Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2160
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: 10604
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Found at i:290 original size:52 final size:51
Alignment explanation
Indices: 212--327 Score: 205
Period size: 52 Copynumber: 2.3 Consensus size: 51
202 AGTTGCTTGT
*
212 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTGCCTGC
*
264 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTGC
315 ATGTATCGATACA
1 ATGTATCGATACA
328 AGATCAGTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 21 0.34
52 41 0.66
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTGC
Found at i:353 original size:13 final size:13
Alignment explanation
Indices: 335--359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325 ACAAGATCAG
335 TGTATCGATACAA
1 TGTATCGATACAA
348 TGTATCGATACA
1 TGTATCGATACA
360 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:441 original size:13 final size:13
Alignment explanation
Indices: 423--447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
413 CAAAAAAATA
423 TGTATCGATACAT
1 TGTATCGATACAT
436 TGTATCGATACA
1 TGTATCGATACA
448 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:443 original size:33 final size:33
Alignment explanation
Indices: 401--467 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
391 AGTAGCTTAA
401 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
434 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
467 A
1 A
468 CATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1512 original size:49 final size:49
Alignment explanation
Indices: 1352--1580 Score: 308
Period size: 49 Copynumber: 4.7 Consensus size: 49
1342 AAAAGGATGT
* * *
1352 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
1404 CAATATGCTGATTCAAGGCCAGCTTTATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
1447 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
1496 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
1545 CAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1581 GAAGGGTTGC
Statistics
Matches: 159, Mismatches: 12, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
43 40 0.25
48 1 0.01
49 87 0.55
52 31 0.19
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:1607 original size:30 final size:30
Alignment explanation
Indices: 1573--1661 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
1563 CCAGCTATAT
*
1573 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
*
1603 TGGGCTTTGGAAAAGGG-TGCCACTGA-TT-TG
1 TGGGC-TT--AGAAGGGTTGCCACTGACTTGTG
*
1633 TGGGCTTTGAA-GGTTGCCACTGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
1662 GGCTTTCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 2 0.04
27 11 0.22
28 2 0.04
29 4 0.08
30 12 0.24
31 4 0.08
32 8 0.16
33 6 0.12
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (30 bp):
TGGGCTTAGAAGGGTTGCCACTGACTTGTG
Found at i:1688 original size:30 final size:29
Alignment explanation
Indices: 1601--2051 Score: 353
Period size: 30 Copynumber: 15.3 Consensus size: 29
1591 CACCGACTTG
* * *
1601 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
* *
1631 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* *
1658 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
*
1688 TGTGGGCTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * * *
1717 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* * *
1747 TGTGGGCTTT-TAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
1775 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* * *
1805 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* *
1835 TGTGGG--TTG-AAAAGAGTGCTA-TAGAGT
1 TGTGGGCTTTGAAAAAGA-TGCCACT-GACT
* * * * *
1862 TATGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT-----TGAAAAAGA-TGCCACTGACT
* * *
1897 TGTGGACTTTGGAAAAGATGCCACCGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * * *
1926 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTT-TGAAAAAGATGCCACTGACT
* *
1956 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* *
1983 TGTGGGCTTTCGAAAAAAATGCCATTGACT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
*
2013 TGTGGGCTTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
2042 TGTGGACTTT
1 TGTGGGCTTT
2052 TGAAGGGTGA
Statistics
Matches: 342, Mismatches: 58, Indels: 43
0.77 0.13 0.10
Matches are distributed among these distances:
26 5 0.01
27 61 0.18
28 23 0.07
29 77 0.23
30 154 0.45
34 1 0.00
35 21 0.06
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAGATGCCACTGACT
Found at i:1808 original size:88 final size:88
Alignment explanation
Indices: 1585--1840 Score: 331
Period size: 88 Copynumber: 2.9 Consensus size: 88
1575 GGCTTAGAAG
* *** * *
1585 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACCGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
1648 GCCACTGACTTGTGGGCTTTCGAAAA
64 GCCACTAACTTGTGGGCTTTC-AAAA
***
1674 AAATGCCACCGACTTGTGGGC-TTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
*
1738 CCACTAACTTGTGGGCTTT-TAAA
65 CCACTAACTTGTGGGCTTTCAAAA
*
1761 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTG
1 GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
1826 CCACTAACTTGTGGG
65 CCACTAACTTGTGGG
1841 TTGAAAAGAG
Statistics
Matches: 147, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
86 24 0.16
87 31 0.21
88 57 0.39
89 35 0.24
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (88 bp):
GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTCAAAA
Found at i:1962 original size:209 final size:206
Alignment explanation
Indices: 1669--2046 Score: 549
Period size: 209 Copynumber: 1.8 Consensus size: 206
1659 GTGGGCTTTC
* * * ** *
1669 GAAAAAAATGCCACCGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAG
1 GAAAAAAATGCCACCGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAG
* *
1734 GGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCA
66 GGTGCCACTAACTTGTGGGC-TTTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCA
***
1799 CTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGTTGAAAAGAGTGCTATAGAGTTA
130 CTGACTTGTGGGC-TTTGAAAAAAATGCCACTAACTTGTGGGTTGAAAAGAGTGCTATAGAGTTA
1864 TGAGCTTACAAAA
194 TGAGCTTACAAAA
* * * *
1877 GAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAA
1 GAAAAA-AATGCCACCGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAA
* * *
1942 GGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCA
65 GGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCA
* *
2007 TTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
130 CTGACTTGTGGGCTTTGAAAAAAATGCCACTAACTTGTGG
2047 ACTTTTGAAG
Statistics
Matches: 149, Mismatches: 20, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
207 23 0.15
208 59 0.40
209 67 0.45
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (206 bp):
GAAAAAAATGCCACCGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAG
GGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCAC
TGACTTGTGGGCTTTGAAAAAAATGCCACTAACTTGTGGGTTGAAAAGAGTGCTATAGAGTTATG
AGCTTACAAAA
Found at i:1985 original size:57 final size:57
Alignment explanation
Indices: 1582--2051 Score: 324
Period size: 59 Copynumber: 7.9 Consensus size: 57
1572 TTGGGCTTAG
* * *
1582 AAGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGCTTTG--
1 AAGGG-TGCCACTGAC-T-TGTGGGCTTT-G-AAAGGATGCCACTGACTTGTGGGCTTTGAA
* ** *
1642 AAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACCGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTT-G-AAAGGATGCCACTGACTTGTGGGCTTTGAA
*** * * *
1701 AAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTT-TA
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA-AGGATGCCACTGACTTGTGGGCTTTGAA
* **
1759 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGC-TTTG-AAAGGATGCCACTGACTTGTGGGC-TTTGAA
* * * * * * *
1819 AAGGGTGCCACTAACTTGTGGG--TTGAAAAGAGTGCTA-TAGAGTTATGAGCTTACAAAAGAAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACT-GACTTGTGGGCTT-----TG-AA
* * * * * * *
1881 AAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTT-TGAA
* *
1940 AAGGGTGCCACTGATTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTCGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAA
*** * ** *
1997 AAAAATGCCATTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGACTTT
1 AAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTT
2052 TGAAGGGTGA
Statistics
Matches: 326, Mismatches: 62, Indels: 45
0.75 0.14 0.10
Matches are distributed among these distances:
56 8 0.02
57 97 0.30
58 48 0.15
59 101 0.31
60 29 0.09
61 1 0.00
62 19 0.06
64 16 0.05
65 7 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (57 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
Found at i:2943 original size:9 final size:10
Alignment explanation
Indices: 2929--2958 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2919 TAAAAAAATG
2929 ATGAAAAAAA
1 ATGAAAAAAA
2939 A-GAAAAAAA
1 ATGAAAAAAA
2948 ATGAAAAAAA
1 ATGAAAAAAA
2958 A
1 A
2959 CAATAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (10 bp):
ATGAAAAAAA
Found at i:4297 original size:31 final size:31
Alignment explanation
Indices: 4259--4604 Score: 478
Period size: 31 Copynumber: 11.3 Consensus size: 31
4249 CAAATCTCTC
*
4259 TTCTCAAAGTCCACGATTCAGTGGCATCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
* *
4290 TTCTCAAAGTTCACGATTCAGTGGCATCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
*
4321 TTCTCAAAGTCCACGACTCAGTGGCATCTCT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
*
4352 TTC-CAAAGTCCACGACTCAGTGGCATC-TC
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
4381 TTCTTCAAAGTCCACGACTCAGTGGCATCTTT
1 TTC-TCAAAGTCCACGACTCAGTGGCATCTTT
4413 ACTTC-C-AAGTCCACGACTCAGTGGCATCTTT
1 --TTCTCAAAGTCCACGACTCAGTGGCATCTTT
*
4444 ACTTC-C-AAGTCCACGACTCAGTGGCATCTCT
1 --TTCTCAAAGTCCACGACTCAGTGGCATCTTT
*
4475 TTC-CAAAGTCCACGACTCAGTGGCATC-TC
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
*
4504 TTCTCAAAGTCCACGATTCAGTGGCATCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
* *
4535 TTCTTAAAGTCCACGACTCAGTGGCATCTCT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
4566 TTC-CAAAGTCCACGACTCAGTGGCATC-TT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
4595 TTCTTCAAAG
1 TTC-TCAAAG
4605 CCCATAACTC
Statistics
Matches: 288, Mismatches: 17, Indels: 20
0.89 0.05 0.06
Matches are distributed among these distances:
29 14 0.05
30 92 0.32
31 177 0.61
32 2 0.01
34 3 0.01
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (31 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTTT
Found at i:4389 original size:61 final size:61
Alignment explanation
Indices: 4255--4596 Score: 498
Period size: 61 Copynumber: 5.6 Consensus size: 61
4245 TCTTCAAATC
* * *
4255 TCTCTTC-TCAAAGTCCACGATTCAGTGGCATCTTTTTCTCAAAGTTCACGATTCAGTGGCA
1 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTTC-CAAAGTCCACGACTCAGTGGCA
* *
4316 TCT-TTTTCTCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCA
1 TCTCTTCT-TCAAAGTCCACGACTCAGTGGCATCTTTTTCCAAAGTCCACGACTCAGTGGCA
4377 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTACTTCC-AAGTCCACGACTCAGTGGCA
1 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTT--TTCCAAAGTCCACGACTCAGTGGCA
* *
4439 TCT-TTACTTCCAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCA
1 TCTCTT-CTTCAAAGTCCACGACTCAGTGGCATCTTTTTCCAAAGTCCACGACTCAGTGGCA
* *
4500 TCTCTTC-TCAAAGTCCACGATTCAGTGGCATCTTTTTCTTAAAGTCCACGACTCAGTGGCA
1 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTTC-CAAAGTCCACGACTCAGTGGCA
*
4561 TCTCTT-TCCAAAGTCCACGACTCAGTGGCATCTTTT
1 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTT
4597 CTTCAAAGCC
Statistics
Matches: 256, Mismatches: 15, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
60 34 0.13
61 133 0.52
62 85 0.33
63 4 0.02
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (61 bp):
TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTTCCAAAGTCCACGACTCAGTGGCA
Found at i:4481 original size:123 final size:120
Alignment explanation
Indices: 4255--4597 Score: 532
Period size: 123 Copynumber: 2.8 Consensus size: 120
4245 TCTTCAAATC
* *
4255 TCTCTTCTCAAAGTCCACGATTCAGTGGCATCTTT-TTCTCAAAGTTCACGATTCAGTGGCATCT
1 TCTCTTCTCAAAGTCCACGATTCAGTGGCATCTTTCTTC-C-AAGTCCACGACTCAGTGGCATCT
4319 TTTTCTCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCA
64 TTTTC-CAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCA
*
4377 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTACTTCCAAGTCCACGACTCAGTGGCATCT
1 TCTCTTC-TCAAAGTCCACGATTCAGTGGCATCTTT-CTTCCAAGTCCACGACTCAGTGGCATCT
4442 TTACTTCC-AAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCA
64 TT--TTCCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCA
*
4500 TCTCTTCTCAAAGTCCACGATTCAGTGGCATCTTT-TTCTTAAAGTCCACGACTCAGTGGCATCT
1 TCTCTTCTCAAAGTCCACGATTCAGTGGCATCTTTCTTC--CAAGTCCACGACTCAGTGGCATCT
*
4564 CTTTCCAAAGTCCACGACTCAGTGGCATCT-TTTC
64 TTTTCCAAAGTCCACGACTCAGTGGCATCTCTTTC
4598 TTCAAAGCCC
Statistics
Matches: 207, Mismatches: 6, Indels: 18
0.90 0.03 0.08
Matches are distributed among these distances:
120 11 0.05
121 23 0.11
122 58 0.28
123 107 0.52
124 2 0.01
125 6 0.03
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.31
Consensus pattern (120 bp):
TCTCTTCTCAAAGTCCACGATTCAGTGGCATCTTTCTTCCAAGTCCACGACTCAGTGGCATCTTT
TTCCAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCA
Found at i:4664 original size:122 final size:121
Alignment explanation
Indices: 4265--4781 Score: 432
Period size: 122 Copynumber: 4.3 Consensus size: 121
4255 TCTCTTCTCA
* * * * * * *
4265 AAGTCCACGATTCAGTGGCATCTTTTTC-TCAAAGTTCACGATTCAGTGGCATCTTTTTCTCAAA
1 AAGTCCACAACTCAGTGGCAACTTTTTCTTTAAAGTCCACGACTCAGTGGCATCTCTTTC-CAAA
* * *
4329 GTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTCTTCTT
65 GTCCACGACTCAGTGGCATCTCTTTCCAAAGCCCACAACTCAGTGGCATCCCTTCTT
* * * ** *
4386 CAAAGTCCACGACTCAGTGGCATC-TTTACTTCCAAGTCCACGACTCAGTGGCATCTTTACTTCC
1 --AAGTCCACAACTCAGTGGCAACTTTTTCTTTAAAGTCCACGACTCAGTGGCATCTCT--TTCC
* * * *
4450 -AAGTCCACGACTCAGTGGCATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTCTTCTCA
62 AAAGTCCACGACTCAGTGGCATCTCTTTCCAAAGCCCACAACTCAGTGGCATCCCTTCT-T
* * *
4510 AAGTCCACGATTCAGTGGCATCTTTTTC-TTAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAG
1 AAGTCCACAACTCAGTGGCAACTTTTTCTTTAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAG
*
4574 TCCACGACTCAGTGGCATCT-TTTCTTCAAAGCCCATAACTCTA-TGGCA-CCCTT-TT
66 TCCACGACTCAGTGGCATCTCTTTC--CAAAGCCCACAACTC-AGTGGCATCCCTTCTT
* * * * * * *
4629 AAGTCCACAACTCCGTGGTAACTTTTTCTTTTTAAAGCCCACAACTCTGTGGCA-CCCTTT--TA
1 AAGTCCACAACTCAGTGGCAACTTTTTC--TTTAAAGTCCACGACTCAGTGGCATCTCTTTCCAA
* * * ** * * *
4691 AGTCCACAACTCCGTGGCACCTTTTTCTTTTTACAGCCCATAACTCTGTGGCA-CCCTT-TT
64 AGTCCACGACTCAGTGGCA----TCTCTTTCCAAAGCCCACAACTCAGTGGCATCCCTTCTT
*
4751 AAGTCCACAACTCTGTGGC-ACATTTTTCTTT
1 AAGTCCACAACTCAGTGGCAAC-TTTTTCTTT
4782 TTTAAAGCCC
Statistics
Matches: 340, Mismatches: 35, Indels: 41
0.82 0.08 0.10
Matches are distributed among these distances:
119 41 0.12
120 12 0.04
121 34 0.10
122 135 0.40
123 111 0.33
124 4 0.01
125 3 0.01
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (121 bp):
AAGTCCACAACTCAGTGGCAACTTTTTCTTTAAAGTCCACGACTCAGTGGCATCTCTTTCCAAAG
TCCACGACTCAGTGGCATCTCTTTCCAAAGCCCACAACTCAGTGGCATCCCTTCTT
Found at i:4669 original size:61 final size:60
Alignment explanation
Indices: 4601--4959 Score: 334
Period size: 61 Copynumber: 5.8 Consensus size: 60
4591 TCTTTTCTTC
* *
4601 AAAGCCCATAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGTAACTTTTTCTTTTT
1 AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGG-AACTTTTTCTTTTT
*
4662 AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGG-AACTTTTTCTTTTT
* * * *
4723 ACAGCCCATAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACATTTTTCTTTTTT
1 AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGAAC-TTTTTC-TTTTT
** * * * *
4785 AAAGCCCACAACTCCATAGCACTCTTTTTCCTTTTAAGTCCATAACTCCGTGGCAC-----CCTT
1 AAAGCCCACAACTCTGTGGCA--C-----CCTTTTAAGTCCACAACTCCGTGGAACTTTTTCTTT
4845 TT
59 TT
* ** * *
4847 -AAGTCCACAACTCTGTGGCACCTTTTTCGTTTTAAAGTCCACAACTCTATGGCACCTTTTTCGT
1 AAAGCCCACAACTCTGTGGCACC-----C-TTTT-AAGTCCACAACTCCGTGG-AACTTTTTCTT
4911 TTT
58 TTT
*
4914 AAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGG
1 AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGG
4960 CATTTTCTCC
Statistics
Matches: 246, Mismatches: 29, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
54 1 0.00
59 2 0.01
60 5 0.02
61 153 0.62
62 30 0.12
63 2 0.01
64 1 0.00
67 5 0.02
68 22 0.09
69 25 0.10
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (60 bp):
AAAGCCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGAACTTTTTCTTTTT
Found at i:4672 original size:34 final size:32
Alignment explanation
Indices: 4623--4959 Score: 174
Period size: 34 Copynumber: 10.8 Consensus size: 32
4613 TCTATGGCAC
*
4623 CCTTTTAAGTCCACAACTCCGTGGTAACTTTTT
1 CCTTTTAAGTCCACAACTCTGTGG-AACTTTTT
* * *
4656 CTTTTTAAAGCCCACAACTCTGTGGCAC-----
1 CCTTTT-AAGTCCACAACTCTGTGGAACTTTTT
* *
4684 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCTGTGG-AACTTTTT
* * * *
4717 CTTTTTACAGCCCATAACTCTGTGGCAC-----
1 CCTTTTA-AGTCCACAACTCTGTGGAACTTTTT
*
4745 CCTTTTAAGTCCACAACTCTGTGGCACATTTTT
1 CCTTTTAAGTCCACAACTCTGTGGAAC-TTTTT
* * ** * *
4778 CTTTTTTAAAGCCCACAACTCCATAGCACTCTTTTT
1 C-CTTTT-AAGTCCACAACTCTGT-GGA-ACTTTTT
* * *
4814 CCTTTTAAGTCCATAACTCCGTGGCAC-----
1 CCTTTTAAGTCCACAACTCTGTGGAACTTTTT
*
4841 CCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCTGTGG-AACTTTTT
* * *
4874 CGTTTTAAAGTCCACAACTCTATGGCACCTTTTT
1 CCTTTT-AAGTCCACAACTCTGTGG-AACTTTTT
* *
4908 CGTTTTAAAGTCCACAACTCTGTGGCAC-----
1 CCTTTT-AAGTCCACAACTCTGTGGAACTTTTT
*
4936 CCTTTTAAGTCCACAACTCCGTGG
1 CCTTTTAAGTCCACAACTCTGTGG
4960 CATTTTCTCC
Statistics
Matches: 236, Mismatches: 43, Indels: 56
0.70 0.13 0.17
Matches are distributed among these distances:
27 73 0.31
28 18 0.08
32 1 0.00
33 22 0.09
34 97 0.41
35 17 0.07
36 7 0.03
37 1 0.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (32 bp):
CCTTTTAAGTCCACAACTCTGTGGAACTTTTT
Found at i:4795 original size:96 final size:94
Alignment explanation
Indices: 4686--4961 Score: 401
Period size: 95 Copynumber: 2.9 Consensus size: 94
4676 TGTGGCACCC
* * *
4686 TTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTACAGCCCATAACTCTGTGGCACCCTTT
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTCCTTTTA-AGTCCATAACTCTGTGGCACCCTTT
*
4750 TAAGTCCACAACTCTGTGGCACATTTTTCTT
65 TAAGTCCACAACTCTGTGGCACATTTTTC-G
* * *
4781 TTTTAAAGCCCACAACTCCATAGCACTCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCCTTT
1 TTTTAAAGTCCACAACTCCATGGCAC-CTTTTTCCTTTTAAGTCCATAACTCTGTGGCACCCTTT
*
4846 TAAGTCCACAACTCTGTGGCACCTTTTTCG
65 TAAGTCCACAACTCTGTGGCACATTTTTCG
* * *
4876 TTTTAAAGTCCACAACTCTATGGCACCTTTTTCGTTTTAAAGTCCACAACTCTGTGGCACCCTTT
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTCCTTTT-AAGTCCATAACTCTGTGGCACCCTTT
*
4941 TAAGTCCACAACTCCGTGGCA
65 TAAGTCCACAACTCTGTGGCA
4962 TTTTCTCCTC
Statistics
Matches: 163, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
94 11 0.07
95 71 0.44
96 69 0.42
97 12 0.07
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (94 bp):
TTTTAAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAAGTCCATAACTCTGTGGCACCCTTTT
AAGTCCACAACTCTGTGGCACATTTTTCG
Found at i:4942 original size:157 final size:150
Alignment explanation
Indices: 4601--4955 Score: 390
Period size: 157 Copynumber: 2.3 Consensus size: 150
4591 TCTTTTCTTC
* * * * * * *
4601 AAAGCCCATAACTCTATGGCACCCTTTTAAGTCCACAACTCCGTGGTAACTTTTTCTTTTTAAAG
1 AAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCATAGCAACTTTTTCCTTTTAAAG
* * *
4666 CCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTACAGCCCA
66 CCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCGTTTTAAAGCCCA
* *
4731 TAACTCTGTGGCACCCTTTT
131 CAACTCTATGGCACCCTTTT
* * *
4751 -AAGTCCACAACTCTGTGGCACATTTTTCTTTTTTAAAGCCCACAACTCCATAGCACTCTTTTTC
1 AAAGTCCACAACTCTGTGGCAC------C-CTTTT-AAGTCCACAACTCCATAGCA-ACTTTTTC
* * *
4815 CTTTT-AAGTCCATAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCGTTT
57 CTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCGTTT
*
4879 TAAAGTCCACAACTCTATGGCACCTTTTTCGTTTT
122 TAAAGCCCACAACTCTATGGCACC-----C-TTTT
4914 AAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCC
1 AAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCC
4956 GTGGCATTTT
Statistics
Matches: 168, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
149 18 0.11
155 1 0.01
156 17 0.10
157 94 0.56
158 12 0.07
162 1 0.01
163 4 0.02
164 21 0.12
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.34
Consensus pattern (150 bp):
AAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCATAGCAACTTTTTCCTTTTAAAG
CCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCGTTTTAAAGCCCA
CAACTCTATGGCACCCTTTT
Found at i:5202 original size:101 final size:100
Alignment explanation
Indices: 5027--5881 Score: 1067
Period size: 101 Copynumber: 8.4 Consensus size: 100
5017 GGTGGCGTCT
* * *
5027 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCGCCTTCATCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGTCCAA
* * *
5092 TGTCGCTGGCCTTGAATCAGCACATTGACACC-T-TCA
63 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCA
* * * *
5128 TCTTTAAGTCTAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGTCCAA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-T--TCATCTTTAAGTCCAA
* *
5193 TGTCGCTGGCCTTGAATCAGCACATTGGCACC-T-TCA
63 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCA
* * * * * * *
5229 TCTTTAAGACCAGTATCGCTGGCCTTGAATCAGCATATTGGTGCCTCCGTCATCTTTCAA-ACCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT-G-G-CACCTTCATCTTT-AAGTCCA
* ** *
5293 ATGTCGCTGGCCTTGAATCAGCATATTGGTGCCTTCATCA
62 ATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCA
* * *
5333 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACTAGTAT
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
* * *
5398 CGCTGGCCTTGAATCAGCATATTAGCGCCTTCATCA
66 CGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCA
* * *
5434 TCTTTCAA-TCCAATGTCGCTGGCCTTGAATCAGTACATTAGCACCTTCATCTTTATGTCCAATA
1 TCTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATA
*
5498 TTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
65 TCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCA
*
5535 TCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-TTAAATCCAATA
1 TC-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATA
*
5599 TCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA
65 TCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCA
* *
5636 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTTCAATAT
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
5701 CGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
66 CGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCA
* *
5737 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAGTAT
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
* * **
5802 CACTGGCCTTGAATTAGCATATTGGCGTCTTCGTCA
66 CGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCA
** * *
5838 TCTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCATATTGGCA
1 TCTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
5882 TTATTCTCAT
Statistics
Matches: 680, Mismatches: 59, Indels: 29
0.89 0.08 0.04
Matches are distributed among these distances:
100 52 0.08
101 498 0.73
102 87 0.13
103 2 0.00
104 41 0.06
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (100 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT
CGCTGGCCTTGAATCAGCATATTGGCACCTTGTCA
Found at i:6704 original size:32 final size:34
Alignment explanation
Indices: 6663--6732 Score: 108
Period size: 32 Copynumber: 2.1 Consensus size: 34
6653 AAGTAACTGT
6663 ATCGATACATAAGTG-TTGTACCGA-TACAATGC
1 ATCGATACATAAGTGTTTGTACCGATTACAATGC
* *
6695 ATCGATACATAAGTGTTTGTATCGATTACAATGT
1 ATCGATACATAAGTGTTTGTACCGATTACAATGC
6729 ATCG
1 ATCG
6733 CTACGAAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 15 0.44
33 8 0.24
34 11 0.32
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (34 bp):
ATCGATACATAAGTGTTTGTACCGATTACAATGC
Found at i:6797 original size:13 final size:13
Alignment explanation
Indices: 6779--6806 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6769 ATTACTCAAA
6779 TGTATCGATACAT
1 TGTATCGATACAT
6792 TGTATCGATACAT
1 TGTATCGATACAT
6805 TG
1 TG
6807 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Done.