Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014496.1 Corchorus capsularis cultivar CVL-1 contig14517, whole genome shotgun sequence
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: 176859
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2051 original size:24 final size:25
Alignment explanation
Indices: 2002--2051 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1992 ATTTTTATTT
* *
2002 TATTTAAATAAATAAAAATAATAAA
1 TATTAAAATAAATAAAAATAAGAAA
*
2027 TATTAAAATAAA-AAAAATCAGAAA
1 TATTAAAATAAATAAAAATAAGAAA
2051 T
1 T
2052 TTATTTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (25 bp):
TATTAAAATAAATAAAAATAAGAAA
Found at i:2447 original size:2 final size:2
Alignment explanation
Indices: 2442--2471 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2432 TGTGTGTGTC
2442 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2472 TTCTTATGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2687 original size:93 final size:92
Alignment explanation
Indices: 2574--2753 Score: 261
Period size: 93 Copynumber: 1.9 Consensus size: 92
2564 AACCTTCAAC
* *
2574 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACTCTTATATGGTCTTAGATGTCCACCC
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTATATGGTC-TAGATATCCACCC
2639 TCAATTAATTAACTCGTCAAAATGCTCA
65 TCAATTAATTAACTCGTCAAAATGCTCA
* * ** * *
2667 TTTCTTAATATTTTGTATGTAATTTTACATGGTGTTCACCCTTATTTGGTCTAGATATTCACCCT
1 TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTATATGGTCTAGATATCCACCCT
* *
2732 CAATTGATTAACTTGTCAAAAT
66 CAATTAATTAACTCGTCAAAAT
2754 ATCTTTGAAT
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
92 32 0.42
93 45 0.58
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (92 bp):
TTTCTTAACATTTTCTATGTAATTTTACATGGTGCCCACCCTTATATGGTCTAGATATCCACCCT
CAATTAATTAACTCGTCAAAATGCTCA
Found at i:3816 original size:66 final size:66
Alignment explanation
Indices: 3737--3869 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
3727 ACACGTCAGA
* *
3737 AAAATAACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGGTCACTGACGTGAGG
1 AAAATAACAGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGGTCACTAACGTGAGG
3802 G
66 G
3803 AAAATAACAGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGGTCACTAACGTGAGG
1 AAAATAACAGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGGTCACTAACGTGAGG
3868 G
66 G
3869 A
1 A
3870 CCTCCGATGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (66 bp):
AAAATAACAGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGGTCACTAACGTGAGG
G
Found at i:4065 original size:25 final size:25
Alignment explanation
Indices: 4031--4082 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4021 GTCAAAATGG
4031 TTGAAATTTCTGAAGTTATTTTTAT
1 TTGAAATTTCTGAAGTTATTTTTAT
4056 TTGAAATTTCTGAAGTTATTTTTAT
1 TTGAAATTTCTGAAGTTATTTTTAT
4081 TT
1 TT
4083 AGATTTTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.58
Consensus pattern (25 bp):
TTGAAATTTCTGAAGTTATTTTTAT
Found at i:10706 original size:25 final size:25
Alignment explanation
Indices: 10647--10706 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
10637 AAAATATGAC
* *
10647 ATCTTGGTTCTTTTTGCAAATTTTT
1 ATCTTGTTTCTTTTTGCAAATTGTT
* *
10672 TTTTTGGTTTC-TTTTGCAAATTGGTT
1 ATCTT-GTTTCTTTTTGCAAATT-GTT
10698 ATCTTGTTT
1 ATCTTGTTT
10707 AGGGCATAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.13, C:0.10, G:0.15, T:0.62
Consensus pattern (25 bp):
ATCTTGTTTCTTTTTGCAAATTGTT
Found at i:10951 original size:22 final size:21
Alignment explanation
Indices: 10907--10950 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
10897 TGTTACTGGA
10907 TTGCTAAACACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
* *
10928 TTGCTAAATACCGTCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
10949 TT
1 TT
10951 TACACTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.41, G:0.09, T:0.32
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:11050 original size:10 final size:10
Alignment explanation
Indices: 11037--11062 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
11027 CATTTCTAAC
11037 AACTTCTTCA
1 AACTTCTTCA
11047 AACTTCTTCA
1 AACTTCTTCA
11057 AACTTC
1 AACTTC
11063 ATTTCTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:11128 original size:26 final size:26
Alignment explanation
Indices: 11099--11166 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
11089 TTCCTTCATT
11099 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
11125 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
11151 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
11167 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:11190 original size:52 final size:51
Alignment explanation
Indices: 11099--11216 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
11089 TTCCTTCATT
* *
11099 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
11151 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
11202 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
11217 TATTAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:11516 original size:21 final size:22
Alignment explanation
Indices: 11481--11526 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
11471 AAAAATTATA
* **
11481 AAAAGGGGGGGCGGTATTTAGC
1 AAAAGGGGGGACGGTAAATAGC
11503 AAAA-GGGGGACGGTAAATAGC
1 AAAAGGGGGGACGGTAAATAGC
11524 AAA
1 AAA
11527 CTAACTGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.39, C:0.09, G:0.39, T:0.13
Consensus pattern (22 bp):
AAAAGGGGGGACGGTAAATAGC
Found at i:12332 original size:15 final size:15
Alignment explanation
Indices: 12307--12352 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
12297 CCCTTCTTTT
12307 TTTTATTTTAATAGTA
1 TTTTATTTTAATA-TA
12323 TTTT-TTTTAATATA
1 TTTTATTTTAATATA
**
12337 TTTGCTTTTAAT-TA
1 TTTTATTTTAATATA
12351 TT
1 TT
12353 GTGTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.32
15 15 0.54
16 4 0.14
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (15 bp):
TTTTATTTTAATATA
Found at i:16350 original size:167 final size:165
Alignment explanation
Indices: 15968--16411 Score: 622
Period size: 167 Copynumber: 2.7 Consensus size: 165
15958 TGATTAATTT
15968 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** *
16033 TTAAGTAATCGGCCAAGTAGGTAAAGACGAAAAATATTAGTTCTCTAGCTCATCATCAATCTTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAATCTTTG
* * ** *
16098 ATGGGGATCTTTTTTTAATTCCACCACTCTATTCAA
130 ATAGGGATATTTTAGTAATTCCACCACTCTATTAAA
* * *
16134 GTCTACTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCTAAAA-TTAGGACA
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATC-AAAAGTTAGGACA
*
16198 TTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGTC-
64 TTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGCAA-TCT
* *
16262 TTGGTAGGGATATTTTAGTAATTCCACTACTCTATTAAA
127 TTGATAGGGATATTTTAGTAATTCCACCACTCTATTAAA
* *
16301 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCTTCAAGAATCAAAAGTTGGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
16366 TTAAGTAATCTGCCAAATAGGAAAAGACGAAAAAAATTATTTCTCT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCT
16412 CGCTCCTCAT
Statistics
Matches: 246, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
166 106 0.43
167 138 0.56
168 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAATCTTTGA
TAGGGATATTTTAGTAATTCCACCACTCTATTAAA
Found at i:17386 original size:19 final size:18
Alignment explanation
Indices: 17362--17398 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17352 TTGAAGATTT
17362 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
17381 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
17399 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:19334 original size:74 final size:74
Alignment explanation
Indices: 19249--19405 Score: 242
Period size: 74 Copynumber: 2.1 Consensus size: 74
19239 CTAAGGAAGG
* * * * * *
19249 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGGCCTTT
1 GAAAAGTGTAATTACGAAAAAAGATAAAAGGAAAAGGAATAGGGGAAACTCATAGAGGGACCTTT
*
19314 TAGTCATCC
66 TAGTCACCC
*
19323 GAAAAGTGTAATTACGAAAAAAGATAAAAGGAAAAGGAATAGGGGAAACTCATAGAGGGACTTTT
1 GAAAAGTGTAATTACGAAAAAAGATAAAAGGAAAAGGAATAGGGGAAACTCATAGAGGGACCTTT
19388 TAGTCACCC
66 TAGTCACCC
19397 GAAAAGTGT
1 GAAAAGTGT
19406 CAAAAGACCA
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.42, C:0.10, G:0.28, T:0.20
Consensus pattern (74 bp):
GAAAAGTGTAATTACGAAAAAAGATAAAAGGAAAAGGAATAGGGGAAACTCATAGAGGGACCTTT
TAGTCACCC
Found at i:21037 original size:33 final size:31
Alignment explanation
Indices: 20985--21062 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
20975 ACGACATCCA
** *
20985 ACGTGGCATGCCATGTGTACCAAAAAAAATGAC
1 ACGTGGCATGCCACATGTA-C-AAAAAAAGGAC
* *
21018 ACGTGGCACGCCACATGTACAAAATAAGGAC
1 ACGTGGCATGCCACATGTACAAAAAAAGGAC
21049 ACGTGGCATGCCAC
1 ACGTGGCATGCCAC
21063 GTTGGGCACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 22 0.56
32 1 0.03
33 16 0.41
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACAAAAAAAGGAC
Found at i:21829 original size:25 final size:26
Alignment explanation
Indices: 21777--21829 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
21767 TTACTCAACT
**
21777 AAAAAATCTATTTTTATTTTTCTGTA
1 AAAAAATCTATTTTTATTTTAATGTA
21803 AAAAAACTCTATTTTTA-TTTAAT-TA
1 AAAAAA-TCTATTTTTATTTTAATGTA
21828 AA
1 AA
21830 TTTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 10 0.42
27 10 0.42
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (26 bp):
AAAAAATCTATTTTTATTTTAATGTA
Found at i:23568 original size:18 final size:18
Alignment explanation
Indices: 23545--23579 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
23535 CTGTCCCATA
23545 TTATAAGTTCCATTCTAG
1 TTATAAGTTCCATTCTAG
23563 TTATAAGTTCCATTCTA
1 TTATAAGTTCCATTCTA
23580 AAAACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46
Consensus pattern (18 bp):
TTATAAGTTCCATTCTAG
Found at i:24565 original size:2 final size:2
Alignment explanation
Indices: 24558--24584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24548 TTCTCTTATT
24558 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
24585 TTTATTCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64870 original size:3 final size:3
Alignment explanation
Indices: 64862--64890 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
64852 CTCGCCAATC
64862 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
64891 GGCTGAACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:79489 original size:17 final size:19
Alignment explanation
Indices: 79467--79503 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
79457 CCATAATCAT
79467 TGAAATAAGA-AACA-AAA
1 TGAAATAAGAGAACAGAAA
79484 TGAAATAAGAGAACAGAAA
1 TGAAATAAGAGAACAGAAA
79503 T
1 T
79504 AGTATCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.16, T:0.14
Consensus pattern (19 bp):
TGAAATAAGAGAACAGAAA
Found at i:112174 original size:134 final size:134
Alignment explanation
Indices: 112018--112287 Score: 404
Period size: 134 Copynumber: 2.0 Consensus size: 134
112008 AAGTTTTTGT
112018 CCTAAAATAAAAGTAGTTATATA-TATATATATTT-TTTTTACTAA-TTCTCCGGTATCCGGTGA
1 CCTAAAATAAAAGTAGTTATATAGT-T-TATATTTCTTTTTACTAACTT-TCCGGTATCCGGTGA
** * * *
112080 CCACATCGGGTCCCT-AGTTAATTCGGAATCAAGCTGCACTCTTCCATTTTTCGTCATTTATAAG
63 CCACATCGGACCCCTGA-TTAATTCGGAATCAAGCTGCACTCTCCCATTTTTCGTCATTTACAAA
112144 ACTCGAAC
127 ACTCGAAC
* *
112152 CCTAAAATAAAAGTAGTTATATAGTTTTTTTTTCTTTTTACTAACTTTCCGGTATCCGGTGACCA
1 CCTAAAATAAAAGTAGTTATATAGTTTATATTTCTTTTTACTAACTTTCCGGTATCCGGTGACCA
*
112217 CATCGGACCCCTGATTAATTCGGAATTAAGCTGCACTCTCCCATTTTTCGTCATTTACAAAACTC
66 CATCGGACCCCTGATTAATTCGGAATCAAGCTGCACTCTCCCATTTTTCGTCATTTACAAAACTC
112282 GAAC
131 GAAC
112286 CC
1 CC
112288 AAGATATTAC
Statistics
Matches: 124, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
133 5 0.04
134 115 0.93
135 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (134 bp):
CCTAAAATAAAAGTAGTTATATAGTTTATATTTCTTTTTACTAACTTTCCGGTATCCGGTGACCA
CATCGGACCCCTGATTAATTCGGAATCAAGCTGCACTCTCCCATTTTTCGTCATTTACAAAACTC
GAAC
Found at i:120698 original size:22 final size:21
Alignment explanation
Indices: 120671--120712 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
120661 TGATTACATA
*
120671 AAGAAAACAAAGCAAGAAAAAG
1 AAGAAAACAAA-AAAGAAAAAG
*
120693 AAGAAAATAAAAAAGAAAAA
1 AAGAAAACAAAAAAGAAAAA
120713 AAAGGTATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.02
Consensus pattern (21 bp):
AAGAAAACAAAAAAGAAAAAG
Found at i:134177 original size:72 final size:72
Alignment explanation
Indices: 134036--134186 Score: 180
Period size: 72 Copynumber: 2.1 Consensus size: 72
134026 TTTTTGCAAG
* * *
134036 CAAACCATCAAGATCAATTTTTGACAATCTAAAAATTTCAGCAAAAAATTTCACATCCAAACCAA
1 CAAACCATCAAGATCAATTTTTGACAACCTAAAAACTTCAGCAAAAAATTTCACATCAAAACCAA
134101 AATCCCA
66 AATCCCA
* * * * * *
134108 CAAACCTTCAA-AGTCAATTTTTGACAACCTCAAGACTTCAGCAGAAAACTTT-GCATCAAAACT
1 CAAACCATCAAGA-TCAATTTTTGACAACCTAAAAACTTCAGCA-AAAAATTTCACATCAAAACC
*
134171 AGAATCCCA
64 AAAATCCCA
134180 CAAACCA
1 CAAACCA
134187 AGACCTTCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
71 1 0.02
72 58 0.88
73 7 0.11
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (72 bp):
CAAACCATCAAGATCAATTTTTGACAACCTAAAAACTTCAGCAAAAAATTTCACATCAAAACCAA
AATCCCA
Found at i:141443 original size:13 final size:14
Alignment explanation
Indices: 141425--141457 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
141415 ATGTGACTTG
141425 TTTTTAAT-AATTT
1 TTTTTAATAAATTT
141438 TTTTTAATAAATTT
1 TTTTTAATAAATTT
141452 TGTTTT
1 T-TTTT
141458 TGCCTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 6 0.33
15 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTTTAATAAATTT
Found at i:142542 original size:2 final size:2
Alignment explanation
Indices: 142535--142566 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
142525 TTCAGCCTAC
142535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
142567 GGCAAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:143505 original size:308 final size:310
Alignment explanation
Indices: 142929--143522 Score: 714
Period size: 308 Copynumber: 1.9 Consensus size: 310
142919 CAAAATTTTG
*
142929 TTTCATATTTTTTTAGAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCACGTAAAAACA
1 TTTCATATTTTTTTA-AATTAATTTCTAATTAAATCAAAACAAAATTCAGATGCACGTAAAAACA
* * * *
142994 AATCTTTAAATCCAATGTGGCTGTGATTTGATTAGATAAATAAAGATAATTCAAGGAGTTCCGAC
65 AATCCTTAAATCCAATGTGGCCGAGATTTGATTAAATAAATAAAGATAATTCAAGGAGTTCCGAC
* * * *** *
143059 GCCAAAAATCATACAAAACACAGCAGTGGCACCGAAATGTGTTTTCAGGCAAAAACCGTGATGGT
130 ACCAAAAATAATACAAAACACAACAGTGGCACCGAAACACGTTTTCAGCCAAAAACCGTGATGGT
** * * * *
143124 TAGTACATGATTTTGGCTAAAATTTTGCAAAAATTAACCCGAAAGATATTTCCTTAATTTTTAGA
195 TAGTACACAATTTCGGCTAAAATTTTGCAAAAATTAACCCAAAAGATATTTCCTCAATTTCTAGA
*
143189 TAAAATACTCATAAAAATATATAATTCGGCTTTTAACGCTTCTAATATTGTT
260 GAAAATACTCATAAAAA-ATATAATTCGGCTTTTAACGCTTCTAATATTGTT
* * * * **
143241 TTTCCTATTTTTTT-AATTAATTTCTAATTAAATCAAAATAAGATTTAGATGCTTGTAAAAA-AA
1 TTTCATATTTTTTTAAATTAATTTCTAATTAAATCAAAACAAAATTCAGATGCACGTAAAAACAA
* * * * *
143304 ATCCTTAAATCCAATGTGGCCGAGATTT-AGTTAAATGAATATAGATATTTCAAGGAG-TCTTGG
66 ATCCTTAAATCCAATGTGGCCGAGATTTGA-TTAAATAAATAAAGATAATTCAAGGAGTTC-CGA
* ** * * *
143367 CACCAAAAATAATGCAAAACTGAACCG-GGTC-CCGAAACACGTTTTTAGCCGAAAACCGTGATG
129 CACCAAAAATAATACAAAACACAACAGTGG-CACCGAAACACGTTTTCAGCCAAAAACCGTGATG
* * * * *
143430 GTTAGTACACAATTTCGGCTTAAATTTTGCAAAAATTGACCCAAAATATTTTTCGTCAATTTCTA
193 GTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATTAACCCAAAAGATATTTCCTCAATTTCTA
* *
143495 GCGAAAATACTCATAAAAAATTTAATTC
258 GAGAAAATACTCATAAAAAATATAATTC
143523 AACGCCAAAA
Statistics
Matches: 236, Mismatches: 43, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
307 8 0.03
308 102 0.43
309 72 0.31
310 41 0.17
312 13 0.06
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (310 bp):
TTTCATATTTTTTTAAATTAATTTCTAATTAAATCAAAACAAAATTCAGATGCACGTAAAAACAA
ATCCTTAAATCCAATGTGGCCGAGATTTGATTAAATAAATAAAGATAATTCAAGGAGTTCCGACA
CCAAAAATAATACAAAACACAACAGTGGCACCGAAACACGTTTTCAGCCAAAAACCGTGATGGTT
AGTACACAATTTCGGCTAAAATTTTGCAAAAATTAACCCAAAAGATATTTCCTCAATTTCTAGAG
AAAATACTCATAAAAAATATAATTCGGCTTTTAACGCTTCTAATATTGTT
Found at i:147037 original size:308 final size:310
Alignment explanation
Indices: 146450--147050 Score: 721
Period size: 308 Copynumber: 1.9 Consensus size: 310
146440 TTTTAGCCAC
* *
146450 AATACTCATAAAAAAAATATAATTCAACGCCTAAAAGATTGAAGCACTTTTTACACATTTAATAT
1 AATACTCATAAAAAAAATATAATTCAACGCCAAAAAGATTGAAGCACTTTTCACACATTTAATAT
** * *
146515 CGTTTTTCATATTTTTTCAGAATAATTTTCTAATTAAATCGAAACAAGATTCAAATGTTCGCAAA
66 AATTTTTCATATTTTTTCAGAATAAGTTTCTAATTAAATCGAAACAAGATTCAAATGCTCG--AA
* * * * *
146580 AAAAATAAATTCTTAAATGCATTGTGGCTAAAATTTTATTAGATGAAAATAGCTATTTCAAGGAG
129 AAAAATAAATTCTTAAATCCAATGTGGCTAAAATTTGATTAGATGAAAATAGATATCTCAAGGAG
* *
146645 TTTCGGTGCCAAAAATCACGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
194 TTTCGGCGCCAAAAATCACGCAAAACTGAGACGGGGCCCCAAAACGCGTTTTTAGCCAAAAACCG
*
146710 TGATGATTAATAAACGATTTTGGTTAAAATTTTTCCTCATTTTTTTGGATAA
259 TGATGATTAATAAACGATTTTGGCTAAAATTTTTCCTCATTTTTTTGGATAA
* * * * * * *
146762 AATACTCATAAAATATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGC-TTTTATAT
1 AATACTCATAAAAAAAATATAATTCAACGCCAAAAAGATTGAAGCACTTTTCACACATTTAATAT
* * * *
146826 AATTTTTCATATTTTTT-ACGAATTAGTTTCTAATTAAATCGAAACAAGATTGAGATGCTCG-TA
66 AATTTTTCATATTTTTTCA-GAATAAGTTTCTAATTAAATCGAAACAAGATTCAAATGCTCGAAA
* *** * * *
146889 AAATTTTTTTTTTAAATCCAATGTGGTTAAGATTTGATTAGAT--AAATATGAATATCTCAAGGA
130 AAAATAAATTCTTAAATCCAATGTGGCTAAAATTTGATTAGATGAAAATA-G-ATATCTCAAGGA
* * * * *
146952 GTATTC-GCGCTAATAATCATGCAAAACTGAGTCGGGGCCCCAAAAACGCTTTTTTAGCCAAAAA
193 GT-TTCGGCGCCAAAAATCACGCAAAACTGAGACGGGGCCCC-AAAACGCGTTTTTAGCCAAAAA
* ** *
147016 CTGTGATG-TTTTTACACGATTTTGGCTAAAATTTT
256 CCGTGATGATTAATAAACGATTTTGGCTAAAATTTT
147051 GTAAAAATTG
Statistics
Matches: 243, Mismatches: 41, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
306 5 0.02
307 1 0.00
308 99 0.41
309 30 0.12
310 1 0.00
311 59 0.24
312 48 0.20
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (310 bp):
AATACTCATAAAAAAAATATAATTCAACGCCAAAAAGATTGAAGCACTTTTCACACATTTAATAT
AATTTTTCATATTTTTTCAGAATAAGTTTCTAATTAAATCGAAACAAGATTCAAATGCTCGAAAA
AAATAAATTCTTAAATCCAATGTGGCTAAAATTTGATTAGATGAAAATAGATATCTCAAGGAGTT
TCGGCGCCAAAAATCACGCAAAACTGAGACGGGGCCCCAAAACGCGTTTTTAGCCAAAAACCGTG
ATGATTAATAAACGATTTTGGCTAAAATTTTTCCTCATTTTTTTGGATAA
Found at i:147821 original size:15 final size:16
Alignment explanation
Indices: 147803--147832 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
147793 ATAAATAATA
147803 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
147818 ATATTATAATCTAAA
1 ATATTATAATCTAAA
147833 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:152688 original size:21 final size:20
Alignment explanation
Indices: 152662--152705 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
152652 GTGGAAAGCA
152662 TTATAACTATTTTAATAAATT
1 TTATAACTATTTTAAT-AATT
* *
152683 TTATAACTTTTTTAGTAATT
1 TTATAACTATTTTAATAATT
152703 TTA
1 TTA
152706 GATTACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATAACTATTTTAATAATT
Found at i:152818 original size:21 final size:20
Alignment explanation
Indices: 152785--152828 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
152775 GTGGAAAGCA
*
152785 TTATAGCTATTTTAATAAATT
1 TTATAACTATTTTAAT-AATT
* *
152806 TTATAACTTTTTTAGTAATT
1 TTATAACTATTTTAATAATT
152826 TTA
1 TTA
152829 GATTACAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
TTATAACTATTTTAATAATT
Found at i:157181 original size:41 final size:43
Alignment explanation
Indices: 157112--157196 Score: 156
Period size: 41 Copynumber: 2.0 Consensus size: 43
157102 ACAAAATTTC
157112 ATTTCTTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
157155 ATTTC-TTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
157196 A
1 A
157197 CAGCCGCACG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 28 0.67
42 9 0.21
43 5 0.12
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (43 bp):
ATTTCTTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Found at i:159269 original size:333 final size:331
Alignment explanation
Indices: 158077--160482 Score: 1910
Period size: 329 Copynumber: 7.3 Consensus size: 331
158067 TAAATCGAAA
* * * * * * * * * *
158077 CTAATTAAATTGAAGCAAGATTTA-ATTACTTGTAAAAACAAATCATTAAATCTAATATGTCTTA
1 CTAATTAAATCGAAACAAGATTCAGA-TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * * * ** * *
158141 GATTTGATTAAAT-AATATAAATATTTCAAGGAGTCTCGGCACCGAAAAT-AGTGCAAAACAGAG
65 GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGTCACAAAAAATCA-TGCAAAACTGAC
* * * * * ** * * * * * * *
158204 TCGTGGCCTTGGAACGTGTTTTAAGTAAAAAACCGTAATGGTTAAATACACGATTTCGGTTGAAA
129 CCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGTGACGGAT-AGTACACGATTTCGGCTAAAA
* * *
158269 TTTTGCAAAAATTGACCCGAAAGATA-TTTCCTTAATTTTTAGCTAAAATACTTATAAAAAGTAT
193 TTTTGCAAAAATTGACCC-AAA-ATATTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATAT
* *** * * * *
158333 ATAATTCGACATAAAAAATATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTTTTTTTTT
256 ATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTT-C--TTTTTTT
158398 TTCTAGAATTAATTT
318 TTCTA-AATTAATTT
* * * *
158413 CTAATTAAATCGAAACAATATTCACATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAT
1 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * *
158478 ATTTGGTTAGGTGAATATATATGGATATTTCAAGGAGTC-TGGCACAAAAAATCATGCTAAACTG
66 ATTTGGTTAGATG-A-ATATA--GATATTTCAAGGAGTCTTGTCACAAAAAATCATGCAAAACTG
** * * * * * * * *
158542 ATTC-GGGTCTTGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCAGCTAAA
127 ACCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGTGACGGATAGTACACGATTTCGGCTAAA
* * * * * *
158606 ATTTTGTAAAAATTGACCCGAAATATTTTCCCTCAATTTATAGCGAAAATACTCATGAAAACTAT
192 ATTTTGCAAAAATTGACCCAAAATATTTT-CCTCAATTTTTAGCTAAAATACTCATAAAAAATAT
** * *
158671 ATAATTCAACGCCAAAAA-A-TGTAAAACCTTTTTAACGCTTCTAATATCGTTTTTCCTATTTTA
256 ATAATTCAACGCCAAAAAGATTG-AAAGGC-TTTTCACGCTTCTAATATCGTTTTT-CT-TTTTT
*
158734 TTTCCAAATTAATTT
317 TTTCTAAATTAATTT
* ** * * * ** *
158749 CTAATTAAATCGAAATAAGATTTTGATACTTGTAAAAACAAATCCTTAAATACAATGTGATTGAA
1 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * *
158814 ATTTGGTTAGATGAATATAGATATATTTCAAAGAGTCTTGACGCAAAAAAATCATGCAAAACTGA
66 ATTTGGTTAGATGAATATAG--ATATTTCAAGGAGTCTTGTCAC-AAAAAATCATGCAAAACTGA
* * ** * * ** * *
158879 TCCAGAGTTCC-GGAACGTGTTTTTATCCAAAAA-A--CCCTGATGGTACACGATTTCGGCTAAA
128 -CCCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGTGACGGATAGTACACGATTTCGGCTAAA
* * * * *
158940 ATTTTACAAAAATTGACCCAAAATATTTTTCTAAATTTTTAGCCACAATACTCATAAAAAATATA
192 ATTTTGCAAAAATTGACCCAAAATATTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATA
* * *
159005 TAATTCAACGCCAAAAAGATTGAAAGGCTTCTCGCGCTTCTAATATCGTTTTTCTTTTTTTTTTT
257 TAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCT
*
159070 AAATGAATTT
322 AAATTAATTT
* * * *
159080 CTAATTAAATCGAAACATGGTTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAG
1 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * *
159145 ATTTGGTTAGATGAATATAGATATTTCAAGGAATTTTGTCACAAAAATTCATACAAAACTGACCC
66 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGTCACAAAAAATCATGCAAAACTGACCC
* * *** *
159210 GGGGCCCTAGAACGCGTTTTTAGCCAAAAAAAAAAAACGTGATGGTACACGATTTCGGCTAAAAT
131 GGGGCCCTGGAACGCGTTTTTAGCC-AAAAACAGTGACG-GATAGTACACGATTTCGGCTAAAAT
* * * * *
159275 TTCGCAAAAATTGACCCGAAATATTTTCCCTCAATTTTTAGCCACAATACTCATAAAATATATAT
194 TTTGCAAAAATTGACCCAAAATATTTT-CCTCAATTTTTAGCTAAAATACTCATAAAAAATATAT
* * * * * * *
159340 ACTTCAACTCCAAAAAGATTG-GAGGACTTTACACGCTTTTAATATCGTTTTTC-ATATTTTTCT
258 AATTCAACGCCAAAAAGATTGAAAGG-CTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCT
*
159403 GAATTAATTT
322 AAATTAATTT
159413 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA--C------CC--T-TGGCTGAG
1 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * ** * * *
159467 AATTGGATAGATGAATATAGATATTTCAAGGAGTCTCAAT-ACAAAAAATAATGCAAAATTGAGC
66 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT-TGTCACAAAAAATCATGCAAAACTGACC
* * * * * * * * * *
159531 TGAGGCCCCGAAACACGTTTTTA-ACAACAAACCGTGAC-CATTACTACATGATTTCGGCTAAAA
130 CGGGGCCCTGGAACGCGTTTTTAGCCAA-AAACAGTGACGGA-TAGTACACGATTTCGGCTAAAA
* *** * * * * * *
159594 TTTTCCAAAAAAAAAACCCGAAATTTTTTTTCTCAATTTTTGGCTGAAAA-ACTCATGAAATATA
193 TTTTGC-AAAAATTGACCC-AAAATATTTTCCTCAATTTTTAGCT-AAAATACTCATAAAAAATA
* * * * * * * * * *
159658 TAAAATTTAACGCCAAAAAGATAGGAAGACTTTTCACGCTTTTCATATCATTTTTCATATTTTTT
255 TATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTT
159723 CTAAATT-ATTT
320 CTAAATTAATTT
* * * * *
159734 CTAATTAAATAGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAA
1 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * * *
159799 ATTTGATTAGATGAATATGGATATCTCAAGGAGTCTTGACACAAAAAATCATGCAAAACTGACTC
66 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGTCACAAAAAATCATGCAAAACTGACCC
* * * * * ** *
159864 GGGGCCCTGGAACGGGTTTTTAGCCAAAAACTGTGA-TGATTATTACATGATTTCCTCTAACATT
131 GGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGTGACGGA-TAGTACACGATTTCGGCTAAAATT
* * * * *
159928 TTGCAAAAAATGACCCAAAAGAAATTTCCTCAATTTTTGGCTAAAATTCTCAT-AAAAA-ATATA
195 TTGCAAAAATTGACCCAAAA-TATTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATA
* * * * * * * ** **
159991 ATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTT-TCAATACCTTTTTTCCTACTTTTTCCG
259 ATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCT-AATATCGTTTTTCTTTTTTTTTCTA
*
160055 AATTGATTT
323 AATTAATTT
* * * * *
160064 CTAATTCAATAGAAACAAGATTTAGATGCTCGTAAAAA-AAATCCTTCAATCCAATGTGGCTGAT
1 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * * * *
160128 ATTTGATTAGATGAATATAGGTATGTCATGGAGTCTTGATGC-C-AAAATTCATGCAAAACTGAG
66 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTG-T-CACAAAAAATCATGCAAAACTGAC
* * ** * * * * * *
160191 ACAGGGCCCCAGAATGCATTTTTAGCCAAAAACTGTGATGGATAATACACGATTTCAGC-AAAAT
129 CCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGTGACGGATAGTACACGATTTCGGCTAAAAT
** * *
160255 TTTATAAAAATTTACCCAAAAGATATTTCCTCAATTTTT-GTCTAAAATACTCATATATATATAT
194 TTTGCAAAAATTGACCCAAAATAT-TTTCCTCAATTTTTAG-CTAAAATACTC--ATA-A-A-A-
* * * * *
160319 ATATATATATATTTCAATGCCAAAAAGATTGAAGGGCTTTTGACGTTTAC-AATATCGTTTTTCC
251 A-ATATATA-A-TTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTT-CTAATATCGTTTTTCT
* **
160383 TATTTTTTCCGAATTAATTT
312 TTTTTTTTCTAAATTAATTT
* * *
160403 CTAATTAAATCGAAA-AAAATTCAGATGCTCAT-AAAACAAATCCTTAAATCCTATGTGGCTGAG
1 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* *
160466 A-TTGATTAGATAAATAT
66 ATTTGGTTAGATGAATAT
160483 TTCAAGTGGT
Statistics
Matches: 1678, Mismatches: 319, Indels: 145
0.78 0.15 0.07
Matches are distributed among these distances:
319 1 0.00
320 25 0.01
321 127 0.08
322 98 0.06
323 3 0.00
325 2 0.00
327 8 0.00
328 78 0.05
329 196 0.12
330 56 0.03
331 123 0.07
332 112 0.07
333 178 0.11
334 146 0.09
335 8 0.00
336 162 0.10
337 62 0.04
338 145 0.09
339 111 0.07
340 21 0.01
341 16 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (331 bp):
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGTCACAAAAAATCATGCAAAACTGACCC
GGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGTGACGGATAGTACACGATTTCGGCTAAAATTT
TGCAAAAATTGACCCAAAATATTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAAT
TCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCTTTTTTTTTCTAAAT
TAATTT
Found at i:159355 original size:667 final size:656
Alignment explanation
Indices: 158250--160482 Score: 2054
Period size: 667 Copynumber: 3.4 Consensus size: 656
158240 AATGGTTAAA
* * * *
158250 TACACGATTTCGGTTGAAATTTTGCAAAAATTGACCCGAAAGATA-TTTCCTTAATTTTTAGCTA
1 TACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAA-ATATTTTCCTCAATTTTTAGCTA
* * * *** * * *
158314 AAATACTTATAAAAAGTATATAATTCGACATAAAAAATATTGAAGGGCTTTTAACGCTTCTAATA
65 AAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATA
* * * *
158379 TTGTTTTTCCTTTTTTTTTTTCTAGAATTAATTTCTAATTAAATCGAAACAATATTCACATGCTC
130 TCGTTTTT-C--TTATTTTTTCTA-AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTC
* * * * *
158444 GTAAAAACAAATCCTTAAATCCAATGTGACTGATATTTGGTTAGGTGAATATATATGGATATTTC
191 GTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATG-A-ATATA--GATATTTC
* * * * * * * *
158509 AAGG-AGTCTGGCACAAAAAATCATGCTAAACTGATTC-GGGTCTTGGAACGCATTTTTAGCCAA
252 AAGGAATTTTGACACAAAAAATCATGCAAAACTGACTCGGGGCCCTGGAACGCGTTTTTAGCCAA
* * * *
158572 AAACCGTGA-TGGTTAGTACACAATTTCAGCTAAAATTTTGTAAAAATTGACCCGAAATATTTTC
317 AAACAGTGAGT-GATAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTC
* *
158636 CCTCAATTTATAGCGAAAATACTCATGAAAACTATATA-ATTCAACGCCAAAAA-ATGTAAAACC
381 CCTCAATTTTTAGCCAAAATACTCAT-AAAA-TATATATATTCAACGCCAAAAAGATGTAAAA-C
* *
158699 TTTTTAACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATTAATTTCTAATTAAATCGAAA
443 TTTTTAACGCTT-TAATATCGTTTTTCCTATATT-TTTCCGAATTAATTTCTAATTAAATCGAAA
* * * *
158764 TAAGATTTTGATACTTGTAAAAACAAATCCTTAAATACAATGTGATTGAAATTTGGTTAGATGAA
506 CAAGATTTAGATGCTCGTAAAAACAAATCCTT-AATACAATGTGA-TGAAATTTGGTTAGATGAA
* * * **
158829 TATAGATATATTTCAAAGAGTCTTGACGCAAAAAAATCATGCAAAACTGATCCAGAGTTCCGGAA
569 TATAG--ATATTTCAAGGAGTCTTGATGC-AAAAAATCATGCAAAACTGA-ACAGAGCCCCGGAA
* *
158894 CGTGTTTTTATCCAAAAAACCCTGATGG
630 CGCGTTTTTA-CCAAAAAACCGTGATGG
* * * *
158922 TACACGATTTCGGCTAAAATTTTACAAAAATTGACCC-AAAATATTTTTCTAAATTTTTAGCCAC
1 TACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAATATTTTCCTCAATTTTTAGCTAA
* *
158986 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTCTCGCGCTTCTAATAT
66 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATAT
* * * * *
159051 CGTTTTTCTTTTTTTTTTTAAATGAATTTCTAATTAAATCGAAACATGGTTCAAATGCTCGTAAA
131 CGTTTTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAA
*
159116 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAATTT
196 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAATTT
* * * * * * ***
159181 TGTCACAAAAATTCATACAAAACTGACCCGGGGCCCTAGAACGCGTTTTTAGCCAAAAAAAAAAA
261 TGACACAAAAAATCATGCAAAACTGACTCGGGGCCCTGGAACGCGTTTTTAGCC-AAAAACAGTG
* * *
159246 ACGTGATGGTACACGATTTCGGCTAAAATTTCGCAAAAATTGACCCGAAATATTTTCCCTCAATT
325 A-GTGATAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTCCCTCAATT
* * * **
159311 TTTAGCCACAATACTCATAAAATATATATACTTCAACTCCAAAAAGATTGGAGGAC--TTTACAC
389 TTTAGCCAAAATACTCATAAAATATATATA-TTCAACGCCAAAAAGA-TGTAAAACTTTTTA-AC
* *
159374 GCTTTTAATATCGTTTTT-C-ATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCA
451 GC-TTTAATATCGTTTTTCCTATATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTA
* ** *
159437 GATGCTCGTAAAAACAAACCCTT--GGC----TGA-G-AA-TTGGATAGATGAATATAGATATTT
515 GATGCTCGTAAAAACAAATCCTTAATACAATGTGATGAAATTTGGTTAGATGAATATAGATATTT
** * * * * * * * *
159493 CAAGGAGTCTCAATACAAAAAATAATGCAAAATTGAGCTGAGGCCCCGAAACACGTTTTTAACAA
580 CAAGGAGTCTTGATGCAAAAAATCATGCAAAACTGAACAGA-GCCCCGGAACGCGTTTTTACCAA
* **
159558 CAAACCGTGACCATTAC
644 AAAACCGTG---A-TGG
* * *** * * * *
159575 TACATGATTTCGGCTAAAATTTTCCAAAAAAAAAACCCGAAATTTTTTTTCTCAATTTTTGGCTG
1 TACACGATTTCGGCTAAAATTTTAC-AAAAATTGACCCGAAAATATTTTCCTCAATTTTTAGCT-
* * * * * * * * *
159640 AAAA-ACTCATGAAATATATAAAATTTAACGCCAAAAAGATAGGAAGACTTTTCACGCTTTTCAT
64 AAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAAT
* * *
159704 ATCATTTTTCATATTTTTTCTAAATT-ATTTCTAATTAAATAGAAACAAGATTCAAATGCTCGTA
129 ATCGTTTTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTA
* * * * *
159768 AAAACAAATCCTTAAATGCAATGTGGCTAAAATTTGATTAGATGAATATGGATATCTCAAGGAGT
194 AAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAAT
* * *
159833 CTTGACACAAAAAATCATGCAAAACTGACTCGGGGCCCTGGAACGGGTTTTTAGCCAAAAACTGT
259 TTTGACACAAAAAATCATGCAAAACTGACTCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGT
* * ** * * * * *
159898 GA-TGATTATTACATGATTTCCTCTAACATTTTGCAAAAAATGACCCAAAAGAAATTT-CCTCAA
324 GAGTGA-TAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAA-TATTTTCCCTCAA
* * * * * *** *
159961 TTTTTGGCTAAAATTCTCATAAAAAATATA-ATTCAACGCCAAAAATAT-TGAAGGGTTTTTTAC
387 TTTTTAGCCAAAATACTCATAAAATATATATATTCAACGCCAAAAAGATGT-AAAACTTTTTAAC
* * * * * *
160024 GCTTTCAATACCTTTTTTCCTA-CTTTTTCCGAATTGATTTCTAATTCAATAGAAACAAGATTTA
451 GCTTT-AATATCGTTTTTCCTATATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTA
* * * * *
160088 GATGCTCGTAAAAA-AAATCCTTCAATCCAATGTGGCTGATATTTGATTAGATGAATATAGGTAT
515 GATGCTCGTAAAAACAAATCCTT-AATACAATGT-GATGAAATTTGGTTAGATGAATATAGATAT
* * * * * * * *
160152 GTCATGGAGTCTTGATGCCAAAATTCATGCAAAACTGAGACAGGGCCCCAGAATGCATTTTTAGC
578 TTCAAGGAGTCTTGATGCAAAAAATCATGCAAAACTGA-ACAGAGCCCCGGAACGCGTTTTTA-C
*
160217 C-AAAAACTGTGATGG
641 CAAAAAACCGTGATGG
* * * *
160232 ATAATACACGATTTCAGC-AAAATTTTATAAAAATTTACCC-AAAAGATATTTCCTCAATTTTT-
1 ----TACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAATAT-TTTCCTCAATTTTTA
* *
160294 GTCTAAAATACTCATATATATATATATATATATATATTTCAATGCCAAAAAGATTGAAGGGCTTT
61 G-CTAAAATACTC--ATA-A-A-A-A-ATATATA-A-TTCAACGCCAAAAAGATTGAAAGGCTTT
* * * ** *
160359 TGACGTTTAC-AATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAA-AAAA
116 TCACGCTT-CTAATATCGTTTTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGA
* * * * *
160422 TTCAGATGCTCAT-AAAACAAATCCTTAAATCCTATGTGGCTGAGA-TTGATTAGATAAATAT
180 TTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATAT
160483 TTCAAGTGGT
Statistics
Matches: 1266, Mismatches: 236, Indels: 124
0.78 0.15 0.08
Matches are distributed among these distances:
649 19 0.02
650 67 0.05
651 75 0.06
652 68 0.05
653 52 0.04
654 154 0.12
655 91 0.07
656 3 0.00
657 5 0.00
658 11 0.01
659 29 0.02
660 9 0.01
661 85 0.07
662 4 0.00
663 13 0.01
664 80 0.06
665 35 0.03
666 38 0.03
667 207 0.16
668 82 0.06
669 22 0.02
670 4 0.00
671 79 0.06
672 34 0.03
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (656 bp):
TACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAATATTTTCCTCAATTTTTAGCTAA
AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATAT
CGTTTTTCTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAA
AACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAATTT
TGACACAAAAAATCATGCAAAACTGACTCGGGGCCCTGGAACGCGTTTTTAGCCAAAAACAGTGA
GTGATAGTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTCCCTCAATTTT
TAGCCAAAATACTCATAAAATATATATATTCAACGCCAAAAAGATGTAAAACTTTTTAACGCTTT
AATATCGTTTTTCCTATATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCT
CGTAAAAACAAATCCTTAATACAATGTGATGAAATTTGGTTAGATGAATATAGATATTTCAAGGA
GTCTTGATGCAAAAAATCATGCAAAACTGAACAGAGCCCCGGAACGCGTTTTTACCAAAAAACCG
TGATGG
Found at i:159698 original size:321 final size:317
Alignment explanation
Indices: 158922--160109 Score: 884
Period size: 321 Copynumber: 3.6 Consensus size: 317
158912 ACCCTGATGG
* * * * * * *
158922 TACACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAATATTTTT-CTAAATTTTTAGCCAC
1 TACATGATTTCGGCTAAAATTTTCCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTA-
* * * * * * *
158986 AATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTCTCGCGCTTCTAATAT
65 AAAACTCAT-AAATATATATAATTCAACGCCAAAAAGA-TGGAAGACTTTTCACGCTTTTAATAT
* * ** * * * * * * *
159051 CGTTTTTCTTTTTTTTTTTAAATGAATTTCTAATTAAATCGAAACATGGTTCAAATGCTCGTAAA
128 CATTTTTCATACTTTTTCTGAAT-TATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAA
* * * *
159116 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGG-TTAGATGAATATAGATATTTCAAGGAATT
192 AACAAA--C------CC--T-TGGCTAA-AATTGGATTAGATGAATATAGATATCTCAAGGAGTC
*** * * * * * * * * ****
159180 TTGTCACAAAAATTCATACAAAACTGACCCG-GGGCCCTAGAACGCGTTTTTAGCCAAAAAAAAA
245 TCAACACAAAAAATAATGCAAAACTGACTCGAGGCCCCGA-AACACGTTTTTAGACAAAAACCGT
* * * **
159244 AAACGTGATGG
309 GACCAT--TAC
* * * * *
159255 TACACGATTTCGGCTAAAA-TTTCGCAAAAATTGACCCGAAATATTTTCCCTCAATTTTTAGCCA
1 TACATGATTTCGGCTAAAATTTTC-CAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTA
* * * * *
159319 CAATACTCATAAAATATATATACTTCAACTCCAAAAAGATTGGAGGACTTTACACGCTTTTAATA
65 -AAAACTCAT-AAATATATATAATTCAACGCCAAAAAGA-TGGAAGACTTTTCACGCTTTTAATA
* *
159384 TCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
127 TCATTTTTCATACTTTTTCTGAATT-ATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAA
* * *
159448 AAACAAACCCTTGGCTGAGAATTGGA-TAGATGAATATAGATATTTCAAGGAGTCTCAATACAAA
191 AAACAAACCCTTGGCT-AAAATTGGATTAGATGAATATAGATATCTCAAGGAGTCTCAACACAAA
*
159512 AAATAATGCAAAATTGAGCT-GAGGCCCCGAAACACGTTTTTA-ACAACAAACCGTGACCATTAC
255 AAATAATGCAAAACTGA-CTCGAGGCCCCGAAACACGTTTTTAGACAA-AAACCGTGACCATTAC
** * *
159575 TACATGATTTCGGCTAAAATTTTCCAAAAAAAAAACCCGAAATTTTTTTTCTCAATTTTTGGCTG
1 TACATGATTTCGGCTAAAATTTTCC-AAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCT-
* * *
159640 AAAAACTCATGAAATATATAAAATTTAACGCCAAAAAGATAGGAAGACTTTTCACGCTTTTCATA
64 AAAAACTCAT-AAATATATATAATTCAACGCCAAAAAGAT-GGAAGACTTTTCACGCTTTTAATA
* * *
159705 TCATTTTTCATATTTTTTCTAAATTATTTCTAATTAAATAGAAACAAGATTCAAATGCTCGTAAA
127 TCATTTTTCATACTTTTTCTGAATTATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAA
* *
159770 AACAAATCCTTAAATGCAATGTGGCTAAAATTTGATTAGATGAATATGGATATCTCAAGGAGTCT
192 AACAAA-CC-------C--T-TGGCTAAAATTGGATTAGATGAATATAGATATCTCAAGGAGTCT
** * * * * ** * *
159835 TGACACAAAAAATCATGCAAAACTGACTCGGGGCCCTGGAACGGGTTTTTAGCCAAAAACTGTGA
246 CAACACAAAAAATAATGCAAAACTGACTCGAGGCCCCGAAACACGTTTTTAGACAAAAACCGTGA
** *
159900 TGATTAT
311 CCATTAC
** * * * * **
159907 TACATGATTTCCTCTAACATTTTGCAAAAAATGACCCAAAAGAAATTTCCTCAATTTTTGGCTAA
1 TACATGATTTCGGCTAAAATTTTCCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAA
* * * * ** * * *
159972 AATTCTCATAAA-AAATATAATTCAACGCCAAAAATATTGAAGGGTTTTTTACGCTTTCAATACC
66 AA-ACTCATAAATATATATAATTCAACGCCAAAAAGATGGAA-GACTTTTCACGCTTTTAATATC
* * * * *
160036 TTTTTTCCTACTTTTTCCGAATTGATTTCTAATTCAATAGAAACAAGATTTAGATGCTCGTAAAA
129 ATTTTTCATACTTTTTCTGAATT-ATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAA
*
160101 A-AAATCCTT
193 ACAAACCCTT
160110 CAATCCAATG
Statistics
Matches: 703, Mismatches: 122, Indels: 75
0.78 0.14 0.08
Matches are distributed among these distances:
318 1 0.00
319 1 0.00
320 21 0.03
321 146 0.21
322 87 0.12
323 9 0.01
325 2 0.00
328 4 0.01
329 59 0.08
330 46 0.07
331 46 0.07
332 106 0.15
333 96 0.14
334 79 0.11
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (317 bp):
TACATGATTTCGGCTAAAATTTTCCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAA
AAACTCATAAATATATATAATTCAACGCCAAAAAGATGGAAGACTTTTCACGCTTTTAATATCAT
TTTTCATACTTTTTCTGAATTATTTCTAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACA
AACCCTTGGCTAAAATTGGATTAGATGAATATAGATATCTCAAGGAGTCTCAACACAAAAAATAA
TGCAAAACTGACTCGAGGCCCCGAAACACGTTTTTAGACAAAAACCGTGACCATTAC
Found at i:161383 original size:106 final size:107
Alignment explanation
Indices: 161101--161468 Score: 584
Period size: 106 Copynumber: 3.5 Consensus size: 107
161091 AATTTTTCTA
* ** * * * *
161101 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATAAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
* * *
161164 CTTCTAAAACCCTATAACAAT--ATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
*
161204 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTG
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
161269 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
*
161311 ACCCTTAAAATAAAAATAAAATTTTAA-TTGGGGCTAAATTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
*
161375 TTTCTAAAACCCTATAACAATAAATTATAAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
161417 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
161469 AGGCTAAATC
Statistics
Matches: 245, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
103 27 0.11
104 15 0.06
105 33 0.13
106 103 0.42
107 67 0.27
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.40
Consensus pattern (107 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
Found at i:163721 original size:38 final size:38
Alignment explanation
Indices: 163678--163751 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
163668 AATAGGCCAC
163678 TTAACTAGTTATCCAAGAAATATCGGGTTAGCCACACG
1 TTAACTAGTTATCCAAGAAATATCGGGTTAGCCACACG
* *
163716 TTAACTAGTTATCTAAGAAATATCGTGTTAGCCACA
1 TTAACTAGTTATCCAAGAAATATCGGGTTAGCCACA
163752 TGAGAGATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (38 bp):
TTAACTAGTTATCCAAGAAATATCGGGTTAGCCACACG
Found at i:165314 original size:13 final size:13
Alignment explanation
Indices: 165298--165322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
165288 AAATTAAGGA
165298 ATTAAATGGTAGT
1 ATTAAATGGTAGT
165311 ATTAAATGGTAG
1 ATTAAATGGTAG
165323 AAAATGTCCA
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:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (13 bp):
ATTAAATGGTAGT
Found at i:168544 original size:166 final size:166
Alignment explanation
Indices: 168237--168679 Score: 577
Period size: 166 Copynumber: 2.7 Consensus size: 166
168227 TGAGTCATTT
* * * *
168237 GTCAATTGAGAAATGATCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTAAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
* * * * * ** * * *
168302 TTAAGTAATCTGCCAAATAGGTAACGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
66 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTCG
* *
168367 ATAGAGATCTTTTATTAATTCCACTACTCTATTCAA
131 ATAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
168403 GTCCATTAAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTAAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
* *
168468 TTAAGTAAT-TGCCAAGTAGGAAAAGACGAAAAAAATAAGTTTTCTAACTCCAAAAGCAAGCCTC
66 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCTC
* *
168532 GGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
130 GATAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
168569 GTCAATTGAGAAATGACCAAAAA-TTCTAATTATTTAATCCCCTCAAGAATCAAAAATTAGGGTA
1 GTCAATTAAGAAATGACCAAAAAGTT-TAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGATA
* * *
168633 TTTAAGTAATCGGTCAAGT-GTGAAAAGACAAAAAAAATTAGTTCTCT
65 TTTAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCT
168680 CGCTCCTCAT
Statistics
Matches: 240, Mismatches: 33, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
165 34 0.14
166 177 0.74
167 29 0.12
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (166 bp):
GTCAATTAAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTCG
ATAGAGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:176596 original size:41 final size:41
Alignment explanation
Indices: 176546--176629 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
176536 TCAACTTGAT
* *
176546 CCTCATAATAATTAAGGAAACAAATTAAATTCAGGTTTAGC
1 CCTCATAATAATTAAGGAAACAAATTAAATCCAGATTTAGC
* *
176587 CCTCCTAATAATTAAGGAAATAAATTAAATCCAGATTTAGC
1 CCTCATAATAATTAAGGAAACAAATTAAATCCAGATTTAGC
176628 CC
1 CC
176630 CTAGTTACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (41 bp):
CCTCATAATAATTAAGGAAACAAATTAAATCCAGATTTAGC
Done.