genome.fa.s572.2.7.7.80.10.50.1000.5.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: VEPZ01000572.1 Hibiscus syriacus cultivar Beakdansim tig00001120_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  2399138

Tables:   1   2   3   4   5   6   7   8   9   

This is table  5  of  9  ( 1076 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)
1112606--1112646	16	2.6	16	81	14	57	31	0	0	68	0.90
1112730--1112806	25	3.1	25	94	0	136	37	19	14	28	1.91
1125502--1125560	23	2.7	21	85	14	84	30	28	16	23	1.97
1125516--1125562	23	2.0	23	100	0	94	31	25	17	25	1.97
1127822--1127878	25	2.2	27	78	15	66	59	0	1	38	1.08
1127829--1127877	25	1.9	26	88	12	75	57	0	2	40	1.10
1127829--1127886	25	2.3	25	82	8	64	51	3	1	43	1.28
1132442--1132467	5	5.2	5	100	0	52	61	0	0	38	0.96
1138320--1138370	24	2.1	24	82	7	59	49	5	3	41	1.45
1149516--1149559	22	2.0	22	100	0	88	45	13	9	31	1.75
1155642--1155732	42	2.2	42	91	0	146	23	16	42	17	1.88
1155653--1155745	42	2.2	41	86	7	125	24	15	43	17	1.87
1161799--1161839	5	8.2	5	100	0	82	0	0	19	80	0.71
1162553--1162596	20	2.3	19	80	7	54	47	9	20	22	1.78
1162746--1162776	15	2.1	15	93	0	53	54	0	0	45	0.99
1164878--1165039	84	1.9	84	98	0	315	56	16	11	16	1.66
1165897--1165944	24	2.0	24	95	0	87	18	12	22	45	1.83
1168800--1168854	22	2.5	22	93	3	92	43	1	0	54	1.10
1168786--1168851	11	5.6	11	75	12	53	43	1	0	54	1.09
1169071--1169119	25	2.0	25	95	0	89	48	14	10	26	1.75
1170268--1170337	33	2.1	33	81	5	79	60	2	0	37	1.12
1173385--1173435	26	2.0	26	92	7	86	49	13	0	37	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1175215--1175256	16	2.5	17	80	11	50	26	9	7	57	1.56
1185413--1185471	28	2.1	27	87	9	84	50	5	3	40	1.41
1185469--1185525	28	1.9	31	89	10	93	50	1	3	43	1.29
1187419--1188296	228	3.9	228	87	0	1105	21	25	23	29	1.99
1189420--1189479	27	2.1	28	84	9	77	43	0	13	43	1.43
1203622--1203674	21	2.5	21	81	0	61	20	24	18	35	1.95
1203714--1203782	20	3.5	20	94	4	113	39	20	18	21	1.93
1203714--1203790	20	3.9	19	70	13	57	37	20	19	22	1.94
1207108--1207195	20	4.4	20	86	2	115	36	25	20	18	1.95
1207374--1207410	14	2.6	14	86	0	56	48	21	0	29	1.50
1209356--1209452	33	2.9	34	78	3	106	48	22	16	12	1.79
1209426--1209512	20	4.3	20	92	0	102	36	19	18	25	1.94
1209521--1209586	19	3.7	19	73	21	61	16	21	19	42	1.89
1209538--1209653	34	3.4	34	97	0	214	16	22	18	42	1.89
1209559--1209656	20	5.5	20	68	26	94	18	21	19	40	1.91
1209577--1209633	14	3.6	14	71	24	51	17	24	17	40	1.91
1211518--1211567	19	2.5	20	80	3	66	46	24	18	12	1.82
1211903--1211964	18	3.0	22	71	22	62	19	14	38	27	1.90
1212137--1212174	20	1.9	20	88	0	58	26	18	18	36	1.94
1212142--1212212	20	3.5	20	75	3	70	19	22	21	36	1.95
1216275--1216328	16	3.4	16	80	14	76	62	5	1	29	1.28
1216268--1216338	31	2.3	31	95	0	133	60	9	4	25	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1217763--1217944	98	1.9	98	100	0	364	40	12	17	29	1.86
1220741--1220832	33	2.8	33	79	0	94	26	16	48	8	1.74
1220801--1221143	27	12.7	27	84	4	370	27	13	44	15	1.83
1220801--1221143	81	4.2	81	85	3	422	27	13	44	15	1.83
1221042--1221646	297	2.0	307	96	3	1122	28	23	24	24	1.99
1221342--1221440	27	3.7	27	89	2	146	26	16	44	13	1.84
1223126--1223195	36	2.0	34	88	5	104	22	21	40	15	1.91
1226286--1226316	14	2.2	14	100	0	62	35	29	6	29	1.82
1228692--1228731	19	2.2	17	86	8	53	27	2	0	70	1.01
1229548--1229577	13	2.3	13	100	0	60	26	0	0	73	0.84
1230393--1230417	6	4.2	6	100	0	50	20	16	64	0	1.30
1230481--1230524	13	3.5	13	90	6	72	18	52	15	13	1.75
1230526--1230622	32	3.0	32	79	10	101	53	0	0	46	1.00
1230622--1230676	24	2.3	24	90	0	83	25	47	14	12	1.80
1230622--1230676	12	4.6	12	81	0	65	25	47	14	12	1.80
1235431--1235480	23	2.0	25	81	11	59	62	4	2	32	1.25
1240029--1240139	17	6.4	17	68	20	61	44	0	7	47	1.36
1240855--1240917	29	2.2	29	88	5	92	30	15	9	44	1.79
1240866--1240925	29	2.1	28	96	3	111	28	13	10	48	1.74
1243101--1243131	12	2.6	12	94	0	53	12	16	45	25	1.83
1243134--1243189	27	2.1	27	89	0	85	46	0	0	53	1.00
1243235--1243283	13	3.8	13	89	2	73	12	16	53	18	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1243235--1243283	25	1.9	26	95	4	91	12	16	53	18	1.73
1246079--1246137	29	2.0	29	96	0	109	23	11	13	50	1.74
1251575--1251627	21	2.5	21	72	6	54	45	1	3	49	1.31
1256148--1256182	18	1.9	18	88	0	52	34	5	5	54	1.48
1256483--1256519	19	2.0	18	89	5	56	45	16	18	18	1.85
1268014--1268291	138	2.0	138	95	0	502	26	24	18	30	1.98
1270151--1270347	20	9.8	20	82	2	232	15	21	22	39	1.91
1270214--1270287	21	3.6	21	74	3	87	21	18	25	33	1.96
1270154--1270350	41	4.9	41	87	1	254	15	21	23	39	1.91
1270339--1270451	22	5.4	21	71	12	99	19	19	23	38	1.94
1270153--1270375	61	3.7	60	77	7	243	15	21	22	39	1.91
1270360--1270469	19	5.5	19	71	12	94	20	20	20	39	1.93
1270154--1270429	122	2.3	121	85	7	364	16	21	22	39	1.92
1270319--1270469	41	3.7	41	95	2	259	18	20	22	38	1.93
1270562--1270603	6	7.5	6	92	7	63	33	50	16	0	1.46
1270562--1270602	16	2.5	16	88	11	57	34	48	17	0	1.47
1271098--1271136	6	6.5	6	100	0	78	0	15	51	33	1.44
1271285--1271381	41	2.4	41	86	6	126	41	22	18	17	1.90
1271367--1271396	15	2.0	15	100	0	60	46	26	20	6	1.75
1271324--1271437	56	2.0	56	96	0	210	39	24	20	15	1.91
1271285--1271478	97	2.0	97	89	6	295	40	24	18	17	1.91
1271385--1271499	21	5.6	21	72	4	108	35	27	17	19	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1271382--1271503	41	3.0	41	91	0	208	37	26	17	18	1.93
1271370--1271512	41	3.6	39	83	9	152	37	27	18	16	1.92
1272038--1272234	10	20.1	10	75	16	78	72	0	3	24	0.99
1272073--1272227	4	39.2	4	79	13	72	71	0	1	27	0.94
1272108--1272142	2	17.5	2	100	0	70	51	0	0	48	1.00
1272138--1272221	23	3.5	25	76	15	79	80	0	1	17	0.77
1272142--1272219	33	2.3	33	86	4	102	83	0	1	15	0.72
1272313--1272459	12	12.6	12	79	11	71	57	0	2	40	1.10
1272356--1272457	2	52.5	2	89	5	147	55	0	0	44	0.99
1272932--1273033	37	2.8	37	86	0	141	31	10	15	42	1.82
1273763--1274907	106	11.0	106	87	4	1525	23	17	24	34	1.96
1275734--1275807	22	3.5	22	73	19	77	24	16	22	36	1.94
1276438--1276500	13	5.2	12	74	16	58	0	14	6	79	0.92
1276416--1276501	35	2.4	37	78	7	88	1	16	8	74	1.11
1276439--1276502	23	2.9	22	81	9	76	0	15	7	76	1.00
1279508--1279593	17	5.1	17	69	16	61	75	0	6	17	1.01
1279509--1279637	30	4.4	27	74	16	80	70	0	7	21	1.12
1279541--1279615	4	18.0	4	82	10	62	70	0	4	25	1.04
1279511--1279617	21	5.0	21	71	18	69	70	0	7	22	1.12
1279678--1279735	29	2.0	30	82	3	73	74	6	0	18	1.04
1280402--1280498	37	2.6	37	85	0	140	31	9	17	41	1.81
1281576--1281836	60	4.3	60	90	1	360	12	24	18	45	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1282312--1282397	33	2.6	33	88	0	127	17	27	22	32	1.96
1295639--1295690	23	2.3	23	96	0	95	50	17	9	23	1.75
1298904--1299033	65	2.0	62	89	4	197	28	16	14	40	1.87
1310679--1310942	138	1.9	138	80	6	302	27	14	32	25	1.94
1322434--1322485	26	2.0	26	100	0	104	30	15	11	42	1.82
1325392--1325451	23	2.6	23	79	10	77	16	26	23	33	1.96
1327138--1327178	21	2.0	21	85	0	55	29	29	24	17	1.97
1328587--1328901	149	2.1	149	96	2	580	26	18	21	33	1.96
1328869--1328913	23	2.0	23	90	0	72	22	26	26	24	2.00
1332174--1332214	21	2.0	21	85	0	55	29	29	24	17	1.97

Tables:   1   2   3   4   5   6   7   8   9