genome.fa.s8527.2.7.7.80.10.50.1000.5.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: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  9057482

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   

This is table  5  of  37  ( 4336 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)
1010180--1010313	60	2.3	58	79	6	144	30	13	26	29	1.94
1010167--1010328	79	2.1	79	80	4	175	30	13	27	28	1.94
1018193--1018219	6	4.5	6	100	0	54	14	51	14	18	1.76
1020106--1020138	15	2.1	17	88	11	52	51	9	0	39	1.34
1027667--1027699	8	4.1	8	100	0	66	63	12	0	24	1.28
1029519--1029564	20	2.3	20	84	0	56	56	0	2	41	1.11
1030956--1030998	21	2.0	21	100	0	86	34	18	18	27	1.95
1032759--1032803	20	2.4	19	81	7	56	40	8	24	26	1.84
1032944--1033029	38	2.2	36	80	11	91	50	3	1	45	1.26
1032949--1033024	37	2.1	37	82	9	93	50	3	0	46	1.20
1039316--1039410	39	2.4	39	75	12	93	54	1	1	43	1.14
1039318--1039709	187	2.1	185	91	2	635	44	2	7	45	1.45
1044679--1044711	8	4.0	8	96	4	57	48	3	12	36	1.56
1061716--1061862	60	2.4	59	81	8	163	27	13	21	36	1.91
1087043--1087159	60	2.0	60	92	0	198	28	14	18	38	1.90
1109361--1109425	29	2.2	28	78	10	67	40	0	3	56	1.15
1112010--1112040	13	2.3	14	94	5	55	54	0	0	45	0.99
1112063--1112100	6	6.5	6	96	3	69	0	84	0	15	0.63
1123351--1123416	15	4.3	16	72	9	50	57	1	0	40	1.08
1123353--1123425	32	2.3	32	81	9	87	58	1	0	39	1.06
1125265--1125298	18	1.9	17	88	5	50	61	2	2	32	1.26
1125380--1125414	17	2.0	18	94	5	63	42	5	0	51	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1127385--1127436	17	3.2	17	75	10	54	51	13	1	32	1.52
1132514--1132599	19	4.2	19	72	16	73	36	4	27	31	1.78
1132564--1132600	19	1.9	19	100	0	74	37	5	29	27	1.79
1132999--1133053	19	2.8	20	77	5	67	36	20	21	21	1.95
1133093--1133138	19	2.4	19	85	3	56	21	17	30	30	1.96
1133104--1133140	19	1.9	19	94	0	65	21	16	29	32	1.95
1133640--1133721	21	4.0	21	79	3	103	35	20	21	21	1.96
1137898--1137962	34	1.9	34	100	0	130	27	10	20	41	1.85
1140291--1140555	136	1.9	136	83	7	342	35	16	21	25	1.94
1140582--1140725	64	2.3	63	83	5	168	40	6	11	40	1.69
1140637--1140818	94	2.0	91	84	7	242	37	8	13	40	1.75
1140728--1140884	66	2.4	68	84	5	205	37	6	15	40	1.73
1140583--1141078	160	3.2	158	87	4	667	38	7	13	40	1.73
1140940--1141051	59	1.9	59	88	0	170	35	7	10	46	1.66
1140998--1141169	80	2.1	81	88	3	258	39	8	14	37	1.77
1141084--1141311	95	2.4	95	93	0	384	37	9	14	39	1.78
1144599--1144652	28	1.9	28	92	0	90	25	7	22	44	1.79
1161519--1161543	13	1.9	13	100	0	50	40	0	0	60	0.97
1161910--1162088	96	1.9	96	84	4	245	26	21	22	30	1.99
1166892--1166958	26	2.5	26	83	11	82	34	5	1	58	1.32
1171949--1171976	2	14.0	2	100	0	56	50	0	0	50	1.00
1172279--1172329	2	25.5	2	100	0	102	49	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1173789--1173813	2	12.5	2	100	0	50	48	0	0	52	1.00
1174287--1174378	32	2.9	31	75	14	89	35	17	15	31	1.91
1174285--1174387	31	3.3	29	72	17	82	33	17	15	33	1.91
1178351--1178395	17	2.6	17	75	0	54	42	2	0	55	1.12
1181273--1181334	31	2.1	31	87	6	92	29	6	3	61	1.37
1206277--1206387	52	2.1	52	100	0	222	29	19	16	34	1.94
1218017--1218077	29	2.2	25	81	16	68	55	1	6	36	1.36
1224150--1224518	20	18.5	20	85	4	458	34	26	18	20	1.96
1225201--1225247	24	2.0	24	87	8	69	25	14	21	38	1.92
1225422--1225446	12	2.1	12	100	0	50	72	0	28	0	0.86
1227729--1228035	19	17.4	19	80	16	376	46	18	20	14	1.83
1227757--1228035	52	5.2	52	93	4	388	46	17	21	14	1.83
1227796--1228035	71	3.4	71	86	11	373	47	17	20	14	1.83
1227729--1228073	142	2.5	138	90	6	518	46	18	20	14	1.84
1227729--1228057	52	6.3	55	88	9	332	46	18	20	14	1.84
1228064--1228165	19	5.6	19	85	12	151	14	23	17	44	1.86
1228272--1228308	14	2.6	14	91	0	65	45	21	0	32	1.52
1230264--1230320	14	3.7	14	77	20	60	45	22	21	10	1.82
1230245--1230337	33	2.8	33	95	0	168	47	21	20	10	1.80
1230208--1230342	19	7.6	19	76	16	128	45	23	19	11	1.82
1230338--1230466	19	7.3	19	75	17	125	8	17	28	45	1.77
1230338--1230429	33	2.8	33	93	3	150	7	18	28	45	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1230510--1231167	93	7.1	93	99	0	1293	46	18	12	22	1.83
1230510--1231167	185	3.5	186	99	0	1293	46	18	12	22	1.83
1230510--1231167	278	2.4	278	99	0	1307	46	18	12	22	1.83
1232871--1232960	14	5.7	14	74	23	81	42	23	25	8	1.83
1232863--1232977	33	3.5	33	95	0	212	45	20	24	9	1.81
1232870--1232982	19	6.8	18	72	23	88	43	22	24	9	1.83
1232994--1233048	14	3.6	14	73	21	56	9	25	23	41	1.83
1232978--1233048	33	2.2	33	94	0	124	8	22	25	43	1.81
1232989--1233070	33	2.5	33	89	2	119	9	25	21	42	1.84
1233001--1233089	20	4.8	20	72	19	75	12	24	19	43	1.85
1233169--1233239	33	2.2	33	92	0	115	47	18	22	11	1.80
1233420--1233474	22	2.5	22	81	0	74	20	16	40	23	1.91
1233616--1233808	20	9.6	20	82	5	219	19	19	25	35	1.95
1233616--1233808	60	3.2	60	83	0	251	19	19	25	35	1.95
1233864--1233915	20	2.6	20	96	0	95	21	13	26	38	1.90
1239594--1239631	19	2.0	19	89	0	58	18	26	31	23	1.97
1239629--1239653	13	1.9	13	100	0	50	16	48	24	12	1.79
1254650--1254675	2	13.0	2	100	0	52	50	0	0	50	1.00
1258612--1258673	29	2.1	29	84	3	79	53	1	3	41	1.27
1260671--1260711	21	2.0	21	95	0	73	24	26	24	24	2.00
1261471--1261572	31	3.3	31	94	0	177	37	22	20	19	1.95
1261822--1261874	26	2.1	25	82	10	63	33	20	3	41	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1262850--1262882	3	11.0	3	93	0	57	63	0	33	3	1.10
1263666--1263707	2	21.0	2	100	0	84	50	0	0	50	1.00
1263978--1264022	21	2.1	21	83	0	54	22	22	17	37	1.94
1264012--1264124	20	5.7	20	94	0	190	39	19	20	20	1.92
1264323--1264366	22	2.0	22	95	0	79	25	40	13	20	1.89
1264773--1264895	20	6.5	20	77	11	98	14	17	24	43	1.86
1264774--1264876	53	1.9	54	84	2	136	15	17	24	42	1.88
1264722--1264896	73	2.4	73	93	0	287	15	17	22	44	1.86
1264862--1264905	20	2.2	20	91	0	70	11	13	20	54	1.69
1266851--1266917	20	3.3	20	89	0	98	38	22	17	20	1.93
1266954--1267016	20	3.2	20	88	0	90	19	15	25	39	1.91
1267501--1267586	21	4.1	21	75	3	84	20	37	19	22	1.95
1268964--1269002	14	2.8	14	84	0	51	35	0	17	46	1.49
1269128--1269180	14	3.5	14	72	18	52	45	20	22	11	1.83
1269128--1269192	32	2.0	32	96	0	121	49	18	20	12	1.79
1269173--1269232	20	3.0	20	85	0	84	55	16	13	15	1.70
1269237--1269309	33	2.2	34	92	2	121	10	21	19	47	1.79
1269252--1269321	33	2.1	33	86	0	95	14	21	17	47	1.82
1269304--1269397	20	4.7	19	85	10	109	21	23	21	34	1.97
1269304--1269397	40	2.4	39	85	10	129	21	23	21	34	1.97
1271813--1271866	24	2.2	24	93	0	90	40	20	18	20	1.91
1272707--1272754	20	2.4	20	82	0	60	25	16	25	33	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1272741--1272813	20	3.7	20	98	0	137	20	21	20	36	1.95
1272811--1272850	21	1.9	21	94	0	71	45	17	20	17	1.86
1274145--1274177	5	6.6	5	100	0	66	21	0	0	78	0.75
1281378--1281421	12	3.7	12	90	0	70	25	0	9	65	1.21
1281379--1281421	6	7.2	6	94	0	59	25	0	6	67	1.15
1281405--1281587	2	94.5	2	63	19	50	44	2	3	48	1.35
1281445--1281482	11	3.5	11	88	0	58	50	2	2	44	1.30
1281488--1281541	17	3.1	17	81	2	63	46	0	3	50	1.19
1281520--1281586	22	2.9	23	80	13	75	44	1	4	49	1.31
1281679--1281751	20	3.4	20	72	17	65	36	8	2	52	1.46

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37