Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 93 of 172
Found at i:31297944 original size:8 final size:8
Alignment explanation
Indices: 31297931--31297957 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31297921 AAACACCGTA
31297931 TTTCGGCT
1 TTTCGGCT
31297939 TTTCGGCT
1 TTTCGGCT
31297947 TTTCGGCT
1 TTTCGGCT
31297955 TTT
1 TTT
31297958 GTTGATTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.22, T:0.56
Consensus pattern (8 bp):
TTTCGGCT
Found at i:31307908 original size:43 final size:43
Alignment explanation
Indices: 31307860--31307967 Score: 139
Period size: 43 Copynumber: 2.5 Consensus size: 43
31307850 GATTAACGAG
* *
31307860 ATGTGATTATGTGTAAGACTATGTCTGGGACATTGACATCATT
1 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGACATCATT
* *
31307903 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGGCATCGTT
1 ATGTGATTATGTGTAAGACCATGTCTAGGACATTGACATCATT
*
31307946 AAT-TAATT-TCGTGTAAGACCAT
1 -ATGTGATTAT-GTGTAAGACCAT
31307968 AACTGGGCTA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
42 1 0.02
43 55 0.95
44 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (43 bp):
ATGTGATTATGTGTAAGACCATGTCTAGGACATTGACATCATT
Found at i:31311696 original size:27 final size:27
Alignment explanation
Indices: 31311666--31311843 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
31311656 ATATTGAGTC
* * *
31311666 CGCACACTCAGTTCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
31311693 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
31311720 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
31311748 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
31311775 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
31311802 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
31311829 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31311844 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:31311807 original size:82 final size:81
Alignment explanation
Indices: 31311687--31311842 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31311677 TTCTATATAA
* *
31311687 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
31311752 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
31311769 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
31311833 CACTTAGTGC
65 CACTTAGTGC
31311843 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:31314070 original size:43 final size:43
Alignment explanation
Indices: 31313982--31314121 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 43
31313972 TGTGATTATG
* * *
31313982 TGTAAGACCATGTCTGGGACATTGGCTTCATTATGTGATTACA
1 TGTAAGACCATATCTGGGACATTGGCATCATTATGTAATTACA
* *
31314025 TGTAAGACCATATTTGGGACATTGGCAT-AGTTAAT-TAATTTCA
1 TGTAAGACCATATCTGGGACATTGGCATCA-TT-ATGTAATTACA
* * * *
31314068 TGTGAGACCATAGCTGGG-CTATTGGCATCGA-TATGTGATAACA
1 TGTAAGACCATATCTGGGAC-ATTGGCATC-ATTATGTAATTACA
31314111 TGTAAGACCAT
1 TGTAAGACCAT
31314122 GTCTTGGATA
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
42 4 0.05
43 72 0.91
44 2 0.03
45 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGACATTGGCATCATTATGTAATTACA
Found at i:31315716 original size:34 final size:32
Alignment explanation
Indices: 31315673--31315763 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 32
31315663 TTAGGGCCTT
* *
31315673 AGCCCATTTCAGTAACAGTAGCAGTCTGGGACTG
1 AGCCCATTTCAGTAACAGTA-CAGT-GGGGACTA
* *
31315707 AGCCCATTTCAATAACAGTATCAGTGGGGCCTA
1 AGCCCATTTCAGTAACAGTA-CAGTGGGGACTA
* *
31315740 AGCCCATTACAGTATCAGTACAGT
1 AGCCCATTTCAGTAACAGTACAGT
31315764 TGCAATTAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 4 0.08
33 22 0.45
34 23 0.47
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (32 bp):
AGCCCATTTCAGTAACAGTACAGTGGGGACTA
Found at i:31323314 original size:43 final size:43
Alignment explanation
Indices: 31323267--31323374 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
31323257 TAGCCCAACT
* *
31323267 ATGGTCTTACACAAAATTA-ATTAACGATGCCAATGTCCCATAC
1 ATGGTCTTACACAAAATCACA-TAACGATGCCAATGTCCCAGAC
* *
31323310 ATGGTCTTACACATAATCACATAATGATGCCAATGTCCCAGAC
1 ATGGTCTTACACAAAATCACATAACGATGCCAATGTCCCAGAC
*
31323353 ATGGTCTTACACATAATCACAT
1 ATGGTCTTACACAAAATCACAT
31323375 CTCATTAATC
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 59 0.98
44 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACAAAATCACATAACGATGCCAATGTCCCAGAC
Found at i:31323361 original size:86 final size:85
Alignment explanation
Indices: 31323208--31323365 Score: 196
Period size: 86 Copynumber: 1.8 Consensus size: 85
31323198 AGCTTGTATA
** * *
31323208 ATGCCATATCCCATACATGGTCTTACATGTTATCACATATCGATAACGATAGCCCAACTATGGTC
1 ATGCCATATCCCATACATGGTCTTACACATAATCACATATCGATAACAATAGCCCAACTATGGTC
31323273 TTACACAAAATTAATTAACG
66 TTACACAAAATTAATTAACG
* **
31323293 ATGCCAATGTCCCATACATGGTCTTACACATAATCACATAAT-GATGCCAAT-GTCCCAGAC-AT
1 ATGCC-ATATCCCATACATGGTCTTACACATAATCACAT-ATCGATAACAATAG-CCCA-ACTAT
31323355 GGTCTTACACA
62 GGTCTTACACA
31323366 TAATCACATC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
85 6 0.10
86 52 0.84
87 4 0.06
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (85 bp):
ATGCCATATCCCATACATGGTCTTACACATAATCACATATCGATAACAATAGCCCAACTATGGTC
TTACACAAAATTAATTAACG
Found at i:31325106 original size:53 final size:53
Alignment explanation
Indices: 31324923--31325124 Score: 217
Period size: 53 Copynumber: 3.8 Consensus size: 53
31324913 GACGTTGAAT
* * * *
31324923 GACCATACCATGTAAGACCGTAACTTGTGGGTTA-TGACATCATATGGAAGGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATTG-CATCATATGGAAAGAA
* * * * *
31324976 GCCCATATCATGTAATACCGTAATTGGTGGGTTATTACATCATATGGAAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATTGCATCATATGGAAAGAA
* * * *
31325029 GACCATATTGTGTAAGAACATAACTGGTGGGTTATTGCATCATATGAAAAGAA
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATTGCATCATATGGAAAGAA
* ** * * *
31325082 GACCATGTCGTGTAAGATTGTAACTAGTGGATTATGGCATCAT
1 GACCATATCGTGTAAGACCGTAACTGGTGGGTTATTGCATCAT
31325125 GTGGGAAAAA
Statistics
Matches: 124, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
53 123 0.99
54 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (53 bp):
GACCATATCGTGTAAGACCGTAACTGGTGGGTTATTGCATCATATGGAAAGAA
Found at i:31325314 original size:29 final size:28
Alignment explanation
Indices: 31325282--31325377 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 28
31325272 TTTAATGACA
*
31325282 CCTTTGTGGCAAAACTTTGGAAAGGTAAG
1 CCTTTGTGGCAAAACTAT-GAAAGGTAAG
*
31325311 CCTTTGTGG-AAAAGCTATGAAAGGCCAA-
1 CCTTTGTGGCAAAA-CTATGAAAGG-TAAG
* * *
31325339 ACTTTGTGCCAAAACTCTAGAAAGGTAAG
1 CCTTTGTGGCAAAACTAT-GAAAGGTAAG
31325368 CCTTTGTGGC
1 CCTTTGTGGC
31325378 GAACTTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 22 0.41
29 32 0.59
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (28 bp):
CCTTTGTGGCAAAACTATGAAAGGTAAG
Found at i:31325439 original size:27 final size:27
Alignment explanation
Indices: 31325282--31325459 Score: 83
Period size: 28 Copynumber: 6.3 Consensus size: 27
31325272 TTTAATGACA
* * *
31325282 CCTTTGTGGCAAAACTTTGGAAAGGTAAG
1 CCTTTGTGGC-AAACTCT-AAAAGGAAAG
* * *
31325311 CCTTTGTGGAAAAGCTATGAAAGGCCAAA-
1 CCTTTGTGGCAAA-CTCTAAAAGG--AAAG
* *
31325340 -CTTTGTGCCAAAACTCTAGAAAGGTAAG
1 CCTTTGTGGC-AAACTCTA-AAAGGAAAG
* * * *
31325368 CCTTTGTGGCGAACTTTTTAAA-GAACG
1 CCTTTGTGGCAAAC-TCTAAAAGGAAAG
* *
31325395 CCTTTATGGAAAATCTCTAAAAGGAAAG
1 CCTTTGTGGCAAA-CTCTAAAAGGAAAG
* ** *
31325423 CCTCTGTGGCAAACTCTAGGCAGGAAAA
1 CCTTTGTGGCAAACTCTA-AAAGGAAAG
31325451 CCTTTGTGG
1 CCTTTGTGG
31325460 TAATATCCAT
Statistics
Matches: 111, Mismatches: 27, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
27 25 0.23
28 54 0.49
29 30 0.27
30 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (27 bp):
CCTTTGTGGCAAACTCTAAAAGGAAAG
Found at i:31325736 original size:23 final size:23
Alignment explanation
Indices: 31325709--31325782 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 23
31325699 GACTCTAAAG
31325709 GTATGGTAAGTGTAAGAAATAAT
1 GTATGGTAAGTGTAAGAAATAAT
* * *
31325732 GTATGGGTCAATTAGAAAGAACTAA-
1 GTAT-GGT-AAGT-GTAAGAAATAAT
31325757 GTA---TAAGTGTAAGAAATAAT
1 GTATGGTAAGTGTAAGAAATAAT
31325777 GTATGG
1 GTATGG
31325783 GTCAATTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 9 0.24
20 6 0.16
21 1 0.03
23 4 0.11
24 3 0.08
25 6 0.16
26 9 0.24
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (23 bp):
GTATGGTAAGTGTAAGAAATAAT
Found at i:31325779 original size:45 final size:45
Alignment explanation
Indices: 31325715--31325805 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
31325705 AAAGGTATGG
31325715 TAAGTGTAAGAAATAATGTATGGGTCAATTAGAAAGAACTAAGTA
1 TAAGTGTAAGAAATAATGTATGGGTCAATTAGAAAGAACTAAGTA
31325760 TAAGTGTAAGAAATAATGTATGGGTCAATTAGAAAGAACTAAGTA
1 TAAGTGTAAGAAATAATGTATGGGTCAATTAGAAAGAACTAAGTA
31325805 T
1 T
31325806 CCAACAAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.27
Consensus pattern (45 bp):
TAAGTGTAAGAAATAATGTATGGGTCAATTAGAAAGAACTAAGTA
Found at i:31325793 original size:22 final size:22
Alignment explanation
Indices: 31325723--31325794 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
31325713 GGTAAGTGTA
31325723 AGAAATAATGTATGGGTCAATT
1 AGAAATAATGTATGGGTCAATT
* ** * *
31325745 AGAAAGAACTAAGTATAAGT--GTA
1 AGAAATAA-T--GTATGGGTCAATT
31325768 AGAAATAATGTATGGGTCAATT
1 AGAAATAATGTATGGGTCAATT
31325790 AGAAA
1 AGAAA
31325795 GAACTAAGTA
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 6 0.17
22 14 0.40
23 9 0.26
25 6 0.17
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.26
Consensus pattern (22 bp):
AGAAATAATGTATGGGTCAATT
Found at i:31328445 original size:40 final size:40
Alignment explanation
Indices: 31328390--31328607 Score: 282
Period size: 40 Copynumber: 5.5 Consensus size: 40
31328380 CGGATGATAA
* *
31328390 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
31328429 CCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* **
31328470 TCGATCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
31328510 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
31328550 CCGGGCTAGGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
31328590 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
31328608 TACTTGGTTT
Statistics
Matches: 159, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.09
40 142 0.89
41 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:31333257 original size:40 final size:40
Alignment explanation
Indices: 31333099--31333243 Score: 263
Period size: 40 Copynumber: 3.6 Consensus size: 40
31333089 NNNNNNNNNN
* *
31333099 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTTTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
31333139 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
31333179 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
31333219 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31333244 AGCTAGTAGC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 101 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:31335564 original size:22 final size:22
Alignment explanation
Indices: 31335539--31335585 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
31335529 AAAGCCGAGG
31335539 AGCTCAGTAT-GGAGAAAAGAAA
1 AGCTCA-TATGGGAGAAAAGAAA
*
31335561 AGCTGATATGGGAGAAAAGAAA
1 AGCTCATATGGGAGAAAAGAAA
31335583 AGC
1 AGC
31335586 AAAGGAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.49, C:0.09, G:0.30, T:0.13
Consensus pattern (22 bp):
AGCTCATATGGGAGAAAAGAAA
Found at i:31336978 original size:150 final size:150
Alignment explanation
Indices: 31336707--31336989 Score: 494
Period size: 150 Copynumber: 1.9 Consensus size: 150
31336697 TATTATCAGT
** *
31336707 TGCGAATTCGAGATTCGGATATACCCAAAACTGCTTTCAGAACGAGATAAGGCCACTACGAGTTC
1 TGCGAATTCGAGATTCGGATATACCCAAAACTGCTTTCAGAACGAGATAAGGCCACTAAAAATTC
*
31336772 TTAGTGATGCCGTTTGGGCTCACTAATGCCCCTGCGGTATTTATGGATTTGATGAATCGGATCTT
66 TTAGTGATGCCGTTTGGGCTCACTAATGCCCCCGCGGTATTTATGGATTTGATGAATCGGATCTT
31336837 CAGTGTAACACCCCGAACCC
131 CAGTGTAACACCCCGAACCC
* *
31336857 TGCGAATTCGAGATTCGGATATACCCAAAACTGCTTTCAGAACGAGATACGGTCACTAAAAATTC
1 TGCGAATTCGAGATTCGGATATACCCAAAACTGCTTTCAGAACGAGATAAGGCCACTAAAAATTC
* *
31336922 TTAGTGATGCCGTTTGGGCTTACTAATGCCCCCGCGGTATTTATGGATTTGATGAATCGGATTTT
66 TTAGTGATGCCGTTTGGGCTCACTAATGCCCCCGCGGTATTTATGGATTTGATGAATCGGATCTT
31336987 CAG
131 CAG
31336990 ACCGTATTTG
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
150 125 1.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (150 bp):
TGCGAATTCGAGATTCGGATATACCCAAAACTGCTTTCAGAACGAGATAAGGCCACTAAAAATTC
TTAGTGATGCCGTTTGGGCTCACTAATGCCCCCGCGGTATTTATGGATTTGATGAATCGGATCTT
CAGTGTAACACCCCGAACCC
Found at i:31340499 original size:40 final size:40
Alignment explanation
Indices: 31340436--31340723 Score: 344
Period size: 40 Copynumber: 7.3 Consensus size: 40
31340426 TATTCGGATG
31340436 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGT-CT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-TACT
* * * *
31340476 A-ATTCCAGGCTAAGTCCCAAAGGCA----TGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
** *
31340512 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
* * * *
31340552 TTATCCGGGCTAAGTTCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
31340592 ATAACCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACT
31340632 ATAACCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACT
*
31340672 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTA-CT
*
31340712 ATATCC-GGCTAA
1 ATAACCGGGCTAA
31340724 ACTCCAAAGG
Statistics
Matches: 222, Mismatches: 16, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
35 1 0.00
36 28 0.13
37 1 0.00
39 9 0.04
40 182 0.82
41 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACT
Found at i:31340714 original size:80 final size:80
Alignment explanation
Indices: 31340436--31340723 Score: 387
Period size: 80 Copynumber: 3.7 Consensus size: 80
31340426 TATTCGGATG
* *
31340436 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGT-CTA-ATTCCAGGCTAAGTCCCAAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-TACTATA-TCCGGGCTAAGTCCCGAAGG
31340499 CA----TGCGAGTTACT
64 CATTTGTGCGAGTTACT
** * * *
31340512 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTTTATCCGGGCTAAGTTCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
31340577 TTTGTGCGAGTTACT
66 TTTGTGCGAGTTACT
*
31340592 ATAACCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATATCCGGGCTAAGTCCCGAAGGC
*
31340656 ATTTGTGTGAGTTACT
65 ATTTGTGCGAGTTACT
*
31340672 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATATCC-GGCTAA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTA-CTATATCCGGGCTAA
31340724 ACTCCAAAGG
Statistics
Matches: 187, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
75 1 0.01
76 54 0.29
77 1 0.01
79 8 0.04
80 122 0.65
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTACT
Found at i:31352440 original size:40 final size:39
Alignment explanation
Indices: 31352346--31352490 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 39
31352336 TACTCGAATG
* *
31352346 ATATCTGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCT-AGCGACT
* *
31352387 ACATCCGGACTAAGATCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCGAAGGCATTTGTGCTAGCGACT
* * *
31352427 ATATCCGGGCTAAGTCTCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTC-CGAAGGCATTTGTGCTAGCGACT
* *
31352467 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAG-TCCGAAGGC
31352491 CTTGTGCGAG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
39 2 0.02
40 59 0.66
41 28 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCGAAGGCATTTGTGCTAGCGACT
Found at i:31354119 original size:26 final size:25
Alignment explanation
Indices: 31354067--31354119 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
31354057 TTAGATTTCA
*
31354067 CCTTAAAGGCTTTTCTTCATACCATG
1 CCTTAAAGGCTTTTCGTCATA-CATG
31354093 CCTTAAAGGCATTTCTCGTCATA-ATG
1 CCTTAAAGGC-TTT-TCGTCATACATG
31354119 C
1 C
31354120 ACCACAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 14 0.58
27 3 0.12
28 7 0.29
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (25 bp):
CCTTAAAGGCTTTTCGTCATACATG
Found at i:31354449 original size:29 final size:28
Alignment explanation
Indices: 31354377--31354500 Score: 128
Period size: 27 Copynumber: 4.5 Consensus size: 28
31354367 ATTTCCATAG
* *
31354377 AGGCTTCCA-TGTCATAG-TTCTCCACAA
1 AGGCTTCCATTTTCATAGATT-GCCACAA
*
31354404 AGGCTACCATTTTCATAGATTGCCACAA
1 AGGCTTCCATTTTCATAGATTGCCACAA
*
31354432 AAGCTTCCATTTCTCATAGATTGCCACAA
1 AGGCTTCCATTT-TCATAGATTGCCACAA
* * ** *
31354461 AGGCTTCCATGTT-ATAGACTATCATAA
1 AGGCTTCCATTTTCATAGATTGCCACAA
31354488 AGGCTTCCATTTT
1 AGGCTTCCATTTT
31354501 TCTAGTGTGT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
27 30 0.37
28 24 0.29
29 28 0.34
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (28 bp):
AGGCTTCCATTTTCATAGATTGCCACAA
Found at i:31361206 original size:3 final size:3
Alignment explanation
Indices: 31361200--31361231 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31361190 CGTACTGGCT
*
31361200 TCA TCA TCA TCA TCA TCA TCA TTA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
31361232 GTCTGGTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:31365294 original size:52 final size:52
Alignment explanation
Indices: 31365215--31365315 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
31365205 TGTATGCGGT
*
31365215 ATCCGAGCACGTTGAGTTGGTTCGAGTTCATGATGGATGCGATACATGTGGC
1 ATCCGAGCACGTTGAGTTGGTTCGAGTTCATAATGGATGCGATACATGTGGC
* *
31365267 ATCCGAGCTCGTTGAGTTGGTTTGAGTTCATAATGGATGCGATACATGT
1 ATCCGAGCACGTTGAGTTGGTTCGAGTTCATAATGGATGCGATACATGT
31365316 AATTGGGTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.32
Consensus pattern (52 bp):
ATCCGAGCACGTTGAGTTGGTTCGAGTTCATAATGGATGCGATACATGTGGC
Found at i:31369538 original size:11 final size:11
Alignment explanation
Indices: 31369522--31369547 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
31369512 TTAGGGAAGA
31369522 TTTCCCAAACC
1 TTTCCCAAACC
31369533 TTTCCCAAACC
1 TTTCCCAAACC
31369544 TTTC
1 TTTC
31369548 TAAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (11 bp):
TTTCCCAAACC
Found at i:31375768 original size:52 final size:52
Alignment explanation
Indices: 31375701--31375804 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 52
31375691 ATATGTATAC
* * *
31375701 GGCACCCGAGCTCGTTGTGTTGGT-TCAAGTTCATGATAGATGTGATACATGT
1 GGCACCCGAGCTCGTTGAGTTGGTCT-AAGTTCATAATAGATGCGATACATGT
* * *
31375753 GGCATCCGAGCTCGTTGAGTTGGTCTGAGTTCATAATGGATGCGATACATGT
1 GGCACCCGAGCTCGTTGAGTTGGTCTAAGTTCATAATAGATGCGATACATGT
31375805 AATTGGGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 44 0.98
53 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (52 bp):
GGCACCCGAGCTCGTTGAGTTGGTCTAAGTTCATAATAGATGCGATACATGT
Found at i:31377659 original size:32 final size:32
Alignment explanation
Indices: 31377621--31377685 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
31377611 CATAAGTGCC
31377621 ATATATGTAGCCAAAGCTACCTCATATTTCAT
1 ATATATGTAGCCAAAGCTACCTCATATTTCAT
31377653 ATATATGTAGCCAAAGCTACCTCATATTTCAT
1 ATATATGTAGCCAAAGCTACCTCATATTTCAT
31377685 A
1 A
31377686 ATACATATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (32 bp):
ATATATGTAGCCAAAGCTACCTCATATTTCAT
Found at i:31379044 original size:27 final size:27
Alignment explanation
Indices: 31379014--31379090 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
31379004 AATTTCATAT
* *
31379014 CTGTAGGCTAGTATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATGCCC
31379041 CTGTAGGGTAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATGCCC
* *
31379068 CTATAGGGTAGAATTATTGAAAT
1 CTGTAGGGTAGAATTACTGAAAT
31379091 ACCCTTGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATGCCC
Found at i:31379192 original size:54 final size:55
Alignment explanation
Indices: 31379130--31379331 Score: 207
Period size: 54 Copynumber: 3.8 Consensus size: 55
31379120 CTTGGTTTAC
* * *
31379130 AAAATTACCAAAATA-CCTTCGATTAGGAAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCGAAATACCCTTCGATTAGGAAAATTACCAAAATACCCCTAATTTGG
* * * * *
31379184 AAAATTACCCAAATACCCTTGGTTTA-TAAAATTACTAAAATACCCCTAATTTGG
1 AAAATTACCGAAATACCCTTCGATTAGGAAAATTACCAAAATACCCCTAATTTGG
* ** *** *
31379238 GAAATTATTGAAATACCC-TCGATTTCTAAAATTACCAACATACCCCTAATTTGG
1 AAAATTACCGAAATACCCTTCGATTAGGAAAATTACCAAAATACCCCTAATTTGG
* * *
31379292 AAAATTACTGAAATACCCTT-AATTTGGAAAATTA-CAAAAT
1 AAAATTACCGAAATACCCTTCGATTAGGAAAATTACCAAAAT
31379332 TACCATTGAC
Statistics
Matches: 123, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
53 9 0.07
54 105 0.85
55 9 0.07
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (55 bp):
AAAATTACCGAAATACCCTTCGATTAGGAAAATTACCAAAATACCCCTAATTTGG
Found at i:31379243 original size:81 final size:79
Alignment explanation
Indices: 31379087--31379389 Score: 252
Period size: 81 Copynumber: 3.7 Consensus size: 79
31379077 AGAATTATTG
* * * * *
31379087 AAATACCCTTGGTTTAC-AAAATTACTAAATACTCTTGGTTTACAAAATTACCAAAATA-CCTTC
1 AAATACCCTAGATTT-CTAAAATTACCAAATACCCTTGGTTTACAAAATTACTAAAATACCCTT-
* *
31379150 GATTAGGAAAATTACCA
64 AATTTGGAAAATTA-CA
* * *
31379167 AAATACCCCTAG-TTTGTAAAATTACCCAAATACCCTTGGTTTATAAAATTACTAAAATACCCCT
1 AAATA-CCCTAGATTTCTAAAATTA-CCAAATACCCTTGGTTTACAAAATTACTAAAATACCCTT
* **
31379231 AATTTGGGAAATTATTG
64 AATTTGGAAAATTA-CA
* * ** ** *
31379248 AAATACCCTCGATTTCTAAAATTACCAACATACCCCTAATTTGGAAAATTACTGAAATACCCTTA
1 AAATACCCTAGATTTCTAAAATTACCAA-ATACCCTTGGTTTACAAAATTACTAAAATACCCTTA
31379313 ATTTGGAAAATTACA
65 ATTTGGAAAATTACA
* * * * * * *
31379328 AAATTACCATTGACTTTCAAAAATTACAGAAATACCATTGGTTTGCAAAATTACTGAAATAC
1 AAA-TACCCTAGA-TTTCTAAAATTAC-CAAATACCCTTGGTTTACAAAATTACTAAAATAC
31379390 TCTTGGTCTG
Statistics
Matches: 180, Mismatches: 34, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
80 27 0.15
81 110 0.61
82 41 0.23
83 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (79 bp):
AAATACCCTAGATTTCTAAAATTACCAAATACCCTTGGTTTACAAAATTACTAAAATACCCTTAA
TTTGGAAAATTACA
Found at i:31379395 original size:27 final size:27
Alignment explanation
Indices: 31379079--31379396 Score: 171
Period size: 27 Copynumber: 11.8 Consensus size: 27
31379069 TATAGGGTAG
* *
31379079 AATTATTGAAATACCCTTGGTTTACAA
1 AATTACTGAAATACCCTTGGTTTGCAA
* *
31379106 AATTACT-AAATACTCTTGGTTTACAA
1 AATTACTGAAATACCCTTGGTTTGCAA
** * * *
31379132 AATTACCAAAATA-CCTTCGATTAGGAA
1 AATTACTGAAATACCCTT-GGTTTGCAA
** * * *
31379159 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACTGAAATACCCTTGGTTTGCAA
** **
31379186 AATTACCCAAATACCCTTGGTTTATAA
1 AATTACTGAAATACCCTTGGTTTGCAA
* * ** **
31379213 AATTACTAAAATACCCCTAATTTGGGA
1 AATTACTGAAATACCCTTGGTTTGCAA
* * *
31379240 AATTATTGAAATACCCTCGATTT-CTAA
1 AATTACTGAAATACCCTTGGTTTGC-AA
* * ** *
31379267 AATTAC-CAACATACCCCTAATTTGGAA
1 AATTACTGAA-ATACCCTTGGTTTGCAA
** *
31379294 AATTACTGAAATACCCTTAATTTGGAA
1 AATTACTGAAATACCCTTGGTTTGCAA
* * *
31379321 AATTAC-AAAATTACCATTGACTTT-CAAA
1 AATTACTGAAA-TACCCTTG-GTTTGC-AA
* *
31379349 AATTACAGAAATACCATTGGTTTGCAA
1 AATTACTGAAATACCCTTGGTTTGCAA
*
31379376 AATTACTGAAATACTCTTGGT
1 AATTACTGAAATACCCTTGGT
31379397 CTGTAGATTT
Statistics
Matches: 229, Mismatches: 50, Indels: 24
0.76 0.17 0.08
Matches are distributed among these distances:
26 32 0.14
27 169 0.74
28 25 0.11
29 3 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGGTTTGCAA
Found at i:31379704 original size:41 final size:41
Alignment explanation
Indices: 31379658--31379778 Score: 188
Period size: 41 Copynumber: 3.0 Consensus size: 41
31379648 CAGAGGAAGA
31379658 AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAAC
1 AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAAC
* * * *
31379699 GATTGAGGATCGCATGGTTGCTTAATGACCGTGGATCCACC
1 AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAAC
* *
31379740 AATTAAGGATCGCATGGTTTCTTGACGACCGTGGATCCA
1 AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCA
31379779 TCAGTGGCTT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (41 bp):
AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAAC
Found at i:31379960 original size:25 final size:25
Alignment explanation
Indices: 31379926--31380071 Score: 184
Period size: 25 Copynumber: 5.8 Consensus size: 25
31379916 AATTATTCTA
*
31379926 TTATCAATGGCTTTGTGCCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
* *
31379951 TTATCGATGGCTTTGTACCGATATG
1 TTATCGATGGCTTTGTGCCGATCTG
* * **
31379976 ATATTGATGGCAATGTGCCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
* *
31380001 TTATCGATGGCATTGTGCCGATATG
1 TTATCGATGGCTTTGTGCCGATCTG
* * *
31380026 ATATTGATGGCTATGTGCCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
31380051 TTATCGATGGCTTTGTGCCGA
1 TTATCGATGGCTTTGTGCCGA
31380072 GTGTATTATC
Statistics
Matches: 100, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 100 1.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (25 bp):
TTATCGATGGCTTTGTGCCGATCTG
Found at i:31380007 original size:50 final size:50
Alignment explanation
Indices: 31379939--31380071 Score: 239
Period size: 50 Copynumber: 2.7 Consensus size: 50
31379929 TCAATGGCTT
*
31379939 TGTGCCGATCTGTTATCGATGGCTTTGTACCGATATGATATTGATGGCAA
1 TGTGCCGATCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCAA
* *
31379989 TGTGCCGATCTGTTATCGATGGCATTGTGCCGATATGATATTGATGGCTA
1 TGTGCCGATCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCAA
31380039 TGTGCCGATCTGTTATCGATGGCTTTGTGCCGA
1 TGTGCCGATCTGTTATCGATGGCTTTGTGCCGA
31380072 GTGTATTATC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (50 bp):
TGTGCCGATCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCAA
Found at i:31384045 original size:40 final size:40
Alignment explanation
Indices: 31383990--31384181 Score: 296
Period size: 40 Copynumber: 4.8 Consensus size: 40
31383980 CGGATGATAA
*
31383990 CCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
31384030 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
*
31384070 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
31384110 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AAT
* *
31384150 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
31384182 AGCTATATCC
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 137 0.99
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
Found at i:31386178 original size:26 final size:27
Alignment explanation
Indices: 31386138--31386211 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 27
31386128 CCTAGAGGGT
31386138 AGAATTACTGAAATACCCTTGGTTTAC
1 AGAATTACTGAAATACCCTTGGTTTAC
*
31386165 AGAATTACTG-AATACTCTTGGTTTAC
1 AGAATTACTGAAATACCCTTGGTTTAC
* **
31386191 AAAATTACCAAAATACCCTTG
1 AGAATTACTGAAATACCCTTG
31386212 ATTAGGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 22 0.54
27 19 0.46
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (27 bp):
AGAATTACTGAAATACCCTTGGTTTAC
Found at i:31386221 original size:27 final size:27
Alignment explanation
Indices: 31386191--31386481 Score: 239
Period size: 27 Copynumber: 10.8 Consensus size: 27
31386181 CTTGGTTTAC
*
31386191 AAAATTACCAAAATACCCTTGATTAGG
1 AAAATTACCAAAATACCCTTGATTTGG
* * *
31386218 AAAATTAGCAAAATACCCCT-AGTTTGT
1 AAAATTACCAAAATACCCTTGA-TTTGG
* * * **
31386245 AAAATTACCCAAATACCCCTGGTTTAT
1 AAAATTACCAAAATACCCTTGATTTGG
31386272 AAAATTACCAAAATACCC-TGATTTGTG
1 AAAATTACCAAAATACCCTTGATTTG-G
** * *
31386299 -AAATTACTGAAATACCCTCGATTTGT
1 AAAATTACCAAAATACCCTTGATTTGG
* * *
31386325 AAAATTACCAACATACCCCTAATTTGG
1 AAAATTACCAAAATACCCTTGATTTGG
* *
31386352 AAAATTATCGAAATACCCTTGATTTGG
1 AAAATTACCAAAATACCCTTGATTTGG
**
31386379 AAAATTA-CAGAAATACCCTTGATTTAC
1 AAAATTACCA-AAATACCCTTGATTTGG
* * * **
31386406 AAAATTACAAAAATATCATTGACTTTCA
1 AAAATTACCAAAATACCCTTGA-TTTGG
* * * *
31386434 AAAATTACAAAAATACCATTGGTTTGC
1 AAAATTACCAAAATACCCTTGATTTGG
* *
31386461 AAAATTACCGAAATACTCTTG
1 AAAATTACCAAAATACCCTTG
31386482 GTCTGTAGAT
Statistics
Matches: 212, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
26 22 0.10
27 166 0.78
28 24 0.11
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGATTTGG
Found at i:31386312 original size:107 final size:108
Alignment explanation
Indices: 31386192--31386403 Score: 266
Period size: 107 Copynumber: 2.0 Consensus size: 108
31386182 TTGGTTTACA
* * * *
31386192 AAATTACCAAAATACCCTTGATTAGGAAAATTAGCAAAATACCCCTAGTTTGTAAAATTACCCAA
1 AAATTACCAAAATACCCTCGATTAGGAAAATTACCAAAATACCCCTAATTTGGAAAATTACCCAA
* *
31386257 ATACCCCTGGTTTATAAAATTACCA-AAATACCC-TGATTTGTG
66 ATACCCCTGATTTAGAAAATTA-CAGAAATACCCTTGATTTGTG
** * * * * *
31386299 AAATTACTGAAATACCCTCGATTTGTAAAATTACCAACATACCCCTAATTTGGAAAATTATCGAA
1 AAATTACCAAAATACCCTCGATTAGGAAAATTACCAAAATACCCCTAATTTGGAAAATTACCCAA
* *
31386364 ATACCCTTGATTTGGAAAATTACAGAAATACCCTTGATTT
66 ATACCCCTGATTTAGAAAATTACAGAAATACCCTTGATTT
31386404 ACAAAATTAC
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
106 2 0.02
107 80 0.91
108 6 0.07
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (108 bp):
AAATTACCAAAATACCCTCGATTAGGAAAATTACCAAAATACCCCTAATTTGGAAAATTACCCAA
ATACCCCTGATTTAGAAAATTACAGAAATACCCTTGATTTGTG
Found at i:31386483 original size:27 final size:27
Alignment explanation
Indices: 31386140--31386481 Score: 235
Period size: 27 Copynumber: 12.7 Consensus size: 27
31386130 TAGAGGGTAG
* * * *
31386140 AATTACTGAAATACCCTTGGTTTACAG
1 AATTACCGAAATACCCTTGATTTGCAA
* * * *
31386167 AATTACTG-AATACTCTTGGTTTACAA
1 AATTACCGAAATACCCTTGATTTGCAA
* * *
31386193 AATTACCAAAATACCCTTGATTAGGAA
1 AATTACCGAAATACCCTTGATTTGCAA
* * * *
31386220 AATTAGCAAAATACCCCT-AGTTTGTAA
1 AATTACCGAAATACCCTTGA-TTTGCAA
* * * **
31386247 AATTACCCAAATACCCCTGGTTTATAA
1 AATTACCGAAATACCCTTGATTTGCAA
* **
31386274 AATTACCAAAATACCC-TGATTTGTGA
1 AATTACCGAAATACCCTTGATTTGCAA
* * *
31386300 AATTACTGAAATACCCTCGATTTGTAA
1 AATTACCGAAATACCCTTGATTTGCAA
* * *
31386327 AATTACC-AACATACCCCTAATTTGGAA
1 AATTACCGAA-ATACCCTTGATTTGCAA
* *
31386354 AATTATCGAAATACCCTTGATTTGGAA
1 AATTACCGAAATACCCTTGATTTGCAA
* *
31386381 AATTACAGAAATACCCTTGATTTACAA
1 AATTACCGAAATACCCTTGATTTGCAA
** * *
31386408 AATTACAAAAATATCATTGACTTT-CAAA
1 AATTACCGAAATACCCTTGA-TTTGC-AA
** * *
31386436 AATTACAAAAATACCATTGGTTTGCAA
1 AATTACCGAAATACCCTTGATTTGCAA
*
31386463 AATTACCGAAATACTCTTG
1 AATTACCGAAATACCCTTG
31386482 GTCTGTAGAT
Statistics
Matches: 260, Mismatches: 46, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
26 46 0.18
27 188 0.72
28 26 0.10
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGATTTGCAA
Found at i:31386803 original size:41 final size:41
Alignment explanation
Indices: 31386745--31386865 Score: 161
Period size: 41 Copynumber: 3.0 Consensus size: 41
31386735 CGTATAAAGA
*
31386745 AATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAAC
1 AATTGAGGATCTCATGGTTGCTTGACGACCGTGGATCCAAC
* * * * * *
31386786 GATTGAGGATCTAATGGTTGTTTGATGACTGTGGATCCACC
1 AATTGAGGATCTCATGGTTGCTTGACGACCGTGGATCCAAC
* *
31386827 AATTAAAGATCTCATGGTTGCTTGACGACCGTGGATCCA
1 AATTGAGGATCTCATGGTTGCTTGACGACCGTGGATCCA
31386866 TCGGTGGCTT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (41 bp):
AATTGAGGATCTCATGGTTGCTTGACGACCGTGGATCCAAC
Found at i:31387047 original size:25 final size:25
Alignment explanation
Indices: 31387013--31387156 Score: 162
Period size: 25 Copynumber: 5.8 Consensus size: 25
31387003 TATTATTCTA
*
31387013 TTATCAATGGCTTTGTGCCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
* *
31387038 TTATCGATGGCTTTGTACCGATATG
1 TTATCGATGGCTTTGTGCCGATCTG
* * **
31387063 ATATTGATGGCAATGTGCCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
* *
31387088 TTATCGATGGCATTGTGCCGATATG
1 TTATCGATGGCTTTGTGCCGATCTG
* * * *
31387113 ATATTGATGGCTATGTGCTGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
*
31387138 TTATCGAAGGCTTTGTGCC
1 TTATCGATGGCTTTGTGCC
31387157 AAGTGTATTA
Statistics
Matches: 95, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 95 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (25 bp):
TTATCGATGGCTTTGTGCCGATCTG
Found at i:31387154 original size:50 final size:50
Alignment explanation
Indices: 31387019--31387156 Score: 222
Period size: 50 Copynumber: 2.8 Consensus size: 50
31387009 TCTATTATCA
* *
31387019 ATGGCTTTGTGCCGATCTGTTATCGATGGCTTTGTACCGATATGATATTG
1 ATGGCTATGTGCCGATCTGTTATCGATGGCTTTGTGCCGATATGATATTG
* *
31387069 ATGGCAATGTGCCGATCTGTTATCGATGGCATTGTGCCGATATGATATTG
1 ATGGCTATGTGCCGATCTGTTATCGATGGCTTTGTGCCGATATGATATTG
* *
31387119 ATGGCTATGTGCTGATCTGTTATCGAAGGCTTTGTGCC
1 ATGGCTATGTGCCGATCTGTTATCGATGGCTTTGTGCC
31387157 AAGTGTATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (50 bp):
ATGGCTATGTGCCGATCTGTTATCGATGGCTTTGTGCCGATATGATATTG
Found at i:31390031 original size:26 final size:27
Alignment explanation
Indices: 31389991--31390064 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 27
31389981 CCTATAGGGT
*
31389991 AGAATTATTGAAATACCCTTGGTTTAC
1 AGAATTACTGAAATACCCTTGGTTTAC
*
31390018 AGAATTACTG-AATACTCTTGGTTTAC
1 AGAATTACTGAAATACCCTTGGTTTAC
* **
31390044 AAAATTACCAAAATACCCTTG
1 AGAATTACTGAAATACCCTTG
31390065 ATTTGGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 22 0.55
27 18 0.45
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (27 bp):
AGAATTACTGAAATACCCTTGGTTTAC
Found at i:31390074 original size:27 final size:27
Alignment explanation
Indices: 31390044--31390335 Score: 207
Period size: 27 Copynumber: 10.8 Consensus size: 27
31390034 CTTGGTTTAC
31390044 AAAATTACCAAAATACCCTTGATTTGG
1 AAAATTACCAAAATACCCTTGATTTGG
* ** *
31390071 AAAATTAGCAAAATACCC-CCAGTTTGT
1 AAAATTACCAAAATACCCTTGA-TTTGG
* * **
31390098 AAAATTACCCAAATACCCCT-AGTTTAT
1 AAAATTACCAAAATACCCTTGA-TTTGG
*
31390125 AAAATTACCAAAATACCCCTGATTTGTG
1 AAAATTACCAAAATACCCTTGATTTG-G
** * *
31390153 -AAATTACTGAAATACCCTCGATTTGT
1 AAAATTACCAAAATACCCTTGATTTGG
* * *
31390179 AAAATTACCAACATACCCCTAATTTGG
1 AAAATTACCAAAATACCCTTGATTTGG
* *
31390206 AAAATTATCGAAATACCCTTGATTTGG
1 AAAATTACCAAAATACCCTTGATTTGG
* **
31390233 AAAATTA-TAGAAATACCCTTGATTTAC
1 AAAATTACCA-AAATACCCTTGATTTGG
* **
31390260 AAAATTA-CAGAAATACCATTGACTTTCA
1 AAAATTACCA-AAATACCCTTGA-TTTGG
* ** * *
31390288 AAAATTACAAAAATACAATTGGTTTGC
1 AAAATTACCAAAATACCCTTGATTTGG
* * *
31390315 AAAATTATCGAAATACTCTTG
1 AAAATTACCAAAATACCCTTG
31390336 GTCTGTAGAT
Statistics
Matches: 211, Mismatches: 46, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.00
27 188 0.89
28 21 0.10
29 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGATTTGG
Found at i:31390249 original size:54 final size:53
Alignment explanation
Indices: 31390043--31390335 Score: 232
Period size: 54 Copynumber: 5.4 Consensus size: 53
31390033 TCTTGGTTTA
* * *
31390043 CAAAATTACCAAAATACCCTTGATTTGGAAAATTAGCAAAATACCCC-CAGTTTG
1 CAAAATTA-CGAAATACCCTTGATTTGGAAAATTACCAAAATACCCCTGA-TTTG
* * * **
31390097 TAAAATTACCCAAATACCCCT-AGTTTATAAAATTACCAAAATACCCCTGATTTG
1 CAAAATTA-CGAAATACCCTTGA-TTTGGAAAATTACCAAAATACCCCTGATTTG
** * * * *
31390151 TGAAATTACTGAAATACCCTCGATTTGTAAAATTACCAACATACCCCTAATTTG
1 CAAAATTAC-GAAATACCCTTGATTTGGAAAATTACCAAAATACCCCTGATTTG
* * * *
31390205 GAAAATTATCGAAATACCCTTGATTTGGAAAATTA-TAGAAATACCCTTGATTTA
1 CAAAATTA-CGAAATACCCTTGATTTGGAAAATTACCA-AAATACCCCTGATTTG
* ** * *** *
31390259 CAAAATTACAGAAATACCATTGACTTTCAAAAATTACAAAAATACAATTGGTTTG
1 CAAAATTAC-GAAATACCCTTGA-TTTGGAAAATTACCAAAATACCCCTGATTTG
*
31390314 CAAAATTATCGAAATACTCTTG
1 CAAAATTA-CGAAATACCCTTG
31390336 GTCTGTAGAT
Statistics
Matches: 195, Mismatches: 34, Indels: 19
0.79 0.14 0.08
Matches are distributed among these distances:
53 4 0.02
54 146 0.75
55 43 0.22
56 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (53 bp):
CAAAATTACGAAATACCCTTGATTTGGAAAATTACCAAAATACCCCTGATTTG
Found at i:31390251 original size:81 final size:81
Alignment explanation
Indices: 31390039--31390276 Score: 272
Period size: 81 Copynumber: 2.9 Consensus size: 81
31390029 ATACTCTTGG
* *
31390039 TTTACAAAATTACCAAAATACCCTTGATTTGGAAAATTAGC-A-AAATACCC-CCAGTTTGTAAA
1 TTTAGAAAATTACCAAAATACCCTTGATTTGGAAAATTA-CTAGAAATACCCTCGA-TTTGTAAA
*
31390101 ATTACCCAAATACCCCTAG
64 ATTA-CCAAATACCCCTAA
* *
31390120 TTTATAAAATTACCAAAATACCCCTGATTTGTG-AAATTACT-GAAATACCCTCGATTTGTAAAA
1 TTTAGAAAATTACCAAAATACCCTTGATTTG-GAAAATTACTAGAAATACCCTCGATTTGTAAAA
31390183 TTACCAACATACCCCTAA
65 TTACCAA-ATACCCCTAA
* * * * **
31390201 TTTGGAAAATTATCGAAATACCCTTGATTTGGAAAATTA-TAGAAATACCCTTGATTTACAAAAT
1 TTTAGAAAATTACCAAAATACCCTTGATTTGGAAAATTACTAGAAATACCCTCGATTTGTAAAAT
*
31390265 TACAGAAATACC
66 TAC-CAAATACC
31390277 ATTGACTTTC
Statistics
Matches: 136, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
80 7 0.05
81 124 0.91
82 5 0.04
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (81 bp):
TTTAGAAAATTACCAAAATACCCTTGATTTGGAAAATTACTAGAAATACCCTCGATTTGTAAAAT
TACCAAATACCCCTAA
Found at i:31390318 original size:55 final size:54
Alignment explanation
Indices: 31390200--31390330 Score: 147
Period size: 55 Copynumber: 2.4 Consensus size: 54
31390190 CATACCCCTA
* * ** * * **
31390200 ATTTGGAAAATTATCGAAATACCCTTGATTTGGAAAATTATAGAAATACCCTTG
1 ATTTGCAAAATTATCGAAATACCATTGATTTCAAAAATTACAAAAATACAATTG
*
31390254 ATTTACAAAATTA-CAGAAATACCATTGACTTTCAAAAATTACAAAAATACAATTG
1 ATTTGCAAAATTATC-GAAATACCATTGA-TTTCAAAAATTACAAAAATACAATTG
*
31390309 GTTTGCAAAATTATCGAAATAC
1 ATTTGCAAAATTATCGAAATAC
31390331 TCTTGGTCTG
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
53 1 0.02
54 23 0.37
55 38 0.60
56 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (54 bp):
ATTTGCAAAATTATCGAAATACCATTGATTTCAAAAATTACAAAAATACAATTG
Found at i:31390337 original size:27 final size:26
Alignment explanation
Indices: 31390000--31390335 Score: 185
Period size: 27 Copynumber: 12.5 Consensus size: 26
31389990 TAGAATTATT
* * *
31390000 GAAATACCCTTGGTTTACAGAATTAC
1 GAAATACCCTTGATTTGCAAAATTAC
* * *
31390026 TG-AATACTCTTGGTTTACAAAATTACC
1 -GAAATACCCTTGATTTGCAAAATTA-C
* *
31390053 AAAATACCCTTGATTTGGAAAATTAGC
1 GAAATACCCTTGATTTGCAAAATTA-C
* ** *
31390080 AAAATACCC-CCAGTTTGTAAAATTACC
1 GAAATACCCTTGA-TTTGCAAAATTA-C
* * **
31390107 CAAATACCCCT-AGTTTATAAAATTACC
1 GAAATACCCTTGA-TTTGCAAAATTA-C
* * **
31390134 AAAATACCCCTGATTTGTGAAATTAC
1 GAAATACCCTTGATTTGCAAAATTAC
* *
31390160 TGAAATACCCTCGATTTGTAAAATTAC
1 -GAAATACCCTTGATTTGCAAAATTAC
* * * *
31390187 CAACATACCCCTAATTTGGAAAATTATC
1 GAA-ATACCCTTGATTTGCAAAATTA-C
* *
31390215 GAAATACCCTTGATTTGGAAAATTATA
1 GAAATACCCTTGATTTGCAAAATTA-C
*
31390242 GAAATACCCTTGATTTACAAAATTAC
1 GAAATACCCTTGATTTGCAAAATTAC
*
31390268 AGAAATACCATTGACTTT-CAAAAATTAC
1 -GAAATACCCTTGA-TTTGC-AAAATTAC
* ** *
31390296 AAAAATACAATTGGTTTGCAAAATTATC
1 -GAAATACCCTTGATTTGCAAAATTA-C
*
31390324 GAAATACTCTTG
1 GAAATACCCTTG
31390336 GTCTGTAGAT
Statistics
Matches: 255, Mismatches: 41, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
26 25 0.10
27 202 0.79
28 28 0.11
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (26 bp):
GAAATACCCTTGATTTGCAAAATTAC
Found at i:31390659 original size:41 final size:41
Alignment explanation
Indices: 31390600--31390719 Score: 145
Period size: 41 Copynumber: 2.9 Consensus size: 41
31390590 GGATGAAGAA
* *
31390600 ATTGAGGATCGCAAGGTTGCTTGACGATCC-TGGATCCAACG
1 ATTGAGGATCGCATGGTTGCTTGACGA-CCGTGGATCCAACC
* *
31390641 ATTGAGGATCGCATGGTTGTTTGATGACCGTGGATCC-ACC
1 ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAACC
* * *
31390681 AGTTAAAGATCGCATGGTTACTTGACGACCGTGGATCCA
1 A-TTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCA
31390720 TCGGTGGCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
40 5 0.07
41 62 0.93
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACCGTGGATCCAACC
Found at i:31390901 original size:25 final size:25
Alignment explanation
Indices: 31390867--31391007 Score: 130
Period size: 25 Copynumber: 5.8 Consensus size: 25
31390857 AATTATTCTA
*
31390867 TTATCAATGGCTTTGTGCCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
*
31390892 TTATCGATGGCTTTGTACCGA----
1 TTATCGATGGCTTTGTGCCGATCTG
* ** *
31390913 -TATTGATGGCAATGTGTCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
* *
31390937 TTATCGATGGCATTGTGCCGATATG
1 TTATCGATGGCTTTGTGCCGATCTG
* * *
31390962 ATATTGATGGCTATGTGCCGATCTG
1 TTATCGATGGCTTTGTGCCGATCTG
* *
31390987 TTATCGATGCCTTTGTACCGA
1 TTATCGATGGCTTTGTGCCGA
31391008 GCGTATTATC
Statistics
Matches: 90, Mismatches: 21, Indels: 10
0.74 0.17 0.08
Matches are distributed among these distances:
20 15 0.17
25 75 0.83
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (25 bp):
TTATCGATGGCTTTGTGCCGATCTG
Found at i:31390986 original size:50 final size:45
Alignment explanation
Indices: 31390873--31391007 Score: 162
Period size: 50 Copynumber: 2.9 Consensus size: 45
31390863 TCTATTATCA
* *
31390873 ATGGCTTTGTGCCGATCTGTTATCGATGGCTTTGTACCGATATTG
1 ATGGCTATGTGCCGATCTGTTATCGATGGCATTGTACCGATATTG
* * *
31390918 ATGGCAATGTGTCGATCTGTTATCGATGGCATTGTGCCGATATGATATTG
1 ATGGCTATGTGCCGATCTGTTATCGATGGCATTGTACC-----GATATTG
* *
31390968 ATGGCTATGTGCCGATCTGTTATCGATGCCTTTGTACCGA
1 ATGGCTATGTGCCGATCTGTTATCGATGGCATTGTACCGA
31391008 GCGTATTATC
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
45 35 0.47
50 40 0.53
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.37
Consensus pattern (45 bp):
ATGGCTATGTGCCGATCTGTTATCGATGGCATTGTACCGATATTG
Found at i:31393708 original size:52 final size:52
Alignment explanation
Indices: 31393646--31393746 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
31393636 CGACTGCACA
*
31393646 TGTGGGAGCTTCGACGTGATGGTTAATGACATCATGAGTGCTCTCGTGGGCT
1 TGTGGGAGCTTCGACGTGATGGTTAAGGACATCATGAGTGCTCTCGTGGGCT
* * *
31393698 TGTGGGAGCTTTGACGTGATGGTTGAGGCCATCATGAGTGCTCTCGTGG
1 TGTGGGAGCTTCGACGTGATGGTTAAGGACATCATGAGTGCTCTCGTGG
31393747 TCTTAGGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.16, C:0.17, G:0.37, T:0.31
Consensus pattern (52 bp):
TGTGGGAGCTTCGACGTGATGGTTAAGGACATCATGAGTGCTCTCGTGGGCT
Found at i:31393905 original size:27 final size:27
Alignment explanation
Indices: 31393873--31393971 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 27
31393863 AATCTCATAT
* * *
31393873 CTGTAGGCTAGTATTACTAAAATATCC
1 CTGTAGGATAGAATTACTAAAATACCC
* *
31393900 CTGTAGGGTAGAATTACTGAAATACCC
1 CTGTAGGATAGAATTACTAAAATACCC
* *
31393927 CTATAGGATAGAATTACTAAAATGCCC
1 CTGTAGGATAGAATTACTAAAATACCC
* * *
31393954 CTATAGGGTAAAATTACT
1 CTGTAGGATAGAATTACT
31393972 GAATACCTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (27 bp):
CTGTAGGATAGAATTACTAAAATACCC
Found at i:31393969 original size:54 final size:53
Alignment explanation
Indices: 31393876--31393978 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
31393866 CTCATATCTG
* * * * *
31393876 TAGGCTAGTATTACTAAAATATCCCTGTAGGGTAGAATTACTGAAATACCCCTA
1 TAGGATAGAATTACTAAAATACCCCTATAGGGTAAAATTACTG-AATACCCCTA
*
31393930 TAGGATAGAATTACTAAAATGCCCCTATAGGGTAAAATTACTGAATACC
1 TAGGATAGAATTACTAAAATACCCCTATAGGGTAAAATTACTGAATACC
31393979 TATAGTTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 6 0.14
54 37 0.86
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (53 bp):
TAGGATAGAATTACTAAAATACCCCTATAGGGTAAAATTACTGAATACCCCTA
Found at i:31394049 original size:27 final size:27
Alignment explanation
Indices: 31393989--31394252 Score: 187
Period size: 27 Copynumber: 9.8 Consensus size: 27
31393979 TATAGTTTAC
* *
31393989 AAAATTACCAAAATAATCC-TGGTTTGT
1 AAAATTACCAAAAT-ACCCTTGATTTGT
* * *
31394016 AAGATTACCTAAATACCCTTGATTTTT
1 AAAATTACCAAAATACCCTTGATTTGT
* ** *
31394043 GAAATTACCAAAAT-GTCTCGATTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* *
31394069 AAAATTACCAAAATACCCCTGATTTGG
1 AAAATTACCAAAATACCCTTGATTTGT
* * *
31394096 AAAATTACCGAAATACCTTTGATTTGA
1 AAAATTACCAAAATACCCTTGATTTGT
* **
31394123 AAAATTA-CAGAAATACCCTTAATTTAC
1 AAAATTACCA-AAATACCCTTGATTTGT
* **
31394150 AAAATTA-TAGAAATACCCTTGACTTTCA
1 AAAATTACCA-AAATACCCTTGA-TTTGT
* * *
31394178 AAAATTA-CAGAAATACCTTTGGTTTGC
1 AAAATTACCA-AAATACCCTTGATTTGT
* * *
31394205 AAAATTACCGAAATACCTTTGGTTTGT
1 AAAATTACCAAAATACCCTTGATTTGT
* * *
31394232 AGATTTACCAAAACACCCTTG
1 AAAATTACCAAAATACCCTTG
31394253 TAGGGTAAAG
Statistics
Matches: 189, Mismatches: 43, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
26 25 0.13
27 141 0.75
28 23 0.12
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTGATTTGT
Found at i:31394128 original size:80 final size:81
Alignment explanation
Indices: 31393984--31394221 Score: 212
Period size: 80 Copynumber: 2.9 Consensus size: 81
31393974 ATACCTATAG
** * * * * * ***
31393984 TTTACAAAATTACCAAAATAATCCTGGTTTGTAAGATTACCTAAATACCCTTGATTTTTGAAATT
1 TTTACAAAATTACCAAAATACCCCTGATTTGAAAAATTACCGAAATACCTTTGATTTGAAAAATT
** *
31394049 ACCAAAAT-GTCTCGA
66 ACCAAAATACCCTCAA
** *
31394064 TTTGTAAAATTACCAAAATACCCCTGATTTGGAAAATTACCGAAATACCTTTGATTTGAAAAATT
1 TTTACAAAATTACCAAAATACCCCTGATTTGAAAAATTACCGAAATACCTTTGATTTGAAAAATT
*
31394129 A-CAGAAATACCCTTAA
66 ACCA-AAATACCCTCAA
* * * * * *
31394145 TTTACAAAATTA-TAGAAATACCCTTGACTTTCAAAAATTACAGAAATACCTTTGGTTTGCAAAA
1 TTTACAAAATTACCA-AAATACCCCTGA-TTTGAAAAATTACCGAAATACCTTTGATTTGAAAAA
*
31394209 TTACCGAAATACC
64 TTACCAAAATACC
31394222 TTTGGTTTGT
Statistics
Matches: 127, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
79 2 0.02
80 59 0.46
81 24 0.19
82 41 0.32
83 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (81 bp):
TTTACAAAATTACCAAAATACCCCTGATTTGAAAAATTACCGAAATACCTTTGATTTGAAAAATT
ACCAAAATACCCTCAA
Found at i:31394139 original size:54 final size:54
Alignment explanation
Indices: 31394026--31394230 Score: 207
Period size: 54 Copynumber: 3.8 Consensus size: 54
31394016 AAGATTACCT
*** * ** * *
31394026 AAATACCCTTGATTTTTGAAATTACCAAAATGTC-TCGATTTGTAAAATTACCA-
1 AAATACCCTTGATTTGCAAAATTACCGAAATACCTTTGATTTGAAAAATTA-CAG
* *
31394079 AAATACCCCTGATTTGGAAAATTACCGAAATACCTTTGATTTGAAAAATTACAG
1 AAATACCCTTGATTTGCAAAATTACCGAAATACCTTTGATTTGAAAAATTACAG
* * ** * *
31394133 AAATACCCTTAATTTACAAAATTATAGAAATACCCTTGACTTTCAAAAATTACAG
1 AAATACCCTTGATTTGCAAAATTACCGAAATACCTTTGA-TTTGAAAAATTACAG
* * *
31394188 AAATACCTTTGGTTTGCAAAATTACCGAAATACCTTTGGTTTG
1 AAATACCCTTGATTTGCAAAATTACCGAAATACCTTTGATTTG
31394231 TAGATTTACC
Statistics
Matches: 123, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
53 29 0.24
54 49 0.40
55 45 0.37
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (54 bp):
AAATACCCTTGATTTGCAAAATTACCGAAATACCTTTGATTTGAAAAATTACAG
Found at i:31394194 original size:55 final size:54
Alignment explanation
Indices: 31394069--31394221 Score: 191
Period size: 55 Copynumber: 2.8 Consensus size: 54
31394059 CTCGATTTGT
* * * *
31394069 AAAATTACCA-AAATACCCCTGATTTGGAAAATTACCGAAATACCTTTGATTTGA
1 AAAATTA-CAGAAATACCCTTGATTTGCAAAATTACCGAAATACCCTTGATTTCA
* * **
31394123 AAAATTACAGAAATACCCTTAATTTACAAAATTATAGAAATACCCTTGACTTTCA
1 AAAATTACAGAAATACCCTTGATTTGCAAAATTACCGAAATACCCTTGA-TTTCA
* *
31394178 AAAATTACAGAAATACCTTTGGTTTGCAAAATTACCGAAATACC
1 AAAATTACAGAAATACCCTTGATTTGCAAAATTACCGAAATACC
31394222 TTTGGTTTGT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 2 0.02
54 39 0.47
55 42 0.51
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (54 bp):
AAAATTACAGAAATACCCTTGATTTGCAAAATTACCGAAATACCCTTGATTTCA
Found at i:31394250 original size:82 final size:81
Alignment explanation
Indices: 31394063--31394252 Score: 211
Period size: 82 Copynumber: 2.3 Consensus size: 81
31394053 AAATGTCTCG
* ** *
31394063 ATTTGTAAAATTACCAAAATACCCCTGATTTGGAAAATTACCGAAATACCTTTGATTTGAAAAAT
1 ATTTGTAAAATTACCAAAATACCCTTGATTTCAAAAATTACAGAAATACCTTTGATTTGAAAAAT
31394128 TACAGAAATACCCTTA
66 TACAGAAATACCCTTA
** * * *
31394144 ATTTACAAAATTA-TAGAAATACCCTTGACTTTCAAAAATTACAGAAATACCTTTGGTTTGCAAA
1 ATTTGTAAAATTACCA-AAATACCCTTGA-TTTCAAAAATTACAGAAATACCTTTGATTTGAAAA
* * *
31394208 ATTACCGAAATACCTTTG
64 ATTACAGAAATACCCTTA
* * * *
31394226 GTTTGTAGATTTACCAAAACACCCTTG
1 ATTTGTAAAATTACCAAAATACCCTTG
31394253 TAGGGTAAAG
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
80 1 0.01
81 22 0.25
82 63 0.72
83 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (81 bp):
ATTTGTAAAATTACCAAAATACCCTTGATTTCAAAAATTACAGAAATACCTTTGATTTGAAAAAT
TACAGAAATACCCTTA
Found at i:31394733 original size:50 final size:50
Alignment explanation
Indices: 31394669--31394944 Score: 489
Period size: 50 Copynumber: 5.5 Consensus size: 50
31394659 AGCAAATTAT
*
31394669 TCTGTTATCAATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
31394719 TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
*
31394769 TCTGTTATCGATGGCTTTGTGCCAATATGATATTGATGGCTATGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
* *
31394819 TCTGTTATCGATGGCTTTATGCCGATATGATATTGATGGCTATGTGTCGA
1 TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
* **
31394869 TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGACTATGTATCGA
1 TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
31394919 TCTGTTATCGATGGCTTTGTGCCGAT
1 TCTGTTATCGATGGCTTTGTGCCGAT
31394945 CGTATTATCG
Statistics
Matches: 218, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 218 1.00
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (50 bp):
TCTGTTATCGATGGCTTTGTGCCGATATGATATTGATGGCTATGTGCCGA
Found at i:31394945 original size:25 final size:25
Alignment explanation
Indices: 31394669--31394954 Score: 311
Period size: 25 Copynumber: 11.4 Consensus size: 25
31394659 AGCAAATTAT
*
31394669 TCTGTTATCAATGGCTTTGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
* * * *
31394694 TATGATATTGATGGCTATGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
31394719 TCTGTTATCGATGGCTTTGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
* * * *
31394744 TATGATATTGATGGCTATGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
*
31394769 TCTGTTATCGATGGCTTTGTGCCAA
1 TCTGTTATCGATGGCTTTGTGCCGA
* * * *
31394794 TATGATATTGATGGCTATGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
*
31394819 TCTGTTATCGATGGCTTTATGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
* * * * *
31394844 TATGATATTGATGGCTATGTGTCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
31394869 TCTGTTATCGATGGCTTTGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
* * * * * **
31394894 TATGATATTGATGACTATGTATCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
31394919 TCTGTTATCGATGGCTTTGTGCCGA
1 TCTGTTATCGATGGCTTTGTGCCGA
*
31394944 TCGTATTATCG
1 TC-TGTTATCG
31394955 TAATAATGTC
Statistics
Matches: 206, Mismatches: 54, Indels: 1
0.79 0.21 0.00
Matches are distributed among these distances:
25 199 0.97
26 7 0.03
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (25 bp):
TCTGTTATCGATGGCTTTGTGCCGA
Found at i:31400824 original size:43 final size:41
Alignment explanation
Indices: 31400746--31400826 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 41
31400736 GTTGAAATTA
*
31400746 CGTGTAAGACCATATCTGGATATGGCATCGATATGAGACTT
1 CGTGTAAGACCATAGCTGGATATGGCATCGATATGAGACTT
*
31400787 CGTGTAAGACCATAGCTGGGCTATTGGCATCGATATGAGA
1 CGTGTAAGACCATAGCT-GGATA-TGGCATCGATATGAGA
31400827 TCCCATGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 16 0.44
42 4 0.11
43 16 0.44
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (41 bp):
CGTGTAAGACCATAGCTGGATATGGCATCGATATGAGACTT
Found at i:31400836 original size:43 final size:42
Alignment explanation
Indices: 31400748--31400854 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 42
31400738 TGAAATTACG
* *
31400748 TGTAAGACCATATCT-GGATATGGCATCGATATGAGACTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGACTCCA
* *
31400789 TGTAAGACCATAGCTGGGCTATTGGCATCGATATGAGA-TCCCA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGACT-CCA
*
31400832 TGTAAGACCTTATCTGGGATATG
1 TGTAAGACCATATCTGGGATATG
31400855 ACATTGGCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
41 14 0.25
42 7 0.12
43 35 0.62
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGACTCCA
Found at i:31400969 original size:20 final size:20
Alignment explanation
Indices: 31400941--31400987 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
31400931 CAGCAAAGTT
31400941 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTATGG
* *
31400961 TATGTTGTGAAAGATTATGG
1 TAAGTTGTGAAAGACTATGG
31400981 TAAGTTG
1 TAAGTTG
31400988 CAAGTTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTATGG
Found at i:31411811 original size:43 final size:42
Alignment explanation
Indices: 31411742--31411822 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
31411732 AATGGCAACA
** *
31411742 TCCCAGACGTAGTCTTACTTGTAATCAAATATCGATGCCTCTG
1 TCCCAGACGTAGTCTTACACGAAATCAAATAT-GATGCCTCTG
31411785 TCCCAGACAG-AGTCTTACACGAAATCAAATATGATGCC
1 TCCCAGAC-GTAGTCTTACACGAAATCAAATATGATGCC
31411823 AACATCCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 6 0.18
43 27 0.79
44 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (42 bp):
TCCCAGACGTAGTCTTACACGAAATCAAATATGATGCCTCTG
Found at i:31417320 original size:49 final size:49
Alignment explanation
Indices: 31417263--31417450 Score: 270
Period size: 49 Copynumber: 3.8 Consensus size: 49
31417253 TAGACAAGGC
* *
31417263 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * *
31417312 TATCTGGTACACGTAGTAGCCTGCACTTAGTATTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-T
* *
31417363 TATC-GAGTACGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTG-GTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
*
31417412 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
31417451 CCTGACCTCA
Statistics
Matches: 124, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
49 77 0.62
50 8 0.06
51 39 0.31
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
Found at i:31417403 original size:100 final size:100
Alignment explanation
Indices: 31417269--31417451 Score: 330
Period size: 100 Copynumber: 1.8 Consensus size: 100
31417259 AGGCTATCTG
* *
31417269 GTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCTGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
*
31417334 GCACTTAGTATTACACACGTGATCGAAGTTATCGA
66 GCACTTAGTACTACACACGTGATCGAAGTTATCGA
*
31417369 GTACGCGTAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
31417434 GCACTTAGTACTACACAC
66 GCACTTAGTACTACACAC
31417452 CTGACCTCAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (100 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
GCACTTAGTACTACACACGTGATCGAAGTTATCGA
Found at i:31417720 original size:27 final size:27
Alignment explanation
Indices: 31417680--31417733 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
31417670 AGGTACAACC
* *
31417680 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
31417707 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
31417734 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:31420843 original size:40 final size:40
Alignment explanation
Indices: 31420769--31420940 Score: 215
Period size: 40 Copynumber: 4.3 Consensus size: 40
31420759 TGATAACCGA
* *
31420769 CTAAGATCCGAAGGCATTCATGCGAGTTGCTATATCCGGG
1 CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
* * * *
31420809 CTATGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGG
1 CTAAGACCCGAAGGCATTTATGCGAGTTG-CTATATCCGGG
* *
31420849 CTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATTCGGG
1 CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
* *
31420889 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCC-GG
1 CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
31420928 CTAA-ATCCCGAAG
1 CTAAGA-CCCGAAG
31420941 ATACTTGGGT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 97 0.84
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
Found at i:31438153 original size:14 final size:15
Alignment explanation
Indices: 31438136--31438164 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31438126 TCACGAAAAT
31438136 TTCACACAT-ATAAA
1 TTCACACATAATAAA
31438150 TTCACACATAATAAA
1 TTCACACATAATAAA
31438165 CACAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:31443155 original size:39 final size:40
Alignment explanation
Indices: 31443110--31443294 Score: 187
Period size: 40 Copynumber: 4.7 Consensus size: 40
31443100 GCTCCTCGTT
* * * *
31443110 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
*
31443150 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
* *
31443189 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
* * * * * * *
31443229 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAATAAC-TCGCA
* *
31443270 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
31443295 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
39 37 0.30
40 77 0.62
41 11 0.09
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
Found at i:31451034 original size:39 final size:40
Alignment explanation
Indices: 31450989--31451173 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
31450979 GCTCCTCGTT
* * *
31450989 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
31451029 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
31451068 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
31451108 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
31451149 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
31451174 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:31451089 original size:40 final size:39
Alignment explanation
Indices: 31450956--31451173 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
31450946 AAATCACGTA
* * **
31450956 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
31450995 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
31451034 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
31451074 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
31451114 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
31451154 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
31451174 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:31459809 original size:93 final size:93
Alignment explanation
Indices: 31459695--31459866 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
31459685 CGCCCATAAG
* * *
31459695 CGAACTCGTACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGAACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
*
31459760 ACGAGTTTGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
31459788 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
31459853 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
31459867 TCAACCATCC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:31459863 original size:46 final size:46
Alignment explanation
Indices: 31459688--31459863 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
31459678 TGTAACCCGC
* * * *
31459688 CCATAAGCGAACTCGTACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * * *
31459734 CCATAAGTGAACTCGAACTCAACTCAACGAGTTTGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
31459784 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
31459827 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
31459864 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.57
47 27 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:31465794 original size:482 final size:482
Alignment explanation
Indices: 31464889--31465852 Score: 1757
Period size: 482 Copynumber: 2.0 Consensus size: 482
31464879 ATCTGAATTA
31464889 TCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAAA
1 TCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAAA
**
31464954 GCTTCTTGCAATTTCCTCCAAAATCGCGAGGTGAATCTCGGATCTCTATCCGATTCGATAGAAAT
66 GCTTCTTGCAATTTCCTCCAAAATCGCGAGGTGAATCTCGGATCTCTATCCGACACGATAGAAAT
*
31465019 AGGTACCCCGTGTAATCTCACAATCTGAGAAACGTACAATTCAACTAGTCTATCCAATGAAAAAT
131 AGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCAACTAGTCTATCCAATGAAAAAT
* *
31465084 CCATACACACGGGGATAAAGTGAGCCTACTTAGTCAGTCTATCGACAACAACCCAAATCGCATCC
196 CCATACACACGGGGATAAAGTGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCATCC
31465149 TTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
261 TTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
*
31465214 GGGTATCATGATCGGCTGAAGTAATCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTTGACATA
326 GGGGATCATGATCGGCTGAAGTAATCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTTGACATA
31465279 TTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCAACGTTTC
391 TTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCAACGTTTC
*
31465344 AAATCGTTGTACATTTTCGTACTCCCC
456 AAATCGTTGTACATTTTCGTACCCCCC
*
31465371 TCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCACA
1 TCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAAA
31465436 GCTTCTTGCAATTTCCTCCAAAATCGCGAGGTGAATCTCGGATCTCTATCCGACACGATAGAAAT
66 GCTTCTTGCAATTTCCTCCAAAATCGCGAGGTGAATCTCGGATCTCTATCCGACACGATAGAAAT
** *
31465501 AGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCGGCTAGTTTATCCAATGAAAAAT
131 AGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCAACTAGTCTATCCAATGAAAAAT
* * *
31465566 CCGTACGCACGGGGATAAGGTGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCATCC
196 CCATACACACGGGGATAAAGTGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCATCC
*
31465631 TTCTTACTTGTTGACCATGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
261 TTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
**
31465696 GGGGATCATGATCGGCTGAAGTCCTCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTTGACATA
326 GGGGATCATGATCGGCTGAAGTAATCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTTGACATA
* *
31465761 TTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAATCGACGTTTC
391 TTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCAACGTTTC
31465826 AAATCGTTGTACATTTTCGTACCCCCC
456 AAATCGTTGTACATTTTCGTACCCCCC
31465853 GGGTGAATTG
Statistics
Matches: 463, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
482 463 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (482 bp):
TCCGCTCAGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAAA
GCTTCTTGCAATTTCCTCCAAAATCGCGAGGTGAATCTCGGATCTCTATCCGACACGATAGAAAT
AGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCAACTAGTCTATCCAATGAAAAAT
CCATACACACGGGGATAAAGTGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCATCC
TTCTTACTTGTTGACAATGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
GGGGATCATGATCGGCTGAAGTAATCCTGAAGGCACTTGATGTTCCGCTTTCACTTGTTGACATA
TTAAACATCTCGAAACAAAGTCGGAGATGTCTCGTTTCATACCATGCCACCAAAACCAACGTTTC
AAATCGTTGTACATTTTCGTACCCCCC
Found at i:31480428 original size:6 final size:6
Alignment explanation
Indices: 31480419--31480447 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31480409 ACTGATACTA
31480419 CAAAAT CAAAAT CAAAAT CAAAAT CAAAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAA
31480448 CTTATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (6 bp):
CAAAAT
Found at i:31482590 original size:14 final size:15
Alignment explanation
Indices: 31482565--31482593 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
31482555 AATTTAGAAT
31482565 TTTTTCTATGTTTTC
1 TTTTTCTATGTTTTC
31482580 TTTTTCT-TGTTTTC
1 TTTTTCTATGTTTTC
31482594 AGAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.03, C:0.14, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTTTCTATGTTTTC
Found at i:31490060 original size:71 final size:71
Alignment explanation
Indices: 31489982--31490125 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
31489972 ATGGCATATG
31489982 TGATTTTCGCATGATTTATAAAATGTGAAATATTGATATAAATTATATATATGTGATTTGCATGT
1 TGATTTTCGCATGATTTATAAAATGTGAAATATTGATATAAATTATATATATGTGATTTGCATGT
31490047 TCAGCA
66 TCAGCA
31490053 TGATTTTCGCATGATTTATAAAATGTGAAATATTGATATAAATTATATATATGTGATTTGCATGT
1 TGATTTTCGCATGATTTATAAAATGTGAAATATTGATATAAATTATATATATGTGATTTGCATGT
31490118 TCAGCA
66 TCAGCA
31490124 TG
1 TG
31490126 CCTATGTGAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (71 bp):
TGATTTTCGCATGATTTATAAAATGTGAAATATTGATATAAATTATATATATGTGATTTGCATGT
TCAGCA
Found at i:31490182 original size:38 final size:38
Alignment explanation
Indices: 31490139--31490228 Score: 153
Period size: 38 Copynumber: 2.4 Consensus size: 38
31490129 ATGTGATTTT
* **
31490139 AAGTGAAAAGTGATATAATGAGCATGTCTCACATGTTA
1 AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
31490177 AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
1 AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
31490215 AAGTGAAAAGTGAT
1 AAGTGAAAAGTGAT
31490229 TTTTAAGTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.24
Consensus pattern (38 bp):
AAGTGAAAAGTGATATAATGAGCATGTCTCACAGGCCA
Found at i:31490238 original size:18 final size:19
Alignment explanation
Indices: 31490215--31490250 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31490205 TCACAGGCCA
31490215 AAGTG-AAAAGTGATTTTT
1 AAGTGAAAAAGTGATTTTT
31490233 AAGTGAAAAAGTGATTTT
1 AAGTGAAAAAGTGATTTT
31490251 GTGGCCATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
AAGTGAAAAAGTGATTTTT
Found at i:31490448 original size:47 final size:47
Alignment explanation
Indices: 31490339--31490448 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
31490329 TATCCACAAC
* * * *
31490339 ATGTGGTAGTTTATCTGCGAAAGTAGTGGCTTGTCCACAATTTTATT
1 ATGTGGTAGTTTATCTACAAAAGTAGTGACTTGTCCACAATTTGATT
* * * * *
31490386 ATGTGGCAATATATCTACAAAAGTGGTGACTTGTCCATAATTTGATT
1 ATGTGGTAGTTTATCTACAAAAGTAGTGACTTGTCCACAATTTGATT
31490433 ATGTGGTAGTTTATCT
1 ATGTGGTAGTTTATCT
31490449 GCATTACCAT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (47 bp):
ATGTGGTAGTTTATCTACAAAAGTAGTGACTTGTCCACAATTTGATT
Found at i:31490860 original size:7 final size:7
Alignment explanation
Indices: 31490850--31490882 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31490840 TTTTGGTTTG
31490850 TGGACTT
1 TGGACTT
31490857 TGGACTT
1 TGGACTT
31490864 TGGACTT
1 TGGACTT
31490871 TGGACTT
1 TGGACTT
31490878 TGGAC
1 TGGAC
31490883 ATTACTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.39
Consensus pattern (7 bp):
TGGACTT
Found at i:31497540 original size:8 final size:8
Alignment explanation
Indices: 31497527--31497552 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31497517 TTATGAGTGA
31497527 TGACATTT
1 TGACATTT
31497535 TGACATTT
1 TGACATTT
31497543 TGACATTT
1 TGACATTT
31497551 TG
1 TG
31497553 GTGCTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (8 bp):
TGACATTT
Found at i:31502592 original size:39 final size:40
Alignment explanation
Indices: 31502497--31502758 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
31502487 TTGAATGATG
*
31502497 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
31502535 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
31502576 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
31502615 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
31502654 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
31502693 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
31502732 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
31502759 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:31511733 original size:39 final size:41
Alignment explanation
Indices: 31511638--31511821 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
31511628 TTGAATGATG
*
31511638 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
31511677 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
31511717 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
31511756 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
31511796 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31511822 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 61 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:31511773 original size:79 final size:81
Alignment explanation
Indices: 31511638--31511821 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
31511628 TTGAATGATG
31511638 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
31511701 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
31511716 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
31511777 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* *
31511796 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31511822 AACGAGGAGC
Statistics
Matches: 92, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.63
80 23 0.25
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:31511843 original size:79 final size:79
Alignment explanation
Indices: 31511690--31511854 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
31511680 GGACTAAGAT
* ** *
31511690 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
31511755 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
31511769 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
31511831 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
31511848 CCGAAGG
1 CCGAAGG
31511855 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.62
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:31515214 original size:6 final size:6
Alignment explanation
Indices: 31515203--31515250 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
31515193 ACTTTTAGAC
* *
31515203 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGAAT TTTATT TTTATT TTTA
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG--T TTTAGT TTTAGT TTTA
31515251 TTTATTAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 34 0.87
8 5 0.13
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (6 bp):
TTTAGT
Found at i:31515226 original size:18 final size:19
Alignment explanation
Indices: 31515188--31515250 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
31515178 AAATTATTTG
*
31515188 TTTAGACTTTTAGACTTTAGT
1 TTTAGA-TTTTAG-TTTTAGT
31515209 TTTAG-TTTTAGTTTTAGT
1 TTTAGATTTTAGTTTTAGT
* *
31515227 TTTAGAATTTTATTTTTATT
1 TTTAG-ATTTTAGTTTTAGT
31515247 TTTA
1 TTTA
31515251 TTTATTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 11 0.30
19 6 0.16
20 15 0.41
21 5 0.14
ACGTcount: A:0.22, C:0.03, G:0.11, T:0.63
Consensus pattern (19 bp):
TTTAGATTTTAGTTTTAGT
Found at i:31517148 original size:26 final size:26
Alignment explanation
Indices: 31517112--31517163 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31517102 GAATCCAAAG
31517112 TAAGGATCAAGGAAGATTTTGAAGAA
1 TAAGGATCAAGGAAGATTTTGAAGAA
31517138 TAAGGATCAAGGAAGATTTTGAAGAA
1 TAAGGATCAAGGAAGATTTTGAAGAA
31517164 CAAATTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.27, T:0.23
Consensus pattern (26 bp):
TAAGGATCAAGGAAGATTTTGAAGAA
Found at i:31518563 original size:27 final size:27
Alignment explanation
Indices: 31518521--31518620 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
31518511 TTGTTCTTTG
*
31518521 CCACAAAGACAATTCTTTCATAATGCT
1 CCACAAAGACATTTCTTTCATAATGCT
* * ** *
31518548 CCGCAAAGGCATTTCTTTTGTGATG-T
1 CCACAAAGACATTTCTTTCATAATGCT
*
31518574 GCCACAAAGACATTTCTTTCATAATGCA
1 -CCACAAAGACATTTCTTTCATAATGCT
* *
31518602 CCAAAAAGGCATTTCTTTC
1 CCACAAAGACATTTCTTTC
31518621 TTGACATGTT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
26 1 0.02
27 56 0.98
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (27 bp):
CCACAAAGACATTTCTTTCATAATGCT
Found at i:31523530 original size:85 final size:85
Alignment explanation
Indices: 31523431--31523610 Score: 288
Period size: 85 Copynumber: 2.1 Consensus size: 85
31523421 ATAGAAATGG
* *
31523431 AAATGAAAATTTGCAATCCTATATGGATTACTTAAAAACTGATGGGAAGAATAAGTTTATATTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAAACAGATGGGAAGAATAAGTTTATATTTT
* *
31523496 TGGACTATTTTGAAGCTTGA
66 TGGACTAATTTGAAGCCTGA
* * *
31523516 AAATGAAAATTTGCAATCTTATATAGATTACTTAAAAACAGATTGGAAGAATAAGTTTATGTTTT
1 AAATGAAAATTTGCAATCCTATATAGATTACTTAAAAACAGATGGGAAGAATAAGTTTATATTTT
*
31523581 TGGACTAATTTGAAGCCTGG
66 TGGACTAATTTGAAGCCTGA
31523601 AAATGAAAAT
1 AAATGAAAAT
31523611 AAACTATTCG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (85 bp):
AAATGAAAATTTGCAATCCTATATAGATTACTTAAAAACAGATGGGAAGAATAAGTTTATATTTT
TGGACTAATTTGAAGCCTGA
Found at i:31526118 original size:50 final size:50
Alignment explanation
Indices: 31525990--31526230 Score: 268
Period size: 50 Copynumber: 4.8 Consensus size: 50
31525980 GATAATAACA
* ** * * * **
31525990 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * ** * *
31526040 -GCCAATGCCATATTCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * **
31526089 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
31526139 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
31526189 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31526231 TTACCCAAAT
Statistics
Matches: 162, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
49 38 0.23
50 124 0.77
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31527338 original size:12 final size:12
Alignment explanation
Indices: 31527323--31527349 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31527313 GAACGAAATT
31527323 TTCAGGAAATCA
1 TTCAGGAAATCA
31527335 TTCAGGAAATCA
1 TTCAGGAAATCA
31527347 TTC
1 TTC
31527350 TGTGAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (12 bp):
TTCAGGAAATCA
Found at i:31532915 original size:21 final size:22
Alignment explanation
Indices: 31532886--31532926 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31532876 AATTTTGAAA
31532886 AAAGAAAAAAAGAAAAGAATTG
1 AAAGAAAAAAAGAAAAGAATTG
*
31532908 AAAG-AAAAAGGAAAAGAAT
1 AAAGAAAAAAAGAAAAGAAT
31532927 GAATAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (22 bp):
AAAGAAAAAAAGAAAAGAATTG
Found at i:31543019 original size:29 final size:28
Alignment explanation
Indices: 31542976--31543053 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
31542966 TCATGAGATT
31542976 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
* *
31543006 -GCACTAAGTGTGCGAGTTTACAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
31543033 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
31543054 GATTATTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.12
29 34 0.81
30 3 0.07
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:31543315 original size:174 final size:174
Alignment explanation
Indices: 31543008--31543333 Score: 501
Period size: 174 Copynumber: 1.9 Consensus size: 174
31542998 ATTGTACAGC
* * * *
31543008 ACTAAGTGTGCGAGTTTACAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTG
1 ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
* * ** *
31543073 TGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATT
66 TGCGAACCCAATATATATTTTCCACAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
31543138 TTGGACAGCGGAAAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
131 TTGGACAGCGG-AAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
* * * * *
31543183 ACTAAGTGTGTGAGTTTAAAGTGCATGGCACTGAGTGTGCGTGGGTGATTACTAAACATTATGTG
1 ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
*
31543248 TGC-AACCCAATATATATTTTCCACAAATTATTTACACGAAGGGTGCGGCTTTACCGAGTCAATT
66 TGCGAACCCAATATATATTTTCCACAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
31543312 TTGGACAGCGGAAAAGGTAAGT
131 TTGGACAGCGGAAAAGGTAAGT
31543334 ACCTTGAGTT
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
173 11 0.08
174 66 0.49
175 59 0.43
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (174 bp):
ACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGGTGATTACTAAACACTATGTG
TGCGAACCCAATATATATTTTCCACAAATTATTTACACGAAGGGTGCGACTTTACCGAGTCAATT
TTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGGT
Found at i:31558382 original size:14 final size:13
Alignment explanation
Indices: 31558367--31558419 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
31558357 TCTATCTTTC
31558367 TTTTCTTTAATTT
1 TTTTCTTTAATTT
*
31558380 CTTTACTTTAATTT
1 -TTTTCTTTAATTT
* *
31558394 TGTTCTTATTATTT
1 TTTTCTT-TAATTT
*
31558408 TTATCTTTAATT
1 TTTTCTTTAATT
31558420 ACTTAATGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTTCTTTAATTT
Found at i:31565027 original size:17 final size:15
Alignment explanation
Indices: 31564995--31565032 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
31564985 TGTTATTGGT
31564995 TGATTGTTGGTTGTG
1 TGATTGTTGGTTGTG
31565010 TGATTGTGTGGTT-TG
1 TGATTGT-TGGTTGTG
31565025 TG-TTGTTG
1 TGATTGTTG
31565033 AAGCGTCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 4 0.18
15 11 0.50
16 5 0.23
ACGTcount: A:0.05, C:0.00, G:0.39, T:0.55
Consensus pattern (15 bp):
TGATTGTTGGTTGTG
Found at i:31573385 original size:71 final size:70
Alignment explanation
Indices: 31573268--31573404 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 70
31573258 TCAAAGTGTT
* * *
31573268 TTTCAACTTGTTTTAAGATATTAGAAGGTTTCTAATGTTACATTGAATTTTTCGTTAAGAATTTT
1 TTTCAACTTGTTTTAACATATTAGAAGGTTTCTAACGTTACATTGAATTTTTCATTAAGAATTTT
31573333 TTGAG
66 TTGAG
*
31573338 TTTCAACTTGTTTTAACATGATTAGAAGGTTTCTAACGTTACTTTGAATTTTTCATTAAGAATTT
1 TTTCAACTTGTTTTAACAT-ATTAGAAGGTTTCTAACGTTACATTGAATTTTTCATTAAGAATTT
31573403 TT
65 TT
31573405 CGGTTTTAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 18 0.29
71 44 0.71
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (70 bp):
TTTCAACTTGTTTTAACATATTAGAAGGTTTCTAACGTTACATTGAATTTTTCATTAAGAATTTT
TTGAG
Found at i:31574065 original size:35 final size:36
Alignment explanation
Indices: 31573992--31574067 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
31573982 TGATGACTGT
* *
31573992 TGTGAAAGAAAATATGTGGATTTGTTATTCATGCCA
1 TGTGAAAGAAAATATGTGGATATGTTATTCATACCA
* *
31574028 TGTGATAGTAAAA-ATGTGGGTATGTT-TTCATACCA
1 TGTGAAAG-AAAATATGTGGATATGTTATTCATACCA
31574063 TGTGA
1 TGTGA
31574068 CAGTGATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 13 0.37
36 18 0.51
37 4 0.11
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (36 bp):
TGTGAAAGAAAATATGTGGATATGTTATTCATACCA
Found at i:31577972 original size:22 final size:21
Alignment explanation
Indices: 31577947--31577988 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
31577937 TTAAATAAAT
*
31577947 TTTAGTTAATTTAGTTTAAGTA
1 TTTAATTAATTTAG-TTAAGTA
31577969 TTTAATTAATTTAGTTAAGT
1 TTTAATTAATTTAGTTAAGT
31577989 GTTAAATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAATTAATTTAGTTAAGTA
Found at i:31589091 original size:19 final size:18
Alignment explanation
Indices: 31589066--31589110 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
31589056 TTATTTATAT
**
31589066 AAATTTTTA-AAATTTTA
1 AAATTTTTATAAAAATTA
31589083 AGAATTTTTATAAAAATTA
1 A-AATTTTTATAAAAATTA
31589102 AAATTTTTA
1 AAATTTTTA
31589111 GATAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 16 0.67
19 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AAATTTTTATAAAAATTA
Found at i:31594469 original size:29 final size:29
Alignment explanation
Indices: 31594403--31594471 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
31594393 CATACACAGT
* *
31594403 CAGATTCAAATTCGGTCTTAAGTCCTTTA
1 CAGATTCAGATTCGATCTTAAGTCCTTTA
31594432 CAGATTCAGATTCAGAT-TTAAGTCCTTTA
1 CAGATTCAGATTC-GATCTTAAGTCCTTTA
31594461 CAGATTCAGAT
1 CAGATTCAGAT
31594472 AACAGAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (29 bp):
CAGATTCAGATTCGATCTTAAGTCCTTTA
Found at i:31602254 original size:43 final size:43
Alignment explanation
Indices: 31602193--31602276 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
31602183 ATGCACAAAG
31602193 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATAT
1 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATAT
31602236 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCAT
1 TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCAT
31602277 CTCAATGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (43 bp):
TAAGCTTTGGAAGCTTAGTAAGCCATAAGAAAATAAATCATAT
Found at i:31602603 original size:41 final size:40
Alignment explanation
Indices: 31602497--31602654 Score: 113
Period size: 43 Copynumber: 3.8 Consensus size: 40
31602487 GCTCGTACAA
* * * *
31602497 ATGCC-ATATCCCAGATATGGTCTTACATGTTAACGCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG--AA-TCATATCG
* * * * *
31602539 ATGCCACTATCCTAGACAGGGTCTTATACGAATCATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATAT-CG
* **
31602580 ATGCCAATGTCCCAAACATGGTCTTACACGTTTTC-TCACTTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCAT-A--TCG
*
31602623 ATGCCAATGTCCCAGACATGGTTTTACACGAA
1 ATGCCAATGTCCCAGACATGGTCTTACACGAA
31602655 GTCACACCTT
Statistics
Matches: 91, Mismatches: 19, Indels: 12
0.75 0.16 0.10
Matches are distributed among these distances:
40 5 0.05
41 29 0.32
42 8 0.09
43 48 0.53
44 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (40 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATCG
Found at i:31602827 original size:30 final size:30
Alignment explanation
Indices: 31602768--31603092 Score: 336
Period size: 30 Copynumber: 10.7 Consensus size: 30
31602758 ATCCAATGCT
*
31602768 CAAATCAATTCGGTAATATATATGTATACATTTA
1 CAAATCAATTCGGTAATATATATCTAT--A--TA
*
31602802 CAAATCAATTTGGTAATATATATAC-ATATA
1 CAAATCAATTCGGTAATATATAT-CTATATA
* *
31602832 CAAATCAATTCGGTAATTTATATCAATATA
1 CAAATCAATTCGGTAATATATATCTATATA
* * *
31602862 CAAAT-AATTCGGCAATGTATATCCATATA
1 CAAATCAATTCGGTAATATATATCTATATA
*
31602891 CAAATCAATTC--AAATATATTTATCTATATA
1 CAAATCAATTCGGTAATATA--TATCTATATA
*
31602921 TAAATCAATTCGGTAATATATATCTATATA
1 CAAATCAATTCGGTAATATATATCTATATA
* * *
31602951 CAAATCAATTCGGCAATTTATATCAATATA
1 CAAATCAATTCGGTAATATATATCTATATA
* * *
31602981 CAAATCAATTCGGCAATGTATATCCATATA
1 CAAATCAATTCGGTAATATATATCTATATA
* *
31603011 CAAATCAATTCCGCT-ATATTTATCTATATA
1 CAAATCAATT-CGGTAATATATATCTATATA
* * *
31603041 TAAATCAATTTGGTAATATATATCCATATA
1 CAAATCAATTCGGTAATATATATCTATATA
* * *
31603071 CAAACCAATTTGGCAATATATA
1 CAAATCAATTCGGTAATATATA
31603093 AAACATATAC
Statistics
Matches: 251, Mismatches: 31, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.02
29 29 0.12
30 184 0.73
31 2 0.01
32 7 0.03
34 24 0.10
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (30 bp):
CAAATCAATTCGGTAATATATATCTATATA
Found at i:31603049 original size:120 final size:118
Alignment explanation
Indices: 31602803--31603092 Score: 472
Period size: 120 Copynumber: 2.4 Consensus size: 118
31602793 ATACATTTAC
*
31602803 AAATCAATTTGGTAATATATATACATATACAAATCAATTCGGTAATTTATATCAATATACAAATA
1 AAATCAATTTGGTAATATATAT-CATATACAAATCAATTCGGCAATTTATATCAATATACAAATA
31602868 ATTCGGCAATGTATATCCATATACAAATCAATTCAAATATATTTATCTATATAT
65 ATTCGGCAATGTATATCCATATACAAATCAATTCAAATATATTTATCTATATAT
*
31602922 AAATCAATTCGGTAATATATATCTATATACAAATCAATTCGGCAATTTATATCAATATACAAATC
1 AAATCAATTTGGTAATATATATC-ATATACAAATCAATTCGGCAATTTATATCAATATACAAAT-
***
31602987 AATTCGGCAATGTATATCCATATACAAATCAATTCCGCTATATTTATCTATATAT
64 AATTCGGCAATGTATATCCATATACAAATCAATTCAAATATATTTATCTATATAT
* * *
31603042 AAATCAATTTGGTAATATATATCCATATACAAACCAATTTGGCAATATATA
1 AAATCAATTTGGTAATATATAT-CATATACAAATCAATTCGGCAATTTATA
31603093 AAACATATAC
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
118 1 0.01
119 60 0.38
120 97 0.61
121 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (118 bp):
AAATCAATTTGGTAATATATATCATATACAAATCAATTCGGCAATTTATATCAATATACAAATAA
TTCGGCAATGTATATCCATATACAAATCAATTCAAATATATTTATCTATATAT
Found at i:31605014 original size:21 final size:20
Alignment explanation
Indices: 31604982--31605021 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
31604972 CCCGATTAAC
*
31604982 CAATGATTCACTAACCAAAA
1 CAATAATTCACTAACCAAAA
*
31605002 CAATAATTACACTTACCAAA
1 CAATAATT-CACTAACCAAA
31605022 CTTACCAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.25, G:0.03, T:0.23
Consensus pattern (20 bp):
CAATAATTCACTAACCAAAA
Found at i:31606811 original size:33 final size:33
Alignment explanation
Indices: 31606760--31606846 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
31606750 CTATCTCTTT
* * * *
31606760 TTTTGTGTTTATTGTCCCAATGTACTATCTATG
1 TTTTGTGTTTACTATCCCAATGGACTATATATG
** *
31606793 TTTTGTGTTTACTATCCCAGCGGACTATATCTG
1 TTTTGTGTTTACTATCCCAATGGACTATATATG
*
31606826 TTATGTGTTTACTATCCCAAT
1 TTTTGTGTTTACTATCCCAAT
31606847 TGGCTATCTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (33 bp):
TTTTGTGTTTACTATCCCAATGGACTATATATG
Found at i:31606859 original size:33 final size:33
Alignment explanation
Indices: 31606733--31606844 Score: 98
Period size: 33 Copynumber: 3.4 Consensus size: 33
31606723 CCCACCCATT
** * * *
31606733 TTTACTATCTAAGTGGACTATCTCTTTTTTTGTG
1 TTTACTATCCCAGCGGACTATCTC-TGTTATGTG
* * ** * * *
31606767 TTTATTGTCCCAATGTACTATCTATGTTTTGTG
1 TTTACTATCCCAGCGGACTATCTCTGTTATGTG
*
31606800 TTTACTATCCCAGCGGACTATATCTGTTATGTG
1 TTTACTATCCCAGCGGACTATCTCTGTTATGTG
31606833 TTTACTATCCCA
1 TTTACTATCCCA
31606845 ATTGGCTATC
Statistics
Matches: 62, Mismatches: 16, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
33 45 0.73
34 17 0.27
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (33 bp):
TTTACTATCCCAGCGGACTATCTCTGTTATGTG
Found at i:31608836 original size:10 final size:10
Alignment explanation
Indices: 31608823--31608855 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
31608813 TGTGATAATG
*
31608823 TGATGCTATT
1 TGATCCTATT
31608833 TGATCCTATT
1 TGATCCTATT
31608843 TGATCCTATT
1 TGATCCTATT
31608853 TGA
1 TGA
31608856 CTTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (10 bp):
TGATCCTATT
Found at i:31609565 original size:55 final size:55
Alignment explanation
Indices: 31609502--31609609 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
31609492 TGAGATTCAT
*
31609502 AAGTTAGTCGTAGCACTGAAATTACGAGAATTTATGGTTCTATTTGAATGAGCAC
1 AAGTTAGTCGGAGCACTGAAATTACGAGAATTTATGGTTCTATTTGAATGAGCAC
* * *
31609557 AAGTTAGTCGGGGCACTGAAATTACGGGAATTTGTGGTTCTATTTGAATGAGC
1 AAGTTAGTCGGAGCACTGAAATTACGAGAATTTATGGTTCTATTTGAATGAGC
31609610 GCGGAAATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (55 bp):
AAGTTAGTCGGAGCACTGAAATTACGAGAATTTATGGTTCTATTTGAATGAGCAC
Found at i:31619864 original size:25 final size:24
Alignment explanation
Indices: 31619830--31619882 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
31619820 AAGTTCAAGT
31619830 GAGCCATATCAGGAAGCTCACAAA
1 GAGCCATATCAGGAAGCTCACAAA
* *
31619854 GAGCCTATATCAGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCACAAA
31619879 GAGC
1 GAGC
31619883 TACGGTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCACAAA
Found at i:31625854 original size:20 final size:21
Alignment explanation
Indices: 31625831--31625878 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
31625821 CACTCTCTTG
*
31625831 GCTTTTATCACACTC-GCAAT
1 GCTTTTATCACACTCACCAAT
*
31625851 GCTTTTA--ACCCTCACCAAT
1 GCTTTTATCACACTCACCAAT
31625870 GCTTTTATC
1 GCTTTTATC
31625879 CGCTCATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 5 0.22
19 11 0.48
20 7 0.30
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (21 bp):
GCTTTTATCACACTCACCAAT
Found at i:31641079 original size:3 final size:3
Alignment explanation
Indices: 31641071--31641097 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31641061 CAAATGTAAA
31641071 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
31641098 CTTATGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31641458 original size:16 final size:16
Alignment explanation
Indices: 31641429--31641495 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
31641419 AAATATAAAT
*
31641429 ATAAATAGACATGAAA
1 ATAAATAAACATGAAA
*
31641445 ATAAATAAAGATG-AA
1 ATAAATAAACATGAAA
31641460 ATAAGA-ATAA-AT--AA
1 ATAA-ATA-AACATGAAA
*
31641474 ATAAATAAACATTAAA
1 ATAAATAAACATGAAA
31641490 ATAAAT
1 ATAAAT
31641496 TGCATAATGG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
13 3 0.07
14 9 0.21
15 9 0.21
16 22 0.51
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.22
Consensus pattern (16 bp):
ATAAATAAACATGAAA
Found at i:31641985 original size:6 final size:6
Alignment explanation
Indices: 31641974--31642008 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
31641964 AATCCTCTTT
31641974 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
31642009 GCAAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Done.