genome.fa.s8087.2.7.7.80.10.50.1000.7.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: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Length:  8279816

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   

This is table  7  of  37  ( 4336 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)
1328493--1328671	90	2.0	89	88	8	267	46	18	12	21	1.83
1330268--1330329	20	3.2	19	77	8	61	45	16	24	14	1.84
1330290--1330377	32	2.8	32	86	11	119	39	20	26	13	1.90
1330360--1330410	19	2.7	19	87	0	75	45	17	21	15	1.86
1330977--1331070	20	4.7	20	80	7	91	23	19	25	31	1.98
1330997--1331091	41	2.3	41	81	3	111	20	21	23	35	1.96
1331141--1331181	21	2.0	21	85	0	55	34	29	17	19	1.94
1333512--1333570	31	1.9	31	85	0	82	44	6	6	42	1.57
1333763--1333805	18	2.4	19	84	11	63	51	4	2	41	1.35
1334903--1334976	37	2.0	37	97	0	139	48	12	27	12	1.76
1346388--1346414	2	13.5	2	100	0	54	51	0	0	48	1.00
1355247--1355594	172	2.0	176	86	9	491	44	10	3	41	1.56
1355574--1355642	26	2.7	26	76	12	72	39	1	5	53	1.34
1362178--1362237	31	2.0	31	86	3	86	45	21	11	21	1.84
1368107--1368133	2	13.5	2	100	0	54	0	48	0	51	1.00
1377598--1377642	21	2.1	21	87	0	63	31	28	24	15	1.96
1379134--1379437	149	2.0	149	96	0	563	27	17	20	34	1.95
1379416--1379460	23	2.0	23	86	0	63	20	24	28	26	1.99
1383782--1383809	2	14.0	2	100	0	56	50	0	0	50	1.00
1384277--1384580	149	2.0	149	94	0	545	28	17	19	34	1.94
1384559--1384602	22	2.0	22	86	0	61	20	25	27	27	1.99
1387087--1387139	23	2.2	24	81	15	58	35	16	9	37	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1389655--1389679	2	12.5	2	100	0	50	52	0	0	48	1.00
1398231--1398269	19	2.1	19	100	0	78	56	0	5	38	1.22
1406242--1406280	15	2.6	16	84	12	55	35	2	0	61	1.10
1406262--1406299	19	2.0	20	84	5	51	44	0	2	52	1.14
1408648--1408703	29	1.9	29	92	7	96	53	10	12	23	1.69
1412066--1412105	21	1.9	21	89	0	62	25	0	22	52	1.47
1423449--1423630	75	2.4	75	81	4	190	41	10	12	35	1.77
1423495--1423651	74	2.1	75	85	1	208	38	11	14	36	1.82
1423605--1423703	52	1.9	52	87	0	144	37	15	12	35	1.84
1423527--1423757	126	1.8	127	85	2	331	40	9	13	36	1.78
1423665--1423927	98	2.7	98	86	0	355	40	11	12	35	1.80
1423830--1423878	23	2.1	23	88	0	71	34	16	14	34	1.89
1424533--1424819	108	2.6	108	85	2	362	36	12	11	39	1.80
1430226--1430294	30	2.2	30	85	15	95	34	5	17	42	1.73
1430235--1430294	30	2.0	30	93	6	104	33	6	16	43	1.74
1430506--1430535	15	2.0	15	93	0	51	20	36	16	26	1.93
1430488--1430558	33	2.1	35	84	5	92	19	30	21	28	1.97
1430585--1430627	21	2.0	21	90	0	68	32	23	18	25	1.97
1431829--1431865	19	1.9	19	88	0	56	40	8	16	35	1.78
1433135--1433194	29	2.0	30	90	6	95	35	6	15	43	1.72
1433396--1433437	21	2.0	21	85	0	57	30	21	23	23	1.99
1437632--1437735	31	3.5	30	81	7	122	52	0	9	36	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1437634--1437735	29	3.4	29	82	5	123	51	0	9	37	1.42
1442251--1442294	15	3.0	15	96	3	81	75	4	0	20	0.98
1455364--1455430	28	2.4	28	89	0	98	46	22	5	25	1.74
1455408--1455487	29	2.8	29	92	0	133	43	23	8	23	1.81
1466022--1466074	24	2.1	25	83	13	65	67	1	1	28	1.11
1469140--1469171	6	5.3	6	100	0	64	50	0	34	15	1.45
1470310--1470455	48	2.9	50	83	8	197	35	25	5	33	1.79
1470700--1470740	22	1.9	22	85	5	57	68	4	12	14	1.36
1481376--1481406	16	1.9	16	100	0	62	19	9	19	51	1.74
1484121--1484263	74	1.9	75	92	1	243	37	11	10	40	1.77
1484664--1484700	17	2.2	17	90	0	56	51	27	13	8	1.69
1485820--1485883	21	3.4	20	66	29	59	31	4	18	45	1.70
1485812--1485933	35	3.4	36	87	6	176	32	4	18	43	1.72
1490426--1490544	35	3.3	36	85	5	152	32	5	18	43	1.72
1493544--1493596	21	2.6	20	78	3	61	7	30	39	22	1.82
1504729--1504781	27	2.0	26	82	10	63	13	52	3	30	1.57
1509176--1509225	24	2.1	24	100	0	100	28	16	16	40	1.89
1509497--1509582	21	4.3	20	85	5	95	6	33	22	37	1.81
1509502--1509573	21	3.5	21	90	1	110	8	36	22	33	1.84
1514619--1514659	21	2.0	21	95	0	73	48	26	0	24	1.51
1514565--1514695	56	2.3	56	86	1	181	44	29	0	26	1.55
1514608--1514667	21	2.9	21	82	5	68	48	25	0	26	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1514643--1514744	41	2.5	42	81	13	122	45	28	0	25	1.60
1515141--1515170	14	2.1	14	93	0	51	43	0	6	50	1.28
1516484--1516527	18	2.4	18	92	0	70	22	4	29	43	1.73
1520447--1520488	21	2.0	21	90	0	66	47	14	0	38	1.44
1526037--1526077	20	2.0	20	90	0	64	56	2	7	34	1.40
1526845--1526887	2	22.0	2	95	4	79	48	0	0	51	1.00
1527097--1527132	16	2.2	17	90	5	56	33	0	5	61	1.19
1529527--1529651	3	42.7	3	85	7	177	62	0	3	34	1.11
1529807--1530326	119	4.5	119	90	6	797	28	20	14	36	1.92
1530938--1531766	52	16.1	52	95	1	1455	36	23	14	25	1.93
1530938--1531766	103	8.1	103	96	1	1497	36	23	14	25	1.93
1532689--1532749	5	13.0	5	80	13	60	0	14	0	85	0.60
1532689--1532749	14	4.4	14	88	10	81	0	14	0	85	0.60
1532693--1532749	29	2.0	29	89	6	89	0	14	0	85	0.59
1532703--1532757	24	2.3	24	90	6	85	0	14	0	85	0.60
1532690--1532751	15	4.3	15	78	17	78	0	12	0	87	0.55
1532690--1532742	1	53.0	1	80	0	52	0	11	0	88	0.51
1543130--1543164	18	1.9	18	88	11	54	65	2	0	31	1.07
1544767--1544816	19	2.5	20	79	17	59	0	24	10	66	1.22
1545256--1545388	3	44.7	3	90	1	214	62	0	3	34	1.11
1550297--1550360	2	32.5	2	96	3	121	0	48	0	51	1.00
1550360--1550397	2	19.0	2	100	0	76	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)
1555436--1555494	23	2.6	23	83	2	75	28	15	23	32	1.95
1557158--1557189	17	1.9	16	93	6	55	34	18	9	37	1.83
1569798--1569872	35	2.2	35	90	2	116	37	25	1	36	1.65
1570440--1570485	23	2.2	20	84	11	56	36	15	13	34	1.86
1570266--1570512	129	1.9	130	88	0	379	35	15	12	36	1.86
1570973--1571009	15	2.4	16	86	13	51	59	5	2	32	1.34
1573869--1573895	4	6.8	4	100	0	54	25	0	22	51	1.48
1575304--1575391	29	3.0	29	84	0	122	14	32	32	19	1.92
1575425--1575468	22	2.0	23	86	4	63	6	50	20	22	1.72
1575392--1575454	29	2.2	29	97	0	117	4	49	22	23	1.69
1575499--1575560	31	2.0	31	93	0	106	24	37	14	24	1.93
1576393--1576460	30	2.3	30	79	2	75	26	8	13	51	1.70
1576411--1576606	108	1.8	109	85	3	279	28	5	9	56	1.54
1593537--1593599	25	2.5	25	80	14	67	34	0	3	61	1.12
1596945--1596980	15	2.4	15	95	0	63	41	0	0	58	0.98
1598922--1598965	22	2.0	21	83	12	54	25	2	0	72	0.96
1599186--1599259	21	3.4	24	77	17	65	29	4	0	66	1.10
1603660--1603739	16	5.1	16	75	15	60	81	7	10	1	0.93
1603660--1603750	23	3.9	23	77	8	76	79	7	12	1	0.99
1604338--1604392	22	2.5	22	96	0	101	36	25	12	25	1.91
1605342--1605638	106	2.8	106	90	1	461	36	25	16	21	1.94
1605554--1605723	85	2.0	85	94	0	295	35	25	15	22	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1605448--1605829	191	2.0	191	92	0	638	35	26	16	21	1.95
1605639--1605922	106	2.7	106	94	0	505	33	26	17	22	1.96
1605639--1606558	212	4.4	211	87	5	1343	33	25	18	22	1.96
1605831--1606009	88	2.0	88	97	0	340	32	26	19	21	1.97
1605919--1606558	106	6.0	106	91	0	1001	33	24	18	22	1.97
1606603--1606697	32	2.9	34	76	6	113	29	29	18	22	1.98
1607754--1607799	14	3.4	14	77	22	53	28	0	0	71	0.86
1607754--1607799	22	2.0	23	88	12	69	28	0	0	71	0.86
1607990--1608023	18	1.9	17	88	5	50	32	2	2	61	1.26
1608043--1608100	21	2.8	20	79	10	71	25	1	0	72	0.94

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