genome.fa.s13.2.7.7.80.10.50.1000.185.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  185  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)
53947905--53947975	28	2.5	27	80	17	74	52	1	0	46	1.09
53947952--53947992	15	2.5	17	80	11	59	65	0	0	34	0.93
53969610--53969637	2	14.0	2	100	0	56	50	0	0	50	1.00
53970386--53970532	41	3.6	39	78	14	147	26	20	25	27	1.99
53976016--53976082	30	2.2	31	92	5	111	29	20	5	43	1.76
53978933--53979219	70	4.2	67	82	6	321	60	3	7	28	1.38
53978933--53979354	69	6.3	69	75	9	367	59	2	7	29	1.40
53978933--53979351	134	3.2	135	80	11	381	59	2	7	29	1.40
53979247--53979354	57	1.9	57	83	5	139	57	1	8	32	1.39
53983745--53983790	9	5.1	9	91	0	65	34	13	39	13	1.83
53985504--53985528	13	1.9	13	100	0	50	16	8	36	40	1.77
53985868--53986099	96	2.4	96	85	1	277	34	18	13	33	1.90
53985913--53986241	51	6.7	51	73	9	270	35	17	13	34	1.88
53985762--53986237	147	3.3	147	80	5	441	34	17	12	34	1.88
53986074--53986286	96	2.2	95	85	5	295	35	18	14	31	1.90
53992082--53992166	9	9.4	9	93	0	125	43	24	8	23	1.81
53992994--53993049	28	2.0	29	85	3	78	37	8	17	35	1.82
53999471--53999536	32	2.1	32	85	2	89	39	16	6	37	1.74
54003643--54003690	25	1.9	25	95	0	87	37	31	14	16	1.89
54007650--54007716	27	2.5	26	76	9	64	37	0	1	61	1.05
54007684--54007722	16	2.5	16	83	4	53	33	0	2	64	1.08
54009178--54009203	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54009306--54009373	33	2.1	33	88	5	102	26	16	10	47	1.78
54016415--54016491	40	1.9	40	86	5	111	31	15	14	38	1.87
54019466--54019495	15	2.0	15	100	0	60	13	26	13	46	1.80
54022942--54022995	24	2.2	24	83	0	72	48	9	3	38	1.53
54027360--54027411	24	2.2	24	85	0	68	48	9	5	36	1.60
54032008--54032045	20	1.9	20	88	0	58	52	10	2	34	1.50
54039938--54040122	41	4.6	41	67	14	134	36	15	15	32	1.88
54039917--54040154	118	2.0	118	94	0	413	36	16	16	31	1.91
54059070--54059106	11	3.4	11	88	0	56	64	0	5	29	1.15
54072789--54072934	43	3.4	43	82	6	188	27	16	24	31	1.96
54075200--54075304	41	2.5	41	89	4	147	36	0	0	61	1.09
54075222--54075268	17	3.0	17	79	14	57	36	0	0	63	0.94
54075222--54075286	31	2.1	29	83	8	76	33	0	0	66	0.92
54076631--54076681	2	26.0	2	96	4	95	49	0	0	50	1.00
54076861--54076918	23	2.5	23	78	18	66	67	1	5	25	1.21
54076970--54077043	2	37.5	2	97	2	141	50	0	0	50	1.00
54077402--54077481	3	26.7	3	74	14	67	66	1	6	26	1.23
54080868--54080937	25	2.9	24	70	4	59	20	25	17	37	1.94
54081228--54081272	21	2.1	22	91	4	74	37	4	20	37	1.73
54084989--54085138	3	50.0	3	94	0	192	32	7	0	59	1.30
54094175--54094222	24	2.0	24	87	0	69	31	20	29	18	1.97
54095971--54095999	14	2.1	14	100	0	58	27	24	27	20	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54100283--54100457	79	2.2	79	96	0	323	35	15	10	38	1.82
54104288--54104321	17	1.9	17	88	5	50	67	2	0	29	1.05
54111394--54111424	2	15.5	2	100	0	62	48	0	0	51	1.00
54124240--54124272	5	6.4	5	96	3	57	78	0	0	21	0.75
54125410--54125460	26	2.1	25	85	10	70	50	1	1	45	1.24
54129029--54129074	22	2.1	22	84	8	58	47	0	6	45	1.28
54129594--54129618	11	2.3	11	100	0	50	0	0	8	92	0.40
54138983--54139059	35	2.2	35	95	0	136	22	14	16	46	1.83
54142282--54142377	48	2.0	48	93	4	167	25	27	21	26	2.00
54143146--54143193	24	2.0	24	84	8	62	45	27	4	22	1.70
54151389--54151438	25	2.0	25	88	7	75	24	32	18	26	1.97
54152194--54152247	26	2.1	26	100	0	108	25	14	22	37	1.93
54153297--54153349	22	2.4	22	90	0	79	11	22	22	43	1.85
54155332--54155376	11	3.9	11	77	11	54	33	4	4	57	1.38
54157011--54157076	26	2.6	26	78	2	71	22	18	18	40	1.91
54168691--54168724	5	6.8	5	100	0	68	0	20	0	79	0.73
54191446--54191510	30	2.2	30	81	8	80	52	10	6	30	1.61
54192560--54192607	22	2.2	21	82	10	53	35	2	2	60	1.20
54193240--54193288	8	6.1	8	78	7	55	28	2	2	67	1.13
54193649--54193693	23	1.9	24	81	4	56	55	2	6	35	1.38
54194758--54194786	15	1.9	15	100	0	58	48	0	17	34	1.47
54195438--54195475	9	4.2	9	89	0	58	21	0	21	57	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54195588--54196160	127	4.6	125	86	5	742	31	16	22	30	1.96
54197638--54197675	20	1.9	20	84	10	51	55	7	2	34	1.43
54198601--54198700	51	2.0	51	86	4	139	45	2	26	27	1.65
54198660--54198714	11	4.9	11	75	20	60	41	1	30	25	1.66
54198660--54198714	22	2.5	22	83	16	69	41	1	30	25	1.66
54200112--54200170	28	2.2	27	84	6	75	59	18	11	10	1.60
54200174--54200271	47	2.1	47	94	0	169	26	23	19	30	1.98
54200817--54200842	11	2.4	11	100	0	52	61	0	0	38	0.96
54201521--54201575	29	1.9	28	85	10	76	36	1	1	60	1.18
54201849--54201873	13	1.9	13	100	0	50	92	0	8	0	0.40
54220770--54220832	17	3.6	17	78	10	65	50	22	0	26	1.49
54221278--54221336	31	1.9	31	92	0	100	45	11	11	30	1.77
54235075--54235100	2	13.0	2	100	0	52	50	0	0	50	1.00
54238703--54238769	28	2.4	28	76	18	68	46	0	4	49	1.22
54252295--54252333	18	2.2	18	85	0	51	38	7	17	35	1.79
54252653--54252690	9	4.2	9	93	0	67	26	10	23	39	1.87
54254522--54254718	67	2.9	67	94	2	342	17	23	18	40	1.91
54254522--54254728	35	6.1	35	84	6	273	17	22	17	41	1.90
54257529--54257573	20	2.1	23	88	12	69	13	8	8	68	1.38
54260937--54260989	13	4.1	13	75	0	61	35	28	7	28	1.84
54264707--54264748	16	2.7	15	80	16	50	52	19	23	4	1.65
54268463--54268514	26	2.0	27	88	3	79	44	1	25	28	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54281077--54281129	25	2.1	25	85	0	70	35	20	26	16	1.94
54281233--54281295	25	2.6	25	74	2	65	34	19	26	19	1.95
54283667--54283709	18	2.4	16	82	17	50	41	13	0	44	1.44
54290476--54290530	19	2.9	19	78	19	62	65	0	1	32	1.03
54290496--54290545	15	3.2	15	78	15	57	66	0	2	32	1.03
54290502--54290539	17	2.2	18	86	13	53	63	0	2	34	1.09
54294799--54294882	9	10.0	8	71	20	57	59	4	1	34	1.26
54298151--54298192	22	1.9	22	85	0	57	64	14	0	21	1.29
54299565--54299605	14	2.9	15	89	10	61	46	0	0	53	1.00
54299906--54299964	30	2.0	29	83	3	73	55	0	0	44	0.99
54317865--54317986	23	5.3	23	85	0	172	22	20	27	29	1.99
54317867--54317986	46	2.6	46	93	0	195	22	20	27	29	1.99
54320846--54320893	24	2.0	25	83	4	62	60	6	0	33	1.22
54323601--54323651	23	2.3	22	90	6	77	49	0	0	50	1.00
54331738--54331768	15	2.0	16	93	6	55	25	6	16	51	1.68
54333339--54333394	22	2.5	22	85	8	69	60	0	5	33	1.19
54334244--54334287	18	2.5	19	85	10	58	6	25	0	68	1.14
54334361--54334394	17	2.0	17	88	0	50	5	5	17	70	1.28
54337208--54337248	15	2.8	15	82	10	50	43	0	2	53	1.13
54337266--54337449	59	3.1	59	67	22	166	41	1	7	50	1.39
54337265--54337452	61	3.1	61	70	14	199	41	1	6	50	1.39
54337317--54337368	15	3.6	15	80	12	56	44	0	1	53	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54337208--54337484	120	2.3	120	98	0	536	41	1	5	51	1.35
54337446--54337487	15	2.7	16	82	14	52	45	0	2	52	1.13
54337437--54337478	15	2.9	15	82	10	52	47	0	0	52	1.00
54337615--54337719	44	2.5	40	76	15	113	31	30	4	33	1.78
54337613--54337722	45	2.6	44	81	8	131	31	30	5	32	1.80
54337816--54337847	9	3.7	9	95	4	57	34	0	9	56	1.32
54346431--54346473	18	2.2	20	80	12	54	44	2	2	51	1.27
54353107--54353134	3	9.3	3	100	0	56	64	0	0	35	0.94
54354855--54355118	15	17.1	16	63	13	88	27	21	22	28	1.99
54354998--54355117	33	3.7	33	86	6	183	29	18	23	29	1.98

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