genome.fa.s13.2.7.7.80.10.50.1000.12.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  12  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)
3720703--3720733	6	5.2	6	100	0	62	51	0	0	48	1.00
3720703--3720738	18	2.1	18	89	5	56	55	0	0	44	0.99
3722304--3722343	21	1.9	21	89	0	62	30	2	0	67	1.04
3727678--3727711	16	2.2	15	89	5	50	52	0	2	44	1.16
3730415--3730473	28	2.3	27	83	16	72	45	1	0	52	1.10
3732634--3732856	95	2.4	95	81	2	252	39	3	17	39	1.67
3732925--3732963	16	2.4	17	79	12	55	43	2	2	51	1.29
3732915--3733034	47	2.5	48	80	8	154	45	5	6	41	1.54
3733301--3733345	21	2.1	21	83	0	54	2	24	44	28	1.66
3737158--3737182	12	2.1	12	100	0	50	0	8	0	92	0.40
3737282--3737314	14	2.4	14	95	5	59	15	0	33	51	1.43
3742787--3742841	3	18.3	3	100	0	110	0	0	65	34	0.93
3743534--3743566	2	16.5	2	100	0	66	0	48	0	51	1.00
3757389--3757424	2	18.0	2	100	0	72	50	0	0	50	1.00
3763872--3764098	36	6.0	36	86	9	310	29	20	12	37	1.90
3763980--3764134	46	3.6	46	78	16	204	28	21	12	36	1.91
3763944--3764134	82	2.3	82	95	0	337	29	21	12	37	1.89
3769668--3769692	12	2.1	12	100	0	50	24	8	36	32	1.84
3776462--3776516	21	2.6	21	82	0	74	23	10	32	32	1.90
3784081--3784119	19	2.2	18	86	9	53	53	2	5	38	1.37
3789184--3789250	3	23.7	3	82	11	79	28	1	1	68	1.07
3793545--3793613	29	2.4	31	76	18	76	56	4	1	37	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3802032--3802069	18	2.2	18	95	4	69	34	0	10	55	1.34
3802372--3802410	16	2.4	16	82	0	51	41	5	23	30	1.76
3802392--3802484	44	2.1	44	90	6	143	35	3	24	36	1.72
3802598--3802719	56	2.2	56	79	8	140	51	4	0	42	1.29
3809428--3809467	10	3.9	10	86	3	53	87	7	5	0	0.66
3820696--3820735	4	10.0	4	100	0	80	25	0	25	50	1.50
3824506--3824565	4	15.0	4	100	0	120	50	25	0	25	1.50
3832329--3832361	14	2.4	14	90	5	50	21	3	0	75	0.93
3832878--3832909	11	2.8	12	95	4	57	84	0	0	15	0.63
3832878--3832909	6	5.5	6	92	7	57	84	0	0	15	0.63
3836866--3837252	146	2.6	149	82	9	443	40	28	8	22	1.84
3844120--3844168	23	2.1	23	100	0	98	34	20	14	30	1.92
3846759--3846821	24	2.6	24	84	0	81	47	15	14	22	1.81
3850737--3850773	18	2.1	18	100	0	74	21	32	5	40	1.76
3852926--3853037	43	2.6	43	82	2	127	31	22	17	28	1.97
3856875--3856943	16	4.3	16	92	0	102	23	33	5	37	1.79
3868160--3868202	24	1.9	22	86	13	61	46	13	20	18	1.83
3882670--3882695	10	2.6	10	100	0	52	19	0	23	57	1.40
3884983--3885060	35	2.2	36	86	4	113	26	2	17	52	1.58
3892213--3892263	25	2.0	25	88	0	75	47	15	17	19	1.83
3892639--3892672	15	2.3	15	89	0	50	47	5	17	29	1.71
3900326--3900374	19	2.3	23	80	16	61	34	2	0	63	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3903242--3903303	31	2.0	31	100	0	124	48	3	12	35	1.58
3906231--3906276	24	2.0	24	86	4	67	26	19	10	43	1.84
3918939--3918978	20	2.0	20	100	0	80	25	10	35	30	1.88
3922121--3922153	3	11.0	3	93	0	57	33	30	0	36	1.58
3925277--3925306	2	15.0	2	100	0	60	50	0	0	50	1.00
3939290--3939362	26	2.9	24	82	11	83	34	21	27	16	1.95
3939615--3939681	18	3.7	18	91	0	107	40	26	7	25	1.82
3939616--3939681	27	2.4	27	87	0	96	39	27	7	25	1.83
3939615--3939673	9	6.6	9	92	0	91	40	27	8	23	1.83
3953698--3953724	6	4.5	6	100	0	54	14	0	0	85	0.61
3954779--3954827	2	24.5	2	95	0	89	48	0	0	51	1.00
3955562--3955623	29	2.2	28	91	8	99	62	16	0	20	1.32
3964370--3964401	10	3.2	10	100	0	64	28	0	31	40	1.57
3964414--3964520	38	2.8	38	83	8	146	36	3	19	40	1.70
3970789--3970834	14	3.2	14	81	3	56	56	8	2	32	1.42
3983940--3983970	16	1.9	16	93	0	53	77	0	16	6	0.97
3983974--3984644	215	3.1	213	79	9	784	36	15	15	33	1.88
3983966--3984621	108	6.1	106	82	7	763	37	14	14	32	1.87
3984839--3985376	211	2.5	212	82	8	644	33	15	13	37	1.86
3985371--3985402	16	2.0	16	93	0	55	9	15	0	75	1.05
3991270--3991345	27	2.8	27	88	4	100	18	26	35	19	1.95
3991399--3991451	22	2.3	23	81	12	65	66	1	28	3	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3994447--3994481	7	5.0	7	100	0	70	42	14	28	14	1.84
3996905--3996983	37	2.1	37	97	0	149	24	39	6	30	1.80
4000786--4000871	21	4.0	23	80	11	110	37	24	22	16	1.93
4000786--4000872	44	2.0	41	86	6	120	36	24	21	17	1.94
4001885--4001929	19	2.2	22	84	11	60	51	2	0	46	1.13
4002072--4002124	27	2.1	26	89	10	83	45	0	0	54	0.99
4002085--4002118	15	2.1	16	89	10	52	44	0	0	55	0.99
4031249--4031280	17	2.0	17	88	11	50	25	15	25	34	1.95
4043211--4043414	110	1.9	107	86	5	293	34	20	16	28	1.94
4043959--4043988	8	3.8	8	100	0	60	66	0	0	33	0.92
4044218--4044276	2	30.0	2	88	10	77	52	0	1	45	1.10
4044316--4044347	3	11.0	3	93	6	57	65	0	0	34	0.93
4045880--4046337	44	10.4	44	63	20	145	28	25	16	30	1.96
4046408--4046607	44	4.5	44	67	16	135	26	23	19	31	1.98
4045715--4046875	132	8.8	132	92	0	1813	27	23	17	30	1.97
4047183--4047239	24	2.4	24	79	5	62	31	26	14	28	1.94
4048019--4048099	42	1.9	42	84	0	108	28	27	13	30	1.94
4051465--4051489	8	3.1	8	100	0	50	72	12	16	0	1.13
4051889--4052093	111	1.9	107	82	6	259	34	18	17	30	1.94
4052638--4052675	8	4.8	8	100	0	76	65	0	0	34	0.93
4052632--4052675	16	2.7	16	92	3	61	68	0	0	31	0.90
4052866--4052959	2	48.5	2	78	6	68	51	3	3	42	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4054054--4054113	30	2.0	29	87	3	84	11	10	38	40	1.75
4054257--4054460	110	1.9	107	86	5	293	34	20	16	28	1.94
4055009--4055038	8	3.8	8	100	0	60	66	0	0	33	0.92
4055003--4055038	16	2.2	16	90	5	54	69	0	0	30	0.89
4055229--4055322	2	48.5	2	78	6	68	51	3	3	42	1.34
4056823--4056879	25	2.3	24	84	6	78	45	17	19	17	1.86
4058739--4058763	2	12.5	2	100	0	50	52	0	0	48	1.00
4059367--4059406	17	2.4	17	95	0	71	42	32	0	25	1.55
4067232--4067302	27	2.6	27	88	4	97	40	12	1	45	1.51
4067254--4067306	27	2.0	27	100	0	106	41	9	0	49	1.35
4067292--4067331	18	2.2	19	90	4	64	72	15	0	12	1.12
4067613--4067668	3	18.3	3	92	3	94	32	0	3	64	1.11
4067667--4067704	3	12.7	3	100	0	76	0	0	31	68	0.90
4074010--4074034	13	1.9	13	100	0	50	8	20	8	64	1.46
4074344--4074540	21	9.5	20	74	17	113	0	33	0	66	0.92
4074358--4074537	22	8.6	21	72	18	103	0	34	0	65	0.93
4074406--4074546	4	34.5	4	75	16	112	0	33	0	66	0.92
4074367--4074483	34	3.6	34	75	14	111	0	34	0	65	0.93
4074372--4074517	63	2.3	65	87	9	203	0	33	0	66	0.92
4074406--4074546	34	4.2	34	82	11	159	0	33	0	66	0.92
4074577--4074652	27	2.8	27	85	0	107	15	28	28	26	1.96
4074724--4074794	27	2.6	28	88	6	101	45	1	12	40	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4078116--4078154	2	19.5	2	94	0	69	51	0	0	48	1.00
4086841--4086902	29	2.1	29	82	5	72	53	16	1	29	1.52
4089979--4090004	3	8.7	3	100	0	52	34	65	0	0	0.93
4098419--4098448	10	3.0	10	95	0	51	26	3	10	60	1.45
4101548--4101573	5	5.2	5	100	0	52	42	19	19	19	1.90
4104755--4104815	18	3.4	18	97	0	113	24	21	37	16	1.93
4104954--4105142	105	1.8	105	94	0	333	38	26	7	26	1.84
4114430--4114481	24	2.2	24	89	0	77	38	1	7	51	1.42
4116179--4116524	31	11.2	31	76	3	268	24	36	13	26	1.92
4116180--4116524	62	5.6	61	77	3	316	24	36	12	26	1.91

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