genome.fa.s64.2.7.7.80.10.50.1000.7.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   

This is table  7  of  45  ( 5312 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)
1354040--1354069	4	7.5	4	100	0	60	73	0	0	26	0.84
1354498--1354553	3	18.7	3	96	0	103	33	1	0	64	1.04
1355407--1355437	2	15.5	2	100	0	62	48	0	0	51	1.00
1355595--1355636	2	21.0	2	100	0	84	50	0	0	50	1.00
1356381--1356443	20	3.3	20	78	12	71	47	0	0	52	1.00
1356381--1356443	18	3.4	19	80	12	69	47	0	0	52	1.00
1356386--1356450	30	2.1	30	83	8	78	53	0	0	46	1.00
1356391--1356438	23	2.0	24	88	4	71	50	0	0	50	1.00
1356477--1356503	3	9.0	3	100	0	54	66	0	0	33	0.92
1356445--1356494	21	2.3	21	82	3	55	60	2	0	38	1.09
1366851--1366876	11	2.4	11	100	0	52	84	0	0	15	0.62
1369302--1369342	2	20.5	2	100	0	82	51	0	0	48	1.00
1371170--1371213	18	2.5	17	78	10	52	34	0	6	59	1.24
1371215--1371253	14	2.8	14	84	0	51	58	0	0	41	0.98
1371895--1371944	17	3.1	17	75	16	52	68	0	0	32	0.90
1371925--1372002	32	2.4	33	80	8	97	55	2	0	42	1.13
1376268--1376485	34	6.5	34	85	5	282	40	27	7	24	1.82
1376266--1376485	67	3.3	67	88	1	323	40	27	7	24	1.82
1380551--1380613	19	3.3	19	90	0	90	34	19	17	28	1.94
1380916--1381131	34	6.4	34	85	5	278	40	27	7	24	1.83
1380914--1381131	67	3.2	67	88	1	319	40	27	7	24	1.82
1381766--1381810	12	3.7	12	87	3	63	13	4	0	82	0.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1381766--1381811	13	3.6	13	82	5	58	13	4	0	82	0.81
1387936--1387991	5	11.4	5	77	11	62	39	1	0	58	1.08
1388298--1388322	5	5.0	5	100	0	50	80	0	0	20	0.72
1388323--1388395	31	2.3	32	79	11	80	52	0	0	47	1.00
1394881--1394964	43	2.0	43	86	9	118	52	0	1	46	1.08
1394927--1394999	26	2.8	26	74	17	62	54	0	2	42	1.14
1394981--1395022	17	2.6	16	85	7	50	45	0	4	50	1.23
1395911--1395974	33	1.9	33	83	0	83	31	10	6	51	1.62
1400432--1400610	91	2.0	91	86	4	254	16	20	21	41	1.90
1403467--1403491	2	12.5	2	100	0	50	48	0	0	52	1.00
1404431--1404464	5	7.0	5	86	6	52	76	0	23	0	0.79
1404422--1404464	14	3.0	14	87	12	61	76	0	20	2	0.89
1408982--1409011	2	15.0	2	100	0	60	50	0	0	50	1.00
1410220--1410270	21	2.4	21	74	6	50	50	3	5	39	1.45
1410153--1410270	54	2.3	51	80	12	132	50	4	5	39	1.46
1413531--1413569	20	1.9	21	89	5	62	51	0	0	48	1.00
1413526--1413573	25	1.9	25	83	8	62	50	0	0	50	1.00
1413524--1413579	25	2.2	25	78	6	60	50	0	0	50	1.00
1413607--1413660	24	2.3	25	81	12	69	51	0	0	48	1.00
1414601--1414644	21	2.0	22	82	4	54	27	2	4	65	1.23
1416245--1416271	13	2.1	13	100	0	54	40	0	44	14	1.46
1419850--1419909	31	1.9	31	89	0	93	45	1	3	50	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1425956--1426021	2	33.5	2	85	8	73	43	3	1	51	1.26
1426721--1426767	14	3.5	13	78	21	53	38	2	0	59	1.09
1426791--1426818	2	14.0	2	100	0	56	50	0	0	50	1.00
1428948--1428977	2	15.0	2	100	0	60	0	50	0	50	1.00
1430920--1430958	17	2.3	17	95	0	69	30	5	5	58	1.41
1433946--1434014	27	2.6	27	97	0	129	31	4	1	62	1.24
1434702--1434875	62	2.8	62	83	0	213	29	16	22	31	1.96
1434688--1434864	93	1.9	93	83	0	228	30	19	21	28	1.98
1434692--1434875	31	5.9	31	83	0	170	28	17	22	30	1.97
1435743--1435771	3	9.7	3	100	0	58	31	0	0	68	0.89
1438785--1438843	24	2.5	24	81	13	77	52	0	0	47	1.00
1438790--1438848	25	2.3	25	80	13	75	49	0	0	50	1.00
1440856--1440927	21	3.5	21	78	14	78	44	0	1	54	1.08
1440886--1440927	18	2.2	20	83	12	52	47	0	0	52	1.00
1440940--1440976	17	2.2	17	90	0	56	40	0	0	59	0.97
1440935--1440994	22	2.7	22	73	21	61	43	0	1	55	1.10
1440946--1441033	28	3.2	26	81	9	86	43	1	2	53	1.20
1441530--1441606	27	2.7	29	75	16	72	48	0	0	51	1.00
1441557--1441600	17	2.4	19	81	11	56	45	0	0	54	0.99
1444028--1444061	14	2.3	15	90	10	61	38	0	0	61	0.96
1444043--1444087	21	2.0	23	83	8	58	40	0	0	60	0.97
1444157--1444208	5	10.4	5	89	6	79	40	0	0	59	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1444263--1444292	2	15.0	2	92	0	51	46	0	0	53	1.00
1444256--1444291	10	3.6	10	92	0	54	41	2	0	55	1.14
1444963--1445029	29	2.5	27	81	13	77	37	4	0	58	1.19
1444974--1445029	29	2.0	27	86	13	78	33	5	0	60	1.19
1446541--1446594	23	2.4	22	75	9	54	44	0	1	53	1.11
1448728--1448764	19	1.9	19	89	10	58	56	0	2	40	1.13
1450312--1450359	6	8.0	6	88	0	60	0	58	0	41	0.98
1451343--1451368	2	13.0	2	100	0	52	50	0	0	50	1.00
1452158--1452229	2	36.0	2	88	0	108	47	0	2	50	1.15
1452229--1452266	2	19.0	2	94	0	67	52	0	47	0	1.00
1457331--1457380	27	1.9	25	88	8	73	56	2	2	40	1.22
1458038--1458109	18	4.0	18	77	12	85	56	0	0	43	0.99
1460707--1460749	14	3.3	12	81	15	50	46	0	0	53	1.00
1460723--1460749	14	1.9	14	100	0	54	55	0	0	44	0.99
1460763--1460810	14	3.5	14	77	5	53	68	0	0	31	0.90
1460752--1460802	23	2.2	24	90	10	81	64	0	0	35	0.94
1460754--1460812	22	2.7	21	82	17	68	67	0	0	32	0.91
1461282--1461315	2	17.0	2	100	0	68	50	0	0	50	1.00
1469678--1469918	120	2.0	120	92	0	401	36	18	15	29	1.92
1475394--1475435	18	2.3	18	84	8	50	69	0	0	30	0.89
1476664--1476705	2	21.5	2	95	4	77	50	0	0	50	1.00
1477780--1477831	21	2.5	21	70	17	54	21	0	3	75	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1477781--1477841	28	2.1	31	90	9	101	22	0	6	70	1.10
1479895--1479931	7	4.9	8	93	6	60	86	0	0	13	0.57
1479898--1479931	15	2.3	15	95	5	61	88	0	0	11	0.52
1483985--1484016	2	16.0	2	100	0	64	0	50	0	50	1.00
1484673--1484709	17	2.1	18	90	5	58	45	0	5	48	1.25
1485822--1485855	6	5.7	6	100	0	68	17	29	17	35	1.93
1486850--1486911	20	3.0	20	79	11	63	37	1	1	59	1.17
1487108--1487155	17	2.6	19	77	16	55	54	0	0	45	0.99
1495922--1495961	15	2.7	14	85	11	53	47	0	0	52	1.00
1495934--1495979	23	2.0	23	82	0	56	52	0	0	47	1.00
1496144--1496169	2	13.0	2	100	0	52	50	0	0	50	1.00
1496651--1496689	20	1.9	21	89	5	62	51	0	0	48	1.00
1496692--1496730	19	2.1	19	85	0	51	66	2	0	30	1.05
1496891--1496953	22	2.7	23	78	16	67	63	0	0	36	0.95
1497066--1497137	37	1.9	35	83	10	90	52	0	0	47	1.00
1499191--1499250	27	2.2	26	82	5	66	38	0	0	61	0.96
1499194--1499282	32	2.8	32	78	16	98	42	0	0	57	0.98
1499236--1499288	15	3.5	15	76	16	56	49	1	0	49	1.12
1500114--1500149	3	12.0	3	93	0	63	63	0	2	33	1.08
1503563--1503678	58	2.0	58	94	0	205	37	15	18	29	1.91
1505589--1505628	14	2.5	17	73	23	50	45	0	0	55	0.99
1505598--1505638	14	3.2	13	80	19	50	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1505585--1505652	31	2.2	32	80	20	81	45	1	0	52	1.09
1516306--1516433	65	2.0	65	90	3	204	38	25	17	18	1.92
1516635--1516686	27	1.9	27	84	7	70	32	9	3	53	1.51
1516894--1516933	21	1.9	21	89	0	62	52	0	0	47	1.00
1518303--1518494	50	3.8	51	77	6	178	36	15	15	32	1.89
1518428--1518542	50	2.3	50	87	0	158	44	12	8	34	1.73
1518788--1518812	2	12.5	2	100	0	50	52	0	0	48	1.00
1519753--1519834	32	2.4	34	81	15	91	36	1	4	57	1.28
1519858--1519914	23	2.5	22	81	10	62	52	1	0	45	1.11
1520015--1520060	15	2.9	16	78	12	51	54	2	0	43	1.12

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