genome.fa.s25.2.7.7.80.10.50.1000.5.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: 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  5  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)
821555--821632	33	2.2	36	86	11	108	48	1	0	50	1.09
821620--821679	28	2.1	29	82	14	72	35	3	0	61	1.12
831514--831566	16	3.2	16	75	19	56	45	0	0	54	0.99
831591--831654	12	5.8	12	74	20	59	32	1	0	65	1.02
831547--831644	28	3.4	30	74	7	87	34	0	3	62	1.11
831598--831644	14	3.2	14	75	19	51	31	0	0	68	0.90
831606--831643	19	2.0	18	90	10	58	36	0	0	63	0.95
832096--832152	28	2.0	29	96	3	107	35	7	7	50	1.56
832146--832205	26	2.3	27	83	13	74	50	1	0	48	1.11
832654--832695	22	2.0	21	85	4	57	50	0	0	50	1.00
833079--833121	3	14.3	3	100	0	86	65	0	0	34	0.93
836685--836714	10	3.0	10	95	0	51	10	0	63	26	1.26
836710--836897	94	1.9	98	84	7	249	42	13	31	12	1.81
839154--839191	19	2.0	20	89	5	60	18	2	0	78	0.86
840247--840278	2	16.0	2	100	0	64	50	0	0	50	1.00
840561--840669	43	2.5	44	78	14	111	57	0	0	42	0.98
846097--846143	23	2.1	21	84	11	58	29	10	8	51	1.66
846673--846728	25	2.2	26	81	9	71	48	0	0	51	1.00
847358--847411	27	2.0	27	82	7	65	61	1	9	27	1.37
847646--847678	3	11.3	3	87	6	50	33	0	0	66	0.92
848894--849015	17	7.9	16	66	19	55	48	0	2	48	1.20
848984--849036	27	2.0	27	81	7	63	58	0	3	37	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
850028--850072	3	15.0	3	95	0	81	64	0	2	33	1.06
851437--851461	2	12.5	2	100	0	50	0	48	0	52	1.00
854935--855315	70	5.4	70	84	2	221	24	16	18	40	1.90
854935--855314	140	2.7	140	80	4	372	24	16	18	40	1.90
855614--855640	3	9.0	3	100	0	54	66	0	0	33	0.92
855760--855806	13	3.4	13	78	16	58	34	0	4	61	1.15
855748--855831	29	2.8	30	83	7	118	45	0	4	50	1.23
856149--856283	67	2.0	67	98	0	261	37	22	24	16	1.94
857061--857096	15	2.5	14	91	8	63	44	0	0	55	0.99
857055--857096	5	8.4	5	82	17	52	45	0	0	54	0.99
857055--857093	20	2.0	20	90	5	62	43	0	0	56	0.99
857425--857457	2	17.0	2	93	6	59	48	0	0	51	1.00
857964--858037	32	2.4	32	80	17	93	58	0	0	41	0.98
859612--859668	22	2.5	24	81	16	68	33	5	7	54	1.50
866902--866940	20	2.0	20	84	0	51	43	0	0	56	0.99
873687--873717	16	1.9	16	93	0	53	83	6	3	6	0.88
875109--875309	109	1.8	112	87	6	302	45	1	10	41	1.48
875620--875680	30	2.0	31	87	3	88	44	1	1	52	1.20
875670--875736	28	2.4	28	87	5	91	59	0	2	37	1.13
879796--879834	14	2.8	13	85	11	51	46	0	0	53	1.00
885903--885958	26	2.2	25	78	6	60	50	7	0	42	1.30
908702--908758	3	19.0	3	77	0	60	56	0	35	8	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
908683--908758	12	6.3	12	77	8	57	55	0	35	9	1.32
911908--911939	2	16.0	2	100	0	64	50	0	0	50	1.00
921733--921786	3	18.0	3	96	0	81	61	0	5	33	1.19
924070--924101	3	10.7	3	100	0	64	68	0	0	31	0.90
924746--924779	14	2.3	15	90	5	52	14	8	32	44	1.76
926886--926925	20	2.0	20	90	9	64	67	0	0	32	0.91
926882--926926	17	2.5	18	80	19	58	66	0	0	33	0.92
928535--928568	17	2.0	17	94	0	59	41	8	0	50	1.34
928541--928576	17	2.1	17	89	0	54	44	5	0	50	1.25
928605--928641	14	2.6	14	82	0	56	48	0	0	51	1.00
928896--928935	17	2.4	16	84	12	53	72	0	0	27	0.85
929476--929506	2	15.5	2	100	0	62	0	48	0	51	1.00
935211--935260	14	3.5	14	89	8	57	50	0	2	48	1.12
935211--935252	2	21.0	2	90	9	68	47	0	2	50	1.14
935891--935916	2	13.0	2	100	0	52	50	0	0	50	1.00
937579--938964	707	2.0	706	88	2	2070	44	12	6	36	1.68
939540--939567	2	14.0	2	100	0	56	0	50	0	50	1.00
943520--943555	18	2.0	18	100	0	72	27	16	11	44	1.82
944019--944044	3	8.7	3	100	0	52	69	0	0	30	0.89
944201--944274	20	3.5	21	80	14	82	56	0	0	43	0.99
944170--944270	28	3.8	26	76	14	100	58	0	0	40	1.05
944170--944267	11	8.7	11	70	20	60	58	0	1	40	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
944191--944285	27	3.5	28	77	11	99	60	0	0	40	0.97
950838--950867	2	15.0	2	100	0	60	50	0	0	50	1.00
951056--951125	27	2.6	28	78	15	76	45	0	0	54	0.99
951074--951112	20	2.0	20	85	5	53	51	0	0	48	1.00
951082--951192	33	3.3	33	75	8	100	43	0	1	54	1.10
960710--960735	2	13.0	2	100	0	52	50	50	0	0	1.00
961655--961752	35	2.9	35	79	11	114	42	0	1	56	1.06
961652--961752	34	3.0	34	77	15	102	43	0	0	55	1.06
968635--968677	20	2.2	19	84	12	52	48	2	4	44	1.36
970854--970878	2	12.5	2	100	0	50	52	0	0	48	1.00
982808--982840	12	2.8	12	100	0	66	66	9	0	24	1.20
983009--983063	27	2.0	27	96	0	101	58	3	0	38	1.16
988815--988850	16	2.2	16	100	0	72	30	13	16	38	1.88
994526--994581	27	2.1	27	87	6	80	48	1	0	50	1.11
999812--999877	20	3.2	20	75	12	53	39	0	0	60	0.97
999818--999896	28	2.8	29	76	12	76	41	0	0	58	0.98
999819--999943	35	3.6	35	76	16	109	40	0	0	58	1.04
999882--999940	13	4.9	13	74	19	56	37	0	1	61	1.07
999874--999939	34	1.9	35	87	3	98	37	0	1	60	1.06
999883--999952	19	3.9	19	74	12	76	38	0	1	60	1.06
1000261--1000291	15	2.1	14	94	5	53	58	3	0	38	1.15
1000766--1000812	23	2.1	23	88	4	69	46	2	6	44	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1001015--1001052	14	2.6	15	84	15	53	47	0	0	52	1.00
1005860--1005893	17	1.9	18	94	5	61	44	8	0	47	1.34
1005954--1005993	21	2.0	21	90	5	64	42	0	0	57	0.98
1012626--1012677	19	2.7	19	75	0	50	80	3	5	9	0.99
1020536--1020572	18	2.2	18	85	9	51	45	0	0	54	1.00
1021096--1021132	14	2.8	14	84	12	51	43	0	2	54	1.14
1021096--1021144	14	3.9	13	79	15	50	44	2	2	51	1.24
1034097--1034134	2	19.0	2	100	0	76	50	0	0	50	1.00
1034585--1034619	2	17.5	2	100	0	70	48	0	0	51	1.00
1041882--1041988	29	3.7	28	81	12	108	32	23	5	38	1.78
1041862--1041997	29	4.7	29	80	6	107	35	25	5	33	1.80
1042688--1042804	60	2.0	60	92	0	198	31	17	11	39	1.85
1058203--1058237	2	17.5	2	100	0	70	51	0	0	48	1.00
1058905--1058959	28	2.0	28	82	7	67	47	3	0	49	1.19
1059028--1059105	5	15.2	5	74	10	50	33	0	0	66	0.92
1059019--1059105	32	2.7	32	82	12	97	35	0	0	64	0.94
1059049--1059102	21	2.5	22	87	9	83	33	0	0	66	0.92
1059049--1059103	11	5.0	11	84	6	67	32	0	0	67	0.91
1060751--1060788	20	1.9	20	94	0	67	47	2	0	50	1.15
1063445--1063488	21	2.0	22	86	4	63	63	0	0	36	0.95
1063956--1064006	20	2.5	21	87	6	70	41	0	0	58	0.98
1063946--1063997	22	2.4	20	81	12	59	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1064933--1065027	33	2.6	37	82	12	101	37	5	1	55	1.29
1066779--1066813	3	11.7	3	100	0	70	34	0	0	65	0.93
1067057--1067095	19	2.1	19	100	0	78	35	10	0	53	1.35
1067491--1067524	2	17.0	2	100	0	68	50	0	0	50	1.00
1067996--1068028	3	11.0	3	93	0	57	30	0	3	66	1.06
1068937--1069003	15	4.5	15	77	9	66	58	0	0	41	0.98
1068976--1069070	32	2.5	37	73	26	92	56	0	0	43	0.99
1069015--1069071	18	3.3	18	73	11	57	61	0	0	38	0.96
1068984--1069055	32	2.2	32	85	9	101	55	0	0	44	0.99
1070063--1070097	2	17.5	2	93	0	61	48	0	2	48	1.16

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