Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 129 of 208
Found at i:42437584 original size:17 final size:15
Alignment explanation
Indices: 42437550--42437609 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
42437540 ATGAGATCTA
42437550 CACATATATCAATAT
1 CACATATATCAATAT
*
42437565 CACATATATGCAATTTT
1 CACATATAT-CAA-TAT
* *
42437582 CACAAACATCACA-AT
1 CACATATATCA-ATAT
42437597 CACATAATATCAA
1 CACAT-ATATCAA
42437610 CACATCACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 15 0.43
16 10 0.29
17 10 0.29
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (15 bp):
CACATATATCAATAT
Found at i:42439190 original size:50 final size:50
Alignment explanation
Indices: 42439077--42439276 Score: 206
Period size: 50 Copynumber: 3.9 Consensus size: 50
42439067 ACATTAAGGG
* *
42439077 AATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGA
1 AATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCA-C--TGA
* ** *
42439128 GATTATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGTGTTGGCACCGA
1 -A--ATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCACTGA
* *
42439181 AATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACTGA
1 AATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCACTGA
* ** * * *
42439231 TATGAGAACTCCCACGTAAGACCATATCTGGGATATGGCATTGGCA
1 AATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCA
42439277 GTATAGAAAA
Statistics
Matches: 126, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
50 81 0.64
52 2 0.02
53 2 0.02
54 6 0.05
55 1 0.01
56 34 0.27
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGGCACTGA
Found at i:42439275 original size:100 final size:104
Alignment explanation
Indices: 42439090--42439276 Score: 238
Period size: 100 Copynumber: 1.8 Consensus size: 104
42439080 GAGATCCCAT
* * ** *
42439090 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTAGGACATGGCATGGGCATCA-T-AGATTATGAGAACTCCCACGTAAGACCA
* **
42439155 TGTCTAGGACATGGTGTTGGCACCGAAATGAGAGGTCCCCC
64 TATCTAGGACATGGCATTGGCACCGAAATGAGAGGTCCCCC
42439196 GTAAGACCATGTCTAGGACATGGCATGGGCA-C-T-GA-TATGAGAACTCCCACGTAAGACCATA
1 GTAAGACCATGTCTAGGACATGGCATGGGCATCATAGATTATGAGAACTCCCACGTAAGACCATA
* *
42439257 TCTGGGATATGGCATTGGCA
66 TCTAGGACATGGCATTGGCA
42439277 GTATAGAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 38 0.54
101 2 0.03
103 1 0.01
105 1 0.01
106 29 0.41
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (104 bp):
GTAAGACCATGTCTAGGACATGGCATGGGCATCATAGATTATGAGAACTCCCACGTAAGACCATA
TCTAGGACATGGCATTGGCACCGAAATGAGAGGTCCCCC
Found at i:42439310 original size:49 final size:49
Alignment explanation
Indices: 42439140--42439335 Score: 144
Period size: 50 Copynumber: 3.9 Consensus size: 49
42439130 TTATGAGAGG
* * ** * * **
42439140 TCCCATGTAAGACCATGTCTAGGACATGGTGTTGGCACCG-AAATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA--GTATATGAAAAC
* * * * *
42439190 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACTGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAGT-ATATGAAAAC
* *
42439240 TCCCACGTAAGACCATATCTGGGATATGGCATTGGCAGTATA-GAAAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAGTATATGAAAAC
* * * * *
42439288 ATCTCATGTAAGACTATGTCTGGGACATAGCTTTGGCATGTATTATGA
1 -TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-GTA-TATGA
42439336 GACAAGAGAC
Statistics
Matches: 117, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
48 5 0.04
49 33 0.28
50 75 0.64
51 2 0.02
52 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (49 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAGTATATGAAAAC
Found at i:42446890 original size:50 final size:50
Alignment explanation
Indices: 42446787--42446979 Score: 179
Period size: 50 Copynumber: 3.7 Consensus size: 50
42446777 GGGAATGAGA
* * **
42446787 TCCCATGTAAGACCATATCCGGGACATGGAATTGGAATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGG---CACCGAG---ATGAGAGG
42446843 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGG
** ** * * * **
42446893 TCCCCCGTAAGACCATGCCTGGGACATGGCATGGGCACCAATATGAGAAT
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGG
* ** *
42446943 TCCCATGTAAGACCATATTTGGGGTATGACATTGGCA
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCA
42446980 GTACAGAAAA
Statistics
Matches: 115, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
50 77 0.67
53 5 0.04
56 33 0.29
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:42463565 original size:14 final size:14
Alignment explanation
Indices: 42463546--42463573 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42463536 AATATTCAAA
42463546 CCTAATAATATTAG
1 CCTAATAATATTAG
42463560 CCTAATAATATTAG
1 CCTAATAATATTAG
42463574 AAATTAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
CCTAATAATATTAG
Found at i:42464190 original size:3 final size:3
Alignment explanation
Indices: 42464182--42464211 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42464172 CATTTGTTAC
42464182 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42464212 AAAATAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42474898 original size:12 final size:12
Alignment explanation
Indices: 42474881--42474906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42474871 AACATCACCA
42474881 AAATAAATGTCC
1 AAATAAATGTCC
42474893 AAATAAATGTCC
1 AAATAAATGTCC
42474905 AA
1 AA
42474907 TGTCTATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AAATAAATGTCC
Found at i:42476365 original size:18 final size:19
Alignment explanation
Indices: 42476334--42476381 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
42476324 TTAAAACCAT
42476334 AAAAT-TTATTT-TTTT-A
1 AAAATATTATTTATTTTCA
*
42476350 AAAATATT-TTTATTTTCC
1 AAAATATTATTTATTTTCA
42476368 AAAATATTATTTAT
1 AAAATATTATTTAT
42476382 CGATTTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 8 0.30
19 5 0.19
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
AAAATATTATTTATTTTCA
Found at i:42479873 original size:45 final size:45
Alignment explanation
Indices: 42479765--42479873 Score: 134
Period size: 45 Copynumber: 2.4 Consensus size: 45
42479755 TTGGCTTGAA
* *
42479765 GAAAAATGATTAAGACCATAGTTGAAAGACATTATGGCACTATACC
1 GAAAAATGA-TAAGACCATAGTTGAAAGACACTATGGCACCATACC
42479811 GGAGAAAA--ATAAGACCATAGTTGAAAGACACTATGGCACCATACC
1 -GA-AAAATGATAAGACCATAGTTGAAAGACACTATGGCACCATACC
*
42479856 -AAAAATGAGTAAAACCAT
1 GAAAAATGA-TAAGACCAT
42479874 GACTGAAAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
42 4 0.07
43 1 0.02
44 1 0.02
45 42 0.76
46 1 0.02
47 2 0.04
48 4 0.07
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (45 bp):
GAAAAATGATAAGACCATAGTTGAAAGACACTATGGCACCATACC
Found at i:42479912 original size:45 final size:45
Alignment explanation
Indices: 42479862--42480018 Score: 208
Period size: 45 Copynumber: 3.5 Consensus size: 45
42479852 TACCAAAAAT
*
42479862 GAGTAAAACCATGACTGAAAGACGTTATGGCATCACAATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATC
* * * * * *
42479907 AAGTAAGACCATGACCGAAAGTCGTTATGGCTTTACGATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATC
* * *
42479952 GAGTAAGACCATGATTGAAAGACGTTATGGCATCACAATTCGATT
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATC
42479997 GAGTAAGACCAT-AGCTGAAAGA
1 GAGTAAGACCATGA-CTGAAAGA
42480019 TGCTATGACA
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 93 0.99
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (45 bp):
GAGTAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATC
Found at i:42479927 original size:90 final size:90
Alignment explanation
Indices: 42479833--42480008 Score: 194
Period size: 90 Copynumber: 2.0 Consensus size: 90
42479823 GACCATAGTT
42479833 GAAAGACACTATGGCACCATACCA-AAAAT-GAGTAAAACCATGACTGAAAGACGTTATGGCATC
1 GAAAGACACTATGG--CCATACCATAAAATCGAGTAAAACCATGACTGAAAGACGTTATGGCATC
*
42479896 ACAATTCTATCAAGTAAGACCATGACC
64 ACAATTCGATCAAGTAAGACCATGACC
* ** ** * *** * *
42479923 GAAAGTCGTTATGGCTTTACGATTCTATCGAGTAAGACCATGATTGAAAGACGTTATGGCATCAC
1 GAAAGACACTATGGCCATACCATAAAATCGAGTAAAACCATGACTGAAAGACGTTATGGCATCAC
**
42479988 AATTCGATTGAGTAAGACCAT
66 AATTCGATCAAGTAAGACCAT
42480009 AGCTGAAAGA
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
88 5 0.07
89 2 0.03
90 63 0.90
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (90 bp):
GAAAGACACTATGGCCATACCATAAAATCGAGTAAAACCATGACTGAAAGACGTTATGGCATCAC
AATTCGATCAAGTAAGACCATGACC
Found at i:42480049 original size:90 final size:90
Alignment explanation
Indices: 42479869--42480069 Score: 217
Period size: 90 Copynumber: 2.2 Consensus size: 90
42479859 AATGAGTAAA
* * *
42479869 ACCATGACTGAAAGACGTTATGGCATCACAATTCTATCAAGTAAGACCATGACCGAAAGTCGTTA
1 ACCATGATTGAAAGACGTTATGGCATCACAATTCGATCAAGTAAGACCATGACCGAAAGTCGCTA
* * * * ** * *
42479934 TGGCTTTACGATTCTATCGAGTAAG
66 TGACATCACGAATAAAACGAATAAG
** *
42479959 ACCATGATTGAAAGACGTTATGGCATCACAATTCGATTGAGTAAGACCAT-AGCTGAAAGAT-GC
1 ACCATGATTGAAAGACGTTATGGCATCACAATTCGATCAAGTAAGACCATGA-CCGAAAG-TCGC
*
42480022 TATGACATCCCGAATAAAACGAATAAG
64 TATGACATCACGAATAAAACGAATAAG
* *
42480049 ACCATGGTTGAAAGACATTAT
1 ACCATGATTGAAAGACGTTAT
42480070 TGCAACACGA
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
89 1 0.01
90 90 0.98
91 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (90 bp):
ACCATGATTGAAAGACGTTATGGCATCACAATTCGATCAAGTAAGACCATGACCGAAAGTCGCTA
TGACATCACGAATAAAACGAATAAG
Found at i:42482765 original size:25 final size:25
Alignment explanation
Indices: 42482734--42482796 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
42482724 TTTTGAACTT
42482734 TATATTATTCATTTTAAATTGTTCAA
1 TATATTATTCATTTTAAATT-TTCAA
* * *
42482760 TA-ATTATTTATTTTAAGTTTTCCA
1 TATATTATTCATTTTAAATTTTCAA
42482784 TATATTA-TCATTT
1 TATATTATTCATTT
42482797 CATTTCCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 11 0.34
25 19 0.59
26 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (25 bp):
TATATTATTCATTTTAAATTTTCAA
Found at i:42483011 original size:16 final size:16
Alignment explanation
Indices: 42482990--42483031 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
42482980 TAAATTATTT
42482990 TTTATTATATATA-TAC
1 TTTATTAT-TATAGTAC
*
42483006 TTTATTATTTTAGTAC
1 TTTATTATTATAGTAC
42483022 TTTATT-TTAT
1 TTTATTATTAT
42483032 TTTTACTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTATTATTATAGTAC
Found at i:42487420 original size:16 final size:16
Alignment explanation
Indices: 42487399--42487434 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
42487389 TTTTCAAAAA
42487399 AAAATCAAAAAAAATC
1 AAAATCAAAAAAAATC
42487415 AAAATCAAAAAAAATC
1 AAAATCAAAAAAAATC
42487431 AAAA
1 AAAA
42487435 AATATTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAATCAAAAAAAATC
Found at i:42487430 original size:26 final size:27
Alignment explanation
Indices: 42487395--42487445 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
42487385 ATGATTTTCA
42487395 AAAAAAAATCAAAAAA-AATCAAAATC
1 AAAAAAAATCAAAAAATAATCAAAATC
*
42487421 AAAAAAAATCAAAAAATATTCAAAA
1 AAAAAAAATCAAAAAATAATCAAAA
42487446 AAATGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (27 bp):
AAAAAAAATCAAAAAATAATCAAAATC
Found at i:42487443 original size:11 final size:10
Alignment explanation
Indices: 42487395--42487448 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
42487385 ATGATTTTCA
42487395 AAAAAAAATC
1 AAAAAAAATC
42487405 AAAAAAAATC
1 AAAAAAAATC
42487415 ----AAAATC
1 AAAAAAAATC
42487421 AAAAAAAATC
1 AAAAAAAATC
*
42487431 AAAAAATATTC
1 AAAAAA-AATC
42487442 AAAAAAA
1 AAAAAAA
42487449 TGAAAATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
6 6 0.16
10 23 0.61
11 9 0.24
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:42487475 original size:5 final size:5
Alignment explanation
Indices: 42487465--42487508 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
42487455 TGAAAATGAT
*
42487465 GAAAA GAAAA GGAAAA GAAAA GAAAA GGAAAA GAAAA AAAAA GA
1 GAAAA GAAAA -GAAAA GAAAA GAAAA -GAAAA GAAAA GAAAA GA
42487509 GTAAAAACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 25 0.71
6 10 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:42487481 original size:11 final size:10
Alignment explanation
Indices: 42487465--42487508 Score: 61
Period size: 11 Copynumber: 4.2 Consensus size: 10
42487455 TGAAAATGAT
42487465 GAAAAGAAAA
1 GAAAAGAAAA
42487475 GGAAAAGAAAA
1 -GAAAAGAAAA
42487486 GAAAAGGAAAA
1 GAAAA-GAAAA
*
42487497 GAAAAAAAAA
1 GAAAAGAAAA
42487507 GA
1 GA
42487509 GTAAAAACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
10 11 0.35
11 20 0.65
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
GAAAAGAAAA
Found at i:42487486 original size:16 final size:16
Alignment explanation
Indices: 42487465--42487507 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
42487455 TGAAAATGAT
42487465 GAAAAGAAAAGGAAAA
1 GAAAAGAAAAGGAAAA
42487481 GAAAAGAAAAGGAAAA
1 GAAAAGAAAAGGAAAA
*
42487497 GAAAAAAAAAG
1 GAAAAGAAAAG
42487508 AGTAAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
GAAAAGAAAAGGAAAA
Found at i:42488507 original size:48 final size:48
Alignment explanation
Indices: 42488455--42488550 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
42488445 AGGGAGAAGG
* * * **
42488455 GACCAAGGTGAAAACCCGCAAAGGGCGCTTTGAGTCTTAAAAATAAAA
1 GACCAAGGTGAAAACCCGAAAAGGACGCATTGAGTCCAAAAAATAAAA
42488503 GACCAAGGTGAAAACCCGAAAAGGACGCATTGAGTCCAAAAAATAAAA
1 GACCAAGGTGAAAACCCGAAAAGGACGCATTGAGTCCAAAAAATAAAA
42488551 ATATAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (48 bp):
GACCAAGGTGAAAACCCGAAAAGGACGCATTGAGTCCAAAAAATAAAA
Found at i:42489426 original size:24 final size:24
Alignment explanation
Indices: 42489394--42489440 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
42489384 AAAGTATAGT
*
42489394 AGATTAAACCTTGAGGATTACAGC
1 AGATTAAACCTTGAAGATTACAGC
42489418 AGATTAAACCTTGAAGATTACAG
1 AGATTAAACCTTGAAGATTACAG
42489441 TGGGAGGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (24 bp):
AGATTAAACCTTGAAGATTACAGC
Found at i:42490007 original size:44 final size:45
Alignment explanation
Indices: 42489923--42490044 Score: 120
Period size: 44 Copynumber: 2.7 Consensus size: 45
42489913 CAAATTGCAG
* * * * * * *
42489923 CAGATCTTATCTTCCTGAAGTTTCAGTGGAACAGATTGAAGCCAC
1 CAGACCTTATCTCCCTAAAGTTGCAGCGGAACAGACTGAAGACAC
* *
42489968 CAG-CCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAG
1 CAGACCTTATCTCCCTAAAGTTGCAGCGGAACAGACTGAAGACAC
* * * *
42490012 CGGATCTTATTTCCCTAAAGTTGCAGTGGAACA
1 CAGACCTTATCTCCCTAAAGTTGCAGCGGAACA
42490045 TATTAAAGCT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 34 0.55
45 28 0.45
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (45 bp):
CAGACCTTATCTCCCTAAAGTTGCAGCGGAACAGACTGAAGACAC
Found at i:42490042 original size:143 final size:143
Alignment explanation
Indices: 42489773--42490763 Score: 1341
Period size: 143 Copynumber: 7.0 Consensus size: 143
42489763 GATTGAAGTT
* * * *
42489773 ATTACGGCGGGTCTTATCTTACTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
* * * ** * **
42489838 TTGAAGTTGTAGCGGAGCAGACTAAAGACAGCAAATCTTATTTCTCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACAG
42489903 ATTAAAGCTACAA
131 ATTAAAGCTACAA
*** * *
42489916 ATTGCAGCAGATCTTATCTTCCTGAAGTTTCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
* * *
42489981 CTAAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTAAAGTTGCAGTGGAACAT
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACAG
42490046 ATTAAAGCTACAA
131 ATTAAAGCTACAA
*
42490059 ATTATGGCGGATCTTATCTTCCTGAAGTTTCAGT-GAAGCAGATTGAAGCCACCAGCCTTATCTC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAA-CAGATTGAAGCCACCAGCCTTATCTC
* * * *
42490123 CATGAAGTTGCAACGGAGCATACTAAAGACAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACA
65 CCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACA
*
42490188 GATTAAAGCTAAAA
130 GATTAAAGCTACAA
* * * *
42490202 ATTATGAC-GATCTTATCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGTCACCAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
* * * * *
42490266 TTGAAGTTACAGCAGAGCAGAATGAAGACAGCGGATCTTA-TTCCCTTGAAGTTGCAGTGGAATA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCC-TGAAGTTGCAGTGGAACA
*
42490330 GATTGAAGCTACAA
130 GATTAAAGCTACAA
*
42490344 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGT-GAAGCAGATTGAAGCCACTAGCCTTAT-TC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAA-CAGATTGAAGCCACCAGCCTTATCTC
* * *
42490407 CCTGAAGTTGCAGTGGAGCACACTGAAGACAACGGATCTTA-TTCCCTGAAGTTGCAGTGGAACA
65 CCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACA
*
42490471 GATTAAAGCTAGAA
130 GATTAAAGCTACAA
* * * *
42490485 GTTACGGCGAATCTTATCTTCTTGAAGTTGCAGT-GAAGCAGATTGAAGCCACCAGCCTTATCTC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAA-CAGATTGAAGCCACCAGCCTTATCTC
* * * *
42490549 CCTGAAGTTGCAGTGGAGCAGACTAAAGACAGCAGATCTTATTTCCCTGAAGTTGTAGTGGAACA
65 CCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACA
*
42490614 AATTAAAGCTACAA
130 GATTAAAGCTACAA
* * *
42490628 ATTATGGCGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAATCCACCAGCCTTATCTCC
1 ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
* * * * * * *
42490693 CTGAAGTTGCAGCGGAGCAGATTGAAGATAGTC-AATCCTATCTCCCTGAAGTTGCAATGGAGCA
66 CTGAAGTTGCAGCGGAGCAGACTGAAGACAG-CGGATCTTATTTCCCTGAAGTTGCAGTGGAACA
42490757 GATTAAA
130 GATTAAA
42490764 ATGATGGATC
Statistics
Matches: 749, Mismatches: 90, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
141 90 0.12
142 203 0.27
143 453 0.60
144 3 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (143 bp):
ATTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAACAGATTGAAGCCACCAGCCTTATCTCC
CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGGATCTTATTTCCCTGAAGTTGCAGTGGAACAG
ATTAAAGCTACAA
Found at i:42490463 original size:44 final size:45
Alignment explanation
Indices: 42490351--42490802 Score: 209
Period size: 44 Copynumber: 9.8 Consensus size: 45
42490341 CAAATTATGG
* * * *
42490351 CGGATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAG-CCA
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAA
* * *
42490395 C-TAGCCTTAT-TCCCTGAAGTTGCAGTGGAGCACACTGAAGACAA
1 CGGA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAA
* **
42490439 CGGATCTTAT-TCCCTGAAGTTGCAGTGGAACAGATTAAAGCTAGAAGTTACGG
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-----A-CT-GAAG--ACAA
* * * * * * *
42490492 CGAATCTTATCTTCTTGAAGTTGCAGTGAAGCAGATTGAAGCCAC
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAA
* * * *
42490537 CAG-CCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAG
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAA
* * * * * * *
42490581 CAGATCTTATTTCCCTGAAGTTGTAGTGGAACAAATTAAAGCTACAAATTA
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--AC--A--A
* * * ** *
42490632 TGGCGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAATCCAC
1 ---CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAA
* * * * * *
42490680 CAG-CCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGATAGT
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACA-A
* * * * * **
42490725 C-AATCCTATCTCCCTGAAGTTGCAATGGAGCAGA-TTAAAATGA
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAA
* * * *
42490768 TGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGA
1 CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
42490803 TCGTATCAGA
Statistics
Matches: 307, Mismatches: 75, Indels: 52
0.71 0.17 0.12
Matches are distributed among these distances:
43 27 0.09
44 136 0.44
45 64 0.21
47 6 0.02
48 1 0.00
49 3 0.01
50 3 0.01
51 4 0.01
52 1 0.00
53 11 0.04
54 51 0.17
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (45 bp):
CGGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAA
Found at i:42492702 original size:16 final size:16
Alignment explanation
Indices: 42492683--42492724 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
42492673 TAAATTATTT
42492683 TTTATTATATATA-TAC
1 TTTATTAT-TATAGTAC
*
42492699 TTTATTATTTTAGTAC
1 TTTATTATTATAGTAC
42492715 TTTATT-TTAT
1 TTTATTATTAT
42492725 TTTTACTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTATTATTATAGTAC
Found at i:42498292 original size:47 final size:47
Alignment explanation
Indices: 42498227--42498860 Score: 880
Period size: 47 Copynumber: 13.4 Consensus size: 47
42498217 CAGCCAAGAG
*
42498227 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
42498274 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
42498321 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
42498372 A--G--TATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * *
42498415 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATAAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
42498462 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
42498509 AGTGTATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
42498560 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * *
42498607 AGTGTATATGTGTGATAATGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
42498654 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
42498701 AGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
42498748 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTAATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * * *
42498795 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
42498842 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
42498861 TCCCGAAAGG
Statistics
Matches: 537, Mismatches: 38, Indels: 24
0.90 0.06 0.04
Matches are distributed among these distances:
43 40 0.07
45 2 0.00
47 403 0.75
49 3 0.01
51 89 0.17
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:42499035 original size:37 final size:37
Alignment explanation
Indices: 42498979--42499057 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42498969 CCGAGCTCTA
* * *
42498979 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
42499016 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
42499053 AAGAC
1 AAGAC
42499058 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:42502055 original size:20 final size:20
Alignment explanation
Indices: 42502023--42502060 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42502013 ATAAAATTAA
42502023 ATTTTCTAAATAT-ATTTTT
1 ATTTTCTAAATATCATTTTT
42502042 ATTTTCTGAAATATCATTT
1 ATTTTCT-AAATATCATTT
42502061 ATCGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTTCTAAATATCATTTTT
Found at i:42502112 original size:22 final size:23
Alignment explanation
Indices: 42502076--42502118 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
42502066 TTTTTTAAAT
42502076 AAAAAATTAAGCTAACTAAATTTA
1 AAAAAATTAAGCTAA-TAAATTTA
42502100 AAAAAATT-A-CTAATAAATT
1 AAAAAATTAAGCTAATAAATT
42502119 CGATTAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 1 0.05
24 8 0.42
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAATTAAGCTAATAAATTTA
Found at i:42504140 original size:6 final size:6
Alignment explanation
Indices: 42504129--42504206 Score: 66
Period size: 6 Copynumber: 12.2 Consensus size: 6
42504119 ACGTTCCCAC
* *
42504129 TTTCTT TTTCTT TATTCTT TTTGTT TTTGTT TTTCTTT CTTTCTT TTTCTT
1 TTTCTT TTTCTT T-TTCTT TTTCTT TTTCTT TTTC-TT -TTTCTT TTTCTT
* * *
42504180 TATTCCT TTTGTT TTTAATT TTTCTT T
1 T-TTCTT TTTCTT TTT-CTT TTTCTT T
42504207 CTTTCTACCA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
6 36 0.60
7 20 0.33
8 4 0.07
ACGTcount: A:0.05, C:0.13, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:42504148 original size:13 final size:13
Alignment explanation
Indices: 42504130--42504189 Score: 68
Period size: 14 Copynumber: 4.5 Consensus size: 13
42504120 CGTTCCCACT
42504130 TTCTTTTTCTTTA
1 TTCTTTTTCTTTA
*
42504143 TTCTTTTTGTTT-
1 TTCTTTTTCTTTA
* *
42504155 TTGTTTTTCTTTCT
1 TTCTTTTTCTTT-A
42504169 TTCTTTTTCTTTA
1 TTCTTTTTCTTTA
42504182 TTCCTTTT
1 TT-CTTTT
42504190 GTTTTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.26
13 13 0.33
14 16 0.41
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (13 bp):
TTCTTTTTCTTTA
Found at i:42504178 original size:39 final size:40
Alignment explanation
Indices: 42504128--42504212 Score: 145
Period size: 39 Copynumber: 2.1 Consensus size: 40
42504118 CACGTTCCCA
* *
42504128 CTTTCTTTTTCTTTATTCTTTTTGTTTTT-GTTTTTCTTT
1 CTTTCTTTTTCTTTATTCCTTTTGTTTTTAATTTTTCTTT
42504167 CTTTCTTTTTCTTTATTCCTTTTGTTTTTAATTTTTCTTT
1 CTTTCTTTTTCTTTATTCCTTTTGTTTTTAATTTTTCTTT
42504207 CTTTCT
1 CTTTCT
42504213 ACCATTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 28 0.65
40 15 0.35
ACGTcount: A:0.05, C:0.15, G:0.04, T:0.76
Consensus pattern (40 bp):
CTTTCTTTTTCTTTATTCCTTTTGTTTTTAATTTTTCTTT
Found at i:42504221 original size:39 final size:38
Alignment explanation
Indices: 42504138--42504221 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 38
42504128 CTTTCTTTTT
* * **
42504138 CTTTATTCTTTTTGTTTTTGTTTTTCTTTCTTTCTTTTT
1 CTTTATTCCTTTTGTTTTTATTTTTCTTTCTTTC-TTAC
42504177 CTTTATTCCTTTTGTTTTTAATTTTTCTTTCTTTC-TAC
1 CTTTATTCCTTTTGTTTTT-ATTTTTCTTTCTTTCTTAC
42504215 CATTTAT
1 C-TTTAT
42504222 ATTTGTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 2 0.05
39 23 0.59
40 14 0.36
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.73
Consensus pattern (38 bp):
CTTTATTCCTTTTGTTTTTATTTTTCTTTCTTTCTTAC
Found at i:42505022 original size:43 final size:43
Alignment explanation
Indices: 42504923--42505180 Score: 195
Period size: 43 Copynumber: 6.0 Consensus size: 43
42504913 ACGCTACTAT
* * * * *
42504923 AGATCATGACCTTTAGCGGCGC-TTTCTCCACAAACGTCGCCAT
1 AGATCAAGACCTTTAGCGGCACTTTTC-CCACAAACGCCGCTAA
* * * *
42504966 AGGT-TAGAACCTTTAGCGACACTTTTCCCACAAACGCCGCTAT
1 AGATCAAG-ACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAA
* * *** *
42505009 AGGTCAAGGCCTTTAGCGGCA-TTTTTTTACAAACGCCGCTTTA
1 AGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGC-TAA
* * * * *
42505052 A-ATCAGGACCTTTAGCGACGCTTTTTTCGA-AAACGCCGCTAA
1 AGATCAAGACCTTTAGCGGCAC-TTTTCCCACAAACGCCGCTAA
** *
42505094 AGATCAAGACCTTTAGCGGCA-TTTTTTCGCAAACGCCGCTAA
1 AGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAA
* * * *
42505136 AAATCAAGACCTTTAACGGCGCTTTTCCCACAAACGTCGCTAA
1 AGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAA
42505179 AG
1 AG
42505181 GTCTCAAAAA
Statistics
Matches: 169, Mismatches: 37, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
41 5 0.03
42 63 0.37
43 89 0.53
44 12 0.07
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
AGATCAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAA
Found at i:42505064 original size:42 final size:42
Alignment explanation
Indices: 42504974--42505179 Score: 191
Period size: 42 Copynumber: 4.8 Consensus size: 42
42504964 ATAGGTTAGA
* ** * **
42504974 ACCTTTAGCGACACTTTTCCCACAAACGCCGCTATAGGTCAAG
1 ACCTTTAGCGGCA-TTTTTTCACAAACGCCGCTAAAAATCAAG
* * ** *
42505017 GCCTTTAGCGGCATTTTTTTACAAACGCCGCTTTAAATCAGG
1 ACCTTTAGCGGCATTTTTTCACAAACGCCGCTAAAAATCAAG
*
42505059 ACCTTTAGCGACGC-TTTTTTCGA-AAACGCCGCTAAAGATCAAG
1 ACCTTTAGCG--GCATTTTTTC-ACAAACGCCGCTAAAAATCAAG
*
42505102 ACCTTTAGCGGCATTTTTTCGCAAACGCCGCTAAAAATCAAG
1 ACCTTTAGCGGCATTTTTTCACAAACGCCGCTAAAAATCAAG
* * ** *
42505144 ACCTTTAACGGCGCTTTTCCCACAAACGTCGCTAAA
1 ACCTTTAGCGGC-ATTTTTTCACAAACGCCGCTAAA
42505180 GGTCTCAAAA
Statistics
Matches: 134, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.01
42 68 0.51
43 61 0.46
44 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (42 bp):
ACCTTTAGCGGCATTTTTTCACAAACGCCGCTAAAAATCAAG
Found at i:42505076 original size:85 final size:85
Alignment explanation
Indices: 42504974--42505183 Score: 278
Period size: 85 Copynumber: 2.5 Consensus size: 85
42504964 ATAGGTTAGA
* * * *
42504974 ACCTTTAGCGACACTTTTCCCACAAACGCCGCTATAGGTCAAGGCCTTTAGCGGCATTTTTTTAC
1 ACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGGTCAAGACCTTTAGCGGCATTTTTTCAC
** *
42505039 AAACGCCGCTTTAAATCAGG
66 AAACGCCGCTAAAAATCAAG
* * * *
42505059 ACCTTTAGCGACGCTTTTTTCGA-AAACGCCGCTAAAGATCAAGACCTTTAGCGGCATTTTTTCG
1 ACCTTTAGCGACGC-TTTTCCCACAAACGCCGCTAAAGGTCAAGACCTTTAGCGGCATTTTTTCA
42505123 CAAACGCCGCTAAAAATCAAG
65 CAAACGCCGCTAAAAATCAAG
* * *
42505144 ACCTTTAACGGCGCTTTTCCCACAAACGTCGCTAAAGGTC
1 ACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGGTC
42505184 TCAAAAACGC
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
84 6 0.06
85 94 0.89
86 6 0.06
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (85 bp):
ACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGGTCAAGACCTTTAGCGGCATTTTTTCAC
AAACGCCGCTAAAAATCAAG
Found at i:42505790 original size:5 final size:5
Alignment explanation
Indices: 42505780--42505805 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42505770 TGTAATGGCA
42505780 AAAAC AAAAC AAAAC AAAAC AAAAC A
1 AAAAC AAAAC AAAAC AAAAC AAAAC A
42505806 TGCTGACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:42509407 original size:7 final size:7
Alignment explanation
Indices: 42509395--42509535 Score: 50
Period size: 7 Copynumber: 19.7 Consensus size: 7
42509385 ACTAATTAAT
42509395 CTAAACC
1 CTAAACC
42509402 CTAAACC
1 CTAAACC
* *
42509409 CTTATCC
1 CTAAACC
42509416 CTTAAACC
1 C-TAAACC
* *
42509424 GTAAATC
1 CTAAACC
* *
42509431 ATAAAAC
1 CTAAACC
* *
42509438 ATAACCC
1 CTAAACC
42509445 CTAAACC
1 CTAAACC
*
42509452 CTTAACCC
1 C-TAAACC
42509460 CTAAACC
1 CTAAACC
* *
42509467 TTAAA-T
1 CTAAACC
*
42509473 CTCAACC
1 CTAAACC
*
42509480 CTTAAACA
1 C-TAAACC
*
42509488 ATAAACC
1 CTAAACC
*
42509495 ATAAACC
1 CTAAACC
* *
42509502 GTAATCC
1 CTAAACC
*
42509509 TTAAACC
1 CTAAACC
*
42509516 CATAATCC
1 C-TAAACC
*
42509524 ATAAACC
1 CTAAACC
*
42509531 TTAAA
1 CTAAA
42509536 ATAGTAACTC
Statistics
Matches: 97, Mismatches: 32, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
6 3 0.03
7 75 0.77
8 19 0.20
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:42509459 original size:15 final size:14
Alignment explanation
Indices: 42509439--42509470 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
42509429 TCATAAAACA
42509439 TAACCCCTAAACCCT
1 TAACCCCTAAA-CCT
42509454 TAACCCCTAAACCT
1 TAACCCCTAAACCT
42509468 TAA
1 TAA
42509471 ATCTCAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACCCCTAAACCT
Found at i:42509498 original size:64 final size:64
Alignment explanation
Indices: 42509414--42509535 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
42509404 AAACCCTTAT
** * * *
42509414 CCCTTAAACCGTAAATCATAAAACATAACCCCTAAACCCTTAACCCCTAAACCTTAAATCTCAA
1 CCCTTAAACAATAAACCATAAAACATAACCCCTAAACCCATAACCCATAAACCTTAAATCTCAA
* * * * *
42509478 CCCTTAAACAATAAACCATAAACCGTAATCCTTAAACCCATAATCCATAAACCTTAAA
1 CCCTTAAACAATAAACCATAAAACATAACCCCTAAACCCATAACCCATAAACCTTAAA
42509536 ATAGTAACTC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 48 1.00
ACGTcount: A:0.44, C:0.32, G:0.02, T:0.22
Consensus pattern (64 bp):
CCCTTAAACAATAAACCATAAAACATAACCCCTAAACCCATAACCCATAAACCTTAAATCTCAA
Found at i:42510102 original size:15 final size:15
Alignment explanation
Indices: 42510067--42510104 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
42510057 TCCCAACCCT
*
42510067 TAAA-CCATAATGCC
1 TAAATCCATAATCCC
42510081 T-AATCCATAATCCC
1 TAAATCCATAATCCC
42510095 TAAATCCATA
1 TAAATCCATA
42510105 TATAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.42, C:0.29, G:0.03, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:42510353 original size:15 final size:14
Alignment explanation
Indices: 42510325--42510425 Score: 66
Period size: 14 Copynumber: 7.2 Consensus size: 14
42510315 CTAGTTAATC
42510325 TAAACCCTAAACCA
1 TAAACCCTAAACCA
42510339 TAAACCCTAAAACCA
1 TAAACCCT-AAACCA
* * *
42510354 AAAACCCTTAACACG
1 TAAACCCTAAAC-CA
*
42510369 T-AA--CTAAACCT
1 TAAACCCTAAACCA
* *
42510380 TAAACCCT-AGCCTT
1 TAAACCCTAAACC-A
*
42510394 TAAACCATAAACCA
1 TAAACCCTAAACCA
*
42510408 TAACCCCTAAACCCA
1 TAAACCCTAAA-CCA
42510423 TAA
1 TAA
42510426 TTCATATACC
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
11 2 0.03
12 7 0.10
13 3 0.04
14 32 0.48
15 23 0.34
ACGTcount: A:0.47, C:0.34, G:0.02, T:0.18
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:42510787 original size:41 final size:41
Alignment explanation
Indices: 42510728--42510962 Score: 319
Period size: 41 Copynumber: 5.7 Consensus size: 41
42510718 AAGAGAATTC
* *
42510728 GCGGCGCTTTCTCAAAAACGCTGCTAAAGCCCTGAGCATTA
1 GCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * * *
42510769 GAGGTGCTTCCTCAAAAACGCTGCTAAAGCCATTAGCATTA
1 GCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
42510810 GC-GTCGCTTTGTCAAAAATGCCGCTAAAGCCATGAGCATTA
1 GCGGT-GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
42510851 GCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTAAGCATTA
1 GCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
42510892 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* **
42510933 GCGGCGCTTTCTCAAAAACATCGCTAAAGC
1 GCGGTGCTTTCTCAAAAACGCCGCTAAAGC
42510963 ACCCGAAAGC
Statistics
Matches: 173, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 2 0.01
41 169 0.98
42 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:42510836 original size:82 final size:82
Alignment explanation
Indices: 42510728--42510962 Score: 353
Period size: 82 Copynumber: 2.9 Consensus size: 82
42510718 AAGAGAATTC
* * * *
42510728 GCGGCGCTTTCTCAAAAACGCTGCTAAAGCCCTGAGCATTAGAGGTGCTTCCTCAAAAACGCTGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTCTCAAAAACGCCGC
*
42510793 TAAAGCCATTAGCATTA
66 TAAAGCCATAAGCATTA
* * * *
42510810 GCGTCGCTTTGTCAAAAATGCCGCTAAAGCCATGAGCATTAGCGGTGCTTTCTCAAAAACGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTCTCAAAAACGCCGC
*
42510875 TAAAGCCCTAAGCATTA
66 TAAAGCCATAAGCATTA
* **
42510892 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCAAAAACATCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTCTCAAAAACGCCGC
42510957 TAAAGC
66 TAAAGC
42510963 ACCCGAAAGC
Statistics
Matches: 136, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 136 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (82 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTCTCAAAAACGCCGC
TAAAGCCATAAGCATTA
Found at i:42510906 original size:123 final size:123
Alignment explanation
Indices: 42510685--42510950 Score: 349
Period size: 123 Copynumber: 2.2 Consensus size: 123
42510675 ATCCCTAAGA
* * * * * *
42510685 ATTAGCGGCGCTTT-TTAGAAAACGCCGCTAAA--AAAGAGAATTCGCGGCGCTTTCTCAAAAAC
1 ATTAGCGGCGCTTTCTCA-AAAATGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTCTCAAAAAC
* * * * *
42510747 GCTGCTAAAGCCCTGAGCATTAGAGGTGCTTCCTCAAAAACGCTGCTAAAGCCATTAGC
65 GCCGCTAAAGCCCTAAGCATTAGAGGCGCTTCCTCAAAAACGCCGCTAAAGCCATGAGC
* * *
42510806 ATTAGCGTCGCTTTGTCAAAAATGCCGCTAAAGCCATGAGCATTAGCGGTGCTTTCTCAAAAACG
1 ATTAGCGGCGCTTTCTCAAAAATGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTCTCAAAAACG
* * *
42510871 CCGCTAAAGCCCTAAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGC
66 CCGCTAAAGCCCTAAGCATTAGAGGCGCTTCCTCAAAAACGCCGCTAAAGCCATGAGC
42510929 ATTAGCGGCGCTTTCTCAAAAA
1 ATTAGCGGCGCTTTCTCAAAAA
42510951 CATCGCTAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
121 26 0.21
122 2 0.02
123 96 0.77
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (123 bp):
ATTAGCGGCGCTTTCTCAAAAATGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTCTCAAAAACG
CCGCTAAAGCCCTAAGCATTAGAGGCGCTTCCTCAAAAACGCCGCTAAAGCCATGAGC
Found at i:42511092 original size:40 final size:40
Alignment explanation
Indices: 42511031--42511130 Score: 134
Period size: 40 Copynumber: 2.5 Consensus size: 40
42511021 AAACGCAGCA
* * *
42511031 GCTAATGCT-TATTTTTAGCGGCGTTTTTCATAAAACGC-C-
1 GCTAATGCTCGATCTTTAGCGGCGTTTTCCA-AAAA-GCTCT
42511070 GCTAATGCTCGATCTTTAGCGGCGTTTTCCAAAAAGCTCT
1 GCTAATGCTCGATCTTTAGCGGCGTTTTCCAAAAAGCTCT
42511110 GCTAATGCTCGATCTTTAGCG
1 GCTAATGCTCGATCTTTAGCG
42511131 CCATTTTTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
38 2 0.04
39 14 0.25
40 39 0.71
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (40 bp):
GCTAATGCTCGATCTTTAGCGGCGTTTTCCAAAAAGCTCT
Found at i:42511297 original size:31 final size:31
Alignment explanation
Indices: 42511261--42511319 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
42511251 AGGCAACTTG
* **
42511261 GGTAGGTCGTGTGGGGCACATGGGCTGGTTA
1 GGTAGGCCGTGTGGACCACATGGGCTGGTTA
42511292 GGTAGGCCGTGTGGACCACATGGGCTGG
1 GGTAGGCCGTGTGGACCACATGGGCTGG
42511320 CCAATTAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.14, C:0.17, G:0.47, T:0.22
Consensus pattern (31 bp):
GGTAGGCCGTGTGGACCACATGGGCTGGTTA
Found at i:42514807 original size:2 final size:2
Alignment explanation
Indices: 42514800--42514825 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42514790 GCACAACCTA
42514800 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42514826 GGATCCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42527409 original size:10 final size:11
Alignment explanation
Indices: 42527381--42527412 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
42527371 AGTATACTTA
42527381 CTATTTTTAAT
1 CTATTTTTAAT
*
42527392 TTATTTTTAAT
1 CTATTTTTAAT
42527403 CTATTTTTAA
1 CTATTTTTAA
42527413 CTAAATAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (11 bp):
CTATTTTTAAT
Found at i:42527976 original size:32 final size:33
Alignment explanation
Indices: 42527928--42528001 Score: 114
Period size: 32 Copynumber: 2.2 Consensus size: 33
42527918 GGTTTTTAAT
42527928 ATATATATATGCGTGCATGGGTGTTATA-TATA
1 ATATATATATGCGTGCATGGGTGTTATAGTATA
* *
42527960 ATATATATTTGGGTGCATGGGTGTTATATGTATA
1 ATATATATATGCGTGCATGGGTGTTATA-GTATA
42527994 ATATATAT
1 ATATATAT
42528002 GTGTGGGTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 26 0.68
34 12 0.32
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (33 bp):
ATATATATATGCGTGCATGGGTGTTATAGTATA
Found at i:42528087 original size:29 final size:28
Alignment explanation
Indices: 42528025--42528100 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 28
42528015 ATATACACAG
*
42528025 TACATAT-ATATATATGCGTGGTTTTGC
1 TACATATAATATATATGCGTGGTTTTAC
* *
42528052 TACATATAATATATATGTGTAGGTTTTAT
1 TACATATAATATATATGCGT-GGTTTTAC
* *
42528081 TATATATAATATGTATGCGT
1 TACATATAATATATATGCGT
42528101 TATAGGTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 7 0.17
28 11 0.27
29 23 0.56
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.46
Consensus pattern (28 bp):
TACATATAATATATATGCGTGGTTTTAC
Found at i:42531064 original size:53 final size:53
Alignment explanation
Indices: 42530993--42531125 Score: 142
Period size: 53 Copynumber: 2.5 Consensus size: 53
42530983 TCGTGACCTT
** * * *
42530993 TTACAAGATTTTTGGAATCTTGCAGTTTGTCAATTTATGATCGCAACC-TATAC
1 TTACAAGATTTTCAGAATCTTGCAGCTT-ACAATTTAAGATCGCAACCTTATAC
* * * * *
42531046 TTACAAGGTTTTCAGAATCTTGCGGCTTACGATTTAAGATCGCAACCTTTTGC
1 TTACAAGATTTTCAGAATCTTGCAGCTTACAATTTAAGATCGCAACCTTATAC
* *
42531099 TTACAAGATTTTCATAATCTTGTAGCT
1 TTACAAGATTTTCAGAATCTTGCAGCT
42531126 AGCCGATCTA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
52 16 0.25
53 49 0.75
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (53 bp):
TTACAAGATTTTCAGAATCTTGCAGCTTACAATTTAAGATCGCAACCTTATAC
Found at i:42535240 original size:28 final size:28
Alignment explanation
Indices: 42535208--42535278 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
42535198 AATGAGATTG
42535208 GCACTAAGTGTGCGAGTTT-AAT-TGTAAA
1 GCACTAAGTGTGCGAGTTTGAATAT-T-AA
*
42535236 GCACTAAGTGTGTGAGTTTGAATATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
42535264 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
42535279 ACTTGTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:42537231 original size:19 final size:19
Alignment explanation
Indices: 42537207--42537247 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
42537197 CGAATCTAAA
** *
42537207 TCAGAAACTTATACAATTT
1 TCAGAAACAGATAAAATTT
42537226 TCAGAAACAGATAAAATTT
1 TCAGAAACAGATAAAATTT
42537245 TCA
1 TCA
42537248 AACTGCAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (19 bp):
TCAGAAACAGATAAAATTT
Found at i:42546444 original size:31 final size:31
Alignment explanation
Indices: 42546406--42546617 Score: 138
Period size: 31 Copynumber: 6.8 Consensus size: 31
42546396 TAAGGGTAAA
42546406 CTCACGAGGTGATCCCATCACGCCTCACCAT
1 CTCACGAGGTGATCCCATCACGCCTCACCAT
* * * * *
42546437 CTCACGAGGCGATCTCACCATGCCACACCAT
1 CTCACGAGGTGATCCCATCACGCCTCACCAT
* * * * *
42546468 CTCGCTAAGTGATCCCACCACGCCTTACCAT
1 CTCACGAGGTGATCCCATCACGCCTCACCAT
* * * *
42546499 CTCACTAAGTGATCCCATCACACCTCACCAC
1 CTCACGAGGTGATCCCATCACGCCTCACCAT
* * * ** *
42546530 CTCATGAGGTAACCCCA-CTGTGCCTTACCAT
1 CTCACGAGGTGATCCCATC-ACGCCTCACCAT
*** * * * *
42546561 CTCGTTAGGTGATCCCATCACACATTACCAC
1 CTCACGAGGTGATCCCATCACGCCTCACCAT
** *
42546592 CTTGCGAGGTGATCCCATCATGCCTC
1 CTCACGAGGTGATCCCATCACGCCTC
42546618 TATCACACAT
Statistics
Matches: 135, Mismatches: 44, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
30 1 0.01
31 133 0.99
32 1 0.01
ACGTcount: A:0.24, C:0.40, G:0.15, T:0.22
Consensus pattern (31 bp):
CTCACGAGGTGATCCCATCACGCCTCACCAT
Found at i:42546604 original size:93 final size:93
Alignment explanation
Indices: 42546406--42546611 Score: 223
Period size: 93 Copynumber: 2.2 Consensus size: 93
42546396 TAAGGGTAAA
* * * * *
42546406 CTCACGAGGTGATCCCATCACGCCTCACCATCTCACGAGGCGATCTCACCATGCCACACCATCTC
1 CTCACGAGGTGATCCCATCACACCTCACCACCTCACGAGGCAACCCCACCATGCCACACCATCTC
* * *
42546471 GCTAAGTGATCCCACCACGCCTTACCAT
66 GCTAAGTGATCCCACCACACATTACCAC
* * * * ** **
42546499 CTCACTAAGTGATCCCATCACACCTCACCACCTCATGAGGTAACCCCACTGTGCCTTACCATCTC
1 CTCACGAGGTGATCCCATCACACCTCACCACCTCACGAGGCAACCCCACCATGCCACACCATCTC
* * *
42546564 GTTAGGTGATCCCATCACACATTACCAC
66 GCTAAGTGATCCCACCACACATTACCAC
**
42546592 CTTGCGAGGTGATCCCATCA
1 CTCACGAGGTGATCCCATCA
42546612 TGCCTCTATC
Statistics
Matches: 90, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (93 bp):
CTCACGAGGTGATCCCATCACACCTCACCACCTCACGAGGCAACCCCACCATGCCACACCATCTC
GCTAAGTGATCCCACCACACATTACCAC
Found at i:42557986 original size:40 final size:40
Alignment explanation
Indices: 42557903--42558127 Score: 224
Period size: 40 Copynumber: 5.7 Consensus size: 40
42557893 TTGAATGCTG
* * ** * *
42557903 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGCGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** *
42557943 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42557983 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * **
42558023 GT-CGGGTTAAGTCCCGAAGGCATTCGTGTGAGTTGTTAAA
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42558063 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42558102 TCCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
42558128 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
39 37 0.23
40 115 0.71
41 9 0.06
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42558102 original size:39 final size:40
Alignment explanation
Indices: 42557956--42558125 Score: 227
Period size: 40 Copynumber: 4.3 Consensus size: 40
42557946 GGACTAAGAT
* *
42557956 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
*
42557996 CCGAAGGCATTCGTGCGAGTTATTAAAGT-CGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-TCCGGGTTAAGTC
* ** *
42558036 CCGAAGGCATTCGTGTGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
42558076 CCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
42558115 CCGAAGGCATT
1 CCGAAGGCATT
42558126 TGAACGAGGA
Statistics
Matches: 119, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 37 0.31
40 81 0.68
41 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:42566187 original size:29 final size:29
Alignment explanation
Indices: 42566153--42566225 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
42566143 ATGTATTAGT
* *
42566153 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
*
42566182 TTAGGACATATTTAAAACTCCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
42566211 TTAGGACATATTTAA
1 TTAGGACATATTTAA
42566226 TAATATCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.33
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:42574740 original size:16 final size:17
Alignment explanation
Indices: 42574719--42574758 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
42574709 ATATCACCGG
42574719 CACAAAGCCTACTA-GA
1 CACAAAGCCTACTAGGA
42574735 CACAAAGCCTACTAGGA
1 CACAAAGCCTACTAGGA
42574752 -ACAAAGC
1 CACAAAGC
42574759 TCAAATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.45, C:0.30, G:0.15, T:0.10
Consensus pattern (17 bp):
CACAAAGCCTACTAGGA
Found at i:42574794 original size:38 final size:38
Alignment explanation
Indices: 42574735--42574895 Score: 182
Period size: 38 Copynumber: 4.2 Consensus size: 38
42574725 GCCTACTAGA
* * *
42574735 CACAAAGCCT-ACTAGGAACAAAGCTCAAATATCACCGG
1 CACAAAGCCTGA-TAGGCACAAAGCCCGAATATCACCGG
* **
42574773 CACAAAGCCTGATAAGCACAAAGCCCGAATATCACTAG
1 CACAAAGCCTGATAGGCACAAAGCCCGAATATCACCGG
* **
42574811 CACAAAGCCTGCTAGGGTCAAAGCCCGAATATCACCGG
1 CACAAAGCCTGATAGGCACAAAGCCCGAATATCACCGG
* * *
42574849 CACAAAGCTTGCTAGGCACGAAGCCCGAAT-TACACCGG
1 CACAAAGCCTGATAGGCACAAAGCCCGAATAT-CACCGG
42574887 CACAAAGCC
1 CACAAAGCC
42574896 CGAATTAATG
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
37 1 0.01
38 102 0.98
39 1 0.01
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.12
Consensus pattern (38 bp):
CACAAAGCCTGATAGGCACAAAGCCCGAATATCACCGG
Found at i:42574826 original size:76 final size:76
Alignment explanation
Indices: 42574729--42574895 Score: 210
Period size: 76 Copynumber: 2.2 Consensus size: 76
42574719 CACAAAGCCT
*
42574729 ACTAGACACAAAGCCTACTAGGAACAAAGCTCAAATATCACCGGCACAAAGCCTGATAAGCACAA
1 ACTAG-CACAAAGCCTACTAGGAACAAAGCCCAAATATCACCGGCACAAAGCCTGATAAGCACAA
42574794 AGCCCGAA-TATC
65 AGCCCGAATTA-C
* ** * * * * *
42574806 ACTAGCACAAAGCCTGCTAGGGTCAAAGCCCGAATATCACCGGCACAAAGCTTGCTAGGCACGAA
1 ACTAGCACAAAGCCTACTAGGAACAAAGCCCAAATATCACCGGCACAAAGCCTGATAAGCACAAA
42574871 GCCCGAATTAC
66 GCCCGAATTAC
**
42574882 ACCGGCACAAAGCC
1 ACTAGCACAAAGCC
42574896 CGAATTAATG
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
76 71 0.91
77 7 0.09
ACGTcount: A:0.38, C:0.31, G:0.19, T:0.13
Consensus pattern (76 bp):
ACTAGCACAAAGCCTACTAGGAACAAAGCCCAAATATCACCGGCACAAAGCCTGATAAGCACAAA
GCCCGAATTAC
Found at i:42577888 original size:17 final size:16
Alignment explanation
Indices: 42577866--42577898 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
42577856 TTTATAAAGG
42577866 TTATAATATATATTATA
1 TTATAATATAT-TTATA
42577883 TTATAATATATTTATA
1 TTATAATATATTTATA
42577899 ATAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATAATATATTTATA
Found at i:42577905 original size:15 final size:17
Alignment explanation
Indices: 42577867--42577905 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
42577857 TTATAAAGGT
*
42577867 TATAATATATATTATAT
1 TATAATATATATTATAA
42577884 TATAATATAT-TTATAA
1 TATAATATATATTATAA
42577900 TA-AATA
1 TATAATA
42577906 AATAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATATATATTATAA
Found at i:42578356 original size:18 final size:19
Alignment explanation
Indices: 42578327--42578362 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42578317 TATATATAAA
42578327 TATATAATGTATTAATATT
1 TATATAATGTATTAATATT
*
42578346 TATAT-ATGTATTTATAT
1 TATATAATGTATTAATAT
42578363 GAATATGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TATATAATGTATTAATATT
Found at i:42583815 original size:53 final size:54
Alignment explanation
Indices: 42583752--42583859 Score: 166
Period size: 53 Copynumber: 2.0 Consensus size: 54
42583742 TTGAAAACCT
* * *
42583752 TATTCCAAAAAACACCATTGTTCAAG-GAGAGGCTACTATTCAGGGGGAGACTAC
1 TATTCCAAAAAACACCATTGTTCAAGAG-GAAGCTACTACTCAAGGGGAGACTAC
42583806 TATT-CAAAAAACACCATTGTTCAAGAGGAAGCTACTACTCAAGGGGAGACTAC
1 TATTCCAAAAAACACCATTGTTCAAGAGGAAGCTACTACTCAAGGGGAGACTAC
42583859 T
1 T
42583860 GTTAAGAAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
53 45 0.90
54 5 0.10
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (54 bp):
TATTCCAAAAAACACCATTGTTCAAGAGGAAGCTACTACTCAAGGGGAGACTAC
Found at i:42587529 original size:20 final size:20
Alignment explanation
Indices: 42587484--42587543 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 20
42587474 AAAAATTACA
*
42587484 AAAAAATTTCAACATAATTT-T
1 AAAAAA-TTCAAAAT-ATTTAT
*
42587505 CAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
*
42587525 -AAAAATTCCAAA-ATTTAT
1 AAAAAATTCAAAATATTTAT
42587543 A
1 A
42587544 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.18
19 15 0.44
20 8 0.24
21 5 0.15
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:42587545 original size:20 final size:19
Alignment explanation
Indices: 42587506--42587543 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42587496 CATAATTTTC
42587506 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
42587525 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
42587543 A
1 A
42587544 TATTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:42588209 original size:59 final size:59
Alignment explanation
Indices: 42588112--42588264 Score: 166
Period size: 59 Copynumber: 2.6 Consensus size: 59
42588102 CTGAGTTAAA
* * *
42588112 TCACATTTGAGGCCTGAA-TTTTTTACTAGTCCAAGTTAGGCTCTAAACTTGACAATTATT-
1 TCACA-TTGAGGCTTGAACTTTTTT--TAGTCCAAGTTAGGCCCTAAACTTGACAATTGTTC
* * *
42588172 TCCACATTGAGGCTTGAACTTTTTTTAGTCCAGGTTAGGCCCTGAACTTGGCAATTGTTC
1 T-CACATTGAGGCTTGAACTTTTTTTAGTCCAAGTTAGGCCCTAAACTTGACAATTGTTC
* * * *
42588232 TTACATTAAGGTTTGAACTTTTTTTTGTCCAAG
1 TCACATTGAGGCTTGAACTTTTTTTAGTCCAAG
42588265 ATATTCCTTG
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
59 56 0.71
60 13 0.16
61 10 0.13
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (59 bp):
TCACATTGAGGCTTGAACTTTTTTTAGTCCAAGTTAGGCCCTAAACTTGACAATTGTTC
Found at i:42589529 original size:19 final size:19
Alignment explanation
Indices: 42589492--42589555 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
42589482 CAAAATAATC
42589492 AAAATAATTTTCAAAAATTT
1 AAAATAATTTT-AAAAATTT
*
42589512 AAAATAATTTTTAAAATTT
1 AAAATAATTTTAAAAATTT
42589531 AAAAT-ATTTATAAAAATTCT
1 AAAATAATTT-TAAAAATT-T
42589551 AAAAT
1 AAAAT
42589556 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.10
19 19 0.47
20 17 0.43
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTT
Found at i:42589544 original size:18 final size:19
Alignment explanation
Indices: 42589504--42589561 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
42589494 AATAATTTTC
42589504 AAAAATTTAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
42589523 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
42589542 AAAAATTCTAAAATTTTTAT
1 AAAAATT-TAAAATATTTAT
42589562 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.12
19 19 0.56
20 11 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:42595162 original size:113 final size:113
Alignment explanation
Indices: 42594980--42595214 Score: 436
Period size: 113 Copynumber: 2.1 Consensus size: 113
42594970 AAAAAAAACC
*
42594980 TAATT-AATTAAAATAAGAGGGAAATTCGGCCAAGGCATTTTTAATGGGCTGCTTGGGCCGAATT
1 TAATTAAAATAAAATAAGAGGGAAATTCGGCCAAGGCATTTTTAATGGGCTGCTTGGGCCGAATT
*
42595044 TTGACAAATAAAATTCTTAAAGTCTAAAAATTAAACTAGATATTCAAA
66 CTGACAAATAAAATTCTTAAAGTCTAAAAATTAAACTAGATATTCAAA
*
42595092 TAATTAAAATAAAATAAGAGGGAAATTTGGCCAAGGCATTTTTAATGGGCTGCTTGGGCCGAATT
1 TAATTAAAATAAAATAAGAGGGAAATTCGGCCAAGGCATTTTTAATGGGCTGCTTGGGCCGAATT
42595157 CTGACAAATAAAATTCTTAAAGTCTAAAAATTAAACTAGATATTCAAA
66 CTGACAAATAAAATTCTTAAAGTCTAAAAATTAAACTAGATATTCAAA
42595205 TAATTAAAAT
1 TAATTAAAAT
42595215 TATTACAAAT
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
112 5 0.04
113 114 0.96
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (113 bp):
TAATTAAAATAAAATAAGAGGGAAATTCGGCCAAGGCATTTTTAATGGGCTGCTTGGGCCGAATT
CTGACAAATAAAATTCTTAAAGTCTAAAAATTAAACTAGATATTCAAA
Found at i:42605435 original size:24 final size:24
Alignment explanation
Indices: 42605403--42605450 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42605393 TTTCCAAAAG
42605403 TAAATTTCACAATATTGTTTATAT
1 TAAATTTCACAATATTGTTTATAT
42605427 TAAATTTCACAATATTGTTTATAT
1 TAAATTTCACAATATTGTTTATAT
42605451 GTGACTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (24 bp):
TAAATTTCACAATATTGTTTATAT
Found at i:42607332 original size:18 final size:18
Alignment explanation
Indices: 42607289--42607332 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
42607279 AGTGAAATTT
* *
42607289 ATATAAAAATCCCTGAAGG
1 ATAT-AAAATCCCAGAACG
*
42607308 ATTTAAAATCCCAGAACG
1 ATATAAAATCCCAGAACG
42607326 ATATAAA
1 ATATAAA
42607333 GTTTCTTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (18 bp):
ATATAAAATCCCAGAACG
Found at i:42612315 original size:21 final size:22
Alignment explanation
Indices: 42612291--42612337 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
42612281 AGGGTGAAAA
42612291 GAAA-GCTAGGATGTGATAGGT
1 GAAAGGCTAGGATGTGATAGGT
* * *
42612312 GAAAGGTTAGGATTTGATGGGT
1 GAAAGGCTAGGATGTGATAGGT
42612334 GAAA
1 GAAA
42612338 CTTTTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.34, C:0.02, G:0.38, T:0.26
Consensus pattern (22 bp):
GAAAGGCTAGGATGTGATAGGT
Found at i:42619461 original size:12 final size:12
Alignment explanation
Indices: 42619446--42619475 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42619436 AAGATGAAAG
*
42619446 TTGATTTATGAC
1 TTGATTTAAGAC
42619458 TTGATTTAAGAC
1 TTGATTTAAGAC
42619470 TTGATT
1 TTGATT
42619476 AATAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.50
Consensus pattern (12 bp):
TTGATTTAAGAC
Found at i:42621468 original size:50 final size:50
Alignment explanation
Indices: 42621294--42621483 Score: 229
Period size: 51 Copynumber: 3.8 Consensus size: 50
42621284 CTATAAACAT
* * * *
42621294 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAGAT-TTGGTCAC
* * * *
42621345 ATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGTTTTGGTCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAAAGATTTGGTCAC
* *
42621396 GTGTGTAGTACTATGTGCAGGCTACTACGTGAACCGAAA-AGTTTGATCAC
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAGA-TTTGGTCAC
* * *
42621446 GTGTGTAGTACTATGTGAAGGCTACTACATGTATCGAA
1 GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
42621484 TGATAATAAT
Statistics
Matches: 119, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
50 45 0.38
51 70 0.59
52 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAGATTTGGTCAC
Found at i:42622744 original size:23 final size:23
Alignment explanation
Indices: 42622714--42622764 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
42622704 ATATCTACTA
42622714 TACCATTTTATATCATCCAACAT
1 TACCATTTTATATCATCCAACAT
42622737 TACCATTTTATATCATCCAACAT
1 TACCATTTTATATCATCCAACAT
42622760 T-CCAT
1 TACCAT
42622765 ATAGATGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (23 bp):
TACCATTTTATATCATCCAACAT
Found at i:42633078 original size:17 final size:17
Alignment explanation
Indices: 42633058--42633111 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
42633048 AAGAGAGTTT
*
42633058 AAGAGACAAGAAAGAGA
1 AAGAGAAAAGAAAGAGA
42633075 AAGAGAAAAGAAAG-GA
1 AAGAGAAAAGAAAGAGA
*
42633091 ATAGGAAAAAAGAAAGAGA
1 A-A-GAGAAAAGAAAGAGA
42633110 AA
1 AA
42633112 AAAGGTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 3 0.09
17 14 0.44
18 12 0.38
19 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.28, T:0.02
Consensus pattern (17 bp):
AAGAGAAAAGAAAGAGA
Found at i:42638137 original size:14 final size:15
Alignment explanation
Indices: 42638118--42638146 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42638108 GACCCTTAAT
42638118 CCCTAAAT-CCTAAC
1 CCCTAAATCCCTAAC
42638132 CCCTAAATCCCTAAC
1 CCCTAAATCCCTAAC
42638147 TCTTAACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCCCTAAC
Found at i:42638140 original size:22 final size:22
Alignment explanation
Indices: 42638110--42638155 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42638100 CCTAACCCGA
*
42638110 CCCTTAATCCCTAAATCCTAAC
1 CCCTAAATCCCTAAATCCTAAC
* *
42638132 CCCTAAATCCCTAACTCTTAAC
1 CCCTAAATCCCTAAATCCTAAC
42638154 CC
1 CC
42638156 TTAACTACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.43, G:0.00, T:0.26
Consensus pattern (22 bp):
CCCTAAATCCCTAAATCCTAAC
Found at i:42638191 original size:21 final size:21
Alignment explanation
Indices: 42638135--42638196 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
42638125 TCCTAACCCC
* *
42638135 TAAATCCCTAACTCTTAACCCT
1 TAAA-CCCTAACCCTTAAACCT
*
42638157 T-AACTACTAA-CCTTAAACCT
1 TAAAC-CCTAACCCTTAAACCT
42638177 TAAACCCTAACCCTTAAACC
1 TAAACCCTAACCCTTAAACC
42638197 ATAATCCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 14 0.42
21 18 0.55
22 1 0.03
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACCCTAACCCTTAAACCT
Found at i:42638297 original size:21 final size:18
Alignment explanation
Indices: 42638255--42638311 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 18
42638245 CAAAACACGC
*
42638255 AAAAAACTGAACTGGATA
1 AAAAAACTGAACCGGATA
42638273 AAAAAACTGAACCGAGCACTA
1 AAAAAACTGAACCG-G-A-TA
*
42638294 AAAATACTGAACCAGGAT
1 AAAAAACTGAACC-GGAT
42638312 GGGATAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 13 0.39
19 2 0.06
20 2 0.06
21 15 0.45
22 1 0.03
ACGTcount: A:0.53, C:0.18, G:0.16, T:0.14
Consensus pattern (18 bp):
AAAAAACTGAACCGGATA
Found at i:42638472 original size:7 final size:7
Alignment explanation
Indices: 42638460--42638503 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
42638450 ACTAGTTAAT
42638460 CTAAACC
1 CTAAACC
42638467 CTAAACC
1 CTAAACC
*
42638474 ATAAA-C
1 CTAAACC
*
42638480 TTAAACC
1 CTAAACC
42638487 CTAAACC
1 CTAAACC
42638494 CATAAACC
1 C-TAAACC
42638502 CT
1 CT
42638504 TAACACATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 5 0.16
7 20 0.62
8 7 0.22
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:42638486 original size:20 final size:21
Alignment explanation
Indices: 42638461--42638500 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
42638451 CTAGTTAATC
42638461 TAAACCCTAAA-CCATAAACT
1 TAAACCCTAAACCCATAAACT
42638481 TAAACCCTAAACCCATAAAC
1 TAAACCCTAAACCCATAAAC
42638501 CCTTAACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (21 bp):
TAAACCCTAAACCCATAAACT
Found at i:42638501 original size:15 final size:15
Alignment explanation
Indices: 42638460--42638513 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 15
42638450 ACTAGTTAAT
42638460 CTAAACCC-TAAACC
1 CTAAACCCATAAACC
* *
42638474 ATAAA--CTTAAACC
1 CTAAACCCATAAACC
42638487 CTAAACCCATAAACC
1 CTAAACCCATAAACC
* *
42638502 CTTAACACATAA
1 CTAAACCCATAA
42638514 CCTTTAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.03
13 10 0.31
14 4 0.12
15 17 0.53
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
CTAAACCCATAAACC
Found at i:42638557 original size:21 final size:21
Alignment explanation
Indices: 42638509--42638557 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42638499 ACCCTTAACA
**
42638509 CATAACCTTTAAACCTTAAAC
1 CATAACCTTTAAACAATAAAC
**
42638530 CCCAACCTTTAAACAATAAAC
1 CATAACCTTTAAACAATAAAC
42638551 CATAACC
1 CATAACC
42638558 CCTAAACCTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (21 bp):
CATAACCTTTAAACAATAAAC
Found at i:42639109 original size:113 final size:114
Alignment explanation
Indices: 42638821--42639735 Score: 1130
Period size: 114 Copynumber: 8.1 Consensus size: 114
42638811 CTGAGCATTA
* * * **
42638821 GCGGCACTTTCTCAAAAATGCCGCTAAAG--C--AGC-TTAGCGGTGCTTTATTAAAAAATACCG
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAAAACGCCG
* * *
42638881 CTAAATCCCTAAAAGCTCAGAAAACGGCGTCGTTAGGCTTAGGTTTTTTT
65 CTAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
* * * * * * * * *
42638931 ACGGCACTTTCCCAAAAATGCTGCTAATGCTCTAAGCATTAGCGGCGCTTTATTAAAAATGCCGC
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* * **
42638996 TAAATCCCCAAAAGCTCAAAAAACGACATCACTGGGCTTAGG-TTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
** ** * *
42639044 GCGGCGCTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCAACGCTTTCCTAAAAACACCGC
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* *
42639109 TAAATCCCCAAAACCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
* * * *
42639158 GCAGCACTTTC-AAAAAATGCCGCTAATGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* * *
42639222 TAAATCCCTAAAAGCTCAGAAAACAGCGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
* ** * *
42639271 ACGGCGCTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGC
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
** * * *
42639336 TAAATCCCTGAAAGCTCAGAAAACGGCACCGTTGGGCATAGTTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
* * * * * *
42639385 GCTGTGCTTTCCCAAAAACGCCGCTAAAGCCTTGAGCATTAGTGTG-GCTTTCTTAAAAACGCCG
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCG-GCGCTTTCTTAAAAACGCCG
*
42639449 CTAAATCCCCAAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTT
65 CTAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
* * *
42639499 GCAGCGCTTTTTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGTCGC
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
* * * *
42639564 TAAATCCTCAAAAGCTCAGAAAATGGCATCTTTGGGCTTAGTTTTTTTT
66 TAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
* * *
42639613 GCGGCGCTTTCTCAAAAATGCCGCTAAAACCCTGAGCATTAGCGGCGCTTCCTTAAAAAACGCTG
1 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAAAACGCCG
* * *
42639678 CTAAATCCCCAAAAGCT-TGAAAAACGGCGTCGTTGGACTTAGG-TTTTTT
65 CTAAATCCCCAAAAGCTCAG-AAAACGGCATCGTTGGGCTTAGGTTTTTTT
42639727 GCGGCGCTT
1 GCGGCGCTT
42639736 CCTGGAAAAC
Statistics
Matches: 693, Mismatches: 101, Indels: 18
0.85 0.12 0.02
Matches are distributed among these distances:
110 25 0.04
112 1 0.00
113 192 0.28
114 417 0.60
115 58 0.08
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (114 bp):
GCGGCGCTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC
TAAATCCCCAAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTT
Found at i:42655364 original size:32 final size:34
Alignment explanation
Indices: 42655303--42655368 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
42655293 TAAAAAAAAA
42655303 GAGAAAAGAAAGAAAAAAAGGAGAGGCCAAGGTG
1 GAGAAAAGAAAGAAAAAAAGGAGAGGCCAAGGTG
* *
42655337 GAGAAAATAAA-AAAAAAA-GAGATGCCAAGGTG
1 GAGAAAAGAAAGAAAAAAAGGAGAGGCCAAGGTG
42655369 AAAACCCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.43
33 7 0.23
34 10 0.33
ACGTcount: A:0.58, C:0.06, G:0.30, T:0.06
Consensus pattern (34 bp):
GAGAAAAGAAAGAAAAAAAGGAGAGGCCAAGGTG
Found at i:42656565 original size:44 final size:44
Alignment explanation
Indices: 42656404--42656894 Score: 260
Period size: 44 Copynumber: 10.9 Consensus size: 44
42656394 GACCATATCA
* * * *** *
42656404 AACCTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTAAAAATAAATC
1 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AAAGCCAA-G
* * *
42656450 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGACCGCCTACA-
1 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT-AA-A--GCC-A-AG
* *
42656499 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAAG
1 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAAG
* * * ** *
42656543 AACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAA-ATAACA
1 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAA-G
* * * * * **
42656587 AACCTTAACTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGCTACT
1 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAAG
* * * * *
42656631 AATCC-TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATG
1 AA-CCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAAG
* * * * *
42656675 AATCATT-TAC-CTCTGAAGTTGCAGTAG-GTCGGATTAAATCTACCATGAC
1 AA-CCTTAT-CTCCCTGAAGTTGCAGTAGAG-CAGATTAAA---GCCA--AG
* * * * *
42656724 AAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGATCAAAGCCACG
1 AA-CCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAAG
* * * * *
42656769 AACCTTATCTCTCTGAAGTTGTAGTAGAGCAGGTTAAAG-TAACA
1 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAA-G
* * ** **
42656813 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACT
1 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAAG
* *
42656857 AATCC-TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAA
1 AA-CCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAA
42656895 ACGATGAATC
Statistics
Matches: 351, Mismatches: 71, Indels: 48
0.75 0.15 0.10
Matches are distributed among these distances:
43 5 0.01
44 226 0.64
45 15 0.04
46 33 0.09
47 8 0.02
48 2 0.01
49 37 0.11
50 23 0.07
51 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCAAG
Found at i:42656693 original size:132 final size:137
Alignment explanation
Indices: 42656404--42656891 Score: 384
Period size: 132 Copynumber: 3.6 Consensus size: 137
42656394 GACCATATCA
* * * *
42656404 AACCTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTAAAAATAAATCAATCTTATCTCCCTGAAGT
1 AACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAAATAAA-CAACCTTAACTCCCTGAAGT
* *
42656469 TGTAGTGGAGCAGATTGAAGACCGCCTACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC
65 TGCAGTGGAGCAGATTGAAGA-CGCCTACAAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATC
*
42656534 AAAGCCAAG
129 AAAACCAAG
42656543 AACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTT-AAAAT-AACAAACCTTAACTCCCTGAAGT
1 AACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAAATAAAC-AACCTTAACTCCCTGAAGT
* * * * *
42656606 TGCAGTGGAGCAGGTTG-A-A-G-CTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTA
65 TGCAGTGGAGCAGATTGAAGACGCCTACAAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATCA
* *
42656667 AAACGATG
130 AAACCAAG
* * ** * *
42656675 AATCATT-TAC-CTCTGAAGTTGCAGTAG-GTCGGATTAAATCTACCATGACAAGTCTTATCTCC
1 AA-CCTTAT-CTCTCTGAAGTTGCAGTAGAGTAGG-TTAAAAATA--A--ACAA-CCTTAACTCC
* * * * *
42656737 CTGAAGTTGCAATGGAGCAGA-TCAA-A-GCC-ACGAA-CCTTATCTCTCTGAAGTTGTAGTAGA
58 CTGAAGTTGCAGTGGAGCAGATTGAAGACGCCTACAAATCC-TATCTCCCTGAAGTTGCAGTAGA
* * *
42656797 GCAGGTTAAAGTAAC-A-
122 GCAGATCAAA--ACCAAG
* * * * * * *
42656813 AACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTT-GAAGT-TACTAATCC-TATCTCCTTGAAG
1 AACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAAATAAAC-AA-CCTTAACTCCCTGAAG
42656875 TTGCAGTGGAGCAGATT
64 TTGCAGTGGAGCAGATT
42656892 AAAACGATGA
Statistics
Matches: 284, Mismatches: 44, Indels: 48
0.76 0.12 0.13
Matches are distributed among these distances:
131 4 0.01
132 91 0.32
133 12 0.04
135 1 0.00
136 3 0.01
137 45 0.16
138 90 0.32
139 37 0.13
140 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (137 bp):
AACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAAATAAACAACCTTAACTCCCTGAAGTT
GCAGTGGAGCAGATTGAAGACGCCTACAAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATCAA
AACCAAG
Found at i:42656757 original size:226 final size:226
Alignment explanation
Indices: 42656496--42656978 Score: 822
Period size: 226 Copynumber: 2.1 Consensus size: 226
42656486 AAGACCGCCT
* *
42656496 ACAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAAGAACCTTATCTCTCTGAAG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGCCAAGAACCTTATCTCTCTGAAG
* *
42656561 TTGCAGTAGAGTAGGTTAAAATAACAAACCTTAACTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG
66 TTGCAGTAGAGCAGGTTAAAATAACAAACCTTAACTCCCTGAAGTTGCAGTAGAGCAGGTTGAAG
* *
42656626 CTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGAATCATTTACCTCTGA
131 CTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCATATACCTCTGA
*
42656691 AGTTGCAGTAGGTCGGATTAAATCTACCATG
196 AGTTGCAGTAGGTCAGATTAAATCTACCATG
* *
42656722 ACAAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGATCAAAGCCACGAACCTTATCTCTCTGAAG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGCCAAGAACCTTATCTCTCTGAAG
* * *
42656787 TTGTAGTAGAGCAGGTTAAAGTAACAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAG
66 TTGCAGTAGAGCAGGTTAAAATAACAAACCTTAACTCCCTGAAGTTGCAGTAGAGCAGGTTGAAG
* * *
42656852 TTACTAATCCTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCCTATACCTCTGA
131 CTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCATATACCTCTGA
*
42656917 AGTTGTAGTAGGTCAGATTAAATCTACCATG
196 AGTTGCAGTAGGTCAGATTAAATCTACCATG
42656948 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGA
42656979 ACATACTAAA
Statistics
Matches: 240, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
226 240 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (226 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAAGCCAAGAACCTTATCTCTCTGAAG
TTGCAGTAGAGCAGGTTAAAATAACAAACCTTAACTCCCTGAAGTTGCAGTAGAGCAGGTTGAAG
CTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCATATACCTCTGA
AGTTGCAGTAGGTCAGATTAAATCTACCATG
Found at i:42656905 original size:44 final size:44
Alignment explanation
Indices: 42656409--42656978 Score: 246
Period size: 44 Copynumber: 12.5 Consensus size: 44
42656399 TATCAAACCT
* * ** * *
42656409 TATCTCCCTGAAGTTGCAGTGGAGTAGGTTAAAAATAAATCAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAA-CGATGAATCC
* * ** *
42656455 TATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGACCGCCTACAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AACG---ATGAATCC
* * * * *
42656504 TATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAGCCAAGAA-CC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCC
* * * * * ** *
42656547 TTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAA-TAACAAACC
1 -TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCC
* * * * *
42656591 TTAACTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGCTACT-AATCC
1 -TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGA-TGAATCC
*
42656636 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGAAT-C
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCC
* * * * *
42656679 -ATTTACCTCTGAAGTTGCAGTAGG-TCGGATTAAATCTACCATGACAAGTCT
1 TATCT-CC-CTGAAGTTGCAGT-GGAGCAGATTAAA---ACGATG--AA-TCC
* * * * *
42656730 TATCTCCCTGAAGTTGCAATGGAGCAGATCAAAGCCACGAA-CC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCC
* * * * ** *
42656773 TTATCTCTCTGAAGTTGTAGTAGAGCAGGTT-AAA-GTAACAAACC
1 -TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACG-ATGAATCC
* * * ***
42656817 TTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACT-AATCC
1 -TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGA-TGAATCC
*
42656862 TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCC
* * * * *
42656906 TATAC-CTCTGAAGTTGTAGTAGG-TCAGATTAAATCTACCATGACAAGTCT
1 TAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTAAA---ACGATG--AA-TCC
42656956 TATCTCCCTGAAGTTGCAGTGGA
1 TATCTCCCTGAAGTTGCAGTGGA
42656979 ACATACTAAA
Statistics
Matches: 405, Mismatches: 81, Indels: 72
0.73 0.15 0.13
Matches are distributed among these distances:
42 3 0.01
43 16 0.04
44 233 0.58
45 20 0.05
46 29 0.07
47 17 0.04
48 2 0.00
49 42 0.10
50 38 0.09
51 2 0.00
52 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACGATGAATCC
Found at i:42657578 original size:22 final size:19
Alignment explanation
Indices: 42657529--42657569 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
42657519 TCAATGTAAT
*
42657529 AAAAAA-ATCGAATACAAA
1 AAAAAAGATTGAATACAAA
42657547 AAAAAAGATTGAATACAAA
1 AAAAAAGATTGAATACAAA
42657566 AAAA
1 AAAA
42657570 TCAAAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAAAGATTGAATACAAA
Found at i:42658518 original size:53 final size:55
Alignment explanation
Indices: 42658455--42658572 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 55
42658445 TATCATTCTC
* * * *
42658455 TTACTTTTAAAATATTTGAATTTAATATTAGGTAT-TATTTTATCTATTT-TTTT
1 TTACTCTTAAAATATTTAAACTTAACATTAGGTATATATTTTATCTATTTCTTTT
*
42658508 TTACTCTTAAAATATTTAAACTTAACATTATGTATACATATTTTATCTATTTCGTTTT
1 TTACTCTTAAAATATTTAAACTTAACATTAGGTAT--ATATTTTATCTATTTC-TTTT
42658566 TTA-TCTT
1 TTACTCTT
42658573 CTGTTATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
53 30 0.55
56 14 0.25
57 4 0.07
58 7 0.13
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (55 bp):
TTACTCTTAAAATATTTAAACTTAACATTAGGTATATATTTTATCTATTTCTTTT
Found at i:42658798 original size:12 final size:12
Alignment explanation
Indices: 42658780--42658814 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
42658770 TTTATTTCTT
42658780 TTCTTTTA-TTG
1 TTCTTTTATTTG
42658791 TGTCTTTTATTTG
1 T-TCTTTTATTTG
42658804 TTCTTTTATTT
1 TTCTTTTATTT
42658815 ATTTGCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 17 0.77
13 4 0.18
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (12 bp):
TTCTTTTATTTG
Found at i:42658898 original size:3 final size:3
Alignment explanation
Indices: 42658846--42658890 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
42658836 AAAATTTAGA
42658846 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42658891 CTTATTATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42659751 original size:43 final size:43
Alignment explanation
Indices: 42659690--42659774 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
42659680 TGGTTTCGAC
42659690 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTG
1 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTG
42659733 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTT
1 ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTT
42659775 AGTGTATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (43 bp):
ATTAAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTG
Found at i:42659789 original size:40 final size:42
Alignment explanation
Indices: 42659694--42659793 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 42
42659684 TTCGACATTA
* *
42659694 AGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTTGATT
1 AGAATATACAATTTATTTGTTGTTGTCCTCTTCAATTTGAGT
*
42659736 AAGAATGTACAATTTATTTGTTGTTGTCCTCTTCAATTT-AGT
1 -AGAATATACAATTTATTTGTTGTTGTCCTCTTCAATTTGAGT
* *
42659778 -GTATATTCAATTTATT
1 AGAATATACAATTTATT
42659794 GTTAATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 13 0.25
42 2 0.04
43 38 0.72
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (42 bp):
AGAATATACAATTTATTTGTTGTTGTCCTCTTCAATTTGAGT
Found at i:42660870 original size:10 final size:10
Alignment explanation
Indices: 42660857--42660928 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 10
42660847 AGATAAAAGA
42660857 TAAAAATTAT
1 TAAAAATTAT
**
42660867 TAAATTTTAAT
1 TAAAAATT-AT
*
42660878 GAAAAA-TA-
1 TAAAAATTAT
*
42660886 TAAAAAATAT
1 TAAAAATTAT
42660896 TAAAAATCTAT
1 TAAAAAT-TAT
42660907 TAAAAATTA-
1 TAAAAATTAT
42660916 T-AAAATTA-
1 TAAAAATTAT
42660924 TAAAA
1 TAAAA
42660929 TTTTATAAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 13 0.26
9 7 0.14
10 15 0.30
11 15 0.30
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:42660934 original size:18 final size:19
Alignment explanation
Indices: 42660880--42660937 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
42660870 ATTTTAATGA
*
42660880 AAAATATAAAAAATATTA-
1 AAAATATATAAAATATTAT
*
42660898 AAAATCTATTAAAA-ATTAT
1 AAAATATA-TAAAATATTAT
*
42660917 AAAAT-TATAAAATTTTAT
1 AAAATATATAAAATATTAT
42660935 AAA
1 AAA
42660938 GTAGTAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.15
18 20 0.59
19 9 0.26
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATATAAAATATTAT
Found at i:42660963 original size:12 final size:12
Alignment explanation
Indices: 42660946--42660970 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42660936 AAGTAGTAAG
42660946 AAAATTATAAAA
1 AAAATTATAAAA
42660958 AAAATTATAAAA
1 AAAATTATAAAA
42660970 A
1 A
42660971 TTATCATACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:42660969 original size:8 final size:9
Alignment explanation
Indices: 42660856--42660974 Score: 55
Period size: 8 Copynumber: 12.2 Consensus size: 9
42660846 AAGATAAAAG
42660856 ATAAAAATT
1 ATAAAAATT
**
42660865 ATTAAATTTT
1 A-TAAAAATT
42660875 AATGAAAAA-T
1 -AT-AAAAATT
*
42660885 ATAAAAAAT
1 ATAAAAATT
42660894 ATTAAAAATCT
1 A-TAAAAAT-T
42660905 ATTAAAAATT
1 A-TAAAAATT
42660915 AT-AAAATT
1 ATAAAAATT
42660923 AT-AAAATT
1 ATAAAAATT
* * *
42660931 TTATAAAGT
1 ATAAAAATT
42660940 AGTAAGAAAATT
1 A-T-A-AAAATT
42660952 ATAAAAAAAATT
1 AT---AAAAATT
42660964 ATAAAAATT
1 ATAAAAATT
42660973 AT
1 AT
42660975 CATACCAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
8 20 0.23
9 19 0.22
10 17 0.20
11 16 0.18
12 13 0.15
13 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:42660969 original size:10 final size:10
Alignment explanation
Indices: 42660879--42660974 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 10
42660869 AATTTTAATG
42660879 AAAAA-TATA
1 AAAAATTATA
*
42660888 AAAAA-TATT
1 AAAAATTATA
*
42660897 AAAAATCTATT
1 AAAAAT-TATA
42660908 AAAAATTAT-
1 AAAAATTATA
42660917 -AAAATTATA
1 AAAAATTATA
**
42660926 AAATTTTATA
1 AAAAATTATA
** *
42660936 AAGTAGTA-A
1 AAAAATTATA
*
42660945 GAAAATTATAAA
1 AAAAATTAT--A
42660957 AAAAATTAT-
1 AAAAATTATA
42660966 AAAAATTAT
1 AAAAATTAT
42660975 CATACCAAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
8 8 0.12
9 27 0.39
10 15 0.22
11 10 0.14
12 9 0.13
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:42661174 original size:17 final size:17
Alignment explanation
Indices: 42661145--42661257 Score: 61
Period size: 17 Copynumber: 6.4 Consensus size: 17
42661135 TTAAAAAGCC
*
42661145 TTTTTATAA-TTTTATA
1 TTTTTTTAATTTTTATA
42661161 TTTTTTTAATTTTTAATAA
1 TTTTTTTAATTTTT-AT-A
* **
42661180 ATTTTAAATATTTTTATA
1 TTTTTTTA-ATTTTTATA
**
42661198 TTTTTATTAAAGTTTA-A
1 TTTTT-TTAATTTTTATA
* *
42661215 TAATTTTTATTTTTTAT-
1 T-TTTTTTAATTTTTATA
*
42661232 TTATTTTTATTTTTTATAA
1 TT-TTTTTAATTTTTAT-A
42661251 TTTTTTT
1 TTTTTTT
42661258 GCCACATGTC
Statistics
Matches: 73, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.11
17 28 0.38
18 20 0.27
19 11 0.15
20 6 0.08
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (17 bp):
TTTTTTTAATTTTTATA
Found at i:42661202 original size:28 final size:28
Alignment explanation
Indices: 42661145--42661230 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 28
42661135 TTAAAAAGCC
* *
42661145 TTTTT-AT-AATTTTATATTTTTTTA-A
1 TTTTTAATAAATTTTAAATATTTTTATA
42661170 TTTTTAATAAATTTTAAATATTTTTATA
1 TTTTTAATAAATTTTAAATATTTTTATA
* *
42661198 TTTTTATTAAAGTTT-AATAATTTTTAT-
1 TTTTTAATAAATTTTAAAT-ATTTTTATA
42661225 TTTTTA
1 TTTTTA
42661231 TTTATTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.09
26 2 0.04
27 24 0.45
28 22 0.42
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTTTAATAAATTTTAAATATTTTTATA
Found at i:42661231 original size:27 final size:27
Alignment explanation
Indices: 42661163--42661232 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
42661153 ATTTTATATT
* * *
42661163 TTTTTAATTTTTAATAAATTTTAAATA
1 TTTTTATTTTTTATTAAAGTTTAAATA
42661190 TTTTTATATTTTTATTAAAGTTT-AATAA
1 TTTTTAT-TTTTTATTAAAGTTTAAAT-A
42661218 TTTTTATTTTTTATT
1 TTTTTATTTTTTATT
42661233 TATTTTTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTTTATTTTTTATTAAAGTTTAAATA
Found at i:42662353 original size:17 final size:17
Alignment explanation
Indices: 42662333--42662375 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
42662323 CTTTCTTATT
*
42662333 TTTATTTTTAATTAATA
1 TTTATTTTTAATAAATA
**
42662350 TTTATAATTAATAAATA
1 TTTATTTTTAATAAATA
42662367 TGTTATTTT
1 T-TTATTTT
42662376 CAAGTTTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTATTTTTAATAAATA
Found at i:42664965 original size:17 final size:16
Alignment explanation
Indices: 42664935--42664968 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
42664925 TTTGGGGGGA
42664935 TTTTCTTTTGATTTTC
1 TTTTCTTTTGATTTTC
*
42664951 TTTTCATTTTTATTTTC
1 TTTTC-TTTTGATTTTC
42664968 T
1 T
42664969 GTAATTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTGATTTTC
Found at i:42670573 original size:15 final size:15
Alignment explanation
Indices: 42670553--42670582 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42670543 GAGAAATCTC
42670553 AAAAAAAATCAAAAT
1 AAAAAAAATCAAAAT
42670568 AAAAAAAATCAAAAT
1 AAAAAAAATCAAAAT
42670583 CAAAGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAAAATCAAAAT
Found at i:42670581 original size:6 final size:6
Alignment explanation
Indices: 42670557--42670605 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
42670547 AATCTCAAAA
* * *
42670557 AAAATC AAAAT- AAAA-- AAAATC AAAATC AAAGTC AAAATG AAAATG
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
42670602 AAAA
1 AAAA
42670606 AGAGAGAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 30 0.79
ACGTcount: A:0.71, C:0.08, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATC
Found at i:42672842 original size:44 final size:44
Alignment explanation
Indices: 42672760--42672844 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
42672750 GCTCCTTGAC
*
42672760 CAGCAGTGGAATAGGTTGAAGATTGCAAGTCTTATCTCCCTGGT
1 CAGCAGTGGAATAGGTTGAAGATTACAAGTCTTATCTCCCTGGT
* *
42672804 CAGCAGTGGAGTAGGTTAGAA-ATTAC-AGATCTTGTCTCCCT
1 CAGCAGTGGAATAGGTT-GAAGATTACAAG-TCTTATCTCCCT
42672845 AAGTAGTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 2 0.06
44 31 0.86
45 3 0.08
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (44 bp):
CAGCAGTGGAATAGGTTGAAGATTACAAGTCTTATCTCCCTGGT
Found at i:42673013 original size:128 final size:128
Alignment explanation
Indices: 42672785--42673293 Score: 788
Period size: 128 Copynumber: 4.0 Consensus size: 128
42672775 TTGAAGATTG
* *
42672785 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTAGAAATTACAGATCTTGTCTCCCTAAGTA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCA
* * * *
42672850 GTAGTGGAGCACATCGAAGACAGCGAATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGCCA
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* *
42672913 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAAATCTTGTCTCCCTAACCA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCA
*
42672978 GTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* *
42673041 CAAGTCCTATCTCCCTGGTCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCA
** * *
42673106 GTAGTAGAGCAGATTGAAGACGGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
* * ** * * *
42673169 CAAGTC--CTGTCCCTGGTCAGCAGCAGAATAGGTTGGAAATTACAGATCTTGTTTCCCTAAGTA
1 CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCA
* *
42673232 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAACAGATTGAAGCC
66 GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC
42673294 GATAATCCTA
Statistics
Matches: 349, Mismatches: 32, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
126 105 0.30
128 244 0.70
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (128 bp):
CAAGTCTTATCTCCCTGGTCAGCAGTGGAGTAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCA
GTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCA
Found at i:42674272 original size:17 final size:16
Alignment explanation
Indices: 42674242--42674275 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
42674232 TTTGGGGGGA
42674242 TTTTCTTTTGATTTTC
1 TTTTCTTTTGATTTTC
*
42674258 TTTTCATTTTTATTTTC
1 TTTTC-TTTTGATTTTC
42674275 T
1 T
42674276 GTAATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTGATTTTC
Found at i:42679007 original size:96 final size:96
Alignment explanation
Indices: 42678892--42679087 Score: 295
Period size: 96 Copynumber: 2.1 Consensus size: 96
42678882 CTTACTTTCT
** * ** *
42678892 TCTCTAGTTGGATATTTAATTGGACATTGGAAACTCTTATGATCTTTTGAACTATACCAATAACA
1 TCTCTAGTTGGATATTTAATTGGACATTAAAAACCCTTACAATCTTTTGAACTACACCAATAACA
*
42678957 TTGCACAAAAGATGATATCTCAATCATATTC
66 TTGCACAAAAGATGATAACTCAATCATATTC
*
42678988 TCTCTATTTGGATATTTAATTGGACATTAAAAACCCTTACAATCTTTTGAACTACACCAATAACA
1 TCTCTAGTTGGATATTTAATTGGACATTAAAAACCCTTACAATCTTTTGAACTACACCAATAACA
* *
42679053 TTGCACAAAAGGTGATAACTCAATCGTATTC
66 TTGCACAAAAGATGATAACTCAATCATATTC
42679084 -CTCT
1 TCTCT
42679088 TTTCGTTTGG
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 4 0.04
96 86 0.96
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (96 bp):
TCTCTAGTTGGATATTTAATTGGACATTAAAAACCCTTACAATCTTTTGAACTACACCAATAACA
TTGCACAAAAGATGATAACTCAATCATATTC
Found at i:42680675 original size:27 final size:25
Alignment explanation
Indices: 42680623--42680675 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
42680613 AAACTCTTCT
*
42680623 AAAAGAAACTCAAGAGGAATTCTTG
1 AAAAGAAACTCAAGAGGAATTATTG
42680648 AAAAGAAAACTCAA-AGAGAATTTATTG
1 AAAAG-AAACTCAAGAG-GAA-TTATTG
42680675 A
1 A
42680676 CTCAAAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.29
26 11 0.46
27 6 0.25
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (25 bp):
AAAAGAAACTCAAGAGGAATTATTG
Found at i:42680898 original size:8 final size:8
Alignment explanation
Indices: 42680885--42680913 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
42680875 AAAAATTCAG
42680885 AATAATAA
1 AATAATAA
42680893 AATAATAA
1 AATAATAA
42680901 AATAATAA
1 AATAATAA
42680909 AATAA
1 AATAA
42680914 CAAGAGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:42683852 original size:17 final size:17
Alignment explanation
Indices: 42683830--42683866 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42683820 GAGTTTTATA
42683830 TACCCAAATTATTCTTT
1 TACCCAAATTATTCTTT
42683847 TACCCAAATTATTCTTT
1 TACCCAAATTATTCTTT
42683864 TAC
1 TAC
42683867 TTTCATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (17 bp):
TACCCAAATTATTCTTT
Done.