genome.fa.s9.2.7.7.80.10.50.1000.28.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  28  of  226  ( 27023 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)
12583527--12583576	21	2.4	21	86	0	64	36	32	6	26	1.81
12583965--12584012	25	2.0	24	87	4	69	52	2	2	43	1.24
12586677--12586702	12	2.2	12	100	0	52	42	7	7	42	1.62
12587339--12587398	20	3.0	20	75	20	70	53	18	0	28	1.45
12588032--12588076	24	1.9	23	82	13	56	48	24	6	20	1.73
12588892--12588943	3	17.7	3	96	4	97	34	0	0	65	0.93
12588962--12589009	5	9.6	5	81	0	51	43	0	6	50	1.27
12591501--12591531	5	6.4	5	96	3	55	0	38	0	61	0.96
12595230--12595286	25	2.2	26	81	6	71	66	0	5	28	1.13
12595725--12595765	19	2.1	20	86	4	57	56	2	9	31	1.45
12608702--12608771	33	2.3	29	80	17	95	45	5	8	40	1.58
12608711--12608776	33	2.0	33	100	0	132	48	3	9	39	1.50
12608769--12608843	31	2.5	31	86	2	107	32	10	12	45	1.75
12610931--12610960	3	10.0	3	100	0	60	33	0	0	66	0.92
12621989--12622122	66	2.0	66	100	0	268	38	20	14	26	1.92
12629222--12629277	22	2.5	23	82	2	69	51	1	1	44	1.22
12629253--12629292	16	2.5	16	91	0	62	47	2	7	42	1.45
12629365--12629392	9	3.1	9	100	0	56	32	0	10	57	1.33
12629281--12629490	68	3.1	68	97	1	388	40	4	9	45	1.57
12629433--12629460	9	3.1	9	100	0	56	32	0	10	57	1.33
12629561--12629603	22	2.0	22	86	13	63	58	2	0	39	1.11
12629925--12629991	25	2.6	26	92	2	109	47	2	1	47	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12632449--12632482	16	2.1	16	94	0	59	79	0	0	20	0.73
12633053--12633124	34	2.1	34	89	5	110	16	5	9	68	1.37
12635721--12635753	14	2.3	15	89	5	50	39	0	6	54	1.25
12640222--12640410	50	3.8	50	87	0	270	26	24	30	19	1.98
12647173--12647205	13	2.5	13	95	0	57	30	0	12	57	1.35
12647300--12647541	50	4.7	50	85	3	277	26	23	28	20	1.99
12647300--12647549	100	2.4	103	86	5	344	26	23	28	21	1.99
12649980--12650010	10	3.1	10	100	0	62	51	0	9	38	1.35
12651808--12651840	8	3.7	9	88	12	50	45	9	0	45	1.35
12658794--12658825	16	2.0	16	100	0	64	25	31	18	25	1.98
12664596--12664648	23	2.5	22	77	20	58	66	3	3	26	1.26
12665047--12665087	21	2.0	21	85	0	55	56	4	7	31	1.48
12665098--12665152	23	2.3	23	84	15	67	76	3	1	18	1.02
12665096--12665153	25	2.3	24	80	8	71	75	3	1	18	1.03
12665633--12665678	22	2.0	22	83	4	56	39	17	4	39	1.69
12665634--12665729	19	4.8	19	81	5	93	39	14	7	38	1.74
12666977--12667004	3	9.3	3	100	0	56	0	35	0	64	0.94
12669220--12669288	31	2.3	30	76	18	81	37	2	11	47	1.55
12672519--12672657	46	3.0	45	89	4	208	36	10	25	28	1.88
12676759--12676815	23	2.4	25	83	13	77	50	7	0	42	1.29
12676759--12676823	23	2.9	24	82	13	59	52	7	1	38	1.40
12688395--12688532	50	2.7	50	83	3	179	22	16	28	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12688392--12688577	51	3.7	48	78	7	183	22	15	28	33	1.95
12690502--12690650	45	3.4	45	85	5	196	21	17	26	34	1.95
12692907--12692933	2	13.5	2	100	0	54	51	0	0	48	1.00
12693129--12693302	41	4.2	41	90	2	260	29	23	20	25	1.99
12693997--12694035	2	19.0	2	94	5	69	48	2	0	48	1.15
12696869--12696920	25	2.3	23	81	18	72	38	5	15	40	1.71
12696876--12696927	25	2.1	25	92	0	86	42	3	13	40	1.62
12697502--12697550	5	9.8	5	100	0	98	40	0	0	59	0.98
12715722--12715773	24	2.2	24	85	0	68	38	3	7	50	1.50
12743527--12743551	2	12.5	2	100	0	50	52	0	0	48	1.00
12743543--12743599	30	1.9	30	92	0	96	33	21	10	35	1.87
12748016--12748057	21	2.1	19	86	8	57	54	4	0	40	1.21
12751585--12751630	21	2.2	21	84	7	58	43	2	13	41	1.55
12752251--12752320	34	1.9	38	83	16	96	51	15	5	27	1.66
12753953--12754010	27	2.1	27	80	6	62	60	1	3	34	1.24
12756683--12756718	17	2.1	17	89	0	54	11	16	8	63	1.49
12779486--12779526	21	2.0	21	85	9	57	36	2	7	53	1.42
12795376--12795431	27	2.0	28	83	10	71	50	14	5	30	1.65
12796615--12796646	2	16.0	2	100	0	64	50	0	0	50	1.00
12807883--12807920	13	2.9	13	96	0	67	39	26	10	23	1.87
12810397--12810454	20	2.8	21	89	5	91	13	17	17	51	1.76
12810401--12810466	21	3.2	21	86	4	89	15	19	18	46	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12810643--12810688	21	2.2	21	88	3	67	39	4	28	28	1.76
12817165--12817345	50	3.6	50	89	0	263	20	29	23	25	1.99
12817688--12817744	30	2.0	28	82	6	69	35	22	3	38	1.72
12823603--12823655	26	2.0	26	85	7	72	45	22	16	15	1.85
12824688--12824821	37	3.4	40	72	14	109	35	24	13	26	1.93
12830024--12830095	25	2.8	26	81	6	94	20	25	18	36	1.95
12830024--12830140	25	4.7	25	75	12	87	20	27	18	33	1.96
12830029--12830173	25	5.8	26	77	11	81	22	25	19	32	1.97
12832233--12832277	20	2.2	21	80	11	58	73	0	26	0	0.84
12833026--12833081	25	2.2	25	83	0	67	17	26	19	35	1.94
12834274--12834307	13	2.7	13	95	4	61	61	0	0	38	0.96
12843699--12843730	3	10.7	3	93	0	55	0	34	0	65	0.93
12844255--12844333	40	2.0	40	97	0	149	32	12	12	41	1.81
12847559--12847599	20	2.0	20	100	0	82	24	12	24	39	1.89
12848776--12848810	3	11.7	3	100	0	70	34	0	34	31	1.58
12851192--12851220	10	3.0	10	95	5	51	31	0	0	68	0.89
12860674--12860707	5	6.8	5	100	0	68	0	41	0	58	0.98
12860674--12860715	15	2.8	15	92	0	57	0	38	2	59	1.10
12870701--12870738	15	2.4	16	82	4	51	34	23	7	34	1.84
12871891--12871932	6	7.0	6	97	0	57	0	0	40	59	0.97
12871891--12871931	12	3.4	12	93	0	64	0	0	41	58	0.98
12875320--12875358	2	19.5	2	100	0	78	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12891585--12891718	44	3.0	45	91	6	213	33	24	14	27	1.94
12903586--12903660	31	2.4	31	76	8	80	49	6	14	29	1.69
12914491--12914549	29	2.0	30	83	9	77	52	1	1	44	1.21
12924656--12924796	66	2.1	66	98	0	273	36	10	14	37	1.81
12925337--12925386	26	1.9	26	83	0	64	36	20	24	20	1.95
12925343--12925403	26	2.3	26	80	5	70	34	21	26	18	1.96
12935571--12935597	13	2.1	13	100	0	54	55	14	7	22	1.64
12946355--12946406	13	3.7	13	76	18	59	13	25	38	23	1.91
12946368--12946423	17	3.6	16	76	18	64	14	26	35	23	1.93
12946352--12946423	30	2.4	30	97	0	135	13	27	36	22	1.92
12951837--12951874	2	19.0	2	100	0	76	0	50	0	50	1.00
12977008--12977035	2	14.0	2	100	0	56	50	0	50	0	1.00
12982975--12983008	11	3.0	11	86	4	50	20	23	0	55	1.43
12983005--12983110	51	2.1	51	82	3	124	27	24	1	46	1.63
12987091--12987195	46	2.3	46	85	1	140	22	19	19	39	1.93
12987282--12987322	19	2.2	19	90	0	64	51	2	12	34	1.52
12988240--12988708	125	3.7	126	88	2	685	28	22	16	32	1.96
12988151--12988708	250	2.3	241	89	3	857	28	22	17	32	1.96
12989238--12989265	6	4.7	6	100	0	56	50	32	0	17	1.47
13004359--13004516	21	7.5	21	66	5	77	17	24	17	41	1.90
13004396--13004477	42	2.0	42	85	0	110	17	26	17	39	1.91
13004358--13004516	63	2.5	63	75	4	160	16	24	16	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13005361--13005442	42	2.0	42	80	9	96	15	28	31	24	1.96
13006210--13006319	21	5.3	21	80	2	116	48	15	20	16	1.82
13006210--13006319	42	2.7	42	87	2	152	48	15	20	16	1.82
13011225--13011302	24	3.2	24	78	3	68	5	8	53	32	1.54
13011271--13011352	24	3.4	24	82	0	83	8	6	50	35	1.58
13011249--13011398	60	2.5	60	81	4	169	10	8	51	30	1.64
13011333--13011431	24	4.1	24	72	5	65	12	11	47	29	1.75
13011460--13011513	12	4.4	12	81	11	56	12	0	64	22	1.27
13014434--13014495	30	2.1	30	100	0	124	51	12	9	25	1.70
13019407--13019455	19	2.7	19	87	6	75	46	8	14	30	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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226