Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold582
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: 29659
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 153 characters in sequence are not A, C, G, or T
Found at i:10052 original size:127 final size:128
Alignment explanation
Indices: 9818--10072 Score: 487
Period size: 127 Copynumber: 2.0 Consensus size: 128
9808 CATTCAGCCG
9818 TACCTTCAAAAGGACCGTCACAAACGTGGGATCTCCGACGGCGGTTTACAGAGCTAACCTGAGTT
1 TACCTTCAAAAGGACCGTCACAAACGTGGGATCTCCGACGGCGGTTTACAGAGCTAACCTGAGTT
9883 TTTCGACAGGTACGTTGAAAATCAGGGTTAACCCCGATGTTCTGTCGTTCACGTCGGTGGGAC
66 TTTCGACAGGTACGTTGAAAATCAGGGTTAACCCCGATGTTCTGTCGTTCACGTCGGTGGGAC
9946 TACCTTC-AAAGGACCGGTC-CAAACGTGGGATCTCCGACGGCGGTTTACAGAGCTAACCTGAGT
1 TACCTTCAAAAGGACC-GTCACAAACGTGGGATCTCCGACGGCGGTTTACAGAGCTAACCTGAGT
10009 TTTTCGACAGGTACGTTGAAAATCAGGGTTAACCCCGATGTTCTGTCGTTCACGTCGGTGGGAC
65 TTTTCGACAGGTACGTTGAAAATCAGGGTTAACCCCGATGTTCTGTCGTTCACGTCGGTGGGAC
10073 AAAAGCTGTC
Statistics
Matches: 126, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
127 116 0.92
128 10 0.08
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (128 bp):
TACCTTCAAAAGGACCGTCACAAACGTGGGATCTCCGACGGCGGTTTACAGAGCTAACCTGAGTT
TTTCGACAGGTACGTTGAAAATCAGGGTTAACCCCGATGTTCTGTCGTTCACGTCGGTGGGAC
Found at i:11014 original size:23 final size:23
Alignment explanation
Indices: 10988--11033 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10978 ACTTTGTTAT
*
10988 ATCA-AATAAAATGAAATACGAAA
1 ATCATAATAAAA-AAAATACGAAA
*
11011 ATCATAGTAAAAAAAATACGAAA
1 ATCATAATAAAAAAAATACGAAA
11034 GCCAATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (23 bp):
ATCATAATAAAAAAAATACGAAA
Found at i:11314 original size:21 final size:21
Alignment explanation
Indices: 11275--11314 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11265 TAACATAAAA
* *
11275 TAATATATGATATACATATTT
1 TAATATATAAAATACATATTT
*
11296 TAATATATAAAATATATAT
1 TAATATATAAAATACATAT
11315 ATATATATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TAATATATAAAATACATATTT
Found at i:11385 original size:3 final size:3
Alignment explanation
Indices: 11372--11431 Score: 79
Period size: 3 Copynumber: 19.7 Consensus size: 3
11362 AAGTTAGAAA
11372 AAT ATAT AAT AAT AAT AAT AAT AAT AA- AGAT AAT AAT AAT AAT AA-
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
11417 AGAT AAT AAT AAT AA
1 A-AT AAT AAT AAT AA
11432 CAAAATATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11404 original size:18 final size:18
Alignment explanation
Indices: 11383--11431 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
11373 ATATATAATA
11383 ATAATAATAATAATAAAG
1 ATAATAATAATAATAAAG
11401 ATAATAATAATAATAAAG
1 ATAATAATAATAATAAAG
11419 ATAATAATAATAA
1 ATAATAATAATAA
11432 CAAAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
ATAATAATAATAATAAAG
Found at i:12984 original size:45 final size:45
Alignment explanation
Indices: 12920--13084 Score: 177
Period size: 45 Copynumber: 3.6 Consensus size: 45
12910 CTAGGAAAGT
* * *
12920 AAGATCCGCTGTTGCAGCTTCAAACTTTTTAACTGCCAGGGAAGC
1 AAGATCCGCTGCTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* * * * *
12965 AAGATCCGTTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGT
1 AAGATCCGCTGCTGTAGCTTCAATCTTTTTAACTG---C-C-AGGGAAGC
* * * *
13015 AAAATACGCTGTTGTAGCTTCAATCTTTTTAACTGCCGGGGAAGC
1 AAGATCCGCTGCTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
13060 AAGATCCGCTGCTGTAGCTTCAATC
1 AAGATCCGCTGCTGTAGCTTCAATC
13085 GCTGTTGTAG
Statistics
Matches: 95, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
45 56 0.59
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 35 0.37
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (45 bp):
AAGATCCGCTGCTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
Found at i:13032 original size:50 final size:50
Alignment explanation
Indices: 12901--13084 Score: 172
Period size: 45 Copynumber: 3.9 Consensus size: 50
12891 ATTCTATTCC
* * *
12901 ACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGCAGCTTCAAACTTTTTA
1 ACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
* * * * * *
12951 ACTG---C-C-AGGGAAGCAAGATCCGTTGCTGTAGCTTCAATCTGTTTC
1 ACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
* *
12996 ACTGCAACGCTAGGAAAGTAAAATACGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
* * *
13046 ACTGC--CG---GGGAAGCAAGATCCGCTGCTGTAGCTTCAATC
1 ACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATC
13085 GCTGTTGTAG
Statistics
Matches: 107, Mismatches: 22, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
45 62 0.58
46 1 0.01
48 3 0.03
49 1 0.01
50 40 0.37
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.28
Consensus pattern (50 bp):
ACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
Found at i:13063 original size:95 final size:95
Alignment explanation
Indices: 12900--13084 Score: 307
Period size: 95 Copynumber: 1.9 Consensus size: 95
12890 TATTCTATTC
* * *
12900 CACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGCAGCTTCAAACTTTTTAACTGCCAGGGAAGC
1 CACTGCAACGCTAGGAAAGTAAAATACGCTGTTGCAGCTTCAAACTTTTTAACTGCCAGGGAAGC
*
12965 AAGATCCGTTGCTGTAGCTTCAATCTGTTT
66 AAGATCCGCTGCTGTAGCTTCAATCTGTTT
* * *
12995 CACTGCAACGCTAGGAAAGTAAAATACGCTGTTGTAGCTTCAATCTTTTTAACTGCCGGGGAAGC
1 CACTGCAACGCTAGGAAAGTAAAATACGCTGTTGCAGCTTCAAACTTTTTAACTGCCAGGGAAGC
13060 AAGATCCGCTGCTGTAGCTTCAATC
66 AAGATCCGCTGCTGTAGCTTCAATC
13085 GCTGTTGTAG
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 83 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (95 bp):
CACTGCAACGCTAGGAAAGTAAAATACGCTGTTGCAGCTTCAAACTTTTTAACTGCCAGGGAAGC
AAGATCCGCTGCTGTAGCTTCAATCTGTTT
Found at i:13093 original size:18 final size:18
Alignment explanation
Indices: 13066--13102 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
13056 AAGCAAGATC
13066 CGCTGCTGTAGCTTCAAT
1 CGCTGCTGTAGCTTCAAT
*
13084 CGCTGTTGTAGCTTCAAT
1 CGCTGCTGTAGCTTCAAT
13102 C
1 C
13103 TATTCCACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (18 bp):
CGCTGCTGTAGCTTCAAT
Found at i:13175 original size:113 final size:113
Alignment explanation
Indices: 12977--13197 Score: 397
Period size: 113 Copynumber: 2.0 Consensus size: 113
12967 GATCCGTTGC
* * *
12977 TGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAAATACGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTATTCCACTGCAACACTAGGAAAGTAAAATACGCTGTTGTAGCTTCAATCTT
13042 TTTAACTGCCGGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCGCTGT
66 TTTAACTGCCGGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCGCTGT
* *
13090 TGTAGCTTCAATCTATTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 TGTAGCTTCAATCTATTCCACTGCAACACTAGGAAAGTAAAATACGCTGTTGTAGCTTCAATCTT
13155 TTTAACTGCCGGGGAAGCAAGATCCGCTGCTGTAGCTTCAATC
66 TTTAACTGCCGGGGAAGCAAGATCCGCTGCTGTAGCTTCAATC
13198 TGCTCCACTG
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 103 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (113 bp):
TGTAGCTTCAATCTATTCCACTGCAACACTAGGAAAGTAAAATACGCTGTTGTAGCTTCAATCTT
TTTAACTGCCGGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCGCTGT
Found at i:13192 original size:45 final size:45
Alignment explanation
Indices: 13128--14100 Score: 805
Period size: 45 Copynumber: 20.6 Consensus size: 45
13118 CTAGGAAAGT
*
13128 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* ** ** * *
13173 AAGATCCGCTGCTGTAGCTTCAATCTGCTCCACTGCAATGCTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGC----C-AGGGAAGC
* * *
13223 AAGATCCGATGTTGTAGCTTCAATCTTTTTAATTGCAAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
** * * * *
13268 AAGATCCGCTACTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG---C-C-AGGGAAGC
* *
13318 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* ** * * **
13363 AAGATCCGCTGCTGTAGCTTCAATCCGTTTCACTGCAAAGCTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGC----C-AGGGAAGC
*
13413 AAGATCCGTTGTTGTAGCTTCAATCTTTTTAACTG-CAGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCA-GGGAAGC
* ** * *
13458 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG---C-C-AGGGAAGC
* *
13508 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCCGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* * * * ** * *
13553 AAGATCCGCTGCTGTAGATTCAATATGTTCCACTGCAATGCTAGGAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCA-G---GGAAGC
13602 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* * * * *
13647 AAGATCCGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG---C-C-AGGGAAGC
* * * *
13697 AAGATCCACTGTTGTAGCTTCAATATTTTTAATTGCAAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* * *
13742 AAGATCCGCTGTTGTAGCTTCAATATTTTTAATTGCAAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* * ** * * **
13787 AAGATCCGCTGCTGTAACTTCAATCCGTTTCACTGCAACACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG---C-C-AGGGAAGC
* * * *
13837 AAGATACGCTGTTGTAGCTTCAATATTTTTAATTGCAAGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* * * * *
13882 AAGATCCGTTGTTGTAGCTTCAATCTGTTTCACTGCAAGGCTAGAAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGG---G--AAGC
*
13932 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCGGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* *
13977 AAGATCCCCTGTTGTAGCTTCAATCTTTTTAACTGCCCGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
* * * ** * *
14022 AAGATCCGTTGCTGTAGCTTCAATCTGTTCCACTGCAATGCTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGC----C-AGGGAAGC
14072 AAGATCCGCTGTTGTAGCTTCAATCTTTT
1 AAGATCCGCTGTTGTAGCTTCAATCTTTT
14101 AAATTGCAAT
Statistics
Matches: 736, Mismatches: 146, Indels: 87
0.76 0.15 0.09
Matches are distributed among these distances:
44 1 0.00
45 405 0.55
46 2 0.00
47 5 0.01
48 5 0.01
49 39 0.05
50 278 0.38
51 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (45 bp):
AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGC
Found at i:13247 original size:95 final size:95
Alignment explanation
Indices: 13084--14109 Score: 1220
Period size: 95 Copynumber: 10.9 Consensus size: 95
13074 TAGCTTCAAT
* * * *
13084 CGCTGTTGTAGCTTCAATCTATTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
**
13149 AATCTTTTTAACTGCCGGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
* * * *
13179 CGCTGCTGTAGCTTCAATCTGCTCCACTGCAATGCTAGGAAAGTAAGATCCGATGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
*
13244 AATCTTTTTAATTGCAAGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
*
13274 CGCTACTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
*
13339 AATCTTTTTAATTGCAAGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
* * * *
13369 CGCTGCTGTAGCTTCAATCCGTTTCACTGCAAAGCTAGGAAAATAAGATCCGTTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
*
13434 AATCTTTTTAACTGCAGGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
* * *
13464 CGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
* **
13529 AATATTTTTAACTGCCGGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
* * * *
13559 CGCTGCTGTAGATTCAATATGTTCCACTGCAATGCTAGG-AAGTAAGATCCGCTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
*
13623 AATCTTTTTAACTGCCAGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
*
13653 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCACTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
* *
13718 AATATTTTTAATTGCAAGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
* * * * * * * *
13748 CGCTGTTGTAGCTTCAATATTTTTAATTGCAA-G---GG-AAGCAAGATCCGCTGCTGTAACTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
** * * ** *
13808 AATCCGTTTCACTGCAACACTAGGAAAATAAGATA
66 AATCTTTTTAACTG---CA--AGGGAAGCAAGATC
* * * * * * *
13843 CGCTGTTGTAGCTTCAATATTTTTAATTGCAA-G---GG-AAGCAAGATCCGTTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
* * *
13903 AATCTGTTTCACTGCAAGGCTAGAAAAGTAAGATC
66 AATCTTTTTAACTGCAAGG---G--AAGCAAGATC
* * * * * *
13938 CGCTGTTGTAGCTTCAATCTTTTTAACTGC--CG---GGGAAGCAAGATCCCCTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
**
13998 AATCTTTTTAACTGCCCGGGAAGCAAGATC
66 AATCTTTTTAACTGCAAGGGAAGCAAGATC
* * *
14028 CGTTGCTGTAGCTTCAATCTGTTCCACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
1 CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
* *
14093 AATCTTTTAAATTGCAA
66 AATCTTTTTAACTGCAA
14110 TGTCGGGGAA
Statistics
Matches: 821, Mismatches: 92, Indels: 36
0.87 0.10 0.04
Matches are distributed among these distances:
90 67 0.08
91 2 0.00
92 4 0.00
93 2 0.00
94 92 0.11
95 654 0.80
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (95 bp):
CGCTGCTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTC
AATCTTTTTAACTGCAAGGGAAGCAAGATC
Found at i:13400 original size:140 final size:135
Alignment explanation
Indices: 13128--14102 Score: 854
Period size: 140 Copynumber: 6.9 Consensus size: 135
13118 CTAGGAAAGT
* ** *
13128 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCGGGGAAGCAAGATCCGCTGCTGTAGCTT
1 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAAGGGAAGCAAGATCCGCTGTTGTAGCTT
** ** * * * * *
13193 CAATCTGCTCCACTGCAATGCTAGGAAAGTAAGATCCGATGTTGTAGCTTCAATCTTTTTAATTG
66 CAATCTTTTTAACTGCAA-G---GG-AAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAACTG
13258 CAAGGGAAGC
126 CAAGGGAAGC
** * * * *
13268 AAGATCCGCTACTGTAGCTTCAATCTGTTTCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGT
1 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAA-G---GG-AAGCAAGATCCGCTGTTGT
* * *
13333 AGCTTCAATCTTTTTAATTGCAAGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCCGTTTCACTG
61 AGCTTCAATCTTTTTAACTGCAAGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAACTG
**
13398 CAAAGCTAGGAAAAT
126 C-AAG---GG-AAGC
* * *
13413 AAGATCCGTTGTTGTAGCTTCAATCTTTTTAACTGCAGGGGAAGCAAGATCCGCTGTTGTAGCTT
1 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAAGGGAAGCAAGATCCGCTGTTGTAGCTT
* ** * * * * *
13478 CAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATATTTTTAACTG
66 CAATCTTTTTAACTG---CA--AGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAACTG
**
13543 CCGGGGAAGC
126 CAAGGGAAGC
* * * ** *
13553 AAGATCCGCTGCTGTAGATTCAATATGTTCCACTGCAATGCTAGGAAGTAAGATCCGCTGTTGTA
1 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAA-G---GGAAGCAAGATCCGCTGTTGTA
* *
13618 GCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTCACTGC
62 GCTTCAATCTTTTTAACTGCAAGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAACTGC
*
13683 AACGCTAGGAAAGT
127 AA-G---GG-AAGC
* *
13697 AAGATCCACTGTTGTAGCTTCAATATTTTTAATTGCAAGGGAAGCAAGATCCGCTGTTGTAGCTT
1 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAAGGGAAGCAAGATCCGCTGTTGTAGCTT
* * * * *
13762 CAATATTTTTAATTGCAAGGGAAGCAAGATCCGCTGCTGTAACTTCAATCCGTTTCACTGCAACA
66 CAATCTTTTTAACTGCAAGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAACTG---CA
* **
13827 CTAGGAAAAT
128 --AGGGAAGC
* * *
13837 AAGATACGCTGTTGTAGCTTCAATATTTTTAATTGCAAGGGAAGCAAGATCCGTTGTTGTAGCTT
1 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAAGGGAAGCAAGATCCGCTGTTGTAGCTT
* * * * *
13902 CAATCTGTTTCACTGCAAGGCTAGAAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG
66 CAATCTTTTTAACTGCAAGG---G--AAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAACTG
**
13967 CCGGGGAAGC
126 CAAGGGAAGC
* * ** * *
13977 AAGATCCCCTGTTGTAGCTTCAATCTTTTTAACTGCCCGGGAAGCAAGATCCGTTGCTGTAGCTT
1 AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAAGGGAAGCAAGATCCGCTGTTGTAGCTT
* ** * *
14042 CAATCTGTTCCACTGCAATGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TTTAA
66 CAATCTTTTTAACTGCAA-G---GG-AAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAA
14103 ATTGCAATGT
Statistics
Matches: 690, Mismatches: 107, Indels: 77
0.79 0.12 0.09
Matches are distributed among these distances:
139 43 0.06
140 403 0.58
141 15 0.02
142 1 0.00
143 8 0.01
144 80 0.12
145 140 0.20
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (135 bp):
AAGATCCGCTGTTGTAGCTTCAATATTTTTAACTGCAAGGGAAGCAAGATCCGCTGTTGTAGCTT
CAATCTTTTTAACTGCAAGGGAAGCAAGATCCGCTGCTGTAGCTTCAATCTGTTTAACTGCAAGG
GAAGC
Found at i:14191 original size:49 final size:49
Alignment explanation
Indices: 14130--14295 Score: 174
Period size: 49 Copynumber: 3.4 Consensus size: 49
14120 GTGAGATTTG
14130 CCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGGAGTAAGATTCA
1 CCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGGAGTAAGATTCA
* * **** * * * *
14179 CCGTTGTGGCTTCAATCT-TTAAATTGCAAT-GTCAGGGAAGTGAGATTCG
1 CCGTTGTAGCTTCAATCTGCTCCGCTGC-ATCGCCTGGG-AGTAAGATTCA
* *
14228 CCGTTATAGCTTCAATCTGCTCCGCTGCATCGCCTAGGAAGTAAGATTCA
1 CCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCT-GGGAGTAAGATTCA
*
14278 CCGTTGTGGCTTCAATCT
1 CCGTTGTAGCTTCAATCT
14296 TTGAATTGCG
Statistics
Matches: 88, Mismatches: 24, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
48 9 0.10
49 46 0.52
50 31 0.35
51 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (49 bp):
CCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCTGGGAGTAAGATTCA
Found at i:14221 original size:98 final size:99
Alignment explanation
Indices: 14034--14304 Score: 395
Period size: 99 Copynumber: 2.7 Consensus size: 99
14024 GATCCGTTGC
* * * * * *
14034 TGTAGCTTCAATCTGTTCCACTGCAAT-G-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATC
1 TGTAGCTTCAATCTGCTCCGCTGC-ATCGCCTAGG-AAGTAAGATTCACCGTTGTGGCTTCAATC
* *
14097 TTTTAAATTGCAATGTCGGGGAAGTGAGATTTGCCGT
64 -TTTAAATTGCAATGTCAGGGAAGTGAGATTCGCCGT
*
14134 TGTAGCTTCAATCTGCTCCGCTGCATCGCCT-GGGAGTAAGATTCACCGTTGTGGCTTCAATCTT
1 TGTAGCTTCAATCTGCTCCGCTGCATCGCCTAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTT
14198 TAAATTGCAATGTCAGGGAAGTGAGATTCGCCGT
66 TAAATTGCAATGTCAGGGAAGTGAGATTCGCCGT
*
14232 TATAGCTTCAATCTGCTCCGCTGCATCGCCTAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTT
1 TGTAGCTTCAATCTGCTCCGCTGCATCGCCTAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTT
*
14297 TGAATTGC
66 TAAATTGC
14305 GAACTATGGT
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
98 64 0.41
99 65 0.42
100 25 0.16
101 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (99 bp):
TGTAGCTTCAATCTGCTCCGCTGCATCGCCTAGGAAGTAAGATTCACCGTTGTGGCTTCAATCTT
TAAATTGCAATGTCAGGGAAGTGAGATTCGCCGT
Found at i:15494 original size:44 final size:43
Alignment explanation
Indices: 15442--15547 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 43
15432 TACCCCGATC
* **
15442 TGAT-CAAAATTTGAGTTGCTCTGATCACCACCATGCCCCAATT
1 TGATCCAAAATTTAAGCCGCTCTGATCA-CACCATGCCCCAATT
** * *
15485 TGATCCAAAATTTAAGCCGCTCTGATCACTTCGTGCCCCATTT
1 TGATCCAAAATTTAAGCCGCTCTGATCACACCATGCCCCAATT
* *
15528 TGTTCCAAAATTTTAGCCGC
1 TGATCCAAAATTTAAGCCGC
15548 CCTTTTTGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 33 0.62
44 20 0.38
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (43 bp):
TGATCCAAAATTTAAGCCGCTCTGATCACACCATGCCCCAATT
Found at i:15681 original size:9 final size:9
Alignment explanation
Indices: 15620--15716 Score: 68
Period size: 9 Copynumber: 9.9 Consensus size: 9
15610 TTGGCCTCTC
*
15620 CTTTTTTTC
1 CTTTTTTTT
15629 CTTTTCTTTT
1 CTTTT-TTTT
*
15639 CTCTTCTTCTT
1 CT-TT-TTTTT
*
15650 CTTCTTTTT
1 CTTTTTTTT
*
15659 CTTCTCGTTCTT
1 CTT-T--TTTTT
15671 CTTTTTTTT
1 CTTTTTTTT
15680 CTTTTTTTTT
1 C-TTTTTTTT
*
15690 CTTTCTTTCT
1 CTTT-TTTTT
15700 CTTTTTTTT
1 CTTTTTTTT
*
15709 GTTTTTTT
1 CTTTTTTT
15717 GTATTTTTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
9 31 0.44
10 23 0.33
11 8 0.11
12 8 0.11
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:15684 original size:6 final size:6
Alignment explanation
Indices: 15623--15705 Score: 51
Period size: 6 Copynumber: 12.8 Consensus size: 6
15613 GCCTCTCCTT
* * *
15623 TTTTTC CTTTTC TTTTCTC TTCTTC TTCTTC TTTTTC TTCTCGTTC TTCTTT-
1 TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TT-T--TTC TT-TTTC
* *
15675 TTTTTC TTTTTTT TTCTTTC TTTCTC TTTTT
1 TTTTTC -TTTTTC TT-TTTC TTTTTC TTTTT
15706 TTTGTTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
5 3 0.05
6 34 0.55
7 18 0.29
9 7 0.11
ACGTcount: A:0.00, C:0.23, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:15688 original size:30 final size:28
Alignment explanation
Indices: 15637--15716 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 28
15627 TCCTTTTCTT
* * *
15637 TTCTCTTCTTCTTCTTCTTTTTCTTCTCG
1 TTCTCTTTTTTTTCTTTTTTTTCTT-TCG
*
15666 TTCTTCTTTTTTTTCTTTTTTTTTCTTTCT
1 TTC-TCTTTTTTTTC-TTTTTTTTCTTTCG
*
15696 TTCTCTTTTTTTTGTTTTTTT
1 TTCTCTTTTTTTTCTTTTTTT
15717 GTATTTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 7 0.16
29 13 0.30
30 14 0.32
31 10 0.23
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (28 bp):
TTCTCTTTTTTTTCTTTTTTTTCTTTCG
Found at i:15716 original size:10 final size:10
Alignment explanation
Indices: 15672--15708 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
15662 CTCGTTCTTC
15672 TTTTTTTTCT
1 TTTTTTTTCT
15682 TTTTTTTTCT
1 TTTTTTTTCT
* *
15692 TTCTTTCTCT
1 TTTTTTTTCT
15702 TTTTTTT
1 TTTTTTT
15709 GTTTTTTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:20660 original size:21 final size:22
Alignment explanation
Indices: 20626--20679 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
20616 ATATGTGGAT
*
20626 TATAAAAATA-ACATAAAATAA
1 TATATAAATATACATAAAATAA
***
20647 TATAT-AATATACATATTTTAA
1 TATATAAATATACATAAAATAA
20668 TATATAAATATA
1 TATATAAATATA
20680 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
TATATAAATATACATAAAATAA
Found at i:20844 original size:3 final size:3
Alignment explanation
Indices: 20836--20903 Score: 68
Period size: 3 Copynumber: 22.0 Consensus size: 3
20826 ATATAAAAAC
* *
20836 ATA ATA ATA ACA ATA ATA TTA ATA A-A TATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
20880 GATA ATA ATA ATA ACTAA ATA ATA
1 -ATA ATA ATA ATA A-T-A ATA ATA
20904 GAATTACTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 2 0.04
3 47 0.85
4 4 0.07
5 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:20879 original size:18 final size:18
Alignment explanation
Indices: 20818--20900 Score: 82
Period size: 18 Copynumber: 4.6 Consensus size: 18
20808 TAAAATTTAC
20818 ATAAGTAAATATAA-AA-A
1 ATAA-TAAATATAATAATA
*
20835 CATAAT-AATAACAATAATA
1 -ATAATAAAT-ATAATAATA
*
20854 TTAATAAATATAATAATA
1 ATAATAAATATAATAATA
*
20872 ATAATAAAGATAATAATA
1 ATAATAAATATAATAATA
20890 ATAACTAAATA
1 ATAA-TAAATA
20901 ATAGAATTAC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 3 0.06
17 4 0.07
18 38 0.70
19 9 0.17
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAATAAATATAATAATA
Found at i:20988 original size:30 final size:31
Alignment explanation
Indices: 20919--20988 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
20909 ACTAAAATAT
* *
20919 GGACTAAATCGAAATAAAAACAAGAGTATAG
1 GGACTAAATCGAAATAAAAACAAGAGAAAAG
* *
20950 GG-CGAAATCGAAATAAGAA-AAG-GCAAAAG
1 GGACTAAATCGAAATAAAAACAAGAG-AAAAG
20979 GGACTAAATC
1 GGACTAAATC
20989 ACGATGCACG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.03
29 8 0.25
30 21 0.66
31 2 0.06
ACGTcount: A:0.53, C:0.11, G:0.23, T:0.13
Consensus pattern (31 bp):
GGACTAAATCGAAATAAAAACAAGAGAAAAG
Found at i:21737 original size:22 final size:22
Alignment explanation
Indices: 21696--21738 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21686 TCACCTTGAA
* * *
21696 TGTTTTTTTTTTTGCTAATATC
1 TGTTTTTTTTGTTACAAATATC
21718 TGTTTTTTTTGTTACAAATAT
1 TGTTTTTTTTGTTACAAATAT
21739 TGCCCGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.65
Consensus pattern (22 bp):
TGTTTTTTTTGTTACAAATATC
Found at i:23713 original size:16 final size:17
Alignment explanation
Indices: 23682--23715 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
23672 TGAATTTGAT
23682 TGAAAATATACAAAAAA
1 TGAAAATATACAAAAAA
*
23699 TGAAAATA-CCAAAAAA
1 TGAAAATATACAAAAAA
23715 T
1 T
23716 TCTAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.09, G:0.06, T:0.18
Consensus pattern (17 bp):
TGAAAATATACAAAAAA
Found at i:24433 original size:10 final size:11
Alignment explanation
Indices: 24411--24438 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
24401 CCCAATACCC
24411 AAAAACATAAA
1 AAAAACATAAA
24422 AAAAACATAAA
1 AAAAACATAAA
24433 AAAAAC
1 AAAAAC
24439 CCTAGCTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.11, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAACATAAA
Found at i:26576 original size:18 final size:18
Alignment explanation
Indices: 26553--26589 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
26543 TCATCATTAT
26553 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
26571 TATTAGTTTATATATTTA
1 TATTAGTTTATATATTTA
26589 T
1 T
26590 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:27709 original size:31 final size:33
Alignment explanation
Indices: 27665--27744 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 33
27655 TTATAACCCC
* *
27665 TATATATATACATATATTC-TTTTTAT-ATATA
1 TATATGTATACATATATTCATTTTGATAATATA
* * *
27696 TCTATGTATACATACATACATTTTGATAATATA
1 TATATGTATACATATATTCATTTTGATAATATA
27729 TATATG--TACATATATT
1 TATATGTATACATATATT
27745 TTATAATTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
31 23 0.59
32 6 0.15
33 10 0.26
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (33 bp):
TATATGTATACATATATTCATTTTGATAATATA
Found at i:27757 original size:26 final size:27
Alignment explanation
Indices: 27702--27772 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
27692 TATATCTATG
* *
27702 TATACATACATACATTTTGATAATATA
1 TATATATACATATATTTTGATAATATA
* *
27729 TATATGTACATATATTTT-ATAATTTA
1 TATATATACATATATTTTGATAATATA
*
27755 TATATATACATATGTTTT
1 TATATATACATATATTTT
27773 TGTCATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 23 0.61
27 15 0.39
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (27 bp):
TATATATACATATATTTTGATAATATA
Done.