Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1463
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: 34411
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Found at i:11583 original size:47 final size:47
Alignment explanation
Indices: 11505--11914 Score: 624
Period size: 47 Copynumber: 8.6 Consensus size: 47
11495 CCCTTCGGGA
* * * * * *
11505 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
11551 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
11599 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11646 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11693 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
11742 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11789 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
11840 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACA--TATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
11889 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
11915 CACAATTATC
Statistics
Matches: 338, Mismatches: 16, Indels: 19
0.91 0.04 0.05
Matches are distributed among these distances:
46 2 0.01
47 194 0.57
48 2 0.01
49 94 0.28
51 46 0.14
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:11739 original size:96 final size:96
Alignment explanation
Indices: 11505--11914 Score: 645
Period size: 96 Copynumber: 4.3 Consensus size: 96
11495 CCCTTCGGGA
* * * * * *
11505 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATATATA
11567 CACTTTCACATTCATCACATCGGCCATTAGGC
65 CACTTTCACATTCATCACATCGGCCATTAGGC
* *
11599 CTCATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
11662 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
11693 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
11758 ACTTTCACATTCATCACATCGGCCATTAGAC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
11789 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATGTAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA--TAT
11854 ATACACTTTCACATTCATCACATCGGCCATTAGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
11889 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
11915 CACAATTATC
Statistics
Matches: 295, Mismatches: 12, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
93 1 0.00
94 87 0.29
95 2 0.01
96 99 0.34
98 61 0.21
100 45 0.15
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:14623 original size:20 final size:20
Alignment explanation
Indices: 14598--14637 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14588 GTGACATTTC
14598 TCACCAAATAGATAGTGGCG
1 TCACCAAATAGATAGTGGCG
14618 TCACCAAATAGATAGTGGCG
1 TCACCAAATAGATAGTGGCG
14638 CCAAATCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (20 bp):
TCACCAAATAGATAGTGGCG
Found at i:14643 original size:17 final size:18
Alignment explanation
Indices: 14600--14643 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
14590 GACATTTCTC
14600 ACCAAATAGATAGTGGCG
1 ACCAAATAGATAGTGGCG
14618 TCACCAAATAGATAGTGGCG
1 --ACCAAATAGATAGTGGCG
14638 -CCAAAT
1 ACCAAAT
14644 CTTCAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
20 18 0.75
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (18 bp):
ACCAAATAGATAGTGGCG
Found at i:21250 original size:42 final size:42
Alignment explanation
Indices: 21189--21352 Score: 186
Period size: 42 Copynumber: 3.7 Consensus size: 42
21179 CTTCGTTTTC
**
21189 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATCTTCACAT-A
* *
21232 T-GATGCCATAGCCCAACTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATCTTCACATA
*
21273 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATGACATATCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC---AT--C-T-TCACATA
* *
21322 TCGATGCCATAACCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAACTATGGTCTTACAC
21353 GAATCACATA
Statistics
Matches: 105, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
41 2 0.02
42 63 0.60
43 1 0.01
45 2 0.02
48 1 0.01
49 36 0.34
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATCTTCACATA
Found at i:21338 original size:49 final size:49
Alignment explanation
Indices: 21260--21441 Score: 198
Period size: 49 Copynumber: 3.8 Consensus size: 49
21250 ATGGTCTTAC
* * *
21260 ACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATG
1 ACATA-TCACATATCGATGCCATATCCCAGATATGGTCTTACACGTAATG
* * *
21310 ACATATCACATATCGATGCCATAACCCAGCTATGGTCTTACACG-AATC
1 ACATATCACATATCGATGCCATATCCCAGATATGGTCTTACACGTAATG
* * *
21358 ACATATCTCA-CT-GATGCCATATCCCAGATATGGTCTTATACAGT-A-G
1 ACATATCACATATCGATGCCATATCCCAGATATGGTCTTACAC-GTAATG
*
21404 -CATAT-ATCACATCGATGCCATATCCCAGATATGGTCTT
1 ACATATCA-CATATCGATGCCATATCCCAGATATGGTCTT
21442 GTACGGAAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
45 7 0.06
46 27 0.23
47 28 0.24
48 12 0.10
49 37 0.32
50 5 0.04
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (49 bp):
ACATATCACATATCGATGCCATATCCCAGATATGGTCTTACACGTAATG
Found at i:21426 original size:47 final size:48
Alignment explanation
Indices: 21272--21441 Score: 181
Period size: 47 Copynumber: 3.6 Consensus size: 48
21262 ATATTCATAT
* * *
21272 ATCGATGCCATAGCCCAGCTATGGTCTTACAC-GTAATGACATATCA-CAT
1 ATCGATGCCATATCCCAGATATGGTCTTACACAGTAA-G-CATAT-ATCAC
* * * * *
21321 ATCGATGCCATAACCCAGCTATGGTCTTACAC-G-AATCACATATCTC
1 ATCGATGCCATATCCCAGATATGGTCTTACACAGTAAGCATATATCAC
*
21367 A-CTGATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC
1 ATC-GATGCCATATCCCAGATATGGTCTTACACAGTAAGCATATATCAC
21414 ATCGATGCCATATCCCAGATATGGTCTT
1 ATCGATGCCATATCCCAGATATGGTCTT
21442 GTACGGAAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
45 2 0.02
46 32 0.30
47 36 0.34
48 3 0.03
49 32 0.30
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (48 bp):
ATCGATGCCATATCCCAGATATGGTCTTACACAGTAAGCATATATCAC
Found at i:21540 original size:31 final size:31
Alignment explanation
Indices: 21464--21550 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
21454 CTTGTCACTT
* * *
21464 GTAGCCGAAGCTACCACTATTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAC
* *
21495 GTAGTCGGTA-CTACCACTTTTCACTGATCAC
1 GTAG-CCGAAGCTACCACTTTTCACTGATCAC
21526 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
21551 TGTCATTTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 3 0.06
31 41 0.87
32 3 0.06
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAC
Found at i:21638 original size:50 final size:50
Alignment explanation
Indices: 21526--21702 Score: 275
Period size: 50 Copynumber: 3.5 Consensus size: 50
21516 CACTGATCAC
* *
21526 GTAGCCGAAGCTACCACTTTTCACTTGTCA-TTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTACCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
*
21577 GTAGCCGAAGCTACCACTTATCACTTTCACTTTTCCTTGATTAGATAAGT
1 GTAGCCGAAGCTACCACTTATCACTTTCACTTTTCCTTGATCAGATAAGT
* *
21627 GTAGCCGAAGCTATCACTTATCACTTTCACTTTTCCTTGATCAGAAAAGT
1 GTAGCCGAAGCTACCACTTATCACTTTCACTTTTCCTTGATCAGATAAGT
*
21677 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTACCACTTATCACTT
21703 GTTTCCATGG
Statistics
Matches: 119, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
50 91 0.76
51 28 0.24
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (50 bp):
GTAGCCGAAGCTACCACTTATCACTTTCACTTTTCCTTGATCAGATAAGT
Found at i:25234 original size:20 final size:20
Alignment explanation
Indices: 25209--25256 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
25199 AATAGGGGTC
25209 ACACACCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
25229 ACACACCCGTGTGGCTTGGG
1 ACACACCCGTGTGGCTTGGG
25249 ACACACCC
1 ACACACCC
25257 ATATGGGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.17
Consensus pattern (20 bp):
ACACACCCGTGTGGCTTGGG
Found at i:27529 original size:64 final size:64
Alignment explanation
Indices: 27455--27595 Score: 178
Period size: 64 Copynumber: 2.2 Consensus size: 64
27445 CATTAATTAT
* * * * *
27455 ATATGTACTTACCATACATGCAATA-TTAAAGCACTTAAAGTATG-GTACATATTGCATAATTTG
1 ATATGAACTTACCATAAATGCAATATTTAAA-CACTTAAAATA-GAGTACATATTGCATAACTCG
27518 C
64 C
* * *
27519 ATATGAACTTACCATAAATGCAATATTTAAACATTTAAAATAGATTACATATTGCATTACTCGC
1 ATATGAACTTACCATAAATGCAATATTTAAACACTTAAAATAGAGTACATATTGCATAACTCGC
27583 ATATGAACTTACC
1 ATATGAACTTACC
27596 CCGATACTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.01
64 61 0.91
65 5 0.07
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (64 bp):
ATATGAACTTACCATAAATGCAATATTTAAACACTTAAAATAGAGTACATATTGCATAACTCGC
Found at i:30305 original size:33 final size:34
Alignment explanation
Indices: 30236--30306 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 34
30226 AACAGTGCAT
* * *
30236 ACAGTAACGGTCTGGGCCTAAGCCCTATTCATTA
1 ACAGTAACAGTCTGGGCCTAAGCCCTATGCAGTA
* *
30270 ACAGT-ACAGTCTTGGCCTAAGCCCTCTGCAGTA
1 ACAGTAACAGTCTGGGCCTAAGCCCTATGCAGTA
30303 ACAG
1 ACAG
30307 AGTTGGCCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (34 bp):
ACAGTAACAGTCTGGGCCTAAGCCCTATGCAGTA
Found at i:33175 original size:26 final size:25
Alignment explanation
Indices: 33144--33211 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 25
33134 CTAGTGGCTA
33144 TGCCACAAATTATCTGTTCTAGT-GC-C
1 TGCCACAAA-TATCTGTT-T-GTGGCAC
**
33170 TGCCACGTATATCTGTTTGTGGCAC
1 TGCCACAAATATCTGTTTGTGGCAC
33195 TGCCACAAAATATCTGT
1 TGCCAC-AAATATCTGT
33212 ATCTGGTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 2 0.06
24 3 0.09
25 15 0.43
26 15 0.43
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (25 bp):
TGCCACAAATATCTGTTTGTGGCAC
Done.