genome.fa.s1.2.7.7.80.10.50.1000.128.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  128  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)
38869597--38869624	14	2.0	14	100	0	56	57	0	7	35	1.26
38874145--38874480	169	2.0	170	97	0	629	42	21	11	24	1.85
38876099--38876175	38	2.0	39	94	2	138	19	24	22	33	1.97
38884834--38884858	12	2.1	12	100	0	50	24	40	28	8	1.83
38891414--38891521	50	2.2	49	79	9	121	30	2	11	55	1.49
38891720--38891955	82	2.9	81	84	6	280	32	13	7	47	1.71
38892061--38892091	12	2.5	13	94	5	55	19	6	25	48	1.72
38892067--38892121	28	1.9	29	85	3	76	29	10	20	40	1.86
38896309--38896452	40	3.6	40	74	11	105	38	19	18	23	1.93
38896482--38896797	41	7.5	41	77	10	271	19	20	26	33	1.97
38896596--38896700	52	2.0	52	83	3	131	19	21	26	32	1.97
38896561--38896736	93	1.9	93	87	6	259	20	21	27	30	1.98
38897264--38897301	14	2.8	13	88	7	58	34	15	23	26	1.95
38900758--38901028	43	6.3	43	90	0	400	21	17	33	27	1.96
38902534--38902803	43	6.3	43	83	4	332	29	31	16	22	1.96
38902534--38902803	85	3.2	86	82	4	350	29	31	16	22	1.96
38907318--38907359	21	2.0	22	95	4	77	23	0	47	28	1.52
38907756--38907799	8	5.8	8	81	10	56	38	43	0	18	1.50
38907773--38907820	15	3.3	15	85	8	55	39	41	0	18	1.51
38907829--38907868	15	2.8	14	85	7	53	47	27	0	25	1.52
38909191--38909463	41	6.1	41	76	20	253	32	29	20	17	1.95
38909240--38909428	52	3.8	52	80	18	260	31	30	21	16	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38909201--38909463	93	2.8	93	94	1	456	31	30	20	17	1.96
38909507--38909621	40	2.9	39	84	3	140	25	20	20	33	1.97
38912757--38912814	6	9.7	6	100	0	116	0	65	0	34	0.93
38916714--38916757	22	2.0	23	86	4	63	43	9	2	45	1.48
38917647--38917681	17	2.0	18	94	5	63	74	0	0	25	0.82
38917780--38917821	15	3.3	12	87	12	50	59	0	9	30	1.29
38917816--38917874	10	5.6	10	78	9	64	66	1	0	32	1.02
38917856--38917939	25	3.4	25	78	18	70	61	1	4	32	1.24
38917918--38917956	18	2.2	17	90	4	60	69	0	0	30	0.89
38917859--38917958	43	2.4	42	77	12	107	65	1	4	30	1.18
38917918--38917959	9	4.7	9	80	11	50	66	0	0	33	0.92
38922636--38922695	31	2.0	31	83	3	77	45	5	11	38	1.63
38922749--38922886	41	3.4	41	72	11	138	28	22	16	31	1.96
38922725--38922900	82	2.1	82	89	0	262	26	18	19	34	1.95
38923226--38923302	34	2.3	32	82	13	84	25	2	5	66	1.26
38925753--38925804	20	2.8	18	76	21	54	50	3	3	42	1.39
38925720--38925864	68	2.1	71	79	7	154	51	4	4	40	1.43
38929299--38929476	89	2.0	89	91	0	284	23	32	17	25	1.97
38936426--38936495	26	2.7	26	75	0	77	24	20	30	25	1.99
38939813--38939867	5	11.0	5	84	7	76	41	20	0	38	1.52
38945707--38945756	20	2.7	18	79	14	57	52	2	2	44	1.24
38953236--38953340	39	2.7	38	86	2	147	38	5	8	47	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38954335--38954396	29	2.1	29	82	5	72	29	20	9	40	1.84
38960156--38960216	26	2.3	26	82	0	77	22	18	18	40	1.91
38961073--38961101	2	14.5	2	100	0	58	48	0	0	51	1.00
38963710--38963734	11	2.3	11	100	0	50	28	0	36	36	1.58
38980903--38981036	46	2.9	45	80	8	128	31	22	20	26	1.98
38984906--38984982	36	2.1	36	83	9	95	59	5	3	31	1.37
38985931--38985974	22	2.0	22	95	0	79	47	13	11	27	1.77
38986509--38986567	20	3.1	19	78	14	68	64	0	5	30	1.15
38986744--38986807	19	3.2	19	69	16	56	3	45	18	32	1.65
38996509--38996546	18	2.1	18	95	0	67	57	0	7	34	1.28
39003236--39003311	40	2.0	40	84	5	102	53	2	7	35	1.44
39009141--39009172	15	2.1	15	94	0	55	15	6	9	68	1.36
39010280--39010306	14	1.9	14	100	0	54	51	0	11	37	1.37
39011050--39011100	25	2.0	26	84	3	68	39	5	11	43	1.66
39013116--39013169	22	2.5	21	81	6	63	31	5	0	62	1.18
39015734--39015762	2	14.5	2	100	0	58	51	0	48	0	1.00
39021376--39021443	25	2.6	26	93	4	111	41	10	1	47	1.47
39021498--39021564	27	2.5	27	97	0	125	25	29	31	13	1.94
39021857--39021941	3	28.7	3	97	2	163	34	0	0	65	0.93
39022672--39022716	18	2.5	18	85	0	63	28	4	46	20	1.69
39026207--39026246	17	2.4	17	86	0	53	10	2	2	85	0.80
39026217--39026248	16	2.0	16	93	0	55	9	0	6	84	0.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39026249--39026318	29	2.6	27	86	13	92	47	1	10	41	1.46
39026353--39026389	19	2.0	18	89	5	56	70	5	0	24	1.08
39026353--39026402	17	2.8	17	84	6	55	66	8	0	26	1.19
39027121--39027247	10	12.8	10	70	18	79	1	31	0	66	1.01
39027121--39027233	38	3.1	37	85	8	126	1	31	0	66	1.02
39027154--39027264	18	6.1	18	74	15	95	1	31	0	66	1.02
39027146--39027255	38	2.9	38	89	2	150	1	33	0	64	1.04
39027175--39027249	34	2.1	36	85	9	100	1	34	0	64	1.02
39027196--39027267	10	6.6	10	73	17	54	1	30	0	68	0.99
39027185--39027267	28	2.8	29	74	22	82	1	31	0	67	0.98
39027369--39027414	19	2.4	18	92	7	74	2	4	6	86	0.75
39027368--39027414	20	2.4	19	89	3	76	2	4	8	85	0.81
39027416--39027484	28	2.5	29	90	6	108	49	1	10	39	1.46
39038894--39038932	18	2.2	18	90	9	62	71	2	20	5	1.17
39040699--39040770	33	2.1	34	92	2	119	38	6	13	40	1.72
39048805--39048844	20	2.0	20	90	0	62	35	5	0	60	1.19
39049741--39049789	24	2.0	24	100	0	98	55	12	8	24	1.64
39053534--39053649	41	2.8	42	85	5	155	29	26	19	24	1.99
39053827--39053872	2	23.0	2	100	0	92	50	0	0	50	1.00
39054584--39054627	15	3.1	14	80	12	54	43	6	0	50	1.29
39056685--39056739	22	2.5	22	96	0	101	10	16	27	45	1.80
39059051--39059089	20	2.0	20	90	10	62	35	20	33	10	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39072990--39073103	44	2.6	44	83	2	131	22	28	13	35	1.92
39081133--39081184	21	2.5	21	87	0	77	30	17	26	25	1.97
39082534--39082594	20	3.1	18	82	15	68	44	21	27	6	1.77
39088211--39088311	32	3.2	32	62	29	79	32	21	14	30	1.94
39088212--39088340	64	2.0	64	98	0	249	34	24	11	30	1.91
39089458--39089487	13	2.3	13	94	0	51	10	23	0	66	1.21
39093102--39093271	48	3.5	48	86	0	214	25	20	30	24	1.99
39093336--39093361	2	13.0	2	100	0	52	50	0	0	50	1.00
39100107--39100225	48	2.5	48	83	2	159	27	23	26	22	2.00
39108473--39108515	18	2.4	18	84	7	61	62	9	4	23	1.44
39112414--39112468	20	2.8	20	81	10	67	47	20	20	12	1.82
39117515--39117578	32	2.0	32	100	0	128	25	12	15	46	1.81
39118908--39119309	201	2.0	201	98	0	768	33	17	14	33	1.91
39121717--39121757	17	2.3	18	80	12	50	68	4	2	24	1.22
39126144--39126189	24	2.0	24	82	4	58	43	0	34	21	1.53
39128290--39128322	17	1.9	17	88	11	50	21	9	3	66	1.33
39129591--39129704	61	1.9	58	89	5	174	42	1	5	50	1.35
39129597--39129726	58	2.2	61	82	9	153	42	3	6	48	1.43
39132877--39134174	259	5.0	259	94	0	2227	31	15	18	34	1.92
39134438--39134481	5	9.0	5	85	5	63	40	2	0	56	1.11
39137096--39137238	41	3.4	42	79	7	157	35	24	16	23	1.94
39137134--39137241	43	2.6	40	81	8	126	34	25	17	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39137180--39137306	67	1.9	68	82	8	161	32	25	15	26	1.96
39137253--39137347	41	2.3	41	83	3	120	28	25	15	30	1.96
39140381--39140448	15	4.2	16	73	12	68	73	4	19	2	1.13
39140384--39140460	16	4.8	16	76	12	52	70	3	23	2	1.17
39141139--39141194	2	28.0	2	100	0	112	0	0	50	50	1.00
39142368--39142401	11	3.0	11	91	4	50	23	0	5	70	1.09
39148494--39148553	29	2.1	29	96	0	111	41	13	16	28	1.86
39153699--39153957	43	6.0	43	87	3	344	27	29	17	26	1.97
39153725--39153957	85	2.7	84	88	6	335	27	30	17	24	1.97
39154221--39154305	43	2.0	43	88	0	125	45	11	7	35	1.68

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