genome.fa.s9586.2.7.7.80.10.50.1000.16.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: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  3773412

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   

This is table  16  of  19  ( 2170 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)
3094160--3094228	23	3.0	23	84	0	84	27	24	26	21	1.99
3094438--3094491	27	2.0	27	89	3	83	29	25	3	40	1.73
3094501--3094566	33	2.0	33	100	0	132	27	24	3	45	1.68
3094813--3094954	64	2.2	65	82	5	164	26	19	19	34	1.96
3095887--3095917	11	2.8	11	100	0	62	35	9	0	54	1.33
3097279--3097319	14	2.8	15	77	7	57	46	4	17	31	1.69
3100071--3100119	25	1.9	25	87	4	71	53	4	12	30	1.57
3102202--3102288	31	2.8	30	83	10	104	42	0	3	54	1.17
3103010--3103093	11	8.3	10	71	18	50	53	3	1	41	1.26
3103010--3103093	29	2.8	29	76	18	82	53	3	1	41	1.26
3103003--3103074	19	3.7	19	72	18	60	54	2	1	41	1.23
3103197--3103230	13	2.6	13	95	0	59	23	5	26	44	1.76
3103463--3103507	23	2.0	22	86	4	63	37	0	6	55	1.26
3103764--3103807	18	2.4	18	92	0	70	38	11	25	25	1.89
3114237--3114564	164	2.0	164	92	0	539	44	12	16	26	1.83
3116948--3116998	19	2.6	20	90	3	77	43	23	17	15	1.88
3116948--3117185	20	11.6	20	73	10	113	39	19	22	18	1.92
3117052--3117185	63	2.1	63	92	0	223	36	17	25	20	1.94
3117288--3117446	6	26.5	6	98	0	309	33	49	16	0	1.46
3118128--3118198	6	12.5	6	98	1	114	0	16	53	29	1.44
3118274--3118576	20	14.8	20	76	7	160	19	22	18	39	1.93
3118274--3118491	40	5.3	40	83	4	238	20	24	17	36	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3118333--3118491	83	1.9	83	93	0	273	20	25	17	35	1.95
3118902--3118947	22	2.0	23	87	4	67	43	2	0	54	1.12
3118896--3118965	32	2.2	32	82	14	83	44	2	0	52	1.15
3119129--3119173	23	2.0	23	86	0	63	53	2	2	42	1.25
3119248--3119317	14	4.9	14	72	8	52	55	0	0	44	0.99
3119254--3119337	20	3.8	22	74	19	77	51	0	1	47	1.08
3119268--3119340	25	3.0	24	79	20	80	49	0	1	49	1.09
3119743--3120289	188	2.9	187	85	4	697	31	19	16	32	1.94
3122700--3122909	71	3.0	68	71	17	157	45	3	8	42	1.51
3122642--3122872	37	6.5	37	73	16	116	43	4	7	44	1.53
3122793--3122860	32	2.1	32	84	10	86	44	4	5	45	1.48
3122957--3123005	19	2.5	20	77	9	57	20	8	0	71	1.11
3128740--3129673	94	9.9	94	97	0	1697	33	25	18	22	1.97
3129686--3129963	80	3.4	80	89	3	394	28	26	20	24	1.99
3130600--3130712	39	2.9	38	72	8	104	41	7	8	42	1.63
3130770--3130812	21	1.9	23	86	13	63	48	0	2	48	1.14
3130770--3130821	18	2.5	20	82	17	54	48	0	1	50	1.12
3130893--3130925	17	1.9	18	88	11	52	36	3	6	54	1.41
3130934--3130986	9	5.9	9	79	12	56	20	11	0	67	1.21
3130934--3130986	27	2.0	27	85	7	72	20	11	0	67	1.21
3132318--3132347	5	5.8	5	96	4	51	16	3	0	80	0.85
3133063--3133121	31	1.9	30	83	10	75	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3133070--3133143	38	1.9	39	83	8	98	59	0	0	40	0.97
3139432--3139611	56	3.3	57	80	6	167	30	12	13	43	1.81
3149478--3149530	21	2.5	21	78	9	54	49	3	0	47	1.19
3153289--3153363	29	2.6	29	84	0	96	18	40	26	14	1.90
3153290--3153377	29	3.0	29	84	0	95	20	37	30	11	1.88
3153594--3153680	29	3.0	29	84	0	120	14	29	39	16	1.88
3157757--3158188	214	2.0	214	98	1	812	30	16	20	32	1.95
3159298--3159335	2	19.0	2	100	0	76	50	0	0	50	1.00
3162598--3162654	28	2.0	28	89	0	87	36	24	10	28	1.88
3164108--3164167	25	2.4	26	88	8	97	48	3	10	38	1.53
3164274--3164317	15	3.0	15	90	9	65	38	2	4	54	1.33
3164280--3164380	15	6.5	15	72	18	66	34	3	1	59	1.27
3164334--3164392	30	2.0	28	84	12	75	28	0	0	71	0.87
3164342--3164384	23	1.9	22	90	4	68	30	0	0	69	0.88
3164327--3164393	32	2.1	33	86	8	93	29	0	0	70	0.88
3165474--3165511	18	2.1	19	90	5	60	23	2	0	73	0.95
3167325--3167408	27	3.0	27	75	17	89	15	7	1	76	1.06
3167424--3167480	23	2.3	25	88	8	82	14	7	3	75	1.14
3171410--3172536	168	6.7	168	85	1	1298	34	24	17	23	1.96
3171409--3172536	333	3.4	335	85	2	1372	34	24	17	23	1.96
3171409--3172536	84	13.5	84	83	2	1176	34	24	17	23	1.96
3172978--3173021	2	22.5	2	95	4	81	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3174119--3174254	4	33.2	4	69	19	59	22	5	1	71	1.14
3175734--3175830	44	2.2	44	81	1	115	50	4	2	43	1.33
3179510--3179551	3	14.0	3	100	0	84	66	0	0	33	0.92
3186665--3186766	34	2.8	37	85	10	149	43	15	13	27	1.85
3187474--3187508	16	2.2	16	89	0	52	31	5	0	62	1.18
3187489--3187539	21	2.4	22	80	3	59	27	3	1	66	1.20
3190844--3190905	23	2.7	22	80	9	72	79	6	14	0	0.93
3190844--3190913	20	3.3	20	82	9	68	78	5	14	1	1.00
3192526--3192649	36	3.4	36	82	6	160	25	20	13	40	1.89
3192625--3192781	68	2.4	68	84	5	205	31	22	8	36	1.85
3193386--3194046	105	6.3	105	91	2	972	33	26	18	22	1.96
3194594--3194695	34	2.8	37	88	10	158	43	14	13	28	1.84
3194594--3194729	37	3.8	35	82	9	159	41	13	13	30	1.84
3195269--3195301	12	2.8	12	95	0	57	21	0	0	78	0.75
3197629--3197682	27	2.0	27	100	0	108	44	18	3	33	1.67
3201413--3201517	52	2.0	52	100	0	210	20	19	10	49	1.77
3205592--3205684	6	15.5	6	100	0	186	51	0	16	32	1.44
3207729--3207828	31	3.2	32	76	9	107	35	15	18	32	1.91
3210839--3210881	21	2.0	21	86	0	59	30	27	25	16	1.97
3211416--3211633	103	2.1	103	98	0	418	25	12	24	37	1.90
3211650--3211712	23	2.7	23	87	4	92	20	26	26	25	1.99
3217631--3217673	21	2.0	21	86	0	59	30	27	25	16	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3218216--3218433	103	2.1	103	96	0	409	24	11	24	38	1.89
3218449--3218512	23	2.8	23	77	13	78	21	26	25	26	2.00
3231841--3231870	15	2.1	14	93	6	51	20	40	16	23	1.91
3232261--3232305	17	2.8	16	83	13	56	42	4	0	53	1.21
3233848--3233877	13	2.3	13	94	0	51	63	0	3	33	1.11
3233998--3234067	28	2.4	27	80	15	70	70	2	1	25	1.10
3234027--3234067	20	2.1	19	86	4	55	73	2	0	24	0.96
3235294--3235352	15	3.6	15	80	15	55	69	0	3	27	1.04
3235377--3235610	35	6.7	33	70	17	136	44	6	3	44	1.48
3236378--3237251	165	5.3	164	89	1	1180	24	20	25	30	1.99
3236378--3237245	329	2.6	328	86	2	1184	24	20	25	30	1.99
3242165--3242196	13	2.5	13	94	0	55	59	0	3	37	1.13
3242346--3242386	20	2.1	19	86	4	55	73	2	0	24	0.96
3242435--3242495	23	2.9	21	74	11	61	73	3	3	19	1.11
3243616--3243665	15	3.3	15	83	11	57	72	0	4	24	1.02
3243732--3243945	35	5.9	38	74	14	143	42	6	5	45	1.53
3250264--3250296	17	1.9	17	93	0	57	18	45	3	33	1.65
3270592--3270632	18	2.3	18	86	0	55	82	4	9	2	0.89
3276642--3276759	58	2.0	58	100	0	236	48	5	10	36	1.59
3278611--3278654	23	1.9	23	95	0	79	15	29	27	27	1.96
3280270--3280308	3	12.7	3	89	5	60	33	0	0	66	0.92
3280270--3280308	16	2.5	15	91	4	60	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3281847--3281892	24	2.0	24	86	4	67	52	0	2	45	1.13
3288927--3289114	93	2.0	93	86	4	263	29	14	19	36	1.92
3290612--3290928	158	2.0	158	98	1	609	32	17	16	33	1.93
3291975--3292029	22	2.5	22	90	0	92	34	12	14	38	1.84
3292545--3292867	165	2.0	166	88	1	488	36	13	10	39	1.80
3292872--3293555	76	9.0	76	96	0	1248	23	22	20	34	1.96
3292872--3293555	302	2.3	303	96	1	1273	23	22	20	34	1.96
3296199--3296291	2	47.5	2	93	4	163	51	0	1	47	1.07
3299676--3299716	21	2.0	21	95	0	73	26	21	24	26	2.00
3303252--3303310	30	2.0	31	86	6	86	32	11	13	42	1.81

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19