Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 126 of 310
Found at i:40436651 original size:46 final size:46
Alignment explanation
Indices: 40436584--40436757 Score: 183
Period size: 46 Copynumber: 3.8 Consensus size: 46
40436574 TTTGGGCATT
*
40436584 CGAACTCATTGAGTAGAGTCCGAGTTCACTTATGGATGCGAACATC
1 CGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATC
* * * * *
40436630 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATC
1 CGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-ACATC
* * * *
40436677 CGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACACC
1 CGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATC
* *
40436723 CGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCATTGAGTTGAGTCCGAGTTCACTTATGG
40436758 GCGGTTTACA
Statistics
Matches: 104, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 61 0.59
47 32 0.31
48 2 0.02
50 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (46 bp):
CGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATC
Found at i:40436696 original size:93 final size:93
Alignment explanation
Indices: 40436578--40436750 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
40436568 CAGATATTTG
* * * *
40436578 GGCATTCGAACTCATTGAGTAGAGTCCGAGTTCACTTATGGATGCGAACATCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTAGAGTCCGAGTTCACTTATGGATACGAACACCCGAACTCATTGAG
40436643 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
40436671 GGCATCCGAACTCGTTGAGCT-GAGTCCGAGTTCACTTATGGATACGAACACCCGAGCTCATTGA
1 GGCATCCGAACTCATTGAG-TAGAGTCCGAGTTCACTTATGGATACGAACACCCGAACTCATTGA
40436735 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
40436751 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTAGAGTCCGAGTTCACTTATGGATACGAACACCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:40442343 original size:27 final size:27
Alignment explanation
Indices: 40442304--40442481 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
40442294 ATATTGAGCC
* * *
40442304 CGCACACTCAGTGCTACATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40442331 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40442358 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40442386 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40442413 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40442440 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40442467 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40442482 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 107 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40442443 original size:82 final size:81
Alignment explanation
Indices: 40442325--40442480 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40442315 TGCTACATAA
* *
40442325 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40442390 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40442407 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40442471 CACTTAGTGC
65 CACTTAGTGC
40442481 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40442668 original size:67 final size:67
Alignment explanation
Indices: 40442560--40442693 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
40442550 CCGAGATCAA
40442560 CAACTCAGTACATCTTACCTCTTTTCTTTCATTCAACAATTTCATCATCACATACGTACATGCAT
1 CAACTCAGTACATCTTACCTCTTTTCTTTCATTCAACAATTTCATCATCACATACGTACATGCAT
40442625 AT
66 AT
*
40442627 CAACTCAGTACATCTTACCTCTTTTCTTTCATTCAACAATTTCATCATCATATACGTACATGCAT
1 CAACTCAGTACATCTTACCTCTTTTCTTTCATTCAACAATTTCATCATCACATACGTACATGCAT
40442692 AT
66 AT
40442694 ATATATGTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (67 bp):
CAACTCAGTACATCTTACCTCTTTTCTTTCATTCAACAATTTCATCATCACATACGTACATGCAT
AT
Found at i:40443111 original size:13 final size:13
Alignment explanation
Indices: 40443093--40443117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40443083 TACTAAATTT
40443093 TCATGGATTCAAG
1 TCATGGATTCAAG
40443106 TCATGGATTCAA
1 TCATGGATTCAA
40443118 TATACCATTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:40444478 original size:62 final size:62
Alignment explanation
Indices: 40444381--40444505 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
40444371 CCTTTACTAA
* *
40444381 CGGAACCTTTTTGTTCCGCAACTCCTTCACTTCACGAGCTAGGATAC-ACATCGGCTCTTCTT
1 CGGAACCCTTTTATTCCGCAACTCCTTCACTTCACGAGCTAGGATACGA-ATCGGCTCTTCTT
* * * *
40444443 CGGAACCCTTTTATTTCGCAACTCTTTCACTTCACGAGTTAGGATACGAATCGGTTCTTCTT
1 CGGAACCCTTTTATTCCGCAACTCCTTCACTTCACGAGCTAGGATACGAATCGGCTCTTCTT
40444505 C
1 C
40444506 ATAGCTCATA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 55 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (62 bp):
CGGAACCCTTTTATTCCGCAACTCCTTCACTTCACGAGCTAGGATACGAATCGGCTCTTCTT
Found at i:40445135 original size:63 final size:63
Alignment explanation
Indices: 40445062--40445185 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
40445052 GCAACATCTC
*
40445062 AACATATCCTCAAGTATCTGAATTATCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGTG
1 AACATATCCTCAAGTATCTGAATTATCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAGTG
*
40445125 AACATATCCTCAAGTATCTGAATTATCCGCTCAGATTGACCATCGGTTTGGGGGTGAAAAG
1 AACATATCCTCAAGTATCTGAATTATCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAG
40445186 CAGTGCTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (63 bp):
AACATATCCTCAAGTATCTGAATTATCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAGTG
Found at i:40448250 original size:63 final size:63
Alignment explanation
Indices: 40448151--40448276 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
40448141 CCGCAGTCGC
40448151 CCTCGACTTATTAATGTCCTCCCTGAACTTCTTTACAGCTAAGAACGGAGCTTTACCCGCCGA
1 CCTCGACTTATTAATGTCCTCCCTGAACTTCTTTACAGCTAAGAACGGAGCTTTACCCGCCGA
* *
40448214 CCTCGACTTATTAATGTCCTCCCTGAACTTCTTTACAGCTGAGAACGGAGCTTTCCCCGCCGA
1 CCTCGACTTATTAATGTCCTCCCTGAACTTCTTTACAGCTAAGAACGGAGCTTTACCCGCCGA
40448277 TCTTTTACGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.29
Consensus pattern (63 bp):
CCTCGACTTATTAATGTCCTCCCTGAACTTCTTTACAGCTAAGAACGGAGCTTTACCCGCCGA
Found at i:40452379 original size:19 final size:19
Alignment explanation
Indices: 40452333--40452382 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
40452323 GGTATAGAGC
*
40452333 ACACGCCCATGTGCTAGGG
1 ACACGCCCGTGTGCTAGGG
40452352 ACACGCCCGTGTGCTAGGG
1 ACACGCCCGTGTGCTAGGG
40452371 ACACGCCCGTGT
1 ACACGCCCGTGT
40452383 CCCGAACCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (19 bp):
ACACGCCCGTGTGCTAGGG
Found at i:40454139 original size:92 final size:92
Alignment explanation
Indices: 40453976--40454790 Score: 1576
Period size: 92 Copynumber: 8.8 Consensus size: 92
40453966 GCCCATAAGT
* ** * *
40453976 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCA-CCATTAGTGAACTCGGACTCAACTCAA
40454041 CGAGCTCGGATGCCTAGTTACATCTCAC
65 CGAGCTCGGATGCCTAGTTACATCTCAC
40454069 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454134 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
40454161 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454226 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
40454253 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454318 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
40454345 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454410 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
40454437 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454502 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
40454529 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454594 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
40454621 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454686 GAGCTCGGATGCCTAGTTACATCTCAC
66 GAGCTCGGATGCCTAGTTACATCTCAC
40454713 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
40454778 GAGCTCGGATGCC
66 GAGCTCGGATGCC
40454791 CAAATATTCC
Statistics
Matches: 717, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 684 0.95
93 33 0.05
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCACCATTAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCAC
Found at i:40454907 original size:57 final size:57
Alignment explanation
Indices: 40454833--40454946 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
40454823 AATCTATTCC
*
40454833 TAAGGTTCAACGAGACCTTTTTCCCAATCATGTGTCTCAACCATCTTCTACGGAATG
1 TAAGGTTCAACGAGACCTTTTTCCCAATCATGTGTCTCAACCATCTCCTACGGAATG
* *
40454890 TAAGGTTCAACGGGACCTTTTTCCCAATCATGTGTCTCAACTATCTCCTACGGAATG
1 TAAGGTTCAACGAGACCTTTTTCCCAATCATGTGTCTCAACCATCTCCTACGGAATG
40454947 CCGATACCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (57 bp):
TAAGGTTCAACGAGACCTTTTTCCCAATCATGTGTCTCAACCATCTCCTACGGAATG
Found at i:40457744 original size:40 final size:40
Alignment explanation
Indices: 40457700--40458012 Score: 255
Period size: 40 Copynumber: 7.6 Consensus size: 40
40457690 GCTCCTCGTT
*
40457700 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
40457740 CAAATGCCTTCGGGACTTAACCCAGATT-TAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGTTATAGTAACTCGCA
**
40457780 CAAATGCCTTCGGG-CTTAGCCCGGATT-TAACCGGATATAGCTCCTCGTT
1 CAAATGCCTTCGGGACTTAGCCCGG-TTAT-A---G-TA-A----CTCGCA
*
40457829 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
40457869 CAAATGCCTTCGGGACTTAACCCAGATT-TAATATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGTTATAGTAACTCGCA
* *
40457909 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
40457948 CAAATGCCTTC-GGATCTTAGTCCGGATATTGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
*
40457989 TAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40458013 ACATCATTCA
Statistics
Matches: 222, Mismatches: 29, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
38 4 0.02
39 39 0.18
40 124 0.56
41 17 0.08
44 3 0.01
45 3 0.01
46 1 0.00
49 21 0.09
50 10 0.05
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:40457800 original size:79 final size:78
Alignment explanation
Indices: 40457700--40458011 Score: 256
Period size: 79 Copynumber: 3.8 Consensus size: 78
40457690 GCTCCTCGTT
* *
40457700 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
1 CAAATGCCTTCGGGACTTAGCCCGGTT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-G
*
40457765 ATTTAATAACTCGCA
64 ATTTAGTAACTCGCA
**
40457780 CAAATGCCTTCGGG-CTTAGCCCGGATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTT-A---G-TA-A----CTCGCACAAATGCCTTCGGGA
* *
40457844 CATAGCCCGGTTATAGTAACTCGCA
55 CTTAGCCCGATT-TAGTAACTCGCA
* * * *
40457869 CAAATGCCTTCGGGACTTAACCCAGATTTAATATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCC-GGTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-G
* *
40457933 AATTAGTATCTCGCA
64 ATTTAGTAACTCGCA
* * * *
40457948 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCATAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGA-CTTAGCCCGG-T-TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCC
40458010 CG
62 CG
40458012 GACATCATTC
Statistics
Matches: 187, Mismatches: 25, Indels: 41
0.74 0.10 0.16
Matches are distributed among these distances:
78 4 0.02
79 58 0.31
80 54 0.29
83 1 0.01
84 2 0.01
85 3 0.02
88 3 0.02
89 51 0.27
90 10 0.05
91 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAT
TTAGTAACTCGCA
Found at i:40457907 original size:129 final size:129
Alignment explanation
Indices: 40457675--40457933 Score: 509
Period size: 129 Copynumber: 2.0 Consensus size: 129
40457665 TACCTTCGGA
40457675 ATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 ATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
40457740 CAAATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGG
66 CAAATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGG
40457804 ATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 ATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
*
40457869 CAAATGCCTTCGGGACTTAACCCAGATTTAATATCTCGCACAAATGCCTTCGGGCTTAGCCCGG
66 CAAATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGG
40457933 A
1 A
40457934 ATTAGTATCT
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (129 bp):
ATTTAACCGGATATAGCTCCTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
CAAATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACAAATGCCTTCGGGCTTAGCCCGG
Found at i:40463166 original size:110 final size:110
Alignment explanation
Indices: 40462973--40463193 Score: 415
Period size: 110 Copynumber: 2.0 Consensus size: 110
40462963 CTTGGTACCA
* *
40462973 AAATATAAAGATTTTTCAATTTAGTCCATAATCTTTTCTTTTCCTCGATCACGACTTGAATCTCG
1 AAATATAAAGATTTTGCAATTTAGTCCACAATCTTTTCTTTTCCTCGATCACGACTTGAATCTCG
40463038 TTTTTCTTGATCTATAATACCAAATTAATCTTATTTAATACATAC
66 TTTTTCTTGATCTATAATACCAAATTAATCTTATTTAATACATAC
*
40463083 AAATATAAAGATTTTGCAATTTAGTCCACAATCTTTTCTTTTCCTCGATCGCGACTTGAATCTCG
1 AAATATAAAGATTTTGCAATTTAGTCCACAATCTTTTCTTTTCCTCGATCACGACTTGAATCTCG
40463148 TTTTTCTTGATCTATAATACCAAATTAATCTTATTTAATACATAC
66 TTTTTCTTGATCTATAATACCAAATTAATCTTATTTAATACATAC
40463193 A
1 A
40463194 TTCATCAAAA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.43
Consensus pattern (110 bp):
AAATATAAAGATTTTGCAATTTAGTCCACAATCTTTTCTTTTCCTCGATCACGACTTGAATCTCG
TTTTTCTTGATCTATAATACCAAATTAATCTTATTTAATACATAC
Found at i:40470318 original size:93 final size:93
Alignment explanation
Indices: 40470211--40470381 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40470201 GCCCATAAGT
* *
40470211 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
40470276 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
40470304 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
40470369 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40470382 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40470378 original size:46 final size:46
Alignment explanation
Indices: 40470203--40470378 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
40470193 TGTAACCCGC
* * *
40470203 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* *
40470249 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
* * *
40470299 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
40470342 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40470379 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
44 1 0.01
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 1 0.01
50 5 0.05
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:40470838 original size:30 final size:30
Alignment explanation
Indices: 40470804--40470863 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40470794 ATTTAATACG
40470804 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
40470834 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40470864 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40474196 original size:45 final size:46
Alignment explanation
Indices: 40474135--40474249 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 46
40474125 TGTGCCATGG
* *
40474135 TGTCTTTCAATAATGGTCTTATTTATTCTCT-TCTTAATGCCATAA
1 TGTCTTTCAACAATGGTCTTATTTATTCTCTGTCGTAATGCCATAA
* * * * * ** *
40474180 TGTCTTTCAACCATGGTTTTATTCATTTTTTGTCGTGTTGCCATAG
1 TGTCTTTCAACAATGGTCTTATTTATTCTCTGTCGTAATGCCATAA
*
40474226 TGTCTTTCAACTATGGTCTTATTT
1 TGTCTTTCAACAATGGTCTTATTT
40474250 CTTTGATTCA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
45 25 0.45
46 31 0.55
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.50
Consensus pattern (46 bp):
TGTCTTTCAACAATGGTCTTATTTATTCTCTGTCGTAATGCCATAA
Found at i:40474321 original size:45 final size:46
Alignment explanation
Indices: 40474284--40474385 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 46
40474274 CTTTCAGCTG
*
40474284 TGGTCTTACTCTG-TAGAATCGTGATGCCATAACGTCTTTCA-ATCA
1 TGGTCTTACTC-GATAGAATCATGATGCCATAACGTCTTTCAGATCA
*
40474329 TGGTCTTACTCGATAGAATCATGATGCCATAATGTCTTTCAG-TCA
1 TGGTCTTACTCGATAGAATCATGATGCCATAACGTCTTTCAGATCA
*
40474374 TGGTTTTACTCG
1 TGGTCTTACTCG
40474386 TTTCTGGTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (46 bp):
TGGTCTTACTCGATAGAATCATGATGCCATAACGTCTTTCAGATCA
Found at i:40474451 original size:46 final size:47
Alignment explanation
Indices: 40474386--40474479 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 47
40474376 GTTTTACTCG
* * *
40474386 TTTCTGGTATGGTGCCATAGTGTTTTTCAACTATGGTCTTATTTATT
1 TTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTAATTATT
*
40474433 TTTC-GGTATAGTGTCATAGTGTCTTTCAACTATGGTCTTAATTATT
1 TTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTAATTATT
40474479 T
1 T
40474480 CTTTCAAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 39 0.91
47 4 0.09
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.50
Consensus pattern (47 bp):
TTTCTGGTATAGTGCCATAGTGTCTTTCAACTATGGTCTTAATTATT
Found at i:40476214 original size:40 final size:42
Alignment explanation
Indices: 40476150--40476242 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 42
40476140 CTATGTTTGT
* *
40476150 CACTTAGTGTGCATATCGAGATAGCTTCAGCTATATA-A-AG
1 CACTTAGTGTGCAAATCGAGATAGCTTCAGATATATATATAG
*
40476190 CACTTAGTGTGCAAATC-AGAATAGCTTCGGATATATATATAG
1 CACTTAGTGTGCAAATCGAG-ATAGCTTCAGATATATATATAG
40476232 CACTTAGTGTG
1 CACTTAGTGTG
40476243 TGAGACTGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
39 2 0.04
40 31 0.66
41 1 0.02
42 13 0.28
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (42 bp):
CACTTAGTGTGCAAATCGAGATAGCTTCAGATATATATATAG
Found at i:40476284 original size:41 final size:41
Alignment explanation
Indices: 40476231--40476324 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
40476221 TATATATATA
*
40476231 GCACTTAGTGTGTGAGACTGTGATAGCTTCGTCTATGAAAG
1 GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
40476272 GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
1 GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
*
40476313 CCACTTAGTGTG
1 GCACTTAGTGTG
40476325 CAAGATTACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (41 bp):
GCACTTAGTGTGTGAGACTGTGATAGCTTCGGCTATGAAAG
Found at i:40476339 original size:41 final size:40
Alignment explanation
Indices: 40476170--40476349 Score: 139
Period size: 41 Copynumber: 4.4 Consensus size: 40
40476160 GCATATCGAG
* * *
40476170 ATAGCTTCAGCTATATAAAGCACTTAGTGTGCAA-A-TCAGA
1 ATAGCTTCGGCTAT-GAAAGCACTTAGTGTGCAAGACT-ATA
* * ** * *
40476210 ATAGCTTCGGATATATATATAGCACTTAGTGTGTGAGACTGTG
1 ATAGCTTCGGCTAT-GA-A-AGCACTTAGTGTGCAAGACTATA
* ** * *
40476253 ATAGCTTCGTCTATGAAAGGCACTTAGTGTGTGAGACTGTG
1 ATAGCTTCGGCTATGAAA-GCACTTAGTGTGCAAGACTATA
* *
40476294 ATAGCTTCGGCTATGAAAGCCACTTAGTGTGCAAGATTACA
1 ATAGCTTCGGCTATGAAAG-CACTTAGTGTGCAAGACTATA
40476335 ATAGCTTCGGCTATG
1 ATAGCTTCGGCTATG
40476350 CTTTGGCACT
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
40 17 0.15
41 71 0.61
42 15 0.13
43 13 0.11
44 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
ATAGCTTCGGCTATGAAAGCACTTAGTGTGCAAGACTATA
Found at i:40479925 original size:27 final size:27
Alignment explanation
Indices: 40479895--40480072 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
40479885 ATATTGAGTC
* *
40479895 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40479922 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
40479949 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
40479977 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40480004 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
40480031 CGGACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
40480058 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40480073 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40480038 original size:82 final size:81
Alignment explanation
Indices: 40479916--40480071 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
40479906 TGCTATATAA
* *
40479916 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40479981 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
40479998 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGGACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40480062 CACTTAGTGC
65 CACTTAGTGC
40480072 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40480086 original size:82 final size:83
Alignment explanation
Indices: 40479895--40480086 Score: 207
Period size: 82 Copynumber: 2.3 Consensus size: 83
40479885 ATATTGAGTC
* * * * *
40479895 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
40479959 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * ** *
40479977 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGGACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
40480038 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
*
40480058 CGCACACTTAGTGCTGTACAATTTAATTC
1 CGCACACTTAGTGCTGTACAATTCAATTC
40480087 CCGTGCACTT
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 69 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:40489592 original size:49 final size:48
Alignment explanation
Indices: 40489438--40489607 Score: 157
Period size: 49 Copynumber: 3.5 Consensus size: 48
40489428 AGATGCCGAC
* *
40489438 GCCATGTCCCAGACATGGTCTTACACTGGCTAGCA-C-ATCAAAGTCGAT
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTATCATCTATC-AGGTCGAT
* * * * * **
40489486 GACATGTCCCAGATAGGTCTTACACTGACTTTCATATATCGAGACCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATC-AGGTCGAT
* * * *
40489535 G-CAGTGTCCTAGATAGGTCTTACACTGGCTCTCATCTATCAGTGTCGAA
1 GCCA-TGTCCCAGACAGGTCTTACACTGGCTATCATCTATCAG-GTCGAT
40489584 GCCATGTCCCAGACAGGTCTTACA
1 GCCATGTCCCAGACAGGTCTTACA
40489608 ATGACACACA
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
47 16 0.16
48 17 0.17
49 63 0.64
50 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (48 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCAGGTCGAT
Found at i:40489771 original size:46 final size:46
Alignment explanation
Indices: 40489670--40489778 Score: 125
Period size: 46 Copynumber: 2.4 Consensus size: 46
40489660 TATATCTCAA
*
40489670 GGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCTTAAT
1 GGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTC-TCATAAT
* ** *
40489717 -GCCAATGCATGTCTGAGACATGTCTTACACTAGCTCT-T-ATAATGT
1 GGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCTCATAA--T
40489762 GGCCGATGCATGTCCCA
1 GGCCGATGCATGTCCCA
40489779 GATGTAACAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
43 3 0.06
44 1 0.02
45 1 0.02
46 46 0.90
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
GGCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCTCATAAT
Found at i:40493484 original size:20 final size:20
Alignment explanation
Indices: 40493459--40493497 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40493449 ACAACTTCAA
40493459 TTATTTTAC-ACATTTACAAC
1 TTATTTTACAAC-TTTACAAC
40493479 TTATTTTACAACTTTACAA
1 TTATTTTACAACTTTACAA
40493498 AATAGCCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATTTTACAACTTTACAAC
Found at i:40498172 original size:28 final size:29
Alignment explanation
Indices: 40498140--40498251 Score: 149
Period size: 29 Copynumber: 3.9 Consensus size: 29
40498130 TACCTGTATC
*
40498140 TGGCCCATTAAGCCC-AATCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
40498168 TGGCCCATTAGGCCCAAATCACCTAT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
40498197 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
40498226 TGGCCCGTTAGGCCC-AGTCACATTCA
1 TGGCCCATTAGGCCCAAATCACATTCA
40498252 ATTCATGCTC
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.32
29 50 0.67
30 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:40498231 original size:58 final size:57
Alignment explanation
Indices: 40498131--40498241 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 57
40498121 AAATTCACAT
* *
40498131 ACCTGTATCTGGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
* * *
40498188 ACCTATATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAAGCCC-AATCACATTCATATGGCCCATTAGGCCCA
40498242 GTCACATTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 21 0.44
58 27 0.56
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (57 bp):
ACCTATATATGGCCCATTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:40504057 original size:26 final size:26
Alignment explanation
Indices: 40504021--40504096 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
40504011 TAAAATTAAC
* *
40504021 CCTAAGGGTATATTGGTCATTTTGTA
1 CCTAGGGGTATATTGGTCATTTTCTA
* * *
40504047 CCTAGGGGTATAATGGTAATTTCCCTA
1 CCTAGGGGTATATTGGTCATTT-TCTA
* * *
40504074 CTTAGGGGTATTTTAGTCATTTT
1 CCTAGGGGTATATTGGTCATTTT
40504097 AACAATTTTC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.42
Consensus pattern (26 bp):
CCTAGGGGTATATTGGTCATTTTCTA
Found at i:40506298 original size:32 final size:32
Alignment explanation
Indices: 40506257--40506322 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
40506247 CATGATATGA
*
40506257 AGTACTATTTCTGGGAAGAACCATACTTGTTT
1 AGTACTATTTCTAGGAAGAACCATACTTGTTT
40506289 AGTACTATTTCTAGGAAGAACCATACTTGTTT
1 AGTACTATTTCTAGGAAGAACCATACTTGTTT
40506321 AG
1 AG
40506323 AAAGTGTGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (32 bp):
AGTACTATTTCTAGGAAGAACCATACTTGTTT
Found at i:40507125 original size:40 final size:40
Alignment explanation
Indices: 40507081--40507161 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
40507071 TAAAGCTTAC
* *
40507081 TGGATGTTAACCTTGCTAAAGAAAAATGGATGTTTCAACT
1 TGGATCTTAACCTTGCTAAAGAAAAATGGATGATTCAACT
40507121 TGGATCTTAACCTTGCTAAAGAAAAATGGATGATTCAACT
1 TGGATCTTAACCTTGCTAAAGAAAAATGGATGATTCAACT
40507161 T
1 T
40507162 AACAAGTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (40 bp):
TGGATCTTAACCTTGCTAAAGAAAAATGGATGATTCAACT
Found at i:40507774 original size:52 final size:52
Alignment explanation
Indices: 40507707--40507811 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
40507697 TCACTTTTGA
*
40507707 TCCAAGTCTTCATTGCAACTCAATTTTCAAATTTTCTTTAAGTCTAAGTACT
1 TCCAAGTCTTAATTGCAACTCAATTTTCAAATTTTCTTTAAGTCTAAGTACT
40507759 TCCAAGTCTTAATTGCAACTCAATTTTCAAATTTTCTTTAAGTCTAAGTACT
1 TCCAAGTCTTAATTGCAACTCAATTTTCAAATTTTCTTTAAGTCTAAGTACT
40507811 T
1 T
40507812 AATTGAATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.43
Consensus pattern (52 bp):
TCCAAGTCTTAATTGCAACTCAATTTTCAAATTTTCTTTAAGTCTAAGTACT
Found at i:40507975 original size:18 final size:18
Alignment explanation
Indices: 40507949--40507983 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40507939 TAAATAGTTT
* *
40507949 ATAATTATATTTATTATA
1 ATAAATATATTAATTATA
40507967 ATAAATATATTAATTAT
1 ATAAATATATTAATTAT
40507984 TATCAACTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAAATATATTAATTATA
Found at i:40510825 original size:27 final size:27
Alignment explanation
Indices: 40510795--40510848 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40510785 TCATACAACC
* *
40510795 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
40510822 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
40510849 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:40513342 original size:15 final size:16
Alignment explanation
Indices: 40513323--40513367 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
40513313 AGAAGCCCAG
40513323 GATAAAGAAATCCAAT
1 GATAAAGAAATCCAAT
*
40513339 -ATAAATAAATCC-AT
1 GATAAAGAAATCCAAT
*
40513353 GATAAGGAAATCCAA
1 GATAAAGAAATCCAA
40513368 ATTACAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 2 0.08
15 21 0.88
16 1 0.04
ACGTcount: A:0.56, C:0.13, G:0.11, T:0.20
Consensus pattern (16 bp):
GATAAAGAAATCCAAT
Found at i:40516216 original size:22 final size:22
Alignment explanation
Indices: 40516188--40516232 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
40516178 TATCTCATAG
40516188 TACGAGACTCGGATAATGCTCT
1 TACGAGACTCGGATAATGCTCT
40516210 TACGAGACTCGGATAATGCTCT
1 TACGAGACTCGGATAATGCTCT
40516232 T
1 T
40516233 GTCTCTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
TACGAGACTCGGATAATGCTCT
Found at i:40517445 original size:27 final size:27
Alignment explanation
Indices: 40517415--40517466 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40517405 TCATACAATC
* *
40517415 CATGTAATAGTAATTTAACATTCAAAT
1 CATGTAACAATAATTTAACATTCAAAT
**
40517442 CATGTAACAATAATTTGTCATTCAA
1 CATGTAACAATAATTTAACATTCAA
40517467 TTTCACATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAAAT
Found at i:40520961 original size:18 final size:19
Alignment explanation
Indices: 40520920--40520961 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
40520910 TTTCAAGCAA
40520920 ACCTTGATGAATTTTTATC
1 ACCTTGATGAATTTTTATC
40520939 ACCTTGATGAATTTTTATC
1 ACCTTGATGAATTTTTATC
40520958 -CCTT
1 ACCTT
40520962 AAAACCCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (19 bp):
ACCTTGATGAATTTTTATC
Found at i:40521879 original size:21 final size:23
Alignment explanation
Indices: 40521850--40521892 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40521840 AATTGTACTT
*
40521850 AAATCATT-AACAAATTGAATTA
1 AAATCATTAAAAAAATTGAATTA
40521872 AAAT-ATTAAAAAAATTGAATT
1 AAATCATTAAAAAAATTGAATT
40521893 TTAATTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (23 bp):
AAATCATTAAAAAAATTGAATTA
Found at i:40521927 original size:10 final size:10
Alignment explanation
Indices: 40521912--40521936 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40521902 TTTATAATAA
40521912 ATTTTGATTT
1 ATTTTGATTT
40521922 ATTTTGATTT
1 ATTTTGATTT
40521932 ATTTT
1 ATTTT
40521937 CGACAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (10 bp):
ATTTTGATTT
Found at i:40522803 original size:20 final size:18
Alignment explanation
Indices: 40522770--40522806 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
40522760 TGTGTTGTTG
40522770 ATATGCTTAATTTAATTA
1 ATATGCTTAATTTAATTA
40522788 ATATGGCTTAAATTTAATT
1 ATAT-GCTT-AATTTAATT
40522807 CGTATTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
ATATGCTTAATTTAATTA
Found at i:40526415 original size:15 final size:15
Alignment explanation
Indices: 40526395--40526426 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40526385 TAATTTCACT
40526395 AAAACCATGTCCATA
1 AAAACCATGTCCATA
40526410 AAAACCATGTCCATA
1 AAAACCATGTCCATA
40526425 AA
1 AA
40526427 CACCCACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAACCATGTCCATA
Found at i:40527995 original size:25 final size:24
Alignment explanation
Indices: 40527967--40528018 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
40527957 ATAGGATACT
**
40527967 TCACAACTTGAAATCTGACCCGTCC
1 TCACAACCCGAAATCTGACCC-TCC
40527992 TCACAACCCGAAATCTGACCCTCC
1 TCACAACCCGAAATCTGACCCTCC
40528016 TCA
1 TCA
40528019 AGAGGTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.29, C:0.40, G:0.10, T:0.21
Consensus pattern (24 bp):
TCACAACCCGAAATCTGACCCTCC
Found at i:40529171 original size:22 final size:22
Alignment explanation
Indices: 40529129--40529188 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
40529119 AAATTTAGTT
*
40529129 TTTAATATTTATATTTTTTTTAG
1 TTTAAT-TTTATATTTTTTTTAA
40529152 TTTAATTTT-TATCTTTTTTTAA
1 TTTAATTTTATAT-TTTTTTTAA
*
40529174 -TTAAATTTA-ATTTTT
1 TTTAATTTTATATTTTT
40529189 AATTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 12 0.36
22 11 0.33
23 6 0.18
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTAATTTTATATTTTTTTTAA
Found at i:40529177 original size:21 final size:20
Alignment explanation
Indices: 40529127--40529188 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 20
40529117 TCAAATTTAG
40529127 TTTTTAA-T-ATTTATATTT
1 TTTTTAATTAATTTATATTT
* *
40529145 TTTTTAGTTTAATTTTTATCTT
1 TTTTTA-ATTAATTTATAT-TT
40529167 TTTTTAATTAAATTTA-ATTT
1 TTTTTAATT-AATTTATATTT
40529187 TT
1 TT
40529189 AATTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 6 0.17
20 5 0.14
21 11 0.31
22 13 0.37
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTAATTAATTTATATTT
Found at i:40529341 original size:17 final size:19
Alignment explanation
Indices: 40529319--40529371 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
40529309 TAAATTTAAA
40529319 AAATATATAAAAATT-AA-
1 AAATATATAAAAATTCAAC
* *
40529336 ATATAT-TTAAAATTCAAC
1 AAATATATAAAAATTCAAC
40529354 AAATATATAAAAAATTCA
1 AAATATAT-AAAAATTCA
40529372 TAAATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 7 0.25
17 7 0.25
18 5 0.18
19 1 0.04
20 8 0.29
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATATATAAAAATTCAAC
Found at i:40546962 original size:47 final size:47
Alignment explanation
Indices: 40546884--40548326 Score: 2441
Period size: 47 Copynumber: 30.6 Consensus size: 47
40546874 CCCTTCGGGA
* * * *
40546884 CTTATCACATTTATACACTTTCACATCCATCACGAT-GGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCAC-ATCGGCCATTAGGC
* *
40546931 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40546978 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40547027 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40547076 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40547125 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTA-G-GC
40547176 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547223 CTTATCACAT-CATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547269 CGTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40547316 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547363 CTTATCACAT-CATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547409 CTTATCACAT-CATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547455 CTTATCACAT-CATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547501 CTTATCACAT-CATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40547547 CTTATCACAT-CATACACTTTCACATTCATCACACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCAT--CACATCGGCCATTAGGC
*
40547595 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATCAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40547642 CTTATCACATATATACACTTTCACGTTCATCACATTGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547689 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547736 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547783 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547830 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547877 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547924 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40547971 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40548018 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40548065 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40548112 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40548159 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40548206 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40548253 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40548300 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
40548327 TATTCAAATA
Statistics
Matches: 1364, Mismatches: 23, Indels: 18
0.97 0.02 0.01
Matches are distributed among these distances:
46 248 0.18
47 841 0.62
48 27 0.02
49 237 0.17
50 1 0.00
51 10 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40547232 original size:22 final size:22
Alignment explanation
Indices: 40547204--40547278 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
40547194 TTTCACATTC
40547204 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
*** *** *
40547226 ATCACATCATACACTTTCACATT
1 ATCACATCGGCCA-TTAGGCCTT
*
40547249 CATCACATCGGCCATTAGGCCGT
1 -ATCACATCGGCCATTAGGCCTT
40547272 ATCACAT
1 ATCACAT
40547279 ATATACACTT
Statistics
Matches: 36, Mismatches: 15, Indels: 4
0.65 0.27 0.07
Matches are distributed among these distances:
22 17 0.47
23 9 0.25
24 10 0.28
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:40551845 original size:16 final size:16
Alignment explanation
Indices: 40551832--40551866 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40551822 GCAAAAGCTG
40551832 AAATACCGAAAAGCCA
1 AAATACCGAAAAGCCA
* *
40551848 AAATGCCGAAAAGTCA
1 AAATACCGAAAAGCCA
40551864 AAA
1 AAA
40551867 ATTTGGGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.14, T:0.09
Consensus pattern (16 bp):
AAATACCGAAAAGCCA
Found at i:40552188 original size:29 final size:29
Alignment explanation
Indices: 40552117--40552195 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
40552107 TATAAATGAG
* **
40552117 ATTGGGCCCAATGCGCTATATGAGTGTGA
1 ATTGGGCCCAATGGGCTATATGAACGTGA
* *
40552146 ATTAGGCCTAATGGGCTATATGAACGTGA
1 ATTGGGCCCAATGGGCTATATGAACGTGA
*
40552175 ATTGGGCCCAATGGGCCATAT
1 ATTGGGCCCAATGGGCTATAT
40552196 AAATGAGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (29 bp):
ATTGGGCCCAATGGGCTATATGAACGTGA
Found at i:40552224 original size:57 final size:58
Alignment explanation
Indices: 40552095--40552224 Score: 140
Period size: 57 Copynumber: 2.3 Consensus size: 58
40552085 GTGATTTGGG
* * * * *
40552095 CTAGATGGGCCATAT-AAATGAGATTGGGCCCAATGCGCTATATGAGTGTGAATTAGGC
1 CTAG-TGGGCCATATGAAATGAGATTGGGCCCAATGCGCCATATAAATGAGAATTACGC
* * * *
40552153 CTAATGGGCTATATGAACGTGA-ATTGGGCCCAATGGGCCATATAAATGAG-ATTACGC
1 CTAGTGGGCCATATGAA-ATGAGATTGGGCCCAATGCGCCATATAAATGAGAATTACGC
40552210 CTAGTGGGCCATATG
1 CTAGTGGGCCATATG
40552225 CATGTATGTA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
57 28 0.47
58 28 0.47
59 3 0.05
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (58 bp):
CTAGTGGGCCATATGAAATGAGATTGGGCCCAATGCGCCATATAAATGAGAATTACGC
Found at i:40558461 original size:54 final size:54
Alignment explanation
Indices: 40558333--40558526 Score: 194
Period size: 54 Copynumber: 3.5 Consensus size: 54
40558323 TAAAATGGTA
* * * * *
40558333 ATTT-TACCCCACAAGGGTATCTCAGTAATTCTACCTTAC-AGGAGTATTTCAAT
1 ATTTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGG-GTATTTCGAT
* *
40558386 AATTCTACCCTACAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGAT
* * *
40558440 ATTTCTACCCTACAGGGGTATTTCGGTATTTCAGTATTTCTACCCTACAAGGATATTTCGAC
1 ATTTCTACCCTACA-----A---GGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGAT
*
40558502 ATTTCTACCCAACAAGGGTATTTCA
1 ATTTCTACCCTACAAGGGTATTTCA
40558527 ATAATTTTGT
Statistics
Matches: 117, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
53 3 0.03
54 61 0.52
55 3 0.03
57 1 0.01
62 49 0.42
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (54 bp):
ATTTCTACCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGAT
Found at i:40558464 original size:27 final size:27
Alignment explanation
Indices: 40558333--40558525 Score: 160
Period size: 27 Copynumber: 6.9 Consensus size: 27
40558323 TAAAATGGTA
* *
40558333 ATTT-TACCCCACAAGGGTATCTC-AGT
1 ATTTCTACCCTACAAGGGTATTTCGA-T
* * *
40558359 AATTCTACCTTAC-AGGAGTATTTCAAT
1 ATTTCTACCCTACAAGG-GTATTTCGAT
* *
40558386 AATTCTACCCTACAGGGGTATTTC-AGT
1 ATTTCTACCCTACAAGGGTATTTCGA-T
40558413 ATTTCTACCCTACAAGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGAT
*
40558440 ATTTCTACCCTACAGGGGTATTTCGGTATTTCAGT
1 ATTTCTACCCTACAAGGGTATTTC-G------A-T
* *
40558475 ATTTCTACCCTACAAGGATATTTCGAC
1 ATTTCTACCCTACAAGGGTATTTCGAT
*
40558502 ATTTCTACCCAACAAGGGTATTTC
1 ATTTCTACCCTACAAGGGTATTTC
40558526 AATAATTTTG
Statistics
Matches: 139, Mismatches: 14, Indels: 27
0.77 0.08 0.15
Matches are distributed among these distances:
26 7 0.05
27 101 0.73
28 6 0.04
34 2 0.01
35 23 0.17
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (27 bp):
ATTTCTACCCTACAAGGGTATTTCGAT
Found at i:40558477 original size:62 final size:62
Alignment explanation
Indices: 40558402--40558525 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
40558392 ACCCTACAGG
* * * *
40558402 GGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGATATTTCTACCCTACAGGGGTATTTC
1 GGTATTTCAGTATTTCTACCCTACAAGGATATTTCGACATTTCTACCCAACAAGGGTATTTC
40558464 GGTATTTCAGTATTTCTACCCTACAAGGATATTTCGACATTTCTACCCAACAAGGGTATTTC
1 GGTATTTCAGTATTTCTACCCTACAAGGATATTTCGACATTTCTACCCAACAAGGGTATTTC
40558526 AATAATTTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (62 bp):
GGTATTTCAGTATTTCTACCCTACAAGGATATTTCGACATTTCTACCCAACAAGGGTATTTC
Found at i:40558506 original size:35 final size:35
Alignment explanation
Indices: 40558439--40558506 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
40558429 GGTATTTCGA
* * **
40558439 TATTTCTACCCTACAGGGGTATTTCGGTATTTCAG
1 TATTTCTACCCTACAAGGATATTTCGACATTTCAG
40558474 TATTTCTACCCTACAAGGATATTTCGACATTTC
1 TATTTCTACCCTACAAGGATATTTCGACATTTC
40558507 TACCCAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (35 bp):
TATTTCTACCCTACAAGGATATTTCGACATTTCAG
Found at i:40558584 original size:27 final size:27
Alignment explanation
Indices: 40558554--40558884 Score: 283
Period size: 27 Copynumber: 12.3 Consensus size: 27
40558544 GGGTAAAATA
* * *
40558554 GTAATTCTATAAATCAAGGGTACTTTG
1 GTAATTTTACAAATCAAGGGTATTTTG
* * **
40558581 GTAATTTTACAAGTTAAGGGTATTTCA
1 GTAATTTTACAAATCAAGGGTATTTTG
* ** ** *
40558608 ATAATTTTACAGGTTGAGGGTATTTTA
1 GTAATTTTACAAATCAAGGGTATTTTG
* *
40558635 GTAATTTCACAAATCAGGGGTATTTTG
1 GTAATTTTACAAATCAAGGGTATTTTG
*
40558662 GTAATTTTACAAA-CTAGGGGTATTTTG
1 GTAATTTTACAAATC-AAGGGTATTTTG
* * *
40558689 ATAATTTTACAAACCAGGGGTATTTTG
1 GTAATTTTACAAATCAAGGGTATTTTG
* * *
40558716 GTAATTTTATAAA-CAAAGGTTATTTTA
1 GTAATTTTACAAATC-AAGGGTATTTTG
* *
40558743 GTAATTTTACAAACCAGGGGTATTTTG
1 GTAATTTTACAAATCAAGGGTATTTTG
* ** *
40558770 ATAATTTTGTAAACCAAGGGTATTTTG
1 GTAATTTTACAAATCAAGGGTATTTTG
* *
40558797 GTAATTTGACAAA-CTAGGGGTATTTTG
1 GTAATTTTACAAATC-AAGGGTATTTTG
* * * *
40558824 GTGATTTTATAAACCAAGGGTATTTTA
1 GTAATTTTACAAATCAAGGGTATTTTG
* *
40558851 GTAATTTTACAAATTAGGGGTATTTTG
1 GTAATTTTACAAATCAAGGGTATTTTG
40558878 GT-ATTTT
1 GTAATTTT
40558885 GGTAAACTAA
Statistics
Matches: 248, Mismatches: 50, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
26 8 0.03
27 237 0.96
28 3 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
GTAATTTTACAAATCAAGGGTATTTTG
Found at i:40558603 original size:81 final size:81
Alignment explanation
Indices: 40558515--40558864 Score: 222
Period size: 81 Copynumber: 4.3 Consensus size: 81
40558505 TCTACCCAAC
** *
40558515 AAGGGTATTTCAATAATTTTGTAAATCGAGGGTAAAATAGTAA-TTCTATAAATCAAGGGTACTT
1 AAGGGTATTTCAATAATTTTACAAATCGAGGGTAAAATAGTAATTTC-ACAAATCAAGGGTACTT
**
40558579 TGGTAATTTTACAAGTT
65 TGGTAATTTTACAAACT
** * *** * *
40558596 AAGGGTATTTCAATAATTTTACAGGTTGAGGGTATTTTAGTAATTTCACAAATCAGGGGTATTTT
1 AAGGGTATTTCAATAATTTTACAAATCGAGGGTAAAATAGTAATTTCACAAATCAAGGGTACTTT
40558661 GGTAATTTTACAAACT
66 GGTAATTTTACAAACT
* ** * *** * * * * *
40558677 AGGGGTATTTTGATAATTTTACAAA-CCAGGGGTATTTTGGTAATTTTATAAA-CAAAGGTTATT
1 AAGGGTATTTCAATAATTTTACAAATCGA-GGGTAAAATAGTAATTTCACAAATC-AAGGGTACT
* *
40558740 TTAGTAATTTTACAAACC
64 TTGGTAATTTTACAAACT
* ** ** * * *** * * * *
40558758 AGGGGTATTTTGATAATTTTGTAAACCAAGGGTATTTTGGTAATTTGACAAA-CTAGGGGTATTT
1 AAGGGTATTTCAATAATTTTACAAATCGAGGGTAAAATAGTAATTTCACAAATC-AAGGGTACTT
* * *
40558822 TGGTGATTTTATAAACC
65 TGGTAATTTTACAAACT
* *
40558839 AAGGGTATTTTAGTAATTTTACAAAT
1 AAGGGTATTTCAATAATTTTACAAAT
40558865 TAGGGGTATT
Statistics
Matches: 221, Mismatches: 44, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
80 2 0.01
81 214 0.97
82 5 0.02
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (81 bp):
AAGGGTATTTCAATAATTTTACAAATCGAGGGTAAAATAGTAATTTCACAAATCAAGGGTACTTT
GGTAATTTTACAAACT
Found at i:40558872 original size:81 final size:81
Alignment explanation
Indices: 40558571--40558885 Score: 321
Period size: 81 Copynumber: 3.9 Consensus size: 81
40558561 TATAAATCAA
* *** ** **** *
40558571 GGGTACTTTGGTAATTTTACAAGTTAAGGGTATTTCAATAATTTTAC-AGGTTGAGGGTATTTTA
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAG-GGGTATTTTG
*
40558635 GTAATTTCACAAA-TCAG
65 GTAATTTGACAAACT-AG
* *
40558652 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGG
* * * *
40558717 TAATTTTATAAACAAA
66 TAATTTGACAAACTAG
* * * ** *
40558733 GGTTATTTTAGTAATTTTACAAACCAGGGGTATTTTGATAATTTTGTAAACCAAGGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGG
40558798 TAATTTGACAAACTAG
66 TAATTTGACAAACTAG
* * **
40558814 GGGTATTTTGGTGATTTTATAAACCAAGGGTATTTT-AGTAATTTTACAAATTAGGGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGA-TAATTTTACAAACCAGGGGTATTTTG
*
40558878 GTATTTTG
65 GTAATTTG
40558886 GTAAACTAAA
Statistics
Matches: 195, Mismatches: 36, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
80 1 0.01
81 192 0.98
82 2 0.01
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGATAATTTTACAAACCAGGGGTATTTTGG
TAATTTGACAAACTAG
Found at i:40558891 original size:54 final size:54
Alignment explanation
Indices: 40558624--40558884 Score: 364
Period size: 54 Copynumber: 4.9 Consensus size: 54
40558614 TTACAGGTTG
* * * *
40558624 AGGGTATTTTAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACTA
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
* *
40558678 GGGGTATTTT-GATAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAA
1 AGGGTATTTTAG-TAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
* * *
40558732 AGGTTATTTTAGTAATTTTACAAACCAGGGGTATTTTGATAATTTTGTAAACCA
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
* * * *
40558786 AGGGTATTTTGGTAATTTGACAAACTAGGGGTATTTTGGTGATTTTATAAACCA
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
**
40558840 AGGGTATTTTAGTAATTTTACAAATTAGGGGTATTTTGGT-ATTTT
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTT
40558885 GGTAAACTAA
Statistics
Matches: 185, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
53 6 0.03
54 178 0.96
55 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
Found at i:40565880 original size:24 final size:24
Alignment explanation
Indices: 40565835--40565880 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40565825 GATAATGATT
*
40565835 TGTTATATTTTTACTATTATTATA
1 TGTTATATTTTTACTATCATTATA
*
40565859 TGTTTTATTTTTA-TAGTCATTA
1 TGTTATATTTTTACTA-TCATTA
40565881 AAAATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63
Consensus pattern (24 bp):
TGTTATATTTTTACTATCATTATA
Found at i:40567991 original size:21 final size:21
Alignment explanation
Indices: 40567967--40568015 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
40567957 AACTGGAAAG
40567967 TAAACCTACCAAGTAATAGCA
1 TAAACCTACCAAGTAATAGCA
40567988 TAAACCTACCAAGTAATAGCA
1 TAAACCTACCAAGTAATAGCA
40568009 TACAACC
1 TA-AACC
40568016 ATATTTAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.47, C:0.27, G:0.08, T:0.18
Consensus pattern (21 bp):
TAAACCTACCAAGTAATAGCA
Found at i:40570145 original size:37 final size:37
Alignment explanation
Indices: 40570089--40570164 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
40570079 ATGCGTAGAG
* *
40570089 TCCATTTAACAAAATTTCCAAAACTTG-CTTGTAGGTA
1 TCCATTTAAAAAAAATTCCAAAACTTGTC-TGTAGGTA
40570126 TCCATTTAAAAAAAATTCCAAAACTTGTCTGTAGGTA
1 TCCATTTAAAAAAAATTCCAAAACTTGTCTGTAGGTA
40570163 TC
1 TC
40570165 AATACTGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (37 bp):
TCCATTTAAAAAAAATTCCAAAACTTGTCTGTAGGTA
Found at i:40574742 original size:55 final size:52
Alignment explanation
Indices: 40574655--40574899 Score: 223
Period size: 55 Copynumber: 4.6 Consensus size: 52
40574645 ATTAGGGTTT
*
40574655 AAGGATACCATGTAAGACCATGTCAAGGCATGGCAATTGGTCAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGC-ATTGGT-A-GTTTCTAAGGC
* * * *
40574710 AAGGATACCATGTAAGGCCATGTTAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGT-AGTT--TCTAAGGC
* * * *
40574765 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCGTTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGT-AGTTTC-TAAGGC
* * *
40574818 AAGGATACCATGTAAGACCAGGTCGAGACATGGCAATGGTAAGTTT-TAA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGT-AGTTTCTAAGGC
* * *
40574867 AAGGATACCACGTAAGACCATGACAAGTCATGG
1 AAGGATACCATGTAAGACCATGTCAAGACATGG
40574900 AAATGGTAAG
Statistics
Matches: 156, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
49 28 0.18
52 8 0.05
53 39 0.25
54 9 0.06
55 68 0.44
56 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (52 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAGTTTCTAAGGC
Found at i:40574861 original size:108 final size:110
Alignment explanation
Indices: 40574662--40574862 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
40574652 TTTAAGGATA
* *
40574662 CCATGTAAGACCATGTCAAGGCATGGCAATTGGTCAGGTTTCTAAGGCAAGGATACCATGTAAGG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTCAGGTTTCTAAGGCAAGGATACCATGTAAGA
* * *
40574727 CCATGTTAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCAGGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
40574772 CCATGTAAGACCATGCCAAGGCATGGC-GTTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTCAGGTTTC-TAAGGCAAGGATACCATGTAAG
* *
40574834 ACCAGGTCGAGACATGGCAATGGTAAGTT
65 ACCAGGTCAAGACATGGCAATGATAAGTT
40574863 TTAAAAGGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.57
109 6 0.07
110 26 0.32
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTCAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCAGGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:40575122 original size:16 final size:16
Alignment explanation
Indices: 40575101--40575131 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40575091 ATAATTTTGA
40575101 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
40575117 TTAAGTAAGTTAGTA
1 TTAAGTAAGTAAGTA
40575132 AGTGAAGAAG
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:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:40581214 original size:20 final size:20
Alignment explanation
Indices: 40581189--40581230 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40581179 AGTACGTATG
40581189 ATACCTATGTGGTAGATGGT
1 ATACCTATGTGGTAGATGGT
40581209 ATACCTATGTGGTAGATGGT
1 ATACCTATGTGGTAGATGGT
40581229 AT
1 AT
40581231 TATGTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.36
Consensus pattern (20 bp):
ATACCTATGTGGTAGATGGT
Found at i:40592205 original size:33 final size:33
Alignment explanation
Indices: 40592168--40592235 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
40592158 TAGATGTTTG
*
40592168 AGAGATT-GAAGGAGTGTTTTGAGGAGTGGATCA
1 AGAGATTGGAA-GAGAGTTTTGAGGAGTGGATCA
40592201 AGAGATTGGAAGAGAGTTTTGAGGAGTGGATCA
1 AGAGATTGGAAGAGAGTTTTGAGGAGTGGATCA
40592234 AG
1 AG
40592236 GAAAGGGGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.40, T:0.25
Consensus pattern (33 bp):
AGAGATTGGAAGAGAGTTTTGAGGAGTGGATCA
Found at i:40595925 original size:40 final size:40
Alignment explanation
Indices: 40595874--40596038 Score: 210
Period size: 40 Copynumber: 4.2 Consensus size: 40
40595864 ATACTATTAA
*
40595874 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAA
1 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAG
*
40595914 CCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAG
1 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAG
* *
40595953 CCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAG
1 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAG
* * * * *
40595993 TCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAG
1 CCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAG
40596033 CCCGGA
1 CCCGGA
40596039 CATCATTCGA
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.02
39 32 0.30
40 63 0.58
41 11 0.10
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAG
Found at i:40596022 original size:79 final size:80
Alignment explanation
Indices: 40595874--40596038 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 80
40595864 ATACTATTAA
* * * *
40595874 CCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAAT
1 CCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAA
40595939 GCCTTCGGG-CTTAG
66 GCCTTCGGGACTTAG
* ** * *
40595953 CCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CA
1 CCCGGAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACCA
40596016 AAGCCTTCGGGACTTAG
64 AAGCCTTCGGGACTTAG
40596033 CCCGGA
1 CCCGGA
40596039 CATCATTCGA
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 3 0.04
79 56 0.76
80 15 0.20
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACCAAA
GCCTTCGGGACTTAG
Found at i:40598555 original size:19 final size:19
Alignment explanation
Indices: 40598531--40598578 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
40598521 CAGGTAAAGG
*
40598531 ACACAGGCGTATCCGAAGC
1 ACACAGGCGTATCCCAAGC
* *
40598550 ACACAGACGTGTCCCAAGC
1 ACACAGGCGTATCCCAAGC
*
40598569 ACACAAGCGT
1 ACACAGGCGT
40598579 GCATTGTCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.10
Consensus pattern (19 bp):
ACACAGGCGTATCCCAAGC
Found at i:40605748 original size:42 final size:42
Alignment explanation
Indices: 40605693--40605808 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
40605683 CATTGACTTA
40605693 TGATTTACGTGTAAGACCATGTTTGGGACATCAGCATCG-TATT
1 TGATTT-CGTGTAAGACCATGTTTGGGACAT-AGCATCGATATT
* * * *
40605736 TGATTTCGTGTAAGACCCTGTCTGGGATAATGGCATCGATATT
1 TGATTTCGTGTAAGACCATGTTTGGGA-CATAGCATCGATATT
* * *
40605779 TGATTACATGTAAGACCACGTTTGGGACAT
1 TGATTTCGTGTAAGACCATGTTTGGGACAT
40605809 TTGCGTTGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
42 27 0.44
43 34 0.56
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTTTGGGACATAGCATCGATATT
Found at i:40614346 original size:25 final size:26
Alignment explanation
Indices: 40614318--40614368 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
40614308 CCTTATAATA
40614318 TGAAAATGACCATTTTG-CCCCTAGG
1 TGAAAATGACCATTTTGACCCCTAGG
40614343 TGAAAATGACCATTTTGACCCCTAGG
1 TGAAAATGACCATTTTGACCCCTAGG
40614369 GATATGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (26 bp):
TGAAAATGACCATTTTGACCCCTAGG
Found at i:40614423 original size:21 final size:21
Alignment explanation
Indices: 40614399--40614439 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40614389 CATGATTTGT
40614399 ACATGATATGCCATCATATGC
1 ACATGATATGCCATCATATGC
*
40614420 ACATGATATGCCATGATATG
1 ACATGATATGCCATCATATG
40614440 TTCATATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (21 bp):
ACATGATATGCCATCATATGC
Found at i:40614430 original size:11 final size:10
Alignment explanation
Indices: 40614400--40614439 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
40614390 ATGATTTGTA
40614400 CATGATATGC
1 CATGATATGC
*
40614410 CATCATATGC
1 CATGATATGC
40614420 ACATGATATGC
1 -CATGATATGC
40614431 CATGATATG
1 CATGATATG
40614440 TTCATATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (10 bp):
CATGATATGC
Found at i:40622675 original size:46 final size:46
Alignment explanation
Indices: 40622608--40622876 Score: 293
Period size: 46 Copynumber: 5.8 Consensus size: 46
40622598 TGTAACCCGC
* *
40622608 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
* *
40622654 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG---GAC--GTTCGCAT
* * *
40622704 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
40622747 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* * *
40622797 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
40622840 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40622877 TGCTCAACCA
Statistics
Matches: 187, Mismatches: 18, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
42 4 0.02
43 6 0.03
44 5 0.03
45 4 0.02
46 92 0.49
47 56 0.30
48 4 0.02
49 5 0.03
50 6 0.03
51 5 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:40622729 original size:93 final size:93
Alignment explanation
Indices: 40622616--40622879 Score: 492
Period size: 93 Copynumber: 2.8 Consensus size: 93
40622606 GCCCATAAGT
* * *
40622616 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
40622681 CGAGTTCGAATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
40622709 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40622774 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
40622802 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40622867 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40622880 TCAACCATCC
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 167 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40622730 original size:47 final size:46
Alignment explanation
Indices: 40622662--40622828 Score: 216
Period size: 47 Copynumber: 3.6 Consensus size: 46
40622652 ATCCATAAGT
40622662 GAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCG-ATGCCTAGTTACATCTCAC
* * * *
40622709 GAACTCGGACTCAACTCAACGAGTTCG--GAC-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGATGCCTAGTT-ACAT-C-TCA-C
40622755 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTC-GATGCCTAGTTACATCTCAC
40622802 GAACTCGGACTCAACTCAACGAGTTCG
1 GAACTCGGACTCAACTCAACGAGTTCG
40622829 GACATTCGCA
Statistics
Matches: 103, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 2 0.02
46 27 0.26
47 54 0.52
48 2 0.02
49 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGATGCCTAGTTACATCTCAC
Found at i:40624766 original size:25 final size:25
Alignment explanation
Indices: 40624720--40624770 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
40624710 CCCTTATAAT
* ** *
40624720 GTGAAAATGATCATTTTTCCCCTAG
1 GTGAAAATGACCATGATACCCCTAG
40624745 GTGAAAATGACCATGATACCCCTAG
1 GTGAAAATGACCATGATACCCCTAG
40624770 G
1 G
40624771 GATATGCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (25 bp):
GTGAAAATGACCATGATACCCCTAG
Found at i:40624815 original size:21 final size:21
Alignment explanation
Indices: 40624791--40624852 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
40624781 AATTAAGATG
*
40624791 CATGATTTGTACATGATATGC
1 CATGATATGTACATGATATGC
*
40624812 CATGATATGCACATGATATGC
1 CATGATATGTACATGATATGC
*
40624833 CATGATATGTTCAT-ATATGC
1 CATGATATGTACATGATATGC
40624853 ATGGGTTGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.16
21 31 0.84
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (21 bp):
CATGATATGTACATGATATGC
Found at i:40624826 original size:11 final size:10
Alignment explanation
Indices: 40624802--40624841 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
40624792 ATGATTTGTA
40624802 CATGATATGC
1 CATGATATGC
40624812 CATGATATGC
1 CATGATATGC
40624822 ACATGATATGC
1 -CATGATATGC
40624833 CATGATATG
1 CATGATATG
40624842 TTCATATATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (10 bp):
CATGATATGC
Found at i:40626903 original size:22 final size:22
Alignment explanation
Indices: 40626878--40626934 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
40626868 TTGTATATGT
*
40626878 ATATGTGAACCCTAGGTGATTA
1 ATATGTGAACCCTAGGAGATTA
** * *
40626900 ATATACGAACTCTAGGAGGTTA
1 ATATGTGAACCCTAGGAGATTA
*
40626922 ACATGTGAACCCT
1 ATATGTGAACCCT
40626935 TAATGTGTAC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (22 bp):
ATATGTGAACCCTAGGAGATTA
Found at i:40628305 original size:33 final size:33
Alignment explanation
Indices: 40628261--40628326 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
40628251 TGGAATTCGG
* *
40628261 TTGTATGCAGTTTAGTCAAGGATTTTTTATCCA
1 TTGTATACAGTTTAGTCAAGGAGTTTTTATCCA
40628294 TTGTATACAGTTTAGTCAAGGAGTTTTTATCCA
1 TTGTATACAGTTTAGTCAAGGAGTTTTTATCCA
40628327 GTCTTTGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (33 bp):
TTGTATACAGTTTAGTCAAGGAGTTTTTATCCA
Found at i:40635599 original size:28 final size:28
Alignment explanation
Indices: 40635567--40635650 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
40635557 AACTTCGATC
40635567 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
40635595 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
40635617 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
40635645 ACGTGT
1 ACGTGT
40635651 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:40635627 original size:50 final size:50
Alignment explanation
Indices: 40635565--40635802 Score: 298
Period size: 50 Copynumber: 4.8 Consensus size: 50
40635555 ATAACTTCGA
*
40635565 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGG
* * *
40635615 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGG
* * * * * * * ***
40635664 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCCA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-AGTTAGG
* * *
40635715 TCATGTGTTTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGG
*
40635765 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTAT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAT
40635803 TGGATAATNA
Statistics
Matches: 158, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
49 40 0.25
50 83 0.53
51 35 0.22
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGG
Found at i:40635743 original size:51 final size:51
Alignment explanation
Indices: 40635532--40635797 Score: 252
Period size: 50 Copynumber: 5.3 Consensus size: 51
40635522 TTGGTCGCAT
* *
40635532 GTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGTAGTACTAA
1 GTGCAGGCTACTACGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAA
* * * ** ***
40635583 GTGCAGGCTACTACGTGTATCAGAT-GGTTAGGTCACGTGTGTAGTACTAA
1 GTGCAGGCTACTACGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAA
* * ** * *
40635633 GTGCAGGCTACTACGTGTACCGGATAA-TT-GGTCGCATGTGTAGTACTAA
1 GTGCAGGCTACTACGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAA
* * *
40635682 GTGCAGGCTACTATGCGTACCCGATAACTTCCATCATGTGTTTAGTACTAA
1 GTGCAGGCTACTACGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAA
* * * ** ***
40635733 GTGCAGGCTACTACGTGTATCAGAT-GGTTAGGTCACGTGTGTAGTACTAA
1 GTGCAGGCTACTACGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAA
*
40635783 GTGTAGGCTACTACG
1 GTGCAGGCTACTACG
40635798 TGTATTGGAT
Statistics
Matches: 178, Mismatches: 34, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
49 42 0.24
50 80 0.45
51 56 0.31
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (51 bp):
GTGCAGGCTACTACGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAA
Found at i:40635808 original size:150 final size:150
Alignment explanation
Indices: 40635532--40635810 Score: 504
Period size: 150 Copynumber: 1.9 Consensus size: 150
40635522 TTGGTCGCAT
*
40635532 GTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGTAGTACTAAGTGCAGGCTACTAC
1 GTGCAGGCTACTATGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAAGTGCAGGCTACTAC
40635597 GTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
66 GTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
40635662 GGTCGCATGTGTAGTACTAA
131 GGTCGCATGTGTAGTACTAA
* *
40635682 GTGCAGGCTACTATGCGTACCCGATAACTTCCATCATGTGTTTAGTACTAAGTGCAGGCTACTAC
1 GTGCAGGCTACTATGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAAGTGCAGGCTACTAC
* **
40635747 GTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATTGGATAAT
66 GTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAAT
40635811 NAAAAATTTT
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 123 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (150 bp):
GTGCAGGCTACTATGCGTACCCGATAACTTCCATCACGTGTGTAGTACTAAGTGCAGGCTACTAC
GTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
GGTCGCATGTGTAGTACTAA
Found at i:40635826 original size:101 final size:100
Alignment explanation
Indices: 40635532--40635797 Score: 264
Period size: 101 Copynumber: 2.6 Consensus size: 100
40635522 TTGGTCGCAT
* * * * *
40635532 GTGCAGGCTACTATGCGTACCCGATAACTTCGATCACGTGTGTAGTACTAAGTGCAGGCTACTAC
1 GTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCACATGTGTAGTACTAAGTGCAGGCTACTAC
* * * ** * ** * *
40635597 GTGTATCAGAT-GGTTAGGTCACGTGTGTAGTACTAA
64 GCGTACCCGATAACTAAAATCATGTGTTTAGTACTAA
* * *
40635633 GTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGC
1 GTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGC
***
40635698 GTACCCGATAACTTCCATCATGTGTTTAGTACTAA
66 GTACCCGATAACTAAAATCATGTGTTTAGTACTAA
* ** * *
40635733 GTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACG
1 GTGCAGGCTACTACGTGTACCAGATAATT-GGTCACATGTGTAGTACTAAGTGCAGGCTACTACG
40635798 TGTATTGGAT
Statistics
Matches: 138, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
99 38 0.28
100 45 0.33
101 55 0.40
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (100 bp):
GTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGC
GTACCCGATAACTAAAATCATGTGTTTAGTACTAA
Found at i:40636513 original size:27 final size:27
Alignment explanation
Indices: 40636483--40636637 Score: 161
Period size: 27 Copynumber: 5.7 Consensus size: 27
40636473 TTAGTTTACC
40636483 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
40636510 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
40636537 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** *
40636564 AAATTACCAAAATA-CCCTCATACTGTA
1 AAATTACCAAAATACCCCTGGT-TTGTA
*** **
40636591 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*
40636618 AAATTACCAAAGTACCCCTG
1 AAATTACCAAAATACCCCTG
40636638 ATTTACAGAA
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
26 5 0.05
27 94 0.90
28 5 0.05
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:40636620 original size:81 final size:81
Alignment explanation
Indices: 40636483--40636637 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
40636473 TTAGTTTACC
** * * **
40636483 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATCACCAAA
1 AAATTACCAAAATACCCCTCATCTGTAAAATTACTAAAATACCCTCGACTTATAAAATCACCAAA
40636548 ATACCCCTGGTTTGTA
66 ATACCCCTGGTTTGTA
* * * *
40636564 AAATTACCAAAATA-CCCTCATACTGTAAAATTATTGAAATACCCTCGACTTGTAAAATTACCAA
1 AAATTACCAAAATACCCCTCAT-CTGTAAAATTACTAAAATACCCTCGACTTATAAAATCACCAA
*
40636628 AGTACCCCTG
65 AATACCCCTG
40636638 ATTTACAGAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
80 5 0.08
81 57 0.92
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTCATCTGTAAAATTACTAAAATACCCTCGACTTATAAAATCACCAAA
ATACCCCTGGTTTGTA
Found at i:40636650 original size:81 final size:81
Alignment explanation
Indices: 40636477--40636652 Score: 192
Period size: 81 Copynumber: 2.2 Consensus size: 81
40636467 AATACTTTAG
* ** * * **
40636477 TTTACCAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATC
1 TTTACAAAATTACCAAAATACCCCTCATCTGTAAAATTACTAAAATACCCTCGACTTATAAAATC
*
40636542 ACCAAAATACCCCTGG
66 ACCAAAATACCCCTGA
** * * *
40636558 TTTGTAAAATTACCAAAATA-CCCTCATACTGTAAAATTATTGAAATACCCTCGACTTGTAAAAT
1 TTTACAAAATTACCAAAATACCCCTCAT-CTGTAAAATTACTAAAATACCCTCGACTTATAAAAT
* *
40636622 TACCAAAGTACCCCTGA
65 CACCAAAATACCCCTGA
*
40636639 TTTACAGAATTACC
1 TTTACAAAATTACC
40636653 GTTTTACCCT
Statistics
Matches: 76, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
80 5 0.07
81 71 0.93
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.30
Consensus pattern (81 bp):
TTTACAAAATTACCAAAATACCCCTCATCTGTAAAATTACTAAAATACCCTCGACTTATAAAATC
ACCAAAATACCCCTGA
Found at i:40636687 original size:27 final size:27
Alignment explanation
Indices: 40636563--40636689 Score: 73
Period size: 27 Copynumber: 4.7 Consensus size: 27
40636553 CCTGGTTTGT
* *
40636563 AAAATTACCAAAATACCCTCATACTGT--
1 AAAATTACCGAAATACCCTCA-A-TTTAC
** * * **
40636590 AAAATTATTGAAATACCCTCGACTTGT
1 AAAATTACCGAAATACCCTCAATTTAC
*
40636617 AAAATTACC-AAAGTACCC-CTGATTTAC
1 AAAATTACCGAAA-TACCCTC-AATTTAC
* ***
40636644 AGAATTACCGTTTTACCCTCAATTTAC
1 AAAATTACCGAAATACCCTCAATTTAC
40636671 AAAATTACCGAAATACCCT
1 AAAATTACCGAAATACCCT
40636690 TGTAGGGTAG
Statistics
Matches: 74, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
25 1 0.01
26 5 0.07
27 67 0.91
28 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.29
Consensus pattern (27 bp):
AAAATTACCGAAATACCCTCAATTTAC
Found at i:40636773 original size:6 final size:6
Alignment explanation
Indices: 40636764--40636931 Score: 103
Period size: 6 Copynumber: 27.3 Consensus size: 6
40636754 TTGCATTCAC
*
40636764 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TTACCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * * *
40636814 ATACTG ATTCTG ATTCTG -TTACCTA ATTCTG ATTTTG ATTTTG ATTTTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * * *
40636863 ATTTTG ATTTTG ATTCT- ATCACCTA ATTCTG ATTCTG GTTCTG ATTCTC
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
*
40636912 ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
40636932 AATGTTTCTT
Statistics
Matches: 131, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
5 9 0.07
6 105 0.80
7 11 0.08
8 6 0.05
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:40636814 original size:19 final size:18
Alignment explanation
Indices: 40636767--40636847 Score: 57
Period size: 19 Copynumber: 4.7 Consensus size: 18
40636757 CATTCACATT
40636767 CTGATTCTGATTCTGTTA
1 CTGATTCTGATTCTGTTA
*
40636785 CCTGATACTGATTCTGATT-
1 -CTGATTCTGATTCTG-TTA
* *
40636804 CTG--T-T-A-CCTGATA
1 CTGATTCTGATTCTGTTA
40636817 CTGATTCTGATTCTGTTA
1 CTGATTCTGATTCTGTTA
*
40636835 CCTAATTCTGATT
1 -CTGATTCTGATT
40636848 TTGATTTTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
12 1 0.02
13 6 0.13
14 1 0.02
15 2 0.04
16 1 0.02
17 1 0.02
18 8 0.17
19 25 0.53
20 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (18 bp):
CTGATTCTGATTCTGTTA
Found at i:40636887 original size:49 final size:49
Alignment explanation
Indices: 40636758--40636922 Score: 152
Period size: 49 Copynumber: 3.3 Consensus size: 49
40636748 ATGGGTTTGC
* * * * * *
40636758 ATTCACATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTG
1 ATTCTCATTTTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTG
* ** * * * *
40636807 -TTACCTGATACTGATTCTGATTCTGTTACCTAATTCTGATTTTGATTTTG
1 ATT--CTCATTTTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTG
* * * *
40636857 ATTTTGATTTTGATTTTGATTCTATCACCTAATTCTGATTCTGGTTCTG
1 ATTCTCATTTTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTG
40636906 ATTCTCATTTTGATTCT
1 ATTCTCATTTTGATTCT
40636923 AGTTCTGATA
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
48 2 0.02
49 51 0.54
50 39 0.41
51 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.50
Consensus pattern (49 bp):
ATTCTCATTTTGATTCTGATTCTATCACCTAATTCTGATTCTGATTCTG
Found at i:40636904 original size:25 final size:25
Alignment explanation
Indices: 40636764--40636905 Score: 153
Period size: 25 Copynumber: 5.7 Consensus size: 25
40636754 TTGCATTCAC
40636764 ATTCTGATTCTGATTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
*
40636789 ATACTGATTCTGATTCTGTTACCTG
1 ATTCTGATTCTGATTCTGTTACCTG
* *
40636814 ATACTGATTCTGATTCTGTTACCTA
1 ATTCTGATTCTGATTCTGTTACCTG
* * *
40636839 ATTCTGATTTTGATTTTGATT--TTG
1 ATTCTGATTCTGATTCTG-TTACCTG
* * * * *
40636863 ATTTTGATTTTGATTCTATCACCTA
1 ATTCTGATTCTGATTCTGTTACCTG
*
40636888 ATTCTGATTCTGGTTCTG
1 ATTCTGATTCTGATTCTG
40636906 ATTCTCATTT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
23 1 0.01
24 16 0.16
25 78 0.80
26 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (25 bp):
ATTCTGATTCTGATTCTGTTACCTG
Found at i:40637215 original size:15 final size:15
Alignment explanation
Indices: 40637195--40637230 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
40637185 ATACTGTTTA
40637195 TGTTACAGTTTTGAT
1 TGTTACAGTTTTGAT
40637210 TGTTACAGTTTTGAT
1 TGTTACAGTTTTGAT
*
40637225 TATTAC
1 TGTTAC
40637231 TTTTAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.53
Consensus pattern (15 bp):
TGTTACAGTTTTGAT
Found at i:40649842 original size:31 final size:31
Alignment explanation
Indices: 40649799--40649861 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
40649789 ATATACCTTT
* *
40649799 TTAGCTTTCCTAATTACTAATTTGGCAGACA
1 TTAGATTTCCTAATTACTAATGTGGCAGACA
*
40649830 TTAGATTTCCTAATTACTAATGTGGTAGACA
1 TTAGATTTCCTAATTACTAATGTGGCAGACA
40649861 T
1 T
40649862 ATTTCCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (31 bp):
TTAGATTTCCTAATTACTAATGTGGCAGACA
Found at i:40650939 original size:20 final size:20
Alignment explanation
Indices: 40650914--40650951 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40650904 AAATCATGTG
40650914 TTAAA-CTCAGTATTTTTAAC
1 TTAAACCTCAGT-TTTTTAAC
40650934 TTAAACCTCAGTTTTTTA
1 TTAAACCTCAGTTTTTTA
40650952 GAAACATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (20 bp):
TTAAACCTCAGTTTTTTAAC
Found at i:40658865 original size:64 final size:63
Alignment explanation
Indices: 40658686--40658868 Score: 181
Period size: 64 Copynumber: 2.8 Consensus size: 63
40658676 CATAATTTTG
* * * * * *
40658686 GCTCTCTTGTACACATGGTGAACACTTAGTACCACCCATGTGACCTAGC--CAGTTTATCTCGTA
1 GCTCTCTTGT-CACATTGTGTACACATAGTACCACCCATGCGACCTAGCTACA-TATATCCCGTA
* * * * * *
40658749 GCTCTCTTGTCACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCCGT
1 GCTCTCTTGTCACAT--TGT-GTACACATAGTACCACCCATGCGACCTAGCTACATATATCCCGT
40658814 A
63 A
*
40658815 GCTCTCTTGTCTACATTGTGTACACATAGTATCACCCATGCGACCTAGCTACAT
1 GCTCTCTTGTC-ACATTGTGTACACATAGTACCACCCATGCGACCTAGCTACAT
40658869 CATAATGTCT
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 5 0.05
63 10 0.10
64 30 0.31
65 25 0.26
66 20 0.21
67 6 0.06
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.30
Consensus pattern (63 bp):
GCTCTCTTGTCACATTGTGTACACATAGTACCACCCATGCGACCTAGCTACATATATCCCGTA
Found at i:40660896 original size:25 final size:24
Alignment explanation
Indices: 40660866--40660985 Score: 174
Period size: 23 Copynumber: 5.0 Consensus size: 24
40660856 GGAGGAAGTG
40660866 TAAAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
40660890 GATAAAGGGCTTATGCCCCAGTTAT
1 TA-AAAGGGCTTATGCCCCAGTTAT
40660915 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
40660938 TAAAAGGGCTT-TGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
40660961 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
40660986 ATGATAAAGC
Statistics
Matches: 89, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
23 42 0.47
24 16 0.18
25 31 0.35
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:40661214 original size:31 final size:31
Alignment explanation
Indices: 40661179--40661241 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
40661169 CGTTTACAGT
40661179 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
40661210 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
40661241 A
1 A
40661242 GTGTGAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:40680514 original size:16 final size:18
Alignment explanation
Indices: 40680483--40680519 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40680473 GTTTAGTTCT
40680483 AATAGCTAAAGGAATT-A
1 AATAGCTAAAGGAATTCA
*
40680500 AATAGCT-ATGGAATTCA
1 AATAGCTAAAGGAATTCA
40680517 AAT
1 AAT
40680520 TTTGAGGTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.27
Consensus pattern (18 bp):
AATAGCTAAAGGAATTCA
Found at i:40681079 original size:14 final size:14
Alignment explanation
Indices: 40681060--40681092 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
40681050 CTTGGAATAA
40681060 GAATTAAATTATAT
1 GAATTAAATTATAT
40681074 GAATTAAATTATAT
1 GAATTAAATTATAT
40681088 GAATT
1 GAATT
40681093 TCATTTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (14 bp):
GAATTAAATTATAT
Found at i:40691472 original size:46 final size:46
Alignment explanation
Indices: 40691324--40691488 Score: 206
Period size: 47 Copynumber: 3.5 Consensus size: 46
40691314 AGTGCGAATA
40691324 TTACCTTGATTTGGCTACGGGCCATGCTATAGGTATTCAGAGAGGAG
1 TTACCTTGATTTGGCTACGGGCCATGCTATAGGTATTCAG-GAGGAG
* * * * * **
40691371 TTACCTTGATTTGGTTACGGGTCATGGTATAGGTACTCTGGTATAAG
1 TTACCTTGATTTGGCTACGGGCCATGCTATAGGTATTCAGG-AGGAG
* *
40691418 TTAACTTGATTTGTCTACGGGCCATGCT-TAGGTATTCAGTGAGGAG
1 TTACCTTGATTTGGCTACGGGCCATGCTATAGGTATTCAG-GAGGAG
*
40691464 TTACCTTGATTTGGGTACGGGCCAT
1 TTACCTTGATTTGGCTACGGGCCAT
40691489 CTTGATTTGG
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
46 35 0.36
47 62 0.64
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (46 bp):
TTACCTTGATTTGGCTACGGGCCATGCTATAGGTATTCAGGAGGAG
Found at i:40691494 original size:21 final size:21
Alignment explanation
Indices: 40691468--40691509 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40691458 GAGGAGTTAC
* *
40691468 CTTGATTTGGGTACGGGCCAT
1 CTTGATTTGGCTACGAGCCAT
40691489 CTTGATTTGGCTACGAGCCAT
1 CTTGATTTGGCTACGAGCCAT
40691510 GGTGTAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (21 bp):
CTTGATTTGGCTACGAGCCAT
Found at i:40694621 original size:40 final size:40
Alignment explanation
Indices: 40694577--40694887 Score: 305
Period size: 40 Copynumber: 7.6 Consensus size: 40
40694567 GCTACTTGTT
* *
40694577 CAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
40694617 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
40694657 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
40694696 CAAATGTTCAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATG--------CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
40694744 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
40694784 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * * *
40694823 CAAATGCCTTC-AGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
40694864 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40694888 ACATCATTCG
Statistics
Matches: 227, Mismatches: 23, Indels: 42
0.78 0.08 0.14
Matches are distributed among these distances:
38 1 0.00
39 57 0.25
40 118 0.52
41 15 0.07
47 8 0.04
48 27 0.12
49 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:40694677 original size:79 final size:80
Alignment explanation
Indices: 40694577--40694888 Score: 323
Period size: 79 Copynumber: 3.8 Consensus size: 80
40694567 GCTACTTGTT
* * *
40694577 CAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
40694642 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
40694657 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGCACAAATGTTCAAATTCCTTCGGGAC
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATG--------CCTTCGGGAC
*
40694720 ATAGCCCGG-TTATAGTAACTCGCA
57 TTAGCCCGGATT-TAGTAACTCGCA
* *
40694744 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
40694807 GAATTAGTAACTCGCA
65 GATTTAGTAACTCGCA
* * * * * *
40694823 CAAATGCCTTC-AGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
40694886 GGA
64 GGA
40694889 CATCATTCGA
Statistics
Matches: 194, Mismatches: 20, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
78 4 0.02
79 81 0.42
80 39 0.20
86 2 0.01
87 42 0.22
88 26 0.13
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATTTAGTAACTCGCA
Found at i:40694799 original size:127 final size:127
Alignment explanation
Indices: 40694573--40694828 Score: 512
Period size: 127 Copynumber: 2.0 Consensus size: 127
40694563 TATAGCTACT
40694573 TGTTCAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 TGTTCAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
40694638 CCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAA
66 CCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAA
40694700 TGTTCAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 TGTTCAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
40694765 CCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAA
66 CCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAA
40694827 TG
1 TG
40694829 CCTTCAGATC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 129 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (127 bp):
TGTTCAAATTCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
CCGGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAA
Found at i:40702109 original size:13 final size:13
Alignment explanation
Indices: 40702091--40702118 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40702081 ACAAAATTGG
40702091 AAAGATGATAAAT
1 AAAGATGATAAAT
40702104 AAAGATGATAAAT
1 AAAGATGATAAAT
40702117 AA
1 AA
40702119 TAAAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:40704048 original size:50 final size:49
Alignment explanation
Indices: 40703918--40704161 Score: 301
Period size: 49 Copynumber: 4.9 Consensus size: 49
40703908 TAGCCGAAGC
* ** * *
40703918 TATCTGGTACGCACAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* *
40703967 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * *
40704017 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-T
* * * * * *
40704068 TATCAGGTACGCATAGTAG-CTGCACTTAGTACTACACATGCGACCAAG
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
*
40704116 AATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
40704162 CCACAATAGC
Statistics
Matches: 164, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
48 15 0.09
49 67 0.41
50 67 0.41
51 15 0.09
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:40704121 original size:99 final size:99
Alignment explanation
Indices: 40703932--40704161 Score: 329
Period size: 99 Copynumber: 2.3 Consensus size: 99
40703922 TGGTACGCAC
* * * *
40703932 AGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTAG
1 AGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTAG
* *
40703997 TACTACACACGTGACCTAACCATCTGATACACGT
66 TACTACACACGCGACCTAACAATCTGATACACGT
* *
40704031 AGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCATAGTAG-CTGCACTT
1 AGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCAGGTACACATAGTAGCCTGCACTT
* * *
40704095 AGTACTACACATGCGACC-AAGAATCTGGTACACGT
64 AGTACTACACACGCGACCTAACAATCTGATACACGT
40704130 AGTAGCCTGCACTTAGTACTACACACGTGACC
1 AGTAGCCTGCACTTAGTACTACACACGTGACC
40704162 CCACAATAGC
Statistics
Matches: 117, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
98 1 0.01
99 72 0.62
100 27 0.23
101 17 0.15
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (99 bp):
AGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCAGGTACACATAGTAGCCTGCACTTAG
TACTACACACGCGACCTAACAATCTGATACACGT
Found at i:40704843 original size:30 final size:30
Alignment explanation
Indices: 40704809--40704868 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40704799 CTTTAATACG
40704809 AACTTTGGAAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGAAAAATTACAC-TTTTGCCCCTA
* * *
40704839 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
40704869 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:40706196 original size:26 final size:26
Alignment explanation
Indices: 40706160--40706211 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40706150 TAGGGTTAGC
*
40706160 CACCTGAAAGCTTTCATTGTCATTCA
1 CACCTGAAAGCTTTCACTGTCATTCA
40706186 CACCTGAAAGCTTTCACTGTCATTCA
1 CACCTGAAAGCTTTCACTGTCATTCA
40706212 TCCTTTCTGA
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:0.27, C:0.29, G:0.12, T:0.33
Consensus pattern (26 bp):
CACCTGAAAGCTTTCACTGTCATTCA
Found at i:40707299 original size:3 final size:3
Alignment explanation
Indices: 40707280--40707313 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
40707270 CCATACGGGT
*
40707280 TAA TAAA TAA AAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40707314 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:40707749 original size:64 final size:65
Alignment explanation
Indices: 40707630--40707759 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 65
40707620 CCCCTAGGGT
* *
40707630 TAAGGTTGACCTGAATGCATGTTTGACTGTTATTATTTATTGCATGCCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
*
40707695 TAAGGTTGACCTGAATGCATGTTTGA-TGTTACTATTTACTGCATGTCATGTTATTATTATCTGA
1 TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
40707759 T
1 T
40707760 GCATGGGACT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 36 0.58
65 26 0.42
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (65 bp):
TAAGGTTGACCTGAATGCATGTTTGACTGTTACTATTTACTGCATGCCATGTTATTATTATCTGA
Done.