genome.fa.s17.2.7.7.80.10.50.1000.4.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: D04
Parameters: 2 7 7 80 10 50 1000
Length:  56598092

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   

This is table  4  of  185  ( 22116 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)
1059456--1059535	24	3.4	23	77	11	74	71	3	1	23	1.10
1064513--1064558	21	2.3	21	88	7	69	69	0	0	30	0.89
1064520--1064569	21	2.4	20	80	9	55	64	2	4	30	1.23
1075861--1075890	15	1.9	15	93	6	51	36	0	6	56	1.26
1077199--1077248	25	2.0	25	100	0	100	24	8	24	44	1.80
1078724--1078777	3	18.0	3	100	0	108	33	0	0	66	0.92
1080639--1080690	25	2.1	25	82	7	61	21	25	17	36	1.94
1088546--1088587	21	2.0	21	86	4	59	33	7	16	42	1.75
1091288--1091327	19	2.0	20	90	4	64	17	15	20	47	1.83
1095614--1095644	15	2.1	15	93	0	53	74	16	3	6	1.16
1096919--1096953	3	11.7	3	100	0	70	0	31	0	68	0.90
1100500--1100553	25	2.2	24	90	6	83	38	0	5	55	1.23
1107009--1107059	19	2.6	19	80	20	61	35	7	1	54	1.40
1107221--1107271	16	3.2	15	78	10	57	45	17	15	21	1.86
1129301--1129335	8	4.4	8	100	0	70	88	11	0	0	0.51
1134635--1134693	29	2.0	29	86	6	82	33	10	18	37	1.85
1140140--1140187	22	2.2	22	85	10	64	64	0	2	33	1.05
1140140--1140187	20	2.2	22	85	10	64	64	0	2	33	1.05
1140520--1140691	43	4.0	43	93	0	272	33	18	6	41	1.76
1140520--1140870	86	4.0	86	73	14	329	35	19	5	38	1.77
1140507--1140878	13	26.9	14	65	20	90	36	19	6	37	1.77
1140563--1140887	179	1.8	179	94	0	578	36	20	6	36	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1140742--1140870	43	3.0	43	92	4	215	34	20	5	39	1.75
1144458--1144509	20	2.5	20	84	9	59	59	7	0	32	1.26
1144472--1144511	20	2.0	20	95	0	71	65	2	0	32	1.06
1149126--1149199	33	2.2	33	82	0	94	27	9	21	41	1.84
1151386--1151441	19	3.1	18	70	12	51	62	7	7	23	1.46
1154239--1154297	30	1.9	31	89	3	93	47	0	20	32	1.50
1156802--1156909	54	2.0	54	98	1	209	48	5	19	26	1.71
1157380--1157467	44	2.0	44	91	4	142	21	12	23	42	1.87
1162891--1162915	11	2.3	11	100	0	50	0	0	8	92	0.40
1187803--1187832	5	6.0	5	96	0	51	16	0	23	60	1.36
1190611--1190645	11	3.3	10	85	14	52	45	0	0	54	0.99
1190842--1190884	22	2.0	22	85	0	59	51	9	11	27	1.69
1194979--1195032	27	2.0	27	88	0	81	11	20	24	44	1.83
1207008--1207083	26	3.0	26	88	5	102	34	17	10	38	1.84
1207363--1207437	28	2.9	27	82	11	93	37	5	29	28	1.79
1208790--1208828	20	2.0	19	85	14	53	61	2	0	35	1.10
1209429--1209509	29	2.8	28	73	14	74	38	18	4	38	1.73
1209529--1209568	17	2.4	17	86	0	53	57	0	2	40	1.12
1210163--1210204	20	2.1	20	91	8	68	33	2	2	61	1.21
1210693--1210745	27	2.0	27	96	0	97	26	20	18	33	1.96
1214240--1214267	5	5.6	5	100	0	56	39	0	0	60	0.97
1215588--1215626	18	2.3	18	86	8	55	64	7	2	25	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1217510--1217558	20	2.4	22	80	13	59	65	0	6	28	1.16
1220241--1220282	22	1.9	23	85	9	61	52	9	0	38	1.34
1220318--1220361	23	1.9	23	81	9	54	54	0	20	25	1.45
1221249--1221274	11	2.4	11	100	0	52	38	7	0	53	1.30
1221249--1221331	11	7.5	11	70	22	50	36	3	0	60	1.14
1221239--1221346	42	2.6	42	85	1	164	35	3	0	61	1.14
1221297--1221349	15	3.5	15	75	14	63	28	3	0	67	1.07
1221300--1221374	31	2.3	33	86	11	111	32	4	1	62	1.22
1221239--1221368	41	3.1	42	77	16	137	32	3	0	63	1.18
1221752--1221790	11	3.5	11	82	0	51	69	23	2	5	1.21
1222379--1222430	18	2.9	17	78	18	61	61	0	0	38	0.96
1222344--1222441	47	2.2	45	82	12	112	59	0	2	38	1.09
1222474--1222527	10	5.4	10	76	8	56	68	1	1	27	1.10
1222472--1222527	29	1.9	30	85	10	80	67	1	1	28	1.10
1222991--1223037	20	2.3	21	88	3	78	38	2	4	55	1.31
1223128--1223191	19	3.3	19	84	6	76	31	3	3	62	1.26
1228640--1228675	17	2.2	17	90	5	56	25	2	0	72	0.98
1235946--1235999	25	2.2	25	83	6	65	11	14	16	57	1.65
1256606--1256679	38	1.9	38	81	5	87	22	13	31	32	1.93
1256685--1256761	38	2.0	38	84	0	100	28	5	29	36	1.79
1257770--1257803	17	2.0	18	88	11	54	41	11	0	47	1.40
1259702--1259776	26	2.9	26	76	9	82	18	20	24	37	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1259740--1259880	73	1.9	73	82	2	176	21	20	21	36	1.96
1259730--1259891	73	2.2	73	76	3	164	19	19	22	38	1.94
1262135--1262200	33	2.0	33	96	0	123	31	4	18	45	1.69
1266438--1266486	18	2.8	18	75	3	55	59	0	0	40	0.98
1268004--1268070	34	1.9	35	88	8	102	34	8	11	44	1.73
1268889--1268922	3	11.3	3	100	0	68	35	0	0	64	0.94
1275966--1276031	31	2.1	31	100	0	132	27	12	12	48	1.76
1277683--1277717	17	2.0	18	88	5	54	60	0	2	37	1.12
1283744--1283768	2	12.5	2	100	0	50	52	0	48	0	1.00
1287926--1287967	6	7.0	6	100	0	84	66	16	0	16	1.25
1290209--1290243	16	2.1	18	89	10	56	45	2	5	45	1.41
1307046--1307096	20	2.5	19	81	12	57	27	3	3	64	1.28
1307155--1307192	7	4.9	8	87	12	53	21	0	2	76	0.91
1317152--1317401	125	2.0	125	98	0	482	22	20	17	39	1.92
1321862--1321913	22	2.3	23	83	6	61	63	1	0	34	1.06
1321961--1322007	24	2.0	23	84	8	60	59	2	0	38	1.09
1324491--1324531	12	3.6	12	77	12	50	39	7	0	53	1.29
1324693--1324734	17	2.5	17	77	11	50	61	2	0	35	1.09
1324721--1324753	16	2.1	16	88	11	50	81	0	3	15	0.80
1341308--1341349	22	2.0	22	86	13	61	80	7	2	9	0.97
1346800--1346831	15	2.1	15	100	0	64	0	0	68	31	0.90
1352792--1352826	15	2.4	15	90	4	54	48	0	8	42	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1357877--1357901	2	12.5	2	100	0	50	48	0	0	52	1.00
1358108--1358157	15	3.3	15	74	20	50	44	4	2	50	1.32
1370053--1370132	30	2.7	30	96	3	144	37	23	10	28	1.87
1375143--1375205	32	2.0	32	93	0	108	28	17	14	39	1.89
1388515--1388593	40	2.0	40	87	0	113	44	18	13	22	1.86
1391498--1391658	35	4.6	35	84	3	216	27	17	16	39	1.90
1391494--1391658	70	2.4	70	90	2	260	27	17	15	39	1.90
1391494--1391678	35	5.3	35	80	6	178	26	17	16	40	1.90
1391494--1391678	70	2.6	69	88	5	248	26	17	16	40	1.90
1414500--1414621	45	2.7	45	79	2	138	40	16	22	20	1.91
1415080--1415136	12	4.5	12	79	20	55	47	5	0	47	1.24
1415657--1415757	9	11.4	9	82	4	134	34	23	8	32	1.86
1415656--1415757	26	3.9	26	85	6	134	35	23	8	32	1.86
1415657--1415757	44	2.3	44	94	0	184	34	23	8	32	1.86
1418224--1418275	18	2.7	19	82	5	61	23	17	19	40	1.91
1427803--1427863	32	1.9	32	93	0	104	27	21	8	42	1.81
1427747--1427937	90	2.1	89	81	5	226	26	15	10	47	1.79
1431890--1432011	23	5.3	23	84	3	165	31	25	20	22	1.98
1431890--1432011	46	2.7	46	92	2	192	31	25	20	22	1.98
1432237--1432275	18	2.2	17	86	13	53	46	20	0	33	1.51
1434352--1434391	9	4.4	9	83	0	53	52	12	2	32	1.52
1435323--1435372	17	2.7	20	78	18	70	10	0	44	46	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1439961--1440010	17	2.7	20	78	18	70	10	0	44	46	1.37
1446979--1447012	16	2.0	18	88	11	54	58	2	5	32	1.37
1446985--1447055	12	6.0	12	70	17	51	64	0	2	32	1.08
1446993--1447061	33	2.1	33	100	0	138	66	0	2	30	1.06
1447013--1447053	21	2.0	21	85	0	55	65	0	2	31	1.05
1447104--1447162	25	2.2	28	82	17	72	62	6	6	23	1.44
1447145--1447193	13	3.6	14	78	10	57	65	8	0	26	1.20
1456760--1456836	37	2.1	37	97	0	145	32	10	11	45	1.75
1463947--1464153	66	3.1	66	94	2	362	26	22	27	24	2.00
1464455--1464544	42	2.1	42	91	0	144	32	21	31	15	1.94

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185