genome.fa.s99.2.7.7.80.10.50.1000.9.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: Scaffold99
Parameters: 2 7 7 80 10 50 1000
Length:  1377724

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

This is table  9  of  10  ( 1130 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)
1179135--1179170	17	2.2	16	95	5	63	91	8	0	0	0.41
1179127--1179185	30	2.0	30	86	6	84	84	15	0	0	0.62
1179133--1179185	14	3.7	15	80	10	65	84	15	0	0	0.61
1180552--1180723	33	5.1	37	76	16	151	20	29	12	37	1.89
1180465--1180823	95	3.8	93	80	9	366	23	27	13	35	1.92
1180454--1180829	31	11.8	31	76	11	332	22	27	12	36	1.91
1180836--1181379	68	8.4	65	80	8	529	20	29	13	36	1.91
1180836--1181361	34	16.2	33	79	10	462	20	29	13	36	1.90
1181159--1181318	61	2.5	61	76	12	144	20	33	12	33	1.90
1180836--1181361	95	5.4	92	83	8	518	20	29	13	36	1.90
1181352--1181476	29	4.3	29	79	7	137	33	31	16	19	1.93
1181352--1181476	57	2.2	58	85	5	164	33	31	16	19	1.93
1181498--1182377	49	19.0	48	69	15	403	25	26	17	30	1.97
1181552--1181708	39	3.8	39	74	14	152	27	28	18	26	1.98
1181498--1182219	87	8.0	87	79	9	730	26	26	17	29	1.98
1181761--1182313	98	5.9	97	78	9	497	25	27	17	30	1.97
1181907--1181984	39	2.0	39	84	0	102	29	28	19	23	1.98
1181499--1182219	273	2.7	271	89	2	1057	26	26	17	29	1.98
1186050--1186152	50	2.1	50	100	0	206	29	18	19	33	1.96
1186284--1186515	79	3.0	79	76	6	240	27	22	13	36	1.92
1186452--1186567	51	2.3	51	83	7	146	30	25	10	34	1.89
1186378--1186615	130	1.8	130	83	1	316	29	22	10	37	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1186501--1186784	79	3.6	78	76	8	227	30	20	11	36	1.89
1192930--1193230	61	4.9	62	85	1	408	23	23	19	32	1.98
1192930--1193231	123	2.5	123	87	1	444	23	24	19	32	1.98
1193209--1193255	24	2.0	24	91	0	76	29	21	21	27	1.98
1193147--1193312	85	1.9	86	82	3	210	27	23	18	30	1.98
1193086--1193383	147	2.0	147	87	2	429	25	24	19	30	1.98
1193025--1193439	208	2.0	208	85	2	566	25	24	18	31	1.98
1193233--1193439	61	3.4	60	82	5	245	26	25	18	29	1.98
1193422--1193939	43	12.3	42	77	8	387	22	24	12	40	1.88
1193418--1193943	85	6.3	83	74	11	367	22	24	12	40	1.88
1193957--1194041	44	1.9	44	83	4	109	14	21	15	49	1.79
1194751--1194818	31	2.2	31	86	0	91	25	17	19	38	1.93
1195797--1195902	53	2.0	53	94	0	185	21	24	22	31	1.98
1195902--1195958	24	2.3	25	87	9	89	29	28	17	24	1.97
1195927--1196204	62	4.5	61	81	4	303	26	25	17	30	1.98
1196180--1196722	42	13.0	42	78	8	459	20	27	12	39	1.88
1196182--1196692	85	6.1	85	77	10	365	20	27	12	39	1.89
1197505--1197618	51	2.2	50	81	4	129	26	14	13	46	1.80
1197521--1197628	51	2.1	51	82	3	137	26	15	14	42	1.86
1199779--1200141	79	4.6	78	80	10	337	28	23	12	35	1.91
1205421--1205460	19	2.0	20	86	13	57	72	5	15	7	1.24
1206630--1206691	30	2.1	30	84	6	81	22	30	12	33	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1206694--1206990	62	4.8	62	80	4	332	26	26	17	29	1.97
1207315--1207370	20	2.8	19	89	5	76	39	14	16	30	1.88
1207429--1207454	13	2.0	13	100	0	52	38	15	15	30	1.88
1207499--1207537	20	1.9	21	94	5	71	43	10	10	35	1.73
1211299--1212359	62	17.1	62	82	3	1202	27	24	19	28	1.98
1211299--1212359	309	3.4	308	83	3	1211	27	24	19	28	1.98
1212331--1212421	33	2.9	32	84	12	109	28	24	18	28	1.98
1213565--1213605	19	2.1	19	86	4	55	63	0	31	4	1.15
1213564--1213609	23	2.0	23	82	0	56	65	0	30	4	1.12
1220645--1220690	22	2.1	22	84	8	58	56	0	0	43	0.99
1220698--1220731	10	3.6	9	88	11	50	47	0	2	50	1.16
1220636--1220782	70	2.0	74	81	12	173	54	0	1	44	1.08
1220760--1220792	15	2.1	17	88	11	52	60	0	0	39	0.97
1221735--1221781	4	11.8	4	93	0	67	53	23	4	19	1.63
1221861--1221887	2	13.5	2	100	0	54	0	48	0	51	1.00
1222590--1222637	23	2.1	23	100	0	96	29	12	18	39	1.88
1223194--1223227	18	2.0	17	88	11	52	82	2	11	2	0.89
1227317--1227371	20	2.8	19	83	5	74	32	10	18	38	1.85
1227420--1227445	13	2.0	13	100	0	52	30	15	15	38	1.88
1233579--1233620	13	3.2	13	86	0	66	28	14	16	40	1.88
1236027--1236079	20	2.7	20	91	2	81	32	13	18	35	1.90
1237466--1237515	20	2.5	20	96	0	91	32	14	18	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1244539--1244573	15	2.3	15	95	0	61	28	28	0	42	1.56
1246163--1246216	20	2.7	19	77	11	56	38	18	11	31	1.86
1250039--1250153	57	2.0	57	94	0	203	36	19	13	31	1.90
1250397--1250443	15	3.0	16	78	15	53	68	0	31	0	0.90
1251684--1251808	51	2.4	52	85	1	162	29	17	11	41	1.84
1251695--1251808	52	2.2	51	84	1	147	28	18	9	42	1.82
1253636--1253674	10	3.8	10	96	3	69	35	12	0	51	1.40
1256867--1257208	140	2.4	139	86	3	472	44	9	11	34	1.73
1258087--1258120	11	3.1	11	95	0	59	0	14	0	85	0.60
1263117--1263170	20	2.7	20	100	0	108	44	14	14	25	1.84
1263155--1263182	13	2.2	13	100	0	56	39	17	14	28	1.89
1263135--1263202	33	2.1	33	88	5	102	39	14	16	29	1.88
1264107--1264314	47	4.4	47	82	2	220	41	15	20	22	1.89
1264107--1264314	94	2.2	94	83	3	258	41	15	20	22	1.89
1264283--1264418	35	3.9	35	79	6	125	46	12	20	20	1.83
1264283--1264382	34	2.9	35	83	5	132	45	13	21	21	1.85
1265789--1265833	21	2.1	21	88	8	65	2	20	0	77	0.87
1265797--1265835	7	5.6	7	85	11	53	0	17	0	82	0.68
1272215--1272339	20	5.7	20	75	18	97	40	10	17	32	1.84
1272263--1272339	40	1.9	40	89	5	120	38	11	16	32	1.85
1273218--1273859	28	22.0	28	82	6	622	22	17	30	28	1.97
1273210--1273859	85	7.4	85	81	7	662	23	17	29	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1275101--1275190	1	90.0	1	79	0	99	1	0	8	90	0.52
1275078--1275189	10	10.8	10	81	16	115	1	1	9	86	0.72
1275102--1275188	9	9.9	9	87	6	117	1	0	9	89	0.53
1275076--1275187	40	2.7	41	82	14	142	1	1	10	85	0.74
1275079--1275189	42	2.7	40	86	8	143	1	1	9	86	0.72
1286397--1286521	52	2.4	52	91	0	205	28	16	18	37	1.92
1286397--1286541	52	2.8	52	85	4	186	29	15	18	35	1.92
1286530--1286554	13	1.9	13	100	0	50	36	16	16	32	1.90
1286596--1286620	13	1.9	13	100	0	50	32	16	16	36	1.90
1290148--1290199	22	2.5	21	81	6	61	42	17	13	26	1.86
1290252--1290284	13	2.4	14	85	15	50	42	15	15	27	1.86
1290259--1290284	13	2.0	13	100	0	52	38	15	15	30	1.88
1290241--1290305	34	2.0	32	88	11	96	38	16	15	29	1.90
1296446--1296483	13	2.9	13	96	0	67	31	15	18	34	1.92
1296616--1296656	22	2.0	19	86	13	55	36	19	0	43	1.51
1296925--1296973	20	2.5	20	100	0	98	14	40	30	14	1.85
1297914--1297958	22	2.0	22	83	8	56	37	0	24	37	1.56
1298609--1298641	13	2.4	14	85	15	50	42	15	15	27	1.86
1298616--1298641	13	2.0	13	100	0	52	38	15	15	30	1.88
1298598--1298662	34	2.0	32	88	11	96	38	16	15	29	1.90
1305034--1305385	78	4.5	78	78	6	336	27	19	13	39	1.89
1305088--1305385	157	1.9	157	82	4	379	27	19	13	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1314716--1314741	13	2.0	13	100	0	52	30	15	15	38	1.88
1314801--1314873	20	3.6	20	81	3	101	31	19	13	35	1.91
1314780--1314873	41	2.3	41	96	0	170	30	18	12	38	1.88
1314780--1314855	21	3.7	21	78	3	91	30	17	11	40	1.85
1315299--1315323	13	1.9	13	100	0	50	32	16	16	36	1.90
1315282--1315343	33	1.9	33	90	3	99	37	19	9	33	1.84
1321624--1321681	21	2.7	22	81	5	75	39	15	13	31	1.86
1321717--1321784	19	3.9	19	78	21	85	35	10	14	39	1.80
1321719--1321779	32	1.9	32	96	0	113	34	9	16	39	1.82
1321824--1321849	13	2.0	13	100	0	52	30	15	15	38	1.88

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