genome.fa.s6.2.7.7.80.10.50.1000.4.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   

This is table  4  of  168  ( 20060 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)
1002389--1002437	20	2.7	18	77	22	57	51	4	2	42	1.32
1002353--1002488	72	1.9	71	82	11	170	51	4	3	40	1.40
1005312--1005356	23	2.0	23	82	8	56	33	4	11	51	1.58
1005563--1005590	2	14.0	2	100	0	56	50	0	0	50	1.00
1005764--1005812	2	24.5	2	100	0	98	48	0	0	51	1.00
1005996--1006205	42	5.1	41	85	7	282	30	20	21	28	1.98
1005996--1006248	41	6.1	41	85	6	291	30	19	22	27	1.98
1005996--1006248	83	3.1	83	85	5	318	30	19	22	27	1.98
1013809--1013870	22	2.8	22	92	0	97	24	25	14	35	1.93
1014083--1014193	31	3.7	29	80	10	107	34	10	12	42	1.78
1016343--1016397	29	2.0	28	82	7	67	58	3	32	5	1.38
1019648--1019681	16	2.1	16	88	0	50	41	2	20	35	1.68
1026993--1027028	2	18.0	2	100	0	72	50	0	0	50	1.00
1030173--1030236	20	3.0	20	70	14	56	37	4	1	56	1.30
1032255--1032301	5	9.2	5	80	13	51	36	14	25	23	1.93
1034567--1034635	10	6.5	10	74	15	59	55	0	2	42	1.15
1034553--1034728	42	4.2	40	85	9	237	60	0	2	36	1.12
1034578--1034666	31	2.9	30	86	6	115	61	0	2	35	1.08
1034631--1034655	11	2.3	11	100	0	50	84	0	0	16	0.63
1035023--1035049	14	1.9	14	100	0	54	37	14	3	44	1.63
1036147--1036231	44	1.9	44	95	0	152	43	3	12	40	1.60
1056730--1056763	17	2.0	17	94	0	59	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1065686--1065716	16	1.9	16	93	0	53	9	6	9	74	1.23
1066798--1066822	13	1.9	13	100	0	50	48	0	12	40	1.40
1067386--1067445	16	3.7	16	69	8	50	45	6	0	48	1.29
1067400--1067440	21	2.0	20	85	4	55	43	7	0	48	1.30
1067398--1067444	11	4.3	12	75	20	50	42	6	0	51	1.27
1069528--1070027	40	12.4	40	80	2	509	35	17	26	21	1.95
1074118--1074239	23	5.3	23	85	3	165	31	24	20	23	1.98
1074118--1074239	46	2.7	46	90	0	190	31	24	20	23	1.98
1075575--1075642	5	13.4	5	77	20	70	42	0	0	57	0.98
1082685--1082735	25	2.0	25	84	0	66	11	5	23	58	1.55
1087546--1087585	19	2.2	19	95	4	73	45	12	5	37	1.64
1091438--1091474	19	1.9	19	94	0	65	43	16	0	40	1.48
1095476--1095548	22	3.3	22	88	0	101	28	27	15	28	1.96
1102848--1102890	16	2.6	17	82	17	56	65	2	9	23	1.34
1104038--1104082	23	2.0	23	91	4	74	46	17	4	31	1.68
1104038--1104092	22	2.5	23	88	5	78	43	18	3	34	1.67
1107195--1107726	264	2.0	264	99	0	1046	25	24	16	32	1.96
1109420--1109477	22	2.6	22	81	7	64	44	17	1	36	1.59
1109433--1109477	22	2.0	23	86	4	65	40	17	2	40	1.62
1109819--1109849	16	1.9	16	93	0	53	22	22	25	29	1.99
1110012--1110073	28	2.2	28	85	0	79	41	9	16	32	1.80
1110632--1110695	21	3.0	20	68	22	51	43	0	3	53	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1112762--1112791	8	3.6	8	95	4	51	3	56	0	40	1.16
1113851--1113875	12	2.1	12	100	0	50	68	0	0	32	0.90
1113789--1113983	66	3.0	63	78	9	205	55	2	3	38	1.27
1113961--1114002	19	2.2	20	86	4	59	54	2	7	35	1.41
1119805--1120499	348	2.0	348	81	3	819	31	15	17	35	1.91
1120153--1120822	210	3.2	209	86	2	862	31	15	16	36	1.91
1135402--1135456	27	2.2	25	80	9	58	63	1	0	34	1.05
1135404--1135465	28	2.3	25	81	13	70	62	1	0	35	1.05
1136102--1136199	49	2.1	45	86	7	133	38	4	2	55	1.31
1144536--1144564	11	2.6	11	100	0	58	0	72	0	27	0.85
1148306--1148349	20	2.3	19	88	4	61	40	2	13	43	1.57
1150147--1150185	15	2.7	15	88	7	55	30	0	23	46	1.53
1153719--1153774	22	2.5	23	82	2	69	51	1	1	44	1.22
1153750--1153789	16	2.5	16	91	0	62	47	2	7	42	1.45
1153800--1153968	59	2.9	59	97	0	313	40	5	9	44	1.59
1154035--1154080	24	1.9	24	91	8	76	60	2	0	36	1.09
1154031--1154082	24	2.3	23	84	15	72	59	1	0	38	1.08
1163214--1163286	24	3.0	24	89	0	119	12	46	4	36	1.61
1163879--1163903	8	3.1	8	100	0	50	0	16	24	60	1.36
1164461--1164730	134	2.0	134	100	0	540	36	9	11	42	1.73
1168050--1168091	20	2.1	20	100	0	84	28	9	11	50	1.70
1168317--1168393	33	2.4	32	82	8	93	46	16	9	27	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1168418--1168457	14	2.9	14	84	0	53	42	17	7	32	1.77
1168383--1168449	34	1.9	35	87	3	100	44	13	10	31	1.77
1175802--1175849	2	24.0	2	95	0	87	52	0	47	0	1.00
1176234--1176478	124	2.0	124	96	0	454	36	10	12	40	1.77
1181144--1181186	5	8.2	5	80	10	50	39	0	4	55	1.20
1183764--1183804	21	2.0	21	90	0	64	17	19	34	29	1.94
1185813--1185918	45	2.4	46	78	12	114	43	5	19	31	1.74
1190645--1190685	22	1.9	22	85	5	57	60	0	9	29	1.28
1191500--1191622	25	5.0	25	79	11	103	26	24	17	31	1.97
1195942--1196088	27	5.4	27	80	1	134	36	17	19	27	1.94
1199094--1199509	205	2.0	205	95	0	751	39	12	16	31	1.86
1201397--1201444	24	2.1	23	81	11	55	10	45	4	39	1.58
1212468--1212527	21	3.0	21	75	15	65	30	31	1	36	1.68
1216562--1216650	44	2.0	44	93	0	151	24	19	13	42	1.87
1218658--1218699	21	2.0	21	85	0	57	14	7	21	57	1.61
1222288--1222328	13	3.2	13	83	13	57	34	24	0	41	1.55
1224829--1224867	19	2.1	19	90	0	60	17	7	7	66	1.40
1226736--1226762	6	4.5	6	100	0	54	14	14	51	18	1.76
1228847--1229534	272	2.5	272	92	3	1119	28	16	14	39	1.88
1234852--1234877	12	2.2	12	100	0	52	23	26	15	34	1.94
1239762--1239836	13	6.1	13	80	12	86	30	8	21	40	1.82
1240119--1240170	27	1.9	26	84	7	68	32	0	5	61	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1253770--1253840	29	2.4	29	79	6	72	35	7	15	42	1.74
1254119--1254178	20	2.9	21	78	12	61	66	5	3	25	1.27
1257567--1257662	46	2.1	46	90	0	147	40	20	11	27	1.87
1264256--1264286	5	6.2	5	100	0	62	38	22	0	38	1.54
1268155--1268179	13	1.9	13	100	0	50	40	0	32	28	1.57
1268421--1268450	10	3.1	10	95	4	53	53	0	0	46	1.00
1279084--1279123	17	2.3	18	91	4	64	47	5	2	45	1.38
1287484--1287578	37	2.5	37	83	11	113	38	4	5	51	1.44
1287509--1287636	69	1.9	68	88	1	193	42	3	4	49	1.39
1292344--1292406	30	2.1	30	100	0	126	38	28	12	20	1.89
1295372--1295440	33	2.1	33	100	0	138	31	2	21	43	1.67
1296365--1296402	18	2.2	18	86	9	53	57	2	23	15	1.51
1296360--1296445	43	2.0	43	88	4	129	53	2	20	23	1.57
1302442--1302484	22	2.0	20	82	8	50	34	0	23	41	1.55
1305652--1305793	75	1.9	75	81	11	175	22	20	18	38	1.93
1306486--1306512	2	13.5	2	100	0	54	48	0	0	51	1.00
1308572--1308624	23	2.3	23	96	0	97	24	20	26	28	1.99
1312982--1313030	22	2.3	22	96	3	91	44	6	16	32	1.72
1313571--1313607	2	18.5	2	100	0	74	51	48	0	0	1.00
1313906--1313956	2	25.5	2	100	0	102	0	49	0	50	1.00
1323973--1324015	9	4.8	9	80	11	52	37	6	0	55	1.27
1324084--1324174	10	9.3	10	74	12	82	37	3	2	57	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1324084--1324173	19	4.6	19	74	10	67	37	3	2	56	1.28
1324559--1324631	38	1.9	38	83	5	94	46	8	13	31	1.73
1327743--1327783	21	1.9	22	85	5	57	43	4	2	48	1.37
1332777--1332842	19	3.4	20	74	16	75	60	3	0	36	1.12
1332776--1332857	38	2.1	39	82	6	96	62	2	2	32	1.22
1334655--1334693	6	6.5	6	87	0	60	64	12	2	20	1.40
1335916--1335981	33	2.0	33	93	0	114	21	25	16	36	1.94
1335952--1336496	44	11.9	44	73	9	270	30	18	16	34	1.93
1346409--1346523	43	2.7	43	81	4	135	29	25	19	26	1.98
1349987--1350041	18	3.2	17	82	10	67	65	1	5	27	1.25

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   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168