genome.fa.s5.2.7.7.80.10.50.1000.43.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   199   200   201   202   203   204   205   206   207   208   

This is table  43  of  208  ( 24913 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)
11823081--11823165	31	2.7	31	78	10	84	27	22	28	22	1.99
11837234--11837327	27	3.5	27	86	0	125	23	17	23	36	1.95
11837868--11837924	28	2.0	28	100	0	114	40	10	10	38	1.74
11849555--11849581	5	5.4	5	100	0	54	40	0	0	59	0.98
11856377--11856525	42	3.5	44	73	13	125	34	24	16	24	1.95
11873493--11873524	6	5.3	6	100	0	64	18	50	0	31	1.48
11878590--11878628	20	2.0	20	90	10	62	15	23	5	56	1.59
11878893--11879025	50	2.7	50	83	2	160	21	30	22	26	1.99
11882963--11882990	9	3.1	9	100	0	56	21	25	0	53	1.46
11886280--11886318	20	2.0	20	90	10	62	15	23	5	56	1.59
11890280--11890317	13	3.0	13	92	3	60	65	5	23	5	1.34
11891379--11891461	25	3.5	24	77	11	91	16	22	20	39	1.92
11892281--11892327	17	2.8	17	90	0	67	38	10	17	34	1.84
11898419--11898525	51	2.1	51	84	3	135	44	8	17	28	1.78
11904217--11904336	57	2.1	57	85	3	161	46	7	19	26	1.76
11907914--11907957	20	2.2	20	100	0	88	25	6	27	40	1.80
11908803--11908837	2	17.5	2	93	0	61	45	2	0	51	1.16
11912784--11912902	57	2.1	57	96	0	220	32	15	13	38	1.86
11920853--11920888	2	18.0	2	94	0	63	47	0	2	50	1.15
11920865--11921115	114	2.2	114	93	1	432	42	3	13	41	1.60
11920895--11921073	60	3.1	60	65	23	164	41	2	14	40	1.60
11921583--11921729	41	3.6	41	89	1	215	28	19	28	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11922631--11922687	11	5.2	11	78	0	60	66	12	3	17	1.37
11924721--11924924	52	3.7	58	84	11	263	27	20	8	43	1.81
11924721--11924924	110	1.9	106	87	6	297	27	20	8	43	1.81
11925820--11925887	33	2.1	33	100	0	136	25	11	20	42	1.86
11929165--11929190	12	2.2	12	100	0	52	42	15	15	26	1.87
11933180--11933536	41	8.7	41	92	0	570	22	28	20	28	1.99
11934008--11934037	2	15.0	2	92	0	51	46	0	0	53	1.00
11941551--11941577	8	3.4	8	100	0	54	33	0	11	55	1.35
11941558--11941868	170	1.8	170	93	2	536	38	14	11	35	1.82
11943555--11943617	30	2.0	33	81	9	78	14	7	11	66	1.43
11957412--11957484	14	5.0	15	75	20	66	43	12	15	28	1.82
11957423--11957453	16	2.0	16	93	6	55	48	12	12	25	1.77
11969425--11969474	26	2.0	25	84	7	66	44	2	0	54	1.11
11974289--11974314	13	2.0	13	100	0	52	15	15	0	69	1.20
11982522--11982647	41	3.0	43	78	11	143	31	26	17	23	1.97
11983386--11983414	10	2.9	10	100	0	58	62	20	6	10	1.50
11983521--11983567	25	2.0	23	84	16	60	38	12	0	48	1.41
11997318--11997383	25	2.6	25	79	9	71	28	21	22	27	1.99
12002862--12002948	33	2.7	32	76	15	88	45	18	8	27	1.77
12002939--12002978	20	2.0	20	100	0	80	45	15	10	30	1.78
12002928--12002992	34	1.9	33	87	9	96	41	15	7	35	1.76
12002962--12002991	14	2.2	13	94	5	51	40	20	6	33	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12005640--12005791	63	2.4	62	77	8	146	22	19	31	26	1.97
12006364--12006414	23	2.2	23	92	0	84	15	3	47	33	1.64
12008688--12008728	3	13.3	3	85	14	57	65	29	4	0	1.13
12009610--12009671	23	2.8	22	78	14	65	37	8	0	54	1.30
12011791--12011856	14	4.5	14	74	23	55	56	1	0	42	1.08
12015405--12015437	12	2.8	12	100	0	66	42	0	0	57	0.98
12017452--12017629	51	3.5	51	94	2	306	35	15	23	25	1.94
12017604--12017642	7	5.6	7	96	0	69	41	10	30	17	1.83
12017401--12017737	115	3.0	114	83	6	386	34	15	24	26	1.94
12017557--12017693	65	2.1	64	86	4	186	36	14	24	24	1.93
12019006--12019104	28	3.5	28	91	0	153	33	14	25	27	1.94
12019831--12020312	23	20.6	23	73	9	359	25	15	16	41	1.88
12019816--12020314	70	7.1	70	88	4	702	25	15	16	42	1.88
12027061--12027126	14	4.5	14	74	23	55	56	1	0	42	1.08
12033226--12033280	27	2.0	29	85	7	78	67	9	0	23	1.19
12038496--12038579	25	3.4	25	73	15	75	26	23	17	32	1.97
12042487--12042783	44	6.6	44	70	14	153	28	21	18	31	1.97
12042516--12042796	141	2.0	142	94	0	492	27	20	18	33	1.96
12042706--12042828	44	2.8	43	85	4	149	27	20	21	30	1.98
12042873--12043282	131	3.2	131	90	1	619	24	24	21	28	1.99
12044080--12044162	25	3.4	24	76	15	80	24	24	19	32	1.97
12048888--12048931	22	1.9	24	86	9	65	34	13	25	27	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12049300--12049331	16	2.0	16	100	0	64	25	6	12	56	1.59
12066539--12066613	22	3.3	22	67	10	60	25	17	5	52	1.66
12071836--12071877	20	2.0	21	86	4	59	40	0	0	59	0.97
12075482--12075535	26	2.1	26	100	0	108	38	14	11	35	1.82
12083192--12083241	12	4.2	12	79	7	57	14	10	2	74	1.16
12083202--12083251	24	2.1	24	89	10	77	16	10	2	72	1.21
12083663--12083694	17	1.9	16	93	6	55	46	0	0	53	1.00
12088272--12088314	21	2.0	21	95	0	77	13	30	18	37	1.90
12092185--12092224	20	2.0	20	95	0	71	32	10	12	45	1.75
12093599--12093659	32	1.9	32	96	0	113	50	18	3	27	1.62
12093599--12093672	32	2.5	30	87	10	100	51	18	2	27	1.60
12093600--12093686	27	3.0	27	83	11	77	51	18	3	26	1.62
12095079--12095139	27	2.3	27	79	0	68	50	6	4	37	1.50
12097058--12097096	18	2.2	18	90	9	62	69	0	25	5	1.09
12098746--12098803	29	2.0	29	93	0	98	34	13	13	37	1.85
12099528--12099574	22	2.1	23	84	11	62	25	21	8	44	1.80
12100096--12100123	14	2.0	14	100	0	56	28	21	0	50	1.49
12103781--12103831	18	2.8	18	69	0	57	13	41	3	41	1.63
12107334--12107410	14	5.0	15	71	20	52	42	15	9	32	1.78
12107350--12107389	20	2.0	20	90	0	62	50	12	10	27	1.72
12107338--12107404	34	1.9	35	90	3	109	46	13	8	31	1.74
12107373--12107412	14	2.9	14	84	0	53	42	17	7	32	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12109055--12109106	18	2.9	18	91	0	86	34	15	11	38	1.83
12112639--12112705	26	2.5	26	77	15	75	47	11	2	37	1.56
12117328--12117389	30	2.2	27	85	8	79	50	0	3	46	1.17
12118425--12118560	38	3.5	39	86	8	190	61	0	4	33	1.16
12118472--12118533	30	2.1	29	82	11	72	62	0	3	33	1.11
12121095--12121142	20	2.3	20	82	7	60	35	2	14	47	1.56
12121277--12121318	23	1.9	23	85	9	61	16	7	11	64	1.48
12128773--12128837	28	2.3	28	72	2	67	55	3	7	33	1.44
12128982--12129062	3	28.0	3	80	7	87	60	2	1	35	1.18
12129048--12129110	18	3.4	18	70	12	56	60	3	6	30	1.37
12129034--12129110	38	2.1	34	86	13	102	57	3	5	33	1.39
12130201--12130265	30	2.2	30	82	0	76	10	3	40	46	1.54
12134871--12134905	18	1.9	18	88	11	54	40	11	22	25	1.88
12144297--12144341	20	2.2	20	88	0	63	26	13	15	44	1.83
12145236--12145399	45	3.6	45	87	1	213	34	29	4	30	1.79
12145267--12145390	23	5.5	22	70	3	86	36	32	4	26	1.78
12145637--12145697	29	2.0	29	84	6	77	70	1	8	19	1.21
12147788--12147872	38	2.1	41	83	10	106	65	2	21	10	1.34
12152073--12152230	23	7.1	22	73	5	138	36	31	3	28	1.75
12152067--12152230	45	3.6	45	90	1	249	36	31	3	28	1.75
12152073--12152262	45	4.3	44	83	5	143	38	30	3	27	1.74
12156211--12156328	34	3.4	35	82	4	150	19	27	33	20	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12159680--12159718	20	2.0	20	84	0	51	33	30	23	12	1.92
12165708--12165758	17	3.1	16	81	15	52	43	1	0	54	1.11
12165722--12165758	17	2.2	17	90	9	58	43	0	0	56	0.99
12172652--12173140	8	61.1	8	91	0	602	24	7	24	42	1.80
12173241--12173940	4	175.5	4	91	1	1109	24	2	25	48	1.62
12176966--12177021	25	2.2	26	90	3	87	23	10	23	42	1.85
12177014--12177104	25	3.6	25	70	5	85	23	19	24	32	1.97
12177042--12177128	25	3.4	25	70	7	77	19	18	26	35	1.95
12177002--12177128	51	2.5	51	93	3	213	21	17	25	35	1.95
12177002--12177151	51	3.0	50	84	8	187	20	16	26	36	1.93

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   199   200   201   202   203   204   205   206   207   208