Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3702
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: 30806
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2942 original size:40 final size:40
Alignment explanation
Indices: 2898--3169 Score: 400
Period size: 40 Copynumber: 6.8 Consensus size: 40
2888 CCAGCATGAT
* * * *
2898 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*** * *
2938 TGCTCTTCAAAACTTAGCCCGGATACATCACTAGTACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
2978 TGCTCTTCGAGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
3018 TGCTCTTCGGGACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
3058 TGCTCTTCGGGACTTAGCTCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
3098 TGCTCTTCAGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
3138 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
3170 CTCAATTCTC
Statistics
Matches: 209, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 209 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:4497 original size:37 final size:37
Alignment explanation
Indices: 4438--4546 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
4428 AGCTCAGACG
* *
4438 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
4475 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
4512 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
4547 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:4816 original size:48 final size:48
Alignment explanation
Indices: 4692--4876 Score: 309
Period size: 48 Copynumber: 3.8 Consensus size: 48
4682 GCACATCGCC
*
4692 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* *
4742 TATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
4790 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
4838 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATA
4877 TGCATGTTCA
Statistics
Matches: 128, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
48 84 0.66
49 2 0.02
50 42 0.33
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:4881 original size:98 final size:97
Alignment explanation
Indices: 4692--4875 Score: 318
Period size: 98 Copynumber: 1.9 Consensus size: 97
4682 GCACATCGCC
*
4692 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATATATTTCACATT
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA-ATACATATTTCACATT
4757 GACCATTCGGCTTTACCACATATGCATATCTCA
65 GACCATTCGGCTTTACCACATATGCATATCTCA
*
4790 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC-ATACATATTTCACATT-
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTG
4853 AGCCATTCGGCTTTACCACATAT
66 A-CCATTCGGCTTTACCACATAT
4876 ATGCATGTTC
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
95 1 0.01
96 36 0.43
98 46 0.55
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (97 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAATACATATTTCACATTG
ACCATTCGGCTTTACCACATATGCATATCTCA
Found at i:4925 original size:47 final size:47
Alignment explanation
Indices: 4846--5039 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
4836 CATACATATT
* * * *
4846 TCACATTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * *
4893 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
4940 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
4987 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
5034 TCACAT
1 TCACAT
5040 AAAATCCTAA
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:4966 original size:22 final size:22
Alignment explanation
Indices: 4939--5010 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
4929 GCTCACATTC
4939 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
4961 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
4985 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
5008 ATC
1 ATC
5011 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:4967 original size:94 final size:94
Alignment explanation
Indices: 4799--5039 Score: 290
Period size: 94 Copynumber: 2.6 Consensus size: 94
4789 ATACATATTT
* * * *
4799 CACATTAGCCATTCGGCTTTA-C-CACATATACATATCTCATACATAT-TTCACATTAGCCATTC
1 CACATTGGCCATTCGGCCTTATCACACATATACACA-CTC--ACAT-TCATCACATTAGCCATTC
* *
4861 GGCTTTACCACATATATGCATGTTCATATTCAC
62 GGCCTTACCACATATATGCATGTTCACATTCAC
* ** *
4894 CACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTGGCCATTCGGCC
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACATTAGCCATTCGGCC
* *
4959 TTATCACATATATGCATGTTCACATTCAT
66 TTACCACATATATGCATGTTCACATTCAC
* * *
4988 CACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACAT
5040 AAAATCCTAA
Statistics
Matches: 127, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
93 1 0.01
94 93 0.73
95 19 0.15
96 4 0.03
97 10 0.08
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (94 bp):
CACATTGGCCATTCGGCCTTATCACACATATACACACTCACATTCATCACATTAGCCATTCGGCC
TTACCACATATATGCATGTTCACATTCAC
Found at i:14678 original size:35 final size:35
Alignment explanation
Indices: 14626--14695 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
14616 AGTCGAAAAG
*
14626 AATAATTTAGGTTTTAGAAGACATGTTACGGTGTT
1 AATAATTTAGGTATTAGAAGACATGTTACGGTGTT
14661 AATAATTT-GGATATTAGAAGACATGTTACGGTGTT
1 AATAATTTAGG-TATTAGAAGACATGTTACGGTGTT
14696 GTGTTCCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (35 bp):
AATAATTTAGGTATTAGAAGACATGTTACGGTGTT
Found at i:16783 original size:49 final size:50
Alignment explanation
Indices: 16654--16843 Score: 158
Period size: 49 Copynumber: 3.9 Consensus size: 50
16644 TCGGCTACGA
* *
16654 GATATGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACATGGATATGT
1 GATA-GTCAGTGTAAGACCATGTCTGGGACATGACATCGACATCGATATGT
* * ** * * *
16705 GAGAG-CTAGTGTAAGACCATCTCTGGGACATGATGTCGGCCTCGAT-TTT
1 GATAGTC-AGTGTAAGACCATGTCTGGGACATGACATCGACATCGATATGT
* * *
16754 GATAGTCAGTGTAAGACCATGTCTAGGACATGGCATCGAC-TTG--ATG-
1 GATAGTCAGTGTAAGACCATGTCTGGGACATGACATCGACATCGATATGT
* * * * *
16800 GATGAGCCAGTGTAAAACCACGTCTGGGACATGGCATCGGCATC
1 GAT-AGTCAGTGTAAGACCATGTCTGGGACATGACATCGACATC
16844 ATACCCTATG
Statistics
Matches: 110, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
46 3 0.03
47 33 0.30
48 3 0.03
49 34 0.31
50 34 0.31
51 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.25
Consensus pattern (50 bp):
GATAGTCAGTGTAAGACCATGTCTGGGACATGACATCGACATCGATATGT
Found at i:17728 original size:34 final size:34
Alignment explanation
Indices: 17685--17791 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
17675 GAGACATGAT
* *
17685 CAAATGCTCGTATTAGCTAATCCATCTAGCACAC
1 CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
*
17719 CAAATGCTCGTATGAGCTAATCGATCCAGCACAC
1 CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
* * *
17753 CAAATGGTTGTATGAGCTAATCCATCCAACACAC
1 CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
17787 CAAAT
1 CAAAT
17792 AACACTGTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (34 bp):
CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
Found at i:19093 original size:79 final size:81
Alignment explanation
Indices: 18961--19185 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
18951 TTGAATGATG
* * * * *
18961 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-ATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGCCCCGAAGGCATTTGTAC-GAGTTACTATAATCCGGACTAAGATCCGAAGGCAT
*
19024 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
*
19041 TCCGGGCTAAG-CCTGAAGGCATTTGTACGAGTTACTA-AATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGCCCCGAAGGCATTTGTACGAGTTACTATAATCCGGACTAAGATCCGAAGGCATT
*
19104 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * *
19120 TCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGCCCCGAAGGCATTTGTACGAGTTACTATAATCCGGACTAAGAT-CCGAAGGCAT
19183 TTG
65 TTG
19186 AACGAGTAGC
Statistics
Matches: 128, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
79 64 0.50
80 62 0.48
81 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGCCCCGAAGGCATTTGTACGAGTTACTATAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:19192 original size:40 final size:40
Alignment explanation
Indices: 18961--19185 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
18951 TTGAATGATG
* * * *
18961 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
19001 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
19041 TCCGGGCTAAG-CCTGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
19080 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
19120 TCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
19161 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
19186 AACGAGTAGC
Statistics
Matches: 157, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
39 33 0.21
40 114 0.73
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:26293 original size:39 final size:40
Alignment explanation
Indices: 26190--26412 Score: 242
Period size: 40 Copynumber: 5.6 Consensus size: 40
26180 TTGAATGATG
* * * *
26190 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
26230 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
26270 TCCGGGCTAAG-CCTGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
26309 TCCGGACTAAAGAT-CCGAAGGCATTT-TGCGAGTTACTAAA
1 TCCGGGCT-AAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
26349 TCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
26390 -CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
26413 GAACGAGTAG
Statistics
Matches: 153, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
39 45 0.29
40 87 0.57
41 21 0.14
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:26420 original size:79 final size:77
Alignment explanation
Indices: 26190--26432 Score: 249
Period size: 79 Copynumber: 3.1 Consensus size: 77
26180 TTGAATGATG
* * * *
26190 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGACTAAGATCCGAAGGCA-T
*
26254 TGTGCGAGATACTAAT
63 TGTGCGAG-TACTAAA
* *
26270 TCCGGGCTAAGCCTGAAGGCATTTGTACGAGTTACTA-AATCCGGACTAAAGATCCGAAGGCATT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGACT-AAGATCCGAAGGCATT
*
26334 TTGCGAGTTACTAAA
64 GTGCGAG-TACTAAA
* * *
26349 TCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATG-TCCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAACCGGACTAAGAT-CCGAAGGCATT
** *
26413 GAACGAGTAGCTATA
64 GTGCGAGTA-CTAAA
26428 TCCGG
1 TCCGG
26433 TTAAATTCCG
Statistics
Matches: 138, Mismatches: 18, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
78 4 0.03
79 71 0.51
80 61 0.44
81 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (77 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATAACCGGACTAAGATCCGAAGGCATTGT
GCGAGTACTAAA
Done.