Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 138 of 378
Found at i:39294942 original size:19 final size:18
Alignment explanation
Indices: 39294918--39294954 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
39294908 ACTAATTGAC
*
39294918 TTCATTCATTCATTTTTTT
1 TTCATT-ATTAATTTTTTT
39294937 TTCATTATTAATTTTTTT
1 TTCATTATTAATTTTTTT
39294955 AAATAAAAAT
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:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (18 bp):
TTCATTATTAATTTTTTT
Found at i:39296396 original size:15 final size:14
Alignment explanation
Indices: 39296353--39296399 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
39296343 TTACTTACTA
*
39296353 TAAAATAAATAAATT
1 TAAAATAAAT-AACT
*
39296368 TAAAATTAAT-ACT
1 TAAAATAAATAACT
39296381 TAATAATAAATAACT
1 TAA-AATAAATAACT
39296396 TAAA
1 TAAA
39296400 TTATAGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 15 0.56
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAAATAAATAACT
Found at i:39297211 original size:3 final size:3
Alignment explanation
Indices: 39297203--39297260 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
39297193 TGTCCTTACT
39297203 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39297251 TTA TTA TTA T
1 TTA TTA TTA T
39297261 CAACTTTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39297459 original size:16 final size:16
Alignment explanation
Indices: 39297422--39297459 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
39297412 TTATAATTTA
39297422 AATAAA-ATAATAATT
1 AATAAATATAATAATT
39297437 -ATAAAATATAATAATT
1 AAT-AAATATAATAATT
39297453 AATAAAT
1 AATAAAT
39297460 TAAGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.10
15 3 0.15
16 13 0.65
17 2 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAATATAATAATT
Found at i:39307689 original size:41 final size:41
Alignment explanation
Indices: 39307575--39307724 Score: 205
Period size: 41 Copynumber: 3.7 Consensus size: 41
39307565 CGCTGACTCA
*
39307575 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGC-C
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
** * * * *
39307615 CGAAGACCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTC
1 AAAAG-CCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
*
39307656 AAAAGCCCTTCGAGACCAAGCTTGGATTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
39307697 AAAAGCCCTTCGAGACCAAGCTCGGATT
1 AAAAGCCCTTCGAGACCAAGCTCGGATT
39307725 TAAACCCCGA
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
40 30 0.33
41 62 0.67
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
Found at i:39314362 original size:41 final size:41
Alignment explanation
Indices: 39314309--39314417 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 41
39314299 CGCTGACTCA
*
39314309 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCCC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCCC
* * * * * * *
39314350 GAAGGCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCCC
39314390 AAAAGCCCTTCGAGACCAAGCTCGGATT
1 AAAAGCCCTTCGAGACCAAGCTCGGATT
39314418 TAAACCCCGA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 32 0.60
41 21 0.40
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCCC
Found at i:39316965 original size:39 final size:40
Alignment explanation
Indices: 39316865--39317046 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
39316855 TCGAATGATG
* * *
39316865 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
39316905 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
*
39316945 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * *
39316984 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
39317025 -CCGGGCTTCGTCCC-AAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
39317047 TGAGCGAGTC
Statistics
Matches: 117, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
39 41 0.35
40 67 0.57
41 9 0.08
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:39317029 original size:79 final size:81
Alignment explanation
Indices: 39316865--39317048 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
39316855 TCGAATGATG
* * *
39316865 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
*
39316929 CGTGCGAGTTAATAAA
66 CGTGCGAGTCAATAAA
* **
39316945 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
*
39317007 TCGTGCGAGTCACTATAA
65 TCGTGCGAGTCAATA-AA
**
39317025 -CCGGGCTTCGTCCC-AAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39317049 AGCGAGTCGT
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 1 0.01
79 66 0.73
80 23 0.26
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTCAATAAA
Found at i:39319353 original size:79 final size:81
Alignment explanation
Indices: 39319252--39319436 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
39319242 ACGACTCGCT
** * *
39319252 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
39319315 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
39319332 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
39319396 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
39319412 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39319437 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:39319436 original size:40 final size:39
Alignment explanation
Indices: 39319245--39319436 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
39319235 GGATATAACG
* ** * *
39319245 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
39319285 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
39319325 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
39319364 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
39319404 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
39319437 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:39321690 original size:49 final size:49
Alignment explanation
Indices: 39321563--39321982 Score: 677
Period size: 49 Copynumber: 8.7 Consensus size: 49
39321553 CCCTTCGGGA
* * * * * * *
39321563 CTTATCACAT-T-TATACACTTCCACATCCATCACTTTGGCCACTCGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39321610 CCTATCACATATAT--ACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39321657 CTTATCACATATATATACACCTTCTCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
39321706 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
39321755 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
39321804 CTTATCACATATATACACACTTTCACATTCATCAAATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
*
39321853 CTGATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
39321902 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
39321951 CTTATCACATATATACACACTTTCACATTCAT
1 CTTATCACATATATACACACTTTCACATTCAT
39321983 TTCACATTCA
Statistics
Matches: 352, Mismatches: 17, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
47 50 0.14
48 1 0.00
49 301 0.86
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39322019 original size:31 final size:31
Alignment explanation
Indices: 39321924--39322020 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
39321914 ATACACACTT
39321924 TCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATTCATCACATCGGCCATTAGGCCTTA
** *
39321955 TCACATAT-ATACACA-CTTTCACATT---CATT-
1 TCACAT-TCAT-CACATC-GGC-CATTAGGCCTTA
39321984 TCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATTCATCACATCGGCCATTAGGCCTTA
39322015 TCACAT
1 TCACAT
39322021 ATATATATCT
Statistics
Matches: 50, Mismatches: 6, Indels: 20
0.66 0.08 0.26
Matches are distributed among these distances:
27 4 0.08
28 6 0.12
29 9 0.18
30 6 0.12
31 15 0.30
32 6 0.12
33 4 0.08
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (31 bp):
TCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:39324233 original size:38 final size:37
Alignment explanation
Indices: 39324186--39324295 Score: 87
Period size: 38 Copynumber: 2.8 Consensus size: 37
39324176 CGGATAGTTC
*
39324186 GAAGCAAAGTTGACACCTAGTGTCTCATCGACCTAGCT
1 GAAGTAAAGTTGACACC-AGTGTCTCATCGACCTAGCT
* ** * * *
39324224 GAAGTAAAGTGGTAC-CCAGTACCTCATCAAATCTATCT
1 GAAGTAAAGTTG-ACACCAGTGTCTCATC-GACCTAGCT
*
39324262 GAAGTAACAATATGACACCCAGTGTCTCATCGAC
1 GAAGTAA-AGT-TGACA-CCAGTGTCTCATCGAC
39324296 TCGAGGTCAA
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
37 9 0.17
38 25 0.47
39 6 0.11
40 2 0.04
41 11 0.21
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (37 bp):
GAAGTAAAGTTGACACCAGTGTCTCATCGACCTAGCT
Found at i:39326724 original size:13 final size:14
Alignment explanation
Indices: 39326706--39326735 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39326696 AGTTTCTCAT
39326706 TTTTTCTTTT-TCC
1 TTTTTCTTTTCTCC
39326719 TTTTTCTTTTCTCC
1 TTTTTCTTTTCTCC
39326733 TTT
1 TTT
39326736 CCTTTCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTCTTTTCTCC
Found at i:39326962 original size:3 final size:3
Alignment explanation
Indices: 39326954--39326982 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39326944 TATTTATTTC
39326954 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
39326983 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:39326987 original size:3 final size:3
Alignment explanation
Indices: 39326981--39327072 Score: 184
Period size: 3 Copynumber: 30.7 Consensus size: 3
39326971 AATAATAATA
39326981 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39327029 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
39327073 CATCATCTTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39327255 original size:16 final size:16
Alignment explanation
Indices: 39327217--39327262 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
39327207 TCTATAATTC
*
39327217 ATATTATAATTTAAATA
1 ATATAATAA-TTAAATA
* *
39327234 AAATAATAATTATATA
1 ATATAATAATTAAATA
39327250 ATATAATAATTAA
1 ATATAATAATTAA
39327263 GAAATTAAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATAATAATTAAATA
Found at i:39328148 original size:124 final size:124
Alignment explanation
Indices: 39327958--39328256 Score: 375
Period size: 124 Copynumber: 2.4 Consensus size: 124
39327948 CGTAACCTTC
* * *
39327958 AAAAACAGCTAGCAGACCTACACTCCCAGCTAATATTCTAAGAGCTTACAGCTCAAACACTACTA
1 AAAAACAGCTAGCGGACCTACGCTCCCAGCTAATATTCTAAGAGCTTGCAGCTCAAACACTACTA
* ** * *
39328023 GCAGACCTATGTTCCCAGCTGATGTTATAAAGGTTTGCCGGTTTATGGTCACAGCCTCA
66 GCAGACCTACGTTCCCAGCTGATGTTATAAAGGTTTGCCGGTACATGATCACAACCTCA
* * * * *
39328082 AAAAACAACTAGCGGACCTATGCTCACAGCTAATATTCTAAGAGCTCGCAGCTCCAACA-TAGCT
1 AAAAACAGCTAGCGGACCTACGCTCCCAGCTAATATTCTAAGAGCTTGCAGCTCAAACACTA-CT
* * * * * *
39328146 AGCGGACTTACGTTTCCAGCTGATGTTATAAAGGTTTGTCGGTACATGATCGCAACCTCC
65 AGCAGACCTACGTTCCCAGCTGATGTTATAAAGGTTTGCCGGTACATGATCACAACCTCA
* ** *
39328206 AAAAACAGTTAGCGGACCTACGCTCCCAATTGATATTCTAAGAGCTTGCAG
1 AAAAACAGCTAGCGGACCTACGCTCCCAGCTAATATTCTAAGAGCTTGCAG
39328257 GGTTAAGCCC
Statistics
Matches: 147, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
123 2 0.01
124 145 0.99
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (124 bp):
AAAAACAGCTAGCGGACCTACGCTCCCAGCTAATATTCTAAGAGCTTGCAGCTCAAACACTACTA
GCAGACCTACGTTCCCAGCTGATGTTATAAAGGTTTGCCGGTACATGATCACAACCTCA
Found at i:39336267 original size:14 final size:11
Alignment explanation
Indices: 39336237--39336264 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39336227 AAAGAACAAT
39336237 AAAACACCACC
1 AAAACACCACC
39336248 AAAACACCACC
1 AAAACACCACC
39336259 AAAACA
1 AAAACA
39336265 ACATTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACACCACC
Found at i:39337060 original size:22 final size:22
Alignment explanation
Indices: 39337035--39337102 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 22
39337025 CCTATACCTA
* *
39337035 AATATAAAAATAGTAACAAAAC
1 AATACAAAAATAGCAACAAAAC
*
39337057 AATACCAAAATAGCAACAAAAC
1 AATACAAAAATAGCAACAAAAC
** * * *
39337079 AGCACCAACATAGCACCAAAAC
1 AATACAAAAATAGCAACAAAAC
39337101 AA
1 AA
39337103 CAACAAAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.62, C:0.22, G:0.06, T:0.10
Consensus pattern (22 bp):
AATACAAAAATAGCAACAAAAC
Found at i:39337181 original size:22 final size:22
Alignment explanation
Indices: 39337121--39337181 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
39337111 TAACACTAAC
* *
39337121 ACAGCA-ATAAAACAACACCAA
1 ACAGCACAAAAAACAGCACCAA
** *
39337142 ACAATACAAAAAATAGCACCAA
1 ACAGCACAAAAAACAGCACCAA
39337164 ACAGCACAAAAAACAGCA
1 ACAGCACAAAAAACAGCA
39337182 TCACCAACAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.62, C:0.26, G:0.07, T:0.05
Consensus pattern (22 bp):
ACAGCACAAAAAACAGCACCAA
Found at i:39342639 original size:19 final size:19
Alignment explanation
Indices: 39342615--39342677 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
39342605 TATTCATTTA
39342615 TTTTTAATTTTTTATGTATT
1 TTTTTAATTTTTTATGTA-T
*
39342635 TTTTATAATTTTATATGTAT
1 TTTT-TAATTTTTTATGTAT
* ** *
39342655 TTTATAAAATCTTATGTAT
1 TTTTTAATTTTTTATGTAT
39342674 TTTT
1 TTTT
39342678 ATCGAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
19 14 0.40
20 8 0.23
21 13 0.37
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTAATTTTTTATGTAT
Found at i:39342645 original size:21 final size:20
Alignment explanation
Indices: 39342615--39342657 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
39342605 TATTCATTTA
*
39342615 TTTTTAATTTTTTATGTATT
1 TTTTTAATTTTATATGTATT
39342635 TTTTATAATTTTATATGTATT
1 TTTT-TAATTTTATATGTATT
39342656 TT
1 TT
39342658 ATAAAATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTAATTTTATATGTATT
Found at i:39343933 original size:47 final size:47
Alignment explanation
Indices: 39343873--39343975 Score: 145
Period size: 47 Copynumber: 2.2 Consensus size: 47
39343863 ATTATAATAA
* * *
39343873 TAAAATTT-TAGTTTTAGTATTTTGATGCCTATTAGAATTAGAATTC
1 TAAATTTTATAGTTTTAGCATTTTGACGCCTATTAGAATTAGAATTC
* * *
39343919 TATATTTTATAGTTTTAGCATTTTGGCGTCTATTAGAATTAGAATTC
1 TAAATTTTATAGTTTTAGCATTTTGACGCCTATTAGAATTAGAATTC
39343966 TAAATTTTAT
1 TAAATTTTAT
39343976 CTCTATAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 6 0.12
47 43 0.88
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.50
Consensus pattern (47 bp):
TAAATTTTATAGTTTTAGCATTTTGACGCCTATTAGAATTAGAATTC
Found at i:39344885 original size:27 final size:27
Alignment explanation
Indices: 39344855--39344912 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
39344845 AGATTATTAA
39344855 AATTCTTCCAAAAG-AAAACTC-AAGAGG
1 AATTCTT-CAAAAGAAAAACTCAAAGA-G
*
39344882 AATTCTTTAAAAGAAAAACTCAAAGAG
1 AATTCTTCAAAAGAAAAACTCAAAGAG
39344909 AATT
1 AATT
39344913 TTATTAACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 19 0.68
28 4 0.14
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (27 bp):
AATTCTTCAAAAGAAAAACTCAAAGAG
Found at i:39347565 original size:43 final size:43
Alignment explanation
Indices: 39347518--39347605 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
39347508 AAATCAAAAT
39347518 GTGTAAGAATCAATCTAACAAAGCAAACCTAATGACACTAGGA
1 GTGTAAGAATCAATCTAACAAAGCAAACCTAATGACACTAGGA
*
39347561 GTGTAAGAATCAATCTAGCAAAGCAAACCTAATGACACTAGGA
1 GTGTAAGAATCAATCTAACAAAGCAAACCTAATGACACTAGGA
39347604 GT
1 GT
39347606 CCAAAATTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.19
Consensus pattern (43 bp):
GTGTAAGAATCAATCTAACAAAGCAAACCTAATGACACTAGGA
Found at i:39351799 original size:18 final size:18
Alignment explanation
Indices: 39351772--39352067 Score: 175
Period size: 18 Copynumber: 16.1 Consensus size: 18
39351762 TCATTAACAA
* *
39351772 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAATTAT
*
39351789 TCAGTAACAATCACTTAT
1 TCAGTAACAATCAATTAT
*
39351807 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAATTAT
* * * *
39351825 TCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTAT
* *
39351843 TCAGTATCGATCAATTGATCAGTT
1 TCAGTAACAATCAA-T--T-A--T
*
39351867 ATCTAGTAACAGTCAATTAT
1 -TC-AGTAACAATCAATTAT
*
39351887 TTAGTAA-AATCAGA-TAT
1 TCAGTAACAATCA-ATTAT
* *
39351904 TCAGTAGCAATTAAGTTAT
1 TCAGTAACAATCAA-TTAT
* * *
39351923 TCAATAACAGTCATTTAT
1 TCAGTAACAATCAATTAT
* *
39351941 TCAGTGACAATCAGTTAT
1 TCAGTAACAATCAATTAT
**
39351959 TCAGTAATGATCAATTAT
1 TCAGTAACAATCAATTAT
* * *
39351977 TCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTAT
* * * *
39351995 TCAGTAATAGTCTATTGT
1 TCAGTAACAATCAATTAT
* *
39352013 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTAT
* *
39352031 TCAGTAACAGTTAATTAT
1 TCAGTAACAATCAATTAT
* *
39352049 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCAATTAT
39352067 T
1 T
39352068 TTATACCTTT
Statistics
Matches: 213, Mismatches: 53, Indels: 25
0.73 0.18 0.09
Matches are distributed among these distances:
17 17 0.08
18 164 0.77
19 14 0.07
20 1 0.00
21 1 0.00
22 2 0.01
23 1 0.00
24 1 0.00
25 3 0.01
26 9 0.04
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (18 bp):
TCAGTAACAATCAATTAT
Found at i:39351825 original size:36 final size:36
Alignment explanation
Indices: 39351772--39352067 Score: 193
Period size: 36 Copynumber: 8.0 Consensus size: 36
39351762 TCATTAACAA
* * *
39351772 TCAG-AACAATTATTTATTCAGTAACAATCACTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
39351807 TCGGTAACAATCAATTATTCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
39351843 TCAGTATCGATCAATTGATCAGTTATCTAGTAACAGTCAATTAT
1 TCAGTAACAATCAA-T--T-A--T-TC-AGTAACAATCAGTTAT
* * *
39351887 TTAGTAA-AATCAGA-TATTCAGTAGCAATTAAGTTAT
1 TCAGTAACAATCA-ATTATTCAGTAACAA-TCAGTTAT
* * * *
39351923 TCAATAACAGTCATTTATTCAGTGACAATCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
** * *
39351959 TCAGTAATGATCAATTATTCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * * * * *
39351995 TCAGTAATAGTCTATTGTCCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * *
39352031 TCAGTAACAGTTAATTATTCAGTAATAATCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
39352067 T
1 T
39352068 TTATACCTTT
Statistics
Matches: 195, Mismatches: 53, Indels: 25
0.71 0.19 0.09
Matches are distributed among these distances:
35 9 0.05
36 141 0.72
37 17 0.09
39 2 0.01
40 2 0.01
42 1 0.01
43 6 0.03
44 17 0.09
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (36 bp):
TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
Found at i:39352323 original size:45 final size:45
Alignment explanation
Indices: 39352237--39352345 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
39352227 CTGAAACAGT
* * *
39352237 AACAGTAACAGTAATAGTATTCAACACACAAAGTACTGAATCGAA
1 AACAGTAACAGTAACAGTATTCAACACACAAAATACCGAATCGAA
* * * *
39352282 AACGGTAACAGTAACAGTATTCGACACACAAAATGCCGAATCGAT
1 AACAGTAACAGTAACAGTATTCAACACACAAAATACCGAATCGAA
39352327 AACAGTAAC-GATAACAGTA
1 AACAGTAACAG-TAACAGTA
39352346 ACAGTAGTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 1 0.02
45 54 0.98
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (45 bp):
AACAGTAACAGTAACAGTATTCAACACACAAAATACCGAATCGAA
Found at i:39352340 original size:12 final size:12
Alignment explanation
Indices: 39352323--39352347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39352313 AATGCCGAAT
39352323 CGATAACAGTAA
1 CGATAACAGTAA
39352335 CGATAACAGTAA
1 CGATAACAGTAA
39352347 C
1 C
39352348 AGTAGTCGGC
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:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (12 bp):
CGATAACAGTAA
Found at i:39354076 original size:5 final size:5
Alignment explanation
Indices: 39354066--39354103 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
39354056 TTACTTATTT
*
39354066 ATATA ATATA ATATA ATATA TTATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
39354104 ACAATTTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:39354235 original size:21 final size:22
Alignment explanation
Indices: 39354196--39354248 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
39354186 CATACAATTG
*
39354196 TTAAAATAATATTATAATATCA
1 TTAAAATAATATTACAATATCA
*
39354218 TTAATATAA-ATTACAATAT-A
1 TTAAAATAATATTACAATATCA
*
39354238 ATAAAATAATA
1 TTAAAATAATA
39354249 ATATAGTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 10 0.38
22 8 0.31
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAAATAATATTACAATATCA
Found at i:39357487 original size:49 final size:49
Alignment explanation
Indices: 39357415--39357511 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
39357405 ATACTGGGTA
* * * *
39357415 TGTGTCCATTACAAGTATGCTTAATTATCTCCAAGTTTTTTCACATATC
1 TGTGTCCACTACAAGTATGCTTAATCATCTCCAAATTTTTTCAAATATC
*
39357464 TGTGTCCACTACAAGTATGCTTAATCATCTCTAAATTTTTTCAAATAT
1 TGTGTCCACTACAAGTATGCTTAATCATCTCCAAATTTTTTCAAATAT
39357512 ATTTAGAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (49 bp):
TGTGTCCACTACAAGTATGCTTAATCATCTCCAAATTTTTTCAAATATC
Found at i:39360835 original size:22 final size:22
Alignment explanation
Indices: 39360805--39360869 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
39360795 AGTAAAAGGA
39360805 TGGAAAGAGGAAACTTTAAAAG
1 TGGAAAGAGGAAACTTTAAAAG
* * **
39360827 TGGATAGAGTAAA----AGGA-
1 TGGAAAGAGGAAACTTTAAAAG
39360844 TGGAAAGAGGAAACTTTAAAAG
1 TGGAAAGAGGAAACTTTAAAAG
39360866 TGGA
1 TGGA
39360870 TAGGAAAAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
21 2 0.07
22 15 0.50
ACGTcount: A:0.48, C:0.03, G:0.31, T:0.18
Consensus pattern (22 bp):
TGGAAAGAGGAAACTTTAAAAG
Found at i:39360849 original size:39 final size:39
Alignment explanation
Indices: 39360795--39360872 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
39360785 TGAACGAAAA
39360795 AGTAAAAGGATGGAAAGAGGAAACTTTAAAAGTGGATAG
1 AGTAAAAGGATGGAAAGAGGAAACTTTAAAAGTGGATAG
39360834 AGTAAAAGGATGGAAAGAGGAAACTTTAAAAGTGGATAG
1 AGTAAAAGGATGGAAAGAGGAAACTTTAAAAGTGGATAG
39360873 GAAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.49, C:0.03, G:0.31, T:0.18
Consensus pattern (39 bp):
AGTAAAAGGATGGAAAGAGGAAACTTTAAAAGTGGATAG
Found at i:39362120 original size:7 final size:7
Alignment explanation
Indices: 39362108--39362137 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
39362098 TCTCTCTCTT
39362108 TGCCTGC
1 TGCCTGC
39362115 TGCCTGC
1 TGCCTGC
39362122 TGCCTGC
1 TGCCTGC
39362129 TGCCTGC
1 TGCCTGC
39362136 TG
1 TG
39362138 GGTTTGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.40, G:0.30, T:0.30
Consensus pattern (7 bp):
TGCCTGC
Found at i:39365395 original size:2 final size:2
Alignment explanation
Indices: 39365384--39365436 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
39365374 ATAATTGTTT
* *
39365384 TA TA -A TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39365425 TA TA TA TA TA TA
1 TA TA TA TA TA TA
39365437 AGAAGAAAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:39365409 original size:16 final size:16
Alignment explanation
Indices: 39365384--39365434 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
39365374 ATAATTGTTT
39365384 TATA-ATATATATATA
1 TATACATATATATATA
39365399 TATACATATATATATA
1 TATACATATATATATA
39365415 TATACATATATATATA
1 TATACATATATATATA
39365431 TATA
1 TATA
39365435 TAAGAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
TATACATATATATATA
Found at i:39370761 original size:40 final size:40
Alignment explanation
Indices: 39370653--39370778 Score: 146
Period size: 40 Copynumber: 3.2 Consensus size: 40
39370643 TCTTCGGAAT
* * *
39370653 TTAG-CCGGATACAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * * * *
39370692 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * *
39370732 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGGC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
39370772 TTAGCCC
1 TTAGCCC
39370779 TGGTATCATT
Statistics
Matches: 70, Mismatches: 16, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
39 3 0.04
40 67 0.96
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
Found at i:39372184 original size:13 final size:13
Alignment explanation
Indices: 39372166--39372191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39372156 TATTTATTCC
39372166 AACATAAAACACT
1 AACATAAAACACT
39372179 AACATAAAACACT
1 AACATAAAACACT
39372192 TACACAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
AACATAAAACACT
Found at i:39372711 original size:51 final size:51
Alignment explanation
Indices: 39372638--39372746 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 51
39372628 GGAGGTTCAA
* *
39372638 GTGTG-TTCTGGAGGGATGTGAAGCCTACAGGCTT-AGCACTTAGTGCCTAG
1 GTGTGTTTCTAGAGGGATGTGAAGCCTACAGGCTTGA-CACTCAGTGCCTAG
* * *
39372688 GTTTGTTTCTAGAGGGATGTGAAGCCTACGGGCTTGACGCTCAGTGCCTAG
1 GTGTGTTTCTAGAGGGATGTGAAGCCTACAGGCTTGACACTCAGTGCCTAG
39372739 GTGTGTTT
1 GTGTGTTT
39372747 ATGGATGGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
50 4 0.08
51 46 0.90
52 1 0.02
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (51 bp):
GTGTGTTTCTAGAGGGATGTGAAGCCTACAGGCTTGACACTCAGTGCCTAG
Found at i:39377498 original size:40 final size:40
Alignment explanation
Indices: 39377435--39377562 Score: 168
Period size: 41 Copynumber: 3.1 Consensus size: 40
39377425 AATATATTTT
* * *
39377435 GTTTTTGCTCAAAATGCCGCT-AAAACTGAGTAATAGCGGC
1 GTTTTTGGTCCAAACGCCGCTAAAAACTGAG-AATAGCGGC
* *
39377475 GTTTTTGGTCCAAACGCCACTAAAAACTTAGAAATAGCGGC
1 GTTTTTGGTCCAAACGCCGCTAAAAACTGAG-AATAGCGGC
*
39377516 GTTTTTAGTCCAAACGCCGCTAAAAACTGAGAAGTAGCGGC
1 GTTTTTGGTCCAAACGCCGCTAAAAACTGAGAA-TAGCGGC
39377557 GTTTTT
1 GTTTTT
39377563 TTAGCAAACA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 19 0.25
41 58 0.75
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
GTTTTTGGTCCAAACGCCGCTAAAAACTGAGAATAGCGGC
Found at i:39377513 original size:41 final size:41
Alignment explanation
Indices: 39377456--39377562 Score: 169
Period size: 41 Copynumber: 2.6 Consensus size: 41
39377446 AAATGCCGCT
* *
39377456 AAAACTGAGTAATAGCGGCGTTTTTGGTCCAAACGCCACTA
1 AAAACTGAGAAATAGCGGCGTTTTTAGTCCAAACGCCACTA
* *
39377497 AAAACTTAGAAATAGCGGCGTTTTTAGTCCAAACGCCGCTA
1 AAAACTGAGAAATAGCGGCGTTTTTAGTCCAAACGCCACTA
*
39377538 AAAACTGAGAAGTAGCGGCGTTTTT
1 AAAACTGAGAAATAGCGGCGTTTTT
39377563 TTAGCAAACA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (41 bp):
AAAACTGAGAAATAGCGGCGTTTTTAGTCCAAACGCCACTA
Found at i:39377571 original size:41 final size:40
Alignment explanation
Indices: 39377450--39377576 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 40
39377440 TGCTCAAAAT
* *
39377450 GCCGCT-AAAACTGAGTAATAGCGGCGTTTTTGGT-CCAAAC
1 GCCGCTAAAAACTGAG-AATAGCGGCGTTTTT-TTAGCAAAC
* *
39377490 GCCACTAAAAACTTAGAAATAGCGGCG--TTTTTAGTCCAAAC
1 GCCGCTAAAAACTGAG-AATAGCGGCGTTTTTTTAG--CAAAC
39377531 GCCGCTAAAAACTGAGAAGTAGCGGCGTTTTTTTAGCAAAC
1 GCCGCTAAAAACTGAGAA-TAGCGGCGTTTTTTTAGCAAAC
*
39377572 ACCGC
1 GCCGC
39377577 AAATAGTTGA
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 7 0.10
41 54 0.75
43 7 0.10
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (40 bp):
GCCGCTAAAAACTGAGAATAGCGGCGTTTTTTTAGCAAAC
Found at i:39378445 original size:20 final size:21
Alignment explanation
Indices: 39378414--39378452 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
39378404 GGGTACATAG
*
39378414 AATTAGGGTTTAGAGTTTAAA
1 AATTAGGGTTTAAAGTTTAAA
39378435 AATTA-GGTTTAAAGTTTA
1 AATTAGGGTTTAAAGTTTA
39378453 GGGTATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (21 bp):
AATTAGGGTTTAAAGTTTAAA
Found at i:39381826 original size:7 final size:7
Alignment explanation
Indices: 39381814--39381849 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
39381804 GGTTTATAGA
39381814 TTTGCTT
1 TTTGCTT
39381821 TTTGCTT
1 TTTGCTT
39381828 TTTGCTT
1 TTTGCTT
39381835 TTTGCTT
1 TTTGCTT
39381842 TTTGCTT
1 TTTGCTT
39381849 T
1 T
39381850 ATAAGTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72
Consensus pattern (7 bp):
TTTGCTT
Found at i:39381885 original size:46 final size:40
Alignment explanation
Indices: 39381822--39381923 Score: 179
Period size: 40 Copynumber: 2.6 Consensus size: 40
39381812 GATTTGCTTT
39381822 TTGCTTTTTGCTTTTTGCTTTTTGC-TTTATAAGTAACAG
1 TTGCTTTTTGCTTTTTGCTTTTTGCGTTTATAAGTAACAG
* *
39381861 TTGTTTTTTGCTTTTTTCTTTTTGCGTTTATAAGTAACAG
1 TTGCTTTTTGCTTTTTGCTTTTTGCGTTTATAAGTAACAG
39381901 TTGCTTTTTGCTTTTTGCTTTTT
1 TTGCTTTTTGCTTTTTGCTTTTT
39381924 TAATCTGTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 23 0.40
40 35 0.60
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.62
Consensus pattern (40 bp):
TTGCTTTTTGCTTTTTGCTTTTTGCGTTTATAAGTAACAG
Found at i:39382867 original size:64 final size:64
Alignment explanation
Indices: 39382657--39382854 Score: 369
Period size: 64 Copynumber: 3.1 Consensus size: 64
39382647 TAATATTTCT
*
39382657 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
39382721 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
* *
39382785 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATTATATATCCCATCTAATATACAA
1 ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
39382849 ATATTT
1 ATATTT
39382855 AATAAAATAT
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 131 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.46
Consensus pattern (64 bp):
ATATTTCTATCACGATTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
Found at i:39382929 original size:24 final size:24
Alignment explanation
Indices: 39382902--39382972 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
39382892 ATTATTATTG
* *
39382902 AAATATTCTCGTCTGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
*
39382926 AAATATTATTGTCCGTTTTATCAC
1 AAATATTATCGTCCGTTTTATCAC
39382950 AAATATTATCGTCCGTTTTATCA
1 AAATATTATCGTCCGTTTTATCA
39382973 TTTAAGTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.45
Consensus pattern (24 bp):
AAATATTATCGTCCGTTTTATCAC
Found at i:39383207 original size:28 final size:29
Alignment explanation
Indices: 39383146--39383215 Score: 106
Period size: 28 Copynumber: 2.4 Consensus size: 29
39383136 AACGACATGT
* * *
39383146 ATATTATTTAATTAAAATATTTTTTTTCA
1 ATATTATTTAATTAAAATATATTTTATAA
39383175 ATATTATTTAATTAAAATA-ATTTTATAA
1 ATATTATTTAATTAAAATATATTTTATAA
39383203 ATATTATTTAATT
1 ATATTATTTAATT
39383216 CGCAACTTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 19 0.50
29 19 0.50
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTATTTAATTAAAATATATTTTATAA
Found at i:39383211 original size:14 final size:15
Alignment explanation
Indices: 39383146--39383215 Score: 67
Period size: 14 Copynumber: 4.9 Consensus size: 15
39383136 AACGACATGT
39383146 ATATTATTTAATTAAA
1 ATATTATTTAATT-AA
* *
39383162 ATATT-TTT-TTTCA
1 ATATTATTTAATTAA
39383175 ATATTATTTAATTAA
1 ATATTATTTAATTAA
* *
39383190 A-ATAATTTTA-TAA
1 ATATTATTTAATTAA
39383203 ATATTATTTAATT
1 ATATTATTTAATT
39383216 CGCAACTTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
13 10 0.24
14 19 0.45
15 8 0.19
16 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTATTTAATTAA
Found at i:39383357 original size:9 final size:9
Alignment explanation
Indices: 39383327--39383543 Score: 185
Period size: 9 Copynumber: 24.4 Consensus size: 9
39383317 AATATTTAAC
*
39383327 ATAACTTAC
1 ATAACTTAT
* *
39383336 AAAACTTAC
1 ATAACTTAT
39383345 ATAACTTAT
1 ATAACTTAT
*
39383354 ATAACTTAG
1 ATAACTTAT
*
39383363 ATAA-ATAT
1 ATAACTTAT
39383371 ATAACTTAT
1 ATAACTTAT
*
39383380 ATAACTTAG
1 ATAACTTAT
*
39383389 ATAA-ATAT
1 ATAACTTAT
39383397 ATAACTTAT
1 ATAACTTAT
*
39383406 ATAACTTAC
1 ATAACTTAT
39383415 ATAACTTAT
1 ATAACTTAT
*
39383424 ATAACTGAT
1 ATAACTTAT
39383433 ATAACTT-T
1 ATAACTTAT
*
39383441 GATAA-ATAT
1 -ATAACTTAT
*
39383450 ATAACTTAC
1 ATAACTTAT
*
39383459 ATAACTTAC
1 ATAACTTAT
39383468 ATAACCTTAT
1 ATAA-CTTAT
*
39383478 ATAACTTAA
1 ATAACTTAT
*
39383487 ATAA-ATAT
1 ATAACTTAT
*
39383495 ATAACTTAC
1 ATAACTTAT
*
39383504 ATAA-ATAT
1 ATAACTTAT
* *
39383512 ATATCATAT
1 ATAACTTAT
*
39383521 CATAACTTAC
1 -ATAACTTAT
*
39383531 ATAACTTAC
1 ATAACTTAT
39383540 ATAA
1 ATAA
39383544 TACTTAAATA
Statistics
Matches: 169, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
8 29 0.17
9 126 0.75
10 14 0.08
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.36
Consensus pattern (9 bp):
ATAACTTAT
Found at i:39383373 original size:17 final size:17
Alignment explanation
Indices: 39383351--39383514 Score: 88
Period size: 17 Copynumber: 10.4 Consensus size: 17
39383341 TTACATAACT
39383351 TATATAACTTAGATAAA
1 TATATAACTTAGATAAA
39383368 TATATAAC-T---T--A
1 TATATAACTTAGATAAA
39383379 T--ATAACTTAGATAAA
1 TATATAACTTAGATAAA
* *
39383394 TATATAACTTATATAACT
1 TATATAACTTAGATAA-A
* * *
39383412 TACATAACTTATATAAC
1 TATATAACTTAGATAAA
*
39383429 TGATATAACTTTGATAAA
1 T-ATATAACTTAGATAAA
* *
39383447 TATATAACTTACATAACT
1 TATATAACTTAGATAA-A
* *
39383465 TACATAAC----CT---
1 TATATAACTTAGATAAA
*
39383475 TATATAACTTAAATAAA
1 TATATAACTTAGATAAA
*
39383492 TATATAACTTACATAAA
1 TATATAACTTAGATAAA
39383509 TATATA
1 TATATA
39383515 TCATATCATA
Statistics
Matches: 113, Mismatches: 16, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
9 5 0.04
10 8 0.07
11 2 0.02
13 2 0.02
14 2 0.02
15 2 0.02
16 1 0.01
17 56 0.50
18 35 0.31
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (17 bp):
TATATAACTTAGATAAA
Found at i:39383378 original size:26 final size:26
Alignment explanation
Indices: 39383345--39383490 Score: 193
Period size: 26 Copynumber: 5.5 Consensus size: 26
39383335 CAAAACTTAC
39383345 ATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTAGATAAATAT
39383371 ATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTAGATAAATAT
* *
39383397 ATAACTTATATAACTTACATAACTTAT
1 ATAACTTATATAACTTAGATAA-ATAT
* *
39383424 ATAACTGATATAACTTTGATAAATAT
1 ATAACTTATATAACTTAGATAAATAT
* * *
39383450 ATAACTTACATAACTTACATAACCTTAT
1 ATAACTTATATAACTTAGATAA--ATAT
*
39383478 ATAACTTAAATAA
1 ATAACTTATATAA
39383491 ATATATAACT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 68 0.65
27 22 0.21
28 15 0.14
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.38
Consensus pattern (26 bp):
ATAACTTATATAACTTAGATAAATAT
Found at i:39383445 original size:79 final size:80
Alignment explanation
Indices: 39383322--39383507 Score: 250
Period size: 79 Copynumber: 2.3 Consensus size: 80
39383312 TGATAAATAT
* * *
39383322 TTAACATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATATATAACTTATATAACTT
1 TTAA-ATAACTTACATAACTTACATAACTGATATAACTTAGATAAATATATAACTTACATAACTT
*
39383387 AGATAA-ATATATAAC
65 ACATAACATATATAAC
* * *
39383402 TTATATAACTTACATAACTTATATAACTGATATAACTTTGATAAATATATAACTTACATAACTTA
1 TTAAATAACTTACATAACTTACATAACTGATATAACTTAGATAAATATATAACTTACATAACTTA
*
39383467 CATAACCTTATATAAC
66 CATAA-CATATATAAC
* *
39383483 TTAAATAA-ATATATAACTTACATAA
1 TTAAATAACTTACATAACTTACATAA
39383508 ATATATATCA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
79 60 0.65
80 17 0.18
81 15 0.16
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (80 bp):
TTAAATAACTTACATAACTTACATAACTGATATAACTTAGATAAATATATAACTTACATAACTTA
CATAACATATATAAC
Found at i:39389341 original size:2 final size:2
Alignment explanation
Indices: 39389334--39389365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39389324 AATTCATTCG
39389334 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39389366 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:39389634 original size:39 final size:39
Alignment explanation
Indices: 39389608--39389712 Score: 183
Period size: 39 Copynumber: 2.7 Consensus size: 39
39389598 TCCCAGCACG
* * *
39389608 TAGCCTGCGGACCTCAAGTCCAGATATATTTCTAGCATA
1 TAGCCTGCGGATCTCATGTCCGGATATATTTCTAGCATA
39389647 TAGCCTGCGGATCTCATGTCCGGATATATTTCTAGCATA
1 TAGCCTGCGGATCTCATGTCCGGATATATTTCTAGCATA
39389686 TAGCCTGCGGATCTCATGTCCGGATAT
1 TAGCCTGCGGATCTCATGTCCGGATAT
39389713 TTCCAATCTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (39 bp):
TAGCCTGCGGATCTCATGTCCGGATATATTTCTAGCATA
Found at i:39391847 original size:10 final size:10
Alignment explanation
Indices: 39391821--39391854 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39391811 TGCTAATATA
*
39391821 ATATATATAT
1 ATATATGTAT
39391831 ATATATGTAT
1 ATATATGTAT
39391841 ATATATGT-T
1 ATATATGTAT
39391850 ATATA
1 ATATA
39391855 ATAATTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:39392632 original size:21 final size:21
Alignment explanation
Indices: 39392597--39392672 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
39392587 ACTTAGAGCG
* *
39392597 GAGGCAGCAGAGAGGGAGGCA
1 GAGGCAACAGCGAGGGAGGCA
*
39392618 GCGGCAACAGCGAGGGAGGCA
1 GAGGCAACAGCGAGGGAGGCA
*
39392639 AAGGC-ACGAGCGAGGGAGGCA
1 GAGGCAAC-AGCGAGGGAGGCA
*
39392660 GAGGCAGCAGCGA
1 GAGGCAACAGCGA
39392673 TGGCAGCAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.04
21 43 0.93
22 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.49, T:0.00
Consensus pattern (21 bp):
GAGGCAACAGCGAGGGAGGCA
Found at i:39392966 original size:31 final size:31
Alignment explanation
Indices: 39392920--39392986 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
39392910 TTGTTGTATT
* *
39392920 TTTTATGCTAAATTTGATGTTTTTGGCTGCA
1 TTTTATACTAAATTTGATGTATTTGGCTGCA
* * * *
39392951 TTTTATACTATATTTGTTGTATTTGGTTGGA
1 TTTTATACTAAATTTGATGTATTTGGCTGCA
39392982 TTTTA
1 TTTTA
39392987 ATGCAAAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.06, G:0.18, T:0.57
Consensus pattern (31 bp):
TTTTATACTAAATTTGATGTATTTGGCTGCA
Found at i:39397907 original size:13 final size:13
Alignment explanation
Indices: 39397874--39397927 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
39397864 ATTTGTTTCA
39397874 AAATAAAATATTT
1 AAATAAAATATTT
* *
39397887 -TATTAAATATTT
1 AAATAAAATATTT
39397899 AAATAAAATATCTT
1 AAATAAAATAT-TT
*
39397913 TAAT-AAATA-TT
1 AAATAAAATATTT
39397924 AAAT
1 AAAT
39397928 TTATAATACA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
11 5 0.15
12 10 0.30
13 13 0.39
14 5 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAATAAAATATTT
Found at i:39397908 original size:25 final size:26
Alignment explanation
Indices: 39397817--39397927 Score: 88
Period size: 26 Copynumber: 4.2 Consensus size: 26
39397807 AAATTTAATA
39397817 AAATACAAATATTTTATTTTAAATATTATT
1 AAATACAAATATTTTA--TTAAATA-T-TT
* *
39397847 AAATACAAATATTTTA--AATTTGTTT
1 AAATACAAATATTTTATTAA-ATATTT
39397872 CAAAATA-AAATATTTTATTAAATATTT
1 --AAATACAAATATTTTATTAAATATTT
*
39397899 AAATA-AAATATCTTTAATAAATA-TT
1 AAATACAAATAT-TTTATTAAATATTT
39397924 AAAT
1 AAAT
39397928 TTATAATACA
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
25 19 0.27
26 23 0.33
27 10 0.14
28 2 0.03
30 16 0.23
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (26 bp):
AAATACAAATATTTTATTAAATATTT
Found at i:39397921 original size:26 final size:24
Alignment explanation
Indices: 39397874--39397927 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
39397864 ATTTGTTTCA
*
39397874 AAATAAAATATTTTATTAAATATTT
1 AAATAAAATATTTTAATAAATA-TT
39397899 AAATAAAATATCTTTAATAAATATT
1 AAATAAAATAT-TTTAATAAATATT
39397924 AAAT
1 AAAT
39397928 TTATAATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.63
26 10 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATAAAATATTTTAATAAATATT
Found at i:39398182 original size:37 final size:36
Alignment explanation
Indices: 39398121--39398195 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 36
39398111 GGCATCATTT
* * * *
39398121 AATTAATTTTTAAATTTTAGAAAATTCAAATATATATA
1 AATTAATTTTTAAAATTAAAAAAATTAAAAT-TAT-TA
39398159 AATT-ATTTTTAAAATTAAAAAAATTAAAATTATTA
1 AATTAATTTTTAAAATTAAAAAAATTAAAATTATTA
39398194 AA
1 AA
39398196 AATATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 4 0.12
36 3 0.09
37 22 0.67
38 4 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (36 bp):
AATTAATTTTTAAAATTAAAAAAATTAAAATTATTA
Found at i:39398187 original size:15 final size:16
Alignment explanation
Indices: 39398167--39398204 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
39398157 TAAATTATTT
39398167 TTAAAATTA-AAAAAA
1 TTAAAATTATAAAAAA
*
39398182 TTAAAATTATTAAAAA
1 TTAAAATTATAAAAAA
39398198 TATAAAA
1 T-TAAAA
39398205 AAAACCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
17 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAATTATAAAAAA
Found at i:39398785 original size:2 final size:2
Alignment explanation
Indices: 39398778--39398802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39398768 TTAAAATAAA
39398778 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39398803 AATTAACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39400312 original size:20 final size:20
Alignment explanation
Indices: 39400289--39400371 Score: 76
Period size: 20 Copynumber: 4.2 Consensus size: 20
39400279 TAAATAATAG
* *
39400289 TAAATTATTACAAATTTTGA
1 TAAATTATTAGAAATATTGA
* *
39400309 TAAATTGTTAAAAATATTGA
1 TAAATTATTAGAAATATTGA
* * *
39400329 TAAAGTACTAGAAATAGTGA
1 TAAATTATTAGAAATATTGA
* * *
39400349 TAAATTGTTAGATATTTTGA
1 TAAATTATTAGAAATATTGA
39400369 TAA
1 TAA
39400372 TTGTTAAGAC
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (20 bp):
TAAATTATTAGAAATATTGA
Found at i:39400852 original size:29 final size:29
Alignment explanation
Indices: 39400820--39400890 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
39400810 TTGGTATGTG
*
39400820 CTTAGAAATTTTGAAAATATTTGTAAACT
1 CTTAGATATTTTGAAAATATTTGTAAACT
39400849 CTTAGATATTTTGAAAATATTTGTAAACT
1 CTTAGATATTTTGAAAATATTTGTAAACT
*
39400878 CCTAGATATTTTG
1 CTTAGATATTTTG
39400891 GTAAAGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (29 bp):
CTTAGATATTTTGAAAATATTTGTAAACT
Found at i:39401001 original size:20 final size:20
Alignment explanation
Indices: 39400976--39401023 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
39400966 CAGAGAAATT
*
39400976 TTAGAAATTTCGGTATAGGC
1 TTAGAAATTTCGATATAGGC
*
39400996 TTAGAAATTTCGATATATGC
1 TTAGAAATTTCGATATAGGC
*
39401016 CTAGAAAT
1 TTAGAAAT
39401024 ATTGGTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (20 bp):
TTAGAAATTTCGATATAGGC
Found at i:39401118 original size:39 final size:40
Alignment explanation
Indices: 39401075--39401170 Score: 126
Period size: 40 Copynumber: 2.4 Consensus size: 40
39401065 TTGGTAGATC
* *
39401075 CTAAGAAAATTTGGTAAAGC-TTAGATA-TTTGAGTAAAGT
1 CTAAGAAATTTTGGTAAAGCGTTAAATATTTTGA-TAAAGT
*
39401114 CTAAGAAATTTTGGTAAATCGTTAAATATTTTGATAAAGT
1 CTAAGAAATTTTGGTAAAGCGTTAAATATTTTGATAAAGT
39401154 -TATAGAAATTTTGGTAA
1 CTA-AGAAATTTTGGTAA
39401171 TTGGTAAGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
39 20 0.39
40 26 0.51
41 5 0.10
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.38
Consensus pattern (40 bp):
CTAAGAAATTTTGGTAAAGCGTTAAATATTTTGATAAAGT
Found at i:39401130 original size:20 final size:19
Alignment explanation
Indices: 39401018--39401170 Score: 80
Period size: 20 Copynumber: 7.7 Consensus size: 19
39401008 ATATATGCCT
* * *
39401018 AGAAATATTGGTAAATTGTT
1 AGAAATTTTGGTAAA-TCTA
*
39401038 AGAAATTCTT-GTAAATCATT
1 AGAAATT-TTGGTAAATC-TA
* *
39401058 AGATATTTTGGTAGATCCTA
1 AGAAATTTTGGTAAAT-CTA
* * *
39401078 AGAAAATTTGGTAAAGCTT
1 AGAAATTTTGGTAAATCTA
*
39401097 AGATA-TTTGAGTAAAGTCTA
1 AGAAATTTTG-GTAAA-TCTA
39401117 AGAAATTTTGGTAAATCGTTA
1 AGAAATTTTGGTAAATC--TA
* *
39401138 A-ATATTTTGATAAAGT-TA
1 AGAAATTTTGGTAAA-TCTA
39401156 TAGAAATTTTGGTAA
1 -AGAAATTTTGGTAA
39401171 TTGGTAAGAC
Statistics
Matches: 103, Mismatches: 18, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
18 6 0.06
19 17 0.17
20 69 0.67
21 11 0.11
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (19 bp):
AGAAATTTTGGTAAATCTA
Found at i:39401364 original size:20 final size:19
Alignment explanation
Indices: 39401354--39401584 Score: 88
Period size: 20 Copynumber: 11.6 Consensus size: 19
39401344 AAAGTTTTAT
39401354 ATAATTTGGTAAATCCTTAG
1 ATAATTTGGTAAAT-CTTAG
39401374 A-AATATTGGTAAAATCTTAG
1 ATAAT-TTGGT-AAATCTTAG
39401394 ATAATTTGGT-AATCCTTTAG
1 ATAATTTGGTAAAT-C-TTAG
* **
39401414 AT-TTTTGGTAAAGTAATAG
1 ATAATTTGGTAAA-TCTTAG
39401433 A-AATTGTGGT-AATCTATAAG
1 ATAATT-TGGTAAATCT-T-AG
* *
39401453 ACT--TTTGGTATAAACTTAT
1 A-TAATTTGGTA-AATCTTAG
*
39401472 A-AATATTGATAAATTCATTAG
1 ATAAT-TTGGTAAA-TC-TTAG
*
39401493 A-AATTCTGCTAAATCGTTAG
1 ATAATT-TGGTAAATC-TTAG
*
39401513 AT-ATCTTGGTAAAGTTTTAG
1 ATAAT-TTGGTAAA-TCTTAG
* *
39401533 ATATTTTGGTAAATCATTGG
1 ATAATTTGGTAAATC-TTAG
* *
39401553 ATTATTTGGTAAAGTCATAG
1 ATAATTTGGTAAA-TCTTAG
39401573 A-AATTTTGGTAA
1 ATAA-TTTGGTAA
39401585 TTGTTAAGAC
Statistics
Matches: 160, Mismatches: 23, Indels: 56
0.67 0.10 0.23
Matches are distributed among these distances:
18 4 0.03
19 30 0.19
20 96 0.60
21 30 0.19
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.41
Consensus pattern (19 bp):
ATAATTTGGTAAATCTTAG
Found at i:39401364 original size:40 final size:40
Alignment explanation
Indices: 39401320--39401410 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
39401310 TTAAAAGTAA
** * * *
39401320 TGGTAAATGGTTAGAAAT-TCAGGTAAAGTTTTATATAATT
1 TGGTAAATCCTTAGAAATAT-AGGTAAAATCTTAGATAATT
*
39401360 TGGTAAATCCTTAGAAATATTGGTAAAATCTTAGATAATT
1 TGGTAAATCCTTAGAAATATAGGTAAAATCTTAGATAATT
39401400 TGGT-AATCCTT
1 TGGTAAATCCTT
39401411 TAGATTTTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 7 0.16
40 36 0.82
41 1 0.02
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (40 bp):
TGGTAAATCCTTAGAAATATAGGTAAAATCTTAGATAATT
Found at i:39401546 original size:40 final size:40
Alignment explanation
Indices: 39401481--39401584 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 40
39401471 TAAATATTGA
* * * *
39401481 TAAATTCATTAGAAATTCTGCTAAATCGTTAGA-TATCTTGG
1 TAAAGTCA-TAGAAATTTTGGTAAATCATTAGATTAT-TTGG
** * *
39401522 TAAAGTTTTAGATATTTTGGTAAATCATTGGATTATTTGG
1 TAAAGTCATAGAAATTTTGGTAAATCATTAGATTATTTGG
39401562 TAAAGTCATAGAAATTTTGGTAA
1 TAAAGTCATAGAAATTTTGGTAA
39401585 TTGTTAAGAC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
40 43 0.84
41 8 0.16
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (40 bp):
TAAAGTCATAGAAATTTTGGTAAATCATTAGATTATTTGG
Found at i:39402161 original size:27 final size:28
Alignment explanation
Indices: 39402114--39402168 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
39402104 ACTAAGATCA
39402114 AAAGTACTAAGAATTAACATCCATAATT
1 AAAGTACTAAGAATTAACATCCATAATT
39402142 AAAGTACTAA-AATTAACATCCATAATT
1 AAAGTACTAAGAATTAACATCCATAATT
39402169 TACAAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAGTACTAAGAATTAACATCCATAATT
Found at i:39404180 original size:47 final size:44
Alignment explanation
Indices: 39404010--39404182 Score: 141
Period size: 46 Copynumber: 3.7 Consensus size: 44
39404000 ATTGTGAGCT
* * * * *
39404010 AGTGTAAGACATGTTTGGGACATGCATCAGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCA-GACGA-AGCC
* ** * *
39404056 AGTGTAAGACCATGCCTGGGACATGGCATCGGTATTTAAGAC-AAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG--CCTCAGACGAA--GCC
*
39404105 AGTGTAAGACATGTATGGGACATGCATCGGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTC-AGACG-AAGCC
39404151 AGTGTAAGACATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC
39404183 ACAGATATGC
Statistics
Matches: 100, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
45 1 0.01
46 37 0.37
47 28 0.28
48 21 0.21
49 12 0.12
50 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCAGACGAAGCC
Found at i:39404205 original size:95 final size:95
Alignment explanation
Indices: 39404008--39404230 Score: 229
Period size: 95 Copynumber: 2.3 Consensus size: 95
39403998 TTATTGTGAG
* * * *
39404008 CTAGTGTAAGACATGTTTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGCCT
1 CTAGTGTAAGACATGTATGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGCCT
* ** **
39404073 GGGACATGGCATCGGTATTTAAGACAAGTG
66 GGGACATGGCATCGGCAGATAAGACAAGAA
* *
39404103 CTAGTGTAAGACATGTATGGGACATGCATCGGCCTCGA-GACGTA-AGCCAGTGTAAGA-CATGT
1 CTAGTGTAAGACATGTATGGGACATGCATCGGCCAC-ATGACG-AGAGCCAGTGTAAGACCATGC
* *
39404165 CTGGGACATGGCATCGGCACAGATATG-CTAGAA
64 CTGGGACATGGCATCGG--CAGATAAGACAAGAA
* *
39404198 CTTGTGTAAGACCATGTATGAGACATGGCATCG
1 CTAGTGTAAGA-CATGTATGGGACAT-GCATCG
39404231 ACATCTTACC
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
94 21 0.20
95 61 0.57
96 19 0.18
97 6 0.06
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (95 bp):
CTAGTGTAAGACATGTATGGGACATGCATCGGCCACATGACGAGAGCCAGTGTAAGACCATGCCT
GGGACATGGCATCGGCAGATAAGACAAGAA
Found at i:39406173 original size:46 final size:47
Alignment explanation
Indices: 39406120--39406287 Score: 163
Period size: 46 Copynumber: 3.6 Consensus size: 47
39406110 ACTGTTGACT
*
39406120 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATT-ATGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCTGCCACATTGA-GACGAGCC
* *
39406166 AGTGTAAGACCATGTCTGGGACATGGCAT-TG--GCATTGAGACGAGAACT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCTGCCACATTGAGACGAG--CC
* * *
39406214 AGTGTAAAACATGTATGGGACATGCAT-TGGC-C-TTGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCTGCCACATTGAGACG--AGCC
39406260 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
39406288 GGCTACGATA
Statistics
Matches: 103, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
45 6 0.06
46 53 0.51
47 29 0.28
48 15 0.15
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCTGCCACATTGAGACGAGCC
Found at i:39406373 original size:140 final size:140
Alignment explanation
Indices: 39406120--39406373 Score: 350
Period size: 140 Copynumber: 1.8 Consensus size: 140
39406110 ACTGTTGACT
39406120 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
* * * *
39406185 GACATGGCATTGGCATTGAGACGAGAACTAGTGTAAAACATGTATGGGACATGCATTGGCCTTGA
66 GACATGGCATCGACATTGAGACGAGAACCAGTGTAAAACATATATGGGACATGCATTGGCCTTGA
39406250 GACGTAAGCC
131 GACGTAAGCC
* * * *
39406260 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-TATGATAGTCAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATTATGAGAGCCAGTGTAAGACCATGTCTG
* * * * * *
39406324 GGCCATGGCATCGAC-TTGAGATGTGAGCCAGTGTAAGACCATATCTGGGA
65 GGACATGGCATCGACATTGAGACGAGAACCAGTGTAA-AACATATATGGGA
39406374 TATGACATCG
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
139 17 0.17
140 80 0.82
141 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGACATTGAGACGAGAACCAGTGTAAAACATATATGGGACATGCATTGGCCTTGA
GACGTAAGCC
Found at i:39406383 original size:47 final size:46
Alignment explanation
Indices: 39406120--39406385 Score: 216
Period size: 47 Copynumber: 5.7 Consensus size: 46
39406110 ACTGTTGACT
* *** * * *
39406120 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTTGA-GACGTGAGCC
* * * *
39406166 AGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGACGAGAACT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGC-TTGAGACGTGAGCC
* * * *
39406214 AGTGTAA-AACATGTATGGGACATGCATTGGCCTTGAGACGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGG-CTTGAGACGTGAGCC
* * * *
39406260 AGTGTAAGA-CATGTCTGGGACATGCATCGGCTACGATATGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCT-TGAGACG-TGAGCC
* * *
39406306 AGTGTAAGACCATGTCTGGGCCATGGCATCGACTTGAGATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTTGAGACGTGAGCC
* *
39406353 AGTGTAAGACCATATCTGGGATATGACATCGGC
1 AGTGTAAGACCATGTCTGGGACATG-CATCGGC
39406386 ACTTTACCTA
Statistics
Matches: 179, Mismatches: 30, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.01
46 70 0.39
47 79 0.44
48 27 0.15
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCTTGAGACGTGAGCC
Found at i:39414596 original size:46 final size:48
Alignment explanation
Indices: 39414456--39414665 Score: 174
Period size: 46 Copynumber: 4.5 Consensus size: 48
39414446 TGAGCTAATA
* * *
39414456 TAAGA-CATGTCTGGGACAT-GCATCAGCCAC-ATTATG-AGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCTCGA-GATGTA-AGCCAGTG
* * * * ** *
39414502 TAAGATCGTGTCTGTGACATGGCATCGGCATTAAGATG-AATGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAA-GCCAGTG
* *
39414550 TAAGA-CATGTCTGAGACAT-GCATCGGCCTCGAGACGTAAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAAGCCAGTG
* *
39414596 TAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGTTGT--GTCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGTAAGCCAGTG
39414640 TAAGACCATGTCTGGGACATGGCATC
1 TAAGACCATGTCTGGGACATGGCATC
39414666 AGCACAAATA
Statistics
Matches: 137, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
44 11 0.08
45 16 0.12
46 60 0.44
47 27 0.20
48 22 0.16
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTAAGCCAGTG
Found at i:39417435 original size:87 final size:86
Alignment explanation
Indices: 39417324--39417482 Score: 210
Period size: 87 Copynumber: 1.8 Consensus size: 86
39417314 TTAATTTCGA
* *
39417324 TGAATTCATTAAGTCCGTCTCAATAAAACCACCCAAACTCTAGGATATGAACTCATTAAGAGTAA
1 TGAATTAATTAAGTCCGTCTCAATAAAACCACCCAAACTATAGGATATGAACTCATTAAGAGTAA
39417389 TAAACTCAACCTCTCAATTCTG
66 -AAACTCAACCTCTCAATTCTG
** * * * * * * *
39417411 TGAATTAATTAAGTTTGTTTCAATAAGACCACCCAAATTATGGGCTATGAATTTATTAAGAGTAA
1 TGAATTAATTAAGTCCGTCTCAATAAAACCACCCAAACTATAGGATATGAACTCATTAAGAGTAA
39417476 AAACTCA
66 AAACTCA
39417483 TCCTTACGCA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
86 7 0.11
87 54 0.89
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (86 bp):
TGAATTAATTAAGTCCGTCTCAATAAAACCACCCAAACTATAGGATATGAACTCATTAAGAGTAA
AAACTCAACCTCTCAATTCTG
Found at i:39439070 original size:18 final size:20
Alignment explanation
Indices: 39439033--39439073 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
39439023 TAATATTTTA
*
39439033 TTTAGTAATTATTAATATTT
1 TTTAGTAATTATTAAAATTT
39439053 TTTA-TAATT-TTAAAATTT
1 TTTAGTAATTATTAAAATTT
39439071 TTT
1 TTT
39439074 TTATAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 5 0.25
20 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTAGTAATTATTAAAATTT
Found at i:39446224 original size:3 final size:3
Alignment explanation
Indices: 39446216--39446256 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
39446206 GCATTTAGTT
39446216 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39446257 GGTTGACAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:39446441 original size:81 final size:75
Alignment explanation
Indices: 39446282--39446462 Score: 193
Period size: 81 Copynumber: 2.3 Consensus size: 75
39446272 AATTGATTTC
* * *
39446282 ATGTTTCGATTATA-ATAAATATATAATATATGCATGTTTTTTATTGACTCAAGATGCATGCTTA
1 ATGTTTCGATTATATATAAATATATAATATATGCATGTTTTTGATTCAATCAAGATGCATGCTTA
* **
39446346 ATTTATATGT
66 ATTCATATAA
* * *
39446356 ATGTTTCAATTATATATAAATATATAATATATGCATGTTCTGATTGATTCAATGTATGAGATGTA
1 ATGTTTCGATTATATATAAATATATAATATATGCATGTT-T--TTGATTCAAT-CA--AGATGCA
39446421 TGCTTAATTCATATAA
60 TGCTTAATTCATATAA
* *
39446437 ATGTTTCGGTTATATAATATATATAT
1 ATGTTTCGATTATAT-ATAAATATAT
39446463 TTTTTTTTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
74 13 0.15
75 24 0.28
76 1 0.01
78 7 0.08
79 1 0.01
81 32 0.37
82 9 0.10
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (75 bp):
ATGTTTCGATTATATATAAATATATAATATATGCATGTTTTTGATTCAATCAAGATGCATGCTTA
ATTCATATAA
Found at i:39446507 original size:2 final size:2
Alignment explanation
Indices: 39446500--39446530 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39446490 TGCTTATTTC
39446500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39446531 ATTCAATTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39447063 original size:29 final size:28
Alignment explanation
Indices: 39446992--39447071 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 28
39446982 ACCACTACCA
* *
39446992 GTACATAGTACCTAGAAATATATCACAG
1 GTACATAGTACCTGGAAATGTATCACAG
* * ** *
39447020 GCACAGAGTGTCTGGAAATTGTATCACTG
1 GTACATAGTACCTGGAAA-TGTATCACAG
39447049 GTACATAGTACCTGGAAACTGTA
1 GTACATAGTACCTGGAAA-TGTA
39447072 ATCTGTAATC
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
28 13 0.33
29 26 0.67
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (28 bp):
GTACATAGTACCTGGAAATGTATCACAG
Found at i:39457195 original size:19 final size:19
Alignment explanation
Indices: 39457136--39457199 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
39457126 AAAAGAATTT
* *
39457136 ATAAAATAACACATAATAT
1 ATAAAATAATACATAATAA
**
39457155 A-AAAAT-AT-CATTTTAA
1 ATAAAATAATACATAATAA
39457171 AGTAAAATAATACATAATAA
1 A-TAAAATAATACATAATAA
39457191 AT-AAATAAT
1 ATAAAATAAT
39457200 TAATAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 17 0.49
19 4 0.11
20 7 0.20
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAAATAATACATAATAA
Found at i:39457527 original size:19 final size:19
Alignment explanation
Indices: 39457469--39457531 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
39457459 ATGTAAAAAC
39457469 AATATATATAAATAAT-TAATA
1 AATATA-AT-AATAATATAA-A
39457490 AATAT-ATAATACA-AGTAAA
1 AATATAATAATA-ATA-TAAA
39457509 AATATAATAATAATATAAA
1 AATATAATAATAATATAAA
39457528 AATA
1 AATA
39457532 ATGATGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 10 0.27
21 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AATATAATAATAATATAAA
Found at i:39457575 original size:7 final size:7
Alignment explanation
Indices: 39457563--39457591 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39457553 AATTTGTGAA
39457563 AAATAAT
1 AAATAAT
39457570 AAATAAT
1 AAATAAT
39457577 AAATAAT
1 AAATAAT
39457584 AAATAAT
1 AAATAAT
39457591 A
1 A
39457592 GTAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:39465195 original size:53 final size:53
Alignment explanation
Indices: 39465115--39465221 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
39465105 TAAGTTATAG
* * *
39465115 CATAATATTGAATATATTCAAGTGTTAAATTCTACGAGAGATGCTTCAAGCGA
1 CATAACATTAAATATATTAAAGTGTTAAATTCTACGAGAGATGCTTCAAGCGA
* *
39465168 CATAACATTAAATATATTAAAGTGTTAAATTCTACGAGAGATGTTTGAAGCGA
1 CATAACATTAAATATATTAAAGTGTTAAATTCTACGAGAGATGCTTCAAGCGA
39465221 C
1 C
39465222 TCTTTAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (53 bp):
CATAACATTAAATATATTAAAGTGTTAAATTCTACGAGAGATGCTTCAAGCGA
Found at i:39466168 original size:18 final size:18
Alignment explanation
Indices: 39466145--39466187 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39466135 GAATAAGTTT
39466145 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
39466163 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
39466181 TTAATTA
1 TTAATTA
39466188 CACATTGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:39483052 original size:19 final size:18
Alignment explanation
Indices: 39483028--39483071 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
39483018 AATATGAATA
*
39483028 AAATTTATCTTCCTAAAT
1 AAATTTATCTACCTAAAT
39483046 AAGATTTATCTACCTAAAT
1 AA-ATTTATCTACCTAAAT
39483065 AAATTTA
1 AAATTTA
39483072 AAATATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (18 bp):
AAATTTATCTACCTAAAT
Found at i:39486979 original size:20 final size:19
Alignment explanation
Indices: 39486948--39486996 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
39486938 CTAGAATATG
*
39486948 AATAAAATTTATCTTCCTA
1 AATAAAATTTATCTACCTA
39486967 AATAAAGATTTATCTACCTA
1 AATAAA-ATTTATCTACCTA
39486987 AAT-AAATTTA
1 AATAAAATTTA
39486997 AAATATATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.18
19 8 0.29
20 15 0.54
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (19 bp):
AATAAAATTTATCTACCTA
Found at i:39491822 original size:18 final size:18
Alignment explanation
Indices: 39491796--39491833 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
39491786 GAAGGCAAGG
39491796 ACTGCGAATGTTTGGAAA
1 ACTGCGAATGTTTGGAAA
*
39491814 ACTGTGAATGTTTGGAAA
1 ACTGCGAATGTTTGGAAA
39491832 AC
1 AC
39491834 CCCTGTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (18 bp):
ACTGCGAATGTTTGGAAA
Found at i:39495049 original size:2 final size:2
Alignment explanation
Indices: 39495044--39495077 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39495034 CCATACACAC
39495044 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
39495078 TTGTCAATTT
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:39510259 original size:49 final size:48
Alignment explanation
Indices: 39510204--39510427 Score: 321
Period size: 49 Copynumber: 4.7 Consensus size: 48
39510194 TAGATTCTAC
* *
39510204 GTGATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCTAT
1 GTGATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCAAT
* *
39510253 GTGATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCGAT
1 GTGATGAATGTGAAAGTGTATA-ATATGTGATAAGGCCTAATGGCCAAT
39510302 GTGATGAATGTGAAAGTGTAT-ATATGTGATAAGGCCTAATGGCCAAT
1 GTGATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCAAT
* ** *
39510349 GTGATGAATGTGAAAGTGTAT-ATATGTGATAGGGCC-GGTGGCCAAC
1 GTGATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCAAT
*
39510395 GTGATGGATGTGAAAGTGTATAA-ATGTGATAAG
1 GTGATGAATGTGAAAGTGTATAATATGTGATAAG
39510428 TCCCGAAGGG
Statistics
Matches: 165, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
46 36 0.22
47 61 0.37
49 68 0.41
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (48 bp):
GTGATGAATGTGAAAGTGTATAATATGTGATAAGGCCTAATGGCCAAT
Found at i:39510343 original size:96 final size:93
Alignment explanation
Indices: 39510202--39510427 Score: 317
Period size: 96 Copynumber: 2.4 Consensus size: 93
39510192 TTTAGATTCT
* *
39510202 ACGTGATGAATGTGAAAGCGTATACATATGTGATAAGGCCTAATGGCCTATGTGATGAATGTGAA
1 ACGTGATGAATGTGAAAGTGTAT--ATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
*
39510267 AGCGTATACATATGTGATAAGGCCTAATGGCCG
64 AGCGTAT--ATATGTGATAAGGCC-AATGGCCA
*
39510300 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
1 ACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
* * **
39510365 TGTATATATGTGATAGGGCCGGTGGCCA
66 CGTATATATGTGATAAGGCCAATGGCCA
* *
39510393 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ACGTGATGAATGTGAAAGTGTATATATGTGATAAG
39510428 TCCCGAAGGG
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
93 37 0.32
94 14 0.12
96 45 0.38
98 21 0.18
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (93 bp):
ACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAG
CGTATATATGTGATAAGGCCAATGGCCA
Found at i:39512725 original size:2 final size:2
Alignment explanation
Indices: 39512718--39512743 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39512708 GTTTGGATGA
39512718 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
39512744 GCATTCGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39514662 original size:47 final size:47
Alignment explanation
Indices: 39514608--39514707 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 47
39514598 TTAGGATTTT
* * *
39514608 ATGTGATGAATGTGAACGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAAGCCGAATGGCCA
* * * *
39514655 ATGTGATGATTGTGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAAGCCGAATGGCCA
39514702 ATGTGA
1 ATGTGA
39514708 AATATATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAAGCCGAATGGCCA
Found at i:39514831 original size:50 final size:50
Alignment explanation
Indices: 39514677--39514812 Score: 254
Period size: 50 Copynumber: 2.7 Consensus size: 50
39514667 TGAACATGCA
39514677 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
39514727 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
* *
39514777 TATATGTGGTAAAGCCGAATGGATAGTGTGAAATAT
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
39514813 GTAGGCGATG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (50 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATG
Found at i:39515018 original size:37 final size:37
Alignment explanation
Indices: 39514962--39515069 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
39514952 GGAAATATAT
* *
39514962 TCCGGGTAAGGCCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTATG
39514999 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCAATGACTACGTGTGGAGATTATG
**
39515036 TCCGGGTAAGACCCAATGACTTTGTGTGGAGATT
1 TCCGGGTAAGACCCAATGACTACGTGTGGAGATT
39515070 TCGTCTGAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCAATGACTACGTGTGGAGATTATG
Found at i:39532958 original size:50 final size:51
Alignment explanation
Indices: 39532839--39533027 Score: 199
Period size: 50 Copynumber: 3.8 Consensus size: 51
39532829 AGGTCGCATG
* * * *
39532839 TGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTTGATCACGTG
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTTAGATCACGTA
* ** *
39532890 TGTAGTACTAAGTGCAGGCTACTATGTGTATCAGAT-GGTTAGGTCACGTA
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTTAGATCACGTA
* * * *
39532940 TGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-TT-GGT--CGCA
1 TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTTAGATCACGTA
* *
39532987 TGTACAGTACTATGTGCAGGCTACTATGCGTACCAGATAAC
1 TGT--AGTACTAAGTGCAGGCTACTATGTGTACCAGATAAC
39533028 CTTGTCTACA
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
47 6 0.05
49 34 0.29
50 44 0.38
51 33 0.28
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (51 bp):
TGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTTAGATCACGTA
Found at i:39541913 original size:5 final size:5
Alignment explanation
Indices: 39541903--39541930 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39541893 AACAACCTTA
39541903 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
39541931 TCCAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:39544163 original size:28 final size:31
Alignment explanation
Indices: 39544116--39544173 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
39544106 TTTTAATAAC
39544116 TTATATTTTTATAATTTTTAA-AGAATTAAA
1 TTATATTTTTATAATTTTTAAGAGAATTAAA
* *
39544146 TTAT-TTTTTATTA-TTTTAAGGGAATTAA
1 TTATATTTTTATAATTTTTAAGAGAATTAA
39544174 TAAAGGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 15 0.60
30 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (31 bp):
TTATATTTTTATAATTTTTAAGAGAATTAAA
Found at i:39555115 original size:21 final size:22
Alignment explanation
Indices: 39555091--39555143 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
39555081 AGTTGAGCAA
* *
39555091 TTTATCTACATCA-TTGAGTGG
1 TTTATCCACACCATTTGAGTGG
39555112 TTTATCCACACCATTTGAGTGG
1 TTTATCCACACCATTTGAGTGG
*
39555134 TTTAACCACA
1 TTTATCCACA
39555144 GTGTACTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (22 bp):
TTTATCCACACCATTTGAGTGG
Found at i:39555277 original size:18 final size:18
Alignment explanation
Indices: 39555254--39555311 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
39555244 CCATTTTATT
39555254 ACTAGTGGTTTATCCACA
1 ACTAGTGGTTTATCCACA
**
39555272 ACTAGTGGTTCGTCCACA
1 ACTAGTGGTTTATCCACA
*
39555290 ACGATGAGTAGTTTATCCACA
1 AC--T-AGTGGTTTATCCACA
39555311 A
1 A
39555312 TGTGCTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.56
20 1 0.03
21 13 0.41
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (18 bp):
ACTAGTGGTTTATCCACA
Found at i:39557901 original size:56 final size:55
Alignment explanation
Indices: 39557837--39557993 Score: 219
Period size: 56 Copynumber: 2.8 Consensus size: 55
39557827 TACAGAGTTT
* * *
39557837 GCCACAAAGGCTT-TTATTTTATAGTTTGCCACAAAAGTCTTCCTTTTTCATAGATC
1 GCCACAAAGGCTTCTT-TTTCATAGATTGCCAC-AAAGACTTCCTTTTTCATAGATC
39557893 GCCACAAAGGCTTCCTTTTTCATAGATTGCCACAAAGACTTCCTTTTTCATAGATC
1 GCCACAAAGGCTT-CTTTTTCATAGATTGCCACAAAGACTTCCTTTTTCATAGATC
* *
39557949 GCCACAAAGGCTTCCTTTTTCATAGATGGCCA-TAAGACTTCCTTT
1 GCCACAAAGGCTT-CTTTTTCATAGATTGCCACAAAGACTTCCTTT
39557994 GTCTGGCATG
Statistics
Matches: 94, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
55 12 0.13
56 66 0.70
57 14 0.15
58 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (55 bp):
GCCACAAAGGCTTCTTTTTCATAGATTGCCACAAAGACTTCCTTTTTCATAGATC
Found at i:39557906 original size:28 final size:28
Alignment explanation
Indices: 39557837--39557993 Score: 194
Period size: 28 Copynumber: 5.6 Consensus size: 28
39557827 TACAGAGTTT
* * *
39557837 GCCACAAAGGCTT--TTATTTTATAGTTT
1 GCCACAAAGGCTTCCTT-TTTCATAGATC
*
39557864 GCCACAAAAGTCTTCCTTTTTCATAGATC
1 GCCAC-AAAGGCTTCCTTTTTCATAGATC
*
39557893 GCCACAAAGGCTTCCTTTTTCATAGATT
1 GCCACAAAGGCTTCCTTTTTCATAGATC
*
39557921 GCCACAAAGACTTCCTTTTTCATAGATC
1 GCCACAAAGGCTTCCTTTTTCATAGATC
*
39557949 GCCACAAAGGCTTCCTTTTTCATAGATG
1 GCCACAAAGGCTTCCTTTTTCATAGATC
* *
39557977 GCCA-TAAGACTTCCTTT
1 GCCACAAAGGCTTCCTTT
39557994 GTCTGGCATG
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
27 16 0.14
28 84 0.73
29 13 0.11
30 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (28 bp):
GCCACAAAGGCTTCCTTTTTCATAGATC
Found at i:39560093 original size:17 final size:17
Alignment explanation
Indices: 39560073--39560131 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
39560063 TCAGTATGAT
39560073 TAAATAATTAAATAATA
1 TAAATAATTAAATAATA
* *
39560090 TAAAT-AGTAAAAAATA
1 TAAATAATTAAATAATA
*
39560106 TGAAATTTAATTCAATAATA
1 T-AAA--TAATTAAATAATA
39560126 TAAATA
1 TAAATA
39560132 GTAGACATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.30
17 10 0.30
19 4 0.12
20 9 0.27
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
TAAATAATTAAATAATA
Found at i:39561586 original size:2 final size:2
Alignment explanation
Indices: 39561579--39561624 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
39561569 TTTGTTCTTA
39561579 AT AT AT AT 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 AT AT AT AT
39561621 AT AT
1 AT AT
39561625 TTGGTGTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39564055 original size:87 final size:88
Alignment explanation
Indices: 39563962--39564124 Score: 256
Period size: 87 Copynumber: 1.9 Consensus size: 88
39563952 CTCAACATTG
* * *
39563962 ATGGATGTTGAGTTCTTCTATAATTCAATTTTCACTATATATTATAAACAAAACCTTAATAAATA
1 ATGGATGTTGAGTTCCTCTATAAATCAATTTTCACTATATACTATAAACAAAACCTTAATAAATA
39564027 TATTAA-TTAAAAGTAGACACAA
66 TATTAAGTTAAAAGTAGACACAA
* ** *
39564049 ATGGATGTTGAGTTCCTCTATAAATCAATTTTCACTATGTACTATAAACTTAACCTTAATAAATG
1 ATGGATGTTGAGTTCCTCTATAAATCAATTTTCACTATATACTATAAACAAAACCTTAATAAATA
39564114 TATTAAGTTAA
66 TATTAAGTTAA
39564125 GTTGACATCC
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
87 64 0.94
88 4 0.06
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.38
Consensus pattern (88 bp):
ATGGATGTTGAGTTCCTCTATAAATCAATTTTCACTATATACTATAAACAAAACCTTAATAAATA
TATTAAGTTAAAAGTAGACACAA
Found at i:39565333 original size:2 final size:2
Alignment explanation
Indices: 39565326--39565358 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39565316 CCCAAATTCT
39565326 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39565359 GATGTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39590229 original size:52 final size:52
Alignment explanation
Indices: 39590154--39590255 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
39590144 AAATCAATAA
* *
39590154 TCAAGAAAGGGAAAGGGATAAAAATAAAAATGGAGAATTTTAGGAGAATTAC
1 TCAAGAAAGGGAAAGGGACAAAAAGAAAAATGGAGAATTTTAGGAGAATTAC
*
39590206 TCAAGAAAGGG-AAGATGACAAAAAGAAAAATGGAGAATTTTAGGAGAATT
1 TCAAGAAAGGGAAAG-GGACAAAAAGAAAAATGGAGAATTTTAGGAGAATT
39590256 TCGACAGAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 3 0.07
52 43 0.93
ACGTcount: A:0.52, C:0.04, G:0.25, T:0.19
Consensus pattern (52 bp):
TCAAGAAAGGGAAAGGGACAAAAAGAAAAATGGAGAATTTTAGGAGAATTAC
Found at i:39592204 original size:18 final size:18
Alignment explanation
Indices: 39592181--39592329 Score: 201
Period size: 18 Copynumber: 8.3 Consensus size: 18
39592171 TATCAATATC
*
39592181 ATTCAGTAAC-GATCAATT
1 ATTCAGTAACAG-TCATTT
* *
39592199 ATTCAGTAATAGTCAGTT
1 ATTCAGTAACAGTCATTT
39592217 ATTCAGTAACAGTCATTT
1 ATTCAGTAACAGTCATTT
39592235 ATTCAGTAACAGTCATTT
1 ATTCAGTAACAGTCATTT
*
39592253 ATTCAGTAGCAGTCATTT
1 ATTCAGTAACAGTCATTT
*
39592271 ATTCAGTAATAGTCATTT
1 ATTCAGTAACAGTCATTT
* *
39592289 ATTCAGTAACAGTTAATT
1 ATTCAGTAACAGTCATTT
* *
39592307 ATTCAGTAGCAGTCAGTT
1 ATTCAGTAACAGTCATTT
39592325 ATTCA
1 ATTCA
39592330 ATACCTTTAT
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
18 116 0.99
19 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTCAGTAACAGTCATTT
Found at i:39592255 original size:54 final size:54
Alignment explanation
Indices: 39592181--39592329 Score: 228
Period size: 54 Copynumber: 2.8 Consensus size: 54
39592171 TATCAATATC
**
39592181 ATTCAGTAAC-GATCAATTATTCAGTAATAGTCAGTTATTCAGTAACAGTCATTT
1 ATTCAGTAACAG-TCAATTATTCAGTAGCAGTCAGTTATTCAGTAACAGTCATTT
* * *
39592235 ATTCAGTAACAGTCATTTATTCAGTAGCAGTCATTTATTCAGTAATAGTCATTT
1 ATTCAGTAACAGTCAATTATTCAGTAGCAGTCAGTTATTCAGTAACAGTCATTT
*
39592289 ATTCAGTAACAGTTAATTATTCAGTAGCAGTCAGTTATTCA
1 ATTCAGTAACAGTCAATTATTCAGTAGCAGTCAGTTATTCA
39592330 ATACCTTTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 85 0.99
55 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (54 bp):
ATTCAGTAACAGTCAATTATTCAGTAGCAGTCAGTTATTCAGTAACAGTCATTT
Found at i:39593266 original size:13 final size:13
Alignment explanation
Indices: 39593250--39593276 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39593240 TACAATATTA
39593250 ATTTACATTTAAT
1 ATTTACATTTAAT
39593263 ATTTACATTTAAT
1 ATTTACATTTAAT
39593276 A
1 A
39593277 CTAATTTCTT
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:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTACATTTAAT
Found at i:39593739 original size:20 final size:20
Alignment explanation
Indices: 39593716--39593767 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
39593706 TCTTTCTTTC
*
39593716 TTTCCTTCCTTCCTTCTCTG
1 TTTCCTTCCTTCCTACTCTG
* * * *
39593736 TTTCGTTTCATGCTACTCTG
1 TTTCCTTCCTTCCTACTCTG
*
39593756 TTTCTTTCCTTC
1 TTTCCTTCCTTC
39593768 TTTTCCTTTC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.04, C:0.33, G:0.08, T:0.56
Consensus pattern (20 bp):
TTTCCTTCCTTCCTACTCTG
Found at i:39593845 original size:13 final size:13
Alignment explanation
Indices: 39593804--39593845 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
39593794 TTTACTTTAT
39593804 ATATATTATAATA
1 ATATATTATAATA
39593817 ATATAATT-TAATA
1 ATAT-ATTATAATA
39593830 ATATACTTATAA-A
1 ATATA-TTATAATA
39593843 ATA
1 ATA
39593846 AGTAAACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.04
13 19 0.73
14 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATATTATAATA
Found at i:39600358 original size:15 final size:17
Alignment explanation
Indices: 39600330--39600361 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
39600320 TTGGTACTGG
39600330 TGAATGTGAGTTTGGTA
1 TGAATGTGAGTTTGGTA
39600347 TGAAT-TGA-TTTGGTA
1 TGAATGTGAGTTTGGTA
39600362 AATTATGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TGAATGTGAGTTTGGTA
Done.