Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1823
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: 21990
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Found at i:254 original size:12 final size:12
Alignment explanation
Indices: 239--268 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
229 GGCAAGTCTT
*
239 TGATGAAGTTCC
1 TGATAAAGTTCC
251 TGATAAAGTTCC
1 TGATAAAGTTCC
263 TGATAA
1 TGATAA
269 TAGCTTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (12 bp):
TGATAAAGTTCC
Found at i:542 original size:30 final size:29
Alignment explanation
Indices: 506--744 Score: 92
Period size: 30 Copynumber: 7.9 Consensus size: 29
496 TGGCACTTCA
*
506 AAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAGCCCACAAATCAGTGGCACTCTTTTCC
* *
535 GAAGCCCACAAGTCGGTGGCA-TC-TTTCC
1 -AAGCCCACAAATCAGTGGCACTCTTTTCC
* * * *
563 AAGTCCACAACTCCGTGGCACTCTTTTTCTTTTGT
1 AAGCCCACAAATCAGTGGCACTC-TTTTC-----C
* * *
598 AAGCTCACAACTCTA-TAGCACTCTTTTTCC
1 AAGCCCACAAATC-AGTGGCACTC-TTTTCC
* * * *
628 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 ----AAGCCCACAAATCAGTGGCACTCTTTTC-C
* * * *
662 AAGCCCATAAGTTAGTGGCATCTCTTTTCA
1 AAGCCCACAAATCAGTGGCA-CTCTTTTCC
* **
692 AAGCCCACAAGTCAGTGGCAAC-C-TTTAA
1 AAGCCCACAAATCAGTGGC-ACTCTTTTCC
* *
720 AAGCCCACAAGTCAGTGGCAATCTT
1 AAGCCCACAAATCAGTGGCACTCTT
745 AAAAGCCCCA
Statistics
Matches: 166, Mismatches: 24, Indels: 39
0.72 0.10 0.17
Matches are distributed among these distances:
27 18 0.11
28 31 0.19
29 3 0.02
30 60 0.36
31 8 0.05
33 6 0.04
34 16 0.10
35 24 0.14
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (29 bp):
AAGCCCACAAATCAGTGGCACTCTTTTCC
Found at i:581 original size:57 final size:53
Alignment explanation
Indices: 485--589 Score: 129
Period size: 57 Copynumber: 1.9 Consensus size: 53
475 TTGCATTTTT
485 GCCCACAAGTCTGGCACTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAA
1 GCCCACAAGTCTGGCACTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAA
* * * * *
538 GCCCACAAGTCGGTGGCATCTTTCCAAGTCCACAACTCCGTGGCACTCTTTT
1 GCCCACAAGTC--TGGCA-C-TTCAAAGCCCACAAATCAGTGGCACCCTTTT
590 TCTTTTGTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
53 11 0.26
55 5 0.12
56 1 0.02
57 26 0.60
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.23
Consensus pattern (53 bp):
GCCCACAAGTCTGGCACTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAA
Found at i:658 original size:34 final size:36
Alignment explanation
Indices: 567--658 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 36
557 CTTTCCAAGT
* *
567 CCACAACTC-CGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCCTTTGTAAGC
* *
602 TCACAACTCTA-TAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCCTTTGTAAGC
* *
636 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCTAGTGGCACTCTTTT
659 CAAAAGCCCA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
33 2 0.04
34 21 0.45
35 24 0.51
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (36 bp):
CCACAACTCTAGTGGCACTCTTTTTCCTTTGTAAGC
Found at i:726 original size:28 final size:28
Alignment explanation
Indices: 632--812 Score: 188
Period size: 28 Copynumber: 6.3 Consensus size: 28
622 TTTTCCTTTT
* *
632 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
* * * *
662 AAGCCCATAAGTTAGTGGCATCTCTTTTCA
1 AAGCCCACAAGTCAGTGGCAAC-C-TTTAA
692 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
720 AAGCCCACAAGTCAGTGGCAATC-TTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
747 AAGCCCCACAAGTCAGTGGCAACCTTCAA
1 AAG-CCCACAAGTCAGTGGCAACCTTTAA
* *
776 AAGCACACAAGT-TGAT-GCAATCCTTTAA
1 AAGCCCACAAGTCAG-TGGCAA-CCTTTAA
804 AAGCCCACA
1 AAGCCCACA
813 CACAAGTTGG
Statistics
Matches: 132, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
27 12 0.09
28 68 0.52
29 7 0.05
30 40 0.30
31 5 0.04
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:4857 original size:52 final size:51
Alignment explanation
Indices: 4772--4895 Score: 203
Period size: 52 Copynumber: 2.4 Consensus size: 51
4762 ATATGAAAAG
* *
4772 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
* *
4823 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
4875 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
4896 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
51 21 0.31
52 47 0.69
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:4908 original size:51 final size:51
Alignment explanation
Indices: 4772--4915 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 51
4762 ATATGAAAAG
*
4772 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
4824 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGTAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
4875 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
4916 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.41
52 47 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:4922 original size:13 final size:13
Alignment explanation
Indices: 4904--4928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4894 CAAAGATCAG
4904 TGTATCGATACAA
1 TGTATCGATACAA
4917 TGTATCGATACA
1 TGTATCGATACA
4929 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:5006 original size:33 final size:33
Alignment explanation
Indices: 4969--5035 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4959 AGTAGCTTAA
4969 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5002 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5035 A
1 A
5036 AATCGTTGAA
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:5009 original size:13 final size:13
Alignment explanation
Indices: 4991--5015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4981 CAAAAAAATA
4991 TGTATCGATACAT
1 TGTATCGATACAT
5004 TGTATCGATACA
1 TGTATCGATACA
5016 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:5983 original size:22 final size:22
Alignment explanation
Indices: 5958--6026 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
5948 ATGCTGATTC
5958 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
5980 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
6001 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
6023 AAGG
1 AAGG
6027 TGAAGGTGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:6052 original size:49 final size:49
Alignment explanation
Indices: 5834--6120 Score: 318
Period size: 49 Copynumber: 5.8 Consensus size: 49
5824 GTGATAAAGA
* * * *
5834 TGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
1 TGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG
* * * *
5888 ATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGG
5941 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
5984 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
6033 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
6082 TGCCAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
6121 GAAGGGTTGC
Statistics
Matches: 205, Mismatches: 20, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
43 41 0.20
48 1 0.00
49 87 0.42
52 34 0.17
53 6 0.03
54 1 0.00
55 34 0.17
56 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
Found at i:6251 original size:30 final size:30
Alignment explanation
Indices: 6141--6594 Score: 359
Period size: 30 Copynumber: 15.5 Consensus size: 30
6131 CACCGACTTG
* * * *
6141 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* *
6171 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* *
6198 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
*
6226 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* * * *
6256 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* *
6286 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
*
6314 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* * *
6344 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* *
6374 TGTGGGC---TG-AAAAGAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAAGA-TGCCACT-GACT
* ** * *
6401 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTGAAAAAGA-TGCCACTGACT
* * *
6436 TGTGGAC-TTTGGAAAAGATGCCACCGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* * *
6465 TGTGGGC-TTCGAAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAA-GATGCCACTGACT
* *
6495 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
* * *
6522 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
*
6552 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTGAAAAAGATGCCACTGACT
*
6581 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
6595 GGGTGATGAA
Statistics
Matches: 347, Mismatches: 55, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
26 5 0.01
27 53 0.15
28 60 0.17
29 51 0.15
30 156 0.45
34 2 0.01
35 20 0.06
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAAGATGCCACTGACT
Found at i:6307 original size:58 final size:59
Alignment explanation
Indices: 6125--6594 Score: 351
Period size: 58 Copynumber: 8.0 Consensus size: 59
6115 GGCTTAGAAG
* * *
6125 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAA
*
6184 GGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTGAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAA
** * *
6241 AATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-AAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAA
***
6300 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAA
* * * * * * **
6360 GGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTT----TTG--AA
6421 A
59 A
* * * * * * *
6422 GAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGC-TTCGAAAAA
1 G-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG--AAA
* * * *
6481 GGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTCGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAA
*** * *** *
6538 AAATGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAA
6595 GGGTGATGAA
Statistics
Matches: 333, Mismatches: 55, Indels: 47
0.77 0.13 0.11
Matches are distributed among these distances:
55 22 0.07
56 7 0.02
57 76 0.23
58 80 0.24
59 61 0.18
60 47 0.14
61 1 0.00
62 19 0.06
63 2 0.01
64 13 0.04
65 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (59 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAA
Found at i:6310 original size:88 final size:87
Alignment explanation
Indices: 6125--6381 Score: 392
Period size: 88 Copynumber: 2.9 Consensus size: 87
6115 GGCTTAGAAG
* * *** * *
6125 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
6188 GCCACTGACTTGTGGGCTTTTAAA
64 GCCACTAACTTGTGGGCTTTTAAA
6212 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
6277 CCACTAACTTGTGGGCTTTTAAA
65 CCACTAACTTGTGGGCTTTTAAA
6300 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
6365 CCACTAACTTGTGGGCT
65 CCACTAACTTGTGGGCT
6382 GAAAAGAGTG
Statistics
Matches: 158, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
85 32 0.20
86 5 0.03
87 13 0.08
88 106 0.67
89 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (87 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTTAAA
Found at i:6467 original size:29 final size:29
Alignment explanation
Indices: 6416--6590 Score: 183
Period size: 29 Copynumber: 6.0 Consensus size: 29
6406 GCTTACAAAA
* * *
6416 GAAAAAGAGTGCCACGGAGTTGTGGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
* * *
6446 GGAAAAGATGCCACCGACTTGTGGGCTTC
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
6475 GAAAAAGGGTGCCACTGATTTGTGGGCTTT
1 GAAAAA-GATGCCACTGACTTGTGGGCTTT
* *
6505 G--AAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
6532 CGAAAAAAATGCCACCGACTTGTGGGCTTT
1 -GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
6562 GAAAAAAATGCCACTGACTTGTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
6591 TGAAGGGTGA
Statistics
Matches: 122, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
27 21 0.17
28 3 0.02
29 49 0.40
30 49 0.40
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:6525 original size:121 final size:116
Alignment explanation
Indices: 6187--6590 Score: 300
Period size: 121 Copynumber: 3.4 Consensus size: 116
6177 CTTTGAAGGT
* * *** * ***
6187 TGCCACTGACTTGTGGGCTTT-TAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCAC
1 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTTCGAAAAGGGTGCCAC
* * * * ** ***
6251 TGACTTGTGGGCTTTTGAACAGGGTGCCACTA-ACTTGTGGGCTT--TTAAAGGT
66 TAACTTGTGGGC---TGAAAAGAGTGCCA-TAGACTTGTGAGCTTACGAAAAAAA
* * *
6303 TGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCA
1 TGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGGCTTTCGAAAAGGGTGCCA
* * *
6368 CTAACTTGTGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGAG
65 CTAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTAC----GAAAAA-AA
* * * * * *
6425 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGC-TTCGAAAAAGGGTGCCA
1 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTTCG-AAAAGGGTGCCA
* * *** * *
6489 CTGATTTGTGGGCTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTCGAAAAAAA
65 CTAACTTGTGGGCTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACGAAAAAAA
*
6541 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGACTTT
1 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTT
6591 TGAAGGGTGA
Statistics
Matches: 232, Mismatches: 42, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
114 2 0.01
115 21 0.09
116 59 0.25
117 11 0.05
118 47 0.20
120 4 0.02
121 72 0.31
122 16 0.07
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (116 bp):
TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTTCGAAAAGGGTGCCAC
TAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACGAAAAAAA
Found at i:8036 original size:1 final size:1
Alignment explanation
Indices: 8032--8110 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
8022 CCGGACCCCC
* * * * * * ** * **
8032 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTCCTTTTGTTTTTTCATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
8097 TTGTTTTTTTTTTT
1 TTTTTTTTTTTTTT
8111 GGAGGACGCC
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.03, C:0.04, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:8052 original size:17 final size:15
Alignment explanation
Indices: 8032--8110 Score: 86
Period size: 17 Copynumber: 4.7 Consensus size: 15
8022 CCGGACCCCC
8032 TTTTTTGTTTTTGTTTG
1 TTTTTT-TTTTT-TTTG
8049 TTTTTTTATTGTTTTTG
1 TTTTTTT-TT-TTTTTG
8066 TTTTTTTTTTCCTTTTG
1 TTTTTTTTTT--TTTTG
8083 TTTTTTCATTTTTTTTG
1 TTTTTT--TTTTTTTTG
8100 TTTTTTTTTTT
1 TTTTTTTTTTT
8111 GGAGGACGCC
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.11
16 3 0.05
17 41 0.73
18 2 0.04
19 4 0.07
ACGTcount: A:0.03, C:0.04, G:0.09, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:8062 original size:21 final size:19
Alignment explanation
Indices: 8032--8110 Score: 76
Period size: 18 Copynumber: 4.3 Consensus size: 19
8022 CCGGACCCCC
8032 TTTTTTGTTTTTGTTTGTTT
1 TTTTTTGTTTTTGTTT-TTT
8052 TTTTATTGTTTTTG--TTTT
1 TTTT-TTGTTTTTGTTTTTT
**
8070 TTTTTTCCTTTTG-TTTTT
1 TTTTTTGTTTTTGTTTTTT
**
8088 TCATTT-TTTTTGTTTTTT
1 TTTTTTGTTTTTGTTTTTT
8106 TTTTT
1 TTTTT
8111 GGAGGACGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 12 0.24
18 23 0.47
19 1 0.02
20 4 0.08
21 9 0.18
ACGTcount: A:0.03, C:0.04, G:0.09, T:0.85
Consensus pattern (19 bp):
TTTTTTGTTTTTGTTTTTT
Found at i:8070 original size:34 final size:33
Alignment explanation
Indices: 8032--8111 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 33
8022 CCGGACCCCC
*
8032 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTG
1 TTTTTT-TTTTTGTTTGTTTTTTCATTGTTTTTG
*
8066 TTTTTTTTTTCCT-TTTGTTTTTTCATTTTTTTTG
1 TTTTTTTTTT--TGTTTGTTTTTTCATTGTTTTTG
8100 TTTTTTTTTTTG
1 TTTTTTTTTTTG
8112 GAGGACGCCG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 1 0.02
33 4 0.10
34 35 0.85
35 1 0.02
ACGTcount: A:0.03, C:0.04, G:0.10, T:0.84
Consensus pattern (33 bp):
TTTTTTTTTTTGTTTGTTTTTTCATTGTTTTTG
Found at i:8104 original size:23 final size:22
Alignment explanation
Indices: 8068--8110 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
8058 TGTTTTTGTT
8068 TTTTTTTTCCTTTTGTTTTTTCA
1 TTTTTTTTCCTTTT-TTTTTTCA
**
8091 TTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTCCTTTTTTTTTT
8111 GGAGGACGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (22 bp):
TTTTTTTTCCTTTTTTTTTTCA
Found at i:17806 original size:10 final size:10
Alignment explanation
Indices: 17791--17817 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17781 ATGTATCAAG
17791 CAAAAACAAA
1 CAAAAACAAA
17801 CAAAAACAAA
1 CAAAAACAAA
17811 CAAAAAC
1 CAAAAAC
17818 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:21963 original size:51 final size:50
Alignment explanation
Indices: 21887--21990 Score: 181
Period size: 51 Copynumber: 2.1 Consensus size: 50
21877 CGAAATATGA
*
21887 AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATT-ATAATGTATCGATACATCTGGGC
*
21938 AAATTTGCCTGCATGTATCGATACATTTTAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTATAATGTATCGATACATCTGGGC
21988 AAA
1 AAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
50 24 0.47
51 27 0.53
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACATTATAATGTATCGATACATCTGGGC
Done.