Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 99 of 240
Found at i:30954219 original size:24 final size:23
Alignment explanation
Indices: 30954171--30954221 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
30954161 CTGAAATACC
**
30954171 AAAAATCAAACAAAACTTGTATA
1 AAAAATCAAACAAAACTCATATA
*
30954194 AAAAATCCAACAAAACTCATACTA
1 AAAAATCAAACAAAACTCATA-TA
30954218 AAAA
1 AAAA
30954222 TGCTGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.63, C:0.18, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAATCAAACAAAACTCATATA
Found at i:30954220 original size:23 final size:23
Alignment explanation
Indices: 30954166--30954222 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
30954156 AAAAACTGAA
* *
30954166 ATACCAAAAATCAAACAAAACTT
1 ATACTAAAAATCAAACAAAACTC
* *
30954189 GTA-TAAAAAATCCAACAAAACTC
1 ATACT-AAAAATCAAACAAAACTC
30954212 ATACTAAAAAT
1 ATACTAAAAAT
30954223 GCTGAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (23 bp):
ATACTAAAAATCAAACAAAACTC
Found at i:30957791 original size:20 final size:20
Alignment explanation
Indices: 30957766--30957803 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30957756 ATTTGTACAA
*
30957766 AAAAATAAATAAATTTGTGT
1 AAAAATAAACAAATTTGTGT
*
30957786 AAAAATGAACAAATTTGT
1 AAAAATAAACAAATTTGT
30957804 TAACAAGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAAATAAACAAATTTGTGT
Found at i:30965041 original size:211 final size:211
Alignment explanation
Indices: 30964677--30965100 Score: 812
Period size: 211 Copynumber: 2.0 Consensus size: 211
30964667 ATAAAAGTCT
* *
30964677 AAAACTTTGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATGAGTAACGCATACA
1 AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
* *
30964742 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTTACGAAAATACA
66 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
30964807 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
131 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
30964872 GAACAATTTTCTTCTC
196 GAACAATTTTCTTCTC
30964888 AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
1 AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
30964953 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
66 AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
30965018 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
131 TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
30965083 GAACAATTTTCTTCTC
196 GAACAATTTTCTTCTC
30965099 AA
1 AA
30965101 CCTGTGAGTG
Statistics
Matches: 209, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 209 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (211 bp):
AAAACTTAGGGTAAAAGCCTCTAGATATGCATTTATGGGTTATGCCTTGATAAGTAACGCATACA
AGTTGCTCAACCTTGATAACAATGTTATAATTGAATCCTTAGATGCCATGTTTCACAAAAATACA
TTTCCCTTTAAGGCTAGAAATAGTGAGGGTGTTGAATCTAGACTAACAATAATCAACAAGCTCTT
GAACAATTTTCTTCTC
Found at i:30972827 original size:24 final size:24
Alignment explanation
Indices: 30972799--30972847 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
30972789 ATAGAGTTGG
30972799 TTTAGATCGAGAATTTTTTTCAAT
1 TTTAGATCGAGAATTTTTTTCAAT
30972823 TTTAGATCGAGAATTTTTTTCAAT
1 TTTAGATCGAGAATTTTTTTCAAT
30972847 T
1 T
30972848 GTTGAACTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (24 bp):
TTTAGATCGAGAATTTTTTTCAAT
Found at i:30974794 original size:32 final size:32
Alignment explanation
Indices: 30974724--30974862 Score: 156
Period size: 32 Copynumber: 4.4 Consensus size: 32
30974714 TAATGGCTAC
* *
30974724 AAGCCATAAGT-ACAGTAATATGAT-TGACACA
1 AAGCCATCAGTAACAGTAATATGATCAG-CACA
* * *
30974755 AACCCATCAGTAGCAGTGATATGATCAGCACA
1 AAGCCATCAGTAACAGTAATATGATCAGCACA
* ** *
30974787 CAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCAGCACA
* *
30974819 AAGCCATCAGTAACGGTAATATGATCAACACA
1 AAGCCATCAGTAACAGTAATATGATCAGCACA
30974851 AAGCCATCAGTA
1 AAGCCATCAGTA
30974863 GCATCGCAAC
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
31 9 0.10
32 80 0.89
33 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCAGCACA
Found at i:30974841 original size:64 final size:64
Alignment explanation
Indices: 30974738--30974862 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 64
30974728 CATAAGTACA
* * * * *
30974738 GTAATATGATTGACACAAACCCATCAGTAGCAGTGATATGATCAGCACACAGCCATCAGTAATG
1 GTAATATGATCGACACAAACCCATCAGTAACAGTAATATGATCAACACAAAGCCATCAGTAATG
* * *
30974802 GTAATATGATCGGCACAAAGCCATCAGTAACGGTAATATGATCAACACAAAGCCATCAGTA
1 GTAATATGATCGACACAAACCCATCAGTAACAGTAATATGATCAACACAAAGCCATCAGTA
30974863 GCATCGCAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (64 bp):
GTAATATGATCGACACAAACCCATCAGTAACAGTAATATGATCAACACAAAGCCATCAGTAATG
Found at i:30975060 original size:11 final size:11
Alignment explanation
Indices: 30975044--30975086 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
30975034 AATCAGTCAT
30975044 ACAAATCACAG
1 ACAAATCACAG
*
30975055 ACAAATCAGTCAT
1 ACAAATCA--CAG
*
30975068 ACCAATCACAG
1 ACAAATCACAG
30975079 ACAAATCA
1 ACAAATCA
30975087 ATCATTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:30975061 original size:24 final size:24
Alignment explanation
Indices: 30975034--30975091 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
30975024 CCATGCTCAG
30975034 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
30975058 AATCAGTCATACCAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
30975082 AATCAATCAT
1 AATCAGTCAT
30975092 TTACACTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.26, G:0.07, T:0.19
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:30975182 original size:17 final size:17
Alignment explanation
Indices: 30975160--30975194 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
30975150 TATAGGAGTA
30975160 TTTTGGTCATTTAACCC
1 TTTTGGTCATTTAACCC
30975177 TTTTGGTCATTTAACCC
1 TTTTGGTCATTTAACCC
30975194 T
1 T
30975195 ATGGGGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTTGGTCATTTAACCC
Found at i:30975210 original size:43 final size:44
Alignment explanation
Indices: 30975137--30975220 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
30975127 GAGGCATTAC
* * *
30975137 GGTCATTTTACCTTATAGGAGTATTTTGGTCATTTAACCCTTTT
1 GGTCATTTAACCCTATAGGAGTATTATGGTCATTTAACCCTTTT
* *
30975181 GGTCATTTAACCCTAT-GGGGTATTATGGTCATTTTACCCT
1 GGTCATTTAACCCTATAGGAGTATTATGGTCATTTAACCCT
30975221 ACAGGGGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 21 0.60
44 14 0.40
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (44 bp):
GGTCATTTAACCCTATAGGAGTATTATGGTCATTTAACCCTTTT
Found at i:30975227 original size:27 final size:27
Alignment explanation
Indices: 30975182--30975300 Score: 152
Period size: 27 Copynumber: 4.4 Consensus size: 27
30975172 AACCCTTTTG
* * **
30975182 GTCATTTAACCCTA-TGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACA
30975208 GTCATTTTACCCTACAGGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTACA
30975235 GTCATTTTACCCTACAGGGGTATTACA
1 GTCATTTTACCCTACAGGGGTATTACA
* *
30975262 ATCATTTTACCCTAC-GAGGGTATTTCA
1 GTCATTTTACCCTACAG-GGGTATTACA
*
30975289 ATCATTTTACCC
1 GTCATTTTACCC
30975301 ATCGAGGGTA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
26 14 0.16
27 71 0.84
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACA
Found at i:30975239 original size:70 final size:69
Alignment explanation
Indices: 30975111--30975247 Score: 159
Period size: 70 Copynumber: 2.0 Consensus size: 69
30975101 AGGGTCAAAA
* * ***
30975111 TGGTCATTTACCCTCAGAGGCATTACGGTCATTTTACCTTATAGGAGTATTTTGGTCATTTAACC
1 TGGTCATTTACCCTCAGAGGCATTACGGTCATTTTACCCTACAGGAGTATTACAGTCATTTAACC
30975176 CTTT
66 CTTT
* * * * *
30975180 TGGTCATTTAACCCT-ATGGGGTATTATGGTCATTTTACCCTACAGGGGTATTACAGTCATTTTA
1 TGGTCATTT-ACCCTCA-GAGGCATTACGGTCATTTTACCCTACAGGAGTATTACAGTCATTTAA
30975244 CCCT
64 CCCT
30975248 ACAGGGGTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
69 10 0.18
70 46 0.82
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (69 bp):
TGGTCATTTACCCTCAGAGGCATTACGGTCATTTTACCCTACAGGAGTATTACAGTCATTTAACC
CTTT
Found at i:30975294 original size:81 final size:81
Alignment explanation
Indices: 30975225--30975621 Score: 503
Period size: 81 Copynumber: 4.9 Consensus size: 81
30975215 TACCCTACAG
* * * *
30975225 GGGTATTACAGTCATTTTACCC-TAC-AGGGGTATTACAATCATTTTACCC-TACGAGGGTATTT
1 GGGTATTTCGGTCATTTTACCCAT-CGA-GGGTATTTCAATAATTTTACCCAT-CGAGGGTATTT
*
30975287 CAATCATTTTACCCATCGA
63 CAATAATTTTACCCATCGA
* * * ** **
30975306 GGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGATAATTTCACCCATTAAGGGTATTTCGG
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
*
30975371 TTATTTTACCCATCGA
66 TAATTTTACCCATCGA
* *
30975387 CGGTATTTCGGTAATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
30975452 TAATTTTACCCATCGA
66 TAATTTTACCCATCGA
* ** * *
30975468 GGGTATTTCGGTCATTTTACCCATTGAGGGTATTTTGATTATTTTACCCATCGAGGGTATTTCGA
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
30975533 TAATTTTACCCATCGA
66 TAATTTTACCCATCGA
* * * * * *
30975549 GGGTATTACGGTTATTTTACCCATCGAAGGTGTTTCGATAATTTTACCCATCGAGGGTATTTCAG
1 GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
*
30975614 TTATTTTA
66 TAATTTTA
30975622 GAGGCCCATT
Statistics
Matches: 274, Mismatches: 39, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
81 271 0.99
82 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (81 bp):
GGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCAATAATTTTACCCATCGAGGGTATTTCAA
TAATTTTACCCATCGA
Found at i:30975306 original size:27 final size:27
Alignment explanation
Indices: 30975265--30975611 Score: 480
Period size: 27 Copynumber: 12.9 Consensus size: 27
30975255 TATTACAATC
* *
30975265 ATTTTACCC-TACGAGGGTATTTCAATC
1 ATTTTACCCAT-CGAGGGTATTTCGATA
*
30975292 ATTTTACCCATCGAGGGTATTTCGATC
1 ATTTTACCCATCGAGGGTATTTCGATA
30975319 ATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* ** * *
30975346 ATTTCACCCATTAAGGGTATTTCGGTT
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
30975373 ATTTTACCCATCGACGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
*
30975400 ATTTTACCCATCGAGGGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCGATA
*
30975427 ATTTTACCCATCGAGGGTATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
30975454 ATTTTACCCATCGAGGGTATTTCGGTC
1 ATTTTACCCATCGAGGGTATTTCGATA
* * *
30975481 ATTTTACCCATTGAGGGTATTTTGATT
1 ATTTTACCCATCGAGGGTATTTCGATA
30975508 ATTTTACCCATCGAGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* * *
30975535 ATTTTACCCATCGAGGGTATTACGGTT
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
30975562 ATTTTACCCATCGAAGGTGTTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
30975589 ATTTTACCCATCGAGGGTATTTC
1 ATTTTACCCATCGAGGGTATTTC
30975612 AGTTATTTTA
Statistics
Matches: 284, Mismatches: 35, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
27 283 1.00
28 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.38
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGATA
Found at i:30975619 original size:27 final size:27
Alignment explanation
Indices: 30975225--30975621 Score: 414
Period size: 27 Copynumber: 14.7 Consensus size: 27
30975215 TACCCTACAG
* *
30975225 GGGTATTACAGTCATTTTACCC-TAC-A
1 GGGTATTTCAGTAATTTTACCCAT-CGA
* * *
30975251 GGGGTATTACAATCATTTTACCC-TACGA
1 -GGGTATTTCAGTAATTTTACCCAT-CGA
* *
30975279 GGGTATTTCAATCATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
*
30975306 GGGTATTTC-GATCATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
* **
30975333 GGGTATTTC-GATAATTTCACCCATTAA
1 GGGTATTTCAG-TAATTTTACCCATCGA
* *
30975360 GGGTATTTCGGTTATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* *
30975387 CGGTATTTCGGTAATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
*
30975414 GGGTATTTCAATAATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
*
30975441 GGGTATTTCAATAATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* * *
30975468 GGGTATTTCGGTCATTTTACCCATTGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* *
30975495 GGGTATTT-TGATTATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
30975522 GGGTATTTC-GATAATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
* * *
30975549 GGGTATTACGGTTATTTTACCCATCGA
1 GGGTATTTCAGTAATTTTACCCATCGA
* *
30975576 AGGTGTTTC-GATAATTTTACCCATCGA
1 GGGTATTTCAG-TAATTTTACCCATCGA
*
30975603 GGGTATTTCAGTTATTTTA
1 GGGTATTTCAGTAATTTTA
30975622 GAGGCCCATT
Statistics
Matches: 328, Mismatches: 33, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
26 2 0.01
27 321 0.98
28 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACCCATCGA
Found at i:30979297 original size:43 final size:43
Alignment explanation
Indices: 30979248--30979546 Score: 411
Period size: 43 Copynumber: 7.0 Consensus size: 43
30979238 CAAATATACT
*
30979248 GACCACGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* * *
30979291 GACCACGACCTTTAGCAGCGCTTTTTCCACAAACGCCGCTACA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* * *
30979334 AACCACGACCTTTAGCGACGCTTTTCCCACTAACGCCGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* * *
30979377 GACTA-TAGCCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATA
1 GACCACGA-CCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
** * *
30979420 GACCACGACCTTTAGCAACACTTTTCCCACAAACGTCGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* *
30979463 GACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTATA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
* **
30979506 GACCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTA
1 GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
30979547 AAGAATAAAC
Statistics
Matches: 224, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
42 1 0.00
43 222 0.99
44 1 0.00
ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23
Consensus pattern (43 bp):
GACCACGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATA
Found at i:30983247 original size:2 final size:2
Alignment explanation
Indices: 30983240--30983280 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30983230 GCAGCATTCG
30983240 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
30983281 GATACTTGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:30983849 original size:13 final size:13
Alignment explanation
Indices: 30983833--30983857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30983823 ACTAAAATCA
30983833 TAACATAAAGATT
1 TAACATAAAGATT
30983846 TAACATAAAGAT
1 TAACATAAAGAT
30983858 CTAAAACATC
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:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (13 bp):
TAACATAAAGATT
Found at i:30983873 original size:19 final size:20
Alignment explanation
Indices: 30983846--30983903 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
30983836 CATAAAGATT
30983846 TAACATAAAGATCTAAAACA
1 TAACATAAAGATCTAAAACA
* *
30983866 T-CCAT-AA-ATC-AAATCA
1 TAACATAAAGATCTAAAACA
30983882 TAACATAAAGATCTAAAACA
1 TAACATAAAGATCTAAAACA
30983902 TA
1 TA
30983904 TATAATGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 6 0.20
17 6 0.20
18 4 0.13
19 6 0.20
20 8 0.27
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.22
Consensus pattern (20 bp):
TAACATAAAGATCTAAAACA
Found at i:30985403 original size:21 final size:22
Alignment explanation
Indices: 30985365--30985406 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
30985355 TTAACCATAT
*
30985365 ATATATATATATACCCTAAACC
1 ATATATATATAAACCCTAAACC
30985387 ATATATAT-TAAACCCTAAAC
1 ATATATATATAAACCCTAAAC
30985407 TATTATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (22 bp):
ATATATATATAAACCCTAAACC
Found at i:30985759 original size:41 final size:40
Alignment explanation
Indices: 30985714--30985875 Score: 180
Period size: 42 Copynumber: 3.9 Consensus size: 40
30985704 TTAAAGCCTC
* * * *
30985714 GAGCATTAGTGGCTCTTTTCCTAAAACGCCGCTAAAGATCT
1 GAGCATTAGCGGCGCTTTT-CAAAAATGCCGCTAAAGATCT
* *
30985755 GAGCAATAGCGACGCTTTTTCAAAAATGCCGCTAAAAGATCT
1 GAGCATTAGCGGCGC-TTTTCAAAAATGCCGCT-AAAGATCT
30985797 GAGCATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGATCT
1 GAGCATTAGCGGCGCTT-TTCAAAAATGCCGCTAAAGATCT
* ** *
30985838 AAGCATTAGCAGTGCTTTTTTTAAAAATGCCGCTAAAG
1 GAGCATTAGC-G-GCGCTTTTCAAAAATGCCGCTAAAG
30985876 CCCCGGAAGG
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
41 41 0.39
42 59 0.57
43 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
GAGCATTAGCGGCGCTTTTCAAAAATGCCGCTAAAGATCT
Found at i:30985794 original size:42 final size:41
Alignment explanation
Indices: 30985736--30985875 Score: 183
Period size: 42 Copynumber: 3.4 Consensus size: 41
30985726 CTCTTTTCCT
* *
30985736 AAAACGCCGCTAAAGATCTGAGCAATAGCGACGCTTTTTCA
1 AAAATGCCGCTAAAGATCTGAGCATTAGCGACGCTTTTTCA
* *
30985777 AAAATGCCGCTAAAAGATCTGAGCATTAGCGGCGCTTCTTCA
1 AAAATGCCGCT-AAAGATCTGAGCATTAGCGACGCTTTTTCA
* * *
30985819 AAAATGCCGCTAAAGATCTAAGCATTAGC-AGTGCTTTTTTTA
1 AAAATGCCGCTAAAGATCTGAGCATTAGCGA-CGC-TTTTTCA
30985861 AAAATGCCGCTAAAG
1 AAAATGCCGCTAAAG
30985876 CCCCGGAAGG
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 29 0.33
42 58 0.67
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (41 bp):
AAAATGCCGCTAAAGATCTGAGCATTAGCGACGCTTTTTCA
Found at i:30985857 original size:83 final size:84
Alignment explanation
Indices: 30985714--30985874 Score: 211
Period size: 83 Copynumber: 1.9 Consensus size: 84
30985704 TTAAAGCCTC
* * * *
30985714 GAGCATTAGTGGCTCTTTTCCTAAAACGCCGCTAAAGATCTGAGCAATAGCGACGC-TTTTTCAA
1 GAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTAAGCAATAGCGACGCTTTTTTCAA
30985778 AAATGCCGCTAAAAGATCT
66 AAATGCCGCTAAAAGATCT
* * * *
30985797 GAGCATTAGCGGCGCTTCTT-CAAAAATGCCGCTAAAGATCTAAGCATTAGC-AGTGCTTTTTTT
1 GAGCATTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAGATCTAAGCAATAGCGA-CGCTTTTTTC
30985860 AAAAATGCCGCTAAA
64 AAAAATGCCGCTAAA
30985875 GCCCCGGAAG
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
82 1 0.01
83 44 0.66
84 22 0.33
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (84 bp):
GAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTAAGCAATAGCGACGCTTTTTTCAA
AAATGCCGCTAAAAGATCT
Found at i:30990126 original size:17 final size:16
Alignment explanation
Indices: 30990096--30990130 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
30990086 GAATTAACTC
30990096 TAAAAATTAATAAAAT
1 TAAAAATTAATAAAAT
*
30990112 TAAAAACTTACTAAAAT
1 TAAAAA-TTAATAAAAT
30990129 TA
1 TA
30990131 TGCTCAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATTAATAAAAT
Found at i:30991770 original size:25 final size:25
Alignment explanation
Indices: 30991736--30991793 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
30991726 GTGTGCCTAG
30991736 CAGGCTTTGTGCTAGTATATATAAT
1 CAGGCTTTGTGCTAGTATATATAAT
* * *
30991761 CAGGCTTTGTTCTGGTGTATATAAT
1 CAGGCTTTGTGCTAGTATATATAAT
*
30991786 TAGGCTTT
1 CAGGCTTT
30991794 ATGCCTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.43
Consensus pattern (25 bp):
CAGGCTTTGTGCTAGTATATATAAT
Found at i:30992957 original size:18 final size:19
Alignment explanation
Indices: 30992921--30992957 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
30992911 TAAGTATTTA
30992921 TATCATAATTAAGTTATGT
1 TATCATAATTAAGTTATGT
30992940 TATCA-AATATAA-TTATGT
1 TATCATAAT-TAAGTTATGT
30992958 GAATTTCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (19 bp):
TATCATAATTAAGTTATGT
Found at i:31004795 original size:41 final size:41
Alignment explanation
Indices: 31004726--31004805 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
31004716 AGGCTTGGTG
*
31004726 CCTAGTAGGCTTTGTGCCAATTTATATAATCAAGCTTTGCT
1 CCTAGTAGGCTTTGTGCCAATGTATATAATCAAGCTTTGCT
* ** *
31004767 CCTAGTAGGCTTTGTGTCGGTGTCTATAATCAAGCTTTG
1 CCTAGTAGGCTTTGTGCCAATGTATATAATCAAGCTTTG
31004806 TGCCGGTGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (41 bp):
CCTAGTAGGCTTTGTGCCAATGTATATAATCAAGCTTTGCT
Found at i:31004812 original size:25 final size:25
Alignment explanation
Indices: 31004775--31004826 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
31004765 CTCCTAGTAG
* *
31004775 GCTTTGTGTCGGTGTCTATAATCAA
1 GCTTTGTGCCGGTGTATATAATCAA
*
31004800 GCTTTGTGCCGGTGTATATTATCAA
1 GCTTTGTGCCGGTGTATATAATCAA
31004825 GC
1 GC
31004827 CTTGAGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (25 bp):
GCTTTGTGCCGGTGTATATAATCAA
Found at i:31008598 original size:8 final size:8
Alignment explanation
Indices: 31008585--31008615 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
31008575 GTATATATGA
31008585 TATTATTT
1 TATTATTT
31008593 TATTATTT
1 TATTATTT
31008601 TATTATTT
1 TATTATTT
31008609 TATTATT
1 TATTATT
31008616 ATGGATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTATTT
Found at i:31013321 original size:29 final size:29
Alignment explanation
Indices: 31013274--31013597 Score: 192
Period size: 29 Copynumber: 11.1 Consensus size: 29
31013264 ATGTACTAAA
* **
31013274 CGATGGTCGTAACTGTCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
31013303 TGATGGTCGAAACCATCCCATTTCATTAAT
1 CGATGGTCGAAACCATCCCTTTTCA-TATT
** *
31013333 CGATGGTCGTCACCATCCCTTTTGATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
** ** * *
31013362 TTATGGTCGTTACCATCCCTTTTTATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
31013391 CGAT-ATCCGAAGCTATCCCTTTTCATAATT
1 CGATGGT-CGAAACCATCCCTTTTCAT-ATT
* * *
31013421 -GATAG-CCAAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
* ** *
31013449 CAATGGTCGTCACCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
31013478 CGATAG-CCAAAGCTATCCCTTTTCATATT
1 CGATGGTCGAAA-CCATCCCTTTTCATATT
* * *
31013507 CAATGGT-TACCACCATCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
* *
31013536 CTATGGTC-ATCACCATCCCTTTTCATATT
1 CGATGGTCGA-AACCATCCCTTTTCATATT
* *** * *
31013565 TGATGGTCTTCATCATCCCTTTTCATAAT
1 CGATGGTCGAAACCATCCCTTTTCATATT
31013594 CGAT
1 CGAT
31013598 ACCCGAAGCT
Statistics
Matches: 227, Mismatches: 56, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
28 9 0.04
29 190 0.84
30 28 0.12
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:31013464 original size:87 final size:87
Alignment explanation
Indices: 31013347--31013616 Score: 276
Period size: 87 Copynumber: 3.1 Consensus size: 87
31013337 GGTCGTCACC
* * * * *
31013347 ATCCCTTTTGATATTTTATGGTCGTTACCATCCCTTTTTATAATCGATATCCGAAGCTATCCCTT
1 ATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATAATCGATATCCAAAGCTATCCCTT
31013412 TTCATAATTGATAGCCAAAGCT
66 TTCATAATTGATAGCCAAAGCT
* *
31013434 ATCCCTTTTCATATTCAATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTT
1 ATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATAATCGATATCCAAAGCTATCCCTT
* * ** * *
31013499 TTCAT-ATTCAATGGTTACCA-CC
66 TTCATAATT-GATAGCCA-AAGCT
* * * * *** *
31013521 ATCCCTTTTCATATTCTATGGTCATCACCATCCCTTTTCATATTTGATGGTCTTCATC-ATCCCT
1 ATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATAATCGAT-ATCCAAAGCTATCCCT
* * *
31013585 TTTCATAATCGATACCCGAAGCT
65 TTTCATAATTGATAGCCAAAGCT
31013608 ATCCCTTTT
1 ATCCCTTTT
31013617 TATTAGTCGA
Statistics
Matches: 146, Mismatches: 32, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
86 4 0.03
87 136 0.93
88 6 0.04
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (87 bp):
ATCCCTTTTCATATTCTATGGTCGTCACCATCCCTTTTCATAATCGATATCCAAAGCTATCCCTT
TTCATAATTGATAGCCAAAGCT
Found at i:31014689 original size:12 final size:12
Alignment explanation
Indices: 31014672--31014696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31014662 ATGACACTCC
31014672 AAAAATATTTAT
1 AAAAATATTTAT
31014684 AAAAATATTTAT
1 AAAAATATTTAT
31014696 A
1 A
31014697 GCTCGATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATATTTAT
Found at i:31021553 original size:40 final size:40
Alignment explanation
Indices: 31021509--31021587 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
31021499 TACGTGGCAA
* * *
31021509 CAAAGCGCGCTTACGTAGACGCGCTTTGTTGCCACGTAGG
1 CAAAGCGCGCTGACGTAGACACGCTTTGCTGCCACGTAGG
* * *
31021549 CAAAGTGCGCTGACGTGGACACGTTTTGCTGCCACGTAG
1 CAAAGCGCGCTGACGTAGACACGCTTTGCTGCCACGTAG
31021588 CACGCCCCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.30, T:0.23
Consensus pattern (40 bp):
CAAAGCGCGCTGACGTAGACACGCTTTGCTGCCACGTAGG
Found at i:31021797 original size:51 final size:51
Alignment explanation
Indices: 31021730--31021827 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
31021720 AATTATTTTC
31021730 TCAATTTGCTCTCAATTTCCT-TCCAAATTTCTCTAAAATCCATATTTAATT
1 TCAATTTGCTCTCAATTTCCTCT-CAAATTTCTCTAAAATCCATATTTAATT
* * *
31021781 TCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTAAAATCCATATTT
31021828 TTAATTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTAAAATCCATATTTAATT
Found at i:31024146 original size:125 final size:126
Alignment explanation
Indices: 31023882--31024195 Score: 513
Period size: 125 Copynumber: 2.5 Consensus size: 126
31023872 CCCAAACATG
** * * * *
31023882 CTACTGTAGCAAAAGCGCGTCCACGAAGGCGTGATTTCAGAAATTTTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTAC
* *
31023947 TTGAAGCATTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCAGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * *
31024008 CTACTGTAGCAAAAGCGTGTCTACGTGGGCACGATTTTAGAAATTCTTCTGATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTAC
31024073 TTGAAGC-GTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCAGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
*
31024133 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAAAAATTCTTCTGATAAAGCATCCT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCT
31024196 GCTTTGATTT
Statistics
Matches: 173, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
125 110 0.64
126 63 0.36
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTTAGAAATTCTTCTGATAAAGCATCCTAC
TTGAAGCAGTTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:31028333 original size:37 final size:36
Alignment explanation
Indices: 31028291--31028432 Score: 110
Period size: 37 Copynumber: 3.8 Consensus size: 36
31028281 TTCTATTCAT
*
31028291 TTGAACTTCACTCAATATAACAGTAGAATTTTCTAAA
1 TTGAACTTCATTCAATATAACAGTA-AATTTTCTAAA
** *
31028328 TTGAACATT-ATTCAATATAATGGTAATATTTGT-TTAA
1 TTGAAC-TTCATTCAATATAACAGTAA-ATTT-TCTAAA
* * * **
31028365 TT-AGGCTGCATTCAATATAACAGTATAATTTACTCGA
1 TTGA-ACTTCATTCAATATAACAGTA-AATTTTCTAAA
*
31028402 TTGAGCTTCATTCAATATAACAGTAAGATTT
1 TTGAACTTCATTCAATATAACAGTAA-ATTT
31028433 GACTCGATAA
Statistics
Matches: 84, Mismatches: 12, Indels: 18
0.74 0.11 0.16
Matches are distributed among these distances:
36 4 0.05
37 75 0.89
38 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (36 bp):
TTGAACTTCATTCAATATAACAGTAAATTTTCTAAA
Found at i:31043579 original size:20 final size:20
Alignment explanation
Indices: 31043550--31043591 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31043540 TACCATTTCT
* *
31043550 AATGAGGTTGGAGGACAAGC
1 AATGAAGTTGGAAGACAAGC
*
31043570 AATGAAGTTGGAAGATAAGC
1 AATGAAGTTGGAAGACAAGC
31043590 AA
1 AA
31043592 CAAAGGGATG
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:0.43, C:0.07, G:0.33, T:0.17
Consensus pattern (20 bp):
AATGAAGTTGGAAGACAAGC
Found at i:31052987 original size:25 final size:25
Alignment explanation
Indices: 31052957--31053020 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
31052947 AACTAAACAC
*
31052957 AACAAAAATTAATAATAAAAAAA-T
1 AACAAAAATTAAAAATAAAAAAACT
*
31052981 AAGCAAATAA-AAAAAATAAAAAAACT
1 AA-CAAA-AATTAAAAATAAAAAAACT
*
31053007 AACAAAATTTAAAA
1 AACAAAAATTAAAA
31053021 CAGGAAATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
24 3 0.09
25 24 0.75
26 5 0.16
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (25 bp):
AACAAAAATTAAAAATAAAAAAACT
Found at i:31060362 original size:27 final size:27
Alignment explanation
Indices: 31060322--31060386 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
31060312 TTAGCCTTCT
* *
31060322 TGGCGTACTTTGAATGGATCACCTATG
1 TGGCATACTCTGAATGGATCACCTATG
* * *
31060349 TGGCATACTCTGAATGGATCGCTTTTG
1 TGGCATACTCTGAATGGATCACCTATG
*
31060376 TTGCATACTCT
1 TGGCATACTCT
31060387 AATTAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (27 bp):
TGGCATACTCTGAATGGATCACCTATG
Found at i:31067968 original size:23 final size:23
Alignment explanation
Indices: 31067920--31067965 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31067910 TAAATTATAT
*
31067920 ATTTTTTTATTTTAACTATTTTA
1 ATTTTTTTATTTTAACTATTTAA
31067943 ATTTTTTTATATTT-A-TATTTAA
1 ATTTTTTTAT-TTTAACTATTTAA
31067965 A
1 A
31067966 ATTAAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTTTTTATTTTAACTATTTAA
Found at i:31069068 original size:31 final size:32
Alignment explanation
Indices: 31069028--31069087 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
31069018 CTAAAAAATA
31069028 CAAAGAAATAT-ATAA-AAATATATAAATATTTT
1 CAAAGAAATATAATAATAAAT-T-TAAATATTTT
31069060 CAAA-AAATATAATAATAAATTTAAATAT
1 CAAAGAAATATAATAATAAATTTAAATAT
31069088 ATTTTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 13 0.50
32 9 0.35
33 4 0.15
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (32 bp):
CAAAGAAATATAATAATAAATTTAAATATTTT
Found at i:31069223 original size:24 final size:24
Alignment explanation
Indices: 31069173--31069236 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
31069163 TTTAAAAAGA
** *
31069173 TAATAATAAATTTAAATTTTATAT
1 TAATAATAAATAAAAATGTTATAT
31069197 TAATAATAAATAAAAATAGTTAT-T
1 TAATAATAAATAAAAAT-GTTATAT
31069221 TAA-ATATAAAATAAAA
1 TAATA-AT-AAATAAAA
31069237 TAAACTCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.03
24 21 0.62
25 12 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
TAATAATAAATAAAAATGTTATAT
Found at i:31069370 original size:17 final size:16
Alignment explanation
Indices: 31069348--31069386 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
31069338 TTTTTTAAAA
*
31069348 ATATTTAAGTATTTTAT
1 ATATTTAA-AATTTTAT
31069365 ATATTTTAAAATTTTAT
1 ATA-TTTAAAATTTTAT
31069382 ATATT
1 ATATT
31069387 ATTATTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATATTTAAAATTTTAT
Found at i:31069391 original size:27 final size:27
Alignment explanation
Indices: 31069295--31069391 Score: 76
Period size: 27 Copynumber: 3.6 Consensus size: 27
31069285 TTTATTTTTA
* *
31069295 TTTAA-TATTAATATAAATTTT-AAAT
1 TTTAACTATTATTATATATTTTAAAAT
* *
31069320 TTATTACTATTATTATATTTTTTTAAAAAT
1 TT-TAACTATTATTATA-TATTTT-AAAAT
*
31069350 ATTTAAGTATT-TTATATATTTTAAAAT
1 -TTTAACTATTATTATATATTTTAAAAT
31069377 TTTATA-TATTATTAT
1 TTTA-ACTATTATTAT
31069392 TTCTGTTCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.04
26 10 0.18
27 19 0.33
28 9 0.16
29 5 0.09
30 10 0.18
31 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTAACTATTATTATATATTTTAAAAT
Found at i:31069436 original size:9 final size:9
Alignment explanation
Indices: 31069409--31069485 Score: 66
Period size: 9 Copynumber: 8.6 Consensus size: 9
31069399 CAACAATTAA
31069409 TTTTTAT-T
1 TTTTTATAT
*
31069417 TTTATATAT
1 TTTTTATAT
*
31069426 TTTTTAAAT
1 TTTTTATAT
31069435 TTTTTATAT
1 TTTTTATAT
* *
31069444 TTTGTATAA
1 TTTTTATAT
* *
31069453 TATTTATGT
1 TTTTTATAT
*
31069462 ATTTTCATAT
1 -TTTTTATAT
*
31069472 TTTTTTTAT
1 TTTTTATAT
31069481 TTTTT
1 TTTTT
31069486 TTAGAATTGG
Statistics
Matches: 52, Mismatches: 15, Indels: 3
0.74 0.21 0.04
Matches are distributed among these distances:
8 6 0.12
9 40 0.77
10 6 0.12
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (9 bp):
TTTTTATAT
Found at i:31075793 original size:27 final size:27
Alignment explanation
Indices: 31075745--31075810 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
31075735 AATGAAATTT
*
31075745 CTCAAAATTTTA-CCGAGAGTAAAATTA
1 CTCAAAATTTTATCAGAGAGTAAAA-TA
* *
31075772 -TCAAAATTTTATCAGTGGGTAAAATA
1 CTCAAAATTTTATCAGAGAGTAAAATA
*
31075798 CTCAAAAATTTAT
1 CTCAAAATTTTAT
31075811 TGGAGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 13 0.39
27 20 0.61
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (27 bp):
CTCAAAATTTTATCAGAGAGTAAAATA
Found at i:31083393 original size:15 final size:15
Alignment explanation
Indices: 31083373--31083402 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31083363 GTCGAGCCTG
*
31083373 CAAACAATGGATTTC
1 CAAACAAAGGATTTC
31083388 CAAACAAAGGATTTC
1 CAAACAAAGGATTTC
31083403 ATTTGCCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (15 bp):
CAAACAAAGGATTTC
Found at i:31089789 original size:13 final size:14
Alignment explanation
Indices: 31089769--31089814 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
31089759 ATAATGTAAG
31089769 TAATAATTATTAAA
1 TAATAATTATTAAA
* *
31089783 -GATAATTA-CAAA
1 TAATAATTATTAAA
31089795 TAATAATTATTAAA
1 TAATAATTATTAAA
*
31089809 AAATAA
1 TAATAA
31089815 AATAATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
12 3 0.12
13 14 0.56
14 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
TAATAATTATTAAA
Found at i:31089802 original size:26 final size:22
Alignment explanation
Indices: 31089769--31089825 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 22
31089759 ATAATGTAAG
31089769 TAATAATTATTAAAGATAATTACAAA
1 TAATAATTATTAAA-A-AA-TA-AAA
31089795 TAATAATTATTAAAAAATAAAA
1 TAATAATTATTAAAAAATAAAA
31089817 TAATAATTA
1 TAATAATTA
31089826 AATTGATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 12 0.39
23 2 0.06
24 2 0.06
25 1 0.03
26 14 0.45
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATAATTATTAAAAAATAAAA
Found at i:31091105 original size:18 final size:18
Alignment explanation
Indices: 31091082--31091143 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
31091072 ATTATTTGTT
31091082 TTAAGTCTGATCAAATTA
1 TTAAGTCTGATCAAATTA
* * *
31091100 TTAAGT-TATATAATTAAATA
1 TTAAGTCT-GATCA--AATTA
31091120 TTAAGTCTGATCAAATTA
1 TTAAGTCTGATCAAATTA
31091138 TTAAGT
1 TTAAGT
31091144 TATATTATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.03
18 19 0.56
20 13 0.38
21 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (18 bp):
TTAAGTCTGATCAAATTA
Found at i:31091133 original size:38 final size:38
Alignment explanation
Indices: 31091082--31091158 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
31091072 ATTATTTGTT
31091082 TTAAGTCTGATCAAATTATTAAGTTATATAATTAAATA
1 TTAAGTCTGATCAAATTATTAAGTTATATAATTAAATA
*
31091120 TTAAGTCTGATCAAATTATTAAGTTATATTATTAAATA
1 TTAAGTCTGATCAAATTATTAAGTTATATAATTAAATA
31091158 T
1 T
31091159 CAATAGGTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (38 bp):
TTAAGTCTGATCAAATTATTAAGTTATATAATTAAATA
Found at i:31096662 original size:42 final size:42
Alignment explanation
Indices: 31096586--31096813 Score: 264
Period size: 42 Copynumber: 5.4 Consensus size: 42
31096576 ACGTCGCTAA
* * *
31096586 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCT-AAAGATCATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAAG-TAATGTT
*
31096630 CTTTAGCGGCGCTTAGGAAAAAACGCTGCTAAAAGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAAGTAATGTT
* * *
31096672 CTATAGCGGCGCTTGGGAAAAAACGCCGCT-AAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAAG-TAATGTT
31096714 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAAGTAATGTT
* * * * *
31096757 CTATAGCGGCGC-TGGGTCAGAAACGCCGCTAAAAGTAGTGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAAGTAATGTT
*
31096799 CTTTAGCGACGCTTA
1 CTTTAGCGGCGCTTA
31096814 TTTCACAAAC
Statistics
Matches: 159, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
41 4 0.03
42 104 0.65
43 34 0.21
44 17 0.11
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAAGTAATGTT
Found at i:31096826 original size:85 final size:84
Alignment explanation
Indices: 31096605--31096813 Score: 325
Period size: 85 Copynumber: 2.5 Consensus size: 84
31096595 CGCTTACAGA
*
31096605 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCTGCTAAAAGTAATG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAAGTAATG
31096670 TTCTATAGCGGCGCTTGGG
66 TTCTATAGCGGCGCTTGGG
31096689 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAAGTAAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAAGTAAT
31096754 GTTCTATAGCGGCGC-TGGG
65 GTTCTATAGCGGCGCTTGGG
* * *
31096773 TCAGAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGACGCTTA
1 -AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
31096814 TTTCACAAAC
Statistics
Matches: 117, Mismatches: 4, Indels: 7
0.91 0.03 0.05
Matches are distributed among these distances:
84 50 0.43
85 67 0.57
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (84 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAAGTAATG
TTCTATAGCGGCGCTTGGG
Found at i:31097283 original size:21 final size:21
Alignment explanation
Indices: 31097259--31097327 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
31097249 GCTTCTATCG
*
31097259 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
31097280 CTGCTTCTCTCACTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
31097301 CTGCTTCCCTCGCTGCCGTCT
1 CTGCTTCTCTCGCTGCAGCCT
31097322 CTGCTT
1 CTGCTT
31097328 TAAGTTGTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.42, G:0.19, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:31102816 original size:9 final size:9
Alignment explanation
Indices: 31102802--31102835 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
31102792 TTATGTATTA
31102802 TGTAAGTAC
1 TGTAAGTAC
31102811 TGTAAGTAC
1 TGTAAGTAC
31102820 TGTAAGTTA-
1 TGTAAG-TAC
31102829 TGTAAGT
1 TGTAAGT
31102836 TACTACATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 1 0.04
9 21 0.88
10 2 0.08
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38
Consensus pattern (9 bp):
TGTAAGTAC
Found at i:31102831 original size:27 final size:26
Alignment explanation
Indices: 31102783--31103099 Score: 283
Period size: 27 Copynumber: 11.9 Consensus size: 26
31102773 TTAAAACGCC
31102783 AGTTATGT-ATTATGT-A-TTATGTA
1 AGTTATGTAATTATGTAAGTTATGTA
*
31102806 AG-TACTGTAAGTACTGTAAGTTATGTA
1 AGTTA-TGTAATTA-TGTAAGTTATGTA
*
31102833 AGTTA-CTACATTTATGTAAGTTATGTA
1 AGTTATGTA-A-TTATGTAAGTTATGTA
*
31102860 AGTTA-CTACATTTATGTAAGTTATGTA
1 AGTTATGTA-A-TTATGTAAGTTATGTA
*
31102887 AGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAA-TTATGTAAGTTATGTA
31102914 AGTTACT-TAATTTATGTAAGTTATGTA
1 AGTTA-TGTAA-TTATGTAAGTTATGTA
* *
31102941 AGATATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAA-TTATGTAAGTTATGTA
*
31102968 AGTTATGTAAGTTACT-TAATTTATGTA
1 AGTTATGTAA-TTA-TGTAAGTTATGTA
* * * *
31102995 AGTTATGTAAGATATTTAATTTTTGTA
1 AGTTATGTAA-TTATGTAAGTTATGTA
*
31103022 AGTTATGTAAGTTACT-TAATTTATGTA
1 AGTTATGTAA-TTA-TGTAAGTTATGTA
* * *
31103049 AGTTATGTAAGTTATTTAATTTTTGTA
1 AGTTATGTAA-TTATGTAAGTTATGTA
31103076 AGTTATGTAATTAATGTAAGTTAT
1 AGTTATGTAATT-ATGTAAGTTAT
31103100 TTAATTTGTG
Statistics
Matches: 261, Mismatches: 17, Indels: 28
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.01
23 5 0.02
24 3 0.01
25 3 0.01
26 8 0.03
27 231 0.89
28 9 0.03
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (26 bp):
AGTTATGTAATTATGTAAGTTATGTA
Found at i:31102860 original size:54 final size:54
Alignment explanation
Indices: 31102792--31103096 Score: 320
Period size: 54 Copynumber: 5.5 Consensus size: 54
31102782 CAGTTATGTA
*
31102792 TTATGT-A-TTATGTAAG-TACTGTAAGTACTGTAAGTTATGTAAGTTA-CTACAT
1 TTATGTAAGTTATGTAAGTTACTGTAAGTA-TGTAAGTTATGTAAGTTATTTA-AT
** **
31102844 TTATGTAAGTTATGTAAGTTACTACATTTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAGTTACTGTAAGTATGTAAGTTATGTAAGTTATTTAAT
* *
31102898 TTATGTAAGTTATGTAAGTTACT-TAATTTATGTAAGTTATGTAAGATATTTAAT
1 TTATGTAAGTTATGTAAGTTACTGTAA-GTATGTAAGTTATGTAAGTTATTTAAT
*
31102952 TTATGTAAGTTATGTAAGTTA-TGTAAGTTACTTAATTTATGTAAGTTATGTAAGATATTTAAT
1 TTATGTAAGTTATGTAAGTTACTGTAAG----------TATGTAAGTTATGTAAGTTATTTAAT
* *
31103015 TTTTGTAAGTTATGTAAGTTACT-TAATTTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAGTTACTGTAA-GTATGTAAGTTATGTAAGTTATTTAAT
* *
31103069 TTTTGTAAGTTATGTAA-TTAATGTAAGT
1 TTATGTAAGTTATGTAAGTTACTGTAAGT
31103097 TATTTAATTT
Statistics
Matches: 220, Mismatches: 14, Indels: 37
0.81 0.05 0.14
Matches are distributed among these distances:
52 6 0.03
53 8 0.04
54 147 0.67
55 9 0.04
63 49 0.22
64 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (54 bp):
TTATGTAAGTTATGTAAGTTACTGTAAGTATGTAAGTTATGTAAGTTATTTAAT
Found at i:31102887 original size:63 final size:56
Alignment explanation
Indices: 31102842--31103085 Score: 340
Period size: 54 Copynumber: 4.3 Consensus size: 56
31102832 AAGTTACTAC
31102842 ATTTATGTAAGTTATGTAAGTTAC-TACATTTATGTAAGTTATGTAAG--TTATTTA
1 ATTTATGTAAGTTATGTAAGTTACTTA-ATTTATGTAAGTTATGTAAGTATTATTTA
31102896 ATTTATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGATATTTAATTTATGTA
1 ATTTATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAG-TA-TT-A--T-T-TA
*
31102959 AGTTATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAG-A-TATTTA
1 ATTTATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTATTATTTA
*
31103013 ATTTTTGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAG--TTATTTA
1 ATTTATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTATTATTTA
*
31103067 ATTTTTGTAAGTTATGTAA
1 ATTTATGTAAGTTATGTAA
31103086 TTAATGTAAG
Statistics
Matches: 176, Mismatches: 3, Indels: 22
0.88 0.01 0.11
Matches are distributed among these distances:
54 116 0.66
55 3 0.02
56 1 0.01
58 3 0.02
59 2 0.01
61 2 0.01
62 1 0.01
63 48 0.27
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (56 bp):
ATTTATGTAAGTTATGTAAGTTACTTAATTTATGTAAGTTATGTAAGTATTATTTA
Found at i:31103104 original size:18 final size:18
Alignment explanation
Indices: 31102799--31103106 Score: 252
Period size: 18 Copynumber: 17.1 Consensus size: 18
31102789 GTATTATGTA
31102799 TTATGTAAG-TACTGTAA-
1 TTATGTAAGTTA-TGTAAT
* *
31102816 GTACTGTAAGTTATGTAAG
1 TTA-TGTAAGTTATGTAAT
* * *
31102835 TTA-CTACATTTATGTAAG
1 TTATGTA-AGTTATGTAAT
*
31102853 TTATGTAAGTTA-CTACAT
1 TTATGTAAGTTATGTA-AT
*
31102871 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAT
* * *
31102889 TTATTTAATTTATGTAAG
1 TTATGTAAGTTATGTAAT
31102907 TTATGTAAGTTACT-TAAT
1 TTATGTAAGTTA-TGTAAT
*
31102925 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAT
* * * *
31102943 ATATTTAATTTATGTAAG
1 TTATGTAAGTTATGTAAT
*
31102961 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAT
* *
31102979 TTACT-TAATTTATGTAAG
1 TTA-TGTAAGTTATGTAAT
* *
31102997 TTATGTAAGATATTTAAT
1 TTATGTAAGTTATGTAAT
* *
31103015 TTTTGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAT
* *
31103033 TTACT-TAATTTATGTAAG
1 TTA-TGTAAGTTATGTAAT
*
31103051 TTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAT
*
31103069 TTTTGTAAGTTATGTAAT
1 TTATGTAAGTTATGTAAT
* *
31103087 TAATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAT
31103105 TT
1 TT
31103107 GTGAACCCTA
Statistics
Matches: 236, Mismatches: 42, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
17 9 0.04
18 216 0.92
19 11 0.05
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATGTAAT
Found at i:31105331 original size:9 final size:8
Alignment explanation
Indices: 31105311--31105346 Score: 54
Period size: 9 Copynumber: 4.2 Consensus size: 8
31105301 AGACATGCAA
31105311 AAATTCCC
1 AAATTCCC
31105319 AAATTCTCC
1 AAATTC-CC
31105328 AAATTCCCC
1 AAATT-CCC
31105337 AAATTCCC
1 AAATTCCC
31105345 AA
1 AA
31105347 CCAAATTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 11 0.42
9 14 0.54
10 1 0.04
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (8 bp):
AAATTCCC
Found at i:31105333 original size:17 final size:17
Alignment explanation
Indices: 31105311--31105346 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
31105301 AGACATGCAA
31105311 AAATT-CCCAAATTCTCC
1 AAATTCCCCAAATTC-CC
31105328 AAATTCCCCAAATTCCC
1 AAATTCCCCAAATTCCC
31105345 AA
1 AA
31105347 CCAAATTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATTCCCCAAATTCCC
Found at i:31106788 original size:14 final size:15
Alignment explanation
Indices: 31106757--31106791 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
31106747 TCTGACCCCA
*
31106757 AAATCCCTAAACCTT
1 AAATCCCTAAACCCT
31106772 AAATCCC-AAACCCT
1 AAATCCCTAAACCCT
31106786 AAATCC
1 AAATCC
31106792 ATACAAGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATCCCTAAACCCT
Found at i:31107596 original size:15 final size:14
Alignment explanation
Indices: 31107571--31107617 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
31107561 ATCTAAATTG
*
31107571 TAAACCATAAACCT
1 TAAAACATAAACCT
31107585 TAAAATCATAAACCCT
1 TAAAA-CATAAA-CCT
*
31107601 TAACACAT-AACCT
1 TAAAACATAAACCT
31107614 TAAA
1 TAAA
31107618 CCTTAAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 9 0.32
16 7 0.25
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAACATAAACCT
Found at i:31107637 original size:21 final size:20
Alignment explanation
Indices: 31107609--31107647 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31107599 CTTAACACAT
*
31107609 AACCTTAAACCTTAAACCCC
1 AACCTTAAACCATAAACCCC
31107629 AACCTTTAAACCATAAACC
1 AACC-TTAAACCATAAACC
31107648 ATAGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCTTAAACCATAAACCCC
Found at i:31108071 original size:113 final size:113
Alignment explanation
Indices: 31107912--31108135 Score: 263
Period size: 113 Copynumber: 2.0 Consensus size: 113
31107902 TTTTGATATA
* *
31107912 CGCCACTAATAACTGTATACATCAAGACAAAACGTTGCGTTTTGGTTACCAAATGTTGCGGCGCT
1 CGCCACTAATAACTGTATACATCAAGACAAAACGTTACGTTTTGGTTAACAAATGTTGCGGCGCT
* ** *
31107977 TCTCTGAAAATGCCGCTAATAGTATGCCTTAGCGGCATGTTCCCTTTG
66 TCCCACAAAACGCCGCTAATAGTATGCCTTAGCGGCATGTTCCCTTTG
* * * * * *
31108025 CGCCACTAAT-TCTAGTATACCTCAAGACCAAAC-TCTACGTTTTGGTTAAGATATTTTGCGGCG
1 CGCCACTAATAACT-GTATACATCAAGACAAAACGT-TACGTTTTGGTTAACAAATGTTGCGGCG
* * * * *
31108088 CTTCCCACTAAACGCCGCTAATATTATGCTTTAGCGGCGTTTTCCCTT
64 CTTCCCACAAAACGCCGCTAATAGTATGCCTTAGCGGCATGTTCCCTT
31108136 AAACGCCACT
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
112 3 0.03
113 89 0.97
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (113 bp):
CGCCACTAATAACTGTATACATCAAGACAAAACGTTACGTTTTGGTTAACAAATGTTGCGGCGCT
TCCCACAAAACGCCGCTAATAGTATGCCTTAGCGGCATGTTCCCTTTG
Found at i:31110995 original size:7 final size:7
Alignment explanation
Indices: 31110983--31111018 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
31110973 TGTATAAAAT
31110983 TATTAAA
1 TATTAAA
31110990 TATTAAA
1 TATTAAA
*
31110997 TATAAAA
1 TATTAAA
31111004 TTATTAAA
1 -TATTAAA
31111012 TATTAAA
1 TATTAAA
31111019 ATAAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATTAAA
Found at i:31110997 original size:15 final size:14
Alignment explanation
Indices: 31110983--31111018 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
31110973 TGTATAAAAT
31110983 TATTAAATATTAAA
1 TATTAAATATTAAA
*
31110997 TATAAAATTATTAAA
1 TATTAAA-TATTAAA
31111012 TATTAAA
1 TATTAAA
31111019 ATAAAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TATTAAATATTAAA
Found at i:31111003 original size:22 final size:22
Alignment explanation
Indices: 31110975--31111024 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
31110965 ATAAAAAATG
31110975 TATAAAATTATTAAATATTAAA
1 TATAAAATTATTAAATATTAAA
31110997 TATAAAATTATTAAATATTAAA
1 TATAAAATTATTAAATATTAAA
31111019 -ATAAAA
1 TATAAAA
31111025 CAATATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TATAAAATTATTAAATATTAAA
Found at i:31116985 original size:5 final size:5
Alignment explanation
Indices: 31116975--31117004 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
31116965 TATATATAAG
31116975 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
31117005 TAATAACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:31118956 original size:18 final size:18
Alignment explanation
Indices: 31118933--31118968 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31118923 GGCTGGTTCT
*
31118933 AGTTCATCTACACCTTGG
1 AGTTCACCTACACCTTGG
31118951 AGTTCACCTACACCTTGG
1 AGTTCACCTACACCTTGG
31118969 TTTTCCTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (18 bp):
AGTTCACCTACACCTTGG
Found at i:31119754 original size:269 final size:269
Alignment explanation
Indices: 31119275--31119815 Score: 1046
Period size: 269 Copynumber: 2.0 Consensus size: 269
31119265 AATGGTTCTA
31119275 CATTACCTATTTTGGCCACTGGGCAGTCCTCGTTAATCACAAGATCTCGACCGTTGTACATGCGA
1 CATTACCTATTTTGGCCACTGGGCAGTCCTCGTTAATCACAAGATCTCGACCGTTGTACATGCGA
31119340 TCTTTACTGCTTGTTCCAGGAATTACTAAAAATCTATTATCTGTGTCAAAGTTTGCTAAAGATAA
66 TCTTTACTGCTTGTTCCAGGAATTACTAAAAATCTATTATCTGTGTCAAAGTTTGCTAAAGATAA
*
31119405 TCAAGTAATGTTTGAGTTCTTTCCTACTCAGTGTCGGGTGCGTGATTTAAGGACCAGAGAAGTGC
131 TCAAGTAATATTTGAGTTCTTTCCTACTCAGTGTCGGGTGCGTGATTTAAGGACCAGAGAAGTGC
31119470 TTCTTCAAGGGTTGGTGCATCATGGGTTATATAAACTTCAGCTCAACAAGTCTCCTTCACCTAGC
196 TTCTTCAAGGGTTGGTGCATCATGGGTTATATAAACTTCAGCTCAACAAGTCTCCTTCACCTAGC
31119535 ACTCTGTCT
261 ACTCTGTCT
* *
31119544 CATTACCTGTTTTGGCCACTGGGCAGTCCTCGTTAATCACAAGATCTCGACCGTTGTACATGTGA
1 CATTACCTATTTTGGCCACTGGGCAGTCCTCGTTAATCACAAGATCTCGACCGTTGTACATGCGA
*
31119609 TCTTTACTGCTTGTTCTAGGAATTACTAAAAATCTATTATCTGTGTCAAAGTTTGCTAAAGATAA
66 TCTTTACTGCTTGTTCCAGGAATTACTAAAAATCTATTATCTGTGTCAAAGTTTGCTAAAGATAA
31119674 TCAAGTAATATTTGAGTTCTTTCCTACTCAGTGTCGGGTGCGTGATTTAAGGACCAGAGAAGTGC
131 TCAAGTAATATTTGAGTTCTTTCCTACTCAGTGTCGGGTGCGTGATTTAAGGACCAGAGAAGTGC
31119739 TTCTTCAAGGGTTGGTGCATCATGGGTTATATAAACTTCAGCTCAACAAGTCTCCTTCACCTAGC
196 TTCTTCAAGGGTTGGTGCATCATGGGTTATATAAACTTCAGCTCAACAAGTCTCCTTCACCTAGC
31119804 ACTCTGTCT
261 ACTCTGTCT
31119813 CAT
1 CAT
31119816 AATGCTCAAT
Statistics
Matches: 268, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
269 268 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (269 bp):
CATTACCTATTTTGGCCACTGGGCAGTCCTCGTTAATCACAAGATCTCGACCGTTGTACATGCGA
TCTTTACTGCTTGTTCCAGGAATTACTAAAAATCTATTATCTGTGTCAAAGTTTGCTAAAGATAA
TCAAGTAATATTTGAGTTCTTTCCTACTCAGTGTCGGGTGCGTGATTTAAGGACCAGAGAAGTGC
TTCTTCAAGGGTTGGTGCATCATGGGTTATATAAACTTCAGCTCAACAAGTCTCCTTCACCTAGC
ACTCTGTCT
Found at i:31123367 original size:49 final size:49
Alignment explanation
Indices: 31123311--31123426 Score: 187
Period size: 49 Copynumber: 2.4 Consensus size: 49
31123301 ATACTTTTAA
*
31123311 GTTAGGCATTGATATCTTTTATTTATCAATAAAGTATCTATCGTTCTGG
1 GTTAGGCATTGATATCTTTTATTTATCAATAAAGTATCTATAGTTCTGG
*
31123360 GTTAGGCATTGATATATTTTATTTATCAATAAAGTATCTATAGTTCTGG
1 GTTAGGCATTGATATCTTTTATTTATCAATAAAGTATCTATAGTTCTGG
* * *
31123409 GTTAAGTATTAATATCTT
1 GTTAGGCATTGATATCTT
31123427 AACAACAAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (49 bp):
GTTAGGCATTGATATCTTTTATTTATCAATAAAGTATCTATAGTTCTGG
Found at i:31126000 original size:39 final size:40
Alignment explanation
Indices: 31125899--31126122 Score: 266
Period size: 40 Copynumber: 5.7 Consensus size: 40
31125889 TTGAATGATG
* *
31125899 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
31125938 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
31125979 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
31126018 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT-AAT
* *
31126058 T-CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31126096 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
31126123 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 9, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.01
39 70 0.42
40 81 0.49
41 12 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31126073 original size:79 final size:80
Alignment explanation
Indices: 31125899--31126122 Score: 280
Period size: 79 Copynumber: 2.8 Consensus size: 80
31125889 TTGAATGATG
* * * *
31125899 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATATCCGGGCTAAGACCCGAAGGCAT
31125962 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAT
31125979 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA-TCCGGGCTAAGACCCGAAGGCATT
*
31126041 TGTGCGAGTTACTAAAT
65 TGTGCGAGATACT-AAT
* * * * *
31126058 T-CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATTT
31126122 G
66 G
31126123 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
78 32 0.25
79 60 0.47
80 35 0.27
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGATACTAAT
Found at i:31126144 original size:79 final size:79
Alignment explanation
Indices: 31125952--31126155 Score: 204
Period size: 79 Copynumber: 2.6 Consensus size: 79
31125942 GGACTAAGAT
** *
31125952 CCGAAGGCATTTGTGCGAGAT-ACT-AATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATAC
1 CCGAAGGCATTTGAACGAG-TGACTAAATTCC-GGTTAAGTCCCGAAGGCATTTGTGCGAGATAC
*
31126014 TAATTCCGGGCTAAGC
64 TAATACCGGGCTAAGC
** * * *
31126030 CCGAAGGCATTTGTGCGAGTTACTAAATTCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTGACTAAATTCCGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
*
31126094 ATAACCGGGCTATGTC
66 AT-ACCGGGCTAAG-C
* * *
31126110 CCGAAGGCATTTGAACGAG-GAGCTATA-TCCGGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACGAGTGA-CTAAATTCCGGTTAAGTCCCGAAGG
31126156 TACGTGATTT
Statistics
Matches: 108, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
77 1 0.01
78 30 0.28
79 55 0.51
80 22 0.20
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATTCCGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
ATACCGGGCTAAGC
Found at i:31134070 original size:39 final size:40
Alignment explanation
Indices: 31134007--31134190 Score: 250
Period size: 39 Copynumber: 4.7 Consensus size: 40
31133997 AGTGACCATA
*
31134007 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
31134047 TCCGGGCTAAG-CCTGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31134086 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31134125 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31134164 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
31134191 AACGAAGAGC
Statistics
Matches: 131, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
39 73 0.56
40 58 0.44
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31134113 original size:78 final size:80
Alignment explanation
Indices: 31133971--31134190 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 80
31133961 ATGATGTCCA
* * * * *
31133971 GGCTAAGTCTCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAACCGGGCTAAG-TCCCGAAGGCATTTG
*
31134033 TGCGAGATACTAATTCCG
63 TGCGAGATACTAAATCCG
* *
31134051 GGCTAAG-CCTGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATA-ACCGGGCTAAGTCCCGAAGGCATTTGTG
*
31134113 CGAGTTACTAAATCCG
65 CGAGATACTAAATCCG
* * *
31134129 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTTG
31134191 AACGAAGAGC
Statistics
Matches: 121, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
78 36 0.30
79 53 0.44
80 31 0.26
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGC
GAGATACTAAATCCG
Found at i:31134212 original size:79 final size:78
Alignment explanation
Indices: 31134020--31134223 Score: 200
Period size: 79 Copynumber: 2.6 Consensus size: 78
31134010 GGACTAAGAT
** * * * *
31134020 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCT-AAGCCTGAAGGCATTTGTGCGAGATACTA
1 CCGAAGGCATTTGAACGAG-TACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTA
*
31134084 ATTCCGGGCTAAGC
65 ATACCGGGCTAAGC
** * *
31134098 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAG-TACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTA
*
31134162 ATAACCGGGCTATGTC
65 AT-ACCGGGCTAAG-C
* *
31134178 CCGAAGGCATTTGAACGAAG-AGCTATATCC-GGTTAAATTCCGAAGG
1 CCGAAGGCATTTGAACG-AGTA-CTAAATCCGGGTTAAATCCCGAAGG
31134224 TACGTGATTT
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
78 34 0.32
79 48 0.45
80 23 0.21
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTTGAACGAGTACTAAATCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTAA
TACCGGGCTAAGC
Found at i:31143941 original size:21 final size:22
Alignment explanation
Indices: 31143912--31143955 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
31143902 GCATCTACTC
* *
31143912 AGGGCAATTATAATCCACAACA
1 AGGGCAATTACAATCAACAACA
31143934 AGGG-AATTACAATCAACAACA
1 AGGGCAATTACAATCAACAACA
31143955 A
1 A
31143956 AACTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (22 bp):
AGGGCAATTACAATCAACAACA
Found at i:31155428 original size:87 final size:87
Alignment explanation
Indices: 31155282--31155457 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
31155272 ATCAGACAGG
* * * *
31155282 GTTGTCCATTATCACCTTACCTTTTTGTGCTATGTGTGGAATGGTTAGGGCACATTATTCACACG
1 GTTGTCCATTACCACCTTACCTTTTTGTGCTATATATGGAATGGTTAGGGCACATTATTCACACA
31155347 AAAATTGATAAAGGTAAGTGGT
66 AAAATTGATAAAGGTAAGTGGT
* * *
31155369 GTTGTCCATTACCACCTTACCTTTTTGTGTTATATATGGAATGGTTAGGGCATATTATTCACGCA
1 GTTGTCCATTACCACCTTACCTTTTTGTGCTATATATGGAATGGTTAGGGCACATTATTCACACA
*
31155434 AAAATTGATAAATGTAAGTGGT
66 AAAATTGATAAAGGTAAGTGGT
31155456 GT
1 GT
31155458 CCAATTCGTC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (87 bp):
GTTGTCCATTACCACCTTACCTTTTTGTGCTATATATGGAATGGTTAGGGCACATTATTCACACA
AAAATTGATAAAGGTAAGTGGT
Found at i:31161615 original size:11 final size:11
Alignment explanation
Indices: 31161592--31161630 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
31161582 TATATTGTCA
31161592 TATGTAT-TTT
1 TATGTATATTT
31161602 TATGTATATTT
1 TATGTATATTT
*
31161613 TATGGATACTTT
1 TATGTATA-TTT
31161625 TATGTA
1 TATGTA
31161631 CATAATCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 7 0.28
11 10 0.40
12 8 0.32
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.59
Consensus pattern (11 bp):
TATGTATATTT
Found at i:31163138 original size:6 final size:6
Alignment explanation
Indices: 31163127--31163152 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31163117 TAAAATACAT
31163127 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
31163153 ATTTATTTTG
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:31164398 original size:25 final size:25
Alignment explanation
Indices: 31164370--31164422 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
31164360 TTATTTTTAC
*
31164370 TTTTAAAAATATTTAAA-ATATTATA
1 TTTTAAAAATAATTAAACATA-TATA
* *
31164395 TTTTCAATATAATTAAACATATATA
1 TTTTAAAAATAATTAAACATATATA
31164420 TTT
1 TTT
31164423 AATTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTAAAAATAATTAAACATATATA
Found at i:31164461 original size:28 final size:30
Alignment explanation
Indices: 31164387--31164463 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 30
31164377 AATATTTAAA
*
31164387 ATATTATATT-TTCAATATAATTAAACATAT
1 ATATTAAATTATT-AATATAATTAAACATAT
* * *
31164417 ATATTTAATTATT--TATATTTAATCATAT
1 ATATTAAATTATTAATATAATTAAACATAT
31164445 A-A-TAAATTATTAATATAAT
1 ATATTAAATTATTAATATAAT
31164464 AAATATAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
26 8 0.21
27 1 0.03
28 19 0.50
30 8 0.21
31 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATTAAATTATTAATATAATTAAACATAT
Found at i:31164471 original size:22 final size:22
Alignment explanation
Indices: 31164446--31164489 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31164436 TAATCATATA
31164446 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
31164468 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
31164490 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:31165225 original size:11 final size:11
Alignment explanation
Indices: 31165203--31165260 Score: 80
Period size: 11 Copynumber: 5.2 Consensus size: 11
31165193 AACTAATCCT
31165203 CTCTCAAATTTC
1 CTCTC-AATTTC
31165215 CTCTCAATTTC
1 CTCTCAATTTC
*
31165226 CTCTAAATTTC
1 CTCTCAATTTC
*
31165237 CTCTCAATTTG
1 CTCTCAATTTC
*
31165248 CTCTCAAATTC
1 CTCTCAATTTC
31165259 CT
1 CT
31165261 TCCAAATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:31165236 original size:22 final size:23
Alignment explanation
Indices: 31165203--31165278 Score: 97
Period size: 22 Copynumber: 3.4 Consensus size: 23
31165193 AACTAATCCT
31165203 CTCTCAAATTTCCTCTCAATTTC
1 CTCTCAAATTTCCTCTCAATTTC
*
31165226 CTCT-AAATTTCCTCTCAATTTG
1 CTCTCAAATTTCCTCTCAATTTC
31165248 CTCTCAAA-TTCCT-TCCAAATTT-
1 CTCTCAAATTTCCTCT-C-AATTTC
31165270 CTCTCAAAT
1 CTCTCAAAT
31165279 CCATATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 1 0.02
22 35 0.73
23 12 0.25
ACGTcount: A:0.25, C:0.32, G:0.01, T:0.42
Consensus pattern (23 bp):
CTCTCAAATTTCCTCTCAATTTC
Found at i:31165252 original size:33 final size:33
Alignment explanation
Indices: 31165202--31165276 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 33
31165192 AAACTAATCC
* *
31165202 TCTCTCAAATTTCCTCTCAATTTCC-TCTAAATT
1 TCTCTC-AATTTCCTCTCAAATTCCTTCCAAATT
*
31165235 TCCTCTCAATTTGCTCTCAAATTCCTTCCAAATT
1 T-CTCTCAATTTCCTCTCAAATTCCTTCCAAATT
31165269 TCTCTCAA
1 TCTCTCAA
31165277 ATCCATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.24, C:0.32, G:0.01, T:0.43
Consensus pattern (33 bp):
TCTCTCAATTTCCTCTCAAATTCCTTCCAAATT
Found at i:31165277 original size:11 final size:11
Alignment explanation
Indices: 31165202--31165278 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
31165192 AAACTAATCC
31165202 TCTCTCAAATT
1 TCTCTCAAATT
31165213 TCCTCTC-AATT
1 T-CTCTCAAATT
31165224 TC-CTCTAAATT
1 TCTCTC-AAATT
31165235 TCCTCTC-AATT
1 T-CTCTCAAATT
31165246 TGCTCTCAAATT
1 T-CTCTCAAATT
*
31165258 CCT-TCCAAATT
1 TCTCT-CAAATT
31165269 TCTCTCAAAT
1 TCTCTCAAAT
31165279 CCATATTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 3 0.05
10 2 0.04
11 36 0.65
12 11 0.20
13 3 0.05
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:31166525 original size:7 final size:7
Alignment explanation
Indices: 31166513--31166538 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31166503 TAGTCGATTG
31166513 GTATTTA
1 GTATTTA
31166520 GTATTTA
1 GTATTTA
31166527 GTATTTA
1 GTATTTA
31166534 GTATT
1 GTATT
31166539 ATGTGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:31171487 original size:21 final size:21
Alignment explanation
Indices: 31171445--31171489 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
31171435 AGATGCCGTA
* *
31171445 CCGGAAGAACCAGAATCCCCG
1 CCGGAAGAACAACAATCCCCG
31171466 CCGGAAGAACAACAA-CCGCCG
1 CCGGAAGAACAACAATCC-CCG
31171487 CCG
1 CCG
31171490 AAAGCTAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.40, G:0.24, T:0.02
Consensus pattern (21 bp):
CCGGAAGAACAACAATCCCCG
Found at i:31171657 original size:45 final size:45
Alignment explanation
Indices: 31171608--31171789 Score: 213
Period size: 45 Copynumber: 3.9 Consensus size: 45
31171598 ATATTTTGAA
* *
31171608 TATTTTGATATTATTTTATGTAATAAAATAGAAATTTTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
* *
31171653 TATTTTGATATTATTTGATGTAATAAGATAGAAGTTTATTTGATGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA-GT
** * *
31171699 AATAAAATAGA-AGTTTATTTGATGTAATAAAATAGAAATTTTTTTGAGT
1 --T-ATTTTGATA--TTATTTGATGTAATAAAATAGAAATTTATTTGAGT
* *
31171748 TATTTTGATATTATTTTATGTAATAAAATAGAAGTTTATTTG
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTG
31171790 GTGTAATAAA
Statistics
Matches: 114, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
45 68 0.60
46 6 0.05
47 2 0.02
48 2 0.02
49 6 0.05
50 30 0.26
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:31171691 original size:25 final size:25
Alignment explanation
Indices: 31171663--31171802 Score: 157
Period size: 25 Copynumber: 5.8 Consensus size: 25
31171653 TATTTTGATA
*
31171663 TTATTTGATGTAATAAGATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
31171688 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
31171713 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
* ** *
31171738 TTTTTTGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
*
31171757 ATTATTTTATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
*
31171783 TTATTTGGTGTAATAAAATA
1 TTATTTGATGTAATAAAATA
31171803 TAAATTTTTT
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.01
20 7 0.07
21 5 0.05
22 1 0.01
23 1 0.01
24 5 0.05
25 74 0.78
26 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:31171729 original size:95 final size:95
Alignment explanation
Indices: 31171618--31171802 Score: 334
Period size: 95 Copynumber: 1.9 Consensus size: 95
31171608 TATTTTGATA
* *
31171618 TTATTTTATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAGATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
31171683 GAAGTTTATTTGATGTAATAAAATAGAAGT
66 GAAGTTTATTTGATGTAATAAAATAGAAGT
*
31171713 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTTATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
*
31171778 GAAGTTTATTTGGTGTAATAAAATA
66 GAAGTTTATTTGATGTAATAAAATA
31171803 TAAATTTTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 86 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (95 bp):
TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
GAAGTTTATTTGATGTAATAAAATAGAAGT
Found at i:31171762 original size:70 final size:70
Alignment explanation
Indices: 31171688--31171843 Score: 285
Period size: 70 Copynumber: 2.2 Consensus size: 70
31171678 AGATAGAAGT
31171688 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTT
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTT
31171753 TGATA
66 TGATA
* * *
31171758 TTATTTTATGTAATAAAATAGAAGTTTATTTGGTGTAATAAAATATAAATTTTTTTGAGTTATTT
1 TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTT
31171823 TGATA
66 TGATA
31171828 TTATTTGATGTAATAA
1 TTATTTGATGTAATAA
31171844 CATGAGATTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 82 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (70 bp):
TTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTT
TGATA
Found at i:31175391 original size:21 final size:22
Alignment explanation
Indices: 31175365--31175419 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
31175355 AACAACGGTG
*
31175365 GCGGTGAGATTAGG-TACTGTA
1 GCGGTGAGATTAGGATACTATA
31175386 GCGGTGAGATT-GGATACTATA
1 GCGGTGAGATTAGGATACTATA
*
31175407 GCAGTGAGATTAG
1 GCGGTGAGATTAG
31175420 AAACAGCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (22 bp):
GCGGTGAGATTAGGATACTATA
Found at i:31175555 original size:19 final size:18
Alignment explanation
Indices: 31175531--31175577 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
31175521 AGAAGTTTTT
*
31175531 AAAATTATTTAACAATTA
1 AAAATTATTAAACAATTA
* *
31175549 CAAAATTAATAAATAATTA
1 -AAAATTATTAAACAATTA
31175568 AAAATTATTA
1 AAAATTATTA
31175578 CAATTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAACAATTA
Found at i:31175680 original size:36 final size:34
Alignment explanation
Indices: 31175639--31175748 Score: 109
Period size: 36 Copynumber: 3.5 Consensus size: 34
31175629 GAAAAATTCA
31175639 AAAATATCAAAATATTTTACAGATTATATTCATAAT
1 AAAATATCAAAATATTTTA-A-ATTATATTCATAAT
31175675 AAAATATCAAAATATTTTAAA-TATA--C--AAT
1 AAAATATCAAAATATTTTAAATTATATTCATAAT
*
31175704 -AAA-AT----AT-TTTTAAATTATATTCATAAC
1 AAAATATCAAAATATTTTAAATTATATTCATAAT
31175731 AAAATATCAAAATATTTT
1 AAAATATCAAAATATTTT
31175749 TACAGATTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 26
0.69 0.01 0.30
Matches are distributed among these distances:
22 7 0.11
23 6 0.10
25 1 0.02
27 4 0.07
28 6 0.10
29 5 0.08
31 1 0.02
33 6 0.10
34 5 0.08
35 1 0.02
36 19 0.31
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (34 bp):
AAAATATCAAAATATTTTAAATTATATTCATAAT
Found at i:31175779 original size:36 final size:32
Alignment explanation
Indices: 31175701--31175781 Score: 83
Period size: 37 Copynumber: 2.3 Consensus size: 32
31175691 TTAAATATAC
31175701 AATAAAATATTTTTAAATTATATTCATAACAAA
1 AATAAAATATTTTTAAATTATATT-ATAACAAA
31175734 ATATCAAAATATTTTTACAGATTATATT-TGAATCAAA
1 A-AT-AAAATATTTTTA-A-ATTATATTAT-AA-CAAA
31175771 TAATAAAATAT
1 -AATAAAATAT
31175782 AAATTAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
33 1 0.02
34 2 0.05
35 13 0.32
36 10 0.24
37 14 0.34
38 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (32 bp):
AATAAAATATTTTTAAATTATATTATAACAAA
Found at i:31178226 original size:34 final size:34
Alignment explanation
Indices: 31178183--31178254 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
31178173 CCAATCCAAG
31178183 TTTAACTTAAACCCAAAATAAGTCCTAAAAGCTT
1 TTTAACTTAAACCCAAAATAAGTCCTAAAAGCTT
31178217 TTTAACTTAAACCCAAAATAAGTCCTAAAAGCTT
1 TTTAACTTAAACCCAAAATAAGTCCTAAAAGCTT
31178251 TTTA
1 TTTA
31178255 TTTTATATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (34 bp):
TTTAACTTAAACCCAAAATAAGTCCTAAAAGCTT
Found at i:31178976 original size:17 final size:18
Alignment explanation
Indices: 31178949--31178985 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
31178939 TTAGTATTTA
*
31178949 ATTATTAATATATGTTTT
1 ATTATTAATATATGTATT
31178967 ATTA-TAATATATGTATT
1 ATTATTAATATATGTATT
31178984 AT
1 AT
31178986 AAACAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
ATTATTAATATATGTATT
Found at i:31179181 original size:24 final size:24
Alignment explanation
Indices: 31179132--31179207 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
31179122 TAGGAAATTA
* **
31179132 GTTACAAGAAGATGAAATGTTTAAG
1 GTTA-AAGAAGATGAAAGGTGAAAG
*
31179157 GTTAAAGAAGATGAAAGGTGGAAG
1 GTTAAAGAAGATGAAAGGTGAAAG
* * * *
31179181 GTTGAGGGAGATGAAAGATGAAAG
1 GTTAAAGAAGATGAAAGGTGAAAG
31179205 GTT
1 GTT
31179208 GAACATCCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 39 0.91
25 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.34, T:0.22
Consensus pattern (24 bp):
GTTAAAGAAGATGAAAGGTGAAAG
Found at i:31182327 original size:51 final size:53
Alignment explanation
Indices: 31182250--31182358 Score: 136
Period size: 51 Copynumber: 2.1 Consensus size: 53
31182240 TGATGATTAA
* *
31182250 TTAGC-AGACTATGAGCCATTGGTTATTTAGCAATCCTTAAGCCGGT-GATAT
1 TTAGCAAGACTATGAGCCATTGATTATTTAGCAAGCCTTAAGCCGGTGGATAT
* * *
31182301 TTAGCAAGA-TATGAGCCGA-TGATTATTTAGCAAGCCTTGAGCTGGTGGTTAT
1 TTAGCAAGACTATGAGCC-ATTGATTATTTAGCAAGCCTTAAGCCGGTGGATAT
31182353 TTAGCA
1 TTAGCA
31182359 GGCCATAAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
51 36 0.72
52 14 0.28
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (53 bp):
TTAGCAAGACTATGAGCCATTGATTATTTAGCAAGCCTTAAGCCGGTGGATAT
Found at i:31182341 original size:26 final size:26
Alignment explanation
Indices: 31182235--31182411 Score: 103
Period size: 26 Copynumber: 6.8 Consensus size: 26
31182225 TAGTAGGCTA
* * *
31182235 TGAGCTGATGATTAATTAGC-AGACT
1 TGAGCCGATGATTATTTAGCAAGCCT
* *
31182260 ATGAGCC-ATTGGTTATTTAGCAATCCT
1 -TGAGCCGA-TGATTATTTAGCAAGCCT
* * *
31182287 TAAGCCGGTGA-TATTTAGCAAG-AT
1 TGAGCCGATGATTATTTAGCAAGCCT
31182311 ATGAGCCGATGATTATTTAGCAAGCCT
1 -TGAGCCGATGATTATTTAGCAAGCCT
* * * * *
31182338 TGAGCTGGTGGTTATTTAGCAGGCCA
1 TGAGCCGATGATTATTTAGCAAGCCT
* * * * *
31182364 TAAGCCGATGTTTATTTTAGTAGGCTT
1 TGAGCCGATGATTA-TTTAGCAAGCCT
*
31182391 TAAGCCGATGAATTA-TTAGCA
1 TGAGCCGATG-ATTATTTAGCA
31182412 GGTACTATTA
Statistics
Matches: 116, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
24 1 0.01
25 20 0.17
26 69 0.59
27 23 0.20
28 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (26 bp):
TGAGCCGATGATTATTTAGCAAGCCT
Found at i:31182368 original size:77 final size:78
Alignment explanation
Indices: 31182199--31182370 Score: 204
Period size: 77 Copynumber: 2.2 Consensus size: 78
31182189 ATGTGATATC
* * * *
31182199 TAGCAGGCCATAAGCCGGTGATTAATTAGTAGGCTATGAGCTGATGATTAATTAGCAGACTATGA
1 TAGCAGGCCATAAGCCGGTGATTAATTAGCAAGATATGAGCCGATGATTAATTAGCAGACTATGA
*
31182264 GCCATTGGTTATT
66 GCCAGTGGTTATT
** * * * *
31182277 TAGCAATCCTTAAGCCGGTGA-TATTTAGCAAGATATGAGCCGATGATTATTTAGCAAGCCT-TG
1 TAGCAGGCCATAAGCCGGTGATTAATTAGCAAGATATGAGCCGATGATTAATTAGC-AGACTATG
**
31182340 AGCTGGTGGTTATT
65 AGCCAGTGGTTATT
31182354 TAGCAGGCCATAAGCCG
1 TAGCAGGCCATAAGCCG
31182371 ATGTTTATTT
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
77 55 0.71
78 22 0.29
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (78 bp):
TAGCAGGCCATAAGCCGGTGATTAATTAGCAAGATATGAGCCGATGATTAATTAGCAGACTATGA
GCCAGTGGTTATT
Found at i:31195006 original size:11 final size:11
Alignment explanation
Indices: 31194992--31195016 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31194982 TCAAAATTGA
31194992 TCTAAGTACGG
1 TCTAAGTACGG
31195003 TCTAAGTACGG
1 TCTAAGTACGG
31195014 TCT
1 TCT
31195017 GAAAATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (11 bp):
TCTAAGTACGG
Found at i:31199395 original size:23 final size:23
Alignment explanation
Indices: 31199348--31199398 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
31199338 ACCCACTTTC
* * * *
31199348 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTCGAGATA
31199371 TTACAGTAGTAATTTTCGAGATA
1 TTACAGTAGTAATTTTCGAGATA
31199394 TTACA
1 TTACA
31199399 CTGCAAACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGAGATA
Found at i:31200862 original size:30 final size:30
Alignment explanation
Indices: 31200788--31201162 Score: 347
Period size: 30 Copynumber: 12.5 Consensus size: 30
31200778 TATATGTAAA
* * *
31200788 CATATACACATC-ATTTCGGCAATATATATG
1 CATATACAAATCAATTT-GGCAATGTATATC
* * *
31200818 TATGTA-AAATTCAATTTGGTAATGTATATC
1 CATATACAAA-TCAATTTGGCAATGTATATC
*
31200848 TATATACAAATCAATTTGGCAATG----T-
1 CATATACAAATCAATTTGGCAATGTATATC
* * *
31200873 --TATACAAAACAATTCGGCAATGTACATC
1 CATATACAAATCAATTTGGCAATGTATATC
31200901 CATATACAAATCAATTTGGCAATGTATATC
1 CATATACAAATCAATTTGGCAATGTATATC
31200931 CATATACAAATCAATTTGGCAATGTATATC
1 CATATACAAATCAATTTGGCAATGTATATC
*
31200961 CATATACAAATCAATTTGGAAATGTATATC
1 CATATACAAATCAATTTGGCAATGTATATC
* * *
31200991 CATATACAAATCAATTCGGCAATATATATGTAAA
1 CATATACAAATCAATTTGGCAATGTATA--T--C
* * *
31201025 CATATACAAATC-ATTTCGACAATATATATA
1 CATATACAAATCAATTT-GGCAATGTATATC
* * *
31201055 CATGTACAATTCAATTCGGCAATGTATATC
1 CATATACAAATCAATTTGGCAATGTATATC
* * *
31201085 CATATACAAATCAATTCGGCTATATATACATC
1 CATATACAAATCAATTTGGC-A-ATGTATATC
* * ** *
31201117 TATATATAAATCAATTCAGCAATATATATC
1 CATATACAAATCAATTTGGCAATGTATATC
31201147 CATATACAAATCAATT
1 CATATACAAATCAATT
31201163 CGACAATATA
Statistics
Matches: 291, Mismatches: 36, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
23 20 0.07
26 1 0.00
27 1 0.00
29 2 0.01
30 204 0.70
31 12 0.04
32 26 0.09
33 3 0.01
34 22 0.08
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
CATATACAAATCAATTTGGCAATGTATATC
Found at i:31200880 original size:23 final size:23
Alignment explanation
Indices: 31200850--31200895 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31200840 TGTATATCTA
* *
31200850 TATACAAATCAATTTGGCAATGT
1 TATACAAAACAATTCGGCAATGT
31200873 TATACAAAACAATTCGGCAATGT
1 TATACAAAACAATTCGGCAATGT
31200896 ACATCCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (23 bp):
TATACAAAACAATTCGGCAATGT
Found at i:31201079 original size:94 final size:90
Alignment explanation
Indices: 31200873--31201174 Score: 347
Period size: 94 Copynumber: 3.3 Consensus size: 90
31200863 TTGGCAATGT
* * * * *
31200873 TATACAAAACAATTCGGCAATGTACATCCATATACAAATCAATTTGGCAATGTATATCCATATAC
1 TATACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATATATATACATATAC
* * *
31200938 AAATCAATTTGGCAATGTATATCCA
66 AAATCAATTTGACAATATATATACA
* *
31200963 TATACAAATCAATTTGGAAATGTATATCCATATACAAATCAATTCGGCAATATATATGTAAACAT
1 TATACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATATATA--T--ACAT
31201028 ATACAAATC-ATTTCGACAATATATATACA
62 ATACAAATCAATTT-GACAATATATATACA
* * * *
31201057 TGTACAATTCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCTATATATACATCTATAT
1 TATACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATATATATA-C-ATAT
* * *
31201122 ATAAATCAA-TTCAGCAATATATATCCA
64 ACAAATCAATTTGA-CAATATATATACA
* *
31201149 TATACAAATCAATTCGACAATATATA
1 TATACAAATCAATTCGGCAATGTATA
31201175 AAACATATAC
Statistics
Matches: 180, Mismatches: 23, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
90 51 0.28
91 2 0.01
92 47 0.26
93 5 0.03
94 75 0.42
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (90 bp):
TATACAAATCAATTCGGCAATGTATATCCATATACAAATCAATTCGGCAATATATATACATATAC
AAATCAATTTGACAATATATATACA
Found at i:31201163 original size:30 final size:30
Alignment explanation
Indices: 31200873--31201174 Score: 352
Period size: 30 Copynumber: 9.9 Consensus size: 30
31200863 TTGGCAATGT
* * *
31200873 TATACAAAACAATTCGGCAATGTACATCCA
1 TATACAAATCAATTCGGCAATATATATCCA
* *
31200903 TATACAAATCAATTTGGCAATGTATATCCA
1 TATACAAATCAATTCGGCAATATATATCCA
* *
31200933 TATACAAATCAATTTGGCAATGTATATCCA
1 TATACAAATCAATTCGGCAATATATATCCA
* * *
31200963 TATACAAATCAATTTGGAAATGTATATCCA
1 TATACAAATCAATTCGGCAATATATATCCA
*
31200993 TATACAAATCAATTCGGCAATATATATGTAAACA
1 TATACAAATCAATTCGGCAATATATA--T--CCA
* * *
31201027 TATACAAATCATTTCGACAATATATATACA
1 TATACAAATCAATTCGGCAATATATATCCA
* * *
31201057 TGTACAATTCAATTCGGCAATGTATATCCA
1 TATACAAATCAATTCGGCAATATATATCCA
* *
31201087 TATACAAATCAATTCGGCTATATATACATCTA
1 TATACAAATCAATTCGGC-A-ATATATATCCA
* *
31201119 TATATAAATCAATTCAGCAATATATATCCA
1 TATACAAATCAATTCGGCAATATATATCCA
*
31201149 TATACAAATCAATTCGACAATATATA
1 TATACAAATCAATTCGGCAATATATA
31201175 AAACATATAC
Statistics
Matches: 238, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
30 184 0.77
31 2 0.01
32 26 0.11
34 26 0.11
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (30 bp):
TATACAAATCAATTCGGCAATATATATCCA
Found at i:31202890 original size:16 final size:17
Alignment explanation
Indices: 31202862--31202895 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
31202852 TGATAATTCA
31202862 TTCTAATCTATTTATTT
1 TTCTAATCTATTTATTT
31202879 TTCTAA-CTATTTATTT
1 TTCTAATCTATTTATTT
31202895 T
1 T
31202896 CTACCCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTAATCTATTTATTT
Found at i:31205090 original size:27 final size:27
Alignment explanation
Indices: 31205055--31205109 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
31205045 AATTAAGTTG
31205055 AAATCAAAACAAAAGGAAATAAAAGAA
1 AAATCAAAACAAAAGGAAATAAAAGAA
31205082 AAATCAAAACAAAAGGAAATAAAAGAA
1 AAATCAAAACAAAAGGAAATAAAAGAA
31205109 A
1 A
31205110 TTGGTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.07
Consensus pattern (27 bp):
AAATCAAAACAAAAGGAAATAAAAGAA
Found at i:31208251 original size:33 final size:34
Alignment explanation
Indices: 31208213--31208276 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
31208203 TAATATAAAG
* *
31208213 ATAAGTAGTTCCTTAAC-AAACTTTCAAGCAAAC
1 ATAAGTAATCCCTTAACAAAACTTTCAAGCAAAC
31208246 ATAAGTAATCCCTTAACAAAACTTTCAAGCA
1 ATAAGTAATCCCTTAACAAAACTTTCAAGCA
31208277 TAACGTAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.27
Consensus pattern (34 bp):
ATAAGTAATCCCTTAACAAAACTTTCAAGCAAAC
Found at i:31224295 original size:11 final size:11
Alignment explanation
Indices: 31224279--31224303 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31224269 AATTATTTTG
31224279 AAAAAAAAAGA
1 AAAAAAAAAGA
31224290 AAAAAAAAAGA
1 AAAAAAAAAGA
31224301 AAA
1 AAA
31224304 TGGATAGGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:31225702 original size:44 final size:43
Alignment explanation
Indices: 31225536--31226259 Score: 461
Period size: 44 Copynumber: 16.7 Consensus size: 43
31225526 ACAGATCGAG
* * * *
31225536 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAGGCA-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AGCCACAA
* * *
31225580 TATTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA-AA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCACAA
* *
31225625 TCATATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ACAA
* * * *
31225669 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA-A
* * * *
31225713 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CG-CATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-C-AA
* *
31225753 TTTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ACAA
* * * *
31225797 T-TCTATCTCCCTGAAATTGTAGTGGAGCAGATTAAAACCTCAGA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA-A
* * * * * *
31225841 TATTATCTCTCTGAAGTTGCAG-AGAGAAGA-T--CG-CATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-C-AA
* * * **
31225881 TTTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAGTAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CAA
* * * **
31225924 GTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATAGCAA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-CAA
* *
31225969 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ACAA
* * * **
31226014 TCCTATCTCCCTGAAGTTGCAGTGGAACTGATTAAAGCCTTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA-A
* * * * *** *
31226058 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCACA--TTTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAA
* *
31226098 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAA-CAGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-CACAA
* * *
31226141 TCCTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAGCCGACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-ACAA
* *
31226185 T-TCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCTCA-AA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CACAA
* *
31226229 TCTTATCTCACTGAAGTTGCAG-AGAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
31226260 CGCGTTTAGT
Statistics
Matches: 539, Mismatches: 100, Indels: 83
0.75 0.14 0.11
Matches are distributed among these distances:
39 2 0.00
40 62 0.12
41 27 0.05
42 6 0.01
43 74 0.14
44 280 0.52
45 81 0.15
46 7 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAA
Found at i:31225773 original size:84 final size:86
Alignment explanation
Indices: 31225536--31226296 Score: 436
Period size: 84 Copynumber: 8.8 Consensus size: 86
31225526 ACAGATCGAG
* * * * * *
31225536 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAGGCAAGTATTATC-CTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAGCA-TCTAGTCTTATCTC-CCTGAAGTTGC
* * *** *
31225600 AGT-GAGGCAGACTGAAGATGGCAAA
63 AGTGGA-GCAGA-TTAAAACCTCAGA
* * * *
31225625 TCATATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGA-C-AATCCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AG-C-ATCTAGTCTTATCTCCCTGAAGTTG
*
31225688 CAGTGGAGCGGATTAAAACCTCAGA
62 CAGTGGAGCAGATTAAAACCTCAGA
* * * *
31225713 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAGTTTTATCTCCCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
*
31225776 GGAGCAGATTAAAGCCGAT-A-A
66 GGAGCAGATTAAAACC--TCAGA
* * ** * * *
31225797 T-TCTATCTCCCTGAAATTGTAGTGGAGCAGATTAAAACCTCAGATATTATCTCTCTGAAGTTGC
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCT-AG-TCTTATCTCCCTGAAGTTGC
* * *** *
31225861 AG-AGAGAAGA-TCGCATCT-AG-
63 AGTGGAGCAGATTAAAACCTCAGA
* * * * * *
31225881 TTTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-CATCTAGTCTTATCTC-CCTGAAGTTGC
* * * *
31225945 AGTGGGGCAGACTGAAGATAGC-AAG-
63 AGTGGAGCAGA-TTAA-A-ACCTCAGA
** * * *
31225970 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATC--TAGTCTTATCTCCCTGAAGTTGCA
* * * *
31226035 GTGGAACTGATTAAAGCCTTAGA
64 GTGGAGCAGATTAAAACCTCAGA
* * * *
31226058 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCA-CATTTAGTCTTATCTCCCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
* **
31226121 GGAGCAGACT-AAACAGACA-A
66 GGAGCAGATTAAAAC-CTCAGA
* * * * *
31226141 TCCTATCTCTCTGAAGTTACAGTGGAGCAGATTAAAGCCGA-CAATTC-TATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AG-C-ATCTAGTCTTATCTCCCTGAAGTTG
* * *
31226204 CAGTGGAGCGGATTAAAATCTCAAA
62 CAGTGGAGCAGATTAAAACCTCAGA
* * * * * *
31226229 TCTTATCTCACTGAAGTTGCAG-AGAGCAGA-TCGCGTTTAGTCTTATCTCCCTGAAGTTGTAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
31226292 GGAGC
66 GGAGC
31226297 TGACTAAGTA
Statistics
Matches: 521, Mismatches: 109, Indels: 89
0.72 0.15 0.12
Matches are distributed among these distances:
82 1 0.00
83 32 0.06
84 166 0.32
85 18 0.03
86 15 0.03
87 68 0.13
88 101 0.19
89 112 0.21
90 7 0.01
92 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (86 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
GGAGCAGATTAAAACCTCAGA
Found at i:31225803 original size:128 final size:128
Alignment explanation
Indices: 31225628--31226296 Score: 633
Period size: 128 Copynumber: 5.2 Consensus size: 128
31225618 TGGCAAATCA
* *
31225628 TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTG
* * *
31225693 GAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTTT
66 GAGCAGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCT
* * *
31225756 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATTCTATCTCCCTGAAATTGTAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTG
* * * *
31225821 GAGCAGATTAAAACCTCAGATATTATCTCTCTGAAGTTGCAGAGAGAAGATCGCATCTAGTTT
66 GAGCAGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCT
* * ** *
31225884 TATCTCCCTGAAGTTACAGTGGAGCAGACT-AAG-TAAGCAAGTCTTATC-CTCCTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA-CAATTC-TATCTC-CCTGAAGTTGCA
* * * * * *** *
31225946 GTGGGGCAGACTGAAGATAGC-AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
63 GTGGAGCAGA-TTAA-A-ACCTCAGATCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-TCGCATC
* *
31226009 GATAATCC
123 --TAGTCT
* * * * *
31226017 TATCTCCCTGAAGTTGCAGTGGAACTGATTAAAGCCTTA-GA-TCTTATCTCTCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-GACAATTC-TATCTCCCTGAAGTTGCAG
* * * * * * ** *
31226080 -AGAGCAGA-TCACA-TTTAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAACAGAC-A
64 TGGAGCAGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCAG-AGAGCAGA-T-CGCA-TCTA
* *
31226140 ATCC
125 GTCT
* *
31226144 TATCTCTCTGAAGTTACAGTGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTG
* * * * * *
31226209 GAGCGGATTAAAATCTCAAATCTTATCTCACTGAAGTTGCAGAGAGCAGATCGCGTTTAGTCT
66 GAGCAGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCT
*
31226272 TATCTCCCTGAAGTTGTAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
31226297 TGACTAAGTA
Statistics
Matches: 442, Mismatches: 75, Indels: 48
0.78 0.13 0.08
Matches are distributed among these distances:
126 2 0.00
127 64 0.14
128 240 0.54
129 30 0.07
130 20 0.05
131 26 0.06
132 6 0.01
133 48 0.11
134 5 0.01
136 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (128 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATTCTATCTCCCTGAAGTTGCAGTG
GAGCAGATTAAAACCTCAGATCTTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCT
Found at i:31225986 original size:217 final size:216
Alignment explanation
Indices: 31225755--31226221 Score: 647
Period size: 217 Copynumber: 2.2 Consensus size: 216
31225745 GCATCTAGTT
* * *
31225755 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATTCTATCTCCCTGAAATTGTAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCTCCCTGAAATTGCAGT
* * *
31225820 GGAGCAGATTAAAACCTCAGATATTATCTCTCTGAAGTTGCAGAGAGAAGATCGCATCTAGTTTT
66 GGAACAGATTAAAACCTCAGATATTATCTCTCTGAAGTTGCAGAGAGAAGATCACATCTAGTCTT
* *
31225885 ATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTA-AG-CAAGTCTTATC-CTCCTGAAGTTGCAG
131 ATCTCCCTGAAGTTACAGTGGAGCAGACTAA--ACAGACAA-TCCTATCTCT-CTGAAGTTACAG
* * *
31225947 TGGGGCAGACTGAAG-ATAGCAAGTC
192 TGGAGCAGACTAAAGCAGA-CAAGTC
*
31225972 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCTCCCTGAAATTGCAGT
* * * * * *
31226037 GGAACTGATTAAAGCCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATTTAGTCTT
66 GGAACAGATTAAAACCTCAGATATTATCTCTCTGAAGTTGCAGAGAGAAGATCACATCTAGTCTT
*
31226102 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAACAGACAATCCTATCTCTCTGAAGTTACAGTGGA
131 ATCTCCCTGAAGTTACAGTGGAGCAGACTAAACAGACAATCCTATCTCTCTGAAGTTACAGTGGA
* * *
31226167 GCAGATTAAAGCCGACAATTC
196 GCAGACTAAAGCAGACAAGTC
*
31226188 -TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA
31226222 TCTCAAATCT
Statistics
Matches: 223, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
215 34 0.15
216 36 0.16
217 153 0.69
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (216 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCGATAATCCTATCTCCCTGAAATTGCAGT
GGAACAGATTAAAACCTCAGATATTATCTCTCTGAAGTTGCAGAGAGAAGATCACATCTAGTCTT
ATCTCCCTGAAGTTACAGTGGAGCAGACTAAACAGACAATCCTATCTCTCTGAAGTTACAGTGGA
GCAGACTAAAGCAGACAAGTC
Done.