Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004017.1 Hibiscus syriacus cultivar Beakdansim tig00008769_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: 139741
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4808 original size:24 final size:24
Alignment explanation
Indices: 4780--4840 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
4770 ATCATGATTA
*
4780 TTCATGAAAATTAAATTAAGTATT
1 TTCATGAAAAATAAATTAAGTATT
*
4804 TTCATGAAAAATAAATTAAGTCTT
1 TTCATGAAAAATAAATTAAGTATT
4828 TTCATGAAAAATA
1 TTCATGAAAAATA
4841 GTTATTTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.38
Consensus pattern (24 bp):
TTCATGAAAAATAAATTAAGTATT
Found at i:4914 original size:21 final size:21
Alignment explanation
Indices: 4885--4943 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
4875 CATGTTAACC
* *
4885 TTTTGATCAAAAGGTTATAAT
1 TTTTAATCAAATGGTTATAAT
4906 TTTTAATCAAATGGTTATAAT
1 TTTTAATCAAATGGTTATAAT
4927 TTTTAATCAAATGGTTA
1 TTTTAATCAAATGGTTA
4944 AGTCATTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (21 bp):
TTTTAATCAAATGGTTATAAT
Found at i:18008 original size:18 final size:18
Alignment explanation
Indices: 17866--17997 Score: 228
Period size: 18 Copynumber: 7.3 Consensus size: 18
17856 GAGAGTCCCC
*
17866 AGCCTGCTGAACCTGAAG
1 AGCCTGTTGAACCTGAAG
* *
17884 AACCTATTGAACCTGAAG
1 AGCCTGTTGAACCTGAAG
17902 AGCCTGTTGAACCTGAAG
1 AGCCTGTTGAACCTGAAG
17920 AGCCTGTTGAACCTGAAG
1 AGCCTGTTGAACCTGAAG
17938 AGCCTGTTGAACCTGAAG
1 AGCCTGTTGAACCTGAAG
*
17956 AGCCTGCTGAACCTGAAG
1 AGCCTGTTGAACCTGAAG
17974 AGCCTGTTGAACCTGAAG
1 AGCCTGTTGAACCTGAAG
17992 AGCCTG
1 AGCCTG
17998 CTGACATTGA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 107 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (18 bp):
AGCCTGTTGAACCTGAAG
Found at i:22340 original size:14 final size:14
Alignment explanation
Indices: 22323--22356 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
22313 ACGACTTTTT
*
22323 ATTATTTTCTTTCA
1 ATTATTTCCTTTCA
22337 ATTACTTTCCTTTCA
1 ATTA-TTTCCTTTCA
22352 ATTAT
1 ATTAT
22357 CCGATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTATTTCCTTTCA
Found at i:23934 original size:26 final size:26
Alignment explanation
Indices: 23882--23946 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
23872 AGTCGACCAT
* *
23882 ATATTATTCAAATGGTAGAGCCAACC
1 ATATTAATCAAATGGTAGAACCAACC
* * *
23908 ATATTAATCAGATGGTATAACCGACC
1 ATATTAATCAAATGGTAGAACCAACC
23934 ATATATCAATCAA
1 ATAT-T-AATCAA
23947 GTGGCAAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 25 0.81
27 1 0.03
28 5 0.16
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (26 bp):
ATATTAATCAAATGGTAGAACCAACC
Found at i:38671 original size:15 final size:15
Alignment explanation
Indices: 38651--38687 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
38641 TAGGTTCTAG
38651 AGGCTTCCAAACTAT
1 AGGCTTCCAAACTAT
38666 AGGCTTCCAAACTAT
1 AGGCTTCCAAACTAT
38681 AGGCTTC
1 AGGCTTC
38688 AAGGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (15 bp):
AGGCTTCCAAACTAT
Found at i:39325 original size:326 final size:323
Alignment explanation
Indices: 38765--39413 Score: 865
Period size: 326 Copynumber: 2.0 Consensus size: 323
38755 CTCCATATCA
* * *
38765 AATTAGTTAAAAATAATAATTTTAAATTGTCCAAATAAGGTACACGTTCGGTAAAAAGTGAAGTT
1 AATTAGTTAAAAATAATAATTTCAAATTGTCCAAAGAAGATACACGTTCGGTAAAAAGTGAAGTT
* ** * * * *
38830 AAAATTTATGTTTTATGAAAATTAAGTTTCATGTATTTATTATTATTTTTATTAAATAGTAAATG
66 AAAATTTACGTTTTACCAAAATCAAGTTTCATGCATTTATTATTATTTTTATCAAATAGTAAATA
* *
38895 ATTATTTAAAAAAGTTGATAGGTCTCGTGCATTATAAAACGCGAGGTTCATTAAACGAGTTTTAT
131 ATTATATAAAAAAGTTGATAGGTCTCGCGCATTATAAAACGCGAGGTTCATTAAACGAGTTTTAT
* * ** * * *
38960 AGAATACGAGATAATCTTACGTAGGTTTTTTGAGGTTATTTTTTTTAACTAATATGACATGGGGT
196 AGAACACGAGATAATCTTACGTAGATTGCTTGAGGTTA-TTTTTCTAACTAATATGACATGAGAT
39025 TATTTCT-AAAAAAAATAATTAAAGGGGATTTTTAATATAATAATACCAAGGAGAAACATGATC
260 TATTTCTCAAAAAAAATAATTAAAGGGGATTTTTAATATAATAATACCAAGGAGAAACATGATC
** *
39088 AATTAGTT-AAAA-AATAATTTCAAATTGTCCACGGAAGATACTTCACGTTCTGTAAAAAGTGAA
1 AATTAGTTAAAAATAATAATTTCAAATTGTCCAAAGAAGATA---CACGTTCGGTAAAAAGTGAA
* * * *
39151 GTTAAATTTTGCGTTTTACCAAAATCAAGTTTTATGCATTTATTATTATTTTTATCAAATATTAA
63 GTTAAAATTTACGTTTTACCAAAATCAAGTTTCATGCATTTATTATTATTTTTATCAAATAGTAA
* * * *
39216 ATAACTTTATATGAAAAAGTTGAT-GGATCTCGCGCATTATAAAACGTGAGGTTTATTAAATGAG
128 ATAA--TTATATAAAAAAGTTGATAGG-TCTCGCGCATTATAAAACGCGAGGTTCATTAAACGAG
* * ** *
39280 TTTTATAGGACGCGAGATAATCTTACGTTTATTGCTTGGGGTTATTTTTCTAACTAATATGACAT
190 TTTTATAGAACACGAGATAATCTTACGTAGATTGCTTGAGGTTATTTTTCTAACTAATATGACAT
** *
39345 GAGATTATTTCTCAAAAAAAATAATTAAAGGGGATTTTTAATATAATAATGTCAAGGAGAAACTT
255 GAGATTATTTCTCAAAAAAAATAATTAAAGGGGATTTTTAATATAATAATACCAAGGAGAAACAT
39410 GATC
320 GATC
39414 GGGACTTGAT
Statistics
Matches: 281, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
321 23 0.08
322 4 0.01
323 8 0.03
324 77 0.27
325 32 0.11
326 137 0.49
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (323 bp):
AATTAGTTAAAAATAATAATTTCAAATTGTCCAAAGAAGATACACGTTCGGTAAAAAGTGAAGTT
AAAATTTACGTTTTACCAAAATCAAGTTTCATGCATTTATTATTATTTTTATCAAATAGTAAATA
ATTATATAAAAAAGTTGATAGGTCTCGCGCATTATAAAACGCGAGGTTCATTAAACGAGTTTTAT
AGAACACGAGATAATCTTACGTAGATTGCTTGAGGTTATTTTTCTAACTAATATGACATGAGATT
ATTTCTCAAAAAAAATAATTAAAGGGGATTTTTAATATAATAATACCAAGGAGAAACATGATC
Found at i:39698 original size:5 final size:5
Alignment explanation
Indices: 39688--39722 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
39678 AATTTGATCA
**
39688 TTAAT TTAAT TTAAT TTAAT TTAAT AAAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
39723 CTCTAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTAAT
Found at i:41945 original size:95 final size:95
Alignment explanation
Indices: 41775--41949 Score: 228
Period size: 95 Copynumber: 1.8 Consensus size: 95
41765 CCCAATCAAT
* * * * * *
41775 GGGGTATCGATACCATGGTAAGGGTATCGATACTAGTAAATATCGAATCTAATTTGTGTATCGGT
1 GGGGTATCGATACCATAGTAAGAGTATCGATACCAATAAATATCGAAGCTAATTTGTGTATCGAT
*
41840 ACCTAGAGGGGGTATTGATACCATAACATA
66 ACATAGAGGGGGTATTGATACCATAACATA
* **
41870 GGGGTATCGATACCATAGTAAGAGTATCTATACCAATCTATATCGAAGCTAATTTAG-GTATCGA
1 GGGGTATCGATACCATAGTAAGAGTATCGATACCAATAAATATCGAAGCTAATTT-GTGTATCGA
41934 TACATCA-AGGGGGTAT
65 TACAT-AGAGGGGGTAT
41950 CAATACCCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
95 66 0.97
96 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (95 bp):
GGGGTATCGATACCATAGTAAGAGTATCGATACCAATAAATATCGAAGCTAATTTGTGTATCGAT
ACATAGAGGGGGTATTGATACCATAACATA
Found at i:46182 original size:79 final size:79
Alignment explanation
Indices: 46050--46198 Score: 228
Period size: 79 Copynumber: 1.9 Consensus size: 79
46040 AACAAATGTG
* * *
46050 AAAGAAAAATGCATATTGGTGCATTATAGGCATGAAAGGATGCCATAGCTGAAATGTATATGGGT
1 AAAGAAAAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCAGAGCTGAAATGCATATGGGT
46115 ACATTGTCAGCATA
66 ACATTGTCAGCATA
* *
46129 AAAGAATAATGCATATGGGTGCATTAGT-GGCATGAAAGGATGCCAGAGTTGAAATGCATATGGG
1 AAAGAAAAATGCATATGGGTGCATTA-TAGGCATGAAAGGATGCCAGAGCTGAAATGCATATGGG
*
46193 TGCATT
65 TACATT
46199 ATCAACAGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 62 0.98
80 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (79 bp):
AAAGAAAAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCAGAGCTGAAATGCATATGGGT
ACATTGTCAGCATA
Found at i:46294 original size:90 final size:91
Alignment explanation
Indices: 46163--46389 Score: 262
Period size: 90 Copynumber: 2.5 Consensus size: 91
46153 TAGTGGCATG
* *
46163 AAAGGATGCCAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAA-TATACTAACGTTGAA
1 AAAGTATGCAAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAAGTATACTAACGTTGAA
* *
46227 ATGCATATGGATGCATTATCAACAGA
66 ATGCATATGGATACATCATCAACAGA
* * * * * * * ** *
46253 AAAGTATGCTAGAGTTGAAATGTATGTAGGTACATTCTCAACA-AAAAAGTATATTATGGTTGAG
1 AAAGTATGCAAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAAGTATACTAACGTTGAA
* * *
46317 ATGTATATGGGTACATCATCAACATA
66 ATGCATATGGATACATCATCAACAGA
*
46343 AAAGTATACAATGA-TTGAAATGCATATGGGTGCATTATCAACAGAAA
1 AAAGTATGCAA-GAGTTGAAATGCATATGGGTGCATTATCAACAGAAA
46390 CGATGTTATA
Statistics
Matches: 111, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
89 5 0.05
90 101 0.91
91 5 0.05
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (91 bp):
AAAGTATGCAAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAAGTATACTAACGTTGAA
ATGCATATGGATACATCATCAACAGA
Found at i:46409 original size:45 final size:45
Alignment explanation
Indices: 46175--46389 Score: 236
Period size: 45 Copynumber: 4.8 Consensus size: 45
46165 AGGATGCCAG
*
46175 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAATATACTA-
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * *
46219 ACGTTGAAATGCATATGGATGCATTATCAACAGAAAAGTATGCTAG
1 A-GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * * * * * *
46265 AGTTGAAATGTATGTAGGTACATTCTCAACAAAAAAGTATATTAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
* * * * * * *
46310 GGTTGAGATGTATATGGGTACATCATCAACATAAAAGTATACAAT
1 AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
46355 -GATTGAAATGCATATGGGTGCATTATCAACAGAAA
1 AG-TTGAAATGCATATGGGTGCATTATCAACAGAAA
46390 CGATGTTATA
Statistics
Matches: 141, Mismatches: 27, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
44 2 0.01
45 138 0.98
46 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (45 bp):
AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACTAT
Found at i:49315 original size:18 final size:18
Alignment explanation
Indices: 49292--49330 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
49282 GTGTAGTGCA
49292 TGTCAATTTGGTAAAGTT
1 TGTCAATTTGGTAAAGTT
49310 TGTCAATTTGGTAAAGTT
1 TGTCAATTTGGTAAAGTT
49328 TGT
1 TGT
49331 AAGTCACCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (18 bp):
TGTCAATTTGGTAAAGTT
Found at i:51950 original size:132 final size:132
Alignment explanation
Indices: 51759--52021 Score: 429
Period size: 132 Copynumber: 2.0 Consensus size: 132
51749 TTATACTTCA
* * *
51759 ACCCCTCATCGTGTAAATAGCCATCCATTTTTTTTCACCATCTAGTTCCCCGAATATTCCAGCCA
1 ACCCCTCATCATGTAAATAGCCATCCATTTTTCTTCACCATCTAGTTCCCCGAATATTCCACCCA
* *
51824 GTCATCATTCATCTTCTTCTCCGTCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACT
66 GTCATCATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACT
51889 TT
131 TT
* * *
51891 ACCCGCTCATCATGTGAATAGTCATCCA-TTTTCTTCACCATCTAGTTCCCCGAATATTCCTCCC
1 ACCC-CTCATCATGTAAATAGCCATCCATTTTTCTTCACCATCTAGTTCCCCGAATATTCCACCC
*
51955 AGTCATCATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCTACCACATTCGCTCAC
65 AGTCATCATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCAC
52020 TT
130 TT
52022 CATTACCATC
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
132 101 0.83
133 20 0.17
ACGTcount: A:0.21, C:0.38, G:0.06, T:0.34
Consensus pattern (132 bp):
ACCCCTCATCATGTAAATAGCCATCCATTTTTCTTCACCATCTAGTTCCCCGAATATTCCACCCA
GTCATCATTCATCTTCCTCTCCATCTCTTTCACCACCATCCATCACTCCACCACATTCGCTCACT
TT
Found at i:57157 original size:2 final size:2
Alignment explanation
Indices: 57150--57174 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57140 ATTTCATCAT
57150 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 T
57175 TATTTTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57213 original size:17 final size:16
Alignment explanation
Indices: 57174--57214 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
57164 TATATATATA
57174 TTATTTTTAAACTCTT
1 TTATTTTTAAACTCTT
57190 TTATTTTTAAACTCTT
1 TTATTTTTAAACTCTT
57206 TTATTTTTA
1 TTATTTTTA
57215 TTTTTTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTTTAAACTCTT
Found at i:57320 original size:19 final size:19
Alignment explanation
Indices: 57298--57343 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
57288 TTTATATATC
57298 TTTACTTTTTT-TCATTTTA
1 TTTA-TTTTTTCTCATTTTA
*
57317 TTTATTTTTTCTCCTTTTA
1 TTTATTTTTTCTCATTTTA
57336 TTTTATTT
1 -TTTATTT
57344 GTTATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 11 0.46
20 7 0.29
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTATTTTTTCTCATTTTA
Found at i:57361 original size:27 final size:26
Alignment explanation
Indices: 57318--57369 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
57308 TTCATTTTAT
*
57318 TTATTTTTTCTCCTTTTATTTTATTTG
1 TTATTTTTTCTCCTTTT-CTTTATTTG
*
57345 TTATTTTTAT-TCTTTTTCTTTATTT
1 TTATTTTT-TCTCCTTTTCTTTATTT
57370 TTTTTTCCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 14 0.64
28 1 0.05
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.77
Consensus pattern (26 bp):
TTATTTTTTCTCCTTTTCTTTATTTG
Found at i:60418 original size:98 final size:95
Alignment explanation
Indices: 60158--60418 Score: 389
Period size: 95 Copynumber: 2.7 Consensus size: 95
60148 CATAATATTA
* * *
60158 TATATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTGTG
1 TATA-ATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
*
60223 GATAATATTCAGCTAGCCTGATAAAGGTGAT
65 GATAATATTCAACTAGCCTGATAAAGGTGAT
*
60254 TATAATATACAATAAAGTTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 TATAATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
60319 ATAATATTCAACTAGCCTGATAAAGGTGAT
66 ATAATATTCAACTAGCCTGATAAAGGTGAT
* * * *
60349 TATAATAT-CTATATAATGATATTGAGCTGTCCCACTAGAGCAATTGGTTAAACGCCCCGACTTT
1 TATAATATAC-A-ATAAAG-T-TTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTT
60413 ATGGAT
62 ATGGAT
60419 CCAGCTAGCT
Statistics
Matches: 151, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
94 1 0.01
95 95 0.63
96 9 0.06
97 1 0.01
98 45 0.30
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
TATAATATACAATAAAGTTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGG
ATAATATTCAACTAGCCTGATAAAGGTGAT
Found at i:61539 original size:151 final size:152
Alignment explanation
Indices: 61369--61745 Score: 569
Period size: 151 Copynumber: 2.5 Consensus size: 152
61359 GTCTGTTAAT
* *
61369 AAACAACTTTCCAGTTTCATTCAGAGTTAATTTCAACTTCACAACAAAGGATATTGGACTCGAAA
1 AAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAAA
* *
61434 CAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCTAATTCAAATCTCAACTTCACAGCG
66 CAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCG
61499 AAGGGGCGACTGTCTG-CCA-A
131 AAGGGGCGACTGTCTGACCATA
* *
61519 CAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGACTTGAA
1 -AAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAA
* * *
61584 ACAACACAAGATTGGATTTCAACTTCACAACGAATGATATCCAATTTAAAGCTCCACTTCACAGC
65 ACAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGC
*
61649 GAAGGGGCGACTGTCTGACGATA
130 GAAGGGGCGACTGTCTGACCATA
* * * * *
61672 AAACAACTTTCCAAGTCTCGTTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGAACTCGAA
1 AAACAACTTTCC-AGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAA
* *
61737 GCGACACAA
65 ACAACACAA
61746 TTTACTCGAG
Statistics
Matches: 204, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
151 137 0.67
152 14 0.07
153 53 0.26
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (152 bp):
AAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAAA
CAACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCG
AAGGGGCGACTGTCTGACCATA
Found at i:61979 original size:121 final size:121
Alignment explanation
Indices: 61817--62278 Score: 599
Period size: 121 Copynumber: 3.8 Consensus size: 121
61807 GAAACAATAC
* * * *
61817 TTGGATTTCAACTTCACAACGAAGGATATCAAATTCAAGGCTCAACTACACAACGAAAGGGCAAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAAGGGCCAT
* * * * *
61882 CCACGATTTCAAATTCACGACAAAGGATATCGTGCCCACAACCAACCATCCCAA-GA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAACAACAAT-ACAACCA
* * * * * *
61938 TTGGATTTCAACTTCACGATGAATGATATCTAATTCAAGGCTCAACTTCACGACGAAGGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAAGGGCCAT
*
62003 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAACAACAATACAACCCA
66 CCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAACAACAATACAA-CCA
* * *
62060 TTGGATTTCAACTTCACGAAGAATGATATCCAATTCAAGGCTCAACTTCACAAC-AAATGAGCCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAA-GGGCCA
* * * * *
62124 TCCACGATTTCAACTTCACGGCGAAA-GATATCGTG-CCACAAGCAGCAATGCAACCT
65 TCCACGATTTCAACTTCACGAC-AAAGGATATCGTGCCCACAAACAACAATACAACCA
* * *
62180 TTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGTAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAAGGGCCAT
**
62245 CCACGATTTCAACTTCACGATGAAGGATATCGTG
66 CCACGATTTCAACTTCACGACAAAGGATATCGTG
62279 GCTAGAAGGG
Statistics
Matches: 299, Mismatches: 36, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
119 2 0.01
120 90 0.30
121 119 0.40
122 86 0.29
123 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (121 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAAGGGCCAT
CCACGATTTCAACTTCACGACAAAGGATATCGTGCCCACAAACAACAATACAACCA
Found at i:62261 original size:242 final size:243
Alignment explanation
Indices: 61817--62278 Score: 664
Period size: 242 Copynumber: 1.9 Consensus size: 243
61807 GAAACAATAC
*
61817 TTGGATTTCAACTTCACAACGAAGGATATCAAATTCAAGGCTCAACTACACAACGAAAGGGCAAT
1 TTGGATTTCAACTTCACAACGAAGGATATCAAATTCAAGGCTCAACTACACAACGAAAGAGCAAT
* *
61882 CCACGATTTCAAATTCACGACAAAGGATATCGTGCCCACAACCAACCATCCCAAGATTGGATTTC
66 CCACGATTTCAAATTCACGACAAAGGATATCGTGCCCACAACCAACAATCCCAACATTGGATTTC
* * * * *
61947 AACTTCACGATGAATGATATCTAATTCAAGGCTCAACTTCACGACGAAGGGGTCATCCACGATTT
131 AACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTT
62012 CAACTTCACGACGAAGGATATCGTGCCCACAAACAACAATACAACCCA
196 CAACTTCACGACGAAGGATATCGTGCCCACAAACAACAATACAACCCA
* * * *
62060 TTGGATTTCAACTTCACGAA-GAATGATATCCAATTCAAGGCTCAACTTCACAAC-AAATGAGCC
1 TTGGATTTCAACTTCAC-AACGAAGGATATCAAATTCAAGGCTCAACTACACAACGAAA-GAGCA
* * * * * *
62123 ATCCACGATTTCAACTTCACGGCGAAA-GATATCGTG-CCACAAGCAGCAAT-GCAACCTTTGGA
64 ATCCACGATTTCAAATTCACGAC-AAAGGATATCGTGCCCACAACCAACAATCCCAA-CATTGGA
* *
62185 TTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGTAGGGGCCATCCACG
127 TTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACG
*
62250 ATTTCAACTTCACGATGAAGGATATCGTG
192 ATTTCAACTTCACGACGAAGGATATCGTG
62279 GCTAGAAGGG
Statistics
Matches: 194, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
241 3 0.02
242 105 0.54
243 81 0.42
244 5 0.03
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (243 bp):
TTGGATTTCAACTTCACAACGAAGGATATCAAATTCAAGGCTCAACTACACAACGAAAGAGCAAT
CCACGATTTCAAATTCACGACAAAGGATATCGTGCCCACAACCAACAATCCCAACATTGGATTTC
AACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTT
CAACTTCACGACGAAGGATATCGTGCCCACAAACAACAATACAACCCA
Found at i:62425 original size:84 final size:84
Alignment explanation
Indices: 62296--62599 Score: 331
Period size: 84 Copynumber: 3.8 Consensus size: 84
62286 GGGTTGTCTA
* *
62296 CCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAATGCACATCATTTGCAGCATAGCTCA
1 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
62361 AGGCGAGAAGAGCTATCTT
66 AGGCGAGAAGAGCTATCTT
* *
62380 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATTATTTGTAGCATAGCTCA
1 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
* *
62445 AGGTGAGAA-AGGCTATCTG
66 AGGCGAGAAGA-GCTATCTT
* *
62464 CCAACAAAAGA-C--C---TTCGATTACACTCAGCTCAAAAGCACATCATTTGCAACATAGCTCA
1 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
*
62523 A---G-G--GA--TATATT
66 AGGCGAGAAGAGCTATCTT
* * * * *
62534 -C--C-AAAGACCTTCAAGTTCGATTACACTCAACTCAAAGGCACGTCATTTTACAGTATAGCTC
1 CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCA-TTTGCAGCATAGCTC
62595 AAGGC
65 AAGGC
62600 AAAAAAGGTT
Statistics
Matches: 190, Mismatches: 18, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
66 5 0.03
67 2 0.01
69 2 0.01
70 4 0.02
72 27 0.14
73 15 0.08
74 1 0.01
75 1 0.01
78 43 0.23
81 1 0.01
83 2 0.01
84 87 0.46
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (84 bp):
CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
AGGCGAGAAGAGCTATCTT
Found at i:64621 original size:20 final size:21
Alignment explanation
Indices: 64593--64639 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
64583 TTTATATATC
*
64593 TTTACTTTTTT-TCATTTTA-
1 TTTATTTTTTTCTCATTTTAT
*
64612 TTTATTTTTTTCTCCTTTTAT
1 TTTATTTTTTTCTCATTTTAT
64633 TTTATTT
1 TTTATTT
64640 GTTATTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 10 0.42
20 7 0.29
21 7 0.29
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATTTTTTTCTCATTTTAT
Found at i:64645 original size:32 final size:34
Alignment explanation
Indices: 64609--64673 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 34
64599 TTTTTTCATT
* *
64609 TTATTTATT-TTTTTCTCCTTT-TATTTTATTTG
1 TTATTTATTATTTTTATCCTTTATATTTAATTTG
* *
64641 TTATTTGTTATTTTTATTCTTTATATTTAATTT
1 TTATTTATTATTTTTATCCTTTATATTTAATTT
64674 TTCCTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 8 0.30
33 10 0.37
34 9 0.33
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (34 bp):
TTATTTATTATTTTTATCCTTTATATTTAATTTG
Found at i:70131 original size:2 final size:2
Alignment explanation
Indices: 70124--70148 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
70114 AGGTGCTGTT
70124 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 T
70149 TAAATTATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:70175 original size:13 final size:14
Alignment explanation
Indices: 70149--70177 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
70139 ATATATATAT
70149 TAAATTATAAAAAA
1 TAAATTATAAAAAA
70163 TAAATTA-AAAAAA
1 TAAATTATAAAAAA
70176 TA
1 TA
70178 CTAAATTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAATTATAAAAAA
Found at i:73372 original size:18 final size:18
Alignment explanation
Indices: 73318--73373 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
73308 TAATCATTAG
* *
73318 TTTTA-TTTTATTTTATTT
1 TTTTATTTTTATATTA-TA
*
73336 TTTTATTTTTA-AATA-A
1 TTTTATTTTTATATTATA
73352 TTTTATTTTTATATTATA
1 TTTTATTTTTATATTATA
73370 TTTT
1 TTTT
73374 CTCTATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 11 0.35
17 3 0.10
18 12 0.39
19 5 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTATATTATA
Found at i:73949 original size:16 final size:17
Alignment explanation
Indices: 73928--73981 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
73918 AAAAAGTATA
73928 AAATTTAT-TTATTTAT
1 AAATTTATATTATTTAT
73944 AAATTTATGA-TATTT-T
1 AAATTTAT-ATTATTTAT
*
73960 AATTTTATATT-TTTAT
1 AAATTTATATTATTTAT
*
73976 ATATTT
1 AAATTT
73982 TTTTGTTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 4 0.13
16 22 0.71
17 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
AAATTTATATTATTTAT
Found at i:75308 original size:64 final size:64
Alignment explanation
Indices: 75172--75332 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 64
75162 AATTGTTCAG
* * * *
75172 TGTGTATCGATGCACAGGAAGTGCATCGATGTA-CCCATTAAAATGGAAACATCGAATACAATT
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGACAATT
* * * * ***
75235 AGTGCATCGATGCATAAGAAGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATT
1 TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGACAATT
*
75299 TGTGTATCGATGCAT-GGTTAGTGCATCGATGCAC
1 TGTGTATCGATGCATAGG-AAGTGCATCGATGCAC
75333 ATATTAAAGA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 29 0.36
64 52 0.64
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (64 bp):
TGTGTATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGACAATT
Found at i:75365 original size:20 final size:20
Alignment explanation
Indices: 75340--75377 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
75330 CACATATTAA
75340 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
75360 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
75378 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:76713 original size:34 final size:32
Alignment explanation
Indices: 76651--76720 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
76641 CCTTACAAAC
* *
76651 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
76683 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
76717 TCCC
1 TCCC
76721 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:77025 original size:21 final size:21
Alignment explanation
Indices: 77001--77045 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
76991 TGCCCAGAAT
*
77001 ATAGGGAATCGGTACCCCTTC
1 ATAGGGAATCGATACCCCTTC
77022 ATAGGGAATCGATACCCCTTC
1 ATAGGGAATCGATACCCCTTC
77043 ATA
1 ATA
77046 ATATTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
ATAGGGAATCGATACCCCTTC
Found at i:77173 original size:15 final size:15
Alignment explanation
Indices: 77153--77182 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
77143 CCCCCTGGGG
77153 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
77168 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
77183 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:77198 original size:36 final size:38
Alignment explanation
Indices: 77130--77203 Score: 116
Period size: 36 Copynumber: 2.0 Consensus size: 38
77120 CTTTAGACAG
*
77130 GGGGTAATCGGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGGTAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
*
77168 GGGGT-ATCTGTACCCCCT-GGGGGGGAATCTGTACCC
1 GGGGTAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
77204 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 17 0.50
37 12 0.35
38 5 0.15
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.22
Consensus pattern (38 bp):
GGGGTAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
Found at i:77204 original size:20 final size:21
Alignment explanation
Indices: 77129--77209 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
77119 GCTTTAGACA
* *
77129 GGGGGTAATCGGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCT-G
*
77151 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
77168 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
77187 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
77208 GG
1 GG
77210 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 20 0.41
22 11 0.22
ACGTcount: A:0.12, C:0.27, G:0.40, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:77486 original size:23 final size:22
Alignment explanation
Indices: 77453--77496 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
77443 TGAATACAAG
77453 TATAGGAAAGATGATATATATATA
1 TATAGGAAAGATGA-AT-TATATA
77477 TATAGG-AAGATGAATTATAT
1 TATAGGAAAGATGAATTATAT
77497 GAATACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 7 0.35
24 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (22 bp):
TATAGGAAAGATGAATTATATA
Found at i:77543 original size:17 final size:18
Alignment explanation
Indices: 77514--77550 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
77504 CATTTAGGTG
77514 ATGAAATGATGAAT-TAT
1 ATGAAATGATGAATATAT
77531 ATGAACATG-TGAATATAT
1 ATGAA-ATGATGAATATAT
77549 AT
1 AT
77551 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.35
Consensus pattern (18 bp):
ATGAAATGATGAATATAT
Found at i:77550 original size:2 final size:2
Alignment explanation
Indices: 77543--77579 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
77533 GAACATGTGA
77543 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 A
77580 AGACATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78010 original size:23 final size:23
Alignment explanation
Indices: 77966--78010 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
77956 AACCTTATAT
* * *
77966 GGCACTTCGATGCATTTTTACGC
1 GGCACTACGATGCAATTATACGC
77989 GGCACTACGATGCAATTATACG
1 GGCACTACGATGCAATTATACG
78011 TGGAACTTCA
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:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (23 bp):
GGCACTACGATGCAATTATACGC
Found at i:81489 original size:45 final size:45
Alignment explanation
Indices: 81423--81521 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
81413 TTCTGTGTGT
* * *
81423 ATCGATGCACCCATTAAAAATGGAAACATCGAATGTAATTAGTGC
1 ATCGATGCACCCATTAAAAATGAAAACATCAAAGGTAATTAGTGC
* * * * *
81468 ATCGATGCACCCCCTT-GAAATGAAAACATCAAAGGTGATTTGTGT
1 ATCGATGCA-CCCATTAAAAATGAAAACATCAAAGGTAATTAGTGC
81513 ATCGATGCA
1 ATCGATGCA
81522 TGGGTAGTGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
45 40 0.89
46 5 0.11
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (45 bp):
ATCGATGCACCCATTAAAAATGAAAACATCAAAGGTAATTAGTGC
Found at i:81574 original size:20 final size:22
Alignment explanation
Indices: 81529--81591 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 22
81519 GCATGGGTAG
81529 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
81553 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
81573 TGTATCGATGCACT-TTAAG
1 TGCATCGATGCACTGTTAAG
81592 GGGAAATAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 1 0.03
23 2 0.06
24 13 0.36
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:82706 original size:2 final size:2
Alignment explanation
Indices: 82694--82731 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
82684 AGTATAGGAA
82694 AT AT GAT 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 A
82732 GAAAGATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:83240 original size:23 final size:22
Alignment explanation
Indices: 83205--83272 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
83195 AACCTTATAT
*
83205 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTT-TACGC
* *
83228 GGCACTACGGTGCAATTTTACGT
1 GGCACTTCGGTGC-ATTTTACGC
*
83251 GGAACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTT-TACG
83273 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 4 0.11
23 30 0.79
24 4 0.11
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (22 bp):
GGCACTTCGGTGCATTTTACGC
Found at i:85124 original size:22 final size:21
Alignment explanation
Indices: 85049--85108 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
85039 AAGAATGAAT
85049 AATATCGATACTTTTAAATAC
1 AATATCGATACTTTTAAATAC
85070 AATATCGATACTTTTAAATAC
1 AATATCGATACTTTTAAATAC
*
85091 AATATCGATACTTCTAAA
1 AATATCGATACTTTTAAA
85109 CTAAGGTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
AATATCGATACTTTTAAATAC
Found at i:87465 original size:17 final size:18
Alignment explanation
Indices: 87445--87478 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
87435 AGATTAATAT
87445 AATTAAAATAC-ATTAAC
1 AATTAAAATACAATTAAC
87462 AATTAAAATACAATTAA
1 AATTAAAATACAATTAA
87479 AATGTCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AATTAAAATACAATTAAC
Found at i:87954 original size:23 final size:23
Alignment explanation
Indices: 87936--87982 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
87926 TTTATGGCAT
*
87936 ATTTTCATATGCTTATATGATAC
1 ATTTTCATATGCTTATATGACAC
*
87959 ATTTTCATATGCTTTTATGACAC
1 ATTTTCATATGCTTATATGACAC
87982 A
1 A
87983 CTATTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.47
Consensus pattern (23 bp):
ATTTTCATATGCTTATATGACAC
Found at i:88214 original size:18 final size:18
Alignment explanation
Indices: 88191--88249 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
88181 TTGGTCTTTA
88191 GTAGTTTGATCTATTGTT
1 GTAGTTTGATCTATTGTT
*
88209 GTAGTTTGGA---ATT-TA
1 GTAGTTT-GATCTATTGTT
* *
88224 GTACTTTGATCTACTGTT
1 GTAGTTTGATCTATTGTT
88242 GTAGTTTG
1 GTAGTTTG
88250 TTTTACTGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 3 0.10
17 2 0.06
18 15 0.48
19 2 0.06
ACGTcount: A:0.19, C:0.07, G:0.24, T:0.51
Consensus pattern (18 bp):
GTAGTTTGATCTATTGTT
Found at i:88232 original size:33 final size:33
Alignment explanation
Indices: 88187--88249 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
88177 GTTGTTGGTC
* *
88187 TTTAGTAGTTTGATCTATTGTTGTAGTTTGGAA
1 TTTAGTACTTTGATCTACTGTTGTAGTTTGGAA
88220 TTTAGTACTTTGATCTACTGTTGTAGTTTG
1 TTTAGTACTTTGATCTACTGTTGTAGTTTG
88250 TTTTACTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.19, C:0.06, G:0.22, T:0.52
Consensus pattern (33 bp):
TTTAGTACTTTGATCTACTGTTGTAGTTTGGAA
Found at i:91232 original size:20 final size:19
Alignment explanation
Indices: 91193--91233 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
91183 TATGGACATA
* *
91193 AGTTGGTTTCAATAATGAT
1 AGTTGGTTTAAAGAATGAT
91212 AGTTGGTTTAAAGACATGAT
1 AGTTGGTTTAAAGA-ATGAT
91232 AG
1 AG
91234 GGGATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (19 bp):
AGTTGGTTTAAAGAATGAT
Found at i:91416 original size:169 final size:165
Alignment explanation
Indices: 91126--91462 Score: 622
Period size: 169 Copynumber: 2.0 Consensus size: 165
91116 AATTTGAAAG
91126 TTTAGTAAGATTCTTAATTTTAAGAATCTTGAAAATATGGAAGATAAATATGATTTATATGGACA
1 TTTAGTAAGATTCTTAATTTTAAGAATCTTGAAAATATGGAAGATAAATATGATTTATATGGACA
91191 TAAGTTGGTTTCAATAATGATAGTTGGTTTAAAGACATGATAGGGGATTAAAATAGAAGAATTGA
66 TAAGTTGGTTTCAATAATGATAGTTGGTTTAAAGACATGATAGGGGATTAAAATAGAAGAATTGA
91256 ATGAAGAATTGATGAATTTCGGGCTTGAAATACAA
131 ATGAAGAATTGATGAATTTCGGGCTTGAAATACAA
91291 TTTAGTAAGATTCTTAA-TTTAAGAATCTTGATGAAATATGGAAGATAAATATGATTTATTATGG
1 TTTAGTAAGATTCTTAATTTTAAGAATCTTGA--AAATATGGAAGATAAATATGATTTA-TAT-G
91355 GACATAAGTTGGTTTCAATAATGATAGTTGAGTTTAAAGACATGATAGGGGATTAAAATAGAAGA
62 GACATAAGTTGGTTTCAATAATGATAGTTG-GTTTAAAGACATGATAGGGGATTAAAATAGAAGA
91420 ATTGAATGAAGAATTGATGAATTTCGGGCTTGAAATACAA
126 ATTGAATGAAGAATTGATGAATTTCGGGCTTGAAATACAA
91460 TTT
1 TTT
91463 CTGGACAAGG
Statistics
Matches: 167, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
164 14 0.08
165 17 0.10
166 25 0.15
167 3 0.02
168 31 0.19
169 77 0.46
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (165 bp):
TTTAGTAAGATTCTTAATTTTAAGAATCTTGAAAATATGGAAGATAAATATGATTTATATGGACA
TAAGTTGGTTTCAATAATGATAGTTGGTTTAAAGACATGATAGGGGATTAAAATAGAAGAATTGA
ATGAAGAATTGATGAATTTCGGGCTTGAAATACAA
Found at i:91610 original size:59 final size:62
Alignment explanation
Indices: 91489--91635 Score: 151
Period size: 59 Copynumber: 2.3 Consensus size: 62
91479 GATCACATTC
*
91489 ATAAGTGCATCGATGCCATTCC-TTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCAT
1 ATAA-TGCATCGATG-CA-TCCTTTTAAAAGAAGAACATC-AATGCCTTTGATGCATCGATGCAC
91553 A
62 A
* * *
91554 GATAATGCATCGATGCATCCTTTTAAAATAA-TACAT-AATG-CTTTTATGCA-CGATGCACA
1 -ATAATGCATCGATGCATCCTTTTAAAAGAAGAACATCAATGCCTTTGATGCATCGATGCACA
*
91613 AGTAGTGCATCGATGCATACCTT
1 A-TAATGCATCGATGCAT-CCTT
91636 CATTGAAAGA
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
58 1 0.01
59 23 0.32
60 13 0.18
61 4 0.05
63 7 0.10
64 11 0.15
65 10 0.14
66 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (62 bp):
ATAATGCATCGATGCATCCTTTTAAAAGAAGAACATCAATGCCTTTGATGCATCGATGCACA
Found at i:93247 original size:35 final size:35
Alignment explanation
Indices: 93205--93279 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
93195 TTCATGTTCA
93205 AAATTCCAAAACACTTTAATTACATTCTAAACCTC
1 AAATTCCAAAACACTTTAATTACATTCTAAACCTC
* * * * *
93240 AAATTCCAAAATACTTTAATTATATTTTGAACCTT
1 AAATTCCAAAACACTTTAATTACATTCTAAACCTC
93275 AAATT
1 AAATT
93280 AAAGTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.37
Consensus pattern (35 bp):
AAATTCCAAAACACTTTAATTACATTCTAAACCTC
Found at i:96330 original size:31 final size:31
Alignment explanation
Indices: 96291--96462 Score: 290
Period size: 31 Copynumber: 5.5 Consensus size: 31
96281 AGGGTCGAGG
96291 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
96322 ATTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
96353 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
96384 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
96415 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
96446 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
96463 AGAATCTATG
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 132 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:96979 original size:21 final size:21
Alignment explanation
Indices: 96954--96996 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
96944 AAAGAATATA
96954 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
96975 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
96996 T
1 T
96997 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:99529 original size:19 final size:18
Alignment explanation
Indices: 99505--99573 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
99495 AGAATGTCCA
99505 GGGGGTA-CAGATTCCCCT
1 GGGGGTATC-GATTCCCCT
99523 GGGGGGTATCGATTCCCC-
1 -GGGGGTATCGATTCCCCT
*
99541 --GGG-AACAGATTCCCCT
1 GGGGGTATC-GATTCCCCT
99557 GGGGGTATCGATTCCCC
1 GGGGGTATCGATTCCCC
99574 CTAAATAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
14 2 0.05
15 11 0.26
18 11 0.26
19 17 0.40
20 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:100423 original size:31 final size:31
Alignment explanation
Indices: 100385--100633 Score: 392
Period size: 31 Copynumber: 8.0 Consensus size: 31
100375 AGGGTCGAGG
100385 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
100416 GTTTACCTATGTTCTTCGGGACATATGTACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
100447 GTTTGCCTACGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
100478 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
100509 GTTTATCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
100540 GTTTACCTATGTTCTTCGTGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
100571 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
100602 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
100633 G
1 G
100634 GTCCTTCGGG
Statistics
Matches: 200, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
31 199 1.00
32 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:101139 original size:21 final size:21
Alignment explanation
Indices: 101114--101156 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
101104 AAAGAATATA
101114 TTGTATAA-GCTTTGAATAATT
1 TTGTA-AATGCTTTGAATAATT
*
101135 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTTTGAATAATT
101156 T
1 T
101157 AAATGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (21 bp):
TTGTAAATGCTTTGAATAATT
Found at i:102953 original size:23 final size:22
Alignment explanation
Indices: 102924--102991 Score: 102
Period size: 21 Copynumber: 3.1 Consensus size: 22
102914 TGCATTCATA
*
102924 AAAGGAATTTGTGAGTTTTTTTT
1 AAAGGAAATTGTGA-TTTTTTTT
102947 AAAGGAAATTGTGA-TTTTTTT
1 AAAGGAAATTGTGATTTTTTTT
*
102968 AAAGTAAATTGTGATTTTTTTT
1 AAAGGAAATTGTGATTTTTTTT
102990 AA
1 AA
102992 TTTTATAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
21 20 0.48
22 9 0.21
23 13 0.31
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (22 bp):
AAAGGAAATTGTGATTTTTTTT
Found at i:103427 original size:75 final size:75
Alignment explanation
Indices: 103305--103450 Score: 256
Period size: 75 Copynumber: 1.9 Consensus size: 75
103295 ATACATTTCA
* *
103305 TTTTTTTATAACGAACTACGTGTTTTTTTCTCGGTGAAAAATTAGAACGTGCATGTTTTTCCCCC
1 TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTGAAAAATTAGAACGTACATGTTTTTCCCCC
103370 TCTTTTTATT
66 TCTTTTTATT
**
103380 TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTGAAAAATTAGAACGTACATGTTTTTTTCCC
1 TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTGAAAAATTAGAACGTACATGTTTTTCCCCC
103445 TCTTTT
66 TCTTTT
103451 CTTTTGCTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (75 bp):
TTTTTTTATAACGAACTACGTGCTTTTTTCTCGGTGAAAAATTAGAACGTACATGTTTTTCCCCC
TCTTTTTATT
Found at i:105385 original size:29 final size:29
Alignment explanation
Indices: 105353--105410 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
105343 TAGATATTAG
105353 CAGCCCTTCCAAGTATAAATTTGGAGCAT
1 CAGCCCTTCCAAGTATAAATTTGGAGCAT
105382 CAGCCCTTCCAAGTATAAATTTGGAGCAT
1 CAGCCCTTCCAAGTATAAATTTGGAGCAT
105411 GTATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (29 bp):
CAGCCCTTCCAAGTATAAATTTGGAGCAT
Found at i:116301 original size:25 final size:24
Alignment explanation
Indices: 116252--116301 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
116242 TAAGGGTTTG
* * *
116252 TTTAATTTTTAAAAATATAATTAT
1 TTTAAATTTTAAAAATAAAAATAT
116276 TTTAAATTTTAAAATATAAAAATAT
1 TTTAAATTTTAAAA-ATAAAAATAT
116301 T
1 T
116302 AAGTTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAAATTTTAAAAATAAAAATAT
Found at i:116303 original size:23 final size:24
Alignment explanation
Indices: 116253--116303 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
116243 AAGGGTTTGT
* ** *
116253 TTAATTTTTAAAAATATAATTATT
1 TTAAATTTTAAAAATATAAAAATA
116277 TTAAATTTT-AAAATATAAAAATA
1 TTAAATTTTAAAAATATAAAAATA
116300 TTAA
1 TTAA
116304 GTTAAATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAATTTTAAAAATATAAAAATA
Found at i:116424 original size:15 final size:15
Alignment explanation
Indices: 116404--116433 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
116394 AATTAAACAT
*
116404 AAATAAAAAGTAAAA
1 AAATAAAAAATAAAA
116419 AAATAAAAAATAAAA
1 AAATAAAAAATAAAA
116434 TATCAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAATAAAAAATAAAA
Found at i:119627 original size:20 final size:19
Alignment explanation
Indices: 119590--119644 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
119580 TTGATCTGAC
* *
119590 CATTGACCATTGAACCGAT
1 CATTGACCGTTGACCCGAT
119609 CATTGACCTGTTGACCCGAT
1 CATTGACC-GTTGACCCGAT
*
119629 CGTTGACCCGTTGACC
1 CATTGA-CCGTTGACC
119645 AGACCCGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.26
20 21 0.68
21 2 0.06
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (19 bp):
CATTGACCGTTGACCCGAT
Found at i:126069 original size:9 final size:9
Alignment explanation
Indices: 126055--126107 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 9
126045 TTTTGTTTTC
126055 AAAAACAAA
1 AAAAACAAA
126064 AAAAACAAAAA
1 AAAAAC--AAA
126075 AAAAACACAA
1 AAAAACA-AA
*
126085 AAAAGGCAAAA
1 AAAA-AC-AAA
126096 AAAAACAAA
1 AAAAACAAA
126105 AAA
1 AAA
126108 GTCAAAAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 13 0.35
10 7 0.19
11 16 0.43
12 1 0.03
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:126077 original size:11 final size:11
Alignment explanation
Indices: 126061--126107 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
126051 TTTCAAAAAC
126061 AAAAAAAACAA
1 AAAAAAAACAA
*
126072 AAAAAAAACAC
1 AAAAAAAACAA
**
126083 AAAAAAGGC-A
1 AAAAAAAACAA
126093 AAAAAAAACAA
1 AAAAAAAACAA
126104 AAAA
1 AAAA
126108 GTCAAAAAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 7 0.24
11 22 0.76
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:126080 original size:20 final size:20
Alignment explanation
Indices: 126055--126107 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
126045 TTTTGTTTTC
126055 AAAAACAAAAAAA-ACAAAAA
1 AAAAACAAAAAAAGAC-AAAA
*
126075 AAAAACACAAAAAAGGCAAAA
1 AAAAACA-AAAAAAGACAAAA
126096 AAAAACAAAAAA
1 AAAAACAAAAAA
126108 GTCAAAAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 12 0.40
21 17 0.57
22 1 0.03
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAAAAGACAAAA
Found at i:126095 original size:19 final size:19
Alignment explanation
Indices: 126072--126115 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
126062 AAAAAAACAA
126072 AAAAAAAACACAAAAAAGGC
1 AAAAAAAA-ACAAAAAAGGC
*
126092 AAAAAAAAACAAAAAAGTC
1 AAAAAAAAACAAAAAAGGC
126111 AAAAA
1 AAAAA
126116 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.80, C:0.11, G:0.07, T:0.02
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAGGC
Done.