genome.fa.s4.2.7.7.80.10.50.1000.128.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  128  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)
40864151--40864244	44	2.1	44	88	0	134	22	31	9	36	1.86
40865879--40865959	35	2.3	35	95	0	144	33	4	3	58	1.37
40865978--40866033	16	3.3	17	80	9	78	37	16	3	42	1.65
40865983--40866055	34	2.3	33	86	11	100	41	16	2	39	1.63
40866083--40866120	19	2.0	19	94	0	67	44	0	0	55	0.99
40866125--40866325	24	9.3	22	65	23	65	48	18	1	31	1.59
40866142--40866251	31	3.4	31	77	10	89	45	18	2	33	1.63
40866256--40866310	12	4.8	12	88	4	78	52	16	1	29	1.54
40866249--40866317	24	3.0	24	87	8	92	53	17	1	27	1.52
40866267--40866326	12	5.7	10	90	5	68	55	16	0	28	1.42
40866267--40866411	34	4.2	34	67	16	91	53	17	0	28	1.49
40866285--40866378	9	10.4	9	75	11	52	58	13	1	26	1.43
40866301--40866707	95	4.5	95	87	9	595	51	18	2	27	1.59
40866363--40866525	52	3.3	52	67	15	164	47	20	2	28	1.63
40866285--40866707	181	2.4	178	81	7	572	51	18	2	27	1.58
40866576--40866705	37	3.3	37	70	21	109	53	15	3	28	1.57
40866642--40866669	12	2.3	12	100	0	56	53	14	0	32	1.41
40870584--40870652	21	3.3	21	87	0	93	36	20	40	2	1.67
40871091--40871231	42	3.3	42	81	7	144	28	24	20	26	1.99
40871343--40871385	16	2.7	16	88	0	59	25	25	2	46	1.65
40875852--40875882	13	2.4	13	94	0	53	51	0	0	48	1.00
40876999--40877059	19	3.1	19	77	13	61	40	9	11	37	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40878052--40878131	21	3.3	23	79	14	74	37	1	7	53	1.37
40879601--40879658	30	1.9	30	89	0	89	41	3	24	31	1.71
40879870--40879901	13	2.5	13	94	0	55	31	0	12	56	1.37
40879996--40880244	50	4.8	50	86	3	318	26	22	28	22	1.99
40889286--40889325	2	20.0	2	100	0	80	50	0	0	50	1.00
40898106--40898130	6	4.2	6	100	0	50	0	16	0	84	0.63
40900588--40900621	14	2.6	13	90	9	52	52	0	0	47	1.00
40900589--40900628	20	2.0	20	90	0	62	55	0	0	45	0.99
40900606--40900710	45	2.5	44	79	15	116	51	1	1	44	1.23
40900749--40900790	20	2.1	20	91	8	68	38	2	0	59	1.10
40912280--40912313	17	1.9	17	94	5	59	47	0	0	52	1.00
40912312--40912350	16	2.4	16	86	0	51	46	2	10	41	1.51
40912424--40912466	9	5.0	9	88	11	72	32	0	11	55	1.36
40912421--40912466	16	2.8	16	86	6	65	34	0	10	54	1.36
40912424--40912472	25	2.0	25	95	0	89	32	2	10	55	1.45
40912421--40912458	16	2.4	16	95	0	67	34	0	10	55	1.34
40916044--40916071	14	2.0	14	100	0	56	7	28	0	64	1.20
40916024--40916068	19	2.5	18	83	16	58	6	26	0	66	1.16
40916132--40916173	6	7.2	6	91	5	59	2	11	19	66	1.34
40918987--40919027	15	2.8	15	82	10	50	43	0	2	53	1.13
40919096--40919147	15	3.6	15	80	12	56	44	0	1	53	1.11
40918987--40919381	120	3.3	120	97	0	745	41	1	6	50	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40919216--40919387	15	11.5	15	69	20	60	43	1	4	51	1.28
40919347--40919387	16	2.6	16	88	7	57	46	0	0	53	1.00
40919515--40919619	44	2.5	40	76	15	113	31	29	4	34	1.78
40919513--40919622	45	2.6	44	81	8	131	31	29	5	33	1.80
40919601--40919638	16	2.4	16	90	0	58	34	34	0	31	1.58
40919751--40919794	21	2.0	21	82	8	52	50	0	0	50	1.00
40920207--40920285	23	3.4	23	68	21	67	46	6	3	43	1.47
40921281--40921312	2	16.0	2	100	0	64	50	0	0	50	1.00
40922752--40922821	31	2.1	33	84	10	90	20	31	15	32	1.94
40927492--40927562	25	2.9	25	82	2	81	32	18	29	19	1.96
40931362--40931448	44	2.0	45	95	2	158	29	11	10	48	1.73
40933490--40933523	11	3.1	11	87	12	52	64	5	8	20	1.43
40938252--40938277	4	6.5	4	100	0	52	76	0	0	23	0.78
40939026--40939365	44	7.8	44	72	12	116	27	25	19	27	1.98
40939125--40939451	44	7.5	43	77	5	228	29	23	18	28	1.97
40940177--40940225	25	2.0	25	84	8	64	22	26	4	46	1.69
40940204--40940294	44	2.1	44	93	0	155	30	13	12	43	1.80
40942573--40942605	17	1.9	17	100	0	66	42	9	0	48	1.35
40943112--40943197	28	2.9	29	70	19	79	20	15	10	53	1.71
40945053--40945079	14	1.9	14	100	0	54	44	0	18	37	1.50
40946443--40946470	14	2.0	14	100	0	56	57	14	7	21	1.61
40946759--40946861	3	33.7	3	96	3	188	66	0	0	32	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40952882--40952925	9	5.1	9	89	10	74	56	11	0	31	1.35
40952891--40952928	16	2.4	16	95	0	67	55	10	0	34	1.34
40957337--40957401	32	2.1	31	82	8	78	64	0	7	27	1.20
40958786--40958838	20	2.7	20	82	5	54	33	1	0	64	1.05
40958886--40959060	89	2.0	89	85	4	237	35	7	19	37	1.80
40958891--40959084	89	2.2	87	78	10	194	36	8	16	39	1.79
40959427--40959476	21	2.6	19	75	15	50	28	8	2	62	1.35
40962273--40962310	15	2.5	15	87	8	51	18	23	0	57	1.40
40964536--40965259	131	5.7	129	76	11	490	38	12	18	30	1.88
40964884--40965106	114	2.0	114	88	0	329	40	13	16	30	1.86
40964749--40965227	245	2.0	245	85	1	647	39	12	17	30	1.87
40970462--40970532	26	2.7	26	88	0	106	22	22	28	26	1.99
40981212--40981287	35	2.2	35	90	2	118	27	3	7	60	1.42
40991636--40991689	3	18.0	3	96	0	99	35	0	64	0	0.94
40991874--40992026	39	3.8	39	73	13	123	33	3	12	50	1.58
40991998--40992036	16	2.4	16	100	0	78	25	0	15	58	1.37
40997245--40998009	154	5.0	153	83	7	1007	30	10	7	51	1.63
40997243--40998011	304	2.5	307	92	3	1284	30	10	7	51	1.63
40998378--40998504	4	29.2	4	74	23	82	1	25	0	72	0.94
40998378--40998507	20	6.4	20	71	16	99	1	26	0	71	0.95
40998343--40998507	44	4.0	42	73	15	121	1	27	0	70	0.99
40998400--40998511	34	3.4	33	77	19	128	1	28	0	69	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40998373--40998512	10	14.2	10	70	22	84	1	27	0	70	0.95
40998395--40998530	62	2.2	62	83	10	163	2	30	0	66	1.03
40999695--40999724	10	3.0	10	95	0	51	66	0	13	20	1.24
41001467--41001516	8	6.1	8	77	13	57	76	0	0	24	0.80
41001469--41001519	17	3.1	16	86	8	68	78	0	0	21	0.75
41001464--41001520	11	5.5	11	73	23	52	77	0	0	22	0.77
41002626--41002652	13	2.1	13	100	0	54	22	7	7	62	1.46
41002758--41002894	50	2.7	52	80	6	156	26	22	27	24	2.00
41015467--41015491	12	2.1	12	100	0	50	16	8	0	76	1.02
41017070--41017108	6	6.5	6	90	0	60	12	0	5	82	0.83
41017070--41017164	18	5.1	18	71	18	61	16	5	6	71	1.25
41018894--41018932	17	2.3	17	95	0	69	43	12	23	20	1.86
41036286--41036337	21	2.5	21	96	0	95	55	3	9	30	1.50
41039987--41040040	25	2.3	24	81	9	67	37	1	7	53	1.40
41042992--41043034	22	2.0	22	81	9	52	67	6	2	23	1.27
41044602--41044641	20	2.1	18	86	9	53	67	0	7	25	1.16
41045493--41045649	43	3.7	42	80	10	176	25	18	25	30	1.98
41052423--41052526	52	2.0	52	96	0	190	36	26	11	25	1.90
41052654--41052695	16	2.6	16	81	7	50	50	0	0	50	1.00
41060702--41060745	3	14.7	3	100	0	88	68	0	0	31	0.90
41062025--41062063	16	2.4	16	82	0	51	51	2	10	35	1.50
41062076--41062142	31	2.2	31	81	5	73	53	1	7	37	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41063445--41063493	15	3.4	15	83	10	59	12	6	40	40	1.67
41063547--41063605	20	3.0	20	85	7	86	40	1	3	54	1.27
41063840--41063865	5	5.2	5	100	0	52	38	19	19	23	1.93
41073621--41073829	37	5.7	37	93	2	343	25	21	15	38	1.92
41081820--41081868	20	2.5	19	77	6	53	24	24	22	28	1.99
41083198--41083233	19	2.0	19	89	10	58	66	0	0	33	0.92
41083225--41083262	17	2.2	18	85	4	51	71	0	13	15	1.16
41083630--41083691	10	6.4	10	71	26	53	40	1	0	58	1.08
41083635--41083689	28	1.9	29	88	3	85	36	0	0	63	0.95
41083711--41083768	15	3.8	16	80	13	61	32	0	0	67	0.91

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