genome.fa.s42.2.7.7.80.10.50.1000.9.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: Scaffold42
Parameters: 2 7 7 80 10 50 1000
Length:  3911082

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   

This is table  9  of  24  ( 2843 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)
1219727--1219773	2	23.5	2	100	0	94	51	0	0	48	1.00
1220849--1220972	14	9.1	14	69	20	68	54	0	1	43	1.09
1220847--1220912	30	2.2	30	84	7	82	57	0	1	40	1.08
1222817--1222850	11	3.1	11	91	8	52	32	0	0	67	0.91
1223797--1223843	24	2.0	24	83	8	60	59	0	0	40	0.97
1224589--1224626	18	2.1	18	85	9	51	60	0	23	15	1.35
1224938--1225000	18	3.3	18	77	12	63	33	3	1	61	1.21
1225046--1225081	18	1.9	19	88	5	56	52	0	0	47	1.00
1226160--1226206	16	3.0	16	75	12	53	36	6	0	57	1.24
1226958--1227033	12	6.1	12	72	15	57	35	0	0	64	0.94
1226974--1227010	17	2.1	19	90	10	60	35	0	0	64	0.94
1226953--1227004	16	3.4	16	77	22	58	36	0	0	63	0.95
1228705--1228771	18	3.7	19	75	13	61	50	4	1	43	1.31
1231099--1231161	27	2.3	28	79	20	71	65	3	3	28	1.24
1231343--1231383	2	20.5	2	100	0	82	51	0	0	48	1.00
1231576--1231781	110	1.9	111	90	3	335	29	21	6	42	1.79
1231832--1231877	17	2.9	16	83	6	58	15	0	4	80	0.86
1237313--1237344	15	2.1	15	94	0	55	43	0	28	28	1.55
1241977--1242053	31	2.5	30	80	10	84	36	22	0	41	1.54
1245642--1245695	20	2.7	20	88	2	81	33	14	11	40	1.82
1250577--1250621	22	2.0	22	91	0	72	40	8	13	37	1.76
1252822--1252847	13	2.0	13	100	0	52	38	15	15	30	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1252800--1252867	33	2.1	32	94	2	118	32	13	17	36	1.89
1252889--1252940	20	2.6	20	81	0	59	28	15	13	42	1.85
1257141--1257207	27	2.7	24	73	24	66	56	0	0	43	0.99
1259940--1260030	36	2.8	32	75	16	96	30	24	13	31	1.93
1260396--1260447	20	2.6	20	100	0	104	40	9	11	38	1.74
1260506--1260551	24	1.9	24	95	0	83	43	6	23	26	1.78
1263953--1264010	19	3.0	20	80	7	75	34	13	15	36	1.87
1263975--1264036	32	1.9	33	87	9	92	38	12	16	32	1.86
1265001--1265057	21	2.7	20	76	10	60	17	24	3	54	1.59
1267190--1267221	10	3.2	10	95	0	55	40	3	28	28	1.71
1267200--1267266	24	2.8	24	83	0	98	43	5	22	28	1.76
1267210--1267260	14	3.9	14	75	19	56	43	7	21	27	1.80
1267822--1267855	14	2.4	14	90	9	52	35	0	23	41	1.55
1269344--1269395	20	2.6	20	84	0	68	38	15	13	32	1.86
1269781--1269825	20	2.2	20	96	0	81	40	15	15	28	1.88
1269872--1269929	22	2.6	22	94	0	107	41	12	17	29	1.85
1270350--1270459	54	2.0	54	98	0	211	32	9	24	33	1.87
1270460--1270553	34	2.8	34	91	0	152	28	15	20	35	1.94
1274264--1274322	30	2.0	30	89	0	91	47	16	15	20	1.83
1276380--1276447	34	2.0	34	94	0	118	29	13	22	35	1.92
1276426--1276494	29	2.3	32	83	11	85	30	8	20	40	1.82
1290821--1290871	22	2.3	21	83	12	59	45	5	9	39	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1290990--1291014	13	1.9	13	100	0	50	32	16	16	36	1.90
1291002--1291054	20	2.6	21	82	8	65	37	15	16	30	1.90
1291085--1291136	20	2.7	20	87	3	70	40	21	9	28	1.84
1297176--1297273	47	2.0	50	84	9	132	35	17	17	29	1.93
1297260--1297298	13	3.0	13	88	0	60	33	20	15	30	1.94
1299572--1299617	22	2.1	21	84	11	58	43	6	10	39	1.66
1299830--1299855	13	2.0	13	100	0	52	30	15	15	38	1.88
1299810--1299877	33	2.1	32	91	2	109	35	19	13	32	1.90
1300887--1300917	13	2.3	14	94	5	55	35	0	0	64	0.94
1300950--1301023	26	2.8	26	97	0	139	47	0	4	48	1.20
1301103--1301177	19	4.0	19	74	10	82	48	8	2	41	1.47
1301287--1301327	19	2.2	19	86	8	57	48	2	0	48	1.14
1301305--1301367	8	8.0	8	75	7	58	55	3	0	41	1.16
1301545--1301602	30	2.0	29	86	3	80	44	0	3	51	1.18
1304971--1304997	13	2.1	13	100	0	54	29	14	14	40	1.86
1304952--1305016	32	2.0	33	87	3	96	26	15	16	41	1.88
1304981--1305037	19	2.9	19	86	5	78	33	15	15	35	1.90
1305224--1305253	11	2.7	11	100	0	60	56	33	10	0	1.32
1316355--1316481	64	2.0	63	85	1	173	22	30	14	32	1.94
1316390--1316539	30	4.9	30	76	8	117	21	26	16	36	1.93
1316639--1317117	34	15.3	34	68	19	213	23	31	11	33	1.90
1316563--1317159	61	9.6	61	79	9	505	22	30	12	34	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1316561--1317097	27	17.5	27	66	20	140	22	31	11	34	1.90
1316563--1317098	34	17.5	28	66	20	129	22	31	11	34	1.90
1316629--1316964	130	2.7	121	83	8	363	23	32	10	33	1.89
1316760--1316995	95	2.6	89	83	5	294	23	32	10	33	1.88
1316760--1317036	95	3.1	89	77	12	276	22	32	11	33	1.89
1317197--1317265	32	2.2	32	82	15	81	33	24	15	26	1.95
1317335--1317768	52	8.7	50	75	7	271	23	25	15	34	1.95
1317371--1317594	45	4.7	46	83	11	220	24	25	15	34	1.95
1317372--1317651	142	1.9	144	81	3	339	25	25	15	34	1.94
1317776--1317828	26	2.0	26	100	0	106	33	26	11	28	1.91
1317629--1317973	187	1.9	182	81	6	426	24	26	14	34	1.94
1317803--1318064	52	4.9	53	81	5	246	24	26	14	34	1.94
1317808--1318064	104	2.4	105	83	7	306	23	26	14	35	1.93
1318657--1318682	13	2.0	13	100	0	52	38	15	15	30	1.88
1324061--1324106	18	2.6	18	86	10	60	23	2	4	69	1.17
1329466--1329499	6	5.7	6	92	0	59	50	0	17	32	1.47
1332064--1332142	31	2.6	29	82	10	77	30	0	2	67	1.04
1332444--1332483	18	2.1	20	86	9	57	10	10	2	77	1.08
1332453--1332492	20	2.1	19	85	4	53	20	7	2	70	1.24
1333337--1333392	29	1.9	30	89	7	89	37	12	12	37	1.81
1333581--1333637	29	2.0	30	86	6	82	36	15	12	35	1.85
1336308--1336409	41	2.4	41	88	3	141	38	14	25	21	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1336380--1336830	123	3.7	121	88	3	638	28	19	27	24	1.99
1336401--1336830	184	2.3	184	90	2	661	29	19	27	24	1.98
1336380--1336830	61	7.4	61	88	3	658	28	19	27	24	1.99
1350076--1350411	74	4.6	74	80	3	345	25	24	14	35	1.94
1350054--1350411	147	2.4	147	83	5	422	25	24	14	35	1.94
1355248--1355305	20	2.8	20	81	2	62	44	8	10	36	1.69
1356091--1356120	14	2.2	13	94	5	51	20	0	13	66	1.24
1365106--1365150	21	2.1	21	84	8	56	53	4	20	22	1.63
1370920--1370944	11	2.3	11	100	0	50	40	0	8	52	1.31
1371688--1371713	13	2.0	13	100	0	52	38	15	15	30	1.88
1373796--1373860	33	2.0	32	87	3	94	29	15	15	40	1.88
1373826--1373877	19	2.7	19	80	14	61	28	17	15	38	1.90
1373954--1373980	13	2.1	13	100	0	54	29	14	14	40	1.86
1374433--1374491	32	1.9	31	90	10	95	32	16	20	30	1.95
1376073--1376130	21	2.8	21	82	15	75	51	1	25	20	1.57
1376710--1376765	19	2.9	19	86	2	85	32	19	14	33	1.92
1378872--1378904	14	2.4	14	90	10	50	18	0	3	78	0.87
1380031--1380073	22	1.9	23	95	4	79	4	23	16	55	1.59
1380999--1381054	18	3.2	18	80	5	62	23	0	1	75	0.90
1381011--1381059	25	2.0	25	84	8	64	24	0	0	75	0.80
1381571--1381895	42	7.7	43	79	5	331	31	18	33	16	1.93
1381567--1381957	127	3.1	127	87	2	520	32	19	31	16	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1390259--1390312	19	2.8	19	81	13	65	29	14	12	42	1.83
1390379--1390405	13	2.1	13	100	0	54	40	14	14	29	1.86
1390362--1390425	33	1.9	33	84	6	85	39	14	17	29	1.88
1397020--1397091	38	1.9	37	86	8	101	29	22	22	26	1.99
1397122--1397154	13	2.4	14	90	5	50	24	0	3	72	0.98
1410796--1410840	13	3.0	16	78	18	60	82	17	0	0	0.68
1410796--1410840	15	3.1	15	77	6	56	82	17	0	0	0.68
1412054--1412927	126	7.1	125	81	7	866	23	27	15	32	1.95
1412054--1412927	251	3.5	250	80	7	835	23	27	15	32	1.95
1412054--1412986	31	30.0	30	75	11	643	24	27	15	32	1.95

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