genome.fa.s11.2.7.7.80.10.50.1000.8.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   

This is table  8  of  210  ( 25152 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)
3193334--3193374	15	2.5	17	80	11	59	65	0	0	34	0.93
3193334--3193396	22	2.8	22	80	4	63	60	1	0	38	1.07
3194341--3194382	14	2.9	14	78	21	50	23	4	21	50	1.68
3203904--3203941	20	1.9	20	89	10	60	57	5	0	36	1.21
3205163--3205220	29	2.0	29	100	0	116	34	3	20	41	1.69
3208043--3208262	37	6.0	37	96	1	390	38	16	20	24	1.93
3219348--3219390	18	2.3	18	84	4	50	2	41	0	55	1.12
3230112--3230177	32	2.0	33	82	8	82	53	4	10	31	1.56
3231246--3231316	21	3.2	24	62	22	64	53	4	2	39	1.35
3237113--3237171	10	5.9	10	76	9	50	22	5	3	69	1.23
3243646--3243712	33	2.0	33	91	5	109	8	25	22	43	1.82
3246892--3246926	17	2.1	17	94	5	63	40	0	5	54	1.24
3252065--3252107	14	2.8	16	79	17	54	37	0	4	58	1.19
3252975--3253291	109	2.9	109	92	2	507	30	16	18	33	1.94
3268006--3268054	25	2.0	24	84	11	64	44	4	0	51	1.20
3268072--3268129	18	3.1	19	74	18	59	41	3	0	55	1.17
3274391--3274428	20	1.9	20	94	0	67	71	5	7	15	1.28
3276448--3276489	23	1.9	23	85	9	61	40	2	9	47	1.49
3279511--3279584	37	2.2	33	85	11	96	31	12	6	50	1.66
3280181--3280253	32	2.3	31	83	7	92	47	8	15	28	1.73
3280552--3280582	15	2.1	15	93	0	53	35	9	6	48	1.62
3283708--3283743	13	2.8	13	91	0	63	38	8	30	22	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3288310--3288369	27	2.2	27	78	0	66	70	0	1	28	0.97
3288324--3288367	21	2.2	20	91	4	70	77	0	0	22	0.77
3288827--3288858	14	2.3	14	94	0	55	50	9	21	18	1.75
3289342--3289382	21	2.0	20	90	4	64	34	21	21	21	1.97
3291634--3291683	21	2.4	20	80	9	55	32	2	4	62	1.25
3292543--3292584	13	3.3	13	78	18	52	59	0	2	38	1.10
3294613--3294653	21	2.0	21	85	4	57	63	12	4	19	1.46
3295550--3295591	3	14.0	3	100	0	84	66	0	0	33	0.92
3295787--3295865	40	2.0	40	87	5	115	32	0	1	65	1.00
3296249--3296315	34	1.9	35	90	3	109	32	8	13	44	1.75
3296306--3296391	33	2.6	33	96	3	156	24	6	20	47	1.75
3297508--3297547	17	2.4	17	95	0	71	70	0	0	30	0.88
3297855--3297891	11	3.5	11	82	14	51	48	0	0	51	1.00
3299720--3299752	18	1.9	17	88	11	50	51	0	12	36	1.39
3301148--3301351	46	4.5	46	95	3	344	32	15	24	28	1.95
3303868--3303911	23	1.9	23	90	0	70	27	6	22	43	1.78
3306132--3306199	31	2.3	31	84	5	95	17	16	13	52	1.74
3321648--3321676	5	6.0	5	92	8	51	0	17	0	82	0.66
3334112--3334180	20	3.5	19	76	5	66	66	0	2	30	1.06
3334107--3334182	39	1.9	39	91	0	125	61	0	3	34	1.14
3334147--3334172	13	2.0	13	100	0	52	61	0	0	38	0.96
3335827--3335896	28	2.5	29	79	9	83	57	0	1	41	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3341199--3341229	2	15.5	2	100	0	62	48	0	0	51	1.00
3346571--3346646	41	1.9	40	82	12	95	55	0	2	42	1.14
3350009--3350340	109	3.1	109	86	2	447	35	16	15	32	1.90
3350641--3350686	24	1.9	24	86	0	65	50	2	2	45	1.26
3350634--3350691	14	3.9	14	73	10	53	51	1	3	43	1.28
3350827--3350908	3	27.3	3	86	9	105	64	2	2	30	1.19
3352321--3352361	3	14.0	3	84	5	57	31	0	2	65	1.05
3352327--3352370	20	2.2	20	83	0	52	31	4	2	61	1.28
3352444--3352475	2	16.0	2	100	0	64	50	0	0	50	1.00
3352778--3352856	2	41.0	2	85	12	112	48	1	0	50	1.08
3353163--3353193	15	2.1	15	93	0	53	19	9	6	64	1.45
3363330--3363369	16	2.5	17	84	11	50	55	35	5	5	1.44
3364563--3364613	3	17.3	3	95	4	95	33	0	0	66	0.92
3364714--3364747	17	2.1	16	88	5	50	44	5	2	47	1.42
3367350--3367415	34	2.0	32	85	5	87	40	1	4	53	1.31
3367926--3367957	3	10.7	3	93	0	55	0	37	0	62	0.95
3382566--3382724	78	2.0	78	95	0	282	35	19	13	32	1.90
3391596--3391627	2	16.0	2	93	0	55	50	3	0	46	1.17
3391650--3391808	47	3.3	47	92	4	248	32	8	11	48	1.68
3391732--3391761	14	2.1	15	93	6	53	43	0	13	43	1.43
3391779--3391808	14	2.1	15	93	6	53	43	0	13	43	1.43
3392305--3392342	15	2.4	16	86	4	51	73	0	0	26	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3395048--3395088	19	2.2	19	86	4	57	36	2	4	56	1.34
3395033--3395089	18	3.1	18	78	19	55	38	1	5	54	1.33
3403888--3403951	31	2.1	31	100	0	128	40	18	28	12	1.87
3406870--3406918	22	2.1	24	82	14	59	55	2	8	34	1.41
3409079--3409516	44	9.8	44	70	12	207	28	22	19	29	1.98
3409002--3409511	87	5.7	88	73	12	360	28	21	19	30	1.98
3409089--3409269	98	1.8	98	88	4	276	28	19	18	33	1.96
3421314--3421364	25	2.0	25	100	0	102	45	7	3	43	1.51
3421864--3421912	22	2.1	24	82	14	59	55	2	8	34	1.41
3422996--3423035	21	2.0	21	90	5	64	77	0	12	10	0.99
3423761--3423819	31	1.9	31	85	0	82	35	10	8	45	1.68
3427314--3427381	25	2.8	24	70	12	59	54	1	7	36	1.37
3427442--3427481	21	1.9	21	89	0	62	65	5	7	22	1.38
3427530--3427560	12	2.6	12	89	0	53	58	0	9	32	1.31
3442929--3442979	4	12.8	4	95	0	93	49	25	0	25	1.51
3451483--3451518	17	2.2	16	90	5	54	52	5	8	33	1.55
3456074--3456117	14	3.1	14	81	15	54	72	2	0	25	0.96
3459334--3459715	74	4.9	80	86	8	481	28	21	14	36	1.92
3459457--3459677	37	6.0	37	93	0	345	28	19	13	38	1.89
3461785--3461833	26	1.9	25	84	12	64	16	18	4	61	1.50
3461721--3461889	84	2.0	85	88	4	252	24	18	3	53	1.60
3463227--3463452	42	5.3	42	84	1	281	29	29	17	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3463260--3463452	85	2.3	85	87	3	264	30	29	18	22	1.97
3471574--3471746	45	4.2	39	81	11	177	18	20	21	39	1.93
3471601--3471800	45	4.4	45	90	0	301	19	20	21	40	1.92
3472971--3473099	9	14.6	9	66	11	61	34	1	16	47	1.56
3472971--3473099	36	3.1	42	79	17	162	34	1	16	47	1.56
3480509--3480859	178	2.0	173	94	2	612	25	19	16	38	1.92
3482214--3482243	2	15.0	2	100	0	60	50	0	0	50	1.00
3489218--3489275	28	2.1	28	96	0	107	29	17	12	41	1.85
3491309--3491338	13	2.3	13	94	0	51	53	26	13	6	1.64
3491891--3491926	19	1.9	18	88	5	54	63	2	13	19	1.41
3492228--3492271	11	4.1	11	85	2	54	61	13	13	11	1.57
3492226--3492267	22	1.9	22	90	0	66	59	14	16	9	1.60
3495711--3495739	12	2.5	12	94	5	51	37	6	0	55	1.27
3503112--3503368	28	8.7	29	76	16	212	29	0	25	45	1.54
3503168--3503237	23	3.0	23	80	12	79	27	0	27	45	1.54
3503178--3503237	23	2.6	23	94	2	102	28	0	26	45	1.54
3503146--3503373	114	2.0	113	86	9	320	30	0	24	45	1.57
3506264--3506321	29	2.0	29	90	6	91	58	1	0	39	1.08
3506412--3506480	22	3.1	21	81	8	84	40	1	27	30	1.65
3506354--3506459	52	2.1	51	82	5	124	34	2	30	32	1.72
3506691--3506748	29	2.1	26	84	9	71	43	18	13	24	1.87
3512180--3512217	18	2.2	18	85	4	51	36	10	23	28	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3512300--3512336	18	2.1	18	94	0	65	29	10	13	45	1.77
3513689--3513732	13	3.4	13	78	12	54	31	6	20	40	1.79
3513679--3513750	26	2.8	26	75	10	76	37	6	15	40	1.74
3517568--3517607	3	13.3	3	100	0	80	67	0	0	32	0.91
3518770--3518798	10	2.9	10	100	0	58	0	41	6	51	1.28
3520896--3520924	7	4.1	7	100	0	58	17	13	27	41	1.87
3529608--3529640	2	16.5	2	100	0	66	51	0	0	48	1.00
3537815--3537842	2	14.0	2	100	0	56	50	0	0	50	1.00
3538133--3538189	27	2.4	24	83	16	66	40	15	8	35	1.79
3545643--3545718	25	3.0	25	84	7	109	30	19	17	32	1.95

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