genome.fa.s17.2.7.7.80.10.50.1000.12.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  12  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)
3290700--3290744	14	3.4	12	80	19	54	77	2	6	13	1.05
3299148--3299172	3	8.3	3	100	0	50	0	32	0	68	0.90
3302900--3302940	20	2.0	20	100	0	82	24	19	26	29	1.98
3306730--3306777	24	2.0	24	87	0	69	62	6	29	2	1.31
3311506--3311553	24	2.0	24	87	0	69	62	6	29	2	1.31
3312003--3312101	1	99.0	1	100	0	198	0	0	0	100	0.00
3328558--3328596	15	2.5	16	83	8	53	25	5	15	53	1.62
3343805--3343896	30	3.1	30	92	6	159	31	9	14	44	1.77
3344428--3344496	9	7.8	9	75	12	63	73	13	13	0	1.09
3344428--3344495	17	3.9	17	81	12	84	73	13	13	0	1.10
3347599--3347694	31	3.1	31	95	3	174	31	9	13	45	1.75
3349512--3349554	22	2.0	21	90	4	68	65	2	4	27	1.25
3351343--3351413	12	6.2	11	70	13	54	59	0	1	39	1.06
3351339--3351413	36	2.0	38	89	7	118	61	0	1	37	1.05
3351825--3351862	16	2.3	17	83	16	53	26	0	7	65	1.19
3351827--3351862	18	2.1	18	90	10	58	25	0	8	66	1.19
3352833--3352857	4	6.2	4	100	0	50	76	0	0	24	0.80
3353195--3353325	69	1.9	69	90	0	208	31	20	20	27	1.98
3355046--3355096	26	2.0	26	85	11	70	49	3	0	47	1.20
3356331--3356488	51	3.2	50	82	12	220	27	24	14	33	1.94
3356328--3356481	44	3.3	44	81	14	193	28	23	14	33	1.94
3358433--3358477	3	14.3	3	90	9	72	31	4	0	64	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3358583--3358650	36	1.9	34	82	11	84	36	8	1	52	1.42
3360176--3360217	3	13.7	3	85	5	57	59	0	4	35	1.19
3361538--3361669	6	22.0	6	100	0	264	50	16	0	33	1.46
3366103--3366189	10	8.5	10	71	13	61	82	3	8	5	0.92
3366104--3366189	20	4.3	19	75	16	75	82	3	8	5	0.93
3366114--3366181	14	4.9	14	77	13	70	82	1	8	7	0.91
3367964--3368103	41	3.3	42	75	10	144	32	25	18	22	1.97
3373621--3373740	35	3.3	35	88	8	186	28	40	8	23	1.83
3373628--3373740	39	3.0	38	92	5	178	28	38	8	24	1.85
3374533--3374568	1	36.0	1	88	0	54	94	0	0	5	0.31
3375570--3375689	35	3.3	35	86	8	177	23	8	40	28	1.83
3375570--3375682	39	3.0	38	91	7	178	24	8	38	28	1.85
3381226--3381338	44	2.7	43	82	6	133	26	22	23	27	1.99
3381215--3381338	41	2.9	43	77	8	146	25	20	25	29	1.99
3382193--3382250	24	2.4	24	82	0	71	31	24	10	34	1.89
3383134--3383203	14	5.2	13	76	17	72	7	8	1	82	0.89
3383130--3383203	19	3.9	18	77	20	64	6	9	1	82	0.90
3383128--3383206	20	3.9	20	76	12	72	6	8	2	82	0.93
3387657--3387782	6	21.0	6	100	0	252	33	0	16	50	1.46
3388658--3388727	36	1.9	36	97	0	131	24	22	31	21	1.98
3389103--3389144	3	13.7	3	85	5	57	35	4	0	59	1.19
3390841--3390884	3	14.3	3	86	13	63	63	0	4	31	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3390844--3390879	17	2.1	18	94	5	65	63	0	2	33	1.08
3390841--3390879	20	1.9	21	94	5	71	64	0	2	33	1.08
3390840--3390884	20	2.2	20	84	7	65	62	0	6	31	1.21
3392817--3392977	51	3.3	50	80	15	219	34	14	23	27	1.94
3392824--3392977	44	3.3	44	80	15	193	33	14	23	28	1.94
3395985--3396115	69	1.9	69	90	0	208	27	20	20	31	1.98
3396453--3396477	4	6.2	4	100	0	50	24	0	0	76	0.80
3397447--3397482	18	2.1	18	90	10	58	66	8	0	25	1.19
3397894--3397964	12	6.2	11	73	9	61	39	1	0	59	1.06
3399746--3399788	22	2.0	21	90	4	68	27	4	2	65	1.25
3401606--3401701	31	3.1	31	95	3	174	45	13	9	31	1.75
3404847--3404908	19	3.3	19	90	2	99	1	14	12	70	1.23
3404845--3404917	9	7.9	9	76	8	67	2	15	10	71	1.25
3405461--3405556	31	3.1	31	95	3	174	45	13	9	31	1.75
3410860--3410916	15	3.9	15	75	9	64	75	0	10	14	1.05
3412809--3412975	50	3.3	50	69	3	138	33	22	21	22	1.97
3412559--3413148	100	5.9	100	84	2	639	31	20	22	25	1.98
3412837--3413089	50	5.1	50	69	9	167	33	22	19	24	1.97
3414648--3414690	22	2.0	21	90	4	68	27	4	2	65	1.25
3416166--3416205	19	2.0	21	85	9	57	52	10	0	37	1.35
3416821--3416862	13	3.4	13	74	12	52	45	9	2	42	1.49
3418690--3418837	77	1.9	77	97	0	278	34	20	10	34	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3420181--3420332	41	3.7	41	91	0	243	34	17	25	22	1.95
3423396--3423435	19	2.0	21	85	9	57	52	10	0	37	1.35
3432729--3432780	22	2.3	22	83	6	59	23	25	19	32	1.97
3432742--3432787	22	2.1	22	100	0	92	19	21	19	39	1.93
3433784--3433843	31	1.9	31	96	0	111	23	1	26	48	1.60
3436285--3436310	6	4.3	6	100	0	52	84	15	0	0	0.62
3437146--3437262	34	3.5	33	75	9	128	40	0	15	43	1.52
3437476--3437501	10	2.6	10	100	0	52	73	7	0	19	1.07
3439758--3439873	46	2.6	45	90	6	175	34	14	23	27	1.94
3440588--3440627	18	2.2	18	90	0	62	42	10	30	17	1.82
3442253--3442308	21	2.7	21	94	0	94	28	8	33	28	1.87
3445294--3445331	6	6.2	6	87	6	58	39	0	60	0	0.97
3445294--3445329	18	2.0	18	100	0	72	38	0	61	0	0.96
3445299--3445339	18	2.3	18	86	0	55	41	0	58	0	0.98
3446609--3446647	20	2.0	20	89	0	60	43	0	7	48	1.31
3448878--3448912	16	2.1	17	89	5	54	77	5	2	14	1.07
3453555--3453603	19	2.7	19	75	12	59	24	16	0	59	1.37
3460035--3460083	18	2.7	19	84	9	66	73	6	4	16	1.19
3464166--3464224	28	2.1	28	90	6	93	44	0	15	40	1.46
3464182--3464314	67	2.0	67	86	4	189	41	0	15	43	1.46
3464190--3464316	34	3.8	33	84	5	175	40	0	15	44	1.47
3467140--3467435	23	12.7	23	81	2	340	26	11	19	42	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3467934--3467971	18	2.1	18	90	0	58	42	10	23	23	1.85
3469374--3469502	43	3.0	42	80	15	156	22	18	28	30	1.97
3470098--3470151	2	27.5	2	81	10	67	42	1	3	51	1.30
3470100--3470147	17	2.8	17	96	3	87	41	2	4	52	1.32
3470124--3470162	12	3.4	12	79	13	55	41	5	5	48	1.47
3470098--3470162	22	3.1	22	91	6	100	41	3	4	50	1.38
3475835--3475927	18	5.2	18	93	0	159	31	17	24	26	1.97
3475835--3475927	36	2.6	36	98	0	177	31	17	24	26	1.97
3484111--3484157	20	2.3	20	86	13	62	34	2	4	59	1.29
3484237--3484296	4	15.0	4	100	0	120	50	25	0	25	1.50
3484437--3484542	38	2.8	37	75	11	101	38	6	0	54	1.26
3484451--3484542	36	2.5	38	80	8	118	39	5	0	55	1.23
3484578--3484603	4	6.5	4	100	0	52	0	23	0	76	0.78
3494681--3494745	7	9.0	7	80	12	69	78	0	0	21	0.75
3494687--3494745	5	11.6	5	76	20	52	77	0	0	22	0.76
3494669--3494763	37	2.6	36	80	9	95	72	0	0	27	0.85
3499000--3499063	7	9.3	7	75	20	55	71	0	6	21	1.07
3499007--3499066	12	5.2	12	75	20	58	73	0	5	21	1.02
3507475--3507745	23	11.7	23	84	1	326	25	12	19	42	1.86
3508245--3508280	18	2.0	18	94	0	63	38	8	27	25	1.84
3509682--3509811	43	3.0	42	82	10	165	21	19	28	30	1.97
3510601--3510772	73	2.4	72	86	1	227	29	22	24	23	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3510672--3511203	114	4.7	114	86	3	705	26	21	25	26	1.99
3510672--3511204	227	2.3	225	83	6	703	26	21	25	26	1.99
3511522--3511555	14	2.4	14	100	0	68	26	0	38	35	1.57
3511498--3511579	21	3.8	21	73	12	60	23	0	39	37	1.55
3511522--3511604	7	11.6	7	78	10	51	21	0	43	34	1.53
3511550--3511604	15	3.7	15	76	11	60	18	0	47	34	1.49
3511568--3511617	23	2.1	24	92	3	84	16	0	50	34	1.45
3512025--3512224	103	1.9	103	89	6	312	50	11	11	27	1.72
3512269--3512587	109	2.9	107	87	4	455	49	12	12	26	1.76
3512030--3512552	261	2.0	255	84	6	669	49	12	12	25	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