genome.fa.s17.2.7.7.80.10.50.1000.181.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  181  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)
55166748--55166783	15	2.3	16	90	4	56	36	2	0	61	1.11
55174040--55174131	38	2.3	40	83	7	116	40	1	7	51	1.38
55181520--55181634	39	2.9	39	64	19	94	37	19	4	39	1.71
55182607--55182638	12	2.6	13	85	14	50	56	6	0	37	1.25
55185644--55185668	5	5.0	5	100	0	50	40	0	0	60	0.97
55186760--55186792	17	1.9	17	88	11	50	39	21	9	30	1.84
55187562--55187720	86	1.8	86	82	5	205	32	18	23	25	1.97
55188137--55188176	17	2.3	18	86	4	55	55	5	0	40	1.22
55188142--55188194	25	2.2	24	83	10	63	54	5	1	37	1.35
55188548--55188581	18	1.9	17	94	5	59	0	58	0	41	0.98
55188641--55188703	25	2.4	27	77	17	71	4	33	1	60	1.27
55191491--55191567	14	5.0	15	71	20	52	42	14	9	33	1.77
55191507--55191546	20	2.0	20	90	0	62	50	12	10	27	1.72
55191495--55191561	34	1.9	35	90	3	109	46	13	8	31	1.74
55193004--55193036	16	2.1	16	100	0	66	48	27	0	24	1.51
55193531--55194246	205	3.5	204	86	3	891	18	15	12	52	1.74
55194331--55194597	112	2.4	111	81	9	305	20	11	13	53	1.70
55198940--55198980	22	1.9	21	85	5	55	39	24	7	29	1.82
55208532--55208875	124	2.8	124	93	0	564	27	14	22	35	1.93
55211851--55212052	37	5.5	37	98	0	377	50	3	6	39	1.46
55212048--55212849	29	27.6	29	88	2	1092	23	0	30	45	1.53
55214029--55214054	7	3.7	7	100	0	52	57	15	0	26	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55215231--55215278	22	2.2	22	96	0	87	43	0	31	25	1.55
55215191--55215356	73	2.3	73	93	0	287	45	1	27	25	1.61
55215303--55215351	22	2.2	22	88	0	71	44	2	30	22	1.64
55216078--55216790	175	4.1	175	88	1	984	21	12	22	43	1.86
55217040--55217095	25	2.2	24	75	9	58	48	21	3	26	1.66
55217052--55217109	25	2.4	25	85	2	73	46	25	1	25	1.62
55220094--55220161	31	2.2	31	89	0	109	52	19	5	22	1.66
55223843--55223879	10	3.6	10	85	7	56	10	10	2	75	1.14
55223839--55223887	21	2.4	20	76	6	62	12	12	2	73	1.18
55240328--55240391	31	2.1	31	100	0	128	40	15	9	34	1.80
55242022--55242072	25	2.0	26	84	3	68	62	5	5	25	1.41
55242200--55242250	15	3.5	15	69	15	52	52	15	9	21	1.71
55251249--55251273	13	1.9	13	100	0	50	40	44	0	16	1.47
55251260--55251376	19	5.5	19	67	21	63	41	34	1	22	1.64
55251277--55251357	25	3.5	24	71	21	84	44	32	2	20	1.65
55251257--55251379	44	2.8	44	95	1	221	43	33	1	21	1.63
55274832--55274869	13	2.9	13	100	0	76	39	28	7	23	1.83
55275988--55276242	87	2.9	87	83	4	327	46	18	11	23	1.82
55280694--55280793	31	3.2	31	76	5	94	24	21	21	34	1.97
55287303--55287335	15	2.2	15	89	10	50	0	30	18	51	1.46
55290561--55290599	18	2.2	18	86	9	53	53	0	0	46	1.00
55295581--55295605	9	2.8	9	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55295805--55295942	69	2.0	69	91	2	224	31	12	10	45	1.75
55296443--55296487	18	2.4	18	85	3	63	35	6	11	46	1.66
55301885--55301943	30	1.9	31	89	3	93	47	16	6	28	1.72
55303622--55303652	3	10.3	3	100	0	62	35	0	0	64	0.94
55305295--55305356	23	2.7	23	85	2	81	50	1	1	46	1.20
55305332--55305371	16	2.5	16	91	0	62	47	2	7	42	1.45
55305382--55305551	59	2.9	59	92	0	295	40	5	9	45	1.59
55305422--55305500	20	4.0	20	65	21	58	39	5	8	46	1.57
55305618--55305661	24	1.9	24	90	9	74	61	2	0	36	1.09
55307208--55307295	30	2.9	30	88	8	126	35	3	0	61	1.13
55307181--55307297	40	3.2	39	74	22	135	34	3	0	61	1.19
55307261--55307303	11	3.9	11	82	11	61	41	2	0	55	1.12
55315602--55315864	132	2.0	131	85	4	359	28	15	19	35	1.93
55316343--55316371	10	2.9	10	100	0	58	10	20	20	48	1.79
55316343--55316381	20	2.0	20	85	10	53	12	20	20	46	1.83
55321629--55321671	18	2.3	19	84	15	54	30	2	2	65	1.18
55329457--55329503	24	2.0	24	86	0	67	57	4	0	38	1.18
55329485--55329529	9	4.7	9	81	10	54	71	2	2	24	1.09
55334692--55334753	30	2.0	30	87	3	88	48	8	14	29	1.72
55337666--55337691	11	2.4	11	100	0	52	0	7	15	76	0.99
55338831--55338983	58	2.6	59	77	10	159	29	23	14	32	1.94
55342572--55343197	262	2.4	262	89	1	923	35	19	14	29	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55346396--55346441	22	2.1	22	100	0	92	30	8	17	43	1.79
55356449--55356476	2	14.0	2	100	0	56	0	0	50	50	1.00
55357471--55357520	8	6.9	8	82	13	56	22	0	2	76	0.89
55358799--55358844	24	1.9	24	82	8	58	54	6	0	39	1.26
55361633--55361815	96	1.9	95	84	7	246	45	16	6	31	1.73
55369885--55369918	4	8.2	4	87	6	50	47	2	0	50	1.16
55372924--55372992	26	2.6	27	73	13	72	55	0	0	44	0.99
55382852--55383196	147	2.3	147	90	2	541	28	20	23	28	1.99
55390390--55390424	12	2.9	12	95	0	61	65	2	25	5	1.28
55394470--55394529	30	2.0	30	83	6	77	31	15	11	41	1.82
55397778--55397829	16	3.2	16	75	17	54	23	1	3	71	1.13
55400566--55400597	6	5.3	6	100	0	64	50	15	0	34	1.45
55402103--55402135	16	2.1	16	88	11	50	42	0	9	48	1.35
55404870--55404920	15	3.1	16	80	11	50	43	1	0	54	1.11
55404885--55404938	26	2.2	25	81	12	67	42	5	0	51	1.25
55404973--55405014	20	2.0	22	86	9	61	45	0	0	54	0.99
55405080--55405136	15	3.5	15	73	17	60	52	1	0	45	1.11
55406419--55406473	23	2.3	24	81	6	67	41	1	5	50	1.36
55408844--55408884	15	2.7	15	80	0	55	26	9	2	60	1.40
55410961--55411012	25	2.1	25	85	0	68	63	1	0	34	1.06
55411037--55411099	20	2.9	23	69	23	55	4	60	6	28	1.42
55412258--55412300	18	2.4	18	76	3	52	30	2	0	67	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55412644--55412688	21	2.1	22	84	12	58	44	11	11	33	1.75
55420537--55420589	23	2.4	22	76	20	56	9	18	1	69	1.25
55435626--55435838	110	1.9	110	84	0	282	39	22	10	27	1.87
55438092--55438141	18	2.9	18	83	13	61	36	4	14	46	1.63
55441659--55441700	16	2.7	15	85	7	66	28	23	23	23	2.00
55443054--55443085	13	2.3	15	89	10	50	40	0	6	53	1.26
55444440--55444790	90	3.8	90	84	5	438	22	17	25	34	1.96
55444723--55444861	70	2.0	70	85	0	188	23	19	20	37	1.94
55471366--55471406	20	2.0	20	95	0	73	29	21	17	31	1.96
55474178--55474339	30	5.4	30	79	9	163	40	1	22	35	1.65
55474148--55474339	89	2.1	89	79	10	205	41	3	21	33	1.69
55474201--55474341	59	2.4	59	79	5	160	40	2	23	34	1.67
55474652--55475600	75	12.6	74	92	3	1296	34	20	16	28	1.94
55474652--55475600	151	6.3	149	91	4	1332	34	20	16	28	1.94
55476469--55476549	1	81.0	1	72	0	63	1	4	7	86	0.75
55476475--55476538	17	3.8	17	89	4	94	0	4	7	87	0.66
55476475--55476537	8	7.6	8	91	7	90	0	4	7	87	0.67
55480510--55480534	4	6.2	4	100	0	50	52	0	24	24	1.48
55482220--55482311	17	5.3	16	71	17	69	45	9	7	36	1.66
55482216--55482283	35	1.9	36	87	3	102	45	8	5	39	1.60
55482255--55482333	18	4.4	18	79	6	88	49	8	10	31	1.67
55482509--55482565	19	2.9	19	79	12	62	38	10	12	38	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55482581--55482605	11	2.3	11	100	0	50	24	0	8	68	1.16
55482726--55482763	16	2.4	16	86	8	51	60	2	2	34	1.24
55482933--55482975	17	2.5	17	84	0	59	2	20	0	76	0.89
55482940--55482975	19	1.9	18	88	5	54	2	19	0	77	0.88
55482928--55482987	26	2.3	26	86	11	79	1	18	1	78	0.92
55483015--55483072	27	2.1	28	90	6	91	5	31	37	25	1.78
55483169--55483226	3	20.3	3	79	13	61	1	29	0	68	0.99
55483329--55483410	28	2.9	27	77	15	76	8	19	3	68	1.31
55483893--55484054	30	5.5	28	78	7	144	38	2	22	36	1.67
55483892--55484054	60	2.7	58	78	10	177	38	3	22	36	1.70

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