genome.fa.s9596.2.7.7.80.10.50.1000.6.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: VEPZ01009596.1 Hibiscus syriacus cultivar Beakdansim tig00116975_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1846166

Tables:   1   2   3   4   5   6   7   8   

This is table  6  of  8  ( 926 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)
1194654--1194701	24	2.0	24	88	4	71	41	0	6	52	1.27
1194668--1194709	17	2.5	17	80	0	57	40	0	2	57	1.12
1197261--1197300	21	1.9	21	100	0	80	57	15	0	27	1.38
1197320--1197380	18	3.8	18	66	29	57	54	6	0	39	1.27
1197320--1197381	29	2.2	27	79	17	81	53	6	0	40	1.27
1197615--1197654	21	1.9	21	100	0	80	57	15	0	27	1.38
1197917--1197951	11	3.1	11	84	8	52	37	20	20	22	1.95
1198066--1198150	29	2.9	29	87	0	116	15	31	30	22	1.95
1201127--1201180	16	3.3	16	75	12	56	42	0	3	53	1.18
1213501--1213531	15	2.1	15	93	0	53	45	9	6	38	1.63
1224064--1224135	31	2.3	31	92	0	117	33	13	27	25	1.94
1224771--1224834	30	2.1	30	88	5	94	34	12	26	26	1.92
1225046--1225074	3	9.7	3	100	0	58	31	0	0	68	0.89
1225102--1225170	25	2.6	27	90	9	124	40	2	18	37	1.66
1227330--1227377	21	2.2	22	81	3	53	62	4	2	31	1.26
1228092--1228119	14	2.0	14	100	0	56	28	14	14	42	1.84
1231588--1231918	6	54.8	6	96	1	599	48	16	1	33	1.54
1232035--1232083	20	2.5	20	93	0	80	36	4	6	53	1.45
1233412--1233436	12	2.1	12	100	0	50	32	36	0	32	1.58
1242418--1242467	23	2.2	23	82	7	57	32	0	6	62	1.20
1244694--1244756	14	5.0	13	70	20	53	34	1	0	63	1.04
1244699--1244742	22	2.0	22	83	12	56	29	2	0	68	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1244692--1244767	36	2.1	36	100	0	152	32	3	0	63	1.13
1244715--1244777	18	3.3	19	71	22	53	31	3	1	63	1.19
1258722--1258783	31	2.0	31	96	0	115	61	4	6	27	1.41
1258722--1258772	16	3.2	16	70	25	54	60	3	5	29	1.38
1258808--1258836	2	14.5	2	100	0	58	48	0	0	51	1.00
1267559--1267593	16	2.2	16	89	0	52	48	0	0	51	1.00
1267735--1267779	23	2.0	23	100	0	90	48	20	8	22	1.76
1272631--1272667	18	2.1	18	100	0	74	37	0	18	43	1.51
1277982--1278220	42	5.8	42	70	10	143	30	15	21	31	1.94
1277987--1278323	83	4.1	83	78	7	303	30	14	21	33	1.93
1279535--1279561	14	1.9	14	100	0	54	40	7	7	44	1.60
1281041--1281078	17	2.2	17	86	9	51	44	7	5	42	1.56
1281404--1281515	43	2.5	45	72	16	108	30	19	25	25	1.98
1281537--1281629	43	2.2	43	84	0	123	22	23	19	34	1.96
1281560--1281674	43	2.7	43	77	4	106	24	24	15	35	1.94
1285989--1286029	2	20.5	2	100	0	82	48	0	0	51	1.00
1290338--1290418	23	3.7	23	75	24	93	23	32	22	22	1.98
1290360--1290437	20	3.8	20	76	21	88	24	29	23	23	1.99
1290346--1290437	43	2.1	43	97	0	175	23	31	21	22	1.98
1291709--1291750	21	2.0	20	86	4	57	59	7	7	26	1.50
1291764--1291807	19	2.3	19	84	4	52	45	6	15	31	1.73
1293138--1293216	21	3.7	21	78	8	88	24	34	18	22	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1293324--1293374	21	2.4	21	93	0	84	31	29	15	23	1.95
1308633--1309020	4	97.2	4	98	0	760	49	25	0	25	1.53
1317661--1317694	11	2.9	12	86	8	52	11	8	44	35	1.72
1317710--1317793	24	3.4	25	73	18	70	46	0	0	53	1.00
1317764--1317793	2	15.5	2	93	6	53	50	0	0	50	1.00
1317814--1317858	13	3.5	13	81	3	56	15	13	48	22	1.79
1323310--1323382	31	2.4	31	81	6	87	45	2	9	42	1.51
1326504--1326543	21	1.9	21	89	0	62	27	25	22	25	2.00
1327371--1327487	19	6.1	19	85	10	130	16	24	29	29	1.96
1327371--1327445	29	2.5	30	91	8	127	16	26	28	29	1.96
1327372--1327464	29	3.2	28	87	6	123	15	25	29	30	1.95
1327503--1327565	5	11.8	5	80	12	72	19	52	22	6	1.68
1327490--1327572	22	3.8	22	100	0	166	18	49	22	9	1.76
1327562--1327599	7	5.4	7	100	0	76	15	28	28	26	1.96
1328497--1328584	32	2.8	31	75	5	79	19	28	28	23	1.98
1334506--1334560	19	2.9	19	97	0	101	14	20	32	32	1.92
1334558--1334596	17	2.3	17	100	0	78	17	46	23	12	1.83
1337939--1337968	2	15.0	2	100	0	60	50	0	0	50	1.00
1345092--1345149	21	2.7	21	94	2	98	13	27	37	20	1.91
1348867--1348911	14	3.1	14	87	6	63	15	13	15	55	1.69
1349785--1349838	21	2.6	21	76	5	56	14	25	1	57	1.48
1353983--1354027	21	2.1	21	87	0	63	31	28	24	15	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1354859--1354954	32	3.0	32	79	14	126	29	17	18	34	1.94
1354946--1355038	30	3.1	30	93	1	152	20	21	26	31	1.98
1358866--1358910	21	2.1	21	87	0	63	31	28	24	15	1.96
1359744--1359839	32	3.0	32	79	14	126	29	17	18	34	1.94
1359831--1359923	30	3.1	30	90	1	134	20	19	26	33	1.96
1360194--1360229	2	18.0	2	88	0	54	44	2	2	50	1.31
1361806--1361852	24	2.0	24	86	0	67	55	2	8	34	1.42
1365379--1365611	93	2.4	93	81	8	236	27	13	10	48	1.75
1379386--1379447	20	3.0	22	70	15	60	59	0	1	38	1.07
1382158--1382200	2	22.0	2	95	4	79	51	0	0	48	1.00
1384171--1384205	16	2.1	17	89	5	54	34	22	14	28	1.93
1389469--1389499	15	2.1	15	93	0	53	45	0	0	54	0.99
1389649--1389690	20	2.2	19	87	8	59	21	16	7	54	1.65
1389660--1389705	20	2.3	20	85	7	58	28	21	2	47	1.62
1392228--1392290	31	2.2	28	81	15	76	30	25	22	22	1.99
1402023--1402091	35	2.0	35	91	0	111	15	33	11	39	1.84
1417268--1417452	92	2.0	92	100	0	370	32	12	19	35	1.90
1417648--1417854	64	3.2	64	85	6	258	33	22	15	28	1.95
1417826--1417874	19	2.6	19	87	9	66	24	28	18	28	1.98
1417970--1417995	13	2.0	13	100	0	52	30	15	0	53	1.42
1419713--1419770	28	2.0	29	96	3	109	50	15	13	20	1.78
1425034--1425081	22	2.2	22	96	0	87	16	8	14	60	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1425348--1425375	12	2.3	12	100	0	56	39	7	0	53	1.28
1425738--1425860	65	1.9	63	83	6	158	34	18	17	29	1.94
1426925--1426991	34	2.0	33	85	8	91	61	13	2	22	1.46
1429284--1429362	21	4.0	21	71	23	64	64	2	0	32	1.07
1429279--1429335	9	6.7	9	74	11	57	64	1	0	33	1.04
1429281--1429333	16	3.2	17	84	10	65	66	1	0	32	1.03
1429287--1429336	17	3.0	17	91	2	75	60	4	0	36	1.16
1429389--1429417	10	2.9	10	100	0	58	41	0	37	20	1.53
1436508--1436864	176	2.0	177	99	0	707	25	24	17	33	1.97
1441485--1441515	2	15.5	2	100	0	62	51	0	0	48	1.00
1458519--1458598	32	2.5	32	93	2	135	48	3	1	46	1.28
1458773--1458833	25	2.5	22	76	19	59	36	6	0	57	1.25
1468783--1468830	21	2.2	21	85	10	62	56	0	6	37	1.25
1468818--1468877	21	2.8	21	89	2	93	56	0	3	40	1.16
1469375--1469443	12	5.2	13	84	13	88	44	0	4	50	1.21
1469382--1469443	14	4.8	12	92	4	70	46	0	3	50	1.17
1469375--1469431	2	29.5	2	89	7	91	47	0	1	50	1.11
1473700--1474168	181	2.6	182	91	1	764	41	14	17	26	1.88
1476362--1476405	21	2.1	21	95	0	79	40	11	34	13	1.81
1476453--1476518	33	2.0	33	90	0	105	31	0	45	22	1.53
1476703--1476743	21	2.0	21	100	0	82	53	0	46	0	1.00
1478125--1478153	10	2.9	10	100	0	58	27	10	20	41	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1479390--1479423	17	2.1	16	88	5	50	14	8	0	76	1.01
1489596--1489629	17	2.1	16	94	5	59	14	5	0	79	0.91
1490156--1490212	29	2.0	29	82	6	71	50	17	21	10	1.75
1490227--1490275	19	2.6	19	96	0	89	32	0	10	57	1.32
1490265--1490315	18	2.8	18	91	5	77	37	0	19	43	1.51
1490643--1491604	201	4.8	201	89	2	1414	37	14	15	32	1.88
1490643--1491604	401	2.4	403	88	2	1400	37	14	15	32	1.88
1493094--1493133	6	6.7	6	91	0	53	42	2	32	22	1.67
1494480--1495589	200	5.7	199	83	7	1407	37	13	16	32	1.88
1494668--1495434	377	2.0	379	94	1	1353	37	13	17	31	1.89

Tables:   1   2   3   4   5   6   7   8