genome.fa.s1165.2.7.7.80.10.50.1000.5.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: scaffold158
Parameters: 2 7 7 80 10 50 1000
Length:  3161772

Tables:   1   2   3   4   5   6   7   8   9   

This is table  5  of  9  ( 1067 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)
1283492--1283565	6	12.0	6	75	15	62	75	0	24	0	0.80
1283498--1283565	21	3.3	21	81	4	86	76	0	23	0	0.79
1284207--1284250	20	2.2	20	91	0	70	36	9	9	45	1.68
1284407--1284814	35	11.5	35	72	14	268	29	13	10	45	1.78
1284472--1284813	18	19.3	18	72	18	170	30	13	11	45	1.78
1284507--1284569	19	3.4	19	78	6	58	33	9	9	47	1.68
1284537--1284579	19	2.3	19	87	0	59	25	9	11	53	1.67
1284586--1284813	17	13.2	17	75	12	178	29	14	10	46	1.77
1286526--1286560	4	9.0	4	93	6	63	25	25	0	48	1.51
1291426--1291934	157	3.3	156	85	5	683	25	17	21	35	1.95
1291402--1291947	78	7.0	76	83	7	627	25	17	21	36	1.94
1292073--1292332	78	3.4	76	86	4	360	25	17	20	36	1.94
1292479--1292602	29	4.2	29	87	2	176	33	24	2	39	1.68
1292479--1292602	59	2.1	59	89	3	187	33	24	2	39	1.68
1292954--1293000	17	2.7	18	81	15	55	76	6	14	2	1.08
1292955--1293013	23	2.7	23	81	5	68	76	5	16	1	1.05
1293096--1293185	7	12.4	7	71	15	58	76	0	23	0	0.78
1293089--1293178	31	2.7	34	81	13	107	75	0	24	0	0.80
1293088--1293184	21	4.6	21	74	8	81	75	0	24	0	0.81
1293106--1293185	42	1.9	42	85	10	110	75	0	25	0	0.81
1293093--1293183	24	3.8	24	77	8	103	75	0	24	0	0.80
1293088--1293183	34	3.0	31	76	16	97	75	0	25	0	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1293418--1293454	10	3.5	11	85	7	51	83	0	16	0	0.64
1293972--1294092	36	3.4	33	79	13	102	30	13	9	46	1.75
1294026--1294364	18	18.5	18	71	14	214	29	12	10	47	1.75
1293969--1294365	35	10.9	36	70	15	212	29	13	10	46	1.77
1296339--1296803	44	10.7	44	75	10	321	30	18	23	28	1.97
1296339--1296905	133	4.3	132	73	11	384	31	18	22	27	1.97
1296327--1296766	177	2.5	177	89	2	649	31	18	23	26	1.97
1298247--1298284	12	3.1	12	85	14	51	34	0	0	65	0.93
1305742--1305821	25	2.9	27	80	15	94	37	1	11	50	1.46
1307662--1307841	51	3.6	50	78	3	184	24	16	27	31	1.96
1307855--1307940	45	1.9	45	95	0	154	25	15	24	34	1.94
1313309--1313338	2	15.0	2	92	0	51	53	0	0	46	1.00
1314157--1314185	7	4.1	7	100	0	58	31	27	13	27	1.94
1316385--1316434	25	2.0	25	84	7	66	12	4	18	66	1.39
1317363--1317404	16	2.7	15	79	17	50	28	2	7	61	1.35
1322215--1322248	15	2.4	14	90	5	50	82	5	0	11	0.83
1324559--1324771	44	4.6	45	67	18	116	33	17	19	28	1.95
1324547--1324733	98	1.9	97	82	6	234	33	18	20	27	1.96
1324858--1324904	23	2.0	23	100	0	94	34	21	27	17	1.95
1324888--1325245	50	7.2	49	71	5	225	33	23	19	23	1.97
1324881--1325245	100	3.7	100	87	0	480	32	23	20	23	1.97
1326750--1326791	16	2.7	15	79	17	50	28	2	7	61	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1326850--1326902	11	4.6	11	76	15	54	28	5	5	60	1.42
1332176--1332327	43	3.6	42	76	13	168	23	17	28	30	1.97
1332214--1332334	41	2.9	42	79	7	129	25	15	26	32	1.96
1332176--1332334	84	1.9	84	84	7	216	23	16	27	31	1.97
1333266--1333319	27	2.0	28	96	3	101	16	9	22	51	1.72
1336783--1336920	40	3.5	39	78	3	100	18	18	21	40	1.91
1336820--1336895	20	3.8	20	67	0	62	18	19	21	40	1.91
1336763--1336898	40	3.5	40	78	5	143	20	19	20	39	1.92
1340383--1340415	12	2.6	13	90	4	50	9	15	0	75	1.03
1341678--1341719	22	1.9	22	85	0	57	45	7	7	40	1.59
1343922--1343952	2	15.5	2	93	0	53	45	0	3	51	1.17
1349858--1349885	6	4.7	6	100	0	56	17	28	0	53	1.44
1359210--1359367	79	2.0	79	98	0	307	39	20	16	23	1.91
1367298--1367366	31	2.3	30	80	7	77	42	20	13	24	1.87
1367495--1367530	3	12.3	3	88	5	56	69	0	30	0	0.89
1369191--1369284	35	2.6	36	84	3	127	44	0	14	40	1.46
1369191--1369298	36	3.0	36	83	4	130	44	0	13	41	1.44
1369385--1369707	124	2.6	124	87	4	452	36	14	18	29	1.91
1371495--1371545	24	2.1	24	81	0	57	19	19	35	25	1.95
1375021--1375077	16	3.6	16	95	0	87	29	0	36	33	1.58
1375323--1375357	18	2.0	17	88	5	52	54	0	0	45	0.99
1385748--1385843	29	3.3	29	82	8	97	34	7	1	57	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1388883--1389161	139	2.0	139	100	0	558	27	16	14	41	1.87
1389736--1389830	29	3.2	29	82	8	95	33	7	1	57	1.33
1396522--1396566	21	2.1	21	100	0	90	35	4	22	37	1.74
1399555--1399592	7	5.4	7	100	0	76	42	0	15	42	1.47
1401193--1401217	12	2.1	12	100	0	50	32	0	36	32	1.58
1402288--1402361	30	2.5	29	77	14	71	47	5	2	44	1.40
1404305--1404365	32	1.9	32	82	0	77	29	4	6	59	1.44
1405591--1405642	24	2.2	24	92	0	86	51	7	3	36	1.49
1405733--1405791	29	2.0	29	93	0	100	33	32	10	23	1.88
1409268--1409320	24	2.2	24	86	3	70	54	7	3	33	1.46
1410148--1410182	19	1.9	19	88	11	56	45	5	8	40	1.58
1412223--1412264	16	2.6	16	78	10	50	45	0	0	54	0.99
1412857--1412896	16	2.5	17	84	11	50	57	2	0	40	1.12
1415852--1415976	66	1.9	65	95	4	225	32	11	21	34	1.89
1416630--1416675	17	2.6	17	86	13	58	69	4	2	23	1.17
1416911--1416957	20	2.3	20	85	0	67	55	0	8	36	1.31
1417546--1417641	19	4.7	21	74	14	65	40	14	6	38	1.71
1417546--1417603	22	2.6	22	81	7	64	41	17	5	36	1.72
1417582--1417654	19	3.8	19	87	0	110	35	13	10	39	1.80
1424287--1424336	18	2.7	20	82	14	63	32	4	4	60	1.34
1426886--1426941	21	2.7	20	83	8	76	53	0	16	30	1.43
1426889--1426961	28	2.6	28	79	12	78	46	0	21	31	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1426882--1426941	7	8.6	7	75	14	61	51	0	16	31	1.45
1427689--1427724	17	2.1	18	89	5	56	55	0	2	41	1.14
1428596--1428652	29	1.9	29	86	10	80	31	1	1	64	1.13
1429510--1429562	21	2.5	22	76	14	56	41	0	1	56	1.10
1429536--1429577	17	2.4	18	84	7	52	40	0	0	59	0.97
1430230--1430262	17	2.0	17	88	5	50	54	0	0	45	0.99
1444785--1444875	44	2.1	44	89	0	137	47	12	12	28	1.76
1445049--1445104	27	2.1	27	90	3	87	48	3	5	42	1.43
1445070--1445110	21	1.9	21	85	5	55	53	4	4	36	1.44
1445550--1445661	58	1.9	59	85	3	154	35	16	2	45	1.61
1449420--1449563	43	3.3	43	85	1	155	34	29	16	19	1.94
1449549--1449682	43	3.1	41	71	14	110	34	22	15	27	1.94
1455196--1455421	14	15.9	14	70	13	113	38	38	0	22	1.58
1455199--1455312	7	16.3	7	77	9	81	34	42	0	23	1.55
1455199--1455421	21	10.5	21	72	15	93	39	38	0	22	1.58
1455324--1455426	7	14.4	7	77	8	64	46	30	0	22	1.58
1455252--1455420	21	8.0	21	76	8	103	39	36	0	23	1.59
1455844--1455965	41	3.0	41	82	1	145	20	23	15	40	1.91
1456293--1456457	40	4.1	40	80	6	163	27	22	21	29	1.99
1456439--1456490	27	2.0	26	84	3	68	19	17	23	40	1.91
1457804--1457867	32	2.0	32	96	0	119	48	17	9	25	1.76
1461312--1461359	12	4.0	12	80	0	60	27	14	14	43	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1461313--1461383	24	3.0	24	81	6	74	23	15	14	46	1.82
1461351--1461383	11	2.8	12	86	9	50	18	18	12	51	1.76
1461552--1461598	12	3.8	12	75	13	51	31	17	12	38	1.87
1461557--1461619	24	2.7	23	87	7	83	33	12	14	39	1.84
1465748--1466195	134	3.4	133	82	2	513	37	16	20	25	1.93
1465745--1466182	200	2.2	201	82	2	524	37	16	20	25	1.93
1465748--1466196	67	6.7	67	79	5	424	37	16	20	25	1.93
1480540--1480590	21	2.5	20	87	6	68	45	19	21	13	1.85
1481111--1481152	17	2.4	18	84	11	52	47	14	0	38	1.44
1483580--1483610	16	1.9	16	93	0	53	25	6	19	48	1.72

Tables:   1   2   3   4   5   6   7   8   9