genome.fa.s64.2.7.7.80.10.50.1000.6.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

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   
          33   34   35   36   37   38   39   40   41   42   43   44   45   

This is table  6  of  45  ( 5312 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)
1149535--1149569	15	2.4	14	90	9	61	22	0	0	77	0.78
1153274--1153317	2	22.0	2	95	0	79	50	2	0	47	1.13
1164695--1164727	2	16.5	2	100	0	66	48	0	0	51	1.00
1165531--1165564	6	5.7	6	96	0	59	20	17	26	35	1.95
1168731--1168765	2	17.5	2	100	0	70	48	0	0	51	1.00
1169747--1170112	184	2.0	184	93	1	635	32	14	20	33	1.92
1171043--1171166	64	1.9	64	95	0	221	28	21	13	36	1.92
1172092--1172147	20	2.8	20	82	12	71	41	1	0	57	1.09
1172851--1172891	21	1.9	22	90	5	66	34	0	0	65	0.93
1176587--1176619	2	16.5	2	93	0	57	48	48	3	0	1.17
1180070--1180116	2	23.5	2	100	0	94	0	48	0	51	1.00
1182521--1182559	2	19.5	2	100	0	78	0	48	0	51	1.00
1182559--1182585	2	13.5	2	100	0	54	48	0	0	51	1.00
1183518--1183542	1	25.0	1	100	0	50	0	100	0	0	0.00
1183788--1183821	2	17.5	2	93	6	61	50	0	0	50	1.00
1184637--1184688	20	2.5	21	87	6	70	38	0	0	61	0.96
1184794--1184823	3	10.0	3	92	0	51	30	0	3	66	1.07
1186309--1186352	18	2.4	19	85	14	58	52	0	2	45	1.13
1186614--1186651	18	2.1	18	85	9	51	52	2	2	42	1.29
1186606--1186650	21	2.1	21	83	0	54	51	2	2	44	1.26
1190294--1190329	2	18.0	2	100	0	72	50	0	0	50	1.00
1191387--1191424	2	19.0	2	100	0	76	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1191482--1191518	2	18.5	2	100	0	74	48	0	0	51	1.00
1192091--1192115	13	1.9	13	100	0	50	56	0	0	44	0.99
1192084--1192123	21	1.9	21	89	0	62	60	0	0	40	0.97
1195633--1195713	23	3.7	22	72	11	60	56	1	2	39	1.20
1195625--1195718	34	2.9	33	80	7	95	56	1	2	40	1.18
1197344--1197412	30	2.4	28	88	9	95	27	1	2	68	1.13
1197345--1197413	27	2.5	26	84	13	84	28	1	2	66	1.14
1202722--1202749	2	14.0	2	100	0	56	50	0	0	50	1.00
1204106--1204139	12	2.8	12	90	0	50	50	8	0	41	1.34
1206368--1206456	40	2.2	41	76	7	94	49	1	0	49	1.08
1207539--1207583	21	2.1	21	88	8	65	37	0	0	62	0.96
1207980--1208013	3	11.3	3	100	0	68	67	0	0	32	0.91
1208543--1208604	19	3.2	20	76	19	60	50	0	0	50	1.00
1208489--1208604	38	3.0	38	79	14	114	52	0	0	46	1.06
1209644--1209690	3	15.7	3	86	8	69	68	0	2	29	1.02
1209948--1210062	59	1.9	59	89	0	176	25	18	15	40	1.90
1214766--1214805	16	2.5	16	88	8	55	45	0	0	55	0.99
1214774--1214826	21	2.3	23	84	12	65	39	0	0	60	0.97
1214774--1214902	8	17.0	8	72	16	62	44	0	0	55	0.99
1214827--1214886	14	4.0	14	74	16	57	50	0	0	50	1.00
1214823--1214886	22	2.8	22	76	6	65	48	0	0	51	1.00
1214836--1214900	32	2.0	33	93	3	114	44	0	0	55	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1215239--1215265	2	13.5	2	100	0	54	51	0	0	48	1.00
1215982--1216036	28	2.0	27	82	6	67	54	3	0	41	1.18
1218636--1218681	9	5.1	9	84	10	67	54	0	0	45	0.99
1218636--1218681	18	2.6	18	96	0	83	54	0	0	45	0.99
1218702--1218780	17	4.5	17	75	16	65	60	1	0	37	1.05
1218821--1218870	21	2.5	19	80	6	55	66	0	0	34	0.92
1219425--1219461	3	12.3	3	100	0	74	64	0	0	35	0.94
1225194--1225219	2	13.0	2	100	0	52	50	0	0	50	1.00
1226403--1226433	10	3.0	10	95	4	53	29	0	0	70	0.87
1231304--1231330	2	13.5	2	100	0	54	51	48	0	0	1.00
1238792--1238821	11	2.6	11	94	5	51	63	0	0	36	0.95
1238930--1238982	22	2.5	21	76	11	54	47	0	0	52	1.00
1248191--1248237	23	2.0	23	95	0	85	36	12	8	42	1.74
1255054--1255274	34	6.5	33	83	8	275	41	25	7	25	1.81
1255054--1255274	102	2.2	101	90	3	363	41	25	7	25	1.81
1259676--1259898	34	6.6	33	79	9	207	41	24	6	26	1.80
1259676--1259898	68	3.3	66	80	5	239	41	24	6	26	1.80
1259676--1259898	102	2.2	101	88	1	347	41	24	6	26	1.80
1261691--1261718	2	14.0	2	100	0	56	50	0	0	50	1.00
1262382--1262439	21	2.7	22	74	12	59	43	8	3	44	1.51
1263442--1263495	23	2.4	23	81	6	67	53	1	0	44	1.11
1263484--1263540	31	1.9	30	86	10	82	59	7	3	29	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1273107--1273150	18	2.4	19	84	3	54	59	0	0	40	0.98
1273281--1273324	19	2.3	19	88	0	61	54	2	4	38	1.33
1274141--1274191	18	2.9	18	77	13	61	54	0	0	45	0.99
1278462--1278524	27	2.3	27	94	0	108	41	12	17	28	1.86
1280611--1280683	13	5.6	13	71	18	53	46	1	0	52	1.09
1280851--1280879	3	9.7	3	100	0	58	68	0	0	31	0.89
1281338--1281372	14	2.4	14	90	4	52	54	11	0	34	1.37
1281525--1281583	26	2.3	26	82	5	66	61	0	0	38	0.96
1281940--1281981	22	1.9	22	90	0	66	16	11	52	19	1.74
1288029--1288060	2	16.5	2	93	6	57	0	46	0	53	1.00
1288031--1288061	15	2.1	15	100	0	62	0	45	0	54	0.99
1288745--1289063	174	1.8	172	84	6	430	46	8	4	39	1.56
1290896--1290930	2	17.5	2	87	0	52	45	0	5	48	1.26
1291928--1291952	13	1.9	13	100	0	50	24	8	24	44	1.80
1292019--1292049	2	16.0	2	93	6	55	48	0	0	51	1.00
1293532--1293577	22	2.1	22	83	0	56	43	0	2	54	1.12
1295168--1295194	3	9.0	3	100	0	54	66	0	0	33	0.92
1297425--1297466	21	2.0	22	90	4	68	50	2	2	45	1.27
1297457--1297506	26	2.0	24	92	7	82	44	0	0	56	0.99
1297435--1297514	21	3.5	23	75	20	69	45	0	1	53	1.08
1297438--1297514	25	3.3	24	72	18	72	44	0	1	54	1.08
1298195--1298252	16	3.7	16	74	17	59	41	1	1	55	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1298308--1298373	23	3.0	22	80	8	64	25	4	0	69	1.07
1298322--1298373	10	5.0	10	76	17	52	26	1	0	71	0.97
1298304--1298392	27	3.3	26	76	13	74	24	3	2	69	1.15
1306152--1306227	35	2.2	34	82	13	93	44	0	0	55	0.99
1306160--1306198	17	2.4	17	82	4	53	46	0	0	53	1.00
1306144--1306224	43	1.9	42	84	2	108	44	0	0	55	0.99
1306178--1306227	26	1.9	26	84	8	66	46	0	0	54	1.00
1307335--1307369	17	1.9	18	88	11	54	48	0	2	48	1.16
1308378--1308429	11	4.8	10	79	13	50	36	1	1	59	1.19
1308384--1308429	12	4.0	12	78	18	53	36	2	0	60	1.09
1312646--1312689	2	22.0	2	100	0	88	50	0	0	50	1.00
1322598--1322652	18	2.8	20	73	18	53	45	0	3	50	1.19
1323140--1323169	3	10.0	3	100	0	60	33	0	0	66	0.92
1323995--1324055	31	2.0	30	83	3	77	26	3	9	60	1.43
1325703--1325732	2	15.0	2	92	0	51	50	3	0	46	1.18
1326708--1326736	2	14.5	2	100	0	58	51	0	0	48	1.00
1327602--1327651	25	2.1	23	85	7	64	30	0	2	68	1.01
1335258--1335301	16	2.8	17	75	25	51	47	0	0	52	1.00
1335742--1335786	8	5.8	8	81	5	56	15	2	0	82	0.77
1335742--1335785	23	1.9	23	90	0	70	13	2	0	84	0.73
1335740--1335786	15	3.1	15	81	3	58	17	2	0	80	0.80
1339694--1339724	16	1.9	16	93	0	53	29	0	0	70	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1341856--1341948	27	3.6	26	80	13	95	63	1	1	34	1.09
1341879--1341942	13	5.0	13	79	14	62	65	0	0	34	0.93
1341899--1341947	24	2.1	22	88	7	71	65	0	0	34	0.93
1341907--1341999	32	2.9	32	84	10	118	54	0	0	45	0.99
1341939--1341992	15	3.2	18	71	26	55	50	0	0	50	1.00
1341909--1342012	32	3.2	32	71	20	83	55	0	0	44	0.99
1346974--1347005	2	16.0	2	93	0	55	53	0	0	46	1.00
1347069--1347112	20	2.3	19	84	11	54	18	11	36	34	1.86
1349240--1349276	2	18.5	2	94	0	65	51	2	0	45	1.15
1352491--1352523	2	16.5	2	93	0	57	51	3	0	45	1.16

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   
          33   34   35   36   37   38   39   40   41   42   43   44   45