Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 99 of 222
Found at i:31205748 original size:27 final size:27
Alignment explanation
Indices: 31205710--31205873 Score: 131
Period size: 27 Copynumber: 6.1 Consensus size: 27
31205700 CGAGGCAAAG
*
31205710 CCTATAGGGGTATTACGGTCATTTTAC
1 CCTACAGGGGTATTACGGTCATTTTAC
* *
31205737 CCTACAGGGGTATTACGATTATTTTAC
1 CCTACAGGGGTATTACGGTCATTTTAC
* ** *
31205764 TCTACAGAAGCATTACGGTCATTTTAC
1 CCTACAGGGGTATTACGGTCATTTTAC
* * *
31205791 CCTATAGGGGCATTACGATCATTTTAC
1 CCTACAGGGGTATTACGGTCATTTTAC
* * *
31205818 CC-ATC-GAGGGTATTTCGTTTATTTTA-
1 CCTA-CAG-GGGTATTACGGTCATTTTAC
31205844 CCTA-ACGAGGGTATCT-CGGTCATTTTAC
1 CCTACA-G-GGGTAT-TACGGTCATTTTAC
31205872 CC
1 CC
31205874 ATCGAGGGTA
Statistics
Matches: 109, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
26 4 0.04
27 102 0.94
28 3 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (27 bp):
CCTACAGGGGTATTACGGTCATTTTAC
Found at i:31205879 original size:27 final size:26
Alignment explanation
Indices: 31205779--31205885 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 26
31205769 AGAAGCATTA
* *
31205779 CGGTCATTTTACCCTATAG-GGGCATT
1 CGGTCATTTTACCC-ATCGAGGGTATT
*
31205805 ACGATCATTTTACCCATCGAGGGTATTT
1 -CGGTCATTTTACCCATCGAGGGTA-TT
* * * *
31205833 CGTTTATTTTACCTAACGAGGGTATCT
1 CGGTCATTTTACCCATCGAGGGTAT-T
31205860 CGGTCATTTTACCCATCGAGGGTATT
1 CGGTCATTTTACCCATCGAGGGTATT
31205886 TTAATCCAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
26 5 0.08
27 59 0.89
28 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (26 bp):
CGGTCATTTTACCCATCGAGGGTATT
Found at i:31207346 original size:17 final size:17
Alignment explanation
Indices: 31207324--31207357 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31207314 CACAAAACCG
*
31207324 AAATGAAGAGTATACCA
1 AAATGAAGAGCATACCA
*
31207341 AAATGAGGAGCATACCA
1 AAATGAAGAGCATACCA
31207358 CTCTAGCCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.15
Consensus pattern (17 bp):
AAATGAAGAGCATACCA
Found at i:31208214 original size:100 final size:100
Alignment explanation
Indices: 31208041--31208242 Score: 350
Period size: 100 Copynumber: 2.0 Consensus size: 100
31208031 ATTGGTGAGA
* * *
31208041 ATGCTAATAGTCTGTTTCAATTGGTGGATTTAGAATTTTGCGATTACTATCGTGATTTCAAACGT
1 ATGCTAATAGTATGTTTCAATTGGTGGATTCAGAATTTTGCGATTACTATCGTGATTTAAAACGT
*
31208106 TACTTAACTTACTCTTTGACAGATGTCAAATTTAT
66 TACTTAACTTACTCTTTGACAAATGTCAAATTTAT
* *
31208141 ATGCTAATAGTATGTTTCAATTGGTGGATTCAGAATTTTGCGATTACTCTCGTGATTTAAAATGT
1 ATGCTAATAGTATGTTTCAATTGGTGGATTCAGAATTTTGCGATTACTATCGTGATTTAAAACGT
31208206 TACTTAACTTACTCTTTGACAAATGTCAAATTTAT
66 TACTTAACTTACTCTTTGACAAATGTCAAATTTAT
31208241 AT
1 AT
31208243 TTGATAAGCC
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (100 bp):
ATGCTAATAGTATGTTTCAATTGGTGGATTCAGAATTTTGCGATTACTATCGTGATTTAAAACGT
TACTTAACTTACTCTTTGACAAATGTCAAATTTAT
Found at i:31212714 original size:40 final size:40
Alignment explanation
Indices: 31212616--31212918 Score: 378
Period size: 40 Copynumber: 7.6 Consensus size: 40
31212606 TCCTCGTTCA
* * * * *
31212616 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
31212655 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
31212695 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
31212735 AATGCCTTCGGGACTTAACCCAGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
31212775 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
31212815 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
31212855 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
31212895 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
31212919 CAGCATTCAA
Statistics
Matches: 236, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.16
40 191 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:31212927 original size:41 final size:41
Alignment explanation
Indices: 31212850--31212927 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
31212840 TTAGTATCTC
* * *
31212850 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
31212891 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
31212928 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:31220437 original size:28 final size:28
Alignment explanation
Indices: 31220401--31220457 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
31220391 ATTGCACTGT
* * *
31220401 ACTGATACTGCGTTGGGCTAAGGCCCAC
1 ACTGATACTACATTGGGCTAAGACCCAC
* *
31220429 ACTGTTACTATATTGGGCTAAGACCCAC
1 ACTGATACTACATTGGGCTAAGACCCAC
31220457 A
1 A
31220458 TTGTACCGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (28 bp):
ACTGATACTACATTGGGCTAAGACCCAC
Found at i:31230969 original size:6 final size:6
Alignment explanation
Indices: 31230951--31230980 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
31230941 ATGCAATACT
31230951 TATTTA TATTTTA TATTTA TATTTA TATTT
1 TATTTA TA-TTTA TATTTA TATTTA TATTT
31230981 GGTTGGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATTTA
Found at i:31239067 original size:27 final size:27
Alignment explanation
Indices: 31238977--31239069 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
31238967 CACGATAGCT
31238977 AAGGATAGCCTTTGTGGCGAACTCTAA
1 AAGGATAGCCTTTGTGGCGAACTCTAA
* *
31239004 AAGAATAGCCTTTGTGGTGAACTCTGAA
1 AAGGATAGCCTTTGTGGCGAACTCT-AA
* * *
31239032 AGGGAT-GCCTTTGTGGCAAATTCTAA
1 AAGGATAGCCTTTGTGGCGAACTCTAA
* *
31239058 ATGGATTGCCTT
1 AAGGATAGCCTT
31239070 ACTGGTGTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 7 0.12
27 43 0.77
28 6 0.11
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AAGGATAGCCTTTGTGGCGAACTCTAA
Found at i:31240925 original size:20 final size:21
Alignment explanation
Indices: 31240873--31240926 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
31240863 AGTAGTGCAG
31240873 AGCTGCTAATAATGCAGATAA
1 AGCTGCTAATAATGCAGATAA
* *
31240894 A-CTGCCAGTAATGCAGA-AA
1 AGCTGCTAATAATGCAGATAA
*
31240913 AGCTGCTGATAATG
1 AGCTGCTAATAATG
31240927 TGGACAAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.11
20 23 0.85
21 1 0.04
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
AGCTGCTAATAATGCAGATAA
Found at i:31245053 original size:21 final size:21
Alignment explanation
Indices: 31245029--31245071 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
31245019 TCCCTAGATG
*
31245029 AACCACCTACC-TTAGAGTTAA
1 AACC-CCTACCTTTAAAGTTAA
*
31245050 AACCTCTACCTTTAAAGTTAA
1 AACCCCTACCTTTAAAGTTAA
31245071 A
1 A
31245072 GTACGCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.28
Consensus pattern (21 bp):
AACCCCTACCTTTAAAGTTAA
Found at i:31258737 original size:33 final size:33
Alignment explanation
Indices: 31258686--31258787 Score: 145
Period size: 33 Copynumber: 3.1 Consensus size: 33
31258676 TTATGGCTTA
*
31258686 AAGGA-GTAAATTATATGAAATACAATTTGGCC
1 AAGGAGGTGAATTATATGAAATACAATTTGGCC
* *
31258718 AAGGAGGTGAATTGTATGAAATACAATTTAGCC
1 AAGGAGGTGAATTATATGAAATACAATTTGGCC
*
31258751 AAAGG-GGTGAATTATATGAAATACAATTTGGCT
1 -AAGGAGGTGAATTATATGAAATACAATTTGGCC
31258784 AAGG
1 AAGG
31258788 GGACGAATGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 9 0.15
33 49 0.79
34 4 0.06
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (33 bp):
AAGGAGGTGAATTATATGAAATACAATTTGGCC
Found at i:31265210 original size:114 final size:114
Alignment explanation
Indices: 31265049--31265316 Score: 312
Period size: 114 Copynumber: 2.4 Consensus size: 114
31265039 GGAATCATTT
* * * * * * * *
31265049 TCACCATCACGAATTCTATCTCTTTCATGCCTTCTATCCCTAAAGGAAGGCTTGTCATCTTCTTC
1 TCACCGTCATGAATTCTCTCTCTTTTACGCCTTCTATCTCTATAGGAAGGCTTGCCATCTTCTTC
* *
31265114 ATCAGAAGATCTTGAACCTTCTTCTCTCC-GCCTATCCTTACCATCATCA
66 ATCAGAAGATCTAGAACCTTCTTCTC-CCTGCCTATCCTTACCACCATCA
*
31265163 TCACCGTCATGAATTCTCTCTCTTTTACGCCTTCTATCTCTATAGGAATGCTTGCCATCTTCTTC
1 TCACCGTCATGAATTCTCTCTCTTTTACGCCTTCTATCTCTATAGGAAGGCTTGCCATCTTCTTC
* * * * *
31265228 ATCAGAGGATCTAGGACGTTTTTCTCCCTGCCTATCCTTACCACCATTA
66 ATCAGAAGATCTAGAACCTTCTTCTCCCTGCCTATCCTTACCACCATCA
* * *
31265277 TCA--G-CATGAATTCTCTCACTTTCTTCG-CTCCTATCTCTAT
1 TCACCGTCATGAATTCTCTCTCTTT-TACGCCTTCTATCTCTAT
31265317 TAGCACGCTT
Statistics
Matches: 133, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
111 29 0.22
112 4 0.03
113 2 0.02
114 98 0.74
ACGTcount: A:0.21, C:0.32, G:0.10, T:0.37
Consensus pattern (114 bp):
TCACCGTCATGAATTCTCTCTCTTTTACGCCTTCTATCTCTATAGGAAGGCTTGCCATCTTCTTC
ATCAGAAGATCTAGAACCTTCTTCTCCCTGCCTATCCTTACCACCATCA
Found at i:31269022 original size:61 final size:61
Alignment explanation
Indices: 31268884--31269022 Score: 167
Period size: 63 Copynumber: 2.2 Consensus size: 61
31268874 ATTTATTCAC
* * *
31268884 ATGTGGTTCGAATGTATGTTCAAATTCTTTGAGCTGAAATTTATGTATGAATCTTATACATAT
1 ATGTGGTTCGAATATAGGTTCAAATTCCTTGAGCTGAAATTTATGTATGAA-CTTATACA-AT
* *
31268947 ATGTGGTTCGAATATAGGTTACAAATTCCTTGAGCTG-TATTTAATGTTGTGAA-TTATAC-AT
1 ATGTGGTTCGAATATAGGTT-CAAATTCCTTGAGCTGAAATTT-ATG-TATGAACTTATACAAT
31269008 ATGTGGTTCGAATAT
1 ATGTGGTTCGAATAT
31269023 GTGTTTACTA
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
61 17 0.25
63 28 0.41
64 18 0.26
65 5 0.07
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.42
Consensus pattern (61 bp):
ATGTGGTTCGAATATAGGTTCAAATTCCTTGAGCTGAAATTTATGTATGAACTTATACAAT
Found at i:31273761 original size:28 final size:28
Alignment explanation
Indices: 31273699--31273847 Score: 203
Period size: 28 Copynumber: 5.4 Consensus size: 28
31273689 TATTAAGTCT
* *
31273699 GCACACTCAGTGCTATATAATC-AACTC
1 GCACACTTAGTGCTACATAATCAAACTC
31273726 GCACACTTAGTGCTACATAATCAAACTC
1 GCACACTTAGTGCTACATAATCAAACTC
*
31273754 GCACACTTAGTGCTACATAGTC-AACTC
1 GCACACTTAGTGCTACATAATCAAACTC
*
31273781 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAATCAAACTC
* * * *
31273809 GCACACTTAGTGCTGCACAATTTAAACCC
1 GCACACTTAGTGCTACATAA-TCAAACTC
31273838 GCACACTTAG
1 GCACACTTAG
31273848 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
27 47 0.42
28 48 0.43
29 16 0.14
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25
Consensus pattern (28 bp):
GCACACTTAGTGCTACATAATCAAACTC
Found at i:31273783 original size:55 final size:55
Alignment explanation
Indices: 31273699--31273822 Score: 212
Period size: 55 Copynumber: 2.3 Consensus size: 55
31273689 TATTAAGTCT
* *
31273699 GCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACTC
1 GCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTC
* *
31273754 GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTC
31273809 GCACACTTAGTGCT
1 GCACACTTAGTGCT
31273823 GCACAATTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
GCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTC
Found at i:31276581 original size:42 final size:42
Alignment explanation
Indices: 31276522--31276604 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
31276512 AAATTCAATA
31276522 GGATAAGAACAAAAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAAGAACAAAAGTTCAAATGTTTGAATTTCAAACGTTTT
*
31276564 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAAAGTTCAAATGTTTGAATTTCAAACGTTT
31276605 CACACATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (42 bp):
GGATAAGAACAAAAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:31280776 original size:61 final size:61
Alignment explanation
Indices: 31280639--31280777 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 61
31280629 ATTTATTCAC
* * *
31280639 ATGTGGTTCGAATGTATGTTCAAATTCTTTGAGCTGAAATTTATGTATGAATCTTATACATAT
1 ATGTGGTTCGAATATAGGTTCAAATTCCTTGAGCTGAAATTTATGTATGAA-CTTATACA-AT
* * *
31280702 ATGTGGTTTGAATATAGGTTACAAATTCCTTGAGCTG-TATTTAATGTTGTGAA-TTATAC-AT
1 ATGTGGTTCGAATATAGGTT-CAAATTCCTTGAGCTGAAATTT-ATG-TATGAACTTATACAAT
31280763 ATGTGGTTCGAATAT
1 ATGTGGTTCGAATAT
31280778 GTGTTTACTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
61 16 0.24
63 27 0.41
64 18 0.27
65 5 0.08
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.42
Consensus pattern (61 bp):
ATGTGGTTCGAATATAGGTTCAAATTCCTTGAGCTGAAATTTATGTATGAACTTATACAAT
Found at i:31281567 original size:18 final size:18
Alignment explanation
Indices: 31281546--31281592 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
31281536 TATAAAATCG
*
31281546 GGAAA-AATGAAAAAACCA
1 GGAAAGAATGAAAAAA-AA
31281564 GGAAAGAAT-AAAAAAAA
1 GGAAAGAATGAAAAAAAA
31281581 GGAAAGAATGAA
1 GGAAAGAATGAA
31281593 GAAAGAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 10 0.38
18 13 0.50
19 3 0.12
ACGTcount: A:0.68, C:0.04, G:0.21, T:0.06
Consensus pattern (18 bp):
GGAAAGAATGAAAAAAAA
Found at i:31285299 original size:40 final size:40
Alignment explanation
Indices: 31285255--31285445 Score: 292
Period size: 40 Copynumber: 4.8 Consensus size: 40
31285245 GATCAAAGGC
* * *
31285255 ACCGAAGTGCAAAGAAGGGCACGTAAGTGCAATCAGGGGT
1 ACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGT
* *
31285295 ACCGAAGTACAAACAGGGGCACATAAGTGTAATCAGGGGT
1 ACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGT
*
31285335 ACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGTT
1 ACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGT
* * * *
31285375 ACTGAAGTACAAACAAGGGCACATAAGTGCAATTAGGGGT
1 ACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGT
31285415 ACCGAAGTACAAACAGGGGCACGTAAGTGCA
1 ACCGAAGTACAAACAGGGGCACGTAAGTGCA
31285446 GTCATTCAAT
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 135 1.00
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.14
Consensus pattern (40 bp):
ACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGT
Found at i:31285442 original size:20 final size:20
Alignment explanation
Indices: 31285271--31285442 Score: 118
Period size: 20 Copynumber: 8.6 Consensus size: 20
31285261 GTGCAAAGAA
* *
31285271 GGGCACGTAAGTGCAATCAG
1 GGGCACGTAAGTACAAACAG
*
31285291 GGGTACCG-AAGTACAAACAG
1 GGGCA-CGTAAGTACAAACAG
* ** *
31285311 GGGCACATAAGTGTAATCAG
1 GGGCACGTAAGTACAAACAG
*
31285331 GGGTACCG-AAGTACAAACAG
1 GGGCA-CGTAAGTACAAACAG
* *
31285351 GGGCACGTAAGTGCAATCAG
1 GGGCACGTAAGTACAAACAG
** *
31285371 GGTTAC-TGAAGTACAAACAA
1 GGGCACGT-AAGTACAAACAG
* * **
31285391 GGGCACATAAGTGCAATTAG
1 GGGCACGTAAGTACAAACAG
*
31285411 GGGTACCG-AAGTACAAACAG
1 GGGCA-CGTAAGTACAAACAG
31285431 GGGCACGTAAGT
1 GGGCACGTAAGT
31285443 GCAGTCATTC
Statistics
Matches: 111, Mismatches: 33, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
19 6 0.05
20 100 0.90
21 5 0.05
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (20 bp):
GGGCACGTAAGTACAAACAG
Found at i:31286782 original size:43 final size:43
Alignment explanation
Indices: 31286715--31287291 Score: 496
Period size: 43 Copynumber: 13.3 Consensus size: 43
31286705 TTGGCACATG
* * **
31286715 AGTGCATCA-CTGGGTAAACTGAAGCAACTATACTGGCACACGT
1 AGTGCATCATC-GGATAAACCGAAGCAACTATACTGGCACACAC
*
31286758 AGTGCATCATCGGATAATCCGAAGCAACTATACTGGCACAC-C
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
* * ** * * * * *
31286800 AATGCATTATTAGATAAACAGAAGCAACTATATTAGCGCAC-G
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
** * * *
31286842 AGTGCATCATCAAATAAACTGAAGCAATTATACTAGCACACTGGCAC
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACA----CAC
* * * *
31286889 ACGCGGTGCATCATCGGATAAACTGAAACAAGTATACTGACACACAC
1 A----GTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
* * * *
31286936 AGTACATCATCAGATAAATCGAAGTAACTATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
* ** * *
31286979 AGTGCATCA-CTAGATAAGTCGAAGCAACTATATTGGCACACAT
1 AGTGCATCATC-GGATAAACCGAAGCAACTATACTGGCACACAC
* * * * *
31287022 AGTGCATCATCGAATAAACCGAAGTAACCATACTAGCATACAC
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
* * * *
31287065 AGTGCATCATCGGATAAACCAAAGGAACTATATTGGCACACAT
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
* * * * *
31287108 AATGCATCGTTGGATAAACCGAAGTAACTATATTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
* * * * ** *
31287151 AATGCATCATCGAATAAACCGAGGTAACTATACTAACACACAT
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
*
31287194 AGTGCATCATCGGATAAACAGAAGCAACTATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
* ** * * *
31287237 AGTGCATCATCGAATAAACTAAAGTAACTGTACTGGCACACAT
1 AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
31287280 AGTGCATCATCG
1 AGTGCATCATCG
31287292 AAGATACCAA
Statistics
Matches: 434, Mismatches: 88, Indels: 24
0.79 0.16 0.04
Matches are distributed among these distances:
42 65 0.15
43 328 0.76
44 2 0.00
46 1 0.00
47 5 0.01
51 33 0.08
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (43 bp):
AGTGCATCATCGGATAAACCGAAGCAACTATACTGGCACACAC
Found at i:31289597 original size:115 final size:117
Alignment explanation
Indices: 31289383--31289618 Score: 431
Period size: 115 Copynumber: 2.0 Consensus size: 117
31289373 TTTTCTGTTG
31289383 AATGCTAATAACAATGGGTGCACACGACTGAACTTAACCTGCACCAAAAAAAAAACAAATTGAAC
1 AATGCTAATAACAATGGGTGCACACGACTGAACTTAACCTGCACC-AAAAAAAAACAAATTGAAC
31289448 GTTGAGCAATCAAATCAATGGCTTTTTTATAACTAATATTATAACATAACA-A
65 GTTGAGCAATCAAATCAATGGCTTTTTTATAACTAATATTATAACATAACAGA
*
31289500 AATGCTAATAACAATGGGTGCACACGACTGGACTTAACCTGCACC-AAAAAAAACAAATTGAACG
1 AATGCTAATAACAATGGGTGCACACGACTGAACTTAACCTGCACCAAAAAAAAACAAATTGAACG
*
31289564 TTGAGCAATCAAATCAGTGGCTTTTTTATAACTAATATTATAACATAACAGA
66 TTGAGCAATCAAATCAATGGCTTTTTTATAACTAATATTATAACATAACAGA
31289616 AAT
1 AAT
31289619 TATGTAGGGA
Statistics
Matches: 116, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
115 68 0.59
116 4 0.03
117 44 0.38
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (117 bp):
AATGCTAATAACAATGGGTGCACACGACTGAACTTAACCTGCACCAAAAAAAAACAAATTGAACG
TTGAGCAATCAAATCAATGGCTTTTTTATAACTAATATTATAACATAACAGA
Found at i:31291838 original size:23 final size:23
Alignment explanation
Indices: 31291812--31291944 Score: 194
Period size: 23 Copynumber: 5.8 Consensus size: 23
31291802 ACTAATATGA
* *
31291812 AGCCGAAGCTACCACTGACACGT
1 AGCCGAAGCTACCACTGAAATGT
*
31291835 AGCCGTAGCTACCACTGAAATGT
1 AGCCGAAGCTACCACTGAAATGT
*
31291858 AGCTGAAGCTACCACTGAAATGT
1 AGCCGAAGCTACCACTGAAATGT
*
31291881 AGCCGAAGCTACCACTGATATGT
1 AGCCGAAGCTACCACTGAAATGT
*
31291904 AGCCGTAGCTACCACTGAAATGT
1 AGCCGAAGCTACCACTGAAATGT
* *
31291927 AACCGAAGCTGCCACTGA
1 AGCCGAAGCTACCACTGA
31291945 TCAATAACAC
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 98 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.19
Consensus pattern (23 bp):
AGCCGAAGCTACCACTGAAATGT
Found at i:31291923 original size:69 final size:69
Alignment explanation
Indices: 31291812--31291944 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 69
31291802 ACTAATATGA
* *
31291812 AGCCGAAGCTACCACTGACACGTAGCCGTAGCTACCACTGAAATGTAGCTGAAGCTACCACTGAA
1 AGCCGAAGCTACCACTGACACGTAGCCGTAGCTACCACTGAAATGTAACCGAAGCTACCACTGAA
31291877 ATGT
66 ATGT
* * *
31291881 AGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGTAACCGAAGCTGCCACTGA
1 AGCCGAAGCTACCACTGACACGTAGCCGTAGCTACCACTGAAATGTAACCGAAGCTACCACTGA
31291945 TCAATAACAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.19
Consensus pattern (69 bp):
AGCCGAAGCTACCACTGACACGTAGCCGTAGCTACCACTGAAATGTAACCGAAGCTACCACTGAA
ATGT
Found at i:31293784 original size:38 final size:38
Alignment explanation
Indices: 31293733--31293812 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
31293723 TTCTAACAGC
*
31293733 TTAATTAACTAAATAAAACAACATAAATGACAAAATGT
1 TTAATTAACTAAATAAAACAACATAAATGACAAAATAT
31293771 TTAATTAACTAAATAAAACAACATAAATGACAAAATAT
1 TTAATTAACTAAATAAAACAACATAAATGACAAAATAT
31293809 TTAA
1 TTAA
31293813 ACAATCTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.28
Consensus pattern (38 bp):
TTAATTAACTAAATAAAACAACATAAATGACAAAATAT
Found at i:31299107 original size:24 final size:26
Alignment explanation
Indices: 31299060--31299117 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
31299050 TGTAGCTACA
*
31299060 ATGTATTATTAGCATTATAAATTTCTC
1 ATGTATTATTAGCA-TATAAATTTATC
* *
31299087 ATGTATTATTAGC-T-TAGATTTATT
1 ATGTATTATTAGCATATAAATTTATC
31299111 ATGTATT
1 ATGTATT
31299118 TGTTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.50
25 1 0.04
27 13 0.46
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (26 bp):
ATGTATTATTAGCATATAAATTTATC
Found at i:31304019 original size:9 final size:9
Alignment explanation
Indices: 31304002--31304038 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31303992 TGAGTTTTTG
31304002 AATTCGAAT
1 AATTCGAAT
*
31304011 AATTTGAAT
1 AATTCGAAT
31304020 AATTCGAAT
1 AATTCGAAT
31304029 AATTCGAAT
1 AATTCGAAT
31304038 A
1 A
31304039 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (9 bp):
AATTCGAAT
Found at i:31304084 original size:29 final size:30
Alignment explanation
Indices: 31304051--31304107 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
31304041 AAACTATAAT
* *
31304051 ATTTTATATTTTTACC-CAAAAGTTTTAAA
1 ATTTTATACTTTTACCTCAAAACTTTTAAA
* *
31304080 ATTTTTTACTTTTCCCTCAAAACTTTTA
1 ATTTTATACTTTTACCTCAAAACTTTTA
31304108 TTCCTTTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.32, C:0.16, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTTATACTTTTACCTCAAAACTTTTAAA
Found at i:31306106 original size:16 final size:17
Alignment explanation
Indices: 31306085--31306116 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31306075 TATTATATTA
31306085 TATTATA-TTATTAAAG
1 TATTATATTTATTAAAG
31306101 TATTATATTTATTAAA
1 TATTATATTTATTAAA
31306117 TAATAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTATATTTATTAAAG
Found at i:31306109 original size:5 final size:5
Alignment explanation
Indices: 31306054--31306095 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
31306044 ATATAAGAAA
31306054 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
31306096 TAAAGTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:31306181 original size:17 final size:17
Alignment explanation
Indices: 31306132--31306171 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
31306122 AACAAAACAT
*
31306132 AAACTAAAAGAATAAAAG
1 AAAC-AAAAGAAGAAAAG
31306150 AAACAAAAGAAGAAAAG
1 AAACAAAAGAAGAAAAG
31306167 AAACA
1 AAACA
31306172 GAATAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.75, C:0.07, G:0.12, T:0.05
Consensus pattern (17 bp):
AAACAAAAGAAGAAAAG
Found at i:31306594 original size:24 final size:23
Alignment explanation
Indices: 31306561--31306607 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
31306551 ATTTGAATAG
31306561 AAATAGAGTGTGAATTGAGTTAGGA
1 AAATAGA--GTGAATTGAGTTAGGA
*
31306586 AAATA-AGTGAATTTAGTTAGGA
1 AAATAGAGTGAATTGAGTTAGGA
31306608 TTAAATTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 15 0.71
24 1 0.05
25 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.30
Consensus pattern (23 bp):
AAATAGAGTGAATTGAGTTAGGA
Found at i:31306876 original size:18 final size:18
Alignment explanation
Indices: 31306855--31306891 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31306845 ATGTGAGGTA
31306855 AGTATGAATATTAGTATT
1 AGTATGAATATTAGTATT
* *
31306873 AGTATTAGTATTAGTATT
1 AGTATGAATATTAGTATT
31306891 A
1 A
31306892 CTATTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (18 bp):
AGTATGAATATTAGTATT
Found at i:31306907 original size:6 final size:6
Alignment explanation
Indices: 31306863--31306903 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
31306853 TAAGTATGAA
* *
31306863 TATTAG TATTAG TATTAG TATTAG TATTAC TATTAT TATTA
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTA
31306904 TTATCATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (6 bp):
TATTAG
Found at i:31306912 original size:6 final size:6
Alignment explanation
Indices: 31306863--31306918 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
31306853 TAAGTATGAA
* * * * * *
31306863 TATTAG TATTAG TATTAG TATTAG TATTAC TATTAT TATTAT TATCAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
31306911 TATTAT TA
1 TATTAT TA
31306919 AAATGAGTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (6 bp):
TATTAT
Found at i:31308583 original size:22 final size:22
Alignment explanation
Indices: 31308538--31308593 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
31308528 GACGGAAAGC
* * *
31308538 AAAAACAAGATAAAAACTTTAA
1 AAAAACAAGAGAAAAACCTAAA
*
31308560 AAAAACAAGAGAAAACCCTAAA
1 AAAAACAAGAGAAAAACCTAAA
**
31308582 AACTACAAGAGA
1 AAAAACAAGAGA
31308594 GACAAAGGCG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAAACAAGAGAAAAACCTAAA
Found at i:31321356 original size:14 final size:14
Alignment explanation
Indices: 31321337--31321376 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31321327 TTGATTGCCA
31321337 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
31321351 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
31321365 GGAAAATGTTTT
1 GTAAAATGTTTT
31321377 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:31321385 original size:20 final size:20
Alignment explanation
Indices: 31321360--31321399 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31321350 CGTAAAATGA
*
31321360 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
31321380 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
31321400 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:31321389 original size:34 final size:35
Alignment explanation
Indices: 31321345--31321411 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
31321335 CAGTAAAATG
*
31321345 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
31321379 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
31321412 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:31321415 original size:14 final size:15
Alignment explanation
Indices: 31321339--31321415 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
31321329 GATTGCCAGT
* *
31321339 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
31321353 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
31321367 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
31321387 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
31321402 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
31321416 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:31330130 original size:12 final size:12
Alignment explanation
Indices: 31330113--31330140 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31330103 TATATGATCT
31330113 TCATACTTGAGA
1 TCATACTTGAGA
31330125 TCATACTTGAGA
1 TCATACTTGAGA
31330137 TCAT
1 TCAT
31330141 CATTGTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (12 bp):
TCATACTTGAGA
Found at i:31330962 original size:138 final size:139
Alignment explanation
Indices: 31330790--31331074 Score: 473
Period size: 139 Copynumber: 2.1 Consensus size: 139
31330780 GAGAACATAG
*
31330790 ATATAATTAATATATGATTTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAA-TTTAT
1 ATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAATTTTAT
* * * *
31330854 TAATATAAAAATTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAGTATTCTT
66 TAATATAAAAAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
31330919 TTGAAAAGA
131 TTGAAAAGA
* *
31330928 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTTGT
1 ATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAATTTTAT
* *
31330993 TAATATAAATAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
66 TAATATAAAAAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
*
31331058 TTGGAAAGA
131 TTGAAAAGA
31331067 ATATAATT
1 ATATAATT
31331075 TCTTTTTCTA
Statistics
Matches: 136, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
138 57 0.42
139 79 0.58
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (139 bp):
ATATAATTAATATATGAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCGAATTTTAT
TAATATAAAAAGTTATATTAATTAATCTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTT
TTGAAAAGA
Found at i:31331177 original size:75 final size:75
Alignment explanation
Indices: 31331050--31331199 Score: 239
Period size: 75 Copynumber: 2.0 Consensus size: 75
31331040 ATGGAAATTA
* * *
31331050 ATATTCTTTTGGAAAGAATATAATTTCTTTTTCTAACTTTCCATTTGTCTTCTTTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
31331115 GAATAATCCT
66 GAATAATCCT
* *
31331125 ATATTTTTTTTGAAAGAATATAATTCCTTTTTC-AGACTTTCCATTTGCCTTCTCTATTAATAAG
1 ATATTCTTTTGGAAAGAATATAATTCCTTTTTCTA-ACTTTCCATTTGCCTTCTCTATTAATAAG
31331189 GGAATAATCCT
65 GGAATAATCCT
31331200 GGTTTTCCTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
74 1 0.01
75 68 0.99
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTCCTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGG
GAATAATCCT
Found at i:31331847 original size:27 final size:27
Alignment explanation
Indices: 31331809--31331866 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
31331799 CGTGCCACTA
31331809 CATTCAACATTAGGATACCAATTCTTT
1 CATTCAACATTAGGATACCAATTCTTT
31331836 CATTCAACATTAGGATACCAATTCTTT
1 CATTCAACATTAGGATACCAATTCTTT
31331863 CATT
1 CATT
31331867 TATAGCCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (27 bp):
CATTCAACATTAGGATACCAATTCTTT
Found at i:31336940 original size:17 final size:17
Alignment explanation
Indices: 31336918--31336951 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
31336908 ATATATGATT
31336918 AATTGAAGATGA-AATGA
1 AATTGAA-ATGAGAATGA
31336935 AATTGAAATGAGAATGA
1 AATTGAAATGAGAATGA
31336952 TATGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AATTGAAATGAGAATGA
Found at i:31339173 original size:14 final size:14
Alignment explanation
Indices: 31339154--31339184 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31339144 GGCATGTTAA
*
31339154 TATATATGTATATG
1 TATATATATATATG
31339168 TATATATATATATG
1 TATATATATATATG
31339182 TAT
1 TAT
31339185 TTGAATTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
TATATATATATATG
Found at i:31340490 original size:10 final size:10
Alignment explanation
Indices: 31340472--31340501 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
31340462 ATCTAGGCAA
31340472 TGGTATGTTT
1 TGGTATGTTT
*
31340482 TGTTATGTTT
1 TGGTATGTTT
31340492 TGGTATGTTT
1 TGGTATGTTT
31340502 GAGTAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (10 bp):
TGGTATGTTT
Found at i:31340780 original size:20 final size:20
Alignment explanation
Indices: 31340755--31340792 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
31340745 GTATCAGTGC
31340755 TTTTTATAAATATCGATAAA
1 TTTTTATAAATATCGATAAA
31340775 TTTTTATAAATATCGATA
1 TTTTTATAAATATCGATA
31340793 CCTCCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTTTATAAATATCGATAAA
Found at i:31344820 original size:40 final size:40
Alignment explanation
Indices: 31344701--31344833 Score: 110
Period size: 40 Copynumber: 3.4 Consensus size: 40
31344691 CTTCGAGTCA
* * * * *
31344701 ATGAGACACTAGGTGTCAATTTACTACTTCAAATTAATTCG
1 ATGAGACAATGGGTGTCAATTTATTACTTCGAATT-ATCCG
* * * ** *
31344742 ATGAGGCACTGGGTGCCAA--T-TTACTTCGGTTTAGCCG
1 ATGAGACAATGGGTGTCAATTTATTACTTCGAATTATCCG
*
31344779 ATGAGACAATGTGTGTCAATTTATTACTTCGAATTATCCG
1 ATGAGACAATGGGTGTCAATTTATTACTTCGAATTATCCG
* *
31344819 ATGAGGCACTGGGTG
1 ATGAGACAATGGGTG
31344834 CCAAACTGGT
Statistics
Matches: 70, Mismatches: 19, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
37 18 0.26
38 8 0.11
39 2 0.03
40 26 0.37
41 16 0.23
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (40 bp):
ATGAGACAATGGGTGTCAATTTATTACTTCGAATTATCCG
Found at i:31350897 original size:10 final size:10
Alignment explanation
Indices: 31350879--31350908 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
31350869 ATCTAGGAAA
31350879 TGGTATGTTT
1 TGGTATGTTT
*
31350889 TGTTATGTTT
1 TGGTATGTTT
31350899 TGGTATGTTT
1 TGGTATGTTT
31350909 GAGTAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (10 bp):
TGGTATGTTT
Found at i:31353927 original size:27 final size:27
Alignment explanation
Indices: 31353913--31354163 Score: 305
Period size: 27 Copynumber: 9.4 Consensus size: 27
31353903 TATAACAGTT
31353913 ATTTTACCCTATA-GGGTATTTCGGTC
1 ATTTTACCCTATAGGGGTATTTCGGTC
* *
31353939 ATTTTATCCTAT-GGGGTATTTTGGTC
1 ATTTTACCCTATAGGGGTATTTCGGTC
*
31353965 ATTTTACCCTATGGGGGTATTTCGGTC
1 ATTTTACCCTATAGGGGTATTTCGGTC
*
31353992 ATTTTACCCTAT-GGGGTATTTTGGTC
1 ATTTTACCCTATAGGGGTATTTCGGTC
* *
31354018 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATAGGGGTATTTCGGTC
* **
31354045 ATTTTACCCTATAAGGGTATTTTAGTC
1 ATTTTACCCTATAGGGGTATTTCGGTC
* *
31354072 ATTTTACCCAAT-GAGGGTATTTCAGTC
1 ATTTTACCCTATAG-GGGTATTTCGGTC
* **
31354099 ATTTTACCCTATAAGGGTATTTTAGTC
1 ATTTTACCCTATAGGGGTATTTCGGTC
* * *
31354126 ATTTTATCCTA-CGGGGTATTTCGATC
1 ATTTTACCCTATAGGGGTATTTCGGTC
31354152 ATTTTACCCTAT
1 ATTTTACCCTAT
31354164 TTTAGGGACT
Statistics
Matches: 194, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
26 79 0.41
27 115 0.59
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTATAGGGGTATTTCGGTC
Found at i:31353988 original size:53 final size:54
Alignment explanation
Indices: 31353913--31354163 Score: 357
Period size: 53 Copynumber: 4.7 Consensus size: 54
31353903 TATAACAGTT
* * * *
31353913 ATTTTACCCTAT-AGGGTATTTCGGTCATTTTATCCTAT-GGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTTAGTC
* *
31353965 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT-GGGGTATTTTGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTTAGTC
*
31354018 ATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATAAGGGTATTTTAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTTAGTC
* * *
31354072 ATTTTACCCAATGAGGGTATTTCAGTCATTTTACCCTATAAGGGTATTTTAGTC
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTTAGTC
* * *
31354126 ATTTTATCCTA-CGGGGTATTTCGATCATTTTACCCTAT
1 ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTAT
31354164 TTTAGGGACT
Statistics
Matches: 182, Mismatches: 15, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
52 12 0.07
53 99 0.54
54 71 0.39
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (54 bp):
ATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAAGGGTATTTTAGTC
Found at i:31357964 original size:17 final size:19
Alignment explanation
Indices: 31357918--31357966 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
31357908 TAAGTATTAA
31357918 ATTAAATATAATATTAAATTT
1 ATTAAA-ATAATATT-AATTT
31357939 ATTAAAATAATATT-ATTT
1 ATTAAAATAATATTAATTT
*
31357957 -TTAGAATAAT
1 ATTAAAATAAT
31357967 TAACTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
20 8 0.30
21 6 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTAAAATAATATTAATTT
Found at i:31359855 original size:20 final size:21
Alignment explanation
Indices: 31359818--31359856 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
31359808 AGTTCGATCA
* *
31359818 GTTTTTAGGTCTCGATTTTGG
1 GTTTTTAGGGCTCAATTTTGG
31359839 GTTTTT-GGGCTCAATTTT
1 GTTTTTAGGGCTCAATTTT
31359857 CAATCTTAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.54
Consensus pattern (21 bp):
GTTTTTAGGGCTCAATTTTGG
Found at i:31360891 original size:12 final size:13
Alignment explanation
Indices: 31360867--31360895 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31360857 GGGCTATAAC
31360867 TATTGCATTTATT
1 TATTGCATTTATT
31360880 TATTGC-TTTATT
1 TATTGCATTTATT
31360892 TATT
1 TATT
31360896 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:31369456 original size:42 final size:43
Alignment explanation
Indices: 31369349--31369464 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
31369339 CTCGTACAAT
* * *
31369349 GCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATAACGAT
1 GCCAATGTCCTAGACATGGTCTTACATGTAATCAAATAACGAA
* * * *
31369392 GTCACTGTCCTAGACAGGGTCTTACATGTAATCATAT-ACGAA
1 GCCAATGTCCTAGACATGGTCTTACATGTAATCAAATAACGAA
* *
31369434 GCCAATGTCCCAGACATGGTCTTACACGTAA
1 GCCAATGTCCTAGACATGGTCTTACATGTAA
31369465 ATCTCAAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 30 0.49
43 31 0.51
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
GCCAATGTCCTAGACATGGTCTTACATGTAATCAAATAACGAA
Found at i:31375375 original size:41 final size:42
Alignment explanation
Indices: 31375273--31375425 Score: 132
Period size: 41 Copynumber: 3.7 Consensus size: 42
31375263 TGTGGTTTCG
* * * * **
31375273 TGTAAGACCATGTCTGGAACATTGGCATCGATATAAGATTGTG
1 TGTAAGACCATATCTGGGACATTGGCACCGATATATGATT-CA
* *
31375316 TGTAAGACCATGTTTGGGACATTGGCACCG-TATATGATTCA
1 TGTAAGACCATATCTGGGACATTGGCACCGATATATGATTCA
* ** * * *
31375357 TGTAAGACCCTATCTGGGACAAAGGCA-TGATATGTGATAACA
1 TGTAAGACCATATCTGGGACATTGGCACCGATATATGAT-TCA
*
31375399 TGTAAGACCATATCTGGGATA-TGGCAC
1 TGTAAGACCATATCTGGGACATTGGCAC
31375426 TGTATGTGAT
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
40 1 0.01
41 33 0.37
42 29 0.32
43 27 0.30
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACATTGGCACCGATATATGATTCA
Found at i:31377838 original size:23 final size:23
Alignment explanation
Indices: 31377801--31377854 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
31377791 AGATTAAGCA
*
31377801 CAAACATTATCTGCATTCAACAC
1 CAAACACTATCTGCATTCAACAC
* *
31377824 CAAACACTATTTGCATTCATCAC
1 CAAACACTATCTGCATTCAACAC
31377847 CAAACACT
1 CAAACACT
31377855 TCCACAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.31, G:0.04, T:0.26
Consensus pattern (23 bp):
CAAACACTATCTGCATTCAACAC
Found at i:31385530 original size:22 final size:24
Alignment explanation
Indices: 31385505--31385554 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
31385495 GACCTATCGG
31385505 ATAATTTA-C-AAT-TAATATACAA
1 ATAATTTATCAAATATAATATA-AA
31385527 ATAA-TTATCAAATATAATATAAA
1 ATAATTTATCAAATATAATATAAA
31385550 ATAAT
1 ATAAT
31385555 CTTAAAGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 9 0.38
24 7 0.29
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATTTATCAAATATAATATAAA
Found at i:31386932 original size:31 final size:31
Alignment explanation
Indices: 31386890--31387187 Score: 424
Period size: 31 Copynumber: 9.7 Consensus size: 31
31386880 ATCTAATGCT
*
31386890 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31386920 CGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
31386951 CAAATC-AATTCGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
31386981 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31387012 CAAATC-AACTCGGCAATGTATATTCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31387042 AAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
31387073 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
31387103 CAAATCAAATTTGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
31387134 CAAATCAAATTCGACAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
31387165 CAATTCAAATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
31387188 AAACATATAC
Statistics
Matches: 238, Mismatches: 26, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
30 88 0.37
31 150 0.63
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:31386987 original size:61 final size:61
Alignment explanation
Indices: 31386890--31387198 Score: 465
Period size: 61 Copynumber: 5.0 Consensus size: 61
31386880 ATCTAATGCT
* * * *
31386890 CAAATCAATTCGGCAATATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
*
31386951 CAAATCAATTCGGCAATGAATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * *
31387012 CAAATCAACTCGGCAATGTATATTCATATAAAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* *
31387073 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * * * *
31387134 CAAATCAAATTCGACAATGTATATCTATAAACAATTCAAATTCGGCAATGTATAAAACATATA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTAT-AACCATATA
31387197 CA
1 CA
31387199 TTTAAATTCA
Statistics
Matches: 225, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
61 175 0.78
62 40 0.18
63 10 0.04
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.28
Consensus pattern (61 bp):
CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
Found at i:31393256 original size:7 final size:7
Alignment explanation
Indices: 31393244--31393281 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
31393234 CTCGGGGAAA
31393244 TTTATTT
1 TTTATTT
31393251 TTTATTT
1 TTTATTT
31393258 TTTATTT
1 TTTATTT
31393265 TTTATTT
1 TTTATTT
31393272 TTTATTT
1 TTTATTT
31393279 TTT
1 TTT
31393282 TGTGTGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTATTT
Found at i:31394525 original size:31 final size:31
Alignment explanation
Indices: 31394483--31394903 Score: 629
Period size: 31 Copynumber: 13.7 Consensus size: 31
31394473 ATACAATGCT
*
31394483 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31394513 CGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31394544 CAAATC-AATTCAGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
31394574 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
31394605 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31394635 CAAATAAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
31394666 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31394696 CAAATCAAATTCCGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
31394727 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
31394757 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
31394788 AAAATCAAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
31394819 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
31394850 CAAATCAAATTTGGCAATGTATATCTATA-A
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
31394880 AAAATTCAAATTCGGCAATGTATA
1 CAAA-TCAAATTCGGCAATGTATA
31394904 AAACATATAC
Statistics
Matches: 356, Mismatches: 29, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
30 121 0.34
31 235 0.66
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.28
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:31394580 original size:61 final size:61
Alignment explanation
Indices: 31394483--31394914 Score: 686
Period size: 61 Copynumber: 7.0 Consensus size: 61
31394473 ATACAATGCT
* * * *
31394483 CAAATCAATTCGGCAATATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* *
31394544 CAAATCAATTCAGCAATGAATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
*
31394605 CAAATCAATTCGGCAATGTATATCCATATACAAATAAAATTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
*
31394666 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCCGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
31394727 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * *
31394788 AAAATCAAATTCGACAATGTATAACCATATACAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
* * * *
31394850 CAAATCAAATTTGGCAATGTATATCTATA-AAAAATTCAAATTCGGCAATGTATAAAACATATA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAA-TCAAATTCGGCAATGTAT-AACCATATA
31394913 CA
1 CA
31394915 TTTAAATTCA
Statistics
Matches: 346, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
61 241 0.70
62 95 0.27
63 10 0.03
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (61 bp):
CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
Found at i:31397246 original size:42 final size:43
Alignment explanation
Indices: 31397189--31397290 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 43
31397179 TGAGATTTAT
* * *
31397189 GTGTAAGACCATGTCTTGGACATTGGCGTCG-TATATGATTAC
1 GTGTAAGACCATGTCTGGGACAATGGCATCGTTATATGATTAC
* * *
31397231 GTGTAAGACCCTGTCTGGGACAATGGTATCGTTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAATGGCATCGTTATATGATTAC
* *
31397274 ATGTAAGACCACGTCTG
1 GTGTAAGACCATGTCTG
31397291 AGACGTTGGC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 26 0.52
43 24 0.48
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACAATGGCATCGTTATATGATTAC
Found at i:31402146 original size:14 final size:15
Alignment explanation
Indices: 31402126--31402166 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
31402116 TTTGTTTGGC
31402126 AGTAAAATGTTTTC-
1 AGTAAAATGTTTTCT
* *
31402140 CGTAAAATGATTTCT
1 AGTAAAATGTTTTCT
31402155 AG-AAAATGTTTT
1 AGTAAAATGTTTT
31402167 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (15 bp):
AGTAAAATGTTTTCT
Found at i:31402179 original size:34 final size:35
Alignment explanation
Indices: 31402135--31402201 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
31402125 CAGTAAAATG
*
31402135 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
31402169 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
31402202 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:31402260 original size:32 final size:31
Alignment explanation
Indices: 31402182--31402268 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
31402172 TCTGTAAAAT
* *
31402182 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
31402215 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
31402247 GATTTCCTGAAAATATTTTCTG
1 GATTT-CTGAAAATATTTTCTG
31402269 AAAAGTTGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.02
32 38 0.86
33 5 0.11
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:31402317 original size:14 final size:14
Alignment explanation
Indices: 31402298--31402325 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31402288 ATTTTACATA
31402298 TATTAATATATATT
1 TATTAATATATATT
31402312 TATTAATATATATT
1 TATTAATATATATT
31402326 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:31402633 original size:72 final size:73
Alignment explanation
Indices: 31402511--31402655 Score: 274
Period size: 72 Copynumber: 2.0 Consensus size: 73
31402501 TAGAAATAAT
31402511 AATATTATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATA
1 AATATTATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATA
31402576 TTACACCA
66 TTACACCA
*
31402584 AATA-TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTCCAAGTGCATAATA
1 AATATTATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATA
31402648 TTACACCA
66 TTACACCA
31402656 CATAAATGTA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 67 0.94
73 4 0.06
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (73 bp):
AATATTATCCAAATACATAATTAATGGTACACCACATAGTAACAACATTGTCCAAGTGCATAATA
TTACACCA
Found at i:31403651 original size:35 final size:36
Alignment explanation
Indices: 31403602--31403670 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
31403592 ATTCAATCAT
31403602 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
*
31403637 TTCAATATCTAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
31403671 TCTAACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:31405166 original size:17 final size:17
Alignment explanation
Indices: 31405111--31405166 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
31405101 ACTACAAAAA
31405111 GATGCCTGTAATTAGTT
1 GATGCCTGTAATTAGTT
* *
31405128 GATGCGTTTTCAATGCTAGTT
1 GATGC-CTGT-AAT--TAGTT
31405149 GATGCCTGTAATTAGTT
1 GATGCCTGTAATTAGTT
31405166 G
1 G
31405167 GATCTGCCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
17 11 0.35
18 2 0.06
19 6 0.19
20 2 0.06
21 10 0.32
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.41
Consensus pattern (17 bp):
GATGCCTGTAATTAGTT
Found at i:31407421 original size:25 final size:25
Alignment explanation
Indices: 31407380--31407477 Score: 80
Period size: 25 Copynumber: 4.1 Consensus size: 25
31407370 AAAATGTCTG
* *
31407380 CTGCTTAGAAG-AGAATGGAAAATGT
1 CTGCTTA-AAGAAAAATGAAAAATGT
31407405 CTGCTTAAAGAAAAATGAAAAATG-
1 CTGCTTAAAGAAAAATGAAAAATGT
** *** *
31407429 -T-CTT-ACCAATTTTGGAAAATGT
1 CTGCTTAAAGAAAAATGAAAAATGT
31407451 CTGCTTAAAGAAAAATGAAAAATGT
1 CTGCTTAAAGAAAAATGAAAAATGT
31407476 CT
1 CT
31407478 TACCAATTTT
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
21 11 0.20
22 3 0.06
23 2 0.04
24 6 0.11
25 32 0.59
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (25 bp):
CTGCTTAAAGAAAAATGAAAAATGT
Found at i:31407445 original size:46 final size:46
Alignment explanation
Indices: 31407395--31407488 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
31407385 TAGAAGAGAA
31407395 TGGAAAATGTCTGCTTAAAGAAAAATGAAAAATGTCTTACCAATTT
1 TGGAAAATGTCTGCTTAAAGAAAAATGAAAAATGTCTTACCAATTT
31407441 TGGAAAATGTCTGCTTAAAGAAAAATGAAAAATGTCTTACCAATTT
1 TGGAAAATGTCTGCTTAAAGAAAAATGAAAAATGTCTTACCAATTT
31407487 TG
1 TG
31407489 AAGCCGTAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (46 bp):
TGGAAAATGTCTGCTTAAAGAAAAATGAAAAATGTCTTACCAATTT
Found at i:31412661 original size:17 final size:17
Alignment explanation
Indices: 31412639--31412672 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31412629 GTTAAATAAC
31412639 TTTACACACTTATTTAA
1 TTTACACACTTATTTAA
31412656 TTTACACACTTATTTAA
1 TTTACACACTTATTTAA
31412673 ATATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTACACACTTATTTAA
Found at i:31413422 original size:13 final size:13
Alignment explanation
Indices: 31413404--31413436 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
31413394 ATTGATAAAT
31413404 CCGAAACGGTACA
1 CCGAAACGGTACA
31413417 CCGAAACGGTACA
1 CCGAAACGGTACA
31413430 CCGAAAC
1 CCGAAAC
31413437 AAACAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.33, G:0.21, T:0.06
Consensus pattern (13 bp):
CCGAAACGGTACA
Found at i:31417042 original size:15 final size:16
Alignment explanation
Indices: 31417022--31417051 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31417012 ATATATAATT
31417022 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
31417037 TAATAAATATTCTTA
1 TAATAAATATTCTTA
31417052 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:31417202 original size:54 final size:58
Alignment explanation
Indices: 31417056--31417353 Score: 189
Period size: 59 Copynumber: 5.1 Consensus size: 58
31417046 TTCTTATATG
*
31417056 AATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 AATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAA-TATTATTA
* * ** * * * * * *
31417115 AATATAATTTAATAAAAATATATAAT-TTAATAAAAT-T-CTTCATAATAA-A-TATTC
1 AATTTACTAAAATCATAATATATAATACT-ATAAAATATAATTCAAAATAATATTATTA
*
31417169 AATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 AATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAA-TATTATTA
* * ** * *** * * *
31417228 AATATAATTTAATAAAAATATATGATTTAATAGCTACT-GTCT-TAA-TAATAAATATTCTTATA
1 AAT-TTA-CTAA-AATCATA-AT-ATATAATA-CTA-TAAAATATAATTCA-AAATAATATTAT-
*
31417290 TG
57 TA
* *
31417292 AATTTACTAAAATCATAATATATAATATTATAAAATATAATTTAAAATAATTATTATTA
1 AATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAA-TATTATTA
31417351 AAT
1 AAT
31417354 ATAATTTAAT
Statistics
Matches: 172, Mismatches: 47, Indels: 40
0.66 0.18 0.15
Matches are distributed among these distances:
54 31 0.18
55 3 0.02
56 8 0.05
57 9 0.05
58 6 0.03
59 53 0.31
60 11 0.06
61 8 0.05
62 8 0.05
63 11 0.06
64 19 0.11
65 4 0.02
66 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (58 bp):
AATTTACTAAAATCATAATATATAATACTATAAAATATAATTCAAAATAATATTATTA
Found at i:31417246 original size:16 final size:17
Alignment explanation
Indices: 31417227--31417259 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31417217 AATTATTATT
31417227 AAATATA-ATTTAATAA
1 AAATATAGATTTAATAA
31417243 AAATATATGATTTAATA
1 AAATATA-GATTTAATA
31417260 GCTACTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATATAGATTTAATAA
Found at i:31417305 original size:123 final size:120
Alignment explanation
Indices: 31416976--31417436 Score: 738
Period size: 123 Copynumber: 3.9 Consensus size: 120
31416966 TTAATCATAT
*
31416976 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
31417041 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
31417096 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTCATAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
31417161 AAATATTC-------AATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
31417209 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTACTGTCTTAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATA--AAAT-TCTTAAT
*
31417274 AATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATATTATAAAATATAA
63 AATAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
31417332 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATA--AAAT-TCTTAAT
31417397 AATAAATATTCTTATATGAATTTACTAAAATCATAATATA
63 AATAAATATTCTTATATGAATTTACTAAAATCATAATATA
31417437 ACTTGAGAAT
Statistics
Matches: 323, Mismatches: 8, Indels: 17
0.93 0.02 0.05
Matches are distributed among these distances:
113 90 0.28
115 2 0.01
116 17 0.05
120 71 0.22
123 143 0.44
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAAT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:31417331 original size:22 final size:24
Alignment explanation
Indices: 31417286--31417332 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
31417276 TAAATATTCT
31417286 TATATGAATTTACTAAAATCATAA
1 TATATGAATTTACTAAAATCATAA
31417310 TATAT-AATATTA-TAAAAT-ATAA
1 TATATGAAT-TTACTAAAATCATAA
31417332 T
1 T
31417333 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TATATGAATTTACTAAAATCATAA
Found at i:31417353 original size:26 final size:25
Alignment explanation
Indices: 31417313--31417371 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
31417303 ATCATAATAT
31417313 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
31417338 ATAATTATTATTAAATATAATTTAATA
1 ATAA-TATTATAAAATATAATTTAA-A
*
31417365 AAAATAT
1 ATAATAT
31417372 ATGATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 4 0.13
26 22 0.73
27 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:31417369 original size:16 final size:17
Alignment explanation
Indices: 31417350--31417382 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31417340 AATTATTATT
31417350 AAATATA-ATTTAATAA
1 AAATATAGATTTAATAA
31417366 AAATATATGATTTAATA
1 AAATATA-GATTTAATA
31417383 GCTATTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATATAGATTTAATAA
Found at i:31417404 original size:64 final size:64
Alignment explanation
Indices: 31417213--31417404 Score: 186
Period size: 64 Copynumber: 3.1 Consensus size: 64
31417203 ATATAATTTA
*
31417213 AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTACTGTCTTAATAAT
1 AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
* * * * * ****
31417277 AAAT-ATTCTTA-T--AT-GAATTTACT-AAAATCATAAT-ATATAATA-TTATAAAATATAAT-
1 AAATAATTATTATTAAATATAATTTAATAAAAAT-AT-ATGATTTAATAGCTATTGTCT-TAATA
*
31417333 TT
63 AT
31417335 AAAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
1 -AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
31417400 AAATA
1 AAATA
31417405 TTCTTATATG
Statistics
Matches: 94, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
58 9 0.10
59 24 0.26
60 10 0.11
61 1 0.01
62 1 0.01
63 10 0.11
64 29 0.31
65 10 0.11
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (64 bp):
AAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAAT
Found at i:31417426 original size:59 final size:58
Alignment explanation
Indices: 31417229--31417426 Score: 186
Period size: 59 Copynumber: 3.3 Consensus size: 58
31417219 TTATTATTAA
*
31417229 ATATAATTTAATAAAAATATATGATTTAATAGCTACTGTCTTAATAATAAATATTCTT
1 ATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
* * ** ** * *
31417287 ATATGAATTTACTAAAATCATAATAT-ATAATATTATAAAATATAAT-TTAA-AATAATTATTAT
1 ATAT-AATTTAATAAAA--AT-ATATGAT--T-TAAT-AGCTATTGTCTTAATAATAAATATTCT
31417349 T
58 T
31417350 AAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
1 --ATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
*
31417410 ATATGAATTTACTAAAA
1 ATAT-AATTTAATAAAA
31417427 TCATAATATA
Statistics
Matches: 108, Mismatches: 18, Indels: 27
0.71 0.12 0.18
Matches are distributed among these distances:
58 13 0.12
59 29 0.27
60 12 0.11
61 8 0.07
62 8 0.07
63 12 0.11
64 18 0.17
65 8 0.07
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (58 bp):
ATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTT
Found at i:31417435 original size:64 final size:64
Alignment explanation
Indices: 31417244--31417436 Score: 206
Period size: 64 Copynumber: 3.1 Consensus size: 64
31417234 ATTTAATAAA
*
31417244 AATATATGATTTAATAGCTACTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
* ** ** * * *
31417308 AATATATAATATT-ATAAAATATAAT-TTAA-AATAATTATTATTAAATAT-AATTTA--ATAA-
1 AATATATGAT-TTAAT-AGCTATTGTCTTAATAATAAATATTCTT--ATATGAATTTACTAAAAT
31417366 -A-
62 CAT
31417367 AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
31417431 AATATA
1 AATATA
31417437 ACTTGAGAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
58 11 0.11
59 21 0.21
60 12 0.12
61 3 0.03
62 3 0.03
63 12 0.12
64 27 0.27
65 10 0.10
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (64 bp):
AATATATGATTTAATAGCTATTGTCTTAATAATAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:31422328 original size:41 final size:41
Alignment explanation
Indices: 31422188--31422300 Score: 208
Period size: 41 Copynumber: 2.8 Consensus size: 41
31422178 GACTTTAAGT
31422188 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
31422229 CTAGCAGGCTACGTGCCGGTGATTTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
31422270 CTAGCAGGCTACATGCCGGTGATCTGAATCA
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCA
31422301 TGCTATAAGT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:31423250 original size:49 final size:49
Alignment explanation
Indices: 31423178--31423281 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 49
31423168 GAAAAAAAAC
* * *
31423178 AAATTAAAATTAAGTTGAATATCATGAATCAAAAGGTGAACACTT-TATA
1 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACA-TTGTATA
31423227 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACATTGTATA
1 AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACATTGTATA
31423276 AAATTA
1 AAATTA
31423282 TAACACATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 2 0.04
49 49 0.96
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACATTGTATA
Found at i:31425094 original size:33 final size:33
Alignment explanation
Indices: 31425050--31425115 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
31425040 GAATTAAAAT
31425050 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
*
31425083 TTGTTGGTATATGTATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
31425116 AATTTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (33 bp):
TTGTAGGTATATGTATAATTGAGCTAAAATTAA
Found at i:31425349 original size:19 final size:19
Alignment explanation
Indices: 31425322--31425358 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31425312 AACAAATTAA
*
31425322 TTGTTGGTATATGTAAAAT
1 TTGTAGGTATATGTAAAAT
31425341 TTGTAGGTATATGTAAAA
1 TTGTAGGTATATGTAAAA
31425359 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGTAGGTATATGTAAAAT
Found at i:31425680 original size:18 final size:18
Alignment explanation
Indices: 31425659--31425693 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31425649 TTAAATATAT
*
31425659 AATTTAATTAGTTTTATG
1 AATTTAAATAGTTTTATG
*
31425677 AATTTAAATATTTTTAT
1 AATTTAAATAGTTTTAT
31425694 TTTAACCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
AATTTAAATAGTTTTATG
Found at i:31435919 original size:13 final size:13
Alignment explanation
Indices: 31435896--31435965 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
31435886 ACTAACTTAT
*
31435896 ATTATATATATTTG
1 ATTA-ATATATTTA
31435910 ATTAATATA-TTA
1 ATTAATATATTTA
*
31435922 ATTAACT-TAATTA
1 ATTAA-TATATTTA
* *
31435935 ATCTTATATATTTG
1 AT-TAATATATTTA
31435949 ATTAATATA-TTA
1 ATTAATATATTTA
31435961 ATTAA
1 ATTAA
31435966 CTTAATTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 16 0.35
13 18 0.39
14 12 0.26
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (13 bp):
ATTAATATATTTA
Found at i:31435920 original size:22 final size:22
Alignment explanation
Indices: 31435893--31435960 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 22
31435883 TCCACTAACT
31435893 TATATTATATATATTTGATTAA
1 TATATTATATATATTTGATTAA
* *
31435915 TATATTA-AT-TAACTTAATT-A
1 TATATTATATAT-ATTTGATTAA
*
31435935 -AT-CT-TATATATTTGATTAA
1 TATATTATATATATTTGATTAA
31435954 TATATTA
1 TATATTA
31435961 ATTAACTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 14
0.62 0.11 0.26
Matches are distributed among these distances:
18 9 0.27
19 4 0.12
20 4 0.12
21 9 0.27
22 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (22 bp):
TATATTATATATATTTGATTAA
Found at i:31435945 original size:39 final size:39
Alignment explanation
Indices: 31435900--31435979 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
31435890 ACTTATATTA
31435900 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
1 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
31435939 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
1 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
31435978 TA
1 TA
31435980 CTTAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (39 bp):
TATATATTTGATTAATATATTAATTAACTTAATTAATCT
Found at i:31436959 original size:25 final size:26
Alignment explanation
Indices: 31436927--31436981 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
31436917 TTATTAAATT
*
31436927 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
31436952 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
31436977 A-ATAT
1 ATATAT
31436982 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:31437215 original size:16 final size:16
Alignment explanation
Indices: 31437194--31437229 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31437184 GATTTGCTAT
31437194 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31437210 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
31437226 TACA
1 TACA
31437230 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:31437502 original size:22 final size:23
Alignment explanation
Indices: 31437475--31437521 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
31437465 ATTATTGACA
31437475 TTTTATAATTAAA-AATTATTAT
1 TTTTATAATTAAACAATTATTAT
*
31437497 TTTTATAATTAAACTATTATTAT
1 TTTTATAATTAAACAATTATTAT
31437520 TT
1 TT
31437522 AATTTAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTATAATTAAACAATTATTAT
Found at i:31437516 original size:20 final size:21
Alignment explanation
Indices: 31437475--31437522 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
31437465 ATTATTGACA
*
31437475 TTTTATAATTAAAAATTATTAT
1 TTTTATAATT-AAAACTATTAT
31437497 TTTTATAATT-AAACTATTAT
1 TTTTATAATTAAAACTATTAT
31437517 TATTTA
1 T-TTTA
31437523 ATTTAAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
22 10 0.42
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATAATTAAAACTATTAT
Found at i:31439271 original size:23 final size:23
Alignment explanation
Indices: 31439245--31439291 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
31439235 TTTGGTGCAG
*
31439245 TGCAGTTGTACTGCCTAGGGTCT
1 TGCAGTTGTACTGCCTAAGGTCT
31439268 TGCAGTTGTACTGCCTAAGGTCT
1 TGCAGTTGTACTGCCTAAGGTCT
31439291 T
1 T
31439292 TTTTCTCTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (23 bp):
TGCAGTTGTACTGCCTAAGGTCT
Found at i:31440195 original size:24 final size:24
Alignment explanation
Indices: 31440158--31440214 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
31440148 CTGTTGTTGA
31440158 AGTTTTCAATTGAAAATGGTTTCTGT
1 AGTTTTC--TTGAAAATGGTTTCTGT
*
31440184 ATTTTTCTTGAAAATGGTTTCTGT
1 AGTTTTCTTGAAAATGGTTTCTGT
31440208 AGTTTTC
1 AGTTTTC
31440215 AATTTGTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 23 0.79
26 6 0.21
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.51
Consensus pattern (24 bp):
AGTTTTCTTGAAAATGGTTTCTGT
Found at i:31441899 original size:45 final size:44
Alignment explanation
Indices: 31441816--31441902 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
31441806 AATATCATTC
* **
31441816 CATTCAACCAAACACAAGAATACTATTATGCCTCTATTCCATCA
1 CATTCAACCAAACACAAGAATACTATTACGCAACTATTCCATCA
31441860 CATTCAACCAAACA-ATTA-AATTACTATTACGCAACTATTCCAT
1 CATTCAACCAAACACA--AGAA-TACTATTACGCAACTATTCCAT
31441903 TACAGCTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 1 0.03
44 16 0.43
45 20 0.54
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.29
Consensus pattern (44 bp):
CATTCAACCAAACACAAGAATACTATTACGCAACTATTCCATCA
Found at i:31445215 original size:44 final size:43
Alignment explanation
Indices: 31445142--31445340 Score: 156
Period size: 43 Copynumber: 4.6 Consensus size: 43
31445132 TGATTTCATA
* *
31445142 TAAGACCATAGCTGGGCTATGGCACCGATATATGAGACTTTGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATATGAGA-TTTGTG
* * *
31445186 TAAGACCATATCTGGGATATAGCATCGATATAT-ATGATTACGTG
1 TAAGACCATAGCTGGGATATGGCATCGATATATGA-GATT-TGTG
* *
31445230 TAAGACCAT-GTCTGGGACATTGGCATCG-T-TATGTGATTTCGTG
1 TAAGACCATAG-CTGGGATA-TGGCATCGATATATGAGATTT-GTG
* * * * ***
31445273 TAAGACCATAGCTGGGCTATTGACATCGATATGTGATA-ACATG
1 TAAGACCATAGCTGGGATA-TGGCATCGATATATGAGATTTGTG
* *
31445316 TAAGGCCATATCTGGGATATGGCAT
1 TAAGACCATAGCTGGGATATGGCAT
31445341 TGTATGTGTT
Statistics
Matches: 123, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
42 5 0.04
43 54 0.44
44 53 0.43
45 11 0.09
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (43 bp):
TAAGACCATAGCTGGGATATGGCATCGATATATGAGATTTGTG
Found at i:31451193 original size:49 final size:45
Alignment explanation
Indices: 31451105--31451206 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 45
31451095 TTCATATAGA
* * *
31451105 ACTACACTTCTTTTATTTTATTTTAGAATAAGGTTTTTCAACCTT
1 ACTACACTTCATTTATTTTATTTTAGAATAAGATGTTTCAACCTT
*
31451150 ATTACACTTCATTTATTTGATATTGATTAGAATAAGATGTTTCAACCTT
1 ACTACACTTCATTTATTT--TATT--TTAGAATAAGATGTTTCAACCTT
31451199 ACTACACT
1 ACTACACT
31451207 CCTTCTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 16 0.33
47 4 0.08
49 28 0.58
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (45 bp):
ACTACACTTCATTTATTTTATTTTAGAATAAGATGTTTCAACCTT
Found at i:31455699 original size:49 final size:49
Alignment explanation
Indices: 31455600--31455699 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 49
31455590 TTATTTTATT
* * * ** *
31455600 TTAGAATAAGGTTTTTCAACCTTATTATACTTTATCTATTTGATATTGA
1 TTAGAATAAGGTGTTTCAACCTTACTACACCCTATCTATTAGATATTGA
31455649 TTAGAATAAGGTGTTTCAACCTTACTACACCCCT-TCTATTAGA-ATATGA
1 TTAGAATAAGGTGTTTCAACCTTACTACA-CCCTATCTATTAGATAT-TGA
31455698 TT
1 TT
31455700 TTACAAGCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
48 2 0.05
49 39 0.91
50 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (49 bp):
TTAGAATAAGGTGTTTCAACCTTACTACACCCTATCTATTAGATATTGA
Found at i:31461990 original size:12 final size:12
Alignment explanation
Indices: 31461973--31461997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31461963 AGCAACAATG
31461973 ATTTTAGTTTTT
1 ATTTTAGTTTTT
31461985 ATTTTAGTTTTT
1 ATTTTAGTTTTT
31461997 A
1 A
31461998 GTTTCTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (12 bp):
ATTTTAGTTTTT
Found at i:31470291 original size:16 final size:16
Alignment explanation
Indices: 31470270--31470310 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31470260 AAATATTATT
31470270 ATTAAATTCAAATGAA
1 ATTAAATTCAAATGAA
* *
31470286 ATTAAACTGAAATGAA
1 ATTAAATTCAAATGAA
*
31470302 ATGAAATTC
1 ATTAAATTC
31470311 CAAAGACTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (16 bp):
ATTAAATTCAAATGAA
Found at i:31471054 original size:19 final size:19
Alignment explanation
Indices: 31471030--31471066 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31471020 TGAAACAAGT
*
31471030 TATAATTTTTTTAAAAATA
1 TATAATATTTTTAAAAATA
*
31471049 TATAATATTTTTAGAAAT
1 TATAATATTTTTAAAAAT
31471067 TACTTGCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATAATATTTTTAAAAATA
Found at i:31471561 original size:15 final size:16
Alignment explanation
Indices: 31471539--31471574 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
31471529 AGGGTGATGA
* *
31471539 TAAAAAAAATATAAAT
1 TAAAAAAATTAAAAAT
31471555 TAAAAAAATTAAAAAT
1 TAAAAAAATTAAAAAT
31471571 TAAA
1 TAAA
31471575 TAAAGGACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAAAAATTAAAAAT
Found at i:31486528 original size:45 final size:45
Alignment explanation
Indices: 31486464--31486552 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
31486454 AATAGATACT
* *
31486464 CGATGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTC
1 CGATGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
* *
31486509 CGATGGAATCAGCACATAGCAACTACCTTACTAATCAATGATGT
1 CGATGGAATCAACACATAGCAACCACCTTACTAATCAATGATGT
31486553 TCAGTTCACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (45 bp):
CGATGGAATCAACACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:31486618 original size:51 final size:50
Alignment explanation
Indices: 31486563--31486746 Score: 199
Period size: 51 Copynumber: 3.6 Consensus size: 50
31486553 TCAGTTCACA
* * * *
31486563 TAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATTTGATCCACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGATACACG
* * * * * * *
31486614 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATTCGATACACG
* * * *
31486665 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCAGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGA-TACACG
31486715 TAGTAGCCTGCACATAGTACTACACACGTGAC
1 TAGTAGCCTGCACATAGTACTACACACGTGAC
31486747 AATCACTTTC
Statistics
Matches: 107, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
49 4 0.04
50 35 0.33
51 66 0.62
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGATACACG
Found at i:31486739 original size:101 final size:101
Alignment explanation
Indices: 31486561--31486745 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
31486551 GTTCAGTTCA
* * ** *
31486561 CATAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATTTGATCCACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATTCCATACACGTAGTAGCCTGCA
31486626 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
*
31486663 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCAGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCCA-TACACGTAGTAGCCTGCA
31486727 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
31486746 CAATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 7 0.09
101 36 0.47
102 33 0.43
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCCATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:31488009 original size:19 final size:19
Alignment explanation
Indices: 31487985--31488022 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
31487975 TTGGGTTAGG
31487985 GACTAAATTGTAA-AAACTA
1 GACTAAATTG-AATAAACTA
31488004 GACTAAATTGAATAAACTA
1 GACTAAATTGAATAAACTA
31488023 TGAAGCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
GACTAAATTGAATAAACTA
Found at i:31490321 original size:42 final size:44
Alignment explanation
Indices: 31490269--31490353 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 44
31490259 TAAACATTAA
*
31490269 AAAATTATTTTAAAAATAAAAAA-AATAAA-AAAAAAT-TATTTT
1 AAAAGTATTTTAAAAATAAAAAATAA-AAATAAAAAATATATTTT
*
31490311 AAAAGTATTTTAAAATTAAAAAATAAAAATAAAAAATATATTT
1 AAAAGTATTTTAAAAATAAAAAATAAAAATAAAAAATATATTT
31490354 ATTATATTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
42 24 0.63
43 9 0.24
44 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (44 bp):
AAAAGTATTTTAAAAATAAAAAATAAAAATAAAAAATATATTTT
Found at i:31491285 original size:6 final size:6
Alignment explanation
Indices: 31491274--31491321 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
31491264 GTCTCCCTGC
* *
31491274 AAAATA AAAATA AAAATA AATAATA AGAAA-A AAAATT AAAATT AAAAT
1 AAAATA AAAATA AAAATA AA-AATA A-AAATA AAAATA AAAATA AAAAT
31491322 GGGTATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
5 3 0.08
6 27 0.71
7 7 0.18
8 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:31491296 original size:16 final size:16
Alignment explanation
Indices: 31491275--31491321 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
31491265 TCTCCCTGCA
31491275 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
* *
31491291 AAATAATAAGAAAAA-
1 AAATAAAAATAAAAAT
* *
31491306 AAATTAAAATTAAAAT
1 AAATAAAAATAAAAAT
31491322 GGGTATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:31493910 original size:14 final size:13
Alignment explanation
Indices: 31493881--31493914 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
31493871 GGTAATTTTT
31493881 TAAAAGAAAAAAA
1 TAAAAGAAAAAAA
*
31493894 TAAAATAAAATAAA
1 TAAAAGAAAA-AAA
31493908 TAAAAGA
1 TAAAAGA
31493915 CGATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
TAAAAGAAAAAAA
Found at i:31505742 original size:7 final size:7
Alignment explanation
Indices: 31505730--31505754 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31505720 TTAAAAGAAG
31505730 AAATTCT
1 AAATTCT
31505737 AAATTCT
1 AAATTCT
31505744 AAATTCT
1 AAATTCT
31505751 AAAT
1 AAAT
31505755 CCAAAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTCT
Found at i:31512626 original size:137 final size:137
Alignment explanation
Indices: 31512396--31512787 Score: 590
Period size: 140 Copynumber: 2.8 Consensus size: 137
31512386 TAGAAAAATG
* * *
31512396 AATTATATTCTTTCC-AAAAGATATTAATTTCCATGCCTTTTATATTTTAACCGAAGTTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAA-TTAATTAA
*
31512460 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATC-AATT
65 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
31512524 CATATATT
130 CATATATT
* *
31512532 AATTATATTCTTTCCAAAAAAATAATAATTTCAATGTCTTTTATATTTTGACCGATATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGA-ATTAATTAA
* * *
31512597 TATAACTATTTATATTAATAAATTTGGTAAAATATAAATATAAATAATATTTTGTATGAATCAAA
65 TATAACTATTTATATTAATAAATTCGGTAAAATAT--ATACAATTAATATTTTGTATGAATCAAA
31512662 TTCATATATT
128 TTCATATATT
* * * *
31512672 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATATTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACC-GAATTAATTAA
* *
31512737 TATATCTATTTATATTAATAAATTCGGTAAAATGTATACAATTAATATTTT
65 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTT
31512788 ATATTTTGAT
Statistics
Matches: 230, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
136 15 0.07
137 75 0.33
138 15 0.07
139 23 0.10
140 101 0.44
141 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACCGAATTAATTAAT
ATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:31516215 original size:18 final size:17
Alignment explanation
Indices: 31516163--31516212 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
31516153 GTTGGGCTTG
*
31516163 GCCTTTCCATTGTCCTTA
1 GCCTTTCCTTTG-CCTTA
* *
31516181 GGCTTTGCCTTAGCCTTA
1 GCCTTT-CCTTTGCCTTA
31516199 GCCTTTCCTTTGCC
1 GCCTTTCCTTTGCC
31516213 CTTGTTCTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.08, C:0.34, G:0.16, T:0.42
Consensus pattern (17 bp):
GCCTTTCCTTTGCCTTA
Done.