Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 139 of 141
Found at i:41991775 original size:30 final size:30
Alignment explanation
Indices: 41991705--41991851 Score: 131
Period size: 30 Copynumber: 5.0 Consensus size: 30
41991695 GACTATCGAT
* *
41991705 TATGAAAAGGGAAGGTGACGACCATC-AAT
1 TATGAAAAGGGATGGTGACGACCATCAAAC
*
41991734 TATGGAAAGGGATGGTGACGACCATCAAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
** * * * *
41991764 TATGAAAAGGGATGGCT-TTGGCTAGCAAAT
1 TATGAAAAGGGATGG-TGACGACCATCAAAC
* * *
41991794 TATG-AAAGGGATGGCGACGCCCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
*
41991823 AATGAAAAGGGATGGTGATC-ACCATCAAA
1 TATGAAAAGGGATGGTGA-CGACCATCAAA
41991852 TTTTTAAAAG
Statistics
Matches: 91, Mismatches: 22, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
29 43 0.47
30 46 0.51
31 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCAAAC
Found at i:41991840 original size:89 final size:90
Alignment explanation
Indices: 41991703--41991931 Score: 239
Period size: 89 Copynumber: 2.6 Consensus size: 90
41991693 TCGACTATCG
* * * *
41991703 ATTATGAAAAGGGAAGGTGACGACCATC-AATTATGGAAAGGGATGGTGA-CGACCATCAAACTA
1 ATTATGAAAAGGGATGGCGACGACCATCGAATAATGAAAAGGGATGGTGATC-ACCATCAAACTA
* *
41991766 TGAAAAGGGATGGCTTTGGCTAGCAA
65 TGAAAAGAGATAGCTTTGGCTAGCAA
* * * *
41991792 ATTATG-AAAGGGATGGCGACGCCCATCGAACAATGAAAAGGGATGGTGATCACCATCAAATTTT
1 ATTATGAAAAGGGATGGCGACGACCATCGAATAATGAAAAGGGATGGTGATCACCATCAAACTAT
* * *
41991856 TAAAAGAGATAGTTTTGGCTATCAA
66 GAAAAGAGATAGCTTTGGCTAGCAA
* * ** * * *
41991881 AATATGAAAAGGGATAGCCTCGGCTATCGAATAAAGAAAAGGGATGTGTGA
1 ATTATGAAAAGGGATGGCGACGACCATCGAATAATGAAAAGGGATG-GTGA
41991932 ACCATCGTAT
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
88 18 0.16
89 60 0.52
90 33 0.29
91 4 0.03
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (90 bp):
ATTATGAAAAGGGATGGCGACGACCATCGAATAATGAAAAGGGATGGTGATCACCATCAAACTAT
GAAAAGAGATAGCTTTGGCTAGCAA
Found at i:41991852 original size:59 final size:60
Alignment explanation
Indices: 41991706--41991853 Score: 160
Period size: 59 Copynumber: 2.5 Consensus size: 60
41991696 ACTATCGATT
* * *
41991706 ATGAAAAGGGAAGGTGA-CGACCATC-AATTATGGAAAGGGATGGTGACGACCATCAAACT
1 ATGAAAAGGGATGGTGATC-ACCATCAAATTATGGAAAGGGATGGCGACGACCATCAAACA
* ** * * * *
41991765 ATGAAAAGGGATGGCT-TTGGCTAGCAAATTAT-GAAAGGGATGGCGACGCCCATCGAACA
1 ATGAAAAGGGATGG-TGATCACCATCAAATTATGGAAAGGGATGGCGACGACCATCAAACA
41991824 ATGAAAAGGGATGGTGATCACCATCAAATT
1 ATGAAAAGGGATGGTGATCACCATCAAATT
41991854 TTTAAAAGAG
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
58 1 0.01
59 62 0.89
60 7 0.10
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (60 bp):
ATGAAAAGGGATGGTGATCACCATCAAATTATGGAAAGGGATGGCGACGACCATCAAACA
Found at i:41995558 original size:20 final size:20
Alignment explanation
Indices: 41995533--41995571 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41995523 TGAGTTATTT
41995533 AAGTAAGCA-AGTAAGTAAAG
1 AAGTAAG-AGAGTAAGTAAAG
41995553 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
41995572 AATGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAG
Found at i:42002115 original size:29 final size:30
Alignment explanation
Indices: 42002073--42002319 Score: 184
Period size: 29 Copynumber: 8.4 Consensus size: 30
42002063 CATTGACGGG
* * *
42002073 TGAAATGGGATAGCTTCGGCTATCGAACT-
1 TGAAAAGGGATAGCTTCGACTATCGAATTA
*
42002102 TGAAAAGGGATAGCTTCAACTATCG-ATTA
1 TGAAAAGGGATAGCTTCGACTATCGAATTA
* * *
42002131 TGAAAAGGGAT-GGTGACGACCATC-AATTA
1 TGAAAAGGGATAGCT-TCGACTATCGAATTA
* * * * * *
42002160 TGGAAGGGGAT-GGTGACGACCATCGAACTA
1 TGAAAAGGGATAGCT-TCGACTATCGAATTA
* * * *
42002190 TGAAAAGGGGTGGCTTCGATTATCG-ATCA
1 TGAAAAGGGATAGCTTCGACTATCGAATTA
* *
42002219 TGAAAAGGGATGGCTTCGACTATCAAATTA
1 TGAAAAGGGATAGCTTCGACTATCGAATTA
* ** *
42002249 TGAAAAGGGATAGTTTCGGTTATCAAATTA
1 TGAAAAGGGATAGCTTCGACTATCGAATTA
* *
42002279 TGAAAAGGGATAGCCTC-AGCTATCGAATAA
1 TGAAAAGGGATAGCTTCGA-CTATCGAATTA
*
42002309 AGAAAAGGGAT
1 TGAAAAGGGAT
42002320 GTGTCAAGCA
Statistics
Matches: 176, Mismatches: 35, Indels: 13
0.79 0.16 0.06
Matches are distributed among these distances:
28 4 0.02
29 89 0.51
30 81 0.46
31 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.24
Consensus pattern (30 bp):
TGAAAAGGGATAGCTTCGACTATCGAATTA
Found at i:42002229 original size:59 final size:60
Alignment explanation
Indices: 42002166--42002289 Score: 135
Period size: 59 Copynumber: 2.1 Consensus size: 60
42002156 ATTATGGAAG
* * * *
42002166 GGGATGG-TGACGACCATCGAACTATGAAAAGGGGTGGCTTCGATTATC-GATCATGAAAA
1 GGGATGGCT-ACGACCATCAAACTATGAAAAGGGATAGCTTCGATTATCAAATCATGAAAA
* * * * * *
42002225 GGGATGGCTTCGACTATCAAATTATGAAAAGGGATAGTTTCGGTTATCAAATTATGAAAA
1 GGGATGGCTACGACCATCAAACTATGAAAAGGGATAGCTTCGATTATCAAATCATGAAAA
42002285 GGGAT
1 GGGAT
42002290 AGCCTCAGCT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
59 38 0.72
60 15 0.28
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (60 bp):
GGGATGGCTACGACCATCAAACTATGAAAAGGGATAGCTTCGATTATCAAATCATGAAAA
Found at i:42002244 original size:88 final size:88
Alignment explanation
Indices: 42002094--42002259 Score: 219
Period size: 88 Copynumber: 1.9 Consensus size: 88
42002084 AGCTTCGGCT
*
42002094 ATCGAACTTGAAAAGGGATAGCTTCAACTATCGATTATGAAAAGGGATGGTGACGACCATC-AAT
1 ATCGAACTTGAAAAGGGATAGCTTCAACTATCGATCATGAAAAGGGATGGTGACGACCATCAAAT
* *
42002158 TATGGAAGGGGATGGTGACGACC
66 TATGAAAAGGGATGGTGACGACC
* * * * * *
42002181 ATCGAACTATGAAAAGGGGTGGCTTCGATTATCGATCATGAAAAGGGATGGCT-TCGACTATCAA
1 ATCGAACT-TGAAAAGGGATAGCTTCAACTATCGATCATGAAAAGGGATGG-TGACGACCATCAA
42002245 ATTATGAAAAGGGAT
64 ATTATGAAAAGGGAT
42002260 AGTTTCGGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 8 0.12
88 44 0.66
89 15 0.22
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (88 bp):
ATCGAACTTGAAAAGGGATAGCTTCAACTATCGATCATGAAAAGGGATGGTGACGACCATCAAAT
TATGAAAAGGGATGGTGACGACC
Found at i:42006685 original size:45 final size:46
Alignment explanation
Indices: 42006610--42006809 Score: 187
Period size: 45 Copynumber: 4.5 Consensus size: 46
42006600 TACACGACGG
* * *
42006610 ATCAGCACACAGC-ACCACCCTTATAGTCAATAGTACTC-GGTGAA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
* * *
42006654 ATCAGCACATAGCAACCAGCTTTATACTCAATGGTAC-CAGGTAAA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
* * * **
42006699 ATCAGCACATAGCAACCACCTATATAAC-CATTGGTTTTC-GGTGAA
1 ATCAGCACATAGCAACCACCTTTAT-ACTCAATAGTACTCAGGTGAA
** * * * *
42006744 ATCAGCACATAGCAACCACCTTTATTTTCATTAATA-TCGGGTGGA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
*
42006789 ATCAGCACATAGCATCCACCT
1 ATCAGCACATAGCAACCACCT
42006810 ATATTTCCAA
Statistics
Matches: 130, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
44 15 0.12
45 112 0.86
46 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (46 bp):
ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
Found at i:42006792 original size:90 final size:90
Alignment explanation
Indices: 42006646--42006813 Score: 237
Period size: 90 Copynumber: 1.9 Consensus size: 90
42006636 TCAATAGTAC
* **
42006646 TCGGTGAAATCAGCACATAGCAACCAGCTTTATACTCAATGGTACCAGGTAAAATCAGCACATAG
1 TCGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCAGGTAAAATCAGCACATAG
42006711 CAACCACCTATATAACCATTGGTTT
66 CAACCACCTATATAACCATTGGTTT
** * * * **
42006736 TCGGTGAAATCAGCACATAGCAACCACCTTTATTTTCATTAATATCGGGTGGAATCAGCACATAG
1 TCGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCAGGTAAAATCAGCACATAG
*
42006801 CATCCACCTATAT
66 CAACCACCTATAT
42006814 TTCCAACGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 67 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (90 bp):
TCGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCAGGTAAAATCAGCACATAG
CAACCACCTATATAACCATTGGTTT
Found at i:42013642 original size:22 final size:22
Alignment explanation
Indices: 42013614--42013659 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
42013604 TCGATACATG
42013614 AAACACATTATGAATTCTTTCT
1 AAACACATTATGAATTCTTTCT
42013636 AAACACATTATGAATTCTTTCT
1 AAACACATTATGAATTCTTTCT
42013658 AA
1 AA
42013660 CTCTATCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.39
Consensus pattern (22 bp):
AAACACATTATGAATTCTTTCT
Found at i:42023296 original size:80 final size:80
Alignment explanation
Indices: 42023163--42023326 Score: 301
Period size: 80 Copynumber: 2.0 Consensus size: 80
42023153 TTGAGCATTC
* *
42023163 GGTCTTCTTTTGGAGCATGCATGGTATTCTTTTTGAGTTTATTTCTAGTAAATTTTATGTTTTTG
1 GGTCTTCTTTTGGAGCATGCATGGTATTCTTTTTGAGTTTATTTCTAGTAAATTTTATGTCTTTC
*
42023228 AAATCGTTGCAACTT
66 AAATCATTGCAACTT
42023243 GGTCTTCTTTTGGAGCATGCATGGTATTCTTTTTGAGTTTATTTCTAGTAAATTTTATGTCTTTC
1 GGTCTTCTTTTGGAGCATGCATGGTATTCTTTTTGAGTTTATTTCTAGTAAATTTTATGTCTTTC
42023308 AAATCATTGCAACTT
66 AAATCATTGCAACTT
42023323 GGTC
1 GGTC
42023327 CAACTAGCAC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (80 bp):
GGTCTTCTTTTGGAGCATGCATGGTATTCTTTTTGAGTTTATTTCTAGTAAATTTTATGTCTTTC
AAATCATTGCAACTT
Found at i:42024315 original size:45 final size:45
Alignment explanation
Indices: 42024016--42024320 Score: 416
Period size: 45 Copynumber: 6.8 Consensus size: 45
42024006 TACTAGAAAT
* *
42024016 GAGTAAGACCATGACT-AGAAGAAGTTATGGCATAACGATTCTATC
1 GAGTAAGACCATGACTGA-AAGACGTTATGGCATCACGATTCTATC
* *
42024061 GAGTAAGACCATGACTGAAATACATTATGGCATCACGATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATC
*
42024106 GAGTAAGACCATGACTGAAAGACATTATGGCATCACGATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATC
* * *
42024151 GAGTAAGACCATGACTGAAAGACGTTATGGCACCACAATTCTAAC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATC
*
42024196 GAGTAAGACCATGAGTGAAAGACGTTATGGCATCACGATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATC
* * * **
42024241 GAGTAAGACCACGATTGAAAAACGTTATGGCATGGCGATTCTATC
1 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATC
* * * *
42024286 GAGCAAGACCAT-AGCTGAAACACGCTATGGTATCA
1 GAGTAAGACCATGA-CTGAAAGACGTTATGGCATCA
42024321 GGAATCAAAC
Statistics
Matches: 232, Mismatches: 26, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
44 1 0.00
45 230 0.99
46 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (45 bp):
GAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATC
Found at i:42024350 original size:135 final size:135
Alignment explanation
Indices: 42024064--42024354 Score: 354
Period size: 135 Copynumber: 2.2 Consensus size: 135
42024054 TTCTATCGAG
* * * *
42024064 TAAGACCATGACTGAAATACATTATGGCATCACGATTCTATCGAGTAAGACCATGACTGAAAGAC
1 TAAGACCATGAGTGAAAGACATTATGGCATCACGATTCTATCGAGTAAGACCACGACTGAAAAAC
* * * *
42024129 ATTATGGCATCACGATTCTATCGAGTAAGACCATGACTGAAAGACGTTATGGCACCACAATTCTA
66 ATTATGGCATCACGATTCTATCGAGCAAGACCATGACTGAAACACGCTATGGCACCACAATTCAA
* *
42024194 ACGAG
131 ACAAA
* *
42024199 TAAGACCATGAGTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCACGATTGAAAAAC
1 TAAGACCATGAGTGAAAGACATTATGGCATCACGATTCTATCGAGTAAGACCACGACTGAAAAAC
* ** * * *
42024264 GTTATGGCATGGCGATTCTATCGAGCAAGACCAT-AGCTGAAACACGCTATGGTATCAGGAA-TC
66 ATTATGGCATCACGATTCTATCGAGCAAGACCATGA-CTGAAACACGCTATGGCACCA-CAATTC
42024327 AAACAAA
129 AAACAAA
* *
42024334 TACGACTATG-GTTGAAAGACA
1 TAAGACCATGAG-TGAAAGACA
42024355 GTATAGAAAC
Statistics
Matches: 132, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
134 2 0.02
135 128 0.97
136 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (135 bp):
TAAGACCATGAGTGAAAGACATTATGGCATCACGATTCTATCGAGTAAGACCACGACTGAAAAAC
ATTATGGCATCACGATTCTATCGAGCAAGACCATGACTGAAACACGCTATGGCACCACAATTCAA
ACAAA
Found at i:42041961 original size:45 final size:45
Alignment explanation
Indices: 42041914--42042219 Score: 380
Period size: 45 Copynumber: 6.8 Consensus size: 45
42041904 ATACCAAAAA
* * * *
42041914 CGAGAAAGACCATGACTGAAAGAAGTCATGGCATCACGATTCTAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
42041959 CGAGTAAGGCCATGACTGAAAGATGTTATGGCATCACAATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* *
42042004 CAAGTAAAACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * * *
42042049 TGAGTAAGACCATGACTGAAAGACGTTATGCCATCACGATTTTAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * * * * ** *
42042094 CAAGTAACACCATGAATGAAAGATGTTACGGCATCATAATTATAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
* * *
42042139 CGAGTAAGACCATGATTGAAAGACGTTACGGCATCATGATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
42042184 CGAGTAAGACCAT-AGCTGAAAGACGTTATGGCATCA
1 CGAGTAAGACCATGA-CTGAAAGACGTTATGGCATCA
42042220 AGAATCAAAC
Statistics
Matches: 224, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 1 0.00
45 223 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (45 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
Found at i:42042127 original size:135 final size:135
Alignment explanation
Indices: 42041914--42042251 Score: 435
Period size: 135 Copynumber: 2.5 Consensus size: 135
42041904 ATACCAAAAA
* * * * ** *
42041914 CGAGAAAGACCATGACTGAAAGAAGTCATGGCATCACGATTCTAACGAGTAAGGCCATGACTGAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAACAAGTAACACCATGAATGAA
* * *
42041979 AGATGTTATGGCATCACAATTCTATCAAGTAAAACCATGACTGAAAGACGTTATGGCATCACGAT
66 AGATGTTACGGCATCACAATTATATCAAGTAAAACCATGACTGAAAGACGTTACGGCATCACGAT
42042044 TCTAT
131 TCTAT
* * *
42042049 TGAGTAAGACCATGACTGAAAGACGTTATGCCATCACGATTTTAACAAGTAACACCATGAATGAA
1 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAACAAGTAACACCATGAATGAA
* * * * *
42042114 AGATGTTACGGCATCATAATTATATCGAGTAAGACCATGATTGAAAGACGTTACGGCATCATGAT
66 AGATGTTACGGCATCACAATTATATCAAGTAAAACCATGACTGAAAGACGTTACGGCATCACGAT
42042179 TCTAT
131 TCTAT
* * * * * **
42042184 CGAGTAAGACCAT-AGCTGAAAGACGTTATGGCATCAAGAATCAAACAAATAAGACCATGGTTGA
1 CGAGTAAGACCATGA-CTGAAAGACGTTATGGCATCACGATTCTAACAAGTAACACCATGAATGA
42042248 AAGA
65 AAGA
42042252 CACTATGGCA
Statistics
Matches: 174, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
134 1 0.01
135 173 0.99
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (135 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAACAAGTAACACCATGAATGAA
AGATGTTACGGCATCACAATTATATCAAGTAAAACCATGACTGAAAGACGTTACGGCATCACGAT
TCTAT
Found at i:42042249 original size:45 final size:45
Alignment explanation
Indices: 42041912--42042261 Score: 346
Period size: 45 Copynumber: 7.8 Consensus size: 45
42041902 CCATACCAAA
* * * *
42041912 AACGAGAAAGACCATGACTGAAAGAAGTCATGGCATCACGATTCT
1 AACGAGTAAGACCATGACTGAAAGACGTTATGGCATCAAGATTCT
* *
42041957 AACGAGTAAGGCCATGACTGAAAGATGTTATGGCATCACA-ATTCT
1 AACGAGTAAGACCATGACTGAAAGACGTTATGGCATCA-AGATTCT
* * * *
42042002 ATCAAGTAAAACCATGACTGAAAGACGTTATGGCATCACGATTCT
1 AACGAGTAAGACCATGACTGAAAGACGTTATGGCATCAAGATTCT
** * * *
42042047 ATTGAGTAAGACCATGACTGAAAGACGTTATGCCATCACGATTTT
1 AACGAGTAAGACCATGACTGAAAGACGTTATGGCATCAAGATTCT
* * * * * *
42042092 AACAAGTAACACCATGAATGAAAGATGTTACGGCATCATA-ATTAT
1 AACGAGTAAGACCATGACTGAAAGACGTTATGGCATCA-AGATTCT
* * * *
42042137 ATCGAGTAAGACCATGATTGAAAGACGTTACGGCATCATGATTCT
1 AACGAGTAAGACCATGACTGAAAGACGTTATGGCATCAAGATTCT
* * *
42042182 ATCGAGTAAGACCAT-AGCTGAAAGACGTTATGGCATCAAGAATCA
1 AACGAGTAAGACCATGA-CTGAAAGACGTTATGGCATCAAGATTCT
* * ** **
42042227 AACAAATAAGACCATGGTTGAAAGACACTATGGCA
1 AACGAGTAAGACCATGACTGAAAGACGTTATGGCA
42042262 ACACGACGAA
Statistics
Matches: 254, Mismatches: 45, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.00
45 253 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (45 bp):
AACGAGTAAGACCATGACTGAAAGACGTTATGGCATCAAGATTCT
Found at i:42044301 original size:43 final size:43
Alignment explanation
Indices: 42044253--42044351 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
42044243 ACTTGGCCTA
* *
42044253 CGACACGGCTGTGAGTC-TTAGCCGTGTGTGACGCACTGCCATG
1 CGACACGGCTGTGAGTCTTTA-CCGTGTGTGACACACGGCCATG
* *
42044296 CGACACGGGC-GTGAGTCTTTACCTTGTGTGACACACGGCTATG
1 CGACAC-GGCTGTGAGTCTTTACCGTGTGTGACACACGGCCATG
*
42044339 CGACACGACTGTG
1 CGACACGGCTGTG
42044352 TCTCCCCTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
42 2 0.04
43 40 0.83
44 6 0.12
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.23
Consensus pattern (43 bp):
CGACACGGCTGTGAGTCTTTACCGTGTGTGACACACGGCCATG
Found at i:42061417 original size:19 final size:19
Alignment explanation
Indices: 42061393--42061436 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
42061383 CGTGAGAGCT
*
42061393 ATGAGAGTTGAGAGAGAGG
1 ATGAGAGATGAGAGAGAGG
* *
42061412 ATGAGAGATGAGAGGGATG
1 ATGAGAGATGAGAGAGAGG
42061431 ATGAGA
1 ATGAGA
42061437 TGAGGGATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.45, T:0.16
Consensus pattern (19 bp):
ATGAGAGATGAGAGAGAGG
Found at i:42061421 original size:7 final size:7
Alignment explanation
Indices: 42061393--42061453 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
42061383 CGTGAGAGCT
42061393 ATGAGAG
1 ATGAGAG
*
42061400 TTGAGAG
1 ATGAGAG
42061407 A-GAG-G
1 ATGAGAG
42061412 ATGAGAG
1 ATGAGAG
42061419 ATGAGAGGG
1 ATGAGA--G
42061428 ATGATGAG
1 ATGA-GAG
*
42061436 ATGAGGG
1 ATGAGAG
*
42061443 ATGAGGG
1 ATGAGAG
42061450 ATGA
1 ATGA
42061454 TTTAAAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 2 0.04
6 6 0.13
7 26 0.57
8 5 0.11
9 5 0.11
10 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.48, T:0.16
Consensus pattern (7 bp):
ATGAGAG
Found at i:42061436 original size:17 final size:16
Alignment explanation
Indices: 42061401--42061446 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
42061391 CTATGAGAGT
42061401 TGAGA-GAGAGGATGA
1 TGAGATGAGAGGATGA
42061416 -GAGATGAGAGGGATGA
1 TGAGATGAGA-GGATGA
42061432 TGAGATGAG-GGATGA
1 TGAGATGAGAGGATGA
42061447 GGGATGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
16 6 0.21
17 8 0.29
ACGTcount: A:0.37, C:0.00, G:0.48, T:0.15
Consensus pattern (16 bp):
TGAGATGAGAGGATGA
Found at i:42065475 original size:17 final size:18
Alignment explanation
Indices: 42065453--42065492 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
42065443 TTCAATCTGC
*
42065453 TGGGCTAAGTT-GGGTTT
1 TGGGCTAAGTTAGAGTTT
*
42065470 TGGGCTAGGTTAGAGTTT
1 TGGGCTAAGTTAGAGTTT
42065488 TGGGC
1 TGGGC
42065493 CCGTTGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.12, C:0.07, G:0.42, T:0.38
Consensus pattern (18 bp):
TGGGCTAAGTTAGAGTTT
Found at i:42066037 original size:132 final size:132
Alignment explanation
Indices: 42065783--42066173 Score: 577
Period size: 132 Copynumber: 3.0 Consensus size: 132
42065773 GCTTCGATCC
** * ** *
42065783 ACTCCACTGCAACATCAGGGAGA-CAGGGCTCGGTAACTTAAACCTACTTCCCACTATCTTGGAA
1 ACTCCACTGCTGC-TCAGGGAGATCA-GGCTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAA
* * *
42065847 AGATAAGATTTTCCGTCTTTGATATGCTCCACTACTGCTTAGGGAGATAAGATTTGCAATCTTCA
64 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCA
42065912 ACCT
129 ACCT
* *
42065916 ACTCCATTGCTGCTCAGGGAGATCAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAG
1 ACTCCACTGCTGCTCAGGGAGATCAGGCTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAG
* *
42065981 ATAATATTTGCCGTCTTTGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
66 ATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
42066046 CT
131 CT
* * * *
42066048 ACTCCGCTGCTGCTCAGGGAGATAAGGCTTGGTGGCTTAAATTTTCTTCCCACTATCTTGGAAAG
1 ACTCCACTGCTGCTCAGGGAGATCAGGCTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAG
* * *
42066113 ATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAAGGAGATAATATCTGCTATCTT
66 ATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTT
42066174 TACTGATCTG
Statistics
Matches: 234, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
132 222 0.95
133 12 0.05
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (132 bp):
ACTCCACTGCTGCTCAGGGAGATCAGGCTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAG
ATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAAC
CT
Found at i:42066159 original size:44 final size:44
Alignment explanation
Indices: 42065847--42066160 Score: 154
Period size: 44 Copynumber: 7.1 Consensus size: 44
42065837 TATCTTGGAA
* * *
42065847 AGATAAGATTTTCCGTCTTTGATATGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
** * * * * * *
42065891 AGATAAGATTTGCAATCTTCAACCTACTCCATTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
42065935 AGATCAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
42065979 AGATAATATTTGCCGTCTTTGATCTGTTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * * * *
42066023 AGATAAGATCTGCAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
** ** * * * * *
42066067 AGATAAGGCTTGGTGGCTTAAATTTTCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* *
42066111 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAAGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
42066155 AGATAA
1 AGATAA
42066161 TATCTGCTAT
Statistics
Matches: 184, Mismatches: 74, Indels: 24
0.65 0.26 0.09
Matches are distributed among these distances:
42 12 0.07
43 8 0.04
44 149 0.81
45 7 0.04
46 8 0.04
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:42097975 original size:16 final size:16
Alignment explanation
Indices: 42097954--42097985 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42097944 TTTGGTTCGC
42097954 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
42097970 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
42097986 CATAATAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:42097991 original size:16 final size:16
Alignment explanation
Indices: 42097956--42097991 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42097946 TGGTTCGCTG
**
42097956 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGCA
42097972 TAATGGAATAGAGGCA
1 TAATGGAATAGAGGCA
42097988 TAAT
1 TAAT
42097992 AGGTAATTCT
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:0.42, C:0.03, G:0.31, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGGCA
Found at i:42098058 original size:44 final size:46
Alignment explanation
Indices: 42097973--42098065 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 46
42097963 ATAGAGGTGT
* *
42097973 AATGGAATAGAGGCATAATAGGTAATTCTTTTGTTTAGTTGAATGG
1 AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTAGTTGAATGG
* *
42098019 AATGGAATAGAGACGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTAGTTGAATGG
42098063 AAT
1 AAT
42098066 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 23 0.53
45 3 0.07
46 17 0.40
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGACATAATAGGTAATTCTTGTGTTTAGTTGAATGG
Found at i:42098360 original size:16 final size:15
Alignment explanation
Indices: 42098339--42098396 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 15
42098329 AATAATTATT
42098339 AAATATATTTTAACTA
1 AAATATATTTTAA-TA
42098355 AAATATATAATTTAATA
1 AAATATAT--TTTAATA
*
42098372 AAAT-TATTAGTAAT-
1 AAATATATT-TTAATA
42098386 AAATAT-TTTTA
1 AAATATATTTTA
42098397 TATGAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
13 2 0.06
14 7 0.19
15 5 0.14
16 11 0.31
17 6 0.17
18 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AAATATATTTTAATA
Found at i:42098368 original size:18 final size:17
Alignment explanation
Indices: 42098341--42098375 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42098331 TAATTATTAA
*
42098341 ATATATTTTAACTAAAAT
1 ATATAATTTAA-TAAAAT
42098359 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42098376 TATTAGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42098406 original size:117 final size:117
Alignment explanation
Indices: 42098217--42098607 Score: 696
Period size: 117 Copynumber: 3.4 Consensus size: 117
42098207 TAACATAATT
* * *
42098217 ATTATTAAAT-TATTTTAATTAATATATATAATTTAATAAAATTCTTAATAGTAAATATTCTTAT
1 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTATTAATAATAAATATTCTTAT
42098281 ATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATA
66 ATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATA
* * *
42098333 ATTATTAAATATATTTTAACTAAAATATATAATTTAATAAAATTATTAGTAATAAATATTTTTAT
1 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTATTAATAATAAATATTCTTAT
42098398 ATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATA
66 ATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATA
42098450 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCA-TAATAATAAATATTCTTA
1 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT-ATTAATAATAAATATTCTTA
*
42098514 TATGAATTTACTAAAATCATAATAAATGATACTATAAAATATAATTTGAAATA
65 TATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATA
42098567 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAA
1 ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAA
42098608 TATTCTTATA
Statistics
Matches: 263, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
116 10 0.04
117 252 0.96
118 1 0.00
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (117 bp):
ATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTATTAATAATAAATATTCTTAT
ATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATA
Found at i:42098499 original size:17 final size:18
Alignment explanation
Indices: 42098458--42098492 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42098448 TAATTATTAA
*
42098458 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
42098476 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
42098493 TCATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:42098611 original size:102 final size:103
Alignment explanation
Indices: 42098476--42098712 Score: 385
Period size: 102 Copynumber: 2.3 Consensus size: 103
42098466 TAATTAAAAT
*
42098476 ATATAATTTAA-TAAAAT-TCATAA-TAATAAATATTCTTATATGAATTTACTAAAATCATAATA
1 ATATATTTTAATTAAAATAT-ATAATTAATAAATATTCTTATATGAATTTACTAAAATCATAATA
42098538 AATGATACTATAAAATATAATTTGAAAT-A-ATTATTAA
65 AATGATACTATAAAATATAATTTGAAATAATATTATTAA
42098575 ATATATTTTAATTAAAATATATAATTTAATAAATATTCTTATATGAATTTACTAAAATCATAATA
1 ATATATTTTAATTAAAATATATAA-TTAATAAATATTCTTATATGAATTTACTAAAATCATAATA
*
42098640 TATGATACTATAAAATATAATTTGAAATAATTATTATTAA
65 AATGATACTATAAAATATAATTTGAAATAA-TATTATTAA
42098680 ATATATTTTAATTAAAATATATAATCTAATAAA
1 ATATATTTTAATTAAAATATATAAT-TAATAAA
42098713 ATTATTAATA
Statistics
Matches: 128, Mismatches: 2, Indels: 10
0.91 0.01 0.07
Matches are distributed among these distances:
99 10 0.08
100 10 0.08
101 1 0.01
102 66 0.52
103 1 0.01
104 1 0.01
105 39 0.30
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (103 bp):
ATATATTTTAATTAAAATATATAATTAATAAATATTCTTATATGAATTTACTAAAATCATAATAA
ATGATACTATAAAATATAATTTGAAATAATATTATTAA
Found at i:42098662 original size:61 final size:61
Alignment explanation
Indices: 42098593--42098777 Score: 206
Period size: 61 Copynumber: 3.1 Consensus size: 61
42098583 TAATTAAAAT
42098593 ATATAATTTAATAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAA
1 ATATAATTTAATAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAA
* * * * * *
42098654 ATATAATTTGAAATAATTATTATTAAAT-ATATTT--T--AATTAAAATATATAAT-CTAATAAA
1 ATATAATTT--AATAAATATTCTTATATGA-ATTTACTAAAATCATAATATATGATACT-ATAAA
42098713 AT-T-ATTAATAATAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAA
1 ATATAATT--TAATAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAA
42098774 ATAT
1 ATAT
42098778 TTTTAATTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
57 21 0.21
58 4 0.04
59 22 0.22
61 30 0.30
62 4 0.04
63 18 0.18
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (61 bp):
ATATAATTTAATAAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAA
Found at i:42100798 original size:22 final size:23
Alignment explanation
Indices: 42100754--42100799 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
42100744 ATCTGACCCC
42100754 CAAAAAATGAAAAACTTACCATAA
1 CAAAAAATGAAAAACTTA-CATAA
**
42100778 CAAAAAATGCCAAACTT-CATAA
1 CAAAAAATGAAAAACTTACATAA
42100800 TTCACTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
24 15 0.75
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (23 bp):
CAAAAAATGAAAAACTTACATAA
Found at i:42101365 original size:9 final size:10
Alignment explanation
Indices: 42101342--42101368 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
42101332 CATTTCCATC
42101342 AAAAAAGAAG
1 AAAAAAGAAG
42101352 AAAAAAGAAG
1 AAAAAAGAAG
42101362 AAAAAAG
1 AAAAAAG
42101369 GAATAAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:42102352 original size:16 final size:16
Alignment explanation
Indices: 42102328--42102365 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
42102318 ACGTAATGGC
*
42102328 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
42102344 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
42102360 TGTAAT
1 TGTAAT
42102366 AGTAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:42102449 original size:39 final size:43
Alignment explanation
Indices: 42102344--42102451 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 43
42102334 GGAATAGAGG
42102344 TGTAATGGAATAGAGGTGTAATAGTAAATCAATTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGTAAATCAATTGTTTGGTT--A
* * *
42102389 TGTAATGGAATAGAGGCGTAATAGT-ATTC-TTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGTAAATCAAT-TGTTTGGTTA
42102429 TG-AATGGAATAGAGGTGTAATAG
1 TGTAATGGAATAGAGGTGTAATAG
42102452 CATAATGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
39 20 0.34
40 2 0.03
43 2 0.03
44 10 0.17
45 24 0.41
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGTAAATCAATTGTTTGGTTA
Found at i:42102616 original size:16 final size:16
Alignment explanation
Indices: 42102579--42102620 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42102569 TTAATCATAT
*
42102579 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
42102595 TT-AAATATATTATAA
1 TTAAAATATATTATAA
42102610 TTAAAATATAT
1 TTAAAATATAT
42102621 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:42102627 original size:14 final size:15
Alignment explanation
Indices: 42102588--42102629 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42102578 TTTAAACATA
*
42102588 ATTATTATTAAATAT
1 ATTATAATTAAATAT
42102603 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
42102617 A-TATAATTTAATA
1 ATTATAATTAAATA
42102630 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:42102731 original size:18 final size:16
Alignment explanation
Indices: 42102699--42102740 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
42102689 TAAAATATAA
*
42102699 ATTAACATA-ATTATT
1 ATTAAAATATATTATT
42102714 ATT-AAATATATTATT
1 ATTAAAATATATTATT
42102729 ATTAAAATATAT
1 ATTAAAATATAT
42102741 AATTTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 12 0.50
16 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAAATATATTATT
Found at i:42102858 original size:16 final size:16
Alignment explanation
Indices: 42102814--42102860 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
42102804 TACTATAAAA
*
42102814 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
42102830 TATTATT-AAATATAT
1 TATAATTAAAATATAT
42102845 TATAATTAAAATATAT
1 TATAATTAAAATATAT
42102861 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:42102980 original size:18 final size:18
Alignment explanation
Indices: 42102959--42103006 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
42102949 TTATTATTAA
42102959 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
42102977 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
42102994 -TAT-TAATAATTAA
1 ATATATTATAATTAA
42103007 TATTCTTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:42102987 original size:14 final size:15
Alignment explanation
Indices: 42102938--42102989 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
42102928 ATAAAATATA
42102938 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
42102953 TATTAAATATATTAT
1 AATTAAATATATTAT
42102968 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
42102981 AATTTAATA
1 AATTAAATA
42102990 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:42103051 original size:120 final size:120
Alignment explanation
Indices: 42102582--42103014 Score: 812
Period size: 120 Copynumber: 3.6 Consensus size: 120
42102572 ATCATATTTA
42102582 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
42102647 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
42102702 AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATCCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
42102767 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
42102822 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
42102887 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
42102942 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
42103007 TATTCTTA
66 TATTCTTA
42103015 CAGTATCATA
Statistics
Matches: 305, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 305 1.00
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:42103109 original size:15 final size:15
Alignment explanation
Indices: 42103074--42103115 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42103064 TTAAGAATTT
*
42103074 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42103088 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42103102 TATTTAATAATAAT
1 TATTTAATTATAAT
42103116 TATGTTNNNN
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42109694 original size:15 final size:15
Alignment explanation
Indices: 42109671--42109701 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42109661 CATATTAGTT
42109671 ATAAGTTTGGTAAAA
1 ATAAGTTTGGTAAAA
*
42109686 ATAATTTTGGTAAAA
1 ATAAGTTTGGTAAAA
42109701 A
1 A
42109702 AACAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (15 bp):
ATAAGTTTGGTAAAA
Found at i:42127909 original size:114 final size:114
Alignment explanation
Indices: 42127709--42127933 Score: 423
Period size: 114 Copynumber: 2.0 Consensus size: 114
42127699 ACTTGGAGTC
42127709 TAATAAATTTTGTTATAAAAATAGTCTGTCATTTTAGTTTTGTTTCTTCAAATTATTTCAATTAT
1 TAATAAATTTTGTTATAAAAATAGTCTGTCATTTTAGTTTTGTTTCTTCAAATTATTTCAATTAT
42127774 AATATAAAATAACAAATCATGCAAAAAAGAAAAACCCTAAAACATTTTA
66 AATATAAAATAACAAATCATGCAAAAAAGAAAAACCCTAAAACATTTTA
*
42127823 TAATAAATTTTGTTATAAAAATAGTTTGTCATTTTAGTTTTGTTTCTTCAAATTATTTCAATTAT
1 TAATAAATTTTGTTATAAAAATAGTCTGTCATTTTAGTTTTGTTTCTTCAAATTATTTCAATTAT
* *
42127888 AATTTAACATAACAAATCATGCAAAAAAGAAAAACCCTAAAACATT
66 AATATAAAATAACAAATCATGCAAAAAAGAAAAACCCTAAAACATT
42127934 ATCCAAAGTT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (114 bp):
TAATAAATTTTGTTATAAAAATAGTCTGTCATTTTAGTTTTGTTTCTTCAAATTATTTCAATTAT
AATATAAAATAACAAATCATGCAAAAAAGAAAAACCCTAAAACATTTTA
Found at i:42128656 original size:18 final size:17
Alignment explanation
Indices: 42128614--42128661 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
42128604 TGTCGTTCGT
42128614 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
42128631 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
42128650 TTTCAAAACATT
1 TTTCAAAACATT
42128662 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:42133410 original size:3 final size:3
Alignment explanation
Indices: 42133404--42133441 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
42133394 ACTAATTGGT
* *
42133404 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA GTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42133442 TCTCTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:42133421 original size:12 final size:12
Alignment explanation
Indices: 42133404--42133441 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
42133394 ACTAATTGGT
*
42133404 TTATTATTATTA
1 TTATTAGTATTA
42133416 TTATTAGTATTA
1 TTATTAGTATTA
42133428 TTATTAGTATTA
1 TTATTAGTATTA
42133440 TT
1 TT
42133442 TCTCTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (12 bp):
TTATTAGTATTA
Found at i:42138834 original size:44 final size:44
Alignment explanation
Indices: 42138771--42139196 Score: 318
Period size: 44 Copynumber: 9.8 Consensus size: 44
42138761 TAAAACCACA
* * *
42138771 AATCCTATCTCCCTGAAGTTGCAGTGTAGCAAATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * *
42138815 AATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATGAC-A-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAA-GCCAAT
* * * * * ***
42138859 GATCTTATCTCTCTGAAGTTGCAG-AGAGAAGA-T--CGCGTTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* ** * * * *
42138899 AGTCTTATCTCCCTGATCTTGTAGCGAAGCAGACTGAATAAG-C-A-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-TA-AAGCCAAT
*
42138943 AATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * ** *
42138987 AATCCTATCTCCCTGAAGTTGCAGCGGAGCAGGCT-AAGCAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * ***
42139030 AGATCTTATCCCCCTGAAGTTGCAGTGGGGCAGATTGAAGATGAT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
*
42139075 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * * **
42139120 AATCCTATCTCCCTAAAGTTGCAGCGGAGCGGATTAAAG-TGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *
42139163 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
42139197 CGCATCTAGT
Statistics
Matches: 295, Mismatches: 69, Indels: 37
0.74 0.17 0.09
Matches are distributed among these distances:
38 1 0.00
40 18 0.06
41 8 0.03
42 3 0.01
43 25 0.08
44 191 0.65
45 45 0.15
46 3 0.01
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:42139351 original size:305 final size:304
Alignment explanation
Indices: 42138771--42139363 Score: 728
Period size: 305 Copynumber: 1.9 Consensus size: 304
42138761 TAAAACCACA
* *
42138771 AATCCTATCTCCCTGAAGTTGCAGTGTAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTTA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTAAAGTTA
* * *
42138836 CAGTGGAGCAGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGAGAGAAGATCGCGTTTAG
66 CAGCGGAGCAGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGAGAGAAGATCGCATCTAG
* * *
42138901 TCTTATCTCCCTGATCTTGTAGCGAAGCAGACTGAATAAGCAAATCTTATCTCCCTGAAGTTGCA
131 TCTTATCTCCCTGAACTTATAGCGAAGCAGACTGAACAAGCAAATCTTATCTCCCTGAAGTTGCA
* ** * * ** * * *
42138966 GTGGAGCATATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGCGGAGCAGGCTAAGCAAATA
196 GTGGAGCAGACGAAAGCAAAAAATCCTATAACCCTGAAGTTACAGCGGAGCAGGATAA-CAAACA
* *
42139031 GATCTTATCCCCCTGAAGTTGCAGTGGGGCAGATTGAAGATGATG
260 GATCTTATACCCCTGAAGATGCAGTGGGGCAGATTGAAGATGATG
* * * *
42139076 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACTAATCCTATCTCCCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTAAAGTTA
* * * *
42139141 CAGCGGAGCGGATTAAAGTGATAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAG
66 CAGCGGAGCAGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGAGAGAAGATCGCATCTAG
* * * **
42139206 TCTTATCTCCCTGAAGTTATAGCGGAGCAGACTGAGCAAGCAGGTCTTATAC-CCCTGAAGTTGC
131 TCTTATCTCCCTGAACTTATAGCGAAGCAGACTGAACAAGCAAATCTTAT-CTCCCTGAAGTTGC
* ** * *
42139270 AGTGGAGCAGACGGAAG-AAAGAAATCCTATAACCCTGTCGTTACAGTGGAG-TGGATCAA-AAC
195 AGTGGAGCAGACGAAAGCAAA-AAATCCTATAACCCTGAAGTTACAGCGGAGCAGGAT-AACAA-
* *
42139332 ACCAG-TTTCTATACCCCTGAGGATGCAGTGGG
257 A-CAGATCT-TATACCCCTGAAGATGCAGTGGG
42139364 TTAAAACGAG
Statistics
Matches: 242, Mismatches: 40, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
303 2 0.01
304 8 0.03
305 231 0.95
306 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (304 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTAAAGTTA
CAGCGGAGCAGATTAAAATGACAGATCTTATCTCTCTGAAGTTGCAGAGAGAAGATCGCATCTAG
TCTTATCTCCCTGAACTTATAGCGAAGCAGACTGAACAAGCAAATCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACGAAAGCAAAAAATCCTATAACCCTGAAGTTACAGCGGAGCAGGATAACAAACAG
ATCTTATACCCCTGAAGATGCAGTGGGGCAGATTGAAGATGATG
Found at i:42141113 original size:18 final size:18
Alignment explanation
Indices: 42141090--42141142 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
42141080 AATCGTGTCG
42141090 TTCATTTTCAAAACATTA
1 TTCATTTTCAAAACATTA
* * *
42141108 TTCATTTACAAATCGTTA
1 TTCATTTTCAAAACATTA
*
42141126 TTCAATTTCAAAACATT
1 TTCATTTTCAAAACATT
42141143 TTTTTATTCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (18 bp):
TTCATTTTCAAAACATTA
Found at i:42142162 original size:219 final size:219
Alignment explanation
Indices: 42141783--42142224 Score: 848
Period size: 219 Copynumber: 2.0 Consensus size: 219
42141773 CTAAGCTGCT
*
42141783 AGTAAATTAGGCTCGAGGCCTTTCAGTACACTTCCTCTGAACATTAAAATCCCCCAACCCAATAT
1 AGTAAATTAGGCTCGAGGCCTTTCAGTACACTTCCTCTGAACATTAAAATCCCCCAACCCAATAC
42141848 AATGCAATATACAGATATGACGTGTTATAACATAATATCATGCATGTAAATAGGGCATACAGTAT
66 AATGCAATATACAGATATGACGTGTTATAACATAATATCATGCATGTAAATAGGGCATACAGTAT
*
42141913 CAAATTAATGGGACATCATCAGGCTTAATCATATCAGTCATACAGTCATTTCAGTCAATTAGGGG
131 CAAATCAATGGGACATCATCAGGCTTAATCATATCAGTCATACAGTCATTTCAGTCAATTAGGGG
*
42141978 TCTAGGTAAGCTTACTGACCCTAC
196 TCTAGGTAAGCTTACCGACCCTAC
42142002 AGTAAATTAGGCTCGAGGCCTTTCAGTACACTTCCTCTGAACATTAAAATCCCCCAACCCAATAC
1 AGTAAATTAGGCTCGAGGCCTTTCAGTACACTTCCTCTGAACATTAAAATCCCCCAACCCAATAC
*
42142067 AATGCAATATACGGATATGACGTGTTATAACATAATATCATGCATGTAAATAGGGCATACAGTAT
66 AATGCAATATACAGATATGACGTGTTATAACATAATATCATGCATGTAAATAGGGCATACAGTAT
42142132 CAAATCAATGGGACATCATCAGGCTTAATCATATCAGTCATACAGTCATTTCAGTCAATTAGGGG
131 CAAATCAATGGGACATCATCAGGCTTAATCATATCAGTCATACAGTCATTTCAGTCAATTAGGGG
42142197 TCTAGGTAAGCTTACCGACCCTAC
196 TCTAGGTAAGCTTACCGACCCTAC
42142221 AGTA
1 AGTA
42142225 GGCCCACAGT
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
219 219 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (219 bp):
AGTAAATTAGGCTCGAGGCCTTTCAGTACACTTCCTCTGAACATTAAAATCCCCCAACCCAATAC
AATGCAATATACAGATATGACGTGTTATAACATAATATCATGCATGTAAATAGGGCATACAGTAT
CAAATCAATGGGACATCATCAGGCTTAATCATATCAGTCATACAGTCATTTCAGTCAATTAGGGG
TCTAGGTAAGCTTACCGACCCTAC
Found at i:42145651 original size:23 final size:22
Alignment explanation
Indices: 42145625--42145672 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
42145615 GACAACAGTC
*
42145625 AGGTAAACAAGGTAGAAAATATA
1 AGGTAAACAAGGCAGAAAATA-A
*
42145648 AGGTAAGCAAGGCAGAAAATAA
1 AGGTAAACAAGGCAGAAAATAA
42145670 AGG
1 AGG
42145673 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.12
Consensus pattern (22 bp):
AGGTAAACAAGGCAGAAAATAA
Found at i:42154231 original size:43 final size:43
Alignment explanation
Indices: 42154183--42154374 Score: 212
Period size: 43 Copynumber: 4.5 Consensus size: 43
42154173 CAGTGCCATA
* * * *
42154183 TCCCAGATATGGACTTACATGTTATCACATATCGATGTCAATAG
1 TCCCAGATATGGTCTTACACGTAATCACATATCGATGCCAAT-G
* *
42154227 -CCCAGCTATGGTCTTACACG-AATCATATATCGATGCCAATG
1 TCCCAGATATGGTCTTACACGTAATCACATATCGATGCCAATG
*
42154268 TCCCAGATATGGTCTTACACGAAATCACATGAT-GATGCCAATG
1 TCCCAGATATGGTCTTACACGTAATCACAT-ATCGATGCCAATG
* * * *
42154311 TCCCAGACATGGTCTTACACGTAATCACATATATCAATACC-ATA
1 TCCCAGATATGGTCTTACACGTAATCAC--ATATCGATGCCAATG
*
42154355 TCCTAGATATGGTCTTACAC
1 TCCCAGATATGGTCTTACAC
42154375 AAAGTCTCAT
Statistics
Matches: 127, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 36 0.28
43 60 0.47
44 24 0.19
45 6 0.05
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (43 bp):
TCCCAGATATGGTCTTACACGTAATCACATATCGATGCCAATG
Found at i:42154326 original size:85 final size:86
Alignment explanation
Indices: 42154178--42154415 Score: 247
Period size: 85 Copynumber: 2.8 Consensus size: 86
42154168 ATATACAGTG
* * ** *
42154178 CCATATCCCAGATATGGACTTACATGTTATCACATATCGATGTCAATAGCCCAGCTATGGTCTTA
1 CCATATCCCAGATATGGTCTTACACGAAATCACATATCGATGCCAATAGCCCAGCTATGGTCTTA
* *
42154243 CACG-AAT-CATATATCGATG
66 CACGTAATACATATATCAATA
*
42154262 CCAATGTCCCAGATATGGTCTTACACGAAATCACATGAT-GATGCCAAT-GTCCCAGAC-ATGGT
1 CC-ATATCCCAGATATGGTCTTACACGAAATCACAT-ATCGATGCCAATAG-CCCAG-CTATGGT
42154324 CTTACACGTAATCACATATATCAATA
62 CTTACACGTAAT-ACATATATCAATA
* * * *
42154350 CCATATCCTAGATATGGTCTTACAC-AAAGTCTCATATATTGATGCC-ATAGCCCAACTATGGTC
1 CCATATCCCAGATATGGTCTTACACGAAA---TCACATATCGATGCCAATAGCCCAGCTATGGTC
42154413 TTA
63 TTA
42154416 TACGAAATCA
Statistics
Matches: 129, Mismatches: 12, Indels: 22
0.79 0.07 0.13
Matches are distributed among these distances:
84 3 0.02
85 54 0.42
86 9 0.07
87 22 0.17
88 29 0.22
89 12 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (86 bp):
CCATATCCCAGATATGGTCTTACACGAAATCACATATCGATGCCAATAGCCCAGCTATGGTCTTA
CACGTAATACATATATCAATA
Found at i:42154374 original size:44 final size:44
Alignment explanation
Indices: 42154183--42154421 Score: 203
Period size: 43 Copynumber: 5.5 Consensus size: 44
42154173 CAGTGCCATA
* * * *
42154183 TCCCAGATATGGACTTACATGTTATCAC--ATATCGATGTCAATAG
1 TCCCAGATATGGTCTTACACG-AATCACATATATCGATGCCAAT-G
*
42154227 -CCCAGCTATGGTCTTACACGAAT--CATATATCGATGCCAATG
1 TCCCAGATATGGTCTTACACGAATCACATATATCGATGCCAATG
*
42154268 TCCCAGATATGGTCTTACACGAAATCACAT-GAT-GATGCCAATG
1 TCCCAGATATGGTCTTACACG-AATCACATATATCGATGCCAATG
* * * *
42154311 TCCCAGACATGGTCTTACACGTAATCACATATATCAATACC-ATA
1 TCCCAGATATGGTCTTACACG-AATCACATATATCGATGCCAATG
* * * *
42154355 TCCTAGATATGGTCTTACACAAAGTCTCATATATTGATGCC-ATAG
1 TCCCAGATATGGTCTTACACGAA-TCACATATATCGATGCCAAT-G
*
42154400 -CCCA-ACTATGGTCTTATACGAA
1 TCCCAGA-TATGGTCTTACACGAA
42154422 ATCATGTAAT
Statistics
Matches: 160, Mismatches: 24, Indels: 22
0.78 0.12 0.11
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 34 0.21
43 61 0.38
44 56 0.35
45 7 0.04
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (44 bp):
TCCCAGATATGGTCTTACACGAATCACATATATCGATGCCAATG
Found at i:42157126 original size:27 final size:27
Alignment explanation
Indices: 42157095--42157153 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
42157085 TAGGTGTAAG
*
42157095 TGATTTTCATAAGTAACTAAGTGTATA
1 TGATTTTCATAAGCAACTAAGTGTATA
* * *
42157122 TGATTTTGATAAGCGACTAAGTGTATG
1 TGATTTTCATAAGCAACTAAGTGTATA
42157149 TGATT
1 TGATT
42157154 CGGATTCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (27 bp):
TGATTTTCATAAGCAACTAAGTGTATA
Found at i:42160826 original size:20 final size:21
Alignment explanation
Indices: 42160801--42160839 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
42160791 TGTGCATGGA
42160801 TGTAAC-TCCTTTT-TCAAATT
1 TGTAACAT-CTTTTCTCAAATT
42160821 TGTAACATCTTTTCTCAAA
1 TGTAACATCTTTTCTCAAA
42160840 GTTATTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (21 bp):
TGTAACATCTTTTCTCAAATT
Found at i:42168529 original size:26 final size:26
Alignment explanation
Indices: 42168467--42168520 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
42168457 AAATAATTAA
**
42168467 TATAAATAAGGATATTTTGATAATTT
1 TATAAATAAAAATATTTTGATAATTT
42168493 TATAAATAAAAATATTTTGATAATTT
1 TATAAATAAAAATATTTTGATAATTT
42168519 TA
1 TA
42168521 CTTGTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (26 bp):
TATAAATAAAAATATTTTGATAATTT
Found at i:42171506 original size:42 final size:42
Alignment explanation
Indices: 42171451--42171543 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
42171441 GCTGGTGTGA
42171451 TATATCAGGCTAAAAGCCTAGCAGGCGTAGTACT-GGTGAATT
1 TATATCAGGCTAAAAGCCTAGCAGGCGTAGT-CTCGGTGAATT
*
42171493 TATATCAGGCTAAAAGCCTAGCAGGCGTAGTGTCGGTGAATT
1 TATATCAGGCTAAAAGCCTAGCAGGCGTAGTCTCGGTGAATT
*
42171535 TTTATCAGG
1 TATATCAGG
42171544 TTTGTGCCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (42 bp):
TATATCAGGCTAAAAGCCTAGCAGGCGTAGTCTCGGTGAATT
Found at i:42172482 original size:13 final size:13
Alignment explanation
Indices: 42172464--42172491 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42172454 TAGGTTAAAT
42172464 TTGGTCATATTGC
1 TTGGTCATATTGC
42172477 TTGGTCATATTGC
1 TTGGTCATATTGC
42172490 TT
1 TT
42172492 TTGACATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (13 bp):
TTGGTCATATTGC
Found at i:42176714 original size:28 final size:27
Alignment explanation
Indices: 42176671--42176767 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 27
42176661 CTGAGATGCA
* *
42176671 TTATCAGAACAGAACATCACCGTAGTGC
1 TTAT-AGAACAAAACAACACCGTAGTGC
* * * *
42176699 TTATCATATCAAAACAAAACCGGAGTGC
1 TTAT-AGAACAAAACAACACCGTAGTGC
*
42176727 TTAATAGAACAGAACAACACCGTAGTGC
1 TT-ATAGAACAAAACAACACCGTAGTGC
*
42176755 TTAACAGAACAAA
1 TT-ATAGAACAAA
42176768 TGGCACACTA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
28 53 0.96
29 2 0.04
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (27 bp):
TTATAGAACAAAACAACACCGTAGTGC
Found at i:42176877 original size:98 final size:98
Alignment explanation
Indices: 42176719--42176904 Score: 273
Period size: 98 Copynumber: 1.9 Consensus size: 98
42176709 AAAACAAAAC
* * *
42176719 CGGAGTGCTTAATAGAACAGAACAACACCGTAGTGCTTAACAGAACAAATGGCACACTAATCCTC
1 CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAAAGGGCACACTAATCCTC
**
42176784 CTTAATGACATGCCATATATATCAGAACAATGT
66 CTTAACAACATGCCATATATATCAGAACAATGT
** *** *
42176817 CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAGGGGGCGTGCTAATTCTC
1 CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAAAGGGCACACTAATCCTC
42176882 CTTAACAACATGCCATATATATC
66 CTTAACAACATGCCATATATATC
42176905 CTAATAGTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 77 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (98 bp):
CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAAAGGGCACACTAATCCTC
CTTAACAACATGCCATATATATCAGAACAATGT
Found at i:42181171 original size:98 final size:98
Alignment explanation
Indices: 42180997--42181182 Score: 273
Period size: 98 Copynumber: 1.9 Consensus size: 98
42180987 AAAGTTAGAC
* * *
42180997 CGGAGTGCTTAATAGAACAGAACAACACCGTAGTGCTTAACAGAACAAATGGCACACTAATCCTC
1 CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAAAGGGCACACTAATCCTC
**
42181062 CTTAATGACATGCCATATATATCAGAACAATGT
66 CTTAACAACATGCCATATATATCAGAACAATGT
** *** *
42181095 CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAGGGGGCGTGCTAATTCTC
1 CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAAAGGGCACACTAATCCTC
42181160 CTTAACAACATGCCATATATATC
66 CTTAACAACATGCCATATATATC
42181183 CTAATAGTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 77 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (98 bp):
CGGAGTGCTTAACAGAACAGAACAACACCGTAGTGCTAAACAGAACAAAGGGCACACTAATCCTC
CTTAACAACATGCCATATATATCAGAACAATGT
Found at i:42203348 original size:28 final size:27
Alignment explanation
Indices: 42203285--42203381 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
42203275 TTATTAAGTC
* *
42203285 CGCACACTCAGTGCTATATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
42203312 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
* *
42203340 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
42203367 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42203382 GCACAATTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
27 39 0.60
28 26 0.40
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:42211329 original size:36 final size:37
Alignment explanation
Indices: 42211279--42211442 Score: 190
Period size: 36 Copynumber: 4.4 Consensus size: 37
42211269 ACAAATGGAA
*
42211279 TACTAATTCTACTGAAAGTGCTC-AACAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAAACAAGCAATATC
* * * * *
42211315 TATTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTCAAACAAGCAATATC
*
42211352 TACTGATTCTACTG-AAGTGCTCAAACGAG-AAGTATC
1 TACTGATTCTACTGAAAGTGCTCAAACAAGCAA-TATC
*
42211388 TACTGATTCTACCGAATAGTTGCTCAAACAAGCAATATC
1 TACTGATTCTACTGAA-AG-TGCTCAAACAAGCAATATC
* *
42211427 CACTGATTATACTGAA
1 TACTGATTCTACTGAA
42211443 TGCTTACTCA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
35 2 0.02
36 49 0.46
37 24 0.22
38 2 0.02
39 28 0.26
40 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (37 bp):
TACTGATTCTACTGAAAGTGCTCAAACAAGCAATATC
Found at i:42211432 original size:39 final size:38
Alignment explanation
Indices: 42211279--42211483 Score: 201
Period size: 39 Copynumber: 5.5 Consensus size: 38
42211269 ACAAATGGAA
* *
42211279 TACTAATTCTACTGAA-AGTGCTC-AACAAGCAATATC
1 TACTGATTCTACTGAATAGTGCTCAAACGAGCAATATC
* * *
42211315 TATTGATCCTACTGAAT-GTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAATAGTGCTCAAACGAGCAATATC
42211352 TACTGATTCTACTG-A-AGTGCTCAAACGAG-AAGTATC
1 TACTGATTCTACTGAATAGTGCTCAAACGAGCAA-TATC
* *
42211388 TACTGATTCTACCGAATAGTTGCTCAAACAAGCAATATC
1 TACTGATTCTACTGAATAG-TGCTCAAACGAGCAATATC
* * * *
42211427 CACTGATTATACTGAAT-GCTTACTCAAACGAGCATTAT-
1 TACTGATTCTACTGAATAG--TGCTCAAACGAGCAATATC
*
42211465 TCACTGATTATACTGAATA
1 T-ACTGATTCTACTGAATA
42211484 AGATTTTCTA
Statistics
Matches: 141, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
35 2 0.01
36 49 0.35
37 24 0.17
38 3 0.02
39 61 0.43
40 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (38 bp):
TACTGATTCTACTGAATAGTGCTCAAACGAGCAATATC
Found at i:42211432 original size:75 final size:72
Alignment explanation
Indices: 42211284--42211446 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 72
42211274 TGGAATACTA
* * *
42211284 ATTCTACTGAAAGTGCTCAACAAGCAATATCTATTGATCCTACTGAATGTGCTCAAACGAGCAAT
1 ATTCTACTG-AAGTGCTCAACAAGCAATATCTACTGATCCTACCGAATGTGCTCAAACAAGCAAT
* *
42211349 GTCTACTG
65 ATCCACTG
* *
42211357 ATTCTACTGAAGTGCTCAAACGAG-AAGTATCTACTGATTCTACCGAATAGTTGCTCAAACAAGC
1 ATTCTACTGAAGTGCTC-AACAAGCAA-TATCTACTGATCCTACCGAAT-G-TGCTCAAACAAGC
42211421 AATATCCACTG
62 AATATCCACTG
*
42211432 ATTATACTGAA-TGCT
1 ATTCTACTGAAGTGCT
42211447 TACTCAAACG
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
72 10 0.13
73 32 0.41
74 5 0.06
75 31 0.40
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (72 bp):
ATTCTACTGAAGTGCTCAACAAGCAATATCTACTGATCCTACCGAATGTGCTCAAACAAGCAATA
TCCACTG
Found at i:42214412 original size:20 final size:20
Alignment explanation
Indices: 42214387--42214425 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42214377 AGAATAAATT
* *
42214387 GGAAAAATTTGGAAATTTTA
1 GGAAAAAGTTGAAAATTTTA
42214407 GGAAAAAGTTGAAAATTTT
1 GGAAAAAGTTGAAAATTTT
42214426 GAACTACAAG
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:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (20 bp):
GGAAAAAGTTGAAAATTTTA
Found at i:42216413 original size:18 final size:19
Alignment explanation
Indices: 42216380--42216420 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
42216370 ATGTTCATAT
42216380 TTTTAAAATAATTTAATTA
1 TTTTAAAATAATTTAATTA
*
42216399 TTTTATAAT-ATTTAATTA
1 TTTTAAAATAATTTAATTA
42216417 TTTT
1 TTTT
42216421 TCGACAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAAATAATTTAATTA
Found at i:42216421 original size:19 final size:20
Alignment explanation
Indices: 42216377--42216421 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
42216367 ATCATGTTCA
42216377 TATTTTTAAAATAATTTAAT
1 TATTTTTAAAATAATTTAAT
*
42216397 TA-TTTTATAAT-ATTTAAT
1 TATTTTTAAAATAATTTAAT
42216415 TATTTTT
1 TATTTTT
42216422 CGACAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 9 0.39
19 12 0.52
20 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTAAAATAATTTAAT
Found at i:42227964 original size:33 final size:33
Alignment explanation
Indices: 42227885--42228036 Score: 180
Period size: 33 Copynumber: 4.5 Consensus size: 33
42227875 TACATCATCC
* * *
42227885 ATCCAACCAAACACACCAGATGCTCACT-TGAGCCA
1 ATCCAACC-ATCACACCA-ATGCTCA-TAAGAGCTA
** *
42227920 ATCCATTCATCACACCAATACTCATAAGAGCTA
1 ATCCAACCATCACACCAATGCTCATAAGAGCTA
*
42227953 ATCCAACCATCACACCAATGCTTATAAGAGCTA
1 ATCCAACCATCACACCAATGCTCATAAGAGCTA
* *
42227986 AACCAACCATCACACTAATGCTCATAAGAGCTA
1 ATCCAACCATCACACCAATGCTCATAAGAGCTA
*
42228019 ATCCAACCAGCACACCAA
1 ATCCAACCATCACACCAA
42228037 ATAGAAAGTA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
32 1 0.01
33 85 0.85
34 8 0.08
35 6 0.06
ACGTcount: A:0.40, C:0.34, G:0.09, T:0.18
Consensus pattern (33 bp):
ATCCAACCATCACACCAATGCTCATAAGAGCTA
Found at i:42234823 original size:23 final size:23
Alignment explanation
Indices: 42234797--42234918 Score: 79
Period size: 23 Copynumber: 5.3 Consensus size: 23
42234787 ATAAGTGCCA
42234797 CACTAATATGTAGCCGATGCTAC
1 CACTAATATGTAGCCGATGCTAC
* *
42234820 CACTGATACGTAGCCG-TAGCTAC
1 CACTAATATGTAGCCGAT-GCTAC
* * *
42234843 CATTGAA-ATGTAGCTGAAGCTAC
1 CACT-AATATGTAGCCGATGCTAC
* * *
42234866 AACTGATATGTAG-CTATAGCTAC
1 CACTAATATGTAGCCGAT-GCTAC
* * * *
42234889 CATTAAAATGTAGCAGAAGCTAC
1 CACTAATATGTAGCCGATGCTAC
*
42234912 TACTAAT
1 CACTAAT
42234919 CAATAACAAT
Statistics
Matches: 70, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
22 3 0.04
23 65 0.93
24 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (23 bp):
CACTAATATGTAGCCGATGCTAC
Found at i:42234871 original size:46 final size:46
Alignment explanation
Indices: 42234804--42234911 Score: 144
Period size: 46 Copynumber: 2.3 Consensus size: 46
42234794 CCACACTAAT
* * * * *
42234804 ATGTAGCCGATGCTACCACTGATACGTAGCCGTAGCTACCATTGAA
1 ATGTAGCAGAAGCTACAACTGATACGTAGCCATAGCTACCATTAAA
* * *
42234850 ATGTAGCTGAAGCTACAACTGATATGTAGCTATAGCTACCATTAAA
1 ATGTAGCAGAAGCTACAACTGATACGTAGCCATAGCTACCATTAAA
42234896 ATGTAGCAGAAGCTAC
1 ATGTAGCAGAAGCTAC
42234912 TACTAATCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25
Consensus pattern (46 bp):
ATGTAGCAGAAGCTACAACTGATACGTAGCCATAGCTACCATTAAA
Found at i:42235404 original size:31 final size:29
Alignment explanation
Indices: 42235365--42235424 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
42235355 GTCCTTGACT
42235365 TAAAATTTGGCAAAATTACAATTTTTCCCC
1 TAAAATTT-GCAAAATTACAATTTTTCCCC
* * *
42235395 TAAATATTTGCATATTTACACTTTTTCCCC
1 TAAA-ATTTGCAAAATTACAATTTTTCCCC
42235425 GAAGCTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.42
Consensus pattern (29 bp):
TAAAATTTGCAAAATTACAATTTTTCCCC
Found at i:42239122 original size:90 final size:90
Alignment explanation
Indices: 42238969--42239148 Score: 360
Period size: 90 Copynumber: 2.0 Consensus size: 90
42238959 TGAGTTAATT
42238969 ACAGATTGCATCCAGAATTGTCGTCCCACTTGACAACTGTCCGGATAAGAACTTAAATTATGTGA
1 ACAGATTGCATCCAGAATTGTCGTCCCACTTGACAACTGTCCGGATAAGAACTTAAATTATGTGA
42239034 GCTATCCAGTTTGGTATAACCAACC
66 GCTATCCAGTTTGGTATAACCAACC
42239059 ACAGATTGCATCCAGAATTGTCGTCCCACTTGACAACTGTCCGGATAAGAACTTAAATTATGTGA
1 ACAGATTGCATCCAGAATTGTCGTCCCACTTGACAACTGTCCGGATAAGAACTTAAATTATGTGA
42239124 GCTATCCAGTTTGGTATAACCAACC
66 GCTATCCAGTTTGGTATAACCAACC
42239149 TGTACGTGCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (90 bp):
ACAGATTGCATCCAGAATTGTCGTCCCACTTGACAACTGTCCGGATAAGAACTTAAATTATGTGA
GCTATCCAGTTTGGTATAACCAACC
Found at i:42245820 original size:32 final size:33
Alignment explanation
Indices: 42245712--42245854 Score: 191
Period size: 33 Copynumber: 4.4 Consensus size: 33
42245702 TCCAATCCAT
** *
42245712 CCATCACAAAAATGCTCATAAGAGCTAACCCAA
1 CCATCACACCAATGCTCATAAGAGCTAAACCAA
*
42245745 CCATCACACCAATGCTCATAAGAG-TGAAACGAA
1 CCATCACACCAATGCTCATAAGAGCT-AAACCAA
42245778 CCATCACACCAATGCTCATAAGAG-TAAACCAA
1 CCATCACACCAATGCTCATAAGAGCTAAACCAA
* *
42245810 CCATCGCACCAATGCTCATAAGAGCTAATCCAA
1 CCATCACACCAATGCTCATAAGAGCTAAACCAA
* *
42245843 CTAGCACACCAA
1 CCATCACACCAA
42245855 ATAGAGAGTA
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
32 30 0.31
33 68 0.69
ACGTcount: A:0.42, C:0.31, G:0.11, T:0.15
Consensus pattern (33 bp):
CCATCACACCAATGCTCATAAGAGCTAAACCAA
Found at i:42245851 original size:65 final size:66
Alignment explanation
Indices: 42245722--42245854 Score: 189
Period size: 65 Copynumber: 2.0 Consensus size: 66
42245712 CCATCACAAA
* * *
42245722 AATGCTCATAAGAGCTAACCCAACCATCACACCAATGCTCATAAGAGTGAAACGAACCATCACAC
1 AATGCTCATAAGAGCTAAACCAACCATCACACCAATGCTCATAAGAGTGAAACCAACCAGCACAC
42245787 C
66 C
* * *
42245788 AATGCTCATAAGAG-TAAACCAACCATCGCACCAATGCTCATAAGAGCT-AATCCAACTAGCACA
1 AATGCTCATAAGAGCTAAACCAACCATCACACCAATGCTCATAAGAG-TGAAACCAACCAGCACA
42245851 CC
65 CC
42245853 AA
1 AA
42245855 ATAGAGAGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 45 0.75
66 15 0.25
ACGTcount: A:0.41, C:0.31, G:0.12, T:0.16
Consensus pattern (66 bp):
AATGCTCATAAGAGCTAAACCAACCATCACACCAATGCTCATAAGAGTGAAACCAACCAGCACAC
C
Found at i:42249372 original size:36 final size:36
Alignment explanation
Indices: 42249315--42249627 Score: 243
Period size: 36 Copynumber: 8.5 Consensus size: 36
42249305 AAAAATGGAA
* * *
42249315 TACTGATTCTACTGAAAGTGCTCAATAAGTAATATC
1 TACTGATTCTACTGAATGTGCTCAATGAGCAATATC
* * * *
42249351 TACTAATCCTACTGAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAATGTGCTC-AATGAGCAATATC
* *
42249388 TACTGATTCTACTGAA-GTACTTAAATGAGCAATATC
1 TACTGATTCTACTGAATGTGC-TCAATGAGCAATATC
* * * *
42249424 TATTGATTCTACTGAAAGTGCTCAACGAGTAATATC
1 TACTGATTCTACTGAATGTGCTCAATGAGCAATATC
* * * * *
42249460 TACTGATCCTACTAAATGTGCTAAAATGAGCCATGTC
1 TACTGATTCTACTGAATGTGCT-CAATGAGCAATATC
* *
42249497 TACTGGTTCTACAGAA-GTGCTCAAATGAGCAATATC
1 TACTGATTCTACTGAATGTGCTC-AATGAGCAATATC
* *
42249533 TACTAATTCTACTGAATTGTTGCTCAAACGAGCAATATC
1 TACTGATTCTACTGAA-TG-TGCTC-AATGAGCAATATC
* * * * * *
42249572 CATTGATTATACTAAATGCTTGCTCAAACGAGCATTATC
1 TACTGATTCTACTGAATG--TGCTC-AATGAGCAATATC
* * *
42249611 CACTGATTATATTGAAT
1 TACTGATTCTACTGAAT
42249628 CAGGTTTTCT
Statistics
Matches: 221, Mismatches: 47, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
36 108 0.49
37 48 0.22
38 3 0.01
39 62 0.28
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (36 bp):
TACTGATTCTACTGAATGTGCTCAATGAGCAATATC
Found at i:42249436 original size:73 final size:74
Alignment explanation
Indices: 42249315--42249627 Score: 292
Period size: 73 Copynumber: 4.2 Consensus size: 74
42249305 AAAAATGGAA
* * * * * *
42249315 TACTGATTCTACTGAAAGTGC-TCAATAAGTAATATCTACTAATCCTACTGAATGTGCTCAAACG
1 TACTGATTCTACTGAATGTGCTTAAATGAGCAATATCTACTGATTCTACTGAATGTGCTCAAACG
*
42249379 AGCAATGTC
66 AGCAATATC
* * *
42249388 TACTGATTCTACTGAA-GTACTTAAATGAGCAATATCTATTGATTCTACTGAAAGTGCTC-AACG
1 TACTGATTCTACTGAATGTGCTTAAATGAGCAATATCTACTGATTCTACTGAATGTGCTCAAACG
*
42249451 AGTAATATC
66 AGCAATATC
* * * * * * * *
42249460 TACTGATCCTACTAAATGTGCTAAAATGAGCCATGTCTACTGGTTCTACAGAA-GTGCTCAAATG
1 TACTGATTCTACTGAATGTGCTTAAATGAGCAATATCTACTGATTCTACTGAATGTGCTCAAACG
42249524 AGCAATATC
66 AGCAATATC
* * * * * * *
42249533 TACTAATTCTACTGAATTGTTGCTCAAACGAGCAATATCCATTGATTATACTAAATGCTTGCTCA
1 TACTGATTCTACTGAA-TG-TGCTTAAATGAGCAATATCTACTGATTCTACTGAATG--TGCTCA
*
42249598 AACGAGCATTATC
62 AACGAGCAATATC
* * *
42249611 CACTGATTATATTGAAT
1 TACTGATTCTACTGAAT
42249628 CAGGTTTTCT
Statistics
Matches: 192, Mismatches: 40, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
72 34 0.18
73 100 0.52
74 2 0.01
75 25 0.13
76 1 0.01
77 1 0.01
78 29 0.15
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (74 bp):
TACTGATTCTACTGAATGTGCTTAAATGAGCAATATCTACTGATTCTACTGAATGTGCTCAAACG
AGCAATATC
Found at i:42249514 original size:109 final size:109
Alignment explanation
Indices: 42249315--42249605 Score: 357
Period size: 109 Copynumber: 2.6 Consensus size: 109
42249305 AAAAATGGAA
** * * *
42249315 TACTGATTCTACTGAAAGTGCTCAATAAGTAATATCTACTAATCCTACTGAATGTGCTCAAACGA
1 TACTGATTCTACTGAAAGTGCTCAACGAGTAATATCTACTGATCCTACTAAATGTGCTAAAACGA
* *
42249380 GCAATGTCTACTGATTCTACTGAAGTACTTAAATGAGCAATATC
66 GCAATGTCTACTGATTCTACAGAAGTACTCAAATGAGCAATATC
* *
42249424 TATTGATTCTACTGAAAGTGCTCAACGAGTAATATCTACTGATCCTACTAAATGTGCTAAAATGA
1 TACTGATTCTACTGAAAGTGCTCAACGAGTAATATCTACTGATCCTACTAAATGTGCTAAAACGA
* * *
42249489 GCCATGTCTACTGGTTCTACAGAAGTGCTCAAATGAGCAATATC
66 GCAATGTCTACTGATTCTACAGAAGTACTCAAATGAGCAATATC
* * * * * ** *
42249533 TACTAATTCTACTGAATTGTTGCTCAAACGAGCAATATCCATTGATTATACTAAATGCTTGCTCA
1 TACTGATTCTACTGAA-AG-TGCTC-AACGAGTAATATCTACTGATCCTACTAAATG--TGCTAA
42249598 AACGAGCA
61 AACGAGCA
42249606 TTATCCACTG
Statistics
Matches: 154, Mismatches: 23, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
109 111 0.72
110 1 0.01
111 5 0.03
112 26 0.17
114 11 0.07
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (109 bp):
TACTGATTCTACTGAAAGTGCTCAACGAGTAATATCTACTGATCCTACTAAATGTGCTAAAACGA
GCAATGTCTACTGATTCTACAGAAGTACTCAAATGAGCAATATC
Found at i:42251698 original size:27 final size:27
Alignment explanation
Indices: 42251668--42251845 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42251658 ATATTGAGTC
* * * *
42251668 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42251695 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42251722 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42251750 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42251777 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42251804 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42251831 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42251846 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42251807 original size:82 final size:81
Alignment explanation
Indices: 42251689--42251844 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42251679 TGCTATATAA
* *
42251689 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42251754 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42251771 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42251835 CACTTAGTGC
65 CACTTAGTGC
42251845 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42259888 original size:27 final size:27
Alignment explanation
Indices: 42259858--42260035 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
42259848 ATATTGAGCC
* * * *
42259858 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
42259885 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42259912 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42259940 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42259967 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42259994 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42260021 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42260036 GTACAATTTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42259997 original size:82 final size:81
Alignment explanation
Indices: 42259879--42260034 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42259869 TGCTATATAA
* *
42259879 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42259944 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42259961 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42260025 CACTTAGTGC
65 CACTTAGTGC
42260035 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 17 0.25
82 50 0.75
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42278321 original size:85 final size:85
Alignment explanation
Indices: 42278173--42278346 Score: 339
Period size: 85 Copynumber: 2.0 Consensus size: 85
42278163 TACTATTAAA
42278173 AAGAGCATAAATATGATTAATATATTATGAGTGGGCTTAAAGCAAGTAACTTATGTTTAGGTAAT
1 AAGAGCATAAATATGATTAATATATTATGAGTGGGCTTAAAGCAAGTAACTTATGTTTAGGTAAT
42278238 AAATGAACTAACTAAATTAG
66 AAATGAACTAACTAAATTAG
*
42278258 AAGAGCATAAATATGATTAATATATTATGAGTGGGCTTAAAGCAAGTAACTTATGTTTTGGTAAT
1 AAGAGCATAAATATGATTAATATATTATGAGTGGGCTTAAAGCAAGTAACTTATGTTTAGGTAAT
42278323 AAATGAACTAACTAAATTAG
66 AAATGAACTAACTAAATTAG
42278343 AAGA
1 AAGA
42278347 TGGTTTCTAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (85 bp):
AAGAGCATAAATATGATTAATATATTATGAGTGGGCTTAAAGCAAGTAACTTATGTTTAGGTAAT
AAATGAACTAACTAAATTAG
Found at i:42281584 original size:27 final size:27
Alignment explanation
Indices: 42281554--42281731 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
42281544 ATATTGAGCC
* *
42281554 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
42281581 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
42281608 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
42281636 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
42281663 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
42281690 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
42281717 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42281732 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42281693 original size:82 final size:81
Alignment explanation
Indices: 42281575--42281730 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
42281565 TGCTATATAA
* *
42281575 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42281640 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
42281657 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42281721 CACTTAGTGC
65 CACTTAGTGC
42281731 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42284052 original size:27 final size:27
Alignment explanation
Indices: 42284022--42284091 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
42284012 TATACGTACA
* *
42284022 ATCCCTACAGAGTTTGTCGCACATACT
1 ATCCCTTCAGAGTTTGTCACACATACT
* ** *
42284049 ATCCCTTTAGAGTTCATCACATATACT
1 ATCCCTTCAGAGTTTGTCACACATACT
42284076 ATCCCTTCAGAGTTTG
1 ATCCCTTCAGAGTTTG
42284092 AATAGAGGTC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (27 bp):
ATCCCTTCAGAGTTTGTCACACATACT
Found at i:42286562 original size:29 final size:28
Alignment explanation
Indices: 42286518--42286601 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 28
42286508 CCACCAAGAA
42286518 TTCCTT-TAATAGAGATAGCCACAAAGG
1 TTCCTTATAATAGAGATAGCCACAAAGG
* **
42286545 TATCCTTATAATAAAGATTTCCACAAAGG
1 T-TCCTTATAATAGAGATAGCCACAAAGG
* * * *
42286574 TTCTTTAGAACAGAGATCGCCACAAAGG
1 TTCCTTATAATAGAGATAGCCACAAAGG
42286602 CTTTCCTACG
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
27 1 0.02
28 26 0.57
29 19 0.41
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (28 bp):
TTCCTTATAATAGAGATAGCCACAAAGG
Found at i:42293819 original size:19 final size:19
Alignment explanation
Indices: 42293795--42293841 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42293785 CAATACCTCT
*
42293795 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
42293814 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
42293833 TATGCATTA
1 TTTGCATTA
42293842 AGTTTCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:42305143 original size:15 final size:15
Alignment explanation
Indices: 42305125--42305175 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
42305115 TCAGCCGTGT
42305125 GTGACACATGGCTTG
1 GTGACACATGGCTTG
*
42305140 GTG--ACATGGCCGTG
1 GTGACACATGG-CTTG
42305154 TGTGACACATGGCTTG
1 -GTGACACATGGCTTG
42305170 GTGACA
1 GTGACA
42305176 TGGTCGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 6 0.20
14 3 0.10
15 12 0.40
16 3 0.10
17 6 0.20
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (15 bp):
GTGACACATGGCTTG
Found at i:42305148 original size:13 final size:13
Alignment explanation
Indices: 42305130--42305178 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
42305120 CGTGTGTGAC
42305130 ACATGGCTTGGTG
1 ACATGGCTTGGTG
*
42305143 ACATGGCCGTGTGTG
1 ACATGG-CTTG-GTG
42305158 ACACATGGCTTGGTG
1 --ACATGGCTTGGTG
42305173 ACATGG
1 ACATGG
42305179 TCGTGTGTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 12 0.40
14 3 0.10
15 6 0.20
16 3 0.10
17 6 0.20
ACGTcount: A:0.18, C:0.18, G:0.37, T:0.27
Consensus pattern (13 bp):
ACATGGCTTGGTG
Found at i:42305152 original size:30 final size:30
Alignment explanation
Indices: 42305118--42305186 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
42305108 ATGTGACTCA
42305118 GCCGTGTGTGACACATGGCTTGGTGACATG
1 GCCGTGTGTGACACATGGCTTGGTGACATG
42305148 GCCGTGTGTGACACATGGCTTGGTGACATG
1 GCCGTGTGTGACACATGGCTTGGTGACATG
*
42305178 GTCGTGTGT
1 GCCGTGTGT
42305187 CCCCTGTAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.14, C:0.19, G:0.38, T:0.29
Consensus pattern (30 bp):
GCCGTGTGTGACACATGGCTTGGTGACATG
Found at i:42305314 original size:13 final size:13
Alignment explanation
Indices: 42305296--42305329 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
42305286 AGCACACAGG
42305296 CGTGTGACTTGGC
1 CGTGTGACTTGGC
42305309 CGTGTGACTTGGC
1 CGTGTGACTTGGC
42305322 CGTGTGAC
1 CGTGTGAC
42305330 CTTACTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.24, G:0.38, T:0.29
Consensus pattern (13 bp):
CGTGTGACTTGGC
Found at i:42308652 original size:40 final size:40
Alignment explanation
Indices: 42308622--42308871 Score: 394
Period size: 40 Copynumber: 6.3 Consensus size: 40
42308612 GGACTAAGAT
* * * *
42308622 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
42308662 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
42308702 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
42308742 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* *
42308782 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
42308822 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
42308861 CCGAAGGCATT
1 CCGAAGGCATT
42308872 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
39 34 0.17
40 165 0.83
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:42308706 original size:80 final size:80
Alignment explanation
Indices: 42308569--42308871 Score: 396
Period size: 80 Copynumber: 3.8 Consensus size: 80
42308559 TTGAATGCTG
* * * * * * * *
42308569 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGCTAAG-TCCCGAAGGCAT
* * *
42308632 TTGTGCGAGATACTAAA
64 TCGTGCGAGTTATTAAA
*
42308649 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGCTAAGTCCCGAAGGCATTC
42308714 GTGCGAGTTATTAAA
66 GTGCGAGTTATTAAA
*
42308729 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGCTAAGTCCCGAAGGCATTC
*
42308794 GTGCGAGTTGTTAAA
66 GTGCGAGTTATTAAA
* * * * *
42308809 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGCTAAGTCCCGAAGGCATT
42308872 TGAACGAGGA
Statistics
Matches: 202, Mismatches: 19, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
79 35 0.17
80 161 0.80
81 6 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGCTAAGTCCCGAAGGCATTC
GTGCGAGTTATTAAA
Found at i:42308782 original size:120 final size:119
Alignment explanation
Indices: 42308569--42308871 Score: 410
Period size: 120 Copynumber: 2.5 Consensus size: 119
42308559 TTGAATGCTG
* * * * * * *
42308569 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
*
42308633 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
64 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
42308689 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTC
* * *
42308754 GTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 GTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * * * *
42308809 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATT
42308872 TGAACGAGGA
Statistics
Matches: 162, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
119 35 0.22
120 123 0.76
121 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:42316682 original size:40 final size:40
Alignment explanation
Indices: 42316599--42316782 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 40
42316589 TTGAATGCTG
* * * * *
42316599 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-T-ACTAAA
* * *
42316639 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACTAAA
* *
42316679 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
* **
42316719 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
* *
42316759 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42316783 TGAACGAGGA
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 115 0.91
41 10 0.08
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:42316736 original size:80 final size:81
Alignment explanation
Indices: 42316599--42316782 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
42316589 TTGAATGCTG
* * *
42316599 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
*
42316663 TGTGCGAGATACTAAA
66 CGTGCGAGATACTAAA
* * * * *
42316679 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCAT
* **
42316742 TCGTGCGAGTTGTTAAA
65 TCGTGCGAGATACTAAA
*
42316759 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42316783 TGAACGAGGA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
79 1 0.01
80 81 0.92
81 6 0.07
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAA
Found at i:42316802 original size:80 final size:80
Alignment explanation
Indices: 42316599--42316817 Score: 203
Period size: 80 Copynumber: 2.8 Consensus size: 80
42316589 TTGAATGCTG
* ** * * * *
42316599 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTATATCCGGGTTAAG-TCCCGAAGGCAT
*
42316662 TTGTGCGAGATACTAAA
64 TCGTGCGAGATACTAAA
* ** * * *
42316679 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTATATCCGGGTTAAGTCCCGAAGGCATTC
* **
42316744 GTGCGAGTTGTTAAA
66 GTGCGAGATACTAAA
* * *
42316759 TCCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTATATCCGGGTTAAGTCCCGAAGG
42316818 TACGTGATTT
Statistics
Matches: 115, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
79 17 0.15
80 92 0.80
81 6 0.05
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTATATCCGGGTTAAGTCCCGAAGGCATTC
GTGCGAGATACTAAA
Found at i:42317770 original size:63 final size:63
Alignment explanation
Indices: 42317671--42317797 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
42317661 GAAACAATCA
42317671 TAGGAACAGTACAGTAAGAGATATTCGGGTTCTTGTGGAACAGGGCCAGAACAGTTTCTGGAT
1 TAGGAACAGTACAGTAAGAGATATTCGGGTTCTTGTGGAACAGGGCCAGAACAGTTTCTGGAT
42317734 TAGGAACAGTACAGTAAGAGATATTCGGGTTCTTGTGGAACAGGGCCAGAACAGTTTCTGGAT
1 TAGGAACAGTACAGTAAGAGATATTCGGGTTCTTGTGGAACAGGGCCAGAACAGTTTCTGGAT
42317797 T
1 T
42317798 CCCTGTTCCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (63 bp):
TAGGAACAGTACAGTAAGAGATATTCGGGTTCTTGTGGAACAGGGCCAGAACAGTTTCTGGAT
Found at i:42318717 original size:59 final size:59
Alignment explanation
Indices: 42318645--42318762 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
42318635 TGACAGAATC
* * * *
42318645 CGAAAACATGGGGCTACTGAATTTAAGGCTATGGATAGCGATGATGCCGAGCAAGCTGA
1 CGAAAACATGGGGCTACTGAATTTAAAGCTACGAATAGCGACGATGCCGAGCAAGCTGA
42318704 CGAAAACATGGGGCTACTGAATTTAAAGCTACGAATAGCGACGATGCCGAGCAAGCTGA
1 CGAAAACATGGGGCTACTGAATTTAAAGCTACGAATAGCGACGATGCCGAGCAAGCTGA
42318763 ATTTTGGTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (59 bp):
CGAAAACATGGGGCTACTGAATTTAAAGCTACGAATAGCGACGATGCCGAGCAAGCTGA
Found at i:42321492 original size:76 final size:76
Alignment explanation
Indices: 42321366--42321509 Score: 252
Period size: 76 Copynumber: 1.9 Consensus size: 76
42321356 ACATTATCTG
* * *
42321366 TTTGGTGAGAAGTGCCATGTATTTTCGGATCACAAAAGTCTCAAATATTTGATGACTCAACGAGA
1 TTTGGTGAGAAGTGCCATATATTTTCGGATCACAAAAGTCTCAAAAATTTGATGACTCAAAGAGA
42321431 CTTGTTACTTA
66 CTTGTTACTTA
*
42321442 TTTGGTGAGAAGTGCCATATATTTTCGGATCACAAAAGTCTCAAAAATTTGATGATTCAAAGAGA
1 TTTGGTGAGAAGTGCCATATATTTTCGGATCACAAAAGTCTCAAAAATTTGATGACTCAAAGAGA
42321507 CTT
66 CTT
42321510 AAATCTGCGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
TTTGGTGAGAAGTGCCATATATTTTCGGATCACAAAAGTCTCAAAAATTTGATGACTCAAAGAGA
CTTGTTACTTA
Found at i:42321935 original size:87 final size:87
Alignment explanation
Indices: 42321789--42321962 Score: 321
Period size: 87 Copynumber: 2.0 Consensus size: 87
42321779 GGAGTCGGAG
* *
42321789 TTTCAAATTGATGATGATGATTGTTTGAGGTTTAGAAATCGTTTGTGTGTTCCAAGGAATTCGGA
1 TTTCAAATTGATGATGATGATTGTTTGAGGTTCAGAAATCGTTTGTGTGTTCCAAGGAATTCGAA
42321854 ACTCATTTCGATGATTCTGAAC
66 ACTCATTTCGATGATTCTGAAC
*
42321876 TTTCAAATTGATGATGATGATTGTTTGAGGTTCAGAAGTCGTTTGTGTGTTCCAAGGAATTCGAA
1 TTTCAAATTGATGATGATGATTGTTTGAGGTTCAGAAATCGTTTGTGTGTTCCAAGGAATTCGAA
42321941 ACTCATTTCGATGATTCTGAAC
66 ACTCATTTCGATGATTCTGAAC
42321963 GAAGCCCATT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (87 bp):
TTTCAAATTGATGATGATGATTGTTTGAGGTTCAGAAATCGTTTGTGTGTTCCAAGGAATTCGAA
ACTCATTTCGATGATTCTGAAC
Found at i:42322256 original size:76 final size:76
Alignment explanation
Indices: 42322130--42322283 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 76
42322120 CTTCAAGATT
42322130 ACTTCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACTTTGTGTCCGGAC
1 ACTTCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACTTTGTGTCCGGAC
42322195 TGCCATTGCCA
66 TGCCATTGCCA
42322206 ACTTCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACTTTGTGTCCGGAC
1 ACTTCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACTTTGTGTCCGGAC
*
42322271 TGCCATTGTCA
66 TGCCATTGCCA
42322282 AC
1 AC
42322284 AAGTAAGAAG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (76 bp):
ACTTCAGCCGATCATGATACCCGAGTGGAAATGGGATCGAGTCACAATGGACTTTGTGTCCGGAC
TGCCATTGCCA
Found at i:42324910 original size:40 final size:40
Alignment explanation
Indices: 42324827--42325010 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
42324817 TTGAATGCTG
* * * * *
42324827 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-T-ACTAAA
* * *
42324867 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACTAAA
* **
42324907 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
* **
42324947 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
* *
42324987 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42325011 TGAACGAGGA
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 115 0.91
41 10 0.08
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:42324964 original size:80 final size:81
Alignment explanation
Indices: 42324827--42325010 Score: 214
Period size: 80 Copynumber: 2.3 Consensus size: 81
42324817 TTGAATGCTG
* * *
42324827 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
*
42324891 TGTGCGAGATACTAAA
66 CGTGCGAGATACTAAA
* * * *
42324907 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* **
42324969 TTCGTGCGAGTTGTTAAA
64 TTCGTGCGAGATACTAAA
*
42324987 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42325011 TGAACGAGGA
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
79 1 0.01
80 79 0.90
81 8 0.09
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAA
Found at i:42325030 original size:80 final size:80
Alignment explanation
Indices: 42324863--42325045 Score: 199
Period size: 80 Copynumber: 2.3 Consensus size: 80
42324853 GCTAAGTGAA
* * * *
42324863 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGG
** ** *
42324927 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * ** *
42324943 TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGC
*
42325008 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
42325023 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
42325046 TACGTGATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
79 16 0.19
80 69 0.81
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:42332587 original size:18 final size:20
Alignment explanation
Indices: 42332551--42332597 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
42332541 AGTTGTAAGT
42332551 ATATATATGTGAATAATTTG
1 ATATATATGTGAATAATTTG
* *
42332571 ATAT-TATGTGATTATTTTG
1 ATATATATGTGAATAATTTG
42332590 ATGATATA
1 AT-ATATA
42332598 ACATGTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATATATATGTGAATAATTTG
Found at i:42333027 original size:50 final size:50
Alignment explanation
Indices: 42332946--42333178 Score: 216
Period size: 50 Copynumber: 4.6 Consensus size: 50
42332936 TCCGTTGTGA
* *
42332946 GTCACTTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTAATAG
* * * ** * *
42332996 GTCGCATGTGTAGTACTAAATGCAGGCTACTATGCATACC-CATTAACTTCG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTAA--TAG
* * * * *** *
42333047 ATCACTTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAA
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTAATAG
** * * * *
42333097 GTCATGTGTGTAGGACTAAGTTCAGGCTATTACGTGCACCAGATTAATAG
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTAATAG
* *
42333147 GTCGCATGTGTAGTACTAAGTGTAGGCTACTA
1 GTCACATGTGTAGTACTAAGTGCAGGCTACTA
42333179 TGCATACCAA
Statistics
Matches: 136, Mismatches: 44, Indels: 6
0.73 0.24 0.03
Matches are distributed among these distances:
49 4 0.03
50 97 0.71
51 33 0.24
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (50 bp):
GTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTAATAG
Found at i:42336836 original size:23 final size:23
Alignment explanation
Indices: 42336799--42337056 Score: 263
Period size: 23 Copynumber: 11.2 Consensus size: 23
42336789 GGAATCTATA
* *
42336799 GGCTACATTTCAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* *
42336822 GGCTACAATATAGTGGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
*
42336845 GGCTAC-ATCTCAGTGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
42336868 GGCTACAATACAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
*
42336891 GGCTACAATATAGTGGTAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* *
42336914 GGCAAC-ATCTCAGTGGTAGCTTC
1 GGCTACAAT-ACAGTGGTAGCTTC
* *
42336937 GGCTTCAATACAGTGGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
* *
42336960 GGATAC-AT-CTTAGTGGTAGCCTC
1 GGCTACAATAC--AGTGGTAGCTTC
*
42336983 GGCTACAATACAGTGGTAGCTTT
1 GGCTACAATACAGTGGTAGCTTC
** *
42337006 GGCTACGTTACAGTGATAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
* *** *
42337029 AGCTATGTTACAGTGATAGCTTC
1 GGCTACAATACAGTGGTAGCTTC
42337052 GGCTA
1 GGCTA
42337057 TATTACAACG
Statistics
Matches: 197, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.01
22 6 0.03
23 183 0.93
24 6 0.03
25 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCTACAATACAGTGGTAGCTTC
Found at i:42336910 original size:69 final size:69
Alignment explanation
Indices: 42336799--42337056 Score: 304
Period size: 69 Copynumber: 3.7 Consensus size: 69
42336789 GGAATCTATA
* * *
42336799 GGCTACATTTCAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTTGGCTACATCTCAGTGGTAG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTAG
42336864 CTTC
66 CTTC
*
42336868 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCAACATCTCAGTGGTAG
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTAG
42336933 CTTC
66 CTTC
* * * * * *
42336937 GGCTTCAATACAGTGGTAGCTTTGGATAC-ATCTTAGTGGTAGCCTCGGCTACAAT-ACAGTGGT
1 GGCTACAATACAGTGGTAGCTTCGGCTACAAT-ATAGTGGTAGCTTCGGCTAC-ATCTCAGTGGT
*
42337000 AGCTTT
64 AGCTTC
** * * *** * *
42337006 GGCTACGTTACAGTGATAGCTTCAGCTATGTTACAGTGATAGCTTCGGCTA
1 GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTA
42337057 TATTACAACG
Statistics
Matches: 161, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
68 2 0.01
69 156 0.97
70 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (69 bp):
GGCTACAATACAGTGGTAGCTTCGGCTACAATATAGTGGTAGCTTCGGCTACATCTCAGTGGTAG
CTTC
Found at i:42346111 original size:93 final size:93
Alignment explanation
Indices: 42346004--42346174 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
42345994 GCCCCTAAGT
* *
42346004 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42346069 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42346097 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42346162 CGAGTTCGGATGC
66 CGAGTTCGGATGC
42346175 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42346171 original size:46 final size:46
Alignment explanation
Indices: 42345999--42346171 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
42345989 AACCCGCCCC
* * *
42345999 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
42346045 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
42346093 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
42346138 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42346172 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:42346628 original size:30 final size:30
Alignment explanation
Indices: 42346594--42346653 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42346584 ATTTAATACG
42346594 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
42346624 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
42346654 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:42355431 original size:36 final size:36
Alignment explanation
Indices: 42355388--42355457 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
42355378 TAAAAATCAA
42355388 CATATCATATAATTAACAT-TAATAACTTAAAAATGG
1 CATATCATATAATTAACATGT-ATAACTTAAAAATGG
*
42355424 CATATCATATGATTAACATGTATAACTTAAAAAT
1 CATATCATATAATTAACATGTATAACTTAAAAAT
42355458 AACAATTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 31 0.97
37 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (36 bp):
CATATCATATAATTAACATGTATAACTTAAAAATGG
Found at i:42355672 original size:30 final size:30
Alignment explanation
Indices: 42355638--42355697 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42355628 ATTTAATACG
42355638 AACTTTAGAAAAATTACACTTTTGCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
* * *
42355668 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAGAAAAATTACACTTTTGCCCCTA
42355698 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTAGAAAAATTACACTTTTGCCCCTA
Found at i:42356846 original size:5 final size:6
Alignment explanation
Indices: 42356817--42356860 Score: 52
Period size: 6 Copynumber: 6.7 Consensus size: 6
42356807 GTTTAAAGAA
42356817 TTTTATT TTTTAT TTTTATGT TTTTAT TTTTAT TTTTAT CTTTT
1 TTTTA-T TTTTAT TTTTA--T TTTTAT TTTTAT TTTTAT -TTTT
42356861 TAAAAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 19 0.56
7 9 0.26
8 6 0.18
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTAT
Done.