genome.fa.s1465.2.7.7.80.10.50.1000.6.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: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  11160956

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   

This is table  6  of  55  ( 6520 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)
992205--992277	23	3.2	23	88	0	101	34	4	21	39	1.73
995555--995579	6	4.2	6	100	0	50	32	16	36	16	1.90
1000427--1000508	40	2.0	40	100	0	164	35	23	12	29	1.91
1004308--1004344	3	12.0	3	94	5	65	67	0	0	32	0.91
1006343--1006391	20	2.5	19	81	15	64	28	16	26	28	1.97
1009093--1009145	2	26.5	2	96	0	97	47	1	0	50	1.12
1011868--1011951	23	3.7	23	75	3	71	20	23	22	33	1.97
1012283--1012359	33	2.5	31	81	8	84	28	3	16	50	1.63
1016125--1016241	45	2.6	45	80	2	119	39	9	18	32	1.83
1016306--1016343	16	2.5	16	87	8	53	28	5	21	44	1.73
1016420--1016512	23	4.1	23	79	6	100	19	22	23	34	1.96
1016509--1016561	24	2.2	24	83	6	63	24	15	16	43	1.87
1016715--1016750	8	4.3	9	89	10	51	47	0	8	44	1.33
1018969--1018995	7	3.9	7	100	0	54	44	25	0	29	1.54
1019200--1019235	18	2.0	18	94	0	63	30	33	19	16	1.94
1019153--1019279	46	2.7	46	91	6	193	34	30	18	16	1.93
1023370--1023427	20	2.6	22	86	10	75	31	18	22	27	1.97
1024335--1024424	2	45.0	2	100	0	180	50	0	0	50	1.00
1024688--1024782	38	2.5	38	80	0	127	23	21	29	26	1.99
1024688--1024781	20	4.9	19	78	8	93	22	21	29	26	1.99
1028035--1028190	64	2.4	64	84	4	181	34	17	24	23	1.96
1028609--1028663	20	2.7	19	81	13	56	52	1	14	30	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1029206--1029246	19	2.2	18	86	4	55	41	0	9	48	1.36
1029616--1029686	18	3.8	18	74	7	70	19	18	29	32	1.96
1033110--1033246	64	2.1	64	81	5	161	34	18	24	23	1.96
1033701--1033742	20	2.3	18	77	18	50	47	0	14	38	1.44
1033712--1033766	20	2.7	20	81	13	58	50	0	16	32	1.45
1034786--1034837	22	2.4	22	96	0	95	48	3	19	28	1.66
1038010--1038169	63	2.5	64	85	5	216	32	17	25	24	1.97
1038575--1038616	20	2.3	18	77	18	50	47	0	14	38	1.44
1038586--1038640	20	2.7	19	83	13	65	52	0	14	32	1.42
1039303--1039344	2	21.0	2	100	0	84	50	0	0	50	1.00
1039607--1039702	20	5.0	20	76	10	83	22	19	30	27	1.98
1039608--1039700	18	4.9	18	80	7	96	21	19	31	27	1.97
1043061--1043182	64	1.9	64	81	3	147	32	17	24	25	1.96
1043170--1043223	20	2.4	23	85	11	69	33	14	24	27	1.94
1043621--1043670	20	2.5	21	84	12	61	54	0	12	34	1.38
1044333--1044366	2	17.0	2	100	0	68	50	0	0	50	1.00
1044629--1044666	20	1.9	20	88	0	58	23	26	26	23	2.00
1044630--1044724	38	2.5	38	78	0	109	25	17	28	28	1.98
1044630--1044722	18	4.9	18	74	7	69	23	18	29	29	1.98
1045087--1046943	4	467.8	4	97	1	3355	25	1	24	48	1.60
1047916--1048038	23	5.6	23	73	6	94	21	23	25	29	1.99
1047919--1048057	21	6.4	21	71	8	93	22	21	25	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1047919--1048057	44	3.2	44	84	4	185	22	21	25	30	1.99
1053817--1053906	45	2.0	46	88	2	137	27	20	24	27	1.99
1056554--1056589	18	2.0	18	100	0	72	27	33	22	16	1.95
1056507--1056633	46	2.7	46	88	3	173	33	29	18	18	1.95
1059651--1059775	23	5.4	23	80	5	92	21	20	25	32	1.97
1059664--1059779	23	5.0	23	86	2	144	22	20	25	31	1.98
1060885--1060938	11	4.7	11	77	8	54	44	1	9	44	1.46
1062074--1062121	15	3.1	15	75	3	51	12	12	25	50	1.75
1062818--1062891	24	3.1	24	83	11	82	48	1	6	43	1.38
1064854--1064887	16	2.2	15	89	5	50	29	5	2	61	1.34
1068106--1068155	27	1.9	25	84	8	64	34	0	14	52	1.42
1068260--1068313	20	2.6	21	80	11	58	38	0	3	57	1.17
1068276--1068315	20	2.0	20	90	9	64	40	0	5	55	1.22
1070880--1070939	20	2.9	21	80	12	79	5	28	0	66	1.12
1070889--1070942	20	2.7	19	86	8	81	3	29	0	66	1.09
1070882--1070949	20	3.3	20	78	13	68	2	32	0	64	1.08
1075673--1075714	21	2.0	21	100	0	84	47	0	0	52	1.00
1076500--1076659	80	2.0	78	92	2	266	39	11	12	36	1.80
1076814--1076861	22	2.1	23	88	7	71	33	18	4	43	1.69
1086898--1086940	21	2.0	21	90	0	68	23	30	4	41	1.74
1094101--1094179	39	2.0	39	95	0	140	22	29	16	31	1.96
1094532--1094621	45	2.0	45	100	0	180	42	20	17	20	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1097999--1098043	21	2.1	21	100	0	90	35	13	20	31	1.91
1098998--1099034	7	5.3	7	96	0	65	13	0	37	48	1.43
1099172--1099234	11	5.9	11	69	14	51	38	1	3	57	1.24
1104752--1104876	23	5.8	22	80	15	129	28	17	25	28	1.98
1104749--1104876	21	6.0	21	79	15	138	28	17	25	28	1.98
1104753--1104876	44	2.8	44	85	8	157	28	17	25	29	1.98
1108674--1108713	21	1.9	21	85	10	55	35	10	2	52	1.48
1110634--1110703	22	3.3	20	79	16	79	24	17	32	25	1.96
1119500--1119611	32	3.4	34	80	12	135	52	12	12	22	1.72
1119496--1119598	32	3.2	32	81	10	138	49	14	14	21	1.79
1121665--1121925	132	2.0	129	81	5	301	37	16	14	31	1.89
1124122--1124188	30	2.2	30	84	12	84	40	2	1	55	1.24
1124119--1124192	31	2.6	29	81	14	82	41	2	1	54	1.23
1124255--1124317	10	6.1	10	75	12	56	23	6	4	65	1.36
1124260--1124317	21	2.8	20	77	12	64	24	5	5	65	1.34
1125567--1125644	3	27.0	3	89	7	126	32	1	0	66	1.00
1127103--1127153	2	27.0	2	82	11	63	43	0	1	54	1.11
1127114--1127169	15	3.2	18	73	19	55	37	0	3	58	1.15
1127103--1127171	9	7.1	10	78	19	51	40	0	2	56	1.14
1128232--1128306	19	3.9	19	75	13	57	30	5	0	64	1.16
1128476--1128518	13	3.4	13	83	6	52	25	4	0	69	1.07
1128486--1128543	21	2.8	20	76	23	59	20	5	1	72	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1128588--1128633	16	2.8	16	79	20	51	34	4	0	60	1.16
1128751--1128803	19	2.7	19	80	11	63	20	9	0	69	1.15
1132841--1133110	100	2.7	99	87	4	366	34	16	16	31	1.92
1134825--1134869	20	2.2	20	96	0	81	31	33	13	22	1.92
1134880--1135041	65	2.5	64	83	1	189	32	22	16	29	1.95
1135565--1135627	33	1.9	33	96	0	117	49	3	17	30	1.62
1139399--1139488	32	2.8	32	80	8	112	32	16	16	34	1.92
1139400--1139505	31	3.4	31	79	8	108	30	16	16	35	1.92
1143134--1143191	20	2.6	22	86	10	75	31	18	22	27	1.97
1144173--1144297	31	4.0	32	79	9	132	28	18	20	32	1.96
1151183--1151220	20	1.9	20	94	0	67	31	34	15	18	1.92
1151251--1151358	19	5.7	19	98	0	207	22	37	14	25	1.93
1151324--1151485	64	2.5	64	85	2	209	30	24	15	29	1.96
1153013--1153050	2	20.0	2	84	10	53	44	0	2	52	1.14
1153016--1153065	9	4.9	10	83	11	50	40	0	4	56	1.18
1154344--1154402	18	3.1	20	79	13	54	40	0	0	59	0.97
1154353--1154420	4	14.4	5	85	11	51	38	0	0	61	0.96
1154367--1154397	2	15.5	2	100	0	62	48	0	0	51	1.00
1154353--1154421	14	5.7	12	80	14	54	37	0	0	62	0.96
1154595--1154639	23	2.0	22	86	4	63	24	6	0	68	1.13
1154595--1154656	22	2.8	22	82	7	63	25	4	0	69	1.08
1154837--1154896	25	2.6	21	80	19	59	18	5	5	71	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1154884--1154935	19	2.8	18	80	14	61	21	7	0	71	1.11
1154970--1155016	20	2.3	20	78	10	51	10	17	0	72	1.12
1155056--1155099	21	2.0	23	82	8	56	18	4	2	75	1.09
1155073--1155156	19	4.3	20	76	16	61	17	4	2	75	1.09
1155078--1155156	5	16.0	5	73	15	58	18	3	2	74	1.08
1156682--1156732	21	2.4	21	96	0	93	25	19	19	35	1.95
1156790--1156837	21	2.3	21	92	0	78	29	16	12	41	1.85
1158205--1158252	20	2.5	19	83	6	60	37	12	4	45	1.61
1158754--1158804	19	2.6	19	96	3	93	5	47	0	47	1.26
1160187--1160244	21	2.8	21	82	10	73	25	15	18	39	1.91

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55