genome.fa.s8027.2.7.7.80.10.50.1000.26.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: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  7662336

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   

This is table  26  of  38  ( 4505 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)
5442137--5442329	63	3.0	63	86	0	269	44	15	9	30	1.78
5442334--5442380	2	23.5	2	100	0	94	48	0	0	51	1.00
5442601--5442724	18	6.9	18	71	6	81	9	4	41	44	1.58
5442601--5442722	6	20.3	6	73	2	66	9	4	40	45	1.57
5442635--5442708	29	2.5	29	79	12	71	8	8	43	40	1.64
5442857--5443215	113	3.1	113	79	10	434	36	6	27	28	1.83
5442967--5443207	125	1.9	125	88	2	360	38	7	26	28	1.82
5443408--5443544	61	2.2	61	84	2	186	35	10	5	47	1.63
5443601--5443747	33	4.7	33	76	15	159	41	8	7	42	1.64
5443689--5443975	18	16.6	18	70	17	189	42	5	6	45	1.53
5443683--5443973	51	5.6	51	82	11	259	42	6	6	45	1.55
5443772--5444172	2	195.0	2	63	24	72	43	3	6	46	1.47
5443740--5443902	33	4.7	33	79	13	175	43	4	6	46	1.48
5443818--5443866	9	5.4	9	77	18	57	38	2	6	53	1.38
5444071--5444173	7	15.1	7	73	11	56	48	1	5	43	1.38
5444200--5444266	33	2.1	31	88	5	98	38	8	10	41	1.71
5444237--5444419	18	9.7	18	72	19	115	43	8	8	39	1.65
5444250--5444300	24	2.1	25	88	3	77	45	9	7	37	1.67
5444237--5444370	42	3.3	40	78	17	143	43	8	8	40	1.64
5444366--5444411	20	2.2	22	76	15	60	45	8	8	36	1.66
5444421--5444493	20	3.4	20	79	17	92	52	2	6	38	1.43
5444404--5444469	33	2.0	32	91	2	105	53	3	6	37	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5444421--5444523	27	4.1	27	67	21	89	50	2	6	39	1.44
5444420--5444480	23	2.7	23	79	16	74	54	1	6	37	1.37
5444433--5444482	13	3.8	13	77	17	59	54	2	6	38	1.37
5444513--5444561	18	2.8	17	78	9	53	44	2	4	48	1.33
5444589--5444671	22	3.9	22	69	21	68	38	8	9	43	1.68
5444556--5444690	64	2.1	63	83	8	164	40	8	8	42	1.67
5444612--5444636	13	1.9	13	100	0	50	40	0	8	52	1.31
5444798--5445028	2	116.5	2	64	23	71	45	3	3	47	1.38
5444798--5445027	20	11.3	21	68	18	96	45	3	3	46	1.38
5444852--5444902	17	2.9	17	82	2	66	49	1	0	49	1.12
5444827--5444945	11	10.6	11	68	16	75	47	2	2	47	1.29
5445110--5445599	217	2.3	216	93	0	827	28	12	7	51	1.66
5447895--5447945	24	2.0	25	85	14	70	49	0	1	49	1.12
5448021--5448054	8	4.4	8	85	7	52	64	0	0	35	0.94
5448004--5448054	23	2.1	25	89	7	79	62	1	0	35	1.06
5448144--5448217	29	2.7	28	82	14	91	55	1	1	41	1.17
5455329--5455383	23	2.4	23	96	0	101	40	10	29	20	1.86
5459492--5462818	303	11.0	303	93	0	5577	29	13	9	47	1.75
5459492--5462818	907	3.7	907	93	1	5606	29	13	9	47	1.75
5466519--5466553	15	2.3	15	90	9	54	37	22	11	28	1.89
5468589--5468631	14	3.0	14	80	6	50	55	11	2	30	1.48
5469413--5469478	23	2.9	22	72	14	62	63	3	9	24	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5472916--5473017	45	2.3	45	85	0	141	25	28	28	17	1.98
5475103--5475236	71	1.9	71	95	0	241	30	5	31	32	1.80
5476009--5476172	82	2.0	82	98	0	319	49	4	8	37	1.55
5476327--5476364	16	2.4	16	95	0	67	23	42	0	34	1.55
5477048--5477340	156	1.9	156	86	2	426	31	16	14	37	1.89
5477076--5477340	79	3.4	78	79	3	271	30	16	13	38	1.89
5476921--5477344	77	5.4	79	78	5	358	29	16	15	38	1.89
5477651--5477690	2	20.0	2	100	0	80	50	0	0	50	1.00
5478996--5479446	225	2.0	223	90	5	712	44	7	12	35	1.70
5479557--5479609	23	2.2	25	86	6	74	54	0	0	45	0.99
5480504--5480550	2	23.5	2	100	0	94	48	0	0	51	1.00
5481167--5481207	2	20.5	2	100	0	82	51	0	0	48	1.00
5483900--5483949	22	2.3	22	78	0	55	30	10	24	36	1.88
5489125--5489149	6	4.2	6	100	0	50	0	16	48	36	1.46
5503586--5503930	173	2.0	172	94	0	609	35	11	14	38	1.82
5504550--5504595	14	3.2	15	90	6	69	30	0	2	67	1.03
5504549--5504599	15	3.5	14	87	10	50	29	0	1	68	1.00
5507679--5507721	21	2.0	21	86	0	59	48	0	20	30	1.50
5509907--5509949	21	2.0	21	86	0	59	48	0	20	30	1.50
5512576--5512614	19	2.1	19	90	0	60	56	5	2	35	1.35
5517280--5517359	32	2.4	33	83	8	101	32	6	0	61	1.21
5517523--5517574	3	17.3	3	81	15	63	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5517932--5517979	20	2.4	20	89	0	78	45	27	8	18	1.78
5518943--5518987	18	2.5	20	79	17	53	33	0	11	55	1.35
5519110--5519200	29	3.1	29	79	1	92	18	13	8	59	1.59
5532317--5532368	26	2.0	26	96	0	95	11	19	9	59	1.59
5534221--5534284	19	3.5	19	83	8	80	76	7	15	0	1.00
5534259--5534288	12	2.4	12	94	5	51	86	6	6	0	0.70
5535538--5535660	36	3.6	37	70	20	115	26	19	14	39	1.90
5535494--5535887	65	6.1	63	80	9	350	29	20	11	38	1.88
5535887--5536242	131	2.7	131	82	3	401	28	30	15	25	1.96
5538595--5538736	64	2.2	63	83	5	169	38	17	18	26	1.93
5539217--5539434	103	2.1	102	93	1	391	25	12	24	37	1.91
5539459--5539513	23	2.4	24	84	9	78	21	25	25	27	2.00
5546182--5546400	103	2.1	103	98	0	420	24	12	25	37	1.91
5546417--5546479	23	2.7	23	85	9	76	22	23	26	26	2.00
5547189--5547251	30	2.1	30	91	2	101	19	12	7	60	1.56
5547189--5547269	30	2.7	29	86	1	99	18	12	8	60	1.57
5550036--5550082	20	2.3	20	88	0	76	40	21	19	19	1.92
5550102--5550154	14	3.4	14	77	22	61	11	20	20	47	1.81
5551737--5551815	42	1.9	42	89	2	124	18	13	43	24	1.87
5551755--5551815	21	2.9	21	73	9	70	21	13	42	22	1.87
5552182--5552249	20	3.4	20	89	0	100	35	23	26	14	1.94
5552162--5552248	40	2.2	40	81	4	95	35	25	21	17	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5552238--5552296	14	3.9	14	76	20	64	47	23	18	10	1.79
5552221--5552312	33	2.8	33	86	1	130	44	23	20	10	1.83
5552308--5552404	19	5.7	18	73	22	84	15	17	19	47	1.83
5552311--5552404	33	2.8	33	88	0	143	15	17	19	47	1.82
5552330--5552388	14	3.9	14	76	20	55	13	15	20	50	1.77
5552398--5552443	20	2.3	20	92	0	74	17	26	23	32	1.97
5552990--5553037	18	2.7	18	90	0	78	16	12	43	27	1.84
5554410--5554449	14	2.9	14	100	0	80	7	15	27	50	1.70
5554902--5554974	20	3.7	20	83	0	101	26	16	27	30	1.97
5564361--5564671	121	2.6	121	93	1	516	32	13	6	47	1.69
5570344--5570398	18	3.1	18	86	5	67	7	23	25	43	1.79
5572024--5572085	19	3.2	18	75	13	52	17	30	27	24	1.97
5572027--5572085	21	2.9	20	75	10	66	18	27	28	25	1.98
5575899--5575938	21	1.9	21	85	10	55	35	10	2	52	1.48
5581582--5581606	11	2.3	11	100	0	50	16	0	0	84	0.63
5584430--5584483	5	10.8	5	85	0	63	9	0	50	40	1.35
5584595--5584636	19	2.3	18	84	12	50	57	0	0	42	0.99
5586526--5586555	9	3.3	9	95	0	51	13	0	3	83	0.77
5591695--5591737	15	2.8	16	79	10	54	23	0	2	74	0.93
5592322--5592435	59	1.9	59	83	1	147	42	12	9	35	1.75
5592322--5592457	60	2.3	59	79	3	148	38	12	11	36	1.80
5596127--5596344	21	10.6	21	79	3	192	21	17	25	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5596123--5596303	41	4.4	41	90	0	281	21	17	25	35	1.95
5596123--5596344	82	2.7	83	84	2	295	21	17	24	36	1.95
5596231--5596364	61	2.2	61	95	0	241	17	20	23	39	1.92
5596152--5596367	102	2.1	103	91	0	344	20	17	24	37	1.94
5596356--5596468	22	5.4	22	71	12	112	18	17	23	39	1.92
5596357--5596490	41	3.3	41	98	0	259	19	17	23	40	1.91
5596295--5596495	82	2.4	81	82	11	241	20	17	21	39	1.92
5596379--5596487	19	5.4	19	69	12	83	19	17	22	41	1.90
5597151--5597177	6	4.5	6	100	0	54	0	14	51	33	1.43
5597253--5597327	22	3.5	22	75	10	93	38	25	17	18	1.92

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