Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3504
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: 45576
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Found at i:1806 original size:28 final size:27
Alignment explanation
Indices: 1737--1914 Score: 114
Period size: 27 Copynumber: 6.6 Consensus size: 27
1727 TATATAAGTC
* *
1737 CGCACACTCAGTGCTAATATAATCAACT
1 CGCACACTTAGTGCT-ACATAATCAACT
* *
1765 CGC-CAATTAGTGCTACCTAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
*
1792 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* ** * *
1819 CGCGGCACTTAGTGCCGC-TATGTCAATT
1 CGC-ACACTTAGTGCTACATA-ATCAACT
* * * **
1847 CGCCCACTTAGTGC-ATATATTCATTT
1 CGCACACTTAGTGCTACATAATCAACT
* *
1873 CGCACACTTTAGTGCAACA-AGATCAA-A
1 CGCACAC-TTAGTGCTACATA-ATCAACT
1900 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1915 GTACAATTAA
Statistics
Matches: 120, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
26 24 0.20
27 52 0.43
28 44 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:9758 original size:27 final size:27
Alignment explanation
Indices: 9728--9905 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
9718 ATATTAAGTC
* * *
9728 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
9755 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
9783 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
9810 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
9837 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
9864 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
9891 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9906 GTACAATTTA
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 106 0.80
28 27 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:17678 original size:27 final size:27
Alignment explanation
Indices: 17646--17822 Score: 203
Period size: 27 Copynumber: 6.6 Consensus size: 27
17636 TATATTAGTC
* * * *
17646 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
17673 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
17700 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
** * *
17727 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
17754 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
17781 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17808 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17823 GTACAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
27 128 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:17784 original size:81 final size:81
Alignment explanation
Indices: 17667--17821 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
17657 TGCTATATAA
* * *
17667 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAACTCGCAC
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
17732 ACTTAGTGCCGCATGG
66 ACTTAGTGCCGCATGG
* * **
17748 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
17812 CACTTAGTGC
65 CACTTAGTGC
17822 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.02
81 65 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:23817 original size:37 final size:37
Alignment explanation
Indices: 23758--23829 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
23748 AGCTCAGACG
*
23758 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
23795 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGA
23830 ATATATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:24099 original size:100 final size:96
Alignment explanation
Indices: 23975--24160 Score: 275
Period size: 100 Copynumber: 1.9 Consensus size: 96
23965 GCACATCGCC
*
23975 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATATTTCACA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTC----ATACATATTTCACA
24040 TT-GACCATTCGACTTTACCACATATGCATATCTCA
62 TTAG-CCATTCGACTTTACCACATATGCATATCTCA
* * *
24075 TACATGTTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
*
24140 CCATTCGATTTTACCACATAT
66 CCATTCGACTTTACCACATAT
24161 ATGCATGTTC
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
96 35 0.44
97 1 0.01
100 44 0.55
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.37
Consensus pattern (96 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTAG
CCATTCGACTTTACCACATATGCATATCTCA
Found at i:24118 original size:48 final size:48
Alignment explanation
Indices: 23975--24161 Score: 250
Period size: 48 Copynumber: 3.8 Consensus size: 48
23965 GCACATCGCC
* *
23975 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATA
1 TACATATTTCACATTAGCCATTCGACTTTACCACATATACATATCTC----A
* *
24027 TATATATTTCACATT-GACCATTCGACTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGACTTTACCACATATACATATCTCA
* * *
24075 TACATGTTTCGCATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGACTTTACCACATATACATATCTCA
*
24123 TACATATTTCACATTAGCCATTCGATTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGACTTTACCACATATA
24162 TGCATGTTCA
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
48 77 0.64
49 1 0.01
51 1 0.01
52 41 0.34
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGACTTTACCACATATACATATCTCA
Found at i:24210 original size:47 final size:47
Alignment explanation
Indices: 24154--24248 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
24144 TCGATTTTAC
* * *
24154 CACATATATGCATGTTCATATTCACCACATTGGCCATTCGGCCTTAT
1 CACACATATGCATGCTCACATTCACCACATTGGCCATTCGGCCTTAT
*
24201 CACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCCTTAT
1 CACACATATGCATGCTCACATTCACCACATTGGCCATTCGGCCTTAT
24248 C
1 C
24249 TCATATATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.32
Consensus pattern (47 bp):
CACACATATGCATGCTCACATTCACCACATTGGCCATTCGGCCTTAT
Found at i:24267 original size:47 final size:47
Alignment explanation
Indices: 24168--24277 Score: 148
Period size: 47 Copynumber: 2.3 Consensus size: 47
24158 TATATGCATG
* * * **
24168 TTCATATTCACCACATTGGCCATTCGGCCTTATCACACATATGCATG
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATACACA
* * *
24215 CTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATACACA
1 TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATACACA
24262 TTCACATTCATCACAT
1 TTCACATTCATCACAT
24278 AAAATCCTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (47 bp):
TTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATACACA
Found at i:26699 original size:85 final size:85
Alignment explanation
Indices: 26570--26750 Score: 344
Period size: 85 Copynumber: 2.1 Consensus size: 85
26560 TATTTTATTG
* *
26570 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCATTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
26635 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
26655 CCCATGCTCATTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCATTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
26720 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
26740 CCCATGCTCAT
1 CCCATGCTCAT
26751 GGCCGGCCAC
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.27, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCATTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:27442 original size:16 final size:16
Alignment explanation
Indices: 27418--27451 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27408 TGGTTCACTT
* *
27418 ATGACATAAATACATC
1 ATGAAATAAAAACATC
27434 ATGAAATAAAAACATC
1 ATGAAATAAAAACATC
27450 AT
1 AT
27452 CAATTCGGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.24
Consensus pattern (16 bp):
ATGAAATAAAAACATC
Found at i:27572 original size:14 final size:15
Alignment explanation
Indices: 27555--27583 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27545 GCACGAAAAT
27555 TTCACACA-AATAAA
1 TTCACACATAATAAA
27569 TTCACACATAATAAA
1 TTCACACATAATAAA
27584 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:29134 original size:27 final size:27
Alignment explanation
Indices: 29104--29281 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29094 ATATTGAGTC
* * * *
29104 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29131 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29158 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29186 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29213 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29240 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29267 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29282 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29243 original size:82 final size:81
Alignment explanation
Indices: 29125--29280 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29115 TGCTATATAA
* *
29125 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29190 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29207 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29271 CACTTAGTGC
65 CACTTAGTGC
29281 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:33403 original size:66 final size:65
Alignment explanation
Indices: 33266--33516 Score: 210
Period size: 68 Copynumber: 3.8 Consensus size: 65
33256 ATATAGTTCG
* * * * *
33266 GCTCTCTTGTAC-ACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGT-TTATCTCG
1 GCTCTCTTGT-CTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACA-TCATATCTCG
33327 TA
64 TA
* * * * *
33329 GCTCTCTTGTCTACATGGTGTCCTTCACTGGAACCACGCATGCGACCTAGCTACAT-ATATCCCG
1 GCTCTCTTGTCTACATGGTGTAC-ACA-TAGAACCACCCATGCGACCTAGCTACATCATATCTCG
33393 TA
64 TA
* *
33395 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTC
1 GCTCTCTTGTCTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATCAT-A--TCTC
33460 GTA
63 GTA
* * * ** *
33463 GCTCTCTTGTAC-ACATGATGTGCAC-TCAGCACCATACATGTGACCTAGCTACAT
1 GCTCTCTTGT-CTACATGGTGTACACAT-AGAACCACCCATGCGACCTAGCTACAT
33517 ACCATCTGTA
Statistics
Matches: 153, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 25 0.16
65 23 0.15
66 32 0.21
67 3 0.02
68 49 0.32
69 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (65 bp):
GCTCTCTTGTCTACATGGTGTACACATAGAACCACCCATGCGACCTAGCTACATCATATCTCGTA
Found at i:34217 original size:30 final size:30
Alignment explanation
Indices: 34183--34243 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
34173 TCCTTAACTC
34183 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
34213 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
34243 A
1 A
34244 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:36625 original size:32 final size:32
Alignment explanation
Indices: 36579--36643 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
36569 GTGTTAAATG
36579 AAATGGAAATGATATCATATTGGAATATGTAT
1 AAATGGAAATGATATCATATTGGAATATGTAT
*
36611 AAATTGAAATGATATCATATTGGAATATGTAT
1 AAATGGAAATGATATCATATTGGAATATGTAT
36643 A
1 A
36644 TTCGACCACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (32 bp):
AAATGGAAATGATATCATATTGGAATATGTAT
Found at i:36632 original size:16 final size:16
Alignment explanation
Indices: 36584--36632 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
36574 AAATGAAATG
36584 GAAATGATATCATATT
1 GAAATGATATCATATT
*
36600 GGAATATG-TAT-AAATT
1 -GAA-ATGATATCATATT
36616 GAAATGATATCATATT
1 GAAATGATATCATATT
36632 G
1 G
36633 GAATATGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 9 0.33
17 6 0.22
18 3 0.11
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (16 bp):
GAAATGATATCATATT
Found at i:37390 original size:40 final size:40
Alignment explanation
Indices: 37342--37467 Score: 177
Period size: 40 Copynumber: 3.2 Consensus size: 40
37332 GGACTAAGAT
37342 CCGAAGGCATTTGTG-GTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCG-AGTGACTATATCCGGGCTAAGTC
*
37382 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
* * *
37422 CCGAAGGCATTTGTGCGAGTTG-TTATATCC-AGCTAAATC
1 CCGAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTC
37461 CCGAAGG
1 CCGAAGG
37468 TACTTGGGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
39 14 0.18
40 63 0.80
41 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTC
Done.