genome.fa.s1.2.7.7.80.10.50.1000.9.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: 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  9  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)
3210306--3210341	18	2.0	18	89	10	56	33	0	5	61	1.19
3212556--3212738	22	8.9	20	68	18	90	32	0	12	55	1.37
3212692--3212942	49	5.2	49	88	1	373	32	0	12	54	1.41
3212724--3213031	27	12.8	26	74	20	253	32	0	12	54	1.43
3212696--3212936	98	2.5	98	92	2	416	31	0	12	55	1.41
3212699--3212985	49	6.0	48	84	7	354	32	0	12	54	1.43
3212696--3213079	98	4.0	91	83	11	375	32	0	13	53	1.44
3212724--3213084	49	7.5	49	76	17	220	31	0	13	54	1.44
3212556--3212955	19	22.2	19	66	22	170	32	0	12	54	1.40
3213131--3213263	27	4.9	27	92	0	203	23	37	22	16	1.93
3220164--3220206	20	2.2	20	100	0	86	23	9	16	51	1.73
3222475--3222507	17	2.0	17	94	5	59	48	0	9	42	1.35
3222474--3222510	16	2.3	15	86	13	56	43	0	8	48	1.32
3230290--3230318	15	1.9	15	100	0	58	24	6	0	68	1.13
3233647--3233691	6	7.3	6	87	2	63	46	17	20	15	1.84
3235227--3235284	2	33.5	2	72	27	53	56	0	0	43	0.99
3235229--3235312	5	16.6	5	79	17	77	57	3	0	39	1.16
3235227--3235284	8	6.6	9	80	20	61	56	0	0	43	0.99
3241583--3241623	9	4.6	9	87	0	64	2	43	0	53	1.13
3241643--3241674	3	10.7	3	93	0	55	3	34	28	34	1.73
3241638--3241677	9	4.4	9	90	0	53	10	35	22	32	1.87
3241638--3241686	12	4.1	12	86	0	62	10	34	20	34	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3241778--3241817	21	1.9	21	90	10	64	15	35	10	40	1.80
3241767--3241825	21	2.6	24	71	20	63	15	40	6	37	1.74
3245415--3245653	100	2.4	101	89	1	372	28	24	15	31	1.95
3251952--3252033	35	2.4	35	85	6	105	59	1	0	39	1.05
3270357--3270427	28	2.5	28	100	0	142	50	11	8	29	1.67
3272882--3273179	75	4.0	75	83	5	324	37	11	23	26	1.89
3277529--3277578	19	2.7	19	76	20	61	38	8	0	54	1.30
3281569--3281620	25	2.0	25	85	3	68	48	5	0	46	1.26
3286798--3286836	14	2.8	14	84	0	51	33	7	15	43	1.75
3291114--3291139	12	2.2	12	100	0	52	15	7	26	50	1.71
3292260--3292297	15	2.5	15	95	0	67	13	47	28	10	1.76
3296512--3296551	3	13.3	3	100	0	80	67	0	0	32	0.91
3298305--3298357	14	3.7	14	76	2	52	66	5	0	28	1.15
3316382--3316427	18	2.5	18	80	20	51	26	2	4	67	1.21
3321577--3321638	22	2.8	22	92	0	97	24	25	14	35	1.93
3335102--3335154	17	3.1	17	83	2	61	58	0	1	39	1.09
3335171--3335216	23	2.0	24	83	12	60	56	4	6	32	1.45
3353645--3353777	38	3.3	38	79	13	158	3	25	11	59	1.48
3353661--3353769	45	2.5	46	85	7	154	2	26	9	61	1.40
3354270--3354316	23	2.0	23	100	0	94	25	12	25	36	1.92
3355856--3355900	15	2.8	16	83	10	56	48	0	0	51	1.00
3355857--3355897	16	2.6	16	88	7	57	46	0	0	53	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3356072--3356104	16	2.1	16	94	0	57	21	33	6	39	1.78
3358264--3358335	31	2.4	30	75	13	76	38	13	12	34	1.83
3364113--3364141	2	14.5	2	100	0	58	48	0	0	51	1.00
3368009--3368045	16	2.2	17	90	4	58	56	2	0	40	1.13
3368585--3368818	118	2.0	118	85	5	321	39	12	11	35	1.81
3373911--3373942	2	17.0	2	87	12	50	53	0	0	46	1.00
3378028--3378137	42	2.6	43	85	1	141	30	24	19	26	1.98
3381571--3381609	18	2.2	18	90	0	60	41	10	12	35	1.77
3384920--3384944	7	3.6	7	100	0	50	88	0	0	12	0.53
3401267--3401328	30	2.1	30	90	0	97	27	1	11	59	1.41
3402114--3402183	29	2.5	28	79	11	79	64	0	1	34	1.03
3404986--3405024	19	2.1	19	85	0	51	10	10	0	79	0.94
3432046--3432076	6	5.2	6	100	0	62	67	32	0	0	0.91
3432974--3433218	133	1.8	133	86	1	357	24	20	22	33	1.97
3438653--3438891	78	3.1	78	93	0	406	39	23	20	16	1.92
3438677--3438894	42	5.5	42	60	14	111	40	24	18	16	1.90
3442203--3442236	2	17.0	2	87	0	50	44	5	0	50	1.26
3444055--3444091	19	1.9	19	89	10	58	45	0	13	40	1.43
3444056--3444097	19	2.3	18	80	15	50	50	0	14	35	1.43
3447467--3447526	26	2.3	26	88	0	93	18	21	21	38	1.94
3452702--3452759	25	2.2	25	84	9	71	44	3	0	51	1.18
3458359--3458403	4	11.2	4	100	0	90	51	24	0	24	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3466731--3466767	14	2.6	15	83	12	51	0	27	10	62	1.28
3470282--3470514	109	2.1	107	88	3	340	31	17	18	33	1.94
3474124--3474180	29	2.0	28	83	13	71	45	7	1	45	1.40
3476734--3476787	27	2.0	27	88	0	81	25	1	20	51	1.57
3479575--3479619	22	2.0	23	86	4	65	57	6	2	33	1.37
3484267--3484292	3	8.7	3	100	0	52	65	0	0	34	0.93
3491837--3491872	2	18.0	2	100	0	72	50	0	0	50	1.00
3492385--3492514	34	3.7	35	80	15	135	60	0	3	36	1.13
3492416--3492520	11	9.0	11	69	17	61	58	0	3	37	1.23
3493293--3493322	13	2.2	14	94	5	53	13	0	13	73	1.10
3493702--3493764	32	2.0	32	93	0	108	19	33	39	7	1.80
3496287--3496854	305	1.9	305	87	1	852	38	10	9	40	1.74
3500374--3500473	47	2.1	48	81	12	116	53	5	3	39	1.38
3504020--3504053	4	8.5	4	100	0	68	76	0	0	23	0.79
3508256--3508453	101	2.0	98	91	3	315	35	24	12	27	1.91
3511594--3511764	52	3.4	52	81	11	203	36	13	23	26	1.92
3511660--3511763	46	2.3	46	93	0	172	38	13	20	27	1.90
3512554--3512706	22	7.0	22	90	0	225	32	14	26	26	1.94
3516334--3516386	21	2.5	21	81	0	61	30	5	33	30	1.81
3520003--3520035	16	2.1	16	100	0	66	36	12	33	18	1.88
3520497--3520549	27	2.0	27	92	0	88	49	9	11	30	1.70
3524615--3524659	22	2.0	23	87	8	67	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3528622--3528670	4	12.2	4	100	0	98	51	24	0	24	1.49
3529526--3529577	18	3.2	15	73	26	52	63	1	0	34	1.06
3530073--3530378	112	2.7	112	78	6	296	32	20	22	25	1.98
3530182--3530548	190	2.0	186	82	3	448	31	19	23	25	1.98
3530373--3530665	113	2.6	114	83	5	344	29	20	24	25	1.99
3530485--3530848	184	2.0	184	86	2	518	31	18	24	25	1.98
3530373--3530940	297	1.9	300	83	4	738	30	19	23	25	1.98
3530668--3530940	115	2.4	114	81	5	327	31	19	22	26	1.98
3530998--3531037	21	1.9	21	89	0	62	20	0	37	42	1.52
3533845--3533895	21	2.4	21	93	0	84	33	17	47	1	1.59
3534609--3534853	116	2.1	117	86	0	339	33	18	20	28	1.96
3544549--3544730	9	19.8	9	66	19	74	33	1	3	62	1.19
3544549--3544730	19	9.9	18	67	18	74	33	1	3	62	1.19
3544558--3544649	21	4.4	21	71	11	64	33	0	3	63	1.11
3544590--3544636	14	3.2	14	75	18	51	31	0	0	68	0.90
3550872--3550915	18	2.4	19	84	3	63	43	15	11	29	1.82
3551206--3551232	13	2.1	13	100	0	54	37	14	0	48	1.45
3561724--3561753	12	2.5	12	94	0	51	66	0	0	33	0.92
3568203--3568250	19	2.4	21	86	13	75	62	0	37	0	0.95
3568203--3568250	20	2.5	18	83	12	60	62	0	37	0	0.95
3569593--3569632	2	20.5	2	94	5	73	47	0	0	52	1.00
3570009--3570099	11	8.5	11	69	19	59	24	29	2	43	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3570009--3570054	22	2.0	23	87	4	67	21	28	2	47	1.62
3570009--3570099	22	4.3	21	69	24	66	24	29	2	43	1.66
3570055--3570088	17	1.9	18	88	5	52	29	29	2	38	1.72
3570037--3570120	40	2.1	40	86	4	116	26	26	2	45	1.66
3571267--3571292	7	3.7	7	100	0	52	26	0	15	57	1.38
3571941--3571975	18	1.9	18	94	0	61	28	28	0	42	1.56
3572411--3572505	34	2.9	33	78	17	85	42	6	5	46	1.51
3576198--3576256	28	2.2	27	90	6	93	25	3	0	71	1.02
3577984--3578018	14	2.5	14	95	0	61	34	20	5	40	1.76
3578980--3579098	49	2.5	48	88	1	175	43	10	10	34	1.75

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