Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_pilon, whole genome shotgun sequence
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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:3172085 original size:21 final size:21
Alignment explanation
Indices: 3172061--3172100 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3172051 CGTAAAACCC
* *
3172061 ATAATGTACATATAGTGCCTA
1 ATAATGCACACATAGTGCCTA
3172082 ATAATGCACACATAGTGCC
1 ATAATGCACACATAGTGCC
3172101 AGATTGCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (21 bp):
ATAATGCACACATAGTGCCTA
Found at i:3172129 original size:19 final size:19
Alignment explanation
Indices: 3172107--3172156 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
3172097 TGCCAGATTG
3172107 CACATAAAGTGCCAAAATA
1 CACATAAAGTGCCAAAATA
*
3172126 CACATAAAGTGCCAAAATG
1 CACATAAAGTGCCAAAATA
3172145 CACATAAAGTGC
1 CACATAAAGTGC
3172157 ATGATAGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.48, C:0.22, G:0.14, T:0.16
Consensus pattern (19 bp):
CACATAAAGTGCCAAAATA
Found at i:3172147 original size:38 final size:40
Alignment explanation
Indices: 3172063--3172156 Score: 111
Period size: 38 Copynumber: 2.4 Consensus size: 40
3172053 TAAAACCCAT
* * * * *
3172063 AATGTACATATAGTGCCTAATAATGCACACATAGTGCCAG
1 AATGCACATAAAGTGCCTAATAATACACACAAAGTGCCAA
* *
3172103 ATTGCACATAAAGTGCC-AA-AATACACATAAAGTGCCAA
1 AATGCACATAAAGTGCCTAATAATACACACAAAGTGCCAA
3172141 AATGCACATAAAGTGC
1 AATGCACATAAAGTGC
3172157 ATGATAGATG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 30 0.65
39 2 0.04
40 14 0.30
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (40 bp):
AATGCACATAAAGTGCCTAATAATACACACAAAGTGCCAA
Found at i:3175344 original size:54 final size:53
Alignment explanation
Indices: 3175272--3175497 Score: 256
Period size: 54 Copynumber: 4.2 Consensus size: 53
3175262 ATTGCACCTA
* * * ** *
3175272 AGTGTCGATATGGAAATTCATAAACTCGTTATGAATTCCATGGTTTGCACACAT
1 AGTGTCGATACGGTAATTCATAAACTCATTATGAATT-TGTGGGTTGCACACAT
* * *
3175326 ACTGTCGATATGGTAATTCACAAACTCATTATGAATTT-TGCGTGTTGCACACAT
1 AGTGTCGATACGGTAATTCATAAACTCATTATGAATTTGTG-G-GTTGCACACAT
* * * * *
3175380 AGTGCCGATACGGTCATTCATTAACTCATTATGAATTTTGTGGGCTGCACAGAT
1 AGTGTCGATACGGTAATTCATAAACTCATTATGAA-TTTGTGGGTTGCACACAT
* *
3175434 AGTGTTGATACGGTCATTCATAAACTCATTATGAATTATGTGGGTTGCACACAT
1 AGTGTCGATACGGTAATTCATAAACTCATTATGAATT-TGTGGGTTGCACACAT
3175488 AGTGTCGATA
1 AGTGTCGATA
3175498 GTACACACAC
Statistics
Matches: 147, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
52 2 0.01
53 3 0.02
54 136 0.93
55 4 0.03
56 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (53 bp):
AGTGTCGATACGGTAATTCATAAACTCATTATGAATTTGTGGGTTGCACACAT
Found at i:3177183 original size:18 final size:19
Alignment explanation
Indices: 3177160--3177220 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
3177150 GTAAGATCGG
3177160 TTCAGACCGG-CAAACCGA
1 TTCAGACCGGTCAAACCGA
* *
3177178 TTCAGACCGGTCAAACTGG
1 TTCAGACCGGTCAAACCGA
3177197 TTCTA-ACCGGTCAAAACCGA
1 TTC-AGACCGGTC-AAACCGA
3177217 TTCA
1 TTCA
3177221 AAATTGGTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 10 0.28
19 17 0.47
20 9 0.25
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (19 bp):
TTCAGACCGGTCAAACCGA
Found at i:3184357 original size:17 final size:17
Alignment explanation
Indices: 3184337--3184374 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3184327 GGTCAAAGGA
3184337 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
3184354 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
3184371 GGTC
1 GGTC
3184375 GGGTTAGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:3184404 original size:9 final size:10
Alignment explanation
Indices: 3184382--3184437 Score: 62
Period size: 9 Copynumber: 5.7 Consensus size: 10
3184372 GTCGGGTTAG
*
3184382 ACCGGTTCAG
1 ACCGGTTCAA
3184392 ACCGG-TCAA
1 ACCGGTTCAA
*
3184401 ACCGGTTCTA
1 ACCGGTTCAA
3184411 ACCGGTTCAAA
1 ACCGGTTC-AA
*
3184422 ATCGGTT-AA
1 ACCGGTTCAA
3184431 ACCGGTT
1 ACCGGTT
3184438 TTCCAGCTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
9 16 0.41
10 16 0.41
11 7 0.18
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:3184406 original size:19 final size:20
Alignment explanation
Indices: 3184382--3184421 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
3184372 GTCGGGTTAG
3184382 ACCGGTTC-AGACCGG-TCAA
1 ACCGGTTCTA-ACCGGTTCAA
3184401 ACCGGTTCTAACCGGTTCAA
1 ACCGGTTCTAACCGGTTCAA
3184421 A
1 A
3184422 ATCGGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (20 bp):
ACCGGTTCTAACCGGTTCAA
Found at i:3187005 original size:21 final size:21
Alignment explanation
Indices: 3186924--3187017 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
3186914 GGTTAAGACC
*
3186924 TTTCGATGAAAGAACTTAACCT
1 TTTC-ATGAAAGGACTTAACCT
* * *
3186946 TTTGATTAAAGGACTTATCCT
1 TTTCATGAAAGGACTTAACCT
* *
3186967 TTTGATGAAAGGGCTTAACCT
1 TTTCATGAAAGGACTTAACCT
* * *
3186988 TTTCATGAAATGATTTAATCT
1 TTTCATGAAAGGACTTAACCT
3187009 TTTCATGAA
1 TTTCATGAA
3187018 GATAATTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
21 57 0.95
22 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (21 bp):
TTTCATGAAAGGACTTAACCT
Found at i:3190006 original size:21 final size:19
Alignment explanation
Indices: 3189959--3190012 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
3189949 TAAAGGACTT
3189959 ATCTTTTTATGAAAGAGGTTA
1 ATCTTTTTATG--AGAGGTTA
*
3189980 ACCTTTTTATGAGAGGATTTA
1 ATCTTTTTATGAGAGG--TTA
*
3190001 ATCTTTTCATGA
1 ATCTTTTTATGA
3190013 AGAGAATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.18
21 23 0.82
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (19 bp):
ATCTTTTTATGAGAGGTTA
Found at i:3190755 original size:122 final size:123
Alignment explanation
Indices: 3190597--3190852 Score: 345
Period size: 122 Copynumber: 2.1 Consensus size: 123
3190587 TTTTTAAATG
*
3190597 CCACTAAATAATGTACTGTAGTTGCGTTTGTATACAAACG-TCGCCAAAGACTCGTACTTTAGTT
1 CCACTAAATAATGTACTGTAGTTGCGTTTGTATACAAACGCT-GCCAAAGACTCATACTTTAGTT
* * * *
3190661 GCGATTTAAGCACAAATGTCGCTAAATACAAGTA-TTTAGTGGCGTTTTTATATAAACA
65 GCGATTTAACCACAAACGCCGCTAAATACAAGTACTTTAGTGGCATTTTTATATAAACA
* * * * *
3190719 CTACTAAATACTGTACTTTAGTTGCGTTTGTTTACAAACGCTGCCAAATACTCATACTTTAGTTG
1 CCACTAAATAATGTACTGTAGTTGCGTTTGTATACAAACGCTGCCAAAGACTCATACTTTAGTTG
* * ** * *
3190784 CGCTTTAACCAGAAACGCCGCTAAATACTTGTACTTTAGTGGTATTTTTATATAAACG
66 CGATTTAACCACAAACGCCGCTAAATACAAGTACTTTAGTGGCATTTTTATATAAACA
3190842 CCACTAAATAA
1 CCACTAAATAA
3190853 ATAAAGCCAA
Statistics
Matches: 114, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
122 83 0.73
123 31 0.27
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (123 bp):
CCACTAAATAATGTACTGTAGTTGCGTTTGTATACAAACGCTGCCAAAGACTCATACTTTAGTTG
CGATTTAACCACAAACGCCGCTAAATACAAGTACTTTAGTGGCATTTTTATATAAACA
Found at i:3190768 original size:40 final size:40
Alignment explanation
Indices: 3190602--3190785 Score: 124
Period size: 40 Copynumber: 4.5 Consensus size: 40
3190592 AAATGCCACT
* * *
3190602 AAATAATGTACTGTAGTTGCGTTTGTATACAAACGTCGCC
1 AAATACTGTACTTTAGTTGCGTTTGTTTACAAACGTCGCC
* **** * *
3190642 AAAGACTCGTACTTTAGTTGCGATTTAAGCACAAATGTCGCT
1 AAATACT-GTACTTTAGTTGCG-TTTGTTTACAAACGTCGCC
* * * * * *
3190684 AAATACAAGTA-TTTAGTGGCGTTT-TTATATAAAC-ACTACT
1 AAATAC-TGTACTTTAGTTGCGTTTGTT-TACAAACGTC-GCC
3190724 AAATACTGTACTTTAGTTGCGTTTGTTTACAAACG-CTGCC
1 AAATACTGTACTTTAGTTGCGTTTGTTTACAAACGTC-GCC
*
3190764 AAATACTCATACTTTAGTTGCG
1 AAATACT-GTACTTTAGTTGCG
3190786 CTTTAACCAG
Statistics
Matches: 110, Mismatches: 25, Indels: 17
0.72 0.16 0.11
Matches are distributed among these distances:
39 4 0.04
40 48 0.44
41 37 0.34
42 21 0.19
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (40 bp):
AAATACTGTACTTTAGTTGCGTTTGTTTACAAACGTCGCC
Found at i:3194041 original size:26 final size:26
Alignment explanation
Indices: 3194004--3194076 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
3193994 TTTCAGTTGT
*
3194004 TTCATTTGAAAAGGCATGTTTAAATG
1 TTCATTTCAAAAGGCATGTTTAAATG
3194030 TTCATTTCAAAAGGCATGTTTAAATG
1 TTCATTTCAAAAGGCATGTTTAAATG
3194056 TTCATTTCAAAAGGCATGTTT
1 TTCATTTCAAAAGGCATGTTT
3194077 CCAATTTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (26 bp):
TTCATTTCAAAAGGCATGTTTAAATG
Found at i:3194601 original size:21 final size:21
Alignment explanation
Indices: 3194541--3194603 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
3194531 TGATTTAGTA
*
3194541 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTATTG
*
3194562 TTATGGATTTCAAGCTTATTG
1 TTATGGATTTCAAGTTTATTG
*
3194583 TTATGGATTTCAAATTTATTG
1 TTATGGATTTCAAGTTTATTG
3194604 GATAATGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTATTG
Found at i:3194872 original size:44 final size:44
Alignment explanation
Indices: 3194818--3194914 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
3194808 TTACATTCAC
* * *
3194818 AAACGTCACTATAT-TACATAACATTTAGCGGTATTTTGGGGAAA
1 AAACGCCACTATATGT-CAGAACATTTAGCGGCATTTTGGGGAAA
* * *
3194862 AAATGCCACTATATGTCAGAACATTTAGCGGCATTTTTGGGATA
1 AAACGCCACTATATGTCAGAACATTTAGCGGCATTTTGGGGAAA
3194906 AAACGCCAC
1 AAACGCCAC
3194915 AAAAGAAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
AAACGCCACTATATGTCAGAACATTTAGCGGCATTTTGGGGAAA
Found at i:3196819 original size:21 final size:21
Alignment explanation
Indices: 3196795--3196842 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3196785 TCTTTCTATT
*
3196795 AAAGAACTT-ATCCTTTTGATG
1 AAAGAACTTCA-CCTTTTCATG
*
3196816 AAAGAAGTTCACCTTTTCATG
1 AAAGAACTTCACCTTTTCATG
3196837 AAAGAA
1 AAAGAA
3196843 TTTAATACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (21 bp):
AAAGAACTTCACCTTTTCATG
Found at i:3198276 original size:9 final size:9
Alignment explanation
Indices: 3198223--3198363 Score: 66
Period size: 9 Copynumber: 15.3 Consensus size: 9
3198213 GTAGATTGTA
3198223 AAATAAAAT
1 AAATAAAAT
*
3198232 AAATATTAAAA
1 AAATA--AAAT
*
3198243 AAATATTAAT
1 AAATA-AAAT
3198253 ATAATAATAAT
1 A-AATAA-AAT
3198264 -AATAAAAT
1 AAATAAAAT
3198272 AAAT-AAAT
1 AAATAAAAT
*
3198280 AAA-ATAGAT
1 AAATA-AAAT
*
3198289 AACA-AAGAT
1 AA-ATAAAAT
3198298 AAATAAAAGTT
1 AAATAAAA--T
*
3198309 AAA-AAAAG
1 AAATAAAAT
3198317 AAA-AATAAT
1 AAATAA-AAT
3198326 -AA-AAAAT
1 AAATAAAAT
3198333 -AATAAAAT
1 AAATAAAAT
3198341 AAATAAAAAT
1 AAAT-AAAAT
3198351 AAATAAAAAT
1 AAAT-AAAAT
3198361 AAA
1 AAA
3198364 AATGACCAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 29
0.75 0.05 0.20
Matches are distributed among these distances:
7 5 0.05
8 25 0.23
9 32 0.29
10 28 0.26
11 19 0.17
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3198290 original size:22 final size:21
Alignment explanation
Indices: 3198250--3198348 Score: 62
Period size: 22 Copynumber: 4.5 Consensus size: 21
3198240 AAAAAATATT
3198250 AATATAATAATAATAATAA-AATA
1 AATA-AATAA-AATAATAACAA-A
3198273 AATAAATAAAATAGATAACAAA
1 AATAAATAAAATA-ATAACAAA
* *
3198295 GATAAATAAAAGTTAA-AAAAAGA
1 AATAAATAAAA--TAATAACAA-A
* *
3198318 AAAATAATAAAA-AATAA-TAA
1 AATA-AATAAAATAATAACAAA
3198338 AATAAATAAAA
1 AATAAATAAAA
3198349 ATAAATAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
19 7 0.11
20 4 0.06
21 7 0.11
22 26 0.41
23 10 0.16
24 9 0.14
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (21 bp):
AATAAATAAAATAATAACAAA
Found at i:3198360 original size:10 final size:10
Alignment explanation
Indices: 3198258--3198363 Score: 67
Period size: 10 Copynumber: 10.2 Consensus size: 10
3198248 TTAATATAAT
*
3198258 AATAATAATA
1 AATAAAAATA
*
3198268 AA-ATAAATA
1 AATAAAAATA
3198277 AAT-AAAATA
1 AATAAAAATA
*
3198286 GATAACAAAGATA
1 AAT-A-AAA-ATA
*
3198299 AATAAAAGTTA
1 AATAAAA-ATA
*
3198310 AA-AAAAGAAA
1 AATAAAA-ATA
3198320 AATAATAAA-A
1 AATAA-AAATA
3198330 AATAATAAAATA
1 AAT-A-AAAATA
3198342 AATAAAAATA
1 AATAAAAATA
3198352 AATAAAAATA
1 AATAAAAATA
3198362 AA
1 AA
3198364 AATGACCAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
9 14 0.18
10 32 0.41
11 16 0.21
12 11 0.14
13 5 0.06
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (10 bp):
AATAAAAATA
Found at i:3199599 original size:19 final size:19
Alignment explanation
Indices: 3199558--3199600 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3199548 CTTGAAATGG
* *
3199558 TATGGAATTGAATCTGTAG
1 TATGGAATTGAATCTGGAA
3199577 TATGGAAATTGAATC-GGAA
1 TATGG-AATTGAATCTGGAA
3199596 TATGG
1 TATGG
3199601 CTTCTCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (19 bp):
TATGGAATTGAATCTGGAA
Found at i:3200162 original size:85 final size:85
Alignment explanation
Indices: 3200014--3200359 Score: 394
Period size: 85 Copynumber: 4.1 Consensus size: 85
3200004 ATGTGTAATC
* * * * * * ** *
3200014 GAGCTGAATGAAATCGAACTCGACA-AT-TTTGTTGATAGATAGCCCTTTTTTCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTGGTTGACAGATAACCCTTCTCCCCTTGAGTTATG
* * * *
3200077 CTGTAAATTTGATTTGCCTCT
65 CTATAAATTGGATGTGCCTTT
*
3200098 GAGCTGAATGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTCCCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCCCCTTGAGTTATGC
* *
3200163 TACAAAATT-GATATGCCTTT
66 TA-TAAATTGGATGTGCCTTT
* * ** *
3200183 TAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGATAGATAACCCTTCTTGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCCCCTTGAGTTATGC
* *
3200248 TGTAAATTGGATGTGCTTTT
66 TATAAATTGGATGTGCCTTT
* * * *
3200268 GAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTC-CCGTCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCC-CCTTGAGTTATG
3200332 CTATAAATTGGATGTGCCTTT
65 CTATAAATTGGATGTGCCTTT
3200353 GAGCTGA
1 GAGCTGA
3200360 GTGTTAGAGT
Statistics
Matches: 222, Mismatches: 35, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
83 1 0.00
84 27 0.12
85 189 0.85
86 5 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCCCCTTGAGTTATGC
TATAAATTGGATGTGCCTTT
Found at i:3200296 original size:170 final size:169
Alignment explanation
Indices: 3200014--3200359 Score: 455
Period size: 170 Copynumber: 2.0 Consensus size: 169
3200004 ATGTGTAATC
* * * *
3200014 GAGCTGAATGAAATCGAACTCGACAATTTTGTTGATAGATAGCCCTTTTTTCCTTGAGCTATGCT
1 GAGCTGAATGAAATCGAACTCGACAATTTGGTTGATAGATAACCCTTCTTGCCTTGAGCTATGCT
* * **
3200079 GTAAATTTGATTTGCCTCTGAGCTGAATGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCC
66 GTAAATTGGATGTGCCTCTGAGCTGAATGTAATCGAACTCAAAGGTCTTGGTTGACAGATAACCC
3200144 TTCTCC-CCTTGAGTTATGCTACAAAATT-GATATGCCTTT
131 TTC-CCGCCTTGAGTTATGCTA-AAAATTGGATATGCCTTT
* * * *
3200183 TAGCTGAATGTAATCGAACTCGA-AGGTCTTGGTTGATAGATAACCCTTCTTGCCTTGAGTTATG
1 GAGCTGAATGAAATCGAACTCGACA-AT-TTGGTTGATAGATAACCCTTCTTGCCTTGAGCTATG
* * * * *
3200247 TTGTAAATTGGATGTGCTTTTGAGCTGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGATAAC
64 CTGTAAATTGGATGTGCCTCTGAGCTGAATGTAATCGAACTCAAAGGTCTTGGTTGACAGATAAC
* * *
3200312 CCTTCCCGTCTTGAGTTATGCTATAAATTGGATGTGCCTTT
129 CCTTCCCGCCTTGAGTTATGCTAAAAATTGGATATGCCTTT
3200353 GAGCTGA
1 GAGCTGA
3200360 GTGTTAGAGT
Statistics
Matches: 152, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
168 1 0.01
169 29 0.19
170 122 0.80
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.36
Consensus pattern (169 bp):
GAGCTGAATGAAATCGAACTCGACAATTTGGTTGATAGATAACCCTTCTTGCCTTGAGCTATGCT
GTAAATTGGATGTGCCTCTGAGCTGAATGTAATCGAACTCAAAGGTCTTGGTTGACAGATAACCC
TTCCCGCCTTGAGTTATGCTAAAAATTGGATATGCCTTT
Found at i:3201475 original size:90 final size:89
Alignment explanation
Indices: 3201366--3201538 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
3201356 TCTCGAATAT
* * * *
3201366 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTTATATGATTAA
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAA
3201431 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
3201455 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTA
* *
3201520 GGGTAACTTGGCTATAAAA
65 AGGTAACTTGGATATAAAA
3201539 TGGTATGTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 70 0.91
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.39
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAA
GGTAACTTGGATATAAAAGGATTA
Found at i:3208112 original size:90 final size:90
Alignment explanation
Indices: 3208002--3208179 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 90
3207992 TAATCTTGAA
* * * * *
3208002 TATTTAATTTTAATTAATTAAATATAGATTAAATTAATTTGAAATAGTAAAATCCCTGATATGAT
1 TATTAAATTCTAATTAATTAAATATAGATTAAATTAATTTGAAATAATAAAAACCCTAATATGAT
3208067 TAAAGTAACTTGGATATAAAAGGAT
66 TAAAGTAACTTGGATATAAAAGGAT
*
3208092 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCTAATTAATTAAATATAGATTAAATTAATTTGAAATAATAAAAACCCTAATATGAT
** *
3208157 TAGGGTAACTTGGCTATAAAAGG
66 TAAAGTAACTTGGATATAAAAGG
3208180 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCTAATTAATTAAATATAGATTAAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAAAGTAACTTGGATATAAAAGGAT
Found at i:3208714 original size:85 final size:83
Alignment explanation
Indices: 3208455--3208729 Score: 320
Period size: 85 Copynumber: 3.3 Consensus size: 83
3208445 GGTCCCAACA
* * *
3208455 CTGAGTGTAATCAAACTTGAAGGTATTGGTTGACAGATAACCTTTCTCACCTTGAGTTATACTGT
1 CTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACC-TTCTCGCCTTGAGTTATACTGT
*
3208520 AAATTGGATGTGCCTTTTAG
65 AAA-TGGATGTGCCTTTGAG
* * * * * *
3208540 CTGAGTATAATCAAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCAC-TGAGCTATTCT
1 CTGAGTGTAATCAAACTCGAAGGTC-TTGGTTGACAGATA-ACCTTCTCGC-CTTGAGTTATACT
** *
3208604 ACAAAT-TATGTGCCTTTGAG
63 GTAAATGGATGTGCCTTTGAG
** *
3208624 CTGAGTGTAATTGAACTCGAAGGTCTTGGTTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGT
1 CTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACAGATAAC-CTTCTCGCCTTGAGTTATACTGT
*
3208689 AAATAGGATGTCCCTTTGAG
65 AAAT-GGATGTGCCTTTGAG
3208709 CTGAGTGTAATCAAACTCGAA
1 CTGAGTGTAATCAAACTCGAA
3208730 TATCTTTTAT
Statistics
Matches: 156, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
82 2 0.01
83 33 0.21
84 34 0.22
85 54 0.35
86 30 0.19
87 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (83 bp):
CTGAGTGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCTTCTCGCCTTGAGTTATACTGTA
AATGGATGTGCCTTTGAG
Found at i:3209738 original size:92 final size:92
Alignment explanation
Indices: 3209531--3209784 Score: 303
Period size: 92 Copynumber: 2.7 Consensus size: 92
3209521 GGCTAGCTGG
* * * * * * *
3209531 ATCCATATAGTCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTTAATATCATTGTATAGATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTATAGAGGGACAAC-TCA-AGC-TT-TATTG-TA
3209596 TTATAATCACCTTTATCAGGCTAACTGAATACT
61 -TATAATCACCTTTATCAGGCTAACTGAATACT
3209629 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATAA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATAA
* ** *
3209694 TCACCTTTATCTGGCTAGTTG-ATTCAT
66 TCACCTTTATCAGGCTAACTGAATAC-T
* * * *
3209721 ATCCATAAAGCCTGGGCGTTTAACCAATTGCTTTAGAGGGATAGCTCAAGCTTTATTGTATATA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATA
3209785 TATAATATTA
Statistics
Matches: 140, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
91 3 0.02
92 84 0.60
93 2 0.01
94 4 0.03
95 2 0.01
96 2 0.01
97 2 0.01
98 41 0.29
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (92 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTATAGAGGGACAACTCAAGCTTTATTGTATATAA
TCACCTTTATCAGGCTAACTGAATACT
Found at i:3211029 original size:9 final size:9
Alignment explanation
Indices: 3211015--3211064 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
3211005 GCTGCTGGAA
3211015 ACCGGTTTG
1 ACCGGTTTG
3211024 ACCGGTTTTG
1 ACCGG-TTTG
*
3211034 ACCGATTTG
1 ACCGGTTTG
*
3211043 ACCGGTCTG
1 ACCGGTTTG
*
3211052 AACCGATTTG
1 -ACCGGTTTG
3211062 ACC
1 ACC
3211065 CGACCCGACC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3211042 original size:19 final size:19
Alignment explanation
Indices: 3211014--3211064 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
3211004 CGCTGCTGGA
* *
3211014 AACCGGTTTGACCGGTTTTG
1 AACCGATTTGACCGG-TCTG
3211034 -ACCGATTTGACCGGTCTG
1 AACCGATTTGACCGGTCTG
3211052 AACCGATTTGACC
1 AACCGATTTGACC
3211065 CGACCCGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.29
Consensus pattern (19 bp):
AACCGATTTGACCGGTCTG
Found at i:3211071 original size:5 final size:5
Alignment explanation
Indices: 3211061--3211134 Score: 71
Period size: 5 Copynumber: 14.8 Consensus size: 5
3211051 GAACCGATTT
* * *
3211061 GACCC GACCC GA-CC AACCC GACCC -AACC GACCC GACCC GACCC GACCGTT
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC--C
* *
3211111 GACAC GACCT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACC
3211135 GTTGACCGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
4 6 0.11
5 46 0.84
7 3 0.05
ACGTcount: A:0.24, C:0.53, G:0.19, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:3211081 original size:9 final size:10
Alignment explanation
Indices: 3211061--3211103 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
3211051 GAACCGATTT
*
3211061 GACCCGACCC
1 GACCCAACCC
3211071 GA-CCAACCC
1 GACCCAACCC
3211080 GACCCAA-CC
1 GACCCAACCC
*
3211089 GACCCGACCC
1 GACCCAACCC
3211099 GACCC
1 GACCC
3211104 GACCGTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 16 0.55
10 13 0.45
ACGTcount: A:0.26, C:0.58, G:0.16, T:0.00
Consensus pattern (10 bp):
GACCCAACCC
Found at i:3211081 original size:14 final size:14
Alignment explanation
Indices: 3211062--3211102 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
3211052 AACCGATTTG
3211062 ACCCGACCCGACCA
1 ACCCGACCCGACCA
* *
3211076 ACCCGACCCAACCG
1 ACCCGACCCGACCA
3211090 ACCCGACCCGACC
1 ACCCGACCCGACC
3211103 CGACCGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.27, C:0.59, G:0.15, T:0.00
Consensus pattern (14 bp):
ACCCGACCCGACCA
Found at i:3211126 original size:27 final size:27
Alignment explanation
Indices: 3211088--3211140 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3211078 CCGACCCAAC
3211088 CGACCCGACCCGACCCGACCGTTGACA
1 CGACCCGACCCGACCCGACCGTTGACA
*
3211115 CGACCTGACCCGACCCGACCGTTGAC
1 CGACCCGACCCGACCCGACCGTTGAC
3211141 CGTTGACTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.47, G:0.23, T:0.09
Consensus pattern (27 bp):
CGACCCGACCCGACCCGACCGTTGACA
Found at i:3218489 original size:10 final size:10
Alignment explanation
Indices: 3218471--3218513 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
3218461 TTTGACCGGT
*
3218471 CTGAACCGAC
1 CTGACCCGAC
*
3218481 CCGACCCGAC
1 CTGACCCGAC
3218491 CGTTGACCCGAC
1 C--TGACCCGAC
3218503 CTGACCCGAC
1 CTGACCCGAC
3218513 C
1 C
3218514 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 19 0.68
12 9 0.32
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (10 bp):
CTGACCCGAC
Found at i:3218500 original size:12 final size:12
Alignment explanation
Indices: 3218483--3218520 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
3218473 GAACCGACCC
3218483 GACCCGACCGTT
1 GACCCGACCGTT
3218495 GACCCGACC--T
1 GACCCGACCGTT
3218505 GACCCGACCGTT
1 GACCCGACCGTT
3218517 GACC
1 GACC
3218521 GTTGACTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:3218502 original size:22 final size:22
Alignment explanation
Indices: 3218476--3218520 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3218466 CCGGTCTGAA
3218476 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
*
3218498 CCGACCTGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
3218520 C
1 C
3218521 GTTGACTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:3220033 original size:17 final size:17
Alignment explanation
Indices: 3219995--3220033 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3219985 GATAGTATAA
*
3219995 TTTATTTATAATTTCAT
1 TTTATTTATAATGTCAT
* *
3220012 GTTATTTATAATGTGAT
1 TTTATTTATAATGTCAT
3220029 TTTAT
1 TTTAT
3220034 ATTGATGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (17 bp):
TTTATTTATAATGTCAT
Found at i:3222252 original size:26 final size:27
Alignment explanation
Indices: 3222223--3222279 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
3222213 GATAACAAAT
*
3222223 ATAAATAAAA-ATTAAAAAAAAGAAAA
1 ATAAATAAAATAATAAAAAAAAGAAAA
* *
3222249 AT-AATAAAATAATAAAATAAATAAAA
1 ATAAATAAAATAATAAAAAAAAGAAAA
3222275 ATAAA
1 ATAAA
3222280 AAGGATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 7 0.27
26 17 0.65
27 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (27 bp):
ATAAATAAAATAATAAAAAAAAGAAAA
Found at i:3222257 original size:9 final size:9
Alignment explanation
Indices: 3222226--3222278 Score: 51
Period size: 8 Copynumber: 6.2 Consensus size: 9
3222216 AACAAATATA
3222226 AATAAAAAT
1 AATAAAAAT
*
3222235 --TAAAAAA
1 AATAAAAAT
*
3222242 AAGAAAAAT
1 AATAAAAAT
3222251 AAT-AAAAT
1 AATAAAAAT
3222259 AAT-AAAAT
1 AATAAAAAT
3222267 AAATAAAAAT
1 -AATAAAAAT
3222277 AA
1 AA
3222279 AAAGGATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
7 6 0.17
8 13 0.36
9 12 0.33
10 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (9 bp):
AATAAAAAT
Found at i:3224414 original size:16 final size:16
Alignment explanation
Indices: 3224395--3224436 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
3224385 TCGTTGACTG
3224395 TTAAGCTCGTTGCTCA
1 TTAAGCTCGTTGCTCA
3224411 TTAAG-TCTGTTGCTCA
1 TTAAGCTC-GTTGCTCA
3224427 TTAAGCTCGT
1 TTAAGCTCGT
3224437 ATCTCGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (16 bp):
TTAAGCTCGTTGCTCA
Found at i:3229147 original size:24 final size:24
Alignment explanation
Indices: 3229111--3229246 Score: 218
Period size: 24 Copynumber: 5.7 Consensus size: 24
3229101 TACAGGTAAA
*
3229111 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3229135 AATACAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3229159 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3229183 AATCCAGGTCAAGTATCCTATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3229207 AATCCATGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3229231 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
3229247 TATAATAGAA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 102 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:3234510 original size:26 final size:26
Alignment explanation
Indices: 3234475--3234540 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
3234465 GCATGGTCTT
3234475 GTGCATCGATGCATCAAATGCACTAA
1 GTGCATCGATGCATCAAATGCACTAA
*
3234501 GTGTATCGATGCATCAAATGCACTAA
1 GTGCATCGATGCATCAAATGCACTAA
3234527 GTGCATCGATGCAT
1 GTGCATCGATGCAT
3234541 GGTATGTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (26 bp):
GTGCATCGATGCATCAAATGCACTAA
Found at i:3243165 original size:45 final size:46
Alignment explanation
Indices: 3243080--3243167 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
3243070 AAAAAGCCTG
* *
3243080 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
3243126 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
3243168 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:3243809 original size:24 final size:24
Alignment explanation
Indices: 3243616--3243801 Score: 273
Period size: 24 Copynumber: 7.8 Consensus size: 24
3243606 ATCAAAACAT
* * *
3243616 AATCCAGGTCAAGTATCAGGTCAA
1 AATCCAGGTCAAGTATCCGATCAG
* * *
3243640 AATCCAAGTCAATTATTCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3243664 AATCCAGGTCAAGTATCCGATCAT
1 AATCCAGGTCAAGTATCCGATCAG
*
3243688 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3243712 AATCCATGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3243736 AATCCAGGTCAAGTATCCAATCAG
1 AATCCAGGTCAAGTATCCGATCAG
3243760 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
3243784 AATCCAGGTCAGGTATCC
1 AATCCAGGTCAAGTATCC
3243802 TAATAGAAAT
Statistics
Matches: 144, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 144 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:3245605 original size:36 final size:36
Alignment explanation
Indices: 3245558--3245666 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
3245548 GATAAATTAT
3245558 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
3245594 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
* *
3245630 AATATACATATCCATGGCTGATTCTGTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
3245666 A
1 A
3245667 TTCCAAAACT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:3254459 original size:16 final size:17
Alignment explanation
Indices: 3254425--3254459 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3254415 ATTATGTTAC
*
3254425 AAGTGTCATAGGTATTA
1 AAGTGTCATAGGAATTA
3254442 AAGTGTCAT-GGAATTA
1 AAGTGTCATAGGAATTA
3254458 AA
1 AA
3254460 ATGTAGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (17 bp):
AAGTGTCATAGGAATTA
Found at i:3257968 original size:13 final size:13
Alignment explanation
Indices: 3257950--3257974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3257940 AACATTAATT
3257950 AAGATGAAAAAAA
1 AAGATGAAAAAAA
3257963 AAGATGAAAAAA
1 AAGATGAAAAAA
3257975 CTTGAAGACA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
AAGATGAAAAAAA
Found at i:3258265 original size:18 final size:18
Alignment explanation
Indices: 3258223--3258266 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3258213 ATTTTGGGTG
*
3258223 TACACAACCACAATATAA
1 TACACAACAACAATATAA
*
3258241 TTCACAACAACAATA-AA
1 TACACAACAACAATATAA
3258258 TACGACAAC
1 TAC-ACAAC
3258267 TAATGTTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.55, C:0.27, G:0.02, T:0.16
Consensus pattern (18 bp):
TACACAACAACAATATAA
Found at i:3262007 original size:19 final size:20
Alignment explanation
Indices: 3261966--3262033 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
3261956 CCGGTTTTCA
* *
3261966 ACCGGTTTTG-ACCTGTTTCG
1 ACCGGTTCTGAACC-GTTTTG
3261986 ACCGGTTC-GAACCGTTTTG
1 ACCGGTTCTGAACCGTTTTG
*
3262005 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGTTTTG
3262024 ACCGG-TCTGA
1 ACCGGTTCTGA
3262034 CCCAACCCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.05
19 31 0.72
20 10 0.23
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (20 bp):
ACCGGTTCTGAACCGTTTTG
Found at i:3262029 original size:9 final size:9
Alignment explanation
Indices: 3261951--3262035 Score: 62
Period size: 10 Copynumber: 8.8 Consensus size: 9
3261941 TGGAAACCAA
3261951 TTTGACCGG
1 TTTGACCGG
*
3261960 TTTTCAACCGG
1 -TTT-GACCGG
*
3261971 TTTTGACCTG
1 -TTTGACCGG
3261981 TTTCGACCGG
1 TTT-GACCGG
* *
3261991 TTCGAACCGT
1 TTTG-ACCGG
3262001 TTTGACCGG
1 TTTGACCGG
*
3262010 TCTGAACCGG
1 TTTG-ACCGG
3262020 TTTGACCGG
1 TTTGACCGG
*
3262029 TCTGACC
1 TTTGACC
3262036 CAACCCGACC
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
9 22 0.37
10 29 0.48
11 9 0.15
ACGTcount: A:0.14, C:0.27, G:0.26, T:0.33
Consensus pattern (9 bp):
TTTGACCGG
Found at i:3262054 original size:14 final size:15
Alignment explanation
Indices: 3262030--3262073 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
3262020 TTTGACCGGT
3262030 CTGACCCAACCCGAC
1 CTGACCCAACCCGAC
3262045 CTGA-CCAACCCGAC
1 CTGACCCAACCCGAC
*
3262059 C-GACCCGACCCGAC
1 CTGACCCAACCCGAC
3262073 C
1 C
3262074 GTTGACTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 2 0.07
14 21 0.78
15 4 0.15
ACGTcount: A:0.25, C:0.55, G:0.16, T:0.05
Consensus pattern (15 bp):
CTGACCCAACCCGAC
Found at i:3262066 original size:5 final size:5
Alignment explanation
Indices: 3262032--3262095 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
3262022 TGACCGGTCT
* * * * *
3262032 GACCC AACCC GACCT GA-CC AACCC GA-CC GACCC GACCC GACCGTT GACTC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC
3262082 GACCC GACCC GACC
1 GACCC GACCC GACC
3262096 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
4 6 0.13
5 36 0.80
7 3 0.07
ACGTcount: A:0.23, C:0.52, G:0.19, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:3262087 original size:22 final size:22
Alignment explanation
Indices: 3262059--3262101 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3262049 CCAACCCGAC
3262059 CGACCCGACCCGACCGTTGACT
1 CGACCCGACCCGACCGTTGACT
3262081 CGACCCGACCCGACCGTTGAC
1 CGACCCGACCCGACCGTTGAC
3262102 CGTTGACCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (22 bp):
CGACCCGACCCGACCGTTGACT
Found at i:3264600 original size:55 final size:55
Alignment explanation
Indices: 3264279--3264640 Score: 360
Period size: 55 Copynumber: 6.6 Consensus size: 55
3264269 CCCACTACCA
* * * * * * *
3264279 ATACGAAAATTCA-CCTACTTATTATGAACTTCTTA-TATTTACACATATATTTCCC
1 ATACGAAAATTCATAC-ACTTAGTATGAATTTCTTAGT-TTTGCACACATAGTGCCC
* * * *
3264334 ATACTAAAATTCATACA-TTAAGTATGAATTTCTTAG-TTCGCACACATACTGTCC
1 ATACGAAAATTCATACACTT-AGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
* * * *
3264388 ATACGTAAATTTATACACATAGTATGAATTTCTTAGTTTTGCACACATAGTGTCC
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
* * *
3264443 ATA--TAAATTCATACACTTAGTATTAATTTCTTAGTTTTGCACACATAGTGCCT
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
* *
3264496 ATATGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTAC-CGACATAGTGCCC
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCAC-ACATAGTGCCC
* * **
3264551 ATACGGAAATTCATACACTTAGTATGAATTTCTTACTTTTAAACACATAGTGCCC
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
* * * * ** *
3264606 AAACGGATATTCATAAACAAATTATGAATTTCTTA
1 ATACGAAAATTCATACACTTAGTATGAATTTCTTA
3264641 ACTTTTTGCA
Statistics
Matches: 263, Mismatches: 35, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
53 48 0.18
54 45 0.17
55 168 0.64
56 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (55 bp):
ATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCC
Found at i:3265121 original size:20 final size:20
Alignment explanation
Indices: 3265075--3265130 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3265065 TCTGTTAACA
*
3265075 ATGGTATCGATACCATCCTC
1 ATGGTATCGATACCACCCTC
*
3265095 ATAGTATCGATACTC-CCCTC
1 ATGGTATCGATAC-CACCCTC
* *
3265115 TTGGTATTGATACCAC
1 ATGGTATCGATACCAC
3265131 TTGATACTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (20 bp):
ATGGTATCGATACCACCCTC
Found at i:3268124 original size:2 final size:2
Alignment explanation
Indices: 3268117--3268151 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3268107 CCAGAAAATC
3268117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3268152 GACACCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3270134 original size:34 final size:34
Alignment explanation
Indices: 3270096--3270162 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
3270086 ATGCACAGTT
*
3270096 AGGCATTTAGTCTTTATTTCAGAACAATTTCTAG
1 AGGCATTTAGTCTTTATTTCAGAAAAATTTCTAG
3270130 AGGCATTTAGTCTTTATTTCAGAAAAATTTCTA
1 AGGCATTTAGTCTTTATTTCAGAAAAATTTCTA
3270163 CTCTAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (34 bp):
AGGCATTTAGTCTTTATTTCAGAAAAATTTCTAG
Found at i:3270477 original size:110 final size:109
Alignment explanation
Indices: 3270355--3270747 Score: 563
Period size: 111 Copynumber: 3.6 Consensus size: 109
3270345 TTTCAATAAG
*
3270355 GAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTCATA
1 GAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATA
* * * *
3270420 CACTTGGTATGAATTTTTTAGTTTTCCACACATTGTGCCCATAC
66 CACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
* * *
3270464 AGAAATTCATACACTTAGTATAAATTTTTTTAGTTTTACACACATAGTGCCCATACGGAAATTCA
1 -GAAATTCATACACTTAGTATGAA-TTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCA
* *
3270529 AACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCTCATAC
64 TACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
* * **
3270575 GCAAATTCATACATTTAGTATGAATTTCTTAGTTTTGCACTCATAGTGCCCATACAAAAATTCAT
1 G-AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCAT
* * *
3270640 ACACGTAGTATGAATTTCTTAGTTTTGCACATATAGT-ACCATAC
65 ACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
* * *
3270684 GGAATTTCATACACTTAGTATGAATTTCTTACTTTTGCACATATAGTGCCCATACGGAAATTCA
1 -GAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCA
3270748 AAAACAAATT
Statistics
Matches: 251, Mismatches: 29, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
109 60 0.24
110 94 0.37
111 97 0.39
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (109 bp):
GAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCATA
CACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
Found at i:3270609 original size:166 final size:164
Alignment explanation
Indices: 3270354--3270747 Score: 590
Period size: 166 Copynumber: 2.4 Consensus size: 164
3270344 TTTTCAATAA
*
3270354 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTCAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCAT
* * * * *
3270419 ACACTTGGTATGAATTTTTTAGTTTTCCACACATTGTGCCCATACAGAAATTCATACACTTAGTA
66 ACACTTAGTATGAATTTCTTAGTTTTCCACACATAGTGCCCATACAAAAATTCATACACGTAGTA
* *
3270484 TAAATTTTTTTAGTTTTACACACATAGTGCCCATAC
131 TAAA-TTTCTTAGTTTTACACACATAGT-ACCATAC
* * *
3270520 GGAAATTCAAACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCTCATACGCAAATTCAT
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCAT
* * *
3270585 ACATTTAGTATGAATTTCTTAGTTTTGCACTCATAGTGCCCATACAAAAATTCATACACGTAGTA
66 ACACTTAGTATGAATTTCTTAGTTTTCCACACATAGTGCCCATACAAAAATTCATACACGTAGTA
* * *
3270650 TGAATTTCTTAGTTTTGCACATATAGTACCATAC
131 TAAATTTCTTAGTTTTACACACATAGTACCATAC
* * *
3270684 GGAATTTCATACACTTAGTATGAATTTCTTACTTTTGCACATATAGTGCCCATACGGAAATTCA
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCA
3270748 AAAACAAATT
Statistics
Matches: 205, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
164 64 0.31
165 20 0.10
166 121 0.59
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (164 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACGGAAATTCAT
ACACTTAGTATGAATTTCTTAGTTTTCCACACATAGTGCCCATACAAAAATTCATACACGTAGTA
TAAATTTCTTAGTTTTACACACATAGTACCATAC
Found at i:3270769 original size:55 final size:55
Alignment explanation
Indices: 3270354--3270747 Score: 574
Period size: 55 Copynumber: 7.2 Consensus size: 55
3270344 TTTTCAATAA
*
3270354 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
* * * *
3270409 GGAAATTCATACACTTGGTATGAATTTTTTAGTTTTCCACACATTGTGCCCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
* * * *
3270464 AGAAATTCATACACTTAGTATAAATTTTTTTAGTTTTACACACATAGTGCCCATAC
1 GGAAATTCATACACTTAGTATGAA-TTTCTTAGTTTTGCACACATAGTGCCCATAC
* *
3270520 GGAAATTCAAACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCTCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
* * *
3270575 GCAAATTCATACATTTAGTATGAATTTCTTAGTTTTGCACTCATAGTGCCCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
** * * *
3270630 AAAAATTCATACACGTAGTATGAATTTCTTAGTTTTGCACATATAGT-ACCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
* * *
3270684 GGAATTTCATACACTTAGTATGAATTTCTTACTTTTGCACATATAGTGCCCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
3270739 GGAAATTCA
1 GGAAATTCA
3270748 AAAACAAATT
Statistics
Matches: 302, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
54 48 0.16
55 204 0.68
56 50 0.17
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (55 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATAC
Found at i:3271236 original size:20 final size:21
Alignment explanation
Indices: 3271208--3271258 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 21
3271198 GTTAACAATG
*
3271208 GTATTGATACCATCCT-CATA
1 GTATCGATACCATCCTCCATA
* *
3271228 GTATCGATA-C-TCCTCCTTG
1 GTATCGATACCATCCTCCATA
3271247 GTATCGATACCA
1 GTATCGATACCA
3271259 CTTAAATCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.16
19 12 0.48
20 9 0.36
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (21 bp):
GTATCGATACCATCCTCCATA
Found at i:3274762 original size:20 final size:20
Alignment explanation
Indices: 3274737--3274789 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
3274727 GCATCAACCC
3274737 TATATTTCC-ACTCAGATACT
1 TATATTTCCTA-TCAGATACT
3274757 TATATTTCCTATCAGATACT
1 TATATTTCCTATCAGATACT
3274777 TATATTTCCTATC
1 TATATTTCCTATC
3274790 TCATTATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATTTCCTATCAGATACT
Found at i:3286370 original size:15 final size:15
Alignment explanation
Indices: 3286346--3286376 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3286336 GGTGCCTATT
*
3286346 ACATTGAAGATTCAC
1 ACATTCAAGATTCAC
3286361 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
3286376 A
1 A
3286377 ACCGGTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (15 bp):
ACATTCAAGATTCAC
Found at i:3291054 original size:14 final size:14
Alignment explanation
Indices: 3291035--3291061 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3291025 AATAAATTTT
3291035 ATTTTTTTTCTTTA
1 ATTTTTTTTCTTTA
3291049 ATTTTTTTTCTTT
1 ATTTTTTTTCTTT
3291062 TTGTTAAGTA
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:0.11, C:0.07, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTTTTCTTTA
Found at i:3293099 original size:20 final size:20
Alignment explanation
Indices: 3293063--3293105 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3293053 CTATTTACAC
* *
3293063 TAAAATATCTAAAATAAAGA
1 TAAAATATCAAAAATAAAAA
3293083 TAAAATAT-AAAATATAAAAA
1 TAAAATATCAAAA-ATAAAAA
3293103 TAA
1 TAA
3293106 TATCCTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAATATCAAAAATAAAAA
Found at i:3297233 original size:192 final size:193
Alignment explanation
Indices: 3296906--3297292 Score: 758
Period size: 192 Copynumber: 2.0 Consensus size: 193
3296896 TTTTGTTTTT
3296906 TGAATGGAATGAATACTCCTTCATAATTCGCTTGCTTTAGCAGCTGGAAAGAACCTGCCAAGAAA
1 TGAATGGAATGAATACTCCTTCATAATTCGCTTGCTTTAGCAGCTGGAAAGAACCTGCCAAGAAA
3296971 ATTTTGATTCATGTCAGCCCATGAATTAACTGAATTTGGAGGTAAATAAAATAATCATTCTTTAG
66 ATTTTGATTCATGTCAGCCCATGAATTAACTGAATTTGGAGGTAAATAAAATAATCATTCTTTAG
3297036 CCAAATTGTCTAAAGAGAAAGGGAAAA-CTCAATTTAATTTGATCCTCAGTAACTCCCTGTGG
131 CCAAATTGTCTAAAGAGAAAGGGAAAACCTCAATTTAATTTGATCCTCAGTAACTCCCTGTGG
3297098 TGAATGGAATGAATACTCCTTCATAATTCGCTTGCTTTAGCAGCTGGAAAGAACCTGCCAAGAAA
1 TGAATGGAATGAATACTCCTTCATAATTCGCTTGCTTTAGCAGCTGGAAAGAACCTGCCAAGAAA
3297163 ATTTTGATTCATGTCAGCCCATGAATTAACTGAATTTGGAGGTAAATAAAATAATCATTCTTTAG
66 ATTTTGATTCATGTCAGCCCATGAATTAACTGAATTTGGAGGTAAATAAAATAATCATTCTTTAG
3297228 CCAAATTGTCTAAAGAGAAAGGGAAAACTCTCAATTTAATTTGATCCTCAGTAACTCCCTGTGG
131 CCAAATTGTCTAAAGAGAAAGGGAAAAC-CTCAATTTAATTTGATCCTCAGTAACTCCCTGTGG
3297292 T
1 T
3297293 TTCATGGTAG
Statistics
Matches: 193, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 157 0.81
194 36 0.19
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (193 bp):
TGAATGGAATGAATACTCCTTCATAATTCGCTTGCTTTAGCAGCTGGAAAGAACCTGCCAAGAAA
ATTTTGATTCATGTCAGCCCATGAATTAACTGAATTTGGAGGTAAATAAAATAATCATTCTTTAG
CCAAATTGTCTAAAGAGAAAGGGAAAACCTCAATTTAATTTGATCCTCAGTAACTCCCTGTGG
Found at i:3299873 original size:30 final size:30
Alignment explanation
Indices: 3299837--3299893 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
3299827 GCATGGTCAT
*
3299837 GCTTAAATAGATTGATATGAGATATCAATG
1 GCTTAAACAGATTGATATGAGATATCAATG
3299867 GCTTAAACAGATTGATATGAGATATCA
1 GCTTAAACAGATTGATATGAGATATCA
3299894 TATGTTGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (30 bp):
GCTTAAACAGATTGATATGAGATATCAATG
Found at i:3301376 original size:202 final size:202
Alignment explanation
Indices: 3300995--3301376 Score: 525
Period size: 202 Copynumber: 1.9 Consensus size: 202
3300985 GCATTCTGGG
* * ** * * *
3300995 AGTGAGTTTGTAGATTTTAGGTTAAAATTGGTACATTTTTTTATGATGAGTAAGTAGGAGGAGAA
1 AGTGAGTTGGTAGATTTTAGGCTAAAATTGGTACATTTTGCTATGATGAGTAAGCAAGAAGAGAA
* * *
3301060 TTCTTCTAGAAACGTAAAACTGTCCAAATCCATTATAATATATTTTAGGATCATTACTGTTTTTC
66 TTCTTCTAGAAACGTAAAACTGTCCAAATCCATTATAATAGATTTTAGGATCATCACTGTTTTCC
* * * * *
3301125 CAAGAGTTAGTGCTAAAAGCAACAATGAGTCGGCTTGCGGTTAGAGGAAATCTTCTATTGGTGGA
131 CAAGAGTCAGTGCTAAAAGCAACAATGAATCAGCTAGCGATTAGAGGAAATCTTCTATTGGTGGA
3301190 TGTTGAA
196 TGTTGAA
*
3301197 AGTGAGTTGGTAGATTTTAGGCTAAAATTGGTACATTTTGCTATGATGAGTCAA-CAAGAAGATA
1 AGTGAGTTGGTAGATTTTAGGCTAAAATTGGTACATTTTGCTATGATGAGT-AAGCAAGAAGAGA
* * **
3301261 ATTCTTCTAGAAACGTACAATTGTCCAAATCCATTATAATAGATTTTAGGATCATCGTTGTTTTC
65 ATTCTTCTAGAAACGTAAAACTGTCCAAATCCATTATAATAGATTTTAGGATCATCACTGTTTTC
* * *
3301326 CCAAGAGTCAGTGGTGAAAGCAACAATGAATCAGC-AGACGATTGGAGGAAA
130 CCAAGAGTCAGTGCTAAAAGCAACAATGAATCAGCTAG-CGATTAGAGGAAA
3301377 CATACAATTG
Statistics
Matches: 155, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
201 1 0.01
202 152 0.98
203 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (202 bp):
AGTGAGTTGGTAGATTTTAGGCTAAAATTGGTACATTTTGCTATGATGAGTAAGCAAGAAGAGAA
TTCTTCTAGAAACGTAAAACTGTCCAAATCCATTATAATAGATTTTAGGATCATCACTGTTTTCC
CAAGAGTCAGTGCTAAAAGCAACAATGAATCAGCTAGCGATTAGAGGAAATCTTCTATTGGTGGA
TGTTGAA
Found at i:3308722 original size:18 final size:19
Alignment explanation
Indices: 3308686--3308722 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
3308676 TCGAATGAGG
3308686 ATCCAGATGAGATTTCTGA
1 ATCCAGATGAGATTTCTGA
3308705 ATCCAG-TGATGA-TTCTGA
1 ATCCAGATGA-GATTTCTGA
3308723 GGTTCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (19 bp):
ATCCAGATGAGATTTCTGA
Found at i:3310330 original size:6 final size:6
Alignment explanation
Indices: 3310319--3310416 Score: 78
Period size: 6 Copynumber: 16.5 Consensus size: 6
3310309 TAAGAGCTAA
** *
3310319 AAAAAG AAAAAG AAAACC AAAAA- AAAAAG -AAAAG -AAAA- AAAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * *
3310363 AAAGAAG AAAAAC AAAAAC AAAAAG AAGAAG AAGAAG AAATATAG AAAAAG
1 AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA-A-AG AAAAAG
3310414 AAA
1 AAA
3310417 GAAATGAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
5 17 0.22
6 48 0.62
7 7 0.09
8 5 0.06
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:3310356 original size:14 final size:14
Alignment explanation
Indices: 3310339--3310431 Score: 64
Period size: 14 Copynumber: 6.3 Consensus size: 14
3310329 AGAAAACCAA
3310339 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
3310353 -AAAAAAAGAGAAAG
1 AAAAAAAAGA-AAAG
*
3310367 AAGAAAAACA-AAAAC
1 AA-AAAAA-AGAAAAG
*
3310382 AAAAAGAAGAAGAAG
1 AAAAAAAAGAA-AAG
*
3310397 AAGAAATATAGAAAAAG
1 AA-AAA-AAAG-AAAAG
* *
3310414 AAAGAAATGAAAAG
1 AAAAAAAAGAAAAG
3310428 AAAA
1 AAAA
3310432 TGGTAGATGT
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
13 10 0.16
14 18 0.30
15 12 0.20
16 11 0.18
17 8 0.13
18 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:3310373 original size:27 final size:24
Alignment explanation
Indices: 3310326--3310431 Score: 60
Period size: 22 Copynumber: 4.4 Consensus size: 24
3310316 TAAAAAAAGA
**
3310326 AAAAGAAAACCAAAAAA-AA-AAG
1 AAAAGAAAAAAAAAAAAGAAGAAG
*
3310348 AAAAGAAAAAAAGAGAAAGAAG-A-
1 AAAAGAAAAAAA-AAAAAGAAGAAG
* *
3310371 AAAA-CAAAAACAAAAAGAAGAAG
1 AAAAGAAAAAAAAAAAAGAAGAAG
* *
3310394 AAGAAGAAATATAGAAAAAGAAAGAAATG
1 AA-AAGAAA-AAAAAAAAAG-AAG-AA-G
3310423 AAAAGAAAA
1 AAAAGAAAA
3310432 TGGTAGATGT
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
21 8 0.12
22 16 0.25
23 10 0.16
24 5 0.08
25 2 0.03
26 8 0.12
27 4 0.06
28 8 0.12
29 3 0.05
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.03
Consensus pattern (24 bp):
AAAAGAAAAAAAAAAAAGAAGAAG
Found at i:3310374 original size:30 final size:29
Alignment explanation
Indices: 3310325--3310429 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 29
3310315 CTAAAAAAAG
* *
3310325 AAAAAGAAAACCAAAAAAAAAAGAAAAGAA
1 AAAAAGAAAA-GAAGAAAAAAAGAAAAGAA
* *
3310355 AAAAAGAGAAAGAAGAAAAACA-AAAACAA
1 AAAAAGA-AAAGAAGAAAAAAAGAAAAGAA
* *
3310384 AAAGAAGAAGAAGAAGAAATATAGAAAAAGAA
1 AAA-AAGAA-AAGAAGAAAAAAAG-AAAAGAA
*
3310416 AGAAATGAAAAGAA
1 A-AAAAGAAAAGAA
3310430 AATGGTAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
29 10 0.16
30 30 0.49
31 8 0.13
32 11 0.18
33 2 0.03
ACGTcount: A:0.77, C:0.04, G:0.16, T:0.03
Consensus pattern (29 bp):
AAAAAGAAAAGAAGAAAAAAAGAAAAGAA
Found at i:3312615 original size:23 final size:23
Alignment explanation
Indices: 3312569--3312639 Score: 124
Period size: 23 Copynumber: 3.0 Consensus size: 23
3312559 TGCATAACAT
*
3312569 TGTACATAGATGTTTAATACATCA
1 TGTACACAGATGTTT-ATACATCA
3312593 TGTACACAGATGTTTATACATCA
1 TGTACACAGATGTTTATACATCA
3312616 TGTACACAGATGTTTATACATCA
1 TGTACACAGATGTTTATACATCA
3312639 T
1 T
3312640 CAGGAAGACT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 32 0.70
24 14 0.30
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (23 bp):
TGTACACAGATGTTTATACATCA
Found at i:3313219 original size:45 final size:45
Alignment explanation
Indices: 3313155--3313241 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
3313145 GTAACCATGC
*
3313155 AAATAAGCTTACGAGCTTATGGGAGAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGAGAAATGATAAATATATTGGTA
* *
3313200 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAATATATTG
1 AAATAAGCTTACGAGCTTATGGGAGAAATGATAAATATATTG
3313242 ATAAGAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGAGAAATGATAAATATATTGGTA
Found at i:3313629 original size:12 final size:12
Alignment explanation
Indices: 3313612--3313641 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3313602 GTTTTTATTG
*
3313612 AACAAATTTGGA
1 AACAAAGTTGGA
3313624 AACAAAGTTGGA
1 AACAAAGTTGGA
3313636 AACAAA
1 AACAAA
3313642 ATGGTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.17
Consensus pattern (12 bp):
AACAAAGTTGGA
Found at i:3313707 original size:13 final size:13
Alignment explanation
Indices: 3313660--3313711 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 13
3313650 TTTATAGAGG
3313660 TGGAAACAAAAATT
1 TGGAAAC-AAAATT
3313674 TGGAAACAAAA--
1 TGGAAACAAAATT
*
3313685 TGGTAACAAAATT
1 TGGAAACAAAATT
3313698 TGGAAAC-AAATT
1 TGGAAACAAAATT
3313710 TG
1 TG
3313712 AGTTTTATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.29
12 7 0.21
13 10 0.29
14 7 0.21
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (13 bp):
TGGAAACAAAATT
Found at i:3313710 original size:12 final size:12
Alignment explanation
Indices: 3313669--3313711 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3313659 GTGGAAACAA
3313669 AAATTTGGAAAC
1 AAATTTGGAAAC
* *
3313681 AAA-ATGGTAAC
1 AAATTTGGAAAC
3313692 AAAATTTGGAAAC
1 -AAATTTGGAAAC
3313705 AAATTTG
1 AAATTTG
3313712 AGTTTTATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 6 0.24
12 13 0.52
13 6 0.24
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (12 bp):
AAATTTGGAAAC
Found at i:3318115 original size:2 final size:2
Alignment explanation
Indices: 3318108--3318138 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3318098 CATATGGTAA
*
3318108 AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3318139 TATATATATA
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:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:3328586 original size:19 final size:19
Alignment explanation
Indices: 3328562--3328608 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
3328552 AACACAATGG
3328562 GAAGCTCAACTCAGCTAGA
1 GAAGCTCAACTCAGCTAGA
* *
3328581 GAAGCTCAACTCAGTTGGA
1 GAAGCTCAACTCAGCTAGA
*
3328600 GGAGCTCAA
1 GAAGCTCAA
3328609 GGCTAGCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (19 bp):
GAAGCTCAACTCAGCTAGA
Found at i:3343093 original size:90 final size:89
Alignment explanation
Indices: 3342980--3343159 Score: 279
Period size: 90 Copynumber: 2.0 Consensus size: 89
3342970 TAATAATCTC
* * *
3342980 GATTATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAGCCCTAATAT
1 GATTATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAA-CCCTAATAT
*
3343045 GATTCGGGTAACTTGGATATAAAAG
65 GATTAGGGTAACTTGGATATAAAAG
* *
3343070 GATTATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTTAAAAAATAAAACTCTAATATG
1 GATTATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAACCCTAATATG
* *
3343135 ATTAGGGTAATTTGGCTATAAAAG
66 ATTAGGGTAACTTGGATATAAAAG
3343159 G
1 G
3343160 GTGTCTTAGG
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 31 0.38
90 51 0.62
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (89 bp):
GATTATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAACCCTAATATG
ATTAGGGTAACTTGGATATAAAAG
Found at i:3349950 original size:46 final size:45
Alignment explanation
Indices: 3349891--3350057 Score: 228
Period size: 46 Copynumber: 3.7 Consensus size: 45
3349881 AAATCTCTTG
* *
3349891 CCATTTATCCCATAAGATCGTAAGCTTATTTTACCAAAATACTTA
1 CCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
* * * * *
3349936 CCATTTAATTCCATAAGCTCATAAACGTATTTTACCAATATACCTA
1 CCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
*
3349982 CCATTTGATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTG
1 CCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
*
3350028 CCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CCATTTATCCCATAAGCTCGTAAGCTTATTT
3350058 GCCAGTTTAT
Statistics
Matches: 106, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
44 24 0.23
45 8 0.08
46 74 0.70
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (45 bp):
CCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
Found at i:3350199 original size:40 final size:40
Alignment explanation
Indices: 3350155--3350235 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
3350145 GCACCTAAGG
* *
3350155 GCTGAGGTCGAGCTTTGCTCACCTAATAATGCATCGTAGT
1 GCTGAGGTCGAGCTTTACTCACCTAATAATGCACCGTAGT
*
3350195 GCTGAGGTCGAGTTTTACTCACCTAATAATGCACCGTAGT
1 GCTGAGGTCGAGCTTTACTCACCTAATAATGCACCGTAGT
3350235 G
1 G
3350236 TTTTGTACCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (40 bp):
GCTGAGGTCGAGCTTTACTCACCTAATAATGCACCGTAGT
Found at i:3356635 original size:30 final size:30
Alignment explanation
Indices: 3356601--3356705 Score: 95
Period size: 30 Copynumber: 3.3 Consensus size: 30
3356591 CCTTGAGACA
3356601 GTTTCTCTTGAAACATAAACATTTGAGATT
1 GTTTCTCTTGAAACATAAACATTTGAGATT
* **
3356631 GTTTCTCTTGAAACA-AATTTTATCTAGCTTGAGACA
1 GTTTCTCTTGAAACATAA----A-C-A-TTTGAGATT
* *
3356667 GTTTATCTTGAAATATAAACATTTGAGATT
1 GTTTCTCTTGAAACATAAACATTTGAGATT
3356697 GTTTCTCTT
1 GTTTCTCTT
3356706 TATACATATT
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
29 2 0.03
30 29 0.50
31 1 0.02
32 1 0.02
33 2 0.03
34 1 0.02
35 1 0.02
36 19 0.33
37 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (30 bp):
GTTTCTCTTGAAACATAAACATTTGAGATT
Found at i:3356698 original size:66 final size:66
Alignment explanation
Indices: 3356592--3356912 Score: 351
Period size: 67 Copynumber: 4.8 Consensus size: 66
3356582 GTCTGTCTCC
*
3356592 CTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAATTTTATCTA
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAATTTCATCTA
3356657 G
66 G
* * * * * **
3356658 CTTGAGACAGTTTATCTTGAAATATAAACATTTGAGATTGTTTCTCTTTATACATATTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAATTTCATCT-
3356723 A-
65 AG
* * * * *
3356724 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTCTAG-AACTAGAGTTTCGTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAAC-A-AATTTCATC
*
3356788 TCG
64 TAG
* **
3356791 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTTCATCT
1 CTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAA-TTTCATCT
*
3356856 CG
65 AG
* * * * * * *
3356858 CTTGAGATAGATTTC-CTTGAAACACAAATATTTTAAATTGTTTCACTTTAAACAA
1 CTTGAGACAG-TTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAA
3356913 GAAATTGATC
Statistics
Matches: 217, Mismatches: 31, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
65 2 0.01
66 103 0.47
67 105 0.48
68 7 0.03
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (66 bp):
CTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAATTTCATCTA
G
Found at i:3356911 original size:67 final size:66
Alignment explanation
Indices: 3356587--3356912 Score: 370
Period size: 66 Copynumber: 4.9 Consensus size: 66
3356577 ATATTGTCTG
* * *
3356587 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAATTTT
1 TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTTAAACAAATTTC
3356652 A
66 A
* * * * * *
3356653 TCTAGCTTGAGACAGTTTATCTTGAAATATAAACATTTGAGATTGTTTCTCTTTATACATATTTT
1 TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTTAAACAAATTTC
*
3356718 G
66 A
* * * *
3356719 TCTCACTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGTTTGTTTCTC--TAGAACTAGAGT
1 TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTTA-AAC-A-AAT
*
3356782 TTCG
63 TTCA
* **
3356786 TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCAAAACAAAGTTT
1 TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTTAAACAAA-TTT
3356851 CA
65 CA
* * * * * *
3356853 TCTCGCTTGAGATAGATTTC-CTTGAAACACAAATATTTTAAATTGTTTCACTTTAAACAA
1 TCTCGCTTGAGACAG-TTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTTAAACAA
3356913 GAAATTGATC
Statistics
Matches: 221, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
64 2 0.01
65 2 0.01
66 105 0.48
67 104 0.47
68 7 0.03
69 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (66 bp):
TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTTAAACAAATTTC
A
Found at i:3357099 original size:103 final size:102
Alignment explanation
Indices: 3356821--3357123 Score: 335
Period size: 103 Copynumber: 2.9 Consensus size: 102
3356811 AACATAAACC
* *
3356821 TTTGAGATTGTTTCTCTCAAAACAAAGTTTCATCTCGCTTGAGATAGA-TTTCCTTGAAACACAA
1 TTTGAGATTGTTTCTCTCAAAACAAAGTTTCATCTCACTTGAGACA-ATTTTCCTTGAAACACAA
* * *
3356885 ATATTTTAAATTGTTTCACTTTAAACAAGAAATTGATCTCA
65 A-ATTTGAAATTGTTTCACTTAAAAC-A-AAATTGATATCA
* * *
3356926 TTTGAGATTGTTT-TCCTAAAAACATA-TTTCATCTCAGTTGAGACAATTTTCCTTTGCAAA-AC
1 TTTGAGATTGTTTCT-CTCAAAACAAAGTTTCATCTCACTTGAGACAATTTTCC-TTG-AAACAC
* * *
3356988 GAATTTTGAAATTGTTTCTCTTAAAACAAAATTGATATCA
63 AAAATTTGAAATTGTTTCACTTAAAACAAAATTGATATCA
* ** *
3357028 TTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCACTTGAGACAATTTTCCTTGAAACATAAA
1 TTTGAGATTGTTTCTCTCAAAACAAAGTTTCATCTCACTTGAGACAATTTTCCTTGAAACACAAA
* * * *
3357093 CCTTTGAGAGTGTTTCACTCAAAACAAAATT
66 -ATTTGAAATTGTTTCACTTAAAACAAAATT
3357124 TCATCTCACA
Statistics
Matches: 166, Mismatches: 24, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
101 3 0.02
102 38 0.23
103 51 0.31
104 42 0.25
105 29 0.17
106 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (102 bp):
TTTGAGATTGTTTCTCTCAAAACAAAGTTTCATCTCACTTGAGACAATTTTCCTTGAAACACAAA
ATTTGAAATTGTTTCACTTAAAACAAAATTGATATCA
Found at i:3357151 original size:67 final size:67
Alignment explanation
Indices: 3357028--3357153 Score: 155
Period size: 67 Copynumber: 1.9 Consensus size: 67
3357018 ATTGATATCA
* * * * ** * *
3357028 TTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCACTTGAGACAATTTTCCTTGAAACATAAA
1 TTTGAGAGTGTTTCACTCAAAACAAAATTTCATCTCACATGAGACAATTCTCCTTGAAACATAAA
3357093 CC
66 CC
*
3357095 TTTGAGAGTGTTTCACTCAAAACAAAATTTCATCTCACATGAGATAACTTCT-CTTGAAA
1 TTTGAGAGTGTTTCACTCAAAACAAAATTTCATCTCACATGAGACAA-TTCTCCTTGAAA
3357154 AAATTATTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
67 46 0.94
68 3 0.06
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (67 bp):
TTTGAGAGTGTTTCACTCAAAACAAAATTTCATCTCACATGAGACAATTCTCCTTGAAACATAAA
CC
Found at i:3358506 original size:2 final size:2
Alignment explanation
Indices: 3358496--3358524 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3358486 ATATACGTGC
3358496 TA TA T- 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
3358525 CTATGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3367620 original size:15 final size:15
Alignment explanation
Indices: 3367595--3367633 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3367585 GTTAAAAACC
*
3367595 TAACCAAAAAT-AAA
1 TAACAAAAAATGAAA
3367609 TAACAGAAAAATGAAA
1 TAACA-AAAAATGAAA
3367625 TAACAAAAA
1 TAACAAAAA
3367634 TAAGTATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.72, C:0.10, G:0.05, T:0.13
Consensus pattern (15 bp):
TAACAAAAAATGAAA
Found at i:3376949 original size:2 final size:2
Alignment explanation
Indices: 3376942--3376994 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
3376932 AAATTTATGA
* * * *
3376942 AT AT AT AT AT AT AT AT AT AT AT AT AA AC AT AA AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3376983 AT AT TT AT AT AT
1 AT AT AT AT AT AT
3376995 TTAAATGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3377989 original size:13 final size:13
Alignment explanation
Indices: 3377971--3377995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3377961 AAATAGATAT
3377971 TCTAAAATATAAG
1 TCTAAAATATAAG
3377984 TCTAAAATATAA
1 TCTAAAATATAA
3377996 AATAATAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (13 bp):
TCTAAAATATAAG
Found at i:3378151 original size:20 final size:20
Alignment explanation
Indices: 3378126--3378192 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
3378116 TATAAATAAA
3378126 AATTAAATTAATTTATATAT
1 AATTAAATTAATTTATATAT
*
3378146 AATT-AATAAATTT-TATA-
1 AATTAAATTAATTTATATAT
* *
3378163 AATGTATATATAATTAAT-TAT
1 AAT-TAAAT-TAATTTATATAT
3378184 AATTAAATT
1 AATTAAATT
3378193 TTGTATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.08
18 5 0.14
19 11 0.30
20 14 0.38
21 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
AATTAAATTAATTTATATAT
Found at i:3378637 original size:30 final size:30
Alignment explanation
Indices: 3378589--3378656 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
3378579 ATTCTTATAA
*
3378589 TATTATATATATTATATTATATTATATCA-T
1 TATTATTTATATTATATTATATTAT-TCATT
* *
3378619 TATTATTTATTATT-TATTATTTTATTTATT
1 TATTATTTA-TATTATATTATATTATTCATT
3378649 TATTATTT
1 TATTATTT
3378657 TAAAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 2 0.06
30 27 0.82
31 4 0.12
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (30 bp):
TATTATTTATATTATATTATATTATTCATT
Found at i:3378639 original size:7 final size:7
Alignment explanation
Indices: 3378532--3378656 Score: 72
Period size: 7 Copynumber: 16.1 Consensus size: 7
3378522 TAGTTTACCC
*
3378532 TATTATA
1 TATTATT
3378539 TATTATAT
1 TATTAT-T
3378547 ATATTATT
1 -TATTATT
*
3378555 TACTATTT
1 TATTA-TT
3378563 TATTTATT
1 TA-TTATT
* *
3378571 AATTTTT
1 TATTATT
*
3378578 TATTCTT
1 TATTATT
*
3378585 ATAATATT
1 -TATTATT
3378593 ATATATATT
1 -TAT-TATT
3378602 ATATTATAT
1 -TATTAT-T
3378611 TA-TATCAT
1 TATTAT--T
3378619 TATTATT
1 TATTATT
3378626 TATTATT
1 TATTATT
3378633 TATTATTT
1 TATTA-TT
3378641 TATTTATT
1 TA-TTATT
3378649 TATTATT
1 TATTATT
3378656 T
1 T
3378657 TAAAAATATA
Statistics
Matches: 97, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
7 41 0.42
8 33 0.34
9 23 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (7 bp):
TATTATT
Found at i:3378649 original size:16 final size:16
Alignment explanation
Indices: 3378550--3378658 Score: 84
Period size: 16 Copynumber: 6.9 Consensus size: 16
3378540 ATTATATATA
*
3378550 TTATTTACTATTTTAT
1 TTATTTATTATTTTAT
*
3378566 TTATTAATT-TTTTAT
1 TTATTTATTATTTTAT
* * *
3378581 TCT-TATAATATTATAT
1 T-TATTTATTATTTTAT
* *
3378597 ATATTATATTATATTAT
1 TTATT-TATTATTTTAT
*
3378614 ATCA-TTATTA-TTTA-
1 -TTATTTATTATTTTAT
3378628 TTATTTATTATTTTAT
1 TTATTTATTATTTTAT
3378644 TTATTTATTATTTTA
1 TTATTTATTATTTTA
3378659 AAAATATATT
Statistics
Matches: 70, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
13 2 0.03
14 6 0.09
15 18 0.26
16 34 0.49
17 9 0.13
18 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTATTATTTTAT
Found at i:3378667 original size:71 final size:69
Alignment explanation
Indices: 3378537--3378680 Score: 161
Period size: 71 Copynumber: 2.1 Consensus size: 69
3378527 TACCCTATTA
* *
3378537 TATATTATATATATTATTTACTATTTTATTTATTAATTTTTTATTCTTATAATATTATATATATT
1 TATATTATATATATTATTTACTATTTTATTTATTAATTTATTATTCTTATAATAATATAT-TATT
3378602 -ATAT
65 AATAT
* *
3378606 TATATTATATCATTATTATTTATTATTTATTATTTTATTTATTTATTATT-TTA-AA-AATATAT
1 TATATTATAT-A-TATTATTTACTA-TT-TTA-TTTATTAATTTATTATTCTTATAATAATATAT
*
3378668 TTTTAATAT
61 TATTAATAT
3378677 TATA
1 TATA
3378681 ATTACTTAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
69 10 0.16
70 4 0.06
71 25 0.39
72 4 0.06
73 6 0.09
74 15 0.23
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (69 bp):
TATATTATATATATTATTTACTATTTTATTTATTAATTTATTATTCTTATAATAATATATTATTA
ATAT
Found at i:3380447 original size:40 final size:39
Alignment explanation
Indices: 3380401--3380527 Score: 114
Period size: 41 Copynumber: 3.1 Consensus size: 39
3380391 TTTATAGCTA
3380401 AAACGCCGCAATAGAGATGTTTATAGTGGCGTTTTTTAAC
1 AAACGCCGCAATAGAG-TGTTTATAGTGGCGTTTTTTAAC
*
3380441 AAACGCCGCAATAGAGTGGTAATT-TAGCGGCG-TTTTTACAC
1 AAACGCCGCAATAGAGT-GT--TTATAGTGGCGTTTTTTA-AC
* ** * * *
3380482 AAACGTCGTGATAGTGTTGTTTATATTGGCGTTTGTTCAAC
1 AAACGCCGCAATAGAG-TGTTTATAGTGGCGTTT-TTTAAC
3380523 AAACG
1 AAACG
3380528 ACACTATAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
39 3 0.04
40 30 0.42
41 32 0.45
42 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (39 bp):
AAACGCCGCAATAGAGTGTTTATAGTGGCGTTTTTTAAC
Found at i:3380455 original size:82 final size:81
Alignment explanation
Indices: 3380345--3380640 Score: 267
Period size: 82 Copynumber: 3.6 Consensus size: 81
3380335 ATACTTTAGC
* * *
3380345 GGCGTTT-TTCAAACAAAAGCCGTAATAGAGTGGTAATTTAGCGGCATTTATAGCTAAAACGCCG
1 GGCGTTTGTTC-AACAAACGCCGCAATAGAGTAGTAATTTAGCGGCATTTATA-C-AAAACGCCG
* *
3380409 CAATAGAGATGTTTATAGT
63 TAATAGAGTTGTTTATAGT
* * * * * *
3380428 GGCGTTT-TTTAACAAACGCCGCAATAGAGTGGTAATTTAGCGGCGTTTTTACACAAACGTCGTG
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCATTTATACA-AAACGCCGTA
* *
3380492 ATAGTGTTGTTTATATT
65 ATAGAGTTGTTTATAGT
* * * * * *
3380509 GGCGTTTGTTCAACAAACGACACTATAGA-TAAGTAATTTCGCGGCGTTTATCAAAAAAACGCCG
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGT-AGTAATTTAGCGGCATTTAT--ACAAAACGCCG
3380573 TAATAGTA-TTGTTTATAGT
63 TAATAG-AGTTGTTTATAGT
* * * * * *
3380592 GACGTTTGTGCAAAAAATGCCGCAATAGAGTAATAATATAGCGGCATTT
1 GGCGTTTGTTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCATTT
3380641 GTCCTACAAA
Statistics
Matches: 172, Mismatches: 34, Indels: 14
0.78 0.15 0.06
Matches are distributed among these distances:
80 1 0.01
81 30 0.17
82 71 0.41
83 67 0.39
84 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (81 bp):
GGCGTTTGTTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCATTTATACAAAACGCCGTAA
TAGAGTTGTTTATAGT
Found at i:3380485 original size:41 final size:41
Alignment explanation
Indices: 3380339--3380486 Score: 153
Period size: 42 Copynumber: 3.6 Consensus size: 41
3380329 AAAATGATAC
* * *
3380339 TTTAGCGGCGTTTTTCAAACAAAAGCCGTAATAGAGTGGTAA
1 TTTAGCGGCGTTTTT-ACACAAACGCCGCAATAGAGTGGTAA
* *
3380381 TTTAGCGGCATTTATAGCTA-AAACGCCGCAATAGAGAT-GT--
1 TTTAGCGGCGTTTTTA-C-ACAAACGCCGCAATAGAG-TGGTAA
*
3380421 TTATAGTGGCGTTTTTTA-ACAAACGCCGCAATAGAGTGGTAA
1 TT-TAGCGGCG-TTTTTACACAAACGCCGCAATAGAGTGGTAA
3380463 TTTAGCGGCGTTTTTACACAAACG
1 TTTAGCGGCGTTTTTACACAAACG
3380487 TCGTGATAGT
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
39 2 0.02
40 26 0.30
41 21 0.24
42 36 0.41
43 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTACACAAACGCCGCAATAGAGTGGTAA
Found at i:3381793 original size:165 final size:165
Alignment explanation
Indices: 3381562--3381866 Score: 389
Period size: 165 Copynumber: 1.8 Consensus size: 165
3381552 AGGACTACAA
* * **
3381562 ATTTAGCGGCGTTTTTATATAAACGCCGCAAAATAATAGAACTTTAGCGGCGTTGTTATTAAAAC
1 ATTTAGCGGCGTTTTTATATAAACACCGCAAAATAATAGAACTTTAGCAGCGTTGTTAAGAAAAC
** * * * *
3381627 GCCGCTATAAAGTG-TTACTTTAGTGTCGTTTTTAAACAAAAACGCCGCAAAATATTTGGACATT
66 GCCGCTATAAAG-GCTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCGCAAAACATTTGGACAGT
3381691 AGTGGCGTTTTATACAAATGCAGCAATAGATTTAAT
130 AGTGGCGTTTTATACAAATGCAGCAATAGATTTAAT
* * * * * *
3381727 ATTTAGTGGCGTTTTT-TAATCAACACTGCAATATAATATAACTTTAGCAGCGTTTTTAAGAAAA
1 ATTTAGCGGCGTTTTTAT-ATAAACACCGCAAAATAATAGAACTTTAGCAGCGTTGTTAAGAAAA
* * * **
3381791 CGCCGCTATAGAGGCTTAAGTTAGTGGCGTTTTGAAACACAAACGCTGCTCAACATTTGGACAGT
65 CGCCGCTATAAAGGCTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCGCAAAACATTTGGACAGT
3381856 AGTGGCGTTTT
130 AGTGGCGTTTT
3381867 TTAAGTAAAC
Statistics
Matches: 117, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
164 2 0.02
165 115 0.98
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (165 bp):
ATTTAGCGGCGTTTTTATATAAACACCGCAAAATAATAGAACTTTAGCAGCGTTGTTAAGAAAAC
GCCGCTATAAAGGCTTAAGTTAGTGGCGTTTTGAAACAAAAACGCCGCAAAACATTTGGACAGTA
GTGGCGTTTTATACAAATGCAGCAATAGATTTAAT
Found at i:3386122 original size:42 final size:42
Alignment explanation
Indices: 3386060--3386167 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 42
3386050 GTGTTATTTA
**
3386060 GCGGCGTTTGTATCAAAAAAACCGCTATATAT-AAGACCTATC
1 GCGGCGTTTGTATCCTAAAAACCGCTATAT-TCAAGACCTATC
* * *
3386102 GCGGCGTTTGTATCCTAAAAATGGCGCTATATTCCAGTCCTATC
1 GCGGCGTTTGTATCCTAAAAA--CCGCTATATTCAAGACCTATC
*
3386146 GCGGCGTTTGTACCCTAAAAAC
1 GCGGCGTTTGTATCCTAAAAAC
3386168 GCAGTTAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
42 19 0.34
43 1 0.02
44 36 0.64
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTGTATCCTAAAAACCGCTATATTCAAGACCTATC
Found at i:3386188 original size:44 final size:44
Alignment explanation
Indices: 3386093--3386198 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
3386083 GCTATATATA
* * * *
3386093 AGACCTATCGCGGCGTTTGTATCCTAAAAATGGCGCTATATTCC
1 AGACCTATCGCGGCGTTTGTACCCTAAAAATCGCGCTAAATACC
* *
3386137 AGTCCTATCGCGGCGTTTGTACCCTAAAAA-CGCAGTTAAATACC
1 AGACCTATCGCGGCGTTTGTACCCTAAAAATCGC-GCTAAATACC
* *
3386181 AGACCTATTGCGCCGTTT
1 AGACCTATCGCGGCGTTT
3386199 TCATAAAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 2 0.04
44 50 0.96
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.28
Consensus pattern (44 bp):
AGACCTATCGCGGCGTTTGTACCCTAAAAATCGCGCTAAATACC
Found at i:3395872 original size:36 final size:37
Alignment explanation
Indices: 3395831--3396010 Score: 213
Period size: 36 Copynumber: 4.9 Consensus size: 37
3395821 GGGCAAGTCA
* * * *
3395831 ATCTTAAGCCTTTACAGAAGAGTAGTAAATCAAA-TC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTC
3395867 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA-TC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTC
* * * *
3395903 CTATTAAGCCATCATGGAAGAGTAGTGAAG-AAATTC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTC
* ** * *
3395939 ATCTTAAGTCTTCACAAAAGAGTAGTGAGGCAAATTA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTC
*
3395976 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGTAAAT
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAT
3396011 CAATTTCAAG
Statistics
Matches: 120, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
35 3 0.03
36 82 0.68
37 35 0.29
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTC
Found at i:3396092 original size:55 final size:55
Alignment explanation
Indices: 3396019--3396427 Score: 523
Period size: 55 Copynumber: 7.4 Consensus size: 55
3396009 ATCAATTTCA
*
3396019 AGTCCTATACTCCTTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGCTT-G
1 AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTG-TTCG
* *
3396074 AGTCCTATACTCCCTGAAAGAATAGGAAGCATACACGTTTGCTGAAGATTGTTCG
1 AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
* * *
3396129 AGTCCTATACTCCCTGAAAGAATAGGGACCAGACACATTTGCTGAAGGTTGTTCG
1 AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
* * * *
3396184 AGTCTTATACTCCCTGAAAGAATAGGGAGCGGACAAGTTTGTTGAAGATTGTTCG
1 AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
* * * * * *
3396239 AGTCCTACACTCTCTGAAAGAATAAGGAGCAGGCATGTTTGCTGAAGATTATTCG
1 AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
* * * ** *
3396294 AGTCCTATATTCCTTGAAAGAATAGGGAGCAAACACGTTTTTTGAATATTGTTCG
1 AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
* * * * * *
3396349 AGTCATATACTCCCCGAAAGAATAGGGTGTAGACCCGTTTGCCGAAGATTGTTCG
1 AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
* * *
3396404 AGTCCTATATTCCATGAAATAATA
1 AGTCCTATACTCCCTGAAAGAATA
3396428 AGGAATGAAC
Statistics
Matches: 300, Mismatches: 53, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
54 2 0.01
55 298 0.99
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (55 bp):
AGTCCTATACTCCCTGAAAGAATAGGGAGCAGACACGTTTGCTGAAGATTGTTCG
Found at i:3402908 original size:118 final size:118
Alignment explanation
Indices: 3402758--3402975 Score: 355
Period size: 118 Copynumber: 1.8 Consensus size: 118
3402748 TCCAAAATAA
*
3402758 TTCTTTAATAATCAAAGTAAATCCATACCATTCGTCATATTTAATCACCTTCACATTAATTCCAA
1 TTCTTTAATAATCAAAGTAAATCCATACCATTCGTCATATTTAATCACCGTCACATTAATTCCAA
* * *
3402823 TCTAATACATTAATTTTGAATAATTACCATTTTACCGCCAATTTTCCCAAAAC
66 TATAATACATTAACTTTAAATAATTACCATTTTACCGCCAATTTTCCCAAAAC
* * * * *
3402876 TTCTTTGATATTCAAATTAAATCCATATCATTCGTCATATTTAATCACCGTCACATTAATTCTAA
1 TTCTTTAATAATCAAAGTAAATCCATACCATTCGTCATATTTAATCACCGTCACATTAATTCCAA
3402941 TATAATACATTAACTTTAAATAATTACCATTTTAC
66 TATAATACATTAACTTTAAATAATTACCATTTTAC
3402976 TGAACTTCTA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 91 1.00
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (118 bp):
TTCTTTAATAATCAAAGTAAATCCATACCATTCGTCATATTTAATCACCGTCACATTAATTCCAA
TATAATACATTAACTTTAAATAATTACCATTTTACCGCCAATTTTCCCAAAAC
Found at i:3405414 original size:23 final size:23
Alignment explanation
Indices: 3405388--3405432 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3405378 TCAATGGAAG
* * *
3405388 ATGGATGATGTTGTTGAAGTTGA
1 ATGGAAGATGGTGATGAAGTTGA
3405411 ATGGAAGATGGTGATGAAGTTG
1 ATGGAAGATGGTGATGAAGTTG
3405433 TATCTCAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (23 bp):
ATGGAAGATGGTGATGAAGTTGA
Found at i:3410071 original size:23 final size:23
Alignment explanation
Indices: 3410042--3410086 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3410032 TCAATGGAAG
**
3410042 ATGGATGATGGTGTTGAAGTTGA
1 ATGGATGATGGTGACGAAGTTGA
3410065 ATGGATGATGGTGACGAAGTTG
1 ATGGATGATGGTGACGAAGTTG
3410087 TATCTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.40, T:0.31
Consensus pattern (23 bp):
ATGGATGATGGTGACGAAGTTGA
Found at i:3414548 original size:17 final size:17
Alignment explanation
Indices: 3414526--3414571 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
3414516 GAAGGTTAAG
3414526 AAAGCAAAAAAAGAAAA
1 AAAGCAAAAAAAGAAAA
* *
3414543 AAAGCATAAAATGAAAA
1 AAAGCAAAAAAAGAAAA
*
3414560 AAAGGAAAAAAA
1 AAAGCAAAAAAA
3414572 TAGACAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.78, C:0.04, G:0.13, T:0.04
Consensus pattern (17 bp):
AAAGCAAAAAAAGAAAA
Found at i:3414896 original size:13 final size:13
Alignment explanation
Indices: 3414878--3414917 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
3414868 GGATAGAACA
3414878 CCAACACAATTAT
1 CCAACACAATTAT
3414891 CCAACACAATTAT
1 CCAACACAATTAT
3414904 CCAACACAACTTAT
1 CCAACACAA-TTAT
3414918 TGTCACAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.23
Consensus pattern (13 bp):
CCAACACAATTAT
Found at i:3415530 original size:36 final size:36
Alignment explanation
Indices: 3415485--3415599 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
3415475 GGTCTCAAGC
*
3415485 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * ** **
3415521 GAAATAAATCTTCTTTCGAGAAAAACAATCTCAAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * *
3415557 GAGACAAAGT-ATGTTTTAAAAAAAACAAAT-TTGAGT
1 GAGATAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGT
3415593 GAGATAA
1 GAGATAA
3415600 TCATCTGCAT
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
36 56 0.93
37 4 0.07
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (36 bp):
GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:3415561 original size:72 final size:75
Alignment explanation
Indices: 3415438--3415599 Score: 199
Period size: 72 Copynumber: 2.2 Consensus size: 75
3415428 AAAAAATAGC
* ** *
3415438 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTTT
1 CTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAATCTCAAGCGAGACAAAGT-ATGTTTT
*
3415502 AAGAAAAAC-AAT
63 AAAAAAAACAAAT
*
3415514 CTTGAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAATCTCAAGTGAGACAAAGTATGTTTTAAA
1 CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAATCTCAAGCGAGACAAAGTATGTTTTAAA
3415577 AAAAACAAAT
66 AAAAACAAAT
*
3415587 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
3415600 TCATCTGCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
72 46 0.60
73 15 0.19
75 4 0.05
76 12 0.16
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (75 bp):
CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAATCTCAAGCGAGACAAAGTATGTTTTAAA
AAAAACAAAT
Found at i:3417024 original size:183 final size:183
Alignment explanation
Indices: 3416716--3417252 Score: 950
Period size: 183 Copynumber: 2.9 Consensus size: 183
3416706 ATTAGGTTTA
* *
3416716 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** * *
3416781 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTAATAAAGCCATGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
* *
3416845 TTCCTCTATAACCAATTTCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATT
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
3416899 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACATCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
3416964 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
3417029 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
3417082 ATTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
3417147 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
3417212 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
3417253 CGGATTTAAT
Statistics
Matches: 340, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
183 339 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:3421077 original size:2 final size:2
Alignment explanation
Indices: 3421072--3421111 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
3421062 AAAAAGGAAA
*
3421072 AT AT AT AT -T AT AT AT AT CT AT AT AT AT AT AT AT A- 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
3421112 CAAAGTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3421144 original size:2 final size:2
Alignment explanation
Indices: 3421139--3421177 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3421129 AAAAAGGAAA
3421139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3421178 CAAAGTATTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3421166 original size:66 final size:67
Alignment explanation
Indices: 3421060--3421185 Score: 236
Period size: 66 Copynumber: 1.9 Consensus size: 67
3421050 GTAATATTTG
*
3421060 AAAAAAAGGAAAATATATATTATATATATCTATATATATATATATAATATATCAAAGTATAAAAT
1 AAAAAAAGGAAAATATATATTATATATATATATATATATATATATAATATATCAAAGTATAAAAT
3421125 AA
66 AA
3421127 AAAAAAAGGAAAATATATA-TATATATATATATATATATATATATAATATATCAAAGTAT
1 AAAAAAAGGAAAATATATATTATATATATATATATATATATATATAATATATCAAAGTAT
3421186 TAATAAATAA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
66 39 0.67
67 19 0.33
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (67 bp):
AAAAAAAGGAAAATATATATTATATATATATATATATATATATATAATATATCAAAGTATAAAAT
AA
Found at i:3421209 original size:66 final size:65
Alignment explanation
Indices: 3421071--3421209 Score: 199
Period size: 66 Copynumber: 2.1 Consensus size: 65
3421061 AAAAAAGGAA
* *
3421071 AATATATATTATATATATCTATATATATATATATAATATATCAAAGTATAAAATAAAAAAAAAGG
1 AATATATATTATATATATATATATATATATATATAATATATCAAAGTATAAAATAAAAAAAAAGC
* * *
3421136 AAAATATATATATATATATATATATATATATATATAATATATCAAAGTAT-TAATAAATAAATAA
1 AATATATAT-TATATATATATATATATATATATATAATATATCAAAGTATAAAATAAA-AAAAAA
3421200 GC
64 GC
*
3421202 TATATATA
1 AATATATA
3421210 CACCAATACT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 14 0.22
66 51 0.78
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (65 bp):
AATATATATTATATATATATATATATATATATATAATATATCAAAGTATAAAATAAAAAAAAAGC
Found at i:3421697 original size:18 final size:17
Alignment explanation
Indices: 3421674--3421707 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3421664 TATATACATA
*
3421674 TAATAATAATAACATGAC
1 TAATAAAAATAA-ATGAC
3421692 TAATAAAAATAAATGA
1 TAATAAAAATAAATGA
3421708 ATAAAATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (17 bp):
TAATAAAAATAAATGAC
Found at i:3422641 original size:2 final size:2
Alignment explanation
Indices: 3422620--3422658 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3422610 ATTCTTAGAG
* * *
3422620 TA TA TA TC TA TC TA TC TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3422659 TGCTAAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3422779 original size:2 final size:2
Alignment explanation
Indices: 3422772--3422800 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3422762 TTGTAAGTAT
3422772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3422801 TATTTCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3426181 original size:15 final size:15
Alignment explanation
Indices: 3426161--3426338 Score: 232
Period size: 15 Copynumber: 11.5 Consensus size: 15
3426151 TAATAAGGTT
3426161 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
3426176 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
3426191 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
3426206 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
3426221 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
3426236 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
3426251 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
3426266 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
3426281 AATTATTATAAAATATGGAA
1 ATTTATT-TTAAA-AT---A
3426301 TGATTTATTTTAAAATA
1 --ATTTATTTTAAAATA
3426318 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
3426332 ATTTATT
1 ATTTATT
3426339 AGTATTGATT
Statistics
Matches: 146, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
14 12 0.08
15 114 0.78
16 4 0.03
17 3 0.02
20 3 0.02
21 4 0.03
22 6 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Done.