genome.fa.s162.2.7.7.80.10.50.1000.8.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: Scaffold162
Parameters: 2 7 7 80 10 50 1000
Length:  1959167

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   

This is table  8  of  12  ( 1418 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)
1175766--1175812	23	2.0	24	84	12	62	61	19	4	14	1.49
1178376--1178442	37	1.9	35	88	11	102	29	25	11	32	1.92
1178921--1178946	13	2.0	13	100	0	52	30	23	15	30	1.95
1179043--1179084	21	2.0	21	95	0	75	38	9	21	30	1.85
1179134--1179270	53	2.6	53	95	1	247	27	17	18	37	1.93
1179240--1179310	20	3.5	20	77	11	74	29	14	16	39	1.88
1179350--1179390	21	2.0	21	85	9	57	39	9	12	39	1.76
1186120--1186168	25	2.0	25	84	8	64	22	12	22	42	1.86
1188233--1188269	14	2.6	14	91	0	56	78	0	8	13	0.96
1188524--1188565	13	3.3	13	77	16	52	0	14	0	85	0.59
1188522--1188565	23	1.9	23	86	9	63	0	15	0	84	0.63
1188513--1188563	12	4.2	12	82	7	59	0	19	0	80	0.71
1188507--1188564	11	4.9	12	74	18	50	1	18	0	79	0.82
1189928--1190026	20	4.8	20	79	9	117	31	12	19	37	1.88
1190013--1190038	13	2.0	13	100	0	52	30	15	15	38	1.88
1189993--1190056	33	2.0	32	90	3	101	26	14	20	39	1.90
1190127--1190151	13	1.9	13	100	0	50	36	16	16	32	1.90
1194924--1195052	52	2.5	52	96	0	240	27	17	18	35	1.94
1195061--1195085	13	1.9	13	100	0	50	36	16	16	32	1.90
1195124--1195224	32	3.1	32	95	1	175	36	16	11	34	1.86
1195148--1195204	13	3.9	13	74	24	51	35	15	14	35	1.88
1195129--1195225	19	5.7	19	68	27	83	37	16	12	34	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1195946--1196068	49	2.5	49	94	0	210	32	15	28	23	1.95
1196137--1196571	101	4.5	95	89	5	547	33	17	24	24	1.97
1196146--1196571	52	8.7	49	80	10	455	32	18	24	24	1.97
1196571--1197031	33	14.0	33	90	2	678	21	18	31	27	1.97
1197044--1197312	27	9.0	27	72	18	178	30	13	33	22	1.92
1197126--1197537	32	13.0	34	77	15	250	32	13	32	22	1.92
1197126--1197345	62	3.5	63	85	6	295	31	12	34	22	1.91
1197286--1197406	34	3.6	34	82	5	124	31	13	33	22	1.92
1197280--1197537	63	4.0	65	77	12	203	33	13	30	22	1.93
1198543--1198585	20	2.1	21	86	4	61	0	6	11	81	0.87
1202393--1202437	20	2.1	21	84	8	56	4	26	48	20	1.68
1205221--1205286	33	2.0	33	100	0	132	42	18	3	36	1.66
1206987--1207024	15	2.4	16	86	4	51	23	7	5	63	1.42
1209053--1209078	13	2.0	13	100	0	52	30	15	15	38	1.88
1209033--1209096	33	2.0	32	90	3	101	26	14	20	39	1.90
1214837--1214911	20	3.8	20	78	0	87	34	13	12	40	1.81
1214837--1214914	40	2.0	39	87	2	111	34	12	12	39	1.82
1215824--1215877	20	2.5	22	82	17	76	18	11	11	59	1.60
1215832--1215877	20	2.2	22	92	7	78	17	8	10	63	1.51
1221975--1222017	15	2.7	17	79	17	56	65	11	18	4	1.42
1221998--1222049	23	2.3	23	83	12	63	75	7	11	5	1.19
1223334--1224807	57	26.0	54	82	8	861	27	32	16	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1223330--1225253	143	13.2	140	86	5	1859	27	32	17	22	1.96
1223334--1225253	28	66.1	29	88	5	1828	27	32	17	22	1.96
1225815--1225889	20	3.8	20	75	7	80	33	14	12	40	1.83
1225815--1225892	40	2.0	39	85	7	104	33	14	12	39	1.84
1226802--1226859	22	2.4	25	83	16	95	17	10	8	63	1.49
1226811--1226859	22	2.2	22	100	0	98	16	8	8	67	1.40
1226812--1226866	22	2.6	21	88	5	58	20	9	9	61	1.52
1232371--1232419	11	4.4	11	92	2	80	55	2	0	42	1.11
1234898--1234941	21	2.1	20	84	16	54	22	31	4	40	1.74
1236749--1236785	13	2.8	13	95	0	65	43	16	10	29	1.82
1238864--1238894	15	2.1	15	93	0	53	12	22	16	48	1.80
1240697--1240741	21	2.1	21	84	8	56	22	20	4	53	1.63
1242967--1242992	13	2.0	13	100	0	52	30	15	15	38	1.88
1248844--1250130	642	2.0	642	99	0	2547	39	12	19	28	1.88
1253864--1253901	20	1.9	20	100	0	76	31	18	10	39	1.85
1256967--1257039	20	3.6	20	81	3	101	35	13	19	31	1.91
1256985--1257060	21	3.7	21	80	3	100	42	11	17	28	1.84
1256967--1257060	41	2.3	41	98	0	179	39	12	18	29	1.88
1257099--1257124	13	2.0	13	100	0	52	38	15	15	30	1.88
1261187--1261217	15	2.1	15	93	0	53	48	16	22	12	1.80
1263297--1263334	13	2.9	13	96	0	67	34	18	15	31	1.92
1265788--1265860	20	3.6	20	81	3	101	35	13	19	31	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1265806--1265881	21	3.7	21	80	3	100	42	11	17	28	1.84
1265788--1265881	41	2.3	41	98	0	179	39	12	18	29	1.88
1265920--1265945	13	2.0	13	100	0	52	38	15	15	30	1.88
1270769--1270809	21	2.0	21	85	9	57	39	12	9	39	1.76
1270849--1270919	20	3.6	19	77	7	70	39	16	14	29	1.88
1270889--1271025	53	2.6	53	96	1	247	37	18	17	27	1.93
1271067--1271122	21	2.6	22	94	5	105	26	25	10	37	1.88
1271184--1271209	13	2.0	13	100	0	52	30	15	23	30	1.95
1279662--1279725	9	6.7	10	84	10	64	85	7	3	3	0.79
1279661--1279724	10	7.0	9	81	12	60	84	9	3	3	0.84
1279688--1279725	10	3.7	10	96	3	67	89	7	2	0	0.57
1279679--1279744	10	6.3	10	81	10	51	83	7	4	4	0.91
1280953--1282203	28	43.6	28	84	6	1433	28	31	17	22	1.97
1280950--1282203	85	14.6	84	85	4	1445	28	31	17	22	1.97
1282598--1282638	21	2.0	21	85	9	57	39	12	9	39	1.76
1282678--1282748	20	3.6	19	75	7	61	39	15	14	30	1.87
1282718--1282854	53	2.6	53	90	3	213	37	18	17	27	1.93
1282878--1282908	10	3.1	10	90	0	53	22	29	6	41	1.78
1282919--1283016	48	2.1	47	92	1	160	29	23	8	38	1.84
1282897--1283001	24	4.5	24	73	13	85	30	21	9	38	1.86
1286468--1286492	13	1.9	13	100	0	50	36	16	16	32	1.90
1287296--1287782	243	2.0	242	98	0	947	41	4	25	28	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1288328--1288368	21	2.0	21	85	9	57	39	12	9	39	1.76
1288408--1288478	20	3.6	19	77	7	70	39	16	14	29	1.88
1288448--1288584	53	2.6	53	95	1	238	37	18	17	26	1.93
1288609--1288639	10	3.1	10	95	0	53	25	29	3	41	1.71
1289039--1289110	20	3.6	20	82	0	99	33	15	11	40	1.82
1294478--1294521	12	3.7	12	75	0	52	50	0	0	50	1.00
1298023--1298054	2	16.0	2	100	0	64	50	0	0	50	1.00
1298054--1298087	2	17.0	2	100	0	68	50	0	50	0	1.00
1298606--1298645	21	1.9	21	89	0	62	75	5	12	7	1.18
1299070--1299113	22	2.0	22	86	4	61	52	0	2	45	1.13
1300076--1300123	20	2.3	21	78	3	53	41	2	6	50	1.39
1300205--1300239	3	11.7	3	100	0	70	34	0	0	65	0.93
1300427--1300469	10	4.1	10	85	8	50	44	2	0	53	1.13
1301273--1301314	21	2.0	21	81	9	50	57	0	0	42	0.99
1302211--1302239	2	14.5	2	100	0	58	0	48	0	51	1.00
1302239--1302267	2	14.5	2	100	0	58	48	0	0	51	1.00
1303105--1303156	18	2.8	18	80	13	61	46	0	0	53	1.00
1304172--1304216	16	2.9	15	80	9	54	33	4	4	57	1.38
1308524--1308563	16	2.5	16	100	0	80	40	0	5	55	1.22
1308835--1308881	25	1.9	24	86	4	67	40	0	6	53	1.27
1308864--1308905	17	2.4	18	80	15	52	33	0	11	54	1.37
1313313--1313360	23	2.1	23	92	0	78	60	0	2	37	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1315457--1315514	28	2.0	29	83	3	73	48	3	0	48	1.18
1315586--1315618	2	16.5	2	100	0	66	51	0	0	48	1.00
1315618--1315678	2	30.5	2	100	0	122	50	0	49	0	1.00
1315941--1316048	57	1.9	57	88	0	162	48	7	6	37	1.57
1317478--1317650	82	2.1	82	96	0	319	35	9	9	45	1.69
1317478--1317676	82	2.4	82	90	3	285	35	9	9	45	1.68
1318020--1318044	7	3.6	7	100	0	50	60	0	0	40	0.97
1319336--1319407	28	2.5	28	76	15	74	61	0	1	37	1.05
1320576--1320634	17	3.4	17	86	9	66	66	0	0	33	0.92
1325310--1325398	9	11.5	8	65	27	50	58	1	0	40	1.05

Tables:   1   2   3   4   5   6   7   8   9   10   11   12