genome.fa.s9.2.7.7.80.10.50.1000.26.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  26  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)
11808997--11809045	20	2.4	21	80	6	57	48	0	0	51	1.00
11810015--11810068	28	2.0	27	92	3	90	44	1	5	48	1.37
11812981--11813231	46	5.5	46	93	2	418	27	23	16	33	1.95
11815650--11815707	30	1.9	30	89	0	89	41	3	24	31	1.71
11824249--11824299	26	1.9	27	84	11	70	50	1	0	47	1.12
11824276--11824335	24	2.7	23	73	19	63	46	0	1	51	1.10
11825344--11825403	31	1.9	32	83	6	79	30	8	8	53	1.60
11837553--11837669	43	2.8	42	86	7	157	55	0	5	37	1.30
11837550--11837834	84	3.4	83	72	12	190	54	1	6	38	1.33
11837758--11837870	37	3.0	37	78	16	99	55	0	2	40	1.20
11837789--11837893	37	2.9	36	76	10	108	56	0	3	39	1.24
11837968--11838026	3	19.7	3	100	0	118	67	0	0	32	0.91
11840092--11840256	51	3.3	51	90	0	260	32	14	25	27	1.95
11842939--11843102	75	2.2	75	87	2	231	33	18	27	20	1.96
11842939--11843094	25	6.2	25	81	3	152	33	18	26	21	1.96
11845043--11845086	18	2.5	17	82	7	52	38	6	0	54	1.27
11851121--11851189	34	2.0	34	100	0	138	15	5	43	34	1.71
11852156--11852185	5	6.0	5	100	0	60	20	60	0	20	1.37
11852157--11852193	15	2.5	15	90	0	56	21	59	0	18	1.38
11853238--11853278	22	1.9	22	90	5	66	46	4	9	39	1.58
11858006--11858044	2	19.5	2	100	0	78	51	0	0	48	1.00
11870568--11870627	22	2.7	23	80	10	61	11	18	10	60	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11876831--11876864	18	2.0	17	88	11	52	44	0	20	35	1.52
11878244--11878359	46	2.6	45	90	4	180	30	15	25	29	1.96
11879522--11879588	29	2.3	29	82	5	73	38	0	2	58	1.14
11879884--11880170	40	7.2	40	85	3	273	43	16	4	35	1.69
11879884--11880170	20	14.4	19	75	9	243	43	16	4	35	1.69
11880289--11880373	20	4.3	19	71	14	64	31	12	10	44	1.77
11880274--11880355	40	2.0	40	90	0	128	37	15	7	39	1.76
11880503--11880573	21	3.5	20	80	5	90	47	9	0	42	1.36
11887860--11887890	16	1.9	16	93	0	53	35	0	0	64	0.94
11888740--11888775	15	2.4	15	90	0	54	52	0	13	33	1.41
11892762--11892810	3	16.3	3	100	0	98	32	0	0	67	0.91
11909603--11909661	29	2.0	29	100	0	118	32	10	40	16	1.82
11915721--11915750	3	10.0	3	92	0	51	33	3	0	63	1.11
11928531--11928577	19	2.5	18	83	13	51	55	2	6	36	1.37
11929331--11929371	20	2.2	20	86	8	59	39	7	0	53	1.29
11937582--11937643	27	2.3	27	97	0	115	29	22	33	14	1.94
11938567--11938604	19	2.0	19	89	0	58	36	5	7	50	1.54
11943537--11943622	21	4.0	23	79	11	101	37	23	22	17	1.94
11943537--11943623	44	2.0	41	84	6	111	36	22	21	18	1.95
11943876--11943915	13	3.0	13	85	3	53	30	7	0	62	1.23
11944231--11944276	3	15.3	3	100	0	92	67	0	0	32	0.91
11944615--11944666	16	3.2	16	83	0	59	28	1	34	34	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11944648--11944737	45	2.0	44	84	2	117	33	5	27	33	1.80
11945110--11945150	15	2.8	15	82	10	50	53	2	0	43	1.13
11947398--11947439	6	7.2	6	91	5	50	66	19	9	4	1.38
11947406--11947439	17	2.0	17	88	0	50	70	17	5	5	1.28
11947510--11947552	17	2.4	18	81	18	54	67	0	20	11	1.22
11949338--11949377	18	2.2	19	90	4	64	57	17	2	22	1.52
11950136--11950193	21	2.7	22	76	17	59	32	0	5	62	1.18
11954467--11954501	16	2.2	16	90	10	54	45	0	0	54	0.99
11958412--11958446	18	2.0	17	88	5	52	82	2	11	2	0.88
11959215--11959279	30	2.1	31	85	2	87	41	9	10	38	1.72
11970588--11970772	46	4.0	46	92	0	307	35	9	27	28	1.88
11994080--11994121	20	2.0	20	90	4	66	54	0	0	45	0.99
11994252--11994296	22	2.0	22	83	8	56	31	0	4	64	1.13
12002763--12002791	15	1.9	15	100	0	58	27	24	34	13	1.93
12007308--12007360	21	2.5	21	96	0	97	28	41	9	20	1.83
12020784--12020817	2	17.0	2	100	0	68	50	0	0	50	1.00
12025521--12025582	27	2.3	26	75	10	63	53	1	8	37	1.40
12026468--12026516	26	2.0	24	88	8	71	55	0	2	42	1.11
12026971--12027075	37	3.0	37	77	13	107	42	9	0	46	1.42
12026971--12027099	68	1.9	68	80	7	154	43	7	2	46	1.45
12029061--12029243	46	4.0	46	91	3	266	36	9	25	28	1.87
12033390--12033427	19	2.0	19	89	0	58	60	2	5	31	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12046217--12046260	22	2.0	22	86	8	63	54	2	0	43	1.12
12054843--12054918	40	1.9	40	97	0	143	38	23	9	28	1.86
12057767--12057792	4	6.5	4	100	0	52	26	0	0	73	0.84
12058041--12058080	20	1.9	22	90	10	66	57	0	0	42	0.98
12058060--12058127	26	2.6	26	73	13	68	55	0	4	39	1.20
12063930--12063988	28	2.1	28	93	3	102	40	20	27	11	1.87
12070796--12070891	49	1.9	51	89	4	151	37	27	8	27	1.85
12085869--12085907	14	2.8	14	80	0	51	35	10	12	41	1.77
12086151--12086200	20	2.4	21	93	6	84	48	0	2	50	1.12
12086151--12086235	10	8.6	10	72	13	61	48	0	3	48	1.18
12086127--12086282	58	2.7	59	80	9	171	44	1	2	50	1.26
12086374--12086480	45	2.4	45	85	4	137	37	27	6	28	1.82
12088495--12088571	31	2.4	32	82	4	84	37	7	3	50	1.50
12089703--12089825	61	2.0	62	82	4	151	39	4	13	42	1.64
12102651--12102681	4	7.8	4	100	0	62	0	22	25	51	1.48
12105237--12105265	2	14.5	2	100	0	58	0	48	0	51	1.00
12109347--12109372	2	13.0	2	100	0	52	50	50	0	0	1.00
12114111--12114171	21	3.0	20	76	7	52	60	8	1	29	1.35
12126700--12126751	27	2.0	28	82	17	69	44	0	1	53	1.11
12127887--12128004	61	2.0	60	83	8	150	40	2	14	42	1.59
12133192--12133217	2	13.0	2	100	0	52	0	50	0	50	1.00
12135843--12135867	10	2.5	10	100	0	50	12	20	60	8	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12141186--12141228	2	21.5	2	95	0	77	51	2	0	46	1.13
12141687--12141720	17	1.9	18	88	5	52	41	0	0	58	0.98
12142066--12142150	43	2.0	43	97	0	161	45	10	10	32	1.73
12142760--12143099	130	2.7	125	89	2	484	29	17	23	29	1.97
12143772--12143809	11	3.4	11	88	3	58	44	2	34	18	1.64
12145260--12145335	9	8.4	9	89	0	98	44	25	6	23	1.77
12145259--12145335	18	4.3	18	93	0	118	45	24	6	23	1.76
12145439--12145485	18	2.6	18	79	0	58	14	2	44	38	1.58
12146832--12146887	15	3.9	15	74	4	53	35	1	0	62	1.06
12146833--12146887	22	2.6	21	80	5	65	36	1	0	61	1.06
12157732--12157765	14	2.5	14	85	4	52	76	0	23	0	0.79
12159030--12159084	27	2.0	29	82	13	71	50	10	1	36	1.48
12164982--12165049	33	2.1	33	97	0	127	25	11	23	39	1.88
12165176--12165224	20	2.4	22	73	16	59	40	0	6	53	1.26
12167429--12167669	50	4.8	50	82	5	274	27	21	28	21	1.99
12168940--12168988	9	5.4	9	92	0	71	42	18	10	28	1.83
12169091--12169134	18	2.4	18	88	0	61	13	0	43	43	1.44
12171969--12172031	30	2.1	30	93	0	108	25	3	14	57	1.52
12172114--12172153	18	2.2	18	86	8	55	20	0	12	67	1.22
12172155--12172188	12	2.8	12	90	0	50	67	0	0	32	0.91
12172770--12172910	70	2.0	70	100	0	282	32	18	24	24	1.97
12174560--12174601	20	2.1	20	82	8	50	21	4	4	69	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12174540--12174601	28	2.3	27	80	2	70	22	3	9	64	1.38
12196958--12197074	22	5.3	22	88	0	162	32	14	25	27	1.95
12206719--12206748	15	2.0	15	100	0	60	66	26	0	6	1.16
12211849--12211898	3	17.3	3	79	8	59	30	0	4	66	1.10
12211852--12211893	18	2.4	18	92	4	68	28	0	4	66	1.12
12212153--12212206	24	2.2	24	80	6	65	35	0	7	57	1.27
12214161--12214208	25	1.9	25	100	0	96	33	35	0	31	1.58
12224962--12225025	23	2.7	23	72	13	60	46	0	10	42	1.39
12225814--12225898	27	3.2	26	75	11	91	36	2	5	55	1.37
12225868--12225902	18	1.9	18	88	0	52	40	2	0	57	1.14

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