genome.fa.s8.2.7.7.80.10.50.1000.9.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: Scaffold8
Parameters: 2 7 7 80 10 50 1000
Length:  6381039

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   

This is table  9  of  33  ( 3942 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)
1185760--1185811	12	4.3	12	76	9	52	30	3	1	63	1.23
1186078--1186134	28	2.1	27	84	15	73	45	1	3	49	1.29
1193832--1193873	20	2.1	20	86	8	59	47	0	2	50	1.14
1195636--1195662	2	13.5	2	100	0	54	48	0	0	51	1.00
1196346--1196406	28	2.2	27	82	8	70	52	6	0	40	1.27
1196618--1196642	12	2.1	12	100	0	50	0	40	36	24	1.55
1200322--1200388	19	3.7	19	77	15	63	38	0	0	61	0.96
1200386--1200422	15	2.5	15	86	0	56	64	0	0	35	0.94
1203933--1203975	2	21.5	2	100	0	86	51	0	0	48	1.00
1204863--1204898	18	2.0	18	88	0	54	50	0	0	50	1.00
1204910--1204989	25	3.4	24	74	17	71	48	0	1	50	1.08
1204910--1204964	21	2.5	21	79	5	56	47	0	1	50	1.11
1204931--1205002	25	2.8	25	75	6	65	48	0	2	48	1.16
1205183--1205224	19	2.3	18	87	4	57	42	2	2	52	1.27
1205465--1205521	15	3.7	15	73	13	53	38	0	1	59	1.08
1205564--1205588	2	12.5	2	100	0	50	48	0	0	52	1.00
1206320--1206356	19	2.0	18	89	5	56	45	0	0	54	1.00
1206984--1207021	17	2.1	19	85	9	53	57	5	2	34	1.35
1208131--1208186	3	18.7	3	96	0	103	32	1	0	66	1.03
1215400--1215453	26	2.1	25	83	10	65	37	0	0	62	0.95
1215651--1215677	14	1.9	14	100	0	54	29	3	0	66	1.09
1221661--1221706	2	23.0	2	95	0	83	50	0	2	47	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1223016--1223040	13	1.9	13	100	0	50	48	0	4	48	1.20
1223044--1223102	28	2.1	28	83	0	73	52	0	0	47	1.00
1223600--1223627	2	14.0	2	100	0	56	50	0	0	50	1.00
1224578--1224615	2	19.0	2	89	10	60	50	0	2	47	1.15
1224752--1224787	15	2.4	15	90	0	54	8	33	27	30	1.86
1226166--1226208	19	2.3	18	84	8	50	67	0	2	30	1.03
1228168--1228216	26	2.0	24	84	15	64	42	0	0	57	0.99
1229218--1229258	21	2.0	21	85	9	57	51	0	2	46	1.14
1231357--1231393	2	18.5	2	100	0	74	51	0	0	48	1.00
1232478--1232528	17	3.0	17	82	0	66	29	3	3	62	1.31
1232514--1232564	25	2.1	24	89	7	77	31	5	1	60	1.31
1233150--1233231	29	2.8	29	76	14	78	50	1	4	43	1.31
1233161--1233231	29	2.4	30	83	2	90	49	1	5	43	1.35
1234733--1234806	36	2.1	34	85	12	96	39	1	4	55	1.27
1251715--1251741	2	13.5	2	100	0	54	48	0	51	0	1.00
1252146--1252183	18	2.2	18	90	4	60	60	2	0	36	1.11
1252330--1252389	27	2.3	25	81	16	68	41	1	0	56	1.09
1252350--1252393	21	2.1	21	82	0	52	45	2	0	52	1.13
1253080--1253110	15	2.1	15	100	0	62	25	0	12	61	1.32
1263903--1263938	2	18.0	2	100	0	72	50	0	0	50	1.00
1265889--1265937	25	2.0	25	84	8	64	51	0	0	48	1.00
1266061--1266099	19	2.0	19	85	5	51	41	20	5	33	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1266895--1266930	2	18.0	2	100	0	72	50	0	0	50	1.00
1270060--1270159	44	2.3	44	82	3	121	31	13	16	40	1.86
1274707--1274838	47	3.0	44	79	9	151	50	10	18	20	1.77
1274982--1275022	21	2.0	21	100	0	82	29	21	4	43	1.73
1275055--1275157	44	2.3	44	86	0	134	29	10	17	42	1.83
1279116--1279154	13	3.2	13	92	7	64	43	0	0	56	0.99
1279122--1279159	13	3.4	11	89	10	51	44	0	0	55	0.99
1279244--1279286	14	3.2	13	80	9	50	51	0	0	48	1.00
1280122--1280184	29	2.1	29	85	8	83	42	4	0	52	1.22
1280836--1280972	7	16.4	8	68	20	52	36	1	2	59	1.22
1280872--1280908	17	2.1	17	90	5	56	48	0	0	51	1.00
1280828--1280908	18	4.4	18	77	14	69	41	0	1	56	1.07
1283784--1283830	19	2.6	18	86	6	67	61	0	0	38	0.96
1283784--1283834	18	2.6	20	87	9	70	60	0	0	39	0.97
1284145--1284169	2	12.5	2	100	0	50	48	0	0	52	1.00
1286307--1286334	4	7.0	4	100	0	56	25	0	25	50	1.50
1286915--1286952	19	2.0	19	94	0	67	34	5	7	52	1.53
1288306--1288339	4	8.5	4	93	0	59	76	2	0	20	0.92
1293015--1293044	2	15.0	2	100	0	60	50	0	50	0	1.00
1293983--1294033	21	2.3	23	83	6	61	37	5	0	56	1.23
1294039--1294271	113	2.0	116	91	5	382	49	6	11	33	1.64
1296413--1296437	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1296554--1296590	15	2.6	15	87	8	51	56	8	2	32	1.43
1297765--1297794	2	15.0	2	92	0	51	53	0	0	46	1.00
1297859--1297919	31	2.0	31	100	0	122	45	3	16	34	1.63
1297960--1298011	20	2.6	21	72	9	54	44	1	0	53	1.11
1299407--1299435	2	14.5	2	100	0	58	0	0	48	51	1.00
1300008--1300079	25	2.7	29	72	18	73	65	0	0	34	0.93
1300010--1300101	8	11.9	8	66	23	54	61	0	0	38	0.96
1299981--1300051	14	5.0	14	72	24	60	69	0	0	30	0.89
1300042--1300078	19	1.9	19	88	0	56	59	0	0	40	0.97
1300010--1300107	34	2.9	34	76	15	96	61	0	0	38	0.96
1300873--1300941	31	2.2	32	82	7	88	39	1	0	59	1.06
1300913--1300951	20	2.0	20	84	0	51	48	0	0	51	1.00
1301090--1301114	2	12.5	2	100	0	50	48	0	0	52	1.00
1301899--1301952	18	3.0	18	79	15	58	62	1	0	35	1.06
1302167--1302232	25	2.6	24	81	9	78	59	1	1	37	1.16
1302720--1302755	18	2.0	18	94	0	63	41	0	0	58	0.98
1303620--1303683	32	2.0	32	96	0	119	60	0	7	31	1.25
1306928--1306974	16	3.0	16	78	12	53	42	0	0	57	0.98
1307122--1307146	2	12.5	2	100	0	50	48	0	0	52	1.00
1308908--1308955	23	2.1	23	81	14	55	66	4	0	29	1.10
1312163--1312211	9	5.2	9	82	7	62	71	0	2	26	0.97
1312178--1312243	33	2.0	33	85	5	89	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1312164--1312274	26	4.4	25	73	13	84	63	0	0	36	1.01
1312163--1312250	19	5.0	19	77	18	84	67	0	1	31	0.99
1312166--1312249	10	8.3	10	69	24	52	65	0	1	33	1.00
1313290--1313332	19	2.1	21	91	8	72	30	9	11	48	1.71
1314488--1314544	22	2.5	22	81	13	55	42	0	0	57	0.98
1315697--1315730	14	2.3	15	85	10	52	50	0	0	50	1.00
1317671--1317722	19	2.7	19	81	0	59	46	3	0	50	1.20
1320068--1320104	2	18.5	2	100	0	74	48	0	0	51	1.00
1320649--1320682	3	11.3	3	93	0	59	70	0	0	29	0.87
1321143--1321168	7	3.7	7	100	0	52	26	30	26	15	1.96
1321137--1321175	14	2.9	14	80	3	53	23	35	23	17	1.95
1326279--1326303	2	12.5	2	100	0	50	48	0	52	0	1.00
1326876--1326904	2	14.5	2	100	0	58	48	0	0	51	1.00
1328620--1328662	21	2.0	21	95	0	77	69	18	11	0	1.17
1330018--1330074	16	3.7	17	76	19	63	68	0	0	31	0.90
1330017--1330064	21	2.5	20	83	10	64	68	0	0	31	0.90
1330062--1330142	32	2.9	27	71	18	74	54	0	0	45	0.99
1330091--1330143	17	3.3	15	76	23	54	58	0	0	41	0.98
1330036--1330166	16	8.2	16	64	24	55	58	0	0	40	1.09
1330851--1330909	30	2.0	30	90	3	93	38	16	5	38	1.71
1340438--1340463	3	8.7	3	100	0	52	69	0	0	30	0.89
1341108--1341135	13	2.2	13	100	0	56	25	14	14	46	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1346272--1346320	22	2.3	20	86	6	62	57	0	4	38	1.18
1348345--1348382	19	2.0	19	90	10	60	57	0	0	42	0.98
1348352--1348418	10	6.7	11	68	25	51	62	0	0	37	0.95
1349589--1349636	19	2.5	19	74	12	53	75	0	6	18	1.01
1350475--1350514	19	2.1	19	85	4	53	62	5	0	32	1.17
1350985--1351024	20	2.0	20	85	9	55	50	0	0	50	1.00
1350981--1351049	26	2.6	26	81	9	68	46	0	1	52	1.09
1350968--1351065	35	2.7	33	79	17	90	42	0	1	56	1.06
1351021--1351051	16	1.9	16	100	0	62	45	0	3	51	1.17
1351858--1351897	21	2.0	21	85	5	55	7	15	12	65	1.47

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