genome.fa.s686.2.7.7.80.10.50.1000.5.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: VEPZ01000686.1 Hibiscus syriacus cultivar Beakdansim tig00001340_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1443669

Tables:   1   2   3   4   5   6   

This is table  5  of  6  ( 696 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)
1021383--1021453	22	3.3	21	69	9	54	16	22	39	21	1.92
1028941--1028975	17	2.1	17	88	0	52	40	8	14	37	1.76
1036839--1036894	18	3.1	18	94	0	94	33	16	17	32	1.92
1037428--1037838	125	3.2	125	89	4	588	33	16	20	28	1.95
1037583--1038424	139	6.1	136	86	4	847	35	16	21	26	1.94
1037678--1038424	139	5.4	139	87	3	936	36	16	21	26	1.94
1039911--1039975	11	6.2	10	78	18	62	18	1	4	75	1.05
1039911--1039975	16	4.1	15	81	15	62	18	1	4	75	1.05
1039911--1039975	5	12.4	5	77	18	62	18	1	4	75	1.05
1039922--1039975	8	6.9	8	74	19	51	18	1	3	75	1.03
1041842--1041899	2	29.0	2	100	0	116	50	0	0	50	1.00
1050513--1050554	2	21.5	2	95	4	77	50	0	0	50	1.00
1051301--1051333	16	2.0	17	88	5	50	27	3	6	63	1.32
1051829--1051875	23	2.1	21	84	7	58	34	19	14	31	1.92
1051802--1052046	130	1.9	130	93	0	427	35	13	14	35	1.86
1052446--1052521	35	2.2	35	90	4	118	34	2	23	39	1.69
1057092--1057147	21	2.7	21	97	0	103	39	23	23	14	1.91
1065088--1065144	30	1.9	30	92	0	96	28	7	14	50	1.68
1073599--1073640	9	4.7	9	80	8	50	66	0	7	26	1.17
1083729--1083786	29	2.0	30	83	10	75	34	18	3	43	1.68
1084841--1084901	33	1.9	31	86	6	86	47	13	8	31	1.71
1085172--1085233	32	1.9	32	93	0	106	14	8	29	48	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1085311--1085362	27	1.9	27	84	0	68	19	7	38	34	1.80
1096347--1097287	55	17.4	55	88	5	1172	29	14	27	28	1.95
1096347--1097287	271	3.5	272	89	3	1341	29	14	27	28	1.95
1096347--1097333	162	6.1	164	85	4	1143	28	14	27	28	1.96
1102224--1102289	30	2.2	31	81	10	82	39	12	7	40	1.71
1104342--1104388	2	24.0	2	95	4	87	51	0	0	48	1.00
1107220--1107358	72	1.9	71	82	7	174	40	21	16	21	1.91
1111920--1111965	21	2.1	22	92	4	76	50	2	0	47	1.13
1111936--1111970	18	1.9	18	88	11	54	51	0	0	48	1.00
1112274--1112497	92	2.4	92	88	3	335	29	16	19	33	1.94
1112458--1112532	36	2.1	36	92	2	125	24	18	20	37	1.94
1112146--1112752	220	2.8	220	84	5	787	28	17	19	34	1.94
1112383--1113009	128	4.9	128	76	15	623	28	16	20	35	1.94
1112494--1112710	93	2.4	92	80	8	253	29	17	19	34	1.94
1112683--1112787	36	2.9	36	95	1	185	24	19	20	35	1.96
1112586--1112915	162	2.0	163	87	4	479	26	17	20	35	1.94
1112383--1113102	383	1.9	385	87	3	1083	28	16	20	35	1.94
1112840--1112915	36	2.1	35	90	2	116	25	15	17	42	1.88
1112876--1113143	93	2.9	94	91	2	409	28	18	17	35	1.94
1113226--1113270	20	2.2	20	84	0	54	42	13	15	28	1.85
1120729--1120762	13	2.7	12	90	9	50	2	23	17	55	1.55
1121113--1121150	19	2.1	19	90	5	60	10	18	39	31	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1121725--1121791	28	2.4	28	100	0	134	31	10	5	52	1.60
1123701--1123738	17	2.3	17	86	4	51	68	2	7	21	1.28
1126863--1126929	11	5.7	11	77	14	55	34	0	0	65	0.93
1126864--1126932	17	4.0	17	81	17	72	31	0	0	68	0.90
1126867--1126928	10	6.9	9	75	21	51	33	0	0	66	0.92
1126979--1127049	33	2.2	33	89	0	115	40	22	12	23	1.88
1127416--1127488	27	2.4	29	78	19	71	30	4	1	64	1.20
1128539--1128577	20	2.0	20	89	0	60	33	2	5	58	1.33
1134964--1135050	27	3.2	27	95	1	147	22	13	18	44	1.85
1136470--1136515	20	2.3	20	92	0	74	36	21	6	34	1.80
1137412--1137771	177	2.0	182	97	2	685	27	15	23	33	1.95
1138470--1138524	2	27.5	2	100	0	110	49	0	0	50	1.00
1139444--1139485	21	2.0	21	100	0	84	9	9	33	47	1.68
1140991--1141181	54	3.5	54	90	1	303	34	13	15	37	1.86
1140987--1141181	108	1.8	108	94	2	347	34	13	14	36	1.86
1143250--1143274	10	2.5	10	100	0	50	32	12	20	36	1.89
1143415--1143482	17	4.0	17	82	3	66	41	10	5	42	1.63
1143416--1143485	34	2.1	34	83	5	88	41	11	5	41	1.65
1145728--1145775	21	2.3	21	96	0	87	29	18	25	27	1.98
1159984--1160076	38	2.4	38	89	3	134	27	8	22	40	1.83
1159981--1160088	38	2.8	38	81	5	130	26	9	23	40	1.84
1160062--1160178	36	3.2	36	85	9	166	39	14	20	25	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1160287--1160476	37	5.4	37	70	16	134	39	13	19	27	1.89
1160260--1160499	102	2.4	102	90	0	381	36	12	20	31	1.89
1160408--1160586	87	2.1	87	93	0	304	36	12	18	32	1.89
1160495--1160695	102	2.0	102	80	2	224	39	11	17	30	1.86
1160306--1160691	189	2.0	189	86	1	540	38	11	18	30	1.87
1160891--1161161	106	2.6	106	88	1	400	21	18	24	35	1.95
1161743--1161851	32	3.4	32	83	3	103	36	19	13	30	1.90
1161761--1161851	33	2.8	32	84	1	110	37	19	12	30	1.88
1162794--1162925	69	1.9	69	93	0	228	27	12	22	37	1.91
1163003--1163048	14	3.5	13	82	11	58	2	15	0	82	0.76
1162982--1163048	21	3.1	21	77	16	57	4	17	0	77	0.93
1164968--1165011	23	2.0	23	81	4	54	50	11	2	36	1.51
1170927--1170986	21	2.7	23	84	5	79	20	38	23	18	1.93
1170968--1171007	21	1.9	21	89	0	62	25	40	25	10	1.86
1179127--1179187	32	1.9	32	96	0	113	6	26	8	59	1.51
1180379--1180419	3	14.0	3	94	5	75	34	0	0	65	0.93
1180379--1180417	20	2.0	20	100	0	78	33	0	0	66	0.92
1184870--1185013	72	2.0	72	87	0	207	25	18	16	38	1.92
1189172--1190020	116	7.3	116	88	3	1231	30	20	20	28	1.98
1189172--1190020	234	3.6	233	90	1	1299	30	20	20	28	1.98
1189643--1189701	21	2.8	21	72	15	59	35	25	22	16	1.95
1189172--1190020	350	2.4	346	89	4	1281	30	20	20	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1201112--1201141	2	15.0	2	100	0	60	50	0	0	50	1.00
1203901--1203992	24	3.7	24	75	18	91	35	17	1	45	1.56
1204316--1204391	30	2.6	30	87	6	102	36	23	19	19	1.95
1206167--1206216	3	17.0	3	76	19	52	32	0	0	68	0.90
1206167--1206216	5	8.5	6	83	14	52	32	0	0	68	0.90
1206167--1206216	22	2.3	22	80	13	59	32	0	0	68	0.90
1207813--1207869	4	13.2	4	75	14	51	21	3	5	70	1.22
1207830--1207891	27	2.2	28	88	2	90	20	4	6	67	1.32
1207828--1207932	31	3.3	31	73	15	97	21	4	5	67	1.31
1215187--1215219	14	2.3	15	89	5	50	36	3	3	57	1.29
1217464--1217501	20	1.9	20	88	0	58	23	21	15	39	1.92
1221855--1221896	20	2.1	20	91	8	68	30	26	9	33	1.88
1223980--1224023	23	1.9	23	95	0	79	52	11	0	36	1.38
1228728--1229211	81	6.0	81	86	1	652	30	22	11	35	1.89
1228728--1229208	239	2.0	242	87	1	698	30	22	11	35	1.89
1230020--1230047	2	14.0	2	100	0	56	50	0	0	50	1.00
1231735--1231846	53	2.1	52	96	3	215	53	27	8	10	1.63
1232068--1232228	60	2.7	60	81	6	166	31	19	5	43	1.74
1233959--1234615	163	4.0	160	81	7	716	31	20	11	36	1.89
1233959--1234615	81	8.1	81	82	6	724	31	20	11	36	1.89
1233962--1234615	244	2.7	243	86	5	883	31	20	11	36	1.89
1234701--1234916	55	3.9	55	90	0	333	34	18	10	37	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1237434--1237764	81	4.1	81	88	0	473	30	22	9	37	1.86
1237850--1238075	55	4.1	55	86	2	303	36	18	10	34	1.84
1242016--1242139	46	2.7	46	76	13	123	26	16	10	45	1.80
1242216--1243593	81	17.1	81	87	1	1899	30	21	11	36	1.89
1243697--1243839	55	2.6	55	92	4	243	33	17	9	39	1.81
1244940--1244966	10	2.7	10	100	0	54	22	18	0	59	1.38
1245421--1245463	19	2.3	19	91	0	68	34	25	16	23	1.95
1245724--1245773	20	2.4	21	76	3	57	36	20	14	30	1.91
1251244--1252035	81	9.8	81	86	2	1002	31	24	11	33	1.90
1252616--1252665	19	2.4	21	87	9	68	30	16	16	38	1.90

Tables:   1   2   3   4   5   6