genome.fa.s9634.2.7.7.80.10.50.1000.60.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: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  17174986

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   

This is table  60  of  78  ( 9351 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)
12158885--12158918	18	2.0	17	88	11	52	70	0	2	26	1.01
12160341--12160366	2	13.0	2	100	0	52	50	0	0	50	1.00
12160418--12160596	2	90.0	2	68	23	67	51	1	7	39	1.37
12160518--12160556	17	2.3	17	86	8	53	56	2	5	35	1.35
12160505--12160621	12	9.5	12	70	21	75	51	2	6	39	1.42
12165747--12165790	8	5.4	8	86	2	61	72	0	27	0	0.85
12165747--12165794	16	2.9	17	93	6	89	68	0	31	0	0.90
12166109--12166191	22	3.8	22	81	9	98	57	3	8	30	1.45
12166084--12166201	43	2.7	43	80	7	116	57	3	7	31	1.43
12166173--12166712	29	19.1	29	69	16	246	52	2	11	33	1.53
12166196--12166689	8	65.8	8	66	22	129	51	3	12	33	1.54
12166174--12166537	37	9.2	37	68	18	155	52	2	11	33	1.51
12166449--12166746	43	6.6	43	81	13	339	52	3	11	32	1.54
12166444--12166746	94	3.3	91	84	9	386	52	3	11	33	1.55
12166126--12166316	90	2.2	90	80	13	157	54	2	10	32	1.48
12166605--12166747	8	19.5	8	68	27	54	51	2	9	35	1.49
12167447--12167517	2	35.5	2	100	0	142	49	0	0	50	1.00
12168077--12168545	57	8.2	57	89	1	652	31	19	12	36	1.89
12168129--12168545	172	2.4	172	96	1	766	31	18	12	37	1.88
12168077--12168545	115	4.1	114	89	1	652	31	19	12	36	1.89
12171953--12172002	23	2.2	23	92	0	82	34	24	20	22	1.97
12175818--12175857	21	1.9	21	89	0	62	30	7	5	57	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12178238--12178267	2	15.0	2	100	0	60	50	0	0	50	1.00
12180069--12180220	81	1.9	82	83	4	200	27	23	11	37	1.89
12180553--12181096	57	9.5	57	87	1	730	32	18	11	37	1.86
12182495--12182525	16	1.9	16	100	0	62	45	0	16	38	1.47
12182486--12182529	16	3.0	14	81	18	54	47	2	13	36	1.56
12182498--12182559	16	4.1	16	73	12	58	53	0	14	32	1.41
12182586--12182832	8	31.2	8	75	19	121	48	0	11	39	1.43
12182579--12182839	14	19.2	14	70	23	71	47	0	11	40	1.43
12182586--12182832	15	15.6	16	72	21	121	48	0	11	39	1.43
12182570--12182632	22	2.8	22	79	13	67	49	3	11	36	1.54
12182654--12182702	4	12.8	4	91	8	84	26	0	22	51	1.49
12182652--12182702	26	2.0	26	100	0	102	27	0	21	50	1.48
12182658--12182702	22	2.0	22	100	0	90	26	0	22	51	1.49
12182699--12182833	7	18.9	7	76	22	81	54	0	8	36	1.32
12182699--12182833	22	6.0	22	80	18	111	54	0	8	36	1.32
12182715--12182832	58	2.0	61	86	11	172	55	0	7	37	1.29
12197447--12197754	85	3.6	85	91	0	474	29	20	17	32	1.96
12203819--12203859	15	2.7	15	92	3	64	7	21	7	63	1.45
12204105--12204142	18	2.1	18	100	0	76	44	31	10	13	1.77
12207283--12207725	228	2.0	226	94	0	787	31	13	19	35	1.90
12209556--12209595	21	2.0	20	85	5	53	40	17	12	30	1.86
12223222--12223273	14	4.0	13	78	16	54	76	3	19	0	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12223223--12223268	11	4.2	11	78	15	51	78	2	19	0	0.86
12223236--12223274	5	7.8	5	83	11	53	76	0	23	0	0.78
12223223--12223274	9	5.6	9	78	14	52	76	1	21	0	0.87
12223228--12223274	14	3.2	14	82	11	58	76	2	21	0	0.89
12233376--12233453	23	3.3	24	85	8	99	48	5	0	46	1.24
12239211--12239251	21	2.0	21	85	0	55	31	14	17	36	1.90
12240465--12241253	287	2.8	283	82	4	940	46	6	15	32	1.71
12242633--12242663	14	2.2	14	94	0	53	35	0	3	61	1.12
12256132--12256169	20	1.9	20	100	0	76	42	5	28	23	1.76
12264759--12264930	55	3.1	55	93	0	292	34	11	18	36	1.86
12264921--12264960	13	3.1	13	100	0	80	22	15	15	47	1.82
12265711--12266195	250	1.9	250	96	0	889	29	18	21	30	1.97
12266588--12266630	22	2.0	22	95	0	77	13	27	41	16	1.86
12268079--12268126	19	2.5	20	82	3	62	29	12	6	52	1.63
12269338--12269379	21	2.0	21	90	0	66	26	26	21	26	1.99
12269492--12269554	21	3.0	20	79	9	72	17	26	36	19	1.94
12275789--12275993	55	3.7	55	91	1	331	37	9	17	35	1.83
12294373--12294681	55	5.6	55	94	0	519	37	9	18	35	1.83
12294378--12294716	110	3.1	109	86	5	461	34	10	19	35	1.86
12295342--12295531	66	2.7	69	77	10	199	30	19	12	38	1.88
12295542--12295792	103	2.4	103	81	3	299	33	16	13	36	1.88
12295542--12295774	104	2.3	102	84	3	288	34	16	12	36	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12295930--12297016	219	5.0	218	85	3	1350	31	25	16	26	1.96
12295933--12296988	437	2.4	434	86	4	1424	31	25	16	26	1.97
12298556--12298667	33	3.4	33	74	14	86	28	16	3	51	1.60
12301064--12301095	16	2.0	16	93	0	55	46	6	15	31	1.71
12301269--12301368	39	2.6	39	81	0	110	47	10	4	39	1.56
12304887--12304935	12	4.2	11	85	12	62	73	0	0	26	0.83
12304888--12304922	6	5.8	6	87	12	54	71	0	0	28	0.86
12304888--12304939	24	2.1	25	89	10	81	73	0	0	26	0.84
12304892--12304950	24	2.4	24	81	16	68	72	0	3	23	0.99
12306100--12306139	11	3.6	11	93	6	64	82	2	0	15	0.77
12306100--12306141	20	2.2	19	87	12	59	83	2	0	14	0.75
12306171--12306276	35	3.0	34	76	14	99	43	9	1	45	1.47
12306195--12306357	40	4.2	40	80	11	160	44	6	3	46	1.45
12306317--12306341	12	2.1	12	100	0	50	36	8	8	48	1.62
12306145--12306545	38	10.9	37	72	17	279	42	7	3	46	1.50
12306344--12306497	39	4.1	38	76	15	131	44	7	4	44	1.52
12306359--12306578	38	5.8	37	77	12	171	44	8	3	44	1.49
12306358--12306578	77	2.9	76	78	11	229	43	8	3	44	1.51
12307218--12307612	85	4.7	85	82	1	445	26	16	22	34	1.95
12308747--12308943	95	2.1	96	88	0	288	32	16	16	34	1.92
12311225--12311267	17	2.4	18	84	3	61	16	0	2	81	0.79
12311227--12311271	22	2.0	22	84	16	58	20	0	2	77	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12311221--12311269	17	3.0	16	82	11	55	16	0	4	79	0.88
12311352--12311381	2	15.5	2	93	6	53	50	0	0	50	1.00
12311364--12311641	37	7.7	37	69	20	164	47	3	6	42	1.45
12311440--12311594	50	3.2	50	77	12	153	50	2	3	43	1.34
12311506--12311543	12	3.2	12	100	0	76	42	7	7	42	1.63
12311520--12311635	37	3.1	37	91	7	182	46	3	6	43	1.45
12311607--12311664	26	2.4	24	83	11	73	43	0	13	43	1.44
12311704--12311741	3	13.0	3	88	5	60	31	2	0	65	1.06
12312933--12312962	4	7.5	4	100	0	60	23	0	0	76	0.78
12314621--12314653	3	11.0	3	100	0	66	33	0	0	66	0.92
12314999--12315110	34	3.3	34	93	0	188	28	25	19	26	1.99
12315027--12315122	27	3.3	27	73	18	75	27	27	18	27	1.98
12315083--12315150	27	2.5	27	97	0	127	25	25	19	30	1.98
12315226--12315295	30	2.3	32	78	14	85	40	0	4	55	1.19
12315272--12315364	15	5.7	16	71	26	63	33	1	6	59	1.30
12315285--12315359	3	24.7	3	75	17	66	33	0	5	61	1.19
12317084--12317214	61	2.2	59	82	10	158	35	8	1	54	1.40
12317084--12317214	30	4.3	30	77	9	140	35	8	1	54	1.40
12317223--12317307	28	3.0	27	77	10	89	55	0	7	37	1.27
12317220--12317307	29	3.0	29	81	5	106	55	0	6	37	1.27
12317385--12317454	30	2.3	30	82	7	79	55	1	8	34	1.39
12317467--12317536	31	2.2	32	85	10	99	65	1	4	28	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12320885--12320942	17	3.4	16	77	13	53	32	10	15	41	1.81
12320895--12320949	18	3.1	18	76	5	58	36	10	14	38	1.81
12320921--12320973	17	3.1	17	91	0	88	35	15	7	41	1.75
12321289--12321322	17	2.0	17	88	0	50	26	20	11	41	1.87
12322336--12322446	45	2.4	46	85	7	138	24	27	4	44	1.73
12322837--12322963	59	2.2	59	94	0	218	30	22	9	37	1.86
12322987--12323269	54	5.2	54	91	0	431	33	21	17	27	1.96
12324909--12324947	17	2.2	17	86	4	51	33	12	12	41	1.82
12328858--12328902	24	1.9	23	86	4	63	66	2	8	22	1.30
12332530--12332561	15	2.1	15	94	0	55	28	21	6	43	1.77

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