Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1519
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: 40358
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Found at i:2917 original size:27 final size:27
Alignment explanation
Indices: 2887--2950 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
2877 ATAAGTTCGG
* *
2887 CACATAGCCATGGATAAATATGATCGA
1 CACATAGCCATCGATAAATATGATAGA
* * * *
2914 CACAGAGTCATCGATAAATTTGATAGG
1 CACATAGCCATCGATAAATATGATAGA
2941 CACATAGCCA
1 CACATAGCCA
2951 AGGGTAAGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (27 bp):
CACATAGCCATCGATAAATATGATAGA
Found at i:4212 original size:27 final size:27
Alignment explanation
Indices: 4165--4220 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
4155 GACAATGAAA
* *
4165 ATCGACACACAGCCATGGATAAATATG
1 ATCGACACACAGCCATCGATAAAAATG
* *
4192 ATCGACACAGAGTCATCGATAAAAATG
1 ATCGACACACAGCCATCGATAAAAATG
4219 AT
1 AT
4221 AGGCACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (27 bp):
ATCGACACACAGCCATCGATAAAAATG
Found at i:4731 original size:54 final size:51
Alignment explanation
Indices: 4673--4848 Score: 138
Period size: 54 Copynumber: 3.3 Consensus size: 51
4663 TTTACCCTAT
*
4673 AGGGGTATTTCGGTAATTTTACACCACAAAGGTATTTCGATAATTTTACAAATC
1 AGGGGTATTTCGGTAATTTTACA-AAC-AAGGTATTTC-ATAATTTTACAAATC
* * * * * *
4727 AGGGGTATTTTGGTTATTTCACAAATTCAGGGTATTTCAGTAATTCCT-CAAATT
1 AGGGGTATTTCGGTAATTTTACAAA--CAAGGTATTTCA-TAATT-TTACAAATC
* * ** *
4781 AGGGGTATTTCAGAAATTTTACAAACCGTGTGTATTTCAATAATTTTACAAGTC
1 AGGGGTATTTCGGTAATTTTACAAA-CAAG-GTATTTC-ATAATTTTACAAATC
*
4835 GGGGGTATTTCGGT
1 AGGGGTATTTCGGT
4849 CCTATTGGTG
Statistics
Matches: 94, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
53 5 0.05
54 86 0.91
55 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (51 bp):
AGGGGTATTTCGGTAATTTTACAAACAAGGTATTTCATAATTTTACAAATC
Found at i:4733 original size:27 final size:27
Alignment explanation
Indices: 4673--4846 Score: 117
Period size: 27 Copynumber: 6.4 Consensus size: 27
4663 TTTACCCTAT
* *
4673 AGGGGTATTTCGGTAATTTTACACCA-C
1 AGGGGTATTTCGATAATTTTACA-AATC
**
4700 AAAGGTATTTCGATAATTTTACAAATC
1 AGGGGTATTTCGATAATTTTACAAATC
* * * *
4727 AGGGGTATTTTGGTTATTTCACAAATTC
1 AGGGGTATTTCGATAATTTTACAAA-TC
* *
4755 A-GGGTATTTC-AGTAATTCCT-CAAATT
1 AGGGGTATTTCGA-TAATT-TTACAAATC
4781 AGGGGTATTTCAGA-AATTTTACAAA-C
1 AGGGGTATTTC-GATAATTTTACAAATC
* * * *
4807 CGTGTGTATTTCAATAATTTTACAAGTC
1 AG-GGGTATTTCGATAATTTTACAAATC
*
4835 GGGGGTATTTCG
1 AGGGGTATTTCG
4847 GTCCTATTGG
Statistics
Matches: 111, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
26 6 0.05
27 99 0.89
28 5 0.05
29 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (27 bp):
AGGGGTATTTCGATAATTTTACAAATC
Found at i:6375 original size:27 final size:27
Alignment explanation
Indices: 6318--6488 Score: 82
Period size: 27 Copynumber: 6.3 Consensus size: 27
6308 ACCCTATAGG
* *
6318 GGTATTTCGGTAATTTTAC-ACTACA-A
1 GGTATTTCGATAATTTTACAAAT-CAGA
6344 GGGTATTTCGATAATTTTACAAATCAGA
1 -GGTATTTCGATAATTTTACAAATCAGA
* * * * *
6372 GGTATTTTGGTAATTTCAAAAATTA-A
1 GGTATTTCGATAATTTTACAAATCAGA
* ** * *
6398 GGGTATTTC-AGTTATTCCACAAATTAGG
1 -GGTATTTCGA-TAATTTTACAAATCAGA
* * * *
6426 GGTGTTTCAAAAATTTTACAAACCATG-
1 GGTATTTCGATAATTTTACAAATCA-GA
* * * *
6453 GGTATTTCAATAATTTTACAAGTCGGG
1 GGTATTTCGATAATTTTACAAATCAGA
6480 GGTATTTCG
1 GGTATTTCG
6489 GTCCTATTGG
Statistics
Matches: 110, Mismatches: 26, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
26 2 0.02
27 103 0.94
28 5 0.05
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTATTTCGATAATTTTACAAATCAGA
Found at i:8013 original size:54 final size:52
Alignment explanation
Indices: 7955--8130 Score: 158
Period size: 54 Copynumber: 3.3 Consensus size: 52
7945 TTCACCCTAT
*
7955 AGGGGTATTTCGGTAATTTTACACTACAAGTGTATTTCGATAATTTTACAAATC
1 AGGGGTATTTCGGTAATTTTACAC-ACGAG-GTATTTCGATAATTTTACAAATC
* * * * * * * *
8009 AGGGGTATTTTGGTAATTTCAAAAATCGAGGATATTTTGGTAATTTCACAAATT
1 AGGGGTATTTCGGTAATTTTACACA-CGAGG-TATTTCGATAATTTTACAAATC
* * *
8063 AGGGGTGA-TTCGGTAATTTTACAACCCGAGGGTATTTCAATAATTTTACAAGTC
1 AGGGGT-ATTTCGGTAATTTTAC-ACACGA-GGTATTTCGATAATTTTACAAATC
8117 -GGGGCTATTTCGGT
1 AGGGG-TATTTCGGT
8131 CCTATTGGTG
Statistics
Matches: 95, Mismatches: 20, Indels: 14
0.74 0.16 0.11
Matches are distributed among these distances:
53 7 0.07
54 84 0.88
55 4 0.04
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.37
Consensus pattern (52 bp):
AGGGGTATTTCGGTAATTTTACACACGAGGTATTTCGATAATTTTACAAATC
Found at i:8016 original size:27 final size:27
Alignment explanation
Indices: 7955--8130 Score: 128
Period size: 27 Copynumber: 6.5 Consensus size: 27
7945 TTCACCCTAT
*
7955 AGGGGTATTTCGGTAATTTTAC-ACTAC
1 AGGGGTATTTCGGTAATTTTACAAAT-C
* * *
7982 AAGTGTATTTCGATAATTTTACAAATC
1 AGGGGTATTTCGGTAATTTTACAAATC
* * *
8009 AGGGGTATTTTGGTAATTTCAAAAATC
1 AGGGGTATTTCGGTAATTTTACAAATC
* * * *
8036 -GAGGATATTTTGGTAATTTCACAAATT
1 AG-GGGTATTTCGGTAATTTTACAAATC
*
8063 AGGGGTGA-TTCGGTAATTTTAC-AACC
1 AGGGGT-ATTTCGGTAATTTTACAAATC
* ** *
8089 CGAGGGTATTTCAATAATTTTACAAGTC
1 AG-GGGTATTTCGGTAATTTTACAAATC
8117 -GGGGCTATTTCGGT
1 AGGGG-TATTTCGGT
8131 CCTATTGGTG
Statistics
Matches: 116, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
26 8 0.07
27 102 0.88
28 6 0.05
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.37
Consensus pattern (27 bp):
AGGGGTATTTCGGTAATTTTACAAATC
Found at i:8333 original size:10 final size:10
Alignment explanation
Indices: 8299--8323 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
8289 AGCCCATTGG
8299 GCCCACTTCA
1 GCCCACTTCA
8309 GCCCACTTCA
1 GCCCACTTCA
8319 GCCCA
1 GCCCA
8324 TTGAGGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.52, G:0.12, T:0.16
Consensus pattern (10 bp):
GCCCACTTCA
Found at i:9121 original size:25 final size:26
Alignment explanation
Indices: 9093--9143 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
9083 TGAAAATCGG
*
9093 GACAC-AGCCATGGATAAATATGATC
1 GACACAAGCCATCGATAAATATGATC
*
9118 GACACAGAGTCATCGATAAATATGAT
1 GACACA-AGCCATCGATAAATATGAT
9144 AGGCACATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
27 17 0.77
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.22
Consensus pattern (26 bp):
GACACAAGCCATCGATAAATATGATC
Found at i:9658 original size:27 final size:27
Alignment explanation
Indices: 9601--9772 Score: 104
Period size: 27 Copynumber: 6.4 Consensus size: 27
9591 CCCTATAGGG
* *
9601 GTATTTAGGTAATTTTAC-ACTACAAGG-
1 GTATTTCGGTAATTTTACAAAT-C-AGGA
*
9628 GTATTTCGATAATTTTACAAATCAGGA
1 GTATTTCGGTAATTTTACAAATCAGGA
* * * *
9655 GTATTTTGGTAATTTCAAAAATAGAGGA
1 GTATTTCGGTAATTTTACAAAT-CAGGA
* *
9683 -TATTTCGGTAATTTCACAAATTATGGA
1 GTATTTCGGTAATTTTACAAATCA-GGA
* **
9710 -TATTTTGGTAATTTTACAACCCGAGG-
1 GTATTTCGGTAATTTTACAAATC-AGGA
** * *
9736 GTATTTCAATAATTTTACAAGTC-GGG
1 GTATTTCGGTAATTTTACAAATCAGGA
9762 GCTATTTCGGT
1 G-TATTTCGGT
9773 CCCATTGGTG
Statistics
Matches: 114, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
25 2 0.02
26 5 0.04
27 100 0.88
28 7 0.06
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (27 bp):
GTATTTCGGTAATTTTACAAATCAGGA
Found at i:9659 original size:54 final size:55
Alignment explanation
Indices: 9601--9755 Score: 165
Period size: 54 Copynumber: 2.9 Consensus size: 55
9591 CCCTATAGGG
* *
9601 GTATTTAGGTAATTTTACACTACAAGGGTATTTCGATAATTTTACAAATCA-GGA
1 GTATTTTGGTAATTTTACACTACGAGGGTATTTCGATAATTTTACAAATCATGGA
* * * * * * *
9655 GTATTTTGGTAATTTCAAAAATA-GAGGATATTTCGGTAATTTCACAAATTATGGA
1 GTATTTTGGTAATTT-TACACTACGAGGGTATTTCGATAATTTTACAAATCATGGA
* *
9710 -TATTTTGGTAATTTTACAAC-CCGAGGGTATTTCAATAATTTTACAA
1 GTATTTTGGTAATTTTAC-ACTACGAGGGTATTTCGATAATTTTACAA
9756 GTCGGGGCTA
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
53 1 0.01
54 72 0.90
55 7 0.09
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (55 bp):
GTATTTTGGTAATTTTACACTACGAGGGTATTTCGATAATTTTACAAATCATGGA
Found at i:10782 original size:27 final size:27
Alignment explanation
Indices: 10723--10788 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
10713 AATGAAAATC
* *
10723 GGCACACAGCCATGGATAAATATGATC
1 GGCACACAGCCATCGATAAATATGATA
* * *
10750 GACACAGAGTCATCGATAAATATGATA
1 GGCACACAGCCATCGATAAATATGATA
*
10777 GGCACATAGCCA
1 GGCACACAGCCA
10789 CTGGTAAGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (27 bp):
GGCACACAGCCATCGATAAATATGATA
Found at i:11291 original size:27 final size:26
Alignment explanation
Indices: 11231--11400 Score: 89
Period size: 27 Copynumber: 6.4 Consensus size: 26
11221 TATCCTATAC
* * *
11231 GGGTATTTAGGTAATTTTAC-ACTACAA
1 GGGTATTTCGATAATTTTACAAAT-C-A
11258 GGGTATTTCGATAATTTTACAAATCA
1 GGGTATTTCGATAATTTTACAAATCA
* * * *
11284 GGGATATTTTGGTAA-TTTCCAAAATTGA
1 GGG-TATTTCGATAATTTTAC-AAA-TCA
* * *
11312 GGCTATTTC-ATAATTTCACAAATTA
1 GGGTATTTCGATAATTTTACAAATCA
* *
11337 GAGGTATTTCGGA-ACTTTTAC-AACCGA
1 G-GGTATTTC-GATAATTTTACAAATC-A
* * *
11364 GGGTATTTCAATAATTTTACAAGTCGG
1 GGGTATTTCGATAATTTTACAAATC-A
11391 GGGTATTTCG
1 GGGTATTTCG
11401 CCCTATTGGT
Statistics
Matches: 108, Mismatches: 24, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
25 4 0.04
26 38 0.35
27 59 0.55
28 7 0.06
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.37
Consensus pattern (26 bp):
GGGTATTTCGATAATTTTACAAATCA
Found at i:11325 original size:26 final size:26
Alignment explanation
Indices: 11259--11346 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
11249 ACACTACAAG
* *
11259 GGTATTTCGATAATTTTACAAATCAG-
1 GGTATTTC-ATAATTTCACAAATTAGA
**
11285 GGATATTTTGGTAATTTC-CAAAATT-GA
1 GG-TA-TTTCATAATTTCAC-AAATTAGA
11312 GGCTATTTCATAATTTCACAAATTAGA
1 GG-TATTTCATAATTTCACAAATTAGA
11339 GGTATTTC
1 GGTATTTC
11347 GGAACTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
26 25 0.51
27 21 0.43
28 3 0.06
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (26 bp):
GGTATTTCATAATTTCACAAATTAGA
Found at i:24775 original size:27 final size:27
Alignment explanation
Indices: 24745--24922 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
24735 ATATTGAGTC
* * * *
24745 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
24772 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
24799 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
24827 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
24854 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
24881 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
24908 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
24923 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:24884 original size:82 final size:81
Alignment explanation
Indices: 24766--24921 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
24756 TGCTATATAA
* *
24766 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
24831 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
24848 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
24912 CACTTAGTGC
65 CACTTAGTGC
24922 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:32895 original size:27 final size:27
Alignment explanation
Indices: 32865--33042 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
32855 ATATTGAGTC
* * * *
32865 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
32892 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
32919 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
32947 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
32974 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
33001 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
33028 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
33043 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:33004 original size:82 final size:81
Alignment explanation
Indices: 32886--33041 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
32876 TGCTATATAA
* *
32886 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
32951 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
32968 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
33032 CACTTAGTGC
65 CACTTAGTGC
33042 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
Done.