Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold130
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: 730134
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:704007 original size:79 final size:78
Alignment explanation
Indices: 703925--704224 Score: 333
Period size: 79 Copynumber: 3.8 Consensus size: 78
703915 TTTCACAATC
* *
703925 GGGGATACTCCAACTCCGATTTTA-TTTCTAAAACACCAATTTCTCACAATC-AGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTTCACAATCGA-GGATACTCCA
703988 ATCCCGTTATTTTC-A
64 A-CCCGTTATTTTCGA
* *** * *
704003 CGGGGATGCTCCAACCCCGGCCTTA-TTTCTAAAGCATCAATTTTTCACAATCGAGGATACTCCA
1 -GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTTCACAATCGAGGATACTCCA
*
704067 ACTCCATTATTTTCGA
64 AC-CCGTTATTTTCGA
* * *
704083 GGGGATACTCCAACCCTGATTTTATTTTCAAAACACCAA-TTTTCTATAATC-AGGGATACTTCA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTC-ACAATCGA-GGATACTCCA
*
704146 ACCCTGTTATTTCCGA
64 ACCC-GTTATTTTCGA
* * *
704162 GGGGATACTCCAACCCCGATTTTATTTTCAGAACACCGATTTTTCATAATCGAGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATACTCCA
704225 CCCCCGTTGT
Statistics
Matches: 188, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
78 9 0.05
79 167 0.89
80 12 0.06
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
CCGTTATTTTCGA
Found at i:704095 original size:237 final size:237
Alignment explanation
Indices: 703641--704076 Score: 556
Period size: 237 Copynumber: 1.8 Consensus size: 237
703631 TTAATCGAGG
* * * *
703641 ATACTCCAACTCCGATTTTATTTCTAAAGCATCGATTTACCGCAATCGAGGATACTCCAACTCCG
1 ATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCACAATCGAGGATACTCCAACTCCG
* * *
703706 ATTTTATTTTCAAAACACCAATTTTTCATAATTAGGGATACTCCAACCCCATTATTTCCGAGGGG
66 ATTTTATTTTCAAAACACCAATTTCTCACAATCAGGGATACTCCAACCCCATTATTTCCGAGGGG
* * * ** * * * * *
703771 ATACTCTAACCCCGGCTTTATATCTAAAATATTGATTTTTTATAATCAGGGGTATTCCAACCCCG
131 ATACTCCAACCCCGGCCTTATATCTAAAACATCAATTTTTCACAATCAGGGATACTCCAACCCCA
703836 TTATGTCATCGAGGATACTCCAATCTCGTTATTTCTGAGCGA
196 TTATGTCATCGAGGATACTCCAATCTCGTTATTTCTGAGCGA
* ** *
703878 ATACTCCAAC-CCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAACTCC
1 ATACTCCAACTCC-GATTTTATTTCTAAAACACCAATTTACCACAATCGAGGATACTCCAACTCC
* * *
703942 GATTTTA-TTTCTAAAACACCAATTTCTCACAATCAGGGATACTCCAATCCCGTTATTTTC-ACG
65 GATTTTATTTTC-AAAACACCAATTTCTCACAATCAGGGATACTCCAACCCCATTATTTCCGA-G
* * *
704005 GGGATGCTCCAACCCCGGCCTTATTTCTAAAGCATCAATTTTTCACAATC-GAGGATACTCCAAC
128 GGGATACTCCAACCCCGGCCTTATATCTAAAACATCAATTTTTCACAATCAG-GGATACTCCAAC
*
704069 TCCATTAT
192 CCCATTAT
704077 TTTCGAGGGG
Statistics
Matches: 167, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
236 8 0.05
237 159 0.95
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (237 bp):
ATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTACCACAATCGAGGATACTCCAACTCCG
ATTTTATTTTCAAAACACCAATTTCTCACAATCAGGGATACTCCAACCCCATTATTTCCGAGGGG
ATACTCCAACCCCGGCCTTATATCTAAAACATCAATTTTTCACAATCAGGGATACTCCAACCCCA
TTATGTCATCGAGGATACTCCAATCTCGTTATTTCTGAGCGA
Found at i:704104 original size:158 final size:158
Alignment explanation
Indices: 703925--704224 Score: 398
Period size: 158 Copynumber: 1.9 Consensus size: 158
703915 TTTCACAATC
703925 GGGGATACTCCAACTCCGATTTTA-TTTCTAAAACACCAA-TTTCTCACAATCAGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTTTC-AAAACACCAATTTTCT-ACAATCAGGGATACTCCA
* * * *
703988 ATCCC-GTTATTTTC-ACGGGGATGCTCCAACCCCGGCCTTA-TTTCTA-AAGCATCAATTTTTC
64 A-CCCTGTTATTTCCGA-GGGGATACTCCAACCCCGACCTTATTTTC-AGAA-CACCAATTTTTC
704049 ACAATCGAGGATACTCCAACTCCATTATTTTCGA
125 ACAATCGAGGATACTCCAACTCCATTATTTTCGA
* *
704083 GGGGATACTCCAAC-CCTGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTTCAA
1 GGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAA
** * *
704147 CCCTGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTCAGAACACCGATTTTTCATAAT
65 CCCTGTTATTTCCGAGGGGATACTCCAACCCCGACCTTATTTTCAGAACACCAATTTTTCACAAT
704212 CGAGGATACTCCA
130 CGAGGATACTCCA
704225 CCCCCGTTGT
Statistics
Matches: 125, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
157 5 0.04
158 104 0.83
159 16 0.13
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (158 bp):
GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAAC
CCTGTTATTTCCGAGGGGATACTCCAACCCCGACCTTATTTTCAGAACACCAATTTTTCACAATC
GAGGATACTCCAACTCCATTATTTTCGA
Found at i:705636 original size:2 final size:2
Alignment explanation
Indices: 705629--705660 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
705619 TCATTGTAAA
705629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
705661 TACAATACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:706535 original size:2 final size:2
Alignment explanation
Indices: 706528--706571 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
706518 GTCTTTCTCC
706528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
706570 AT
1 AT
706572 CACAAAATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:707158 original size:3 final size:3
Alignment explanation
Indices: 707144--707194 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
707134 GTAGGTATAG
*
707144 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
707192 ATT
1 ATT
707195 GTTGTTGTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:714964 original size:7 final size:7
Alignment explanation
Indices: 714952--714989 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
714942 AGGAAGAAGA
714952 AAAAAAG
1 AAAAAAG
714959 AAAAAA-
1 AAAAAAG
714965 AAAAGAA-
1 AAAA-AAG
714972 AAAAAAG
1 AAAAAAG
714979 AAAAAAG
1 AAAAAAG
714986 AAAA
1 AAAA
714990 CATCCTGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:714965 original size:11 final size:11
Alignment explanation
Indices: 714945--714989 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
714935 AAATTGGAGG
*
714945 AAGAAGAAAAA
1 AAGAAAAAAAA
714956 AAGAAAAAAAA
1 AAGAAAAAAAA
714967 AAG--AAAAAA
1 AAGAAAAAAAA
714976 AAGAAAAAAGAA
1 AAGAAAAAA-AA
714988 AA
1 AA
714990 CATCCTGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 9 0.30
11 17 0.57
12 4 0.13
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:714974 original size:20 final size:21
Alignment explanation
Indices: 714951--714989 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
714941 GAGGAAGAAG
714951 AAAAAAAGAAAAAA-AAAAGA
1 AAAAAAAGAAAAAAGAAAAGA
714971 AAAAAAAGAAAAAAGAAAA
1 AAAAAAAGAAAAAAGAAAA
714990 CATCCTGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAAAAAGAAAAGA
Found at i:715894 original size:17 final size:17
Alignment explanation
Indices: 715872--715926 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
715862 AATAGAAAGA
*
715872 AATTTTCTTTTCTTTTC
1 AATTTTCTTCTCTTTTC
* *
715889 AATTTTCTCCTCTTCT-
1 AATTTTCTTCTCTTTTC
*
715905 AATTTTC-TCTATTTTC
1 AATTTTCTTCTCTTTTC
715921 AATTTT
1 AATTTT
715927 ATGTGCACTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 5 0.16
16 13 0.42
17 13 0.42
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTTCTTCTCTTTTC
Found at i:716894 original size:3 final size:3
Alignment explanation
Indices: 716886--716930 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
716876 GTATCTTTTT
*
716886 ATA ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
716931 CCAAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:722756 original size:50 final size:50
Alignment explanation
Indices: 722681--722825 Score: 193
Period size: 51 Copynumber: 2.9 Consensus size: 50
722671 AAAAGTCATA
* * * *
722681 TTTTTATCTAGATATATCGATACATTTTCAATGTATCGATACATTTTGTC
1 TTTTTATCCAGATGTATCGATACATTTTCAATGTATCGATACATTCTATC
* * *
722731 TTTTTATCCAGATGTATTGATACATTTTTTAATGTATTGATACATTCTATC
1 TTTTTATCCAGATGTATCGATACA-TTTTCAATGTATCGATACATTCTATC
*
722782 TTTTTATCCAGATGTATCGATACA-TTGCAAATGTATCGATACAT
1 TTTTTATCCAGATGTATCGATACATTTTC-AATGTATCGATACAT
722826 CTAGTTAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.02
50 35 0.43
51 45 0.55
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (50 bp):
TTTTTATCCAGATGTATCGATACATTTTCAATGTATCGATACATTCTATC
Found at i:729008 original size:2 final size:2
Alignment explanation
Indices: 728997--729036 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
728987 CCAAAATCAT
728997 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
729037 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:729041 original size:2 final size:2
Alignment explanation
Indices: 729036--729065 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
729026 TCTCTCTCTC
729036 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
729066 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.