genome.fa.s4.2.7.7.80.10.50.1000.195.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  195  of  198  ( 23681 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)
60784981--60785076	27	3.5	27	97	2	183	50	4	3	42	1.37
60785905--60786007	18	5.6	19	73	5	95	48	0	11	38	1.46
60785905--60786003	37	2.7	37	93	0	162	46	1	12	40	1.48
60786240--60786304	26	2.5	26	87	7	87	46	0	12	41	1.41
60790785--60790842	25	2.3	25	80	14	66	74	8	10	6	1.23
60791236--60791270	13	2.6	13	90	4	52	68	0	20	11	1.20
60793432--60793473	3	14.0	3	100	0	84	66	0	0	33	0.92
60803214--60803257	20	2.3	19	88	4	61	22	0	9	68	1.18
60813916--60814004	44	2.0	44	95	0	160	35	21	14	28	1.93
60815508--60815553	20	2.2	22	84	7	60	39	0	8	52	1.33
60818359--60818393	5	7.4	5	93	6	56	40	0	0	60	0.97
60828598--60828626	2	14.5	2	100	0	58	51	0	0	48	1.00
60836090--60836147	30	1.9	30	92	0	98	37	8	10	43	1.70
60837359--60837397	14	2.7	15	84	8	53	23	10	0	66	1.22
60838952--60839024	36	2.0	36	100	0	146	36	2	16	43	1.62
60843720--60843783	32	2.0	32	100	0	128	34	15	15	34	1.90
60845475--60845509	18	2.0	18	88	5	54	48	14	11	25	1.77
60852907--60852960	23	2.5	21	75	6	54	38	11	7	42	1.68
60856333--60856365	15	2.1	16	88	5	50	36	6	6	51	1.51
60856372--60856396	9	2.8	9	100	0	50	32	0	0	68	0.90
60858353--60858410	20	3.0	20	73	17	59	50	10	0	39	1.37
60864713--60864748	12	3.0	12	83	0	54	2	22	30	44	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60866273--60866319	16	3.0	16	73	17	53	38	0	2	59	1.09
60874895--60875118	111	2.0	111	97	0	421	36	12	16	34	1.87
60900832--60900888	28	2.0	28	83	6	71	35	1	15	47	1.56
60902192--60902250	31	1.9	31	82	6	75	32	8	16	42	1.79
60904085--60904144	27	2.2	27	93	0	102	40	13	0	46	1.43
60904296--60904359	18	3.5	18	80	4	83	48	0	10	40	1.38
60904280--60904375	37	2.6	37	98	0	183	50	0	11	38	1.39
60904280--60904375	19	5.2	19	79	5	124	50	0	11	38	1.39
60904551--60904602	26	2.0	26	88	3	79	67	1	0	30	1.02
60904582--60904613	14	2.3	14	100	0	64	87	0	0	12	0.54
60905003--60905040	20	1.9	20	89	10	60	39	5	7	47	1.55
60905308--60905386	27	2.9	27	94	0	131	13	31	21	32	1.93
60909696--60909753	29	2.1	27	87	12	84	39	17	8	34	1.80
60915521--60915554	18	2.0	17	88	11	52	58	0	0	41	0.98
60924341--60924428	31	2.8	31	81	3	97	39	6	2	51	1.41
60933856--60933895	20	2.0	20	100	0	80	35	15	15	35	1.88
60933937--60934011	32	2.5	28	77	14	87	36	1	1	61	1.13
60935050--60935074	12	2.1	12	100	0	50	68	0	0	32	0.90
60937410--60937510	15	6.7	15	71	8	80	26	39	15	17	1.90
60937406--60937668	72	3.6	72	84	3	271	25	37	15	21	1.93
60937766--60937808	21	2.0	21	86	0	59	13	44	18	23	1.86
60937789--60937826	15	2.5	15	91	0	58	10	42	15	31	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60938038--60938080	21	2.0	21	86	0	59	13	44	18	23	1.86
60938061--60938098	15	2.5	15	91	0	58	10	42	15	31	1.81
60944234--60944272	18	2.2	18	86	9	53	25	0	10	64	1.25
60959257--60959286	5	6.0	5	100	0	60	0	60	0	40	0.97
60962842--60962888	20	2.3	20	88	0	67	59	0	0	40	0.97
60962872--60962935	11	6.4	11	77	17	68	59	0	1	39	1.07
60962863--60962945	38	2.2	39	93	2	141	62	0	1	36	1.03
60963773--60963803	15	2.1	15	93	0	53	38	0	3	58	1.15
60964258--60964313	21	2.5	22	80	8	60	53	3	0	42	1.18
60964286--60964329	19	2.2	21	84	8	56	59	0	0	40	0.98
60964268--60964329	21	3.0	20	81	11	63	53	1	0	45	1.10
60967782--60967822	3	13.7	3	94	0	73	34	0	29	36	1.58
60969358--60969389	6	5.5	6	96	3	57	0	12	0	87	0.54
60970964--60971006	13	3.4	13	78	18	54	65	6	2	25	1.30
60971410--60971441	2	16.0	2	100	0	64	50	0	0	50	1.00
60972463--60972524	31	2.0	32	90	3	99	19	4	22	53	1.64
60983798--60983823	12	2.2	12	100	0	52	50	30	0	19	1.48
60987554--60987636	11	7.9	11	70	20	61	38	2	1	57	1.19
60987536--60987621	41	2.1	41	95	0	154	30	2	1	66	1.12
60987595--60987636	21	2.0	22	90	9	52	45	2	0	52	1.13
60987593--60987642	22	2.3	23	82	6	68	46	2	0	52	1.12
60993833--60993874	21	2.0	21	85	0	57	19	4	7	69	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61006203--61006265	31	2.0	31	81	0	72	58	1	7	31	1.36
61009275--61009319	22	2.0	24	83	16	60	53	24	6	15	1.66
61024280--61024332	16	3.4	16	73	5	63	54	3	3	37	1.36
61024274--61024347	31	2.4	31	100	0	148	58	2	2	36	1.27
61024296--61024348	15	3.5	15	74	5	61	60	1	1	35	1.19
61025385--61025438	2	27.0	2	100	0	108	50	0	0	50	1.00
61041183--61041223	13	3.2	13	82	3	57	39	2	0	58	1.11
61050169--61050352	98	1.9	97	85	3	253	22	12	15	49	1.78
61050459--61050516	28	2.0	29	93	3	100	17	8	17	56	1.64
61050838--61050879	8	5.1	8	82	5	57	69	0	0	30	0.89
61050839--61050878	17	2.4	17	86	0	53	67	0	0	32	0.91
61050838--61050885	25	1.9	25	86	0	69	68	2	2	27	1.11
61051149--61051187	21	1.9	20	89	5	60	43	0	0	56	0.99
61051149--61051195	20	2.3	21	85	3	60	40	2	0	57	1.11
61051149--61051193	21	2.1	21	84	8	56	40	2	0	57	1.11
61051291--61051323	13	2.5	14	90	9	52	39	9	15	36	1.79
61051330--61051579	86	2.8	92	77	12	225	32	7	16	43	1.76
61051405--61051579	86	2.1	86	86	6	241	32	6	16	45	1.73
61054725--61054749	9	2.8	9	100	0	50	52	0	0	48	1.00
61055487--61055638	83	1.9	81	86	5	216	22	14	13	49	1.78
61055461--61055822	184	2.0	182	84	9	479	21	14	11	52	1.73
61055667--61055831	82	2.0	80	83	9	199	22	16	10	50	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61064584--61064627	23	2.0	23	86	13	65	56	4	0	38	1.20
61069640--61069697	30	1.9	30	89	0	89	41	3	24	31	1.71
61069909--61069940	13	2.5	13	94	0	55	31	0	12	56	1.37
61070035--61070227	50	3.8	50	90	0	305	25	23	31	20	1.98
61075114--61075245	44	3.0	44	90	0	201	38	15	13	31	1.87
61074954--61075447	247	2.0	248	90	2	780	40	16	15	27	1.88
61075361--61075447	44	2.0	44	95	0	156	40	14	13	31	1.86
61076422--61076463	20	2.0	21	86	13	61	47	0	14	38	1.44
61076526--61076597	31	2.3	32	83	6	87	26	6	11	55	1.60
61076881--61076909	8	3.8	8	95	4	51	55	0	0	44	0.99
61076908--61076938	14	2.1	15	94	5	55	67	0	6	25	1.14
61080610--61080646	17	2.2	17	95	0	65	35	2	16	45	1.61
61080768--61080812	24	1.9	23	90	4	72	35	2	2	60	1.22
61081117--61081148	2	16.5	2	93	6	57	53	0	0	46	1.00
61089806--61089839	16	2.0	18	88	11	54	47	5	5	41	1.52
61098755--61098779	7	3.6	7	100	0	50	44	28	12	16	1.83
61102018--61102057	21	1.9	21	89	0	62	15	7	0	77	0.98
61102010--61102076	32	2.1	32	83	5	82	11	10	4	73	1.24
61114065--61114106	20	2.2	19	86	4	57	66	2	2	28	1.16
61115382--61115438	15	3.5	15	69	17	51	45	3	1	49	1.29
61115460--61115496	16	2.3	17	86	13	60	40	0	0	59	0.97
61115510--61115559	16	3.2	16	70	18	52	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
61121593--61121725	71	1.9	71	82	4	169	31	16	20	31	1.95
61124495--61124870	179	2.1	177	88	4	551	20	16	19	43	1.88
61136574--61136615	18	2.2	20	87	8	61	50	0	0	50	1.00
61136564--61136618	27	2.0	27	82	6	67	49	1	0	49	1.11
61136973--61137064	29	3.1	30	79	7	89	31	8	6	53	1.57
61136993--61137064	30	2.5	28	81	4	81	33	8	5	52	1.55
61145582--61145639	27	2.3	26	82	14	68	34	0	10	55	1.34
61146571--61146606	6	6.0	6	100	0	72	0	16	16	66	1.25
61147188--61147221	2	17.0	2	100	0	68	50	0	0	50	1.00
61149181--61149244	31	2.1	29	82	5	74	46	14	3	35	1.60

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