genome.fa.s9070.2.7.7.80.10.50.1000.5.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: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2268343

Tables:   1   2   3   4   5   6   7   8   9   

This is table  5  of  9  ( 1013 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)
1122041--1123122	106	10.3	106	89	3	1600	23	18	24	33	1.96
1127000--1127031	6	5.2	6	96	3	55	68	0	0	31	0.90
1128083--1128142	3	20.7	3	77	19	65	65	0	0	35	0.93
1128078--1128124	16	2.8	16	90	6	67	68	0	0	31	0.90
1128085--1128137	16	3.6	14	82	14	54	66	0	0	33	0.92
1128084--1128142	25	2.4	26	83	16	81	66	0	0	33	0.92
1128099--1128143	5	9.2	5	83	16	51	62	0	0	37	0.96
1128083--1128140	22	2.6	22	89	5	82	65	0	0	34	0.93
1128912--1128979	14	5.2	13	77	7	57	27	1	30	39	1.66
1129994--1130064	29	2.4	29	95	0	124	43	22	1	32	1.62
1135057--1135488	220	2.0	216	84	7	559	47	6	5	40	1.52
1136342--1136377	15	2.4	15	90	0	54	55	0	2	41	1.14
1137008--1137039	2	15.5	2	93	6	55	50	0	3	46	1.17
1138191--1138237	15	3.0	15	90	6	67	42	2	0	55	1.12
1138238--1138268	16	1.9	16	93	0	53	35	16	6	41	1.74
1140800--1141019	114	1.9	114	88	1	334	20	25	16	36	1.94
1145515--1145545	12	2.6	12	89	0	53	9	19	48	22	1.78
1145569--1145637	2	37.5	2	75	16	69	49	0	0	50	1.00
1145704--1145772	35	1.9	36	88	2	104	20	33	11	34	1.89
1148340--1148381	15	2.6	16	77	7	50	45	4	4	45	1.45
1148647--1148682	17	2.1	17	89	0	54	66	0	2	30	1.06
1153822--1153855	16	2.1	16	89	10	52	64	0	0	35	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1167534--1167579	22	2.2	21	85	14	60	36	4	0	58	1.18
1169131--1169179	21	2.3	22	82	13	66	44	0	2	53	1.12
1171162--1171217	19	2.9	19	85	12	78	16	21	28	33	1.95
1171162--1171210	10	4.8	11	83	16	70	16	20	26	36	1.93
1171163--1171217	9	5.6	10	83	12	78	14	21	29	34	1.93
1171230--1171260	13	2.4	13	94	0	53	16	48	19	16	1.81
1171272--1171347	29	2.6	29	89	0	107	22	9	26	42	1.83
1178431--1178466	11	3.6	10	88	11	56	13	22	30	33	1.93
1178479--1178515	13	2.8	13	95	0	65	16	45	18	18	1.85
1178523--1178598	29	2.6	29	87	0	98	21	10	27	40	1.86
1183432--1183800	20	18.5	20	84	4	449	34	26	18	20	1.96
1184483--1184529	24	2.0	24	87	8	69	25	14	21	38	1.92
1186897--1187093	33	5.8	33	82	14	242	47	18	20	13	1.82
1186886--1187112	52	4.4	52	91	5	338	47	17	21	14	1.83
1186897--1187134	85	2.8	85	89	6	351	46	18	21	14	1.83
1186930--1187134	52	3.9	52	90	6	214	46	18	20	14	1.83
1187141--1187243	20	5.6	19	83	14	144	14	23	17	44	1.85
1187350--1187386	14	2.6	14	91	0	65	45	21	0	32	1.52
1189367--1189423	14	3.7	14	77	20	60	45	22	21	10	1.82
1189348--1189440	33	2.8	33	91	0	150	48	21	18	11	1.80
1189311--1189445	19	7.6	19	74	16	110	46	23	17	11	1.81
1189441--1189569	19	7.3	19	75	17	125	8	17	28	45	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1189441--1189532	33	2.8	33	93	3	150	7	18	28	45	1.76
1189601--1190067	93	5.0	93	98	0	909	46	18	12	22	1.83
1189601--1190067	185	2.5	186	98	0	909	46	18	12	22	1.83
1191774--1191863	14	5.7	14	74	23	81	42	22	25	10	1.84
1191766--1191880	33	3.5	33	93	0	203	45	20	25	9	1.81
1191773--1191885	19	6.8	18	72	23	79	43	21	25	9	1.83
1191897--1191951	14	3.6	14	73	21	56	10	25	21	41	1.86
1191881--1191951	33	2.2	33	92	0	115	9	22	23	43	1.83
1191892--1191973	33	2.5	33	87	2	110	10	25	20	42	1.85
1191904--1191992	20	4.8	20	72	19	75	13	24	17	43	1.85
1192075--1192143	32	2.2	32	91	0	111	46	20	21	11	1.82
1192094--1192143	16	3.0	18	69	22	54	44	22	22	12	1.85
1192323--1192377	22	2.5	22	81	0	74	20	16	40	23	1.91
1192523--1192715	20	9.6	20	82	5	219	19	19	25	35	1.95
1192523--1192715	60	3.2	60	83	0	251	19	19	25	35	1.95
1192771--1192822	20	2.6	20	96	0	95	21	13	26	38	1.90
1193809--1193841	2	16.5	2	100	0	66	48	0	0	51	1.00
1198796--1198854	31	1.9	31	86	10	86	37	6	20	35	1.79
1199842--1199917	31	2.5	31	91	0	125	23	18	19	38	1.93
1199842--1199933	31	3.0	31	88	0	103	23	18	21	35	1.95
1210874--1210911	14	2.7	14	95	0	67	57	5	36	0	1.21
1212271--1212299	2	15.0	2	92	7	51	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1215517--1215739	121	1.8	122	86	0	322	45	10	8	35	1.69
1221773--1221877	31	3.4	31	74	10	90	24	25	29	20	1.99
1222990--1223117	30	4.2	30	92	1	193	34	24	17	23	1.96
1223078--1223153	31	2.4	32	86	4	102	34	21	14	30	1.93
1223078--1223170	31	3.0	31	81	6	91	35	20	16	27	1.94
1223345--1223369	4	6.2	4	100	0	50	48	24	0	28	1.52
1224230--1224290	21	2.7	24	80	15	83	9	39	26	24	1.86
1224245--1224290	21	2.2	21	100	0	92	8	43	21	26	1.81
1224318--1224360	21	2.0	21	81	0	50	16	25	30	27	1.97
1227678--1227780	30	3.4	30	93	0	170	33	24	18	24	1.97
1227678--1227805	60	2.1	61	85	1	168	34	25	17	22	1.96
1227766--1227858	31	3.0	31	79	3	98	34	21	17	26	1.95
1228972--1229014	21	2.0	21	81	0	50	16	25	30	27	1.97
1233035--1233166	59	2.2	60	85	4	169	34	18	4	41	1.71
1235904--1235931	2	14.0	2	100	0	56	50	0	0	50	1.00
1236186--1236278	32	2.9	31	81	7	107	46	16	17	20	1.84
1241000--1241676	91	7.5	91	87	2	904	24	20	17	37	1.93
1241000--1241663	181	3.7	182	86	5	904	24	20	17	37	1.93
1240947--1241677	272	2.7	273	85	5	933	24	20	17	38	1.93
1242032--1242473	66	6.6	67	76	9	334	40	13	19	27	1.88
1242021--1242402	131	2.9	133	82	6	465	39	12	20	28	1.89
1242352--1242872	36	15.4	35	70	16	268	40	13	19	26	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1242460--1242770	65	4.8	65	76	13	296	40	12	19	27	1.88
1242597--1242700	32	3.1	33	74	10	93	42	15	19	23	1.89
1242525--1242815	133	2.2	131	82	8	345	41	13	19	26	1.88
1242388--1242749	196	1.8	198	87	2	539	39	13	19	26	1.89
1242352--1242872	101	5.1	101	74	15	416	40	13	19	26	1.89
1242763--1242887	65	1.9	65	91	0	205	42	12	18	27	1.85
1243685--1243757	36	2.0	36	83	0	92	32	13	6	46	1.70
1245583--1245866	148	1.9	149	89	3	448	21	24	19	34	1.96
1246998--1247036	17	2.4	17	95	4	71	43	0	5	51	1.24
1250750--1250792	14	3.0	15	83	10	54	76	6	0	16	0.99
1257837--1257912	27	2.6	30	78	18	88	44	0	1	53	1.08
1257858--1257895	18	2.0	19	85	10	51	36	0	0	63	0.95
1257975--1258067	19	4.5	19	75	17	55	56	2	1	39	1.18
1257967--1258085	45	2.8	42	85	10	113	56	1	1	40	1.19
1257999--1258081	23	3.7	23	83	3	114	53	2	1	43	1.21
1257990--1258086	45	2.2	44	92	3	167	53	2	1	43	1.19
1260063--1260168	35	2.9	38	87	8	157	46	19	3	30	1.68
1260114--1260174	21	3.2	21	63	29	55	42	19	4	32	1.73
1265236--1265282	25	1.9	24	86	4	67	63	0	0	36	0.94
1269080--1269134	25	2.0	26	83	13	67	60	0	0	40	0.97
1271936--1272005	31	2.3	31	82	7	81	25	24	2	47	1.66
1276899--1276941	16	2.8	16	89	3	61	32	11	6	48	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1280256--1280286	2	15.5	2	100	0	62	48	0	0	51	1.00
1280273--1280336	27	2.4	27	78	2	67	46	3	0	50	1.17
1306234--1306279	21	2.2	21	77	11	51	41	6	0	52	1.27
1307556--1307628	38	2.0	38	91	5	123	54	6	2	35	1.41
1322145--1322205	31	2.0	31	93	0	104	42	18	4	34	1.71
1325674--1325712	12	3.1	13	81	7	53	20	25	2	51	1.60
1331220--1331248	2	14.5	2	100	0	58	48	0	0	51	1.00
1331425--1331469	2	22.5	2	100	0	90	51	0	0	48	1.00
1333379--1333429	2	26.5	2	76	7	52	50	0	0	49	1.00
1333384--1333440	17	3.1	17	70	18	51	50	0	0	49	1.00

Tables:   1   2   3   4   5   6   7   8   9