genome.fa.s1162.2.7.7.80.10.50.1000.7.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: VEPZ01001162.1 Hibiscus syriacus cultivar Beakdansim tig00002317_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  1560963

Tables:   1   2   3   4   5   6   7   8   9   

This is table  7  of  9  ( 971 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)
1154753--1154865	52	2.2	51	93	6	192	43	17	25	13	1.86
1154855--1155061	19	11.7	19	76	19	209	14	21	17	45	1.85
1154861--1155073	52	4.1	51	85	10	276	14	21	18	46	1.84
1154855--1155061	70	2.9	71	84	9	246	14	21	17	45	1.85
1157535--1157581	24	2.0	24	87	8	69	38	21	14	25	1.92
1158269--1158454	20	9.3	20	87	4	232	19	18	26	34	1.95
1158961--1159189	20	11.4	20	85	1	235	18	17	25	37	1.93
1157759--1159144	692	2.0	695	97	1	2640	30	17	20	32	1.95
1159976--1160016	4	10.2	4	89	0	64	24	0	21	53	1.46
1161998--1162035	11	3.5	11	100	0	76	55	10	0	34	1.34
1169454--1169480	11	2.5	11	100	0	54	55	11	0	33	1.35
1169454--1169495	21	2.0	21	82	17	52	52	9	2	35	1.47
1169537--1169562	11	2.4	11	100	0	52	53	11	0	34	1.37
1173647--1173697	22	2.4	20	78	12	57	47	3	21	27	1.68
1180792--1180842	22	2.3	22	89	3	75	27	21	19	31	1.97
1185143--1185209	34	1.9	34	82	14	84	20	13	19	46	1.83
1189742--1189808	34	1.9	34	82	14	84	19	11	20	47	1.81
1190795--1191066	35	7.8	35	83	0	328	22	24	19	34	1.96
1190798--1191067	105	2.6	104	87	2	380	22	24	18	34	1.96
1193624--1193683	31	1.9	31	86	0	84	50	8	1	40	1.43
1193874--1193899	2	13.0	2	100	0	52	50	0	0	50	1.00
1194561--1194585	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1194494--1194638	77	1.9	76	98	1	281	33	8	15	42	1.76
1194860--1194913	21	2.6	21	100	0	108	33	7	33	25	1.84
1195381--1195427	2	23.5	2	100	0	94	48	0	0	51	1.00
1195653--1195845	103	1.9	103	84	6	266	34	14	12	37	1.85
1196338--1196389	17	3.2	17	75	10	54	32	3	13	50	1.60
1196439--1196471	16	2.0	17	88	5	50	42	0	6	51	1.26
1203453--1203508	2	28.0	2	100	0	112	50	0	0	50	1.00
1209463--1209537	29	2.5	30	72	10	73	56	6	12	25	1.60
1211513--1211649	35	3.9	34	82	10	141	45	4	14	35	1.65
1211513--1211650	71	1.9	72	82	4	172	46	4	14	34	1.64
1211545--1211608	20	3.4	19	69	30	57	42	1	15	40	1.57
1211550--1211672	35	3.4	36	87	4	167	47	6	13	31	1.68
1219984--1220031	23	2.1	23	84	0	60	35	10	18	35	1.85
1220457--1220519	23	2.7	23	90	0	90	38	19	4	38	1.73
1220098--1221146	426	2.5	429	97	1	2000	38	11	7	41	1.71
1220873--1220945	23	3.2	22	88	3	83	39	20	5	34	1.76
1220883--1220945	23	2.7	23	92	0	99	38	19	6	36	1.77
1221361--1221446	39	2.2	39	93	0	145	18	13	18	48	1.80
1221703--1221739	18	2.1	18	89	0	56	51	10	5	32	1.60
1222170--1222222	22	2.3	23	93	3	90	39	16	5	37	1.73
1224702--1225357	181	3.6	183	94	2	1132	34	16	14	35	1.89
1225661--1225723	21	2.7	23	78	11	67	50	9	11	28	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1226815--1226889	3	25.0	3	76	0	69	24	34	5	36	1.78
1226815--1226901	12	7.2	12	81	0	93	22	34	6	35	1.81
1226823--1226901	36	2.2	36	93	0	131	21	35	7	35	1.82
1226843--1226904	18	3.4	18	79	0	79	19	35	8	37	1.81
1226819--1226904	6	14.3	6	78	0	64	20	34	6	37	1.80
1228358--1229827	197	7.5	197	96	1	2756	32	16	14	36	1.90
1228358--1229827	393	3.7	393	97	1	2761	32	16	14	36	1.90
1229952--1230000	19	2.6	19	93	0	80	57	10	2	30	1.43
1231883--1231947	21	3.1	21	80	6	69	15	29	15	40	1.88
1234321--1234365	19	2.3	20	85	14	67	17	17	8	55	1.67
1235774--1235827	28	1.9	27	82	14	65	29	7	3	59	1.42
1238540--1238581	21	2.0	21	100	0	84	28	14	23	33	1.94
1239130--1239599	126	3.7	126	87	2	660	21	22	22	34	1.97
1238882--1239599	252	2.8	257	83	6	871	21	22	22	33	1.97
1239735--1239837	23	4.8	22	67	17	72	42	0	20	35	1.59
1239729--1239856	63	2.0	63	96	0	238	39	0	23	36	1.61
1240606--1240666	21	3.0	20	79	9	59	27	19	32	19	1.96
1240630--1240669	21	1.9	21	100	0	80	27	20	32	20	1.97
1242309--1242360	25	2.2	23	82	6	59	63	1	0	34	1.06
1242436--1242473	20	1.9	20	89	10	60	65	7	2	23	1.32
1242462--1242552	14	6.3	15	69	20	61	59	0	0	40	0.97
1242462--1242545	29	2.9	29	80	16	95	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1242462--1242549	32	2.8	33	76	11	94	59	0	0	40	0.98
1242460--1242554	19	4.4	22	69	21	58	60	0	0	40	0.97
1243157--1243285	64	2.0	64	92	0	213	43	10	13	32	1.78
1243193--1243477	87	3.3	87	96	0	525	41	10	15	32	1.81
1243344--1243395	23	2.3	23	93	0	86	38	7	21	32	1.82
1243909--1243955	20	2.3	20	96	0	85	34	12	4	48	1.61
1243487--1243939	203	2.3	200	85	5	605	30	14	15	39	1.87
1244520--1244564	21	2.1	21	88	8	65	37	15	0	46	1.46
1244806--1244889	42	2.0	43	81	6	100	51	0	1	47	1.08
1244843--1244936	30	3.2	30	79	11	81	50	1	1	47	1.15
1244854--1244940	14	6.2	14	69	9	52	47	1	1	50	1.16
1244868--1244936	28	2.5	28	74	6	70	49	1	1	47	1.19
1245089--1245150	2	31.5	2	96	3	117	50	0	0	50	1.00
1245617--1245709	33	2.9	32	84	4	98	40	18	4	36	1.70
1245638--1245708	33	2.2	33	92	0	115	38	15	2	43	1.61
1250358--1250804	117	3.8	117	93	0	770	21	24	23	30	1.99
1250358--1250810	233	1.9	233	94	0	800	22	24	23	30	1.99
1250945--1251047	23	4.7	23	70	20	87	43	0	18	36	1.57
1250942--1251066	63	2.0	63	92	3	207	40	0	21	37	1.59
1250963--1251041	40	2.0	41	82	7	99	37	1	20	40	1.60
1251257--1251329	34	2.1	34	92	0	119	36	4	6	52	1.48
1251865--1251904	21	1.9	21	100	0	80	30	20	30	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1251886--1251968	42	2.0	42	80	0	94	24	20	33	21	1.97
1253647--1253711	15	4.2	15	75	11	51	58	0	1	40	1.07
1254481--1254515	18	1.9	18	88	0	52	62	0	2	34	1.10
1257990--1258025	19	1.9	19	94	5	65	47	11	22	19	1.80
1267208--1267271	32	2.0	32	93	0	110	31	15	21	31	1.95
1269266--1269326	29	2.1	29	100	0	122	26	13	14	45	1.81
1270053--1270090	2	19.0	2	100	0	76	50	0	0	50	1.00
1277979--1278041	29	2.2	28	83	8	74	30	1	4	63	1.24
1278270--1278311	20	2.2	19	86	4	57	35	0	0	64	0.94
1278178--1278402	119	1.9	117	81	7	276	40	6	7	46	1.58
1278361--1278424	29	2.2	30	82	2	85	46	1	1	50	1.20
1278945--1279029	42	2.0	42	100	0	170	35	22	14	28	1.93
1311863--1311897	17	2.1	17	88	0	52	34	25	22	17	1.96
1321438--1321468	16	1.9	16	93	0	53	61	0	3	35	1.12
1327087--1327179	21	4.5	21	72	4	82	40	17	23	18	1.90
1327087--1327179	41	2.3	41	94	0	168	40	17	23	18	1.90
1327165--1327215	20	2.5	20	77	3	57	45	17	15	21	1.86
1327213--1327252	19	2.0	20	90	4	64	32	30	12	25	1.92
1327972--1328016	18	2.5	18	88	0	72	26	44	15	13	1.83
1328494--1328560	20	3.4	20	81	2	73	38	23	22	14	1.92
1328549--1328594	14	3.2	14	80	17	58	52	23	15	8	1.70
1328541--1328641	24	3.8	26	75	15	89	46	20	20	11	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1328580--1328621	11	3.5	12	77	9	50	45	21	19	14	1.85
1328699--1328753	20	2.8	19	89	5	83	16	25	23	34	1.95
1330627--1330694	19	3.8	19	81	14	92	48	17	20	13	1.80
1330712--1330769	20	2.9	20	94	0	98	17	22	22	37	1.93
1334330--1334456	33	3.8	33	86	4	193	42	18	22	15	1.89
1334331--1334463	66	2.0	66	95	0	239	41	18	22	17	1.90
1334456--1334498	20	2.2	20	87	4	61	16	18	23	41	1.89
1334484--1334517	14	2.4	14	85	0	50	8	23	20	47	1.78
1334639--1334675	14	2.6	14	91	0	65	45	24	0	29	1.53
1336022--1336088	21	3.2	21	68	4	55	19	20	35	23	1.95

Tables:   1   2   3   4   5   6   7   8   9