Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1504
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: 12659
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Found at i:1047 original size:52 final size:52
Alignment explanation
Indices: 914--1054 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
904 TGAAAAGTTA
914 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
966 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
1018 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
1055 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1061 original size:13 final size:13
Alignment explanation
Indices: 1043--1067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1033 CAAAAATCAG
1043 TGTATCGATACAA
1 TGTATCGATACAA
1056 TGTATCGATACA
1 TGTATCGATACA
1068 TGTGAGTAAT
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:1151 original size:13 final size:13
Alignment explanation
Indices: 1133--1157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1123 CAAAAAAATA
1133 TGTATCGATACAT
1 TGTATCGATACAT
1146 TGTATCGATACA
1 TGTATCGATACA
1158 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:1153 original size:33 final size:33
Alignment explanation
Indices: 1111--1177 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1101 AGTAGCTTAA
1111 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1144 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1177 A
1 A
1178 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:6247 original size:48 final size:52
Alignment explanation
Indices: 6135--6250 Score: 197
Period size: 48 Copynumber: 2.3 Consensus size: 52
6125 GAAAATTTAT
6135 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
6187 CTGCA-GTATCGATACATTTAA-A-TGTATCGATACATCT-GGCAAA-TTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
6234 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
6251 AAGATCAGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
47 9 0.14
48 17 0.27
49 15 0.24
50 1 0.02
51 16 0.25
52 5 0.08
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:6277 original size:13 final size:13
Alignment explanation
Indices: 6259--6283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6249 CAAAGATCAG
6259 TGTATCGATACAA
1 TGTATCGATACAA
6272 TGTATCGATACA
1 TGTATCGATACA
6284 TGTGAGTAAT
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:7435 original size:49 final size:49
Alignment explanation
Indices: 7269--8011 Score: 909
Period size: 49 Copynumber: 15.7 Consensus size: 49
7259 AAAAGGATGT
*
7269 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
7321 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
7369 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
7418 CAATGTGCTGAGTCAAGGCCAGCTACAGTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7467 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
7510 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7559 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
7602 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7651 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
7694 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
7743 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
7786 CAATGTGCTAATTCAAGGCCAGCTACATTAGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7829 CAATGTGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
7878 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
7927 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
7976 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
8012 GAAGGGTTGC
Statistics
Matches: 606, Mismatches: 60, Indels: 53
0.84 0.08 0.07
Matches are distributed among these distances:
43 192 0.32
45 4 0.01
47 4 0.01
48 45 0.07
49 323 0.53
51 1 0.00
52 37 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:7542 original size:92 final size:92
Alignment explanation
Indices: 7313--8011 Score: 881
Period size: 92 Copynumber: 7.5 Consensus size: 92
7303 TAAAGATGGA
* *
7313 AAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-AGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
* *
7377 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * * * *
7404 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAGTGGACTTAAAGATGATGATGCCA
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
*
7469 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 ATGTGCTGATTCAAGGCCAGCGATATTGGACTT
* *
7502 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
7567 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
7594 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
7659 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
7686 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGTCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * *
7751 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
7778 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTAGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
7837 TGATTCAAGGCCAGCAATATTGGACTTAAAGAT
66 TGATTCAAGGCCAGCGATATTGGAC-T-----T
* * * *
7870 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGTCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * *
7935 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
7962 AAAGATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
8012 GAAGGGTTGC
Statistics
Matches: 542, Mismatches: 41, Indels: 39
0.87 0.07 0.06
Matches are distributed among these distances:
86 36 0.07
87 1 0.00
88 1 0.00
92 343 0.63
94 1 0.00
95 1 0.00
96 1 0.00
97 45 0.08
98 113 0.21
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:7619 original size:21 final size:21
Alignment explanation
Indices: 7552--7619 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
7542 CTTAAAGATG
7552 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
7573 AA-G-GCCAGCGATAT--TGGACTTA
1 AAGGTGCCA---ATATGCT-GA-TTC
7595 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
7616 AAGG
1 AAGG
7620 CCAGCTACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 14 0.39
22 10 0.28
23 2 0.06
24 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:8055 original size:33 final size:35
Alignment explanation
Indices: 8011--8080 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
8001 TATTGGGCTT
8011 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
8045 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
8079 AG
1 AG
8081 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:8123 original size:34 final size:33
Alignment explanation
Indices: 8085--9143 Score: 959
Period size: 34 Copynumber: 32.8 Consensus size: 33
8075 AGGAAGGGAG
* * *
8085 AAAGATGCCACGGAATTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-GGAA
8119 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-GAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8153 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
**
8183 --A-GTGCCACGGAGTCATGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8214 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
8248 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
8280 AAA-GTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8313 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8347 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
8379 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
* *
8413 AAAAGTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
8444 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
8473 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8507 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
8537 --A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8568 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * **
8602 AAAGAGTGCTACAGAGTTGTGGGCTTTTAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
8634 AAA-GTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8667 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8701 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAA-AGGAA
* *
8736 AAAAGTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
8767 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
8796 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8830 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
8860 --A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8891 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
8925 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
8957 AAA-GTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8990 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
9024 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAA-AGGAA
* * *
9059 AAAAGTGCCACGAAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
9090 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
9119 AAAGGTGCCACGGAGTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
9144 TGAAGAAAAA
Statistics
Matches: 875, Mismatches: 80, Indels: 142
0.80 0.07 0.13
Matches are distributed among these distances:
27 68 0.08
28 74 0.08
29 3 0.00
30 53 0.06
31 6 0.01
32 123 0.14
33 70 0.08
34 340 0.39
35 132 0.15
36 6 0.01
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.22
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:8349 original size:194 final size:189
Alignment explanation
Indices: 8085--9144 Score: 1071
Period size: 194 Copynumber: 5.5 Consensus size: 189
8075 AGGAAGGGAG
* * *
8085 AAAGATGCCACGGAATTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAG-TGCCACGGAGTTGTGGGCTTTAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGCTTTAAA
**
8149 AGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGAGTGCCACGGAGTCATGGGCTTTAAAAGGA
62 AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGA
* *
8213 AAAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAA
127 AAAA-GGTGCCACGGAGTTGTGGGCTT-GAA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTTAA
8278 AA
188 AA
8280 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAAG
* *
8345 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGAC-TTAAAGA
64 AAGAAGGTGCCACGGAGTTGTGGGCTTT-AA--AAGA-GTGCCACGGAGTTGTGGGCTTTAAA-A
* * * * *
8409 TGAAAAAAGTGCCACGGAATTGTGGGCTT---TAAAAGGGTGCCACGGAGTTGTGGGC-TTTAAA
124 GGAAAAAGGTGCCACGGAGTTGTGGGCTTGAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAAA
8470 GGA
189 --A
8473 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT---A-
1 AAA-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
* * *
8534 AAG-A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGC-TTAG
64 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAA-G----A--GTGCCACGGAGTTGTGGGCTTTAA
* * *
8596 AAGGAAAAAGAGTGCTACAGAGTTGTGGGCTTTTAA-AAAAA-GTGCCACGGAGTTGTGGGCTTT
122 AAGGAAAAAG-GTGCCACGGAGTTGTGGGC-TTGAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
*
8659 GAAAAGA
185 -TAAA-A
8666 AGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAG
1 A-AA-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA-
* * * *
8731 ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGGCTTT-AAAGG
62 A-GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGG
*
8795 -AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGC-TTT--
126 AAAAAGGTGCCACGGAGTTGTGGGC-TTG--AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAA
8856 AA
188 AA
* * * * *
8858 AGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGC-TTAGAAG
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAA-GAAGAA-GGTGCCACGGAGTTGTGGGCTTTA-AAA
* * *
8922 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAA
63 GAAGAAG-GTGCCACGGAGTTGTGGGC-TTT-AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA
* * *
8987 -GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTA
124 GGAAAAAGGTGCCACGGAGTTGTGGGC-TT--GAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-
*
9051 AAGATGAAA
185 ----TAAAA
* * *
9060 AAAGTGCCACGAAATTGTGGGCTTT--AA-AAG--GGTGCCACGGAGTTGTGGGCTTTAAAGGAA
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAA
9120 -AAGGTGCCACGGAGTTGTGGGCTTT
66 GAAGGTGCCACGGAGTTGTGGGCTTT
9145 GAAGAAAAAA
Statistics
Matches: 749, Mismatches: 57, Indels: 121
0.81 0.06 0.13
Matches are distributed among these distances:
184 2 0.00
186 2 0.00
187 21 0.03
188 1 0.00
189 21 0.03
190 85 0.11
191 33 0.04
192 68 0.09
193 80 0.11
194 237 0.32
195 57 0.08
196 16 0.02
197 19 0.03
198 30 0.04
199 23 0.03
200 5 0.01
201 2 0.00
202 47 0.06
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.22
Consensus pattern (189 bp):
AAAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAA
GAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAA
GGTGCCACGGAGTTGTGGGCTTGAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAAAA
Found at i:8827 original size:323 final size:323
Alignment explanation
Indices: 8118--9147 Score: 1667
Period size: 323 Copynumber: 3.2 Consensus size: 323
8108 TTAAAAGGGA
* *
8118 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT----
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAA-AAGGTGCCACGGAGTTGTGGGCTTTGAAA
** **
8179 A-AAG-A-GTGCCACGGAGTCATGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGC-TT
65 AGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAA-G----A--GTGCCACGGAGTCGTGGGCTTT
* * * * ** *
8240 AGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT-TTA--AAAAA-AGTGCCACGGAGTTGTGGG
122 AAAAGGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGG
* *
8301 CTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGT
187 CTTT-TAAA-AA-AA-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGT
* *
8366 GGGCTTT-AAAGGAA-AAGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAA
248 GGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGGAA
8428 TTGTGGGCTTT
313 TTGTGGGCTTT
8439 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
8504 GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAA
66 GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAA
*
8569 AAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCTACAGAGTTGTGGGCTTTTAAAA
131 AAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAAAA
8634 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
196 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
8699 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
261 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
8762 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
8827 GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAA
66 GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAA
8892 AAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAAAA
131 AAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAAAA
8957 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
196 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
9022 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGAAATTGTGGGCTTT
261 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
9085 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
9148 GAAAAAAGCC
Statistics
Matches: 674, Mismatches: 20, Indels: 28
0.93 0.03 0.04
Matches are distributed among these distances:
319 17 0.03
320 112 0.17
321 43 0.06
322 23 0.03
323 429 0.64
324 22 0.03
325 4 0.01
326 4 0.01
327 20 0.03
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.22
Consensus pattern (323 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAA
AAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAAAA
AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
Found at i:9188 original size:60 final size:62
Alignment explanation
Indices: 9124--9267 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 62
9114 AAGGAAAAGG
* * * *
9124 TGCCACGGAGTTGTGGGCTTTGAAGAAAAA-A-GCCATTGAGTCGTGGACCTTGAGACAAAA
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACCTTGAGACAAAA
* * *
9184 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACCTTGAGACA-A-AA
*
9247 TGCCACTGAGTCGTGGACTTT
1 TGCCACGGAGTCGTGGACTTT
9268 TTTTTTTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 26 0.36
61 3 0.04
62 22 0.30
63 22 0.30
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (62 bp):
TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACCTTGAGACAAAA
Found at i:9194 original size:30 final size:30
Alignment explanation
Indices: 9124--9267 Score: 148
Period size: 30 Copynumber: 4.7 Consensus size: 30
9114 AAGGAAAAGG
* * *
9124 TGCCACGGAGTTGTGGGCTTTGAAGA-AAAA
1 TGCCACTGAGTCGTGGACTTTG-AGACAAAA
* * *
9154 AGCCATTGAGTCGTGGACCTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
9184 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTT-GAGACAAA-A
*
9216 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
9247 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
9268 TTTTTTTTTT
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
29 3 0.03
30 39 0.41
31 30 0.32
32 23 0.24
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:10309 original size:15 final size:15
Alignment explanation
Indices: 10289--10328 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
10279 CTCACCGAGA
*
10289 TTTTCTGTTTTGTTT
1 TTTTCTGTTTTCTTT
*
10304 TTTTCTTTTTTCTTT
1 TTTTCTGTTTTCTTT
*
10319 TTTTGTGTTT
1 TTTTCTGTTT
10329 GGAAAAGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.82
Consensus pattern (15 bp):
TTTTCTGTTTTCTTT
Done.