genome.fa.s401.2.7.7.80.10.50.1000.9.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: Scaffold401
Parameters: 2 7 7 80 10 50 1000
Length:  1910012

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   

This is table  9  of  13  ( 1464 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)
1240647--1240731	15	5.8	14	73	17	57	58	1	2	37	1.18
1240639--1240731	13	6.3	15	71	21	72	58	1	3	37	1.22
1244171--1244210	2	20.0	2	94	0	71	47	0	0	52	1.00
1250783--1250809	14	1.9	14	100	0	54	74	0	0	25	0.83
1252796--1252838	23	2.0	22	90	9	70	48	4	2	44	1.36
1252942--1252988	19	2.5	18	77	16	51	36	8	2	53	1.44
1255251--1255283	7	4.7	7	96	0	57	63	0	0	36	0.95
1255667--1255704	19	1.9	19	89	5	58	52	0	0	47	1.00
1255780--1255814	2	18.0	2	88	5	54	51	0	0	48	1.00
1256192--1256244	23	2.3	23	83	6	63	41	0	3	54	1.18
1256314--1256402	29	2.9	29	77	11	72	48	1	2	48	1.21
1258908--1258989	24	3.4	25	75	14	82	43	0	0	56	0.99
1258899--1259001	47	2.2	45	81	13	111	43	0	0	56	0.99
1258997--1259047	12	4.2	12	79	0	57	17	1	5	74	1.11
1260445--1260470	3	8.7	3	100	0	52	34	0	0	65	0.93
1261665--1261728	21	3.0	22	73	13	62	46	0	1	51	1.10
1261753--1261789	15	2.4	16	82	13	51	64	0	0	35	0.94
1267203--1267294	5	18.0	5	70	14	55	36	0	2	60	1.09
1267199--1267289	27	3.3	26	76	14	85	36	0	2	61	1.08
1268964--1269025	27	2.3	26	81	8	79	64	3	0	32	1.09
1269257--1269294	20	1.9	20	88	0	58	44	0	0	55	0.99
1269284--1269341	23	2.6	23	83	8	66	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1269279--1269326	16	3.0	16	75	6	53	41	0	0	58	0.98
1269762--1269901	20	7.2	20	69	21	68	39	1	0	59	1.06
1269771--1269811	19	2.2	18	91	4	64	31	2	0	65	1.05
1269783--1269886	45	2.2	48	81	13	128	44	0	0	55	0.99
1269787--1269888	16	6.5	16	72	15	79	44	0	0	55	0.99
1270542--1270567	3	8.7	3	100	0	52	69	0	0	30	0.89
1272811--1272930	38	3.1	39	80	12	117	49	0	0	50	1.00
1273317--1273487	85	2.0	84	95	1	306	43	7	17	30	1.77
1273605--1273689	43	2.0	42	88	2	125	37	0	4	57	1.20
1274173--1274199	3	9.0	3	100	0	54	66	0	0	33	0.92
1276184--1276238	24	2.2	26	78	12	62	52	0	1	45	1.11
1276394--1276432	12	3.3	12	85	3	53	48	0	0	51	1.00
1276702--1276792	20	5.1	18	75	15	66	50	0	1	48	1.08
1276735--1276777	14	2.9	14	80	13	50	51	0	2	46	1.13
1276722--1276785	32	2.0	33	87	3	94	51	0	1	46	1.10
1276697--1276795	18	5.2	18	67	21	51	47	0	1	51	1.07
1276705--1276811	16	6.2	17	71	16	62	45	0	0	53	1.06
1276804--1276853	19	2.6	19	78	15	57	34	2	0	64	1.05
1277145--1277214	18	4.0	17	74	9	61	51	1	0	47	1.09
1277145--1277181	17	2.1	18	90	5	58	54	0	0	45	1.00
1277195--1277286	29	3.3	29	75	11	86	52	0	1	46	1.07
1281731--1281766	2	18.0	2	88	0	54	44	0	5	50	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1283257--1283288	17	1.9	16	93	6	55	53	0	0	46	1.00
1286061--1286092	15	2.1	15	94	0	55	46	9	6	37	1.61
1286214--1286241	2	14.0	2	100	0	56	50	0	0	50	1.00
1286263--1286306	19	2.2	21	80	15	58	45	0	6	47	1.29
1286337--1286377	22	1.9	21	90	5	64	63	2	2	31	1.20
1286581--1286627	15	3.1	15	76	14	51	55	0	0	44	0.99
1301911--1301998	27	3.3	27	81	0	113	31	10	47	10	1.71
1301890--1301998	54	2.0	54	87	3	157	31	14	44	9	1.77
1302410--1302454	23	1.9	24	86	4	65	60	0	2	37	1.09
1302577--1302661	16	5.5	16	69	18	54	38	7	0	54	1.28
1307066--1307110	22	2.1	21	83	4	54	46	2	2	48	1.26
1307476--1307515	21	1.9	21	85	10	55	37	2	5	55	1.35
1309542--1309596	29	2.0	29	85	7	78	50	1	0	47	1.11
1310595--1310633	2	19.5	2	83	0	51	43	0	7	48	1.31
1311735--1311765	9	3.4	9	95	0	53	0	38	3	58	1.15
1312787--1312812	2	13.0	2	100	0	52	50	0	0	50	1.00
1313981--1314019	3	13.0	3	100	0	78	66	0	0	33	0.92
1318105--1318139	16	2.2	16	90	10	54	62	0	0	37	0.95
1318126--1318158	16	2.1	16	88	11	50	75	0	0	24	0.80
1318142--1318194	25	2.1	24	82	6	61	62	0	0	37	0.96
1318178--1318231	17	3.3	17	69	27	53	50	1	1	46	1.23
1319643--1319720	30	2.7	29	80	9	79	57	1	2	38	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1319663--1319739	29	2.5	29	85	8	91	51	3	1	42	1.28
1324047--1324093	16	3.0	15	75	22	51	51	0	2	46	1.13
1326215--1326448	120	2.0	119	95	0	423	20	20	22	36	1.95
1327288--1327322	2	18.0	2	88	5	54	48	0	2	48	1.16
1329877--1329933	16	3.7	16	71	21	50	56	0	0	43	0.99
1329856--1329908	21	2.6	21	79	8	56	64	1	0	33	1.05
1330198--1330257	21	2.8	22	72	12	61	60	0	0	40	0.97
1330199--1330259	27	2.3	26	81	10	79	60	0	0	39	0.97
1330200--1330259	15	3.8	16	75	18	63	60	0	0	40	0.97
1330934--1330988	24	2.2	25	83	3	67	27	3	1	67	1.17
1337702--1337751	17	2.9	18	78	21	54	56	2	2	40	1.22
1340395--1340459	26	2.5	26	82	7	69	49	0	3	47	1.17
1340484--1340517	16	2.2	15	89	5	50	47	0	0	52	1.00
1353932--1353981	12	4.5	11	74	16	50	44	0	0	56	0.99
1353932--1353981	17	3.0	17	80	13	68	44	0	0	56	0.99
1353932--1354000	5	12.8	5	73	14	57	46	0	2	50	1.16
1353972--1354009	16	2.3	17	86	4	51	47	0	7	44	1.32
1353951--1354000	21	2.3	22	86	3	66	50	0	4	46	1.20
1360212--1360273	16	3.7	17	78	14	67	43	0	0	56	0.99
1366698--1366731	17	1.9	17	88	5	50	50	0	0	50	1.00
1369172--1369216	16	2.8	17	80	12	51	44	0	0	55	0.99
1369176--1369226	19	2.7	20	76	11	54	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1369329--1369416	27	3.3	27	75	15	69	64	1	3	30	1.17
1369747--1369785	20	1.9	21	89	5	62	12	10	0	76	1.01
1372856--1372915	27	2.2	26	83	13	77	58	3	0	38	1.15
1372905--1372976	15	4.9	14	74	16	58	56	0	1	41	1.07
1373344--1373373	2	15.0	2	100	0	60	50	0	0	50	1.00
1374468--1374567	33	2.9	35	80	16	120	37	1	0	62	1.02
1374677--1374722	14	3.4	14	85	8	51	56	0	2	41	1.11
1374686--1374724	14	2.7	15	88	7	55	58	0	2	38	1.12
1374696--1374827	47	2.6	48	75	15	117	57	0	0	40	1.09
1375657--1375702	21	2.3	18	82	17	56	50	0	0	50	1.00
1375657--1375723	26	3.0	21	72	27	59	50	0	0	49	1.00
1376295--1376324	15	1.9	16	93	6	53	46	0	3	50	1.18
1380191--1380223	3	11.0	3	100	0	66	33	0	0	66	0.92
1383112--1383136	1	25.0	1	100	0	50	0	100	0	0	0.00
1384534--1384568	2	17.5	2	100	0	70	51	0	0	48	1.00
1385165--1385195	13	2.4	13	88	0	53	58	3	0	38	1.15
1393072--1393119	21	2.3	21	78	7	53	35	0	2	62	1.07
1394894--1394923	3	10.0	3	92	0	51	66	3	0	30	1.07
1400516--1400588	22	3.2	22	73	21	60	47	0	0	52	1.00
1400523--1400588	24	2.9	21	72	20	60	46	0	0	53	1.00
1400762--1400786	10	2.5	10	100	0	50	60	0	8	32	1.26
1402057--1402109	18	2.9	17	81	10	61	45	1	1	50	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1404094--1404127	17	2.0	17	88	0	50	47	0	0	52	1.00
1404238--1404293	28	2.0	29	82	3	69	51	1	0	46	1.11
1404268--1404302	18	1.9	18	88	0	52	51	0	0	48	1.00
1404407--1404446	21	2.0	21	85	5	55	50	2	0	47	1.14
1407104--1407140	19	2.0	20	84	10	51	16	16	21	45	1.84
1414571--1414595	4	6.2	4	100	0	50	0	24	0	76	0.80
1414924--1414959	4	8.8	4	93	6	63	22	2	0	75	0.94
1415772--1415818	12	3.8	12	81	13	60	42	0	0	57	0.98
1416101--1416151	15	3.5	15	79	10	52	41	0	0	58	0.98
1416148--1416212	32	2.0	33	85	5	89	36	1	0	61	1.05

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13