genome.fa.s7.2.7.7.80.10.50.1000.28.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  28  of  204  ( 24458 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)
10283049--10283121	23	3.2	23	90	0	119	26	21	21	30	1.99
10283592--10283633	16	2.6	16	88	0	66	40	7	26	26	1.81
10283613--10283705	45	2.1	43	90	9	143	34	4	24	36	1.75
10283818--10283934	55	2.1	54	82	7	137	51	4	0	43	1.27
10285202--10285278	38	2.0	38	90	5	120	45	19	19	15	1.85
10287992--10288131	49	2.9	49	91	0	226	25	13	27	32	1.94
10290001--10290249	50	4.8	50	84	3	291	20	28	23	27	1.99
10290000--10290249	100	2.4	104	86	5	337	20	28	23	27	1.99
10290344--10290375	13	2.5	13	94	0	55	56	12	0	31	1.37
10294450--10294569	41	2.9	41	86	0	141	26	19	25	29	1.98
10298350--10298400	25	2.0	26	81	11	61	62	1	11	23	1.39
10300821--10300858	18	2.1	18	90	9	60	0	18	0	81	0.69
10300824--10300856	10	3.4	10	91	4	50	0	12	0	87	0.53
10300824--10300863	11	3.7	11	83	6	55	0	15	0	85	0.61
10300824--10300887	26	2.7	23	83	13	69	4	17	0	78	0.92
10301780--10301819	3	13.3	3	100	0	80	0	0	32	67	0.91
10307486--10307511	6	4.3	6	100	0	52	15	0	53	30	1.42
10315918--10316056	68	2.0	69	90	1	217	46	10	17	24	1.80
10318206--10318234	15	1.9	15	100	0	58	48	6	3	41	1.47
10321361--10321394	2	17.5	2	93	6	61	47	0	0	52	1.00
10324801--10324840	18	2.2	18	86	8	55	12	10	2	75	1.15
10327437--10327521	41	2.1	41	97	0	161	29	23	20	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10327926--10327968	2	21.5	2	100	0	86	48	0	0	51	1.00
10338275--10338351	9	8.4	9	81	8	75	42	24	9	23	1.83
10338436--10338464	6	4.8	6	100	0	58	17	0	13	68	1.20
10338503--10338532	13	2.3	13	100	0	60	16	0	43	40	1.48
10343515--10343595	22	3.7	22	86	0	117	29	25	13	30	1.94
10345858--10345921	31	2.1	31	90	0	101	43	14	10	31	1.79
10346803--10346835	7	4.7	7	96	0	57	81	15	3	0	0.80
10353452--10353493	16	2.8	16	82	7	52	85	0	14	0	0.59
10358822--10358900	39	2.0	40	95	2	142	31	1	10	56	1.40
10367266--10367361	46	2.1	47	96	2	176	31	13	27	28	1.94
10367717--10367747	12	2.6	12	89	0	53	16	6	32	45	1.72
10377483--10377535	23	2.4	21	79	14	61	62	0	0	37	0.96
10377486--10377533	16	2.8	16	79	14	51	66	0	0	33	0.92
10378330--10378391	29	2.2	28	91	2	97	43	3	8	45	1.49
10381772--10381805	12	2.7	13	90	9	61	61	0	0	38	0.96
10381786--10381838	27	2.0	27	89	7	83	49	3	3	43	1.38
10381888--10381948	29	2.1	28	81	3	68	24	14	19	40	1.89
10382187--10382534	122	2.8	124	94	1	612	29	16	22	32	1.95
10384060--10384114	25	2.2	25	83	6	67	45	7	1	45	1.41
10384116--10384151	18	2.0	18	88	0	54	44	0	0	55	0.99
10386719--10387011	50	5.8	50	93	0	478	21	31	22	25	1.98
10387106--10387136	13	2.4	13	94	0	53	54	12	0	32	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10387349--10387406	30	1.9	30	85	0	80	31	22	3	43	1.70
10393320--10393365	24	2.0	24	83	12	60	6	17	21	54	1.65
10394620--10394687	35	1.9	35	96	0	127	52	10	20	16	1.72
10395345--10395396	21	2.5	21	90	0	77	30	34	9	25	1.88
10402172--10402196	2	12.5	2	100	0	50	52	48	0	0	1.00
10411552--10411593	15	2.9	15	82	10	52	47	0	0	52	1.00
10411722--10411831	45	2.6	43	81	8	129	31	28	5	34	1.80
10411812--10411863	16	3.2	16	94	0	86	34	36	0	28	1.58
10420810--10420856	24	2.0	24	91	0	76	63	6	2	27	1.30
10421002--10421127	40	3.2	39	75	15	116	40	5	7	46	1.54
10428648--10428684	14	2.6	15	83	12	51	40	5	5	48	1.49
10431877--10431941	21	3.1	21	82	12	89	58	1	0	40	1.07
10433334--10433366	6	5.5	6	100	0	66	54	15	0	30	1.41
10445158--10445208	25	2.0	25	96	0	93	31	27	9	31	1.89
10448923--10448973	18	2.7	19	78	3	59	35	0	0	64	0.94
10448927--10448977	25	2.1	24	81	3	57	41	0	0	58	0.98
10449271--10449300	3	10.0	3	92	0	51	63	0	3	33	1.11
10452700--10452752	21	2.5	21	72	22	56	28	0	7	64	1.21
10455202--10455743	46	12.6	46	82	13	690	28	20	15	34	1.94
10455472--10455706	36	6.0	36	78	18	254	27	19	16	37	1.93
10455341--10455743	82	4.9	82	95	2	664	29	19	15	35	1.92
10455246--10455743	164	2.9	165	91	5	739	29	20	15	35	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10480241--10480301	26	2.4	25	81	13	70	34	3	3	59	1.30
10488552--10488759	91	2.3	91	91	0	326	45	2	3	48	1.35
10488552--10488690	47	3.0	44	68	18	122	45	2	5	46	1.39
10488663--10488734	26	2.6	28	84	8	85	41	0	4	54	1.20
10488584--10488727	47	3.1	47	69	16	138	43	1	4	51	1.29
10488592--10488734	44	3.2	43	68	16	119	44	1	3	50	1.27
10488775--10489070	120	2.5	119	89	3	445	42	3	5	48	1.40
10489018--10489059	15	2.9	15	82	10	52	50	0	0	50	1.00
10489169--10489203	18	2.0	17	88	5	52	45	0	0	54	0.99
10489002--10489316	155	2.0	157	93	1	535	47	5	3	44	1.41
10489364--10489456	45	2.1	44	87	2	132	33	26	6	33	1.82
10489437--10489506	16	4.4	16	85	7	88	32	34	0	32	1.58
10489685--10489899	115	1.9	114	82	2	270	30	6	12	51	1.64
10491896--10491926	15	2.1	15	94	5	55	61	0	0	38	0.96
10501905--10501957	24	2.2	24	82	0	61	56	9	3	30	1.49
10503748--10503774	3	9.0	3	100	0	54	0	33	0	66	0.92
10504361--10504443	25	3.3	25	98	1	157	14	12	22	50	1.76
10504689--10504783	49	2.0	47	89	4	145	23	12	6	57	1.57
10513724--10513749	12	2.2	12	100	0	52	42	0	50	7	1.31
10523913--10523957	23	2.0	22	91	8	74	68	0	6	24	1.13
10525407--10525445	4	9.8	4	100	0	78	25	0	25	48	1.51
10533466--10533503	17	2.2	18	86	9	53	60	0	10	28	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10533606--10533642	18	2.1	18	95	5	67	32	0	0	67	0.91
10536670--10536731	22	2.7	22	80	5	61	37	3	1	58	1.24
10544798--10544832	3	11.7	3	93	0	61	0	34	0	65	0.93
10545501--10545533	2	17.0	2	93	6	59	51	0	0	48	1.00
10546534--10546569	16	2.2	16	95	0	63	30	25	22	22	1.99
10551380--10551455	23	3.3	23	82	12	102	31	25	19	23	1.98
10555179--10555222	21	2.1	21	83	8	54	22	9	25	43	1.82
10557720--10557774	23	2.4	24	81	9	69	7	20	30	41	1.79
10561585--10561615	12	2.6	12	94	0	53	22	41	29	6	1.78
10563293--10563414	23	5.3	23	86	2	174	24	19	25	30	1.98
10563293--10563414	46	2.7	46	88	2	192	24	19	25	30	1.98
10566036--10566114	25	3.2	25	87	1	97	22	27	18	30	1.98
10567251--10567283	12	2.8	12	95	0	57	21	45	27	6	1.75
10568613--10568665	17	3.1	17	88	2	79	18	22	26	32	1.97
10569569--10569593	2	12.5	2	100	0	50	52	0	0	48	1.00
10571090--10571144	25	2.3	24	81	12	60	56	16	5	21	1.60
10571899--10572005	22	4.9	22	87	0	142	31	14	26	27	1.95
10575023--10575113	22	4.0	22	72	25	66	50	1	4	43	1.29
10576668--10576723	31	1.9	29	82	13	71	35	7	3	53	1.46
10581086--10581127	21	2.0	21	86	9	59	73	0	11	14	1.09
10582401--10583067	132	5.0	132	92	1	1018	27	20	25	26	1.99
10582736--10582916	44	4.1	44	67	11	118	25	23	25	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10583011--10583148	45	3.1	46	72	9	124	31	18	22	28	1.97
10594852--10594934	39	2.2	39	86	2	114	20	19	20	39	1.92
10594852--10595017	45	4.0	39	75	16	127	21	19	19	39	1.92
10594879--10595028	45	3.3	45	83	2	194	20	20	18	40	1.92
10595424--10595490	11	6.4	11	72	20	54	35	2	0	61	1.12
10595375--10595520	40	3.6	40	92	2	231	33	3	0	63	1.12
10595433--10595545	31	3.4	30	69	26	93	35	2	0	61	1.10
10595455--10595545	31	3.0	30	86	3	128	35	2	0	62	1.07
10595375--10595542	79	2.1	77	84	6	221	33	2	0	63	1.10
10595375--10595539	40	4.2	39	89	3	215	32	3	0	64	1.09

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