genome.fa.s1432.2.7.7.80.10.50.1000.5.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: scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  1915636

Tables:   1   2   3   4   5   6   

This is table  5  of  6  ( 644 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)
1316995--1317037	22	2.0	20	82	8	50	34	0	23	41	1.55
1319104--1319152	25	2.0	25	84	8	64	38	14	22	24	1.91
1319096--1319234	26	5.3	26	77	9	106	39	22	16	21	1.92
1319097--1319236	52	2.7	52	83	6	151	39	23	15	21	1.92
1319148--1319242	26	3.6	25	80	9	109	41	25	14	18	1.89
1319161--1319263	53	1.9	52	81	11	120	39	26	15	18	1.90
1326588--1326728	26	5.4	26	85	5	178	36	21	17	24	1.94
1326586--1326728	52	2.7	52	87	5	200	37	21	17	23	1.94
1327128--1327195	33	2.0	36	85	8	97	25	20	26	27	1.99
1327481--1327525	21	2.1	22	88	12	67	35	20	4	40	1.72
1327673--1327722	24	2.1	24	88	0	73	34	14	12	40	1.82
1327945--1328159	75	2.9	74	76	11	179	20	20	23	36	1.95
1340637--1340801	90	1.8	90	84	0	222	24	14	23	37	1.92
1340641--1340840	45	4.5	44	78	6	152	23	14	26	37	1.92
1353823--1353858	15	2.4	15	85	0	54	11	22	8	58	1.59
1356122--1356322	27	7.5	27	84	3	226	19	18	19	41	1.90
1357790--1358177	27	14.4	27	83	0	407	19	17	20	43	1.89
1359543--1359805	27	9.8	25	80	7	204	20	16	20	43	1.88
1359543--1359805	54	4.9	53	82	3	296	20	16	20	43	1.88
1359543--1359805	81	3.3	78	84	4	321	20	16	20	43	1.88
1368802--1368835	17	1.9	18	88	5	52	55	8	2	32	1.45
1368795--1368841	18	2.5	19	76	13	53	59	6	4	29	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1381795--1381938	41	3.5	41	88	0	207	25	22	21	30	1.99
1386807--1386907	21	4.8	20	76	11	87	47	0	18	32	1.56
1386814--1386880	7	9.6	7	76	12	66	52	1	13	32	1.50
1393138--1393175	2	19.0	2	100	0	76	50	0	50	0	1.00
1394078--1394108	5	6.2	5	100	0	62	41	0	0	58	0.98
1397056--1397086	16	2.0	16	93	6	55	41	12	0	45	1.42
1400814--1400846	11	2.9	11	95	4	57	36	6	12	45	1.66
1412021--1412351	147	2.3	145	86	6	456	42	4	9	42	1.58
1412470--1412494	13	1.9	13	100	0	50	0	12	0	88	0.53
1415753--1415794	21	2.0	21	90	0	66	35	16	2	45	1.61
1418013--1418055	19	2.4	17	78	21	52	34	0	18	46	1.50
1418135--1418245	51	2.2	51	98	0	213	32	14	23	29	1.94
1426047--1426089	12	3.4	12	81	9	50	76	18	4	0	0.95
1426495--1427009	42	12.3	42	85	0	652	20	17	24	36	1.94
1427842--1428161	145	2.2	145	81	10	359	40	4	10	45	1.59
1429267--1429310	3	14.7	3	100	0	88	68	0	0	31	0.90
1430014--1430057	3	14.7	3	100	0	88	68	0	0	31	0.90
1428649--1430136	747	2.0	744	93	1	2581	36	8	11	43	1.72
1430815--1430886	20	3.7	20	81	7	69	58	4	1	36	1.26
1430823--1430879	19	2.9	19	84	7	71	56	1	1	40	1.20
1437354--1437397	22	2.0	22	100	0	88	59	13	9	18	1.60
1447018--1447201	96	1.9	96	100	0	368	25	29	14	30	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1461144--1461169	12	2.2	12	100	0	52	57	7	15	19	1.62
1463530--1463570	20	2.0	21	85	4	57	14	9	19	56	1.66
1469240--1469303	13	4.5	14	70	16	51	59	1	1	37	1.16
1472201--1472242	21	2.0	21	95	0	75	14	26	19	40	1.89
1472222--1472398	40	4.5	40	86	3	234	14	19	27	38	1.90
1472221--1472398	79	2.3	79	93	0	302	14	19	26	39	1.90
1480858--1480882	10	2.5	10	100	0	50	8	12	0	80	0.92
1484578--1484611	17	1.9	18	88	5	52	52	0	8	38	1.33
1484829--1484870	3	14.0	3	84	0	57	64	2	2	30	1.19
1484829--1484870	15	2.8	15	92	0	66	64	2	2	30	1.19
1484829--1484886	15	3.7	15	88	6	62	63	1	3	31	1.21
1486416--1486628	44	4.8	45	82	3	243	27	20	21	31	1.98
1486416--1486632	89	2.4	86	81	7	220	27	20	21	31	1.98
1486768--1487110	44	7.9	44	74	12	293	26	21	20	31	1.98
1486729--1487119	129	3.0	129	90	3	585	27	20	20	30	1.98
1486768--1487110	85	4.0	85	75	11	279	26	21	20	31	1.98
1486792--1487169	44	8.7	44	72	12	230	25	21	21	31	1.98
1496898--1496938	13	3.1	14	79	10	50	51	17	14	17	1.77
1498109--1498160	6	8.7	6	100	0	104	84	0	0	15	0.62
1501415--1501445	14	2.2	14	100	0	62	80	0	12	6	0.89
1503125--1503178	23	2.2	24	81	18	60	18	12	27	40	1.87
1504803--1505099	50	5.8	52	79	8	272	28	21	27	21	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1512260--1512555	50	5.8	50	82	6	276	27	21	29	21	1.99
1512260--1512551	100	2.9	99	81	7	304	27	21	28	21	1.99
1518917--1518978	21	2.9	21	73	4	52	30	4	3	61	1.33
1528740--1528771	14	2.3	14	100	0	64	18	31	0	50	1.48
1531677--1531713	17	2.2	17	100	0	74	37	10	21	29	1.88
1545863--1545920	30	1.9	31	82	10	75	39	3	3	53	1.35
1547780--1547826	24	2.0	24	92	8	80	59	0	0	40	0.97
1547783--1547838	24	2.6	22	81	16	64	60	0	0	39	0.97
1551317--1551512	99	2.0	99	93	0	338	41	13	22	22	1.88
1552339--1552363	6	4.2	6	100	0	50	16	0	0	84	0.63
1564448--1564710	131	2.0	132	98	0	510	41	17	12	29	1.86
1568977--1569051	38	2.0	38	84	10	100	17	17	28	37	1.92
1573682--1573719	13	3.0	13	80	7	51	42	0	0	57	0.98
1576207--1576253	3	15.7	3	95	0	58	57	8	0	34	1.29
1585931--1585989	29	2.0	29	100	0	118	35	16	13	33	1.88
1590149--1590240	29	3.1	29	85	1	130	19	11	11	56	1.66
1590157--1590250	29	3.2	29	76	11	95	21	12	12	53	1.72
1596627--1596660	16	2.1	17	88	5	52	11	0	11	76	1.02
1621689--1621769	40	2.0	40	100	0	162	35	24	17	22	1.95
1622799--1622829	15	2.1	15	93	0	53	35	25	16	22	1.94
1632025--1632119	25	3.8	25	76	5	84	31	18	24	25	1.98
1632009--1632119	50	2.2	50	85	3	143	30	19	24	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1637512--1637537	11	2.4	11	100	0	52	50	7	0	42	1.31
1639743--1639788	23	2.0	24	82	4	58	28	2	15	54	1.53
1640790--1640819	16	1.9	16	93	6	53	50	20	0	30	1.49
1649659--1649701	21	2.0	21	91	8	70	32	4	18	44	1.71
1658931--1658966	19	2.0	17	89	10	54	44	0	25	30	1.54
1666212--1666891	345	2.0	345	100	0	1360	36	18	8	36	1.81
1684106--1684156	25	2.0	25	88	0	75	25	11	23	39	1.89
1686602--1686626	13	1.9	13	100	0	50	36	0	16	48	1.46
1692154--1692181	13	2.2	13	100	0	56	46	7	25	21	1.76
1710907--1710988	34	2.4	34	85	4	112	43	0	12	43	1.41
1711393--1711428	18	2.0	18	94	0	63	38	8	27	25	1.84
1712934--1713000	30	2.2	30	79	12	75	62	2	5	28	1.33
1716563--1716588	3	8.7	3	100	0	52	34	0	0	65	0.93
1724650--1724685	2	18.0	2	100	0	72	50	0	50	0	1.00
1725940--1726013	37	2.0	38	83	2	96	41	10	18	28	1.84
1726496--1726526	15	2.1	15	93	0	53	38	6	29	25	1.81
1727456--1727485	15	2.0	15	93	0	51	23	6	46	23	1.75
1730830--1730860	15	2.1	15	100	0	62	38	6	32	22	1.80
1733311--1733340	15	1.9	16	93	6	53	73	0	3	23	0.98
1740410--1740643	69	3.4	69	89	1	337	34	25	20	20	1.96
1740657--1740809	57	2.7	57	90	0	243	26	19	13	39	1.89
1744379--1744495	25	4.8	24	78	4	108	17	25	21	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1744405--1744502	49	2.0	49	84	7	128	17	25	20	36	1.94
1757969--1758365	70	5.7	70	82	2	431	27	18	23	30	1.98
1757969--1758367	140	2.9	140	86	1	550	27	18	23	31	1.97
1758730--1758780	23	2.2	23	89	0	75	41	19	9	29	1.84
1769551--1769604	21	2.6	21	83	13	60	48	0	7	44	1.31
1771767--1771793	14	1.9	14	100	0	54	55	14	14	14	1.70
1777546--1777590	22	2.0	22	95	0	81	31	11	8	48	1.69
1782133--1782157	3	8.3	3	100	0	50	32	0	68	0	0.90
1782660--1782703	19	2.2	20	96	4	81	6	22	0	70	1.11
1782662--1782719	20	2.8	22	76	12	68	5	25	0	68	1.10

Tables:   1   2   3   4   5   6