Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold626
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: 37015
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Found at i:775 original size:13 final size:13
Alignment explanation
Indices: 757--783 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
747 ACACTAGTGT
757 GATAATTGCAAGA
1 GATAATTGCAAGA
770 GATAATTGCAAGA
1 GATAATTGCAAGA
783 G
1 G
784 TTGAAAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (13 bp):
GATAATTGCAAGA
Found at i:4627 original size:19 final size:19
Alignment explanation
Indices: 4603--4639 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4593 TTTATTTATA
*
4603 TTATATTTTAATTATTTTT
1 TTATATTATAATTATTTTT
*
4622 TTATATTATATTTATTTT
1 TTATATTATAATTATTTT
4640 GTATATCGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATATTATAATTATTTTT
Found at i:7642 original size:177 final size:177
Alignment explanation
Indices: 7346--7699 Score: 620
Period size: 177 Copynumber: 2.0 Consensus size: 177
7336 CCAGAAAGGT
* * *
7346 GCCTCAAAGTTCAAACAATCTGATTTGATGTTTTAAGCTACATGTTATGCAATAGGGCAGAGTAT
1 GCCTCAAAGTTCAAACAATCTGATTTAATGTTTTAAACTACATGGTATGCAATAGGGCAGAGTAT
* *
7411 TCAAACTGAGAAAACTGGAAATTGGGAACCAAGAGCTGAGTTTCTTTGATGGGATTTTTCTTCCA
66 TCAAACTGAGAAAACTGGAAATTGGGAACCAAGAGCTGAGTTTCTTTGATGGGATTTTACCTCCA
*
7476 TTTTTGGGTGATCATTTTATGAACTTTTGAAGGCATCTGATTTCTCA
131 TTTTTGGGTGATCATTTTATGAACTTTTGAAGGCATCTGATATCTCA
*
7523 GCCTCAAAGTTCAAACAATCTGATTTAATG-TTTAACACTACATGGTATGCAATAGGGGAGAGTA
1 GCCTCAAAGTTCAAACAATCTGATTTAATGTTTTAA-ACTACATGGTATGCAATAGGGCAGAGTA
7587 TTCAAACTGAGAAAACTGGAAATTGGGAACCAAGAGCTGAGTTTCTTTGATGGGATTTTACCTCC
65 TTCAAACTGAGAAAACTGGAAATTGGGAACCAAGAGCTGAGTTTCTTTGATGGGATTTTACCTCC
*
7652 ATTTTTGGGTGATCATTTTCTGAACTTTTGAAGGCATCTGATATCTCA
130 ATTTTTGGGTGATCATTTTATGAACTTTTGAAGGCATCTGATATCTCA
7700 ATTTGGATAA
Statistics
Matches: 168, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
176 5 0.03
177 163 0.97
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (177 bp):
GCCTCAAAGTTCAAACAATCTGATTTAATGTTTTAAACTACATGGTATGCAATAGGGCAGAGTAT
TCAAACTGAGAAAACTGGAAATTGGGAACCAAGAGCTGAGTTTCTTTGATGGGATTTTACCTCCA
TTTTTGGGTGATCATTTTATGAACTTTTGAAGGCATCTGATATCTCA
Found at i:10492 original size:23 final size:23
Alignment explanation
Indices: 10462--10507 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
10452 TTTTCTCAAC
* *
10462 CCTAACTGAGTTATAATCCAGAT
1 CCTAACTGAGGTATAATACAGAT
10485 CCTAACTGAGGTATAATACAGAT
1 CCTAACTGAGGTATAATACAGAT
10508 GCGGTTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (23 bp):
CCTAACTGAGGTATAATACAGAT
Found at i:11968 original size:5 final size:5
Alignment explanation
Indices: 11958--11998 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
11948 TTCAAAACCG
11958 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA A
11999 GAGAAGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:12556 original size:2 final size:2
Alignment explanation
Indices: 12549--12599 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
12539 GTTGATTGAG
12549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12590 AT GT AT AT AT
1 AT AT AT AT AT
12600 CACGATGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14461 original size:2 final size:2
Alignment explanation
Indices: 14454--14502 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
14444 CTGTCATCCT
14454 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
14496 AC AC AC A
1 AC AC AC A
14503 TATATATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15243 original size:13 final size:13
Alignment explanation
Indices: 15225--15252 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15215 TTTTTTAATA
15225 AATTAATTAAATT
1 AATTAATTAAATT
15238 AATTAATTAAATT
1 AATTAATTAAATT
15251 AA
1 AA
15253 AAAATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTAATTAAATT
Found at i:15333 original size:23 final size:24
Alignment explanation
Indices: 15306--15367 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 24
15296 AATTTTTTAT
*
15306 TAATTTTTATTTTTTAT-TAAATA
1 TAATTTTTAATTTTTATCTAAATA
15329 TAA-TTTTAATTTTTATCCATAAATA
1 TAATTTTTAATTTTTAT-C-TAAATA
15354 TAATTTTATAATTT
1 TAATTTT-TAATTT
15368 ATAAATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 12 0.36
23 3 0.09
25 9 0.27
26 3 0.09
27 6 0.18
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATTTTTAATTTTTATCTAAATA
Found at i:15334 original size:17 final size:17
Alignment explanation
Indices: 15295--15335 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
15285 TTAATGTATT
* *
15295 TAATTTTTTATTAATTT
1 TAATTTTTTATTAAATA
*
15312 TTATTTTTTATTAAATA
1 TAATTTTTTATTAAATA
15329 TAATTTT
1 TAATTTT
15336 AATTTTTATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TAATTTTTTATTAAATA
Found at i:15629 original size:19 final size:19
Alignment explanation
Indices: 15587--15632 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
15577 TAATAATTTT
* *
15587 TAAATTTTAATATGTTGAA
1 TAAATTTTTATATATTGAA
*
15606 T-AATTTTTATCTATTGAA
1 TAAATTTTTATATATTGAA
15624 TAAATTTTT
1 TAAATTTTT
15633 TTCATACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (19 bp):
TAAATTTTTATATATTGAA
Found at i:16065 original size:21 final size:21
Alignment explanation
Indices: 16026--16065 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16016 AATAAAAGAT
**
16026 TATTTTATATTTATGTTTATA
1 TATTTTATATTTAAATTTATA
16047 TATTTTATATTTAAATTTA
1 TATTTTATATTTAAATTTA
16066 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TATTTTATATTTAAATTTATA
Found at i:24824 original size:10 final size:10
Alignment explanation
Indices: 24809--24858 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
24799 TAACATTTTC
24809 ATTAAATCAA
1 ATTAAATCAA
*
24819 ATTAAATTAA
1 ATTAAATCAA
*
24829 ATTTCAATCAA
1 A-TTAAATCAA
24840 ATTAAAT-AA
1 ATTAAATCAA
24849 ATTCAAATCA
1 ATT-AAATCA
24859 GCTTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 5 0.15
10 19 0.58
11 9 0.27
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (10 bp):
ATTAAATCAA
Found at i:24838 original size:21 final size:20
Alignment explanation
Indices: 24813--24851 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
24803 ATTTTCATTA
24813 AATCAAATTAAATTAAATTTC
1 AATCAAATTAAA-TAAATTTC
24834 AATCAAATTAAATAAATT
1 AATCAAATTAAATAAATT
24852 CAAATCAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
AATCAAATTAAATAAATTTC
Found at i:25489 original size:2 final size:2
Alignment explanation
Indices: 25482--25510 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25472 GTATTGAAGG
25482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25511 AATTGTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26463 original size:25 final size:23
Alignment explanation
Indices: 26414--26479 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 23
26404 TATGTGATTC
* *
26414 ATTAATAATATATAAATTTATTT
1 ATTAATAATATATAAATTAAATT
26437 ATTAATAATATATTAAATATAAATT
1 ATTAATAATATA-TAAAT-TAAATT
** *
26462 ATTTTTAATATAAAAATT
1 ATTAATAATATATAAATT
26480 GTAATTTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 13 0.36
24 9 0.25
25 14 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTAATAATATATAAATTAAATT
Found at i:27455 original size:23 final size:22
Alignment explanation
Indices: 27425--27478 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
27415 CTTAATGATA
27425 AAATTAAATTA-ATATAGTTTAT
1 AAATTAAATTAGATATA-TTTAT
27447 AAATATAAATTAGATATATTTA-
1 AAAT-TAAATTAGATATATTTAT
27469 AAGATTAAAT
1 AA-ATTAAAT
27479 AATTTGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.38
23 13 0.45
24 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (22 bp):
AAATTAAATTAGATATATTTAT
Found at i:30727 original size:22 final size:22
Alignment explanation
Indices: 30674--30717 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
30664 TATTTTTTAT
30674 ATATT-TATTATTATATATAAA
1 ATATTATATTATTATATATAAA
*
30695 ATATTAAATTATTATATA-AAA
1 ATATTATATTATTATATATAAA
30716 AT
1 AT
30718 TGATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTATATTATTATATATAAA
Found at i:30756 original size:18 final size:17
Alignment explanation
Indices: 30687--30763 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 17
30677 TTTATTATTA
30687 TATATAAAATATTAAATTAT
1 TATATAAAAT-TT-AA-TAT
* *
30707 TATATAAAAATTGATA-
1 TATATAAAATTTAATAT
30723 TAT-TAAAGATTT-ATAT
1 TATATAAA-ATTTAATAT
30739 TATATAAAATTTTAATAT
1 TATATAAAA-TTTAATAT
30757 TATATAA
1 TATATAA
30764 TTATAATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 7 0.14
16 10 0.20
17 9 0.18
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TATATAAAATTTAATAT
Found at i:30768 original size:31 final size:32
Alignment explanation
Indices: 30704--30774 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
30694 AATATTAAAT
*
30704 TATTATATAAAAATTGATATATTAAAGATTTA
1 TATTATATAAAAATTGATATATTAAAGAATTA
* * * *
30736 TATTATATAAAATTTTA-ATATTATATAATTA
1 TATTATATAAAAATTGATATATTAAAGAATTA
*
30767 TAATATAT
1 TATTATAT
30775 TTATATTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 18 0.55
32 15 0.45
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (32 bp):
TATTATATAAAAATTGATATATTAAAGAATTA
Found at i:30780 original size:24 final size:25
Alignment explanation
Indices: 30753--30822 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 25
30743 TAAAATTTTA
30753 ATATTATATAATTATAATATAT-TT
1 ATATTATATAATTATAATATATATT
**
30777 ATATTAT-TTTTATATAATA-ATATT
1 ATATTATATAAT-TATAATATATATT
*
30801 ATATT-TAAAATTATCAATATAT
1 ATATTATATAATTAT-AATATAT
30823 CAGTGTGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
23 8 0.22
24 26 0.72
25 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (25 bp):
ATATTATATAATTATAATATATATT
Found at i:30791 original size:19 final size:18
Alignment explanation
Indices: 30734--30807 Score: 51
Period size: 19 Copynumber: 4.0 Consensus size: 18
30724 ATTAAAGATT
* *
30734 TATATTATATAAAATTTTA
1 TATATTATAT-TATTTTTA
* * *
30753 -ATATTATATAATTATAA
1 TATATTATATTATTTTTA
30770 TATATTTATATTATTTTTA
1 TATA-TTATATTATTTTTA
* *
30789 TATAATAATATTATATTTA
1 TAT-ATTATATTATTTTTA
30808 AAATTATCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.11
18 12 0.27
19 26 0.59
20 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTATATTATTTTTA
Found at i:31330 original size:17 final size:16
Alignment explanation
Indices: 31300--31339 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
31290 TTTTTTAATA
31300 TTTAAATTTAAATTTAT
1 TTTAAATTTAAA-TTAT
* *
31317 TTTAATTTTGAATTAT
1 TTTAAATTTAAATTAT
31333 TTTAAAT
1 TTTAAAT
31340 ATAATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:34836 original size:17 final size:16
Alignment explanation
Indices: 34788--34836 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
34778 TGTTTAACAT
*
34788 ATTTTATAATTTATATA
1 ATTTTATTATTTA-ATA
34805 ATTTTATTATGTTAATA
1 ATTTTATTAT-TTAATA
*
34822 ATTTATTTTATTTAA
1 ATTT-TATTATTTAA
34837 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTTTATTATTTAATA
Found at i:35492 original size:36 final size:36
Alignment explanation
Indices: 35448--35518 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
35438 TGGCTTGAAA
* **
35448 TTTTTTATTTATATTTATATTAGGTTAATTTAAAAT
1 TTTTTTATTTATATTCATATTAAATTAATTTAAAAT
*
35484 TTTTTTATTTATATTCATGTTAAATTAATTTAAAA
1 TTTTTTATTTATATTCATATTAAATTAATTTAAAA
35519 GTTTAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (36 bp):
TTTTTTATTTATATTCATATTAAATTAATTTAAAAT
Found at i:35637 original size:46 final size:49
Alignment explanation
Indices: 35545--35643 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 49
35535 AGATATATAA
*
35545 AAATAATAAAAAATATTTTTATATTAATATTATTATTTATAATTAAATTT
1 AAATAATAAAAAATATTTTTATATTAATA-TATAATTTATAATTAAATTT
* *
35595 AAATAA-AAATAATA-TTTTATTATTAATA-ATAATTTA-ATTTAAATTT
1 AAATAATAAAAAATATTTTTA-TATTAATATATAATTTATAATTAAATTT
35641 AAA
1 AAA
35644 AAATTTAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
46 12 0.27
47 7 0.16
48 5 0.11
49 15 0.33
50 6 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (49 bp):
AAATAATAAAAAATATTTTTATATTAATATATAATTTATAATTAAATTT
Found at i:36088 original size:19 final size:19
Alignment explanation
Indices: 36064--36103 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
36054 AATAGATATT
36064 TAATAAGATA-AAAATAATA
1 TAATAA-ATATAAAATAATA
*
36083 TAATAAATATAAAATTATA
1 TAATAAATATAAAATAATA
36102 TA
1 TA
36104 TTTAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
TAATAAATATAAAATAATA
Done.