genome.fa.s17.2.7.7.80.10.50.1000.13.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: D04
Parameters: 2 7 7 80 10 50 1000
Length:  56598092

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   

This is table  13  of  185  ( 22116 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)
3515126--3515289	29	5.5	30	70	22	116	46	18	0	34	1.54
3515241--3515287	9	5.4	9	77	7	53	48	19	0	31	1.49
3515391--3515454	25	2.5	26	84	2	85	42	14	3	40	1.61
3515953--3516174	43	5.2	43	87	1	320	28	20	29	21	1.98
3521332--3521386	28	2.0	28	100	0	110	16	21	14	47	1.82
3521453--3521567	57	2.0	57	93	3	196	26	17	9	46	1.79
3521642--3521694	15	3.5	15	75	10	54	37	0	7	54	1.29
3521839--3521881	19	2.3	18	80	11	59	69	0	2	27	1.00
3522010--3522042	17	2.0	17	88	5	50	6	30	0	63	1.18
3522975--3522999	8	3.1	8	100	0	50	36	0	0	64	0.94
3528292--3528331	20	2.0	20	100	0	80	40	0	20	40	1.52
3530150--3530178	3	9.7	3	100	0	58	68	31	0	0	0.89
3530177--3530216	3	13.3	3	100	0	80	67	0	0	32	0.91
3530464--3530540	27	2.9	27	94	0	127	16	28	27	27	1.97
3532106--3532439	23	14.7	23	75	5	94	29	4	23	42	1.74
3532151--3532536	23	16.9	22	77	10	237	29	6	23	40	1.79
3532174--3532536	114	3.2	113	81	6	396	29	6	23	40	1.79
3532074--3532499	137	3.1	137	95	0	755	29	5	23	40	1.78
3533514--3533636	42	2.9	43	88	2	185	21	17	31	29	1.96
3533647--3533688	22	1.9	22	90	0	66	40	23	21	14	1.90
3534691--3534738	18	2.5	20	77	19	57	50	6	0	43	1.27
3535718--3535765	14	3.5	14	80	5	53	58	8	2	31	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3536227--3536262	3	12.3	3	88	5	56	63	0	2	33	1.08
3538475--3538529	26	2.1	26	96	0	101	34	3	5	56	1.40
3542947--3543012	33	2.0	33	93	0	114	12	30	16	40	1.85
3543033--3543064	15	2.1	16	94	5	57	18	25	12	43	1.85
3543429--3543457	1	29.0	1	100	0	58	0	0	0	100	0.00
3544522--3544558	7	5.1	7	93	6	65	13	0	0	86	0.57
3544522--3544556	15	2.3	15	100	0	70	11	0	0	88	0.51
3544872--3544899	14	2.0	14	100	0	56	50	0	0	50	1.00
3546139--3546199	3	20.3	3	86	6	88	32	3	0	63	1.10
3548092--3548125	15	2.2	15	89	5	50	32	2	0	64	1.08
3551257--3551288	15	2.1	16	94	5	57	18	25	12	43	1.85
3552737--3552773	7	5.1	7	93	6	65	13	0	0	86	0.57
3552737--3552771	15	2.3	15	100	0	70	11	0	0	88	0.51
3553088--3553115	14	2.0	14	100	0	56	50	0	0	50	1.00
3558111--3558160	24	2.0	26	84	7	68	38	2	0	60	1.09
3558111--3558150	15	2.5	16	84	8	55	35	2	0	62	1.09
3559097--3559194	42	2.3	42	92	1	160	19	29	13	37	1.90
3559622--3559768	42	3.4	42	94	2	240	18	29	12	39	1.87
3564879--3564908	13	2.3	13	100	0	60	63	0	0	36	0.95
3576756--3576820	32	2.0	32	100	0	130	38	9	15	36	1.79
3584516--3584572	25	2.1	27	78	18	66	40	8	1	49	1.44
3585041--3585090	21	2.4	20	74	9	55	42	40	6	12	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3590885--3591051	88	1.9	88	83	7	221	37	16	12	33	1.87
3591141--3591185	19	2.3	19	84	3	54	66	0	0	33	0.92
3591304--3591356	19	2.7	19	77	13	54	71	3	5	18	1.21
3591478--3591540	19	3.4	19	73	10	67	33	4	4	57	1.41
3591495--3591619	56	2.2	55	81	13	139	34	3	2	60	1.26
3592374--3592446	30	2.4	30	84	6	85	56	1	4	38	1.27
3596639--3596682	19	2.2	20	88	4	63	50	6	2	40	1.42
3596655--3596694	18	2.2	19	86	4	55	52	10	2	35	1.48
3605778--3605823	13	3.6	13	85	2	67	32	0	2	65	1.05
3605800--3605849	13	3.8	13	86	0	64	30	0	2	68	1.01
3609311--3609358	24	2.0	24	100	0	96	37	12	20	29	1.90
3616974--3617103	59	2.2	61	80	5	140	39	4	15	40	1.68
3622471--3622515	23	2.0	23	86	0	63	11	11	2	75	1.13
3629872--3629942	28	2.5	28	93	2	115	56	8	8	26	1.58
3637149--3637193	19	2.4	19	85	10	65	28	0	2	68	1.01
3637663--3637735	27	2.6	28	79	12	71	50	0	8	41	1.32
3637928--3638190	141	1.9	142	83	5	345	37	14	15	32	1.88
3638458--3638620	69	2.3	74	77	15	196	40	5	15	38	1.70
3638239--3638714	237	2.0	238	81	4	550	39	6	17	36	1.76
3639293--3639322	6	5.0	6	100	0	60	83	0	0	16	0.65
3640324--3640369	23	2.0	23	86	0	65	28	8	17	45	1.78
3643184--3643225	13	3.3	13	80	3	50	66	19	0	14	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3645287--3645365	33	2.5	33	87	6	110	58	8	8	24	1.57
3645614--3645652	12	3.3	12	82	7	53	35	0	0	64	0.94
3645771--3645833	30	2.1	30	90	0	99	58	14	1	25	1.45
3645864--3645894	14	2.2	14	94	0	53	61	12	6	19	1.53
3653127--3653181	19	2.8	20	78	13	60	43	9	12	34	1.74
3653499--3653550	20	2.6	20	84	0	68	26	5	21	46	1.74
3657509--3657549	19	2.0	21	86	9	59	56	4	0	39	1.21
3662998--3663050	9	5.7	9	78	8	61	26	0	0	73	0.83
3662999--3663030	10	3.3	10	95	4	57	18	0	0	81	0.70
3662997--3663096	19	5.1	20	75	16	84	36	1	0	63	1.02
3663010--3663070	27	2.2	28	80	16	83	34	0	0	65	0.93
3663027--3663096	10	6.9	11	72	18	55	41	1	0	57	1.08
3663050--3663104	22	2.4	23	81	3	76	45	1	0	52	1.11
3670046--3670081	17	2.0	19	89	10	58	61	5	0	33	1.19
3673266--3673293	8	3.5	8	100	0	56	25	10	28	35	1.89
3673380--3673455	23	3.3	23	84	12	111	25	19	26	28	1.99
3681739--3681785	7	6.7	7	100	0	94	12	44	0	42	1.42
3694678--3694744	31	2.2	31	83	5	82	31	22	16	29	1.96
3694709--3694883	90	2.0	88	85	6	237	25	19	16	38	1.92
3694791--3694857	30	2.2	31	89	2	100	31	20	17	29	1.96
3697139--3697195	29	2.0	29	86	6	80	15	33	21	29	1.94
3700096--3700151	23	2.6	22	76	18	55	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3700107--3700151	23	1.9	24	86	13	67	51	0	0	48	1.00
3700154--3700205	17	3.2	17	83	8	63	55	0	1	42	1.10
3700178--3700241	29	2.2	29	83	10	78	53	0	1	45	1.10
3700201--3700235	16	2.2	16	89	0	52	57	0	0	42	0.99
3700099--3700242	13	10.0	15	68	20	78	51	0	0	47	1.05
3706386--3706476	3	30.3	3	100	0	182	65	0	0	34	0.93
3707404--3707473	31	2.3	31	80	9	81	30	21	15	32	1.94
3707508--3707574	30	2.2	31	89	2	100	31	20	17	29	1.96
3707427--3707622	89	2.2	89	84	4	252	25	18	16	39	1.91
3712531--3712904	148	2.5	151	84	8	508	49	8	12	29	1.69
3723409--3723499	41	2.2	43	80	9	107	46	1	2	50	1.20
3723576--3723657	34	2.4	34	76	11	87	50	1	2	46	1.22
3724001--3724667	154	4.4	155	87	6	945	50	8	11	29	1.67
3725699--3725737	20	2.0	20	94	0	69	15	41	5	38	1.69
3726117--3726173	30	1.9	30	82	13	73	47	1	0	50	1.11
3726349--3726412	26	2.5	26	84	0	92	35	23	6	34	1.80
3726349--3726414	13	5.1	13	79	0	78	36	22	6	34	1.79
3726502--3726529	13	2.2	13	100	0	56	57	21	7	14	1.61
3732245--3732270	6	4.3	6	100	0	52	65	0	0	34	0.93
3737056--3737091	18	1.9	18	88	5	54	58	2	0	38	1.13
3737189--3737215	13	2.1	13	100	0	54	40	0	0	59	0.98
3737550--3737579	3	10.0	3	100	0	60	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3737578--3737602	3	8.3	3	100	0	50	36	32	0	32	1.58
3739436--3739556	43	2.8	43	76	18	135	24	20	25	28	1.99
3740475--3740638	23	7.0	23	77	6	123	26	14	18	40	1.88
3740484--3740642	70	2.2	72	84	7	218	27	14	18	39	1.89
3741030--3741091	5	12.2	5	85	11	74	43	0	0	56	0.99
3741031--3741092	2	35.0	2	73	23	59	45	0	0	54	0.99
3742095--3742169	19	4.0	19	69	20	68	36	1	25	37	1.65
3748726--3748757	14	2.3	14	94	0	55	78	0	0	21	0.76
3750170--3750236	30	2.2	30	84	5	82	26	22	19	31	1.98
3750091--3750260	88	2.0	85	83	8	218	24	21	17	37	1.94

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