genome.fa.s15.2.7.7.80.10.50.1000.9.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: D02
Parameters: 2 7 7 80 10 50 1000
Length:  70731513

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   

This is table  9  of  222  ( 26535 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)
3005545--3005601	21	2.8	21	86	7	73	36	0	7	56	1.27
3016905--3017165	50	5.5	50	71	21	173	31	20	18	29	1.97
3017059--3017209	44	3.3	44	70	21	121	34	19	19	26	1.96
3016902--3017267	94	3.9	94	86	2	493	32	20	19	27	1.97
3019400--3019612	106	2.0	106	87	1	311	30	16	13	39	1.87
3026474--3026677	72	2.8	72	79	2	239	29	19	17	33	1.95
3054731--3054784	27	2.0	27	100	0	108	25	18	37	18	1.94
3055580--3056513	193	4.8	193	92	0	1449	35	15	19	29	1.93
3055580--3056513	385	2.4	386	90	1	1462	35	15	19	29	1.93
3057791--3057878	2	44.0	2	100	0	176	50	0	50	0	1.00
3074120--3074148	6	4.8	6	100	0	58	0	51	0	48	1.00
3078752--3078829	24	3.1	24	72	16	77	33	23	17	25	1.96
3085983--3086017	7	4.9	7	96	3	61	45	0	11	42	1.40
3086176--3086241	28	2.4	28	80	10	82	42	1	4	51	1.31
3091475--3091512	16	2.2	18	86	9	53	31	15	2	50	1.58
3096404--3096452	25	2.0	25	88	4	73	36	6	0	57	1.24
3096433--3096461	14	2.1	14	93	6	51	34	0	0	65	0.93
3096976--3097062	45	1.9	46	83	4	115	43	1	6	48	1.37
3098248--3098299	24	2.2	24	82	0	59	50	5	3	40	1.45
3100900--3100977	29	2.6	30	75	17	81	28	10	5	56	1.54
3112927--3113031	52	2.0	52	100	0	210	52	11	7	28	1.65
3115798--3116128	161	2.1	161	98	0	646	34	19	13	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3125950--3125997	11	4.3	11	76	5	51	25	8	2	64	1.32
3142772--3142800	14	2.1	14	93	6	51	41	0	0	58	0.98
3142870--3142912	19	2.4	18	81	11	52	44	9	0	46	1.35
3143680--3143741	29	2.2	29	85	8	83	43	11	1	43	1.50
3144002--3144036	17	2.1	17	89	5	54	40	0	0	60	0.97
3147489--3147545	30	1.9	30	85	7	80	36	3	7	52	1.46
3154043--3154081	16	2.4	16	87	8	53	41	17	5	35	1.72
3158549--3158590	16	2.6	16	80	0	57	35	0	16	47	1.47
3170873--3171009	65	2.1	65	81	0	157	29	31	19	19	1.97
3190296--3190332	19	1.9	19	94	0	65	27	10	24	37	1.88
3193165--3193198	17	2.0	17	100	0	68	41	0	0	58	0.98
3193127--3193238	54	2.1	55	81	8	131	44	1	3	50	1.29
3193358--3193450	46	2.1	44	89	4	141	36	30	4	29	1.77
3193432--3193497	16	4.1	16	94	0	105	24	33	4	37	1.76
3206702--3206782	31	2.6	31	82	0	99	37	13	19	29	1.90
3213664--3213706	21	2.0	21	86	8	61	67	0	2	30	1.03
3213673--3213706	10	3.3	10	84	8	50	70	0	0	29	0.87
3214146--3214207	30	2.1	30	100	0	124	48	9	19	22	1.78
3214312--3214368	24	2.4	25	88	5	82	45	0	0	54	0.99
3214759--3214784	7	3.7	7	100	0	52	84	0	0	15	0.62
3217547--3217595	24	2.1	24	85	7	66	48	6	12	32	1.65
3222045--3222120	25	2.6	31	73	25	85	50	5	7	36	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3226093--3226173	41	2.0	41	97	0	153	30	17	24	27	1.97
3228419--3228461	19	2.3	19	95	0	77	34	23	16	25	1.95
3233690--3233733	20	2.2	20	84	8	54	40	0	15	43	1.47
3234069--3234107	4	9.8	4	94	0	60	76	5	0	17	0.96
3238291--3238336	22	2.2	21	88	7	67	26	0	2	71	0.97
3238319--3238371	14	3.7	14	78	12	54	35	0	3	60	1.15
3243608--3243635	13	2.2	13	100	0	56	32	32	0	35	1.58
3244179--3244271	18	5.2	18	81	0	105	34	15	20	30	1.93
3244177--3244271	36	2.6	37	91	3	149	33	15	20	30	1.94
3244804--3244846	11	4.0	11	84	3	61	30	2	46	20	1.63
3244804--3244846	21	2.0	21	90	4	68	30	2	46	20	1.63
3246497--3246525	9	3.3	9	95	4	51	44	6	0	48	1.29
3254370--3254992	252	2.5	252	97	1	1160	38	15	11	35	1.82
3256447--3256548	35	2.9	34	81	4	123	24	7	15	51	1.70
3258167--3258209	21	2.0	22	81	4	52	62	4	2	30	1.28
3265554--3265602	22	2.3	22	89	3	73	38	4	0	57	1.18
3267673--3267764	5	20.4	5	80	10	78	34	3	1	60	1.20
3267678--3267761	32	2.6	32	87	9	118	34	3	1	60	1.21
3268568--3268608	3	13.7	3	89	0	55	34	4	2	58	1.32
3269831--3269874	20	2.2	20	84	8	54	40	0	15	43	1.47
3270200--3270238	4	9.8	4	88	0	60	79	2	0	17	0.84
3270635--3270660	8	3.2	8	100	0	52	88	0	11	0	0.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3270792--3270824	5	6.6	5	100	0	66	78	0	0	21	0.75
3271873--3272548	133	5.1	131	72	5	444	29	24	16	30	1.96
3271962--3272137	89	2.0	89	88	0	262	28	24	16	30	1.96
3271989--3272541	89	6.2	90	70	7	220	29	23	16	30	1.96
3271873--3272286	222	1.9	221	90	1	659	28	24	15	30	1.96
3271940--3272548	44	13.7	44	69	8	266	29	23	16	30	1.96
3272080--3272479	177	2.3	178	89	1	624	30	23	16	30	1.96
3271967--3272548	177	3.3	177	80	3	591	29	24	16	30	1.96
3282901--3282944	20	2.2	20	84	8	54	40	0	15	43	1.47
3283267--3283305	4	9.8	4	94	0	60	76	5	0	17	0.96
3283708--3283732	13	1.9	13	100	0	50	88	0	0	12	0.53
3287485--3287530	22	2.2	21	88	7	67	26	0	2	71	0.97
3287513--3287565	14	3.7	14	78	12	54	35	0	3	60	1.15
3293215--3293243	9	3.3	9	95	4	51	44	6	0	48	1.29
3297475--3297568	23	4.1	23	87	0	125	48	4	24	22	1.68
3310018--3310060	19	2.3	19	95	0	77	34	23	16	25	1.95
3311457--3311487	15	2.1	15	100	0	62	38	6	32	22	1.80
3313079--3313107	15	1.9	15	100	0	58	41	6	34	17	1.76
3313266--3313304	18	2.3	17	86	8	53	38	5	12	43	1.65
3320024--3320103	26	3.0	26	75	10	99	42	10	10	37	1.72
3320013--3320093	27	3.0	27	75	10	103	41	11	12	34	1.78
3319991--3320148	53	3.0	53	80	9	198	39	9	11	39	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3321654--3321755	35	2.9	34	81	4	123	24	7	15	51	1.70
3323121--3323265	73	2.0	73	90	0	227	28	15	17	38	1.90
3326994--3327052	26	2.3	26	82	8	68	42	3	1	52	1.28
3332869--3332935	31	2.2	31	86	0	89	38	16	7	37	1.77
3341197--3341250	16	3.3	15	80	15	54	50	11	7	31	1.66
3341320--3341355	17	2.2	17	90	5	56	47	8	8	36	1.64
3341550--3341587	20	1.9	20	88	0	58	42	7	13	36	1.73
3342602--3342703	30	3.4	30	81	5	118	46	3	20	29	1.69
3342973--3343399	54	8.0	54	88	6	642	37	17	15	29	1.91
3342973--3343392	104	4.0	103	90	5	653	37	17	15	29	1.91
3342973--3343399	211	2.0	213	94	2	743	37	17	15	29	1.91
3343347--3344753	72	19.7	72	92	3	2276	34	17	16	31	1.92
3343347--3344753	217	6.6	216	92	3	2294	34	17	16	31	1.92
3343347--3344753	289	4.9	289	93	2	2307	34	17	16	31	1.92
3344757--3344930	68	2.5	70	85	2	210	32	21	14	31	1.93
3356658--3356721	17	3.4	19	73	18	62	39	10	10	39	1.76
3356654--3356725	38	1.9	38	91	8	121	40	11	13	34	1.81
3356662--3356729	18	3.7	17	74	16	57	41	13	11	33	1.81
3356679--3356744	19	3.5	20	72	14	59	39	10	13	36	1.80
3356715--3356782	17	3.9	17	73	9	66	41	10	19	29	1.84
3356808--3356890	17	4.9	17	77	9	82	57	10	9	21	1.61
3356883--3356929	23	2.1	21	92	7	76	48	10	2	38	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3356775--3357009	127	1.8	129	89	3	375	51	10	8	29	1.67
3356935--3357046	17	6.4	17	79	14	113	50	9	13	26	1.73
3356935--3357045	35	3.2	35	82	10	113	50	9	13	26	1.72
3356775--3357087	127	2.4	127	84	7	373	49	9	9	30	1.67
3358338--3358454	30	3.9	29	77	11	94	44	3	21	30	1.69
3358353--3358454	30	3.4	30	83	2	125	44	3	21	30	1.70
3358450--3358486	15	2.4	16	90	4	58	24	0	2	72	0.97
3358452--3358486	16	2.2	16	89	0	52	20	0	2	77	0.90
3362674--3362708	17	2.0	18	88	5	54	45	5	5	42	1.51
3362676--3362716	17	2.5	17	80	11	50	39	2	7	51	1.43

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