Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 90 of 322
Found at i:29208674 original size:79 final size:79
Alignment explanation
Indices: 29208576--29208758 Score: 212
Period size: 79 Copynumber: 2.3 Consensus size: 79
29208566 TACTCGTTCA
*
29208576 AATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGA
1 AATGCCTTCGGGACTTAGCCCGGATT--AGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGA
* *
29208639 ATTTAGTAAC-TCGCACC
63 ATATAGTAACTTAGCA-C
* ** *
29208656 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGAAT
*
29208720 ATAGTCACTTAGCAC
65 ATAGTAACTTAGCAC
*
29208735 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
29208759 CATCATTCAA
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 26 0.29
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
AATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGAATA
TAGTAACTTAGCAC
Found at i:29208758 original size:40 final size:40
Alignment explanation
Indices: 29208555--29208758 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
29208545 CGGAATTTAA
** *
29208555 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
29208595 CCGGTTACAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
29208635 CCGAATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29208674 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
29208714 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29208754 CCGGA
1 CCGGA
29208759 CATCATTCAA
Statistics
Matches: 136, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 31 0.23
40 91 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29214798 original size:43 final size:44
Alignment explanation
Indices: 29214678--29214800 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 44
29214668 ACATAGGATT
*
29214678 TCGATATGTGATT-GGTGTAAGACCACGTCTGGGAC-GTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGTTGGCA
* * * *
29214720 TCGATTTTTAATTTACGTGTAAGACC-CTGTGTGGGACAG-TGGCA
1 TCGATATGTGA-TTACGTGTAAGACCAC-GTCTGGGACAGTTGGCA
* *
29214764 TCGATATGTGATTACATGTAAGACCACATCTGGGACA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACA
29214801 TTCGTGTTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
42 8 0.12
43 24 0.37
44 32 0.49
45 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (44 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGTTGGCA
Found at i:29216110 original size:42 final size:43
Alignment explanation
Indices: 29216027--29216175 Score: 128
Period size: 42 Copynumber: 3.5 Consensus size: 43
29216017 TCTGAGATGT
* * *
29216027 CGTATAAGACCATGTCTGGGACACCGGCCTCGAT-TGAGATTTA
1 CGTATAAGACCATGTCTGGGACACAGGCATCGATAT-TGATTTA
*
29216070 CGTATAAGACCAT-TCTGGGACATAGGCATC-ATATCTGATTTCA
1 CGTATAAGACCATGTCTGGGACACAGGCATCGATAT-TGATTT-A
* * * * *
29216113 C--ATAAAACCTTGTCTAGGACAGAGGCATCGATATTGAATTA
1 CGTATAAGACCATGTCTGGGACACAGGCATCGATATTGATTTA
* * *
29216154 CATGTAAGACCACGTCTGGGAC
1 CGTATAAGACCATGTCTGGGAC
29216176 GTCGGCATTG
Statistics
Matches: 85, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
41 12 0.14
42 40 0.47
43 33 0.39
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
CGTATAAGACCATGTCTGGGACACAGGCATCGATATTGATTTA
Found at i:29217034 original size:64 final size:65
Alignment explanation
Indices: 29216966--29217089 Score: 146
Period size: 64 Copynumber: 1.9 Consensus size: 65
29216956 CAGTATTCTC
* **
29216966 CTAAGAATCACACGGTCT-T-GACACACGGGAGTGTCTA-TGGCCGTGGGCTAAAGTCAGTAGCT
1 CTAAGAATCACACGG-CTATAG-CACACGGGAGTGACTATTGGCCGTGGGAAAAAGTCAGTAGCT
29217028 AG
64 AG
* * * *
29217030 CTAAGTATCACATGGCTATAGCACACGGGCGTGACTATTGGCCGTGTGAAAAAGTCAGTA
1 CTAAGAATCACACGGCTATAGCACACGGGAGTGACTATTGGCCGTGGGAAAAAGTCAGTA
29217090 TTGGACCTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.04
64 28 0.56
65 20 0.40
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (65 bp):
CTAAGAATCACACGGCTATAGCACACGGGAGTGACTATTGGCCGTGGGAAAAAGTCAGTAGCTAG
Found at i:29225764 original size:15 final size:15
Alignment explanation
Indices: 29225740--29225779 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
29225730 TGTAAATTGT
*
29225740 ATTTCCTTATCATGG
1 ATTTCTTTATCATGG
*
29225755 ATTTCTTTATCTTGG
1 ATTTCTTTATCATGG
*
29225770 AATTCTTTAT
1 ATTTCTTTAT
29225780 TCTGGGCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (15 bp):
ATTTCTTTATCATGG
Found at i:29226390 original size:21 final size:21
Alignment explanation
Indices: 29226366--29226410 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
29226356 TGAAATGATC
29226366 ATTGTTTATCTTTGAGTACAA
1 ATTGTTTATCTTTGAGTACAA
29226387 ATTGTTTATCTTTGAGTACAA
1 ATTGTTTATCTTTGAGTACAA
29226408 ATT
1 ATT
29226411 CTTGAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (21 bp):
ATTGTTTATCTTTGAGTACAA
Found at i:29230733 original size:315 final size:315
Alignment explanation
Indices: 29230161--29230791 Score: 1217
Period size: 315 Copynumber: 2.0 Consensus size: 315
29230151 GGTTATGTGA
*
29230161 TTGTGCTTGTTCACTATGTATGAGAAGTATATGGCATATGTACATGATGAATTCCATTGAAATCG
1 TTGTGCTTGTTCACTATGTATGAGAAGTATATAGCATATGTACATGATGAATTCCATTGAAATCG
*
29230226 TGTATGTGTGTGTATGTAAAGATGACAAAAAGGCTTGGAAATTAGCCTAAGTCTTGACCATAAGG
66 TGTATGTGTGTGTAAGTAAAGATGACAAAAAGGCTTGGAAATTAGCCTAAGTCTTGACCATAAGG
*
29230291 GTAGAGACATGGCCGTGTGTCTCAGCCATATGGAGGACACGGCCTCTGGCCACGAGTGTGTGCCT
131 GTAGAAACATGGCCGTGTGTCTCAGCCATATGGAGGACACGGCCTCTGGCCACGAGTGTGTGCCT
29230356 TGGCCGTGTGCCCTTAAACGGTTGTTGACGTTATAAACAGAGAGTTACACAGGCTGAGGACACGG
196 TGGCCGTGTGCCCTTAAACGGTTGTTGACGTTATAAACAGAGAGTTACACAGGCTGAGGACACGG
29230421 GTGTGTCCCAAGCCACACGGACGTGTGCGACTAGATGGCCCAACCCACATGGGCT
261 GTGTGTCCCAAGCCACACGGACGTGTGCGACTAGATGGCCCAACCCACATGGGCT
*
29230476 TTGTGCTTGTTCACTATGTATGAGAAGTATATAGCATATGTACATGATGAGTTCCATTGAAATCG
1 TTGTGCTTGTTCACTATGTATGAGAAGTATATAGCATATGTACATGATGAATTCCATTGAAATCG
*
29230541 TGTATGTGTGTGTAAGTAGAGATGACAAAAAGGCTTGGAAATTAGCCTAAGTCTTGACCATAAGG
66 TGTATGTGTGTGTAAGTAAAGATGACAAAAAGGCTTGGAAATTAGCCTAAGTCTTGACCATAAGG
29230606 GTAGAAACATGGCCGTGTGTCTCAGCCATATGGAGGACACGGCCTCTGGCCACGAGTGTGTGCCT
131 GTAGAAACATGGCCGTGTGTCTCAGCCATATGGAGGACACGGCCTCTGGCCACGAGTGTGTGCCT
29230671 TGGCCGTGTGCCCTTAAACGGTTGTTGACGTTATAAACAGAGAGTTACACAGGCTGAGGACACGG
196 TGGCCGTGTGCCCTTAAACGGTTGTTGACGTTATAAACAGAGAGTTACACAGGCTGAGGACACGG
29230736 GTGTGTCCCAAGCCACACGGACGTGTGCGACTAGATGGCCCAACCCACATGGGCT
261 GTGTGTCCCAAGCCACACGGACGTGTGCGACTAGATGGCCCAACCCACATGGGCT
29230791 T
1 T
29230792 GTGACTCTCC
Statistics
Matches: 311, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
315 311 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (315 bp):
TTGTGCTTGTTCACTATGTATGAGAAGTATATAGCATATGTACATGATGAATTCCATTGAAATCG
TGTATGTGTGTGTAAGTAAAGATGACAAAAAGGCTTGGAAATTAGCCTAAGTCTTGACCATAAGG
GTAGAAACATGGCCGTGTGTCTCAGCCATATGGAGGACACGGCCTCTGGCCACGAGTGTGTGCCT
TGGCCGTGTGCCCTTAAACGGTTGTTGACGTTATAAACAGAGAGTTACACAGGCTGAGGACACGG
GTGTGTCCCAAGCCACACGGACGTGTGCGACTAGATGGCCCAACCCACATGGGCT
Found at i:29233140 original size:25 final size:25
Alignment explanation
Indices: 29233102--29233155 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
29233092 CAGTGAGAAT
29233102 AAGATACACAGGGTCGATTTGATCA
1 AAGATACACAGGGTCGATTTGATCA
*
29233127 AAGATACACGGGGTCGATTTGATCA
1 AAGATACACAGGGTCGATTTGATCA
29233152 AAGA
1 AAGA
29233156 GACTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (25 bp):
AAGATACACAGGGTCGATTTGATCA
Found at i:29233571 original size:13 final size:13
Alignment explanation
Indices: 29233553--29233577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29233543 TATATTATAT
29233553 GTGTGAAAATTTC
1 GTGTGAAAATTTC
29233566 GTGTGAAAATTT
1 GTGTGAAAATTT
29233578 TATCATTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:29234751 original size:44 final size:43
Alignment explanation
Indices: 29234687--29234813 Score: 145
Period size: 44 Copynumber: 3.0 Consensus size: 43
29234677 TAGGATTCCG
29234687 ATATGTGATT-CGA-GTAAGACCACGTCTGGGACGTTGGCATCA
1 ATATGTGATTAC-ATGTAAGACCACGTCTGGGACGTTGGCATCA
* * * *
29234729 ATTTGTGATTTACGTGTAAGACC-CTGTCTGGGATAG-TGGCATCG
1 ATATGTGA-TTACATGTAAGACCAC-GTCTGGGA-CGTTGGCATCA
*
29234773 ATATGTGATTACATGTAAGACCACGTCTGGGACGTTAGCAT
1 ATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
29234814 TGCACGAGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
42 8 0.11
43 29 0.41
44 32 0.46
45 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (43 bp):
ATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATCA
Found at i:29242287 original size:52 final size:51
Alignment explanation
Indices: 29242222--29242320 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 51
29242212 ATAAATTTTT
* * *
29242222 TAAAATATGTTAGAATTTTTAAGAA-ATTATAAAAAAAATTATAAAAATACTA
1 TAAAATATATTAGAAATTCTAA-AATATTAT-AAAAAAATTATAAAAATACTA
* *
29242274 TAAAATATATTAGAAATTCTAAAATATTGTAAAAAATTTATAAAAAT
1 TAAAATATATTAGAAATTCTAAAATATTATAAAAAAATTATAAAAAT
29242321 TATCAGAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 18 0.44
52 23 0.56
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (51 bp):
TAAAATATATTAGAAATTCTAAAATATTATAAAAAAATTATAAAAATACTA
Found at i:29242891 original size:20 final size:19
Alignment explanation
Indices: 29242868--29242906 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29242858 TTTTTATTTA
*
29242868 CAAATTAATATATTGGTCTT
1 CAAATAAATA-ATTGGTCTT
*
29242888 CAAATAAATAATTTGTCTT
1 CAAATAAATAATTGGTCTT
29242907 GGGATGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (19 bp):
CAAATAAATAATTGGTCTT
Found at i:29243180 original size:10 final size:10
Alignment explanation
Indices: 29243165--29243193 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29243155 TTAAAAATAA
29243165 TAAATTTTAG
1 TAAATTTTAG
29243175 TAAATTTTAG
1 TAAATTTTAG
29243185 TAAATTTTA
1 TAAATTTTA
29243194 ATTTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TAAATTTTAG
Found at i:29251888 original size:13 final size:13
Alignment explanation
Indices: 29251870--29251894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29251860 CATACTAAAA
29251870 TAATTCATTTAAG
1 TAATTCATTTAAG
29251883 TAATTCATTTAA
1 TAATTCATTTAA
29251895 TATATTATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TAATTCATTTAAG
Found at i:29252148 original size:42 final size:42
Alignment explanation
Indices: 29252087--29252200 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
29252077 GTGCTAAATG
* * * * * *
29252087 GAAACCCGTAAGGGCTAAACGGAAGTTCATAGGAGCTGAACA
1 GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTAAACA
* * **
29252129 GAAACTCATAAGGGTTAAACTGAAGCTCAAAAGAGCTAAATG
1 GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTAAACA
* *
29252171 GAAACCCATTAGGGTTAAACGGAAACTCAA
1 GAAACCCATAAGGGTTAAACGGAAGCTCAA
29252201 GTGAGTTAAC
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.17
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTAAACA
Found at i:29253674 original size:61 final size:61
Alignment explanation
Indices: 29253579--29253701 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
29253569 TCAGTTTATG
29253579 AATTTATTCACTTGTGACGTTCATAGTGTGACATACCTTAATCCTGAGTGCATGATGAACT
1 AATTTATTCACTTGTGACGTTCATAGTGTGACATACCTTAATCCTGAGTGCATGATGAACT
*
29253640 AATTTATTCACTTGTGACGTTCATAGTGTGACATACCTTAATCCTGAGTGGATGATGAACT
1 AATTTATTCACTTGTGACGTTCATAGTGTGACATACCTTAATCCTGAGTGCATGATGAACT
29253701 A
1 A
29253702 TGTATGTGTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (61 bp):
AATTTATTCACTTGTGACGTTCATAGTGTGACATACCTTAATCCTGAGTGCATGATGAACT
Found at i:29256714 original size:27 final size:27
Alignment explanation
Indices: 29256674--29256748 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
29256664 TTACCTAGAC
* ** * *
29256674 CCCTTATGTCGTAAAATGGTTGTTTTT
1 CCCTTATGTGGTAAAATGACTGTCTTG
*
29256701 CCTTTATGTGGTAAAATGACTGTCTTG
1 CCCTTATGTGGTAAAATGACTGTCTTG
*
29256728 CCCTTATGTGGTGAAATGACT
1 CCCTTATGTGGTAAAATGACT
29256749 ATTTTTGTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.41
Consensus pattern (27 bp):
CCCTTATGTGGTAAAATGACTGTCTTG
Found at i:29259090 original size:50 final size:47
Alignment explanation
Indices: 29258926--29259245 Score: 178
Period size: 46 Copynumber: 6.7 Consensus size: 47
29258916 GGTATAATGT
* * **
29258926 CGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCATCCATCAAGT--
1 CGATGCTATGTCCCAGACAT-GTCTTACACTAGCTTCA--CATCTCGTGC
* * * **
29258973 CGATGCCATGTACCAGACATGGTCTTACACT-GACTATCGAAATCGAG-GC
1 CGATGCTATGTCCCAGACAT-GTCTTACACTAG-CT-TC-ACATCTCGTGC
* * * *
29259022 CGACGCAACGTCCCAGACATTGTCTTACACTAGCTCTCACATATCCGTGC
1 CGATGCTATGTCCCAGACA-TGTCTTACACTAGCT-TCACATCT-CGTGC
* * *
29259072 CGATGCTATGTCCCAGACATGGTCTTACA-TTG--ACACATCTCATAGC
1 CGATGCTATGTCCCAGACAT-GTCTTACACTAGCTTCACATCTCGT-GC
* *
29259118 CGATG-TATGTCCCAAACATGTCTTACACTAGCTT-ACATCTCGAGGC
1 CGATGCTATGTCCCAGACATGTCTTACACTAGCTTCACATCTCG-TGC
* * * * *
29259164 CGATGC-ATTTCCCAGACATGTCTTACACTAGC-ACTCGTCTCAATGC
1 CGATGCTATGTCCCAGACATGTCTTACACTAGCTTCACATCTC-GTGC
* * * *
29259210 CGAAGCCATATCCCAGATATGGTCTTACACTAGCTT
1 CGATGCTATGTCCCAGACAT-GTCTTACACTAGCTT
29259246 ACAATAACCC
Statistics
Matches: 216, Mismatches: 35, Indels: 42
0.74 0.12 0.14
Matches are distributed among these distances:
44 8 0.04
45 17 0.08
46 64 0.30
47 42 0.19
48 21 0.10
49 35 0.16
50 29 0.13
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (47 bp):
CGATGCTATGTCCCAGACATGTCTTACACTAGCTTCACATCTCGTGC
Found at i:29260115 original size:27 final size:27
Alignment explanation
Indices: 29260084--29260389 Score: 394
Period size: 27 Copynumber: 11.6 Consensus size: 27
29260074 GCTGTTACAA
*
29260084 TTTTGCCCTTATGTGGTGAAATGATTG
1 TTTTGCCCTTATGTGGTGAAATGACTG
* * *
29260111 TTTTGTCCTTATGTGGTAAAATGATTG
1 TTTTGCCCTTATGTGGTGAAATGACTG
* * *
29260138 TTTTGCCCTTATGTGATAAAATGACTA
1 TTTTGCCCTTATGTGGTGAAATGACTG
*
29260165 TTTTGCCCTTATATGGTGAAATGACTG
1 TTTTGCCCTTATGTGGTGAAATGACTG
29260192 TTTTGCCCTTATGTGGTGAAATGACTG
1 TTTTGCCCTTATGTGGTGAAATGACTG
* * *
29260219 TTTTGTCCTTATGTGGTAAAATGATTG
1 TTTTGCCCTTATGTGGTGAAATGACTG
*
29260246 TTTTGCCCTTATGTGGTAAAATGACTG
1 TTTTGCCCTTATGTGGTGAAATGACTG
*
29260273 TTTTGCCCTTATGTGGTGAAATGACTA
1 TTTTGCCCTTATGTGGTGAAATGACTG
* *
29260300 TTTTTCCCTTATGT-G-G---TGACTA
1 TTTTGCCCTTATGTGGTGAAATGACTG
29260322 TTTTGCCCTTATGTGGT-AAGATGACTG
1 TTTTGCCCTTATGTGGTGAA-ATGACTG
*
29260349 TTTTGCCCTTATTTGGT-AAGATGACTG
1 TTTTGCCCTTATGTGGTGAA-ATGACTG
29260376 TTTTGCCC-TATGTG
1 TTTTGCCCTTATGTG
29260390 ATGTATATAT
Statistics
Matches: 250, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
22 19 0.08
23 1 0.00
25 1 0.00
26 6 0.02
27 223 0.89
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (27 bp):
TTTTGCCCTTATGTGGTGAAATGACTG
Found at i:29260322 original size:22 final size:22
Alignment explanation
Indices: 29260267--29260338 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 22
29260257 TGTGGTAAAA
*
29260267 TGACTGTTTTGCCCTTATGTGGTG
1 TGACTATTTTGCCCTTATGT-G-G
*
29260291 AAATGACTATTTTTCCCTTATGTGG
1 ---TGACTATTTTGCCCTTATGTGG
29260316 TGACTATTTTGCCCTTATGTGG
1 TGACTATTTTGCCCTTATGTGG
29260338 T
1 T
29260339 AAGATGACTG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 22 0.52
25 1 0.02
26 1 0.02
27 18 0.43
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (22 bp):
TGACTATTTTGCCCTTATGTGG
Found at i:29265838 original size:31 final size:31
Alignment explanation
Indices: 29265800--29265895 Score: 129
Period size: 31 Copynumber: 3.0 Consensus size: 31
29265790 TCATACATAT
29265800 GTATGATAAACATGCCATATTGTTTAGGGAA
1 GTATGATAAACATGCCATATTGTTTAGGGAA
*
29265831 GTATGATAAACATGCCATATAATAATTTAGGGAA
1 GTATGATAAACATGCCATAT--T-GTTTAGGGAA
* * *
29265865 GCATGATAAACATGCCATATAGTTTAAGGAA
1 GTATGATAAACATGCCATATTGTTTAGGGAA
29265896 AGAATGTCAC
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
31 28 0.49
33 1 0.02
34 28 0.49
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (31 bp):
GTATGATAAACATGCCATATTGTTTAGGGAA
Found at i:29265865 original size:34 final size:32
Alignment explanation
Indices: 29265800--29265885 Score: 129
Period size: 34 Copynumber: 2.7 Consensus size: 32
29265790 TCATACATAT
*
29265800 GTATGATAAACATGCCATAT-TGTTTAGGGAA
1 GTATGATAAACATGCCATATATATTTAGGGAA
29265831 GTATGATAAACATGCCATATAATAATTTAGGGAA
1 GTATGATAAACATGCCATAT-AT-ATTTAGGGAA
*
29265865 GCATGATAAACATGCCATATA
1 GTATGATAAACATGCCATATA
29265886 GTTTAAGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
31 20 0.40
33 2 0.04
34 28 0.56
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (32 bp):
GTATGATAAACATGCCATATATATTTAGGGAA
Found at i:29266729 original size:46 final size:46
Alignment explanation
Indices: 29266676--29266769 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
29266666 AAAAAATAAG
**
29266676 ATTAAGGAGTTGCAATGTTGATTAGGAAAATTGGGATTACTGATGC
1 ATTAAGGAACTGCAATGTTGATTAGGAAAATTGGGATTACTGATGC
* *
29266722 ATTAAGGAACTGCAATGTTGATTAGGACAATTGGGATTATTGATGC
1 ATTAAGGAACTGCAATGTTGATTAGGAAAATTGGGATTACTGATGC
29266768 AT
1 AT
29266770 CTACCTTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (46 bp):
ATTAAGGAACTGCAATGTTGATTAGGAAAATTGGGATTACTGATGC
Found at i:29276156 original size:35 final size:35
Alignment explanation
Indices: 29276104--29276173 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
29276094 AGTCGGAAAG
*
29276104 AATAATTTAGGTTTTAGAAGACATGTTACGGTGTT
1 AATAATTTAGGTATTAGAAGACATGTTACGGTGTT
29276139 AATAATTT-GGATATTAGAAGACATGTTACGGTGTT
1 AATAATTTAGG-TATTAGAAGACATGTTACGGTGTT
29276174 GTGTTCCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (35 bp):
AATAATTTAGGTATTAGAAGACATGTTACGGTGTT
Found at i:29278122 original size:44 final size:44
Alignment explanation
Indices: 29278072--29278161 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 44
29278062 TTTGTGTGCT
29278072 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATATGTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACG-GATATGTG
*
29278116 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATGGATATGTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGTG
29278160 AG
1 AG
29278162 AGCTAGTGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
44 19 0.44
45 16 0.37
46 8 0.19
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (44 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGTG
Found at i:29278237 original size:49 final size:50
Alignment explanation
Indices: 29278116--29278297 Score: 160
Period size: 49 Copynumber: 3.7 Consensus size: 50
29278106 GAGATATGTG
* *
29278116 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGACATCGGCATCGATATGTGAGAGCT
* ** * * *
29278166 AGTGTAAGACCATTTCTGGGACATGATGTCGGCCTCGAT-TTTGATAG-T
1 AGTGTAAGACCATGTCTGGGACATGACATCGGCATCGATATGTGAGAGCT
* * * * *
29278214 CAGTGTAAGACCATGTCTAGGACATGGCATCGAC-TTG--ATG-GATGAGCC
1 -AGTGTAAGACCATGTCTGGGACATGACATCGGCATCGATATGTGA-GAGCT
* * *
29278262 AGTGTAAAACCACGTCTGGGACATGGCATCGGCATC
1 AGTGTAAGACCATGTCTGGGACATGACATCGGCATC
29278298 ATACCCTATG
Statistics
Matches: 104, Mismatches: 23, Indels: 12
0.75 0.17 0.09
Matches are distributed among these distances:
46 2 0.02
47 32 0.31
48 4 0.04
49 33 0.32
50 33 0.32
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTGGGACATGACATCGGCATCGATATGTGAGAGCT
Found at i:29279182 original size:34 final size:34
Alignment explanation
Indices: 29279139--29279245 Score: 178
Period size: 34 Copynumber: 3.1 Consensus size: 34
29279129 GAGACATGAT
*
29279139 CAAATGCTCGTATGAGCTAATCCATCTAGCACAC
1 CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
*
29279173 CAAATGCTCGTATGAGCTAATCGATCCAGCACAC
1 CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
* *
29279207 CAAATGGTCGTATGAGCTAATCCATCCAACACAC
1 CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
29279241 CAAAT
1 CAAAT
29279246 AACACTGTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (34 bp):
CAAATGCTCGTATGAGCTAATCCATCCAGCACAC
Found at i:29308467 original size:38 final size:38
Alignment explanation
Indices: 29308408--29308538 Score: 118
Period size: 38 Copynumber: 3.2 Consensus size: 38
29308398 TCTCAAATTA
*
29308408 ACATGTATAACCGTGGCATATCCACTTAGCACGACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * *
29308446 ACATGTTTAACTGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
* * *
29308487 GAATCGATATATGTAACAGTGGCATATCCAGTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
29308531 ACATGTAT
1 ACATGTAT
29308539 CAATATGTGT
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
38 33 0.45
39 1 0.01
40 4 0.05
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 3 0.04
46 1 0.01
47 26 0.35
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:29308570 original size:48 final size:47
Alignment explanation
Indices: 29308453--29308575 Score: 167
Period size: 48 Copynumber: 2.6 Consensus size: 47
29308443 GTTACATGTT
* *
29308453 TAACTGTGGTATATCCACTTAGCACCACGTTAATGAATCGATATATG
1 TAACAGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
* * * *
29308500 TAACAGTGGCATATCCAGTTAGCACCACGTTACATGTATCAATATGTG
1 TAACAGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
29308548 TAATC-GTGGTATATCCACTTAGCACCAC
1 TAA-CAGTGGTATATCCACTTAGCACCAC
29308576 ATTTTTCCAT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 29 0.44
48 36 0.55
49 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (47 bp):
TAACAGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
Found at i:29309483 original size:84 final size:84
Alignment explanation
Indices: 29309342--29309589 Score: 496
Period size: 84 Copynumber: 3.0 Consensus size: 84
29309332 GGATTTCAAA
29309342 AATGCAAAGAACATTAAAAACGGGGCAAAGATGGACTTACAATCAAGCTTGGAAGTTTTAAAACC
1 AATGCAAAGAACATTAAAAACGGGGCAAAGATGGACTTACAATCAAGCTTGGAAGTTTTAAAACC
29309407 CCTAGCCATGTCTTCAGTC
66 CCTAGCCATGTCTTCAGTC
29309426 AATGCAAAGAACATTAAAAACGGGGCAAAGATGGACTTACAATCAAGCTTGGAAGTTTTAAAACC
1 AATGCAAAGAACATTAAAAACGGGGCAAAGATGGACTTACAATCAAGCTTGGAAGTTTTAAAACC
29309491 CCTAGCCATGTCTTCAGTC
66 CCTAGCCATGTCTTCAGTC
29309510 AATGCAAAGAACATTAAAAACGGGGCAAAGATGGACTTACAATCAAGCTTGGAAGTTTTAAAACC
1 AATGCAAAGAACATTAAAAACGGGGCAAAGATGGACTTACAATCAAGCTTGGAAGTTTTAAAACC
29309575 CCTAGCCATGTCTTC
66 CCTAGCCATGTCTTC
29309590 CATCTCCATA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 164 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (84 bp):
AATGCAAAGAACATTAAAAACGGGGCAAAGATGGACTTACAATCAAGCTTGGAAGTTTTAAAACC
CCTAGCCATGTCTTCAGTC
Found at i:29314455 original size:48 final size:48
Alignment explanation
Indices: 29314329--29314456 Score: 150
Period size: 48 Copynumber: 2.7 Consensus size: 48
29314319 TAACATGAAT
* *
29314329 AACCATAGCATATCCACTTAGCACCACGTTA-ATGAATCGATATATGC
1 AACCATCGCATATCCACTTAGCACCACGTTACATGAATCAATATATGC
* * * *
29314376 AACCATCGCATATCCACTTAGCACCATGTTACATGTATCAATATGTGT
1 AACCATCGCATATCCACTTAGCACCACGTTACATGAATCAATATATGC
* * * * *
29314424 AATCGTGGTATATCCACTTAGCACTACGTTACA
1 AACCATCGCATATCCACTTAGCACCACGTTACA
29314457 CATATAACCG
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 29 0.43
48 39 0.57
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (48 bp):
AACCATCGCATATCCACTTAGCACCACGTTACATGAATCAATATATGC
Found at i:29318875 original size:19 final size:19
Alignment explanation
Indices: 29318851--29318887 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29318841 ATTATTTCCT
*
29318851 ACGCTAGCTACGGATGTAA
1 ACGCTAGCTACAGATGTAA
29318870 ACGCTAGCTACAGATGTA
1 ACGCTAGCTACAGATGTA
29318888 GCCTGAGTCC
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:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (19 bp):
ACGCTAGCTACAGATGTAA
Found at i:29331428 original size:28 final size:29
Alignment explanation
Indices: 29331392--29331495 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 29
29331382 GTAAGCATGA
*
29331392 ATATGAATGT-AATTGGGCCTAACAGGCC
1 ATATAAATGTGAATTGGGCCTAACAGGCC
* **
29331420 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGAATTGGGCCTAACAGGCC
* * * * **
29331449 ATATACAGGTGATTTAGGCCTAATGGGCC
1 ATATAAATGTGAATTGGGCCTAACAGGCC
* *
29331478 ATATGAATATG-ATTGGGC
1 ATATAAATGTGAATTGGGC
29331496 TTAATGGGCC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
28 14 0.23
29 48 0.77
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (29 bp):
ATATAAATGTGAATTGGGCCTAACAGGCC
Found at i:29331441 original size:29 final size:29
Alignment explanation
Indices: 29331404--29331506 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
29331394 ATGAATGTAA
**
29331404 TTGGGCCTAACAGGCCATATAAATGTGAT
1 TTGGGCCTAATGGGCCATATAAATGTGAT
* *
29331433 TTGGGCCTAATGGGCCATATACAGGTGAT
1 TTGGGCCTAATGGGCCATATAAATGTGAT
* * *
29331462 TTAGGCCTAATGGGCCATATGAATATGA-
1 TTGGGCCTAATGGGCCATATAAATGTGAT
*
29331490 TTGGGCTTAATGGGCCA
1 TTGGGCCTAATGGGCCA
29331507 AATATAGATA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
28 15 0.24
29 48 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATAAATGTGAT
Found at i:29334430 original size:7 final size:7
Alignment explanation
Indices: 29334418--29334443 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29334408 CTTAGATGAA
29334418 TTGGGCT
1 TTGGGCT
29334425 TTGGGCT
1 TTGGGCT
29334432 TTGGGCT
1 TTGGGCT
29334439 TTGGG
1 TTGGG
29334444 TTTCATATAA
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:0.00, C:0.12, G:0.46, T:0.42
Consensus pattern (7 bp):
TTGGGCT
Found at i:29335668 original size:16 final size:16
Alignment explanation
Indices: 29335638--29335681 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
29335628 TATGAATCGA
*
29335638 CAAAA-GCCAAAATGC
1 CAAAATGCCGAAATGC
29335653 CAAAATGCCGAAATGC
1 CAAAATGCCGAAATGC
**
29335669 TGAAATGCCGAAA
1 CAAAATGCCGAAA
29335682 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (16 bp):
CAAAATGCCGAAATGC
Found at i:29335673 original size:8 final size:8
Alignment explanation
Indices: 29335647--29335681 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
29335637 ACAAAAGCCA
*
29335647 AAATGCCA
1 AAATGCCG
29335655 AAATGCCG
1 AAATGCCG
*
29335663 AAATGCTG
1 AAATGCCG
29335671 AAATGCCG
1 AAATGCCG
29335679 AAA
1 AAA
29335682 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (8 bp):
AAATGCCG
Found at i:29335947 original size:29 final size:29
Alignment explanation
Indices: 29335905--29336003 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
29335895 TGAATGTGCC
* *
29335905 TGGGCCTGACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
29335934 TGGGCCTAATGGGCCATATACAA-GTGATT
1 TGGGCCTAATGGGCCATATA-AATGTGATT
* * *
29335963 TGGGCCTAATGGGTCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
*
29335991 TGGGCTTAATGGG
1 TGGGCCTAATGGG
29336004 TCAGATACAG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
28 15 0.24
29 45 0.73
30 2 0.03
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.29
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:29339876 original size:32 final size:32
Alignment explanation
Indices: 29339802--29339877 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
29339792 TGATATTGAA
* * * * *
29339802 ATGGGCTAGGCCCAATTGATATTGGTTCTGAT
1 ATGGGCTAGGCCAAACTGATATTGATTCTAAG
*
29339834 ATGCGCTAGGCCAAACTGATATTGATTCTAAG
1 ATGGGCTAGGCCAAACTGATATTGATTCTAAG
*
29339866 ATGGGATAGGCC
1 ATGGGCTAGGCC
29339878 CAATTGAGTC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (32 bp):
ATGGGCTAGGCCAAACTGATATTGATTCTAAG
Found at i:29354008 original size:42 final size:42
Alignment explanation
Indices: 29353944--29354093 Score: 185
Period size: 42 Copynumber: 3.5 Consensus size: 42
29353934 TGAGATTACG
* *
29353944 TGTAAGACCATATCTGGAATATGGCATCGATATAAGACTTCA
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTCA
* * *
29353986 CGTAAGACCATATCTGGGATATGGCATCGATGTGAGACTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTCA
* * * *
29354028 TGTAAGACCATAGCTAGGCTATTGGCATCGATACGAGA-TTACA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGACTT-CA
*
29354071 TGTAAGGCCATATCTGGGATATG
1 TGTAAGACCATATCTGGGATATG
29354094 ACATTGGTAC
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
42 58 0.64
43 32 0.36
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGACTTCA
Found at i:29354082 original size:85 final size:84
Alignment explanation
Indices: 29353934--29354093 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 84
29353924 TTAGGGTTAC
* *
29353934 TGAGATTACGTGTAAGACCATATCTGGAATATGGCATCGATATAAGACTTCACGTAAGACCATAT
1 TGAGATTACGTGTAAGACCATAGCTGGAATATGGCATCGATACAAGACTTCACGTAAGACCATAT
29353999 CTGGGATATGGCATCGATG
66 CTGGGATATGGCATCGATG
* * * *
29354018 TGAGACTT-CGTGTAAGACCATAGCTAGG-CTATTGGCATCGATACGAGA-TTACATGTAAGGCC
1 TGAGA-TTACGTGTAAGACCATAGCT-GGAATA-TGGCATCGATACAAGACTT-CACGTAAGACC
29354080 ATATCTGGGATATG
62 ATATCTGGGATATG
29354094 ACATTGGTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
84 25 0.38
85 41 0.62
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (84 bp):
TGAGATTACGTGTAAGACCATAGCTGGAATATGGCATCGATACAAGACTTCACGTAAGACCATAT
CTGGGATATGGCATCGATG
Found at i:29368665 original size:47 final size:47
Alignment explanation
Indices: 29368609--29368713 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
29368599 TGTATTTGTT
*
29368609 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
29368656 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
29368703 AATGTGATAAG
1 TATGTGATAAG
29368714 TCCCGAAGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
Found at i:29373335 original size:8 final size:7
Alignment explanation
Indices: 29373312--29373343 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
29373302 GGACCCTATA
29373312 CCTAAAC
1 CCTAAAC
29373319 CCTAAAC
1 CCTAAAC
29373326 CCTAAAAC
1 CCT-AAAC
29373334 CCTAAAC
1 CCTAAAC
29373341 CCT
1 CCT
29373344 CGTTCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.16
Consensus pattern (7 bp):
CCTAAAC
Found at i:29373335 original size:15 final size:15
Alignment explanation
Indices: 29373315--29373343 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29373305 CCCTATACCT
29373315 AAACCCTAAACCCTA
1 AAACCCTAAACCCTA
29373330 AAACCCTAAACCCT
1 AAACCCTAAACCCT
29373344 CGTTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACCCTAAACCCTA
Found at i:29381765 original size:40 final size:40
Alignment explanation
Indices: 29381706--29382069 Score: 602
Period size: 40 Copynumber: 9.1 Consensus size: 40
29381696 GAGCATTGGA
*
29381706 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
29381746 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
29381786 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
29381826 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
29381866 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
29381906 ATATATCCGGGCTAAGACCCGAAAGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
29381946 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
29381986 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
29382026 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
29382066 ATAT
1 ATAT
29382070 NNNNNNNNNN
Statistics
Matches: 310, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 310 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:29387761 original size:30 final size:30
Alignment explanation
Indices: 29387717--29387805 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
29387707 CAAAGATAAC
29387717 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
29387746 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
29387776 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
29387806 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:29387765 original size:15 final size:15
Alignment explanation
Indices: 29387717--29387796 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
29387707 CAAAGATAAC
*
29387717 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
29387731 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
29387746 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
29387761 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
29387776 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
29387791 AAGAAA
1 AAGAAA
29387797 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:29387805 original size:15 final size:15
Alignment explanation
Indices: 29387728--29387805 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
29387718 AGAAAACCGA
29387728 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
29387743 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
29387757 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
29387772 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
29387788 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
29387803 ATA
1 ATA
29387806 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:29390421 original size:46 final size:45
Alignment explanation
Indices: 29390354--29390515 Score: 168
Period size: 46 Copynumber: 3.5 Consensus size: 45
29390344 GTAACCCGCC
* * *
29390354 CCATAAGCGAACTCGGACTCAACTCAATGAGATCTGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCAT
* *
29390400 CCATAGGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* * *
29390446 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT
29390493 CCATAAGTGAACTCGGACTCAAC
1 CCATAAGTGAACTCGGACTCAAC
29390516 CATCCTAGTG
Statistics
Matches: 94, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 4 0.04
46 48 0.51
47 31 0.33
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:29394696 original size:41 final size:42
Alignment explanation
Indices: 29394627--29394716 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 42
29394617 AAATAGCAAC
* *
29394627 AAGTGTGCGATGTGGAATAGCTTTGGCTATAT-GA-GGCACT
1 AAGTGTGCGATCTGGAATAGCTTCGGCTATATAGATGGCACT
*
29394667 AAGTGTGCGATACT-GAGATAGCTTCGGCTATTTGAGATGGCACT
1 AAGTGTGCGAT-CTGGA-ATAGCTTCGGCTATAT-AGATGGCACT
29394711 AAGTGT
1 AAGTGT
29394717 ATGGGATCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 13 0.31
41 15 0.36
43 2 0.05
44 12 0.29
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (42 bp):
AAGTGTGCGATCTGGAATAGCTTCGGCTATATAGATGGCACT
Found at i:29407123 original size:145 final size:146
Alignment explanation
Indices: 29406859--29407152 Score: 538
Period size: 145 Copynumber: 2.0 Consensus size: 146
29406849 ACAGGCTAAT
*
29406859 TTGCCCATCTCTTACCCATATTGGTCCGTAAGCCCATTGGGCCTAGTTTTTGGCCCATCGAGGCC
1 TTGCCCATCTCTTACCCATATTGGTCCGTAAGCCCATTGGGCCCAGTTTTTGGCCCATCGAGGCC
*
29406924 CTCTTTTCCTGAAGTATGCTAAGACGTCACACAAACTTACTTACCACCTTGCGGTGCTAGATCTA
66 CTCTTTTCCTGAAGTACGCTAAGACGTCACACAAACTTACTTACCACCTTGCGGTGCTAGATCTA
29406989 ACAATTACTCCACGTC
131 ACAATTACTCCACGTC
29407005 TTGCCCATCTCTTACCCATATTGGTCCGTAAGCCCATTGGGCCCAG-TTTTGGCCCATCGAGGCC
1 TTGCCCATCTCTTACCCATATTGGTCCGTAAGCCCATTGGGCCCAGTTTTTGGCCCATCGAGGCC
*
29407069 CTCTTTTTCC-GAAGTACGTTAAGACGTCACACAAACTTACTTACCACCTTGCGGTGCTAGATCT
66 CTC-TTTTCCTGAAGTACGCTAAGACGTCACACAAACTTACTTACCACCTTGCGGTGCTAGATCT
29407133 AACAATTACTCCACGTC
130 AACAATTACTCCACGTC
29407150 TTG
1 TTG
29407153 AGAGCATTCG
Statistics
Matches: 144, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
145 93 0.65
146 51 0.35
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.30
Consensus pattern (146 bp):
TTGCCCATCTCTTACCCATATTGGTCCGTAAGCCCATTGGGCCCAGTTTTTGGCCCATCGAGGCC
CTCTTTTCCTGAAGTACGCTAAGACGTCACACAAACTTACTTACCACCTTGCGGTGCTAGATCTA
ACAATTACTCCACGTC
Found at i:29413761 original size:61 final size:61
Alignment explanation
Indices: 29413686--29413803 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
29413676 TGCCATATAT
*
29413686 ATAGCCGAAGCTATCTCCATCTCATATCACATACACTACTCACACTAGAGCTATCAACGGG
1 ATAGCCGAAGCTATCTCAATCTCATATCACATACACTACTCACACTAGAGCTATCAACGGG
* *
29413747 ATAGCCGAAGCTATCTCAATCTCATATCACATATACTGCTCACACTAGAGCTATCAA
1 ATAGCCGAAGCTATCTCAATCTCATATCACATACACTACTCACACTAGAGCTATCAA
29413804 TGGCCCTGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.34, C:0.30, G:0.12, T:0.25
Consensus pattern (61 bp):
ATAGCCGAAGCTATCTCAATCTCATATCACATACACTACTCACACTAGAGCTATCAACGGG
Found at i:29417016 original size:21 final size:21
Alignment explanation
Indices: 29416990--29417035 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
29416980 AGCACAGGCA
29416990 TGTCCCAGGGTCAAACGGGCG
1 TGTCCCAGGGTCAAACGGGCG
*
29417011 TGTCCCAGGGTCACACGGGCG
1 TGTCCCAGGGTCAAACGGGCG
29417032 TGTC
1 TGTC
29417036 TCTTGGACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.30, G:0.37, T:0.17
Consensus pattern (21 bp):
TGTCCCAGGGTCAAACGGGCG
Found at i:29419899 original size:31 final size:29
Alignment explanation
Indices: 29419864--29419923 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 29
29419854 ATACCTCACA
29419864 TTGTTCATTATCGGCTTAAACTAACCCCAGG
1 TTGTTCATTATCGGCTT-AA-TAACCCCAGG
*
29419895 TTGTTCATTTTCGGCTTAATAACCCCAGG
1 TTGTTCATTATCGGCTTAATAACCCCAGG
29419924 CAAAATGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 2 0.07
31 16 0.57
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (29 bp):
TTGTTCATTATCGGCTTAATAACCCCAGG
Found at i:29435234 original size:94 final size:91
Alignment explanation
Indices: 29434979--29435246 Score: 265
Period size: 94 Copynumber: 2.9 Consensus size: 91
29434969 CTCCATCGAG
* * *
29434979 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCGTGTATAC-ATGCTGATGCATGTCC
1 GCCAATGCCATGTCCCAGAC-TGGTCTTACACTGGCTATCATG-AT-CGA-GCTGATGCATGTCC
*
29435043 CAGACATGTCTTACGCTAGCAAGAAACTTA
62 CAGACATGTCTTACACTAGCAAGAAACTTA
** * * ** * *
29435073 GCTGATG-TATGTCCCAAACACGTCTTACACTGGCTAACATCATCGAGGCTGATGCATGTCCCAG
1 GCCAATGCCATGTCCCAGACTGGTCTTACACTGGCTATCATGATCGA-GCTGATGCATGTCCCAG
* *** *
29435137 ACATGTCTTACACTGGCACTCACCTCTA
65 ACATGTCTTACACTAGCAAGAAACT-TA
*
29435165 CGCCAATGCCATGTCCCAGACGTGGTCTTACACGGGCTATCATGATGCGA-CTGATGCATGTCCC
1 -GCCAATGCCATGTCCCAGAC-TGGTCTTACACTGGCTATCATGAT-CGAGCTGATGCATGTCCC
29435229 AGACATGTCTTA-ACTAGC
63 AGACATGTCTTACACTAGC
29435247 CCTCCTCTCA
Statistics
Matches: 140, Mismatches: 28, Indels: 13
0.77 0.15 0.07
Matches are distributed among these distances:
90 1 0.01
91 39 0.28
92 17 0.12
93 20 0.14
94 41 0.29
95 19 0.14
96 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (91 bp):
GCCAATGCCATGTCCCAGACTGGTCTTACACTGGCTATCATGATCGAGCTGATGCATGTCCCAGA
CATGTCTTACACTAGCAAGAAACTTA
Found at i:29435690 original size:30 final size:30
Alignment explanation
Indices: 29435633--29435690 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29435623 AAATTTATAT
* *
29435633 CTTTGATAAAATGACCATTTTGCCCCTAGA
1 CTTTGACAAAATGACCATTTTACCCCTAGA
*
29435663 CTTTGACAAAATGACCATTTTATCCCTA
1 CTTTGACAAAATGACCATTTTACCCCTA
29435691 TGCTCGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (30 bp):
CTTTGACAAAATGACCATTTTACCCCTAGA
Found at i:29438402 original size:57 final size:56
Alignment explanation
Indices: 29438310--29438422 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 56
29438300 CTCGGGGCAC
29438310 AGGCTATAACCTTGCCTTTTGCATTAGCACACTCCCTAAACCGTTTAGGGAGGCGT
1 AGGCTATAACCTTGCCTTTTGCATTAGCACACTCCCTAAACCGTTTAGGGAGGCGT
29438366 AGGCTATAACCTTGCCTTTTTGCATTAGCACACTCCCTAAACCGTTTAGGGAGGCGT
1 AGGCTATAACCTTGCC-TTTTGCATTAGCACACTCCCTAAACCGTTTAGGGAGGCGT
29438423 CATTAAAAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 16 0.29
57 40 0.71
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (56 bp):
AGGCTATAACCTTGCCTTTTGCATTAGCACACTCCCTAAACCGTTTAGGGAGGCGT
Found at i:29441680 original size:55 final size:54
Alignment explanation
Indices: 29441621--29441739 Score: 134
Period size: 55 Copynumber: 2.2 Consensus size: 54
29441611 CGTGTGCGAC
* * * **
29441621 ACTGACTTTAGGGCACGGCCATGACACACGC-CTGTGTGGCCTACCCGTGGGTAAT
1 ACTGACTTTA-GACACAGCCATGACACACGCTC-GTGTGGCCTAACCGTGGACAAT
* *
29441676 ACTGACTTATAGACACAGCTATGGCACACGCTCGTGTGGCCTAACCGTGGACAAT
1 ACTGACTT-TAGACACAGCCATGACACACGCTCGTGTGGCCTAACCGTGGACAAT
29441731 ACTGA-TTTA
1 ACTGACTTTA
29441740 AAAATTTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 48 0.87
56 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (54 bp):
ACTGACTTTAGACACAGCCATGACACACGCTCGTGTGGCCTAACCGTGGACAAT
Found at i:29442604 original size:49 final size:48
Alignment explanation
Indices: 29442499--29442860 Score: 193
Period size: 47 Copynumber: 7.7 Consensus size: 48
29442489 AAGTTACCGC
*
29442499 TGCCATGTCCCAGACATGGTCTTACGCTAGCTATCTCCATCGAGGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCTCCATC-AGGTCGA
* ** *
29442548 TGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTGTAT-ATGTGCTGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATC-TCCATCAGGT-C-GA
*** *
29442598 TG-CATGTCCCAGACAT-GTCTTACACTAGC-A-CGAAACTCA-GCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCTCCA-TCAGGTCGA
* ** * * *
29442642 TG-CATGTCCCTGACA-CATCTTACACTGGCTAACAT-CATCGAGGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATC-TCCATC-AGGTCGA
* * * * *
29442689 TG-CATGTCCTAGACAT-GTCTTACACTGGC-A-CTCACCTCTACGCCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATCTC-CATC-AGGTCGA
* * ** * * *
29442735 TGCCATGTCCCAGACGTAGTCTTACACGGGCTATCAT-GATGTAGCT-GA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATC-TCCAT-CAGGTCGA
** * * *
29442783 TG-CATGTCCCAGACAT-GTCTTACACTAGCCCTCGT-CTTAATGTCGA
1 TGCCATGTCCCAGACATGGTCTTACACTAGCTATC-TCCATCAGGTCGA
*
29442829 TGCCATGTCCCAGACATGGTCTTATACTAGCT
1 TGCCATGTCCCAGACATGGTCTTACACTAGCT
29442861 CTCACATAAC
Statistics
Matches: 247, Mismatches: 43, Indels: 47
0.73 0.13 0.14
Matches are distributed among these distances:
44 28 0.11
45 8 0.03
46 37 0.15
47 70 0.28
48 44 0.18
49 51 0.21
50 8 0.03
51 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
TGCCATGTCCCAGACATGGTCTTACACTAGCTATCTCCATCAGGTCGA
Found at i:29442788 original size:94 final size:93
Alignment explanation
Indices: 29442502--29442852 Score: 320
Period size: 94 Copynumber: 3.7 Consensus size: 93
29442492 TTACCGCTGC
* * * * *
29442502 CATGTCCCAGACATGGTCTTACGCTAGCTATCTCCA-TCGAGGTCGATGCCATGTCCCAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGC-A-CTCAACTCTA-GCCGATGCCATGTCCCAGACATA
* * *
29442566 GTCTTACACTAGCTCTCGTGTATATGT-GCTGATG
62 GTCTTACACTGGCTATCATG---ATGTAGCTGATG
** * *
29442600 CATGTCCCAGACATGTCTTACACTAGCACGAAACTC-AGCCGATG-CATGTCCCTGACACA-TCT
1 CATGTCCCAGACATGTCTTACACTAGCACTCAACTCTAGCCGATGCCATGTCCCAGACATAGTCT
* * *
29442662 TACACTGGCTAACATCATCG-AGGCCGATG
66 TACACTGGCTATCATGAT-GTA-GCTGATG
* * * *
29442691 CATGTCCTAGACATGTCTTACACTGGCACTCACCTCTACGCCGATGCCATGTCCCAGACGTAGTC
1 CATGTCCCAGACATGTCTTACACTAGCACTCAACTCTA-GCCGATGCCATGTCCCAGACATAGTC
*
29442756 TTACACGGGCTATCATGATGTAGCTGATG
65 TTACACTGGCTATCATGATGTAGCTGATG
* ** * *
29442785 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCT-TAATGTCGATGCCATGTCCCAGACATGGT
1 CATGTCCCAGACATGTCTTACACTAGCACTCAACTCT-A-GCCGATGCCATGTCCCAGACATAGT
29442849 CTTA
64 CTTA
29442853 TACTAGCTCT
Statistics
Matches: 208, Mismatches: 35, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
89 2 0.01
90 1 0.00
91 37 0.18
92 15 0.07
93 20 0.10
94 82 0.39
95 22 0.11
96 3 0.01
97 12 0.06
98 14 0.07
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCAACTCTAGCCGATGCCATGTCCCAGACATAGTCT
TACACTGGCTATCATGATGTAGCTGATG
Found at i:29445921 original size:21 final size:21
Alignment explanation
Indices: 29445891--29445944 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
29445881 GTTCCATTTG
* *
29445891 GTATCGGTAGAACCCGTTAAA
1 GTATCAGTAGAACCCGTCAAA
29445912 GTATCAGTAGAACCCGTCAAA
1 GTATCAGTAGAACCCGTCAAA
* *
29445933 TTATCAATAGAA
1 GTATCAGTAGAA
29445945 GTGCAGGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
GTATCAGTAGAACCCGTCAAA
Found at i:29447236 original size:8 final size:8
Alignment explanation
Indices: 29447223--29447253 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
29447213 AAGCAAATTA
29447223 AAAAAAAC
1 AAAAAAAC
29447231 AAAAAAAC
1 AAAAAAAC
29447239 AAAAAAAC
1 AAAAAAAC
29447247 AAAAAAA
1 AAAAAAA
29447254 AAGTGAACAA
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:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:29452847 original size:75 final size:75
Alignment explanation
Indices: 29452745--29452891 Score: 231
Period size: 75 Copynumber: 2.0 Consensus size: 75
29452735 AATTTCACGT
* * * * *
29452745 TCCCTCTCTTGATCGCGTTCACTCTCGTGTCTCCTCAACCTACTACTGCTTCTCTCTCTCCTATC
1 TCCCTCTCTAGATCACGATCACTCTCGTGCCTCCTCAACCTACTACTGCTCCTCTCTCTCCTATC
29452810 TCTCTCCCGC
66 TCTCTCCCGC
* *
29452820 TCCCTCTCTAGCTCACGATCACTCTCGTGCCTCCTCGACCTACTACTGCTCCTCTCTCTCCTATC
1 TCCCTCTCTAGATCACGATCACTCTCGTGCCTCCTCAACCTACTACTGCTCCTCTCTCTCCTATC
29452885 TCTCTCC
66 TCTCTCC
29452892 ACTGCTTCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.10, C:0.46, G:0.09, T:0.35
Consensus pattern (75 bp):
TCCCTCTCTAGATCACGATCACTCTCGTGCCTCCTCAACCTACTACTGCTCCTCTCTCTCCTATC
TCTCTCCCGC
Found at i:29453445 original size:9 final size:9
Alignment explanation
Indices: 29453431--29453457 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
29453421 GGATACGATA
29453431 TGTGTGAAG
1 TGTGTGAAG
29453440 TGTGTGAAG
1 TGTGTGAAG
29453449 TGTGTGAAG
1 TGTGTGAAG
29453458 CGTACGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (9 bp):
TGTGTGAAG
Found at i:29453789 original size:20 final size:18
Alignment explanation
Indices: 29453752--29453790 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
29453742 TTTATTTTTA
*
29453752 AAAATATTTAAAATTATT
1 AAAATATTTAAAAATATT
29453770 AAAATATTAATAAAAATATT
1 AAAATATT--TAAAAATATT
29453790 A
1 A
29453791 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTTAAAAATATT
Found at i:29453833 original size:26 final size:26
Alignment explanation
Indices: 29453772--29453821 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
29453762 AAATTATTAA
*
29453772 AATATTAATAAAAATATTATATTTTT
1 AATATTATTAAAAATATTATATTTTT
*
29453798 AATATTATTAAACATA-TATATTTT
1 AATATTATTAAAAATATTATATTTT
29453822 ATTATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATTATTAAAAATATTATATTTTT
Found at i:29453854 original size:94 final size:98
Alignment explanation
Indices: 29453756--29453976 Score: 276
Period size: 95 Copynumber: 2.3 Consensus size: 98
29453746 TTTTTAAAAA
* * *
29453756 TATTTAAAATTATTAAAATATTAATAAAAATATTATAT-TTTTAATATTATTAAACATATATATT
1 TATTTATAATTATTAAAATATTAATAAAAATATTATATCTTTCAATATTATTAAACATACATATT
*
29453820 TTATTATTT-TATTATA-TT-GATAATAAATT-T
66 TAATTATTTATATT-TAGTTAGATAATAAATTAT
* *
29453850 TATTT-TTATTTTTAAAAATATTAATAAAAATATTATATCTTTCAATATTATTAAACATACATAT
1 TATTTATAATTATT-AAAATATTAATAAAAATATTATATCTTTCAATATTATTAAACATACATAT
*
29453914 TTAATTATTTATATTTAGTTATATAATAAATTAT
65 TTAATTATTTATATTTAGTTAGATAATAAATTAT
**
29453948 T-TTTATAATTAATATAATTTATTAATAAA
1 TATTTATAATT-AT-TAAAATATTAATAAA
29453977 TTATTTAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
93 5 0.05
94 29 0.27
95 34 0.32
96 6 0.06
97 13 0.12
98 6 0.06
99 13 0.12
100 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (98 bp):
TATTTATAATTATTAAAATATTAATAAAAATATTATATCTTTCAATATTATTAAACATACATATT
TAATTATTTATATTTAGTTAGATAATAAATTAT
Found at i:29453956 original size:16 final size:16
Alignment explanation
Indices: 29453935--29453982 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
29453925 TATTTAGTTA
29453935 TATAATAAATTATTTT
1 TATAATAAATTATTTT
* *
29453951 TATAATTAA-TATAATT
1 TATAATAAATTAT-TTT
29453967 TATTAATAAATTATTT
1 TA-TAATAAATTATTT
29453983 AATATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 12 0.48
17 7 0.28
18 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATAATAAATTATTTT
Found at i:29453993 original size:33 final size:34
Alignment explanation
Indices: 29453932--29454012 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
29453922 TTATATTTAG
*
29453932 TTATATAATAAATTATTTTTATAATTAA-TATAAT
1 TTAT-TAATAAATTATTTATATAATTAATTATAAT
* * *
29453966 TTATTAATAAATTATTTA-ATATTTTAATTTTATT
1 TTATTAATAAATTATTTATATA-ATTAATTATAAT
*
29454000 TTAATAATAAATT
1 TTATTAATAAATT
29454013 TTAAAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 3 0.08
33 17 0.43
34 20 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TTATTAATAAATTATTTATATAATTAATTATAAT
Found at i:29454037 original size:16 final size:17
Alignment explanation
Indices: 29454001--29454037 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
29453991 AATTTTATTT
29454001 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
29454018 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
29454033 TAATA
1 TAATA
29454038 TTATTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:29454875 original size:16 final size:15
Alignment explanation
Indices: 29454842--29454878 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
29454832 AGCACTCAAA
29454842 TTTTCAACATTTATT
1 TTTTCAACATTTATT
*
29454857 TTTTCAACATTTAAT
1 TTTTCAACATTTATT
29454872 TTTTCAA
1 TTTTCAA
29454879 TTTATCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTCAACATTTATT
Found at i:29455504 original size:20 final size:22
Alignment explanation
Indices: 29455468--29455514 Score: 80
Period size: 20 Copynumber: 2.2 Consensus size: 22
29455458 CTTTTAATAA
29455468 TAAATTTTAACAATAATATTTT
1 TAAATTTTAACAATAATATTTT
29455490 TAAATTTT-A-AATAATATTTT
1 TAAATTTTAACAATAATATTTT
29455510 TAAAT
1 TAAAT
29455515 AATATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 16 0.64
21 1 0.04
22 8 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATTTTAACAATAATATTTT
Found at i:29455512 original size:13 final size:13
Alignment explanation
Indices: 29455494--29455520 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29455484 TATTTTTAAA
29455494 TTTTAAATAATAT
1 TTTTAAATAATAT
29455507 TTTTAAATAATAT
1 TTTTAAATAATAT
29455520 T
1 T
29455521 GAAAAATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAATAATAT
Found at i:29455624 original size:22 final size:24
Alignment explanation
Indices: 29455574--29455625 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
29455564 AATTTATAGA
* *
29455574 TATTTAATAATAAATAAAATATTAT
1 TATTTAATAAT-AATAAAATATAAG
29455599 TATTTAATAAT-AT-AAATATAAG
1 TATTTAATAATAATAAAATATAAG
29455621 TATTT
1 TATTT
29455626 GTTTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.48
23 2 0.08
25 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TATTTAATAATAATAAAATATAAG
Found at i:29455624 original size:25 final size:24
Alignment explanation
Indices: 29455574--29455624 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
29455564 AATTTATAGA
*
29455574 TATTTAATAATAAATAAAATATTAT
1 TATTTAATAAT-AATAAAATAGTAT
29455599 TATTTAATAAT-ATAAATATAAGTAT
1 TATTTAATAATAATAAA-AT-AGTAT
29455624 T
1 T
29455625 TGTTTAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
24 2 0.09
25 16 0.70
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TATTTAATAATAATAAAATAGTAT
Found at i:29456591 original size:22 final size:22
Alignment explanation
Indices: 29456549--29456593 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
29456539 AAATATGTCG
*
29456549 TTTTTTTTAATTGGTTAAAAATA
1 TTTTTTTTAATT-GTAAAAAATA
29456572 TTTTTTTTAATT-TAAGAAAATA
1 TTTTTTTTAATTGTAA-AAAATA
29456594 GGTTGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 6 0.30
23 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
TTTTTTTTAATTGTAAAAAATA
Found at i:29462081 original size:14 final size:14
Alignment explanation
Indices: 29462058--29462090 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29462048 ATGGAAATTC
*
29462058 GATTTCTACTAGTT
1 GATTTATACTAGTT
29462072 GATTTATACTAGTT
1 GATTTATACTAGTT
29462086 GATTT
1 GATTT
29462091 CCTAACATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (14 bp):
GATTTATACTAGTT
Found at i:29462702 original size:26 final size:26
Alignment explanation
Indices: 29462651--29462702 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29462641 TTTTCTTCAT
*
29462651 GTTTTTAATAACATAAAGAGCTATGA
1 GTTTTTAATAACATAAAGAGCAATGA
*
29462677 GTTTTTGAATAACATAAA-ATCAATGA
1 GTTTTT-AATAACATAAAGAGCAATGA
29462703 TTATGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (26 bp):
GTTTTTAATAACATAAAGAGCAATGA
Found at i:29463135 original size:34 final size:35
Alignment explanation
Indices: 29463091--29463165 Score: 104
Period size: 34 Copynumber: 2.2 Consensus size: 35
29463081 TTCTTAATAA
29463091 TAAT-ATTATATTAA-AATTGTTATTAAATAT-TA-T
1 TAATAATTATATTAAGAA-TGTTATTAAAT-TGTATT
29463124 TAATAATTATATTAAGAATGTTATTAAATTGTATT
1 TAATAATTATATTAAGAATGTTATTAAATTGTATT
29463159 TAATAAT
1 TAATAAT
29463166 AATTATGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
33 5 0.13
34 23 0.61
35 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (35 bp):
TAATAATTATATTAAGAATGTTATTAAATTGTATT
Found at i:29463245 original size:25 final size:26
Alignment explanation
Indices: 29463196--29463245 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
29463186 AAATTATTTT
*
29463196 TTATTAAAATATATTTAACAATAATC
1 TTATTAAAATATATATAACAATAATC
*
29463222 TTATTAAAATTTA-ATAACAATAAT
1 TTATTAAAATATATATAACAATAAT
29463246 TAACTATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TTATTAAAATATATATAACAATAATC
Found at i:29463508 original size:16 final size:16
Alignment explanation
Indices: 29463476--29463510 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29463466 TGGTTGGGGG
*
29463476 AATGGAATAGGACTGT
1 AATGGAATAGAACTGT
*
29463492 AATGGAATAGAATTGT
1 AATGGAATAGAACTGT
29463508 AAT
1 AAT
29463511 TAGTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.29
Consensus pattern (16 bp):
AATGGAATAGAACTGT
Found at i:29464163 original size:26 final size:27
Alignment explanation
Indices: 29464136--29464225 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
29464126 ATAAAAAATC
29464136 AAAACTCATAGTTTTTTATGTTATTCA
1 AAAACTCATAGTTTTTTATGTTATTCA
*
29464163 AAAAC-CATAATTCTTGATTTTATGTTATTCA
1 AAAACTCAT-A--GTT--TTTTATGTTATTCA
* * * *
29464194 AAAACTTATAGTTCTTTATATTATTAA
1 AAAACTCATAGTTTTTTATGTTATTCA
29464221 AAAAC
1 AAAAC
29464226 ATGAAGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
26 3 0.06
27 22 0.43
29 4 0.08
31 20 0.39
32 2 0.04
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (27 bp):
AAAACTCATAGTTTTTTATGTTATTCA
Found at i:29464848 original size:25 final size:25
Alignment explanation
Indices: 29464819--29464869 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29464809 CAAAGGAAAA
**
29464819 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29464844 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29464869 T
1 T
29464870 TTATAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:29469513 original size:25 final size:25
Alignment explanation
Indices: 29469484--29469534 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29469474 CAAAAGAAAA
**
29469484 TCCTAATCTAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29469509 TCCTAATAGAATTCCTAATTTAAAG
1 TCCTAATAGAATTCCTAATTTAAAG
29469534 T
1 T
29469535 TTATAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (25 bp):
TCCTAATAGAATTCCTAATTTAAAG
Found at i:29470712 original size:30 final size:30
Alignment explanation
Indices: 29470619--29470715 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
29470609 GTTTAAATAC
29470619 ATAAACCTATACCTTTCCCAGCATATGCTCAT
1 ATAAACCTATACCTTTCCCAGC--ATGCTCAT
* * *
29470651 ACAAACTTATACCCTTCCCAGCATGCTCAT
1 ATAAACCTATACCTTTCCCAGCATGCTCAT
* *
29470681 ATAAACCTATACCTTTTCTAGCATGCTCAT
1 ATAAACCTATACCTTTCCCAGCATGCTCAT
29470711 ATAAA
1 ATAAA
29470716 ATTTCAAACC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 38 0.67
32 19 0.33
ACGTcount: A:0.33, C:0.30, G:0.06, T:0.31
Consensus pattern (30 bp):
ATAAACCTATACCTTTCCCAGCATGCTCAT
Found at i:29471175 original size:133 final size:129
Alignment explanation
Indices: 29471023--29471262 Score: 374
Period size: 133 Copynumber: 1.8 Consensus size: 129
29471013 GTTTGCCAAT
29471023 AGCTAAGAACAATAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTACAAAAGAAAAAG
1 AGCTAAGAACAATAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGT---AAAGAAAAAG
* *
29471088 TAAAAACAGACAAACCCATTTAAATTTGAACTGAAAGAACACAAAAACAAAGATTGTAATTTACA
63 TAAAAACAAACAAACCCATTTAAA-TTGAACTAAAAGAACACAAAAACAAAGATTGTAATTTACA
29471153 AAG
127 AAG
* * *
29471156 AGCTAAGAAC-ATCAAAATCAACAAAAGGGGCAATCAATAAGAATCAAATAGTATAGAAAAAGTA
1 AGCTAAGAACAAT-AAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTAAAGAAAAAGTA
*
29471220 AAAACAAACAAACCCATTTTAATTGAACTAAAAGAACACAAAA
65 AAAACAAACAAACCCATTTAAATTGAACTAAAAGAACACAAAA
29471263 GCGAAGACCG
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
129 20 0.20
130 31 0.31
132 2 0.02
133 47 0.47
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.16
Consensus pattern (129 bp):
AGCTAAGAACAATAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTAAAGAAAAAGTAA
AAACAAACAAACCCATTTAAATTGAACTAAAAGAACACAAAAACAAAGATTGTAATTTACAAAG
Found at i:29471303 original size:133 final size:130
Alignment explanation
Indices: 29471025--29471291 Score: 362
Period size: 133 Copynumber: 2.1 Consensus size: 130
29471015 TTGCCAATAG
29471025 CTAAGAACAAT-AAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTACAAAAGAAAAAGT
1 CTAAGAAC-ATCAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGT--AAAAGAAAAAGT
* * **
29471089 AAAAACAGACAAACCCATTTAAATTTGAACTGAAAGAACACAAAAACAAAGATTGTAATTTACAA
63 AAAAACAAACAAACCCATTTAAATTTGAACTAAAAGAACACAAAAACAAAGACCGTAATTTA-AA
*
29471154 AGAG
127 AGAA
* * *
29471158 CTAAGAACATCAAAATCAACAAAAGGGGCAATCAATAAGAATCAAATAGT-ATAGAAAAAGTAAA
1 CTAAGAACATCAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTAAAAGAAAAAGTAAA
* * * *
29471222 AACAAACAAACCCATTTTAA-TTGAACTAAAAGAACACAAAAGCGAAGACCGTAGTTT-AAAGAA
66 AACAAACAAACCCATTTAAATTTGAACTAAAAGAACACAAAAACAAAGACCGTAATTTAAAAGAA
29471285 CTAAGAA
1 CTAAGAA
29471292 TAGCTAAATC
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
127 12 0.10
129 31 0.26
130 31 0.26
132 2 0.02
133 45 0.37
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.16
Consensus pattern (130 bp):
CTAAGAACATCAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTAAAAGAAAAAGTAAA
AACAAACAAACCCATTTAAATTTGAACTAAAAGAACACAAAAACAAAGACCGTAATTTAAAAGAA
Found at i:29472106 original size:16 final size:16
Alignment explanation
Indices: 29472070--29472117 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29472060 GATTGTTTCA
* *
29472070 CTGTAATAGAATAGGG
1 CTGTAATTGAATAGAG
*
29472086 TTGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
29472102 CTGTAA-TGTAATAGAG
1 CTGTAATTG-AATAGAG
29472118 TTATAATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 2 0.07
16 25 0.93
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:29472391 original size:17 final size:17
Alignment explanation
Indices: 29472369--29472401 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29472359 AATTATTATT
29472369 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
29472386 AAATATAATTTAATAA
1 AAATATAATTTAATAA
29472402 CATTCTTAAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:29472810 original size:14 final size:14
Alignment explanation
Indices: 29472791--29472817 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29472781 ACAAACACAA
29472791 AAAAATACAAAATG
1 AAAAATACAAAATG
29472805 AAAAATACAAAAT
1 AAAAATACAAAAT
29472818 AAATTCACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAAATACAAAATG
Found at i:29473236 original size:28 final size:30
Alignment explanation
Indices: 29473190--29473249 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
29473180 AAAGGACTTG
29473190 AAAATTAAATATAAGTTAACTTTAAT-TTTT
1 AAAATTAAATATAAGTTAA-TTTAATATTTT
* *
29473220 AAAATTATAT-TAA-TTAATTTATTATTTT
1 AAAATTAAATATAAGTTAATTTAATATTTT
29473248 AA
1 AA
29473250 CTATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 10 0.37
29 3 0.11
30 9 0.33
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
AAAATTAAATATAAGTTAATTTAATATTTT
Found at i:29475695 original size:3 final size:3
Alignment explanation
Indices: 29475689--29475720 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
29475679 AGTGAAAAAA
*
29475689 AAG AAG AAG AAT AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
29475721 AAATGGTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:29480998 original size:19 final size:19
Alignment explanation
Indices: 29480974--29481068 Score: 149
Period size: 19 Copynumber: 5.0 Consensus size: 19
29480964 CTTTAAGGAC
29480974 ATGCAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
29480993 ATGCAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
29481012 A--CAATCTTAGATATGAT
1 ATGCAATCTTAGATATGAT
*
29481029 ATGCAATCTTAAATATGAT
1 ATGCAATCTTAGATATGAT
29481048 ATGCAATCTTGAAGATATGAT
1 ATGCAATCTT--AGATATGAT
29481069 CTTGTAATCT
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
17 17 0.24
19 45 0.64
21 8 0.11
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGCAATCTTAGATATGAT
Found at i:29481001 original size:36 final size:35
Alignment explanation
Indices: 29480961--29481038 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
29480951 ATGGAAATAT
29480961 AATCTTTAAGGACATG-CAATCTTAGATATGATATGC
1 AATCTTT-A-GACATGACAATCTTAGATATGATATGC
*
29480997 AATC-TTAGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAGACATG--ACAATCTTAGATATGATATGC
29481033 AATCTT
1 AATCTT
29481039 AAATATGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
33 5 0.14
34 1 0.03
35 2 0.05
36 28 0.76
37 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (35 bp):
AATCTTTAGACATGACAATCTTAGATATGATATGC
Found at i:29481009 original size:14 final size:15
Alignment explanation
Indices: 29480990--29481027 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
29480980 TCTTAGATAT
29480990 GATATG-CAATCTTA
1 GATATGACAATCTTA
29481004 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
29481021 GATATGA
1 GATATGA
29481028 TATGCAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:29481039 original size:36 final size:37
Alignment explanation
Indices: 29480976--29481068 Score: 143
Period size: 36 Copynumber: 2.5 Consensus size: 37
29480966 TTAAGGACAT
*
29480976 GCAATCTTAGATATGATATGCAATCTTAGATATGATA
1 GCAATCTTAGATATGATATGCAATCTTAAATATGATA
29481013 -CAATCTTAGATATGATATGCAATCTTAAATATGATA
1 GCAATCTTAGATATGATATGCAATCTTAAATATGATA
29481049 TGCAATCTTGAAGATATGAT
1 -GCAATCTT--AGATATGAT
29481069 CTTGTAATCT
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
36 35 0.69
38 7 0.14
40 9 0.18
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (37 bp):
GCAATCTTAGATATGATATGCAATCTTAAATATGATA
Found at i:29482841 original size:24 final size:24
Alignment explanation
Indices: 29482814--29482861 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29482804 TGTAATTTTA
29482814 AATCTTGAAAAATTTTTAATCATT
1 AATCTTGAAAAATTTTTAATCATT
29482838 AATCTTGAAAAATTTTTAATCATT
1 AATCTTGAAAAATTTTTAATCATT
29482862 CTTTTTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (24 bp):
AATCTTGAAAAATTTTTAATCATT
Found at i:29483232 original size:13 final size:14
Alignment explanation
Indices: 29483208--29483236 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29483198 TTCATCCAAA
29483208 ATAATCCTTTTTTG
1 ATAATCCTTTTTTG
29483222 ATAAT-CTTTTTTG
1 ATAATCCTTTTTTG
29483235 AT
1 AT
29483237 TGCTTTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (14 bp):
ATAATCCTTTTTTG
Found at i:29489233 original size:209 final size:213
Alignment explanation
Indices: 29488872--29489263 Score: 643
Period size: 209 Copynumber: 1.9 Consensus size: 213
29488862 ACTGTTTTGC
* *
29488872 AAATTTTCAAGTTTTTCTAAAACTTTCTGATTTGATTCAATTTGATCCTGGATCATCCTCAAATT
1 AAATTTTCAAGTTTTTCTAAAACTTTCTGATTTGATGCAATTTGATCCTAGATCATCCTCAAATT
*
29488937 GTTTTTTAGGGCTCCATAAGTTCGATTTAAGGTCCATAAGTGATTTATTCTATAAATTGATTTCG
66 GTTTTTTAGGGCTCCATAAGTTCGATTTAAGGTCCATAAGTGATTTATTCTATAAATTGATTTCA
* *
29489002 TTTGTTATATGTTTGTT-A-ATT-ATTTGTTTAATTGGTCTGAAATGAAATGAAATGTTCTATAT
131 TTTGTTACATGTTTGTTAATATTAATTTGGTTAATTGGTCTGAAATGAAATGAAATGTTCTATAT
29489064 TGCTTAGTAACACTCTGT
196 TGCTTAGTAACACTCTGT
29489082 AAATTTTCAAGATTTTT-TAAAACTTTCTGATTTGATGCAATTTGATCCTAGATC-TCCTCAAAT
1 AAATTTTCAAG-TTTTTCTAAAACTTTCTGATTTGATGCAATTTGATCCTAGATCATCCTCAAAT
* * *
29489145 TGTTTTTTAGGGCTCCGT-ATTTCGATTTAAGGTGCATAAGTGTATTTATTCTATAAATTGATTT
65 TGTTTTTTAGGGCTCCATAAGTTCGATTTAAGGTCCATAAGTG-ATTTATTCTATAAATTGATTT
29489209 CATTTGTTACATGTTTGTTAATTATTAATTTGGTTAATTGGTCTGAAATGAAATG
129 CATTTGTTACATGTTTGTTAA-TATTAATTTGGTTAATTGGTCTGAAATGAAATG
29489264 TTCTATATTG
Statistics
Matches: 168, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
208 22 0.13
209 64 0.38
210 47 0.28
211 5 0.03
212 3 0.02
213 27 0.16
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (213 bp):
AAATTTTCAAGTTTTTCTAAAACTTTCTGATTTGATGCAATTTGATCCTAGATCATCCTCAAATT
GTTTTTTAGGGCTCCATAAGTTCGATTTAAGGTCCATAAGTGATTTATTCTATAAATTGATTTCA
TTTGTTACATGTTTGTTAATATTAATTTGGTTAATTGGTCTGAAATGAAATGAAATGTTCTATAT
TGCTTAGTAACACTCTGT
Found at i:29489334 original size:209 final size:206
Alignment explanation
Indices: 29488904--29489334 Score: 480
Period size: 209 Copynumber: 2.1 Consensus size: 206
29488894 CTTTCTGATT
* *
29488904 TGATTCAATTTGATCCTGGATCATCCTCAAATTGTTTTTTAGGGCTCCATAAGTTCGATTTAAGG
1 TGATACAATTTGATCCTAGATCATCCTCAAATTGTTTTTTAGGGCTCCATAAGTTCGATTTAAGG
* * *
29488969 TCCATAAGTGATTTATTCTATAAATTGATTTCGTTTGTTATATGTTTGTTAATTATTTGTTTAAT
66 TCCATAAGTGATTTATTCTATAAATTGATTTCATTTGTTACATGTTTGTTAATTATTTGGTTAAT
* ** * * **
29489034 TGGTCTGAAATGAAATGAAATGTTCTATATTGCTTAGTAACACTCTGTAAATTTTCAAGATTTTT
131 TGGTC----ATGAAATGAAATGTTCTATATTGCTCAGTAACACTCTGTAAACCTTCAACATATAA
* * **
29489099 TAAAACTTTCTGATT
192 TAAAACGTTCGGAGG
* * *
29489114 TGATGCAATTTGATCCTAGATC-TCCTCAAATTGTTTTTTAGGGCTCCGT-ATTTCGATTTAAGG
1 TGATACAATTTGATCCTAGATCATCCTCAAATTGTTTTTTAGGGCTCCATAAGTTCGATTTAAGG
*
29489177 TGCATAAGTGTATTTATTCTATAAATTGATTTCATTTGTTACATGTTTGTTAATTATTAATTTGG
66 TCCATAAGTG-ATTTATTCTATAAATTGATTTCATTTGTTACATGTTTGTT-A--ATT-ATTTGG
* *
29489242 TTAATTGGTC-TGAAATGAAATGTTCTATATTGCTCGGTAACATTCTGT-AACCTT-AACCCA-A
126 TTAATTGGTCATGAAATGAAATGTTCTATATTGCTCAGTAACACTCTGTAAACCTTCAA--CATA
29489303 TAATAAAGACAAGTT-GGAGG
189 TAATAAA-AC--GTTCGGAGG
*
29489323 TGTTACAATTTG
1 TGATACAATTTG
29489335 GATTAATAAA
Statistics
Matches: 188, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
206 2 0.01
207 9 0.05
208 60 0.32
209 76 0.40
210 23 0.12
212 3 0.02
213 15 0.08
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (206 bp):
TGATACAATTTGATCCTAGATCATCCTCAAATTGTTTTTTAGGGCTCCATAAGTTCGATTTAAGG
TCCATAAGTGATTTATTCTATAAATTGATTTCATTTGTTACATGTTTGTTAATTATTTGGTTAAT
TGGTCATGAAATGAAATGTTCTATATTGCTCAGTAACACTCTGTAAACCTTCAACATATAATAAA
ACGTTCGGAGG
Found at i:29498693 original size:11 final size:11
Alignment explanation
Indices: 29498677--29498724 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
29498667 TTAATTTTAG
29498677 TTATTTTAATT
1 TTATTTTAATT
*
29498688 TTATTTTATTT
1 TTATTTTAATT
29498699 TTCGATTATTAATT
1 TT--ATT-TTAATT
*
29498713 TTATTTCAATT
1 TTATTTTAATT
29498724 T
1 T
29498725 CTCTTAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 18 0.58
12 3 0.10
13 3 0.10
14 7 0.23
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (11 bp):
TTATTTTAATT
Found at i:29500629 original size:9 final size:9
Alignment explanation
Indices: 29500612--29500641 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
29500602 GTTCATGGAT
*
29500612 TGAATTGAA
1 TGAAATGAA
29500621 TGAAATGAA
1 TGAAATGAA
29500630 TGAAATGAA
1 TGAAATGAA
29500639 TGA
1 TGA
29500642 TTGAATGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (9 bp):
TGAAATGAA
Found at i:29502319 original size:19 final size:19
Alignment explanation
Indices: 29502295--29502332 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29502285 ATATCTGTGA
29502295 TTCTGTATTGTCT-GTAATG
1 TTCTGTATT-TCTGGTAATG
*
29502314 TTCTGTCTTTCTGGTAATG
1 TTCTGTATTTCTGGTAATG
29502333 CCCCTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (19 bp):
TTCTGTATTTCTGGTAATG
Found at i:29522183 original size:19 final size:19
Alignment explanation
Indices: 29522159--29522196 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
29522149 ATATCTGTGA
29522159 TTCTGTATTGTCT-GTAATG
1 TTCTGTATT-TCTGGTAATG
*
29522178 TTCTGTCTTTCTGGTAATG
1 TTCTGTATTTCTGGTAATG
29522197 CCCCTTACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (19 bp):
TTCTGTATTTCTGGTAATG
Found at i:29532920 original size:66 final size:66
Alignment explanation
Indices: 29532839--29532971 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
29532829 ACTTGTGTGA
29532839 GCAGACCCATTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGAGATAGCTTCGACTA
1 GCAGACCCATTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGAGATAGCTTCGACTA
29532904 T
66 T
29532905 GCAGACCCATTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGAGATAGCTTCGACTA
1 GCAGACCCATTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGAGATAGCTTCGACTA
29532970 T
66 T
29532971 G
1 G
29532972 TATTGACACT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (66 bp):
GCAGACCCATTGATAGCTCGAGAGTGAGCATTATATGAGATATGAGATTGAGATAGCTTCGACTA
T
Found at i:29538706 original size:18 final size:19
Alignment explanation
Indices: 29538683--29538718 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29538673 AACTTGGCAC
*
29538683 CATAA-TCATTTAATTTAA
1 CATAATTCAATTAATTTAA
29538701 CATAATTCAATTAATTTA
1 CATAATTCAATTAATTTA
29538719 CTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (19 bp):
CATAATTCAATTAATTTAA
Found at i:29539048 original size:30 final size:30
Alignment explanation
Indices: 29539014--29539074 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29539004 TCCTTAACTC
29539014 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
29539044 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
29539074 A
1 A
29539075 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:29543009 original size:12 final size:11
Alignment explanation
Indices: 29542979--29543008 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
29542969 TATACAAGTT
29542979 AAAAAAAATCC
1 AAAAAAAATCC
29542990 AAAAAAAATCC
1 AAAAAAAATCC
29543001 AAAAAAAA
1 AAAAAAAA
29543009 AGGAAGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAATCC
Found at i:29545735 original size:40 final size:40
Alignment explanation
Indices: 29545657--29545880 Score: 310
Period size: 40 Copynumber: 5.5 Consensus size: 40
29545647 ACCCAAGTAT
* *
29545657 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
29545696 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
29545736 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
29545776 CTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
29545819 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
29545859 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
29545881 CATCCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 12 0.07
40 117 0.70
41 1 0.01
43 36 0.22
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:29545853 original size:83 final size:80
Alignment explanation
Indices: 29545657--29545880 Score: 317
Period size: 83 Copynumber: 2.8 Consensus size: 80
29545647 ACCCAAGTAT
* * * *
29545657 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
29545721 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
29545736 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
29545800 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
29545819 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
29545881 CATCCGAATA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.10
80 49 0.38
83 67 0.52
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:29554467 original size:34 final size:34
Alignment explanation
Indices: 29554424--29554526 Score: 116
Period size: 37 Copynumber: 2.9 Consensus size: 34
29554414 TTTTAATTAA
29554424 ACTCATTTTAGTTAATTGAGTTGCTGGAATAAAT
1 ACTCATTTTAGTTAATTGAGTTGCTGGAATAAAT
*
29554458 ACTCATTTTAGTTATTAATTGAGTTGCTAGAATAAAT
1 ACTCATTTTAG---TTAATTGAGTTGCTGGAATAAAT
* * * * * *
29554495 GCTTATCTTAGTTAATTTAGATGTTGGAATAA
1 ACTCATTTTAGTTAATTGAGTTGCTGGAATAA
29554527 TTTATTGTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
34 28 0.48
37 30 0.52
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (34 bp):
ACTCATTTTAGTTAATTGAGTTGCTGGAATAAAT
Found at i:29554583 original size:9 final size:9
Alignment explanation
Indices: 29554571--29554629 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
29554561 AGTTAATTAA
*
29554571 GTTTAATAT
1 GTTTAATGT
29554580 GTTTAATGT
1 GTTTAATGT
*
29554589 GCTTAATGT
1 GTTTAATGT
* *
29554598 GCTTAAAGT
1 GTTTAATGT
*
29554607 GTTTAATTT
1 GTTTAATGT
29554616 GTTTTAATGT
1 G-TTTAATGT
29554626 GTTT
1 GTTT
29554630 GTTAATGAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
9 34 0.81
10 8 0.19
ACGTcount: A:0.24, C:0.03, G:0.19, T:0.54
Consensus pattern (9 bp):
GTTTAATGT
Found at i:29560434 original size:85 final size:85
Alignment explanation
Indices: 29560306--29560568 Score: 517
Period size: 85 Copynumber: 3.1 Consensus size: 85
29560296 ATTTTATTGT
*
29560306 CCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTT
1 CCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTT
29560371 AGCCATAACATCTTGTCCAC
66 AGCCATAACATCTTGTCCAC
29560391 CCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTT
1 CCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTT
29560456 AGCCATAACATCTTGTCCAC
66 AGCCATAACATCTTGTCCAC
29560476 CCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTT
1 CCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTT
29560541 AGCCATAACATCTTGTCCAC
66 AGCCATAACATCTTGTCCAC
29560561 CCATGCTC
1 CCATGCTC
29560569 ATGGCCGGCC
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 177 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (85 bp):
CCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTTT
AGCCATAACATCTTGTCCAC
Found at i:29564296 original size:43 final size:41
Alignment explanation
Indices: 29564247--29564338 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
29564237 TCCGAGACGT
*
29564247 GGTCTTACATGTAATCAAACATCGATGCC-ACTGTCCCAAACA
1 GGTCTTACATGAAATCAAACA-CGATGCCGA-TGTCCCAAACA
* * * *
29564289 GGATCTTACATGAAATTAGATACGATGCCGATGTCCCAGACA
1 GG-TCTTACATGAAATCAAACACGATGCCGATGTCCCAAACA
29564331 GGTCTTAC
1 GGTCTTAC
29564339 GCGTAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 6 0.14
42 21 0.49
43 16 0.37
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (41 bp):
GGTCTTACATGAAATCAAACACGATGCCGATGTCCCAAACA
Found at i:29565947 original size:11 final size:12
Alignment explanation
Indices: 29565921--29565954 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
29565911 GGACAAGGGC
29565921 AAAGGCAAAGGA
1 AAAGGCAAAGGA
29565933 AAAGGCAAA-GA
1 AAAGGCAAAGGA
*
29565944 AAAGGCTAAGG
1 AAAGGCAAAGG
29565955 CTAAGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.32, T:0.03
Consensus pattern (12 bp):
AAAGGCAAAGGA
Found at i:29571155 original size:140 final size:138
Alignment explanation
Indices: 29570877--29571282 Score: 634
Period size: 140 Copynumber: 2.9 Consensus size: 138
29570867 GAGAACATAG
* *
29570877 ATATAATTAATATATAAATTTGATTCATGCAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATT
* * ** * * *
29570942 AACATAAATAGTTATATTAATT-ATTTTTTTCAAAATGTAAAAGACATGGAAATTAATATTATTT
66 AATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTA
29571006 TGGAAAGA
131 TGGAAAGA
* *
29571014 ATATAATTAATATATTAATTTGATTCATACAAAATATTAATTGTATTTATATTTTACTGAATTTA
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTA--TATATTTTACTAAATTTA
*
29571079 TTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGAAATGGAAATTAATATTCT
64 TTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCT
29571144 TATGGAAAGA
129 TATGGAAAGA
* *
29571154 ATATAATTAATATATGAATTTGATTCATACAAAATGTTAATTGTATATATTTTACTAAATTTATT
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATT
* * *
29571219 AATATAAACAGTTATATTAATGAAGTTTGGTCAAAATATAAAAGACATAGAAATTAATATTCTT
66 AATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
29571283 TTAGATATAA
Statistics
Matches: 247, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
137 43 0.17
138 79 0.32
139 38 0.15
140 87 0.35
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (138 bp):
ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATT
AATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTA
TGGAAAGA
Found at i:29571295 original size:138 final size:137
Alignment explanation
Indices: 29570877--29571299 Score: 630
Period size: 138 Copynumber: 3.1 Consensus size: 137
29570867 GAGAACATAG
* *
29570877 ATATAATTAATATATAAATTTGATTCATGCAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATT
* * * ** * *
29570942 AACATAAATAGTTATATTAATTATTTTTTTCAAAATGTAAAAGACATGGAAATTAATATTATTTT
66 AATATAAACAGTTATATTAATAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTT
29571007 GGAAAGA
131 GGAAAGA
* *
29571014 ATATAATTAATATATTAATTTGATTCATACAAAATATTAATTGTATTTATATTTTACTGAATTTA
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTA--TATATTTTACTAAATTTA
*
29571079 TTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGAAATGGAAATTAATATTCT
64 TTAATATAAACAGTTATATTAA-TAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCT
*
29571144 TATGGAAAGA
128 TTTGGAAAGA
* *
29571154 ATATAATTAATATATGAATTTGATTCATACAAAATGTTAATTGTATATATTTTACTAAATTTATT
1 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATT
* *
29571219 AATATAAACAGTTATATTAATGAAGTTTGGTCAAAATATAAAAGACATAGAAATTAATATTCTTT
66 AATATAAACAGTTATATTAAT-AATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
* * *
29571284 TAGATATA
130 TGGAAAGA
29571292 ATATAATT
1 ATATAATT
29571300 CATTTTTCCA
Statistics
Matches: 259, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
137 44 0.17
138 91 0.35
139 36 0.14
140 88 0.34
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (137 bp):
ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTACTAAATTTATT
AATATAAACAGTTATATTAATAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTT
GGAAAGA
Found at i:29574673 original size:27 final size:27
Alignment explanation
Indices: 29574643--29574732 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
29574633 TTTAGTTTAC
29574643 TAAAATTA-TCGAAATACGCTTAG-TTTG
1 TAAAATTACT-GAAATAC-CTTAGATTTG
* * *
29574670 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACTGAAATACCTTAGATTTG
* *
29574697 TAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACTGAAATACCTTAGATTTG
29574724 TAAAATTAC
1 TAAAATTAC
29574733 CAAAGTACCC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.05
27 51 0.93
28 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (27 bp):
TAAAATTACTGAAATACCTTAGATTTG
Found at i:29574741 original size:27 final size:27
Alignment explanation
Indices: 29574667--29574732 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
29574657 TACGCTTAGT
* *
29574667 TTGTAAAAATACTGAAATACCCTCGAT
1 TTGTAAAATTACTGAAATACCCTCGAC
*
29574694 TTGTAAAATTACTGAAATACCTTCGAC
1 TTGTAAAATTACTGAAATACCCTCGAC
29574721 TTGTAAAATTAC
1 TTGTAAAATTAC
29574733 CAAAGTACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (27 bp):
TTGTAAAATTACTGAAATACCCTCGAC
Done.