Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 11 of 205
Found at i:3195364 original size:37 final size:37
Alignment explanation
Indices: 3195322--3195498 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
3195312 AGCTGAAGCT
* **
3195322 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
3195359 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
3195396 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
3195433 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
3195470 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
3195499 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:3203012 original size:45 final size:46
Alignment explanation
Indices: 3202945--3203068 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
3202935 CATATGACCT
*
3202945 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3202988 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
3203034 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3203069 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:3203051 original size:46 final size:45
Alignment explanation
Indices: 3202945--3203216 Score: 216
Period size: 37 Copynumber: 6.8 Consensus size: 45
3202935 CATATGACCT
*
3202945 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3202988 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
3203034 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3203071 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
3203108 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
3203145 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
3203182 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
3203217 CACTTATCAC
Statistics
Matches: 210, Mismatches: 9, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
37 134 0.64
39 2 0.01
40 3 0.01
42 1 0.00
43 9 0.04
44 6 0.03
45 21 0.10
46 34 0.16
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:3203072 original size:37 final size:37
Alignment explanation
Indices: 3203031--3203243 Score: 363
Period size: 37 Copynumber: 5.8 Consensus size: 37
3203021 GCTGAAGCTA
* *
3203031 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3203068 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3203105 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3203142 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3203179 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3203216 CCACTTATCACTTTGTTTCTTGATCAGA
1 CCACTTATCACTTTGTCTCTTGATCAGA
3203244 AGTACTCAAA
Statistics
Matches: 167, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 167 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:3205885 original size:18 final size:19
Alignment explanation
Indices: 3205864--3205902 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3205854 ATATATAGAT
3205864 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
3205882 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
3205901 AT
1 AT
3205903 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:3206250 original size:39 final size:39
Alignment explanation
Indices: 3206140--3206274 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 39
3206130 GACCTCAAGT
* * * *
3206140 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
3206181 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
*
3206219 CGATGAGACACTGGGTGTCAAATATTGCTTCGAGCTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
3206258 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
3206275 CCATATTGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 18 0.24
39 35 0.47
40 5 0.07
41 16 0.22
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:3206418 original size:18 final size:19
Alignment explanation
Indices: 3206397--3206437 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3206387 AATGAAATGA
3206397 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
3206415 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
3206434 GAAA
1 GAAA
3206438 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:3212450 original size:467 final size:467
Alignment explanation
Indices: 3211577--3212500 Score: 1839
Period size: 467 Copynumber: 2.0 Consensus size: 467
3211567 ATCAAGTATG
3211577 AGGTTGCAGAAGTCAGGACCCCATTGAGACGGATGTGGAAAGAGATGGTTAAGAGATGATTAATC
1 AGGTTGCAGAAGTCAGGACCCCATTGAGACGGATGTGGAAAGAGATGGTTAAGAGATGATTAATC
3211642 GTGTTGAATTTGAGAGAAGAATCTGAAGAAAAGAGGAACTACTGTGAGTTCCACAACGAGGTGGG
66 GTGTTGAATTTGAGAGAAGAATCTGAAGAAAAGAGGAACTACTGTGAGTTCCACAACGAGGTGGG
3211707 GCATGAAATTCAAGAGTGTGTGGAGTTCAGGGCCCTCGTGCAGGACATGATAAACAATAGAGAAA
131 GCATGAAATTCAAGAGTGTGTGGAGTTCAGGGCCCTCGTGCAGGACATGATAAACAATAGAGAAA
3211772 TAGAGTTTTATGAAGAAATCGAAAACCCCAAAGAAGGAGATATATGCTCATCAGAGGGAGAATCA
196 TAGAGTTTTATGAAGAAATCGAAAACCCCAAAGAAGGAGATATATGCTCATCAGAGGGAGAATCA
3211837 ACGACACAGAACCAAACAGTTAATTACCCCGTGGTCATCATATCACGACCCAAAAGTAATGAAAC
261 ACGACACAGAACCAAACAGTTAATTACCCCGTGGTCATCATATCACGACCCAAAAGTAATGAAAC
3211902 AGTAGTGCAAATGCCACCGAAAGTCATAATCCAAATACCTGCAGTCTTCCCCTATAAAGATAGTA
326 AGTAGTGCAAATGCCACCGAAAGTCATAATCCAAATACCTGCAGTCTTCCCCTATAAAGATAGTA
3211967 AGAGGGTCCCATGAAATTACGACTGTAATGTGACGATCTCAGGAAAAGAGAACCTGGTTAACGAT
391 AGAGGGTCCCATGAAATTACGACTGTAATGTGACGATCTCAGGAAAAGAGAACCTGGTTAACGAT
3212032 TCCCCTATAAAT
456 TCCCCTATAAAT
3212044 AGGTTGCAGAAGTCAGGACCCCATTGAGACGGATGTGGAAAGAGATGGTTAAGAGATGATTAATC
1 AGGTTGCAGAAGTCAGGACCCCATTGAGACGGATGTGGAAAGAGATGGTTAAGAGATGATTAATC
3212109 GTGTTGAATTTGAGAGAAGAATCTGAAGAAAAGAGGAACTACTGTGAGTTCCACAACGAGGTGGG
66 GTGTTGAATTTGAGAGAAGAATCTGAAGAAAAGAGGAACTACTGTGAGTTCCACAACGAGGTGGG
3212174 GCATGAAATTCAAGAGTGTGTGGAGTTCAGGGCCCTCGTGCAGGACATGATAAACAATAGAGAAA
131 GCATGAAATTCAAGAGTGTGTGGAGTTCAGGGCCCTCGTGCAGGACATGATAAACAATAGAGAAA
*
3212239 TAGAGTTTTATGAAGAAATCGAAAACCCCGAAGAAGGAGATATATGCTCATCAGAGGGAGAATCA
196 TAGAGTTTTATGAAGAAATCGAAAACCCCAAAGAAGGAGATATATGCTCATCAGAGGGAGAATCA
3212304 ACGACACAGAACCAAACAGTTAATTACCCCGTGGTCATCATATCACGACCCAAAAGTAATGAAAC
261 ACGACACAGAACCAAACAGTTAATTACCCCGTGGTCATCATATCACGACCCAAAAGTAATGAAAC
3212369 AGTAGTGCAAATGCCACCGAAAGTCATAATCCAAATACCTGCAGTCTTCCCCTATAAAGATAGTA
326 AGTAGTGCAAATGCCACCGAAAGTCATAATCCAAATACCTGCAGTCTTCCCCTATAAAGATAGTA
3212434 AGAGGGTCCCATGAAATTACGACTGTAATGTGACGATCTCAGGAAAAGAGAACCTGGTTAACGAT
391 AGAGGGTCCCATGAAATTACGACTGTAATGTGACGATCTCAGGAAAAGAGAACCTGGTTAACGAT
3212499 TC
456 TC
3212501 AAAAGAGGAC
Statistics
Matches: 456, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
467 456 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (467 bp):
AGGTTGCAGAAGTCAGGACCCCATTGAGACGGATGTGGAAAGAGATGGTTAAGAGATGATTAATC
GTGTTGAATTTGAGAGAAGAATCTGAAGAAAAGAGGAACTACTGTGAGTTCCACAACGAGGTGGG
GCATGAAATTCAAGAGTGTGTGGAGTTCAGGGCCCTCGTGCAGGACATGATAAACAATAGAGAAA
TAGAGTTTTATGAAGAAATCGAAAACCCCAAAGAAGGAGATATATGCTCATCAGAGGGAGAATCA
ACGACACAGAACCAAACAGTTAATTACCCCGTGGTCATCATATCACGACCCAAAAGTAATGAAAC
AGTAGTGCAAATGCCACCGAAAGTCATAATCCAAATACCTGCAGTCTTCCCCTATAAAGATAGTA
AGAGGGTCCCATGAAATTACGACTGTAATGTGACGATCTCAGGAAAAGAGAACCTGGTTAACGAT
TCCCCTATAAAT
Found at i:3218826 original size:81 final size:82
Alignment explanation
Indices: 3218704--3218866 Score: 231
Period size: 81 Copynumber: 2.0 Consensus size: 82
3218694 AGGCTGAAGA
* * *
3218704 TTGTAGATCTTGTCTCCCTGAAGCAACAGTGGAATAGATCAAACAAAGTGATCCTTAACCCCCTA
1 TTGTAGATCTTGTCTCCCTGAAGCAACAGTGGAACAAATCAAACAAAGTGAGCCTTAACCCCCTA
3218769 AGTAGTAGGGTAACAGG
66 AGTAGTAGGGTAACAGG
* * * **
3218786 TTGTAGATCTTGTCTCTCT-AAGC-ACTAGTGGAGCAAATCAAAGACGGTGAGCCTTAACCCCCT
1 TTGTAGATCTTGTCTCCCTGAAGCAAC-AGTGGAACAAATCAAACAAAGTGAGCCTTAACCCCCT
3218849 AAGTAGTAGGGTAACAGG
65 AAGTAGTAGGGTAACAGG
3218867 CCGAAGATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
80 2 0.03
81 52 0.72
82 18 0.25
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (82 bp):
TTGTAGATCTTGTCTCCCTGAAGCAACAGTGGAACAAATCAAACAAAGTGAGCCTTAACCCCCTA
AGTAGTAGGGTAACAGG
Found at i:3218985 original size:45 final size:45
Alignment explanation
Indices: 3218885--3219000 Score: 146
Period size: 45 Copynumber: 2.6 Consensus size: 45
3218875 TAGCAGATTT
* * *
3218885 TATCTTCCTGAAGTTGCAGTGGAGC-GGATCAAAATCACAATCCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGATCAAAATCACAAACCA
* * * *
3218929 TATCTCTCTGAAGCTGCAGTAGAGCAGGAT-AAAATAGACAAACCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGGATCAAAAT-CACAAACCA
3218974 TATCTCCCTGAAGTTGCAGTGGAGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAG
3219001 TTGCAGTAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 26 0.43
45 34 0.57
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGGATCAAAATCACAAACCA
Found at i:3219004 original size:14 final size:14
Alignment explanation
Indices: 3218985--3219014 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3218975 ATCTCCCTGA
*
3218985 AGTTGCAGTGGAGC
1 AGTTGCAGTAGAGC
3218999 AGTTGCAGTAGAGC
1 AGTTGCAGTAGAGC
3219013 AG
1 AG
3219015 ACTGAAGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.40, T:0.20
Consensus pattern (14 bp):
AGTTGCAGTAGAGC
Found at i:3220822 original size:19 final size:20
Alignment explanation
Indices: 3220795--3220833 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3220785 TTAAATAATT
* *
3220795 ATTTTTAAATTTAT-ATATG
1 ATTTATAAATCTATGATATG
3220814 ATTTATAAATCTATGATATG
1 ATTTATAAATCTATGATATG
3220834 TATGGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTTATAAATCTATGATATG
Found at i:3220878 original size:15 final size:14
Alignment explanation
Indices: 3220854--3220883 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3220844 CTCCCTAGAT
3220854 TATATTTCATTATA
1 TATATTTCATTATA
3220868 TATATTTTCATTATA
1 TATA-TTTCATTATA
3220883 T
1 T
3220884 TTTCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTTCATTATA
Found at i:3221570 original size:128 final size:129
Alignment explanation
Indices: 3221405--3221652 Score: 390
Period size: 128 Copynumber: 1.9 Consensus size: 129
3221395 GAAGATTCGT
** ** * *
3221405 TAAAACAAAGGCAATATTTGATGTTTGGAAATTCGGGGAATAGTGCCCTATCGTTCTGGGTTTCG
1 TAAAACAAAGGCAATATCAGATGTTTCAAAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTTCA
* *
3221470 ATTTCCCGTTTGTTCAAAATAATCAAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACGC
66 ATTTCCCGTTTGTTCAAAATAATCAAATATCCCTTTAGAATTTCACTCGTGTTTTTCCAAACGC
*
3221534 TAAAAC-AAGGCAATATCAGATGTTTCAAAATTCGGGGAATAGTGCCTTATCGTGCTGGGTTTCA
1 TAAAACAAAGGCAATATCAGATGTTTCAAAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTTCA
* *
3221598 ATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTGGAATTTCACTCGTGTTTT
66 ATTTCCCGTTTGTTCAAAATAATCAAATATCCCTTTAGAATTTCACTCGTGTTTT
3221653 CTAAAGCAAG
Statistics
Matches: 108, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
128 102 0.94
129 6 0.06
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (129 bp):
TAAAACAAAGGCAATATCAGATGTTTCAAAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTTCA
ATTTCCCGTTTGTTCAAAATAATCAAATATCCCTTTAGAATTTCACTCGTGTTTTTCCAAACGC
Found at i:3222247 original size:18 final size:19
Alignment explanation
Indices: 3222193--3222249 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
3222183 TTCGACACAT
*
3222193 ATATTTAAT-ATTAAATAG
1 ATATTTATTAATTAAATAG
* *
3222211 ATATTTATTATTTTATAAAAG
1 ATATTTATTA-ATTA-AATAG
3222232 ATATTTATTAATTAAATA
1 ATATTTATTAATTAAATA
3222250 ATTATATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.26
19 3 0.10
20 6 0.19
21 14 0.45
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (19 bp):
ATATTTATTAATTAAATAG
Found at i:3223986 original size:46 final size:46
Alignment explanation
Indices: 3223929--3224283 Score: 410
Period size: 46 Copynumber: 7.7 Consensus size: 46
3223919 AGTGTGCTCT
* *
3223929 CTGAAATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3223975 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3224021 CTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * *
3224067 ATGAAATAAAATGTGTGAGACCATGGTTGAAAGATATCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** * *
3224113 GTGACATGAAAAGAATAAGACTATGGTTGAAAGATACTATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ** * ** *
3224159 ATGA-CGGGAATGAATAAGACCATGGTTGAAAGATACCATGGCAAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
3224204 GTAATATGAAATG-GATAAGACCATGGTTGAAAGATACCATGGTAAC
1 CTGATATGAAATGTG-TAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
3224250 CTGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGA
3224284 CTATGGCATC
Statistics
Matches: 266, Mismatches: 39, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
45 37 0.14
46 228 0.86
47 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3226630 original size:17 final size:17
Alignment explanation
Indices: 3226593--3226631 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3226583 TTATTTATTC
*
3226593 TATTGTTGGAATTGAAT
1 TATTGTTGGAATTGAAA
3226610 TATTGTTGGAATT-ATAA
1 TATTGTTGGAATTGA-AA
3226627 TATTG
1 TATTG
3226632 AATTGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAATTGAAA
Found at i:3237360 original size:46 final size:47
Alignment explanation
Indices: 3237295--3237434 Score: 169
Period size: 46 Copynumber: 3.0 Consensus size: 47
3237285 TTATCTTTGA
* * * *
3237295 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
* * *
3237341 CATGTTGCCATGGTATCTTTCAACCATGGCCTTATTC-TTTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
* * *
3237387 CACGTTACCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
3237433 CA
1 CA
3237435 GAGAGCACAC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
45 5 0.06
46 74 0.94
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (47 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATAT
Found at i:3239303 original size:11 final size:11
Alignment explanation
Indices: 3239287--3239334 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
3239277 CTTTATATAC
3239287 TAATAAAATAA
1 TAATAAAATAA
3239298 TAATAAAATATA
1 TAATAAAATA-A
* *
3239310 TTATTAAAATAT
1 -TAATAAAATAA
3239322 TAATAAAATAA
1 TAATAAAATAA
3239333 TA
1 TA
3239335 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 21 0.68
12 1 0.03
13 9 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:3239317 original size:24 final size:24
Alignment explanation
Indices: 3239281--3239336 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
3239271 TTCTTTCTTT
*
3239281 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* *
3239305 ATATATTATTAAAATATTAATAAA
1 ATATATTAATAAAATAATAATAAA
3239329 ATAATATT
1 AT-ATATT
3239337 TATCTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:3246793 original size:18 final size:19
Alignment explanation
Indices: 3246766--3246808 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
3246756 AGTATTAAAA
*
3246766 ATTGTGCATATTTTCGAAC
1 ATTGTACATATTTTCGAAC
3246785 -TTGTACATATTTTCGAAC
1 ATTGTACATATTTTCGAAC
3246803 ATTGTA
1 ATTGTA
3246809 AAATAAGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (19 bp):
ATTGTACATATTTTCGAAC
Found at i:3250694 original size:21 final size:21
Alignment explanation
Indices: 3250670--3250732 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
3250660 GCATATTGAC
3250670 ATGTAATTTTGCAATTTCTAA
1 ATGTAATTTTGCAATTTCTAA
* * *
3250691 ATGTAGA-TAT-CAAATT-GAA
1 ATGTA-ATTTTGCAATTTCTAA
*
3250710 ATGTTATTTTGCAATTTCTAA
1 ATGTAATTTTGCAATTTCTAA
3250731 AT
1 AT
3250733 TGTAGGATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 8
0.67 0.15 0.17
Matches are distributed among these distances:
18 1 0.03
19 8 0.26
20 10 0.32
21 11 0.35
22 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (21 bp):
ATGTAATTTTGCAATTTCTAA
Found at i:3255058 original size:3 final size:3
Alignment explanation
Indices: 3255052--3255077 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3255042 AGAAGAAGAA
3255052 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
3255078 AAAGGGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3259392 original size:6 final size:6
Alignment explanation
Indices: 3259381--3259413 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3259371 CGGCCACGAG
3259381 TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCA
1 TCAGGC TCAGGC TCAGGC TCAGGC TCAGGC TCA
3259414 AGCCGGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.18
Consensus pattern (6 bp):
TCAGGC
Found at i:3262831 original size:21 final size:20
Alignment explanation
Indices: 3262798--3262836 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3262788 TTTTGAGCTT
*
3262798 TTTAATGAGAATTTCTAAATA
1 TTTAATGAAAATTT-TAAATA
*
3262819 TTTAATTAAAATTTTAAA
1 TTTAATGAAAATTTTAAA
3262837 AAATTTCCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTAATGAAAATTTTAAATA
Found at i:3276681 original size:153 final size:153
Alignment explanation
Indices: 3276473--3276777 Score: 583
Period size: 153 Copynumber: 2.0 Consensus size: 153
3276463 TAAATAGACC
3276473 ATATCGTAACTCAAAATTGAAAAATCAATATGCAAGGATGTCAGAATGCTTACAGCTACACCACC
1 ATATCGTAACTCAAAATTGAAAAATCAATATGCAAGGATGTCAGAATGCTTACAGCTACACCACC
*
3276538 CAGACCACCACTCAGAATTCCAATTCCCATATCAACCAAATTGTTGTGGTCAGATGAACCAGATT
66 CAGACCACCACTCAGAATTCCAATTCCCATATCAACCAAATTGTTATGGTCAGATGAACCAGATT
* *
3276603 TTAGTTGTAAGTGCATATAATAA
131 TTAGCTGTAAATGCATATAATAA
3276626 ATATCGTAACTCAAAATTGAAAAATCAATATGCAAGGATGTCAGAATGCTTACAGCTACACCACC
1 ATATCGTAACTCAAAATTGAAAAATCAATATGCAAGGATGTCAGAATGCTTACAGCTACACCACC
3276691 CAGACCACCACTCAGAATTCCAATTCCCATATCAACCAAATTGTTATGGTCAGATGAACCAGATT
66 CAGACCACCACTCAGAATTCCAATTCCCATATCAACCAAATTGTTATGGTCAGATGAACCAGATT
3276756 TTAGCTGTAAATGCATATAATA
131 TTAGCTGTAAATGCATATAATA
3276778 GCGGACATAT
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 149 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (153 bp):
ATATCGTAACTCAAAATTGAAAAATCAATATGCAAGGATGTCAGAATGCTTACAGCTACACCACC
CAGACCACCACTCAGAATTCCAATTCCCATATCAACCAAATTGTTATGGTCAGATGAACCAGATT
TTAGCTGTAAATGCATATAATAA
Found at i:3278512 original size:15 final size:16
Alignment explanation
Indices: 3278494--3278532 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3278484 CATTCCCAGC
3278494 AATCATATTCCAGT-G
1 AATCATATTCCAGTGG
* *
3278509 AATCACATTCCATTGG
1 AATCATATTCCAGTGG
3278525 AATCATAT
1 AATCATAT
3278533 CATAGAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (16 bp):
AATCATATTCCAGTGG
Found at i:3278529 original size:16 final size:15
Alignment explanation
Indices: 3278475--3278520 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3278465 TTAACTTCCT
3278475 CAGT-AATCACATTCC
1 CAGTGAATCACATT-C
* *
3278490 CAG-CAATCATATTC
1 CAGTGAATCACATTC
3278504 CAGTGAATCACATTC
1 CAGTGAATCACATTC
3278519 CA
1 CA
3278521 TTGGAATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (15 bp):
CAGTGAATCACATTC
Found at i:3280011 original size:30 final size:30
Alignment explanation
Indices: 3279977--3280039 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
3279967 ATTTATTTTA
3279977 TTGTTAATTTTTTTATTATTTTA-AAGACAT
1 TTGTTAATTTTTTTATTATTTTAGAAG-CAT
3280007 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTTTTATTATTTTAGAAGCAT
3280037 TTG
1 TTG
3280040 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTTTTATTATTTTAGAAGCAT
Found at i:3283948 original size:28 final size:30
Alignment explanation
Indices: 3283879--3283946 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
3283869 GAATAAAATT
*
3283879 TTAATTTTTTATAATTTTTAAAAAATTAAA
1 TTAAATTTTTATAATTTTTAAAAAATTAAA
3283909 TTAAATTTTTATAA-TTTT-AAAAATTAATA
1 TTAAATTTTTATAATTTTTAAAAAATTAA-A
*
3283938 TTTAATTTT
1 TTAAATTTT
3283947 ATCTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 9 0.26
29 13 0.37
30 13 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTAAATTTTTATAATTTTTAAAAAATTAAA
Found at i:3291107 original size:102 final size:102
Alignment explanation
Indices: 3290931--3291134 Score: 390
Period size: 102 Copynumber: 2.0 Consensus size: 102
3290921 ACCATGCCCC
*
3290931 TTGGACTCCATAATATTACTACCATCTGCATTGAAGAAAAACTCAATCAAAATGACAAGAAATAA
1 TTGGACTCCAAAATATTACTACCATCTGCATTGAAGAAAAACTCAATCAAAATGACAAGAAATAA
3290996 CCATCATTTCCGGTCAGACTATGAAATAGCCTTTAAT
66 CCATCATTTCCGGTCAGACTATGAAATAGCCTTTAAT
3291033 TTGGACTCCAAAATATTACTACCATCTGCATTGAAGAAAAACTCAATCAAAATGACAAGAAATAA
1 TTGGACTCCAAAATATTACTACCATCTGCATTGAAGAAAAACTCAATCAAAATGACAAGAAATAA
*
3291098 CCATCATTTCTGGTCAGACTATGAAATAGCCTTTAAT
66 CCATCATTTCCGGTCAGACTATGAAATAGCCTTTAAT
3291135 CAGATCTATA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (102 bp):
TTGGACTCCAAAATATTACTACCATCTGCATTGAAGAAAAACTCAATCAAAATGACAAGAAATAA
CCATCATTTCCGGTCAGACTATGAAATAGCCTTTAAT
Found at i:3294569 original size:22 final size:22
Alignment explanation
Indices: 3294541--3294587 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3294531 TTTGAGATTT
*
3294541 ATTAGGCACTAGAATGCCTTTG
1 ATTAGGCACTAGAATGCCTCTG
*
3294563 ATTAGGCATTAGAATGCCTCTG
1 ATTAGGCACTAGAATGCCTCTG
3294585 ATT
1 ATT
3294588 GGGGCGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (22 bp):
ATTAGGCACTAGAATGCCTCTG
Found at i:3296757 original size:22 final size:22
Alignment explanation
Indices: 3296729--3296775 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3296719 TTTGAGATTT
*
3296729 ATTAGGCACTAGAATGCCTTTG
1 ATTAGGCACTAGAATGCCTCTG
*
3296751 ATTAGGCATTAGAATGCCTCTG
1 ATTAGGCACTAGAATGCCTCTG
3296773 ATT
1 ATT
3296776 GGGGCGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (22 bp):
ATTAGGCACTAGAATGCCTCTG
Found at i:3303235 original size:44 final size:44
Alignment explanation
Indices: 3303178--3303288 Score: 168
Period size: 44 Copynumber: 2.5 Consensus size: 44
3303168 TGTTTCCGTG
* * * *
3303178 AAAAGTAATGGAGCCCATTACTGTAATCTTAACCGTATTTAAGT
1 AAAACTAACGGAGCCCATTACTGTAATCTCAACCATATTTAAGT
*
3303222 AAAACTAACGGAGCCCATTACTGTAATCTCAACCATATTTACGT
1 AAAACTAACGGAGCCCATTACTGTAATCTCAACCATATTTAAGT
*
3303266 AAAACTAACGGAGCCAATTACTG
1 AAAACTAACGGAGCCCATTACTG
3303289 ATTTTAACAG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (44 bp):
AAAACTAACGGAGCCCATTACTGTAATCTCAACCATATTTAAGT
Found at i:3314466 original size:23 final size:22
Alignment explanation
Indices: 3314440--3314494 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
3314430 CTGAATCTTG
3314440 AATTTTAAAAATAAAAATAAATA
1 AATTTTAAAAATAAAAATAAA-A
** *
3314463 AATTTTTTGAAATAAAAATATAA
1 AA-TTTTAAAAATAAAAATAAAA
3314486 AATTTTAAA
1 AATTTTAAA
3314495 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 5 0.19
23 5 0.19
24 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTTTAAAAATAAAAATAAAA
Found at i:3315450 original size:8 final size:8
Alignment explanation
Indices: 3315437--3315461 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3315427 AGGGTTCTTT
3315437 GTTTTCGG
1 GTTTTCGG
3315445 GTTTTCGG
1 GTTTTCGG
3315453 GTTTTCGG
1 GTTTTCGG
3315461 G
1 G
3315462 GATTAGTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.40, T:0.48
Consensus pattern (8 bp):
GTTTTCGG
Found at i:3321025 original size:47 final size:47
Alignment explanation
Indices: 3320916--3321026 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
3320906 CCGGGATAAG
* * *
3320916 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
3320963 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
3321010 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
3321027 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:3326535 original size:16 final size:15
Alignment explanation
Indices: 3326510--3326547 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3326500 ACAAAATTTG
3326510 AAAGAAAAAGAAAGAA
1 AAAGAAAAAG-AAGAA
*
3326526 AAAGAGAAAGAAGAA
1 AAAGAAAAAGAAGAA
3326541 AAAGAAA
1 AAAGAAA
3326548 GAGACCCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAGAA
Found at i:3326541 original size:19 final size:18
Alignment explanation
Indices: 3326512--3326551 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3326502 AAAATTTGAA
3326512 AGAAAAAGAAAGAA-AAAG
1 AGAAAAAGAAA-AAGAAAG
3326530 AGAAAGAAGAAAAAGAAAG
1 AGAAA-AAGAAAAAGAAAG
3326549 AGA
1 AGA
3326552 CCCGTGGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAAAAGAAAG
Found at i:3327959 original size:21 final size:21
Alignment explanation
Indices: 3327933--3327975 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3327923 GCAGGTTAGG
3327933 TACTTAACTTTTAATCACCGA
1 TACTTAACTTTTAATCACCGA
3327954 TACTTAACTTTTAATCACCGA
1 TACTTAACTTTTAATCACCGA
3327975 T
1 T
3327976 TCAGCATCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.40
Consensus pattern (21 bp):
TACTTAACTTTTAATCACCGA
Found at i:3335805 original size:13 final size:13
Alignment explanation
Indices: 3335787--3335813 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3335777 GATATAGGAT
3335787 CACTTATGTTCGC
1 CACTTATGTTCGC
3335800 CACTTATGTTCGC
1 CACTTATGTTCGC
3335813 C
1 C
3335814 TAAATGCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.15, T:0.37
Consensus pattern (13 bp):
CACTTATGTTCGC
Found at i:3349436 original size:26 final size:25
Alignment explanation
Indices: 3349407--3349466 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
3349397 TCATACATCT
*
3349407 TTTAATATCATT-TTAAATAATAATAA
1 TTTAATAT-ATTATTAAAAAATAA-AA
3349433 TTTAATATATTAATTAAAAAATAAAA
1 TTTAATATATT-ATTAAAAAATAAAA
*
3349459 TTAAATAT
1 TTTAATAT
3349467 GAAAAAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 3 0.10
26 17 0.57
27 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTAATATATTATTAAAAAATAAAA
Found at i:3353470 original size:13 final size:13
Alignment explanation
Indices: 3353437--3353463 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3353427 CCAGTCAATC
3353437 ATTCAAAGCATAA
1 ATTCAAAGCATAA
3353450 ATTCAAAGCATAA
1 ATTCAAAGCATAA
3353463 A
1 A
3353464 ATTAAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ATTCAAAGCATAA
Found at i:3357863 original size:30 final size:30
Alignment explanation
Indices: 3357824--3357880 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
3357814 TTTTATAAGT
3357824 AATTAATATTT-A-TTACTTAAAAATATTTAA
1 AATTAATATTTCATTTA-TT-AAAATATTTAA
*
3357854 AATTTATATTTCATTTATTAAAATATT
1 AATTAATATTTCATTTATTAAAATATT
3357881 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 3 0.12
32 3 0.12
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTAATATTTCATTTATTAAAATATTTAA
Found at i:3358665 original size:45 final size:45
Alignment explanation
Indices: 3358601--3358690 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
3358591 ATGTCAGATA
3358601 GAATTGCGGGATGAAATAAACAAACCTATTGAATGGGGCATTCAT
1 GAATTGCGGGATGAAATAAACAAACCTATTGAATGGGGCATTCAT
3358646 GAATTGCGGGATGAAATAAACAAACCTATTGAATGGGGCATTCAT
1 GAATTGCGGGATGAAATAAACAAACCTATTGAATGGGGCATTCAT
3358691 TTTGGCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (45 bp):
GAATTGCGGGATGAAATAAACAAACCTATTGAATGGGGCATTCAT
Found at i:3364264 original size:26 final size:26
Alignment explanation
Indices: 3364130--3364263 Score: 232
Period size: 26 Copynumber: 5.2 Consensus size: 26
3364120 TGGTACAAAT
*
3364130 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3364156 TGATAATGGGCTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3364182 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3364208 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3364234 TGATGATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3364260 TGAT
1 TGAT
3364264 GGGAATTTCA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3365982 original size:27 final size:27
Alignment explanation
Indices: 3365885--3365989 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
3365875 AGGAAGCGTC
*
3365885 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
3365912 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
3365939 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
3365966 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
3365990 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:3370345 original size:14 final size:14
Alignment explanation
Indices: 3370328--3370366 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3370318 CTGAATGTTG
*
3370328 AAACTTTAAATCTT
1 AAACTTTAAACCTT
*
3370342 AAACCTTAAACCTT
1 AAACTTTAAACCTT
*
3370356 AAATTTTAAAC
1 AAACTTTAAAC
3370367 ATTTGACTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
AAACTTTAAACCTT
Found at i:3373301 original size:2 final size:2
Alignment explanation
Indices: 3373294--3373333 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3373284 ATCCCCACTT
3373294 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3373334 GCTGCGTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3382152 original size:22 final size:23
Alignment explanation
Indices: 3382116--3382169 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
3382106 AGATTTGACG
*
3382116 TTTAAA-AAATATTA-TGTTAATA
1 TTTAAATAAATATTATTATTAA-A
*
3382138 TTTATATAAAT-TTATTATTAAA
1 TTTAAATAAATATTATTATTAAA
3382160 TTTAAATAAA
1 TTTAAATAAA
3382170 ATAACTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTAAATAAATATTATTATTAAA
Found at i:3412497 original size:38 final size:39
Alignment explanation
Indices: 3412413--3412547 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
3412403 ACCAATATGG
*
3412413 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
3412452 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
3412490 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
3412531 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
3412548 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:3414129 original size:5 final size:5
Alignment explanation
Indices: 3414111--3414151 Score: 73
Period size: 5 Copynumber: 8.0 Consensus size: 5
3414101 TTTCTTTTAT
3414111 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA
3414152 CTTAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:3414833 original size:11 final size:11
Alignment explanation
Indices: 3414819--3414859 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3414809 TATTTTCTCC
3414819 CTATTTTGCTA
1 CTATTTTGCTA
*
3414830 CTATTTTACTA
1 CTATTTTGCTA
* *
3414841 TTATGTTGCTA
1 CTATTTTGCTA
3414852 CTATTTTG
1 CTATTTTG
3414860 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:3414931 original size:30 final size:30
Alignment explanation
Indices: 3414896--3414958 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
3414886 TTTTATTTTA
*
3414896 TTGTTAATTTTTTTATTATTTTA-AACACAT
1 TTGTTAATTTTGTTATTATTTTAGAA-ACAT
3414926 TTGTTAATTTTGTTATTATTTTAGAAACAT
1 TTGTTAATTTTGTTATTATTTTAGAAACAT
3414956 TTG
1 TTG
3414959 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAAACAT
Found at i:3423249 original size:27 final size:26
Alignment explanation
Indices: 3423189--3423250 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
3423179 ATTTTATTTT
3423189 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * *
3423215 ATAATTATTAGGATTATTCAA-ATTTAGG
1 AT-TTTATTAGGATAATT-AATA-TTAAG
3423243 ATTTTATT
1 ATTTTATT
3423251 TTAATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:3427801 original size:549 final size:549
Alignment explanation
Indices: 3426763--3427861 Score: 2198
Period size: 549 Copynumber: 2.0 Consensus size: 549
3426753 CGCACATCTG
3426763 AAGTATGCATTTTTAGGAAAAGGTAATACATTACCCATTATAATTTCAAATAAACTCTCTAAACC
1 AAGTATGCATTTTTAGGAAAAGGTAATACATTACCCATTATAATTTCAAATAAACTCTCTAAACC
3426828 CAAAGAGAAAAGTTTGATCCAGGTACTAAAGAGTCATAAGGAGGCGATTGGCTGGACCATTGTTG
66 CAAAGAGAAAAGTTTGATCCAGGTACTAAAGAGTCATAAGGAGGCGATTGGCTGGACCATTGTTG
3426893 ACTTGAAGGGGATAAGCCATTTGACATGCACCCACAAGATTTACTTGGAGGAGAACACGAAACCA
131 ACTTGAAGGGGATAAGCCATTTGACATGCACCCACAAGATTTACTTGGAGGAGAACACGAAACCA
3426958 AGGAGAGAGGCACAATGACGTTTAAACCCGAATATGATAGAGGTGGTAAAAAAGGAAATAATTAA
196 AGGAGAGAGGCACAATGACGTTTAAACCCGAATATGATAGAGGTGGTAAAAAAGGAAATAATTAA
3427023 GTTGCTAGATGCTGACAACATCTTCCCTATTTCTGACAGCAGATGGGTAAGTCCGGTACAAGTCG
261 GTTGCTAGATGCTGACAACATCTTCCCTATTTCTGACAGCAGATGGGTAAGTCCGGTACAAGTCG
3427088 TGCCCAAGAAGAGACAAATGAGCAGGTCATTCCAGGCTACATCCAAAAGACCAAAGGAGTTTTCT
326 TGCCCAAGAAGAGACAAATGAGCAGGTCATTCCAGGCTACATCCAAAAGACCAAAGGAGTTTTCT
3427153 ACCAGGTCTAGTTTCTCAGCCGGATATTCTAGTCAGAATAGAGGCAGCAGATTTAAGGATTCGAA
391 ACCAGGTCTAGTTTCTCAGCCGGATATTCTAGTCAGAATAGAGGCAGCAGATTTAAGGATTCGAA
3427218 GGCTCAGAACACCTCGACTGCGAGTGTAGGTAATGTTGGACAGTAGATCAGGGTGTTCACGGTGT
456 GGCTCAGAACACCTCGACTGCGAGTGTAGGTAATGTTGGACAGTAGATCAGGGTGTTCACGGTGT
3427283 GGTAGACTTCATTATGGTCCTTGTCGGGA
521 GGTAGACTTCATTATGGTCCTTGTCGGGA
3427312 AAGTATGCATTTTTAGGAAAAGGTAATACATTACCCATTATAATTTCAAATAAACTCTCTAAACC
1 AAGTATGCATTTTTAGGAAAAGGTAATACATTACCCATTATAATTTCAAATAAACTCTCTAAACC
3427377 CAAAGAGAAAAGTTTGATCCAGGTACTAAAGAGTCATAAGGAGGCGATTGGCTGGACCATTGTTG
66 CAAAGAGAAAAGTTTGATCCAGGTACTAAAGAGTCATAAGGAGGCGATTGGCTGGACCATTGTTG
3427442 ACTTGAAGGGGATAAGCCATTTGACATGCACCCACAAGATTTACTTGGAGGAGAACACGAAACCA
131 ACTTGAAGGGGATAAGCCATTTGACATGCACCCACAAGATTTACTTGGAGGAGAACACGAAACCA
3427507 AGGAGAGAGGCACAATGACGTTTAAACCCGAATATGATAGAGGTGGTAAAAAAGGAAATAATTAA
196 AGGAGAGAGGCACAATGACGTTTAAACCCGAATATGATAGAGGTGGTAAAAAAGGAAATAATTAA
3427572 GTTGCTAGATGCTGACAACATCTTCCCTATTTCTGACAGCAGATGGGTAAGTCCGGTACAAGTCG
261 GTTGCTAGATGCTGACAACATCTTCCCTATTTCTGACAGCAGATGGGTAAGTCCGGTACAAGTCG
3427637 TGCCCAAGAAGAGACAAATGAGCAGGTCATTCCAGGCTACATCCAAAAGACCAAAGGAGTTTTCT
326 TGCCCAAGAAGAGACAAATGAGCAGGTCATTCCAGGCTACATCCAAAAGACCAAAGGAGTTTTCT
3427702 ACCAGGTCTAGTTTCTCAGCCGGATATTCTAGTCAGAATAGAGGCAGCAGATTTAAGGATTCGAA
391 ACCAGGTCTAGTTTCTCAGCCGGATATTCTAGTCAGAATAGAGGCAGCAGATTTAAGGATTCGAA
3427767 GGCTCAGAACACCTCGACTGCGAGTGTAGGTAATGTTGGACAGTAGATCAGGGTGTTCACGGTGT
456 GGCTCAGAACACCTCGACTGCGAGTGTAGGTAATGTTGGACAGTAGATCAGGGTGTTCACGGTGT
3427832 GGTAGACTTCATTATGGTCCTTGTCGGGA
521 GGTAGACTTCATTATGGTCCTTGTCGGGA
3427861 A
1 A
3427862 GGCGAAAATG
Statistics
Matches: 550, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
549 550 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (549 bp):
AAGTATGCATTTTTAGGAAAAGGTAATACATTACCCATTATAATTTCAAATAAACTCTCTAAACC
CAAAGAGAAAAGTTTGATCCAGGTACTAAAGAGTCATAAGGAGGCGATTGGCTGGACCATTGTTG
ACTTGAAGGGGATAAGCCATTTGACATGCACCCACAAGATTTACTTGGAGGAGAACACGAAACCA
AGGAGAGAGGCACAATGACGTTTAAACCCGAATATGATAGAGGTGGTAAAAAAGGAAATAATTAA
GTTGCTAGATGCTGACAACATCTTCCCTATTTCTGACAGCAGATGGGTAAGTCCGGTACAAGTCG
TGCCCAAGAAGAGACAAATGAGCAGGTCATTCCAGGCTACATCCAAAAGACCAAAGGAGTTTTCT
ACCAGGTCTAGTTTCTCAGCCGGATATTCTAGTCAGAATAGAGGCAGCAGATTTAAGGATTCGAA
GGCTCAGAACACCTCGACTGCGAGTGTAGGTAATGTTGGACAGTAGATCAGGGTGTTCACGGTGT
GGTAGACTTCATTATGGTCCTTGTCGGGA
Found at i:3428509 original size:20 final size:20
Alignment explanation
Indices: 3428484--3428523 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3428474 ATTTAAGTAT
3428484 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
3428504 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
3428524 AATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:3428762 original size:20 final size:18
Alignment explanation
Indices: 3428733--3428777 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
3428723 AACGAAAAGC
3428733 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
3428751 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
3428770 AGGGAAAA
1 AGGGAAAA
3428778 TTGAAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:3439754 original size:28 final size:29
Alignment explanation
Indices: 3439701--3439760 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
3439691 AGATGATTTG
* *
3439701 ATAAAAATATAAATTTAAATATTAAAAAA
1 ATAAAAATATAAATATAAATAGTAAAAAA
*
3439730 ATAAAAA-ATAAA-ATAAATGAGTAAAATA
1 ATAAAAATATAAATATAAAT-AGTAAAAAA
3439758 ATA
1 ATA
3439761 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 15 0.56
29 7 0.26
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (29 bp):
ATAAAAATATAAATATAAATAGTAAAAAA
Found at i:3444157 original size:12 final size:12
Alignment explanation
Indices: 3444142--3444239 Score: 56
Period size: 12 Copynumber: 8.2 Consensus size: 12
3444132 CTTCGTCGGG
3444142 GGCTGAGTTGGA
1 GGCTGAGTTGGA
*
3444154 GGCTTG-GTTGGT
1 GGC-TGAGTTGGA
* * *
3444166 GGCTTAGTCGGG
1 GGCTGAGTTGGA
*
3444178 GGCTGAGTTGGT
1 GGCTGAGTTGGA
* * *
3444190 GGCTTAGTCGGG
1 GGCTGAGTTGGA
*
3444202 GGTTGAGTTGGA
1 GGCTGAGTTGGA
* *
3444214 GGTTTG-GTTGGT
1 GG-CTGAGTTGGA
*
3444226 GGCTTAGTTGGA
1 GGCTGAGTTGGA
3444238 GG
1 GG
3444240 TTGAACTGGT
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 2 0.03
12 57 0.89
13 5 0.08
ACGTcount: A:0.09, C:0.08, G:0.50, T:0.33
Consensus pattern (12 bp):
GGCTGAGTTGGA
Found at i:3444164 original size:36 final size:36
Alignment explanation
Indices: 3444124--3444194 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
3444114 TGGTGGGTGT
*
3444124 GTTGGTGGCTTCGTCGGGGGCTGAGTTGGAGGCTTG
1 GTTGGTGGCTTAGTCGGGGGCTGAGTTGGAGGCTTG
*
3444160 GTTGGTGGCTTAGTCGGGGGCTGAGTTGGTGGCTT
1 GTTGGTGGCTTAGTCGGGGGCTGAGTTGGAGGCTT
3444195 AGTCGGGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.06, C:0.13, G:0.49, T:0.32
Consensus pattern (36 bp):
GTTGGTGGCTTAGTCGGGGGCTGAGTTGGAGGCTTG
Found at i:3444169 original size:24 final size:24
Alignment explanation
Indices: 3444114--3444287 Score: 93
Period size: 24 Copynumber: 7.2 Consensus size: 24
3444104 GAGGATGAGA
* * *
3444114 TGGTGGGTGTGTTGGTGGCTTCGT
1 TGGTGGCTGAGTTGGTGGCTTGGT
* * *
3444138 CGGGGGCTGAGTTGGAGGCTTGGT
1 TGGTGGCTGAGTTGGTGGCTTGGT
* * *
3444162 TGGTGGCTTAGTCGGGGGC-TGAGT
1 TGGTGGCTGAGTTGGTGGCTTG-GT
* * *
3444186 TGGTGGCTTAGTCGG-GGGTTGAGT
1 TGGTGGCTGAGTTGGTGGCTTG-GT
* * *
3444210 TGGAGGTTTG-GTTGGTGGCTTAGT
1 TGGTGG-CTGAGTTGGTGGCTTGGT
* * ** *
3444234 TGGAGGTTGAACTGGTGGCTTGGG
1 TGGTGGCTGAGTTGGTGGCTTGGT
* **
3444258 TGGTGGGTGAACTGGTGGCTTGGT
1 TGGTGGCTGAGTTGGTGGCTTGGT
3444282 TGGTGG
1 TGGTGG
3444288 TTGCACTGGC
Statistics
Matches: 120, Mismatches: 25, Indels: 10
0.77 0.16 0.06
Matches are distributed among these distances:
23 7 0.06
24 108 0.90
25 5 0.04
ACGTcount: A:0.07, C:0.09, G:0.51, T:0.33
Consensus pattern (24 bp):
TGGTGGCTGAGTTGGTGGCTTGGT
Found at i:3444250 original size:60 final size:60
Alignment explanation
Indices: 3444126--3444254 Score: 186
Period size: 60 Copynumber: 2.1 Consensus size: 60
3444116 GTGGGTGTGT
* * **
3444126 TGGTGGCTTCGTCGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGGGGCTGAGT
1 TGGTGGCTTAGTCGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAAC
* * * *
3444186 TGGTGGCTTAGTCGGGGGTTGAGTTGGAGGTTTGGTTGGTGGCTTAGTTGGAGGTTGAAC
1 TGGTGGCTTAGTCGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAAC
3444246 TGGTGGCTT
1 TGGTGGCTT
3444255 GGGTGGTGGG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.09, C:0.10, G:0.48, T:0.33
Consensus pattern (60 bp):
TGGTGGCTTAGTCGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAAC
Found at i:3444262 original size:36 final size:36
Alignment explanation
Indices: 3444186--3444263 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
3444176 GGGGCTGAGT
* ** * *
3444186 TGGTGGCTTAGTCGGGGGTTGAGTTGGAGGTTTGGT
1 TGGTGGCTTAGTCGGAGGTTGAACTGGAGGCTTGGG
* *
3444222 TGGTGGCTTAGTTGGAGGTTGAACTGGTGGCTTGGG
1 TGGTGGCTTAGTCGGAGGTTGAACTGGAGGCTTGGG
3444258 TGGTGG
1 TGGTGG
3444264 GTGAACTGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.09, C:0.06, G:0.50, T:0.35
Consensus pattern (36 bp):
TGGTGGCTTAGTCGGAGGTTGAACTGGAGGCTTGGG
Found at i:3444277 original size:48 final size:48
Alignment explanation
Indices: 3444222--3444320 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 48
3444212 GAGGTTTGGT
* * *
3444222 TGGTGGCTTAGTTGGAGGTTGAACTGGTGGCTTGGGTGGTGGGTGAAC
1 TGGTGGCTTAGTTGGAGGTTGAACTGGCGCCTTGGGTGGTGGATGAAC
* * *
3444270 TGGTGGCTTGGTTGGTGGTTGCACTGGCGCCTTGGGTGGTGGATGAAC
1 TGGTGGCTTAGTTGGAGGTTGAACTGGCGCCTTGGGTGGTGGATGAAC
3444318 TGG
1 TGG
3444321 AGGAGGAGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.10, C:0.11, G:0.47, T:0.31
Consensus pattern (48 bp):
TGGTGGCTTAGTTGGAGGTTGAACTGGCGCCTTGGGTGGTGGATGAAC
Found at i:3444281 original size:60 final size:60
Alignment explanation
Indices: 3444126--3444287 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 60
3444116 GTGGGTGTGT
* * ** * **
3444126 TGGTGGCTTCGTCGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGGGGCTGAGT
1 TGGTGGCTTAGTCGGGGGTTGAACTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAAC
** * * *
3444186 TGGTGGCTTAGTCGGGGGTTGAGTTGGAGGTTTGGTTGGTGGCTTAGTTGGAGGTTGAAC
1 TGGTGGCTTAGTCGGGGGTTGAACTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAAC
* *
3444246 TGGTGGCTTGGGT-GGTGGG-TGAACTGGTGGCTTGGTTGGTGG
1 TGGTGGCTT-AGTCGG-GGGTTGAACTGGAGGCTTGGTTGGTGG
3444288 TTGCACTGGC
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
60 82 0.94
61 5 0.06
ACGTcount: A:0.08, C:0.09, G:0.50, T:0.33
Consensus pattern (60 bp):
TGGTGGCTTAGTCGGGGGTTGAACTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAAC
Found at i:3444295 original size:24 final size:24
Alignment explanation
Indices: 3444222--3444320 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
3444212 GAGGTTTGGT
* * *
3444222 TGGTGGCTTAGTTGGAGGTTGAAC
1 TGGTGGCTTGGGTGGTGGTTGAAC
*
3444246 TGGTGGCTTGGGTGGTGGGTGAAC
1 TGGTGGCTTGGGTGGTGGTTGAAC
* *
3444270 TGGTGGCTTGGTTGGTGGTTGCAC
1 TGGTGGCTTGGGTGGTGGTTGAAC
* * *
3444294 TGGCGCCTTGGGTGGTGGATGAAC
1 TGGTGGCTTGGGTGGTGGTTGAAC
3444318 TGG
1 TGG
3444321 AGGAGGAGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.10, C:0.11, G:0.47, T:0.31
Consensus pattern (24 bp):
TGGTGGCTTGGGTGGTGGTTGAAC
Found at i:3444392 original size:12 final size:12
Alignment explanation
Indices: 3444349--3444402 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
3444339 GGGCTTAGTG
*
3444349 GGTGGATGAGGAT
1 GGTGG-TGAGGGT
*
3444362 GGGGGTGAGGGT
1 GGTGGTGAGGGT
3444374 GAG-GGTGAGGGT
1 G-GTGGTGAGGGT
*
3444386 GGTGGTGATGGT
1 GGTGGTGAGGGT
3444398 GGTGG
1 GGTGG
3444403 GTTGGTGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 1 0.03
12 30 0.83
13 5 0.14
ACGTcount: A:0.13, C:0.00, G:0.65, T:0.22
Consensus pattern (12 bp):
GGTGGTGAGGGT
Found at i:3447308 original size:42 final size:42
Alignment explanation
Indices: 3447260--3447339 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
3447250 AAAATAAATC
*
3447260 CACTCCAAATTTATATCTTCCTACACCGACAATAGTGTCGAT
1 CACTCCAAATTTATATCCTCCTACACCGACAATAGTGTCGAT
3447302 CACTCCAAATTTATATCCTCCTACACCGACAATAGTGT
1 CACTCCAAATTTATATCCTCCTACACCGACAATAGTGT
3447340 TGATACAGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (42 bp):
CACTCCAAATTTATATCCTCCTACACCGACAATAGTGTCGAT
Found at i:3451325 original size:9 final size:9
Alignment explanation
Indices: 3451311--3451344 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
3451301 GACGAAATTG
3451311 AAAAGAAGA
1 AAAAGAAGA
3451320 AAAAGAAGA
1 AAAAGAAGA
3451329 AAAAGAAGA
1 AAAAGAAGA
*
3451338 AGAAGAA
1 AAAAGAA
3451345 CAACAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:3451768 original size:30 final size:31
Alignment explanation
Indices: 3451734--3451804 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
3451724 TAACCATCGT
** *
3451734 AATTTTAAAAAAAATATT-GTAATTAACTTG
1 AATTTTAAAAAAAATATTAACAATTAACTTA
3451764 AATTTTAAAAAAAATATTAACAATTAACTTA
1 AATTTTAAAAAAAATATTAACAATTAACTTA
*
3451795 AAATTTAAAA
1 AATTTTAAAA
3451805 TTTAAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (31 bp):
AATTTTAAAAAAAATATTAACAATTAACTTA
Found at i:3452275 original size:18 final size:18
Alignment explanation
Indices: 3452252--3452287 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3452242 GTTGTTTTGA
3452252 ATGCTAATAATGCATGAT
1 ATGCTAATAATGCATGAT
3452270 ATGCTAATAATGCATGAT
1 ATGCTAATAATGCATGAT
3452288 TTGGGGACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (18 bp):
ATGCTAATAATGCATGAT
Found at i:3453561 original size:64 final size:64
Alignment explanation
Indices: 3453425--3453554 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 64
3453415 ACTTCAATGT
*
3453425 TAAATTAATGTAAGTTTACACTTTTTTATAAATTTTTTGTATGATTGATATTTTAACAATCAAG
1 TAAATTAAAGTAAGTTTACACTTTTTTATAAATTTTTTGTATGATTGATATTTTAACAATCAAG
* *
3453489 TAAATTAAAGTAAGTTTACACTTTTTTATTATTATTTTTGTATGATTGATATTTTAACAATCAAG
1 TAAATTAAAGTAAGTTTACACTTTTTTATAAAT-TTTTTGTATGATTGATATTTTAACAATCAAG
3453554 T
1 T
3453555 CCTTAAACAT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 30 0.48
65 32 0.52
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.49
Consensus pattern (64 bp):
TAAATTAAAGTAAGTTTACACTTTTTTATAAATTTTTTGTATGATTGATATTTTAACAATCAAG
Found at i:3463993 original size:28 final size:28
Alignment explanation
Indices: 3463953--3464031 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
3463943 GCAATCAAAT
* * *
3463953 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
3463981 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
3464009 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
3464032 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:3482873 original size:19 final size:19
Alignment explanation
Indices: 3482851--3482889 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3482841 TTTTAAATAG
*
3482851 ATACACATGTATTAATAAT
1 ATACACATGTATAAATAAT
3482870 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
3482889 A
1 A
3482890 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:3483223 original size:19 final size:19
Alignment explanation
Indices: 3483201--3483239 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3483191 TTTTAAATAG
*
3483201 ATACACATGTATTAATAAT
1 ATACACATGTATAAATAAT
3483220 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
3483239 A
1 A
3483240 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:3483311 original size:349 final size:349
Alignment explanation
Indices: 3482638--3483337 Score: 1382
Period size: 350 Copynumber: 2.0 Consensus size: 349
3482628 ATGACTAAAT
*
3482638 TGAATAAAGGATAAAAGTTGAATTGTAGATTAAAAGAAAATAAAAAGGACCAAAATGGAAAATAG
1 TGAATAAAGGATAAAAGTTGAATTGTAGATTAAAAGAAAATAAAAAGGACCAAAATGGAAAAAAG
3482703 ACCATTTAGTATAGTTGAGGCGGCAAACAATGAAAAATCTAAAGATTTTTCTAGATTATTGTTGA
66 ACCATTTAGTATAGTTGAGGCGGCAAACAATGAAAAATCTAAAGATTTTTCTAGATTATTGTTGA
3482768 ATTATAAATTATAAATTATTATTAACTATTATTATTAAATAAATTAAAAAAAAGAAAAGTGACAA
131 ATTATAAATTATAAATTATTATTAACTATTATTATTAAATAAATTAAAAAAAAGAAAAGTGACAA
3482833 ATGTATGGTTTTAAATAGATACACATGTATTAATAATATACACATGTATAAATAATAAATAAGTA
196 ATGTATGGTTTTAAATAGATACACATGTATTAATAATATACACATGTATAAATAATAAATAAGTA
3482898 TTACTTATTATTTAAGTATAAATAATATTACATATATATATGTATATAAAACAAAAGAAAAAAAA
261 TTACTTATTATTTAAGTATAAATAATATTACATATATATATGTATATAAAACAAAAGAAAAAAAA
3482963 AAGAAGAAGGGAAGAAACAGAATA
326 AAGAAGAAGGGAAGAAACAGAATA
3482987 TGAATAAAGGATAAAAGTTGAATTGTAGATTAAAAGAAAATAAAAAGGACCAAAATGGAAAAAAG
1 TGAATAAAGGATAAAAGTTGAATTGTAGATTAAAAGAAAATAAAAAGGACCAAAATGGAAAAAAG
3483052 ACCATTTAGTATAGTTGAGGCGGCAAACAATGAAAAATCTAAAGATTTTTCTAGATTATTGTTGA
66 ACCATTTAGTATAGTTGAGGCGGCAAACAATGAAAAATCTAAAGATTTTTCTAGATTATTGTTGA
3483117 ATTATAAATTATAAATTATTATTAACTATTATTATTAAATAAATTAAAAAAAAAGAAAAGTGACA
131 ATTATAAATTATAAATTATTATTAACTATTATTATTAAATAAATT-AAAAAAAAGAAAAGTGACA
3483182 AATGTATGGTTTTAAATAGATACACATGTATTAATAATATACACATGTATAAATAATAAATAAGT
195 AATGTATGGTTTTAAATAGATACACATGTATTAATAATATACACATGTATAAATAATAAATAAGT
3483247 ATTACTTATTATTTAAGTATAAATAATATTACATATATATATGTATATAAAACAAAAGAAAAAAA
260 ATTACTTATTATTTAAGTATAAATAATATTACATATATATATGTATATAAAACAAAAGAAAAAAA
3483312 AAAGAAGAAGGGAAGAAACAGAATA
325 AAAGAAGAAGGGAAGAAACAGAATA
3483337 T
1 T
3483338 TAGAAACGAA
Statistics
Matches: 349, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
349 174 0.50
350 175 0.50
ACGTcount: A:0.52, C:0.05, G:0.13, T:0.30
Consensus pattern (349 bp):
TGAATAAAGGATAAAAGTTGAATTGTAGATTAAAAGAAAATAAAAAGGACCAAAATGGAAAAAAG
ACCATTTAGTATAGTTGAGGCGGCAAACAATGAAAAATCTAAAGATTTTTCTAGATTATTGTTGA
ATTATAAATTATAAATTATTATTAACTATTATTATTAAATAAATTAAAAAAAAGAAAAGTGACAA
ATGTATGGTTTTAAATAGATACACATGTATTAATAATATACACATGTATAAATAATAAATAAGTA
TTACTTATTATTTAAGTATAAATAATATTACATATATATATGTATATAAAACAAAAGAAAAAAAA
AAGAAGAAGGGAAGAAACAGAATA
Found at i:3483688 original size:15 final size:15
Alignment explanation
Indices: 3483665--3483714 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
3483655 TTTATCAAAT
3483665 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* *
3483680 TTATTTTGATTGAAT
1 TTATATTGATTGAAA
3483695 TTATATTGATTGAAA
1 TTATATTGATTGAAA
3483710 -TATAT
1 TTATAT
3483715 AATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:3484107 original size:23 final size:23
Alignment explanation
Indices: 3484079--3484136 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
3484069 TAATATTCCG
3484079 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
3484102 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
3484125 GGTGTGTTTGGG
1 GGTGTGTTTGGG
3484137 AGGAATCCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.07, C:0.03, G:0.43, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:3484262 original size:18 final size:19
Alignment explanation
Indices: 3484241--3484281 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3484231 AATGAAATGA
3484241 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
3484259 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
3484278 GAAA
1 GAAA
3484282 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:3486359 original size:10 final size:10
Alignment explanation
Indices: 3486344--3486373 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3486334 TCTATCTTTC
3486344 TTTTCTTTTT
1 TTTTCTTTTT
3486354 TTTTCTTTTT
1 TTTTCTTTTT
3486364 TTTT-TTTTT
1 TTTTCTTTTT
3486373 T
1 T
3486374 GCCTCTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:3486372 original size:15 final size:15
Alignment explanation
Indices: 3486340--3486371 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3486330 TATTTCTATC
3486340 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
3486355 TTTCTTTT-TTTTTT
1 TTTCTTTTCTTTTTT
3486369 TTT
1 TTT
3486372 TTGCCTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:3491811 original size:4 final size:4
Alignment explanation
Indices: 3491793--3491839 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
3491783 TCTGGGAGGG
* *
3491793 TTCT TT-T TCTCT TTCT TTCT TTCT TTCT TTCT ATCT CTCT TTCT TTC
1 TTCT TTCT T-TCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
3491840 AAGTTCTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
3 2 0.05
4 34 0.89
5 2 0.05
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:3502414 original size:167 final size:167
Alignment explanation
Indices: 3502138--3502471 Score: 650
Period size: 167 Copynumber: 2.0 Consensus size: 167
3502128 ATCTCCAAAT
3502138 TTTCTAGATTTGATAACTCGTTCTGTCTTCCTGTTGATGCTTTGGAATATGATACCACTGTCATA
1 TTTCTAGATTTGATAACTCGTTCTGTCTTCCTGTTGATGCTTTGGAATATGATACCACTGTCATA
*
3502203 ACATCCATCTGAGCAAACATTCATTTCTTGCAATTGTGTCATGATGAGCATGGCACGGTTGGTCG
66 ACATCCATCTGAGCAAACATTCATTTCTTGCAATTGTGTCATGATAAGCATGGCACGGTTGGTCG
3502268 AATTTGCAGCTTACACATACATCAAATGTAAATCTTC
131 AATTTGCAGCTTACACATACATCAAATGTAAATCTTC
3502305 TTTCTAGATTTGATAACTCGTTCTGTCTTCCTGTTGATGCTTTGGAATATGATACCACTGTCATA
1 TTTCTAGATTTGATAACTCGTTCTGTCTTCCTGTTGATGCTTTGGAATATGATACCACTGTCATA
*
3502370 ACATCCATCTGAGCAAACATTCATTTCTTTCAATTGTGTCATGATAAGCATGGCACGGTTGGTCG
66 ACATCCATCTGAGCAAACATTCATTTCTTGCAATTGTGTCATGATAAGCATGGCACGGTTGGTCG
3502435 AATTTGCAGCTTACACATACATCAAATGTAAATCTTC
131 AATTTGCAGCTTACACATACATCAAATGTAAATCTTC
3502472 GATTCTTTTT
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 165 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (167 bp):
TTTCTAGATTTGATAACTCGTTCTGTCTTCCTGTTGATGCTTTGGAATATGATACCACTGTCATA
ACATCCATCTGAGCAAACATTCATTTCTTGCAATTGTGTCATGATAAGCATGGCACGGTTGGTCG
AATTTGCAGCTTACACATACATCAAATGTAAATCTTC
Found at i:3521375 original size:176 final size:175
Alignment explanation
Indices: 3521076--3521427 Score: 478
Period size: 176 Copynumber: 2.0 Consensus size: 175
3521066 ATCTTCCCCC
* * * *
3521076 TACCACCGCCCCTCTTCTCTCCCTTGTCTCTGCAAATCAGTTTTTTTTTCTTCTCATCTCAGTTC
1 TACCACCGCCCCTCTTCTCTCCCTCGTATCTACAAATCAGTTTTTTTCTCTTCTCATCTCAGTTC
* * * *
3521141 TCGCCCACCGCCGTCTCCGCTGATTTTTTCTGGATCTGACCCGTATTCCGTGTCGGATCGTGTTG
66 TAGCCCACCGCCG-CTCCGCTGATTTTTGCCGGATCTGACCCGTATTCCGTGTCGGATCGTGTCG
* *
3521206 ACACAGGTACTGCACCCCAAATTG-CCGAGTCAGGGTAACGAAGCT
130 ACACAAGTACTGCACCCCAAATTGCCCGAGCCAGGGTAACGAAGCT
* *
3521251 TACCATCGCCCCTCTTCTCTCTCTCGTATCTACAAATCAGGTTTCTTCATTCTCTTCTCATCTCA
1 TACCACCGCCCCTCTTCTCTCCCTCGTATCTACAAATCA-GTTT-TT--TTCTCTTCTCATCTCA
*
3521316 GTTCTAGCCCACCG-C-CTCCGCTGGTTTTTGCCGGATCTGACCCGTA-TCGCGTGTCGGATCGT
62 GTTCTAGCCCACCGCCGCTCCGCTGATTTTTGCCGGATCTGACCCGTATTC-CGTGTCGGATCGT
* *
3521378 GTCGACACAAGTACTGCATCCCAAATTGCTCCGAGCCCGGGTAACGAAGC
126 GTCGACACAAGTACTGCACCCCAAATTGC-CCGAGCCAGGGTAACGAAGC
3521428 CTATACTTTT
Statistics
Matches: 155, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
175 36 0.23
176 70 0.45
177 2 0.01
178 19 0.12
179 28 0.18
ACGTcount: A:0.17, C:0.34, G:0.18, T:0.31
Consensus pattern (175 bp):
TACCACCGCCCCTCTTCTCTCCCTCGTATCTACAAATCAGTTTTTTTCTCTTCTCATCTCAGTTC
TAGCCCACCGCCGCTCCGCTGATTTTTGCCGGATCTGACCCGTATTCCGTGTCGGATCGTGTCGA
CACAAGTACTGCACCCCAAATTGCCCGAGCCAGGGTAACGAAGCT
Found at i:3532447 original size:23 final size:24
Alignment explanation
Indices: 3532403--3532447 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
3532393 TTGTTCGCAT
**
3532403 ATCATGTTTATATTTTTCTTTTGC
1 ATCATGTTTATATTTTAATTTTGC
*
3532427 ATCATG-TTGTATTTTAATTTT
1 ATCATGTTTATATTTTAATTTT
3532448 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (24 bp):
ATCATGTTTATATTTTAATTTTGC
Found at i:3542096 original size:9 final size:9
Alignment explanation
Indices: 3542084--3542110 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3542074 TAACTCATTT
3542084 ATTATTCAA
1 ATTATTCAA
3542093 ATTATTCAA
1 ATTATTCAA
3542102 ATTATTCAA
1 ATTATTCAA
3542111 TTCAGTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTATTCAA
Found at i:3578928 original size:21 final size:21
Alignment explanation
Indices: 3578902--3578942 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3578892 ATCTGCTCAA
* *
3578902 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3578923 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3578943 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3581800 original size:5 final size:5
Alignment explanation
Indices: 3581790--3581814 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3581780 ATGTGAAATG
3581790 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
3581815 AACAAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:3582510 original size:26 final size:27
Alignment explanation
Indices: 3582461--3582512 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
3582451 GGTTTGTGAT
3582461 AATTATATATTTAAAAATAATTATAAA
1 AATTATATATTTAAAAATAATTATAAA
3582488 AATTATA-ATGTT-AAAATAATTATAA
1 AATTATATAT-TTAAAAATAATTATAA
3582513 TTGAAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AATTATATATTTAAAAATAATTATAAA
Found at i:3591965 original size:31 final size:30
Alignment explanation
Indices: 3591929--3591992 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3591919 ATTTTTTTTA
3591929 ATATTTACATTATAATAT-TATATAATAATAT
1 ATATTTA-ATTATAATATGTATAT-ATAATAT
* * *
3591960 ATATTTAATTTTTATGTGTATATATAATAT
1 ATATTTAATTATAATATGTATATATAATAT
3591990 ATA
1 ATA
3591993 AAATAACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATTTAATTATAATATGTATATATAATAT
Found at i:3601295 original size:21 final size:20
Alignment explanation
Indices: 3601265--3601305 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
3601255 ATTCGGGTGG
*
3601265 ATTAACTCTTTTGAGCTTCT
1 ATTAACTCTTATGAGCTTCT
3601285 ATTAAGCTCTTATGAGCTTCT
1 ATTAA-CTCTTATGAGCTTCT
3601306 GTTGGTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTAACTCTTATGAGCTTCT
Found at i:3603068 original size:30 final size:29
Alignment explanation
Indices: 3603034--3603098 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3603024 TAATCCACCA
3603034 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
3603064 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
3603094 CCCAA
1 CCCAA
3603099 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:3603072 original size:31 final size:30
Alignment explanation
Indices: 3603041--3603098 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3603031 CCACCCAACT
3603041 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
3603071 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
3603099 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:3618931 original size:16 final size:16
Alignment explanation
Indices: 3618910--3618948 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
3618900 AAAATTACAT
3618910 AAAAATATGAAAAGAC
1 AAAAATATGAAAAGAC
3618926 AAAAATATGAAAAGAC
1 AAAAATATGAAAAGAC
3618942 AAAAATA
1 AAAAATA
3618949 ATAATAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.72, C:0.05, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAAATATGAAAAGAC
Found at i:3621929 original size:20 final size:20
Alignment explanation
Indices: 3621892--3621929 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3621882 TGATGGGGAG
*
3621892 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
3621912 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
3621930 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:3623606 original size:20 final size:20
Alignment explanation
Indices: 3623581--3623620 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3623571 ATTTAAGTAT
3623581 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
3623601 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
3623621 AATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:3623864 original size:19 final size:19
Alignment explanation
Indices: 3623834--3623874 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3623824 GAAAAGAAAG
3623834 AAAGAAAGGAAGAAAGGAGA
1 AAAGAAAGGAAGAAAGG-GA
3623854 AAAGAAA-GAAGAAAGGGA
1 AAAGAAAGGAAGAAAGGGA
3623872 AAA
1 AAA
3623875 TTGAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 9 0.43
20 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAAGAAAGGAAGAAAGGGA
Found at i:3625093 original size:46 final size:46
Alignment explanation
Indices: 3625026--3625294 Score: 378
Period size: 46 Copynumber: 5.8 Consensus size: 46
3625016 NNNNNNNNNN
* * *
3625026 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAGCCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
*
3625072 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
* *
3625118 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
** *
3625164 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
** * *
3625210 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
* * *
3625256 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
3625295 TCATGTCAAA
Statistics
Matches: 209, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 208 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
Found at i:3627987 original size:33 final size:32
Alignment explanation
Indices: 3627941--3628004 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
3627931 TCCTTCCCAT
** *
3627941 ATTTTTAGGTTAGGTTTCTTTTCTTATCTTTTC
1 ATTTTTAAATTAGGTTT-TTCTCTTATCTTTTC
*
3627974 ATTTTTAAATTAGGTTTTTCTCTTTTCTTTT
1 ATTTTTAAATTAGGTTTTTCTCTTATCTTTT
3628005 TAGAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.14, C:0.11, G:0.09, T:0.66
Consensus pattern (32 bp):
ATTTTTAAATTAGGTTTTTCTCTTATCTTTTC
Found at i:3628921 original size:41 final size:40
Alignment explanation
Indices: 3628836--3628962 Score: 128
Period size: 41 Copynumber: 3.1 Consensus size: 40
3628826 TTTTCTTAAA
* * * * *
3628836 AAACGCCGCAAAAGGCAAGGTAATAGCAGCGTTTCTCTCGT
1 AAACGCAGCAAAAGGTAAGGCAATAGCAGCGTTTTTC-CAT
* *
3628877 AAACGCTGCAAAAGGTAAGGCAATAGCAGCATTTTTACCAT
1 AAACGCAGCAAAAGGTAAGGCAATAGCAGCGTTTTT-CCAT
* * * *
3628918 AAACGCAGCAAATGGTAAAGCAACAGCGGCGTTTTTCCCAT
1 AAACGCAGCAAAAGGTAAGGCAATAGCAGCGTTTTT-CCAT
3628959 AAAC
1 AAAC
3628963 ATTGCGAATT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 71 0.99
42 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (40 bp):
AAACGCAGCAAAAGGTAAGGCAATAGCAGCGTTTTTCCAT
Found at i:3629057 original size:22 final size:22
Alignment explanation
Indices: 3629027--3629101 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
3629017 ACTGGTTCCC
*
3629027 TTTTCTTTCGCAAACGATGCTG
1 TTTTATTTCGCAAACGATGCTG
* *** * *
3629049 TTTTATTTCTCCCCCGATTCTC
1 TTTTATTTCGCAAACGATGCTG
* * *
3629071 TTTTCTTTCGCAAATGATGTTG
1 TTTTATTTCGCAAACGATGCTG
3629093 TTTTATTTC
1 TTTTATTTC
3629102 TCTCCCCCGA
Statistics
Matches: 36, Mismatches: 17, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTTATTTCGCAAACGATGCTG
Found at i:3629095 original size:44 final size:46
Alignment explanation
Indices: 3629022--3629125 Score: 167
Period size: 44 Copynumber: 2.3 Consensus size: 46
3629012 TACAAACTGG
3629022 TTCCCTTTTCTTTCGCAAACGATGCTGTTTTA-TT-TCTCCCCCGA
1 TTCCCTTTTCTTTCGCAAACGATGCTGTTTTATTTCTCTCCCCCGA
* * *
3629066 TTCTCTTTTCTTTCGCAAATGATGTTGTTTTATTTCTCTCCCCCGA
1 TTCCCTTTTCTTTCGCAAACGATGCTGTTTTATTTCTCTCCCCCGA
3629112 TTCCCTTTTCTTTC
1 TTCCCTTTTCTTTC
3629126 TTAGCCTTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 29 0.54
45 2 0.04
46 23 0.43
ACGTcount: A:0.12, C:0.30, G:0.10, T:0.49
Consensus pattern (46 bp):
TTCCCTTTTCTTTCGCAAACGATGCTGTTTTATTTCTCTCCCCCGA
Found at i:3630809 original size:12 final size:12
Alignment explanation
Indices: 3630792--3630816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3630782 AGTAATTTCG
3630792 GGTCGGTTAACC
1 GGTCGGTTAACC
3630804 GGTCGGTTAACC
1 GGTCGGTTAACC
3630816 G
1 G
3630817 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:3633030 original size:6 final size:6
Alignment explanation
Indices: 3633014--3633061 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
3633004 TTTCCTTTCC
3633014 TTTTATA TTTTTA TTTTTA TTTTTGA -TTTTA -TTTT- TTTTTA TTTTTA
1 TTTT-TA TTTTTA TTTTTA TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA
3633061 T
1 T
3633062 AATTTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 9 0.24
6 24 0.63
7 5 0.13
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:3633128 original size:23 final size:23
Alignment explanation
Indices: 3633102--3633150 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
3633092 AATACTATGT
3633102 TAAATTATATTTT-TACATTTTTA
1 TAAATTATATTTTATA-ATTTTTA
*
3633125 TAAATTTTATTTTATAATTTTTA
1 TAAATTATATTTTATAATTTTTA
3633148 TAA
1 TAA
3633151 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TAAATTATATTTTATAATTTTTA
Found at i:3633161 original size:23 final size:23
Alignment explanation
Indices: 3633118--3633161 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
3633108 ATATTTTTAC
*
3633118 ATTTTTATAAATTTTATTTTATA
1 ATTTTTATAAATTTTAATTTATA
3633141 ATTTTTAT-AATTTTAAATTTA
1 ATTTTTATAAATTTT-AATTTA
3633162 GCTAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTTTATAAATTTTAATTTATA
Found at i:3636961 original size:21 final size:21
Alignment explanation
Indices: 3636899--3636962 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
3636889 CCTGATCAGT
** * *
3636899 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
3636920 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
3636941 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
3636962 A
1 A
3636963 AGCCGAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:3639183 original size:23 final size:23
Alignment explanation
Indices: 3639153--3639200 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3639143 TCTTTTCATG
3639153 AATGATTAGGGCAAATTGTATGC
1 AATGATTAGGGCAAATTGTATGC
3639176 AATGATTAGGGCAAATTGTATGC
1 AATGATTAGGGCAAATTGTATGC
3639199 AA
1 AA
3639201 CTGAAGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (23 bp):
AATGATTAGGGCAAATTGTATGC
Found at i:3642117 original size:17 final size:17
Alignment explanation
Indices: 3642095--3642130 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3642085 CGTCAGGCAG
3642095 GAAACCTGGGCCGACAA
1 GAAACCTGGGCCGACAA
3642112 GAAACCTGGGCCGACAA
1 GAAACCTGGGCCGACAA
3642129 GA
1 GA
3642131 GACCGTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.28, G:0.31, T:0.06
Consensus pattern (17 bp):
GAAACCTGGGCCGACAA
Found at i:3644230 original size:17 final size:17
Alignment explanation
Indices: 3644210--3644244 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3644200 TTATATACTT
*
3644210 AATATAATATTATATAA
1 AATATAATATAATATAA
*
3644227 AATATATTATAATATAA
1 AATATAATATAATATAA
3644244 A
1 A
3644245 TAAGAGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAATATAATATAA
Found at i:3647918 original size:31 final size:31
Alignment explanation
Indices: 3647875--3647936 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3647865 AATGGATAAG
3647875 TATTGAGAGTTAAATTGATAAATTTTGTAAA
1 TATTGAGAGTTAAATTGATAAATTTTGTAAA
* * * * *
3647906 TATTGAGGGTTAAGTTTATTAATTTTTTAAA
1 TATTGAGAGTTAAATTGATAAATTTTGTAAA
3647937 AATTTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (31 bp):
TATTGAGAGTTAAATTGATAAATTTTGTAAA
Found at i:3648934 original size:21 final size:21
Alignment explanation
Indices: 3648910--3648949 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3648900 ATTTTCACTG
3648910 ATTAAAATTT-TATATATAGGC
1 ATTAAAATTTATAT-TATAGGC
*
3648931 ATTAATATTTATATTATAG
1 ATTAAAATTTATATTATAG
3648950 TATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
ATTAAAATTTATATTATAGGC
Found at i:3648954 original size:20 final size:21
Alignment explanation
Indices: 3648918--3648969 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 21
3648908 TGATTAAAAT
3648918 TTTATATATAGGCATTA-ATA
1 TTTATATATAGGCATTATATA
*
3648938 TTTATATTATA-GTATTATATA
1 TTTATA-TATAGGCATTATATA
3648959 TTACTATATAT
1 TT--TATATAT
3648970 TTAATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 11 0.41
21 9 0.33
22 3 0.11
23 4 0.15
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (21 bp):
TTTATATATAGGCATTATATA
Found at i:3649110 original size:29 final size:29
Alignment explanation
Indices: 3649063--3649151 Score: 79
Period size: 31 Copynumber: 3.0 Consensus size: 29
3649053 TTGATTTAAA
*
3649063 GTGCACTTGTATACATGAACTTTAATTTG
1 GTGCAATTGTATACATGAACTTTAATTTG
* * *
3649092 GTGCAATTGTAAACGTGAAACTCTAATTGTG
1 GTGCAATTGTATACATG-AACTTTAATT-TG
* * * *
3649123 GTTCAAATGTATACTTAAAACTTTAATTT
1 GTGCAATTGTATACAT-GAACTTTAATTT
3649152 TGATTTAATC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 14 0.30
30 10 0.21
31 23 0.49
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (29 bp):
GTGCAATTGTATACATGAACTTTAATTTG
Found at i:3652159 original size:42 final size:42
Alignment explanation
Indices: 3652112--3652210 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 42
3652102 GAAGTCCAAA
** *
3652112 GGTTGAACAGAAGCTCATGGGAGCAAAACAGAAACCCATAAG
1 GGTTGAACAGAAGCTCATAAGAACAAAACAGAAACCCATAAG
* ** *
3652154 GGTTGAAC-GAAAGCTCGTAAGAACTGAACGGAAACCCATAAG
1 GGTTGAACAG-AAGCTCATAAGAACAAAACAGAAACCCATAAG
**
3652196 GGTCAAACAGAAGCT
1 GGTTGAACAGAAGCT
3652211 TAAAAGAGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.13
Consensus pattern (42 bp):
GGTTGAACAGAAGCTCATAAGAACAAAACAGAAACCCATAAG
Found at i:3655852 original size:25 final size:25
Alignment explanation
Indices: 3655823--3655874 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3655813 TTTGGCTTGA
**
3655823 CATTTACTAA-GCAATATTGAATATT
1 CATTTA-TAAGGCAATATCAAATATT
3655848 CATTTATAAGGCAATATCAAATATT
1 CATTTATAAGGCAATATCAAATATT
3655873 CA
1 CA
3655875 AATTATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (25 bp):
CATTTATAAGGCAATATCAAATATT
Found at i:3657100 original size:11 final size:11
Alignment explanation
Indices: 3657084--3657108 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3657074 TTCAGCTGAT
3657084 GAAAATGAAGA
1 GAAAATGAAGA
3657095 GAAAATGAAGA
1 GAAAATGAAGA
3657106 GAA
1 GAA
3657109 TTCTAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:3659703 original size:39 final size:41
Alignment explanation
Indices: 3659612--3659707 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 41
3659602 CTGTTACCGC
* * *
3659612 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAACATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGT---ACA-TGA
3659657 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGT-CA-GA
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTACATGA
*
3659696 TATTGTTACCGT
1 TACTGTTACCGT
3659708 ACTATTACTG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 12 0.26
41 2 0.04
45 33 0.70
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (41 bp):
TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTACATGA
Found at i:3667633 original size:54 final size:54
Alignment explanation
Indices: 3667551--3667693 Score: 286
Period size: 54 Copynumber: 2.6 Consensus size: 54
3667541 TATAAAGGGC
3667551 CAAAACCTTGGATTGGAGTGATGTTAATGCTGATTTATTAGCACATTTTTCTCA
1 CAAAACCTTGGATTGGAGTGATGTTAATGCTGATTTATTAGCACATTTTTCTCA
3667605 CAAAACCTTGGATTGGAGTGATGTTAATGCTGATTTATTAGCACATTTTTCTCA
1 CAAAACCTTGGATTGGAGTGATGTTAATGCTGATTTATTAGCACATTTTTCTCA
3667659 CAAAACCTTGGATTGGAGTGATGTTAATGCTGATT
1 CAAAACCTTGGATTGGAGTGATGTTAATGCTGATT
3667694 AATGCTGATT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 89 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (54 bp):
CAAAACCTTGGATTGGAGTGATGTTAATGCTGATTTATTAGCACATTTTTCTCA
Done.