Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007172.1 Hibiscus syriacus cultivar Beakdansim tig00018823_pilon, whole genome shotgun sequence
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: 164432
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12202 original size:812 final size:812
Alignment explanation
Indices: 10596--12181 Score: 2769
Period size: 812 Copynumber: 2.0 Consensus size: 812
10586 AATTAGTATT
10596 TCAAAAATACTATTTATGCAGTAAGCATAATTTCCATAATTCCATAATTAATATTATCATATACC
1 TCAAAAATACTATTTATGCAGTAAGCATAATTTCCATAATTCCATAATTAATATTATCATATACC
*
10661 AATGAAAATCAATAATCATATATCAGTCATATTCCATAAACCATCACCAGTAAATAGGTGGATTA
66 AATGAAAACCAATAATCATATATCAGTCATATTCCATAAACCATCACCAGTAAATAGGTGGATTA
*
10726 ATAAAACATTAAACCATAGCTTTCAATATACCATATTTCAAAACATATAAAACAATCAAGTAGTA
131 ATAAAACATTAAACCATAACTTTCAATATACCATATTTCAAAACATATAAAACAATCAAGTAGTA
*
10791 CACAGGGAACACACCTCGACAATAGGTTTAAATAGTAGATCTAGTGATTGTTGGCCTCGCCACGC
196 CACAGGGAACACACCTCGACAATAGGTTTAAATAGTAGATCTAGTGATTGCTGGCCTCGCCACGC
*
10856 TCTGCTACTGTTTTCGAACCTAATCCATAATAATACTATATTACTAATGGGTAACAAAATTAATT
261 TCTGCTACTGTTTTCGAACCTAATCCATAATAACACTATATTACTAATGGGTAACAAAATTAATT
* *
10921 TCTGAAATCATAAAATTTACGGGTCTTACGGGTGAATACTAGCACACGTGGCTTAACTGATCTAG
326 TCTGAAATCATAAAATTTACGGGTCTTACGGGTGAATACTAGCACACGCGGCTTAACTAATCTAG
*
10986 AGGAGCTGGGTCGAGCTGTCGAACGGTCAGGAGAGTCTCTTGTACCTTCAAACATTAATAATTTA
391 AGGAGCTAGGTCGAGCTGTCGAACGGTCAGGAGAGTCTCTTGTACCTTCAAACATTAATAATTTA
* * * *
11051 TCAGTCCCAAGTCTTACTCAACCATTCAAAGCTTAAACTCTTTAGTATATAAGCATTTTTCTGGT
456 TCAGTCCCAAGTCTTACTCAACCATTCAAAGCTTAAACTCTTTAGTATATAAACATTTTCCGGGC
11116 TTGACTATCAATTTGAAGGCTTTCGAGTCTGAATTTTACCAAACGGAGTGTGGAATCGGAATCAG
521 TTGACTATCAATTTGAAGGCTTTCGAGTCTGAATTTTACCAAACGGAGTGTGGAATCGGAATCAG
11181 GGCGTCGAACAACATAAAGTATGACTTTTCAAAAATTCAAATTCTTGGTCAAAATCAAAGTCAAC
586 GGCGTCGAACAACATAAAGTATGACTTTTCAAAAATTCAAATTCTTGGTCAAAATCAAAGTCAAC
* * * * * * *
11246 GGGTTTGACTGACGATTCGGAGACTTTTGGTTTTGAATTTTGTGAAACCGACCCCAAAAACGGAT
651 GGGTTTGACTGACGATTCGGAGACCTTCGGGTTCGAATTTGGCGAAACAGACCCCAAAAACGGAT
* * * ** * * * * *
11311 TCGAAACGTCGAAAACTATCAGGATAGGTATTCTCGGAAAAGATTAACGGTTGTTTAATAGCCGG
716 TCGAAACATCAAAAAATATCAAAATAGGTATACTCGGAAAAAATCAAAGGTCGTTTAATAGCCGG
11376 TCAAAGCCGGTCAAAGTTCTGGTCAAAAGTGG
781 TCAAAGCCGGTCAAAGTTCTGGTCAAAAGTGG
*
11408 TCAACAATACTATTTATGCAGTAAGCATAATTTCCATAATTCCATAATTAATATTATCATATACC
1 TCAAAAATACTATTTATGCAGTAAGCATAATTTCCATAATTCCATAATTAATATTATCATATACC
11473 AATGAAAACCAATAATCATATATCAGTCATATTCCATAAACCATCACCAGTAAATAGGTGGATTA
66 AATGAAAACCAATAATCATATATCAGTCATATTCCATAAACCATCACCAGTAAATAGGTGGATTA
11538 ATAAAACATTAAACCATAACTTTCAATATACCATATTTCAAAACATATAAAACAATCAAGTAGTA
131 ATAAAACATTAAACCATAACTTTCAATATACCATATTTCAAAACATATAAAACAATCAAGTAGTA
11603 CACAGGGAACACACCTCGACAATAGGTTTAAATAGTAGATCTAGTGATTGCTGGCCTCGCCACGC
196 CACAGGGAACACACCTCGACAATAGGTTTAAATAGTAGATCTAGTGATTGCTGGCCTCGCCACGC
*
11668 TCTGCTACTGTTTTCGAACCTAATCCATAATAACATTATATTACTAATGGGTAACAAAATTAATT
261 TCTGCTACTGTTTTCGAACCTAATCCATAATAACACTATATTACTAATGGGTAACAAAATTAATT
11733 TCTGAAATCATAAAATTTACGGGTCTTACGGGTGAATACTAGCACACGCGGCTTAACTAATCTAG
326 TCTGAAATCATAAAATTTACGGGTCTTACGGGTGAATACTAGCACACGCGGCTTAACTAATCTAG
11798 AGGAGCTAGGTCGAGCTGTCGAACGGTCAGGAGAGTCTCTTGTACCTTCAAACATTAATAATTTA
391 AGGAGCTAGGTCGAGCTGTCGAACGGTCAGGAGAGTCTCTTGTACCTTCAAACATTAATAATTTA
*
11863 TCAGTCGCAAGTCTTACTCAACCATTCAAAGCTTAAACTCTTTAGTATATAAACATTTTCCGGGC
456 TCAGTCCCAAGTCTTACTCAACCATTCAAAGCTTAAACTCTTTAGTATATAAACATTTTCCGGGC
*
11928 TTGACTATCAATTTGAAGGCTTTCGAGTCTGAATTTTACCAAACTGAGTGTGGAATCGGAATCAG
521 TTGACTATCAATTTGAAGGCTTTCGAGTCTGAATTTTACCAAACGGAGTGTGGAATCGGAATCAG
*
11993 GGCGTCGAACAACATAAAGTATGACTTTTCGAAAATTCAAATTCTTGGTCAAAATCAAAGTCAAC
586 GGCGTCGAACAACATAAAGTATGACTTTTCAAAAATTCAAATTCTTGGTCAAAATCAAAGTCAAC
* * * ** **
12058 GGGTTTGACTGATGATTTGGAGGCCTTCGGGTTCGAATTTGGCGAAACAGACTTCGGAAACGGAT
651 GGGTTTGACTGACGATTCGGAGACCTTCGGGTTCGAATTTGGCGAAACAGACCCCAAAAACGGAT
* * *
12123 TCGGAACATCAAAAAATGTCAAAATATGTATACTC-GAACAAAATCAAAGGTCGTTTAAT
716 TCGAAACATCAAAAAATATCAAAATAGGTATACTCGGAA-AAAATCAAAGGTCGTTTAAT
12182 GGTTGTTTAA
Statistics
Matches: 730, Mismatches: 43, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
811 3 0.00
812 727 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (812 bp):
TCAAAAATACTATTTATGCAGTAAGCATAATTTCCATAATTCCATAATTAATATTATCATATACC
AATGAAAACCAATAATCATATATCAGTCATATTCCATAAACCATCACCAGTAAATAGGTGGATTA
ATAAAACATTAAACCATAACTTTCAATATACCATATTTCAAAACATATAAAACAATCAAGTAGTA
CACAGGGAACACACCTCGACAATAGGTTTAAATAGTAGATCTAGTGATTGCTGGCCTCGCCACGC
TCTGCTACTGTTTTCGAACCTAATCCATAATAACACTATATTACTAATGGGTAACAAAATTAATT
TCTGAAATCATAAAATTTACGGGTCTTACGGGTGAATACTAGCACACGCGGCTTAACTAATCTAG
AGGAGCTAGGTCGAGCTGTCGAACGGTCAGGAGAGTCTCTTGTACCTTCAAACATTAATAATTTA
TCAGTCCCAAGTCTTACTCAACCATTCAAAGCTTAAACTCTTTAGTATATAAACATTTTCCGGGC
TTGACTATCAATTTGAAGGCTTTCGAGTCTGAATTTTACCAAACGGAGTGTGGAATCGGAATCAG
GGCGTCGAACAACATAAAGTATGACTTTTCAAAAATTCAAATTCTTGGTCAAAATCAAAGTCAAC
GGGTTTGACTGACGATTCGGAGACCTTCGGGTTCGAATTTGGCGAAACAGACCCCAAAAACGGAT
TCGAAACATCAAAAAATATCAAAATAGGTATACTCGGAAAAAATCAAAGGTCGTTTAATAGCCGG
TCAAAGCCGGTCAAAGTTCTGGTCAAAAGTGG
Found at i:12259 original size:28 final size:28
Alignment explanation
Indices: 12227--12379 Score: 155
Period size: 29 Copynumber: 5.4 Consensus size: 28
12217 CACATTTGAA
*
12227 AATTACAAAAATATCACCTTTTAAAAAT
1 AATTACCAAAATATCACCTTTTAAAAAT
*
12255 AATTACCAAAATATCACTATTTTAAAAAT
1 AATTACCAAAATATCAC-CTTTTAAAAAT
* *
12284 AATTACCAAAATATCACCGTTTACAAAT
1 AATTACCAAAATATCACCTTTTAAAAAT
* * * *
12312 AATTCCCAAAATGTTATCGTTTTAAAAAT
1 AATTACCAAAATATCA-CCTTTTAAAAAT
* * * *
12341 AATTACCAGAATGTCACTATTTTTAAAA-
1 AATTACCAAAATATCAC-CTTTTAAAAAT
*
12369 AATTCCCAAAA
1 AATTACCAAAA
12380 ATGTAACTGG
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
28 47 0.45
29 57 0.55
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (28 bp):
AATTACCAAAATATCACCTTTTAAAAAT
Found at i:12295 original size:57 final size:57
Alignment explanation
Indices: 12227--12379 Score: 175
Period size: 57 Copynumber: 2.7 Consensus size: 57
12217 CACATTTGAA
* *
12227 AATTACAAAAATATCACCTTTTAAAAATAATTACCAAAATATCA-CTATTTTAAAAAT
1 AATTACCAAAATATCACCTTTTAAAAATAATTCCCAAAATATCATC-ATTTTAAAAAT
* * * * *
12284 AATTACCAAAATATCACCGTTTACAAATAATTCCCAAAATGTTATCGTTTTAAAAAT
1 AATTACCAAAATATCACCTTTTAAAAATAATTCCCAAAATATCATCATTTTAAAAAT
* * * *
12341 AATTACCAGAATGTCACTATTTTTAAAA-AATTCCCAAAA
1 AATTACCAAAATATCAC-CTTTTAAAAATAATTCCCAAAA
12380 ATGTAACTGG
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
57 74 0.91
58 7 0.09
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (57 bp):
AATTACCAAAATATCACCTTTTAAAAATAATTCCCAAAATATCATCATTTTAAAAAT
Found at i:16585 original size:13 final size:14
Alignment explanation
Indices: 16553--16585 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
16543 AAACACAAAC
*
16553 TTAGGGTTTATAAT
1 TTAGGGTTTATAAG
16567 TTAGGGTTT-TAAG
1 TTAGGGTTTATAAG
16580 TTAGGG
1 TTAGGG
16586 GAAGGGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTATAAG
Found at i:23724 original size:17 final size:18
Alignment explanation
Indices: 23686--23726 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
23676 TAAATGATTA
23686 ATTATTTAAAATATAAAT
1 ATTATTTAAAATATAAAT
* *
23704 -TTATTT-AAATATTATT
1 ATTATTTAAAATATAAAT
23720 ATTATTT
1 ATTATTT
23727 CATAGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTTAAAATATAAAT
Found at i:25870 original size:306 final size:306
Alignment explanation
Indices: 25317--25929 Score: 1208
Period size: 306 Copynumber: 2.0 Consensus size: 306
25307 AAAAATTGGA
25317 AAAGTATAGACGAAGGGTTATCAATCATTCTCAAAACTTAGTTACCTATAAGTGCAAAATTAAAC
1 AAAGTATAGACGAAGGGTTATCAATCATTCTCAAAACTTAGTTACCTATAAGTGCAAAATTAAAC
25382 AACTTTAGATCTCTGAAGCACAAACCGCCATCTCTTTTAGCCTGACAATGTTGTAACGCCCCAAA
66 AACTTTAGATCTCTGAAGCACAAACCGCCATCTCTTTTAGCCTGACAATGTTGTAACGCCCCAAA
* *
25447 TTCCAAATTAGTAGTTTCGGGTTAACCCTAGTAGGCCTTTGAATAAATTTCTTAGTCTATAGGAA
131 TTCCAAATTAGTAGTTTCGGGTTAACCCTAGTAGGCCTCTGAATAAATTTCTTAGCCTATAGGAA
25512 GCCTTGACCCAAATTAAAGTGGAATTGGGCTTGGGTTGAGCCCAACAGTTGATAATTATGTGATT
196 GCCTTGACCCAAATTAAAGTGGAATTGGGCTTGGGTTGAGCCCAACAGTTGATAATTATGTGATT
25577 TTTTAGAGTTGACTAAAACTTGAAGGACCAAGAGTACAATTCACCC
261 TTTTAGAGTTGACTAAAACTTGAAGGACCAAGAGTACAATTCACCC
25623 AAAGTATAGACGAAGGGTTATCAATCATTCTCAAAACTTAGTTACCTATAAGTGCAAAATTAAAC
1 AAAGTATAGACGAAGGGTTATCAATCATTCTCAAAACTTAGTTACCTATAAGTGCAAAATTAAAC
25688 AACTTTAGATCTCTGAAGCACAAACCGCCATCTCTTTTAGCCTGACAATGTTGTAACGCCCCAAA
66 AACTTTAGATCTCTGAAGCACAAACCGCCATCTCTTTTAGCCTGACAATGTTGTAACGCCCCAAA
25753 TTCCAAATTAGTAGTTTCGGGTTAACCCTAGTAGGCCTCTGAATAAATTTCTTAGCCTATAGGAA
131 TTCCAAATTAGTAGTTTCGGGTTAACCCTAGTAGGCCTCTGAATAAATTTCTTAGCCTATAGGAA
25818 GCCTTGACCCAAATTAAAGTGGAATTGGGCTTGGGTTGAGCCCAACAGTTGATAATTATGTGATT
196 GCCTTGACCCAAATTAAAGTGGAATTGGGCTTGGGTTGAGCCCAACAGTTGATAATTATGTGATT
25883 TTTTAGAGTTGACTAAAACTTGAAGGACCAAGAGTACAATTCACCC
261 TTTTAGAGTTGACTAAAACTTGAAGGACCAAGAGTACAATTCACCC
25929 A
1 A
25930 TTTTCTTTAT
Statistics
Matches: 305, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
306 305 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (306 bp):
AAAGTATAGACGAAGGGTTATCAATCATTCTCAAAACTTAGTTACCTATAAGTGCAAAATTAAAC
AACTTTAGATCTCTGAAGCACAAACCGCCATCTCTTTTAGCCTGACAATGTTGTAACGCCCCAAA
TTCCAAATTAGTAGTTTCGGGTTAACCCTAGTAGGCCTCTGAATAAATTTCTTAGCCTATAGGAA
GCCTTGACCCAAATTAAAGTGGAATTGGGCTTGGGTTGAGCCCAACAGTTGATAATTATGTGATT
TTTTAGAGTTGACTAAAACTTGAAGGACCAAGAGTACAATTCACCC
Found at i:27204 original size:19 final size:18
Alignment explanation
Indices: 27168--27218 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
27158 AAGCTTTTAG
*
27168 ATAAGTGAAGAAAAAAAT
1 ATAAGTGAGGAAAAAAAT
*
27186 A-AGAGTGAGTGAAAGAAAT
1 ATA-AGTGAG-GAAAAAAAT
27205 ATAAGTGAGGAAAA
1 ATAAGTGAGGAAAA
27219 GTGTGAGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.04
18 10 0.37
19 15 0.56
20 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (18 bp):
ATAAGTGAGGAAAAAAAT
Found at i:27266 original size:14 final size:15
Alignment explanation
Indices: 27237--27269 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
27227 AGAGAGAAAA
*
27237 AGAAAAACATACGAG
1 AGAAAAAAATACGAG
27252 AGAAAAAAATA-GAG
1 AGAAAAAAATACGAG
27266 AGAA
1 AGAA
27270 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.67, C:0.06, G:0.21, T:0.06
Consensus pattern (15 bp):
AGAAAAAAATACGAG
Found at i:31800 original size:2 final size:2
Alignment explanation
Indices: 31793--31850 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
31783 GGTTTATTGC
31793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31835 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
31851 GTGAGCAAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31922 original size:19 final size:18
Alignment explanation
Indices: 31872--31920 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
31862 AAGCTTTTAG
*
31872 ATAAGTGAAGAAA-AAAT
1 ATAAGTGAGGAAAGAAAT
31889 A-ATAGTGAGTGAAAGAAAT
1 ATA-AGTGAG-GAAAGAAAT
31908 ATAAGTGAGGAAA
1 ATAAGTGAGGAAA
31921 AGTGTGAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.04
17 6 0.22
18 8 0.30
19 11 0.41
20 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.18
Consensus pattern (18 bp):
ATAAGTGAGGAAAGAAAT
Found at i:31970 original size:13 final size:15
Alignment explanation
Indices: 31940--31971 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
31930 AAAGAGAAAA
31940 AGAAAAACATACGAG
1 AGAAAAACATACGAG
31955 AGAAAAA-ATA-GAG
1 AGAAAAACATACGAG
31968 AGAA
1 AGAA
31972 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.66, C:0.06, G:0.22, T:0.06
Consensus pattern (15 bp):
AGAAAAACATACGAG
Found at i:32454 original size:24 final size:23
Alignment explanation
Indices: 32417--32464 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
32407 TTCATTGAAA
32417 AACCGAAAAACCGAACCGAACCG
1 AACCGAAAAACCGAACCGAACCG
32440 AACCGAAAAACCCGAACCGAACCG
1 AACCGAAAAA-CCGAACCGAACCG
32464 A
1 A
32465 TAAAACCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.48, C:0.35, G:0.17, T:0.00
Consensus pattern (23 bp):
AACCGAAAAACCGAACCGAACCG
Found at i:32456 original size:19 final size:20
Alignment explanation
Indices: 32432--32471 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
32422 AAAAACCGAA
32432 CCGAACCGAACCGA-AAAAC
1 CCGAACCGAACCGATAAAAC
32451 CCGAACCGAACCGATAAAAC
1 CCGAACCGAACCGATAAAAC
32471 C
1 C
32472 GGTTTCGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.45, C:0.38, G:0.15, T:0.03
Consensus pattern (20 bp):
CCGAACCGAACCGATAAAAC
Found at i:32674 original size:20 final size:20
Alignment explanation
Indices: 32630--32675 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
32620 CAGAAGGTAG
*
32630 GTATCGATACTCAGGGGCCA
1 GTATCGATACTCAAGGGCCA
* * *
32650 ATATCGATACTGAAGGGTCA
1 GTATCGATACTCAAGGGCCA
32670 GTATCG
1 GTATCG
32676 GTACCAACGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (20 bp):
GTATCGATACTCAAGGGCCA
Found at i:34615 original size:15 final size:15
Alignment explanation
Indices: 34592--34623 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
34582 AGAAATGAAC
34592 TCATAAAAATTGTTT
1 TCATAAAAATTGTTT
*
34607 TCATGAAAATTGTTT
1 TCATAAAAATTGTTT
34622 TC
1 TC
34624 TAACTAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (15 bp):
TCATAAAAATTGTTT
Found at i:41132 original size:30 final size:30
Alignment explanation
Indices: 41096--41249 Score: 130
Period size: 30 Copynumber: 5.0 Consensus size: 30
41086 TAAATTATTT
* * *
41096 AATTATTAAATATATTATATTTTTACCTTA
1 AATTAATAAATATATTATATTCTTATCTTA
* *
41126 AATTATTAAATATTATT-TATTCTTATATTA
1 AATTAATAAATA-TATTATATTCTTATCTTA
* * *
41156 AATTAATATATATATATATATATATTATTTTA
1 AATTAATAAATATAT-TATAT-TCTTATCTTA
* * * *
41188 ATTTAAAAATATATATTTTATTCTTATTTTA
1 AATTAATAA-ATATATTATATTCTTATCTTA
* * *
41219 ATTTAATAAATATATTTTATTTTTATCTTA
1 AATTAATAAATATATTATATTCTTATCTTA
41249 A
1 A
41250 CTATAAATTT
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
29 3 0.03
30 53 0.51
31 24 0.23
32 18 0.17
33 6 0.06
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTAATAAATATATTATATTCTTATCTTA
Found at i:41188 original size:27 final size:27
Alignment explanation
Indices: 41149--41203 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
41139 TATTTATTCT
* *
41149 TATATTAAATTAATATATATATATATA
1 TATATTAAATTAATATAAAAATATATA
** *
41176 TATATTATTTTAATTTAAAAATATATA
1 TATATTAAATTAATATAAAAATATATA
41203 T
1 T
41204 TTTATTCTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TATATTAAATTAATATAAAAATATATA
Found at i:41199 original size:25 final size:26
Alignment explanation
Indices: 41171--41219 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
41161 ATATATATAT
41171 ATATATATATTATT-TTAATTTAAAA
1 ATATATATATTATTCTTAATTTAAAA
* *
41196 ATATATATTTTATTCTTATTTTAA
1 ATATATATATTATTCTTAATTTAA
41220 TTTAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATATATATATTATTCTTAATTTAAAA
Found at i:41203 original size:31 final size:32
Alignment explanation
Indices: 41105--41238 Score: 123
Period size: 31 Copynumber: 4.3 Consensus size: 32
41095 TAATTATTAA
* ** * *
41105 ATATATTATATTTTTACCTTAAATTATTAAAT
1 ATATATTATATTATTATTTTAATTTAATAAAT
* * * *
41137 AT-TATT-TATTCTTATATTAAATTAATATAT
1 ATATATTATATTATTATTTTAATTTAATAAAT
41167 ATATA-TATATATATTATTTTAATTTAA-AAAT
1 ATATATTATAT-TATTATTTTAATTTAATAAAT
* *
41198 ATATATTTTATTCTTATTTTAATTTAATAAAT
1 ATATATTATATTATTATTTTAATTTAATAAAT
*
41230 ATATTTTAT
1 ATATATTAT
41239 TTTTATCTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
30 22 0.26
31 32 0.38
32 30 0.36
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (32 bp):
ATATATTATATTATTATTTTAATTTAATAAAT
Found at i:41242 original size:25 final size:26
Alignment explanation
Indices: 41171--41243 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 26
41161 ATATATATAT
*
41171 ATATATATATTA-TTTTAATTTAAAA
1 ATATATATTTTATTTTTAATTTAAAA
*
41196 ATATATATTTTATTCTTATTTTAATTTAATA
1 ATATATATTTTA----T-TTTTAATTTAAAA
41227 A-ATATATTTTATTTTTA
1 ATATATATTTTATTTTTA
41244 TCTTAACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
25 16 0.40
26 1 0.03
30 10 0.25
31 13 0.32
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (26 bp):
ATATATATTTTATTTTTAATTTAAAA
Found at i:41465 original size:18 final size:18
Alignment explanation
Indices: 41442--41479 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41432 TTAAGAATTT
41442 AAAATTAAACTAAGATAC
1 AAAATTAAACTAAGATAC
41460 AAAATTAAACTAAGATAC
1 AAAATTAAACTAAGATAC
41478 AA
1 AA
41480 GTTATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAATTAAACTAAGATAC
Found at i:42087 original size:25 final size:25
Alignment explanation
Indices: 42058--42109 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
42048 AAAATACAAA
* *
42058 TATACAGAACATATTAATATTTTAT
1 TATACAAAACATATTAATATATTAT
*
42083 TATACAAAACATATTCATATATTAT
1 TATACAAAACATATTAATATATTAT
42108 TA
1 TA
42110 GTTGTATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (25 bp):
TATACAAAACATATTAATATATTAT
Found at i:42667 original size:22 final size:21
Alignment explanation
Indices: 42636--42683 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
42626 TAAATTTACA
* *
42636 AAAAATTAAATTTGAAAATACT
1 AAAAAGTAAAATT-AAAATACT
*
42658 AAAAAGTAAAATTAAATTACT
1 AAAAAGTAAAATTAAAATACT
42679 AAAAA
1 AAAAA
42684 ATTAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAGTAAAATTAAAATACT
Found at i:42684 original size:22 final size:22
Alignment explanation
Indices: 42626--42691 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
42616 TTAAAATATA
*
42626 TAAATTTAC-AAAAAATTAAATT
1 TAAA-TTACTAAAAAATTAAAAT
* *
42648 TGAAAATACT-AAAAAGTAAAAT
1 T-AAATTACTAAAAAATTAAAAT
42670 TAAATTACTAAAAAATTAAAAT
1 TAAATTACTAAAAAATTAAAAT
42692 ATATATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 7 0.19
22 26 0.72
23 3 0.08
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (22 bp):
TAAATTACTAAAAAATTAAAAT
Found at i:42763 original size:19 final size:18
Alignment explanation
Indices: 42719--42764 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
42709 ATTGAAAATG
42719 TTATTTTTA-AATAATTT
1 TTATTTTTATAATAATTT
*
42736 TTATTTTTATAATATTTT
1 TTATTTTTATAATAATTT
*
42754 ATTATATTTAT
1 -TTATTTTTAT
42765 TTAATTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 7 0.28
19 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTTATAATAATTT
Found at i:44019 original size:132 final size:132
Alignment explanation
Indices: 43775--44069 Score: 344
Period size: 132 Copynumber: 2.2 Consensus size: 132
43765 CATCGGAAAG
* * * * * **
43775 AAAGAGGCAATTGTCCGACAGTCGACCGCTGGTTTAAGTTGTGAGCATTGGCACCAATGGAGAAA
1 AAAG-GGCAATGGTCCGACAGTCGACTGCTGGTCTAAGTTGCGAGAACGGGCACCAATGGAGAAA
* * * *
43840 GGGTTTATATTTGTTTGTCTTGGCCTTGGTGACGTCGGATTCCAGTTGTTCACCTTCGAT-TGGA
65 GGGTTTATATTTGTTTCTATTGGCCTTAGTGACGTCGGATTCCAGTTGTTCACCGTCGATCT-GA
43904 ACGA
129 ACGA
* *
43908 AAATGGCAATGGTCGGACAGTCGACTGCTGGTCTACA-TTGCGAGAACGGGCACCAATGGA-ATA
1 AAAGGGCAATGGTCCGACAGTCGACTGCTGGTCTA-AGTTGCGAGAACGGGCACCAATGGAGA-A
* * ** * *
43971 AGGGTTTCTATTTGTTTCTATTGGCCTTATTGGTGTCGGATTCGAGTTGTTCCCCGTCGATCTGA
64 AGGGTTTATATTTGTTTCTATTGGCCTTAGTGACGTCGGATTCCAGTTGTTCACCGTCGATCTGA
44036 ACGA
129 ACGA
* *
44040 AACGGGCAGTGGTCCGACAGTCGACTGCTG
1 AAAGGGCAATGGTCCGACAGTCGACTGCTG
44070 ATTTAACGCG
Statistics
Matches: 136, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
131 1 0.01
132 130 0.96
133 5 0.04
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (132 bp):
AAAGGGCAATGGTCCGACAGTCGACTGCTGGTCTAAGTTGCGAGAACGGGCACCAATGGAGAAAG
GGTTTATATTTGTTTCTATTGGCCTTAGTGACGTCGGATTCCAGTTGTTCACCGTCGATCTGAAC
GA
Found at i:44083 original size:132 final size:132
Alignment explanation
Indices: 43824--44121 Score: 316
Period size: 132 Copynumber: 2.3 Consensus size: 132
43814 TGTGAGCATT
* * *
43824 GGCACCAATGGAGAAAGGGTTTATATTTGTTTGTCTTGGCCTTGGTGACGTCGGATTCCAGTTGT
1 GGCACCAATGGAGAAAGGGTTTATATTTGTTTCTATTGGCCTTAGTGACGTCGGATTCCAGTTGT
* * * * **
43889 TCACCTTCGATTGGAACGAAAATGGCAATGGTCGGACAGTCGACTGCTGGTCTACATTGCGAGAA
66 TCACCGTCGATTGGAACGAAAAGGGCAATGGTCCGACAGTCGACTGCTGATCTACAGCGCGAGAA
43954 CG
131 CG
* * ** *
43956 GGCACCAATGGA-ATAAGGGTTTCTATTTGTTTCTATTGGCCTTATTGGTGTCGGATTCGAGTTG
1 GGCACCAATGGAGA-AAGGGTTTATATTTGTTTCTATTGGCCTTAGTGACGTCGGATTCCAGTTG
* * * *
44020 TTCCCCGTCGATCT-GAACGAAACGGGCAGTGGTCCGACAGTCGACTGCTGATTTA-ACGCGCGA
65 TTCACCGTCGAT-TGGAACGAAAAGGGCAATGGTCCGACAGTCGACTGCTGATCTACA-GCGCGA
**
44083 GCATTG
128 G-AACG
* * * *
44089 GG-TCCAACGGAGAAAGGGTTCATATTTATTTCT
1 GGCACCAATGGAGAAAGGGTTTATATTTGTTTCT
44122 CTCGGCGGCA
Statistics
Matches: 136, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
131 2 0.01
132 128 0.94
133 6 0.04
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (132 bp):
GGCACCAATGGAGAAAGGGTTTATATTTGTTTCTATTGGCCTTAGTGACGTCGGATTCCAGTTGT
TCACCGTCGATTGGAACGAAAAGGGCAATGGTCCGACAGTCGACTGCTGATCTACAGCGCGAGAA
CG
Found at i:48921 original size:8 final size:8
Alignment explanation
Indices: 48908--48962 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
48898 TAATATTTTT
48908 TTAAAATA
1 TTAAAATA
48916 TTAAAATA
1 TTAAAATA
* *
48924 ATAATATTA
1 TTAA-AATA
48933 TTAAAATA
1 TTAAAATA
48941 -TAAAA-A
1 TTAAAATA
* *
48947 ATATAATA
1 TTAAAATA
48955 TTAAAATA
1 TTAAAATA
48963 AGAATATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
6 1 0.03
7 9 0.24
8 21 0.57
9 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TTAAAATA
Found at i:48931 original size:14 final size:14
Alignment explanation
Indices: 48912--48971 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
48902 ATTTTTTTAA
48912 AATATTAAAATAAT
1 AATATTAAAATAAT
*
48926 AATATT--ATTAA-
1 AATATTAAAATAAT
*
48937 AATA-TAAAAAATAT
1 AATATTAAAATA-AT
*
48951 AATATTAAAATAAG
1 AATATTAAAATAAT
48965 AATATTA
1 AATATTA
48972 TATTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
10 1 0.03
11 4 0.11
12 6 0.17
13 1 0.03
14 18 0.50
15 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AATATTAAAATAAT
Found at i:48936 original size:17 final size:17
Alignment explanation
Indices: 48914--48972 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 17
48904 TTTTTTAAAA
*
48914 TATTAAAATAATAATAT
1 TATTAAAATAAAAATAT
48931 TATTAAAATATAAAAAATAT
1 TATT-AAA-AT-AAAAATAT
*
48951 AATATTAAAATAAGAATAT
1 --TATTAAAATAAAAATAT
48970 TAT
1 TAT
48973 ATTATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 7 0.20
18 3 0.09
19 9 0.26
20 9 0.26
21 3 0.09
22 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TATTAAAATAAAAATAT
Found at i:48946 original size:25 final size:25
Alignment explanation
Indices: 48862--48957 Score: 83
Period size: 25 Copynumber: 3.9 Consensus size: 25
48852 TATAAACATC
*
48862 AAATATAATAAATAATATTATTTATTA
1 AAATATAA-AAATAATAATA-TTATTA
* * * *
48889 ACA-A-AATAATAAT-ATTTTTTTA
1 AAATATAAAAATAATAATATTATTA
*
48911 AAATATTAAAATAATAATATTATTA
1 AAATATAAAAATAATAATATTATTA
48936 AAATATAAAAA-ATATAATATTA
1 AAATATAAAAATA-ATAATATTA
48958 AAATAAGAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
22 7 0.13
23 2 0.04
24 14 0.26
25 28 0.52
26 1 0.02
27 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATATAAAAATAATAATATTATTA
Found at i:49076 original size:22 final size:19
Alignment explanation
Indices: 49026--49073 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
49016 TTTTTATGAA
*
49026 ATTAATAAATAATATTAAT
1 ATTATTAAATAATATTAAT
*
49045 TTTATT-AATAATTATTATAT
1 ATTATTAAATAA-TATTA-AT
49065 ATTATTAAA
1 ATTATTAAA
49074 ATAAAAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 7 0.30
21 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATTAAATAATATTAAT
Found at i:49105 original size:29 final size:29
Alignment explanation
Indices: 49060--49116 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
49050 TAATAATTAT
*
49060 TATATATTATTAAAATAAAAGTATAACAC
1 TATATATTACTAAAATAAAAGTATAACAC
* *
49089 TATATATT-CTAATAATATAATTATAACA
1 TATATATTACTAA-AATAAAAGTATAACA
49117 ATAAAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.39
Consensus pattern (29 bp):
TATATATTACTAAAATAAAAGTATAACAC
Found at i:52035 original size:30 final size:31
Alignment explanation
Indices: 51933--52035 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
51923 ATTAATGTCA
* * *
51933 TATTCTTTTCCCAACATGTTATTTAATACAT
1 TATTCTTTTCCCAATATGCTATTTATTACAT
* *
51964 TATAT-TTTTCCAAATTATGAC-ATTAATGT-CAT
1 TAT-TCTTTTCCCAA-TATG-CTATTTAT-TACAT
51996 T-TTCTTTTCCCAATATGCTATTTATTACAT
1 TATTCTTTTCCCAATATGCTATTTATTACAT
52026 TATT-TTTTCC
1 TATTCTTTTCC
52036 TCAACAGTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
29 2 0.04
30 20 0.35
31 22 0.39
32 12 0.21
33 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.51
Consensus pattern (31 bp):
TATTCTTTTCCCAATATGCTATTTATTACAT
Found at i:53792 original size:27 final size:26
Alignment explanation
Indices: 53762--53826 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
53752 ATATCTTATC
53762 TTTAAATTAAACATTA-AATTATAAAAT
1 TTTAAATTAAA-ATTATAATT-TAAAAT
*
53789 TTTAAATCTTAAATTATAATTTAAAAT
1 TTTAAAT-TAAAATTATAATTTAAAAT
*
53816 TTTAAGTTAAA
1 TTTAAATTAAA
53827 GGTAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 3 0.09
27 23 0.70
28 7 0.21
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (26 bp):
TTTAAATTAAAATTATAATTTAAAAT
Found at i:53815 original size:20 final size:21
Alignment explanation
Indices: 53775--53820 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
53765 AAATTAAACA
*
53775 TTAAATTATAAAATTTTAAATC
1 TTAAATTAT-AAATTTAAAATC
*
53797 TTAAATTAT-AATTTAAAATT
1 TTAAATTATAAATTTAAAATC
53817 TTAA
1 TTAA
53821 GTTAAAGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
22 9 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATTATAAATTTAAAATC
Found at i:54254 original size:20 final size:20
Alignment explanation
Indices: 54225--54262 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54215 TTTCAAGGGT
54225 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
* *
54245 ATGCATCGATGCATCAAT
1 ATGCACCGATGCACCAAT
54263 TAATTTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:54331 original size:45 final size:46
Alignment explanation
Indices: 54282--54372 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
54272 GAACATCGAA
* *
54282 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
54327 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
54373 GCTTTTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 21 0.49
46 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:56316 original size:21 final size:20
Alignment explanation
Indices: 56230--56387 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
56220 AAATGACCAA
**
56230 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
56249 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
56269 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
56289 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
56310 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
56331 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
56351 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
56372 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
56388 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:56416 original size:20 final size:20
Alignment explanation
Indices: 56354--56547 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
56344 CGATTTTCCA
* ** *
56354 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
56374 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
56394 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
56414 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
56434 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
56454 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
56474 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
56494 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
56514 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
56535 AAATCGCAACGCG
1 AAATCGCAACGCG
56548 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:56438 original size:60 final size:60
Alignment explanation
Indices: 56354--56547 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
56344 CGATTTTCCA
* ** * *
56354 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
56414 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
56474 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
56535 AAATCGCAACGCG
1 AAATCGCAACGCG
56548 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:56720 original size:21 final size:22
Alignment explanation
Indices: 56694--56747 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
56684 CTCTCTACGG
56694 CGAAGAAATCC-TCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
56715 CGAAGATTTCCGTCCCCATCTC
1 CGAAGAAATCCGTCCCCATCTC
**
56737 CGGCGAAATCC
1 CGAAGAAATCC
56748 CTCACAACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTC
Found at i:56963 original size:32 final size:32
Alignment explanation
Indices: 56925--56993 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
56915 ATTTCACTTA
*
56925 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
56957 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
56989 GATTT
1 GATTT
56994 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:56974 original size:18 final size:18
Alignment explanation
Indices: 56925--56974 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
56915 ATTTCACTTA
*
56925 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
56943 GA-TTC-TGT--CGTTGC
1 GATTTCATTTCGCGTTGC
56957 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
56975 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:57100 original size:21 final size:20
Alignment explanation
Indices: 57076--57181 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
57066 TGCAGAAGAG
*
57076 TCGCAATGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
57097 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
57117 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
57138 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
57152 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
57171 TCGCAACGAGA
1 TCGCAACGAGA
57182 GAATCGCAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 16 0.24
21 25 0.37
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:57120 original size:20 final size:20
Alignment explanation
Indices: 57089--57185 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
57079 CAATGAGATA
57089 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
57109 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
57129 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
57148 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
57163 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
57183 AAT
1 AAT
57186 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:57133 original size:41 final size:38
Alignment explanation
Indices: 57069--57185 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
57059 TTCAATTTGC
* * *
57069 AGAAGAGTCGCAATGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
57107 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
57148 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
57181 AGAAT
1 AGAAT
57186 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
33 23 0.33
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.16, G:0.26, T:0.12
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:57155 original size:14 final size:14
Alignment explanation
Indices: 57136--57192 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
57126 GAGAAATGAA
57136 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
57150 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
57169 AATCGCAACGAGAG
1 AATCGCAACGAGAG
57183 AATCGCAACG
1 AATCGCAACG
57193 CGAACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:57168 original size:33 final size:33
Alignment explanation
Indices: 57128--57196 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
57118 CGCAACGAGA
57128 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57161 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57194 GAA
1 GAA
57197 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.25, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:57230 original size:19 final size:19
Alignment explanation
Indices: 57203--57300 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
57193 CGAACCAAAA
*
57203 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
57222 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
57236 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
57255 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
57269 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
57288 TCGCGTTGCGATT
1 TCGCGTTGCGATT
57301 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:57244 original size:14 final size:14
Alignment explanation
Indices: 57225--57314 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
57215 TTTCATTTCG
57225 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57239 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57258 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57272 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
57291 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
57305 CGTTGCGATT
1 CGTTGCGATT
57315 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:57250 original size:33 final size:33
Alignment explanation
Indices: 57208--57322 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
57198 CAAAATCGCA
57208 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
57241 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
57274 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
57307 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
57323 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:57663 original size:19 final size:19
Alignment explanation
Indices: 57647--57744 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
57637 AAAAATGACT
57647 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
57666 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
57685 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
57699 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
57718 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
57738 ATCGCAA
1 ATCGCAA
57745 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:57776 original size:53 final size:53
Alignment explanation
Indices: 57647--57762 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
57637 AAAAATGACT
57647 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
57699 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
57752 ATCGCAATGCG
1 ATCGCAATGCG
57763 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:57806 original size:33 final size:33
Alignment explanation
Indices: 57769--57921 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
57759 TGCGTTTATA
57769 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * *
57802 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTAC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC
* * *
57833 AATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 -ATT-TCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
57873 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
57906 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
57922 TTCATTTCGC
Statistics
Matches: 98, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.53
35 6 0.06
36 3 0.03
37 1 0.01
38 11 0.11
39 4 0.04
40 7 0.07
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:57815 original size:19 final size:19
Alignment explanation
Indices: 57791--58007 Score: 222
Period size: 19 Copynumber: 12.4 Consensus size: 19
57781 GATTCTCTCG
57791 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57810 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
57829 TTAC-A-ATTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
57843 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57862 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
57881 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
57895 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
57914 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
57933 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
57947 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
57967 TTACGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
57981 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
58000 TTGCGATT
1 TTGCGATT
58008 CTCTCGTTGC
Statistics
Matches: 163, Mismatches: 14, Indels: 42
0.74 0.06 0.19
Matches are distributed among these distances:
14 25 0.15
15 1 0.01
16 23 0.14
17 20 0.12
18 4 0.02
19 79 0.48
20 11 0.07
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:57826 original size:52 final size:52
Alignment explanation
Indices: 57769--57979 Score: 386
Period size: 52 Copynumber: 4.0 Consensus size: 52
57759 TGCGTTTATA
57769 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
57821 ATTTCGCATTACAATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
57873 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
57925 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTACGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
57978 AT
1 AT
57980 GTTGGGATTT
Statistics
Matches: 153, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 137 0.90
53 16 0.10
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:58029 original size:33 final size:33
Alignment explanation
Indices: 57810--58021 Score: 207
Period size: 33 Copynumber: 6.2 Consensus size: 33
57800 TCATTTCGCA
* *
57810 TTGCGATTTTCATTTCGCATTACAATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
57843 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
57879 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
57914 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
57947 TTGCGATTTTCATTTCCGCATTACGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
57981 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
58014 TTGCGATT
1 TTGCGATT
58022 GTAATTTCCG
Statistics
Matches: 145, Mismatches: 20, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 70 0.48
34 28 0.19
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.06
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:60308 original size:12 final size:12
Alignment explanation
Indices: 60291--60315 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60281 TCTTCGGGGA
60291 CTTTTTCTTCTT
1 CTTTTTCTTCTT
60303 CTTTTTCTTCTT
1 CTTTTTCTTCTT
60315 C
1 C
60316 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:60521 original size:24 final size:24
Alignment explanation
Indices: 60487--60533 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
60477 CTGAAACATC
60487 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
60511 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
60534 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:61237 original size:20 final size:20
Alignment explanation
Indices: 61209--61438 Score: 221
Period size: 20 Copynumber: 11.5 Consensus size: 20
61199 AAATTTCAGT
* * *
61209 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
61229 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
61249 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
61269 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
61289 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
61309 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
61329 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
61349 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
61369 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
61389 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
61409 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
61429 GTTGCGATTT
1 GTTGCGATTT
61439 TGGAAAATCG
Statistics
Matches: 181, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
19 3 0.02
20 173 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:61455 original size:21 final size:21
Alignment explanation
Indices: 61425--61507 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
61415 ATTTTAATAT
*
61425 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
61446 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
61467 TCGCATTGCAATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
61488 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
61508 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:61498 original size:42 final size:43
Alignment explanation
Indices: 61405--61503 Score: 98
Period size: 42 Copynumber: 2.4 Consensus size: 43
61395 ATTTATGTGT
* * *
61405 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCAATTTTGCAAAA
** *
61446 TCGCAATGCGAATTTGTACTA-TCGCATTGCAATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCAATTTTGCAA-AA
*
61488 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
61504 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 10 0.22
42 32 0.70
43 4 0.09
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCAATTTTGCAAAA
Found at i:64660 original size:29 final size:29
Alignment explanation
Indices: 64618--64676 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
64608 CTCATTTTTT
64618 TTGGGACTCCAAATCAAGCAAAGAAAAGA
1 TTGGGACTCCAAATCAAGCAAAGAAAAGA
64647 TTGGGACTCCAAATCAAGCAAAGAAAAGA
1 TTGGGACTCCAAATCAAGCAAAGAAAAGA
64676 T
1 T
64677 GACATCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (29 bp):
TTGGGACTCCAAATCAAGCAAAGAAAAGA
Found at i:68534 original size:20 final size:20
Alignment explanation
Indices: 68509--68547 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
68499 TTTTCAATGG
68509 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
68529 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
68548 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:68616 original size:45 final size:46
Alignment explanation
Indices: 68567--68657 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
68557 GAACATCGAA
* *
68567 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
68612 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
68658 ATTTTTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 21 0.49
46 22 0.51
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:71510 original size:29 final size:29
Alignment explanation
Indices: 71441--71534 Score: 152
Period size: 29 Copynumber: 3.2 Consensus size: 29
71431 ACGTGGGGGC
* *
71441 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATA-AAA
71471 ATGGTAGTGGCATGGGATGTTGAATAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAA
71500 ATGGTAGTGGCATGGGATGTTGAATAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAA
71529 TATGGT
1 -ATGGT
71535 GGAATAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 32 0.52
30 29 0.48
ACGTcount: A:0.33, C:0.03, G:0.34, T:0.30
Consensus pattern (29 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAA
Found at i:72680 original size:15 final size:15
Alignment explanation
Indices: 72660--72706 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
72650 CGCCCCGCAT
*
72660 CCGCCCTGCATCCGC
1 CCGCCCCGCATCCGC
72675 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
** *
72690 CTACCCCACATCCGC
1 CCGCCCCGCATCCGC
72705 CC
1 CC
72707 ACCCAGCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.64, G:0.15, T:0.11
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:72710 original size:15 final size:15
Alignment explanation
Indices: 72668--72710 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
72658 ATCCGCCCTG
* *
72668 CATCCGCCCGCCCCG
1 CATCCGCCCACCCCA
*
72683 CATCCGCCTACCCCA
1 CATCCGCCCACCCCA
72698 CATCCGCCCACCC
1 CATCCGCCCACCC
72711 AGCTAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.14, C:0.65, G:0.12, T:0.09
Consensus pattern (15 bp):
CATCCGCCCACCCCA
Found at i:79722 original size:18 final size:18
Alignment explanation
Indices: 79696--79730 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
79686 ACTGAATATT
*
79696 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
79714 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
79731 GATAATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:84465 original size:15 final size:15
Alignment explanation
Indices: 84445--84484 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
84435 GCAATAAAGA
84445 ATATTGATACTCATT
1 ATATTGATACTCATT
84460 ATATTGATACTCATT
1 ATATTGATACTCATT
84475 ATATTGATAC
1 ATATTGATAC
84485 AATAGAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.45
Consensus pattern (15 bp):
ATATTGATACTCATT
Found at i:89544 original size:16 final size:16
Alignment explanation
Indices: 89523--89556 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
89513 TTTGTTGGAA
89523 GTCTACTGTTCAATCT
1 GTCTACTGTTCAATCT
89539 GTCTACTGTTCAATCT
1 GTCTACTGTTCAATCT
89555 GT
1 GT
89557 TGTGGCACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (16 bp):
GTCTACTGTTCAATCT
Found at i:91508 original size:29 final size:30
Alignment explanation
Indices: 91455--91512 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
91445 TCACAATGAT
*
91455 CATTTTACAACGTTTGATAAATTTAATAAC
1 CATTTTACAACGTTTGAAAAATTTAATAAC
* *
91485 CATTTTATAAC-TTTTAAAAATTTAATAA
1 CATTTTACAACGTTTGAAAAATTTAATAA
91513 TCAGAGTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (30 bp):
CATTTTACAACGTTTGAAAAATTTAATAAC
Found at i:98590 original size:6 final size:6
Alignment explanation
Indices: 98579--99558 Score: 818
Period size: 6 Copynumber: 164.5 Consensus size: 6
98569 TACTAGTAGT
*
98579 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AAAAGA AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
98627 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
98675 AGAAGA AGAAGG AGAAGA AGGAGA AG-AGG AGAAGG AGGAGA AGGAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * *
98722 AGAAGG AGGAGA AGGAGG AGAAGG AGGAGA AGGAGGA A-AAGG AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA
* * * * * * *
98770 AGAAGG AGAAGG AGAAGC AGAAGA AGGAGA AGGAGG AGAAGA AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
98818 AGAAGG AGAAGA AGAAGA AGGAGA AGGAGA AGGAGA ATG-AGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA
* * * * *
98866 AGAAAA AGAAGA AGAAGG AGAAGG AGAAGA AGGAAG- AGAAGG AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA
* * * * * * * * *
98914 AGAAGG AGAAGG AGGAGA AGGAGG AGGAGA AGGAGA AGGAGA AGGATG-
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA
* *
98962 AGAAGA AGAAG- AGAAGA AGAAGA AGGAAGG AGAAGG AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA A-GAAGA AGAAGA AGAAGA AGAAGA
* * * * *
99010 A-AA-A AGAAGA AGGAGA AGGAGG AGAAGA AGGAGA AGGAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * *
99056 AGAAGG AGAAGG AGGAGA AGAAGGG AGAAG- AGAAG- AGAAGA AG-AGA
1 AGAAGA AGAAGA AGAAGA AGAA-GA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * *
99102 AGGAGA AGGAGA AGAAGA A-AA-A AGAAGA AGGAGA AGGAGG AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
99148 AGAAGG AG-AGA AGAGAGG AGAAGG AGAAGG AGAAGG AGAAGG AGGAGA
1 AGAAGA AGAAGA AGA-AGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * *
99196 AGAAGA AGGAGA AGGAGA AGGAGA AGAAGA AGGAGA AGGAGG AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
99244 AGAAGA AGGAGA AGGAGG AGAAGG AGAAGA AGGAGA AGAAGG AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * * * *
99292 AGGAGG AGAAGG AGGAGG AGAAGG AGGAGA AGAAGG AGAAGA AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
99340 AGAAGG AGGAGA AGAAGG AGAAGA AGGAGG AGAAGA AGAAGG AGAAGG
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * * *
99388 AGAAGA AGGAGG AGAAGA AGAAGG AGAAGA AGGAGG AGAAGG AGGAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * * * * *
99436 AGAAGG AGGAGA AGAAGA AGAAGG AGGAGG AGAAGA AGAAGG AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
* * *
99484 AGGAGG AGAAGA AGAAGG AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA AGAAGA
99532 AGAAGA AGAAGA AGAAGA AGAAGA AGA
1 AGAAGA AGAAGA AGAAGA AGAAGA AGA
99559 TAGACGTAAG
Statistics
Matches: 818, Mismatches: 136, Indels: 40
0.82 0.14 0.04
Matches are distributed among these distances:
4 4 0.00
5 47 0.06
6 741 0.91
7 26 0.03
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AGAAGA
Found at i:98593 original size:9 final size:9
Alignment explanation
Indices: 98579--99558 Score: 818
Period size: 9 Copynumber: 109.7 Consensus size: 9
98569 TACTAGTAGT
98579 AGAAGAAGA
1 AGAAGAAGA
98588 AGAAGAAGA
1 AGAAGAAGA
98597 AGAAGAAGA
1 AGAAGAAGA
*
98606 AGAAAAAGA
1 AGAAGAAGA
98615 AGAAGAAGA
1 AGAAGAAGA
98624 AGAAGAAGA
1 AGAAGAAGA
98633 AGAAGAAGA
1 AGAAGAAGA
98642 AGAAGAAGA
1 AGAAGAAGA
98651 AGAAGAAGA
1 AGAAGAAGA
98660 AGAAGAAGA
1 AGAAGAAGA
98669 AGAAGAAGA
1 AGAAGAAGA
*
98678 AGAAGAAGG
1 AGAAGAAGA
*
98687 AGAAGAAGG
1 AGAAGAAGA
*
98696 AGAAG-AGG
1 AGAAGAAGA
* *
98704 AGAAGGAGG
1 AGAAGAAGA
* *
98713 AGAAGGAGG
1 AGAAGAAGA
* *
98722 AGAAGGAGG
1 AGAAGAAGA
* *
98731 AGAAGGAGG
1 AGAAGAAGA
* *
98740 AGAAGGAGG
1 AGAAGAAGA
*
98749 AGAAGGAGGA
1 AGAA-GAAGA
*
98759 A-AAGGAGA
1 AGAAGAAGA
*
98767 AGAAGAAGG
1 AGAAGAAGA
*
98776 AGAAGGAGA
1 AGAAGAAGA
*
98785 AGCAGAAGA
1 AGAAGAAGA
* *
98794 AGGAGAAGG
1 AGAAGAAGA
*
98803 AGGAGAAGA
1 AGAAGAAGA
*
98812 AGAAGGAGA
1 AGAAGAAGA
*
98821 AGGAGAAGA
1 AGAAGAAGA
*
98830 AGAAGAAGG
1 AGAAGAAGA
*
98839 AGAAGGAGA
1 AGAAGAAGA
*
98848 AGGAGAATG-
1 AGAAGAA-GA
98857 AGAAGAAGA
1 AGAAGAAGA
*
98866 AGAAAAAGA
1 AGAAGAAGA
*
98875 AGAAGAAGG
1 AGAAGAAGA
*
98884 AGAAGGAGA
1 AGAAGAAGA
98893 AGAAGGAAG-
1 AGAA-GAAGA
* *
98902 AGAAGGAGG
1 AGAAGAAGA
*
98911 AGAAGAAGG
1 AGAAGAAGA
* *
98920 AGAAGGAGG
1 AGAAGAAGA
* *
98929 AGAAGGAGG
1 AGAAGAAGA
* *
98938 AGGAGAAGG
1 AGAAGAAGA
*
98947 AGAAGGAGA
1 AGAAGAAGA
*
98956 AGGATG-AGA
1 A-GAAGAAGA
98965 AGAAGAAG-
1 AGAAGAAGA
98973 AGAAGAAGA
1 AGAAGAAGA
*
98982 AGAAGGAAGG
1 AGAA-GAAGA
*
98992 AGAAGGAGA
1 AGAAGAAGA
99001 AGAAGAAGA
1 AGAAGAAGA
99010 A-AA-AAGA
1 AGAAGAAGA
*
99017 AGAAGGAGA
1 AGAAGAAGA
* *
99026 AGGAGGAGA
1 AGAAGAAGA
*
99035 AGAAGGAGA
1 AGAAGAAGA
*
99044 AGGAGAAGA
1 AGAAGAAGA
*
99053 AGAAGAAGG
1 AGAAGAAGA
* *
99062 AGAAGGAGG
1 AGAAGAAGA
*
99071 AGAAGAAGGG
1 AGAAGAA-GA
99081 AGAAG-AGA
1 AGAAGAAGA
99089 AG-AGAAGA
1 AGAAGAAGA
*
99097 AG-AGAAGG
1 AGAAGAAGA
*
99105 AGAAGGAGA
1 AGAAGAAGA
99114 AGAAGAA-A
1 AGAAGAAGA
99122 A-AAGAAGA
1 AGAAGAAGA
* *
99130 AGGAGAAGG
1 AGAAGAAGA
*
99139 AGGAGAAGA
1 AGAAGAAGA
*
99148 AGAAGGAG-
1 AGAAGAAGA
*
99156 AGAAGAGAGG
1 AGAAGA-AGA
*
99166 AGAAGGAGA
1 AGAAGAAGA
* *
99175 AGGAGAAGG
1 AGAAGAAGA
* *
99184 AGAAGGAGG
1 AGAAGAAGA
99193 AGAAGAAGA
1 AGAAGAAGA
* *
99202 AGGAGAAGG
1 AGAAGAAGA
*
99211 AGAAGGAGA
1 AGAAGAAGA
*
99220 AGAAGAAGG
1 AGAAGAAGA
* *
99229 AGAAGGAGG
1 AGAAGAAGA
99238 AGAAGAAGA
1 AGAAGAAGA
*
99247 AGAAGGAGA
1 AGAAGAAGA
* *
99256 AGGAGGAGA
1 AGAAGAAGA
*
99265 AGGAGAAGA
1 AGAAGAAGA
*
99274 AGGAGAAGA
1 AGAAGAAGA
* *
99283 AGGAGGAGA
1 AGAAGAAGA
* *
99292 AGGAGGAGA
1 AGAAGAAGA
* * *
99301 AGGAGGAGG
1 AGAAGAAGA
* *
99310 AGAAGGAGG
1 AGAAGAAGA
*
99319 AGAAGAAGG
1 AGAAGAAGA
*
99328 AGAAGAAGG
1 AGAAGAAGA
*
99337 AGAAGAAGG
1 AGAAGAAGA
*
99346 AGGAGAAGA
1 AGAAGAAGA
*
99355 AGGAGAAGA
1 AGAAGAAGA
* *
99364 AGGAGGAGA
1 AGAAGAAGA
*
99373 AGAAGAAGG
1 AGAAGAAGA
*
99382 AGAAGGAGA
1 AGAAGAAGA
* *
99391 AGAAGGAGG
1 AGAAGAAGA
99400 AGAAGAAGA
1 AGAAGAAGA
*
99409 AGGAGAAGA
1 AGAAGAAGA
* *
99418 AGGAGGAGA
1 AGAAGAAGA
* *
99427 AGGAGGAGA
1 AGAAGAAGA
* *
99436 AGAAGGAGG
1 AGAAGAAGA
99445 AGAAGAAGA
1 AGAAGAAGA
* *
99454 AGAAGGAGG
1 AGAAGAAGA
*
99463 AGGAGAAGA
1 AGAAGAAGA
*
99472 AGAAGGAGA
1 AGAAGAAGA
* *
99481 AGAAGGAGG
1 AGAAGAAGA
99490 AGAAGAAGA
1 AGAAGAAGA
*
99499 AGGAGAAGA
1 AGAAGAAGA
99508 AGAAGAAGA
1 AGAAGAAGA
99517 AGAAGAAGA
1 AGAAGAAGA
99526 AGAAGAAGA
1 AGAAGAAGA
99535 AGAAGAAGA
1 AGAAGAAGA
99544 AGAAGAAGA
1 AGAAGAAGA
99553 AGAAGA
1 AGAAGA
99559 TAGACGTAAG
Statistics
Matches: 828, Mismatches: 123, Indels: 40
0.84 0.12 0.04
Matches are distributed among these distances:
7 12 0.01
8 55 0.07
9 731 0.88
10 30 0.04
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
AGAAGAAGA
Found at i:100333 original size:64 final size:64
Alignment explanation
Indices: 100265--100442 Score: 245
Period size: 64 Copynumber: 2.8 Consensus size: 64
100255 CATAAAATAT
*
100265 ATTCGATGTTGT-ATTATTACTGGGATGCATCGATGCACTACTTATGCATCAATGCACGAATTGC
1 ATTCGATGTT-TCATTATTAATGGGATGCATCGATGCACTACTTATGCATCAATGCACGAATTGC
*
100329 ATTCGATGTTTCATTATTAATGGGATGCATCGATGCACTACTTATGCATCGATGCACGAATTGC
1 ATTCGATGTTTCATTATTAATGGGATGCATCGATGCACTACTTATGCATCAATGCACGAATTGC
* ** **
100393 ATTCGATGTATTTATT-TTAA-AAGAGTGCATCGATGCACTACCAATGCATC
1 ATTCGATGT-TTCATTATTAATGGGA-TGCATCGATGCACTACTTATGCATC
100443 GATACACCTT
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
63 3 0.03
64 96 0.92
65 5 0.05
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (64 bp):
ATTCGATGTTTCATTATTAATGGGATGCATCGATGCACTACTTATGCATCAATGCACGAATTGC
Found at i:100443 original size:64 final size:64
Alignment explanation
Indices: 100225--100445 Score: 241
Period size: 64 Copynumber: 3.5 Consensus size: 64
100215 TAATGAAGGT
* * * ** * ** ** *
100225 ATGCATTGATGCACTACTGATGCATCGGTGCATAAAATATATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TCATTATTAAAGAG
* * *
100289 ATGCATCGATGCACTACTTATGCATCAATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
*
100353 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAAAGAG
**
100416 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
100446 ACACCTTCAA
Statistics
Matches: 138, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
63 3 0.02
64 130 0.94
65 5 0.04
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:103643 original size:31 final size:31
Alignment explanation
Indices: 103605--103667 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
103595 CCCGAAGGAC
*
103605 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
103636 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
103667 C
1 C
103668 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:104437 original size:64 final size:62
Alignment explanation
Indices: 104329--104549 Score: 266
Period size: 64 Copynumber: 3.5 Consensus size: 62
104319 TAATGAAGGT
* * * * *
104329 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGTATTATTACTAGG
1 ATGCATCGATGCACTACTAATGCATCGATGCATGAATTGCATTCGATGTT-TATTATTA-TAGG
* *
104393 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTA-ATGG
1 ATGCATCGATGCACTACTAATGCATCGATGCATGAATTGCATTCGATGTTT-ATTATTATA-GG
* *
104456 TATGCATCGATGCACTACTAATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAAAAG
1 -ATGCATCGATGCACTACTAATGCATCGATGCATGAATTGCATTCGATG--TTTATTATTATAGG
*
104520 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTAATGCATCGAT
104550 ACACCTTCAA
Statistics
Matches: 140, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 128 0.91
65 4 0.03
66 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCACTACTAATGCATCGATGCATGAATTGCATTCGATGTTTATTATTATAGG
Found at i:105473 original size:9 final size:9
Alignment explanation
Indices: 105459--105492 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
105449 ATTTATATTG
105459 AAGAAGAAA
1 AAGAAGAAA
105468 AAGAAGAAA
1 AAGAAGAAA
*
105477 AA-AAGAAG
1 AAGAAGAAA
105485 AAGAAGAA
1 AAGAAGAA
105493 GAGTCAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGAAGAAA
Found at i:105609 original size:30 final size:29
Alignment explanation
Indices: 105570--105640 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 29
105560 GTAGTAACGA
* *
105570 TTTGTTAACAACTATTACATTGAGTGA-CAAT
1 TTTG-TAACAACAATAACATT-AGTGATC-AT
*
105601 TTTGTAACAAACAATAACGTTAGTGATCAT
1 TTTGTAAC-AACAATAACATTAGTGATCAT
105631 TTTGTAACAA
1 TTTGTAACAA
105641 ATGATAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 2 0.06
30 19 0.54
31 14 0.40
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (29 bp):
TTTGTAACAACAATAACATTAGTGATCAT
Found at i:105654 original size:30 final size:30
Alignment explanation
Indices: 105586--105656 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
105576 AACAACTATT
105586 ACATTGAGTGA-CAATTTTGTAACAAACAATA
1 ACATT-AGTGATC-ATTTTGTAACAAACAATA
* **
105617 ACGTTAGTGATCATTTTGTAACAAATGATA
1 ACATTAGTGATCATTTTGTAACAAACAATA
*
105647 ATATTAGTGA
1 ACATTAGTGA
105657 CCAATTAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 29 0.85
31 5 0.15
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (30 bp):
ACATTAGTGATCATTTTGTAACAAACAATA
Found at i:111645 original size:33 final size:33
Alignment explanation
Indices: 111603--111685 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
111593 GGGCCGATTA
*
111603 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTACATTTTTATATTAAT
111636 TATATATATAATATTTTACATTTTTATATTAAT
1 TATATATATAATATTTTACATTTTTATATTAAT
*
111669 TATGTATATAATATTTT
1 TATATATATAATATTTT
111686 CGGGTTCGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (33 bp):
TATATATATAATATTTTACATTTTTATATTAAT
Found at i:116624 original size:2 final size:2
Alignment explanation
Indices: 116617--116670 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
116607 TTATAATACG
116617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116659 AT AT AT AT AT AT
1 AT AT AT AT AT AT
116671 TTGTTACGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:117050 original size:19 final size:19
Alignment explanation
Indices: 117026--117065 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
117016 AAGAACAAAG
117026 ATCAATAATGTACAAATAC
1 ATCAATAATGTACAAATAC
117045 ATCAATAATGTACAAATAC
1 ATCAATAATGTACAAATAC
117064 AT
1 AT
117066 TGTATTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (19 bp):
ATCAATAATGTACAAATAC
Found at i:121320 original size:2 final size:2
Alignment explanation
Indices: 121307--121345 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
121297 GTGAGGCATA
*
121307 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
121346 ATGCATTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:121623 original size:18 final size:18
Alignment explanation
Indices: 121596--121664 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
121586 AATATTTGTA
*
121596 CCGAAGGACCACTATGTC
1 CCGAAAGACCACTATGTC
*
121614 CCGAAAGACCACTGATTGTT
1 CCGAAAGACCACT-A-TGTC
*
121634 CCG-AAGAACCACTATGCC
1 CCGAAAG-ACCACTATGTC
*
121652 CCGAAGGACCACT
1 CCGAAAGACCACT
121665 GATAATCCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 23 0.55
19 7 0.17
20 12 0.29
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.16
Consensus pattern (18 bp):
CCGAAAGACCACTATGTC
Found at i:121639 original size:38 final size:38
Alignment explanation
Indices: 121591--121667 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
121581 CACTGAATAT
* *
121591 TTGTACCGAAGGACCACTATGTCCCGAAAGACCACTGA
1 TTGTACCGAAGAACCACTATGCCCCGAAAGACCACTGA
* *
121629 TTGTTCCGAAGAACCACTATGCCCCGAAGGACCACTGA
1 TTGTACCGAAGAACCACTATGCCCCGAAAGACCACTGA
121667 T
1 T
121668 AATCCCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (38 bp):
TTGTACCGAAGAACCACTATGCCCCGAAAGACCACTGA
Found at i:122307 original size:64 final size:64
Alignment explanation
Indices: 122236--122380 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 64
122226 ATCCCTTGAC
* * *
122236 GGGTGCATCGATGCACAA-TCTATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAG
1 GGGTGCATCGATGCACAACTC-ATGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAA
122299 G
64 G
* * * *
122300 GGGTGCATCGATGCACTACTCGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACAACTCATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
**
122364 AAGTGCATCGATGCACA
1 GGGTGCATCGATGCACA
122381 TTGAACAATT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 66 0.96
65 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (64 bp):
GGGTGCATCGATGCACAACTCATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
Found at i:128405 original size:18 final size:20
Alignment explanation
Indices: 128356--128415 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 20
128346 CACTGAATAT
128356 TTGTCCCCGAAGGACCACTGA
1 TTGT-CCCGAAGGACCACTGA
* *
128377 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
128396 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
128415 T
1 T
128416 AATCCCTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 15 0.45
19 2 0.06
20 12 0.36
21 4 0.12
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:129110 original size:65 final size:66
Alignment explanation
Indices: 128984--129130 Score: 158
Period size: 65 Copynumber: 2.3 Consensus size: 66
128974 ATCCCTTGAC
* * *
128984 GGGTGCATCGATGCAC-AATCTATGCATCGGTACATAAATCCCATTCGATGTTTGTATTTTTAAG
1 GGGTGCATCGATGCACTAATCTATGCATCGATACATAAATCACATTCGATGTTTGTATTTTTAAA
129048 G
66 G
* * * *
129049 GGGTGCATCGATGCACTACT-TGTGCATCGATACACT-AATGACATTCGATGTTT-TTTATTTTA
1 GGGTGCATCGATGCACTAATCTATGCATCGATACA-TAAATCACATTCGATGTTTGTAT-TTTTA
129111 AAG
64 AAG
** *
129114 AAGTGCATCGATACACT
1 GGGTGCATCGATGCACT
129131 TCATGTGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
64 2 0.03
65 64 0.93
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (66 bp):
GGGTGCATCGATGCACTAATCTATGCATCGATACATAAATCACATTCGATGTTTGTATTTTTAAA
G
Found at i:133252 original size:18 final size:17
Alignment explanation
Indices: 133230--133262 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
133220 ATATATATAT
*
133230 TTTTTTAATATTTTATG
1 TTTTTTAATAATTTATG
133247 TTTTTTAATAATTTAT
1 TTTTTTAATAATTTAT
133263 CATTTTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTTAATAATTTATG
Found at i:133268 original size:18 final size:17
Alignment explanation
Indices: 133225--133287 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
133215 ATAATATATA
*
133225 TATATTTTTTTAATATTT
1 TATA-TTTTTTAATAATT
*
133243 TATGTTTTTTAATAATT
1 TATATTTTTTAATAATT
* *
133260 TATCATTTTATAAT-TTAT
1 TAT-ATTTTTTAATAAT-T
133278 TATATTTTTT
1 TATATTTTTT
133288 TTAATTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 22 0.59
18 15 0.41
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (17 bp):
TATATTTTTTAATAATT
Found at i:133361 original size:22 final size:24
Alignment explanation
Indices: 133336--133385 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
133326 TTTTTTGGTA
*
133336 ATTTAATTTTTT-ATTATTT-TAT
1 ATTTAATTTTTTAAATATTTGTAT
*
133358 ATTTATTTTTTTAAATATTTGTAT
1 ATTTAATTTTTTAAATATTTGTAT
133382 ATTT
1 ATTT
133386 TAAATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 6 0.25
24 7 0.29
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTAATTTTTTAAATATTTGTAT
Found at i:133423 original size:24 final size:24
Alignment explanation
Indices: 133368--133423 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
133358 ATTTATTTTT
*
133368 TTAAAT-ATTTGTATATTTTAAAT
1 TTAAATAATTTGTATATTTTAAAA
* *
133391 TTGAAATAATTTTTATTTTTTAAAA
1 TT-AAATAATTTGTATATTTTAAAA
133416 TTAAATAA
1 TTAAATAA
133424 GCTTCTGGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 10 0.36
25 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TTAAATAATTTGTATATTTTAAAA
Found at i:133825 original size:23 final size:23
Alignment explanation
Indices: 133798--133841 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
133788 CAAATGTACA
133798 TTTAAATAAA-AAAATAAATAAGT
1 TTTAAA-AAATAAAATAAATAAGT
*
133821 TTTAAAAAATAAAATTAATAA
1 TTTAAAAAATAAAATAAATAA
133842 ATAAAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
TTTAAAAAATAAAATAAATAAGT
Found at i:140203 original size:61 final size:61
Alignment explanation
Indices: 140108--140233 Score: 216
Period size: 61 Copynumber: 2.1 Consensus size: 61
140098 ATCGGGAGAT
*
140108 CATTTGGTAACTTTTAATAATTGAAGAACTTGATAAAGTTGCTTCCCTATAGTCAGAGGAC
1 CATTTGGTAACTTTTAATAATCGAAGAACTTGATAAAGTTGCTTCCCTATAGTCAGAGGAC
* * *
140169 CATTTTGTAACTTTTAATAATCGATGAAGTTGATAAAGTTGCTTCCCTATAGTCAGAGGAC
1 CATTTGGTAACTTTTAATAATCGAAGAACTTGATAAAGTTGCTTCCCTATAGTCAGAGGAC
140230 CATT
1 CATT
140234 GTATACTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (61 bp):
CATTTGGTAACTTTTAATAATCGAAGAACTTGATAAAGTTGCTTCCCTATAGTCAGAGGAC
Found at i:143630 original size:28 final size:28
Alignment explanation
Indices: 143588--143642 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
143578 CTCTGTTTAC
143588 ATTATGTCGTCGAGCCAATGCTTGAAAT
1 ATTATGTCGTCGAGCCAATGCTTGAAAT
* *
143616 ATTATGTTGTTGAGCCAATGCTTGAAA
1 ATTATGTCGTCGAGCCAATGCTTGAAA
143643 ATAACGGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (28 bp):
ATTATGTCGTCGAGCCAATGCTTGAAAT
Found at i:146858 original size:33 final size:33
Alignment explanation
Indices: 146807--146888 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
146797 CCACCTATCA
*
146807 AAGATGAATTTTCTAATAAGTTGGCCACCAACC
1 AAGATGAATTTTCCAATAAGTTGGCCACCAACC
* *
146840 AATATGAAATTTCCAATAAGTTGGCCACCAACC
1 AAGATGAATTTTCCAATAAGTTGGCCACCAACC
146873 AAGATGAATTTTCCAA
1 AAGATGAATTTTCCAA
146889 CTTGCCAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (33 bp):
AAGATGAATTTTCCAATAAGTTGGCCACCAACC
Found at i:149312 original size:20 final size:20
Alignment explanation
Indices: 149287--149369 Score: 123
Period size: 20 Copynumber: 4.1 Consensus size: 20
149277 CCGTTAGATA
149287 GGGGGAATCGGTACCCCTTG
1 GGGGGAATCGGTACCCCTTG
149307 GGGGGAATCGGTACCCCTTG
1 GGGGGAATCGGTACCCCTTG
149327 GGGGGAATCGGTACCCCCTCT-
1 GGGGGAATCGGTA-CCCCT-TG
* *
149348 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTACCCCTTG
149368 GG
1 GG
149370 CAATCAAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.02
20 39 0.67
21 17 0.29
22 1 0.02
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.19
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTTG
Found at i:149362 original size:41 final size:40
Alignment explanation
Indices: 149287--149369 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 40
149277 CCGTTAGATA
*
149287 GGGGGAATCGGTACCCCTTGGGGGGAATCGGTACCCCTTG
1 GGGGGAATCGGTACCCCTTGGGGGGAATCGGTACCCCCTG
*
149327 GGGGGAATCGGTACCCCCTCT-GGGGGAATCTGTACCCCCTG
1 GGGGGAATCGGTA-CCCCT-TGGGGGGAATCGGTACCCCCTG
149368 GG
1 GG
149370 CAATCAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
40 13 0.33
41 25 0.64
42 1 0.03
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.19
Consensus pattern (40 bp):
GGGGGAATCGGTACCCCTTGGGGGGAATCGGTACCCCCTG
Found at i:149849 original size:21 final size:22
Alignment explanation
Indices: 149811--149856 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
149801 GTCTGCTGAA
* **
149811 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGAGGAGTACT
149832 ACTCCACCTGCTGAGGAGTACT
1 ACTCCACCTGCTGAGGAGTACT
149854 ACT
1 ACT
149857 TGTCTGGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGAGGAGTACT
Found at i:152505 original size:33 final size:33
Alignment explanation
Indices: 152468--152546 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
152458 TCACATACCA
* *
152468 AAGATGAATTTTTCAATAAATTAACCACCAACT
1 AAGATGAATTTTCCAATAAATTAACCACCAACC
* * *
152501 AAGATGAAATTTCCAATAAATTGATCACCAACC
1 AAGATGAATTTTCCAATAAATTAACCACCAACC
*
152534 GAGATGAATTTTC
1 AAGATGAATTTTC
152547 TTACTTGGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (33 bp):
AAGATGAATTTTCCAATAAATTAACCACCAACC
Found at i:159241 original size:20 final size:21
Alignment explanation
Indices: 159202--159242 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
159192 TAAGGGTTCA
**
159202 AGTATCGATTTTGAGATGAAT
1 AGTATCGATACTGAGATGAAT
159223 AGTATCGATACTG-GATGAAT
1 AGTATCGATACTGAGATGAAT
159243 TGGGGCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
AGTATCGATACTGAGATGAAT
Found at i:160532 original size:10 final size:10
Alignment explanation
Indices: 160517--160542 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
160507 AATACACTTT
160517 AAATATTTAA
1 AAATATTTAA
160527 AAATATTTAA
1 AAATATTTAA
160537 AAATAT
1 AAATAT
160543 GATTAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATATTTAA
Found at i:160883 original size:64 final size:64
Alignment explanation
Indices: 160805--160943 Score: 154
Period size: 64 Copynumber: 2.2 Consensus size: 64
160795 GGATCCTGGT
* * * *
160805 AGGTCGGGTAAAATCAGATACAGGTCA-AGTCAGGTAAATTTAACATCAGATCCAGATCGGGTTC
1 AGGTCAGGTCAAATCAG-TACAGGTCATAGTCAGGTAAATTTAACACCAGATCCAAATCGGGTTC
* * * ** ** *
160869 AGGTCAGGTCAAATCAGTTCGGGTTATTTTCAGGTTGATTTGACACCAGATCCAAATCGGGTTC
1 AGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTAACACCAGATCCAAATCGGGTTC
160933 AGGTCAGGTCA
1 AGGTCAGGTCA
160944 TTTTCAGTTC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
63 6 0.10
64 56 0.90
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (64 bp):
AGGTCAGGTCAAATCAGTACAGGTCATAGTCAGGTAAATTTAACACCAGATCCAAATCGGGTTC
Found at i:161683 original size:13 final size:13
Alignment explanation
Indices: 161628--161693 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
161618 ATTATAAATA
*
161628 ATATATATTGTAT
1 ATATATATAGTAT
* *
161641 ACATTATATAGTTT
1 ATA-TATATAGTAT
*
161655 AT-TA-ATA-TAA
1 ATATATATAGTAT
*
161665 AT-TATATAGTTT
1 ATATATATAGTAT
161677 ATATATATAGTAT
1 ATATATATAGTAT
161690 ATAT
1 ATAT
161694 GGTTTAGGGT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
10 5 0.12
11 6 0.15
12 5 0.12
13 15 0.38
14 9 0.22
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (13 bp):
ATATATATAGTAT
Found at i:162555 original size:21 final size:21
Alignment explanation
Indices: 162530--162570 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
162520 AGTATGTGCA
162530 GGGGG-AACAGATTCCCCCCTG
1 GGGGGTAAC-GATTCCCCCCTG
*
162551 GGGGGTATCGATTCCCCCCT
1 GGGGGTAACGATTCCCCCCT
162571 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.15, C:0.34, G:0.32, T:0.20
Consensus pattern (21 bp):
GGGGGTAACGATTCCCCCCTG
Found at i:162999 original size:7 final size:6
Alignment explanation
Indices: 162972--163179 Score: 54
Period size: 7 Copynumber: 31.5 Consensus size: 6
162962 CTATGTGACT
*
162972 ATATGA A-ATGA TATATGA ATATGCA ATACTTGA TACATGA TGATATGA
1 ATATGA ATATGA -ATATGA ATATG-A ATA--TGA -ATATGA --ATATGA
* *
163020 A-ATGA CATATGA ATATGTA ATACGTGA TACATGTG ATATG- ATATGA
1 ATATGA -ATATGA ATATG-A ATA--TGA -ATATG-A ATATGA ATATGA
* *
163066 A-ATGA CATATGA ATATGTA ATACGTGA TACATGTG ATATG- ATATGA
1 ATATGA -ATATGA ATATG-A ATA--TGA -ATATG-A ATATGA ATATGA
* *
163112 A-ATGA CATATGA ATATGTA ATACGTGA TACATGTG ATATG- ATATGA
1 ATATGA -ATATGA ATATG-A ATA--TGA -ATATG-A ATATGA ATATGA
163158 A-ATGA CATATGA ATATGTA ATA
1 ATATGA -ATATGA ATATG-A ATA
163180 CGTGATACAT
Statistics
Matches: 156, Mismatches: 12, Indels: 67
0.66 0.05 0.29
Matches are distributed among these distances:
5 35 0.22
6 35 0.22
7 61 0.39
8 9 0.06
9 16 0.10
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (6 bp):
ATATGA
Found at i:163035 original size:18 final size:18
Alignment explanation
Indices: 162972--163036 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
162962 CTATGTGACT
*
162972 ATATGAAATGATATATGA
1 ATATGAAATGACATATGA
162990 ATATGCAATACTTGATACATGATG-
1 ATATG-AA-A--TG--ACAT-ATGA
163014 ATATGAAATGACATATGA
1 ATATGAAATGACATATGA
163032 ATATG
1 ATATG
163037 TAATACGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 16
0.69 0.02 0.29
Matches are distributed among these distances:
17 3 0.08
18 14 0.37
19 2 0.05
20 3 0.08
22 3 0.08
23 2 0.05
24 8 0.21
25 3 0.08
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (18 bp):
ATATGAAATGACATATGA
Found at i:163078 original size:46 final size:46
Alignment explanation
Indices: 162972--163210 Score: 416
Period size: 46 Copynumber: 5.3 Consensus size: 46
162962 CTATGTGACT
* * *
162972 ATATGAAATGATATATGAATATGCAATACTTGATACA--TG--ATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
163014 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
163060 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
163106 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
163152 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
163198 ATATGAAAT-ACAT
1 ATATGAAATGACAT
163211 GGTTACACAT
Statistics
Matches: 190, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
42 34 0.18
44 2 0.01
45 4 0.02
46 150 0.79
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
Found at i:163428 original size:17 final size:17
Alignment explanation
Indices: 163388--163431 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
163378 ACAGATTACA
*
163388 TCCTTCAGGATGACAGG
1 TCCTTCGGGATGACAGG
*
163405 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGACAGG
163422 TCCTTCGGGA
1 TCCTTCGGGA
163432 CATTTATACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Done.