Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1233
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: 12712
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Found at i:1045 original size:52 final size:52
Alignment explanation
Indices: 912--1052 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
902 TGAAAAGTTA
912 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
964 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
1016 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
1053 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:1059 original size:13 final size:13
Alignment explanation
Indices: 1041--1065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1031 CAAAAATCAG
1041 TGTATCGATACAA
1 TGTATCGATACAA
1054 TGTATCGATACA
1 TGTATCGATACA
1066 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:1149 original size:13 final size:13
Alignment explanation
Indices: 1131--1155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1121 CAAAAAAATA
1131 TGTATCGATACAT
1 TGTATCGATACAT
1144 TGTATCGATACA
1 TGTATCGATACA
1156 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:1151 original size:33 final size:33
Alignment explanation
Indices: 1109--1175 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1099 AGTAGCTTAA
1109 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1142 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1175 A
1 A
1176 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:6220 original size:52 final size:53
Alignment explanation
Indices: 6150--6271 Score: 219
Period size: 52 Copynumber: 2.3 Consensus size: 53
6140 GAAAATTTAT
*
6150 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTG-C
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
6202 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
6255 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
6272 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 49 0.73
53 18 0.27
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (53 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:6284 original size:53 final size:51
Alignment explanation
Indices: 6150--6291 Score: 205
Period size: 52 Copynumber: 2.7 Consensus size: 51
6140 GAAAATTTAT
6150 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
6202 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTG-C
*
6255 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
6292 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
52 51 0.62
53 31 0.38
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:6298 original size:13 final size:13
Alignment explanation
Indices: 6280--6304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6270 CAAAGATCAG
6280 TGTATCGATACAA
1 TGTATCGATACAA
6293 TGTATCGATACA
1 TGTATCGATACA
6305 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:6387 original size:13 final size:13
Alignment explanation
Indices: 6369--6393 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6359 CAAAAAAATA
6369 TGTATCGATACAT
1 TGTATCGATACAT
6382 TGTATCGATACA
1 TGTATCGATACA
6394 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:6389 original size:33 final size:33
Alignment explanation
Indices: 6347--6413 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
6337 AGTAGCTTAA
6347 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
6380 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
6413 A
1 A
6414 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:7454 original size:49 final size:49
Alignment explanation
Indices: 7288--8030 Score: 909
Period size: 49 Copynumber: 15.7 Consensus size: 49
7278 AAAAGGATGT
*
7288 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
7340 CGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
7388 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
7437 CAATGTGCTGAGTCAAGGCCAGCTACAGTGGACTTAAAGATGATGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7486 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
7529 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7578 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
7621 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7670 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
7713 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
7762 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
7805 CAATGTGCTAATTCAAGGCCAGCTACATTAGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
7848 CAATGTGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
7897 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
7946 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
7995 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
8031 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:7561 original size:92 final size:92
Alignment explanation
Indices: 7332--8030 Score: 881
Period size: 92 Copynumber: 7.5 Consensus size: 92
7322 TAAAGATGGA
* *
7332 AAAGGTGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-AGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
* *
7396 TGATTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * * * *
7423 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAGTGGACTTAAAGATGATGATGCCA
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
*
7488 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 ATGTGCTGATTCAAGGCCAGCGATATTGGACTT
* *
7521 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
7586 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
7613 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
7678 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
7705 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGTCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * *
7770 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
7797 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTAGACTT----A--AAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
7856 TGATTCAAGGCCAGCAATATTGGACTTAAAGAT
66 TGATTCAAGGCCAGCGATATTGGAC-T-----T
* * * *
7889 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGTCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * *
7954 TGAGTCAAGGCCAGCTACATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * *
7981 AAAGATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
8031 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:7638 original size:21 final size:21
Alignment explanation
Indices: 7571--7638 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
7561 CTTAAAGATG
7571 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
*
7592 AA-G-GCCAGCGATAT--TGGACTTA
1 AAGGTGCCA---ATATGCT-GA-TTC
7614 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
7635 AAGG
1 AAGG
7639 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:8057 original size:30 final size:30
Alignment explanation
Indices: 8023--8100 Score: 111
Period size: 32 Copynumber: 2.5 Consensus size: 30
8013 CCAGCTATAT
8023 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
*
8053 TGGGCTTGGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAG--GGTTGCCACCGACTTGTG
8085 TGGGCTTTAGGAAGGG
1 TGGGC-TTA-GAAGGG
8101 AGAAAGATGC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 11 0.26
32 25 0.60
33 2 0.05
34 4 0.10
ACGTcount: A:0.18, C:0.17, G:0.40, T:0.26
Consensus pattern (30 bp):
TGGGCTTAGAAGGGTTGCCACCGACTTGTG
Found at i:8073 original size:32 final size:33
Alignment explanation
Indices: 8030--8091 Score: 117
Period size: 32 Copynumber: 1.9 Consensus size: 33
8020 TATTGGGCTT
8030 AGAAGGGTTGCCACCGACTTGTGTGGGCTTGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTGGA
8063 AGAA-GGTTGCCACCGACTTGTGTGGGCTT
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTT
8092 TAGGAAGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.18, C:0.19, G:0.37, T:0.26
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTGGA
Found at i:8141 original size:34 final size:33
Alignment explanation
Indices: 8103--9163 Score: 929
Period size: 34 Copynumber: 32.8 Consensus size: 33
8093 AGGAAGGGAG
* * *
8103 AAAGATGCCACGGAATTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
8137 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8172 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
**
8202 --A-GTGCCACGGAGTCATGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8233 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
8267 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
8299 AAA-GTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8332 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8366 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
8398 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
* *
8432 AAAAGTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
8463 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
8492 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8526 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
8556 --A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8587 AAATGGGTGCCACGGAGTTATGGGCTTAGAAGGAAA
1 AAA--GGTGCCACGGAGTTGTGGGCTTAAAAGG-AA
* * **
8623 AAAGAGTGCTACAGAGTTGTGGGCTTTTAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
8655 AAA-GTGCCACGGAG-TGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8687 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8721 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAA-A-GGAA
* *
8757 AAAAGTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
8788 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
8817 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
8851 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
8881 --A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
8912 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
8946 AAAGAGTGCCACAGAGTTGTGGGCTT-TAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
8977 AAA-GTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* *
9010 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
9044 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAA-AGGAA
* * *
9079 AAAAGTGCCACGAAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
9110 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
9139 AAAGGTGCCACGGAGTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
9164 TGAAGAAAAA
Statistics
Matches: 871, Mismatches: 81, Indels: 152
0.79 0.07 0.14
Matches are distributed among these distances:
27 68 0.08
28 74 0.08
29 28 0.03
30 31 0.04
31 9 0.01
32 115 0.13
33 63 0.07
34 307 0.35
35 120 0.14
36 56 0.06
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:8357 original size:194 final size:190
Alignment explanation
Indices: 8103--9164 Score: 1045
Period size: 194 Copynumber: 5.5 Consensus size: 190
8093 AGGAAGGGAG
* * *
8103 AAAGATGCCACGGAATTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAG-TGCCACGGAGTTGTGGGCTTTAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGCTTTAAA
**
8167 AAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGAGTGCCACGGAGTCATGGGCTTTAAAAGG
62 AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGG
* *
8231 AAAAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTA
127 AAAAA-GGTGCCACGGAGTTGTGGGCTT-GAA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTTA
8296 AAA
188 AAA
8299 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* *
8364 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGAC-TTAAAGA
65 AAGAAGGTGCCACGGAGTTGTGGGCTTT-AA--AAGA-GTGCCACGGAGTTGTGGGCTTTAAA-A
* * * * *
8428 TGAAAAAAGTGCCACGGAATTGTGGGCTT---TAAAAGGGTGCCACGGAGTTGTGGGC-TTTAAA
125 GGAAAAAGGTGCCACGGAGTTGTGGGCTTGAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAAA
8489 GGA
190 --A
8492 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT----A
1 AAA-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
* *
8553 -AAG-A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAATGGGTGCCACGGAGTTATGGGC-TT
64 GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAA-G----A---GTGCCACGGAGTTGTGGGCTTT
* * * *
8614 AGAAGGAAAAAAGAGTGCTACAGAGTTGTGGGCTTTTAA-AAAAA-GTGCCACGGAG-TGTGGGC
121 AAAAGG-AAAAAG-GTGCCACGGAGTTGTGGGC-TTGAAGAAAAAGGTGCCACGGAGTTGTGGGC
*
8676 TTTGAAAAGA
183 TTT-TAAA-A
8686 AGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAG
1 A-AA-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA-
* * * * *
8751 ATGAAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGGCTTT-AAAG
62 AAG-AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
8815 G-AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGC-TTT-
126 GAAAAAGGTGCCACGGAGTTGTGGGC-TTG--AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTA
8877 -AA
188 AAA
* * * * * *
8879 AGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGC-TTAGAAG
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAA-GAAGAA-GGTGCCACGGAGTTGTGGGCTTTAAAAA
* * *
8943 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAA-
64 GAAGAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* * *
9007 GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
126 GAAAAAGGTGCCACGGAGTTGTGGGC-TT--GAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT--
*
9072 AGATGAAA
186 ---TAAAA
* * *
9080 AAAGTGCCACGAAATTGTGGGCTTT--AA-AAG--GGTGCCACGGAGTTGTGGGCTTT-AAAGGA
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
9139 A-AAGGTGCCACGGAGTTGTGGGCTTT
66 AGAAGGTGCCACGGAGTTGTGGGCTTT
9165 GAAGAAAAAA
Statistics
Matches: 746, Mismatches: 60, Indels: 124
0.80 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 9 0.01
190 29 0.04
191 89 0.12
192 76 0.10
193 100 0.13
194 161 0.22
195 91 0.12
196 33 0.04
197 21 0.03
198 34 0.05
199 26 0.03
201 23 0.03
202 2 0.00
203 2 0.00
204 24 0.03
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.22
Consensus pattern (190 bp):
AAAGTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
AGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAA
AGGTGCCACGGAGTTGTGGGCTTGAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTTAAAA
Found at i:9205 original size:30 final size:30
Alignment explanation
Indices: 9144--9288 Score: 157
Period size: 31 Copynumber: 4.7 Consensus size: 30
9134 AAGGAAAAGG
* * * *
9144 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTG-AGACAAAA
* *
9175 TGCCATTGAGTCGTGGACCTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
9205 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTT-GAGACAAA-A
*
9237 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
9268 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
9289 TTTTTTTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
30 27 0.28
31 47 0.48
32 23 0.24
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:9241 original size:93 final size:93
Alignment explanation
Indices: 9112--9285 Score: 224
Period size: 93 Copynumber: 1.9 Consensus size: 93
9102 TTTAAAAGGG
* * * * * *
9112 TGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG-AAAAAAT
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTG-AGCAAAAAAT
*
9176 GCCATTGAGTCGTGGACCTTGAGACAAAA
65 GCCACTGAGTCGTGGACCTTGAGACAAAA
* * * * *
9205 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTG
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
9270 CCACTGAGTCGTGGAC
66 CCACTGAGTCGTGGAC
9286 TTTTTTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (93 bp):
TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
CCACTGAGTCGTGGACCTTGAGACAAAA
Done.