Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 99 of 185
Found at i:31183391 original size:18 final size:18
Alignment explanation
Indices: 31183370--31183409 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31183360 AAAGGGAATT
* *
31183370 GAAAAAGTGAGTGAAAAG
1 GAAAAAGAGAGTGAAAAA
*
31183388 GAAAAAGAGATTGAAAAA
1 GAAAAAGAGAGTGAAAAA
31183406 GAAA
1 GAAA
31183410 TTGAAAGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (18 bp):
GAAAAAGAGAGTGAAAAA
Found at i:31196441 original size:40 final size:40
Alignment explanation
Indices: 31196202--31196427 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
31196192 TTGAATGATG
* * * *
31196202 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
31196242 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31196282 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
31196322 TTCGGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31196362 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31196403 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31196428 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 156 0.93
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31214825 original size:27 final size:27
Alignment explanation
Indices: 31214795--31214972 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31214785 ATATTGAGTC
* * * *
31214795 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
31214822 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31214849 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
31214877 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
31214904 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
31214931 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
31214958 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31214973 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:31214934 original size:82 final size:81
Alignment explanation
Indices: 31214816--31214971 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31214806 TGCTATATAA
* *
31214816 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31214881 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31214898 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31214962 CACTTAGTGC
65 CACTTAGTGC
31214972 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31220203 original size:45 final size:45
Alignment explanation
Indices: 31220152--31220366 Score: 240
Period size: 45 Copynumber: 4.8 Consensus size: 45
31220142 TACTGAGTAT
* ***
31220152 CATTGATTATAAATGTGGTTGCTATGTGCTGATTCCATTTGGTAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGGTAC
31220197 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGGTAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGGTAC
** * *
31220242 TTTTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCGAAGT--
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG-GGTAC
** * ** *
31220286 CATTGAAAATAAAGGTGGTTGTTATGTGCTGATTCCACCGAATAT
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGGTAC
* * *
31220331 AATTGATTATAAGGGTGG-TGCTATGTGTTGA-TCCAC
1 CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCAC
31220367 TGTGTAACTG
Statistics
Matches: 146, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
43 7 0.05
44 45 0.31
45 92 0.63
46 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGGTAC
Found at i:31220317 original size:89 final size:87
Alignment explanation
Indices: 31220153--31220366 Score: 245
Period size: 89 Copynumber: 2.4 Consensus size: 87
31220143 ACTGAGTATC
* ** **
31220153 ATTGATTATAAATGTGGTTGCTATGTGCTGATTCCATTTGGTACCATTGATTATAAAGGTGGTTG
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGA-TCCA-CCGGTA-CATTGAAAATAAAGGTGGTTG
**
31220218 CTATGTGCTGATTCCACCGGGTACT-
63 CTATGTGCTGATTCCACCGAATA-TA
*
31220243 TTTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCGAAGT-CATTGAAAATAAAGGTGGTTG
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGA-TCCACCG--GTACATTGAAAATAAAGGTGGTTG
*
31220307 TTATGTGCTGATTCCACCGAATATA
63 CTATGTGCTGATTCCACCGAATATA
* *
31220332 ATTGATTATAAGGGTGG-TGCTATGTGTTGATCCAC
1 ATTGATTATAAAGGTGGTTGCTATGTGCTGATCCAC
31220367 TGTGTAACTG
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
87 5 0.05
88 13 0.12
89 55 0.51
90 33 0.31
91 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (87 bp):
ATTGATTATAAAGGTGGTTGCTATGTGCTGATCCACCGGTACATTGAAAATAAAGGTGGTTGCTA
TGTGCTGATTCCACCGAATATA
Found at i:31222884 original size:16 final size:17
Alignment explanation
Indices: 31222863--31222898 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
31222853 TCAATCATCC
31222863 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
31222879 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
31222896 CTC
1 CTC
31222899 TCAACTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:31225903 original size:16 final size:16
Alignment explanation
Indices: 31225882--31225913 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31225872 GTTTTGTTGC
*
31225882 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
31225898 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
31225914 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:31232156 original size:20 final size:20
Alignment explanation
Indices: 31232131--31232170 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31232121 AATGTTTTCT
31232131 AATTTAAATTATTT-TGTTAA
1 AATTTAAATT-TTTATGTTAA
31232151 AATTTAAATTTTTATGTTAA
1 AATTTAAATTTTTATGTTAA
31232171 TAAAGGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
AATTTAAATTTTTATGTTAA
Found at i:31236025 original size:16 final size:17
Alignment explanation
Indices: 31236000--31236034 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
31235990 CATTCTTCAA
31236000 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
31236016 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
31236033 TC
1 TC
31236035 TCAAGTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:31252534 original size:42 final size:42
Alignment explanation
Indices: 31252482--31252571 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
31252472 TTTTATGATG
* *
31252482 GATTATTAAGCCTGATGGTTAAATAGTACTATTTTGTAAAGT
1 GATTTTTAAGCCTGATGGTTAAATAGGACTATTTTGTAAAGT
31252524 GATTTTTAAGCCTGATGGTTAAATAGGACTATTTTGTAAAGT
1 GATTTTTAAGCCTGATGGTTAAATAGGACTATTTTGTAAAGT
31252566 GATTTT
1 GATTTT
31252572 AGTTAATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (42 bp):
GATTTTTAAGCCTGATGGTTAAATAGGACTATTTTGTAAAGT
Found at i:31253163 original size:26 final size:26
Alignment explanation
Indices: 31253121--31253189 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
31253111 CATTAGGGCG
* * *
31253121 TAGTAGGCTTTGTGCTGGTGTATATT
1 TAGTAGGCTTTGAGCTGATGTACATT
31253147 TAGTAGGCTTCT-AGCTGATGTACATT
1 TAGTAGGCTT-TGAGCTGATGTACATT
* *
31253173 TAGAAGGCTTTGTGCTG
1 TAGTAGGCTTTGAGCTG
31253190 GTGTTGTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.03
26 34 0.94
27 1 0.03
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.41
Consensus pattern (26 bp):
TAGTAGGCTTTGAGCTGATGTACATT
Found at i:31258685 original size:39 final size:40
Alignment explanation
Indices: 31258640--31258811 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
31258630 GCTCCTCGTT
* * *
31258640 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
31258680 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
31258719 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
31258759 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
31258799 CAAATGCCTTCGG
1 CAAATGCCTTCGG
31258812 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:31258740 original size:40 final size:39
Alignment explanation
Indices: 31258642--31258864 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
31258632 TCCTCGTTCA
* * * *
31258642 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
31258681 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
31258720 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
31258760 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
31258800 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
31258841 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31258865 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:31258824 original size:80 final size:79
Alignment explanation
Indices: 31258640--31258864 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
31258630 GCTCCTCGTT
* * * * *
31258640 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
31258704 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
31258719 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
31258784 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
31258799 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
31258863 GA
63 GA
31258865 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:31258873 original size:41 final size:41
Alignment explanation
Indices: 31258796--31258873 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31258786 TTTGTATCTC
* * *
31258796 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31258837 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31258874 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31266628 original size:39 final size:40
Alignment explanation
Indices: 31266583--31266754 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
31266573 GCTCCTCGTT
* * *
31266583 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
31266623 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
31266662 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
31266702 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
31266742 CAAATGCCTTCGG
1 CAAATGCCTTCGG
31266755 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:31266683 original size:40 final size:39
Alignment explanation
Indices: 31266585--31266807 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
31266575 TCCTCGTTCA
* * * *
31266585 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
31266624 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
31266663 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
31266703 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
31266743 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
31266784 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31266808 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:31266767 original size:80 final size:79
Alignment explanation
Indices: 31266583--31266807 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
31266573 GCTCCTCGTT
* * * * *
31266583 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
31266647 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
31266662 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
31266727 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
31266742 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
31266806 GA
63 GA
31266808 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:31266816 original size:41 final size:41
Alignment explanation
Indices: 31266739--31266816 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31266729 TTTGTATCTC
* * *
31266739 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31266780 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31266817 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31269517 original size:61 final size:61
Alignment explanation
Indices: 31269447--31269573 Score: 220
Period size: 61 Copynumber: 2.1 Consensus size: 61
31269437 ATGAAGGTGA
31269447 TTGATCTATGAAA-TCGAAACTAGAAAAGCATAGTATGATGATTATGCTATTGCATGAATGT
1 TTGATCTATGAAACT-GAAACTAGAAAAGCATAGTATGATGATTATGCTATTGCATGAATGT
* *
31269508 TTGATCTATGAAACTGAAACTAGAAAAGTATGGTATGATGATTATGCTATTGCATGAATGT
1 TTGATCTATGAAACTGAAACTAGAAAAGCATAGTATGATGATTATGCTATTGCATGAATGT
31269569 TTGAT
1 TTGAT
31269574 GGACTTTGCA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 62 0.98
62 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (61 bp):
TTGATCTATGAAACTGAAACTAGAAAAGCATAGTATGATGATTATGCTATTGCATGAATGT
Found at i:31270055 original size:27 final size:27
Alignment explanation
Indices: 31270017--31270101 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
31270007 ACACGCTAGA
31270017 AAAATGATGCCTTTGTGGAAATCTATG
1 AAAATGATGCCTTTGTGGAAATCTATG
31270044 AAAATAGA-GCCTTTGTGGAAATCTATG
1 AAAAT-GATGCCTTTGTGGAAATCTATG
* * * * * *
31270071 AAAAGGAAGCATTTATGGAAAACTATA
1 AAAATGATGCCTTTGTGGAAATCTATG
31270098 AAAA
1 AAAA
31270102 GGAATCCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 2 0.04
27 47 0.92
28 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (27 bp):
AAAATGATGCCTTTGTGGAAATCTATG
Found at i:31270230 original size:79 final size:79
Alignment explanation
Indices: 31270126--31270291 Score: 271
Period size: 79 Copynumber: 2.1 Consensus size: 79
31270116 CGATCTATGA
31270126 TAAG-GAAGCCTTTTCGACGCACTCTAAAGAATGACCTTTATGGCAACCATCTGAAGGCAATGCA
1 TAAGAGAAGCCTTTTCGACGCACTCTAAAGAATGACCTTTATGGCAACCATCTGAAGGCAATGCA
*
31270190 TTTGTGGTCGACCC
66 TCTGTGGTCGACCC
* * *
31270204 TAAGAGAAGCCTTTTCGGCGCACTCTAAAGAATGACCTTTGTGGCAACCATCTGAAGGCAATGCC
1 TAAGAGAAGCCTTTTCGACGCACTCTAAAGAATGACCTTTATGGCAACCATCTGAAGGCAATGCA
*
31270269 TCTGTGGTGGACCC
66 TCTGTGGTCGACCC
*
31270283 TAAAAGAAG
1 TAAGAGAAG
31270292 GAAATGGTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
78 4 0.05
79 77 0.95
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (79 bp):
TAAGAGAAGCCTTTTCGACGCACTCTAAAGAATGACCTTTATGGCAACCATCTGAAGGCAATGCA
TCTGTGGTCGACCC
Found at i:31272103 original size:27 final size:27
Alignment explanation
Indices: 31272037--31272396 Score: 426
Period size: 27 Copynumber: 13.4 Consensus size: 27
31272027 ATTCGTGGGC
* *
31272037 AAAATGAATGAAATATCCT-GAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
31272063 AAAATGACCGAAATACCCTCAAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* * *
31272090 AAAATAACTAAAATACCCTTGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
31272117 AAAATGA-TCGAAATACCCCCGAAGGGT
1 AAAATGACT-GAAATACCCTCGAAGGGT
*
31272144 AAAATGA-TCGAAATACCCTTGAA-GGT
1 AAAATGACT-GAAATACCCTCGAAGGGT
*
31272170 AAACTGACTGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
31272197 AAAATGACTAAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
31272224 AAACTGA-TCGAAATACCCTCGAAGGGT
1 AAAATGACT-GAAATACCCTCGAAGGGT
* * *
31272251 AAAATGACTAAAATACCCTCAAAAGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
31272278 AAAATGACCGAAATACCCTTGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* **
31272305 AAAATGACCGAAATACCCTTAAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
*
31272332 AAAATGACCGAAATACCCTCGAAGGGT
1 AAAATGACTGAAATACCCTCGAAGGGT
* *
31272359 AAAATGA-TCGAAATACCCCCAATAGGGT
1 AAAATGACT-GAAATACCCTCGA-AGGGT
31272387 AAAATGACTG
1 AAAATGACTG
31272397 TTATACTCCT
Statistics
Matches: 289, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
26 40 0.14
27 234 0.81
28 14 0.05
29 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
AAAATGACTGAAATACCCTCGAAGGGT
Found at i:31272597 original size:26 final size:26
Alignment explanation
Indices: 31272568--31272619 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
31272558 TTGTCACATA
*
31272568 TACTGTTACTGGTAGCCTTGCTGCGT
1 TACTGTTACTGGCAGCCTTGCTGCGT
* *
31272594 TACTGTTATTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCCTTGCTGCGT
31272620 CATTATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.21, G:0.27, T:0.40
Consensus pattern (26 bp):
TACTGTTACTGGCAGCCTTGCTGCGT
Found at i:31283070 original size:76 final size:75
Alignment explanation
Indices: 31282972--31283125 Score: 272
Period size: 76 Copynumber: 2.0 Consensus size: 75
31282962 GAATTTGATT
*
31282972 TGGAAATTAGAATAGGAAAGGGATAGAAAATCAAGTGGCTGATCACTTGTCTTGAATTGAAGCAG
1 TGGAAATTAGAATAGGAAAGGGATAAAAAATCAAGTGGCTGATCACTTGTCTTGAATTGAAGCAG
31283037 GAAATGAAGA
66 GAAATGAAGA
*
31283047 TGGAAATTAGAGATAGGACAGGGATAAAAAATCAAGTGGCTGATCACTTGTCTTGAATTGAAGCA
1 TGGAAATTAGA-ATAGGAAAGGGATAAAAAATCAAGTGGCTGATCACTTGTCTTGAATTGAAGCA
*
31283112 GGAAATGAATA
65 GGAAATGAAGA
31283123 TGG
1 TGG
31283126 TAATATTCAG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 11 0.15
76 64 0.85
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.23
Consensus pattern (75 bp):
TGGAAATTAGAATAGGAAAGGGATAAAAAATCAAGTGGCTGATCACTTGTCTTGAATTGAAGCAG
GAAATGAAGA
Found at i:31300588 original size:28 final size:29
Alignment explanation
Indices: 31300531--31300588 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 29
31300521 TTTAAATAAA
* *
31300531 TATGGACTTTTATTTATGATTTGGATTTT
1 TATGGACTTTTATTGATGATTTGGACTTT
*
31300560 TATGGAC-TTTATTGCT-ATTTGGGACTTT
1 TATGGACTTTTATTGATGATTT-GGACTTT
31300588 T
1 T
31300589 TATGTTCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 4 0.16
28 14 0.56
29 7 0.28
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.55
Consensus pattern (29 bp):
TATGGACTTTTATTGATGATTTGGACTTT
Found at i:31300588 original size:29 final size:29
Alignment explanation
Indices: 31300531--31300592 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
31300521 TTTAAATAAA
*
31300531 TATGGACTTTTATTTATGATTTGGATTTT
1 TATGGACTTTTATTGATGATTTGGATTTT
*
31300560 TATGGAC-TTTATTGCT-ATTTGGGACTTTT
1 TATGGACTTTTATTGATGATTT-GGA-TTTT
31300589 TATG
1 TATG
31300593 TTCAATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.14
28 10 0.34
29 15 0.52
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (29 bp):
TATGGACTTTTATTGATGATTTGGATTTT
Found at i:31304618 original size:13 final size:14
Alignment explanation
Indices: 31304600--31304628 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31304590 AAAATTGTTT
31304600 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
31304613 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
31304627 AA
1 AA
31304629 GCCACTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:31318056 original size:19 final size:19
Alignment explanation
Indices: 31318032--31318069 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31318022 CTAGAGCAGA
31318032 GGTATCGATAATCGAGTTT
1 GGTATCGATAATCGAGTTT
*
31318051 GGTATCGATAATTGAGTTT
1 GGTATCGATAATCGAGTTT
31318070 TAAAATCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (19 bp):
GGTATCGATAATCGAGTTT
Found at i:31320930 original size:40 final size:40
Alignment explanation
Indices: 31320893--31321078 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
31320883 GCTACTCGTT
* *
31320893 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
31320933 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
31320973 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
31321013 CCAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
31321054 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
31321079 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.89
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:31339829 original size:18 final size:19
Alignment explanation
Indices: 31339806--31339853 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
31339796 ACATTTTTGG
31339806 TGCCTTTGTCC-CCCTTAT
1 TGCCTTTGTCCTCCCTTAT
*
31339824 TGCCTTTTTCCCTCCCTTAT
1 TGCCTTTGT-CCTCCCTTAT
31339844 TGCCTTTGTC
1 TGCCTTTGTC
31339854 TCCTCCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 3 0.12
20 15 0.58
ACGTcount: A:0.04, C:0.38, G:0.10, T:0.48
Consensus pattern (19 bp):
TGCCTTTGTCCTCCCTTAT
Found at i:31340165 original size:19 final size:19
Alignment explanation
Indices: 31340141--31340178 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31340131 ATATCACATC
31340141 ATATATCTA-ATTATTTTTT
1 ATATAT-TATATTATTTTTT
*
31340160 ATATATTATGTTATTTTTT
1 ATATATTATATTATTTTTT
31340179 GTCTAGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
ATATATTATATTATTTTTT
Found at i:31342225 original size:28 final size:27
Alignment explanation
Indices: 31342193--31342289 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 27
31342183 TTAATAAGTA
* *
31342193 CGCACACTTAGTGCTTAATAATCACACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
*
31342221 CGCACACTTAGTGCTT-TACCATTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
31342249 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
31342277 CGCACACTTAGTG
1 CGCACACTTAGTG
31342290 TTGGGGGTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.03
28 56 0.90
29 3 0.05
30 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:31343967 original size:35 final size:35
Alignment explanation
Indices: 31343935--31344017 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
31343925 TTCTGATTTG
* *
31343935 CATATTGAGCATG-CTATTATTCTGATTATGATTCA
1 CATATTAAGCATGTC-ATGATTCTGATTATGATTCA
* *
31343970 CATGTTAAGCATGTCATGATTCTGATTCTGATTCA
1 CATATTAAGCATGTCATGATTCTGATTATGATTCA
* *
31344005 CATGTTAAACATG
1 CATATTAAGCATG
31344018 CCACTATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 41 0.98
36 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (35 bp):
CATATTAAGCATGTCATGATTCTGATTATGATTCA
Found at i:31346235 original size:11 final size:10
Alignment explanation
Indices: 31346189--31346253 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
31346179 AAAAGGTTAT
31346189 AAAATTATT-
1 AAAATTATTA
* *
31346198 AATATTA-CA
1 AAAATTATTA
*
31346207 AAAACTATTA
1 AAAATTATTA
31346217 AAAATTATTA
1 AAAATTATTA
* *
31346227 AAATTTTATAAA
1 AAA-ATTAT-TA
31346239 AAAATTATTA
1 AAAATTATTA
31346249 AAAAT
1 AAAAT
31346254 ACTAAAAAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
9 11 0.26
10 19 0.45
11 8 0.19
12 4 0.10
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTATTA
Found at i:31346261 original size:22 final size:22
Alignment explanation
Indices: 31346216--31346261 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31346206 AAAAACTATT
**
31346216 AAAAATTATTAAAATTTTATAA
1 AAAAATTATTAAAATACTATAA
31346238 AAAAATTATTAAAAATACTA-AA
1 AAAAATTATT-AAAATACTATAA
31346260 AA
1 AA
31346262 GTTAAATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATTATTAAAATACTATAA
Found at i:31346702 original size:11 final size:11
Alignment explanation
Indices: 31346686--31346711 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31346676 TATTTTTTAA
31346686 TTTTAAAATAC
1 TTTTAAAATAC
31346697 TTTTAAAATAC
1 TTTTAAAATAC
31346708 TTTT
1 TTTT
31346712 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:31346733 original size:17 final size:17
Alignment explanation
Indices: 31346711--31346783 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 17
31346701 AAAATACTTT
31346711 TTTTAAAATTTTTTAAA
1 TTTTAAAATTTTTTAAA
*
31346728 TTTTAAATTTTTTTTAAATA
1 TTTTAAA-ATTTTTT-AA-A
** *
31346748 CTTTTTTAATTTTTTTAA
1 -TTTTAAAATTTTTTAAA
31346766 TTTTAAAATATTTTTAAA
1 TTTTAAAAT-TTTTTAAA
31346784 ATACTTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
17 14 0.33
18 14 0.33
19 3 0.07
20 7 0.16
21 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAAAATTTTTTAAA
Found at i:31356839 original size:19 final size:19
Alignment explanation
Indices: 31356815--31356856 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
31356805 TGAGTAGAGA
31356815 TATTTTAGTTATTAAATAG
1 TATTTTAGTTATTAAATAG
31356834 TATTTTAGTTATTAAATAG
1 TATTTTAGTTATTAAATAG
31356853 TATT
1 TATT
31356857 CTTTTGATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (19 bp):
TATTTTAGTTATTAAATAG
Found at i:31357005 original size:41 final size:41
Alignment explanation
Indices: 31356960--31357042 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
31356950 CATTACATCA
31356960 GGTTATATAATGACATGTATTTCTAGACTCGTACATGCTAT
1 GGTTATATAATGACATGTATTTCTAGACTCGTACATGCTAT
31357001 GGTTATATAATGACATGTATTTCTAGACTCGTACATGCTAT
1 GGTTATATAATGACATGTATTTCTAGACTCGTACATGCTAT
31357042 G
1 G
31357043 TTCAGTTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (41 bp):
GGTTATATAATGACATGTATTTCTAGACTCGTACATGCTAT
Found at i:31358968 original size:12 final size:12
Alignment explanation
Indices: 31358951--31358994 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
31358941 AACCAACAAG
31358951 ATAAGTCATATC
1 ATAAGTCATATC
*
31358963 ATAAGTCATA-G
1 ATAAGTCATATC
31358974 ATAAGTCA-ATC
1 ATAAGTCATATC
*
31358985 ATAACTCATA
1 ATAAGTCATA
31358995 CATTAACACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 1 0.04
11 15 0.56
12 11 0.41
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (12 bp):
ATAAGTCATATC
Found at i:31358988 original size:22 final size:23
Alignment explanation
Indices: 31358949--31358994 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
31358939 ACAACCAACA
*
31358949 AGATAAGTCATATCATAAGTCAT
1 AGATAAGTCATATCATAACTCAT
31358972 AGATAAGTCA-ATCATAACTCAT
1 AGATAAGTCATATCATAACTCAT
31358994 A
1 A
31358995 CATTAACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (23 bp):
AGATAAGTCATATCATAACTCAT
Found at i:31364764 original size:19 final size:19
Alignment explanation
Indices: 31364740--31364778 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31364730 AAGGAGTTAA
31364740 TTAGAAAATGCATGATGTC
1 TTAGAAAATGCATGATGTC
31364759 TTAGAAAATGCATGATGTC
1 TTAGAAAATGCATGATGTC
31364778 T
1 T
31364779 GGTTTTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (19 bp):
TTAGAAAATGCATGATGTC
Found at i:31375907 original size:22 final size:22
Alignment explanation
Indices: 31375882--31375973 Score: 130
Period size: 22 Copynumber: 4.2 Consensus size: 22
31375872 AGGTCATGCC
* *
31375882 ACCACTGATTTGCATATAAACT
1 ACCACTGAATTGCAGATAAACT
*
31375904 ACCACTGAATTGTAGATAAACT
1 ACCACTGAATTGCAGATAAACT
*
31375926 ACCATTGAATTGCAGATAAACT
1 ACCACTGAATTGCAGATAAACT
* *
31375948 GCCACTGATTTGCAGATAAACT
1 ACCACTGAATTGCAGATAAACT
31375970 ACCA
1 ACCA
31375974 TTAATAACAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (22 bp):
ACCACTGAATTGCAGATAAACT
Found at i:31379577 original size:34 final size:33
Alignment explanation
Indices: 31379514--31379577 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
31379504 ATGTGAATGA
*
31379514 AATGAGTGAAAGAGAGAGAGAGCTTAAACAAGG
1 AATGAGTGAAAGAGAGAGAGAGCTCAAACAAGG
*
31379547 AATGAGTG-AAGAAGAAGAGAGTGCTCAAACA
1 AATGAGTGAAAG-AG-AGAGAGAGCTCAAACA
31379578 CAATGGAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 3 0.11
33 10 0.37
34 14 0.52
ACGTcount: A:0.48, C:0.08, G:0.31, T:0.12
Consensus pattern (33 bp):
AATGAGTGAAAGAGAGAGAGAGCTCAAACAAGG
Found at i:31409311 original size:20 final size:20
Alignment explanation
Indices: 31409286--31409324 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31409276 TGAGTTATTT
31409286 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
31409306 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
31409325 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:31416664 original size:39 final size:39
Alignment explanation
Indices: 31416608--31416793 Score: 170
Period size: 39 Copynumber: 4.7 Consensus size: 39
31416598 TTGAATGATG
*
31416608 TCCGGGCTAAG-TCCCGAAGGC-TTGTGCTAAG-TGAC-AATA
1 TCCGGACTAAGAT-CCGAAGGCATTGTGC-AAGAT-ACTAA-A
*
31416647 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
*
31416687 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
* * * *
31416727 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAGATCCGAAGGCA-TTGTGCAAGATACTAAA
*
31416766 TCCAGG-CTAAG-CCCGAAGGCATTTGTGC
1 TCC-GGACTAAGATCCGAAGGCA-TTGTGC
31416794 GAGGAGCTAT
Statistics
Matches: 136, Mismatches: 5, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
39 69 0.51
40 58 0.43
41 9 0.07
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
TCCGGACTAAGATCCGAAGGCATTGTGCAAGATACTAAA
Found at i:31416696 original size:40 final size:39
Alignment explanation
Indices: 31416646--31416796 Score: 232
Period size: 39 Copynumber: 3.8 Consensus size: 39
31416636 AAGTGACAAT
*
31416646 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAA
*
31416686 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAG-CCCGAAGGCATTTGTGCGAGATACTAA
*
31416726 ATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAA
*
31416765 TTCCAGG-CTAAGCCCGAAGGCATTTGTGCGAG
1 ATCC-GGACTAAGCCCGAAGGCATTTGTGCGAG
31416797 GAGCTATATC
Statistics
Matches: 107, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
39 54 0.50
40 53 0.50
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (39 bp):
ATCCGGACTAAGCCCGAAGGCATTTGTGCGAGATACTAA
Found at i:31416823 original size:78 final size:79
Alignment explanation
Indices: 31416646--31416796 Score: 234
Period size: 79 Copynumber: 1.9 Consensus size: 79
31416636 AAGTGACAAT
* *
31416646 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATT
1 ATCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGACCCGAAGGCATT
31416711 TGTGCGAGATACTAA
65 TGTGCGAGATACTAA
* *
31416726 ATCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAATTCCAGG-CTAAG-CCCGAAGGCATT
1 ATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCC-GGACTAAGACCCGAAGGCATT
31416789 TGTGCGAG
65 TGTGCGAG
31416797 GAGCTATATC
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
78 19 0.29
79 34 0.52
80 13 0.20
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGACTAAGACCCGAAGGCATTT
GTGCGAGATACTAA
Found at i:31424631 original size:27 final size:26
Alignment explanation
Indices: 31424600--31424651 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
31424590 GACTAAGATC
31424600 CGAAGGCATTTGTGCGAGATACTAATT
1 CGAAGGCATTTGTGCGAG-TACTAATT
31424627 CGAAGGCATTTGTGCGAGTACTAAT
1 CGAAGGCATTTGTGCGAGTACTAAT
31424652 CCGGGTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (26 bp):
CGAAGGCATTTGTGCGAGTACTAATT
Found at i:31424717 original size:40 final size:40
Alignment explanation
Indices: 31424627--31424755 Score: 194
Period size: 40 Copynumber: 3.3 Consensus size: 40
31424617 GATACTAATT
31424627 CGAAGGCATTTGTGCGAG-TACT-AATCCGGGTTAAG-CC
1 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
31424664 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
* * *
31424704 CGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCC
1 CGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTCC
31424744 CGAAGGCATTTG
1 CGAAGGCATTTG
31424756 AACGAGGAGC
Statistics
Matches: 85, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
37 18 0.21
38 4 0.05
39 13 0.15
40 48 0.56
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCC
Found at i:31424773 original size:80 final size:76
Alignment explanation
Indices: 31424627--31424788 Score: 182
Period size: 80 Copynumber: 2.1 Consensus size: 76
31424617 GATACTAATT
* * ** *
31424627 CGAAGGCATTTGTGCGAGTACTAATCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 CGAAGGCATTTGTGCGAGTACTAAACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATC
*
31424692 CGGGTTAAGTCC
66 C-GGTTAAATCC
* *
31424704 CGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTA
1 CGAAGGCATTTGTGCG-AGTACTA-AACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTA
* *
31424768 TATCCGGTTAAATTC
62 AATCCGGTTAAATCC
31424783 CGAAGG
1 CGAAGG
31424789 TACGTGATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
77 16 0.23
78 6 0.08
79 24 0.34
80 25 0.35
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (76 bp):
CGAAGGCATTTGTGCGAGTACTAAACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATC
CGGTTAAATCC
Found at i:31432603 original size:39 final size:40
Alignment explanation
Indices: 31432508--31432729 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
31432498 TTGAATGATG
*
31432508 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
31432546 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
31432587 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31432626 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
31432665 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
31432703 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
31432730 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.01
39 123 0.76
40 26 0.16
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31432751 original size:78 final size:78
Alignment explanation
Indices: 31432560--31432762 Score: 209
Period size: 78 Copynumber: 2.6 Consensus size: 78
31432550 GGACTAAGAT
** * * *
31432560 CCGAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGATACTA
*
31432624 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
** *
31432638 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGA-ATTACT-
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGA-TACTA
*
31432701 ATAACCGGGCTATGTC
65 AT-ACCGGGCTAAG-C
* *
31432717 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTT-AAGTCCGAAGG
31432763 TACGTGATTT
Statistics
Matches: 109, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
77 4 0.04
78 70 0.64
79 35 0.32
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGATACTAA
TACCGGGCTAAGC
Found at i:31434055 original size:1 final size:1
Alignment explanation
Indices: 31434049--31434090 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
31434039 TTCGCTCCGG
31434049 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31434091 ATCTCATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31436037 original size:6 final size:6
Alignment explanation
Indices: 31436026--31436051 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31436016 ACTTTTAGAC
31436026 TTTAGT TTTAGT TTTAGT TTTAGT TT
1 TTTAGT TTTAGT TTTAGT TTTAGT TT
31436052 AGAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTAGT
Found at i:31436059 original size:19 final size:18
Alignment explanation
Indices: 31436010--31436066 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
31436000 TAAATTATTT
*
31436010 GTTTAGACTTTTAGACTTTA
1 GTTTAGA-TTTTAG-TTTTA
31436030 GTTTTAG-TTTTAGTTTTA
1 G-TTTAGATTTTAGTTTTA
*
31436048 GTTTAGAATTTTATTTTTA
1 GTTTAG-ATTTTAGTTTTA
31436067 TTTTTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 5 0.16
18 5 0.16
19 16 0.50
20 1 0.03
21 5 0.16
ACGTcount: A:0.23, C:0.04, G:0.14, T:0.60
Consensus pattern (18 bp):
GTTTAGATTTTAGTTTTA
Found at i:31439322 original size:27 final size:27
Alignment explanation
Indices: 31439292--31439379 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
31439282 CACAAGACAA
*
31439292 TTCTTTCATAATGCTCCGCAAAGGCAT
1 TTCTTTCATAATGCTCCACAAAGGCAT
** * *
31439319 TTCTTTTGTGATG-TGCCACAAAGACAT
1 TTCTTTCATAATGCT-CCACAAAGGCAT
* *
31439346 TTCTTTCATAATGCACCAAAAAGGCAT
1 TTCTTTCATAATGCTCCACAAAGGCAT
31439373 TTCTTTC
1 TTCTTTC
31439380 TTGACATGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
26 1 0.02
27 47 0.98
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (27 bp):
TTCTTTCATAATGCTCCACAAAGGCAT
Found at i:31444210 original size:84 final size:84
Alignment explanation
Indices: 31444112--31444289 Score: 284
Period size: 84 Copynumber: 2.1 Consensus size: 84
31444102 ATAGAAATGG
* *
31444112 AAATGAAAATTTGCAATCCTATATGGATTACTTAAAACTGATGGGAAGAATAAGTTTATATTTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAACAGATGGGAAGAATAAGTTTATATTTTT
* *
31444177 GGACTATTTTGAAGCTTGA
66 GGACTAATTTGAAGCCTGA
* * *
31444196 AAATGAAAATTTGCAATCTTATATAGATTACTTAAAACAGATTGGAAGAATAAGTTTATGTTTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAACAGATGGGAAGAATAAGTTTATATTTTT
*
31444261 GGACTAATTTGAAGCCTGG
66 GGACTAATTTGAAGCCTGA
31444280 AAATGAAAAT
1 AAATGAAAAT
31444290 AAACTATTCG
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (84 bp):
AAATGAAAATTTGCAATCCTATATAGATTACTTAAAACAGATGGGAAGAATAAGTTTATATTTTT
GGACTAATTTGAAGCCTGA
Found at i:31446778 original size:50 final size:50
Alignment explanation
Indices: 31446650--31446890 Score: 268
Period size: 50 Copynumber: 4.8 Consensus size: 50
31446640 GATAATAACA
* ** * * * **
31446650 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * ** * *
31446700 -GCCAATGCCATATTCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * **
31446749 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
31446799 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
31446849 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31446891 TTACCCAAAT
Statistics
Matches: 162, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
49 38 0.23
50 124 0.77
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31447997 original size:12 final size:12
Alignment explanation
Indices: 31447982--31448008 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31447972 GAACGAAATT
31447982 TTCAGGAAATCA
1 TTCAGGAAATCA
31447994 TTCAGGAAATCA
1 TTCAGGAAATCA
31448006 TTC
1 TTC
31448009 TGTGAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (12 bp):
TTCAGGAAATCA
Found at i:31465846 original size:19 final size:19
Alignment explanation
Indices: 31465822--31465868 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
31465812 TTTAAAAGTA
*
31465822 TAAAAAAATA-TACGAGTGT
1 TAAAAAAATAGTA-AAGTGT
*
31465841 TAAAAAAACAGTAAAGTGT
1 TAAAAAAATAGTAAAGTGT
31465860 TAAAAAAAT
1 TAAAAAAAT
31465869 CTTTGTTGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (19 bp):
TAAAAAAATAGTAAAGTGT
Found at i:31466789 original size:15 final size:15
Alignment explanation
Indices: 31466753--31466789 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
31466743 AACTCAAATG
*
31466753 AAAGAAAAAGAAAAT
1 AAAGAAAAAGAAAAA
*
31466768 AATGAAAAAGAAAAA
1 AAAGAAAAAGAAAAA
31466783 AAAGAAA
1 AAAGAAA
31466790 GTGAAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAGAAAAAGAAAAA
Found at i:31466833 original size:19 final size:19
Alignment explanation
Indices: 31466753--31466834 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
31466743 AACTCAAATG
31466753 AAAGAAAAAGAAAATAATGAA
1 AAAGAAAAAGAAAA-AAT-AA
*
31466774 AAAGAAAAA-AAAGAAAGTGA
1 AAAGAAAAAGAAA-AAA-TAA
* ** * **
31466794 AAAGAACATTAGAAACGAA
1 AAAGAAAAAGAAAAAATAA
31466813 AAAGAAAAAGAAAAAATAA
1 AAAGAAAAAGAAAAAATAA
31466832 AAA
1 AAA
31466835 AAAGTTTGAT
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
19 17 0.38
20 15 0.33
21 13 0.29
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAGAAAAAGAAAAAATAA
Found at i:31469188 original size:10 final size:11
Alignment explanation
Indices: 31469163--31469211 Score: 59
Period size: 10 Copynumber: 4.7 Consensus size: 11
31469153 GAACAAGCTC
*
31469163 ATTGAGCTAAA
1 ATTGAGCTAGA
31469174 ATTGAGCT-GA
1 ATTGAGCTAGA
*
31469184 ATTGAGCTCG-
1 ATTGAGCTAGA
31469194 ATTGAGCTAG-
1 ATTGAGCTAGA
31469204 ATTGAGCT
1 ATTGAGCT
31469212 TTATTTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
10 26 0.74
11 9 0.26
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (11 bp):
ATTGAGCTAGA
Found at i:31471821 original size:13 final size:13
Alignment explanation
Indices: 31471805--31471841 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
31471795 TCGTGCCTTT
31471805 CACCTCTCGAATC
1 CACCTCTCGAATC
31471818 CACCTCTCGAATC
1 CACCTCTCGAATC
*
31471831 CGCCTCTCGAA
1 CACCTCTCGAA
31471842 CTTCTTAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.22, C:0.46, G:0.11, T:0.22
Consensus pattern (13 bp):
CACCTCTCGAATC
Found at i:31472148 original size:12 final size:12
Alignment explanation
Indices: 31472114--31472147 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31472104 AACCACGTAC
*
31472114 AAATTTTTGTTG
1 AAATTTTTTTTG
31472126 AAATTTTTTTTG
1 AAATTTTTTTTG
31472138 -AATTTTTTTT
1 AAATTTTTTTT
31472148 TCACAATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (12 bp):
AAATTTTTTTTG
Found at i:31474270 original size:20 final size:20
Alignment explanation
Indices: 31474247--31474300 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
31474237 AGTTTTTCCC
*
31474247 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
31474267 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
31474287 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
31474301 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:31474282 original size:30 final size:30
Alignment explanation
Indices: 31474247--31474320 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
31474237 AGTTTTTCCC
31474247 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
31474277 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
31474307 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
31474321 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:31474310 original size:20 final size:20
Alignment explanation
Indices: 31474247--31474311 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31474237 AGTTTTTCCC
* * * *
31474247 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
31474267 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
31474286 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
31474307 AGCTC
1 AGCTC
31474312 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:31475833 original size:12 final size:11
Alignment explanation
Indices: 31475809--31475847 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
31475799 ATGGTATTGT
31475809 AAAAAAAAT--
1 AAAAAAAATCG
31475818 AAAAAAAATCG
1 AAAAAAAATCG
*
31475829 AAAAAAAATTG
1 AAAAAAAATCG
31475840 AAAAAAAA
1 AAAAAAAA
31475848 CTTATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:31476855 original size:21 final size:21
Alignment explanation
Indices: 31476815--31476873 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
31476805 AATCTTGAAT
*
31476815 GAAATTAAGAGAAGAA-AAAAA
1 GAAA-TAAGAGAAAAAGAAAAA
*
31476836 GAAATGAGAGAAAAAGAAAAA
1 GAAATAAGAGAAAAAGAAAAA
*
31476857 GAAATAAAAGAAAAAGA
1 GAAATAAGAGAAAAAGA
31476874 TGAAAATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAATAAGAGAAAAAGAAAAA
Found at i:31476865 original size:15 final size:14
Alignment explanation
Indices: 31476826--31476873 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
31476816 AAATTAAGAG
31476826 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
31476840 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
31476855 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
31476870 AAGA
1 AAGA
31476874 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:31476929 original size:12 final size:12
Alignment explanation
Indices: 31476912--31476943 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31476902 AGTGAAAAGC
*
31476912 AAAAAGAGATTG
1 AAAAAGAAATTG
31476924 AAAAAGAAATTG
1 AAAAAGAAATTG
31476936 AAAAAGAA
1 AAAAAGAA
31476944 GAAAAGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:31478676 original size:82 final size:82
Alignment explanation
Indices: 31478517--31478679 Score: 220
Period size: 82 Copynumber: 2.0 Consensus size: 82
31478507 TTGTGTCTGC
* * * *
31478517 AGGTCATTAAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTAAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
31478582 GGAACGACATTTAAAGA
66 GGAACGACATTTAAAGA
* **
31478599 AGGTCATTGAAATTTGGCTACTTAATGGCAAAGGAAACATGCA-TTAAGGAGATGTTCCCATGCA
1 AGGTCATT-AAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCA
* **
31478663 TGGAACGGTATTTAAAG
65 AGGAACGACATTTAAAG
31478680 GGAAGTAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
82 39 0.56
83 31 0.44
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (82 bp):
AGGTCATTAAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
GGAACGACATTTAAAGA
Found at i:31483844 original size:30 final size:30
Alignment explanation
Indices: 31483808--31483912 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 30
31483798 AATGAAAGAG
31483808 AAGAAAAAGAAAAAGAAAGTGAAAAAGAAA
1 AAGAAAAAGAAAAAGAAAGTGAAAAAGAAA
* * *
31483838 AAGAAAAATAAAAAGAAATTGCAAAAGAAA
1 AAGAAAAAGAAAAAGAAAGTGAAAAAGAAA
** ** *
31483868 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAGAAAAAGAAAAAGAAAGTGAAAAAGAAA
*
31483898 ATGAAGAAAAGAAAA
1 AAG-A-AAAAGAAAA
31483913 TTTAAAAAGA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
30 51 0.86
31 1 0.02
32 7 0.12
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (30 bp):
AAGAAAAAGAAAAAGAAAGTGAAAAAGAAA
Found at i:31483868 original size:5 final size:6
Alignment explanation
Indices: 31483808--31483912 Score: 84
Period size: 6 Copynumber: 17.2 Consensus size: 6
31483798 AATGAAAGAG
** *
31483808 AAGAAA AAGAAA AAGAAA GTGAAA AAGAAA AAGAAA AATAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * ** ** * *
31483856 TTGCAA AAGAAA AAGAAA TCGAAA AAGTGA GAGAAA AAGAAA ATGAAGAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-A-AA
31483906 AAGAAA A
1 AAGAAA A
31483913 TTTAAAAAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
6 67 0.92
7 2 0.03
8 4 0.05
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (6 bp):
AAGAAA
Found at i:31486505 original size:25 final size:25
Alignment explanation
Indices: 31486471--31486540 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
31486461 AATAAATTAG
*
31486471 CATGCATGTTTCCTTGAATGTCGTT
1 CATGCATGTTTCCTTTAATGTCGTT
*
31486496 CATGCATGTTTCTTTTAATGTCGTT
1 CATGCATGTTTCCTTTAATGTCGTT
*
31486521 CATGCATGCTTCCTTTAATG
1 CATGCATGTTTCCTTTAATG
31486541 CTCTCCTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (25 bp):
CATGCATGTTTCCTTTAATGTCGTT
Found at i:31486975 original size:20 final size:20
Alignment explanation
Indices: 31486950--31486991 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31486940 AATTTAAACC
31486950 AAGCTCAAACGAGTTGAATT
1 AAGCTCAAACGAGTTGAATT
***
31486970 AAGCTCATGTGAGTTGAATT
1 AAGCTCAAACGAGTTGAATT
31486990 AA
1 AA
31486992 AAATCATGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (20 bp):
AAGCTCAAACGAGTTGAATT
Found at i:31487000 original size:21 final size:20
Alignment explanation
Indices: 31486960--31487008 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
31486950 AAGCTCAAAC
**
31486960 GAGTTGAATTAAGCTCATGT
1 GAGTTGAATTAAAATCATGT
31486980 GAGTTGAATTAAAAATCATGT
1 GAGTTGAATT-AAAATCATGT
*
31487001 GAGCTGAA
1 GAGTTGAA
31487009 CCAAGCTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (20 bp):
GAGTTGAATTAAAATCATGT
Found at i:31489069 original size:14 final size:15
Alignment explanation
Indices: 31489042--31489071 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31489032 TCTCTTTCAA
31489042 TTTCTTTTTCCACTC
1 TTTCTTTTTCCACTC
31489057 TTTCTTTTT-CACTC
1 TTTCTTTTTCCACTC
31489071 T
1 T
31489072 CAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTCTTTTTCCACTC
Found at i:31489161 original size:22 final size:23
Alignment explanation
Indices: 31489127--31489169 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31489117 TCAATCTCTT
31489127 TTTCAATTTTC-TTTTCTTTTTC
1 TTTCAATTTTCTTTTTCTTTTTC
31489149 TTTC-ATTTCTCTTTTTCTTTT
1 TTTCAATTT-TCTTTTTCTTTT
31489170 GGTTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTCAATTTTCTTTTTCTTTTTC
Found at i:31490114 original size:26 final size:25
Alignment explanation
Indices: 31490077--31490150 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
31490067 CTTCACTCTC
*
31490077 TTTTTTTCGAATTTTTTTATTTATT
1 TTTTTTTTGAATTTTTTTATTTATT
**
31490102 ATTTTTTTTGAATTTTTTT-TGAATT
1 -TTTTTTTTGAATTTTTTTATTTATT
*
31490127 TATTTTTTTGAATTTTTTAATTTA
1 T-TTTTTTTGAATTTTTTTATTTA
31490151 ATACAATGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 1 0.03
25 20 0.50
26 19 0.47
ACGTcount: A:0.20, C:0.01, G:0.05, T:0.73
Consensus pattern (25 bp):
TTTTTTTTGAATTTTTTTATTTATT
Found at i:31490119 original size:10 final size:11
Alignment explanation
Indices: 31490102--31490144 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
31490092 TTTATTTATT
31490102 ATTTTTTTTGA
1 ATTTTTTTTGA
31490113 ATTTTTTTTGA
1 ATTTTTTTTGA
31490124 ATTTATTTTTTTGA
1 A--T-TTTTTTTGA
31490138 ATTTTTT
1 ATTTTTT
31490145 AATTTAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 17 0.59
12 1 0.03
13 1 0.03
14 10 0.34
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:31497117 original size:20 final size:21
Alignment explanation
Indices: 31497073--31497118 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
31497063 CAATGTGTCT
31497073 TGTCTTAACCGAATTAATTAG
1 TGTCTTAACCGAATTAATTAG
**
31497094 -GTCTTAACTTAATTAATT-G
1 TGTCTTAACCGAATTAATTAG
31497113 TGTCTT
1 TGTCTT
31497119 GTTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (21 bp):
TGTCTTAACCGAATTAATTAG
Found at i:31498447 original size:13 final size:13
Alignment explanation
Indices: 31498426--31498459 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
31498416 ATAGGTACGT
31498426 AAAAAAATTTGAA
1 AAAAAAATTTGAA
*
31498439 AAGAAAATTTGAA
1 AAAAAAATTTGAA
31498452 AAAAAAAT
1 AAAAAAAT
31498460 ATACATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAAAAATTTGAA
Found at i:31500658 original size:17 final size:19
Alignment explanation
Indices: 31500630--31500678 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
31500620 AGAAAAAGAA
*
31500630 AAGAATGAAAAATCAAAAG
1 AAGAAAGAAAAATCAAAAG
* *
31500649 -A-AAAGAAAAATGAGAAG
1 AAGAAAGAAAAATCAAAAG
31500666 AAGAAAGAAAAAT
1 AAGAAAGAAAAAT
31500679 TGAAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 2 0.08
19 10 0.40
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.08
Consensus pattern (19 bp):
AAGAAAGAAAAATCAAAAG
Found at i:31500688 original size:19 final size:19
Alignment explanation
Indices: 31500644--31500688 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
31500634 ATGAAAAATC
31500644 AAAAGAAAAGAAAAATGAGA
1 AAAAG-AAAGAAAAATGAGA
*
31500664 AGAAGAAAGAAAAATTGA-A
1 AAAAGAAAGAAAAA-TGAGA
31500683 AAAAGA
1 AAAAGA
31500689 GTGTGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (19 bp):
AAAAGAAAGAAAAATGAGA
Found at i:31503792 original size:20 final size:21
Alignment explanation
Indices: 31503748--31503793 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
31503738 CAATGTGTAT
31503748 TGTCTTAACCGAATTAATTAG
1 TGTCTTAACCGAATTAATTAG
**
31503769 -GTCTTAACTTAATTAATT-G
1 TGTCTTAACCGAATTAATTAG
31503788 TGTCTT
1 TGTCTT
31503794 GTTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (21 bp):
TGTCTTAACCGAATTAATTAG
Found at i:31511775 original size:20 final size:20
Alignment explanation
Indices: 31511732--31511775 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31511722 GGGTTAAGAT
*
31511732 TGAGTTGAATTGAGCTTGAA
1 TGAGTTGAATTGAGCTCGAA
* *
31511752 TGAGTTGACTTGAGCTCGAG
1 TGAGTTGAATTGAGCTCGAA
31511772 TGAG
1 TGAG
31511776 CTGGAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.34, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTGAGCTCGAA
Found at i:31522311 original size:39 final size:40
Alignment explanation
Indices: 31522101--31522331 Score: 313
Period size: 40 Copynumber: 5.8 Consensus size: 40
31522091 GGATATAACT
* * *
31522101 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
31522141 ACTCGCACAATTCCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
31522181 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
31522221 ATTCGCACAAATGCCTTCGGGACTTAGCCCGGGTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
31522261 ACTCGCACAGATGCCTTCGGAACTTAGCCCGGA-TTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* ** *
31522300 ACTAGTGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
31522332 TTTTCATCCA
Statistics
Matches: 172, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
39 33 0.19
40 137 0.80
41 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:31524821 original size:40 final size:40
Alignment explanation
Indices: 31524730--31524898 Score: 207
Period size: 39 Copynumber: 4.3 Consensus size: 40
31524720 TCCTCGTTCA
* * * * *
31524730 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
31524769 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
31524809 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
31524849 AATGCC-TCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
31524888 AAGGCCTTCGG
1 AATGCCTTCGG
31524899 ATCTTAGTCC
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
39 66 0.59
40 46 0.41
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:31524831 original size:79 final size:79
Alignment explanation
Indices: 31524728--31524898 Score: 218
Period size: 79 Copynumber: 2.2 Consensus size: 79
31524718 GCTCCTCGTT
* * * *
31524728 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCC-TCGGGACGTAACCCGG
31524792 ATTTAACAACTCGCA
65 ATTTAACAACTCGCA
* * * *
31524807 CGAATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACGAATGCCTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCTCGGGACGTAACCCGGA
** *
31524872 TTTAGTATCTCGCA
66 TTTAACAACTCGCA
*
31524886 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
31524899 ATCTTAGTCC
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 73 0.94
80 5 0.06
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCTCGGGACGTAACCCGGA
TTTAACAACTCGCA
Found at i:31532824 original size:40 final size:40
Alignment explanation
Indices: 31532641--31532810 Score: 234
Period size: 40 Copynumber: 4.3 Consensus size: 40
31532631 TCCTCGTTCA
* * * *
31532641 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
31532680 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
31532720 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
31532760 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
31532800 AAGGCCTTCGG
1 AATGCCTTCGG
31532811 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 35 0.30
40 83 0.70
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:31535657 original size:24 final size:25
Alignment explanation
Indices: 31535630--31535685 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
31535620 TTTAACTTGA
31535630 TTTTTTTTGCTC-ACTTTTTTTT-CT
1 TTTTTTTTGCTCGA-TTTTTTTTACT
31535654 TTTTTTTTGCTCGATTTTTTTTACT
1 TTTTTTTTGCTCGATTTTTTTTACT
31535679 TTTTTTT
1 TTTTTTT
31535686 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.67
25 10 0.33
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.77
Consensus pattern (25 bp):
TTTTTTTTGCTCGATTTTTTTTACT
Found at i:31535692 original size:11 final size:11
Alignment explanation
Indices: 31535667--31535704 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
31535657 TTTTTGCTCG
31535667 ATTTTTTTT-A
1 ATTTTTTTTGA
*
31535677 CTTTTTTTTGA
1 ATTTTTTTTGA
31535688 ATTTTTTTTTGA
1 A-TTTTTTTTGA
31535700 ATTTT
1 ATTTT
31535705 GATTTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.33
11 5 0.21
12 11 0.46
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:31535693 original size:12 final size:12
Alignment explanation
Indices: 31535678--31535704 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31535668 TTTTTTTTAC
31535678 TTTTTTTTGAAT
1 TTTTTTTTGAAT
31535690 TTTTTTTTGAAT
1 TTTTTTTTGAAT
31535702 TTT
1 TTT
31535705 GATTTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:31537208 original size:20 final size:20
Alignment explanation
Indices: 31537185--31537231 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31537175 GGGTTAAGAT
*
31537185 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
31537205 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
31537225 TGAGCTG
1 TGAGCTG
31537232 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:31539948 original size:18 final size:18
Alignment explanation
Indices: 31539927--31540045 Score: 100
Period size: 18 Copynumber: 6.6 Consensus size: 18
31539917 TAAATCTCAA
31539927 TTTCTTTTTCAATTTTCTTT
1 TTTCTTTTTC-ATTTTC-TT
* * *
31539947 TCTTCATTTTCTTTTTCTC
1 T-TTCTTTTTCATTTTCTT
** *
31539966 TCACTTTTTCAATTTCTT
1 TTTCTTTTTCATTTTCTT
* *
31539984 TTTCTTTTGCAATTTCTT
1 TTTCTTTTTCATTTTCTT
31540002 TTTCTTTTTC-TTCTTCTT
1 TTTCTTTTTCATT-TTCTT
*
31540020 TTTC--TTTCACTTTCTT
1 TTTCTTTTTCATTTTCTT
31540036 TTTCTTTTTC
1 TTTCTTTTTC
31540046 TTCTTTTTTG
Statistics
Matches: 79, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
16 13 0.16
17 2 0.03
18 48 0.61
19 2 0.03
20 6 0.08
21 8 0.10
ACGTcount: A:0.08, C:0.21, G:0.01, T:0.71
Consensus pattern (18 bp):
TTTCTTTTTCATTTTCTT
Found at i:31539964 original size:6 final size:6
Alignment explanation
Indices: 31539927--31540047 Score: 84
Period size: 6 Copynumber: 20.0 Consensus size: 6
31539917 TAAATCTCAA
* * * ** **
31539927 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCAA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** *
31539978 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCTT CTTCTT TTTC--
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
**
31540024 TTTCAC TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT
31540048 CTTTTTTGTT
Statistics
Matches: 86, Mismatches: 25, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
4 4 0.05
6 70 0.81
7 9 0.10
8 3 0.03
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:31540059 original size:15 final size:15
Alignment explanation
Indices: 31539939--31540053 Score: 65
Period size: 15 Copynumber: 7.3 Consensus size: 15
31539929 TCTTTTTCAA
*
31539939 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTCT
31539953 TTTTCTTTTTCTCTCACT
1 TTTTCTTTTTCT-T--CT
*
31539971 TTTTCAATTTCTTTTTCT
1 TTTTC--TTT-TTCTTCT
* **
31539989 TTTGCAATTTCTT-T
1 TTTTCTTTTTCTTCT
31540003 TTCTT-TTTCTTCTTCT
1 TT-TTCTTT-TTCTTCT
**
31540019 TTTTCTTTCACTTTCT
1 TTTTCTTTTTC-TTCT
31540035 TTTTCTTTTTCTTCT
1 TTTTCTTTTTCTTCT
31540050 TTTT
1 TTTT
31540054 TGTTTTTATT
Statistics
Matches: 76, Mismatches: 13, Indels: 23
0.68 0.12 0.21
Matches are distributed among these distances:
14 9 0.12
15 27 0.36
16 21 0.28
18 12 0.16
20 4 0.05
21 3 0.04
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:31544792 original size:18 final size:18
Alignment explanation
Indices: 31544743--31544808 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
31544733 TTACTCAATA
31544743 TCTTTTCTCTCTTCAA-TT
1 TCTTTTCTCT-TTCAATTT
* * *
31544761 TCAATCTCTTTTTCAATTT
1 TC-TTTTCTCTTTCAATTT
31544780 TCTTTTCTCTTTCACATTT
1 TCTTTTCTCTTTCA-ATTT
31544799 T-TTTTACTCT
1 TCTTTT-CTCT
31544809 CAAACTCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 20 0.53
19 18 0.47
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTTTCTCTTTCAATTT
Found at i:31547635 original size:19 final size:19
Alignment explanation
Indices: 31547611--31547655 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
31547601 TTTCCAACAC
31547611 TTTTTTTTGAAGTTTAGTT
1 TTTTTTTTGAAGTTTAGTT
* *
31547630 TTTTTTTTGAATTTTTGTT
1 TTTTTTTTGAAGTTTAGTT
31547649 TTTTTTT
1 TTTTTTT
31547656 CAATACTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (19 bp):
TTTTTTTTGAAGTTTAGTT
Found at i:31549202 original size:50 final size:52
Alignment explanation
Indices: 31549084--31549207 Score: 155
Period size: 50 Copynumber: 2.4 Consensus size: 52
31549074 ATGAGTTGCT
* *
31549084 TAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGGGAGTTACA
1 TAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGAAGTTACA
** * *
31549136 TAATGCATGTCATTATTT-ATGATGCATACTT-AACTAACATGGAAGTTACA
1 TAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGAAGTTACA
*
31549186 TAATGCATAACTTTATTAAATG
1 TAATGCATAACTTTATTTAATG
31549208 CAAAACACAC
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
50 32 0.53
51 15 0.25
52 13 0.22
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
TAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGAAGTTACA
Found at i:31556074 original size:16 final size:16
Alignment explanation
Indices: 31556053--31556086 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31556043 TATTGAGCCA
31556053 TAATTAAACACTTAAT
1 TAATTAAACACTTAAT
**
31556069 TAATTAAGTACTTAAT
1 TAATTAAACACTTAAT
31556085 TA
1 TA
31556087 GGAAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
TAATTAAACACTTAAT
Found at i:31556167 original size:17 final size:18
Alignment explanation
Indices: 31556129--31556172 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
31556119 TCCAAGTTTT
*
31556129 TTTAAC-AAATTAATTAA
1 TTTAACTAAATTAACTAA
*
31556146 CTTAACTAAA-TAACTAA
1 TTTAACTAAATTAACTAA
31556163 TTTAACTAAA
1 TTTAACTAAA
31556173 GACAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAACTAAATTAACTAA
Found at i:31558098 original size:40 final size:40
Alignment explanation
Indices: 31558014--31558238 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
31558004 TTGAATGATG
* * * *
31558014 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
31558054 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31558094 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31558133 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
31558173 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* * *
31558214 -CCGGGATATGTCCCGAAGGTATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31558239 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 16, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31558256 original size:80 final size:80
Alignment explanation
Indices: 31558014--31558271 Score: 226
Period size: 80 Copynumber: 3.2 Consensus size: 80
31558004 TTGAATGATG
* * * * * *
31558014 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC-GGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGA-TAAG-TCCCGAAGGCA
** *
31558076 TTTGTGCGAGAT-ACTAAT
63 TTTGAACGAG-TGACTAAA
* *
31558094 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGATAAGTCCCGAAGGCATTT
** *
31558158 GTGCGAGTTACTAAA
66 GAACGAGTGACTAAA
* * *
31558173 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGATATGTCCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGATAAGTCCCGAAGGCATT
*
31558237 TGAACGAG-GAGCTATA
65 TGAACGAGTGA-CTAAA
* *
31558253 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
31558272 TACGTGATTT
Statistics
Matches: 153, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.01
79 72 0.47
80 77 0.50
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGATAAGTCCCGAAGGCATTT
GAACGAGTGACTAAA
Found at i:31566159 original size:105 final size:105
Alignment explanation
Indices: 31565993--31566201 Score: 265
Period size: 105 Copynumber: 2.0 Consensus size: 105
31565983 GTCTACCTCT
* * *
31565993 AAGGGAAGTCAGTCCAACTCGGATTAGGACATCCATCGCATCAAGTCAATCCCAAAACTCAACTT
1 AAGGGAAGTCAGTCCAACTCGGATGAGAACATCCAGCGCATCAAGTCAATCCCAAAACTCAACTT
* * * *
31566058 CAGTTCTCAGTTCAACTTCAAGAGGAGTCGGTCCAACTCC
66 CAGTTATAAGTTCAACTTCAAGAGGAGCCAGTCCAACTCC
* * * ** * * *
31566098 AAGGGTAGTGAGTCCAACTCGGATGAGAACATCGAGCTTATCGAGTCAATCCCATAGCTCAACTT
1 AAGGGAAGTCAGTCCAACTCGGATGAGAACATCCAGCGCATCAAGTCAATCCCAAAACTCAACTT
* *
31566163 CAGTTATAAGTTTAACTTCAAGTGGAGCCAGTCCAACTC
66 CAGTTATAAGTTCAACTTCAAGAGGAGCCAGTCCAACTC
31566202 GGATGAGGGC
Statistics
Matches: 87, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (105 bp):
AAGGGAAGTCAGTCCAACTCGGATGAGAACATCCAGCGCATCAAGTCAATCCCAAAACTCAACTT
CAGTTATAAGTTCAACTTCAAGAGGAGCCAGTCCAACTCC
Found at i:31566264 original size:84 final size:84
Alignment explanation
Indices: 31566108--31566264 Score: 208
Period size: 84 Copynumber: 1.9 Consensus size: 84
31566098 AAGGGTAGTG
* * * * *
31566108 AGTCCAACTCGGATGAGAACATCGAGCTTATCGAGTCAATCCCATAGCTCAACTTCAGTTATAAG
1 AGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATATAAG
*
31566173 TTTAACTTCAAGTGGAGCC
66 TTCAACTTCAAGTGGAGCC
** * *
31566192 AGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCA-ATAGTTA
1 AGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATA-TAA
31566256 GTTCAACTT
65 GTTCAACTT
31566265 TAAGAGGGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
83 2 0.03
84 60 0.97
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (84 bp):
AGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATATAAG
TTCAACTTCAAGTGGAGCC
Found at i:31566279 original size:84 final size:84
Alignment explanation
Indices: 31566108--31566285 Score: 205
Period size: 84 Copynumber: 2.1 Consensus size: 84
31566098 AAGGGTAGTG
* * * * *
31566108 AGTCCAACTCGGATGAGAACATCGAGCTTATCGAGTCAATCCCATAGCTCAACTTCAGTTATAAG
1 AGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATATAAG
* *
31566173 TTTAACTTCAAGTGGAGCC
66 TTCAACTTCAAGAGGAGCC
** * *
31566192 AGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCA-ATAGTTA
1 AGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATA-TAA
* * *
31566256 GTTCAACTTTAAGAGGGGTC
65 GTTCAACTTCAAGAGGAGCC
*
31566276 AGTCCTACTC
1 AGTCCAACTC
31566286 CAAGGGTAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 2 0.03
84 76 0.97
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (84 bp):
AGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATATAAG
TTCAACTTCAAGAGGAGCC
Found at i:31566341 original size:189 final size:189
Alignment explanation
Indices: 31566002--31566357 Score: 460
Period size: 189 Copynumber: 1.9 Consensus size: 189
31565992 TAAGGGAAGT
* * * * * *
31566002 CAGTCCAACTCGGATTAGGACATCCATCGCATCAAGTCAATCCCAAAACTCAACTTCAGTTCTCA
1 CAGTCCAACTCGGATGAGGACATCAACCGCATCAAGTCAATCCCAAAACTCAACTCCAATACTCA
* * * * *
31566067 GTTCAACTTCAAGAGGAGTCGGTCCAACTCCAAGGGTAGTGAGTCCAACTCGGATGAGAACATCG
66 GTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGAACATCC
* *
31566132 AGCTTATCGAGTCAATCCCATAGCTCAACTTCAGTTATAAGTTTAACTTCAAGTGGAGC
131 ACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATAAGTTTAACTTCAAGTGGAGC
* ** * * * * *
31566191 CAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCAATAGTTA
1 CAGTCCAACTCGGATGAGGACATCAACCGCATCAAGTCAATCCCAAAACTCAACTCCAATACTCA
* * * *
31566256 GTTCAACTTTAAGAGGGGTCAGTCCTACTCCAAGGGTAATCAGTCCAACTCGAATGAGTACATCC
66 GTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGAACATCC
* * *
31566321 ACCTCATTGAGTCTATCCCATAGCTCAACTTTAGTTA
131 ACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTA
31566358 GTTCAACTCC
Statistics
Matches: 139, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
189 139 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (189 bp):
CAGTCCAACTCGGATGAGGACATCAACCGCATCAAGTCAATCCCAAAACTCAACTCCAATACTCA
GTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGAACATCC
ACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATAAGTTTAACTTCAAGTGGAGC
Found at i:31566387 original size:21 final size:21
Alignment explanation
Indices: 31566361--31566408 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31566351 TTAGTTAGTT
31566361 CAACTCCAAGAGG-AGTCAATC
1 CAACTCCAAG-GGTAGTCAATC
* *
31566382 CAACTCCAAGGGTAGTGAGTC
1 CAACTCCAAGGGTAGTCAATC
31566403 CAACTC
1 CAACTC
31566409 GGATAAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (21 bp):
CAACTCCAAGGGTAGTCAATC
Found at i:31566508 original size:105 final size:105
Alignment explanation
Indices: 31566191--31567121 Score: 840
Period size: 105 Copynumber: 8.9 Consensus size: 105
31566181 CAAGTGGAGC
* * * * * * * *
31566191 CAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCA-ATAGTT
1 CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTA-TC
** * * *
31566255 AGTTCAACTTTAAGAGGGGTCAGTCCTACTCCAAGGGTAAT
65 AGTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
* * * * *
31566296 CAGTCCAACTCGAATGAGTACATCCACCTCATTGAGTCTATCCCATAGCTCAACTTTAG-T-T-A
1 CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
*
31566358 GTTCAACTCCAAGAGGAGTCAATCCAACTCCAAGGGTAGT
66 GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
* * * *
31566398 GAGTCCAACTCGGATAAGGACATACACCTCATCGAGTCAATCCCATAGTTCAACTTCAGTTATCA
1 CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
* *
31566463 GTTCAACTCCAAGAGGAGTCATTCCAACTCCAAGGGTACT
66 GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
* * * * *
31566503 GAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCTCA
1 CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
* * *
31566568 TTTCAACCCCAAGAGGAGTCAGTCCAACTTCAAGGGTAGT
66 GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
* ** * * * * * *
31566608 CAGTCCAATTCAAATAAGAACATCCAGCAT-ATTGAGTCAATCCCATAGCTCGACTTCAGTTATT
1 CAGTCCAACTCGGATGAGGACATCCA-CCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATC
* * *
31566672 AGTTCAACTCCAAG-GGTAGTCAGTCCAACTCGGATGGG-A-A
65 AGTTCAACTCCAAGAGG-AGTCAGTCCAACTC-CAAGGGTAGT
* * * * * * * * *
31566712 CA-TCCACCTC--ATCGA-GTCAATCC-CAT-AGCTCAACTTCAGT--TATCAGTTCAACTCCAA
1 CAGTCCAACTCGGAT-GAGGAC-ATCCACCTCA--TCGA-GTCAATCCCAT-AGCTCAACTTC-A
** * * * * * * * *
31566769 GAGGAGTAAGTCCAACTCCAA-ATGTTA-TCATTTCAATTCCAAGGGGACT
59 G-TTA-TCAGTTCAACTCCAAGA-G-GAGTCAGTCCAACTCCAAGGGTAGT
* ** * * * *
31566818 CAATCCAACTCCAATCAGGACATCCACCTCATCTAGTCAATCCTATAGCTCCACTTCAGTTATCA
1 CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
*
31566883 GTTCAACTCCAAGAGGATTCAGTCCAACTCCAAGGGTAGT
66 GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
*
31566923 TAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATC-
1 CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
*
31566987 GATTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGT
66 G-TTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
* * * *
31567028 TAGTCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCA
1 CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
* * *
31567093 GTCCAACTCCAATG-GTAGTTAGTCCAACT
66 GTTCAACTCCAA-GAGGAGTCAGTCCAACT
31567122 TGGATGAGGA
Statistics
Matches: 671, Mismatches: 121, Indels: 68
0.78 0.14 0.08
Matches are distributed among these distances:
100 4 0.01
101 5 0.01
102 100 0.15
103 14 0.02
104 12 0.02
105 484 0.72
106 13 0.02
107 13 0.02
108 16 0.02
109 9 0.01
110 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (105 bp):
CAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
Found at i:31566666 original size:210 final size:208
Alignment explanation
Indices: 31566191--31566702 Score: 575
Period size: 207 Copynumber: 2.5 Consensus size: 208
31566181 CAAGTGGAGC
** * * * * * * * * *
31566191 CAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCA-ATAGTT
1 CAGTCCAACTCAAATAAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTA-TC
** * * * * *
31566255 AGTTCAACTTTAAGAGGGGTCAGTCCTACTCCAAGGGTAATCAGTCCAACTCGAATGAGTACATC
65 AGTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTACT-AGTCCAACTCGGATGAGGACATC
* ** * * *
31566320 CACCTCATTGAGTCTATCCCATAGCTCAACTTTAG-TT-AGTTCAACTCCAAGAGGAGTCAATCC
129 CAACTCATCAAGTCAATCCCATAGCTCAACTTCAGTTTCAGTTCAACTCCAAGAGGAGTCAGTCC
31566383 AACTCCAAGGGTAGT
194 AACTCCAAGGGTAGT
* ** * *
31566398 GAGTCCAACTCGGATAAGGACATACACCTCATCGAGTCAATCCCATAGTTCAACTTCAGTTATCA
1 CAGTCCAACTCAAATAAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
* *
31566463 GTTCAACTCCAAGAGGAGTCATTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCC
66 GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTACT-AGTCCAACTCGGATGAGGACATCC
* *
31566528 AACTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCTCATTTCAACCCCAAGAGGAGTCAGTCC
130 AACTCATCAAGTCAATCCCATAGCTCAACTTCAGTT-TCAGTTCAACTCCAAGAGGAGTCAGTCC
*
31566593 AACTTCAAGGGTAGT
194 AACTCCAAGGGTAGT
* * * * * *
31566608 CAGTCCAATTCAAATAAGAACATCCAGCAT-ATTGAGTCAATCCCATAGCTCGACTTCAGTTATT
1 CAGTCCAACTCAAATAAGGACATCCA-CCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATC
31566672 AGTTCAACTCCAAG-GGTAGTCAGTCCAACTC
65 AGTTCAACTCCAAGAGG-AGTCAGTCCAACTC
31566703 GGATGGGAAC
Statistics
Matches: 256, Mismatches: 43, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
207 134 0.52
208 3 0.01
209 3 0.01
210 114 0.45
211 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (208 bp):
CAGTCCAACTCAAATAAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTACTAGTCCAACTCGGATGAGGACATCCA
ACTCATCAAGTCAATCCCATAGCTCAACTTCAGTTTCAGTTCAACTCCAAGAGGAGTCAGTCCAA
CTCCAAGGGTAGT
Found at i:31566733 original size:84 final size:84
Alignment explanation
Indices: 31566586--31566791 Score: 263
Period size: 84 Copynumber: 2.4 Consensus size: 84
31566576 CCAAGAGGAG
* * * *
31566586 TCAGTCCAACTTCAAGGGTAGTCAGTCCAATTCAAATAAGAACATCCAGCATATTGAGTCAATCC
1 TCAGTTCAACTCCAAGGGTAGTCAGTCCAACTCAAATAAGAACATCCAGCATATCGAGTCAATCC
*
31566651 CATAGCTCGACTTCAGTTA
66 CATAGCTCAACTTCAGTTA
* ** ** *
31566670 TTAGTTCAACTCCAAGGGTAGTCAGTCCAACTCGGATGGGAACATCCA-CCTCATCGAGTCAATC
1 TCAGTTCAACTCCAAGGGTAGTCAGTCCAACTCAAATAAGAACATCCAGCAT-ATCGAGTCAATC
31566734 CCATAGCTCAACTTCAGTTA
65 CCATAGCTCAACTTCAGTTA
*
31566754 TCAGTTCAACTCCAAGAGG-AGTAAGTCCAACTCCAAAT
1 TCAGTTCAACTCCAAG-GGTAGTCAGTCCAACT-CAAAT
31566792 GTTATCATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
83 2 0.02
84 97 0.93
85 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (84 bp):
TCAGTTCAACTCCAAGGGTAGTCAGTCCAACTCAAATAAGAACATCCAGCATATCGAGTCAATCC
CATAGCTCAACTTCAGTTA
Found at i:31566798 original size:42 final size:42
Alignment explanation
Indices: 31566750--31566831 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
31566740 CTCAACTTCA
*
31566750 GTTATCAGTTCAACTCCAAGAGGAGT-AAGTCCAACTCCAAAT
1 GTTATCAGTTCAACTCCAAGAGGACTCAA-TCCAACTCCAAAT
* * *
31566792 GTTATCATTTCAATTCCAAGGGGACTCAATCCAACTCCAA
1 GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAA
31566832 TCAGGACATC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAAAT
Found at i:31566894 original size:420 final size:420
Alignment explanation
Indices: 31566414--31567209 Score: 1211
Period size: 420 Copynumber: 1.9 Consensus size: 420
31566404 AACTCGGATA
*
31566414 AGGACATACACCTCATCGAGTCAATCCCATAGTTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
1 AGGACATACACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
*
31566479 AGTCATTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
66 AGTCAGTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
* * *
31566544 CCCATAGCTCAACTTCAGTTCTC-ATTTCAACCCCAAGAGGAGTCAGTCCAACTTCAAGGGTAGT
131 CCCATAGCTCAACTTCAGTTATCGA-TTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGT
* * * * **
31566608 CAGTCCAATTCAAATAAGAACATCCAGCAT-ATTGAGTCAATCCCATAGCTCGACTTCAGTTATT
195 CAGTCCAACTCAAATAAGAACATCCA-CATCATCGAGTCAATCCCATAGCTCAACTTCAATTACC
*
31566672 AGTTCAACTCCAAGGGTAGTCAGTCCAACTCGGATG-GGAACATCCACCTCATCGAGTCAATCCC
259 AGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGG-ACATCCACCTCATCGAGTCAATCCC
*
31566736 ATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATT
323 ATAGCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATT
31566801 TCAATTCCAAGGGGACTCAATCCAACTCCAATC
388 TCAATTCCAAGGGGACTCAATCCAACTCCAATC
* * * *
31566834 AGGACATCCACCTCATCTAGTCAATCCTATAGCTCCACTTCAGTTATCAGTTCAACTCCAAGAGG
1 AGGACATACACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
* * * * * *
31566899 ATTCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAAT
66 AGTCAGTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
* *
31566964 CCCATAGCTCAACTTCAGTTATCGATTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTT
131 CCCATAGCTCAACTTCAGTTATCGATTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTC
* * * *
31567029 AGTCCAACTCAGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
196 AGTCCAACTCAAATAAGAACATCCACATCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
* * * * * *
31567094 TCCAACTCCAATGGTAGTTAGTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCTCATA
261 TCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATA
* *
31567159 GCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAA
326 GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA
31567210 GGGTAGTTAG
Statistics
Matches: 336, Mismatches: 37, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
419 2 0.01
420 331 0.99
421 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (420 bp):
AGGACATACACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
AGTCAGTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
CCCATAGCTCAACTTCAGTTATCGATTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTC
AGTCCAACTCAAATAAGAACATCCACATCATCGAGTCAATCCCATAGCTCAACTTCAATTACCAG
TCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATA
GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCA
ATTCCAAGGGGACTCAATCCAACTCCAATC
Found at i:31566927 original size:21 final size:21
Alignment explanation
Indices: 31566880--31566933 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
31566870 ACTTCAGTTA
*
31566880 TCAGTTCAACTCCAAGAGGAT
1 TCAGTCCAACTCCAAGAGGAT
31566901 TCAGTCCAACTCCAAG-GGTAGT
1 TCAGTCCAACTCCAAGAGG-A-T
31566923 T-AGTCCAACTC
1 TCAGTCCAACTC
31566934 GGATGAGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAT
Done.