genome.fa.s78.2.7.7.80.10.50.1000.9.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: Scaffold78
Parameters: 2 7 7 80 10 50 1000
Length:  2238306

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   

This is table  9  of  15  ( 1751 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)
1246652--1246685	17	2.0	17	94	0	59	23	26	23	26	2.00
1246897--1246968	23	3.0	24	88	8	78	48	0	0	51	1.00
1246911--1246968	11	5.2	11	75	22	50	44	0	0	55	0.99
1246909--1246968	23	2.6	24	92	5	97	45	0	0	55	0.99
1248220--1248244	6	4.2	6	100	0	50	0	68	16	16	1.22
1251581--1251646	31	2.1	31	83	5	80	36	10	15	37	1.82
1253088--1253218	39	3.3	40	83	6	117	36	16	22	24	1.94
1253129--1253218	39	2.3	39	92	0	144	38	15	22	23	1.92
1253054--1253249	78	2.5	78	76	4	198	37	14	23	24	1.93
1257098--1257135	18	2.1	18	85	9	51	26	15	34	23	1.95
1257469--1257507	2	19.5	2	100	0	78	51	0	0	48	1.00
1259172--1259221	26	1.9	26	84	8	66	38	0	4	58	1.17
1261030--1261233	99	2.1	99	93	0	345	29	8	14	47	1.74
1265121--1265183	23	2.7	23	76	11	67	49	1	0	49	1.10
1265907--1265933	4	6.8	4	100	0	54	22	0	0	77	0.76
1266600--1266628	12	2.3	13	94	5	51	13	6	0	79	0.93
1268558--1268640	23	3.5	22	73	15	76	45	0	0	54	0.99
1268501--1268665	84	2.0	84	80	9	185	45	0	1	52	1.11
1271547--1271580	15	2.3	15	94	0	59	38	2	0	58	1.13
1274526--1274579	18	3.0	17	84	10	72	48	0	1	50	1.11
1274564--1274601	15	2.4	16	86	4	51	60	0	0	39	0.97
1274568--1274638	17	4.1	18	75	18	71	57	0	1	40	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1274570--1274648	19	4.4	18	73	16	58	55	0	1	43	1.07
1274683--1274713	6	5.2	6	100	0	62	48	0	0	51	1.00
1275883--1275910	2	14.0	2	100	0	56	50	0	0	50	1.00
1278279--1278371	42	2.2	43	82	5	118	23	13	8	53	1.67
1279003--1279042	22	1.9	22	90	10	66	47	0	0	52	1.00
1281295--1281320	9	2.9	9	100	0	52	57	0	7	34	1.27
1282430--1282470	19	2.1	20	86	13	59	56	2	0	41	1.13
1284295--1284333	20	2.0	20	90	10	62	46	10	15	28	1.78
1285119--1285284	57	3.0	56	93	5	284	50	3	4	42	1.39
1286077--1286126	2	25.0	2	87	0	73	44	0	6	50	1.26
1286179--1286206	11	2.5	11	100	0	56	32	10	0	57	1.33
1286395--1286461	28	2.4	27	83	11	75	64	1	1	32	1.12
1286638--1286705	33	2.1	33	100	0	136	41	20	2	35	1.68
1289963--1290036	15	5.1	15	72	16	66	39	1	1	58	1.15
1290175--1290229	20	2.8	19	77	20	60	47	0	1	50	1.11
1290446--1290499	18	2.9	18	81	10	65	44	1	0	53	1.11
1290433--1290499	37	1.9	33	88	11	98	41	1	0	56	1.08
1290450--1290507	19	3.1	19	72	2	55	46	1	0	51	1.11
1290484--1290541	26	2.2	27	84	9	75	44	0	0	55	0.99
1290471--1290531	30	2.0	31	84	15	83	47	1	0	50	1.10
1290497--1290543	23	2.0	24	91	4	78	44	0	0	55	0.99
1290573--1290632	24	2.5	24	80	0	75	40	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1290600--1290666	21	3.3	21	89	6	95	34	1	1	62	1.13
1290760--1290784	10	2.5	10	100	0	50	20	20	40	20	1.92
1294581--1294646	31	2.1	31	86	5	89	65	3	1	30	1.17
1297219--1297256	17	2.2	17	86	9	51	34	0	2	63	1.09
1297228--1297270	17	2.5	17	85	7	52	27	0	0	72	0.85
1297810--1297834	2	12.5	2	100	0	50	52	0	0	48	1.00
1299388--1299458	17	4.1	17	80	9	63	39	2	0	57	1.13
1299409--1299467	16	3.8	16	74	14	61	40	0	0	59	0.97
1299397--1299477	33	2.5	33	86	9	105	39	1	0	59	1.05
1299410--1299490	37	2.1	38	80	8	94	41	1	0	56	1.07
1300241--1300315	38	2.0	38	84	5	98	53	0	1	45	1.08
1300347--1300379	11	2.8	12	86	9	50	63	0	0	36	0.95
1300769--1300809	21	2.0	20	86	13	57	68	0	4	26	1.10
1301229--1301271	2	21.5	2	100	0	86	48	0	0	51	1.00
1301251--1301698	227	2.0	227	93	1	774	45	8	6	40	1.60
1301679--1301743	28	2.3	27	82	10	78	64	1	0	33	1.03
1305591--1305643	26	2.0	26	85	7	72	41	1	3	52	1.30
1305663--1305719	30	1.9	29	86	10	80	47	0	0	52	1.00
1306179--1306216	20	1.9	20	89	10	60	47	0	0	52	1.00
1306176--1306229	20	2.7	19	73	18	56	53	0	0	46	1.00
1306211--1306252	17	2.7	15	76	16	50	66	0	0	33	0.92
1306565--1306619	26	2.1	26	86	6	76	49	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1306700--1306752	21	2.4	21	75	9	52	43	9	0	47	1.36
1307319--1307360	22	2.0	22	86	13	61	54	0	0	45	0.99
1308859--1308900	19	2.4	17	78	17	50	76	2	2	19	1.01
1310685--1310719	16	2.1	17	89	5	54	34	2	0	62	1.10
1312053--1312082	16	1.9	15	93	6	51	53	3	16	26	1.59
1314672--1314827	80	1.9	82	96	2	289	52	10	12	25	1.69
1315833--1316017	73	2.5	73	91	2	284	36	2	7	53	1.42
1315894--1315995	30	4.2	23	64	26	59	37	0	6	54	1.34
1316068--1316110	16	2.6	16	82	14	52	41	2	0	55	1.12
1316259--1316375	16	7.2	16	82	1	126	32	34	22	11	1.89
1316285--1316408	48	2.6	48	87	2	178	34	33	20	10	1.87
1316366--1316414	16	3.1	16	75	0	53	42	34	14	8	1.75
1316318--1316440	32	3.8	32	76	0	111	34	34	18	12	1.88
1322397--1322424	8	3.5	8	100	0	56	78	0	0	21	0.75
1322403--1322455	26	2.0	27	82	10	65	58	0	3	37	1.16
1323597--1323652	28	2.0	28	93	3	96	41	0	0	58	0.98
1324127--1324171	2	22.5	2	100	0	90	51	0	0	48	1.00
1324705--1324745	20	2.0	20	90	9	66	70	0	4	24	1.06
1325052--1325092	2	20.5	2	100	0	82	48	0	0	51	1.00
1325181--1325225	2	22.5	2	100	0	90	48	0	0	51	1.00
1328787--1328820	13	2.5	14	85	4	52	79	0	0	20	0.73
1328788--1328827	14	3.0	13	86	13	55	75	0	0	25	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1329326--1329378	26	2.0	26	85	7	72	41	1	3	52	1.30
1329398--1329454	30	1.9	29	86	10	80	47	0	0	52	1.00
1329880--1329917	20	1.9	20	89	10	60	47	0	0	52	1.00
1330183--1330328	63	2.3	63	80	8	163	42	1	2	54	1.20
1330267--1330321	26	2.1	26	86	6	76	49	0	0	50	1.00
1330382--1330457	21	3.2	24	72	23	70	39	3	0	56	1.18
1331021--1331062	22	2.0	22	86	13	61	54	0	0	45	0.99
1332561--1332602	19	2.4	17	78	17	50	76	2	2	19	1.01
1334388--1334422	16	2.1	17	89	5	54	34	2	0	62	1.10
1335757--1335786	16	1.9	15	93	6	51	53	3	16	26	1.59
1338372--1338531	82	1.9	84	94	2	288	53	9	11	25	1.67
1339547--1339732	73	2.5	73	86	3	268	35	2	9	52	1.47
1339720--1339758	17	2.3	17	86	0	51	35	5	2	56	1.35
1340003--1340095	16	5.8	16	78	5	89	32	29	25	12	1.93
1339987--1340096	32	3.4	32	80	5	132	32	30	24	12	1.92
1340001--1340095	48	2.0	48	83	4	120	31	29	25	13	1.94
1340034--1340140	48	2.2	48	80	6	119	35	28	20	14	1.93
1346110--1346137	8	3.5	8	100	0	56	78	0	0	21	0.75
1346116--1346168	26	2.0	27	82	10	65	58	0	3	37	1.16
1347303--1347343	21	2.0	21	90	0	64	43	0	0	56	0.99
1347835--1347873	2	19.5	2	100	0	78	51	0	0	48	1.00
1348755--1348781	2	13.5	2	100	0	54	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1348874--1348913	2	20.0	2	100	0	80	50	0	0	50	1.00
1349094--1349158	28	2.3	27	82	10	78	64	1	0	33	1.03
1353073--1353116	21	2.0	22	83	12	56	45	0	0	54	0.99
1353099--1353145	20	2.3	21	78	10	53	48	0	0	51	1.00
1353466--1353532	34	2.0	34	85	5	91	40	1	0	58	1.07
1353499--1353550	22	2.4	22	90	6	79	46	0	0	53	1.00
1353670--1353736	32	2.1	32	83	5	82	59	0	0	40	0.97
1353946--1354029	18	4.9	17	83	12	102	40	0	0	59	0.97
1353963--1354029	16	3.9	16	76	18	55	43	0	0	56	0.99
1354076--1354156	40	2.0	40	83	7	101	40	1	0	58	1.06

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15