genome.fa.s7.2.7.7.80.10.50.1000.143.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  143  of  204  ( 24458 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)
43203952--43203979	6	4.7	6	100	0	56	85	0	0	14	0.59
43206355--43206483	61	2.1	58	83	14	163	41	2	6	48	1.43
43210903--43210965	14	4.6	14	72	18	60	38	15	6	39	1.73
43211236--43211293	30	1.9	30	85	0	80	31	24	3	41	1.71
43212362--43212391	8	3.8	8	100	0	60	66	0	0	33	0.92
43212339--43212389	24	2.1	25	85	10	70	66	0	1	31	1.03
43214250--43214280	16	1.9	16	93	0	53	54	9	0	35	1.33
43215213--43215285	36	2.0	36	100	0	146	24	27	17	30	1.97
43223981--43224019	20	2.0	20	85	9	55	43	7	15	33	1.75
43225318--43225387	36	1.9	37	97	2	133	22	22	17	37	1.94
43241505--43241537	11	2.9	12	86	13	52	33	0	0	66	0.92
43241539--43241578	18	2.2	18	86	8	55	67	12	0	20	1.22
43254028--43254064	16	2.3	16	90	0	56	48	2	8	40	1.47
43262553--43262601	21	2.4	21	96	3	91	46	12	0	40	1.41
43263779--43263810	15	2.1	15	94	0	55	68	9	6	15	1.36
43268096--43268140	20	2.1	22	84	12	58	13	11	8	66	1.44
43272254--43272338	22	3.9	22	84	0	98	29	15	27	28	1.96
43272464--43272518	21	2.6	21	94	0	101	43	5	12	38	1.66
43272930--43272965	15	2.4	15	95	0	63	13	2	5	77	1.05
43273363--43273516	7	21.7	7	68	12	64	42	36	1	20	1.60
43273667--43273739	21	3.5	20	77	3	65	38	46	0	15	1.46
43273667--43273710	7	6.3	7	84	7	54	31	54	0	13	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43273665--43273717	13	3.8	13	80	11	61	37	49	0	13	1.42
43273709--43273820	7	15.9	7	68	12	59	46	29	0	23	1.58
43273656--43273820	14	11.7	14	69	13	88	44	33	0	20	1.56
43273212--43273902	300	2.3	299	91	2	1127	44	23	2	30	1.64
43274209--43274325	40	2.9	40	82	7	130	29	22	17	30	1.96
43274618--43274652	18	1.9	18	100	0	70	37	17	22	22	1.94
43275620--43275653	7	4.9	7	100	0	68	14	11	58	14	1.63
43281301--43281390	43	2.1	43	87	2	128	35	8	10	45	1.69
43282784--43282855	36	2.0	36	81	5	83	63	1	2	31	1.17
43284905--43284955	25	2.1	25	82	13	63	41	0	9	49	1.36
43286863--43286918	3	18.7	3	100	0	112	32	0	0	67	0.91
43291399--43291471	10	7.9	10	68	17	50	42	0	1	56	1.08
43291396--43291471	28	2.9	27	78	7	84	43	0	1	55	1.08
43291529--43291564	18	2.0	18	100	0	72	44	0	0	55	0.99
43291711--43291816	39	2.5	43	83	11	130	35	30	3	30	1.75
43291724--43291816	44	2.1	46	89	4	145	37	29	4	29	1.76
43291798--43291850	16	3.3	16	97	0	97	24	32	5	37	1.79
43298497--43298542	21	2.2	21	80	3	58	21	36	17	23	1.94
43304450--43304527	40	2.0	40	87	5	113	30	23	28	17	1.97
43304445--43304560	40	2.9	39	79	6	99	35	19	25	19	1.96
43304611--43304763	41	3.7	41	97	0	279	15	24	30	30	1.95
43304864--43305068	42	4.9	42	83	3	200	15	24	26	33	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43305921--43305951	16	1.9	16	93	0	53	19	0	51	29	1.47
43307161--43307217	25	2.4	22	80	13	60	19	42	1	36	1.62
43307193--43307231	16	2.6	15	84	11	53	23	35	5	35	1.77
43307175--43307497	160	2.0	160	99	0	637	20	28	11	39	1.87
43307353--43307391	16	2.6	15	84	11	53	23	35	5	35	1.77
43309269--43309321	24	2.2	24	96	0	97	43	3	3	49	1.38
43309427--43309472	22	2.1	22	88	8	67	45	10	4	39	1.59
43309437--43309697	31	8.1	31	76	9	247	47	11	3	37	1.55
43309412--43309697	56	4.7	56	75	18	257	47	11	3	37	1.55
43309493--43309817	9	37.7	9	66	19	72	45	13	2	38	1.58
43309483--43309561	22	3.8	21	66	27	60	49	11	1	37	1.47
43309437--43309697	96	2.7	96	97	0	486	47	11	3	37	1.55
43309697--43309775	34	2.3	34	80	0	86	43	13	1	41	1.53
43315272--43315442	66	2.6	65	84	4	200	40	19	26	13	1.89
43315424--43315525	42	2.4	42	86	0	132	38	16	41	3	1.67
43315414--43315525	21	5.3	21	82	4	109	37	16	41	4	1.69
43315831--43316036	43	4.7	42	82	10	220	21	19	29	29	1.97
43315830--43316036	89	2.4	89	81	11	232	21	19	29	29	1.98
43316024--43316168	43	3.3	43	84	10	179	35	25	19	19	1.95
43316304--43316346	22	2.0	22	90	0	68	44	27	18	9	1.80
43318530--43318557	12	2.3	12	100	0	56	85	7	0	7	0.73
43321827--43321857	5	6.2	5	92	0	53	38	22	19	19	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43322593--43322618	7	3.7	7	100	0	52	15	0	69	15	1.20
43322619--43322678	30	2.0	30	83	3	75	45	0	35	20	1.51
43322892--43322928	18	2.1	18	94	0	65	29	5	13	51	1.63
43323264--43323294	16	1.9	16	100	0	62	32	12	25	29	1.93
43323263--43323299	16	2.5	15	87	12	58	37	13	21	27	1.91
43323692--43323731	20	2.0	21	85	5	55	15	20	15	50	1.79
43329693--43329765	4	18.2	4	100	0	146	24	0	24	50	1.49
43331968--43332040	34	2.1	35	90	5	114	49	9	12	28	1.72
43332159--43332384	90	2.6	84	84	5	283	38	18	11	32	1.86
43338926--43338950	13	1.9	13	100	0	50	24	8	28	40	1.83
43339650--43339771	60	2.0	60	100	0	244	50	8	11	29	1.67
43342871--43343000	9	13.9	9	69	22	63	24	3	14	56	1.55
43342871--43342952	25	3.2	25	85	10	119	25	3	14	56	1.55
43342935--43343004	21	3.5	20	73	9	63	25	4	12	57	1.54
43342871--43343080	30	7.2	29	77	9	200	25	4	13	56	1.55
43342924--43343080	15	10.5	15	64	27	50	25	4	12	57	1.54
43342869--43343080	60	3.6	59	81	8	240	25	4	13	56	1.55
43347018--43347211	27	7.3	27	83	5	234	17	17	22	43	1.88
43347018--43347212	77	2.5	80	86	4	252	16	16	22	43	1.87
43349519--43349737	9	23.7	9	65	19	69	27	2	12	57	1.46
43349527--43349608	25	3.2	25	78	10	92	26	3	12	57	1.51
43349523--43349737	30	7.4	30	76	11	180	27	2	12	58	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43349580--43349737	60	2.6	61	84	5	203	27	1	12	59	1.40
43350098--43350131	17	2.0	17	100	0	68	29	11	17	41	1.85
43350168--43350242	26	2.9	26	97	0	141	18	5	22	53	1.65
43352251--43352395	69	2.1	69	89	2	220	40	13	6	40	1.70
43353564--43353697	61	2.2	61	84	7	175	42	5	8	43	1.58
43371181--43371227	21	2.2	22	88	3	69	23	19	36	21	1.95
43374224--43374268	15	3.0	15	84	9	65	66	0	0	33	0.92
43374226--43374269	16	2.8	15	83	10	61	70	0	0	29	0.88
43374387--43374443	30	1.9	30	89	7	89	33	8	15	42	1.78
43381623--43381690	34	2.0	35	85	2	93	44	13	7	35	1.71
43385567--43385600	2	17.0	2	100	0	68	50	0	0	50	1.00
43387134--43387183	20	2.4	22	80	6	59	54	16	2	28	1.53
43390301--43390362	22	2.8	22	85	0	79	6	12	9	70	1.31
43390515--43390565	23	2.3	22	78	18	52	35	0	5	58	1.22
43390554--43390593	16	2.3	18	87	8	57	27	0	5	67	1.11
43392075--43392127	28	1.9	27	85	11	72	35	0	3	60	1.15
43392108--43392147	19	2.0	21	90	9	66	45	0	0	55	0.99
43400123--43400169	16	3.1	16	87	6	71	55	0	2	42	1.12
43402476--43402538	27	2.2	29	83	5	76	39	1	25	33	1.65
43403023--43403059	19	2.1	19	90	10	60	48	0	8	43	1.32
43403560--43403589	2	15.0	2	100	0	60	50	0	0	50	1.00
43404147--43404235	35	2.5	36	82	7	94	33	16	10	39	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43404525--43404834	41	7.6	41	91	0	476	22	27	20	29	1.99
43405795--43405822	2	14.0	2	100	0	56	50	0	0	50	1.00
43406633--43406683	26	2.0	26	84	7	68	43	7	0	49	1.32
43414221--43414277	30	1.9	29	86	10	80	24	5	8	61	1.46
43418460--43418502	13	3.3	13	82	17	54	48	2	2	46	1.27
43419042--43419097	6	9.2	6	79	11	60	33	1	44	19	1.61
43419042--43419097	13	4.1	13	77	18	60	33	1	44	19	1.61
43419134--43419174	6	6.5	6	91	8	64	31	0	53	14	1.41
43419134--43419174	13	3.2	13	93	3	66	31	0	53	14	1.41
43419134--43419174	19	2.2	19	91	8	66	31	0	53	14	1.41

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