genome.fa.s1129.2.7.7.80.10.50.1000.8.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  8  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)
1507947--1508010	29	2.3	27	84	10	76	81	12	4	1	0.92
1514582--1514618	18	2.1	18	89	0	56	29	32	5	32	1.80
1515411--1515458	22	2.2	21	85	10	62	33	8	0	58	1.28
1515475--1515505	15	2.1	15	93	0	53	45	0	3	51	1.17
1518193--1518299	53	2.0	53	98	0	205	25	24	15	34	1.95
1519335--1519381	18	2.7	17	86	3	67	34	8	29	27	1.87
1519692--1519716	12	2.1	12	100	0	50	64	16	0	20	1.30
1519915--1519986	38	1.9	38	94	2	128	36	37	13	12	1.83
1520421--1520449	14	2.1	14	100	0	58	27	6	34	31	1.83
1529510--1529552	4	10.8	4	100	0	86	76	23	0	0	0.78
1529824--1529870	21	2.3	21	85	3	69	38	12	19	29	1.89
1533189--1533247	30	2.0	29	83	6	73	50	5	16	27	1.66
1534507--1534552	21	2.2	21	88	0	65	43	6	2	47	1.41
1534645--1534692	22	2.2	22	92	0	78	45	6	0	47	1.27
1535232--1535273	14	3.0	14	82	0	57	57	4	0	38	1.20
1545848--1545944	42	2.3	41	78	1	104	24	20	23	30	1.98
1546064--1546153	42	2.1	42	93	0	153	25	24	17	32	1.97
1546195--1546274	42	1.9	41	87	7	117	30	22	20	27	1.98
1546195--1546297	42	2.5	42	83	10	115	27	23	21	28	1.99
1546073--1546294	122	1.8	122	86	1	320	29	22	19	29	1.98
1546716--1546925	53	3.9	53	84	1	233	29	20	26	23	1.99
1550176--1550231	21	2.7	21	97	0	103	17	35	28	17	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1550271--1550312	21	2.0	21	95	0	75	23	21	28	26	1.99
1550341--1550380	20	1.9	22	90	10	66	37	40	10	12	1.77
1550595--1550664	34	2.1	32	89	5	104	31	15	31	21	1.95
1552239--1552283	12	4.0	12	75	13	51	68	2	0	28	1.01
1552252--1552294	21	2.0	22	90	4	70	74	4	0	20	1.00
1552252--1552294	22	1.9	23	86	13	63	74	4	0	20	1.00
1552735--1554046	113	11.7	112	88	3	1786	28	19	15	37	1.92
1552627--1554044	449	3.2	446	86	5	1898	28	19	15	36	1.92
1557361--1557580	114	1.9	114	91	0	359	29	20	16	33	1.94
1559710--1559782	8	9.1	8	73	16	62	2	23	0	73	0.95
1559721--1559814	8	10.8	9	75	21	67	4	21	0	74	0.99
1559715--1559774	16	3.6	17	82	6	79	3	20	0	76	0.92
1559715--1559842	7	16.3	7	70	23	78	4	19	1	74	1.08
1559715--1559783	17	4.4	15	82	12	77	2	21	0	75	0.93
1559753--1559831	37	2.1	38	83	6	99	6	17	2	73	1.16
1564072--1564149	33	2.4	33	95	0	138	37	2	11	48	1.53
1564148--1564198	22	2.3	24	77	16	56	43	5	11	39	1.66
1564881--1564931	2	26.0	2	96	4	95	50	0	0	49	1.00
1565529--1565568	18	2.3	18	91	4	64	37	5	0	57	1.21
1565533--1565576	19	2.4	17	85	14	61	36	6	0	56	1.26
1565929--1565971	14	3.2	13	81	18	52	44	0	11	44	1.40
1566895--1566927	15	2.2	15	100	0	66	12	51	30	6	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1570733--1570796	17	3.7	17	75	17	60	34	0	0	65	0.93
1570733--1570797	25	2.5	27	82	9	82	33	0	0	66	0.92
1571267--1571335	30	2.4	30	79	16	74	26	5	1	66	1.22
1573495--1573547	21	2.5	21	79	11	56	50	11	28	9	1.69
1576106--1576637	110	4.9	110	88	4	762	33	23	18	25	1.97
1576106--1576637	215	2.4	216	89	2	789	33	23	18	25	1.97
1576749--1577173	84	5.1	84	77	4	428	32	24	19	24	1.98
1576840--1577186	165	2.1	162	81	5	401	32	24	19	24	1.97
1577745--1577787	13	3.2	13	87	6	59	72	0	4	23	1.04
1577869--1577895	2	13.5	2	100	0	54	51	0	0	48	1.00
1578295--1578381	14	6.2	14	72	18	65	68	0	0	31	0.89
1578295--1578335	3	14.3	3	80	10	50	73	0	0	26	0.84
1578303--1578382	12	7.5	11	76	17	62	67	0	0	32	0.91
1579224--1579294	33	2.2	33	94	0	124	25	9	21	43	1.83
1579372--1579400	2	14.5	2	100	0	58	51	0	0	48	1.00
1580330--1580370	17	2.7	14	80	20	55	46	34	14	4	1.66
1582529--1582572	21	2.2	20	83	4	52	52	2	2	43	1.26
1582508--1582894	184	2.1	183	91	0	614	42	3	8	45	1.50
1585537--1585591	2	27.5	2	100	0	110	50	0	0	49	1.00
1591453--1591526	23	3.3	23	75	3	78	41	13	10	33	1.79
1591893--1591931	17	2.5	17	88	12	57	20	12	10	56	1.65
1596739--1596788	23	2.2	23	85	0	64	40	10	8	42	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1598129--1598188	31	1.9	31	93	6	104	41	6	8	43	1.61
1598728--1598810	40	2.2	36	85	12	105	54	1	0	44	1.08
1598707--1598862	63	2.5	64	91	7	250	57	1	0	41	1.10
1598761--1598843	25	3.2	26	80	14	93	56	1	0	42	1.07
1598824--1598874	12	4.3	12	76	18	54	66	1	0	31	1.03
1607592--1607631	3	13.3	3	84	10	55	67	0	2	30	1.04
1607591--1607637	24	1.9	25	95	4	87	68	0	4	27	1.08
1609099--1609181	28	3.0	27	71	13	69	45	4	2	46	1.37
1609107--1609171	26	2.6	24	72	15	60	47	6	3	43	1.43
1610047--1610227	74	2.4	74	81	3	195	24	17	18	39	1.92
1613700--1613742	17	2.6	17	96	3	79	20	23	4	51	1.66
1615697--1615732	7	5.6	7	90	9	51	72	0	0	27	0.85
1617316--1617357	23	1.9	21	85	9	57	54	0	0	45	0.99
1617499--1617539	16	2.6	16	92	0	64	53	2	0	43	1.13
1618810--1618839	12	2.4	13	94	5	53	53	0	0	46	1.00
1631141--1631219	42	1.9	42	82	7	99	59	7	3	29	1.43
1631756--1631843	41	2.2	40	88	7	128	27	15	31	25	1.96
1632645--1632684	19	2.2	18	86	4	53	72	0	5	22	1.04
1632732--1632786	19	2.9	19	74	15	60	65	1	9	23	1.31
1632836--1632925	37	2.3	37	81	9	99	73	1	4	21	1.07
1632870--1632999	19	6.5	18	71	23	84	64	1	3	30	1.20
1632864--1632977	3	38.0	3	69	20	53	65	0	3	29	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1632881--1632990	13	8.1	13	67	27	52	65	0	3	30	1.16
1632863--1633054	16	11.8	16	66	22	55	65	1	4	28	1.22
1632864--1632999	40	3.4	38	77	15	114	65	1	3	29	1.18
1632870--1633019	19	7.1	22	68	23	67	64	1	4	30	1.20
1633118--1633169	10	4.9	10	78	17	52	57	0	3	38	1.17
1633649--1633744	37	2.6	37	89	0	138	32	10	15	41	1.81
1634486--1635337	106	8.0	106	91	0	1285	22	18	24	34	1.96
1636950--1636991	14	2.8	16	82	14	61	0	16	4	78	0.91
1636942--1636998	22	2.6	22	76	15	64	1	14	7	77	1.06
1638651--1638705	23	2.4	23	87	3	76	29	20	29	21	1.98
1638738--1638932	100	2.0	98	90	4	311	35	25	11	27	1.90
1639215--1639283	23	3.0	23	86	0	93	27	26	26	20	1.99
1639299--1639516	103	2.1	103	93	0	373	37	23	12	26	1.91
1645073--1645128	20	2.9	19	75	19	62	66	1	8	23	1.30
1645206--1645246	17	2.4	17	88	12	57	70	0	2	26	0.99
1645215--1645255	21	2.0	21	90	9	66	73	0	0	26	0.84
1645394--1645419	13	2.0	13	100	0	52	69	0	7	23	1.14
1645437--1645489	22	2.4	21	82	14	63	60	0	1	37	1.08
1645968--1646057	37	2.4	37	88	0	126	33	7	15	43	1.76
1649493--1649527	2	17.5	2	100	0	70	51	0	0	48	1.00
1650166--1650256	42	2.2	42	85	0	119	19	13	19	47	1.82
1650565--1650638	25	3.0	25	69	17	64	44	0	0	55	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1650497--1650638	50	2.9	50	77	15	120	48	1	0	49	1.15
1651015--1651053	20	2.0	20	84	0	51	33	17	7	41	1.79
1660533--1660571	15	2.6	15	100	0	78	10	35	5	48	1.59
1672365--1672417	20	2.7	20	90	0	88	26	28	20	24	1.99
1672604--1672647	22	2.0	22	95	0	79	20	45	15	18	1.85
1672899--1672956	20	2.9	20	86	0	71	17	17	22	43	1.88
1673093--1673147	25	2.2	24	78	15	58	20	9	18	52	1.71
1674272--1674316	18	2.5	18	88	0	63	28	42	15	13	1.85
1674809--1674864	20	2.9	19	76	12	60	41	21	21	16	1.90
1674853--1674910	14	3.9	14	79	16	71	48	24	17	10	1.78

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