genome.fa.s4.2.7.7.80.10.50.1000.78.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: chr4
Parameters: 2 7 7 80 10 50 1000
Length:  31929104

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   

This is table  78  of  82  ( 9773 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)
29353938--29353993	27	2.1	27	83	6	69	71	0	1	26	0.96
29353980--29354096	56	2.1	55	95	1	207	35	10	3	50	1.53
29354254--29354313	25	2.4	24	81	8	66	31	10	1	56	1.42
29370235--29370275	12	3.4	12	89	0	64	65	0	34	0	0.93
29381940--29381977	4	9.8	4	88	5	60	73	0	26	0	0.83
29397285--29397309	13	1.9	13	100	0	50	24	0	8	68	1.16
29397288--29397329	19	2.2	20	83	8	52	33	0	7	59	1.25
29402060--29402159	24	4.0	24	72	17	60	7	5	56	32	1.48
29402194--29402309	30	3.9	29	74	5	97	20	1	56	21	1.52
29402117--29402468	158	2.2	158	97	1	663	16	3	57	22	1.54
29402368--29402585	60	3.6	60	87	0	301	20	3	54	22	1.58
29402382--29402585	30	6.8	30	75	3	169	18	3	55	22	1.58
29402533--29402630	48	2.0	48	98	0	187	18	5	53	23	1.64
29402566--29402606	18	2.3	18	91	0	64	19	4	53	21	1.63
29402650--29402774	60	2.1	60	90	0	196	24	2	51	21	1.60
29402650--29402777	30	4.3	30	84	4	152	24	2	51	21	1.59
29402754--29402804	24	2.1	24	85	0	66	17	0	52	29	1.45
29402664--29402834	54	3.1	54	80	8	173	21	1	51	25	1.57
29402845--29402882	12	3.2	12	92	0	58	7	7	60	23	1.51
29402896--29402925	12	2.5	12	94	0	51	20	0	60	20	1.37
29402927--29402969	18	2.4	18	92	0	68	2	2	58	37	1.24
29402941--29402996	12	4.7	12	79	0	58	8	1	62	26	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29402959--29402993	6	5.8	6	93	0	61	14	2	65	17	1.38
29402992--29403029	18	2.1	18	95	0	67	7	5	57	28	1.49
29419472--29419955	202	2.4	202	88	1	693	33	22	17	26	1.96
29431277--29431310	2	17.5	2	93	6	61	52	0	0	47	1.00
29433851--29433906	2	30.5	2	83	16	77	46	0	0	53	1.00
29435151--29435180	2	15.5	2	93	6	53	0	50	0	50	1.00
29444324--29444370	24	2.0	25	83	8	62	48	6	6	38	1.54
29444974--29445004	14	2.2	14	100	0	62	45	0	0	54	0.99
29445066--29445113	21	2.3	21	82	13	55	64	0	2	33	1.05
29453034--29453076	21	2.0	22	81	4	52	46	6	9	37	1.63
29456403--29456448	2	24.0	2	91	8	78	52	0	0	47	1.00
29456437--29456724	139	2.1	140	97	0	560	28	13	18	38	1.89
29457785--29458099	107	2.9	107	97	0	585	46	9	11	32	1.71
29459486--29459543	29	2.0	29	90	6	91	36	0	0	63	0.94
29459683--29459797	59	1.9	59	87	0	167	38	6	10	44	1.66
29472331--29473975	411	4.0	411	97	0	3076	33	12	14	40	1.83
29472331--29473975	824	2.0	825	97	0	3100	33	12	14	40	1.83
29475201--29475244	20	2.3	19	84	7	54	15	22	6	54	1.65
29475685--29475803	29	4.2	29	70	12	95	33	7	11	47	1.69
29475677--29475767	29	3.1	29	82	1	110	39	8	10	40	1.72
29475710--29475822	54	2.1	53	85	3	145	32	8	13	45	1.74
29475688--29475901	82	2.6	81	76	8	209	35	9	12	42	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29476130--29476161	13	2.5	13	94	0	55	50	0	0	50	1.00
29486971--29487006	16	2.2	16	90	0	54	50	2	0	47	1.15
29487475--29487543	15	4.5	15	77	12	59	69	1	0	28	0.97
29487490--29487537	12	3.9	13	84	13	66	70	0	0	29	0.87
29487499--29487532	3	11.3	3	87	12	52	70	0	0	29	0.87
29487490--29487882	196	2.0	196	96	3	720	53	1	6	39	1.33
29487686--29487733	12	3.9	13	84	13	66	70	0	0	29	0.87
29487695--29487728	3	11.3	3	87	12	52	70	0	0	29	0.87
29488303--29488344	20	2.1	20	86	0	57	50	11	2	35	1.52
29490366--29490408	17	2.5	17	92	0	77	74	0	0	25	0.82
29492427--29492484	28	2.1	28	83	6	73	44	27	6	20	1.77
29512907--29512953	17	2.7	17	90	9	69	74	0	0	25	0.82
29512920--29512957	13	2.8	14	80	8	51	76	0	0	23	0.79
29519216--29519411	63	3.1	63	85	4	252	33	7	2	57	1.37
29520201--29520243	22	2.0	22	85	0	59	32	9	6	51	1.61
29524194--29524287	45	2.1	45	84	4	118	50	4	1	44	1.28
29529917--29529941	12	2.1	12	100	0	50	16	20	24	40	1.91
29531116--29531196	24	3.2	25	83	16	96	48	1	3	46	1.27
29531124--29531195	20	3.5	20	92	5	110	50	0	4	45	1.21
29531123--29531195	2	37.0	2	80	17	82	50	0	4	45	1.20
29544713--29544751	20	2.0	20	90	5	62	46	0	0	53	1.00
29545118--29545340	74	3.0	74	86	3	290	33	17	21	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29545605--29545629	7	3.6	7	100	0	50	12	16	24	48	1.79
29547147--29547179	3	11.0	3	100	0	66	66	0	33	0	0.92
29557406--29557436	16	1.9	16	93	0	53	0	12	25	61	1.32
29566696--29566753	29	2.0	29	100	0	116	48	10	17	24	1.78
29568381--29568425	16	2.8	16	89	0	63	48	0	2	48	1.13
29568936--29568979	15	3.1	15	78	18	58	47	0	0	52	1.00
29568976--29569017	18	2.3	19	84	12	52	69	4	0	26	1.08
29569020--29569049	7	4.1	7	91	8	51	13	3	0	83	0.77
29569020--29569049	15	2.1	15	93	6	53	13	3	0	83	0.77
29571378--29571610	117	2.0	117	97	0	439	22	20	18	38	1.93
29577923--29577966	2	22.0	2	100	0	88	50	0	0	50	1.00
29579320--29579387	35	2.0	34	88	5	102	35	8	14	41	1.77
29579365--29579527	44	3.5	42	73	24	159	33	14	16	36	1.89
29579342--29579546	96	2.1	96	100	0	410	33	13	17	36	1.89
29580703--29580751	21	2.3	20	77	16	55	61	2	0	36	1.08
29580707--29580759	22	2.4	22	75	9	54	60	1	0	37	1.08
29583660--29583717	2	31.0	2	77	19	63	44	0	1	51	1.11
29595477--29595579	44	2.3	44	100	0	206	41	6	18	33	1.77
29599863--29599944	41	2.0	41	100	0	164	43	12	19	24	1.85
29612082--29612112	2	15.5	2	93	0	53	0	45	0	54	0.99
29615454--29615520	30	2.3	31	82	10	86	47	25	5	20	1.73
29642989--29643020	10	3.1	10	91	8	55	40	18	9	31	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29643023--29643072	18	2.8	19	84	6	61	26	10	20	44	1.82
29643197--29643266	23	3.0	24	78	13	76	30	0	4	65	1.11
29663446--29663498	19	2.8	19	79	0	52	37	1	0	60	1.08
29664079--29664122	19	2.3	19	96	0	79	25	27	15	31	1.96
29664450--29664474	2	12.5	2	100	0	50	48	0	0	52	1.00
29667657--29667743	43	2.0	43	93	0	147	33	11	21	33	1.89
29673361--29673502	74	1.9	74	85	2	196	26	12	8	52	1.67
29678592--29678631	17	2.2	18	91	8	64	60	0	2	37	1.11
29679683--29679707	9	2.8	9	100	0	50	32	8	12	48	1.69
29680754--29680811	28	2.1	28	93	0	98	20	8	18	51	1.72
29684269--29684349	2	41.0	2	90	7	130	48	0	1	49	1.09
29689514--29689563	18	2.8	18	85	8	66	22	10	38	30	1.86
29695582--29695619	19	2.0	19	85	10	51	50	5	13	31	1.63
29696347--29696386	3	13.3	3	83	0	53	5	2	60	32	1.32
29697145--29697182	16	2.2	18	86	9	53	21	15	13	50	1.78
29699700--29699767	35	2.0	35	94	2	120	23	13	22	41	1.89
29715856--29715889	5	7.2	5	96	3	54	85	0	14	0	0.60
29725361--29725499	6	22.8	6	73	8	93	38	4	10	46	1.59
29725340--29725501	12	13.2	12	79	7	148	40	3	9	46	1.55
29725340--29725481	14	9.9	14	78	6	131	40	3	9	46	1.53
29725617--29725655	18	2.1	18	85	4	51	41	2	5	51	1.38
29744971--29745063	31	3.1	30	81	4	100	32	8	5	53	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29746186--29746215	2	15.0	2	92	0	51	50	3	0	46	1.18
29747719--29747796	38	2.1	38	100	0	156	43	7	12	35	1.72
29752277--29752347	30	2.6	25	73	25	63	45	1	9	43	1.46
29752975--29753018	24	1.9	24	81	9	56	43	2	11	43	1.53
29753360--29753418	30	2.1	29	84	9	77	23	8	5	62	1.43
29756871--29756937	33	2.0	33	100	0	134	34	11	14	38	1.84
29756972--29757118	26	5.3	26	76	13	123	39	20	21	19	1.93
29756964--29757040	35	2.2	35	90	0	127	42	20	19	16	1.89
29757008--29757118	52	2.1	52	88	0	159	39	20	21	18	1.92
29757372--29757455	29	2.9	28	77	8	87	16	28	7	47	1.73

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   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82