genome.fa.s25.2.7.7.80.10.50.1000.6.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  6  of  56  ( 6609 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)
1070451--1070481	16	1.9	16	93	0	53	64	0	0	35	0.94
1073576--1073643	23	3.1	23	67	16	72	48	2	11	36	1.55
1074129--1074178	24	2.0	24	88	11	75	40	2	0	58	1.10
1074134--1074196	19	3.3	19	76	12	67	34	1	1	61	1.15
1074142--1074206	30	2.2	30	78	8	71	38	1	1	58	1.17
1074677--1074728	19	2.7	20	80	17	65	32	0	0	67	0.91
1074663--1074725	24	2.6	24	82	7	83	31	0	0	68	0.90
1081185--1081217	2	16.5	2	100	0	66	51	0	0	48	1.00
1081908--1081937	15	2.0	15	93	0	51	3	20	0	76	0.92
1082113--1082146	17	1.9	18	94	5	61	64	0	0	35	0.94
1082307--1082343	17	2.2	18	85	9	51	29	2	0	67	1.04
1082460--1082513	21	2.4	22	82	14	58	57	0	3	38	1.17
1082483--1082539	21	2.7	22	83	5	73	52	0	0	47	1.00
1082486--1082550	21	3.1	21	78	12	55	49	0	0	50	1.00
1090013--1090054	2	21.0	2	100	0	84	0	50	0	50	1.00
1095566--1095599	2	17.0	2	100	0	68	50	0	50	0	1.00
1095666--1095693	2	14.0	2	100	0	56	50	0	50	0	1.00
1099661--1099694	2	17.0	2	93	0	59	47	2	0	50	1.16
1099890--1100040	78	1.9	78	94	0	266	41	11	23	23	1.87
1100432--1100463	2	16.5	2	93	6	57	53	46	0	0	1.00
1111141--1111196	21	2.6	22	80	2	60	46	1	5	46	1.36
1113660--1113749	46	2.0	45	88	2	135	33	4	5	56	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1121821--1121884	19	3.1	21	80	12	71	53	6	0	40	1.26
1122283--1122320	3	12.7	3	100	0	76	34	0	0	65	0.93
1122558--1122614	17	3.2	18	72	18	57	59	0	0	40	0.97
1122512--1122613	43	2.5	39	74	18	93	53	0	0	44	1.13
1122586--1122615	15	2.0	15	93	0	51	56	0	0	43	0.99
1122539--1122607	21	3.3	20	71	13	50	59	0	0	40	0.97
1124276--1124346	25	3.0	25	80	10	69	42	1	1	54	1.17
1124334--1124367	13	2.5	14	90	4	52	44	2	0	52	1.16
1124287--1124363	23	3.3	23	78	10	84	45	1	0	53	1.08
1124296--1124361	25	2.7	24	81	6	71	45	1	0	53	1.09
1127463--1127513	17	2.8	18	82	8	68	52	1	1	43	1.23
1130062--1130103	20	2.1	20	95	0	75	28	19	16	35	1.93
1135286--1135311	2	13.0	2	100	0	52	50	0	0	50	1.00
1135332--1135362	2	15.5	2	100	0	62	51	0	0	48	1.00
1138470--1138509	2	20.5	2	94	5	73	50	0	0	50	1.00
1138816--1138862	24	2.0	24	82	0	58	36	2	0	61	1.08
1139390--1139423	3	11.7	3	87	6	52	64	2	32	0	1.08
1139783--1139835	22	2.3	24	81	18	69	50	0	0	49	1.00
1144957--1145018	22	2.9	21	85	9	72	41	0	0	58	0.98
1146544--1146587	19	2.3	19	84	7	54	50	2	0	47	1.13
1146533--1146604	22	3.0	23	76	13	74	54	1	0	44	1.08
1147381--1147423	18	2.6	16	80	16	52	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1148572--1148657	38	2.3	38	82	9	104	51	0	0	48	1.00
1148571--1148671	39	2.6	38	81	9	107	48	0	0	51	1.00
1148697--1148722	12	2.2	12	100	0	52	80	0	0	19	0.71
1157918--1157966	2	24.5	2	95	0	89	48	0	2	48	1.12
1163573--1163651	9	8.3	9	74	18	54	43	0	0	56	0.99
1163576--1163620	22	2.0	23	91	4	74	35	0	0	64	0.94
1163968--1164026	14	4.2	14	77	12	59	8	0	13	77	0.97
1164035--1164079	19	2.4	19	84	0	63	11	2	6	80	0.99
1164113--1164163	26	1.9	27	84	11	70	29	1	1	66	1.13
1164880--1164912	11	3.0	11	90	0	57	51	3	0	45	1.16
1165368--1165393	2	13.0	2	100	0	52	50	0	0	50	1.00
1167503--1167528	2	13.0	2	100	0	52	50	0	0	50	1.00
1167838--1167889	3	17.3	3	95	0	95	67	1	0	30	1.02
1170275--1170304	10	2.8	11	90	10	53	70	0	0	30	0.88
1171306--1171356	12	4.4	12	76	16	54	45	0	0	54	0.99
1171314--1171356	21	2.0	22	86	4	61	44	0	0	55	0.99
1174377--1174435	14	4.7	13	70	21	54	35	0	0	64	0.94
1174383--1174426	23	1.9	24	90	9	74	43	0	0	56	0.99
1176671--1176713	20	2.2	20	83	8	52	62	0	0	37	0.95
1178415--1178472	22	2.8	20	78	17	55	43	0	0	56	0.99
1182124--1182167	24	1.9	24	86	9	65	31	0	0	68	0.90
1184827--1184865	19	2.0	21	85	10	55	53	2	0	43	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1185763--1185822	26	2.4	25	83	5	75	65	0	0	35	0.93
1186994--1187072	30	2.7	30	92	2	124	39	0	2	58	1.12
1187209--1187296	36	2.4	36	83	5	97	54	3	0	42	1.17
1192183--1192219	2	18.5	2	94	0	65	54	0	0	45	1.00
1193152--1193184	16	2.1	16	88	5	50	69	0	0	30	0.88
1193158--1193193	16	2.2	16	90	0	54	69	0	0	30	0.89
1208012--1208166	77	2.0	77	98	0	301	40	22	7	29	1.82
1208124--1208172	25	2.1	22	88	11	71	53	12	4	30	1.57
1208381--1208410	2	15.0	2	92	0	51	50	3	0	46	1.18
1213161--1213203	2	21.5	2	100	0	86	48	0	0	51	1.00
1219627--1219662	18	2.0	18	100	0	72	44	16	16	22	1.86
1222530--1222559	6	5.0	6	95	0	51	80	0	3	16	0.85
1224008--1224042	13	2.5	14	90	9	54	51	0	0	48	1.00
1225480--1225527	15	3.1	15	82	8	53	58	10	0	31	1.32
1226021--1226066	23	2.0	23	83	8	58	54	0	0	45	0.99
1228693--1228726	3	11.3	3	100	0	68	64	0	0	35	0.94
1232621--1232647	3	9.0	3	100	0	54	66	33	0	0	0.92
1235040--1235081	19	2.2	20	86	4	59	66	0	0	33	0.92
1235413--1235451	20	2.0	20	85	9	55	71	2	2	23	1.10
1235553--1235628	40	1.9	40	91	0	125	10	7	11	69	1.36
1235553--1235628	20	3.7	21	71	15	68	10	7	11	69	1.36
1236597--1236650	28	1.9	28	85	7	74	51	1	0	46	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1237064--1237102	19	2.1	19	85	0	51	58	2	2	35	1.25
1244052--1244102	14	3.4	16	78	15	63	58	0	0	41	0.98
1246848--1246904	28	2.0	28	96	0	105	36	8	14	40	1.76
1247652--1247680	12	2.3	13	94	5	51	3	13	0	82	0.79
1252591--1252746	81	1.9	82	93	1	269	26	10	17	46	1.80
1259552--1259590	18	2.1	19	90	4	62	35	20	15	28	1.93
1261758--1261815	26	2.2	26	93	0	98	41	0	0	58	0.98
1261761--1261823	33	2.0	31	87	6	90	41	0	0	58	0.98
1261683--1261824	56	2.5	55	75	10	135	44	2	0	52	1.17
1261814--1261855	18	2.4	18	85	14	61	57	0	0	42	0.99
1262865--1262907	14	2.9	15	82	6	52	30	0	4	65	1.13
1264084--1264114	14	2.2	14	94	0	53	67	0	0	32	0.91
1264123--1264147	12	2.1	12	100	0	50	68	0	0	32	0.90
1269062--1269122	21	3.2	21	60	26	53	37	24	13	24	1.91
1270395--1270437	2	21.5	2	95	0	77	0	46	0	53	1.00
1282087--1282125	15	2.6	15	83	0	51	48	15	35	0	1.45
1293122--1293151	4	7.5	4	100	0	60	50	0	26	23	1.50
1296261--1296288	13	2.2	13	100	0	56	50	7	7	35	1.57
1297124--1297175	13	4.2	13	82	4	63	34	0	0	65	0.93
1297126--1297175	26	1.9	26	91	0	82	36	0	0	64	0.94
1299486--1299521	17	2.1	18	89	5	56	44	2	0	52	1.15
1299892--1299967	16	4.8	16	75	12	75	21	14	21	43	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1299891--1299984	32	2.9	32	76	10	93	23	15	19	41	1.90
1299896--1299984	16	5.6	16	78	2	72	24	15	17	41	1.89
1300963--1300988	1	26.0	1	100	0	52	0	0	100	0	0.00
1305771--1305812	15	2.8	15	81	0	57	38	19	38	4	1.73
1308891--1308950	31	2.0	30	83	9	77	40	1	5	53	1.33
1309842--1309869	2	14.0	2	100	0	56	0	50	0	50	1.00
1311813--1311859	18	2.6	18	86	0	58	17	14	53	14	1.74
1325071--1325116	24	1.9	24	82	8	58	60	2	0	36	1.09
1325131--1325174	23	1.9	23	85	0	61	52	0	2	45	1.13
1325144--1325184	13	2.9	14	85	14	57	51	0	2	46	1.14

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   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56