Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001130.1 Hibiscus syriacus cultivar Beakdansim tig00002239_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: 226092
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
File 1 of 2
Found at i:7607 original size:60 final size:60
Alignment explanation
Indices: 7489--7650 Score: 154
Period size: 60 Copynumber: 2.7 Consensus size: 60
7479 ATCATATGTG
* * * *
7489 CTCAAAGTATGAC-TCTCACTT-TAAATTGGTCCTTAAACTTTTAAATGTCTCAAATTCATC
1 CTCAAACTATGACAT-TCA-TTCTAAATTAGTCCTCAAACTTTTAAATATCTCAAATTCATC
* * * * *
7549 C-CTAAATTTTGAC-TATCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAACTTCATC
1 CTC-AAACTATGACAT-TCATTCTAAATTAGTCCTCAAACTTTTAAATATCTCAAATTCATC
*
7609 CTCAAACTATGGCATTCATTCTAAATTAGT-CTCTAAACTTTT
1 CTCAAACTATGACATTCATTCTAAATTAGTCCTC-AAACTTTT
7651 TTAACATTCC
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
59 6 0.07
60 77 0.91
61 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (60 bp):
CTCAAACTATGACATTCATTCTAAATTAGTCCTCAAACTTTTAAATATCTCAAATTCATC
Found at i:7675 original size:60 final size:60
Alignment explanation
Indices: 7564--7678 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
7554 ATTTTGACTA
* *
7564 TCATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAACTTCATCCTCAAACTATGGCAT
1 TCATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAACTTCATCCTCAAACTATGGCAT
* * *
7624 TCATTCTAAATTAGT-CTCTAAACTTTTTTAACATTCCAATTTTATCC-CAAACTAT
1 TCATTCTAAATTAGTCCTC-AAAC-TTTTGAACATTCCAACTTCATCCTCAAACTAT
7679 ACGTATATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.06
60 27 0.56
61 18 0.38
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCTCAAACTTTTGAACATTCCAACTTCATCCTCAAACTATGGCAT
Found at i:7911 original size:60 final size:60
Alignment explanation
Indices: 7788--7964 Score: 175
Period size: 60 Copynumber: 3.0 Consensus size: 60
7778 ATATATTTGG
* ** * * *
7788 ATAAATTTGGGGATGAAATTGGAAGATTC-AAAGTTT-GGAGACCAATTTATAAA-GAGGGTC
1 ATAAA-TTGAGGATGAAATTAAAATATTCAAAAGTTTAAG-GACTAATTTA-AAATGAGGGTC
* * * *
7848 AT-AATTTATGGATGGAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAGG-C
1 ATAAATTGA-GGATGAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAAAATGAG-GGTC
*
7908 ATAAATTGAGGATGAAATTAAAATATTCAAAAGTTTAAGGACTAATTCAAAATGAGG
1 ATAAATTGAGGATGAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGG
7965 ATTATAGTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
58 2 0.02
59 21 0.21
60 67 0.68
61 8 0.08
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (60 bp):
ATAAATTGAGGATGAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGGTC
Found at i:8113 original size:60 final size:61
Alignment explanation
Indices: 8049--8222 Score: 162
Period size: 60 Copynumber: 2.9 Consensus size: 61
8039 GTCCTCAAAG
* * * *
8049 TATGACTCTTATTTTAAATTGGTTC-TTAAACTTTTAAATATTTCAGTTTCATC-CCTAGAC
1 TATGACTCTTATTCTAAATTGGTTCATCAAACTTTTAAACATTTCAATTTCATCTCCTA-AC
* * * * *
8109 TATGACTATCATTCTAAATTAG-TCATCAAACTTTTGAACATTTCAATTTCATCTCCTAAT
1 TATGACTCTTATTCTAAATTGGTTCATCAAACTTTTAAACATTTCAATTTCATCTCCTAAC
* * *
8169 TATGAC-CTTCATTCTAAATTGG-TC-TCCAAGCTTTTTGAACATTCCAATTTCATC
1 TATGACTCTT-ATTCTAAATTGGTTCAT-CAAAC-TTTTAAACATTTCAATTTCATC
8223 CTAAACTATA
Statistics
Matches: 95, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
59 4 0.04
60 66 0.69
61 25 0.26
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.43
Consensus pattern (61 bp):
TATGACTCTTATTCTAAATTGGTTCATCAAACTTTTAAACATTTCAATTTCATCTCCTAAC
Found at i:8545 original size:553 final size:551
Alignment explanation
Indices: 7468--8556 Score: 1397
Period size: 553 Copynumber: 2.0 Consensus size: 551
7458 ATATTTAATG
* *
7468 GAGTTAATTGTATCATATGTGCTCAAAGTATGACTCTCACTTTAAATTGGTCCTTAAACTTTTAA
1 GAGTTAATTGCATCATATGTCCTCAAAGTATGACTCTCACTTTAAATTGGTCCTTAAACTTTTAA
* * * * *
7533 ATGTCTCAAATTCATCCCTAAATTTTGACTATCATTCTAAATTAGTCCTCAAACTTTTGAATATT
66 ATATCTCAAATTCATCCCTAAACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAACATT
* * *
7598 TCAACTTCATCCTCAAACTATGGCATTCATTCTAAATTAGTCTCTAAACTTTTTTAACATTCCAA
131 TCAACTTCATCCTCAAACTATGACATTCATTCTAAATTAGTCTCCAAACTTTTTGAACATTCCAA
* * * * *
7663 TTTTATCCCAAACTATACGTATATACTAATCACATCTCTTGTTAATAAAAGCGTTAGGCCGTGTT
196 TTTCATCCCAAACTATACATATATACTAATCACATATCTTGTTAATAAAAGCATTAGGCCGAGTT
* * *
7728 ATATTTTATATGTTTGAAAAAAATAAGTTAAACTATGGTTGAAACTAATGATATATTTGGATAAA
261 ATATTTTATATGTTTGAAAAAAATAAGTTAAAATAAGGTTGAAACTAATGACATATTTGGATAAA
* ** * *
7793 TTTGGGGATGAAATTGGAAGATTCAAAGTTTGGAGACCAATTTATAAAGAGGGTCATAATTTATG
326 TTTAGGGATGAAATTAAAAGATTCAAAGTTTGGAGACCAATTTAGAAAGAGGGTCATAATTCATG
* * *
7858 GATGGAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAGAGGCATAAATTGAGGATGA
391 GATGAAATTAGAATGGTCAAAAGTTTAAGGACTAATTTAAAATGAGACGCATAAATTGAGGATGA
* * *
7923 AATTAAAATATTCAAAAGTTTAAGGACTAATTCAAAATGAGGATTATAGTTTGGGGATATATAAT
456 AATTAAAATATTCAAAAGTTTAAGGACCAATT--AAATGAGGATTATAGTCTGGGGACATATAAT
7988 GCAATTAACTCTATTTAATTGATATGGACTTAA
519 GCAATTAACTCTATTTAATTGATATGGACTTAA
* * *
8021 GAGTTAATTGCATCATATGTCCTCAAAGTATGACTCTTATTTTAAATTGGTTCTTAAACTTTTAA
1 GAGTTAATTGCATCATATGTCCTCAAAGTATGACTCTCACTTTAAATTGGTCCTTAAACTTTTAA
* ** *
8086 ATATTTCAGTTTCATCCCTAGACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAACATT
66 ATATCTCAAATTCATCCCTAAACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAACATT
* * * * * *
8151 TCAATTTCAT-CTCCTAATTATGACCTTCATTCTAAATTGGTCTCCAAGCTTTTTGAACATTCCA
131 TCAACTTCATCCT-CAAACTATGACATTCATTCTAAATTAGTCTCCAAACTTTTTGAACATTCCA
* * *
8215 ATTTCATCCTAAACTATACATATATACTAATCACATATCTTGTTAATAAAATCATTAGG-TGAAG
195 ATTTCATCCCAAACTATACATATATACTAATCACATATCTTGTTAATAAAAGCATTAGGCCG-AG
* *
8279 TTATATTATTATATGTTTGAAAAAACAAAATTGAGGTTAAAATAAGGTTGAAACTAATTACATAT
259 TTATATT-TTATATGTTTG---AAA-AAAA-T-AAGTTAAAATAAGGTTGAAACTAATGACATAT
* *
8344 TTGGATGAATTTAGGGATGAAATTAAAATATTCAAAGGTTTAGG-GACCAATTTAGAAAGAGGGT
317 TTGGATAAATTTAGGGATGAAATTAAAAGATTCAAA-GTTT-GGAGACCAATTTAGAAAGAGGGT
* * * * ***
8408 CATAGTTCA-GTGATGAAATTATAATGGT-AAAAGTTTAAGGACTAATTTATAATGGGACTTGTA
380 CATAATTCATG-GATGAAATTAGAATGGTCAAAAGTTTAAGGACTAATTTAAAATGAGACGCATA
** * *** * *
8471 GTTTGGGGATGAAATTGGGATATTTAAAAGTTTAAGGACCAA-T-AA-G-GG-TTATTGTCTGGG
444 AATTGAGGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTAAATGAGGATTATAGTCTGGG
*
8531 GACATATGATGCAATTAACTCTATTT
509 GACATATAATGCAATTAACTCTATTT
8557 GTTATAATCT
Statistics
Matches: 459, Mismatches: 65, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
552 3 0.01
553 263 0.57
554 13 0.03
555 1 0.00
556 2 0.00
557 3 0.01
558 4 0.01
559 2 0.00
560 122 0.27
561 44 0.10
562 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (551 bp):
GAGTTAATTGCATCATATGTCCTCAAAGTATGACTCTCACTTTAAATTGGTCCTTAAACTTTTAA
ATATCTCAAATTCATCCCTAAACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAACATT
TCAACTTCATCCTCAAACTATGACATTCATTCTAAATTAGTCTCCAAACTTTTTGAACATTCCAA
TTTCATCCCAAACTATACATATATACTAATCACATATCTTGTTAATAAAAGCATTAGGCCGAGTT
ATATTTTATATGTTTGAAAAAAATAAGTTAAAATAAGGTTGAAACTAATGACATATTTGGATAAA
TTTAGGGATGAAATTAAAAGATTCAAAGTTTGGAGACCAATTTAGAAAGAGGGTCATAATTCATG
GATGAAATTAGAATGGTCAAAAGTTTAAGGACTAATTTAAAATGAGACGCATAAATTGAGGATGA
AATTAAAATATTCAAAAGTTTAAGGACCAATTAAATGAGGATTATAGTCTGGGGACATATAATGC
AATTAACTCTATTTAATTGATATGGACTTAA
Found at i:25201 original size:21 final size:21
Alignment explanation
Indices: 25172--25215 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25162 TAATTGAAAT
*
25172 ATTTTATAATAA-TTTAATAAA
1 ATTTCATAATAATTTTAA-AAA
25193 ATTTCATAATAATTTTAAAAA
1 ATTTCATAATAATTTTAAAAA
25214 AT
1 AT
25216 ATTGATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCATAATAATTTTAAAAA
Found at i:41731 original size:29 final size:29
Alignment explanation
Indices: 41685--41767 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
41675 GAAATTGTCT
41685 TAGGTCGCCATGCACTCCGGGCGACTTTG
1 TAGGTCGCCATGCACTCCGGGCGACTTTG
*
41714 TAGGTCGCCATGCCCTCCGGGCGACTTTG
1 TAGGTCGCCATGCACTCCGGGCGACTTTG
41743 TAGGTCGCCATGCACTCCGGGCGAC
1 TAGGTCGCCATGCACTCCGGGCGAC
41768 CTACCCTCGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.13, C:0.34, G:0.31, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACTTTG
Found at i:41851 original size:14 final size:14
Alignment explanation
Indices: 41829--41909 Score: 63
Period size: 14 Copynumber: 5.4 Consensus size: 14
41819 CCTCGCATAG
*
41829 CTCGTTCGGATGAC
1 CTCGGTCGGATGAC
* *
41843 CTCGGTCGGGTGGC
1 CTCGGTCGGATGAC
41857 CTCAGATGCTCTCGGATGAC
1 CTC-G--G-TC--GGATGAC
41877 CTCGGTCGGATGAC
1 CTCGGTCGGATGAC
* *
41891 CTCGGTTGGATGGC
1 CTCGGTCGGATGAC
41905 CTCGG
1 CTCGG
41910 ATGCCCAGCG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
14 38 0.70
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 1 0.02
20 8 0.15
ACGTcount: A:0.11, C:0.28, G:0.36, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGAC
Found at i:44355 original size:21 final size:20
Alignment explanation
Indices: 44329--44484 Score: 136
Period size: 21 Copynumber: 7.3 Consensus size: 20
44319 CATATCCGCA
*
44329 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
44350 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
*
44371 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
44392 TTGCGATTTATTCCAAGTTCGCG
1 TTGCGA-TTATTCCAAGTT--CG
*
44415 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAGTTCG
* *
44436 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT--CG
*
44457 TTGCGATTTATTCTAAGTTCG
1 TTGCGA-TTATTCCAAGTTCG
44478 TTGCGAT
1 TTGCGAT
44485 AGTCCAAAAT
Statistics
Matches: 118, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.07
20 1 0.01
21 71 0.60
23 38 0.32
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATTATTCCAAGTTCG
Found at i:44394 original size:42 final size:43
Alignment explanation
Indices: 44348--44484 Score: 190
Period size: 42 Copynumber: 3.2 Consensus size: 43
44338 TCCAAGTTCG
*
44348 CGTTGCGATTTATTCCAAATT-CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTTCCGTTGCGATTTATTCCAAATT
44390 CGTTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTTC-CGTTGCGATTTATTCCAAATT
* * * *
44434 CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCTAAGTT
1 CGTTGCGATTTATTCCAAGTTC-CGTTGCGATTTATTCCAAATT
44476 CGTTGCGAT
1 CGTTGCGAT
44485 AGTCCAAAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
42 58 0.67
44 29 0.33
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (43 bp):
CGTTGCGATTTATTCCAAGTTCCGTTGCGATTTATTCCAAATT
Found at i:44412 original size:65 final size:64
Alignment explanation
Indices: 44338--44484 Score: 210
Period size: 65 Copynumber: 2.3 Consensus size: 64
44328 ATTGCGATAG
*
44338 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT-CGTTGCGATTTA
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAATTCCGTTGCGATTTA
44402 T
64 T
* *
44403 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAATTC-CGTTGCGATTTAT
*
44468 TCTAAGTT--CGTTGCGAT
1 TCCAAGTTCGCGTTGCGAT
44485 AGTCCAAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
63 17 0.22
65 59 0.78
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (64 bp):
TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAATTCCGTTGCGATTTAT
Found at i:44485 original size:42 final size:42
Alignment explanation
Indices: 44369--44491 Score: 192
Period size: 42 Copynumber: 2.9 Consensus size: 42
44359 ATTCCAAATT
*
44369 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTTCG
*
44413 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
* *
44455 CGTTGCGATTTATTCTAAGTTCGTTGCGATAGTCCAA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
44492 AATCGCAACG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
42 45 0.61
44 29 0.39
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:44802 original size:21 final size:21
Alignment explanation
Indices: 44776--44865 Score: 87
Period size: 21 Copynumber: 4.3 Consensus size: 21
44766 CACCAGTCGT
*
44776 TGCGATTTTGGACTATCGCAA
1 TGCGATATTGGACTATCGCAA
* * *
44797 TGCGATAGTCGACTATCGTAA
1 TGCGATATTGGACTATCGCAA
44818 TGCGA-ACTTGGACTATCGCAA
1 TGCGATA-TTGGACTATCGCAA
* *
44839 TGCGA-ATATGTA-AATCGCAA
1 TGCGATAT-TGGACTATCGCAA
44859 TGCGATA
1 TGCGATA
44866 GTCGAAGTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
20 14 0.25
21 43 0.75
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (21 bp):
TGCGATATTGGACTATCGCAA
Found at i:44883 original size:21 final size:20
Alignment explanation
Indices: 44853--44966 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 20
44843 AATATGTAAA
*
44853 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAA-T
*
44874 TCGCATTGCGAT-TTAC-ATAT
1 TCGCATTGCGATAGT-CGA-AT
* *
44894 TCGCATTGCGATAGCCGACT
1 TCGCATTGCGATAGTCGAAT
*
44914 ATCGCATTGCGAT-TTAC-ATAT
1 -TCGCATTGCGATAGT-CGA-AT
**
44935 TCGTGTTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAA-T
*
44956 TCGCGTTGCGA
1 TCGCATTGCGA
44967 ATTTGGAAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
20 30 0.42
21 41 0.58
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (20 bp):
TCGCATTGCGATAGTCGAAT
Found at i:44898 original size:20 final size:20
Alignment explanation
Indices: 44873--44937 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
44863 ATAGTCGAAG
44873 TTCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
***
44893 TTCGCATTGCGATAGCCGACTA
1 TTCGCATTGCGATTTAC-A-TA
44915 -TCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
44934 TTCG
1 TTCG
44938 TGTTGCGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.06
20 18 0.50
21 14 0.39
22 2 0.06
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
TTCGCATTGCGATTTACATA
Found at i:44898 original size:41 final size:41
Alignment explanation
Indices: 44853--44966 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
44843 AATATGTAAA
*
44853 TCGCAATGCGATAGTCGAAGTTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATTTACATAT
* *
44894 TCGCATTGCGATAGCCG-ACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCGAAGT-TCGCATTGCGATTTACATAT
** *
44935 TCGTGTTGCGATAGTCGAAGTTCGCGTTGCGA
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGA
44967 ATTTGGAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.03
41 59 0.94
42 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (41 bp):
TCGCATTGCGATAGTCGAAGTTCGCATTGCGATTTACATAT
Found at i:46067 original size:16 final size:17
Alignment explanation
Indices: 46035--46067 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46025 TTTTATAATT
46035 TTATATTTATCAAATAA
1 TTATATTTATCAAATAA
*
46052 TTATCTTTAT-AAATAA
1 TTATATTTATCAAATAA
46068 ATAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATATTTATCAAATAA
Found at i:62025 original size:2 final size:2
Alignment explanation
Indices: 62018--62042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62008 TCAAGATCAG
62018 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 A
62043 CACACACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74715 original size:13 final size:14
Alignment explanation
Indices: 74690--74718 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
74680 TCACTCTTTA
74690 TTATTTCTATCCAC
1 TTATTTCTATCCAC
74704 TTATTT-TATCCAC
1 TTATTTCTATCCAC
74717 TT
1 TT
74719 TGTTTTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATTTCTATCCAC
Found at i:74819 original size:2 final size:2
Alignment explanation
Indices: 74812--74840 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
74802 TAAAGAATCA
74812 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 A
74841 GAAAGAACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76236 original size:29 final size:29
Alignment explanation
Indices: 76203--76274 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
76193 CGAGCTAGGG
* *
76203 GTAGGTCACCATGCCTTCCGGACGACCTT
1 GTAGGTCGCCATGCCCTCCGGACGACCTT
* * *
76232 GTAGGTCGTCATGCCCTCTGGGCGACCTT
1 GTAGGTCGCCATGCCCTCCGGACGACCTT
76261 GTAGGTCGCCATGC
1 GTAGGTCGCCATGC
76275 ACGACGTCGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.14, C:0.32, G:0.29, T:0.25
Consensus pattern (29 bp):
GTAGGTCGCCATGCCCTCCGGACGACCTT
Found at i:76524 original size:25 final size:25
Alignment explanation
Indices: 76503--76580 Score: 126
Period size: 25 Copynumber: 3.2 Consensus size: 25
76493 TATTGCAACG
76503 TTCAACGGTTGAAAAATTTGCAGCC
1 TTCAACGGTTGAAAAATTTGCAGCC
*
76528 TTCAAC-G-TG-AAAATTTGTAGCC
1 TTCAACGGTTGAAAAATTTGCAGCC
76550 TTCAACGGTTGAAAAATTTGCAGCC
1 TTCAACGGTTGAAAAATTTGCAGCC
76575 TTCAAC
1 TTCAAC
76581 CGTGCAAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
22 18 0.38
23 3 0.06
24 3 0.06
25 24 0.50
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (25 bp):
TTCAACGGTTGAAAAATTTGCAGCC
Found at i:76589 original size:25 final size:24
Alignment explanation
Indices: 76503--76589 Score: 106
Period size: 25 Copynumber: 3.6 Consensus size: 24
76493 TATTGCAACG
*
76503 TTCAACGGTTGAAAAATTTGCAGCC
1 TTCAACCG-TGAAAAATTTGCAGCC
*
76528 TTCAA-CGTG-AAAATTTGTAGCC
1 TTCAACCGTGAAAAATTTGCAGCC
*
76550 TTCAACGGTTGAAAAATTTGCAGCC
1 TTCAACCG-TGAAAAATTTGCAGCC
*
76575 TTCAACCGTGCAAAA
1 TTCAACCGTGAAAAA
76590 CTCATTATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
22 17 0.32
23 3 0.06
24 9 0.17
25 24 0.45
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (24 bp):
TTCAACCGTGAAAAATTTGCAGCC
Found at i:76826 original size:21 final size:21
Alignment explanation
Indices: 76801--76844 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
76791 AATTTAGTTA
76801 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
76822 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
76843 AT
1 AT
76845 ATTATATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:76927 original size:25 final size:25
Alignment explanation
Indices: 76798--76927 Score: 76
Period size: 25 Copynumber: 5.2 Consensus size: 25
76788 ATAAATTTAG
*
76798 TTAATTAGTTTGTTAGTATAA---A
1 TTAATTAGTTTGTTAGTTTAAGTTA
76820 TT-ATTAGTTTGTTAGTTTAAGTTATA
1 TTAATTAGTTTGTTAGTTTAAG-T-TA
76846 TTATATATTAGTTTGTTAGTTTAAGTTA
1 -T-TA-ATTAGTTTGTTAGTTTAAGTTA
* * ** *
76874 -TATATTAGATT-ATA-TAAAAAATTA
1 TTA-ATTAGTTTGTTAGT-TTAAGTTA
*
76898 GTTAATTAGTTTCTTAGTTTAAGTTA
1 -TTAATTAGTTTGTTAGTTTAAGTTA
76924 TTAA
1 TTAA
76928 ATGTAAAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
21 17 0.20
22 2 0.02
23 1 0.01
24 7 0.08
25 21 0.25
26 10 0.12
27 2 0.02
28 3 0.04
29 1 0.01
30 19 0.23
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (25 bp):
TTAATTAGTTTGTTAGTTTAAGTTA
Found at i:77411 original size:20 final size:20
Alignment explanation
Indices: 77386--77436 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
77376 CAATTAGGGA
77386 ACCGATTCCCCATGAGGGGT
1 ACCGATTCCCCATGAGGGGT
77406 ACCGATTCCCCATGAGGGGT
1 ACCGATTCCCCATGAGGGGT
77426 ACCGATTCCCC
1 ACCGATTCCCC
77437 CCACGCTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
ACCGATTCCCCATGAGGGGT
Found at i:79512 original size:19 final size:20
Alignment explanation
Indices: 79470--79512 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
79460 TGACCTTAAT
** *
79470 TTTTTTTAATGATTATGCAT
1 TTTTTTTAATGATTATAAAG
79490 TTTTTTTAAT-ATTATAAAG
1 TTTTTTTAATGATTATAAAG
79509 TTTT
1 TTTT
79513 AATGCATACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (20 bp):
TTTTTTTAATGATTATAAAG
Found at i:79512 original size:20 final size:20
Alignment explanation
Indices: 79467--79512 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
79457 TTTTGACCTT
*
79467 AATTTTTTTTAATGATTATG
1 AATTTTTTTTAATGATTATA
*
79487 CATTTTTTTTAAT-ATTATA
1 AATTTTTTTTAATGATTATA
*
79506 AAGTTTT
1 AATTTTT
79513 AATGCATACC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (20 bp):
AATTTTTTTTAATGATTATA
Found at i:82764 original size:22 final size:23
Alignment explanation
Indices: 82738--82788 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
82728 ATAGGGCAGA
*
82738 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATACCCCCTTTGAAG
* *
82760 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATACCCCCTTTGAAG
82783 GGGAAC
1 GGGAAC
82789 TGATTCCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
GGGAACCGATACCCCCTTTGAAG
Found at i:82780 original size:23 final size:22
Alignment explanation
Indices: 82738--82796 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
82728 ATAGGGCAGA
* *
82738 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
*
82760 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCC-TTGAAG
*
82783 GGGAACTGATTCCC
1 GGGAACCGATTCCC
82797 TTCTTTAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:85965 original size:14 final size:14
Alignment explanation
Indices: 85946--85972 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
85936 GTAATTTATT
85946 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
85960 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
85973 GTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:86067 original size:17 final size:17
Alignment explanation
Indices: 86045--86082 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
86035 ATTTATTCCC
86045 GTTTAAAAAAATATTGT
1 GTTTAAAAAAATATTGT
*
86062 GTTT--AAAAATATTTT
1 GTTTAAAAAAATATTGT
86077 GTTTAA
1 GTTTAA
86083 TTTATATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
15 14 0.78
17 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (17 bp):
GTTTAAAAAAATATTGT
Found at i:86069 original size:15 final size:15
Alignment explanation
Indices: 86051--86082 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
86041 TCCCGTTTAA
86051 AAAAATATTGTGTTT
1 AAAAATATTGTGTTT
*
86066 AAAAATATTTTGTTT
1 AAAAATATTGTGTTT
86081 AA
1 AA
86083 TTTATATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (15 bp):
AAAAATATTGTGTTT
Found at i:89146 original size:60 final size:60
Alignment explanation
Indices: 89066--89208 Score: 250
Period size: 60 Copynumber: 2.4 Consensus size: 60
89056 TTATTTAGTC
* * * *
89066 ATGATTAATAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGGTA
1 ATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGATA
89126 ATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGATA
1 ATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGATA
89186 ATGATTAGTAATCATGAAATTAT
1 ATGATTAGTAATCATGAAATTAT
89209 AATAATGATT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 79 1.00
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (60 bp):
ATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGATA
Found at i:89194 original size:21 final size:21
Alignment explanation
Indices: 89110--89225 Score: 70
Period size: 21 Copynumber: 5.9 Consensus size: 21
89100 AATGATTTGA
*
89110 TAGTAATGATTTGGTAATGAT
1 TAGTAATGATTTGATAATGAT
* *
89131 TAGTAATCA--TGA-AATTAT
1 TAGTAATGATTTGATAATGAT
* * *
89149 TATTAAT-ATTTAATGATTTGA-
1 TAGTAATGATTTGAT-A-ATGAT
89170 TAGTAATGATTTGATAATGAT
1 TAGTAATGATTTGATAATGAT
* *
89191 TAGTAATCA--TGA-AATTA-
1 TAGTAATGATTTGATAATGAT
*
89208 TAATAATGATTTGATAAT
1 TAGTAATGATTTGATAAT
89226 AATGATTTAA
Statistics
Matches: 71, Mismatches: 14, Indels: 21
0.67 0.13 0.20
Matches are distributed among these distances:
17 8 0.11
18 15 0.21
19 10 0.14
20 6 0.08
21 24 0.34
22 8 0.11
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.43
Consensus pattern (21 bp):
TAGTAATGATTTGATAATGAT
Found at i:89231 original size:14 final size:14
Alignment explanation
Indices: 89159--89233 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
89149 TATTAATATT
*
89159 TAATGATTTGATAG
1 TAATGATTTGATAA
89173 TAATGATTTG---A
1 TAATGATTTGATAA
*
89184 TAATGATTAG-TAA
1 TAATGATTTGATAA
* *
89197 TCATGAAATT-ATAA
1 TAATG-ATTTGATAA
89211 TAATGATTTGATAA
1 TAATGATTTGATAA
89225 TAATGATTT
1 TAATGATTT
89234 AATGGGGTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
11 9 0.18
13 8 0.16
14 32 0.65
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:89237 original size:60 final size:60
Alignment explanation
Indices: 89066--89231 Score: 208
Period size: 60 Copynumber: 2.8 Consensus size: 60
89056 TTATTTAGTC
* * * * * * *
89066 ATGATTAATAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGGTA
1 ATGATTAGTAATCATGAAATTATTAATAATATTTAATAATATGATAGTAATGATTTGATA
* * *
89126 ATGATTAGTAATCATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGATA
1 ATGATTAGTAATCATGAAATTATTAATAATATTTAATAATATGATAGTAATGATTTGATA
*
89186 ATGATTAGTAATCATGAAATTA-TAATAATGATTTGATAATAATGAT
1 ATGATTAGTAATCATGAAATTATTAATAAT-ATTTAATAAT-ATGAT
89232 TTAATGGGGT
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
59 6 0.06
60 86 0.90
61 4 0.04
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (60 bp):
ATGATTAGTAATCATGAAATTATTAATAATATTTAATAATATGATAGTAATGATTTGATA
Found at i:89384 original size:23 final size:20
Alignment explanation
Indices: 89345--89421 Score: 100
Period size: 20 Copynumber: 3.6 Consensus size: 20
89335 GATATGACAT
89345 TTAATAATGATTTATTATTA
1 TTAATAATGATTTATTATTA
89365 TTAATAATGATTAGTAATTATTA
1 TTAATAATGATT--T-ATTATTA
89388 TTAATAATGATTTATTATTA
1 TTAATAATGATTTATTATTA
* *
89408 ATATTTAATGATTT
1 TTA-ATAATGATTT
89422 GATATTAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
20 21 0.41
21 10 0.20
22 1 0.02
23 19 0.37
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
TTAATAATGATTTATTATTA
Found at i:89413 original size:13 final size:13
Alignment explanation
Indices: 89359--89414 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
89349 TAATGATTTA
*
89359 TTATTATTAATAA
1 TTATTATTAATAT
* *
89372 TGATTAGTAAT-T
1 TTATTATTAATAT
*
89384 ATTATTAATAATGAT
1 -TTATTATTAAT-AT
89399 TTATTATTAATAT
1 TTATTATTAATAT
89412 TTA
1 TTA
89415 ATGATTTGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 23 0.68
14 10 0.29
15 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (13 bp):
TTATTATTAATAT
Found at i:89436 original size:21 final size:21
Alignment explanation
Indices: 89349--89430 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 21
89339 TGACATTTAA
* *
89349 TAATGATTTATTATTATTA-A
1 TAATGATTTATTATTAATATT
* *
89369 TAATGATTAGTAATTATTATTA-A
1 TAATGATT--T-ATTATTAATATT
89392 TAATGATTTATTATTAATATT
1 TAATGATTTATTATTAATATT
89413 TAATGATTTGA-TATTAAT
1 TAATGATTT-ATTATTAAT
89431 GATTAAGTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
20 17 0.31
21 17 0.31
22 2 0.04
23 19 0.35
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
TAATGATTTATTATTAATATT
Found at i:89713 original size:11 final size:11
Alignment explanation
Indices: 89697--89883 Score: 71
Period size: 11 Copynumber: 15.6 Consensus size: 11
89687 TAATAATTAT
89697 ATGATTTAATA
1 ATGATTTAATA
89708 ATGATTTGATAATA
1 ATGA-TT--TAATA
89722 ATGATTTAATA
1 ATGATTTAATA
*
89733 AT-ATTGGACAATA
1 ATGATT---TAATA
89746 AT-ATTTAATA
1 ATGATTTAATA
89756 ATGATTT--TA
1 ATGATTTAATA
89765 AT-ATTTGATAGTA
1 ATGATTT-A-A-TA
*
89778 ATGATTTACTA
1 ATGATTTAATA
*
89789 ATGATTACTAGTA
1 ATGATT--TAATA
*
89802 ATGAAATT-ATA
1 ATG-ATTTAATA
* *
89813 ATGATGATAGTA
1 ATGAT-TTAATA
89825 ATGATTTGATACTA
1 ATGATTT-A-A-TA
*
89839 ATGATTTACTA
1 ATGATTTAATA
*
89850 ATGATTACTAGTA
1 ATGATT--TAATA
89863 ATGAAATTATAATA
1 ATG--ATT-TAATA
89877 ATGATTT
1 ATGATTT
89884 GATACTAATA
Statistics
Matches: 136, Mismatches: 15, Indels: 50
0.68 0.07 0.25
Matches are distributed among these distances:
8 4 0.03
9 4 0.03
10 10 0.07
11 39 0.29
12 14 0.10
13 31 0.23
14 31 0.23
15 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:89717 original size:16 final size:16
Alignment explanation
Indices: 89685--89728 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
89675 ATAGGATTTT
* *
89685 TTTAATAATTATATGA
1 TTTAATAATGATTTGA
89701 TTTAATAATGATTTGA
1 TTTAATAATGATTTGA
89717 --TAATAATGATTT
1 TTTAATAATGATTT
89729 AATAATATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 12 0.46
16 14 0.54
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TTTAATAATGATTTGA
Found at i:89722 original size:14 final size:14
Alignment explanation
Indices: 89703--89735 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
89693 TTATATGATT
*
89703 TAATAATGATTTGA
1 TAATAATGATTTAA
89717 TAATAATGATTTAA
1 TAATAATGATTTAA
89731 TAATA
1 TAATA
89736 TTGGACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (14 bp):
TAATAATGATTTAA
Found at i:89834 original size:14 final size:14
Alignment explanation
Indices: 89817--89892 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 14
89807 ATTATAATGA
*
89817 TGATAGTAATGATT
1 TGATACTAATGATT
89831 TGATACTAATGA-T
1 TGATACTAATGATT
89844 T--TACTAATGA-T
1 TGATACTAATGATT
* *
89855 T-ACTAGTAATGAAAT
1 TGA-TACTAATG-ATT
*
89870 T-ATAATAATGATT
1 TGATACTAATGATT
89883 TGATACTAAT
1 TGATACTAAT
89893 AATCATTATA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
11 11 0.21
13 12 0.23
14 26 0.50
15 3 0.06
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (14 bp):
TGATACTAATGATT
Found at i:89844 original size:61 final size:61
Alignment explanation
Indices: 89706--89881 Score: 222
Period size: 61 Copynumber: 3.0 Consensus size: 61
89696 TATGATTTAA
* * **
89706 TAATGATTTGATAATAATGATTTAATAAT-ATTGGAC-AATAAT---ATT-TAATAATGATTT
1 TAATGATTTGATAATAATGATTTACTAATGATT--ACTAGTAATGAAATTATAATAATGATAG
* *
89763 TAAT-ATTTGATAGTAATGATTTACTAATGATTACTAGTAATGAAATTATAATGATGATAG
1 TAATGATTTGATAATAATGATTTACTAATGATTACTAGTAATGAAATTATAATAATGATAG
*
89823 TAATGATTTGATACTAATGATTTACTAATGATTACTAGTAATGAAATTATAATAATGAT
1 TAATGATTTGATAATAATGATTTACTAATGATTACTAGTAATGAAATTATAATAATGAT
89882 TTGATACTAA
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
55 2 0.02
56 27 0.26
57 7 0.07
59 3 0.03
60 13 0.12
61 52 0.50
ACGTcount: A:0.43, C:0.03, G:0.12, T:0.41
Consensus pattern (61 bp):
TAATGATTTGATAATAATGATTTACTAATGATTACTAGTAATGAAATTATAATAATGATAG
Found at i:89879 original size:38 final size:37
Alignment explanation
Indices: 89811--89883 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
89801 AATGAAATTA
* *
89811 TAATGATGATAGTAATGATTTGATACTAATGATTTAC
1 TAATGATGATAGTAATGAATTGATAATAATGATTTAC
*
89848 TAATGATTACTAGTAATGAAATT-ATAATAATGATTT
1 TAATGATGA-TAGTAATG-AATTGATAATAATGATTT
89884 GATACTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 8 0.26
38 20 0.65
39 3 0.10
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (37 bp):
TAATGATGATAGTAATGAATTGATAATAATGATTTAC
Found at i:92204 original size:16 final size:16
Alignment explanation
Indices: 92171--92217 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
92161 CAAAAAAAGT
*
92171 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
92186 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
92202 TAA-ACTAAAAAACTAA
1 TAATA-TAATAAACTAA
92218 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:92540 original size:21 final size:22
Alignment explanation
Indices: 92516--92556 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
92506 TTTATGTATA
*
92516 ATATAA-CTTAAACTAACAATC
1 ATATAACCATAAACTAACAATC
92537 ATATAACCATAAACTAACAA
1 ATATAACCATAAACTAACAA
92557 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (22 bp):
ATATAACCATAAACTAACAATC
Found at i:92738 original size:26 final size:26
Alignment explanation
Indices: 92696--92779 Score: 134
Period size: 26 Copynumber: 3.3 Consensus size: 26
92686 CCCTTCCTTT
* *
92696 CTTTC-TCGACTGTAATCTCTTCTCC
1 CTTTCTTCGGCTGCAATCTCTTCTCC
92721 CTTTCTTCGGCTGCAATCTCTTCTCC
1 CTTTCTTCGGCTGCAATCTCTTCTCC
*
92747 ATTTCTTCGGCTGCAATCTCTTCTCC
1 CTTTCTTCGGCTGCAATCTCTTCTCC
92773 CTTTCTT
1 CTTTCTT
92780 TCTTTTATGT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
25 5 0.09
26 49 0.91
ACGTcount: A:0.10, C:0.36, G:0.10, T:0.45
Consensus pattern (26 bp):
CTTTCTTCGGCTGCAATCTCTTCTCC
Found at i:97961 original size:23 final size:23
Alignment explanation
Indices: 97914--97963 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
97904 AATAACATAT
**
97914 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
97937 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
97960 TAGG
1 TAGG
97964 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:98023 original size:87 final size:87
Alignment explanation
Indices: 97877--98039 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
97867 AATGTTATAT
*
97877 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
97942 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
**
97964 CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGTTCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
98029 AGCGTTTATAT
66 AGCGCTTATAT
98040 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:98675 original size:200 final size:199
Alignment explanation
Indices: 98034--98764 Score: 730
Period size: 200 Copynumber: 3.6 Consensus size: 199
98024 TAGGTAGCGT
* * * *
98034 TTATATTGACCTATTTTCGAAGT-AAACCGGTATATTTATACCGATAACATTGTAAATTTACCTA
1 TTATATTGACCTATTTTCTAA-TAAAACCGGAATATTTATACCGGTTACATTGTAAATTTACCTA
* * * * *
98098 TTATATTATTATTATCGGTTTCAATATTTTTTA-GATCGATACAATTT--TAAATGTATCGACAC
65 TTACATTATAATTATCGTTTTCGAT-GTTTTTAGGATCGATAC-ATTTAATAAATGTATCGACAC
* * * *
98160 TTTATGCTTGCACCTCGTTGGACATTCATATTTCATTCTGGAAAAAAGTATCGACACAAACTAAA
128 TTTATGCATGCACCTCGTTTG--A--C--A-TTCATTCTGGACAAAAGTATCGACACAAATTAAA
*
98225 AAAGTGTCGATACA
186 CAAGTGTCGATACA
* * * * *
98239 TTAT-TTAGACTTATTTTCTCATAAAACC-GATAAATTTATATCGGGTACATTGTAAATTTACCT
1 TTATATT-GACCTATTTTCTAATAAAACCGGA-ATATTTATACCGGTTACATTGTAAATTTACCT
* * * * * *
98302 ATCACATTGTAATTTTCG-TTTCGATGTTTTT-GAGATCGATACTTTTAATAATTGTATTGACAC
64 ATTACATTATAATTATCGTTTTCGATGTTTTTAG-GATCGATACATTTAATAAATGTATCGACAC
* ** * * *
98365 TCTATGTGTGCACCCCGTTTGACATAT-ATTATGGACAAAATGTATCGACACAAATTTAACAAGT
128 TTTATGCATGCACCTCGTTTGACAT-TCATTCTGGACAAAA-GTATCGACACAAATTAAACAAGT
*
98429 GTCGATACT
191 GTCGATACA
* * * * * *
98438 TTATGTTGACCTATTTTCTCATAAAATCGGTATATTTATATCGGTTACATTGTAAATTTACATAT
1 TTATATTGACCTATTTTCTAATAAAACCGGAATATTTATACCGGTTACATTGTAAATTTACCTAT
* *
98503 TACATTAAAATTATCGTTTTCGATGTTTTTAGGATCGATACTTTTAATAAATGTATCGACACTTT
66 TACATTATAATTATCGTTTTCGATGTTTTTAGGATCGATACATTTAATAAATGTATCGACACTTT
* **
98568 ATGCATGCACCTCGTTTGAGCATTCATTCTAGACAATAAGTATCGACACAAATTCCACAAGTGTC
131 ATGCATGCACCTCGTTTGA-CATTCATTCTGGACAA-AAGTATCGACACAAATTAAACAAGTGTC
98633 GATACA
194 GATACA
* * * * * *
98639 TTATATTGACTTGTTTTCTAAT-TAACCGGAATATTTATACCAGTTACATTGTTAATTTACTTAT
1 TTATATTGACCTATTTTCTAATAAAACCGGAATATTTATACCGGTTACATTGTAAATTTACCTAT
* * * *
98703 TACATTATAATTATTGGTTTT-GATGTTTTTTGGGTCGATACATGTAGA-AAATGTATCGACAC
66 TACATTATAATTA-TCGTTTTCGATGTTTTTAGGATCGATACATTTA-ATAAATGTATCGACAC
98765 ATATTTAGGT
Statistics
Matches: 440, Mismatches: 68, Indels: 41
0.80 0.12 0.07
Matches are distributed among these distances:
198 12 0.03
199 96 0.22
200 145 0.33
201 68 0.15
202 2 0.00
203 9 0.02
204 19 0.04
205 89 0.20
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (199 bp):
TTATATTGACCTATTTTCTAATAAAACCGGAATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGTTTTCGATGTTTTTAGGATCGATACATTTAATAAATGTATCGACACTTT
ATGCATGCACCTCGTTTGACATTCATTCTGGACAAAAGTATCGACACAAATTAAACAAGTGTCGA
TACA
Found at i:109756 original size:20 final size:20
Alignment explanation
Indices: 109733--109796 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
109723 GTTTCCAGAT
*
109733 TCGCAACGCGATTTTAACTA
1 TCGCAACGCGATTCTAACTA
* *
109753 TCGCAATGCGAATATGTAA--A
1 TCGCAACGCG-AT-TCTAACTA
*
109773 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTAACTA
109793 TCGC
1 TCGC
109797 GTTGCGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 24 0.69
21 2 0.06
22 4 0.11
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGATTCTAACTA
Found at i:109990 original size:22 final size:22
Alignment explanation
Indices: 109964--110043 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
109954 TCACTCTCTA
* *
109964 CGACGACATCCGTCCACATCTC
1 CGACGAAATCCGTCCCCATCTC
*
109986 TGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
110008 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
110030 CGACGAAATCCGTC
1 CGACGAAATCCGTC
110044 TATCTCCATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.24, C:0.42, G:0.15, T:0.19
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:110456 original size:20 final size:20
Alignment explanation
Indices: 110433--110477 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
110423 TTAGTTTCAC
*
110433 GTTGCAATAGTCATTTTCGT
1 GTTGCAATAGTCATTTCCGT
* **
110453 GTTGCGATTTTCATTTCCGT
1 GTTGCAATAGTCATTTCCGT
110473 GTTGC
1 GTTGC
110478 GATTTTAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
GTTGCAATAGTCATTTCCGT
Found at i:110478 original size:20 final size:20
Alignment explanation
Indices: 110443--110483 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
110433 GTTGCAATAG
*
110443 TCATTTTCGTGTTGCGATTT
1 TCATTTCCGTGTTGCGATTT
110463 TCATTTCCGTGTTGCGATTT
1 TCATTTCCGTGTTGCGATTT
110483 T
1 T
110484 AAGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.20, T:0.54
Consensus pattern (20 bp):
TCATTTCCGTGTTGCGATTT
Found at i:112543 original size:30 final size:30
Alignment explanation
Indices: 112509--112581 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
112499 CCCGAAGGAC
112509 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
112539 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
112569 CTATCCATAGGTC
1 CTATCCAGAGGTC
112582 CCGAAGAACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:112598 original size:30 final size:30
Alignment explanation
Indices: 112509--112608 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 30
112499 CCCGAAGGAC
* *
112509 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
* *
112539 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGATCCTCGGTAA
* * * *
112569 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCACAAAGATCCTCGGT-AA
*
112600 CTGTCCATA
1 CTATCCATA
112609 TGTTCCTTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 52 0.84
31 10 0.16
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGATCCTCGGTAA
Found at i:112688 original size:32 final size:31
Alignment explanation
Indices: 112567--112695 Score: 118
Period size: 32 Copynumber: 4.1 Consensus size: 31
112557 GATCCTCGGT
* * * * *
112567 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
112598 AACTGTCCATATGTTCCTTAGAACATATTGTA
1 AACTGTCCATATGTTCCGTAGAACATA-GGTA
* * *
112630 TACTGTACATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
112662 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
112693 AAC
1 AAC
112696 CCTCGACTCT
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
31 31 0.40
32 42 0.55
33 4 0.05
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:113885 original size:21 final size:20
Alignment explanation
Indices: 113855--113898 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
113845 TGTTGTTCGT
* *
113855 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
113875 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
113896 TTG
1 TTG
113899 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:115221 original size:20 final size:20
Alignment explanation
Indices: 115198--115266 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
115188 GAAACTTAAA
115198 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
115218 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
115238 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAAAATGACT
115258 ATCGCAACG
1 ATCGCAACG
115267 GGATAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:115297 original size:33 final size:34
Alignment explanation
Indices: 115258--115333 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
115248 GAATTTGACT
* * *
115258 ATCGCAACGGGATAATCGCAATTCG-AAATAAAA
1 ATCGCAACGGGAAAAGCGCAATGCGAAAATAAAA
* *
115291 ATCGCAACGTGAAAAGCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAAGCGCAATGCGAAAATAAAA
115325 ATCGCAACG
1 ATCGCAACG
115334 CGAATTTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAAGCGCAATGCGAAAATAAAA
Found at i:115325 original size:20 final size:20
Alignment explanation
Indices: 115300--115337 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
115290 AATCGCAACG
*
115300 TGAAAAGCGCAATGCGAAAA
1 TGAAAAGCGCAACGCGAAAA
*
115320 TGAAAATCGCAACGCGAA
1 TGAAAAGCGCAACGCGAA
115338 TTTAGTTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (20 bp):
TGAAAAGCGCAACGCGAAAA
Found at i:115421 original size:20 final size:20
Alignment explanation
Indices: 115396--115483 Score: 99
Period size: 20 Copynumber: 4.4 Consensus size: 20
115386 CGATTATCTT
*
115396 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
115416 GTTGCGATAGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
* *
115436 ATTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAATTTCGC
* *
115456 GTTGCGAT-GTTAAGTTTCGT
1 GTTGCGATAGTCAA-TTTCGC
115476 GTTGCGAT
1 GTTGCGAT
115484 TTTAAGTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 6 0.10
20 49 0.84
21 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:115488 original size:20 final size:20
Alignment explanation
Indices: 115450--115493 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
115440 CGATAGTCAT
115450 TTTCGCGTTGCGATGTTAAG
1 TTTCGCGTTGCGATGTTAAG
* *
115470 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATGTTAAG
115490 TTTC
1 TTTC
115494 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGATGTTAAG
Found at i:117644 original size:20 final size:20
Alignment explanation
Indices: 117619--117680 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
117609 AACGCTAAAC
117619 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
117639 TCAAAATCGCAATGCGAAA-
1 TCAAAATCGCAATGCGAAAG
*
117658 TCCAAAATCGCAACGCGAAAG
1 T-CAAAATCGCAATGCGAAAG
117679 TC
1 TC
117681 TAATACGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.15
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:117727 original size:20 final size:20
Alignment explanation
Indices: 117702--117792 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
117692 GCGATTTTCT
117702 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
117722 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
117742 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
117756 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
117776 CCTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
117793 GAATGTGTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
14 11 0.19
16 1 0.02
18 1 0.02
20 46 0.78
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:117772 original size:54 final size:54
Alignment explanation
Indices: 117672--117792 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 54
117662 AAATCGCAAC
* * * * *
117672 GCGAAAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATACGCGTTGCGATTTTCTCGTTACGATAGTCAAATTCGCCTT
*
117726 GCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTTACGATAGTCAAATTCGCCTT
1 GCGATAGTCAAATACGCGTTGCGATTTTCT-CGTTACGATAGTCAAATTCGCCTT
*
117780 GCGATATTCAAAT
1 GCGATAGTCAAAT
117793 GAATGTGTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.02
54 58 0.98
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (54 bp):
GCGATAGTCAAATACGCGTTGCGATTTTCTCGTTACGATAGTCAAATTCGCCTT
Found at i:118018 original size:140 final size:140
Alignment explanation
Indices: 117763--118045 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
117753 TTGCGTTACG
117763 ATAGTCAAATTCGCCTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCCTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
117828 TAGCAATGTTCAAACTCAAGTTTCTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
117893 AATACACATA
131 AATACACATA
*
117903 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCCTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
117968 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
118033 AATACACATA
131 AATACACATA
118043 ATA
1 ATA
118046 CAACGTTTGC
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCCTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAAAGTTAAAAGTTTACACATAA
AATACACATA
Found at i:118124 original size:18 final size:18
Alignment explanation
Indices: 118098--118138 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
118088 AGGTGAAGCC
*
118098 GATTGTGATTGGGATTTT
1 GATTGTGATTGCGATTTT
*
118116 GATTTTGATTGCGATTTT
1 GATTGTGATTGCGATTTT
118134 GATTG
1 GATTG
118139 CCTTTTACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.51
Consensus pattern (18 bp):
GATTGTGATTGCGATTTT
Found at i:120390 original size:24 final size:24
Alignment explanation
Indices: 120363--120416 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
120353 TTGAAACATC
120363 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
120387 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
120411 ATCAAA
1 ATCAAA
120417 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:121316 original size:21 final size:20
Alignment explanation
Indices: 121292--121357 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
121282 ATTTACATAT
*
121292 TCGCATTGCGATTTTCTAAAA
1 TCGCAATGCGATTTTC-AAAA
* **
121313 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCG-ATTTTCAAAA
**
121334 TCGCAATGCGATAGTCAAAA
1 TCGCAATGCGATTTTCAAAA
121354 TCGC
1 TCGC
121358 TTTGCGAATC
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
20 10 0.29
21 21 0.60
22 4 0.11
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGATTTTCAAAA
Found at i:122094 original size:16 final size:16
Alignment explanation
Indices: 122039--122096 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
122029 TTTAGAACAT
122039 GTAAATAAGTAA-AAGAA
1 GTAAATAA-TAATAA-AA
*
122056 GTAAAATAATAATAAAT
1 GT-AAATAATAATAAAA
* *
122073 GAAAATTATAATAAAA
1 GTAAATAATAATAAAA
122089 GTAAATAA
1 GTAAATAA
122097 AGTATAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 18 0.55
17 7 0.21
18 8 0.24
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (16 bp):
GTAAATAATAATAAAA
Found at i:123321 original size:29 final size:29
Alignment explanation
Indices: 123264--123326 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
123254 AATAAATCAC
* * **
123264 CCTTTCCCTCTTTATTTTCCTGTCAAACA
1 CCTTTCCATCTTTATTTCCCCATCAAACA
*
123293 CCTTTCCATCTTTATTTCCCCATCTAACA
1 CCTTTCCATCTTTATTTCCCCATCAAACA
*
123322 TCTTT
1 CCTTT
123327 TGCAGAAAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.17, C:0.35, G:0.02, T:0.46
Consensus pattern (29 bp):
CCTTTCCATCTTTATTTCCCCATCAAACA
Found at i:124161 original size:11 final size:10
Alignment explanation
Indices: 124140--124195 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
124130 CTCATATATT
124140 TAAAAATCAA
1 TAAAAATCAA
124150 TAAAAATACAA
1 TAAAAAT-CAA
124161 TAAAAA--AA
1 TAAAAATCAA
* *
124169 TTAAAAGTGAA
1 -TAAAAATCAA
*
124180 TAAAATTCAA
1 TAAAAATCAA
124190 TAAAAA
1 TAAAAA
124196 ATGTAAAGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 2 0.05
9 5 0.13
10 20 0.53
11 11 0.29
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:131707 original size:17 final size:17
Alignment explanation
Indices: 131685--131717 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
131675 ATATATATAA
131685 TAAACTAAACCTAATAT
1 TAAACTAAACCTAATAT
131702 TAAACTAAACCTAATA
1 TAAACTAAACCTAATA
131718 GCCGTATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAACTAAACCTAATAT
Found at i:131761 original size:15 final size:15
Alignment explanation
Indices: 131729--131767 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
131719 CCGTATATCA
131729 TACTCCTCTCACCCTC
1 TACT-CTCTCACCCTC
131745 TACTCTCTC-CCCATC
1 TACTCTCTCACCC-TC
131760 TACTCTCT
1 TACTCTCT
131768 TCCTCACGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 15 0.68
16 4 0.18
ACGTcount: A:0.13, C:0.51, G:0.00, T:0.36
Consensus pattern (15 bp):
TACTCTCTCACCCTC
Found at i:132962 original size:55 final size:55
Alignment explanation
Indices: 132898--133336 Score: 513
Period size: 55 Copynumber: 8.1 Consensus size: 55
132888 TGATAAGTCT
* * *
132898 GCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACATGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* * * *
132953 GCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* * *
133008 GCTCCCTATTCATTCATG-GAGTATAAGACTCGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCA-GAGAGTATAAGACTCGAACAATCTTCAA-CAAACGTGTCC
* * ** *
133064 GCTCTCTATTCCTTC--AGTGTAT-AGAACTCGAACAATCTTCAACAAATATGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCC
* * *
133117 GCTCCCTATTTCTTCAGAGAGTATAGGACTTG----ATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
* * *
133168 GCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACAATCTTCATA-AAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAAACGTGTCC
* *
133223 GCTCTCTATTCCTTCAGAGAGTATATA-ACTCGAACAATCTTCAACAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAACGTGTCC
* * *
133278 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGAGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGTGTCC
133333 GCTC
1 GCTC
133337 TCTCTTTCTC
Statistics
Matches: 338, Mismatches: 30, Indels: 32
0.85 0.08 0.08
Matches are distributed among these distances:
51 47 0.14
53 22 0.07
54 23 0.07
55 222 0.66
56 24 0.07
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGTGTCC
Found at i:133355 original size:55 final size:54
Alignment explanation
Indices: 132913--133744 Score: 533
Period size: 54 Copynumber: 15.4 Consensus size: 54
132903 CTATTCCTTC
** *
132913 AGGGAGTATA-AGACTCGAACAATCTTCAACAAACATG-TCTGCTCCCT-ATTCAT-T
1 AGGGAGTATAGA-ACTCGAAC-ATCTTCAACAAACGGGTTC-GCTCCCTCTTTC-TCT
* * *
132967 CAGGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTG-TCTGCTCCCT-ATTCAT-T
1 -AGGGAGTATAGA-ACTCGAAC-ATCTTCAACAAACGGGTTC-GCTCCCTCTTTC-TCT
* * *
133022 CATGGAGTATA-AGACTCGAACAATCTTCAATAAAACGGGTCCGCT--CTCTATTC-CT
1 -AGGGAGTATAGA-ACTCGAAC-ATCTTCAA-CAAACGGGTTCGCTCCCTCT-TTCTCT
*** * *** *
133077 TCAGTGTATAGAACTCGAACAATCTTCAACAAATATG-TCTGCTCCCTATTTCT-T
1 AGGGAGTATAGAACTCGAAC-ATCTTCAACAAACGGGTTC-GCTCCCTCTTTCTCT
* * * * * *
133131 CAGAGAGTATAGGACTTG---ATCTTCAACAAACGTGTCCGCTCCCTATTTCT-T
1 -AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* * * * * *
133182 CAGAGAGTATAGGACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCCT-T
1 -AGGGAGTATAGAACTCGAAC-ATCTTCA-ACAAACGGGTTCGCTCCCTCTTTCTCT
* * * * * *
133237 CAGAGAGTATATAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCT-T
1 -AGGGAGTATAGAACTCGAAC-ATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* * *
133292 CAGAGAGTATAGAACTCGAACAATCTTCAACAAACGAGTTCGCTCTCTCTTTCTCT
1 -AGGGAGTATAGAACTCGAAC-ATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* * * ** ** *
133348 ATGGAGTATAAAACTCTAACATCTTCTTCTTACGGGTTCGCTCCCTTTTTCTCT
1 AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* ** **
133402 AGGGAGTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCT-CCTCTTTCTCT
1 AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* ** **
133455 AGGGAGTATGGAACTCGAACAT-TTCTTCTTACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* * ** **
133508 AGGGAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCGCTCCCTCTTTCTCT
1 AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* ** ** *
133562 AGGGAGTATGGAACTCGAACAT-TTCTTCTTACGGGTTCGCTCCCTCTTTCTTT
1 AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* * ** ** *
133615 AGGGAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCACTCCCTCTTTCTCT
1 AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
* * ** ** *
133669 AGGGAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCGCTCTCTCTTTCTCT
1 AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
*
133723 AGGGAGTATGGAACTCGAACAT
1 AGGGAGTATAGAACTCGAACAT
133745 TTTCTTCTAC
Statistics
Matches: 697, Mismatches: 58, Indels: 45
0.87 0.07 0.06
Matches are distributed among these distances:
51 45 0.06
52 21 0.03
53 124 0.18
54 251 0.36
55 241 0.35
56 14 0.02
57 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (54 bp):
AGGGAGTATAGAACTCGAACATCTTCAACAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:133474 original size:53 final size:54
Alignment explanation
Indices: 133329--133752 Score: 728
Period size: 54 Copynumber: 7.9 Consensus size: 54
133319 CAACAAACGA
* * ** * *
133329 GTTCGCTCTCTCTTTCTCTATGGAGTATAAAACTCTAACATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
* *
133383 GTTCGCTCCCTTTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
133437 GTTCGCT-CCTCTTTCTCTAGGGAGTATGGAACTCGAACA-TTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
133489 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
133543 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACA-TTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
*
133596 GTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
*
133650 GTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
*
133704 GTTCGCTCTCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCT
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCT
133753 ACTTTATTAC
Statistics
Matches: 354, Mismatches: 13, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
52 19 0.05
53 115 0.32
54 220 0.62
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (54 bp):
GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
Found at i:133605 original size:107 final size:107
Alignment explanation
Indices: 133329--133752 Score: 733
Period size: 107 Copynumber: 4.0 Consensus size: 107
133319 CAACAAACGA
* * ** *
133329 GTTCGCTCTCTCTTTCTCTATGGAGTATAAAACTCTAACATCTTCTTCTTACGGGTTCGCTCCCT
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACAT-TTCTTCTTACGGGTTCGCTCCCT
* *
133394 TTTTCTCTAGGGAGTATGGAACTCGAACATCTTCTTCTTACGG
65 CTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
133437 GTTCGCT-CCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTCTTCTTACGGGTTCGCTCCCTC
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTCTTCTTACGGGTTCGCTCCCTC
133501 TTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
66 TTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
133543 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTCTTCTTACGGGTTCGCTCCCTC
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTCTTCTTACGGGTTCGCTCCCTC
*
133608 TTTCTTTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
66 TTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
* *
133650 GTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGGGTTCGCTCTCT
1 GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACA-TTTCTTCTTACGGGTTCGCTCCCT
133715 CTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCT
65 CTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCT
133753 ACTTTATTAC
Statistics
Matches: 303, Mismatches: 11, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
106 71 0.23
107 165 0.54
108 67 0.22
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (107 bp):
GTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTCTTCTTACGGGTTCGCTCCCTC
TTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTTACGG
Found at i:134200 original size:36 final size:37
Alignment explanation
Indices: 134125--134248 Score: 169
Period size: 37 Copynumber: 3.4 Consensus size: 37
134115 TTGCGCCAAC
* * * *
134125 ACTCTTCCGAGAAGGCTTAAAAAGGATATGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
134162 ACTCTTCGGTGAAGGCTTAAGATGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
* *
134198 ACTCTTTGGTGAAGGCTCAAAATGGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
134235 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
134249 ACTTGACTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 32 0.41
37 46 0.59
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:135673 original size:125 final size:125
Alignment explanation
Indices: 135473--135699 Score: 316
Period size: 125 Copynumber: 1.8 Consensus size: 125
135463 GCAGGTAAGA
* *
135473 GCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTTCAGTGCCTTCTTGGTCTGAATC
1 GCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTTCAGTGACTTCTTGGTCTAAATC
*
135538 TTATCATCTCAACATGATGTGGGTTCAGTCGTGCCCCGACATTACCTCATACTGGTACGG
66 TTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCGACATTACCTCATACTGGTACGG
* * * *
135598 GCCTTCAAAATGCCCCATCACCTCAATTTGTAAGGCTCATTCTTCA-TTAC-TCATTGGT-TCAA
1 GCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATT-TTCAGTGACTTC-TTGGTCT-AA
* * *
135660 ATCTTGTCATCTCACCATGATGTGGGTTTAGTCATGCCCC
63 ATCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCC
135700 AATGTGGGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
124 3 0.03
125 82 0.92
126 4 0.04
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.32
Consensus pattern (125 bp):
GCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCTCATTTTCAGTGACTTCTTGGTCTAAATC
TTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCGACATTACCTCATACTGGTACGG
Found at i:139210 original size:72 final size:72
Alignment explanation
Indices: 139093--139239 Score: 258
Period size: 72 Copynumber: 2.0 Consensus size: 72
139083 TAACAGGTTA
*
139093 TTGATCAGTTGTTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
1 TTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
*
139158 TCTGTTC
66 TATGTTC
*
139165 TTGATCATTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
1 TTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
*
139230 TATTTTC
66 TATGTTC
139237 TTG
1 TTG
139240 TGTAATAGGG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (72 bp):
TTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTCTTCA
TATGTTC
Found at i:139995 original size:55 final size:55
Alignment explanation
Indices: 139919--140031 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
139909 TTCTTTGTAG
* *
139919 ATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATTGGATGTCCTTCTTCATGA
1 ATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATTGAATGTCCTTCTTCATGA
* *
139974 ATCGTTCTTCAGTCAGGTTCAAATTTCTTCATTCATTGAATGTCCTTCTTCATGA
1 ATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATTGAATGTCCTTCTTCATGA
140029 ATC
1 ATC
140032 ATTTGAACGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (55 bp):
ATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATTGAATGTCCTTCTTCATGA
Found at i:140435 original size:46 final size:45
Alignment explanation
Indices: 140348--140435 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 45
140338 TGCAAAAAAT
*
140348 CCTAACCGCATGATATCTAATTCACATGCTTGTTCGAGAAAATAAA
1 CCTAACCGCATGATATCTAATTCACATGCTTATTC-AGAAAATAAA
* *
140394 CCTAACCGCATGATATCTAGTTCGCATGCATTTATTC-GAAAA
1 CCTAACCGCATGATATCTAATTCACATGC--TTATTCAGAAAA
140436 ATGAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 32 0.86
48 5 0.14
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (45 bp):
CCTAACCGCATGATATCTAATTCACATGCTTATTCAGAAAATAAA
Found at i:142428 original size:17 final size:17
Alignment explanation
Indices: 142406--142438 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
142396 ATATATATAA
142406 TAAACTAAACCTAATAT
1 TAAACTAAACCTAATAT
142423 TAAACTAAACCTAATA
1 TAAACTAAACCTAATA
142439 GCCGTATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAACTAAACCTAATAT
Found at i:142482 original size:15 final size:15
Alignment explanation
Indices: 142450--142488 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
142440 CCGTATATCA
142450 TACTCCTCTCACCCTC
1 TACT-CTCTCACCCTC
142466 TACTCTCTC-CCCATC
1 TACTCTCTCACCC-TC
142481 TACTCTCT
1 TACTCTCT
142489 TCCTCACGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 15 0.68
16 4 0.18
ACGTcount: A:0.13, C:0.51, G:0.00, T:0.36
Consensus pattern (15 bp):
TACTCTCTCACCCTC
Found at i:152252 original size:106 final size:106
Alignment explanation
Indices: 152067--152278 Score: 415
Period size: 106 Copynumber: 2.0 Consensus size: 106
152057 GCCTGAGACT
152067 CTCTCTTCTTGGAAAATTTAAAATCTGGGGGCAATCCTATAAGGCGATAACATTGTTCTTTGTTG
1 CTCTCTTCTTGGAAAATTTAAAATCTGGGGGCAATCCTATAAGGCGATAACATTGTTCTTTGTTG
*
152132 TGACCCTTAAGCTTGCAGTGATCCCAAAAGCCATTGAACCG
66 TGACCCTTAAGCTTGCAGTGATCACAAAAGCCATTGAACCG
152173 CTCTCTTCTTGGAAAATTTAAAATCTGGGGGCAATCCTATAAGGCGATAACATTGTTCTTTGTTG
1 CTCTCTTCTTGGAAAATTTAAAATCTGGGGGCAATCCTATAAGGCGATAACATTGTTCTTTGTTG
152238 TGACCCTTAAGCTTGCAGTGATCACAAAAGCCATTGAACCG
66 TGACCCTTAAGCTTGCAGTGATCACAAAAGCCATTGAACCG
152279 GCACGATTAG
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (106 bp):
CTCTCTTCTTGGAAAATTTAAAATCTGGGGGCAATCCTATAAGGCGATAACATTGTTCTTTGTTG
TGACCCTTAAGCTTGCAGTGATCACAAAAGCCATTGAACCG
Found at i:165456 original size:21 final size:20
Alignment explanation
Indices: 165418--165474 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
165408 TTTTTCATAT
* * *
165418 TAATTTTAAATGTAATTTTA
1 TAATTTTAAATATTATTTAA
165438 TAATATTTAAATATTATTTAA
1 TAAT-TTTAAATATTATTTAA
* *
165459 TAAGTTTAAAAATTAT
1 TAATTTTAAATATTAT
165475 AAATATGATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TAATTTTAAATATTATTTAA
Found at i:167806 original size:41 final size:41
Alignment explanation
Indices: 167706--167788 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
167696 GGATGATCTA
167706 TTTTAGAAAATCTATTTTATTTAAATTTAATTTCACTACTT
1 TTTTAGAAAATCTATTTTATTTAAATTTAATTTCACTACTT
167747 TTTTAGAAAATCTATTTTATTTAAATTTAATTTCACTACTT
1 TTTTAGAAAATCTATTTTATTTAAATTTAATTTCACTACTT
167788 T
1 T
167789 AATTTTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (41 bp):
TTTTAGAAAATCTATTTTATTTAAATTTAATTTCACTACTT
Found at i:169853 original size:22 final size:24
Alignment explanation
Indices: 169828--169880 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 24
169818 TGTATTTTTG
169828 TATTATTATA-TATATCATAT-AA
1 TATTATTATATTATATCATATAAA
* *
169850 TATTA-TAAATTATATTATATAAA
1 TATTATTATATTATATCATATAAA
169873 TATT-TTAT
1 TATTATTAT
169881 TTACCTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTATTATATTATATCATATAAA
Found at i:169950 original size:24 final size:25
Alignment explanation
Indices: 169918--169964 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
169908 CTATTTTTTA
*
169918 TTATTTTTTA-TATTTTTTTCATCT
1 TTATTTTTTATTATTTTCTTCATCT
169942 TTATTTTTTATTATTTTCTTCAT
1 TTATTTTTTATTATTTTCTTCAT
169965 TTGTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (25 bp):
TTATTTTTTATTATTTTCTTCATCT
Found at i:176161 original size:54 final size:54
Alignment explanation
Indices: 176070--176488 Score: 461
Period size: 54 Copynumber: 7.8 Consensus size: 54
176060 CTATGTGTAC
* * * * *
176070 TATCGACATTATATATGCAACCCACATAATTCATAATGAGTTTTTGAATTACCG
1 TATCGACACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACTG
* * * * *
176124 TGTCGGCACTATATGTGCAACCTACATAATTCATAATGAGTTTATGAATTACTG
1 TATCGACACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACTG
* * * * *
176178 TATCGATACTAAGTGTGTAACCCACATAATTCATAACGAGTTTGTGAATTATTG
1 TATCGACACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACTG
* * *
176232 TATCGACACCATGTATGCAACCCACATAATTCATAATTAGTTTGTGAATTACCT-
1 TATCGACACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTA-CTG
* * * * * *
176286 TATCGATACTATGCGTACAACCCA-AGGAATTCA-AATGAGTTTGAGAATTATTG
1 TATCGACACTATGTGTGCAACCCACA-TAATTCATAATGAGTTTGTGAATTACTG
* *
176339 TATCGACACTATGTGTGTAACCCACATAATTCATAATGAGTTTGTGAATTATTG
1 TATCGACACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACTG
* * * * *
176393 TATTGGCACTATGTGTGTAACCCACGA-AATTCATAATGAGTTTATGAATTACCG
1 TATCGACACTATGTGTGCAACCCAC-ATAATTCATAATGAGTTTGTGAATTACTG
* * *
176447 TATTGACACTATGTATGCAACCCAC-TGAATTTATAATGAGTT
1 TATCGACACTATGTGTGCAACCCACAT-AATTCATAATGAGTT
176489 GTAATATTTA
Statistics
Matches: 308, Mismatches: 49, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.00
53 42 0.14
54 263 0.85
55 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (54 bp):
TATCGACACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGAATTACTG
Found at i:176374 original size:161 final size:162
Alignment explanation
Indices: 176083--176488 Score: 514
Period size: 161 Copynumber: 2.5 Consensus size: 162
176073 CGACATTATA
* * * ** * *
176083 TATGCAACCCACATAATTCATAATGAGTTTTTGAATTACCGTGTCGGCACTATATGTGCAACCTA
1 TATGCAACCCACATAATTCATAATGAGTTTATGAATTACCGTATCGACACTATGCGTACAACCCA
* *
176148 CATAATTCATAATGAGTTTATGAATTACTGTATCGATACTAAGTGTGTAACCCACATAATTCATA
66 CAGAATTCATAATGAGTTTATGAATTACTGTATCGACACTAAGTGTGTAACCCACATAATTCATA
176213 ACGAGTTTGTGAATTATTGTATCGACACCATG
131 ACGAGTTTGTGAATTATTGTATCGACACCATG
* * * *
176245 TATGCAACCCACATAATTCATAATTAGTTTGTGAATTACCTTATCGATACTATGCGTACAACCCA
1 TATGCAACCCACATAATTCATAATGAGTTTATGAATTACCGTATCGACACTATGCGTACAACCCA
* *
176310 -AGGAATTCA-AATGAGTTTGA-GAATTATTGTATCGACACTATGTGTGTAACCCACATAATTCA
66 CA-GAATTCATAATGAGTTT-ATGAATTACTGTATCGACACTAAGTGTGTAACCCACATAATTCA
* * * *
176372 TAATGAGTTTGTGAATTATTGTATTGGCACTATG
129 TAACGAGTTTGTGAATTATTGTATCGACACCATG
* * * ** *
176406 TGTGTAACCCACGA-AATTCATAATGAGTTTATGAATTACCGTATTGACACTATGTATGCAACCC
1 TATGCAACCCAC-ATAATTCATAATGAGTTTATGAATTACCGTATCGACACTATGCGTACAACCC
* *
176470 ACTGAATTTATAATGAGTT
65 ACAGAATTCATAATGAGTT
176489 GTAATATTTA
Statistics
Matches: 209, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
161 138 0.66
162 71 0.34
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (162 bp):
TATGCAACCCACATAATTCATAATGAGTTTATGAATTACCGTATCGACACTATGCGTACAACCCA
CAGAATTCATAATGAGTTTATGAATTACTGTATCGACACTAAGTGTGTAACCCACATAATTCATA
ACGAGTTTGTGAATTATTGTATCGACACCATG
Found at i:179980 original size:14 final size:14
Alignment explanation
Indices: 179961--179993 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
179951 AATTCCCTAA
179961 ATACCATTAATGTC
1 ATACCATTAATGTC
179975 ATACCATTAATGTC
1 ATACCATTAATGTC
179989 ATACC
1 ATACC
179994 CATTTTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (14 bp):
ATACCATTAATGTC
Found at i:181837 original size:23 final size:22
Alignment explanation
Indices: 181805--181850 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
181795 TATGTATCAA
181805 TAAAAATAAAAATAAATATTTTT
1 TAAAAATAAAAATAAAT-TTTTT
* * *
181828 TAAAACTAAACATATATTTTTT
1 TAAAAATAAAAATAAATTTTTT
181850 T
1 T
181851 CTTTGAGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAAATAAAAATAAATTTTTT
Found at i:194858 original size:49 final size:49
Alignment explanation
Indices: 194792--194918 Score: 186
Period size: 48 Copynumber: 2.6 Consensus size: 49
194782 CGTTAAATGC
* *
194792 TGATTTGGAGTCACGTGGGTATAGTGCGCCCCCTATCCCGCGATATAC-G
1 TGATCTGGCGTCACGTGGGTATAG-GCGCCCCCTATCCCGCGATATACGG
*
194841 TGATCTGGCGTCACGTGGGTATA-ACGCCCCCTATCCCGCGATATACGG
1 TGATCTGGCGTCACGTGGGTATAGGCGCCCCCTATCCCGCGATATACGG
*
194889 TGATCTGACGTCACGTGGGTATAGCGCGCC
1 TGATCTGGCGTCACGTGGGTATAG-GCGCC
194919 ACTGATCCTC
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
47 22 0.31
48 23 0.33
49 21 0.30
50 4 0.06
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.24
Consensus pattern (49 bp):
TGATCTGGCGTCACGTGGGTATAGGCGCCCCCTATCCCGCGATATACGG
Found at i:195926 original size:12 final size:12
Alignment explanation
Indices: 195911--195940 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
195901 TGTCATCATT
195911 GTCGTCACCATC
1 GTCGTCACCATC
*
195923 GTCGTCATCATC
1 GTCGTCACCATC
195935 GTCGTC
1 GTCGTC
195941 GTCCTGAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.37, G:0.20, T:0.30
Consensus pattern (12 bp):
GTCGTCACCATC
Found at i:198030 original size:3 final size:3
Alignment explanation
Indices: 197952--198019 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
197942 TTTTACTTAA
* *
197952 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
197999 A-T ATAT ATT A-A ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT A
198020 AATAATTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 5 0.09
3 47 0.85
4 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:198447 original size:18 final size:18
Alignment explanation
Indices: 198408--198449 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
198398 GACACAGAGA
**
198408 ACAGAAGAAAAAAAAGGG
1 ACAGAAGAAAAAAAAGAC
198426 ACAGAGAGAAAAAAAA-AC
1 ACAGA-AGAAAAAAAAGAC
198444 ACAGAA
1 ACAGAA
198450 ACGAGAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 10 0.48
19 10 0.48
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (18 bp):
ACAGAAGAAAAAAAAGAC
Found at i:199499 original size:31 final size:33
Alignment explanation
Indices: 199464--199527 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
199454 ATAATTAAAC
199464 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
199495 ATTATTAAAATTTTAATATTTATTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
199528 TAATATCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 12 0.43
32 1 0.04
33 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:199732 original size:15 final size:15
Alignment explanation
Indices: 199712--199762 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
199702 CTTTTTCTGA
199712 AATTTTTAAATAAAT
1 AATTTTTAAATAAAT
**
199727 AATTTTTTTATAAAT
1 AATTTTTAAATAAAT
* *
199742 -ATATTTAAATTAAT
1 AATTTTTAAATAAAT
199756 ATATTTT
1 A-ATTTT
199763 CTTAAAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
14 10 0.37
15 13 0.48
16 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTAAATAAAT
Found at i:200282 original size:17 final size:19
Alignment explanation
Indices: 200253--200294 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
200243 TCTTTTAAAT
* * *
200253 TTTTTATATATATTTATTA
1 TTTTCATATATGTATATTA
200272 TTTTCATATATGTATATTA
1 TTTTCATATATGTATATTA
200291 TTTT
1 TTTT
200295 ATTAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTCATATATGTATATTA
Found at i:202650 original size:7 final size:7
Alignment explanation
Indices: 202630--202678 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
202620 TTTTCATATA
202630 TGCATTT
1 TGCATTT
202637 T-CATTT
1 TGCATTT
202643 TGCATTTT
1 TGCA-TTT
202651 TGCATCTT
1 TGCAT-TT
202659 TGCATTT
1 TGCATTT
*
202666 TTCATTT
1 TGCATTT
*
202673 TTCATT
1 TGCATT
202679 CATACTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
6 6 0.16
7 18 0.47
8 14 0.37
ACGTcount: A:0.14, C:0.16, G:0.08, T:0.61
Consensus pattern (7 bp):
TGCATTT
Found at i:202653 original size:8 final size:8
Alignment explanation
Indices: 202640--202678 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
202630 TGCATTTTCA
202640 TTTTGCAT
1 TTTTGCAT
202648 TTTTGCAT
1 TTTTGCAT
*
202656 CTTTGCAT
1 TTTTGCAT
202664 TTTT-CAT
1 TTTTGCAT
202671 TTTT-CAT
1 TTTTGCAT
202678 T
1 T
202679 CATACTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 11 0.38
8 18 0.62
ACGTcount: A:0.13, C:0.15, G:0.08, T:0.64
Consensus pattern (8 bp):
TTTTGCAT
Found at i:202662 original size:16 final size:14
Alignment explanation
Indices: 202620--202678 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
202610 AGTAAACACC
*
202620 TTTTCATATATGCA-
1 TTTTCAT-TTTGCAT
202634 TTTTCATTTTGCAT
1 TTTTCATTTTGCAT
202648 TTTTGCATCTTTGCAT
1 TTTT-CAT-TTTGCAT
*
202664 TTTTCATTTTTCAT
1 TTTTCATTTTGCAT
202678 T
1 T
202679 CATACTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.12
14 18 0.45
15 6 0.15
16 11 0.28
ACGTcount: A:0.17, C:0.15, G:0.07, T:0.61
Consensus pattern (14 bp):
TTTTCATTTTGCAT
Found at i:204938 original size:2 final size:2
Alignment explanation
Indices: 204931--204998 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
204921 TTATCCTTTA
204931 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
204973 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
204999 CCTTTGTTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:205302 original size:23 final size:22
Alignment explanation
Indices: 205271--205344 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
205261 ACTCATCCAG
*
205271 TAAAGAAAGGAAAAAGAAAAAGA
1 TAAAAAAAGGAAAAA-AAAAAGA
*
205294 TGAAAAAA-GAAAAAAAAGAAGA
1 TAAAAAAAGGAAAAAAAA-AAGA
* *
205316 AAAAAAAAGGAAATAAAAAA-A
1 TAAAAAAAGGAAAAAAAAAAGA
205337 TAAAAAAA
1 TAAAAAAA
205345 AACAAAAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 11 0.26
22 18 0.42
23 14 0.33
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (22 bp):
TAAAAAAAGGAAAAAAAAAAGA
Found at i:205305 original size:22 final size:21
Alignment explanation
Indices: 205280--205369 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 21
205270 GTAAAGAAAG
**
205280 GAAAAAGAAAAAGATGAAAAAA
1 GAAAAA-AAAAAGAAAAAAAAA
205302 GAAAAAAAAGAAGAAAAAAAAA
1 GAAAAAAAA-AAGAAAAAAAAA
*
205324 GGAAATAAAAAAATAAAAAAAAA
1 -GAAA-AAAAAAAGAAAAAAAAA
*
205347 CAAAAAGGAAAAA-AATAAAAAAA
1 GAAAAA--AAAAAGAA-AAAAAAA
205370 TTGAATCAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
21 5 0.09
22 21 0.36
23 27 0.47
24 5 0.09
ACGTcount: A:0.82, C:0.01, G:0.12, T:0.04
Consensus pattern (21 bp):
GAAAAAAAAAAGAAAAAAAAA
Found at i:205342 original size:33 final size:32
Alignment explanation
Indices: 205281--205370 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 32
205271 TAAAGAAAGG
* *
205281 AAAAAGAAAAAGATGAAAAAAGA-AAAAAAAGAAG
1 AAAAAGAAAAAAAT-AAAAAA-ATAAAAAAA-AAC
205315 AAAAA-AAAAGGAAATAAAAAAATAAAAAAAAAC
1 AAAAAGAAAA--AAATAAAAAAATAAAAAAAAAC
205348 AAAAAGGAAAAAAATAAAAAAAT
1 AAAAA-GAAAAAAATAAAAAAAT
205371 TGAATCAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
33 24 0.49
34 18 0.37
35 7 0.14
ACGTcount: A:0.82, C:0.01, G:0.11, T:0.06
Consensus pattern (32 bp):
AAAAAGAAAAAAATAAAAAAATAAAAAAAAAC
Found at i:205344 original size:9 final size:9
Alignment explanation
Indices: 205281--205369 Score: 58
Period size: 9 Copynumber: 9.4 Consensus size: 9
205271 TAAAGAAAGG
205281 AAAAAGAAA
1 AAAAAGAAA
* *
205290 AAGATGAAA
1 AAAAAGAAA
205299 AAAGAA-AAA
1 AAA-AAGAAA
205308 AAAGAAGAAAA
1 AAA-AAG-AAA
205319 AAAAAGGAAA
1 AAAAA-GAAA
205329 TAAAAA-AATA
1 -AAAAAGAA-A
205339 AAAAA-AAA
1 AAAAAGAAA
*
205347 CAAAAAGGAA
1 -AAAAAGAAA
*
205357 AAAAATAAA
1 AAAAAGAAA
205366 AAAA
1 AAAA
205370 TTGAATCAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
8 1 0.02
9 43 0.66
10 9 0.14
11 12 0.18
ACGTcount: A:0.83, C:0.01, G:0.11, T:0.04
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:205367 original size:45 final size:46
Alignment explanation
Indices: 205271--205368 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 46
205261 ACTCATCCAG
*
205271 TAAAGAAAGGAAAAAGAAAAAGATGAAAAAAGAAAAAAAAGAAGAAA
1 TAAA-AAAGGAAAAAGAAAAAGATGAAAAAAGAAAAAAAAGAAAAAA
*
205318 -AAAAAAGGAAATA-AAAAA-AT-AAAAAA-AAACAAAAAGGAAAAAAA
1 TAAAAAAGGAAAAAGAAAAAGATGAAAAAAGAAA-AAAAA-G-AAAAAA
205362 TAAAAAA
1 TAAAAAA
205369 ATTGAATCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
41 3 0.07
42 11 0.24
43 3 0.07
44 10 0.22
45 15 0.33
46 3 0.07
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.05
Consensus pattern (46 bp):
TAAAAAAGGAAAAAGAAAAAGATGAAAAAAGAAAAAAAAGAAAAAA
Found at i:209838 original size:54 final size:53
Alignment explanation
Indices: 209756--209913 Score: 171
Period size: 54 Copynumber: 3.0 Consensus size: 53
209746 TGATTGAGAA
*
209756 ATTTGAGCAGAAGCCACAGAAAAAGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATTTGAGCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATG-TTTACGAAC
* * * *
209810 ATTTGAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAGTGTTT---TAC
1 ATTTGAGCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTACGAAC
* * * * *
209860 ATCTGAGCAGAAACCAAATG-AGATGATGCATGTGTTGTCAAATGTTTTACGAAC
1 ATTTGAGCAGAAACCACA-GAAAAAGATGAATGTGTTGTCAAATG-TTTACGAAC
209914 CAGTTATTCT
Statistics
Matches: 86, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
50 37 0.43
51 4 0.05
53 3 0.03
54 42 0.49
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (53 bp):
ATTTGAGCAGAAACCACAGAAAAAGATGAATGTGTTGTCAAATGTTTACGAAC
Found at i:209893 original size:50 final size:50
Alignment explanation
Indices: 209759--209909 Score: 142
Period size: 50 Copynumber: 2.9 Consensus size: 50
209749 TTGAGAAATT
* * * * * *
209759 TGAGCAGAAGCCACAGAAAAAGATGAATGTGTTGTCAAATGCTTTACGAACATT
1 TGAGCAGAAACCAAAGAAAAGGATGAATGTGTTATCAAATG-TTT---TACATC
* *
209813 TGAGCAGAAACCACAGAAAAGGATGAATGTGTTATCAAGTGTTTTACATC
1 TGAGCAGAAACCAAAGAAAAGGATGAATGTGTTATCAAATGTTTTACATC
* * * *
209863 TGAGCAGAAACCAAATG-AGATGATGCATGTGTTGTCAAATGTTTTAC
1 TGAGCAGAAACCAAA-GAAAAGGATGAATGTGTTATCAAATGTTTTAC
209910 GAACCAGTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 43 0.51
51 1 0.01
53 3 0.04
54 37 0.44
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (50 bp):
TGAGCAGAAACCAAAGAAAAGGATGAATGTGTTATCAAATGTTTTACATC
Found at i:210304 original size:22 final size:22
Alignment explanation
Indices: 210278--210354 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
210268 ATCTACACTC
210278 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
210300 TTCAAAGATGATATATTCTTTT
1 TTCAAAGATGATAGATTCTCTT
* *
210322 TTTAAAGATAATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
210344 TTCAAAGATGA
1 TTCAAAGATGA
210355 AAGCTTTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:211216 original size:184 final size:185
Alignment explanation
Indices: 210901--211270 Score: 663
Period size: 184 Copynumber: 2.0 Consensus size: 185
210891 CTAATCGACA
*
210901 TGTTATTTCTAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTATTTCTAAAAATAACGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
*
210966 AAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCCACATC
66 AAATTATTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCCACATC
*
211031 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGT
131 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGT
**
211086 TGTTATTT-TGAAAAATAACGAGAAAACGATTTCCATAGTTTCTCATTTTATCTTTTCT-AAAAT
1 TGTTATTTCT-AAAAATAACGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAAT
*
211149 GAAATTATTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCTACAT
65 GAAATTATTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCCACAT
211214 CTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGT
130 CTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGT
211270 T
1 T
211271 TTCAAAGCCT
Statistics
Matches: 178, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
184 125 0.70
185 53 0.30
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (185 bp):
TGTTATTTCTAAAAATAACGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
AAATTATTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCCACATC
TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGT
Found at i:211310 original size:76 final size:76
Alignment explanation
Indices: 211211--211771 Score: 1025
Period size: 76 Copynumber: 7.4 Consensus size: 76
211201 CTATTTCCTA
*
211211 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
211276 AGCCTTAGGGT
66 AGCCTTAGGGT
211287 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
211352 AGCCTTAGGGT
66 AGCCTTAGGGT
*
211363 CATCTGTAAGTCCTGCAGTGCATGATGTTTACAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
211428 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
211439 CATTTGTAAGTCATGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
211504 AGCCTTAGGGT
66 AGCCTTAGGGT
*
211515 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
211580 AGCCTTAGGGT
66 AGCCTTAGGGT
*
211591 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
211656 AGCCTTAGGGT
66 AGCCTTAGGGT
*
211667 CATCTGTAAGTCCTGCAGTGCATGATATTTCCAAAAAGCCTT-GGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
211731 AACCTTAGGGT
66 AGCCTTAGGGT
* *
211742 CATTTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
211772 TTAAGACCTC
Statistics
Matches: 470, Mismatches: 15, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
75 59 0.13
76 411 0.87
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:211939 original size:15 final size:14
Alignment explanation
Indices: 211917--212002 Score: 63
Period size: 14 Copynumber: 6.0 Consensus size: 14
211907 TTCATTTTAC
211917 TTAAATTATTATTA
1 TTAAATTATTATTA
211931 TTAAAATTATTATTATTA
1 TT--AA--ATTATTATTA
*
211949 TTATAAATATTATTA
1 TTA-AATTATTATTA
*
211964 TTATATTA-TATATA
1 TTAAATTATTAT-TA
211978 TT--A-TATTATTA
1 TTAAATTATTATTA
*
211989 TTAAATAATTATTA
1 TTAAATTATTATTA
212003 CAAGCCCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
11 6 0.10
12 4 0.07
13 4 0.07
14 16 0.28
15 12 0.21
16 3 0.05
17 1 0.02
18 12 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTAAATTATTATTA
Found at i:211942 original size:18 final size:19
Alignment explanation
Indices: 211921--212002 Score: 91
Period size: 18 Copynumber: 4.4 Consensus size: 19
211911 TTTTACTTAA
211921 ATTATTATTATTA-AAATT
1 ATTATTATTATTATAAATT
211939 ATTATTATTATTATAAA-T
1 ATTATTATTATTATAAATT
*
211957 ATTATTATTA-TATTATATAT
1 ATTATTATTATTA-TAAAT-T
*
211977 ATTA-TATTATTATTAAATA
1 ATTATTATTATTA-TAAATT
211996 ATTATTA
1 ATTATTA
212003 CAAGCCCAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.04
18 27 0.49
19 12 0.22
20 14 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTATTATTATAAATT
Done.