genome.fa.s13.2.7.7.80.10.50.1000.20.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  20  of  199  ( 23770 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)
5987076--5987107	15	2.1	15	94	0	55	68	9	6	15	1.36
5990634--5990686	23	2.4	22	81	9	63	32	9	22	35	1.86
5990634--5990722	24	3.9	23	73	7	65	32	13	19	34	1.90
5992604--5992650	22	2.1	23	84	4	60	36	4	8	51	1.52
5993597--5993650	27	2.0	27	82	7	65	31	9	1	57	1.41
5999700--5999742	23	1.9	23	86	13	63	27	4	18	48	1.68
6004847--6004899	19	3.0	17	78	10	61	35	9	18	35	1.84
6004871--6004915	23	2.0	23	91	4	74	37	4	17	40	1.70
6005100--6005138	19	2.0	21	85	10	55	15	10	5	69	1.34
6030541--6030583	17	2.5	17	92	3	68	18	46	25	9	1.79
6034398--6034434	17	2.2	17	90	0	56	67	0	13	18	1.23
6039652--6039703	16	3.2	16	94	0	86	28	0	36	34	1.58
6040409--6040588	91	2.0	90	87	1	261	46	4	2	46	1.37
6040446--6040503	28	2.2	26	84	12	73	51	5	0	43	1.24
6040443--6040586	44	3.2	43	68	16	112	48	3	2	45	1.31
6042646--6042706	30	2.0	30	87	0	86	24	6	27	40	1.80
6043507--6043540	16	2.1	16	88	0	50	70	0	26	2	1.01
6054093--6054148	23	2.4	23	87	3	76	66	0	5	28	1.14
6054360--6054385	10	2.6	10	100	0	52	88	0	11	0	0.52
6055828--6056033	44	4.7	44	77	8	138	28	24	18	28	1.98
6055831--6056349	223	2.3	224	85	3	713	28	21	18	31	1.97
6055874--6056398	44	11.8	44	71	10	318	28	21	18	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6056144--6056497	181	2.0	181	85	2	487	28	19	19	32	1.96
6056540--6056692	22	7.0	22	90	0	225	26	26	14	32	1.94
6056953--6057247	44	6.7	44	77	6	258	28	22	18	30	1.97
6056944--6057247	88	3.4	88	77	3	331	28	21	18	31	1.97
6056936--6057259	178	1.8	178	89	0	513	27	22	17	32	1.96
6058470--6058604	50	2.5	51	84	8	164	10	25	21	42	1.84
6058507--6058604	50	1.9	51	93	2	171	12	22	21	43	1.85
6059541--6059573	12	3.0	11	87	12	50	0	18	0	81	0.68
6059583--6059650	31	2.2	30	92	7	111	25	2	2	69	1.17
6063562--6063592	4	7.8	4	100	0	62	25	0	22	51	1.48
6063761--6063816	23	2.5	21	75	11	58	58	3	3	33	1.32
6070499--6070580	28	2.9	28	87	0	128	30	12	18	39	1.87
6074620--6074962	44	7.8	44	72	8	234	26	25	18	29	1.98
6074550--6075066	218	2.4	217	88	0	748	28	23	18	29	1.97
6074601--6075066	44	10.7	45	69	12	181	27	23	19	29	1.98
6075054--6075697	128	5.0	127	85	5	674	25	25	18	30	1.98
6075059--6075697	132	4.9	129	84	6	690	25	25	18	30	1.98
6075470--6075652	44	4.2	44	64	8	102	26	25	18	28	1.98
6076912--6076945	15	2.3	15	94	0	59	14	8	0	76	1.01
6080654--6080853	108	1.9	106	91	2	328	35	17	17	30	1.93
6081802--6081932	3	41.3	3	75	11	61	58	3	5	33	1.36
6081832--6081887	30	1.9	28	85	7	76	53	0	7	39	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6081850--6081918	24	3.1	24	74	16	76	57	1	1	39	1.16
6081858--6081929	34	2.2	34	83	14	89	61	2	2	33	1.25
6082411--6082436	11	2.4	11	100	0	52	7	46	26	19	1.77
6083558--6084288	50	14.7	49	69	7	364	22	22	23	30	1.99
6083545--6084018	100	4.7	100	89	1	664	24	21	23	30	1.99
6083589--6084088	200	2.5	200	86	2	610	23	22	23	31	1.99
6083556--6084286	100	7.3	100	85	2	546	22	22	23	30	1.99
6084006--6084298	99	2.9	99	91	1	453	22	22	24	30	1.99
6083556--6084176	149	4.1	150	74	3	579	23	22	23	30	1.99
6083613--6084286	149	4.5	148	74	4	519	22	22	23	31	1.99
6085595--6085663	6	12.0	6	78	18	67	1	17	0	81	0.77
6085596--6085665	17	4.1	18	77	12	76	1	15	0	82	0.73
6089343--6089542	108	1.9	106	92	2	337	35	17	17	30	1.93
6090469--6090529	3	20.3	3	75	6	52	62	6	3	27	1.36
6094830--6094863	10	3.3	10	84	8	50	85	0	8	5	0.75
6098590--6098689	27	3.5	28	72	22	68	63	3	3	31	1.25
6098618--6098711	31	3.2	30	76	10	72	63	4	3	28	1.28
6099013--6099072	20	3.0	21	81	13	72	31	10	1	56	1.42
6099043--6099079	20	1.9	20	94	5	67	21	8	0	70	1.13
6098885--6099079	19	9.9	20	65	14	68	29	8	1	60	1.36
6100823--6100881	26	2.3	26	90	0	91	18	5	20	55	1.61
6102021--6102104	24	3.8	24	80	18	117	29	42	5	21	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6102037--6102075	18	2.2	18	100	0	78	28	46	0	25	1.53
6103218--6103282	33	2.0	32	88	5	96	15	7	18	58	1.60
6109732--6109769	20	1.9	20	88	0	58	44	0	7	47	1.32
6110259--6110314	29	1.9	29	85	0	76	51	3	0	44	1.18
6111272--6111314	22	2.0	21	86	13	61	23	11	9	55	1.64
6113488--6113531	20	2.2	20	88	8	63	20	4	6	68	1.31
6117365--6117414	17	2.9	17	82	8	57	44	0	32	24	1.54
6117500--6117559	30	2.0	31	86	3	86	43	0	36	20	1.52
6119164--6119253	25	3.6	25	74	12	78	42	11	14	32	1.81
6124792--6124848	28	2.0	28	93	0	96	33	24	21	21	1.97
6125007--6125072	22	3.0	21	73	4	60	43	16	21	18	1.87
6125273--6125303	16	1.9	16	93	0	53	29	12	25	32	1.93
6125308--6125394	24	3.6	24	79	0	84	45	19	8	26	1.78
6128322--6128387	22	3.0	22	77	4	62	43	18	21	16	1.87
6128395--6128516	32	3.8	32	80	10	133	36	22	19	21	1.95
6128652--6128682	16	1.9	16	93	0	53	29	12	25	32	1.93
6128692--6128745	24	2.2	24	83	0	63	46	20	9	24	1.79
6128902--6129066	79	2.1	79	95	2	296	21	27	22	29	1.99
6136400--6136431	15	2.1	15	94	0	55	40	6	9	43	1.62
6136620--6136660	15	2.7	15	88	3	55	46	2	2	48	1.28
6137300--6137344	22	2.1	21	87	4	63	11	11	8	68	1.39
6146353--6146394	23	1.9	21	90	9	66	66	0	4	28	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6146393--6146431	16	2.4	17	86	4	53	56	7	7	28	1.55
6148622--6148668	18	2.7	17	78	12	51	36	8	0	55	1.31
6148809--6148865	30	1.9	29	89	3	87	31	14	3	50	1.59
6154217--6154315	49	2.0	49	98	0	189	52	6	6	35	1.51
6156107--6156232	44	2.8	45	74	9	125	25	26	18	30	1.98
6156011--6156553	218	2.5	217	85	1	694	28	22	18	30	1.97
6156541--6156836	128	2.3	128	89	0	466	24	23	19	32	1.97
6156887--6157111	44	5.1	44	65	6	105	28	25	16	28	1.97
6156839--6157114	132	2.1	132	95	0	498	28	24	18	28	1.98
6158309--6158342	15	2.3	15	94	0	59	14	8	0	76	1.01
6162054--6162256	108	1.9	105	89	5	318	35	16	17	30	1.92
6163192--6163278	3	29.0	3	80	4	86	60	3	5	29	1.36
6164899--6165592	50	13.9	50	70	6	356	23	21	23	31	1.99
6164858--6165312	100	4.6	100	89	1	644	23	21	24	31	1.98
6164850--6165380	100	5.3	100	85	2	467	23	21	23	31	1.99
6164858--6165382	200	2.6	200	84	2	588	22	22	23	31	1.99
6165300--6165592	99	2.9	99	87	1	408	24	22	22	30	1.99
6164872--6165462	149	3.9	150	75	5	442	23	22	23	30	1.99
6166889--6166965	6	13.0	6	81	13	79	1	20	0	77	0.83
6166906--6166966	16	3.8	16	81	12	54	1	21	0	77	0.86
6166885--6166965	13	6.2	13	77	9	85	1	20	0	77	0.83
6170694--6170893	108	1.9	106	89	2	310	35	18	17	30	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6171891--6171981	3	30.3	3	78	4	94	61	4	4	29	1.35
6177039--6177080	21	2.0	21	100	0	84	38	19	19	23	1.93
6177922--6177969	16	2.9	15	79	14	51	66	0	2	31	1.03
6177933--6177969	16	2.2	17	90	4	58	70	0	0	29	0.88
6177981--6178005	5	5.0	5	100	0	50	80	0	0	20	0.72
6179783--6179882	27	3.5	28	72	22	68	63	3	3	31	1.25
6179811--6179904	31	3.2	30	76	10	72	63	4	3	28	1.28
6180207--6180266	20	3.0	21	81	13	72	31	10	1	56	1.42
6180237--6180273	20	1.9	20	94	5	67	21	8	0	70	1.13
6180079--6180273	19	9.9	20	65	14	68	29	8	1	60	1.36

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