genome.fa.s4.2.7.7.80.10.50.1000.12.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: At_chr8
Parameters: 2 7 7 80 10 50 1000
Length:  78745976

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   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   

This is table  12  of  235  ( 28198 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)
3219306--3219335	15	2.0	15	100	0	60	46	0	0	53	1.00
3219440--3219629	9	20.6	9	74	10	107	47	13	1	37	1.52
3219474--3219629	17	8.9	17	71	11	93	47	12	1	39	1.49
3219413--3219620	96	2.1	96	80	5	231	47	12	1	38	1.52
3225658--3225789	43	3.0	43	91	1	210	24	31	18	25	1.98
3231517--3231555	19	2.0	20	85	5	53	56	5	5	33	1.43
3233596--3233808	30	7.1	30	90	0	345	27	47	5	19	1.72
3233660--3233713	18	3.3	18	66	28	57	24	50	7	18	1.72
3233596--3233805	90	2.3	90	97	0	393	27	47	5	20	1.72
3233720--3233775	18	3.4	18	65	27	52	26	48	5	19	1.70
3240106--3240262	39	4.0	39	87	2	174	30	29	22	17	1.96
3249857--3249901	13	3.4	13	87	6	72	13	11	6	68	1.37
3249795--3250370	99	5.8	99	95	1	967	23	18	18	38	1.93
3250368--3250967	74	8.2	74	88	5	774	29	16	20	33	1.94
3251044--3251076	14	2.4	14	100	0	66	18	15	6	60	1.54
3250943--3251430	89	5.3	90	76	8	378	26	17	17	38	1.92
3250880--3251232	89	3.9	88	83	6	415	27	17	18	36	1.94
3250880--3251230	179	2.0	179	85	4	476	27	17	18	35	1.94
3251144--3251332	102	1.8	103	88	4	292	28	14	16	39	1.89
3251270--3251497	87	2.6	87	81	4	237	30	16	19	33	1.94
3252119--3253017	30	30.0	30	92	0	1512	28	48	5	18	1.69
3252117--3253019	60	15.1	60	99	0	1763	28	48	5	18	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3253499--3253550	24	2.2	23	83	10	61	36	3	0	59	1.16
3253499--3253630	23	5.6	25	74	10	91	35	6	3	55	1.40
3253566--3253708	25	5.7	25	72	15	80	31	7	4	55	1.49
3253593--3253700	27	4.0	28	70	15	86	29	6	4	59	1.43
3253656--3253727	25	2.8	25	77	10	67	30	5	4	59	1.39
3253578--3253750	78	2.2	77	79	7	188	31	6	4	57	1.42
3253774--3253829	25	2.3	24	79	14	62	37	16	3	42	1.65
3254680--3254730	22	2.3	22	86	0	66	11	13	7	66	1.43
3255192--3255225	15	2.3	15	89	0	50	61	2	0	35	1.11
3255902--3255935	10	3.4	10	95	0	59	55	11	23	8	1.63
3256357--3256408	18	2.9	17	83	11	59	50	5	0	44	1.26
3257450--3257485	16	2.1	16	90	10	54	55	0	0	44	0.99
3267681--3267720	20	2.0	20	85	9	55	55	25	17	2	1.55
3271454--3271495	20	2.1	20	100	0	84	28	21	23	26	1.99
3271601--3271625	13	1.9	13	100	0	50	48	0	16	36	1.46
3273351--3273458	26	4.2	26	89	2	164	34	8	23	34	1.85
3273351--3273458	52	2.1	52	92	3	182	34	8	23	34	1.85
3276595--3276619	12	2.1	12	100	0	50	8	24	52	16	1.70
3281511--3281617	26	4.2	26	85	2	153	33	7	24	34	1.83
3285655--3285692	19	2.1	19	85	9	53	60	5	2	31	1.33
3295906--3295953	24	2.0	24	87	0	69	35	20	10	33	1.87
3297093--3297202	42	2.6	43	81	8	134	23	19	29	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3298025--3298053	13	2.1	14	93	6	51	55	10	0	34	1.34
3301961--3301994	14	2.4	14	85	0	50	41	26	8	23	1.83
3302040--3302105	14	4.6	14	73	14	53	50	27	3	19	1.63
3319887--3320048	84	1.9	84	80	5	184	30	25	14	29	1.94
3321477--3321950	29	16.3	29	75	4	301	36	14	27	22	1.93
3321452--3321950	58	8.6	58	72	7	343	36	14	27	22	1.93
3321459--3321878	116	3.6	115	85	1	491	36	13	27	22	1.92
3325381--3325424	18	2.6	16	82	7	52	11	13	4	70	1.31
3325485--3325670	21	8.7	21	68	20	68	25	8	4	61	1.43
3325569--3325678	3	36.7	3	73	17	77	28	6	2	62	1.33
3325612--3325665	20	2.7	20	80	5	56	31	3	5	59	1.38
3325608--3325666	23	2.7	22	82	7	68	30	5	5	59	1.41
3325757--3325807	3	17.0	3	84	15	70	29	3	0	66	1.09
3331692--3331739	24	2.0	24	100	0	96	33	12	25	29	1.92
3338019--3338083	31	2.1	31	85	0	85	30	13	12	43	1.81
3340555--3340634	31	2.6	32	84	6	110	48	11	8	31	1.69
3341116--3341149	4	8.8	4	87	6	52	23	2	23	50	1.63
3341119--3341148	15	2.0	15	93	0	51	23	3	26	46	1.68
3346860--3347731	188	4.6	188	98	1	1627	17	17	14	50	1.78
3347923--3347959	19	1.9	20	88	5	58	59	0	18	21	1.38
3359524--3360081	175	3.2	175	89	2	879	26	19	20	34	1.96
3359582--3360032	87	5.2	85	66	18	291	25	18	20	35	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3360000--3360566	284	2.0	284	97	1	1084	25	20	22	32	1.98
3361513--3361552	15	2.7	15	84	0	53	2	12	0	85	0.71
3376043--3376152	55	2.0	55	94	0	193	28	26	21	23	1.99
3376333--3376384	25	2.1	25	82	7	61	21	21	19	38	1.94
3376429--3376490	25	2.5	25	97	0	115	22	30	19	27	1.98
3382379--3382406	11	2.5	11	100	0	56	17	10	32	39	1.84
3384527--3384553	13	2.1	13	100	0	54	14	37	33	14	1.88
3385552--3385610	26	2.2	25	88	8	82	44	23	15	16	1.86
3385556--3385674	25	4.9	25	68	16	88	44	19	17	18	1.87
3387101--3387289	94	2.0	94	98	0	369	33	12	10	43	1.76
3389723--3389890	40	4.2	40	81	4	97	25	27	23	23	2.00
3389746--3389890	40	3.6	40	84	4	184	24	26	24	25	2.00
3398158--3398216	31	1.9	31	96	0	109	20	22	30	27	1.98
3398189--3398292	42	2.5	42	77	13	106	24	17	25	33	1.96
3402984--3403060	40	1.9	40	86	5	111	24	18	31	25	1.97
3406716--3406745	14	2.1	14	93	0	51	16	0	36	46	1.47
3407653--3407794	67	2.1	67	86	5	194	30	21	28	19	1.97
3407724--3407775	27	2.0	26	84	3	68	34	21	26	17	1.95
3413593--3413626	17	2.0	17	100	0	68	35	5	5	52	1.50
3417539--3417601	24	2.6	24	89	0	90	34	4	12	47	1.63
3422956--3422997	21	2.0	22	85	4	59	42	0	0	57	0.99
3425397--3425436	21	2.0	21	85	9	57	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3426905--3426938	14	2.3	15	90	10	52	70	0	20	8	1.13
3429768--3429818	22	2.5	20	84	9	66	31	23	3	41	1.73
3429770--3429812	22	2.0	21	90	4	68	25	25	4	44	1.73
3431010--3431057	20	2.4	20	73	10	53	4	29	4	62	1.32
3431084--3431112	5	5.8	5	100	0	58	58	0	0	41	0.98
3440153--3440249	48	2.0	48	95	0	176	38	6	20	35	1.78
3453632--3453675	22	2.0	22	82	8	54	36	9	18	36	1.82
3458627--3458747	60	2.0	60	93	0	206	34	17	17	30	1.93
3459917--3459956	19	2.2	18	90	4	62	42	12	2	42	1.56
3464508--3464555	19	2.6	19	90	3	71	52	12	0	35	1.40
3472184--3472209	7	3.7	7	100	0	52	57	0	42	0	0.98
3479926--3479985	32	1.9	30	87	12	86	56	1	0	41	1.09
3480592--3481249	326	2.0	327	98	0	1273	29	11	19	39	1.87
3484519--3484564	22	2.0	23	83	4	58	56	17	8	17	1.65
3489039--3489139	46	2.2	46	98	0	193	36	7	20	34	1.82
3493452--3493500	13	3.8	13	80	0	62	51	2	6	40	1.38
3493449--3493500	26	2.0	26	96	0	95	51	3	5	38	1.44
3493836--3493893	31	1.9	29	82	6	71	36	3	5	55	1.39
3493925--3493972	17	2.8	18	80	17	50	43	2	0	54	1.12
3500476--3500519	19	2.4	19	88	11	65	70	0	0	29	0.88
3503241--3503623	184	2.1	184	89	1	588	36	10	11	42	1.76
3511978--3512027	21	2.4	21	83	6	66	18	14	18	50	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3511973--3512127	42	3.7	42	77	5	143	17	19	16	46	1.84
3514155--3514246	40	2.3	40	98	0	175	34	17	20	27	1.95
3514155--3514289	40	3.4	40	84	7	159	32	16	23	27	1.96
3532773--3533034	39	6.7	40	87	7	337	25	22	27	24	2.00
3535896--3535954	21	2.8	21	76	7	66	54	5	0	40	1.23
3537544--3537592	25	2.0	25	91	0	80	44	14	14	26	1.83
3538612--3538676	23	3.0	22	71	15	71	41	23	20	15	1.89
3538886--3538995	38	2.8	38	75	6	96	31	27	20	20	1.97
3541048--3541157	38	2.8	38	75	6	96	31	27	20	20	1.97
3553581--3553677	40	2.4	40	82	0	113	23	16	26	32	1.96

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   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235