genome.fa.s4.2.7.7.80.10.50.1000.119.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  119  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)
38255079--38255126	3	15.7	3	95	4	87	66	0	2	31	1.03
38255668--38256299	145	4.3	146	94	0	1117	44	15	15	24	1.84
38256130--38256167	20	1.9	20	88	0	58	71	2	0	26	1.00
38255668--38256299	291	2.2	291	95	1	1126	44	15	15	24	1.84
38256573--38256602	15	2.0	15	100	0	60	33	33	13	20	1.91
38260765--38260807	13	3.3	13	80	0	50	55	4	2	37	1.33
38262270--38262435	43	3.9	43	83	3	201	25	21	25	27	1.99
38267926--38267955	7	4.3	7	100	0	60	0	43	0	56	0.99
38269336--38269587	128	2.0	128	99	0	495	36	13	20	29	1.90
38281845--38281870	3	8.7	3	100	0	52	30	0	0	69	0.89
38296427--38296459	16	2.1	16	94	0	57	78	0	15	6	0.93
38299542--38299580	17	2.3	17	86	8	53	38	0	20	41	1.53
38300239--38300302	19	3.3	20	78	8	87	6	29	21	42	1.78
38300227--38300302	19	3.9	20	77	6	84	6	28	22	42	1.78
38306816--38306869	28	1.9	28	85	7	74	40	22	9	27	1.84
38308137--38308169	12	2.8	12	95	0	57	21	33	12	33	1.90
38312804--38312836	12	2.8	12	95	0	57	21	33	12	33	1.90
38317885--38317927	18	2.3	18	84	8	50	37	6	6	48	1.57
38320037--38320253	51	4.3	51	94	0	371	27	25	15	31	1.96
38323325--38323385	30	2.0	30	96	0	113	44	24	3	27	1.69
38325287--38325342	25	2.2	25	84	9	69	53	1	7	37	1.39
38328233--38328261	2	14.5	2	100	0	58	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38332413--38332510	28	3.5	28	91	0	142	30	11	28	29	1.91
38333245--38333956	93	7.7	93	96	0	1298	28	12	17	40	1.87
38333904--38333987	29	3.1	28	71	22	79	29	13	14	42	1.83
38340789--38340855	25	2.7	25	85	0	71	37	14	13	34	1.86
38347412--38347480	32	2.2	30	84	7	84	52	10	5	31	1.59
38351283--38351334	3	17.3	3	100	0	104	67	0	0	32	0.91
38352628--38352739	43	2.6	44	84	1	127	31	20	16	31	1.95
38352768--38353233	132	3.5	132	92	2	747	31	24	15	27	1.96
38352768--38353236	44	10.7	44	77	9	438	31	24	15	28	1.95
38359870--38359917	13	3.6	13	75	5	51	62	0	2	35	1.07
38364037--38364112	38	2.0	38	100	0	152	18	18	18	44	1.87
38367800--38367856	28	1.9	28	86	10	78	49	0	8	42	1.34
38370950--38371029	41	2.0	41	82	0	97	41	30	12	16	1.85
38371028--38371073	22	2.1	22	87	0	65	34	36	17	10	1.85
38371041--38371127	38	2.3	38	93	0	147	33	33	24	9	1.87
38373965--38373999	2	17.5	2	100	0	70	48	0	0	51	1.00
38374493--38374533	18	2.2	19	86	4	57	60	2	0	36	1.10
38378919--38378975	16	2.8	22	63	31	54	38	0	0	61	0.96
38380176--38380216	18	2.2	19	86	4	57	56	14	0	29	1.39
38381939--38382047	10	11.5	10	66	21	56	59	1	0	38	1.08
38381937--38382016	20	4.3	20	76	17	84	58	0	0	41	0.98
38381937--38382016	40	2.2	36	80	19	94	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38381970--38382024	26	2.2	25	83	3	65	60	1	0	38	1.08
38382005--38382045	19	2.2	18	91	4	64	65	4	0	29	1.13
38382935--38382989	19	2.8	20	78	10	60	25	9	1	63	1.34
38383002--38383113	10	11.6	10	68	17	51	28	4	1	65	1.22
38383032--38383152	57	2.1	58	80	13	135	31	3	2	62	1.24
38382993--38383152	19	8.3	18	69	19	58	31	3	1	62	1.23
38385812--38385889	33	2.5	30	78	15	88	47	1	1	50	1.17
38385809--38385904	21	4.6	19	73	18	68	48	1	2	47	1.20
38388940--38389055	11	10.8	11	66	21	52	61	0	2	36	1.10
38388931--38388988	30	2.0	29	86	10	82	58	0	1	39	1.08
38388931--38389072	38	3.7	38	94	4	241	62	0	2	35	1.07
38401535--38401651	39	3.0	39	91	2	189	39	23	5	32	1.76
38401664--38401800	39	3.6	36	77	12	130	46	14	4	34	1.65
38401873--38401921	21	2.3	21	89	0	71	40	2	4	53	1.32
38401884--38401923	21	1.9	21	100	0	80	40	0	2	57	1.12
38401886--38401954	21	3.2	21	84	11	70	34	2	2	59	1.27
38405543--38405572	15	2.0	15	100	0	60	53	13	6	26	1.64
38405764--38405827	3	21.3	3	93	0	110	31	1	0	67	1.00
38414320--38414350	15	2.1	15	93	0	53	48	9	0	41	1.36
38414457--38414645	61	3.2	56	77	10	182	52	4	2	40	1.35
38418909--38419028	44	2.8	43	78	16	140	28	27	20	24	1.99
38420942--38420982	20	2.0	20	100	0	82	46	0	9	43	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38420942--38420991	20	2.5	20	90	6	66	46	0	12	42	1.41
38421528--38421676	63	2.4	63	80	2	174	29	6	31	32	1.82
38425560--38425593	13	2.5	13	85	4	50	26	0	2	70	1.01
38429638--38429747	55	2.0	55	98	0	211	30	31	13	23	1.93
38430297--38430345	21	2.4	20	86	6	71	22	28	8	40	1.82
38430518--38430626	21	5.3	21	73	7	82	45	16	22	15	1.84
38430531--38430626	21	4.6	21	77	0	111	44	16	21	16	1.86
38432544--38432583	18	2.2	18	95	0	71	30	2	17	50	1.59
38439633--38439901	124	2.2	125	89	2	425	28	15	22	33	1.94
38443031--38443705	23	30.2	23	83	7	797	25	0	25	48	1.52
38443041--38443709	44	15.0	43	85	7	740	25	0	25	48	1.53
38443041--38443709	67	10.0	67	89	4	964	25	0	25	48	1.53
38443736--38443777	9	4.8	9	94	2	68	57	11	0	30	1.35
38443767--38443891	25	5.3	24	76	14	136	47	13	0	39	1.43
38443769--38443901	69	1.9	69	100	0	266	48	12	0	38	1.41
38444320--38444359	18	2.2	18	90	0	62	42	7	30	20	1.79
38445010--38445034	7	3.6	7	100	0	50	60	12	0	28	1.32
38445205--38445242	20	1.9	20	84	10	51	55	7	2	34	1.43
38446136--38446178	11	3.8	12	81	6	54	58	0	0	41	0.98
38446248--38446287	11	3.6	11	93	6	64	42	0	35	22	1.54
38447060--38447099	20	2.0	20	90	0	62	27	10	12	50	1.72
38447039--38447115	14	5.0	15	71	20	52	35	6	14	44	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38447404--38447475	37	1.9	37	100	0	144	40	15	5	38	1.70
38448760--38448865	44	2.4	44	93	1	176	43	29	6	20	1.77
38449137--38449180	14	3.1	14	90	0	70	15	9	54	20	1.68
38449446--38449478	14	2.4	14	94	0	57	15	9	60	15	1.58
38468188--38468260	29	2.5	29	97	0	137	43	13	8	34	1.74
38468277--38468316	9	4.4	9	87	0	53	40	25	7	27	1.82
38468445--38468498	18	2.9	18	86	2	72	11	1	46	40	1.50
38470641--38470992	178	2.0	178	96	0	650	37	11	23	27	1.89
38473706--38473823	62	1.9	61	82	3	148	41	6	2	49	1.43
38473932--38473984	25	2.1	26	85	3	72	39	9	13	37	1.77
38477743--38477823	26	3.2	26	78	3	94	20	19	18	40	1.91
38477817--38477873	25	2.3	25	90	0	87	24	24	15	35	1.95
38477754--38477932	25	7.2	26	68	13	74	21	19	19	39	1.92
38490851--38490911	22	2.8	22	78	14	63	44	1	3	50	1.28
38492671--38492705	15	2.4	14	85	4	52	65	0	0	34	0.93
38492671--38492713	16	2.8	15	82	13	52	65	0	0	34	0.93
38506845--38506896	4	13.0	4	95	0	95	26	0	23	50	1.50
38513043--38513068	2	13.0	2	100	0	52	50	0	0	50	1.00
38518818--38518844	2	13.5	2	100	0	54	48	0	0	51	1.00
38518935--38518987	26	1.9	27	81	11	63	39	18	7	33	1.79
38520548--38520587	17	2.4	16	87	4	53	77	0	20	2	0.88
38520943--38520969	8	3.4	8	100	0	54	22	0	0	77	0.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38530729--38530763	18	1.9	18	94	0	61	31	34	14	20	1.92
38530776--38530805	15	2.0	15	93	0	51	16	50	13	20	1.78
38530786--38530931	63	2.3	63	78	4	161	19	36	19	23	1.94
38544350--38544412	30	2.0	32	87	6	94	58	0	1	39	1.07
38544347--38544383	19	1.9	19	94	0	65	64	0	0	35	0.94
38548376--38548406	5	6.2	5	92	0	53	38	3	0	58	1.15
38553214--38553325	56	2.0	57	87	1	163	43	15	12	28	1.83
38554129--38554182	18	2.9	18	86	2	72	11	1	46	40	1.50
38554462--38554578	24	4.5	25	69	18	71	67	2	0	29	1.09
38555600--38555637	20	1.9	20	88	0	58	36	5	5	52	1.47

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