genome.fa.s4.2.7.7.80.10.50.1000.132.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   186   187   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  132  of  198  ( 23681 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)
42112050--42112204	21	7.4	21	65	16	79	20	10	11	56	1.64
42112048--42112280	42	5.5	43	83	7	262	20	11	12	55	1.68
42112063--42112324	42	6.0	44	79	9	254	20	11	11	56	1.65
42112067--42112270	21	9.6	21	65	16	80	20	12	11	54	1.69
42113009--42113219	42	4.9	42	79	6	208	18	9	12	59	1.59
42113044--42113203	86	1.9	86	90	0	257	18	8	13	60	1.57
42113007--42113165	21	7.5	20	68	16	70	20	8	13	57	1.62
42113150--42113214	24	2.9	23	79	9	80	18	6	9	66	1.41
42113575--42113604	16	1.9	15	93	6	51	20	6	0	73	1.05
42120191--42120217	14	1.9	14	100	0	54	22	18	7	51	1.70
42120599--42120639	21	2.0	21	85	0	55	36	31	17	14	1.90
42127447--42127472	11	2.4	11	100	0	52	38	7	0	53	1.30
42127432--42127561	39	3.3	39	81	11	176	34	3	0	61	1.14
42130513--42130548	19	1.9	18	88	5	54	58	2	5	33	1.36
42132436--42132720	129	2.2	129	89	1	437	27	22	21	29	1.99
42132436--42132720	44	6.6	43	67	17	155	27	22	21	29	1.99
42132752--42132911	46	3.5	45	82	3	178	28	21	18	31	1.97
42145073--42146149	298	3.6	298	94	0	1807	28	19	19	32	1.96
42147624--42147648	10	2.5	10	100	0	50	28	8	0	64	1.22
42148192--42148279	45	2.0	45	95	0	158	34	22	18	25	1.96
42148286--42148426	51	2.8	51	84	0	183	33	28	15	22	1.95
42151986--42152028	21	2.2	19	83	8	50	32	2	0	65	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42152451--42152509	26	2.1	31	84	15	83	30	1	5	62	1.26
42157575--42157651	21	3.7	21	89	0	109	42	16	20	19	1.89
42157620--42157691	21	3.4	21	78	5	74	48	18	22	11	1.79
42157562--42157691	42	3.1	43	78	12	146	46	15	22	15	1.83
42164556--42164586	16	1.9	16	100	0	62	70	9	0	19	1.14
42164557--42164594	16	2.4	16	90	0	58	76	7	0	15	1.01
42166224--42166282	30	2.0	30	86	6	84	20	38	0	40	1.53
42166370--42166430	19	3.2	18	79	9	61	22	36	0	40	1.55
42171365--42171393	12	2.3	13	94	5	51	6	6	13	72	1.26
42184537--42184708	25	7.4	25	75	10	107	19	23	18	39	1.92
42184565--42184652	44	2.0	44	86	0	122	21	23	17	37	1.94
42184590--42184626	19	1.9	19	94	0	65	24	29	10	35	1.89
42184621--42184707	47	1.9	44	83	6	111	17	24	19	39	1.92
42184621--42184708	22	3.9	22	79	10	88	17	23	19	39	1.92
42194588--42194823	50	4.6	50	78	7	201	28	20	27	23	1.99
42203809--42203839	9	3.3	9	91	8	53	77	0	22	0	0.77
42203809--42203838	5	6.2	5	92	7	53	80	0	20	0	0.72
42203809--42203838	14	2.1	15	93	6	53	80	0	20	0	0.72
42207523--42208025	252	2.0	252	96	0	918	31	15	15	37	1.89
42208437--42208477	18	2.3	18	80	20	50	73	14	2	9	1.19
42209324--42209763	227	1.9	228	90	2	706	29	17	14	38	1.90
42228175--42228370	27	7.3	27	80	3	218	42	21	19	15	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42228175--42228368	53	3.6	52	82	6	219	42	22	19	15	1.88
42228175--42228368	80	2.4	80	83	1	237	42	22	19	15	1.88
42234667--42234745	20	4.0	20	73	6	70	34	13	35	16	1.88
42234643--42234748	40	2.7	40	83	5	117	34	14	33	16	1.89
42241563--42241750	51	3.7	51	82	4	211	22	15	29	31	1.95
42241876--42241948	37	1.9	37	84	13	96	42	1	23	32	1.63
42245193--42245299	55	1.9	55	90	0	169	25	21	14	39	1.90
42254974--42255000	2	13.5	2	100	0	54	51	0	48	0	1.00
42258421--42259429	503	2.0	503	91	0	1653	26	11	21	40	1.88
42260099--42260238	72	1.9	72	100	0	280	37	5	7	50	1.54
42263658--42263704	24	2.0	24	100	0	94	27	12	4	55	1.56
42275083--42275150	32	2.1	32	86	10	95	47	11	0	41	1.40
42275311--42275346	13	2.8	13	95	0	63	50	16	0	33	1.46
42279217--42279409	50	3.7	51	81	5	210	25	21	29	23	1.99
42285619--42285666	25	1.9	25	91	0	78	20	18	25	35	1.95
42299387--42299471	9	9.4	9	88	0	107	43	22	8	25	1.81
42299395--42299471	27	2.9	27	90	0	118	42	23	9	24	1.83
42299616--42299659	18	2.4	18	92	0	70	11	2	45	40	1.53
42306290--42306360	29	2.4	29	85	0	88	49	1	15	33	1.54
42306325--42306407	34	2.5	33	78	5	94	42	0	16	40	1.49
42306513--42306902	124	3.1	126	87	4	565	38	16	16	28	1.91
42313254--42313291	19	2.0	19	85	10	51	50	2	5	42	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42316570--42316681	54	2.1	52	82	11	131	49	1	3	45	1.30
42322084--42322117	17	2.1	16	88	5	50	70	0	29	0	0.87
42328106--42328209	54	1.9	54	84	0	136	33	14	25	25	1.94
42331458--42331550	39	2.5	37	80	7	98	27	29	22	20	1.98
42331708--42331762	24	2.2	26	81	15	71	29	25	0	45	1.54
42332865--42332910	14	3.3	14	93	0	83	56	2	0	41	1.11
42337738--42337780	21	2.0	21	82	8	52	23	20	4	51	1.66
42339339--42339378	6	6.7	6	85	0	53	50	10	0	40	1.36
42339342--42339376	18	1.9	18	94	0	61	54	5	0	40	1.24
42339339--42339378	12	3.3	12	89	0	62	50	10	0	40	1.36
42340415--42340481	5	14.2	5	80	12	79	61	1	0	37	1.05
42340414--42340478	7	8.9	7	71	15	51	60	1	0	38	1.07
42340413--42340479	22	3.0	22	79	12	75	58	1	0	40	1.07
42342782--42342898	54	2.2	53	83	7	137	31	19	22	26	1.98
42342801--42342908	54	2.0	54	87	0	153	32	20	20	26	1.97
42345648--42345688	17	2.3	19	88	12	61	53	2	0	43	1.13
42345664--42345715	26	2.0	26	85	11	70	51	1	1	44	1.23
42346665--42346703	11	3.5	11	80	19	53	28	2	0	69	1.02
42346657--42346709	23	2.6	19	73	21	54	33	5	0	60	1.20
42351008--42351044	19	1.9	19	88	0	56	59	2	8	29	1.40
42352977--42353022	21	2.2	21	84	0	56	26	28	34	10	1.90
42353721--42353819	25	3.9	25	82	1	117	36	24	17	22	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42359339--42359430	3	29.7	3	82	8	105	30	4	1	64	1.20
42362074--42362180	30	3.8	28	74	14	85	41	0	4	53	1.28
42362133--42362181	19	2.6	18	78	9	53	44	2	2	51	1.24
42366145--42366715	127	4.5	126	90	2	855	30	16	23	29	1.97
42366145--42366715	253	2.3	251	89	2	860	30	16	23	29	1.97
42369786--42369995	114	1.8	114	98	0	411	41	7	9	40	1.66
42369995--42370691	43	16.1	43	84	8	864	26	0	30	42	1.60
42370177--42370245	15	4.7	15	85	8	72	26	0	33	40	1.56
42370193--42370232	8	5.2	8	88	11	66	25	0	32	42	1.55
42370634--42370682	15	3.5	15	69	25	52	22	0	34	42	1.54
42369995--42370660	64	10.3	63	85	6	626	26	0	30	42	1.61
42370630--42370688	27	2.1	28	96	3	111	20	0	37	42	1.52
42369995--42370691	22	32.1	22	84	8	873	26	0	30	42	1.60
42371230--42371273	18	2.4	18	84	0	61	50	6	27	15	1.70
42371919--42371943	7	3.6	7	100	0	50	60	12	0	28	1.32
42372113--42372150	20	1.9	20	89	10	60	55	5	2	36	1.37
42373165--42373197	11	2.8	12	86	9	50	42	3	30	24	1.70
42377883--42377925	19	2.3	19	83	0	50	34	0	4	60	1.17
42386252--42386377	62	2.0	62	90	0	198	31	11	11	45	1.76
42391858--42391893	12	3.0	12	91	0	54	52	16	2	27	1.57
42395148--42395268	39	3.1	39	90	0	206	29	21	13	35	1.91
42399494--42399534	21	2.0	21	85	0	55	63	12	9	14	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42403527--42403560	15	2.2	16	89	5	52	50	0	8	41	1.34
42405587--42405622	16	2.2	16	90	0	54	41	11	16	30	1.83
42407555--42407614	31	1.9	32	83	10	79	21	6	41	30	1.79
42408657--42408743	42	2.1	42	91	4	140	34	21	20	22	1.97
42408720--42408767	24	2.0	24	95	0	87	27	16	25	31	1.97
42408678--42408809	66	2.0	66	91	5	214	31	19	21	27	1.97
42408657--42408851	108	1.8	108	92	2	329	34	21	20	24	1.97
42408744--42409010	42	6.3	42	86	2	383	33	20	20	24	1.97
42408757--42409001	127	1.9	126	92	0	409	35	20	19	23	1.95
42409395--42409444	21	2.4	21	82	0	64	4	44	16	36	1.66

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   186   187   188   189   190   191   192   
          193   194   195   196   197   198