genome.fa.s9582.2.7.7.80.10.50.1000.6.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: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  4978262

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   

This is table  6  of  24  ( 2799 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)
1236527--1236561	17	1.9	17	88	11	52	45	11	0	42	1.40
1237016--1237082	32	2.2	32	86	5	93	38	7	0	53	1.29
1239103--1239170	24	2.8	24	73	8	66	55	16	10	17	1.67
1239105--1239174	12	5.8	12	75	6	52	54	17	11	17	1.71
1239103--1239211	48	2.3	47	80	3	110	51	16	12	19	1.76
1239152--1239211	24	2.5	24	78	10	77	46	16	16	20	1.84
1241678--1241712	12	2.8	13	87	12	56	60	5	5	28	1.43
1244907--1244951	20	2.3	19	84	3	54	40	0	22	37	1.54
1247491--1247556	32	2.1	32	94	0	114	43	10	16	28	1.81
1254122--1254197	2	38.0	2	100	0	152	50	0	0	50	1.00
1257839--1257883	22	2.0	22	95	0	81	35	17	15	31	1.92
1267853--1268232	182	2.1	178	89	5	579	46	8	2	42	1.49
1277537--1277570	11	2.9	11	87	12	50	23	0	0	76	0.79
1281420--1281448	14	2.0	15	93	6	51	31	13	6	48	1.69
1283230--1283277	3	16.7	3	86	4	64	70	0	2	27	0.98
1286667--1286711	2	23.0	2	95	4	83	51	0	0	48	1.00
1289197--1289226	2	15.0	2	92	0	51	46	0	53	0	1.00
1289944--1289974	5	6.2	5	100	0	62	41	0	0	58	0.98
1290994--1291041	2	24.0	2	100	0	96	50	0	0	50	1.00
1292523--1292586	6	10.8	6	96	3	121	82	0	0	17	0.66
1292520--1292586	23	2.9	23	97	2	125	82	0	0	17	0.68
1292582--1292691	7	15.7	7	100	0	220	58	0	13	28	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1292688--1292718	4	7.8	4	100	0	62	77	0	0	22	0.77
1292910--1293397	132	3.7	130	80	7	527	30	16	20	32	1.95
1292930--1293397	136	3.5	130	82	8	525	30	16	19	33	1.94
1293631--1293754	63	2.0	62	90	4	196	39	8	10	41	1.71
1294239--1296070	4	466.0	4	94	3	3201	24	1	25	48	1.57
1303344--1303379	2	18.5	2	94	5	65	52	0	0	47	1.00
1305942--1305983	2	21.5	2	95	4	77	50	0	0	50	1.00
1310226--1310269	20	2.3	19	81	11	54	34	4	0	61	1.16
1312804--1312831	14	2.0	14	100	0	56	92	7	0	0	0.37
1321499--1321555	7	7.7	7	81	11	53	66	5	0	28	1.13
1321524--1321570	13	3.6	14	83	11	64	59	6	0	34	1.23
1321507--1321565	22	2.7	22	89	5	84	61	8	0	30	1.26
1321517--1321584	34	2.2	29	82	15	75	57	8	1	32	1.39
1321561--1321600	16	2.3	18	87	8	57	52	5	5	37	1.45
1321609--1321745	36	3.9	35	80	11	145	46	7	4	41	1.51
1321644--1321745	37	2.8	36	87	1	141	47	5	4	42	1.49
1321609--1321745	73	1.9	71	86	5	195	46	7	4	41	1.51
1321709--1321761	26	2.1	26	96	3	99	43	5	3	47	1.45
1323272--1323428	43	3.7	43	88	0	224	26	17	22	33	1.96
1323271--1323455	86	2.1	86	82	3	228	25	18	21	34	1.96
1329346--1329461	29	4.0	29	87	0	169	44	18	2	33	1.64
1330190--1330257	2	34.0	2	100	0	136	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1336836--1336995	29	5.5	29	85	0	212	45	16	5	33	1.69
1342872--1343119	134	1.9	134	90	0	397	34	18	15	31	1.92
1344604--1345151	208	2.6	206	87	2	767	27	20	17	33	1.95
1346072--1346149	3	26.0	3	73	10	61	38	3	0	57	1.17
1346072--1346149	24	3.4	23	81	13	81	38	3	0	57	1.17
1346620--1346676	17	3.4	16	78	14	53	57	8	17	15	1.63
1351711--1351742	10	3.2	10	100	0	64	21	37	28	12	1.90
1351816--1351872	20	3.0	20	76	7	55	35	40	15	8	1.79
1352411--1352476	33	2.0	33	96	0	123	12	22	24	40	1.88
1353613--1353664	3	17.3	3	76	7	52	36	5	0	57	1.23
1353613--1353661	21	2.3	21	89	0	71	36	6	0	57	1.24
1360273--1360340	33	2.1	33	97	0	127	11	25	23	39	1.88
1361682--1361722	21	2.0	21	90	0	64	29	7	0	63	1.21
1361692--1361733	15	3.0	15	83	10	54	28	11	0	59	1.33
1363041--1363067	11	2.5	11	100	0	54	18	0	0	81	0.69
1365955--1365993	20	2.0	20	94	0	69	25	17	12	43	1.85
1367907--1368013	24	4.5	24	87	4	144	26	14	20	39	1.90
1367907--1368013	48	2.2	48	90	3	162	26	14	20	39	1.90
1367907--1368030	24	5.2	24	85	3	124	26	12	20	40	1.88
1368231--1368270	2	20.0	2	100	0	80	50	0	0	50	1.00
1370253--1370280	10	2.8	10	100	0	56	17	32	28	21	1.96
1372736--1372798	12	5.2	12	72	14	58	26	12	22	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1372721--1372835	24	4.8	24	89	4	169	25	13	20	40	1.89
1373016--1373046	2	15.5	2	100	0	62	48	0	0	51	1.00
1373756--1373811	29	1.9	29	85	7	78	41	10	17	30	1.84
1374336--1374384	21	2.3	21	85	0	62	38	6	0	55	1.25
1374914--1374954	18	2.2	20	86	8	59	63	7	17	12	1.50
1379578--1379642	33	2.0	33	96	0	121	13	20	24	41	1.88
1380955--1380996	20	2.1	20	86	8	59	35	0	2	61	1.09
1380988--1381036	21	2.3	21	89	0	71	36	6	0	57	1.24
1385832--1385878	20	2.3	20	92	0	76	36	31	17	14	1.90
1386418--1386482	33	2.0	33	93	0	112	12	18	24	44	1.84
1387828--1387876	21	2.3	21	89	0	71	36	6	0	57	1.24
1387839--1387879	12	3.7	11	81	18	50	34	9	0	56	1.32
1387838--1387878	21	2.0	21	95	0	73	31	9	0	58	1.31
1388933--1388967	16	2.2	16	95	5	63	42	8	11	37	1.72
1389219--1389302	6	11.7	7	73	13	50	29	2	3	64	1.23
1389272--1389314	23	1.9	22	86	13	61	30	0	4	65	1.13
1389686--1389714	9	3.3	9	95	4	51	62	0	0	37	0.96
1389445--1389724	147	1.9	147	83	8	365	38	6	6	47	1.56
1390232--1390294	26	2.4	25	82	10	65	28	1	1	68	1.08
1390253--1390289	15	2.4	16	82	13	51	24	0	2	72	0.97
1391676--1391762	43	2.0	44	86	2	122	31	11	22	34	1.90
1397865--1398049	75	2.5	75	84	3	221	33	16	18	31	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1398991--1399128	54	2.6	54	79	6	154	39	14	19	26	1.90
1400196--1400438	74	3.3	74	91	0	378	27	19	20	32	1.97
1400329--1400703	118	3.2	118	87	2	540	28	21	20	28	1.98
1400849--1400880	3	10.7	3	93	0	55	34	3	0	62	1.11
1402099--1402198	28	3.5	31	75	18	83	34	10	3	53	1.50
1402226--1402267	22	2.0	21	86	13	59	30	0	4	64	1.14
1402618--1402646	9	3.3	9	95	4	51	62	0	0	37	0.96
1403182--1403225	17	2.5	17	85	3	52	63	6	15	13	1.49
1406143--1406181	14	2.6	16	84	15	57	51	0	0	48	1.00
1406143--1406184	17	2.4	18	84	8	59	52	0	0	47	1.00
1406529--1407094	236	2.4	230	89	4	850	24	22	13	39	1.90
1407308--1407417	20	5.5	20	77	6	107	39	19	14	27	1.90
1414968--1415014	20	2.3	20	92	0	76	36	31	17	14	1.90
1415547--1415611	33	2.0	33	93	0	112	12	18	24	44	1.84
1416443--1416469	13	2.1	13	100	0	54	22	25	14	37	1.93
1418222--1418261	19	2.0	20	85	4	55	32	42	17	7	1.77
1418765--1418832	33	2.1	33	91	0	109	13	23	23	39	1.90
1419936--1419975	3	13.3	3	84	10	55	32	5	0	62	1.17
1419938--1419975	15	2.5	15	95	0	67	31	5	0	63	1.17
1422239--1422277	2	20.0	2	94	5	71	51	0	0	48	1.00
1422379--1422463	44	2.0	43	85	2	116	18	10	2	68	1.30
1422432--1422479	19	2.6	18	80	9	51	18	6	2	72	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1422447--1422509	22	2.7	24	76	14	69	14	11	0	74	1.07
1422450--1422541	31	3.1	29	76	16	82	13	10	0	76	1.03
1426553--1426739	95	2.0	94	87	5	270	31	19	18	31	1.95
1428145--1428207	21	3.3	20	70	25	64	30	20	3	46	1.66
1428143--1428198	15	3.2	17	72	23	53	33	17	1	46	1.59
1428114--1428230	36	3.2	36	85	1	153	31	19	9	39	1.84
1428253--1428353	36	2.8	36	85	4	125	27	17	9	44	1.81
1428331--1428493	65	2.5	65	85	1	209	25	21	10	42	1.85
1428115--1428432	138	2.3	138	86	3	446	29	19	9	41	1.83
1428243--1428363	34	3.4	36	80	5	129	25	19	10	43	1.83

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