genome.fa.s89.2.7.7.80.10.50.1000.9.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: Scaffold89
Parameters: 2 7 7 80 10 50 1000
Length:  5168001

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   

This is table  9  of  27  ( 3236 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)
1221301--1221333	6	5.5	6	92	0	57	36	0	15	48	1.45
1221487--1221528	2	21.0	2	100	0	84	50	0	50	0	1.00
1221877--1221908	2	16.0	2	100	0	64	0	50	0	50	1.00
1221880--1221934	10	5.5	10	86	0	65	7	49	1	41	1.41
1222388--1222413	3	8.7	3	100	0	52	30	0	0	69	0.89
1229908--1229948	22	1.9	21	85	5	55	43	0	0	56	0.99
1229937--1229988	24	2.4	21	73	17	52	59	1	0	38	1.08
1234109--1234164	26	2.2	26	93	0	94	33	10	12	42	1.77
1238268--1238314	23	2.0	23	91	0	76	63	2	8	25	1.34
1239767--1239802	19	1.9	19	88	5	56	47	0	2	50	1.15
1245491--1245523	2	16.5	2	100	0	66	51	0	48	0	1.00
1250167--1250213	21	2.2	22	84	3	60	51	4	0	44	1.21
1250190--1250237	15	3.2	15	83	13	55	52	2	0	45	1.12
1250189--1250293	16	6.6	16	69	21	60	51	2	1	43	1.27
1250166--1250226	31	2.0	31	87	3	88	50	3	0	45	1.17
1255492--1255526	2	17.5	2	87	0	52	48	2	2	45	1.32
1258562--1258607	23	2.0	22	84	12	58	52	17	2	28	1.56
1258650--1258680	2	15.5	2	100	0	62	51	0	0	48	1.00
1269624--1269666	22	2.0	22	86	4	61	69	2	0	27	1.00
1271180--1271212	17	1.9	17	93	0	57	27	3	6	63	1.32
1271223--1271288	20	3.4	18	71	19	53	48	0	1	50	1.10
1272116--1272175	24	2.5	24	79	15	70	56	0	0	43	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1274270--1274394	42	2.9	42	91	2	205	24	20	24	31	1.98
1278447--1278486	20	2.0	20	90	0	62	60	0	0	40	0.97
1278510--1278565	26	2.1	26	83	9	69	50	0	0	50	1.00
1281160--1281230	5	14.2	5	73	16	58	61	2	1	33	1.19
1281180--1281219	21	1.9	21	84	0	53	62	2	2	32	1.22
1281246--1281303	11	5.4	10	76	12	53	56	1	1	39	1.19
1281326--1281361	11	3.5	11	88	11	58	66	0	0	33	0.92
1281156--1281363	26	8.2	26	66	18	82	60	1	0	36	1.14
1281625--1281670	22	2.3	18	82	17	56	45	0	0	54	0.99
1282064--1282116	23	2.2	25	80	10	65	41	0	0	58	0.98
1282371--1282425	21	2.8	20	74	17	60	50	0	0	49	1.00
1298196--1298249	2	27.0	2	100	0	108	50	0	50	0	1.00
1300802--1300881	24	3.5	24	75	11	78	35	21	26	17	1.95
1300964--1301148	24	7.7	24	79	7	178	23	21	36	18	1.95
1300964--1301148	72	2.6	72	79	6	203	23	21	36	18	1.95
1301045--1301162	24	5.0	22	75	16	69	22	18	38	19	1.93
1301790--1301825	2	18.0	2	100	0	72	50	0	0	50	1.00
1303322--1303346	2	12.5	2	100	0	50	52	0	48	0	1.00
1304405--1304436	16	2.0	16	93	0	55	28	0	3	68	1.04
1305961--1305996	18	1.9	19	88	5	56	41	0	0	58	0.98
1305961--1306000	19	2.1	19	86	9	55	42	0	0	57	0.98
1305825--1306090	141	1.9	140	80	6	308	51	1	6	40	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1306196--1306236	20	2.1	20	86	4	57	73	0	4	21	1.02
1307192--1307232	21	2.0	20	90	4	64	73	0	14	12	1.11
1309371--1309413	3	14.3	3	86	13	54	30	2	0	67	1.03
1310222--1310262	21	1.9	22	85	5	57	17	29	31	21	1.96
1312303--1312343	18	2.3	17	84	12	55	58	0	0	41	0.98
1313441--1313500	19	3.0	19	74	16	50	53	6	3	36	1.44
1313980--1314024	23	2.0	22	83	16	56	44	8	8	37	1.67
1315489--1315519	2	15.5	2	93	0	53	51	0	45	3	1.17
1318159--1318239	8	10.4	8	70	15	53	53	4	0	41	1.22
1318083--1318178	51	1.9	50	82	6	122	44	2	5	47	1.37
1318366--1318419	22	2.4	23	75	6	58	70	1	3	24	1.13
1318767--1318825	31	1.9	30	83	10	75	42	1	1	54	1.20
1318808--1318901	44	2.2	44	87	9	133	45	1	1	52	1.15
1318789--1318926	42	3.4	40	71	18	108	41	1	1	55	1.17
1319471--1319537	35	2.0	33	94	5	116	35	2	1	59	1.22
1322221--1322267	23	2.0	24	84	12	62	70	0	6	23	1.10
1322440--1322479	21	1.9	21	85	10	55	62	0	0	37	0.95
1322631--1322673	15	3.0	14	76	6	50	46	0	0	53	1.00
1325121--1325151	3	10.3	3	100	0	62	67	0	32	0	0.91
1325524--1325553	5	6.0	5	96	0	51	20	56	0	23	1.42
1326010--1326041	15	2.1	16	94	5	57	18	3	0	78	0.89
1326070--1326108	20	2.0	20	84	0	51	46	7	7	38	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1326775--1326826	26	2.0	25	81	3	59	55	0	0	44	0.99
1326771--1326832	31	2.0	31	81	6	72	54	0	0	45	0.99
1326768--1326866	42	2.4	41	82	14	114	53	0	0	46	1.00
1328003--1328041	2	19.5	2	94	0	69	51	0	48	0	1.00
1330907--1330936	15	1.9	16	93	6	53	43	0	6	50	1.28
1330938--1330988	21	2.4	21	75	15	52	41	1	1	54	1.22
1331527--1331553	13	2.1	13	100	0	54	37	0	7	55	1.28
1336709--1336736	6	4.7	6	100	0	56	17	46	0	35	1.49
1338600--1338637	3	12.7	3	100	0	76	65	0	0	34	0.93
1338861--1338897	3	12.3	3	100	0	74	64	0	0	35	0.94
1339185--1339256	22	3.2	22	71	13	56	45	0	1	52	1.09
1339211--1339283	24	3.0	25	82	13	82	36	0	2	60	1.11
1342201--1342239	3	13.0	3	100	0	78	33	0	0	66	0.92
1349199--1349240	20	2.2	19	86	4	57	50	0	0	50	1.00
1349477--1349536	30	2.0	31	83	9	79	56	5	3	35	1.37
1352579--1352620	16	2.7	16	85	3	50	52	2	0	45	1.13
1352788--1352822	18	2.0	18	88	5	54	45	0	0	54	0.99
1352781--1352859	26	2.7	32	70	25	82	43	0	0	56	0.99
1352739--1352867	27	4.8	25	71	14	98	41	0	0	58	0.98
1352829--1352875	17	2.8	17	87	6	60	34	2	0	63	1.06
1353640--1353692	22	2.3	22	83	6	61	47	0	1	50	1.12
1353952--1354007	26	2.2	26	83	3	69	57	0	0	42	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1354315--1354345	2	15.5	2	100	0	62	51	0	0	48	1.00
1354665--1354708	20	2.3	19	85	11	63	27	4	0	68	1.09
1354727--1354821	17	5.5	17	69	23	56	45	3	7	44	1.47
1354726--1354821	2	47.5	2	70	17	56	44	3	7	44	1.47
1355447--1355516	30	2.3	31	85	11	92	62	2	0	34	1.10
1359214--1359268	21	2.5	22	82	5	76	54	0	5	40	1.23
1359214--1359286	21	3.5	20	78	16	67	54	0	4	41	1.19
1359195--1359286	43	2.1	43	82	9	107	51	2	3	43	1.30
1362597--1362637	3	13.7	3	94	0	73	2	0	63	34	1.08
1364199--1364228	2	15.0	2	100	0	60	50	0	0	50	1.00
1366197--1366280	8	9.4	9	70	21	52	53	0	1	45	1.08
1366263--1366335	14	5.7	13	75	13	53	39	0	1	58	1.06
1366296--1366343	12	4.1	11	76	12	51	33	0	0	66	0.92
1369658--1369688	2	15.5	2	100	0	62	0	48	0	51	1.00
1369905--1369976	15	4.4	17	75	17	64	38	0	0	61	0.96
1369937--1369982	15	3.0	15	83	3	56	34	2	0	63	1.07
1374382--1374423	12	3.6	12	80	3	50	47	0	0	52	1.00
1375684--1375759	20	3.7	20	79	12	73	46	1	3	48	1.29
1375674--1375759	11	8.0	11	72	17	65	44	1	3	51	1.26
1375674--1375755	31	2.6	32	83	11	98	43	1	3	51	1.27
1376526--1376597	33	2.2	33	94	0	135	31	37	9	20	1.85
1377164--1377197	2	17.0	2	100	0	68	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)
1378579--1378624	16	2.8	16	80	3	56	52	4	2	41	1.33
1383310--1383401	11	8.8	11	69	23	56	34	0	1	64	1.01
1383307--1383387	18	4.8	18	69	14	66	35	0	1	62	1.03
1383295--1383394	32	3.2	32	77	18	104	38	0	1	61	1.03
1383312--1383412	40	2.5	42	75	16	104	35	0	0	63	1.01
1383314--1383411	29	3.7	27	79	11	96	34	0	1	64	1.01
1383295--1383387	18	5.4	18	67	19	56	37	0	1	61	1.03
1383370--1383426	22	2.6	24	76	18	61	36	0	0	63	0.95
1383346--1383420	20	3.5	23	70	26	58	32	0	0	68	0.90
1383572--1383608	2	18.5	2	100	0	74	48	0	51	0	1.00

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