genome.fa.s17.2.7.7.80.10.50.1000.19.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: D04
Parameters: 2 7 7 80 10 50 1000
Length:  56598092

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   

This is table  19  of  185  ( 22116 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)
5262778--5262821	20	2.2	20	87	0	61	68	4	2	25	1.20
5276840--5276879	21	1.9	21	84	0	53	45	37	5	12	1.64
5279039--5279070	16	1.9	17	93	6	57	43	0	0	56	0.99
5279069--5279108	16	2.5	16	91	0	62	47	2	7	42	1.45
5279044--5279093	22	2.3	22	85	0	64	52	2	2	44	1.24
5279119--5279258	59	2.4	59	98	0	271	39	4	9	47	1.55
5279240--5279267	9	3.1	9	100	0	56	32	0	10	57	1.33
5279367--5279410	24	1.9	24	90	9	74	61	2	0	36	1.09
5280334--5280379	22	2.1	22	84	8	58	2	19	13	65	1.37
5286269--5286302	7	4.9	7	92	0	50	29	8	26	35	1.87
5286270--5286318	21	2.3	21	89	10	73	28	4	28	38	1.75
5286464--5286496	14	2.4	14	94	0	57	3	6	18	72	1.18
5290971--5291019	21	2.3	21	89	10	73	30	4	26	38	1.75
5298625--5298691	31	2.2	31	89	5	100	22	20	11	44	1.84
5300231--5300306	30	2.5	31	82	2	91	35	9	13	42	1.76
5309328--5309419	27	3.4	27	90	3	141	20	20	36	21	1.95
5309481--5309527	18	2.5	20	79	10	62	63	2	34	0	1.06
5309477--5309530	22	2.4	23	84	12	76	64	1	33	0	1.04
5310324--5310659	19	18.5	19	63	24	88	54	12	0	32	1.43
5310318--5310530	49	4.3	49	86	5	304	53	13	0	32	1.46
5310318--5310530	97	2.2	99	92	3	358	53	13	0	32	1.46
5310484--5310549	19	3.1	21	82	12	91	54	12	0	33	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5310483--5310657	41	4.4	41	68	20	129	56	12	0	31	1.37
5310596--5310657	22	3.0	21	90	4	90	58	9	0	32	1.31
5310483--5310693	115	1.8	116	84	11	288	54	12	0	31	1.42
5310823--5310860	14	2.5	15	87	12	60	0	39	0	60	0.97
5311115--5311157	17	2.6	16	85	3	50	37	0	0	62	0.95
5324079--5324115	3	12.3	3	100	0	74	67	0	0	32	0.91
5331888--5331943	29	1.9	29	88	0	85	50	7	21	21	1.72
5332485--5332532	13	3.5	13	78	15	51	50	2	2	45	1.25
5333120--5333164	3	15.3	3	90	4	74	64	0	35	0	0.94
5333112--5333160	20	2.5	20	93	0	80	61	0	38	0	0.96
5333112--5333163	23	2.3	23	93	0	86	61	0	38	0	0.96
5333335--5333520	22	9.0	21	72	15	154	32	0	12	54	1.42
5333335--5333520	41	4.5	40	73	17	166	32	0	12	54	1.42
5333618--5333675	22	2.9	19	71	14	53	34	1	12	51	1.49
5333469--5333691	97	2.3	99	92	3	369	32	1	13	53	1.48
5333469--5333692	49	4.5	49	85	8	319	32	1	13	53	1.48
5333892--5333965	37	1.9	39	91	5	125	54	4	2	39	1.34
5335739--5335791	6	8.8	6	85	0	70	32	28	37	1	1.68
5338997--5339336	19	18.5	19	66	23	151	54	12	0	32	1.41
5339002--5339201	74	2.7	75	76	19	209	53	13	0	33	1.43
5339003--5339334	22	14.9	22	67	21	151	55	12	0	31	1.41
5339095--5339334	41	5.5	42	71	19	165	55	12	0	31	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5339003--5339043	21	2.0	21	95	0	73	53	14	2	29	1.54
5338991--5339201	52	4.3	51	83	10	271	54	13	0	32	1.43
5338991--5339201	48	4.3	48	85	8	300	54	13	0	32	1.43
5339505--5339561	3	19.3	3	92	3	98	0	35	0	64	0.93
5341247--5341315	34	2.1	34	83	8	88	40	18	4	36	1.71
5345596--5345637	9	4.7	9	80	8	50	33	0	0	66	0.92
5351611--5351666	29	1.9	29	82	7	69	30	16	16	37	1.90
5351830--5351923	48	2.0	48	85	8	129	40	26	12	20	1.88
5354346--5354439	48	2.0	48	85	8	129	40	26	12	20	1.88
5355726--5355785	29	2.1	28	81	6	68	46	18	11	23	1.81
5379851--5379885	5	7.0	5	100	0	70	60	0	0	40	0.97
5382958--5382983	6	4.3	6	100	0	52	53	15	0	30	1.42
5386109--5386144	18	2.0	18	100	0	72	33	22	5	38	1.77
5386328--5386380	25	2.1	25	89	0	79	37	13	9	39	1.77
5386561--5386625	23	2.8	24	90	4	91	32	20	29	18	1.96
5387769--5387838	8	9.0	8	68	6	54	57	2	4	35	1.33
5387767--5387838	24	3.1	23	84	9	85	56	2	4	36	1.33
5395649--5395697	5	9.4	5	80	6	53	71	4	4	20	1.19
5396075--5396100	12	2.2	12	100	0	52	38	0	15	46	1.46
5404172--5404220	21	2.3	20	80	10	53	71	2	4	22	1.13
5404180--5404227	20	2.3	20	80	13	53	70	0	4	25	1.04
5407026--5407069	14	3.1	14	80	6	52	34	6	15	43	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5409155--5409200	20	2.2	21	81	14	60	63	19	6	10	1.48
5411084--5411297	109	2.0	109	80	5	245	31	19	14	33	1.93
5411289--5411321	16	2.1	16	88	5	50	63	12	0	24	1.28
5415801--5415838	16	2.4	16	86	4	51	60	0	2	36	1.11
5417884--5417923	20	2.0	20	85	9	55	55	25	17	2	1.55
5420347--5420387	20	2.0	20	90	9	66	36	2	2	58	1.24
5422178--5422209	6	5.3	6	100	0	64	15	0	0	84	0.63
5422170--5422210	18	2.3	19	83	12	59	24	0	0	75	0.80
5431604--5431674	24	2.9	24	81	8	81	11	16	14	57	1.64
5437090--5437130	21	2.0	21	95	0	73	31	21	26	19	1.97
5451043--5451106	15	4.1	15	78	11	65	29	45	1	23	1.62
5451043--5451120	6	13.0	6	78	5	50	28	42	1	28	1.64
5451043--5451120	9	8.7	9	73	5	50	28	42	1	28	1.64
5455349--5455492	72	2.0	72	97	0	270	32	13	22	31	1.92
5465926--5466139	44	4.5	44	75	17	205	32	15	22	29	1.95
5466017--5466048	7	4.6	7	96	0	55	40	9	31	18	1.83
5465973--5466086	58	2.0	58	92	0	192	35	14	21	28	1.93
5465929--5466137	102	2.0	102	93	0	355	32	15	22	29	1.95
5467345--5467416	30	2.4	31	84	11	103	29	18	13	38	1.89
5468229--5468258	7	4.3	7	95	0	51	43	40	0	16	1.48
5477058--5477082	13	1.9	13	100	0	50	32	0	4	64	1.12
5491179--5491226	24	2.0	24	91	0	78	41	20	12	25	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5491702--5491735	17	2.0	18	88	11	54	26	0	17	55	1.42
5509419--5509455	13	2.8	13	87	0	56	45	21	0	32	1.52
5515197--5515392	96	2.0	96	99	0	383	33	22	15	28	1.95
5520915--5520958	22	1.9	24	86	9	65	43	2	13	40	1.57
5521047--5521238	97	2.0	97	95	0	348	43	13	11	31	1.80
5521326--5521369	20	2.2	20	84	8	54	27	11	15	45	1.81
5522894--5522984	27	3.4	27	83	6	112	27	23	26	23	2.00
5523283--5523320	20	1.9	20	88	0	58	36	7	10	44	1.68
5528290--5528408	60	2.0	60	91	0	193	52	11	0	35	1.44
5528312--5528429	60	2.0	59	85	5	139	55	11	1	32	1.45
5528660--5528731	27	2.7	27	80	0	72	18	27	26	27	1.98
5529584--5529647	3	21.3	3	100	0	128	65	0	34	0	0.93
5562954--5563096	60	2.4	59	88	2	196	47	13	15	23	1.81
5582005--5582134	57	2.3	56	79	15	133	32	17	10	39	1.84
5592638--5592687	20	2.5	19	84	9	64	36	2	10	52	1.47
5600954--5601148	97	2.0	97	96	0	363	36	17	15	30	1.91
5602760--5602883	28	4.4	27	79	8	99	24	22	18	34	1.96
5602915--5602979	24	2.9	22	73	8	67	26	29	21	23	1.99
5619457--5619498	21	2.0	21	85	0	57	26	9	14	50	1.73
5623164--5623195	15	2.2	14	94	5	55	25	31	0	43	1.55
5623917--5623948	16	2.1	16	88	11	50	34	0	0	65	0.93
5623915--5623954	19	2.0	19	85	9	53	37	0	0	62	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5625805--5625888	28	3.1	26	70	21	66	58	3	2	35	1.28
5639365--5639396	2	16.0	2	100	0	64	50	0	50	0	1.00
5639518--5639568	23	2.2	23	89	0	75	25	13	29	31	1.94
5652345--5652382	18	2.1	18	95	0	67	0	55	0	44	0.99
5652442--5652491	25	2.0	25	84	0	64	4	28	4	64	1.30
5655821--5655873	15	3.2	15	80	17	52	54	1	1	41	1.22
5655904--5655942	20	2.0	20	94	0	69	48	0	2	48	1.15
5662280--5662422	71	2.0	69	95	2	259	35	18	6	39	1.76
5663926--5663960	15	2.4	15	90	4	54	48	0	8	42	1.33
5665786--5665940	26	6.2	25	69	13	90	35	23	23	17	1.95

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