genome.fa.s4117.2.7.7.80.10.50.1000.5.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: VEPZ01004117.1 Hibiscus syriacus cultivar Beakdansim tig00009009_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2456583

Tables:   1   2   3   4   5   6   7   8   9   

This is table  5  of  9  ( 1080 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)
1112095--1112167	28	2.7	26	73	8	83	36	5	6	50	1.52
1118661--1118701	22	1.9	21	90	5	64	46	2	7	43	1.44
1119701--1120445	333	2.2	328	82	5	858	31	15	17	35	1.91
1120975--1121026	23	2.3	23	86	6	70	23	48	23	5	1.72
1122982--1123037	23	2.4	23	100	0	112	44	5	10	39	1.62
1124525--1124552	14	2.0	14	100	0	56	21	7	35	35	1.81
1125094--1125156	18	3.5	18	78	4	56	11	9	38	41	1.73
1126421--1126446	2	13.0	2	100	0	52	50	0	0	50	1.00
1128936--1129034	42	2.4	42	94	0	171	38	23	25	13	1.91
1134410--1134436	14	1.9	14	100	0	54	40	0	7	51	1.30
1137343--1137372	2	15.0	2	92	0	51	53	0	0	46	1.00
1158399--1158436	17	2.2	17	90	0	58	28	5	5	60	1.40
1158405--1158439	17	2.1	17	100	0	70	31	11	5	51	1.61
1160736--1160839	50	2.1	50	98	1	201	35	14	11	38	1.82
1161599--1161635	2	18.5	2	100	0	74	48	0	0	51	1.00
1171293--1171646	192	1.8	192	88	1	539	29	23	25	22	1.99
1173978--1174036	19	3.1	19	78	11	75	45	16	15	22	1.84
1177278--1177320	22	2.0	22	90	9	70	20	0	4	74	1.00
1179602--1179650	3	16.0	3	87	4	71	32	2	0	65	1.04
1200688--1200770	41	2.0	41	97	0	157	16	21	24	37	1.94
1202201--1202250	15	3.3	15	91	0	82	20	24	10	46	1.81
1204941--1205839	420	2.1	424	94	2	1574	42	12	10	34	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1209162--1209266	42	2.5	42	92	0	165	13	24	24	37	1.92
1215115--1215169	22	2.5	22	75	0	56	29	9	23	38	1.85
1219177--1219228	26	2.0	26	81	7	61	32	5	1	59	1.32
1220670--1220699	15	2.0	15	93	0	51	50	0	43	6	1.28
1221832--1222291	232	2.0	232	98	0	893	24	18	22	34	1.96
1222491--1222544	20	2.7	20	83	11	74	72	7	3	16	1.22
1239283--1239329	20	2.3	20	100	0	94	53	4	4	38	1.40
1239822--1239946	57	2.1	60	88	5	184	19	13	21	45	1.84
1244974--1245043	30	2.3	30	92	0	122	31	12	12	42	1.81
1249081--1249123	22	1.9	23	90	4	70	11	0	20	67	1.22
1253529--1253667	65	2.1	65	93	1	233	33	17	7	41	1.78
1258725--1258803	39	2.0	39	95	0	140	43	7	27	21	1.80
1268194--1268231	2	19.0	2	100	0	76	50	0	0	50	1.00
1270792--1270820	6	4.8	6	100	0	58	65	0	34	0	0.93
1273775--1273809	13	2.8	13	95	4	63	31	17	37	14	1.89
1273823--1274018	93	2.1	91	96	2	356	33	21	32	12	1.90
1273823--1274017	61	3.2	64	84	10	248	33	21	32	11	1.90
1274049--1274157	29	3.8	29	95	2	184	14	31	32	22	1.94
1274241--1274275	18	1.9	18	100	0	70	28	17	25	28	1.97
1274377--1274422	23	2.0	23	100	0	92	47	4	39	8	1.54
1274426--1274491	4	16.5	4	76	9	55	63	0	34	1	1.04
1274377--1274437	23	2.6	23	86	5	59	50	6	36	6	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1274425--1274483	21	2.9	21	94	2	102	62	0	35	1	1.05
1274618--1274706	41	2.2	41	78	8	92	42	1	10	46	1.45
1274687--1274777	45	2.0	47	87	8	134	41	0	12	46	1.41
1274646--1274777	45	3.0	44	80	14	132	40	0	12	46	1.41
1274818--1274894	34	2.3	33	81	14	88	40	0	12	46	1.42
1277136--1277168	17	1.9	17	93	0	57	45	12	6	36	1.66
1277267--1277612	26	12.9	26	73	20	177	45	9	2	43	1.47
1277289--1277324	11	3.4	11	88	3	56	58	5	0	36	1.22
1277261--1277670	124	3.3	124	94	2	682	45	9	1	43	1.47
1277636--1277661	11	2.4	11	100	0	52	34	7	0	57	1.27
1280486--1280542	26	2.2	24	77	17	60	40	1	8	49	1.44
1281349--1281409	27	2.2	29	88	11	92	55	13	0	31	1.38
1281353--1281416	27	2.4	27	82	15	87	54	12	0	32	1.38
1281387--1281434	21	2.3	20	85	7	69	52	16	0	31	1.45
1281936--1281993	25	2.3	25	79	5	64	22	43	17	17	1.88
1282052--1282131	29	2.8	29	96	0	142	16	28	33	21	1.95
1282474--1282613	60	2.3	62	83	4	169	43	5	18	32	1.74
1282474--1282634	60	2.6	59	80	9	164	42	5	18	33	1.73
1282536--1282650	60	1.9	60	80	7	135	45	6	16	32	1.72
1295038--1295063	2	13.0	2	100	0	52	50	0	0	50	1.00
1297158--1297191	16	2.0	18	88	11	54	64	5	2	26	1.30
1297310--1297352	21	2.0	21	100	0	86	39	0	13	46	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1297321--1297406	35	2.5	35	84	0	100	37	1	20	40	1.61
1297537--1297594	29	2.0	29	86	6	82	27	8	29	34	1.87
1301164--1301201	20	1.9	20	94	0	67	34	2	5	57	1.35
1310167--1310200	6	5.7	6	89	0	50	38	14	32	14	1.87
1311886--1311950	18	3.6	18	80	0	85	6	7	27	58	1.50
1313554--1313607	6	9.0	6	93	0	90	18	31	1	48	1.59
1315713--1315865	78	2.0	79	85	5	213	33	12	13	40	1.81
1318594--1318636	22	2.0	22	86	9	61	46	4	2	46	1.36
1330982--1331008	2	13.5	2	100	0	54	51	0	0	48	1.00
1331622--1331716	24	4.0	24	73	0	82	46	13	14	25	1.82
1336680--1337515	334	2.5	334	92	1	1390	22	29	11	35	1.90
1336677--1337517	168	5.0	168	92	1	1420	22	29	11	35	1.90
1346273--1346324	23	2.2	24	83	10	63	38	1	3	55	1.29
1346380--1346429	15	3.3	15	76	15	57	62	0	0	38	0.96
1354703--1354736	17	2.0	17	100	0	68	35	17	17	29	1.93
1360700--1360772	31	2.4	31	88	0	101	52	5	0	42	1.24
1366289--1366319	11	2.7	12	95	5	55	38	9	3	48	1.52
1372625--1372655	2	15.5	2	100	0	62	51	0	0	48	1.00
1375492--1375550	11	5.5	11	68	11	50	52	11	6	28	1.63
1375491--1375550	21	2.8	21	84	2	84	53	11	6	28	1.62
1379837--1379899	14	4.4	14	74	4	54	49	4	17	28	1.67
1379849--1379891	15	2.9	15	79	3	52	44	4	18	32	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1382725--1382772	22	2.2	22	100	0	96	12	14	25	47	1.79
1387510--1387631	59	2.1	59	82	0	145	34	25	15	24	1.95
1389240--1389276	14	2.6	15	83	8	51	59	0	2	37	1.12
1398741--1398881	7	20.3	7	70	15	53	50	28	0	21	1.49
1398738--1398822	21	4.1	20	74	17	66	51	27	0	21	1.48
1398738--1398787	20	2.5	20	87	9	66	52	30	0	18	1.46
1398745--1398787	13	3.2	13	81	15	52	53	27	0	18	1.45
1398833--1398885	14	3.7	14	78	12	63	52	28	0	18	1.46
1398831--1398905	28	2.6	28	79	6	80	49	30	0	20	1.49
1407258--1407379	59	2.1	59	87	0	172	34	26	13	25	1.93
1408980--1409016	14	2.6	15	83	8	51	59	0	2	37	1.12
1410499--1410618	18	7.0	18	77	11	135	29	27	19	24	1.98
1412495--1412525	14	2.2	14	100	0	62	19	6	29	45	1.75
1420031--1420057	6	4.5	6	100	0	54	33	0	14	51	1.43
1421359--1421769	201	2.0	202	93	1	709	36	12	13	37	1.82
1423727--1423808	41	2.0	41	95	0	146	26	19	8	45	1.79
1424451--1424495	11	4.0	11	94	5	81	53	2	8	35	1.45
1424451--1424495	23	2.0	22	95	4	81	53	2	8	35	1.45
1431859--1431884	2	13.0	2	100	0	52	50	0	0	50	1.00
1434409--1434469	29	2.1	29	87	3	88	47	9	1	40	1.46
1435734--1435799	28	2.4	27	80	7	78	31	3	3	62	1.26
1435884--1435948	31	2.1	31	88	2	96	44	4	0	50	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1435970--1436049	29	2.8	29	79	9	92	57	0	8	33	1.30
1436200--1436287	29	3.0	30	81	6	108	64	2	4	28	1.25
1436464--1436492	11	2.7	11	94	5	51	62	0	0	37	0.96
1436559--1436625	31	2.2	31	94	0	116	43	4	4	47	1.43
1437077--1437128	17	2.8	18	75	16	52	57	0	0	42	0.98
1437457--1437481	3	8.3	3	100	0	50	36	0	0	64	0.94
1444342--1444371	9	3.3	9	95	0	51	16	13	0	70	1.18
1447870--1447930	14	4.4	14	75	19	56	34	0	18	47	1.49
1448149--1448186	2	19.0	2	100	0	76	50	0	0	50	1.00
1449353--1449380	2	14.0	2	100	0	56	50	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9