genome.fa.s6.2.7.7.80.10.50.1000.16.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  16  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)
5440639--5440664	5	5.2	5	100	0	52	80	0	0	19	0.71
5442109--5442327	116	1.9	116	90	0	348	26	24	18	31	1.97
5448060--5448102	21	2.0	21	95	0	77	65	9	2	23	1.34
5450461--5451406	129	7.3	129	98	0	1822	28	21	18	31	1.97
5450476--5451832	44	31.7	42	69	9	408	28	21	19	31	1.97
5451399--5451470	36	2.0	36	91	0	117	23	18	25	33	1.97
5451458--5451832	129	2.9	129	89	2	536	27	23	19	29	1.98
5453073--5453119	7	7.0	7	80	9	62	17	17	0	65	1.27
5453073--5453117	13	3.4	14	84	9	58	17	17	0	64	1.29
5453073--5453119	20	2.3	20	92	0	76	17	17	0	65	1.27
5467562--5467627	28	2.3	29	84	5	89	40	1	4	53	1.31
5474368--5474564	97	2.0	98	99	1	387	54	7	10	27	1.60
5484210--5484252	19	2.2	20	88	12	63	39	0	4	55	1.20
5488123--5488151	14	2.1	14	100	0	58	34	0	27	37	1.57
5488174--5488220	24	1.9	25	86	4	69	48	2	23	25	1.62
5489541--5489577	2	19.5	2	83	10	51	54	0	0	45	1.00
5500339--5500373	9	4.0	9	85	7	54	65	0	0	34	0.93
5507566--5507599	17	2.0	17	94	0	59	50	11	8	29	1.69
5508584--5508639	22	2.5	22	94	0	94	32	25	0	42	1.55
5508611--5508669	30	2.0	30	86	0	82	30	32	0	37	1.58
5508641--5508682	22	1.9	22	90	0	66	33	33	0	33	1.58
5508725--5508781	29	2.0	29	86	6	80	38	1	1	57	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5508727--5508788	29	2.1	29	82	5	72	38	1	1	58	1.18
5508879--5508912	15	2.3	15	90	5	52	26	0	5	67	1.13
5508877--5508934	24	2.3	23	78	21	64	27	0	5	67	1.12
5515494--5515532	17	2.3	17	86	8	53	58	15	0	25	1.37
5516202--5516299	44	2.2	44	87	5	135	31	5	28	34	1.79
5516412--5516540	57	2.2	56	76	18	129	51	3	1	42	1.29
5520110--5520163	14	3.2	17	82	15	60	62	3	22	11	1.43
5520110--5520149	19	2.2	18	86	8	55	62	5	20	12	1.48
5520139--5520183	19	2.5	18	82	17	58	66	0	26	6	1.16
5521650--5521700	25	2.0	26	92	3	86	37	1	0	60	1.08
5522645--5522680	17	2.0	19	89	10	58	63	0	8	27	1.23
5523188--5523218	8	3.9	8	91	0	53	64	0	9	25	1.24
5535379--5535442	25	2.5	24	85	5	74	56	1	3	39	1.25
5535397--5535443	25	1.9	25	91	4	78	55	2	2	40	1.24
5538500--5538543	23	1.9	23	85	0	61	43	0	0	56	0.99
5541051--5541156	56	1.9	56	86	0	149	20	10	21	47	1.80
5546512--5546554	18	2.4	18	88	7	61	46	0	0	53	1.00
5549687--5549729	22	2.0	22	100	0	86	32	18	18	30	1.95
5549948--5550011	23	2.6	25	78	9	78	21	14	25	39	1.91
5552123--5552172	26	1.9	27	88	8	77	50	6	14	30	1.66
5552128--5552184	24	2.3	25	82	8	64	49	8	8	33	1.65
5553277--5553305	11	2.6	11	100	0	58	17	6	55	20	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5553758--5554661	44	20.6	44	69	12	232	27	20	20	31	1.97
5553901--5554228	129	2.5	127	86	6	439	27	21	19	31	1.97
5553933--5554396	129	3.6	129	82	6	428	27	20	19	32	1.97
5554053--5554529	172	2.7	172	84	2	587	27	19	19	32	1.97
5554205--5554440	128	1.8	129	85	2	332	27	18	21	33	1.96
5554452--5554677	89	2.6	87	80	6	249	27	22	18	31	1.97
5554421--5554661	133	1.8	133	80	5	290	28	21	19	30	1.98
5553937--5554680	44	17.1	42	72	9	300	27	20	19	31	1.97
5554668--5555643	50	19.4	50	72	5	635	25	20	21	32	1.98
5554671--5555335	100	6.6	100	83	3	767	25	21	21	31	1.98
5554698--5555640	150	6.3	150	75	3	732	25	20	21	31	1.98
5555261--5555640	199	1.9	200	90	3	606	25	21	21	31	1.98
5568317--5568364	20	2.3	21	78	7	53	45	2	4	47	1.33
5569905--5569956	24	2.2	24	92	0	86	51	7	3	36	1.49
5571646--5571841	100	2.0	100	88	0	293	31	16	12	38	1.87
5574373--5574427	24	2.5	21	78	16	65	47	7	1	43	1.41
5574382--5574427	24	1.9	24	90	0	74	47	6	2	43	1.41
5574647--5575158	255	2.0	255	95	0	925	37	14	14	34	1.86
5581007--5581058	26	2.0	27	85	11	72	0	32	1	65	1.04
5581264--5581313	12	3.9	13	77	12	59	60	2	0	38	1.09
5592539--5592574	17	2.0	19	89	10	58	52	0	8	38	1.32
5594655--5594749	38	2.5	38	89	3	147	38	22	8	30	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5606055--5606153	45	2.2	44	86	8	146	22	21	2	54	1.55
5612470--5612494	13	1.9	13	100	0	50	36	0	16	48	1.46
5612699--5612739	17	2.4	17	91	0	73	0	19	14	65	1.26
5612700--5612739	8	4.7	9	84	12	57	0	20	12	67	1.22
5613354--5613392	16	2.3	16	86	8	51	43	0	0	56	0.99
5631729--5631791	27	2.3	27	81	5	65	44	14	22	19	1.86
5640193--5640224	15	2.1	15	94	0	55	68	9	6	15	1.36
5641597--5641792	41	4.8	41	88	1	286	30	22	20	26	1.98
5641597--5641792	81	2.4	82	88	0	304	30	22	20	26	1.98
5643385--5643625	119	2.0	121	95	1	441	40	20	7	31	1.81
5647399--5647438	14	2.9	14	84	0	53	40	12	0	47	1.41
5647440--5647526	38	2.3	38	88	11	126	33	21	1	43	1.60
5647469--5647527	20	3.0	20	80	9	86	33	22	0	44	1.53
5647464--5647521	18	3.1	19	78	11	75	32	20	0	46	1.51
5647517--5647891	105	3.6	105	92	3	623	25	18	1	53	1.55
5647517--5647891	157	2.4	158	91	4	607	25	18	1	53	1.55
5647880--5647919	14	2.9	14	96	0	71	32	15	0	52	1.43
5647553--5647891	52	6.5	52	94	2	590	25	18	1	54	1.53
5647947--5647999	14	3.0	19	71	28	62	30	18	1	49	1.59
5651006--5653074	114	18.5	113	93	4	2765	24	15	15	44	1.85
5651478--5651506	10	2.7	11	94	5	51	10	0	3	86	0.69
5651711--5651739	10	2.7	11	94	5	51	10	0	3	86	0.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5651825--5651853	10	2.7	11	94	5	51	10	0	3	86	0.69
5651939--5651967	10	2.7	11	94	5	51	10	0	3	86	0.69
5652053--5652081	10	2.7	11	94	5	51	10	0	3	86	0.69
5652167--5652195	10	2.7	11	94	5	51	10	0	3	86	0.69
5652281--5652309	10	2.7	11	94	5	51	10	0	3	86	0.69
5652395--5652423	10	2.7	11	94	5	51	10	0	3	86	0.69
5657063--5657101	20	2.0	20	85	10	53	38	10	12	38	1.78
5657639--5657671	16	2.1	16	100	0	66	18	0	12	69	1.18
5657705--5657770	19	3.4	19	91	4	105	19	6	6	68	1.33
5657686--5657770	39	2.2	39	87	8	120	20	4	7	68	1.32
5663623--5663672	9	5.6	9	95	0	91	36	20	34	10	1.86
5664595--5664636	16	2.6	16	88	0	57	42	4	2	50	1.36
5665613--5665672	3	19.7	3	89	3	93	33	3	0	63	1.11
5671897--5672115	98	2.2	98	92	1	359	30	19	18	31	1.96
5672083--5672204	44	2.8	42	85	3	145	27	22	19	30	1.98
5690821--5691114	150	2.0	150	100	0	588	43	3	4	49	1.37
5691085--5691154	24	2.8	24	75	12	70	41	2	5	50	1.41
5693723--5693754	15	2.1	15	94	0	55	68	9	6	15	1.36
5696255--5696280	12	2.2	12	100	0	52	7	15	30	46	1.74
5696348--5696577	113	2.0	114	88	0	345	25	23	24	26	2.00
5719556--5719712	42	3.7	42	82	7	194	25	20	20	33	1.97
5723851--5724094	19	13.5	17	68	14	89	40	10	12	36	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5723851--5724050	37	5.6	35	78	9	117	41	10	12	37	1.76
5723851--5724106	17	14.2	17	70	14	120	41	9	12	36	1.76
5724851--5724906	7	8.7	7	76	11	50	0	19	0	80	0.71
5724852--5724919	19	3.9	18	83	11	88	0	22	0	77	0.76
5724851--5724918	12	5.2	13	76	13	68	0	20	0	79	0.73
5724852--5724909	6	9.3	6	78	14	64	0	20	0	79	0.74
5724854--5724919	22	3.0	22	80	12	82	0	22	0	77	0.77
5725531--5725592	30	2.1	30	87	3	90	38	1	25	33	1.66
5725622--5725730	29	3.7	29	75	11	98	41	6	22	30	1.78
5725921--5725946	5	5.2	5	100	0	52	80	0	0	19	0.71

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