genome.fa.s61.2.7.7.80.10.50.1000.9.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: Scaffold61
Parameters: 2 7 7 80 10 50 1000
Length:  1437555

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  9  of  10  ( 1115 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)
1262912--1262964	21	2.5	21	81	6	63	37	26	1	33	1.68
1267500--1267555	30	1.9	29	82	7	69	60	0	5	33	1.19
1269175--1269206	16	2.0	16	93	0	55	53	0	0	46	1.00
1271043--1271080	5	7.6	5	90	0	58	63	5	18	13	1.48
1271955--1271994	19	2.1	19	85	0	53	27	27	10	35	1.89
1282272--1282318	24	2.0	24	95	0	85	23	17	12	46	1.82
1288000--1288128	52	2.5	52	97	0	240	29	17	17	35	1.93
1288171--1288223	19	2.7	20	88	2	81	37	18	11	32	1.87
1288965--1289302	48	6.9	48	83	4	390	30	18	26	24	1.98
1288963--1289302	149	2.3	145	88	2	493	30	18	26	24	1.98
1289322--1289469	28	5.2	28	85	5	174	18	15	29	36	1.92
1289322--1289476	84	1.8	85	81	12	194	20	15	27	36	1.93
1289464--1289538	35	2.2	34	86	9	107	34	10	32	22	1.89
1289368--1289687	29	10.7	29	76	7	191	25	15	28	29	1.96
1289523--1289693	86	2.0	86	83	2	218	23	16	29	29	1.96
1291141--1291189	14	3.3	15	88	5	73	0	0	10	89	0.48
1291125--1291187	25	2.4	26	86	10	92	0	0	14	85	0.59
1291126--1291199	37	2.0	38	86	2	105	1	1	12	85	0.74
1291125--1291187	11	5.9	11	78	14	69	0	0	14	85	0.59
1291124--1291189	30	2.2	30	89	5	98	0	0	13	86	0.57
1291136--1291199	14	4.9	13	80	17	71	1	1	9	87	0.68
1291124--1291199	25	3.2	25	83	9	88	1	1	11	85	0.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1291136--1291199	1	64.0	1	74	0	56	1	1	9	87	0.68
1305009--1305141	52	2.6	52	95	0	230	30	16	16	36	1.91
1305161--1305225	32	2.0	33	90	3	105	38	13	12	35	1.83
1310809--1310853	23	2.0	23	82	8	56	60	0	0	40	0.97
1310834--1310869	16	2.1	18	90	10	58	66	0	0	33	0.92
1310814--1310890	39	2.0	39	81	0	91	61	0	1	37	1.05
1310952--1311010	21	2.9	21	82	12	61	45	0	0	54	0.99
1310965--1311010	18	2.3	19	82	17	58	43	0	0	56	0.99
1310975--1311010	18	1.9	19	94	5	65	44	0	0	55	0.99
1311361--1311386	4	6.5	4	100	0	52	76	0	0	23	0.78
1311617--1311670	26	2.0	27	85	7	74	66	0	0	33	0.92
1311623--1311677	16	3.2	17	85	12	69	70	0	0	29	0.87
1311623--1311684	17	3.6	17	78	12	56	72	0	0	27	0.85
1312491--1312549	20	3.0	21	83	13	65	59	3	5	32	1.36
1312967--1313021	21	2.6	21	82	5	67	58	0	1	40	1.09
1312965--1313004	15	2.5	17	80	19	50	62	0	0	37	0.95
1313894--1313935	15	2.7	15	78	14	50	38	0	0	61	0.96
1321440--1321610	44	3.9	43	87	3	225	43	25	4	27	1.72
1321440--1321610	88	2.0	87	92	1	288	43	25	4	27	1.72
1322586--1322625	21	1.9	21	90	10	64	60	0	0	40	0.97
1324693--1324807	16	7.3	16	75	9	85	57	3	1	37	1.26
1324711--1324772	32	1.9	33	90	3	99	61	3	3	32	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1326377--1326413	2	18.5	2	88	0	56	54	0	2	43	1.14
1329842--1330026	97	1.9	96	84	5	248	40	10	20	29	1.85
1331469--1331658	52	3.7	51	77	10	192	43	11	14	30	1.80
1331868--1331893	2	13.0	2	100	0	52	50	0	0	50	1.00
1332297--1332330	3	11.3	3	100	0	68	32	0	0	67	0.91
1332681--1332710	15	1.9	16	93	6	53	60	0	0	40	0.97
1339121--1339159	20	2.0	20	94	0	69	33	17	10	38	1.84
1339624--1339668	13	3.5	13	82	8	56	28	2	0	68	1.01
1341447--1341489	17	2.3	19	84	11	54	37	2	0	60	1.10
1342123--1342156	16	2.1	16	88	0	50	47	20	5	26	1.73
1343896--1343933	20	1.9	20	84	10	51	52	2	7	36	1.45
1350067--1350105	20	2.0	20	89	0	60	41	17	5	35	1.72
1354844--1354879	2	19.0	2	88	11	58	50	0	0	50	1.00
1355100--1355147	20	2.3	20	78	3	51	62	0	2	35	1.07
1355195--1355227	18	1.9	18	88	11	52	39	3	0	57	1.14
1355717--1355853	64	2.2	63	88	4	195	42	8	15	34	1.76
1356347--1356389	16	2.7	16	85	7	52	58	16	9	16	1.63
1357149--1357183	16	2.2	16	89	0	52	5	17	0	77	0.96
1358027--1358111	42	2.0	43	88	2	127	31	3	8	56	1.46
1358671--1358712	22	1.9	22	90	9	68	38	0	0	61	0.96
1361026--1361060	2	17.5	2	100	0	70	51	0	0	48	1.00
1362059--1362277	52	4.3	50	78	9	210	54	4	1	39	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1362150--1362214	25	2.7	24	69	4	67	56	7	0	35	1.28
1362068--1362277	51	4.1	51	80	9	223	53	4	1	40	1.31
1362061--1362261	100	2.0	100	85	4	271	52	4	1	40	1.32
1362067--1362279	49	4.2	52	79	7	170	53	4	1	39	1.30
1362058--1362290	101	2.3	97	76	12	227	54	5	1	39	1.31
1363136--1363190	20	2.8	19	76	13	58	43	12	10	32	1.78
1363160--1363221	33	1.9	32	86	3	88	45	16	9	29	1.79
1363807--1363870	26	2.5	26	94	0	110	39	6	15	39	1.73
1364129--1364186	31	1.9	31	85	3	82	44	15	12	27	1.82
1370404--1370428	3	8.3	3	100	0	50	32	32	0	36	1.58
1372489--1372523	18	1.9	18	88	0	52	57	2	2	37	1.29
1372498--1372546	22	2.2	23	82	10	57	51	4	2	42	1.32
1374465--1374502	18	2.1	18	90	0	58	42	21	5	31	1.75
1374550--1374600	26	2.0	26	88	0	75	41	0	5	52	1.25
1374906--1374931	7	3.7	7	100	0	52	73	0	0	26	0.84
1375873--1375934	24	2.6	24	92	2	99	62	3	0	33	1.11
1377241--1377567	157	2.1	155	82	3	379	40	16	15	27	1.88
1378172--1378228	17	3.3	17	80	14	55	28	0	1	70	0.98
1377838--1378302	184	2.5	182	86	2	619	42	9	7	40	1.66
1378753--1378791	3	13.0	3	94	0	69	30	33	0	35	1.58
1379059--1379092	10	3.3	10	88	8	50	0	14	0	85	0.60
1379731--1380138	164	2.5	163	81	8	483	50	7	10	31	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1381058--1381340	85	3.3	84	81	3	309	43	15	21	19	1.87
1381142--1381282	43	3.3	42	70	13	119	46	17	20	16	1.85
1381484--1381652	41	4.2	41	71	11	132	43	12	22	21	1.85
1381590--1381676	40	2.2	39	81	6	104	43	13	24	18	1.86
1381484--1381702	121	1.8	122	79	5	255	43	12	24	19	1.86
1381630--1381764	71	1.9	71	87	3	200	43	14	25	16	1.85
1381718--1381833	61	1.9	61	87	0	169	39	13	31	15	1.86
1382130--1382156	13	2.1	13	100	0	54	29	14	14	40	1.86
1384444--1384560	51	2.4	51	81	12	138	30	23	11	34	1.91
1384501--1384720	80	2.8	77	82	6	255	27	26	13	32	1.94
1384656--1384773	52	2.3	52	81	7	141	32	27	9	31	1.88
1385568--1385609	1	42.0	1	92	0	57	92	0	2	4	0.44
1385565--1385609	23	2.0	23	100	0	90	86	0	4	8	0.69
1385569--1385611	22	2.0	22	100	0	86	88	0	2	9	0.60
1385614--1385670	21	2.7	21	97	0	105	33	10	19	36	1.86
1385726--1385793	19	3.9	19	78	21	85	35	11	14	38	1.83
1385747--1385771	13	1.9	13	100	0	50	36	16	16	32	1.90
1385728--1385790	32	2.0	32	96	0	117	34	12	15	36	1.86
1385833--1385858	13	2.0	13	100	0	52	30	15	15	38	1.88
1385813--1385879	33	2.0	33	88	0	98	25	14	16	43	1.86
1388387--1388557	51	3.3	51	80	4	207	29	25	11	33	1.91
1388540--1388621	28	2.9	28	83	7	105	25	31	15	26	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1389079--1390094	507	2.0	507	93	1	1761	27	23	21	26	1.99
1390108--1390546	41	10.4	41	69	13	239	42	15	22	18	1.88
1390251--1390471	48	4.9	48	72	14	170	41	15	24	18	1.89
1390182--1390556	129	2.9	127	82	4	430	42	15	23	18	1.88
1391036--1391292	87	2.9	89	81	2	342	29	16	27	25	1.97
1393638--1393710	27	2.7	27	86	2	92	20	20	35	23	1.96
1393699--1393825	51	2.4	53	82	10	152	35	11	22	31	1.89
1396121--1396146	13	2.0	13	100	0	52	38	15	15	30	1.88
1396100--1396166	33	2.0	33	88	0	98	43	16	14	25	1.86
1396189--1396251	32	2.0	32	90	0	99	34	14	14	36	1.86

Tables:   1   2   3   4   5   6   7   8   9   10