genome.fa.s1.2.7.7.80.10.50.1000.46.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  46  of  52  ( 6211 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)
7419347--7419401	16	3.4	16	78	9	58	43	14	14	27	1.84
7419440--7419481	21	2.0	22	85	4	59	50	2	4	42	1.36
7419484--7419534	19	2.7	18	79	8	57	43	0	5	50	1.26
7419759--7419802	21	2.0	22	83	12	56	43	0	2	54	1.12
7421319--7421422	6	18.5	6	68	20	64	35	0	0	64	0.94
7421319--7421384	35	1.9	34	87	9	98	36	0	0	63	0.95
7421327--7421437	22	5.1	23	74	14	76	36	0	0	63	1.01
7421323--7421409	8	10.9	8	75	19	67	37	0	0	62	0.96
7426832--7426902	27	2.7	27	77	2	72	28	9	18	43	1.81
7427782--7427811	12	2.6	11	90	10	51	50	0	0	50	1.00
7427791--7427840	17	2.9	17	78	0	64	56	0	0	44	0.99
7427816--7427878	31	2.1	31	90	3	101	57	1	0	41	1.08
7433285--7433329	22	2.1	21	87	4	63	46	0	0	53	1.00
7433619--7433643	2	12.5	2	100	0	50	52	0	0	48	1.00
7433659--7433691	17	2.0	17	88	5	50	72	6	15	6	1.24
7434755--7434787	2	16.5	2	100	0	66	48	0	0	51	1.00
7436611--7436653	22	2.0	21	86	4	59	46	9	0	44	1.35
7438019--7438058	16	2.6	16	84	15	57	40	0	0	60	0.97
7438042--7438127	22	3.8	23	77	14	72	50	1	1	47	1.16
7438377--7438418	14	3.0	14	76	10	50	40	0	0	59	0.97
7439237--7439293	12	4.6	12	72	23	55	66	0	0	33	0.92
7439280--7439342	23	2.7	23	75	4	65	55	6	0	38	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7439450--7439482	14	2.4	14	90	10	50	51	0	0	48	1.00
7439532--7439570	21	1.9	21	94	5	71	61	0	0	38	0.96
7441391--7441422	17	1.9	16	93	6	55	28	0	0	71	0.86
7441439--7441490	22	2.4	22	81	9	63	61	5	0	32	1.20
7442200--7442241	22	1.9	22	90	0	66	47	7	0	45	1.30
7450045--7450082	19	2.1	18	90	5	58	28	0	2	68	1.03
7450726--7450787	33	1.9	33	87	9	83	54	6	1	37	1.36
7451208--7451361	29	5.2	28	71	18	86	40	0	1	57	1.10
7452116--7452156	11	3.6	12	74	12	50	58	0	0	41	0.98
7452258--7452319	32	1.9	32	87	6	90	20	4	11	62	1.46
7453634--7453664	2	15.5	2	93	0	53	0	48	3	48	1.17
7456106--7456256	57	2.6	57	80	0	167	25	25	23	25	2.00
7459829--7459854	3	8.7	3	100	0	52	69	0	0	30	0.89
7461216--7461240	2	12.5	2	100	0	50	0	0	48	52	1.00
7462609--7462640	2	16.0	2	100	0	64	0	50	0	50	1.00
7464971--7465032	23	2.6	23	82	10	63	66	0	0	33	0.92
7465479--7465519	2	20.5	2	84	0	55	41	2	4	51	1.36
7469792--7469821	13	2.4	12	94	5	51	13	3	0	83	0.77
7469787--7469829	22	2.0	22	85	0	59	18	6	0	74	1.04
7471130--7471169	18	2.1	19	86	9	55	52	2	0	45	1.14
7471163--7471217	23	2.3	25	87	6	78	47	0	0	52	1.00
7471114--7471217	12	8.7	12	68	18	56	46	0	0	52	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7472899--7472937	3	13.0	3	100	0	78	33	0	0	66	0.92
7478262--7478288	12	2.2	12	100	0	54	62	0	0	37	0.95
7478768--7478794	3	9.0	3	100	0	54	66	0	0	33	0.92
7479034--7479080	17	2.7	18	87	9	62	61	0	4	34	1.15
7479414--7479457	15	2.8	16	83	13	56	50	0	0	50	1.00
7481469--7481505	16	2.4	16	90	4	58	72	2	0	24	0.97
7483490--7483551	30	2.1	30	96	0	115	40	16	6	37	1.74
7484973--7485042	15	4.2	18	68	17	62	60	0	1	38	1.06
7484968--7485046	25	3.2	24	79	10	90	58	0	1	40	1.06
7486450--7486479	2	15.0	2	100	0	60	50	0	0	50	1.00
7502249--7502676	139	3.0	137	80	9	463	51	16	10	21	1.74
7506142--7506196	28	2.0	28	92	0	92	40	16	18	25	1.91
7507980--7508022	22	2.0	22	90	0	68	20	0	0	79	0.74
7509209--7509531	171	1.9	171	83	2	416	26	18	23	30	1.98
7510593--7510803	72	2.9	72	80	4	237	25	26	18	28	1.98
7514945--7514999	6	9.2	6	95	0	56	7	14	61	16	1.54
7514950--7515015	12	5.5	12	85	7	80	9	16	57	16	1.63
7514954--7515012	6	9.8	6	94	0	82	6	16	59	16	1.58
7528211--7528239	15	1.9	15	100	0	58	51	0	0	48	1.00
7528214--7528247	14	2.3	15	90	5	52	55	0	0	44	0.99
7528708--7528885	85	2.1	85	98	0	347	37	8	6	46	1.62
7529360--7529396	19	1.9	19	88	0	56	27	0	0	72	0.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7537843--7537877	15	2.3	16	90	9	56	37	0	0	62	0.95
7537859--7537901	22	1.9	23	85	4	61	34	0	2	62	1.08
7538551--7538592	21	1.9	23	85	9	61	45	0	0	54	0.99
7539031--7539093	31	2.0	31	81	6	74	44	0	1	53	1.10
7539026--7539094	22	3.0	22	72	12	68	46	0	1	52	1.09
7540694--7540760	28	2.4	28	76	11	66	40	0	0	59	0.97
7540716--7540757	19	2.2	20	86	4	59	40	0	0	59	0.97
7540918--7540988	28	2.6	27	79	14	74	54	1	2	40	1.23
7540925--7541019	25	3.7	25	75	12	68	53	1	1	44	1.14
7540974--7541023	19	2.7	19	76	11	50	62	0	0	38	0.96
7541217--7541241	2	12.5	2	100	0	50	52	0	0	48	1.00
7541241--7541271	2	15.5	2	100	0	62	51	0	48	0	1.00
7541364--7541394	14	2.2	14	94	0	53	58	3	0	38	1.15
7541411--7541492	29	2.8	29	70	17	71	46	0	1	52	1.08
7541871--7541910	20	2.0	21	90	5	64	45	0	0	55	0.99
7543947--7543976	2	15.0	2	100	0	60	50	0	0	50	1.00
7545147--7545186	20	2.0	19	85	9	53	52	0	0	47	1.00
7545185--7545217	13	2.4	14	85	10	50	42	9	0	48	1.35
7545419--7545451	3	11.3	3	90	6	50	39	0	27	33	1.57
7545455--7545506	18	2.9	18	74	23	56	40	0	0	59	0.97
7546865--7546954	41	2.2	41	82	7	105	43	2	0	54	1.12
7551905--7551936	16	2.0	16	93	0	55	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7553745--7553799	27	2.0	27	83	13	69	65	5	0	29	1.15
7554287--7554366	35	2.4	33	85	8	99	43	0	0	56	0.99
7554310--7554360	26	1.9	27	96	4	95	45	0	0	54	0.99
7562707--7562753	23	2.0	23	100	0	94	36	4	25	34	1.76
7563429--7563498	24	3.1	23	78	13	74	62	0	0	37	0.95
7563421--7563476	28	2.0	28	82	10	69	58	0	0	41	0.98
7563437--7563503	23	3.0	23	82	6	75	61	0	0	38	0.96
7563457--7563496	15	2.5	15	84	8	53	67	0	0	32	0.91
7563990--7564066	30	2.7	30	80	6	97	51	0	2	45	1.14
7564330--7564467	20	6.5	22	66	18	60	57	0	0	42	1.04
7564329--7564367	15	2.5	15	87	8	51	61	0	0	38	0.96
7564396--7564468	20	3.3	20	74	18	65	60	1	0	38	1.06
7564322--7564483	11	15.5	11	67	20	53	56	0	1	41	1.12
7565487--7565546	10	6.3	9	78	19	52	55	0	1	43	1.10
7565499--7565532	10	3.6	10	92	7	54	50	0	0	50	1.00
7567049--7567345	150	2.0	149	89	2	452	30	26	21	20	1.98
7567337--7567394	25	2.3	25	96	0	107	15	41	24	18	1.89
7573536--7573603	23	3.1	23	66	25	56	29	4	0	66	1.11
7574043--7574094	27	1.9	27	92	0	86	44	3	9	42	1.55
7574042--7574086	14	3.3	14	78	6	56	48	2	8	40	1.47
7580515--7580625	57	2.0	54	85	5	150	22	17	12	47	1.81
7581150--7581191	15	2.6	16	81	11	50	66	7	2	23	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7586267--7586321	27	2.0	26	89	6	83	18	9	10	61	1.54
7586934--7586979	16	3.1	15	85	11	60	36	0	0	63	0.95
7587062--7587094	15	2.2	16	89	10	52	63	0	0	36	0.95
7588130--7588173	17	2.8	17	80	16	51	56	0	0	43	0.99
7588580--7588636	21	2.7	21	84	7	80	38	3	0	57	1.16
7588580--7588655	21	3.5	22	78	8	75	35	5	0	59	1.20
7589202--7589244	2	21.5	2	95	0	77	51	2	0	46	1.13
7590202--7590244	23	1.9	22	85	4	59	51	2	0	46	1.13
7590836--7590869	18	1.9	18	88	5	52	64	0	0	35	0.94
7591107--7591141	3	11.7	3	93	0	61	34	28	0	37	1.58

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