genome.fa.s109.2.7.7.80.10.50.1000.9.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: Scaffold109
Parameters: 2 7 7 80 10 50 1000
Length:  1855911

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

This is table  9  of  13  ( 1516 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)
1187399--1187449	24	2.1	24	96	0	93	31	11	7	49	1.68
1188370--1188442	27	2.7	27	83	12	87	24	35	20	19	1.95
1201006--1201039	13	2.6	13	90	0	50	88	5	5	0	0.64
1202050--1203200	55	19.9	55	83	9	1160	26	28	19	24	1.99
1202050--1203200	116	10.0	115	86	7	1416	26	28	19	24	1.99
1202019--1203200	235	5.1	234	88	6	1555	26	28	19	25	1.99
1203069--1203155	26	3.2	26	66	20	70	31	29	17	21	1.96
1203184--1203272	42	2.1	42	81	4	99	17	24	15	41	1.89
1218307--1218340	14	2.3	15	90	5	52	88	5	5	0	0.64
1219320--1220499	55	20.4	55	82	10	1137	26	28	19	25	1.99
1219350--1220499	116	10.0	115	87	6	1412	26	28	19	25	1.99
1219319--1220499	235	5.1	233	88	5	1547	26	28	19	25	1.99
1220338--1220427	29	3.2	29	65	13	80	28	30	17	23	1.97
1221858--1221891	16	2.1	17	88	5	52	35	14	5	44	1.70
1223668--1223707	20	2.0	20	95	0	71	52	5	7	35	1.51
1224910--1224984	21	3.6	21	85	3	98	37	12	16	34	1.85
1225022--1225089	19	3.9	19	76	21	76	35	13	14	36	1.85
1225043--1225067	13	1.9	13	100	0	50	36	16	16	32	1.90
1225024--1225086	32	2.0	32	93	0	108	34	14	15	34	1.88
1229430--1229485	20	2.7	21	86	5	78	39	14	17	28	1.89
1232049--1232099	24	2.1	24	96	0	93	31	11	7	49	1.68
1232111--1232160	26	1.9	26	95	0	91	20	28	20	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1233450--1233479	11	2.7	11	100	0	60	93	6	0	0	0.35
1236738--1236918	52	3.5	52	93	0	308	28	17	17	37	1.92
1236927--1236951	13	1.9	13	100	0	50	36	16	16	32	1.90
1236994--1237090	19	5.7	19	68	27	74	38	18	9	34	1.83
1236989--1237089	32	3.1	32	94	1	175	37	18	8	34	1.82
1237127--1237168	21	2.0	21	90	0	66	35	14	14	35	1.86
1238054--1238137	28	2.9	31	77	18	99	17	19	28	34	1.95
1238113--1238434	29	11.0	29	87	3	448	23	16	30	28	1.97
1238108--1238434	59	5.6	59	90	1	505	24	16	30	28	1.96
1238115--1238433	88	3.6	88	86	4	457	23	16	30	28	1.97
1238417--1238501	34	2.5	34	86	5	111	31	9	35	23	1.87
1239952--1240039	1	88.0	1	72	0	59	2	4	7	85	0.81
1239937--1240019	26	3.1	26	84	6	94	1	4	9	84	0.82
1239952--1240041	43	2.2	43	86	9	125	2	4	8	84	0.84
1239937--1240039	43	2.4	40	84	12	118	1	3	10	83	0.85
1239959--1240039	23	3.3	23	77	10	65	1	4	8	85	0.79
1251782--1251806	13	1.9	13	100	0	50	36	16	16	32	1.90
1251848--1251945	13	5.8	18	68	28	72	33	17	12	36	1.87
1251844--1251944	32	3.1	32	92	1	166	33	17	11	36	1.87
1252291--1252470	88	2.1	87	90	1	279	30	13	7	47	1.71
1252857--1253078	58	3.8	58	80	7	229	28	14	13	43	1.83
1255951--1255999	5	10.2	5	75	16	50	38	0	2	59	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1255964--1256032	20	3.6	20	77	15	74	42	4	1	52	1.30
1255939--1256005	24	2.9	23	80	12	66	40	1	1	56	1.17
1255951--1255999	14	3.4	14	77	5	53	38	0	2	59	1.09
1255940--1255997	32	1.9	32	86	10	86	41	0	1	56	1.09
1255941--1256012	37	1.9	37	86	5	101	41	1	1	55	1.17
1257428--1257467	19	2.1	20	86	9	57	70	2	2	25	1.13
1257631--1257711	22	3.6	22	80	6	83	67	11	1	19	1.27
1257675--1257724	23	2.2	23	82	10	59	72	4	0	24	1.02
1257630--1257733	22	4.7	22	76	9	77	67	9	0	22	1.26
1258087--1258161	27	2.8	27	87	0	114	44	18	10	26	1.83
1260034--1260079	21	2.1	22	84	4	58	19	30	19	30	1.97
1262523--1262589	33	2.0	33	88	0	98	34	11	13	40	1.81
1262543--1262567	13	1.9	13	100	0	50	36	16	16	32	1.90
1262630--1262654	13	1.9	13	100	0	50	32	16	16	36	1.90
1270984--1271040	30	1.9	30	100	0	114	24	26	19	29	1.98
1271044--1271638	34	17.9	34	81	12	623	20	34	12	32	1.91
1271042--1271196	29	5.2	27	76	20	148	22	34	12	30	1.92
1271137--1271638	71	7.4	69	84	10	630	20	34	12	32	1.90
1271207--1271599	98	3.9	97	85	10	453	20	34	13	31	1.91
1271073--1271638	169	3.4	165	90	5	879	20	34	12	32	1.90
1271469--1271638	70	2.4	70	92	5	281	20	34	11	34	1.89
1271016--1271659	105	6.4	102	81	12	650	20	34	12	31	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1271641--1271747	33	3.2	33	93	1	187	27	35	16	20	1.94
1271747--1272968	49	24.7	49	80	8	1264	24	25	17	32	1.97
1271747--1272968	147	8.2	147	83	8	1436	24	25	17	32	1.97
1272252--1273034	389	2.0	384	90	3	1210	24	25	17	32	1.97
1273902--1273968	33	2.0	33	88	0	98	34	11	13	40	1.81
1273922--1273946	13	1.9	13	100	0	50	36	16	16	32	1.90
1274009--1274033	13	1.9	13	100	0	50	32	16	16	36	1.90
1274042--1274161	52	2.3	52	94	4	208	33	18	18	30	1.95
1278166--1278247	41	2.0	41	88	4	121	25	19	8	46	1.78
1278168--1278258	41	2.3	40	83	9	114	26	16	8	48	1.75
1282593--1282644	11	4.7	11	73	7	52	48	3	0	48	1.20
1282764--1282809	19	2.4	19	82	13	58	58	4	0	36	1.18
1286042--1286074	11	2.9	12	82	17	52	66	0	0	33	0.92
1286033--1286116	35	2.4	35	78	11	100	59	0	1	39	1.05
1286036--1286110	19	4.1	20	75	25	51	60	0	1	38	1.06
1286042--1286095	27	2.0	28	88	3	83	61	0	1	37	1.07
1286328--1286359	2	16.0	2	93	0	55	50	3	0	46	1.17
1286534--1286594	23	2.6	22	77	10	59	60	0	3	36	1.13
1287082--1287114	16	1.9	18	88	11	52	21	3	3	72	1.11
1288551--1288616	22	3.0	22	78	17	73	59	1	1	37	1.16
1293215--1293258	11	3.6	12	80	14	54	59	0	0	40	0.98
1293712--1293750	21	1.9	20	84	5	51	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1293722--1293787	20	3.3	18	70	22	51	53	0	0	46	1.00
1293854--1293914	26	2.3	27	78	18	74	52	0	0	47	1.00
1294371--1294396	2	13.0	2	100	0	52	50	0	0	50	1.00
1295345--1295438	26	3.6	25	72	14	75	26	6	1	65	1.23
1297474--1297506	11	2.8	12	95	4	59	57	0	0	42	0.98
1297537--1297582	17	2.5	18	79	13	58	39	0	2	58	1.10
1297882--1297908	2	13.5	2	100	0	54	51	0	0	48	1.00
1298765--1298834	29	2.5	27	77	8	68	50	0	0	50	1.00
1300631--1300659	2	14.5	2	100	0	58	0	48	0	51	1.00
1301444--1301512	15	4.3	15	73	20	59	65	1	0	33	1.02
1301457--1301509	20	2.7	20	80	13	65	62	1	0	35	1.06
1301449--1301489	5	8.2	5	84	10	57	65	0	0	34	0.93
1301482--1301556	33	2.3	31	81	9	87	53	2	0	44	1.14
1301975--1302019	22	2.1	21	84	12	56	28	0	4	66	1.11
1303075--1303119	15	3.0	15	83	0	63	42	26	0	31	1.56
1305328--1305369	22	2.0	22	90	4	68	45	16	4	33	1.69
1306836--1306886	15	3.8	13	79	18	52	39	1	0	58	1.09
1306854--1306882	15	1.9	15	100	0	58	37	0	0	62	0.96
1308828--1308868	17	2.4	17	87	4	64	34	2	24	39	1.69
1309052--1309080	2	15.0	2	92	7	51	51	0	0	48	1.00
1309570--1309600	2	15.5	2	93	0	53	54	0	0	45	0.99
1312114--1312170	2	28.5	2	89	0	87	47	1	3	47	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1315943--1315981	2	19.5	2	100	0	78	51	0	0	48	1.00
1319253--1319297	24	1.9	24	90	4	74	51	0	0	48	1.00
1319523--1319556	17	1.9	17	94	5	59	67	2	0	29	1.05
1320610--1320673	14	4.7	13	75	14	58	50	0	0	50	1.00
1320618--1320679	20	3.0	20	79	15	65	53	0	0	46	1.00
1320723--1320778	26	2.2	24	82	14	69	53	7	0	39	1.28
1322428--1322490	17	3.9	16	71	23	51	47	0	1	50	1.10
1323393--1323429	19	1.9	19	88	0	56	45	8	0	45	1.32
1323431--1323473	16	2.6	17	82	7	54	55	0	0	44	0.99
1324037--1324159	35	3.4	34	78	9	120	52	0	3	43	1.23

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