genome.fa.s16.2.7.7.80.10.50.1000.9.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: Scaffold16
Parameters: 2 7 7 80 10 50 1000
Length:  5287347

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   25   26   27   28   29   30   31   32   
          33   34   35   

This is table  9  of  35  ( 4175 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)
1229840--1230196	45	8.0	44	77	7	285	22	24	14	38	1.91
1229955--1230196	44	5.5	44	75	5	202	21	23	15	39	1.91
1231625--1231697	38	1.9	38	86	5	103	21	8	9	60	1.54
1231737--1232166	159	2.7	161	83	6	555	28	12	6	52	1.63
1231958--1231999	21	2.0	20	82	13	50	23	14	7	54	1.64
1231737--1232247	166	3.1	164	79	8	562	30	12	6	51	1.64
1232442--1232473	8	4.2	8	92	7	50	18	0	0	81	0.70
1232763--1232823	30	2.0	32	84	12	83	73	0	19	6	1.04
1233411--1233510	50	2.0	50	96	0	182	20	6	22	52	1.68
1233973--1233998	5	5.2	5	100	0	52	61	0	0	38	0.96
1233874--1234074	98	2.0	99	87	0	287	38	8	12	40	1.73
1240916--1241076	50	3.1	49	81	15	184	38	0	3	57	1.21
1240918--1241077	52	3.1	52	80	13	188	37	0	3	58	1.21
1247753--1247854	46	2.2	46	89	0	150	29	6	22	41	1.80
1247823--1247945	47	2.6	49	77	2	124	33	4	18	43	1.72
1253973--1254101	52	2.5	52	96	0	231	30	17	17	34	1.93
1253973--1254121	52	2.9	51	89	4	219	31	17	17	33	1.93
1254110--1254134	13	1.9	13	100	0	50	36	16	16	32	1.90
1255224--1255248	13	1.9	13	100	0	50	36	16	16	32	1.90
1255289--1255355	33	2.0	33	88	0	98	40	14	11	32	1.83
1255311--1255335	13	1.9	13	100	0	50	32	16	16	36	1.90
1256504--1256633	46	2.8	45	76	10	129	30	8	19	41	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1259685--1259836	52	2.8	54	80	3	182	35	15	23	25	1.94
1259793--1259878	42	2.0	42	93	0	145	29	18	24	27	1.98
1259999--1260521	28	17.7	30	77	10	354	25	16	28	29	1.97
1260405--1260456	27	2.0	26	88	3	77	17	17	30	34	1.93
1261937--1262010	1	74.0	1	79	0	76	0	1	9	89	0.55
1261937--1262010	28	2.6	28	87	12	107	0	1	9	89	0.55
1271697--1271723	10	2.7	10	100	0	54	77	22	0	0	0.76
1275880--1275932	20	2.7	20	100	0	106	33	11	18	35	1.87
1275900--1276015	52	2.2	52	93	3	198	30	17	18	33	1.94
1275900--1276035	52	2.6	51	86	4	191	31	16	19	32	1.94
1276024--1276048	13	1.9	13	100	0	50	36	16	16	32	1.90
1276087--1276144	20	3.0	20	84	2	73	46	13	10	29	1.77
1277291--1277420	46	2.8	45	76	10	129	30	8	19	41	1.81
1279586--1279861	139	2.0	138	83	4	351	34	8	15	41	1.78
1285517--1285586	33	2.1	33	86	0	95	34	12	14	38	1.84
1285659--1285780	52	2.3	53	94	4	212	34	18	18	29	1.94
1293878--1293915	16	2.3	17	86	4	51	44	23	5	26	1.74
1294039--1294127	31	2.9	31	91	3	146	23	33	19	23	1.97
1294039--1294280	63	3.9	62	83	10	169	23	33	15	27	1.95
1294114--1294414	34	9.2	33	84	11	295	20	33	13	32	1.92
1294114--1294419	63	4.7	62	81	14	316	20	33	13	33	1.91
1294128--1294419	97	3.0	97	82	10	341	20	33	13	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1294123--1294472	139	2.6	137	80	14	335	21	34	12	31	1.91
1294427--1294553	33	3.9	33	88	8	188	29	33	18	18	1.95
1294421--1294557	65	2.1	65	90	2	213	27	35	17	19	1.95
1294558--1295661	49	22.7	49	84	5	1372	25	25	17	31	1.97
1294553--1295576	98	10.5	98	91	4	1513	25	26	17	31	1.97
1294558--1295927	195	6.9	196	84	8	1553	25	25	17	31	1.97
1295244--1295605	92	3.9	93	90	5	468	25	25	18	30	1.98
1295746--1295927	43	3.8	48	83	10	239	25	25	18	30	1.98
1295746--1295936	95	2.0	92	88	5	276	25	26	17	30	1.97
1295837--1295975	52	2.6	52	82	4	161	25	25	15	33	1.95
1295476--1296056	266	2.2	265	96	0	1063	24	25	15	34	1.95
1296822--1296846	13	1.9	13	100	0	50	36	16	16	32	1.90
1296802--1296871	33	2.1	33	89	0	104	34	11	14	40	1.82
1296943--1297063	52	2.3	52	94	2	208	33	18	18	29	1.94
1308584--1308919	109	3.1	108	86	1	442	33	15	17	33	1.91
1309276--1309300	12	2.1	12	100	0	50	24	20	32	24	1.98
1309505--1309558	7	7.6	7	82	12	56	0	22	0	77	0.76
1309504--1309571	11	6.3	11	75	14	70	0	26	0	73	0.83
1309504--1309558	18	3.3	18	75	14	64	0	23	0	76	0.79
1309504--1309558	25	2.2	24	84	9	74	0	23	0	76	0.79
1309525--1309567	18	2.3	18	84	4	50	0	27	0	72	0.85
1310177--1310209	9	3.7	9	95	0	57	3	0	15	81	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1310527--1310935	28	15.0	27	77	7	330	22	17	29	31	1.96
1310695--1310901	108	1.9	105	84	7	274	20	18	28	31	1.97
1310599--1311040	54	8.4	52	73	14	241	21	17	29	31	1.96
1310942--1311040	26	3.7	26	84	2	126	17	16	32	34	1.92
1310942--1311054	54	2.1	54	80	6	122	20	16	29	33	1.95
1310827--1311055	122	1.9	121	85	3	316	20	16	30	32	1.95
1312221--1312254	14	2.3	15	85	5	52	0	2	8	88	0.62
1312251--1312280	15	1.9	16	93	6	53	0	10	10	80	0.92
1312232--1312287	27	2.1	27	83	12	71	3	8	10	76	1.12
1316728--1316794	33	2.0	33	88	0	98	34	11	13	40	1.81
1316748--1316772	13	1.9	13	100	0	50	36	16	16	32	1.90
1316835--1316859	13	1.9	13	100	0	50	32	16	16	36	1.90
1316868--1316987	52	2.3	52	94	4	208	33	18	18	30	1.95
1326239--1326264	13	2.0	13	100	0	52	30	15	15	38	1.88
1328234--1328363	51	2.5	51	86	1	170	45	9	16	29	1.78
1328327--1328383	20	2.8	20	89	0	78	40	14	12	33	1.83
1328724--1328778	20	2.8	20	85	0	74	43	14	9	32	1.77
1328725--1328786	20	3.1	20	79	9	72	41	16	9	32	1.80
1328702--1328849	79	1.9	79	87	2	217	43	15	14	27	1.85
1332653--1332678	13	2.0	13	100	0	52	30	15	15	38	1.88
1332632--1332696	32	2.0	33	90	6	105	29	12	15	43	1.83
1334650--1334692	20	2.1	20	82	4	50	11	30	41	16	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1335133--1335168	13	2.8	13	95	0	63	30	13	19	36	1.91
1337236--1337271	15	2.3	15	90	4	54	11	19	16	52	1.73
1339073--1339117	21	2.1	21	84	8	56	22	20	4	53	1.63
1341841--1341866	13	2.0	13	100	0	52	30	15	15	38	1.88
1341820--1341884	32	2.0	34	90	6	107	27	12	15	44	1.82
1341938--1341991	20	2.7	20	88	5	74	25	14	18	40	1.89
1344169--1344344	32	5.5	32	77	5	133	19	13	32	35	1.90
1344182--1344318	64	2.1	64	87	2	195	18	13	33	33	1.91
1344441--1344516	35	2.2	34	84	11	93	48	7	18	25	1.74
1344468--1344549	33	2.5	33	82	9	96	52	8	17	21	1.71
1348111--1348165	20	2.8	20	83	5	67	32	12	12	41	1.81
1359236--1359396	84	1.9	84	82	7	202	52	3	18	25	1.60
1361469--1362234	49	16.1	49	84	6	1022	32	17	24	24	1.97
1361474--1362229	92	8.0	92	90	4	1152	31	18	24	25	1.97
1361469--1362229	141	5.4	141	84	7	970	32	18	24	25	1.97
1362441--1362595	27	5.2	27	78	13	121	29	14	38	18	1.90
1362508--1362629	60	2.0	63	88	7	189	27	13	37	20	1.91
1362563--1363553	37	27.8	35	87	6	1240	34	11	34	19	1.88
1362563--1363553	71	13.9	71	87	6	1270	34	11	34	19	1.88
1362563--1363553	108	9.3	105	87	7	1260	34	11	34	19	1.88
1371852--1371992	52	2.7	52	91	2	230	31	17	17	33	1.94
1371981--1372005	13	1.9	13	100	0	50	36	16	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1372071--1372095	13	1.9	13	100	0	50	32	16	16	36	1.90
1372049--1372115	33	2.0	33	88	0	98	40	13	11	34	1.81
1372153--1372194	21	2.0	21	90	0	66	35	14	14	35	1.86
1373463--1373487	13	1.9	13	100	0	50	36	16	16	32	1.90
1374342--1374444	46	2.2	46	96	0	188	30	4	34	30	1.78
1380721--1380851	52	2.5	52	92	0	208	31	16	18	34	1.93
1380721--1380871	52	2.9	51	86	3	196	32	15	18	33	1.93
1389806--1390174	182	2.0	182	90	4	575	31	18	16	33	1.93
1393927--1394141	93	2.3	93	84	0	277	28	10	27	33	1.89
1397177--1397302	55	2.3	55	94	0	216	29	18	11	40	1.86

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   25   26   27   28   29   30   31   32   
          33   34   35