Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2052
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: 42937
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:9984 original size:79 final size:81
Alignment explanation
Indices: 9848--10032 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
9838 TTGAATGATG
* *
9848 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
9912 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
9927 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
9989 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
10007 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
10033 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:10046 original size:40 final size:40
Alignment explanation
Indices: 9849--10032 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
9839 TGAATGATGT
* * * *
9849 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
9889 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
9929 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
9967 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
10008 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
10033 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:10054 original size:79 final size:79
Alignment explanation
Indices: 9901--10065 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
9891 GGACTAAGAT
* * **
9901 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
9966 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
9980 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
10043 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
10059 CCGAAGG
1 CCGAAGG
10066 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:12288 original size:86 final size:86
Alignment explanation
Indices: 12065--12290 Score: 217
Period size: 86 Copynumber: 2.6 Consensus size: 86
12055 TACTCGGAAT
* * *
12065 CACATAAAGCACA-TACAATGCC-ATATCCCAGATATGGTCTTACATGTTATCAC-ATATCGACG
1 CACA-AAATCACACTACAATGCCAATATCCCAGA-ATGGTCTTACATGTAATCACAATATCAACG
* *
12127 CCACTATCCTAGACAGGGTCTTA
64 CCAATATCCCAGACAGGGTCTTA
* * * ** * * * * *
12150 CACGAAATCAAACAATGATGCTAATGTCCCAGAATTGGTCTTACAAGAAATCACAATA-CAATGC
1 CACAAAATCACACTACAATGCCAATATCCCAGAA-TGGTCTTACATGTAATCACAATATCAACGC
* *
12214 CAATGTCCCAGACATGGTCTTA
65 CAATATCCCAGACAGGGTCTTA
* *
12236 TACAAAATCACACTACAATGCCAATATCCCAGACATGGTCTTAGATGTAATCACA
1 CACAAAATCACACTACAATGCCAATATCCCAGA-ATGGTCTTACATGTAATCACA
12291 TCTCGGTAAC
Statistics
Matches: 108, Mismatches: 28, Indels: 9
0.74 0.19 0.06
Matches are distributed among these distances:
84 6 0.06
85 9 0.08
86 89 0.82
87 4 0.04
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (86 bp):
CACAAAATCACACTACAATGCCAATATCCCAGAATGGTCTTACATGTAATCACAATATCAACGCC
AATATCCCAGACAGGGTCTTA
Found at i:12290 original size:43 final size:42
Alignment explanation
Indices: 12074--12278 Score: 184
Period size: 43 Copynumber: 4.8 Consensus size: 42
12064 TCACATAAAG
* * **
12074 CACATACAATGCC-ATATCCCAGATATGGTCTTACATGTTAT
1 CACATACAATGCCAATATCCCAGACATGGTCTTACACGAAAT
* * * * *
12115 CACATATCGACGCCACTATCCTAGACAGGGTCTTACACGAAAT
1 CACATA-CAATGCCAATATCCCAGACATGGTCTTACACGAAAT
* * *
12158 CA-A-ACAATGATGCTAATGTCCCAGA-ATTGGTCTTACAAGAAAT
1 CACATAC-A--ATGCCAATATCCCAGACA-TGGTCTTACACGAAAT
* * *
12201 CACAATACAATGCCAATGTCCCAGACATGGTCTTATACAAAAT
1 CAC-ATACAATGCCAATATCCCAGACATGGTCTTACACGAAAT
12244 CACACTACAATGCCAATATCCCAGACATGGTCTTA
1 CACA-TACAATGCCAATATCCCAGACATGGTCTTA
12279 GATGTAATCA
Statistics
Matches: 131, Mismatches: 22, Indels: 20
0.76 0.13 0.12
Matches are distributed among these distances:
40 1 0.01
41 7 0.05
42 8 0.06
43 110 0.84
44 1 0.01
45 2 0.02
46 2 0.02
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.25
Consensus pattern (42 bp):
CACATACAATGCCAATATCCCAGACATGGTCTTACACGAAAT
Found at i:15962 original size:42 final size:41
Alignment explanation
Indices: 15911--16039 Score: 132
Period size: 42 Copynumber: 3.1 Consensus size: 41
15901 GGATACGACG
*
15911 TTGATATGAGACTTCGTGTAAGACCACATCTAGGACATGGCA
1 TTGATATGAGA-TTCGTGTAAGACCACATCTGGGACATGGCA
* * * *
15953 TTGAAATGAGATTTCGTATAAGACCATATCTGGGATATGGCA
1 TTGATATGAGA-TTCGTGTAAGACCACATCTGGGACATGGCA
* * * * * *
15995 TCGATGTGAGATCCAATGTAAGACCACGTTTGGGACATGGCA
1 TTGATATGAGATTC-GTGTAAGACCACATCTGGGACATGGCA
16037 TTG
1 TTG
16040 GCATCTTATT
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
41 2 0.03
42 67 0.97
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (41 bp):
TTGATATGAGATTCGTGTAAGACCACATCTGGGACATGGCA
Found at i:18654 original size:194 final size:194
Alignment explanation
Indices: 18315--18706 Score: 676
Period size: 194 Copynumber: 2.0 Consensus size: 194
18305 AACGTTTATA
* *
18315 GTAGCCAGCTAGTCCTAGAAAATTGCAGACTTCGGATACATTTCTCAGAGGCTTCCAATCTATTA
1 GTAGCCAGCTAGTCCTAGAAAACTACAGACTTCGGATACATTTCTCAGAGGCTTCCAATCTATTA
*
18380 TTGCAGAAATCTTACTCAGGTCAACACGAATACCCGCAGCTGAAACTATATGCCCCAGAAAACCA
66 TTGCAAAAATCTTACTCAGGTCAACACGAATACCCGCAGCTGAAACTATATGCCCCAGAAAACCA
*
18445 ACCTCAGGAAGCCAAAATTCACATTTGCTAAATTTTGCATACAACTGCTTATCTCGCAGAGTCT
131 ACCTCAGGAAGCCAAAATTCACATTTGCTAAATTTTGCATACAACTACTTATCTCGCAGAGTCT
* *
18509 GTAGCCAGCTAGTCCTAGAAAACTACAGACTTCGGATACATTTGTCGGAGGCTTCCAATCTATTA
1 GTAGCCAGCTAGTCCTAGAAAACTACAGACTTCGGATACATTTCTCAGAGGCTTCCAATCTATTA
* ** *
18574 TTGCAAAAATCTTACTCGGGTCAACTTGAATACCGGCAGCTGAAACTATATGCCCCAGAAAACCA
66 TTGCAAAAATCTTACTCAGGTCAACACGAATACCCGCAGCTGAAACTATATGCCCCAGAAAACCA
* *
18639 ACCTCGGGCAGCCAAAATTCACATTTGCTAAATTTTGCATACAACTACTTATCTCGCAGAGTCT
131 ACCTCAGGAAGCCAAAATTCACATTTGCTAAATTTTGCATACAACTACTTATCTCGCAGAGTCT
18703 GTAG
1 GTAG
18707 TACAATTCTC
Statistics
Matches: 186, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
194 186 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (194 bp):
GTAGCCAGCTAGTCCTAGAAAACTACAGACTTCGGATACATTTCTCAGAGGCTTCCAATCTATTA
TTGCAAAAATCTTACTCAGGTCAACACGAATACCCGCAGCTGAAACTATATGCCCCAGAAAACCA
ACCTCAGGAAGCCAAAATTCACATTTGCTAAATTTTGCATACAACTACTTATCTCGCAGAGTCT
Found at i:25024 original size:48 final size:48
Alignment explanation
Indices: 24969--25219 Score: 287
Period size: 48 Copynumber: 5.2 Consensus size: 48
24959 TGGTCCAGCT
* * * *
24969 ATGGTCTTACACAATG-TCTCATATCGATGCCAATGTCATATCCCAGAT
1 ATGGTCTTACA-AAGGATCTCATATCGATGCCAATGCCATGTCCCAGAC
** *
25017 ATGGTCTTACATGGGATCTCATATCAATGCCAATGCCATGTCCCA-AGC
1 ATGGTCTTACAAAGGATCTCATATCGATGCCAATGCCATGTCCCAGA-C
*
25065 ATGGTCTTAC-ATGGAATCTCATATCGATGCCAAT-CTCATGTCCCAGAC
1 ATGGTCTTACAAAGG-ATCTCATATCGATGCCAATGC-CATGTCCCAGAC
** * *
25113 ATGGTCTTACATGGGATCTCATATCGGTGCCAATGCCATGTCCCAAAC
1 ATGGTCTTACAAAGGATCTCATATCGATGCCAATGCCATGTCCCAGAC
* * *
25161 ATAGTCTTA-AATGGAATCTCATATCGATGCCAATGCCATGTCCTAGAC
1 ATGGTCTTACAAAGG-ATCTCATATCGATGCCAATGCCATGTCCCAGAC
25209 ATGGTCTTACA
1 ATGGTCTTACA
25220 TGGGATCTAA
Statistics
Matches: 173, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
47 8 0.05
48 160 0.92
49 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (48 bp):
ATGGTCTTACAAAGGATCTCATATCGATGCCAATGCCATGTCCCAGAC
Found at i:25089 original size:96 final size:96
Alignment explanation
Indices: 24985--25232 Score: 397
Period size: 96 Copynumber: 2.6 Consensus size: 96
24975 TTACACAATG
* *
24985 TCTCATATCGATGCCAATGTCATATCCCAGATATGGTCTTACATGGGATCTCATATCAATGCCAA
1 TCTCATATCGATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCATATCAATGCCAA
* * *
25050 TGCCATGTCCCAAGCATGGTCTTACATGGAA
66 TGCCATGTCCCAAACATAGTCTTAAATGGAA
* **
25081 TCTCATATCGATGCCAATCTCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGGTGCCAA
1 TCTCATATCGATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCATATCAATGCCAA
25146 TGCCATGTCCCAAACATAGTCTTAAATGGAA
66 TGCCATGTCCCAAACATAGTCTTAAATGGAA
* * *
25177 TCTCATATCGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTAATAT
1 TCTCATATCGATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCATAT
25233 AACCGTAATG
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 140 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (96 bp):
TCTCATATCGATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCATATCAATGCCAA
TGCCATGTCCCAAACATAGTCTTAAATGGAA
Found at i:30347 original size:46 final size:46
Alignment explanation
Indices: 30194--30371 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
30184 TAACCGCCCC
* * *
30194 TAAGTGAACTCGGACTCAACTCAATGAGCTCGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTC-A--A---CGAGTTCGGACATTCGCATCCA
* *
30246 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--TCCA
* *
30292 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
30338 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
30372 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 71 0.66
47 2 0.02
48 4 0.04
49 2 0.02
51 1 0.01
52 22 0.20
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:30822 original size:30 final size:30
Alignment explanation
Indices: 30788--30847 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
30778 ATTTAATACG
30788 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
30818 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
30848 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.