Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1792
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: 22762
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:4089 original size:48 final size:48
Alignment explanation
Indices: 3967--4284 Score: 386
Period size: 48 Copynumber: 6.6 Consensus size: 48
3957 TCGTTTAACC
* *
3967 GTATTGGCGTTAGGACCTGGTCAAACTCTTTTCATCCCTCATTTGACT
1 GTATTGGCGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
*
4015 G-ATTGGCATTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
1 GTATTGGCGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
* * ** * **
4062 GTATTGGTGTTAAGGCCCGGTCAAACTCTTTTCATCCTTTGTTTGACT
1 GTATTGGCGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
* *
4110 GTATTGGTGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGATT
1 GTATTGGCGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
* * * **
4158 GCATTGGAGTTAGGGCCTAGTCAAACTCTTTTCATGCCTTGTTTGACT
1 GTATTGGCGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
* * * *
4206 ATATTAGCGTTAGGGCCTAGTTAAACTCTTTTTATCCCTCATTTGACT
1 GTATTGGCGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
* * * * * *
4254 GCATTGGTGTTAAGGCTTGGTTAAACTCTTT
1 GTATTGGCGTTAGGGCCTAGTCAAACTCTTT
4285 GCACCTTTGT
Statistics
Matches: 229, Mismatches: 40, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
47 44 0.19
48 185 0.81
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (48 bp):
GTATTGGCGTTAGGGCCTAGTCAAACTCTTTTCATCCCTCATTTGACT
Found at i:4147 original size:96 final size:96
Alignment explanation
Indices: 3969--4306 Score: 450
Period size: 96 Copynumber: 3.5 Consensus size: 96
3959 GTTTAACCGT
* * ** * *
3969 ATTGGCGTT-AGGACCTGGTCAAACTCTTTTCATCCCTCATTTGACT-GATTGGCATTAGGGCCT
1 ATTGGTGTTAAGG-CCTGGTCAAACTCTTTTCATCCTTTGTTTGACTATATTGGCGTTAGGGCCT
*
4032 AGTCAAACTCTTTTCATCCCTCATTTGACTGT
65 AGTCAAACTCTTTTCATCCCTCATTTGACTGC
* * *
4064 ATTGGTGTTAAGGCCCGGTCAAACTCTTTTCATCCTTTGTTTGACTGTATTGGTGTTAGGGCCTA
1 ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTTGTTTGACTATATTGGCGTTAGGGCCTA
*
4129 GTCAAACTCTTTTCATCCCTCATTTGATTGC
66 GTCAAACTCTTTTCATCCCTCATTTGACTGC
* * * *
4160 ATTGGAGTTAGGGCCTAGTCAAACTCTTTTCATGCC-TTGTTTGACTATATTAGCGTTAGGGCCT
1 ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCAT-CCTTTGTTTGACTATATTGGCGTTAGGGCCT
* *
4224 AGTTAAACTCTTTTTATCCCTCATTTGACTGC
65 AGTCAAACTCTTTTCATCCCTCATTTGACTGC
* * *
4256 ATTGGTGTTAAGGCTTGGTTAAACTCTTTGCA-CCTTTGTTTGACTATATTG
1 ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTTGTTTGACTATATTG
4307 ATGATAGAAC
Statistics
Matches: 212, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
94 2 0.01
95 52 0.25
96 156 0.74
97 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (96 bp):
ATTGGTGTTAAGGCCTGGTCAAACTCTTTTCATCCTTTGTTTGACTATATTGGCGTTAGGGCCTA
GTCAAACTCTTTTCATCCCTCATTTGACTGC
Found at i:4682 original size:84 final size:84
Alignment explanation
Indices: 4565--4754 Score: 213
Period size: 84 Copynumber: 2.3 Consensus size: 84
4555 TTAGTCTCGG
* ** * * *
4565 GTAAA-TCCTTTACCCTTTATTGACTTATTGGTTCAGCCTTGGTCAACCATT-TATCACTTGTTT
1 GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACC-TTCCATCACTTGTTT
* *
4628 ACTTGGCAGTTTAGTGCCCA
65 ACCTAGCAGTTTAGTGCCCA
*
4648 GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACCTTCCATCCCTTGTTTA
1 GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACCTTCCATCACTTGTTTA
* * **
4713 CCTATCATTTTAGTGCCTG
66 CCTAGCAGTTTAGTGCCCA
* * *
4732 GTAAACTCGTTTATCCTATGTTG
1 GTAAACTCCTTTACCCTTTGTTG
4755 GTTTGTCGGT
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
83 7 0.08
84 82 0.92
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (84 bp):
GTAAACTCCTTTACCCTTTGTTGACTTAACGGTTCAGCCCTAGTCAACCTTCCATCACTTGTTTA
CCTAGCAGTTTAGTGCCCA
Found at i:6158 original size:168 final size:166
Alignment explanation
Indices: 5837--7047 Score: 950
Period size: 164 Copynumber: 7.4 Consensus size: 166
5827 TTAAAGATTT
* * * * * **
5837 TCAAATATTATCATTTAATTT--TCATTAAATAAATTTTTAAAACTTTATTCATTTTTATTCA-T
1 TCAAATATTATTATTT-ATTTCAT-ATTAAATCAATTTTTAAAAATTCATTCATTTTCA-AGAGT
* * ** * *
5899 TCTTCA-TTTTTCCTAAAAATTTTCCTATTTTCGAAATACAAAGTTTTCTA-ATC-TATAATTTT
63 TTTTTATTTTTTCCTTGAAATTTTCCTATTTTCAAAATACAAAGTTTTCTACTTCATA-AATTTT
* *
5961 TTTCGAGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
127 TTTGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * *
6001 TCAAATATTATTGTTTATGTCATATTAAATCAATTTTTAAAAATTCATTCCTTTTCAAGAGTTTT
1 TCAAATATTATTATTTATTTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCAAGAG--TT
* **
6066 TTTTATTTTTTCCTTAAAATTTTCCTA-TTTCTAAAATACGGAGTTTTCTACTTCATAAATTTTT
64 TTTTATTTTTTCCTTGAAATTTTCCTATTTTC-AAAATACAAAGTTTTCTACTTCATAAATTTTT
**
6130 TTGGATAGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
128 TTGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * * *
6169 TTAAATATTATTATTTACTTCATATTAAATCACTTTTTAAAAATTCATTCATTCTCATA-AGTTT
1 TCAAATATTATTATTTATTTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCA-AGAGTTT
* * * * * * *
6233 TTCA-TTTTTCCTCGAAA-TTTCTCTATTTCCAAAATACGAAGTTTTTTAC-TCTGTAATTTTTT
65 TTTATTTTTTCCTTGAAATTTTC-CTATTTTCAAAATACAAAGTTTTCTACTTC-ATAAATTTTT
*
6295 TTAGG-GGGA----TCTTGGTTTTTAATTTTTAAAATTTA
128 TT-GGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * * *
6330 TCAAATATTATTATTTATTTCATATTAAATTATTTTTTAAAAATTTATTCATTTTCAGGAGTTTT
1 TCAAATATTATTATTTATTTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCAAGAGTTTT
* * * * * * * * ** ** * **
6395 TT-GTTTTTCTTTCAAATTCTCATATTTTCGAAATACAGAGTTTTCTGCTTTGTTGACTTTTTCA
66 TTATTTTTTCCTTGAAATTTTCCTATTTTCAAAATACAAAGTTTTCTACTTCATAAATTTTTTTG
* *
6459 GAGGGATTTTTCTTGGTTTTGAATTTTTAAAATCCA
131 GAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * *
6495 T--AA-A--A-TA-TTATTTCATATTAACT-TATTTTTTAAAA--C-TTCA--TTC---A-TTTT
1 TCAAATATTATTATTTATTTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCAAGAGTTTT
* * * * * *
6543 TCATTTTTTTCTCGAAATTTTCCTA-TTTCTTAAATACAAAGCTTTCTACTCCAT-AA-TTTTTT
66 TTATTTTTTCCTTGAAATTTTCCTATTTTC-AAAATACAAAGTTTTCTACTTCATAAATTTTTTT
* *
6605 GGGGGAGATTTTTCTTAGTTTTTAATTTTTAAAATTCA
130 GGAGG-GATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * * *
6643 TCAAATATTATTATTTATTTCATAGTAAATC-TTTTTTAAAAAATTCATTTATTTTCATGAGTTT
1 TCAAATATTATTATTTATTTCATATTAAATCAATTTTT-AAAAATTCATTCATTTTCAAGAGTTT
* * *
6707 TTTATTTTTT-CTTGAAATTTCCCTATTTTCAAAATACGAAA-TTTTCGACTGCATAAATTTTTT
65 TTTATTTTTTCCTTGAAATTTTCCTATTTTCAAAATAC-AAAGTTTTCTACTTCATAAATTTTTT
* * **
6770 TCGAGGGATTTTTATTGGTTTTT--TTTAAAAAAATTCA
129 TGGAGGGATTTTTCTTGGTTTTTAATTT-TTAAAATTCA
* * * **
6807 TCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCATTCA-TTT
1 TCAAATATTATTATTTATTTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCA-AGAGTTT
* * * * ** * *
6871 TTCATTTTTTTACTTGAAATTTTCTTATTTTTGAAAA-ACTGAGTTTTCTACTCCATAAATGTTT
65 TTTA-TTTTTTCCTTGAAATTTTCCTA-TTTTCAAAATACAAAGTTTTCTACTTCATAAATTTTT
* * ** *
6935 TCGGAGGGATTTTTCTTGATTTAAAATTTTTAAAATTTA
128 TTGGAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * * ** * * *
6974 TCTAATATTGTTATTAACCTC-TCATTAAATC-ATTTTCTAAAAATTCAATTTA-TTTCATGAAT
1 TCAAATATTATTATTTATTTCAT-ATTAAATCAATTTT-TAAAAATTC-ATTCATTTTCAAGAGT
*
7036 TTTTAATTTTTT
63 TTTTTATTTTTT
7048 TGTATACATT
Statistics
Matches: 840, Mismatches: 146, Indels: 120
0.76 0.13 0.11
Matches are distributed among these distances:
147 8 0.01
148 40 0.05
149 33 0.04
150 2 0.00
151 1 0.00
152 3 0.00
153 1 0.00
154 6 0.01
155 19 0.02
156 4 0.00
157 9 0.01
158 16 0.02
159 5 0.01
160 2 0.00
161 127 0.15
162 5 0.01
163 9 0.01
164 140 0.17
165 117 0.14
166 93 0.11
167 92 0.11
168 105 0.12
169 3 0.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (166 bp):
TCAAATATTATTATTTATTTCATATTAAATCAATTTTTAAAAATTCATTCATTTTCAAGAGTTTT
TTATTTTTTCCTTGAAATTTTCCTATTTTCAAAATACAAAGTTTTCTACTTCATAAATTTTTTTG
GAGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
Found at i:7381 original size:9 final size:9
Alignment explanation
Indices: 7367--7411 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
7357 AGCAAAAAAA
*
7367 AAAAGAGAG
1 AAAAGAAAG
7376 AAAAGAAAG
1 AAAAGAAAG
7385 AAAAGAAAG
1 AAAAGAAAG
7394 --AAGAAA-
1 AAAAGAAAG
7400 AAAAGAAA-
1 AAAAGAAAG
7408 AAAA
1 AAAA
7412 TAGTGAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
7 6 0.18
8 10 0.30
9 17 0.52
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:7404 original size:20 final size:20
Alignment explanation
Indices: 7360--7411 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
7350 GCAACTCAGC
7360 AAAA-AAAAAAAGAGAGAAA
1 AAAAGAAAAAAAGAGAGAAA
7379 AGAAAGAAAAGAAAGA-AGAAA
1 A-AAAGAAAA-AAAGAGAGAAA
7400 AAAAGAAAAAAA
1 AAAAGAAAAAAA
7412 TAGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 10 0.33
22 5 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAGAGAGAAA
Found at i:15748 original size:21 final size:21
Alignment explanation
Indices: 15724--15763 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
15714 AATCATTCAT
15724 CACGTGTAACTGAATCTTGAC
1 CACGTGTAACTGAATCTTGAC
*
15745 CACGTGTAACTGACTCTTG
1 CACGTGTAACTGAATCTTG
15764 GAACCTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (21 bp):
CACGTGTAACTGAATCTTGAC
Found at i:21901 original size:20 final size:21
Alignment explanation
Indices: 21861--21903 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
21851 AATGATAAAT
*
21861 TCTAGATTTAGATTTTCCATC
1 TCTAGATTTAGATTCTCCATC
*
21882 TCTAGGTTTAG-TTCTCCATC
1 TCTAGATTTAGATTCTCCATC
21902 TC
1 TC
21904 ATCTTTCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.47
Consensus pattern (21 bp):
TCTAGATTTAGATTCTCCATC
Done.