genome.fa.s4.2.7.7.80.10.50.1000.192.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  192  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)
59567917--59568121	86	2.6	78	83	9	220	24	18	32	24	1.97
59567983--59568121	43	3.2	43	94	0	251	23	17	33	25	1.97
59572900--59572945	21	2.2	20	81	11	58	65	2	0	32	1.05
59572901--59572953	19	2.6	21	85	11	67	62	1	0	35	1.06
59572918--59572973	27	2.0	28	83	10	71	58	0	1	39	1.08
59572927--59572984	29	2.0	30	86	10	84	56	1	1	39	1.19
59572935--59572996	30	2.1	30	81	6	72	59	1	1	37	1.17
59573383--59573492	10	11.0	10	68	19	52	34	8	0	57	1.29
59573403--59573448	21	2.1	22	84	4	58	32	10	0	56	1.34
59573384--59573474	30	3.1	30	77	13	91	34	7	0	58	1.27
59573383--59573494	20	5.5	21	71	18	78	34	8	0	57	1.28
59573487--59573562	28	2.8	26	72	18	66	34	3	1	60	1.23
59581063--59581123	26	2.3	26	88	5	88	40	22	22	13	1.89
59582529--59582570	2	21.0	2	90	0	66	52	0	2	45	1.13
59583161--59583346	41	4.5	41	91	1	284	29	17	27	25	1.98
59583827--59583916	45	2.0	45	100	0	180	28	8	15	46	1.76
59590105--59590158	2	27.5	2	92	3	92	51	0	0	48	1.00
59600245--59600712	124	3.8	124	75	8	432	38	20	13	27	1.90
59600252--59600715	248	1.9	248	82	0	588	37	21	13	27	1.91
59600626--59600852	120	1.9	122	82	11	292	39	18	11	30	1.86
59605917--59605962	16	2.8	17	96	3	85	43	0	21	34	1.53
59606991--59607519	216	2.4	214	85	3	682	29	13	14	42	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59616890--59616925	14	2.6	14	100	0	72	30	0	33	36	1.58
59627169--59627205	15	2.4	16	86	8	51	45	0	5	48	1.25
59629402--59629445	17	2.5	18	82	14	56	65	0	0	34	0.93
59629400--59629452	17	3.1	16	76	13	52	66	1	0	32	1.03
59629818--59630088	58	4.8	54	83	6	301	10	10	22	56	1.63
59634196--59634234	5	8.6	5	78	21	50	58	0	0	41	0.98
59634192--59634234	17	2.5	17	81	11	52	60	0	0	39	0.97
59634197--59634234	14	2.9	13	92	7	60	57	0	0	42	0.98
59636160--59636252	43	2.2	42	82	7	116	30	20	12	36	1.90
59636205--59636313	36	3.0	36	89	0	173	31	19	11	38	1.86
59640845--59641151	151	2.0	151	94	0	533	34	13	21	30	1.92
59643786--59644422	218	2.9	215	90	1	968	39	21	14	24	1.90
59650210--59650244	15	2.2	16	90	5	54	65	11	5	17	1.43
59650430--59650459	3	10.0	3	100	0	60	66	0	33	0	0.92
59652833--59652861	2	14.5	2	100	0	58	48	0	0	51	1.00
59659492--59659524	16	2.0	17	88	5	50	39	0	0	60	0.97
59662173--59662547	204	1.8	206	83	6	501	45	15	12	26	1.81
59662376--59662746	197	1.9	198	82	6	466	45	15	11	27	1.81
59666109--59666153	23	1.9	24	90	4	74	53	0	2	44	1.13
59684232--59684279	23	2.1	23	100	0	96	39	8	12	39	1.73
59693670--59693710	16	2.7	15	85	7	55	48	12	7	31	1.68
59693677--59693712	16	2.2	16	95	0	63	50	11	8	30	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59698786--59698835	23	2.2	23	85	3	66	52	6	6	36	1.51
59698786--59698830	22	2.1	22	84	12	58	53	4	6	35	1.47
59700985--59701011	9	3.0	9	100	0	54	66	0	0	33	0.92
59704037--59704102	31	2.2	29	82	12	80	53	13	1	31	1.49
59705154--59705186	15	2.1	17	88	11	52	18	15	12	54	1.71
59710211--59710241	3	10.3	3	100	0	62	67	0	0	32	0.91
59710787--59710867	41	2.0	41	97	0	153	49	13	6	30	1.67
59714649--59714729	41	2.0	41	92	0	135	48	14	6	30	1.69
59714767--59714807	19	2.2	19	95	0	73	46	12	4	36	1.63
59717184--59717224	20	2.0	20	86	9	57	73	4	7	14	1.22
59720179--59720213	14	2.5	14	90	0	52	20	5	11	62	1.48
59723849--59723879	14	2.2	14	94	0	53	58	6	6	29	1.48
59737693--59737722	11	2.6	11	94	5	51	36	3	0	60	1.14
59739979--59740044	26	2.6	25	81	11	71	40	1	4	53	1.31
59740760--59740808	25	2.0	25	95	0	89	6	30	22	40	1.78
59746167--59746202	2	18.0	2	100	0	72	50	0	0	50	1.00
59746627--59746666	21	1.9	21	85	10	55	42	27	7	22	1.80
59748295--59748342	24	2.0	24	87	0	69	43	6	4	45	1.48
59748305--59748350	24	1.9	24	91	8	76	43	6	2	47	1.41
59757302--59757499	98	2.0	98	100	0	396	37	9	13	39	1.77
59770324--59770360	4	9.2	4	93	0	65	45	27	2	24	1.66
59770830--59770856	7	3.9	7	100	0	54	59	0	0	40	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59783533--59783576	2	22.0	2	100	0	88	50	0	0	50	1.00
59802424--59802871	232	1.9	232	94	0	781	38	20	13	27	1.90
59808291--59808346	23	2.5	22	76	15	62	46	0	1	51	1.11
59810629--59810676	24	2.0	24	88	4	71	33	0	2	64	1.05
59810635--59810685	23	2.2	24	82	3	59	39	0	1	58	1.09
59813145--59813170	3	8.7	3	100	0	52	30	0	0	69	0.89
59813691--59813729	7	5.6	7	90	0	60	28	0	30	41	1.57
59814003--59814029	2	13.5	2	100	0	54	51	0	0	48	1.00
59822270--59822405	41	3.4	41	78	10	158	33	25	16	24	1.96
59822569--59822614	24	2.0	23	83	12	58	50	15	2	32	1.56
59823368--59823458	35	2.6	34	77	16	87	42	5	2	49	1.38
59844475--59844535	3	21.0	3	77	12	65	34	0	3	62	1.12
59844677--59844719	21	2.0	21	86	8	61	76	9	4	9	1.14
59844849--59844889	21	2.0	20	86	13	57	36	0	17	46	1.48
59844910--59844967	29	2.0	29	80	12	66	31	1	25	41	1.66
59845585--59845693	38	2.8	39	81	6	123	22	19	26	32	1.97
59845585--59845717	38	3.5	37	79	9	108	22	19	27	30	1.98
59845978--59846004	8	3.4	8	100	0	54	40	0	11	48	1.39
59846854--59846920	34	2.1	33	83	8	84	47	16	11	23	1.80
59846864--59846931	34	2.0	34	85	0	91	44	19	11	25	1.84
59851631--59851752	23	5.3	23	96	0	226	30	28	21	19	1.98
59851978--59852016	18	2.2	17	86	13	53	46	20	0	33	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59856410--59856456	22	2.2	21	84	3	58	65	4	4	25	1.29
59862723--59862799	32	2.4	33	93	6	133	58	2	2	36	1.26
59865270--59865316	22	2.1	22	84	0	58	36	4	21	38	1.73
59865222--59865355	53	2.5	51	81	9	144	38	3	20	37	1.71
59870450--59870623	95	1.8	96	86	2	251	40	14	15	29	1.87
59873564--59873618	28	2.0	27	85	3	74	20	18	10	50	1.76
59874562--59874595	18	1.9	18	88	5	52	70	2	0	26	1.01
59885987--59886232	134	1.8	133	87	0	366	40	20	8	30	1.83
59897019--59897062	23	1.9	23	85	0	61	22	31	15	29	1.95
59897018--59897069	23	2.2	23	79	3	59	23	30	13	32	1.93
59898717--59898793	25	3.1	24	81	9	75	40	20	20	18	1.92
59906065--59906140	32	2.4	32	84	0	98	50	11	17	21	1.77
59909815--59909884	34	2.1	34	100	0	140	35	8	8	47	1.65
59915975--59916084	13	8.5	13	70	20	54	64	0	2	32	1.08
59915986--59916055	10	6.8	11	73	23	64	64	0	1	34	1.03
59915989--59916073	9	9.0	9	73	16	66	68	0	1	30	0.97
59915988--59916084	50	1.9	50	100	0	194	64	0	2	32	1.05
59915955--59916045	40	2.2	40	90	5	146	65	0	2	31	1.04
59916367--59916419	8	6.8	8	76	23	51	58	0	1	39	1.09
59916336--59916438	31	3.3	31	85	12	133	58	0	2	38	1.13
59916425--59916459	17	2.2	16	90	10	54	48	0	11	40	1.39
59916820--59916859	18	2.3	18	86	4	55	55	2	2	40	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59926879--59926937	20	3.1	20	69	30	65	67	5	1	25	1.20
59926880--59926937	19	3.1	18	72	22	57	67	5	1	25	1.21
59927723--59927765	22	2.0	22	86	9	61	37	0	2	60	1.10
59927723--59927768	23	2.0	22	84	12	58	36	0	2	60	1.09
59927707--59927808	29	3.5	29	75	18	97	43	0	0	54	1.13
59930275--59930326	18	2.9	18	69	11	52	63	5	0	30	1.18
59930275--59930354	36	2.2	36	82	4	90	60	6	3	30	1.39
59937456--59937519	29	2.2	29	94	0	119	40	9	3	46	1.52
59939598--59939922	164	2.0	164	91	0	524	27	11	20	40	1.87
59946333--59946440	47	2.3	46	84	9	137	41	11	9	37	1.73

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