genome.fa.s2.2.7.7.80.10.50.1000.5.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: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2131600

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

This is table  5  of  10  ( 1119 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)
1208984--1209177	94	2.1	93	79	5	203	36	12	26	24	1.91
1209480--1209809	54	6.1	54	94	1	547	33	14	16	35	1.89
1210704--1210759	28	2.0	27	86	10	78	16	5	3	75	1.13
1213297--1213338	20	2.2	20	86	4	59	35	33	0	30	1.58
1216150--1216211	21	3.0	21	84	9	74	59	0	0	40	0.97
1216715--1216786	25	2.6	28	76	12	78	52	5	1	40	1.33
1218770--1218807	18	2.1	18	100	0	76	21	28	10	39	1.86
1227648--1227741	27	3.4	26	80	15	75	29	7	6	56	1.52
1227677--1227741	27	2.4	27	89	5	96	30	4	7	56	1.48
1227739--1227821	29	2.7	29	75	21	80	28	7	8	55	1.56
1227909--1228043	72	1.9	72	83	6	175	32	10	5	51	1.58
1227979--1228059	43	1.9	42	82	7	101	35	12	2	49	1.54
1228431--1228462	12	2.7	12	95	0	55	31	37	0	31	1.58
1235375--1235424	20	2.6	18	77	22	57	32	4	4	60	1.34
1236013--1236094	35	2.3	35	82	0	110	46	12	9	31	1.74
1236010--1236091	18	4.7	18	77	4	78	45	13	9	31	1.76
1237002--1237056	29	2.0	27	82	10	67	50	9	5	34	1.57
1238700--1238785	30	2.8	31	72	19	83	37	18	2	41	1.63
1258253--1258362	31	3.5	31	97	0	193	15	12	26	45	1.82
1258411--1258500	23	3.9	23	83	2	108	55	20	12	12	1.68
1258373--1258500	24	5.4	24	74	2	107	53	18	15	11	1.71
1260818--1260877	7	9.0	7	75	10	54	41	25	1	31	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1260820--1260857	20	1.9	20	88	0	58	39	28	0	31	1.57
1263573--1263610	19	2.0	20	89	5	60	52	2	13	31	1.54
1264367--1264447	36	2.2	36	84	6	110	41	2	1	54	1.21
1264440--1264471	2	16.5	2	93	6	57	50	0	0	50	1.00
1264855--1264891	16	2.3	16	90	0	65	43	16	13	27	1.85
1271926--1271950	13	1.9	13	100	0	50	44	16	32	8	1.76
1273053--1273486	44	9.9	44	88	5	601	41	12	20	25	1.88
1273053--1273489	132	3.3	131	91	1	687	41	12	20	25	1.88
1273356--1273472	25	5.2	24	61	23	65	39	15	21	23	1.91
1276601--1276633	11	2.8	12	90	9	50	75	9	0	15	1.03
1281403--1281452	20	2.5	20	87	3	66	54	4	12	30	1.55
1290734--1290797	24	2.7	23	80	4	65	37	28	12	21	1.90
1298412--1298577	38	4.4	37	77	13	151	40	3	12	43	1.60
1298453--1298577	37	3.3	36	78	13	117	40	4	14	41	1.64
1298546--1298590	23	2.0	23	95	0	81	44	2	11	42	1.52
1298547--1298601	23	2.3	23	84	3	65	49	3	9	38	1.52
1298603--1298654	24	2.1	25	89	3	79	53	3	1	40	1.30
1298696--1298743	22	2.3	20	85	7	69	43	4	6	45	1.48
1298756--1298837	4	19.8	4	81	16	96	29	0	0	70	0.87
1298756--1298837	25	3.3	25	81	16	107	29	0	0	70	0.87
1305232--1305258	14	1.9	14	100	0	54	22	40	7	29	1.81
1307631--1307695	29	2.2	29	78	10	78	35	4	24	35	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1308321--1308457	59	2.3	59	83	2	195	28	18	24	28	1.98
1315237--1315342	33	2.9	37	67	24	91	28	19	13	38	1.89
1318458--1318494	11	3.4	11	96	0	65	67	0	16	16	1.23
1324051--1324111	24	2.6	24	86	2	79	26	21	26	26	1.99
1325667--1325716	1	50.0	1	87	0	73	0	6	0	94	0.33
1325669--1325730	12	5.1	12	88	3	88	0	11	0	88	0.51
1325667--1325714	17	2.8	17	96	3	87	0	6	0	93	0.34
1325661--1325728	20	3.5	20	88	8	95	0	11	0	88	0.52
1325668--1325730	25	2.6	25	87	5	76	0	11	0	88	0.50
1325677--1325730	4	14.2	4	86	3	51	0	12	0	87	0.56
1327042--1327083	20	2.0	21	86	4	59	64	9	2	23	1.35
1327042--1327095	21	2.6	20	82	5	63	62	7	3	25	1.38
1331500--1331658	79	2.0	79	98	0	309	33	7	22	37	1.82
1332276--1332317	20	2.0	21	86	4	59	45	7	19	28	1.76
1337396--1337569	87	2.0	87	91	0	285	33	14	13	37	1.86
1337529--1337695	82	2.0	83	97	2	318	31	13	16	37	1.88
1337750--1337921	85	2.0	86	91	2	283	33	15	12	38	1.85
1338144--1338221	38	2.1	38	90	0	120	19	21	16	42	1.89
1338839--1338876	19	2.1	18	85	9	51	36	13	7	42	1.73
1341257--1341300	19	2.3	19	88	0	61	22	9	11	56	1.62
1344100--1344756	57	11.5	57	85	3	813	36	10	18	34	1.86
1345420--1345660	45	5.4	45	93	0	374	43	7	23	25	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1349340--1349825	57	8.5	57	90	0	720	34	11	19	33	1.89
1350489--1350630	45	3.2	45	84	2	196	43	7	24	24	1.79
1350595--1350658	28	2.3	28	88	0	92	46	4	23	25	1.71
1358680--1358849	68	2.5	69	85	4	211	34	22	20	22	1.97
1358692--1358849	69	2.3	68	85	5	194	34	22	19	24	1.97
1358692--1358881	69	2.8	69	82	5	181	33	22	21	23	1.97
1360450--1360501	15	3.5	15	83	0	77	11	15	63	9	1.52
1363896--1363955	27	2.4	25	75	21	63	50	15	5	30	1.65
1366610--1366732	22	5.3	25	80	11	111	52	21	0	25	1.53
1366762--1366854	17	5.8	17	72	20	67	66	1	2	30	1.10
1366761--1366864	24	4.3	23	73	22	72	67	0	1	29	1.08
1366832--1366864	10	3.0	11	86	13	50	75	0	0	24	0.80
1368433--1368644	106	2.0	105	88	2	318	20	21	26	31	1.98
1368594--1368773	64	2.8	64	97	0	333	19	21	25	33	1.97
1369866--1369906	1	41.0	1	90	0	64	0	0	4	95	0.28
1369866--1369917	12	4.1	13	87	9	72	0	3	5	90	0.55
1369855--1369910	24	2.4	23	84	3	76	1	5	3	89	0.65
1380954--1381074	23	5.3	22	79	8	116	52	21	0	25	1.53
1380942--1381074	47	2.9	46	78	6	135	51	21	0	25	1.53
1380953--1381074	22	5.3	24	80	11	121	51	22	0	25	1.53
1381099--1381132	2	17.5	2	87	6	52	55	0	0	44	0.99
1381101--1381138	8	4.3	9	87	12	53	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1381174--1381206	16	2.0	17	88	5	50	72	0	0	27	0.85
1382500--1382530	2	15.5	2	100	0	62	48	0	0	51	1.00
1387102--1387132	2	15.5	2	100	0	62	48	0	0	51	1.00
1390262--1390365	46	2.3	47	88	6	160	31	10	18	39	1.85
1390333--1390407	39	1.9	39	86	0	105	32	10	17	40	1.84
1390581--1390781	58	3.5	58	88	2	280	34	6	15	42	1.74
1391714--1391780	24	2.8	25	68	23	63	25	22	0	52	1.47
1391772--1391817	18	2.6	18	96	0	83	28	28	2	41	1.68
1393842--1393875	3	11.3	3	100	0	68	64	0	35	0	0.94
1394650--1394800	38	4.0	39	83	6	188	31	6	13	47	1.69
1394750--1394823	31	2.3	33	88	6	107	32	8	6	52	1.57
1396929--1397079	54	2.7	56	79	8	146	21	32	14	31	1.93
1412240--1412487	130	1.9	129	93	0	424	35	14	12	36	1.85
1412946--1412979	16	2.0	18	88	11	54	64	5	2	26	1.30
1413096--1413138	21	2.0	21	100	0	86	39	0	13	46	1.44
1413107--1413192	35	2.5	35	84	0	100	37	1	20	40	1.61
1413810--1414436	128	4.9	129	78	5	518	27	16	29	27	1.97
1414914--1414971	24	2.5	22	76	15	62	46	1	13	37	1.54
1416916--1416962	13	3.5	13	78	16	51	48	12	19	19	1.80
1416916--1416985	27	2.6	27	86	0	95	48	10	18	22	1.78
1417713--1417787	32	2.3	32	84	4	98	58	6	13	21	1.57
1420710--1420761	20	2.5	22	82	17	76	32	17	30	19	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1421262--1421517	46	5.4	46	84	7	352	46	10	21	22	1.81
1421287--1421762	26	20.0	26	72	20	400	46	10	20	22	1.81
1421359--1421630	119	2.3	119	94	1	465	46	10	20	21	1.81
1421333--1421727	166	2.4	168	86	8	565	46	10	20	22	1.81
1421504--1421762	46	5.6	46	92	1	401	46	10	20	22	1.81
1421504--1421762	93	2.8	93	92	0	430	46	10	20	22	1.81
1437180--1437240	3	20.7	3	86	9	90	34	0	0	65	0.93
1437525--1437560	19	1.9	19	88	5	56	27	22	22	27	1.99
1438539--1438567	12	2.4	12	100	0	58	31	6	0	62	1.22
1441123--1441160	14	2.7	14	91	0	67	34	15	0	50	1.45

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