genome.fa.s1279.2.7.7.80.10.50.1000.25.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: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  6984689

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   

This is table  25  of  29  ( 3433 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)
5843003--5843164	84	1.9	83	86	6	229	25	19	24	30	1.98
5843194--5843269	20	3.8	20	92	0	125	17	14	36	31	1.90
5843066--5843229	65	2.5	63	79	9	161	24	17	23	34	1.96
5844086--5844141	20	2.8	20	76	10	53	23	3	3	69	1.20
5845333--5845452	4	28.0	4	67	12	60	32	3	3	60	1.29
5845333--5845452	26	4.3	26	76	14	114	32	3	3	60	1.29
5845336--5845455	30	4.1	30	80	9	140	33	3	3	60	1.30
5845354--5845451	22	3.8	24	76	19	83	32	4	4	59	1.35
5850121--5850147	11	2.5	11	100	0	54	18	0	14	66	1.25
5850152--5850185	16	2.2	15	89	5	50	29	5	20	44	1.75
5850127--5850289	83	2.0	84	91	1	265	34	7	16	41	1.78
5850237--5850268	16	2.0	16	93	0	55	34	12	18	34	1.89
5851620--5851645	2	13.0	2	100	0	52	50	0	0	50	1.00
5861356--5861423	21	3.3	21	62	25	54	30	10	22	36	1.87
5861349--5861432	41	2.0	41	100	0	168	28	9	23	38	1.86
5866678--5866757	26	3.1	26	67	22	78	37	13	7	41	1.73
5866688--5866768	26	3.2	26	68	16	78	34	16	7	41	1.76
5874477--5874574	21	4.8	20	75	10	81	37	21	18	22	1.94
5874476--5874593	21	5.8	20	73	10	78	38	23	17	20	1.93
5874541--5874733	20	9.6	20	83	4	228	35	25	20	18	1.95
5875233--5875307	19	3.8	20	84	7	98	44	18	25	12	1.84
5875326--5875409	19	4.7	19	80	14	106	10	22	22	44	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5875367--5875423	14	3.7	14	75	20	60	8	24	24	42	1.83
5875348--5875431	33	2.5	33	96	0	159	9	23	21	45	1.81
5877109--5877577	93	5.1	93	98	0	904	22	12	19	46	1.83
5877625--5877753	19	7.3	19	75	17	125	45	28	17	8	1.77
5877661--5877753	33	2.8	32	91	4	150	46	27	18	7	1.76
5877625--5877753	52	2.5	52	74	14	140	45	28	17	8	1.77
5877749--5877867	19	6.8	18	74	19	110	8	19	25	47	1.77
5877771--5877827	14	3.7	14	72	20	51	7	19	28	45	1.76
5877754--5877846	33	2.8	33	91	0	159	8	19	24	47	1.77
5877749--5877883	19	7.6	19	73	20	105	9	18	25	45	1.80
5879808--5879843	14	2.6	14	95	0	63	33	0	22	44	1.53
5879946--5880043	19	5.4	19	84	13	143	45	17	22	14	1.84
5879946--5880062	53	2.2	53	98	1	227	44	17	23	13	1.85
5880052--5880273	19	12.7	19	77	18	250	14	20	18	46	1.84
5880058--5880245	52	3.6	52	97	0	340	14	21	17	47	1.82
5880076--5880287	33	6.2	33	76	14	207	13	20	18	47	1.82
5882591--5882615	12	2.1	12	100	0	50	0	28	0	72	0.86
5882790--5882836	24	2.0	24	87	8	69	38	21	14	25	1.92
5883548--5883792	20	12.2	20	88	1	267	19	18	24	36	1.94
5883779--5883861	21	4.0	21	73	6	78	25	16	24	33	1.96
5883759--5883857	42	2.4	43	77	11	100	21	18	23	37	1.94
5884601--5884650	24	2.1	24	96	0	91	30	8	12	50	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5884642--5884684	18	2.4	19	80	11	54	37	0	9	53	1.33
5884672--5884724	27	2.0	27	85	3	72	39	3	9	47	1.54
5887494--5887571	33	2.4	33	84	0	102	21	47	12	17	1.81
5890430--5890478	19	2.4	21	83	10	66	57	2	10	30	1.43
5890430--5890478	20	2.5	20	86	6	64	57	2	10	30	1.43
5892020--5892074	20	2.7	20	83	8	58	29	27	12	30	1.93
5892562--5892696	60	2.2	59	80	5	153	30	16	19	34	1.94
5899487--5899531	19	2.4	19	100	0	90	24	26	17	31	1.97
5903012--5903071	28	2.1	28	100	0	120	25	18	30	26	1.98
5905035--5905140	31	3.4	31	79	6	115	31	16	17	33	1.93
5905084--5905171	31	2.8	32	84	5	101	29	17	20	32	1.95
5905490--5905524	2	17.5	2	100	0	70	0	0	48	51	1.00
5909147--5909270	31	4.0	31	76	8	108	29	18	20	31	1.96
5909594--5909657	2	32.0	2	96	0	119	0	0	48	51	1.00
5911577--5911633	23	2.5	23	85	0	78	31	28	21	19	1.97
5912235--5912285	20	2.5	20	78	6	59	27	25	15	31	1.96
5912257--5912415	64	2.5	64	84	4	187	26	16	20	36	1.94
5915426--5915476	24	2.1	24	85	0	66	27	11	29	31	1.92
5922811--5922844	17	2.0	17	100	0	68	23	35	5	35	1.79
5929634--5929694	29	2.1	29	87	3	88	36	16	26	21	1.94
5929650--5929715	29	2.3	29	83	0	78	43	13	19	22	1.86
5940616--5940763	76	1.9	76	90	2	235	49	13	10	26	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5949868--5949914	23	2.0	23	83	0	58	34	8	2	55	1.42
5962529--5962567	20	2.0	20	84	0	51	25	20	17	35	1.95
5962655--5962717	23	2.7	23	85	4	83	17	25	25	31	1.97
5963918--5963959	5	8.0	5	84	10	57	19	54	21	4	1.62
5978327--5978358	15	2.1	15	94	0	55	59	9	6	25	1.52
5980872--5980906	18	1.9	18	88	0	52	28	31	17	22	1.96
5985407--5985462	28	2.0	28	100	0	112	50	10	17	21	1.77
5986761--5987190	165	2.6	165	86	2	580	30	24	16	28	1.97
5986761--5987196	55	7.9	54	86	5	484	30	24	16	28	1.97
5988565--5988642	26	2.7	29	75	17	90	8	16	1	73	1.15
5988585--5988648	14	4.8	13	81	14	85	7	17	1	73	1.14
5988567--5988696	14	8.8	14	73	22	74	9	17	0	72	1.15
5988565--5988647	29	2.9	28	75	21	84	8	15	1	74	1.11
5995124--5995228	45	2.2	44	80	12	111	37	23	9	29	1.87
5995147--5995257	45	2.3	47	86	7	154	40	20	10	27	1.86
5996799--5996859	27	2.1	30	82	11	74	65	9	4	19	1.40
5997153--5997206	28	1.9	28	100	0	108	50	9	18	22	1.75
5999982--6000021	13	3.0	13	81	3	53	40	42	0	17	1.49
6002655--6002730	29	2.6	29	93	0	125	13	32	28	25	1.93
6002784--6002811	14	2.0	14	100	0	56	7	21	42	28	1.79
6003583--6003632	18	2.7	19	79	11	59	12	4	8	76	1.15
6004199--6004270	30	2.3	32	81	13	80	48	11	6	33	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6006158--6006187	13	2.2	13	94	5	51	83	0	16	0	0.65
6006632--6006700	25	2.8	25	93	0	120	21	27	24	26	1.99
6006815--6006859	23	2.0	23	82	8	56	24	24	22	28	1.99
6012873--6012915	21	2.0	21	86	0	59	30	23	25	20	1.99
6012984--6013016	15	2.2	15	94	0	57	78	0	21	0	0.75
6013463--6013531	25	2.8	25	100	0	138	20	28	26	24	1.99
6015860--6015894	2	17.5	2	100	0	70	51	0	0	48	1.00
6016923--6016968	13	3.5	13	81	0	56	39	13	19	28	1.89
6019525--6019623	23	4.5	22	81	11	105	34	25	24	16	1.95
6019717--6019786	28	2.4	30	80	15	85	35	20	10	34	1.86
6019717--6019756	14	2.9	14	82	10	55	37	17	5	40	1.72
6022588--6022647	29	2.0	31	90	6	97	35	6	16	41	1.75
6022725--6022778	19	2.8	19	91	0	81	42	12	11	33	1.79
6022883--6022924	21	2.0	21	95	0	75	23	21	28	26	1.99
6023207--6023276	34	2.1	32	89	5	104	31	15	31	21	1.95
6024043--6024102	20	3.0	20	85	2	68	35	15	18	31	1.91
6024069--6024107	20	2.0	20	100	0	78	35	17	20	25	1.95
6025177--6025215	2	19.5	2	100	0	78	51	0	0	48	1.00
6025517--6025561	21	2.1	21	87	4	63	31	24	20	24	1.98
6025547--6025615	23	3.0	23	89	0	111	31	21	27	18	1.97
6028751--6028821	28	2.4	29	77	11	83	52	2	4	40	1.36
6037501--6037535	15	2.3	15	90	0	52	11	5	20	62	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6048396--6048478	12	6.9	12	94	0	76	37	30	12	20	1.89
6048405--6048475	6	11.8	6	93	0	124	36	32	14	16	1.89
6048977--6049017	14	2.9	14	88	3	64	43	12	34	9	1.75
6050399--6050450	21	2.5	21	84	6	61	25	13	1	59	1.44
6053420--6053453	17	2.1	16	88	5	50	50	0	0	50	1.00
6059921--6059954	16	2.1	16	88	0	50	50	0	2	47	1.16
6059996--6060029	16	2.0	18	88	11	54	26	2	5	64	1.30
6060529--6060575	23	2.1	23	84	7	62	34	14	14	36	1.88
6060502--6060749	130	1.9	130	91	0	406	35	12	15	36	1.86
6061146--6061221	35	2.2	35	90	0	116	36	2	25	35	1.70

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