genome.fa.s17.2.7.7.80.10.50.1000.11.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  11  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)
3136718--3136749	3	10.7	3	100	0	64	31	0	0	68	0.90
3138467--3138545	39	2.0	39	97	0	149	37	15	8	37	1.78
3139810--3139965	33	4.6	33	70	24	92	15	20	29	34	1.93
3139807--3140173	103	3.6	103	90	3	544	17	21	29	31	1.96
3141552--3141589	19	2.0	19	100	0	76	21	10	21	47	1.80
3166900--3166935	18	1.9	19	94	5	65	13	0	8	77	0.98
3169350--3169473	26	4.7	26	87	2	176	28	23	11	37	1.89
3170091--3170134	19	2.3	19	84	11	54	50	0	0	50	1.00
3176361--3176410	6	8.3	6	97	0	91	18	0	48	34	1.48
3177136--3177193	28	2.1	27	90	9	91	48	0	15	36	1.45
3177569--3177602	16	2.1	16	100	0	68	11	23	17	47	1.81
3180718--3180751	4	8.8	4	93	6	61	20	0	0	79	0.73
3182863--3183056	3	65.0	3	70	3	86	56	5	5	32	1.45
3184082--3184111	2	15.0	2	100	0	60	50	50	0	0	1.00
3184946--3185018	38	1.9	37	86	8	103	31	21	1	45	1.61
3185006--3185049	23	1.9	22	82	17	54	38	22	0	38	1.55
3185148--3185246	23	4.3	23	92	0	171	33	26	20	20	1.97
3185148--3185246	46	2.2	46	98	0	189	33	26	20	20	1.97
3188590--3188621	14	2.3	14	100	0	64	12	0	0	87	0.54
3194353--3194400	25	1.9	25	83	8	62	33	4	2	60	1.27
3200533--3200584	20	2.8	18	71	8	50	69	3	0	26	1.06
3200687--3200741	20	2.8	21	75	10	62	25	3	3	67	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3200667--3200804	10	13.8	9	66	18	51	30	5	2	61	1.31
3200712--3200792	31	2.7	31	81	11	89	33	4	0	61	1.17
3205331--3205393	32	2.0	31	84	9	83	65	6	1	26	1.26
3214268--3214433	29	5.6	29	75	6	136	25	15	20	38	1.91
3214270--3214439	89	1.9	90	79	6	193	25	14	21	37	1.92
3216382--3216564	51	3.6	51	79	7	194	23	16	27	32	1.96
3216575--3216663	45	2.0	45	93	0	151	23	17	25	32	1.97
3220126--3220206	6	13.0	6	78	7	72	17	62	0	19	1.32
3220134--3220184	18	2.8	18	93	0	84	13	66	0	19	1.24
3220150--3220201	15	3.5	15	79	10	61	19	65	0	15	1.27
3220240--3220297	3	19.3	3	78	0	53	22	65	0	12	1.25
3220243--3220292	9	5.6	9	85	0	73	22	66	0	12	1.24
3220240--3220302	12	5.2	12	81	7	74	22	63	0	14	1.30
3220135--3220471	114	3.1	107	83	12	404	20	55	4	19	1.59
3220287--3220325	18	2.2	18	90	0	60	23	46	2	28	1.65
3220354--3220416	12	5.2	12	84	0	72	20	65	1	12	1.35
3220357--3220406	9	5.6	9	87	0	73	20	68	2	10	1.29
3220354--3220411	15	3.9	15	86	0	62	20	67	1	10	1.29
3220498--3220546	3	16.3	3	86	0	53	22	67	2	8	1.28
3220489--3220546	15	3.9	15	83	0	62	20	65	3	10	1.38
3220560--3220595	18	2.0	18	94	0	63	25	38	8	27	1.84
3220609--3220643	9	3.9	9	84	0	52	22	68	0	8	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3220609--3220645	15	2.5	15	95	0	65	24	67	0	8	1.17
3220609--3220645	18	2.1	18	94	0	65	24	67	0	8	1.17
3220513--3220704	99	1.9	99	83	0	249	26	50	5	18	1.67
3220729--3220760	3	10.7	3	93	0	55	28	68	0	3	1.04
3222324--3222365	9	4.7	9	80	11	50	30	0	2	66	1.04
3222323--3222367	18	2.4	19	88	3	65	31	0	2	66	1.04
3222323--3222367	10	4.8	10	81	15	51	31	0	2	66	1.04
3222898--3222960	25	2.6	23	76	14	63	58	7	1	31	1.36
3223213--3223258	19	2.4	19	82	13	58	21	0	4	73	1.00
3226475--3226539	21	3.1	21	78	8	69	15	61	3	20	1.47
3226600--3226658	30	2.0	30	86	6	84	18	61	5	15	1.52
3226608--3226658	15	3.2	15	79	15	57	19	62	3	13	1.46
3226675--3226714	18	2.2	18	95	0	71	25	50	5	20	1.68
3226711--3226760	15	3.3	15	77	0	55	18	62	8	12	1.53
3226723--3226774	15	3.3	15	77	15	59	21	65	3	9	1.38
3230008--3230422	42	9.9	42	91	2	575	31	21	21	25	1.98
3230490--3230523	14	2.4	14	95	0	59	52	20	8	17	1.71
3230747--3230817	21	3.4	21	80	0	79	2	45	18	33	1.64
3236265--3236757	7	57.0	9	61	33	76	32	0	20	46	1.55
3236279--3236748	18	24.6	19	65	24	99	32	0	20	46	1.55
3236310--3236767	26	18.1	26	89	5	683	32	0	20	47	1.55
3236821--3236936	34	3.2	34	65	15	88	42	5	1	50	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3236816--3236938	41	3.2	40	64	19	107	42	4	1	51	1.33
3236804--3236952	75	2.0	75	98	0	289	40	6	1	51	1.35
3239817--3239868	27	1.9	27	88	0	77	50	9	0	40	1.35
3239936--3239972	10	3.7	10	92	0	65	43	13	0	43	1.44
3240871--3241047	82	2.2	82	97	0	336	35	20	15	28	1.93
3241227--3241380	41	3.8	41	80	6	186	38	22	22	16	1.92
3241187--3241382	82	2.4	82	94	1	349	39	21	22	15	1.92
3242698--3242775	21	3.7	21	77	6	77	15	60	2	21	1.47
3242754--3242791	6	6.3	6	93	0	58	15	57	0	26	1.38
3242820--3242881	15	3.9	16	79	14	67	19	62	3	14	1.44
3242703--3243013	132	2.4	132	85	2	401	18	55	5	19	1.62
3242892--3242942	24	2.1	24	85	7	68	27	47	5	19	1.73
3242898--3242955	18	3.2	18	82	0	71	27	46	6	18	1.75
3242963--3243015	18	2.9	18	77	0	61	18	64	7	9	1.47
3242952--3243001	15	3.3	15	74	0	55	16	62	10	12	1.55
3242964--3243015	15	3.3	15	77	15	59	19	65	5	9	1.42
3247796--3247846	18	2.8	18	90	0	84	31	41	5	21	1.77
3247850--3247905	15	3.5	15	81	13	76	14	67	0	17	1.22
3247850--3247919	21	3.3	21	85	0	86	17	65	0	17	1.27
3247850--3247907	12	5.1	12	77	12	68	13	67	0	18	1.23
3247856--3247917	6	10.8	6	77	10	67	16	66	0	17	1.26
3247982--3248034	18	2.9	18	80	0	70	24	66	1	7	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3247985--3248050	30	2.3	27	87	7	87	24	63	1	10	1.35
3247982--3248037	15	3.7	15	80	0	76	23	66	1	8	1.30
3247982--3248034	3	17.7	3	84	0	61	24	66	1	7	1.28
3248114--3248156	6	7.3	6	81	5	52	13	72	2	11	1.22
3248110--3248166	23	2.4	23	82	2	69	17	66	3	12	1.37
3248176--3248228	12	4.4	12	74	9	54	32	37	13	16	1.88
3248176--3248228	24	2.2	24	83	6	63	32	37	13	16	1.88
3252273--3252343	30	2.5	28	84	10	99	46	5	0	47	1.26
3252563--3252633	27	2.6	29	84	6	94	69	0	30	0	0.89
3252469--3252666	66	3.0	65	83	10	228	66	0	32	0	0.96
3252515--3252670	33	4.6	33	77	15	151	70	0	28	0	0.92
3252513--3252671	16	9.9	15	65	18	54	71	0	28	0	0.91
3253401--3253456	27	2.1	27	93	0	94	44	14	32	8	1.76
3258438--3258482	18	2.5	18	88	0	72	15	48	6	28	1.70
3259181--3259216	19	1.9	18	88	5	54	66	8	0	25	1.19
3258777--3259653	438	2.0	437	99	0	1718	42	16	6	34	1.74
3259869--3259910	11	3.9	11	87	6	68	0	30	0	69	0.89
3259871--3259910	21	1.9	21	94	0	71	0	30	0	70	0.88
3259990--3260062	27	2.7	27	86	0	110	13	30	28	27	1.94
3260108--3260178	26	2.6	28	85	14	103	45	0	8	46	1.33
3267752--3267790	20	2.0	20	89	0	60	71	7	0	20	1.10
3269273--3269312	21	2.0	21	85	9	57	37	0	12	50	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3275560--3275624	32	2.1	31	91	2	103	36	10	6	46	1.64
3278229--3278493	85	3.1	85	95	0	458	34	18	20	27	1.95
3278494--3278563	37	2.0	35	83	8	88	40	17	12	30	1.87
3284235--3284313	41	1.9	41	82	5	97	20	1	32	45	1.59
3284319--3284366	14	3.4	14	82	5	62	18	0	35	45	1.50
3284311--3284367	21	2.7	21	77	2	60	17	0	36	45	1.49
3284834--3284895	20	3.1	20	85	0	79	37	9	8	45	1.67
3284846--3284902	20	2.8	20	86	0	60	35	14	7	43	1.72
3288221--3288263	15	2.9	14	77	12	50	39	4	0	55	1.20
3288689--3288717	14	2.1	14	93	6	51	31	0	6	62	1.22

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