genome.fa.s371.2.7.7.80.10.50.1000.5.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: scaffold160
Parameters: 2 7 7 80 10 50 1000
Length:  1852349

Tables:   1   2   3   4   5   6   

This is table  5  of  6  ( 718 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)
1168789--1168851	27	2.3	26	86	5	81	41	23	20	14	1.89
1178024--1178085	28	2.2	29	79	2	72	27	6	12	53	1.63
1181221--1181258	18	2.1	18	90	0	58	42	21	15	21	1.89
1181406--1181483	38	2.0	39	90	7	124	51	25	2	20	1.60
1181614--1181679	17	3.7	17	71	11	60	34	3	15	46	1.61
1181611--1181682	37	1.9	37	91	0	117	36	2	15	45	1.60
1182619--1182650	8	3.9	8	95	4	55	0	12	0	87	0.54
1182617--1182651	18	1.9	18	94	0	61	0	11	0	88	0.51
1185156--1185192	18	2.1	18	89	0	56	48	10	16	24	1.77
1188315--1188388	27	2.7	28	74	17	82	31	14	9	44	1.77
1204000--1204126	48	2.7	48	77	10	118	27	3	3	66	1.22
1204075--1204121	9	4.8	10	84	12	53	34	0	0	65	0.93
1204088--1204185	9	10.5	10	69	15	50	32	3	1	63	1.17
1204007--1204185	19	9.6	18	68	17	80	30	3	2	63	1.25
1204095--1204144	26	1.9	26	84	8	66	36	0	2	62	1.07
1204084--1204153	35	2.0	35	83	5	88	34	1	1	62	1.13
1204882--1204933	23	2.3	23	80	6	61	28	11	1	57	1.44
1205274--1205328	25	2.2	25	100	0	110	67	14	7	10	1.41
1214887--1214918	11	2.6	13	90	9	50	37	12	12	37	1.81
1218788--1218824	18	2.0	19	89	5	58	70	5	2	21	1.20
1220484--1220650	45	3.7	45	82	4	169	25	26	20	27	1.99
1220805--1221329	267	2.0	267	87	0	755	25	25	20	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1222226--1222274	25	1.9	26	87	4	73	59	10	16	14	1.61
1227476--1227592	52	2.3	49	83	9	139	28	14	8	48	1.73
1228906--1228960	25	2.1	27	93	6	96	54	3	10	30	1.52
1230757--1230824	31	2.2	31	83	0	91	30	14	11	42	1.82
1235041--1235081	5	8.6	5	81	10	50	73	2	2	21	1.07
1235028--1235073	18	2.5	18	83	13	58	67	4	2	26	1.21
1235041--1235077	18	2.1	18	89	0	56	72	2	2	21	1.09
1237583--1238970	282	4.9	282	86	3	1814	25	22	18	33	1.96
1237638--1238955	561	2.3	562	87	2	1860	25	22	17	33	1.96
1245543--1245605	31	2.0	31	100	0	126	46	15	3	34	1.62
1248410--1248569	56	2.8	56	82	4	205	33	13	22	30	1.92
1250252--1250339	45	2.0	44	95	2	158	45	9	13	31	1.75
1251485--1251514	15	2.0	15	93	0	51	56	10	0	33	1.32
1276041--1276117	33	2.3	33	100	0	154	45	22	16	15	1.85
1276460--1276523	33	1.9	33	84	6	85	21	23	23	31	1.99
1278566--1278657	42	2.2	42	98	0	175	20	28	29	21	1.98
1284153--1284177	13	1.9	13	100	0	50	40	24	8	28	1.83
1293855--1293894	12	3.2	13	86	10	57	30	40	22	7	1.81
1302759--1302814	25	2.4	22	78	16	67	21	14	48	16	1.81
1302765--1302818	25	2.2	25	93	0	90	22	12	48	16	1.80
1303274--1303305	10	3.2	10	95	0	55	9	46	0	43	1.35
1303984--1304631	27	23.7	27	82	5	683	39	19	15	24	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1304082--1304149	34	2.0	35	88	2	102	36	17	20	25	1.94
1307739--1307792	25	2.2	25	89	0	81	22	12	46	18	1.83
1307903--1307945	13	3.3	14	78	18	56	37	0	34	27	1.57
1308946--1309367	27	15.6	27	83	2	499	39	20	15	24	1.91
1309993--1310018	10	2.6	10	100	0	52	11	7	11	69	1.37
1312780--1312843	12	5.5	12	74	7	60	26	6	17	50	1.69
1312769--1312848	23	3.5	23	92	0	142	28	7	15	48	1.71
1315025--1315089	27	2.4	27	87	2	87	33	15	10	40	1.82
1315230--1315275	6	7.5	6	83	11	58	19	15	0	65	1.28
1317945--1317974	15	2.0	15	93	0	51	13	20	36	30	1.90
1323555--1323598	21	2.1	21	83	8	54	63	2	9	25	1.35
1328530--1328722	51	3.8	51	81	4	201	32	30	13	23	1.94
1328527--1328720	102	1.9	102	83	2	255	32	30	13	23	1.93
1331529--1331602	26	2.8	25	79	8	76	47	1	4	47	1.29
1331493--1331701	90	2.3	90	99	0	409	44	1	6	47	1.39
1331619--1331692	26	2.8	25	79	8	76	47	1	4	47	1.29
1336059--1336092	6	5.7	6	96	0	59	17	26	0	55	1.42
1337902--1337987	45	1.9	45	90	0	136	37	6	2	53	1.41
1349012--1349043	2	16.0	2	100	0	64	50	0	0	50	1.00
1349126--1349158	15	2.2	15	89	10	50	30	0	12	57	1.35
1351123--1351159	9	4.1	9	92	0	56	37	29	0	32	1.58
1351106--1351159	18	3.0	18	86	0	63	37	27	5	29	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1352279--1352308	13	2.3	13	94	0	51	53	13	10	23	1.69
1352889--1352933	23	2.0	23	82	8	56	24	15	6	53	1.66
1370252--1370284	17	1.9	17	88	11	50	66	6	0	27	1.15
1370074--1370426	176	2.0	176	99	0	697	48	9	13	28	1.73
1395140--1395183	15	2.9	15	89	0	70	31	36	13	18	1.90
1395212--1395272	18	3.6	18	68	28	51	21	34	21	22	1.97
1395203--1395270	33	2.1	33	91	0	109	22	36	22	19	1.95
1395479--1395519	21	2.0	21	85	9	57	21	26	21	29	1.99
1397328--1397405	28	2.8	28	84	5	95	44	1	6	47	1.36
1409423--1409455	16	2.1	16	88	11	50	57	3	0	39	1.14
1409604--1409636	16	2.1	16	88	11	50	57	3	0	39	1.14
1409364--1409726	181	2.0	182	99	0	719	52	9	6	31	1.59
1409936--1409988	14	3.7	14	77	5	52	15	11	5	67	1.38
1411395--1411445	18	2.7	19	81	3	50	35	1	3	58	1.28
1413833--1413900	21	3.3	21	77	4	84	22	7	14	55	1.63
1417154--1417209	28	2.0	28	100	0	112	28	42	0	28	1.56
1422671--1422735	29	2.2	31	88	8	107	24	26	3	46	1.67
1441853--1441990	67	2.0	68	80	5	154	55	13	10	20	1.67
1447629--1447685	30	1.9	30	82	13	73	24	28	28	19	1.98
1458014--1458040	5	5.4	5	100	0	54	18	0	0	81	0.69
1459120--1459199	42	1.9	42	84	5	108	27	12	23	36	1.91
1472906--1472942	18	2.1	18	100	0	74	62	10	10	16	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1472949--1472996	24	1.9	26	83	8	64	0	31	4	64	1.12
1473724--1473785	31	2.0	31	93	0	106	40	20	14	24	1.90
1490915--1490960	22	2.1	22	95	0	83	63	8	4	23	1.42
1492344--1492390	22	2.1	22	92	0	76	14	23	17	44	1.85
1494318--1494371	26	2.1	26	89	6	83	22	31	7	38	1.82
1499150--1499175	1	26.0	1	100	0	52	0	0	0	100	0.00
1499221--1499247	1	27.0	1	100	0	54	0	0	0	100	0.00
1513528--1513661	40	3.3	40	76	5	110	40	23	18	17	1.91
1513840--1513947	54	2.0	54	94	0	189	22	25	22	29	1.99
1513904--1514036	41	3.2	41	81	2	133	21	24	26	27	1.99
1514036--1514071	18	2.1	18	94	5	65	52	5	5	36	1.48
1525038--1525202	65	2.5	64	83	7	190	38	18	28	13	1.90
1525062--1525202	66	2.2	65	86	8	189	38	17	29	14	1.89
1525575--1526104	43	12.4	43	88	1	724	25	20	29	24	1.99
1532348--1532400	26	2.0	26	88	0	79	32	7	24	35	1.84
1532348--1532398	13	3.9	13	78	0	66	31	7	25	35	1.85
1535110--1535149	19	2.1	19	100	0	80	70	5	10	15	1.32
1536539--1536622	21	4.2	20	76	8	64	34	7	3	54	1.45
1537480--1537506	14	1.9	14	100	0	54	51	0	3	44	1.19
1545776--1545829	24	2.2	25	83	9	67	44	0	1	53	1.11
1545953--1546057	44	2.5	40	76	15	113	31	29	4	34	1.78
1545951--1546060	45	2.6	44	81	8	131	31	29	5	33	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1546039--1546092	16	3.4	16	94	0	90	31	35	0	33	1.58
1546455--1546490	17	2.1	17	90	10	56	52	0	5	41	1.24
1547425--1547506	30	2.7	30	94	0	137	21	30	30	17	1.96
1552342--1552402	21	2.8	23	78	14	76	14	24	26	34	1.94
1552353--1552415	21	3.0	21	83	2	83	15	25	25	33	1.95
1555093--1555155	29	2.2	31	78	16	73	14	9	3	73	1.21
1555690--1555734	11	3.9	12	77	16	51	24	31	2	42	1.67
1555690--1555742	22	2.4	21	81	15	54	26	28	1	43	1.65
1555702--1555801	51	2.0	51	90	4	157	26	25	2	47	1.63
1555804--1555844	14	2.9	15	78	10	50	56	0	0	43	0.99

Tables:   1   2   3   4   5   6