genome.fa.s49.2.7.7.80.10.50.1000.8.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: Scaffold49
Parameters: 2 7 7 80 10 50 1000
Length:  1668912

Tables:   1   2   3   4   5   6   7   8   9   

This is table  8  of  9  ( 1071 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)
1266661--1266710	19	2.5	20	84	12	68	26	18	16	40	1.90
1269029--1269144	51	2.3	51	81	0	133	30	26	9	33	1.88
1269127--1269199	28	2.6	27	89	8	103	21	31	20	26	1.98
1269234--1269310	28	2.7	29	88	7	106	23	29	19	27	1.98
1269293--1269462	51	3.3	50	76	13	159	28	25	12	32	1.93
1269077--1269357	110	2.6	108	80	7	363	27	24	14	33	1.94
1269416--1269614	79	2.5	78	77	9	224	30	23	11	35	1.90
1274568--1274602	18	1.9	18	94	0	61	22	25	11	40	1.88
1280646--1280691	3	15.0	3	90	4	74	30	0	0	69	0.89
1281727--1281776	19	2.7	18	87	6	73	34	0	0	66	0.92
1282244--1282313	18	3.9	17	80	12	70	62	0	0	37	0.95
1282264--1282306	22	2.0	22	90	4	70	62	0	0	37	0.95
1282256--1282306	22	2.3	23	86	3	68	60	0	0	39	0.97
1282330--1282372	21	2.0	21	86	0	59	39	0	0	60	0.97
1282334--1282382	23	2.0	25	84	7	66	36	0	4	59	1.17
1282442--1282466	13	1.9	13	100	0	50	68	0	0	32	0.90
1282937--1282993	16	3.6	16	87	0	87	54	0	0	45	0.99
1284100--1284172	25	2.9	24	77	18	69	43	0	2	53	1.15
1284140--1284217	28	2.9	27	74	14	81	48	1	0	50	1.09
1284153--1284199	14	3.4	15	80	13	57	44	0	0	55	0.99
1287572--1287620	10	4.7	10	82	9	62	83	0	14	2	0.73
1287573--1287621	16	3.0	17	80	17	59	81	0	14	4	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1288424--1288473	4	12.2	4	83	12	66	70	0	2	28	0.99
1288767--1289208	156	2.9	156	79	8	406	24	15	19	40	1.91
1288815--1289208	147	2.6	151	79	3	436	25	15	19	39	1.91
1290956--1290989	15	2.3	15	94	0	59	29	14	5	50	1.67
1291546--1291670	40	3.1	41	74	12	125	36	11	8	43	1.72
1291519--1291647	40	3.2	41	72	13	126	37	10	8	42	1.71
1291527--1291689	80	2.0	80	85	2	220	38	14	7	40	1.73
1291531--1291719	80	2.4	80	82	3	211	38	13	8	39	1.77
1297520--1297558	21	1.9	20	94	5	69	35	10	12	41	1.77
1299238--1299292	19	2.8	19	91	2	83	36	14	18	30	1.91
1299277--1299303	13	2.1	13	100	0	54	40	14	14	29	1.86
1305943--1305975	13	2.5	13	95	0	57	27	15	0	57	1.38
1308030--1308054	13	1.9	13	100	0	50	32	16	16	36	1.90
1308104--1308159	19	2.9	19	86	2	76	35	12	17	33	1.88
1308125--1308187	32	1.9	33	87	9	94	41	12	15	30	1.85
1310435--1310468	18	1.9	18	94	5	61	85	0	2	11	0.71
1311979--1312168	28	6.8	28	76	1	166	28	28	19	23	1.98
1312211--1312468	43	5.6	43	68	17	131	27	25	14	32	1.95
1312211--1312519	95	3.3	95	82	2	345	26	25	15	32	1.95
1312418--1312532	52	2.2	51	89	1	167	26	27	13	31	1.94
1312555--1312683	61	2.1	61	89	0	195	22	25	12	39	1.89
1312660--1312693	18	1.9	17	88	5	50	17	29	0	52	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1313384--1313446	33	1.9	33	86	0	90	36	14	11	38	1.81
1313417--1313547	50	2.6	51	83	6	160	30	16	13	39	1.87
1319023--1319047	13	1.9	13	100	0	50	32	16	16	36	1.90
1319003--1319070	33	2.1	32	88	2	100	35	14	14	35	1.87
1325237--1325275	13	3.0	13	96	0	69	30	17	15	35	1.91
1327812--1327879	33	2.1	33	91	2	111	35	16	14	33	1.89
1327832--1327856	13	1.9	13	100	0	50	32	16	16	36	1.90
1330085--1330137	27	2.0	26	82	10	63	43	3	7	45	1.50
1330213--1330263	6	8.5	6	86	0	75	29	0	21	49	1.50
1330213--1330263	12	4.2	12	97	0	93	29	0	21	49	1.50
1330698--1330740	22	2.0	21	86	9	59	30	0	9	60	1.28
1332007--1332107	48	2.1	48	82	8	118	44	16	13	24	1.85
1332625--1333000	157	2.4	155	81	6	402	38	17	12	31	1.87
1334490--1334515	12	2.2	12	100	0	52	69	0	0	30	0.89
1336939--1337090	29	5.2	29	64	12	78	48	16	10	24	1.77
1336902--1337246	116	3.0	116	79	5	336	44	15	12	26	1.83
1336899--1337091	58	3.3	58	71	3	145	47	16	10	25	1.79
1336943--1337245	58	5.2	58	71	8	166	45	16	12	25	1.82
1336922--1337296	117	3.2	116	76	7	328	44	16	13	25	1.84
1343986--1344039	3	18.0	3	92	0	90	64	3	0	31	1.11
1351345--1351446	52	2.0	52	90	3	161	33	10	7	48	1.67
1356075--1356109	2	17.5	2	100	0	70	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1356177--1356212	18	2.0	18	88	0	54	41	2	8	47	1.48
1358765--1358815	20	2.5	20	96	0	93	31	15	13	39	1.87
1361477--1361519	21	2.0	21	86	0	59	53	27	4	13	1.60
1369418--1369459	13	3.2	13	89	0	66	38	21	11	28	1.89
1369459--1369490	10	3.2	10	90	0	55	40	3	28	28	1.71
1373718--1373770	6	8.8	6	97	0	97	49	15	1	33	1.55
1374082--1374121	15	2.6	16	84	4	55	70	5	2	22	1.19
1376525--1376680	84	1.8	85	87	1	233	36	14	17	31	1.90
1379349--1379407	7	8.3	7	73	17	50	81	0	15	3	0.82
1379351--1379406	9	6.4	9	76	15	55	83	0	12	3	0.76
1379351--1379397	24	1.9	25	91	4	78	82	0	12	4	0.80
1386242--1386276	2	17.5	2	100	0	70	48	0	0	51	1.00
1403145--1403204	30	2.1	28	87	9	86	30	3	1	65	1.19
1403149--1403212	30	2.2	29	86	5	85	31	1	3	64	1.19
1409373--1409412	17	2.4	17	100	0	80	25	22	25	27	2.00
1411085--1411113	2	14.5	2	100	0	58	51	0	0	48	1.00
1412225--1412269	20	2.2	20	84	7	56	40	0	0	60	0.97
1412236--1412312	40	1.9	40	86	0	109	33	1	3	61	1.23
1412386--1412438	25	2.2	25	80	9	67	37	3	1	56	1.28
1412778--1412810	13	2.4	14	95	5	59	51	0	0	48	1.00
1412975--1413021	3	16.7	3	86	8	55	65	0	0	34	0.93
1412935--1413021	39	2.2	39	82	8	106	60	5	0	33	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1413169--1413223	13	4.2	13	78	17	51	43	3	0	52	1.18
1414689--1414714	13	2.0	13	100	0	52	23	15	30	30	1.95
1415035--1415067	2	16.5	2	93	0	57	48	3	0	48	1.17
1430189--1430233	23	1.9	23	82	13	56	44	8	20	26	1.80
1437585--1437755	79	2.2	78	81	5	193	34	17	23	23	1.96
1440343--1440473	34	3.7	35	81	10	142	37	16	27	18	1.92
1440525--1441328	61	13.1	61	81	6	759	29	18	25	26	1.98
1440525--1441339	183	4.4	183	82	7	907	29	18	24	26	1.98
1440533--1441328	122	6.5	123	82	7	861	29	18	25	26	1.98
1443092--1443162	28	2.5	28	80	13	83	22	16	35	25	1.95
1443100--1443323	108	2.1	109	88	2	326	28	13	28	29	1.95
1443208--1443274	27	2.4	27	85	2	80	23	20	31	23	1.98
1443259--1443389	51	2.5	51	80	9	156	32	10	25	31	1.90
1445774--1445839	10	7.0	9	77	19	55	3	10	3	83	0.87
1445777--1445811	15	2.2	16	90	5	54	0	17	0	82	0.66
1445797--1445840	11	3.9	11	85	5	52	4	4	6	84	0.88
1445789--1445838	18	2.8	18	80	14	50	4	6	4	86	0.80
1458149--1458354	79	2.6	79	79	5	200	36	12	23	27	1.91
1458299--1458407	51	2.1	51	84	3	148	32	14	23	29	1.94
1460206--1460237	14	2.2	15	94	5	57	12	0	46	40	1.42
1462790--1462887	51	1.9	50	85	6	135	42	9	19	28	1.82
1462930--1463211	78	3.6	78	78	13	267	36	10	23	29	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1462903--1463258	79	4.5	77	79	12	334	37	10	23	28	1.88
1462915--1463258	157	2.2	156	82	7	412	38	10	22	28	1.87
1465591--1465647	20	2.7	21	81	8	71	43	8	14	33	1.76
1466120--1466300	68	2.7	68	81	0	209	35	25	12	25	1.92
1467556--1467605	22	2.3	22	78	0	55	34	10	18	38	1.84
1469923--1470582	79	8.3	79	78	7	484	28	21	11	39	1.88
1469923--1470582	237	2.8	236	80	6	669	28	21	11	39	1.88
1469922--1470580	158	4.2	158	79	6	611	28	21	11	39	1.88
1471372--1471630	135	1.9	135	86	0	356	23	21	21	33	1.97
1473711--1473752	20	2.1	20	82	8	50	69	11	7	11	1.37

Tables:   1   2   3   4   5   6   7   8   9