genome.fa.s1709.2.7.7.80.10.50.1000.7.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: VEPZ01001709.1 Hibiscus syriacus cultivar Beakdansim tig00003435_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1326839

Tables:   1   2   3   4   5   6   7   8   

This is table  7  of  8  ( 866 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)
1037379--1037418	19	2.1	19	95	0	71	42	10	12	35	1.76
1037819--1037872	24	2.2	24	90	0	81	24	18	14	42	1.88
1040143--1040178	18	2.0	18	94	0	63	55	22	2	19	1.56
1040573--1040622	25	2.0	25	96	0	91	26	8	22	44	1.80
1040999--1041051	24	2.2	24	89	0	79	37	1	13	47	1.54
1041988--1042022	6	5.8	6	86	0	52	60	20	2	17	1.49
1041989--1042029	18	2.3	18	95	0	73	56	24	2	17	1.53
1042014--1042519	150	3.4	150	96	0	933	30	16	14	38	1.88
1045372--1045426	23	2.5	21	80	11	65	23	25	25	25	2.00
1050814--1050864	20	2.5	20	83	0	75	23	23	37	15	1.93
1053249--1053367	21	5.7	21	81	3	132	21	20	36	21	1.96
1053249--1053369	42	2.9	42	87	0	170	22	20	35	21	1.96
1053511--1053556	4	11.5	4	85	0	65	69	2	2	26	1.11
1055527--1055565	20	1.9	21	89	5	62	15	10	20	53	1.70
1055911--1055953	22	2.0	22	100	0	86	20	13	41	23	1.88
1056113--1056158	20	2.3	20	92	0	74	19	13	26	41	1.88
1056800--1056831	13	2.3	15	89	10	50	68	9	3	18	1.30
1061270--1061341	2	36.0	2	100	0	144	50	0	0	50	1.00
1061566--1061644	2	39.5	2	100	0	158	49	0	0	50	1.00
1066096--1066248	58	2.6	58	80	8	166	28	22	7	41	1.81
1074538--1074634	21	4.6	21	77	14	92	43	0	2	54	1.11
1074538--1074632	24	4.2	23	80	7	81	43	0	2	54	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1074589--1074634	13	3.7	13	80	16	53	43	0	0	56	0.99
1074759--1074796	17	2.2	17	100	0	76	39	39	15	5	1.70
1075066--1075108	19	2.3	19	95	0	77	20	32	25	20	1.97
1075302--1075330	2	14.5	2	100	0	58	48	0	0	51	1.00
1076079--1076109	14	2.2	14	94	0	53	54	25	19	0	1.44
1077013--1077064	21	2.5	21	100	0	104	30	34	15	19	1.93
1077188--1077226	19	2.1	19	85	0	51	33	28	7	30	1.85
1080253--1080331	35	2.3	34	85	12	99	34	6	5	54	1.48
1083856--1084009	80	1.9	80	96	1	283	33	8	1	55	1.41
1084636--1084684	23	2.1	23	84	0	62	38	8	20	32	1.82
1084600--1084759	87	1.8	87	95	0	293	41	10	14	33	1.79
1084756--1085478	199	3.6	198	87	3	992	30	15	14	38	1.88
1088202--1088249	19	2.5	19	96	0	87	52	10	6	31	1.60
1089699--1090450	200	3.8	200	83	3	932	32	14	14	38	1.87
1091970--1092025	24	2.3	24	84	6	78	50	12	5	32	1.63
1091970--1092006	18	2.1	18	89	0	56	51	10	5	32	1.60
1096901--1096954	23	2.3	23	83	0	63	27	18	33	20	1.96
1100808--1101029	117	1.9	117	82	5	279	27	14	9	48	1.75
1103246--1103295	15	3.1	15	83	13	64	24	6	40	30	1.79
1103602--1105682	199	10.4	199	92	0	3217	33	14	14	38	1.86
1107543--1107571	14	2.0	15	93	6	51	10	41	0	48	1.37
1110080--1110555	180	2.6	179	87	2	650	26	15	13	43	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1119726--1119757	2	16.0	2	100	0	64	50	0	0	50	1.00
1125142--1125174	15	2.2	15	100	0	66	66	12	0	21	1.23
1125452--1125483	2	16.5	2	93	6	57	46	0	0	53	1.00
1133226--1133263	20	2.1	19	85	14	53	76	15	5	2	1.08
1134051--1134105	22	2.5	22	77	19	53	21	0	30	47	1.51
1134123--1134156	18	1.9	18	88	5	52	50	0	2	47	1.16
1136296--1136322	4	6.8	4	100	0	54	25	0	0	74	0.83
1140269--1140297	2	14.5	2	100	0	58	48	0	0	51	1.00
1143421--1143472	24	2.1	25	92	3	88	28	23	34	13	1.92
1143421--1143460	14	3.1	14	73	26	52	27	22	37	12	1.90
1145377--1145421	23	2.0	23	86	0	63	26	26	26	20	1.99
1151536--1151632	18	5.4	18	87	0	140	30	31	17	19	1.95
1151533--1151632	36	2.8	36	92	0	164	32	31	17	20	1.95
1152261--1152308	19	2.5	19	96	0	87	20	29	16	33	1.95
1152901--1152944	2	22.0	2	100	0	88	50	0	0	50	1.00
1155244--1155310	23	2.9	23	86	0	98	29	25	26	17	1.98
1155811--1155843	2	16.5	2	100	0	66	48	0	0	51	1.00
1162853--1162930	2	39.0	2	100	0	156	50	0	0	50	1.00
1163127--1163277	53	2.9	53	92	1	250	50	9	8	31	1.64
1164509--1164749	129	1.9	129	82	1	304	35	14	18	31	1.91
1164756--1164784	14	2.1	14	100	0	58	41	20	24	13	1.89
1168151--1168211	3	20.7	3	83	3	79	34	3	1	60	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1169573--1169636	30	2.1	30	85	0	83	14	6	10	68	1.37
1175595--1175764	60	2.7	64	82	6	213	36	21	14	27	1.92
1176198--1176304	40	2.7	40	94	0	178	23	34	14	27	1.94
1176499--1176577	3	26.7	3	94	2	142	32	0	1	65	1.00
1177918--1177979	30	2.1	30	81	0	70	14	8	11	66	1.45
1183817--1183859	20	2.2	20	84	8	54	48	9	20	20	1.77
1184195--1184267	37	2.0	37	91	2	121	46	13	10	28	1.77
1184709--1184745	2	19.0	2	94	5	67	48	0	0	51	1.00
1185079--1185125	19	2.5	19	96	0	76	25	2	55	17	1.53
1191029--1191161	61	2.2	61	100	0	266	21	29	15	33	1.95
1191217--1191278	24	2.6	23	84	5	70	53	1	0	45	1.10
1192697--1192729	16	2.1	16	100	0	66	60	15	12	12	1.59
1193117--1193149	2	16.5	2	100	0	66	51	0	0	48	1.00
1198257--1198572	35	8.9	34	76	10	226	41	2	7	48	1.45
1198282--1198415	34	3.8	34	77	9	126	37	2	7	52	1.42
1198323--1198566	73	3.4	74	79	13	219	43	2	6	47	1.45
1198533--1198575	22	2.0	21	86	4	59	41	0	6	51	1.29
1198537--1198575	21	1.9	19	85	10	51	43	0	5	51	1.24
1198641--1198695	4	14.0	4	75	11	51	25	3	0	70	1.03
1198850--1198880	16	2.0	15	93	6	53	19	41	25	12	1.87
1199920--1199962	22	2.0	22	86	9	61	18	2	2	76	1.00
1199931--1199963	13	2.3	15	85	15	52	21	0	3	75	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1200106--1200165	10	5.5	10	75	16	57	10	3	6	80	1.01
1201930--1201975	19	2.4	19	89	7	67	10	13	8	67	1.42
1205330--1206224	84	10.8	83	82	4	932	29	25	21	23	1.99
1205330--1206224	165	5.4	165	83	3	998	29	25	21	23	1.99
1206854--1207157	35	8.7	34	75	10	213	41	2	7	47	1.47
1206879--1207158	36	7.9	35	76	12	195	41	2	7	48	1.45
1206920--1207161	35	6.8	35	77	13	228	42	2	7	47	1.45
1207125--1207167	22	2.0	21	86	4	59	41	0	6	51	1.29
1207129--1207167	21	1.9	19	85	10	51	43	0	5	51	1.24
1207232--1207298	34	1.9	35	81	3	82	22	4	2	70	1.19
1207440--1207470	16	2.0	15	93	6	53	19	41	25	12	1.87
1208507--1208549	22	2.0	22	86	9	61	18	2	2	76	1.00
1208518--1208550	13	2.3	15	85	15	52	21	0	3	75	0.93
1208693--1208752	10	5.5	10	75	16	57	10	3	6	80	1.01
1211692--1211737	20	2.3	20	78	14	58	23	0	19	56	1.42
1213985--1214093	45	2.3	47	84	7	152	38	20	12	28	1.89
1215964--1216183	115	1.9	115	88	0	332	36	9	10	43	1.71
1218295--1218353	30	2.0	30	86	0	82	16	11	6	64	1.47
1220792--1220821	2	15.0	2	100	0	60	50	0	0	50	1.00
1225538--1225703	54	3.1	54	92	1	253	36	15	22	24	1.93
1226061--1226139	22	3.6	22	82	0	86	34	17	10	37	1.84
1226690--1226790	40	2.5	40	98	0	193	47	8	24	18	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1226730--1227362	113	5.3	113	83	9	598	39	15	19	26	1.91
1226578--1226903	153	2.1	153	97	0	607	40	12	20	26	1.88
1226939--1227362	123	3.4	124	88	2	586	40	15	19	25	1.90
1227721--1227926	76	2.8	76	88	2	292	25	31	23	20	1.98
1233682--1233742	23	3.0	20	79	11	70	21	34	26	18	1.96
1235674--1235721	17	2.9	17	80	17	57	14	0	27	58	1.37
1236306--1236514	77	2.7	77	87	5	291	24	32	22	19	1.97
1238827--1239046	115	1.9	115	88	0	332	36	9	10	43	1.71
1244481--1244534	24	2.2	24	96	0	99	59	3	7	29	1.42
1245106--1245150	2	22.5	2	100	0	90	48	0	0	51	1.00

Tables:   1   2   3   4   5   6   7   8