genome.fa.s1.2.7.7.80.10.50.1000.114.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  114  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)
34169324--34169376	24	2.2	24	93	0	88	32	3	24	39	1.73
34171175--34171218	22	2.0	23	86	4	63	34	9	2	54	1.44
34183045--34183091	13	3.5	13	81	16	60	46	0	17	36	1.48
34186153--34186288	41	3.2	42	81	9	136	24	16	27	30	1.97
34190570--34190594	5	5.0	5	100	0	50	20	0	0	80	0.72
34192525--34192569	21	2.3	19	88	7	63	2	15	4	77	1.02
34193099--34193185	26	3.3	26	86	0	111	14	25	41	18	1.89
34203911--34203973	31	2.0	31	100	0	126	44	3	12	39	1.59
34205251--34205323	33	2.2	33	85	0	92	46	17	19	16	1.84
34205301--34205353	27	2.0	27	84	0	70	32	20	28	18	1.97
34214048--34214080	16	2.1	16	94	0	57	69	3	3	24	1.16
34225815--34225961	41	3.6	41	92	0	249	31	20	24	23	1.98
34239662--34239724	15	3.9	16	75	20	69	42	0	1	55	1.09
34239646--34239731	32	2.7	33	80	18	94	41	0	1	56	1.06
34241715--34241836	34	3.6	34	86	4	158	44	13	7	34	1.72
34241715--34241836	32	3.6	32	81	8	136	44	13	7	34	1.72
34248476--34248599	34	3.6	36	80	8	143	41	12	8	36	1.75
34250898--34251134	41	5.8	41	80	0	267	38	24	19	17	1.93
34254769--34254815	21	2.2	22	77	11	53	31	29	23	14	1.95
34256339--34256373	13	2.8	12	87	8	52	14	8	2	74	1.17
34265581--34265648	23	3.0	23	66	20	61	38	13	19	29	1.89
34265562--34265721	45	3.6	44	82	3	169	42	15	20	22	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34268855--34268933	39	2.0	39	97	0	149	26	8	27	36	1.86
34271196--34271228	11	2.8	12	81	9	50	15	21	15	48	1.81
34271503--34271548	23	2.0	23	83	8	58	39	10	17	32	1.84
34273641--34274067	43	10.1	43	81	3	456	29	28	18	24	1.98
34273821--34273892	37	1.9	37	94	0	126	25	27	19	27	1.99
34274401--34274491	43	2.1	43	87	2	130	45	9	10	34	1.73
34278650--34278759	7	15.0	7	70	16	53	40	36	0	21	1.60
34278706--34278752	24	1.9	25	91	4	78	34	42	2	21	1.65
34278877--34278923	15	3.3	15	79	8	53	40	29	0	29	1.57
34282319--34282366	18	2.7	18	77	9	53	62	0	4	33	1.14
34286514--34286543	7	4.1	7	91	8	51	86	0	13	0	0.57
34286514--34286543	15	2.0	15	100	0	60	86	0	13	0	0.57
34288271--34288412	71	2.0	71	92	0	239	35	19	18	27	1.95
34288873--34288926	26	2.1	26	82	6	65	46	3	9	40	1.54
34288956--34289076	58	2.0	59	82	4	145	47	4	11	36	1.59
34289179--34289211	3	10.7	3	93	6	57	69	0	0	30	0.88
34290827--34290941	44	2.6	44	81	8	144	29	24	20	26	1.99
34291283--34291380	51	1.9	51	82	0	124	30	24	14	30	1.94
34291372--34294205	50	56.6	50	75	2	2356	26	19	21	32	1.97
34291315--34294205	100	28.9	100	87	1	3192	26	19	21	31	1.97
34295611--34295666	6	8.8	6	77	11	58	0	17	0	82	0.68
34295609--34295668	11	5.7	10	79	16	68	0	16	0	83	0.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34295610--34295667	26	2.2	27	87	9	93	0	17	0	82	0.66
34300738--34300874	70	1.9	71	91	1	222	37	18	16	27	1.92
34301309--34301411	26	3.8	28	73	19	76	49	2	5	41	1.42
34301309--34301411	28	3.9	25	73	16	75	49	2	5	41	1.42
34313998--34314087	42	2.2	41	78	9	94	23	30	26	20	1.98
34317480--34317577	42	2.3	42	92	0	160	36	10	25	27	1.88
34320798--34320841	22	2.1	20	87	8	61	54	4	0	40	1.21
34327120--34327186	32	2.1	32	97	0	125	35	11	11	40	1.79
34329063--34329118	28	2.1	27	84	12	73	25	3	5	66	1.29
34329572--34329613	8	5.4	8	88	2	59	33	2	0	64	1.07
34346691--34346754	34	1.9	32	84	12	85	34	3	39	23	1.71
34354720--34354757	20	1.9	20	88	0	58	60	0	5	34	1.19
34356556--34356594	12	3.2	12	85	0	51	20	23	5	51	1.67
34356797--34357035	49	4.7	49	77	3	172	23	27	21	27	1.99
34378301--34378340	17	2.4	17	91	8	64	32	0	2	65	1.06
34378745--34378782	20	1.9	20	88	0	58	50	5	7	36	1.54
34382237--34382433	62	3.0	68	73	18	207	41	3	5	49	1.43
34383310--34383348	21	1.9	21	94	5	71	30	25	10	33	1.89
34390558--34390597	15	2.6	15	84	15	55	42	0	5	52	1.23
34398029--34398055	14	1.9	14	100	0	54	37	22	25	14	1.93
34407929--34407993	34	2.0	32	87	6	94	20	9	1	69	1.24
34408274--34408334	20	3.1	19	73	19	61	26	1	4	67	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34408273--34408331	21	2.9	19	75	18	57	25	1	5	67	1.20
34418478--34418502	12	2.1	12	100	0	50	60	0	24	16	1.36
34426735--34426777	15	2.7	16	85	7	52	65	16	0	18	1.28
34437222--34437259	19	2.1	19	95	5	69	39	26	5	28	1.78
34441200--34441240	15	2.7	15	88	0	64	21	7	24	46	1.77
34442758--34442785	3	9.3	3	100	0	56	67	32	0	0	0.91
34446336--34446616	140	2.0	140	99	0	553	36	19	17	26	1.94
34449861--34449898	17	2.2	17	90	0	58	13	5	31	50	1.63
34460154--34460287	39	3.4	40	82	5	148	42	30	14	11	1.82
34460158--34460292	40	3.4	40	84	2	164	43	28	14	12	1.82
34461952--34462008	13	4.4	13	82	4	62	52	14	5	28	1.62
34466995--34467032	18	2.1	19	85	5	51	71	13	2	13	1.26
34473012--34473049	16	2.4	17	82	13	53	36	0	52	10	1.36
34475190--34475223	16	2.1	16	88	0	50	58	11	5	23	1.55
34476622--34476646	10	2.5	10	100	0	50	24	32	8	36	1.84
34481639--34481673	16	2.1	17	89	5	54	37	0	51	11	1.38
34482123--34482151	14	2.1	14	100	0	58	51	0	6	41	1.28
34498831--34498932	35	2.9	35	75	4	116	26	28	11	33	1.92
34509406--34509489	4	20.5	4	78	18	77	22	3	0	73	0.98
34511169--34511203	15	2.4	15	90	4	54	48	0	8	42	1.33
34521539--34521657	57	2.1	58	82	1	141	46	8	19	26	1.78
34524384--34524454	34	2.1	34	97	0	133	40	25	14	19	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34527550--34527596	3	15.7	3	100	0	94	0	31	0	68	0.90
34528131--34528165	7	5.0	7	92	0	61	28	2	28	40	1.71
34529915--34529961	22	2.1	22	88	0	67	31	27	14	25	1.95
34529926--34530000	22	3.4	22	84	0	87	26	30	21	21	1.98
34529942--34530040	22	4.5	22	79	5	83	29	31	20	19	1.97
34529754--34530323	287	2.0	289	85	2	781	29	20	22	27	1.98
34530252--34530345	44	2.1	44	86	0	125	25	35	21	18	1.95
34530202--34530358	22	7.1	22	78	5	102	24	29	24	21	1.99
34539639--34539663	13	1.9	13	100	0	50	0	12	0	88	0.53
34540229--34540261	17	1.9	17	93	0	57	63	15	3	18	1.43
34542284--34542347	31	2.1	31	85	5	85	68	6	3	21	1.26
34542378--34542458	21	3.8	21	76	11	67	71	2	6	19	1.19
34546070--34546099	14	2.1	14	93	0	51	46	13	0	40	1.43
34549743--34549790	23	2.1	23	84	7	62	37	16	10	35	1.83
34553922--34553946	13	1.9	13	100	0	50	64	0	0	36	0.94
34567438--34567472	3	11.7	3	100	0	70	65	0	0	34	0.93
34568254--34568288	17	1.9	19	88	11	56	48	2	5	42	1.41
34572583--34572615	2	16.5	2	100	0	66	51	0	0	48	1.00
34583342--34583460	57	2.1	57	84	13	156	27	21	5	45	1.74
34601413--34601446	17	2.0	17	100	0	68	35	23	5	35	1.79
34605881--34605916	18	2.0	18	88	0	54	25	2	0	72	0.98
34615143--34615190	24	2.0	24	87	0	69	47	6	27	18	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34615240--34615421	21	8.7	21	78	0	141	14	24	18	42	1.88
34615259--34615416	42	3.8	42	79	1	165	15	24	18	41	1.89
34621489--34621557	14	4.6	14	67	22	50	66	0	5	27	1.14
34621463--34621516	20	2.8	19	79	17	58	70	0	5	24	1.08
34621487--34621581	47	2.0	47	100	0	190	63	0	6	30	1.19
34626415--34626468	19	2.8	19	79	17	58	68	3	5	22	1.26
34628634--34628666	17	1.9	17	93	0	57	63	12	0	24	1.28
34633174--34633204	4	7.8	4	100	0	62	77	0	22	0	0.77
34634518--34634615	13	7.5	14	74	20	54	48	0	2	48	1.12
34634548--34634591	23	2.0	22	86	13	63	47	0	4	47	1.22

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