genome.fa.s25.2.7.7.80.10.50.1000.43.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  43  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)
7248604--7248668	32	2.0	33	87	3	96	26	15	16	41	1.88
7248634--7248690	19	2.9	19	89	5	78	29	17	17	35	1.93
7248735--7248765	13	2.4	13	94	0	53	35	16	12	35	1.87
7248723--7248785	33	1.9	32	87	12	92	38	14	17	30	1.89
7248877--7248903	10	2.7	10	100	0	54	51	37	11	0	1.37
7256809--7256880	36	1.9	38	88	5	112	38	2	22	36	1.69
7258237--7258484	79	3.2	78	80	6	286	31	15	26	26	1.96
7258362--7258772	107	3.9	107	71	12	326	30	13	27	28	1.94
7258496--7258839	52	6.6	52	67	13	204	31	11	27	29	1.92
7258385--7258832	211	2.1	211	95	0	799	30	12	28	28	1.93
7261248--7261299	13	3.5	13	73	26	50	36	17	13	32	1.89
7261256--7261318	19	3.7	18	76	24	73	36	15	12	34	1.86
7261248--7261320	32	2.3	32	97	0	137	35	16	12	35	1.86
7261287--7261348	19	3.2	19	73	13	63	27	14	14	43	1.84
7261827--7261883	19	2.8	20	89	5	80	33	15	15	35	1.90
7264884--7264910	2	13.5	2	100	0	54	51	0	0	48	1.00
7266636--7266661	13	2.0	13	100	0	52	23	7	7	61	1.49
7267540--7267570	2	15.5	2	100	0	62	51	0	0	48	1.00
7269014--7269147	69	1.9	71	79	14	154	41	0	3	54	1.23
7269362--7269390	2	14.5	2	100	0	58	48	0	0	51	1.00
7272198--7272269	27	2.9	26	71	20	66	52	2	0	44	1.15
7276700--7276738	21	1.9	20	89	5	60	38	15	10	35	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7276797--7276866	31	2.2	32	92	2	115	34	11	18	35	1.87
7276797--7276858	19	3.6	19	70	28	66	33	11	19	35	1.87
7279142--7279209	26	2.6	26	100	0	136	23	39	20	16	1.91
7286487--7286566	13	6.4	12	75	12	63	77	8	6	7	1.12
7287925--7288305	96	4.0	95	79	5	342	29	31	17	22	1.96
7287939--7288303	160	2.3	158	84	6	461	28	31	17	21	1.96
7288202--7288281	31	2.6	31	81	0	88	25	30	22	22	1.99
7287940--7288315	32	11.8	32	78	8	306	28	31	18	21	1.97
7289137--7289190	21	2.6	21	84	0	81	46	7	14	31	1.73
7298186--7298236	20	2.6	20	90	3	77	35	17	15	31	1.92
7298208--7298269	32	1.9	33	87	9	92	38	12	16	32	1.86
7305481--7305905	27	15.5	27	82	4	485	24	32	14	28	1.95
7305481--7305916	55	7.9	55	82	4	513	24	33	14	27	1.94
7305481--7305916	82	5.3	82	81	6	497	24	33	14	27	1.94
7305517--7305916	109	3.6	108	83	6	466	25	32	14	28	1.94
7305901--7306008	32	3.5	31	71	14	107	29	31	15	23	1.95
7305939--7306577	28	22.6	28	84	2	778	31	27	17	24	1.97
7305743--7306577	84	9.9	84	82	5	747	29	28	16	24	1.97
7313640--7313718	7	12.7	6	82	7	63	34	0	1	64	1.02
7313641--7313672	7	4.6	7	100	0	64	25	0	0	75	0.81
7313681--7313731	5	10.0	5	85	12	52	39	0	0	60	0.97
7314122--7314158	2	18.5	2	100	0	74	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7317042--7317118	26	3.0	26	86	0	109	35	7	12	44	1.72
7327232--7327321	1	90.0	1	77	0	72	86	5	7	0	0.70
7327230--7327321	31	3.0	31	89	9	143	84	5	9	0	0.76
7331940--7332060	26	4.7	26	81	4	145	37	8	13	41	1.74
7331940--7332060	52	2.3	52	86	0	170	37	8	13	41	1.74
7344663--7344702	21	1.9	21	85	10	55	42	5	0	52	1.23
7344790--7344840	16	3.2	16	75	5	50	15	15	25	43	1.86
7352362--7352401	20	2.0	20	95	5	71	40	0	0	60	0.97
7352369--7352401	11	3.2	11	83	16	52	39	0	0	60	0.97
7354282--7354389	48	2.2	48	90	0	171	58	1	15	24	1.47
7357054--7357134	21	4.2	20	75	13	62	43	0	0	56	0.99
7357074--7357149	37	2.1	35	83	9	91	42	0	0	57	0.98
7357080--7357148	27	2.5	27	77	13	70	42	0	0	57	0.98
7357706--7357752	3	15.7	3	95	0	85	63	0	0	36	0.94
7363516--7363561	23	2.0	23	87	4	67	41	30	0	28	1.56
7364016--7364081	17	3.8	17	72	21	57	45	0	1	53	1.09
7364013--7364097	20	3.8	23	73	14	72	42	0	1	56	1.07
7364031--7364106	20	3.6	20	69	23	57	39	0	2	57	1.12
7364057--7364132	35	2.2	35	83	2	91	42	0	1	56	1.07
7364863--7364893	2	15.5	2	100	0	62	51	0	0	48	1.00
7365106--7365141	18	2.0	18	88	0	54	55	0	2	41	1.14
7366647--7366690	2	22.0	2	100	0	88	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)
7366974--7367014	17	2.4	18	80	12	50	53	0	0	46	1.00
7376467--7376551	28	2.9	29	80	16	104	48	1	1	49	1.16
7376454--7376616	31	5.4	31	70	19	112	44	1	0	52	1.16
7376560--7376609	24	2.1	23	88	3	73	40	4	0	56	1.18
7376560--7376616	24	2.4	24	85	5	62	40	3	0	56	1.17
7376678--7376751	3	25.3	3	69	20	50	36	0	1	62	1.04
7376693--7376751	25	2.4	25	80	11	75	38	0	1	59	1.08
7379535--7379577	22	2.0	20	86	8	59	72	9	0	18	1.11
7379674--7379740	6	10.8	6	92	6	107	65	0	0	34	0.93
7381057--7381090	17	2.0	18	88	11	54	47	11	0	41	1.40
7382241--7382278	19	2.0	19	90	10	60	5	15	0	78	0.91
7382334--7382384	25	2.0	25	100	0	102	35	15	11	37	1.84
7382599--7382743	71	2.0	71	98	0	281	35	8	4	51	1.53
7388091--7388150	20	3.0	21	87	7	88	38	11	16	33	1.85
7394874--7394919	21	2.2	20	85	11	58	39	6	15	39	1.73
7398291--7398361	27	2.7	27	75	14	67	71	5	0	22	1.06
7398304--7398338	17	2.0	18	88	5	54	77	5	0	17	0.96
7402739--7402815	7	10.9	7	72	18	61	15	2	3	77	1.02
7402748--7402815	35	1.9	36	82	14	88	16	1	4	77	0.99
7402738--7402814	22	3.6	21	75	16	70	15	2	3	77	1.02
7403276--7403388	41	2.8	41	76	9	104	18	24	15	41	1.89
7403837--7403964	66	1.9	66	81	9	154	21	23	13	42	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7405403--7405440	6	6.3	6	82	11	51	34	0	0	65	0.93
7405406--7405445	17	2.3	18	87	8	57	32	0	0	67	0.91
7405546--7405628	12	7.0	12	68	22	59	39	1	4	54	1.30
7405964--7405994	15	2.1	15	93	0	53	32	19	9	38	1.84
7406161--7406214	3	18.0	3	100	0	108	66	0	0	33	0.92
7407827--7407884	29	2.0	28	83	9	73	44	3	20	31	1.68
7407895--7407968	29	2.6	29	91	0	121	37	6	17	37	1.76
7410610--7410702	29	3.1	29	77	16	84	55	0	2	41	1.11
7411438--7411488	9	5.3	9	82	17	59	84	0	15	0	0.63
7411453--7411488	11	3.3	11	96	0	63	88	0	11	0	0.50
7412576--7412605	15	1.9	16	93	6	53	40	0	0	60	0.97
7412615--7412661	4	11.8	4	100	0	94	25	23	0	51	1.49
7412734--7412790	29	2.0	29	89	3	89	77	0	22	0	0.77
7413179--7413215	15	2.5	15	80	20	51	64	8	0	27	1.21
7413198--7413288	36	2.4	35	79	15	85	61	5	4	28	1.38
7413327--7413369	13	3.1	14	81	12	54	0	11	0	88	0.52
7413335--7413371	19	1.9	19	94	0	65	0	13	0	86	0.57
7414161--7414203	2	21.5	2	95	0	77	0	51	0	48	1.00
7414161--7414212	12	4.5	12	92	4	72	0	51	0	48	1.00
7414861--7414895	15	2.3	15	90	0	52	0	8	25	65	1.21
7422116--7422189	16	4.5	16	77	17	71	22	0	12	64	1.26
7422114--7422177	33	1.9	33	87	6	94	21	0	10	67	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7422118--7422189	33	2.2	33	82	5	83	23	0	12	63	1.28
7422174--7422215	21	2.0	21	85	0	57	19	0	16	64	1.30
7430145--7430263	49	2.4	49	84	2	150	31	15	13	40	1.85
7431337--7431388	19	2.7	20	88	8	72	44	15	13	26	1.84
7435228--7435279	10	5.0	10	81	9	59	73	1	23	1	1.04
7436168--7436414	97	2.5	97	87	0	341	28	28	13	29	1.94
7441121--7441169	19	2.6	18	84	9	62	75	10	10	4	1.17
7442489--7443230	27	27.1	27	84	1	746	24	29	15	30	1.95
7442489--7443539	28	38.0	28	81	5	728	25	29	15	29	1.96
7442481--7443230	109	6.9	109	84	1	829	24	29	15	30	1.96

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