genome.fa.s13.2.7.7.80.10.50.1000.113.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   199   

This is table  113  of  199  ( 23770 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)
34347044--34347086	2	21.5	2	100	0	86	51	0	0	48	1.00
34347172--34347204	3	11.0	3	100	0	66	66	0	0	33	0.92
34351272--34351325	22	2.5	21	75	6	54	55	1	0	42	1.10
34351568--34351598	16	1.9	16	93	0	53	29	12	6	51	1.65
34355834--34355891	29	2.1	27	87	12	84	43	3	3	50	1.36
34358975--34359028	26	2.1	26	85	0	72	27	16	11	44	1.82
34358986--34359044	26	2.3	26	88	5	84	28	10	13	47	1.75
34359191--34359232	6	7.0	6	88	0	57	16	23	0	59	1.37
34359191--34359233	12	3.6	12	87	0	68	16	25	0	58	1.38
34359191--34359233	18	2.4	18	96	0	77	16	25	0	58	1.38
34362631--34362677	25	1.9	25	82	4	60	14	23	21	40	1.90
34362752--34362823	26	2.8	25	72	12	74	16	23	23	36	1.94
34362783--34362866	24	3.5	24	66	19	57	16	20	21	41	1.90
34370002--34370066	27	2.5	26	82	7	78	16	26	21	35	1.95
34370094--34370152	25	2.4	24	77	8	64	20	25	16	37	1.93
34372878--34372950	40	1.9	37	84	13	96	15	27	21	35	1.93
34376087--34376171	38	2.2	38	81	8	93	32	23	22	21	1.98
34382678--34382745	35	1.9	35	82	11	86	27	23	17	30	1.97
34386503--34386608	30	3.5	30	92	2	169	42	0	22	33	1.60
34387986--34388094	41	2.7	41	85	2	148	23	27	19	29	1.98
34390376--34390470	41	2.3	41	96	0	172	26	24	21	28	1.99
34392112--34392140	13	2.3	13	94	5	51	44	20	3	31	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34394266--34394296	13	2.4	13	94	0	53	35	0	58	6	1.24
34394288--34394322	18	1.9	18	88	0	52	48	0	51	0	1.00
34403600--34403645	19	2.4	19	89	10	67	56	0	6	36	1.25
34403630--34403706	30	2.6	30	87	6	113	51	0	0	48	1.00
34403600--34403762	19	8.1	20	67	17	63	51	0	4	43	1.26
34403653--34403742	32	3.0	29	69	20	67	51	1	1	46	1.15
34406076--34406124	16	3.0	17	82	5	57	34	2	2	61	1.19
34406097--34406146	16	3.1	16	72	16	50	36	2	0	62	1.07
34406103--34406148	23	2.0	24	87	8	69	39	0	0	60	0.97
34406883--34407059	91	1.9	91	82	0	219	25	22	29	22	1.99
34417638--34417914	51	5.6	51	89	6	451	33	15	22	28	1.94
34417638--34417910	95	2.8	95	91	3	429	32	15	22	28	1.95
34417652--34417917	146	1.8	146	95	0	487	33	15	22	28	1.94
34419351--34419400	21	2.5	20	81	15	59	40	6	10	44	1.63
34422873--34422913	2	20.5	2	100	0	82	51	0	0	48	1.00
34422986--34423022	18	2.0	19	89	5	58	43	0	13	43	1.44
34423161--34423199	16	2.6	15	88	11	62	76	5	0	17	0.96
34425567--34425635	35	2.0	35	88	0	102	56	0	2	40	1.14
34425766--34425805	20	2.1	19	86	9	55	50	5	0	45	1.23
34426348--34426393	3	15.3	3	95	0	83	69	0	30	0	0.89
34431859--34431982	56	2.1	58	83	5	153	50	4	0	45	1.26
34431942--34432016	33	2.3	33	79	9	82	54	2	1	41	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34435487--34435775	93	3.1	92	97	1	553	40	6	4	48	1.50
34435778--34436171	9	45.7	9	67	14	143	46	19	4	30	1.70
34435888--34435958	37	1.9	37	100	0	142	50	16	2	29	1.60
34435865--34436005	55	2.6	55	88	0	210	49	17	4	29	1.65
34435990--34436111	16	8.0	16	68	20	82	45	18	5	29	1.73
34436010--34436141	25	5.3	25	71	5	70	43	20	5	31	1.74
34442743--34442785	22	2.0	22	95	0	77	41	27	20	9	1.83
34452842--34453004	63	2.6	62	76	6	175	28	27	17	26	1.98
34462885--34462934	25	2.0	25	100	0	100	40	16	4	40	1.67
34466554--34466633	34	2.4	34	84	0	106	47	21	7	23	1.76
34475597--34475638	22	1.9	22	95	0	75	38	0	38	23	1.55
34481507--34481538	16	2.0	16	93	0	55	46	0	0	53	1.00
34491698--34491751	25	2.2	25	83	6	65	79	1	7	11	1.00
34491698--34491753	12	4.6	12	80	12	60	80	1	7	10	0.97
34491672--34491753	11	7.3	10	77	13	56	79	2	6	12	1.01
34491914--34491943	4	7.8	4	92	7	53	76	0	0	23	0.78
34492049--34492091	21	2.0	21	100	0	86	39	23	4	32	1.75
34495543--34495584	2	21.0	2	95	0	75	50	0	2	47	1.14
34495684--34495761	38	2.0	39	87	9	115	48	7	11	32	1.68
34500717--34500756	20	2.0	20	100	0	80	35	30	10	25	1.88
34504338--34504365	14	2.0	14	100	0	56	35	14	21	28	1.92
34504987--34505034	22	2.0	24	84	11	64	50	2	8	39	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34505137--34505188	20	2.7	18	82	14	59	44	7	11	36	1.70
34505137--34505197	20	3.1	18	76	21	52	40	8	11	39	1.71
34507849--34508033	41	4.5	41	84	2	210	33	22	21	22	1.97
34517215--34517257	19	2.3	18	84	15	52	23	23	11	41	1.87
34519515--34519577	10	6.4	10	78	10	67	82	0	15	1	0.74
34519515--34519575	17	3.5	18	80	6	72	81	0	16	1	0.76
34519515--34519571	16	3.4	17	87	4	71	82	0	15	1	0.75
34519513--34519572	18	3.4	17	80	17	61	83	0	15	1	0.73
34520809--34521023	44	4.8	45	72	6	177	27	22	25	24	2.00
34520809--34521035	89	2.6	89	89	0	337	28	22	25	24	1.99
34521197--34521414	115	1.9	115	83	3	287	35	20	20	23	1.96
34522874--34522933	31	2.0	30	83	9	77	26	0	1	71	0.95
34522962--34523007	8	6.1	8	82	12	62	32	0	0	67	0.91
34523362--34523390	6	4.8	6	100	0	58	86	0	13	0	0.58
34523406--34523447	13	3.2	13	80	9	50	38	9	7	45	1.64
34523784--34523850	35	1.9	35	90	0	107	46	8	7	37	1.64
34530038--34530064	14	1.9	14	100	0	54	37	22	14	25	1.93
34542027--34542091	30	2.2	30	88	5	96	18	21	38	21	1.93
34547830--34547868	18	2.2	18	90	4	62	48	12	0	38	1.42
34548470--34548506	9	4.1	9	92	0	65	45	13	10	29	1.77
34549532--34549557	5	5.2	5	100	0	52	19	19	19	42	1.90
34559308--34559409	50	2.1	49	85	5	134	24	24	19	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34559308--34559393	25	3.5	25	81	7	95	24	24	18	32	1.97
34559312--34559413	25	4.1	25	79	10	77	25	24	18	31	1.98
34566349--34567146	134	6.0	134	80	3	838	35	13	18	32	1.90
34567387--34567428	17	2.5	17	84	0	57	23	30	21	23	1.99
34579242--34580351	222	5.0	222	96	0	2058	37	16	9	36	1.82
34582554--34582597	22	2.0	22	82	8	54	50	11	9	29	1.69
34588890--34588958	36	1.9	35	91	2	111	24	21	13	40	1.89
34590595--34590630	18	2.0	18	88	0	54	63	0	16	19	1.30
34600271--34600341	25	2.8	25	86	0	97	18	29	19	32	1.96
34606599--34606712	23	4.8	23	75	9	97	21	25	20	33	1.97
34606599--34606729	45	2.8	46	77	9	131	22	24	19	33	1.97
34606649--34606720	23	3.2	21	77	15	56	20	25	22	31	1.98
34606899--34606943	20	2.2	20	84	0	54	35	11	15	37	1.83
34608511--34608549	7	5.6	7	91	8	62	38	2	0	58	1.12
34608734--34608793	31	1.9	31	86	0	84	40	13	18	28	1.88
34608747--34608807	31	2.0	31	83	6	79	39	18	16	26	1.91
34614950--34614992	18	2.5	17	85	7	52	46	4	0	48	1.22
34618315--34618368	20	2.7	20	80	8	65	40	1	14	42	1.57
34620618--34620643	1	26.0	1	100	0	52	0	0	0	100	0.00
34623849--34623902	24	2.2	25	83	3	65	24	1	1	72	1.05
34636664--34636705	18	2.3	18	84	8	50	40	2	0	57	1.12
34636670--34636821	27	5.5	28	70	17	111	39	0	3	56	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34636968--34637037	16	4.4	16	90	0	104	25	32	2	38	1.71
34641443--34641587	47	3.1	47	68	16	122	43	2	5	48	1.37
34641424--34641631	91	2.3	91	90	0	317	44	3	4	47	1.41
34641464--34641606	44	3.2	43	68	20	112	45	2	4	48	1.33
34641888--34641922	18	2.0	17	88	5	52	40	0	0	60	0.97
34641898--34641943	15	3.2	15	82	11	53	43	0	2	54	1.12
34642021--34642062	15	2.7	16	82	14	52	45	0	2	52	1.13
34642012--34642053	15	2.9	15	82	10	52	47	0	0	52	1.00
34642276--34642329	16	3.4	16	86	0	81	25	35	3	35	1.74
34647730--34647795	13	5.1	13	83	0	87	36	24	7	31	1.83

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   199