genome.fa.s13.2.7.7.80.10.50.1000.112.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  112  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)
34006683--34006752	16	4.2	16	75	12	61	20	2	22	54	1.58
34011381--34011425	23	2.0	23	95	0	81	35	8	15	40	1.79
34023256--34023323	27	2.6	25	83	9	73	19	35	2	42	1.66
34023676--34023713	19	2.0	19	94	0	67	28	5	28	36	1.79
34024964--34024994	16	1.9	16	93	0	53	48	12	9	29	1.73
34025990--34026038	24	2.0	24	100	0	98	16	24	8	51	1.71
34026073--34026131	25	2.4	26	86	8	79	62	10	11	15	1.54
34032543--34032588	21	2.2	23	81	14	55	47	10	8	32	1.69
34035835--34035866	15	2.2	15	94	5	57	37	3	6	53	1.42
34039149--34039178	12	2.5	12	100	0	60	33	40	20	6	1.78
34039322--34039392	35	2.0	35	94	0	124	21	18	12	47	1.81
34040544--34040628	42	2.0	43	95	2	154	43	4	27	24	1.74
34041648--34041688	16	2.6	16	81	14	50	58	4	7	29	1.46
34042167--34042344	66	2.7	65	79	2	187	25	24	26	22	2.00
34043617--34043688	36	2.0	35	86	7	101	26	25	13	34	1.93
34045120--34045202	35	2.4	34	80	6	87	25	28	25	20	1.99
34046093--34046125	15	2.3	15	89	5	50	0	30	0	69	0.88
34046193--34046240	3	16.3	3	95	4	89	31	0	0	68	0.90
34048416--34048478	31	2.0	31	96	0	117	46	17	3	33	1.64
34048898--34049035	41	3.4	41	89	0	204	20	22	26	30	1.98
34048892--34049090	41	4.8	40	83	2	191	19	23	28	28	1.98
34049764--34049814	22	2.3	23	80	10	61	11	0	47	41	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34050833--34050908	40	1.9	40	94	0	134	52	14	13	19	1.74
34055474--34055783	43	7.2	43	84	0	404	23	16	31	28	1.96
34055803--34055865	22	2.9	22	95	0	108	41	28	20	9	1.84
34057441--34057849	202	2.0	202	93	1	696	42	3	15	38	1.64
34059960--34060016	29	1.9	30	92	3	98	26	21	19	33	1.97
34066669--34066699	2	15.5	2	93	0	53	0	51	0	48	1.00
34069181--34069256	9	8.4	9	86	5	109	25	9	23	42	1.83
34069181--34069256	27	2.8	27	91	0	134	25	9	23	42	1.83
34084638--34084677	9	4.4	9	84	12	55	17	0	2	80	0.83
34093812--34093862	19	2.7	19	80	19	63	33	0	11	54	1.37
34095899--34095944	25	1.9	23	82	8	56	52	2	4	41	1.33
34100838--34100894	26	2.2	25	75	9	62	17	24	5	52	1.65
34104603--34104628	7	3.7	7	100	0	52	30	42	15	11	1.82
34105307--34105358	24	2.2	24	86	6	70	11	11	13	63	1.52
34107224--34107269	6	7.5	6	82	2	56	45	17	19	17	1.85
34107256--34107355	45	2.2	45	83	3	130	41	17	19	23	1.90
34107555--34107638	40	2.1	40	84	0	105	41	20	7	30	1.79
34108432--34108468	5	7.4	5	93	0	65	56	0	2	40	1.13
34108890--34108921	17	1.9	17	93	6	57	18	34	12	34	1.89
34110150--34110220	34	2.1	34	100	0	142	42	23	2	30	1.69
34114456--34114555	45	2.2	45	89	0	155	45	17	16	22	1.86
34114756--34114842	40	2.2	40	82	0	102	43	17	6	32	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34115629--34115759	5	26.2	5	98	0	253	59	0	0	39	1.03
34117104--34117167	33	1.9	34	84	9	87	28	14	9	48	1.74
34118535--34118589	20	2.7	20	80	2	56	25	29	25	20	1.99
34118544--34118589	21	2.2	20	84	3	56	26	23	26	23	2.00
34119462--34119491	15	1.9	16	93	6	53	40	33	6	20	1.78
34125550--34125582	12	3.0	11	87	12	50	21	0	0	78	0.75
34134758--34134803	24	1.9	24	95	0	83	26	8	23	41	1.83
34137521--34137715	41	4.8	41	82	5	250	19	26	16	37	1.93
34143666--34144179	31	16.7	31	87	2	664	32	8	15	42	1.78
34143666--34144179	61	8.4	61	83	4	606	32	8	15	42	1.78
34143666--34144179	92	5.6	92	88	3	653	32	8	15	42	1.78
34144310--34144417	42	2.6	42	96	0	198	28	14	30	25	1.95
34145927--34146012	30	2.8	31	87	3	113	46	2	18	32	1.62
34152613--34152638	4	6.5	4	100	0	52	53	0	0	46	1.00
34157879--34157925	21	2.2	22	85	11	62	38	6	0	55	1.26
34158140--34158173	2	17.5	2	87	6	52	50	2	0	47	1.16
34163058--34163120	33	1.9	33	96	0	117	41	17	7	33	1.79
34166387--34166438	16	3.2	16	100	0	104	38	36	0	25	1.56
34166949--34166979	15	2.0	16	93	6	55	61	0	0	38	0.96
34167016--34167048	15	2.2	15	94	0	57	57	0	0	42	0.98
34189198--34189265	30	2.3	30	97	0	127	20	29	29	20	1.98
34189204--34189255	13	3.7	13	72	18	50	17	25	34	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34190534--34190654	41	2.9	41	86	1	161	46	18	19	16	1.85
34190514--34190656	21	6.9	21	68	7	76	47	18	17	16	1.83
34192528--34192567	12	3.2	12	89	3	53	10	15	0	75	1.05
34192570--34192613	17	2.6	17	85	7	54	20	2	6	70	1.21
34192998--34193036	17	2.2	18	86	4	53	48	12	2	35	1.55
34194585--34194632	26	1.9	26	83	8	64	25	4	2	68	1.18
34194618--34194694	23	3.3	23	71	12	66	35	1	0	63	1.03
34206431--34206479	2	25.0	2	89	4	73	53	2	0	44	1.12
34213990--34214182	50	3.8	50	88	0	287	20	30	22	26	1.98
34213990--34214182	100	1.9	101	91	1	316	20	30	22	26	1.98
34214520--34214576	30	1.9	29	82	10	71	31	24	3	40	1.72
34220109--34220148	2	20.0	2	100	0	80	50	0	0	50	1.00
34225798--34225839	17	2.4	18	80	4	50	50	7	0	42	1.30
34243351--34243527	39	4.5	39	87	0	237	43	20	5	29	1.75
34255853--34255892	2	20.0	2	100	0	80	50	0	0	50	1.00
34265675--34265722	10	4.8	10	78	0	60	66	2	4	27	1.21
34265675--34265729	20	2.7	19	78	10	56	67	1	5	25	1.22
34272884--34273070	60	3.1	60	85	1	241	14	24	17	44	1.85
34272861--34273080	20	11.0	20	74	5	124	14	24	17	43	1.86
34272862--34273077	60	3.6	60	77	6	213	14	24	18	43	1.86
34274631--34274674	15	2.9	15	96	3	79	36	25	25	13	1.92
34276232--34276273	11	3.6	11	81	12	57	35	0	4	59	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34276298--34276327	15	2.0	15	93	0	51	70	0	26	3	1.03
34289412--34289436	5	5.0	5	100	0	50	20	0	0	80	0.72
34295777--34295805	11	2.6	11	100	0	58	37	0	0	62	0.96
34297084--34297136	22	2.5	20	84	9	61	18	3	3	73	1.14
34297091--34297136	21	2.1	21	84	11	58	19	4	2	73	1.10
34297083--34297152	25	2.7	25	82	8	70	20	4	4	71	1.20
34297176--34297235	19	3.1	20	81	9	63	40	5	3	51	1.40
34309282--34309378	29	3.3	29	71	8	90	32	19	18	28	1.96
34311470--34311506	17	2.2	17	90	0	56	48	27	8	16	1.74
34318289--34318337	3	16.3	3	100	0	98	65	0	0	34	0.93
34318990--34319023	12	2.7	13	86	9	52	76	5	17	0	0.98
34324762--34324791	16	1.9	15	93	6	51	56	3	26	13	1.52
34325166--34325205	20	2.0	20	90	0	62	27	10	12	50	1.72
34325151--34325217	34	1.9	35	90	3	109	31	8	13	46	1.74
34325145--34325221	14	5.0	15	71	20	52	33	9	14	42	1.77
34325902--34325941	20	2.1	19	86	9	55	40	0	7	52	1.30
34326115--34326150	9	4.1	9	85	7	56	44	13	11	30	1.79
34326116--34326151	17	2.1	17	94	0	63	41	13	11	33	1.80
34326363--34326422	30	2.0	31	90	3	95	20	38	0	41	1.52
34327366--34327396	16	1.9	16	93	0	53	41	6	25	25	1.79
34327575--34327717	58	2.5	60	82	7	170	52	3	0	43	1.23
34337277--34337321	14	3.4	14	73	20	51	57	6	0	35	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34337298--34337355	30	1.9	31	86	10	84	56	3	3	36	1.33
34337329--34337376	23	2.1	23	85	11	64	60	4	2	33	1.27
34337297--34337376	24	3.2	24	77	13	81	58	3	2	35	1.29
34337608--34337636	2	14.5	2	100	0	58	51	0	0	48	1.00
34337728--34337757	3	10.0	3	100	0	60	66	0	0	33	0.92
34339337--34339456	44	2.8	42	81	5	141	30	18	18	32	1.95
34339337--34339457	43	2.8	45	82	3	149	30	18	18	33	1.94
34339465--34339671	99	2.1	100	89	0	317	25	22	22	30	1.99
34339874--34340121	44	5.7	44	90	2	360	29	27	17	26	1.97
34342741--34342808	34	2.0	34	100	0	136	20	20	17	41	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