genome.fa.s5.2.7.7.80.10.50.1000.10.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  10  of  208  ( 24913 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)
3187894--3187937	21	2.0	21	86	4	61	63	11	9	15	1.51
3192891--3192915	2	12.5	2	100	0	50	52	0	0	48	1.00
3196483--3196553	30	2.4	31	79	6	76	40	0	2	56	1.14
3197346--3197376	15	2.1	15	100	0	62	54	0	12	32	1.38
3197874--3197961	31	2.9	31	79	12	110	48	4	2	44	1.35
3199496--3199531	7	5.3	7	96	3	65	27	0	11	61	1.30
3200060--3200102	18	2.4	18	92	0	68	20	27	9	41	1.83
3201388--3201461	23	3.5	23	75	22	90	60	4	6	28	1.40
3201394--3201437	17	2.8	15	83	12	61	59	4	6	29	1.44
3201781--3201818	15	2.5	15	91	0	58	39	7	28	23	1.83
3202359--3202553	97	2.0	97	86	0	273	29	14	21	34	1.93
3203216--3203248	2	16.5	2	100	0	66	48	0	0	51	1.00
3206420--3206455	14	2.6	14	100	0	72	55	13	0	30	1.39
3207234--3207268	6	5.8	6	96	0	61	51	37	11	0	1.38
3207268--3207311	2	22.0	2	100	0	88	50	0	0	50	1.00
3208310--3208372	30	2.1	30	93	0	108	57	14	3	25	1.52
3208682--3208724	22	2.0	22	85	0	59	55	9	13	20	1.66
3211490--3211549	9	6.7	9	72	12	52	61	0	3	35	1.12
3211578--3211649	21	3.6	21	78	16	55	59	1	8	30	1.35
3211593--3211649	19	3.0	19	73	14	55	61	0	8	29	1.26
3211605--3211649	19	2.4	18	85	10	56	64	0	6	28	1.19
3211890--3211914	7	3.6	7	100	0	50	44	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3216099--3217008	356	2.6	354	86	5	1191	34	17	24	24	1.96
3219184--3219254	35	2.0	35	100	0	142	49	11	8	30	1.68
3224932--3224974	14	3.2	12	87	12	50	32	0	2	65	1.06
3224938--3224974	7	5.4	7	84	15	51	35	0	2	62	1.10
3229174--3229295	23	5.3	23	88	0	190	31	27	20	21	1.98
3229174--3229293	46	2.6	46	95	0	213	30	27	20	20	1.98
3232835--3232886	15	3.6	15	80	12	56	44	0	1	53	1.11
3233291--3233395	44	2.5	40	76	15	113	31	29	4	34	1.78
3233289--3233398	45	2.6	44	81	8	131	31	29	5	33	1.80
3233377--3233414	16	2.4	16	90	0	58	34	34	0	31	1.58
3242492--3242522	10	3.1	10	95	0	53	16	19	12	51	1.76
3245603--3245635	16	2.1	16	100	0	66	30	6	12	51	1.63
3246098--3246187	29	3.0	30	80	9	96	40	14	13	32	1.85
3246484--3246528	23	2.0	23	82	8	56	20	8	13	57	1.62
3247947--3248013	27	2.5	27	84	15	86	34	47	8	8	1.66
3247941--3248014	30	2.5	30	95	0	130	32	50	9	8	1.64
3247886--3248189	120	2.5	120	90	0	455	28	47	8	16	1.75
3248061--3248130	30	2.3	30	87	4	97	34	47	11	7	1.67
3248350--3248664	12	26.8	12	72	11	179	14	25	18	40	1.89
3248361--3248664	42	7.4	42	77	10	295	15	25	18	40	1.90
3248364--3248666	48	6.4	48	77	12	231	15	25	18	40	1.90
3248350--3248664	60	5.2	60	74	8	258	14	25	18	40	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3248355--3248641	84	3.4	83	83	4	337	14	26	19	39	1.90
3248354--3248644	18	16.5	18	74	13	194	15	26	19	39	1.91
3249013--3250103	444	2.4	448	85	5	1423	23	36	9	30	1.86
3250482--3250546	18	3.6	18	72	15	71	23	60	6	10	1.52
3253244--3253285	16	2.7	16	77	3	50	4	16	0	78	0.91
3253894--3253952	3	19.7	3	78	0	55	8	3	61	27	1.41
3255113--3255433	18	18.5	18	72	10	195	41	17	26	14	1.88
3255111--3255428	24	13.5	24	76	6	166	41	17	26	15	1.88
3255106--3255410	42	7.4	42	77	5	255	40	17	26	15	1.89
3255645--3255719	30	2.5	31	84	6	109	8	12	46	33	1.70
3255789--3255815	3	9.0	3	100	0	54	0	0	66	33	0.92
3255594--3255807	117	1.8	117	91	0	356	14	7	47	30	1.72
3255679--3255896	96	2.3	93	82	11	286	15	7	47	29	1.72
3258955--3258979	13	1.9	13	100	0	50	36	0	16	48	1.46
3258956--3259018	26	2.4	26	74	10	74	34	6	22	36	1.80
3260124--3260224	24	4.3	24	79	13	102	40	5	1	51	1.38
3264295--3264353	27	2.2	27	96	0	109	25	13	32	28	1.94
3264517--3264547	2	15.5	2	100	0	62	0	48	0	51	1.00
3267640--3267695	12	4.7	12	75	6	51	1	28	17	51	1.56
3267637--3267760	24	5.2	24	79	3	88	3	26	21	48	1.65
3267703--3267784	12	6.8	12	80	0	92	7	28	23	41	1.81
3267703--3267784	6	13.7	6	72	0	56	7	28	23	41	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3267668--3267772	24	4.4	24	81	4	122	3	25	23	46	1.69
3267855--3268003	12	12.4	12	75	11	81	10	26	18	44	1.82
3267898--3268149	6	42.0	6	74	4	132	16	23	15	44	1.86
3267910--3268149	18	13.0	18	73	8	151	17	23	15	43	1.87
3267898--3268155	30	8.8	30	74	8	199	16	23	15	44	1.85
3267910--3268141	42	5.5	42	83	3	243	16	23	15	43	1.86
3268128--3268515	156	2.5	156	94	0	677	20	34	7	38	1.80
3268466--3268623	54	2.9	54	92	0	253	18	36	5	40	1.73
3277842--3278213	43	8.7	43	90	0	496	28	30	16	24	1.97
3278422--3278459	19	2.0	19	90	10	60	57	2	7	31	1.41
3278560--3278707	66	2.2	66	83	7	176	16	26	17	39	1.90
3278598--3278724	66	1.9	66	84	6	168	16	25	15	42	1.87
3284194--3284275	25	3.3	25	84	6	112	35	1	15	47	1.54
3284219--3284616	34	12.4	34	69	17	223	30	1	20	46	1.61
3284474--3284603	25	5.5	24	66	19	78	30	0	22	46	1.57
3284591--3284838	12	23.1	12	63	26	69	33	2	13	49	1.57
3284654--3284798	31	4.6	32	70	16	115	33	2	12	51	1.51
3284587--3284826	95	2.5	95	97	0	444	34	2	13	49	1.58
3284205--3284698	9	58.0	9	68	19	224	31	1	19	46	1.60
3284959--3284991	15	2.3	15	89	5	50	57	3	0	39	1.14
3285040--3285191	45	3.4	44	79	14	161	50	5	4	40	1.46
3285105--3285137	13	2.5	13	95	0	57	48	6	9	36	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3285412--3285454	22	2.0	22	90	4	70	18	13	25	41	1.88
3285656--3285707	20	2.5	21	81	9	61	46	21	7	25	1.77
3287179--3287213	15	2.2	16	95	5	63	51	11	0	37	1.38
3290968--3291048	41	2.0	41	87	0	117	23	28	19	28	1.98
3291017--3291079	31	2.0	31	87	0	90	25	25	20	28	1.99
3292800--3292828	14	2.0	15	93	6	51	55	20	0	24	1.44
3295040--3295090	25	2.0	25	88	0	75	35	17	21	25	1.95
3296907--3296946	9	4.4	9	81	12	55	27	7	20	45	1.78
3300630--3300675	23	2.0	23	83	8	58	39	8	4	47	1.54
3301996--3302041	14	3.3	14	79	14	51	45	4	0	50	1.21
3302220--3302310	28	3.3	27	69	22	80	43	18	1	36	1.58
3302231--3302320	24	3.4	24	68	21	72	44	17	1	36	1.57
3302220--3302334	56	2.1	56	96	0	212	43	20	0	35	1.58
3302246--3302334	28	3.2	28	71	23	96	43	21	0	34	1.53
3304062--3304111	24	2.1	24	84	0	64	40	34	8	18	1.79
3304103--3304317	66	3.3	66	90	2	326	22	45	6	26	1.75
3304103--3305084	132	7.3	127	77	12	764	23	44	5	25	1.75
3304310--3305084	66	11.3	66	85	5	870	24	44	5	25	1.75
3305029--3305304	90	3.1	90	90	0	417	26	38	2	31	1.71
3305337--3305372	18	2.0	18	94	0	63	36	25	16	22	1.94
3311481--3311606	66	1.9	67	88	1	191	22	44	6	26	1.76
3311530--3311693	90	1.8	90	95	0	301	23	47	6	23	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3311481--3311762	156	1.8	157	87	0	422	23	45	5	26	1.74
3311620--3312326	66	10.7	66	86	3	976	23	45	5	24	1.74
3312982--3313020	18	2.2	18	90	0	60	43	15	5	35	1.69
3313611--3313654	2	22.0	2	100	0	88	50	0	0	50	1.00
3317301--3317394	47	2.0	46	97	2	179	37	8	2	52	1.44
3320803--3321097	146	2.0	146	87	3	425	41	25	7	26	1.81
3326001--3326049	22	2.3	21	83	13	57	26	2	4	67	1.19
3327249--3327314	17	4.1	16	77	13	64	30	4	3	62	1.30
3327276--3327314	15	2.5	16	87	8	62	28	5	2	64	1.28
3327276--3327322	15	2.9	16	81	9	60	25	4	4	65	1.29

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