genome.fa.s3.2.7.7.80.10.50.1000.11.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   25   26   27   28   29   30   31   32   

This is table  11  of  32  ( 3795 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)
1326632--1326700	15	4.5	15	72	13	50	62	0	1	36	1.04
1326696--1326728	11	2.9	12	86	13	52	54	3	0	42	1.15
1326712--1326763	20	2.4	22	81	9	63	42	0	0	57	0.98
1326712--1326767	22	2.7	20	81	15	60	41	0	0	58	0.98
1326872--1326903	16	2.0	16	93	0	55	65	3	0	31	1.08
1327481--1327520	19	2.0	20	86	13	57	52	0	0	47	1.00
1328526--1328552	14	1.9	14	100	0	54	85	0	14	0	0.61
1330269--1330322	17	3.1	18	77	15	60	42	0	0	57	0.98
1330395--1330432	11	3.5	11	86	10	51	52	0	2	44	1.14
1331852--1331882	2	15.5	2	100	0	62	51	0	0	48	1.00
1332097--1332136	2	19.5	2	94	5	71	47	0	2	50	1.14
1332543--1332654	37	3.0	37	87	7	163	27	7	15	50	1.70
1332542--1332662	38	3.2	38	83	9	167	27	6	14	51	1.67
1332990--1333038	19	2.5	19	76	3	53	24	2	0	73	0.94
1332972--1333042	11	6.2	12	72	21	55	29	2	0	67	1.05
1336409--1336466	15	3.9	15	72	22	59	43	0	0	56	0.99
1336409--1336481	29	2.5	28	78	8	76	46	0	0	53	1.00
1338692--1338743	15	3.5	16	80	12	58	59	0	0	40	0.97
1338719--1338767	25	1.9	25	87	4	71	55	0	0	44	0.99
1344350--1344385	12	3.0	12	95	0	63	55	8	36	0	1.30
1344862--1344891	2	15.0	2	92	0	51	50	0	3	46	1.18
1345538--1345611	37	2.0	38	89	7	116	28	6	14	50	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1345915--1345993	32	2.5	32	82	8	92	35	1	0	63	1.03
1346264--1346306	11	4.0	11	87	3	52	32	0	0	67	0.91
1346276--1346306	11	2.8	11	95	0	53	38	0	0	61	0.96
1346266--1346306	22	1.9	22	90	5	66	34	0	0	65	0.93
1346794--1346987	100	1.9	101	89	5	302	39	10	8	41	1.70
1348162--1348222	20	3.0	20	80	15	72	32	1	0	65	1.02
1348177--1348218	16	2.6	17	74	11	52	30	2	0	66	1.04
1348983--1349013	16	1.9	16	93	0	53	70	0	3	25	1.02
1349845--1349873	9	3.0	10	90	10	51	58	0	0	41	0.98
1351039--1351071	14	2.4	14	90	10	50	63	0	0	36	0.95
1352213--1352243	15	2.1	15	93	0	53	0	3	6	90	0.55
1352683--1352717	16	2.1	16	89	5	52	42	0	0	57	0.99
1353369--1353418	17	3.1	16	83	11	66	30	4	0	66	1.10
1353395--1353435	12	3.6	12	87	9	59	31	2	0	65	1.05
1353392--1353435	22	2.0	22	82	8	54	34	2	0	63	1.07
1355490--1355541	15	3.4	14	75	15	50	61	0	1	36	1.07
1360237--1360268	2	16.0	2	100	0	64	50	0	0	50	1.00
1362445--1362495	25	2.0	25	85	7	68	50	0	0	49	1.00
1362445--1362520	23	3.3	24	70	18	72	50	0	0	50	1.00
1362449--1362536	46	1.9	46	84	13	119	47	0	1	51	1.08
1362550--1362623	22	3.3	22	79	9	69	41	1	0	56	1.07
1362584--1362632	22	2.4	21	80	12	57	44	2	0	53	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1363795--1363848	20	2.8	20	78	13	67	38	1	0	59	1.08
1364242--1364344	35	3.0	35	89	2	163	37	9	13	38	1.78
1366346--1366396	20	2.6	19	84	9	59	29	0	3	66	1.09
1367012--1367058	21	2.3	20	85	3	58	42	2	2	53	1.25
1368062--1368102	21	2.0	20	86	13	57	36	0	2	60	1.10
1368481--1368507	3	9.0	3	100	0	54	66	0	0	33	0.92
1370191--1370229	13	2.8	13	85	11	51	51	2	0	46	1.14
1373689--1373730	19	2.2	20	82	4	50	64	0	0	35	0.94
1374601--1374651	2	25.5	2	87	0	75	45	0	5	49	1.26
1376275--1376319	21	2.1	21	84	8	56	46	0	4	48	1.22
1376954--1376985	2	16.0	2	100	0	64	50	0	50	0	1.00
1378326--1378353	3	9.3	3	100	0	56	32	0	0	67	0.91
1381074--1381103	10	3.0	10	95	0	51	43	0	0	56	0.99
1384400--1384431	14	2.3	14	100	0	64	28	12	9	50	1.71
1389214--1389242	15	1.9	15	100	0	58	20	0	0	79	0.74
1389535--1389656	64	1.9	65	84	5	167	54	1	4	40	1.29
1392530--1392564	2	17.5	2	100	0	70	51	0	0	48	1.00
1393247--1393441	98	2.0	98	96	0	363	38	10	4	46	1.58
1394593--1394627	2	17.5	2	100	0	70	51	0	48	0	1.00
1394847--1394909	16	3.8	17	72	14	51	53	0	0	46	1.00
1394859--1394959	27	3.7	26	73	17	80	54	0	0	44	1.06
1394855--1394962	38	2.9	36	75	24	93	55	0	0	43	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1395571--1395599	2	14.5	2	100	0	58	48	0	0	51	1.00
1395877--1395976	50	2.0	49	96	1	182	40	17	25	18	1.91
1397190--1397361	11	17.8	10	65	22	50	37	0	1	61	1.08
1397189--1397343	18	8.8	17	66	19	52	38	0	1	59	1.10
1397220--1397270	20	2.5	20	81	12	68	39	0	0	60	0.97
1397306--1397349	22	1.9	24	90	9	74	31	2	2	63	1.19
1399120--1399157	11	3.6	11	82	13	53	63	0	0	36	0.95
1399119--1399162	20	2.1	21	91	4	72	61	0	0	38	0.96
1399233--1399270	20	1.9	20	84	10	51	39	13	5	42	1.66
1399375--1399643	136	2.0	130	95	5	477	50	3	7	37	1.48
1401346--1401387	21	2.0	21	85	0	57	42	4	0	52	1.22
1401439--1401469	15	2.1	15	93	0	53	48	22	0	29	1.51
1407879--1407924	13	3.7	12	78	21	58	36	0	0	63	0.95
1407921--1407997	39	2.0	39	92	0	127	59	3	2	33	1.29
1411266--1411308	22	2.0	22	85	0	59	62	2	4	30	1.28
1413325--1413349	4	6.2	4	100	0	50	76	0	0	24	0.80
1419350--1419384	15	2.3	15	95	0	61	0	42	8	48	1.33
1424360--1424402	16	2.9	14	77	12	50	60	0	0	39	0.97
1424599--1424642	20	2.3	18	81	14	52	47	6	0	45	1.29
1425043--1425113	32	2.2	33	80	12	85	43	0	0	56	0.99
1425621--1425676	18	3.1	18	77	10	51	69	0	5	25	1.09
1426562--1426589	11	2.5	11	100	0	56	64	0	0	35	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1427039--1427072	11	3.1	11	91	0	50	73	0	0	26	0.83
1427303--1427592	149	2.0	148	84	6	381	43	9	7	40	1.64
1428272--1428318	23	2.1	22	88	4	67	57	2	2	38	1.23
1430652--1430678	2	13.5	2	100	0	54	48	0	0	51	1.00
1430775--1430824	22	2.3	21	77	19	50	46	2	2	50	1.24
1434748--1434777	2	15.0	2	100	0	60	50	0	50	0	1.00
1436257--1436291	2	17.5	2	100	0	70	51	0	48	0	1.00
1438883--1438933	25	2.0	25	82	14	61	37	0	0	62	0.95
1439247--1439280	16	2.2	15	89	5	50	61	0	2	35	1.11
1439500--1439532	2	16.5	2	93	0	57	48	0	0	51	1.00
1440967--1441027	26	2.4	25	71	17	61	52	3	4	39	1.39
1441467--1441596	16	7.4	17	70	17	70	65	2	0	32	1.05
1441428--1441542	59	1.9	59	81	10	137	63	4	0	31	1.20
1441501--1441605	24	4.5	24	67	17	78	65	0	0	33	0.99
1441487--1441607	33	3.5	33	79	9	118	64	1	0	33	1.04
1441423--1441564	24	6.0	22	71	20	92	65	3	0	30	1.14
1441492--1441607	35	3.4	34	80	8	119	64	1	0	33	1.04
1441290--1441594	155	2.0	157	80	8	356	60	5	1	32	1.30
1441870--1441925	15	3.6	15	87	4	67	62	0	1	35	1.06
1443311--1443341	15	2.1	15	93	0	53	19	3	45	32	1.66
1448241--1448287	10	4.7	10	82	7	60	51	0	0	48	1.00
1448243--1448287	21	2.3	19	88	7	63	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1448192--1448274	43	2.0	44	83	11	111	53	0	0	46	1.00
1448426--1448473	19	2.5	19	82	0	60	35	0	2	62	1.07
1450056--1450109	26	2.1	26	100	0	108	22	11	25	40	1.87
1456961--1457000	20	2.0	20	100	0	80	20	15	15	50	1.79
1457434--1457489	26	2.2	26	96	0	103	23	8	17	50	1.74
1458495--1458530	3	12.0	3	100	0	72	33	0	0	66	0.92
1459792--1459848	21	2.5	22	80	13	62	56	3	1	38	1.27
1463167--1463201	2	17.5	2	100	0	70	51	0	0	48	1.00
1463242--1463276	2	17.5	2	100	0	70	48	0	0	51	1.00
1464845--1464903	29	2.0	29	80	6	66	59	0	0	40	0.97

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   25   26   27   28   29   30   31   32