Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009645.1 Hibiscus syriacus cultivar Beakdansim tig00117063_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: 1081801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:393180 original size:16 final size:17
Alignment explanation
Indices: 393145--393181 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
393135 CATGAGATAA
393145 AAAAATAGTATTATTGT
1 AAAAATAGTATTATTGT
393162 AAAAAT-GTAATTATT-T
1 AAAAATAGT-ATTATTGT
393178 AAAA
1 AAAA
393182 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (17 bp):
AAAAATAGTATTATTGT
Found at i:393554 original size:16 final size:18
Alignment explanation
Indices: 393515--393589 Score: 75
Period size: 19 Copynumber: 4.2 Consensus size: 18
393505 AAACAAGATA
*
393515 ATAATAATATAATATTCT
1 ATAATAATATTATATTCT
393533 CATAATAATATTATATT-T
1 -ATAATAATATTATATTCT
393551 -TAATAATATTAT-TTCT
1 ATAATAATATTATATTCT
* * *
393567 AAATATAATCTTACATTCT
1 ATA-ATAATATTATATTCT
393586 ATAA
1 ATAA
393590 ATCAAACGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 2 0.04
16 13 0.28
17 1 0.02
18 10 0.21
19 21 0.45
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
ATAATAATATTATATTCT
Found at i:397052 original size:15 final size:16
Alignment explanation
Indices: 397032--397064 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
397022 ATTTGGTCCT
*
397032 TAATTT-ATTTTTTAA
1 TAATTTAATTTTGTAA
397047 TAATTTAATTTTGTAA
1 TAATTTAATTTTGTAA
397063 TA
1 TA
397065 TTTTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TAATTTAATTTTGTAA
Found at i:397991 original size:2 final size:2
Alignment explanation
Indices: 397984--398023 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
397974 TGCCTACGAT
397984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
398024 AATAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:402099 original size:144 final size:144
Alignment explanation
Indices: 401622--402598 Score: 953
Period size: 144 Copynumber: 6.8 Consensus size: 144
401612 AACGGCGATT
* ** * * *
401622 GTGATCTTCTTGGT-TTCAGTGTGGGTTGGTCTCTTTCTTTAACATGATCATTATGTTCCTTACC
1 GTGATCTTCTTGGTCTT-AGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATC
* * * * *
401686 TTGTTC-GAAATTCTCCATTTC--CG-ACTGCTTCATCATCACCAACGCGTTCTTTCT-A-C-CC
65 TTGCTCAG-AATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACC
* *
401744 AACGGTATCGGCGATG
129 ATCGGTATCGGTGATG
* * * *
401760 GTGATCTTCTTGTTCTTAGTATGGGTTGTTC-ACTTTCTTTATCTCGATCAATATGTTCCTTATC
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGA-TTTCTTTATCACGATCATTATGTTCCTTATC
* * * *
401824 TTGCTCAGAATCCTCTATTTCGGAGTGCTGCTTCATCGTCACCAACGAGGCCTTTCTC--C-CCA
65 TTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCA
*
401886 TCAGTATCGGTGATG
130 TCGGTATCGGTGATG
* * * * *
401901 GTGATCTTGTTGGTCTTAGTGTAGGTTGTTCGCTTTCTTTATCTCGATCATTATGTTCATTATCT
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
* * ** * **** *
401966 TGCTCAGAATCCCCCATTTCGGGGCGCTGCTTCATTGTTGTTAATGCGGTCTTTCTCATCACCAT
66 TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
*
402031 CGGTATTGGTGATG
131 CGGTATCGGTGATG
* * * * * * * **
402045 GTGATCTTCTCGGTGTTAATGTGGGTTGTTCGATGTCTTTGTCCCGATCGTTATGTTCCCCATCT
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
* * * * *
402110 TGCTCAGAATCATCTATTTCGGAGTACTGCTTCATTGTCACCACCGCAGTCTTTCTCATCACCAT
66 TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
402175 CGGTATCGGAT-ATG
131 CGGTATCGG-TGATG
** * * *
402189 GTGATCTTCTTGGTGC-TAGTGCAGGTTGTTCGCTTTCTTTATCAGGATCATTATGTTCCGTATC
1 GTGATCTTCTTGGT-CTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATC
* ** * * * * *
402253 TTGTTCAGAATTTTCCATGTCCGAGTACTGCTTCACCGTTACCACCGCGGTCTTTCTCATCACCA
65 TTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCA
402318 TCGGTATCGGTGATG
130 TCGGTATCGGTGATG
* * * * * * * * *
402333 GTGTTCTTCTTGTTCTTTGTGTGAGTTCTTCGCTTTCTTTATCAGGATCATTATGTTCTTTGTCT
1 GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
* * * * *
402398 TGCTCAGAATCCTCCGTTTCGGAGTACTGCTTCACCGTCATCAATGCGGTCTTCCTCATCACCAT
66 TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
* **
402463 CGGAATCGGCAATG
131 CGGTATCGGTGATG
* *
402477 GTGATCTTCTCGGTCTTAGTGTGGG-TGTTTC-ACTTTCTATT-TCACGATCATTATGTTTCTTA
1 GTGATCTTCTTGGTCTTAGTGTGGGTTG-TTCGA-TTTCT-TTATCACGATCATTATGTTCCTTA
** ** * *
402539 TCTTGCTCAGAATCCTCCATTTCATAGTGTTGCTTCATCGTCATCAACGCGGTCCTTCTC
63 TCTTGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTC
402599 GCCGGTGATC
Statistics
Matches: 685, Mismatches: 136, Indels: 30
0.80 0.16 0.04
Matches are distributed among these distances:
138 67 0.10
139 3 0.00
140 1 0.00
141 144 0.21
143 4 0.01
144 463 0.68
145 3 0.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (144 bp):
GTGATCTTCTTGGTCTTAGTGTGGGTTGTTCGATTTCTTTATCACGATCATTATGTTCCTTATCT
TGCTCAGAATCCTCCATTTCGGAGTACTGCTTCATCGTCACCAACGCGGTCTTTCTCATCACCAT
CGGTATCGGTGATG
Found at i:404587 original size:32 final size:32
Alignment explanation
Indices: 404551--404618 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
404541 AAACTTATCT
*
404551 TAAAGACATACTTATTAAAAATA-AAAA-AACAA
1 TAAAGACATA-ATA-TAAAAATATAAAAGAACAA
* *
404583 TAAAGATATAATATAAAAATATAAAAGTACAA
1 TAAAGACATAATATAAAAATATAAAAGAACAA
404615 TAAA
1 TAAA
404619 AATTATTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 8 0.26
31 6 0.19
32 17 0.55
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.24
Consensus pattern (32 bp):
TAAAGACATAATATAAAAATATAAAAGAACAA
Found at i:411386 original size:20 final size:20
Alignment explanation
Indices: 411361--411492 Score: 203
Period size: 20 Copynumber: 6.6 Consensus size: 20
411351 TTTTTCGACT
*
411361 ATCGCAATGCGAATATATAA
1 ATCGCAATGCGAATATGTAA
411381 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
411401 ATCACAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
411421 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
411441 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* * *
411461 ATCGCAATGTGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
411481 ATCGCAATGCGA
1 ATCGCAATGCGA
411493 TTCGGACTGT
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 1 0.01
20 103 0.99
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:411494 original size:20 final size:20
Alignment explanation
Indices: 411357--411585 Score: 132
Period size: 20 Copynumber: 11.6 Consensus size: 20
411347 GTGATTTTTC
411357 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
411377 -A-TAAATCGCAATGCGAATAT
1 GACT--ATCGCAATGCGAATAT
* *
411397 GTA-AATCACAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
*
411417 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
*
411437 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGAATAT
* * *
411457 GTA-AATCGCAATGTGATTAT
1 G-ACTATCGCAATGCGAATAT
* **
411477 GACTATCGCAATGCGATTCG
1 GACTATCGCAATGCGAATAT
* * * *
411497 GACTGTCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
* * * *
411517 GACTGTCGCAACGCGATTCT
1 GACTATCGCAATGCGAATAT
* **
411537 GACTGTCGCAACACG-A-AT
1 GACTATCGCAATGCGAATAT
* * *
411555 GACTGTCGCAACGCGAAAAT
1 GACTATCGCAATGCGAATAT
411575 GACTATCGCAA
1 GACTATCGCAA
411586 CGAGAGAATC
Statistics
Matches: 185, Mismatches: 17, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
18 16 0.09
19 3 0.02
20 165 0.89
22 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:411578 original size:38 final size:39
Alignment explanation
Indices: 411497--411586 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 39
411487 ATGCGATTCG
* * ***
411497 GACTGTCGCAACGCGATTCTGACTGTCGCAACGCGATTCT
1 GACTGTCGCAACACGA-TATGACTGTCGCAACGCGAAAAT
411537 GACTGTCGCAACACGA-ATGACTGTCGCAACGCGAAAAT
1 GACTGTCGCAACACGATATGACTGTCGCAACGCGAAAAT
*
411575 GACTATCGCAAC
1 GACTGTCGCAAC
411587 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
38 29 0.66
40 15 0.34
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (39 bp):
GACTGTCGCAACACGATATGACTGTCGCAACGCGAAAAT
Found at i:413364 original size:19 final size:19
Alignment explanation
Indices: 413305--413429 Score: 180
Period size: 19 Copynumber: 6.5 Consensus size: 19
413295 TCTGAAACTT
413305 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
413325 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
*
413345 AAAATCGCAACGCGAAATG
1 AAAATCGCAACACGAAATG
*
413364 AAAATCGCAACTCGAAATG
1 AAAATCGCAACACGAAATG
*
413383 AAAATCGCAACTCGAAATG
1 AAAATCGCAACACGAAATG
*
413402 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAA-TG
413421 AAAATCGCA
1 AAAATCGCA
413430 TTGCGATTCT
Statistics
Matches: 101, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
19 67 0.66
20 34 0.34
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:413843 original size:22 final size:22
Alignment explanation
Indices: 413811--413867 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
413801 GATGGAGATA
*
413811 GACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
413833 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
413855 GACGGATGTCGCC
1 GACGGATTTCGCC
413868 TTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:414063 original size:20 final size:20
Alignment explanation
Indices: 414031--414144 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
414021 GCGCTTTGAA
*
414031 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
414051 CATCACGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
414071 AATCGCGTTGCGATAATCAG
1 AATCGCGTTGCGATAGTCAG
*
414091 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
414111 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
414131 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
414145 TTACATATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:414162 original size:60 final size:60
Alignment explanation
Indices: 414031--414168 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
414021 GCGCTTTGAA
* *
414031 AATCGCATTGCGATAGTCAGCATCACGTTGCGACAGTCAGAATCGCGTTGCGATAATCAG
1 AATCGCATTGCGATAGTCAGAATCACGTTGCGACAGTCAGAATCGCATTGCGATAATCAG
* * * * * * *
414091 AATCTCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCACGTTGCGACAGTCAGAATCGCATTGCGATAAT-CAG
*
414151 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
414169 GAAAAATCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 64 0.98
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCACGTTGCGACAGTCAGAATCGCATTGCGATAATCAG
Found at i:414184 original size:22 final size:22
Alignment explanation
Indices: 414153--414211 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
414143 ATTTACATAT
*
414153 TCGCATTGCGATAGTCGAAAAA
1 TCGCAATGCGATAGTCGAAAAA
* * *
414175 TCGCAATGCGA-ATTTGGAAAA
1 TCGCAATGCGATAGTCGAAAAA
414196 TCGCAATGCGATAGTC
1 TCGCAATGCGATAGTC
414212 AGAATCGCGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (22 bp):
TCGCAATGCGATAGTCGAAAAA
Found at i:414219 original size:20 final size:20
Alignment explanation
Indices: 414031--414226 Score: 153
Period size: 20 Copynumber: 9.7 Consensus size: 20
414021 GCGCTTTGAA
414031 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * * *
414051 CATCACGTTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
414071 AATCGCGTTGCGATAATCAG
1 AATCGCATTGCGATAGTCAG
* *
414091 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
414111 AATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* *
414131 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
414151 ATTCGCATTGCGATAGTCGAAA
1 AATCGCATTGCGATAGTC--AG
* * * *
414173 AATCGCAATGCGA-ATTTGGAA
1 AATCGCATTGCGATA-GT-CAG
*
414194 AATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
414214 AATCGCGTTGCGA
1 AATCGCATTGCGA
414227 ATCTGGAAAC
Statistics
Matches: 143, Mismatches: 26, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.01
20 110 0.77
21 18 0.13
22 14 0.10
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:429426 original size:2 final size:2
Alignment explanation
Indices: 429419--429446 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
429409 AGAAATAGGG
429419 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
429447 TCAATTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:434621 original size:17 final size:16
Alignment explanation
Indices: 434599--434667 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
434589 CCGTGTCTCG
*
434599 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
434616 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
* *
434631 ACCCTGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
434648 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
434663 ACCCG
1 ACCCG
434668 ATACCCAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.17, C:0.28, G:0.32, T:0.23
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:434631 original size:15 final size:15
Alignment explanation
Indices: 434611--434667 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
434601 CCGGATGTTA
434611 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
434626 CGGGTACCCTGATTTT
1 CGGGTACCC-GGTAAT
434642 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
434658 CGGGTACCCG
1 CGGGTACCCG
434668 ATACCCAGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 19 0.56
16 6 0.18
17 9 0.26
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:436484 original size:23 final size:24
Alignment explanation
Indices: 436441--436497 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
436431 TGTCACTCAT
* *
436441 TATTTTTATTTTGTAGAATTTTCAA
1 TATTTTTATTTTATAGAA-TTTAAA
*
436466 T-TTTTTATTTTATA-TATTTAAA
1 TATTTTTATTTTATAGAATTTAAA
436488 TATTTTTATT
1 TATTTTTATT
436498 ATTTTGGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 6 0.21
23 9 0.32
24 12 0.43
25 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (24 bp):
TATTTTTATTTTATAGAATTTAAA
Found at i:437165 original size:22 final size:24
Alignment explanation
Indices: 437140--437183 Score: 58
Period size: 22 Copynumber: 1.9 Consensus size: 24
437130 AAAATTCAAT
437140 AAATA-AATTGAA-AAAA-AGTTGA
1 AAATATAA-TGAATAAAATAGTTGA
437162 AAATATAATGAATAAAATAGTT
1 AAATATAATGAATAAAATAGTT
437184 TCTGCAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.27
Consensus pattern (24 bp):
AAATATAATGAATAAAATAGTTGA
Found at i:448437 original size:157 final size:154
Alignment explanation
Indices: 448135--448447 Score: 581
Period size: 157 Copynumber: 2.0 Consensus size: 154
448125 TGCGTCGTCT
448135 TAAGGATTTAATTAAAAAATACAATTTGTAAGAAATTACATTATTATCCTAGGGATTGTTGGAGT
1 TAAGGATTTAATTAAAAAATACAATTTGTAAGAAATTACATTATTATCCTAGGGATTGTTGGAGT
448200 TTTTTACCCTCCACTCGGCCCGAACTGACCTTGTACCTAAAAAATCTGACTCGACTTGAACTCGA
66 TTTTTACCCTCCACTCGGCCCGAACTGACCTTGTACCTAAAAAATCTGACTCGACTTGAACTCGA
448265 TTTTTGACATAAAAAAATCGACCC
131 TTTTTGACATAAAAAAATCGACCC
*
448289 TAAGGATTTAATTAAAAAATAACAAATTTGTAAGAAAATTACATTATTATCCTAGGTATTGTTGG
1 TAAGGATTTAATTAAAAAAT-AC-AATTTGTAAG-AAATTACATTATTATCCTAGGGATTGTTGG
448354 AGTTTTTTACCCTCCACTCGGCCCGAACTGACCTTGTACCTTAAAAAATCTGACTCGACTTGAAC
63 AGTTTTTTACCCTCCACTCGGCCCGAACTGACCTTGTACC-TAAAAAATCTGACTCGACTTGAAC
448419 TCGATTTTTGACATAAAAAAATCGACCC
127 TCGATTTTTGACATAAAAAAATCGACCC
448447 T
1 T
448448 CTAGTCAGGT
Statistics
Matches: 154, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
154 20 0.13
155 2 0.01
156 10 0.06
157 69 0.45
158 53 0.34
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (154 bp):
TAAGGATTTAATTAAAAAATACAATTTGTAAGAAATTACATTATTATCCTAGGGATTGTTGGAGT
TTTTTACCCTCCACTCGGCCCGAACTGACCTTGTACCTAAAAAATCTGACTCGACTTGAACTCGA
TTTTTGACATAAAAAAATCGACCC
Found at i:454371 original size:30 final size:30
Alignment explanation
Indices: 454335--454402 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
454325 CCGGTTCTAG
454335 TGAACCGTAAGGAACTGTTCGAATCAGCTT
1 TGAACCGTAAGGAACTGTTCGAATCAGCTT
454365 TGAACCGTAAGGAACTGTTCGAATCAGCTT
1 TGAACCGTAAGGAACTGTTCGAATCAGCTT
*
454395 TTAACCGT
1 TGAACCGT
454403 TAGAATCGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (30 bp):
TGAACCGTAAGGAACTGTTCGAATCAGCTT
Found at i:454474 original size:23 final size:21
Alignment explanation
Indices: 454436--454490 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
454426 CGGTTCAACC
**
454436 TAAATTTTTTTTTATTTTTTAT
1 TAAATTTTTTAGTA-TTTTTAT
454458 TAAATATTTTTAGTATTTTTAT
1 TAAAT-TTTTTAGTATTTTTAT
*
454480 TTAATTTTTTA
1 TAAATTTTTTA
454491 AATAATTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 16 0.55
23 7 0.24
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TAAATTTTTTAGTATTTTTAT
Found at i:455042 original size:39 final size:39
Alignment explanation
Indices: 454999--455082 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 39
454989 GCACTCCTGG
* *
454999 GTCTTC-TCAATTTGCCTGAAAACGCCATACAGTCATGGA
1 GTCTTCTTC-ATTTACCTGAAAACGCCATACAATCATGGA
* * * *
455038 GTCTTCTTCATTTACTTGAAGACGCCATGCAATCGTGGA
1 GTCTTCTTCATTTACCTGAAAACGCCATACAATCATGGA
455077 GTCTTC
1 GTCTTC
455083 AATAAAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (39 bp):
GTCTTCTTCATTTACCTGAAAACGCCATACAATCATGGA
Found at i:455049 original size:125 final size:126
Alignment explanation
Indices: 454826--455076 Score: 495
Period size: 125 Copynumber: 2.0 Consensus size: 126
454816 CATATTATTT
454826 CTCGAACTAGGGTTTTTTATTTGTCTAAAGACGCATTGCACTCCCTGGGTCTTCTCAATTTGCCT
1 CTCGAACTAGGGTTTTTTATTTGTCTAAAGACGCATTGCACTCCCTGGGTCTTCTCAATTTGCCT
454891 GAAAACGCCATACAGTCATGGAGTCTTCTTCATTTACTTGAAGACGCCATGCAATCGTGGA
66 GAAAACGCCATACAGTCATGGAGTCTTCTTCATTTACTTGAAGACGCCATGCAATCGTGGA
454952 CTCGAACTAGGGTTTTTTATTTGTCTAAAGACGCATTGCACT-CCTGGGTCTTCTCAATTTGCCT
1 CTCGAACTAGGGTTTTTTATTTGTCTAAAGACGCATTGCACTCCCTGGGTCTTCTCAATTTGCCT
455016 GAAAACGCCATACAGTCATGGAGTCTTCTTCATTTACTTGAAGACGCCATGCAATCGTGGA
66 GAAAACGCCATACAGTCATGGAGTCTTCTTCATTTACTTGAAGACGCCATGCAATCGTGGA
455077 GTCTTCAATA
Statistics
Matches: 125, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 83 0.66
126 42 0.34
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (126 bp):
CTCGAACTAGGGTTTTTTATTTGTCTAAAGACGCATTGCACTCCCTGGGTCTTCTCAATTTGCCT
GAAAACGCCATACAGTCATGGAGTCTTCTTCATTTACTTGAAGACGCCATGCAATCGTGGA
Found at i:462739 original size:28 final size:24
Alignment explanation
Indices: 462688--462771 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 24
462678 TGTTATCAAG
462688 AAATTCTTTCTTTTTAATCGAATC
1 AAATTCTTTCTTTTTAATCGAATC
462712 AAATTCTTAATCTTTTTAGAATCGAATC
1 AAATTCTT--TCTTTTT--AATCGAATC
* *
462740 AAATTCTTGTTTTTTTTTAATCAAATC
1 AAATTC---TTTCTTTTTAATCGAATC
462767 AAATT
1 AAATT
462772 TTAGTGACCT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
24 8 0.16
26 7 0.14
27 13 0.25
28 15 0.29
29 6 0.12
31 2 0.04
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (24 bp):
AAATTCTTTCTTTTTAATCGAATC
Found at i:470675 original size:30 final size:31
Alignment explanation
Indices: 470641--470701 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
470631 AAAACTTAAC
470641 GTATTTTTTAGTAGCC-AAACTATC-ATTTTT
1 GTATTTTTTAGTA-CCTAAACTATCAATTTTT
*
470671 GTATTTTTTAGTACCTAAACTTTCAATTTTT
1 GTATTTTTTAGTACCTAAACTATCAATTTTT
470702 TAAAACTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 2 0.07
30 20 0.71
31 6 0.21
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.52
Consensus pattern (31 bp):
GTATTTTTTAGTACCTAAACTATCAATTTTT
Found at i:474844 original size:81 final size:81
Alignment explanation
Indices: 474709--474883 Score: 296
Period size: 81 Copynumber: 2.2 Consensus size: 81
474699 CTTCATGGAT
*
474709 TACAACCCAATTCAGTTAACATGTGCATGTTTTCACAATCATCTGTTAATAGTTTCATTTCGTTG
1 TACAACCCAATTCAGTTAACATGTGCATGTTTTCACAATCATCTGTTAACAGTTTCATTTCGTTG
474774 GGGTGTATATATAGAG
66 GGGTGTATATATAGAG
* * * *
474790 TACAACCCAATTCTGTTAACATGTGCATGTTTTCACTATCATCTGTTCACAGTTTCTTTTCGTTG
1 TACAACCCAATTCAGTTAACATGTGCATGTTTTCACAATCATCTGTTAACAGTTTCATTTCGTTG
*
474855 GTGTGTATATATAGAG
66 GGGTGTATATATAGAG
474871 TACAACCCAATTC
1 TACAACCCAATTC
474884 CGTATAACCA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (81 bp):
TACAACCCAATTCAGTTAACATGTGCATGTTTTCACAATCATCTGTTAACAGTTTCATTTCGTTG
GGGTGTATATATAGAG
Found at i:498672 original size:31 final size:31
Alignment explanation
Indices: 498629--498701 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
498619 TGGTTCAGTG
* *
498629 ACCAAAATTTAATAAAACGATAACGTAAGTA
1 ACCAAAACTTAATAAAACGATAACGTAAATA
* *
498660 ACCAAAACTTAATAAAACGATAATGTAAATT
1 ACCAAAACTTAATAAAACGATAACGTAAATA
498691 ACCAAAACTTA
1 ACCAAAACTTA
498702 TTTTTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (31 bp):
ACCAAAACTTAATAAAACGATAACGTAAATA
Found at i:504102 original size:186 final size:186
Alignment explanation
Indices: 503788--504159 Score: 744
Period size: 186 Copynumber: 2.0 Consensus size: 186
503778 CAGAGTCGAC
503788 CGTTCCACCACTGAAAATTATGTTTGTCATTATGTCCAACGTGATAACGGATGCAACTGACTGGT
1 CGTTCCACCACTGAAAATTATGTTTGTCATTATGTCCAACGTGATAACGGATGCAACTGACTGGT
503853 TCATGTATCGAAGAGGAAAAATAATATATGAGAACAAACAATATACAACGGTCTTCACACATCCT
66 TCATGTATCGAAGAGGAAAAATAATATATGAGAACAAACAATATACAACGGTCTTCACACATCCT
503918 GTGCTGGGGGGATCAACCAAGATCGTCCAAACTTGGACTCTGACATTATCTGCCAA
131 GTGCTGGGGGGATCAACCAAGATCGTCCAAACTTGGACTCTGACATTATCTGCCAA
503974 CGTTCCACCACTGAAAATTATGTTTGTCATTATGTCCAACGTGATAACGGATGCAACTGACTGGT
1 CGTTCCACCACTGAAAATTATGTTTGTCATTATGTCCAACGTGATAACGGATGCAACTGACTGGT
504039 TCATGTATCGAAGAGGAAAAATAATATATGAGAACAAACAATATACAACGGTCTTCACACATCCT
66 TCATGTATCGAAGAGGAAAAATAATATATGAGAACAAACAATATACAACGGTCTTCACACATCCT
504104 GTGCTGGGGGGATCAACCAAGATCGTCCAAACTTGGACTCTGACATTATCTGCCAA
131 GTGCTGGGGGGATCAACCAAGATCGTCCAAACTTGGACTCTGACATTATCTGCCAA
504160 GCCATCATGC
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 186 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (186 bp):
CGTTCCACCACTGAAAATTATGTTTGTCATTATGTCCAACGTGATAACGGATGCAACTGACTGGT
TCATGTATCGAAGAGGAAAAATAATATATGAGAACAAACAATATACAACGGTCTTCACACATCCT
GTGCTGGGGGGATCAACCAAGATCGTCCAAACTTGGACTCTGACATTATCTGCCAA
Found at i:511115 original size:100 final size:100
Alignment explanation
Indices: 510985--511166 Score: 301
Period size: 100 Copynumber: 1.8 Consensus size: 100
510975 TATTGTGTTG
* *
510985 AAAGATTATGAACTGCTTTCTAAGTGATATATATCAGCTTCAAAAATTAATTTAGTATCTAATAC
1 AAAGATTACGAACTGCTTTCTAAGTGATATATATCAACTTCAAAAATTAATTTAGTATCTAATAC
511050 ATTTTTTATTATGTTTCCTAATTGATATATGCTGA
66 ATTTTTTATTATGTTTCCTAATTGATATATGCTGA
* * * *
511085 AAAGATTACGAATTGTTTTCTAATTGATATATATCAACTTCAAAAATTAATTTAGTATCTAATAT
1 AAAGATTACGAACTGCTTTCTAAGTGATATATATCAACTTCAAAAATTAATTTAGTATCTAATAC
*
511150 TTTTTTTATTATGTTTC
66 ATTTTTTATTATGTTTC
511167 TTGACAAATT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (100 bp):
AAAGATTACGAACTGCTTTCTAAGTGATATATATCAACTTCAAAAATTAATTTAGTATCTAATAC
ATTTTTTATTATGTTTCCTAATTGATATATGCTGA
Found at i:512465 original size:32 final size:31
Alignment explanation
Indices: 512427--512503 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
512417 CGGGGCTGTG
*
512427 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
512459 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
512490 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
512504 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:513385 original size:7 final size:7
Alignment explanation
Indices: 513373--513409 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
513363 GTCAAAGAAA
513373 GTCAACG
1 GTCAACG
513380 GTCAACG
1 GTCAACG
*
513387 GTC-ACA
1 GTCAACG
513393 GTCAACG
1 GTCAACG
513400 GTCAACG
1 GTCAACG
513407 GTC
1 GTC
513410 GGGTCAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:513397 original size:20 final size:20
Alignment explanation
Indices: 513372--513409 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
513362 GGTCAAAGAA
513372 AGTCAACGGTCAACGGTCAC
1 AGTCAACGGTCAACGGTCAC
513392 AGTCAACGGTCAACGGTC
1 AGTCAACGGTCAACGGTC
513410 GGGTCAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (20 bp):
AGTCAACGGTCAACGGTCAC
Found at i:513452 original size:19 final size:19
Alignment explanation
Indices: 513428--513495 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
513418 AGTCGGGTCG
*
513428 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
513447 GGTCAAACCGGTTCAGATC
1 GGTCAAACCGGTTCAGACC
* *
513466 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
513486 GGTCAAACCG
1 GGTCAAACCG
513496 ATTTTCCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 31 0.72
20 12 0.28
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:513481 original size:10 final size:9
Alignment explanation
Indices: 513428--513495 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
513418 AGTCGGGTCG
*
513428 GGTCAACCC
1 GGTCAAACC
*
513437 GGTTCAGACC
1 GG-TCAAACC
513447 GGTCAAACC
1 GGTCAAACC
* *
513456 GGTTCAGATC
1 GG-TCAAACC
513466 GGTCAAACC
1 GGTCAAACC
*
513475 GGTTCAAAACT
1 GG-TC-AAACC
513486 GGTCAAACC
1 GGTCAAACC
513495 G
1 G
513496 ATTTTCCATC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 22 0.48
10 18 0.39
11 6 0.13
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (9 bp):
GGTCAAACC
Found at i:514380 original size:20 final size:20
Alignment explanation
Indices: 514355--514393 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
514345 ATATTATGCA
514355 GGGGGTA-CAGATTCCCCCTG
1 GGGGGTATC-GATTCCCCCTG
514375 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
514394 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.31, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:515278 original size:22 final size:22
Alignment explanation
Indices: 515250--515309 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
515240 GGTCTGCGCT
*
515250 GTCCTTCGGGACATATACAGTA-
1 GTCCTTCGGGACAAATACA-TAG
515272 GTCCTTCGGGACAAATACATAG
1 GTCCTTCGGGACAAATACATAG
*
515294 GTCCTTTGGGACAAAT
1 GTCCTTCGGGACAAAT
515310 TTCATATGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 2 0.06
22 33 0.94
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (22 bp):
GTCCTTCGGGACAAATACATAG
Found at i:517170 original size:30 final size:30
Alignment explanation
Indices: 517136--517203 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
517126 TAACGGTCAC
517136 TGATGTTTGAATAAAATTTTATTTTCTGAT
1 TGATGTTTGAATAAAATTTTATTTTCTGAT
* * *
517166 TGATGTTTGAATAAATTTTTCTTTTCTGTT
1 TGATGTTTGAATAAAATTTTATTTTCTGAT
517196 TGATGTTT
1 TGATGTTT
517204 CAAAAGTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.24, C:0.04, G:0.15, T:0.57
Consensus pattern (30 bp):
TGATGTTTGAATAAAATTTTATTTTCTGAT
Found at i:527869 original size:32 final size:32
Alignment explanation
Indices: 527822--527943 Score: 120
Period size: 32 Copynumber: 3.8 Consensus size: 32
527812 TAGTATCAGC
*
527822 ATTGCATTCAGATAGTGCATAACATATTCAAT
1 ATTGCATTCAGATAGTGCATAACAGATTCAAT
* * *
527854 ATTGTATTCAAATAGTGCATAGCAGATTCAAT
1 ATTGCATTCAGATAGTGCATAACAGATTCAAT
* * * * *
527886 ATTACATTCAGATAATGCATATCAGAGTCATT
1 ATTGCATTCAGATAGTGCATAACAGATTCAAT
* * *
527918 ATTTCATTTAGAT-GATGCACAACAGA
1 ATTGCATTCAGATAG-TGCATAACAGA
527944 GTTATTGTTG
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
32 73 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (32 bp):
ATTGCATTCAGATAGTGCATAACAGATTCAAT
Found at i:527944 original size:32 final size:32
Alignment explanation
Indices: 527876--528007 Score: 113
Period size: 32 Copynumber: 4.1 Consensus size: 32
527866 TAGTGCATAG
* * * *
527876 CAGATTCAATATTACATTCAGATAATGCATAT
1 CAGAGTCATTATTTCATTCAGATAATGCACAT
* * *
527908 CAGAGTCATTATTTCATTTAGATGATGCACAA
1 CAGAGTCATTATTTCATTCAGATAATGCACAT
* * *
527940 CAGAGTTATTGTTGT-ATTCAGATAAAGCACAT
1 CAGAGTCATTATT-TCATTCAGATAATGCACAT
* * * * *
527972 GAGCGTCAGTATTGCATTTAGATAATGCACAT
1 CAGAGTCATTATTTCATTCAGATAATGCACAT
528004 CAGA
1 CAGA
528008 TACAATCATT
Statistics
Matches: 75, Mismatches: 23, Indels: 4
0.74 0.23 0.04
Matches are distributed among these distances:
32 74 0.99
33 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (32 bp):
CAGAGTCATTATTTCATTCAGATAATGCACAT
Found at i:530843 original size:317 final size:317
Alignment explanation
Indices: 530268--530908 Score: 1151
Period size: 317 Copynumber: 2.0 Consensus size: 317
530258 AATTTTTAAT
*
530268 TCATTTTAACCAGTAAATGACAAAAGTACATAGATTTTTAATTAGAATTTTCATGAATTTGGTTC
1 TCATTTTAACCAGTAAATGACAAAAGTAAATAGATTTTTAATTAGAATTTTCATGAATTTGGTTC
530333 ATCTTAAAGCTCTTGGCCGTGACCTCCATTAGTAAGGTAAGAAAATTTTATTTTTGTTTTTCAAG
66 ATCTTAAAGCTCTTGGCCGTGACCTCCATTAGTAAGGTAAGAAAATTTTATTTTTGTTTTTCAAG
*
530398 CCAATTTCTTTGGTTTTAAGATGAAAGCATGAAATAGAAAATTAACCTACATGAAATTCTCTATC
131 CCAATTTCTTTGGTTTTAAGATGAAAGAATGAAATAGAAAATTAACCTACATGAAATTCTCTATC
*
530463 ATTTGGTACCATTTGTTCCTGCTTTCCATGCTTGAAATCATAAGTTCATGAATAGGGTGGATCAA
196 ATTTAGTACCATTTGTTCCTGCTTTCCATGCTTGAAATCATAAGTTCATGAATAGGGTGGATCAA
530528 TAG-GAGGTTTGATTTTGATGTTTTATGGATAGATTTGATGTTATTGATGTTATAGAA
261 -AGAGAGGTTTGATTTTGATGTTTTATGGATAGATTTGATGTTATTGATGTTATAGAA
* *
530585 TCATTTTAGCCAGTAAATGACAAAGGTAAATAGATTTTTAATTAGAATTTTCATGAATTTGGTTC
1 TCATTTTAACCAGTAAATGACAAAAGTAAATAGATTTTTAATTAGAATTTTCATGAATTTGGTTC
* *
530650 ATCTTCAAGCTCTTGGCCGTGACCTCCATTAGTAAGGTAAGAAAGTTTTATTTTTGTTTTTCAAG
66 ATCTTAAAGCTCTTGGCCGTGACCTCCATTAGTAAGGTAAGAAAATTTTATTTTTGTTTTTCAAG
* *
530715 CCAATTTCTTTGGTTTTAGGATGAAAGAATGAAATAGAAAATTAACCTATATGAAATTCTCTATC
131 CCAATTTCTTTGGTTTTAAGATGAAAGAATGAAATAGAAAATTAACCTACATGAAATTCTCTATC
*
530780 ATTTAGTACTATTTG-TCCATGCTTTCCATGCTTGAAATCATAAGTTCATGAATAGGGTGGATCA
196 ATTTAGTACCATTTGTTCC-TGCTTTCCATGCTTGAAATCATAAGTTCATGAATAGGGTGGATCA
*
530844 AGGAGAGGTTTGATTTTGATGTTTTATGGATAGATTTGATGTTATTGATGTTATAGAA
260 AAGAGAGGTTTGATTTTGATGTTTTATGGATAGATTTGATGTTATTGATGTTATAGAA
530902 TCATTTT
1 TCATTTT
530909 CATGCTTGTA
Statistics
Matches: 311, Mismatches: 11, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
316 4 0.01
317 307 0.99
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.40
Consensus pattern (317 bp):
TCATTTTAACCAGTAAATGACAAAAGTAAATAGATTTTTAATTAGAATTTTCATGAATTTGGTTC
ATCTTAAAGCTCTTGGCCGTGACCTCCATTAGTAAGGTAAGAAAATTTTATTTTTGTTTTTCAAG
CCAATTTCTTTGGTTTTAAGATGAAAGAATGAAATAGAAAATTAACCTACATGAAATTCTCTATC
ATTTAGTACCATTTGTTCCTGCTTTCCATGCTTGAAATCATAAGTTCATGAATAGGGTGGATCAA
AGAGAGGTTTGATTTTGATGTTTTATGGATAGATTTGATGTTATTGATGTTATAGAA
Found at i:532199 original size:31 final size:31
Alignment explanation
Indices: 532164--532233 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
532154 TACATTGGAC
532164 TATGATTTGAATATATGAA-AAGTACATGTTA
1 TATGATTTGAATATATGAACAA-TACATGTTA
* *
532195 TATGATTTGAATATGTGAACTATACATGTTA
1 TATGATTTGAATATATGAACAATACATGTTA
*
532226 TTTGATTT
1 TATGATTT
532234 CAGATGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (31 bp):
TATGATTTGAATATATGAACAATACATGTTA
Found at i:532360 original size:2 final size:2
Alignment explanation
Indices: 532347--532401 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
532337 AAGTCTATTT
*
532347 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
532389 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
532402 CACCAAGTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:536015 original size:16 final size:17
Alignment explanation
Indices: 535982--536015 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
535972 CAGAGATGAG
*
535982 CAACTTGATATTTTAAC
1 CAACTTGATATATTAAC
535999 CAACTTG-TATATTAAC
1 CAACTTGATATATTAAC
536015 C
1 C
536016 TCCAACGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (17 bp):
CAACTTGATATATTAAC
Found at i:540153 original size:2 final size:2
Alignment explanation
Indices: 540146--540196 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
540136 TGTTAACAAT
540146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
540188 TA TA TA TA T
1 TA TA TA TA T
540197 GAAATTATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:540326 original size:16 final size:17
Alignment explanation
Indices: 540305--540346 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
540295 AAACTGTAGA
540305 CAAAATATATTT-AAAT
1 CAAAATATATTTAAAAT
540321 CAAAATA-ATTTAGAAAT
1 CAAAATATATTTA-AAAT
*
540338 TAAAATATA
1 CAAAATATA
540347 ATTTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 7 0.32
17 10 0.45
18 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (17 bp):
CAAAATATATTTAAAAT
Found at i:541248 original size:13 final size:13
Alignment explanation
Indices: 541230--541256 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
541220 TATTTATATT
541230 TTTTTAAAAAATA
1 TTTTTAAAAAATA
541243 TTTTTAAAAAATA
1 TTTTTAAAAAATA
541256 T
1 T
541257 AAAATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:541771 original size:33 final size:33
Alignment explanation
Indices: 541727--541793 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
541717 GCATGTAATT
* * *
541727 TTTTTCGATTAGTTACTTATTTTACTGATGATG
1 TTTTTCAATTAGTTACTTATTTTACAGACGATG
541760 TTTTTCAATTAGTTACTTATTTTACAGACGATG
1 TTTTTCAATTAGTTACTTATTTTACAGACGATG
541793 T
1 T
541794 CAACCCTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.52
Consensus pattern (33 bp):
TTTTTCAATTAGTTACTTATTTTACAGACGATG
Found at i:544454 original size:13 final size:13
Alignment explanation
Indices: 544438--544462 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
544428 CTGATGCTCT
544438 GCTTTGGTGCTAG
1 GCTTTGGTGCTAG
544451 GCTTTGGTGCTA
1 GCTTTGGTGCTA
544463 TGCATGGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40
Consensus pattern (13 bp):
GCTTTGGTGCTAG
Found at i:544520 original size:61 final size:61
Alignment explanation
Indices: 544451--544570 Score: 213
Period size: 61 Copynumber: 2.0 Consensus size: 61
544441 TTGGTGCTAG
*
544451 GCTTTGGTGCTATGCATGGACCATGTACGGGGCATGGGATAGGTCACCAAGAGCTTTGTCT
1 GCTTTGGTGCTATGCATGGACCATGCACGGGGCATGGGATAGGTCACCAAGAGCTTTGTCT
* *
544512 GCTTTGGTGCTATGCATGGGCCATGCACGGGGCATGGGATAGGTCGCCAAGAGCTTTGT
1 GCTTTGGTGCTATGCATGGACCATGCACGGGGCATGGGATAGGTCACCAAGAGCTTTGT
544571 TCACGTGGTC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.18, C:0.20, G:0.35, T:0.27
Consensus pattern (61 bp):
GCTTTGGTGCTATGCATGGACCATGCACGGGGCATGGGATAGGTCACCAAGAGCTTTGTCT
Found at i:545060 original size:18 final size:17
Alignment explanation
Indices: 545039--545093 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
545029 AATAATTATT
545039 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATT-TTA
545057 TAAATTA--TTA--TT-
1 TAAATTAGTTTATTTTA
545069 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATT-TTA
545086 TAAATTAG
1 TAAATTAG
545094 GGTAAAACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 5 0.17
16 5 0.17
17 1 0.03
18 13 0.43
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TAAATTAGTTTATTTTA
Found at i:545074 original size:29 final size:30
Alignment explanation
Indices: 545033--545092 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
545023 AAAAAGAATA
*
545033 ATTATTTAAATTAGTTTATTGTTATAAATT
1 ATTATTTAAATTAGTTTATTATTATAAATT
545063 ATTATTT-AATTAGTTTATTATTATAAATT
1 ATTATTTAAATTAGTTTATTATTATAAATT
545092 A
1 A
545093 GGGTAAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (30 bp):
ATTATTTAAATTAGTTTATTATTATAAATT
Found at i:545394 original size:29 final size:29
Alignment explanation
Indices: 545357--545434 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
545347 TAGTAATAAA
545357 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
545387 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
545417 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
545435 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:545403 original size:22 final size:22
Alignment explanation
Indices: 545378--545458 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
545368 AATCATTTAT
*
545378 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
545400 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAGTTTA--AG-T----T-ATATTAAAGAA
*
545430 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
545452 TAGTTTA
1 TAGTTTA
545459 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 24 0.50
23 1 0.02
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 1 0.02
30 16 0.33
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:545538 original size:16 final size:16
Alignment explanation
Indices: 545506--545552 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
545496 TTTAAAAAGT
545506 TTAGTTTATTAGT-TTA
1 TTAGTTTATTA-TATTA
*
545522 TTAGTTTAATATATTA
1 TTAGTTTATTATATTA
*
545538 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
545553 AATTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:546769 original size:23 final size:23
Alignment explanation
Indices: 546741--546785 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
546731 TTTAATTATT
*
546741 ATTTAAATTAACTATATTATTTG
1 ATTTAAATAAACTATATTATTTG
* *
546764 ATTTAAATAAATTTTATTATTT
1 ATTTAAATAAACTATATTATTT
546786 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAACTATATTATTTG
Found at i:546785 original size:18 final size:20
Alignment explanation
Indices: 546735--546785 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
546725 GTTATTTTTA
546735 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATTAAC-AT
546756 ATTATTTGATTTAAA-TAA-AT
1 ATTA-TT-ATTTAAATTAACAT
*
546776 TTTATTATTT
1 ATTATTATTT
546786 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 2 0.07
20 5 0.19
21 4 0.15
22 5 0.19
23 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTTAAATTAACAT
Found at i:547701 original size:18 final size:18
Alignment explanation
Indices: 547680--547759 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 18
547670 TACTAAATCA
547680 TTAAATATTAATAATAAT
1 TTAAATATTAATAATAAT
* * *
547698 TTAATTATTACTAATCAT
1 TTAAATATTAATAATAAT
547716 TACTAAATCATTAAT-ATCAAAT
1 T--TAAAT-ATTAATAAT--AAT
547738 AATTAAATATTAATAATAAT
1 --TTAAATATTAATAATAAT
547758 TT
1 TT
547760 CATTATTACT
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
18 18 0.38
20 9 0.19
21 11 0.23
22 9 0.19
24 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATATTAATAATAAT
Found at i:547728 original size:21 final size:21
Alignment explanation
Indices: 547681--547788 Score: 54
Period size: 18 Copynumber: 5.5 Consensus size: 21
547671 ACTAAATCAT
*
547681 TAAAT-ATTAATAATAATT--
1 TAAATCATTAATAATCATTAC
* *
547699 T-AATTATTACTAATCATTAC
1 TAAATCATTAATAATCATTAC
* *
547719 TAAATCATTAAT-ATCAAATAAT
1 TAAATCATTAATAATC--ATTAC
*
547741 TAAAT-ATTAATAATAATT--
1 TAAATCATTAATAATCATTAC
* * *
547759 T-CATTATTACTAATCATTAC
1 TAAATCATTAATAATCATTAC
547779 TAAATCATTA
1 TAAATCATTA
547789 TTATAATTTC
Statistics
Matches: 66, Mismatches: 13, Indels: 19
0.67 0.13 0.19
Matches are distributed among these distances:
17 5 0.08
18 24 0.36
20 7 0.11
21 20 0.30
22 10 0.15
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATCATTAATAATCATTAC
Found at i:547748 original size:60 final size:60
Alignment explanation
Indices: 547674--548030 Score: 262
Period size: 60 Copynumber: 5.8 Consensus size: 60
547664 AATCATTACT
547674 AAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTAAATCATTAATATC
1 AAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTAAATCATTAATATC
* * *
547734 AAATAATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTATTAT-
1 AAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTAAATCATTAATATC
* * * * * * ** **
547793 AATTTCATTACTAGTTATGTAACGAA-AATATGGTGAATTGA--ACCAAACATT-GTTCATTGTT
1 AA-ATCATTA--A-ATAT-TAA-TAATAAT-T--T-AATT-ATTACTAATCATTACTAAATCATT
*
547854 CAA-GTC
55 -AATATC
* * * * * * * * * *
547860 GTAAATCATT-ACTATCAAATCATTAAATATTAATAATAAATTATTATTACT-AATTATTACTAT
1 --AAATCATTAAATAT-TAAT-AAT-AAT-TTAATTATTACTAATCATTACTAAATCATTAATAT
547923 C
60 C
*
547924 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATC
1 AAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTAAATCATTAATATC
*
547984 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA
1 AAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTA
548031 TCAAATCATT
Statistics
Matches: 228, Mismatches: 45, Indels: 48
0.71 0.14 0.15
Matches are distributed among these distances:
59 18 0.08
60 122 0.54
61 2 0.01
62 13 0.06
63 11 0.05
64 25 0.11
65 5 0.02
66 11 0.05
67 10 0.04
68 8 0.04
69 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (60 bp):
AAATCATTAAATATTAATAATAATTTAATTATTACTAATCATTACTAAATCATTAATATC
Found at i:547891 original size:21 final size:21
Alignment explanation
Indices: 547861--547939 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 21
547851 GTTCAAGTCG
547861 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATCAAATCAT
* * *
547883 TAAATATTAATAATAAATTATTAT
1 TAAATATTACT-ATCAA--ATCAT
547907 TACTAATTATTACTATCAAATCAT
1 TA--AA-TATTACTATCAAATCAT
547931 TAAATATTA
1 TAAATATTA
547940 ATAATAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
21 10 0.22
22 11 0.24
24 12 0.27
26 6 0.13
27 6 0.13
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTACTATCAAATCAT
Found at i:547915 original size:24 final size:24
Alignment explanation
Indices: 547888--547962 Score: 57
Period size: 24 Copynumber: 3.1 Consensus size: 24
547878 ATCATTAAAT
547888 ATTAATAATAAATTATTATTACTA
1 ATTAATAATAAATTATTATTACTA
* * *
547912 ATTATTACTATCAAATCATTA--AAT-
1 ATTAATA--AT-AAATTATTATTACTA
*
547936 ATTAATAATAATTTCATTATTACTA
1 ATTAATAATAAATT-ATTATTACTA
547961 AT
1 AT
547963 CATTACTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 13
0.65 0.12 0.23
Matches are distributed among these distances:
21 3 0.08
22 6 0.16
24 14 0.38
25 4 0.11
26 2 0.05
27 8 0.22
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTAATAATAAATTATTATTACTA
Found at i:547938 original size:48 final size:49
Alignment explanation
Indices: 547863--547970 Score: 191
Period size: 48 Copynumber: 2.2 Consensus size: 49
547853 TCAAGTCGTA
547863 AATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
* *
547911 AATTATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
547960 AATCATTACTA
1 AATCATTACTA
547971 AATCATTAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
48 37 0.66
49 19 0.34
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
AATCATTACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
Found at i:548085 original size:48 final size:48
Alignment explanation
Indices: 547964--548281 Score: 465
Period size: 48 Copynumber: 6.4 Consensus size: 48
547954 ATTACTAATC
* *
547964 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
548014 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
*
548062 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTATTAAT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAAT--A--A--ATTA-T--T
548119 CATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 -ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
*
548168 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* *
548216 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
548265 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
548282 AATCATTAAT
Statistics
Matches: 249, Mismatches: 8, Indels: 23
0.89 0.03 0.08
Matches are distributed among these distances:
48 131 0.53
49 58 0.23
50 7 0.03
51 1 0.00
52 5 0.02
54 5 0.02
55 1 0.00
56 1 0.00
57 1 0.00
58 39 0.16
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:548125 original size:58 final size:58
Alignment explanation
Indices: 548062--548362 Score: 302
Period size: 58 Copynumber: 5.5 Consensus size: 58
548052 ATAAATTATT
*
548062 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTATTAATC
1 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATC
*
548120 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATC
1 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATC
* * *
548178 ATTACTATTAAAT-C-ATTAAAT-ATT--A-A----TAATAAATTATTATTACTAATC
1 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATC
* *
548226 ATTAC---T-A-T-C----AAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATT-ATTATTACTAATC
* * * * *
548275 ATTACTAAATCATTAATATCAAATTATTAAATACTAATAATAATTTCATTATTACTAATC
1 ATTACT-AATCATTACTATTAAATCATTAAATATTAATAATAAATT-ATTATTACTAATC
*
548335 ATTACTAAATCATTACTA-TCAATCATTA
1 ATTACT-AATCATTACTATTAAATCATTA
548363 TTATTAAATC
Statistics
Matches: 208, Mismatches: 15, Indels: 39
0.79 0.06 0.15
Matches are distributed among these distances:
40 4 0.02
41 3 0.01
43 3 0.01
44 2 0.01
45 1 0.00
48 35 0.17
49 18 0.09
52 1 0.00
53 2 0.01
54 1 0.00
55 4 0.02
56 6 0.03
57 1 0.00
58 66 0.32
59 7 0.03
60 54 0.26
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (58 bp):
ATTACTAATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTACTAATC
Found at i:548150 original size:106 final size:106
Alignment explanation
Indices: 547863--548281 Score: 517
Period size: 106 Copynumber: 4.1 Consensus size: 106
547853 TCAAGTCGTA
* *
547863 AATCATTACTATCAAATCATTAAATATTAATAAT--A-A--ATTA-T--T-ATTACTAATTATTA
1 AATCATTACTATTAAATCATTAAATATTAATAATAAATATTATTATTAATCATTACTAATCATTA
*
547919 CTATCAAATCATTAAATATTAATAATAATTTCATTATTACT
66 CTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
* * * *
547960 AATCATTAC---TAAATCATT-AATATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
1 AATCATTACTATTAAATCATTAAATAT-TAAT-AATAAATATT-AT--T-A-TTAATCATTACTA
548021 ATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
59 ATCATTACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
548068 AATCATTACTATTAAATCATTAAATATTAATAATAAATTATTATTATTAATCATTACTAATCATT
1 AATCATTACTATTAAATCATTAAATATTAATAATAAA-TATTATTATTAATCATTACTAATCATT
548133 ACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
65 ACTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
548174 AATCATTACTATTAAATCATTAAATATTAATAAT--A-A--ATTA-T--T-ATTACTAATCATTA
1 AATCATTACTATTAAATCATTAAATATTAATAATAAATATTATTATTAATCATTACTAATCATTA
* *
548230 CTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
66 CTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
548271 AATCATTACTA
1 AATCATTACTA
548282 AATCATTAAT
Statistics
Matches: 289, Mismatches: 11, Indels: 44
0.84 0.03 0.13
Matches are distributed among these distances:
93 5 0.02
94 11 0.04
95 2 0.01
96 43 0.15
97 31 0.11
98 1 0.00
99 1 0.00
100 4 0.01
101 2 0.01
102 1 0.00
103 1 0.00
104 2 0.01
106 93 0.32
107 1 0.00
108 20 0.07
109 43 0.15
110 7 0.02
111 16 0.06
112 5 0.02
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (106 bp):
AATCATTACTATTAAATCATTAAATATTAATAATAAATATTATTATTAATCATTACTAATCATTA
CTATCAAATCATTAAATATTAATAATAAATTCATTATTACT
Found at i:548289 original size:21 final size:21
Alignment explanation
Indices: 548265--548352 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
548255 TAATTTCATT
548265 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* *
548286 ATTAAT-ATCAAATTATTAAAT-
1 ATTACTAATC--ATTACTAAATC
* * * * *
548307 ACTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
548325 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
548346 ATTACTA
1 ATTACTA
548353 TCAATCATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
17 2 0.04
18 11 0.22
20 7 0.14
21 19 0.38
22 11 0.22
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:548289 original size:60 final size:60
Alignment explanation
Indices: 548216--548428 Score: 247
Period size: 60 Copynumber: 3.5 Consensus size: 60
548206 ATAAATTATT
548216 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
* * * *
548275 ATTACTAAATCATTAATATCAAATTATTAAATACTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
548335 ATTACTAAATCATTACTATCAATCATTATTATTAAATCATTATTATAATAATTT--TTATTA--A
1 ATTACTAAATCATTACTATCAA--ATCATTA--AAA--ATTA--ATAATAATTTCATTATTACTA
548396 ATC
58 ATC
* *
548399 ATTACTATAATGATTATTATCAAATCATTA
1 ATTACTA-AATCATTACTATCAAATCATTA
548429 CTAAATCATC
Statistics
Matches: 134, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
59 6 0.04
60 70 0.52
62 7 0.05
63 6 0.04
64 13 0.10
65 13 0.10
66 9 0.07
68 10 0.07
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:548347 original size:11 final size:11
Alignment explanation
Indices: 548325--548362 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
548315 TAATTTCATT
548325 ATTACT-AATC
1 ATTACTAAATC
548335 ATTACTAAATC
1 ATTACTAAATC
548346 ATTACTATCAATC
1 ATTACTA--AATC
548359 ATTA
1 ATTA
548363 TTATTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 6 0.24
11 11 0.44
13 8 0.32
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:548399 original size:26 final size:26
Alignment explanation
Indices: 548144--548555 Score: 186
Period size: 26 Copynumber: 16.6 Consensus size: 26
548134 CTATCAAATC
548144 ATTAAAT-ATTA--ATAATAAATTATT
1 ATTAAATCATTACTATAAT-AATTATT
*
548168 ATTACTAATCATTACTAT--TAA--ATC
1 ATTA--AATCATTACTATAATAATTATT
548192 ATTAAAT-ATTA--ATAATAAATTATT
1 ATTAAATCATTACTATAAT-AATTATT
* *
548216 ATTACTAATCATTACTATCA-AATCATT
1 ATTA--AATCATTACTATAATAATTATT
548243 A--AAA--ATTA--ATAATAATTTCATT
1 ATTAAATCATTACTATAATAA-TT-ATT
* *
548265 ATTACTAATCATTACTA-AATCATTAAT
1 ATTA--AATCATTACTATAATAATTATT
* * * * * *
548292 ATCAAATTATTA-AATACTAATAATA
1 ATTAAATCATTACTATAATAATTATT
* *
548317 ATT---TCATTA-T-TACTAATCATT
1 ATTAAATCATTACTATAATAATTATT
* *
548338 ACTAAATCATTACTATCAATCATTATT
1 ATTAAATCATTACTAT-AATAATTATT
* *
548365 ATTAAATCATTATTATAATAATTTTT
1 ATTAAATCATTACTATAATAATTATT
*
548391 ATTAAATCATTACTATAATGATTATT
1 ATTAAATCATTACTATAATAATTATT
* * * *
548417 ATCAAATCATTACTA-AATCATCAAATC
1 ATTAAATCATTACTATAATAAT--TATT
*
548444 ATTAAAT-A-T--T-T-A-AATCATT
1 ATTAAATCATTACTATAATAATTATT
* *
548463 ATTAAATCATTATTATAATGATTATT
1 ATTAAATCATTACTATAATAATTATT
* * *
548489 ACTAAATCATTATTATAATGATTATT
1 ATTAAATCATTACTATAATAATTATT
* * *
548515 ATCAAATCATTATTATAATGATTATT
1 ATTAAATCATTACTATAATAATTATT
* *
548541 ATCATATCATTACTA
1 ATTAAATCATTACTA
548556 AATCATCAAA
Statistics
Matches: 298, Mismatches: 47, Indels: 84
0.69 0.11 0.20
Matches are distributed among these distances:
19 14 0.05
20 3 0.01
21 24 0.08
22 15 0.05
23 4 0.01
24 25 0.08
25 23 0.08
26 124 0.42
27 50 0.17
28 6 0.02
29 9 0.03
30 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (26 bp):
ATTAAATCATTACTATAATAATTATT
Found at i:548472 original size:72 final size:68
Alignment explanation
Indices: 548389--548620 Score: 210
Period size: 72 Copynumber: 3.5 Consensus size: 68
548379 ATAATAATTT
548389 TTATTAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATT
1 TTATTAAATCA-T--TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA-T
548454 TAAATCA
62 TAAATCA
* *
548461 TTATTAAATCATTATTATAATGATTATTA-CTAAATCATTA-T---T-AT--AATGATT-ATTAT
1 TTATTAAATC---ATTATAATGATTATTATC-AAATCATTACTAAATCATCAAATCATTAAATAT
*
548517 CAAATCA
62 TAAATCA
* * *
548524 TTATT--AT-AAT-GA----TTATTATCATATCATTACTAAATCATCAAATCATTAAATATTAAA
1 TTATTAAATCATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAA
548581 TTCA
66 -TCA
548585 TTATTAAATCATTATAATGATTATTATCAAATCATT
1 TTATTAAATCATTATAATGATTATTATCAAATCATT
548621 TTTATGGTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 47
0.68 0.06 0.25
Matches are distributed among these distances:
52 14 0.11
53 2 0.02
56 2 0.02
57 4 0.03
59 6 0.05
60 7 0.06
61 10 0.08
63 14 0.11
64 5 0.04
65 7 0.06
67 2 0.02
68 1 0.01
69 15 0.12
71 2 0.02
72 33 0.26
74 1 0.01
75 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (68 bp):
TTATTAAATCATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAA
TCA
Found at i:548503 original size:124 final size:122
Alignment explanation
Indices: 548331--548625 Score: 434
Period size: 124 Copynumber: 2.4 Consensus size: 122
548321 CATTATTACT
* * * * *
548331 AATCATTACTAAATCATTACTATCAATCATTATTATTAAATCATTATTATAATAATTTTTATTAA
1 AATCATTATTAAATCATTATTAT-AATGATTATTA-TAAATCATTATTATAATAATTATTATCAA
548396 ATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTA
64 ATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA-TTA
*
548456 AATCATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAA
1 AATCATTATTAAATCATTATTATAATGATTATTA-TAAATCATTATTATAATAATTATTATCAAA
* *
548521 TCATTATTATAATGATTATTATCATATCATTACTAAATCATCAAATCATTAAATATTA
65 TCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTA
*
548579 AATTCATTATTAAATC---ATTATAATGATTATTATCAAATCATTTTTAT
1 AA-TCATTATTAAATCATTATTATAATGATTATTAT-AAATCATTATTAT
548626 GGTTTATTGA
Statistics
Matches: 158, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
120 1 0.01
121 28 0.18
123 5 0.03
124 103 0.65
125 21 0.13
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (122 bp):
AATCATTATTAAATCATTATTATAATGATTATTATAAATCATTATTATAATAATTATTATCAAAT
CATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTA
Found at i:548616 original size:23 final size:23
Alignment explanation
Indices: 548474--548620 Score: 99
Period size: 26 Copynumber: 6.1 Consensus size: 23
548464 TTAAATCATT
548474 ATTATAATGATTATTA-CTAAATC
1 ATTATAATGATTATTATC-AAATC
548497 ATTATTATAATGATTATTATCAAATC
1 ---ATTATAATGATTATTATCAAATC
*
548523 ATTATTATAATGATTATTATCATATC
1 ---ATTATAATGATTATTATCAAATC
*
548549 ATTACT-A--A--ATCATCAAATC
1 ATTA-TAATGATTATTATCAAATC
* * *
548568 ATTAAATATTAAATTCATTATTAAATC
1 ATT--ATAAT-GATT-ATTATCAAATC
548595 ATTATAATGATTATTATCAAATC
1 ATTATAATGATTATTATCAAATC
548618 ATT
1 ATT
548621 TTTATGGTTT
Statistics
Matches: 101, Mismatches: 9, Indels: 25
0.75 0.07 0.19
Matches are distributed among these distances:
19 12 0.12
20 1 0.01
21 2 0.02
23 18 0.18
24 5 0.05
25 4 0.04
26 46 0.46
27 13 0.13
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (23 bp):
ATTATAATGATTATTATCAAATC
Found at i:548815 original size:17 final size:18
Alignment explanation
Indices: 548795--548884 Score: 67
Period size: 18 Copynumber: 4.8 Consensus size: 18
548785 TATTAGTAAA
548795 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
548812 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
*
548830 ACTAATTATTACTATCAAATAA-T
1 --TCATTATTA-T-T--AATAATT
* * *
548853 TAAATATTAATAATAATT
1 TCATTATTATTAATAATT
*
548871 TCATTATTACTAAT
1 TCATTATTATTAAT
548885 CATTACTATC
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
17 16 0.27
18 18 0.31
19 1 0.02
20 8 0.14
21 9 0.15
22 1 0.02
23 1 0.02
24 5 0.08
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:548837 original size:20 final size:17
Alignment explanation
Indices: 548797--548840 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
548787 TTAGTAAATC
*
548797 ATTATTATTATAATTTC
1 ATTATTATTATAATTTA
548814 ATTATTATTAATAATTACTA
1 ATTATTATT-ATAATT--TA
548834 ATTATTA
1 ATTATTA
548841 CTATCAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
18 6 0.26
20 8 0.35
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTATTATAATTTA
Found at i:551910 original size:26 final size:24
Alignment explanation
Indices: 551850--551910 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
551840 TACTAATATT
*
551850 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
551874 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
551901 ATTTAATAAT
1 A-TTAATAAT
551911 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:552166 original size:18 final size:18
Alignment explanation
Indices: 552143--552208 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
552133 ACAATATAAA
552143 TAAAACAAAATATTTTTT
1 TAAAACAAAATATTTTTT
* *
552161 TAAAACAACACTAAATATTTT
1 TAAAACAA-A--ATATTTTTT
* *
552182 T-AAACACAATCTTTTTT
1 TAAAACAAAATATTTTTT
*
552199 TTAAACAAAA
1 TAAAACAAAA
552209 ATTATCTCGC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 7 0.19
18 15 0.41
19 2 0.05
20 5 0.14
21 8 0.22
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAACAAAATATTTTTT
Found at i:553356 original size:36 final size:36
Alignment explanation
Indices: 553309--553390 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
553299 GACCTACACG
553309 CCCCGAGTGCCCCATGCATGAATCGATCATTGGTCA
1 CCCCGAGTGCCCCATGCATGAATCGATCATTGGTCA
* *
553345 CCCCGAGTGCCCCATGCATGAATCGATCCTTGGTCG
1 CCCCGAGTGCCCCATGCATGAATCGATCATTGGTCA
553381 CCCCGAGTGC
1 CCCCGAGTGC
553391 ATGGCATGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.18, C:0.37, G:0.24, T:0.21
Consensus pattern (36 bp):
CCCCGAGTGCCCCATGCATGAATCGATCATTGGTCA
Found at i:553461 original size:29 final size:29
Alignment explanation
Indices: 553429--553494 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
553419 CATGAACTGA
553429 TCCTTGGTCGCCCCGAGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
**** *
553458 TCCTTGGTCGTTGGGCGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
*
553487 TCTTTGGT
1 TCCTTGGT
553495 TACTGTACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.08, C:0.30, G:0.33, T:0.29
Consensus pattern (29 bp):
TCCTTGGTCGCCCCGAGTGCATGGCGACC
Found at i:554107 original size:32 final size:32
Alignment explanation
Indices: 554071--554157 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
554061 TTCGTGTTAC
*
554071 TTCAGGTTGCTTTCGGTTTGGGTTATTTTCAG
1 TTCAGGTTGCTTTCGGTTTGGGTTAATTTCAG
* * *
554103 TTCAGGTTGCTTTTGGTTTGGATTAATTTCGG
1 TTCAGGTTGCTTTCGGTTTGGGTTAATTTCAG
* * *
554135 TACAAGTTGTTTTCGGTTTGGGT
1 TTCAGGTTGCTTTCGGTTTGGGT
554158 CAAATTGGAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.11, C:0.10, G:0.29, T:0.49
Consensus pattern (32 bp):
TTCAGGTTGCTTTCGGTTTGGGTTAATTTCAG
Found at i:554792 original size:39 final size:39
Alignment explanation
Indices: 554718--554793 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
554708 CATAAATAAC
* * *
554718 TAATTTCTTAAATTATTTCATCATAAAATTTTAAATTCT
1 TAATTTATTAAATTATTTCACCATAAAATTGTAAATTCT
* **
554757 TAATTTATTAAATTATTTCACCCTATCATTGTAAATT
1 TAATTTATTAAATTATTTCACCATAAAATTGTAAATT
554794 ATTTTTCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (39 bp):
TAATTTATTAAATTATTTCACCATAAAATTGTAAATTCT
Found at i:556846 original size:15 final size:15
Alignment explanation
Indices: 556804--556838 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
556794 TAAAATTATA
556804 AAATTTAAATTACA-G
1 AAATTTAAATTA-ATG
556819 AAATTTAAATTAATG
1 AAATTTAAATTAATG
556834 AAATT
1 AAATT
556839 AAGATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (15 bp):
AAATTTAAATTAATG
Found at i:556959 original size:12 final size:13
Alignment explanation
Indices: 556924--556966 Score: 61
Period size: 12 Copynumber: 3.2 Consensus size: 13
556914 ATGTCAAATT
556924 AATATATCTTTAAA
1 AATATAT-TTTAAA
556938 AATTATATTTTAAA
1 AA-TATATTTTAAA
556952 AA-ATATTTTAAA
1 AATATATTTTAAA
556964 AAT
1 AAT
556967 TAAAAGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.44
14 10 0.37
15 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATTTTAAA
Found at i:563446 original size:44 final size:44
Alignment explanation
Indices: 563395--563483 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
563385 AAAATTTTCT
* * * **
563395 TTAAAAATAAGTGATTAACCTTTTTAATTTTATAATTTTAGGTG
1 TTAAAAATAAGTGACTAACATTTTCAACGTTATAATTTTAGGTG
*
563439 TTAAAAATAAGTGACTAACATTTTCAACGTTATACTTTTAGGTG
1 TTAAAAATAAGTGACTAACATTTTCAACGTTATAATTTTAGGTG
563483 T
1 T
563484 CTAGACCGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (44 bp):
TTAAAAATAAGTGACTAACATTTTCAACGTTATAATTTTAGGTG
Found at i:563571 original size:25 final size:24
Alignment explanation
Indices: 563542--563588 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
563532 TATATAACTT
* *
563542 TTTAAAATTTTTATATAAAAAAATA
1 TTTAAAATTATAAT-TAAAAAAATA
*
563567 TTTAATATTATAATTAAAAAAA
1 TTTAAAATTATAATTAAAAAAA
563589 CAAAAAATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAAATTATAATTAAAAAAATA
Found at i:565139 original size:35 final size:35
Alignment explanation
Indices: 565100--565167 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
565090 CCGCGAGGAG
* *
565100 GTGAAAATCGTGTACAATAGATCACACTCTAAGAA
1 GTGAAAATCCTGTACAATAGATCACACGCTAAGAA
*
565135 GTGAAAATCCTGTACAATAGGTCACACGCTAAG
1 GTGAAAATCCTGTACAATAGATCACACGCTAAG
565168 GAGCTGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (35 bp):
GTGAAAATCCTGTACAATAGATCACACGCTAAGAA
Found at i:575252 original size:56 final size:56
Alignment explanation
Indices: 575166--575277 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
575156 CCCCTGTCCT
575166 CTTTACTAATATATTTATAAGCCATACCTTACATCAACCTATGCCCAAAGCAAATG
1 CTTTACTAATATATTTATAAGCCATACCTTACATCAACCTATGCCCAAAGCAAATG
575222 CTTTACTAATATATTTATAAGCCATACCTTACATCAACCTATGCCCAAAGCAAATG
1 CTTTACTAATATATTTATAAGCCATACCTTACATCAACCTATGCCCAAAGCAAATG
575278 TAGAACATGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (56 bp):
CTTTACTAATATATTTATAAGCCATACCTTACATCAACCTATGCCCAAAGCAAATG
Found at i:575476 original size:63 final size:63
Alignment explanation
Indices: 575377--575504 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
575367 GCTACTTTCC
575377 CTTGTGCTAGTGTGCCGAGCTCCTCTTCTCCTTTGGCTTCAACATCTGTGATTGCTCCTTGCG
1 CTTGTGCTAGTGTGCCGAGCTCCTCTTCTCCTTTGGCTTCAACATCTGTGATTGCTCCTTGCG
575440 CTTGTGCTAGTGTGCCGAGCTCCTCTTCTCCTTTGGCTTCAACATCTGTGATTGCTCCTTGCG
1 CTTGTGCTAGTGTGCCGAGCTCCTCTTCTCCTTTGGCTTCAACATCTGTGATTGCTCCTTGCG
575503 CT
1 CT
575505 CGAGCTCCCG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.09, C:0.30, G:0.22, T:0.38
Consensus pattern (63 bp):
CTTGTGCTAGTGTGCCGAGCTCCTCTTCTCCTTTGGCTTCAACATCTGTGATTGCTCCTTGCG
Found at i:577750 original size:26 final size:26
Alignment explanation
Indices: 577721--577772 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
577711 TTAAATAAAT
*
577721 TAGTAAATAAACAATTAGATGTCAGC
1 TAGTAAATAAACAATTAGATGCCAGC
577747 TAGTAAATAAACAATTAGATGCCAGC
1 TAGTAAATAAACAATTAGATGCCAGC
577773 CGGCAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (26 bp):
TAGTAAATAAACAATTAGATGCCAGC
Found at i:584851 original size:25 final size:25
Alignment explanation
Indices: 584822--584884 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
584812 ATATAATATG
*
584822 ATTTTATATATATTAATT-TAAAAAT
1 ATTTTATATAT-TAAATTATAAAAAT
*
584847 ATTTT-TATATTAAATTAGTAAATAT
1 ATTTTATATATTAAATTA-TAAAAAT
584872 ATTTTAT-TATTAA
1 ATTTTATATATTAA
584885 CTTCATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 5 0.15
24 5 0.15
25 22 0.67
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTTATATATTAAATTATAAAAAT
Found at i:584856 original size:22 final size:24
Alignment explanation
Indices: 584830--584884 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
584820 TGATTTTATA
*
584830 TATATTAATTTA-AAAATAT-TTT
1 TATATTAAATTAGAAAATATATTT
*
584852 TATATTAAATTAGTAAATATATTT
1 TATATTAAATTAGAAAATATATTT
584876 TATTATTAA
1 TA-TATTAA
584885 CTTCATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.39
23 6 0.21
24 5 0.18
25 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATATTAAATTAGAAAATATATTT
Found at i:615202 original size:20 final size:20
Alignment explanation
Indices: 615179--615216 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
615169 ATACCTATAT
615179 TTTCATTTGTTTCAAAATCA
1 TTTCATTTGTTTCAAAATCA
615199 TTTCATTTGTTTCAAAAT
1 TTTCATTTGTTTCAAAAT
615217 TATACTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTCATTTGTTTCAAAATCA
Found at i:616206 original size:14 final size:14
Alignment explanation
Indices: 616189--616216 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
616179 TTAATGCACA
616189 AGAGATCGATCCTT
1 AGAGATCGATCCTT
616203 AGAGATCGATCCTT
1 AGAGATCGATCCTT
616217 TTTCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (14 bp):
AGAGATCGATCCTT
Found at i:616342 original size:20 final size:21
Alignment explanation
Indices: 616297--616351 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
616287 AGAATTCAAT
616297 GGATCGATCCTTTGGTCAAAG
1 GGATCGATCCTTTGGTCAAAG
* * *
616318 GGATCGATCCTTTTG-CTAGG
1 GGATCGATCCTTTGGTCAAAG
616338 GGATCGATCCTTTG
1 GGATCGATCCTTTG
616352 AGCCAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (21 bp):
GGATCGATCCTTTGGTCAAAG
Found at i:618992 original size:48 final size:48
Alignment explanation
Indices: 618921--619017 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
618911 TTGCAGAAAC
618921 ATCCAATCCCTTATAACCTATTATTTATAGAGATAACCATCCATGCAT
1 ATCCAATCCCTTATAACCTATTATTTATAGAGATAACCATCCATGCAT
618969 ATCCAATCCCTTATAACCTATTATTTATAGAGATAACCATCCATGCAT
1 ATCCAATCCCTTATAACCTATTATTTATAGAGATAACCATCCATGCAT
619017 A
1 A
619018 AGAACTCATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (48 bp):
ATCCAATCCCTTATAACCTATTATTTATAGAGATAACCATCCATGCAT
Found at i:624570 original size:18 final size:17
Alignment explanation
Indices: 624547--624580 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
624537 CAGTCTGTAT
624547 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
624565 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
624581 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:625243 original size:16 final size:16
Alignment explanation
Indices: 625222--625252 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
625212 TTCTAGAAAA
625222 TGATGCCCCTACATGT
1 TGATGCCCCTACATGT
*
625238 TGATGCCCTTACATG
1 TGATGCCCCTACATG
625253 CTGCCCTGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.32
Consensus pattern (16 bp):
TGATGCCCCTACATGT
Found at i:625464 original size:31 final size:31
Alignment explanation
Indices: 625429--625492 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
625419 AAATATACAT
625429 TTTGA-TACCTAAAATCTCCCTTAAT-ATTTAA
1 TTTGATTACCTAAAA-CT-CCTTAATGATTTAA
* *
625460 TTTGATTACTTAAAACTCCTTTATGATTTAA
1 TTTGATTACCTAAAACTCCTTAATGATTTAA
625491 TT
1 TT
625493 AAATCCTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.21
31 15 0.52
32 8 0.28
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTGATTACCTAAAACTCCTTAATGATTTAA
Found at i:631596 original size:2 final size:2
Alignment explanation
Indices: 631589--631628 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
631579 TATTACTGTG
631589 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
631629 TTAACAAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:632741 original size:15 final size:16
Alignment explanation
Indices: 632721--632758 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
632711 TATCCGTTCA
632721 ATATTATAATT-TTTT
1 ATATTATAATTATTTT
632736 ATATTAT-ATTATTTT
1 ATATTATAATTATTTT
632751 ATA-TATAA
1 ATATTATAA
632759 ATAAATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTATAATTATTTT
Found at i:633990 original size:16 final size:16
Alignment explanation
Indices: 633965--633998 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
633955 CAATAACTCA
633965 TTTTACGTAAATCAAT
1 TTTTACGTAAATCAAT
* *
633981 TTTTAGGTAATTCAAT
1 TTTTACGTAAATCAAT
633997 TT
1 TT
633999 ATTTTCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (16 bp):
TTTTACGTAAATCAAT
Found at i:634133 original size:30 final size:32
Alignment explanation
Indices: 634089--634154 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
634079 GAAATTGTTT
*
634089 TTTTTAATATAATTTATTTTATGT-AAAATAA
1 TTTTTAATATAATTTATTTTACGTAAAAATAA
634120 TTTTTAA-ATAATTTATTTTACGTAAAAATAA
1 TTTTTAATATAATTTATTTTACGTAAAAATAA
634151 TTTT
1 TTTT
634155 GACGGACCGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTTTAATATAATTTATTTTACGTAAAAATAA
Found at i:635665 original size:16 final size:18
Alignment explanation
Indices: 635633--635667 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
635623 ATATAAAAAC
635633 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
635651 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
635667 A
1 A
635668 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:635703 original size:20 final size:20
Alignment explanation
Indices: 635678--635715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
635668 AATGAGTAAA
635678 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
635698 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
635716 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:636328 original size:34 final size:35
Alignment explanation
Indices: 636246--636343 Score: 153
Period size: 34 Copynumber: 2.8 Consensus size: 35
636236 ATAGTAGAAC
636246 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA--AAAAT
*
636283 TTTATCCTATTTTTAGGAGTTTGAATCCT-AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
*
636317 TCTATCATATTTTTAGGAGTTTGAATC
1 TCTATCCTATTTTTAGGAGTTTGAATC
636344 TTAGTATGAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
34 30 0.52
37 28 0.48
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:637202 original size:105 final size:105
Alignment explanation
Indices: 636895--637831 Score: 1461
Period size: 105 Copynumber: 9.0 Consensus size: 105
636885 CATTGTTCCA
* * * ** * * *
636895 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * * *
636960 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* **
637001 AGTCCAATATCCTTCGTTATGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
637061 AGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
637101 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
637166 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
637206 AATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
637271 ATCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
637311 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
637376 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
637416 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
637481 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
637521 AGTCCAATATCCTTCATTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGTCAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
637586 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
637626 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
637691 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
637731 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
637796 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
637832 CCTCGAGTGC
Statistics
Matches: 775, Mismatches: 50, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
100 82 0.11
101 1 0.00
102 4 0.01
103 4 0.01
104 3 0.00
105 606 0.78
106 75 0.10
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:638638 original size:67 final size:66
Alignment explanation
Indices: 638503--638660 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 66
638493 AAGATATCTG
* * **
638503 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
638568 TT
65 TT
* * * * *
638570 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
638634 TT
65 TT
*
638636 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
638661 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:638676 original size:65 final size:67
Alignment explanation
Indices: 638504--638896 Score: 198
Period size: 65 Copynumber: 5.7 Consensus size: 67
638494 AGATATCTGT
* * * * * ** *
638504 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
638569 TTG
65 TTG
* * * *
638572 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
638636 T-
66 TG
* * * * *
638637 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AG
638699 AGATAAAACTT-
62 AG-T-----TTG
* * * * * * * * * * *
638710 AGTTCCAAAAGAAACTGTCTCAAGGGAGACG-GAATTTGTTTCAAAGAAAACATATTCAAATA-T
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGT
638773 TT-
65 TTG
* * * * *
638775 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--GTCTCAAGATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-A
*
638838 GACGAAATT-
61 GA-G--TTTG
* *
638847 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAA
638897 CTGTCTCAAG
Statistics
Matches: 254, Mismatches: 47, Indels: 44
0.74 0.14 0.13
Matches are distributed among these distances:
64 2 0.01
65 84 0.33
66 11 0.04
67 24 0.09
68 34 0.13
70 1 0.00
72 54 0.21
73 43 0.17
74 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:638687 original size:36 final size:35
Alignment explanation
Indices: 638636--638916 Score: 263
Period size: 36 Copynumber: 8.0 Consensus size: 35
638626 TTCAAAGGTT
* *
638636 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
638672 TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
638707 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
638745 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
638774 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
638809 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
638846 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
638881 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
638917 CTCTTCTAGT
Statistics
Matches: 202, Mismatches: 27, Indels: 32
0.77 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 133 0.66
37 32 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:638746 original size:138 final size:137
Alignment explanation
Indices: 638584--638897 Score: 414
Period size: 138 Copynumber: 2.3 Consensus size: 137
638574 TTTCAAGAGT
* * * * *
638584 AACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * *
638649 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
638713 TCCAAAAGA
129 TCCAAAAGA
** * * * *
638722 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
638787 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
638852 CAAGAGA
131 CAAAAGA
*
638859 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
638898 TGTCTCAAGA
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.33
138 101 0.67
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:638852 original size:101 final size:103
Alignment explanation
Indices: 638672--638860 Score: 283
Period size: 102 Copynumber: 1.9 Consensus size: 103
638662 TAGACGAAAA
* *
638672 TTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
*
638737 GACGGAATTTGTTTCAA-AGAAAACATATTCAAATATT
66 GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
* * * ** *
638774 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
638838 GACGAAATTTGTTTCAAGAGAAA
66 GACGAAATTTGTTTCAAGAGAAA
638861 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 36 0.47
102 41 0.53
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (103 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACGAAATTTGTTTCAAGAGAAAACATATTCAAATATT
Found at i:638938 original size:35 final size:36
Alignment explanation
Indices: 638778--638950 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
638768 AATATTTTGT
* * **
638778 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
638814 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
638850 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
638886 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
638920 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
638951 TCTTGTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 92 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:639924 original size:22 final size:22
Alignment explanation
Indices: 639847--639917 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
639837 TTGTGTTTGG
*
639847 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
639869 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
* *
639891 TCAATGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
639913 TCAAA
1 TCAAA
639918 AGATTGATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:640589 original size:16 final size:15
Alignment explanation
Indices: 640570--640652 Score: 62
Period size: 16 Copynumber: 5.1 Consensus size: 15
640560 TCTTTTTGAT
640570 TTTTGCTCTTTTTTTC
1 TTTTGCT-TTTTTTTC
640586 TTTTG-TTCTTGTTTCTC
1 TTTTGCTT-TT-TTT-TC
* *
640603 TTTTTCTTTGTTTTTT
1 TTTTGCTTT-TTTTTC
640619 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTT--TTC
640636 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTT-TTC
640651 TT
1 TT
640653 GATTGGATCT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
14 1 0.02
15 11 0.20
16 24 0.44
17 16 0.29
18 3 0.05
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.77
Consensus pattern (15 bp):
TTTTGCTTTTTTTTC
Found at i:640600 original size:15 final size:15
Alignment explanation
Indices: 640554--640643 Score: 60
Period size: 16 Copynumber: 5.7 Consensus size: 15
640544 CTTTTTGTCC
*
640554 CTTTTTTCTTT-TTG
1 CTTTTTTCTTTGTTT
* *
640568 ATTTTTGCTCTTTTTTT
1 CTTTTT--TCTTTGTTT
640585 CTTTTGTTC-TTGTTT
1 CTTTT-TTCTTTGTTT
640600 CTCTTTTTCTTTGTTT
1 CT-TTTTTCTTTGTTT
*
640616 TTTTTTTGCTTT-TTT
1 CTTTTTT-CTTTGTTT
640631 GCTTCTTTTCTTT
1 -CTT-TTTTCTTT
640644 TTTGTTCTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
14 5 0.08
15 18 0.30
16 27 0.44
17 10 0.16
18 1 0.02
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (15 bp):
CTTTTTTCTTTGTTT
Found at i:643873 original size:16 final size:18
Alignment explanation
Indices: 643841--643875 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
643831 ATATAAAAAC
643841 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
643859 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
643875 A
1 A
643876 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:644469 original size:37 final size:35
Alignment explanation
Indices: 644428--644555 Score: 132
Period size: 37 Copynumber: 3.6 Consensus size: 35
644418 GGATCTTATC
* **
644428 TTTAGGAATTTAAATAATAGTAGAATTCTATCCTATT
1 TTTAGGAATTTGAATCCTAG-A-AATTCTATCCTATT
* *
644465 TTTAGGAGTTTGAATCCTAGCAAAATTTTATCCTATT
1 TTTAGGAATTTGAATCCTAG--AAATTCTATCCTATT
* *
644502 TTTAGGAGTTTGAATCCTA-AAATTCTATCATATT
1 TTTAGGAATTTGAATCCTAGAAATTCTATCCTATT
* *
644536 TTTAAGAATTTGAATTCTAG
1 TTTAGGAATTTGAATCCTAG
644556 TAAGACGAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 29 0.37
37 48 0.62
38 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (35 bp):
TTTAGGAATTTGAATCCTAGAAATTCTATCCTATT
Found at i:644536 original size:34 final size:35
Alignment explanation
Indices: 644451--644550 Score: 139
Period size: 37 Copynumber: 2.8 Consensus size: 35
644441 ATAATAGTAG
644451 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAGCAA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTA--AA
*
644488 AATTTTATCCTATTTTTAGGAGTTTGAATCCT-AA
1 AATTCTATCCTATTTTTAGGAGTTTGAATCCTAAA
* * *
644522 AATTCTATCATATTTTTAAGAATTTGAAT
1 AATTCTATCCTATTTTTAGGAGTTTGAAT
644551 TCTAGTAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
34 27 0.47
37 31 0.53
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (35 bp):
AATTCTATCCTATTTTTAGGAGTTTGAATCCTAAA
Found at i:645196 original size:16 final size:16
Alignment explanation
Indices: 645177--645207 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
645167 ATTACACTCT
645177 TAATAAATTTTTATTA
1 TAATAAATTTTTATTA
*
645193 TAATTAATTTTTATT
1 TAATAAATTTTTATT
645208 TTTAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATAAATTTTTATTA
Done.