genome.fa.s54.2.7.7.80.10.50.1000.8.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: 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  8  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)
1225833--1225876	14	3.1	14	83	0	52	50	0	0	50	1.00
1232587--1232611	3	8.3	3	100	0	50	68	0	0	32	0.90
1232868--1232908	21	2.0	21	90	0	64	39	9	7	43	1.65
1233204--1233248	23	1.9	24	82	13	58	44	0	2	53	1.13
1234356--1234417	26	2.4	25	81	7	63	61	4	3	30	1.33
1234702--1234737	4	9.0	4	93	0	54	69	0	5	25	1.10
1234953--1234984	15	2.1	16	94	5	57	46	0	0	53	1.00
1235039--1235071	15	2.2	15	89	10	50	57	0	0	42	0.98
1235689--1235718	2	15.0	2	100	0	60	50	0	0	50	1.00
1236686--1236724	2	19.5	2	100	0	78	48	0	0	51	1.00
1237294--1237331	20	1.9	19	89	5	58	42	0	2	55	1.14
1237370--1237410	22	1.9	22	90	5	66	65	0	0	34	0.93
1237900--1237933	15	2.3	15	90	10	52	64	0	0	35	0.94
1239980--1240019	2	20.0	2	100	0	80	50	0	0	50	1.00
1240162--1240207	23	1.9	25	86	8	69	67	4	0	28	1.10
1241843--1241875	12	2.7	13	81	18	52	48	0	0	51	1.00
1242197--1242253	22	2.7	21	84	15	73	33	0	5	61	1.18
1242214--1242257	22	2.0	22	100	0	88	36	0	4	59	1.18
1242212--1242273	22	2.9	21	86	11	81	33	1	4	59	1.28
1242246--1242317	36	2.0	37	81	8	85	44	4	1	50	1.30
1246781--1246850	30	2.5	26	82	17	79	34	0	1	64	1.03
1248820--1248844	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1251143--1251220	21	3.5	22	74	19	81	43	0	0	56	0.99
1251156--1251187	13	2.4	14	90	10	50	31	0	0	68	0.90
1251136--1251219	24	3.6	24	71	20	72	42	0	0	57	0.99
1256310--1256340	2	15.5	2	100	0	62	51	0	0	48	1.00
1256725--1256764	20	2.0	21	85	14	57	25	5	2	67	1.23
1257290--1257329	16	2.5	16	88	8	55	60	2	0	37	1.11
1259596--1259629	2	17.0	2	100	0	68	50	0	0	50	1.00
1260231--1260261	7	4.4	7	100	0	62	41	0	0	58	0.98
1260685--1260722	20	1.9	20	89	10	60	39	2	7	50	1.46
1260988--1261050	26	2.6	23	79	18	74	41	1	0	57	1.08
1261067--1261092	13	2.0	13	100	0	52	53	0	0	46	1.00
1261162--1261206	13	3.6	13	75	22	51	62	0	0	37	0.96
1261157--1261220	24	2.6	24	85	2	83	62	0	0	37	0.95
1261209--1261302	41	2.3	41	80	8	104	53	0	1	45	1.07
1261264--1261348	44	1.9	46	83	7	113	51	1	0	47	1.08
1262542--1262589	25	2.0	25	88	12	73	45	0	0	54	0.99
1262813--1262841	12	2.5	12	94	5	51	86	0	0	13	0.58
1262977--1263024	25	2.0	24	83	4	60	54	0	2	43	1.12
1263414--1263443	2	15.0	2	100	0	60	50	0	0	50	1.00
1263733--1263761	2	14.5	2	100	0	58	51	0	0	48	1.00
1267553--1267587	18	1.9	18	88	11	54	57	0	5	37	1.23
1270349--1270393	23	2.0	23	90	0	72	46	0	4	48	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1270345--1270418	23	3.2	22	77	12	69	44	1	2	51	1.24
1270505--1270542	18	2.1	19	85	5	51	52	0	10	36	1.36
1271031--1271079	17	3.0	17	71	20	50	40	0	0	59	0.98
1271034--1271091	22	2.6	23	81	5	66	44	0	0	55	0.99
1271087--1271144	11	5.4	11	82	12	75	34	1	0	63	1.04
1271021--1271102	33	2.6	32	83	11	89	45	0	0	54	0.99
1271025--1271134	27	4.2	26	73	16	84	40	0	0	59	1.04
1271087--1271144	16	3.6	16	83	2	80	34	1	0	63	1.04
1271087--1271144	27	2.1	27	87	6	82	34	1	0	63	1.04
1279112--1279153	11	3.8	11	87	9	59	28	0	0	71	0.86
1279136--1279208	26	2.6	28	79	10	87	49	0	0	50	1.00
1279136--1279212	21	3.5	22	78	8	77	49	0	0	50	1.00
1279142--1279206	7	8.6	8	71	23	52	49	0	0	50	1.00
1280105--1280176	36	2.0	36	97	0	135	23	22	19	34	1.96
1280814--1280871	21	2.8	20	75	19	55	48	0	3	48	1.18
1280883--1280930	24	2.0	25	84	12	64	56	2	2	39	1.23
1281682--1281743	20	3.1	20	80	11	56	51	1	1	45	1.20
1282173--1282226	2	27.0	2	88	0	81	44	0	5	50	1.25
1282619--1282651	17	1.9	17	93	0	57	51	0	3	45	1.16
1283385--1283439	28	2.0	28	82	3	67	47	0	0	52	1.00
1283411--1283446	16	2.2	16	90	9	56	44	0	0	55	0.99
1283423--1283473	22	2.3	23	86	3	68	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1283417--1283473	24	2.4	23	85	5	78	40	0	0	59	0.97
1283433--1283544	16	7.8	15	66	25	64	41	0	0	58	1.04
1284220--1284282	24	2.6	24	79	0	72	14	58	3	23	1.50
1284220--1284299	24	3.3	24	78	0	70	12	60	3	23	1.49
1290970--1291168	100	2.0	99	90	1	308	38	13	18	29	1.89
1295560--1295592	15	2.1	16	88	5	50	45	0	3	51	1.16
1295623--1295664	21	2.0	21	90	4	66	59	0	0	40	0.97
1295929--1295978	23	2.2	23	88	0	73	38	0	6	56	1.24
1296425--1296460	19	1.9	18	88	5	54	66	0	0	33	0.92
1300794--1300841	3	16.0	3	100	0	96	33	0	0	66	0.92
1310253--1310294	20	2.2	20	91	8	70	26	0	0	73	0.83
1310262--1310306	20	2.3	20	88	3	65	35	0	0	64	0.94
1310312--1310352	14	2.9	15	82	10	50	46	0	0	53	1.00
1310317--1310355	20	1.9	20	89	5	60	41	0	0	58	0.98
1310912--1310956	3	15.0	3	90	0	72	4	0	64	31	1.13
1315137--1315161	11	2.3	11	100	0	50	92	0	8	0	0.40
1321206--1321256	25	2.0	25	92	0	84	35	19	7	37	1.81
1321692--1321729	14	2.6	15	83	8	51	81	2	15	0	0.80
1321958--1322008	20	2.3	23	87	12	72	52	0	1	45	1.12
1321948--1322008	26	2.4	26	86	8	81	50	0	1	47	1.10
1324478--1324503	2	13.0	2	100	0	52	0	0	50	50	1.00
1327106--1327134	10	2.7	11	89	10	51	79	0	0	20	0.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1327576--1327654	42	1.9	40	86	0	95	34	13	6	45	1.69
1327585--1327671	42	2.1	42	97	0	165	33	13	5	47	1.67
1334878--1334902	2	12.5	2	100	0	50	52	0	48	0	1.00
1336940--1336970	2	15.5	2	93	0	53	51	3	0	45	1.17
1337975--1338021	22	2.2	21	81	11	51	46	0	0	53	1.00
1338129--1338220	10	8.7	10	67	19	53	34	1	1	63	1.09
1338243--1338288	22	2.0	23	83	4	58	41	0	2	56	1.11
1338606--1338660	28	1.9	30	89	10	89	60	1	0	38	1.08
1353237--1353287	25	2.0	26	85	7	70	35	0	0	64	0.94
1353619--1353647	2	14.5	2	100	0	58	51	0	0	48	1.00
1354695--1354738	20	2.2	20	95	0	79	29	29	27	13	1.94
1355041--1355093	27	2.0	26	92	3	88	43	18	1	35	1.62
1362508--1362603	24	3.5	27	69	24	76	34	0	0	65	0.93
1362518--1362566	16	3.2	16	75	13	50	36	0	0	63	0.95
1362533--1362573	21	1.9	22	95	5	75	34	0	0	65	0.93
1362535--1362579	16	2.9	16	80	3	56	33	0	0	66	0.92
1362511--1362623	28	4.1	28	82	8	135	34	0	0	65	0.93
1362643--1362714	30	2.4	30	88	9	103	56	0	4	38	1.18
1362912--1362941	2	15.0	2	100	0	60	50	0	0	50	1.00
1373785--1373829	22	2.0	22	87	8	65	42	8	4	44	1.56
1374384--1374415	2	16.0	2	100	0	64	50	0	0	50	1.00
1374528--1374676	9	16.4	9	69	19	71	57	0	0	41	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1374536--1374698	39	4.1	39	73	20	126	55	0	0	43	1.04
1374535--1374657	11	10.9	12	67	30	60	55	0	0	43	1.05
1374575--1374649	23	3.0	24	77	16	64	53	0	1	45	1.08
1374562--1374668	20	5.4	21	70	15	68	54	0	0	44	1.06
1374562--1374676	60	1.9	60	83	15	148	53	0	0	45	1.06
1374601--1374663	10	6.0	11	77	15	71	53	0	0	46	1.00
1374538--1374706	90	1.9	88	82	9	209	56	0	0	43	1.03
1374641--1374700	8	7.4	8	77	19	54	53	0	0	46	1.00
1374655--1374705	22	2.3	23	76	10	61	56	0	0	43	0.99
1377300--1377329	2	15.0	2	100	0	60	50	0	0	50	1.00

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