genome.fa.s3.2.7.7.80.10.50.1000.10.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   

This is table  10  of  32  ( 3795 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)
1197507--1197570	23	2.8	23	75	15	62	57	0	4	37	1.19
1198231--1198274	18	2.4	18	84	0	52	27	6	2	63	1.31
1198424--1198448	6	4.2	6	100	0	50	16	0	0	84	0.63
1198651--1198693	18	2.4	17	77	11	50	27	4	2	65	1.25
1200185--1200522	144	2.3	144	78	8	330	30	8	14	46	1.75
1201065--1201148	29	3.0	28	84	5	98	47	2	13	36	1.55
1201065--1201148	27	3.0	28	82	8	91	47	2	13	36	1.55
1204670--1205060	201	2.0	199	85	4	527	33	14	15	37	1.87
1210330--1210399	28	2.4	29	75	11	72	31	1	4	62	1.23
1210347--1210414	35	2.0	33	82	8	82	30	1	7	60	1.33
1210345--1210421	34	2.3	34	80	8	86	31	1	6	61	1.30
1211015--1211086	14	5.1	14	76	17	78	81	0	16	1	0.75
1211015--1211087	28	2.6	27	81	14	94	80	0	16	2	0.82
1211015--1211086	22	3.3	21	75	12	83	81	0	16	1	0.75
1211676--1211723	23	2.0	24	92	4	80	16	2	12	68	1.29
1211859--1211911	14	3.4	15	71	19	54	41	0	0	58	0.98
1211867--1211917	14	3.4	14	75	19	57	45	0	0	54	0.99
1211934--1212014	35	2.4	34	78	10	94	32	4	0	62	1.16
1211894--1212020	22	5.7	22	66	25	54	33	4	0	60	1.23
1212006--1212094	29	3.3	27	67	21	69	42	0	0	57	0.98
1212015--1212124	43	2.4	47	74	18	117	47	0	0	52	1.00
1216885--1216986	31	3.0	33	77	12	84	38	0	0	60	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1216872--1216947	17	4.4	17	74	15	59	42	1	0	56	1.07
1216912--1216964	24	2.3	23	84	12	65	39	0	0	60	0.97
1222616--1222663	15	3.1	15	80	14	53	39	0	0	60	0.97
1223111--1223156	18	2.5	19	83	13	60	26	4	2	67	1.21
1223425--1223494	32	2.2	32	82	7	79	44	4	0	51	1.21
1225214--1225275	32	2.1	29	82	11	72	46	3	1	48	1.28
1225254--1225296	18	2.5	16	88	11	59	48	0	0	51	1.00
1225254--1225308	17	2.9	19	82	15	62	50	0	1	47	1.11
1225254--1225300	17	2.7	17	87	12	69	48	0	0	51	1.00
1225795--1225842	25	1.9	25	91	0	78	50	0	0	50	1.00
1228631--1228669	20	2.0	20	100	0	78	15	10	30	43	1.80
1229028--1229090	21	3.3	20	70	30	57	50	0	0	49	1.00
1229041--1229072	15	2.1	15	100	0	64	59	0	0	40	0.97
1229059--1229098	21	1.9	21	94	0	71	50	0	0	50	1.00
1229205--1229229	6	4.2	6	100	0	50	80	0	0	20	0.72
1229232--1229263	6	5.3	6	100	0	64	37	0	0	62	0.95
1229192--1229284	18	5.1	18	67	11	55	53	0	0	46	1.00
1235827--1235968	69	2.1	69	90	2	223	43	14	9	33	1.76
1239286--1239315	15	2.0	15	93	0	51	20	6	10	63	1.47
1246120--1246164	20	2.3	18	79	17	54	42	0	0	57	0.98
1247087--1247170	19	4.6	18	70	16	66	47	4	0	47	1.23
1247415--1247445	16	1.9	16	100	0	62	80	0	6	12	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1247418--1247468	16	3.1	16	83	5	57	78	1	3	15	0.99
1247424--1247486	24	2.5	24	78	14	58	73	1	1	23	1.01
1248057--1248093	2	18.5	2	100	0	74	51	0	0	48	1.00
1252774--1252799	3	8.7	3	100	0	52	34	0	34	30	1.58
1255562--1256226	108	6.2	108	93	1	1084	44	13	12	29	1.80
1256446--1256534	36	2.5	36	82	10	96	37	0	0	62	0.95
1256457--1256515	25	2.3	25	83	13	68	37	0	0	62	0.95
1256455--1256515	26	2.4	26	76	17	65	37	0	0	62	0.96
1256446--1256534	17	5.0	19	81	11	84	37	0	0	62	0.95
1258774--1258829	19	3.0	19	76	2	51	42	0	1	55	1.10
1259684--1259738	20	2.8	20	77	2	58	49	0	5	45	1.25
1259731--1259768	12	3.3	12	82	14	53	52	0	0	47	1.00
1259734--1259784	24	2.2	24	86	6	70	54	0	0	45	0.99
1259726--1259784	24	2.6	23	78	10	68	50	0	1	47	1.11
1262524--1262562	20	2.0	20	84	0	51	23	5	7	64	1.40
1267562--1267600	18	2.2	18	90	9	62	43	2	12	41	1.56
1267868--1267911	20	2.2	20	84	4	54	61	0	0	38	0.96
1268511--1268540	15	1.9	16	93	6	53	63	0	3	33	1.11
1272301--1272341	3	13.7	3	100	0	82	31	0	0	68	0.90
1272566--1272622	3	19.0	3	96	0	105	64	0	1	33	1.04
1274742--1274811	2	35.0	2	79	0	50	42	7	7	42	1.59
1274746--1274806	32	1.9	32	93	0	104	40	8	8	42	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1280688--1280741	19	3.1	18	82	12	69	44	0	0	55	0.99
1280699--1280750	19	2.8	19	85	8	72	42	0	0	57	0.98
1281039--1281100	21	2.9	22	70	15	58	66	4	1	27	1.21
1281929--1281968	2	20.0	2	84	0	53	42	0	2	55	1.13
1282096--1282148	5	10.2	5	82	13	63	60	0	1	37	1.08
1282081--1282158	25	2.9	28	78	20	85	57	0	1	41	1.07
1282761--1282848	31	2.7	31	77	7	77	55	0	0	44	0.99
1282803--1282858	19	2.9	19	81	0	67	62	0	0	37	0.95
1283059--1283094	2	18.0	2	100	0	72	50	0	0	50	1.00
1283426--1283485	27	2.2	28	82	8	70	66	1	1	30	1.11
1283437--1283477	16	2.5	17	88	4	57	63	2	0	34	1.08
1283438--1283498	28	2.3	25	83	13	77	65	1	0	32	1.02
1283437--1283500	27	2.4	28	82	10	80	64	1	0	34	1.03
1283440--1283509	26	2.5	29	75	17	76	61	1	0	37	1.05
1283486--1283539	17	3.2	18	70	17	53	48	0	0	51	1.00
1283478--1283544	14	4.4	15	74	20	59	53	0	0	46	1.00
1283550--1283584	11	3.2	11	95	0	61	65	0	0	34	0.93
1283756--1283804	24	2.0	25	88	4	73	38	4	0	57	1.18
1283761--1283806	5	9.6	5	76	9	51	39	2	0	58	1.10
1284502--1284583	15	5.8	15	70	21	52	64	0	0	35	0.94
1284531--1284590	27	2.2	26	85	14	77	60	0	0	40	0.97
1284530--1284576	12	3.5	13	78	16	51	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)
1286279--1286326	25	1.9	25	83	8	62	45	6	4	43	1.48
1286576--1286623	17	2.9	17	79	20	57	64	0	0	35	0.94
1290035--1290071	14	2.5	15	83	16	51	43	0	0	56	0.99
1290047--1290121	22	3.8	20	74	20	68	48	0	0	52	1.00
1290090--1290154	29	2.4	29	80	10	75	53	0	0	46	1.00
1290142--1290205	25	2.6	25	76	16	71	59	3	0	37	1.13
1290142--1290205	23	2.6	26	72	25	66	59	3	0	37	1.13
1297988--1298048	30	2.0	31	90	3	97	62	1	1	34	1.15
1298145--1298211	31	2.1	31	84	13	84	53	4	1	40	1.30
1298946--1298986	8	4.8	9	80	19	52	36	0	0	63	0.95
1299420--1299488	27	2.6	27	84	9	88	34	2	13	49	1.56
1302043--1302088	21	2.1	22	84	4	58	34	19	26	19	1.96
1304759--1304842	32	2.8	30	76	15	93	46	3	0	50	1.19
1308028--1308071	23	1.9	23	86	9	63	54	0	0	45	0.99
1308468--1308526	27	2.2	27	78	3	66	55	1	0	42	1.09
1308530--1308607	40	1.9	41	82	7	97	50	8	3	37	1.52
1308634--1308672	16	2.4	16	82	0	51	61	0	0	38	0.96
1309355--1309393	19	2.0	20	90	5	62	51	0	0	48	1.00
1310107--1310215	31	3.6	30	77	9	89	35	4	3	55	1.38
1310763--1310836	22	3.2	24	79	5	73	50	0	0	50	1.00
1314431--1314468	11	3.5	11	86	10	51	52	0	2	44	1.14
1315887--1315917	2	15.5	2	100	0	62	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)
1316132--1316158	2	13.5	2	100	0	54	48	0	0	51	1.00
1316567--1316688	38	3.2	38	83	12	162	26	8	14	50	1.71
1317363--1317396	11	3.1	11	91	0	50	38	2	0	58	1.13
1320849--1321064	34	6.4	34	80	1	229	28	7	23	40	1.82
1320849--1321065	102	2.1	101	84	1	281	28	7	23	40	1.82
1322661--1323002	171	2.0	171	99	0	675	31	17	25	24	1.97
1325643--1325860	34	6.4	34	86	2	287	25	7	26	40	1.82
1325643--1325861	102	2.2	102	91	0	350	25	7	26	40	1.82
1326239--1326266	4	7.0	4	100	0	56	75	0	0	25	0.81
1326634--1326690	15	3.6	16	81	11	64	59	0	1	38	1.08

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