genome.fa.s6.2.7.7.80.10.50.1000.2.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  2  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)
390084--390126	16	2.7	16	81	0	59	30	0	18	51	1.47
390856--390893	17	2.2	17	100	0	76	42	5	13	39	1.66
393832--393857	12	2.2	12	100	0	52	38	7	15	38	1.76
393932--393962	15	2.1	15	93	0	53	45	9	0	45	1.36
395651--395706	27	2.1	27	96	0	103	30	16	23	30	1.96
398506--398536	15	2.1	15	93	0	53	45	9	0	45	1.36
398585--398638	27	2.0	27	100	0	108	37	14	7	40	1.74
399302--399344	16	2.7	16	81	0	59	30	0	18	51	1.47
401235--401331	46	2.1	46	90	0	149	41	13	14	30	1.84
401281--401429	56	2.6	57	92	2	246	40	11	17	30	1.85
401501--401559	29	2.0	29	96	0	109	23	20	10	45	1.81
404014--404234	120	1.8	121	97	2	419	36	4	8	50	1.53
409789--409819	16	1.9	16	100	0	62	45	22	12	19	1.84
421627--421664	20	1.9	20	84	10	51	55	10	2	31	1.48
427615--427675	17	3.4	17	68	12	50	32	3	11	52	1.54
427593--427684	37	2.5	37	89	7	134	33	5	13	47	1.65
427689--427794	9	11.8	9	75	13	67	28	6	17	47	1.73
427683--427795	18	6.3	18	79	8	113	28	6	17	47	1.72
427691--427794	27	3.9	27	79	5	102	28	6	17	47	1.73
428747--428792	4	11.5	4	100	0	92	50	26	0	23	1.50
436496--436563	32	2.1	32	100	0	136	35	5	10	48	1.61
451549--451606	30	1.9	30	89	0	89	12	25	41	20	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
456058--456084	8	3.4	8	100	0	54	59	0	0	40	0.98
456392--456442	21	2.5	20	81	15	59	58	1	0	39	1.09
456392--456438	7	6.6	7	79	11	51	57	2	0	40	1.11
456611--456818	107	1.9	107	92	0	344	45	12	11	30	1.78
457565--457720	38	4.1	38	100	0	312	37	41	2	18	1.64
492256--492297	21	2.0	21	95	0	75	28	11	14	45	1.80
494238--494277	21	2.0	20	85	14	55	32	2	22	42	1.67
498907--498949	21	2.0	21	82	8	52	58	13	2	25	1.48
499687--499722	16	2.2	16	100	0	72	50	11	8	30	1.67
501252--501277	13	2.0	13	100	0	52	30	23	23	23	1.99
501997--502096	28	3.6	29	89	8	154	40	11	2	47	1.50
502174--502249	19	4.1	18	77	5	80	35	9	0	55	1.32
502179--502249	37	1.9	37	94	0	124	38	9	0	52	1.35
502548--502621	37	2.0	37	94	0	130	48	2	5	43	1.40
502552--502626	18	4.1	18	76	19	75	52	1	5	41	1.33
502595--502635	19	2.1	19	86	4	55	53	0	9	36	1.34
502845--502915	37	1.9	37	94	0	124	49	0	8	42	1.33
502845--502919	18	4.1	19	81	6	93	52	0	8	40	1.31
502888--502928	19	2.1	19	86	4	55	53	0	9	36	1.34
502992--503042	27	1.9	26	92	4	84	21	31	23	23	1.98
503132--503229	28	3.5	28	91	2	162	48	1	12	37	1.47
520487--520547	15	4.1	15	97	0	113	19	54	8	18	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
530675--530876	68	3.0	68	99	0	395	23	17	13	45	1.84
531773--531805	13	2.6	13	90	4	50	36	12	0	51	1.39
538774--538823	19	2.4	21	87	12	77	38	0	2	60	1.09
541513--541553	3	13.7	3	100	0	82	65	0	0	34	0.93
545676--545715	6	6.7	6	100	0	80	32	35	15	17	1.91
546627--546663	19	1.9	19	89	10	58	48	0	2	48	1.15
548682--548707	10	2.6	10	100	0	52	76	7	0	15	0.99
548681--548709	10	2.7	11	89	10	51	75	6	0	17	1.01
561086--561114	2	14.5	2	100	0	58	51	0	0	48	1.00
562427--562464	18	2.2	17	90	9	60	47	0	0	52	1.00
568140--568169	16	1.9	15	93	6	51	26	0	6	66	1.16
569193--569248	29	2.0	28	86	10	78	41	1	21	35	1.64
569236--569271	18	1.9	19	88	5	56	38	0	27	33	1.57
570145--570184	14	2.9	14	84	0	53	32	7	17	42	1.77
570153--570219	35	1.9	35	87	3	100	31	10	13	44	1.77
570168--570207	20	2.0	20	85	0	53	27	12	12	47	1.77
574163--574207	23	2.0	23	95	0	81	20	22	24	33	1.97
574519--574673	77	2.0	78	94	2	276	23	16	23	36	1.95
575582--575678	40	2.5	39	77	6	108	24	17	27	29	1.97
604248--604309	29	2.2	29	94	2	108	48	0	4	46	1.23
605349--605385	19	1.9	19	88	0	56	67	0	2	29	1.04
605733--605801	31	2.2	30	80	10	77	46	4	13	36	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
617944--617989	15	2.8	16	83	12	58	58	0	0	41	0.98
617943--617989	17	2.8	17	84	15	71	57	0	0	42	0.98
620570--620653	44	1.9	44	82	0	105	16	15	28	39	1.89
623262--623961	236	3.0	236	90	3	1039	33	17	18	30	1.94
628311--628349	18	2.0	20	85	9	55	43	0	0	56	0.99
628349--628413	29	2.1	32	83	8	82	35	4	0	60	1.18
630800--630875	32	2.3	34	86	6	111	48	10	5	35	1.60
630854--630892	13	3.0	13	92	0	69	53	10	7	28	1.62
630866--631002	67	2.0	67	93	5	233	49	12	10	27	1.72
632647--632783	49	2.7	51	88	4	190	29	12	28	29	1.93
634168--634275	41	2.6	41	86	2	155	58	0	3	37	1.22
634212--634271	30	2.0	31	83	9	79	51	1	3	43	1.28
634228--634283	29	1.9	29	85	7	78	57	1	1	39	1.20
635127--635197	36	2.0	36	94	0	124	28	11	12	47	1.76
638370--638841	236	2.0	236	86	2	653	33	15	19	30	1.93
643129--643825	236	3.0	233	90	2	1052	35	16	17	31	1.92
646215--646318	51	2.0	51	92	3	174	43	20	18	18	1.89
647522--647571	9	5.6	9	75	15	50	52	2	0	46	1.12
651616--651660	18	2.5	18	85	0	63	40	48	11	0	1.39
651617--651657	14	2.9	14	85	0	55	36	51	12	0	1.40
653559--653606	24	2.0	25	92	8	82	29	29	14	27	1.95
658155--658192	6	6.3	6	100	0	76	50	18	0	31	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
677213--677408	89	2.2	91	84	2	254	37	22	9	31	1.85
677454--677503	19	2.6	19	81	6	57	62	0	2	36	1.07
677472--677584	38	3.0	38	75	6	104	60	1	2	35	1.21
678375--678426	19	2.8	19	77	13	54	59	3	1	34	1.27
683713--683787	23	3.3	23	90	3	116	17	21	29	32	1.96
684806--684831	2	13.0	2	100	0	52	50	0	0	50	1.00
687826--687867	17	2.5	17	82	17	52	35	2	0	61	1.09
687948--687988	17	2.5	16	92	4	64	63	4	0	31	1.15
687965--688012	22	2.1	23	85	11	64	62	4	2	31	1.26
696784--696843	9	6.7	9	77	7	59	26	0	5	68	1.10
696796--696853	28	2.1	27	81	9	64	36	0	3	60	1.14
708888--708920	8	4.1	8	85	14	50	84	0	3	12	0.72
711664--711695	3	10.7	3	93	0	55	31	3	0	65	1.08
714700--714739	14	2.9	14	84	0	53	32	7	17	42	1.77
714708--714774	35	1.9	35	87	3	100	31	10	13	44	1.77
714723--714762	20	2.0	20	85	0	53	27	12	12	47	1.77
721025--721078	6	9.0	6	79	0	63	64	22	12	0	1.27
721025--721078	24	2.2	24	96	0	99	64	22	12	0	1.27
723494--723525	1	32.0	1	93	0	55	96	3	0	0	0.20
728814--728863	21	2.4	22	80	6	59	42	2	0	56	1.11
729227--729255	12	2.5	12	94	5	51	48	0	0	51	1.00
732983--733034	21	2.5	21	84	3	70	26	19	1	51	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
745803--746826	518	2.0	517	95	1	1829	24	13	16	46	1.82
751088--751446	179	2.0	180	99	0	711	38	15	23	22	1.92
763672--763713	18	2.3	18	91	0	66	28	14	21	35	1.92
763955--764020	31	2.2	31	97	2	125	31	16	6	45	1.72
764101--764148	24	2.0	24	84	8	62	56	4	4	35	1.38
768414--768478	32	2.0	32	93	0	112	33	18	12	35	1.88
769504--769554	21	2.4	22	80	3	59	45	0	7	47	1.32
775103--775139	18	2.1	18	100	0	74	32	16	40	10	1.83
776016--776104	46	2.0	46	84	4	119	35	29	3	31	1.74
776086--776138	16	3.3	15	82	10	61	24	30	3	41	1.72

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