genome.fa.s6.2.7.7.80.10.50.1000.10.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: Chr1
Parameters: 2 7 7 80 10 50 1000
Length:  35726063

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   

This is table  10  of  109  ( 13028 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)
3223560--3223759	107	1.9	107	92	0	337	26	25	15	32	1.95
3224812--3224956	41	3.6	40	84	3	173	25	18	24	31	1.98
3225429--3225454	7	3.7	7	100	0	52	15	0	53	30	1.42
3225550--3225587	13	2.8	13	81	18	51	13	0	47	39	1.42
3225498--3225641	74	1.9	76	85	2	202	28	1	26	43	1.63
3225629--3225659	7	4.4	7	95	0	53	19	0	48	32	1.49
3228908--3229085	43	4.2	43	84	2	198	25	17	28	28	1.98
3228929--3229085	43	3.7	43	85	1	201	26	18	28	27	1.98
3231086--3231110	13	1.9	13	100	0	50	40	0	0	60	0.97
3234025--3234076	23	2.3	23	93	0	86	40	5	11	42	1.65
3235224--3235253	6	5.0	6	95	0	51	30	16	0	53	1.44
3235442--3235500	21	2.8	21	97	0	109	32	28	27	11	1.92
3235430--3235558	21	6.0	22	80	4	86	35	23	23	17	1.95
3235749--3235847	36	2.7	38	80	13	91	33	20	1	45	1.58
3237005--3237042	18	2.0	20	90	10	62	57	13	0	28	1.36
3246737--3246848	40	2.7	42	83	9	140	33	2	0	64	1.08
3246740--3246805	18	3.4	18	76	13	69	36	3	0	60	1.12
3246810--3246835	12	2.2	12	100	0	52	15	0	0	84	0.62
3247098--3247137	21	1.9	21	84	0	53	2	32	2	62	1.22
3247222--3247270	19	2.4	21	76	10	57	10	24	0	65	1.23
3251092--3251138	19	2.4	19	85	7	58	63	2	10	23	1.37
3267476--3267626	56	2.7	56	86	0	221	37	11	22	28	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3272901--3272952	20	2.6	19	78	6	59	9	21	21	48	1.78
3273746--3273789	23	1.9	23	90	0	70	61	4	2	31	1.28
3273750--3273792	11	3.8	11	80	17	52	65	2	2	30	1.18
3277543--3277622	40	2.0	40	100	0	160	27	27	10	35	1.89
3282336--3282368	17	1.9	17	93	0	57	48	21	3	27	1.64
3288221--3288306	30	2.9	30	80	5	111	33	18	13	33	1.91
3291516--3291577	3	20.7	3	93	0	106	62	0	35	1	1.05
3291773--3291812	19	2.2	18	86	4	53	25	0	12	62	1.30
3291738--3291923	57	3.2	59	75	16	194	33	3	10	53	1.51
3291889--3291953	18	3.0	22	72	21	66	29	1	10	58	1.41
3291801--3292308	155	3.3	154	71	21	538	31	2	11	54	1.51
3291974--3292088	42	2.8	41	73	17	112	35	4	12	47	1.61
3292100--3292173	30	2.6	27	82	6	94	27	1	10	60	1.38
3291851--3292384	173	3.4	159	73	20	447	32	3	11	52	1.54
3292267--3292312	17	2.8	16	83	6	65	28	2	13	56	1.48
3291793--3292384	306	1.9	305	97	0	1121	32	3	11	53	1.53
3295209--3295251	8	5.4	8	97	0	77	25	0	23	51	1.49
3295194--3295251	16	3.7	16	90	2	73	27	0	22	50	1.50
3295201--3295251	24	2.2	23	89	3	75	23	0	23	52	1.47
3298167--3298211	23	2.0	22	82	4	54	40	4	17	37	1.70
3298373--3298413	20	2.2	19	86	8	57	4	14	17	63	1.47
3299903--3300508	302	2.0	302	100	0	1212	41	15	3	40	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3300540--3300566	3	9.0	3	100	0	54	0	33	0	66	0.92
3305655--3305691	9	4.1	9	92	0	65	29	10	13	45	1.77
3305746--3305776	9	3.4	9	90	0	53	38	22	12	25	1.90
3306189--3306235	20	2.5	19	75	6	51	55	2	2	40	1.24
3307990--3308039	19	2.6	19	83	0	64	44	8	22	26	1.80
3313353--3313430	39	2.0	39	100	0	156	33	7	20	38	1.81
3321834--3322006	94	1.8	96	86	2	251	27	7	12	52	1.66
3322001--3322047	21	2.2	22	84	3	60	46	2	0	51	1.13
3322316--3322378	27	2.3	27	81	13	74	60	0	1	38	1.07
3323250--3323289	21	1.9	21	89	0	62	37	0	2	60	1.11
3323431--3323476	22	2.0	23	87	12	67	45	0	6	47	1.28
3324731--3324763	17	1.9	17	100	0	66	48	0	9	42	1.35
3325160--3325213	16	3.4	16	81	0	63	40	1	27	29	1.67
3325195--3325288	44	2.1	46	86	4	129	29	4	28	37	1.76
3329888--3330004	62	1.9	62	98	1	227	40	5	14	39	1.71
3330185--3330234	26	1.9	26	84	8	66	58	4	6	32	1.41
3331000--3331030	15	2.1	15	100	0	62	32	25	12	29	1.93
3335420--3335454	2	17.5	2	100	0	70	0	48	0	51	1.00
3341866--3341911	25	1.9	24	82	8	58	41	17	0	41	1.49
3355264--3355308	6	7.5	6	89	0	63	28	15	33	22	1.95
3355264--3355307	12	3.7	12	90	0	70	27	15	34	22	1.95
3355264--3355308	18	2.5	18	92	0	81	28	15	33	22	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3365788--3366416	312	2.0	312	89	0	954	40	15	25	18	1.90
3379760--3379808	24	2.0	24	96	0	89	40	18	16	24	1.90
3380678--3380733	27	2.1	27	83	12	71	10	17	0	71	1.14
3384422--3384466	20	2.2	20	85	14	58	53	13	4	28	1.59
3389508--3390070	280	2.0	281	99	0	1119	36	14	17	31	1.90
3391062--3391122	14	4.5	14	73	21	58	26	0	4	68	1.09
3391093--3391131	19	2.1	19	85	9	53	17	0	7	74	1.05
3397280--3397332	6	8.8	6	100	0	106	49	0	0	50	1.00
3397280--3397358	18	4.2	20	88	9	98	46	0	0	53	1.00
3407384--3407972	194	3.0	193	87	4	866	48	12	10	29	1.74
3412592--3412651	31	1.9	32	86	6	88	41	8	13	36	1.74
3420821--3420860	20	2.0	20	85	5	53	30	12	45	12	1.79
3426247--3426294	19	2.5	19	93	0	87	60	4	18	16	1.51
3437193--3437220	14	2.0	14	100	0	56	14	42	7	35	1.73
3437563--3437683	52	2.4	53	90	5	187	28	30	13	27	1.94
3442256--3442284	10	2.7	11	89	10	51	44	0	20	34	1.52
3442835--3442888	24	2.2	24	83	0	63	16	24	24	35	1.95
3445585--3445618	17	1.9	18	94	5	61	64	0	5	29	1.17
3449498--3449535	18	2.1	18	85	9	51	21	10	0	68	1.19
3458064--3458091	14	2.0	14	100	0	56	50	0	0	50	1.00
3460216--3460268	24	2.2	24	96	0	97	66	5	7	20	1.38
3461276--3461322	23	2.0	23	100	0	94	25	38	8	27	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3465024--3465082	25	2.5	24	88	5	84	61	1	1	35	1.16
3468147--3468181	18	1.9	18	88	11	54	8	2	34	54	1.46
3469325--3469366	21	2.0	21	85	0	57	14	38	21	26	1.91
3471372--3471439	18	3.7	18	82	5	75	69	0	7	23	1.14
3471367--3471439	12	5.9	12	72	16	53	68	0	6	24	1.14
3483581--3483632	19	2.7	19	85	8	70	71	1	3	23	1.13
3483948--3483986	15	2.6	15	88	8	53	35	0	0	64	0.94
3487265--3487298	17	2.1	16	89	10	52	64	2	0	32	1.08
3488966--3488994	14	2.0	15	93	6	51	34	10	27	27	1.89
3492519--3492634	41	2.8	41	81	0	124	37	18	28	15	1.91
3492698--3492790	34	2.7	34	88	1	132	33	32	0	34	1.58
3494063--3494087	5	5.0	5	100	0	50	20	0	0	80	0.72
3494336--3494391	29	1.9	29	85	7	78	39	5	3	51	1.42
3498233--3498257	5	5.0	5	100	0	50	20	0	20	60	1.37
3502429--3502532	42	2.4	43	79	7	113	28	14	24	32	1.94
3504706--3504741	6	6.0	6	100	0	72	33	0	16	50	1.46
3504708--3504751	18	2.4	18	88	7	63	31	0	18	50	1.47
3506784--3506962	43	4.2	43	80	4	173	31	22	18	26	1.97
3506768--3506962	86	2.3	86	85	1	257	31	24	17	26	1.97
3506949--3507071	43	2.9	41	70	7	111	26	17	21	33	1.96
3507727--3507975	123	2.0	123	96	0	462	22	29	20	28	1.98
3516292--3516323	3	10.7	3	100	0	64	31	34	0	34	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3517097--3517353	128	2.0	129	99	0	507	40	8	13	38	1.75
3522497--3522762	3	88.7	3	100	0	532	33	0	0	66	0.92
3528098--3528206	55	2.0	55	90	0	173	50	12	24	11	1.74
3557096--3557134	16	2.5	15	83	4	51	51	10	28	10	1.68
3558450--3558886	50	8.9	49	67	10	246	32	24	20	22	1.98
3558450--3558929	98	4.9	99	91	1	750	32	24	21	21	1.98
3558450--3558929	197	2.4	197	90	1	748	32	24	21	21	1.98
3559762--3559796	17	2.1	17	88	0	52	2	11	0	85	0.69
3560225--3560292	3	22.7	3	100	0	136	33	0	0	66	0.92
3562268--3562334	29	2.3	30	79	10	75	38	7	11	41	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