genome.fa.s5.2.7.7.80.10.50.1000.12.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: Scaffold5
Parameters: 2 7 7 80 10 50 1000
Length:  1536239

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   

This is table  12  of  14  ( 1571 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)
1355434--1355469	19	1.9	19	88	5	56	52	0	0	47	1.00
1355925--1355963	3	13.0	3	94	0	69	33	2	0	64	1.08
1363668--1363757	45	2.0	45	86	4	128	37	16	15	30	1.90
1364476--1364518	3	14.3	3	100	0	86	32	0	0	67	0.91
1365540--1365627	24	3.7	24	69	10	72	65	1	1	31	1.07
1365582--1365627	17	2.8	16	80	9	56	69	0	2	28	1.00
1365800--1365824	6	4.2	6	100	0	50	84	0	0	16	0.63
1368269--1368320	26	2.0	25	85	3	68	59	0	1	38	1.08
1368282--1368325	23	2.0	22	86	13	63	59	0	2	38	1.10
1368267--1368371	28	3.8	28	74	16	76	52	1	4	40	1.33
1369384--1369421	17	2.3	17	86	4	51	52	5	0	42	1.24
1369830--1369896	30	2.3	29	85	10	84	56	0	1	41	1.08
1370830--1370885	24	2.4	23	85	8	69	48	3	3	44	1.37
1370883--1370934	14	3.9	13	80	12	61	50	0	0	50	1.00
1370883--1370934	26	2.1	24	89	7	77	50	0	0	50	1.00
1371266--1371324	16	3.6	16	82	11	57	61	1	0	37	1.07
1371336--1371388	22	2.5	21	81	9	63	50	1	0	47	1.12
1372633--1372673	19	2.1	19	86	9	55	39	0	0	60	0.96
1372787--1372839	26	2.1	25	82	3	61	43	1	0	54	1.11
1372958--1373015	20	3.0	18	73	14	53	60	0	0	39	0.97
1373453--1373518	12	5.7	12	79	13	75	39	0	4	56	1.20
1373439--1373516	24	3.4	22	84	12	95	38	0	6	55	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1374251--1374352	27	3.5	28	72	11	73	50	0	0	49	1.07
1374609--1374665	22	2.6	21	83	8	69	57	0	1	40	1.09
1374783--1374821	18	2.2	18	86	9	53	56	0	0	43	0.99
1374791--1374834	19	2.3	20	84	7	56	50	0	2	47	1.13
1374975--1375013	19	2.1	19	85	0	51	41	5	2	51	1.38
1375167--1375248	42	2.0	42	90	4	130	67	2	14	15	1.34
1375606--1375639	14	2.5	13	85	4	50	38	2	0	58	1.13
1375595--1375674	16	5.0	16	75	13	67	41	1	0	57	1.07
1375595--1375654	30	2.0	29	83	3	75	41	1	0	56	1.09
1375649--1375678	13	2.2	14	94	5	53	36	0	0	63	0.95
1376553--1376617	31	2.1	31	82	0	76	21	7	9	61	1.51
1376629--1376657	11	2.5	12	94	5	51	34	0	0	65	0.93
1377098--1377180	19	4.5	19	72	13	57	56	1	2	39	1.20
1377924--1377954	16	1.9	16	93	0	53	22	12	16	48	1.80
1378551--1378630	41	2.0	40	92	4	135	37	17	17	27	1.92
1385663--1385734	25	2.8	27	78	15	82	54	1	0	44	1.08
1386790--1386844	28	2.0	28	96	0	101	54	7	5	32	1.51
1391748--1391777	2	15.0	2	100	0	60	50	0	0	50	1.00
1392960--1393022	31	2.0	31	100	0	126	46	6	6	41	1.55
1399015--1399042	5	5.6	5	100	0	56	64	35	0	0	0.94
1399635--1399664	15	2.1	14	93	6	51	43	0	0	56	0.99
1399660--1399716	18	3.0	18	85	12	62	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1399683--1399721	20	1.9	20	94	5	69	64	0	0	35	0.94
1399696--1399731	13	2.7	14	91	8	58	63	0	0	36	0.94
1399852--1399889	18	2.1	18	95	5	67	50	0	0	50	1.00
1399854--1399905	26	2.0	25	85	3	68	53	1	0	44	1.11
1400345--1400393	20	2.5	20	83	6	55	57	0	0	42	0.99
1400356--1400393	10	3.8	10	90	10	60	55	0	0	44	0.99
1400809--1400838	15	2.0	15	93	0	51	40	10	0	50	1.36
1401123--1401162	21	1.9	21	90	10	64	37	0	0	62	0.95
1403595--1403643	2	24.5	2	100	0	98	48	0	0	51	1.00
1404240--1404295	24	2.3	25	78	12	62	39	0	3	57	1.16
1404967--1405022	25	2.2	25	96	0	103	53	7	3	35	1.46
1405557--1405599	23	2.0	21	81	9	50	44	9	11	34	1.73
1406685--1406715	13	2.4	13	94	0	53	38	0	3	58	1.15
1407053--1407087	2	18.0	2	88	5	54	48	0	0	51	1.00
1407061--1407089	15	1.9	15	100	0	58	44	0	0	55	0.99
1407492--1407534	22	1.9	22	85	4	59	37	0	4	58	1.19
1407671--1407756	43	2.0	43	93	4	147	34	22	6	36	1.81
1409948--1409982	5	6.6	5	96	3	52	42	0	0	57	0.99
1409997--1410076	33	2.5	32	78	13	83	46	0	0	53	1.00
1410218--1410260	16	2.8	15	83	13	52	37	0	2	60	1.10
1410247--1410293	18	2.7	18	83	3	51	46	0	0	53	1.00
1411135--1411182	21	2.2	22	77	3	53	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1411240--1411283	18	2.4	18	88	0	70	38	2	0	59	1.10
1411275--1411344	19	3.9	19	74	17	62	51	1	0	47	1.09
1411815--1411870	20	2.9	20	72	12	55	62	0	0	37	0.95
1411796--1411870	38	2.1	35	87	7	105	58	0	0	41	0.98
1411823--1411879	27	2.1	27	83	6	71	56	0	3	40	1.17
1412470--1412505	15	2.4	15	90	0	54	33	0	0	66	0.92
1413490--1413533	2	22.0	2	100	0	88	50	0	0	50	1.00
1413931--1414000	36	2.0	34	83	8	88	58	0	0	41	0.98
1416545--1416591	20	2.4	21	82	10	55	44	0	0	55	0.99
1416530--1416586	18	3.1	19	80	5	55	47	0	0	52	1.00
1416761--1416826	32	2.1	32	85	5	89	53	1	0	45	1.09
1416462--1416921	236	2.0	226	84	8	597	43	7	5	43	1.56
1417691--1417749	16	3.7	16	67	15	50	64	0	1	33	1.04
1418010--1418076	11	5.8	11	72	16	55	64	0	0	35	0.94
1418006--1418076	35	1.9	36	83	8	90	61	0	0	38	0.96
1418355--1418408	18	3.2	17	72	20	51	51	0	0	48	1.00
1418373--1418440	18	3.4	21	73	22	67	58	0	0	41	0.98
1418398--1418458	21	3.0	22	74	11	58	65	0	0	34	0.93
1418426--1418466	5	8.4	5	79	15	50	65	0	0	34	0.93
1418374--1418469	27	3.5	28	70	17	76	62	0	0	37	0.95
1418898--1418965	6	11.8	6	75	17	56	39	0	0	60	0.97
1418898--1419004	11	10.1	11	67	17	57	42	0	0	57	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1419695--1419762	35	1.9	36	84	3	93	52	0	2	44	1.16
1419733--1419796	27	2.4	24	73	19	56	57	1	4	35	1.29
1420052--1420156	25	4.4	24	78	16	112	62	0	0	37	0.95
1420041--1420141	49	2.0	51	90	7	163	62	0	0	37	0.96
1420097--1420178	36	2.2	36	86	6	110	59	0	0	40	0.97
1420076--1420266	29	6.6	29	74	17	114	58	0	0	41	1.02
1420048--1420180	49	2.8	49	80	12	154	60	0	0	39	0.97
1420091--1420223	32	3.9	33	78	18	116	56	0	0	43	0.99
1420099--1420207	30	3.6	30	81	9	116	56	0	0	43	0.99
1420166--1420274	26	4.0	26	75	15	80	54	0	0	44	1.06
1420197--1420265	19	3.3	21	78	15	72	59	0	1	39	1.06
1420120--1420252	46	2.8	47	73	13	121	55	0	0	44	0.99
1420386--1420436	25	2.0	26	85	11	70	50	1	0	47	1.12
1420451--1420509	21	2.9	21	72	20	61	47	0	0	52	1.00
1420597--1420644	22	2.1	23	85	11	64	66	0	0	33	0.92
1420597--1420659	22	2.8	21	81	13	63	66	0	0	33	0.92
1420874--1420904	2	15.5	2	100	0	62	0	48	0	51	1.00
1425160--1425215	23	2.5	23	82	8	71	62	1	3	32	1.23
1425355--1425429	31	2.5	31	81	14	86	61	0	8	30	1.25
1425660--1425703	20	2.1	21	83	4	54	45	0	4	50	1.22
1425659--1425705	21	2.2	22	77	11	53	44	0	4	51	1.21
1426157--1426206	19	2.7	19	84	3	66	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1426154--1426266	36	3.2	35	69	15	97	46	0	0	53	1.00
1426207--1426255	24	1.9	24	84	12	62	48	0	0	51	1.00
1426214--1426275	20	3.0	20	75	13	54	51	1	0	46	1.10
1426475--1426538	21	2.9	23	81	9	87	56	0	4	39	1.20
1426481--1426575	28	3.7	27	77	13	85	56	1	2	40	1.18
1426833--1426866	18	1.9	17	88	5	50	67	2	0	29	1.05
1426971--1427007	18	2.0	20	84	10	51	43	0	0	56	0.99
1427073--1427114	2	21.5	2	85	4	59	47	2	0	50	1.14
1427931--1428018	27	3.4	27	68	22	73	53	1	0	45	1.07
1428853--1428957	32	3.1	31	79	18	95	38	0	0	60	1.03

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14