genome.fa.s13.2.7.7.80.10.50.1000.11.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  11  of  199  ( 23770 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)
3448341--3448383	17	2.5	17	88	0	68	60	0	4	34	1.17
3449837--3450307	100	4.7	100	90	0	710	24	18	23	33	1.97
3449849--3450304	50	9.1	50	71	6	314	23	18	23	33	1.97
3451596--3451648	7	7.4	7	82	16	65	15	15	0	69	1.19
3451605--3451645	8	5.5	8	88	11	61	12	12	0	75	1.05
3451596--3451648	21	2.5	21	93	3	88	15	15	0	69	1.19
3457677--3457735	24	2.4	23	77	22	59	35	1	3	59	1.24
3463109--3463134	12	2.2	12	100	0	52	84	0	15	0	0.62
3465556--3465607	18	2.9	18	94	2	88	34	11	11	42	1.77
3466551--3466603	6	8.8	6	100	0	106	33	0	15	50	1.44
3466739--3466768	2	14.5	2	93	6	51	50	0	3	46	1.18
3466739--3466784	16	2.8	17	84	12	53	52	0	6	41	1.27
3468219--3468426	44	4.6	44	72	7	125	26	25	19	28	1.98
3468350--3468662	136	2.3	136	87	2	450	30	19	18	30	1.96
3468827--3468934	44	2.5	44	81	0	117	29	17	19	33	1.95
3468855--3468949	44	2.2	44	82	0	118	28	17	17	35	1.93
3469411--3469729	89	3.6	88	89	1	458	21	23	24	30	1.99
3469484--3469618	44	3.0	44	65	18	107	20	24	26	28	1.99
3470612--3470831	107	2.1	107	86	3	300	48	7	17	26	1.73
3471100--3471137	11	3.4	11	85	7	58	0	18	0	81	0.69
3471094--3471138	12	3.8	12	85	8	65	0	20	0	80	0.72
3475931--3475980	3	17.3	3	75	8	50	58	0	4	38	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3477599--3477837	72	3.3	71	91	1	381	24	6	14	54	1.63
3478246--3478359	40	2.8	40	84	7	133	20	18	28	32	1.96
3478705--3478754	14	3.5	15	83	8	68	26	0	36	38	1.57
3479011--3479052	15	2.9	15	85	3	59	33	0	28	38	1.58
3479072--3479139	15	4.7	15	76	10	54	23	1	42	32	1.63
3479068--3479122	22	2.5	22	85	2	67	23	1	40	34	1.66
3479082--3479122	21	1.9	22	90	5	66	24	2	41	31	1.68
3478632--3479231	306	2.0	301	86	4	852	28	2	27	41	1.69
3484501--3484727	43	5.3	43	78	5	192	25	16	26	31	1.96
3486559--3486583	13	1.9	13	100	0	50	40	20	8	32	1.81
3488864--3489000	46	3.0	46	91	2	222	27	26	8	37	1.86
3494609--3494652	11	3.9	11	79	5	52	56	2	0	40	1.11
3497731--3497775	3	15.0	3	100	0	90	66	0	0	33	0.92
3498412--3498461	22	2.2	24	82	10	61	64	8	22	6	1.43
3507559--3507656	31	3.3	30	72	17	80	37	10	12	39	1.77
3507896--3507947	20	2.5	20	81	3	59	61	5	5	26	1.42
3509642--3509705	29	2.2	29	97	0	119	32	18	6	42	1.76
3529435--3529481	23	2.0	23	92	8	78	61	2	0	36	1.08
3533133--3533322	45	4.2	45	89	0	254	22	18	17	41	1.90
3533307--3533342	18	1.9	19	94	5	65	25	19	11	44	1.83
3536444--3536755	43	7.3	43	85	0	417	30	29	16	23	1.96
3536444--3536757	86	3.7	86	93	0	493	30	29	16	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3540628--3540732	14	7.4	14	68	12	61	46	29	1	21	1.62
3540907--3541115	41	5.1	41	88	0	265	31	28	18	22	1.97
3542463--3542546	37	2.3	37	95	2	152	42	16	2	38	1.61
3545924--3545948	8	3.1	8	100	0	50	52	36	12	0	1.39
3549226--3549323	31	3.3	30	72	17	80	37	10	12	39	1.77
3549563--3549614	20	2.5	20	81	3	59	61	5	5	26	1.42
3554822--3554858	5	7.6	5	96	3	67	0	16	0	83	0.64
3556102--3556162	3	20.3	3	80	12	72	32	3	0	63	1.10
3556108--3556169	15	4.1	15	80	14	65	33	3	0	62	1.11
3556102--3556166	24	2.7	24	83	11	87	33	3	0	63	1.10
3556186--3556260	28	2.8	27	82	9	91	32	1	1	65	1.09
3556123--3556310	96	1.9	96	80	10	218	31	4	4	59	1.37
3556106--3556315	96	2.2	96	77	17	213	31	4	4	59	1.36
3560563--3560614	21	2.4	21	93	3	86	28	34	11	25	1.91
3561833--3561867	15	2.3	15	85	0	52	31	2	0	65	1.07
3568200--3568243	16	2.6	16	85	7	52	52	20	2	25	1.58
3578633--3578672	18	2.2	18	86	0	53	30	2	5	62	1.29
3602644--3602700	29	2.0	29	83	13	73	50	3	3	42	1.36
3604038--3604080	14	2.9	15	80	12	54	65	0	0	34	0.93
3605407--3605464	18	3.3	18	68	27	52	51	3	3	41	1.35
3609918--3609946	2	14.5	2	100	0	58	51	0	0	48	1.00
3612866--3612922	21	2.5	23	72	8	55	52	1	40	5	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3615191--3615417	116	2.0	116	93	0	391	42	9	9	38	1.70
3615416--3616018	23	24.4	23	73	21	410	28	0	24	46	1.57
3615416--3616033	29	24.7	27	71	24	372	28	0	24	46	1.57
3615457--3615507	22	2.5	21	87	9	70	25	0	29	45	1.54
3615467--3615580	22	4.9	21	76	19	102	28	0	27	44	1.54
3615416--3616033	124	5.0	126	78	14	617	28	0	24	46	1.57
3615405--3616034	205	3.1	202	84	8	831	28	0	24	46	1.57
3615959--3616004	22	2.2	20	88	11	67	26	0	28	45	1.54
3616135--3616250	25	4.6	25	94	1	205	40	14	0	43	1.51
3616218--3616304	44	2.0	45	90	2	140	49	12	0	37	1.41
3616726--3616760	18	1.9	18	94	0	61	34	8	31	25	1.86
3617409--3617440	7	4.6	7	100	0	64	59	12	0	28	1.34
3618634--3618662	10	2.7	11	89	10	51	55	0	27	17	1.42
3618941--3618985	18	2.5	19	89	10	76	42	0	0	57	0.98
3618957--3618995	12	3.0	13	88	7	53	43	0	0	56	0.99
3623363--3623403	15	2.7	15	88	3	55	51	0	4	43	1.23
3626112--3626184	28	2.5	30	88	6	114	50	1	1	46	1.18
3626701--3626752	14	3.5	15	75	19	56	57	28	0	13	1.36
3637799--3637832	17	2.0	17	94	0	59	41	8	23	26	1.83
3644897--3644922	11	2.4	11	100	0	52	7	0	0	92	0.39
3651063--3651115	21	2.5	21	93	0	88	30	37	9	22	1.86
3653950--3653991	16	2.6	16	81	14	50	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3653952--3653991	17	2.4	16	88	12	55	50	0	0	50	1.00
3653969--3654019	23	2.2	24	82	3	59	41	1	0	56	1.10
3653967--3654020	24	2.2	24	83	6	65	40	1	0	57	1.09
3653985--3654050	35	1.9	33	85	11	89	36	3	1	59	1.22
3653986--3654055	17	4.1	17	69	7	52	38	2	1	57	1.23
3654764--3654807	16	2.9	16	80	10	56	38	2	0	59	1.10
3665767--3665808	11	3.8	11	93	0	57	19	0	7	73	1.05
3665771--3665848	19	3.9	19	69	21	61	20	2	8	67	1.30
3665771--3665850	30	2.7	30	90	0	115	21	2	8	67	1.30
3665783--3665834	11	5.1	10	76	19	54	21	1	9	67	1.29
3667570--3667633	32	2.0	33	87	3	94	18	31	20	29	1.96
3668663--3668801	69	2.0	69	100	0	278	39	18	17	24	1.92
3673638--3673672	15	2.4	15	95	4	63	34	2	5	57	1.37
3674718--3674776	26	2.3	26	88	5	86	62	1	0	35	1.05
3674784--3674823	7	5.7	7	93	0	71	75	0	0	25	0.81
3675659--3675690	15	2.1	15	100	0	64	25	12	15	46	1.81
3675969--3676013	22	2.0	22	95	4	81	73	0	0	26	0.84
3676543--3676578	17	2.0	19	89	10	58	47	11	2	38	1.54
3679396--3679456	24	2.4	25	86	8	79	60	0	32	6	1.22
3687255--3687349	48	2.0	48	91	0	154	31	16	21	30	1.95
3691837--3692323	172	2.8	172	83	5	554	39	18	11	30	1.86
3708687--3708854	31	5.5	31	72	8	139	39	3	4	52	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3708720--3708823	30	3.4	30	74	10	104	41	2	5	50	1.41
3708693--3708857	61	2.7	61	90	3	253	40	3	4	51	1.41
3709921--3709969	9	5.4	9	85	9	73	26	12	20	40	1.87
3710257--3710312	26	2.2	25	84	6	76	42	10	14	32	1.80
3717183--3717230	24	2.0	23	84	11	62	25	2	0	72	0.95
3717766--3717818	24	2.2	23	83	12	63	56	0	0	43	0.99
3719595--3719627	18	1.9	17	88	11	50	48	3	0	48	1.17
3720629--3720667	10	4.0	10	83	6	53	69	0	0	30	0.89
3720629--3720692	29	2.1	32	85	8	89	64	1	0	34	1.03
3720566--3720701	28	4.6	28	70	15	80	60	1	2	36	1.18

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