Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3674
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: 17638
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4664 original size:41 final size:40
Alignment explanation
Indices: 4618--4696 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
4608 ATGTATGTTT
* * * *
4618 AACCAACTATAGTGTAGAATCACTCAATACAAAGTACAACA
1 AACCAACTACAATGTAAAACCACTC-ATACAAAGTACAACA
*
4659 AACCAATTACAATGTAAAACCACTCATACAAAGTACAA
1 AACCAACTACAATGTAAAACCACTCATACAAAGTACAA
4697 TGGGCAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 13 0.39
41 20 0.61
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.19
Consensus pattern (40 bp):
AACCAACTACAATGTAAAACCACTCATACAAAGTACAACA
Found at i:11961 original size:21 final size:21
Alignment explanation
Indices: 11921--11961 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11911 TGTTAAGAAA
* *
11921 GAAGTTGCTACTGCAGAAGAT
1 GAAGTTGCTACTGAAAAAGAT
*
11942 GAAGTTGTTACTGAAAAAGA
1 GAAGTTGCTACTGAAAAAGA
11962 AATTGCTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (21 bp):
GAAGTTGCTACTGAAAAAGAT
Found at i:11993 original size:13 final size:13
Alignment explanation
Indices: 11975--12000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11965 TGCTGAAAAG
11975 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
11988 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
12001 GATTCTGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:15038 original size:20 final size:18
Alignment explanation
Indices: 14998--15032 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
14988 TATTGAACCT
14998 AAAATGATAATAGAGAGC
1 AAAATGATAATAGAGAGC
15016 AAAATGATAATAGAGAG
1 AAAATGATAATAGAGAG
15033 TACAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (18 bp):
AAAATGATAATAGAGAGC
Found at i:17135 original size:30 final size:30
Alignment explanation
Indices: 17082--17158 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
17072 TGGTTAACCC
* *
17082 ATCCCTTTTTCGTAATTCAATAACAGAAGTT
1 ATCCC-TTTTCATAATTCAATAACAGAAGCT
* * *
17113 ATCCCTTTTCATAGTTCGATAACCGAAGCT
1 ATCCCTTTTCATAATTCAATAACAGAAGCT
*
17143 ATTCCTTTTCATAATT
1 ATCCCTTTTCATAATT
17159 TGATGGTTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 34 0.87
31 5 0.13
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCAATAACAGAAGCT
Found at i:17199 original size:29 final size:29
Alignment explanation
Indices: 17158--17213 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
17148 TTTTCATAAT
*
17158 TTGATGGTTGTCACCATCCCTTTTCATTG
1 TTGATGGTCGTCACCATCCCTTTTCATTG
17187 TTGATGGTCGTCACCATCCCTTTTCAT
1 TTGATGGTCGTCACCATCCCTTTTCAT
17214 AATCTGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (29 bp):
TTGATGGTCGTCACCATCCCTTTTCATTG
Found at i:17260 original size:30 final size:30
Alignment explanation
Indices: 17113--17360 Score: 163
Period size: 30 Copynumber: 8.4 Consensus size: 30
17103 AACAGAAGTT
* *
17113 ATCCCTTTTCATAGTTCGATAACCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
* * * * ** *
17143 ATTCCTTTTCATAATTTGATGGTTGTCA-CC
1 ATCCCTTTTCATAGTTCGATAGCCG-AAGCC
* * * *
17173 ATCCCTTTTCATTGTT-GATGGTCGTCA-CC
1 ATCCCTTTTCATAGTTCGATAGCCG-AAGCC
* * **
17202 ATCCCTTTTCATA-ATCTGAAAGTTGAAGCC
1 ATCCCTTTTCATAGTTC-GATAGCCGAAGCC
17232 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
* * *
17262 ATCCTTTTTCATAGTTCGAT-GATCGTCA-CC
1 ATCCCTTTTCATAGTTCGATAG-CCG-AAGCC
* *
17292 AT-CCTTTTCATAG-TCGATAGCCAAAGCT
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
* * *
17320 ATCCCTTTTCGTA-TTCGATAGCCGAAACT
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCC
17349 ATCCCTTTTCAT
1 ATCCCTTTTCAT
17361 TTGTCGATGA
Statistics
Matches: 172, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 10 0.06
29 70 0.41
30 87 0.51
31 4 0.02
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATAGCCGAAGCC
Found at i:17268 original size:59 final size:59
Alignment explanation
Indices: 17113--17329 Score: 169
Period size: 59 Copynumber: 3.7 Consensus size: 59
17103 AACAGAAGTT
* * * ** *
17113 ATCCCTTTTCATAGTTCGATAACCGAAGCTATTCCTTTTCATAATTTGATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCCA-TCCTTTTCATAATCTGAAAGTTGTAACC
* * * *
17173 ATCCCTTTTCATTGTT-GATGGTCGTCA-CCATCCCTTTTCATAATCTGAAAGTTG-AAGCC
1 ATCCCTTTTCATAGTTCGATAGCCG-AAGCCAT-CCTTTTCATAATCTGAAAGTTGTAA-CC
* * * *
17232 ATCCCTTTTCATAGTTCGATAGCCGAAGCCATCCTTTTTCATAGT-TCG-ATGATCGTCACC
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCCATCC-TTTTCATAATCT-GAAAG-TTGTAACC
* *
17292 AT-CCTTTTCATAG-TCGATAGCCAAAGCTATCCCTTTTC
1 ATCCCTTTTCATAGTTCGATAGCCGAAGCCAT-CCTTTTC
17330 GTATTCGATA
Statistics
Matches: 127, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
58 22 0.17
59 62 0.49
60 42 0.33
61 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (59 bp):
ATCCCTTTTCATAGTTCGATAGCCGAAGCCATCCTTTTCATAATCTGAAAGTTGTAACC
Found at i:17326 original size:29 final size:30
Alignment explanation
Indices: 17227--17360 Score: 134
Period size: 29 Copynumber: 4.6 Consensus size: 30
17217 CTGAAAGTTG
*
17227 AAGCCATCCCTTTTCATAGTTCGATAGCCG
1 AAGCCATCCCTTTTCATAGTTCGATAGCCA
* * **
17257 AAGCCATCCTTTTTCATAGTTCGATGATCGT
1 AAGCCATCCCTTTTCATAGTTCGAT-AGCCA
*
17288 CA-CCAT-CCTTTTCATAG-TCGATAGCCA
1 AAGCCATCCCTTTTCATAGTTCGATAGCCA
* *
17315 AAGCTATCCCTTTTCGTA-TTCGATAGCCGA
1 AAGCCATCCCTTTTCATAGTTCGATAGCC-A
*
17345 AA-CTATCCCTTTTCAT
1 AAGCCATCCCTTTTCAT
17361 TTGTCGATGA
Statistics
Matches: 86, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.03
28 8 0.09
29 41 0.48
30 31 0.36
31 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.34
Consensus pattern (30 bp):
AAGCCATCCCTTTTCATAGTTCGATAGCCA
Found at i:17356 original size:58 final size:60
Alignment explanation
Indices: 17230--17360 Score: 153
Period size: 58 Copynumber: 2.2 Consensus size: 60
17220 AAAGTTGAAG
* * * **
17230 CCATCCCTTTTCATAGTTCGATAGCCGAAGCCATCCTTTTTCATAGTTCGATGATCGTCA
1 CCATCCCTTTTCATAGTTCGATAGCCAAAGCCATCCCTTTTCATAGTTCGATGACCGAAA
* *
17290 CCAT-CCTTTTCATAG-TCGATAGCCAAAGCTATCCCTTTTCGTA-TTCGAT-AGCCGAAA
1 CCATCCCTTTTCATAGTTCGATAGCCAAAGCCATCCCTTTTCATAGTTCGATGA-CCGAAA
*
17347 CTATCCCTTTTCAT
1 CCATCCCTTTTCAT
17361 TTGTCGATGA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 1 0.02
57 12 0.20
58 33 0.54
59 11 0.18
60 4 0.07
ACGTcount: A:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (60 bp):
CCATCCCTTTTCATAGTTCGATAGCCAAAGCCATCCCTTTTCATAGTTCGATGACCGAAA
Found at i:17358 original size:87 final size:89
Alignment explanation
Indices: 17170--17373 Score: 245
Period size: 87 Copynumber: 2.3 Consensus size: 89
17160 GATGGTTGTC
* ***
17170 ACCATCCCTTTTCATTGTT-GATGGTCGTCACCATCCCTTTTCATAATCTGAAAGTTGAAGCCAT
1 ACCATCCCTTTTCA-TGTTCGATGATCGTCACCATCCCTTTTCATAATCTGAAAGCCAAAGCCAT
17234 CCCTTTTCATAGTTCGATAGCCGAA
65 CCCTTTTCATAGTTCGATAGCCGAA
* * * * *
17259 GCCATCCTTTTTCATAGTTCGATGATCGTCACCAT-CCTTTTCATAGTC-GATAGCCAAAGCTAT
1 ACCATCCCTTTTCAT-GTTCGATGATCGTCACCATCCCTTTTCATAATCTGAAAGCCAAAGCCAT
*
17322 CCCTTTTCGTA-TTCGATAGCCGAA
65 CCCTTTTCATAGTTCGATAGCCGAA
* *
17346 ACTATCCCTTTTCATTTGTCGATGATCG
1 ACCATCCCTTTTCATGT-TCGATGATCG
17374 ACATTATGCC
Statistics
Matches: 98, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
86 1 0.01
87 35 0.36
88 21 0.21
89 27 0.28
90 14 0.14
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.36
Consensus pattern (89 bp):
ACCATCCCTTTTCATGTTCGATGATCGTCACCATCCCTTTTCATAATCTGAAAGCCAAAGCCATC
CCTTTTCATAGTTCGATAGCCGAA
Done.