genome.fa.s1.2.7.7.80.10.50.1000.37.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  37  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)
6117504--6117598	27	3.4	27	75	15	77	51	0	2	46	1.12
6117770--6117813	3	14.7	3	90	0	70	36	0	0	63	0.95
6117756--6117842	12	7.2	12	71	17	56	45	1	0	52	1.08
6117772--6117844	24	3.0	24	82	7	85	49	0	0	50	1.00
6123226--6123292	16	4.1	17	72	18	61	55	0	1	43	1.09
6123227--6123316	15	5.6	17	70	17	68	57	0	1	41	1.06
6123288--6123331	5	9.0	5	80	14	56	61	0	0	38	0.96
6126119--6126196	12	6.6	12	75	8	61	42	0	0	57	0.98
6131650--6131708	27	2.1	27	82	14	68	47	1	0	50	1.11
6131641--6131702	32	2.0	32	84	9	85	48	0	0	51	1.00
6132150--6132182	14	2.4	14	95	5	59	30	12	9	48	1.71
6135525--6135576	19	2.7	19	81	3	59	38	0	0	61	0.96
6136104--6136475	193	1.9	193	79	4	419	38	10	9	41	1.72
6138803--6138854	12	4.3	12	73	7	52	57	0	0	42	0.98
6138803--6138878	25	3.2	24	81	10	86	59	0	0	40	0.98
6138818--6138881	22	2.8	23	83	11	78	60	0	0	39	0.97
6143552--6143715	48	3.0	56	79	17	209	44	14	17	23	1.85
6144953--6145027	30	2.5	30	95	0	132	45	21	9	24	1.81
6146306--6146342	18	2.1	18	90	5	58	72	2	2	21	1.09
6146333--6146381	21	2.4	22	77	16	61	55	2	4	38	1.31
6148378--6148443	28	2.4	28	84	5	80	50	10	13	25	1.74
6148702--6148746	20	2.2	20	84	7	56	62	6	0	31	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6151338--6151384	21	2.2	21	92	0	76	53	14	6	25	1.65
6153645--6153687	18	2.4	18	84	7	61	34	0	0	65	0.93
6153685--6153747	27	2.3	27	76	13	67	55	0	1	42	1.09
6153966--6154009	18	2.4	18	78	10	54	25	4	2	68	1.20
6156085--6156115	15	2.1	15	93	0	53	51	0	0	48	1.00
6156628--6156677	12	4.2	12	76	16	50	40	2	0	58	1.10
6156707--6156756	12	4.2	12	76	16	50	40	2	0	58	1.10
6156642--6156760	24	4.7	24	66	19	71	40	5	1	52	1.33
6160328--6160404	30	2.4	31	85	12	95	54	0	3	41	1.19
6160687--6160861	20	8.5	20	66	21	69	60	0	1	37	1.08
6160706--6160758	27	2.0	26	85	3	70	66	0	0	33	0.92
6160700--6160860	18	8.6	18	67	21	64	60	0	0	37	1.06
6160761--6160867	17	6.7	15	68	24	60	58	0	0	39	1.11
6160743--6160869	18	7.8	16	71	19	77	57	0	0	40	1.10
6160715--6160868	8	17.5	8	68	18	51	59	0	0	39	1.07
6163231--6163265	18	2.0	18	88	5	54	48	0	0	51	1.00
6163831--6163883	26	2.0	27	85	10	74	54	1	3	39	1.29
6165279--6165304	2	13.0	2	100	0	52	50	0	0	50	1.00
6167421--6167463	17	2.6	17	79	13	54	55	0	0	44	0.99
6167494--6167535	21	2.0	21	86	9	59	57	2	0	40	1.12
6168903--6168937	18	1.9	18	100	0	70	40	2	0	57	1.14
6169415--6169465	16	3.1	16	80	8	59	37	1	1	58	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6169751--6169802	16	3.3	16	76	7	54	34	0	0	65	0.93
6170584--6170632	20	2.4	20	76	10	55	59	4	4	32	1.35
6170968--6170995	4	7.0	4	100	0	56	50	0	0	50	1.00
6171080--6171144	23	2.6	25	78	16	71	30	3	6	60	1.37
6171080--6171154	25	2.9	26	78	15	75	29	2	6	61	1.35
6171496--6171542	22	2.1	23	84	11	62	44	0	4	51	1.21
6171598--6171674	27	2.8	27	79	11	86	51	2	0	45	1.14
6172986--6173023	20	1.9	20	88	0	58	63	0	2	34	1.09
6173138--6173181	23	1.9	23	85	0	61	43	0	0	56	0.99
6173127--6173181	23	2.5	21	72	11	56	47	0	0	52	1.00
6176257--6176293	17	2.2	17	90	0	56	54	21	0	24	1.45
6179731--6179787	29	2.0	28	83	10	71	50	0	1	47	1.11
6180150--6180217	27	2.5	27	85	4	84	44	0	2	52	1.16
6182212--6182236	7	3.6	7	100	0	50	32	0	28	40	1.57
6188596--6188620	3	8.3	3	100	0	50	32	0	0	68	0.90
6191002--6191068	25	2.8	25	74	17	70	52	0	0	47	1.00
6191028--6191147	52	2.3	51	87	5	152	50	3	2	44	1.32
6191824--6191862	17	2.3	17	91	8	62	38	2	2	56	1.27
6192109--6192155	19	2.5	18	76	10	58	29	8	4	57	1.48
6193507--6193610	16	6.4	16	71	20	56	39	1	0	57	1.16
6193458--6193565	37	3.0	36	69	27	86	39	2	1	55	1.25
6193603--6193633	14	2.1	14	94	5	53	32	6	0	61	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6196212--6196246	16	2.2	16	94	0	61	34	14	5	45	1.68
6196385--6196434	2	26.0	2	77	22	54	46	4	0	50	1.20
6197148--6197187	18	2.3	18	91	4	64	45	0	0	55	0.99
6198209--6198247	20	2.0	20	89	0	60	56	2	5	35	1.35
6201566--6201642	20	3.8	20	77	6	84	38	12	15	32	1.86
6202155--6202196	21	2.1	21	87	12	63	52	7	4	35	1.50
6203225--6203263	19	2.1	19	85	9	53	23	7	2	66	1.30
6204661--6204764	16	6.4	16	71	20	56	39	1	0	57	1.16
6204612--6204719	37	3.0	36	69	27	86	39	2	1	55	1.25
6204757--6204787	14	2.1	14	94	5	53	32	6	0	61	1.21
6207048--6207105	21	2.8	21	78	5	55	37	3	24	34	1.72
6210822--6211197	153	2.4	156	82	6	410	41	18	11	28	1.85
6210920--6211197	154	1.8	152	85	4	398	41	19	10	27	1.85
6213648--6213758	55	2.0	55	96	0	204	45	12	9	33	1.74
6215821--6215850	15	2.0	15	93	0	51	63	0	0	36	0.95
6216551--6216595	14	3.2	14	77	22	58	37	13	6	42	1.70
6218726--6218774	22	2.1	22	85	7	62	59	0	0	40	0.98
6218900--6218944	3	15.0	3	95	0	81	66	2	0	31	1.04
6219816--6219850	18	1.9	18	88	0	52	34	8	5	51	1.56
6219858--6219891	18	1.9	17	88	5	50	38	0	5	55	1.24
6220417--6220460	19	2.2	20	84	4	54	43	0	0	56	0.99
6222463--6222509	5	9.8	5	90	4	62	0	14	2	82	0.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6223602--6223646	20	2.2	21	96	4	83	62	0	0	37	0.96
6223595--6223655	16	3.9	17	77	14	69	63	0	0	36	0.94
6223585--6223669	11	7.5	11	75	10	64	63	1	2	32	1.15
6223708--6223733	2	13.0	2	100	0	52	50	0	0	50	1.00
6224047--6224092	3	15.3	3	100	0	92	67	0	0	32	0.91
6224138--6224192	24	2.3	23	81	12	58	47	0	0	52	1.00
6224570--6224614	21	2.3	19	84	7	54	51	0	2	46	1.13
6224866--6224891	2	13.0	2	100	0	52	50	0	0	50	1.00
6225750--6225791	18	2.3	18	87	4	57	71	0	2	26	0.98
6225791--6225849	19	3.4	19	68	22	65	52	0	0	47	1.00
6225777--6225851	33	2.2	33	90	6	116	58	0	0	41	0.98
6226847--6226913	13	5.1	13	73	18	50	44	0	0	55	0.99
6226890--6226932	11	3.8	11	79	14	52	34	2	0	62	1.08
6227064--6227093	14	2.1	14	100	0	60	40	0	20	40	1.52
6228171--6228219	20	2.6	19	75	12	57	46	0	0	53	1.00
6228214--6228255	22	1.9	22	90	9	68	61	2	0	35	1.09
6228960--6229021	22	2.7	23	76	11	65	59	1	0	38	1.07
6230420--6230461	22	1.9	22	90	9	68	61	0	0	38	0.96
6230664--6230710	24	2.0	24	88	12	71	65	0	4	29	1.11
6230664--6230710	23	2.0	23	88	12	69	65	0	4	29	1.11
6232109--6232155	24	2.0	24	88	12	71	65	0	4	29	1.11
6232109--6232155	23	2.0	23	88	12	69	65	0	4	29	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6233329--6233370	22	1.9	22	90	9	68	61	0	0	38	0.96
6233576--6233622	23	2.0	23	84	15	62	65	0	0	34	0.93
6234793--6234834	22	1.9	22	90	9	68	61	0	0	38	0.96
6235041--6235087	23	2.0	23	84	15	62	65	0	0	34	0.93
6237468--6237688	74	3.0	74	97	0	406	40	16	15	27	1.88
6239554--6239608	22	2.6	22	78	13	55	49	0	1	49	1.11
6239642--6239681	21	1.9	21	90	10	64	40	0	0	60	0.97
6240183--6240218	16	2.3	16	90	4	56	69	8	0	22	1.15
6240213--6240262	19	2.7	18	81	9	64	52	16	0	32	1.44
6240297--6240342	14	3.2	13	85	11	56	52	2	0	45	1.13

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