oyster.v9_M.fa.s3.2.7.7.80.10.50.500.4.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.04

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: scaffold150
Parameters: 2 7 7 80 10 50 500
Length:  1854615

Tables:   1   2   3   4   5   6   

This is table  4  of  6  ( 642 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)
1155476--1155750	148	1.9	148	92	0	469	33	19	18	27	1.96
1155624--1155734	43	2.6	43	94	0	204	31	19	22	26	1.98
1160576--1160664	46	1.9	46	93	0	151	25	21	13	39	1.90
1160626--1160741	56	2.1	56	90	0	178	26	16	15	41	1.88
1163059--1163105	4	12.0	4	88	4	60	0	31	25	42	1.55
1163059--1163108	20	2.5	20	96	3	93	0	32	26	42	1.56
1163059--1163101	16	2.8	16	92	3	70	0	32	25	41	1.56
1163278--1164824	166	9.2	165	88	3	2150	32	15	26	25	1.96
1169590--1170593	80	12.7	80	84	7	1316	28	17	19	35	1.94
1170125--1170580	73	6.1	73	84	7	597	30	16	18	34	1.93
1169590--1170593	153	6.3	155	92	3	1430	28	17	19	35	1.94
1174061--1174098	2	19.0	2	100	0	76	0	50	0	50	1.00
1176067--1176139	28	2.6	28	91	4	112	31	15	24	28	1.95
1176090--1176146	13	4.2	13	78	8	69	33	12	26	28	1.92
1181212--1181254	20	2.1	20	86	0	59	37	23	20	18	1.94
1181291--1181589	20	14.9	20	83	2	314	33	19	23	24	1.97
1181301--1181399	41	2.4	41	91	1	155	32	18	17	32	1.94
1186143--1186206	29	2.2	29	94	0	110	29	9	20	40	1.84
1186550--1186597	2	24.0	2	100	0	96	0	0	50	50	1.00
1186597--1186637	2	20.5	2	94	0	73	46	0	51	2	1.14
1186830--1186856	2	13.5	2	100	0	54	48	0	51	0	1.00
1196878--1197065	35	5.3	35	75	9	159	25	37	20	17	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1196890--1197007	38	3.2	37	78	8	116	22	43	19	14	1.87
1199242--1200296	39	27.6	39	77	8	778	41	20	14	24	1.89
1199242--1200296	78	13.8	77	84	5	959	41	20	14	24	1.89
1199242--1200222	117	8.5	116	81	7	1017	41	20	13	24	1.88
1199505--1199637	67	2.0	67	100	0	266	40	19	12	27	1.87
1200396--1200527	41	3.1	41	74	18	126	43	17	18	21	1.88
1200401--1200533	45	3.2	39	76	15	133	42	18	18	21	1.89
1207672--1207698	8	3.4	8	100	0	54	0	11	0	88	0.50
1210318--1210346	15	1.9	15	100	0	58	17	48	0	34	1.47
1212432--1212563	66	2.0	66	98	0	255	28	29	13	28	1.94
1212536--1212605	35	2.0	35	97	0	131	44	14	12	28	1.82
1214103--1214527	22	19.4	22	75	9	207	24	14	29	31	1.94
1214192--1214564	44	8.5	44	92	0	568	26	13	30	29	1.94
1214192--1214564	22	17.0	22	84	2	453	26	13	30	29	1.94
1221715--1221747	17	1.9	17	93	0	57	66	15	6	12	1.42
1221967--1222002	18	2.0	18	88	0	54	58	19	8	13	1.61
1222395--1222453	22	2.7	22	86	0	82	23	10	20	45	1.81
1222443--1223386	22	42.5	22	81	1	1006	30	11	15	43	1.82
1222485--1223386	132	6.8	132	90	0	1257	30	11	15	43	1.82
1225614--1225648	4	8.8	4	100	0	70	22	25	0	51	1.48
1226621--1227005	22	17.9	22	77	12	182	33	13	17	35	1.89
1226676--1227007	64	5.1	62	71	12	168	35	13	17	33	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1226684--1226918	84	2.7	84	75	10	217	37	14	17	30	1.90
1226684--1227010	22	15.1	21	78	10	191	36	13	16	33	1.88
1228017--1228051	2	17.5	2	100	0	70	51	0	48	0	1.00
1230426--1230473	5	9.6	5	78	17	55	2	0	20	77	0.88
1233267--1233311	19	2.3	20	88	11	67	15	11	2	71	1.24
1237164--1237339	90	2.0	90	82	6	214	48	9	10	32	1.68
1241944--1241976	17	2.0	17	88	5	50	51	0	27	21	1.48
1242081--1242117	12	3.1	12	88	11	58	0	0	16	83	0.64
1242078--1242114	18	2.1	18	90	10	58	0	0	21	78	0.75
1242081--1242131	24	2.0	24	85	7	66	0	0	21	78	0.75
1242618--1242668	16	3.2	16	91	5	77	80	17	1	0	0.81
1242614--1242657	22	2.1	20	87	8	61	84	15	0	0	0.63
1242618--1242659	15	2.9	14	86	10	57	80	19	0	0	0.70
1260064--1261005	19	48.4	19	88	5	1296	31	15	16	36	1.90
1260064--1261005	59	16.1	57	88	5	1235	31	15	16	36	1.90
1260861--1260947	45	1.9	45	88	4	131	31	17	13	37	1.89
1261813--1261845	17	1.9	17	100	0	66	24	21	24	30	1.99
1268512--1268765	63	4.0	63	90	4	391	31	24	23	21	1.98
1268512--1268765	130	2.0	126	89	3	391	31	24	23	21	1.98
1268828--1268857	13	2.3	13	94	0	51	43	13	13	30	1.82
1268911--1269031	38	3.2	38	63	15	95	41	11	14	33	1.81
1268914--1269114	77	2.6	77	98	0	384	41	13	13	31	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1270145--1270387	54	4.4	55	83	12	311	19	21	13	45	1.84
1270153--1270244	27	3.4	27	69	21	75	19	19	13	47	1.81
1270298--1270382	27	3.1	27	65	34	74	15	24	12	47	1.81
1271106--1271166	30	2.0	30	100	0	122	16	29	19	34	1.94
1272818--1272880	33	1.9	33	83	0	81	41	17	20	20	1.91
1272866--1272986	54	2.2	54	92	0	197	44	14	23	18	1.85
1273257--1273392	33	4.1	33	79	0	137	36	15	22	25	1.93
1274685--1274725	2	20.5	2	84	0	55	0	41	0	58	0.98
1274684--1274726	14	3.1	14	93	0	77	0	39	0	60	0.97
1274689--1274740	10	5.5	10	76	19	58	0	38	0	61	0.96
1274805--1274844	21	1.9	21	89	0	62	12	32	0	55	1.38
1274830--1274864	16	2.2	16	89	0	52	22	40	0	37	1.55
1277619--1277676	28	2.1	28	100	0	116	32	20	17	29	1.95
1279032--1279089	28	2.1	28	100	0	116	32	20	17	29	1.95
1296613--1296658	2	23.0	2	95	0	74	54	0	0	45	0.99
1297358--1297383	13	2.0	13	100	0	52	38	38	7	15	1.76
1300743--1300796	29	2.0	28	85	10	76	24	3	20	51	1.63
1304170--1304595	33	12.9	33	74	5	342	38	9	27	24	1.86
1304168--1304595	66	6.5	66	80	3	423	38	9	27	24	1.87
1304404--1304592	98	1.9	98	88	2	281	40	7	25	26	1.83
1305568--1306391	38	21.8	38	90	1	1199	33	12	28	25	1.92
1307475--1307545	2	35.5	2	100	0	142	50	0	49	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1320726--1320763	2	19.0	2	94	0	67	50	0	47	2	1.15
1320893--1321008	2	58.0	2	91	0	187	49	3	46	0	1.24
1322304--1322328	9	2.8	9	100	0	50	36	0	8	56	1.29
1323592--1323644	2	26.5	2	96	0	97	50	0	49	0	1.00
1327063--1327093	15	2.1	15	100	0	62	35	12	0	51	1.40
1327929--1328130	65	3.1	65	99	0	395	35	11	12	41	1.79
1329182--1329218	2	18.5	2	100	0	74	51	0	48	0	1.00
1329934--1330357	214	2.0	210	100	0	812	28	22	19	29	1.97
1334183--1334225	23	2.0	23	86	9	63	46	13	16	23	1.83
1337217--1337272	2	28.0	2	100	0	112	0	50	0	50	1.00
1337670--1337734	2	32.5	2	100	0	130	0	49	0	50	1.00
1348701--1349542	31	27.3	31	85	1	1066	40	23	10	24	1.87
1365310--1365453	30	4.9	28	77	11	126	22	47	12	17	1.81
1365313--1365453	60	2.3	61	85	3	196	22	47	12	17	1.81
1366517--1366576	2	30.0	2	89	0	93	5	46	0	48	1.24
1368098--1368160	15	4.2	15	76	15	58	36	6	11	46	1.65
1368136--1368176	15	2.7	15	88	0	55	31	12	14	41	1.83
1368510--1368560	18	2.6	20	81	12	70	37	15	7	39	1.77
1368558--1368611	28	1.9	28	88	0	81	31	9	3	55	1.49
1368559--1368618	28	2.1	28	84	0	75	33	8	5	53	1.53
1368822--1368855	16	2.1	16	94	0	59	29	23	23	23	1.99
1369470--1369505	15	2.4	15	95	0	63	27	5	13	52	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1369470--1369511	15	2.9	14	86	13	59	28	7	14	50	1.69
1369674--1369721	15	3.2	15	73	8	53	37	6	12	43	1.68
1370409--1370443	18	2.0	17	94	5	61	45	17	0	37	1.48
1370486--1370521	17	2.1	17	90	10	56	36	2	13	47	1.58
1371921--1371976	2	28.0	2	100	0	112	0	50	0	50	1.00
1373259--1373590	166	2.0	165	98	0	637	38	11	11	37	1.78
1377252--1377276	13	1.9	13	100	0	50	56	8	12	24	1.62
1377910--1378197	29	9.9	29	88	0	324	43	24	11	20	1.84
1377910--1378197	58	5.0	58	85	4	366	43	24	11	20	1.84
1377910--1378197	87	3.3	87	84	4	384	43	24	11	20	1.84

Tables:   1   2   3   4   5   6