Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3167
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: 14822
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Found at i:1365 original size:37 final size:37
Alignment explanation
Indices: 1315--1393 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1305 TTATTACGAA
* * *
1315 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
1352 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
1389 GTCTT
1 GTCTT
1394 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:1646 original size:47 final size:47
Alignment explanation
Indices: 1510--1974 Score: 682
Period size: 47 Copynumber: 10.1 Consensus size: 47
1500 GCCTTCGGGA
* * * * * * * *
1510 CTTATCACATTTATGCACTTCCACATCCAT-ACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1556 CTTGTCACATATATATAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1602 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1648 CTTATCACACATATACACTTTCACATTCAT--CATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1693 CTTATCACACATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1739 C-TATCACACATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1784 CTTATCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1829 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1876 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1923 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1971 CTTA
1 CTTA
1975 CTATCATTTC
Statistics
Matches: 391, Mismatches: 16, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
44 40 0.10
45 102 0.26
46 93 0.24
47 115 0.29
48 39 0.10
49 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1707 original size:91 final size:93
Alignment explanation
Indices: 1553--1974 Score: 637
Period size: 91 Copynumber: 4.6 Consensus size: 93
1543 TTGGCCACTC
* * *
1553 GGCCTTGTCACATATATATAC-TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 GGCCTTATCACATATATACACTTTCACATTCAT-ACATCGGCCATTAGGCCTTATCACACATATA
*
1617 CACTTTCACATTCATCACATCGGCTATTA
65 CACTTTCACATTCATCACATCGGCCATTA
* *
1646 -GCCTTATCACACATATACACTTTCACATTCAT-CATCGGCTATTAGGCCTTATCACACATATAC
1 GGCCTTATCACATATATACACTTTCACATTCATACATCGGCCATTAGGCCTTATCACACATATAC
1709 ACTTTCACATTCATCACATCGG-CATTA
66 ACTTTCACATTCATCACATCGGCCATTA
*
1736 GGCC-TATCACACATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTAT--CACATATA
1 GGCCTTATCACATATATACACTTTCACATTCAT-ACATCGGCCATTAGGCCTTATCACACATATA
1797 CACTTTCACATTCATCACATCGGCCATTA
65 CACTTTCACATTCATCACATCGGCCATTA
* **
1826 GGCCTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATA
1 GGCCTTATCACATATATACACTTTCACATTCAT-ACATCGGCCATTAGGCCTTATCACACATATA
1891 CACTTTCACATTCATCACATCGGCCATTA
65 CACTTTCACATTCATCACATCGGCCATTA
1920 GGCC-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 GGCCTTATCAC--ATATATACACTTTCACATTCAT-ACATCGGCCATTAGGCCTTA
1975 CTATCATTTC
Statistics
Matches: 306, Mismatches: 12, Indels: 20
0.91 0.04 0.06
Matches are distributed among these distances:
89 31 0.10
90 41 0.13
91 100 0.33
92 36 0.12
93 17 0.06
94 39 0.13
95 42 0.14
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (93 bp):
GGCCTTATCACATATATACACTTTCACATTCATACATCGGCCATTAGGCCTTATCACACATATAC
ACTTTCACATTCATCACATCGGCCATTA
Found at i:1792 original size:136 final size:139
Alignment explanation
Indices: 1510--1974 Score: 667
Period size: 136 Copynumber: 3.4 Consensus size: 139
1500 GCCTTCGGGA
** * * * * * * * * *
1510 CTTATCACATTTATGCACTTCCACATCCATACGTTGGCCACTCGGCCTTGTCACATATATATAC-
1 CTTATCACACATATACACTTTCACATTCATACATCGGCCATTAGGCCTTATCACATATATACACT
1574 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
66 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
1639 GCTATTA-GC
131 GC-ATTAGGC
* *
1648 CTTATCACACATATACACTTTCACATTCAT-CATCGGCTATTAGGCCTTATCACACATATACACT
1 CTTATCACACATATACACTTTCACATTCATACATCGGCCATTAGGCCTTATCACATATATACACT
*
1712 TTCACATTCATCACATCGG-CATTAGGCC-TATCACACATATACACTTTCACATTCATCACATCG
66 TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
1775 GCATTAGGC
131 GCATTAGGC
*
1784 CTTAT--CACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACAC
1 CTTATCACACATATACACTTTCACATTCAT-ACATCGGCCATTAGGCCTTATCACATATATACAC
*
1847 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCACATTCATCACATC
65 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
1912 GGCCATTAGGC
130 GG-CATTAGGC
*
1923 C-TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 CTTATCAC--ACATATACACTTTCACATTCAT-ACATCGGCCATTAGGCCTTA
1975 CTATCATTTC
Statistics
Matches: 296, Mismatches: 20, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
134 23 0.08
135 4 0.01
136 93 0.31
137 43 0.15
138 81 0.27
139 9 0.03
140 1 0.00
142 42 0.14
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (139 bp):
CTTATCACACATATACACTTTCACATTCATACATCGGCCATTAGGCCTTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
GCATTAGGC
Found at i:5525 original size:39 final size:39
Alignment explanation
Indices: 5431--5663 Score: 297
Period size: 39 Copynumber: 5.9 Consensus size: 39
5421 CGAATACACG
* * * * *
5431 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATA
1 TCACTAGCATGAATGCTCTTCGGG-CTTAGCCCGGATACA
* * * * * *
5471 ACACCAGCACGAATGCTCTTCGGGTTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTCGGGCTTAGCCCGGATACA
* *
5510 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGG-GCTTAGCCCGGATACA
5550 TCACTAGCATGAATGCTC-TCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGG-CTTAGCCCGGATACA
*
5589 TCACTAGCATGAATGCTCTTCGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGCTTAGCCCGGATACA
5628 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGA
1 TCACTAGCATGAATGCTCTTCGGG-CTTAGCCCGGA
5664 CATCATTCAA
Statistics
Matches: 172, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 107 0.62
40 65 0.38
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (39 bp):
TCACTAGCATGAATGCTCTTCGGGCTTAGCCCGGATACA
Found at i:5579 original size:79 final size:79
Alignment explanation
Indices: 5444--5663 Score: 318
Period size: 79 Copynumber: 2.8 Consensus size: 79
5434 CCAGCATGAT
* * * * * * * *
5444 TGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGG-TTTAGCACGGATA
1 TGCTCTTC-GGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATA
*
5508 TATCACTAGCACGAA
65 CATCACTAGCACGAA
5523 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATGCTC-TCGGGACTTAGCCCGGATA
1 TGCTCTTCGG-ACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATA
*
5587 CATCACTAGCATGAA
65 CATCACTAGCACGAA
5602 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGA
5664 CATCATTCAA
Statistics
Matches: 128, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
78 41 0.32
79 87 0.68
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.24
Consensus pattern (79 bp):
TGCTCTTCGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATAC
ATCACTAGCACGAA
Found at i:5658 original size:118 final size:119
Alignment explanation
Indices: 5431--5663 Score: 333
Period size: 118 Copynumber: 2.0 Consensus size: 119
5421 CGAATACACG
* * **
5431 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTCGGGT
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGAC
*
5496 TTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
66 TTAGCACGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
* * * * * *
5550 TCACTAGCATGAATGCTC-TCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGAC
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGAC
* * *
5614 TTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGA
66 TTAGCACGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGA
5664 CATCATTCAA
Statistics
Matches: 100, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
118 84 0.84
119 16 0.16
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (119 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACACAACACCAGCACGAATGCTCTTCGGAC
TTAGCACGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
Found at i:6008 original size:29 final size:30
Alignment explanation
Indices: 5974--6048 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
5964 TAATCAACCA
* *
5974 CGCACACTTAGTGCCATGTACTTT-AAA-CT
1 CGCACACTTAGTGCCATGCA-TTTCAAAGCC
6003 CGCACACTTAGTGCCATGCATTTCAAAGCC
1 CGCACACTTAGTGCCATGCATTTCAAAGCC
6033 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
6049 ATCTCACAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
28 3 0.07
29 22 0.52
30 17 0.40
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (30 bp):
CGCACACTTAGTGCCATGCATTTCAAAGCC
Found at i:7987 original size:37 final size:37
Alignment explanation
Indices: 7937--8015 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
7927 TTATTACGAA
* * *
7937 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
7974 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
8011 GTCTT
1 GTCTT
8016 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:8221 original size:47 final size:47
Alignment explanation
Indices: 8134--8606 Score: 723
Period size: 47 Copynumber: 10.1 Consensus size: 47
8124 CCTTTCGGGA
* * * * * * * * *
8134 CTTATCACATTTATGCACTTCCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8181 CTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8228 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
8275 CTTATCACACACATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
8322 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
8369 C-TATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8415 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8462 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8509 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
8556 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
8603 CTTA
1 CTTA
8607 CTATCATTTC
Statistics
Matches: 400, Mismatches: 25, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 0.11
47 355 0.89
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:8555 original size:234 final size:234
Alignment explanation
Indices: 8178--8604 Score: 746
Period size: 234 Copynumber: 1.8 Consensus size: 234
8168 TTGGCCACTC
* *
8178 GGCCTTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
*
8243 CACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACACATACACTTTCACATTCATCAC
66 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACACATACACTTTCACATTCATCAC
* * * *
8308 GTCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGCCTAT
131 ATCGGCCATTAGGCCCTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTAT
8373 CACACATATACACTTTCACATTCATCACGTCGGCTATTA
196 CACACATATACACTTTCACATTCATCACGTCGGCTATTA
*
8412 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATA
1 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
** *
8477 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACGTATATACACTTTCACATTCATCAC
66 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACACATACACTTTCACATTCATCAC
*
8542 ATCGGCCATTAGGCCCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
131 ATCGGCCATTAGGCCCTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
8605 TACTATCATT
Statistics
Matches: 181, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
234 181 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.31
Consensus pattern (234 bp):
GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACACATACACTTTCACATTCATCAC
ATCGGCCATTAGGCCCTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTAT
CACACATATACACTTTCACATTCATCACGTCGGCTATTA
Found at i:11125 original size:46 final size:46
Alignment explanation
Indices: 11075--11248 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 46
11065 GTTGAGCATT
*
11075 CGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* * * *
11121 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TC
* * *
11168 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *
11214 CGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11249 GCGGGTACAT
Statistics
Matches: 106, Mismatches: 13, Indels: 18
0.77 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.58
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Done.