Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3135
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: 34957
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:5859 original size:27 final size:27
Alignment explanation
Indices: 5829--6006 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5819 ATATTGAGTC
* * * *
5829 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
5856 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5883 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
5911 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
5938 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
5965 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5992 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
6007 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:5968 original size:82 final size:81
Alignment explanation
Indices: 5850--6005 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5840 TGCTATATAA
* *
5850 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
5915 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
5932 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
5996 CACTTAGTGC
65 CACTTAGTGC
6006 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:12569 original size:24 final size:24
Alignment explanation
Indices: 12518--12571 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
12508 AATATCCAAT
* * *
12518 GCACTATGTGTGCGGTTTACTATG
1 GCACTATGTGTGCGGTGTAATATA
12542 GCACTATGTGTGCGAGTGTAAT-TA
1 GCACTATGTGTGCG-GTGTAATATA
12566 GCACTA
1 GCACTA
12572 CGTGCGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (24 bp):
GCACTATGTGTGCGGTGTAATATA
Found at i:20423 original size:24 final size:24
Alignment explanation
Indices: 20372--20432 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
20362 AATATCCAAT
* * *
20372 GCACTATGTGTGTGGTTTAATATG
1 GCACTATGTGTGCGGTGTAATATA
20396 GCACTATGTGTGCGAGTGTAAT-TA
1 GCACTATGTGTGCG-GTGTAATATA
*
20420 GCACTACGTGTGC
1 GCACTATGTGTGC
20433 AAATTCGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGGTGTAATATA
Found at i:22571 original size:16 final size:15
Alignment explanation
Indices: 22552--22587 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
22542 TTTCATTAAG
22552 TTTTTAAGACTCATT
1 TTTTTAAGACTCATT
*
22567 TTTTTAAGATTCATT
1 TTTTTAAGACTCATT
22582 TGTTTT
1 T-TTTT
22588 CTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.61
Consensus pattern (15 bp):
TTTTTAAGACTCATT
Found at i:27317 original size:49 final size:50
Alignment explanation
Indices: 27237--27482 Score: 266
Period size: 49 Copynumber: 4.9 Consensus size: 50
27227 ATCTATTGTG
* * *
27237 AGGTCACGTGTGTAGTACTAAGTGCAAGCTACTATGTGTACCAAATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
* * * *
27287 -GGTCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TT
* * * * * **
27337 CGGTCACGTGTGTATTACTAGGTGCAGGCTACTACT-TGTATCAGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTA-TGTGTACCAGATAATT
* * * *
27387 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACCACGTGTACCGGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
*
27437 -GGTCACATGTGTAGTACTAAGTGTAGGCTACTAT-TCGTACCAGATA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGT-GTACCAGATA
27483 GCTTCGGCTA
Statistics
Matches: 160, Mismatches: 31, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 79 0.49
50 44 0.28
51 35 0.22
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT
Found at i:27434 original size:101 final size:98
Alignment explanation
Indices: 27238--27478 Score: 279
Period size: 100 Copynumber: 2.4 Consensus size: 98
27228 TCTATTGTGA
* *
27238 GGTCACGTGTGTAGTACTAAGTGCAAGCTACTATGTGTACCAAATAATTGGTCGCATGTGTAGTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATAATTGGTCACATGTGTAGTA
* * *
27303 CTAAGTGTAGGCTACTATGCGTACCCGATAACTT
66 CTAAGTGCAGGCTACCACGCGTACCCGATAA-TT
* * * * ** *
27337 CGGTCACGTGTGTATTACTAGGTGCAGGCTACTACT-TGTATCAGATGGTTAGGTCACGTGTGTA
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA-TGTGTACCAAATAATT-GGTCACATGTGTA
* *
27401 GTACTAAGTGCAGGCTACCACGTGTACCGGATAATT
63 GTACTAAGTGCAGGCTACCACGCGTACCCGATAATT
* *
27437 GGTCACATGTGTAGTACTAAGTGTAGGCTACTAT-TCGTACCA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGT-GTACCA
27479 GATAGCTTCG
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
98 2 0.02
99 34 0.29
100 42 0.35
101 41 0.34
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (98 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAAATAATTGGTCACATGTGTAGTA
CTAAGTGCAGGCTACCACGCGTACCCGATAATT
Found at i:27512 original size:150 final size:150
Alignment explanation
Indices: 27237--27515 Score: 409
Period size: 150 Copynumber: 1.9 Consensus size: 150
27227 ATCTATTGTG
* * *
27237 AGGTCACGTGTGTAGTACTAAGTGCAAGCTACTATGTGTACCAAATAATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAAGCTACCACGTGTACCAAATAATTGGTCACATGTGTAGT
* * * *
27302 ACTAAGTGTAGGCTACTATGCGTACCCGATAACTTCGGTCACGTGTGTATTACTAGGTGCAGGCT
66 ACTAAGTGTAGGCTACTATGCGTACCAGATAACTTCGGTCAAGTGTGTATAAATAGGTGCAGGCT
27367 ACTACTTGTATCAGATGGTT
131 ACTACTTGTATCAGATGGTT
* **
27387 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACCACGTGTACCGGATAATTGGTCACATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAAGCTACCACGTGTACCAAATAATTGGTCACATGTGTAGT
* * *
27452 ACTAAGTGTAGGCTACTATTCGTACCAGATAGCTTCGGCTACAAGTGTG-A-AAATATGTGCAGG
66 ACTAAGTGTAGGCTACTATGCGTACCAGATAACTTCGG-T-CAAGTGTGTATAAATAGGTGCAGG
27515 C
129 C
27516 AACTGAGTAT
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
150 105 0.92
151 2 0.02
152 7 0.06
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (150 bp):
AGGTCACGTGTGTAGTACTAAGTGCAAGCTACCACGTGTACCAAATAATTGGTCACATGTGTAGT
ACTAAGTGTAGGCTACTATGCGTACCAGATAACTTCGGTCAAGTGTGTATAAATAGGTGCAGGCT
ACTACTTGTATCAGATGGTT
Found at i:29189 original size:50 final size:50
Alignment explanation
Indices: 29114--29216 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
29104 ATGGAAGTCC
29114 TTAATATAAAGGGGATAATCTAGCATGTATAAAAATTGATGAGATGAGGT
1 TTAATATAAAGGGGATAATCTAGCATGTATAAAAATTGATGAGATGAGGT
29164 TTAATATAAAGGGGATAATCTAGCATGTATAAAAATTGATGAGATGAGGT
1 TTAATATAAAGGGGATAATCTAGCATGTATAAAAATTGATGAGATGAGGT
29214 TTA
1 TTA
29217 CATGTAATGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (50 bp):
TTAATATAAAGGGGATAATCTAGCATGTATAAAAATTGATGAGATGAGGT
Found at i:31895 original size:29 final size:29
Alignment explanation
Indices: 31863--31946 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
31853 ATTCGATGGT
*
31863 CGTCACCATCCCTTTTCATAGTTGATTGC
1 CGTCACCATCCCTTTTCATAGTTGATAGC
* *
31892 CGTCACCATCCCTTTTCATAATTGATAGT
1 CGTCACCATCCCTTTTCATAGTTGATAGC
* *
31921 CG-AAGCTATCCCTTTTCATAGTTGAT
1 CGTCA-CCATCCCTTTTCATAGTTGAT
31947 GATCGTCGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 1 0.02
29 47 0.98
ACGTcount: A:0.21, C:0.27, G:0.13, T:0.38
Consensus pattern (29 bp):
CGTCACCATCCCTTTTCATAGTTGATAGC
Found at i:34932 original size:12 final size:12
Alignment explanation
Indices: 34915--34940 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34905 ACAGTTTTGG
34915 CACAGCCTAGCA
1 CACAGCCTAGCA
34927 CACAGCCTAGCA
1 CACAGCCTAGCA
34939 CA
1 CA
34941 TGGGCGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.42, G:0.15, T:0.08
Consensus pattern (12 bp):
CACAGCCTAGCA
Done.