Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008214.1 Hibiscus syriacus cultivar Beakdansim tig00110840_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: 2117680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:443218 original size:45 final size:45
Alignment explanation
Indices: 443154--443369 Score: 312
Period size: 45 Copynumber: 4.8 Consensus size: 45
443144 GGTAAACACG
*
443154 AAAATAAGCTTACGAGCTTATGGCA-T-AATGGCAAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGG-AGTAAATGG-TAAGTATATTGGT
443199 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
* *
443244 AAAATAAGCTTACGAGCTTATAGAGTAAATGGTAAGTATATTTGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
* *
443289 AAAATAAGCTTACGAGCTTATTGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
* * *
443334 AGATTAAGCTTACGAGCTTATAGGA-TAAATGATAAG
1 AAAATAAGCTTACGAGCTTAT-GGAGTAAATGGTAAG
443370 AAATTTTATA
Statistics
Matches: 158, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.01
45 150 0.95
46 7 0.04
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAGTAAATGGTAAGTATATTGGT
Found at i:459317 original size:23 final size:23
Alignment explanation
Indices: 459270--459318 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
459260 AATAACATAT
* **
459270 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
459293 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
459316 TAG
1 TAG
459319 ACATTTAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:459379 original size:87 final size:87
Alignment explanation
Indices: 459233--459395 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
459223 TATGTTATAT
*
459233 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTACCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
459298 AACGCTTATATAATAAAATAGA
66 AACGCTTATATAATAAAATAGA
*
459320 CATTTAACCGGAAATATTACCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTACCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
459385 AGCGCTTATAT
66 AACGCTTATAT
459396 TGGTCTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (87 bp):
CATTTAACCGGAAATATTACCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AACGCTTATATAATAAAATAGA
Found at i:459974 original size:200 final size:196
Alignment explanation
Indices: 459400--460166 Score: 880
Period size: 200 Copynumber: 3.8 Consensus size: 196
459390 TTATATTGGT
* * * * *
459400 CTATTTTCTCATAAAACCGGTAAATTTCA-ACAGGTTACATTGTAAATTGATCTATTACATTATA
1 CTATTTTCTCAT-AAACCGGTATATTT-AGACTGGTTACATTGTTAATTTACCTATTACATTATA
* * ** *
459464 ATTATCGGTTTCGATGTTTTTGGGATCGATA-TAATTTTAAATGTATCGACACTTTATGCGTGCA
64 ATTAT-GTTTTCGATG-TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-T-CGTGCA
* *** * * * *
459528 CCT-GTTTGTGCATTCATTTTGGAAAAAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTC
125 CTTGGTTTGAAAATACATTATGG--ACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTT
459592 TATGTATAC
188 TATGTATAC
* * * * * * *
459601 CTATTTTCTTATAAAACCGATAAATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAA
1 CTATTTTCTCAT-AAACCGGTATATTTAGACTGGTTACATTGTTAATTTACCTATTACATTATAA
* * * *
459666 TTATG-TTTCGATGTATTTGGGATCGACACATATTATAAAAGTATCGACACTTTTTTGTGCA-TT
65 TTATGTTTTCGATGT-TTTGGGATCGACACTTGTTATAAATGTATCGACAC-TTTTCGTGCACTT
459729 GGTTTGGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATG
128 GGTTT-GAAAATACATTATGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATG
459794 TATAC
192 TATAC
* * * * * * *
459799 TTGTTTTCTCATAAACTGGTGTATTTAGGCCGGTTACATTGTTATTTTACCTATTACATTAT-AT
1 CTATTTTCTCATAAACCGGTATATTTAGACTGGTTACATTGTTAATTTACCTATTACATTATAAT
* *
459863 CTATGTATTTCGATGATTTTAGTATCGACACTTGTTATAAATGTATCGACACTTTGTCGTGCACT
66 -TATGT-TTTCGATG-TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TCGTGCACT
*
459928 TGGTTTGAAAAATACATTCTGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTAT
127 TGGTTTG-AAAATACATTATGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTAT
459993 GTATAC
191 GTATAC
* * *
459999 CTATTTTCTCAAAAACCGGTTTATTTAGACTGGTTACATTGTTAATTTACTTATTACATTATAAT
1 CTATTTTCTCATAAACCGGTATATTTAGACTGGTTACATTGTTAATTTACCTATTACATTATAAT
*
460064 TATGTGTTTCGATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTTCTTGTGCACT
66 TATGT-TTTCGATG-TTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTC--GTGCACT
* * * *
460129 TGGTTTGGAAATACATTATAGACAACATGTATCGACAC
127 TGGTTTGAAAATACATTATGGACAAAAAGTATCGACAC
460167 GAATGAATAA
Statistics
Matches: 491, Mismatches: 59, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
196 2 0.00
197 43 0.09
198 61 0.12
199 76 0.15
200 228 0.46
201 81 0.16
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (196 bp):
CTATTTTCTCATAAACCGGTATATTTAGACTGGTTACATTGTTAATTTACCTATTACATTATAAT
TATGTTTTCGATGTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTCGTGCACTTGGT
TTGAAAATACATTATGGACAAAAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATA
C
Found at i:460367 original size:24 final size:24
Alignment explanation
Indices: 460340--460398 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
460330 AGTGGAGCCG
*
460340 AAATTTACATTTAAATTCAAACTC
1 AAATTTAAATTTAAATTCAAACTC
460364 AAATTTAAATTTAAATTCAAACTC
1 AAATTTAAATTTAAATTCAAACTC
*
460388 TAATTATAAAT
1 AAATT-TAAAT
460399 GAAATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATTTAAATTTAAATTCAAACTC
Found at i:460371 original size:18 final size:18
Alignment explanation
Indices: 460348--460384 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
460338 CGAAATTTAC
460348 ATTTAAATTCAAACTCAA
1 ATTTAAATTCAAACTCAA
* *
460366 ATTTAAATTTAAATTCAA
1 ATTTAAATTCAAACTCAA
460384 A
1 A
460385 CTCTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTAAATTCAAACTCAA
Found at i:461666 original size:3 final size:3
Alignment explanation
Indices: 461658--461701 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
461648 ACTTGTTTGG
* * *
461658 ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC GTC ATC TTC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
461702 TGACCGCTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:462893 original size:15 final size:15
Alignment explanation
Indices: 462869--462912 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
462859 AAGAGGTTGT
462869 GGTTGAGAAGAGCTG
1 GGTTGAGAAGAGCTG
*
462884 GGTT-ATGAAGAGTTG
1 GGTTGA-GAAGAGCTG
462899 GGTTGAGAAGAGCT
1 GGTTGAGAAGAGCT
462913 TTGAGAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 1 0.04
15 23 0.92
16 1 0.04
ACGTcount: A:0.27, C:0.05, G:0.43, T:0.25
Consensus pattern (15 bp):
GGTTGAGAAGAGCTG
Found at i:463728 original size:199 final size:199
Alignment explanation
Indices: 463258--464356 Score: 1741
Period size: 199 Copynumber: 5.5 Consensus size: 199
463248 TTTTCAAATT
* * * ** * * * *
463258 AAACCGGTATAATTATACCGGTTATATTGCAAAATAACCTATTACATTAAAATTTTGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * * * *
463323 TGTTCTTAGGATCGATACTTATTATAAATGTATCCACACTTTTTCATGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
* * *
463388 CATTCTAGACCAAAAGTATCGACACTTGTTTTATTTATGTCGATACTTTTT-TACACATATTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
463452 TCAA
196 TCAA
** *
463456 AAACTAGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCAA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * *
463521 TGTTTTTGGGATCGACACTTGTTATAAATGGATCGACACTTATTCGTGCACTTGTTTTAGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
**
463586 CATTCTGGAAAAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
463651 TCAA
196 TCAA
* * * *
463655 AAACCGGTATATTTAGACCAGTTACATTGTTAATTTACATATTACATTAAAATTTTGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
463720 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
* *
463785 CATTCTGGACCAAAAGTATCTACACTTGTTTTATTTGTGTCGATACTTTTTGTACACTTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
463850 TCAA
196 TCAA
*
463854 AAACCGGTATATTTAGACTGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
463919 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTAGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
*
463984 CATTCTGGACCAAAAGTATCTACACTTGTTTTATTTGTGTCGATACTTTTTTGTACACATGTTTT
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATAC-TTTTTGTACACATGTTTT
464049 CTCAA
195 CTCAA
* *
464054 AAATCGGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * *
464119 TGTTTTTGGGATCGACATTTGTTATAAATGTATCAACACCTTTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
* * * * *
464184 CATTCTGGACCAAAATTATCGACACTTGCTTTATTTTTGTCGATATTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
464249 TCAA
196 TCAA
* *
464253 AAACCTGTATATTTAGACCGGTTGCATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
464318 TGTTTTTGGGATCGATACTTGTTATAAATGTATCGACAC
66 TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
464357 ATAAGTTTAC
Statistics
Matches: 830, Mismatches: 69, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
198 156 0.19
199 488 0.59
200 186 0.22
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (199 bp):
AAACCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGTTTTC
TCAA
Found at i:464248 original size:399 final size:398
Alignment explanation
Indices: 463258--464356 Score: 1777
Period size: 399 Copynumber: 2.8 Consensus size: 398
463248 TTTTCAAATT
* * ** * *
463258 AAACCGGTATAATTATACCGGTTATATTGCAAAATAACCTATTACATTAAAATTTTGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTAAAATTTTGGGTTTCGA
* * * * *
463323 TGTTCTTAGGATCGATACTTATTATAAATGTATCCACACTTTTTCATGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCAACACTTTTTCGTGCACTTGGTTTAGAAATA
* *
463388 CATTCTAGACCAAAAGTATCGACACTTGTTTTATTTATGTCGATACTTTTT-TACACATATTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTATGTCGATACTTTTTGTACACATGTTTTC
*
463452 TCAAAAACTAGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTT
196 TCAAAAACCAGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTT
* * * *
463517 TCAATGTTTTTGGGATCGACACTTGTTATAAATGGATCGACACTTATTCGTGCACTTGTTTTAGA
261 TCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTATTCGTGCACTAGGTTTAGA
463582 AATACATTCTGGAAAAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGT
326 AATACATTCTGGAAAAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGT
463647 TTTCTCAA
391 TTTCTCAA
* * *
463655 AAACCGGTATATTTAGACCAGTTACATTGTTAATTTACATATTACATTAAAATTTTGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTAAAATTTTGGGTTTCGA
*
463720 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCAACACTTTTTCGTGCACTTGGTTTAGAAATA
* * *
463785 CATTCTGGACCAAAAGTATCTACACTTGTTTTATTTGTGTCGATACTTTTTGTACACTTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTATGTCGATACTTTTTGTACACATGTTTTC
* *
463850 TCAAAAACCGGTATATTTAGACTGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTT
196 TCAAAAACCAGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTT
*
463915 TCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGCACTAGGTTTAGA
261 TCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTATTCGTGCACTAGGTTTAGA
** *
463980 AATACATTCTGGACCAAAAGTATCTACACTTGTTTTATTTGTGTCGATACTTTTTTGTACACATG
326 AATACATTCTGGAAAAAAAGTATCGACACTTGTTTTATTTGTGTCGATAC-TTTTTGTACACATG
464045 TTTTCTCAA
390 TTTTCTCAA
* * *
464054 AAATCGGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTAAAATTTTGGGTTTCGA
* * *
464119 TGTTTTTGGGATCGACATTTGTTATAAATGTATCAACACCTTTTCGTGCACTTGGTTTAGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCAACACTTTTTCGTGCACTTGGTTTAGAAATA
* * * * *
464184 CATTCTGGACCAAAATTATCGACACTTGCTTTATTTTTGTCGATATTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTATGTCGATACTTTTTGTACACATGTTTTC
* *
464249 TCAAAAACCTGTATATTTAGACCGGTTGCATTGTTAATTTACCTATTACATTATAATTATGGGTT
196 TCAAAAACCAGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTT
*
464314 TCGATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACAC
261 TCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
464357 ATAAGTTTAC
Statistics
Matches: 650, Mismatches: 50, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
397 164 0.25
398 180 0.28
399 306 0.47
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (398 bp):
AAACCGGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTAAAATTTTGGGTTTCGA
TGTTTTTGGGATCGACACTTATTATAAATGTATCAACACTTTTTCGTGCACTTGGTTTAGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTATGTCGATACTTTTTGTACACATGTTTTC
TCAAAAACCAGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTT
TCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTATTCGTGCACTAGGTTTAGA
AATACATTCTGGAAAAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACATGT
TTTCTCAA
Found at i:464754 original size:19 final size:19
Alignment explanation
Indices: 464730--464774 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
464720 ATTCACAAAT
464730 AAAATTATAAATCATATAC
1 AAAATTATAAATCATATAC
*
464749 AAAATTATAAATCTTATAC
1 AAAATTATAAATCATATAC
464768 AAAATTA
1 AAAATTA
464775 ACCCTACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATAAATCATATAC
Found at i:466283 original size:18 final size:18
Alignment explanation
Indices: 466245--466283 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
466235 TTCTCACCAT
* *
466245 TTCCTCCATCTTTTGTAC
1 TTCCTCCATCTTCTCTAC
*
466263 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTCTCTAC
466281 TTC
1 TTC
466284 AAATTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.38, G:0.03, T:0.51
Consensus pattern (18 bp):
TTCCTCCATCTTCTCTAC
Found at i:466717 original size:18 final size:18
Alignment explanation
Indices: 466691--466733 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
466681 CTTCTTCCTT
*
466691 TTCCACTGCCTCCACTAC
1 TTCCTCTGCCTCCACTAC
*
466709 TTCCTCTGCCTCCTCTAC
1 TTCCTCTGCCTCCACTAC
*
466727 CTCCTCT
1 TTCCTCT
466734 ATCTCCTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.51, G:0.05, T:0.35
Consensus pattern (18 bp):
TTCCTCTGCCTCCACTAC
Found at i:466999 original size:22 final size:21
Alignment explanation
Indices: 466971--467027 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
466961 AACATGCATT
*
466971 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
466993 TATAATAACTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
*
467017 TATAAAAAAAC
1 TATAATAAAAC
467028 AAAAACATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 9 0.30
24 18 0.60
25 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:468474 original size:16 final size:15
Alignment explanation
Indices: 468453--468497 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 15
468443 ACTTGTTGAC
468453 TTGACCCGTTGACCCG
1 TTGA-CCGTTGACCCG
468469 TTGACCGTTGACCCCG
1 TTGACCGTTGA-CCCG
468485 TTGACCGTTGACC
1 TTGACCGTTGACC
468498 AAAACTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.13, C:0.36, G:0.24, T:0.27
Consensus pattern (15 bp):
TTGACCGTTGACCCG
Found at i:468478 original size:7 final size:8
Alignment explanation
Indices: 468453--468497 Score: 67
Period size: 7 Copynumber: 5.8 Consensus size: 8
468443 ACTTGTTGAC
468453 TTGACCCG
1 TTGACCCG
468461 TTGACCCG
1 TTGACCCG
468469 TTGA-CCG
1 TTGACCCG
468476 TTGACCCCG
1 TTGA-CCCG
468485 TTGA-CCG
1 TTGACCCG
468492 TTGACC
1 TTGACC
468498 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.41
8 13 0.38
9 7 0.21
ACGTcount: A:0.13, C:0.36, G:0.24, T:0.27
Consensus pattern (8 bp):
TTGACCCG
Found at i:468479 original size:23 final size:23
Alignment explanation
Indices: 468453--468497 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
468443 ACTTGTTGAC
468453 TTGA-CCCGTTGACCCGTTGACCG
1 TTGACCCCGTTGA-CCGTTGACCG
468476 TTGACCCCGTTGACCGTTGACC
1 TTGACCCCGTTGACCGTTGACC
468498 AAAACTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.13, C:0.36, G:0.24, T:0.27
Consensus pattern (23 bp):
TTGACCCCGTTGACCGTTGACCG
Found at i:469857 original size:43 final size:42
Alignment explanation
Indices: 469805--469885 Score: 144
Period size: 43 Copynumber: 1.9 Consensus size: 42
469795 AAATGATGAG
*
469805 ATTGAATTAAATAATAAGATCGGATGGAGGAAAAAGATATAA
1 ATTGAATTAAATAATAAGACCGGATGGAGGAAAAAGATATAA
469847 ATTGTAATTAAATAATAAGACCGGATGGAGGAAAAAGAT
1 ATTG-AATTAAATAATAAGACCGGATGGAGGAAAAAGAT
469886 TGAAATACCG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
42 4 0.11
43 33 0.89
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.23
Consensus pattern (42 bp):
ATTGAATTAAATAATAAGACCGGATGGAGGAAAAAGATATAA
Found at i:471009 original size:24 final size:24
Alignment explanation
Indices: 470992--471129 Score: 179
Period size: 24 Copynumber: 5.8 Consensus size: 24
470982 TTGATTTGAT
470992 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
471016 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
471040 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
471064 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* * * *
471088 TTTTGATATGATACTTGACGTGAA
1 TTCTGATCTGATACTTGACATGGA
* * *
471112 TTATGATTTGATATTTGA
1 TTCTGATCTGATACTTGA
471130 TATATCCGTT
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
23 1 0.01
24 101 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:472471 original size:19 final size:18
Alignment explanation
Indices: 472445--472537 Score: 105
Period size: 19 Copynumber: 4.9 Consensus size: 18
472435 ATCCATATTT
*
472445 ATTTTCTACCTATAATATA
1 ATTTT-TACCTATAATATC
* * *
472464 ACTTTCTACATGTAATATC
1 A-TTTTTACCTATAATATC
472483 ATTTTTACCTATAATATC
1 ATTTTTACCTATAATATC
*
472501 ATTGTTTACGTATAATATC
1 ATT-TTTACCTATAATATC
472520 ATTTTTTACCTATAATAT
1 A-TTTTTACCTATAATAT
472538 TAAATAAAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.27
19 40 0.65
20 5 0.08
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (18 bp):
ATTTTTACCTATAATATC
Found at i:472497 original size:37 final size:37
Alignment explanation
Indices: 472445--472537 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
472435 ATCCATATTT
*
472445 ATTTTCTACCTATAATATAACTT-TCTACATGTAATATC
1 ATTTT-TACCTATAATATAA-TTGTCTACATATAATATC
* * *
472483 ATTTTTACCTATAATATCATTGTTTACGTATAATATC
1 ATTTTTACCTATAATATAATTGTCTACATATAATATC
472520 ATTTTTTACCTATAATAT
1 A-TTTTTACCTATAATAT
472538 TAAATAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 2 0.04
37 26 0.53
38 21 0.43
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (37 bp):
ATTTTTACCTATAATATAATTGTCTACATATAATATC
Found at i:473214 original size:182 final size:181
Alignment explanation
Indices: 473003--473779 Score: 1023
Period size: 182 Copynumber: 4.3 Consensus size: 181
472993 GTAGCGCTTT
* *
473003 ACCGGTTTTGTCACATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTAC-TGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
* * * * * *
473068 TATTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATATTTATATTAAAGT
65 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATT
* * *
473133 ATCGACACTTTCAATATATCCTATAGTTCTTTATCGGTTTTTTCATTTTGAG
130 ATCGACACTTTCAACATATCCTATAGTTCTTTACCGGTTTTGTCATTTTGAG
* **
473185 ATCGGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTA-CTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
*
473250 CACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATT
65 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATT
* * ** * *
473315 ATCGACACTTTCAACATAT-ATGGTAGCGCTTTACCGGATTTGTCATTTTGGG
130 ATCGACACTTTCAACATATCCT-ATAGTTCTTTACCGGTTTTGTCATTTTGAG
** *
473367 ACCTATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTAC-TGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
**
473432 CACTTTATAGGCGCTATAA---CTTCTCTTTTAAATT-AAAAAAAATCGATACTTATATTAAATT
65 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATT
** * *
473493 ATCGACACTTTCAACATATCCGGTA-TTATTTTACTGGTTTTGTCATTTTTGAG
130 ATCGACACTTTCAACATATCCTATAGTT-CTTTACCGGTTTTGTCA-TTTTGAG
**
473546 ACAAGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTTTAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTA-CTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGA
* * *
473610 CACTTTATAGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATT
65 CACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATT
* * *
473675 ATCGACACTTTCAACATATCCGGTATCG-T-TTTACCGATTTTGTCATTTCGAG
130 ATCGACACTTTCAACATATCC--TATAGTTCTTTACCGGTTTTGTCATTTTGAG
* * * *
473727 ACCGATTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCGATACATTTTT
1 ACCGGTTTTGTCATATTTTTA-CTGTTATATTGTTATGGATCGATACATTTTT
473780 CATTTGTATC
Statistics
Matches: 521, Mismatches: 59, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
178 95 0.18
179 63 0.12
180 1 0.00
181 65 0.12
182 294 0.56
183 1 0.00
184 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (181 bp):
ACCGGTTTTGTCATATTTTTACTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGAC
ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATTA
TCGACACTTTCAACATATCCTATAGTTCTTTACCGGTTTTGTCATTTTGAG
Found at i:473673 original size:360 final size:362
Alignment explanation
Indices: 473003--473779 Score: 1136
Period size: 360 Copynumber: 2.1 Consensus size: 362
472993 GTAGCGCTTT
* *
473003 ACCGGTTTTGTCACATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGA
1 ACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGA
* * * *** *
473068 TATTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATATTTATATTAAAGT
66 CACTTTATAGGCGCTATAA--TCTTCTCTTTTAAATTCAAAAAAAATCGATACTTATATTAAAGT
* * * *
473133 ATCGACACTTTCAATATATCCTATAGTTCTTTATCGGTTTTTTCATTTTGAGATCGGTTTTGTCA
129 ATCGACACTTTCAACATATCCGATAGTTCTTTATCGGTTTTGTCATTTTGAGATCAGTTTTGTCA
* *
473198 TATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCG
194 TATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTATAGGCG
473263 CTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATTATCGACACTTTCA
259 CTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATTATCGACACTTTCA
* * *
473328 ACATATATGGTAGCGCTTTACCGGA-TTTGTCATTTTGGG
324 ACATATACGGTAGCGCTTTACC-GATTTTGTCATTTCGAG
*
473367 ACCTATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGA
1 ACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGA
*
473432 CACTTTATAGGCGCTATAA-CTTCTCTTTTAAATT-AAAAAAAATCGATACTTATATTAAATTAT
66 CACTTTATAGGCGCTATAATCTTCTCTTTTAAATTCAAAAAAAATCGATACTTATATTAAAGTAT
* *
473495 CGACACTTTCAACATATCCGGTA-TTATTT-TACTGGTTTTGTCATTTTTGAGA-CAAGTTTTGT
131 CGACACTTTCAACATATCCGATAGTTCTTTAT-C-GGTTTTGTCA-TTTTGAGATC-AGTTTTGT
*
473557 CATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT-TTAAAGTATCGACACTTTATAGG
192 CATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTATAGG
* * *
473621 TGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCGACACTTT
257 CGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATTATCGACACTTT
* * *
473686 CAACATATCCGGTATCGTTTTACCGATTTTGTCATTTCGAG
322 CAACATATACGGTAGCGCTTTACCGATTTTGTCATTTCGAG
* * * * *
473727 ACCGATTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCGATACATTTTT
1 ACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTT
473780 CATTTGTATC
Statistics
Matches: 373, Mismatches: 35, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
358 1 0.00
359 8 0.02
360 215 0.58
361 70 0.19
364 79 0.21
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (362 bp):
ACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGA
CACTTTATAGGCGCTATAATCTTCTCTTTTAAATTCAAAAAAAATCGATACTTATATTAAAGTAT
CGACACTTTCAACATATCCGATAGTTCTTTATCGGTTTTGTCATTTTGAGATCAGTTTTGTCATA
TTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTATAGGCGCT
ATAACTTCTTCTCTTTTAAATTCAAAAAGTATCGATACTTATATTAAATTATCGACACTTTCAAC
ATATACGGTAGCGCTTTACCGATTTTGTCATTTCGAG
Found at i:474337 original size:19 final size:19
Alignment explanation
Indices: 474315--474353 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
474305 TTTTCTTAAT
* *
474315 AAAATAATATATATTCATA
1 AAAAAAATATAAATTCATA
*
474334 AAAAAAATTTAAATTCATA
1 AAAAAAATATAAATTCATA
474353 A
1 A
474354 TCTTCTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAAATATAAATTCATA
Found at i:483333 original size:20 final size:20
Alignment explanation
Indices: 483308--483348 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
483298 TTACTTTAGG
483308 TATCGATACTACAAGAACAA
1 TATCGATACTACAAGAACAA
**
483328 TATCGATACTGTAAGAACAA
1 TATCGATACTACAAGAACAA
483348 T
1 T
483349 GTCAGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.24
Consensus pattern (20 bp):
TATCGATACTACAAGAACAA
Found at i:485240 original size:20 final size:20
Alignment explanation
Indices: 485217--485255 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
485207 GCAAAGAGAG
485217 TATTGATACTGTAAGGCCAA
1 TATTGATACTGTAAGGCCAA
485237 TATTGATACTGTAAGGCCA
1 TATTGATACTGTAAGGCCA
485256 GTATCAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (20 bp):
TATTGATACTGTAAGGCCAA
Found at i:485265 original size:20 final size:20
Alignment explanation
Indices: 485222--485265 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
485212 GAGAGTATTG
**
485222 ATACTGTAAGGCCAATATTG
1 ATACTGTAAGGCCAATATCA
*
485242 ATACTGTAAGGCCAGTATCA
1 ATACTGTAAGGCCAATATCA
485262 ATAC
1 ATAC
485266 CAAGGGTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (20 bp):
ATACTGTAAGGCCAATATCA
Found at i:485832 original size:27 final size:28
Alignment explanation
Indices: 485794--485852 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
485784 TGAAAAATAA
*
485794 ATAAATAAATATTAAAATA-ATTTA-TAT
1 ATAAAAAAATA-TAAAATATATTTATTAT
485821 ATAAAAAAATATAAAATATTATTTATTAT
1 ATAAAAAAATATAAAATA-TATTTATTAT
485850 ATA
1 ATA
485853 TATATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.25
27 10 0.36
28 5 0.18
29 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAAAAAAATATAAAATATATTTATTAT
Found at i:487268 original size:3 final size:3
Alignment explanation
Indices: 487262--487325 Score: 96
Period size: 3 Copynumber: 21.7 Consensus size: 3
487252 TAATATTTAT
487262 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
487309 TGA TAA T-A TAAA TAA TA
1 TAA TAA TAA T-AA TAA TA
487326 TTTAAATGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 50 0.89
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:487690 original size:120 final size:120
Alignment explanation
Indices: 487465--487750 Score: 384
Period size: 120 Copynumber: 2.4 Consensus size: 120
487455 TGAATAAATT
* * * * *
487465 CTTCTTTTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCGCTGG---GGATGATGTTGACCT
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGATGATGCTAACCT
* * **
487527 ATTTCCTTCTGTGATAGAGTTATTCAAAAGGTTGAATGAGCTCTTCTCATTATGAA
65 ATTTCCTTCTGTGATAAAATTATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
** *
487583 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTTTGATGCTAATCTA
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
* *
487648 TTTGCTTCTGTGATAAAATTATGT-AAAAGGTTGAACAAGCTCTTCTCATTGTGAA
66 TTTCCTTCTGTGATAAAATTAT-TCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
*
487703 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
487751 AGCTGATCCA
Statistics
Matches: 149, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
117 5 0.03
118 38 0.26
119 11 0.07
120 94 0.63
121 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (120 bp):
CTTCTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTA
TTTCCTTCTGTGATAAAATTATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAA
Found at i:488003 original size:225 final size:222
Alignment explanation
Indices: 487672--488185 Score: 733
Period size: 226 Copynumber: 2.3 Consensus size: 222
487662 AAAATTATGT
** *
487672 AAAAGGTTGAACAAGCTCTTCTCATTGTGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
*
487736 GAAC-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
66 GAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
* * * *
487800 CTTATTATGAA-T-TTCTT-CTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTAC-CTGGC
131 CTCATTATGAATTCTTCTTCCTTCTTCAGATG--AA-TTCTTATCATTACGAACT-TACTCTGGA
487861 AA-TGTTAATCCATCAAATGATGAATTTAAAC
192 AAGT-TTAATCCATCAAATGATGAATTTAAAC
487892 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
487957 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATT
63 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATT
*
488022 CTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTATCATTACGAACTTCCTCTGGA
128 CTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAATTCTTATCATTACGAACTTACTCTGGA
* * ** *
488087 AAGTTTGATCCATCAAGTGATGGTTTTGAAC
192 AAGTTTAATCCATCAAATGATGAATTTAAAC
*
488118 AAAAAGTTGAACAAATTCTTCTCATTATGAAT-TTCTTC-T-TTCAGATGAGTTCTTCTCATTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
*
488180 GGACTT
66 GAACTT
488186 CTTCTTCTTC
Statistics
Matches: 267, Mismatches: 16, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
220 56 0.21
221 1 0.00
222 1 0.00
223 11 0.04
224 32 0.12
225 71 0.27
226 74 0.28
227 4 0.01
228 5 0.02
229 12 0.04
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (222 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
CTCATTATGAATTCTTCTTCCTTCTTCAGATGAATTCTTATCATTACGAACTTACTCTGGAAAGT
TTAATCCATCAAATGATGAATTTAAAC
Found at i:488008 original size:113 final size:110
Alignment explanation
Indices: 487672--488185 Score: 666
Period size: 113 Copynumber: 4.6 Consensus size: 110
487662 AAAATTATGT
** *
487672 AAAAGGTTGAACAAGCTCTTCTCATTGTGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
* *
487736 GAAC-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
66 GAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
*
487780 AAAAGGTTGAACAAATTCTTCTTATTATGAAT-TTCTTCTTCTTCAGATGACAAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATG---AGTTCTTCTCAT
* * * * * * *
487844 TATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAAC
63 TATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
487892 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
*
487957 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
63 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
* *
488005 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTATCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
* * * * *
488070 TACGAACTTCCTCTGG-AAAGTTTGATCCATCAAGTGATGGTTTTGAAC
63 TATGAACTTTCTCTGGAAAAG-CTGATCCATCAAATGATGGATTTGAAC
*
488118 AAAAAGTTGAACAAATTCTTCTCATTATGAAT-TTCTTC-T-TTCAGATGAGTTCTTCTCATTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
*
488180 GGACTT
66 GAACTT
488186 CTTCTTCTTC
Statistics
Matches: 358, Mismatches: 36, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
107 25 0.07
108 45 0.13
109 1 0.00
110 5 0.01
111 20 0.06
112 64 0.18
113 180 0.50
114 1 0.00
115 5 0.01
116 12 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (110 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAAC
Found at i:488170 original size:17 final size:17
Alignment explanation
Indices: 488150--488209 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
488140 CATTATGAAT
488150 TTCTTCTTTCAGATGAG
1 TTCTTCTTTCAGATGAG
* *
488167 TTCTTC--TCATTATGGAC
1 TTCTTCTTTCA-GAT-GAG
488184 TTCTTCTTCTTCAGATGAG
1 TTCTTC-T-TTCAGATGAG
488203 TTCTTCT
1 TTCTTCT
488210 CATTATGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 14 0.42
18 1 0.03
19 8 0.24
20 2 0.06
21 3 0.09
ACGTcount: A:0.15, C:0.22, G:0.13, T:0.50
Consensus pattern (17 bp):
TTCTTCTTTCAGATGAG
Found at i:488176 original size:34 final size:36
Alignment explanation
Indices: 488133--488224 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 36
488123 GTTGAACAAA
488133 TTCTTCTCATTATGAATTTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
* *
488167 TTCTTCTCATTATGGACTTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
488203 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
488225 CTGGAAAAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 21 0.41
35 1 0.02
36 25 0.49
37 4 0.08
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (36 bp):
TTCTTCTCATTATGAATTTCTTCTTCTTCAGATGAG
Found at i:488220 original size:143 final size:149
Alignment explanation
Indices: 488020--488334 Score: 455
Period size: 143 Copynumber: 2.1 Consensus size: 149
488010 GTTGAACAAA
488020 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTATCATTACGAACTTCCTCTG
1 TTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAATTCTTATCATTACGAACTTCCTCTG
* *
488085 G-AAAGTTTGATCCATCAAGTGATGGTTTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
63 GAAAAG-CTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAA
488149 -T-TTCTT-C-T-TTCAGATGAG
127 CTCTTCTTCCTTCTTCAGATGAG
* * * * *
488167 TTCTTCTCATTATGGACTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTATCATTACGAACTTCCTCTGGAA
* *
488231 AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTC
66 AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC-TC
488296 TTCTTCCTTCTTCAGATGAG
130 TTCTTCCTTCTTCAGATGAG
488316 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
488335 TCTCTGGAAA
Statistics
Matches: 151, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
143 90 0.60
144 10 0.07
145 1 0.01
146 5 0.03
147 16 0.11
148 1 0.01
149 28 0.19
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (149 bp):
TTCTTCTCATTATGAACTTCTTCCTTCTTCAGATGAATTCTTATCATTACGAACTTCCTCTGGAA
AAGCTGATCCATCAAGTGATGGATTTGAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTCT
TCTTCCTTCTTCAGATGAG
Found at i:489282 original size:115 final size:114
Alignment explanation
Indices: 489065--489282 Score: 305
Period size: 115 Copynumber: 1.9 Consensus size: 114
489055 GATCATGCAG
* * * * *
489065 TTCATCTTTTAATTCTAATAATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATAATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
489130 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCACA
66 ACACTTCCAGAAGATGCTATTGAGTCATATTATTTCTACTATGAGCACA
* *
489179 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATTAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATAATTGGTTCTGTGG-TTCATACCAAACCAGATCAGATAACTCAAAG
489244 AACACTTCCAGAAGATGCTA-TGAG-CATATTCATCTTCTA
65 AACACTTCCAGAAGATGCTATTGAGTCATATT-AT-TTCTA
489283 AATTCAATTA
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
113 4 0.04
114 34 0.37
115 53 0.58
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATAATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCATATTATTTCTACTATGAGCACA
Found at i:489328 original size:93 final size:93
Alignment explanation
Indices: 489168--489550 Score: 642
Period size: 93 Copynumber: 4.1 Consensus size: 93
489158 CTTATTTCTA
* * * * *
489168 CTATGAGCACATTCATCTTTCAAATCCAATGATTGG-TTCTGTGGTTTCATACCAAACCAGATTA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTG-GGGTTCATACCAAACCAGATCA
489232 GATAACTCAAAGAACACTTCCAGAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
* * * *
489261 CTATGAGCATATTCATCTTCTAAATTCAATTATTGGTTTTTGGGGTTCATACTAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
489326 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
489354 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
489419 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* * *
489447 TTATGAGCACATTTATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATTAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
489512 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
489540 CTATGAGCACA
1 CTATGAGCACA
489551 CGACACTTGT
Statistics
Matches: 272, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
93 268 0.99
94 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:490558 original size:10 final size:10
Alignment explanation
Indices: 490558--490625 Score: 64
Period size: 10 Copynumber: 6.5 Consensus size: 10
490548 TTTTTCCCTT
490558 TTTTTTTCTTTC
1 TTTTTTTC--TC
*
490570 TCTTTTTTCCC
1 T-TTTTTTCTC
*
490581 TTTTTTTTTC
1 TTTTTTTCTC
* *
490591 TTTCTTTCTT
1 TTTTTTTCTC
490601 TTTTTTTCTC
1 TTTTTTTCTC
*
490611 TTTTTTTTTC
1 TTTTTTTCTC
490621 TTTTT
1 TTTTT
490626 CTTTTTTTCT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
10 36 0.78
11 2 0.04
12 1 0.02
13 7 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:490598 original size:29 final size:28
Alignment explanation
Indices: 490545--490634 Score: 118
Period size: 25 Copynumber: 3.3 Consensus size: 28
490535 TGACCCCCCC
490545 CTTTTTTTCCCTTTTTTTTTCTTTC--T
1 CTTTTTTTCCCTTTTTTTTTCTTTCTTT
490571 C-TTTTTTCCCTTTTTTTTTCTTTCTTT
1 CTTTTTTTCCCTTTTTTTTTCTTTCTTT
*
490598 CTTTTTTTTTCTCTTTTTTTTTC-TT-TTT
1 C--TTTTTTTCCCTTTTTTTTTCTTTCTTT
490626 CTTTTTTTC
1 CTTTTTTTC
490635 TTCAAGCATA
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
25 23 0.40
26 9 0.16
27 2 0.03
28 4 0.07
29 2 0.03
30 18 0.31
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (28 bp):
CTTTTTTTCCCTTTTTTTTTCTTTCTTT
Found at i:490603 original size:18 final size:17
Alignment explanation
Indices: 490545--490632 Score: 81
Period size: 18 Copynumber: 5.0 Consensus size: 17
490535 TGACCCCCCC
**
490545 CTTTTTTTCCCTTTTTT
1 CTTTTTTTTTCTTTTTT
* *
490562 -TTTCTTTCTCTTTTTT
1 CTTTTTTTTTCTTTTTT
490578 CCCTTTTTTTTTCTTTCTTT
1 --CTTTTTTTTTCTTT-TTT
490598 CTTTTTTTTTCTCTTTTT
1 CTTTTTTTTTCT-TTTTT
490616 -TTTTCTTTTTCTTTTTT
1 CTTTT-TTTTTCTTTTTT
490633 TCTTCAAGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
16 14 0.23
17 9 0.15
18 22 0.36
19 13 0.21
20 3 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
CTTTTTTTTTCTTTTTT
Found at i:498000 original size:15 final size:15
Alignment explanation
Indices: 497977--498008 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
497967 TGAAATGAAT
497977 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
497992 AATGTATGTATGCAA
1 AATGAATGTATGCAA
498007 AA
1 AA
498009 AGGTATTGAT
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:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:502023 original size:27 final size:28
Alignment explanation
Indices: 501974--502031 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
501964 TGAAAAATAA
501974 ATAAATAAATATTAAAATAATTTA-TAT
1 ATAAATAAATATTAAAATAATTTATTAT
502001 ATAAA-AAATA-TAAAATATTATTTATTAT
1 ATAAATAAATATTAAAATA--ATTTATTAT
502029 ATA
1 ATA
502032 TATATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.25
26 5 0.18
27 10 0.36
28 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAAATAAATATTAAAATAATTTATTAT
Found at i:502036 original size:18 final size:18
Alignment explanation
Indices: 502015--502052 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
502005 AAAATATAAA
*
502015 ATATTATTTATTA-TATAT
1 ATATT-TTTATGACTATAT
502033 ATATTTTTATGACTATAT
1 ATATTTTTATGACTATAT
502051 AT
1 AT
502053 TAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
ATATTTTTATGACTATAT
Found at i:503452 original size:3 final size:3
Alignment explanation
Indices: 503446--503502 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
503436 TAATATTTAT
503446 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
503493 TAA TAA TAA T
1 TAA TAA TAA T
503503 GATGATGATG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:504658 original size:60 final size:59
Alignment explanation
Indices: 504550--504661 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
504540 GTCAGATGAT
* * *
504550 CATTTTGTAACTTTTAATAATCGATGACTCAATAAAGCAATACCCTATAATCAAGAGAC
1 CATTTTGTAACTTTCAATAATCGATGACTCAACAAAGCAATACACTATAATCAAGAGAC
*
504609 CATTTTGTAACTTTCAATAGTCGA-GATACTCAACAAAGC-ATCACACTATAATC
1 CATTTTGTAACTTTCAATAATCGATG--ACTCAACAAAGCAAT-ACACTATAATC
504662 GAGGAACTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 1 0.02
59 24 0.52
60 21 0.46
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (59 bp):
CATTTTGTAACTTTCAATAATCGATGACTCAACAAAGCAATACACTATAATCAAGAGAC
Found at i:505576 original size:28 final size:29
Alignment explanation
Indices: 505540--505637 Score: 105
Period size: 28 Copynumber: 3.4 Consensus size: 29
505530 ATTATATTAA
505540 TATTAAATATATAAATAATATTAT-TCA-T
1 TATTAAATATATAAATAATATTATAT-ATT
*
505568 TATTAAATATATAAAAAATATTATATATT
1 TATTAAATATATAAATAATATTATATATT
* *
505597 TATTAAA-ATAAAAAT-ATAATATAATATAT
1 TATTAAATATATAAATAATATTAT-ATAT-T
505626 TATTATAATATA
1 TATTA-AATATA
505638 ATTGATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
27 6 0.10
28 34 0.57
29 15 0.25
30 2 0.03
31 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
TATTAAATATATAAATAATATTATATATT
Found at i:505632 original size:18 final size:18
Alignment explanation
Indices: 505611--505701 Score: 65
Period size: 18 Copynumber: 5.5 Consensus size: 18
505601 AAAATAAAAA
505611 TATAATATAATATATTAT
1 TATAATATAATATATTAT
505629 TATAATATAAT-TGATTAT
1 TATAATATAATAT-ATTAT
* * *
505647 TTTATTATAATAT-TCA-
1 TATAATATAATATATTAT
*
505663 -A-AATATAATATAATAT
1 TATAATATAATATATTAT
*
505679 TAT--TATAA-ATATTAA
1 TATAATATAATATATTAT
505694 TA-AATATA
1 TATAATATA
505702 TTTTAAATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
14 9 0.16
15 8 0.14
16 9 0.16
17 4 0.07
18 25 0.45
19 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
TATAATATAATATATTAT
Found at i:505635 original size:23 final size:24
Alignment explanation
Indices: 505609--505711 Score: 72
Period size: 23 Copynumber: 4.2 Consensus size: 24
505599 TTAAAATAAA
505609 AATATAATAT-AATATATTATTAT
1 AATATAATATAAATATATTATTAT
* * *
505632 AATATAAT-TGATTATTTTATTAT
1 AATATAATATAAATATATTATTAT
505655 AATATTCAAAATATAATATAATATTATTAT
1 AATA-T---AATATAA-AT-ATATTATTAT
*
505685 AA-ATATTAATAAATATATT-TTA-
1 AATATAAT-ATAAATATATTATTAT
505707 AATAT
1 AATAT
505712 TTTAATAGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
22 3 0.05
23 28 0.44
24 6 0.09
25 4 0.06
26 4 0.06
27 3 0.05
28 3 0.05
29 2 0.03
30 11 0.17
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
AATATAATATAAATATATTATTAT
Found at i:505671 original size:32 final size:32
Alignment explanation
Indices: 505616--505701 Score: 86
Period size: 32 Copynumber: 2.6 Consensus size: 32
505606 AAAAATATAA
* * *
505616 TATAATATATTATTATAATATAATTGATTATTTTAT
1 TATAA-ATATTAATA-AATATAA-T-ATAATATTAT
*
505652 TAT-AATATTCA-AAATATAATATAATATTAT
1 TATAAATATTAATAAATATAATATAATATTAT
505682 TATAAATATTAATAAATATA
1 TATAAATATTAATAAATATA
505702 TTTTAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
30 11 0.26
31 8 0.19
32 14 0.33
33 1 0.02
34 5 0.12
35 1 0.02
36 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (32 bp):
TATAAATATTAATAAATATAATATAATATTAT
Found at i:505717 original size:23 final size:23
Alignment explanation
Indices: 505663--505712 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
505653 ATAATATTCA
505663 AAATA-TAATATAATATTATTAT
1 AAATATTAATATAATATTATTAT
*
505685 AAATATTAATA-AATA-TATTTT
1 AAATATTAATATAATATTATTAT
505706 AAATATT
1 AAATATT
505713 TTAATAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTAATATAATATTATTAT
Found at i:506474 original size:21 final size:21
Alignment explanation
Indices: 506448--506491 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
506438 TATCCATCTG
506448 TACATAATTTAAACATTAAAT
1 TACATAATTTAAACATTAAAT
*
506469 TACATAATTTAACCATTAAAT
1 TACATAATTTAAACATTAAAT
506490 TA
1 TA
506492 TGACTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (21 bp):
TACATAATTTAAACATTAAAT
Found at i:506678 original size:14 final size:15
Alignment explanation
Indices: 506659--506691 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
506649 TTAAAAAAAT
506659 AAAATA-TTTTTAAA
1 AAAATATTTTTTAAA
506673 AAAATATTTTTTAAA
1 AAAATATTTTTTAAA
506688 AAAA
1 AAAA
506692 AATCTAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATTTTTTAAA
Found at i:511306 original size:27 final size:27
Alignment explanation
Indices: 511268--511321 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
511258 TATATATGGG
*
511268 GTAAGGGGGAGGTAAGATAGTAGGCTA
1 GTAAGGGAGAGGTAAGATAGTAGGCTA
511295 GTAAGGGAGAGGTAAGATAGTAGGCTA
1 GTAAGGGAGAGGTAAGATAGTAGGCTA
511322 CTACTCAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.43, T:0.19
Consensus pattern (27 bp):
GTAAGGGAGAGGTAAGATAGTAGGCTA
Found at i:512838 original size:33 final size:33
Alignment explanation
Indices: 512800--512864 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
512790 GGGTTATATG
*
512800 ACAAGGATTTATGAGATCATACAAGAATGTTAT
1 ACAAGGATCTATGAGATCATACAAGAATGTTAT
512833 ACAAGGATCTATGAGATCATACAAGAATGTTA
1 ACAAGGATCTATGAGATCATACAAGAATGTTA
512865 CATAAGCTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (33 bp):
ACAAGGATCTATGAGATCATACAAGAATGTTAT
Found at i:513330 original size:28 final size:28
Alignment explanation
Indices: 513299--513364 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
513289 AATGTATTAT
* * * *
513299 ATGATATGTTACAAATGTTGAGTATAAG
1 ATGACATGTTACAAAGGTTAAGTACAAG
513327 ATGACATGTTACAAAGGTTAAGTACAAG
1 ATGACATGTTACAAAGGTTAAGTACAAG
513355 ATGACATGTT
1 ATGACATGTT
513365 TTAAATGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (28 bp):
ATGACATGTTACAAAGGTTAAGTACAAG
Found at i:518315 original size:45 final size:45
Alignment explanation
Indices: 518241--518350 Score: 152
Period size: 45 Copynumber: 2.4 Consensus size: 45
518231 AGGAACGGAA
*
518241 TATTTCACCAATATA-TATATCATTTAATCCATAAGCTAGTAAGCT
1 TATTTTACCAATATACT-TATCATTTAATCCATAAGCTAGTAAGCT
* * *
518286 TATTTTACCAATATACTTA-CCTTTAAATCCCTAAGCTCGTAAGCT
1 TATTTTACCAATATACTTATCATTT-AATCCATAAGCTAGTAAGCT
518331 TATTTTACCAATATACTTAT
1 TATTTTACCAATATACTTAT
518351 TATAGTTTAC
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
44 4 0.07
45 53 0.91
46 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (45 bp):
TATTTTACCAATATACTTATCATTTAATCCATAAGCTAGTAAGCT
Found at i:518519 original size:59 final size:57
Alignment explanation
Indices: 518440--519405 Score: 735
Period size: 59 Copynumber: 16.4 Consensus size: 57
518430 AATTCGTACA
* * * * *
518440 ATTTCCTTATAATATTAGCACTCTTAGTGCTCTATCTAGAATATCATATACTTAATATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAA-ATCATACA-TTAATATG
* * ** * *
518499 ATTTCCTTCTTATTTTAGCACACGAAGTGC-CTTAT-TCGAGAATCCATACCATTAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTC-TATCTGGA-AAT-CATA-CATTAATATG
* * * * * * *
518558 A-TTCCTTTACCATTTTTAGCAC-CTGAAGTGC-CTTATATGAAAATCCATACTGTTAGTATA
1 ATTTCC-TTATCA-TTTTAGCACACT-TAGTGCTC-TATCTGGAAAT-CATAC-ATTAATATG
* * * * * * * *
518618 ATTTCCTTATCCTTGTAGCTCCCTTAGTGCTTTTTCTGGAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAAT-CATACA-TTAATATG
* * * * * *
518677 ATTCCCTTACCATTTTAGCACA-TATAATGCCCTATCTGAAAATCTATATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCTATCTGGAAATC-ATACATT-AATATG
* * * * * *
518736 ATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAAT-CATACA-TTAATATG
* * * * *
518795 ATTTACTTATCATTTTAGCACACTCAGTACTCTATATGGAAATTCATACATTCATTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAA-TCATACATT-AATATG
* * *
518854 ATTTCCTTATCATTTTAGCACA-TATAATGCCCTATCTGGAAATCCATATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCTATCTGGAAAT-CATACATT-AATATG
* * * * *
518913 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGTAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAAT-CATACA-TTAATATG
* * *
518972 ATTTACTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATTCATACATTCAATATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAA-TCATACATT-AATATG
* * * *
519031 ATTTCCTTATCATTTTAGCA-AATATAATGCCCTATCTGGAAATCCATATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCTATCTGGAAAT-CATACATT-AATATG
* * * * *
519090 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGTAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAAT-CATACA-TTAATATG
* * * * *
519149 ATTTTCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACAATCAATATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAA-TCATAC-ATTAATATG
* * *
519208 ATTTCCTTATCATTTTAGCACA-TATAATGCCCTATCTGGAAATCCATATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCTATCTGGAAAT-CATACATT-AATATG
* * * * * *
519267 ATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAAT-CATACA-TTAATATG
* * * * * *
519326 ATTTACTTATCATTTTTAGCACACTCAGTGCTCCATATGGAAATTCATACGTTCAGTATG
1 ATTTCCTTATCA-TTTTAGCACACTTAGTGCTCTATCTGGAAA-TCATACATT-AATATG
519386 ATTTCCTTATCATTTTAGCA
1 ATTTCCTTATCATTTTAGCA
519406 GAAATAATGC
Statistics
Matches: 742, Mismatches: 124, Indels: 82
0.78 0.13 0.09
Matches are distributed among these distances:
58 24 0.03
59 603 0.81
60 108 0.15
61 7 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (57 bp):
ATTTCCTTATCATTTTAGCACACTTAGTGCTCTATCTGGAAATCATACATTAATATG
Found at i:518586 original size:60 final size:61
Alignment explanation
Indices: 518511--518625 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 61
518501 TTCCTTCTTA
* *
518511 TTTTAGCACACGAAGTGCCTTAT-TCGAGAATCCATACCATTAGTATGA-TTCCTTTACCAT
1 TTTTAGCACACGAAGTGCCTTATAT-GAAAATCCATACCATTAGTATAATTTCCTTTACCAT
**
518571 TTTTAGCAC-CTGAAGTGCCTTATATGAAAATCCATACTGTTAGTATAATTTCCTT
1 TTTTAGCACAC-GAAGTGCCTTATATGAAAATCCATACCATTAGTATAATTTCCTT
518626 ATCCTTGTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 1 0.02
60 40 0.83
61 7 0.15
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (61 bp):
TTTTAGCACACGAAGTGCCTTATATGAAAATCCATACCATTAGTATAATTTCCTTTACCAT
Found at i:518766 original size:118 final size:118
Alignment explanation
Indices: 518440--519405 Score: 918
Period size: 118 Copynumber: 8.2 Consensus size: 118
518430 AATTCGTACA
* * * * * * *
518440 ATTTCCTTATAATATTAGCACTCTTAGTGCTCTATCTAGAATAT-CATATACTT-AATATGATTT
1 ATTTCCTTATCATTTTAGCACACTTAGTGCCCTATAT-GAAAATCCATACA-TTCAATATGATTT
* * ** * *
518503 CCTTCTTATTTTAGCACACGAAGTGC-CT-TATTCGAGAATCCATAC-CATTAGTATG
64 CCTTATCATTTTAGCACACTTAGTGCTCTATA-TGGA-AATCCATACAC-TCAGTATG
* * * * * *
518558 A-TTCCTTTACCATTTTTAGCAC-CTGAAGTGCCTTATATGAAAATCCATAC-TGTTAGTATAAT
1 ATTTCC-TTATCA-TTTTAGCACACT-TAGTGCCCTATATGAAAATCCATACAT-TCAATATGAT
* * * * * * *
518620 TTCCTTATCCTTGTAGCTCCCTTAGTGCTTTTTCTGGAAATCCATACACTCAGTATG
62 TTCCTTATCATTTTAGCACACTTAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * * * *
518677 ATTCCCTTACCATTTTAGCACA-TATAATGCCCTATCTGAAAATCTATATATTCAATATGATTTC
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCCCTATATGAAAATCCATACATTCAATATGATTTC
* * *
518741 CTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATACACTCAGTATG
65 CTTATCATTTTAGCACACTTAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * * * * *
518795 ATTTACTTATCATTTTAGCACACTCAGTACTCTATATGGAAATTCATACATTCATTATGATTTCC
1 ATTTCCTTATCATTTTAGCACACTTAGTGCCCTATATGAAAATCCATACATTCAATATGATTTCC
* * * * * *
518860 TTATCATTTTAGCACA-TATAATGCCCTATCTGGAAATCCATATATTCAATATG
66 TTATCATTTTAGCACACT-TAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * *
518913 ATTTCCTTATCATTTTAGCACACTTAGTGCTCC-ATATGTAAATCCATACACTCAGTATGATTTA
1 ATTTCCTTATCATTTTAGCACACTTAGTGC-CCTATATGAAAATCCATACATTCAATATGATTTC
* * * *
518977 CTTATCATTTTAGCACACTCAGTGCTCTATATGGAAATTCATACATTCAATATG
65 CTTATCATTTTAGCACACTTAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * * *
519031 ATTTCCTTATCATTTTAGCA-AATATAATGCCCTATCTGGAAATCCATATATTCAATATGATTTC
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCCCTATATGAAAATCCATACATTCAATATGATTTC
* *
519095 CTTATCATTTTAGCACACTTAGTGCTCCATATGTAAATCCATACACTCAGTATG
65 CTTATCATTTTAGCACACTTAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * * *
519149 ATTTTCTTATCATTTTAGCACACTCAGTGCTCC-ATATGGAAATTCATACAATCAATATGATTTC
1 ATTTCCTTATCATTTTAGCACACTTAGTGC-CCTATATGAAAATCCATACATTCAATATGATTTC
* * * * * *
519213 CTTATCATTTTAGCACA-TATAATGCCCTATCTGGAAATCCATATATTCAATATG
65 CTTATCATTTTAGCACACT-TAGTGCTCTATATGGAAATCCATACACTCAGTATG
* * * * *
519267 ATTTCCTTATCATTTTAGCACACTCAGTGCTCC-ATATGTAAATCCATACACTCAGTATGATTTA
1 ATTTCCTTATCATTTTAGCACACTTAGTGC-CCTATATGAAAATCCATACATTCAATATGATTTC
* * * **
519331 CTTATCATTTTTAGCACACTCAGTGCTCCATATGGAAATTCATACGTTCAGTATG
65 CTTATCA-TTTTAGCACACTTAGTGCTCTATATGGAAATCCATACACTCAGTATG
519386 ATTTCCTTATCATTTTAGCA
1 ATTTCCTTATCATTTTAGCA
519406 GAAATAATGC
Statistics
Matches: 699, Mismatches: 126, Indels: 45
0.80 0.14 0.05
Matches are distributed among these distances:
117 11 0.02
118 544 0.78
119 134 0.19
120 9 0.01
121 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (118 bp):
ATTTCCTTATCATTTTAGCACACTTAGTGCCCTATATGAAAATCCATACATTCAATATGATTTCC
TTATCATTTTAGCACACTTAGTGCTCTATATGGAAATCCATACACTCAGTATG
Found at i:518837 original size:177 final size:177
Alignment explanation
Indices: 518654--519416 Score: 1337
Period size: 177 Copynumber: 4.3 Consensus size: 177
518644 GTGCTTTTTC
* * * * * *
518654 TGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGAAAA
1 TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
*
518719 TCTATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
* *
518784 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTACTCTATA
131 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
*
518831 TGGAAATTCATACATTCATTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
1 TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
*
518896 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGTAAATCCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
*
518961 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCTATA
131 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
*
519008 TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTAGCAAATATAATGCCCTATCTGGAAA
1 TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
*
519073 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGTAAATCCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
*
519138 CACTCAGTATGATTTTCTTATCATTTTAGCACACTCAGTGCTCCATA
131 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
*
519185 TGGAAATTCATACAATCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
1 TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
519250 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
519315 CACTCAGTATGATTTACTTATCATTTTTAGCACACTCAGTGCTCCATA
131 CACTCAGTATGATTTACTTATCA-TTTTAGCACACTCAGTGCTCCATA
* * * *
519363 TGGAAATTCATACGTTCAGTATGATTTCCTTATCATTTTAGCAGAAATAATGCC
1 TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTAGCACATATAATGCC
519417 GTTTGGTAAC
Statistics
Matches: 563, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
177 490 0.87
178 73 0.13
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (177 bp):
TGGAAATTCATACATTCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
Found at i:522361 original size:3 final size:3
Alignment explanation
Indices: 522353--522408 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
522343 ACAAACTTAG
522353 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
522401 TTA TTA TT
1 TTA TTA TT
522409 TTTAGTTCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:522484 original size:21 final size:20
Alignment explanation
Indices: 522448--522486 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
522438 CATGACTAAG
522448 AAAATCAACTTCTGATAGCC
1 AAAATCAACTTCTGATAGCC
522468 AAAACTCACACTT-TGATAG
1 AAAA-TCA-ACTTCTGATAG
522487 TTTAGCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAATCAACTTCTGATAGCC
Found at i:524116 original size:29 final size:30
Alignment explanation
Indices: 524047--524105 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
524037 AATTTAAGGC
524047 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
524078 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
524106 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:524211 original size:21 final size:21
Alignment explanation
Indices: 524185--524241 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
524175 AGGGTGTCAA
*
524185 AGTGCATCCAAGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
524206 AGTGCATACATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
524227 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
524242 ATGCACTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.37, G:0.19, T:0.19
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:524254 original size:22 final size:23
Alignment explanation
Indices: 524227--524269 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
524217 GCATCCCTGC
*
524227 AGTGCATCCATGCA-CATGCACT
1 AGTGCATCAATGCACCATGCACT
524249 AGTGCATCAATGCACCATGCA
1 AGTGCATCAATGCACCATGCA
524270 ATACATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (23 bp):
AGTGCATCAATGCACCATGCACT
Found at i:524329 original size:20 final size:20
Alignment explanation
Indices: 524304--524378 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
524294 AATGTAATTA
*
524304 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
* **
524324 GTGCATCGTTGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
524345 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
* *
524365 GTTCATCCATGCAT
1 GTGCATCGATGCAT
524379 GAAGGCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:524349 original size:41 final size:41
Alignment explanation
Indices: 524304--524386 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
524294 AATGTAATTA
* **
524304 GTGCATCGATGCATCCTTCTGTGCATCGTTGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
* *
524345 GTGCATCGATGCATCCTGCTGTTCATCCATGCATGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
524386 G
1 G
524387 CAACAGCTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATGCATCAAGGCT
Found at i:525705 original size:19 final size:19
Alignment explanation
Indices: 525669--525721 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
525659 TGAAAATGAT
**
525669 TTGATTTTGAAAGCCAAAA
1 TTGATTTTGAAAATCAAAA
525688 TTGATTTTGAAAATCAAAA
1 TTGATTTTGAAAATCAAAA
525707 -TGAAATTTTGAAAAT
1 TTG--ATTTTGAAAAT
525722 TGATTTAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 17 0.57
20 11 0.37
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (19 bp):
TTGATTTTGAAAATCAAAA
Found at i:530240 original size:24 final size:24
Alignment explanation
Indices: 530190--530255 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
530180 TTAGTGCAGA
* * *
530190 GGGAATCAATACCCCC-CTTGAAG
1 GGGAATCAATTCCCCCTTTTAAAG
*
530213 GGGAATCAATTCCCCCTTTTAAAT
1 GGGAATCAATTCCCCCTTTTAAAG
*
530237 GGGAATCGATTCCCTCCTT
1 GGGAATCAATTCCC-CCTT
530256 GAGGAAATCG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 15 0.42
24 17 0.47
25 4 0.11
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (24 bp):
GGGAATCAATTCCCCCTTTTAAAG
Found at i:532426 original size:45 final size:46
Alignment explanation
Indices: 532377--532464 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
532367 GAACATCGAA
* * *
532377 TGCATTTTATGCATTGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
*
532422 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
532465 CAGGCTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:534063 original size:12 final size:12
Alignment explanation
Indices: 534046--534070 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
534036 GCATCGATGC
534046 ACTGCTACAGTA
1 ACTGCTACAGTA
534058 ACTGCTACAGTA
1 ACTGCTACAGTA
534070 A
1 A
534071 ATTCCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:534208 original size:170 final size:171
Alignment explanation
Indices: 533919--534262 Score: 645
Period size: 170 Copynumber: 2.0 Consensus size: 171
533909 AATTTAATGT
* *
533919 AAAATATTTTTTTTATGAACTGTGAACAGTGTACAAATGCATTGCTACAGTGACGTGAACAGTGC
1 AAAATATTTTTTTTATGAACTGTGAAAAGTGTACAAATGCATAGCTACAGTGACGTGAACAGTGC
*
533984 ACCGATGCATAAAACATCGAATTAACATTGTGTATCGATGCACTGCTACAATGCATCGATGCACT
66 ACCAATGCATAAAACATCGAATTAACATTGTGTATCGATGCACTGCTACAATGCATCGATGCACT
534049 GCTACAGTAACTGCTACAGTAAATTCCGAAAAATGCATATA
131 GCTACAGTAACTGCTACAGTAAATTCCGAAAAATGCATATA
534090 AAAATA-TTTTTTTATGAACTGTGAAAAGTGTACAAATGCATAGCTACAGTGACGTGAACAGTGC
1 AAAATATTTTTTTTATGAACTGTGAAAAGTGTACAAATGCATAGCTACAGTGACGTGAACAGTGC
534154 ACCAATGCATAAAACATCGAATTAACATTGTGTATCGATGCACTGCTACAATGCATCGATGCACT
66 ACCAATGCATAAAACATCGAATTAACATTGTGTATCGATGCACTGCTACAATGCATCGATGCACT
*
534219 GCTACAGTAACTGTTACAGTAAATTCCGAAAAATGCATATA
131 GCTACAGTAACTGCTACAGTAAATTCCGAAAAATGCATATA
534260 AAA
1 AAA
534263 CTCATAGAAA
Statistics
Matches: 169, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
170 163 0.96
171 6 0.04
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (171 bp):
AAAATATTTTTTTTATGAACTGTGAAAAGTGTACAAATGCATAGCTACAGTGACGTGAACAGTGC
ACCAATGCATAAAACATCGAATTAACATTGTGTATCGATGCACTGCTACAATGCATCGATGCACT
GCTACAGTAACTGCTACAGTAAATTCCGAAAAATGCATATA
Found at i:535028 original size:59 final size:59
Alignment explanation
Indices: 534772--535739 Score: 865
Period size: 59 Copynumber: 16.4 Consensus size: 59
534762 AATTCGTACA
* * * * * * * *
534772 ATTTCCTTATAATATTAGCACTCTTAGTGCTCTATCTAGAATAT-CATATACTT-AATATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAA-ATCCATACA-TTCAGTATG
* * * * * *
534831 ATTTCCTTCTTATTTTAGCAAACGTAGTGC-CC-TATTCGAGAACCCATACCATT-AGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATA-TGGA-AATCCATA-CATTCAGTATG
* * * * * * *
534890 A-TTCCTTTACCATTTTTAGCAC-CTGAAGTGC-CTTATATGAAAATCCATACTTTTAGTATA
1 ATTTCC-TTATCA-TTTTAGCACACT-TAGTGCTC-CATATGGAAATCCATACATTCAGTATG
* * * * * *** * *
534950 ATTTCATTCTCCTTGTAGCACCCTTAGTGCTTTTTCTGGAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
* * * * * * * * *
535009 ATTCCCTTACCATTTTAGCACA-TATAATGC-CCTATCTAGAAGTCCCTATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCC-ATATGGAAATCCATACATTCAGTATG
* * *
535068 ATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
* *
535127 ATTTACTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATTCATACATTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
* * * * *
535186 ATTTCCTTATCATTTTAGCATA-TATAATGC-CCTATCTGGAAATCCATATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCC-ATATGGAAATCCATACATTCAGTATG
* * * *
535245 ATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATTCATACACTC-GTTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAG-TATG
* * *
535304 ATTTACTTATCATTTTAGCACACTCT-GTGCTCCATATGGAAATTCATACATTCATTATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCCATATGGAAATCCATACATTCAGTATG
* * * * *
535363 ATTTCCTTATCATTTTAGCACA-TATAATGC-CCTATCTAGAAATCCATATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCC-ATATGGAAATCCATACATTCAGTATG
** *
535422 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATATAAATCCATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
* * * *
535481 ATTTACTTATCATTTTAGCACACTCAGTGTTCCATATGGAAATTCATACATTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
* * * * * *
535540 ATTTACTTATCATTTTTGCACA-TATAATGC-CCTATCTGGAAATCCATATATTCAATATG
1 ATTTCCTTATCATTTTAGCACACT-TAGTGCTCC-ATATGGAAATCCATACATTCAGTATG
* * * * * *
535599 ATTTCCTTATCATTTTAGCACACTCAGAGCTCTATATGTAAATCGATACACTCAGTATG
1 ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
* * * *
535658 ATTTGCTTATCATGTTTAGCACACTCAGTGCTCCATATGGAAATTCATACATTCATTATG
1 ATTTCCTTATCAT-TTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
535718 ATTTCCTTATCATTTTAGCACA
1 ATTTCCTTATCATTTTAGCACA
535740 TATAATGCCA
Statistics
Matches: 733, Mismatches: 143, Indels: 66
0.78 0.15 0.07
Matches are distributed among these distances:
57 1 0.00
58 20 0.03
59 610 0.83
60 95 0.13
61 5 0.01
62 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (59 bp):
ATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATGGAAATCCATACATTCAGTATG
Found at i:535169 original size:177 final size:177
Alignment explanation
Indices: 534986--535748 Score: 1294
Period size: 177 Copynumber: 4.3 Consensus size: 177
534976 GTGCTTTTTC
* * * * *
534986 TGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTAGAAG
1 TGGAAATTCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAA
*
535051 TCCCTATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
*
535116 CACTCAGTATGATTTACTTATCATTTTAGCACACTTAGTGCTCCATA
131 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
* *
535163 TGGAAATTCATACATTCAGTATGATTTCCTTATCATTTTAGCATATATAATGCCCTATCTGGAAA
1 TGGAAATTCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAA
*
535228 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATTCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
*
535293 CACTC-GTTATGATTTACTTATCATTTTAGCACACTCTGTGCTCCATA
131 CACTCAG-TATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
*
535340 TGGAAATTCATACATTCATTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAA
1 TGGAAATTCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAA
* *
535405 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTTAGTGCTCCATATATAAATCCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
*
535470 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGTTCCATA
131 CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
* * *
535517 TGGAAATTCATACATTCAGTATGATTTACTTATCATTTTTGCACATATAATGCCCTATCTGGAAA
1 TGGAAATTCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAA
* * *
535582 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGAGCTCTATATGTAAATCGATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
*
535647 CACTCAGTATGATTTGCTTATCATGTTTAGCACACTCAGTGCTCCATA
131 CACTCAGTATGATTTACTTATCAT-TTTAGCACACTCAGTGCTCCATA
*
535695 TGGAAATTCATACATTCATTATGATTTCCTTATCATTTTAGCACATATAATGCC
1 TGGAAATTCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCC
535749 ATTTGATAAT
Statistics
Matches: 550, Mismatches: 33, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
176 1 0.00
177 475 0.86
178 74 0.13
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.38
Consensus pattern (177 bp):
TGGAAATTCATACATTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTAGAAA
TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGTAAATCCATA
CACTCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
Found at i:541133 original size:12 final size:12
Alignment explanation
Indices: 541116--541140 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
541106 GTATTGATGC
541116 ACTGCTACAGTA
1 ACTGCTACAGTA
541128 ACTGCTACAGTA
1 ACTGCTACAGTA
541140 A
1 A
541141 ATTTCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:541547 original size:45 final size:45
Alignment explanation
Indices: 541481--541581 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 45
541471 ATCATGTTAT
*
541481 CAATATA-TATACCATTTAATCCATAAGCTAGTAAGCTTATTTTAC
1 CAATATACT-TACCATTAAATCCATAAGCTAGTAAGCTTATTTTAC
* *
541526 CAATATACTTACCATTAAATCCCTAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTAAATCCATAAGCTAGTAAGCTTATTTTAC
541571 CAATATACTTA
1 CAATATACTTA
541582 TTATAATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (45 bp):
CAATATACTTACCATTAAATCCATAAGCTAGTAAGCTTATTTTAC
Found at i:541928 original size:59 final size:59
Alignment explanation
Indices: 541886--542285 Score: 484
Period size: 59 Copynumber: 6.8 Consensus size: 59
541876 GTGCTTTTTC
* * * * * *
541886 TGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACA-TATAATGC-CCTATC
1 TGGAAATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACACT-CAGTGCTCC-ATA
* * *
541945 TGGAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGTTCCATA
1 TGGAAATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
* * *
542004 TGTAAATCCATACAATCAGTATGATTTACTTATCATTTTAGCACACTCAGTGCTCCATA
1 TGGAAATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
* * * * * *
542063 TGCAAATTCATACATTTAGTATGATTTCCTTATCATTTTAGCACA-TATAATGC-CCTATC
1 TGGAAATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACACT-CAGTGCTCC-ATA
* * *
542122 TGGAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAATGCTCCATA
1 TGGAAATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
* * * *
542181 TGTAAATCCATACACTCGGTATGATTTACTTATCATTTTTAGCACACTCAGTGCTCCATA
1 TGGAAATCCATACATTCAGTATGATTTCCTTATCA-TTTTAGCACACTCAGTGCTCCATA
* *
542241 TGGAAATTCATACATTTAGTATGATTTCCTTATCATTTTAGCACA
1 TGGAAATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACA
542286 TATAATGCCA
Statistics
Matches: 291, Mismatches: 43, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
58 3 0.01
59 230 0.79
60 58 0.20
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.38
Consensus pattern (59 bp):
TGGAAATCCATACATTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
Found at i:546962 original size:17 final size:17
Alignment explanation
Indices: 546924--546962 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
546914 ATATGTTGTT
*
546924 TATTATTTATGTTATAA
1 TATTATTTATATTATAA
546941 TATTATTTATTATTATAA
1 TATTATTTA-TATTATAA
546959 -ATTA
1 TATTA
546963 AATTTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTATTTATATTATAA
Found at i:548176 original size:51 final size:51
Alignment explanation
Indices: 548067--548211 Score: 129
Period size: 51 Copynumber: 2.8 Consensus size: 51
548057 CCCGATCTAA
* * * * * * *
548067 CACC-CGTAGCAGTAAAGCGCGCCCCCTGAATCGCGCTATATGCTGATTTGG
1 CACCACGTAGGAGTATAGCGCG-CCCCTGTACCGCGCTATACGCTGACTGGG
548118 CACCACGT-GGAGTATAGCGCGCCCCTTGTACCGCGCTATACGCTGACTGGG
1 CACCACGTAGGAGTATAGCGCGCCCC-TGTACCGCGCTATACGCTGACTGGG
* *
548169 TTA-CACGTAGG-GTATAGCGTGCCTCCTGCT-CCGCGCTATACGC
1 -CACCACGTAGGAGTATAGCGCGCC-CCTG-TACCGCGCTATACGC
548212 CACGTAGGGG
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
50 4 0.05
51 66 0.84
52 9 0.11
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (51 bp):
CACCACGTAGGAGTATAGCGCGCCCCTGTACCGCGCTATACGCTGACTGGG
Found at i:551890 original size:35 final size:34
Alignment explanation
Indices: 551805--551891 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
551795 ATTTGGCATT
*
551805 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
551839 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
551877 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
551892 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:552148 original size:9 final size:9
Alignment explanation
Indices: 552112--552152 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
552102 GATGTCATCA
552112 TCATCGTCG
1 TCATCGTCG
*
552121 TCGTCGTCG
1 TCATCGTCG
* *
552130 TCACCATCG
1 TCATCGTCG
552139 TCATCGTCG
1 TCATCGTCG
552148 TCATC
1 TCATC
552153 CTGAGCAGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.12, C:0.37, G:0.20, T:0.32
Consensus pattern (9 bp):
TCATCGTCG
Found at i:554205 original size:111 final size:111
Alignment explanation
Indices: 554011--554338 Score: 558
Period size: 111 Copynumber: 3.0 Consensus size: 111
554001 ATTACAAAAA
*
554011 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
554076 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
554122 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
554187 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
554233 TTAATTCTTAATCTATTAATCATGCATTAAATAAATCAACTAAATATTACTAATAA--T---TTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
554293 AATTAAAGCGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
554339 ATGATTTCCA
Statistics
Matches: 209, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
106 46 0.22
109 1 0.00
111 162 0.78
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:554488 original size:10 final size:10
Alignment explanation
Indices: 554465--554504 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
554455 TTAAAAAGAT
*
554465 AGAGTATTTG
1 AGAGAATTTG
554475 AGAGATATTT-
1 AGAGA-ATTTG
554485 AGAGAATTTG
1 AGAGAATTTG
554495 AGAGAATTTG
1 AGAGAATTTG
554505 GTGTGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 4 0.15
10 19 0.70
11 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.35
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:554493 original size:20 final size:19
Alignment explanation
Indices: 554464--554503 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
554454 CTTAAAAAGA
*
554464 TAGAGTATTTGAGAGATATT
1 TAGAGAATTTGAGAGA-ATT
554484 TAGAGAATTTGAGAGAATT
1 TAGAGAATTTGAGAGAATT
554503 T
1 T
554504 GGTGTGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (19 bp):
TAGAGAATTTGAGAGAATT
Found at i:554763 original size:30 final size:29
Alignment explanation
Indices: 554701--554763 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
554691 TACTGCTACG
** *
554701 GGTGTTAGATCGGGAAATATAATTTGACC
1 GGTGTTAGATCGGGAAATATAAGATCACC
* *
554730 GGTGTTAGATCGGTAAATATACCGATCACC
1 GGTGTTAGATCGGGAAATATA-AGATCACC
554760 GGTG
1 GGTG
554764 ATTTATTGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAAGATCACC
Found at i:555291 original size:12 final size:13
Alignment explanation
Indices: 555269--555301 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
555259 ATTCCTTCAA
555269 AATATGCCTTTAT
1 AATATGCCTTTAT
*
555282 -ATATGTCTTTAT
1 AATATGCCTTTAT
555294 AATATGCC
1 AATATGCC
555302 ATGGTTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (13 bp):
AATATGCCTTTAT
Found at i:555584 original size:15 final size:15
Alignment explanation
Indices: 555564--555597 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
555554 TTAGATTGCT
555564 TTTGTAATCCATATG
1 TTTGTAATCCATATG
*
555579 TTTGTAATCTATATG
1 TTTGTAATCCATATG
555594 TTTG
1 TTTG
555598 AAAATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (15 bp):
TTTGTAATCCATATG
Found at i:563841 original size:2 final size:2
Alignment explanation
Indices: 563834--563924 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
563824 AAAGTTTGTT
563834 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
563876 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
563918 TG TG TG T
1 TG TG TG T
563925 ATTTTCATCT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:565742 original size:12 final size:12
Alignment explanation
Indices: 565727--565766 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
565717 ATCCTTCTTT
565727 TTCTTCCCCTTC
1 TTCTTCCCCTTC
565739 TTCTTCCCCTTC
1 TTCTTCCCCTTC
*
565751 TT-TTCCATCTTC
1 TTCTTCC-CCTTC
565763 TTCT
1 TTCT
565767 ACTCTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 4 0.16
12 20 0.80
13 1 0.04
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (12 bp):
TTCTTCCCCTTC
Found at i:565765 original size:27 final size:27
Alignment explanation
Indices: 565697--565766 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
565687 TGCCAATGAT
* *
565697 TTTTCCTTCTTCTTCTTGTTATCCTTC
1 TTTTCCTTCTTCTTCTTCTTACCCTTC
* ** *
565724 TTTTTCTTCCCCTTCTTCTTCCCCTTC
1 TTTTCCTTCTTCTTCTTCTTACCCTTC
*
565751 TTTTCCATCTTCTTCT
1 TTTTCCTTCTTCTTCT
565767 ACTCTTTCTC
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.03, C:0.36, G:0.01, T:0.60
Consensus pattern (27 bp):
TTTTCCTTCTTCTTCTTCTTACCCTTC
Found at i:565795 original size:15 final size:15
Alignment explanation
Indices: 565769--565807 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
565759 CTTCTTCTAC
*
565769 TCTTTCTCCTTTTTCT
1 TCTTT-TCCTTTTCCT
565785 TCTTTTCCTTTTCCT
1 TCTTTTCCTTTTCCT
565800 TCTCTTTC
1 TCT-TTTC
565808 TTCTCTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTTTTCCTTTTCCT
Found at i:566579 original size:83 final size:83
Alignment explanation
Indices: 566489--566649 Score: 270
Period size: 83 Copynumber: 1.9 Consensus size: 83
566479 ATTTTGATAA
*
566489 AGTTTTACTCCAACTAAA-ACTTTTTTAATATCTAAATTTAAACAGATAATAATATATTTTAAAT
1 AGTTTTACTCCAACTAAACA-TATTTTAATATCTAAATTTAAACAGATAATAATATATTTTAAAT
566553 TTAAAATATTAAAATTGAG
65 TTAAAATATTAAAATTGAG
* * *
566572 AGTTTTACTCCAACTAAACATATTTTAATATCTAAATTTAAATAGATAATAATGTCTTTTAAATT
1 AGTTTTACTCCAACTAAACATATTTTAATATCTAAATTTAAACAGATAATAATATATTTTAAATT
566637 TAAAATATTAAAA
66 TAAAATATTAAAA
566650 AGATATGCAC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
83 72 0.99
84 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (83 bp):
AGTTTTACTCCAACTAAACATATTTTAATATCTAAATTTAAACAGATAATAATATATTTTAAATT
TAAAATATTAAAATTGAG
Found at i:570198 original size:12 final size:12
Alignment explanation
Indices: 570147--570201 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
570137 ATTTTAATAA
570147 TGTTATTATTAT
1 TGTTATTATTAT
* *
570159 TGTT-TT-TAAA
1 TGTTATTATTAT
*
570169 TGATTATTTTTA-
1 TG-TTATTATTAT
570181 TGTTATTATTAT
1 TGTTATTATTAT
570193 TGTTATTAT
1 TGTTATTAT
570202 GAATAAAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 4 0.11
11 12 0.34
12 17 0.49
13 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.65
Consensus pattern (12 bp):
TGTTATTATTAT
Found at i:573108 original size:26 final size:25
Alignment explanation
Indices: 573079--573128 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
573069 CCATCGAATA
* *
573079 TTAACTATAATATATAATATATATTT
1 TTAACTATAACAAAT-ATATATATTT
573105 TTAACTATAACAAATATATATATT
1 TTAACTATAACAAATATATATATT
573129 ATAATTTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAACTATAACAAATATATATATTT
Found at i:573331 original size:2 final size:2
Alignment explanation
Indices: 573326--573360 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
573316 TTATGATTTC
573326 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 A
573361 ATCATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:573539 original size:181 final size:180
Alignment explanation
Indices: 573167--573499 Score: 497
Period size: 181 Copynumber: 1.8 Consensus size: 180
573157 TGATTTCATG
* *
573167 TATATGTATATATAATCATTCAAAATAAATATGAAAACAATAATTTAATTTAAAAATACTAAAAT
1 TATATATATATATAATCATTAAAAATAAATATGAAAACAATAATTTAATTTAAAAATACTAAAAT
* *
573232 CTTAAACCAATTATAAATAAACTATTAGATTTATTTTAGTGATTTAAGTGTTGTCATATTTTCAA
66 CTTAAACCAATTATAAATAAACTATTAGATTTATTTTAGTGATTTAAGTGTTGGCATATTCTCAA
** * * *
573297 TAGGACTAGAATTATTTTTTTATGATTTCATATATATATATATATATATA
131 TAGGACTAGAATTAAGTTCTCATGATTCCATATATATATATATATATATA
* * *
573347 TATATATATATATAATCATTAAAAATAAATATGAAAGCGATAAATTTAATTTAAAGATACTAAAA
1 TATATATATATATAATCATTAAAAATAAATATGAAAACAAT-AATTTAATTTAAAAATACTAAAA
* *
573412 TCTTAAATCAATTATAAATAAACTATTATATTTATTTTAGTGATTTAAGTGTTGGCATATTCTCA
65 TCTTAAACCAATTATAAATAAACTATTAGATTTATTTTAGTGATTTAAGTGTTGGCATATTCTCA
* *
573477 AT-TGACGTAGACTTAAGTTCTCA
130 ATAGGAC-TAGAATTAAGTTCTCA
573500 CTTATCCGTT
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
180 40 0.29
181 96 0.71
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (180 bp):
TATATATATATATAATCATTAAAAATAAATATGAAAACAATAATTTAATTTAAAAATACTAAAAT
CTTAAACCAATTATAAATAAACTATTAGATTTATTTTAGTGATTTAAGTGTTGGCATATTCTCAA
TAGGACTAGAATTAAGTTCTCATGATTCCATATATATATATATATATATA
Found at i:575090 original size:18 final size:18
Alignment explanation
Indices: 575067--575102 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
575057 GATTTGTAAC
*
575067 TTTACTTTAGATTCATAG
1 TTTACTTCAGATTCATAG
*
575085 TTTACTTCATATTCATAG
1 TTTACTTCAGATTCATAG
575103 CCCAATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (18 bp):
TTTACTTCAGATTCATAG
Found at i:579540 original size:23 final size:21
Alignment explanation
Indices: 579502--579552 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
579492 ATAATTATTT
579502 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
579523 AAAAACATTTAATAAAAAATA--
1 AAAAA-ATTAAAT-AAAAATACC
579544 AAAAAATTA
1 AAAAAATTA
579553 GGTTGAACCG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.12
21 10 0.38
22 6 0.23
23 7 0.27
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:579548 original size:22 final size:21
Alignment explanation
Indices: 579502--579552 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
579492 ATAATTATTT
579502 AAAAAATTAAATAAAAATACCA
1 AAAAAATTAAATAAAAATA-CA
* * *
579524 AAAACATTTAATAAAAA-ATA
1 AAAAAATTAAATAAAAATACA
579544 AAAAAATTA
1 AAAAAATTA
579553 GGTTGAACCG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACA
Found at i:581266 original size:11 final size:11
Alignment explanation
Indices: 581252--581312 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
581242 GTATAATTAT
581252 AAATTATTTAA
1 AAATTATTTAA
*** *
581263 AAATTAAAGAT
1 AAATTATTTAA
581274 AAATTATTTAA
1 AAATTATTTAA
*** *
581285 AAATTAAAGAT
1 AAATTATTTAA
581296 AAATTATTTAA
1 AAATTATTTAA
581307 AAATTA
1 AAATTA
581313 AAGGTAAAGT
Statistics
Matches: 34, Mismatches: 16, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAATTATTTAA
Found at i:581275 original size:22 final size:22
Alignment explanation
Indices: 581250--581330 Score: 144
Period size: 22 Copynumber: 3.7 Consensus size: 22
581240 ACGTATAATT
581250 ATAAATTATTTAAAAATTAAAG
1 ATAAATTATTTAAAAATTAAAG
581272 ATAAATTATTTAAAAATTAAAG
1 ATAAATTATTTAAAAATTAAAG
581294 ATAAATTATTTAAAAATTAAAG
1 ATAAATTATTTAAAAATTAAAG
* *
581316 GTAAAGTATTTAAAA
1 ATAAATTATTTAAAA
581331 TAAAGGGTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (22 bp):
ATAAATTATTTAAAAATTAAAG
Found at i:583765 original size:6 final size:6
Alignment explanation
Indices: 583749--583780 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
583739 CAATTATGTC
583749 TTTAT- TTTATG TTTATG TTTATG TTTATG TTT
1 TTTATG TTTATG TTTATG TTTATG TTTATG TTT
583781 TTATTATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (6 bp):
TTTATG
Found at i:595812 original size:33 final size:33
Alignment explanation
Indices: 595770--595843 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
595760 CACACACCCC
595770 ATGCATACTCATGCATTCATTTAATAGGAGCAT
1 ATGCATACTCATGCATTCATTTAATAGGAGCAT
595803 ATGCATACTCATGCATTCATTTAATAGGAGCAT
1 ATGCATACTCATGCATTCATTTAATAGGAGCAT
595836 ATGCATAC
1 ATGCATAC
595844 ATCAAGTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (33 bp):
ATGCATACTCATGCATTCATTTAATAGGAGCAT
Found at i:596171 original size:44 final size:44
Alignment explanation
Indices: 596121--596325 Score: 144
Period size: 44 Copynumber: 4.6 Consensus size: 44
596111 AACTTTTAGC
* *
596121 TCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAACATCGACATCTCGT
* * * **** * *
596165 TCGATTCCATCATAGAAAGAGGTGGATCAACCTTTTTATTTTCGC
1 TCGATTCCATCACAGAAGGAGGTGGATCAACATCGACA-TCTCGT
* * * * * * * *
596210 TCAAATCCATCGCAGAAGGAGTTGGATCAACGTC-AAATTTTAGT
1 TCGATTCCATCACAGAAGGAGGTGGATCAACATCGACA-TCTCGT
* * * *
596254 TCGATTCTATCACAGAATGAGGTAGATCAGA-ACCGACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTGGATCA-ACATCGACATCTCGT
* *
596298 TCGATTCCATCACAGAAAGAGATGGATC
1 TCGATTCCATCACAGAAGGAGGTGGATC
596326 GACCTTTTTA
Statistics
Matches: 119, Mismatches: 39, Indels: 6
0.73 0.24 0.04
Matches are distributed among these distances:
44 86 0.72
45 33 0.28
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
TCGATTCCATCACAGAAGGAGGTGGATCAACATCGACATCTCGT
Found at i:596213 original size:133 final size:131
Alignment explanation
Indices: 595976--596706 Score: 926
Period size: 133 Copynumber: 5.6 Consensus size: 131
595966 AAGAACTTAT
595976 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
1 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * ** *
596041 TCACAGAAGGAGGTGGATCGACCTTTTTATTATCGCTCAAATATATTGCAAAGGGAGTTGGATCA
66 TCACAGAAAGAGGTGGATC-ACCTTTTTATTTTCGCTCAAATCCATCGCAAA-GGAGTTGGATCA
*
596106 GCT
129 GCG
* *
596109 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAACATCGACATCTCGTTCGATTCCA
1 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
*
596174 TCATAGAAAGAGGTGGATCAACCTTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAAGAGGTGGATC-ACCTTTTTATTTTCGCTCAAATCCATCGCA-AAGGAGTTGGATCA
*
596239 ACG
129 GCG
* * * *
596242 TCAAATTTTAGTTCGATTCTATCACAGAATGAGGTAGATCAGA-ACCGACATCTCGTTCGATTCC
1 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCA-ACACCGACATCTCGTTCGATTCC
* * **
596306 ATCACAGAAAGAGATGGATCGACCTTTTTATTTTCGCTCAAATCCATTGCAGAAGGAGTCAGATC
65 ATCACAGAAAGAGGTGGATC-ACCTTTTTATTTTCGCTCAAATCCATCGCA-AAGGAGTTGGATC
596371 AGCG
128 AGCG
* * * * *
596375 TCAACTTTCAGCTTGATTCTATAATAGAAGAAGGTAGATCAACACCAACATCTCGTTCGATTCCA
1 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * *
596440 TCACATAAAGAGGTGGATCA-TTTTTTATTTTCGCTCAAATCCATCGCAAAAGGAGTTGGATCAA
66 TCACAGAAAGAGGTGGATCACCTTTTTATTTTCGCTCAAATCCATCGC-AAAGGAGTTGGATCAG
596504 CG
130 CG
* * * ** *
596506 TCAACTTTTAGCTCGATTCTATAACAGAATGAGGTAGATCAGTACCGACATCTCGTTCTATTCCA
1 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
* * *
596571 TCACA-AAATGAGGTGG---A-----TTATTTTCACTCAAATCCATCGCAAAAGAAATTGGATCA
66 TCACAGAAA-GAGGTGGATCACCTTTTTATTTTCGCTCAAATCCATCGC-AAAGGAGTTGGATCA
596627 GCG
129 GCG
* * * * * *
596630 TCAACTTTCAACTCGATTCTATCGCAGAATGAGGTAGATCAGCACCGATATCTCGTTAGATTCCA
1 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
596695 TCACAGAAAGAG
66 TCACAGAAAGAG
596707 AGATCGACAT
Statistics
Matches: 533, Mismatches: 59, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
124 103 0.19
125 3 0.01
128 1 0.00
130 3 0.01
131 107 0.20
132 3 0.01
133 310 0.58
134 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (131 bp):
TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCGACATCTCGTTCGATTCCA
TCACAGAAAGAGGTGGATCACCTTTTTATTTTCGCTCAAATCCATCGCAAAGGAGTTGGATCAGC
G
Found at i:600134 original size:37 final size:36
Alignment explanation
Indices: 600062--600135 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
600052 TACTATAATT
**
600062 AATTTATATATATTTTTTAAAAATTTAAATTGATAA
1 AATTTATATATATTTTTTAAAAATTTAAAAAGATAA
*
600098 AATTTATATAATTTTTTTTATAAAA-TTAAAAAGATAA
1 AATTTATAT-ATATTTTTTA-AAAATTTAAAAAGATAA
600135 A
1 A
600136 TATGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 9 0.27
37 20 0.61
38 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (36 bp):
AATTTATATATATTTTTTAAAAATTTAAAAAGATAA
Found at i:600924 original size:17 final size:17
Alignment explanation
Indices: 600889--600941 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
600879 TAAGGATATT
* *
600889 TTTAAAATTAATCATAA
1 TTTAAATTTAATTATAA
*
600906 TTTAAATTTAATTAAAA
1 TTTAAATTTAATTATAA
* *
600923 TTTTAATATAATTATAA
1 TTTAAATTTAATTATAA
600940 TT
1 TT
600942 AATTTATAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATTTAATTATAA
Found at i:601763 original size:19 final size:19
Alignment explanation
Indices: 601708--601769 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
601698 CATGAAAATA
* *
601708 TTAATTTTGATACGTAAATT
1 TTAATTTTGAT-CATTAATT
* *
601728 TTAATATTGATCATTAACT
1 TTAATTTTGATCATTAATT
601747 TTAATTTTGATGC-TTAATT
1 TTAATTTTGAT-CATTAATT
601766 TTAA
1 TTAA
601770 CTTGATATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 24 0.69
20 11 0.31
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (19 bp):
TTAATTTTGATCATTAATT
Found at i:602231 original size:24 final size:25
Alignment explanation
Indices: 602203--602254 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
602193 ATATAATGAA
* *
602203 TAAAAT-AAAGTATTAATTGTT-AAT
1 TAAAATCAAAGAATAAATT-TTAAAT
602227 TAAAATCAAAGAATAAATTTTAAAT
1 TAAAATCAAAGAATAAATTTTAAAT
602252 TAA
1 TAA
602255 TTATCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
TAAAATCAAAGAATAAATTTTAAAT
Found at i:602862 original size:31 final size:32
Alignment explanation
Indices: 602806--602865 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
602796 TTAAATTACT
*
602806 TAAATTAATTATTATTTTTAGTAAAAGTATTA
1 TAAATTAATTATTAATTTTAGTAAAAGTATTA
*
602838 TAAATTAATTA-TAATTTTATTAAAAGTA
1 TAAATTAATTATTAATTTTAGTAAAAGTA
602866 AAATTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (32 bp):
TAAATTAATTATTAATTTTAGTAAAAGTATTA
Found at i:602874 original size:32 final size:33
Alignment explanation
Indices: 602805--602875 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
602795 ATTAAATTAC
* **
602805 TTAAATTAATTATTATTTTTAGTAAAAGTATTA
1 TTAAATTAATTATTAATTTTAGTAAAAGTAAAA
*
602838 -TAAATTAATTA-TAATTTTATTAAAAGTAAAA
1 TTAAATTAATTATTAATTTTAGTAAAAGTAAAA
602869 TTAAATT
1 TTAAATT
602876 TTATTTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (33 bp):
TTAAATTAATTATTAATTTTAGTAAAAGTAAAA
Found at i:603730 original size:18 final size:19
Alignment explanation
Indices: 603693--603732 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
603683 GTGACGTCTT
*
603693 AATATTTTGTTGACTGAAA
1 AATATTTTGTTAACTGAAA
*
603712 AATATTTT-TTAATTGAAA
1 AATATTTTGTTAACTGAAA
603730 AAT
1 AAT
603733 GATAAGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (19 bp):
AATATTTTGTTAACTGAAA
Found at i:605559 original size:64 final size:64
Alignment explanation
Indices: 605443--605565 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
605433 TGACCGTAGC
* *
605443 TGTTTCTGTTCTTCAATTATGATTGGATTTACAGTTAAAAAGTTTCTTAGATTGTTGTTATAAT
1 TGTTTCTGTTCTTCAATTATGATTGGATTTACAGTTAAAAAGTTTCTGAGATTGATGTTATAAT
* * *
605507 TGTTTCTGTTCTTCAGTTATGCTTGGATTTACCA-TTAGAAAGTTGT-TGAGATTGATGTT
1 TGTTTCTGTTCTTCAATTATGATTGGATTTA-CAGTTAAAAAGTT-TCTGAGATTGATGTT
605566 CATACTTCGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
64 49 0.94
65 3 0.06
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.49
Consensus pattern (64 bp):
TGTTTCTGTTCTTCAATTATGATTGGATTTACAGTTAAAAAGTTTCTGAGATTGATGTTATAAT
Found at i:605794 original size:21 final size:21
Alignment explanation
Indices: 605769--605819 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
605759 GCTATGTATT
*
605769 GCAGCAACATCAATTTGAACA
1 GCAGCAACATCAATTCGAACA
*
605790 GCAGCAACATCAATTCGAGCA
1 GCAGCAACATCAATTCGAACA
605811 GCAGCAACA
1 GCAGCAACA
605820 GCATCCGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (21 bp):
GCAGCAACATCAATTCGAACA
Found at i:608100 original size:27 final size:27
Alignment explanation
Indices: 608062--608149 Score: 158
Period size: 27 Copynumber: 3.3 Consensus size: 27
608052 AAAATAACCC
608062 AAGCAAAGATGCTTAGATTCTCAACGG
1 AAGCAAAGATGCTTAGATTCTCAACGG
*
608089 AAGCAAAGATGCTTAGATTCTCAATGG
1 AAGCAAAGATGCTTAGATTCTCAACGG
*
608116 AAGCAAAGATGCTTAGATTCTCAGCGG
1 AAGCAAAGATGCTTAGATTCTCAACGG
608143 AAGCAAA
1 AAGCAAA
608150 AACAAGAGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.22
Consensus pattern (27 bp):
AAGCAAAGATGCTTAGATTCTCAACGG
Found at i:609362 original size:95 final size:96
Alignment explanation
Indices: 609208--609390 Score: 287
Period size: 95 Copynumber: 1.9 Consensus size: 96
609198 CGATATTGTA
* * * *
609208 TCAGTAGTATCGGTACTACTACTCTTAAGTAGTATCGATATCATATATGGTATCAGTACCATTTT
1 TCAGAAGTATCGATACTACAACTCTTAAGTAGTATCGATATCATATATGGTATCAGTACCAATTT
*
609273 AGCATTCTGTTTTGACAATATCGGTACTGCC
66 AGCATTATGTTTTGACAATATCGGTACTGCC
* *
609304 TCAGAAGTATCGATACTAGAACTC-TAAGTAGTATCGATATCATATATGGTATCGGTACCAATTT
1 TCAGAAGTATCGATACTACAACTCTTAAGTAGTATCGATATCATATATGGTATCAGTACCAATTT
*
609368 AGCATTATGTTTTGACAGTATCG
66 AGCATTATGTTTTGACAATATCG
609391 ATACCATAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 59 0.75
96 20 0.25
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (96 bp):
TCAGAAGTATCGATACTACAACTCTTAAGTAGTATCGATATCATATATGGTATCAGTACCAATTT
AGCATTATGTTTTGACAATATCGGTACTGCC
Found at i:612559 original size:45 final size:47
Alignment explanation
Indices: 612507--612595 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 47
612497 TCGAATAAAT
612507 GCATGCGAACTAGATATCATGCAGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCAGTTAGGATTTATTTTTGTGAACAA
* *
612552 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCAGTTAGGATTTATTTTTGTGAA
612596 TAACAAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCAGTTAGGATTTATTTTTGTGAACAA
Found at i:622259 original size:18 final size:18
Alignment explanation
Indices: 622232--622359 Score: 58
Period size: 16 Copynumber: 7.2 Consensus size: 18
622222 AAGAAGAAAT
622232 AAAA-GAGAAAAAATGAA
1 AAAATGAGAAAAAATGAA
*
622249 AAAATGAGAAAAAA--CA
1 AAAATGAGAAAAAATGAA
* **
622265 ATAATGATGGAAAAAACAAA
1 AAAATGA--GAAAAAATGAA
* * *
622285 AAGAAAGAAAAAGAAGAAGAA
1 AA-AATGAGAAA-AA-ATGAA
*
622306 AAAATG-GAAAAAGGAAGAA
1 AAAATGAGAAAAA--ATGAA
622325 AAAAT--G-AAAAATGAA
1 AAAATGAGAAAAAATGAA
622340 AAAA-GAG-AAAAATGAA
1 AAAATGAGAAAAAATGAA
622356 AAAA
1 AAAA
622360 AAAAGAAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
15 8 0.09
16 21 0.24
17 8 0.09
18 19 0.21
19 17 0.19
20 7 0.08
21 9 0.10
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAATGAGAAAAAATGAA
Found at i:622270 original size:16 final size:17
Alignment explanation
Indices: 622251--622283 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
622241 AAAATGAAAA
622251 AATGA-GAAAAAACAAT
1 AATGAGGAAAAAACAAT
622267 AATGATGGAAAAAACAA
1 AATGA-GGAAAAAACAA
622284 AAAGAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
18 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.15, T:0.12
Consensus pattern (17 bp):
AATGAGGAAAAAACAAT
Found at i:622294 original size:17 final size:18
Alignment explanation
Indices: 622255--622296 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
622245 TGAAAAAATG
* *
622255 AGAAAAAACAATAATGAT
1 AGAAAAAACAATAAAGAA
*
622273 GGAAAAAACAA-AAAGAA
1 AGAAAAAACAATAAAGAA
622290 AGAAAAA
1 AGAAAAA
622297 GAAGAAGAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.07
Consensus pattern (18 bp):
AGAAAAAACAATAAAGAA
Done.