Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2111
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: 26307
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2180 original size:39 final size:39
Alignment explanation
Indices: 2123--2223 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
2113 CGAATACACG
*
2123 TCACCAGCATGATGCTCTTCGGGACCTAGCCCGGATATA
1 TCACCAGCATGATGCTCTTCGGGACCTAGCCCGGATACA
* **
2162 -CACCAGCACGAATGCTCTTC-GGAATTAGCCCGGATACA
1 TCACCAGCATG-ATGCTCTTCGGGACCTAGCCCGGATACA
*
2200 TCACTAGCATGA-GCTCTTCGGGAC
1 TCACCAGCATGATGCTCTTCGGGAC
2224 TTACCCGATT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
37 7 0.13
38 28 0.54
39 17 0.33
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.22
Consensus pattern (39 bp):
TCACCAGCATGATGCTCTTCGGGACCTAGCCCGGATACA
Found at i:2721 original size:29 final size:30
Alignment explanation
Indices: 2644--2723 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
2634 GCTTATAATC
* *
2644 AACCACGCACACTTAGTGCCATGTACTTTTA
1 AACC-CGCACACTTAGTGCCATGCACTTTCA
*
2675 AACTCGCACACTTAGTGCCATGCA-TTTCA
1 AACCCGCACACTTAGTGCCATGCACTTTCA
*
2704 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
2724 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 22 0.50
30 19 0.43
31 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGCACTTTCA
Found at i:4555 original size:36 final size:37
Alignment explanation
Indices: 4495--4572 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
4485 TTATTACGAA
* * *
4495 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
4532 GTCTTA-CCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
4568 GTCTT
1 GTCTT
4573 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:4813 original size:47 final size:47
Alignment explanation
Indices: 4691--5201 Score: 448
Period size: 49 Copynumber: 11.1 Consensus size: 47
4681 CCCTTCGGGA
* * * * * *
4691 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
4738 CCTGTCACATATAT--ACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4783 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4830 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
4879 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * **
4928 CTTATCACGTATATACTCTTTCACATTCATCACATCGGCATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGC-CAT-TAGGC
** * *
4977 ACTT-TCAC--AT-T-CA---TCACA-TCGGC-CATTAGGCC-TTA-TC
1 -CTTATCACATATATACACTTTCACATTCATCACA-TCGGCCATTAGGC
* * *
5014 ACGTATAT-ACACT-T-T-CACATTCATCA--CATCGGCCATTAGGCC--T----
1 -C-T-TATCACA-TATATACACTTTCA-CATTCATC--ACA-TCGGCCATTAGGC
5057 --TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5102 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5151 CTTATCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
5198 CTTA
1 CTTA
5202 CTATCATTTC
Statistics
Matches: 396, Mismatches: 31, Indels: 74
0.79 0.06 0.15
Matches are distributed among these distances:
37 3 0.01
38 7 0.02
39 13 0.03
40 8 0.02
41 19 0.05
42 9 0.02
44 5 0.01
45 41 0.10
46 2 0.01
47 136 0.34
48 2 0.01
49 148 0.37
50 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:4888 original size:96 final size:96
Alignment explanation
Indices: 4693--5198 Score: 426
Period size: 96 Copynumber: 5.5 Consensus size: 96
4683 CTTCGGGACT
* * * * * * *
4693 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATAT--AC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC
*
4754 TTTCACATTCATCACATCGGCCATTAGGCCT
66 TTTCACATTCATCACATCGGCCATTAGGCCC
*
4785 TATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGCCCTATCACATATATATACAC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC
4850 TTTCACATTCATCACATCGGCCATTAGGCCC
66 TTTCACATTCATCACATCGGCCATTAGGCCC
* *
4881 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--GTATATAC
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
* * ** *
4944 TCTTTCACATTCATCACATCGGCATATATATACAC
64 ACTTTCACATTCATCACATCGGC-CAT-TAGGCCC
* ** * * * * *
4979 TTTCAC--AT-T-CA---TCACA-TCGGC-CATTAGGCC-TTA-TCACGTAT---ATACACT-TT
1 TATCACATATATACACTTTCACATTCATCACA-TCGGCCATTAGGC-CCTATCACATATA-TATA
* * *
5029 CACATTCATCA--CATCGGCCATTAGGCC--T------
63 CACTTTCA-CATTCATC--ACA-TCGGCCATTAGGCCC
*
5057 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC
*
5122 TTTCACATTCATCACATCGGCCATTAGGCCT
66 TTTCACATTCATCACATCGGCCATTAGGCCC
*
5153 TATCACATATATACACTTTCACGTTCATCACATCGGCCATTAGGCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
5199 TTACTATCAT
Statistics
Matches: 331, Mismatches: 41, Indels: 80
0.73 0.09 0.18
Matches are distributed among these distances:
78 5 0.02
80 2 0.01
81 1 0.00
82 2 0.01
84 1 0.00
85 9 0.03
86 17 0.05
87 23 0.07
88 18 0.05
89 10 0.03
90 13 0.04
91 4 0.01
92 49 0.15
93 1 0.00
94 8 0.02
96 112 0.34
97 2 0.01
98 54 0.16
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (96 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:4976 original size:33 final size:33
Alignment explanation
Indices: 4937--4999 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
4927 CCTTATCACG
*
4937 TATATACTCTTTCACATTCATCACATCGGCATA
1 TATATACACTTTCACATTCATCACATCGGCATA
4970 TATATACACTTTCACATTCATCACATCGGC
1 TATATACACTTTCACATTCATCACATCGGC
5000 CATTAGGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (33 bp):
TATATACACTTTCACATTCATCACATCGGCATA
Found at i:4977 original size:80 final size:80
Alignment explanation
Indices: 4886--5046 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
4876 GGCCCTATCA
*
4886 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACTCTTTCA
1 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCA
4951 CATTCATCACATCGG
66 CATTCATCACATCGG
4966 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCA
1 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCA
5031 CATTCATCACATCGG
66 CATTCATCACATCGG
5046 C
1 C
5047 CATTAGGCCT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (80 bp):
CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCA
CATTCATCACATCGG
Found at i:5033 original size:38 final size:42
Alignment explanation
Indices: 4981--5201 Score: 217
Period size: 47 Copynumber: 4.7 Consensus size: 42
4971 ATATACACTT
*
4981 TCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACA
1 TCACATT-ATCACATCGGCCATTAGGCCTTATCACATATATA-A
5025 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 ---TCACATT-ATCACATCGGCCATTAGGCCTTATCACATATATA-A
5072 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
1 ---TCACATT-ATCACATCGGCCATTAGGCCTTATCAC--ATATATA-A
5121 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
1 ---TCACATT-ATCACATCGGCCATTAGGCCTTATCACATATATA-A
*
5168 CTTTCACGTTCATCACATCGGCCATTAGGCCTTA
1 ---TCACATT-ATCACATCGGCCATTAGGCCTTA
5202 CTATCATTTC
Statistics
Matches: 170, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
47 123 0.72
49 47 0.28
ACGTcount: A:0.29, C:0.30, G:0.10, T:0.32
Consensus pattern (42 bp):
TCACATTATCACATCGGCCATTAGGCCTTATCACATATATAA
Found at i:5068 original size:127 final size:128
Alignment explanation
Indices: 4837--5093 Score: 462
Period size: 127 Copynumber: 2.0 Consensus size: 128
4827 GGCCCTATCA
4837 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATACACTTT
1 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACA-ATATATACACTTT
* *
4902 CACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACTCTTTCACATTCATCACATCGG
65 CACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
* *
4966 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-GTATATACACTTTC
1 CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACACTTTC
5030 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
5093 C
1 C
5094 CATTAGGCCT
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
127 75 0.60
129 49 0.40
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (128 bp):
CATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACAATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
Found at i:5199 original size:96 final size:94
Alignment explanation
Indices: 4969--5201 Score: 430
Period size: 96 Copynumber: 2.5 Consensus size: 94
4959 ACATCGGCAT
*
4969 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
5034 TCATCACATCGGCCATTAGGCCTTATCAC
66 TCATCACATCGGCCATTAGGCCTTATCAC
5063 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCAC
5128 ATTCATCACATCGGCCATTAGGCCTTATCAC
64 ATTCATCACATCGGCCATTAGGCCTTATCAC
*
5159 ATATATACACTTTCACGTTCATCACATCGGCCATTAGGCCTTA
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
5202 CTATCATTTC
Statistics
Matches: 135, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
94 47 0.35
96 88 0.65
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (94 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCAC
Found at i:12824 original size:27 final size:26
Alignment explanation
Indices: 12776--12852 Score: 84
Period size: 26 Copynumber: 2.9 Consensus size: 26
12766 TCTTATCCCT
12776 ATTTTACCCCCGATAAAATTTTGACA
1 ATTTTACCCCCGATAAAATTTTGACA
* *
12802 ATTTTACCCCC-AGTAAATTTTTTGACG
1 ATTTTACCCCCGA-TAAA-ATTTTGACA
***
12829 ATTTTACCAATGATAAAATTTTGA
1 ATTTTACCCCCGATAAAATTTTGA
12853 GAAAATATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
25 1 0.02
26 21 0.50
27 19 0.45
28 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (26 bp):
ATTTTACCCCCGATAAAATTTTGACA
Found at i:19983 original size:26 final size:26
Alignment explanation
Indices: 19948--19998 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
19938 AATGTGAAAG
*
19948 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
19974 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
19999 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:20010 original size:103 final size:104
Alignment explanation
Indices: 19870--20092 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 104
19860 TGTATATAAA
** * *
19870 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
19934 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
19973 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
20038 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
20077 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
20093 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 90 0.80
104 22 0.20
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:20144 original size:71 final size:72
Alignment explanation
Indices: 20011--20162 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
20001 TCATTGGTGG
* *
20011 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
20076 GAGGGGT
66 GAGGGGT
***
20083 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
20147 GAGGGGT
66 GAGGGGT
20154 TGCTAAGTG
1 TGCTAAGTG
20163 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Done.