Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2073
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: 52499
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Found at i:5206 original size:27 final size:27
Alignment explanation
Indices: 5168--5249 Score: 155
Period size: 27 Copynumber: 3.0 Consensus size: 27
5158 GCACATCCCT
5168 ATAATGTTCATGAAAGTTTCAATCACC
1 ATAATGTTCATGAAAGTTTCAATCACC
5195 ATAATGTTCATGAAAGTTTCAATCACC
1 ATAATGTTCATGAAAGTTTCAATCACC
*
5222 ATAATGTTCGTGAAAGTTTCAATCACC
1 ATAATGTTCATGAAAGTTTCAATCACC
5249 A
1 A
5250 GGCAATTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (27 bp):
ATAATGTTCATGAAAGTTTCAATCACC
Found at i:10116 original size:155 final size:155
Alignment explanation
Indices: 9926--10233 Score: 607
Period size: 155 Copynumber: 2.0 Consensus size: 155
9916 CAACCATGAA
*
9926 CACTAGTTATGGTTCTAACTACAAAAAAGCAATTTTCTTCACGGTGCCCGATGTCAATATCATCA
1 CACTAGTTATGGTTCTAACTACAAAAAAGCAATTTTCTTCACGGTGCCCCATGTCAATATCATCA
9991 AGAGAATTCTATCATACTCAATGCATCTGTTTCAGGTAGTGCAAAATCTTACTATACCATGCGAC
66 AGAGAATTCTATCATACTCAATGCATCTGTTTCAGGTAGTGCAAAATCTTACTATACCATGCGAC
10056 AAATAGCAGCTATCACATATGCTAT
131 AAATAGCAGCTATCACATATGCTAT
10081 CACTAGTTATGGTTCTAACTACAAAAAAGCAATTTTCTTCACGGTGCCCCATGTCAATATCATCA
1 CACTAGTTATGGTTCTAACTACAAAAAAGCAATTTTCTTCACGGTGCCCCATGTCAATATCATCA
10146 AGAGAATTCTATCATACTCAATGCATCTGTTTCAGGTAGTGCAAAATCTTACTATACCATGCGAC
66 AGAGAATTCTATCATACTCAATGCATCTGTTTCAGGTAGTGCAAAATCTTACTATACCATGCGAC
10211 AAATAGCAGCTATCACATATGCT
131 AAATAGCAGCTATCACATATGCT
10234 TGTATTTTGA
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 152 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30
Consensus pattern (155 bp):
CACTAGTTATGGTTCTAACTACAAAAAAGCAATTTTCTTCACGGTGCCCCATGTCAATATCATCA
AGAGAATTCTATCATACTCAATGCATCTGTTTCAGGTAGTGCAAAATCTTACTATACCATGCGAC
AAATAGCAGCTATCACATATGCTAT
Found at i:16990 original size:23 final size:23
Alignment explanation
Indices: 16964--17017 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
16954 ACATAACGAC
16964 CCTAGCCTAATATACAAAAGATT
1 CCTAGCCTAATATACAAAAGATT
*
16987 CCTAACCTAATATACAAAAGATT
1 CCTAGCCTAATATACAAAAGATT
17010 CCTAGCCT
1 CCTAGCCT
17018 TCCCTGACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (23 bp):
CCTAGCCTAATATACAAAAGATT
Found at i:21790 original size:27 final size:27
Alignment explanation
Indices: 21760--21817 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
21750 CAAGAATGTC
*
21760 TGAATAATTCTATATCTATAATGACAG
1 TGAATAATTCTATATCTATAATGACAA
21787 TGAATAATTCTATATCTATAATGACAA
1 TGAATAATTCTATATCTATAATGACAA
21814 TGAA
1 TGAA
21818 CAATGAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
TGAATAATTCTATATCTATAATGACAA
Found at i:22810 original size:5 final size:5
Alignment explanation
Indices: 22800--22847 Score: 69
Period size: 5 Copynumber: 9.0 Consensus size: 5
22790 ATAATTGGAT
22800 TTATA TTATA TTATA TTATA TTATA TTATTA TTATTA TTATTA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTA-TA TTA-TA TTA-TA TTATA
22848 AAAATATAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 25 0.60
6 17 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:22831 original size:3 final size:3
Alignment explanation
Indices: 22803--22846 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
22793 ATTGGATTTA
22803 TAT TA- TAT TA- TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
22847 AAAAATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:27021 original size:230 final size:228
Alignment explanation
Indices: 26403--27095 Score: 1000
Period size: 230 Copynumber: 3.0 Consensus size: 228
26393 GCAAAACCCA
*
26403 TTGCTTCATTGTCTACCACTTGGCCTATTTAACAAACTACAAGAAGGCAAGCAGAATGCATTACA
1 TTGCTTCATTGTCT-CCACTTGGCCTA--TAACAAACTACAAGAAGGCAAGCAGAATACATTACA
*
26468 AAAAAGAAACCTTTTAAAATTAAAATAAAACAGAAATCCGGAACACCAAGGCCAAATCCAGCACC
63 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* * * * *
26533 TTGCCTACTCACTCTAAATCAGTTGGCTTAATAAAAAGATTTGCTTGGAAATGGACGAATCATTC
128 TTGCCTACTTACTCTAAATCAATTGG-TTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTC
* *
26598 AAAAAAACTCTTTCACCAGTATCCTTTCTAGAACCGAT
192 -AAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* *
26636 TTGCTTCATTGTCTTCCACTTGGCCTAT--CTAACTACAAGGAGGCAAGCAGAATACATTACAAA
1 TTGCTTCATTGTC-TCCACTTGGCCTATAACAAACTACAAGAAGGCAAGCAGAATACATTACAAA
* * * *
26699 AAAGGAACCTTTT-AAACTAAAATAAAAACGAAATCCGGCACACCAAGGCC-AATCCAGCACCTT
65 AAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACCTT
26762 GCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAA
130 GCCTACTTACTCTAAATCAATT-GGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAA
* *
26827 AAAACTCTTTCAACAGAATCCTTTCTAGAACTGGT
194 AAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
*
26862 TTGCTTCATTGTCATCCACTTGGCCTATCGAACAAACTACAAGAAGGCAAGCAGAATACATTA-T
1 TTGCTTCATTGTC-TCCACTTGGCCTAT--AACAAACTACAAGAAGGCAAGCAGAATACATTACA
* *
26926 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCATCACC
63 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* *
26991 TTGCCTACTTACTCTAAATCAATTGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCATT
128 TTGCCTACTTACTCTAAATCAATTGGTTCATAAAAAGAATAGCTTGG--AAATGGACGAATCATT
** * *
27056 CAGAAATCCTCTTTCACCAGTTTCCTTGCTAGAACTGGT
191 CA-AAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
27095 T
1 T
27096 GTCAATGCCT
Statistics
Matches: 414, Mismatches: 35, Indels: 22
0.88 0.07 0.05
Matches are distributed among these distances:
226 60 0.14
227 68 0.16
228 35 0.08
229 58 0.14
230 84 0.20
231 35 0.08
232 17 0.04
233 56 0.14
234 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (228 bp):
TTGCTTCATTGTCTCCACTTGGCCTATAACAAACTACAAGAAGGCAAGCAGAATACATTACAAAA
AAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACCTTG
CCTACTTACTCTAAATCAATTGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAAA
AACTCTTTCACCAGTATCCTTTCTAGAACTGGT
Found at i:34586 original size:12 final size:12
Alignment explanation
Indices: 34569--34593 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34559 TCATATAGAC
34569 ATCTTTGACTAA
1 ATCTTTGACTAA
34581 ATCTTTGACTAA
1 ATCTTTGACTAA
34593 A
1 A
34594 GTATAAGGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:35643 original size:13 final size:14
Alignment explanation
Indices: 35612--35644 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35602 ATTAAATTTT
*
35612 TTTTAATTATATCA
1 TTTTATTTATATCA
35626 TTTTATTTATAT-A
1 TTTTATTTATATCA
35639 TTTTAT
1 TTTTAT
35645 ATTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTTATATCA
Found at i:35702 original size:22 final size:22
Alignment explanation
Indices: 35677--35722 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
35667 TACTCCAAAT
*
35677 TTATTTAAATATAAATAAAAAA
1 TTATTTAAATAAAAATAAAAAA
** *
35699 TTATTTTGATAAAAATTAAAAA
1 TTATTTAAATAAAAATAAAAAA
35721 TT
1 TT
35723 TAAAACAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
TTATTTAAATAAAAATAAAAAA
Found at i:35727 original size:29 final size:29
Alignment explanation
Indices: 35701--35756 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
35691 ATAAAAAATT
35701 ATTTT-GATAAAAATTAAAAATTTAAAACA
1 ATTTTAGATAAAAATT-AAAATTTAAAACA
*
35730 ATTTTAGATAGAAATTAAAATTTAAAA
1 ATTTTAGATAAAAATTAAAATTTAAAA
35757 ATTTATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
ATTTTAGATAAAAATTAAAATTTAAAACA
Found at i:37145 original size:22 final size:22
Alignment explanation
Indices: 37110--37163 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
37100 AAAGAAAAAT
37110 AAAAAA-TAATAAAA-TTGAACAA
1 AAAAAACTAATAAAACTT--ACAA
37132 AAAAAACTAA-AAAACTTACAA
1 AAAAAACTAATAAAACTTACAA
37153 AAAAAATCTAA
1 AAAAAA-CTAA
37164 CATTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.34
22 14 0.48
23 5 0.17
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (22 bp):
AAAAAACTAATAAAACTTACAA
Done.