genome.fa.s1.2.7.7.80.10.50.1000.110.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  110  of  187  ( 22383 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)
32777913--32778132	117	1.9	116	85	0	305	39	20	15	25	1.91
32801591--32801622	15	2.2	14	94	5	55	56	0	3	40	1.15
32802701--32802747	21	2.2	22	96	3	87	42	14	0	42	1.46
32808719--32808813	29	3.3	29	73	7	86	22	14	24	38	1.91
32813767--32813804	19	2.0	19	90	10	60	34	26	5	34	1.79
32815957--32816210	121	2.1	121	96	0	472	44	7	9	38	1.64
32819310--32819345	3	12.0	3	100	0	72	33	0	0	66	0.92
32820633--32820667	10	3.2	11	88	12	54	17	37	0	45	1.48
32820648--32820758	51	2.2	51	95	1	197	29	26	0	44	1.55
32821902--32821926	7	3.6	7	100	0	50	28	0	12	60	1.32
32822578--32822612	18	1.9	18	94	0	61	25	31	8	34	1.86
32823089--32823241	22	7.0	22	90	0	225	26	26	14	32	1.94
32823624--32824032	23	17.3	23	80	15	446	45	24	1	28	1.61
32823616--32823687	29	2.5	29	100	0	144	44	33	0	22	1.53
32823653--32824061	45	8.8	46	79	14	409	45	24	1	28	1.61
32823695--32824008	118	2.7	118	94	1	558	46	23	1	28	1.60
32824019--32824062	23	2.0	21	91	8	70	43	29	0	27	1.55
32823624--32824008	118	3.3	116	89	6	530	45	24	1	28	1.60
32824064--32824275	111	1.9	111	94	0	370	40	9	7	42	1.67
32827122--32827473	126	2.8	126	87	5	518	33	21	15	30	1.94
32827978--32828013	12	3.0	12	91	0	63	44	33	16	5	1.71
32827978--32828013	18	2.0	18	88	0	54	44	33	16	5	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32835126--32835201	32	2.4	32	84	0	89	25	23	5	46	1.73
32839621--32839696	32	2.4	32	84	0	89	25	23	5	46	1.73
32846838--32846904	33	2.0	33	100	0	134	23	20	17	37	1.94
32849481--32849559	39	2.0	39	81	13	92	26	31	10	31	1.89
32860262--32860353	41	2.2	41	80	0	112	21	23	38	16	1.93
32866542--32866584	20	2.2	20	91	8	70	0	25	2	72	0.97
32875458--32875549	48	1.9	48	93	0	157	41	19	17	21	1.90
32875774--32875827	17	2.9	19	71	20	60	46	14	12	25	1.81
32875757--32875827	36	2.0	36	94	0	124	46	14	12	26	1.80
32875756--32875819	17	3.6	17	72	15	58	46	12	12	28	1.78
32880866--32880929	17	3.6	17	74	15	67	46	14	12	26	1.79
32880884--32880937	17	2.9	19	71	20	60	46	16	12	24	1.82
32880867--32880937	36	2.0	36	97	0	133	46	15	12	25	1.81
32893087--32893154	35	1.9	35	96	0	127	44	16	23	16	1.86
32905024--32905048	13	1.9	13	100	0	50	60	0	0	40	0.97
32908864--32908981	37	3.2	37	85	2	166	22	13	25	38	1.91
32913539--32913565	13	2.1	13	100	0	54	25	22	14	37	1.93
32914194--32914275	28	2.9	28	71	10	69	42	1	0	56	1.07
32914463--32914515	16	3.3	16	97	0	97	22	35	3	37	1.72
32926920--32926963	23	2.0	23	86	13	65	50	13	11	25	1.75
32927975--32928034	29	2.1	28	81	9	68	26	18	3	51	1.61
32929010--32929047	20	1.9	20	88	0	58	39	23	23	13	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32929794--32929835	19	2.2	20	83	12	52	42	21	2	33	1.66
32932572--32932915	171	2.0	171	97	0	643	34	18	15	31	1.92
32934907--32934959	14	3.8	14	77	7	54	33	30	1	33	1.69
32935606--32935659	24	2.2	24	83	6	65	59	11	7	22	1.56
32939263--32939337	26	2.9	26	91	0	114	18	22	22	36	1.95
32939440--32939531	28	2.9	33	76	15	104	22	22	25	29	1.99
32939476--32939544	33	2.1	34	83	2	86	23	21	24	30	1.99
32947911--32948017	26	4.1	26	77	0	106	22	22	19	35	1.96
32961738--32961796	31	1.9	31	93	6	102	30	28	0	40	1.57
32978816--32978995	94	1.9	94	90	0	288	33	16	17	32	1.92
32987525--32987563	7	5.6	7	81	0	51	15	0	35	48	1.45
32987730--32987914	7	26.6	7	72	3	131	18	1	32	47	1.59
32987763--32987881	62	1.9	62	86	3	168	18	2	30	48	1.61
32988949--32988995	18	2.6	18	93	6	78	23	38	12	25	1.90
32989140--32989178	20	2.0	20	90	10	62	15	23	5	56	1.59
32993337--32993660	161	2.0	159	94	1	567	32	5	32	29	1.81
32995238--32995302	34	1.9	34	84	6	87	35	18	18	27	1.94
32995315--32995404	43	2.1	43	83	4	110	30	18	21	30	1.97
33004500--33004755	56	4.8	51	88	6	309	22	29	23	24	1.99
33008414--33008448	17	2.1	17	94	0	61	37	22	17	22	1.94
33012079--33012368	50	5.7	50	80	3	269	21	26	23	28	1.99
33025458--33025633	33	5.3	33	72	6	142	30	18	26	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33025419--33025663	133	1.8	133	85	3	350	31	17	25	25	1.97
33040978--33041100	57	2.1	57	85	4	167	47	4	17	29	1.68
33045398--33045435	20	2.0	19	85	10	51	34	10	15	39	1.82
33058784--33058810	14	1.9	14	100	0	54	37	22	25	14	1.93
33064980--33065033	27	2.0	27	85	0	72	70	0	7	22	1.12
33064998--33065054	17	3.3	17	82	2	60	75	1	3	19	1.04
33067407--33067470	32	1.9	34	81	6	78	37	4	10	46	1.60
33071912--33071959	25	1.9	25	86	0	69	35	8	4	52	1.51
33075018--33075049	2	16.0	2	100	0	64	50	0	0	50	1.00
33075044--33075114	26	3.0	24	77	16	76	60	1	14	23	1.42
33075880--33075928	19	2.5	21	71	15	52	26	0	10	63	1.26
33078532--33078562	2	15.0	2	93	6	53	48	3	0	48	1.17
33084874--33084937	26	2.5	26	87	5	85	21	26	23	28	1.99
33095703--33095741	20	2.0	20	90	10	62	15	23	5	56	1.59
33097480--33097704	51	4.4	50	82	6	249	29	26	14	29	1.95
33099520--33099545	5	5.2	5	100	0	52	38	19	19	23	1.93
33099494--33099545	26	2.0	26	81	7	61	34	15	26	23	1.94
33100186--33100245	30	2.0	31	83	3	77	41	0	38	20	1.52
33100547--33100577	9	3.4	9	90	0	53	38	22	12	25	1.90
33103646--33103716	26	2.7	26	82	4	81	19	16	25	38	1.93
33103862--33103982	28	4.3	28	76	5	93	28	20	21	29	1.98
33103862--33103961	28	3.5	28	80	1	101	26	21	22	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33105849--33105894	23	2.0	24	82	4	58	43	2	30	23	1.66
33111320--33111346	12	2.2	12	100	0	54	48	0	18	33	1.49
33114668--33114849	92	1.9	91	84	10	242	28	26	24	21	1.99
33114799--33114991	106	1.8	106	88	2	298	29	18	25	26	1.98
33114957--33115120	74	2.2	73	93	1	274	25	22	25	27	2.00
33115121--33115209	13	7.2	13	80	14	98	25	3	5	65	1.31
33115130--33115217	9	10.0	9	74	10	76	27	2	4	65	1.23
33115130--33115217	26	3.3	26	82	7	124	27	2	4	65	1.23
33115121--33115217	52	1.9	52	89	10	157	26	3	5	64	1.29
33115116--33115169	21	2.6	21	82	5	65	27	1	3	66	1.19
33115565--33115598	14	2.3	15	95	5	61	38	0	26	35	1.57
33119964--33120099	43	3.2	43	78	2	130	25	18	29	27	1.98
33120763--33120808	19	2.4	20	78	10	60	45	2	2	50	1.26
33121819--33121867	23	2.1	23	85	7	64	48	12	0	38	1.41
33122166--33122219	24	2.2	24	87	6	83	33	0	0	66	0.92
33122169--33122212	16	2.8	16	79	3	54	29	0	0	70	0.88
33122199--33122246	19	2.6	18	78	21	55	33	0	2	64	1.05
33122199--33122252	18	2.9	18	75	5	54	31	0	1	66	1.02
33123891--33124077	30	6.3	30	73	7	114	40	15	24	19	1.91
33123858--33124045	60	3.2	59	71	10	168	39	15	25	19	1.91
33125151--33125180	12	2.5	12	94	0	51	23	40	30	6	1.80
33131537--33131611	29	2.6	29	84	2	105	42	12	28	17	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33131584--33131699	30	3.8	30	75	3	90	35	13	22	28	1.92
33139756--33139786	7	4.4	7	100	0	62	29	12	25	32	1.93
33142266--33142318	25	2.1	26	85	3	72	35	22	9	32	1.86
33146405--33146447	18	2.3	19	88	4	61	25	23	0	51	1.49
33146422--33146507	43	2.0	43	88	0	127	23	22	2	52	1.59
33146901--33146951	25	2.0	27	84	7	70	47	13	0	39	1.43
33150231--33150281	16	2.9	18	75	21	54	78	0	15	5	0.93
33150232--33150296	6	10.7	6	72	21	55	78	1	15	4	0.99
33150257--33150312	18	3.3	17	73	16	62	73	1	16	8	1.17
33150689--33150719	9	3.6	9	95	4	55	29	0	0	70	0.87

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