Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016452.1 Corchorus olitorius cultivar O-4 contig16485, whole genome shotgun sequence
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: 4731
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Found at i:39 original size:31 final size:30
Alignment explanation
Indices: 1--487 Score: 361
Period size: 31 Copynumber: 16.7 Consensus size: 30
1 AATCATATAGTTGCATATTCAGTAAGGCCAT
1 AATCATATAGTTGCATATTCAGTAAGG-CAT
* *
32 AATCATATAGTTGCATATTTAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAAGG-CAT
* * *
63 AATCACATAGTTACATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAAGG-CAT
*
94 AATCATATAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAAGG-CAT
*
125 AATCATATAGTTGCATATTCAGTAGGGC--
1 AATCATATAGTTGCATATTCAGTAAGGCAT
*
153 ---CATATAGTTGCATATTCAGT-AGG--G
1 AATCATATAGTTGCATATTCAGTAAGGCAT
177 AATCATATAGTTGCATATTCAGT-AGG-A-
1 AATCATATAGTTGCATATTCAGTAAGGCAT
* *
204 AATCATATAGTTGCATATTCAGTAGGGAAT
1 AATCATATAGTTGCATATTCAGTAAGGCAT
*
234 CATAT-AGTGGGCCATATAGTTGCATATTTAGT-AGG-A-
1 -A-ATCA-T-----ATA--GTTGCATATTCAGTAAGGCAT
* * *
270 AATCATATAGTTGCATAATCAAT-AGG--G
1 AATCATATAGTTGCATATTCAGTAAGGCAT
297 AATCATATAGTTGCATATTCAGT-AGG---
1 AATCATATAGTTGCATATTCAGTAAGGCAT
* * *
323 -GTCATGTAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAAGG-CAT
*
353 AATCATATAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAAGG-CAT
*
384 AATCATATAGTTGCATATTTAGT-AGG---
1 AATCATATAGTTGCATATTCAGTAAGGCAT
** * * *
410 GGTCATGTAGTTGCATATTCCGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAAGG-CAT
* **
441 AATTATATAGTTGCATATTCAGT-AGGGGT
1 AATCATATAGTTGCATATTCAGTAAGGCAT
470 --T-ATATAGTTGCATATTCA
1 AATCATATAGTTGCATATTCA
488 ATAGGGGCCA
Statistics
Matches: 388, Mismatches: 37, Indels: 67
0.79 0.08 0.14
Matches are distributed among these distances:
24 2 0.01
25 40 0.10
26 37 0.10
27 87 0.22
28 2 0.01
29 5 0.01
30 5 0.01
31 183 0.47
32 3 0.01
34 3 0.01
35 2 0.01
37 4 0.01
38 2 0.01
39 13 0.03
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (30 bp):
AATCATATAGTTGCATATTCAGTAAGGCAT
Found at i:98 original size:62 final size:60
Alignment explanation
Indices: 1--2161 Score: 1983
Period size: 62 Copynumber: 37.9 Consensus size: 60
* *
1 AATCATATAGTTGCATATTCAGTAAGGCCATAATCATATAGTTGCATATTTAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGT-AGGGCA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* *
63 AATCACATAGTTACATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
125 AATCATATAGTTGCATATTCAGTAGGGC----CATATAGTTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
177 AATCATATAGTTGCATATTCAGTA-GG-AAATCATATAGTTGCATATTCAGTAGGGAATCAT
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGG--CCAT
* * *
237 ATAGTGGGCCATATAGTTGCATATTTAGTA-GG-AAATCATATAGTTGCATAATCAATAGGG---
1 A-A-T----CATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCA
297 -
60 T
*
297 AATCATATAGTTGCATATTCAGTAGGG----TCATGTAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
353 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTTAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* * * * *
411 -GTCATGTAGTTGCATATTCCGTAGGGTCATAATTATATAGTTGCATATTCAGTAGGG--GT
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* *
470 --T-ATATAGTTGCATATTCAATAGGGGC----CATATAGTTGCATATTCAG-AGGGGC--
1 AATCATATAGTTGCATATTCAGTA-GGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
521 ---CATATAGTTGCATATTCAGGAGGGC----CATATAGTTGCATATTCAGTAGGGCC--
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
* * * * *
572 -AT-ATA-A-TTACATATTCTGTAGGG----TTAAATAGTTGCATATTCTGTAGGG-C--
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
* * **
621 ---CATATAGTTGCATATTTATTAGGGCCATAATCATATAGTTGCATATTCAGTAGGTTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* * *
680 GATCATATATTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* ** *
742 AATCATATAGTTGTATATTCAGTAGGGC----CATATTCTTGCATATTCAGCAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
* *
798 AATCATATAGTTGCATATTCAGTAGGGGC----CATATAGTTGCATATTTAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTA-GGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
855 AATCATATAGTTGCATATTCAGTAGGGC----CATATAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
* * *
911 AATCATATAGTTGCTTATTCAGTAGGTTCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGG-GCA-AATCATATAGTTGCATATTCAGTAGGGCCAT
*
973 AATCATATAGTTACATACTT-AGCT-GGGC----CATATAGTTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATA-TTCAG-TAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
1025 AATCATATAGTTGCATATTCAATAGGG--AATCATATAGTTGCATATTCAGTAGGG-C--
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
**
1080 -ATCATATAGTTGCATATTCAGTAGGG--TGTCATATAGTTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
* * * *
1133 AATCATATAGTTGCATATTTAGCA-GG-AAGTCATATAATTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
* * *
1187 AATCATATAGTTGCATATTCAGTAGGACCATAATTATATAGTTGGATATTCAGTAGGG-C--
1 AATCATATAGTTGCATATTCAGTAGG-GCA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* *
1246 ---CATATAGTTGCATATTCAGTAGGG----TCATGTAGTTTCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
1299 AATCATATAGTTGCATATTCAGTAGGG--GATCATATAGTTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
* *
1353 GATCATATAGTTGCATATTCAGTAGGG-AAGTCATATAGTTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
1408 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
*
1470 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATGTAGTTGCATATTCAGTAGGG-C--
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* *
1529 ---CATATAGGTGCATATTCAGTAGGGC---T-ATATAGTTACATATTCAGTAGGG-C--
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
1579 ---CATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
* * * *
1638 ACTCATATAGTTCCATATTCAGTAGGG---GTCATATAGTTCCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
*
1695 AATCATATAGTTGCATATTCAGTAGGGTCATTATCATATAGTTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAGTAGGGCCAT
*
1753 -GTCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTTA-GGCCAT
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAG-TAGGGCCAT
*
1814 AATCATATAGTTGCATATTCAGTAGGGGC----CATATAGTTGCATA-TCTAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTA-GGGCAAATCATATAGTTGCATATTC-AGTAGGGCCAT
*
1871 AATCATATAGTTGCATATTCAGTAGGAGCATAATCATATAGTTGCATATTTAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGG-GCA-AATCATATAGTTGCATATTCAGTAGGGCCAT
1929 --TCATATAGTTGCATATTCAGTAGGAGCATAATCATATAGTTGCATATTCAGTAGGG----
1 AATCATATAGTTGCATATTCAGTAGG-GCA-AATCATATAGTTGCATATTCAGTAGGGCCAT
*
1985 --TCATATAGTTGCATATTCAGTAGGG----TCATATAGTCGCATATTCAGTAGGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTA-GGGCCAT
* *
2040 ATAGTCGCATATTATAGTTGCATATTCAGTATGGTCATAATCATATATTTGCATATTCAGTAGGG
1 A-A-T--C--A-TATAGTTGCATATTCAGTA-GGGCA-AATCATATAGTTGCATATTCAGTAGGG
*
2105 TCAT
57 CCAT
*
2109 AATCATATATTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAG
1 AATCATATAGTTGCATATTCAGTAGGG-CA-AATCATATAGTTGCATATTCAG
2162 GGGCCTCCAA
Statistics
Matches: 1829, Mismatches: 125, Indels: 290
0.82 0.06 0.13
Matches are distributed among these distances:
48 3 0.00
49 2 0.00
50 158 0.09
51 39 0.02
52 87 0.05
53 2 0.00
54 212 0.12
55 57 0.03
56 375 0.21
57 275 0.15
58 79 0.04
59 2 0.00
60 2 0.00
61 11 0.01
62 417 0.23
63 9 0.00
64 19 0.01
65 3 0.00
66 48 0.03
67 1 0.00
68 1 0.00
69 7 0.00
70 20 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (60 bp):
AATCATATAGTTGCATATTCAGTAGGGCAAATCATATAGTTGCATATTCAGTAGGGCCAT
Found at i:162 original size:25 final size:25
Alignment explanation
Indices: 97--2052 Score: 1196
Period size: 31 Copynumber: 70.6 Consensus size: 25
87 GGGCCATAAT
97 CATATAGTTGCATATTCAGTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
123 ATAATCATATAGTTGCATATTCAGTAGGGC
1 -----CATATAGTTGCATATTCAGTAGGGC
*
153 CATATAGTTGCATATTCAGTAGGGAAT
1 CATATAGTTGCATATTCAGTAGGG--C
**
180 CATATAGTTGCATATTCAGTAGGAAAT
1 CATATAGTTGCATATTCAGTAGG--GC
*
207 CATATAGTTGCATATTCAGTAGGGAAT
1 CATATAGTTGCATATTCAGTAGGG--C
* *
234 CATATAGTGGGCCATA-T-AGT--TG-
1 CATATAGT-TG-CATATTCAGTAGGGC
* * * * *
256 CATATTTAGTAGGA-AATCATATAGTTG-
1 CATA--TAGTTGCATATTCA-GTAG-GGC
* ***
283 CATA-A--T-CA-A-T-AG-GGAAT
1 CATATAGTTGCATATTCAGTAGGGC
*
300 CATATAGTTGCATATTCAGTAGGGT
1 CATATAGTTGCATATTCAGTAGGGC
*
325 CATGTAGTTGCATATTCAGTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
351 ATAATCATATAGTTGCATATTCAGTAGGGCC
1 -----CATATAGTTGCATATTCAGTAGGG-C
* *
382 ATAATCATATAGTTGCATATTTAGTAGGGGT
1 -----CATATAGTTGCATATTCAGTA-GGGC
* *
413 CATGTAGTTGCATATTCCGTAGGGTC
1 CATATAGTTGCATATTCAGTAGGG-C
* *
439 ATAATTATATAGTTGCATATTCAGTAGGGGT
1 -----CATATAGTTGCATATTCAGTA-GGGC
* *
470 TATATAGTTGCATATTCAATAGGGGC
1 CATATAGTTGCATATTCAGTA-GGGC
496 CATATAGTTGCATATTCAG-AGGGGC
1 CATATAGTTGCATATTCAGTA-GGGC
*
521 CATATAGTTGCATATTCAGGAGGGC
1 CATATAGTTGCATATTCAGTAGGGC
546 CATATAGTTGCATATTCAGTAGGGC
1 CATATAGTTGCATATTCAGTAGGGC
* * * *
571 CATATAATTACATATTCTGTAGGGT
1 CATATAGTTGCATATTCAGTAGGGC
* * *
596 TAAATAGTTGCATATTCTGTAGGGC
1 CATATAGTTGCATATTCAGTAGGGC
* *
621 CATATAGTTGCATATTTATTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
*
647 ATAATCATATAGTTGCATATTCAGTAGGTTCATGAT
1 -----CATATAGTTGCATATTCAGTAGG-----G-C
*
683 CATATATTTGCATATTCAGTAGGGTC
1 CATATAGTTGCATATTCAGTAGGG-C
709 ATAATCATATAGTTGCATATTCAGTAGGGTC
1 -----CATATAGTTGCATATTCAGTAGGG-C
*
740 ATAATCATATAGTTGTATATTCAGTAGGGC
1 -----CATATAGTTGCATATTCAGTAGGGC
** *
770 CATATTCTTGCATATTCAGCAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
796 ATAATCATATAGTTGCATATTCAGTAGGGGC
1 -----CATATAGTTGCATATTCAGTA-GGGC
*
827 CATATAGTTGCATATTTAGTAGGGTC
1 CATATAGTTGCATATTCAGTAGGG-C
853 ATAATCATATAGTTGCATATTCAGTAGGGC
1 -----CATATAGTTGCATATTCAGTAGGGC
883 CATATAGTTGCATATTCAGTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
* *
909 ATAATCATATAGTTGCTTATTCAGTAGGTTC
1 -----CATATAGTTGCATATTCAGTAGG-GC
940 ATAATCATATAGTTGCATATTCAGTAGGGTC
1 -----CATATAGTTGCATATTCAGTAGGG-C
*
971 ATAATCATATAGTTACATACTT-AGCT-GGGC
1 -----CATATAGTTGCATA-TTCAG-TAGGGC
*
1001 CATATAGTTGCATATTCAGTAGGGAAT
1 CATATAGTTGCATATTCAGTAGGG--C
* *
1028 CATATAGTTGCATATTCAATAGGGAAT
1 CATATAGTTGCATATTCAGTAGGG--C
1055 CATATAGTTGCATATTCAGTAGGGC
1 CATATAGTTGCATATTCAGTAGGGC
*
1080 ATCATATAGTTGCATATTCAGTAGGGTGT
1 --CATATAGTTGCATATTCAGTA-GG-GC
*
1109 CATATAGTTGCATATTCAGTAGGGAAT
1 CATATAGTTGCATATTCAGTAGGG--C
* * *
1136 CATATAGTTGCATATTTAGCAGGAAGT
1 CATATAGTTGCATATTCAGTAGG--GC
* *
1163 CATATAATTGCATATTCAGTAGGGAAT
1 CATATAGTTGCATATTCAGTAGGG--C
*
1190 CATATAGTTGCATATTCAGTAGGAC
1 CATATAGTTGCATATTCAGTAGGGC
*
1215 CATAATTATATAGTTGGATATTCAGTAGGGC
1 C------ATATAGTTGCATATTCAGTAGGGC
*
1246 CATATAGTTGCATATTCAGTAGGGT
1 CATATAGTTGCATATTCAGTAGGGC
* *
1271 CATGTAGTTTCATATTCAGTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
*
1297 ATAATCATATAGTTGCATATTCAGTAGGGGAT
1 -----CATATAGTTGCATATTCAGTA-GGG-C
*
1329 CATATAGTTGCATATTCAGTAGGGGAT
1 CATATAGTTGCATATTCAGTA-GGG-C
*
1356 CATATAGTTGCATATTCAGTAGGGAAGT
1 CATATAGTTGCATATTCAGTA-GG--GC
*
1384 CATATAGTTGCATATTCAGTAGGGAAT
1 CATATAGTTGCATATTCAGTAGGG--C
1411 CATATAGTTGCATATTCAGTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
1437 ATAATCATATAGTTGCATATTCAGTAGGGTC
1 -----CATATAGTTGCATATTCAGTAGGG-C
1468 ATAATCATATAGTTGCATATTCAGTAGGGC
1 -----CATATAGTTGCATATTCAGTAGGGC
1498 CATAATCATGTAGTTGCATATTCAGTAGGGC
1 C---AT-A--TAGTTGCATATTCAGTAGGGC
*
1529 CATATAGGTGCATATTCAGTAGGGC
1 CATATAGTTGCATATTCAGTAGGGC
* *
1554 TATATAGTTACATATTCAGTAGGGC
1 CATATAGTTGCATATTCAGTAGGGC
1579 CATATAGTTGCATATTCAGTAGGGTC
1 CATATAGTTGCATATTCAGTAGGG-C
1605 ATAATCATATAGTTGCATATTCAGTAGGGTCATAC
1 -----CATATAGTTGCATATTCAGTAGGG-----C
* *
1640 TCATATAGTTCCATATTCAGTAGGGGT
1 -CATATAGTTGCATATTCAGTA-GGGC
*
1667 CATATAGTTCCATATTCAGTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
1693 ATAATCATATAGTTGCATATTCAGTAGGGTC
1 -----CATATAGTTGCATATTCAGTAGGG-C
*
1724 ATTATCATATAGTTGCATATTCAGTAGGGGT
1 -----CATATAGTTGCATATTCAGTA-GGGC
1755 CATATAGTTGCATATTCAGTAGGGCC
1 CATATAGTTGCATATTCAGTAGGG-C
*
1781 ATAATCATATAGTTGCATATTCAGTTAGGCC
1 -----CATATAGTTGCATATTCAG-TAGGGC
1812 ATAATCATATAGTTGCATATTCAGTAGGGGC
1 -----CATATAGTTGCATATTCAGTA-GGGC
1843 CATATAGTTGCATA-TCTAGTAGGGTC
1 CATATAGTTGCATATTC-AGTAGGG-C
1869 ATAATCATATAGTTGCATATTCAGTAGGAGC
1 -----CATATAGTTGCATATTCAGTAGG-GC
* *
1900 ATAATCATATAGTTGCATATTTAGTAGGGT
1 -----CATATAGTTGCATATTCAGTAGGGC
1930 CATATAGTTGCATATTCAGTAGGAGC
1 CATATAGTTGCATATTCAGTAGG-GC
*
1956 ATAATCATATAGTTGCATATTCAGTAGGGT
1 -----CATATAGTTGCATATTCAGTAGGGC
*
1986 CATATAGTTGCATATTCAGTAGGGT
1 CATATAGTTGCATATTCAGTAGGGC
*
2011 CATATAGTCGCATATTCAGTAGGGGC
1 CATATAGTTGCATATTCAGTA-GGGC
*
2037 CATATAGTCGCATATT
1 CATATAGTTGCATATT
2053 ATAGTTGCAT
Statistics
Matches: 1638, Mismatches: 124, Indels: 331
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.00
18 1 0.00
19 1 0.00
20 2 0.00
21 5 0.00
22 7 0.00
23 3 0.00
24 11 0.01
25 422 0.26
26 169 0.10
27 301 0.18
28 30 0.02
29 8 0.00
30 9 0.01
31 634 0.39
32 28 0.02
35 1 0.00
36 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (25 bp):
CATATAGTTGCATATTCAGTAGGGC
Found at i:164 original size:56 final size:54
Alignment explanation
Indices: 1--2034 Score: 1652
Period size: 56 Copynumber: 36.0 Consensus size: 54
* *
1 AATCATATAGTTGCATATTCAGTAAGGCCATAATCATATAGTTGCATATTTAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGT-AGGGC-----CATATAGTTGCATATTCAGTAGGG-C-T
* *
63 AATCACATAGTTACATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGG-C-T
125 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGCT
**
177 AATCATATAGTTGCATATTCAGTAGGAAATCATATAGTTGCATATTCAGTAGGGAATCAT
1 AATCATATAGTTGCATATTCAGTAGG--GCCATATAGTTGCATATTCAGTAGGG---C-T
* ** * *
237 ATAGTGGGCCATATAGTTGCATATTTAGTAGGAAATCATATAGTTGCATAATCAATAGGG--
1 A-A-T----CATATAGTTGCATATTCAGTAGG--GCCATATAGTTGCATATTCAGTAGGGCT
* *
297 AATCATATAGTTGCATATTCAGTAGGGTCATGTAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGG-C-T
*
353 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTTAGTAGGG--
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGGCT
* * * * *
411 -GTCATGTAGTTGCATATTCCGTAGGGTCATAATTATATAGTTGCATATTCAGTAGGGGT
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGGCT
*
470 --T-ATATAGTTGCATATTCAATAGGGGCCATATAGTTGCATATTCAG-AGGGGC-
1 AATCATATAGTTGCATATTCAGTA-GGGCCATATAGTTGCATATTCAGTA-GGGCT
*
521 ---CATATAGTTGCATATTCAGGAGGGCCATATAGTTGCATATTCAGTAGGGC-
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGCT
* * * ** * *
571 ---CATATAATTACATATTCTGTAGGGTTAAATAGTTGCATATTCTGTAGGGC-
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGCT
* * *
621 ---CATATAGTTGCATATTTATTAGGGCCATAATCATATAGTTGCATATTCAGTAGGTTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGG-GC-T
* *
680 GATCATATATTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGG-C-T
* ** *
742 AATCATATAGTTGTATATTCAGTAGGGCCATATTCTTGCATATTCAGCAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGG-C-T
*
798 AATCATATAGTTGCATATTCAGTAGGGGCCATATAGTTGCATATTTAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTA-GGGCCATATAGTTGCATATTCAGTAGGG-C-T
855 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGG-C-T
* *
911 AATCATATAGTTGCTTATTCAGTAGGTTCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGG-GC-----CATATAGTTGCATATTCAGTAGGG-C-T
*
973 AATCATATAGTTACATACTT-AGCT-GGGCCATATAGTTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATA-TTCAG-TAGGGCCATATAGTTGCATATTCAGTAGGGCT
* *
1025 AATCATATAGTTGCATATTCAATAGGGAATCATATAGTTGCATATTCAGTAGGGC-
1 AATCATATAGTTGCATATTCAGTAGGG--CCATATAGTTGCATATTCAGTAGGGCT
*
1080 -ATCATATAGTTGCATATTCAGTAGGGTGTCATATAGTTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATATTCAGTA-GG-GCCATATAGTTGCATATTCAGTAGGGCT
* * * *
1133 AATCATATAGTTGCATATTTAGCAGGAAGTCATATAATTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATATTCAGTAGG--GCCATATAGTTGCATATTCAGTAGGGCT
* *
1187 AATCATATAGTTGCATATTCAGTAGGACCATAATTATATAGTTGGATATTCAGTAGGGC-
1 AATCATATAGTTGCATATTCAGTAGGGCC------ATATAGTTGCATATTCAGTAGGGCT
* * *
1246 ---CATATAGTTGCATATTCAGTAGGGTCATGTAGTTTCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGG-C-T
*
1299 AATCATATAGTTGCATATTCAGTAGGGGATCATATAGTTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATATTCAGTA-GGG-CCATATAGTTGCATATTCAGTAGGGCT
* *
1353 GATCATATAGTTGCATATTCAGTAGGGAAGTCATATAGTTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATATTCAGTA-GG--GCCATATAGTTGCATATTCAGTAGGGCT
1408 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGG-C-T
1470 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATGTAGTTGCATATTCAGTAGGGC-
1 AATCATATAGTTGCATATTCAGTAGGGCC---AT-A--TAGTTGCATATTCAGTAGGGCT
* * *
1529 ---CATATAGGTGCATATTCAGTAGGGCTATATAGTTACATATTCAGTAGGGC-
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGCT
1579 ---CATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGG-C-T
* * * *
1638 ACTCATATAGTTCCATATTCAGTAGGGGTCATATAGTTCCATATTCAGTAGGGCCAT
1 AATCATATAGTTGCATATTCAGTA-GGGCCATATAGTTGCATATTCAGTAGGG-C-T
1695 AATCATATAGTTGCATATTCAGTAGGGTCATTATCATATAGTTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAGTAGGGCT
* *
1753 -GTCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTTAGGCCAT
1 AATCATATAGTTGCATATTCAGTAGGG-C-----CATATAGTTGCATATTCAG-TAGGGC-T
1814 AATCATATAGTTGCATATTCAGTAGGGGCCATATAGTTGCATA-TCTAGTAGGGTCAT
1 AATCATATAGTTGCATATTCAGTA-GGGCCATATAGTTGCATATTC-AGTAGGG-C-T
*
1871 AATCATATAGTTGCATATTCAGTAGGAGCATAATCATATAGTTGCATATTTAGTAGGG--
1 AATCATATAGTTGCATATTCAGTAGG-GC-----CATATAGTTGCATATTCAGTAGGGCT
1929 --TCATATAGTTGCATATTCAGTAGGAGCATAATCATATAGTTGCATATTCAGTAGGG--
1 AATCATATAGTTGCATATTCAGTAGG-GC-----CATATAGTTGCATATTCAGTAGGGCT
* *
1985 --TCATATAGTTGCATATTCAGTAGGGTCATATAGTCGCATATTCAGTAGGG
1 AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGG
2035 GCCATATAGT
Statistics
Matches: 1719, Mismatches: 124, Indels: 270
0.81 0.06 0.13
Matches are distributed among these distances:
50 174 0.10
51 25 0.01
52 92 0.05
53 4 0.00
54 215 0.13
55 51 0.03
56 381 0.22
57 268 0.16
58 77 0.04
59 3 0.00
60 3 0.00
61 9 0.01
62 359 0.21
63 10 0.01
66 48 0.03
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (54 bp):
AATCATATAGTTGCATATTCAGTAGGGCCATATAGTTGCATATTCAGTAGGGCT
Found at i:194 original size:93 final size:85
Alignment explanation
Indices: 1--2161 Score: 2072
Period size: 88 Copynumber: 25.3 Consensus size: 85
* *
1 AATCATATAGTTGCATATTCAGTAAGGCCATAATCATATAGTTGCATATTTAGTAGGGCCATAAT
1 AATCATATAGTTGCATATTCAGT-AGG-GATAATCATATAGTTGCATATTCAGTAGGGCC---AT
*
66 CACATAGTTACATATTCAGTAGGGCCAT
61 ---ATAGTTGCATATTCAGTAGGGCCAT
94 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGCCATATA
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTAGGGCCATATA
159 GTTGCATATTCAGTAGGG----
64 GTTGCATATTCAGTAGGGCCAT
177 AATCATATAGTTGCATATTCAGTA-GGA-AATCATATAGTTGCATATTCAGTAGGGAATCATATA
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTA--G---------
*
240 GTGGGCCATATAGTTGCATATTTAGTA-GG--A-
55 G---GCCATATAGTTGCATATTCAGTAGGGCCAT
* * * *
270 AATCATATAGTTGCATAATCAATAGGG--AATCATATAGTTGCATATTCAGTAGGGTCATGTAGT
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGGCCATATAGT
333 TGCATATTCAGTAGGGCCAT
66 TGCATATTCAGTAGGGCCAT
* * *
353 AATCATATAGTTGCATATTCAGTAGGGCCATAATCATATAGTTGCATATTTAGTAGGGGTCATGT
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTA-GGGCCATAT
* *
418 AGTTGCATATTCCGTAGGGTCAT
63 AGTTGCATATTCAGTAGGGCCAT
* * *
441 AATTATATAGTTGCATATTCAGTAGGGGT--T-ATATAGTTGCATATTCAATAGGGGCCATATAG
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTA-GGGCCATATAG
*
503 TTGCATATTCAG-AGGGGC--
65 TTGCATATTCAGTAGGGCCAT
* * *
521 ---CATATAGTTGCATATTCAGGAGGG----CCATATAGTTGCATATTCAGTAGGGCCATATAAT
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGGCCATATAGT
* *
579 TACATATTCTGTAGGG---T
66 TGCATATTCAGTAGGGCCAT
* * * * *
596 --T-AAATAGTTGCATATTCTGTAGGG----CCATATAGTTGCATATTTATTAGGGCCATAATCA
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGG-C-----CA
**
654 TATAGTTGCATATTCAGTAGGTTCAT
60 TATAGTTGCATATTCAGTAGGGCCAT
* *
680 GATCATATATTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGTCATAAT
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTAGGG-C-----
*
745 CATATAGTTGTATATTCAGTAGGGCC--
58 CATATAGTTGCATATTCAGTAGGGCCAT
* *
771 -AT-AT-T-CTTGCATATTCAGCAGGGCCATAATCATATAGTTGCATATTCAGTAGGGGCCATAT
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTA-GGGCCATAT
* *
832 AGTTGCATATTTAGTAGGGTCAT
63 AGTTGCATATTCAGTAGGGCCAT
*
855 AATCATATAGTTGCATATTCAGTAGGG----CCATATAGTTGCATATTCAGTAGGGCCATAATCA
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGG-C-----CA
* **
916 TATAGTTGCTTATTCAGTAGGTTCAT
60 TATAGTTGCATATTCAGTAGGGCCAT
*
942 AATCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTACATACTT-AGCT-GGGCCATA
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATA-TTCAG-TAGGGCCATA
1005 TAGTTGCATATTCAGTAGGG----
62 TAGTTGCATATTCAGTAGGGCCAT
*
1025 AATCATATAGTTGCATATTCAATAGGG--AATCATATAGTTGCATATTCAGTAGGGCATCATATA
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGGC--CATATA
1088 GTTGCATATTCAGTAGGG---T
64 GTTGCATATTCAGTAGGGCCAT
* * * *
1107 -GTCATATAGTTGCATATTCAGTAGGG--AATCATATAGTTGCATATTTAGCAGGAAGTCATATA
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGG--GCCATATA
*
1169 ATTGCATATTCAGTAGGG----
64 GTTGCATATTCAGTAGGGCCAT
* * *
1187 AATCATATAGTTGCATATTCAGTAGGACCATAATTATATAGTTGGATATTCAGTAGGGCCATATA
1 AATCATATAGTTGCATATTCAGTAGG--GATAATCATATAGTTGCATATTCAGTAGGGCCATATA
1252 GTTGCATATTCAGTAGGG----
64 GTTGCATATTCAGTAGGGCCAT
* * *
1270 --TCATGTAGTTTCATATTCAGTAGGGCCATAATCATATAGTTGCATATTCAGTAGGGGATCATA
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTA-GGG-CCATA
1333 TAGTTGCATATTCAGTAGGG----
62 TAGTTGCATATTCAGTAGGGCCAT
* * *
1353 GATCATATAGTTGCATATTCAGTAGGGA-AGTCATATAGTTGCATATTCAGTAGGGAATCATATA
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGG--CCATATA
1417 GTTGCATATTCAGTAGGGCCAT
64 GTTGCATATTCAGTAGGGCCAT
1439 AATCATATAGTTGCATATTCAGTAGGGTCATAATCATATAGTTGCATATTCAGTAGGGCCATAAT
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTAGGGCC---AT
1504 CATGTAGTTGCATATTCAGTAGGG-C--
61 -A--TAGTTGCATATTCAGTAGGGCCAT
* * *
1529 ---CATATAGGTGCATATTCAGTAGGG---CT-ATATAGTTACATATTCAGTAGGGCCATATAGT
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGGCCATATAGT
*
1587 TGCATATTCAGTAGGGTCAT
66 TGCATATTCAGTAGGGCCAT
* * *
1607 AATCATATAGTTGCATATTCAGTAGGGTCATACTCATATAGTTCCATATTCAGTAGGGGTCATAT
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTA-GGGCCATAT
*
1672 AGTTCCATATTCAGTAGGGCCAT
63 AGTTGCATATTCAGTAGGGCCAT
* *
1695 AATCATATAGTTGCATATTCAGTAGGGTCATTATCATATAGTTGCATATTCAGTAGGGGTCATAT
1 AATCATATAGTTGCATATTCAGTAGGG--ATAATCATATAGTTGCATATTCAGTA-GGGCCATAT
1760 AGTTGCATATTCAGTAGGGCCAT
63 AGTTGCATATTCAGTAGGGCCAT
*
1783 AATCATATAGTTGCATATTCAGTTAGGCCATAATCATATAGTTGCATATTCAGTAGGGGCCATAT
1 AATCATATAGTTGCATATTCAG-TAGG-GATAATCATATAGTTGCATATTCAGTA-GGGCCATAT
*
1848 AGTTGCATA-TCTAGTAGGGTCAT
63 AGTTGCATATTC-AGTAGGGCCAT
* *
1871 AATCATATAGTTGCATATTCAGTAGGAGCATAATCATATAGTTGCATATTTAGTAGGGTCATATA
1 AATCATATAGTTGCATATTCAGTAGG-G-ATAATCATATAGTTGCATATTCAGTAGGGCCATATA
1936 GTTGCATATTCAGTAGGAG-CAT
64 GTTGCATATTCAGTAGG-GCCAT
*
1958 AATCATATAGTTGCATATTCAGTAGGG----TCATATAGTTGCATATTCAGTAGGGTCATATAGT
1 AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGGCCATATAGT
*
2019 CGCATATTCAGTAGGGGCCAT
66 TGCATATTCAGTA-GGGCCAT
* *
2040 ATAGTCGCATATTATAGTTGCATATTCAGTATGGTCATAATCATATATTTGCATATTCAGTAGGG
1 A-A-T--C--A-TATAGTTGCATATTCAGTA-GG-GATAATCATATAGTTGCATATTCAGTAGGG
* *
2105 TCATAATCATATATTTGCATATTCAGTAGGGTCAT
57 -C-----CATATAGTTGCATATTCAGTAGGGCCAT
2140 AATCATATAGTTGCATATTCAG
1 AATCATATAGTTGCATATTCAG
2162 GGGCCTCCAA
Statistics
Matches: 1806, Mismatches: 120, Indels: 284
0.82 0.05 0.13
Matches are distributed among these distances:
75 83 0.05
76 25 0.01
77 23 0.01
78 5 0.00
79 66 0.04
80 3 0.00
81 285 0.16
82 113 0.06
83 165 0.09
84 3 0.00
85 47 0.03
86 34 0.02
87 283 0.16
88 316 0.17
89 51 0.03
90 9 0.00
91 2 0.00
92 7 0.00
93 227 0.13
94 6 0.00
95 24 0.01
96 1 0.00
98 1 0.00
99 1 0.00
100 7 0.00
101 19 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (85 bp):
AATCATATAGTTGCATATTCAGTAGGGATAATCATATAGTTGCATATTCAGTAGGGCCATATAGT
TGCATATTCAGTAGGGCCAT
Found at i:257 original size:66 final size:66
Alignment explanation
Indices: 180--307 Score: 229
Period size: 66 Copynumber: 1.9 Consensus size: 66
170 AGTAGGGAAT
* *
180 CATATAGTTGCATATTCAGTAGGAAATCATATAGTTGCATATTCAGTAGGGAATCATATAGTGGG
1 CATATAGTTGCATATTCAGTAGGAAATCATATAGTTGCATAATCAATAGGGAATCATATAGTGGG
245 C
66 C
*
246 CATATAGTTGCATATTTAGTAGGAAATCATATAGTTGCATAATCAATAGGGAATCATATAGT
1 CATATAGTTGCATATTCAGTAGGAAATCATATAGTTGCATAATCAATAGGGAATCATATAGT
308 TGCATATTCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (66 bp):
CATATAGTTGCATATTCAGTAGGAAATCATATAGTTGCATAATCAATAGGGAATCATATAGTGGG
C
Found at i:656 original size:31 final size:30
Alignment explanation
Indices: 599--2034 Score: 1469
Period size: 31 Copynumber: 50.7 Consensus size: 30
589 GTAGGGTTAA
*
599 ATAGTTGCATATTCTGTAGGGC-----CAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
* *
624 ATAGTTGCATATTTATTAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
* *
655 ATAGTTGCATATTCAGTAGGTTCATGATCAT
1 ATAGTTGCATATTCAGTAGG-GCATAATCAT
*
686 ATATTTGCATATTCAGTAGGGTCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
717 ATAGTTGCATATTCAGTAGGGTCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
748 ATAGTTGTATATTCAGTAGGGC-----CAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
** *
773 ATTCTTGCATATTCAGCAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
804 ATAGTTGCATATTCAGTAGGGGC-----CAT
1 ATAGTTGCATATTCAGTA-GGGCATAATCAT
*
830 ATAGTTGCATATTTAGTAGGGTCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
861 ATAGTTGCATATTCAGTAGGGC-----CAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
886 ATAGTTGCATATTCAGTAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
* *
917 ATAGTTGCTTATTCAGTAGGTTCATAATCAT
1 ATAGTTGCATATTCAGTAGG-GCATAATCAT
948 ATAGTTGCATATTCAGTAGGGTCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
979 ATAGTTACATACTT-AGCT-GGGC-----CAT
1 ATAGTTGCATA-TTCAG-TAGGGCATAATCAT
1004 ATAGTTGCATATTCAGTAGGG---AATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1031 ATAGTTGCATATTCAATAGGG---AATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1058 ATAGTTGCATATTCAGTAGGGC---ATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1085 ATAGTTGCATATTCAGTAGGG--T-GTCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1112 ATAGTTGCATATTCAGTAGGG---AATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
* * *
1139 ATAGTTGCATATTTAGCA-GG-A-AGTCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1166 ATAATTGCATATTCAGTAGGG---AATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
* *
1193 ATAGTTGCATATTCAGTAGGACCATAATTAT
1 ATAGTTGCATATTCAGTAGG-GCATAATCAT
*
1224 ATAGTTGGATATTCAGTAGGGC-----CAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1249 ATAGTTGCATATTCAGTAGGG-----TCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
* *
1274 GTAGTTTCATATTCAGTAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
1305 ATAGTTGCATATTCAGTAGGG---GATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1332 ATAGTTGCATATTCAGTAGGG---GATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1359 ATAGTTGCATATTCAGTAGGG-A-AGTCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1387 ATAGTTGCATATTCAGTAGGG---AATCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1414 ATAGTTGCATATTCAGTAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
1445 ATAGTTGCATATTCAGTAGGGTCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
1476 ATAGTTGCATATTCAGTAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
1507 GTAGTTGCATATTCAGTAGGGC-----CAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1532 ATAGGTGCATATTCAGTAGGGC----T-AT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1557 ATAGTTACATATTCAGTAGGGC-----CAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1582 ATAGTTGCATATTCAGTAGGGTCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
1613 ATAGTTGCATATTCAGTAGGGTCATACTCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
* *
1644 ATAGTTCCATATTCAGTAGGG----GTCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
1670 ATAGTTCCATATTCAGTAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
1701 ATAGTTGCATATTCAGTAGGGTCATTATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
1732 ATAGTTGCATATTCAGTAGGG----GTCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1758 ATAGTTGCATATTCAGTAGGGCCATAATCAT
1 ATAGTTGCATATTCAGTAGGG-CATAATCAT
*
1789 ATAGTTGCATATTCAGTTAGGCCATAATCAT
1 ATAGTTGCATATTCAG-TAGGGCATAATCAT
1820 ATAGTTGCATATTCAGTAGGGGC-----CAT
1 ATAGTTGCATATTCAGTA-GGGCATAATCAT
1846 ATAGTTGCATA-TCTAGTAGGGTCATAATCAT
1 ATAGTTGCATATTC-AGTAGGG-CATAATCAT
1877 ATAGTTGCATATTCAGTAGGAGCATAATCAT
1 ATAGTTGCATATTCAGTAGG-GCATAATCAT
*
1908 ATAGTTGCATATTTAGTAGGG-----TCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1933 ATAGTTGCATATTCAGTAGGAGCATAATCAT
1 ATAGTTGCATATTCAGTAGG-GCATAATCAT
1964 ATAGTTGCATATTCAGTAGGG-----TCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
1989 ATAGTTGCATATTCAGTAGGG-----TCAT
1 ATAGTTGCATATTCAGTAGGGCATAATCAT
*
2014 ATAGTCGCATATTCAGTAGGG
1 ATAGTTGCATATTCAGTAGGG
2035 GCCATATAGT
Statistics
Matches: 1244, Mismatches: 75, Indels: 184
0.83 0.05 0.12
Matches are distributed among these distances:
24 3 0.00
25 271 0.22
26 97 0.08
27 243 0.20
28 27 0.02
30 9 0.01
31 581 0.47
32 13 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (30 bp):
ATAGTTGCATATTCAGTAGGGCATAATCAT
Found at i:1517 original size:16 final size:16
Alignment explanation
Indices: 1408--1517 Score: 70
Period size: 16 Copynumber: 7.1 Consensus size: 16
1398 TTCAGTAGGG
*
1408 AATCATATAGTTGCAT
1 AATCATGTAGTTGCAT
* *
1424 ATTCA-GTAG-GGCCAT
1 AATCATGTAGTTG-CAT
*
1439 AATCATATAGTTGCAT
1 AATCATGTAGTTGCAT
* *
1455 ATTCA-GTAG-GGTCAT
1 AATCATGTAGTTG-CAT
*
1470 AATCATATAGTTGCAT
1 AATCATGTAGTTGCAT
* *
1486 ATTCA-GTAG-GGCCAT
1 AATCATGTAGTTG-CAT
1501 AATCATGTAGTTGCAT
1 AATCATGTAGTTGCAT
1517 A
1 A
1518 TTCAGTAGGG
Statistics
Matches: 68, Mismatches: 17, Indels: 18
0.66 0.17 0.17
Matches are distributed among these distances:
14 3 0.04
15 30 0.44
16 32 0.47
17 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (16 bp):
AATCATGTAGTTGCAT
Found at i:1532 original size:15 final size:14
Alignment explanation
Indices: 1420--2034 Score: 84
Period size: 15 Copynumber: 43.1 Consensus size: 14
1410 TCATATAGTT
1420 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1434 GCCATAATCATATAGTT
1 G-CATATTCA-GTAG-G
1451 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1465 GTCATAATCATATAGTT
1 G-CATATTCA-GTAG-G
1482 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* *
1496 GCCATAATCATGTAGTT
1 G-CATATTCA-GTAG-G
1513 GCATATTCAGTAGG
1 GCATATTCAGTAGG
*
1527 GCCATA-T-AG--GT
1 G-CATATTCAGTAGG
1538 GCATATTCAGTAGG
1 GCATATTCAGTAGG
1552 GC-TATAT-AGTTA--
1 GCATAT-TCAG-TAGG
1564 -CATATTCAGTAGG
1 GCATATTCAGTAGG
*
1577 GCCATA-T-AGT--T
1 G-CATATTCAGTAGG
1588 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1602 GTCATAATCATATAGTT
1 G-CATATTCA-GTAG-G
1619 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1633 GTCATACTCATATAGTT
1 G-CATATTCA-GTAG-G
*
1650 CCATATTCAGTAGGG
1 GCATATTCAGTA-GG
*
1665 GTCATA-T-AGT--T
1 G-CATATTCAGTAGG
*
1676 CCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1690 GCCATAATCATATAGTT
1 G-CATATTCA-GTAG-G
1707 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* *
1721 GTCAT-TATCATATAGTT
1 G-CATAT-TCA-GTAG-G
1738 GCATATTCAGTAGGG
1 GCATATTCAGTA-GG
*
1753 GTCATA-T-AGT--T
1 G-CATATTCAGTAGG
1764 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1778 GCCATAATCATATAGTT
1 G-CATATTCA-GTAG-G
1795 GCATATTCAGTTAGG
1 GCATATTCAG-TAGG
* * * *
1810 CCATAATCATATAGTT
1 GCATATTCA-GTAG-G
1826 GCATATTCAGTAGGG
1 GCATATTCAGTA-GG
*
1841 GCCATA-T-AGT--T
1 G-CATATTCAGTAGG
1852 GCATA-TCTAGTAGG
1 GCATATTC-AGTAGG
* * *
1866 GTCATAATCATATAGTT
1 G-CATATTCA-GTAG-G
1883 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1897 AGCATAATCATATAGTT
1 -GCATATTCA-GTAG-G
*
1914 GCATATTTAGTAGG
1 GCATATTCAGTAGG
*
1928 GTCATA-T-AGT--T
1 G-CATATTCAGTAGG
1939 GCATATTCAGTAGG
1 GCATATTCAGTAGG
* * *
1953 AGCATAATCATATAGTT
1 -GCATATTCA-GTAG-G
1970 GCATATTCAGTAGG
1 GCATATTCAGTAGG
*
1984 GTCATA-T-AGT--T
1 G-CATATTCAGTAGG
1995 GCATATTCAGTAGG
1 GCATATTCAGTAGG
*
2009 GTCATA-T-AGT--C
1 G-CATATTCAGTAGG
2020 GCATATTCAGTAGG
1 GCATATTCAGTAGG
2034 G
1 G
2035 GCCATATAGT
Statistics
Matches: 422, Mismatches: 90, Indels: 178
0.61 0.13 0.26
Matches are distributed among these distances:
10 33 0.08
11 19 0.05
12 28 0.07
13 19 0.05
14 34 0.08
15 142 0.34
16 138 0.33
17 9 0.02
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (14 bp):
GCATATTCAGTAGG
Found at i:2092 original size:31 final size:31
Alignment explanation
Indices: 2052--2161 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
2042 AGTCGCATAT
*
2052 TATAGTTGCATATTCAGTATGGTCATAATCA
1 TATAGTTGCATATTCAGTAGGGTCATAATCA
*
2083 TATATTTGCATATTCAGTAGGGTCATAATCA
1 TATAGTTGCATATTCAGTAGGGTCATAATCA
*
2114 TATATTTGCATATTCAGTAGGGTCATAATCA
1 TATAGTTGCATATTCAGTAGGGTCATAATCA
2145 TATAGTTGCATATTCAG
1 TATAGTTGCATATTCAG
2162 GGGCCTCCAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (31 bp):
TATAGTTGCATATTCAGTAGGGTCATAATCA
Done.