Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold554
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: 62044
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 2231 characters in sequence are not A, C, G, or T
Found at i:657 original size:17 final size:17
Alignment explanation
Indices: 621--673 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
611 TTCAATCAAC
*
621 ATTAATAAATAATTTA-A
1 ATTAAT-AATTATTTATA
638 ATTAATAATTATTTATA
1 ATTAATAATTATTTATA
* * *
655 ATTTATATTTATCTATA
1 ATTAATAATTATTTATA
672 AT
1 AT
674 GCATAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 8 0.26
17 23 0.74
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATAATTATTTATA
Found at i:2423 original size:2 final size:2
Alignment explanation
Indices: 2416--2443 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2406 TGCTAGTGAC
2416 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2444 CCGAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13099 original size:2 final size:2
Alignment explanation
Indices: 13087--13116 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
13077 ATATTACAAA
13087 AT AT CAT 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
13117 ATTTGCATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19770 original size:20 final size:20
Alignment explanation
Indices: 19745--19785 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19735 TAATCCTATC
19745 CCATTTCCATTCTGGGATCT
1 CCATTTCCATTCTGGGATCT
*
19765 CCATTTCCATTTTGGGATCT
1 CCATTTCCATTCTGGGATCT
19785 C
1 C
19786 TAATAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (20 bp):
CCATTTCCATTCTGGGATCT
Found at i:28762 original size:27 final size:26
Alignment explanation
Indices: 28732--28791 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
28722 TGTTTAAATT
28732 TTAATGAATAATAATGTTAGTTATAT-C
1 TTAATGAATAATAATG-T-GTTATATGC
* *
28759 TTAAATG-ATTATTATGTGTTATATGC
1 TT-AATGAATAATAATGTGTTATATGC
28785 TTAATGA
1 TTAATGA
28792 GATTAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
25 11 0.39
26 4 0.14
27 9 0.32
28 4 0.14
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (26 bp):
TTAATGAATAATAATGTGTTATATGC
Found at i:29129 original size:26 final size:26
Alignment explanation
Indices: 29063--29129 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
29053 CATCCCAACC
*
29063 CACAGCTCGTGTGACCAAGCCCATTT
1 CACAGCTCGTGTGAGCAAGCCCATTT
*
29089 CACTGCTCGTGTGAGCAAGCCCATTT
1 CACAGCTCGTGTGAGCAAGCCCATTT
*
29115 CACAGCTTGTGTGAG
1 CACAGCTCGTGTGAG
29130 TATTACAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAAGCCCATTT
Found at i:31944 original size:6 final size:6
Alignment explanation
Indices: 31900--31931 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
31890 GTCTACCTGC
31900 AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
31932 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:44693 original size:25 final size:27
Alignment explanation
Indices: 44663--44730 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
44653 AAAATTGGTA
44663 AGACATTTTCCATTCT-TCTCTAAGCA-
1 AGACATTTTCCATTCTCT-TCTAAGCAC
44689 A-ACATTTTCCATTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAAGCA-C
44716 AGACATTTTCCATTC
1 AGACATTTTCCATTC
44731 CTCAAAGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 22 0.58
26 2 0.05
27 1 0.03
28 13 0.34
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.38
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAAGCAC
Found at i:46179 original size:32 final size:33
Alignment explanation
Indices: 46138--46222 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
46128 AACTTTTCCG
* * *
46138 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
46170 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
46202 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
46223 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:46221 original size:14 final size:15
Alignment explanation
Indices: 46199--46275 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
46189 TTACCAAACA
46199 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
46213 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
46228 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
46248 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
46262 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
46276 ACTGCCAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:46240 original size:20 final size:20
Alignment explanation
Indices: 46215--46254 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46205 AATATTTTCC
*
46215 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
46235 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
46255 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:46260 original size:34 final size:35
Alignment explanation
Indices: 46203--46269 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
46193 CAAACACCAG
*
46203 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
46238 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
46270 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:46276 original size:14 final size:14
Alignment explanation
Indices: 46238--46277 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
46228 ACAGAAAAGT
*
46238 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
46252 AAATCATTTTACGG
1 AAAACATTTTACAG
46266 AAAACATTTTAC
1 AAAACATTTTAC
46278 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:47448 original size:13 final size:13
Alignment explanation
Indices: 47430--47458 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47420 GCCCAAACTT
47430 AATTACCCAACCC
1 AATTACCCAACCC
47443 AATTACCCAACCC
1 AATTACCCAACCC
47456 AAT
1 AAT
47459 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.17
Consensus pattern (13 bp):
AATTACCCAACCC
Found at i:57372 original size:22 final size:22
Alignment explanation
Indices: 57344--57396 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
57334 GAATTGGCAA
57344 TGGAGCAAGTTT-TCTCCCTAAT
1 TGGAGCAAGTTTGT-TCCCTAAT
57366 TGGAGCAAGTTTGTTCCCTAAT
1 TGGAGCAAGTTTGTTCCCTAAT
*
57388 TGGACCAAG
1 TGGAGCAAG
57397 CTAGCTTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (22 bp):
TGGAGCAAGTTTGTTCCCTAAT
Found at i:60166 original size:53 final size:53
Alignment explanation
Indices: 60109--60274 Score: 128
Period size: 53 Copynumber: 3.1 Consensus size: 53
60099 TTATTTTTTA
60109 TTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATAT
1 TTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATAT
* * * ** * * ** *
60162 TTTAAAAATTT-TATATATTTAA---A--AAATTTTCCAGCCACTAATAAATTATTTTTT
1 TTT-AATATTTCTCTAAAAATAAGCTATTACA-TTTCC--CC-TTAATAAA-TA-AATAT
60216 ATTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATAT
1 -TTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATAT
60270 TTTAA
1 TTTAA
60275 AAATTTTATA
Statistics
Matches: 79, Mismatches: 20, Indels: 28
0.62 0.16 0.22
Matches are distributed among these distances:
48 2 0.03
49 5 0.06
50 1 0.01
51 2 0.03
52 7 0.09
53 17 0.22
54 16 0.20
55 12 0.15
56 7 0.09
57 2 0.03
58 1 0.01
59 5 0.06
60 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.44
Consensus pattern (53 bp):
TTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATAT
Found at i:60185 original size:59 final size:59
Alignment explanation
Indices: 60122--60294 Score: 172
Period size: 59 Copynumber: 3.1 Consensus size: 59
60112 AATATTTCTC
60122 TAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATATTTTAAAAATTTTATATATT
1 TAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATATTTTAAAAATTTTATATATT
* * * * ** * *
60181 T-AAAA-AA--TTTTCCA--GCCAC-TAATAAAT---TATTTT--TTATTTAATATTTCT
1 TAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATATTTTAAAAATTTTATATAT-T
60229 CTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATATTTTAAAAATTTTATATATT
1 -TAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATATTTTAAAAATTTTATATATT
60289 TAAAAA
1 TAAAAA
60295 ATTTTACAGC
Statistics
Matches: 84, Mismatches: 16, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
47 9 0.11
48 1 0.01
49 7 0.08
50 4 0.05
51 2 0.02
52 8 0.10
53 8 0.10
55 8 0.10
56 8 0.10
57 2 0.02
58 4 0.05
59 13 0.15
60 1 0.01
61 9 0.11
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (59 bp):
TAAAAATAAGCTATTACATTTCCCCTTAATAAATAAATATTTTAAAAATTTTATATATT
Found at i:60219 original size:108 final size:108
Alignment explanation
Indices: 60095--60311 Score: 425
Period size: 108 Copynumber: 2.0 Consensus size: 108
60085 GGTACAATTC
60095 TAAATTATTTTTTATTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAAT
1 TAAATTATTTTTTATTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAAT
*
60160 ATTTTAAAAATTTTATATATTTAAAAAATTTTCCAGCCACTAA
66 ATTTTAAAAATTTTATATATTTAAAAAATTTTACAGCCACTAA
60203 TAAATTATTTTTTATTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAAT
1 TAAATTATTTTTTATTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAAT
60268 ATTTTAAAAATTTTATATATTTAAAAAATTTTACAGCCACTAA
66 ATTTTAAAAATTTTATATATTTAAAAAATTTTACAGCCACTAA
60311 T
1 T
60312 GTATACCTCA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.45
Consensus pattern (108 bp):
TAAATTATTTTTTATTTAATATTTCTCTAAAAATAAGCTATTACATTTCCCCTTAATAAATAAAT
ATTTTAAAAATTTTATATATTTAAAAAATTTTACAGCCACTAA
Found at i:60289 original size:18 final size:18
Alignment explanation
Indices: 60266--60300 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
60256 TAATAAATAA
*
60266 ATATTTTAAAAATTTTAT
1 ATATTTAAAAAATTTTAT
60284 ATATTTAAAAAATTTTA
1 ATATTTAAAAAATTTTA
60301 CAGCCACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTAAAAAATTTTAT
Found at i:60803 original size:86 final size:85
Alignment explanation
Indices: 60693--60859 Score: 255
Period size: 86 Copynumber: 2.0 Consensus size: 85
60683 AGCGTTTACA
* * *
60693 AAAATAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCTCTTAGAAAAAAAACGCCGCGAAAGATC
1 AAAATAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTGAG-AAAAAAACGCCGCGAAAGATC
60758 ATATTCCTTTAGCGGCGCACAT
65 ATATT-CTTTAGCGGCGCACAT
* *
60780 AAAA-AAACGCCGCTGAAGATCATGTTCTTTAGCGGCGCTGAGAAAAAAACGCCGCTAAAGATCA
1 AAAATAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTGAGAAAAAAACGCCGCGAAAGATCA
*
60844 TGTTCTTTAGCGGCGC
66 TATTCTTTAGCGGCGC
60860 TTTCTTCACA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 12 0.16
85 24 0.32
86 34 0.46
87 4 0.05
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (85 bp):
AAAATAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTGAGAAAAAAACGCCGCGAAAGATCA
TATTCTTTAGCGGCGCACAT
Found at i:60860 original size:42 final size:42
Alignment explanation
Indices: 60693--60860 Score: 228
Period size: 42 Copynumber: 3.9 Consensus size: 42
60683 AGCGTTTACA
* * *
60693 AAAATAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCTCTTAG
1 AAAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTCAG
* * * *
60736 AAAAAAAACGCCGCGAAAGATCATATTCCTTTAGCGGCGCACAT
1 -AAAAAAACGCCGCTAAAGATCATGTT-CTTTAGCGGCGCTCAG
* *
60780 AAAAAAACGCCGCTGAAGATCATGTTCTTTAGCGGCGCTGAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTCAG
60822 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCT
60861 TTCTTCACAA
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 51 0.47
43 42 0.39
44 16 0.15
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTCAG
Found at i:61315 original size:21 final size:21
Alignment explanation
Indices: 61291--61341 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
61281 TTCTTTTGAA
* *
61291 CCTCTACTTCTCTCACTGTAG
1 CCTCTACTTCCCTCACTGCAG
* * *
61312 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTACTTCCCTCACTGCAG
61333 CCTCTACTT
1 CCTCTACTT
61342 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.08, C:0.45, G:0.12, T:0.35
Consensus pattern (21 bp):
CCTCTACTTCCCTCACTGCAG
Done.