Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold426
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: 43809
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:6897 original size:27 final size:27
Alignment explanation
Indices: 6859--6915 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
6849 AGGTTATCGA
6859 GTAATCGATCCGATTCGTCAATTTCAT
1 GTAATCGATCCGATTCGTCAATTTCAT
*
6886 GTAATCGATCCGATTTGTCAATTTCAT
1 GTAATCGATCCGATTCGTCAATTTCAT
6913 GTA
1 GTA
6916 CGAGGTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (27 bp):
GTAATCGATCCGATTCGTCAATTTCAT
Found at i:15635 original size:29 final size:29
Alignment explanation
Indices: 15603--16044 Score: 311
Period size: 29 Copynumber: 15.1 Consensus size: 29
15593 AGCTTTAGCT
* * * *
15603 ATCAATTATGGAAAGGCATAGTGATGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* *
15632 ATCAACTATGAATAGGGATGGTGACGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* * ** * *
15661 ATTGAATTATGAAAAGGGATAGCT-TTGGCT
1 A-TCAATTATGAAAAGGGAT-GGTGACGACC
* *
15691 ATCGATTATGAAAAGGGATGGTGATGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* *
15720 ATCAACTATGAAAAGGGATGGTGACGTCC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* *
15749 ATCAACTATGAAAAGGAATGGTGACGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* * * ** * *
15778 ATAGAATTATGAAAAAGGATAGCT-TTGGCT
1 AT-CAATTATGAAAAGGGAT-GGTGACGACC
* *
15808 ATCGATTAT-ATAAAGTGATGGTGACGACC
1 ATCAATTATGA-AAAGGGATGGTGACGACC
* * * *
15837 ATCAACTATGAAAAGGGATGATGATGACT
1 ATCAATTATGAAAAGGGATGGTGACGACC
* * * * *
15866 ATTGAATTATGAAAAGGGATAGCT-TCGGCT
1 A-TCAATTATGAAAAGGGAT-GGTGACGACC
* * * *
15896 ATCGATTATGAAACGTGATGGTGATGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* *
15925 ATCAACTATGAAAAGGGATGATGACGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* * *
15954 ATCTAATTATGAAAAGGGATAGCT-TC-AGCT
1 ATC-AATTATGAAAAGGGAT-GGTGACGA-CC
*
15984 ATCAATTATGAAATGGGATGGTGACGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* * *
16013 ATCAACTATGAAATGGGATGGTGATGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
16042 ATC
1 ATC
16045 GTGATTACAC
Statistics
Matches: 316, Mismatches: 81, Indels: 32
0.74 0.19 0.07
Matches are distributed among these distances:
28 9 0.03
29 222 0.70
30 77 0.24
31 8 0.03
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (29 bp):
ATCAATTATGAAAAGGGATGGTGACGACC
Found at i:15715 original size:88 final size:87
Alignment explanation
Indices: 15581--16031 Score: 298
Period size: 88 Copynumber: 5.1 Consensus size: 87
15571 TCATTGACCA
* *
15581 ATGAAAAGGGATAGCTTTAGCTATCAATTATGGAAAGGCATAGTGATGACCATCAACTATGAATA
1 ATGAAAAGGGATAGCTTTAGCTATCAATTATGAAAAGGCATAGTGATGACCATCAACTATGAAAA
* *
15646 GGGATGGTGACGACCATTGAATT
66 GGGATGGTGACGACCA-TCAACT
* * * *
15669 ATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAGGGATGGTGATGACCATCAACTATGAAAA
1 ATGAAAAGGGATAGCTTTAGCTATCAATTATGAAAAGGCATAGTGATGACCATCAACTATGAAAA
*
15734 GGGATGGTGACGTCCATCAACT
66 GGGATGGTGACGACCATCAACT
* * * * * * * * * *
15756 ATGAAAAGGAAT-G-GTGACGACCATAGAATTATGAAAAAGG-ATAGCT-TTGGCTATCGATTAT
1 ATGAAAAGGGATAGCTTTA-G-CTAT-CAATTATG-AAAAGGCATAG-TGATGACCATCAACTAT
*
15817 -ATAAAGTGATGGTGACGACCATCAACT
61 GA-AAAGGGATGGTGACGACCATCAACT
* * * * * * * *
15844 ATGAAAAGGGAT-G-ATGATGACTATTGAATTATGAAAAGGGATAGCT--TCGGCTATCGATTAT
1 ATGAAAAGGGATAGCTTTA-G-CTA-TCAATTATGAAAAGGCATAG-TGAT-GACCATCAACTAT
* * *
15905 GAAACGTGATGGTGATGACCATCAACT
61 GAAAAGGGATGGTGACGACCATCAACT
* * * * * * *
15932 ATGAAAAGGGAT-G-ATGACGACCATCTAATTATGAAAAGGGATAGCT--TCAGCTATCAATTAT
1 ATGAAAAGGGATAGCTTTA-G-CTATC-AATTATGAAAAGGCATAG-TGATGA-CCATCAACTAT
*
15993 GAAATGGGATGGTGACGACCATCAACT
61 GAAAAGGGATGGTGACGACCATCAACT
*
16020 ATGAAATGGGAT
1 ATGAAAAGGGAT
16032 GGTGATGACC
Statistics
Matches: 311, Mismatches: 40, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
85 1 0.00
86 2 0.01
87 27 0.09
88 272 0.87
89 9 0.03
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (87 bp):
ATGAAAAGGGATAGCTTTAGCTATCAATTATGAAAAGGCATAGTGATGACCATCAACTATGAAAA
GGGATGGTGACGACCATCAACT
Found at i:15787 original size:117 final size:117
Alignment explanation
Indices: 15603--15856 Score: 384
Period size: 117 Copynumber: 2.2 Consensus size: 117
15593 AGCTTTAGCT
* * * * * * * *
15603 ATCAATTATGGAAAGGCATAGTGATGACCATCAACTATGAATAGGGATGGTGACGACCATTGAAT
1 ATCAACTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGAATGGTGACGACCATAGAAT
* *
15668 TATGAAAAGGGATAGCTTTGGCTATCGATTATGA-AAAGGGATGGTGATGACC
66 TATGAAAAAGGATAGCTTTGGCTATCGATTAT-ATAAAGGGATGGTGACGACC
*
15720 ATCAACTATGAAAAGGGATGGTGACGTCCATCAACTATGAAAAGGAATGGTGACGACCATAGAAT
1 ATCAACTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGAATGGTGACGACCATAGAAT
*
15785 TATGAAAAAGGATAGCTTTGGCTATCGATTATATAAAGTGATGGTGACGACC
66 TATGAAAAAGGATAGCTTTGGCTATCGATTATATAAAGGGATGGTGACGACC
15837 ATCAACTATGAAAAGGGATG
1 ATCAACTATGAAAAGGGATG
15857 ATGATGACTA
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
116 1 0.01
117 123 0.99
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (117 bp):
ATCAACTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGAATGGTGACGACCATAGAAT
TATGAAAAAGGATAGCTTTGGCTATCGATTATATAAAGGGATGGTGACGACC
Found at i:15933 original size:205 final size:206
Alignment explanation
Indices: 15581--15970 Score: 604
Period size: 205 Copynumber: 1.9 Consensus size: 206
15571 TCATTGACCA
* * * *
15581 ATGAAAAGGGATAGCTTTAGCTATCAATTATGGAAAGGCATAGTGATGACCATCAACTATGAATA
1 ATGAAAAAGGATAGCTTTAGCTATCAATTATAGAAAGGCATAGTGACGACCATCAACTATGAAAA
* *
15646 GGGATGGTGACGACCATTGAATTATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAGGGATG
66 GGGATGATGACGACCATTGAATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATG
* *
15711 GTGATGACCATCAACTATGAAAAGGGATGGTGACGTCCATC-AACTATGAAAAGGAATGGTGACG
131 GTGATGACCATCAACTATGAAAAGGGATGATGACGACCATCTAACTATGAAAAGGAATGGTGACG
15775 ACCATAGAATT
196 ACCATAGAATT
* * * *
15786 ATGAAAAAGGATAGCTTTGGCTATCGATTATATAAAGTG-ATGGTGACGACCATCAACTATGAAA
1 ATGAAAAAGGATAGCTTTAGCTATCAATTATAGAAAG-GCATAGTGACGACCATCAACTATGAAA
* * * *
15850 AGGGATGATGATGACTATTGAATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAACGTGAT
65 AGGGATGATGACGACCATTGAATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGAT
*
15915 GGTGATGACCATCAACTATGAAAAGGGATGATGACGACCATCTAATTATGAAAAGG
130 GGTGATGACCATCAACTATGAAAAGGGATGATGACGACCATCTAACTATGAAAAGG
15971 GATAGCTTCA
Statistics
Matches: 166, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
205 153 0.92
206 13 0.08
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (206 bp):
ATGAAAAAGGATAGCTTTAGCTATCAATTATAGAAAGGCATAGTGACGACCATCAACTATGAAAA
GGGATGATGACGACCATTGAATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAGGGATG
GTGATGACCATCAACTATGAAAAGGGATGATGACGACCATCTAACTATGAAAAGGAATGGTGACG
ACCATAGAATT
Found at i:16032 original size:88 final size:88
Alignment explanation
Indices: 15720--16044 Score: 429
Period size: 88 Copynumber: 3.7 Consensus size: 88
15710 GGTGATGACC
* * * * **
15720 ATCAACTATGAAAAGGGATGGTGACGTCCATCAACTATGAAAAGGAATGGTGACGACCATAGAAT
1 ATCAATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGATGACGACCATCTAAT
* *
15785 TATGAAAAAGGATAGCTTTGGCT
66 TATGAAAAGGGATAGCTTCGGCT
* * * *
15808 ATCGATTAT-ATAAAGTGATGGTGACGACCATCAACTATGAAAAGGGATGATGATGACTAT-TGA
1 ATCAATTATGA-AAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGATGACGACCATCT-A
15871 ATTATGAAAAGGGATAGCTTCGGCT
64 ATTATGAAAAGGGATAGCTTCGGCT
* * * *
15896 ATCGATTATGAAACGTGATGGTGATGACCATCAACTATGAAAAGGGATGATGACGACCATCTAAT
1 ATCAATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGATGACGACCATCTAAT
*
15961 TATGAAAAGGGATAGCTTCAGCT
66 TATGAAAAGGGATAGCTTCGGCT
* * * *
15984 ATCAATTATGAAATGGGATGGTGACGACCATCAACTATGAAATGGGATGGTGATGACCATC
1 ATCAATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGATGACGACCATC
16045 GTGATTACAC
Statistics
Matches: 210, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
87 1 0.00
88 207 0.99
89 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (88 bp):
ATCAATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGATGACGACCATCTAAT
TATGAAAAGGGATAGCTTCGGCT
Found at i:17290 original size:13 final size:13
Alignment explanation
Indices: 17270--17301 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17260 TGTGAGTCAT
17270 ACGGCCTGGCCAC
1 ACGGCCTGGCCAC
*
17283 ATGGCCTGGCCAC
1 ACGGCCTGGCCAC
17296 ACGGCC
1 ACGGCC
17302 ATGTGACTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.44, G:0.31, T:0.09
Consensus pattern (13 bp):
ACGGCCTGGCCAC
Found at i:18850 original size:39 final size:39
Alignment explanation
Indices: 18794--18909 Score: 108
Period size: 39 Copynumber: 2.9 Consensus size: 39
18784 TACTATTTGA
* * * * *
18794 TTCAAGGTTACCAAAGTATATATAGGGCACGTATGTGTG
1 TTCAAGGCTACCAAAGTACAAACAGAGCACGTATGTGTG
**
18833 TTCAAGGCTA-CAGAAGTACAAACAGAGCACGTATGTGCA
1 TTCAAGGCTACCA-AAGTACAAACAGAGCACGTATGTGTG
* * * *
18872 TTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTG
1 TTCAAGGCTACCAAAGTACAAAC-AGAGCACGTATGTG
18910 CATTCAACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
38 2 0.03
39 47 0.75
40 14 0.22
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (39 bp):
TTCAAGGCTACCAAAGTACAAACAGAGCACGTATGTGTG
Found at i:18910 original size:40 final size:39
Alignment explanation
Indices: 18817--18916 Score: 137
Period size: 39 Copynumber: 2.5 Consensus size: 39
18807 AAGTATATAT
**
18817 AGGGCACGTATGTGTGTTCAAGGCTACAGAAGTACAAAC
1 AGGGCACGTATGTGCATTCAAGGCTACAGAAGTACAAAC
* * * *
18856 AGAGCACGTATGTGCATTCAGGGGTACCGAAGTACAAAC
1 AGGGCACGTATGTGCATTCAAGGCTACAGAAGTACAAAC
18895 AAGGGCACGTATGTGCATTCAA
1 -AGGGCACGTATGTGCATTCAA
18917 CAATAATTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 33 0.63
40 19 0.37
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (39 bp):
AGGGCACGTATGTGCATTCAAGGCTACAGAAGTACAAAC
Found at i:24821 original size:40 final size:40
Alignment explanation
Indices: 24758--24868 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 40
24748 ATTTAGGATT
* * * * *
24758 ACCAAAGTATAAACAA-GGAACGTATGTACGTTAAGGGGT
1 ACCAAAGTACAAATAAGGGCACGTATGTACATTAAGGGGC
** * * *
24797 ACTGAAGTACAAATAGGGGCACGTATGTGCATTCAGGGGC
1 ACCAAAGTACAAATAAGGGCACGTATGTACATTAAGGGGC
*
24837 ACCAAAGTATAAATAAGGGCAC-TATGTACATT
1 ACCAAAGTACAAATAAGGGCACGTATGTACATT
24869 CATCAATAAT
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
39 20 0.36
40 36 0.64
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (40 bp):
ACCAAAGTACAAATAAGGGCACGTATGTACATTAAGGGGC
Found at i:31241 original size:49 final size:49
Alignment explanation
Indices: 31075--31312 Score: 287
Period size: 49 Copynumber: 4.8 Consensus size: 49
31065 TGAGGTCGCA
* * * * *
31075 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACG
* * **
31126 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
*
31176 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * * * *
31225 TGTTTAGTACTAAGTGCAGGCTACTATGTGTACCAAATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
31274 TGTGTAGTACTACGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
31313 GCTTTGGCTA
Statistics
Matches: 162, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
49 86 0.53
50 44 0.27
51 32 0.20
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Done.