genome.fa.s25.2.7.7.80.10.50.1000.4.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   

This is table  4  of  56  ( 6609 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)
593822--593886	22	2.9	21	72	19	60	44	1	0	53	1.09
593880--593925	19	2.4	18	86	13	65	52	0	0	47	1.00
594003--594053	20	2.4	20	80	9	57	43	0	1	54	1.11
594016--594088	20	3.5	20	72	18	60	46	0	0	53	1.00
593996--594084	28	3.2	28	69	13	67	47	0	2	50	1.13
602644--602673	2	15.0	2	100	0	60	50	0	0	50	1.00
602673--602704	2	16.0	2	100	0	64	0	0	50	50	1.00
603946--603991	4	11.5	4	85	0	56	47	0	6	45	1.28
603946--603991	6	7.7	6	82	0	56	47	0	6	45	1.28
603946--603991	10	4.6	10	86	0	56	47	0	6	45	1.28
606866--606914	25	2.0	25	95	0	89	30	20	12	36	1.89
610774--610847	39	1.9	38	81	13	89	56	1	4	37	1.27
611075--611130	28	2.0	29	82	3	69	53	3	1	41	1.29
612965--612993	2	14.5	2	100	0	58	48	0	0	51	1.00
613887--613926	8	4.9	8	90	3	53	50	7	0	42	1.30
613887--613920	2	17.0	2	87	0	50	50	5	0	44	1.26
614805--614844	15	2.5	17	80	16	57	47	0	0	52	1.00
616636--616671	2	18.0	2	94	0	63	50	2	0	47	1.15
619796--619927	65	2.0	65	91	0	210	28	15	16	39	1.90
620409--620440	3	10.7	3	100	0	64	0	31	0	68	0.90
638276--638325	25	2.0	25	88	0	73	34	4	0	62	1.14
639009--639033	2	12.5	2	100	0	50	0	48	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
646997--647056	28	2.1	29	82	14	72	30	13	8	48	1.71
647646--647728	32	2.5	33	86	3	114	42	9	31	16	1.81
649155--649182	2	14.0	2	100	0	56	50	0	0	50	1.00
651931--651983	27	2.0	27	84	0	70	26	11	37	24	1.89
651941--652003	27	2.3	27	88	0	90	23	12	42	20	1.86
652701--652747	21	2.2	21	92	0	76	21	4	36	38	1.73
652779--652893	45	2.6	45	95	0	203	15	6	42	35	1.72
659826--659854	2	14.5	2	100	0	58	48	0	51	0	1.00
660176--660211	18	2.1	17	89	5	54	63	2	0	33	1.08
660225--660258	12	2.8	12	86	4	50	47	0	0	52	1.00
672433--672505	18	4.2	17	81	10	76	43	2	9	43	1.51
672447--672524	18	4.3	18	85	3	93	47	3	7	41	1.50
672447--672524	37	2.1	36	83	2	93	47	3	7	41	1.50
675337--675415	37	2.2	36	86	2	104	50	5	5	39	1.46
675337--675415	18	4.3	18	79	3	86	50	5	5	39	1.46
675482--675516	18	1.9	18	88	0	52	22	2	0	74	0.95
676031--676068	16	2.6	14	88	12	51	28	0	2	68	1.03
676081--676116	16	2.2	16	90	0	54	27	8	13	50	1.71
677731--677836	14	7.8	14	69	23	50	40	0	0	57	1.11
677687--677882	67	2.9	67	98	0	376	39	1	1	57	1.15
681636--681666	4	7.8	4	100	0	62	51	22	0	25	1.48
682696--682731	17	2.1	17	100	0	72	30	0	33	36	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
684501--684640	69	2.0	69	100	0	280	26	8	22	42	1.82
695484--695681	99	2.0	99	87	2	281	21	32	17	27	1.96
696841--696869	2	14.5	2	100	0	58	48	0	0	51	1.00
697966--698016	3	17.0	3	79	0	57	33	35	7	23	1.84
697976--698018	6	7.2	6	91	0	68	32	34	11	20	1.89
697966--698016	12	4.2	12	89	0	75	33	35	7	23	1.84
697976--698024	24	2.0	24	92	0	80	30	34	16	18	1.93
698930--698967	2	19.0	2	94	0	67	0	47	0	52	1.00
712060--712190	16	8.5	16	66	19	64	61	0	0	38	1.02
712072--712183	44	2.6	44	77	11	124	58	0	0	40	1.04
712126--712190	18	3.3	19	72	20	53	63	0	0	36	0.95
712120--712186	32	2.1	32	83	13	84	64	0	0	35	0.94
712120--712186	31	2.1	33	83	13	86	64	0	0	35	0.94
712120--712206	31	2.8	31	78	16	83	59	1	0	39	1.05
717812--717856	13	3.7	13	82	11	51	53	0	0	46	1.00
718710--718753	14	2.9	15	83	6	54	50	0	0	50	1.00
718721--718775	23	2.3	23	84	3	65	45	0	1	52	1.11
719507--719540	9	3.7	9	92	7	59	26	0	0	73	0.83
719482--719540	19	3.1	19	83	7	75	27	0	3	69	1.04
721814--721865	14	3.6	14	77	15	52	53	0	0	46	1.00
721814--721855	14	3.1	14	89	3	59	54	0	0	45	0.99
722344--722397	16	3.3	16	75	12	56	42	5	3	48	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
722410--722465	26	2.3	23	79	14	58	44	0	5	50	1.25
723656--723688	2	16.5	2	100	0	66	48	0	51	0	1.00
729044--729070	2	13.5	2	100	0	54	51	0	0	48	1.00
730121--730148	4	7.0	4	100	0	56	75	0	0	25	0.81
730907--731079	17	9.6	19	66	18	86	62	1	0	36	1.03
730924--730970	11	4.2	11	83	5	58	68	0	0	31	0.90
730930--731006	19	4.3	18	76	12	70	66	1	0	32	1.00
730907--731057	40	3.6	41	71	15	112	60	1	0	37	1.05
730989--731050	20	3.2	20	75	11	67	54	0	0	45	0.99
731273--731308	11	3.2	11	88	7	54	83	0	16	0	0.65
731764--731788	8	3.1	8	100	0	50	0	12	0	88	0.53
733285--733343	29	2.1	28	87	9	86	47	0	0	52	1.00
736379--736408	2	15.0	2	100	0	60	50	0	0	50	1.00
736707--736756	3	16.7	3	91	0	82	68	4	0	28	1.08
737345--737406	30	2.1	29	80	19	67	56	0	0	43	0.99
738416--738468	26	2.0	26	96	0	97	37	7	11	43	1.69
748651--748744	4	23.5	4	84	0	98	40	48	7	3	1.47
748651--748744	6	15.7	6	81	0	98	40	48	7	3	1.47
748651--748744	18	5.3	18	83	2	111	40	48	7	3	1.47
753200--753239	2	20.5	2	94	5	73	0	50	0	50	1.00
756829--756863	18	1.9	18	88	11	54	51	5	2	40	1.40
757486--757556	16	4.5	15	70	19	56	54	4	1	39	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
759262--759408	46	3.2	46	68	22	146	38	7	4	49	1.50
759229--759409	91	2.0	91	100	0	362	37	6	4	51	1.48
759976--760001	9	2.9	9	100	0	52	92	0	0	7	0.39
759976--760004	10	3.0	10	95	5	51	89	0	0	10	0.48
766912--766943	2	16.0	2	100	0	64	50	0	0	50	1.00
768239--768286	6	8.3	6	75	25	50	62	0	0	37	0.95
768248--768299	19	2.8	19	85	8	72	57	0	0	42	0.98
769308--769351	19	2.2	20	88	4	63	50	4	2	43	1.35
775225--775271	22	2.0	23	84	8	60	27	2	4	65	1.22
784863--784894	2	16.0	2	100	0	64	50	0	0	50	1.00
785687--785725	11	3.5	11	96	3	69	64	0	0	35	0.94
785687--785725	6	6.8	6	88	11	64	64	0	0	35	0.94
790709--790733	5	5.0	5	100	0	50	80	0	0	20	0.72
793759--793829	23	3.0	22	74	10	61	53	7	0	39	1.28
794291--794337	21	2.2	21	85	7	60	44	0	0	55	0.99
794469--794501	2	17.0	2	93	6	59	51	0	0	48	1.00
802007--802054	17	2.7	18	75	18	55	31	0	0	68	0.90
802956--803032	28	2.5	31	83	10	88	53	0	0	46	1.00
803024--803053	16	1.9	15	93	6	51	53	0	0	46	1.00
803656--803694	16	2.4	16	82	0	51	33	0	2	64	1.08
804089--804133	22	2.0	22	91	0	72	15	11	15	57	1.64
804300--804357	24	2.4	24	82	5	73	56	3	8	31	1.46
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
804331--804488	80	2.0	80	96	0	289	51	5	6	35	1.52
804452--804823	179	2.1	178	87	3	534	43	6	6	43	1.55
808971--809035	34	1.9	34	84	6	87	64	1	3	30	1.18
809345--809376	2	16.0	2	100	0	64	50	0	0	50	1.00
816953--816982	15	1.9	16	93	6	53	76	23	0	0	0.78
817430--817458	3	9.7	3	100	0	58	65	0	0	34	0.93
817709--817744	19	1.9	18	88	5	54	55	2	0	41	1.14
819599--819664	17	3.9	16	76	18	62	53	0	1	45	1.09
821057--821090	2	18.0	2	88	11	54	50	0	0	50	1.00
821563--821645	19	4.5	19	68	28	63	45	0	0	54	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   48   
          49   50   51   52   53   54   55   56