genome.fa.s5946.2.7.7.80.10.50.1000.7.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: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2465359

Tables:   1   2   3   4   5   6   7   8   9   10   11   

This is table  7  of  11  ( 1316 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)
1294443--1294495	22	2.5	22	84	3	63	52	1	5	39	1.36
1295199--1295239	4	10.2	4	100	0	82	48	0	0	51	1.00
1296307--1296341	2	17.5	2	100	0	70	51	0	0	48	1.00
1299523--1299551	2	14.5	2	100	0	58	51	0	0	48	1.00
1306369--1306448	15	5.4	15	86	3	108	37	7	20	35	1.81
1306363--1306448	45	1.9	44	88	2	127	40	6	18	33	1.78
1306382--1306448	30	2.3	30	97	2	127	38	7	19	34	1.80
1306431--1306480	20	2.5	20	100	0	100	40	10	16	34	1.81
1306679--1306780	28	3.6	29	77	12	104	52	1	0	44	1.18
1306679--1306820	28	4.9	28	76	9	101	50	1	1	46	1.18
1306764--1306830	15	4.4	16	68	22	54	49	0	1	49	1.10
1306790--1306849	10	6.2	9	75	19	50	51	0	0	48	1.00
1307038--1307157	42	2.9	42	96	0	213	43	19	20	16	1.88
1311062--1311165	37	2.8	37	85	0	136	40	14	13	31	1.85
1311582--1311628	23	2.0	24	84	12	62	27	2	0	70	0.99
1311663--1311694	2	16.5	2	93	6	57	46	0	0	53	1.00
1311722--1311748	14	1.9	14	100	0	54	22	7	0	70	1.12
1311897--1311929	12	2.6	13	90	4	50	15	0	0	84	0.61
1313047--1313076	4	7.5	4	100	0	60	23	0	0	76	0.78
1316366--1316417	14	3.6	13	82	17	59	78	7	13	0	0.94
1318033--1318574	106	5.1	106	92	0	913	35	24	18	21	1.96
1318033--1319283	212	6.0	212	88	4	1880	34	25	18	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1318574--1319283	106	6.7	106	91	2	1097	33	25	18	22	1.97
1318169--1319283	404	2.7	388	89	4	1244	34	24	18	22	1.96
1320033--1320129	37	2.6	37	83	0	122	42	15	9	32	1.79
1320551--1320596	23	2.0	23	84	16	60	28	2	0	69	1.00
1320606--1320653	5	8.8	5	82	13	51	37	2	0	60	1.09
1320774--1320895	15	8.0	15	67	21	51	30	4	1	63	1.22
1325605--1325635	16	1.9	16	100	0	62	38	0	61	0	0.96
1325851--1325876	2	13.0	2	100	0	52	50	0	0	50	1.00
1326942--1326973	15	2.1	15	94	0	55	0	15	21	62	1.32
1330555--1330609	3	18.3	3	77	7	58	40	0	0	60	0.97
1330555--1330609	24	2.4	24	85	8	71	40	0	0	60	0.97
1332009--1332045	11	3.3	11	92	3	56	29	2	2	64	1.21
1332006--1332047	12	3.6	12	83	6	59	30	2	2	64	1.19
1331959--1332073	28	4.2	26	71	19	74	29	4	2	63	1.27
1336241--1336268	2	14.0	2	100	0	56	50	0	0	50	1.00
1336563--1336647	15	5.2	15	74	16	64	82	2	14	1	0.83
1336578--1336649	1	72.0	1	77	0	54	86	2	11	0	0.68
1336567--1336649	30	3.0	26	80	16	96	83	2	13	1	0.81
1336603--1336649	21	2.3	20	85	7	67	87	4	8	0	0.67
1336585--1336649	31	2.2	30	91	5	105	86	3	10	0	0.69
1336567--1336638	7	10.4	7	71	14	51	81	2	13	1	0.86
1340950--1341100	54	2.9	53	85	5	184	35	14	24	25	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1340950--1341103	50	3.0	50	85	5	175	35	14	24	25	1.94
1341474--1341528	22	2.5	22	93	0	101	38	10	10	40	1.76
1342038--1342364	167	2.0	167	92	3	543	36	13	11	38	1.82
1342371--1343080	76	9.3	76	95	0	1258	23	19	22	34	1.96
1343246--1343304	3	19.3	3	82	3	73	38	0	0	61	0.96
1343237--1343306	15	4.6	15	82	3	68	41	0	0	58	0.98
1344686--1344716	12	2.6	12	89	0	53	29	0	3	67	1.06
1344639--1344723	19	4.7	17	67	25	50	27	3	3	65	1.25
1344871--1345137	146	1.8	148	82	7	348	37	7	7	47	1.60
1347026--1347073	23	2.1	23	88	0	69	35	12	18	33	1.89
1347501--1347563	23	2.7	23	92	0	99	38	20	4	36	1.74
1348627--1348762	62	2.2	62	81	5	150	25	13	13	48	1.78
1348654--1348762	31	3.5	30	78	5	119	21	13	15	49	1.79
1350101--1350177	31	2.5	31	82	4	102	49	12	14	23	1.78
1362089--1362218	54	2.4	55	88	2	181	44	10	3	41	1.55
1363065--1363100	2	18.0	2	100	0	72	0	50	0	50	1.00
1365827--1366337	275	1.9	275	96	0	943	31	14	11	42	1.81
1378153--1378206	27	2.0	28	85	3	74	31	5	25	37	1.79
1380921--1381002	31	2.6	31	82	3	94	24	10	15	48	1.77
1383988--1384080	3	30.0	3	70	16	57	34	2	5	58	1.33
1384000--1384087	23	4.0	22	72	19	76	34	2	5	57	1.34
1389564--1389600	15	2.5	15	90	0	56	8	70	13	8	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1391537--1391583	24	2.0	24	91	0	76	34	44	6	14	1.71
1392595--1392623	12	2.4	12	100	0	58	13	20	20	44	1.85
1398730--1398782	25	2.1	25	82	0	61	47	16	7	28	1.74
1398927--1398967	21	2.0	21	100	0	82	26	0	4	68	1.10
1404996--1405035	21	1.9	21	89	0	62	10	25	40	25	1.86
1405018--1405078	20	2.9	21	87	7	79	18	26	34	21	1.96
1413899--1413953	20	2.6	20	83	11	65	23	29	29	18	1.98
1413899--1413960	23	2.9	21	83	7	72	20	33	25	19	1.96
1413942--1413981	21	1.9	21	84	0	53	25	37	25	12	1.91
1415895--1415946	9	6.4	8	75	20	54	13	0	26	59	1.34
1415898--1415941	17	2.6	17	85	7	63	13	0	29	56	1.38
1416510--1416717	76	2.7	77	86	4	289	20	24	32	22	1.98
1429878--1429902	13	1.9	13	100	0	50	52	8	16	24	1.70
1430210--1430264	21	2.6	20	78	18	58	43	1	0	54	1.10
1436078--1436500	216	2.0	216	91	0	693	27	16	18	37	1.92
1437245--1438147	451	2.0	451	98	0	1734	32	16	21	30	1.95
1438285--1438357	32	2.3	32	83	4	94	30	12	24	32	1.92
1439661--1439691	15	2.1	15	93	0	53	58	3	6	32	1.40
1448876--1448938	32	2.0	32	81	12	76	68	0	1	30	0.99
1454175--1454310	59	2.3	60	82	8	163	33	13	17	36	1.89
1454916--1454960	21	2.1	21	87	0	63	46	22	2	28	1.63
1458735--1458774	15	2.7	15	84	3	55	60	0	10	30	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1458841--1458879	20	2.0	20	100	0	78	20	10	10	58	1.59
1465223--1465254	15	2.0	17	88	11	50	31	15	6	46	1.71
1465378--1465406	6	4.8	6	100	0	58	86	13	0	0	0.58
1472206--1472529	55	5.9	55	82	6	358	28	25	17	28	1.98
1472232--1472529	108	2.7	109	83	8	363	30	25	17	27	1.97
1472225--1472533	163	1.9	164	86	4	446	30	24	17	27	1.97
1472539--1472609	37	1.9	36	91	2	115	21	19	18	40	1.91
1473889--1473950	27	2.4	26	83	5	72	6	12	3	77	1.08
1473904--1474090	48	3.9	47	77	16	147	9	13	1	75	1.10
1473985--1474029	18	2.6	18	96	3	83	13	11	0	75	1.05
1473964--1474082	58	2.1	56	84	12	154	10	12	0	77	1.00
1473985--1474090	18	5.6	18	77	13	72	12	11	0	76	1.02
1474048--1474088	11	4.0	11	81	12	52	17	4	0	78	0.93
1474001--1474101	24	4.5	21	71	19	71	12	10	0	76	1.03
1486646--1486770	60	2.1	60	82	8	148	33	12	13	40	1.83
1487024--1487110	32	2.8	31	84	3	120	37	21	14	25	1.92
1488614--1488657	3	14.7	3	100	0	88	31	0	0	68	0.90
1491980--1492038	29	2.0	30	83	9	77	38	5	5	50	1.46
1494399--1494428	14	2.1	14	93	0	51	53	10	0	36	1.35
1495961--1496045	34	2.5	34	96	0	152	58	0	0	41	0.98
1499476--1499518	22	1.9	23	95	4	79	58	0	0	41	0.98
1499462--1499525	23	2.8	23	82	17	89	54	3	0	42	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1500350--1500385	3	12.0	3	93	0	63	63	0	2	33	1.08
1505563--1505595	17	1.9	17	88	11	50	39	3	0	57	1.14
1505778--1505845	32	2.2	32	86	2	93	48	10	10	30	1.71
1506489--1506520	2	16.0	2	93	0	55	46	0	3	50	1.17
1506594--1506672	27	3.0	27	85	5	99	40	3	7	48	1.50
1506632--1506924	39	8.0	36	80	11	283	45	4	5	44	1.45
1506688--1506742	29	1.9	28	81	3	65	43	1	5	49	1.36
1506632--1506923	76	4.0	73	76	13	255	45	3	5	44	1.44
1506891--1506945	28	2.1	26	87	12	78	43	3	7	45	1.49
1508302--1508346	24	1.9	23	86	13	65	13	8	0	77	0.98

Tables:   1   2   3   4   5   6   7   8   9   10   11