Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 10 of 66
Found at i:3289082 original size:22 final size:22
Alignment explanation
Indices: 3289057--3289098 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3289047 ACGTTACGCA
3289057 ATACATA-ACAACAAGTCACGAT
1 ATACATACA-AACAAGTCACGAT
*
3289079 ATACATACAAACTAGTCACG
1 ATACATACAAACAAGTCACG
3289099 CAATGTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.48, C:0.24, G:0.10, T:0.19
Consensus pattern (22 bp):
ATACATACAAACAAGTCACGAT
Found at i:3289988 original size:22 final size:22
Alignment explanation
Indices: 3289962--3290049 Score: 131
Period size: 22 Copynumber: 4.0 Consensus size: 22
3289952 AATGCAATTA
* * *
3289962 CTACAAATAAGTCATGAAATGC
1 CTACAAACAAGTCACGTAATGC
*
3289984 TTACAAACAAGTCACGTAATGC
1 CTACAAACAAGTCACGTAATGC
3290006 CTACAAACAAGTCACGTAATGC
1 CTACAAACAAGTCACGTAATGC
*
3290028 CTACAAACAAGTCACGCAATGC
1 CTACAAACAAGTCACGTAATGC
3290050 ACAACTCAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (22 bp):
CTACAAACAAGTCACGTAATGC
Found at i:3294347 original size:16 final size:16
Alignment explanation
Indices: 3294323--3294353 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3294313 TTCCAACGAA
*
3294323 AATTTCGTTGGAAAAT
1 AATTCCGTTGGAAAAT
3294339 AATTCCGTTGGAAAA
1 AATTCCGTTGGAAAA
3294354 GGCAATTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (16 bp):
AATTCCGTTGGAAAAT
Found at i:3294394 original size:31 final size:31
Alignment explanation
Indices: 3294339--3294402 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3294329 GTTGGAAAAT
*
3294339 AATTCCGTTGGAAAAGGCAATTCCAACGGAA
1 AATTCCGTTGGAAAAGCCAATTCCAACGGAA
* *
3294370 AATTCCGTTGG-AAAGCCTATTTCCAATGGAA
1 AATTCCGTTGGAAAAGCC-AATTCCAACGGAA
3294401 AA
1 AA
3294403 AATAGTTGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (31 bp):
AATTCCGTTGGAAAAGCCAATTCCAACGGAA
Found at i:3294570 original size:30 final size:30
Alignment explanation
Indices: 3294534--3294590 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3294524 AACATTTAGA
3294534 ATTTCCAACGAAAATTTT-CGTTGGAAAAAT
1 ATTTCCAACG-AAATTTTCCGTTGGAAAAAT
*
3294564 ATTTCCAATGAAATTTTCCGTTGGAAA
1 ATTTCCAACGAAATTTTCCGTTGGAAA
3294591 TATTTTGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (30 bp):
ATTTCCAACGAAATTTTCCGTTGGAAAAAT
Found at i:3296251 original size:2 final size:2
Alignment explanation
Indices: 3296244--3296293 Score: 57
Period size: 2 Copynumber: 24.0 Consensus size: 2
3296234 AATATGTATG
*
3296244 TA TA TA TA TA TA TA TA T- TGA AA CTA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA -TA TA TA TA
3296286 TA TA TA TA
1 TA TA TA TA
3296294 GTGTATACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3296300 original size:17 final size:17
Alignment explanation
Indices: 3296246--3296300 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3296236 TATGTATGTA
*
3296246 TATATATATATATATTG
1 TATATATATATATACTG
* *
3296263 -AAACTATATATATACTA
1 TATA-TATATATATACTG
*
3296280 TATATATATATATAGTG
1 TATATATATATATACTG
3296297 TATA
1 TATA
3296301 CTTCAAATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (17 bp):
TATATATATATATACTG
Found at i:3297063 original size:23 final size:23
Alignment explanation
Indices: 3297033--3297078 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
3297023 TGAATATAGA
3297033 ATAGGAATCACAAAAAGTTTTCT
1 ATAGGAATCACAAAAAGTTTTCT
*
3297056 ATAGGAATCACAAAATGTTTTCT
1 ATAGGAATCACAAAAAGTTTTCT
3297079 TACATGTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (23 bp):
ATAGGAATCACAAAAAGTTTTCT
Found at i:3297927 original size:19 final size:19
Alignment explanation
Indices: 3297903--3297939 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3297893 AATACTGGTT
3297903 TTGAAAATAGAGTAATTGA
1 TTGAAAATAGAGTAATTGA
3297922 TTGAAAATAGAGTAATTG
1 TTGAAAATAGAGTAATTG
3297940 GAGATTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (19 bp):
TTGAAAATAGAGTAATTGA
Found at i:3304357 original size:11 final size:11
Alignment explanation
Indices: 3304343--3304374 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3304333 AATTAAATTT
3304343 CGTTGGAAATC
1 CGTTGGAAATC
*
3304354 CGTTGCAAATC
1 CGTTGGAAATC
3304365 CGTTGGAAAT
1 CGTTGGAAAT
3304375 ACAATGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (11 bp):
CGTTGGAAATC
Found at i:3322108 original size:34 final size:34
Alignment explanation
Indices: 3322065--3322197 Score: 119
Period size: 34 Copynumber: 3.9 Consensus size: 34
3322055 GCTTTGATTG
3322065 AAGCTTTGACCA-TGGCATGTAACATCTAGTGTTA
1 AAGCTTTGA-CATTGGCATGTAACATCTAGTGTTA
* *
3322099 AAGCTTTGACATTGGCATGTAACATCTGGTGTTG
1 AAGCTTTGACATTGGCATGTAACATCTAGTGTTA
* * * * * *
3322133 AAGCTTT-ACCCTTGGCGTATAACATC-CGTTGCTG
1 AAGCTTTGA-CATTGGCATGTAACATCTAG-TGTTA
** *
3322167 AAGCTTTGATGTTGGCATGTAACATTTAGTG
1 AAGCTTTGACATTGGCATGTAACATCTAGTG
3322198 GTGACATCTG
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
33 4 0.05
34 75 0.93
35 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (34 bp):
AAGCTTTGACATTGGCATGTAACATCTAGTGTTA
Found at i:3322295 original size:115 final size:115
Alignment explanation
Indices: 3322086--3322295 Score: 280
Period size: 115 Copynumber: 1.8 Consensus size: 115
3322076 ATGGCATGTA
* * *
3322086 ACATCTAGTGTTAAAGCTTTGACATTGGCATGTAACATCTGGTGTTGAAGCTTTACCCTTGGCGT
1 ACATCTAGTGTTAAAGCTTTGACATTGGCATGTAACATCTGATGATGAAGCTTTACCCTTGACGT
*
3322151 ATAACATCCGTTGCTGAAGCTTTGATGTTGGCATGTAACATTTAGTGGTG
66 ATAACATCAGTTGCTGAAGCTTTGATGTTGGCATGTAACATTTAGTGGTG
* * * *
3322201 ACATCT-GATGTTGAAGCTTTGATATTGGCATGTAACATCTGATGATGAAGCTTTAGCCTTGATG
1 ACATCTAG-TGTTAAAGCTTTGACATTGGCATGTAACATCTGATGATGAAGCTTTACCCTTGACG
* * * *
3322265 TGTAACATCTAG-TGTTGAAGTTTTGGTGTTG
65 TATAACATC-AGTTGCTGAAGCTTTGATGTTG
3322296 CTTAATTGTT
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
114 1 0.01
115 79 0.98
116 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (115 bp):
ACATCTAGTGTTAAAGCTTTGACATTGGCATGTAACATCTGATGATGAAGCTTTACCCTTGACGT
ATAACATCAGTTGCTGAAGCTTTGATGTTGGCATGTAACATTTAGTGGTG
Found at i:3322777 original size:33 final size:34
Alignment explanation
Indices: 3322724--3322797 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
3322714 ATAATCATAA
* * * *
3322724 AAAGATTCAACATCAAATGTTATATGCCAAGG-G
1 AAAGCTTCAACACCAAATGTTACATGCCAAGGTC
* *
3322757 AAAGCTTCAACACCAGATGTTACATGCTAAGGTC
1 AAAGCTTCAACACCAAATGTTACATGCCAAGGTC
3322791 AAAGCTT
1 AAAGCTT
3322798 TAGCACTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 27 0.79
34 7 0.21
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (34 bp):
AAAGCTTCAACACCAAATGTTACATGCCAAGGTC
Found at i:3326102 original size:250 final size:254
Alignment explanation
Indices: 3325810--3326371 Score: 866
Period size: 250 Copynumber: 2.2 Consensus size: 254
3325800 CAACAAATTA
3325810 ATTAATTTAAATATTTTAAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAA
1 ATTAATTTAAATATTTTAAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAA
*
3325875 AATTTTATTCATTTCGTTAGTTTA-ATTATTTAA-TTATTTATGTCAAAACCTTAATTAATTTAA
66 AATTTTATTCATTTCGTTAG-TTACATTA-TTAAGTTATTTATGTAAAAACCTTAATTAATTTAA
*
3325938 ATAATTTTTAATTATCTTCAATTAACTAATTAAATTATTTGACTAATGAGTAAT-CTTATAATTA
129 ATAATTTTTAATTATCTTCAATTAACTAATTAAATTATTTGACTAATGACTAATACTTATAATTA
* *
3326002 ATACATTATATTACTTAATTAACTTAATCATTTAACTTCGTTATTAACAC-CTT-A-AGTC
194 ATACATTACATTACTTAATTAACTTAATCATTTAACTACGTTATTAACACTCTTAATAGTC
* * *
3326060 ATTAATTTAAATATTTTCAAAATTCAATAATATTACTAATTTTGTTAATTGCTTAGTTACTAAAA
1 ATTAATTTAAATATTTTAAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAA
* *
3326125 AATTTTATTGATTTCGTTAGTTACATTATTAAGTTATTTCTGTAAAAACCTTAATTAATTTAAAT
66 AATTTTATTCATTTCGTTAGTTACATTATTAAGTTATTTATGTAAAAACCTTAATTAATTTAAAT
* * *
3326190 AATTTTTAATTATCTTCAATTAACTTATTTAATTATTTGATTAATGACTAATACTTATAATTAAT
131 AATTTTTAATTATCTTCAATTAACTAATTAAATTATTTGACTAATGACTAATACTTATAATTAAT
*
3326255 ACATTACATTACTTAATTAACTTAATCATTTAACTACGTTATTAACACTTTTAATTAGTC
196 ACATTACATTACTTAATTAACTTAATCATTTAACTACGTTATTAACACTCTTAA-TAGTC
** ** * * * *
3326315 ATTAATTTAAATATTTTTTACGTTAAATAATATTACTTATGTAGTTCATTGCTTAAT
1 ATTAATTTAAATATTTTAAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAAT
3326372 ATGTCACGAC
Statistics
Matches: 282, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
249 7 0.02
250 163 0.58
251 58 0.21
252 2 0.01
253 1 0.00
255 51 0.18
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (254 bp):
ATTAATTTAAATATTTTAAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAA
AATTTTATTCATTTCGTTAGTTACATTATTAAGTTATTTATGTAAAAACCTTAATTAATTTAAAT
AATTTTTAATTATCTTCAATTAACTAATTAAATTATTTGACTAATGACTAATACTTATAATTAAT
ACATTACATTACTTAATTAACTTAATCATTTAACTACGTTATTAACACTCTTAATAGTC
Found at i:3334533 original size:14 final size:14
Alignment explanation
Indices: 3334514--3334543 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3334504 TTTTGTTCTA
3334514 CATCACCACATCAT
1 CATCACCACATCAT
*
3334528 CATCACCACGTCAT
1 CATCACCACATCAT
3334542 CA
1 CA
3334544 CTGCCATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.43, G:0.03, T:0.20
Consensus pattern (14 bp):
CATCACCACATCAT
Found at i:3339834 original size:19 final size:19
Alignment explanation
Indices: 3339807--3339844 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3339797 CCATTTGACT
*
3339807 TATTGGAGTATTATTTGAG
1 TATTGGAGTATAATTTGAG
*
3339826 TATTTGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
3339845 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:3339850 original size:19 final size:19
Alignment explanation
Indices: 3339812--3339850 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3339802 TGACTTATTG
* *
3339812 GAGTATTATTTGAGTATTT
1 GAGTATAATTTGAGGATTT
*
3339831 GAGTATAATTTGAGGGTTT
1 GAGTATAATTTGAGGATTT
3339850 G
1 G
3339851 GCAGTGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.46
Consensus pattern (19 bp):
GAGTATAATTTGAGGATTT
Found at i:3345999 original size:2 final size:2
Alignment explanation
Indices: 3345994--3346037 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3345984 NNNATATATA
3345994 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3346036 TG
1 TG
3346038 AGATATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3347057 original size:22 final size:22
Alignment explanation
Indices: 3347012--3347057 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3347002 TGAACGACAG
*
3347012 AAGAAAGAAGAAAAAAGAGGGA
1 AAGAAAGAAGAAAAAAGAGAGA
3347034 AAGAAAGAAGAGAAAAAGA-AGA
1 AAGAAAGAAGA-AAAAAGAGAGA
3347056 AA
1 AA
3347058 AAGGCTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAGAAAGAAGAAAAAAGAGAGA
Found at i:3350296 original size:18 final size:19
Alignment explanation
Indices: 3350273--3350310 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3350263 TCTAACGAAA
*
3350273 TTTTCCATTGGAATT-TTT
1 TTTTCCAATGGAATTCTTT
3350291 TTTTCCAATGGAATTCTTT
1 TTTTCCAATGGAATTCTTT
3350310 T
1 T
3350311 CACAGTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTTCCAATGGAATTCTTT
Found at i:3350689 original size:2 final size:2
Alignment explanation
Indices: 3350682--3350713 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3350672 TACTCTTAAG
3350682 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
3350714 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:3352931 original size:20 final size:20
Alignment explanation
Indices: 3352908--3352954 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3352898 GGTAAAGAAA
* *
3352908 GAATTTCGTTGGTAATTGAT
1 GAATTTCATTGGTAATAGAT
* *
3352928 GAATTCCATTGTTAATAGAT
1 GAATTTCATTGGTAATAGAT
3352948 GAATTTC
1 GAATTTC
3352955 TTCTGTAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (20 bp):
GAATTTCATTGGTAATAGAT
Found at i:3355306 original size:43 final size:42
Alignment explanation
Indices: 3355132--3355353 Score: 273
Period size: 42 Copynumber: 5.2 Consensus size: 42
3355122 CTTTTTGTAT
* * *
3355132 GCTGATGATGACCTAGCCATGTGCTTGTAGGAGTGTACATGA
1 GCTGATGATGACCCAGCCATGTGCGTGTAGGAGTGCACATGA
* * *
3355174 GTTGATGATGACCCAGCCATGTGCGTGTAGGAATGTACATGA
1 GCTGATGATGACCCAGCCATGTGCGTGTAGGAGTGCACATGA
* * *
3355216 GTTGATGATGACCTAGCCATGTGCGTGTAGGAGTGCATATGA
1 GCTGATGATGACCCAGCCATGTGCGTGTAGGAGTGCACATGA
* * *
3355258 GCTGATGATGACCCAACCATGTGCGAGTGGGGAGTGCACATGA
1 GCTGATGATGACCCAGCCATGTGCGTGT-AGGAGTGCACATGA
* * * * *
3355301 GCTGATGCTAACCCAGCTATGTGCGAGTGGGGAGTGCACATGA
1 GCTGATGATGACCCAGCCATGTGCGTGT-AGGAGTGCACATGA
3355344 GCTGATGATG
1 GCTGATGATG
3355354 GTGGGATGGT
Statistics
Matches: 159, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 100 0.63
43 59 0.37
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (42 bp):
GCTGATGATGACCCAGCCATGTGCGTGTAGGAGTGCACATGA
Found at i:3360772 original size:56 final size:57
Alignment explanation
Indices: 3360711--3360824 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3360701 TATGGTACAC
3360711 TAATTAATGAAGGATGAACAAGCCACG-TTGCCAACAGCTTTGAAAATGAAGGAGAT
1 TAATTAATGAAGGATGAACAAGCCACGTTTGCCAACAGCTTTGAAAATGAAGGAGAT
* *
3360767 TAATTAATGAAGGATGAACAAGTCACGTTTGCCAACGGCTTTGAAAATGAAGGAGAT
1 TAATTAATGAAGGATGAACAAGCCACGTTTGCCAACAGCTTTGAAAATGAAGGAGAT
3360824 T
1 T
3360825 CGATGAAGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 26 0.47
57 29 0.53
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (57 bp):
TAATTAATGAAGGATGAACAAGCCACGTTTGCCAACAGCTTTGAAAATGAAGGAGAT
Found at i:3368369 original size:46 final size:46
Alignment explanation
Indices: 3368299--3368390 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
3368289 ATATATGGTG
* * * * *
3368299 TTGAAGCTTTGATCTTGGCATGTAACATCTGGTGCTGAAGCTTTGA
1 TTGAAGCTTTGACCATGACATGTAACATCTAGTGCTAAAGCTTTGA
*
3368345 TTGAAGCTTTGACCATGACGTGTAACATCTAGTGCTAAAGCTTTGA
1 TTGAAGCTTTGACCATGACATGTAACATCTAGTGCTAAAGCTTTGA
3368391 CATTTACATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (46 bp):
TTGAAGCTTTGACCATGACATGTAACATCTAGTGCTAAAGCTTTGA
Found at i:3369030 original size:33 final size:34
Alignment explanation
Indices: 3368977--3369073 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 34
3368967 TAATCATAAA
* * * * *
3368977 AAAGATTCAACATCATATGTTATATGCCAAGG-G
1 AAAGCTTCAACACCAGATGTTACATGCCAAGGTC
3369010 AAAGCTTCAACACCAGATGTTACATGCCAAGGTC
1 AAAGCTTCAACACCAGATGTTACATGCCAAGGTC
* * * * *
3369044 AAAGCTTTAGCACCATATATTACACGCCAA
1 AAAGCTTCAACACCAGATGTTACATGCCAA
3369074 AGCTTTTTTC
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
33 28 0.53
34 25 0.47
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (34 bp):
AAAGCTTCAACACCAGATGTTACATGCCAAGGTC
Found at i:3369695 original size:134 final size:133
Alignment explanation
Indices: 3369542--3369809 Score: 527
Period size: 134 Copynumber: 2.0 Consensus size: 133
3369532 ATTAAAAAGA
3369542 AGGTTGTTTTTGAAAATACTCTACCTTTGAGGGCTAAAAACAAAATTGTCCCTAAATTAAAATAT
1 AGGTTGTTTTTGAAAATACTCTACCTTTGAGGGCTAAAAACAAAATTGTCCCTAAATTAAAATAT
3369607 CCTTCATTATAATTTATGAATTTTAATTTAAAATATTAAAAATTTATAACACTATAAAACCAGAG
66 CCTTCATTATAATTTATGAATTTTAATTTAAAATATTAAAAATTTATAACACTATAAAACCAGAG
3369672 GGC
131 GGC
3369675 NAGGTTGTTTTTGAAAATACTCTACCTTTGAGGGCTAAAAACAAAATTGTCCCTAAATTAAAATA
1 -AGGTTGTTTTTGAAAATACTCTACCTTTGAGGGCTAAAAACAAAATTGTCCCTAAATTAAAATA
3369740 TCCTTCATTATAATTTATGAATTTTAATTTAAAATATTAAAAATTTATAACACTATAAAACCAGA
65 TCCTTCATTATAATTTATGAATTTTAATTTAAAATATTAAAAATTTATAACACTATAAAACCAGA
3369805 GGGC
130 GGGC
3369809 A
1 A
3369810 TTATTGATGA
Statistics
Matches: 134, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
133 1 0.01
134 133 0.99
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (133 bp):
AGGTTGTTTTTGAAAATACTCTACCTTTGAGGGCTAAAAACAAAATTGTCCCTAAATTAAAATAT
CCTTCATTATAATTTATGAATTTTAATTTAAAATATTAAAAATTTATAACACTATAAAACCAGAG
GGC
Found at i:3372494 original size:251 final size:253
Alignment explanation
Indices: 3372203--3372765 Score: 740
Period size: 251 Copynumber: 2.2 Consensus size: 253
3372193 CAACAAATTA
3372203 ATTAATTTAAATATTTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAA
1 ATTAATTTAAAT-TTTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAA
* * *
3372268 AATTTTATTCATTTCGTGAGTT-TAATTATTTAA-TTACTTATGTCAAAACCTTAATTCATTTAA
65 AATTTTATTCATTTCGTGAGTTAT-ATTA-TTAAGTTACTTACGTAAAAACCTTAATTAATTTAA
* * * *
3372331 ATAATTTTTAACTATCTTCAATTAACTAATTAAATTGTTTGACTGATGAGTAATACTTATAATTA
128 ATAATTTTTAACTATCTTCAATTAACTAATTAAATTATTTGACTAATAACTAATACTTATAATTA
* * *
3372396 ATACATTACATTATTTAATTAACTTAATCATTTAACTTCATTATTAATAC-CTT-A-AGTC
193 ATACATTACATTACTTAATTAACTTAATCATTTAACTACATTATTAACACTCTTAATAGTC
* * * *
3372454 ATTAATTTAAATGTTTTCAAAATTCAATAATATTACTAATTTTGTTAATTGCCTAGTTACTAAAA
1 ATTAATTTAAAT-TTTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAA
* * * * * * *
3372519 ATTTTTTTTGATTTTGTTAGTTATATTATTAAGTTATTTCCGTAAAAACCTTAATTAATTTAAAT
65 AATTTTATTCATTTCGTGAGTTATATTATTAAGTTACTTACGTAAAAACCTTAATTAATTTAAAT
* *
3372584 AATTTTTAATTATCTTCAATTAACTAATTTAATTATTTGACTAATAACTAATACTTATAATTAAT
130 AATTTTTAACTATCTTCAATTAACTAATTAAATTATTTGACTAATAACTAATACTTATAATTAAT
* * * *
3372649 ACATTACATTACTTAATTCACTTAATCTTTTAACTACGTTATTAACACTTTTAATTAGTC
195 ACATTACATTACTTAATTAACTTAATCATTTAACTACATTATTAACACTCTTAA-TAGTC
* * * * * *
3372709 ATTAATTTAAATTATTTTTAAGTTAAATAATATTACTGATATAGTTCATTGCTTAAT
1 ATTAATTTAAATT-TTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAAT
3372766 AATTAATTTG
Statistics
Matches: 267, Mismatches: 38, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
250 4 0.01
251 209 0.78
252 3 0.01
253 1 0.00
254 1 0.00
255 49 0.18
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (253 bp):
ATTAATTTAAATTTTTTAAAATTAAATAATATTACTAATTTTGTTAATTGCTTAATTACTAAAAA
ATTTTATTCATTTCGTGAGTTATATTATTAAGTTACTTACGTAAAAACCTTAATTAATTTAAATA
ATTTTTAACTATCTTCAATTAACTAATTAAATTATTTGACTAATAACTAATACTTATAATTAATA
CATTACATTACTTAATTAACTTAATCATTTAACTACATTATTAACACTCTTAATAGTC
Found at i:3372712 original size:20 final size:21
Alignment explanation
Indices: 3372675--3372713 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3372665 TTCACTTAAT
*
3372675 CTTTTAACTACGTTATTAACA
1 CTTTTAACTACGTCATTAACA
*
3372696 CTTTTAATTA-GTCATTAA
1 CTTTTAACTACGTCATTAA
3372714 TTTAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.46
Consensus pattern (21 bp):
CTTTTAACTACGTCATTAACA
Found at i:3373207 original size:24 final size:24
Alignment explanation
Indices: 3373154--3373207 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3373144 CAACCAAAGT
*
3373154 CACAAATATTCAAACAAAAGAATC
1 CACAAATATTCAAACAAAAGAAAC
* *
3373178 CTCAAATATTCAATCAATAA-AAAC
1 CACAAATATTCAAACAA-AAGAAAC
3373202 CACAAA
1 CACAAA
3373208 ACCACAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.57, C:0.22, G:0.02, T:0.19
Consensus pattern (24 bp):
CACAAATATTCAAACAAAAGAAAC
Found at i:3374111 original size:21 final size:21
Alignment explanation
Indices: 3374085--3374133 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3374075 TAATGGAGCA
*
3374085 TTGATCTGGCCATTATAATGT
1 TTGATCAGGCCATTATAATGT
3374106 TTGATCAGGCCATTATAATGT
1 TTGATCAGGCCATTATAATGT
3374127 TTGATCA
1 TTGATCA
3374134 ATGCTTCCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (21 bp):
TTGATCAGGCCATTATAATGT
Found at i:3377782 original size:39 final size:39
Alignment explanation
Indices: 3377704--3377786 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 39
3377694 TTTTGGCCAT
* * *
3377704 TGTTCACCTTAGTGGGATTTTTTGACCTTGCCAAGATTGG
1 TGTTCACCTTAGTGGGA-TTTCTAACCTTACCAAGATTGG
3377744 TGTTCACCTTAGTAGGG-TTTCTAACCTTACCACA-ATTGG
1 TGTTCACCTTAGT-GGGATTTCTAACCTTACCA-AGATTGG
3377783 TGTT
1 TGTT
3377787 TTCACAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 21 0.55
40 14 0.37
41 3 0.08
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (39 bp):
TGTTCACCTTAGTGGGATTTCTAACCTTACCAAGATTGG
Found at i:3377972 original size:14 final size:14
Alignment explanation
Indices: 3377953--3377983 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3377943 TTTTTTTCTA
3377953 CATCACCACATCAT
1 CATCACCACATCAT
*
3377967 CATCACCACGTCAT
1 CATCACCACATCAT
3377981 CAT
1 CAT
3377984 TGCCATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.23
Consensus pattern (14 bp):
CATCACCACATCAT
Found at i:3387617 original size:40 final size:40
Alignment explanation
Indices: 3387573--3387650 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
3387563 AATATTTCAT
3387573 ATGAACTCCATAGGTAAAAGAAGAATTTCATTGGTAATTG
1 ATGAACTCCATAGGTAAAAGAAGAATTTCATTGGTAATTG
* * * * * * *
3387613 ATGAATTCCATTGTTAATAGATGAATTTCGTTTGTAAT
1 ATGAACTCCATAGGTAAAAGAAGAATTTCATTGGTAAT
3387651 ACTTGCAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (40 bp):
ATGAACTCCATAGGTAAAAGAAGAATTTCATTGGTAATTG
Found at i:3387618 original size:20 final size:20
Alignment explanation
Indices: 3387585--3387651 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
3387575 GAACTCCATA
* *
3387585 GGTAAAAGAAGAATTTCATT
1 GGTAATAGATGAATTTCATT
* *
3387605 GGTAATTGATGAATTCCATT
1 GGTAATAGATGAATTTCATT
* *
3387625 GTTAATAGATGAATTTCGTT
1 GGTAATAGATGAATTTCATT
*
3387645 TGTAATA
1 GGTAATA
3387652 CTTGCAAAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (20 bp):
GGTAATAGATGAATTTCATT
Found at i:3388343 original size:2 final size:2
Alignment explanation
Indices: 3388336--3388380 Score: 63
Period size: 2 Copynumber: 21.5 Consensus size: 2
3388326 GGTAAGTAAC
*
3388336 AT AT AT AT CAA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
3388380 A
1 A
3388381 GGAGCACATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 36 0.92
3 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3393686 original size:21 final size:21
Alignment explanation
Indices: 3393660--3393729 Score: 140
Period size: 21 Copynumber: 3.3 Consensus size: 21
3393650 TTCTCAGTTC
3393660 GCTGTTGCTGAAGCTGCAGGT
1 GCTGTTGCTGAAGCTGCAGGT
3393681 GCTGTTGCTGAAGCTGCAGGT
1 GCTGTTGCTGAAGCTGCAGGT
3393702 GCTGTTGCTGAAGCTGCAGGT
1 GCTGTTGCTGAAGCTGCAGGT
3393723 GCTGTTG
1 GCTGTTG
3393730 AGGCGCTTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.13, C:0.19, G:0.39, T:0.30
Consensus pattern (21 bp):
GCTGTTGCTGAAGCTGCAGGT
Found at i:3393785 original size:24 final size:24
Alignment explanation
Indices: 3393758--3393815 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
3393748 TTGTGGCTTT
* *
3393758 TCATGCTGCTTCTCCTATTG-CTCC
1 TCATGCTGCTACTCCT-GTGACTCC
3393782 TCATGCTGCTACTCCTGTGACTCC
1 TCATGCTGCTACTCCTGTGACTCC
*
3393806 TCACGCTGCT
1 TCATGCTGCT
3393816 CTTCCTCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.10, C:0.38, G:0.16, T:0.36
Consensus pattern (24 bp):
TCATGCTGCTACTCCTGTGACTCC
Found at i:3394031 original size:24 final size:24
Alignment explanation
Indices: 3393975--3394031 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
3393965 GTAGATGCAT
* *
3393975 GCAATGCAATTGGAGATCTAGCAG
1 GCAATGCAGTTGGAGATCCAGCAG
**
3393999 GCAATGCAGTTGGAGATCCAGTGG
1 GCAATGCAGTTGGAGATCCAGCAG
3394023 GCAATGCAG
1 GCAATGCAG
3394032 ATGCAAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.33, T:0.19
Consensus pattern (24 bp):
GCAATGCAGTTGGAGATCCAGCAG
Found at i:3394044 original size:24 final size:24
Alignment explanation
Indices: 3393998--3394044 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3393988 AGATCTAGCA
* * *
3393998 GGCAATGCAGTTGGAGATCCAGTG
1 GGCAATGCAGATGCAAATCCAGTG
*
3394022 GGCAATGCAGATGCAAATGCAGT
1 GGCAATGCAGATGCAAATCCAGT
3394045 CACTACATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.34, T:0.19
Consensus pattern (24 bp):
GGCAATGCAGATGCAAATCCAGTG
Found at i:3396248 original size:26 final size:23
Alignment explanation
Indices: 3396192--3396797 Score: 198
Period size: 23 Copynumber: 26.2 Consensus size: 23
3396182 GTGGCGTTAG
3396192 TAGTTATTATGGAATCGCGTGAC
1 TAGTTATTATGGAATCGCGTGAC
* *
3396215 TAGTTATTATGGAATTGCGTTAC
1 TAGTTATTATGGAATCGCGTGAC
* * *
3396238 TAGTTGA-TATTGAGTC-CGTGAG
1 TAGTT-ATTATGGAATCGCGTGAC
* * *
3396260 TAG-TATATATGGAGTAGCGTTAC
1 TAGTTAT-TATGGAATCGCGTGAC
*
3396283 TAGTTATTATGGAATCGCATGAC
1 TAGTTATTATGGAATCGCGTGAC
* * ** *
3396306 TGGTTCATTAT-AAAGTCATGTGAG
1 TAGTT-ATTATGGAA-TCGCGTGAC
** * ** * *
3396330 TAGCAAATATGGGTTCTCATGAC
1 TAGTTATTATGGAATCGCGTGAC
* * *
3396353 TGGTTATTATGGAATCACGTTAC
1 TAGTTATTATGGAATCGCGTGAC
* * * * *
3396376 TGGTTGA-TATTGAGTCACGTGAG
1 TAGTT-ATTATGGAATCGCGTGAC
* * * *
3396399 TAG-TATATGTGGAGT-GACATTAC
1 TAGTTAT-TATGGAATCG-CGTGAC
*
3396422 TAGTTATTATGGAATCGCATGAC
1 TAGTTATTATGGAATCGCGTGAC
* * *
3396445 TGGTTCATTAT-AAAGTCGCGTGAG
1 TAGTT-ATTATGGAA-TCGCGTGAC
** * ** *
3396469 TAGCAAATATGGCTTCGCGTGCC
1 TAGTTATTATGGAATCGCGTGAC
* *
3396492 TGGTTATTATGGAATCGCGTTAC
1 TAGTTATTATGGAATCGCGTGAC
* * *
3396515 TAGTTGA-TATTGAATCTCGTGAG
1 TAGTT-ATTATGGAATCGCGTGAC
* * *
3396538 TAG-TATATATGGAGTGGCGTTAC
1 TAGTTAT-TATGGAATCGCGTGAC
* *
3396561 TAGTTATTGTGGAATCGCATGAC
1 TAGTTATTATGGAATCGCGTGAC
* * *
3396584 TGGTTCATTAT-AAAGTCGCGTGAG
1 TAGTT-ATTATGGAA-TCGCGTGAC
** * ** *
3396608 TAGCAAATATGGGTTCGCGTGAT
1 TAGTTATTATGGAATCGCGTGAC
* * *
3396631 TGGTTCTTATGGAATCGCGTTAC
1 TAGTTATTATGGAATCGCGTGAC
* * * *
3396654 TAGTTGA-TATTGAGTCGTGTGAG
1 TAGTT-ATTATGGAATCGCGTGAC
* *
3396677 TAG-TATATATGGAGT-GACGTTAC
1 TAGTTAT-TATGGAATCG-CGTGAC
*
3396700 TAGTTATTATGGAATCGCATGAC
1 TAGTTATTATGGAATCGCGTGAC
* *
3396723 TAGTTCATTAT-AAAGTCGCGTGAG
1 TAGTT-ATTATGGAA-TCGCGTGAC
** * ** *
3396747 TAGCAAATATGGCTTCGTGTGAC
1 TAGTTATTATGGAATCGCGTGAC
* * *
3396770 TGGTTATTATGGAATCGGGTTAC
1 TAGTTATTATGGAATCGCGTGAC
3396793 TAGTT
1 TAGTT
3396798 GATATTGAGT
Statistics
Matches: 402, Mismatches: 148, Indels: 66
0.65 0.24 0.11
Matches are distributed among these distances:
20 1 0.00
21 4 0.01
22 18 0.04
23 308 0.77
24 71 0.18
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (23 bp):
TAGTTATTATGGAATCGCGTGAC
Found at i:3396280 original size:91 final size:93
Alignment explanation
Indices: 3396149--3396316 Score: 259
Period size: 91 Copynumber: 1.8 Consensus size: 93
3396139 GCATGAGTAT
* * *
3396149 TTGATATTGACTCACGTGAGTAGTAAATACGGAGTGGCGTTAGTAGTTATTATGGAATCGCGTGA
1 TTGATATTGACTCACGTGAGTAGTAAATACGGAGTAGCGTTACTAGTTATTATGGAATCGCATGA
3396214 CTAGTT-ATTATGGAATTGCGTTACTAG
66 CTAGTTCATTATGGAATTGCGTTACTAG
* * *
3396241 TTGATATTGAGTC-CGTGAGTAGTATATATGGAGTAGCGTTACTAGTTATTATGGAATCGCATGA
1 TTGATATTGACTCACGTGAGTAGTAAATACGGAGTAGCGTTACTAGTTATTATGGAATCGCATGA
*
3396305 CTGGTTCATTAT
66 CTAGTTCATTAT
3396317 AAAGTCATGT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
91 51 0.75
92 17 0.25
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (93 bp):
TTGATATTGACTCACGTGAGTAGTAAATACGGAGTAGCGTTACTAGTTATTATGGAATCGCATGA
CTAGTTCATTATGGAATTGCGTTACTAG
Found at i:3396446 original size:139 final size:139
Alignment explanation
Indices: 3396206--3396862 Score: 1005
Period size: 139 Copynumber: 4.7 Consensus size: 139
3396196 TATTATGGAA
* *
3396206 TCGCGTGACTAGTTATTATGGAATTGCGTTACTAGTTGATATTGAGTC-CGTGAGTAGTATATAT
1 TCGCGTGACTGGTTATTATGGAATCGCGTTACTAGTTGATATTGAGTCACGTGAGTAGTATATAT
**
3396270 GGAGT-AGCGTTACTAGTTATTATGGAATCGCATGACTGGTTCATTATAAAGTCATGTGAGTAGC
66 GGAGTGA-CGTTACTAGTTATTATGGAATCGCATGACTGGTTCATTATAAAGTCGCGTGAGTAGC
*
3396334 AAATATGGGT
130 AAATATGGCT
* * * * *
3396344 TCTCATGACTGGTTATTATGGAATCACGTTACTGGTTGATATTGAGTCACGTGAGTAGTATATGT
1 TCGCGTGACTGGTTATTATGGAATCGCGTTACTAGTTGATATTGAGTCACGTGAGTAGTATATAT
*
3396409 GGAGTGACATTACTAGTTATTATGGAATCGCATGACTGGTTCATTATAAAGTCGCGTGAGTAGCA
66 GGAGTGACGTTACTAGTTATTATGGAATCGCATGACTGGTTCATTATAAAGTCGCGTGAGTAGCA
3396474 AATATGGCT
131 AATATGGCT
* * *
3396483 TCGCGTGCCTGGTTATTATGGAATCGCGTTACTAGTTGATATTGAATCTCGTGAGTAGTATATAT
1 TCGCGTGACTGGTTATTATGGAATCGCGTTACTAGTTGATATTGAGTCACGTGAGTAGTATATAT
* *
3396548 GGAGTGGCGTTACTAGTTATTGTGGAATCGCATGACTGGTTCATTATAAAGTCGCGTGAGTAGCA
66 GGAGTGACGTTACTAGTTATTATGGAATCGCATGACTGGTTCATTATAAAGTCGCGTGAGTAGCA
*
3396613 AATATGGGT
131 AATATGGCT
* * **
3396622 TCGCGTGATTGGTTCTTATGGAATCGCGTTACTAGTTGATATTGAGTCGTGTGAGTAGTATATAT
1 TCGCGTGACTGGTTATTATGGAATCGCGTTACTAGTTGATATTGAGTCACGTGAGTAGTATATAT
*
3396687 GGAGTGACGTTACTAGTTATTATGGAATCGCATGACTAGTTCATTATAAAGTCGCGTGAGTAGCA
66 GGAGTGACGTTACTAGTTATTATGGAATCGCATGACTGGTTCATTATAAAGTCGCGTGAGTAGCA
3396752 AATATGGCT
131 AATATGGCT
* * *
3396761 TCGTGTGACTGGTTATTATGGAATCGGGTTACTAGTTGATATTGAGTCATGTGAGTAGTATATAT
1 TCGCGTGACTGGTTATTATGGAATCGCGTTACTAGTTGATATTGAGTCACGTGAGTAGTATATAT
* * * * *
3396826 AGAGTGGCGTTACCA-TTTTTAATGGAATCGCGTGACT
66 GGAGTGACGTTACTAGTTATT-ATGGAATCGCATGACT
3396863 AGTTGATATG
Statistics
Matches: 473, Mismatches: 43, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
138 46 0.10
139 426 0.90
140 1 0.00
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (139 bp):
TCGCGTGACTGGTTATTATGGAATCGCGTTACTAGTTGATATTGAGTCACGTGAGTAGTATATAT
GGAGTGACGTTACTAGTTATTATGGAATCGCATGACTGGTTCATTATAAAGTCGCGTGAGTAGCA
AATATGGCT
Found at i:3396873 original size:23 final size:22
Alignment explanation
Indices: 3396192--3396885 Score: 142
Period size: 23 Copynumber: 30.0 Consensus size: 22
3396182 GTGGCGTTAG
3396192 TAGTTATTATGGAATCGCGTGAC
1 TAGTTA-TATGGAATCGCGTGAC
* *
3396215 TAGTTATTATGGAATTGCGTTAC
1 TAGTTA-TATGGAATCGCGTGAC
* * *
3396238 TAGTTGATATTGAGTC-CGTGAG
1 TAGTT-ATATGGAATCGCGTGAC
* * *
3396260 TAGTATATATGGAGTAGCGTTAC
1 TAGT-TATATGGAATCGCGTGAC
*
3396283 TAGTTATTATGGAATCGCATGAC
1 TAGTTA-TATGGAATCGCGTGAC
* * ** *
3396306 TGGTTCATTAT-AAAGTCATGTGAG
1 TAGTT-A-TATGGAA-TCGCGTGAC
** ** * *
3396330 TAGCAAATATGGGTTCTCATGAC
1 TAG-TTATATGGAATCGCGTGAC
* * *
3396353 TGGTTATTATGGAATCACGTTAC
1 TAGTTA-TATGGAATCGCGTGAC
* * * * *
3396376 TGGTTGATATTGAGTCACGTGAG
1 TAGTT-ATATGGAATCGCGTGAC
* * * *
3396399 TAGTATATGTGGAGT-GACATTAC
1 TAGT-TATATGGAATCG-CGTGAC
*
3396422 TAGTTATTATGGAATCGCATGAC
1 TAGTTA-TATGGAATCGCGTGAC
* * *
3396445 TGGTTCATTAT-AAAGTCGCGTGAG
1 TAGTT-A-TATGGAA-TCGCGTGAC
** ** *
3396469 TAGCAAATATGGCTTCGCGTGCC
1 TAG-TTATATGGAATCGCGTGAC
* *
3396492 TGGTTATTATGGAATCGCGTTAC
1 TAGTTA-TATGGAATCGCGTGAC
* * *
3396515 TAGTTGATATTGAATCTCGTGAG
1 TAGTT-ATATGGAATCGCGTGAC
* * *
3396538 TAGTATATATGGAGTGGCGTTAC
1 TAGT-TATATGGAATCGCGTGAC
* *
3396561 TAGTTATTGTGGAATCGCATGAC
1 TAGTTA-TATGGAATCGCGTGAC
* * *
3396584 TGGTTCATTAT-AAAGTCGCGTGAG
1 TAGTT-A-TATGGAA-TCGCGTGAC
** ** *
3396608 TAGCAAATATGGGTTCGCGTGAT
1 TAG-TTATATGGAATCGCGTGAC
* * *
3396631 TGGTTCTTATGGAATCGCGTTAC
1 TAGTT-ATATGGAATCGCGTGAC
* * * *
3396654 TAGTTGATATTGAGTCGTGTGAG
1 TAGTT-ATATGGAATCGCGTGAC
* *
3396677 TAGTATATATGGAGT-GACGTTAC
1 TAGT-TATATGGAATCG-CGTGAC
*
3396700 TAGTTATTATGGAATCGCATGAC
1 TAGTTA-TATGGAATCGCGTGAC
* *
3396723 TAGTTCATTAT-AAAGTCGCGTGAG
1 TAGTT-A-TATGGAA-TCGCGTGAC
** ** *
3396747 TAGCAAATATGGCTTCGTGTGAC
1 TAG-TTATATGGAATCGCGTGAC
* * *
3396770 TGGTTATTATGGAATCGGGTTAC
1 TAGTTA-TATGGAATCGCGTGAC
* * ** *
3396793 TAGTTGATATTGAGTCATGTGAG
1 TAGTT-ATATGGAATCGCGTGAC
* * * *
3396816 TAGTATATATAGAGTGGCGTTAC
1 TAGT-TATATGGAATCGCGTGAC
* * *
3396839 CATTTTTAATGGAATCGCGTGAC
1 TAGTTAT-ATGGAATCGCGTGAC
* *
3396862 TAGTTGATATGGAATTGTGTGAC
1 TAGTT-ATATGGAATCGCGTGAC
3396885 T
1 T
3396886 CACTTAATGT
Statistics
Matches: 466, Mismatches: 165, Indels: 80
0.66 0.23 0.11
Matches are distributed among these distances:
22 30 0.06
23 367 0.79
24 69 0.15
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.36
Consensus pattern (22 bp):
TAGTTATATGGAATCGCGTGAC
Found at i:3405406 original size:26 final size:28
Alignment explanation
Indices: 3405348--3405411 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 28
3405338 CTCTTAAATA
* * *
3405348 TATTTTTAATGTCATATATTTTATCTTT
1 TATTTTTATTGTCATATATTATATATTT
*
3405376 AATTTTTATTGT-A-ATATTATATATTT
1 TATTTTTATTGTCATATATTATATATTT
3405402 TATTTTTATT
1 TATTTTTATT
3405412 TTTAATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.65
27 1 0.03
28 10 0.32
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (28 bp):
TATTTTTATTGTCATATATTATATATTT
Found at i:3405406 original size:38 final size:37
Alignment explanation
Indices: 3405364--3405446 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 37
3405354 TAATGTCATA
* *
3405364 TATTTTATCTTTAATTTTTATTGTAATATTATATATTT
1 TATTTTATCTTTAA-TATAATTGTAATATTATATATTT
* * *
3405402 TATTTTTATTTTTAATATAATTTTTATATTATATATTT
1 TA-TTTTATCTTTAATATAATTGTAATATTATATATTT
3405440 TATTTTA
1 TATTTTA
3405447 ATTTCTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 5 0.13
38 23 0.59
39 11 0.28
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (37 bp):
TATTTTATCTTTAATATAATTGTAATATTATATATTT
Found at i:3405429 original size:33 final size:33
Alignment explanation
Indices: 3405361--3405445 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
3405351 TTTTAATGTC
* *
3405361 ATATATTTTATCTTTAATTTTTATTGTAATATT
1 ATATATTTTATCTTTAATTTTTAATATAATATT
*
3405394 ATATATTTTAT-TTTTATTTTTAATATAAT-TT
1 ATATATTTTATCTTTAATTTTTAATATAATATT
* * * *
3405425 TTATATTATATATTTTATTTT
1 ATATATTTTATCTTTAATTTT
3405446 AATTTCTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 11 0.24
32 24 0.52
33 11 0.24
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (33 bp):
ATATATTTTATCTTTAATTTTTAATATAATATT
Found at i:3405436 original size:71 final size:73
Alignment explanation
Indices: 3405344--3405519 Score: 181
Period size: 71 Copynumber: 2.4 Consensus size: 73
3405334 TCATCTCTTA
*
3405344 AATAT-ATTTTTA-ATGTCATATATTTTATCTTTAATTTTTATTGTA-ATATTATAT-ATTTT-A
1 AATATAATTTTTATAT-T-ATATATTTTAT-TTTAATTTCT-TT-TACATATTATATAATTTTAA
3405404 TTT-TTAT-TTTT
61 TTTCTTATATTTT
3405415 AATATAATTTTTATATTATATATTTTATTTTAATTTCTTTTACCTATATTATATAAATTTTAATT
1 AATATAATTTTTATATTATATATTTTATTTTAATTTCTTTTA-C-ATATTATAT-AATTTTAATT
3405480 TCTTATATTTT
63 TCTTATATTTT
* *
3405491 -ATNCTAATTCTTATATTATATA-TTTATTT
1 AAT-ATAATTTTTATATTATATATTTTATTT
3405520 AATGTTTTTT
Statistics
Matches: 91, Mismatches: 3, Indels: 18
0.81 0.03 0.16
Matches are distributed among these distances:
68 2 0.02
69 2 0.02
70 9 0.10
71 25 0.27
72 8 0.09
73 7 0.08
74 4 0.04
75 13 0.14
76 21 0.23
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (73 bp):
AATATAATTTTTATATTATATATTTTATTTTAATTTCTTTTACATATTATATAATTTTAATTTCT
TATATTTT
Found at i:3405448 original size:26 final size:26
Alignment explanation
Indices: 3405419--3405532 Score: 67
Period size: 26 Copynumber: 4.5 Consensus size: 26
3405409 ATTTTTAATA
3405419 TAATTTTTATATTATATATTTTATTT
1 TAATTTTTATATTATATATTTTATTT
* ** * *
3405445 TAATTTCT-T-TTACCTATATTATAT
1 TAATTTTTATATTATATATTTTATTT
* * * **
3405469 AAATTTTAAT-TTCTTATATTTTATNC
1 TAATTTTTATATT-ATATATTTTATTT
*
3405495 TAATTCTTATATTATATA-TTTA-TT
1 TAATTTTTATATTATATATTTTATTT
*
3405519 TAATGTTTTTTATT
1 TAAT-TTTTATATT
3405533 TTAATTATAC
Statistics
Matches: 62, Mismatches: 22, Indels: 9
0.67 0.24 0.10
Matches are distributed among these distances:
24 20 0.32
25 15 0.24
26 25 0.40
27 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (26 bp):
TAATTTTTATATTATATATTTTATTT
Found at i:3406035 original size:60 final size:62
Alignment explanation
Indices: 3405937--3406067 Score: 221
Period size: 60 Copynumber: 2.1 Consensus size: 62
3405927 ATGCCAACAT
* *
3405937 AACCAGTCGCATAATGGCCCGCTGTCATGTAATGCATAACTATAGGTCACGTAATATACAAA
1 AACCAGTCACATAATGGCCCGCTGTCATGTAATACATAACTATAGGTCACGTAATATACAAA
*
3405999 AACCAGTCACGTAATGG-CC-CTGTCATGTAATACATAACTATAGGTCACGTAATATACAAA
1 AACCAGTCACATAATGGCCCGCTGTCATGTAATACATAACTATAGGTCACGTAATATACAAA
3406059 AACCAGTCA
1 AACCAGTCA
3406068 TGCACTGCCT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
60 49 0.74
61 2 0.03
62 15 0.23
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (62 bp):
AACCAGTCACATAATGGCCCGCTGTCATGTAATACATAACTATAGGTCACGTAATATACAAA
Found at i:3406257 original size:22 final size:22
Alignment explanation
Indices: 3406227--3406278 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
3406217 CTGGCCTAAT
* *
3406227 GTCATGCAATACATAACAA-CA
1 GTCACGCAATACATAAAAACCA
3406248 GGTCACGCAATACATAAAAACCA
1 -GTCACGCAATACATAAAAACCA
3406271 GTCACGCA
1 GTCACGCA
3406279 TGCAATGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.44, C:0.27, G:0.13, T:0.15
Consensus pattern (22 bp):
GTCACGCAATACATAAAAACCA
Found at i:3406374 original size:207 final size:208
Alignment explanation
Indices: 3406027--3406690 Score: 733
Period size: 207 Copynumber: 3.2 Consensus size: 208
3406017 CCTGTCATGT
* * * * * * *
3406027 AATACATAACTATAGGTCACGTAATATACAAAAACCAGT----CATGCACTGCCTAAAAACAAGT
1 AATACATAACAACAGGTCACGCAATACATAAAAACCAGTCACGCATGCAATGCCTAAAAACTAGT
* * * * * *
3406088 GACCAAAAGCCTCTAAACAAGAAATGAATTGCACAAATCAGTCACGCATCGCCAGTCTCACAATA
66 GAACAAAAGCCTCAAAACAAGAGATGAATTGCAC-AATCAGTCACACAACG--ACTCTCACAATA
* * * *
3406153 CCTAAGAATAAGTCACTCAATGCCTTATACCCACTCACATTATGCTAACATAACCAATCACGTAC
128 CCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACCAATCACGTAC
*
3406218 TGGCCTAATGTCATGC
193 TGGCCTAATGTCACGC
3406234 AATACATAACAACAGGTCACGCAATACATAAAAACCAGTCACGCATGCAATGCCTAAAAACTAGT
1 AATACATAACAACAGGTCACGCAATACATAAAAACCAGTCACGCATGCAATGCCTAAAAACTAGT
* *
3406299 GAACAAAAGCCTCAAAATAAGAGATGAATTGCACAATTCACG-CAC-CACCG-CTCTCACAATAC
66 GAACAAAAGCCTCAAAACAAGAGATGAATTGCACAA-TCA-GTCACACAACGACTCTCACAATAC
* * * * * * * *
3406361 CGAATAATAAGTCACTAAATGCGTAATATCCATTCACATTATGCCAATATAACTAGTCACGTAAT
129 CTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACCAATCACGTACT
*
3406426 GG-CTCAATGTCACAC
194 GGCCT-AATGTCACGC
*
3406441 AATACATAACAACAGGTCACGCAATATATAAAAACCAGTCACGC-T---ATGCCTAAAAACTAGT
1 AATACATAACAACAGGTCACGCAATACATAAAAACCAGTCACGCATGCAATGCCTAAAAACTAGT
* * * * * *
3406502 GAACAAAAGCCTCAAAACAATAGATAAATTTGCACAACCTAGTCACACATAGGTAGTCTCGCAAT
66 GAACAAAAGCCTCAAAACAAGAGATGAA-TTGCACAATC-AGTCACACA-ACG-ACTCTCACAAT
** * *
3406567 ACCTAATAATAAGTCACTCGTTGCCTAATATCCACTCACGTTATGCCAACATAACCATTCACGTA
127 ACCTAATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACCAATCACGTA
* *
3406632 CTGCCCCAATGTCACGC
192 CTGGCCTAATGTCACGC
* * *
3406649 AATACATAACAACACGTCAC-CATATACATATAAACCAATCAC
1 AATACATAACAACAGGTCACGCA-ATACATAAAAACCAGTCAC
3406691 ATAATGTCTC
Statistics
Matches: 387, Mismatches: 54, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
203 43 0.11
204 12 0.03
205 2 0.01
206 4 0.01
207 153 0.40
208 109 0.28
209 1 0.00
210 6 0.02
211 56 0.14
212 1 0.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (208 bp):
AATACATAACAACAGGTCACGCAATACATAAAAACCAGTCACGCATGCAATGCCTAAAAACTAGT
GAACAAAAGCCTCAAAACAAGAGATGAATTGCACAATCAGTCACACAACGACTCTCACAATACCT
AATAATAAGTCACTCAATGCCTAATATCCACTCACATTATGCCAACATAACCAATCACGTACTGG
CCTAATGTCACGC
Found at i:3406465 original size:22 final size:22
Alignment explanation
Indices: 3406434--3406484 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3406424 ATGGCTCAAT
* *
3406434 GTCACACAATACATAACAA-CA
1 GTCACGCAATACATAAAAACCA
*
3406455 GGTCACGCAATATATAAAAACCA
1 -GTCACGCAATACATAAAAACCA
3406478 GTCACGC
1 GTCACGC
3406485 TATGCCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.16
Consensus pattern (22 bp):
GTCACGCAATACATAAAAACCA
Found at i:3408082 original size:22 final size:22
Alignment explanation
Indices: 3408057--3408140 Score: 89
Period size: 22 Copynumber: 3.6 Consensus size: 22
3408047 TAGGTAGATA
3408057 AAGTCACGCAATGCCTACAAAC
1 AAGTCACGCAATGCCTACAAAC
* *
3408079 AAGTCACACAATGCTCAACAAATATTC
1 AAGTCACGCAATGC-CTAC-AA-A--C
*
3408106 AA-TCACGTAATGCCTACAAAC
1 AAGTCACGCAATGCCTACAAAC
3408127 AAGTCACGCAATGC
1 AAGTCACGCAATGC
3408141 TCAACAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
21 3 0.06
22 23 0.46
23 4 0.08
24 4 0.08
25 4 0.08
26 9 0.18
27 3 0.06
ACGTcount: A:0.42, C:0.29, G:0.12, T:0.18
Consensus pattern (22 bp):
AAGTCACGCAATGCCTACAAAC
Found at i:3408117 original size:26 final size:26
Alignment explanation
Indices: 3408088--3408164 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
3408078 CAAGTCACAC
3408088 AATGCTCAACAAATATTCAATCACGT
1 AATGCTCAACAAATATTCAATCACGT
* *
3408114 AATGC-CTAC-AA-A--CAAGTCACGC
1 AATGCTCAACAAATATTCAA-TCACGT
*
3408136 AATGCTCAACAAATATTAAATCACGT
1 AATGCTCAACAAATATTCAATCACGT
3408162 AAT
1 AAT
3408165 ATTCAGTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 3 0.08
22 10 0.25
23 4 0.10
24 4 0.10
25 4 0.10
26 13 0.32
27 2 0.05
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.23
Consensus pattern (26 bp):
AATGCTCAACAAATATTCAATCACGT
Found at i:3408131 original size:48 final size:48
Alignment explanation
Indices: 3408055--3408164 Score: 184
Period size: 48 Copynumber: 2.3 Consensus size: 48
3408045 ATTAGGTAGA
*
3408055 TAAAGTCACGCAATGCCTACAAACAAGTCACACAATGCTCAACAAATAT
1 TAAA-TCACGTAATGCCTACAAACAAGTCACACAATGCTCAACAAATAT
* *
3408104 TCAATCACGTAATGCCTACAAACAAGTCACGCAATGCTCAACAAATAT
1 TAAATCACGTAATGCCTACAAACAAGTCACACAATGCTCAACAAATAT
3408152 TAAATCACGTAAT
1 TAAATCACGTAAT
3408165 ATTCAGTCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 54 0.95
49 3 0.05
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (48 bp):
TAAATCACGTAATGCCTACAAACAAGTCACACAATGCTCAACAAATAT
Found at i:3408198 original size:63 final size:63
Alignment explanation
Indices: 3408099--3408244 Score: 213
Period size: 63 Copynumber: 2.3 Consensus size: 63
3408089 ATGCTCAACA
* *
3408099 AATATTCAATCACGTAATGCCTACAAACAAGTCACGCAATGCTCAACAAATATTAAATCACGT
1 AATATTCAGTCACGTAATGCCTACAAACAAGTCACGCAATGCTCAACAAATATTAAATCACAT
* * * *
3408162 AATATTCAGTCATGTAATTCCTACCAAA-AAGTCACGCAATGCTCAACAAATATTCAGTCACAT
1 AATATTCAGTCACGTAATGCCTA-CAAACAAGTCACGCAATGCTCAACAAATATTAAATCACAT
*
3408225 AATATTTAGTCACGTAATGC
1 AATATTCAGTCACGTAATGC
3408245 TAAATAAACA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 69 0.95
64 4 0.05
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (63 bp):
AATATTCAGTCACGTAATGCCTACAAACAAGTCACGCAATGCTCAACAAATATTAAATCACAT
Found at i:3411595 original size:16 final size:16
Alignment explanation
Indices: 3411566--3411606 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3411556 TTATCAATAA
3411566 TTAAA-TTT-AAAATT
1 TTAAATTTTAAAAATT
3411580 TTAAATTTTAAAAATT
1 TTAAATTTTAAAAATT
*
3411596 TTAATTTTTAA
1 TTAAATTTTAA
3411607 TTTTTTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.21
15 3 0.12
16 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAATTTTAAAAATT
Found at i:3411596 original size:23 final size:23
Alignment explanation
Indices: 3411568--3411611 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3411558 ATCAATAATT
3411568 AAATTTAAAATTTTAAATTTTAA
1 AAATTTAAAATTTTAAATTTTAA
* * *
3411591 AAATTTTAATTTTTAATTTTT
1 AAATTTAAAATTTTAAATTTT
3411612 TTAACTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATTTAAAATTTTAAATTTTAA
Found at i:3422519 original size:2 final size:2
Alignment explanation
Indices: 3422512--3422536 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3422502 TACATAAATA
3422512 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3422537 ATAGAGAGAG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3426513 original size:30 final size:30
Alignment explanation
Indices: 3426467--3426526 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3426457 TAATTAAACC
*
3426467 TTTATACTTTTGTTTTAAGCCAAAAAAGCT
1 TTTATACTTTTATTTTAAGCCAAAAAAGCT
* * *
3426497 TTTATATTTTTATTTTAAGCTAAATAAGCT
1 TTTATACTTTTATTTTAAGCCAAAAAAGCT
3426527 ATTGTGACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTATACTTTTATTTTAAGCCAAAAAAGCT
Found at i:3428571 original size:21 final size:20
Alignment explanation
Indices: 3428518--3428576 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
3428508 CGTAAAAACT
3428518 AATAAAT-AATAACTAAATTAA
1 AATAAATAAATAA--AAATTAA
*
3428539 GATAAATAAATATAAAATTAA
1 AATAAATAAATA-AAAATTAA
* *
3428560 AATAACTTAATAAAAAT
1 AATAAATAAATAAAAAT
3428577 AAACTGAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 5 0.16
21 22 0.69
22 4 0.12
23 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAAATAAATAAAAATTAA
Found at i:3435535 original size:29 final size:29
Alignment explanation
Indices: 3435503--3435558 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
3435493 TATTTGAAAG
*
3435503 TAAGTCAAGATATTTGTTCAGCTACAACA
1 TAAGTCAAGATACTTGTTCAGCTACAACA
* *
3435532 TAAGTCAAGATGCTTGTTCAGTTACAA
1 TAAGTCAAGATACTTGTTCAGCTACAA
3435559 GATGGGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (29 bp):
TAAGTCAAGATACTTGTTCAGCTACAACA
Found at i:3436580 original size:67 final size:67
Alignment explanation
Indices: 3436504--3436639 Score: 191
Period size: 67 Copynumber: 2.0 Consensus size: 67
3436494 GAAAAGTTAG
* * *
3436504 TTTTGGGTTTTGGTTGATCCCGAAAAAAACCATTGTTAAAGGTTGTGGCTGAGCCTGTGACAAGC
1 TTTTGGGTTTTGGTTGATCCCGAAAAAAACCATTATTAAAGGTTGTGGCTGAGCATGTGAAAAGC
3436569 CA
66 CA
** ** * *
3436571 TTTTGGGTTTTGGTTGATCTTGTGAAAAATCTTTATTAAAGGTTGTGGCTGAGCATGTGAAAAGC
1 TTTTGGGTTTTGGTTGATCCCGAAAAAAACCATTATTAAAGGTTGTGGCTGAGCATGTGAAAAGC
3436636 CA
66 CA
3436638 TT
1 TT
3436640 ATAAAAGCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.36
Consensus pattern (67 bp):
TTTTGGGTTTTGGTTGATCCCGAAAAAAACCATTATTAAAGGTTGTGGCTGAGCATGTGAAAAGC
CA
Found at i:3438819 original size:2 final size:2
Alignment explanation
Indices: 3438814--3438849 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3438804 AAGTAAAAAC
3438814 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3438850 GGTATAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3438968 original size:2 final size:2
Alignment explanation
Indices: 3438963--3439011 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3438953 TATATGTAAG
*
3438963 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3439005 TA TA TA T
1 TA TA TA T
3439012 GAGAAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3440106 original size:14 final size:14
Alignment explanation
Indices: 3440071--3440098 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3440061 TAAATTAGTG
3440071 AAAGAAAATAGAAT
1 AAAGAAAATAGAAT
3440085 AAAGAAAATAGAAT
1 AAAGAAAATAGAAT
3440099 TGAGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAGAAAATAGAAT
Found at i:3443025 original size:18 final size:19
Alignment explanation
Indices: 3443002--3443045 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
3442992 ATAATAACAC
*
3443002 AGAAAAAGATTTAAA-AAT
1 AGAAAAAGATTTAAATAAA
3443020 AGAAAAAGATTTAAATAAA
1 AGAAAAAGATTTAAATAAA
3443039 AGAAAAA
1 AGAAAAA
3443046 AAAGAAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.18
Consensus pattern (19 bp):
AGAAAAAGATTTAAATAAA
Found at i:3447406 original size:20 final size:19
Alignment explanation
Indices: 3447381--3447446 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
3447371 TAGACACCTC
*
3447381 TAAAATAAAAAAAATGATAA
1 TAAAATAAAAAAAAT-AAAA
* *
3447401 TAAAATATAAAATATAAAA
1 TAAAATAAAAAAAATAAAA
* *
3447420 TAAAATAATAAAATTAAAA
1 TAAAATAAAAAAAATAAAA
3447439 -AAAA-AAAA
1 TAAAATAAAA
3447447 GAAGGAATGG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
17 3 0.08
18 4 0.11
19 18 0.47
20 13 0.34
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (19 bp):
TAAAATAAAAAAAATAAAA
Found at i:3447413 original size:27 final size:24
Alignment explanation
Indices: 3447381--3447446 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 24
3447371 TAGACACCTC
3447381 TAAAATAAAAAAAATGATAATAAAAT
1 TAAAATAAAAAAAA--ATAATAAAAT
3447407 ATAAAATATAAAATAAAATAATAAAAT
1 -TAAAATA-AAAA-AAAATAATAAAAT
3447434 TAAAA-AAAAAAAA
1 TAAAATAAAAAAAA
3447447 GAAGGAATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
23 3 0.08
24 4 0.11
25 1 0.03
26 5 0.14
27 17 0.46
28 4 0.11
29 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (24 bp):
TAAAATAAAAAAAAATAATAAAAT
Found at i:3447421 original size:19 final size:19
Alignment explanation
Indices: 3447399--3447442 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3447389 AAAAAATGAT
3447399 AATAAAAT-ATAAAATATAA
1 AATAAAATAATAAAAT-TAA
3447418 AATAAAATAATAAAATTAA
1 AATAAAATAATAAAATTAA
3447437 AA-AAAA
1 AATAAAA
3447443 AAAAGAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAAAATAATAAAATTAA
Found at i:3448031 original size:11 final size:11
Alignment explanation
Indices: 3448015--3448039 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3448005 GGGAGGAGAA
3448015 AAAGAAAAAAG
1 AAAGAAAAAAG
3448026 AAAGAAAAAAG
1 AAAGAAAAAAG
3448037 AAA
1 AAA
3448040 AAAGAGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:3448059 original size:18 final size:17
Alignment explanation
Indices: 3448011--3448058 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
3448001 AAGAGGGAGG
*
3448011 AGAAAAAGAAAAAAGAA
1 AGAAAAAAAAAAAAGAA
3448028 AGAAAAAAGAAAAAAG--
1 AGAAAAAA-AAAAAAGAA
3448044 AGCAAAAAAAAAAAA
1 AG-AAAAAAAAAAAA
3448059 ACAAAAGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.29
17 13 0.46
18 7 0.25
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAAAGAA
Found at i:3454076 original size:2 final size:2
Alignment explanation
Indices: 3454071--3454101 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3454061 AAAAAAAATT
*
3454071 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3454102 TGTGTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3454248 original size:26 final size:24
Alignment explanation
Indices: 3454211--3454262 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3454201 TTATTTTTTT
*
3454211 ATATTCATATTTGTGTATGTTTAAAA
1 ATATTCATATTTGT-TA-CTTTAAAA
3454237 ATATTC-TGATTTGTTACTTTAAAA
1 ATATTCAT-ATTTGTTACTTTAAAA
3454261 AT
1 AT
3454263 GTAAACTGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.38
25 3 0.12
26 12 0.50
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (24 bp):
ATATTCATATTTGTTACTTTAAAA
Found at i:3455502 original size:15 final size:15
Alignment explanation
Indices: 3455482--3455513 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3455472 TTAAAATGCC
3455482 CATTTTTCTTTCTCT
1 CATTTTTCTTTCTCT
*
3455497 CATTTTTTTTTCTCT
1 CATTTTTCTTTCTCT
3455512 CA
1 CA
3455514 AACAATATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (15 bp):
CATTTTTCTTTCTCT
Found at i:3456577 original size:14 final size:14
Alignment explanation
Indices: 3456558--3456584 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3456548 CAAAAATTAT
3456558 AACTTATAAAAAAG
1 AACTTATAAAAAAG
3456572 AACTTATAAAAAA
1 AACTTATAAAAAA
3456585 AATTTACCAA
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:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:3470414 original size:5 final size:5
Alignment explanation
Indices: 3470404--3470429 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3470394 TCCCTAGGGT
3470404 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
3470430 GCAGGTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:3473477 original size:29 final size:28
Alignment explanation
Indices: 3473430--3473518 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
3473420 AACTCTTACA
*
3473430 ATGGCTTTTAACGAGTTCAACCACAAACCC
1 ATGG-TTTTAACGAGTTC-ACCACAAAACC
3473460 ATGGTTTTAACTG-GTTCACCACAAAACC
1 ATGGTTTTAAC-GAGTTCACCACAAAACC
* * * *
3473488 ATGGTTTTTAACAAGATCACCGCAAATCC
1 ATGG-TTTTAACGAGTTCACCACAAAACC
3473517 AT
1 AT
3473519 ACTAACTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 14 0.27
29 32 0.63
30 5 0.10
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (28 bp):
ATGGTTTTAACGAGTTCACCACAAAACC
Found at i:3473489 original size:28 final size:29
Alignment explanation
Indices: 3473430--3473495 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
3473420 AACTCTTACA
*
3473430 ATGGCTTTTAACGAGTTCAACCACAAACCC
1 ATGG-TTTTAACGAGTTCAACCACAAAACC
3473460 ATGGTTTTAACTG-GTTC-ACCACAAAACC
1 ATGGTTTTAAC-GAGTTCAACCACAAAACC
3473488 ATGGTTTT
1 ATGGTTTT
3473496 TAACAAGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 18 0.53
29 11 0.32
30 5 0.15
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (29 bp):
ATGGTTTTAACGAGTTCAACCACAAAACC
Found at i:3482543 original size:7 final size:7
Alignment explanation
Indices: 3482528--3482570 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
3482518 ATTAATAAGA
3482528 AATATAAT
1 AATA-AAT
3482536 AATAAAT
1 AATAAAT
3482543 AATAAAT
1 AATAAAT
3482550 AAATAAAT
1 -AATAAAT
*
3482558 AGTAAA-
1 AATAAAT
3482564 AATAAAT
1 AATAAAT
3482571 TAGTGAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 5 0.16
7 15 0.48
8 11 0.35
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:3482546 original size:15 final size:14
Alignment explanation
Indices: 3482528--3482570 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
3482518 ATTAATAAGA
3482528 AATATAATAATAAAT
1 AATA-AATAATAAAT
3482543 AATAAATAAATAAAT
1 AATAAAT-AATAAAT
*
3482558 AGTAAA-AATAAAT
1 AATAAATAATAAAT
3482571 TAGTGAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 7 0.27
14 3 0.12
15 16 0.62
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (14 bp):
AATAAATAATAAAT
Found at i:3482596 original size:18 final size:18
Alignment explanation
Indices: 3482562--3482596 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3482552 ATAAATAGTA
* *
3482562 AAAATAAATTAGTGAAAG
1 AAAATAAAATAGAGAAAG
3482580 AAAATAAAATAGAGAAA
1 AAAATAAAATAGAGAAA
3482597 AATAACACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (18 bp):
AAAATAAAATAGAGAAAG
Found at i:3484092 original size:52 final size:51
Alignment explanation
Indices: 3484032--3484134 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 51
3484022 GGAGGGAGAA
*
3484032 GAAAGAGAGATTTATTGAGAGAGATGGGTATTTCTTGAAAAACTGACGTGT
1 GAAAGAGAGATTGATTGAGAGAGATGGGTATTTCTTGAAAAACTGACGTGT
3484083 NGAAAGAGAGATTGATTGAGAGAGATGGGTATTTCTTGAAAAACTGACGTGT
1 -GAAAGAGAGATTGATTGAGAGAGATGGGTATTTCTTGAAAAACTGACGTGT
3484135 TTTTAAAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.28
Consensus pattern (51 bp):
GAAAGAGAGATTGATTGAGAGAGATGGGTATTTCTTGAAAAACTGACGTGT
Found at i:3486148 original size:21 final size:23
Alignment explanation
Indices: 3486101--3486161 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
3486091 GGTGAGATTG
*
3486101 ATGGTGGTGGTGGTGACGGCACTA
1 ATGGTGGAGGTGGTGACGGCAC-A
3486125 ATGGTGGAGGTGGTGACGG-A-A
1 ATGGTGGAGGTGGTGACGGCACA
*
3486146 ATGGTGGCGGTGGTGA
1 ATGGTGGAGGTGGTGA
3486162 TGGGGGTGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 16 0.46
23 1 0.03
24 18 0.51
ACGTcount: A:0.18, C:0.08, G:0.51, T:0.23
Consensus pattern (23 bp):
ATGGTGGAGGTGGTGACGGCACA
Found at i:3486164 original size:15 final size:15
Alignment explanation
Indices: 3486146--3486242 Score: 77
Period size: 15 Copynumber: 6.3 Consensus size: 15
3486136 GGTGACGGAA
* *
3486146 ATGGTGGCGGTGGTG
1 ATGGTGGTGGGGGTG
* *
3486161 ATGGGGGTGGGAGTG
1 ATGGTGGTGGGGGTG
* * *
3486176 ATGGAGGAGGGGGCG
1 ATGGTGGTGGGGGTG
* *
3486191 ATGGTGGTGGAGATG
1 ATGGTGGTGGGGGTG
3486206 ATGGTGGTGGGGAAGTG
1 ATGGTGGTGGGG--GTG
*
3486223 ATGGGTGGTGGTGGTG
1 AT-GGTGGTGGGGGTG
3486239 ATGG
1 ATGG
3486243 GAGTAATGGA
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
15 45 0.71
16 5 0.08
17 4 0.06
18 9 0.14
ACGTcount: A:0.14, C:0.02, G:0.61, T:0.23
Consensus pattern (15 bp):
ATGGTGGTGGGGGTG
Found at i:3487975 original size:81 final size:82
Alignment explanation
Indices: 3487853--3488057 Score: 212
Period size: 82 Copynumber: 2.6 Consensus size: 82
3487843 GTGTAATTAA
* * * *
3487853 ATGTTTTTAAATATGGCATGTAACAACAATA--T-GTTTTCAACAT-AGCGTGAAATAA-CATTT
1 ATGTTTTTATATATGACGTGTAACAACAATATTTATTTTTCAACATGA-CGTGAAATAATC-TTT
3487913 TCCAAT-ATGACGTGTAAC
64 TCCAATCATGACGTGTAAC
* * * *
3487931 ATGTTTTTGCATATA-G-TGTGTAACAATAATATTTTTTTTTCAACATGACGTGTAATAATCTTT
1 ATGTTTTT--ATATATGACGTGTAACAACAATATTTATTTTTCAACATGACGTGAAATAATCTTT
** *
3487994 TTTAATCATGGCGTGTAAC
64 TCCAATCATGACGTGTAAC
3488013 ATGTTTTTATATATGACGTGTAACAACAATATTTATTTTT-AACAT
1 ATGTTTTTATATATGACGTGTAACAACAATATTTATTTTTCAACAT
3488058 TGAGTGTAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
78 20 0.19
79 1 0.01
80 10 0.10
81 32 0.30
82 42 0.40
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (82 bp):
ATGTTTTTATATATGACGTGTAACAACAATATTTATTTTTCAACATGACGTGAAATAATCTTTTC
CAATCATGACGTGTAAC
Found at i:3487987 original size:26 final size:26
Alignment explanation
Indices: 3487957--3488035 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
3487947 TGTGTAACAA
3487957 TAATATTTTTTTTTCAA-CATGACGTG
1 TAATATTTTTTTTT-AATCATGACGTG
* * *
3487983 TAATAATCTTTTTTAATCATGGCGTG
1 TAATATTTTTTTTTAATCATGACGTG
* * *
3488009 TAACATGTTTTTAT-AT-ATGACGTG
1 TAATATTTTTTTTTAATCATGACGTG
3488033 TAA
1 TAA
3488036 CAACAATATT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 10 0.23
25 4 0.09
26 29 0.67
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (26 bp):
TAATATTTTTTTTTAATCATGACGTG
Found at i:3488032 original size:24 final size:24
Alignment explanation
Indices: 3487966--3488037 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
3487956 ATAATATTTT
* *
3487966 TTTTTCAA-CATGACGTGTAATAATCT
1 TTTTT-AATCATGACGTGTAA-CAT-G
*
3487992 TTTTTAATCATGGCGTGTAACATG
1 TTTTTAATCATGACGTGTAACATG
3488016 TTTTTATAT-ATGACGTGTAACA
1 TTTTTA-ATCATGACGTGTAACA
3488038 ACAATATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 18 0.45
25 6 0.15
26 16 0.40
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (24 bp):
TTTTTAATCATGACGTGTAACATG
Found at i:3488072 original size:55 final size:55
Alignment explanation
Indices: 3487992--3488123 Score: 149
Period size: 55 Copynumber: 2.4 Consensus size: 55
3487982 GTAATAATCT
* * *
3487992 TTTTTAATCATGGCGTGTAACATGTTTTTATATATGACGTGTAACAACAATATTTA
1 TTTTTAA-CATTGAGTGTAACATGTTTTTATACATGACGTGTAACAACAATATTTA
* ** * * *
3488048 TTTTTAACATTGAGTGTAATATGTTTTTATACATGGTGTGTAATAACAGTATTTG
1 TTTTTAACATTGAGTGTAACATGTTTTTATACATGACGTGTAACAACAATATTTA
*
3488103 TTTTCAACA-TGACGTGTAACA
1 TTTTTAACATTGA-GTGTAACA
3488124 ATCTAACCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
54 3 0.05
55 54 0.84
56 7 0.11
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (55 bp):
TTTTTAACATTGAGTGTAACATGTTTTTATACATGACGTGTAACAACAATATTTA
Found at i:3488081 original size:24 final size:23
Alignment explanation
Indices: 3488048--3488092 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3488038 ACAATATTTA
*
3488048 TTTTTAACATTGAGTGTAATATG
1 TTTTTAACATGGAGTGTAATATG
*
3488071 TTTTTATACATGGTGTGTAATA
1 TTTTTA-ACATGGAGTGTAATA
3488093 ACAGTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (23 bp):
TTTTTAACATGGAGTGTAATATG
Found at i:3494883 original size:2 final size:2
Alignment explanation
Indices: 3494876--3494932 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
3494866 CTCCCATTAA
3494876 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * *
3494918 AT CA CT CT CT TT CT C
1 CT CT CT CT CT CT CT C
3494933 ATACACAGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3499185 original size:23 final size:23
Alignment explanation
Indices: 3499152--3499205 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
3499142 ATTTCAATCG
**
3499152 ATGTGTCTGTTGTGTTTTAATAT
1 ATGTGTCTGTTAAGTTTTAATAT
* *
3499175 ATGTGTTTGTTAAGTTTTAATAG
1 ATGTGTCTGTTAAGTTTTAATAT
*
3499198 ATGGGTCT
1 ATGTGTCT
3499206 AGTGAACAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (23 bp):
ATGTGTCTGTTAAGTTTTAATAT
Found at i:3499560 original size:20 final size:21
Alignment explanation
Indices: 3499513--3499561 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3499503 TCACTCAACT
3499513 TTAC-ATTTTTTTAATTTATA
1 TTACTATTTTTTTAATTTATA
* * *
3499533 TTATTATTTTTTTCATTTCTA
1 TTACTATTTTTTTAATTTATA
3499554 TT-CTATTT
1 TTACTATTT
3499562 GTTCATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (21 bp):
TTACTATTTTTTTAATTTATA
Found at i:3507563 original size:2 final size:2
Alignment explanation
Indices: 3507556--3507594 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3507546 GAGAAATTAC
3507556 AT AT AT AT 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 AT AT AT AT A
3507595 CACGCATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3508908 original size:35 final size:34
Alignment explanation
Indices: 3508800--3508914 Score: 106
Period size: 35 Copynumber: 3.3 Consensus size: 34
3508790 TGAAACACGT
* * *
3508800 AGAACAACTAGAACAAGTAAAATACTATTTCATGC
1 AGAACAACTAAAACAAGT-AAACACTATTTCAAGC
* * * * *
3508835 AAAACAATTAAAACAAATAAAGGACTATTTCAAAC
1 AGAACAACTAAAACAAGTAAA-CACTATTTCAAGC
*
3508870 AGAACAACTAAAACAAGTGAAACACTACTTT-ACGC
1 AGAACAACTAAAACAAGT-AAACACTA-TTTCAAGC
3508905 AGAACAACTA
1 AGAACAACTA
3508915 CAATAAATGG
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
34 3 0.05
35 55 0.86
36 6 0.09
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.19
Consensus pattern (34 bp):
AGAACAACTAAAACAAGTAAACACTATTTCAAGC
Found at i:3508932 original size:70 final size:70
Alignment explanation
Indices: 3508800--3508933 Score: 153
Period size: 70 Copynumber: 1.9 Consensus size: 70
3508790 TGAAACACGT
* * * * *
3508800 AGAACAACTAGAACAAGTAAAATACTATTTCATGCAAAACAATTAAAACAAATAAAGGACTATTT
1 AGAACAACTAAAACAAGTAAAACACTATTTCACGCAAAACAACTAAAACAAATAAAGCACTATTT
3508865 CAAAC
66 CAAAC
* * * * **
3508870 AGAACAACTAAAACAAGTGAAACACTACTTT-ACGCAGAACAACTACAATAAATGGAGCACTATT
1 AGAACAACTAAAACAAGTAAAACACTA-TTTCACGCAAAACAACTAAAACAAATAAAGCACTATT
3508934 CCATGTAGAA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
70 49 0.94
71 3 0.06
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.20
Consensus pattern (70 bp):
AGAACAACTAAAACAAGTAAAACACTATTTCACGCAAAACAACTAAAACAAATAAAGCACTATTT
CAAAC
Found at i:3509183 original size:29 final size:28
Alignment explanation
Indices: 3509151--3509226 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 28
3509141 CTCTTGTACC
*
3509151 TATTCACGTATACCTTTTTCTTTTATACT
1 TATTCACGTATACCTTTTTCTCTTA-ACT
*
3509180 TATTCACAG-ACACCTTTTTCTCTTAACT
1 TATTCAC-GTATACCTTTTTCTCTTAACT
* * *
3509208 TCTTCTCGTATAACTTTTT
1 TATTCACGTATACCTTTTT
3509227 ATGTATATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.03
28 16 0.41
29 21 0.54
30 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.04, T:0.51
Consensus pattern (28 bp):
TATTCACGTATACCTTTTTCTCTTAACT
Found at i:3509792 original size:64 final size:64
Alignment explanation
Indices: 3509675--3509796 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
3509665 TTTACTTATC
* ** **
3509675 CTCAATCATTATTCTACTATTCATTAATTCTCTTCCATCGTCATGATGTTTAGTACTTCAGAAA
1 CTCAATCATCATTCTACTATTCATTAATTCTCTTCCATCGTCACAATACTTAGTACTTCAGAAA
* * *
3509739 CTCAATCATCATTTTACTATTCATTAGTTCTTTTCCATCGTCACAATACTTAGTACTT
1 CTCAATCATCATTCTACTATTCATTAATTCTCTTCCATCGTCACAATACTTAGTACTT
3509797 TAGGAACTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (64 bp):
CTCAATCATCATTCTACTATTCATTAATTCTCTTCCATCGTCACAATACTTAGTACTTCAGAAA
Found at i:3510677 original size:25 final size:25
Alignment explanation
Indices: 3510649--3510706 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
3510639 TTATTTAAAG
* * *
3510649 GGTTGAATTAATCTCCTTTATGTCA
1 GGTTGAATTAACCTCCTTGATGTAA
*
3510674 GGTTTGAGTTAACCTCCTTGATGTAA
1 GG-TTGAATTAACCTCCTTGATGTAA
*
3510700 AGTTGAA
1 GGTTGAA
3510707 AGTTCCTCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (25 bp):
GGTTGAATTAACCTCCTTGATGTAA
Found at i:3513695 original size:13 final size:13
Alignment explanation
Indices: 3513679--3513715 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
3513669 TTTATTTTTG
3513679 AAAATCACTTGAA
1 AAAATCACTTGAA
*
3513692 AAAATCACTTGAG
1 AAAATCACTTGAA
3513705 AAAATCACTTG
1 AAAATCACTTG
3513716 CTTTAGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (13 bp):
AAAATCACTTGAA
Found at i:3520439 original size:30 final size:30
Alignment explanation
Indices: 3520403--3520464 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
3520393 AATTAGGGTA
*
3520403 ATCAAAAGGTAAATAAGACTCACCACATGT
1 ATCAAAAGGTAAAGAAGACTCACCACATGT
*
3520433 ATCAAAAGGTAAAGAAGACTCACCATATGT
1 ATCAAAAGGTAAAGAAGACTCACCACATGT
3520463 AT
1 AT
3520465 TTTTAAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (30 bp):
ATCAAAAGGTAAAGAAGACTCACCACATGT
Found at i:3538885 original size:67 final size:68
Alignment explanation
Indices: 3538813--3538943 Score: 212
Period size: 67 Copynumber: 1.9 Consensus size: 68
3538803 TATTTTTTAT
*
3538813 TTGTATTAATAATTTAATAAAAAATTATTTTAGGGGCCT-ATTAAAATATATATAT-ATATATAA
1 TTGTATTAATAATTTAATAAAAAATTATTTT-GGGGCCTCATTAAAAAATATATATAATATATAA
3538876 CATA
65 CATA
* *
3538880 TTGTATTAATAATTTAATAAAAAATTATTTTGGGGGCTCATTAAAAAATATATGTAATATATAA
1 TTGTATTAATAATTTAATAAAAAATTATTTTGGGGCCTCATTAAAAAATATATATAATATATAA
3538944 AAATTTTTAA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
66 6 0.10
67 45 0.76
68 8 0.14
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (68 bp):
TTGTATTAATAATTTAATAAAAAATTATTTTGGGGCCTCATTAAAAAATATATATAATATATAAC
ATA
Found at i:3542168 original size:4 final size:4
Alignment explanation
Indices: 3542159--3542200 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
3542149 ATGATGTTAT
* * *
3542159 ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAT ATAT ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
3542201 CTCGATCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (4 bp):
ATAC
Found at i:3542176 original size:12 final size:12
Alignment explanation
Indices: 3542156--3542200 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
3542146 TCCATGATGT
3542156 TATATACATACA
1 TATATACATACA
*
3542168 TACATACATACA
1 TATATACATACA
*
3542180 TATATACATATA
1 TATATACATACA
3542192 TATATACAT
1 TATATACAT
3542201 CTCGATCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TATATACATACA
Found at i:3544184 original size:9 final size:10
Alignment explanation
Indices: 3544163--3544191 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
3544153 CTAAGGTAGT
3544163 TTTTATGAAA
1 TTTTATGAAA
3544173 TTTTAT-AAA
1 TTTTATGAAA
3544182 TTTTATGAAA
1 TTTTATGAAA
3544192 AATGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TTTTATGAAA
Found at i:3547497 original size:58 final size:57
Alignment explanation
Indices: 3547389--3547508 Score: 177
Period size: 58 Copynumber: 2.1 Consensus size: 57
3547379 AAAATCTCAT
* ** * *
3547389 CTTTGCATGCATAGCATTTATTAAATCGCATAAAATAAATCTATTGCATGCATACTA
1 CTTTGCATGCATAGCATTCATTAAATCGCATAAAATAAATCTATCACATGCAAACAA
*
3547446 CTTTGCATTGCATAGCATTCATTAAATCGCATAAAATAAATCTGTCACATGCAAACAA
1 CTTTGCA-TGCATAGCATTCATTAAATCGCATAAAATAAATCTATCACATGCAAACAA
3547504 CTTTG
1 CTTTG
3547509 GATGATTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 7 0.12
58 49 0.88
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (57 bp):
CTTTGCATGCATAGCATTCATTAAATCGCATAAAATAAATCTATCACATGCAAACAA
Found at i:3557930 original size:2 final size:2
Alignment explanation
Indices: 3557925--3557954 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3557915 AATATATATA
3557925 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3557955 CTCAGGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3561867 original size:54 final size:54
Alignment explanation
Indices: 3561803--3561925 Score: 203
Period size: 54 Copynumber: 2.3 Consensus size: 54
3561793 AACATTTTAT
*
3561803 CTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAG-TCAGACACCACAC
1 CTCACCCAGCTCATGTGCATCCCACCACACCGTGCACATAGCT-AGACACCACAC
* *
3561857 CTCACCCAGCTCATGTGCATCCCACCACACCGTGCACATAGCTAGACAGCACAT
1 CTCACCCAGCTCATGTGCATCCCACCACACCGTGCACATAGCTAGACACCACAC
3561911 CTCACCCAGCTCATG
1 CTCACCCAGCTCATG
3561926 CATGGTTACA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
54 64 0.98
55 1 0.02
ACGTcount: A:0.27, C:0.42, G:0.14, T:0.17
Consensus pattern (54 bp):
CTCACCCAGCTCATGTGCATCCCACCACACCGTGCACATAGCTAGACACCACAC
Found at i:3561976 original size:2 final size:2
Alignment explanation
Indices: 3561969--3562034 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3561959 ATGACAGTGC
3561969 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
3562011 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
3562035 GTGTCTGTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3562590 original size:21 final size:21
Alignment explanation
Indices: 3562548--3562590 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3562538 GGTAACAATT
**
3562548 TCGCTGCAGCGAAATTCATTC
1 TCGCTGCAGCGAAAAACATTC
*
3562569 TCGCTGCAGCGAAAAACTTTC
1 TCGCTGCAGCGAAAAACATTC
3562590 T
1 T
3562591 ATTTTGTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (21 bp):
TCGCTGCAGCGAAAAACATTC
Found at i:3573428 original size:18 final size:18
Alignment explanation
Indices: 3573391--3573430 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3573381 CACCCCTTTA
*
3573391 ATTTTTATTTATTTTTAT
1 ATTTTTATTTATTTTAAT
3573409 ATTTTTATTT-TGTTTAAT
1 ATTTTTATTTAT-TTTAAT
3573427 ATTT
1 ATTT
3573431 CAAGTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
ATTTTTATTTATTTTAAT
Found at i:3576434 original size:2 final size:2
Alignment explanation
Indices: 3576429--3576454 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3576419 ATATATAGAT
3576429 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3576455 TTTGAATCCA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3577734 original size:13 final size:13
Alignment explanation
Indices: 3577716--3577740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3577706 TTACATATAT
3577716 TATATTATATTTA
1 TATATTATATTTA
3577729 TATATTATATTT
1 TATATTATATTT
3577741 CCACGTAAAG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTATATTTA
Found at i:3577908 original size:2 final size:2
Alignment explanation
Indices: 3577901--3577925 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3577891 CCACCCTAGA
3577901 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 T
3577926 AACTAAAAGA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3578272 original size:3 final size:3
Alignment explanation
Indices: 3578264--3578297 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3578254 TGCTTTCCTT
*
3578264 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3578298 ATTGAGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:3580544 original size:5 final size:5
Alignment explanation
Indices: 3580534--3580558 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3580524 TTAAGTGTAA
3580534 GGGAG GGGAG GGGAG GGGAG GGGAG
1 GGGAG GGGAG GGGAG GGGAG GGGAG
3580559 AGGGGGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:3580701 original size:2 final size:2
Alignment explanation
Indices: 3580692--3580730 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3580682 CNCCGAACGA
3580692 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3580731 TTGTTAATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:3584445 original size:20 final size:20
Alignment explanation
Indices: 3584408--3584445 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3584398 CTGTAAAGTC
* *
3584408 AAATAATATAATTAAAAATA
1 AAATAAAATAATAAAAAATA
3584428 AAATAAAATAATAAAAAA
1 AAATAAAATAATAAAAAA
3584446 CCTGTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATAAAATAATAAAAAATA
Found at i:3585818 original size:2 final size:2
Alignment explanation
Indices: 3585811--3585837 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3585801 TACTGAGAAG
3585811 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
3585838 CTTTCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Done.