genome.fa.s190.2.7.7.80.10.50.1000.44.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  14308945

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   

This is table  44  of  62  ( 7381 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10242299--10242411	21	5.2	21	75	16	72	30	23	20	24	1.98
10242364--10242421	21	2.8	21	84	5	73	34	24	18	22	1.96
10245482--10245542	22	2.8	22	89	0	95	29	22	22	24	1.99
10256405--10256499	23	4.3	22	72	17	74	33	27	14	24	1.94
10258322--10258357	14	2.6	14	95	0	63	36	5	0	58	1.22
10259586--10259887	117	2.6	117	92	1	491	31	33	16	18	1.93
10260839--10260943	29	3.6	29	85	8	142	39	24	5	30	1.79
10260956--10260980	13	1.9	13	100	0	50	16	16	48	20	1.82
10267051--10267352	117	2.6	117	89	2	457	31	34	15	18	1.92
10268279--10268404	58	2.2	57	85	4	173	38	25	5	30	1.79
10268299--10268403	29	3.6	29	88	3	158	38	25	5	30	1.79
10269906--10269956	23	2.0	27	85	14	74	54	3	0	41	1.19
10273845--10273887	19	2.3	19	87	0	59	16	32	30	20	1.95
10273848--10273919	23	3.4	22	81	12	87	19	23	36	20	1.95
10280036--10280074	19	2.1	19	85	0	51	35	5	10	48	1.59
10280095--10280147	26	2.0	26	92	0	88	32	5	9	52	1.57
10280559--10280704	60	2.4	60	85	4	197	36	19	13	30	1.90
10281271--10281301	16	1.9	16	93	0	53	41	16	19	22	1.89
10281302--10281344	15	2.8	15	85	3	50	55	2	0	41	1.12
10281308--10281354	7	6.4	7	77	18	51	55	2	0	42	1.12
10281308--10281354	15	3.2	14	82	11	51	55	2	0	42	1.12
10281313--10281354	22	1.9	22	90	9	68	57	2	0	40	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10283137--10283174	6	6.5	6	84	3	51	73	0	0	26	0.83
10284371--10284429	23	2.6	23	100	0	118	37	23	20	18	1.94
10287347--10287408	29	2.1	29	84	0	79	43	16	8	32	1.77
10287593--10287664	29	2.5	29	90	0	108	30	20	4	44	1.71
10288708--10288745	20	1.9	20	100	0	76	18	26	31	23	1.97
10290923--10290956	13	2.6	13	95	0	59	44	5	14	35	1.70
10295320--10295359	21	1.9	21	89	0	62	30	7	7	55	1.56
10300616--10300648	13	2.7	13	90	9	52	6	6	6	81	0.97
10300600--10300741	9	16.0	9	70	17	50	18	3	3	74	1.10
10308579--10308631	21	2.5	21	81	6	72	41	5	35	16	1.73
10313792--10313834	21	2.0	21	86	0	59	39	6	37	16	1.75
10315137--10315350	66	3.2	67	76	13	210	29	19	13	37	1.90
10315384--10315695	131	2.4	132	81	2	376	25	30	18	25	1.98
10317143--10317172	15	2.0	15	93	0	51	20	3	6	70	1.25
10318752--10318796	21	2.1	21	95	0	81	24	11	53	11	1.68
10319882--10319932	15	3.3	15	78	21	61	35	17	0	47	1.48
10321083--10321120	11	3.5	11	92	0	67	21	0	42	36	1.53
10321855--10321985	65	2.0	66	98	1	255	32	16	21	29	1.95
10322693--10323270	81	7.1	81	90	1	897	31	20	12	35	1.89
10324713--10324756	23	2.0	21	83	16	54	38	4	15	40	1.68
10331461--10331494	16	2.1	16	100	0	68	26	17	11	44	1.83
10332600--10332659	21	2.8	21	74	5	57	36	30	15	18	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10333515--10333564	24	2.1	24	85	7	66	60	12	2	26	1.43
10343140--10343169	9	3.3	9	100	0	60	76	0	0	23	0.78
10343655--10343704	24	2.1	24	88	7	75	60	10	2	28	1.40
10353576--10353618	3	14.3	3	80	9	52	2	39	0	58	1.11
10363640--10363683	15	2.9	15	80	13	54	75	0	22	2	0.92
10364697--10364759	27	2.6	24	78	12	67	46	4	4	44	1.45
10366369--10366398	3	10.0	3	100	0	60	66	0	0	33	0.92
10366708--10366986	110	2.5	110	84	2	346	26	18	22	31	1.97
10366670--10366981	165	1.9	166	84	4	425	26	19	22	32	1.97
10366670--10366986	55	5.7	55	81	5	311	26	19	22	31	1.97
10366993--10367262	37	7.4	37	84	3	341	22	20	14	41	1.89
10366993--10367262	73	3.7	73	84	3	323	22	20	14	41	1.89
10367003--10367262	110	2.4	110	82	5	321	23	20	15	41	1.90
10368506--10368550	14	3.1	14	87	3	63	4	17	0	77	0.92
10368504--10368550	15	3.2	15	90	3	78	4	19	0	76	0.95
10381391--10381722	131	2.5	132	80	2	371	25	15	33	26	1.95
10381896--10382022	36	3.5	36	76	5	114	43	10	15	30	1.80
10381891--10382031	71	1.9	73	82	5	178	41	9	17	31	1.82
10381891--10382001	36	3.0	37	78	5	125	41	9	18	30	1.83
10381912--10382061	71	2.1	73	80	5	162	39	12	18	30	1.86
10383207--10383250	15	2.9	16	80	10	56	0	15	4	79	0.89
10383216--10383298	30	2.8	31	78	12	77	2	16	4	75	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10386075--10386136	22	2.6	24	80	17	76	43	4	1	50	1.33
10391235--10391301	29	2.2	31	84	10	86	44	2	13	38	1.59
10397113--10397279	90	1.9	89	93	1	289	44	5	11	38	1.65
10403909--10404081	90	1.9	89	92	1	292	44	7	10	36	1.68
10405651--10405689	21	1.9	20	85	15	53	38	17	12	30	1.88
10414722--10414755	2	17.0	2	100	0	68	50	0	0	50	1.00
10422109--10422245	20	6.8	20	83	0	166	23	18	22	35	1.95
10422108--10422245	60	2.3	60	87	5	199	23	18	22	35	1.95
10422309--10422404	42	2.3	42	82	7	115	34	18	21	25	1.96
10422450--10422524	36	2.2	35	80	7	82	40	16	25	18	1.91
10422460--10422529	36	1.9	36	88	0	104	37	17	25	20	1.94
10422754--10422791	19	2.1	18	85	14	51	44	5	0	50	1.24
10431436--10431601	20	8.3	20	84	0	197	22	18	22	36	1.95
10431645--10431752	42	2.5	42	85	7	130	35	18	23	23	1.96
10431774--10431877	36	2.8	36	85	7	127	36	14	26	22	1.92
10446864--10446905	19	2.3	18	92	8	68	33	19	14	33	1.91
10451175--10451211	2	18.5	2	100	0	74	48	0	0	51	1.00
10451828--10451883	22	2.5	24	80	11	66	57	7	12	23	1.60
10455429--10455464	17	2.1	17	94	0	63	27	30	19	22	1.98
10456771--10456840	28	2.5	28	85	2	86	24	4	35	35	1.75
10456786--10456842	21	2.7	21	83	0	69	22	3	33	40	1.71
10456786--10456842	7	8.1	7	84	0	51	22	3	33	40	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10456779--10456842	14	4.6	14	78	0	65	23	3	34	39	1.71
10457910--10457950	20	2.1	19	86	13	57	63	0	0	36	0.95
10461013--10461048	2	18.5	2	94	5	65	52	0	0	47	1.00
10465332--10465359	2	14.0	2	100	0	56	50	0	0	50	1.00
10466405--10466437	2	16.5	2	100	0	66	51	0	0	48	1.00
10466629--10466716	31	2.9	31	83	5	99	36	17	17	29	1.92
10467478--10467591	24	4.8	24	79	5	115	43	17	12	26	1.84
10467474--10467626	72	2.1	72	78	7	159	45	15	11	28	1.81
10471961--10472034	35	2.1	35	90	5	114	36	27	27	9	1.87
10472110--10472223	24	4.8	24	83	5	142	41	19	14	25	1.89
10478092--10478124	16	2.1	16	94	0	57	12	9	0	78	0.95
10480833--10480875	22	1.9	22	90	4	68	13	2	4	79	1.00
10480833--10480878	14	3.3	14	82	11	58	15	2	4	78	1.01
10480831--10480883	22	2.4	23	81	12	58	16	1	5	75	1.08
10482798--10482842	16	2.8	16	83	10	56	40	17	6	35	1.76
10487538--10487625	31	2.9	31	85	8	101	35	18	17	29	1.93
10487754--10487798	16	2.8	16	83	10	56	40	17	6	35	1.76
10493338--10493540	31	6.5	31	96	0	370	20	19	21	38	1.93
10494036--10494078	21	2.0	21	82	8	52	32	4	13	48	1.63
10496600--10496702	19	5.9	18	70	25	80	16	29	33	21	1.95
10496628--10496684	15	3.5	15	70	25	53	19	33	28	19	1.96
10496606--10496702	34	2.9	34	98	1	187	17	30	29	21	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10496738--10496802	20	3.3	20	75	12	80	38	10	10	40	1.75
10496725--10496803	39	2.0	39	100	0	158	39	12	10	37	1.77
10497691--10497908	31	7.0	31	93	1	357	21	18	22	38	1.93
10504979--10505005	2	13.5	2	100	0	54	51	0	0	48	1.00
10509751--10509795	15	2.9	15	90	6	63	20	33	24	22	1.97
10514681--10515096	43	9.8	43	91	3	657	16	27	24	31	1.96
10519985--10520214	42	5.6	43	94	5	383	15	30	26	28	1.96
10522239--10522269	13	2.4	13	94	0	53	19	48	16	16	1.81
10525039--10525494	43	10.8	43	92	3	716	17	27	24	30	1.97
10525039--10525494	127	3.6	127	91	4	744	17	27	24	30	1.97

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62