genome.fa.s8620.2.7.7.80.10.50.1000.3.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: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  13158977

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   63   64   

This is table  3  of  64  ( 7674 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)
530973--531041	21	3.5	20	72	20	65	52	0	7	40	1.29
531207--531269	3	21.0	3	83	6	83	31	1	3	63	1.19
539637--539661	10	2.5	10	100	0	50	20	8	20	52	1.71
556082--556154	9	7.8	9	74	17	51	80	0	16	2	0.82
556092--556141	17	2.8	17	81	6	55	78	0	22	0	0.76
556083--556155	26	2.6	28	78	8	78	80	0	16	2	0.82
557378--557884	135	3.7	136	86	4	673	28	20	18	32	1.96
557381--557896	271	1.9	272	86	3	736	28	19	18	32	1.96
557626--558084	231	2.0	233	84	3	604	28	19	18	34	1.95
557762--557980	95	2.3	95	84	3	280	28	18	17	34	1.94
558358--558404	25	1.9	25	86	4	69	19	4	6	70	1.26
558418--558535	12	9.9	12	69	18	61	50	0	5	44	1.26
558446--558523	2	38.0	2	80	10	77	48	0	5	46	1.24
558495--558541	14	3.7	14	68	26	50	44	0	8	46	1.33
558417--558590	23	7.7	22	72	17	135	50	0	6	43	1.27
558552--558605	23	2.2	26	80	12	60	48	1	3	46	1.30
558483--558635	67	2.2	68	82	12	172	47	0	6	45	1.33
563298--563379	20	4.4	19	80	12	89	23	29	21	25	1.99
563487--563525	21	1.9	20	84	5	51	30	25	23	20	1.98
563553--563592	20	1.9	21	90	10	64	40	37	5	17	1.72
566516--566556	21	2.0	21	90	0	64	26	12	9	51	1.70
566831--566868	20	1.9	20	88	0	58	21	34	21	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
566976--567015	20	1.9	22	90	10	66	37	40	10	12	1.77
567231--567301	34	2.1	33	89	2	106	30	12	29	26	1.93
570558--570653	43	2.3	43	96	3	178	35	30	0	34	1.58
572881--572942	20	2.9	21	80	9	63	16	25	35	22	1.94
579111--579139	2	14.5	2	100	0	58	48	0	0	51	1.00
580121--580189	23	3.0	23	84	0	93	18	23	26	31	1.97
580935--580986	21	2.3	23	80	9	72	65	3	1	28	1.21
582406--582463	3	20.0	3	86	13	86	68	0	0	31	0.89
582407--582463	21	2.6	22	97	2	107	70	0	0	29	0.88
582406--582463	25	2.2	25	90	6	89	68	0	0	31	0.89
582406--582463	16	3.8	15	84	10	73	68	0	0	31	0.89
582754--583221	122	3.9	120	87	6	609	26	20	13	38	1.90
583028--583247	113	2.0	113	89	2	345	27	20	15	37	1.92
584388--584428	21	2.0	21	95	0	73	58	7	7	26	1.51
588316--588347	9	3.6	9	100	0	64	53	0	25	21	1.46
596049--596112	29	2.2	30	83	8	78	64	0	0	35	0.94
597716--597777	3	21.0	3	81	15	76	67	0	1	30	1.00
597716--597777	26	2.3	27	88	5	99	67	0	1	30	1.00
598331--598369	18	2.1	19	85	4	53	41	2	7	48	1.45
598828--598877	18	2.9	17	74	25	52	30	4	6	60	1.39
598632--599408	276	2.8	275	93	2	1341	38	7	8	45	1.64
604779--604830	20	2.6	21	75	9	54	30	11	30	26	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
605578--605850	137	2.0	135	91	2	440	25	13	18	42	1.86
609482--609521	21	1.9	21	100	0	80	62	5	0	32	1.17
615638--615663	2	13.0	2	100	0	52	50	0	0	50	1.00
620027--620397	45	8.3	45	84	3	498	24	18	15	40	1.90
620066--620142	26	3.2	25	67	24	67	23	18	15	42	1.88
620027--620397	179	2.1	180	87	3	525	24	18	15	40	1.90
624616--624816	63	3.1	64	77	18	225	24	24	15	34	1.95
626436--626651	45	4.8	45	82	2	254	27	15	15	41	1.88
626435--626651	90	2.4	90	82	0	290	27	15	15	41	1.88
626656--627019	45	8.1	45	90	2	545	24	20	15	39	1.92
626773--626894	25	5.3	24	64	22	73	22	21	16	40	1.91
626779--626900	26	5.2	26	59	28	67	21	19	16	42	1.89
626656--627019	134	2.7	135	90	2	556	24	20	15	39	1.92
626656--627019	179	2.0	179	91	1	586	24	20	15	39	1.92
628309--628349	17	2.4	17	100	0	82	34	19	4	41	1.73
641153--641928	304	2.6	304	82	2	891	36	11	12	39	1.79
641234--642131	203	4.4	203	77	8	739	36	10	13	40	1.78
641144--642131	101	9.8	101	76	5	667	36	10	13	39	1.79
642301--643192	304	2.9	299	80	6	879	36	10	14	39	1.79
642303--643192	203	4.4	202	79	7	765	36	10	13	39	1.79
642293--643193	101	8.9	101	77	9	735	35	10	14	39	1.79
644768--644877	45	2.5	45	86	1	141	30	22	8	38	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
646643--646676	8	4.2	8	100	0	68	47	0	0	52	1.00
653498--653549	23	2.3	23	100	0	104	15	26	25	32	1.95
679441--679472	16	2.0	16	100	0	64	43	12	12	31	1.80
682399--682475	25	3.1	25	78	9	77	45	0	1	53	1.08
682478--682523	17	2.8	17	81	18	62	54	0	4	41	1.20
682610--682650	21	1.9	21	85	5	55	51	0	2	46	1.14
684853--684891	18	2.2	18	100	0	78	17	51	20	10	1.74
689135--689183	23	2.1	23	96	0	89	30	24	22	22	1.99
695621--696403	407	1.9	407	97	0	1485	36	16	12	34	1.87
697106--697162	20	2.6	24	79	20	72	28	31	10	29	1.90
698681--698749	30	2.2	30	85	15	95	34	5	17	42	1.73
698690--698749	30	2.0	30	93	6	104	33	6	16	43	1.74
698826--698866	22	1.9	21	90	5	64	26	36	17	19	1.94
698906--698979	20	3.7	20	83	3	94	20	28	22	28	1.99
699035--699088	21	2.6	21	100	0	108	24	29	24	22	1.99
699113--699152	20	1.9	22	90	10	66	37	35	10	17	1.83
699369--699438	34	2.1	33	89	5	106	35	14	25	24	1.93
700884--700924	19	2.1	19	86	4	55	56	17	0	26	1.41
700932--700968	19	1.9	19	88	0	56	45	2	16	35	1.61
702404--702484	21	3.9	21	78	16	80	22	35	20	20	1.96
702505--702579	20	3.7	20	82	3	96	17	28	24	30	1.97
702505--702584	41	2.0	41	89	0	124	18	26	26	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
703660--703698	20	2.0	20	94	0	69	15	10	10	64	1.50
703656--703699	10	4.4	10	85	0	52	15	9	9	65	1.45
703660--703750	37	2.6	35	78	14	114	14	14	13	58	1.64
703715--703746	14	2.3	14	94	0	55	9	15	18	56	1.66
704791--704843	27	1.9	28	85	11	74	39	7	7	45	1.61
705051--705096	24	1.9	24	86	0	65	21	23	10	43	1.84
710633--710703	36	1.9	37	83	8	92	15	14	23	46	1.82
712987--713053	28	2.4	28	92	0	107	22	10	25	41	1.85
725653--725705	19	2.7	20	85	11	74	30	33	16	18	1.94
725673--725806	65	2.1	64	83	9	166	29	24	20	25	1.99
731537--731617	24	3.5	24	70	20	75	22	24	23	29	1.99
737410--737439	2	15.0	2	100	0	60	50	0	0	50	1.00
739203--739322	35	3.3	36	88	5	172	43	18	5	33	1.72
739254--739314	21	3.2	21	61	29	55	42	19	4	32	1.73
739225--739349	35	3.5	35	86	7	130	42	16	7	33	1.76
743823--743942	35	3.3	36	89	5	181	43	20	5	31	1.73
743874--743934	21	3.2	21	65	29	64	42	21	4	31	1.74
743825--743969	35	4.1	36	82	11	133	41	18	6	33	1.76
753190--753218	14	2.0	15	93	6	51	20	6	10	62	1.50
758949--759039	20	4.6	20	73	14	82	34	21	14	29	1.93
762600--762648	22	2.3	21	76	10	55	34	22	14	28	1.93
763094--763138	24	1.9	23	90	4	72	33	2	13	51	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
763106--763142	18	2.1	18	89	0	56	32	5	10	51	1.60
763098--763150	24	2.2	24	86	0	70	37	3	11	47	1.58
763454--763540	39	2.2	39	93	0	156	45	21	14	17	1.84
763788--763926	61	2.2	60	85	8	172	51	15	1	30	1.52
765281--765333	21	2.5	21	81	6	63	22	26	32	18	1.97
765301--765399	21	4.7	21	76	8	94	22	20	34	23	1.97
765300--765399	42	2.4	42	78	6	121	23	20	34	23	1.97
765543--765576	4	8.5	4	86	0	50	70	2	0	26	1.01
765724--765845	63	1.9	63	80	3	138	32	34	13	19	1.90
767527--767577	20	2.5	20	75	12	59	50	19	13	15	1.77

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   63   64