genome.fa.s1.2.7.7.80.10.50.1000.10.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  10  of  187  ( 22383 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)
3586719--3586753	17	2.0	18	94	5	63	17	2	0	80	0.84
3587979--3588026	21	2.3	20	80	13	53	20	39	20	18	1.92
3588358--3588454	42	2.3	43	85	1	133	15	34	34	16	1.90
3589387--3589463	33	2.3	32	82	6	91	25	23	18	32	1.97
3589469--3589534	33	2.0	33	96	0	123	24	28	15	31	1.95
3589502--3589739	105	2.3	104	87	5	342	26	22	17	34	1.96
3599688--3599736	21	2.3	21	79	6	55	61	10	18	10	1.55
3603250--3603280	2	16.0	2	93	6	55	51	0	0	48	1.00
3620139--3620186	19	2.5	19	82	0	69	66	2	4	27	1.21
3627732--3627771	21	2.0	20	85	5	53	40	2	0	57	1.12
3627776--3627813	16	2.4	16	86	8	51	26	0	15	57	1.38
3630267--3630306	15	2.9	15	85	10	50	37	15	5	42	1.68
3632255--3632307	21	2.6	21	87	3	81	54	0	3	41	1.18
3632298--3632330	17	1.9	17	93	0	57	72	0	9	18	1.10
3632388--3632444	27	2.2	26	81	15	64	64	1	1	31	1.13
3632485--3632525	21	2.0	21	90	0	64	26	17	17	39	1.91
3632679--3632729	20	2.5	21	90	3	77	54	0	1	43	1.11
3632809--3632868	27	2.2	26	77	13	68	65	1	1	31	1.13
3632802--3632842	19	2.1	20	86	4	57	63	2	4	29	1.28
3639585--3639673	44	2.0	45	86	8	128	53	3	4	38	1.38
3639599--3639684	44	1.9	44	88	2	127	54	4	4	36	1.42
3657891--3657976	39	2.2	39	87	0	118	31	19	17	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3663798--3663852	25	2.2	25	84	9	69	52	1	0	45	1.11
3667391--3667429	3	12.7	3	94	5	69	33	0	0	66	0.92
3667708--3667741	15	2.4	14	90	5	50	38	5	2	52	1.41
3669383--3669464	38	2.2	38	100	0	164	28	7	14	50	1.70
3676335--3676380	23	2.0	23	83	8	58	17	13	0	69	1.19
3679918--3679957	16	2.5	16	91	0	62	47	2	7	42	1.45
3679968--3680137	59	2.9	59	97	0	313	40	4	9	45	1.57
3680204--3680247	24	1.9	24	90	9	74	61	2	0	36	1.09
3682174--3682215	18	2.2	20	79	12	52	47	4	0	47	1.23
3682180--3682216	18	2.0	19	89	5	58	40	5	0	54	1.24
3683047--3683093	23	2.1	23	88	4	69	34	0	4	61	1.15
3690086--3690226	44	3.0	44	82	9	158	29	19	17	33	1.95
3690027--3690191	51	3.3	50	89	0	240	27	23	15	33	1.95
3692604--3692690	40	2.2	40	81	4	95	27	16	20	35	1.94
3692622--3692760	41	3.4	40	84	6	172	24	15	26	33	1.95
3693027--3693126	42	2.4	42	96	0	182	35	9	28	28	1.87
3696160--3696209	25	2.0	25	84	7	66	54	2	2	42	1.23
3703378--3703425	17	2.9	17	81	3	53	35	2	0	62	1.07
3703388--3703444	28	2.1	28	83	9	73	31	1	0	66	1.02
3715981--3716169	63	2.8	67	81	13	237	44	11	19	24	1.83
3723922--3724133	90	2.4	90	94	0	370	26	14	23	35	1.93
3723891--3724150	135	1.9	135	80	7	305	28	14	22	35	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3723888--3724133	45	5.5	45	80	10	270	26	14	23	34	1.94
3736647--3736755	31	3.4	31	85	8	137	35	1	0	62	1.06
3736649--3736759	35	3.4	33	85	12	147	36	1	0	61	1.07
3736726--3736779	25	2.2	25	89	0	81	37	0	1	61	1.07
3736732--3736785	25	2.2	25	82	0	63	46	0	1	51	1.11
3737001--3737086	30	2.9	29	74	8	75	36	8	10	45	1.68
3738855--3738902	15	3.1	16	90	6	80	37	4	37	20	1.72
3738882--3738990	45	2.6	43	80	10	127	34	5	28	31	1.80
3739114--3739157	16	2.8	16	82	10	54	50	2	0	47	1.13
3739119--3739531	120	3.4	120	96	0	738	49	5	1	43	1.36
3739235--3739277	15	2.8	15	82	10	52	51	2	0	46	1.13
3739231--3739277	16	3.0	16	81	12	53	51	2	0	46	1.13
3739355--3739406	15	3.6	15	80	12	56	53	1	0	44	1.11
3739572--3739632	28	2.2	28	85	5	81	50	3	0	45	1.17
3739579--3739720	47	3.1	46	66	24	118	50	3	2	44	1.31
3739538--3739754	91	2.4	89	86	6	299	47	4	3	45	1.38
3739572--3739714	44	3.2	43	70	20	130	48	2	2	46	1.28
3740714--3740760	3	15.7	3	90	0	76	36	0	0	63	0.94
3746273--3746303	6	5.2	6	100	0	62	64	0	0	35	0.94
3747132--3747217	43	2.0	44	90	2	138	51	9	9	30	1.65
3759982--3760008	13	2.1	13	100	0	54	55	0	0	44	0.99
3772935--3772965	6	5.2	6	92	0	53	29	0	3	67	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3773881--3773912	12	2.7	12	95	0	55	40	9	6	43	1.62
3792545--3792648	52	2.0	52	98	0	199	32	8	1	56	1.41
3792752--3792797	10	4.6	10	80	0	56	34	4	2	58	1.30
3802608--3802712	53	2.0	53	94	0	183	31	31	8	28	1.87
3813730--3813781	19	2.5	21	78	12	63	42	1	1	53	1.23
3815138--3815175	17	2.2	17	90	0	58	50	10	7	31	1.66
3824466--3824493	3	9.3	3	100	0	56	64	0	0	35	0.94
3827951--3827987	5	7.4	5	100	0	74	40	0	0	59	0.97
3829967--3830002	2	18.0	2	100	0	72	50	0	0	50	1.00
3830120--3830167	22	2.2	22	100	0	96	68	8	8	14	1.37
3836720--3836936	107	2.0	108	95	0	391	32	18	18	29	1.95
3837559--3837612	25	2.2	24	83	9	65	55	3	5	35	1.41
3837570--3837624	29	1.9	28	82	10	67	56	1	5	36	1.33
3837665--3837695	3	10.7	3	93	6	55	70	0	0	29	0.87
3847248--3847282	18	2.0	17	94	5	61	45	0	0	54	0.99
3848726--3848788	30	2.1	30	96	0	117	23	3	15	57	1.53
3853951--3853995	17	2.6	17	76	13	56	28	8	22	40	1.84
3869497--3869546	22	2.5	20	83	9	66	50	0	0	50	1.00
3875069--3875133	3	21.7	3	100	0	130	66	0	0	33	0.92
3875867--3875902	16	2.2	16	90	0	54	55	0	2	41	1.14
3879519--3879551	17	2.0	17	94	5	59	42	6	0	51	1.26
3879521--3879563	17	2.5	17	81	11	52	44	11	0	44	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3880666--3880693	11	2.5	11	100	0	56	42	0	10	46	1.38
3880912--3881134	111	2.0	111	91	3	360	34	12	10	43	1.77
3888853--3888919	34	1.9	35	90	3	109	34	8	10	46	1.70
3890140--3890185	24	1.9	24	95	0	83	36	4	45	13	1.63
3904837--3905075	119	2.0	120	98	0	462	26	12	17	43	1.85
3906975--3907012	20	2.0	20	89	5	60	21	7	0	71	1.11
3906984--3907026	10	4.4	9	85	11	50	18	6	2	72	1.19
3914507--3914548	3	14.3	3	90	5	50	23	0	7	69	1.13
3924964--3925012	24	2.0	24	84	0	62	63	6	2	28	1.30
3924962--3925012	13	4.1	13	75	10	52	60	7	1	29	1.36
3925015--3925059	20	2.3	19	82	14	56	62	0	0	37	0.96
3925029--3925067	20	2.0	20	85	10	53	61	2	2	33	1.23
3925296--3925338	14	2.9	15	86	6	52	34	0	4	60	1.17
3931249--3931313	30	2.2	30	83	10	80	58	1	3	36	1.23
3936975--3937024	13	3.8	13	76	7	57	34	6	22	38	1.78
3938795--3939005	111	1.9	108	85	8	293	49	9	4	36	1.54
3942922--3942963	19	2.2	20	91	4	68	23	7	0	69	1.13
3943069--3943113	19	2.3	20	81	11	58	33	0	4	62	1.15
3943079--3943120	19	2.3	19	84	12	52	35	0	9	54	1.33
3943223--3943248	11	2.4	11	100	0	52	38	7	7	46	1.61
3943222--3943250	11	2.5	12	88	11	51	37	6	6	48	1.57
3947144--3947203	22	2.8	22	79	2	59	51	3	1	43	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3954115--3954161	17	2.5	20	87	12	66	53	4	4	38	1.40
3955122--3955168	20	2.4	20	89	3	69	29	12	2	55	1.49
3956443--3956484	21	2.0	21	100	0	84	28	9	33	28	1.88
3956805--3956953	3	49.0	3	69	7	68	27	8	3	60	1.42
3957078--3957131	24	2.3	24	81	9	58	14	7	5	72	1.26
3960930--3960965	17	2.2	16	90	5	54	0	25	0	75	0.81
3961052--3961117	11	5.7	11	75	21	64	0	31	0	68	0.90
3961053--3961119	9	8.0	9	69	15	54	0	32	0	67	0.91
3961079--3961119	13	3.2	13	76	16	50	0	29	0	70	0.87
3961062--3961119	24	2.4	25	88	5	91	0	31	0	68	0.89

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