Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 65 of 126
Found at i:18961018 original size:22 final size:22
Alignment explanation
Indices: 18960990--18961047 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
18960980 TTAGCACGTA
18960990 TTGTGCTCTCCGTTTAACACAT
1 TTGTGCTCTCCGTTTAACACAT
* *
18961012 TTGTGCTCTCCGTTTAGCACCT
1 TTGTGCTCTCCGTTTAACACAT
**
18961034 CGGTGCTCTCCGTT
1 TTGTGCTCTCCGTT
18961048 CATTGTGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.10, C:0.31, G:0.19, T:0.40
Consensus pattern (22 bp):
TTGTGCTCTCCGTTTAACACAT
Found at i:18962345 original size:31 final size:31
Alignment explanation
Indices: 18962287--18962345 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
18962277 TAAGATTAAA
* *
18962287 TTTTGAAAAGTTGAGAATATTGAGATAATTT
1 TTTTGAAAAGTTAAAAATATTGAGATAATTT
* * *
18962318 TTTTGAAAATTTAAAAATCTTGGGATAA
1 TTTTGAAAAGTTAAAAATATTGAGATAA
18962346 AATTTACATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.41
Consensus pattern (31 bp):
TTTTGAAAAGTTAAAAATATTGAGATAATTT
Found at i:18964578 original size:17 final size:16
Alignment explanation
Indices: 18964546--18964590 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
18964536 AATATTAATT
*
18964546 ATTAAATCAA-TT-TA
1 ATTAAATAAATTTCTA
18964560 ATTAAATTAAATTTCTA
1 ATTAAA-TAAATTTCTA
18964577 ATTAAATAAATTTC
1 ATTAAATAAATTTC
18964591 CCAACCCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.22
15 3 0.11
16 10 0.37
17 8 0.30
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAATAAATTTCTA
Found at i:18966320 original size:85 final size:85
Alignment explanation
Indices: 18966177--18966336 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 85
18966167 GACACTTCAC
* * * * * *
18966177 ATACTTGTGTTCTTGCAGGTATGTCATAGGATCATCCGAAGTTGGATTTTGACCTTATCTCTGAC
1 ATACTTGTATTCTTGCAAGTATGTCACAGGATCATCCGAAATTGGATTCTAACCTTATCTCTGAC
*
18966242 ATTGTCTTACTTATGGTGAA
66 ATAGTCTTACTTATGGTGAA
* * * *
18966262 ATACTTGTATTTTTTCAAGTATGTCACATGATCATTCGAAATTGGATTCTAACCTTATCTCTGAC
1 ATACTTGTATTCTTGCAAGTATGTCACAGGATCATCCGAAATTGGATTCTAACCTTATCTCTGAC
18966327 ATAGTCTTAC
66 ATAGTCTTAC
18966337 CTATATTATG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (85 bp):
ATACTTGTATTCTTGCAAGTATGTCACAGGATCATCCGAAATTGGATTCTAACCTTATCTCTGAC
ATAGTCTTACTTATGGTGAA
Found at i:18969743 original size:4 final size:4
Alignment explanation
Indices: 18969734--18969764 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
18969724 AAGGGTATTA
18969734 TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TAT
18969765 ATAGATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:18970058 original size:20 final size:20
Alignment explanation
Indices: 18970033--18970085 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
18970023 ATAGCCCGTA
18970033 TGCACTTCGGTGCCCCTGTT
1 TGCACTTCGGTGCCCCTGTT
* *
18970053 TGCACTTTGGTGCCCTTGTT
1 TGCACTTCGGTGCCCCTGTT
18970073 TGCACTTCGGTGC
1 TGCACTTCGGTGC
18970086 GGCTGTCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.06, C:0.30, G:0.26, T:0.38
Consensus pattern (20 bp):
TGCACTTCGGTGCCCCTGTT
Found at i:18973514 original size:16 final size:16
Alignment explanation
Indices: 18973485--18973542 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
18973475 ATCTTCTTTG
18973485 AATCCCTAAAATATTAA
1 AATCCCT-AAATATTAA
18973502 AATCCCTAAATATTAA
1 AATCCCTAAATATTAA
**
18973518 AATCCCTAAATATTTG
1 AATCCCTAAATATTAA
18973534 AATCCCTAA
1 AATCCCTAA
18973543 CCCAAGATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
16 32 0.82
17 7 0.18
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (16 bp):
AATCCCTAAATATTAA
Found at i:18974442 original size:33 final size:33
Alignment explanation
Indices: 18974405--18974483 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
18974395 TGTTGACTGT
* **
18974405 TGGGGAAGGTGATGGTGAAGTTATAGAAGT-TGA
1 TGGGGAAGGTGATGATGAAGGGATAGAA-TCTGA
* *
18974438 TGGGGAGGGTGATGATGAAGGGGTAGAATCTGA
1 TGGGGAAGGTGATGATGAAGGGATAGAATCTGA
*
18974471 TGGTGAAGGTGAT
1 TGGGGAAGGTGAT
18974484 CTGGAAAGGG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.28, C:0.01, G:0.46, T:0.25
Consensus pattern (33 bp):
TGGGGAAGGTGATGATGAAGGGATAGAATCTGA
Found at i:18974533 original size:33 final size:33
Alignment explanation
Indices: 18974428--18974558 Score: 92
Period size: 33 Copynumber: 4.0 Consensus size: 33
18974418 GGTGAAGTTA
* * * *
18974428 TAGAAGTTGATGGGGAGGGTGATG-ATGAAGGGG
1 TAGAAGCTGATGAGGAAGGTGATGTAAG-AGGGG
* *
18974461 TAGAATCTGATG-GTGAAGGTGATCTGGAA-A-GGG
1 TAGAAGCTGATGAG-GAAGGTGA--TGTAAGAGGGG
*
18974494 TAGAAGCT-ATTGAGGAAGGTGATGTAGGAGGGG
1 TAGAAGCTGA-TGAGGAAGGTGATGTAAGAGGGG
* * *
18974527 TTGAAGCTGATGTGGAGGGTGATGTAAGAGGG
1 TAGAAGCTGATGAGGAAGGTGATGTAAGAGGG
18974559 TCTACTGTTA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
31 3 0.04
32 3 0.04
33 66 0.85
34 3 0.04
35 2 0.03
36 1 0.01
ACGTcount: A:0.28, C:0.03, G:0.46, T:0.23
Consensus pattern (33 bp):
TAGAAGCTGATGAGGAAGGTGATGTAAGAGGGG
Found at i:18974682 original size:51 final size:51
Alignment explanation
Indices: 18974596--18974705 Score: 148
Period size: 51 Copynumber: 2.2 Consensus size: 51
18974586 GAAGTTGCTG
* * *
18974596 CTGATGAATATGCTGATGATTTTGCAACATTAGATGGAGAGGATAATGTTA
1 CTGATGAATATGATGATAATTTTGCAACATCAGATGGAGAGGATAATGTTA
* * * * *
18974647 CTGGTGAATATGATGCTAATTTTGCAATATCAGATGGAGTGGATAATGTTG
1 CTGATGAATATGATGATAATTTTGCAACATCAGATGGAGAGGATAATGTTA
18974698 CTGATGAA
1 CTGATGAA
18974706 GTTACTGATA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (51 bp):
CTGATGAATATGATGATAATTTTGCAACATCAGATGGAGAGGATAATGTTA
Found at i:18975974 original size:52 final size:53
Alignment explanation
Indices: 18975917--18976052 Score: 193
Period size: 52 Copynumber: 2.6 Consensus size: 53
18975907 GTGGGATTTG
* * ** * * *
18975917 TATACTCACAATGGCACAGAGTCATCGGATCTCTTAATCCGTAAAGGA-TCCA
1 TATACTCACGATGACACTTAGTCATCGGACCTCTAAATCCATAAAGGATTCCA
*
18975969 TATACTCACGATGACACTTAGTCATCGGACCTCTAAATCCATAAAGGATTTCA
1 TATACTCACGATGACACTTAGTCATCGGACCTCTAAATCCATAAAGGATTCCA
18976022 TATACTCACGATGACACTTAGTCATCGGACC
1 TATACTCACGATGACACTTAGTCATCGGACC
18976053 CTTATTTCAT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
52 41 0.55
53 34 0.45
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (53 bp):
TATACTCACGATGACACTTAGTCATCGGACCTCTAAATCCATAAAGGATTCCA
Found at i:18983157 original size:52 final size:53
Alignment explanation
Indices: 18983101--18983227 Score: 141
Period size: 52 Copynumber: 2.4 Consensus size: 53
18983091 GTATAGTCTT
** * *
18983101 GATGACACAGAGTCATCGGACCTCTT-AATCCGTAAAGGA-TCCATATACACAC
1 GATGACACTTAGTCATCGGACCT-TTAAATCCATAAAAGATTCCATATACACAC
* * * *
18983153 GATGACACTTAGTCATCAGATCTTTAAATCCATAAAAGATTTCATATACTCAC
1 GATGACACTTAGTCATCGGACCTTTAAATCCATAAAAGATTCCATATACACAC
* *
18983206 TATGATACTTAGTCATCGGACC
1 GATGACACTTAGTCATCGGACC
18983228 CCTTTTTCAT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
51 2 0.03
52 30 0.49
53 29 0.48
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (53 bp):
GATGACACTTAGTCATCGGACCTTTAAATCCATAAAAGATTCCATATACACAC
Found at i:18986465 original size:40 final size:40
Alignment explanation
Indices: 18986405--18986555 Score: 223
Period size: 40 Copynumber: 3.8 Consensus size: 40
18986395 GGGAAATCTC
*
18986405 CTACTGCTTAGCAGGCTTTGAGCCGATGATATATTTCAAG
1 CTACGGCTTAGCAGGCTTTGAGCCGATGATATATTTCAAG
* * * *
18986445 CTACGGCTTAGCAGGTTTTGAGCCGGTGATCTATTTTAAG
1 CTACGGCTTAGCAGGCTTTGAGCCGATGATATATTTCAAG
* *
18986485 CTACGGCTTAGTAGGCTTTGAGCCGGTGATATATTTCAAG
1 CTACGGCTTAGCAGGCTTTGAGCCGATGATATATTTCAAG
18986525 CTACGGCTTTA-CAGGCTTTGAGCCGATGATA
1 CTACGGC-TTAGCAGGCTTTGAGCCGATGATA
18986556 GGATTCGGGC
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 96 0.97
41 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (40 bp):
CTACGGCTTAGCAGGCTTTGAGCCGATGATATATTTCAAG
Found at i:18986587 original size:80 final size:80
Alignment explanation
Indices: 18986413--18986594 Score: 208
Period size: 80 Copynumber: 2.3 Consensus size: 80
18986403 TCCTACTGCT
* * *
18986413 TAGCAGGCTTTGAGCCGATGATATATTTCAAGCTACGGCTTAGCAGGTTTTGAGCCGGTGATCTA
1 TAGCAGGCTTTGAGCCGATGATATATTTCAAGCTACGGCTTAGCAGGCTTTGAGCCGATGATCGA
* * *
18986478 TTTTAAGCTACGGCT
66 TTTCAAGCTACAGCC
* * *
18986493 TAGTAGGCTTTGAGCCGGTGATATATTTCAAGCTACGGCTTTA-CAGGCTTTGAGCCGATGATAG
1 TAGCAGGCTTTGAGCCGATGATATATTTCAAGCTACGGC-TTAGCAGGCTTTGAGCCGATGAT-C
** *
18986557 GA-TTCGGGCTATAGCC
64 GATTTCAAGCTACAGCC
18986573 TAGCAGG-TTATGAGCCGATGAT
1 TAGCAGGCTT-TGAGCCGATGAT
18986595 GTTGTAAAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
79 2 0.02
80 79 0.93
81 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (80 bp):
TAGCAGGCTTTGAGCCGATGATATATTTCAAGCTACGGCTTAGCAGGCTTTGAGCCGATGATCGA
TTTCAAGCTACAGCC
Found at i:18993867 original size:7 final size:7
Alignment explanation
Indices: 18993857--18993909 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
18993847 ACATATTACT
18993857 TTTAGGG
1 TTTAGGG
*
18993864 TTTAAGG
1 TTTAGGG
*
18993871 TTTAAGG
1 TTTAGGG
*
18993878 CTTAGGG
1 TTTAGGG
*
18993885 CTTAGGG
1 TTTAGGG
18993892 TTTAGGG
1 TTTAGGG
18993899 TTTAGGG
1 TTTAGGG
18993906 TTTA
1 TTTA
18993910 AGGTACTGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.19, C:0.04, G:0.36, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:18998998 original size:3 final size:3
Alignment explanation
Indices: 18998990--18999036 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
18998980 CAGAGAGATA
*
18998990 ATG ATG ATG ATG ATG ATG ATG ATA ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
18999037 CCGATCTTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:19001035 original size:41 final size:40
Alignment explanation
Indices: 19000988--19001074 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 40
19000978 CATATTTAGC
19000988 ATTCATAATAAGCATTAGATACTTAGTTTTTATATTTTCTA
1 ATTCATAATAAGCATTAGATACTTAGTTTTTATA-TTTCTA
19001029 ATTCATAATAAGCATTAGATACTTAGTTTTTATATTTCTA
1 ATTCATAATAAGCATTAGATACTTAGTTTTTATATTTCTA
*
19001069 ACTCAT
1 ATTCAT
19001075 TGTTGTTTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 11 0.24
41 34 0.76
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.47
Consensus pattern (40 bp):
ATTCATAATAAGCATTAGATACTTAGTTTTTATATTTCTA
Found at i:19005249 original size:21 final size:21
Alignment explanation
Indices: 19005223--19005269 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
19005213 GGTTGGTTTG
* *
19005223 AAGGACAAAAAGAGGAAGCGC
1 AAGGACAAAAAGAAGAAACGC
19005244 AAGGACAAAAAGAAGAAACGC
1 AAGGACAAAAAGAAGAAACGC
19005265 AAGGA
1 AAGGA
19005270 GGAATGGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.13, G:0.30, T:0.00
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAACGC
Found at i:19005427 original size:34 final size:34
Alignment explanation
Indices: 19005389--19005454 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
19005379 CTGTAGTATA
*
19005389 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCCTGCATCTA-CAATGTCATTGCATTTTT
** *
19005423 ATTGTTGCTGCATCTACATTGTCATTGCATTT
1 ATTGTCCCTGCATCTACAATGTCATTGCATTT
19005455 CCATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 25 0.93
35 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (34 bp):
ATTGTCCCTGCATCTACAATGTCATTGCATTTTT
Found at i:19009616 original size:84 final size:85
Alignment explanation
Indices: 19009472--19009638 Score: 219
Period size: 84 Copynumber: 2.0 Consensus size: 85
19009462 GCTTCACGTA
* * * * * *
19009472 CTTGTGTTGTTGCAGGTATGTCACAGGATCATCCGAAATTGGATTTTGACCTTATCTTTGACATT
1 CTTGTATTGTTGCAAGTATGTCACAGGATAATCCGAAATTGGATTCTAACCTTATCTTTGACATC
* *
19009537 GTCTTACTTATGGTGAAATG
66 ATCTTACATATGGTGAAATG
* * * *
19009557 CTTGTATTGTTGCAAGTATGTCATATGATAATTCG-AATTGGATTCTAACCTTGTCTTTGACATC
1 CTTGTATTGTTGCAAGTATGTCACAGGATAATCCGAAATTGGATTCTAACCTTATCTTTGACATC
19009621 ATCTTACATATGGTGAAA
66 ATCTTACATATGGTGAAA
19009639 GCAAATCCTA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
84 41 0.59
85 29 0.41
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (85 bp):
CTTGTATTGTTGCAAGTATGTCACAGGATAATCCGAAATTGGATTCTAACCTTATCTTTGACATC
ATCTTACATATGGTGAAATG
Found at i:19012288 original size:20 final size:20
Alignment explanation
Indices: 19012263--19012300 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
19012253 GGAGAAGAAT
19012263 TAAATCTTGCTAACAAGTAC
1 TAAATCTTGCTAACAAGTAC
19012283 TAAATCTTGCTAACAAGT
1 TAAATCTTGCTAACAAGT
19012301 TTACAACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (20 bp):
TAAATCTTGCTAACAAGTAC
Found at i:19021264 original size:27 final size:27
Alignment explanation
Indices: 19021230--19021284 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
19021220 AGTAGCAGAA
* *
19021230 CAAACATTATATGCAATCTCTCAGTTT
1 CAAACATTATATGCAATCGCCCAGTTT
19021257 CAAACATTATATGCAATCGCCCAGTTT
1 CAAACATTATATGCAATCGCCCAGTTT
19021284 C
1 C
19021285 TCTCATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (27 bp):
CAAACATTATATGCAATCGCCCAGTTT
Found at i:19022636 original size:22 final size:22
Alignment explanation
Indices: 19022604--19022655 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
19022594 TAGGAAGTGT
19022604 GCTTT-CACCTTCTCTCCCGGC
1 GCTTTCCACCTTCTCTCCCGGC
19022625 GCTTTCCACCTTCTCTCCCGGC
1 GCTTTCCACCTTCTCTCCCGGC
19022647 GCTTTCCAC
1 GCTTTCCAC
19022656 ACACTTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.06, C:0.48, G:0.13, T:0.33
Consensus pattern (22 bp):
GCTTTCCACCTTCTCTCCCGGC
Found at i:19035492 original size:12 final size:12
Alignment explanation
Indices: 19035477--19035505 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
19035467 TCAAGACGAG
19035477 GAAGAGAAAGAA
1 GAAGAGAAAGAA
19035489 GAAGAGAAAGAA
1 GAAGAGAAAGAA
19035501 GAAGA
1 GAAGA
19035506 AGAACCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAAGAGAAAGAA
Found at i:19036573 original size:20 final size:20
Alignment explanation
Indices: 19036548--19036593 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
19036538 TCACTTGAAA
*
19036548 AATAAA-AAAATGAGAAAAAG
1 AATAAAGAAAAAG-GAAAAAG
*
19036568 AATAAAGAAAAAGGAAACAG
1 AATAAAGAAAAAGGAAAAAG
19036588 AATAAA
1 AATAAA
19036594 TTGCTGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (20 bp):
AATAAAGAAAAAGGAAAAAG
Found at i:19045869 original size:95 final size:95
Alignment explanation
Indices: 19045695--19045888 Score: 300
Period size: 95 Copynumber: 2.0 Consensus size: 95
19045685 CAAATAAACC
* *
19045695 TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTTATTTAAAGTATAATTTGTTCCCATTATA
1 TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTGATTTAAAGTATAATTTGTTCACATTATA
* * *
19045760 TCATTTTTGACATGCATTTTTAGTATTTTA
66 CCATTTTAGACATGCATTTTTAGCATTTTA
* * *
19045790 TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTGATTTAGAGTATAATTTGTTCACTTTGTA
1 TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTGATTTAAAGTATAATTTGTTCACATTATA
19045855 CCATGTTTAG-CATGCATTTTTAGCATTTTA
66 CCAT-TTTAGACATGCATTTTTAGCATTTTA
19045885 TATT
1 TATT
19045889 TGTAATTGCA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 86 0.96
96 4 0.04
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (95 bp):
TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTGATTTAAAGTATAATTTGTTCACATTATA
CCATTTTAGACATGCATTTTTAGCATTTTA
Found at i:19050282 original size:18 final size:18
Alignment explanation
Indices: 19050256--19050296 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
19050246 GCAAGCACAT
* *
19050256 CATGATCAGATGCAGTCA
1 CATGCTCAGATGCAATCA
19050274 CATGCTCAGATGCAATCA
1 CATGCTCAGATGCAATCA
19050292 CATGC
1 CATGC
19050297 AGCCACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (18 bp):
CATGCTCAGATGCAATCA
Found at i:19068045 original size:12 final size:12
Alignment explanation
Indices: 19068028--19068090 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
19068018 GGGTATTGAG
19068028 GAAGAGAAAGAA
1 GAAGAGAAAGAA
19068040 GAAGAGAAAG-A
1 GAAGAGAAAGAA
* *
19068051 GGAGAAAAAGGAA
1 GAAGAGAAA-GAA
*
19068064 GAAGAAAAAGAA
1 GAAGAGAAAGAA
*
19068076 TG-AGAGAAGGAA
1 -GAAGAGAAAGAA
19068088 GAA
1 GAA
19068091 ATTTTATTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 9 0.21
12 23 0.55
13 10 0.24
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (12 bp):
GAAGAGAAAGAA
Found at i:19068085 original size:24 final size:23
Alignment explanation
Indices: 19068025--19068090 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
19068015 TGTGGGTATT
* *
19068025 GAGGAAGAGAAAGAAGAAGAGAAA
1 GAGG-AGAGAAGGAAGAAGAAAAA
*
19068049 GAGGAGAAAAAGGAAGAAGAAAAA
1 GAGGAG-AGAAGGAAGAAGAAAAA
*
19068073 GAATGAGAGAAGGAAGAA
1 G-AGGAGAGAAGGAAGAA
19068091 ATTTTATTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.06
24 29 0.83
25 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (23 bp):
GAGGAGAGAAGGAAGAAGAAAAA
Found at i:19072850 original size:24 final size:25
Alignment explanation
Indices: 19072818--19072874 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
19072808 ACTTTGTCTA
*
19072818 GGCTCGTAAAAGCTAA-CCTATTTG
1 GGCTCGTAAAAGCTAATCCTATCTG
* *
19072842 GGCTCGTAAGAGCTAATTCTATCTG
1 GGCTCGTAAAAGCTAATCCTATCTG
19072867 GGCTCGTA
1 GGCTCGTA
19072875 TGAGCTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (25 bp):
GGCTCGTAAAAGCTAATCCTATCTG
Found at i:19072869 original size:25 final size:24
Alignment explanation
Indices: 19072818--19072882 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 24
19072808 ACTTTGTCTA
* *
19072818 GGCTCGTAAAAGCTAACCTATTTG
1 GGCTCGTAAGAGCTAACCTATCTG
*
19072842 GGCTCGTAAGAGCTAATTCTATCTG
1 GGCTCGTAAGAGCTAA-CCTATCTG
*
19072867 GGCTCGTATGAGCTAA
1 GGCTCGTAAGAGCTAA
19072883 AATCTGGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 15 0.42
25 21 0.58
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAACCTATCTG
Found at i:19074105 original size:37 final size:36
Alignment explanation
Indices: 19074059--19074207 Score: 172
Period size: 37 Copynumber: 4.0 Consensus size: 36
19074049 AGCCCGATTC
* * * *
19074059 CACCAGCACGAAACCTGCTAGGCACACAACTCGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGC-CGAATA
*
19074096 CACCGGCACGAAGCCTGCTAAGCACATAGCCTGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAGCC-GAATA
*
19074133 CATCGGCACGAAGCCTGCTAGGCACATAGCCCGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAG-CCGAATA
* * * *
19074170 CACTGGCATGAAGCCTACTAGGAACATAGCCCGAATA
1 CACCGGCACGAAGCCTGCTAGGCACATAG-CCGAATA
19074207 C
1 C
19074208 TTAGATGCAA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
36 1 0.01
37 95 0.97
38 2 0.02
ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13
Consensus pattern (36 bp):
CACCGGCACGAAGCCTGCTAGGCACATAGCCGAATA
Found at i:19074155 original size:74 final size:74
Alignment explanation
Indices: 19074064--19074207 Score: 198
Period size: 74 Copynumber: 1.9 Consensus size: 74
19074054 GATTCCACCA
* * * *
19074064 GCACGAAACCTGCTAGGCACACAACTCGAATACACCGGCACGAAGCCTGCTAAGCACATAGCCTG
1 GCACGAAACCTGCTAGGCACACAACCCGAATACACCGGCACGAAGCCTACTAAGAACATAGCCCG
19074129 AATACATCG
66 AATACATCG
* * * * * *
19074138 GCACGAAGCCTGCTAGGCACATAGCCCGAATACACTGGCATGAAGCCTACTAGGAACATAGCCCG
1 GCACGAAACCTGCTAGGCACACAACCCGAATACACCGGCACGAAGCCTACTAAGAACATAGCCCG
19074203 AATAC
66 AATAC
19074208 TTAGATGCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (74 bp):
GCACGAAACCTGCTAGGCACACAACCCGAATACACCGGCACGAAGCCTACTAAGAACATAGCCCG
AATACATCG
Found at i:19077261 original size:17 final size:17
Alignment explanation
Indices: 19077235--19077267 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19077225 TCTTCAAAAC
*
19077235 TTCCCTCATTTTGAAGG
1 TTCCCCCATTTTGAAGG
19077252 TTCCCCCATTTTGAAG
1 TTCCCCCATTTTGAAG
19077268 TGTTTGGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (17 bp):
TTCCCCCATTTTGAAGG
Found at i:19090421 original size:44 final size:45
Alignment explanation
Indices: 19090371--19090458 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
19090361 GTGTGTGTGA
* * *
19090371 CTTCAATCTGTCCTTGTGGATTAGGGGTA-AAGAGTGGATGGTGG
1 CTTCAATCTGCCCCTCTGGATTAGGGGTAGAAGAGTGGATGGTGG
*
19090415 CTTCAATCTGCCCCTCTGGATTAGGGGTAGAAGATTGGATGGTG
1 CTTCAATCTGCCCCTCTGGATTAGGGGTAGAAGAGTGGATGGTG
19090459 ATGTTCACTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 26 0.67
45 13 0.33
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.31
Consensus pattern (45 bp):
CTTCAATCTGCCCCTCTGGATTAGGGGTAGAAGAGTGGATGGTGG
Found at i:19090864 original size:189 final size:189
Alignment explanation
Indices: 19090602--19091074 Score: 635
Period size: 189 Copynumber: 2.5 Consensus size: 189
19090592 TTTAGATTTA
* * * * *
19090602 CTTCATTATTTTCATCCGACCGACACTGTAATTTAGGGGTATAGGATTCTGGTGCTTCACTCCAG
1 CTTCATTATTTTCATCCGACC--CACTGCAACTCAGGGGTATAGGATTCTGCTGCTTCACTCCAC
* * * *
19090667 TCCACTGTAACCTCAGGGATGTTGAGATCTACTACCTGTTTTAACCTACTTCTCTTTACCTCACC
64 TCCACTGTAACCTCAGGGACGTTGAGATCTACTACCTATTTTAACCCACTTCTCTATACCTCACC
*
19090732 AAGAAGATGGGATTTGAAGATTCAATCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTG
129 AAGAAGATAGGATTTGAAGATTCAATCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTG
* * *
19090793 CTTCATTATTTTCATCCGACCCAATGCAACTCAGGGGTATAGAATTCTACTGCTTCACTCCACTC
1 CTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGCTGCTTCACTCCACTC
* * * * * * * *
19090858 CACTGTAACTTGAGGGGCATTGAGATCTGCTACCTATTTTAACCCATTTCTCTATACCTTACCAG
66 CACTGTAACCTCAGGGACGTTGAGATCTACTACCTATTTTAACCCACTTCTCTATACCTCACCAA
*
19090923 GAAGATAGGATTTGAAGATTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTG
131 GAAGATAGGATTTGAAGATTCAATCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTG
* * * *
19090982 CTTCATTATTTTTAAT-CGACCCACTGCAACTCAAGGCTATAGGATTTTGGC-GCTTCACTCCAC
1 CTTCATTA-TTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCT-GCTGCTTCACTCCAC
* * *
19091045 TCCACTATAACCTCAAGGACGTTAAGATCT
64 TCCACTGTAACCTCAGGGACGTTGAGATCT
19091075 GCTTTGTTGT
Statistics
Matches: 244, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
189 216 0.89
190 7 0.03
191 21 0.09
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (189 bp):
CTTCATTATTTTCATCCGACCCACTGCAACTCAGGGGTATAGGATTCTGCTGCTTCACTCCACTC
CACTGTAACCTCAGGGACGTTGAGATCTACTACCTATTTTAACCCACTTCTCTATACCTCACCAA
GAAGATAGGATTTGAAGATTCAATCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTG
Found at i:19091056 original size:94 final size:93
Alignment explanation
Indices: 19090752--19091078 Score: 282
Period size: 94 Copynumber: 3.5 Consensus size: 93
19090742 GATTTGAAGA
* * * *
19090752 TTCAATCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTGCTTCATTATTTTCATCCGACCCAA
1 TTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCTGCTTCATTATTTTAAT-CGACCCAC
* * * *
19090817 TGCAACTCAGGGGTATAGAATTCT-ACTGC
65 TGCAACTCAAGGATATAGGATTTTGAC-GC
* * * * * * * * * ** *
19090846 TTCACTCCACTCCACTGTAACTTGAGGGGCATTGAGATCTGCTAC-CTATTTTAACCCATTTCTC
1 TTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCTGCTTCATTATTTTAATCGA-CCCAC
** * * * * *
19090910 TATACCTTACCAGGAAGATAGGA-TTTGAAGA
65 TGCAAC-T-CAAGG-ATATAGGATTTTGACGC
*
19090941 TTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTGCTTCATTATTTTTAATCGACCCAC
1 TTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCTGCTTCATTA-TTTTAATCGACCCAC
* *
19091006 TGCAACTCAAGGCTATAGGATTTTGGCGC
65 TGCAACTCAAGGATATAGGATTTTGACGC
* *
19091035 TTCACTCCACTCCACTATAACCTCAAGGACGTTAAGATCTGCTT
1 TTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCTGCTT
19091079 TGTTGTTTTA
Statistics
Matches: 173, Mismatches: 52, Indels: 16
0.72 0.22 0.07
Matches are distributed among these distances:
92 2 0.01
93 17 0.10
94 88 0.51
95 45 0.26
96 13 0.08
97 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (93 bp):
TTCACTCCACTCCACTGTAACCTCAAGGACGTTGAGATCTGCTTCATTATTTTAATCGACCCACT
GCAACTCAAGGATATAGGATTTTGACGC
Found at i:19091276 original size:49 final size:49
Alignment explanation
Indices: 19091209--19092120 Score: 850
Period size: 49 Copynumber: 18.7 Consensus size: 49
19091199 TTGCCTTTGT
* * * * *
19091209 GGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAAGATTCATCATTGT
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * *
19091258 GGCTTCAACCTTTTCCTTCACATCTCAAGGGTATAAGGTTCGTCGTTGC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * *
19091307 GGCTTCAACCTTTCCCTCCATATCTCTAGGGTACAAGATTCG-CTGTTGC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTC-GTTGC
* ** * * * * * *
19091356 GACTTCAATTTTTCCCATCAGATCTCTAAGGTATAAGGTTCGTTGTTGT
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * * *
19091405 AGCTTCAACCTTTCCCTCCACATCTTTAGGGTATAAGATTCGTCATTAC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
** * * *
19091454 AACTTCAATCTTTCCCAT--CATCT-TCAAGGTATAAGATTCGTCGTTGC
1 GGCTTCAACCTTTCCCTTCACATCTCT-AGGGTATAAGATTCGTCGTTGC
* * * *
19091501 GGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCGTCGTTAC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * * **
19091550 AGCTTCAACCTTTCCCTCCATATTTCTAGGGTATAAGATTCACCGTTGC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * *
19091599 GGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAAGGTTCGTTGTTG-
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * * * * * *
19091647 GGCTTCAACCTTTCCCTCCATATCTCTAAGATATAAGGTTTGTCATTAC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * ** * *
19091696 GGCTTCAACCTTTCCCTCCATATATCTAGGGTATAAGATTTTTCATTGT
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * **
19091745 GTCTTCAATCTTTCCCTTCACATCTCTAGGGTATAAGGTTCACCGTTGC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * * *
19091794 GGCTTTAACCTTTCCCTTAATATTTCTAGGGTATAAGATTCGCCGTTGC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * *
19091843 GGCTTCAATCTTTCCCTTCACATCTCTAGGGTATAA-AGTTCATCGTTGT
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGA-TTCGTCGTTGC
* * * * ** * *
19091892 GACTTCAACCTTTCCCTCCGCATCTCTAGGGTATAAGGTTCACCATTGT
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * *
19091941 GGCTTGAACCTTT-CCTTCCATATCTCTAGGGTATAAGATTCGCCGTTGC
1 GGCTTCAACCTTTCCCTT-CACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * * *
19091990 AGCTTCAATCTTTCCCTCCACATCTCTAGGGTATAAGATTCGCCGTTAC
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * * *
19092039 GGCCTCAATCTTTCCC-TCTACATCTCTAGGGTATAAGGTTCATTGTTGC
1 GGCTTCAACCTTTCCCTTC-ACATCTCTAGGGTATAAGATTCGTCGTTGC
* * * *
19092088 GGCTTCATCCTTTCCCTCCACGTCTTTAGGGTA
1 GGCTTCAACCTTTCCCTTCACATCTCTAGGGTA
19092121 CATGATTCAA
Statistics
Matches: 701, Mismatches: 149, Indels: 26
0.80 0.17 0.03
Matches are distributed among these distances:
46 1 0.00
47 39 0.06
48 46 0.07
49 610 0.87
50 5 0.01
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (49 bp):
GGCTTCAACCTTTCCCTTCACATCTCTAGGGTATAAGATTCGTCGTTGC
Found at i:19092757 original size:112 final size:112
Alignment explanation
Indices: 19092568--19092772 Score: 311
Period size: 112 Copynumber: 1.8 Consensus size: 112
19092558 ACTAACTGTC
* *
19092568 ATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAAGTGGATAAAATTGAATTTTATTGGAGGCAA
1 ATTTCAATGCAAAAATGCTTGAACAAGGTCGTAAAGTGGATAAAATTGAATTTTATTGGAGGCAA
* * *
19092633 AGCTCGCGTGAATGAAAAGATTAAAAATCATTAGTCCACTAACCATT
66 AACTCACATGAATGAAAAGATTAAAAATCATTAGTCCACTAACCATT
** * *
19092680 ATTTCAATGCAAATTTGCTTGAACAAGGTCGTAAGGTGGATAATATTGAATTTTATTGGAGGCAA
1 ATTTCAATGCAAAAATGCTTGAACAAGGTCGTAAAGTGGATAAAATTGAATTTTATTGGAGGCAA
**
19092745 AACTCACATGAATTTAAAGATTAAAAAT
66 AACTCACATGAATGAAAAGATTAAAAAT
19092773 GAAAAACATT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
112 82 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (112 bp):
ATTTCAATGCAAAAATGCTTGAACAAGGTCGTAAAGTGGATAAAATTGAATTTTATTGGAGGCAA
AACTCACATGAATGAAAAGATTAAAAATCATTAGTCCACTAACCATT
Found at i:19093094 original size:7 final size:7
Alignment explanation
Indices: 19093082--19093142 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
19093072 TGACCTCTCC
19093082 TTTTTCT
1 TTTTTCT
19093089 TTTTTCT
1 TTTTTCT
*
19093096 TCTCTTCT
1 T-TTTTCT
* *
19093104 CTTTTGT
1 TTTTTCT
*
19093111 TTTTTAT
1 TTTTTCT
19093118 TTTTT-T
1 TTTTTCT
19093124 CTTTTTCT
1 -TTTTTCT
*
19093132 TTTTCCT
1 TTTTTCT
19093139 TTTT
1 TTTT
19093143 GGGTGAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
6 1 0.02
7 37 0.84
8 6 0.14
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:19093108 original size:22 final size:21
Alignment explanation
Indices: 19093076--19093135 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
19093066 TCACCTTGAC
* *
19093076 CTCTCCTTTTTCTTTTTTCTT
1 CTCTTCTTTTTCTTTTTTATT
*
19093097 CTCTTCTCTTTTGTTTTTTATT
1 CTCTTCT-TTTTCTTTTTTATT
* *
19093119 TTTTTCTTTTTCTTTTT
1 CTCTTCTTTTTCTTTTT
19093136 CCTTTTTGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.47
22 17 0.53
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (21 bp):
CTCTTCTTTTTCTTTTTTATT
Found at i:19094796 original size:21 final size:19
Alignment explanation
Indices: 19094772--19094820 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
19094762 AAGAGACATA
19094772 AAAAGTAAATAAGTGAAAAAT
1 AAAAGTAAATAA-T-AAAAAT
* *
19094793 AAAAGGAAATAATATAAAT
1 AAAAGTAAATAATAAAAAT
19094812 AAAA-TAAAT
1 AAAAGTAAAT
19094821 GAAAACAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 1 0.04
21 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.20
Consensus pattern (19 bp):
AAAAGTAAATAATAAAAAT
Found at i:19095867 original size:14 final size:14
Alignment explanation
Indices: 19095820--19095861 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
19095810 AATACATTTG
19095820 TTTTTTCTTGTTGTC
1 TTTTTTCTT-TTGTC
* *
19095835 TTGTTGCTTTTGTC
1 TTTTTTCTTTTGTC
19095849 TTTTTTCTTTTGT
1 TTTTTTCTTTTGT
19095862 TATTTTCTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.00, C:0.12, G:0.14, T:0.74
Consensus pattern (14 bp):
TTTTTTCTTTTGTC
Found at i:19100284 original size:12 final size:13
Alignment explanation
Indices: 19100260--19100355 Score: 50
Period size: 12 Copynumber: 7.9 Consensus size: 13
19100250 ATTTATCTAC
*
19100260 AAGA-TAAACATT
1 AAGATTAAATATT
19100272 AA-ATTAAATATT
1 AAGATTAAATATT
*
19100284 AAGA-TAATCATTTT
1 AAGATTAA--ATATT
*
19100298 AATATT-AA-ATT
1 AAGATTAAATATT
*
19100309 -A-ATAAAATAATT
1 AAGATTAAAT-ATT
19100321 AAGA-TAAATATT
1 AAGATTAAATATT
19100333 AA-ATTAAAT-TT
1 AAGATTAAATATT
*
19100344 AATATTAAATAT
1 AAGATTAAATAT
19100356 ATTAAAATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
9 2 0.03
10 3 0.05
11 8 0.12
12 35 0.54
13 7 0.11
14 9 0.14
15 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (13 bp):
AAGATTAAATATT
Found at i:19100322 original size:37 final size:37
Alignment explanation
Indices: 19100276--19100368 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 37
19100266 AACATTAAAT
*
19100276 TAAAT-ATTAAGATAATCATTTTAATATTAAA-TTAATA
1 TAAATAATTAAGATAAT-ATATTAA-ATTAAATTTAATA
19100313 -AAATAATTAAGATAA-ATATTAAATTAAATTTAATA
1 TAAATAATTAAGATAATATATTAAATTAAATTTAATA
*
19100348 TTAAATATATTAAAATAATAT
1 -TAAATA-ATTAAGATAATAT
19100369 TATTTTTGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
34 6 0.12
35 12 0.25
36 4 0.08
37 15 0.31
38 9 0.19
39 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (37 bp):
TAAATAATTAAGATAATATATTAAATTAAATTTAATA
Found at i:19100364 original size:17 final size:17
Alignment explanation
Indices: 19100269--19100353 Score: 58
Period size: 17 Copynumber: 5.1 Consensus size: 17
19100259 CAAGATAAAC
19100269 ATTAAATTAAATATTAA
1 ATTAAATTAAATATTAA
*
19100286 GA-TAATCATTTTAATATTAA
1 -ATTAA--A-TTAAATATTAA
19100306 ATT-AA-TAAA-A-T-A
1 ATTAAATTAAATATTAA
19100318 ATTAAGA-TAAATATTAA
1 ATTAA-ATTAAATATTAA
*
19100335 ATTAAATTTAATATTAA
1 ATTAAATTAAATATTAA
19100352 AT
1 AT
19100354 ATATTAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 21
0.69 0.04 0.27
Matches are distributed among these distances:
12 4 0.07
13 2 0.04
14 6 0.11
15 4 0.07
16 2 0.04
17 21 0.39
18 1 0.02
19 3 0.06
20 11 0.20
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTAAATTAAATATTAA
Found at i:19115288 original size:18 final size:19
Alignment explanation
Indices: 19115265--19115301 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
19115255 TCTGAAAACA
*
19115265 TTAACAAACCTT-ATAAGT
1 TTAACAAAACTTAATAAGT
19115283 TTAACAAAACTTAATAAGT
1 TTAACAAAACTTAATAAGT
19115302 GTTGAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (19 bp):
TTAACAAAACTTAATAAGT
Found at i:19116173 original size:4 final size:4
Alignment explanation
Indices: 19116164--19116198 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
19116154 ACACCATAAA
19116164 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
19116199 TTATGCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:19122934 original size:18 final size:19
Alignment explanation
Indices: 19122900--19122935 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19122890 CGGAAGGTAA
19122900 GGGTTTCGGGATAGGGTTG
1 GGGTTTCGGGATAGGGTTG
*
19122919 GGGTTT-GGGTTAGGGTT
1 GGGTTTCGGGATAGGGTT
19122936 AGGGATTGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.08, C:0.03, G:0.53, T:0.36
Consensus pattern (19 bp):
GGGTTTCGGGATAGGGTTG
Found at i:19123547 original size:30 final size:31
Alignment explanation
Indices: 19123495--19123557 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
19123485 TAGTAAAAAT
* *
19123495 AAAATTTTATTTTATTCTTTTAAAAATTATA
1 AAAATTTAATTTAATTCTTTTAAAAATTATA
19123526 AAAATTTAATTTAATTC-TTTAAAAATTATA
1 AAAATTTAATTTAATTCTTTTAAAAATTATA
19123556 AA
1 AA
19123558 GATAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (31 bp):
AAAATTTAATTTAATTCTTTTAAAAATTATA
Found at i:19126715 original size:2 final size:2
Alignment explanation
Indices: 19126708--19126741 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19126698 CCAGCACCCA
19126708 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19126742 TCCTAATGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19131562 original size:36 final size:36
Alignment explanation
Indices: 19131512--19131612 Score: 132
Period size: 36 Copynumber: 2.8 Consensus size: 36
19131502 GGTAACAAGC
* *
19131512 ATGACCTTTGGGTCAACAGGGAG-AAACATGAACATA
1 ATGACCTTTAGGTCAACAGGGAGTAAA-ACGAACATA
* *
19131548 ATGACCTTTAGGTCAACAGGGAGTAAAACGAGCATT
1 ATGACCTTTAGGTCAACAGGGAGTAAAACGAACATA
* *
19131584 ATAACCTTTAGGTCAATAGGGAGTAAAAC
1 ATGACCTTTAGGTCAACAGGGAGTAAAAC
19131613 AAATAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
36 55 0.95
37 3 0.05
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.22
Consensus pattern (36 bp):
ATGACCTTTAGGTCAACAGGGAGTAAAACGAACATA
Found at i:19144568 original size:17 final size:17
Alignment explanation
Indices: 19144548--19144605 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
19144538 ATTGTCATCA
19144548 CATTTCTTTTGTCCTTG
1 CATTTCTTTTGTCCTTG
19144565 CATTT-TTATTGTCAC-TG
1 CATTTCTT-TTGTC-CTTG
*
19144582 CATTTGCATTTT-TCATTG
1 CATTT-C-TTTTGTCCTTG
19144600 CATTTC
1 CATTTC
19144606 CATATATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
16 2 0.06
17 18 0.53
18 10 0.29
19 2 0.06
20 2 0.06
ACGTcount: A:0.14, C:0.21, G:0.10, T:0.55
Consensus pattern (17 bp):
CATTTCTTTTGTCCTTG
Found at i:19145454 original size:20 final size:21
Alignment explanation
Indices: 19145429--19145467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19145419 TCATTTTTTA
*
19145429 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
19145449 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
19145468 TGCTCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:19152433 original size:36 final size:36
Alignment explanation
Indices: 19152386--19152460 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
19152376 CTCAAAAGCT
*
19152386 AGGTTGAAGAAGATAATATTGTAAAATGGGAGACTA
1 AGGTTGAAGAAGATAATATTGCAAAATGGGAGACTA
19152422 AGGTTGAAGAAGATAATATTGCAAAATGGGAGACTA
1 AGGTTGAAGAAGATAATATTGCAAAATGGGAGACTA
19152458 AGG
1 AGG
19152461 GAAAGAGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.44, C:0.04, G:0.29, T:0.23
Consensus pattern (36 bp):
AGGTTGAAGAAGATAATATTGCAAAATGGGAGACTA
Found at i:19152833 original size:37 final size:37
Alignment explanation
Indices: 19152787--19152862 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
19152777 TATTCCTGTG
* *
19152787 GCGACAGTTTTGGGTGTAATCTGGAAGTGCTCACGCA
1 GCGACAGTTTTGGGCGTAATCTAGAAGTGCTCACGCA
* *
19152824 GCGATAGTTTTGGGCGTAATCTAGAAGTGCTCATGCA
1 GCGACAGTTTTGGGCGTAATCTAGAAGTGCTCACGCA
19152861 GC
1 GC
19152863 AACATTAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (37 bp):
GCGACAGTTTTGGGCGTAATCTAGAAGTGCTCACGCA
Found at i:19153848 original size:17 final size:17
Alignment explanation
Indices: 19153809--19153857 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
19153799 ATATATATGG
* **
19153809 AAATGCAGTGACAATGT
1 AAATGCAGCGACAATAA
*
19153826 AGATGCAGCGACAATAA
1 AAATGCAGCGACAATAA
*
19153843 AAATGCAGGGACAAT
1 AAATGCAGCGACAAT
19153858 TATACTACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.16
Consensus pattern (17 bp):
AAATGCAGCGACAATAA
Found at i:19154553 original size:12 final size:12
Alignment explanation
Indices: 19154536--19154560 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19154526 TTTGTCTCGA
19154536 CATCTTTTTCTT
1 CATCTTTTTCTT
19154548 CATCTTTTTCTT
1 CATCTTTTTCTT
19154560 C
1 C
19154561 CTCCACACGA
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:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (12 bp):
CATCTTTTTCTT
Found at i:19157650 original size:37 final size:37
Alignment explanation
Indices: 19157600--19157675 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
19157590 GCAATTTAAA
*
19157600 AAATATTTATGCAGCG-TCAGTCTTGGATGCATTCTGG
1 AAATATTTATGCAGCGAT-AGTCTTGGATGCAATCTGG
* *
19157637 AAATATTCT-TGCAGCGATAGTTTTGGGTGCAATCTGG
1 AAATATT-TATGCAGCGATAGTCTTGGATGCAATCTGG
19157674 AA
1 AA
19157676 GTGCTCATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 32 0.94
38 2 0.06
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (37 bp):
AAATATTTATGCAGCGATAGTCTTGGATGCAATCTGG
Found at i:19157692 original size:37 final size:37
Alignment explanation
Indices: 19157651--19157722 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
19157641 ATTCTTGCAG
*
19157651 CGATAGTTTTGGGTGCAATCTGGAAGTGCTCATGCGA
1 CGATAGTTTTGGGTGCAATCTAGAAGTGCTCATGCGA
19157688 CGATAGTTTTGGGTGCAATCTAGAAGTGCTCATGC
1 CGATAGTTTTGGGTGCAATCTAGAAGTGCTCATGC
19157723 AACAACATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.31
Consensus pattern (37 bp):
CGATAGTTTTGGGTGCAATCTAGAAGTGCTCATGCGA
Found at i:19160932 original size:22 final size:22
Alignment explanation
Indices: 19160904--19160969 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
19160894 AAAAGAACAA
19160904 ATAGAGTACTCTATTCCTAGTT
1 ATAGAGTACTCTATTCCTAGTT
19160926 ATAGAGTACTCTATTCCTAGTT
1 ATAGAGTACTCTATTCCTAGTT
19160948 ATAGAGTACTCTATTCCTAGTT
1 ATAGAGTACTCTATTCCTAGTT
19160970 TACTCGAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (22 bp):
ATAGAGTACTCTATTCCTAGTT
Found at i:19180292 original size:24 final size:24
Alignment explanation
Indices: 19180263--19180313 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
19180253 CTAGACAGAA
19180263 TTAGCTCTTACAAGCCCAGAAAGG
1 TTAGCTCTTACAAGCCCAGAAAGG
**
19180287 TTAGCTCTTATGAGCCCAGAAAGG
1 TTAGCTCTTACAAGCCCAGAAAGG
19180311 TTA
1 TTA
19180314 ACTAGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (24 bp):
TTAGCTCTTACAAGCCCAGAAAGG
Found at i:19184630 original size:26 final size:26
Alignment explanation
Indices: 19184594--19184647 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
19184584 ATTCTGGGTT
*
19184594 CAATTCTGGACACGTTCATGCAGCGA
1 CAATTATGGACACGTTCATGCAGCGA
* *
19184620 CAATTATGGACATGTTCATGCAGTGA
1 CAATTATGGACACGTTCATGCAGCGA
19184646 CA
1 CA
19184648 TTCCTGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (26 bp):
CAATTATGGACACGTTCATGCAGCGA
Found at i:19184698 original size:37 final size:38
Alignment explanation
Indices: 19184651--19184722 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
19184641 AGTGACATTC
* *
19184651 CTGGGTGCAA-TTAAAGAATACTTATGTAGCGATAGTT
1 CTGGATGCAATTTAAAGAATACTTATGCAGCGATAGTT
* *
19184688 CTGGATGCAATTTGAAGAATATTTATGCAGCGATA
1 CTGGATGCAATTTAAAGAATACTTATGCAGCGATA
19184723 ATCTTGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 9 0.30
38 21 0.70
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (38 bp):
CTGGATGCAATTTAAAGAATACTTATGCAGCGATAGTT
Found at i:19188725 original size:26 final size:26
Alignment explanation
Indices: 19188664--19188718 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
19188654 AATTCTAGGC
19188664 ACAATTCTGGACACGTTCATGCAGCG
1 ACAATTCTGGACACGTTCATGCAGCG
* *
19188690 ACAATTCTGGACATGTTCATGCAGTG
1 ACAATTCTGGACACGTTCATGCAGCG
19188716 ACA
1 ACA
19188719 TTCCTGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (26 bp):
ACAATTCTGGACACGTTCATGCAGCG
Found at i:19188876 original size:36 final size:36
Alignment explanation
Indices: 19188829--19188899 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
19188819 CGGCAATAGT
* * * *
19188829 TTTGGGTGCAATCGAGAAGTGGTCATGCAGCGACAG
1 TTTGGGCGCAATCGAAAAGTGCTCATGCAACGACAG
*
19188865 TTTGGGCGCAATCTAAAAGTGCTCATGCAACGACA
1 TTTGGGCGCAATCGAAAAGTGCTCATGCAACGACA
19188900 TTAGTAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (36 bp):
TTTGGGCGCAATCGAAAAGTGCTCATGCAACGACAG
Found at i:19199217 original size:15 final size:15
Alignment explanation
Indices: 19199194--19199227 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19199184 GAGAAGGATA
* *
19199194 AAGACAAGGAATAAG
1 AAGAAAAGGAAGAAG
19199209 AAGAAAAGGAAGAAG
1 AAGAAAAGGAAGAAG
19199224 AAGA
1 AAGA
19199228 GCCTCCCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.29, T:0.03
Consensus pattern (15 bp):
AAGAAAAGGAAGAAG
Found at i:19199663 original size:17 final size:18
Alignment explanation
Indices: 19199641--19199681 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
19199631 TTAGTTTTAA
19199641 TGCATTCTT-ATTGTGC-C
1 TGCATTCTTAATTGT-CAC
19199658 TGCATT-TTAATTGTCAC
1 TGCATTCTTAATTGTCAC
19199675 TGCATTC
1 TGCATTC
19199682 CTTTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (18 bp):
TGCATTCTTAATTGTCAC
Found at i:19203717 original size:52 final size:52
Alignment explanation
Indices: 19203494--19203832 Score: 387
Period size: 53 Copynumber: 6.5 Consensus size: 52
19203484 CAAAAGGGCT
* * * * * *
19203494 GATGACTCTCTGTCATCGTGAGTTACATGAATCCTATTACGGATTA-AAGGTTC
1 GATGACTATGTGTCATCGTGAG-TATATGAATCCT-TTACGAATTATGAGGTCC
* * * *
19203547 GATTACTCTGTGTCATCATGAGTTATATGAATCCTTTACGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAG-TATATGAATCCTTTACGAATTATGAGGTCC
* *
19203600 GATGACTATGTGTCATCATGAGTTATATGAATCATTTACGAATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAG-TATATGAATCCTTTACGAATTATGAGGTCC
* * *
19203653 GATGACTATGTGTCATCGTGAGTATCTAAATCCTTTATGAATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCC
* * * **
19203705 GATGACTATGTGTCATCGTGAGTATATGAATCTTTTAC-AGATT-TCAAGTTT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGA-ATTATGAGGTCC
* * * * *
19203756 AATGACTATGTGTCATTGTGACTATATGAATCCTTTATGAATTATGAGGTCT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCC
19203808 GATGACTATGTGTCATCGTGAGTAT
1 GATGACTATGTGTCATCGTGAGTAT
19203833 TAAATGAGAA
Statistics
Matches: 248, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
51 41 0.17
52 101 0.41
53 106 0.43
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCC
Found at i:19203802 original size:103 final size:104
Alignment explanation
Indices: 19203494--19203832 Score: 371
Period size: 103 Copynumber: 3.2 Consensus size: 104
19203484 CAAAAGGGCT
* * * * * * * * *
19203494 GATGACTCTCTGTCATCGTGAGTTACATGAATCCTATTACGGATTA--AAGGTTCGATTACTCTG
1 GATGACTATGTGTCATCGTGAG-TATATGAATCAT-TTACGAATTATCAA-GTCCAATGACTATG
* * * *
19203557 TGTCATCATGAGTTATATGAATCCTTTACGGATTATGAGGTCC
63 TGTCATCGTGA-CTATATGAATCCTTTATGAATTATGAGGTCC
* * * *
19203600 GATGACTATGTGTCATCATGAGTTATATGAATCATTTACGAATTATGAGGTCCGATGACTATGTG
1 GATGACTATGTGTCATCGTGAG-TATATGAATCATTTACGAATTATCAAGTCCAATGACTATGTG
* * *
19203665 TCATCGTGAGTATCTAAATCCTTTATGAATTATGAGGTCC
65 TCATCGTGACTATATGAATCCTTTATGAATTATGAGGTCC
* **
19203705 GATGACTATGTGTCATCGTGAGTATATGAATCTTTTAC-AGATT-TCAAGTTTAATGACTATGTG
1 GATGACTATGTGTCATCGTGAGTATATGAATCATTTACGA-ATTATCAAGTCCAATGACTATGTG
* *
19203768 TCATTGTGACTATATGAATCCTTTATGAATTATGAGGTCT
65 TCATCGTGACTATATGAATCCTTTATGAATTATGAGGTCC
19203808 GATGACTATGTGTCATCGTGAGTAT
1 GATGACTATGTGTCATCGTGAGTAT
19203833 TAAATGAGAA
Statistics
Matches: 202, Mismatches: 28, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
103 76 0.38
104 18 0.09
105 56 0.28
106 51 0.25
107 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (104 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCATTTACGAATTATCAAGTCCAATGACTATGTGT
CATCGTGACTATATGAATCCTTTATGAATTATGAGGTCC
Found at i:19204604 original size:21 final size:20
Alignment explanation
Indices: 19204570--19204618 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
19204560 GATTTGTTTC
**
19204570 GGTAGAAACTTCACTTGTATT
1 GGTAG-AACTTCACAGGTATT
19204591 GGTAGAACTGTCACAGGTATT
1 GGTAGAACT-TCACAGGTATT
*
19204612 GATAGAA
1 GGTAGAA
19204619 TTTTTCACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (20 bp):
GGTAGAACTTCACAGGTATT
Found at i:19205553 original size:23 final size:23
Alignment explanation
Indices: 19205487--19205812 Score: 398
Period size: 23 Copynumber: 14.4 Consensus size: 23
19205477 ATATTAATTC
*
19205487 TTTAAGCACAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
19205510 TTTAATCATAAAATCATATTAATA
1 TTTAAGCAT-AAATCACATTAATA
*
19205534 TTTAAGCACAAATCACATTAAT-
1 TTTAAGCATAAATCACATTAATA
19205556 TTTAAAGCATAAATCACATTAATA
1 TTT-AAGCATAAATCACATTAATA
* * * *
19205580 TTTGAGCACAAACCATATTAATA
1 TTTAAGCATAAATCACATTAATA
19205603 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
19205626 TTTAAGCATAAATCATATTTATA
1 TTTAAGCATAAATCACATTAATA
*
19205649 TTTAAGCATAAATTACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
19205672 TTTGAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
19205695 TTTAAGCAAAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
19205718 TTTGAGCACAAAT--C----ATA
1 TTTAAGCATAAATCACATTAATA
19205735 -TTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
*
19205757 CTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* *
19205780 TTTAATCATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
19205803 TTTAAGCATA
1 TTTAAGCATA
19205813 GATATAAGAA
Statistics
Matches: 258, Mismatches: 35, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
16 10 0.04
17 3 0.01
18 1 0.00
21 1 0.00
22 6 0.02
23 214 0.83
24 23 0.09
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:19205756 original size:85 final size:85
Alignment explanation
Indices: 19205650--19205810 Score: 241
Period size: 85 Copynumber: 1.9 Consensus size: 85
19205640 ATATTTATAT
* * * *
19205650 TTAAGCATAAATTACATTAATATTTGAGCACAAATCATATTAATATTTAAGCAAAAATCACATTA
1 TTAAGCATAAATCACATTAATACTTAAGCACAAATCACATTAATATTTAAGCAAAAATCACATTA
*
19205715 ATATTTGAGCACAAATCATA
66 ATATTTAAGCACAAATCATA
* * * *
19205735 TTAAGCATAAATCACATTAATACTTAAGCATAAATCACATTAATATTTAATCATAAATCATATTA
1 TTAAGCATAAATCACATTAATACTTAAGCACAAATCACATTAATATTTAAGCAAAAATCACATTA
19205800 ATATTTAAGCA
66 ATATTTAAGCA
19205811 TAGATATAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (85 bp):
TTAAGCATAAATCACATTAATACTTAAGCACAAATCACATTAATATTTAAGCAAAAATCACATTA
ATATTTAAGCACAAATCATA
Found at i:19205778 original size:62 final size:62
Alignment explanation
Indices: 19205676--19205800 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
19205666 TTAATATTTG
* * *
19205676 AGCACAAATCATATTAATATTTAAGCAAAAATCACATTAATATTTGAGCACAAATCATATTA
1 AGCACAAATCACATTAATACTTAAGCAAAAATCACATTAATATTTAAGCACAAATCATATTA
* * * *
19205738 AGCATAAATCACATTAATACTTAAGCATAAATCACATTAATATTTAATCATAAATCATATTA
1 AGCACAAATCACATTAATACTTAAGCAAAAATCACATTAATATTTAAGCACAAATCATATTA
19205800 A
1 A
19205801 TATTTAAGCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (62 bp):
AGCACAAATCACATTAATACTTAAGCAAAAATCACATTAATATTTAAGCACAAATCATATTA
Found at i:19205787 original size:39 final size:39
Alignment explanation
Indices: 19205696--19205777 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
19205686 ATATTAATAT
* * * *
19205696 TTAAGCAAAAATCACATTAATATTTGAGCACAAATCATA
1 TTAAGCATAAATCACATTAATACTTAAGCACAAATCACA
*
19205735 TTAAGCATAAATCACATTAATACTTAAGCATAAATCACA
1 TTAAGCATAAATCACATTAATACTTAAGCACAAATCACA
19205774 TTAA
1 TTAA
19205778 TATTTAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (39 bp):
TTAAGCATAAATCACATTAATACTTAAGCACAAATCACA
Found at i:19215061 original size:25 final size:23
Alignment explanation
Indices: 19215033--19215078 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
19215023 GTTGGATCCA
19215033 AATTAAATTCTAAAAAGATAATTAT
1 AATTAAA-TCTAAAAA-ATAATTAT
*
19215058 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
19215079 GCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAT
Found at i:19216871 original size:18 final size:19
Alignment explanation
Indices: 19216832--19216875 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
19216822 ATTGTATGGA
*
19216832 TATTGTATAATTTTTGTTT
1 TATTGTATAATTTTTGTAT
19216851 TATTGT-TAA-TTTTGCTAT
1 TATTGTATAATTTTTG-TAT
19216869 TATTGTA
1 TATTGTA
19216876 ACAACCCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 11 0.50
19 6 0.27
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.64
Consensus pattern (19 bp):
TATTGTATAATTTTTGTAT
Found at i:19217462 original size:18 final size:18
Alignment explanation
Indices: 19217435--19217516 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 18
19217425 CTCTCTCTAA
*
19217435 GGTTAGGGTTTTTTTAAG
1 GGTTAAGGTTTTTTTAAG
* *
19217453 GGTTAAGG--TTATTAGG
1 GGTTAAGGTTTTTTTAAG
19217469 GGTT-AGG-TTTTTTAAG
1 GGTTAAGGTTTTTTTAAG
* * * *
19217485 GTTTAGGGTATTTTCAAG
1 GGTTAAGGTTTTTTTAAG
19217503 GTGTTCAAGGTTTT
1 G-GTT-AAGGTTTT
19217517 CGACCGAAGC
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
15 3 0.06
16 19 0.40
17 2 0.04
18 15 0.32
19 2 0.04
20 6 0.13
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (18 bp):
GGTTAAGGTTTTTTTAAG
Found at i:19218584 original size:31 final size:31
Alignment explanation
Indices: 19218546--19218607 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
19218536 TGTCGAGGAG
*
19218546 AATGTGTGCTGCAAGGCAGTAGATGAAGATC
1 AATGTGTGCTGCAAGGCAATAGATGAAGATC
*
19218577 AATGTGTGCTGCAAGGCAATAGATGACGATC
1 AATGTGTGCTGCAAGGCAATAGATGAAGATC
19218608 GCATGGAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.23
Consensus pattern (31 bp):
AATGTGTGCTGCAAGGCAATAGATGAAGATC
Found at i:19219983 original size:85 final size:86
Alignment explanation
Indices: 19219834--19219998 Score: 244
Period size: 85 Copynumber: 1.9 Consensus size: 86
19219824 CAGATAAATT
* *
19219834 CGTAATTAATGAATTGCGCACTGCGATGGCCAGTAAAACCGTCAATAAATGTGCCCAGCACTAGT
1 CGTAATTAATGAATTGCACACTGCGATGGCCAGTAAAACCGACAATAAATGTGCCCAGCACTAGT
*
19219899 CGATATAACAAACAATAGATC
66 CGATAAAACAAACAATAGATC
* * *
19219920 CGTAA-TAATGAATTGCACCCTGCGTTGGCCGGT-AAACTCGACAATAAATGTGCCCAGCACTAG
1 CGTAATTAATGAATTGCACACTGCGATGGCCAGTAAAAC-CGACAATAAATGTGCCCAGCACTAG
*
19219983 TCGATAAAACAGACAA
65 TCGATAAAACAAACAA
19219999 ATAGGGTGCC
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
84 4 0.06
85 62 0.87
86 5 0.07
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (86 bp):
CGTAATTAATGAATTGCACACTGCGATGGCCAGTAAAACCGACAATAAATGTGCCCAGCACTAGT
CGATAAAACAAACAATAGATC
Found at i:19221798 original size:3 final size:3
Alignment explanation
Indices: 19221790--19221816 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19221780 ACTAAATCAT
19221790 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
19221817 ATTCTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19223100 original size:20 final size:20
Alignment explanation
Indices: 19223075--19223114 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19223065 TACCCAATTT
19223075 ATATATCACAATTTATATTC
1 ATATATCACAATTTATATTC
* *
19223095 ATATATTACAATTTCTATTC
1 ATATATCACAATTTATATTC
19223115 GAATCATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATATCACAATTTATATTC
Found at i:19223942 original size:72 final size:71
Alignment explanation
Indices: 19223810--19223989 Score: 209
Period size: 72 Copynumber: 2.5 Consensus size: 71
19223800 ACACACCAAT
* ** * *
19223810 TTGGCACCCAGTGCCTCATTGAAATGTCCGAAGTAATATGCACCCAGCGCTAATCGGTATATAAC
1 TTGGCACCCAGTGCCTCATCGAAACATCCGAAGTAATATGCACCCAACGCTAATCAG--TATAAC
19223875 CGAAG-AA
64 CGAAGAAA
* ** * * *
19223882 TTGGCACCCAATGCCTCATCGAAACATCCGAAGTAATATGTGCCCAATGCTTATCAGTATAACTG
1 TTGGCACCCAGTGCCTCATCGAAACATCCGAAGTAATATGCACCCAACGCTAATCAGTATAACCG
19223947 AAGTAAA
66 AAG-AAA
* *
19223954 TTGGCACCCAGTACCTCATCGGAACATCCGAAGTAA
1 TTGGCACCCAGTGCCTCATCGAAACATCCGAAGTAA
19223990 CCTGTACTTG
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
70 10 0.11
72 82 0.89
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (71 bp):
TTGGCACCCAGTGCCTCATCGAAACATCCGAAGTAATATGCACCCAACGCTAATCAGTATAACCG
AAGAAA
Found at i:19225702 original size:2 final size:2
Alignment explanation
Indices: 19225695--19225729 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19225685 AAATGATCAC
19225695 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19225730 CTTATTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:19225717 original size:17 final size:17
Alignment explanation
Indices: 19225695--19225727 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19225685 AAATGATCAC
19225695 ATATATATATATATATT
1 ATATATATATATATATT
19225712 ATATATATATATATAT
1 ATATATATATATATAT
19225728 ATCTTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:19229540 original size:18 final size:18
Alignment explanation
Indices: 19229517--19229566 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
19229507 ACCGACCCTC
19229517 AACCGAATTAATTCAATT
1 AACCGAATTAATTCAATT
*
19229535 AACCGAATTCGA-TCAATT
1 AACCGAATT-AATTCAATT
**
19229553 AAATGAATTAATTC
1 AACCGAATTAATTC
19229567 GATTTTGCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (18 bp):
AACCGAATTAATTCAATT
Found at i:19231127 original size:14 final size:13
Alignment explanation
Indices: 19231110--19231159 Score: 66
Period size: 14 Copynumber: 3.8 Consensus size: 13
19231100 AATAATTACA
19231110 TTTTTAAGAAATAG
1 TTTTTAA-AAATAG
19231124 TTTTTCAAAAATAG
1 TTTTT-AAAAATAG
19231138 TTTTTAAAAATAG
1 TTTTTAAAAATAG
*
19231151 -ATTTAAAAA
1 TTTTTAAAAA
19231160 AATAACAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.24
13 8 0.24
14 16 0.47
15 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (13 bp):
TTTTTAAAAATAG
Found at i:19235675 original size:30 final size:30
Alignment explanation
Indices: 19235640--19235700 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
19235630 CTACTTGTAA
19235640 TTGACTTTCTATTCGTTCAACTATTATATT
1 TTGACTTTCTATTCGTTCAACTATTATATT
19235670 TTGACTTTCTATTCGTTCAACTATTATATT
1 TTGACTTTCTATTCGTTCAACTATTATATT
19235700 T
1 T
19235701 CGATTTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (30 bp):
TTGACTTTCTATTCGTTCAACTATTATATT
Found at i:19236506 original size:29 final size:35
Alignment explanation
Indices: 19236434--19236527 Score: 143
Period size: 35 Copynumber: 2.7 Consensus size: 35
19236424 TTTTGTTGCT
* *
19236434 ATTCTTATTCGCATGTTAAGTATGTCATTATACTG
1 ATTCTGATTCGCATGTTAAGCATGTCATTATACTG
*
19236469 ATTCTGATTCGCATGTTAAGCATGTCATTATATTG
1 ATTCTGATTCGCATGTTAAGCATGTCATTATACTG
* *
19236504 ATTCCGATTCGCATGTAAAGCATG
1 ATTCTGATTCGCATGTTAAGCATG
19236528 CCACTGCGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (35 bp):
ATTCTGATTCGCATGTTAAGCATGTCATTATACTG
Found at i:19238975 original size:15 final size:15
Alignment explanation
Indices: 19238955--19238984 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19238945 AAGTCATTGC
*
19238955 ATGATGGGTCTATGT
1 ATGATGAGTCTATGT
19238970 ATGATGAGTCTATGT
1 ATGATGAGTCTATGT
19238985 TTGTCTCTAG
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:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (15 bp):
ATGATGAGTCTATGT
Found at i:19239286 original size:28 final size:27
Alignment explanation
Indices: 19239263--19239321 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
19239253 CTATCTTTGT
**
19239263 TAAAGAATGCCTTTGTGACAATCTCTA
1 TAAAGAACACCTTTGTGACAATCTCTA
* *
19239290 TAAAGGACACCTTTGTGACAATCCCTA
1 TAAAGAACACCTTTGTGACAATCTCTA
19239317 TAAAG
1 TAAAG
19239322 GATGCCTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (27 bp):
TAAAGAACACCTTTGTGACAATCTCTA
Found at i:19239302 original size:27 final size:27
Alignment explanation
Indices: 19239272--19239342 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
19239262 TTAAAGAATG
19239272 CCTTTGTGACAATCTCTATAAAGGACA
1 CCTTTGTGACAATCTCTATAAAGGACA
* **
19239299 CCTTTGTGACAATCCCTATAAAGGATG
1 CCTTTGTGACAATCTCTATAAAGGACA
* *
19239326 CCTTAGTGGCAATCTCT
1 CCTTTGTGACAATCTCT
19239343 GGATATGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (27 bp):
CCTTTGTGACAATCTCTATAAAGGACA
Found at i:19240488 original size:19 final size:19
Alignment explanation
Indices: 19240461--19240497 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19240451 ACATGTAATG
19240461 TTCACATCAATTTCACATA
1 TTCACATCAATTTCACATA
*
19240480 TTCAGATCAATTTCACAT
1 TTCACATCAATTTCACAT
19240498 GTTTTCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (19 bp):
TTCACATCAATTTCACATA
Found at i:19242044 original size:29 final size:30
Alignment explanation
Indices: 19241983--19242044 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
19241973 GGTAAATTGG
* *
19241983 AATCAATTTGAGTGATAAGGGGGATTACAC
1 AATCAATTTGAGTGAAAAAGGGGATTACAC
*
19242013 AATCAATTTGAGT-AAAAAGGGGATTGCAC
1 AATCAATTTGAGTGAAAAAGGGGATTACAC
19242042 AAT
1 AAT
19242045 TAAAGGGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (30 bp):
AATCAATTTGAGTGAAAAAGGGGATTACAC
Found at i:19246693 original size:26 final size:26
Alignment explanation
Indices: 19246657--19246709 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
19246647 CGATTATTTG
19246657 TTCCAATTTGGGCACCCGTCATTCGC
1 TTCCAATTTGGGCACCCGTCATTCGC
19246683 TTCCAATTTGGGCACCCGTCATTCGC
1 TTCCAATTTGGGCACCCGTCATTCGC
19246709 T
1 T
19246710 CTAGTACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.34, G:0.19, T:0.32
Consensus pattern (26 bp):
TTCCAATTTGGGCACCCGTCATTCGC
Found at i:19249570 original size:30 final size:30
Alignment explanation
Indices: 19249536--19249597 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
19249526 AATTAGAATC
*
19249536 AATTTGAGTGATAAAGG-GGATTACACAATT
1 AATTTGA-TGAAAAAGGAGGATTACACAATT
*
19249566 AATTTGATTAAAAAGGAGGATTACACAATT
1 AATTTGATGAAAAAGGAGGATTACACAATT
19249596 AA
1 AA
19249598 AGGGAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (30 bp):
AATTTGATGAAAAAGGAGGATTACACAATT
Found at i:19250483 original size:28 final size:31
Alignment explanation
Indices: 19250426--19250492 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 31
19250416 CTTTGCCTCT
* *
19250426 TAAACTTGTTTATTTGTACTTAGTTGGTATC
1 TAAACTTGTTTATTTGTAATTAATTGGTATC
*
19250457 TAAACTT-TTT-TTT-TAATTAATTGGTATT
1 TAAACTTGTTTATTTGTAATTAATTGGTATC
*
19250485 TGAACTTG
1 TAAACTTG
19250493 GATTTAGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 18 0.58
29 3 0.10
30 3 0.10
31 7 0.23
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.54
Consensus pattern (31 bp):
TAAACTTGTTTATTTGTAATTAATTGGTATC
Found at i:19250652 original size:16 final size:16
Alignment explanation
Indices: 19250613--19250658 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
19250603 GACAAACACA
*
19250613 AATATAAATATAAATT
1 AATAAAAATATAAATT
* *
19250629 ATTTAAAATATAAATT
1 AATAAAAATATAAATT
19250645 AATAAAAATTATAA
1 AATAAAAA-TATAA
19250659 TTTTTTTGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATAAAAATATAAATT
Found at i:19250834 original size:8 final size:8
Alignment explanation
Indices: 19250806--19250863 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
19250796 TGTTATTTTG
19250806 AAAT-TAA
1 AAATATAA
*
19250813 AAATTTATA
1 AAATATA-A
19250822 AAATATAA
1 AAATATAA
19250830 AAATATAA
1 AAATATAA
19250838 AAATATAGA
1 AAATATA-A
*
19250847 AACTAATAA
1 AAAT-ATAA
19250856 AAAGTATA
1 AAA-TATA
19250864 TTTTTAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
7 4 0.09
8 18 0.42
9 17 0.40
10 4 0.09
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (8 bp):
AAATATAA
Found at i:19250857 original size:18 final size:16
Alignment explanation
Indices: 19250806--19250863 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
19250796 TGTTATTTTG
*
19250806 AAAT-TAAAAATTTATA
1 AAATATAAAAATATA-A
19250822 AAATATAAAAATATAA
1 AAATATAAAAATATAA
*
19250838 AAATATAGAAACTAATAA
1 AAATATA-AAAAT-ATAA
19250856 AAAGTATA
1 AAA-TATA
19250864 TTTTTAGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
16 12 0.33
17 13 0.36
18 7 0.19
19 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (16 bp):
AAATATAAAAATATAA
Found at i:19251951 original size:27 final size:27
Alignment explanation
Indices: 19251900--19251951 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
19251890 ACGGTATTTA
* *
19251900 ACTATAATTTTATTATATTAAAAAAAC
1 ACTATAATTGTATTATATAAAAAAAAC
*
19251927 ACTATAATTGTATTA-ATAAATAAAA
1 ACTATAATTGTATTATATAAAAAAAA
19251952 TAAATTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (27 bp):
ACTATAATTGTATTATATAAAAAAAAC
Found at i:19257399 original size:14 final size:14
Alignment explanation
Indices: 19257380--19257418 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
19257370 CGTTCATCTC
19257380 CTCTCTTTTCTTAA
1 CTCTCTTTTCTTAA
* *
19257394 CTCTCTTTTTTTAG
1 CTCTCTTTTCTTAA
*
19257408 CTTTCTTTTCT
1 CTCTCTTTTCT
19257419 CTCTTCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.26, G:0.03, T:0.64
Consensus pattern (14 bp):
CTCTCTTTTCTTAA
Found at i:19257817 original size:136 final size:135
Alignment explanation
Indices: 19257557--19257850 Score: 380
Period size: 136 Copynumber: 2.2 Consensus size: 135
19257547 GATCTTTCAC
* * * ***
19257557 GGTTCTTAAATAATTGGTTTCTCAATTTGATTTTTTCTAATTTGAATCGACTTGTTTGTTCACAA
1 GGTTCTTGAATAATTGGTTTCTCAATCTGATTTTTTCTAATCTGAATCGACTTGTTTACCCACAA
* * * * *
19257622 TCCCTTTGTGGGTATTCCTGATTTTTTTTTATTGCTGATTTTGTGTTGATTTACCTTTGTGGGTA
66 TCCCTTTGTCGGTATTCCAGATTTTTTTTTATTACTGATTTTGTGCTGATTTACCTTTGTGCGTA
19257687 TTCCA
131 TTCCA
* *
19257692 GGTTCTTGAATAATTGGTTTCTCAATCCT-ATTTTTT-T-ATCTGGATCGGCTTGTTTACCCACA
1 GGTTCTTGAATAATTGGTTTCTCAAT-CTGATTTTTTCTAATCTGAATCGACTTGTTTACCCACA
* *
19257754 ATCTCTTTGTCGGTATTCCAGATTTTTCTTTCTTATTATTGATTTTGTGCTGATTTACCTTTGTG
65 ATCCCTTTGTCGGTATTCCAGA-TTTT-TTT-TTATTACTGATTTTGTGCTGATTTACCTTTGTG
*
19257819 CGTATTCCG
127 CGTATTCCA
19257828 GGTTCTTGAATAATTGG-TTCTCA
1 GGTTCTTGAATAATTGGTTTCTCA
19257851 TTCCGATTGT
Statistics
Matches: 139, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
133 38 0.27
134 5 0.04
135 41 0.29
136 55 0.40
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (135 bp):
GGTTCTTGAATAATTGGTTTCTCAATCTGATTTTTTCTAATCTGAATCGACTTGTTTACCCACAA
TCCCTTTGTCGGTATTCCAGATTTTTTTTTATTACTGATTTTGTGCTGATTTACCTTTGTGCGTA
TTCCA
Found at i:19259227 original size:24 final size:24
Alignment explanation
Indices: 19259199--19259249 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
19259189 GTATACTGGT
* *
19259199 TAACCTTTCTAGGTTCGTAAGAGC
1 TAACCTATCTAGGCTCGTAAGAGC
*
19259223 TAACCTATCTGGGCTCGTAAGAGC
1 TAACCTATCTAGGCTCGTAAGAGC
19259247 TAA
1 TAA
19259250 ATCTGTTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
TAACCTATCTAGGCTCGTAAGAGC
Found at i:19259271 original size:25 final size:26
Alignment explanation
Indices: 19259232--19259281 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
19259222 CTAACCTATC
*
19259232 TGGGCTCGTAAGAGCTAAA-TCTGTT
1 TGGGCTCATAAGAGCTAAATTCTGTT
*
19259257 TGGGCTCATATGAGCTAAATTCTGT
1 TGGGCTCATAAGAGCTAAATTCTGT
19259282 AAGACCGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (26 bp):
TGGGCTCATAAGAGCTAAATTCTGTT
Found at i:19259986 original size:21 final size:21
Alignment explanation
Indices: 19259962--19260021 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
19259952 ATGATATGTT
*
19259962 TCGGTAGAAGTCTCACTTGTA
1 TCGGTAGAAGTCTCACTAGTA
* * * *
19259983 TCGGTAGAATTTTCCCAAGTA
1 TCGGTAGAAGTCTCACTAGTA
19260004 TCGGTAGAAGTCTGCACT
1 TCGGTAGAAGTCT-CACT
19260022 GTTCTAAATT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (21 bp):
TCGGTAGAAGTCTCACTAGTA
Found at i:19262314 original size:13 final size:14
Alignment explanation
Indices: 19262291--19262323 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
19262281 TTCTAATAAG
19262291 TTTTTTCTTATAGA
1 TTTTTTCTTATAGA
19262305 TTTTTT-TTATAGA
1 TTTTTTCTTATAGA
19262318 TTTTTT
1 TTTTTT
19262324 AGGGCCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (14 bp):
TTTTTTCTTATAGA
Found at i:19268394 original size:22 final size:22
Alignment explanation
Indices: 19268336--19268396 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
19268326 TAAAAATAAT
* * **
19268336 AAAATTTTAATTTAATCTTTTA
1 AAAATTATAATTTAATATCGTA
**
19268358 AAAATTATCTTTTTAATATCGTA
1 AAAATTAT-AATTTAATATCGTA
19268381 AAAATTATAATTTAAT
1 AAAATTATAATTTAAT
19268397 TTAGATCCCT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
AAAATTATAATTTAATATCGTA
Found at i:19269369 original size:41 final size:41
Alignment explanation
Indices: 19269324--19269557 Score: 233
Period size: 41 Copynumber: 5.7 Consensus size: 41
19269314 ATAAAGGCCA
* * *
19269324 CAAAAGGTAAAAGCATTAGTGGCGTTTATGACAAAACACCG
1 CAAAAGGTAAGAGCATTAGCGGCGTTTATGACAAAACGCCG
* * ** *
19269365 CAAAAGGTAAGAGCATTAGCGTCGTTTATGATAAAAATCCA
1 CAAAAGGTAAGAGCATTAGCGGCGTTTATGACAAAACGCCG
* *
19269406 CAAAAAGATAAGAGCATTAGCGGCGTTT-TG-CGATAAATGCCG
1 C-AAAAGGTAAGAGCATTAGCGGCGTTTATGAC-A-AAACGCCG
* * *
19269448 CAAAAGGTATGAGCATTAGCGGCGTTTATGAGAAAACGCTG
1 CAAAAGGTAAGAGCATTAGCGGCGTTTATGACAAAACGCCG
* * * *
19269489 CTAAAA-GTAAGAGAATTAGCAGCGTTTATGGGA-AAAATGCCA
1 C-AAAAGGTAAGAGCATTAGCGGCGTTTAT--GACAAAACGCCG
19269531 CAAAAGGTAAGAGCATTAGCGGCGTTT
1 CAAAAGGTAAGAGCATTAGCGGCGTTT
19269558 TCCCATAAAC
Statistics
Matches: 158, Mismatches: 26, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
41 93 0.59
42 63 0.40
43 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (41 bp):
CAAAAGGTAAGAGCATTAGCGGCGTTTATGACAAAACGCCG
Found at i:19269431 original size:83 final size:81
Alignment explanation
Indices: 19269320--19269557 Score: 257
Period size: 83 Copynumber: 2.9 Consensus size: 81
19269310 TCCCATAAAG
* * **
19269320 GCCACAAAAGGTAAAAGCATTAGTGGCGTTTATGACAAAACACCGCAAAAGGTAAGAGCATTAGC
1 GCCACAAAA-GTAAGAGCATTAGCGGCGTTTATGACAAAATGCCGCAAAAGGTAAGAGCATTAGC
* *
19269385 GTCGTTTATGATAAAAA
65 GGCGTTTATGAGAAAAA
* *
19269402 TCCACAAAAAGATAAGAGCATTAGCGGCGTTT-TG-CGATAAATGCCGCAAAAGGTATGAGCATT
1 GCCAC-AAAAG-TAAGAGCATTAGCGGCGTTTATGAC-A-AAATGCCGCAAAAGGTAAGAGCATT
*
19269465 AGCGGCGTTTATGAGAAAAC
62 AGCGGCGTTTATGAGAAAAA
** * * *
19269485 GCTGCTAAAAGTAAGAGAATTAGCAGCGTTTATGGGA-AAAATGCCACAAAAGGTAAGAGCATTA
1 GCCAC-AAAAGTAAGAGCATTAGCGGCGTTTAT--GACAAAATGCCGCAAAAGGTAAGAGCATTA
19269549 GCGGCGTTT
63 GCGGCGTTT
19269558 TCCCATAAAC
Statistics
Matches: 131, Mismatches: 17, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
81 1 0.01
82 26 0.20
83 102 0.78
84 1 0.01
85 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (81 bp):
GCCACAAAAGTAAGAGCATTAGCGGCGTTTATGACAAAATGCCGCAAAAGGTAAGAGCATTAGCG
GCGTTTATGAGAAAAA
Found at i:19269442 original size:124 final size:124
Alignment explanation
Indices: 19269299--19269566 Score: 353
Period size: 124 Copynumber: 2.2 Consensus size: 124
19269289 GATAAAAAAA
* *
19269299 TAGCGACGTTTTCCCATAAAGGCCACAAAAGGTAAAAGCATTAGTGGCGTTTATGACAAAACACC
1 TAGCGGCGTTTTCCCATAAAGGCCACAAAAGGTAAAAGCATTAGCGGCGTTTATGACAAAACACC
* *
19269364 GC-AAAAGGTAAGAGCATTAGC-GTCGTTTATGATAAAAAT-CCACAAAAAGATAAGAGCAT
66 GCTAAAA-GTAAGAGAATTAGCAG-CGTTTATGAGAAAAATGCCAC-AAAAGATAAGAGCAT
* * * * ** * * *
19269423 TAGCGGCGTTTTGCGATAAATGCCGCAAAAGGTATGAGCATTAGCGGCGTTTATGAGAAAACGCT
1 TAGCGGCGTTTTCCCATAAAGGCCACAAAAGGTAAAAGCATTAGCGGCGTTTATGACAAAACACC
* *
19269488 GCTAAAAGTAAGAGAATTAGCAGCGTTTATGGGAAAAATGCCACAAAAGGTAAGAGCAT
66 GCTAAAAGTAAGAGAATTAGCAGCGTTTATGAGAAAAATGCCACAAAAGATAAGAGCAT
19269547 TAGCGGCGTTTTCCCATAAA
1 TAGCGGCGTTTTCCCATAAA
19269567 CGTTACTAAT
Statistics
Matches: 124, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
124 115 0.93
125 9 0.07
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.22
Consensus pattern (124 bp):
TAGCGGCGTTTTCCCATAAAGGCCACAAAAGGTAAAAGCATTAGCGGCGTTTATGACAAAACACC
GCTAAAAGTAAGAGAATTAGCAGCGTTTATGAGAAAAATGCCACAAAAGATAAGAGCAT
Found at i:19270149 original size:42 final size:42
Alignment explanation
Indices: 19270102--19270271 Score: 166
Period size: 42 Copynumber: 4.0 Consensus size: 42
19270092 GTCACTATAG
*
19270102 AACATGGTCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAA
1 AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
* *
19270144 AACATGGTCTTTAGCGGCGC-TTTCCTCAAAAACGCCACTAAA
1 AACATGGTCTTTAGCGGCGCTTTTCC-CACAAACGCCGCTAAA
* * * * *
19270186 GAACATGGTCTTTCGCTGCG-TTTTTCCACAAACGCGGTTATAGA
1 -AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA-A-A
* * * * *
19270230 TA-ATGTTTTTTAGTGGCGTTTTTCCCACAAACGCCGCTAAA
1 AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
19270271 A
1 A
19270272 TTAACAGATT
Statistics
Matches: 102, Mismatches: 20, Indels: 13
0.76 0.15 0.10
Matches are distributed among these distances:
41 6 0.06
42 55 0.54
43 40 0.39
44 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (42 bp):
AACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
Found at i:19276433 original size:36 final size:34
Alignment explanation
Indices: 19276392--19276503 Score: 99
Period size: 36 Copynumber: 3.3 Consensus size: 34
19276382 AAATATTTTC
19276392 AATTAAATATTTGGGTTTAGGGTTTAATAAATAATT
1 AATTAAATATTT-GGTTTAGGGTTTAATAAATAA-T
*** *
19276428 AATTAAATAATTAAATATTTGGGTTT--T---TAAT
1 AATTAAAT-ATTTGGT-TTAGGGTTTAATAAATAAT
19276459 AATTAAATAGTTTGGTTTAGGGTTTAATAAATAACT
1 AATTAAATA-TTTGGTTTAGGGTTTAATAAATAA-T
19276495 AATTAAATA
1 AATTAAATA
19276504 AGTAATTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
30 9 0.15
31 12 0.20
32 4 0.07
35 4 0.07
36 19 0.32
37 11 0.19
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (34 bp):
AATTAAATATTTGGTTTAGGGTTTAATAAATAAT
Found at i:19276676 original size:92 final size:90
Alignment explanation
Indices: 19276559--19276755 Score: 297
Period size: 92 Copynumber: 2.2 Consensus size: 90
19276549 AATATAATTA
* *
19276559 AATAATTTAATATTTTGAATTAAATATTTGAATTT-AGGATTTAAAAAATAACTAATTAAATAAT
1 AATAATTTAATATTTTAAATTAAATATTTAAATTTAAGG-TTTAAAAAATAACTAATTAAATAAT
19276623 TAATTATTTAAATAGTTCGATTGTTTTT
65 TAATTATTTAAATA-TT-GATTGTTTTT
*
19276651 AATAATTTAATATTTTAAATTAAATATTTAAATTTAAGGTTTAATAAATAACTAATTAAATAATT
1 AATAATTTAATATTTTAAATTAAATATTTAAATTTAAGGTTTAAAAAATAACTAATTAAATAATT
* * **
19276716 AATTTTTTTAATATTTTTTGTTTTT
66 AATTATTTAAATATTGATTGTTTTT
19276741 AATAATTTAATATTT
1 AATAATTTAATATTT
19276756 ATTTAATATA
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
90 23 0.24
91 2 0.02
92 69 0.71
93 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (90 bp):
AATAATTTAATATTTTAAATTAAATATTTAAATTTAAGGTTTAAAAAATAACTAATTAAATAATT
AATTATTTAAATATTGATTGTTTTT
Found at i:19276776 original size:119 final size:120
Alignment explanation
Indices: 19276651--19276956 Score: 490
Period size: 120 Copynumber: 2.6 Consensus size: 120
19276641 GATTGTTTTT
* *
19276651 AATAATTTAATATTTTAAATTAAATATTTAAATTTAAGGTTTAATAAATAACTAATTAAATAATT
1 AATAATTTAATATTTTGAATTAAATATTTAAGTTTAAGGTTTAATAAATAACTAATTAAATAATT
* * *
19276716 AATTTTTTTAATATTTTTTGT-TTTTAATAATTTAATATTTATTTAATATAATTA
66 AATTATTTTAATATTTGTTCTATTTTAATAATTTAATATTTATTTAATATAATTA
* * *
19276770 AATAATTTAATATTTTGAATTAAATATTTTAGTTTAGGGTTTAATAAATAACTAATTAAATAAAT
1 AATAATTTAATATTTTGAATTAAATATTTAAGTTTAAGGTTTAATAAATAACTAATTAAATAATT
*
19276835 AATTATTTTAATATTTGTTCTATTTTAATAATTTAATATTTATTTATTATAATTA
66 AATTATTTTAATATTTGTTCTATTTTAATAATTTAATATTTATTTAATATAATTA
* *
19276890 AATAATTTAATATTTTGAATTAAATATTTGAGTTT-AGAATTTAATAAATAACTAATTAAATAAT
1 AATAATTTAATATTTTGAATTAAATATTTAAGTTTAAG-GTTTAATAAATAACTAATTAAATAAT
19276954 TAA
65 TAA
19276957 ATATATGTAT
Statistics
Matches: 172, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
119 79 0.46
120 93 0.54
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (120 bp):
AATAATTTAATATTTTGAATTAAATATTTAAGTTTAAGGTTTAATAAATAACTAATTAAATAATT
AATTATTTTAATATTTGTTCTATTTTAATAATTTAATATTTATTTAATATAATTA
Found at i:19276821 original size:211 final size:208
Alignment explanation
Indices: 19276474--19276875 Score: 601
Period size: 211 Copynumber: 1.9 Consensus size: 208
19276464 AATAGTTTGG
*
19276474 TTTAGGGTTTAATAAATAACTAATTAAATAAGTAATTATTTAAATAATTCAGTTTTTAATAATTT
1 TTTAAGGTTTAATAAATAACTAATTAAATAAGTAATTATTTAAATAATTCAGTTTTTAATAATTT
19276539 AAATATTTTAAATATAATTAAATAATTTAATATTTTGAATTAAATATTTGAATTTAGGATTTAAA
66 AAATATTTTAAATATAATTAAATAATTTAATATTTTGAATTAAATATTTGAATTTAGGATTTAAA
* *
19276604 AAATAACTAATTAAATAATTAATTATTTAAATAGTTCGATTGT-TTTTAATAATTTAATATTTTA
131 AAATAACTAATTAAATAAATAATTATTTAAATA-TTCG-TTCTATTTTAATAATTTAATATTTTA
19276668 AATTAAATATTTAAA
194 AATTAAATATTTAAA
* * * * **
19276683 TTTAAGGTTTAATAAATAACTAATTAAATAATTAATTTTTTTAATATTTTTTGTTTTTAATAATT
1 TTTAAGGTTTAATAAATAACTAATTAAATAAGTAATTATTTAAATA-ATTCAGTTTTTAATAATT
* * * *
19276748 T-AATATTTATTTAATATAATTAAATAATTTAATATTTTGAATTAAATATTTTAGTTTAGGGTTT
65 TAAATA-TT-TTAAATATAATTAAATAATTTAATATTTTGAATTAAATATTTGAATTTAGGATTT
* * *
19276812 AATAAATAACTAATTAAATAAATAATTATTTTAATATTTGTTCTATTTTAATAATTTAATATTT
128 AAAAAATAACTAATTAAATAAATAATTATTTAAATATTCGTTCTATTTTAATAATTTAATATTT
19276876 ATTTATTATA
Statistics
Matches: 173, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
209 49 0.28
210 40 0.23
211 84 0.49
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (208 bp):
TTTAAGGTTTAATAAATAACTAATTAAATAAGTAATTATTTAAATAATTCAGTTTTTAATAATTT
AAATATTTTAAATATAATTAAATAATTTAATATTTTGAATTAAATATTTGAATTTAGGATTTAAA
AAATAACTAATTAAATAAATAATTATTTAAATATTCGTTCTATTTTAATAATTTAATATTTTAAA
TTAAATATTTAAA
Found at i:19276847 original size:16 final size:16
Alignment explanation
Indices: 19276809--19276847 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19276799 TAGTTTAGGG
19276809 TTTAATAAATAACTAA
1 TTTAATAAATAACTAA
* * *
19276825 TTAAATAAATAATTAT
1 TTTAATAAATAACTAA
19276841 TTTAATA
1 TTTAATA
19276848 TTTGTTCTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAATAAATAACTAA
Found at i:19277069 original size:28 final size:28
Alignment explanation
Indices: 19277015--19277090 Score: 125
Period size: 28 Copynumber: 2.6 Consensus size: 28
19277005 AAAAGAGTTC
19277015 AAATTATTGTATATATTATTAACTTATAAT
1 AAATTATTG--TATATTATTAACTTATAAT
*
19277045 AAATTATTGTATATTATTAATTTATAAT
1 AAATTATTGTATATTATTAACTTATAAT
19277073 AAATTATTGTATATTATT
1 AAATTATTGTATATTATT
19277091 GATGCTGGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 36 0.80
30 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (28 bp):
AAATTATTGTATATTATTAACTTATAAT
Found at i:19279012 original size:23 final size:22
Alignment explanation
Indices: 19278982--19279024 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
19278972 GGTATAGGCT
19278982 GAATTTTGTGATGACTGGTGGCA
1 GAATTTTGTGATGA-TGGTGGCA
19279005 GAATTTTGTGATGATGGTGG
1 GAATTTTGTGATGATGGTGG
19279025 TGGTCGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.21, C:0.05, G:0.37, T:0.37
Consensus pattern (22 bp):
GAATTTTGTGATGATGGTGGCA
Found at i:19279111 original size:50 final size:50
Alignment explanation
Indices: 19279036--19279145 Score: 175
Period size: 50 Copynumber: 2.2 Consensus size: 50
19279026 GGTCGGTCGG
* *
19279036 TGGGTGTTGATGGAGATTGGAGTGGAGAAGGAAATGGAGGAGGTAGACGA
1 TGGGTGTTGGTGGAGATTGGAGTGGAGAAGGAAATGGAGGAGGTAAACGA
* *
19279086 TGGGTGTTGGTGTAGATTGGAGTGGAGAATGAAATGGAGGAGGTAAACGA
1 TGGGTGTTGGTGGAGATTGGAGTGGAGAAGGAAATGGAGGAGGTAAACGA
*
19279136 TGGGTATTGG
1 TGGGTGTTGG
19279146 AGGAAATTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.28, C:0.02, G:0.46, T:0.24
Consensus pattern (50 bp):
TGGGTGTTGGTGGAGATTGGAGTGGAGAAGGAAATGGAGGAGGTAAACGA
Done.