genome.fa.s25.2.7.7.80.10.50.1000.26.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  26  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)
4447749--4447782	17	2.0	17	88	0	50	76	0	0	23	0.79
4447789--4447838	25	2.0	26	84	4	66	54	0	2	44	1.11
4447808--4447968	35	4.6	34	70	13	112	54	1	3	41	1.24
4447883--4447913	15	2.1	15	93	0	53	45	0	3	51	1.17
4447898--4447977	29	2.9	27	75	15	83	56	2	1	40	1.21
4448500--4448810	157	2.0	157	88	3	466	39	14	5	41	1.68
4448884--4448918	16	2.2	16	89	0	52	37	0	5	57	1.23
4449831--4451272	22	69.1	20	71	20	312	10	2	80	6	0.97
4449831--4449923	21	4.2	22	81	12	86	9	7	78	4	1.08
4449823--4449900	12	6.6	12	80	12	72	7	8	80	2	0.98
4449972--4450009	16	2.4	16	95	0	67	18	5	76	0	0.97
4449880--4450112	15	15.8	15	69	20	50	12	3	78	4	1.03
4450012--4451316	67	20.3	64	69	17	426	9	2	81	6	0.95
4450028--4450114	1	87.0	1	77	0	75	5	3	87	3	0.74
4449997--4451231	47	24.6	49	70	20	266	9	2	81	6	0.94
4449831--4451365	28	52.7	28	70	16	455	10	2	80	6	0.98
4450171--4450207	1	37.0	1	88	0	56	2	0	94	2	0.36
4450622--4451376	305	2.4	300	79	8	746	7	2	84	5	0.84
4449756--4451381	52	30.0	51	69	14	539	10	2	80	6	0.99
4450487--4451221	1	735.0	1	74	0	525	7	1	85	4	0.79
4450932--4451350	53	7.6	58	78	14	241	4	2	87	5	0.73
4451287--4451376	25	3.6	26	76	23	79	8	3	78	8	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4449823--4451376	33	48.5	30	70	17	592	9	2	80	6	0.98
4450487--4451380	20	40.0	21	74	15	515	7	2	84	5	0.86
4451432--4451493	23	2.6	24	82	5	72	19	0	72	8	1.09
4451920--4452129	1	210.0	1	93	0	348	0	1	1	96	0.29
4460716--4460749	16	2.1	16	88	0	50	26	14	11	47	1.79
4460754--4460828	16	4.7	16	78	6	80	45	4	5	45	1.45
4460868--4460938	16	4.4	16	76	0	70	45	11	2	40	1.55
4462379--4462429	3	17.3	3	76	11	52	35	0	1	62	1.06
4464216--4464259	21	2.0	22	86	4	63	40	0	0	59	0.98
4465078--4465122	21	2.1	21	87	0	63	48	0	0	51	1.00
4496140--4496165	13	2.0	13	100	0	52	53	7	0	38	1.30
4496312--4496355	18	2.5	17	82	10	52	52	2	0	45	1.13
4496265--4496338	21	3.0	25	67	23	59	54	1	1	43	1.17
4497070--4497101	3	10.7	3	100	0	64	34	0	0	65	0.93
4497527--4497579	16	3.0	18	78	18	58	43	1	0	54	1.11
4501652--4501690	14	2.8	13	85	14	51	15	0	0	84	0.62
4501652--4501690	20	2.0	19	90	5	60	15	0	0	84	0.62
4502023--4502085	28	2.2	29	85	5	92	46	0	1	52	1.10
4502039--4502085	13	3.2	14	79	14	51	42	0	2	55	1.12
4502359--4502403	18	2.5	19	82	10	67	68	0	0	31	0.89
4502342--4502399	19	3.0	20	80	10	57	67	0	0	32	0.91
4502413--4502446	16	2.2	15	94	5	59	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4502437--4502483	24	2.0	24	83	4	60	65	4	2	27	1.22
4502562--4502594	16	2.1	16	94	0	57	69	3	0	27	1.03
4502582--4502672	45	2.0	45	80	4	103	37	1	4	57	1.26
4502634--4502691	26	2.2	26	87	6	80	31	1	3	63	1.21
4502885--4502930	16	3.1	15	75	18	51	50	0	0	50	1.00
4502886--4502948	29	2.2	29	82	5	74	50	0	1	47	1.10
4502998--4503044	23	2.0	23	95	0	85	17	27	17	38	1.91
4503828--4503889	20	3.5	20	66	32	59	45	0	0	54	0.99
4504275--4504305	4	7.8	4	100	0	62	22	0	0	77	0.77
4504287--4504808	232	2.2	230	84	5	642	39	6	5	47	1.55
4505569--4505627	29	2.0	29	100	0	118	42	6	10	40	1.65
4506264--4506506	82	2.9	82	82	3	272	31	9	8	49	1.66
4510582--4510614	2	16.5	2	100	0	66	0	48	0	51	1.00
4511379--4511411	2	16.5	2	93	0	57	0	0	45	54	0.99
4515884--4515908	1	25.0	1	100	0	50	0	0	0	100	0.00
4519053--4519085	13	2.6	13	90	4	50	15	24	6	54	1.63
4527003--4527051	21	2.4	20	89	3	71	44	0	0	55	0.99
4527964--4528000	19	1.9	19	94	0	65	75	2	0	21	0.92
4531734--4531784	2	26.5	2	92	7	88	52	0	47	0	1.00
4534177--4534216	21	2.0	20	85	5	53	22	0	17	60	1.37
4535373--4535408	3	12.0	3	93	0	63	2	0	33	63	1.08
4535926--4535959	17	2.0	18	88	11	54	29	2	0	67	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4535934--4535969	14	2.6	13	87	12	54	27	0	0	72	0.85
4535987--4536021	3	11.7	3	100	0	70	65	0	0	34	0.93
4536036--4536082	23	2.0	23	84	8	60	25	6	2	65	1.27
4536345--4536444	30	3.3	29	75	14	105	47	0	8	45	1.32
4537139--4537174	3	11.7	3	94	5	63	66	0	0	33	0.92
4537555--4537585	16	2.0	15	93	6	53	48	0	0	51	1.00
4537595--4537637	20	2.0	20	86	8	59	51	2	0	46	1.13
4537685--4537738	11	5.4	10	80	14	67	61	0	5	33	1.19
4537685--4537739	20	2.8	20	94	2	94	60	0	5	34	1.20
4537699--4537739	11	3.9	11	87	12	68	58	0	4	36	1.20
4537929--4537989	12	5.2	12	71	9	54	52	3	1	42	1.27
4539502--4539573	28	2.5	31	82	11	89	54	2	6	36	1.42
4540766--4540809	13	3.5	13	81	6	54	61	0	0	38	0.96
4541994--4542051	28	2.0	28	86	6	80	48	3	0	48	1.18
4542405--4542435	2	15.5	2	100	0	62	48	0	0	51	1.00
4544560--4544625	24	2.4	28	76	19	68	46	1	1	50	1.20
4544583--4544630	20	2.4	20	75	6	53	45	0	0	54	0.99
4544687--4544736	18	2.8	19	82	14	63	46	0	0	54	1.00
4545143--4545174	3	10.7	3	93	0	55	65	3	0	31	1.08
4545384--4545431	19	2.5	20	86	3	71	54	0	0	45	0.99
4546770--4546816	8	6.2	8	77	22	57	63	0	0	36	0.94
4546759--4546837	29	2.8	27	85	12	106	63	0	1	35	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4546763--4546837	14	5.4	14	73	9	64	65	0	1	33	1.01
4549269--4549321	20	2.6	20	80	14	63	45	0	9	45	1.36
4549516--4549592	16	4.9	15	77	15	75	35	0	1	63	1.03
4549516--4549595	32	2.5	31	78	15	92	35	0	1	63	1.02
4549519--4549602	17	5.4	15	69	25	50	38	0	1	60	1.04
4550746--4550776	16	1.9	16	93	0	53	48	0	6	45	1.28
4550783--4550843	9	7.4	9	75	15	53	50	0	0	49	1.00
4550787--4550841	16	3.5	16	82	2	67	50	0	0	49	1.00
4553707--4553746	2	20.0	2	100	0	80	50	0	0	50	1.00
4553809--4553854	23	2.0	23	83	8	58	17	2	15	65	1.37
4553950--4553999	20	2.6	19	81	12	50	46	0	2	52	1.12
4554762--4554811	26	1.9	26	95	0	91	32	18	14	36	1.90
4561490--4561552	33	1.9	32	90	3	99	69	6	12	11	1.34
4563360--4563403	2	22.0	2	100	0	88	50	0	0	50	1.00
4563567--4563592	11	2.4	11	100	0	52	92	0	0	7	0.39
4564220--4564288	15	4.4	15	72	7	57	46	4	0	49	1.21
4567609--4567648	2	20.0	2	94	0	71	47	0	2	50	1.14
4571516--4571558	2	22.0	2	95	4	79	51	0	0	48	1.00
4571559--4571692	68	2.0	69	90	1	216	30	26	11	31	1.92
4571859--4571905	23	2.0	23	95	0	85	36	10	27	25	1.89
4572612--4572642	16	1.9	16	93	0	53	9	6	32	51	1.60
4576956--4576983	2	14.0	2	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4576983--4577018	2	18.0	2	100	0	72	50	0	50	0	1.00
4579648--4579748	50	2.1	47	83	5	121	31	6	16	44	1.74
4579688--4579950	50	5.3	49	82	8	250	29	13	18	38	1.89
4579689--4579950	100	2.6	99	80	5	280	29	13	18	38	1.89
4584314--4584569	50	5.1	50	86	2	345	28	20	18	32	1.96
4588330--4588395	28	2.3	29	76	5	71	43	6	4	45	1.49
4591698--4591730	15	2.1	16	88	5	50	45	0	6	48	1.27
4591888--4591935	25	1.9	24	83	8	60	37	2	6	54	1.38
4592076--4592254	69	2.5	72	87	3	267	47	6	11	35	1.64
4592076--4592254	72	2.6	69	86	7	263	47	6	11	35	1.64

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