genome.fa.s13.2.7.7.80.10.50.1000.68.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  68  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)
20409351--20409407	6	9.2	6	80	14	62	17	1	3	77	1.00
20409430--20409475	3	15.3	3	100	0	92	32	0	0	67	0.91
20409501--20409537	17	2.1	18	95	5	67	27	8	5	59	1.48
20414648--20414681	12	2.8	12	95	0	59	73	14	0	11	1.10
20414613--20414713	41	2.5	41	83	3	132	75	10	6	6	1.19
20414655--20414733	29	2.7	31	82	9	103	69	12	7	10	1.36
20414660--20414748	29	3.0	28	78	14	90	70	10	7	11	1.33
20415632--20415665	7	5.0	7	92	7	61	70	0	14	14	1.17
20415636--20415665	13	2.3	13	100	0	60	73	0	13	13	1.10
20416923--20416973	21	2.4	22	83	6	61	7	21	1	68	1.25
20418819--20418855	18	2.1	18	100	0	74	45	0	27	27	1.54
20427028--20427077	26	1.9	26	91	0	82	44	4	0	52	1.20
20430383--20430425	21	2.1	20	82	4	50	25	18	2	53	1.56
20432566--20432724	50	3.2	50	69	0	156	27	22	27	23	1.99
20436626--20436650	12	2.1	12	100	0	50	36	24	16	24	1.94
20440830--20440878	23	2.1	23	92	0	80	32	14	10	42	1.79
20441385--20441858	43	11.0	43	79	5	294	28	24	22	24	1.99
20441555--20441794	129	1.9	129	84	0	327	27	22	23	25	2.00
20442300--20442345	21	2.2	21	84	0	56	4	39	17	39	1.69
20442219--20442395	87	2.0	87	90	2	275	11	31	18	38	1.86
20447915--20448200	9	32.8	9	70	17	194	32	2	20	45	1.64
20447942--20448200	34	8.2	33	73	19	180	31	2	20	45	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20447958--20448107	62	2.4	62	92	4	241	32	2	18	46	1.63
20447998--20448107	28	3.8	27	71	23	89	30	1	19	48	1.59
20447904--20448204	62	5.0	61	77	12	216	31	2	19	45	1.63
20447915--20448200	43	6.6	44	71	17	143	32	2	20	45	1.64
20448292--20448332	13	2.8	15	85	14	59	34	0	19	46	1.50
20448291--20448369	16	5.0	16	75	13	74	34	1	17	46	1.56
20448420--20448470	21	2.4	22	80	9	70	50	1	0	47	1.12
20451136--20451162	11	2.5	11	100	0	54	55	0	18	25	1.43
20452155--20452208	2	28.5	2	74	10	51	46	7	0	46	1.31
20453483--20453549	14	4.9	14	78	14	59	41	31	0	26	1.56
20454043--20454241	41	4.8	41	73	8	136	37	22	22	18	1.94
20454084--20454239	83	1.9	83	83	2	206	37	23	19	19	1.94
20458105--20458149	16	2.7	17	86	6	65	42	0	0	57	0.98
20458142--20458181	21	1.9	21	89	0	62	37	2	0	60	1.11
20458141--20458199	22	2.8	21	80	14	59	40	1	3	54	1.27
20459466--20459518	21	2.6	21	77	11	58	73	1	13	11	1.18
20465796--20465828	14	2.4	14	100	0	66	9	27	15	48	1.74
20465760--20465872	58	1.9	59	89	1	174	23	26	15	34	1.94
20465863--20466927	132	8.1	132	92	1	1638	27	24	19	29	1.98
20465929--20466927	44	22.7	44	63	12	249	27	23	19	29	1.98
20466921--20467290	50	7.4	50	74	2	330	26	24	20	29	1.99
20466944--20467290	100	3.5	98	92	5	563	26	24	20	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20468643--20468795	7	22.0	7	79	15	167	13	16	0	69	1.19
20471852--20471886	16	2.2	16	94	0	61	42	17	14	25	1.86
20476821--20476855	2	17.5	2	100	0	70	51	0	0	48	1.00
20479915--20479957	4	10.8	4	84	0	59	53	18	0	27	1.45
20479913--20479965	12	4.4	12	82	0	61	52	15	0	32	1.42
20479919--20479968	8	6.2	8	88	0	64	52	14	0	34	1.42
20481091--20481122	2	16.0	2	100	0	64	50	0	0	50	1.00
20481509--20481570	22	2.8	22	95	0	106	33	27	0	38	1.57
20481542--20481600	30	2.0	30	93	0	100	30	35	0	33	1.58
20481520--20481622	52	2.0	51	86	1	143	33	31	0	34	1.58
20481572--20481613	22	1.9	22	90	0	66	33	33	0	33	1.58
20481655--20481711	30	2.0	30	86	6	82	35	0	1	63	1.05
20481810--20481843	15	2.3	15	90	5	52	26	0	5	67	1.13
20483922--20484598	28	25.8	28	87	11	935	46	19	0	34	1.53
20483906--20484598	51	13.3	51	91	6	916	46	19	0	33	1.53
20484056--20484102	23	2.3	19	82	17	51	46	21	0	31	1.51
20484191--20484237	23	2.3	19	82	17	51	46	21	0	31	1.51
20484242--20484288	23	2.3	19	82	17	51	46	21	0	31	1.51
20484429--20484511	23	3.7	20	100	0	85	49	18	0	32	1.48
20484611--20484720	56	1.9	57	87	5	161	35	12	10	41	1.77
20488625--20488869	126	2.0	125	93	0	418	31	22	15	29	1.95
20488625--20488907	126	2.3	126	88	3	412	31	23	15	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20493056--20493256	108	1.9	108	96	0	375	25	31	23	19	1.98
20497056--20497117	21	3.1	21	84	8	78	59	3	0	37	1.13
20497055--20497151	9	10.3	9	69	18	56	54	3	1	41	1.23
20497876--20497918	22	2.0	22	90	0	68	9	18	27	44	1.80
20498046--20498232	43	4.4	43	85	3	252	19	20	31	29	1.97
20498071--20498405	43	7.8	43	80	2	141	24	26	22	26	2.00
20498216--20498425	43	4.8	43	79	1	204	29	31	15	23	1.95
20498277--20498468	88	2.2	87	80	0	213	30	29	15	25	1.95
20498776--20498888	21	5.4	21	83	0	109	4	40	17	37	1.70
20508227--20508260	16	2.1	16	94	0	59	32	0	14	52	1.42
20508298--20508381	9	9.8	9	70	10	68	36	2	19	41	1.64
20508300--20508352	16	3.2	16	83	5	70	32	3	22	41	1.72
20508451--20508496	22	2.1	22	91	0	74	43	0	10	45	1.39
20508418--20508607	56	3.2	56	86	9	254	41	1	10	46	1.48
20508505--20508614	9	11.6	9	68	24	50	38	0	10	50	1.37
20508505--20508607	22	4.7	22	68	24	67	38	0	10	50	1.37
20508489--20508642	31	4.8	31	83	9	159	42	0	10	46	1.43
20508489--20508614	65	2.0	62	90	4	198	40	0	10	48	1.43
20508502--20508638	65	2.1	64	86	8	188	41	0	10	47	1.39
20508473--20508642	34	5.2	31	84	11	182	42	0	11	45	1.44
20509991--20510260	76	3.3	83	76	14	247	32	24	17	25	1.97
20510554--20510606	20	2.6	20	79	8	54	24	1	7	66	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20513541--20513873	114	2.9	113	91	1	551	26	22	20	29	1.99
20521239--20521361	64	1.9	65	94	1	221	51	8	8	30	1.64
20521276--20521587	145	2.2	145	96	1	572	47	8	9	34	1.66
20525070--20525160	45	2.0	45	85	2	121	37	28	6	27	1.82
20525141--20525209	16	4.2	16	96	3	129	37	37	0	24	1.56
20525141--20525209	33	2.1	32	97	2	129	37	37	0	24	1.56
20526718--20526751	14	2.5	13	85	4	50	26	0	2	70	1.01
20527260--20527413	42	3.6	42	86	0	191	16	38	23	22	1.93
20530457--20530517	30	2.0	30	100	0	122	44	39	13	3	1.60
20530464--20530512	15	3.3	15	70	30	50	44	38	14	2	1.56
20538923--20538960	16	2.3	17	82	17	53	78	5	5	10	1.06
20539054--20539518	237	2.0	237	98	0	894	23	16	13	46	1.82
20551869--20551926	26	2.2	26	100	0	116	31	12	32	24	1.91
20552207--20552246	20	2.0	20	90	0	62	27	10	12	50	1.72
20552192--20552258	34	1.9	35	90	3	109	31	8	13	46	1.74
20552186--20552262	14	5.0	15	71	20	52	33	9	14	42	1.77
20553021--20553473	18	25.7	17	67	15	190	46	11	13	29	1.77
20553018--20553400	17	21.9	17	68	17	94	45	11	13	29	1.78
20553154--20553473	35	9.1	35	75	10	260	45	10	13	30	1.78
20553250--20553473	52	4.2	52	76	12	174	45	10	12	32	1.76
20553150--20553474	18	18.4	18	70	14	196	45	10	13	30	1.78
20553722--20553768	19	2.5	20	79	10	53	48	4	14	31	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20555710--20555870	45	3.6	45	80	3	200	30	18	25	25	1.98
20555704--20555899	88	2.2	88	94	0	338	30	17	26	25	1.97
20555710--20555899	45	4.3	45	78	3	197	31	17	25	25	1.97
20556112--20556201	44	2.0	45	86	2	128	31	14	26	27	1.95
20560632--20560827	88	2.2	89	92	0	322	26	26	16	30	1.97
20560632--20560827	45	4.4	43	78	5	203	26	26	16	30	1.97
20562314--20562409	50	1.9	49	89	2	147	11	23	16	47	1.79
20562315--20562420	50	2.1	50	83	0	131	11	25	15	48	1.78
20568584--20568618	11	3.2	11	95	0	61	62	0	0	37	0.95
20568584--20568615	16	2.0	16	93	0	55	65	0	0	34	0.93

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