genome.fa.s54.2.7.7.80.10.50.1000.9.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: Scaffold54
Parameters: 2 7 7 80 10 50 1000
Length:  3629595

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  9  of  20  ( 2342 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)
1378808--1378841	6	5.8	6	86	6	52	2	44	0	52	1.16
1378877--1378957	42	1.9	42	90	9	130	30	19	24	24	1.98
1379005--1379044	21	2.0	19	90	9	62	35	0	0	65	0.93
1379079--1379123	19	2.4	18	88	3	63	37	2	0	60	1.09
1379682--1379715	2	17.0	2	100	0	68	50	0	0	50	1.00
1380477--1380519	21	2.0	21	90	0	68	46	0	0	53	1.00
1381199--1381236	20	1.9	20	88	0	58	44	0	0	55	0.99
1384110--1384149	21	1.9	21	89	0	62	47	2	7	42	1.45
1384709--1384743	6	5.8	6	89	0	52	2	11	0	85	0.69
1385305--1385359	29	1.9	29	85	3	76	36	0	3	60	1.15
1385485--1385558	31	2.3	31	81	4	85	43	12	1	43	1.50
1386074--1386148	23	3.1	23	77	17	71	50	0	0	49	1.00
1386145--1386208	30	2.1	32	82	11	80	46	3	1	48	1.27
1392116--1392150	2	17.5	2	87	0	52	45	2	2	48	1.32
1393371--1393419	16	3.1	16	73	26	50	42	0	0	57	0.99
1393388--1393446	27	2.2	28	82	11	79	44	0	1	54	1.10
1393365--1393439	32	2.5	30	76	20	75	44	0	1	54	1.08
1393392--1393443	15	3.8	15	72	27	53	44	0	1	53	1.11
1393401--1393492	27	3.4	26	79	13	80	40	0	1	58	1.05
1393449--1393490	16	2.5	16	85	14	50	35	0	0	64	0.94
1393448--1393490	18	2.5	18	82	17	56	37	0	0	62	0.95
1395323--1395356	13	2.5	14	85	4	52	47	0	2	50	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1395373--1395430	27	2.0	29	83	9	75	56	1	1	39	1.19
1395808--1395846	2	19.5	2	89	0	60	43	5	0	51	1.24
1401423--1401468	16	2.9	16	81	12	51	50	2	0	47	1.13
1401865--1401905	18	2.3	18	87	8	57	41	0	0	58	0.98
1401871--1401932	14	4.4	13	76	15	61	35	1	0	62	1.05
1401844--1402006	31	5.3	30	66	20	95	39	2	0	57	1.12
1405753--1405777	11	2.3	11	100	0	50	8	0	0	92	0.40
1406019--1406059	2	20.5	2	100	0	82	48	0	0	51	1.00
1407200--1407226	13	2.1	13	100	0	54	0	7	0	92	0.38
1407668--1407727	12	4.8	12	71	18	50	63	0	3	33	1.11
1408352--1408400	23	2.2	22	82	10	55	57	2	2	38	1.22
1409193--1409220	2	14.0	2	100	0	56	0	50	0	50	1.00
1417152--1417187	2	18.0	2	94	0	63	47	50	2	0	1.15
1419055--1419103	19	2.6	19	83	3	64	61	0	0	38	0.96
1419061--1419149	32	2.9	31	79	15	105	56	0	0	43	0.99
1419073--1419136	15	3.7	18	72	25	57	53	0	0	46	1.00
1419045--1419180	50	2.8	47	75	18	134	59	0	0	39	1.03
1419128--1419173	21	2.1	22	84	4	58	63	2	0	34	1.07
1425978--1426015	2	19.0	2	94	0	67	50	0	47	2	1.15
1426898--1426932	2	17.5	2	93	0	61	48	0	51	0	1.00
1429064--1429088	1	25.0	1	100	0	50	0	0	0	100	0.00
1433561--1433591	1	31.0	1	100	0	62	0	100	0	0	0.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1436397--1436431	18	1.9	18	88	11	54	57	0	0	42	0.99
1436677--1436705	15	1.9	15	100	0	58	27	0	0	72	0.85
1437184--1437227	23	2.0	23	86	8	65	9	4	11	75	1.19
1437676--1437716	17	2.6	17	81	11	52	46	0	0	53	1.00
1438070--1438150	35	2.3	34	77	10	92	64	1	1	33	1.10
1438322--1438373	22	2.4	21	87	6	68	65	1	3	28	1.21
1438326--1438376	21	2.4	21	81	18	70	64	1	3	29	1.22
1438685--1438730	16	2.9	16	83	6	58	6	10	0	82	0.83
1438695--1438736	19	2.2	20	91	4	68	4	14	0	80	0.86
1438691--1438744	27	2.0	27	85	7	74	3	16	0	79	0.87
1438694--1438739	20	2.3	21	85	11	69	4	15	0	80	0.86
1438769--1438840	25	2.9	25	91	0	117	34	23	15	26	1.94
1439470--1439632	82	2.0	82	89	1	247	14	17	14	53	1.72
1444622--1444655	17	2.0	17	100	0	68	35	23	5	35	1.79
1448110--1450830	911	3.0	910	86	6	3610	38	16	21	24	1.92
1453590--1453629	12	3.1	13	85	10	55	67	0	15	17	1.23
1453592--1453641	25	2.0	25	88	7	75	72	0	10	18	1.12
1456539--1456575	18	2.1	18	100	0	74	37	10	10	40	1.75
1456532--1456573	18	2.4	17	92	8	66	42	9	9	38	1.70
1463848--1463885	18	2.1	18	95	0	67	42	13	31	13	1.82
1464329--1464359	15	2.1	15	100	0	62	38	12	6	41	1.69
1465419--1465780	179	2.0	179	98	0	706	43	18	12	26	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1470487--1470548	30	2.1	30	93	0	106	51	4	19	24	1.66
1477285--1477323	16	2.4	16	82	0	51	10	30	2	56	1.46
1479211--1479256	18	2.5	18	85	3	56	23	21	10	43	1.84
1481289--1481333	23	2.0	23	95	0	81	44	15	17	22	1.86
1485261--1485308	16	3.1	16	90	3	71	14	31	6	47	1.69
1485261--1485309	15	3.2	15	88	5	71	14	32	6	46	1.69
1486456--1486536	39	2.0	41	92	7	139	55	2	22	19	1.55
1486685--1486717	16	2.1	16	100	0	66	24	33	12	30	1.91
1493598--1493807	102	2.1	103	83	8	277	43	10	6	39	1.64
1501472--1501504	17	1.9	17	93	0	57	84	0	12	3	0.72
1507896--1508051	76	2.1	76	98	0	303	50	13	11	25	1.75
1512874--1512904	7	4.4	7	100	0	62	16	0	0	83	0.64
1513733--1513770	2	19.0	2	88	0	58	47	2	50	0	1.15
1515956--1515990	15	2.5	15	90	9	56	68	0	0	31	0.90
1515989--1516072	25	3.6	25	64	23	65	45	1	3	50	1.27
1515970--1516059	45	2.0	44	87	8	128	51	0	2	46	1.13
1516019--1516045	13	2.1	13	100	0	54	48	0	0	51	1.00
1519988--1520093	54	1.9	55	96	1	196	24	9	20	45	1.81
1535539--1535591	27	1.9	28	84	3	72	43	0	1	54	1.11
1535607--1535648	14	3.2	13	77	9	50	57	0	0	42	0.99
1535624--1535698	21	3.6	21	70	19	68	58	0	0	41	0.98
1535607--1535700	49	2.0	46	84	14	120	57	0	0	42	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1535630--1535711	27	3.0	27	73	7	67	58	0	0	41	0.98
1540950--1540992	24	1.9	21	86	13	59	25	23	0	51	1.49
1541144--1541176	9	3.7	9	92	8	50	0	12	0	87	0.53
1541145--1541176	15	2.2	14	94	5	55	0	9	0	90	0.45
1545412--1545513	21	4.7	22	80	11	104	52	0	4	41	1.29
1545398--1545511	10	10.9	10	72	12	52	53	1	5	39	1.34
1545664--1545918	21	12.7	21	67	18	87	51	7	5	35	1.52
1545738--1545918	80	2.3	79	82	0	218	53	6	4	35	1.48
1546095--1546148	21	2.6	20	83	13	65	55	7	1	35	1.39
1550071--1550099	2	14.5	2	100	0	58	48	0	0	51	1.00
1554794--1554818	12	2.1	12	100	0	50	24	16	0	60	1.36
1554901--1554925	6	4.2	6	100	0	50	52	0	48	0	1.00
1555317--1555366	2	25.5	2	79	4	57	44	2	6	48	1.39
1558211--1558237	14	1.9	14	100	0	54	51	11	0	37	1.37
1558509--1558537	2	14.5	2	100	0	58	51	0	0	48	1.00
1558537--1558572	2	18.0	2	100	0	72	50	0	50	0	1.00
1560924--1560965	16	2.4	19	80	19	63	42	0	0	57	0.99
1562014--1562082	22	3.0	23	74	16	63	53	0	0	46	1.00
1562022--1562072	21	2.4	21	87	9	68	56	0	0	43	0.99
1562284--1562375	32	2.8	34	80	15	120	54	0	0	45	0.99
1563042--1563108	22	3.1	21	80	6	64	43	0	0	56	0.99
1563117--1563182	28	2.3	28	82	7	71	39	4	0	56	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1565944--1565970	3	9.0	3	100	0	54	66	0	0	33	0.92
1576973--1577028	27	2.1	27	83	6	69	19	16	17	46	1.84
1580228--1580259	3	10.7	3	100	0	64	68	0	0	31	0.90
1580255--1580280	4	6.5	4	100	0	52	76	0	0	23	0.78
1581020--1581064	11	4.0	11	80	5	54	24	2	0	73	0.95
1581013--1581054	23	1.9	23	90	9	70	30	0	0	69	0.89
1581022--1581106	29	2.9	29	79	10	102	34	2	0	63	1.07
1581194--1581259	20	3.4	20	74	16	59	54	0	0	45	0.99
1581247--1581316	30	2.4	29	79	9	72	47	2	2	47	1.32
1581344--1581394	24	2.1	24	81	0	57	45	0	1	52	1.12

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20