genome.fa.s12.2.7.7.80.10.50.1000.3.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   

This is table  3  of  120  ( 14336 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)
882256--882293	20	2.0	20	89	5	60	42	0	5	52	1.24
882258--882329	18	3.9	18	71	10	56	36	0	9	54	1.34
882256--882299	20	2.3	20	84	7	56	45	0	6	47	1.29
885629--885674	20	2.3	20	85	10	60	28	10	17	43	1.82
892489--892519	12	2.6	12	94	0	53	32	0	19	48	1.49
895639--895764	31	4.2	31	75	13	118	26	15	11	46	1.79
895724--895836	60	1.9	60	83	3	147	23	17	12	46	1.82
895639--895828	90	2.1	90	85	1	245	25	17	11	45	1.82
904032--904135	50	2.1	50	100	0	208	40	16	19	24	1.91
912282--912385	50	2.1	50	98	0	199	25	18	16	40	1.90
912868--912971	50	2.1	50	96	0	190	25	17	16	41	1.89
920110--920208	50	2.0	50	100	0	198	22	20	16	41	1.90
922412--922458	20	2.6	18	75	15	51	44	0	2	53	1.12
927912--928039	67	1.9	68	90	1	204	42	17	13	26	1.87
941095--941154	21	2.7	22	85	12	79	51	11	0	36	1.38
942631--942707	40	1.9	40	100	0	154	53	12	16	16	1.73
948009--948055	23	2.0	23	100	0	94	48	12	12	25	1.77
950561--950587	14	1.9	14	100	0	54	22	14	14	48	1.81
953168--953271	44	2.4	44	100	0	208	46	2	6	44	1.44
953355--953403	16	3.1	16	93	0	89	48	6	2	42	1.39
954112--954237	61	2.1	61	82	5	148	50	7	5	36	1.55
958701--958755	20	2.7	20	78	16	58	63	1	16	18	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
961125--961184	20	3.0	20	79	11	54	38	1	5	55	1.32
961125--961162	19	2.1	19	90	5	60	42	0	2	55	1.14
965283--965320	2	19.0	2	94	0	67	47	2	50	0	1.15
974549--974585	19	1.9	20	88	5	58	81	0	16	2	0.81
983305--983412	51	2.1	52	83	6	132	47	5	15	31	1.69
988457--988507	15	3.5	15	69	15	52	21	9	15	52	1.71
988636--988683	24	2.0	25	83	4	62	18	6	6	68	1.32
988812--988845	14	2.5	14	90	4	52	50	32	0	17	1.47
990022--990051	15	1.9	16	93	6	53	23	3	6	66	1.30
996347--996441	49	1.9	49	97	0	181	22	20	35	22	1.96
998988--999023	6	6.0	6	100	0	72	33	66	0	0	0.92
1002641--1002667	12	2.2	12	100	0	54	25	37	0	37	1.57
1008659--1008693	15	2.3	15	95	0	61	42	0	8	48	1.33
1010508--1010566	8	7.2	8	73	22	52	50	0	1	47	1.11
1010641--1010689	17	2.9	17	90	3	73	63	6	28	2	1.30
1011524--1011658	40	3.4	40	78	9	143	26	17	22	33	1.96
1011802--1011841	20	2.0	20	100	0	80	40	10	20	30	1.85
1015618--1015668	23	2.2	24	85	3	68	23	0	3	72	1.01
1027170--1027335	65	2.5	67	84	4	212	24	11	19	44	1.84
1027560--1027697	72	1.9	70	86	2	195	36	6	31	26	1.82
1030241--1030269	2	14.5	2	100	0	58	48	0	0	51	1.00
1030551--1030637	44	2.0	44	82	8	106	56	4	5	33	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1037518--1037556	17	2.4	16	83	8	51	69	5	2	23	1.21
1037625--1037689	24	2.8	24	77	13	73	72	3	1	23	1.07
1042676--1042725	21	2.4	20	80	9	55	64	2	4	30	1.23
1044567--1044703	39	3.5	40	83	4	163	32	5	18	43	1.72
1055900--1055929	15	1.9	15	93	6	51	36	0	6	56	1.26
1057237--1057286	25	2.0	25	100	0	100	24	8	24	44	1.80
1058518--1058551	16	2.0	18	88	11	54	50	0	20	29	1.49
1060642--1060697	25	2.2	25	84	6	69	21	25	17	35	1.95
1060683--1060731	25	2.0	25	83	0	62	32	20	18	28	1.96
1071236--1071275	19	2.0	20	85	4	55	20	15	17	47	1.83
1076213--1076245	17	1.9	17	88	11	50	39	0	3	57	1.14
1076235--1076267	10	3.0	11	86	13	50	27	0	0	72	0.85
1076326--1076392	27	2.5	27	97	0	125	31	23	32	11	1.91
1076462--1076505	21	2.1	21	95	0	79	29	0	11	59	1.32
1076593--1076636	16	2.8	16	82	0	61	56	2	2	38	1.24
1076669--1076750	38	2.2	38	95	0	146	40	2	2	54	1.26
1076783--1076904	60	2.0	60	85	3	165	53	13	1	31	1.49
1076919--1077076	8	18.4	8	67	20	79	50	14	0	34	1.48
1076966--1077159	19	10.1	19	70	21	120	54	12	0	33	1.38
1076945--1077076	27	5.1	27	92	5	213	52	12	0	34	1.40
1076999--1077156	67	2.5	61	80	13	167	55	11	0	33	1.36
1077155--1077221	27	2.5	27	100	0	134	13	32	22	31	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1078205--1078233	1	29.0	1	100	0	58	0	0	0	100	0.00
1079271--1079352	22	3.7	22	90	0	110	28	14	28	29	1.95
1081784--1081836	24	2.3	23	83	12	72	39	0	5	54	1.24
1081787--1081836	22	2.2	23	89	7	75	38	0	6	56	1.24
1088359--1088409	19	2.6	19	80	20	61	35	7	1	54	1.40
1088571--1088621	16	3.2	15	78	10	57	45	17	15	21	1.86
1092369--1092394	12	2.2	12	100	0	52	61	7	7	23	1.49
1105210--1105235	12	2.2	12	100	0	52	23	34	7	34	1.83
1113140--1113166	8	3.4	8	100	0	54	88	11	0	0	0.50
1118464--1118522	29	2.0	29	86	6	82	33	10	18	37	1.85
1123977--1124024	22	2.2	22	85	10	64	64	0	2	33	1.05
1123977--1124024	20	2.2	22	85	10	64	64	0	2	33	1.05
1124357--1124707	43	8.0	43	76	15	315	35	19	5	38	1.76
1124462--1124536	13	5.5	13	71	12	51	38	18	6	36	1.77
1124564--1124715	13	11.1	13	69	17	67	36	20	5	36	1.77
1124400--1124724	179	1.8	179	93	0	569	36	20	6	36	1.78
1128309--1128364	18	3.3	18	75	12	64	62	0	0	37	0.95
1132983--1133056	33	2.2	33	80	0	85	27	9	20	43	1.82
1135247--1135302	19	3.1	18	70	12	51	62	7	7	23	1.46
1138097--1138155	30	1.9	31	89	3	93	47	0	20	32	1.50
1140661--1140768	54	2.0	54	98	1	209	48	5	19	26	1.71
1141477--1141564	44	2.0	44	91	4	142	21	12	23	42	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1153338--1153370	2	16.5	2	100	0	66	51	0	0	48	1.00
1165774--1165803	5	6.0	5	96	0	51	16	0	23	60	1.36
1168808--1168850	22	2.0	22	85	0	59	51	9	11	27	1.69
1172944--1172997	27	2.0	27	88	0	81	11	20	24	44	1.83
1181728--1182255	224	2.3	222	84	6	681	33	15	21	29	1.94
1181723--1182303	114	5.1	113	70	10	427	33	15	21	30	1.94
1182103--1182503	188	2.1	188	92	0	658	31	15	22	30	1.95
1182238--1182377	74	1.9	75	86	4	203	31	17	21	29	1.96
1182238--1182396	74	2.1	75	82	4	196	34	17	20	27	1.95
1182313--1182530	114	1.9	113	79	8	246	31	15	22	30	1.95
1182919--1182969	7	7.6	7	86	8	79	15	0	50	33	1.44
1182912--1182969	21	2.8	20	90	10	91	17	0	48	34	1.47
1182924--1182991	33	2.1	33	83	5	84	19	0	47	33	1.50
1183068--1183164	7	13.9	7	81	4	88	22	1	46	29	1.59
1183068--1183164	21	4.6	21	76	5	97	22	1	46	29	1.59
1183125--1183319	95	2.0	96	81	5	225	28	1	29	41	1.65
1183390--1183416	14	1.9	14	100	0	54	48	0	7	44	1.31
1183418--1183458	20	2.0	20	85	0	55	60	4	7	26	1.43
1183466--1183498	8	4.1	8	88	11	50	84	3	0	12	0.72
1183466--1183498	15	2.1	16	94	5	59	84	3	0	12	0.72
1184862--1184886	10	2.5	10	100	0	50	48	12	8	32	1.69
1188023--1188171	48	3.0	46	70	25	133	40	6	2	50	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1188225--1188276	13	4.0	13	92	0	77	46	9	1	42	1.47
1188244--1188379	53	2.6	53	85	0	200	38	11	5	45	1.62
1188524--1188773	9	28.8	9	69	11	130	44	20	4	30	1.70
1194240--1194410	66	2.6	65	84	4	209	41	18	26	12	1.87
1194401--1194491	21	4.3	21	76	5	85	34	18	41	5	1.74
1195201--1195243	22	2.0	22	95	0	77	41	27	20	9	1.83
1198622--1198697	26	3.0	25	86	9	100	36	17	7	38	1.79
1198979--1199047	24	2.7	25	84	8	77	39	5	27	27	1.79
1200405--1200453	19	2.5	20	78	15	57	61	2	0	36	1.08
1201041--1201121	29	2.8	28	73	14	74	38	18	4	38	1.73

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