genome.fa.s40.2.7.7.80.10.50.1000.11.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:  3440810

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   

This is table  11  of  24  ( 2833 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)
1498625--1498665	16	2.6	16	96	0	73	9	7	19	63	1.48
1498679--1498709	16	1.9	16	100	0	62	29	0	6	64	1.18
1508946--1509033	46	1.9	46	81	4	106	45	4	4	45	1.44
1509032--1509075	23	1.9	23	81	9	54	34	4	4	56	1.40
1511073--1511098	13	2.0	13	100	0	52	38	15	15	30	1.88
1514704--1514728	13	1.9	13	100	0	50	36	16	16	32	1.90
1515564--1515616	27	2.0	27	100	0	106	30	1	30	37	1.68
1516772--1516797	13	2.0	13	100	0	52	38	15	15	30	1.88
1521342--1521565	111	2.0	112	87	4	328	38	13	10	37	1.80
1522409--1522464	16	3.4	16	75	25	55	32	1	1	64	1.14
1522409--1522451	15	2.9	14	83	16	52	34	0	0	65	0.93
1522662--1522707	19	2.6	18	83	10	58	30	13	0	56	1.37
1523094--1523141	12	4.0	11	77	17	51	39	0	0	60	0.97
1526097--1526148	16	3.3	15	79	10	59	25	3	0	71	1.03
1526639--1526679	15	2.8	15	88	3	57	73	7	0	19	1.07
1527315--1527354	18	2.2	18	86	8	55	65	2	0	32	1.06
1527632--1527714	2	43.0	2	73	7	64	50	1	1	46	1.16
1527670--1527722	6	8.7	6	81	4	52	60	1	0	37	1.08
1530694--1530732	12	3.4	11	82	10	51	53	0	0	46	1.00
1531248--1531279	2	16.0	2	100	0	64	50	0	0	50	1.00
1543619--1543714	42	2.3	42	92	0	165	30	16	14	38	1.89
1543703--1543753	19	2.6	19	84	3	66	29	17	11	41	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1543700--1543794	20	4.8	20	76	5	84	29	17	14	37	1.90
1546077--1546276	79	2.5	79	82	1	258	27	24	14	34	1.94
1546238--1546351	50	2.3	51	82	1	149	30	28	10	30	1.90
1546336--1546407	28	2.6	29	82	10	96	22	26	20	30	1.98
1546288--1546480	107	1.8	107	82	4	255	26	25	13	33	1.94
1546365--1546762	79	5.1	78	71	14	277	27	23	14	34	1.94
1552267--1552293	13	2.1	13	100	0	54	29	14	14	40	1.86
1552332--1552405	20	3.7	19	87	7	103	28	16	13	41	1.86
1554612--1554790	51	3.5	51	85	2	227	27	26	11	35	1.90
1554726--1555030	79	3.9	79	84	4	384	27	25	14	32	1.95
1554881--1555129	129	1.9	130	84	4	333	29	26	12	31	1.93
1554961--1555080	50	2.4	50	84	4	161	28	30	12	29	1.93
1554676--1555311	284	2.2	279	88	4	936	27	26	13	32	1.94
1555011--1555495	79	6.2	78	84	4	579	26	26	15	32	1.95
1557425--1557612	62	3.0	61	85	3	241	26	28	17	28	1.97
1557429--1557647	61	3.5	61	81	6	226	26	27	16	29	1.97
1557855--1557895	21	2.0	21	85	9	57	39	12	9	39	1.76
1557929--1558005	20	3.8	20	75	10	68	41	15	14	28	1.86
1558082--1558112	10	3.1	10	90	0	53	22	29	6	41	1.78
1558100--1558154	21	2.5	22	94	5	103	27	25	10	36	1.89
1558224--1558249	13	2.0	13	100	0	52	30	15	23	30	1.95
1559168--1560077	61	14.8	62	85	4	1071	25	26	19	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1559168--1560077	184	4.9	184	86	2	1231	25	26	19	28	1.99
1559994--1560227	105	2.2	105	93	0	396	22	31	17	28	1.97
1560178--1560783	134	4.5	134	88	1	854	19	28	12	39	1.88
1560166--1560798	269	2.4	269	87	2	898	20	28	12	39	1.88
1560699--1560848	42	3.5	42	79	9	126	20	24	14	40	1.90
1561621--1561673	19	2.7	19	82	2	70	24	16	16	41	1.89
1561657--1561687	13	2.4	13	94	0	53	29	12	19	38	1.89
1563830--1564022	79	2.4	79	85	0	269	27	24	14	32	1.94
1563830--1564049	79	2.8	78	81	4	262	29	25	13	32	1.93
1563988--1564105	51	2.3	51	75	2	130	32	26	11	30	1.91
1564090--1564163	28	2.7	27	85	8	87	21	27	21	29	1.99
1564119--1564296	79	2.2	79	80	3	205	24	25	17	32	1.97
1567357--1567391	17	2.0	18	88	5	54	54	11	2	31	1.51
1567469--1567500	14	2.4	14	94	5	57	12	9	0	78	0.97
1568347--1568404	27	2.1	27	81	6	64	44	1	1	51	1.21
1568352--1568404	28	1.9	27	84	3	70	43	1	1	52	1.23
1568359--1568416	21	2.7	21	75	17	57	37	3	1	56	1.26
1568925--1569023	13	7.8	13	65	20	50	37	1	0	61	1.03
1568963--1569014	22	2.3	22	83	3	68	36	0	0	63	0.95
1568953--1569023	35	2.0	35	86	10	101	36	0	0	63	0.95
1578095--1579021	288	3.3	279	77	8	791	23	21	13	41	1.88
1578872--1578905	16	2.2	15	89	5	50	2	20	0	76	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1580548--1580582	13	2.7	13	100	0	70	22	0	0	77	0.78
1581629--1581687	31	1.9	31	89	0	91	33	11	13	40	1.81
1581705--1581746	21	2.0	21	100	0	84	42	9	19	28	1.82
1581733--1581758	13	2.0	13	100	0	52	30	15	15	38	1.88
1584125--1584225	52	1.9	53	86	6	143	31	22	9	35	1.87
1584115--1584508	51	7.6	51	70	10	215	29	26	11	32	1.91
1584520--1584771	79	3.2	79	80	2	299	25	28	16	29	1.97
1586140--1586186	13	3.6	13	75	11	51	76	0	4	19	0.95
1586421--1586465	20	2.2	20	88	0	63	42	22	8	26	1.83
1593567--1593597	16	1.9	16	93	0	53	29	3	16	51	1.59
1599941--1599972	2	16.0	2	100	0	64	0	50	0	50	1.00
1602045--1602095	6	8.8	6	76	23	56	35	1	0	62	1.06
1602052--1602105	23	2.4	23	84	6	67	37	1	0	61	1.07
1602040--1602105	23	3.1	23	81	12	63	36	1	0	62	1.05
1611677--1611735	21	2.8	21	97	0	109	33	10	18	37	1.85
1611858--1611898	21	2.0	21	100	0	82	34	17	14	34	1.90
1612534--1613593	52	21.6	51	80	8	964	31	18	26	23	1.97
1612538--1613416	101	8.8	100	87	5	1160	32	18	26	22	1.97
1613241--1613319	39	2.0	39	90	0	122	25	20	24	30	1.98
1613281--1613687	48	8.9	49	72	15	307	31	18	25	24	1.98
1612991--1613546	136	4.0	137	82	8	635	31	18	25	24	1.98
1613378--1613455	39	2.0	39	84	0	102	26	19	23	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1613328--1613688	181	2.0	179	89	2	544	31	19	25	24	1.98
1613706--1613800	30	3.3	29	72	10	88	15	14	33	35	1.89
1613791--1614154	34	11.3	33	72	16	239	34	12	31	21	1.91
1613773--1614154	33	11.9	32	75	13	259	34	12	31	21	1.91
1613791--1613974	67	2.8	67	89	2	273	36	11	31	20	1.88
1613791--1614035	67	3.8	62	82	9	214	37	11	30	20	1.88
1613791--1614161	95	3.9	94	80	10	292	35	12	30	21	1.90
1614038--1614096	28	2.1	28	93	6	102	28	10	33	27	1.89
1614049--1614252	31	6.7	30	76	14	118	30	14	30	25	1.94
1614121--1614247	31	4.1	31	80	11	154	29	17	27	25	1.97
1615004--1615062	24	2.5	24	97	0	109	37	23	16	22	1.94
1615553--1615591	14	2.7	15	84	11	55	2	0	20	76	0.90
1624764--1624835	28	2.6	28	86	0	90	25	19	33	22	1.97
1624823--1624993	52	3.3	50	76	10	164	31	13	26	28	1.94
1624976--1625051	27	2.8	28	87	2	100	21	21	32	25	1.97
1624759--1625163	212	1.9	212	88	4	611	31	13	26	28	1.94
1627515--1627540	13	2.0	13	100	0	52	38	15	15	30	1.88
1627494--1627560	33	2.0	33	88	0	98	43	16	14	25	1.86
1627580--1627647	19	3.9	18	76	23	83	38	14	11	35	1.83
1627602--1627626	13	1.9	13	100	0	50	32	16	16	36	1.90
1627583--1627645	32	2.0	32	96	0	117	36	15	12	34	1.86
1627705--1627759	21	2.6	21	97	0	101	36	20	10	32	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1631852--1631884	16	2.1	16	88	5	50	30	27	0	42	1.56
1633011--1633107	37	2.6	36	80	9	106	52	12	6	28	1.63
1633039--1633109	37	1.9	37	88	5	108	53	12	4	29	1.57
1634999--1635033	12	2.9	12	82	0	52	31	8	2	57	1.44
1637151--1637210	30	2.0	30	96	0	111	35	23	11	30	1.90
1641324--1641365	22	1.9	22	85	9	59	38	0	2	59	1.10
1641652--1641725	37	2.1	36	90	7	116	39	24	8	28	1.84
1641913--1641944	2	16.0	2	93	0	55	50	3	0	46	1.17
1646370--1646429	18	3.4	18	71	15	54	48	0	1	50	1.11
1646374--1646442	34	2.0	35	88	2	104	43	0	2	53	1.15

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