genome.fa.s13.2.7.7.80.10.50.1000.187.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  187  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)
54570058--54570115	26	2.1	28	84	6	75	53	0	3	43	1.17
54572564--54572958	132	3.0	132	92	0	639	26	23	20	29	1.99
54584168--54584281	49	2.3	49	80	4	124	28	21	19	30	1.97
54585423--54585518	30	3.3	28	72	20	72	51	4	4	40	1.41
54586497--54586601	33	3.3	33	68	12	112	22	7	17	52	1.69
54586486--54586607	61	2.0	61	100	0	244	24	8	14	52	1.69
54604487--54604552	25	2.5	26	90	4	98	37	10	1	50	1.47
54604609--54604687	27	2.9	27	87	7	99	27	24	29	18	1.98
54604734--54604886	18	8.4	17	72	15	78	67	0	32	0	0.96
54604736--54604889	10	15.1	10	65	16	57	68	0	31	0	0.95
54604736--54604837	24	4.3	23	71	11	73	66	0	33	0	0.92
54604754--54604915	38	4.3	38	81	9	174	66	0	33	0	0.97
54605603--54605654	19	2.7	19	82	8	61	26	0	7	65	1.20
54605661--54605688	14	2.0	14	100	0	56	78	0	0	21	0.75
54605695--54605764	28	2.6	28	88	8	101	45	10	1	42	1.46
54605842--54605900	31	1.9	31	100	0	118	52	0	13	33	1.41
54607941--54608100	27	5.9	27	92	5	245	16	29	26	27	1.97
54608150--54608218	28	2.5	29	90	6	108	49	1	10	39	1.46
54615189--54615286	28	3.5	28	80	6	117	50	19	13	17	1.78
54621819--54621865	16	2.7	17	78	15	51	44	0	0	55	0.99
54623004--54623042	19	2.2	19	86	9	55	71	17	10	0	1.12
54624154--54624261	3	36.0	3	98	0	207	33	0	0	65	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54624558--54624607	4	12.5	4	100	0	100	50	24	0	26	1.50
54625395--54625430	11	3.4	10	85	14	54	11	8	0	80	0.90
54642663--54642688	6	4.3	6	100	0	52	15	0	0	84	0.62
54647512--54647596	29	2.9	29	72	6	73	49	7	7	36	1.57
54649626--54649691	3	22.0	3	84	0	87	59	4	1	34	1.27
54650702--54650753	12	4.1	13	78	11	63	59	1	0	38	1.08
54658121--54658160	7	5.7	7	90	0	62	77	0	0	22	0.77
54658120--54658161	13	3.2	13	86	6	57	76	0	0	23	0.79
54658422--54658554	9	13.9	9	67	18	65	62	1	5	30	1.26
54658423--54658492	29	2.5	29	81	9	83	62	0	1	35	1.04
54659856--54659894	12	3.2	12	85	7	53	0	25	0	74	0.82
54660161--54660216	18	3.1	18	82	10	53	0	28	0	71	0.86
54660179--54660211	11	2.9	11	95	4	57	0	27	0	72	0.85
54660319--54660377	31	1.9	30	83	10	75	11	18	3	66	1.38
54660586--54660739	30	5.2	30	82	3	168	42	2	18	36	1.65
54660600--54660745	29	5.0	29	83	2	166	44	2	19	33	1.65
54660600--54660748	59	2.5	59	88	0	217	44	2	18	34	1.64
54660862--54661177	79	4.1	79	74	11	271	35	19	16	28	1.94
54660871--54661175	151	2.0	151	85	6	407	36	20	17	26	1.94
54660868--54661176	74	4.0	74	76	13	245	35	20	16	27	1.94
54660871--54661198	78	4.3	78	75	13	288	37	19	16	26	1.93
54662057--54662112	11	5.3	11	82	18	50	0	7	8	83	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54662057--54662120	12	5.6	11	74	18	51	0	6	9	84	0.78
54662063--54662124	18	3.4	19	78	14	69	0	6	11	82	0.84
54662063--54662132	20	3.8	19	75	22	69	1	5	10	82	0.88
54669632--54670100	18	26.3	18	71	11	277	42	9	15	32	1.79
54669635--54670031	53	7.5	53	71	15	162	43	10	15	30	1.80
54669632--54670118	35	13.6	35	72	12	273	42	9	14	32	1.79
54669986--54670110	56	2.2	57	79	9	132	40	8	15	35	1.78
54670115--54670141	10	2.7	10	100	0	54	14	0	7	77	0.97
54670247--54670303	5	11.2	5	88	3	87	61	0	0	38	0.96
54670326--54670408	29	2.9	28	84	7	121	45	2	18	33	1.62
54670326--54670423	29	3.4	28	81	4	115	47	2	15	34	1.57
54675615--54675676	4	15.5	4	100	0	124	50	24	0	25	1.50
54676436--54676460	3	8.3	3	100	0	50	32	0	0	68	0.90
54679750--54679786	18	1.9	18	89	10	56	45	2	10	40	1.53
54680716--54680744	13	2.3	13	94	5	51	0	17	3	79	0.87
54681312--54681338	8	3.4	8	100	0	54	74	0	0	25	0.83
54682535--54682588	20	2.7	20	94	0	90	62	0	24	12	1.30
54683757--54683806	24	2.1	24	81	3	57	24	16	14	46	1.83
54692098--54692206	55	2.0	55	90	0	173	23	6	26	43	1.78
54697314--54697346	3	11.0	3	93	0	57	30	0	36	33	1.58
54698415--54698475	31	2.0	31	87	6	88	24	21	21	32	1.98
54701420--54701483	3	21.7	3	96	3	121	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54708107--54708136	2	15.0	2	100	0	60	50	0	0	50	1.00
54708612--54708669	30	1.9	30	82	10	73	25	12	15	46	1.80
54711696--54711735	2	20.0	2	90	10	64	47	2	0	50	1.14
54714232--54714290	30	1.9	31	89	3	93	42	10	11	35	1.76
54718837--54718870	17	2.0	17	88	0	50	29	11	2	55	1.50
54723781--54723822	16	2.6	16	84	0	57	28	21	11	38	1.89
54725837--54725877	18	2.1	20	86	13	59	63	2	4	29	1.28
54728510--54728644	37	3.4	40	72	7	123	33	24	17	25	1.96
54728510--54728645	41	3.4	41	73	12	131	33	24	16	25	1.96
54728764--54728830	21	3.2	21	74	16	59	49	13	0	37	1.42
54728801--54728847	24	2.0	24	84	16	62	51	17	0	31	1.46
54729167--54729202	18	1.9	19	88	5	56	33	27	0	38	1.57
54730463--54730524	11	5.6	11	69	7	54	20	17	9	51	1.73
54730463--54730523	22	2.7	23	75	7	63	21	18	8	52	1.71
54730760--54730790	7	4.4	7	100	0	62	0	12	0	87	0.55
54731700--54731751	25	2.1	24	82	3	59	13	15	1	69	1.28
54734643--54734684	16	2.7	15	89	10	59	69	7	2	21	1.25
54735525--54735558	17	2.0	17	88	0	50	5	5	5	82	0.95
54739503--54739530	9	3.1	9	100	0	56	25	0	10	64	1.26
54742590--54742646	27	2.1	28	83	9	73	24	8	5	61	1.46
54748961--54749035	23	3.5	22	69	22	70	33	5	18	42	1.73
54748947--54749065	40	3.0	40	96	0	211	31	5	17	45	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54748984--54749052	17	3.7	17	70	20	57	30	2	18	47	1.63
54751078--54751164	33	2.6	33	96	0	165	31	24	24	20	1.98
54758673--54758829	63	2.5	63	97	0	296	42	15	20	21	1.89
54763590--54763624	16	2.2	16	89	0	52	48	20	2	28	1.63
54766668--54766740	31	2.4	29	78	12	85	27	13	4	54	1.57
54767517--54767541	12	2.1	12	100	0	50	60	0	8	32	1.26
54769623--54769659	13	2.8	13	91	0	65	45	24	0	29	1.53
54776848--54776872	7	3.6	7	100	0	50	52	16	16	16	1.76
54781699--54781864	43	3.9	43	83	7	203	18	18	29	33	1.95
54786314--54786379	19	3.4	20	76	14	50	36	1	1	60	1.15
54786334--54786378	20	2.3	19	88	7	63	37	0	2	60	1.09
54786313--54786379	21	3.5	19	73	15	57	37	1	1	59	1.16
54786388--54786442	26	2.0	28	89	6	87	36	0	5	58	1.21
54787384--54787428	8	5.6	8	84	10	65	55	0	2	42	1.12
54787384--54787430	25	1.9	24	91	4	76	55	0	2	42	1.12
54788200--54788246	24	2.0	24	84	16	62	31	0	17	51	1.46
54788405--54788543	40	3.5	40	72	13	128	28	17	24	29	1.98
54791058--54791089	16	2.1	16	88	11	50	15	21	0	62	1.32
54802229--54802280	26	2.0	26	92	0	86	61	1	0	36	1.07
54805244--54805308	30	2.1	32	83	8	82	38	6	16	38	1.74
54808618--54808680	31	2.0	31	93	0	108	39	6	14	39	1.71
54810779--54810824	16	3.0	16	71	9	51	58	6	0	34	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54811332--54811416	22	3.8	22	71	3	62	65	11	7	15	1.44
54812851--54812909	30	2.0	29	83	6	75	37	1	3	57	1.25
54813394--54813429	7	5.3	7	86	6	56	61	0	0	38	0.96
54813402--54813441	20	2.1	20	86	9	57	65	0	0	35	0.93
54827543--54827590	22	2.1	23	85	11	64	33	0	0	66	0.92
54827556--54827644	28	3.2	28	83	7	94	35	0	0	64	0.94
54827591--54827654	11	6.4	11	77	22	70	39	1	0	59	1.07
54827584--54827662	37	2.1	38	95	2	142	36	1	0	62	1.04
54827563--54827664	37	2.7	36	86	8	141	36	0	0	62	1.02
54827637--54827675	20	2.0	20	89	0	60	38	2	0	58	1.12

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