Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1465
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: 28031
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:11567 original size:49 final size:49
Alignment explanation
Indices: 11510--11970 Score: 228
Period size: 49 Copynumber: 9.6 Consensus size: 49
11500 ACATCTAAAT
*
11510 CGATGCCATGTCCCAAACAGGTCTTACACTGACTTCCATACATCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTCCATACATCGAGGC
* * * * * * *
11559 CAATGCCATGTCCTAGACAGGTTTTACACTGGC-TCTCAGT-TATCTG-TGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTC-CA-TACATC-GAGGC
* * *
11608 CGATGCCATGTCCCAGACAGGTCTTACACTGA----CACACCTC-AAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTCCATACATCGAGGC
* * * * * * *
11652 TGATGTCATGTCCTAGACAAGTCTTACACT-AGCTTGCATATC-TTGAGGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTTCCATA-CATCGAGGC
* * * * *
11701 TGATGCCGTGTACCAGATAGGTCTTACACTGACTTCCATACATTGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTCCATACATCGAGGC
* * * * * *
11750 CAATGCCATGTCCTAGACAGGTCTTACACTGGCTCTCACTTATC-TC--TGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACT-TC-CATA-CATCGAGGC
* * * * *
11799 CGATGCCATGTCCCAGATAGGTCTTACACTGA----CACACCTC-AAGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTCCATACATCGAGGC
* * * * * *
11843 TGATGTCATGTCCTAGACAGGTCTTACACT-AGCTTGCATATCCT-GAGGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTTCCATA-CATCGAGGC
* * * * * * *
11892 TGATGCCGTGTACCAGATAGGTCTTACACTGGC-TCTCAT-CTATCGATGT
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTC-CATAC-ATCGAGGC
*
11941 GGATGCCATGTCCCAGACAGGTCTTACACT
1 CGATGCCATGTCCCAGACAGGTCTTACACT
11971 AGCACACACA
Statistics
Matches: 312, Mismatches: 70, Indels: 60
0.71 0.16 0.14
Matches are distributed among these distances:
42 1 0.00
43 6 0.02
44 55 0.18
45 4 0.01
47 1 0.00
48 12 0.04
49 223 0.71
50 5 0.02
51 4 0.01
52 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGACTTCCATACATCGAGGC
Found at i:11723 original size:93 final size:93
Alignment explanation
Indices: 11565--11922 Score: 372
Period size: 93 Copynumber: 3.8 Consensus size: 93
11555 AGGCCAATGC
* * * * * *
11565 CATGTCCTAGACAGGTTTTACACTGGCTCT-CAGTTATC-TG-TGTCGATGCCATGTCCCAGACA
1 CATGTCCTAGACAGGTCTTACACTAGCT-TGCA--TATCTTGAGGTTGATGCCATGTACCAGATA
11627 GGTCTTACACTGACACACCTCAAGCTGATGT
63 GGTCTTACACTGACACACCTCAAGCTGATGT
* *
11658 CATGTCCTAGACAAGTCTTACACTAGCTTGCATATCTTGAGGTTGATGCCGTGTACCAGATAGGT
1 CATGTCCTAGACAGGTCTTACACTAGCTTGCATATCTTGAGGTTGATGCCATGTACCAGATAGGT
* * ** *
11723 CTTACACTGACTTC-CATACATTGAGGCCAATGC
66 CTTACACTGAC-ACACCT-CA---A-GCTGATGT
* * *
11756 CATGTCCTAGACAGGTCTTACACTGGCTCT-CACTTATCTCT---GTCGATGCCATGTCCCAGAT
1 CATGTCCTAGACAGGTCTTACACTAGCT-TGCA--TATCT-TGAGGTTGATGCCATGTACCAGAT
*
11817 AGGTCTTACACTGACACACCTCAAGTTGATGT
62 AGGTCTTACACTGACACACCTCAAGCTGATGT
* *
11849 CATGTCCTAGACAGGTCTTACACTAGCTTGCATATCCTGAGGTTGATGCCGTGTACCAGATAGGT
1 CATGTCCTAGACAGGTCTTACACTAGCTTGCATATCTTGAGGTTGATGCCATGTACCAGATAGGT
11914 CTTACACTG
66 CTTACACTG
11923 GCTCTCATCT
Statistics
Matches: 218, Mismatches: 29, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
90 1 0.00
91 8 0.04
92 4 0.02
93 123 0.56
94 4 0.02
97 4 0.02
98 67 0.31
99 1 0.00
100 5 0.02
101 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (93 bp):
CATGTCCTAGACAGGTCTTACACTAGCTTGCATATCTTGAGGTTGATGCCATGTACCAGATAGGT
CTTACACTGACACACCTCAAGCTGATGT
Found at i:11804 original size:98 final size:95
Alignment explanation
Indices: 11482--11831 Score: 383
Period size: 98 Copynumber: 3.6 Consensus size: 95
11472 CTCCAAACAT
** *
11482 GGTCTTACACTGGCTCTCAC-ATCTAAATCGATGCCATGTCCCAAACAGGTCTTACACTGACTTC
1 GGTCTTACACTGGCTCTCACTATCT-TGTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTC
11546 CATACATCGAGGCCAATGCCATGTCCTAGACA
65 CATACAT-GAGGCCAATGCCATGTCCTAGACA
* * *
11578 GGTTTTACACTGGCTCTCAGTTATCTGTGTCGATGCCATGTCCCAGACAGGTCTTACACTGAC-A
1 GGTCTTACACTGGCTCTCA-CTATCT-TGTCGATGCCATGTCCCAGACAGGTCTTACACTGACTT
* ** *
11642 CACCT-CA--A-GCTGATGTCATGTCCTAGACA
64 C-CATACATGAGGCCAATGCCATGTCCTAGACA
* * * * * *
11671 AGTCTTACACTAGCT-TGCA-TATCTTGAGGTTGATGCCGTGTACCAGATAGGTCTTACACTGAC
1 GGTCTTACACTGGCTCT-CACTATCTT---GTCGATGCCATGTCCCAGACAGGTCTTACACTGAC
11734 TTCCATACATTGAGGCCAATGCCATGTCCTAGACA
62 TTCCATACA-TGAGGCCAATGCCATGTCCTAGACA
*
11769 GGTCTTACACTGGCTCTCACTTATCTCTGTCGATGCCATGTCCCAGATAGGTCTTACACTGAC
1 GGTCTTACACTGGCTCTCAC-TATCT-TGTCGATGCCATGTCCCAGACAGGTCTTACACTGAC
11832 ACACCTCAAG
Statistics
Matches: 209, Mismatches: 28, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
90 1 0.00
91 5 0.02
92 1 0.00
93 65 0.31
94 4 0.02
96 18 0.09
97 4 0.02
98 104 0.50
99 1 0.00
100 5 0.02
101 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (95 bp):
GGTCTTACACTGGCTCTCACTATCTTGTCGATGCCATGTCCCAGACAGGTCTTACACTGACTTCC
ATACATGAGGCCAATGCCATGTCCTAGACA
Found at i:11845 original size:142 final size:144
Alignment explanation
Indices: 11699--11979 Score: 342
Period size: 142 Copynumber: 2.0 Consensus size: 144
11689 ATATCTTGAG
* * *
11699 GTTGATGCCGTGTACC-AGATAGGTCTTACACT-GACTTCCATA-CATTGAGGCCAATGCCATGT
1 GTTGATGCCATGT-CCTAGACAGGTCTTACACTAG-CTTCCATATC-CTGAGGCCAATGCCATGT
** *
11761 -CCTAGACAGGTCTTACACTGGCTCTCA-CTTATCTCTGTCGATGCCATGTCCCAGATAGGTCTT
63 ACC-AGACAGGTCTTACACTGGCTCTCATC-TATCGATGTCGATGCCATGTCCCAGACAGGTCTT
11824 ACACT-G-ACACACCTCAA
126 ACACTAGCACACACCTCAA
* * *** *
11841 GTTGATGTCATGTCCTAGACAGGTCTTACACTAGCTTGCATATCCTGAGGTTGATGCCGTGTACC
1 GTTGATGCCATGTCCTAGACAGGTCTTACACTAGCTTCCATATCCTGAGGCCAATGCCATGTACC
* *
11906 AGATAGGTCTTACACTGGCTCTCATCTATCGATGTGGATGCCATGTCCCAGACAGGTCTTACACT
66 AGACAGGTCTTACACTGGCTCTCATCTATCGATGTCGATGCCATGTCCCAGACAGGTCTTACACT
11971 AGCACACAC
131 AGCACACAC
11980 ATCACCCAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
141 2 0.02
142 104 0.88
143 6 0.05
144 6 0.05
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (144 bp):
GTTGATGCCATGTCCTAGACAGGTCTTACACTAGCTTCCATATCCTGAGGCCAATGCCATGTACC
AGACAGGTCTTACACTGGCTCTCATCTATCGATGTCGATGCCATGTCCCAGACAGGTCTTACACT
AGCACACACCTCAA
Found at i:11852 original size:191 final size:191
Alignment explanation
Indices: 11528--11970 Score: 728
Period size: 191 Copynumber: 2.3 Consensus size: 191
11518 TGTCCCAAAC
*
11528 AGGTCTTACACTGACTTCCATACATCGAGGCCAATGCCATGTCCTAGACAGGTTTTACACTGGCT
1 AGGTCTTACACTGACTTCCATACATCGAGGCCAATGCCATGTCCTAGACAGGTCTTACACTGGCT
* *
11593 CTCAGTTATCTGTGTCGATGCCATGTCCCAGACAGGTCTTACACTGACACACCTCAAGCTGATGT
66 CTCACTTATCTCTGTCGATGCCATGTCCCAGACAGGTCTTACACTGACACACCTCAAGCTGATGT
*
11658 CATGTCCTAGACAAGTCTTACACTAGCTTGCATATCTTGAGGTTGATGCCGTGTACCAGAT
131 CATGTCCTAGACAAGTCTTACACTAGCTTGCATATCCTGAGGTTGATGCCGTGTACCAGAT
*
11719 AGGTCTTACACTGACTTCCATACATTGAGGCCAATGCCATGTCCTAGACAGGTCTTACACTGGCT
1 AGGTCTTACACTGACTTCCATACATCGAGGCCAATGCCATGTCCTAGACAGGTCTTACACTGGCT
* *
11784 CTCACTTATCTCTGTCGATGCCATGTCCCAGATAGGTCTTACACTGACACACCTCAAGTTGATGT
66 CTCACTTATCTCTGTCGATGCCATGTCCCAGACAGGTCTTACACTGACACACCTCAAGCTGATGT
*
11849 CATGTCCTAGACAGGTCTTACACTAGCTTGCATATCCTGAGGTTGATGCCGTGTACCAGAT
131 CATGTCCTAGACAAGTCTTACACTAGCTTGCATATCCTGAGGTTGATGCCGTGTACCAGAT
* * *** *
11910 AGGTCTTACACTGGC-TCTCAT-CTATCGATGTGGATGCCATGTCCCAGACAGGTCTTACACT
1 AGGTCTTACACTGACTTC-CATAC-ATCGAGGCCAATGCCATGTCCTAGACAGGTCTTACACT
11971 AGCACACACA
Statistics
Matches: 235, Mismatches: 15, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
190 3 0.01
191 232 0.99
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (191 bp):
AGGTCTTACACTGACTTCCATACATCGAGGCCAATGCCATGTCCTAGACAGGTCTTACACTGGCT
CTCACTTATCTCTGTCGATGCCATGTCCCAGACAGGTCTTACACTGACACACCTCAAGCTGATGT
CATGTCCTAGACAAGTCTTACACTAGCTTGCATATCCTGAGGTTGATGCCGTGTACCAGAT
Found at i:22522 original size:28 final size:27
Alignment explanation
Indices: 22459--22610 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
22449 ATATTAAGTC
* * *
22459 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
22486 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
22514 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
22541 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
22569 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
22596 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
22611 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:22543 original size:55 final size:55
Alignment explanation
Indices: 22459--22610 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
22449 ATATTAAGTC
* * *
22459 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
22514 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
22569 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
22611 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:26260 original size:40 final size:40
Alignment explanation
Indices: 26205--26348 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
26195 TATTCGAATG
* * *
26205 ATATCCGGGTTAAGTCCCGAGGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
26245 ATATCTGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
26285 ATATCCGGGCTAAGACCCGAAGGCATCTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
26325 ATATCC-GGCTAAATCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCA
26349 CTTGAGTTTG
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 16 0.18
40 71 0.80
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Done.