Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 21 of 144
Found at i:5276182 original size:59 final size:59
Alignment explanation
Indices: 5276118--5276487 Score: 530
Period size: 59 Copynumber: 6.3 Consensus size: 59
5276108 CTTGGACTAT
** *
5276118 CCAAAAATTACCATTTTACCC-CAAAACTTTCTGAAA-TCATATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTC-CATTTTTAACCCCGATTTCA
5276177 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
5276236 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
5276295 CCAAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCA-TTTTAACCCCAATTTCG
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* **
5276353 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTTGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * **
5276412 CCAAAAATTACTATTTTACCCTCAAATTTTCCAAAATTCCCTTTTTGACCCTAATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
5276471 CCAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
5276488 GCCCCCGTAA
Statistics
Matches: 284, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
58 52 0.18
59 229 0.81
60 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:5276413 original size:176 final size:177
Alignment explanation
Indices: 5276118--5276492 Score: 569
Period size: 176 Copynumber: 2.1 Consensus size: 177
5276108 CTTGGACTAT
* * *
5276118 CCAAAAATTACCATTTTACCCCAAAACTTTCTGAAATCATATTTTTAACCCCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCAAAACTTTCTAAAATCACATTTTTAACCCCAATTTCACCAAAA
5276183 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
66 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
* *
5276248 ATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGA-CCTCGATTTCA
131 ATTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCCT-AATTTCA
* *
5276295 CCAAAAATTACCATTTTACCCTC-GAACTTTCTAAAATTC-CA-TTTTAACCCCAATTTCGCCAA
1 CCAAAAATTACCATTTTACCC-CAAAACTTTCTAAAA-TCACATTTTTAACCCCAATTTCACCAA
* **
5276357 AAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCTTGATTTCACCAAAAATTA
64 AAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTA
* * *
5276422 CTATTTTACCCTCAAATTTTCCAAAATTCCCTTTTTGACCCTAATTTCA
129 CCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCCTAATTTCA
*
5276471 CCAAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
5276493 CGTAAGTCCA
Statistics
Matches: 181, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
175 1 0.01
176 141 0.78
177 36 0.20
178 3 0.02
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (177 bp):
CCAAAAATTACCATTTTACCCCAAAACTTTCTAAAATCACATTTTTAACCCCAATTTCACCAAAA
ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACC
ATTTTACCCTCAAACTTTCCAAAATTCCATTTTTGACCCTAATTTCA
Found at i:5280941 original size:30 final size:30
Alignment explanation
Indices: 5280907--5281069 Score: 108
Period size: 30 Copynumber: 5.5 Consensus size: 30
5280897 ATTTTATTTA
5280907 AAAATTACATTTTGACCTTCAAACTTTTCT
1 AAAATTACATTTTGACCTTCAAACTTTTCT
* * * *
5280937 AAAATCT-TATTTTGGCC-TCTAAACATTTCC
1 AAAAT-TACATTTTGACCTTC-AAACTTTTCT
* *
5280967 AAAATTATATTTTGACCCTT-AAA-TTTTTT
1 AAAATTACATTTTGA-CCTTCAAACTTTTCT
* * *
5280996 CAAAATTACATTTTGA-CTCCTAAAATTTTCC
1 -AAAATTACATTTTGACCTTC-AAACTTTTCT
* *
5281027 AAAATTACA--TTGA-CTCCCAAACTTTCCT
1 AAAATTACATTTTGACCT-TCAAACTTTTCT
*
5281055 AAAATCACATTTTGA
1 AAAATTACATTTTGA
5281070 TTTTTGAATT
Statistics
Matches: 105, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
28 23 0.22
29 8 0.08
30 66 0.63
31 7 0.07
32 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTGACCTTCAAACTTTTCT
Found at i:5281009 original size:60 final size:60
Alignment explanation
Indices: 5280907--5281069 Score: 153
Period size: 60 Copynumber: 2.8 Consensus size: 60
5280897 ATTTTATTTA
* *
5280907 AAAATTACATTTTGACCTTCAAACTTTTCTAAAATCTTATTTTGGC-CTCTAAACA-TTTCC
1 AAAATTACATTTTGACCTTCAAACTTTTCTAAAATCTCATTTTGACTC-CTAAA-ATTTTCC
* *
5280967 AAAATTATATTTTGACCCTT-AAA-TTTTTTCAAAAT-TACATTTTGACTCCTAAAATTTTCC
1 AAAATTACATTTTGA-CCTTCAAACTTTTCT-AAAATCT-CATTTTGACTCCTAAAATTTTCC
* * *
5281027 AAAATTACA--TTGA-CTCCCAAACTTTCCTAAAATCACATTTTGA
1 AAAATTACATTTTGACCT-TCAAACTTTTCTAAAATCTCATTTTGA
5281070 TTTTTGAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
56 2 0.02
58 20 0.24
59 11 0.13
60 47 0.55
61 5 0.06
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.40
Consensus pattern (60 bp):
AAAATTACATTTTGACCTTCAAACTTTTCTAAAATCTCATTTTGACTCCTAAAATTTTCC
Found at i:5281058 original size:28 final size:28
Alignment explanation
Indices: 5280996--5281065 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
5280986 TAAATTTTTT
*
5280996 CAAAATTACATTTTGACTCCTAAAATTTTC
1 CAAAATTACA--TTGACTCCTAAAACTTTC
*
5281026 CAAAATTACATTGACTCC-CAAACTTTC
1 CAAAATTACATTGACTCCTAAAACTTTC
*
5281053 CTAAAATCACATT
1 C-AAAATTACATT
5281066 TTGATTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 8 0.22
28 18 0.50
30 10 0.28
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (28 bp):
CAAAATTACATTGACTCCTAAAACTTTC
Found at i:5282024 original size:14 final size:14
Alignment explanation
Indices: 5282005--5282035 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5281995 TTATTACTTT
*
5282005 AATATTTGAGCACA
1 AATATTTAAGCACA
5282019 AATATTTAAGCACA
1 AATATTTAAGCACA
5282033 AAT
1 AAT
5282036 CACATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (14 bp):
AATATTTAAGCACA
Found at i:5288387 original size:30 final size:30
Alignment explanation
Indices: 5288346--5288402 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5288336 GTAAATTGGG
*
5288346 AGGGTTTTAGTTGAGCCACAAAAACTAAGA
1 AGGGTTCTAGTTGAGCCACAAAAACTAAGA
* *
5288376 AGGGTTCTAGTTTAGCCATAAAAACTA
1 AGGGTTCTAGTTGAGCCACAAAAACTA
5288403 GGGGGAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (30 bp):
AGGGTTCTAGTTGAGCCACAAAAACTAAGA
Found at i:5290449 original size:24 final size:24
Alignment explanation
Indices: 5290389--5290481 Score: 100
Period size: 24 Copynumber: 3.8 Consensus size: 24
5290379 TTCCAGAAAT
*
5290389 TTAGCTCATACGAGCCCAGACA-AAA
1 TTAGCTCATACGAGCCCA-A-ATAAG
*
5290414 TTAGCTCATACGAAG-CCAAATAGG
1 TTAGCTCATACG-AGCCCAAATAAG
* *
5290438 TTAGCTCTTACGAGCCCAGATAAG
1 TTAGCTCATACGAGCCCAAATAAG
*
5290462 TTAGCTCATTCGAGCCCAAA
1 TTAGCTCATACGAGCCCAAA
5290482 CAGAGTTTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
23 3 0.05
24 37 0.65
25 15 0.26
26 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (24 bp):
TTAGCTCATACGAGCCCAAATAAG
Found at i:5291661 original size:20 final size:19
Alignment explanation
Indices: 5291621--5291662 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
5291611 TCTTTTATAA
*
5291621 TTAACTTAATTAACCTTAC
1 TTAACTTAATTAACATTAC
5291640 TTAAGCTTAATTAA-ATTCAC
1 TTAA-CTTAATTAACATT-AC
5291660 TTA
1 TTA
5291663 TTACATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAACTTAATTAACATTAC
Found at i:5293535 original size:28 final size:28
Alignment explanation
Indices: 5293484--5293538 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
5293474 TGTCCACTTC
*
5293484 TCCCAGATTGGTACCTAAAGTTTTTTTG
1 TCCCAGATTGGTACCTAAACTTTTTTTG
* * *
5293512 TCCCAGATTTGTACTTGAACTTTTTTT
1 TCCCAGATTGGTACCTAAACTTTTTTT
5293539 TTGTCTACTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (28 bp):
TCCCAGATTGGTACCTAAACTTTTTTTG
Found at i:5303679 original size:24 final size:24
Alignment explanation
Indices: 5303652--5303699 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5303642 TTTTGTGATC
*
5303652 TTTCTTTCTTTAGATTAGGCCAAA
1 TTTCTTTCTTTAAATTAGGCCAAA
5303676 TTTCTTTCTTTAAATTAGGCCAAA
1 TTTCTTTCTTTAAATTAGGCCAAA
5303700 AGTCCACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (24 bp):
TTTCTTTCTTTAAATTAGGCCAAA
Found at i:5309008 original size:16 final size:17
Alignment explanation
Indices: 5308982--5309014 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5308972 TTAACTTAGC
5308982 TAAATTAATTTCTCAAT
1 TAAATTAATTTCTCAAT
*
5308999 TAAA-TAATTTTTCAAT
1 TAAATTAATTTCTCAAT
5309015 CCAATTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATTAATTTCTCAAT
Found at i:5311236 original size:3 final size:3
Alignment explanation
Indices: 5311228--5311286 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
5311218 AATATTTAAG
5311228 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
5311276 CTT ATT ATT AT
1 ATT ATT ATT AT
5311287 ATTGTTTATA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5311399 original size:25 final size:23
Alignment explanation
Indices: 5311358--5311403 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
5311348 CCAATTAGAG
5311358 AATTATTATTTAGATTTAATTCT
1 AATTATTATTTAGATTTAATTCT
*
5311381 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
5311404 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCT
Found at i:5315734 original size:98 final size:98
Alignment explanation
Indices: 5315558--5315753 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
5315548 CTTGTGTGGA
5315558 GAGGGTCTTTCTACCCTTATGAATATGGCTGTTCAGGATGGTTTGATTTCGGGGGTAAAAGCTAG
1 GAGGGTCTTTCTACCCTTATGAATATGGCTGTTCAGGATGGTTTGATTTCGGGGGTAAAAGCTAG
5315623 TAAAAGAGATCCGGTGGTTTCACATCTCCTATT
66 TAAAAGAGATCCGGTGGTTTCACATCTCCTATT
5315656 GAGGGTCTTTCTACCCTTATGAATATGGCTGTTCAGGATGGTTTGATTTCGGGGGTAAAAGCTAG
1 GAGGGTCTTTCTACCCTTATGAATATGGCTGTTCAGGATGGTTTGATTTCGGGGGTAAAAGCTAG
* *
5315721 TAAAGGAGGTCCGGTGGTTTCACATCTCCTATT
66 TAAAAGAGATCCGGTGGTTTCACATCTCCTATT
5315754 TACTGATGAC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (98 bp):
GAGGGTCTTTCTACCCTTATGAATATGGCTGTTCAGGATGGTTTGATTTCGGGGGTAAAAGCTAG
TAAAAGAGATCCGGTGGTTTCACATCTCCTATT
Found at i:5319149 original size:49 final size:49
Alignment explanation
Indices: 5319096--5319193 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
5319086 ATTACCTTTC
5319096 ATGTTAAATGGTACTGGAATTTGTTGAGTTTGATATGCGCGTTCTTTTT
1 ATGTTAAATGGTACTGGAATTTGTTGAGTTTGATATGCGCGTTCTTTTT
5319145 ATGTTAAATGGTACTGGAATTTGTTGAGTTTGATATGCGCGTTCTTTTT
1 ATGTTAAATGGTACTGGAATTTGTTGAGTTTGATATGCGCGTTCTTTTT
5319194 TTAAAGCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.47
Consensus pattern (49 bp):
ATGTTAAATGGTACTGGAATTTGTTGAGTTTGATATGCGCGTTCTTTTT
Found at i:5326750 original size:57 final size:59
Alignment explanation
Indices: 5326661--5326781 Score: 210
Period size: 57 Copynumber: 2.1 Consensus size: 59
5326651 GACATAAATA
5326661 TTAAAATAAAAATATTTTTAAAGATATGAAAATTTGGTGGATTGTG-TTTTTTATGTAT
1 TTAAAATAAAAATATTTTTAAAGATATGAAAATTTGGTGGATTGTGTTTTTTTATGTAT
* *
5326719 TTAAAATATAAATA-TTTTAAAGGTATGAAAATTTGGTGGATTGTGTTTTTTTATGTAT
1 TTAAAATAAAAATATTTTTAAAGATATGAAAATTTGGTGGATTGTGTTTTTTTATGTAT
5326777 TTAAA
1 TTAAA
5326782 TAGTGAAATT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
57 30 0.50
58 30 0.50
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (59 bp):
TTAAAATAAAAATATTTTTAAAGATATGAAAATTTGGTGGATTGTGTTTTTTTATGTAT
Found at i:5331824 original size:63 final size:63
Alignment explanation
Indices: 5331725--5331851 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
5331715 AATGTACATT
5331725 GTCTTTTTTATGGGTGGAAAGATTGTGGAGATTTAGACATAATTTTTATGACTTCCAAAATGA
1 GTCTTTTTTATGGGTGGAAAGATTGTGGAGATTTAGACATAATTTTTATGACTTCCAAAATGA
5331788 GTCTTTTTTATGGGTGGAAAGATTGTGGAGATTTAGACATAATTTTTATGACTTCCAAAATGA
1 GTCTTTTTTATGGGTGGAAAGATTGTGGAGATTTAGACATAATTTTTATGACTTCCAAAATGA
5331851 G
1 G
5331852 GGATAAGTAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (63 bp):
GTCTTTTTTATGGGTGGAAAGATTGTGGAGATTTAGACATAATTTTTATGACTTCCAAAATGA
Found at i:5334801 original size:34 final size:34
Alignment explanation
Indices: 5334763--5334842 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 34
5334753 CAATTTATTT
* *
5334763 AACTAGTGTTGGGC-ACACATTCGTTGGTTTATCC
1 AACTAGAGTTGGGCGAAACATT-GTTGGTTTATCC
* * *
5334797 AACTAGCGCTGGGCGTAAATATTGTTGGTTTATCC
1 AACTAGAGTTGGGCG-AAACATTGTTGGTTTATCC
5334832 AACTAGAGTTG
1 AACTAGAGTTG
5334843 AGCTCACTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 12 0.32
35 21 0.55
36 5 0.13
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (34 bp):
AACTAGAGTTGGGCGAAACATTGTTGGTTTATCC
Found at i:5336493 original size:75 final size:75
Alignment explanation
Indices: 5336388--5336545 Score: 212
Period size: 81 Copynumber: 2.1 Consensus size: 75
5336378 CTGTTGTATT
* *
5336388 TTGGACTTTTGCTTATGTTTTTTATTATAATCTTG-TTG-TGTTGTTGTTGTTTACTTCGACTCA
1 TTGGACTTTTGCTTATGTTTTTTATTATAATCTTGTTTGTTGTTGTTATTGTTTACTTAGACTCA
5336451 TGTTGTTTAC
66 TGTTGTTTAC
*
5336461 TTGGATTTTTGCTTATGTTTTTTTTATTATAATCTTGTTCTATTGTTGTTGTTATTGTTTACTTA
1 TTGGACTTTTGCTTATG--TTTTTTATTATAATCTTG---T-TTGTTGTTGTTATTGTTTACTTA
*
5336526 GACTCATGTTGTTTAT
60 GACTCATGTTGTTTAC
5336542 TTGG
1 TTGG
5336546 GCTGATATTA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
73 16 0.22
75 18 0.25
80 3 0.04
81 36 0.49
ACGTcount: A:0.15, C:0.09, G:0.17, T:0.59
Consensus pattern (75 bp):
TTGGACTTTTGCTTATGTTTTTTATTATAATCTTGTTTGTTGTTGTTATTGTTTACTTAGACTCA
TGTTGTTTAC
Found at i:5336942 original size:31 final size:31
Alignment explanation
Indices: 5336889--5336968 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
5336879 AATCTGTCAT
* * * * *
5336889 CCCGGATTGCCTGGCTATGATGACCTATCAC
1 CCCGAATTGCCTGACAACGATGACCTACCAC
*
5336920 CCCGGATTG-CTCGACAACGATGACCTACCAC
1 CCCGAATTGCCT-GACAACGATGACCTACCAC
*
5336951 CTCGAATTGCCTGACAAC
1 CCCGAATTGCCTGACAAC
5336969 TATGGTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 2 0.05
31 37 0.90
32 2 0.05
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (31 bp):
CCCGAATTGCCTGACAACGATGACCTACCAC
Found at i:5346310 original size:7 final size:8
Alignment explanation
Indices: 5346293--5346358 Score: 55
Period size: 8 Copynumber: 7.8 Consensus size: 8
5346283 CTAATTTTTT
5346293 AAATATAA
1 AAATATAA
5346301 AAAT-TAAA
1 AAATAT-AA
5346309 AAAGTATAA
1 AAA-TATAA
5346318 AAATATTAA
1 AAATA-TAA
5346327 AAA-ATTCAAA
1 AAATA-T--AA
5346337 AAATATAA
1 AAATATAA
*
5346345 AAATATGA
1 AAATATAA
5346353 AAATAT
1 AAATAT
5346359 TTTTAATTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
7 1 0.02
8 29 0.58
9 12 0.24
10 7 0.14
11 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.26
Consensus pattern (8 bp):
AAATATAA
Found at i:5346319 original size:9 final size:9
Alignment explanation
Indices: 5346293--5346347 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
5346283 CTAATTTTTT
5346293 AAATAT-AA
1 AAATATAAA
5346301 AAAT-TAAA
1 AAATATAAA
5346309 AAAGTAT-AA
1 AAA-TATAAA
5346318 AAATATTAAA
1 AAATA-TAAA
5346328 AAAT-TCAAA
1 AAATAT-AAA
5346337 AAATATAAA
1 AAATATAAA
5346346 AA
1 AA
5346348 TATGAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
7 1 0.03
8 12 0.30
9 19 0.47
10 8 0.20
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (9 bp):
AAATATAAA
Found at i:5346327 original size:19 final size:18
Alignment explanation
Indices: 5346293--5346359 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 18
5346283 CTAATTTTTT
5346293 AAATAT-AAAA-ATTAAA
1 AAATATAAAAATATTAAA
5346309 AAAGTATAAAAATATTAAA
1 AAA-TATAAAAATATTAAA
5346328 AAAT-TCAAAAA-A-TATAA
1 AAATAT-AAAAATATTA-AA
*
5346345 AAATATGAAAATATT
1 AAATATAAAAATATT
5346360 TTTAATTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.12
17 15 0.36
18 12 0.29
19 10 0.24
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (18 bp):
AAATATAAAAATATTAAA
Found at i:5346337 original size:27 final size:27
Alignment explanation
Indices: 5346299--5346355 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
5346289 TTTTAAATAT
* *
5346299 AAAAATTAAAAAAGTATAAAAATATTA
1 AAAAATTAAAAAAATATAAAAATATGA
*
5346326 AAAAATTCAAAAAATATAAAAATATGA
1 AAAAATTAAAAAAATATAAAAATATGA
5346353 AAA
1 AAA
5346356 TATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAAATTAAAAAAATATAAAAATATGA
Found at i:5349899 original size:2 final size:2
Alignment explanation
Indices: 5349894--5349974 Score: 57
Period size: 2 Copynumber: 42.5 Consensus size: 2
5349884 ATATAATAAA
* * *
5349894 AT AT AT AT A- AT GAT AT AT AT AT AT AT AT AT AT A- AC AT TT TT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5349935 A- AC AT A- AT GAT AT AT A- AT AT AT AT AT AT AT TT AT -T AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5349974 A
1 A
5349975 ATTACATATT
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
1 6 0.09
2 55 0.85
3 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5349899 original size:22 final size:22
Alignment explanation
Indices: 5349866--5349927 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
5349856 ATATAAATAA
* *
5349866 AATAATAAATATGTAATTATAT
1 AATAATAAATATATAATGATAT
5349888 AATAA-AATATATATAATGATAT
1 AATAATAA-ATATATAATGATAT
*
5349910 ATATATATATATATATAA
1 A-ATA-ATAAATATATAA
5349928 CATTTTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 18 0.55
23 3 0.09
24 9 0.27
25 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
AATAATAAATATATAATGATAT
Found at i:5349902 original size:14 final size:14
Alignment explanation
Indices: 5349883--5349916 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5349873 AATATGTAAT
5349883 TATATAATAAAATA
1 TATATAATAAAATA
* *
5349897 TATATAATGATATA
1 TATATAATAAAATA
5349911 TATATA
1 TATATA
5349917 TATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
TATATAATAAAATA
Found at i:5350539 original size:9 final size:9
Alignment explanation
Indices: 5350503--5350570 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 9
5350493 ACATGTGACA
*
5350503 AAAAACTAT
1 AAAAATTAT
5350512 AAAAA--AT
1 AAAAATTAT
*
5350519 AAAAATCAAT
1 AAAAAT-TAT
5350529 AAAAATTAT
1 AAAAATTAT
*
5350538 AAAAAATTGT
1 -AAAAATTAT
**
5350548 AAACTTTTAT
1 AAA-AATTAT
5350558 AAAAATTAT
1 AAAAATTAT
5350567 AAAA
1 AAAA
5350571 TACATCAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
7 7 0.15
9 18 0.38
10 22 0.47
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5350785 original size:20 final size:20
Alignment explanation
Indices: 5350760--5350830 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
5350750 GTATGATATT
5350760 TTTTATAATTTTTTTACAAA
1 TTTTATAATTTTTTTACAAA
* *
5350780 TTTTAT-ATTTCTTTA-AAT
1 TTTTATAATTTTTTTACAAA
* **
5350798 TTTTATACTTTTCCTACAAA
1 TTTTATAATTTTTTTACAAA
*
5350818 TTTATAAAATTTT
1 TTT-TATAATTTT
5350831 ATAATCTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 8 0.21
19 13 0.33
20 11 0.28
21 7 0.18
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATAATTTTTTTACAAA
Found at i:5350893 original size:19 final size:19
Alignment explanation
Indices: 5350869--5350919 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
5350859 TTTATAATTT
5350869 TTTTACGATTTTTATAAAA
1 TTTTACGATTTTTATAAAA
*
5350888 TTTTAC-AATTTTATAAAA
1 TTTTACGATTTTTATAAAA
*
5350906 TTTTAAGATTTTTA
1 TTTTACGATTTTTA
5350920 AGATTTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 16 0.57
19 12 0.43
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTTACGATTTTTATAAAA
Found at i:5350989 original size:30 final size:28
Alignment explanation
Indices: 5350917--5350989 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 28
5350907 TTTAAGATTT
*
5350917 TTAAG-ATTTTTCTATTTTTTAATAAAA
1 TTAAGTATTTTTATATTTTTTAATAAAA
*
5350944 TTAAGTATTTGTTATAGTTTTTTATTAAAA
1 TTAAGTATTT-TTATA-TTTTTTAATAAAA
5350974 TTTAA-TAATTTTTATA
1 -TTAAGT-ATTTTTATA
5350990 ACTTTTATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 5 0.13
28 4 0.10
29 4 0.10
30 18 0.46
31 8 0.21
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (28 bp):
TTAAGTATTTTTATATTTTTTAATAAAA
Found at i:5351245 original size:85 final size:82
Alignment explanation
Indices: 5351080--5351277 Score: 202
Period size: 85 Copynumber: 2.3 Consensus size: 82
5351070 ATTTGGGATG
* * ****
5351080 GTTCAAGTACCAATTGAGTGCAAAAAGAATCAGGGCTTAATTGTTTTTTTTTTAATTTGAGGACC
1 GTTCAAGTACCAATTGAGTG-AAAAA-AAGCAGGGCTTAATTGCTTTTTGAAGAATTTGAGGACC
*
5351145 TTTTTTTATGCATTTTGAAA
64 TTTTTATAT-CATTTTGAAA
*
5351165 GTTCAAGTACCCAATTGAGTGAAAAAAAGCAGGGCTTAATTGCCTTTTTGAAGAAGTTTGAATG-
1 GTTCAAGTA-CCAATTGAGTGAAAAAAAGCAGGGCTTAATTG-CTTTTTGAAGAA-TTTG-AGGA
*
5351229 CCTTTTTGATAT-ATTTTGACA
62 CCTTTTT-ATATCATTTTGAAA
* *
5351250 GTTCAAGTATCAAATAGAGTGAAAAAAA
1 GTTCAAGTA-CCAATTGAGTGAAAAAAA
5351278 TTTAATTGCT
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
84 15 0.16
85 54 0.56
86 22 0.23
87 5 0.05
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (82 bp):
GTTCAAGTACCAATTGAGTGAAAAAAAGCAGGGCTTAATTGCTTTTTGAAGAATTTGAGGACCTT
TTTATATCATTTTGAAA
Found at i:5361631 original size:16 final size:16
Alignment explanation
Indices: 5361610--5361643 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5361600 GCAACTGATT
*
5361610 AAGTATATATTTTTTA
1 AAGTATATATATTTTA
5361626 AAGTATATATATTTTA
1 AAGTATATATATTTTA
5361642 AA
1 AA
5361644 AATTATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AAGTATATATATTTTA
Found at i:5363877 original size:17 final size:18
Alignment explanation
Indices: 5363855--5363889 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5363845 GGTTTAGGGT
5363855 TTAAAA-ATTTTAATTAA
1 TTAAAATATTTTAATTAA
*
5363872 TTAAAATTTTTTAATTAA
1 TTAAAATATTTTAATTAA
5363890 AGATTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAAAATATTTTAATTAA
Found at i:5363887 original size:14 final size:15
Alignment explanation
Indices: 5363858--5363895 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
5363848 TTAGGGTTTA
5363858 AAAATTTTAATTAATT
1 AAAATTTT-ATTAATT
5363874 AAAATTTT-TTAATT
1 AAAATTTTATTAATT
5363888 AAAGATTT
1 AAA-ATTT
5363896 ATTCTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AAAATTTTATTAATT
Found at i:5364037 original size:15 final size:15
Alignment explanation
Indices: 5364017--5364062 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5364007 ACAAAATACT
5364017 AACATAAGTGACTAA
1 AACATAAGTGACTAA
* *
5364032 AACATAA-T-ATTTCA
1 AACATAAGTGA-CTAA
5364046 AACATAAGTGACTAA
1 AACATAAGTGACTAA
5364061 AA
1 AA
5364063 TGTAACCTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (15 bp):
AACATAAGTGACTAA
Found at i:5365223 original size:19 final size:20
Alignment explanation
Indices: 5365200--5365286 Score: 97
Period size: 20 Copynumber: 4.2 Consensus size: 20
5365190 AAAATTACAA
*
5365200 AAAAAATCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
5365220 AAAAATTAAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
5365240 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTTT
5365258 AAAAATTCTAAAATTTATATTTTT
1 AAAAATTC-AAAA--TA-ATTTTT
5365282 AAAAA
1 AAAAA
5365287 AATTATATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
18 5 0.09
19 18 0.32
20 22 0.39
22 1 0.02
24 10 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:5365231 original size:20 final size:20
Alignment explanation
Indices: 5365208--5365264 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
5365198 AAAAAAAATC
5365208 AAAATAATTTTTAAAAATTA
1 AAAATAATTTTTAAAAATTA
*
5365228 AAAATAATTTTT-AAAATTC
1 AAAATAATTTTTAAAAATTA
*
5365247 AAAAT-ATTTATAAAAATT
1 AAAATAATTTTTAAAAATT
5365265 CTAAAATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 5 0.15
19 17 0.50
20 12 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAATTTTTAAAAATTA
Found at i:5365273 original size:18 final size:19
Alignment explanation
Indices: 5365200--5365276 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 19
5365190 AAAATTACAA
* *
5365200 AAAAAATCAAAATAATTTTT
1 AAAAATTCAAAAT-ATTTAT
*
5365220 AAAAATTAAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
5365239 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
5365258 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
5365276 A
1 A
5365277 TTTTTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.22
19 23 0.46
20 16 0.32
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:5365445 original size:16 final size:16
Alignment explanation
Indices: 5365426--5365456 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5365416 TTAAAACAGT
5365426 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
5365442 TTTCAAATTTATATG
1 TTTCAAATATATATG
5365457 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:5369835 original size:18 final size:18
Alignment explanation
Indices: 5369812--5369846 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5369802 AAATAAATAG
5369812 TATATATA-ATGATGTATC
1 TATATATATAT-ATGTATC
5369830 TATATATATATATGTAT
1 TATATATATATATGTAT
5369847 AAATGGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (18 bp):
TATATATATATATGTATC
Found at i:5375110 original size:6 final size:6
Alignment explanation
Indices: 5375090--5375196 Score: 87
Period size: 6 Copynumber: 18.2 Consensus size: 6
5375080 CTAAACCCAT
* ** **
5375090 TTTAAA TTT-AT TTTAAA TTTAAA TTTATT TTTAAA TTTATT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * *
5375137 TTTAAA TTT-GT TTTAAAA TTTAAA TTTATA TTTAAA TTTAAA ATT--A
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5375183 TTCTAAA TTTAAA T
1 TT-TAAA TTTAAA T
5375197 GATGAAAGTC
Statistics
Matches: 77, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
4 2 0.03
5 8 0.10
6 61 0.79
7 6 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:5375121 original size:18 final size:17
Alignment explanation
Indices: 5375090--5375196 Score: 125
Period size: 18 Copynumber: 6.4 Consensus size: 17
5375080 CTAAACCCAT
5375090 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
5375107 TTTAAATTTA--TT---
1 TTTAAATTTATTTTAAA
5375119 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
5375137 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
5375155 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
5375173 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
5375190 TTTAAAT
1 TTTAAAT
5375197 GATGAAAGTC
Statistics
Matches: 77, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
12 10 0.13
15 4 0.05
17 25 0.32
18 35 0.45
19 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5375136 original size:30 final size:29
Alignment explanation
Indices: 5375089--5375176 Score: 122
Period size: 30 Copynumber: 3.0 Consensus size: 29
5375079 ACTAAACCCA
5375089 TTTTAAATTTATTTTAAATTTAAATTTAT
1 TTTTAAATTTATTTTAAATTTAAATTTAT
*
5375118 TTTTAAATTTATTTTTAAATTTAAATTTGT
1 TTTTAAATTTA-TTTTAAATTTAAATTTAT
* * *
5375148 TTTAAAATTTAAATTTATATTTAAATTTA
1 TTTTAAATTT-ATTTTAAATTTAAATTTA
5375177 AAATTATTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 11 0.21
30 40 0.77
31 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTAAATTTATTTTAAATTTAAATTTAT
Found at i:5377044 original size:29 final size:29
Alignment explanation
Indices: 5377011--5377242 Score: 165
Period size: 29 Copynumber: 8.0 Consensus size: 29
5377001 TTGACCCTCG
*
5377011 AAACTTTTAAAAATTACCATTTTACCCCC
1 AAACTTTCAAAAATTACCATTTTACCCCC
*
5377040 AAACTTCCAAAAATTA-CATTTTAACCCCC
1 AAACTTTCAAAAATTACCATTTT-ACCCCC
* * *
5377069 AAACATTCCAAAATT-CCATTTTAACCCC
1 AAACTTTCAAAAATTACCATTTTACCCCC
*
5377097 AAACTTTCCAAAAATTA-CATTTTTACCCTC
1 AAACTTT-CAAAAATTACCA-TTTTACCCCC
* * * **
5377127 AAA-TCATCCAAAA-TCCCATTTTTAACCCTG
1 AAACT-TTCAAAAATTACCA-TTTT-ACCCCC
* * **
5377157 AACCTTCCAAAAATTACCATTTTACCCTT
1 AAACTTTCAAAAATTACCATTTTACCCCC
* * *
5377186 AAA-TGTCCAAAA-TACCATTTTTGA-CCCT
1 AAACTTTCAAAAATTACCA-TTTT-ACCCCC
5377214 AAACTTTTCAAAAATTACCATTTTACCCC
1 AAAC-TTTCAAAAATTACCATTTTACCCC
5377243 GATTGTCCAA
Statistics
Matches: 160, Mismatches: 27, Indels: 31
0.73 0.12 0.14
Matches are distributed among these distances:
27 5 0.03
28 34 0.21
29 69 0.43
30 42 0.26
31 10 0.06
ACGTcount: A:0.38, C:0.29, G:0.01, T:0.32
Consensus pattern (29 bp):
AAACTTTCAAAAATTACCATTTTACCCCC
Found at i:5377165 original size:59 final size:59
Alignment explanation
Indices: 5377020--5377241 Score: 242
Period size: 58 Copynumber: 3.8 Consensus size: 59
5377010 GAAACTTTTA
* * *
5377020 AAAATTACCA-TTTTACCCCCAAA-CTTCCAAAAATTA-CATTTTAACCCCCAAA-CATTCC
1 AAAA-TACCATTTTTAACCCTAAACCTTCCAAAAATTACCATTTT-ACCCTCAAATCA-TCC
* * *
5377078 AAAATTCCA-TTTTAACCCCAAACTTTCCAAAAATTA-CATTTTTACCCTCAAATCATCC
1 AAAATACCATTTTTAACCCTAAACCTTCCAAAAATTACCA-TTTTACCCTCAAATCATCC
* * * *
5377136 AAAATCCCATTTTTAACCCTGAACCTTCCAAAAATTACCATTTTACCCTTAAAT-GTCC
1 AAAATACCATTTTTAACCCTAAACCTTCCAAAAATTACCATTTTACCCTCAAATCATCC
* * *
5377194 AAAATACCATTTTTGACCCTAAACTTTTCAAAAATTACCATTTTACCC
1 AAAATACCATTTTTAACCCTAAACCTTCCAAAAATTACCATTTTACCC
5377242 CGATTGTCCA
Statistics
Matches: 144, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
57 16 0.11
58 83 0.58
59 43 0.30
60 2 0.01
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.32
Consensus pattern (59 bp):
AAAATACCATTTTTAACCCTAAACCTTCCAAAAATTACCATTTTACCCTCAAATCATCC
Found at i:5380047 original size:24 final size:22
Alignment explanation
Indices: 5379999--5380103 Score: 74
Period size: 24 Copynumber: 4.7 Consensus size: 22
5379989 AAAAATACAT
5379999 AAAAATAACATCC--AA-ACAAC
1 AAAAATAACA-CCAAAACACAAC
*
5380019 CAAAATAACTACCAAAACAGCAAC
1 AAAAATAAC-ACCAAAACA-CAAC
* * *
5380043 AAAAATAACAGCAAAATA-AAA
1 AAAAATAACACCAAAACACAAC
* *
5380064 AAAAATAGCAACAAAAACATCAAC
1 AAAAATAAC-ACCAAAACA-CAAC
*
5380088 AAAAATAACAGCAAAA
1 AAAAATAACACCAAAA
5380104 ATAGCACCAA
Statistics
Matches: 64, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
20 10 0.16
21 11 0.17
22 8 0.12
23 13 0.20
24 22 0.34
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.09
Consensus pattern (22 bp):
AAAAATAACACCAAAACACAAC
Found at i:5380057 original size:12 final size:12
Alignment explanation
Indices: 5380013--5380106 Score: 77
Period size: 12 Copynumber: 8.1 Consensus size: 12
5380003 ATAACATCCA
*
5380013 AACAACCAAAAT
1 AACAACAAAAAT
* * *
5380025 AACTACCAAAAC
1 AACAACAAAAAT
*
5380037 AGCAACAAAAAT
1 AACAACAAAAAT
*
5380049 AACAGC-AAAAT
1 AACAACAAAAAT
5380060 AA-AA-AAAAAT
1 AACAACAAAAAT
* *
5380070 AGCAACAAAAAC
1 AACAACAAAAAT
*
5380082 ATCAACAAAAAT
1 AACAACAAAAAT
*
5380094 AACAGCAAAAAT
1 AACAACAAAAAT
5380106 A
1 A
5380107 GCACCAAAAC
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
10 7 0.11
11 9 0.14
12 48 0.75
ACGTcount: A:0.68, C:0.19, G:0.04, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:5380091 original size:33 final size:33
Alignment explanation
Indices: 5380032--5380148 Score: 92
Period size: 33 Copynumber: 3.5 Consensus size: 33
5380022 AATAACTACC
* * *
5380032 AAAACAGCAACAAAAATAACAGCAAAATAAAAA
1 AAAATAGCAACAAAAACAACAACAAAATAAAAA
* *
5380065 AAAATAGCAACAAAAACATCAACAAAAATAACAGCA
1 AAAATAGCAACAAAAACAACAAC-AAAATAA-A-AA
* * * **
5380101 AAAATAGC-ACCAAAACAGCAACCAAAACAGTAA
1 AAAATAGCAACAAAAACAACAA-CAAAATAAAAA
*
5380134 AAAATAGCACCAAAA
1 AAAATAGCAACAAAA
5380149 TAATAATATA
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
33 28 0.42
34 11 0.17
35 17 0.26
36 10 0.15
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (33 bp):
AAAATAGCAACAAAAACAACAACAAAATAAAAA
Found at i:5380114 original size:12 final size:12
Alignment explanation
Indices: 5380064--5380148 Score: 52
Period size: 12 Copynumber: 7.3 Consensus size: 12
5380054 CAAAATAAAA
*
5380064 AAAAATAGCAAC
1 AAAAATAGCACC
* * *
5380076 AAAAACATCAAC
1 AAAAATAGCACC
* *
5380088 AAAAATAACAGC
1 AAAAATAGCACC
5380100 AAAAATAGCACC
1 AAAAATAGCACC
*
5380112 -AAAACAGCAACC
1 AAAAATAGC-ACC
* *
5380124 -AAAACAGTA--
1 AAAAATAGCACC
5380133 AAAAATAGCACC
1 AAAAATAGCACC
5380145 AAAA
1 AAAA
5380149 TAATAATATA
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
10 7 0.12
11 8 0.14
12 43 0.74
ACGTcount: A:0.65, C:0.21, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAATAGCACC
Found at i:5380114 original size:24 final size:24
Alignment explanation
Indices: 5380015--5380115 Score: 86
Period size: 24 Copynumber: 4.3 Consensus size: 24
5380005 AACATCCAAA
* *
5380015 CAACCAAAATAACTA-CCAAAACAG
1 CAACAAAAATAAC-AGCAAAAACAG
5380039 CAACAAAAATAACAGCAAAATA-A-
1 CAACAAAAATAACAGCAAAA-ACAG
* * *
5380062 -AA-AAAAATAGCAACAAAAACAT
1 CAACAAAAATAACAGCAAAAACAG
*
5380084 CAACAAAAATAACAGCAAAAATAG
1 CAACAAAAATAACAGCAAAAACAG
*
5380108 CACCAAAA
1 CAACAAAA
5380116 CAGCAACCAA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 15 0.24
22 2 0.03
23 3 0.05
24 40 0.65
25 1 0.02
ACGTcount: A:0.66, C:0.21, G:0.05, T:0.08
Consensus pattern (24 bp):
CAACAAAAATAACAGCAAAAACAG
Found at i:5380806 original size:167 final size:170
Alignment explanation
Indices: 5380510--5380878 Score: 390
Period size: 167 Copynumber: 2.2 Consensus size: 170
5380500 TAAACATGTT
* * * * * *
5380510 TTTTTTAAATTGTACTTAAAAAGTTTTATTTTATACCTAAGAATTATAGATAATTTTTTATAATG
1 TTTTTT-AACTGTACTTAAAAAG--TT-TTTTATA-ATAAAAAGTATAAATAAATTTTTATAATG
* *
5380575 TATAATTTAAACATTCTGGAAGTATTTCAATATAATATTAGAAACCCCACTTCTAGAAGTTTTTT
61 TACAATTTAAACATTCTGGAAGTATTTCAATATAATATTAGAAACCACACTTCTAGAAG-TTTTT
* *
5380640 TTCTTTATTTCAATGAAG-GGA-TTTGT-TTTTACACTTAAA-ATA
125 TTCTCTATTTAAATGAAGTGGATTTTGTATTTTACACTTAAACATA
* *
5380682 TTTTTTAAACTGTACTTAGATAGTTTTTTATAATAAAAAGTATAAATAAATTTTTA-AATGTACA
1 TTTTTT-AACTGTACTTAAAAAGTTTTTTATAATAAAAAGTATAAATAAATTTTTATAATGTACA
* ** * ** ** * *
5380746 GTTTAAACATTCTGTCATTATTTCAATATAATATTAGAAATGATGCTTGT-GTAGGTTTTTTTCT
65 ATTTAAACATTCTGGAAGTATTTCAATATAATATTAGAAACCACACTTCTAG-AAGTTTTTTTCT
* *
5380810 CTATTTAAATGAAGTGTATTTTTTTATTTTACACTTAAACATA
129 CTATTTAAATGAAGTGGA-TTTTGTATTTTACACTTAAACATA
*
5380853 TTTTTTAATTGTACTTAAAAAGTTTT
1 TTTTTTAACTGTACTTAAAAAGTTTT
5380879 ATTTTATACT
Statistics
Matches: 164, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
166 22 0.13
167 51 0.31
168 19 0.12
169 11 0.07
170 32 0.20
171 9 0.05
172 20 0.12
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.47
Consensus pattern (170 bp):
TTTTTTAACTGTACTTAAAAAGTTTTTTATAATAAAAAGTATAAATAAATTTTTATAATGTACAA
TTTAAACATTCTGGAAGTATTTCAATATAATATTAGAAACCACACTTCTAGAAGTTTTTTTCTCT
ATTTAAATGAAGTGGATTTTGTATTTTACACTTAAACATA
Found at i:5382314 original size:6 final size:6
Alignment explanation
Indices: 5382303--5382385 Score: 75
Period size: 6 Copynumber: 14.2 Consensus size: 6
5382293 TTTAAATTAT
** *
5382303 TTTAAA TTTAAA TTT-GT TTTAAAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
5382350 TTTATA TTTAAA TTTAAA ATT--A TTCTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA T
5382386 GATGAAAGTC
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
4 2 0.03
5 9 0.15
6 44 0.72
7 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:5382329 original size:18 final size:17
Alignment explanation
Indices: 5382293--5382385 Score: 116
Period size: 18 Copynumber: 5.4 Consensus size: 17
5382283 CTAAACCCAT
5382293 TTTAAA-TTATTTTAAA
1 TTTAAATTTATTTTAAA
*
5382309 TTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
5382327 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
5382344 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
5382362 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
5382379 TTTAAAT
1 TTTAAAT
5382386 GATGAAAGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
16 6 0.09
17 29 0.45
18 30 0.46
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5382348 original size:35 final size:34
Alignment explanation
Indices: 5382293--5382385 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 34
5382283 CTAAACCCAT
* *
5382293 TTTAAATTATTTTAAATTTAAATTTGT-TTTAAAA
1 TTTAAATTAATTTAAATTTAAATTTATATTT-AAA
*
5382327 TTTAAATTTAATTTAAGTTTAAATTTATATTTAAA
1 TTTAAA-TTAATTTAAATTTAAATTTATATTTAAA
5382362 TTTAAAATT-ATTCTAAATTTAAAT
1 TTT-AAATTAATT-TAAATTTAAAT
5382386 GATGAAAGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
34 9 0.18
35 36 0.71
36 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (34 bp):
TTTAAATTAATTTAAATTTAAATTTATATTTAAA
Found at i:5382365 original size:24 final size:26
Alignment explanation
Indices: 5382303--5382366 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 26
5382293 TTTAAATTAT
5382303 TTTAAATTTAAATTT--GTTTTAAAA
1 TTTAAATTTAAATTTAAGTTTTAAAA
5382327 TTTAAATTT-AATTTAAG-TTT-AAA
1 TTTAAATTTAAATTTAAGTTTTAAAA
*
5382350 TTTATATTTAAATTTAA
1 TTTAAATTTAAATTTAA
5382367 AATTATTCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 16 0.44
24 19 0.53
25 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTAAATTTAAATTTAAGTTTTAAAA
Found at i:5384221 original size:28 final size:27
Alignment explanation
Indices: 5384189--5384416 Score: 140
Period size: 28 Copynumber: 8.0 Consensus size: 27
5384179 TTGACCCTCG
**
5384189 AAACTTTTGAAAATTACCATTTTACCCC
1 AAACTTTCCAAAATTA-CATTTTACCCC
5384217 AAAC-TTCCAAAAATTACATTTTTACCCC
1 AAACTTTCC-AAAATTACA-TTTTACCCC
* * *
5384245 AAACATTCCAAAATTCCATTTTAACCCT
1 AAACTTTCCAAAATTACATTTT-ACCCC
*
5384273 GAACTTTCCAAAATTTACATTTTACCCC
1 AAACTTTCCAAAA-TTACATTTTACCCC
**
5384301 TAAA-TCTTCCAAAATCCCATTTTTAACCCC
1 -AAACT-TTCCAAAATTACA-TTTT-ACCCC
* *
5384331 GAACCTTCCAAAAATTACTATTTTACCCC
1 AAACTTTCC-AAAATTAC-ATTTTACCCC
* * *
5384360 TAGA-TGTCCAAAA-TACCATTTTTGACCCT
1 -AAACTTTCCAAAATTA-CA-TTTT-ACCCC
* *
5384389 AAACTTTTCAAAAATCACCATTTTACCC
1 AAAC-TTTCCAAAATTA-CATTTTACCC
5384417 TCGGATGTCC
Statistics
Matches: 157, Mismatches: 24, Indels: 37
0.72 0.11 0.17
Matches are distributed among these distances:
27 11 0.07
28 66 0.42
29 48 0.31
30 27 0.17
31 5 0.03
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.33
Consensus pattern (27 bp):
AAACTTTCCAAAATTACATTTTACCCC
Found at i:5384310 original size:29 final size:26
Alignment explanation
Indices: 5384198--5384359 Score: 144
Period size: 28 Copynumber: 5.7 Consensus size: 26
5384188 GAAACTTTTG
5384198 AAAATTACCATTTTACCCCAAACTTCC
1 AAAATTA-CATTTTACCCCAAACTTCC
5384225 AAAAATTACATTTTTACCCCAAACATTCC
1 -AAAATTACA-TTTTACCCCAAAC-TTCC
* **
5384254 AAAATTCCATTTTAACCCTGAACTTTCC
1 AAAATTACATTTT-ACCCCAAAC-TTCC
5384282 AAAATTTACATTTTACCCCTAAATCTTCC
1 AAAA-TTACATTTTACCCC-AAA-CTTCC
** *
5384311 AAAATCCCATTTTTAACCCCGAACCTTCC
1 AAAATTACA-TTTT-ACCCC-AAACTTCC
5384340 AAAAATTACTATTTTACCCC
1 -AAAATTAC-ATTTTACCCC
5384360 TAGATGTCCA
Statistics
Matches: 111, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
27 6 0.05
28 50 0.45
29 36 0.32
30 18 0.16
31 1 0.01
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (26 bp):
AAAATTACATTTTACCCCAAACTTCC
Found at i:5384370 original size:58 final size:57
Alignment explanation
Indices: 5384198--5384430 Score: 208
Period size: 58 Copynumber: 4.1 Consensus size: 57
5384188 GAAACTTTTG
* * *
5384198 AAAATTACCA-TTTT-ACCCC-AAACTTCCAAAAATTACATTTTTACCCCAAACAT-TCC
1 AAAA-TACCATTTTTAACCCCGAACCTTCCAAAAATTACA-TTTTACCCC-TAGATGTCC
* * * * * *
5384254 AAAATTCCA-TTTTAACCCTGAACTTTCCAAAATTTACATTTTACCCCTAAATCTTCC
1 AAAATACCATTTTTAACCCCGAACCTTCCAAAAATTACATTTTACCCCTAGAT-GTCC
*
5384311 AAAATCCCATTTTTAACCCCGAACCTTCCAAAAATTACTATTTTACCCCTAGATGTCC
1 AAAATACCATTTTTAACCCCGAACCTTCCAAAAATTAC-ATTTTACCCCTAGATGTCC
* ** * * * *
5384369 AAAATACCATTTTTGACCCTAAACTTTTCAAAAATCACCATTTTA-CCCTCGGATGTCC
1 AAAATACCATTTTTAACCCCGAACCTTCCAAAAATTA-CATTTTACCCCT-AGATGTCC
5384427 AAAA
1 AAAA
5384431 ATTCCGTTTT
Statistics
Matches: 148, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
55 11 0.07
56 17 0.11
57 30 0.20
58 75 0.51
59 15 0.10
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (57 bp):
AAAATACCATTTTTAACCCCGAACCTTCCAAAAATTACATTTTACCCCTAGATGTCC
Found at i:5384467 original size:58 final size:57
Alignment explanation
Indices: 5384311--5384487 Score: 155
Period size: 58 Copynumber: 3.1 Consensus size: 57
5384301 TAAATCTTCC
* * ** * *
5384311 AAAATCCCATTTTTAACCCCGAAC-CTTCCAAAAATTACTATTTTACCCCTAGATGTCC-
1 AAAATACCATTTTTGACCCTAAACTCTT-CAAAAA-TACCATTTTACCCC-GGATGTCCA
*
5384369 AAAATACCATTTTTGACCCTAAACTTTTCAAAAATCACCATTTTACCCTCGGATGTCCA
1 AAAATACCATTTTTGACCCTAAACTCTTCAAAAAT-ACCATTTTACCC-CGGATGTCCA
* * * * *
5384428 AAAATTCCGTTTTTG-CCCTCGAAGTCTTCAAAAATACCATTTTAACCCCGG-TATCCA
1 AAAATACCATTTTTGACCCT-AAACTCTTCAAAAATACCATTTT-ACCCCGGATGTCCA
5384485 AAA
1 AAA
5384488 TCATATTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
57 9 0.09
58 59 0.59
59 32 0.32
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.31
Consensus pattern (57 bp):
AAAATACCATTTTTGACCCTAAACTCTTCAAAAATACCATTTTACCCCGGATGTCCA
Found at i:5384470 original size:29 final size:29
Alignment explanation
Indices: 5384369--5384470 Score: 75
Period size: 29 Copynumber: 3.4 Consensus size: 29
5384359 CTAGATGTCC
* * *
5384369 AAAATACCATTTTTGACCCT-AAACTTTTCA
1 AAAATACCA-TTTTG-CCCTCGAAGTCTTCA
* *
5384399 AAAATCACCATTTTACCCTCGGATGTC--CA
1 AAAAT-ACCATTTTGCCCTC-GAAGTCTTCA
* *
5384428 AAAATTCCGTTTTTGCCCTCGAAGTCTTCA
1 AAAATACC-ATTTTGCCCTCGAAGTCTTCA
5384458 AAAATACCATTTT
1 AAAATACCATTTT
5384471 AACCCCGGTA
Statistics
Matches: 55, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
28 7 0.13
29 24 0.44
30 18 0.33
31 6 0.11
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAATACCATTTTGCCCTCGAAGTCTTCA
Found at i:5387207 original size:12 final size:12
Alignment explanation
Indices: 5387190--5387332 Score: 112
Period size: 12 Copynumber: 11.9 Consensus size: 12
5387180 ATAACATCCG
*
5387190 AACAACCAAAAT
1 AACAACAAAAAT
* *
5387202 AACAACCAAAAC
1 AACAACAAAAAT
* *
5387214 AGCAGCAAAAAT
1 AACAACAAAAAT
* *
5387226 AACAGCAAAACAAA
1 AACAAC-AAA-AAT
5387240 AACAA-AAAAAT
1 AACAACAAAAAT
*
5387251 AGCAAC-AAAAT
1 AACAACAAAAAT
*
5387262 CAGCAACAAAAAT
1 -AACAACAAAAAT
5387275 AACAACAAAAAT
1 AACAACAAAAAT
*
5387287 CACAACAAAAAT
1 AACAACAAAAAT
*
5387299 AACAGCAAAAAT
1 AACAACAAAAAT
* *
5387311 AGC-ACCAAAAT
1 AACAACAAAAAT
*
5387322 AGCAACAAAAA
1 AACAACAAAAA
5387333 CAGTAAAAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
11 20 0.19
12 73 0.68
13 8 0.07
14 6 0.06
ACGTcount: A:0.67, C:0.21, G:0.06, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:5387225 original size:24 final size:24
Alignment explanation
Indices: 5387192--5387355 Score: 108
Period size: 24 Copynumber: 7.0 Consensus size: 24
5387182 AACATCCGAA
*
5387192 CAACCAAAATAACAACCAAAACAG
1 CAACAAAAATAACAACCAAAACAG
* * *
5387216 CAGCAAAAATAAC-AGCAAAACAA
1 CAACAAAAATAACAACCAAAACAG
* *
5387239 AAACAAAAAAATAGCAA-CAAAATCAG
1 CAAC--AAAAATAACAACCAAAA-CAG
*
5387265 CAACAAAAATAACAACAAAAATCA-
1 CAACAAAAATAACAACCAAAA-CAG
* * *
5387289 CAACAAAAATAACAGCAAAAATAG
1 CAACAAAAATAACAACCAAAACAG
* * *
5387313 C-ACCAAAATAGCAACAAAAACAG
1 CAACAAAAATAACAACCAAAACAG
* *
5387336 -TA-AAAAATAGC-ACCAAAACA
1 CAACAAAAATAACAACCAAAACA
5387356 ATAATATAAT
Statistics
Matches: 114, Mismatches: 19, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
21 8 0.07
22 8 0.07
23 30 0.26
24 42 0.37
25 20 0.18
26 6 0.05
ACGTcount: A:0.66, C:0.21, G:0.06, T:0.07
Consensus pattern (24 bp):
CAACAAAAATAACAACCAAAACAG
Found at i:5387729 original size:25 final size:25
Alignment explanation
Indices: 5387701--5387779 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
5387691 TTTAATTTTA
5387701 TACCTAAACATGTTTTTTTAAATTG
1 TACCTAAACATGTTTTTTTAAATTG
* *
5387726 TACCTAAAC-TGTTTTATT---TTA
1 TACCTAAACATGTTTTTTTAAATTG
5387747 TACCTAAACATGTTTTTTTAAATTG
1 TACCTAAACATGTTTTTTTAAATTG
5387772 TACCTAAA
1 TACCTAAA
5387780 AAGTTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.24
22 8 0.17
24 8 0.17
25 19 0.41
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (25 bp):
TACCTAAACATGTTTTTTTAAATTG
Found at i:5387750 original size:21 final size:22
Alignment explanation
Indices: 5387690--5387799 Score: 89
Period size: 25 Copynumber: 4.8 Consensus size: 22
5387680 GAAGTGCATT
5387690 TTTTAATTTTATACCTAAACATG
1 TTTT-ATTTTATACCTAAACATG
* *
5387713 TTTTTTTAAATTGTACCTAAAC-TG
1 TTTTATT---TTATACCTAAACATG
5387737 TTTTATTTTATACCTAAACATG
1 TTTTATTTTATACCTAAACATG
* * *
5387759 TTTTTTTAAATTGTACCTAAA-AAG
1 TTTTATT---TTATACCTAAACATG
*
5387783 TTTTATTTTAAACCTAA
1 TTTTATTTTATACCTAA
5387800 GAATTATAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
21 19 0.27
22 10 0.14
23 4 0.06
24 16 0.23
25 21 0.30
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTATTTTATACCTAAACATG
Found at i:5387758 original size:46 final size:46
Alignment explanation
Indices: 5387690--5387799 Score: 184
Period size: 46 Copynumber: 2.4 Consensus size: 46
5387680 GAAGTGCATT
**
5387690 TTTTAATTTTATACCTAAACATGTTTTTTTAAATTGTACCTAAACTG
1 TTTT-ATTTTATACCTAAACATGTTTTTTTAAATTGTACCTAAAAAG
5387737 TTTTATTTTATACCTAAACATGTTTTTTTAAATTGTACCTAAAAAG
1 TTTTATTTTATACCTAAACATGTTTTTTTAAATTGTACCTAAAAAG
*
5387783 TTTTATTTTAAACCTAA
1 TTTTATTTTATACCTAA
5387800 GAATTATAGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
46 56 0.93
47 4 0.07
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (46 bp):
TTTTATTTTATACCTAAACATGTTTTTTTAAATTGTACCTAAAAAG
Found at i:5390170 original size:26 final size:26
Alignment explanation
Indices: 5390141--5390240 Score: 110
Period size: 26 Copynumber: 3.8 Consensus size: 26
5390131 ATATTTCCTT
* * *
5390141 AAATTTTATTAGGGGCAAAATCGTCA
1 AAATTTTACTAGGGGTAAAATAGTCA
* *
5390167 AAATTTTACTAGGGGTAAACTTGTCA
1 AAATTTTACTAGGGGTAAAATAGTCA
* *
5390193 AAATTTAACTAGGGGTAAAATAGTTA
1 AAATTTTACTAGGGGTAAAATAGTCA
* **
5390219 AAATTTTGCTAGGAATAAAATA
1 AAATTTTACTAGGGGTAAAATA
5390241 AGGATGATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (26 bp):
AAATTTTACTAGGGGTAAAATAGTCA
Found at i:5390390 original size:6 final size:6
Alignment explanation
Indices: 5390379--5390441 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
5390369 TGAGATTTAT
** * *
5390379 TTTAAA TTTAAA TTT-GT TTTAAG TTTAAA TTT-AT TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
5390426 TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
5390442 ATAAATAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 4 0.09
5 7 0.16
6 30 0.67
7 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5390443 original size:17 final size:17
Alignment explanation
Indices: 5390373--5390441 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
5390363 TCATTTTGAG
5390373 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
5390390 ATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAA
5390407 ATTTATTTTAAAATTTAA
1 ATTTATTTT-AAATTTAA
5390425 ATTTA-TTTAAATTTAA
1 ATTTATTTTAAATTTAA
5390441 A
1 A
5390442 ATAAATAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
16 9 0.19
17 26 0.55
18 12 0.26
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:5391121 original size:18 final size:19
Alignment explanation
Indices: 5391098--5391135 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5391088 AAAACCATTA
5391098 ATTAATAAATA-TAATAAT
1 ATTAATAAATATTAATAAT
5391116 ATTAATAAATATTAATAAT
1 ATTAATAAATATTAATAAT
5391135 A
1 A
5391136 AAAAAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTAATAAATATTAATAAT
Found at i:5391128 original size:10 final size:10
Alignment explanation
Indices: 5391098--5391133 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
5391088 AAAACCATTA
5391098 ATTAATAAAT
1 ATTAATAAAT
5391108 A-TAAT-AAT
1 ATTAATAAAT
5391116 ATTAATAAAT
1 ATTAATAAAT
5391126 ATTAATAA
1 ATTAATAA
5391134 TAAAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.17
9 8 0.33
10 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAATAAAT
Found at i:5391481 original size:20 final size:21
Alignment explanation
Indices: 5391456--5391494 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5391446 CCAAATGACT
5391456 CAGATTCA-AGGTTTAAAACC
1 CAGATTCATAGGTTTAAAACC
*
5391476 CAGATTTATAGGTTTAAAA
1 CAGATTCATAGGTTTAAAA
5391495 TGAAAGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
CAGATTCATAGGTTTAAAACC
Found at i:5392254 original size:60 final size:60
Alignment explanation
Indices: 5392166--5392346 Score: 163
Period size: 60 Copynumber: 3.0 Consensus size: 60
5392156 CCTAGAAGGT
* * * * * * *
5392166 CCCCGAACTGTAC-AAAAATCATATTTTGATCCTTAAATTTTCCAAAAATTACATTTTTAC
1 CCCCGAACT-TTCTAAAAATTATAGTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
* * * * *
5392226 TCTCGAACTTTCTAAAAATTATAGTTTGACCCTCGACCTTTCTAAAAATTACATTTTGAC
1 CCCCGAACTTTCTAAAAATTATAGTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
* * * * *
5392286 CCCCGAACTTTCTAAAAATTACA-TTT-TCCTCCCGAACTTTCCAAAAATTATATTTT-AC
1 CCCCGAACTTTCTAAAAATTATAGTTTGACC-CTCAAACTTTCCAAAAATTACATTTTGAC
5392344 CCC
1 CCC
5392347 AAAATGTCCA
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
58 7 0.07
59 27 0.27
60 65 0.66
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (60 bp):
CCCCGAACTTTCTAAAAATTATAGTTTGACCCTCAAACTTTCCAAAAATTACATTTTGAC
Found at i:5392375 original size:29 final size:28
Alignment explanation
Indices: 5392269--5392369 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 28
5392259 CGACCTTTCT
* * * *
5392269 AAAAATTACATTTTGACCCCCGAACTTTCT
1 AAAAATTACATTTT-A-CCCCAAAATGTCC
* * * *
5392299 AAAAATTACATTTTCCTCCCGAACTTTCC
1 AAAAATTACATTTTAC-CCCAAAATGTCC
*
5392328 AAAAATTATATTTTACCCCAAAATGTCC
1 AAAAATTACATTTTACCCCAAAATGTCC
5392356 AAAAATTACATTTT
1 AAAAATTACATTTT
5392370 TGCCCCTTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 23 0.37
29 25 0.40
30 14 0.23
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAAATTACATTTTACCCCAAAATGTCC
Found at i:5392431 original size:29 final size:30
Alignment explanation
Indices: 5392204--5392434 Score: 206
Period size: 30 Copynumber: 7.8 Consensus size: 30
5392194 ATCCTTAAAT
* *
5392204 TTTCCAAAAATTACATTTTTACTCTCGAAC
1 TTTCTAAAAATTACATTTTTACCCTCGAAC
* * * *
5392234 TTTCTAAAAATTATAGTTTGACCCTCGACC
1 TTTCTAAAAATTACATTTTTACCCTCGAAC
* *
5392264 TTTCTAAAAATTACATTTTGACCCCCGAAC
1 TTTCTAAAAATTACATTTTTACCCTCGAAC
*
5392294 TTTCTAAAAATTACA-TTTT-CCTCCCGAAC
1 TTTCTAAAAATTACATTTTTACC-CTCGAAC
* * * *
5392323 TTTCCAAAAATTATA-TTTTACCC-CAAAA
1 TTTCTAAAAATTACATTTTTACCCTCGAAC
* * * * *
5392351 TGTCCAAAAATTACATTTTTGCCCCTTG-AG
1 TTTCTAAAAATTACATTTTT-ACCCTCGAAC
5392381 TTTCTAAAAATTACCATTTTTACCCTCGAAC
1 TTTCTAAAAATTA-CATTTTTACCCTCGAAC
*
5392412 -ATCTAAAAATTACCA-TTTTACCC
1 TTTCTAAAAATTA-CATTTTTACCC
5392435 CAAGCATCCA
Statistics
Matches: 167, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
28 18 0.11
29 40 0.24
30 101 0.60
31 8 0.05
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
TTTCTAAAAATTACATTTTTACCCTCGAAC
Found at i:5392448 original size:29 final size:30
Alignment explanation
Indices: 5392386--5392458 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 30
5392376 TTGAGTTTCT
*
5392386 AAAAATTACCATTTTTACCCTCGAACATCT
1 AAAAATTACCATTTTTACCCTCGAACATCA
*
5392416 AAAAATTACCA-TTTTACCC-C-AAGCATCC
1 AAAAATTACCATTTTTACCCTCGAA-CATCA
*
5392444 AAAAATCA-CATTTTT
1 AAAAATTACCATTTTT
5392459 GACTCTGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 4 0.10
28 16 0.41
29 8 0.21
30 11 0.28
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAAATTACCATTTTTACCCTCGAACATCA
Found at i:5392449 original size:88 final size:87
Alignment explanation
Indices: 5392269--5392461 Score: 209
Period size: 88 Copynumber: 2.2 Consensus size: 87
5392259 CGACCTTTCT
*
5392269 AAAAATTACA-TTTTGACCCCCGAACTTTCTAAAAATTACATTTTCCTCCCGAACTTTCCAAAAA
1 AAAAATTACATTTTTGACCCCCGAACTTTCTAAAAATTACATTTTCCTCCCGAACTATCCAAAAA
*
5392333 TTATATTTTACCCCAAAATGTCC
66 TTACATTTTACCCCAAAA-GTCC
* * * *
5392356 AAAAATTACATTTTTG-CCCCTTG-AGTTTCTAAAAATTACCATTTTTACC-CTCGAAC-ATCTA
1 AAAAATTACATTTTTGACCCC-CGAACTTTCTAAAAATTA-CA-TTTT-CCTCCCGAACTATCCA
*
5392417 AAAATTACCATTTTACCCCAAGCA-TCC
62 AAAATTA-CATTTTACCCCAA-AAGTCC
*
5392444 AAAAATCACATTTTTGAC
1 AAAAATTACATTTTTGAC
5392462 TCTGTTTGCT
Statistics
Matches: 90, Mismatches: 8, Indels: 14
0.80 0.07 0.12
Matches are distributed among these distances:
87 28 0.31
88 36 0.40
89 23 0.26
90 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (87 bp):
AAAAATTACATTTTTGACCCCCGAACTTTCTAAAAATTACATTTTCCTCCCGAACTATCCAAAAA
TTACATTTTACCCCAAAAGTCC
Found at i:5397644 original size:4 final size:4
Alignment explanation
Indices: 5397620--5397705 Score: 65
Period size: 4 Copynumber: 21.8 Consensus size: 4
5397610 CGATTTAACG
* *
5397620 AAGA AA-A AATA AATA AA-A AAGA AAGA AAGAA AAGA AAGAA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AAGA AAG-A AAGA AAGA
* *
5397668 AAAA AAG- AATA AA-A AAGA AAGAA AAGA AA-A AAGGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AA-GA AAG
5397706 GAAAAAGGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
3 14 0.20
4 41 0.59
5 15 0.21
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:5397652 original size:13 final size:13
Alignment explanation
Indices: 5397636--5397738 Score: 90
Period size: 13 Copynumber: 7.9 Consensus size: 13
5397626 AAATAAATAA
5397636 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
5397649 AAAAGAAAGAAA-
1 AAAAGAAAGAAAG
*
5397661 AGAAAGAAAAAAAG
1 A-AAAGAAAGAAAG
*
5397675 AATAAAAAAGAAAG
1 AA-AAGAAAGAAAG
5397689 AAAAGAAA-AAAGG
1 AAAAGAAAGAAA-G
* *
5397702 AAAGGAAA-AAGG
1 AAAAGAAAGAAAG
5397714 AAATAGAAA-AAAGG
1 AAA-AGAAAGAAA-G
5397728 AAAA-AAAGAAA
1 AAAAGAAAGAAA
5397739 AGGAGAGGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
12 11 0.15
13 48 0.64
14 16 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:5397666 original size:26 final size:26
Alignment explanation
Indices: 5397636--5397740 Score: 101
Period size: 26 Copynumber: 4.0 Consensus size: 26
5397626 AAATAAATAA
5397636 AAAAGAAAGAAAGAAAAGAAAGAAAAG
1 AAAAGAAA-AAAGAAAAGAAAGAAAAG
*
5397663 -AAAGAAAAAAAGAATAAAAAAG-AAAG
1 AAAAG-AAAAAAGAA-AAGAAAGAAAAG
* * *
5397689 AAAAGAAAAAAGGAAAGGAA-AAAGG
1 AAAAGAAAAAAGAAAAGAAAGAAAAG
5397714 AAATAGAAAAAAGGAAAA-AAAGAAAAG
1 AAA-AGAAAAAA-GAAAAGAAAGAAAAG
5397741 GAGAGGTCGA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
25 10 0.16
26 32 0.51
27 21 0.33
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (26 bp):
AAAAGAAAAAAGAAAAGAAAGAAAAG
Found at i:5397722 original size:35 final size:32
Alignment explanation
Indices: 5397639--5397740 Score: 59
Period size: 34 Copynumber: 3.1 Consensus size: 32
5397629 TAAATAAAAA
*
5397639 AGAAAGAAAGAAAAGAAAGAAAAGAAAGAAA-AAA
1 AGAAA-AAAGAAAAGAAA-AAGA-AAAGAAAGAAA
* *
5397673 AGAATAAAAAAGAAAG-AAAAGAAAA-AAGGAAA
1 AGAA-AAAAGA-AAAGAAAAAGAAAAGAAAGAAA
* *
5397705 GGAAAAAGGAAATAGAAAAAAGGAAAA-AAAGAAA
1 AGAAAAAAGAAA-AG-AAAAA-GAAAAGAAAGAAA
5397739 AG
1 AG
5397741 GAGAGGTCGA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
30 2 0.04
31 8 0.15
32 9 0.17
33 7 0.13
34 22 0.42
35 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (32 bp):
AGAAAAAAGAAAAGAAAAAGAAAAGAAAGAAA
Found at i:5397740 original size:40 final size:38
Alignment explanation
Indices: 5397639--5397742 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 38
5397629 TAAATAAAAA
5397639 AGAAAGAAAGAAAAGAAAGAAAA-GAAAGAAAAAAAGAAT
1 AGAAA-AAAGAAAA-AAAGAAAAGGAAAGAAAAAAAGAAT
* *
5397678 --AAAAAAGAAAGAAAAGAAAAAAGGAAAGGAAAAAGGAAAT
1 AGAAAAAAGAAA-AAAAG--AAAAGGAAAGAAAAAAAG-AAT
5397718 AGAAAAAAGGAAAAAAAGAAAAGGA
1 AGAAAAAA-GAAAAAAAGAAAAGGA
5397743 GAGGTCGAGG
Statistics
Matches: 55, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
36 11 0.20
37 4 0.07
38 4 0.07
39 11 0.20
40 10 0.18
42 11 0.20
43 4 0.07
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (38 bp):
AGAAAAAAGAAAAAAAGAAAAGGAAAGAAAAAAAGAAT
Found at i:5398732 original size:50 final size:50
Alignment explanation
Indices: 5398678--5398949 Score: 264
Period size: 50 Copynumber: 5.5 Consensus size: 50
5398668 AAGACTTGAA
*
5398678 GGGAAAGGTTGAGGCCACAACGGTGAACCCGGTACCTAAGAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTAAGAAGATGTGAT
* * * *
5398728 GGGAAAGGTTGA-GCCTGCAACGGTGAACCCGGTACC-ATGAAAATTTGAA
1 GGGAAAGGTTGAGGCC-GCAACGGTGAACCCGGTACCTAAGAAGATGTGAT
* * * * *
5398777 GGG-AAGGATTGAGGCCACGACGGTGAATCTGGTACCGT-ATAAGATGTGAT
1 GGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTACC-TAAGAAGATGTGAT
* * * ** * *
5398827 GGGAAAGGTTGAGGCCGTAACGGTGAACCTGATAGATAAAAAGATGTGAA
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTAAGAAGATGTGAT
* *** * * *
5398877 GGAAAAGGTTGAGGCCGCAACGACAAACCCGATACCAAACAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTAAGAAGATGTGAT
*
5398927 AGGAAAGGTTGAGGCCGCAACGG
1 GGGAAAGGTTGAGGCCGCAACGG
5398950 CAAACCCAGT
Statistics
Matches: 178, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
48 4 0.02
49 36 0.20
50 134 0.75
51 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.17
Consensus pattern (50 bp):
GGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTAAGAAGATGTGAT
Found at i:5398835 original size:99 final size:99
Alignment explanation
Indices: 5398664--5398967 Score: 319
Period size: 99 Copynumber: 3.1 Consensus size: 99
5398654 CTGAGAAAAA
*
5398664 CATGAAGACTTGAAGGGAAAGGTTGAGGCCACAACGGTGAACCCGGTACCTAAGAAGATGTGATG
1 CATGAAAACTTGAAGGGAAAGGTTGAGGCCACAACGGTGAACCCGGTACCTAAGAAGATGTGATG
5398729 GGAAAGGTTGA-GCCTGCAACGGTGAACCCGGTAC
66 GGAAAGGTTGAGGCC-GCAACGGTGAACCCGGTAC
* * * * *
5398763 CATGAAAATTTGAAGGG-AAGGATTGAGGCCACGACGGTGAATCTGGTACCGT-ATAAGATGTGA
1 CATGAAAACTTGAAGGGAAAGG-TTGAGGCCACAACGGTGAACCCGGTACC-TAAGAAGATGTGA
* * *
5398826 TGGGAAAGGTTGAGGCCGTAACGGTGAACCTGATA-
64 TGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
* * * * * *** * * *
5398861 GATAAAAAGATGTGAAGGAAAAGGTTGAGGCCGCAACGACAAACCCGATACCAAACAAGATGTGA
1 CATGAAAA-CT-TGAAGGGAAAGGTTGAGGCCACAACGGTGAACCCGGTACCTAAGAAGATGTGA
* ** *
5398926 TAGGAAAGGTTGAGGCCGCAACGGCAAACCCAGTAC
64 TGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
5398962 CATGAA
1 CATGAA
5398968 GAGATGATAA
Statistics
Matches: 165, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
98 10 0.06
99 79 0.48
100 68 0.41
101 8 0.05
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.16
Consensus pattern (99 bp):
CATGAAAACTTGAAGGGAAAGGTTGAGGCCACAACGGTGAACCCGGTACCTAAGAAGATGTGATG
GGAAAGGTTGAGGCCGCAACGGTGAACCCGGTAC
Found at i:5399009 original size:100 final size:99
Alignment explanation
Indices: 5398686--5399012 Score: 297
Period size: 100 Copynumber: 3.3 Consensus size: 99
5398676 AAGGGAAAGG
* * * *
5398686 TTGAGGCCACAACGGTGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTGA-GCCTGCAACG
1 TTGAGGCCACAACGGCGAACCCGATACCAAACAAGATGTGATGGGAAAGGTTGAGGCC-GCAACG
* *
5398750 GTGAACCCGGTACCATGAAA-ATTTGAAGGGAAGGA
65 GTGAACCCAGTACCATGAAAGATGTGAAGGG-AGGA
* * * * * ** * *
5398785 TTGAGGCCACGACGGTGAATCTGGTACCGTATAAGATGTGATGGGAAAGGTTGAGGCCGTAACGG
1 TTGAGGCCACAACGGCGAACCCGATACCAAACAAGATGTGATGGGAAAGGTTGAGGCCGCAACGG
* * * *
5398850 TGAA-CCTGATA-GATAAAAAGATGTGAAGGAAAAGG-
66 TGAACCCAG-TACCAT-GAAAGATGTGAAGG--GAGGA
* * * *
5398885 TTGAGGCCGCAACGACAAACCCGATACCAAACAAGATGTGATAGGAAAGGTTGAGGCCGCAACGG
1 TTGAGGCCACAACGGCGAACCCGATACCAAACAAGATGTGATGGGAAAGGTTGAGGCCGCAACGG
**
5398950 CAAACCCAGTACCATGAAGAGATGAT-AAGGGAGGA
66 TGAACCCAGTACCATGAA-AGATG-TGAAGGGAGGA
* *
5398985 TTGAGGCCATAACGGCGAATCCGATACC
1 TTGAGGCCACAACGGCGAACCCGATACC
5399013 TTAAAAAGAG
Statistics
Matches: 181, Mismatches: 36, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
98 5 0.03
99 66 0.36
100 92 0.51
101 17 0.09
102 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.17
Consensus pattern (99 bp):
TTGAGGCCACAACGGCGAACCCGATACCAAACAAGATGTGATGGGAAAGGTTGAGGCCGCAACGG
TGAACCCAGTACCATGAAAGATGTGAAGGGAGGA
Found at i:5399101 original size:17 final size:17
Alignment explanation
Indices: 5399076--5399134 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
5399066 TCATTTTGAG
5399076 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
5399093 ATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAA
5399110 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
*
5399127 ATTAATTT
1 ATTTATTT
5399135 GAATTTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:5399131 original size:5 final size:6
Alignment explanation
Indices: 5399082--5399169 Score: 57
Period size: 6 Copynumber: 16.0 Consensus size: 6
5399072 TGAGATTTAT
** * *
5399082 TTTAAA TTTAAA TTT-GT TTTAAG TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
5399128 -TT-AA TTTGAA TTT--G TTTGAA TTTAAA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5399170 ATAAATAAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
4 9 0.14
5 11 0.17
6 44 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5399149 original size:16 final size:16
Alignment explanation
Indices: 5399076--5399169 Score: 74
Period size: 17 Copynumber: 6.1 Consensus size: 16
5399066 TCATTTTGAG
5399076 ATTTATTTTAAATTTAA
1 ATTTA-TTTAAATTTAA
* *
5399093 ATTTGTTTTAAGTTTAA
1 ATTT-ATTTAAATTTAA
5399110 ATTTATTTTAAATTT-A
1 ATTTA-TTTAAATTTAA
*
5399126 A---A-TT-AATTTGA
1 ATTTATTTAAATTTAA
* *
5399137 ATTTGTTTGAATTTAA
1 ATTTATTTAAATTTAA
5399153 ATTTATTTAAATTTAA
1 ATTTATTTAAATTTAA
5399169 A
1 A
5399170 ATAAATAAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
10 5 0.08
11 4 0.07
13 1 0.02
15 2 0.03
16 23 0.38
17 26 0.43
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
ATTTATTTAAATTTAA
Found at i:5399844 original size:18 final size:19
Alignment explanation
Indices: 5399821--5399858 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5399811 AAAACCATTA
5399821 ATTAATAAATA-TAATAAT
1 ATTAATAAATATTAATAAT
5399839 ATTAATAAATATTAATAAT
1 ATTAATAAATATTAATAAT
5399858 A
1 A
5399859 AAAAAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTAATAAATATTAATAAT
Found at i:5399851 original size:10 final size:10
Alignment explanation
Indices: 5399821--5399856 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
5399811 AAAACCATTA
5399821 ATTAATAAAT
1 ATTAATAAAT
5399831 A-TAAT-AAT
1 ATTAATAAAT
5399839 ATTAATAAAT
1 ATTAATAAAT
5399849 ATTAATAA
1 ATTAATAA
5399857 TAAAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.17
9 8 0.33
10 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAATAAAT
Found at i:5401169 original size:50 final size:50
Alignment explanation
Indices: 5401111--5401706 Score: 421
Period size: 50 Copynumber: 11.9 Consensus size: 50
5401101 AATGAAGACT
*
5401111 TGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTAAGAAGATG
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG
* * * *
5401161 TGATGGGAAAGGTTGAGGCTGCAACGGCGAACCCGATACC-ATGAAGA-G
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG
* * * * * *
5401209 TTGAAGGG-AAGGATTGAGGCCACAACGGTGAATCTGATACCGT-ATAAGATG
1 -TGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACC-TAAGAAGATG
* * * * * *
5401260 TGATGAGAAAGGTTGAGGCCGTAACAGCAAACCCGGTAGCTAAGAAGATG
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG
* * * *
5401310 TGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACCAAAGAAGATG
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG
* * *
5401360 TGATA-GGAAAGGTTGAGGCCGCAACGGCTAACCCAGCACCATGAAG-AGATG
1 TGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC-T-AAGAAGATG
* * * * *
5401411 AT-AAGGG--AGGATTGAGGCCGCAATGACGAATCCGATACCTTAAAAAGATG
1 -TGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACC-TAAGAAGATG
* * * * * *
5401461 TAAAGGGAAAGGCTGAGGTCGTAACAGTGAACCCGGTACCTAAGAAGATG
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG
* * ** * *
5401511 TGATGGGAAAGGTTGAGGCTGCAAC-GAAAAACCGAGTACC-ATGAAGA-G
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCG-GTACCTAAGAAGATG
* * *** * *
5401559 ATGACAGGG-AAGGATTAAGTCCGCAACGGCGAATTTGATACCTTAAAAAGATG
1 -TGA-AGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGGTACC-TAAGAAGATG
* * * * ** *
5401612 TAAAGGAAAAGGTTGAGGCTGCAACGACGAACCTAGTACC-ATGAAGA-G
1 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG
* * * *
5401660 ATGAAGGGAAAGGTTGAGGCTGCAACGGTGAGCCCGGTACCTTAGAA
1 -TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAA
5401707 AAAAATATGG
Statistics
Matches: 417, Mismatches: 101, Indels: 56
0.73 0.18 0.10
Matches are distributed among these distances:
48 7 0.02
49 99 0.24
50 232 0.56
51 60 0.14
52 18 0.04
53 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.32, T:0.16
Consensus pattern (50 bp):
TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTAAGAAGATG
Found at i:5401494 original size:151 final size:151
Alignment explanation
Indices: 5401304--5401686 Score: 427
Period size: 151 Copynumber: 2.5 Consensus size: 151
5401294 GGTAGCTAAG
*
5401304 AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACCAAAGAAGATGTGATAGGAA
1 AAGATGTAAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACCAAAGAAGATGTGATAGGAA
*** *
5401369 AGGTTGAGGCCGCAACGGCTAACCCAGCACCATGAAGAGATGATAAGGG-AGGATTGAGGCCGCA
66 AGGTTGAGGCCGCAACGAAAAACCCAGCACCATGAAGAGATGA-AAGGGAAGGATTAAGGCCGCA
*
5401433 ATGACGAATCCGATACCTTAAA
130 ACGACGAATCCGATACCTTAAA
* * * ** * * *
5401455 AAGATGTAAAGGGAAAGGCTGAGGTCGTAAC-AGTGAACCCGGTACCTAAGAAGATGTGATGGGA
1 AAGATGTAAAGGGAAAGGTTGAGGCCGCAACGA-CAAACCCGATACCAAAGAAGATGTGATAGGA
* * * * *
5401519 AAGGTTGAGGCTGCAACGAAAAACCGAGTACCATGAAGAGATGACAGGGAAGGATTAAGTCCGCA
65 AAGGTTGAGGCCGCAACGAAAAACCCAGCACCATGAAGAGATGAAAGGGAAGGATTAAGGCCGCA
* **
5401584 ACGGCGAATTTGATACCTTAAA
130 ACGACGAATCCGATACCTTAAA
* * * * *
5401606 AAGATGTAAAGGAAAAGGTTGAGGCTGCAACGACGAA-CCTAGTACC-ATGAAGA-GATGA-AGG
1 AAGATGTAAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGA-TACCAAAGAAGATG-TGATA-G
*
5401667 GAAAGGTTGAGGCTGCAACG
63 GAAAGGTTGAGGCCGCAACG
5401687 GTGAGCCCGG
Statistics
Matches: 194, Mismatches: 32, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
149 1 0.01
150 37 0.19
151 155 0.80
152 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.31, T:0.15
Consensus pattern (151 bp):
AAGATGTAAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGATACCAAAGAAGATGTGATAGGAA
AGGTTGAGGCCGCAACGAAAAACCCAGCACCATGAAGAGATGAAAGGGAAGGATTAAGGCCGCAA
CGACGAATCCGATACCTTAAA
Found at i:5402132 original size:39 final size:39
Alignment explanation
Indices: 5401970--5402156 Score: 109
Period size: 39 Copynumber: 4.8 Consensus size: 39
5401960 AGCCCGAGGT
* *
5401970 AGATCACCATCAGCCAATCTCATACCCCGAGCCTAGGGC
1 AGATCACCATTAGCCAATCTCTTACCCCGAGCCTAGGGC
* *
5402009 AAATTGCAGCCA-T--CCGATCTCTTACCCCGAGCCT-GGGTC
1 AGA-T-CA-CCATTAGCCAATCTCTTACCCCGAGCCTAGGG-C
* * * * * * *
5402048 AGATTATCGCCTT--TCGATCAT-TTACCCCGAGCTTGGGGT
1 AGATCA-C-CATTAGCCAATC-TCTTACCCCGAGCCTAGGGC
* *
5402087 AAATCACCATTAGCCAATCTTTTACCCCGAGCCTAGGGC
1 AGATCACCATTAGCCAATCTCTTACCCCGAGCCTAGGGC
* * * *
5402126 AGATCACTATCAGCCTATCTCTTACCTCGAG
1 AGATCACCATTAGCCAATCTCTTACCCCGAG
5402157 ATAGGGGCAG
Statistics
Matches: 112, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
37 5 0.04
38 7 0.06
39 90 0.80
40 5 0.04
41 2 0.02
42 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (39 bp):
AGATCACCATTAGCCAATCTCTTACCCCGAGCCTAGGGC
Found at i:5402210 original size:117 final size:116
Alignment explanation
Indices: 5401943--5402286 Score: 273
Period size: 117 Copynumber: 2.9 Consensus size: 116
5401933 GAATGAAGAT
* *
5401943 TCCGATCTTTTACCTCGAGCCCGAGGTAGATCACCATCAGCCAATCTCATACCCCGAGCCTAGGG
1 TCCGATCTTTTACCCCGA-CCTGAGGTAGATCACCATCAGCCAATCTCATACCCCGAGCCTAGGG
** * * * * * *
5402008 CAAATTGCAGCCATCCGATCTCTTACCCCGAGCCTGGGTCAGATTATCGCCT
65 CAAATCACAGCCAGCCGATCTCTTACCCCGAGCATGGGGCAGATTAGCACCA
* * * * * * **
5402060 TTCGATCATTTACCCCGAGCTTGGGGTAAATCACCATTAGCCAATCTTTTACCCCGAGCCTAGGG
1 TCCGATCTTTTACCCCGA-CCTGAGGTAGATCACCATCAGCCAATCTCATACCCCGAGCCTAGGG
* * * *
5402125 CAGATCACTA-TCAGCCTATCTCTTACCTCGAG-ATAGGGGCAGATT-GCAACCA
65 CAAATCAC-AGCCAGCCGATCTCTTACCCCGAGCAT-GGGGCAGATTAGC-ACCA
* * * * *** *
5402177 TCCGATCTTTTACCCCGACCATGAGGTAGATCA-CAGCCATCCAATCTCTTACCACGATAATGGG
1 TCCGATCTTTTACCCCGACC-TGAGGTAGATCACCA-TCAGCCAATCTCATACCCCGAGCCTAGG
* * * * * *
5402241 GCAGATCACAGCCATCCAATTTCTTACCTCGATCATGGGGCAGATT
64 GCAAATCACAGCCAGCCGATCTCTTACCCCGAGCATGGGGCAGATT
5402287 GCAGTTATCC
Statistics
Matches: 179, Mismatches: 41, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
116 6 0.03
117 170 0.95
118 3 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (116 bp):
TCCGATCTTTTACCCCGACCTGAGGTAGATCACCATCAGCCAATCTCATACCCCGAGCCTAGGGC
AAATCACAGCCAGCCGATCTCTTACCCCGAGCATGGGGCAGATTAGCACCA
Found at i:5402298 original size:39 final size:39
Alignment explanation
Indices: 5402142--5402285 Score: 137
Period size: 39 Copynumber: 3.7 Consensus size: 39
5402132 CTATCAGCCT
* * ** * *
5402142 ATCTCTTACCTCGA-GATAGGGGCAGATTGCAACCATCCG
1 ATCTCTTACCACGATAAT-GGGGCAGATCACAGCCATCCA
* * ** * *
5402181 ATCTTTTACCCCGACCATGAGGTAGATCACAGCCATCCA
1 ATCTCTTACCACGATAATGGGGCAGATCACAGCCATCCA
5402220 ATCTCTTACCACGATAATGGGGCAGATCACAGCCATCCA
1 ATCTCTTACCACGATAATGGGGCAGATCACAGCCATCCA
* * *
5402259 ATTTCTTACCTCGATCATGGGGCAGAT
1 ATCTCTTACCACGATAATGGGGCAGAT
5402286 TGCAGTTATC
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
39 84 0.98
40 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCACGATAATGGGGCAGATCACAGCCATCCA
Found at i:5402746 original size:124 final size:124
Alignment explanation
Indices: 5402502--5402734 Score: 387
Period size: 124 Copynumber: 1.9 Consensus size: 124
5402492 AAAGAAACTT
* *
5402502 ATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTAAGAAGTAGACCAAATCAATGAAAC
1 ATTAAAACAAATGATGCAGTCATCTTCCTGATGAGATACTAAGAAGTAGACCAAATCAATGAAAC
* *
5402567 CAAGCTCAATGTGAGCGAAACTTTGAACCCCAGCTTCCTGATGAGACACAGAGAAGTGG
66 CAAGCTCAAAGTGAGCGAAACTTTGAACCCCAGCTTCATGATGAGACACAGAGAAGTGG
*
5402626 ATTAAAACAAATGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAAC
1 ATTAAAACAAATGATGCAGTCATCTTCCTGATGAGATACTAAGAAGTAGACCAAATCAATGAAAC
* *
5402691 CAGGCTCAAAGTGAGC-AAATCTTTGAACCTCAGCTTCATGATGA
66 CAAGCTCAAAGTGAGCGAAA-CTTTGAACCCCAGCTTCATGATGA
5402735 ATTATTGAGA
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
123 3 0.03
124 98 0.97
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (124 bp):
ATTAAAACAAATGATGCAGTCATCTTCCTGATGAGATACTAAGAAGTAGACCAAATCAATGAAAC
CAAGCTCAAAGTGAGCGAAACTTTGAACCCCAGCTTCATGATGAGACACAGAGAAGTGG
Found at i:5402859 original size:209 final size:209
Alignment explanation
Indices: 5402600--5403208 Score: 956
Period size: 206 Copynumber: 2.9 Consensus size: 209
5402590 TGAACCCCAG
* * *
5402600 CTTCCTGATGAGACACAGAGAAGTGGATTAAAACAAATGATGCAGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
* * *
5402665 TGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTTGAACCTCAGCTTCAT
66 TGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCT
* *
5402730 GATGA-ATTATTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTTATGAGATACAGAGAA
131 GATGAGA-TACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAGAGAA
*
5402794 CTGAACCAAATCTGT
195 CTGAACCAAATCCGT
* * *
5402809 CTTCCTGATGAGACATAGAGAAGTGGATCAAAACAAGTGATGTGGTCATCTTCTTGATGAGATAC
1 CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
*
5402874 TGAGAAGTAGACCAAATAAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCT
66 TGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCT
* * *
5402939 GATGAGATACT---AAGTAGGTCGAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAAAGAAG
131 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAGAGAAC
*
5403001 TGAACCAGATCCGT
196 TGAACCAAATCCGT
*
5403015 CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATAT
1 CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
* *
5403080 TGAGAAGTAGACCAAATCAATGAAACTAGACTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCT
66 TGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCT
* * * * *
5403145 GATGAGATACTGAGAAGCAGGTAGAAGTAATAAAGTGATTACCTTCCTGATGAGATACAGAGAA
131 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAGAGAA
5403209 GTAAACTGAG
Statistics
Matches: 365, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
206 193 0.53
209 171 0.47
210 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (209 bp):
CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
TGAGAAGTAGACCAAATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCT
GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTACCTTCCTAATGAGATACAGAGAAC
TGAACCAAATCCGT
Found at i:5403615 original size:18 final size:17
Alignment explanation
Indices: 5403583--5403659 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
5403573 TCATTTTGAG
5403583 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
*
5403600 ATTTCTTTTAAAATTTAA
1 ATTTATTTT-AAATTTAA
** * *
5403618 ATTTAAATCAAGTTTAA
1 ATTTATTTTAAATTTAA
5403635 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
*
5403652 ATTAATTT
1 ATTTATTT
5403660 GAATTTGTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 35 0.73
18 13 0.27
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:5403656 original size:5 final size:6
Alignment explanation
Indices: 5403589--5403694 Score: 68
Period size: 6 Copynumber: 19.0 Consensus size: 6
5403579 TGAGATTTAT
** * *
5403589 TTTAAA TTTAAA TTT-CT TTTAAAA TTTAAA TTTAAA -TCAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * *
5403636 TTT-AT TTTAAA TTTAAA -TT-AA TTTGAA TTT--G TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5403679 TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
5403695 ATAAATAAGT
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
4 9 0.12
5 14 0.18
6 51 0.66
7 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:5403674 original size:16 final size:16
Alignment explanation
Indices: 5403583--5403694 Score: 74
Period size: 16 Copynumber: 7.1 Consensus size: 16
5403573 TCATTTTGAG
5403583 ATTTATTTTAAATTTAA
1 ATTTA-TTTAAATTTAA
*
5403600 ATTTCTTTTAAAATTTAA
1 ATTT-ATTT-AAATTTAA
* * *
5403618 ATTTAAATCAAGTTTAA
1 ATTT-ATTTAAATTTAA
5403635 ATTTATTTTAAATTT-A
1 ATTTA-TTTAAATTTAA
*
5403651 A---A-TT-AATTTGA
1 ATTTATTTAAATTTAA
* *
5403662 ATTTGTTTGAATTTAA
1 ATTTATTTAAATTTAA
5403678 ATTTATTTAAATTTAA
1 ATTTATTTAAATTTAA
5403694 A
1 A
5403695 ATAAATAAGT
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
10 5 0.07
11 4 0.05
13 1 0.01
15 2 0.03
16 24 0.33
17 24 0.33
18 13 0.18
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (16 bp):
ATTTATTTAAATTTAA
Found at i:5404375 original size:18 final size:19
Alignment explanation
Indices: 5404352--5404389 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5404342 AAAACCATTA
5404352 ATTAATAAATA-TAATAAT
1 ATTAATAAATATTAATAAT
5404370 ATTAATAAATATTAATAAT
1 ATTAATAAATATTAATAAT
5404389 A
1 A
5404390 AAAAAAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTAATAAATATTAATAAT
Found at i:5404382 original size:10 final size:10
Alignment explanation
Indices: 5404352--5404387 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
5404342 AAAACCATTA
5404352 ATTAATAAAT
1 ATTAATAAAT
5404362 A-TAAT-AAT
1 ATTAATAAAT
5404370 ATTAATAAAT
1 ATTAATAAAT
5404380 ATTAATAA
1 ATTAATAA
5404388 TAAAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.17
9 8 0.33
10 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAATAAAT
Found at i:5405469 original size:30 final size:30
Alignment explanation
Indices: 5405435--5405594 Score: 184
Period size: 30 Copynumber: 5.4 Consensus size: 30
5405425 CAGAAATCAT
*
5405435 ATTTTGACCCTCAAATTTTCCAAAAATTAC
1 ATTTTGACCCTCAAACTTTCCAAAAATTAC
* *
5405465 ATTTTGACCTTCGAACTTTCC-AAAATTAC
1 ATTTTGACCCTCAAACTTTCCAAAAATTAC
**
5405494 ATTTTGACCCTCAAACTTTTTAAAAATTAC
1 ATTTTGACCCTCAAACTTTCCAAAAATTAC
* * * *
5405524 ATTTTAATCCTCAAACTTTCTAAAAATTAT
1 ATTTTGACCCTCAAACTTTCCAAAAATTAC
*
5405554 ATTTTTGTCCCT-AAA-TTTCCAAAAATTACC
1 A-TTTTGACCCTCAAACTTTCCAAAAATTA-C
5405584 ATTTTG-CCCTC
1 ATTTTGACCCTC
5405595 GGACGTCCCA
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.04
29 42 0.38
30 57 0.52
31 7 0.06
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.40
Consensus pattern (30 bp):
ATTTTGACCCTCAAACTTTCCAAAAATTAC
Found at i:5405499 original size:29 final size:29
Alignment explanation
Indices: 5405435--5405621 Score: 157
Period size: 29 Copynumber: 6.3 Consensus size: 29
5405425 CAGAAATCAT
*
5405435 ATTTTGACCCTCAAATTTTCCAAAAATTAC
1 ATTTTGACCCTCAAACTTTCC-AAAATTAC
* *
5405465 ATTTTGACCTTCGAACTTTCCAAAATTAC
1 ATTTTGACCCTCAAACTTTCCAAAATTAC
**
5405494 ATTTTGACCCTCAAACTTTTTAAAAATTAC
1 ATTTTGACCCTCAAAC-TTTCCAAAATTAC
* * * *
5405524 ATTTTAATCCTCAAACTTTCTAAAAATTAT
1 ATTTTGACCCTCAAACTTTC-CAAAATTAC
*
5405554 ATTTTTGTCCCT-AAA-TTTCCAAAAATTACC
1 A-TTTTGACCCTCAAACTTTCC-AAAATTA-C
** * *
5405584 ATTTTG-CCCTCGGACGTCCCAAAATTACC
1 ATTTTGACCCTCAAACTTTCCAAAATTA-C
5405613 ATTTT-ACCC
1 ATTTTGACCC
5405622 CCGAGCATCC
Statistics
Matches: 129, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.03
29 59 0.46
30 59 0.46
31 7 0.05
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
ATTTTGACCCTCAAACTTTCCAAAATTAC
Found at i:5405527 original size:59 final size:57
Alignment explanation
Indices: 5405417--5405621 Score: 189
Period size: 59 Copynumber: 3.5 Consensus size: 57
5405407 GAAGGTCCCT
* * *
5405417 GAACTATCCAGAAATCATATTTTGACCCTCAAATTTTCCAAAAATTACATTTTGACCTTC
1 GAACTTTCCA-AAATTACATTTTGACCCTCAAATTTT-CAAAAATTACATTTTGACC-TC
* *
5405477 GAACTTTCCAAAATTACATTTTGACCCTCAAACTTTTTAAAAATTACATTTTAATCCTC
1 GAACTTTCCAAAATTACATTTTGACCCTCAAA-TTTTCAAAAATTACATTTTGA-CCTC
* * * * * *
5405536 AAACTTTCTAAAAATTATATTTTTGTCCCT-AAATTTCCAAAAATTACCATTTTGCCCTC
1 GAACTTTC-CAAAATTACA-TTTTGACCCTCAAATTTTCAAAAATTA-CATTTTGACCTC
* * *
5405595 GGACGTCCCAAAATTACCATTTT-ACCC
1 GAACTTTCCAAAATTA-CATTTTGACCC
5405622 CCGAGCATCC
Statistics
Matches: 119, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
57 3 0.03
58 11 0.09
59 64 0.54
60 32 0.27
61 9 0.08
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (57 bp):
GAACTTTCCAAAATTACATTTTGACCCTCAAATTTTCAAAAATTACATTTTGACCTC
Found at i:5405636 original size:29 final size:29
Alignment explanation
Indices: 5405571--5405637 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
5405561 TCCCTAAATT
* * *
5405571 TCCAAAAATTACCATTTTGCCCTCGGACG
1 TCCAAAAATTACCATTTTACCCCCGGACA
*
5405600 TCCCAAAATTACCATTTTACCCCC-GAGCA
1 TCCAAAAATTACCATTTTACCCCCGGA-CA
5405629 TCCAAAAAT
1 TCCAAAAAT
5405638 CGCATTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGGACA
Found at i:5407787 original size:38 final size:38
Alignment explanation
Indices: 5407732--5407810 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
5407722 ACAATTCATT
5407732 TATAGTTTCAACAAGTTAGCGGAGGGACCGATTAGCCA
1 TATAGTTTCAACAAGTTAGCGGAGGGACCGATTAGCCA
* *
5407770 TATAGTTTCAACGAGTTAGCGGAGGGACCGATTGGCCA
1 TATAGTTTCAACAAGTTAGCGGAGGGACCGATTAGCCA
5407808 TAT
1 TAT
5407811 GTAGTTGAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (38 bp):
TATAGTTTCAACAAGTTAGCGGAGGGACCGATTAGCCA
Found at i:5410632 original size:2 final size:2
Alignment explanation
Indices: 5410625--5410651 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5410615 CTATTAAAAG
5410625 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 T
5410652 GTTTTGGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5415119 original size:27 final size:27
Alignment explanation
Indices: 5415088--5415140 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5415078 AAATTTAAAT
*
5415088 TCCTACTCCTACTAACAAGTTAACAAC
1 TCCTACTCCTACTAACAAGGTAACAAC
5415115 TCCTACTCCTACTAACAAGGTAACAA
1 TCCTACTCCTACTAACAAGGTAACAA
5415141 ATCTCCCTAG
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:0.38, C:0.32, G:0.06, T:0.25
Consensus pattern (27 bp):
TCCTACTCCTACTAACAAGGTAACAAC
Found at i:5416395 original size:6 final size:6
Alignment explanation
Indices: 5416384--5416457 Score: 71
Period size: 6 Copynumber: 11.7 Consensus size: 6
5416374 TTTTTCCTTC
*
5416384 TTTTTA TTTTTA TTTTTA -TTTTA TTTATTTA TTGTTTA TGTTTA TTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA -TT-TTTA TT-TTTA TTTTTA TT-TTTA
5416435 TTTTTA TTTGTT- TATTTTA TTTT
1 TTTTTA TTT-TTA T-TTTTA TTTT
5416458 ATTATATATA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
5 5 0.09
6 30 0.52
7 19 0.33
8 4 0.07
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:5416462 original size:13 final size:13
Alignment explanation
Indices: 5416385--5416532 Score: 58
Period size: 13 Copynumber: 11.0 Consensus size: 13
5416375 TTTTCCTTCT
5416385 TTTTA-TTT-TTA
1 TTTTATTTTATTA
5416396 TTTTTATTTTATT-
1 -TTTTATTTTATTA
*
5416409 TATTTATTGT-TTA
1 T-TTTATTTTATTA
*
5416422 TGTTTATTAT-TTA
1 T-TTTATTTTATTA
5416435 TTTTTATTTGT-TTA
1 -TTTTATTT-TATTA
5416449 TTTTATTTTATTA
1 TTTTATTTTATTA
* * * **
5416462 TATATATATAAGCA
1 T-TTTATTTTATTA
5416476 TATTTATTATTATTA
1 T-TTTATT-TTATTA
5416491 TTATTATTATTATTA
1 TT-TTATT-TTATTA
*
5416506 -TTTATATTACTTA
1 TTTTATTTTA-TTA
*
5416519 TTTTCATTTCATTA
1 TTTT-ATTTTATTA
5416533 CATTTTTATT
Statistics
Matches: 106, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
12 12 0.11
13 46 0.43
14 28 0.26
15 20 0.19
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:5416487 original size:3 final size:3
Alignment explanation
Indices: 5416479--5416520 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
5416469 ATAAGCATAT
5416479 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TATA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TT
5416521 TTCATTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 1 0.03
3 31 0.86
4 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5418296 original size:109 final size:109
Alignment explanation
Indices: 5418152--5418354 Score: 282
Period size: 109 Copynumber: 1.9 Consensus size: 109
5418142 CATTTATTGA
* * * * * * * *
5418152 TTTTAAATAGGATATTCAATTATTTTGGTTTAAAGAAAAATCATACCCTGCACGTTAGGGCACAA
1 TTTTAAATAGAATATCCAATTACTTAGATTCAAAGAAAAATCATACCCAGCACGTTAAGGCACAA
*
5418217 -TTCTTCGAGTTCCCTAAAATAAAAAAACACTGAACATTTATCAG
66 TTTC-TCGAATTCCCTAAAATAAAAAAACACTGAACATTTATCAG
*
5418261 TTTTAAATAGAATATCCAATTACTTAGATTCAAAGAAAAATCATACTCAGCACGTTAAGGCACAA
1 TTTTAAATAGAATATCCAATTACTTAGATTCAAAGAAAAATCATACCCAGCACGTTAAGGCACAA
* *
5418326 TTTCTCGAATTTCCTAAAATAAAATAACA
66 TTTCTCGAATTCCCTAAAATAAAAAAACA
5418355 TTGTCTCATT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 78 0.96
110 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (109 bp):
TTTTAAATAGAATATCCAATTACTTAGATTCAAAGAAAAATCATACCCAGCACGTTAAGGCACAA
TTTCTCGAATTCCCTAAAATAAAAAAACACTGAACATTTATCAG
Found at i:5420524 original size:99 final size:100
Alignment explanation
Indices: 5420298--5421045 Score: 431
Period size: 99 Copynumber: 7.8 Consensus size: 100
5420288 CTTTAGGAAG
* * * * * *
5420298 ATAGGATTTGGTGTTG-AAGCTTCTCTCCATTCCACTGTTACCTTAGGGACATTCAGA-TCTGCT
1 ATAGGATTTGATGTTGTAA-CTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGC-
* * *
5420361 TTTGTTGTTCTAATCCGACCCACTGCAAC-T----GT
64 TTCGTTGTTTTAATCCGACCCACTACAACTTAGGGGT
* * * * *
5420393 ATAGGATTTGGTGTTGTAATTTCACTCCATTCCATTGTAAACTCAGGGACATTGAGATTC-GCTT
1 ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
5420457 CGTTGCTTTT-ATCCGACCCACTACAACTTAGGGGT
66 CGTTG-TTTTAATCCGACCCACTACAACTTAGGGGT
* * * * * *
5420492 ATAGGAGTTGATGTTGTAACTTCTCTCTATTCCATTATAACCTCAAGGATATTGAGA-TCTG-TT
1 ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
* * * * *
5420555 AC-TCGTTTTGATCCGATCCACTACAATTTAAGGGAT
66 -CGTTGTTTTAATCCGACCCACTACAACTT-AGGGGT
* * * *
5420591 ATAGGATCTG--G-TG---CTTCACTCTATTCCACTGTAACCTCAAGGACATT-AAAATCTGCTT
1 ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
* * * *
5420649 TGTTGTTTTAATCCGACCCACTGCAACTCAAGGGT
66 CGTTGTTTTAATCCGACCCACTACAACTTAGGGGT
* * * * * *
5420684 ATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTAGGGACATTAAGA-TCCG-TT
1 ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
** * * * ** *
5420747 AC-TCATTTTGATCTGATCCACTGTAACTTCAGGGAT
66 -CGTTGTTTTAATCCGACCCACTACAACTT-AGGGGT
* * * * * **
5420783 ATAGGATCTG--G-TG---CTTCACTCTATTCTACTATAACCTCAAGAACATTGAGA-TCCACTT
1 ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
* * * * *
5420841 TGTTGCTTTAATCCGACCTACTGCAACTTACGGGT
66 CGTTGTTTTAATCCGACCCACTACAACTTAGGGGT
* * * * * * * *
5420876 ATGGGATTTAATGTTGTAACATCTCTCCATTCCACTGTAACCTTAAGGGCATTGAG-CTC-GGTT
1 ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
* * * *
5420939 AC-TTATTTTGATCCGATCCACTACAACTTCAGGGAT
66 -CGTTGTTTTAATCCGACCCACTACAACTT-AGGGGT
* * * * * * *
5420975 ATAGGA--T-ATG--GT-GCTTCACTTCATTCCACTATAATCTTAGGGATATTGAGATT-TGCTT
1 ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
*
5421033 TGTTGTTTTAATC
66 CGTTGTTTTAATC
5421046 TGCTTCACTG
Statistics
Matches: 499, Mismatches: 116, Indels: 77
0.72 0.17 0.11
Matches are distributed among these distances:
92 2 0.00
93 119 0.24
94 81 0.16
95 55 0.11
96 15 0.03
97 7 0.01
98 68 0.14
99 150 0.30
100 2 0.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (100 bp):
ATAGGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACATTGAGATTCTGCTT
CGTTGTTTTAATCCGACCCACTACAACTTAGGGGT
Found at i:5420626 original size:93 final size:93
Alignment explanation
Indices: 5420511--5421026 Score: 365
Period size: 93 Copynumber: 5.4 Consensus size: 93
5420501 GATGTTGTAA
* * * *
5420511 CTTCTCTCTATTCCATTATAACCTCAAGGATATTGAGATCTGTTACTCGTTTTGATCCGATCCAC
1 CTTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTGATCCGATCCAC
* *
5420576 TACAATTTAAGGGATATAGGATCTGGTG
66 TGCAACTTAAGGGATATAGGATCTGGTG
* * * ** * *
5420604 CTTCACTCTATTCCACTGTAACCTCAAGGACATTAAAATCTGCTTTGTTGTTTTAATCCGACCCA
1 CTTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCTG-TTACTTGTTTTGATCCGATCCA
* * *
5420669 CTGCAACTCAAGGG-TATGGGATTTGATGTTG
65 CTGCAACTTAAGGGATATAGGATCTG--G-TG
* * * * * * * ** *
5420700 TAACTTCTCTCCATTCCACTGTAACCTTAGGGACATTAAGATCCGTTACTCATTTTGATCTGATC
1 ---CTTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTGATCCGATC
* *
5420765 CACTGTAACTTCAGGGATATAGGATCTGGTG
63 CACTGCAACTTAAGGGATATAGGATCTGGTG
* * ** ** * *
5420796 CTTCACTCTATTCTACTATAACCTCAAGAACATTGAGATCCACTTTGTTGCTTTAATCCGA-CCT
1 CTTCACTCTATTCCACTATAACCTCAAGGACATTGAGAT-CTGTTACTTGTTTTGATCCGATCC-
* * * **
5420860 ACTGCAACTTACGGG-TATGGGATTTAATG
64 ACTGCAACTTAAGGGATATAGGATCTGGTG
* * * * * * *
5420889 TTGTAACATCTCTCCATTCCACTGTAACCTTAAGGGCATTGAGCTCGGTTACTTATTTTGATCCG
1 CT-T--CA-CTCT--ATTCCACTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTGATCCG
* * *
5420954 ATCCACTACAACTTCAGGGATATAGGATATGGTG
60 ATCCACTGCAACTTAAGGGATATAGGATCTGGTG
* * * *
5420988 CTTCACT-TCATTCCACTATAATCTTAGGGATATTGAGAT
1 CTTCACTCT-ATTCCACTATAACCTCAAGGACATTGAGAT
5421027 TTGCTTTGTT
Statistics
Matches: 319, Mismatches: 86, Indels: 36
0.72 0.20 0.08
Matches are distributed among these distances:
93 114 0.36
94 54 0.17
95 3 0.01
96 8 0.03
97 5 0.02
98 53 0.17
99 82 0.26
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (93 bp):
CTTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCTGTTACTTGTTTTGATCCGATCCAC
TGCAACTTAAGGGATATAGGATCTGGTG
Found at i:5420697 original size:192 final size:192
Alignment explanation
Indices: 5420413--5421045 Score: 795
Period size: 192 Copynumber: 3.3 Consensus size: 192
5420403 GTGTTGTAAT
* * * * * *
5420413 TTCACTCCATTCCATTGTAAACTCAGGGACATTGAGAT-TCGCTTCGTTGCTTTT-ATCCGACCC
1 TTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCT-GCTTTGTTG-TTTTAATCCGACCC
* * * * * * * *
5420476 ACTACAACTTAGGGGTATAGGAGTTGATGTTGTAACTTCTCTCTATTCCATTATAACCTCAAGGA
64 ACTGCAACTTAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTAAGGA
* * * * *
5420541 TATTGAGATCTGTTACTCGTTTTGATCCGATCCACTACAATTTAAGGGATATAGGATCTGGTGC
129 CATTGAGATCCGTTACTCATTTTGATCCGATCCACTACAACTTCAGGGATATAGGATCTGGTGC
* * *
5420605 TTCACTCTATTCCACTGTAACCTCAAGGACATTAAAATCTGCTTTGTTGTTTTAATCCGACCCAC
1 TTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAATCCGACCCAC
* *
5420670 TGCAACTCAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTAGGGACA
66 TGCAACTTAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTAAGGACA
* * **
5420735 TTAAGATCCGTTACTCATTTTGATCTGATCCACTGTAACTTCAGGGATATAGGATCTGGTGC
131 TTGAGATCCGTTACTCATTTTGATCCGATCCACTACAACTTCAGGGATATAGGATCTGGTGC
* * ** * *
5420797 TTCACTCTATTCTACTATAACCTCAAGAACATTGAGATCCACTTTGTTGCTTTAATCCGACCTAC
1 TTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAATCCGACCCAC
* * * *
5420862 TGCAACTTACGGGTATGGGATTTAATGTTGTAACATCTCTCCATTCCACTGTAACCTTAAGGGCA
66 TGCAACTTAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTAAGGACA
* * * *
5420927 TTGAGCTCGGTTACTTATTTTGATCCGATCCACTACAACTTCAGGGATATAGGATATGGTGC
131 TTGAGATCCGTTACTCATTTTGATCCGATCCACTACAACTTCAGGGATATAGGATCTGGTGC
* * * * *
5420989 TTCACT-TCATTCCACTATAATCTTAGGGATATTGAGATTTGCTTTGTTGTTTTAATC
1 TTCACTCT-ATTCCACTATAACCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAATC
5421046 TGCTTCACTG
Statistics
Matches: 379, Mismatches: 59, Indels: 6
0.85 0.13 0.01
Matches are distributed among these distances:
191 5 0.01
192 373 0.98
193 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (192 bp):
TTCACTCTATTCCACTATAACCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAATCCGACCCAC
TGCAACTTAAGGGTATGGGATTTGATGTTGTAACTTCTCTCCATTCCACTGTAACCTTAAGGACA
TTGAGATCCGTTACTCATTTTGATCCGATCCACTACAACTTCAGGGATATAGGATCTGGTGC
Found at i:5421235 original size:42 final size:42
Alignment explanation
Indices: 5421121--5421235 Score: 112
Period size: 42 Copynumber: 2.7 Consensus size: 42
5421111 TAGGGACGTA
* * * *
5421121 AGATTCATCTTTGCAGCTTCAATCTAGC-CCTTTATAGCTTTG
1 AGATTCACCTTTGCGGCTTCAATCT-GCTTCTTTACAGCTTTG
* *
5421163 AGATTCACCTTTTCGGCTTTAATTCT-CTTCTTTACAG-TCTTG
1 AGATTCACCTTTGCGGCTTCAA-TCTGCTTCTTTACAGCT-TTG
5421205 AGATT-AGCCTTTGCGGCTTCAATCTGCTTCT
1 AGATTCA-CCTTTGCGGCTTCAATCTGCTTCT
5421236 CCTCATCTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
41 6 0.10
42 51 0.85
43 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (42 bp):
AGATTCACCTTTGCGGCTTCAATCTGCTTCTTTACAGCTTTG
Found at i:5421292 original size:49 final size:49
Alignment explanation
Indices: 5421246--5421581 Score: 404
Period size: 49 Copynumber: 6.9 Consensus size: 49
5421236 CCTCATCTTC
*** * * *
5421246 AGGGTATAAGATTTACCGTTCCGGCTTCAATCTTTTCCTTAACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* *
5421295 AGGGTACAAGATTCGTCGTTGCGACTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
*
5421344 AGGGTATAAGATTCGTCGTTGCAGCTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * ** *
5421393 AGGGTATAAGGTTTGTCATTGTAGCTTCAATCTTTCCCTCCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* *
5421442 AGGGTATAAGATTCGTCATTGCAGC-TCTAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTC-AATCTTTCCCTTCACATCTCT
* * * * * * * *
5421491 AGTGTATAATATTCGTTGTTGCGGCTTTAATCTTTCCCTCCACGTTTTT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * *
5421540 AGGGTATAAGATTCGCCATTACGGCTTCAATCTTTCCCTTCA
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCA
5421582 TGTCTTCTAA
Statistics
Matches: 247, Mismatches: 38, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
48 2 0.01
49 244 0.99
50 1 0.00
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (49 bp):
AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
Found at i:5422594 original size:16 final size:15
Alignment explanation
Indices: 5422563--5422610 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
5422553 ATCTCACTTG
*
5422563 TTTCTTTTTCTCTCTT
1 TTTC-TTTTCTTTCTT
*
5422579 TTTTTTCTTCTTTCTT
1 TTTCTT-TTCTTTCTT
5422595 TTTCTTTTCTTT-TT
1 TTTCTTTTCTTTCTT
5422609 TT
1 TT
5422611 GGGGTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 16 0.57
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Done.