Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2720
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: 38163
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Found at i:306 original size:28 final size:27
Alignment explanation
Indices: 181--336 Score: 120
Period size: 28 Copynumber: 5.6 Consensus size: 27
171 GTACGTAATC
*
181 AATCGCACACTTAGTGCGCTACATACGTTC-
1 AATCGCACACTTAGT--GCAACATA-G-TCA
* ** *
211 AACCGCACACTTAGTGCCGCATGGTC-
1 AATCGCACACTTAGTGCAACATAGTCA
* * *
237 ATTCGCACACTTAGTGCATTCAT-TTCA
1 AATCGCACACTTAGTGCA-ACATAGTCA
**
264 TGTCGCAACACTTAGTGCAACATAGTCCA
1 AATCGC-ACACTTAGTGCAACATAGT-CA
* *
293 AATCGCACATTTAGTGCTACATAGTCA
1 AATCGCACACTTAGTGCAACATAGTCA
320 AATCGCACACTTAGTGC
1 AATCGCACACTTAGTGC
337 TGTAAATTAC
Statistics
Matches: 103, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
26 19 0.18
27 29 0.28
28 35 0.34
29 6 0.06
30 14 0.14
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (27 bp):
AATCGCACACTTAGTGCAACATAGTCA
Found at i:8509 original size:27 final size:27
Alignment explanation
Indices: 8472--8668 Score: 215
Period size: 27 Copynumber: 7.4 Consensus size: 27
8462 TAAATTGTAC
8472 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
8499 AGCACTAAGTGT-CGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
8525 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8551 ATGCACT-A--GTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
8576 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
8604 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
8631 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
8658 AGCACTGAGTG
1 AGCACTAAGTG
8669 AGCGGACTCA
Statistics
Matches: 144, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
24 18 0.12
25 1 0.01
26 26 0.18
27 76 0.53
28 23 0.16
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:11618 original size:26 final size:26
Alignment explanation
Indices: 11589--11641 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
11579 CTGTCTATTG
11589 TTTCATCAGATGTGATTGGAATGCTT
1 TTTCATCAGATGTGATTGGAATGCTT
11615 TTTCATCAGATGTGATTGGAATGCTT
1 TTTCATCAGATGTGATTGGAATGCTT
11641 T
1 T
11642 CCTTGGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (26 bp):
TTTCATCAGATGTGATTGGAATGCTT
Found at i:24154 original size:21 final size:21
Alignment explanation
Indices: 24107--24148 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
24097 TCGTGGTAAC
24107 GAGTTCAACCACTATTTAGCT
1 GAGTTCAACCACTATTTAGCT
*
24128 GAGTTCAACCACTGTTTAGCT
1 GAGTTCAACCACTATTTAGCT
24149 TTGTTCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (21 bp):
GAGTTCAACCACTATTTAGCT
Found at i:26827 original size:79 final size:79
Alignment explanation
Indices: 26691--26914 Score: 220
Period size: 79 Copynumber: 2.8 Consensus size: 79
26681 TTGAATGCTG
* * * * * * * *
26691 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGAGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
26755 TGTGCGAGATA-CAAGT
64 TGTGCGAGATATCAA-A
* * * * *
26771 TCCGGGTTAAG-CCCGAAGGCCTTTGAGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CATTGAGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* *
26835 GTGCGAGTTATTAAA
65 GTGCGAGATATCAAA
* * *
26850 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGAGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
26915 AACGAGGAGC
Statistics
Matches: 120, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 1 0.01
79 92 0.77
80 27 0.22
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:26841 original size:40 final size:40
Alignment explanation
Indices: 26691--26914 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
26681 TTGAATGCTG
* * *
26691 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
26731 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
* * * *
26771 TCCGGGTTAAG-CCCGAAGGCCTTTGAGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
26810 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
26850 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
26889 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
26915 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
39 64 0.41
40 83 0.54
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:26932 original size:79 final size:80
Alignment explanation
Indices: 26771--26947 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
26761 AGATACAAGT
* * * *
26771 TCCGGGTTAAG-CCCGAAGGCCTTTGAGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGAGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
26835 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
26850 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGAGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
26914 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
26929 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
26948 TACGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 16 0.20
79 58 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGAGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:34352 original size:40 final size:40
Alignment explanation
Indices: 34228--34479 Score: 196
Period size: 40 Copynumber: 6.7 Consensus size: 40
34218 TTGAATGCTG
* * * * *
34228 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAA
** * * *
34268 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAA-A
* *
34308 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
*
34348 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
34388 TCC-GGTTAAGT--C----G----T-T-CGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
34415 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
34454 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
34480 AACGAGGAGC
Statistics
Matches: 171, Mismatches: 23, Indels: 36
0.74 0.10 0.16
Matches are distributed among these distances:
27 15 0.09
28 9 0.05
30 1 0.01
33 1 0.01
34 1 0.01
37 2 0.01
38 1 0.01
39 38 0.22
40 93 0.54
41 10 0.06
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
Found at i:34401 original size:27 final size:28
Alignment explanation
Indices: 34371--34427 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
34361 CCGAAGGCAT
34371 TCGTGCGAGTTATTAAATCC-GGTTAAG
1 TCGTGCGAGTTATTAAATCCGGGTTAAG
*
34398 TCGTTCGAGTTATTAAATCCGGGTTAAG
1 TCGTGCGAGTTATTAAATCCGGGTTAAG
34426 TC
1 TC
34428 CCGAAGGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (28 bp):
TCGTGCGAGTTATTAAATCCGGGTTAAG
Found at i:34497 original size:106 final size:107
Alignment explanation
Indices: 34308--34502 Score: 250
Period size: 106 Copynumber: 1.8 Consensus size: 107
34298 AGATACAAGT
* * * *
34308 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGCCCCGAAGGCCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
34373 GTGCGAGTTATTAAATCCGGTTAAGTCGTTCGAGTTATTAAA
66 GAACGAGTGACTAAATCCGGTTAAGTCGTTCGAGTTATTAAA
* * * *
34415 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGCCCCGAAGGCCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
34479 GAACGAG-GAGCTATATCCGGTTAA
66 GAACGAGTGA-CTAAATCCGGTTAA
34503 ATCCCGAAGG
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
105 1 0.01
106 54 0.73
107 19 0.26
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (107 bp):
TCCGGGTTAAGCCCCGAAGGCCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAATCCGGTTAAGTCGTTCGAGTTATTAAA
Found at i:36970 original size:43 final size:42
Alignment explanation
Indices: 36922--37087 Score: 181
Period size: 43 Copynumber: 3.9 Consensus size: 42
36912 GTTACTGAGA
* *
36922 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATTGTCT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT-T
*
36965 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTT
** * * * * *
37007 AATCGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATA
1 TGT-GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TT
* * *
37051 TGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
37088 TGTACGAGCT
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
42 8 0.08
43 94 0.90
44 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (42 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTT
Done.