Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 91 of 199
Found at i:28018617 original size:50 final size:50
Alignment explanation
Indices: 28018506--28018751 Score: 258
Period size: 50 Copynumber: 4.8 Consensus size: 50
28018496 ATTTGGGTAA
* * *
28018506 AGAGATCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
28018562 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
28018612 AGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
28018662 AGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCTATATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
28018712 AGAACTCTCATGTAAAACCATATCTGGGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
28018752 TAGTACAAGA
Statistics
Matches: 165, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 122 0.74
53 3 0.02
55 1 0.01
56 39 0.24
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28020693 original size:13 final size:12
Alignment explanation
Indices: 28020664--28020706 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
28020654 GTTCCAAATA
* *
28020664 CAAAAGCTCTCT
1 CAAAAACTCTCC
*
28020676 CAAAAACTGTCC
1 CAAAAACTCTCC
28020688 CAAAAACTCTCCC
1 CAAAAACTCT-CC
28020701 CAAAAA
1 CAAAAA
28020707 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.44, C:0.35, G:0.05, T:0.16
Consensus pattern (12 bp):
CAAAAACTCTCC
Found at i:28021387 original size:24 final size:24
Alignment explanation
Indices: 28021360--28021409 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
28021350 AAAGACAATT
*
28021360 AATAAATAAT-AAAATAATATTTAA
1 AATAAATAATCAAAATAA-ATTAAA
**
28021384 AATATTTAATCAAAATAAATTAAA
1 AATAAATAATCAAAATAAATTAAA
28021408 AA
1 AA
28021410 GGTAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AATAAATAATCAAAATAAATTAAA
Found at i:28031906 original size:34 final size:35
Alignment explanation
Indices: 28031862--28031928 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28031852 CAGTAAAATG
*
28031862 TTTTCCGTAAAATAATTTA-TGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
28031896 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
28031929 CTTGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:28032111 original size:22 final size:24
Alignment explanation
Indices: 28032086--28032136 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
28032076 TTATTTATAA
28032086 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
28032106 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
28032132 ATAAA
1 ATAAA
28032137 AGCATTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:28039188 original size:33 final size:33
Alignment explanation
Indices: 28039114--28039198 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
28039104 GTGAACTGGG
* * ** *
28039114 ACTGCGAACTCCCTTCGACTCCTACGAGTTGAT
1 ACTGCGAGCTCCCTTCAACTCCTACGAGCCGAC
*
28039147 ACCT-CGAGCTCCTTTCAACTCCTACGAGCCGAC
1 A-CTGCGAGCTCCCTTCAACTCCTACGAGCCGAC
28039180 ACTGCGAGCTCCCTT-AACT
1 ACTGCGAGCTCCCTTCAACT
28039199 GTCCTCATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
32 6 0.14
33 35 0.81
34 2 0.05
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (33 bp):
ACTGCGAGCTCCCTTCAACTCCTACGAGCCGAC
Found at i:28042251 original size:140 final size:140
Alignment explanation
Indices: 28042040--28042545 Score: 494
Period size: 140 Copynumber: 3.6 Consensus size: 140
28042030 TAGCTTGAGT
* * * ** * * * * ** * *
28042040 TCTCGCTAACTGTTTTGGATGCTACAATATTGAACCTACAAGTCTTAAGTTCATAGCTAGGAGTT
1 TCTCGCTAACTGTTTTGGAGGTTGCGGTATTGAACCTGCTAGCCTTAAGTTCACAATTGGGAGCT
* * * * * *
28042105 TGAGCTCTCGTTAACTGTTTTAATGGTTGCGGTATTGAACTTGCGAACCTTAAGATTACAATTGG
66 TGAGCTCTCGCTAACTGTTTTGATGGTTGCGGTATTAAACTTACGAGCCTTAAGATTACAGTTGG
*
28042170 GAGCTTTAGC
131 GAGCCTTAGC
* * * * *
28042180 TCTCGCTAACTATTTTGGAAGCTGCGGTATTGAACTTGCTAGCTTTAAGTTCACAATTGGGAGCT
1 TCTCGCTAACTGTTTTGGAGGTTGCGGTATTGAACCTGCTAGCCTTAAGTTCACAATTGGGAGCT
* *** * * *
28042245 TGAGCTCTCGCTAACTATTTTGATGGTCATGGTATTAAACCTACGAGCCCTAAGATTATAGTTGG
66 TGAGCTCTCGCTAACTGTTTTGATGGTTGCGGTATTAAACTTACGAGCCTTAAGATTACAGTTGG
*
28042310 AAGCCTTAGC
131 GAGCCTTAGC
* * * * * * * *
28042320 TCTCACTGACTGTTTTGGAGGTTACGGTATTAAACCTACAAGCCTTAAGTTCACAATTAGGAGCC
1 TCTCGCTAACTGTTTTGGAGGTTGCGGTATTGAACCTGCTAGCCTTAAGTTCACAATTGGGAGCT
* * * *
28042385 TGAGCTCTCGCTAAATGTTTTGATGGTTGCGATTTTAAACTTACGAGCCTTAAGATTACAGTTAG
66 TGAGCTCTCGCTAACTGTTTTGATGGTTGCGGTATTAAACTTACGAGCCTTAAGATTACAGTTGG
28042450 GAGCCTTAGC
131 GAGCCTTAGC
* * * * * * * *
28042460 TTTTGCTAACTGTTTTAGAGGTTGCAGTACTGAACCAG-TGAGCCTTAAGATT-ACAGTTGGAAG
1 TCTCGCTAACTGTTTTGGAGGTTGCGGTATTGAACCTGCT-AGCCTTAAG-TTCACAATTGGGAG
*
28042523 CGTGAGCTCTCGCTAACTGTTTT
64 CTTGAGCTCTCGCTAACTGTTTT
28042546 TGGGGTGGAT
Statistics
Matches: 292, Mismatches: 72, Indels: 4
0.79 0.20 0.01
Matches are distributed among these distances:
140 290 0.99
141 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (140 bp):
TCTCGCTAACTGTTTTGGAGGTTGCGGTATTGAACCTGCTAGCCTTAAGTTCACAATTGGGAGCT
TGAGCTCTCGCTAACTGTTTTGATGGTTGCGGTATTAAACTTACGAGCCTTAAGATTACAGTTGG
GAGCCTTAGC
Found at i:28042279 original size:70 final size:70
Alignment explanation
Indices: 28042031--28042545 Score: 323
Period size: 70 Copynumber: 7.4 Consensus size: 70
28042021 TTACGTTCAT
* * ** * * *
28042031 AGCTTGAGTTCTCGCTAACTGTTTTGGATGCT-ACAATATTGAACCTACAAGTCTTAAG-TT-CA
1 AGCTTGAGCTCTCGCTAACTGTTTT-GATGGTCACGGTATTAAACCTACGAGCCTTAAGATTACA
* *
28042093 TAGCTAGG
65 -A-TTGGG
* * * ** * * * *
28042101 AGTTTGAGCTCTCGTTAACTGTTTTAATGGTTGCGGTATTGAACTTGCGAACCTTAAGATTACAA
1 AGCTTGAGCTCTCGCTAACTGTTTTGATGGTCACGGTATTAAACCTACGAGCCTTAAGATTACAA
28042166 TTGGG
66 TTGGG
* * * * * * * * * *
28042171 AGCTTTAGCTCTCGCTAACTATTTTGGAAGCT-GCGGTATTGAACTTGCTAGCTTTAAG-TTCAC
1 AGCTTGAGCTCTCGCTAACTGTTTT-GATGGTCACGGTATTAAACCTACGAGCCTTAAGATT-AC
28042234 AATTGGG
64 AATTGGG
* * * * *
28042241 AGCTTGAGCTCTCGCTAACTATTTTGATGGTCATGGTATTAAACCTACGAGCCCTAAGATTATAG
1 AGCTTGAGCTCTCGCTAACTGTTTTGATGGTCACGGTATTAAACCTACGAGCCTTAAGATTACAA
*
28042306 TTGGA
66 TTGGG
* * * *
28042311 AGCCTT-AGCTCTCACTGACTGTTTTGGA-GGTTACGGTATTAAACCTACAAGCCTTAAG-TTCA
1 AG-CTTGAGCTCTCGCTAACTGTTTT-GATGGTCACGGTATTAAACCTACGAGCCTTAAGATT-A
*
28042373 CAATTAGG
63 CAATTGGG
* * ** * * * *
28042381 AGCCTGAGCTCTCGCTAAATGTTTTGATGGTTGCGATTTTAAACTTACGAGCCTTAAGATTACAG
1 AGCTTGAGCTCTCGCTAACTGTTTTGATGGTCACGGTATTAAACCTACGAGCCTTAAGATTACAA
*
28042446 TTAGG
66 TTGGG
* * ** * * * *
28042451 AGCCTT-AGCTTTTGCTAACTGTTTTAGA-GGTTGCAGTACTGAACC-AGTGAGCCTTAAGATTA
1 AG-CTTGAGCTCTCGCTAACTGTTTT-GATGGTCACGGTATTAAACCTA-CGAGCCTTAAGATTA
* *
28042513 CAGTTGGA
63 CAATTGGG
*
28042521 AGCGTGAGCTCTCGCTAACTGTTTT
1 AGCTTGAGCTCTCGCTAACTGTTTT
28042546 TGGGGTGGAT
Statistics
Matches: 352, Mismatches: 76, Indels: 34
0.76 0.16 0.07
Matches are distributed among these distances:
69 19 0.05
70 312 0.89
71 19 0.05
72 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (70 bp):
AGCTTGAGCTCTCGCTAACTGTTTTGATGGTCACGGTATTAAACCTACGAGCCTTAAGATTACAA
TTGGG
Found at i:28048928 original size:22 final size:23
Alignment explanation
Indices: 28048903--28048947 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
28048893 TAAAGGGTAG
28048903 TTAATATTAT-TATAAAAATATT
1 TTAATATTATATATAAAAATATT
* *
28048925 TTAATCTTTTCATATAAAAATAT
1 TTAATATTAT-ATATAAAAATAT
28048948 CATTTAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
24 11 0.58
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATATTATATATAAAAATATT
Found at i:28049184 original size:15 final size:16
Alignment explanation
Indices: 28049159--28049189 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
28049149 TTAATTCTTT
28049159 TTAATATTTATTTTAA
1 TTAATATTTATTTTAA
28049175 TTAA-ATTTATTTTAA
1 TTAATATTTATTTTAA
28049190 CCAAGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATATTTATTTTAA
Found at i:28050476 original size:19 final size:19
Alignment explanation
Indices: 28050454--28050491 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28050444 TTAATTTGAT
28050454 TTCTTTTATAGAATTTATA
1 TTCTTTTATAGAATTTATA
28050473 TTCTTTTATAGAATTTATA
1 TTCTTTTATAGAATTTATA
28050492 AATTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (19 bp):
TTCTTTTATAGAATTTATA
Found at i:28052144 original size:20 final size:21
Alignment explanation
Indices: 28052107--28052149 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
28052097 AGCTATTTTA
28052107 ATATTTATATTATTATATCAT
1 ATATTTATATTATTATATCAT
* *
28052128 ATATTTA-ATTTTTATATGAT
1 ATATTTATATTATTATATCAT
28052148 AT
1 AT
28052150 TTAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
ATATTTATATTATTATATCAT
Found at i:28052407 original size:17 final size:18
Alignment explanation
Indices: 28052375--28052409 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28052365 AATAAATTTT
28052375 AAATCCAAAATGTTTATAA
1 AAATCCAAAA-GTTTATAA
28052394 AAATCCAAAA-TTTATA
1 AAATCCAAAAGTTTATA
28052410 TTTTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATCCAAAAGTTTATAA
Found at i:28052457 original size:19 final size:19
Alignment explanation
Indices: 28052435--28052485 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
28052425 AAATTTTTTT
28052435 AAAAATATTAAAAAATCTA
1 AAAAATATTAAAAAATCTA
** *
28052454 AAAAATATATAAAATTTTTA
1 AAAAATAT-TAAAAAATCTA
28052474 AAAAA-ATTAAAA
1 AAAAATATTAAAA
28052486 TAATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.18
19 10 0.36
20 13 0.46
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATATTAAAAAATCTA
Found at i:28052467 original size:28 final size:30
Alignment explanation
Indices: 28052434--28052491 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
28052424 TAAATTTTTT
*
28052434 TAAAAATATT-AAAAAATCTAAAA-AATATA
1 TAAAATTATTAAAAAAAT-TAAAATAATATA
*
28052463 TAAAATTTTTAAAAAAATTAAAATAATAT
1 TAAAATTATTAAAAAAATTAAAATAATAT
28052492 TTTTTAGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (30 bp):
TAAAATTATTAAAAAAATTAAAATAATATA
Found at i:28055107 original size:18 final size:19
Alignment explanation
Indices: 28055073--28055108 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28055063 AAAAAAATAT
*
28055073 TCAAAATAATTTTTAAAAC
1 TCAAAATAATTTATAAAAC
28055092 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
28055109 ATTTCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAC
Found at i:28055743 original size:29 final size:29
Alignment explanation
Indices: 28055710--28055767 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
28055700 CATTAACTAT
*
28055710 TTGAACTAATTAATAATATTATAAAAATA
1 TTGAACTAATTAATAACATTATAAAAATA
*
28055739 TTGAACTGATTAATAACATTATAAAAATA
1 TTGAACTAATTAATAACATTATAAAAATA
28055768 AAGAAACGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (29 bp):
TTGAACTAATTAATAACATTATAAAAATA
Found at i:28058117 original size:75 final size:75
Alignment explanation
Indices: 28057994--28058144 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
28057984 AAAATAAGGC
28057994 AAAAAAAAGAAAAAGAAAGATAACATCTGATATTTAACAAATTAAAGAAATTATTGAAGGCAAAA
1 AAAAAAAAGAAAAAGAAAGATAACATCTGATATTTAACAAATTAAAGAAATTATTGAAGGCAAAA
28058059 CATGCAAAAT
66 CATGCAAAAT
28058069 AAAAAAAAGAAAAAGAAAGATAACATCTGATATTTAACAAATTAAAGAAATTATTGAAGGCAAAA
1 AAAAAAAAGAAAAAGAAAGATAACATCTGATATTTAACAAATTAAAGAAATTATTGAAGGCAAAA
28058134 CATGCAAAAT
66 CATGCAAAAT
28058144 A
1 A
28058145 TTGATAAGAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (75 bp):
AAAAAAAAGAAAAAGAAAGATAACATCTGATATTTAACAAATTAAAGAAATTATTGAAGGCAAAA
CATGCAAAAT
Found at i:28062099 original size:2 final size:2
Alignment explanation
Indices: 28062092--28062145 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
28062082 TGTTCGTTCT
28062092 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
28062134 TC TC TC AC TC TC
1 TC TC TC TC TC TC
28062146 ACATTTGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:28062477 original size:16 final size:17
Alignment explanation
Indices: 28062444--28062484 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
28062434 TATACATGAT
28062444 ATTAAAATAAAAATTAA
1 ATTAAAATAAAAATTAA
* *
28062461 ATTAAATTATAAA-TAA
1 ATTAAAATAAAAATTAA
28062477 ATTAAAAT
1 ATTAAAAT
28062485 TTAAACACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAAATAAAAATTAA
Found at i:28062485 original size:17 final size:18
Alignment explanation
Indices: 28062444--28062489 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
28062434 TATACATGAT
*
28062444 ATTAAAA-TAAAAATTAA
1 ATTAAAATTATAAATTAA
28062461 ATT-AAATTATAAA-TAA
1 ATTAAAATTATAAATTAA
28062477 ATTAAAATT-TAAA
1 ATTAAAATTATAAA
28062490 CACATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTAAAATTATAAATTAA
Found at i:28066115 original size:2 final size:2
Alignment explanation
Indices: 28066108--28066132 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28066098 AGAAGTGTAA
28066108 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28066133 AATGTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28066813 original size:14 final size:14
Alignment explanation
Indices: 28066760--28066814 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
28066750 CCATCCACCG
*
28066760 GAAGAGAGAAAGAA
1 GAAGAAAGAAAGAA
*
28066774 -AAGAGAGAAA-AGA
1 GAAGAAAGAAAGA-A
28066787 GAAGAAA-ATAAGAA
1 GAAGAAAGA-AAGAA
28066801 GAAGAAAGAAAGAA
1 GAAGAAAGAAAGAA
28066815 AGAAAAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 1 0.03
13 12 0.34
14 20 0.57
15 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (14 bp):
GAAGAAAGAAAGAA
Found at i:28067065 original size:60 final size:60
Alignment explanation
Indices: 28066986--28067104 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
28066976 TTGCTTTTTA
* * *
28066986 TAATTATTTTAAAATTAATTTGCTAGTAAATAAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTACTAGTAAATAAGGATTAAGTTATAAATTGTTGTGTTTG
* * *
28067046 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTACTAGTAAATAAGGATTAAGTTATAAATTGTTGTGTTT
28067105 AGTTTTGTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTACTAGTAAATAAGGATTAAGTTATAAATTGTTGTGTTTG
Found at i:28069479 original size:20 final size:19
Alignment explanation
Indices: 28069454--28069499 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
28069444 ATGCATGTAT
*
28069454 ATAAAACATAAAGTATAAAA
1 ATAAAAAATAAA-TATAAAA
28069474 ATAAAAAAATAAATATAAAA
1 AT-AAAAAATAAATATAAAA
*
28069494 ACAAAA
1 ATAAAA
28069500 GTAACAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (19 bp):
ATAAAAAATAAATATAAAA
Found at i:28071807 original size:98 final size:98
Alignment explanation
Indices: 28071633--28071830 Score: 326
Period size: 98 Copynumber: 2.0 Consensus size: 98
28071623 AGTACGGTCC
* *
28071633 ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACTTGTTCATATAGTTGGGGGTCCGCA
1 ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTCCGCA
28071698 GTTTTACCCATGCTGTATCGCAAAC-TTGATCGG
66 GTTTTACCCATGCTGTATCGCAAACTTTG-TCGG
*
28071731 ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTTCGCA
1 ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTCCGCA
* * *
28071796 GTTTTAGCCATGTTGTATCGCGAACTTTGTCGG
66 GTTTTACCCATGCTGTATCGCAAACTTTGTCGG
28071829 AC
1 AC
28071831 GACAGATCCT
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 90 0.97
99 3 0.03
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (98 bp):
ACTTGATGTACTTACCCCTATTATCCAATTTGCATAACACCTGCTCATATAGTTGGGGGTCCGCA
GTTTTACCCATGCTGTATCGCAAACTTTGTCGG
Found at i:28072667 original size:18 final size:18
Alignment explanation
Indices: 28072644--28072678 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28072634 GCATCATGCA
*
28072644 CCAGAGCCAGAGCCGGAG
1 CCAGAGCCAGAGACGGAG
*
28072662 CCAGAGGCAGAGACGGA
1 CCAGAGCCAGAGACGGA
28072679 ACTACATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.29, G:0.40, T:0.00
Consensus pattern (18 bp):
CCAGAGCCAGAGACGGAG
Found at i:28072832 original size:33 final size:31
Alignment explanation
Indices: 28072790--28072900 Score: 96
Period size: 33 Copynumber: 3.4 Consensus size: 31
28072780 GCCCACTACA
*
28072790 ACCTCAGTACTCCATTCATCCTAGCTCGTATCC
1 ACCTCAGTACTCC-TCCATCC-AGCTCGTATCC
* *
28072823 ACCTCAGTACTTCGCTCCTTCCAGCTCGTATCT
1 ACCTCAGTAC-TC-CTCCATCCAGCTCGTATCC
* * * *
28072856 ACCTTAGTACTCCGCTCCTTTCGGCTCGTATCC
1 ACCTCAGTACT-C-CTCCATCCAGCTCGTATCC
*
28072889 ACCTTAGTACTC
1 ACCTCAGTACTC
28072901 TGCTCCTTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
32 2 0.03
33 58 0.85
34 7 0.10
35 1 0.01
ACGTcount: A:0.17, C:0.39, G:0.12, T:0.32
Consensus pattern (31 bp):
ACCTCAGTACTCCTCCATCCAGCTCGTATCC
Found at i:28072906 original size:33 final size:33
Alignment explanation
Indices: 28072812--28072909 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
28072802 CATTCATCCT
*
28072812 AGCTCGTATCCACCTCAGTACT-TCGCTCCTTCC
1 AGCTCGTATCCACCTTAGTACTCT-GCTCCTTCC
* * *
28072845 AGCTCGTATCTACCTTAGTACTCCGCTCCTTTC
1 AGCTCGTATCCACCTTAGTACTCTGCTCCTTCC
*
28072878 GGCTCGTATCCACCTTAGTACTCTGCTCCTTC
1 AGCTCGTATCCACCTTAGTACTCTGCTCCTTC
28072910 TGACCCGTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.14, C:0.39, G:0.13, T:0.34
Consensus pattern (33 bp):
AGCTCGTATCCACCTTAGTACTCTGCTCCTTCC
Found at i:28072919 original size:33 final size:33
Alignment explanation
Indices: 28072814--28072924 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 33
28072804 TTCATCCTAG
* *
28072814 CTCGTATCCACCTCAGTACT-TCGCTCCTTC-CA
1 CTCGTATCCACCTTAGTACTCT-GCTCCTTCTGA
* * *
28072846 GCTCGTATCTACCTTAGTACTCCGCTCCTT-TCGG
1 -CTCGTATCCACCTTAGTACTCTGCTCCTTCT-GA
28072880 CTCGTATCCACCTTAGTACTCTGCTCCTTCTGA
1 CTCGTATCCACCTTAGTACTCTGCTCCTTCTGA
*
28072913 CCCGTATCCACC
1 CTCGTATCCACC
28072925 GCCATACTCC
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
33 64 0.98
34 1 0.02
ACGTcount: A:0.14, C:0.41, G:0.13, T:0.32
Consensus pattern (33 bp):
CTCGTATCCACCTTAGTACTCTGCTCCTTCTGA
Found at i:28077447 original size:17 final size:16
Alignment explanation
Indices: 28077420--28077451 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28077410 TTATTCATTG
28077420 TTTTGAATTTTTAAAT
1 TTTTGAATTTTTAAAT
28077436 TTTTGAAATTTTTAAA
1 TTTTG-AATTTTTAAA
28077452 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTTGAATTTTTAAAT
Found at i:28077601 original size:23 final size:24
Alignment explanation
Indices: 28077575--28077634 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
28077565 ACTTTTTAAA
*
28077575 TTTTAAAATTATATATTTTATATT
1 TTTTAAAAATATATATTTTATATT
* *
28077599 TTTTAAAAA-ATATTTTTTTTATGT
1 TTTTAAAAATATATATTTTATAT-T
28077623 TTTTAAAAATAT
1 TTTTAAAAATAT
28077635 TTGAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 11 0.35
24 18 0.58
25 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTAAAAATATATATTTTATATT
Found at i:28077635 original size:23 final size:22
Alignment explanation
Indices: 28077575--28077636 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 22
28077565 ACTTTTTAAA
*
28077575 TTTTAAAATTATATATTTTATATT
1 TTTTAAAA--ATATTTTTTATATT
*
28077599 TTTTAAAAAATATTTTTTTTATGT
1 TTTT-AAAAATATTTTTTATAT-T
28077623 TTTTAAAAATATTT
1 TTTTAAAAATATTT
28077637 GAATTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 21 0.62
24 9 0.26
25 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTAAAAATATTTTTTATATT
Found at i:28077643 original size:23 final size:24
Alignment explanation
Indices: 28077598--28077643 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
28077588 TATTTTATAT
***
28077598 TTTTTAAAAAATATTTTTTTTATG
1 TTTTTAAAAAATATTTGAATTATG
28077622 TTTTT-AAAAATATTTGAATTAT
1 TTTTTAAAAAATATTTGAATTAT
28077644 TTATATATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTTTAAAAAATATTTGAATTATG
Found at i:28080406 original size:71 final size:71
Alignment explanation
Indices: 28080282--28080430 Score: 201
Period size: 71 Copynumber: 2.1 Consensus size: 71
28080272 AACCAAAGTG
* * * * *
28080282 CTACTGATACCTTGAGGACTTCTTCCAAAACAAGTCAAGTCAGTAGCCAAAGTTCAGCAT-CTCT
1 CTACCGATACCTTAAAGACTTCTACCAAAACAAGTCAAGTCAGTAGCCAAAGTTCAACATCCTC-
*
28080346 TGCACTT
65 TACACTT
* **
28080353 CTACCGATACCTTAAAGACTTCTACCAAAATAAGTCAAGTCAGTAGCTGAAGTTCAACATCCTCT
1 CTACCGATACCTTAAAGACTTCTACCAAAACAAGTCAAGTCAGTAGCCAAAGTTCAACATCCTCT
28080418 ACACTT
66 ACACTT
28080424 CTACCGA
1 CTACCGA
28080431 CACTCTGATG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 65 0.96
72 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (71 bp):
CTACCGATACCTTAAAGACTTCTACCAAAACAAGTCAAGTCAGTAGCCAAAGTTCAACATCCTCT
ACACTT
Found at i:28083734 original size:43 final size:43
Alignment explanation
Indices: 28083686--28083784 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
28083676 TATCCCGAAT
* *
28083686 ATGGTCTTACATGCTAACACA-TATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACACGCTAACACACT-TCGATGCCAATGTCCCAGAC
* ** *
28083729 ATGGTCTTACACGTTTCCTCACTTCGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGCTAACACACTTCGATGCCAATGTCCCAGAC
28083772 ATGGTCTTACACG
1 ATGGTCTTACACG
28083785 AAATTACACC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 48 0.98
44 1 0.02
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGCTAACACACTTCGATGCCAATGTCCCAGAC
Found at i:28083967 original size:16 final size:16
Alignment explanation
Indices: 28083942--28083977 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28083932 CATATTTAGG
* *
28083942 CATTTTTTCATCATAT
1 CATTTATTCATCAAAT
28083958 CATTTATTCATCAAAT
1 CATTTATTCATCAAAT
28083974 CATT
1 CATT
28083978 CAATTCAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (16 bp):
CATTTATTCATCAAAT
Found at i:28086441 original size:20 final size:20
Alignment explanation
Indices: 28086396--28086441 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
28086386 TCATCGTGGA
*
28086396 AGAAAGTTTTGAGGTTTGGT
1 AGAAAGTTTTAAGGTTTGGT
* *
28086416 ACAAAGTTTTAAGGTTTTGT
1 AGAAAGTTTTAAGGTTTGGT
28086436 AGAAAG
1 AGAAAG
28086442 GGTAAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (20 bp):
AGAAAGTTTTAAGGTTTGGT
Found at i:28097091 original size:9 final size:9
Alignment explanation
Indices: 28097077--28097196 Score: 97
Period size: 9 Copynumber: 13.6 Consensus size: 9
28097067 TATTTATGTA
28097077 TTATGTAAG
1 TTATGTAAG
28097086 TTATGTAAG
1 TTATGTAAG
*
28097095 TTATGATATG
1 TTATG-TAAG
* * *
28097105 ATATAT-AT
1 TTATGTAAG
28097113 TTATGTAAG
1 TTATGTAAG
*
28097122 TTATGTAAA
1 TTATGTAAG
28097131 TTATGTAAG
1 TTATGTAAG
28097140 TTATGTAAG
1 TTATGTAAG
*
28097149 TTGTG-ATA-
1 TTATGTA-AG
* * *
28097157 TGATTTATAT
1 TTATGTA-AG
28097167 TTATGT-A-
1 TTATGTAAG
28097174 TTATGTAAG
1 TTATGTAAG
28097183 TTATGTAAG
1 TTATGTAAG
28097192 TTATG
1 TTATG
28097197 ATCCAAAATT
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
7 6 0.07
8 9 0.10
9 63 0.72
10 10 0.11
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28097140 original size:54 final size:52
Alignment explanation
Indices: 28097076--28097196 Score: 197
Period size: 54 Copynumber: 2.3 Consensus size: 52
28097066 ATATTTATGT
28097076 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
1 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGT-A-TTATGTAA
* *
28097130 ATTATGTAAGTTATGTAAGTTGTGATATGATTTATATTTATGTATTATGTAA
1 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAA
*
28097182 GTTATGTAAGTTATG
1 ATTATGTAAGTTATG
28097197 ATCCAAAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 22 0.34
53 1 0.02
54 41 0.64
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (52 bp):
ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTATTATGTAA
Found at i:28097255 original size:35 final size:35
Alignment explanation
Indices: 28097216--28097282 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
28097206 TTTTTTTATT
*
28097216 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGTAAGTTATAATAATCATAAA
*
28097251 CTTTAAATGTTTATGTAAGTTATAATTATCAT
1 CTTTAAATGTTTATGTAAGTTATAATAATCAT
28097283 CTTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.46
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGTTATAATAATCATAAA
Found at i:28097287 original size:32 final size:32
Alignment explanation
Indices: 28097215--28097294 Score: 108
Period size: 35 Copynumber: 2.4 Consensus size: 32
28097205 TTTTTTTTAT
*
28097215 TCTTTAAATGTTTATGTAAGTTATGATAATCA
1 TCTTTAAATGTTTATGTAAGTTATAATAATCA
*
28097247 TAAACTTTAAATGTTTATGTAAGTTATAATTATCA
1 T---CTTTAAATGTTTATGTAAGTTATAATAATCA
28097282 TCTTTAAAT-TTTA
1 TCTTTAAATGTTTA
28097295 ACCTTTTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 4 0.09
32 9 0.21
35 30 0.70
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (32 bp):
TCTTTAAATGTTTATGTAAGTTATAATAATCA
Found at i:28097615 original size:11 final size:11
Alignment explanation
Indices: 28097601--28097671 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
28097591 CGGCCCGAAT
28097601 TATATATTAAA
1 TATATATTAAA
**
28097612 TATATATTTTTA
1 TATATA-TTAAA
* * *
28097624 TTTTTAATCAAA
1 TATAT-ATTAAA
**
28097636 TATATATTTTA
1 TATATATTAAA
28097647 TATATATTAAA
1 TATATATTAAA
*
28097658 TATATATTTAA
1 TATATATTAAA
28097669 TAT
1 TAT
28097672 GGGTCGGGCC
Statistics
Matches: 43, Mismatches: 15, Indels: 4
0.69 0.24 0.06
Matches are distributed among these distances:
11 31 0.72
12 11 0.26
13 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATATTAAA
Found at i:28097636 original size:24 final size:23
Alignment explanation
Indices: 28097601--28097666 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
28097591 CGGCCCGAAT
*
28097601 TATATATTAAATATATATTTTTA
1 TATATATCAAATATATATTTTTA
* *
28097624 TTTTTAATCAAATATATA-TTTTA
1 TATAT-ATCAAATATATATTTTTA
*
28097647 TATATATTAAATATATATTT
1 TATATATCAAATATATATTT
28097667 AATATGGGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 11 0.31
23 13 0.37
24 11 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATATCAAATATATATTTTTA
Found at i:28099046 original size:24 final size:24
Alignment explanation
Indices: 28099014--28099066 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
28099004 AGTATTTTAT
*
28099014 AATATAATATTAATTTTAGATGCA
1 AATATAATATTAATTTTAGATACA
*
28099038 AATATAATATTAATTTTAGTTACA
1 AATATAATATTAATTTTAGATACA
28099062 AATAT
1 AATAT
28099067 TATACAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:28099606 original size:17 final size:17
Alignment explanation
Indices: 28099586--28099626 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28099576 ACATACCTCT
*
28099586 TAAAGTCCACAAGGAAG
1 TAAAGGCCACAAGGAAG
**
28099603 TAAAGGCTGCAAGGAAG
1 TAAAGGCCACAAGGAAG
28099620 TAAAGGC
1 TAAAGGC
28099627 TGCAAGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.12
Consensus pattern (17 bp):
TAAAGGCCACAAGGAAG
Found at i:28099627 original size:17 final size:17
Alignment explanation
Indices: 28099595--28099632 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
28099585 TTAAAGTCCA
28099595 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
28099612 CAAGGAAGTAAAGGCTG
1 CAAGGAAGTAAAGGCTG
28099629 CAAG
1 CAAG
28099633 TCCTTGGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.34, T:0.11
Consensus pattern (17 bp):
CAAGGAAGTAAAGGCTG
Found at i:28100904 original size:24 final size:23
Alignment explanation
Indices: 28100864--28100938 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 23
28100854 TTGGGGAAAA
* *
28100864 GAAATTGGGAAAGAATAGCTTGGG
1 GAAATTGGGGAAGAATA-ATTGGG
*
28100888 GAAATTAGGGGAA-AATAATTTGG
1 GAAATT-GGGGAAGAATAATTGGG
*
28100911 GAAATTGGGGAATG-A-AATCGGG
1 GAAATTGGGGAA-GAATAATTGGG
28100933 GAAATT
1 GAAATT
28100939 TGACTTGGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
22 17 0.40
23 11 0.26
24 10 0.23
25 5 0.12
ACGTcount: A:0.40, C:0.03, G:0.35, T:0.23
Consensus pattern (23 bp):
GAAATTGGGGAAGAATAATTGGG
Found at i:28101181 original size:116 final size:115
Alignment explanation
Indices: 28101025--28101701 Score: 731
Period size: 116 Copynumber: 5.9 Consensus size: 115
28101015 GCTTTTATCA
* * * *
28101025 AAAACGCCACTAACACATAACTTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAC
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCCACTAAAAATGCAGCTAA
* * * *
28101090 AAACGACGCCGTTTTGCAAATTGTTAATACATATTCGTGGCGTTTTTGGTG
66 AAAAGACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGTG
* *
28101141 AAAACGCCACTAACGCATAACCTTTTGCGGCATTTTAGTCAAAACACCACTAAAAATGCAGCTAA
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCCACTAAAAATGCAGCTAA
* * * *
28101206 AAAGGGCACCGTTTTGCAAAATTTTAATACATATTTGCGGCGTTTTTGGTG
66 AAAAGACACCGTTTTGC-AAACTTTAATACATATTCGCGGCGTTTTTGGTG
* * *
28101257 AAAATGCCACTAACGCATAACC-TTTGACGAG-GTTGTAGCCAAAACGCCACTAAAAATGCAGCT
1 AAAACGCCACTAACGCATAACCTTTTG-CG-GCGTTTTAGTCAAAACGCCACTAAAAATGCAGCT
* * *
28101320 AAAAATGGCACCATTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTG
64 AAAAAAGACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGTG
* *
28101373 AAAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAAAGCCACTAAAAACGCAGCT-
1 -AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCCACTAAAAATGCAGCTA
* *
28101437 AAAAAGTACACCGTTTTGCAAACTCTTAATACATATTCGCTGCATTTTTGGTG
65 AAAAAG-ACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGTG
* * ** *
28101490 AAAATGCCACTAACGCATAACCTTTTGCGGCGTTTTAGCCAAAATACCACTAAAAA--C-GGT--
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCCACTAAAAATGCAGCTAA
* * * ** *
28101550 ----G---TCGTTTTTCAAACTCTTAATACATATTCACACCATTTTTGGTG
66 AAAAGACACCGTTTTGCAAACT-TTAATACATATTCGCGGCGTTTTTGGTG
* * * * * **
28101594 AAAACGCCA-TTA-GCACAACCTTTTGCAGCGTTTTAGTCGAAACGCCGCTAAAAACACAGCTAA
1 AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCCACTAAAAATGCAGCTAA
* * * *
28101657 AAACGACAACGTTTTGCAATCTTTTAATATATATTCGCGGCGTTT
66 AAAAGACACCGTTTTGCAAAC-TTTAATACATATTCGCGGCGTTT
28101702 GGACAAAAAA
Statistics
Matches: 481, Mismatches: 59, Indels: 44
0.82 0.10 0.08
Matches are distributed among these distances:
102 35 0.07
103 2 0.00
104 47 0.10
105 2 0.00
108 1 0.00
111 1 0.00
113 2 0.00
114 28 0.06
115 9 0.02
116 252 0.52
117 98 0.20
118 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (115 bp):
AAAACGCCACTAACGCATAACCTTTTGCGGCGTTTTAGTCAAAACGCCACTAAAAATGCAGCTAA
AAAAGACACCGTTTTGCAAACTTTAATACATATTCGCGGCGTTTTTGGTG
Found at i:28101451 original size:233 final size:228
Alignment explanation
Indices: 28101025--28101701 Score: 788
Period size: 233 Copynumber: 3.0 Consensus size: 228
28101015 GCTTTTATCA
* * * *
28101025 AAAACGCCACTAACACATAACTTTTTGCGGCGTTTTAGTCAAAATGCCACTAAAAATGCAGCTAC
1 AAAATGCCACTAACGCATAAC-CTTTGCGGCGTTTTAGCCAAAATGCCACTAAAAATGCAGCTA-
* * * * *
28101090 AAACGACGCCGTTTTGCAAATTGTTAATACATATTCGTGGCGTTTTTGGTGAAAACGCCACTAAC
64 AAATGGC-CCGTTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTGAAAACGCCACTAAC
* * *
28101155 GCATAACCTTTTGCGGCATTTTAGTCAAAACA-CCACTAAAAATGCAGCTAAAAAGGGCACCGTT
128 GCATAACCTTTTGCGGCGTTTTAGTCAAAA-AGCCACTAAAAACGCAGCTAAAAA-GACACCGTT
* *
28101219 TTGCAAAATTTTAATACATATTTGCGGCGTTTTTGGTG
191 TTGCAAACTTTTAATACATATTCGCGGCGTTTTTGGTG
* *
28101257 AAAATGCCACTAACGCATAACCTTTGACGAG-GTTGTAGCCAAAACGCCACTAAAAATGCAGCTA
1 AAAATGCCACTAACGCATAACCTTTG-CG-GCGTTTTAGCCAAAATGCCACTAAAAATGCAGCT-
*
28101321 AAAATGGCACCATTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTGAAAAACGCCACTA
63 AAAATGGC-CCGTTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTG-AAAACGCCACTA
28101386 ACGCATAACCTTTTGCGGCGTTTTAGTCAAAAAGCCACTAAAAACGCAGCTAAAAAGTACACCGT
126 ACGCATAACCTTTTGCGGCGTTTTAGTCAAAAAGCCACTAAAAACGCAGCTAAAAAG-ACACCGT
* * *
28101451 TTTGCAAACTCTTAATACATATTCGCTGCATTTTTGGTG
190 TTTGCAAACTTTTAATACATATTCGCGGCGTTTTTGGTG
*
28101490 AAAATGCCACTAACGCATAACCTTTTGCGGCGTTTTAGCCAAAATACCACTAAAAA--C-G----
1 AAAATGCCACTAACGCATAACC-TTTGCGGCGTTTTAGCCAAAATGCCACTAAAAATGCAGCTAA
* * * * * ** * *
28101548 -GT-G-TCGTTTTTCAAACTCTTAATACATATTCACACCATTTTTGGTGAAAACGCCA-TTA-GC
65 AATGGCCCGTTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTGAAAACGCCACTAACGC
* * * * * * *
28101608 ACAACCTTTTGCAGCGTTTTAGTCGAAACGCCGCTAAAAACACAGCTAAAAACGACAACGTTTTG
130 ATAACCTTTTGCGGCGTTTTAGTCAAAAAGCCACTAAAAACGCAGCTAAAAA-GACACCGTTTTG
* *
28101673 CAATCTTTTAATATATATTCGCGGCGTTT
194 CAAACTTTTAATACATATTCGCGGCGTTT
28101702 GGACAAAAAA
Statistics
Matches: 390, Mismatches: 46, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
218 82 0.21
219 3 0.01
220 9 0.02
221 35 0.09
223 1 0.00
224 1 0.00
230 1 0.00
231 5 0.01
232 97 0.25
233 152 0.39
234 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (228 bp):
AAAATGCCACTAACGCATAACCTTTGCGGCGTTTTAGCCAAAATGCCACTAAAAATGCAGCTAAA
ATGGCCCGTTTTGCAAACTATTAATACATATTCGCGGCGTTTTTGGTGAAAACGCCACTAACGCA
TAACCTTTTGCGGCGTTTTAGTCAAAAAGCCACTAAAAACGCAGCTAAAAAGACACCGTTTTGCA
AACTTTTAATACATATTCGCGGCGTTTTTGGTG
Found at i:28102203 original size:15 final size:15
Alignment explanation
Indices: 28102177--28102238 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
28102167 CGAAATTTGT
*
28102177 TTTTAGGGTTTAAGG
1 TTTTAAGGTTTAAGG
* *
28102192 TTTTAAGATTTATGG
1 TTTTAAGGTTTAAGG
*
28102207 TTTT-AGGTTTTAGG
1 TTTTAAGGTTTAAGG
* *
28102221 GTTTAAGGTTTAGGG
1 TTTTAAGGTTTAAGG
28102236 TTT
1 TTT
28102239 AGAGAAAGCC
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
14 10 0.28
15 26 0.72
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (15 bp):
TTTTAAGGTTTAAGG
Found at i:28102208 original size:22 final size:22
Alignment explanation
Indices: 28102178--28102238 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
28102168 GAAATTTGTT
*
28102178 TTTAGGGTTTAAGGTTTTAAGA
1 TTTAAGGTTTAAGGTTTTAAGA
* * * *
28102200 TTTATGGTTTTAGGTTTTAGGG
1 TTTAAGGTTTAAGGTTTTAAGA
*
28102222 TTTAAGGTTTAGGGTTT
1 TTTAAGGTTTAAGGTTT
28102239 AGAGAAAGCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.51
Consensus pattern (22 bp):
TTTAAGGTTTAAGGTTTTAAGA
Found at i:28102240 original size:7 final size:7
Alignment explanation
Indices: 28102178--28102240 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
28102168 GAAATTTGTT
28102178 TTTAGGG
1 TTTAGGG
*
28102185 TTTAAGGT
1 TTT-AGGG
* *
28102193 TTTAAGA
1 TTTAGGG
*
28102200 TTTATGGT
1 TTTA-GGG
*
28102208 TTTAGGT
1 TTTAGGG
28102215 TTTAGGG
1 TTTAGGG
*
28102222 TTTAAGG
1 TTTAGGG
28102229 TTTAGGG
1 TTTAGGG
28102236 TTTAG
1 TTTAG
28102241 AGAAAGCCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
7 35 0.76
8 11 0.24
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:28104663 original size:22 final size:22
Alignment explanation
Indices: 28104633--28104675 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28104623 ACACCAAAAC
*
28104633 AGGCTTTTAGCAACGCTTTTTT
1 AGGCCTTTAGCAACGCTTTTTT
**
28104655 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCAACGCTTTTT
28104676 AGCGCCCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCAACGCTTTTTT
Found at i:28104808 original size:43 final size:43
Alignment explanation
Indices: 28104747--28104952 Score: 358
Period size: 43 Copynumber: 4.8 Consensus size: 43
28104737 GCGTCGCTAA
28104747 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
28104790 CTTTAGCGGCGTTTTTCCCACAAACGCCGCTAAAGACTAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
28104833 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
*
28104876 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* **
28104919 CTTTAGAGGCGCTTTTATCACAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
28104953 AACATAATAT
Statistics
Matches: 154, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 154 1.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.21
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:28110199 original size:41 final size:41
Alignment explanation
Indices: 28110150--28110307 Score: 237
Period size: 41 Copynumber: 3.9 Consensus size: 41
28110140 AATATTTTTT
28110150 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
*
28110191 GCGACGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * * *
28110232 GCGGCGCCTCTTTAAAAACGCTGCTAAAGACCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* *
28110273 GCGGCGCTTTCTT-AAAAACGCCACTAAAGCCCCGA
1 GCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCCCGA
28110308 AAACTCAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 102 0.96
42 4 0.04
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
Found at i:28110406 original size:39 final size:39
Alignment explanation
Indices: 28110358--28110473 Score: 133
Period size: 40 Copynumber: 2.9 Consensus size: 39
28110348 GCGCATTTTG
*
28110358 GAAAACGCCGCTAATGCTCATTTTTAGCGGCGTTTTCCT
1 GAAAGCGCCGCTAATGCTCATTTTTAGCGGCGTTTTCCT
* * * *
28110397 GAAAGCGCCGCTAATACTCTATCTTTAGTGGCGTTTTCTT
1 GAAAGCGCCGCTAATGCTC-ATTTTTAGCGGCGTTTTCCT
* * * *
28110437 AAAAGCGTCGGTAATGCTTAATTTTTAGCGGCGTTTT
1 GAAAGCGCCGCTAATGC-TCATTTTTAGCGGCGTTTT
28110474 TTATCCAAAC
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 17 0.27
40 45 0.71
41 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (39 bp):
GAAAGCGCCGCTAATGCTCATTTTTAGCGGCGTTTTCCT
Found at i:28119068 original size:46 final size:46
Alignment explanation
Indices: 28119018--28119153 Score: 220
Period size: 46 Copynumber: 3.0 Consensus size: 46
28119008 AAAAATCAAA
28119018 CAAACTAAAAAATCCCCAATTTCATATGAACCCTAAAATAAAATTG
1 CAAACTAAAAAATCCCCAATTTCATATGAACCCTAAAATAAAATTG
* * * *
28119064 CAAACTAAAAAATCCTCAATTTCATATAAAACCTAAAATAATATTG
1 CAAACTAAAAAATCCCCAATTTCATATGAACCCTAAAATAAAATTG
*
28119110 CAAACTAAAAAA-ACCCAATTTCATATGAACCCTAAAATAAAATT
1 CAAACTAAAAAATCCCCAATTTCATATGAACCCTAAAATAAAATT
28119154 ACTAAATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
45 27 0.33
46 54 0.67
ACGTcount: A:0.52, C:0.20, G:0.03, T:0.25
Consensus pattern (46 bp):
CAAACTAAAAAATCCCCAATTTCATATGAACCCTAAAATAAAATTG
Found at i:28120276 original size:7 final size:7
Alignment explanation
Indices: 28120258--28120303 Score: 78
Period size: 7 Copynumber: 6.9 Consensus size: 7
28120248 TACTACATTT
28120258 AGTTTT-
1 AGTTTTA
28120264 AGTTTTA
1 AGTTTTA
28120271 AGTTTTA
1 AGTTTTA
28120278 A-TTTTA
1 AGTTTTA
28120284 AGTTTTA
1 AGTTTTA
28120291 AGTTTTA
1 AGTTTTA
28120298 AGTTTT
1 AGTTTT
28120304 GTTTTACTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.32
7 26 0.68
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (7 bp):
AGTTTTA
Found at i:28120276 original size:13 final size:13
Alignment explanation
Indices: 28120258--28120309 Score: 79
Period size: 13 Copynumber: 4.0 Consensus size: 13
28120248 TACTACATTT
28120258 AGTTTTAGTTTTA
1 AGTTTTAGTTTTA
*
28120271 AGTTTTAATTTTA
1 AGTTTTAGTTTTA
28120284 AGTTTTAAGTTTTA
1 AGTTTT-AGTTTTA
28120298 AGTTTT-GTTTTA
1 AGTTTTAGTTTTA
28120310 CTGCCCGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
12 6 0.17
13 18 0.50
14 12 0.33
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (13 bp):
AGTTTTAGTTTTA
Found at i:28120289 original size:20 final size:19
Alignment explanation
Indices: 28120255--28120309 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
28120245 ATATACTACA
*
28120255 TTTAGTTTTAGTTTTAAGT
1 TTTAATTTTAGTTTTAAGT
28120274 TTTAATTTTAAGTTTTAAGT
1 TTTAATTTT-AGTTTTAAGT
28120294 TTTAAGTTTT-GTTTTA
1 TTTAA-TTTTAGTTTTA
28120310 CTGCCCGACA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 14 0.42
20 15 0.45
21 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.64
Consensus pattern (19 bp):
TTTAATTTTAGTTTTAAGT
Found at i:28120414 original size:14 final size:14
Alignment explanation
Indices: 28120395--28120431 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
28120385 TCAAGCTACT
28120395 TCCACCTCCACCAA
1 TCCACCTCCACCAA
**
28120409 TCCACCTCCACCGG
1 TCCACCTCCACCAA
28120423 TCCACCTCC
1 TCCACCTCC
28120432 GGTCCTTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.59, G:0.05, T:0.16
Consensus pattern (14 bp):
TCCACCTCCACCAA
Found at i:28120922 original size:44 final size:44
Alignment explanation
Indices: 28120868--28121013 Score: 247
Period size: 44 Copynumber: 3.3 Consensus size: 44
28120858 AGTAGAGATA
28120868 TTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTGAT
1 TTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTGAT
* * *
28120912 TTGAGTATGTTTTGGGATGACTCGGTGTTTTGAGTTTAGGTGAT
1 TTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTGAT
*
28120956 TTGAACATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTGAT
1 TTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTGAT
*
28121000 TTGAGCATTTTTTG
1 TTGAGCATGTTTTG
28121014 AAAGCCTACA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 93 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.45
Consensus pattern (44 bp):
TTGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGTGAT
Found at i:28121235 original size:23 final size:23
Alignment explanation
Indices: 28121208--28121254 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
28121198 ACTTAATTGT
28121208 CGTTGTATTTTGCTTAAATTTCG
1 CGTTGTATTTTGCTTAAATTTCG
*
28121231 CGTTGTATTTTGCTTAATTTTCG
1 CGTTGTATTTTGCTTAAATTTCG
28121254 C
1 C
28121255 ATTTGAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (23 bp):
CGTTGTATTTTGCTTAAATTTCG
Found at i:28124177 original size:29 final size:29
Alignment explanation
Indices: 28124117--28124177 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
28124107 TAACTATTTC
*
28124117 AATTAATTAATAATATTATAAAAATATTA
1 AATTAATTAATAATATTATAAAAATATAA
28124146 AATTAATTAATAACT-TTATAAAAA-ACTAA
1 AATTAATTAATAA-TATTATAAAAATA-TAA
28124175 AAT
1 AAT
28124178 ATTAACCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 1 0.03
29 27 0.93
30 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
AATTAATTAATAATATTATAAAAATATAA
Found at i:28126208 original size:20 final size:20
Alignment explanation
Indices: 28126172--28126268 Score: 92
Period size: 20 Copynumber: 4.8 Consensus size: 20
28126162 ACCTAAAATA
28126172 TTTTAAACTCAAGTGAAACAG
1 TTTTAAA-TCAAGTGAAACAG
* *
28126193 TTTTAAATCGAGTGAAA-AT
1 TTTTAAATCAAGTGAAACAG
*
28126212 TTTTAAAATCAAGTGACACAG
1 TTTT-AAATCAAGTGAAACAG
* * *
28126233 TTTTAAATCGATTGAAA-ACT
1 TTTTAAATCAAGTGAAACA-G
28126253 TTTTAAA-CAAGTGAAA
1 TTTTAAATCAAGTGAAA
28126269 AACTGTTCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
19 13 0.21
20 37 0.60
21 12 0.19
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (20 bp):
TTTTAAATCAAGTGAAACAG
Found at i:28126224 original size:40 final size:40
Alignment explanation
Indices: 28126166--28126268 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
28126156 CAAAACACCT
*
28126166 AAAATATTTTAAACTCAAGTGAAACAGTTTTAAATCGAGTG
1 AAAAT-TTTTAAAATCAAGTGAAACAGTTTTAAATCGAGTG
* *
28126207 AAAATTTTTAAAATCAAGTGACACAGTTTTAAATCGATTG
1 AAAATTTTTAAAATCAAGTGAAACAGTTTTAAATCGAGTG
28126247 AAAACTTTTT-AAA-CAAGTGAAA
1 AAAA-TTTTTAAAATCAAGTGAAA
28126269 AACTGTTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 8 0.14
40 39 0.68
41 10 0.18
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.32
Consensus pattern (40 bp):
AAAATTTTTAAAATCAAGTGAAACAGTTTTAAATCGAGTG
Found at i:28141884 original size:47 final size:48
Alignment explanation
Indices: 28141776--28141887 Score: 172
Period size: 48 Copynumber: 2.4 Consensus size: 48
28141766 GTGGAATAAG
* *
28141776 GTGGCAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAAATTTTATTAT
1 GTGGCAGTTTATCTACAAAAGTGGTGGCTTGTCCACAAATTTGATTAT
* * *
28141824 GTGGCAGTATATCTACAAGAGTGGTTGCTTGTCCAC-AATTTGATTAT
1 GTGGCAGTTTATCTACAAAAGTGGTGGCTTGTCCACAAATTTGATTAT
28141871 GTGGCAGTTTATCTACA
1 GTGGCAGTTTATCTACA
28141888 TTACAGTGAC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 26 0.45
48 32 0.55
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (48 bp):
GTGGCAGTTTATCTACAAAAGTGGTGGCTTGTCCACAAATTTGATTAT
Found at i:28157041 original size:26 final size:26
Alignment explanation
Indices: 28156930--28157031 Score: 114
Period size: 26 Copynumber: 3.9 Consensus size: 26
28156920 TATGAGTGAA
* * * *
28156930 CCACAAAGGCATTTCTTACAGATTTTT
1 CCACAAAGGC-TTTCTTTCATATTATG
* * * *
28156957 CCACAAAGGCATTCTTTTATAATACG
1 CCACAAAGGCTTTCTTTCATATTATG
*
28156983 CCACAAAGGCTTTCTTTTATATTATG
1 CCACAAAGGCTTTCTTTCATATTATG
28157009 CCACAAAGGCTTTCTTTCATATT
1 CCACAAAGGCTTTCTTTCATATT
28157032 CTGCACCAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
26 53 0.84
27 10 0.16
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (26 bp):
CCACAAAGGCTTTCTTTCATATTATG
Found at i:28157047 original size:26 final size:26
Alignment explanation
Indices: 28156968--28157051 Score: 64
Period size: 26 Copynumber: 3.3 Consensus size: 26
28156958 CACAAAGGCA
* * * **
28156968 TTCTTTTATAATACGCCACAAAGGCT
1 TTCTTTCATATTATGCCACAAACACT
* **
28156994 TTCTTTTATATTATGCCACAAAGGCT
1 TTCTTTCATATTATGCCACAAACACT
*
28157020 TTCTTTCATATTCTG-CACCAAACACT
1 TTCTTTCATATTATGCCA-CAAACACT
28157046 TT-TTTC
1 TTCTTTC
28157052 CCTAACGTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
25 6 0.12
26 45 0.88
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (26 bp):
TTCTTTCATATTATGCCACAAACACT
Found at i:28160441 original size:28 final size:27
Alignment explanation
Indices: 28160315--28160440 Score: 148
Period size: 27 Copynumber: 4.6 Consensus size: 27
28160305 AAAATTTGTT
* * *
28160315 AAATTACCGAAATACTCTCGAAAGGTA
1 AAATTAACGAAATACCCTCGAAGGGTA
*
28160342 AAATTATCGAAATACCCTCGAAGGGTA
1 AAATTAACGAAATACCCTCGAAGGGTA
* *
28160369 AAATTATCGAAATACCGTCGAAGGGTA
1 AAATTAACGAAATACCCTCGAAGGGTA
28160396 AAATT-ACTGAAATACCCCTCGAAGAGG-A
1 AAATTAAC-GAAATA-CCCTCGAAG-GGTA
*
28160424 AAATGAACGAAATACCC
1 AAATTAACGAAATACCC
28160441 CCATGGGGTA
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
26 1 0.01
27 64 0.73
28 19 0.22
29 4 0.05
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATTAACGAAATACCCTCGAAGGGTA
Found at i:28160450 original size:55 final size:54
Alignment explanation
Indices: 28160338--28160454 Score: 132
Period size: 55 Copynumber: 2.1 Consensus size: 54
28160328 ACTCTCGAAA
* * * *
28160338 GGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTATCGAAATACCGTCGAAG
1 GGTAAAATTATCGAAATACCCTCGAAGGGTAAAATGAACGAAATACCGCCCAAG
*
28160392 GGTAAAATTA-CTGAAATACCCCTCGAAGAGG-AAAATGAACGAAATACC-CCCATGG
1 GGTAAAATTATC-GAAATA-CCCTCGAAG-GGTAAAATGAACGAAATACCGCCCA-AG
28160447 GGTAAAAT
1 GGTAAAAT
28160455 GACCGTTATG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
53 1 0.02
54 18 0.33
55 33 0.61
56 2 0.04
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.20
Consensus pattern (54 bp):
GGTAAAATTATCGAAATACCCTCGAAGGGTAAAATGAACGAAATACCGCCCAAG
Found at i:28160676 original size:22 final size:22
Alignment explanation
Indices: 28160625--28160690 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
28160615 GGAGCAAGTG
28160625 TATGGCTTATAGCTGTTCTGTT
1 TATGGCTTATAGCTGTTCTGTT
* ** *
28160647 CAACGCTTATTATCT-TTCTGTT
1 TATGGCTTA-TAGCTGTTCTGTT
* *
28160669 TATGGCTTTTAGCCGTTCTGTT
1 TATGGCTTATAGCTGTTCTGTT
28160691 AACTGCAGCG
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
21 3 0.09
22 25 0.78
23 4 0.12
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (22 bp):
TATGGCTTATAGCTGTTCTGTT
Found at i:28165172 original size:45 final size:45
Alignment explanation
Indices: 28165123--28165208 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
28165113 ACCTGTTTAC
*
28165123 CATGATGTCATAGCGTCTTTCAGCCATGGTCTTACTCATTTCCGT
1 CATGATGTCATAGCATCTTTCAGCCATGGTCTTACTCATTTCCGT
* * * *
28165168 CATGATGTGATAGCATCTTTTAGCTATGGTGTTACTCATTT
1 CATGATGTCATAGCATCTTTCAGCCATGGTCTTACTCATTT
28165209 TAGGCGTATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (45 bp):
CATGATGTCATAGCATCTTTCAGCCATGGTCTTACTCATTTCCGT
Found at i:28168171 original size:34 final size:34
Alignment explanation
Indices: 28168128--28168351 Score: 160
Period size: 34 Copynumber: 6.5 Consensus size: 34
28168118 GTAACTAACT
* *
28168128 TTGTTCCCAGCGCTAGTCGGATAACTGACGATGG
1 TTGTGCCCAGCACTAGTCGGATAACTGACGATGG
* *
28168162 TTGTGCCCAGCACTAGTCGGATAACCGACAATGG
1 TTGTGCCCAGCACTAGTCGGATAACTGACGATGG
* * * * ** * *
28168196 TTATGCCCAGTACTAGTTGAACGAGTCGACGATGTT
1 TTGTGCCCAGCACTAGTCGGATAACT-GACGATG-G
* * * *
28168232 TTGCGCCCAGCGCTAGTCGAATAACTGACGATAG
1 TTGTGCCCAGCACTAGTCGGATAACTGACGATGG
* * * ***
28168266 TTGTGCCTAGCACTAGTCAGATAAACTGACAAAAA
1 TTGTGCCCAGCACTAGTCGGAT-AACTGACGATGG
* * * * *
28168301 TTGGGCCCAGCGCTAGTTGGAGAACCGACGATGG
1 TTGTGCCCAGCACTAGTCGGATAACTGACGATGG
* *
28168335 CTGTGCCCTGCACTAGT
1 TTGTGCCCAGCACTAGT
28168352 TGAATGAATC
Statistics
Matches: 140, Mismatches: 47, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
34 85 0.61
35 37 0.26
36 18 0.13
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (34 bp):
TTGTGCCCAGCACTAGTCGGATAACTGACGATGG
Found at i:28168317 original size:35 final size:34
Alignment explanation
Indices: 28168236--28168317 Score: 85
Period size: 35 Copynumber: 2.4 Consensus size: 34
28168226 GATGTTTTGC
* * * *
28168236 GCCCAGCGCTAGTCGAATAACTGACGATAGTTGT
1 GCCCAGCGCTAGTCGAATAACTGACAAAAATTGG
* *
28168270 GCCTAGCACTAGTC-AGATAAACTGACAAAAATTGG
1 GCCCAGCGCTAGTCGA-AT-AACTGACAAAAATTGG
28168305 GCCCAGCGCTAGT
1 GCCCAGCGCTAGT
28168318 TGGAGAACCG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 1 0.03
34 14 0.37
35 23 0.61
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (34 bp):
GCCCAGCGCTAGTCGAATAACTGACAAAAATTGG
Found at i:28168330 original size:104 final size:104
Alignment explanation
Indices: 28168133--28168333 Score: 251
Period size: 104 Copynumber: 1.9 Consensus size: 104
28168123 TAACTTTGTT
* * * ***
28168133 CCCAGCGCTAGTCGGATAACTGACGATGGTTGTGCCCAGCACTAGTCGGATAACCGACAATGGTT
1 CCCAGCGCTAGTCGAATAACTGACGATAGTTGTGCCCAGCACTAGTCAGATAACCGACAAAAATT
* * **
28168198 ATGCCCAGTACTAGTTGAACGAGTCGACGATGTTTTGCG
66 AGGCCCAGCACTAGTTGAACGAACCGACGATGTTTTGCG
* *
28168237 CCCAGCGCTAGTCGAATAACTGACGATAGTTGTGCCTAGCACTAGTCAGATAAACTGACAAAAAT
1 CCCAGCGCTAGTCGAATAACTGACGATAGTTGTGCCCAGCACTAGTCAGAT-AACCGACAAAAAT
* * *
28168302 TGGGCCCAGCGCTAGTTGGA-GAACCGACGATG
65 TAGGCCCAGCACTAGTTGAACGAACCGACGATG
28168334 GCTGTGCCCT
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
104 57 0.70
105 24 0.30
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (104 bp):
CCCAGCGCTAGTCGAATAACTGACGATAGTTGTGCCCAGCACTAGTCAGATAACCGACAAAAATT
AGGCCCAGCACTAGTTGAACGAACCGACGATGTTTTGCG
Found at i:28171404 original size:25 final size:25
Alignment explanation
Indices: 28171370--28171422 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
28171360 CTAACACAGA
28171370 GTAAGCATTTAAGCTTAGTAAGTTT
1 GTAAGCATTTAAGCTTAGTAAGTTT
28171395 GTAAGCATTTAAGCTTAGTAAGTTT
1 GTAAGCATTTAAGCTTAGTAAGTTT
28171420 GTA
1 GTA
28171423 TATCATAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (25 bp):
GTAAGCATTTAAGCTTAGTAAGTTT
Found at i:28171841 original size:25 final size:24
Alignment explanation
Indices: 28171802--28171908 Score: 81
Period size: 25 Copynumber: 4.3 Consensus size: 24
28171792 TCTTGCACAT
* * *
28171802 GTATGGTCATACGAGCTATGAATCG
1 GTATGCTCACACGAGCTGT-AATCG
* *
28171827 GTATGCTCACTCGAGCTGTAGACCG
1 GTATGCTCACACGAGCTGTA-ATCG
*
28171852 GTATGCTCTCACGAGCTGTAAATCG
1 GTATGCTCACACGAGCTGT-AATCG
* * *
28171877 GTATGCCCTA-ACGACCTGTAAATCA
1 GTATGCTC-ACACGAGCTGT-AATCG
28171902 GTATGCT
1 GTATGCT
28171909 TTCATGAGCT
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
24 1 0.02
25 64 0.97
26 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (24 bp):
GTATGCTCACACGAGCTGTAATCG
Found at i:28174023 original size:13 final size:13
Alignment explanation
Indices: 28174005--28174030 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28173995 TCTGTCTGAT
28174005 GTGCTAAAATGCA
1 GTGCTAAAATGCA
28174018 GTGCTAAAATGCA
1 GTGCTAAAATGCA
28174031 ACCGCGTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GTGCTAAAATGCA
Found at i:28180803 original size:24 final size:24
Alignment explanation
Indices: 28180755--28180844 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
28180745 ATCTATCAAT
* *
28180755 TCATATTCAGGAATGCTCATTTGAG
1 TCATATTCGGGAA-GCTCATATGAG
* *
28180780 TCATATTTGGGAAGCTCATGTGAG
1 TCATATTCGGGAAGCTCATATGAG
* * * *
28180804 TCATGTAACGGAAAGCTCATAAGAG
1 TCATAT-TCGGGAAGCTCATATGAG
*
28180829 TCATATTTGGGAAGCT
1 TCATATTCGGGAAGCT
28180845 TATACGATCC
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
24 22 0.43
25 29 0.57
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (24 bp):
TCATATTCGGGAAGCTCATATGAG
Found at i:28181077 original size:24 final size:25
Alignment explanation
Indices: 28180991--28181078 Score: 90
Period size: 24 Copynumber: 3.6 Consensus size: 25
28180981 CAACCAATCA
* * *
28180991 GGAAGCTCATAAGAGCTAT-TAACG
1 GGAAGCTCATGAGAGCCATATATCG
*
28181015 GGAAGCTCATGAGAGCCATATATCA
1 GGAAGCTCATGAGAGCCATATATCG
* * *
28181040 GGAAGCTCAAGAGATCCA-ATTTCG
1 GGAAGCTCATGAGAGCCATATATCG
*
28181064 GGATGCTCATGAGAG
1 GGAAGCTCATGAGAG
28181079 TTATTATCGA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 33 0.63
25 19 0.37
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCATATATCG
Found at i:28182691 original size:25 final size:25
Alignment explanation
Indices: 28182662--28182779 Score: 114
Period size: 25 Copynumber: 4.7 Consensus size: 25
28182652 TCCTGTACAT
* *
28182662 GTATGGTCATACGAGCTGTAAATCG
1 GTATGCTCTTACGAGCTGTAAATCG
*
28182687 GTATG--CTTACTGGAGCTGTAGATCG
1 GTATGCTCTTAC--GAGCTGTAAATCG
* *
28182712 GTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCTTACGAGCTGTAAATCG
* *
28182737 GTATGCCCTTACGAGCTGTAGATCG
1 GTATGCTCTTACGAGCTGTAAATCG
* * *
28182762 ATATGCTCTCATGAGCTG
1 GTATGCTCTTACGAGCTG
28182780 CAGGTCGAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
23 4 0.05
25 68 0.89
27 4 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (25 bp):
GTATGCTCTTACGAGCTGTAAATCG
Found at i:28182727 original size:50 final size:49
Alignment explanation
Indices: 28182672--28182779 Score: 155
Period size: 50 Copynumber: 2.2 Consensus size: 49
28182662 GTATGGTCAT
*
28182672 ACGAGCTGTAAATCGGTATG-CTTACTGGAGCTGTAGATCGGTATGCTCTC
1 ACGAGCTGTAAATCGGTATGCCTTAC--GAGCTGTAGATCGATATGCTCTC
*
28182722 ACGAGCTATAAATCGGTATGCCCTTACGAGCTGTAGATCGATATGCTCTC
1 ACGAGCTGTAAATCGGTATG-CCTTACGAGCTGTAGATCGATATGCTCTC
*
28182772 ATGAGCTG
1 ACGAGCTG
28182780 CAGGTCGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
50 47 0.90
52 5 0.10
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (49 bp):
ACGAGCTGTAAATCGGTATGCCTTACGAGCTGTAGATCGATATGCTCTC
Found at i:28184117 original size:15 final size:16
Alignment explanation
Indices: 28184083--28184117 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
28184073 AAAAACGAGA
28184083 TGTGTTTAAACCATAT
1 TGTGTTTAAACCATAT
28184099 TGTGTTTAAACCA-AT
1 TGTGTTTAAACCATAT
28184114 TGTG
1 TGTG
28184118 GTAAATTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (16 bp):
TGTGTTTAAACCATAT
Found at i:28189858 original size:21 final size:21
Alignment explanation
Indices: 28189820--28189859 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28189810 ATTTGATTTT
*
28189820 TATATTATTAAATTATCATTA
1 TATATTATTAAATAATCATTA
* *
28189841 TATATTTTTATATAATCAT
1 TATATTATTAAATAATCAT
28189860 AAATTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTATTAAATAATCATTA
Found at i:28190831 original size:17 final size:18
Alignment explanation
Indices: 28190811--28190845 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28190801 AATTTTTTTC
28190811 CTAAATTATATTT-TTAT
1 CTAAATTATATTTATTAT
*
28190828 CTAAATTCTATTTATTAT
1 CTAAATTATATTTATTAT
28190846 TATTTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
CTAAATTATATTTATTAT
Found at i:28196975 original size:29 final size:29
Alignment explanation
Indices: 28196942--28197012 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
28196932 AATCCCGAGA
*
28196942 TATTTTTTCAGAACCCATCTTGTCAAAAT
1 TATTTTTTCAGAACCCATCTCGTCAAAAT
* *
28196971 TATTTTTTCAGAACTCATCTCGTCAAACT
1 TATTTTTTCAGAACCCATCTCGTCAAAAT
28197000 TATTTTTTCAGAA
1 TATTTTTTCAGAA
28197013 TCCCTAAACC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.44
Consensus pattern (29 bp):
TATTTTTTCAGAACCCATCTCGTCAAAAT
Found at i:28197178 original size:22 final size:22
Alignment explanation
Indices: 28197153--28197203 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
28197143 ATAATAAAAT
* *
28197153 CCTAATTCAATTAACCCTAAAC
1 CCTAATTCAATAAACCATAAAC
* *
28197175 CCTAATTTAATAAACTATAAAC
1 CCTAATTCAATAAACCATAAAC
28197197 CCTAATT
1 CCTAATT
28197204 AAACAATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.25, G:0.00, T:0.31
Consensus pattern (22 bp):
CCTAATTCAATAAACCATAAAC
Found at i:28198385 original size:5 final size:5
Alignment explanation
Indices: 28198375--28198403 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28198365 TGGCTTATCT
28198375 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
28198404 GTCTTTATGA
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:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:28203461 original size:24 final size:23
Alignment explanation
Indices: 28203434--28203484 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 23
28203424 TTGAATATTA
28203434 TTTAATT-TTTTTCATTTATATAAT
1 TTTAATTATTTTT-ATTT-TATAAT
28203458 TTTAATTAATTTTTATTTTATAAT
1 TTTAATT-ATTTTTATTTTATAAT
28203482 TTT
1 TTT
28203485 TTTATAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 16 0.64
25 4 0.16
26 5 0.20
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTAATTATTTTTATTTTATAAT
Found at i:28208780 original size:114 final size:114
Alignment explanation
Indices: 28208633--28208854 Score: 345
Period size: 114 Copynumber: 1.9 Consensus size: 114
28208623 ATTTTTTCAG
* * *
28208633 AACCTTCTTCTCAAAATTATTTTTCAGGAACTACTACAAAAAAAGAGTGTCCACGTGGGAGCTTT
1 AACCGTCTTCTCAAAATTATTTTTCAGAAACTACTACAAAAAAAGAGCGTCCACGTGGGAGCTTT
* *
28208698 TTTTAGTACTTTTGCTGACAGTGCATCCTGCTTGAAGCATTTTTGACAC
66 TTTTAGTACTTTTGCTGACAGTACACCCTGCTTGAAGCATTTTTGACAC
* ** *
28208747 AACCGTCTTCTCAAAATTATTTTTTAGAAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTT
1 AACCGTCTTCTCAAAATTATTTTTCAGAAACTACTACAAAAAAAGAGCGTCCACGTGGGAGCTTT
* *
28208812 TTTTAGTACTTTTGTTGATAGTACACCCTGCTTGAAGCATTTT
66 TTTTAGTACTTTTGCTGACAGTACACCCTGCTTGAAGCATTTT
28208855 ACACATTAAT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (114 bp):
AACCGTCTTCTCAAAATTATTTTTCAGAAACTACTACAAAAAAAGAGCGTCCACGTGGGAGCTTT
TTTTAGTACTTTTGCTGACAGTACACCCTGCTTGAAGCATTTTTGACAC
Found at i:28209085 original size:33 final size:34
Alignment explanation
Indices: 28209005--28209095 Score: 121
Period size: 35 Copynumber: 2.7 Consensus size: 34
28208995 AAACACAAAA
* * *
28209005 TTATTTTTAAAAATCCCCAAACCCTAATTTAATTT
1 TTATTTTAAAAAAACCCTAAACCCTAATTTAA-TT
* *
28209040 TTCTTTTAAAAAAACCTTAAACCCTAATTTAA-T
1 TTATTTTAAAAAAACCCTAAACCCTAATTTAATT
28209073 TTATTTTAAAAAAACCCTAAACC
1 TTATTTTAAAAAAACCCTAAACC
28209096 TTAACCCCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 22 0.45
35 27 0.55
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (34 bp):
TTATTTTAAAAAAACCCTAAACCCTAATTTAATT
Found at i:28210433 original size:18 final size:18
Alignment explanation
Indices: 28210396--28210434 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28210386 AATTGAAATT
*
28210396 TATTTTATAATAAGATAA
1 TATTTTATAATAAGAAAA
*
28210414 TATTTTATAATAATAAAA
1 TATTTTATAATAAGAAAA
28210432 TAT
1 TAT
28210435 CATATATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTTTATAATAAGAAAA
Found at i:28210660 original size:27 final size:27
Alignment explanation
Indices: 28210630--28210686 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28210620 TTGTAATTTG
*
28210630 TAATATATATATTTATT-AATAAAATAT
1 TAATATAAATATTT-TTCAATAAAATAT
*
28210657 TAATATAAATATTTTTCAATAATATAT
1 TAATATAAATATTTTTCAATAAAATAT
28210684 TAA
1 TAA
28210687 GAATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATATAAATATTTTTCAATAAAATAT
Found at i:28210782 original size:22 final size:21
Alignment explanation
Indices: 28210720--28210784 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
28210710 ATTATGGTTA
28210720 AATT-TATTATTAAAAT-AA-
1 AATTATATTATTAAAATAAAT
* * *
28210738 AATTGTAATATT-AAATAATT
1 AATTATATTATTAAAATAAAT
28210758 AATTATATTATTAAATATAAAT
1 AATTATATTATTAAA-ATAAAT
28210780 AATTA
1 AATTA
28210785 AATAGGTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 10 0.27
21 2 0.05
22 10 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTATATTATTAAAATAAAT
Found at i:28211502 original size:25 final size:25
Alignment explanation
Indices: 28211474--28211549 Score: 66
Period size: 26 Copynumber: 2.9 Consensus size: 25
28211464 GAGAGGGCAG
28211474 GAAGGGAAAAAGAAAGAAAAAAAGA
1 GAAGGGAAAAAGAAAGAAAAAAAGA
*
28211499 GAAGGAGAAAAGAGAGAGGAAAGGAGAAAGA
1 GAAGG-GAAAA-AGA-AAGAAA--A-AAAGA
*
28211530 GAA-GGAAAAA-AAATAAAAAA
1 GAAGGGAAAAAGAAAGAAAAAA
28211550 GAAAAGGTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
23 2 0.05
24 1 0.02
25 5 0.12
26 9 0.21
27 4 0.10
28 6 0.14
29 5 0.12
30 2 0.05
31 8 0.19
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (25 bp):
GAAGGGAAAAAGAAAGAAAAAAAGA
Found at i:28211530 original size:18 final size:18
Alignment explanation
Indices: 28211500--28211537 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
28211490 AAAAAAAGAG
28211500 AAGGAGAAAAGAGAGAGGA
1 AAGGAGAAAAGAGA-AGGA
28211519 AAGGAG-AAAGAGAAGGA
1 AAGGAGAAAAGAGAAGGA
28211536 AA
1 AA
28211538 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (18 bp):
AAGGAGAAAAGAGAAGGA
Found at i:28212460 original size:36 final size:37
Alignment explanation
Indices: 28212395--28212470 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
28212385 TATGATGTGG
*
28212395 AAAAATTTGTTTGGTATTTTTTTTTTGTAATTAAAAGC
1 AAAAAATTGTTTGGTA-TTTTTTTTTGTAATTAAAAGC
28212433 AAAAAATTGTTTGGTA-TTTTTTTTGTAATTAAAAGC
1 AAAAAATTGTTTGGTATTTTTTTTTGTAATTAAAAGC
28212469 AA
1 AA
28212471 TATATAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 22 0.59
38 15 0.41
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (37 bp):
AAAAAATTGTTTGGTATTTTTTTTTGTAATTAAAAGC
Found at i:28214381 original size:33 final size:33
Alignment explanation
Indices: 28214308--28214391 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
28214298 GATATCTTTG
*
28214308 GGTCGTATCCACCGCAGTACAGACTCCTCCCGA
1 GGTCGTATCCACCGCAGTACACACTCCTCCCGA
** * *
28214341 CAT-GTATCCACCGCAGTACTCCACTCCT-CCTA
1 GGTCGTATCCACCGCAGTAC-ACACTCCTCCCGA
28214373 GGTCGTATCCACCGCAGTA
1 GGTCGTATCCACCGCAGTA
28214392 TGGCACTCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 20 0.48
33 22 0.52
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.21
Consensus pattern (33 bp):
GGTCGTATCCACCGCAGTACACACTCCTCCCGA
Found at i:28214399 original size:33 final size:32
Alignment explanation
Indices: 28214308--28214403 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 32
28214298 GATATCTTTG
*
28214308 GGTCGTATCCACCGCAGTACAG-ACTCCTCCCGA
1 GGTCGTATCCACCGCAGTA-TGCACTCCT-CCGA
** * *
28214341 CAT-GTATCCACCGCAGTACTCCACTCCTCCTA
1 GGTCGTATCCACCGCAGTA-TGCACTCCTCCGA
28214373 GGTCGTATCCACCGCAGTATGGCACTCCTCC
1 GGTCGTATCCACCGCAGTAT-GCACTCCTCC
28214404 CAGCTTAAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
32 21 0.40
33 31 0.60
ACGTcount: A:0.20, C:0.41, G:0.18, T:0.22
Consensus pattern (32 bp):
GGTCGTATCCACCGCAGTATGCACTCCTCCGA
Found at i:28215402 original size:19 final size:19
Alignment explanation
Indices: 28215378--28215432 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
28215368 CGGCCGGCAT
28215378 GGTGGCCAACGGTCGGTAC
1 GGTGGCCAACGGTCGGTAC
**
28215397 GGTGGCCAACGGTCGACAC
1 GGTGGCCAACGGTCGGTAC
*
28215416 GGTGGCCAACGGCCGGT
1 GGTGGCCAACGGTCGGT
28215433 TCCCAGGCCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.42, T:0.13
Consensus pattern (19 bp):
GGTGGCCAACGGTCGGTAC
Found at i:28216234 original size:6 final size:6
Alignment explanation
Indices: 28216235--28216272 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
28216225 ATTTTTATTT
*
28216235 TTTTTA TTTTTA TTTTTA CTTTTA TTTTT- TTATTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TT
28216273 CTCATTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 2 0.07
6 24 0.86
7 2 0.07
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:28217645 original size:16 final size:16
Alignment explanation
Indices: 28217624--28217658 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28217614 TGTTGTTTTG
*
28217624 TTTTGACTGCATGGCA
1 TTTTGACTACATGGCA
28217640 TTTTGACTACATGGCA
1 TTTTGACTACATGGCA
28217656 TTT
1 TTT
28217659 CATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (16 bp):
TTTTGACTACATGGCA
Found at i:28223731 original size:50 final size:50
Alignment explanation
Indices: 28223538--28224039 Score: 294
Period size: 50 Copynumber: 10.1 Consensus size: 50
28223528 TTACCCATAC
* ***
28223538 CCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAATAATGAATCTTACTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
* * ** * * * * *
28223588 CCCCGACATTGCAAT-TAAAAGATTAAAGCTACAACGGTGAATCTTGCTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
* **** * * * * *
28223637 CCCCGATATTGCAAT-TAAAAGATT-AAGGCCACAACGGTGAATCTTATTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAA-GCTACAACGGTGAATCTTACTT
* * * *
28223686 CCGTGGCGGGGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
* * ** * * * * ** *
28223736 CCCCGACATTGCAGT-TAAAAGATTGAGGCCACAACGACGAATCTTATTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
* * *
28223785 CCCTGGTGTTGCAGTGGAATAGATTGAAGCTACAACGGTGAATCTTACTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
* * * *
28223835 CCCTAGCGGTGCAGTGGAACATATTGAAGCTACAACGGCGAATCTTGCTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
*** ** * * * * * **
28223885 CCCCAACATTGCAAT-TAAAAGATTGATGCCACAACGGCAAATCTTACTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
* * *** *
28223934 CCCTGGCAGTGCAGTGGAATAGATTGAAGCTACAACAACGAATCTTTCTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
* * ** * ** * * **
28223984 CCCCGACATTGCAATTAAATAGATTAAAGCTACAATAGTGAATCTTACTT
1 CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
28224034 CCCTGG
1 CCCTGG
28224040 TGAACAAATT
Statistics
Matches: 345, Mismatches: 102, Indels: 10
0.75 0.22 0.02
Matches are distributed among these distances:
48 2 0.01
49 149 0.43
50 192 0.56
51 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
CCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTACTT
Found at i:28223848 original size:99 final size:101
Alignment explanation
Indices: 28223546--28224037 Score: 374
Period size: 99 Copynumber: 5.0 Consensus size: 101
28223536 ACCCCTAGCG
* * ** * * * *
28223546 GTGCAGTGGAACAGATTGAAGCTACAATAATGAATCTTACTTCCCCGACATTGCAAT-TAAAAGA
1 GTGCAGTGGAAAAGATTGAAGCCACAACGACGAATCTTATTTCCCCGACATTGCAATGGAATAGA
* * *
28223610 TTAAAGCTACAACGGTGAATCTTGCTTCCC-CGATA
66 TTGAAGCTACAACGGTGAATCTTACTTCCCTCGACA
* * * ** ** * *** * *
28223645 TTGCAAT-TAAAAGATT-AAGGCCACAACGGTGAATCTTATTTCCGTGGCGGGGCAGTGGAACAG
1 GTGCAGTGGAAAAGATTGAA-GCCACAACGACGAATCTTATTTCCCCGACATTGCAATGGAATAG
* *
28223708 ATTGAAGCTACAATGGTGAATCTTGCTTCCC-CGACA
65 ATTGAAGCTACAACGGTGAATCTTACTTCCCTCGACA
* * * * *** *
28223744 TTGCAGT-TAAAAGATTGAGGCCACAACGACGAATCTTATTTCCCTGGTGTTGCAGTGGAATAGA
1 GTGCAGTGGAAAAGATTGAAGCCACAACGACGAATCTTATTTCCCCGACATTGCAATGGAATAGA
* *
28223808 TTGAAGCTACAACGGTGAATCTTACTTCCCTAG-CG
66 TTGAAGCTACAACGGTGAATCTTACTTCCCTCGACA
* * * * ** * * *
28223843 GTGCAGTGGAACATATTGAAGCTACAACGGCGAATCTTGCTTCCCCAACATTGCAAT-TAAAAGA
1 GTGCAGTGGAAAAGATTGAAGCCACAACGACGAATCTTATTTCCCCGACATTGCAATGGAATAGA
* * ** *
28223907 TTGATGCCACAACGGCAAATCTTACTTCCCT-GGCA
66 TTGAAGCTACAACGGTGAATCTTACTTCCCTCGACA
* * * **
28223942 GTGCAGTGGAATAGATTGAAGCTACAACAACGAATCTT-TCTTCCCCGACATTGCAATTAAATAG
1 GTGCAGTGGAAAAGATTGAAGCCACAACGACGAATCTTAT-TTCCCCGACATTGCAATGGAATAG
* **
28224006 ATTAAAGCTACAATAGTGAATCTTACTTCCCT
65 ATTGAAGCTACAACGGTGAATCTTACTTCCCT
28224038 GGTGAACAAA
Statistics
Matches: 314, Mismatches: 71, Indels: 15
0.79 0.18 0.04
Matches are distributed among these distances:
97 2 0.01
98 33 0.11
99 213 0.68
100 66 0.21
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.27
Consensus pattern (101 bp):
GTGCAGTGGAAAAGATTGAAGCCACAACGACGAATCTTATTTCCCCGACATTGCAATGGAATAGA
TTGAAGCTACAACGGTGAATCTTACTTCCCTCGACA
Found at i:28223879 original size:149 final size:149
Alignment explanation
Indices: 28223538--28223969 Score: 564
Period size: 149 Copynumber: 2.9 Consensus size: 149
28223528 TTACCCATAC
** *
28223538 CCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAATAATGAATCTTACTTCCCCGACATTGCAAT
1 CCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAAT
* * * * * * * * * *
28223603 TAAAAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGATATTGCAAT-TAAAAGATT-AAGGC
66 TAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGTTGCAGTGGAATAGATTGAA-GC
* *
28223666 CACAACGGTGAATCTTATTT
130 TACAACGGTGAATCTTACTT
* * * *
28223686 CCGTGGCGGGGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAGT
1 CCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAAT
* * *
28223751 TAAAAGATTGAGGCCACAACGACGAATCTTATTTCCCTGGTGTTGCAGTGGAATAGATTGAAGCT
66 TAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGTTGCAGTGGAATAGATTGAAGCT
28223816 ACAACGGTGAATCTTACTT
131 ACAACGGTGAATCTTACTT
* * * *
28223835 CCCTAGCGGTGCAGTGGAACATATTGAAGCTACAACGGCGAATCTTGCTTCCCCAACATTGCAAT
1 CCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAAT
* * *
28223900 TAAAAGATTGATGCCACAACGGCAAATCTTACTTCCCTGGCAG-TGCAGTGGAATAGATTGAAGC
66 TAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGG-TGTTGCAGTGGAATAGATTGAAGC
28223964 TACAAC
130 TACAAC
28223970 AACGAATCTT
Statistics
Matches: 246, Mismatches: 35, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
148 96 0.39
149 147 0.60
150 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (149 bp):
CCCTAGCGGTGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAAT
TAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGTTGCAGTGGAATAGATTGAAGCT
ACAACGGTGAATCTTACTT
Found at i:28224014 original size:149 final size:149
Alignment explanation
Indices: 28223546--28224036 Score: 427
Period size: 149 Copynumber: 3.3 Consensus size: 149
28223536 ACCCCTAGCG
* * ** * *
28223546 GTGCAGTGGAACAGATTGAAGCTACAATAATGAATCTTACTTCCCCGACATTGCAATTAAAAGAT
1 GTGCAATGAAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCAACATTGCAATTAAAAGAT
* * * *** * * * * * * * *
28223611 TAAAGCTACAACGGTGAATCTTGCTTCCC-CGATATTGCAAT-TAAAAGATT-AAGGCCACAACG
66 TGAGGCCACAACGACAAATCTTACTTCCCTGGA-GTTGCAGTGGAATAGATTGAA-GCTACAACA
** * * *
28223673 GTGAATCTTA-TTTCCGTGGCG
129 ACGAATCTTACTTCCCG-AGCA
* * * * *
28223694 GGGCAGTGGAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAGAT
1 GTGCAATGAAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCAACATTGCAATTAAAAGAT
* * * ***
28223759 TGAGGCCACAACGACGAATCTTATTTCCCTGGTGTTGCAGTGGAATAGATTGAAGCTACAACGGT
66 TGAGGCCACAACGACAAATCTTACTTCCCTGGAGTTGCAGTGGAATAGATTGAAGCTACAACAAC
* *
28223824 GAATCTTACTTCCCTAGCG
131 GAATCTTACTTCCCGAGCA
* * * * *
28223843 GTGCAGTGGAACATATTGAAGCTACAACGGCGAATCTTGCTTCCCCAACATTGCAATTAAAAGAT
1 GTGCAATGAAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCAACATTGCAATTAAAAGAT
* *
28223908 TGATGCCACAACGGCAAATCTTACTTCCCTGGCAG-TGCAGTGGAATAGATTGAAGCTACAACAA
66 TGAGGCCACAACGACAAATCTTACTTCCCTGG-AGTTGCAGTGGAATAGATTGAAGCTACAACAA
*
28223972 CGAATCTTTCTTCCCCGA-CA
130 CGAATCTTACTT-CCCGAGCA
* * * * * *
28223992 TTGCAATTAAATAGATTAAAGCTACAATAGTGAATCTTACTTCCC
1 GTGCAATGAAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCC
28224037 TGGTGAACAA
Statistics
Matches: 287, Mismatches: 50, Indels: 11
0.82 0.14 0.03
Matches are distributed among these distances:
148 88 0.31
149 188 0.66
150 11 0.04
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (149 bp):
GTGCAATGAAACAGATTGAAGCTACAATGGTGAATCTTGCTTCCCCAACATTGCAATTAAAAGAT
TGAGGCCACAACGACAAATCTTACTTCCCTGGAGTTGCAGTGGAATAGATTGAAGCTACAACAAC
GAATCTTACTTCCCGAGCA
Found at i:28225756 original size:33 final size:31
Alignment explanation
Indices: 28225718--28225783 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 31
28225708 ATACATGTCC
28225718 ATATATA-TCTATATATATTTTCTATTTTTATGA
1 ATATATATTCT-TATATATTTT-TATTTTT-TGA
*
28225751 ATATATATTTCTTATTTATTTTTATTTTTTGA
1 ATATATA-TTCTTATATATTTTTATTTTTTGA
28225783 A
1 A
28225784 ACTTTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 4 0.13
33 14 0.47
34 9 0.30
35 3 0.10
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (31 bp):
ATATATATTCTTATATATTTTTATTTTTTGA
Found at i:28225768 original size:21 final size:23
Alignment explanation
Indices: 28225728--28225769 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28225718 ATATATATCT
*
28225728 ATATATATTTTCTATTTTTATGA
1 ATATATATTTTCTATATTTATGA
28225751 ATATATA-TTTCT-TATTTAT
1 ATATATATTTTCTATATTTAT
28225770 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATATATTTTCTATATTTATGA
Found at i:28230092 original size:27 final size:27
Alignment explanation
Indices: 28230054--28230129 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
28230044 ACTAGGTGTA
*
28230054 CCGCCAATCAGATAGCCACCACCAGTG
1 CCGCCTATCAGATAGCCACCACCAGTG
* ** *
28230081 CCGCCTGTCAGATAGCCATAACCGGTG
1 CCGCCTATCAGATAGCCACCACCAGTG
*
28230108 CTGCCTATCAGATATG-CACCAC
1 CCGCCTATCAGATA-GCCACCAC
28230130 TACTAAAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.26, C:0.37, G:0.20, T:0.17
Consensus pattern (27 bp):
CCGCCTATCAGATAGCCACCACCAGTG
Found at i:28231089 original size:69 final size:69
Alignment explanation
Indices: 28231008--28231230 Score: 249
Period size: 69 Copynumber: 3.3 Consensus size: 69
28230998 ATATTGACTA
* ** * *
28231008 ACTCTCATAGCTCACTGCTTTGCTAATTTCATTAAAAAGTTAATTTTAATCTAACATTGGCTAGA
1 ACTCTCATAGCTCACTACTTAACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGGCTAGA
28231073 GAAT
66 GAAT
* * * * * *
28231077 ACTCTCGTAGCTCACTTCTAAACTATTTTCCTTAAAAAGTTAATTTTAACCTCACATTGACTAGA
1 ACTCTCATAGCTCACTACTTAACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGGCTAGA
28231142 GAAT
66 GAAT
* * * * * *
28231146 ACTCTCATAGC-C-C-ACTTCACTATTTTTATTAGAAAGTTAATTTTAATCCCATATTGGTTAGA
1 ACTCTCATAGCTCACTACTTAACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGGCTAGA
*
28231208 GAAC
66 GAAT
28231212 ACTCTCAT-GCTCAC-ACTTA
1 ACTCTCATAGCTCACTACTTA
28231231 CCTTATAATA
Statistics
Matches: 128, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
65 2 0.02
66 50 0.39
67 6 0.05
68 1 0.01
69 69 0.54
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (69 bp):
ACTCTCATAGCTCACTACTTAACTATTTTCATTAAAAAGTTAATTTTAATCTCACATTGGCTAGA
GAAT
Found at i:28232136 original size:60 final size:61
Alignment explanation
Indices: 28232016--28232141 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 61
28232006 AACTTTTAGA
* * * * ** *
28232016 ATTAGAATTAGAATTAAATTAACAAATTTTGTAAATGTTCATGACTAAATTTATTGAATTT
1 ATTAGAAGTAGAACTAAATTAACAAATCTTGAAAACATTCATGACTAAATTTAGTGAATTT
* *
28232077 ATTAGAAGTAGAACTAAA-TAACAAATCTTGAAAACATTGATGATTAAATTT-GTGAAATTT
1 ATTAGAAGTAGAACTAAATTAACAAATCTTGAAAACATTCATGACTAAATTTAGTG-AATTT
28232137 -TTAGA
1 ATTAGA
28232142 TTTAGGATCA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
59 7 0.13
60 32 0.58
61 16 0.29
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (61 bp):
ATTAGAAGTAGAACTAAATTAACAAATCTTGAAAACATTCATGACTAAATTTAGTGAATTT
Found at i:28242941 original size:24 final size:25
Alignment explanation
Indices: 28242878--28242942 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
28242868 AAGGGAATAG
*
28242878 GGGAAGGAA-ATGAGGAAAAATGGAA
1 GGGAATGAAGATGA-GAAAAATGGAA
28242903 GGGAATGAAGA-GAGAAAAATGAGAA
1 GGGAATGAAGATGAGAAAAATG-GAA
*
28242928 GTGAA-G-AGATGAGAA
1 GGGAATGAAGATGAGAA
28242943 GGGTTGAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
23 3 0.09
24 14 0.40
25 17 0.49
26 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.38, T:0.09
Consensus pattern (25 bp):
GGGAATGAAGATGAGAAAAATGGAA
Found at i:28244128 original size:2 final size:2
Alignment explanation
Indices: 28244117--28244146 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
28244107 GTTGTTATAT
28244117 AC AC ATC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC A-C AC AC AC AC AC AC AC AC AC AC AC A
28244147 ATGAACTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:28246388 original size:16 final size:16
Alignment explanation
Indices: 28246357--28246409 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
28246347 GTTTTATCAA
*
28246357 TTTAGTCATTTGTTTAT
1 TTTA-TCATTTATTTAT
* *
28246374 TTTATCGTTTCTTTAT
1 TTTATCATTTATTTAT
28246390 TTTATCATTTATTTAT
1 TTTATCATTTATTTAT
28246406 TTTA
1 TTTA
28246410 ATTATTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 28 0.88
17 4 0.12
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTATCATTTATTTAT
Found at i:28252964 original size:27 final size:26
Alignment explanation
Indices: 28252925--28252978 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
28252915 TGTTGTAGGT
*
28252925 TAAATGTATAAATATG-ATTTTTGTGA
1 TAAATGTATAAAT-TGAATTATTGTGA
*
28252951 TAAATTGTTTAAATTGAATTATTGTGA
1 TAAA-TGTATAAATTGAATTATTGTGA
28252978 T
1 T
28252979 TTTGAGCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (26 bp):
TAAATGTATAAATTGAATTATTGTGA
Found at i:28253421 original size:35 final size:36
Alignment explanation
Indices: 28253294--28253423 Score: 106
Period size: 35 Copynumber: 3.7 Consensus size: 36
28253284 TCATTGTAGA
* *
28253294 TTTATCCGACTAGTGC-AGCGCACACCTATCGCCAG
1 TTTATCCGACTAGTGCTAGGGCACACCTATCGTCAG
** ** * * * * *
28253329 TTTATCTTACTAGCACTGGGCGCAAAAC-ATTGTCGG
1 TTTATCCGACTAGTGCTAGG-GCACACCTATCGTCAG
* *
28253365 TTTATTCAACTAGTG-TAGGGCACACCTATCGTCAG
1 TTTATCCGACTAGTGCTAGGGCACACCTATCGTCAG
28253400 TTTATCCGACTAGTGCT-GGGCACA
1 TTTATCCGACTAGTGCTAGGGCACA
28253424 AAACATTGTA
Statistics
Matches: 68, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
34 5 0.07
35 41 0.60
36 17 0.25
37 5 0.07
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (36 bp):
TTTATCCGACTAGTGCTAGGGCACACCTATCGTCAG
Found at i:28253451 original size:71 final size:71
Alignment explanation
Indices: 28253257--28253452 Score: 248
Period size: 71 Copynumber: 2.8 Consensus size: 71
28253247 GTATTTGTTG
* * *
28253257 GTTTGTCCAACTAGCGCTGGGCGCAAATCATTGTAGATTTATCCGACTAGTGCAGCGCACACCTA
1 GTTTATCCAACTAGCGCTGGGCGCAAAACATTGTAGATTTATCCGACTAGTGTAGCGCACACCTA
28253322 TCGCCA
66 TCGCCA
** * * * * * *
28253328 GTTTATCTTACTAGCACTGGGCGCAAAACATTGTCGGTTTATTCAACTAGTGTAGGGCACACCTA
1 GTTTATCCAACTAGCGCTGGGCGCAAAACATTGTAGATTTATCCGACTAGTGTAGCGCACACCTA
*
28253393 TCGTCA
66 TCGCCA
* * * *
28253399 GTTTATCCGACTAGTGCTGGGCACAAAACATTGTAAATTTATCCGACTAGTGTA
1 GTTTATCCAACTAGCGCTGGGCGCAAAACATTGTAGATTTATCCGACTAGTGTA
28253453 ACCCATCGTC
Statistics
Matches: 103, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 103 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (71 bp):
GTTTATCCAACTAGCGCTGGGCGCAAAACATTGTAGATTTATCCGACTAGTGTAGCGCACACCTA
TCGCCA
Found at i:28258652 original size:13 final size:13
Alignment explanation
Indices: 28258634--28258658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28258624 CTTATTTAAA
28258634 TAAAATAAAATAG
1 TAAAATAAAATAG
28258647 TAAAATAAAATA
1 TAAAATAAAATA
28258659 AAAGTAAAAT
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
TAAAATAAAATAG
Done.