genome.fa.s39.2.7.7.80.10.50.1000.6.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: scaffold165.1
Parameters: 2 7 7 80 10 50 1000
Length:  1724686

Tables:   1   2   3   4   5   6   7   8   

This is table  6  of  8  ( 876 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)
1171924--1171964	19	2.1	20	82	13	50	46	0	4	48	1.23
1172686--1172777	7	12.3	7	73	13	76	31	48	0	19	1.49
1172686--1172782	22	4.6	22	81	12	123	32	46	0	20	1.51
1172707--1172752	17	2.9	16	83	6	58	32	47	0	19	1.50
1172686--1172774	39	2.4	37	88	3	133	32	47	0	20	1.50
1172685--1172784	15	6.7	14	73	18	55	33	47	0	20	1.50
1173404--1173562	41	3.8	40	75	7	140	38	25	16	19	1.93
1173385--1173538	82	1.9	83	84	8	208	38	27	16	16	1.90
1177692--1177728	13	2.9	14	88	11	53	0	27	0	72	0.84
1178497--1178545	18	2.6	19	83	9	64	53	0	0	46	1.00
1178535--1178591	20	3.0	19	89	5	80	38	0	7	54	1.28
1180187--1180492	46	6.6	46	90	5	465	29	22	15	33	1.94
1181493--1181525	18	1.9	17	88	11	50	36	15	0	48	1.45
1181952--1181995	17	2.6	17	96	0	79	27	9	4	59	1.48
1183513--1183585	27	2.5	29	78	13	87	42	4	6	46	1.49
1183496--1183595	27	3.6	27	75	9	83	41	3	9	47	1.50
1186046--1186101	27	2.1	27	82	0	67	33	3	12	50	1.58
1186532--1186819	42	6.8	42	78	3	265	25	21	20	33	1.97
1186529--1186822	126	2.3	126	79	7	310	25	20	20	32	1.97
1192845--1192925	9	9.0	9	71	15	60	37	1	17	44	1.57
1192849--1192927	16	5.0	16	75	14	74	37	1	16	44	1.56
1192942--1193021	34	2.3	35	93	2	135	61	2	5	31	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1194659--1194745	44	2.0	44	95	0	156	32	8	33	26	1.85
1203669--1204237	9	67.2	9	68	18	237	29	1	18	50	1.56
1203694--1203883	25	7.6	25	87	3	276	29	2	21	47	1.62
1203828--1203923	40	2.4	40	98	0	183	29	4	18	47	1.67
1203669--1204068	25	15.6	25	77	12	126	29	1	19	49	1.59
1203658--1203973	16	18.6	17	74	16	205	30	1	19	47	1.60
1203956--1204136	95	1.9	95	98	0	353	27	1	16	54	1.49
1204083--1204182	25	4.2	25	63	27	63	28	2	14	56	1.49
1204051--1204206	71	2.2	70	96	1	285	27	1	15	55	1.48
1204122--1204322	94	2.1	95	97	0	377	27	0	17	53	1.51
1203956--1204301	165	2.1	166	97	0	658	27	1	17	54	1.50
1204152--1204294	51	3.1	45	71	16	146	27	1	17	53	1.52
1204286--1204337	24	2.2	24	92	0	86	26	1	19	51	1.57
1204289--1204343	24	2.5	22	85	8	67	27	1	21	49	1.60
1204523--1204603	9	9.0	9	71	15	60	37	1	17	44	1.57
1204527--1204605	16	5.0	16	75	14	74	37	1	16	44	1.56
1204620--1204699	34	2.3	35	93	2	135	61	2	5	31	1.31
1206338--1206424	44	2.0	44	95	0	156	32	8	33	26	1.85
1207628--1207667	15	2.7	15	92	3	64	45	30	0	25	1.54
1207983--1208615	114	5.5	114	77	7	572	27	22	18	32	1.97
1207983--1208582	229	2.6	227	80	3	650	27	22	18	31	1.97
1208514--1208689	75	2.3	75	81	1	210	27	23	15	33	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1208420--1208784	187	2.0	187	80	5	416	25	20	17	35	1.95
1209585--1209617	15	2.1	16	88	5	50	66	3	0	30	1.06
1209817--1209928	41	2.8	40	70	9	95	32	24	17	25	1.97
1211584--1211643	17	3.5	17	75	8	59	45	0	3	51	1.17
1211609--1211647	19	2.0	20	85	14	55	35	0	7	56	1.28
1211787--1211849	32	2.0	32	84	6	83	38	19	9	33	1.84
1213730--1213815	29	2.9	29	87	1	109	44	2	8	45	1.46
1213736--1213829	30	3.3	28	81	8	100	41	2	7	48	1.43
1216407--1216436	16	1.9	16	93	6	53	26	0	6	66	1.16
1216452--1216507	27	2.1	27	82	0	67	33	3	12	50	1.58
1218554--1218618	30	2.1	32	82	5	80	64	6	3	26	1.32
1219541--1219584	22	2.0	22	86	4	61	4	4	45	45	1.44
1220044--1220083	20	2.0	20	90	0	62	15	25	45	15	1.84
1220189--1220232	22	2.0	22	86	4	61	4	4	45	45	1.44
1220640--1220709	27	2.6	27	79	2	77	45	4	7	42	1.51
1221881--1221906	4	6.5	4	100	0	52	23	0	0	76	0.78
1224322--1224353	13	2.3	15	89	10	50	31	0	0	68	0.90
1227689--1227724	19	1.9	18	88	5	54	41	2	2	52	1.30
1227772--1227827	25	2.1	27	87	6	80	51	1	0	46	1.11
1229595--1229813	43	5.1	43	77	7	187	37	26	13	22	1.91
1229611--1229813	86	2.4	84	80	5	219	36	26	13	23	1.92
1230895--1230952	25	2.4	23	80	11	62	32	17	41	8	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1231678--1231739	22	2.8	22	85	0	88	45	30	0	24	1.54
1231753--1231797	14	3.2	15	78	12	51	51	20	0	28	1.48
1231679--1231790	37	3.0	36	80	6	100	47	25	0	26	1.58
1232040--1232215	84	2.1	84	93	1	298	33	18	17	30	1.94
1231948--1232339	209	1.9	207	87	3	572	32	19	17	31	1.95
1232120--1232528	124	3.3	122	85	3	514	33	19	15	31	1.93
1237409--1237489	42	2.0	41	97	2	146	17	9	8	62	1.49
1254766--1254814	25	2.0	25	84	11	66	28	4	4	63	1.31
1255052--1255081	15	2.0	15	93	0	51	50	6	0	43	1.28
1260444--1260489	20	2.3	20	85	7	58	28	4	17	50	1.65
1264449--1264587	46	3.0	46	92	0	224	27	28	10	33	1.89
1267969--1268014	20	2.3	20	85	7	58	28	4	17	50	1.65
1272871--1272909	10	3.9	10	80	12	53	51	0	2	46	1.14
1278434--1278461	3	9.3	3	100	0	56	67	0	0	32	0.91
1282385--1282429	23	2.0	23	83	12	58	44	0	0	55	0.99
1282385--1282447	25	2.6	24	87	5	83	46	1	3	49	1.27
1284448--1284479	15	2.1	15	94	0	55	68	0	9	21	1.17
1288277--1288339	15	4.0	16	73	10	58	49	9	3	38	1.51
1296930--1297044	55	2.0	56	88	5	169	53	25	13	6	1.65
1300494--1300569	23	3.3	23	90	0	125	21	21	27	30	1.98
1304023--1304150	25	5.2	25	69	16	79	35	19	23	21	1.96
1304104--1304153	26	1.9	26	95	0	91	38	24	20	18	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1306056--1306093	18	2.1	18	95	0	67	36	47	15	0	1.46
1308969--1309007	11	3.6	11	89	6	62	43	0	0	56	0.99
1311545--1311780	42	5.6	42	83	2	267	30	28	17	23	1.97
1312164--1312291	66	1.9	66	87	3	186	12	27	17	42	1.85
1313983--1314023	20	2.0	20	100	0	82	26	29	19	24	1.98
1317486--1317510	13	1.9	13	100	0	50	28	16	16	40	1.89
1318315--1318353	19	2.1	18	85	4	51	69	2	2	25	1.14
1320345--1320399	10	5.3	10	78	8	65	23	16	14	45	1.84
1320344--1320402	21	2.8	21	97	0	109	23	16	13	45	1.83
1322790--1322846	27	2.1	27	90	0	87	14	24	40	21	1.90
1322987--1323100	59	1.9	59	94	0	201	51	14	0	33	1.43
1323241--1323294	27	2.0	27	88	0	81	16	29	33	20	1.95
1348520--1348879	190	1.9	189	86	4	510	42	13	7	36	1.73
1357586--1357633	20	2.3	21	86	10	64	66	6	0	27	1.15
1357610--1357656	19	2.3	21	85	7	62	65	8	2	23	1.31
1357622--1357666	21	2.2	20	80	11	56	68	6	2	22	1.24
1357610--1357680	19	3.9	17	73	14	54	67	5	1	25	1.20
1357734--1357821	9	9.6	9	75	10	63	63	2	2	31	1.19
1357733--1357822	37	2.4	37	83	8	121	63	2	2	32	1.19
1357818--1357910	39	2.3	40	88	5	143	53	0	2	44	1.12
1358705--1358741	19	1.9	19	88	0	56	43	2	5	48	1.40
1362262--1362358	30	3.2	30	72	13	99	53	9	1	36	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1362225--1362401	61	2.9	61	94	0	309	56	7	2	33	1.39
1362379--1362418	17	2.4	18	80	16	50	60	0	0	40	0.97
1374599--1374678	19	4.1	20	70	13	76	63	0	1	35	1.02
1374652--1374698	17	2.8	17	80	0	58	65	0	0	34	0.93
1377997--1378026	15	2.0	15	100	0	60	46	6	6	40	1.56
1378289--1378376	6	14.3	6	73	11	72	73	4	20	1	1.07
1378302--1378361	17	3.6	17	82	10	72	73	6	20	0	1.05
1378340--1378377	11	3.4	11	86	13	51	73	0	26	0	0.83
1378316--1378376	17	3.4	17	86	6	68	72	4	22	0	1.04
1379254--1379370	41	3.0	40	70	13	107	24	14	23	37	1.92

Tables:   1   2   3   4   5   6   7   8