genome.fa.s1129.2.7.7.80.10.50.1000.16.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: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  21326069

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   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   

This is table  16  of  89  ( 10573 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)
2968426--2968467	3	14.0	3	82	9	50	30	2	0	66	1.04
2968522--2968566	24	1.9	23	86	4	63	42	40	8	8	1.67
2970549--2970861	131	2.4	131	83	5	409	31	11	16	39	1.84
2973782--2973815	16	2.1	16	94	0	59	23	23	23	29	1.99
2976824--2976877	22	2.5	22	87	6	74	38	11	18	31	1.86
2977303--2977670	45	8.2	45	92	0	610	44	12	22	21	1.85
2977353--2977424	19	3.4	19	70	23	63	41	13	22	22	1.89
2977596--2977665	21	3.2	21	66	25	54	42	11	24	21	1.85
2992078--2992140	4	15.8	4	73	18	51	77	0	15	6	0.96
2992077--2992156	16	4.5	17	73	19	56	77	0	13	8	0.99
2992077--2992156	19	4.5	16	72	22	54	77	0	13	8	0.99
2992074--2992143	23	3.1	24	81	16	71	78	0	15	5	0.93
2992589--2992620	15	2.1	15	100	0	64	40	31	0	28	1.57
2993399--2993973	134	4.3	134	81	2	573	33	21	13	31	1.93
2993399--2993973	268	2.1	268	81	3	638	33	21	13	31	1.93
2994874--2994907	10	3.3	10	87	4	50	11	0	38	50	1.39
2996259--2996502	131	1.9	131	88	0	371	32	10	16	40	1.83
3000459--3000516	15	3.9	15	72	17	50	56	3	1	37	1.26
3001291--3001391	47	2.0	49	90	9	161	58	5	7	27	1.50
3001312--3001414	47	2.2	46	82	5	125	64	2	5	27	1.31
3001361--3001426	30	2.1	31	81	15	75	68	0	4	27	1.09
3001517--3001591	21	3.2	23	71	21	66	61	4	0	34	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3001526--3001597	23	3.0	25	70	17	71	59	4	1	34	1.25
3007083--3007129	20	2.3	20	100	0	94	12	17	27	42	1.85
3007593--3007619	13	2.1	13	100	0	54	29	7	48	14	1.71
3007775--3007813	21	2.0	20	85	10	53	41	17	12	28	1.87
3012060--3012104	18	2.6	18	85	3	56	53	0	0	46	1.00
3013674--3013706	15	2.1	17	88	11	52	42	36	6	15	1.71
3013782--3013876	27	3.6	27	92	2	158	31	11	14	42	1.82
3014610--3014649	22	1.9	21	90	10	64	25	20	15	40	1.90
3017605--3017699	27	3.6	27	91	2	158	31	11	14	42	1.82
3021286--3021360	32	2.3	32	90	2	123	41	37	9	12	1.74
3021347--3021447	33	3.2	33	72	12	88	52	20	8	17	1.71
3040343--3040391	24	2.0	24	100	0	98	26	24	12	36	1.91
3054749--3054874	62	2.0	62	95	0	225	26	13	24	34	1.93
3064927--3064974	21	2.3	21	100	0	96	33	14	8	43	1.75
3068129--3068174	20	2.3	20	100	0	92	47	0	30	21	1.51
3069113--3069180	23	3.0	23	88	0	91	20	25	26	27	1.99
3070228--3070261	17	2.0	17	94	0	59	17	20	26	35	1.95
3077582--3077615	17	2.1	16	88	5	50	14	8	0	76	1.01
3089827--3089940	32	3.6	32	76	0	111	29	17	15	36	1.91
3092709--3092755	21	2.2	21	88	7	69	44	21	10	23	1.83
3102321--3102362	18	2.3	19	88	12	61	35	0	11	52	1.38
3103058--3103085	2	14.0	2	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3106836--3106890	21	2.6	21	85	0	74	30	10	21	36	1.88
3107419--3107463	23	2.0	23	86	0	63	26	26	26	20	1.99
3107431--3107746	150	2.1	149	93	1	535	34	21	16	26	1.95
3108230--3108267	20	1.9	20	88	0	58	10	31	34	23	1.89
3114365--3114409	23	2.0	23	81	0	54	26	24	26	22	2.00
3114377--3114692	150	2.1	149	93	1	535	33	20	17	27	1.95
3117941--3117991	18	2.8	19	75	16	54	3	33	0	62	1.13
3119508--3119558	21	2.4	21	83	6	68	41	25	19	13	1.88
3119437--3119614	92	1.9	92	82	6	218	35	21	16	26	1.94
3121115--3121156	2	21.0	2	100	0	84	50	0	0	50	1.00
3121598--3121633	18	2.0	18	94	0	63	22	33	19	25	1.97
3122022--3122048	4	6.8	4	100	0	54	48	25	0	25	1.52
3122126--3122175	25	2.0	25	92	0	82	24	20	12	44	1.85
3133311--3133367	29	1.9	30	85	3	80	38	1	5	54	1.33
3133332--3133378	23	2.1	23	84	7	62	42	2	0	55	1.12
3139513--3139569	29	2.0	29	100	0	114	31	14	21	33	1.92
3139879--3139923	22	2.0	22	87	8	65	22	6	17	53	1.67
3140913--3140987	40	1.9	39	86	5	107	36	20	18	25	1.95
3142085--3142130	24	1.9	24	86	0	65	32	0	50	17	1.47
3152906--3152931	2	13.0	2	100	0	52	50	0	0	50	1.00
3160401--3160516	56	2.1	57	88	1	171	42	17	7	32	1.78
3164625--3164769	53	2.6	58	74	13	151	42	2	17	36	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3164937--3164983	24	2.0	24	91	0	76	23	29	17	29	1.97
3168687--3168747	15	3.9	15	83	10	70	24	1	3	70	1.11
3168709--3168796	44	2.0	44	82	8	108	15	5	6	71	1.27
3168872--3168908	8	4.3	9	89	3	51	18	0	0	81	0.70
3168873--3168908	12	2.8	13	87	8	56	19	0	0	80	0.71
3171660--3172052	196	2.0	196	96	3	729	38	3	20	37	1.71
3172883--3173169	144	2.0	138	91	7	461	26	15	22	35	1.94
3173146--3173188	22	2.0	22	85	0	59	20	27	27	23	1.99
3173933--3173958	12	2.2	12	100	0	52	57	7	7	26	1.54
3176104--3176411	157	2.0	155	87	2	447	39	20	11	27	1.87
3179746--3179828	31	2.6	32	90	1	123	14	16	9	59	1.61
3180230--3180277	12	3.9	13	84	13	57	22	18	39	18	1.92
3180236--3180277	12	3.5	12	93	0	75	26	19	35	19	1.95
3180272--3180359	35	2.5	35	98	0	167	27	32	21	18	1.96
3180347--3180401	26	2.1	26	100	0	110	20	36	25	18	1.94
3180442--3180561	29	4.1	29	98	0	231	10	30	35	23	1.89
3180424--3180561	58	2.4	58	92	2	233	12	31	34	22	1.91
3180562--3180593	13	2.5	13	100	0	64	21	46	0	31	1.52
3180758--3180809	25	2.1	25	100	0	104	26	11	34	26	1.91
3180821--3180866	23	2.0	23	100	0	92	47	4	39	8	1.54
3180870--3180952	4	20.5	4	74	9	62	62	0	36	1	1.03
3180821--3180881	23	2.6	23	86	5	59	50	6	36	6	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3180871--3180944	21	3.5	21	98	0	139	62	0	36	1	1.04
3180873--3180944	13	5.4	13	72	16	58	62	0	36	1	1.04
3181104--3181235	45	3.0	45	80	14	134	40	0	12	47	1.41
3183579--3183611	17	1.9	17	93	0	57	45	12	6	36	1.66
3183596--3183664	22	3.0	22	73	19	77	47	7	4	40	1.51
3183828--3183875	19	2.5	20	89	3	71	47	14	0	37	1.44
3183888--3184351	26	18.6	25	79	14	369	43	10	2	43	1.52
3183842--3184409	124	4.6	124	98	0	1111	44	10	2	42	1.51
3183888--3184415	26	21.4	23	74	12	192	44	10	2	43	1.51
3184093--3184148	19	3.1	18	77	15	62	50	14	0	35	1.43
3183842--3184409	247	2.3	248	98	0	1111	44	10	2	42	1.51
3188095--3188156	28	2.2	29	94	2	108	58	11	0	30	1.33
3188133--3188181	21	2.3	21	85	3	71	53	16	0	30	1.43
3188737--3188800	15	4.1	15	80	11	83	17	54	7	20	1.67
3188738--3188808	17	4.4	16	82	7	90	16	52	9	21	1.73
3188728--3188794	16	4.2	16	79	7	73	16	55	7	20	1.65
3188738--3188808	33	2.2	32	92	2	115	16	52	9	21	1.73
3188848--3188936	29	3.1	29	100	0	178	17	37	31	13	1.89
3193714--3193794	24	3.6	23	73	17	71	29	24	23	22	1.99
3197611--3197650	21	1.9	21	85	10	55	35	10	2	52	1.48
3209507--3209638	57	2.3	57	96	0	237	34	18	12	33	1.89
3209978--3210018	22	1.9	21	90	5	64	26	17	14	41	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3220376--3220435	24	2.2	29	83	16	76	55	8	1	35	1.40
3220822--3221078	57	4.5	57	96	0	462	36	18	10	35	1.85
3221418--3221471	19	2.7	19	82	8	63	29	18	14	37	1.91
3233051--3233103	2	26.5	2	92	0	88	47	0	3	49	1.19
3234563--3234612	25	2.0	25	100	0	100	44	12	0	44	1.41
3235806--3235857	20	2.6	20	87	6	79	23	21	19	36	1.95
3239447--3239515	27	2.4	29	81	11	72	42	2	20	34	1.67
3240119--3240172	2	27.5	2	92	3	92	50	0	0	50	1.00
3247442--3247517	2	38.0	2	100	0	152	50	0	0	50	1.00
3247693--3247738	20	2.3	20	100	0	92	41	21	0	36	1.54

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   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89