Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold564
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 34502
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:11566 original size:58 final size:56
Alignment explanation
Indices: 11460--11567 Score: 128
Period size: 58 Copynumber: 1.9 Consensus size: 56
11450 TTTATGAACG
* * * *
11460 TTGATGTCATTTAAATCATTTCATGATCTAAGAACTTTGATGTAATTTTATAAATT
1 TTGATGTCATGTAAATCATTTCATAATCTAAGAACTTTCATGCAATTTTATAAATT
**
11516 TTGATGTCATGTAGGTCATTTTCTATAATCTAATG-ACTTTCATGCAATTTTA
1 TTGATGTCATGTAAATCA-TTTC-ATAATCTAA-GAACTTTCATGCAATTTTA
11568 CACATCTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
56 15 0.35
57 4 0.09
58 23 0.53
59 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (56 bp):
TTGATGTCATGTAAATCATTTCATAATCTAAGAACTTTCATGCAATTTTATAAATT
Found at i:12886 original size:29 final size:29
Alignment explanation
Indices: 12849--12904 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
12839 TTTTTTAATA
* *
12849 ATATTAATATTTGTTATCATATATATTAT
1 ATATGAATATTTATTATCATATATATTAT
* *
12878 ATATGAATATTTATTATCTTATTTATT
1 ATATGAATATTTATTATCATATATATT
12905 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (29 bp):
ATATGAATATTTATTATCATATATATTAT
Found at i:14983 original size:21 final size:21
Alignment explanation
Indices: 14959--14998 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
14949 TACTTAAATC
*
14959 AAAATCAAATTAAATTAAAGA
1 AAAATCAAATGAAATTAAAGA
* *
14980 AAAATTAAATGAATTTAAA
1 AAAATCAAATGAAATTAAA
14999 TTTAAATAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAATCAAATGAAATTAAAGA
Found at i:14989 original size:26 final size:25
Alignment explanation
Indices: 14960--15028 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
14950 ACTTAAATCA
*
14960 AAATCAAATTAAATTAAAGAAAAATT
1 AAATAAAATTAAATTAAAGAAAAA-T
* * *
14986 AAATGAATTTAAATTTAAATAAAAAT
1 AAATAAAATTAAA-TTAAAGAAAAAT
*
15012 AATTAAAATTAAATTAA
1 AAATAAAATTAAATTAA
15029 TTTTTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 4 0.11
26 22 0.61
27 10 0.28
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (25 bp):
AAATAAAATTAAATTAAAGAAAAAT
Found at i:15005 original size:21 final size:19
Alignment explanation
Indices: 14981--15028 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
14971 AATTAAAGAA
*
14981 AAATTAAATGAATTTAAATTT
1 AAATTAAAT-AA-TTAAAATT
*
15002 AAATAAAAATAATTAAAATT
1 AAAT-TAAATAATTAAAATT
15022 AAATTAA
1 AAATTAA
15029 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 11 0.48
21 6 0.26
22 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATTAAATAATTAAAATT
Found at i:15335 original size:16 final size:15
Alignment explanation
Indices: 15307--15350 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
15297 AAAATGTTAA
15307 TATTATTTTTTAAAAT
1 TATT-TTTTTTAAAAT
*
15323 TTTTTTATTTTAAAAT
1 TATTTT-TTTTAAAAT
15339 TATTTTTTTTAA
1 TATTTTTTTTAA
15351 TGTTAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTTTAAAAT
Found at i:15378 original size:9 final size:9
Alignment explanation
Indices: 15360--15438 Score: 56
Period size: 9 Copynumber: 8.6 Consensus size: 9
15350 ATGTTAATTA
15360 TTTATAATAT
1 TTTAT-ATAT
15370 TTTATATAT
1 TTTATATAT
15379 ATTTA-AT-T
1 -TTTATATAT
* *
15387 TTTAAATTT
1 TTTATATAT
15396 TTTATAT-T
1 TTTATATAT
15404 TTTAATATAT
1 TTT-ATATAT
*
15414 TTTATGAGAT
1 TTTAT-ATAT
*
15424 ATTTATATTT
1 -TTTATATAT
15434 TTTAT
1 TTTAT
15439 TAATATATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
7 4 0.07
8 7 0.12
9 24 0.41
10 18 0.31
11 5 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTATATAT
Found at i:15395 original size:24 final size:25
Alignment explanation
Indices: 15359--15409 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
15349 AATGTTAATT
15359 ATTTATAATATTTTATATATATTTA
1 ATTTATAATATTTTATATATATTTA
* * *
15384 ATTTTTAA-ATTTTTTATATTTTTA
1 ATTTATAATATTTTATATATATTTA
15408 AT
1 AT
15410 ATATTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
ATTTATAATATTTTATATATATTTA
Found at i:15846 original size:20 final size:20
Alignment explanation
Indices: 15799--15846 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
15789 TTGATTTGAT
* *
15799 AATAATTT-GATTAAATTTT
1 AATAATTTAAATTAAATTTA
**
15818 AATTTTTTAAATTAAATTTA
1 AATAATTTAAATTAAATTTA
15838 AATAATTTA
1 AATAATTTA
15847 TAAATATAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AATAATTTAAATTAAATTTA
Found at i:19694 original size:22 final size:21
Alignment explanation
Indices: 19636--19700 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
19626 AAAACTTACG
*
19636 ATAGAGTAAAACTATAAGTAC
1 ATAGAGTAAAACTATATGTAC
* *
19657 ATATAGTATAACTATATGTAC
1 ATAGAGTAAAACTATATGTAC
19678 ATAGAGTAAAAACTATATGTAC
1 ATAGAGT-AAAACTATATGTAC
19700 A
1 A
19701 AATAGCTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
21 24 0.63
22 14 0.37
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.29
Consensus pattern (21 bp):
ATAGAGTAAAACTATATGTAC
Found at i:19880 original size:30 final size:35
Alignment explanation
Indices: 19796--19872 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
19786 CAATAAGTAG
*
19796 ATATAATACAGCTATATGTACATATAGTAAAAATA
1 ATATAATACAGTTATATGTACATATAGTAAAAATA
19831 ATATAATACAGTTATATGTACATATAGTAAAAATA
1 ATATAATACAGTTATATGTACATATAGTAAAAATA
19866 ATATAAT
1 ATATAAT
19873 TATATGTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (35 bp):
ATATAATACAGTTATATGTACATATAGTAAAAATA
Found at i:20309 original size:21 final size:21
Alignment explanation
Indices: 20253--20325 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
20243 TAAATTTGAT
* *
20253 AAAGGTTGGTTCTCTTAGTGT
1 AAAGGTTGATTCTCTTAGTGA
*
20274 GAAGGAATT-AGTTCTCTTAGTGA
1 AAAGG--TTGA-TTCTCTTAGTGA
*
20297 AAAGGTTGATTCTCTTTGTGA
1 AAAGGTTGATTCTCTTAGTGA
20318 AAAGGTTG
1 AAAGGTTG
20326 GCTCTCATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 25 0.58
22 1 0.02
23 17 0.40
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.38
Consensus pattern (21 bp):
AAAGGTTGATTCTCTTAGTGA
Found at i:20331 original size:21 final size:21
Alignment explanation
Indices: 20286--20331 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
20276 AGGAATTAGT
*
20286 TCTCTTAGTGAAAAGGTTGAT
1 TCTCTTAGTGAAAAGGTTGAC
* *
20307 TCTCTTTGTGAAAAGGTTGGC
1 TCTCTTAGTGAAAAGGTTGAC
20328 TCTC
1 TCTC
20332 ATATTATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (21 bp):
TCTCTTAGTGAAAAGGTTGAC
Found at i:21528 original size:42 final size:43
Alignment explanation
Indices: 21481--21565 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
21471 AATTGATATG
*
21481 TACATATACCTTAAAATTAATAAAAAT-AATAA-ACACAAATTT
1 TACATATACCTCAAAATTAATAAAAATCAA-AATACACAAATTT
* *
21523 TACATATATCTCAAAATTGATAAAAATCAAAATACACAAATTT
1 TACATATACCTCAAAATTAATAAAAATCAAAATACACAAATTT
21566 AAGAAAGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 26 0.68
43 12 0.32
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (43 bp):
TACATATACCTCAAAATTAATAAAAATCAAAATACACAAATTT
Found at i:22614 original size:16 final size:15
Alignment explanation
Indices: 22586--22637 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
22576 ATAACTTGAA
22586 TTAAATTATTTAAAT
1 TTAAATTATTTAAAT
22601 TTAAATTAATTTAAAT
1 TTAAATT-ATTTAAAT
* *
22617 GTAAA-TATGTGAAAT
1 TTAAATTAT-TTAAAT
22632 TTAAAT
1 TTAAAT
22638 AATAATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.06
15 17 0.55
16 12 0.39
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TTAAATTATTTAAAT
Found at i:23551 original size:21 final size:20
Alignment explanation
Indices: 23527--23576 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
23517 TTAAATTTAA
23527 TAATTATTTAAAATAA-AATTT
1 TAATTA-TTAAAA-AATAATTT
23548 TAA-TATTAAAAAATAATTT
1 TAATTATTAAAAAATAATTT
23567 TAA-TATTAAA
1 TAATTATTAAA
23577 TATAACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.07
19 21 0.75
20 2 0.07
21 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATTATTAAAAAATAATTT
Found at i:23558 original size:19 final size:20
Alignment explanation
Indices: 23534--23587 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 20
23524 TAATAATTAT
23534 TTAAAATAA-AATTTTAATA
1 TTAAAATAATAATTTTAATA
23553 TTAAAA-AATAATTTTAATA
1 TTAAAATAATAATTTTAATA
23572 TTAAATATAACTAATT
1 TTAAA-ATAA-TAATT
23588 AATAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.06
19 21 0.68
20 1 0.03
21 2 0.06
22 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAAATAATAATTTTAATA
Found at i:23943 original size:8 final size:8
Alignment explanation
Indices: 23860--23966 Score: 51
Period size: 8 Copynumber: 13.0 Consensus size: 8
23850 ATATTATAAT
23860 TATATTTA
1 TATATTTA
*
23868 AATATTTTA
1 TATA-TTTA
* *
23877 TAAATATA
1 TATATTTA
*
23885 TAAAATTTAA
1 T-ATATTT-A
*
23895 TATATTAA
1 TATATTTA
23903 TA-ATTTA
1 TATATTTA
*
23910 TAT-TATA
1 TATATTTA
*
23917 AATATGTTAA
1 TATAT-TT-A
23927 TATATTTA
1 TATATTTA
23935 TATATTTA
1 TATATTTA
*
23943 TATCATATTT
1 TAT-AT-TTA
23953 TATA-TTA
1 TATATTTA
23960 TAT-TTTA
1 TATATTTA
23967 ATTATTTTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
7 19 0.25
8 23 0.31
9 21 0.28
10 12 0.16
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (8 bp):
TATATTTA
Found at i:23950 original size:19 final size:17
Alignment explanation
Indices: 23928--23962 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
23918 ATATGTTAAT
23928 ATATTTATATATTTATATC
1 ATATTT-TATA-TTATATC
23947 ATATTTTATATTATAT
1 ATATTTTATATTATAT
23963 TTTAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTATATTATATC
Found at i:23956 original size:40 final size:40
Alignment explanation
Indices: 23849--23973 Score: 95
Period size: 40 Copynumber: 3.2 Consensus size: 40
23839 GTATATTTTT
*
23849 TATATTATAATTATATT--TAA-ATATTTTATAAATATATAA
1 TATATT-TAA-TATATTAATAATATATTTTATAAATATTTAA
* *
23888 -A-ATTTAATATATTAATAATTTATATTATAAATATGTTAA
1 TATATTTAATATATTAATAATATATTTTATAAATAT-TTAA
* *
23927 TATATTT-ATATATTTAT-ATCATATTTTATATTATATTTTAA
1 TATATTTAATATATTAATAAT-ATATTTTATA-AATA-TTTAA
23968 T-TATTT
1 TATATTT
23974 TTTATTGTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
35 6 0.09
36 3 0.04
37 6 0.09
38 14 0.20
39 5 0.07
40 23 0.33
41 12 0.17
42 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (40 bp):
TATATTTAATATATTAATAATATATTTTATAAATATTTAA
Found at i:23970 original size:11 final size:12
Alignment explanation
Indices: 23927--23978 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
23917 AATATGTTAA
23927 TATATTTATATATT
1 TATA-TTATAT-TT
*
23941 TATATCATATTT
1 TATATTATATTT
23953 TATATTATATTT
1 TATATTATATTT
*
23965 TA-ATTATTTTT
1 TATATTATATTT
23976 TAT
1 TAT
23979 TGTTGCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.29
12 15 0.44
13 5 0.15
14 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTATATTT
Found at i:25188 original size:24 final size:23
Alignment explanation
Indices: 25147--25194 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
25137 CGATATAATT
* *
25147 ATATGATATAAAAAATAATTAAA
1 ATATGACATAAAAAATAAATAAA
25170 ATATGACATGAAAAAATAAATAAA
1 ATATGACAT-AAAAAATAAATAAA
25194 A
1 A
25195 AAATTACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (23 bp):
ATATGACATAAAAAATAAATAAA
Found at i:25195 original size:25 final size:24
Alignment explanation
Indices: 25147--25204 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
25137 CGATATAATT
* *
25147 ATATGATAT-AAAAAATAATTAAA
1 ATATGACATGAAAAAATAATAAAA
25170 ATATGACATGAAAAAATAAATAAAA
1 ATATGACATGAAAAAAT-AATAAAA
* *
25195 AAATTACATG
1 ATATGACATG
25205 GATACAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 8 0.28
24 7 0.24
25 14 0.48
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (24 bp):
ATATGACATGAAAAAATAATAAAA
Found at i:25961 original size:19 final size:21
Alignment explanation
Indices: 25939--25987 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
25929 ATTATTAAAA
25939 ATATTAAAAATTAT-T-TTTT
1 ATATTAAAAATTATATATTTT
* *
25958 ATATTAATATTTATATATTTT
1 ATATTAAAAATTATATATTTT
25979 ATAATTAAA
1 AT-ATTAAA
25988 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.50
20 1 0.04
21 6 0.25
22 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTAAAAATTATATATTTT
Found at i:33688 original size:2 final size:2
Alignment explanation
Indices: 33681--33711 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
33671 ATGAATATGC
33681 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33712 CTGAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.