genome.fa.s8488.2.7.7.80.10.50.1000.39.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: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  12876159

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   

This is table  39  of  54  ( 6450 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)
9457669--9457730	21	3.0	21	76	9	63	41	14	38	4	1.67
9457738--9457777	21	1.9	21	89	0	62	45	22	32	0	1.53
9458102--9458253	44	3.5	43	79	7	157	30	19	17	32	1.94
9458502--9458563	31	2.0	31	84	6	81	33	30	11	24	1.90
9462209--9462246	19	2.0	19	100	0	76	36	5	21	36	1.76
9465348--9465405	30	1.9	30	82	6	73	17	6	3	72	1.21
9465751--9465775	11	2.3	11	100	0	50	92	8	0	0	0.40
9475094--9475148	16	3.6	16	76	16	62	30	0	0	69	0.89
9475118--9475149	16	2.0	16	100	0	64	25	0	0	75	0.81
9475730--9475775	2	23.0	2	100	0	92	50	50	0	0	1.00
9475818--9475904	43	2.1	40	82	6	102	11	31	6	50	1.65
9475887--9475946	3	20.0	3	89	0	84	0	26	3	70	1.03
9475889--9475938	18	2.8	18	100	0	100	0	24	4	72	1.02
9475887--9475946	18	3.3	18	92	0	93	0	26	3	70	1.03
9475925--9476041	52	2.2	52	82	5	139	14	25	1	58	1.46
9478661--9478907	122	2.0	122	95	0	440	22	13	20	43	1.87
9486721--9486759	20	2.0	20	89	0	60	33	23	10	33	1.88
9496616--9496680	30	2.1	31	83	13	82	29	13	29	27	1.95
9496977--9497015	20	2.0	20	89	0	60	33	23	10	33	1.88
9497489--9497542	2	27.0	2	92	0	90	46	0	3	50	1.19
9499955--9499979	13	1.9	13	100	0	50	24	8	12	56	1.62
9510107--9510143	14	2.6	14	95	0	65	37	29	0	32	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9516472--9516540	32	2.2	32	91	0	111	26	21	2	49	1.64
9516482--9516546	32	2.0	32	100	0	130	24	23	3	49	1.64
9516779--9516817	20	1.9	19	85	10	51	43	23	2	30	1.67
9522148--9522287	38	3.8	37	86	6	194	40	4	11	43	1.60
9522148--9522287	74	1.9	76	88	5	214	40	4	11	43	1.60
9523632--9523682	4	12.0	4	83	8	57	21	0	1	76	0.88
9523632--9523682	17	2.9	17	91	2	75	21	0	1	76	0.88
9523632--9523674	13	3.3	12	87	12	59	20	0	0	79	0.74
9524135--9524212	23	3.3	23	92	1	120	57	24	5	12	1.55
9526011--9526749	376	2.0	376	91	0	1190	35	12	23	28	1.92
9527799--9527862	15	4.3	15	76	7	67	43	25	6	25	1.77
9527803--9527861	30	2.0	30	90	6	93	42	23	6	27	1.79
9528346--9528395	21	2.4	21	87	9	68	34	24	12	30	1.91
9537033--9537170	64	2.2	63	82	10	156	28	18	22	30	1.97
9538515--9538590	24	3.1	24	79	9	66	30	19	23	26	1.98
9538578--9538657	23	3.4	23	74	3	79	33	25	22	18	1.97
9538764--9538830	15	4.4	15	76	10	64	47	22	4	25	1.70
9545580--9546096	261	2.0	250	95	4	928	32	18	10	38	1.85
9552646--9552719	22	3.5	22	83	8	93	31	32	21	14	1.94
9556621--9556665	22	2.1	21	87	4	63	42	0	11	46	1.39
9556666--9556783	37	3.3	36	75	15	118	44	4	11	39	1.59
9556727--9556753	13	2.1	13	100	0	54	44	7	7	40	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9556666--9556783	35	3.3	35	78	13	123	44	4	11	39	1.59
9556654--9556796	71	2.0	73	86	2	200	46	3	9	39	1.54
9558541--9558595	25	2.1	27	83	6	69	43	1	0	54	1.10
9558691--9558977	5	57.8	5	69	20	110	17	6	1	74	1.11
9558696--9558977	9	31.1	9	70	17	138	17	6	1	74	1.12
9558781--9558828	4	11.8	4	83	16	55	25	0	0	75	0.81
9558751--9558841	46	2.0	46	82	8	114	21	3	0	74	0.96
9558835--9558882	16	3.1	16	80	19	66	4	10	2	83	0.87
9558893--9558978	19	4.6	19	78	9	97	17	4	1	76	1.01
9558874--9558978	38	2.7	39	88	7	144	17	6	1	74	1.12
9563856--9563898	22	2.0	22	81	9	52	37	0	2	60	1.10
9563937--9564232	5	59.2	5	68	20	131	17	7	1	73	1.14
9563939--9564232	9	31.0	9	66	14	85	17	7	1	73	1.14
9563984--9564232	14	17.9	15	69	23	122	18	6	1	73	1.13
9563980--9564220	69	3.8	64	74	17	173	18	7	1	73	1.15
9564145--9564232	22	4.2	23	77	15	68	15	6	0	77	0.97
9564005--9564232	106	2.2	103	81	12	263	17	6	1	73	1.13
9564864--9564920	28	2.0	30	86	6	82	26	3	1	68	1.15
9569388--9569449	21	3.0	21	85	0	88	30	24	14	30	1.95
9574294--9574332	17	2.3	17	86	0	51	56	0	2	41	1.13
9583679--9583761	23	3.8	21	77	10	69	24	30	22	22	1.99
9583680--9583744	23	2.8	23	83	4	78	21	29	23	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9583680--9583761	22	3.7	22	78	9	69	23	30	23	23	1.99
9593231--9593283	24	2.2	24	82	0	70	58	16	15	9	1.62
9593377--9593415	17	2.4	16	84	16	53	38	2	17	41	1.64
9600688--9600788	7	14.3	7	80	13	50	17	0	30	51	1.46
9600700--9600788	21	4.2	21	79	2	97	16	0	31	51	1.45
9600688--9600788	14	7.1	14	78	6	89	17	0	30	51	1.46
9600700--9600780	29	2.8	29	85	9	112	16	0	30	53	1.43
9601182--9601214	17	1.9	18	88	11	52	60	18	9	12	1.57
9604215--9604287	23	3.2	23	92	0	119	34	4	21	39	1.73
9606328--9606462	62	2.2	62	90	0	207	58	3	2	34	1.31
9607148--9607194	5	9.4	5	77	9	51	74	4	4	17	1.14
9607106--9607201	31	3.2	30	72	18	85	73	8	4	13	1.20
9607232--9607290	23	2.8	20	76	7	55	76	5	3	15	1.10
9607358--9607406	2	24.5	2	100	0	98	51	0	0	48	1.00
9608515--9608561	20	2.3	21	85	3	60	48	0	4	46	1.21
9610249--9610292	7	6.7	7	84	10	58	0	13	0	86	0.57
9610244--9610290	6	7.7	6	84	11	51	0	12	0	87	0.55
9610244--9610289	10	4.4	10	84	15	58	0	13	0	86	0.56
9610254--9610284	9	3.3	9	91	8	53	0	9	0	90	0.46
9610244--9610292	16	3.0	16	88	11	73	0	14	0	85	0.59
9610254--9610393	75	1.9	75	82	4	176	10	16	10	62	1.53
9617459--9617495	17	2.2	17	95	0	65	29	27	0	43	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9620021--9620071	13	3.9	13	76	19	52	74	11	1	11	1.15
9620073--9620119	5	9.4	5	81	9	60	76	2	4	17	1.04
9620030--9620102	18	3.9	18	72	16	60	73	9	2	13	1.18
9620461--9620846	20	19.1	20	69	13	114	38	24	17	19	1.93
9620513--9620843	41	8.2	41	82	5	361	38	25	16	19	1.92
9620527--9620823	20	14.7	21	72	13	164	38	24	16	19	1.92
9620513--9620845	60	5.5	61	86	4	424	38	25	16	19	1.93
9621120--9621395	20	13.6	20	68	15	113	38	23	17	20	1.93
9621120--9621392	40	6.7	40	80	8	202	38	23	17	20	1.93
9621159--9621392	41	5.8	41	86	5	280	37	23	17	21	1.94
9621606--9621738	21	6.5	20	77	9	99	37	23	18	20	1.94
9620592--9622011	549	2.6	549	92	1	2280	37	22	15	24	1.93
9621730--9621943	20	10.6	20	73	6	162	38	23	17	20	1.93
9621730--9621941	41	5.2	41	84	2	266	39	23	16	20	1.92
9622559--9622642	38	2.4	33	82	9	96	48	21	17	11	1.79
9622504--9622633	19	6.9	19	73	14	108	49	20	16	13	1.79
9622670--9622733	20	3.1	21	82	8	78	10	25	17	46	1.80
9626300--9626398	19	5.7	19	70	24	67	46	21	20	12	1.82
9626300--9626393	33	2.8	33	90	3	136	45	21	20	12	1.84
9626332--9626408	19	4.3	19	79	18	85	45	24	16	12	1.83
9626408--9626502	33	2.9	33	93	0	154	10	25	20	44	1.83
9626441--9626554	52	2.2	53	90	4	178	10	21	22	44	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9628776--9628807	9	3.6	9	95	0	55	0	25	0	75	0.81
9628983--9629036	24	2.2	24	93	0	90	40	20	18	20	1.91
9628983--9629050	24	2.8	24	84	0	64	38	20	17	23	1.93
9630246--9630287	22	1.9	22	100	0	84	19	42	14	23	1.87
9630629--9630699	20	3.5	20	84	5	90	52	18	16	12	1.75
9630713--9630791	33	2.4	33	89	2	113	8	24	25	41	1.83
9630756--9630811	20	2.8	20	77	20	71	14	21	21	42	1.88
9632836--9632902	21	3.2	21	66	6	55	23	35	20	19	1.95
9632784--9632902	42	2.8	42	81	5	107	22	36	18	22	1.95
9634233--9634268	14	2.6	14	95	0	63	33	0	22	44	1.53

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