genome.fa.s4.2.7.7.80.10.50.1000.13.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: A04
Parameters: 2 7 7 80 10 50 1000
Length:  82679320

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   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255   

This is table  13  of  255  ( 30512 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)
3744303--3744434	20	6.3	20	71	22	69	62	1	3	32	1.22
3752459--3752491	6	5.5	6	100	0	66	48	18	15	18	1.81
3753921--3753961	21	2.0	21	90	0	64	29	21	29	19	1.98
3764139--3764396	131	2.0	131	89	1	401	27	17	18	35	1.94
3765498--3765522	13	1.9	13	100	0	50	24	0	20	56	1.43
3765850--3766181	130	2.6	129	87	4	451	27	17	19	35	1.94
3767761--3767805	21	2.1	21	83	0	54	57	0	2	40	1.11
3768196--3768286	18	5.5	15	76	21	76	38	9	15	36	1.81
3768184--3768300	17	6.5	17	85	11	146	38	10	14	36	1.80
3768184--3768300	35	3.3	35	92	3	189	38	10	14	36	1.80
3774019--3774074	15	3.7	15	78	7	69	87	0	12	0	0.54
3774019--3774074	23	2.5	22	79	2	67	87	0	12	0	0.54
3774399--3774431	13	2.4	14	90	5	50	69	3	0	27	1.03
3774427--3774528	30	3.4	30	83	2	125	30	22	2	44	1.68
3775385--3775456	16	4.1	17	84	15	85	80	1	18	0	0.78
3775389--3775446	28	2.0	29	86	3	82	82	0	17	0	0.66
3775389--3775457	8	8.0	8	79	17	68	82	1	15	0	0.74
3775393--3775458	17	4.0	16	86	11	89	81	1	16	0	0.76
3775609--3775646	5	7.6	5	93	0	67	36	2	0	60	1.11
3775645--3775674	5	6.0	5	100	0	60	20	0	0	80	0.72
3776001--3776482	17	26.7	18	67	18	198	31	12	8	47	1.71
3776003--3776123	36	3.4	37	78	7	135	33	10	5	50	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3776224--3776481	52	4.9	51	74	15	152	31	14	8	45	1.75
3776213--3776357	69	2.1	69	83	5	177	34	11	8	44	1.72
3776260--3776482	35	6.3	34	74	12	121	31	15	8	44	1.77
3776364--3776519	73	2.2	73	81	8	169	31	15	9	43	1.79
3776544--3776585	21	2.0	22	90	4	68	40	2	9	47	1.49
3776644--3776698	18	3.1	18	89	5	94	27	12	10	49	1.74
3777183--3777275	45	2.1	45	97	0	177	23	13	10	51	1.73
3781140--3781259	43	2.9	41	73	12	127	33	22	21	22	1.97
3781379--3782094	207	3.5	207	93	0	1193	29	18	23	28	1.98
3782489--3782613	19	6.9	18	78	17	100	36	11	15	36	1.83
3782496--3782613	35	3.3	35	95	3	200	37	11	14	36	1.83
3788830--3788872	20	2.2	20	91	0	68	25	11	11	51	1.72
3789976--3790145	85	2.0	85	92	0	286	28	7	30	34	1.84
3791368--3791417	20	2.5	20	84	9	66	60	2	4	34	1.27
3791659--3791747	27	3.4	26	75	10	83	55	3	5	35	1.40
3793270--3793331	16	3.9	16	86	0	88	40	1	29	29	1.66
3793270--3793339	32	2.2	32	94	0	122	40	2	27	30	1.71
3793286--3793341	16	3.5	16	87	0	76	42	3	25	28	1.71
3793578--3793617	21	2.0	20	90	5	62	55	2	0	42	1.13
3793789--3793823	13	2.8	12	91	8	61	60	0	8	31	1.27
3796396--3796473	38	2.1	38	100	0	156	61	2	5	30	1.31
3798599--3798730	44	3.0	43	70	17	119	25	25	21	27	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3798614--3798748	44	3.1	43	66	16	105	24	22	24	28	1.99
3798626--3798764	45	3.1	44	66	15	106	23	22	21	32	1.98
3798788--3798922	42	3.2	42	69	10	139	26	22	22	27	2.00
3798538--3798935	88	4.6	86	85	5	455	24	23	21	30	1.99
3800617--3800666	26	1.9	26	83	0	64	8	6	6	80	1.04
3803247--3803295	19	2.5	20	80	6	57	42	12	18	26	1.85
3805143--3805220	38	2.1	38	100	0	156	61	2	5	30	1.31
3810395--3810468	34	2.1	34	82	9	87	36	8	13	41	1.74
3810445--3810521	32	2.4	33	76	6	86	35	7	14	42	1.74
3812795--3812837	13	3.3	13	75	12	52	65	9	9	16	1.47
3812906--3813136	3	75.7	3	66	18	52	59	3	8	28	1.42
3812901--3813039	37	3.9	36	69	20	105	58	0	10	30	1.31
3812943--3812972	16	1.9	15	93	6	51	76	0	0	23	0.78
3812944--3812996	22	2.7	19	80	11	54	71	0	3	24	1.02
3812939--3812998	19	3.2	20	80	15	67	66	0	6	26	1.16
3813151--3813206	3	18.7	3	96	0	103	32	0	33	33	1.58
3813205--3813241	3	12.3	3	88	0	56	64	0	5	29	1.15
3814740--3814778	11	3.6	10	83	16	51	61	2	17	17	1.46
3814740--3814789	23	2.2	22	85	7	64	62	4	18	16	1.48
3817260--3817302	18	2.5	17	85	7	59	18	25	39	16	1.91
3817612--3817711	30	3.3	30	83	2	130	28	48	4	20	1.67
3818198--3818258	24	2.6	23	78	14	61	34	3	3	59	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3818275--3818339	2	34.5	2	72	17	50	40	1	1	56	1.18
3818265--3818335	25	2.8	26	82	6	92	38	4	2	54	1.34
3818275--3818339	27	2.3	26	80	12	76	40	1	1	56	1.18
3818357--3818415	25	2.5	24	78	10	68	33	8	6	50	1.59
3818373--3818421	25	2.0	25	91	0	80	34	8	6	51	1.57
3818578--3818625	16	3.1	15	90	6	69	31	2	2	64	1.16
3818578--3818629	8	6.5	8	82	8	61	30	1	1	65	1.14
3829477--3830078	74	8.0	73	77	10	525	29	16	20	33	1.94
3829699--3830444	221	3.2	219	77	15	524	29	17	19	33	1.95
3829709--3830069	147	2.4	148	85	4	469	31	16	19	32	1.94
3830074--3830484	77	5.2	76	82	10	434	26	19	20	33	1.97
3830224--3830258	14	2.5	14	95	0	61	20	20	2	57	1.54
3829912--3830412	166	3.0	162	84	6	614	27	18	19	33	1.95
3830147--3830336	89	2.1	92	88	3	287	27	19	18	34	1.95
3830467--3830510	13	3.3	13	81	6	52	18	13	4	63	1.46
3830467--3830529	14	4.5	14	82	7	65	22	12	3	61	1.45
3830494--3830526	15	2.2	15	94	0	57	21	9	0	69	1.15
3830690--3830724	14	2.5	14	90	0	52	14	20	5	60	1.54
3830779--3830841	14	4.5	14	82	7	74	20	14	4	60	1.52
3830691--3830929	117	2.1	115	82	5	284	24	17	15	42	1.88
3831702--3831864	30	5.4	30	89	1	222	26	47	3	22	1.67
3831717--3831799	18	5.3	18	61	31	55	24	49	3	22	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3832352--3832481	22	5.5	22	68	22	70	36	3	3	56	1.33
3832417--3832487	25	2.8	26	82	6	92	38	4	2	54	1.34
3832352--3832483	25	5.6	23	67	21	60	36	3	3	56	1.33
3832521--3832569	25	2.0	25	87	0	71	36	8	4	51	1.51
3832727--3832774	16	3.1	15	90	6	69	31	2	2	64	1.16
3832727--3832778	8	6.5	8	82	8	61	30	1	1	65	1.14
3835050--3835090	22	1.9	22	90	5	66	58	0	0	41	0.98
3844355--3844392	18	2.1	19	85	5	51	60	0	7	31	1.25
3844422--3844487	24	2.8	24	73	13	64	56	1	15	27	1.48
3844497--3844528	6	5.5	6	96	3	57	68	0	0	31	0.90
3844755--3844788	3	11.3	3	90	0	50	58	2	2	35	1.28
3844764--3844798	18	1.9	18	88	0	52	51	2	11	34	1.53
3844962--3845077	3	38.7	3	73	11	71	63	1	6	28	1.28
3847258--3847302	21	2.1	21	84	8	56	53	0	2	44	1.13
3848188--3848237	25	2.0	25	100	0	100	20	24	12	44	1.85
3848263--3848305	21	2.2	19	83	8	50	51	0	0	48	1.00
3848386--3848441	25	2.2	25	100	0	112	58	14	7	19	1.58
3848469--3848495	8	3.4	8	100	0	54	62	0	22	14	1.31
3851552--3851639	43	2.0	43	84	4	115	36	4	6	52	1.49
3853353--3853393	13	3.1	14	82	10	50	48	14	17	19	1.81
3863002--3863047	18	2.6	18	96	0	83	13	26	10	50	1.74
3865563--3865686	62	2.0	62	95	0	221	28	10	22	38	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3867657--3867700	21	2.1	21	95	0	79	18	0	15	65	1.27
3881648--3881717	36	1.9	36	88	0	104	48	10	8	32	1.67
3886993--3887031	20	2.0	20	94	0	69	25	23	15	35	1.94
3887405--3887446	21	2.0	21	95	0	75	28	26	4	40	1.76
3898659--3898695	15	2.5	16	87	12	53	45	10	24	18	1.81
3902815--3902869	26	2.0	28	86	6	78	63	5	0	30	1.17
3905085--3905131	22	2.1	22	96	0	85	31	19	12	36	1.89
3906019--3906066	24	2.0	24	84	8	62	58	0	2	39	1.10
3909063--3909403	160	2.2	151	87	8	472	35	13	11	39	1.80
3911386--3911432	24	2.0	24	87	8	69	40	6	6	46	1.55

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   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   227   228   229   230   231   232   233   234   235   236   237   238   239   240   
          241   242   243   244   245   246   247   248   249   250   251   252   253   254   255