genome.fa.s520.2.7.7.80.10.50.1000.8.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: VEPZ01000520.1 Hibiscus syriacus cultivar Beakdansim tig00000991_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1956684

Tables:   1   2   3   4   5   6   7   8   9   10   11   

This is table  8  of  11  ( 1212 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)
1340290--1340384	35	2.6	34	83	9	109	77	1	5	15	0.99
1340333--1340390	31	1.9	29	86	6	80	77	0	6	15	0.97
1340328--1340389	9	6.4	9	75	18	54	77	1	4	16	1.02
1340333--1340408	31	2.5	30	77	8	73	73	0	5	21	1.02
1340414--1340452	15	2.5	16	83	4	53	74	0	7	17	1.05
1340499--1340540	13	3.2	12	87	12	57	66	2	0	30	1.04
1341082--1341110	12	2.3	13	94	5	51	58	3	0	37	1.15
1341801--1341845	23	1.9	23	81	4	54	48	4	0	46	1.22
1342379--1342420	17	2.3	19	88	8	61	30	16	11	40	1.85
1347248--1347390	22	6.2	22	72	18	96	44	0	9	45	1.40
1347248--1347328	22	3.6	23	80	14	105	50	0	4	44	1.23
1347248--1347364	50	2.5	46	84	9	139	46	0	7	45	1.38
1347473--1347556	16	4.9	16	74	18	55	21	4	1	72	1.10
1347495--1347554	24	2.5	25	84	13	81	16	6	1	75	1.10
1347476--1347556	19	4.5	17	74	22	51	20	4	1	72	1.10
1348827--1348864	3	12.7	3	94	0	67	31	2	0	65	1.06
1350192--1350230	16	2.4	16	91	0	69	17	33	0	48	1.48
1351922--1351954	2	16.5	2	100	0	66	48	0	0	51	1.00
1357489--1357552	26	2.5	26	79	5	67	1	21	15	60	1.43
1358247--1358462	113	1.9	111	96	1	396	28	18	15	37	1.92
1358864--1358916	21	2.5	21	90	0	88	35	15	13	35	1.86
1361237--1361459	114	2.0	112	90	1	356	31	19	14	34	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1363968--1363996	2	15.0	2	92	7	51	51	0	0	48	1.00
1370857--1370920	26	2.5	26	79	5	67	1	21	15	60	1.43
1371595--1371661	35	1.9	35	84	0	89	26	4	14	53	1.60
1372245--1372300	24	2.5	24	83	13	66	60	5	1	32	1.29
1374463--1374505	16	2.6	17	77	3	52	58	0	0	41	0.98
1380105--1380223	43	2.8	43	82	0	148	29	17	25	27	1.98
1380667--1380715	21	2.3	21	89	0	71	6	38	14	40	1.71
1380704--1380764	21	2.9	21	80	0	77	4	39	14	40	1.68
1384422--1384580	52	3.1	52	97	0	300	43	15	7	33	1.75
1385849--1385941	42	2.2	42	80	10	102	34	24	12	27	1.92
1388723--1388770	21	2.3	21	96	0	87	41	12	18	27	1.86
1393370--1393417	21	2.3	21	96	0	87	41	12	18	27	1.86
1395334--1395466	3	44.3	3	98	0	257	65	0	0	33	0.98
1395821--1395898	34	2.3	34	82	4	86	51	0	1	47	1.09
1399334--1399367	3	11.3	3	100	0	68	32	0	0	67	0.91
1403061--1403393	167	2.0	164	97	2	623	41	10	21	26	1.86
1407060--1407131	22	3.0	25	71	22	73	75	0	13	11	1.06
1407063--1407122	18	3.2	18	81	11	66	76	0	13	10	1.01
1407074--1407144	22	3.1	22	74	20	58	78	0	12	8	0.95
1407739--1407772	15	2.2	16	89	5	52	50	20	20	8	1.75
1409137--1409312	44	4.0	43	91	2	262	28	14	30	26	1.95
1409137--1409312	87	2.0	87	88	2	264	28	14	30	26	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1409591--1409714	36	3.4	36	83	6	133	22	20	18	38	1.93
1410171--1410873	44	15.9	44	67	5	263	29	20	20	29	1.98
1410180--1411145	134	7.3	133	88	2	1334	29	20	20	29	1.98
1410180--1411145	397	2.4	398	88	2	1379	29	20	20	29	1.98
1414224--1414285	31	2.2	28	83	13	74	29	29	24	17	1.97
1414939--1414972	2	17.0	2	93	0	59	47	0	2	50	1.16
1419152--1419560	116	3.5	115	77	7	310	36	14	21	26	1.92
1420214--1420254	3	13.7	3	100	0	82	31	0	0	68	0.90
1420802--1420829	9	3.1	9	100	0	56	32	0	42	25	1.55
1423382--1423408	14	1.9	14	100	0	54	44	25	0	29	1.54
1427647--1427694	3	15.3	3	79	16	53	64	0	33	2	1.05
1432513--1432545	2	16.5	2	100	0	66	51	0	0	48	1.00
1441696--1441795	5	18.8	5	73	15	67	70	3	6	21	1.23
1441730--1441768	21	1.9	21	89	5	62	69	0	7	23	1.14
1447328--1448140	408	2.0	408	95	0	1457	30	23	18	26	1.98
1454022--1454987	182	5.3	182	88	0	1360	43	13	15	28	1.84
1458063--1458120	20	2.6	22	86	10	75	31	18	22	27	1.97
1459684--1459752	23	3.0	23	76	0	75	18	26	24	30	1.98
1463184--1463239	20	2.6	20	80	11	58	33	17	21	26	1.96
1464027--1464317	2	147.0	2	88	2	435	48	3	1	46	1.27
1465084--1465151	23	3.0	23	77	0	73	17	26	25	30	1.97
1466317--1466356	18	2.2	18	100	0	80	55	0	40	5	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1469168--1469452	128	2.2	128	82	6	344	44	11	12	30	1.79
1469317--1470283	199	4.8	197	87	4	1305	40	13	15	31	1.85
1470914--1470952	20	2.0	19	95	5	69	41	30	7	20	1.80
1473049--1473093	24	1.9	23	86	4	63	33	2	13	51	1.53
1473053--1473105	24	2.2	24	82	0	61	37	3	11	47	1.58
1474279--1474325	2	23.5	2	100	0	94	48	0	0	51	1.00
1474774--1474823	23	2.2	23	88	0	73	32	16	12	40	1.84
1474644--1475009	157	2.3	156	93	1	633	32	13	13	40	1.83
1474913--1475084	87	2.0	86	88	1	254	32	14	10	42	1.80
1486290--1486357	11	6.4	11	83	8	79	80	10	0	8	0.89
1486290--1486380	42	2.2	42	84	7	114	79	8	4	7	1.06
1486463--1486489	2	13.5	2	100	0	54	51	0	0	48	1.00
1487764--1487814	2	26.0	2	96	4	95	49	0	0	50	1.00
1488347--1488644	85	3.5	85	85	1	400	27	17	19	35	1.95
1489030--1489783	64	11.7	64	91	1	1177	29	12	21	35	1.91
1490596--1490895	95	3.1	98	85	5	398	32	18	16	33	1.93
1493937--1494000	21	3.0	21	86	0	83	25	17	31	26	1.97
1497516--1497631	5	22.8	5	71	16	69	76	5	2	15	1.07
1497553--1497631	21	3.7	21	80	12	90	78	7	0	13	0.95
1497562--1497630	11	6.3	11	78	11	79	79	8	0	11	0.93
1497529--1497631	16	6.3	15	73	12	62	77	5	2	13	1.06
1497562--1497631	32	2.2	33	84	7	90	78	8	0	12	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1498974--1499032	2	31.0	2	90	10	97	49	0	0	50	1.00
1501382--1501426	22	2.1	22	88	12	67	44	2	0	53	1.13
1501382--1501447	21	3.2	21	75	16	66	46	1	0	51	1.10
1501390--1501516	42	3.0	43	79	8	136	48	2	0	48	1.20
1506286--1506325	3	13.3	3	89	10	64	65	0	0	35	0.93
1506513--1506839	135	2.5	133	81	2	363	25	18	30	25	1.98
1506869--1507070	65	3.1	66	85	7	277	39	13	20	26	1.90
1506940--1507056	37	3.4	36	70	20	124	39	14	19	26	1.90
1508390--1508434	23	1.9	24	90	4	74	2	13	4	80	0.97
1508415--1508448	13	2.5	14	85	9	52	2	11	8	76	1.12
1508395--1508468	36	2.1	35	87	7	105	1	9	8	81	0.94
1508394--1508468	23	3.2	23	76	21	68	1	10	8	80	0.98
1508510--1508717	69	3.0	69	98	0	398	14	21	23	40	1.90
1520438--1520499	16	3.4	19	74	19	60	32	12	19	35	1.90
1521025--1521058	12	2.8	12	90	4	50	38	11	2	47	1.55
1522498--1522556	20	2.9	20	82	12	59	23	0	16	59	1.37
1523298--1523353	20	2.8	20	94	0	103	35	21	23	19	1.96
1526712--1526781	3	23.3	3	94	5	124	67	0	0	32	0.91
1527115--1527150	2	18.0	2	94	0	63	47	0	0	52	1.00
1530070--1530110	3	14.3	3	85	10	59	34	0	0	65	0.93
1530070--1530110	14	2.9	14	92	3	64	34	0	0	65	0.93
1534639--1534716	3	26.0	3	94	0	138	33	1	1	64	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1535175--1535226	24	2.2	24	82	0	59	65	7	23	3	1.35
1536011--1536056	17	2.7	17	89	0	74	15	4	4	76	1.11
1536811--1536852	23	1.9	23	85	9	61	28	0	2	69	1.01
1536845--1536881	15	2.7	15	88	12	53	24	5	8	62	1.44
1547455--1547503	12	4.0	12	82	12	55	79	0	16	4	0.88
1547455--1547492	13	3.0	13	88	3	51	81	0	13	5	0.85
1547477--1547505	11	2.6	11	100	0	58	75	0	24	0	0.80
1548628--1549059	83	5.2	84	96	1	782	27	14	21	36	1.92
1549769--1550546	113	6.9	112	96	1	1360	38	12	20	29	1.89
1549766--1550546	337	2.3	335	94	1	1357	38	12	20	29	1.89

Tables:   1   2   3   4   5   6   7   8   9   10   11