genome.fa.s7960.2.7.7.80.10.50.1000.16.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: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  7905731

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   

This is table  16  of  39  ( 4646 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)
3160100--3160161	16	4.1	15	78	13	58	70	0	3	25	1.02
3160100--3160132	16	2.1	16	94	5	59	72	0	0	27	0.85
3160100--3160162	10	5.7	10	79	20	56	71	0	3	25	1.01
3168270--3168329	21	2.8	22	72	23	56	66	1	5	26	1.21
3168281--3168311	14	2.2	14	94	0	53	77	0	3	19	0.90
3168433--3168491	31	1.9	31	89	6	93	57	3	0	38	1.15
3168423--3168492	31	2.2	30	82	9	86	60	2	0	37	1.12
3170249--3170286	20	1.9	20	100	0	76	31	21	23	23	1.98
3171823--3171867	23	2.0	23	90	0	72	17	26	26	28	1.98
3177126--3177164	3	13.0	3	84	10	53	61	2	0	35	1.10
3178307--3178803	254	2.0	254	87	2	730	35	12	9	42	1.76
3185368--3185444	23	3.4	23	74	13	79	31	20	20	27	1.98
3189271--3189310	21	1.9	21	89	0	62	30	7	7	55	1.56
3189454--3189492	15	2.6	15	91	0	69	17	30	12	38	1.88
3191241--3191396	64	2.4	65	84	3	208	29	21	21	28	1.98
3192946--3192970	2	12.5	2	100	0	50	48	0	0	52	1.00
3195126--3195152	3	9.0	3	100	0	54	33	0	0	66	0.92
3195826--3195885	21	2.7	23	72	17	63	75	1	18	5	1.07
3197889--3197926	2	19.0	2	100	0	76	50	0	0	50	1.00
3204320--3204557	99	2.3	102	83	7	279	34	15	12	38	1.84
3204946--3205367	138	3.1	139	82	3	485	33	26	15	25	1.95
3205378--3205600	122	1.8	122	85	0	311	36	22	14	26	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3205764--3205828	3	21.7	3	100	0	130	33	32	0	33	1.58
3206495--3206570	11	6.3	12	69	22	52	73	2	18	5	1.14
3211339--3211395	19	3.2	18	74	20	57	59	0	1	38	1.08
3211348--3211403	17	3.2	18	76	19	57	60	0	3	35	1.14
3225899--3225929	12	2.6	12	100	0	62	64	6	9	19	1.45
3226700--3226751	26	2.0	26	85	7	70	25	23	21	30	1.99
3227160--3227196	18	2.0	19	94	5	67	48	10	5	35	1.61
3231634--3231691	23	2.6	23	94	5	102	39	3	12	44	1.58
3231705--3231739	13	2.8	13	91	4	54	57	0	0	42	0.99
3235307--3235406	33	3.0	34	83	2	139	39	3	4	54	1.35
3235926--3236019	21	4.5	21	89	5	120	20	25	35	19	1.96
3236023--3236070	21	2.3	21	85	0	60	22	12	39	25	1.89
3239175--3239216	21	2.0	22	81	13	52	40	11	4	42	1.63
3239191--3239237	14	3.4	14	77	11	51	44	17	0	38	1.48
3239213--3239292	28	2.8	28	81	5	99	50	21	0	28	1.49
3242951--3243094	41	3.5	41	85	11	179	33	15	22	27	1.95
3244570--3244723	41	3.7	41	74	11	134	34	17	19	28	1.95
3244650--3244788	43	3.4	41	76	5	111	28	17	21	31	1.97
3247767--3247890	21	5.9	21	87	0	158	41	14	38	5	1.70
3247769--3247905	42	3.2	42	83	2	157	42	15	35	6	1.73
3247767--3247890	63	2.0	63	86	0	176	41	14	38	5	1.70
3248872--3249034	64	2.5	63	82	5	193	33	16	22	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3249022--3249099	20	3.7	20	93	6	120	30	20	23	25	1.98
3249006--3249099	40	2.3	43	85	12	126	30	19	24	25	1.98
3249632--3250380	374	2.0	373	97	1	1401	36	19	4	38	1.74
3250486--3250618	30	4.4	30	96	0	230	34	23	18	24	1.96
3250486--3250635	60	2.5	60	87	2	194	35	23	18	22	1.96
3251551--3251608	20	2.6	22	89	10	84	25	22	20	31	1.98
3251596--3251757	64	2.5	63	82	5	182	27	22	16	33	1.95
3261308--3261369	2	31.0	2	100	0	124	50	0	0	50	1.00
3266007--3266055	21	2.3	21	100	0	98	22	4	44	28	1.71
3272448--3272514	18	3.6	19	82	9	77	14	10	0	74	1.07
3272466--3272526	23	2.9	21	76	23	65	11	9	0	78	0.96
3272501--3272696	38	5.6	34	70	20	104	14	7	3	74	1.16
3272624--3272653	15	1.9	16	93	6	53	13	10	0	76	1.01
3272596--3272655	26	2.3	27	85	8	79	13	8	0	78	0.96
3277500--3277671	64	2.7	64	94	0	290	35	22	13	29	1.92
3277638--3277795	64	2.6	60	82	7	167	36	20	14	27	1.92
3277821--3278341	124	4.2	124	91	0	817	33	24	15	26	1.95
3277886--3278400	58	8.5	58	68	16	283	33	23	15	27	1.95
3280042--3280075	2	17.0	2	100	0	68	50	0	0	50	1.00
3280363--3280509	4	35.8	4	68	14	59	18	7	2	72	1.18
3280315--3280384	32	2.3	31	80	12	81	17	12	0	70	1.18
3280363--3280402	21	1.9	21	89	0	62	22	2	2	72	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3280420--3280558	9	14.9	9	70	18	63	15	7	2	74	1.13
3280433--3280553	50	2.4	50	83	8	149	14	8	1	75	1.11
3286151--3286226	27	2.8	27	97	0	143	43	11	14	30	1.81
3296392--3296434	20	2.2	20	83	8	52	37	4	2	55	1.33
3305181--3305221	20	2.0	20	100	0	82	51	24	0	24	1.49
3308226--3308288	32	1.9	33	84	9	85	42	3	1	52	1.27
3308299--3308333	2	17.5	2	100	0	70	48	0	0	51	1.00
3309012--3309054	18	2.4	18	100	0	86	13	30	6	48	1.69
3309257--3309299	17	2.5	17	96	0	77	44	0	13	41	1.44
3311959--3312216	2	140.0	2	68	25	144	41	1	3	53	1.28
3311959--3312233	111	2.5	109	80	10	274	41	1	3	53	1.28
3316667--3316717	24	2.1	25	82	10	61	17	19	5	56	1.61
3316676--3316711	15	2.2	17	90	9	58	13	19	5	61	1.52
3321853--3321943	42	2.2	42	84	4	112	49	28	3	18	1.63
3324529--3324579	23	2.3	22	79	3	57	50	0	3	45	1.20
3324670--3324717	17	2.6	19	80	16	64	47	6	10	35	1.63
3326592--3326832	119	2.0	121	90	3	387	35	15	9	40	1.79
3338004--3338039	14	2.6	14	95	0	63	25	44	8	22	1.80
3343909--3343954	2	23.0	2	81	0	56	58	0	0	41	0.98
3351899--3352008	36	3.0	36	81	4	139	40	21	18	19	1.91
3352059--3352760	54	12.9	54	78	9	399	33	16	23	25	1.96
3352059--3352418	108	3.3	107	82	7	440	33	16	25	24	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3352383--3352666	55	5.1	55	86	4	358	33	14	22	29	1.94
3352938--3352988	3	17.7	3	78	15	54	39	0	1	58	1.09
3352948--3353005	25	2.3	25	84	3	71	43	1	0	55	1.10
3360824--3360876	22	2.4	22	93	0	88	20	18	43	16	1.88
3361510--3361575	32	2.1	32	91	0	105	21	19	15	43	1.87
3362287--3362504	111	2.0	112	88	4	334	43	17	16	22	1.88
3364045--3364977	469	2.0	469	95	0	1686	29	22	15	32	1.95
3369132--3369183	20	2.6	20	100	0	104	32	11	28	26	1.91
3369649--3369919	49	5.5	49	91	0	452	39	14	21	23	1.91
3369885--3369949	30	2.2	30	100	0	130	36	16	23	23	1.94
3369836--3369998	79	2.1	79	92	0	272	39	15	20	24	1.91
3369787--3370047	128	2.0	128	90	0	414	39	15	20	24	1.91
3369915--3370168	49	5.2	49	86	0	357	38	16	19	25	1.92
3369738--3370096	177	2.0	177	91	1	576	39	15	20	23	1.91
3369689--3370145	226	2.0	226	90	0	718	38	15	21	24	1.92
3369649--3370168	275	1.9	275	88	0	790	39	15	20	24	1.91
3376483--3376519	19	1.9	19	100	0	74	43	0	2	54	1.14
3376533--3376706	76	2.3	77	85	8	234	50	5	1	42	1.33
3376746--3376842	46	2.1	45	92	1	158	55	10	20	13	1.67
3380538--3380599	30	2.1	30	96	0	115	30	19	16	33	1.94
3392101--3392441	126	2.7	127	79	9	388	34	21	14	29	1.93
3392080--3392456	131	2.9	130	80	9	421	34	21	15	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3392426--3393126	131	5.3	129	77	8	560	33	20	17	29	1.95
3392266--3392681	217	1.9	217	87	1	602	33	21	16	27	1.95
3392140--3392806	348	1.9	343	85	2	906	34	21	16	27	1.95
3392367--3392829	86	5.3	86	68	11	246	33	21	16	28	1.95
3393961--3394021	10	5.9	10	85	11	70	75	1	22	0	0.89
3393961--3394036	32	2.3	33	86	6	102	73	1	25	0	0.91
3393970--3394035	11	5.8	12	79	16	70	72	1	25	0	0.93
3397577--3397619	22	2.0	22	85	0	59	30	0	0	69	0.88
3399874--3399902	5	5.8	5	100	0	58	20	58	20	0	1.39
3401305--3401342	18	2.1	19	90	5	60	42	2	0	55	1.14

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