Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008162.1 Hibiscus syriacus cultivar Beakdansim tig00110733_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3688897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2367458 original size:192 final size:192
Alignment explanation
Indices: 2367185--2367675 Score: 560
Period size: 192 Copynumber: 2.5 Consensus size: 192
2367175 CTAAAGTATC
* * * *
2367185 GATACTATGGTACATATACTTATAAAAGTATCGATACCGTCAACATATCCGGTAGCGCTTTACCG
1 GATACTTTGGTACATATACTTATAAAAGTATTGATACTGTCAACAT-TCCGGTAGCTCTTTACCG
* *
2367250 GATTTGTCAAATTGAAACCGGTTTTGTCAGATTTCAACATGTTATATT-TCTTGTATCGATACAT
65 GTTTTGTCAAATTGAAACCGGTTTTGTCA-ATTTCAACATGTTATATTGTCATGTATCGATACAT
* * *
2367314 GCGTATAAGATATCGATACTTT-ATA-G-GCGCTATTATTCAATTCTTTTCAATTCCTACAATAC
129 GCGTATAAGATATCAATACTTTCAGATGTGC-CT-TTATTCAATTCTTTTAAATTCCTACAATAC
2367376 T
192 T
* * * *
2367377 GATACTTTGGTAAACATACTTATAAAAGTATTGATACTGTCAAGACTTCCGATAGCTCTTTACCG
1 GATACTTTGGTACATATACTTATAAAAGTATTGATACTGTCAACA-TTCCGGTAGCTCTTTACCG
* * *
2367442 GTTTTTTCAAATTGAAACTGGTTTTGTCCAATTTCAACATGTTATATTGTCATGTATCGATATAT
65 GTTTTGTCAAATTGAAACCGGTTTTGT-CAATTTCAACATGTTATATTGTCATGTATCGATACAT
* * * * * * *
2367507 GTGTGTAAGGTATCAATACTTTCGAGATGTTTTCCTTTTTTTATTTCTTTTAAATTCCTACAATA
129 GCGTATAAGATATCAATACTTTC-AGATG--TGCCTTTATTCAATTCTTTTAAATTCCTACAATA
2367572 CT
191 CT
* * *
2367574 GATACTTTGGTACATATACTTATAAACGT-TTCGATACAAATTTCAACAATTCCGGTAGCTTTTT
1 GATACTTTGGTACATATACTTATAAAAGTATT-GATAC---TGTCAAC-ATTCCGGTAGCTCTTT
** *
2367638 ACCGGTTTTGTCAAATTTCAACCGGTTTTGTCATTTTC
61 ACCGGTTTTGTCAAATTGAAACCGGTTTTGTCAATTTC
2367676 CAATTGGTTT
Statistics
Matches: 250, Mismatches: 35, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
192 97 0.39
193 35 0.14
195 2 0.01
196 3 0.01
197 58 0.23
198 2 0.01
199 7 0.03
200 45 0.18
201 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (192 bp):
GATACTTTGGTACATATACTTATAAAAGTATTGATACTGTCAACATTCCGGTAGCTCTTTACCGG
TTTTGTCAAATTGAAACCGGTTTTGTCAATTTCAACATGTTATATTGTCATGTATCGATACATGC
GTATAAGATATCAATACTTTCAGATGTGCCTTTATTCAATTCTTTTAAATTCCTACAATACT
Found at i:2369702 original size:24 final size:23
Alignment explanation
Indices: 2369652--2369703 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2369642 TATTATATTT
* * *
2369652 TTAATATTTTATATTTAATTTAT
1 TTAATATTTAATATTTAACTTAA
*
2369675 TTAAGTATTTAATATTTTACTTAA
1 TTAA-TATTTAATATTTAACTTAA
2369699 TTAAT
1 TTAAT
2369704 TTTTTTGCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTAATATTTAATATTTAACTTAA
Found at i:2371929 original size:13 final size:13
Alignment explanation
Indices: 2371909--2371955 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
2371899 TATTTAATAC
*
2371909 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
2371922 TGTTTATTGGACT
1 TTTTTATTGTAAT
2371935 TTTTTATTGTAAT
1 TTTTTATTGTAAT
2371948 TTTTTATT
1 TTTTTATT
2371956 ATTTATCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.02, G:0.13, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:2375429 original size:16 final size:16
Alignment explanation
Indices: 2375404--2375434 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2375394 TATTTTTTCA
*
2375404 AATAATTATAATAAAC
1 AATAAGTATAATAAAC
2375420 AATAAGTATAATAAA
1 AATAAGTATAATAAA
2375435 AAAATTATCA
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:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAGTATAATAAAC
Found at i:2377682 original size:15 final size:16
Alignment explanation
Indices: 2377660--2377702 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2377650 ACCCAGAAGT
2377660 TCCGGGTACCCGAAAA
1 TCCGGGTACCCGAAAA
**
2377676 T-CGGGTACATGAAAA
1 TCCGGGTACCCGAAAA
*
2377691 TCCGGATACCCG
1 TCCGGGTACCCG
2377703 GATTTACACA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (16 bp):
TCCGGGTACCCGAAAA
Found at i:2377778 original size:21 final size:21
Alignment explanation
Indices: 2377754--2377804 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2377744 TATCTTGAAC
* * * *
2377754 TATCATGTCAGTATCGTAAAT
1 TATCATATCAATACCGTAAAA
2377775 TATCATATCAATACCGTAAAA
1 TATCATATCAATACCGTAAAA
2377796 TATCATATC
1 TATCATATC
2377805 GGTATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (21 bp):
TATCATATCAATACCGTAAAA
Found at i:2381504 original size:16 final size:16
Alignment explanation
Indices: 2381485--2381527 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
2381475 TACATTTTAT
2381485 TTGAGTTTAAAATTAA
1 TTGAGTTTAAAATTAA
*
2381501 TTGAGTTAAAAAAATTAA
1 TTGAGTT--TAAAATTAA
2381519 -TGAGTTTAA
1 TTGAGTTTAA
2381528 GGTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 2 0.09
16 7 0.30
17 6 0.26
18 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (16 bp):
TTGAGTTTAAAATTAA
Found at i:2381589 original size:14 final size:14
Alignment explanation
Indices: 2381570--2381617 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
2381560 AGGGTTTGGA
2381570 GAACATAAACAAAT
1 GAACATAAACAAAT
2381584 GAACATAAAC----
1 GAACATAAACAAAT
*
2381594 GAAAATAAACAAAT
1 GAACATAAACAAAT
2381608 GAACATAAAC
1 GAACATAAAC
2381618 GAACATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.32
14 19 0.68
ACGTcount: A:0.65, C:0.15, G:0.08, T:0.12
Consensus pattern (14 bp):
GAACATAAACAAAT
Found at i:2381601 original size:24 final size:24
Alignment explanation
Indices: 2381574--2381620 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2381564 TTTGGAGAAC
2381574 ATAAACAAATGAACATAAACGAAA
1 ATAAACAAATGAACATAAACGAAA
2381598 ATAAACAAATGAACATAAACGAA
1 ATAAACAAATGAACATAAACGAA
2381621 CATATTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.66, C:0.13, G:0.09, T:0.13
Consensus pattern (24 bp):
ATAAACAAATGAACATAAACGAAA
Found at i:2383308 original size:22 final size:22
Alignment explanation
Indices: 2383280--2383337 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
2383270 AATTATTTAA
2383280 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2383302 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2383324 ATTTATTTTTAAAA
1 ATTTA-TTTTAAAA
2383338 AATTTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 27 0.77
23 8 0.23
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:2383418 original size:31 final size:31
Alignment explanation
Indices: 2383361--2383419 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2383351 AGTTGTATGG
* *
2383361 ATTATTTAAATTTCATTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
2383392 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
2383420 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:2385908 original size:31 final size:31
Alignment explanation
Indices: 2385838--2385961 Score: 117
Period size: 31 Copynumber: 4.0 Consensus size: 31
2385828 GTCGAGGGTT
2385838 TACCTATGTTCTACGGAACATATGGACAGA-A
1 TACCTATGTTCTACGGAACATATGGACA-ATA
* *
2385869 TTACCTATG-TCTTTCGGGACATATGGACAATA
1 -TACCTATGTTC-TACGGAACATATGGACAATA
* * * *
2385901 TACCTATGTTCTAAGGAATATATGGACATTT
1 TACCTATGTTCTACGGAACATATGGACAATA
* * * *
2385932 TACCTAGGTTCTTCGGGACCTATGGACAAT
1 TACCTATGTTCTACGGAACATATGGACAAT
2385962 TGCCGAGGTT
Statistics
Matches: 74, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
31 48 0.65
32 26 0.35
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAATA
Found at i:2386994 original size:18 final size:18
Alignment explanation
Indices: 2386958--2387008 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
2386948 TATACAACGT
* *
2386958 ATAATTATAAATTAGTTAA
1 ATAATT-TAAAATAATTAA
2386977 A-AATTTACAAATAATTAA
1 ATAATTTA-AAATAATTAA
*
2386995 ATTATTTAAAATAA
1 ATAATTTAAAATAA
2387009 AGGGTAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 2 0.07
18 19 0.70
19 6 0.22
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
ATAATTTAAAATAATTAA
Found at i:2393328 original size:2 final size:2
Alignment explanation
Indices: 2393323--2393350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2393313 GAAAAAATAG
2393323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2393351 GGAGTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2394510 original size:15 final size:15
Alignment explanation
Indices: 2394490--2394557 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
2394480 CGAAGTTGAT
2394490 GATGATGATGAGGAA
1 GATGATGATGAGGAA
* *
2394505 GATGATGTTGTGGAA
1 GATGATGATGAGGAA
*
2394520 GTTCATGAT-ATTGGGGATA
1 G---ATGATGA-TGAGGA-A
2394539 G-TGATGATGAGGAA
1 GATGATGATGAGGAA
2394553 GATGA
1 GATGA
2394558 CATAGACGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
14 2 0.05
15 26 0.63
16 1 0.02
18 10 0.24
19 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.38, T:0.28
Consensus pattern (15 bp):
GATGATGATGAGGAA
Found at i:2398176 original size:22 final size:21
Alignment explanation
Indices: 2398134--2398177 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2398124 CTTGATAATG
*
2398134 ATATTTTTAATTATTTTTTTA
1 ATATTTTTAATTATTTATTTA
2398155 ATATTTTATAATT-TTTAATTTA
1 ATATTTT-TAATTATTT-ATTTA
2398177 A
1 A
2398178 AAATACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATATTTTTAATTATTTATTTA
Found at i:2398837 original size:28 final size:29
Alignment explanation
Indices: 2398805--2398895 Score: 85
Period size: 32 Copynumber: 3.0 Consensus size: 29
2398795 GAAACCGACT
2398805 CGAGTTCGAACTGG-TGTGGATCTGAACC
1 CGAGTTCGAACTGGATGTGGATCTGAACC
* *
2398833 CGAGTTGGACCTGGAAATTGTGGATCTGAACC
1 CGAGTTCGAACTGG--A-TGTGGATCTGAACC
* *
2398865 CGAGTTGGACCTGGAAATTGTGGATCTGAAC
1 CGAGTTCGAACTGG--A-TGTGGATCTGAAC
2398896 TCGACCTGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
28 12 0.21
32 45 0.79
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (29 bp):
CGAGTTCGAACTGGATGTGGATCTGAACC
Found at i:2398860 original size:32 final size:32
Alignment explanation
Indices: 2398819--2398895 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
2398809 TTCGAACTGG
2398819 TGTGGATCTGAACCCGAGTTGGACCTGGAAAT
1 TGTGGATCTGAACCCGAGTTGGACCTGGAAAT
2398851 TGTGGATCTGAACCCGAGTTGGACCTGGAAAT
1 TGTGGATCTGAACCCGAGTTGGACCTGGAAAT
2398883 TGTGGATCTGAAC
1 TGTGGATCTGAAC
2398896 TCGACCTGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (32 bp):
TGTGGATCTGAACCCGAGTTGGACCTGGAAAT
Found at i:2398901 original size:26 final size:28
Alignment explanation
Indices: 2398840--2398903 Score: 69
Period size: 32 Copynumber: 2.2 Consensus size: 28
2398830 ACCCGAGTTG
*
2398840 GACCTGGAAATTGTGGATCTGAACCCGAGTTG
1 GACCTGGAAATTGTGGATCTGAA-CC--G-TC
2398872 GACCTGGAAATTGTGGATCTGAA-C-TC
1 GACCTGGAAATTGTGGATCTGAACCGTC
2398898 GACCTG
1 GACCTG
2398904 CACCCGATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 7 0.23
30 1 0.03
32 23 0.74
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (28 bp):
GACCTGGAAATTGTGGATCTGAACCGTC
Found at i:2400409 original size:20 final size:20
Alignment explanation
Indices: 2400386--2400425 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2400376 TATAATGTAC
2400386 ATTAT-ATATACATGCATCAT
1 ATTATCATA-ACATGCATCAT
*
2400406 ATTATCATAACATTCATCAT
1 ATTATCATAACATGCATCAT
2400426 GCATACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (20 bp):
ATTATCATAACATGCATCAT
Found at i:2404272 original size:21 final size:21
Alignment explanation
Indices: 2404248--2404302 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2404238 CCCCTATGGG
*
2404248 GAGTATCAATACTCTATGAAT
1 GAGTATCAATACTATATGAAT
*
2404269 GAGTATCGATACTATATGAAT
1 GAGTATCAATACTATATGAAT
2404290 GAGTATCAATACT
1 GAGTATCAATACT
2404303 GGCCTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (21 bp):
GAGTATCAATACTATATGAAT
Found at i:2405299 original size:2 final size:2
Alignment explanation
Indices: 2405292--2405401 Score: 79
Period size: 2 Copynumber: 56.0 Consensus size: 2
2405282 AATCTATACT
* *
2405292 TA TA TA TA TA TA TA TA TA TA T- TA TA TA CTT TT TA GTA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * *
2405334 TA TA TT TA TA TA TT TA TA TA T- TA TA TA TA TA CA TA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
2405375 TA TA GA TA TT TA CT- TA TA TA TA T- TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
2405402 AGTATAATGT
Statistics
Matches: 86, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
1 6 0.07
2 75 0.87
3 5 0.06
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2407624 original size:19 final size:20
Alignment explanation
Indices: 2407596--2407649 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
2407586 TACTATTCAT
*
2407596 AGTTTGGAAAATTT-GTAAG
1 AGTTTCGAAAATTTAGTAAG
* * *
2407615 AGTTTTGAAACTTTATTAAG
1 AGTTTCGAAAATTTAGTAAG
*
2407635 AGTTTCGAAACTTTA
1 AGTTTCGAAAATTTA
2407650 TAAATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (20 bp):
AGTTTCGAAAATTTAGTAAG
Found at i:2407634 original size:20 final size:19
Alignment explanation
Indices: 2407596--2407667 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
2407586 TACTATTCAT
* * *
2407596 AGTTTGGAAAATTTGTAAG
1 AGTTTTGAAACTTTATAAG
2407615 AGTTTTGAAACTTTATTAAG
1 AGTTTTGAAACTTTA-TAAG
*
2407635 AGTTTCGAAACTTTATAA-
1 AGTTTTGAAACTTTATAAG
*
2407653 ATTTTTTGAAACTTT
1 A-GTTTTGAAACTTT
2407668 GCACCCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 1 0.02
19 26 0.58
20 18 0.40
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (19 bp):
AGTTTTGAAACTTTATAAG
Found at i:2407665 original size:19 final size:20
Alignment explanation
Indices: 2407611--2407667 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
2407601 GGAAAATTTG
2407611 TAAGAGTTTTGAAACTTTAT
1 TAAGAGTTTTGAAACTTTAT
*
2407631 TAAGAGTTTCGAAACTTTA-
1 TAAGAGTTTTGAAACTTTAT
*
2407650 TAA-ATTTTTTGAAACTTT
1 TAAGA-GTTTTGAAACTTT
2407668 GCACCCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 14 0.42
20 18 0.55
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (20 bp):
TAAGAGTTTTGAAACTTTAT
Found at i:2411160 original size:14 final size:14
Alignment explanation
Indices: 2411141--2411168 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2411131 TACTTATTCT
2411141 CCATTGTTGAATTA
1 CCATTGTTGAATTA
2411155 CCATTGTTGAATTA
1 CCATTGTTGAATTA
2411169 TTTTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
CCATTGTTGAATTA
Found at i:2411716 original size:20 final size:21
Alignment explanation
Indices: 2411686--2411737 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
2411676 TTTAAGTAAG
* *
2411686 AGTTTCAAAACTTTTATTAAA
1 AGTTTCGAAACTTTTATCAAA
*
2411707 A-TTTCGAAAC-TTTCTCAAA
1 AGTTTCGAAACTTTTATCAAA
2411726 AGTTTCGAAACT
1 AGTTTCGAAACT
2411738 ACATGTGCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.31
20 17 0.65
21 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (21 bp):
AGTTTCGAAACTTTTATCAAA
Found at i:2417755 original size:21 final size:21
Alignment explanation
Indices: 2417729--2417792 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
2417719 TTTTGGTGCA
*
2417729 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
2417750 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
2417771 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
2417793 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:2417799 original size:21 final size:21
Alignment explanation
Indices: 2417731--2417812 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
2417721 TTGGTGCAGA
*
2417731 GGGAATCGA-TCCCCCC-CATG
1 GGGAACCGATTCCCCCCACA-G
*
2417751 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
2417775 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
2417796 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
2417813 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 25 0.50
22 6 0.12
23 16 0.32
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.38, G:0.24, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:2425603 original size:19 final size:19
Alignment explanation
Indices: 2425562--2425607 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2425552 TCTTCAGTAT
* * *
2425562 TTTTATTGTTGTTTTTTCC
1 TTTTATTTTTATTTTTTCA
*
2425581 TTTTATTTTTATTTTTTTA
1 TTTTATTTTTATTTTTTCA
2425600 TTTTATTT
1 TTTTATTT
2425608 GTTTATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTATTTTTATTTTTTCA
Found at i:2425617 original size:13 final size:13
Alignment explanation
Indices: 2425582--2425617 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2425572 GTTTTTTCCT
*
2425582 TTTATTTTTATTTT
1 TTTA-TTTTATTTG
2425596 TTTATTTTATTTG
1 TTTATTTTATTTG
2425609 TTTATTTTA
1 TTTATTTTA
2425618 GCCTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTATTTTATTTG
Found at i:2427099 original size:55 final size:55
Alignment explanation
Indices: 2426999--2427364 Score: 543
Period size: 55 Copynumber: 6.7 Consensus size: 55
2426989 CCCACAACCA
* * * * ** *
2426999 ATACGAAAATTTATACACTTAGTATGAATTTCCTATTTTTGCACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
** **
2427054 ATACAAAAATTCATAAACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
2427109 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCA
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* * **
2427164 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAATTTTACACATAAAGTTTCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
2427219 ATACGGAAATTCATCCACTTAGTATTAATTTATTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
2427274 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTACCT
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
2427329 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAA
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAA
2427365 CTTTTTGCAC
Statistics
Matches: 283, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 283 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (55 bp):
ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
Found at i:2429429 original size:23 final size:23
Alignment explanation
Indices: 2429399--2429462 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
2429389 TGAAAGAGGT
*
2429399 TTTTTTTCTTTTATTTAAAGAGA
1 TTTTTTTCTTTTATTAAAAGAGA
*
2429422 TTTTTTTCTTTCATTAAAAGAGA
1 TTTTTTTCTTTTATTAAAAGAGA
2429445 TTTATTTCATCTTTTATT
1 TTT-TTT--TCTTTTATT
2429463 GGAATAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 24 0.69
24 3 0.09
26 8 0.23
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (23 bp):
TTTTTTTCTTTTATTAAAAGAGA
Found at i:2432178 original size:131 final size:130
Alignment explanation
Indices: 2431857--2432215 Score: 423
Period size: 131 Copynumber: 2.7 Consensus size: 130
2431847 GAGAATAGTA
* * * *
2431857 ATATCTTTTTATTTCGGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGATCATTTATTCTC
1 ATATCTATTCATTTCGATTGGAGTAATAAATG-ATGTTTTAAGGCATGAGAGATCATTTATTCTC
* * * * ** * *
2431922 AATTGGAAATAATTCGATATTACCATTTTCTCTAGAATCAATATTGTTTTTTTTAAGATGGAATA
65 GATTGGAAAT-ATTAGATATTATCATTTTCACTAGAATCAATATTG-TAATTTTAAGACGAAATA
2431987 ATG
128 ATG
* * * * * *
2431990 ATATATATTCATTTCGATTGGAGCAATAAATGATTTCTTTAAGGTATGAGAGGTCATTTATTCTT
1 ATATCTATTCATTTCGATTGGAGTAATAAATGATGT-TTTAAGGCATGAGAGATCATTTATTCTC
* * *
2432055 GATTGGAAAATATTAGATATGATCATTTTCACTATAATCGATATTG-AATTTTAAGACGAAATAA
65 GATTGG-AAATATTAGATATTATCATTTTCACTAGAATCAATATTGTAATTTTAAGACGAAATAA
2432119 TG
129 TG
* * *
2432121 ATATCTCTTCATTTCGACTGGAGTAATAAATGACTGTTTTAAGGCATGAAAGATCATTTATTCTC
1 ATATCTATTCATTTCGATTGGAGTAATAAATGA-TGTTTTAAGGCATGAGAGATCATTTATTCTC
*
2432186 GATTGGAAATACTTAGATATTATAATTTTC
65 GATTGGAAATA-TTAGATATTATCATTTTC
2432216 TCTCTTAAAA
Statistics
Matches: 190, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
130 5 0.03
131 91 0.48
132 4 0.02
133 86 0.45
134 4 0.02
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.41
Consensus pattern (130 bp):
ATATCTATTCATTTCGATTGGAGTAATAAATGATGTTTTAAGGCATGAGAGATCATTTATTCTCG
ATTGGAAATATTAGATATTATCATTTTCACTAGAATCAATATTGTAATTTTAAGACGAAATAATG
Found at i:2435311 original size:2 final size:2
Alignment explanation
Indices: 2435304--2435335 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2435294 GTTTTCTTTT
2435304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2435336 ATGTTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2435979 original size:15 final size:15
Alignment explanation
Indices: 2435961--2435999 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
2435951 AAAAAATTAA
2435961 ATTATAAAATAATAT
1 ATTATAAAATAATAT
2435976 ATTAT-AAATAA-AT
1 ATTATAAAATAATAT
2435989 -TTA-AAAATAAT
1 ATTATAAAATAAT
2436000 TATAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 6 0.27
15 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTATAAAATAATAT
Found at i:2436414 original size:30 final size:26
Alignment explanation
Indices: 2436380--2436454 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
2436370 TTTTAATGAA
*
2436380 AATAAAAATAAATTATTTTTAAATTAAGTT
1 AATAAAAA-AAA-TATATTT-AA-TAAGTT
*
2436410 AATAATAAAAATATATTTAATAAGTT
1 AATAAAAAAAATATATTTAATAAGTT
* *
2436436 AAT-ATAGAAATATATTTAA
1 AATAAAAAAAATATATTTAA
2436455 GTTAATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.36
26 9 0.21
27 2 0.05
28 6 0.14
29 3 0.07
30 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
AATAAAAAAAATATATTTAATAAGTT
Found at i:2436452 original size:25 final size:26
Alignment explanation
Indices: 2436404--2436454 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
2436394 ATTTTTAAAT
2436404 TAAGTTAATAATAAAAATATATTTAA
1 TAAGTTAATAATAAAAATATATTTAA
*
2436430 TAAGTTAAT-ATAGAAATATATTTAA
1 TAAGTTAATAATAAAAATATATTTAA
2436455 GTTAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (26 bp):
TAAGTTAATAATAAAAATATATTTAA
Found at i:2436475 original size:26 final size:25
Alignment explanation
Indices: 2436403--2436477 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 25
2436393 TATTTTTAAA
2436403 TTAAGTTAATA-ATA-AAAATATAT
1 TTAAGTTAATATATATAAAATATAT
2436426 TTAA--TAAGT-TAATATAGAAATATAT
1 TTAAGTTAA-TAT-ATATA-AAATATAT
2436451 TTAAGTTAATATATATAAAATTATAT
1 TTAAGTTAATATATATAAAA-TATAT
2436477 T
1 T
2436478 ATATATAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
21 3 0.07
22 1 0.02
23 7 0.16
24 1 0.02
25 15 0.35
26 12 0.28
27 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (25 bp):
TTAAGTTAATATATATAAAATATAT
Found at i:2437246 original size:31 final size:31
Alignment explanation
Indices: 2437211--2437277 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2437201 GGTGATCACT
* * *
2437211 TCTTAATTAAATAAAAATGAAAGTGACTATA
1 TCTTAATTAAATAAAAATAAAAGTAACCATA
*
2437242 TCTTAATTAAATAATAATAAAAGTAACCATA
1 TCTTAATTAAATAAAAATAAAAGTAACCATA
2437273 TCTTA
1 TCTTA
2437278 TGTTTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (31 bp):
TCTTAATTAAATAAAAATAAAAGTAACCATA
Found at i:2441130 original size:20 final size:21
Alignment explanation
Indices: 2441105--2441156 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2441095 GGATCCTAAG
*
2441105 TATCGATACTCCATGAACA-A
1 TATCGATACTCCAAGAACAGA
* * *
2441125 TATCGATACCCCAAGAATAGG
1 TATCGATACTCCAAGAACAGA
2441146 TATCGATACTC
1 TATCGATACTC
2441157 TTCTTATAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (21 bp):
TATCGATACTCCAAGAACAGA
Found at i:2442715 original size:57 final size:57
Alignment explanation
Indices: 2442651--2443080 Score: 621
Period size: 57 Copynumber: 7.5 Consensus size: 57
2442641 GTGCAAAATA
2442651 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
2442708 TAAGAAATCATAATAAGTGTATGAATTTTAGATAGAGCGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* ** *
2442765 TAAGAAATCATACCAAGTGTATGAATTTCAGATAGGGTATTTCGTACGTTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
2442822 TATGAAATCATACTAAGTGTATGAATTTCATG-TAGGGCATTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCA-GATAGGGCGTTTCGTACGCTAAAATGT
* * *
2442879 TAAGAAATCATACCAAGTGTATGAATTTCA-TTAGGGCGTTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
2442935 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
** ** * *
2442992 TAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCGTGTGCTATAATGA
1 TAA-GAAATCATACTAAGTGTATGAATTT-CAGATAGGGCGTTTCGTACGCTAAAATGT
2443051 TAAGAAATTCATACTAAGTGTATGAATTTC
1 TAAGAAA-TCATACTAAGTGTATGAATTTC
2443081 TGTATTGGAC
Statistics
Matches: 338, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
56 53 0.16
57 206 0.61
58 31 0.09
59 48 0.14
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:2443138 original size:58 final size:59
Alignment explanation
Indices: 2442825--2443143 Score: 210
Period size: 58 Copynumber: 5.5 Consensus size: 59
2442815 AAAATGTTAT
* * * ** * * **
2442825 GAAA-TCATACTAAGTGTATGAATTTCA-TGTAGGGCATTTCGTATGCTAAAATGTTAA
1 GAAATTCATACTAAGTGTATGAATTTCAGTATAGGACACTTCGGGTGCTATAAGGACAA
* * ** ** * * **
2442882 GAAA-TCATACCAAGTGTATGAATTTCA-T-TAGGGCGTTTCGTATGCTAAAATGTTAA
1 GAAATTCATACTAAGTGTATGAATTTCAGTATAGGACACTTCGGGTGCTATAAGGACAA
* ** *** * * *
2442938 GAAA-TCATACTAAGTGTATGAATTTCAG-ATAGGGCGTTTCGTACGCTAAAATGATAA
1 GAAATTCATACTAAGTGTATGAATTTCAGTATAGGACACTTCGGGTGCTATAAGGACAA
* * * *
2442995 GGAAA-TCATACTAAGTGTATGAATTTCCAG-ATAGGGCACTTCGTGTGCTATAATGATAA
1 -GAAATTCATACTAAGTGTATGAATTT-CAGTATAGGACACTTCGGGTGCTATAAGGACAA
* *
2443054 GAAATTCATACTAAGTGTATGAATTTCTGTATTGGACATCTT-GGGTGCTA-AAGGACAA
1 GAAATTCATACTAAGTGTATGAATTTCAGTATAGGACA-CTTCGGGTGCTATAAGGACAA
* *
2443112 GAAATTCATACTATGTGTATGAATTTCCGTAT
1 GAAATTCATACTAAGTGTATGAATTTCAGTAT
2443144 GGGAAACATA
Statistics
Matches: 237, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
56 53 0.22
57 53 0.22
58 67 0.28
59 61 0.26
60 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (59 bp):
GAAATTCATACTAAGTGTATGAATTTCAGTATAGGACACTTCGGGTGCTATAAGGACAA
Found at i:2443794 original size:45 final size:45
Alignment explanation
Indices: 2443730--2443844 Score: 140
Period size: 45 Copynumber: 2.6 Consensus size: 45
2443720 GCATAATTGT
* * * **
2443730 ATGAAATGATGTCATAAATGAAATGTATAATAGTGTATCAAAGGG
1 ATGAAAGGATGACATAAATGAAATGTATAATAGTGTATAAAAGAC
* * *
2443775 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGTATAAAATAC
1 ATGAAAGGATGACATAAATGAAATGTATAATAGTGTATAAAAGAC
* *
2443820 ATGTAAGGATGACATAATTGAAATG
1 ATGAAAGGATGACATAAATGAAATG
2443845 AATATATGTG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.27
Consensus pattern (45 bp):
ATGAAAGGATGACATAAATGAAATGTATAATAGTGTATAAAAGAC
Found at i:2445700 original size:77 final size:79
Alignment explanation
Indices: 2445597--2445749 Score: 179
Period size: 77 Copynumber: 2.0 Consensus size: 79
2445587 TTTCAAATTA
* *
2445597 AAAAACTTATTTAATTAATTCAAAATACATAT-ACAGT-AAAGAATTATAATCAGAATTAAAATC
1 AAAAACTTATTTAATTAATTCAAAATAAATATCA-AGTAAAAGAATTATAATCAAAATTAAAATC
2445660 -TTTAATGTTTATTT
65 TTTTAATGTTTATTT
* * * * * * *
2445674 AAAATCTTATTTAATT-ATTCCGAAATAAATATCAATTAAAAGAGTTGTAATCAAAATTATATTC
1 AAAAACTTATTTAATTAATT-CAAAATAAATATCAAGTAAAAGAATTATAATCAAAATTAAAATC
2445738 TTTTAATGTTTA
65 TTTTAATGTTTA
2445750 CTTACTATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
76 3 0.05
77 27 0.43
78 22 0.35
79 11 0.17
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (79 bp):
AAAAACTTATTTAATTAATTCAAAATAAATATCAAGTAAAAGAATTATAATCAAAATTAAAATCT
TTTAATGTTTATTT
Found at i:2445802 original size:15 final size:15
Alignment explanation
Indices: 2445782--2445817 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2445772 AAATCATCTG
2445782 TATATTAAATATACA
1 TATATTAAATATACA
* *
2445797 TATATTAACTATAGA
1 TATATTAAATATACA
2445812 TATATT
1 TATATT
2445818 TTAGTAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
TATATTAAATATACA
Found at i:2448995 original size:20 final size:19
Alignment explanation
Indices: 2448967--2449062 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 19
2448957 ACCACTTCGG
*
2448967 GTATTGATACCAAGCCTTCA
1 GTATGGATACCAA-CCTTCA
*
2448987 GTATGGATACTCAATCTTCA
1 GTATGGATAC-CAACCTTCA
* * *
2449007 ATATGGATACCAATCCATCCG
1 GTATGGATACCAA-CC-TTCA
*
2449028 GTATGGATACCAACCCTCTA
1 GTATGGATACCAACCTTC-A
*
2449048 GTATGGATATCAACC
1 GTATGGATACCAACC
2449063 CACCGATATC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.07
20 40 0.66
21 17 0.28
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (19 bp):
GTATGGATACCAACCTTCA
Found at i:2450552 original size:17 final size:15
Alignment explanation
Indices: 2450530--2450563 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
2450520 TGTATATTTC
2450530 TCTTTATCTTCTTCTTT
1 TCTTTAT-TTCTT-TTT
2450547 TCTTTATTTCTTTTT
1 TCTTTATTTCTTTTT
2450562 TC
1 TC
2450564 CTTCTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTATTTCTTTTT
Found at i:2450567 original size:27 final size:27
Alignment explanation
Indices: 2450524--2450577 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2450514 GAAGGTTGTA
2450524 TATTTCTCTTTATCTTCTTC-TTTTCTT
1 TATTTCTCTTTATCTTC-TCATTTTCTT
*
2450551 TATTTCT-TTTTTCCTTCTCATTTTCTT
1 TATTTCTCTTTAT-CTTCTCATTTTCTT
2450578 CTCTTCCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.70
Consensus pattern (27 bp):
TATTTCTCTTTATCTTCTCATTTTCTT
Found at i:2461830 original size:2 final size:2
Alignment explanation
Indices: 2461825--2461890 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
2461815 AATCTTATTC
2461825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2461867 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
2461891 TATCAGCATG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2474819 original size:18 final size:18
Alignment explanation
Indices: 2474796--2474830 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2474786 AGGTATTATC
2474796 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
2474814 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2474831 AATTCATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2475832 original size:33 final size:33
Alignment explanation
Indices: 2475795--2475869 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
2475785 TGTTTGTAAG
* *
2475795 ACATGTTAGATGTTTATATTTTCAAGACAATTT
1 ACATGTTAGATGTGTATATTTGCAAGACAATTT
*
2475828 ACATGTTACATGTGTATATTTGCAAGACAATTT
1 ACATGTTAGATGTGTATATTTGCAAGACAATTT
2475861 ACATGTTAG
1 ACATGTTAG
2475870 TAAGATCGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (33 bp):
ACATGTTAGATGTGTATATTTGCAAGACAATTT
Found at i:2479241 original size:21 final size:21
Alignment explanation
Indices: 2479215--2479257 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
2479205 TGAGTTAAGA
*
2479215 TCATATTGGGTATAGGTTGTT
1 TCATATTAGGTATAGGTTGTT
2479236 TCATATTAGGTATAGGTTGTT
1 TCATATTAGGTATAGGTTGTT
2479257 T
1 T
2479258 GTCTCCAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.49
Consensus pattern (21 bp):
TCATATTAGGTATAGGTTGTT
Found at i:2486805 original size:21 final size:21
Alignment explanation
Indices: 2486779--2486838 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
2486769 TAAAATTTGG
* *
2486779 CCCGAATGACCTCATATATGA
1 CCCGAAGGACCTCGTATATGA
*
2486800 CCCGAAGGACCTCGTATATGT
1 CCCGAAGGACCTCGTATATGA
*
2486821 CCCAAAGGACCTCGTATA
1 CCCGAAGGACCTCGTATA
2486839 ACTCTCGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (21 bp):
CCCGAAGGACCTCGTATATGA
Found at i:2493713 original size:21 final size:21
Alignment explanation
Indices: 2493689--2493740 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
2493679 GTCTCGAATA
* *
2493689 ACCTCATATATGTCCCGAAGG
1 ACCTCGTATATATCCCGAAGG
2493710 ACCTCGTATATATCCCGAAGG
1 ACCTCGTATATATCCCGAAGG
2493731 ACCTCGTATA
1 ACCTCGTATA
2493741 ACCCTCGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (21 bp):
ACCTCGTATATATCCCGAAGG
Found at i:2497359 original size:160 final size:160
Alignment explanation
Indices: 2497095--2497420 Score: 652
Period size: 160 Copynumber: 2.0 Consensus size: 160
2497085 TTTTATAAAA
2497095 TAAAATGTTTTATTAAAATTACCTGATTTTAGGTGTTCTAATCTCACCTTAAAAAGAACTAGTGG
1 TAAAATGTTTTATTAAAATTACCTGATTTTAGGTGTTCTAATCTCACCTTAAAAAGAACTAGTGG
2497160 TGACTCCCTTCTTTTCACAAAAATCTTTTAAAAAATCCCATTGTCATAATTAGTTGGCTTTTCTC
66 TGACTCCCTTCTTTTCACAAAAATCTTTTAAAAAATCCCATTGTCATAATTAGTTGGCTTTTCTC
2497225 CAATGAAGGGCCGATTTGACACGTAAATGT
131 CAATGAAGGGCCGATTTGACACGTAAATGT
2497255 TAAAATGTTTTATTAAAATTACCTGATTTTAGGTGTTCTAATCTCACCTTAAAAAGAACTAGTGG
1 TAAAATGTTTTATTAAAATTACCTGATTTTAGGTGTTCTAATCTCACCTTAAAAAGAACTAGTGG
2497320 TGACTCCCTTCTTTTCACAAAAATCTTTTAAAAAATCCCATTGTCATAATTAGTTGGCTTTTCTC
66 TGACTCCCTTCTTTTCACAAAAATCTTTTAAAAAATCCCATTGTCATAATTAGTTGGCTTTTCTC
2497385 CAATGAAGGGCCGATTTGACACGTAAATGT
131 CAATGAAGGGCCGATTTGACACGTAAATGT
2497415 TAAAAT
1 TAAAAT
2497421 ATTGAACTTG
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 166 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (160 bp):
TAAAATGTTTTATTAAAATTACCTGATTTTAGGTGTTCTAATCTCACCTTAAAAAGAACTAGTGG
TGACTCCCTTCTTTTCACAAAAATCTTTTAAAAAATCCCATTGTCATAATTAGTTGGCTTTTCTC
CAATGAAGGGCCGATTTGACACGTAAATGT
Found at i:2507965 original size:20 final size:21
Alignment explanation
Indices: 2507920--2507965 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
2507910 AAAAATTTAT
2507920 TTATTT-TTTCCAAAATCCAA
1 TTATTTCTTTCCAAAATCCAA
2507940 TT-TTTCTTT-CAAAA-CCAAA
1 TTATTTCTTTCCAAAATCC-AA
2507959 TTATTTC
1 TTATTTC
2507966 CATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATTTCTTTCCAAAATCCAA
Found at i:2508447 original size:12 final size:12
Alignment explanation
Indices: 2508429--2508472 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2508419 TGATTCATAC
2508429 CTTATTCTTCTT
1 CTTATTCTTCTT
*
2508441 GTTATTCTCTTCTT
1 CTTA-T-TCTTCTT
*
2508455 CTTTTTCTTCTT
1 CTTATTCTTCTT
2508467 CTTATT
1 CTTATT
2508473 TCCTTTGGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 15 0.58
13 2 0.08
14 9 0.35
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.68
Consensus pattern (12 bp):
CTTATTCTTCTT
Found at i:2513248 original size:19 final size:20
Alignment explanation
Indices: 2513219--2513260 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
2513209 GGCCTGCTAT
*
2513219 GTTATTTGGGCTTGAACTGG
1 GTTATTTGGGCCTGAACTGG
2513239 GTTA-TTGGGCCTGAACTGG
1 GTTATTTGGGCCTGAACTGG
2513258 GTT
1 GTT
2513261 GTTGTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.14, C:0.12, G:0.36, T:0.38
Consensus pattern (20 bp):
GTTATTTGGGCCTGAACTGG
Found at i:2513577 original size:36 final size:36
Alignment explanation
Indices: 2513537--2513671 Score: 198
Period size: 36 Copynumber: 3.8 Consensus size: 36
2513527 ATTTGCATAT
** *
2513537 CTTCACTACTCTTCCGTGAAGGTTGAAAACCATTGA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATAATTTA
* *
2513573 CTTCACTACTCTTCTGTGAAGGTTGAAAATGATTTA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATAATTTA
*
2513609 CTTCACTACTCTTTCGTGAAGGTTGAAAATAATTTA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATAATTTA
**
2513645 CTTCACTACTCTTTTGTGAAGGTTGAA
1 CTTCACTACTCTTCCGTGAAGGTTGAA
2513672 TGATGAACTT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (36 bp):
CTTCACTACTCTTCCGTGAAGGTTGAAAATAATTTA
Found at i:2513618 original size:72 final size:72
Alignment explanation
Indices: 2513537--2513671 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
2513527 ATTTGCATAT
*
2513537 CTTCACTACTCTTCCGTGAAGGTTGAAAACCATTGACTTCACTACTCTTCTGTGAAGGTTGAAAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAACAATTGACTTCACTACTCTTCTGTGAAGGTTGAAAA
2513602 TGATTTA
66 TGATTTA
* * * *
2513609 CTTCACTACTCTTTCGTGAAGGTTGAAAATAATTTACTTCACTACTCTTTTGTGAAGGTTGAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAACAATTGACTTCACTACTCTTCTGTGAAGGTTGAA
2513672 TGATGAACTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (72 bp):
CTTCACTACTCTTCCGTGAAGGTTGAAAACAATTGACTTCACTACTCTTCTGTGAAGGTTGAAAA
TGATTTA
Found at i:2513742 original size:36 final size:36
Alignment explanation
Indices: 2513695--2513788 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 36
2513685 AAGAATTTGT
** *
2513695 TTCACTACTCTTTCGTGAAGGTTGAATTTGCATT-TC
1 TTCACTACTCTTTCGTGAAGGTTGAAAATG-ATTAAC
2513731 TTCACTACTCTTTCGTGAAGGTTGAAAATGATTAAC
1 TTCACTACTCTTTCGTGAAGGTTGAAAATGATTAAC
2513767 TTCACTACTC-TTCTGTGAAGGT
1 TTCACTACTCTTTC-GTGAAGGT
2513789 CAGATTCGAG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
35 6 0.11
36 47 0.89
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (36 bp):
TTCACTACTCTTTCGTGAAGGTTGAAAATGATTAAC
Found at i:2519909 original size:45 final size:47
Alignment explanation
Indices: 2519858--2519949 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 47
2519848 TTTGTTGAGT
** * *
2519858 CCTAACCTTATATTTTCTAGTTC-CATGC-TTTATTTGAAAAATAAA
1 CCTAACCGCATATTTTATAGTTCGCATGCATTTATTAGAAAAATAAA
* *
2519903 CCTAACCGCATGTTTTATAGTTCGCATGCATTTATTAGGAAAATAAA
1 CCTAACCGCATATTTTATAGTTCGCATGCATTTATTAGAAAAATAAA
2519950 ACAATATTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 19 0.49
46 5 0.13
47 15 0.38
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (47 bp):
CCTAACCGCATATTTTATAGTTCGCATGCATTTATTAGAAAAATAAA
Found at i:2523341 original size:31 final size:30
Alignment explanation
Indices: 2523293--2523400 Score: 137
Period size: 31 Copynumber: 3.6 Consensus size: 30
2523283 CGGAAAATAA
* *
2523293 TTTACGTAAAATGAATTACCTGAAAACTGT
1 TTTACGTAAAATAAATTACCTGAAAATTGT
* *
2523323 TTTATGTAAAAATAAATTACATGAAAATTGT
1 TTTACGT-AAAATAAATTACCTGAAAATTGT
* *
2523354 TTTACGTAAAATGAATTACCT-AAAATTGC
1 TTTACGTAAAATAAATTACCTGAAAATTGT
*
2523383 TTTACATAAAATAAATTA
1 TTTACGTAAAATAAATTA
2523401 TATTTTTTGG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.34
30 18 0.27
31 26 0.39
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (30 bp):
TTTACGTAAAATAAATTACCTGAAAATTGT
Found at i:2523364 original size:15 final size:15
Alignment explanation
Indices: 2523339--2523394 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
2523329 TAAAAATAAA
*
2523339 TTACATGAAAATTGTT
1 TTACAT-AAAATTGAT
* *
2523355 TTACGTAAAA-TGAA
1 TTACATAAAATTGAT
* *
2523369 TTACCTAAAATTGCT
1 TTACATAAAATTGAT
2523384 TTACATAAAAT
1 TTACATAAAAT
2523395 AAATTATATT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.34
15 16 0.50
16 5 0.16
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38
Consensus pattern (15 bp):
TTACATAAAATTGAT
Found at i:2523708 original size:19 final size:19
Alignment explanation
Indices: 2523675--2523725 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2523665 AGTATTTTGT
* *
2523675 TAAAATAATACTAAAT-TA
1 TAAATTAATATTAAATGTA
*
2523693 TTATATTAATATTAAATGTA
1 -TAAATTAATATTAAATGTA
2523713 TAAATTAATATTA
1 TAAATTAATATTA
2523726 TTCATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAATTAATATTAAATGTA
Found at i:2523891 original size:13 final size:13
Alignment explanation
Indices: 2523849--2523947 Score: 52
Period size: 13 Copynumber: 7.7 Consensus size: 13
2523839 AAGTGGGTAC
2523849 ATATT-AATATAAT
1 ATATTAAATAT-AT
2523862 ATTATTAAA-AT-T
1 A-TATTAAATATAT
*
2523874 ATATTATATATAT
1 ATATTAAATATAT
*
2523887 ATATTAAATATTTT
1 ATATTAAATA-TAT
2523901 AATAATT-AATAT-T
1 -AT-ATTAAATATAT
*
2523914 TTCATTAAA-ATA-
1 AT-ATTAAATATAT
2523926 ATATTAAA-ATATT
1 ATATTAAATATA-T
2523939 ATATTAAAT
1 ATATTAAAT
2523948 TTAAATAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
11 15 0.22
12 11 0.16
13 22 0.32
14 9 0.13
15 8 0.12
16 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:2523944 original size:24 final size:24
Alignment explanation
Indices: 2523849--2523946 Score: 72
Period size: 25 Copynumber: 3.9 Consensus size: 24
2523839 AAGTGGGTAC
* *
2523849 ATATTAATATAATATTATTAAAATT
1 ATATTAAAATATTA-TATTAAAATT
*
2523874 ATATT-ATATATATATATTAAATATT
1 ATATTAAAATAT-TATATTAAA-ATT
* * * *
2523899 TTAATAATTAATATTTTCATTAAAATA
1 ATATTAA--AATATTAT-ATTAAAATT
2523926 ATATTAAAATATTATATTAAA
1 ATATTAAAATATTATATTAAA
2523947 TTTAAATAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
24 18 0.31
25 20 0.34
26 1 0.02
27 9 0.16
28 10 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTAAAATATTATATTAAAATT
Found at i:2524146 original size:42 final size:43
Alignment explanation
Indices: 2524080--2524184 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 43
2524070 AACAAACTAC
** *
2524080 AACTATCAAACA-TTGAAAATCATTTT-TCGAAATATATTTT-T
1 AACTATCAAACACAAGAAAATCATTTTATAGAAA-ATATTTTCT
* *
2524121 CAGCTATCAAACACAATAAAA-CATTTTATAGAAAATATTTTCT
1 -AACTATCAAACACAAGAAAATCATTTTATAGAAAATATTTTCT
2524164 AACTATCAAACACAAGAAAAT
1 AACTATCAAACACAAGAAAAT
2524185 GAGAAAAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
42 42 0.81
43 10 0.19
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (43 bp):
AACTATCAAACACAAGAAAATCATTTTATAGAAAATATTTTCT
Found at i:2524584 original size:23 final size:23
Alignment explanation
Indices: 2524558--2524602 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2524548 TCTAACATGT
*
2524558 TCTTTACCTTTATGGCACGTTTA
1 TCTTTACCTTTATGACACGTTTA
*
2524581 TCTTTACCTTTGTGACACGTTT
1 TCTTTACCTTTATGACACGTTT
2524603 TTCTCTGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.13, T:0.49
Consensus pattern (23 bp):
TCTTTACCTTTATGACACGTTTA
Found at i:2524613 original size:23 final size:23
Alignment explanation
Indices: 2524562--2524614 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2524552 ACATGTTCTT
* *
2524562 TACCTTTATGGCACGTTTATCTT
1 TACCTTTATGACACGTTTATCTC
* *
2524585 TACCTTTGTGACACGTTTTTCTC
1 TACCTTTATGACACGTTTATCTC
*
2524608 TGCCTTT
1 TACCTTT
2524615 TGGTAGGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.25, G:0.13, T:0.49
Consensus pattern (23 bp):
TACCTTTATGACACGTTTATCTC
Found at i:2526673 original size:16 final size:17
Alignment explanation
Indices: 2526645--2526676 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2526635 TTAATATCTG
2526645 TTTTTAATATAAATATA
1 TTTTTAATATAAATATA
2526662 TTTTTAAT-TAAATAT
1 TTTTTAATATAAATAT
2526677 TAAATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAATATAAATATA
Found at i:2530000 original size:35 final size:35
Alignment explanation
Indices: 2529951--2530088 Score: 179
Period size: 35 Copynumber: 3.9 Consensus size: 35
2529941 AAGTCTCTGC
2529951 AGGTTCA-ACTCGATCAAACTGGTAATTCCTTATAT
1 AGGTTCAGAC-CGATCAAACTGGTAATTCCTTATAT
* *
2529986 AGGTTCAGACCGATCGAACTGGTAATTCCTTACGAT
1 AGGTTCAGACCGATCAAACTGGTAATTCCTTA-TAT
* * * *
2530022 AGATTTAGATCGATCAAATTGGTAATTCCTTATAT
1 AGGTTCAGACCGATCAAACTGGTAATTCCTTATAT
* *
2530057 AGGTTCAGACCGATCGAGCTGGTAATTCCTTA
1 AGGTTCAGACCGATCAAACTGGTAATTCCTTA
2530089 CGGATATAAG
Statistics
Matches: 87, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
35 56 0.64
36 31 0.36
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (35 bp):
AGGTTCAGACCGATCAAACTGGTAATTCCTTATAT
Found at i:2532538 original size:22 final size:22
Alignment explanation
Indices: 2532513--2532555 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2532503 ACCTGACTCG
* *
2532513 TTGACATGTCTGACCGTTGAAC
1 TTGACAGGTATGACCGTTGAAC
*
2532535 TTGACAGGTATGACTGTTGAA
1 TTGACAGGTATGACCGTTGAA
2532556 TGGTGACTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (22 bp):
TTGACAGGTATGACCGTTGAAC
Found at i:2543315 original size:19 final size:19
Alignment explanation
Indices: 2543259--2543321 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
2543249 CTATTTAAAC
**
2543259 TAAAATAACTAAAAAATAAT
1 TAAAAT-ACTAAAACCTAAT
*
2543279 ATAATAAT-CTAAATCCTAAT
1 -TAA-AATACTAAAACCTAAT
*
2543299 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
2543318 TAAA
1 TAAA
2543322 CTAAAATACA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 3 0.09
19 17 0.49
20 9 0.26
21 3 0.09
22 3 0.09
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:2543369 original size:69 final size:69
Alignment explanation
Indices: 2543224--2543414 Score: 252
Period size: 69 Copynumber: 2.8 Consensus size: 69
2543214 TAAAACATCT
* * * * *
2543224 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAAT---AA-CTAAAAAAT-AATATAA
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAGATAAAATATAAAAATAA
2543283 TAATC
65 TAATC
*
2543288 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAAAAATAAT
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAAAAATAAT
2543353 -ATCC
66 AAT-C
*
2543357 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAA
2543415 TGTTTAAAAT
Statistics
Matches: 114, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
63 5 0.04
64 34 0.30
67 2 0.02
68 9 0.08
69 64 0.56
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.28
Consensus pattern (69 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAAAAATAAT
AATC
Found at i:2544019 original size:46 final size:46
Alignment explanation
Indices: 2543949--2544249 Score: 507
Period size: 46 Copynumber: 6.6 Consensus size: 46
2543939 CACATTAACA
*
2543949 CATCCATTT-ATGCATTTTAATTATGGCATCCTTGCATGCCTTAATG
1 CATCC-TTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
* *
2543995 CATCATTTCATGCATTTTAATTATGGCATCATTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
2544041 CATCCTTTAATGCATTTTAATTATGGCATCC-TTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
2544086 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
2544132 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
2544178 CATCATTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
*
2544224 CATCCTTTCATCCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
2544250 ATTTGATTTA
Statistics
Matches: 241, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
45 46 0.19
46 195 0.81
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
Found at i:2544167 original size:137 final size:138
Alignment explanation
Indices: 2543949--2544248 Score: 505
Period size: 137 Copynumber: 2.2 Consensus size: 138
2543939 CACATTAACA
*
2543949 CATCCATTT-ATGCATTTTAATTATGGCATCCTTGCATGCCTTAATGCATCATTTCATGCATTTT
1 CATCC-TTTCATGCATTTTAATTATGACATCCTTGCATGCCTTAATGCATCATTTCATGCATTTT
* *
2544013 AATTATGGCATCATTTCATGCCTTAATGCATCCTTTAATGCATTTTAATTATGGCATCC-TTCAT
65 AATTATGACATCATTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGCATCCTTTCAT
2544077 GCCTTAATG
130 GCCTTAATG
* *
2544086 CATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAATTATGACATCCTTGCATGCCTTAATGCATCATTTCATGCATTTTA
* *
2544151 ATTATGACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATG
66 ATTATGACATCATTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGCATCCTTTCATG
2544216 CCTTAATG
131 CCTTAATG
*
2544224 CATCCTTTCATCCATTTTAATTATG
1 CATCCTTTCATGCATTTTAATTATG
2544249 GATTTGATTT
Statistics
Matches: 153, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
136 3 0.02
137 112 0.73
138 38 0.25
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (138 bp):
CATCCTTTCATGCATTTTAATTATGACATCCTTGCATGCCTTAATGCATCATTTCATGCATTTTA
ATTATGACATCATTTCATGCCTTAATGCATCATTTAATGCATTTTAATTATGGCATCCTTTCATG
CCTTAATG
Found at i:2544687 original size:22 final size:20
Alignment explanation
Indices: 2544642--2544695 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
2544632 TGGCTCCTCA
*
2544642 GTATCGATACCCCTACCATG
1 GTATCGATACCCATACCATG
*
2544662 GTATCGATACTACCATACTATG
1 GTATCGATAC--CCATACCATG
*
2544684 GTATTGATACCC
1 GTATCGATACCC
2544696 TATTATGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
22 17 0.59
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCATACCATG
Found at i:2544762 original size:20 final size:18
Alignment explanation
Indices: 2544737--2544787 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 18
2544727 GTTTTGAAAT
2544737 GGTATCGATACCTTCCCTTC
1 GGTATCGATACC--CCCTTC
2544757 GGTATCGATAAGCCCCCTTC
1 GGTATCGAT-A-CCCCCTTC
2544777 GGTATCGATAC
1 GGTATCGATAC
2544788 TGATTGAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 24 0.83
21 1 0.03
22 2 0.07
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (18 bp):
GGTATCGATACCCCCTTC
Found at i:2546067 original size:35 final size:35
Alignment explanation
Indices: 2546027--2546139 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
2546017 GTCTCTGCAT
2546027 GTTCAGATCGATCAAACTGGTAATTCCTTATATAG
1 GTTCAGATCGATCAAACTGGTAATTCCTTATATAG
* * * * *
2546062 GTTCAGA-CGGATCGAACTGATAATTCCTTACGACAT
1 GTTCAGATC-GATCAAACTGGTAATTCCTTA-TATAG
* * *
2546098 GTTCA-ACTCGGTCAAATTGGTAATTTCTTATATAG
1 GTTCAGA-TCGATCAAACTGGTAATTCCTTATATAG
2546133 GTTCAGA
1 GTTCAGA
2546140 CCAATCGAGC
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
34 1 0.02
35 34 0.57
36 24 0.40
37 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (35 bp):
GTTCAGATCGATCAAACTGGTAATTCCTTATATAG
Found at i:2554418 original size:184 final size:184
Alignment explanation
Indices: 2554109--2554473 Score: 667
Period size: 184 Copynumber: 2.0 Consensus size: 184
2554099 ATAGGTTGAA
* * *
2554109 TGAATGGAAAATAATTGGTTGTATAACATTATAGGTTGGTGTTAGTAAAATAAGTAGAATGTAAC
1 TGAATGGAAAATAATTAGTTGTATAACATTATAGGTTGGTGTTAATAAAACAAGTAGAATGTAAC
*
2554174 ATTATAGGTTGAATGGTAAAGATTGGGTTGTAAATAACATTATAAGTTGTAACTGAAATTGTAAT
66 ATTATAGGTTGAATGGTAAAGATTGAGTTGTAAATAACATTATAAGTTGTAACTGAAATTGTAAT
2554239 GAAATTGAAAAATTATTCCTTTGTACATAATCGGTTACTATAATAATCATAGGT
131 GAAATTGAAAAATTATTCCTTTGTACATAATCGGTTACTATAATAATCATAGGT
2554293 TGAATGGAAAATAATTAGTTGTATAACATTATAGGTTGGTGTTAATAAAACAAGTAGAATGTAAC
1 TGAATGGAAAATAATTAGTTGTATAACATTATAGGTTGGTGTTAATAAAACAAGTAGAATGTAAC
*
2554358 ATTATAGGTTGAATGGTAAAGATTGAGTTGTAAATAACATTATAAGTTGTAATTGAAATTGTAAT
66 ATTATAGGTTGAATGGTAAAGATTGAGTTGTAAATAACATTATAAGTTGTAACTGAAATTGTAAT
* *
2554423 GAAATTGAGAAATTATTCCTTTGTACATAATCGGTTATTATAATAATCATA
131 GAAATTGAAAAATTATTCCTTTGTACATAATCGGTTACTATAATAATCATA
2554474 TAGAATTTAT
Statistics
Matches: 174, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 174 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (184 bp):
TGAATGGAAAATAATTAGTTGTATAACATTATAGGTTGGTGTTAATAAAACAAGTAGAATGTAAC
ATTATAGGTTGAATGGTAAAGATTGAGTTGTAAATAACATTATAAGTTGTAACTGAAATTGTAAT
GAAATTGAAAAATTATTCCTTTGTACATAATCGGTTACTATAATAATCATAGGT
Found at i:2558076 original size:18 final size:19
Alignment explanation
Indices: 2558056--2558090 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2558046 ACAATATTTA
2558056 AAAACA-AT-AAATAAATT
1 AAAACATATAAAATAAATT
2558073 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
2558091 GACTAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:2558556 original size:13 final size:13
Alignment explanation
Indices: 2558538--2558563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2558528 CGTACTCCGC
2558538 CGCCGGCCACCGT
1 CGCCGGCCACCGT
2558551 CGCCGGCCACCGT
1 CGCCGGCCACCGT
2558564 AACGGTGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:2559236 original size:3 final size:3
Alignment explanation
Indices: 2559228--2559459 Score: 358
Period size: 3 Copynumber: 77.3 Consensus size: 3
2559218 TTATTTATTA
*
2559228 AAT AAT AAT AAT AAAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * *
2559274 AAT AAT GCT AAT AAT AAT AAT AAT ACT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2559322 ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2559370 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2559417 AAT AAT AAT CAT AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2559460 TGGATAAAAA
Statistics
Matches: 207, Mismatches: 20, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
2 2 0.01
3 202 0.98
4 3 0.01
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2560277 original size:112 final size:113
Alignment explanation
Indices: 2559705--2560554 Score: 1240
Period size: 112 Copynumber: 7.5 Consensus size: 113
2559695 GCTCTTGATG
* *
2559705 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTAC-
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CT
* * * * *
2559769 CTGGTAATGTTGATCCATCAAATGATGAATTCACGCAAAAGGTTGAACA
65 CTGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
2559818 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
2559883 GGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
2559931 AGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
2559996 TGGAAAAGAATGATTCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
2560045 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
2560110 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTAAACA
66 TGGAAAAG-ATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* *
2560159 AGTTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
2560223 TGGAAAAAATAATTCATCAAGTGATGAATTCAGGGAAAAGGTTGAACA
66 TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* * * * * **
2560271 AATTCTTCTTATTATGAATTTCTTCTTCC-TCTTCAAATGAGTTCTTCTCATTATGAACTCTAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* ** * * ** * *
2560335 TGGCACTGCTGATCCACCGGGTGATGAATTTAAGCAAAAAGTTGAACA
66 TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
* * **
2560383 AGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * * *
2560447 TGGTAATGATGATCCATCAAATGATGAATTTAAGCAAAAAGTTGAACA
66 TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
2560495 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
2560555 CGACCTGGAA
Statistics
Matches: 677, Mismatches: 56, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
111 1 0.00
112 254 0.38
113 245 0.36
114 177 0.26
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:2561014 original size:22 final size:22
Alignment explanation
Indices: 2560989--2561043 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
2560979 GATAAAGCTT
* *
2560989 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
*
2561011 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
2561033 TCATCTTTAAA
1 TCATCTTTAAA
2561044 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:2563571 original size:83 final size:82
Alignment explanation
Indices: 2563435--2563905 Score: 726
Period size: 83 Copynumber: 5.7 Consensus size: 82
2563425 GTTCCTACCA
* * * * *
2563435 AACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
*
2563500 CAATGATTGGTTTTGCC
66 CAATGATTGGTTCTGCC
*
2563517 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAAT
*
2563582 TCAATGATTGATTCTGTCC
65 TCAATGATTGGTTCTG-CC
* *
2563601 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTAACAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
2563666 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTG-CC
* * * * *
2563684 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACATTCATCTTCCCAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
*
2563749 CAATGATTGGTTCTGCT
66 CAATGATTGGTTCTGCC
* * *
2563766 AACCAGGTCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTAACAAATTCATCTTCCCAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
*
2563831 CAATGATTGGTTCTGCT
66 CAATGATTGGTTCTGCC
*
2563848 AACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTT
2563906 TCAGTTAATG
Statistics
Matches: 363, Mismatches: 24, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
82 134 0.37
83 227 0.63
84 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (82 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATT
CAATGATTGGTTCTGCC
Found at i:2568033 original size:27 final size:27
Alignment explanation
Indices: 2568003--2568058 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
2567993 GTAATTATGT
*
2568003 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGCAAATACAAACGTA
* * *
2568030 AAAAATGCAAATGCAAATTCAAATGTA
1 AAAAATGAAAATGCAAATACAAACGTA
2568057 AA
1 AA
2568059 TATGTGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGCAAATACAAACGTA
Found at i:2568131 original size:14 final size:14
Alignment explanation
Indices: 2568097--2568149 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
2568087 TTGTGCAATA
*
2568097 CAAATGCAAAAATG
1 CAAATGTAAAAATG
*
2568111 CCAAATGTAAATATG
1 -CAAATGTAAAAATG
2568126 CAAATGTAAAAATG
1 CAAATGTAAAAATG
*
2568140 TAAATGTAAA
1 CAAATGTAAA
2568150 TTATTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.23
Consensus pattern (14 bp):
CAAATGTAAAAATG
Found at i:2570549 original size:19 final size:19
Alignment explanation
Indices: 2570528--2570563 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2570518 AATATATTTA
2570528 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
2570546 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
2570564 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:2571029 original size:13 final size:13
Alignment explanation
Indices: 2571011--2571039 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2571001 CCACCGTACT
2571011 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
2571024 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
2571037 CCG
1 CCG
2571040 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:2571718 original size:3 final size:3
Alignment explanation
Indices: 2571710--2571951 Score: 367
Period size: 3 Copynumber: 80.3 Consensus size: 3
2571700 TTATTTATTA
*
2571710 AAT AAT AAT AAT AAAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * *
2571756 AAT GCT AAT AAT AAT AAT AAT ACT GAT AAT AAT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2571804 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
2571852 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
2571900 AAT AAT GAT AAT AAT AAT CAT AAT ATT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2571948 AAT A
1 AAT A
2571952 TGGATAAAAA
Statistics
Matches: 214, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
3 211 0.99
4 3 0.01
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2575546 original size:13 final size:13
Alignment explanation
Indices: 2575528--2575552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2575518 TTTATTTCGA
2575528 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
2575541 TTTTTTTCTTTT
1 TTTTTTTCTTTT
2575553 TGCTTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:2580056 original size:33 final size:33
Alignment explanation
Indices: 2580011--2580076 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2580001 ACATAATATG
*
2580011 GAGCAATTAACCAACAACTCATCAAAAAATCTC
1 GAGCAATCAACCAACAACTCATCAAAAAATCTC
* * *
2580044 GAGCAATCAACCAACAACTTATCACAATATCTC
1 GAGCAATCAACCAACAACTCATCAAAAAATCTC
2580077 AACCAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.20
Consensus pattern (33 bp):
GAGCAATCAACCAACAACTCATCAAAAAATCTC
Found at i:2582055 original size:18 final size:18
Alignment explanation
Indices: 2582032--2582067 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2582022 AGTATGGATT
2582032 CTATAAGGCATCCTCTTC
1 CTATAAGGCATCCTCTTC
2582050 CTATAAGGCATCCTCTTC
1 CTATAAGGCATCCTCTTC
2582068 TTGTGGCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (18 bp):
CTATAAGGCATCCTCTTC
Found at i:2587051 original size:29 final size:28
Alignment explanation
Indices: 2587010--2587090 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 28
2587000 TTCCATATGT
2587010 TCATGTACTCATGTCATTTCTCTTGTGA
1 TCATGTACTCATGTCATTTCTCTTGTGA
*
2587038 TCATGTAACTCATGTTATTTCTCTTGTGA
1 TCATGT-ACTCATGTCATTTCTCTTGTGA
*
2587067 TCATGTTGCTCATGTCATGTTCTC
1 TCATG-TACTCATGTCAT-TTCTC
2587091 ATATCACATA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
28 6 0.13
29 35 0.74
30 6 0.13
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.47
Consensus pattern (28 bp):
TCATGTACTCATGTCATTTCTCTTGTGA
Found at i:2587553 original size:45 final size:45
Alignment explanation
Indices: 2587486--2587591 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
2587476 TGCACTACTT
* * *
2587486 GTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATT-AATGG
1 GTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAGA
* *
2587530 GATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 G-TGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
2587576 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
2587592 CTGTGCATCG
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
44 1 0.02
45 40 0.75
46 12 0.23
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (45 bp):
GTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:2588716 original size:74 final size:74
Alignment explanation
Indices: 2588634--2588774 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 74
2588624 AACTTTGTTA
* * * *
2588634 ATGTTACAACGTATCAACCATCATAGATTAATTATCGATATTTTACATTTCAAACTATTTTCTTA
1 ATGTTACAAAGTATCAACCATCATAGATTAAGTATCGATATTTTACATTTCAAACTAATTTATTA
2588699 ATTTGTTTT
66 ATTTGTTTT
* * *
2588708 ATGTTACAAAGTATCAATCATCATAGATTAAGTATCGATATTTTATATTTCGAACTAATTTATTA
1 ATGTTACAAAGTATCAACCATCATAGATTAAGTATCGATATTTTACATTTCAAACTAATTTATTA
2588773 AT
66 AT
2588775 CATTTTAACT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (74 bp):
ATGTTACAAAGTATCAACCATCATAGATTAAGTATCGATATTTTACATTTCAAACTAATTTATTA
ATTTGTTTT
Found at i:2589844 original size:76 final size:77
Alignment explanation
Indices: 2589713--2589871 Score: 241
Period size: 76 Copynumber: 2.1 Consensus size: 77
2589703 CTCTGATAAG
*
2589713 ATTTTAGGCGCAACCTAAAATGTTAATAATATTCATGACTATTATAATTTATAACTCATTTTCTT
1 ATTTTAGGCGCAACCTAAAATGTTAATAATATTCATGACTATTATAATTTATAACTCACTTTCTT
*
2589778 ACCTTTCAAAAT
66 ACCCTTCAAAAT
* * *
2589790 ATTTTATGCGC-ACCTAAAATGTTAATAATATTCATGAC-ATTTATCATTTGTAACTCACTTTCT
1 ATTTTAGGCGCAACCTAAAATGTTAATAATATTCATGACTA-TTATAATTTATAACTCACTTTCT
*
2589853 TACCCTTCATAAT
65 TACCCTTCAAAAT
2589866 ATTTTA
1 ATTTTA
2589872 AATGTAACTG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 1 0.01
76 64 0.85
77 10 0.13
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (77 bp):
ATTTTAGGCGCAACCTAAAATGTTAATAATATTCATGACTATTATAATTTATAACTCACTTTCTT
ACCCTTCAAAAT
Found at i:2594543 original size:2 final size:2
Alignment explanation
Indices: 2594536--2594576 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2594526 GTTCGTCATC
2594536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2594577 GTACATGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2600090 original size:13 final size:13
Alignment explanation
Indices: 2600060--2600103 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
2600050 TTTAATATTT
*
2600060 ATCGGGTCGGGT-
1 ATCGGGCCGGGTA
2600072 ATCGGGCCGGGTA
1 ATCGGGCCGGGTA
2600085 ATCGGGCCGGGTA
1 ATCGGGCCGGGTA
2600098 ATCGGG
1 ATCGGG
2600104 GTGGGGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (13 bp):
ATCGGGCCGGGTA
Found at i:2603176 original size:15 final size:15
Alignment explanation
Indices: 2603134--2603176 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2603124 TTTAATTTTT
2603134 TTTTAAAATTAATTTA
1 TTTT-AAATTAATTTA
** *
2603150 TTACAAACTAATTTA
1 TTTTAAATTAATTTA
2603165 TTTTAAATTAAT
1 TTTTAAATTAAT
2603177 AATAAAAGCT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAAATTAATTTA
Found at i:2609743 original size:6 final size:6
Alignment explanation
Indices: 2609727--2609786 Score: 93
Period size: 6 Copynumber: 9.7 Consensus size: 6
2609717 AAAACAAAGC
*
2609727 AAAATA AAAGAAA AAGAATA AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAA-ATA AA-AATA AAAATA AAAATA AAAATA AAAATA AAAATA
2609777 AAAATA AAAA
1 AAAATA AAAA
2609787 GGTAGTGATA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 41 0.82
7 8 0.16
8 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:2609845 original size:17 final size:17
Alignment explanation
Indices: 2609806--2609851 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2609796 AATGTATTAT
2609806 ATATATATATATTAAAAA
1 ATATATA-ATATTAAAAA
*
2609824 CTATATAAT-TTCAAAAA
1 ATATATAATATT-AAAAA
2609841 ATATATAATAT
1 ATATATAATAT
2609852 ATTATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.08
17 15 0.62
18 7 0.29
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATATAATATTAAAAA
Found at i:2609853 original size:42 final size:42
Alignment explanation
Indices: 2609806--2609936 Score: 135
Period size: 42 Copynumber: 3.1 Consensus size: 42
2609796 AATGTATTAT
*
2609806 ATATATATATATT-AAAAACTATATAATTTCAAAAAATATATA
1 ATATATATATTTTAAAAAACTATAT-ATTTCAAAAAATATATA
* *
2609848 ATATATTATATTTTCAAAAACTATGT-TTT-AAAAAATGATATA
1 ATATA-TATATTTTAAAAAACTATATATTTCAAAAAAT-ATATA
* * * *
2609890 TTATATATGTTTTAAAAAATTATATATTTTC-AAAATTATATA
1 ATATATATATTTTAAAAAACTATATA-TTTCAAAAAATATATA
2609932 ATATA
1 ATATA
2609937 CTTTCAAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
41 23 0.31
42 26 0.35
43 15 0.20
44 10 0.14
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (42 bp):
ATATATATATTTTAAAAAACTATATATTTCAAAAAATATATA
Found at i:2609919 original size:17 final size:16
Alignment explanation
Indices: 2609893--2609931 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2609883 TGATATATTA
*
2609893 TATATGTTTTAAAAAAT
1 TATATATTTT-AAAAAT
*
2609910 TATATATTTTCAAAAT
1 TATATATTTTAAAAAT
2609926 TATATA
1 TATATA
2609932 ATATACTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
TATATATTTTAAAAAT
Found at i:2609949 original size:22 final size:22
Alignment explanation
Indices: 2609911--2609977 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
2609901 TTAAAAAATT
2609911 ATATATTTTC-AAAATTATATA
1 ATATATTTTCAAAAATTATATA
* *
2609932 ATATACTTTCAAAAATTATATT
1 ATATATTTTCAAAAATTATATA
*
2609954 ATATATTTTTCAAAACTATATATA
1 ATATA-TTTTCAAAAAT-TATATA
2609978 TTTATATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 9 0.24
22 15 0.39
23 9 0.24
24 5 0.13
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATATTTTCAAAAATTATATA
Found at i:2610844 original size:72 final size:71
Alignment explanation
Indices: 2610714--2610886 Score: 179
Period size: 72 Copynumber: 2.4 Consensus size: 71
2610704 CCCTTCGTGA
* * * * * * ** *
2610714 TTTAAGTCGGTCTTGATTCATTGGACGACTCCCTTTCGCGGGAAAGCCAAGTGGGATGACTCACA
1 TTTAAGTCGGTCTCGATTCTTTGGATGACTCCATTTCACGGGAAAGCCAAATAAGATGAATCAC-
2610779 TTCACAG
65 TTCACAG
2610786 TTTAAGTCGGTCTCGATTCTTTGGATGACT-CATATTCACGGGAAAGCCAAATAAGATGAATCAC
1 TTTAAGTCGGTCTCGATTCTTTGGATGACTCCAT-TTCACGGGAAAGCCAAATAAGATGAATCAC
* *
2610850 TTTACCG
65 TTCACAG
* * *
2610857 TTCAAGTCGGTC-CTACTTCTTTTGATGACT
1 TTTAAGTCGGTCTCGA-TTCTTTGGATGACT
2610887 ACCCTTCATG
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
70 2 0.02
71 31 0.36
72 52 0.61
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (71 bp):
TTTAAGTCGGTCTCGATTCTTTGGATGACTCCATTTCACGGGAAAGCCAAATAAGATGAATCACT
TCACAG
Found at i:2611665 original size:27 final size:27
Alignment explanation
Indices: 2611635--2611688 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2611625 CTTCAATCGA
2611635 TTTTAGAGAAAATATGTCTTGTCTGAG
1 TTTTAGAGAAAATATGTCTTGTCTGAG
2611662 TTTTAGAGAAAATATGTCTTGTCTGAG
1 TTTTAGAGAAAATATGTCTTGTCTGAG
2611689 AGATGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (27 bp):
TTTTAGAGAAAATATGTCTTGTCTGAG
Found at i:2616563 original size:16 final size:16
Alignment explanation
Indices: 2616519--2616570 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
2616509 GTATTACCCA
2616519 ACCTAGTTTCAA-CTG
1 ACCTAGTTTCAACCTG
* *
2616534 A-CTTGTTATGAACCTG
1 ACCTAGTT-TCAACCTG
*
2616550 ACCTAGTTTCAACCTA
1 ACCTAGTTTCAACCTG
2616566 ACCTA
1 ACCTA
2616571 TAAATGATTC
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 5 0.17
15 4 0.14
16 15 0.52
17 5 0.17
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (16 bp):
ACCTAGTTTCAACCTG
Found at i:2619762 original size:18 final size:18
Alignment explanation
Indices: 2619735--2619796 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
2619725 GTTCAGCCGA
*
2619735 GTTTGAGTTCAGGTTTGG
1 GTTTGGGTTCAGGTTTGG
2619753 GTTTGGGTTCAGGTTTGG
1 GTTTGGGTTCAGGTTTGG
**
2619771 G-TTGGGTTTGGGTTTGG
1 GTTTGGGTTCAGGTTTGG
*
2619788 GTTAGGGTT
1 GTTTGGGTT
2619797 AGAAAAGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.38
18 24 0.62
ACGTcount: A:0.06, C:0.03, G:0.45, T:0.45
Consensus pattern (18 bp):
GTTTGGGTTCAGGTTTGG
Found at i:2619790 original size:23 final size:23
Alignment explanation
Indices: 2619749--2619796 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2619739 GAGTTCAGGT
*
2619749 TTGGGTTTGGGTTCAGGTTTGGG
1 TTGGGTTTGGGTTCAGGTTAGGG
**
2619772 TTGGGTTTGGGTTTGGGTTAGGG
1 TTGGGTTTGGGTTCAGGTTAGGG
2619795 TT
1 TT
2619797 AGAAAAGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.04, C:0.02, G:0.48, T:0.46
Consensus pattern (23 bp):
TTGGGTTTGGGTTCAGGTTAGGG
Found at i:2619798 original size:6 final size:6
Alignment explanation
Indices: 2619746--2619796 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
2619736 TTTGAGTTCA
** *
2619746 GGTTTG GGTTTG GGTTCA GGTTTG GG-TTG GGTTTG GGTTTG GGTTAG
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG
2619793 GGTT
1 GGTT
2619797 AGAAAAGATG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.04, C:0.02, G:0.49, T:0.45
Consensus pattern (6 bp):
GGTTTG
Found at i:2620481 original size:61 final size:61
Alignment explanation
Indices: 2620415--2620550 Score: 193
Period size: 61 Copynumber: 2.2 Consensus size: 61
2620405 TCCTAGTTTT
* * * *
2620415 AAATTTTTTCATATT-AGTCCAAATTTAATCATGCAATGTATTAATTTAAGCTTCGTATTTA
1 AAATTTGTTCA-ATTAAGTCCAAATTTAATCATACAATGTATTAATTGAAGCTTCATATTTA
* *
2620476 AAATTTGTTCAATTAAGTCCAAATTTAATCTTACAATTTATTAATTGAAGCTTCATATTTA
1 AAATTTGTTCAATTAAGTCCAAATTTAATCATACAATGTATTAATTGAAGCTTCATATTTA
*
2620537 AAATTTGGTCAATT
1 AAATTTGTTCAATT
2620551 TGATCCTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 3 0.04
61 64 0.96
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (61 bp):
AAATTTGTTCAATTAAGTCCAAATTTAATCATACAATGTATTAATTGAAGCTTCATATTTA
Found at i:2620641 original size:51 final size:51
Alignment explanation
Indices: 2620585--2620702 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 51
2620575 TTTCAATTAA
* * *
2620585 TATATAGTTTATA-TTAATAAATTAATATATAGGATATATATACTAATGAAC
1 TATATAATATATAGTTAATAAA-TAATATATAGGATATATATACTAATAAAC
* ** * **
2620636 TATATAATATATAGTTTATGTATACTATATAGTTTATATATACTAATAAAC
1 TATATAATATATAGTTAATAAATAATATATAGGATATATATACTAATAAAC
*
2620687 TATATAATACATAGTT
1 TATATAATATATAGTT
2620703 TGTATATATC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 51 0.91
52 5 0.09
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (51 bp):
TATATAATATATAGTTAATAAATAATATATAGGATATATATACTAATAAAC
Found at i:2620664 original size:18 final size:18
Alignment explanation
Indices: 2620636--2620814 Score: 135
Period size: 18 Copynumber: 10.3 Consensus size: 18
2620626 ACTAATGAAC
*
2620636 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
*
2620654 TGTATACTATATAGTTTA
1 TATATACTATATAGTTTA
***
2620672 TATATACTA-ATAAACTA
1 TATATACTATATAGTTTA
* *
2620689 TATA-A-TACATAGTTTG
1 TATATACTATATAGTTTA
2620705 TATATA-TCATATAGTTTA
1 TATATACT-ATATAGTTTA
*
2620723 TATATACTATATAATTTA
1 TATATACTATATAGTTTA
*
2620741 TATATACTA-AT-G--AA
1 TATATACTATATAGTTTA
* *
2620755 CTATACAATATATAGTTTA
1 -TATATACTATATAGTTTA
* *
2620774 TATATACCATATACTTTA
1 TATATACTATATAGTTTA
*
2620792 TATATA-TATAGT-TTTTA
1 TATATACTATA-TAGTTTA
2620809 TATATA
1 TATATA
2620815 GTTCATATGT
Statistics
Matches: 127, Mismatches: 24, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
14 1 0.01
15 9 0.07
16 11 0.09
17 27 0.21
18 77 0.61
19 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:2620703 original size:51 final size:50
Alignment explanation
Indices: 2620609--2620814 Score: 184
Period size: 51 Copynumber: 4.1 Consensus size: 50
2620599 TAATAAATTA
** * * *
2620609 ATATATAGGATATATATACTAATGAACTATATAATATATAGTTTATGTAT
1 ATATATAGTTTATATATACTAATAAACTATATAATACATAGTTTATATAT
*
2620659 ACTATATAGTTTATATATACTAATAAACTATATAATACATAGTTTGTATAT
1 A-TATATAGTTTATATATACTAATAAACTATATAATACATAGTTTATATAT
** * ** *
2620710 ATCATATAGTTTATATATACTATATAATTTATAT-ATAC-TAATGAACTATACA
1 AT-ATATAGTTTATATATACTA-ATAAACTATATAATACATAGTTTA-TATA-T
* * * * *
2620762 ATATATAGTTTATATATAC-CATATACTTTATATATATATAGTTTTTATAT
1 ATATATAGTTTATATATACTAATAAACTATATA-ATACATAGTTTATATAT
2620812 ATA
1 ATA
2620815 GTTCATATGT
Statistics
Matches: 124, Mismatches: 24, Indels: 16
0.76 0.15 0.10
Matches are distributed among these distances:
49 7 0.06
50 8 0.06
51 95 0.77
52 14 0.11
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.45
Consensus pattern (50 bp):
ATATATAGTTTATATATACTAATAAACTATATAATACATAGTTTATATAT
Found at i:2620717 original size:69 final size:68
Alignment explanation
Indices: 2620636--2620812 Score: 236
Period size: 69 Copynumber: 2.6 Consensus size: 68
2620626 ACTAATGAAC
*
2620636 TATATA-AT-ATATAGTTTATGTATACTATATAGTTTATATATACTAATAAACTATATAATACAT
1 TATATATATCATATAGTTTAT-TATACTATATAGTTTATATATACTAATAAACTATACAATACAT
2620699 AGTT
65 AGTT
* * * *
2620703 TGTATATATCATATAGTTTATATATACTATATAATTTATATATACTAATGAACTATACAATATAT
1 TATATATATCATATAGTTTAT-TATACTATATAGTTTATATATACTAATAAACTATACAATACAT
2620768 AGTT
65 AGTT
* * *
2620772 TATATATACCATATACTTTA-TATA-TATATAGTTTTTATATA
1 TATATATATCATATAGTTTATTATACTATATAGTTTATATATA
2620813 TAGTTCATAT
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
66 15 0.15
67 9 0.09
68 2 0.02
69 71 0.73
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (68 bp):
TATATATATCATATAGTTTATTATACTATATAGTTTATATATACTAATAAACTATACAATACATA
GTT
Found at i:2620994 original size:18 final size:18
Alignment explanation
Indices: 2620980--2621107 Score: 77
Period size: 18 Copynumber: 6.8 Consensus size: 18
2620970 AACTATACTA
2620980 TATAGTTTATATATAAAC
1 TATAGTTTATATATAAAC
*
2620998 TATAGTTTATATAGTTTTATA-
1 TATAGTTTATATA----TAAAC
* *
2621019 TATAGTTCATATGTAAAC
1 TATAGTTTATATATAAAC
* *
2621037 CATA--CTATATATAATA-
1 TATAGTTTATATATAA-AC
2621053 TATAGTTTATATATATAA-
1 TATAGTTTATATATA-AAC
*
2621071 TATAAGGTATATAAATATAAAC
1 TAT-A-GT-T-TATATATAAAC
2621093 TATAGTTTATATATA
1 TATAGTTTATATATA
2621108 TTATATACTA
Statistics
Matches: 84, Mismatches: 12, Indels: 28
0.68 0.10 0.23
Matches are distributed among these distances:
16 10 0.12
17 4 0.05
18 35 0.42
19 3 0.04
20 4 0.05
21 15 0.18
22 13 0.15
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (18 bp):
TATAGTTTATATATAAAC
Done.