Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 37
Found at i:3385387 original size:153 final size:153
Alignment explanation
Indices: 3385204--3385530 Score: 627
Period size: 153 Copynumber: 2.1 Consensus size: 153
3385194 TTTCCAGAGA
3385204 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
3385269 CAACCTTTTGCCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAG
66 CAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAG
3385334 AACTCATCTGAAGAAGGAAGAAG
131 AACTCATCTGAAGAAGGAAGAAG
*
3385357 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
3385422 CAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAG
66 CAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAG
3385487 AACTCATCTGAAGAAGGAAGAAG
131 AACTCATCTGAAGAAGGAAGAAG
3385510 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
3385531 TGTTCAACTT
Statistics
Matches: 171, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 171 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (153 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAG
Found at i:3385389 original size:266 final size:266
Alignment explanation
Indices: 3385086--3385647 Score: 912
Period size: 266 Copynumber: 2.1 Consensus size: 266
3385076 CAACATTTCC
3385086 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * * **
3385151 TTGTTCAACTTTTTGCTTGAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATG
66 TTGTTCAACCTTTTACCTGAACCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATG
3385216 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCC
131 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCC
* * * * **
3385281 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
196 TAAATCCATCATTTGATGGATCAACATGGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGA
3385345 AGAAGGA
260 AGAAGGA
3385352 AGA-AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 AGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * *
3385416 TTTGTTCAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAAT
65 CTTGTTCAACCTTTTACCTGAACCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAAT
* *
3385481 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
130 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
3385546 TTAAATTCATCATTTGATGGATCAACATGGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGA
195 CTAAATCCATCATTTGATGGATCAACATGGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGA
3385611 AGAAGGA
260 AGAAGGA
3385618 AGAGAAAGTTCATAATGAGAAGAACTCATC
1 AGAGAAAGTTCATAATGAGAAGAACTCATC
3385648 AAGAGCTTAT
Statistics
Matches: 273, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
265 2 0.01
266 270 0.99
267 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (266 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTACCTGAACCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCC
TAAATCCATCATTTGATGGATCAACATGGCCAGGTAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGA
Found at i:3385474 original size:113 final size:113
Alignment explanation
Indices: 3385357--3385643 Score: 425
Period size: 113 Copynumber: 2.5 Consensus size: 113
3385347 AAGGAAGAAG
*
3385357 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * **
3385422 CAACCTTTTACCTGAACCCATCATTTGGTGGATCATCTTTTCCAGAG-A
66 CAACCTTTTACCTAAACCCATCATTTGATGGATCAACATGGCCAG-GTA
3385470 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *** **
3385535 CAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATGGCCAGGTA
66 CAACCTTTTACCTAAACCCATCATTTGATGGATCAACATGGCCAGGTA
3385583 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGAGAAGAACT
3385644 CATCAAGAGC
Statistics
Matches: 159, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
112 3 0.02
113 156 0.98
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTACCTAAACCCATCATTTGATGGATCAACATGGCCAGGTA
Found at i:3385898 original size:3 final size:3
Alignment explanation
Indices: 3385890--3386011 Score: 158
Period size: 3 Copynumber: 40.7 Consensus size: 3
3385880 TTTTATCCAT
* * * *
3385890 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TCA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3385938 -TA TTA TTA TTA TTA TTTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
3385984 TTA ATA -TA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3386012 TAACAAATAA
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
2 4 0.04
3 96 0.91
4 5 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3387280 original size:19 final size:19
Alignment explanation
Indices: 3387242--3387277 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3387232 CAATTTAGTC
3387242 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
3387261 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
3387278 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:3387352 original size:16 final size:15
Alignment explanation
Indices: 3387331--3387363 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3387321 AAATATTTTG
*
3387331 ATATATAT-TCATAA
1 ATATATATATAATAA
3387345 ATATATATATAATAA
1 ATATATATATAATAA
3387360 ATAT
1 ATAT
3387364 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATAATAA
Found at i:3388251 original size:2 final size:2
Alignment explanation
Indices: 3388244--3388316 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
3388234 AAGAATGAGG
3388244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3388286 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 A
3388317 GTAACCCTGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3393373 original size:21 final size:21
Alignment explanation
Indices: 3393349--3393394 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
3393339 TATCGTAAAT
*
3393349 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGAAAA
3393370 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
3393391 TCGC
1 TCGC
3393395 ACGATTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:3393617 original size:21 final size:21
Alignment explanation
Indices: 3393591--3393767 Score: 144
Period size: 21 Copynumber: 8.6 Consensus size: 21
3393581 GAAATGGAAA
3393591 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
3393612 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
3393633 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
* * *
3393653 ATCGTAACGCAAATTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** * **
3393674 ATCGCAATGCGA-AATGAAAA
1 ATCGCAACGCGATTTTCAACT
3393694 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * **
3393715 ATCGCAACGCGA-AATGAAAA
1 ATCGCAACGCGATTTTCAACT
*
3393735 AACGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
3393756 ATCGCAATGCGA
1 ATCGCAACGCGA
3393768 AATGCAACGT
Statistics
Matches: 115, Mismatches: 38, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
20 42 0.37
21 73 0.63
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:3393662 original size:41 final size:41
Alignment explanation
Indices: 3393612--3393771 Score: 257
Period size: 41 Copynumber: 3.9 Consensus size: 41
3393602 ATTTTCAACT
*
3393612 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
* * * *
3393653 ATCGTAACGCAAATTTCAACTATCGCAATGCGAAATGAAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
3393694 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
* *
3393735 AACGCAACGCGATTTTCAACTATCGCAATGCGAAATG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
3393772 CAACGTGAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGAAAA
Found at i:3393670 original size:62 final size:62
Alignment explanation
Indices: 3393568--3393685 Score: 200
Period size: 62 Copynumber: 1.9 Consensus size: 62
3393558 ACCACTGCAG
* *
3393568 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCAAATTTCAACTATCGCAACGCGATTTTCA
* *
3393630 ACTATCGCAACGCGAAATGGAAAATCGTAACGCAAATTTCAACTATCGCAATGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCAAATTTCAACTATCGCAACGCGA
3393686 AATGAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCAAATTTCAACTATCGCAACGCGATTTTCA
Found at i:3402834 original size:39 final size:39
Alignment explanation
Indices: 3402780--3402857 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
3402770 TTCATGGGGT
*
3402780 ACTGAATAAATATCCTTCATGGTAGAACAAAATCACAGA
1 ACTGAATAAAAATCCTTCATGGTAGAACAAAATCACAGA
* *
3402819 ACTGATTAAAAATCCTTCATGGTAGGACAAAATCACAGA
1 ACTGAATAAAAATCCTTCATGGTAGAACAAAATCACAGA
3402858 TCCGCCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (39 bp):
ACTGAATAAAAATCCTTCATGGTAGAACAAAATCACAGA
Found at i:3408436 original size:19 final size:20
Alignment explanation
Indices: 3408414--3408451 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3408404 ATATTTTTTT
3408414 AAAATATT-TTTAAAAAATA
1 AAAATATTATTTAAAAAATA
*
3408433 AAAATATTATTTTAAAAAT
1 AAAATATTATTTAAAAAAT
3408452 CATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATATTATTTAAAAAATA
Found at i:3408732 original size:18 final size:18
Alignment explanation
Indices: 3408709--3408747 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3408699 GTCGGGTAAC
3408709 GGGTGGACAACGATATGT
1 GGGTGGACAACGATATGT
3408727 GGGTGGACAACGATATGT
1 GGGTGGACAACGATATGT
3408745 GGG
1 GGG
3408748 CGGCCGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.44, T:0.21
Consensus pattern (18 bp):
GGGTGGACAACGATATGT
Found at i:3412301 original size:36 final size:36
Alignment explanation
Indices: 3412254--3412326 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
3412244 TACCATCAGG
3412254 TCAGATGAACACTAAATTATAAATAAAACTTTTTAT
1 TCAGATGAACACTAAATTATAAATAAAACTTTTTAT
3412290 TCAGATGAACACTAAATTATAAATAAAACTTTTTAT
1 TCAGATGAACACTAAATTATAAATAAAACTTTTTAT
3412326 T
1 T
3412327 TGGAAATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (36 bp):
TCAGATGAACACTAAATTATAAATAAAACTTTTTAT
Found at i:3415397 original size:23 final size:23
Alignment explanation
Indices: 3415346--3415398 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3415336 AAAATAATTT
* *
3415346 TGTCTTTGTGATATGTTTATCTA
1 TGTCTTTATGATACGTTTATCTA
* * *
3415369 TATCTTTATGATACGTTTTTCTC
1 TGTCTTTATGATACGTTTATCTA
3415392 TGTCTTT
1 TGTCTTT
3415399 GTGGTATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (23 bp):
TGTCTTTATGATACGTTTATCTA
Found at i:3419447 original size:7 final size:7
Alignment explanation
Indices: 3419435--3419464 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3419425 GAGTGGGATG
3419435 AGGTTTT
1 AGGTTTT
3419442 AGGTTTT
1 AGGTTTT
3419449 AGGTTTT
1 AGGTTTT
*
3419456 AGGTCTT
1 AGGTTTT
3419463 AG
1 AG
3419465 TTAAGTTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.30, T:0.50
Consensus pattern (7 bp):
AGGTTTT
Found at i:3423451 original size:249 final size:249
Alignment explanation
Indices: 3423010--3423510 Score: 858
Period size: 249 Copynumber: 2.0 Consensus size: 249
3423000 TACTTTTAGC
*
3423010 TTGGAAGTCAAGTATATTCTCGTAAATGTCTCTATCATTTCTCCAAGAATGCATCAATAAATTTG
1 TTGGAAGTCAAGTATATTATCGTAAATGTCTCTATCATTTCTCCAAGAATGCATCAATAAATTTG
* * **
3423075 GGAAATCCGGATGATCACTCCAAGCATCAATGTATCGAAAAGGTCGATTATGAGAAGTCTCCTGT
66 GGAAATCCGGATGATCACTCCAAGCATCAATGTATCGAAAAGATCGATTATGAGAAGTCTCATAC
* * * *
3423140 TGGTCCCCAAACTTAAGGAGAATGGATCGATGATCCGAATCCAATTTTTAGAGATGAAAGACTTC
131 TGGTCCCCAAACTTAAGAAGAATAGATCGATGATCCGAACCCAATTTTTAGAGATAAAAGACTTC
* *
3423205 TGGATTTTCAAAATAATCATACCACTCAGTATTGCAAATACACCTATTCAACTG
196 TGAATTTTCAAAATAATCATACCACTCAGTATTGCAAATACACCTATTCAACCG
*
3423259 TTGGAAGTCAAGTATATTATCGTAAATGTCTCTATCATTTCTCCAAGAATGCATCAGTAAATTTG
1 TTGGAAGTCAAGTATATTATCGTAAATGTCTCTATCATTTCTCCAAGAATGCATCAATAAATTTG
3423324 GGAAATCCGGATGATCACTCCAAGCATCAATGTATCGAAAAGATCGATTATGAGAAGTCTCATAC
66 GGAAATCCGGATGATCACTCCAAGCATCAATGTATCGAAAAGATCGATTATGAGAAGTCTCATAC
* * *
3423389 TGGTCCCCAAACTTAAGAAGAATAGATCGATTATCTGAACCCAATTTTTGGAGATAAAAGACTTC
131 TGGTCCCCAAACTTAAGAAGAATAGATCGATGATCCGAACCCAATTTTTAGAGATAAAAGACTTC
*
3423454 TGAATTTTCAAAATAATCATATCACTCAGTATTGCAAATACACCTATTCAACCG
196 TGAATTTTCAAAATAATCATACCACTCAGTATTGCAAATACACCTATTCAACCG
3423508 TTG
1 TTG
3423511 AGAAAGAGTT
Statistics
Matches: 236, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
249 236 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (249 bp):
TTGGAAGTCAAGTATATTATCGTAAATGTCTCTATCATTTCTCCAAGAATGCATCAATAAATTTG
GGAAATCCGGATGATCACTCCAAGCATCAATGTATCGAAAAGATCGATTATGAGAAGTCTCATAC
TGGTCCCCAAACTTAAGAAGAATAGATCGATGATCCGAACCCAATTTTTAGAGATAAAAGACTTC
TGAATTTTCAAAATAATCATACCACTCAGTATTGCAAATACACCTATTCAACCG
Found at i:3430616 original size:32 final size:33
Alignment explanation
Indices: 3430552--3430614 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
3430542 ATTACTCTTA
3430552 ATTTAGTTGATAATCTTTGTTATAGGAATTTTG
1 ATTTAGTTGATAATCTTTGTTATAGGAATTTTG
3430585 ATTT-GTTGATAATCTTTGTTA-AGGAATTTT
1 ATTTAGTTGATAATCTTTGTTATAGGAATTTT
3430615 TGCATATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 9 0.30
32 17 0.57
33 4 0.13
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.52
Consensus pattern (33 bp):
ATTTAGTTGATAATCTTTGTTATAGGAATTTTG
Found at i:3435921 original size:21 final size:22
Alignment explanation
Indices: 3435880--3435941 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
3435870 GACAAAAAGG
* *
3435880 TGTCACAAAGATATAAGAAA-ACA
1 TGTCACAAA-A-ATAAAAAATAAA
3435903 TGTCACAAAAATAAAAAAATAAA
1 TGTCACAAAAAT-AAAAAATAAA
*
3435926 TATCACAAAAATAAAA
1 TGTCACAAAAATAAAA
3435942 TTATTCTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 10 0.29
23 22 0.65
ACGTcount: A:0.65, C:0.11, G:0.06, T:0.18
Consensus pattern (22 bp):
TGTCACAAAAATAAAAAATAAA
Found at i:3442730 original size:23 final size:23
Alignment explanation
Indices: 3442704--3442751 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3442694 ATAAAGTACA
*
3442704 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
3442727 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
3442750 AT
1 AT
3442752 TTACCTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:3443211 original size:23 final size:23
Alignment explanation
Indices: 3443185--3443243 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
3443175 AACCACTACC
3443185 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
3443208 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
3443231 TATTACATCATAT
1 TATTACATTATAT
3443244 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:3443411 original size:434 final size:434
Alignment explanation
Indices: 3442825--3443884 Score: 2024
Period size: 434 Copynumber: 2.5 Consensus size: 434
3442815 TTATAATATG
*
3442825 TTGAAAGTGTCCATAATTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
*
3442890 TCAA-TTTTTTGAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
3442954 CAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACAT
131 CAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACAT
3443019 TAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTA
196 TAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTA
3443084 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTA
261 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTA
3443149 TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTAC
326 TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTAC
3443214 ATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 ATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
3443258 TTTAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
3443323 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
3443388 CAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACAT
131 CAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACAT
3443453 TAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTA
196 TAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTA
3443518 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTA
261 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTA
*
3443583 TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTAC
326 TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTAC
3443648 ATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 ATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
3443692 TTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
3443757 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTAC---A--AATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
*
3443817 CAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAAATTTTAATTTAACAACAT
131 CAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACAT
3443882 TAA
196 TAA
3443885 CCAAAGATAA
Statistics
Matches: 619, Mismatches: 7, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
429 88 0.14
431 1 0.00
433 67 0.11
434 463 0.75
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41
Consensus pattern (434 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAACAACAT
TAAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCTTA
AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTA
TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTAC
ATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:3443641 original size:23 final size:23
Alignment explanation
Indices: 3443615--3443677 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
3443605 ATATAACCAC
3443615 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
3443638 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
3443661 TACCTATTACATCATAT
1 TACCTATTACATTATAT
3443678 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:3444146 original size:39 final size:39
Alignment explanation
Indices: 3444092--3444177 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
3444082 CAAGTTGTAG
*
3444092 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
3444131 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
3444170 ATTTTGAT
1 ATTTTGAT
3444178 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:3447737 original size:183 final size:183
Alignment explanation
Indices: 3447429--3448238 Score: 1458
Period size: 183 Copynumber: 4.4 Consensus size: 183
3447419 CGACACATTT
* * *
3447429 TAGGTTGTAGACATATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
*
3447494 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTAGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
3447559 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
*
3447612 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
3447677 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
3447742 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
*
3447795 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCTGTTATATTACAAAATTATCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
3447860 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
3447925 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
* * *
3447978 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCGGTTATATTGCAAATTTACCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
**
3448043 ATTTTATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
66 ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
3448108 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
131 TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
* * * * *
3448161 TAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATTTACCT
1 TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
**
3448226 ATTTTATTATAAT
66 ATTACATTATAAT
3448239 ATGTTGAAAG
Statistics
Matches: 614, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 614 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
TAGGTTGTAGACCTATTCGCTCATACAACCGGTATATTTATACCGGTTATATTACAAAATTATCT
ATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACAT
TTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATA
Found at i:3449716 original size:3 final size:3
Alignment explanation
Indices: 3449708--3449782 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
3449698 ACTTGTTTGG
* * * ** * *
3449708 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
3449756 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
3449783 GTCAACTTCA
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:3449725 original size:12 final size:12
Alignment explanation
Indices: 3449712--3449792 Score: 90
Period size: 12 Copynumber: 6.8 Consensus size: 12
3449702 GTTTGGATCA
*
3449712 TCATCTTCATCA
1 TCATCTTCATCG
* * *
3449724 TCATCATCGTCA
1 TCATCTTCATCG
3449736 TCATCTTCATCG
1 TCATCTTCATCG
* *
3449748 CCAGCTTCATCG
1 TCATCTTCATCG
*
3449760 TCATCATCATCG
1 TCATCTTCATCG
3449772 TCATCTTCATCG
1 TCATCTTCATCG
*
3449784 TCAACTTCA
1 TCATCTTCA
3449793 CCTTCTGCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:3449756 original size:36 final size:36
Alignment explanation
Indices: 3449716--3449792 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
3449706 GGATCATCAT
* *
3449716 CTTCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAA
* * *
3449752 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAA
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAA
3449788 CTTCA
1 CTTCA
3449793 CCTTCTGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAA
Found at i:3451836 original size:198 final size:199
Alignment explanation
Indices: 3451257--3453136 Score: 3630
Period size: 199 Copynumber: 9.5 Consensus size: 199
3451247 TTTAAATTAG
3451257 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3451322 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3451387 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3451452 AAAA
196 AAAA
3451456 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
3451521 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3451586 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3451650 AAAA
196 AAAA
3451654 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
3451718 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3451783 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3451848 AAAA
196 AAAA
3451852 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
3451917 ATTGTACCGGTTATATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
3451982 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
3452047 AAAAA
195 AAAAA
3452052 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3452117 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452181 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3452246 AAAA
196 AAAA
3452250 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
3452315 ACTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452380 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3452444 AAAA
196 AAAA
3452448 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3452513 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452578 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3452642 AAAA
196 AAAA
*
3452646 TATCGACACAAACTATATTAGTATCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3452711 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452776 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
3452840 AAAAA
195 AAAAA
3452845 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
3452910 ATTGTACCGGTTAGATTGAAAAATTACATATTATATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452974 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3453039 AAAA
196 AAAA
3453043 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3453108 ATTGTACCGGTTAGATTGAAAAATTACAT
66 ATTGTACCGGTTAGATTGAAAAATTACAT
3453137 CCTTTTGGCC
Statistics
Matches: 1662, Mismatches: 11, Indels: 17
0.98 0.01 0.01
Matches are distributed among these distances:
197 215 0.13
198 655 0.39
199 664 0.40
200 128 0.08
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:3451990 original size:396 final size:398
Alignment explanation
Indices: 3451257--3453136 Score: 3639
Period size: 396 Copynumber: 4.7 Consensus size: 398
3451247 TTTAAATTAG
3451257 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3451322 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3451387 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3451452 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
*
3451517 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
3451582 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGA
3451646 AAAAAAAA
391 AAAAAAAA
3451654 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
3451718 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCAATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3451783 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3451848 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
*
3451913 TATAATTGTACCGGTTATATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
3451978 GGATCGACACTTTTTATATATGGATCGACACTTTATGGATGCACCCTGTTTTCCATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGG-TGCACCCTGTTTTCCATTCATTCTGG
3452043 AAAAAAAAA
390 AAAAAAAAA
3452052 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3452117 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452181 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3452246 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
*
3452311 TATAACTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
3452376 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-
326 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGA
3452440 AAAAAAAA
391 AAAAAAAA
3452448 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
3452513 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452578 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
3452642 AAAATATCGACACAAACTATATTAGTATCGACACATTATTTAGACATATTCTCACATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
3452707 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
261 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
3452772 GGATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
326 GGATCGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGG
3452836 AAAAAAAAA
390 AAAAAAAAA
3452845 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
3452910 ATTGTACCGGTTAGATTGAAAAATTACATATTATATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
3452974 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
3453039 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
196 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
3453104 TATAATTGTACCGGTTAGATTGAAAAATTACAT
261 TATAATTGTACCGGTTAGATTGAAAAATTACAT
3453137 CCTTTTGGCC
Statistics
Matches: 1466, Mismatches: 10, Indels: 14
0.98 0.01 0.01
Matches are distributed among these distances:
395 25 0.02
396 726 0.50
397 349 0.24
398 247 0.17
399 119 0.08
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (398 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGA
AAAAAAAA
Found at i:3453292 original size:19 final size:18
Alignment explanation
Indices: 3453261--3453308 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
3453251 TTATATTCAC
3453261 ATACGAAAA-TATAAATCGT
1 ATAC-AAAATTAT-AATCGT
*
3453280 ATACAAAATTATAATCTT
1 ATACAAAATTATAATCGT
3453298 ATACAAAATTA
1 ATACAAAATTA
3453309 ACCTACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:3455129 original size:32 final size:32
Alignment explanation
Indices: 3455093--3455156 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
3455083 CATCTTAATA
*
3455093 TCACCCCTTAACACCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCAACTTCTTTCACCACT
* *
3455125 TCACCCCTCAACACTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCAACTTCTTTCACCACT
3455157 CCATCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (32 bp):
TCACCCCTCAACACCCAACTTCTTTCACCACT
Found at i:3455230 original size:21 final size:21
Alignment explanation
Indices: 3455190--3455254 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3455180 CCCCTTATGC
* *
3455190 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
3455211 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
3455232 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
3455253 CT
1 CT
3455255 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:3457494 original size:17 final size:18
Alignment explanation
Indices: 3457472--3457514 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
3457462 ATATATCCGG
3457472 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
3457489 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
3457509 TATCAT
1 TATCAT
3457515 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:3457523 original size:20 final size:19
Alignment explanation
Indices: 3457477--3457523 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
3457467 TCCGGTATCA
3457477 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
3457496 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
3457517 TTTTACC
1 TTTTACC
3457524 TGTTATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:3457671 original size:20 final size:20
Alignment explanation
Indices: 3457645--3457690 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
3457635 CACTTTTAAA
3457645 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
3457664 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
3457685 TTTACC
1 TTTACC
3457691 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:3462161 original size:6 final size:6
Alignment explanation
Indices: 3462146--3462182 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
3462136 TCCTATACTA
*
3462146 GTGCTC GTGCTT GTGCTT GTGCTT GTGCTT GTGCTT G
1 GTGCTT GTGCTT GTGCTT GTGCTT GTGCTT GTGCTT G
3462183 AGAGTCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.19, G:0.35, T:0.46
Consensus pattern (6 bp):
GTGCTT
Found at i:3466972 original size:20 final size:20
Alignment explanation
Indices: 3466947--3467016 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
3466937 TCTACAGTGT
3466947 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * * *
3466967 CGTTGCAATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
3466987 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
3467008 CGTTGCGAT
1 CGTTGCGAT
3467017 AGTTGAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
19 4 0.11
20 19 0.51
21 10 0.27
22 4 0.11
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:3466979 original size:41 final size:41
Alignment explanation
Indices: 3466926--3467208 Score: 258
Period size: 41 Copynumber: 6.9 Consensus size: 41
3466916 TCTACAGTGT
3466926 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
*
3466967 CGTTGCAATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
* * * * *
3467008 CGTTGCGATAGT-TGAAAAT-TGCGTTGCGATAGTGTACA-GT-G
1 CGTTGCGATAGTCT-ACAGTGT-CGTTGCGAT--TTTCCATTTCG
* * * * *** *
3467049 TCATTGCGAT--TTTCCA-TTTCGCGTTGCGATAGTTGAAAATT-G
1 -CGTTGCGATAGTCTACAGTGT--CGTTGCGAT--TTTCCATTTCG
* * *
3467091 CGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATCTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
* *
3467132 CATTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
3467173 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCA
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCA
3467209 AATTCGTCGC
Statistics
Matches: 200, Mismatches: 29, Indels: 26
0.78 0.11 0.10
Matches are distributed among these distances:
39 1 0.00
40 9 0.05
41 161 0.81
42 19 0.09
43 8 0.04
44 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:3467033 original size:103 final size:101
Alignment explanation
Indices: 3466926--3467208 Score: 338
Period size: 103 Copynumber: 2.8 Consensus size: 101
3466916 TCTACAGTGT
* *
3466926 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCAATAGTCTACAGTGTCGT
1 CGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGT
* * * *
3466991 TGCGATTTTCCA-TTTCGCGTTGCGATAGTTGAAAATTG
66 TGCGATTTTCCAGTGT--CATTGCGAT-GTTCAAAATCG
* * *
3467029 CGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAAT-TGC
1 CGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTGT-C
* * * * **
3467092 GTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATCTCG
64 GTTGCGAT--TTTCCAGTGTCATTGCGATGTTCAAAATCG
*
3467132 CATTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGT
1 CGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGT
3467197 TGCGATTTTCCA
66 TGCGATTTTCCA
3467209 AATTCGTCGC
Statistics
Matches: 152, Mismatches: 21, Indels: 16
0.80 0.11 0.08
Matches are distributed among these distances:
101 4 0.03
102 2 0.01
103 130 0.86
104 10 0.07
105 4 0.03
106 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.37
Consensus pattern (101 bp):
CGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGT
TGCGATTTTCCAGTGTCATTGCGATGTTCAAAATCG
Found at i:3467161 original size:62 final size:62
Alignment explanation
Indices: 3466877--3467143 Score: 317
Period size: 62 Copynumber: 4.3 Consensus size: 62
3466867 ATTCGCGTTG
* * * * * * *
3466877 CATTTCGCGTTGCAATAGTTGAAAATCGTGTTGCGATAGTCTACAGTGTCGTTGCGATAGTCTA
1 CATTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATAGTGTACAGTGTCATTGCGAT--TTTC
* *** * * * *
3466941 CA-GT-GTCGTTGCGAT--TTTCCATTTCGCGTTGCAATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCG-CGTTGCGATAGTTGAAAATT-GCGTTGCGATAGTGTACAGTGTCATTGCGATTTTC
3467001 CATTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATAGTGTACAGTGTCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATAGTGTACAGTGTCATTGCGATTTTC
3467063 CATTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATAGTGTACAGTGTCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATAGTGTACAGTGTCATTGCGATTTTC
* *
3467125 CATCTCGCATTGCGATAGT
1 CATTTCGCGTTGCGATAGT
3467144 GTACAGTGTC
Statistics
Matches: 176, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
60 4 0.02
61 14 0.08
62 142 0.81
63 14 0.08
64 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (62 bp):
CATTTCGCGTTGCGATAGTTGAAAATTGCGTTGCGATAGTGTACAGTGTCATTGCGATTTTC
Found at i:3468352 original size:30 final size:30
Alignment explanation
Indices: 3468316--3468379 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
3468306 CACCCCGCAT
* *
3468316 CCGCACCGCATCCACCCGA-TCCTCATCCGC
1 CCGCACCGCATCCACCC-ACCCCACATCCGC
3468346 CCGCACCGCATCCACCCACCCCACATCCGC
1 CCGCACCGCATCCACCCACCCCACATCCGC
3468376 CCGC
1 CCGC
3468380 CCAACTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.17, C:0.61, G:0.12, T:0.09
Consensus pattern (30 bp):
CCGCACCGCATCCACCCACCCCACATCCGC
Found at i:3468357 original size:15 final size:15
Alignment explanation
Indices: 3468316--3468362 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3468306 CACCCCGCAT
3468316 CCGCACCGCATCCAC
1 CCGCACCGCATCCAC
* *
3468331 CCG-ATCCTCATCCGC
1 CCGCA-CCGCATCCAC
3468346 CCGCACCGCATCCAC
1 CCGCACCGCATCCAC
3468361 CC
1 CC
3468363 ACCCCACATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.92
16 1 0.04
ACGTcount: A:0.17, C:0.60, G:0.13, T:0.11
Consensus pattern (15 bp):
CCGCACCGCATCCAC
Found at i:3471054 original size:2 final size:2
Alignment explanation
Indices: 3471047--3471083 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3471037 TGTTTAAATT
3471047 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3471084 TTTAAATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3471894 original size:43 final size:43
Alignment explanation
Indices: 3471837--3472019 Score: 222
Period size: 43 Copynumber: 4.3 Consensus size: 43
3471827 TGGTAACAAA
*** *
3471837 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * *
3471880 AAATGCCGCAATAGGTGTTGATATTTGGCGGCATTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * *
3471923 AAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* * * * *
3471966 AAACACCGCAATAGGTCTTGAGATTTAGCGACGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
*
3472009 AAACACCGCAA
1 AAACGCCGCAA
3472020 AAGATATGGT
Statistics
Matches: 125, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 125 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
Found at i:3472046 original size:43 final size:43
Alignment explanation
Indices: 3471913--3472045 Score: 117
Period size: 43 Copynumber: 3.1 Consensus size: 43
3471903 TTTGGCGGCA
* * * * ** * *
3471913 TTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGACG
1 TTTTTCCCACAAACACCGCAAAAGATCATGAGATATAACGACG
* * * * *
3471956 TTTTTCCCACAAACACCGCAATAGGTCTTGAGATTTAGCGACG
1 TTTTTCCCACAAACACCGCAAAAGATCATGAGATATAACGACG
*
3471999 TTTTTCCCACAAACACCGCAAAAGAT-ATG-GTATATAACGGCG
1 TTTTTCCCACAAACACCGCAAAAGATCATGAG-ATATAACGACG
3472041 TTTTT
1 TTTTT
3472046 TAGAACAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
41 1 0.01
42 15 0.19
43 64 0.80
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
TTTTTCCCACAAACACCGCAAAAGATCATGAGATATAACGACG
Found at i:3472046 original size:86 final size:87
Alignment explanation
Indices: 3471858--3472045 Score: 211
Period size: 86 Copynumber: 2.2 Consensus size: 87
3471848 TAGGTAACGA
** * * * *
3471858 TATATAGCGGCGTTTTTCCAACAAATGCCGCAATAGGTGTTGATATTTGGCGGCATTTTTCCAAC
1 TATATAGCGGCGTTTTTCCAACAAACACCGCAATAGGTCTTGAGATTTAGCGACATTTTTCCAAC
* * * *
3471923 AAACGCCGCAATAGGTGTTGAG
66 AAACACCGCAAAAGATGATGAG
* * * * *
3471945 -ATTTAGCGACGTTTTTCCCACAAACACCGCAATAGGTCTTGAGATTTAGCGACGTTTTTCCCAC
1 TATATAGCGGCGTTTTTCCAACAAACACCGCAATAGGTCTTGAGATTTAGCGACATTTTTCCAAC
3472009 AAACACCGCAAAAGAT-ATG-G
66 AAACACCGCAAAAGATGATGAG
*
3472029 TATATAACGGCGTTTTT
1 TATATAGCGGCGTTTTT
3472046 TAGAACAAAC
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
84 1 0.01
85 15 0.18
86 66 0.80
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (87 bp):
TATATAGCGGCGTTTTTCCAACAAACACCGCAATAGGTCTTGAGATTTAGCGACATTTTTCCAAC
AAACACCGCAAAAGATGATGAG
Found at i:3472239 original size:21 final size:21
Alignment explanation
Indices: 3472215--3472273 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3472205 ATTTTCCAAT
*
3472215 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
3472236 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
3472257 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
3472274 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:3475515 original size:41 final size:41
Alignment explanation
Indices: 3475449--3475957 Score: 500
Period size: 41 Copynumber: 12.3 Consensus size: 41
3475439 TTGTAAACTT
* * * * *
3475449 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* * *
3475492 GCGGCATTTGAATAAAAATGCCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
3475533 ACGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
3475574 GTGGCGTTTGTATAAAAATGCCACTAAATTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * * * *
3475615 GTGACGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* * * *
3475658 ACGGCGTTTGAATAAAAATGCCACTAAAGTACGTGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
3475699 GCAGAGTTTGTATAAAAAACACCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTAT-AAAAACGCCACTAAAGTACGAGTCTTTA
* * *
3475741 GCGGCGTTTGTATAAAAACGCCCCT-AATTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
3475781 GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGA-GTCTTTA
* ** * *
3475824 ACGGCGTTTGTATAAAAACGCCACTAAAGTATAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
3475865 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * *
3475906 GCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
3475947 GCGGCGTTTGT
1 GCGGCGTTTGT
3475958 TGAAAAAATG
Statistics
Matches: 381, Mismatches: 77, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
40 27 0.07
41 245 0.64
42 50 0.13
43 59 0.15
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:3475686 original size:125 final size:124
Alignment explanation
Indices: 3475449--3475973 Score: 506
Period size: 125 Copynumber: 4.2 Consensus size: 124
3475439 TTGTAAACTT
* ** * * * * *
3475449 GCGGCGTTTGTA-AACACAAACGCCACTATAGTACAAGTGTATAGCGGCATTTGAATAAAAATGC
1 GCGGCGTTTGTATAA-A-AAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGC
* * * *
3475513 CACTAAAGTACGAGTCTTTAACGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTA
64 CACTAAAGTACGAGTCTTTAACGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * * *
3475574 GTGGCGTTTGTAT-AAAAATGCCACTAAATTATGAGTCTTTAGTGACGTTTGTAAACACAAACGC
1 GCGGCGTTTGTATAAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATA-A-AAACGC
* * * * * *
3475638 CACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTAAAGTACGTGTCTTTA
64 CACTAAAGTACGAGTCTTTAACGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
3475699 GCAGAGTTTGTATAAAAAACACCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCC
1 GCGGCGTTTGTATAAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCA
* * * * * *
3475764 CT-AATTATGAGTCTTTAGCGGCGTTTGTAA-ACACAAACGCCACTATAGTAC-ATGTGTATA
66 CTAAAGTACGAGTCTTTAACGGCGTTTG-AATA-A-AAACGCCACTAAAGTACGA-GTCTTTA
* * * * *
3475824 ACGGCGTTTGTAT-AAAAACGCCACTAAAGTATAATTCTATAGCGGCGTTTGTATAAAAATGCCA
1 GCGGCGTTTGTATAAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCA
* * * * * *
3475888 CTAAATTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
66 CTAAAGTACGAGTCTTTAACGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTA
*
3475947 GCGGCGTTTGT-TGAAAAAATGCCACTA
1 GCGGCGTTTGTAT-AAAAAACGCCACTA
3475974 TCGATGAACC
Statistics
Matches: 325, Mismatches: 62, Indels: 27
0.79 0.15 0.07
Matches are distributed among these distances:
122 1 0.00
123 76 0.23
124 76 0.23
125 136 0.42
126 36 0.11
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (124 bp):
GCGGCGTTTGTATAAAAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTACGAGTCTTTAACGGCGTTTGAATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:3475772 original size:166 final size:165
Alignment explanation
Indices: 3475453--3475932 Score: 719
Period size: 166 Copynumber: 2.9 Consensus size: 165
3475443 AAACTTGCGG
* *
3475453 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAGCGGCATTTGAATAAAAATGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
* * * * *
3475518 AAGTACGAGTCTTTAACGGCGTTTGTATAAAAATGTCAATAAAGTACGAGTCTTTAGTGGCGTTT
66 AAGTACGTGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTT
* *
3475583 GTATAAAAATGCCACTAAATTATGAGTCTTTAGTGA
131 GTATAAAAACGCCACT-AATTATGAGTCTTTAGCGA
3475619 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
* * ** *
3475684 AAGTACGTGTCTTTAGCAGAGTTTGTATAAAAAACACCACTAAAGTATGAGTCTTTAGCGGCGTT
66 AAGTACGTGTCTTTAGCGGCGTTTGTAT-AAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTT
* *
3475749 TGTATAAAAACGCCCCTAATTATGAGTCTTTAGCGG
130 TGTATAAAAACGCCACTAATTATGAGTCTTTAGCGA
* * *
3475785 CGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAACGCCACTA
1 CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
** * *
3475850 AAGTATAAT-TCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTAGCGGCGTT
66 AAGTA-CGTGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTT
3475914 TGTATAAAAACGCCACTAA
130 TGTATAAAAACGCCACTAA
3475933 AGTACTACTC
Statistics
Matches: 283, Mismatches: 29, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
165 50 0.18
166 187 0.66
167 46 0.16
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (165 bp):
CGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCCACTA
AAGTACGTGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCGTTT
GTATAAAAACGCCACTAATTATGAGTCTTTAGCGA
Found at i:3477786 original size:15 final size:15
Alignment explanation
Indices: 3477766--3477804 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3477756 TATAATTAAT
*
3477766 AATAAAAATGAAAAA
1 AATAAAAATCAAAAA
* *
3477781 AATAAAATTCAAATA
1 AATAAAAATCAAAAA
3477796 AATAAAAAT
1 AATAAAAAT
3477805 TTAAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAAAAATCAAAAA
Found at i:3479468 original size:31 final size:30
Alignment explanation
Indices: 3479425--3479514 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 30
3479415 CACTACAATG
3479425 GTTGAGGGACTAAAATTGAATGAAATTAACA
1 GTTGA-GGACTAAAATTGAATGAAATTAACA
3479456 GTTGAGGAACTAAAATTGAATGAAATTAACA
1 GTTGAGG-ACTAAAATTGAATGAAATTAACA
* * *
3479487 ATTGATGGATTAAAACTGAATG-AATTAA
1 GTTGA-GGACTAAAATTGAATGAAATTAA
3479515 TAATATTAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
30 8 0.15
31 44 0.81
32 2 0.04
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.28
Consensus pattern (30 bp):
GTTGAGGACTAAAATTGAATGAAATTAACA
Found at i:3479491 original size:17 final size:17
Alignment explanation
Indices: 3479438--3479491 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
3479428 GAGGGACTAA
3479438 AATTGAATGAAATTAAC
1 AATTGAATGAAATTAAC
* * *
3479455 AGTTG-A-GGAACTAA-
1 AATTGAATGAAATTAAC
3479469 AATTGAATGAAATTAAC
1 AATTGAATGAAATTAAC
3479486 AATTGA
1 AATTGA
3479492 TGGATTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 4 0.14
15 7 0.25
16 7 0.25
17 10 0.36
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (17 bp):
AATTGAATGAAATTAAC
Found at i:3479513 original size:15 final size:15
Alignment explanation
Indices: 3479435--3479514 Score: 65
Period size: 15 Copynumber: 5.2 Consensus size: 15
3479425 GTTGAGGGAC
3479435 TAAAATTGAATGAAAT
1 TAAAATTGAATG-AAT
* * *
3479451 TAACAGTTG-AGGAAC
1 TAA-AATTGAATGAAT
3479466 TAAAATTGAATGAAAT
1 TAAAATTGAATG-AAT
*
3479482 TAACAATTG-ATGGAT
1 TAA-AATTGAATGAAT
*
3479497 TAAAACTGAATGAAT
1 TAAAATTGAATGAAT
3479512 TAA
1 TAA
3479515 TAATATTAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
14 8 0.16
15 20 0.40
16 13 0.26
17 9 0.18
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (15 bp):
TAAAATTGAATGAAT
Found at i:3479528 original size:31 final size:31
Alignment explanation
Indices: 3479426--3479532 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
3479416 ACTACAATGG
* * * *
3479426 TTGAGGGACTAAAATTGAATGAAATTAACAG
1 TTGAAGGATTAAAACTGAATGAAATTAACAA
* *
3479457 TTG-AGGAACTAAAATTGAATGAAATTAACAA
1 TTGAAGG-ATTAAAACTGAATGAAATTAACAA
* *
3479488 TTGATGGATTAAAACTGAATG-AATTAATAA
1 TTGAAGGATTAAAACTGAATGAAATTAACAA
*
3479518 TATTAAGGATTAAAA
1 T-TGAAGGATTAAAA
3479533 TCGTATAGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.17
31 52 0.80
32 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.29
Consensus pattern (31 bp):
TTGAAGGATTAAAACTGAATGAAATTAACAA
Found at i:3486363 original size:21 final size:20
Alignment explanation
Indices: 3486339--3486480 Score: 124
Period size: 21 Copynumber: 6.8 Consensus size: 20
3486329 TTTTGTAATG
*
3486339 AACCTTAAATCCTAAACTATA
1 AACCTTAAACCCTAAAC-ATA
*
3486360 AACCTTAAACCCTAAATTATA
1 AACCTTAAACCCTAAA-CATA
**
3486381 AA-CTCTAAACTTTAAATCATA
1 AACCT-TAAACCCTAAA-CATA
* * *
3486402 AACCTTAAGCCATCAACACTA
1 AACCTTAAACCCTAAACA-TA
*
3486423 AACCTTAAACCATAAAGCATA
1 AACCTTAAACCCTAAA-CATA
*
3486444 AACCATAAACCCTAAAACATA
1 AACCTTAAACCCT-AAACATA
*
3486465 AACCCTAAACCCTAAA
1 AACCTTAAACCCTAAA
3486481 TTCTAAAACA
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
20 7 0.07
21 87 0.86
22 7 0.07
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (20 bp):
AACCTTAAACCCTAAACATA
Found at i:3486433 original size:7 final size:7
Alignment explanation
Indices: 3486339--3486480 Score: 51
Period size: 7 Copynumber: 20.3 Consensus size: 7
3486329 TTTTGTAATG
3486339 AACCTTA
1 AACCTTA
3486346 AATCC-TA
1 AA-CCTTA
3486353 AA-CTATA
1 AACCT-TA
3486360 AACCTTA
1 AACCTTA
*
3486367 AACCCTA
1 AACCTTA
3486374 AA--TTA
1 AACCTTA
*
3486379 TAAACTCTA
1 -AACCT-TA
*
3486388 AACTTTA
1 AACCTTA
* *
3486395 AATCATA
1 AACCTTA
3486402 AACCTTA
1 AACCTTA
* * *
3486409 AGCCATC
1 AACCTTA
3486416 AACAC-TA
1 AAC-CTTA
3486423 AACCTTA
1 AACCTTA
*
3486430 AACCATA
1 AACCTTA
* *
3486437 AAGCATA
1 AACCTTA
*
3486444 AACCATA
1 AACCTTA
*
3486451 AACCCTA
1 AACCTTA
* *
3486458 AAACATA
1 AACCTTA
*
3486465 AACCCTA
1 AACCTTA
*
3486472 AACCCTA
1 AACCTTA
3486479 AA
1 AA
3486481 TTCTAAAACA
Statistics
Matches: 103, Mismatches: 22, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
5 3 0.03
6 3 0.03
7 86 0.83
8 9 0.09
9 2 0.02
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (7 bp):
AACCTTA
Found at i:3486445 original size:14 final size:14
Alignment explanation
Indices: 3486358--3486480 Score: 77
Period size: 14 Copynumber: 8.8 Consensus size: 14
3486348 TCCTAAACTA
*
3486358 TAAACCTTAAACCC
1 TAAACCATAAACCC
** *
3486372 TAAATTATAAACTC
1 TAAACCATAAACCC
** * *
3486386 TAAACTTTAAATCA
1 TAAACCATAAACCC
* * *
3486400 TAAACCTTAAGCCA
1 TAAACCATAAACCC
* *
3486414 TCAA-CACTAAACCT
1 TAAACCA-TAAACCC
* *
3486428 TAAACCATAAAGCA
1 TAAACCATAAACCC
3486442 TAAACCATAAACCC
1 TAAACCATAAACCC
*
3486456 TAAAACATAAACCC
1 TAAACCATAAACCC
*
3486470 TAAACCCTAAA
1 TAAACCATAAA
3486481 TTCTAAAACA
Statistics
Matches: 83, Mismatches: 24, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
13 1 0.01
14 80 0.96
15 2 0.02
ACGTcount: A:0.50, C:0.27, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:3487256 original size:11 final size:11
Alignment explanation
Indices: 3487240--3487315 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
3487230 GCCGTATGGT
3487240 TCGAGCTTGAA
1 TCGAGCTTGAA
**
3487251 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
3487263 TTGAGCTTGAA
1 TCGAGCTTGAA
*
3487274 TCGAGCTTAAA
1 TCGAGCTTGAA
* * *
3487285 TCGTGCTCGAGTT
1 TCGAGCTTGA--A
*
3487298 TCGAGCTTCAA
1 TCGAGCTTGAA
3487309 TCGAGCT
1 TCGAGCT
3487316 CTTGATTTTT
Statistics
Matches: 47, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
11 32 0.68
12 8 0.17
13 7 0.15
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:3497631 original size:200 final size:191
Alignment explanation
Indices: 3497282--3497675 Score: 540
Period size: 200 Copynumber: 2.0 Consensus size: 191
3497272 TGCAGAGGCA
*
3497282 GATGGAAAATTTAGGCTCCTGGTCCTTCAAGTTCAGAACTGTTTAGGAGTAGGTCACAGTCACAA
1 GATGAAAAATTTAGGCTCCTGGTCCTTCAAGTTCAGAACTGTTTAGGAGTAGGTCACAGTCACAA
* *
3497347 TATAGATCAAACCATTCTTCTGAACCTGGCAGCAGAGGACTCAAACAAAGGTATTATGGCGATTT
66 TAAACATCAAACCATTCTTCTGAACCTGGCAGCAGAGGACTCAAACAAAGGTATTATGGCGATTT
* *
3497412 TGAAGATGAAGGCCCTCCCGGAGTTGACTTTAGATTTAGCTCGCCCTACCCCCCAAGGTAT
131 TGAAGATGAAGGCCCTCCCGGAGTCGACTCTAGATTTAGCTCGCCCTACCCCCCAAGGTAT
*
3497473 GATGAAAAACTTTGGGCTCCTGGTCCTTCAAGTTCAGAA-TCGTTTAGGAGTAGGTCACA-TCCC
1 GATGAAAAA-TTTAGGCTCCTGGTCCTTCAAGTTCAGAACT-GTTTAGGAGTAGGTCACAGT--C
* * * *
3497536 ACTATAAATTAAACCATTCTAACCATTCTTCTGAACCTGGCAGCAGAGGGCTCGAACGAAGGTAT
62 AC----AA-TAAA-CA-TCAAACCATTCTTCTGAACCTGGCAGCAGAGGACTCAAACAAAGGTAT
* * * * *
3497601 TATGGTGATTTTGAAGATGAAGGTCCTCCCGGAGTCGACTCTAGATTTTGCTTGCCCTATCCCCC
120 TATGGCGATTTTGAAGATGAAGGCCCTCCCGGAGTCGACTCTAGATTTAGCTCGCCCTACCCCCC
3497666 AAGGTAT
185 AAGGTAT
3497673 GAT
1 GAT
3497676 AATTATGATT
Statistics
Matches: 177, Mismatches: 15, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
191 10 0.06
192 46 0.26
193 3 0.02
197 2 0.01
198 3 0.02
199 1 0.01
200 112 0.63
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (191 bp):
GATGAAAAATTTAGGCTCCTGGTCCTTCAAGTTCAGAACTGTTTAGGAGTAGGTCACAGTCACAA
TAAACATCAAACCATTCTTCTGAACCTGGCAGCAGAGGACTCAAACAAAGGTATTATGGCGATTT
TGAAGATGAAGGCCCTCCCGGAGTCGACTCTAGATTTAGCTCGCCCTACCCCCCAAGGTAT
Found at i:3504107 original size:26 final size:26
Alignment explanation
Indices: 3504078--3504129 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3504068 AATTTACTTT
3504078 GACCATTAATTTATAATTCATCACTC
1 GACCATTAATTTATAATTCATCACTC
* *
3504104 GACCATTAATTTCTCATTCATCACTC
1 GACCATTAATTTATAATTCATCACTC
3504130 AACAATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (26 bp):
GACCATTAATTTATAATTCATCACTC
Found at i:3518832 original size:2 final size:2
Alignment explanation
Indices: 3518825--3518860 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3518815 AATAATTTTA
3518825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3518861 TCATAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3521739 original size:15 final size:15
Alignment explanation
Indices: 3521716--3521749 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3521706 CGACTTCCCC
*
3521716 TACATATTTACCTAT
1 TACAAATTTACCTAT
3521731 TACAAATTTACCTAT
1 TACAAATTTACCTAT
3521746 TACA
1 TACA
3521750 TTATAATATG
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:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
TACAAATTTACCTAT
Found at i:3522197 original size:23 final size:23
Alignment explanation
Indices: 3522162--3522234 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
3522152 ATGCTTTACA
*
3522162 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3522185 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3522208 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
3522231 ATAT
1 ATAT
3522235 TTTTATCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:3522686 original size:23 final size:23
Alignment explanation
Indices: 3522656--3522717 Score: 92
Period size: 21 Copynumber: 2.8 Consensus size: 23
3522646 CAATATAGCA
3522656 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
*
3522679 CTACCTATTACA-T-TATAAGCG
1 CTACCTATTACATTATATAAACG
*
3522700 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
3522718 TTTTACCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 19 0.54
22 1 0.03
23 15 0.43
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.35
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:3522701 original size:21 final size:21
Alignment explanation
Indices: 3522643--3522712 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
3522633 GATAGATACT
* *
3522643 TTACAATAT-AGCACTACCTA
1 TTACATTATAAGCGCTACCTA
*
3522663 TTACATTATATAAACGCTACCTA
1 TTACA-T-TATAAGCGCTACCTA
3522686 TTACATTATAAGCGCTACCTA
1 TTACATTATAAGCGCTACCTA
3522707 TTACAT
1 TTACAT
3522713 CATATTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 5 0.12
21 20 0.47
22 4 0.09
23 14 0.33
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (21 bp):
TTACATTATAAGCGCTACCTA
Found at i:3523157 original size:21 final size:21
Alignment explanation
Indices: 3523127--3523197 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
3523117 GATAGATACT
* *
3523127 TTACAATATAAGCACTACCTA
1 TTACATTATAAGCGCTACCTA
*
3523148 TTACATTATATAAACGCTACCTA
1 TTACA-T-TATAAGCGCTACCTA
3523171 TTACATTATAAGCGCTACCTA
1 TTACATTATAAGCGCTACCTA
3523192 TTACAT
1 TTACAT
3523198 CATATTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 25 0.57
22 1 0.02
23 18 0.41
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (21 bp):
TTACATTATAAGCGCTACCTA
Found at i:3523167 original size:23 final size:23
Alignment explanation
Indices: 3523132--3523202 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
3523122 ATACTTTACA
*
3523132 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3523155 ATATAAACGCTACCTATTACA-T
1 ATATAAGCGCTACCTATTACATT
*
3523177 -TATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
3523199 ATAT
1 ATAT
3523203 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.45
22 1 0.02
23 22 0.52
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:3523619 original size:485 final size:489
Alignment explanation
Indices: 3521760--3523918 Score: 3898
Period size: 484 Copynumber: 4.4 Consensus size: 489
3521750 TTATAATATG
* *
3521760 TTGAAAGTGTCTATACTTTTTTATAAAAAAGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGT
* **
3521825 TTCAA--TTTTTTAATAGTGTTTCATGTTTTCCACATACAATATTAATTTAATAATTTCATTTGT
64 TTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
*
3521888 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
129 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGTATTTAAATTTAACAATA
*
3521953 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
194 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* **** * *
3522018 TACCGTAACATAAAAAATAAATCATTAGATATATATAATTACTACATTGATATCTTAAAACTCAC
259 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
* **
3522083 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTTTATAAAAATA
324 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
*
3522148 ATAGATGCTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
389 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
3522213 AGCGCTACCTATTACATCATATTTTTATCTATTATA
454 AGCGCTACCTATTACATCATATTTTTACCTATTATA
3522249 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTT
*
3522314 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
3522379 CAAAAAAATATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGTATTTAAATTTAACAATAT
3522444 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
3522509 --CGTAACGTAAAAAA-AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
3522571 CAAAA-ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
325 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
3522635 TAGATACTTTACAATAT-AGCACTACCTATTACATTATATAAACGCTACCTATTACA-T-TATAA
390 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
3522697 GCGCTACCTATTACATCATATTTTTACCTATTATA
455 GCGCTACCTATTACATCATATTTTTACCTATTATA
3522732 TTGAAAGTGTCCATACTTTTTAT-AAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTT
*
3522796 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTACAC
66 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
*
3522861 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGTATTTAAATTTAACAATATT
3522926 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
*
3522991 TCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
*
3523056 AAAAGATAACCTTAAATTAATGTTTTCTACAGTG-AAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
3523120 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACA-T-TATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
3523183 CGCTACCTATTACATCATATTTTTACCTATTATA
456 CGCTACCTATTACATCATATTTTTACCTATTATA
3523217 TTGAAAGTGTCCATAC-TTTTATAAAAAGGATCGATAC-TTTTTAAAGTTATGTAATTTATGTTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTT
*
3523280 CAATTTTTTTTAATAATGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
*
3523345 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGTATTTAAATTTAACAATATT
3523410 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* *
3523475 CCGTAACGTAAAAAATAAATCATTAGACGTCTATAATTATTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
3523540 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
326 AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
3523605 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
391 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
3523670 CGCTACCTATTACATCATATTTTTACCTATTATA
456 CGCTACCTATTACATCATATTTTTACCTATTATA
*
3523704 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATATTTTTTTAAAGTTATGTAATTTATGTTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTT
*
3523769 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTACAC
66 CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
3523834 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGTATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGTATTTAAATTTAACAATATT
3523899 AACCAAAGATAATAATAAAT
196 AACCAAAGATAATAATAAAT
3523919 CATTAGACGC
Statistics
Matches: 1623, Mismatches: 34, Indels: 26
0.96 0.02 0.02
Matches are distributed among these distances:
481 216 0.13
482 14 0.01
483 76 0.05
484 420 0.26
485 263 0.16
486 73 0.04
487 103 0.06
488 85 0.05
489 188 0.12
490 185 0.11
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (489 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTT
CAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGTATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
CGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:3523652 original size:23 final size:23
Alignment explanation
Indices: 3523617--3523689 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
3523607 ATACTTTACA
*
3523617 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3523640 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3523663 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
3523686 ATAT
1 ATAT
3523690 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:3526783 original size:183 final size:183
Alignment explanation
Indices: 3526471--3527775 Score: 2403
Period size: 183 Copynumber: 7.1 Consensus size: 183
3526461 TACTTAAAAT
*
3526471 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
*
3526536 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTATAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
3526601 CGACACTTTTTTACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
3526654 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
*
3526719 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
3526784 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATTTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
3526837 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
*
3526902 TTTATACCGGTTATATTACAAAGTTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
3526967 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
3527020 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTTGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
* *
3527085 TTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCTGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
3527150 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGAACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
3527203 TATCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
* * *
3527268 TTTATACCGGTTATATTACAAAATTATCTATTATATTATAATTCTGGGTTCTGATGTATAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
3527333 CGACACTTTTTCACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
3527386 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
*
3527451 TTTATACCGGTTATATTACACAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
3527516 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTAGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
3527569 TGCCGACTCAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
*
3527634 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
3527699 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACGTAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
**
3527752 TACATACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
3527776 GAAAACTTTG
Statistics
Matches: 1085, Mismatches: 37, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 1085 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTGTTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:3529002 original size:12 final size:12
Alignment explanation
Indices: 3528986--3529085 Score: 128
Period size: 12 Copynumber: 8.3 Consensus size: 12
3528976 CTTGTTTGGA
* *
3528986 TCATCATCATCA
1 TCATCTTCATCG
* * *
3528998 TCATCATCGTCA
1 TCATCTTCATCG
3529010 TCATCTTCATCG
1 TCATCTTCATCG
3529022 TCATCTTCATCG
1 TCATCTTCATCG
*
3529034 TCATCATCATCG
1 TCATCTTCATCG
3529046 TCATCTTCATCG
1 TCATCTTCATCG
3529058 TCATCTTCATCG
1 TCATCTTCATCG
* *
3529070 TCAACTTCATCT
1 TCATCTTCATCG
3529082 TCAT
1 TCAT
3529086 TGACAGCTCG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 79 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:3529083 original size:6 final size:6
Alignment explanation
Indices: 3528986--3529085 Score: 92
Period size: 6 Copynumber: 16.7 Consensus size: 6
3528976 CTTGTTTGGA
* * * * * * *
3528986 TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
3529034 TCATCA TCATCG TCATCT TCATCG TCATCT TCATCG TCAACT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
3529082 TCAT
1 TCAT
3529086 TGACAGCTCG
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 79 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:3530911 original size:200 final size:200
Alignment explanation
Indices: 3530587--3531350 Score: 1350
Period size: 200 Copynumber: 3.8 Consensus size: 200
3530577 AACATTAAAC
* *
3530587 AGTGTCGACACATTATTAAGACATATTCTCTCATAAAACCGATATACTTATACCGGTTAGATTGA
1 AGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGATATACTTGTACCGGTTAGATTGA
*
3530652 AAAATTACCTATTACATTATACTTTTGGTTTTCGATGTCTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
3530717 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
3530782 ACAAA
196 ACAAA
*
3530787 AGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGATATACTTGTACCGGTTAGATTGA
3530852 AAAATTACCTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
3530917 GATCGACACTTTATGGTTGCACCCTGTTTGCAATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
3530982 ACAAA
196 ACAAA
*
3530987 AGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGATATACTTGTACTGGTTAGATTGA
1 AGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGATATACTTGTACCGGTTAGATTGA
* *
3531052 AAAATTACATATTACATTATTCTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
3531117 GATCGACACTTTATGGTTGCACCCTGTTTGCTATTCATTCTGGACCAGAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
3531182 ACAAA
196 ACAAA
* * * *
3531187 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACC-AGTATACTTGCACCGATTAGATTG
1 AGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGA-TATACTTGTACCGGTTAGATTG
* * *
3531251 AAAAATTACCTATTACATTATAATTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATAT
*
3531316 GGATCAACACTTTATGGTTGCACCCTGTTTGCCAT
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
3531351 ATTGTAAATT
Statistics
Matches: 540, Mismatches: 23, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
199 1 0.00
200 539 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTAAGACCTATTCTCTCATAAAACCGATATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTTTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:3531474 original size:18 final size:18
Alignment explanation
Indices: 3531451--3531511 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
3531441 TCTCATTCAT
*
3531451 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
3531469 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
3531488 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
3531507 AATTA
1 AATTA
3531512 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:3531487 original size:19 final size:19
Alignment explanation
Indices: 3531463--3531511 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3531453 TTATATTCAC
3531463 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
3531482 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
3531501 ATACAAAATTA
1 ATACAAAATTA
3531512 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:3533099 original size:26 final size:24
Alignment explanation
Indices: 3533065--3533118 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
3533055 CATCGACTTC
3533065 CTTCCTCCTCATTTCTTCTATCTCTT
1 CTTCCTCCTCATTTC-TCT-TCTCTT
* * *
3533091 CTTCTTCCTCCTTTCTCTTTTCTT
1 CTTCCTCCTCATTTCTCTTCTCTT
3533115 CTTC
1 CTTC
3533119 ATATTTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.36
25 3 0.12
26 13 0.52
ACGTcount: A:0.04, C:0.39, G:0.00, T:0.57
Consensus pattern (24 bp):
CTTCCTCCTCATTTCTCTTCTCTT
Found at i:3533339 original size:33 final size:33
Alignment explanation
Indices: 3533302--3533367 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3533292 CATCTTAATA
*
3533302 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
3533335 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
3533368 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:3533426 original size:21 final size:21
Alignment explanation
Indices: 3533401--3533465 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
3533391 CCCCTTATGC
* *
3533401 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3533422 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
3533443 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3533464 CT
1 CT
3533466 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:3535893 original size:20 final size:20
Alignment explanation
Indices: 3535866--3535912 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3535856 TCCGGTAACG
3535866 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
3535885 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
3535906 TTTTACC
1 TTTTACC
3535913 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:3535956 original size:181 final size:182
Alignment explanation
Indices: 3535652--3536124 Score: 698
Period size: 181 Copynumber: 2.6 Consensus size: 182
3535642 CGTACTTACG
* * * **
3535652 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTATCGGTTTTATCATTTTGATACCTATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
3535717 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
3535782 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
3535833 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
3535898 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
3535963 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * **
3536015 AAAGTATCGACA-TTTTAAAAGTATCCGGTAGCGCTTTACCGATTTTATCATTTCAATACCGGTT
1 AAAGTATCGACACTTTCAATA-TATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTT
* * *
3536079 TTTTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
3536125 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 171 0.65
182 92 0.35
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:3536598 original size:42 final size:42
Alignment explanation
Indices: 3536550--3536631 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
3536540 AGTTTAATTT
3536550 ATTAATGAAAATAAAAGAAAAAAATTACATATTCGAATTTAA
1 ATTAATGAAAATAAAAGAAAAAAATTACATATTCGAATTTAA
* *
3536592 ATTAATGGAAATAAAAGAAAAAAATTACATATTTGAATTT
1 ATTAATGAAAATAAAAGAAAAAAATTACATATTCGAATTT
3536632 TTTTAGAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (42 bp):
ATTAATGAAAATAAAAGAAAAAAATTACATATTCGAATTTAA
Found at i:3539952 original size:23 final size:23
Alignment explanation
Indices: 3539919--3539962 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3539909 GAGTAGAGGG
3539919 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
*
3539942 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
3539963 TATATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:3540155 original size:24 final size:25
Alignment explanation
Indices: 3540075--3540165 Score: 95
Period size: 24 Copynumber: 3.8 Consensus size: 25
3540065 CAATCTTATA
*
3540075 TGGCACTACGGTG-C-AATTCTACG
1 TGGCACTTCGGTGACAAATTCTACG
3540098 TGGCACTTCGGTG-CAAATTTCTACG
1 TGGCACTTCGGTGACAAA-TTCTACG
* *
3540123 CAGTC-CTTCGG-GACAAATTCTACG
1 -TGGCACTTCGGTGACAAATTCTACG
3540147 TGGCACTTCGGTGA-AAATT
1 TGGCACTTCGGTGACAAATT
3540166 TATACGAGCT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
23 15 0.26
24 21 0.37
25 19 0.33
26 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (25 bp):
TGGCACTTCGGTGACAAATTCTACG
Found at i:3543133 original size:29 final size:28
Alignment explanation
Indices: 3543068--3543135 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
3543058 AATAAAAAGA
*
3543068 ATATAATAATTTTTCCTAAAAATTTAAT
1 ATATAATAATTTTTCATAAAAATTTAAT
* *
3543096 ATAAAAATAATTTTT-ATATAATATTATAAT
1 AT-ATAATAATTTTTCATA-AAAATT-TAAT
3543126 ATATAATAAT
1 ATATAATAAT
3543136 ACAAGCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 4 0.12
29 23 0.70
30 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATAATAATTTTTCATAAAAATTTAAT
Found at i:3543314 original size:22 final size:22
Alignment explanation
Indices: 3543286--3543335 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3543276 ATTATAGCAT
3543286 GAAACAAGAAAACATCACAATA
1 GAAACAAGAAAACATCACAATA
3543308 GAAACAAGAAAACATCACAATA
1 GAAACAAGAAAACATCACAATA
3543330 GAAACA
1 GAAACA
3543336 CCATAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.64, C:0.18, G:0.10, T:0.08
Consensus pattern (22 bp):
GAAACAAGAAAACATCACAATA
Found at i:3545270 original size:89 final size:89
Alignment explanation
Indices: 3545114--3545339 Score: 337
Period size: 89 Copynumber: 2.5 Consensus size: 89
3545104 AGGACTTATG
*
3545114 CATCATGCTCGAAAGACATACTGATGGCCCGAAGGACTTACGAATCAAGAAACCCCTAAAGGCTT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACGAATCAAGAAACCCCTAAAGGCTT
3545179 AGTTTCTAAAATCTCATTTGAAAA
66 AGTTTCTAAAATCTCATTTGAAAA
* * *
3545203 CATCATGCTCGAAAGACTTACTGATGGCCTGAAGGACTTACGAATCAAGAAACCCCTGAAGGTTT
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACGAATCAAGAAACCCCTAAAGGCTT
*
3545268 AGTTTCTTAAATCTCATTTGAAAA
66 AGTTTCTAAAATCTCATTTGAAAA
* * * * *
3545292 CATCCTGCACTGAAGGTCTTA-TGGATGGCCCGAAGGACTTACGCATCA
1 CATCATGCTC-GAAAGACTTACT-GATGGCCCGAAGGACTTACGAATCA
3545340 TGCTCGAAAG
Statistics
Matches: 124, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
89 93 0.75
90 31 0.25
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (89 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACGAATCAAGAAACCCCTAAAGGCTT
AGTTTCTAAAATCTCATTTGAAAA
Found at i:3545332 original size:20 final size:20
Alignment explanation
Indices: 3545303--3545374 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
3545293 ATCCTGCACT
*
3545303 GAAGGTCTTATGGATGGCCC
1 GAAGGACTTATGGATGGCCC
* * * *
3545323 GAAGGACTTACGCATCATGCTC
1 GAAGGACTTATGGAT--GGCCC
*
3545345 GAAAGACTTACT-GATGGCCC
1 GAAGGACTTA-TGGATGGCCC
3545365 GAAGGACTTA
1 GAAGGACTTA
3545375 CAAATCAAGA
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
20 24 0.63
22 14 0.37
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (20 bp):
GAAGGACTTATGGATGGCCC
Found at i:3545359 original size:221 final size:220
Alignment explanation
Indices: 3545004--3545539 Score: 885
Period size: 221 Copynumber: 2.4 Consensus size: 220
3544994 AGGTCTTATG
*
3545004 GATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
1 GATGGCCCGAAGGACTTACGAATCAAGAAA-CCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
* *
3545069 AACATCCTGCACTGAATA-TTTTATGGATGGCCCGAAGGACTTATGCATCATGCTCGAAAGACAT
65 AACATCCTGCACTGAA-AGTCTTATGGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGACAT
* * *
3545133 ACTGATGGCCCGAAGGACTTACGAATCAAGAAACCCCTAAAGGCTTAGTTTCTAAAATCTCATTT
129 ACTGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTATAAAATCTCATTT
* *
3545198 GAAAACATCATGCTCGAAAGACTTACT
194 GAAAACATCATGCCCAAAAGACTTACT
* *
3545225 GATGGCCTGAAGGACTTACGAATCAAGAAACCCCTGAAGGTTTAGTTTCTTAAATCTCATTTGAA
1 GATGGCCCGAAGGACTTACGAATCAAGAAACCCC-GAAGGCTTAGTTTCTTAAATCTCATTTGAA
* *
3545290 AACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGACTTA
65 AACATCCTGCACTGAAAGTCTTATGGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGACATA
*
3545355 CTGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTATAAAATCTCATTTG
130 CTGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTATAAAATCTCATTTG
3545420 AAAACATCATGCCCAAAAGACTTACT
195 AAAACATCATGCCCAAAAGACTTACT
* * *
3545446 GATGGCCCGAAGAACTTACGAATCAAGAAACCCCAAAGGCTTAGTTTCTTAAACCTCATTTGAAA
1 GATGGCCCGAAGGACTTACGAATCAAGAAACCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAA
*
3545511 ACATCCTGCACTGAAAGTCTTATAGATGG
66 ACATCCTGCACTGAAAGTCTTATGGATGG
3545540 TGTAACACCC
Statistics
Matches: 293, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
220 59 0.20
221 234 0.80
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (220 bp):
GATGGCCCGAAGGACTTACGAATCAAGAAACCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAA
ACATCCTGCACTGAAAGTCTTATGGATGGCCCGAAGGACTTACGCATCATGCTCGAAAGACATAC
TGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCAAAGGCTTAGTTTATAAAATCTCATTTGA
AAACATCATGCCCAAAAGACTTACT
Found at i:3545375 original size:20 final size:19
Alignment explanation
Indices: 3545315--3545375 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
3545305 AGGTCTTATG
3545315 GATGGCCCGAAGGACTTAC
1 GATGGCCCGAAGGACTTAC
* * *
3545334 GCATCATGCTCGAAAGACTTAC
1 G-AT--GGCCCGAAGGACTTAC
3545356 TGATGGCCCGAAGGACTTAC
1 -GATGGCCCGAAGGACTTAC
3545376 AAATCAAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
22 15 0.47
23 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (19 bp):
GATGGCCCGAAGGACTTAC
Found at i:3545539 original size:89 final size:89
Alignment explanation
Indices: 3545335--3545515 Score: 283
Period size: 89 Copynumber: 2.0 Consensus size: 89
3545325 AGGACTTACG
* * * *
3545335 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTT
1 CATCATGCCCAAAAGACTTACTGATGGCCCGAAGAACTTACAAATCAAGAAACCCCCAAAGGCTT
*
3545400 AGTTTATAAAATCTCATTTGAAAA
66 AGTTTATAAAACCTCATTTGAAAA
*
3545424 CATCATGCCCAAAAGACTTACTGATGGCCCGAAGAACTTACGAATCAAGAAA-CCCCAAAGGCTT
1 CATCATGCCCAAAAGACTTACTGATGGCCCGAAGAACTTACAAATCAAGAAACCCCCAAAGGCTT
* *
3545488 AGTTTCTTAAACCTCATTTGAAAA
66 AGTTTATAAAACCTCATTTGAAAA
3545512 CATC
1 CATC
3545516 CTGCACTGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 36 0.43
89 48 0.57
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.23
Consensus pattern (89 bp):
CATCATGCCCAAAAGACTTACTGATGGCCCGAAGAACTTACAAATCAAGAAACCCCCAAAGGCTT
AGTTTATAAAACCTCATTTGAAAA
Found at i:3546463 original size:25 final size:25
Alignment explanation
Indices: 3546403--3546450 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3546393 CTCATATAAA
*
3546403 TTGCACCGAAGTGCCGCGTAGAGTT
1 TTGCACCGAAGTGCCGCGTAGAATT
3546428 TTGCACCGAAGTGCCGCGTAGAA
1 TTGCACCGAAGTGCCGCGTAGAA
3546451 ATTTATCCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (25 bp):
TTGCACCGAAGTGCCGCGTAGAATT
Found at i:3551058 original size:43 final size:43
Alignment explanation
Indices: 3550980--3551327 Score: 506
Period size: 43 Copynumber: 8.1 Consensus size: 43
3550970 GCAAAAATGA
* * * * *
3550980 TAAGGTCTTATCCTTGCACATAACAAA-AGAGCCTGGGGAAACTT
1 TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGAAACTG
**
3551024 TAAGGCTTACCCTTGCACACAGCAAAGAAACCT-GGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
*
3551066 TAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGG-GAAACTG
*
3551110 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
*
3551153 TAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
*
3551196 TAAGGCTTACCCTTGCACACAACAAAGGGACCTGAGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTG-GGGAAACTG
*
3551239 TAAGGTTTACCCTTGCACACAGCAAAGGGACCTGAGGG-AACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTG-GGGAAACTG
*
3551282 TAAGGCTTACCCTTGCACACAGCAAAGAGACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
3551325 TAA
1 TAA
3551328 CGGTAATTAA
Statistics
Matches: 283, Mismatches: 16, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
42 43 0.15
43 189 0.67
44 51 0.18
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGAAACTG
Found at i:3552839 original size:17 final size:18
Alignment explanation
Indices: 3552806--3552839 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3552796 TCCATTCTGT
*
3552806 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
3552824 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
3552840 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:3555961 original size:25 final size:25
Alignment explanation
Indices: 3555909--3555981 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
3555899 CTCATATAAA
* * **
3555909 TTGCATCGAAGTGCCACGTAGAGTT
1 TTGCACCGAAGTGCCGCGTAGAAAT
3555934 TTGCACCGAAGTGCCGCGTAGAAAT
1 TTGCACCGAAGTGCCGCGTAGAAAT
3555959 TTGTC-CCGAAG-GACCGCGTAGAA
1 TTG-CACCGAAGTG-CCGCGTAGAA
3555982 TTTTTCCCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.02
25 40 0.95
26 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (25 bp):
TTGCACCGAAGTGCCGCGTAGAAAT
Found at i:3555989 original size:24 final size:24
Alignment explanation
Indices: 3555925--3555997 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
3555915 CGAAGTGCCA
* *
3555925 CGTAGAGTTTTGCACCGAAGTG-CCG
1 CGTAGAATTTTTC-CCGAAG-GACCG
*
3555950 CGTAGAAATTTGTCCCGAAGGACCG
1 CGTAG-AATTTTTCCCGAAGGACCG
3555975 CGTAGAATTTTTCCCGAAGGACC
1 CGTAGAATTTTTCCCGAAGGACC
3555998 ACATAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 18 0.43
25 19 0.45
26 5 0.12
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTTTCCCGAAGGACCG
Found at i:3556004 original size:24 final size:24
Alignment explanation
Indices: 3555956--3556005 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3555946 GCCGCGTAGA
* *
3555956 AATTTGTCCCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACCACATAG
*
3555980 AATTTTTCCCGAAGGACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
3556004 AA
1 AA
3556006 AAATTCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACATAG
Found at i:3556012 original size:24 final size:24
Alignment explanation
Indices: 3555962--3556012 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
3555952 TAGAAATTTG
* * ***
3555962 TCCCGAAGGACCGCGTAGAATTTT
1 TCCCGAAGGACCACATAGAAAAAT
3555986 TCCCGAAGGACCACATAGAAAAAT
1 TCCCGAAGGACCACATAGAAAAAT
3556010 TCC
1 TCC
3556013 TTTAGAATCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (24 bp):
TCCCGAAGGACCACATAGAAAAAT
Found at i:3558193 original size:16 final size:15
Alignment explanation
Indices: 3558172--3558278 Score: 105
Period size: 15 Copynumber: 7.3 Consensus size: 15
3558162 GATCTGCCTA
3558172 TTTTCTTCTTTCTTCT
1 TTTTCTTCTTT-TTCT
3558188 TTTTCTTCTTTTTTCT
1 TTTTCTTC-TTTTTCT
3558204 TTTT-TTCTTTTT-T
1 TTTTCTTCTTTTTCT
* *
3558217 TTTT-TTTTTTTTTT
1 TTTTCTTCTTTTTCT
* * *
3558231 TTTTTTTTTTTTTTT
1 TTTTCTTCTTTTTCT
*
3558246 TTTTCTT-TTTTTTT
1 TTTTCTTCTTTTTCT
*
3558260 TTTTTTTCTTTTTCT
1 TTTTCTTCTTTTTCT
3558275 TTTT
1 TTTT
3558279 GTGTTTTTTC
Statistics
Matches: 83, Mismatches: 4, Indels: 9
0.86 0.04 0.09
Matches are distributed among these distances:
13 12 0.14
14 23 0.28
15 29 0.35
16 16 0.19
17 3 0.04
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTCTTCTTTTTCT
Found at i:3558214 original size:23 final size:22
Alignment explanation
Indices: 3558188--3558287 Score: 118
Period size: 20 Copynumber: 4.6 Consensus size: 22
3558178 TCTTTCTTCT
*
3558188 TTTTCTTCTTTTTTCTTTTTTTC
1 TTTT-TTCTTTTTTTTTTTTTTC
3558211 -TTTTT-TTTTTTTTTTTTTT-
1 TTTTTTCTTTTTTTTTTTTTTC
3558230 TTTTTT-TTTTTTTTTTTTTTC
1 TTTTTTCTTTTTTTTTTTTTTC
*
3558251 TTTTTTTTTTTTTTTTCTTTTTC
1 TTTTTTCTTTTTTTTT-TTTTTC
*
3558274 TTTTTGTGTTTTTT
1 TTTTT-TCTTTTTT
3558288 CTATATCTCT
Statistics
Matches: 70, Mismatches: 2, Indels: 9
0.86 0.02 0.11
Matches are distributed among these distances:
20 32 0.46
21 8 0.11
22 12 0.17
23 11 0.16
24 7 0.10
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.91
Consensus pattern (22 bp):
TTTTTTCTTTTTTTTTTTTTTC
Found at i:3558287 original size:1 final size:1
Alignment explanation
Indices: 3558196--3558278 Score: 121
Period size: 1 Copynumber: 83.0 Consensus size: 1
3558186 CTTTTTCTTC
* * *
3558196 TTTTTTCTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
3558261 TTTTTTCTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTT
3558279 GTGTTTTTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:3562349 original size:18 final size:18
Alignment explanation
Indices: 3562326--3562360 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3562316 ATCCTCCACG
*
3562326 TGTTGTTAGGCTGTTAAA
1 TGTTGTTAGGATGTTAAA
3562344 TGTTGTTAGGATGTTAA
1 TGTTGTTAGGATGTTAA
3562361 GGGTTAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.29, T:0.46
Consensus pattern (18 bp):
TGTTGTTAGGATGTTAAA
Found at i:3563733 original size:18 final size:19
Alignment explanation
Indices: 3563706--3563744 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3563696 ATTTAACTAA
*
3563706 TTAAAAAATAA-TATGATT
1 TTAAAAAATAAGGATGATT
*
3563724 TTAAACAATAAGGATGATT
1 TTAAAAAATAAGGATGATT
3563743 TT
1 TT
3563745 GTAATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (19 bp):
TTAAAAAATAAGGATGATT
Found at i:3575281 original size:2 final size:2
Alignment explanation
Indices: 3575276--3575309 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3575266 TTTCCATCAA
3575276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3575310 AATTCGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3575816 original size:2 final size:2
Alignment explanation
Indices: 3575809--3575845 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3575799 ATTTATACAA
3575809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3575846 CTTTTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3575965 original size:5 final size:5
Alignment explanation
Indices: 3575955--3575983 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3575945 TCGATCAATT
3575955 TCCCA TCCCA TCCCA TCCCA TCCCA TCCC
1 TCCCA TCCCA TCCCA TCCCA TCCCA TCCC
3575984 TTGCTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.62, G:0.00, T:0.21
Consensus pattern (5 bp):
TCCCA
Found at i:3601242 original size:26 final size:26
Alignment explanation
Indices: 3601191--3601245 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3601181 GATTTTTCAA
* * *
3601191 ATTTTATAAAAAATATTTATTTTTTT
1 ATTTTATAAAAAATATTAAATATTTT
3601217 ATTTT-TAAAAAATAATTAAATATTTT
1 ATTTTATAAAAAAT-ATTAAATATTTT
3601243 ATT
1 ATT
3601246 ATATCATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTTATAAAAAATATTAAATATTTT
Found at i:3621046 original size:11 final size:12
Alignment explanation
Indices: 3621024--3621048 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3621014 GGATCGACTG
3621024 AAAACCGAAAAA
1 AAAACCGAAAAA
3621036 AAAACCGAAAAA
1 AAAACCGAAAAA
3621048 A
1 A
3621049 TCGGAAATTT
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:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAACCGAAAAA
Found at i:3623205 original size:21 final size:19
Alignment explanation
Indices: 3623181--3623220 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
3623171 TTCGAATACT
3623181 TTTAGACATTATATATTTATA
1 TTTAGACA-TAT-TATTTATA
*
3623202 TTTATACATATTATTTATA
1 TTTAGACATATTATTTATA
3623221 ATTGTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTAGACATATTATTTATA
Found at i:3643287 original size:18 final size:18
Alignment explanation
Indices: 3643264--3643323 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
3643254 ACTGAATATT
3643264 TGTCTCGAAGGACCACTA
1 TGTCTCGAAGGACCACTA
3643282 TGTCTCGAAGGACCACTAA
1 TGTCTCGAAGGACCACT-A
*
3643301 TTGT-TCCGAAGAACCACTA
1 -TGTCT-CGAAGGACCACTA
3643320 TGTC
1 TGTC
3643324 CCTGAATTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 20 0.54
19 3 0.08
20 14 0.38
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (18 bp):
TGTCTCGAAGGACCACTA
Found at i:3643801 original size:19 final size:19
Alignment explanation
Indices: 3643777--3643845 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
3643767 TTTAAACGAG
3643777 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
3643796 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
3643815 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
3643834 TGCATCGATGCA
1 TGCATCGATGCA
3643846 TTAATGGTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:3651628 original size:23 final size:23
Alignment explanation
Indices: 3651600--3651647 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3651590 CATGACTATC
*
3651600 CATGAAAAATAATTAAGTCATTT
1 CATGAAAAAAAATTAAGTCATTT
**
3651623 CATGAAAAAAAATTATTTCATTT
1 CATGAAAAAAAATTAAGTCATTT
3651646 CA
1 CA
3651648 CCCTAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (23 bp):
CATGAAAAAAAATTAAGTCATTT
Found at i:3651752 original size:20 final size:20
Alignment explanation
Indices: 3651727--3651768 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3651717 TCATTTCATT
3651727 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3651747 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3651767 TA
1 TA
3651769 CAAATTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:3652262 original size:18 final size:18
Alignment explanation
Indices: 3652239--3652282 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3652229 TATCGTGATA
3652239 ATATATTTAGGTTAATAT
1 ATATATTTAGGTTAATAT
* * *
3652257 ATATATTTCGTTTCATAT
1 ATATATTTAGGTTAATAT
3652275 -TATATTTA
1 ATATATTTA
3652283 TTATTTCGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (18 bp):
ATATATTTAGGTTAATAT
Found at i:3656943 original size:23 final size:23
Alignment explanation
Indices: 3656895--3656944 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3656885 ATCATGACTA
*
3656895 TTCATGAAAAATAATTAAGTCCT
1 TTCATGAAAAATAATTAAGTCAT
**
3656918 TTCATGAAAAATAATTATTTCAT
1 TTCATGAAAAATAATTAAGTCAT
3656941 TTCA
1 TTCA
3656945 CCCCAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (23 bp):
TTCATGAAAAATAATTAAGTCAT
Found at i:3657050 original size:20 final size:20
Alignment explanation
Indices: 3657025--3657066 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3657015 TCATTTCATT
3657025 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3657045 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
3657065 TA
1 TA
3657067 CAAATTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:3660099 original size:2 final size:2
Alignment explanation
Indices: 3660092--3660118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3660082 ATGCATAAAT
3660092 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3660119 GAAAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3660244 original size:2 final size:2
Alignment explanation
Indices: 3660233--3660291 Score: 56
Period size: 2 Copynumber: 31.5 Consensus size: 2
3660223 TTCTACATAC
* *
3660233 TA TA -A TA TA TA TA TA TA TA TA TA TA -A TA CA CT- TA AA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
3660272 TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
3660292 GCTTACAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
1 5 0.11
2 42 0.89
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Done.