genome.fa.s2.2.7.7.80.10.50.1000.8.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   
          33   34   35   36   37   38   

This is table  8  of  38  ( 4457 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)
1202847--1202901	20	2.8	19	88	5	74	41	16	12	29	1.85
1202953--1203004	19	2.7	20	90	6	88	44	15	11	28	1.81
1203442--1203508	37	1.9	35	88	11	102	32	11	25	29	1.92
1204601--1204642	21	2.0	21	85	0	57	42	4	28	23	1.74
1205031--1205195	84	2.0	84	83	7	210	52	3	18	24	1.61
1206500--1206524	13	1.9	13	100	0	50	36	16	16	32	1.90
1207318--1207469	46	3.3	46	98	0	286	29	3	32	33	1.76
1208616--1208679	20	3.7	18	74	25	66	43	15	12	28	1.83
1208634--1208659	13	2.0	13	100	0	52	38	15	15	30	1.88
1208616--1208679	32	2.0	33	93	3	112	43	15	12	28	1.83
1209117--1209183	37	1.9	35	88	11	102	32	11	25	29	1.92
1211792--1212403	79	7.8	78	69	17	300	32	13	24	29	1.93
1212082--1212144	28	2.2	29	83	8	85	31	22	22	23	1.98
1212128--1212246	51	2.3	51	89	2	177	31	10	26	32	1.89
1214760--1214842	20	3.7	20	69	27	67	40	16	16	25	1.90
1214738--1214841	50	2.1	49	94	1	181	40	18	16	25	1.90
1217709--1217733	13	1.9	13	100	0	50	24	16	20	40	1.91
1217768--1217813	19	2.3	20	88	3	67	36	13	13	36	1.83
1219297--1219329	11	3.1	11	82	8	50	27	6	9	57	1.53
1220994--1221044	19	2.6	20	84	3	68	37	11	17	33	1.86
1229697--1229721	13	1.9	13	100	0	50	36	16	16	32	1.90
1229770--1229823	19	2.8	20	80	2	65	40	16	14	27	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1234555--1234580	2	13.0	2	100	0	52	50	0	0	50	1.00
1239251--1239311	5	11.0	5	75	16	50	73	3	3	19	1.11
1239250--1239312	11	5.5	11	80	12	56	73	3	3	20	1.12
1239250--1239312	23	2.7	23	78	9	67	73	3	3	20	1.12
1241291--1241347	20	2.8	20	83	0	69	38	14	15	31	1.87
1241333--1241394	13	5.2	13	72	21	64	30	14	16	38	1.88
1241316--1241393	33	2.4	33	97	0	147	30	14	17	37	1.90
1241297--1241380	20	4.6	20	74	19	83	33	15	16	34	1.91
1241316--1241412	33	2.9	32	89	6	106	31	15	17	35	1.91
1241382--1241434	20	2.6	21	81	3	63	39	15	16	28	1.89
1241486--1241510	13	1.9	13	100	0	50	32	16	16	36	1.90
1241466--1241532	32	2.1	32	91	5	109	31	20	13	34	1.92
1250136--1250192	20	2.8	20	83	0	69	38	14	15	31	1.87
1250178--1250206	13	2.2	13	100	0	58	31	17	13	37	1.89
1250194--1250246	20	2.6	21	84	3	72	39	16	16	26	1.91
1250298--1250324	13	2.1	13	100	0	54	29	14	14	40	1.86
1254129--1254187	32	1.9	30	83	13	75	59	10	10	20	1.58
1254447--1254496	19	2.5	19	80	6	55	24	10	16	50	1.75
1254550--1254605	20	2.8	20	89	5	78	28	17	16	37	1.91
1258063--1258113	20	2.5	20	87	0	75	45	3	13	37	1.63
1259915--1259961	21	2.2	22	85	11	62	68	0	2	29	1.02
1259914--1259965	22	2.3	24	81	15	67	67	0	1	30	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1261860--1261893	18	1.9	18	88	5	52	73	0	20	5	1.04
1264648--1264699	17	3.1	16	79	17	52	32	0	5	61	1.20
1266311--1266350	21	1.9	21	90	10	64	60	5	0	35	1.19
1267252--1267277	13	2.0	13	100	0	52	30	15	15	38	1.88
1267232--1267295	32	2.0	33	90	3	103	28	14	15	42	1.86
1269835--1269872	13	3.0	12	88	11	58	31	18	18	31	1.95
1271939--1271974	15	2.3	15	90	4	54	19	19	16	44	1.87
1276020--1276071	19	2.7	20	87	6	79	28	13	15	42	1.85
1276861--1276989	27	4.7	28	86	1	127	28	27	23	20	1.99
1276909--1276986	27	2.9	27	92	0	129	26	30	21	20	1.98
1276856--1276989	14	9.7	14	71	3	101	27	26	23	22	2.00
1277647--1277702	23	2.4	23	90	0	94	30	7	14	48	1.70
1278024--1278067	20	2.2	21	84	15	67	70	2	4	22	1.17
1278328--1278374	2	23.5	2	91	0	76	44	0	0	55	0.99
1281059--1281151	24	4.0	23	76	10	82	26	26	16	30	1.96
1281084--1281150	23	2.9	23	82	10	82	28	29	17	23	1.97
1282007--1282475	117	4.0	118	86	4	586	36	17	15	30	1.91
1292681--1292709	3	9.7	3	100	0	58	65	0	0	34	0.93
1293532--1293569	14	2.6	15	87	4	51	36	2	52	7	1.45
1294897--1294930	18	1.9	18	88	5	52	70	0	23	5	1.09
1296544--1296568	5	5.0	5	100	0	50	0	20	40	40	1.52
1296861--1296901	3	13.7	3	94	0	73	31	0	2	65	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1297050--1297138	44	2.0	45	82	8	110	42	0	0	57	0.98
1297107--1297189	19	4.9	18	69	26	58	42	1	0	56	1.07
1297083--1297204	8	14.3	9	65	22	50	39	1	0	59	1.08
1298062--1298117	11	5.2	11	73	18	55	66	8	1	23	1.30
1298308--1298365	27	2.1	28	84	9	75	56	3	1	37	1.26
1298381--1298422	17	2.4	17	92	4	66	2	11	2	83	0.84
1298381--1298438	18	3.1	19	79	18	59	1	18	1	77	0.94
1298887--1298926	13	2.9	15	78	17	50	55	5	2	37	1.35
1298985--1299033	15	3.3	15	80	11	57	59	0	0	40	0.98
1299003--1299049	21	2.3	20	78	14	51	63	2	0	34	1.06
1298949--1299068	6	19.2	6	69	19	50	63	1	0	35	1.05
1300246--1300275	15	2.1	14	93	6	51	46	0	0	53	1.00
1300641--1300675	2	17.5	2	93	0	61	45	2	0	51	1.16
1302428--1302478	3	17.0	3	100	0	102	66	0	0	33	0.92
1310635--1310690	16	3.4	17	72	22	57	42	0	0	57	0.99
1310634--1310680	17	2.7	17	80	9	51	40	0	0	59	0.97
1310667--1310730	31	2.1	32	91	5	105	56	0	1	42	1.09
1317902--1317947	10	4.5	11	84	10	62	80	0	19	0	0.71
1317902--1317943	21	2.0	21	90	0	66	80	0	19	0	0.70
1318916--1318971	20	2.8	19	81	13	60	32	14	16	37	1.88
1327256--1327600	78	4.4	79	80	4	369	35	13	22	28	1.93
1327246--1327600	157	2.3	157	81	5	416	34	13	22	29	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1330498--1330570	34	2.3	33	83	9	89	36	15	30	17	1.91
1330647--1330920	45	6.4	45	71	14	188	40	13	25	21	1.89
1331162--1331623	178	2.6	180	85	3	585	41	7	9	41	1.65
1337130--1337756	310	2.0	306	84	3	814	29	12	18	40	1.86
1336944--1337594	155	4.2	153	74	7	557	29	11	18	41	1.85
1341914--1341939	13	2.0	13	100	0	52	30	15	15	38	1.88
1342637--1342680	21	2.1	21	83	8	54	25	31	4	38	1.76
1346572--1346602	15	2.1	15	93	0	53	12	22	16	48	1.80
1348406--1348454	21	2.4	21	86	10	66	22	18	4	55	1.60
1350665--1350690	13	2.0	13	100	0	52	30	15	15	38	1.88
1351072--1351111	20	2.0	20	90	0	62	30	17	12	40	1.86
1351942--1351996	20	2.7	20	80	8	58	34	10	20	34	1.87
1360110--1360160	24	2.1	24	85	0	66	37	15	7	39	1.77
1368089--1368117	2	14.5	2	100	0	58	51	0	0	48	1.00
1370864--1370939	21	3.7	21	78	3	91	30	17	11	40	1.85
1370885--1370957	20	3.6	20	79	17	96	32	19	13	34	1.91
1370864--1370957	41	2.3	41	96	0	170	30	18	12	38	1.88
1373413--1373450	13	2.9	13	96	0	67	31	15	18	34	1.92
1373439--1373515	20	3.6	20	74	19	66	44	15	14	25	1.84
1377358--1377402	21	2.1	21	84	8	56	22	20	4	53	1.63
1379613--1379638	13	2.0	13	100	0	52	30	15	15	38	1.88
1379677--1379752	21	3.7	21	78	3	91	30	17	11	40	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1379698--1379770	20	3.6	20	79	17	96	32	19	13	34	1.91
1379677--1379770	41	2.3	41	96	0	170	30	18	12	38	1.88
1384533--1384573	21	2.0	21	90	9	66	21	21	17	39	1.93
1387839--1387865	13	2.1	13	100	0	54	48	0	0	51	1.00
1392639--1392689	20	2.5	21	87	3	68	37	11	17	33	1.86
1394453--1394491	21	1.9	20	84	5	51	51	5	0	43	1.24
1399103--1399244	52	2.7	52	91	4	225	30	17	17	33	1.94
1402220--1402244	13	1.9	13	100	0	50	60	0	0	40	0.97
1402718--1402783	24	2.6	28	77	20	81	54	6	4	34	1.45
1404832--1404865	16	2.1	17	94	5	61	38	0	0	61	0.96

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   
          33   34   35   36   37   38