Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1898
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: 33748
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:4004 original size:80 final size:78
Alignment explanation
Indices: 3920--4091 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
3910 GGACTAAGAT
*
3920 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
3983 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
4000 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
4065 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
4079 CCGAAGGCATTTG
1 CCGAAGGCATTTG
4092 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:4082 original size:39 final size:39
Alignment explanation
Indices: 3867--4089 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
3857 TTGAATGCTG
* * * * * *
3867 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
3907 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
3947 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
3987 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
4027 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
4066 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
4090 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:4109 original size:79 final size:80
Alignment explanation
Indices: 3947--4124 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
3937 AGATACAAGT
* * * *
3947 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
4012 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
4027 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
4091 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
4106 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
4125 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:13308 original size:17 final size:17
Alignment explanation
Indices: 13286--13320 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
13276 TGGGGAAGAA
*
13286 GATGATAATTATAATAT
1 GATGATAATTACAATAT
13303 GATGATAATTACAATAT
1 GATGATAATTACAATAT
13320 G
1 G
13321 TTATTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (17 bp):
GATGATAATTACAATAT
Found at i:15501 original size:28 final size:28
Alignment explanation
Indices: 15436--15614 Score: 288
Period size: 28 Copynumber: 6.4 Consensus size: 28
15426 GAGATTGGCG
* * * *
15436 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
15465 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
15493 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
15521 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
15549 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
15577 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
15604 CTGAGTGTGCG
1 CTAAGTGTGCG
15615 GACTTAATAT
Statistics
Matches: 143, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
27 24 0.17
28 104 0.73
29 15 0.10
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:23695 original size:28 final size:28
Alignment explanation
Indices: 23630--23808 Score: 288
Period size: 28 Copynumber: 6.4 Consensus size: 28
23620 GAGATTGGCG
* * * *
23630 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
23659 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
23687 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
23715 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
23743 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
23771 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
23798 CTGAGTGTGCG
1 CTAAGTGTGCG
23809 GACTTAATAT
Statistics
Matches: 143, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
27 24 0.17
28 104 0.73
29 15 0.10
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:25732 original size:62 final size:62
Alignment explanation
Indices: 25666--25790 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
25656 CATATTTGCA
*
25666 TGAACTTGATTGTCACGTATATTTAAAAATATATCAAACGTTTCATTAAAATGAGTCAAACG
1 TGAACTTGATTGTCACGTATATTTAAAAATATATCAAACATTTCATTAAAATGAGTCAAACG
25728 TGAACTTGATTGTCACGTATATTTAAAAATATATCAAACATTTCATTAAAATGAGTCAAACG
1 TGAACTTGATTGTCACGTATATTTAAAAATATATCAAACATTTCATTAAAATGAGTCAAACG
25790 T
1 T
25791 TATAATGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (62 bp):
TGAACTTGATTGTCACGTATATTTAAAAATATATCAAACATTTCATTAAAATGAGTCAAACG
Found at i:29198 original size:96 final size:95
Alignment explanation
Indices: 29029--29355 Score: 356
Period size: 96 Copynumber: 3.4 Consensus size: 95
29019 AAGAGGGTGG
* * * * *
29029 ATTGTCGATGCCATGTTCCAAACATGGTCTTACACTGG-T-TCACATGTCGAAGTCGATGCCATG
1 ATTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAAATGT-G--GCCGATGCCATG
* * * *
29092 TCCCAGACATGATCTTACACTAGCTCTTATCTC
63 TCCCAAACATGGTCTTACACTAGCTCTCATATC
* *
29125 ATTACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTT
1 ATTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-AATGTGGCCGATGCCATGTC
* *
29190 CCAAACATGGTCTTACATTAG-TGCACATATC
65 CCAAACATGGTCTTACACTAGCT-CTCATATC
* ** * *
29221 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACAA-GATCACTGATTCCATGT
1 ATTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-AATG-TGGCCGATGCCATGT
*
29285 CCCAAACATGGTCTTACACTGGCTCTCATATC
64 CCCAAACATGGTCTTACACTAGCTCTCATATC
* * * *
29317 GTGGCCGGTGCCATGCCCCAGACATGGTCTTACACTGGC
1 ATTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGC
29356 ACACATATCA
Statistics
Matches: 196, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
95 2 0.01
96 184 0.94
97 2 0.01
98 4 0.02
99 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (95 bp):
ATTGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAAATGTGGCCGATGCCATGTCC
CAAACATGGTCTTACACTAGCTCTCATATC
Found at i:29294 original size:144 final size:144
Alignment explanation
Indices: 29034--29352 Score: 428
Period size: 144 Copynumber: 2.2 Consensus size: 144
29024 GGTGGATTGT
* * * *
29034 CGATGCCATGTTCCAAACATGGTCTTACACTGGTTCACATGTCGAAGTCGATGCCATGTCCCAGA
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGTGCACATATCGAAGCCGATGCCATGTCCCAGA
* * * *
29099 CATGATCTTACACTAGCTCTTATCTCATTACCGATGCCATGTCCCAGACATGGTCTTACACTGGC
66 CATGATCTTACACTAGCTCTCATCACATCACCGATGCCATGTCCCAAACATGGTCTTACACTGGC
29164 TCTCATAAT-GTGGC
131 TCTCAT-ATCGTGGC
*
29178 CGATGCCATGTTCCAAACATGGTCTTACATTAGTGCACATATC-AATGCCGATGCCATGTCCCAG
1 CGATGCCATGTTCCAAACATGGTCTTACACTAGTGCACATATCGAA-GCCGATGCCATGTCCCAG
* * * * *
29242 ACATGGTCTTACACTGGCTCTCA-CAAGATCACTGATTCCATGTCCCAAACATGGTCTTACACTG
65 ACATGATCTTACACTAGCTCTCATC-ACATCACCGATGCCATGTCCCAAACATGGTCTTACACTG
29306 GCTCTCATATCGTGGC
129 GCTCTCATATCGTGGC
* ** *
29322 CGGTGCCATGCCCCAGACATGGTCTTACACT
1 CGATGCCATGTTCCAAACATGGTCTTACACT
29353 GGCACACATA
Statistics
Matches: 153, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
143 5 0.03
144 148 0.97
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (144 bp):
CGATGCCATGTTCCAAACATGGTCTTACACTAGTGCACATATCGAAGCCGATGCCATGTCCCAGA
CATGATCTTACACTAGCTCTCATCACATCACCGATGCCATGTCCCAAACATGGTCTTACACTGGC
TCTCATATCGTGGC
Found at i:29355 original size:48 final size:48
Alignment explanation
Indices: 29034--29364 Score: 310
Period size: 48 Copynumber: 6.9 Consensus size: 48
29024 GGTGGATTGT
* * * * * ** *
29034 CGATGCCATGTTCCAAACATGGTCTTACACTGGTTCACATGTCGAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGTGGC
* * * * * **
29082 CGATGCCATGTCCCAGACATGATCTTACACTAGCTCTTATCTCATTAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGTGGC
29130 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCGTGGC
* * * * * *
29178 CGATGCCATGTTCCAAACATGGTCTTACATTAG-TGCACATATCAAT-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-CTCATATC-GTGGC
* * **
29226 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACA-AGATCAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCG-TGGC
* * *
29274 TGATTCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATCGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGTGGC
* * * *
29322 CGGTGCCATGCCCCAGACATGGTCTTACACTGGCACACATATC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATC
29365 ACCCAAATGT
Statistics
Matches: 226, Mismatches: 49, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
47 4 0.02
48 218 0.96
49 4 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCGTGGC
Found at i:29605 original size:18 final size:19
Alignment explanation
Indices: 29563--29605 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
29553 AGTTGGATTT
* *
29563 AGTTTACTAAAAATTTCCT
1 AGTTTACTAAAAATTACCC
*
29582 AGTTTACT-AAACTTACCC
1 AGTTTACTAAAAATTACCC
29600 AGTTTA
1 AGTTTA
29606 GGTTTGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (19 bp):
AGTTTACTAAAAATTACCC
Found at i:31153 original size:18 final size:17
Alignment explanation
Indices: 31126--31160 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
31116 ATAAATAAAC
31126 TTTTAACACAAATCTAA
1 TTTTAACACAAATCTAA
31143 TTTTCAACACAAATCTAA
1 TTTT-AACACAAATCTAA
31161 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (17 bp):
TTTTAACACAAATCTAA
Found at i:33445 original size:45 final size:46
Alignment explanation
Indices: 33381--33555 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
33371 TGTAACCCGC
*
33381 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
33426 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
33476 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
33519 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
33556 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 36 0.32
46 29 0.26
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:33546 original size:93 final size:92
Alignment explanation
Indices: 33388--33558 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 92
33378 CGCCCATAAG
*
33388 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
33453 CGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
33480 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
33545 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
33559 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 28 0.37
93 48 0.63
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Done.