genome.fa.s1.2.7.7.80.10.50.1000.139.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  139  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)
41626121--41626170	25	2.0	25	84	0	64	18	10	16	56	1.67
41628447--41628485	16	2.4	16	91	0	60	53	2	7	35	1.43
41630327--41630367	19	2.2	19	86	8	57	46	9	2	41	1.50
41644509--41644783	41	6.7	41	94	0	460	16	22	29	31	1.96
41645303--41645340	7	5.4	7	87	0	58	13	0	50	36	1.42
41645300--41645340	21	1.9	22	90	5	66	12	0	51	36	1.40
41649591--41649638	22	2.0	23	84	11	62	54	2	2	41	1.24
41649652--41649742	42	2.2	42	84	4	112	23	14	27	35	1.93
41649754--41649944	43	4.4	43	92	0	283	17	17	39	25	1.91
41649784--41650012	43	5.3	43	85	4	167	20	20	32	26	1.97
41649784--41649962	86	2.1	86	84	0	232	18	18	35	26	1.95
41649933--41650034	42	2.4	44	86	3	136	33	25	18	22	1.97
41652286--41652696	44	9.7	41	69	11	191	27	20	21	30	1.98
41652389--41652564	85	2.1	85	91	0	280	27	19	22	30	1.98
41652290--41652523	129	1.8	129	82	5	303	27	20	21	31	1.98
41652414--41652608	85	2.3	85	85	3	250	27	21	22	29	1.99
41652464--41652749	129	2.2	129	90	1	466	25	20	22	31	1.98
41652155--41652737	214	2.8	214	81	5	679	28	20	20	30	1.98
41652205--41652737	85	6.2	85	72	9	228	28	20	20	30	1.97
41652771--41653651	50	17.7	50	68	2	498	25	22	22	29	1.99
41652761--41653659	100	9.0	100	86	0	1183	25	22	22	29	1.99
41654930--41654995	16	3.9	17	84	9	82	12	0	7	80	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41654947--41654994	23	2.1	23	84	7	62	12	0	8	79	0.94
41654932--41654988	9	6.6	9	91	4	82	14	0	7	78	0.94
41657698--41657751	24	2.2	25	86	3	74	46	5	22	25	1.73
41663168--41663271	43	2.4	43	93	0	172	23	33	20	23	1.97
41663244--41663301	30	1.9	30	96	0	107	22	31	22	24	1.99
41663201--41663344	73	2.0	73	95	0	261	25	34	20	20	1.97
41663171--41663387	116	1.9	116	92	0	362	24	33	20	21	1.97
41663274--41663445	43	4.0	43	87	0	220	29	32	19	18	1.96
41664169--41664220	23	2.3	23	79	0	59	34	7	30	26	1.85
41668082--41668113	13	2.3	15	89	10	50	56	0	0	43	0.99
41668788--41668920	7	18.7	7	71	11	56	45	33	0	21	1.52
41668788--41668978	14	13.4	14	69	14	70	46	30	0	22	1.56
41668840--41668879	21	1.9	21	89	0	62	42	37	0	20	1.52
41669276--41669473	41	4.9	41	85	6	242	31	30	20	18	1.96
41669276--41669459	81	2.2	81	85	6	239	30	30	20	17	1.96
41669506--41669640	40	3.4	40	81	8	143	21	17	23	37	1.93
41672061--41672109	24	2.0	24	100	0	98	36	20	4	38	1.72
41673684--41673737	27	2.0	28	85	10	76	42	3	3	50	1.38
41682461--41682525	32	2.1	32	97	2	123	30	9	12	47	1.72
41683051--41683093	12	3.5	12	81	15	52	74	4	18	2	1.10
41687959--41688021	32	2.0	32	93	3	110	33	9	11	46	1.72
41696857--41696915	30	2.0	30	96	0	109	57	8	3	30	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41697326--41697372	16	2.9	16	93	0	76	40	8	31	19	1.81
41697587--41697628	15	2.7	16	82	14	52	52	2	0	45	1.13
41697596--41697637	15	2.9	15	82	10	52	52	0	0	47	1.00
41697622--41697929	61	5.1	61	66	17	230	49	6	2	42	1.41
41697702--41697748	16	3.0	16	78	12	53	51	2	2	44	1.25
41697585--41697981	120	3.3	121	95	1	710	49	5	2	42	1.38
41697823--41697868	16	2.9	16	78	12	51	52	2	0	45	1.13
41697823--41697877	15	3.7	15	79	13	53	52	1	0	45	1.11
41702777--41702906	64	2.0	64	100	0	260	31	18	23	26	1.97
41706717--41706743	11	2.5	11	100	0	54	14	0	0	85	0.61
41707527--41707551	2	12.5	2	100	0	50	48	0	0	52	1.00
41712497--41712535	5	7.6	5	82	5	51	79	2	17	0	0.84
41712497--41712535	16	2.5	16	91	4	62	79	2	17	0	0.84
41713489--41713862	45	8.4	45	80	3	389	28	16	26	28	1.97
41713856--41714104	129	1.9	129	90	0	399	32	19	20	28	1.97
41714042--41714493	129	3.5	129	89	1	656	32	20	21	25	1.97
41713862--41714318	214	2.1	214	88	0	680	32	20	20	26	1.97
41713991--41714443	85	5.3	85	74	9	357	31	21	21	26	1.98
41713855--41714491	44	14.8	43	70	11	322	32	20	20	26	1.98
41715452--41715480	5	6.0	5	92	8	51	17	0	0	82	0.66
41716468--41716501	17	2.0	17	94	0	59	17	5	2	73	1.16
41723150--41723178	12	2.5	12	94	5	51	41	0	34	24	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41728524--41728611	44	2.0	44	97	0	167	42	13	6	37	1.71
41735393--41735563	60	2.9	59	83	11	163	22	7	29	40	1.81
41735393--41735533	29	4.8	29	74	15	119	23	7	29	39	1.81
41735437--41735563	60	2.1	59	88	5	193	20	7	30	40	1.81
41735452--41735563	30	3.8	30	71	10	86	20	8	30	41	1.81
41740831--41740864	8	4.1	8	85	7	50	82	0	0	17	0.67
41745597--41745661	16	4.1	16	95	0	103	36	3	35	24	1.71
41745875--41745916	15	2.7	16	82	14	52	52	2	0	45	1.13
41745884--41745925	15	2.9	15	82	10	52	52	0	0	47	1.00
41745994--41746045	15	3.6	15	80	12	56	53	1	0	44	1.11
41746114--41746165	15	3.6	15	80	12	56	53	1	0	44	1.11
41745878--41746290	120	3.4	120	96	0	738	50	5	2	41	1.39
41746331--41746391	28	2.2	28	85	5	81	50	3	0	45	1.17
41746306--41746513	91	2.3	90	87	4	299	47	4	3	44	1.41
41746429--41746472	17	2.7	16	83	13	54	56	0	2	40	1.11
41746429--41746478	18	3.0	17	85	8	59	56	2	2	40	1.22
41746287--41746473	44	4.1	43	67	17	103	48	3	3	44	1.36
41746356--41746490	44	3.0	43	66	17	103	49	4	2	42	1.38
41746356--41746494	47	3.0	47	66	17	128	50	4	2	42	1.37
41746783--41746815	2	16.5	2	100	0	66	51	48	0	0	1.00
41747514--41747559	15	3.0	16	87	12	78	56	26	6	10	1.58
41750860--41750921	7	9.3	7	75	19	53	74	0	4	20	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41755214--41755244	16	1.9	16	93	0	53	29	9	22	38	1.86
41765536--41765595	20	3.1	18	79	18	50	70	3	23	3	1.18
41766798--41766835	20	1.9	20	84	10	51	28	21	21	28	1.98
41772404--41772508	43	2.5	43	93	1	176	30	29	17	22	1.96
41779028--41779072	18	2.3	20	88	11	67	75	4	2	17	1.07
41782247--41782288	23	1.9	22	85	9	59	21	2	2	73	1.06
41783322--41783365	21	2.1	21	82	0	52	40	4	2	52	1.34
41783572--41783608	13	2.7	14	80	20	51	21	5	8	64	1.40
41783615--41783649	15	2.3	15	95	0	61	17	0	17	65	1.27
41787453--41787512	21	2.9	21	92	0	93	11	21	16	50	1.77
41796512--41796561	26	1.9	26	84	8	66	50	2	10	38	1.48
41796652--41796727	33	2.3	32	78	10	82	34	15	22	27	1.95
41796618--41796812	101	1.9	101	86	2	275	31	13	24	30	1.94
41796665--41796812	33	4.4	33	73	9	111	31	12	25	31	1.93
41796618--41796845	101	2.3	101	80	3	262	32	15	23	29	1.95
41800407--41800458	19	2.6	20	77	22	56	11	23	23	42	1.86
41803979--41804045	9	7.4	9	93	0	116	40	22	11	25	1.88
41803979--41804047	27	2.6	27	100	0	138	39	21	11	27	1.88
41804171--41804203	2	16.5	2	100	0	66	51	0	0	48	1.00
41807171--41807237	29	2.3	29	81	0	80	34	22	22	20	1.97
41809832--41809867	4	9.0	4	100	0	72	25	0	25	50	1.50
41810852--41811030	42	4.3	42	80	2	200	32	20	18	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41810873--41811034	84	1.9	83	87	1	234	33	20	17	27	1.95
41818056--41818244	41	4.5	42	81	7	192	29	19	23	27	1.98
41826004--41827069	539	2.0	539	89	0	1641	23	22	15	38	1.92
41830533--41830568	3	12.0	3	100	0	72	66	0	0	33	0.92
41839321--41839382	32	1.9	32	83	9	81	17	12	16	53	1.73
41844402--41844445	18	2.4	19	81	14	56	50	0	2	47	1.13
41852993--41853029	3	12.3	3	100	0	74	67	0	0	32	0.91
41857388--41857540	22	7.0	22	90	0	225	26	26	14	32	1.94
41863863--41863989	41	3.0	43	81	4	159	24	17	28	29	1.97
41872723--41872777	27	2.0	27	92	0	92	34	9	21	34	1.85

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