genome.fa.s196.2.7.7.80.10.50.1000.5.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: Scaffold196
Parameters: 2 7 7 80 10 50 1000
Length:  7488280

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   

This is table  5  of  47  ( 5587 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)
552121--552187	16	4.5	16	71	21	56	43	0	0	56	0.99
552526--552551	6	4.3	6	100	0	52	15	0	0	84	0.62
552565--552592	3	9.3	3	100	0	56	0	32	0	67	0.91
557201--557251	22	2.3	24	74	19	56	58	0	3	37	1.16
557526--557556	3	10.3	3	100	0	62	64	0	0	35	0.94
558447--558479	2	17.0	2	93	6	59	51	0	0	48	1.00
558479--558524	2	23.0	2	100	0	92	50	0	50	0	1.00
561299--561364	32	2.1	32	85	0	87	25	9	13	51	1.70
562322--562423	15	6.9	15	70	12	68	44	2	0	52	1.16
562485--562539	20	2.6	20	78	18	58	54	1	0	43	1.10
562555--562598	12	3.8	11	81	18	54	47	0	0	52	1.00
563193--563330	70	2.0	71	83	1	179	44	11	4	39	1.61
568817--568851	13	2.6	14	86	9	54	82	5	11	0	0.82
575619--575644	2	13.0	2	100	0	52	50	0	0	50	1.00
578080--578119	21	1.9	21	89	0	62	42	2	15	40	1.60
583351--583480	68	1.9	68	82	6	165	50	13	3	33	1.59
583473--583575	31	3.3	32	82	5	122	49	2	1	45	1.28
583504--583575	9	7.0	10	71	20	51	51	1	1	45	1.18
590296--590333	20	1.9	20	94	0	67	57	5	2	34	1.35
593314--593366	2	26.5	2	96	0	97	0	47	0	52	1.00
595057--595085	3	9.7	3	100	0	58	31	0	0	68	0.89
597543--597608	29	2.5	26	90	9	98	42	6	4	46	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
597655--597726	37	2.0	36	86	2	99	48	1	0	50	1.09
598135--598175	21	2.0	21	85	9	57	53	0	0	46	1.00
598148--598190	15	2.9	14	80	13	50	46	0	2	51	1.13
598173--598212	20	2.0	20	85	9	55	37	0	5	57	1.21
598198--598253	23	2.4	23	79	8	60	44	0	1	53	1.11
600223--600252	2	15.0	2	100	0	60	50	0	0	50	1.00
600270--600302	2	16.5	2	93	0	57	48	0	48	3	1.17
602065--602232	83	2.0	83	100	0	336	26	16	15	41	1.88
606339--606380	21	2.0	21	86	13	61	61	0	0	38	0.96
607024--607082	25	2.4	25	81	13	70	57	0	0	42	0.98
608275--608306	16	2.0	17	88	11	50	65	0	0	34	0.93
608766--608801	18	1.9	19	88	5	56	41	0	0	58	0.98
609954--610012	30	2.0	29	83	9	75	35	0	1	62	1.05
610047--610093	15	2.9	17	78	18	55	53	2	0	44	1.12
610065--610131	23	2.8	24	70	14	59	53	2	0	43	1.16
616507--616566	29	2.0	29	84	9	77	38	3	1	56	1.26
616550--616602	16	3.2	17	76	17	67	45	0	1	52	1.11
616551--616628	32	2.5	31	87	6	104	42	0	1	56	1.07
616543--616637	17	5.3	17	72	19	68	41	0	1	57	1.05
616619--616654	11	3.3	11	88	11	56	27	0	0	72	0.85
617366--617393	2	14.0	2	100	0	56	50	0	0	50	1.00
621369--621438	24	3.0	23	76	2	68	55	8	12	22	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
628321--628349	2	14.5	2	100	0	58	48	0	0	51	1.00
628775--628804	3	10.0	3	100	0	60	33	0	0	66	0.92
629492--629524	12	2.7	13	86	13	52	18	0	0	81	0.68
629661--629708	24	2.0	25	87	4	71	45	4	0	50	1.21
630787--630820	2	17.0	2	100	0	68	50	0	0	50	1.00
631244--631302	27	2.1	28	81	3	66	44	0	0	55	0.99
631220--631301	34	2.4	34	78	13	89	46	0	0	53	1.00
631455--631513	27	2.2	28	85	11	79	42	1	3	52	1.28
632894--632925	6	5.3	6	100	0	64	65	0	34	0	0.93
634367--634394	2	14.0	2	100	0	56	50	0	0	50	1.00
637147--637178	4	8.5	4	93	6	50	46	0	0	53	1.00
637416--637447	2	16.0	2	93	0	55	53	0	0	46	1.00
637877--637915	17	2.3	17	86	0	60	28	2	0	69	1.02
644524--644570	12	3.9	12	78	15	53	34	0	2	63	1.06
644531--644578	24	1.9	24	83	8	60	37	0	2	60	1.09
644684--644743	30	2.0	31	90	3	95	35	3	0	61	1.12
645564--645623	30	2.0	29	83	3	75	56	3	0	40	1.16
646154--646191	17	2.2	17	95	0	67	60	0	0	39	0.97
646163--646205	21	2.2	19	87	8	59	60	0	0	39	0.97
646774--646822	2	24.5	2	100	0	98	51	0	0	48	1.00
647180--647238	17	3.5	17	74	17	52	55	5	0	38	1.22
648308--648423	27	3.9	29	76	12	119	50	0	3	44	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
648308--648417	57	1.9	57	83	3	139	50	0	3	45	1.25
648302--648433	57	2.4	54	78	13	135	53	0	3	43	1.21
648302--648440	59	2.4	57	79	8	138	53	0	2	42	1.20
648444--648482	17	2.4	16	91	4	60	46	0	0	53	1.00
648435--648489	16	3.4	17	75	12	53	54	0	0	45	0.99
649023--649127	25	4.2	24	71	18	72	40	0	0	59	0.98
649024--649075	17	2.8	19	83	13	65	46	0	0	53	1.00
649022--649075	19	3.1	17	84	12	65	46	0	0	53	1.00
649072--649125	22	2.5	21	78	21	58	33	0	0	66	0.92
650240--650336	32	2.8	34	81	13	108	43	0	0	56	0.99
650276--650343	24	3.0	24	80	20	92	44	0	0	55	0.99
650230--650343	44	2.6	45	77	17	114	43	0	0	56	0.99
650780--650815	3	12.0	3	100	0	72	33	0	0	66	0.92
652401--652438	20	2.0	18	90	10	58	55	2	0	42	1.14
652433--652465	16	2.1	16	88	11	50	36	6	9	48	1.60
652534--652592	16	3.7	16	78	13	68	50	8	1	38	1.43
655150--655232	41	2.0	42	92	2	141	36	2	13	48	1.55
658825--658863	2	20.0	2	92	5	62	46	0	0	53	1.00
660201--660227	2	13.5	2	100	0	54	51	0	0	48	1.00
673252--673284	10	3.0	11	86	13	50	36	0	0	63	0.95
673817--673884	32	2.1	32	83	5	84	51	2	4	41	1.37
676251--676472	115	2.0	111	85	3	300	34	21	15	28	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
677162--677233	32	2.2	32	80	0	81	16	9	23	50	1.75
677427--677505	23	3.4	23	72	16	81	40	8	10	40	1.70
677408--677506	47	2.1	47	94	0	171	39	10	10	40	1.73
677703--677732	15	2.0	15	100	0	60	66	0	0	33	0.92
677699--677735	15	2.6	14	88	12	58	59	0	0	40	0.97
678317--678401	16	5.5	15	70	12	55	41	1	1	56	1.14
678350--678401	15	3.4	14	76	12	50	40	1	0	57	1.10
678349--678401	16	3.4	16	75	12	56	39	1	0	58	1.09
678348--678411	16	4.1	16	73	15	53	37	1	0	60	1.06
678590--678675	39	2.2	39	84	12	106	17	8	3	70	1.25
679458--679509	17	3.4	15	75	12	52	57	1	1	38	1.21
680630--680705	16	4.8	16	67	16	50	47	27	10	14	1.77
680629--680695	31	2.1	32	88	2	100	46	28	13	11	1.79
680784--680822	2	19.5	2	100	0	78	51	0	0	48	1.00
683518--683545	2	14.0	2	100	0	56	50	0	0	50	1.00
684737--684768	14	2.3	14	94	0	55	25	37	28	9	1.87
686597--686666	27	2.6	27	79	0	68	20	37	15	27	1.93
686697--686789	27	3.4	27	77	0	87	13	34	22	29	1.93
688900--688924	10	2.5	10	100	0	50	84	0	0	16	0.63
692112--692344	116	2.0	116	95	0	421	42	16	17	23	1.88
698264--698293	15	2.0	15	100	0	60	26	20	13	40	1.89
698700--698822	61	2.0	61	91	0	201	39	15	8	36	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
699288--699329	16	2.6	16	80	0	57	28	2	4	64	1.26
700382--700489	33	3.3	33	88	0	153	42	6	12	37	1.69
701779--701805	2	13.5	2	100	0	54	48	0	0	51	1.00
702137--702203	5	13.4	5	75	17	59	23	2	2	70	1.15
702137--702203	9	6.7	10	77	16	59	23	2	2	70	1.15
702140--702203	24	2.9	20	78	17	56	23	3	3	70	1.16
702313--702352	21	1.9	21	84	0	53	45	0	2	52	1.14
703785--703832	17	2.8	18	78	9	55	60	0	6	33	1.22
704105--704144	21	1.9	21	84	0	53	40	2	17	40	1.63
709152--709189	15	2.4	16	86	4	60	44	0	0	55	0.99

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