Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 132 of 185
Found at i:40452460 original size:100 final size:99
Alignment explanation
Indices: 40452173--40453010 Score: 962
Period size: 100 Copynumber: 8.5 Consensus size: 99
40452163 TAACCATAGT
* * * * * * * *
40452173 TTGCAATTTAAAAGATTGAGGCCACAACGGCGAACCTTACTTTCTCAAGCGGTGCAGCGGAACAG
1 TTGCAA-TTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTC-CTAGCGTTGCAGTGGAACAG
* *
40452238 ATTGAAGCTACAACGGCGGATCTCACTTCCCTGACA
64 ATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * * * * * *
40452274 TTGCAATCAAAAGATTGAGGCCATAACGGTGAATCTTACTTTCCTAGCATTGCGGTGGAACAGAT
1 TTGCAATTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGAT
*
40452339 TGAAGCTACAATAGCGGATCTTACTTCCCTGACA
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
40452373 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAGCAGA
1 TTGCAATTAA-AAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* **
40452438 TTGAAGCTATAACAGCAAATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
40452473 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAATAGA
1 TTGCAATTAA-AAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
40452538 TTGAAGCTACAATAGCGGATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
40452573 TTGCAATTAAAAAGATTGAAGCTACAACAGCAGATCTTACTTTCCCAGCGTTGCAGTGGAACAGA
1 TTGCAATT-AAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
40452638 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
40452673 TTGCAATTAAGAAGATTGAAGCTACAACAACGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
1 TTGCAATTAA-AAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
40452738 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * * ** *
40452773 TTGCAATTAAAAGATTGAAGCTACAACAACGAATATT-GTTTCC--CCG--GCAGTTAAAAAGAT
1 TTGCAATTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGAT
* **
40452833 TGAAGCTACAACAGCGGATCTTACTTTCCT-AGTG
66 TGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * * * * * ** *
40452867 TTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGC-TTCC---C-TGGCAGTTAAAAAGA
1 TTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* * *
40452927 TTGAAACTACAATAGCGGATCTTACTTTCCT-AGCA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CA
* * * * * * *
40452962 TTGCAGTGGAACAGATTGAAGTTATAGCAGCGGATCTTACTTCCCTAGC
1 TTGCAAT-TAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC
40453011 AATTAAAAAA
Statistics
Matches: 658, Mismatches: 67, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
93 1 0.00
94 47 0.07
95 109 0.17
96 4 0.01
98 5 0.01
99 85 0.13
100 399 0.61
101 8 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (99 bp):
TTGCAATTAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGAT
TGAAGCTACAACAGCGGATCTTACTTCCCTGACA
Found at i:40453384 original size:15 final size:15
Alignment explanation
Indices: 40453356--40453405 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
40453346 AACCCAACCA
*
40453356 AAACCAAACCAGCCC
1 AAACCAAACAAGCCC
*
40453371 AAACCCAACAAGCCC
1 AAACCAAACAAGCCC
* *
40453386 AAACTAACCCAAGCCC
1 AAACCAA-ACAAGCCC
40453402 AAAC
1 AAAC
40453406 ACTTAAGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.48, C:0.44, G:0.06, T:0.02
Consensus pattern (15 bp):
AAACCAAACAAGCCC
Found at i:40453396 original size:25 final size:26
Alignment explanation
Indices: 40453341--40453403 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
40453331 ACCTAAATCT
40453341 ACCCAAACCCAACCAAAACCAAACCA
1 ACCCAAACCCAACCAAAACCAAACCA
* ** *
40453367 GCCCAAACCCAA-CAAGCCCAAACTA
1 ACCCAAACCCAACCAAAACCAAACCA
*
40453392 ACCCAAGCCCAA
1 ACCCAAACCCAA
40453404 ACACTTAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.48, C:0.46, G:0.05, T:0.02
Consensus pattern (26 bp):
ACCCAAACCCAACCAAAACCAAACCA
Found at i:40456109 original size:20 final size:20
Alignment explanation
Indices: 40456086--40456153 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
40456076 CCTTGATCCT
40456086 TGTCTCAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
* *** *
40456106 TGTCTCAAGACCTTG-ATCCT
1 TGTCTCAATACAACGAAT-CG
40456126 TGTCTCAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
40456146 TGTCTCAA
1 TGTCTCAA
40456154 GACCTTGGAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTCTCAATACAACGAATCG
Found at i:40456121 original size:40 final size:40
Alignment explanation
Indices: 40456073--40456160 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
40456063 CTATGTCTGG
40456073 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
40456113 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
40456153 AGACCTTG
1 AGACCTTG
40456161 GATCGAATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (40 bp):
AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
Found at i:40456165 original size:20 final size:20
Alignment explanation
Indices: 40456102--40456165 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
40456092 AATACAACGA
40456102 ATCGTGTCTCAAGACCTT-G
1 ATCGTGTCTCAAGACCTTGG
* * *** *
40456121 ATCCTTGTCTCAATACAACGA
1 AT-CGTGTCTCAAGACCTTGG
40456142 ATCGTGTCTCAAGACCTTGG
1 ATCGTGTCTCAAGACCTTGG
40456162 ATCG
1 ATCG
40456166 AATTTGATTG
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
ATCGTGTCTCAAGACCTTGG
Found at i:40459601 original size:181 final size:174
Alignment explanation
Indices: 40459294--40459644 Score: 470
Period size: 181 Copynumber: 2.0 Consensus size: 174
40459284 TATATATATA
* *
40459294 TTTATCTATTTAACCAGCTTTCTGCGACTAATATTTTTTTCAGCTTGCACATGTGTCTTGTGAGC
1 TTTATCTATTTAACCAGCTTTCTGCAACTAATATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
** * * *
40459359 AGTTGAATTCATCAAAAGACATTACAGAAGAAATTCTTTTATCATATTCTTGGTTGCATCACCTA
66 ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATATTCTCGGTAGCATCACCTA
* * * *
40459424 TTAAGGAAACATATATTTCCTTAGTATGTCTCTCAATAAGGCATTTCT
131 TTAA-G-AA-A-ACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
* *
40459472 TTTATCTATTTAACCAGCTTTCTGCAAGTAA-ATTTTTCCTTCATCTTGCAGGCACGTGTCTTGT
1 TTTATCTATTTAACCAGCTTTCTGCAACTAATATTTTT--TTCAGCTTGCA--CACGTGTCTTGT
* * * *
40459536 GAGTACATGAATTCATCTAAAGACATTACAAAAGAAATTCTTTTGTCATGTTCTCGGTAGCATCA
62 GAGCACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATATTCTCGGTAGCATCA
40459601 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
127 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
40459645 CTTTTTTTGG
Statistics
Matches: 152, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
177 34 0.22
178 30 0.20
179 12 0.08
180 1 0.01
181 75 0.49
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (174 bp):
TTTATCTATTTAACCAGCTTTCTGCAACTAATATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATATTCTCGGTAGCATCACCTA
TTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
Found at i:40461704 original size:21 final size:20
Alignment explanation
Indices: 40461675--40461713 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
40461665 GTCAAATATA
40461675 AATGCCACAAGCGCCAATAG
1 AATGCCACAAGCGCCAATAG
*
40461695 AATGCACACAAGTGCCAAT
1 AATGC-CACAAGCGCCAAT
40461714 CTTCCTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.28, G:0.18, T:0.13
Consensus pattern (20 bp):
AATGCCACAAGCGCCAATAG
Found at i:40478828 original size:920 final size:926
Alignment explanation
Indices: 40476577--40478970 Score: 4269
Period size: 920 Copynumber: 2.6 Consensus size: 926
40476567 AACATAAACT
* * * *
40476577 ATTTGTTGGGGATGAGGAGGAGCAAATGAAGAAAATAAAGAGCACAGAACAATGAAACAAGATGC
1 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
*
40476642 AAGAAATATTTTTACTTGCTCACAAATGTGCAGCAAGGGAGCTTATGGCTAATAGCTCATTTTGC
66 AAGAAATATTTTTACTTGCTCACAAATGTGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
*
40476707 TCATTCATTCAAGTAGAAAAAATAATACATTTATAGCCAAATACATCACCAAATACTACCTACTA
131 TCATTCATTCAACTAGAAAAAATAATACATTTATAGCCAAATACATCACCAAATACTACCTACTA
*
40476772 CCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAGCA
196 CCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAACA
*
40476837 CCTAAAAATATCAAAACAATACCAACCTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACTA
261 CCTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACTA
40476902 AACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAACC
326 AACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAACC
*
40476967 AAAAATATAACAGTAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAAT
391 AAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAAT
40477032 ACCAATCATTCATCAAGTTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCT
456 ACCAATCATTCATCAAG-TTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCT
* * *
40477097 GCTCAAGAAATTCATTTTCAACCTTGGCTTTATTCTCAACCAAATCTGACTTGCACGCTTGACTA
520 GCTCAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATCTGACTTACACGCTTGACTA
*
40477162 TCCCAGTCTTTTGATCCAAAGATTTGTTCATCAAATGGAGTCTTCTCCTCCTTCACGGCCTTGGT
585 TCCCAGTCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTCTTCTCCTCCTT-----CCTTGGT
* *
40477227 TGACAACTTGCCTTCAAAAACATCTTGCCTTGTTTCTTTGTTCATTACAGTCATGTTTCTTCTTG
645 TGACAACTTACCTTCAAAAACATATTGCCTTGTTTCTTTGTTCATTACAGTCATGTTTCTTCTTG
* *
40477292 CACATACTCCCTCCTGCTGTAGAGTGTCTTCATGCACACACTCCATCAACTCCTCCTTTAGCTTA
710 CACATACTCCCTCCTGCTGTAGAGTGACTTCATGCACACACTCCATCAACTCCTCCTTCAGCTTA
*
40477357 TCCCAAGCTTGTTTAGGAGTCTCACATGGGTGAGCTGTTGCTATCTTTTTTACAAGTAGTCCTCA
775 TCCCAAGCTTGTTTAGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGTAGTCCTCA
40477422 AAGATGACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGCAAAAACAAGCCCTC
840 AAGATGACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGCAAAAACAAGCCCTC
*
40477487 AAAGAGTTGGGCTCATGATACC
905 AAAGACTTGGGCTCATGATACC
* *
40477509 ATTTGTTGGGGATGAGGAGGAGTAAAGGAAGAAAACAGAGAGTACAGAACAATGAAGCAAGATGC
1 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
* *
40477574 AAGAAATATTTTTACTTACTCACAAATATGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
66 AAGAAATATTTTTACTTGCTCACAAATGTGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
40477639 TCATTCATTCAACTAGAAAAAAATAATACATTTATAGCCAAATACATCACCAAATACTACCTACT
131 TCATTCATTCAACTAG-AAAAAATAATACATTTATAGCCAAATACATCACCAAATACTACCTACT
40477704 ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
195 ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
*
40477769 ACCTAAAAATATTAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACT
260 ACCTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACT
40477834 AAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAAC
325 AAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAAC
40477899 CAAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAA
390 CAAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAA
*
40477964 TACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCATTAGATGCTTTGTTTCAAGCTGACTCT
455 TACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCT
* *
40478029 GCTTAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATCTGGCTTACACGCTTGACTA
520 GCTCAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATCTGACTTACACGCTTGACTA
40478094 TCCCAGTCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTC-T-T-CTCCTT-CTT-GTTGACA
585 TCCCAGTCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTCTTCTCCTCCTTCCTTGGTTGACA
* *
40478154 ACTTACCTTCAAACACATATTGCCTTGTTTCTTTGTTCATTACAGTCCTGTTTCTTCTTGCACAT
650 ACTTACCTTCAAAAACATATTGCCTTGTTTCTTTGTTCATTACAGTCATGTTTCTTCTTGCACAT
40478219 ACTCCCTCCTGCTGTAGAGTGACTTCATGCACACACTCCATCAACTCCTCCTTCAGCTTATCCCA
715 ACTCCCTCCTGCTGTAGAGTGACTTCATGCACACACTCCATCAACTCCTCCTTCAGCTTATCCCA
*
40478284 AGCTTGTTTGGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGTAGTCCTCAAAGAT
780 AGCTTGTTTAGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGTAGTCCTCAAAGAT
* * *
40478349 GACAGGCTTTAATAGCTTCTTGTCTTTCTTAACAAGCAGCAGAAGC-AAAACAAGCCTTCAAAGA
845 GACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGCAAAAACAAGCCCTCAAAGA
40478413 CTTGGGCTCATGATACC
910 CTTGGGCTCATGATACC
* *
40478430 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAAAAAACAGAGAGCATAGAACAATGAAGCAAGATGC
1 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
40478495 AAGAAATATTTTTACTTGCTCACAAATGTGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
66 AAGAAATATTTTTACTTGCTCACAAATGTGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
*
40478560 TCATTCATTCAACTAGAAAAAATAATACATTTATAGCCAAATACATCACCAAATACTATCTACTA
131 TCATTCATTCAACTAGAAAAAATAATACATTTATAGCCAAATACATCACCAAATACTACCTACTA
* *
40478625 CCACTAGTCATACTTTGAAACAAGTAAAACTTAACTTGCGCACAAGCTGATTATGTCAATCAACA
196 CCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAACA
* * *
40478690 CCTAAAAATGTCAAAACAATACCAACTTTGTTCATTTTCAACTAAGTAGCTTAACAATGTAACTA
261 CCTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACTA
* *
40478755 AACAACCTTGCTATTACAACAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAACC
326 AACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAACC
* *
40478820 AAAAATATAACAGCAACATGGTTGGCCAATTTTCAACACTCTTCCTTGGACTCCATGCCGCAAAT
391 AAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAAT
*
40478885 ACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCAG
456 ACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCTG
40478950 CTCAAGCAATTCATTTTCAAC
521 CTCAAGCAATTCATTTTCAAC
40478971 ACTATTATCA
Statistics
Matches: 1408, Mismatches: 53, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
920 381 0.27
921 173 0.12
922 238 0.17
923 3 0.00
929 6 0.00
930 1 0.00
931 1 0.00
932 283 0.20
933 322 0.23
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (926 bp):
ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
AAGAAATATTTTTACTTGCTCACAAATGTGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
TCATTCATTCAACTAGAAAAAATAATACATTTATAGCCAAATACATCACCAAATACTACCTACTA
CCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAACA
CCTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACTA
AACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAACC
AAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAAT
ACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCTG
CTCAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATCTGACTTACACGCTTGACTAT
CCCAGTCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTCTTCTCCTCCTTCCTTGGTTGACAA
CTTACCTTCAAAAACATATTGCCTTGTTTCTTTGTTCATTACAGTCATGTTTCTTCTTGCACATA
CTCCCTCCTGCTGTAGAGTGACTTCATGCACACACTCCATCAACTCCTCCTTCAGCTTATCCCAA
GCTTGTTTAGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGTAGTCCTCAAAGATG
ACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGCAAAAACAAGCCCTCAAAGAC
TTGGGCTCATGATACC
Found at i:40486525 original size:41 final size:41
Alignment explanation
Indices: 40486467--40486746 Score: 381
Period size: 41 Copynumber: 6.8 Consensus size: 41
40486457 TTAAACAGAT
** * * *
40486467 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAAT--GTA
* *
40486509 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
40486549 TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
40486590 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
40486631 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
40486672 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
40486711 CTTCACCGGCATTAAGCCTGCTAGACGTAACGTCTG
1 --TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG
40486747 TATTATATTC
Statistics
Matches: 222, Mismatches: 10, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
39 2 0.01
40 8 0.04
41 208 0.94
42 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
Found at i:40487119 original size:2 final size:2
Alignment explanation
Indices: 40487070--40487099 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40487060 TATTCGACTT
*
40487070 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40487100 ATCATTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:40496491 original size:144 final size:143
Alignment explanation
Indices: 40496227--40496517 Score: 510
Period size: 144 Copynumber: 2.0 Consensus size: 143
40496217 TTATTTAGAC
* *
40496227 CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAATTTAATGTATTTTAGTTTCTT
1 CTTTAGTCCATTTCTTTGCTTGTAATGAATTTTCAACCTTTTAATTTAATGTATTTTAATTTCTT
* * *
40496292 TTAATTTAATCTGTTAAAGGCTTCAACTTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATACC
66 TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATACC
*
40496357 TCTCATTACTTTT
131 TCCCATTACTTTT
*
40496370 CTTTGAGTCCATTTCTTTGCTTGTAATGAATTTTCAACCTTTTAGTTTAATGTATTTTAATTTCT
1 CTTT-AGTCCATTTCTTTGCTTGTAATGAATTTTCAACCTTTTAATTTAATGTATTTTAATTTCT
40496435 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATAC
65 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATAC
40496500 CTCCCATTACTTTT
130 CTCCCATTACTTTT
40496514 CTTT
1 CTTT
40496518 TATGTTTTCT
Statistics
Matches: 140, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
143 4 0.03
144 136 0.97
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.55
Consensus pattern (143 bp):
CTTTAGTCCATTTCTTTGCTTGTAATGAATTTTCAACCTTTTAATTTAATGTATTTTAATTTCTT
TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATACC
TCCCATTACTTTT
Found at i:40498718 original size:187 final size:188
Alignment explanation
Indices: 40498402--40498777 Score: 691
Period size: 187 Copynumber: 2.0 Consensus size: 188
40498392 TGGAAGAAAA
40498402 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
1 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
*
40498467 TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGTATTGTTTACAGTTCTTGTTAACAATT
66 TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
40498532 GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAATTT
131 GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAATTT
* *
40498590 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATATGAATTGCTTGTGAATTTATTGCA
1 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
*
40498655 -TATCCTTAGCATGTAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
66 TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
* *
40498719 GGTATCTTAGTTTAAGTATCAATTAGTATCTTCATTAGTCATGAATTTGGTTGAATTT
131 GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAATTT
40498777 T
1 T
40498778 TATGCAATTA
Statistics
Matches: 182, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
187 119 0.65
188 63 0.35
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (188 bp):
TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAATTT
Found at i:40499734 original size:22 final size:22
Alignment explanation
Indices: 40499678--40499735 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
40499668 TGGTAGTTAA
*
40499678 GTCTCAAGACATAAGACCATAT
1 GTCTCAAGACATGAGACCATAT
*
40499700 GTCTCAAGACATGGGACCATAT
1 GTCTCAAGACATGAGACCATAT
40499722 GTCTCAAGACATGA
1 GTCTCAAGACATGA
40499736 AAGTTCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (22 bp):
GTCTCAAGACATGAGACCATAT
Found at i:40500141 original size:14 final size:15
Alignment explanation
Indices: 40500122--40500150 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40500112 TGAGTCCAAA
40500122 AATAACCC-AATTAC
1 AATAACCCAAATTAC
40500136 AATAACCCAAATTAC
1 AATAACCCAAATTAC
40500151 TAGCCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAACCCAAATTAC
Found at i:40500358 original size:23 final size:23
Alignment explanation
Indices: 40500303--40500348 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40500293 GCACCGCACA
* *
40500303 CCTCCGTACGTGCCACGTCCGCG
1 CCTCTGTACGTGCCACGTCCCCG
40500326 CCTCTGTACGTGCCACGTCCCCG
1 CCTCTGTACGTGCCACGTCCCCG
40500349 ATCTTGTACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.48, G:0.24, T:0.20
Consensus pattern (23 bp):
CCTCTGTACGTGCCACGTCCCCG
Found at i:40503673 original size:19 final size:20
Alignment explanation
Indices: 40503649--40503702 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
40503639 GCAATTAAGC
*
40503649 CTAGAAATTTTGGTAT-AGG
1 CTAGAAATTTTGGTATCAGA
*
40503668 CTAGAAATTTTAGTATCAGA
1 CTAGAAATTTTGGTATCAGA
*
40503688 TTA-AAATTTTGGTAT
1 CTAGAAATTTTGGTAT
40503703 TGCTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (20 bp):
CTAGAAATTTTGGTATCAGA
Found at i:40508332 original size:18 final size:18
Alignment explanation
Indices: 40508309--40508344 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40508299 ATGACGAACT
40508309 TGCGGAGGCATGTTGTTA
1 TGCGGAGGCATGTTGTTA
40508327 TGCGGAGGCATGTTGTTA
1 TGCGGAGGCATGTTGTTA
40508345 GGGAAGACAA
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:0.17, C:0.11, G:0.39, T:0.33
Consensus pattern (18 bp):
TGCGGAGGCATGTTGTTA
Found at i:40509948 original size:21 final size:21
Alignment explanation
Indices: 40509905--40510018 Score: 95
Period size: 21 Copynumber: 5.5 Consensus size: 21
40509895 TCGAAAACTG
* * *
40509905 AACAGAAGCTCATGATAGCTA
1 AACAGAAGCTCATAAGAGTTA
40509926 AACAGAAGCTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGTTA
* * * * * *
40509947 AATAAAAACACATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTA
* *
40509968 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGTTA
* * *
40509989 AACAAAAACTCATAA-AGTTG
1 AACAGAAGCTCATAAGAGTTA
40510009 AACAGAAGCT
1 AACAGAAGCT
40510019 TGTGAGAGCT
Statistics
Matches: 69, Mismatches: 24, Indels: 1
0.73 0.26 0.01
Matches are distributed among these distances:
20 11 0.16
21 58 0.84
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGTTA
Found at i:40510038 original size:42 final size:42
Alignment explanation
Indices: 40509926--40510075 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 42
40509916 ATGATAGCTA
* * * *
40509926 AACAGAAGCTCATAAGAGTTAAATAAAAACACATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAAAAACACATAAGAGTTG
*
40509968 AACAGAAGCTCGTAAGAGCTAAACAAAAACTCATAA-AGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAAAAACACATAAGAGTTG
* * * ** * *
40510009 AACAGAAGCTTGTGAGAGCTGAACAAAAA-ATTGTATGAGTTA
1 AACAGAAGCTCGTAAGAGCTAAACAAAAACA-CATAAGAGTTG
* *
40510051 AACGGAAGCTCGTAAGAGCTTAACA
1 AACAGAAGCTCGTAAGAGCTAAACA
40510076 GAAAGTAAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 32 0.36
42 57 0.64
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAACAAAAACACATAAGAGTTG
Found at i:40513241 original size:18 final size:18
Alignment explanation
Indices: 40513220--40513267 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
40513210 AAAAAGCCTA
40513220 ACACAATATTTTTTTCTG
1 ACACAATATTTTTTTCTG
*
40513238 ACACAAT-TTTTTATCTG
1 ACACAATATTTTTTTCTG
40513255 ACA-AATATTTTTT
1 ACACAATATTTTTT
40513268 AAAATTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 3 0.11
17 17 0.63
18 7 0.26
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (18 bp):
ACACAATATTTTTTTCTG
Found at i:40513254 original size:17 final size:17
Alignment explanation
Indices: 40513220--40513268 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
40513210 AAAAAGCCTA
*
40513220 ACACAATATTTTTTTCTG
1 ACACAAT-TTTTTATCTG
40513238 ACACAATTTTTTATCTG
1 ACACAATTTTTTATCTG
*
40513255 ACAAATATTTTTTA
1 ACACA-ATTTTTTA
40513269 AAATTTCTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (17 bp):
ACACAATTTTTTATCTG
Found at i:40522981 original size:27 final size:28
Alignment explanation
Indices: 40522929--40522983 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
40522919 TAAATATTGA
40522929 AATTTATGATTTAAAATAAATTAATAATAT
1 AATTTAT-ATTTAAAATAAA-TAATAATAT
40522959 AATTTAT-TTTAAATATAAA-AATAAT
1 AATTTATATTTAAA-ATAAATAATAAT
40522984 TTTTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 6 0.25
28 6 0.25
29 5 0.21
30 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTTATATTTAAAATAAATAATAATAT
Found at i:40524296 original size:14 final size:15
Alignment explanation
Indices: 40524279--40524316 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
40524269 TTTATTTTTT
40524279 ATTAATTATAAAA-A
1 ATTAATTATAAAATA
* *
40524293 ATTAATTTTAAAATT
1 ATTAATTATAAAATA
40524308 ATTAATTAT
1 ATTAATTAT
40524317 TATCATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAATTATAAAATA
Found at i:40526622 original size:12 final size:12
Alignment explanation
Indices: 40526605--40526629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40526595 TTATGAAATT
40526605 AATTAATTATTG
1 AATTAATTATTG
40526617 AATTAATTATTG
1 AATTAATTATTG
40526629 A
1 A
40526630 TGTTACATAT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
AATTAATTATTG
Found at i:40530728 original size:3 final size:3
Alignment explanation
Indices: 40530720--40530745 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40530710 CAAAAAGGAA
40530720 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
40530746 ACATGAAAGC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40541038 original size:20 final size:21
Alignment explanation
Indices: 40540992--40541070 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
40540982 TACTAATTAC
40540992 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
40541013 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
* *
40541033 ATATATTCTAATTAATT-T-TAT
1 AAATATT-TAA-TAATTATATTT
* *
40541054 AAATAATTAATATTTAT
1 AAATATTTAATAATTAT
40541071 TGCTTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
19 8 0.17
20 15 0.32
21 20 0.43
23 3 0.06
24 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:40541286 original size:28 final size:26
Alignment explanation
Indices: 40541240--40541311 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
40541230 ATTTTATTTC
40541240 TCAAAAACACTGCTAAACACCAAACTTT
1 TCAAAAACACTGCTAAACA--AAACTTT
* * *
40541268 TCAAAAACACTTCTCAACAATACTTT
1 TCAAAAACACTGCTAAACAAAACTTT
* * *
40541294 TCAAGAACATTGTTAAAC
1 TCAAAAACACTGCTAAAC
40541312 GTTAGCGGCT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
26 19 0.53
28 17 0.47
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.26
Consensus pattern (26 bp):
TCAAAAACACTGCTAAACAAAACTTT
Found at i:40553244 original size:12 final size:12
Alignment explanation
Indices: 40553227--40553253 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40553217 ACATTCATTC
40553227 AAAATAAAAATG
1 AAAATAAAAATG
40553239 AAAATAAAAATG
1 AAAATAAAAATG
40553251 AAA
1 AAA
40553254 CAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:40553629 original size:3 final size:3
Alignment explanation
Indices: 40553621--40553667 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
40553611 AAAAACAATT
*
40553621 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
40553668 GCTAAAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40554973 original size:39 final size:39
Alignment explanation
Indices: 40554929--40555281 Score: 177
Period size: 39 Copynumber: 8.5 Consensus size: 39
40554919 ATCTACTCTG
* *
40554929 CTGTAACCTCAGAGAGATAAGATCCTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTAATCTGCTCCA
* * * * ** * **
40554968 CTGTAACTTCGGGGAGATAGGATAGTGTCTTCGATCTACTCTG
1 CTGTAACCTCAGGGAGATA--AGA-T-CCTTTAATCTGCTCCA
* *
40555011 CTGTAACCTCAGAGAGATAAGATCCTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTAATCTGCTCCA
* * * * ** *
40555050 CTGTAACTTCGGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATA--AGA-T-CCTTTAATCTGCTCCA
* *
40555093 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATC-CT---TT-AATCTGCTCCA
** *
40555137 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAACCTCAGGGAGATAAGATC-------CTTTAATCTGCTCCA
* * * *
40555183 CTGTAATCTCAGGGAGATAAGA-CCTGATGTGATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCCT--T-TAATCTGCTCCA
* * *
40555224 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTAATCTGCTCCA
* * *
40555263 TTGTAATCTCAAGGAGATA
1 CTGTAACCTCAGGGAGATA
40555282 GGATTACTAT
Statistics
Matches: 231, Mismatches: 60, Indels: 46
0.69 0.18 0.14
Matches are distributed among these distances:
38 2 0.01
39 63 0.27
40 6 0.03
41 35 0.15
42 5 0.02
43 53 0.23
44 33 0.14
45 1 0.00
46 28 0.12
47 2 0.01
50 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (39 bp):
CTGTAACCTCAGGGAGATAAGATCCTTTAATCTGCTCCA
Found at i:40555010 original size:82 final size:82
Alignment explanation
Indices: 40554917--40555116 Score: 364
Period size: 82 Copynumber: 2.4 Consensus size: 82
40554907 AGACTTGATG
40554917 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAACTTCGGGG
1 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAACTTCGGGG
40554982 AGATAGGATAGTGTCTT
66 AGATAGGATAGTGTCTT
40554999 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAACTTCGGGG
1 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAACTTCGGGG
40555064 AGATAGGATAGTGTCTT
66 AGATAGGATAGTGTCTT
* * * *
40555081 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
1 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC
40555117 TCTGGCTTCA
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 114 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (82 bp):
CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAACTTCGGGG
AGATAGGATAGTGTCTT
Found at i:40555140 original size:44 final size:44
Alignment explanation
Indices: 40554919--40555161 Score: 177
Period size: 43 Copynumber: 5.8 Consensus size: 44
40554909 ACTTGATGCG
* * *
40554919 ATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CT---TT-A
1 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCA
* * * * * ** * *
40554958 ATCCGCTCCACTGTAACTTCGGGGAGATAGGAT-AGTGTCTTCG
1 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCA
* * *
40555001 ATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CT---TT-A
1 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCA
* * * * * ** * *
40555040 ATCCGCTCCACTGTAACTTCGGGGAGATAGGAT-AGTGTCTTCG
1 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCA
*
40555083 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCA
40555127 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCT
1 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCT
40555162 GAAATTCTTT
Statistics
Matches: 151, Mismatches: 41, Indels: 19
0.72 0.19 0.09
Matches are distributed among these distances:
39 52 0.34
40 2 0.01
42 4 0.03
43 53 0.35
44 40 0.26
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCA
Found at i:40555201 original size:46 final size:45
Alignment explanation
Indices: 40555077--40555374 Score: 205
Period size: 44 Copynumber: 6.8 Consensus size: 45
40555067 TAGGATAGTG
* * * *
40555077 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CT
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* ** * * *
40555120 GGCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* *
40555167 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-A-
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * *
40555210 --TGTGATCT-TCTCTACTGTAA-CTTCAGAGAGATAAGATC-----
1 TCTTTGATCTGT-TCCACTGTAATC-TCAGGGAGATAAGATCTGAAT
* * * * * * *
40555248 -CTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACT
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* *
40555290 ATCCTTGATCTGTTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
*
40555337 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGA
40555375 CCTGTATAAT
Statistics
Matches: 199, Mismatches: 38, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
39 25 0.13
40 3 0.02
41 29 0.15
44 69 0.35
45 1 0.01
46 69 0.35
47 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Found at i:40564435 original size:39 final size:39
Alignment explanation
Indices: 40564390--40564469 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
40564380 CAATCTAGTA
* *
40564390 GACTCTTTTCCAAGGCGACTTCTCGAGCTCGAGTATCCT
1 GACTCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCT
40564429 GACTCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCT
1 GACTCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCT
40564468 GA
1 GA
40564470 AATCTCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.19, C:0.33, G:0.21, T:0.28
Consensus pattern (39 bp):
GACTCTTTCCCAAGGCGACTTCTCGAGCCCGAGTATCCT
Found at i:40569193 original size:3 final size:3
Alignment explanation
Indices: 40569185--40569227 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
40569175 AAAAACAATT
* *
40569185 ATA ATA ATA ATA ATA ACA ATA ATA ATA GTA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40569228 AATTGCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:40574461 original size:19 final size:19
Alignment explanation
Indices: 40574437--40574480 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
40574427 TAGCAAAAAC
*
40574437 ATAAAATGTTAAAATATAA
1 ATAAAATATTAAAATATAA
*
40574456 ATAAAATATTATAATATAA
1 ATAAAATATTAAAATATAA
*
40574475 TTAAAA
1 ATAAAA
40574481 GTTGTCCAAA
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:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAAATATTAAAATATAA
Found at i:40576143 original size:1 final size:1
Alignment explanation
Indices: 40576137--40576162 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
40576127 GCAATCTCCC
40576137 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
40576163 AGGCAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40590966 original size:17 final size:17
Alignment explanation
Indices: 40590944--40590978 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40590934 ATTAAAAAAT
* *
40590944 ATTTTTATACTTTTAAA
1 ATTTTTAAAATTTTAAA
40590961 ATTTTTAAAATTTTAAA
1 ATTTTTAAAATTTTAAA
40590978 A
1 A
40590979 AATTAATTAA
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:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTAAAATTTTAAA
Found at i:40592713 original size:22 final size:22
Alignment explanation
Indices: 40592681--40592728 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40592671 AATTATGATC
*
40592681 ATTACTTTAATTGCACT-ATTTA
1 ATTACTATAATT-CACTGATTTA
*
40592703 ATTACTATAATTCATTGATTTA
1 ATTACTATAATTCACTGATTTA
40592725 ATTA
1 ATTA
40592729 TTAATTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTACTATAATTCACTGATTTA
Found at i:40594854 original size:20 final size:21
Alignment explanation
Indices: 40594815--40594855 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
40594805 GTAATTATAT
*
40594815 TAATTAAATGAAATAAAAATA
1 TAATTAAATGAAACAAAAATA
*
40594836 TAATTAACT-AAACAAAAATA
1 TAATTAAATGAAACAAAAATA
40594856 ATTACACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
TAATTAAATGAAACAAAAATA
Found at i:40596605 original size:66 final size:66
Alignment explanation
Indices: 40596482--40596614 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
40596472 GCTTAGGTAC
* * *
40596482 AAACTTGGCTCTAAAAACATGTTCCTCTCGATGAACAAAATAAGTGCTTTCTCTAATTTGTACAC
1 AAACTTGGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTTCCTCTAATTTGTACAC
40596547 A
66 A
* * * * *
40596548 AAACTTTGG-TCTAAATACATATTTCTTTCGATAAACAAAATAAGTGC-TCCATTTAATTTTTAC
1 AAAC-TTGGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTTCC-TCTAATTTGTAC
40596611 ACA
64 ACA
40596614 A
1 A
40596615 TTAAATAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
65 2 0.04
66 51 0.89
67 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (66 bp):
AAACTTGGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTTCCTCTAATTTGTACAC
A
Found at i:40607698 original size:30 final size:31
Alignment explanation
Indices: 40607643--40607707 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 31
40607633 TTTCAAAACT
40607643 AAATGATTAACACATAGTTTTTTTTTACTTAA
1 AAATGATTAACACATAG-TTTTTTTTACTTAA
40607675 AAATGATTAACACATAG-TTTTTTTACTTAA
1 AAATGATTAACACATAGTTTTTTTTACTTAA
40607705 AAA
1 AAA
40607708 CCCATACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 16 0.48
32 17 0.52
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (31 bp):
AAATGATTAACACATAGTTTTTTTTACTTAA
Found at i:40611097 original size:33 final size:32
Alignment explanation
Indices: 40611045--40611188 Score: 93
Period size: 34 Copynumber: 4.5 Consensus size: 32
40611035 GGTTTGAGAA
40611045 TTTTTTAAA--AA-TAAATTAGGGTTTATAATT
1 TTTTTTAAATTAATTAAATTAGGGTTT-TAATT
40611075 TTTTTTAAATTAATTAAATTA-GGTTTTAAGGGTT
1 TTTTTTAAATTAATTAAATTAGGGTTTTAA---TT
*** * *
40611109 TTAAATAAATAAATTAAATTAAGG-TTTAGAGTT
1 TTTTTTAAATTAATTAAATTAGGGTTTTA-A-TT
***
40611142 TTTAAGAAAATTAATTAAATTAGGG-TTTAATT
1 TTT-TTTAAATTAATTAAATTAGGGTTTTAATT
* *
40611174 TTTTTAAAAATAATT
1 TTTTTTAAATTAATT
40611189 TTGTGTTTAG
Statistics
Matches: 93, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
30 9 0.10
31 12 0.13
32 12 0.13
33 13 0.14
34 44 0.47
35 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (32 bp):
TTTTTTAAATTAATTAAATTAGGGTTTTAATT
Found at i:40611178 original size:34 final size:33
Alignment explanation
Indices: 40611056--40611183 Score: 118
Period size: 34 Copynumber: 3.8 Consensus size: 33
40611046 TTTTTAAAAA
**
40611056 TAAATTAGGGTTTATAAT-TTTTT-TTAAATTAAT
1 TAAATTAGGG-TT-TAATGTTTTTAAAAAATTAAT
* * * *
40611089 TAAATTAGGTTTTAAGGGTTTTAAATAAATAAAT
1 TAAATTAGGGTTTAATGTTTTTAAA-AAATTAAT
*
40611123 TAAATTAAGGTTTAGA-GTTTTTAAGAAAATTAAT
1 TAAATTAGGGTTTA-ATGTTTTTAA-AAAATTAAT
*
40611157 TAAATTAGGGTTTAATTTTTTTAAAAA
1 TAAATTAGGGTTTAATGTTTTTAAAAA
40611184 TAATTTTGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
31 3 0.04
32 6 0.08
33 13 0.17
34 53 0.69
35 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (33 bp):
TAAATTAGGGTTTAATGTTTTTAAAAAATTAAT
Found at i:40611512 original size:125 final size:126
Alignment explanation
Indices: 40611274--40611921 Score: 852
Period size: 126 Copynumber: 5.2 Consensus size: 126
40611264 TTTTGTTTTT
** * * * * *
40611274 TTTTTCTTTAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCGAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * *
40611339 ACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
*
40611400 TTTTTCTACAGTTGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * **
40611465 A-GCTTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAATGCTCCCATGTAGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
* * * * * * *
40611525 TTTTTCTATAGTAGTTCTTGAAAAAATGATTTTGAAAAGACAATTCTAAAAAAATAGTATCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * * * *
40611590 ACGCTTCAAGCAAGATGCACTGTCAGCAAAGTTACTGAAAAATGCTCCCACATGGACGGTT
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
* *
40611651 TTTTTCTACAGTAGTTCTTGAAAAAATTATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
40611716 ACGCTTCAAACAGGATGCACTGTTAGCAAAATTATTG-AAAAAGCTCCTACATAGACGCCC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
* * * *
40611776 TTTTTGTACAATAGTTCCTGAAAAAATAATATTT-AGAAGACGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAAT-TTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAA
** * * * * *
40611840 AATACTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTC
65 AACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
40611902 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
40611922 CTTGGCCTTA
Statistics
Matches: 455, Mismatches: 64, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
125 214 0.47
126 241 0.53
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACATAGACGCTC
Found at i:40611773 original size:251 final size:251
Alignment explanation
Indices: 40611274--40611921 Score: 897
Period size: 251 Copynumber: 2.6 Consensus size: 251
40611264 TTTTGTTTTT
* * * *
40611274 TTTTTCTTTAGTAGTT-TCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCGAA
1 TTTTTCTATAGTAGTTCT-TGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAA
* *
40611338 AACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTCTTT
65 AACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTT
*
40611403 TTCTACAGTTGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAGC
130 TTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAGC
* * ** *
40611468 TTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAATGCTCCCATGTAGACGCTC
195 TTCAAACAAGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACATAGACGCCC
* * ** * *
40611525 TTTTTCTATAGTAGTTCTTGAAAAAATGATTTTGAAAAGACAATTCTAAAAAAATAGTATCAAAA
1 TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
40611590 ACGCTTCAAGCAAGATGCACTGTCAGCAAAGTTACTGAAAAATGCTCCCACATGGACGGTTTTTT
66 ACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTTT
* *
40611655 TCTACAGTAGTTCTTGAAAAAATTATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAACGC
131 TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAA-GC
* * * *
40611720 TTCAAACAGGATGCACTGTTAGCAAAATTATTGAAAAA-GCTCCTACATAGACGCCC
195 TTCAAACAAGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACATAGACGCCC
* * * * *
40611776 TTTTTGTACAATAGTTCCTGAAAAAATAATATTT-AGAAGACGGTTCTGAAAAAATAGTGTAAAA
1 TTTTTCTATAGTAGTTCTTGAAAAAATAAT-TTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAA
** * *
40611840 AATACTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTCTTT
65 AACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTT
40611905 TTCTACAGTAGTTCCTG
130 TTCTACAGTAGTTCCTG
40611922 CTTGGCCTTA
Statistics
Matches: 342, Mismatches: 52, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
251 303 0.89
252 39 0.11
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (251 bp):
TTTTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACGCTCTTTT
TCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAAAGCT
TCAAACAAGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACATAGACGCCC
Found at i:40617723 original size:16 final size:16
Alignment explanation
Indices: 40617698--40617728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40617688 ATTTGATGTG
*
40617698 TATCTCTTTTTTTAAA
1 TATCTATTTTTTTAAA
40617714 TATCTATTTTTTTAA
1 TATCTATTTTTTTAA
40617729 TATTTTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
TATCTATTTTTTTAAA
Found at i:40619673 original size:25 final size:24
Alignment explanation
Indices: 40619645--40619691 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
40619635 CAAATATTTA
40619645 ATAGTTATAT-TTAAATATTTAAAAT
1 ATAGTTATATATT--ATATTTAAAAT
*
40619670 ATAGTTTTATATTATATTTAAA
1 ATAGTTATATATTATATTTAAA
40619692 TTTTATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
ATAGTTATATATTATATTTAAAAT
Found at i:40625467 original size:16 final size:16
Alignment explanation
Indices: 40625418--40625470 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
40625408 AAAGAAATTT
*
40625418 AAAAATAAAATATTCA
1 AAAAATAATATATTCA
* *
40625434 AAAAATAATA-AGT-G
1 AAAAATAATATATTCA
*
40625448 AAAAATGATATATTCA
1 AAAAATAATATATTCA
40625464 AAAAATA
1 AAAAATA
40625471 CTATGTCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 15 0.54
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAAATAATATATTCA
Found at i:40628570 original size:38 final size:39
Alignment explanation
Indices: 40628515--40628652 Score: 154
Period size: 38 Copynumber: 3.4 Consensus size: 39
40628505 GGCTACCACT
* *
40628515 TATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAGC
*
40628554 TATCAC-TTATCACTTGATGAGATAAGTGTAGTTAAAGCTACCAC
1 TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAG------C
*
40628598 TTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAAAGC
1 -TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAGC
*
40628638 TACCAC-TTATCACTT
1 TATCACTTTATCACTT
40628653 TGTCACTTGA
Statistics
Matches: 84, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
38 36 0.43
39 11 0.13
40 1 0.01
44 1 0.01
45 6 0.07
46 29 0.35
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (39 bp):
TATCACTTTATCACTTGATCAGATAAGTGTAGTTAAAGC
Found at i:40628605 original size:84 final size:83
Alignment explanation
Indices: 40628472--40628652 Score: 283
Period size: 84 Copynumber: 2.2 Consensus size: 83
40628462 TACGATCTCT
* * *
40628472 TATCACTTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGATCA
1 TATCACTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCA
40628536 GATAAGTGTAGCTAAAGC
66 GATAAGTGTAGCTAAAGC
* *
40628554 TATCACTTATCACTTGATGAGATAAGTGTAGTTAAAGCTACCACTTATCACTTTGTCACTTGATC
1 TATCACTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACTTGATC
*
40628619 AGATAAGTGTAGTTAAAGC
65 AGATAAGTGTAGCTAAAGC
*
40628638 TACCACTTATCACTT
1 TATCACTTATCACTT
40628653 TGTCACTTGA
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 10 0.11
83 18 0.20
84 62 0.69
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (83 bp):
TATCACTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACTTGATCA
GATAAGTGTAGCTAAAGC
Found at i:40628613 original size:46 final size:46
Alignment explanation
Indices: 40628470--40628667 Score: 274
Period size: 46 Copynumber: 4.5 Consensus size: 46
40628460 CATACGATCT
* *
40628470 CTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
40628513 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
40628559 CTTATCAC-TTG--A--TG---AGATAAGTGTAGTTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
40628597 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
40628643 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
40628668 AGTACTCAAA
Statistics
Matches: 139, Mismatches: 5, Indels: 19
0.85 0.03 0.12
Matches are distributed among these distances:
38 30 0.22
39 3 0.02
41 3 0.02
43 11 0.08
44 5 0.04
45 23 0.17
46 64 0.46
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
Found at i:40630187 original size:13 final size:13
Alignment explanation
Indices: 40630169--40630198 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40630159 AAAAAATTCT
40630169 AAAATTATGATAA
1 AAAATTATGATAA
*
40630182 AAAATTATTATAA
1 AAAATTATGATAA
40630195 AAAA
1 AAAA
40630199 CTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATTATGATAA
Found at i:40630657 original size:16 final size:16
Alignment explanation
Indices: 40630636--40630666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40630626 TAGTGGTTTA
40630636 ATATAAATAAATATAG
1 ATATAAATAAATATAG
*
40630652 ATATAAATATATATA
1 ATATAAATAAATATA
40630667 ATCATTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
ATATAAATAAATATAG
Found at i:40645389 original size:84 final size:84
Alignment explanation
Indices: 40645248--40645411 Score: 301
Period size: 84 Copynumber: 2.0 Consensus size: 84
40645238 TGCCACTACA
* *
40645248 AAAAAAAATGCAGCCCAAGCTTTTTTTGAACATATTTCACCAAAACTAAGAATTTGAGAGAGAGA
1 AAAAAAAATGCAGCCCAAGCTTTTCTTGAACATATTTAACCAAAACTAAGAATTTGAGAGAGAGA
*
40645313 GAGAGAGAGAATGAGTAGT
66 GAAAGAGAGAATGAGTAGT
40645332 AAAAAAAATGCAGCCCAAGCTTTTCTTGAACATATTTAACCAAAACTAAGAATTTGAGAGAGAGA
1 AAAAAAAATGCAGCCCAAGCTTTTCTTGAACATATTTAACCAAAACTAAGAATTTGAGAGAGAGA
40645397 GAAAGAGAGAATGAG
66 GAAAGAGAGAATGAG
40645412 CAGTTGAATA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (84 bp):
AAAAAAAATGCAGCCCAAGCTTTTCTTGAACATATTTAACCAAAACTAAGAATTTGAGAGAGAGA
GAAAGAGAGAATGAGTAGT
Found at i:40648508 original size:16 final size:16
Alignment explanation
Indices: 40648487--40648524 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40648477 AATGTTGGTC
*
40648487 TTTTTT-TTACAGTTT
1 TTTTTTATTAAAGTTT
40648502 ATTTTTTATTAAAGTTT
1 -TTTTTTATTAAAGTTT
40648519 TTTTTT
1 TTTTTT
40648525 GTTGTTCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTTTTATTAAAGTTT
Found at i:40650733 original size:24 final size:24
Alignment explanation
Indices: 40650701--40650746 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
40650691 AGTTTAATAA
40650701 CAGAAAGCTCATAAGAGCTTAAAT
1 CAGAAAGCTCATAAGAGCTTAAAT
**
40650725 CAGAAAGCTCATGCGAGCTTAA
1 CAGAAAGCTCATAAGAGCTTAA
40650747 CGGGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (24 bp):
CAGAAAGCTCATAAGAGCTTAAAT
Found at i:40650962 original size:24 final size:23
Alignment explanation
Indices: 40650926--40650980 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
40650916 AAAAACCATG
40650926 TATCAGAAAGCTCAAGAGAGCTTA
1 TATCAGAAAGCTCAAGAGAG-TTA
* * * *
40650950 TATCAGGATGCTCATGTGAGTTA
1 TATCAGAAAGCTCAAGAGAGTTA
40650973 TATCAGAA
1 TATCAGAA
40650981 CGCTTGCGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (23 bp):
TATCAGAAAGCTCAAGAGAGTTA
Found at i:40654854 original size:161 final size:161
Alignment explanation
Indices: 40654666--40654986 Score: 624
Period size: 161 Copynumber: 2.0 Consensus size: 161
40654656 AAAATCATAT
40654666 CTCGAGTTACGAAACTCGAAATCAAGATCCGTAAATTTTTTCTGAATCTAGACTCATATACCTAT
1 CTCGAGTTACGAAACTCGAAATCAAGATCCGTAAATTTTTTCTGAATCTAGACTCATATACCTAT
40654731 CTACTAAATTTTTTCTAGAATTTTTCGTTGGTCCAATTAGTACAGTTTATTAGTTAAAGTTACCC
66 CTACTAAATTTTTTCTAGAATTTTTCGTTGGTCCAATTAGTACAGTTTATTAGTTAAAGTTACCC
*
40654796 CTGTTTCAGGACTCGACTGGTCTGACCTCTG
131 CTGTTTCAGGACTCGACTGATCTGACCTCTG
40654827 CTCGAGTTACGAAACTCGAAATCAAGATCCGTAAATTTTTTCTGAATCTAGACTCATATACCTAT
1 CTCGAGTTACGAAACTCGAAATCAAGATCCGTAAATTTTTTCTGAATCTAGACTCATATACCTAT
40654892 CTACTAAATTTTTTCTAGAATTTTTCGTTGGTCCAATTAGTACAGTTTATTAGTTAAAGTTACCC
66 CTACTAAATTTTTTCTAGAATTTTTCGTTGGTCCAATTAGTACAGTTTATTAGTTAAAGTTACCC
*
40654957 CTGTTTCAGGACTCGACTGATCTGCCCTCT
131 CTGTTTCAGGACTCGACTGATCTGACCTCT
40654987 ATTTACTACG
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 158 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (161 bp):
CTCGAGTTACGAAACTCGAAATCAAGATCCGTAAATTTTTTCTGAATCTAGACTCATATACCTAT
CTACTAAATTTTTTCTAGAATTTTTCGTTGGTCCAATTAGTACAGTTTATTAGTTAAAGTTACCC
CTGTTTCAGGACTCGACTGATCTGACCTCTG
Found at i:40656051 original size:46 final size:46
Alignment explanation
Indices: 40655984--40656155 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
40655974 TGTAACCCGC
*
40655984 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
40656030 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
40656080 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
40656123 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTT
40656156 TGGATGCTCA
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.55
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:40656104 original size:93 final size:93
Alignment explanation
Indices: 40655991--40656162 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
40655981 CGCCCATAAG
* *
40655991 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40656056 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
40656084 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
40656149 ACGAGTTTGGATGC
66 ACGAGTTCGGATGC
40656163 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40656997 original size:71 final size:71
Alignment explanation
Indices: 40656881--40657023 Score: 225
Period size: 71 Copynumber: 2.0 Consensus size: 71
40656871 ATGGGTATTT
* *
40656881 TTCCAAATATGAACCCTAAGTTGAATTATTGTTAGCATAAGCTTAATCGAGCTAACGGGA-TCTT
1 TTCCAAATATAAACCCTAAGTTGAATTATTGCTAGCATAAGCTTAATCGAGCTAACGGGATTC-T
40656945 AAAAACG
65 AAAAACG
* **
40656952 TTCCAAATATAAACCCTAGGTTGAATTATTGCTAGCATAAGCTTAATCGAGCTTCCGGGATTCTA
1 TTCCAAATATAAACCCTAAGTTGAATTATTGCTAGCATAAGCTTAATCGAGCTAACGGGATTCTA
40657017 AAAACG
66 AAAACG
40657023 T
1 T
40657024 AAAGAACATT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 64 0.97
72 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (71 bp):
TTCCAAATATAAACCCTAAGTTGAATTATTGCTAGCATAAGCTTAATCGAGCTAACGGGATTCTA
AAAACG
Found at i:40657748 original size:44 final size:44
Alignment explanation
Indices: 40657676--40657760 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
40657666 ACATGTATCA
* * * *
40657676 CATCCATAATGAACTCGGACCAATTCAACGAGTTCGGATGCTCG
1 CATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTCG
*
40657720 CATCCATAATGAACTCAGACTAACTCAACGAGCTCAGATGC
1 CATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGC
40657761 CTCATATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (44 bp):
CATCCATAATGAACTCAGACCAACTCAACGAGCTCAGATGCTCG
Found at i:40658515 original size:12 final size:12
Alignment explanation
Indices: 40658498--40658522 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40658488 TATTTCACAC
40658498 ATTTACAACTTT
1 ATTTACAACTTT
40658510 ATTTACAACTTT
1 ATTTACAACTTT
40658522 A
1 A
40658523 CAAAATAGCC
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTACAACTTT
Found at i:40661211 original size:45 final size:45
Alignment explanation
Indices: 40661154--40661302 Score: 262
Period size: 45 Copynumber: 3.3 Consensus size: 45
40661144 TCTAATTTAT
40661154 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACATGTCATTTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACATGTCATTTAAA
*
40661199 ATTACAAAGTTTGTTACAAGTTTGTTTCAACACATGTCATTTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACATGTCATTTAAA
* * *
40661244 ATTATAAAGTTTGTTCCAAGTTTCTTTCAACACATGTCATTCAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACATGTCATTTAAA
40661289 ATTACAAAGTTTGT
1 ATTACAAAGTTTGT
40661303 ATTTTTGCAT
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (45 bp):
ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACATGTCATTTAAA
Found at i:40664566 original size:49 final size:49
Alignment explanation
Indices: 40664502--40664933 Score: 549
Period size: 49 Copynumber: 8.7 Consensus size: 49
40664492 CTGGTACGCA
*
40664502 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCAGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACG
* * * *
40664551 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCAGGTACACG
*
40664602 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCAGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACG
* ** * *
40664651 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC-AATTATCAGGTACACG
* * * *
40664701 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCAGGTACACG
* ** *
40664752 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACG
* * * * ** *
40664801 TAGTAGCCTGCACTTAGTACTACACAAGTGATCACAGTTTTCGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAATTATCAGGTACACG
* *
40664852 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACG
40664901 TAGTAGCCTGCACTTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
40664934 TCACAATAGT
Statistics
Matches: 326, Mismatches: 50, Indels: 14
0.84 0.13 0.04
Matches are distributed among these distances:
49 153 0.47
50 56 0.17
51 117 0.36
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACG
Found at i:40664656 original size:100 final size:98
Alignment explanation
Indices: 40664488--40664933 Score: 568
Period size: 100 Copynumber: 4.5 Consensus size: 98
40664478 GTAGCCGAAG
* * * *
40664488 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCAGGTACACGTA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACATA
* *
40664553 GTAGCCTGCACTTAGTACTACACACGTGATCGAA
66 GTAGCCTGCACTTAGTACTACACACGCGA-CCAA
* * * * * *
40664587 GTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCAGGTACACGT
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACAT
*
40664652 AGTAGCCTGCACTTAGTACTACACACGTGACCTAA
65 AGTAGCCTGCACTTAGTACTACACACGCGACC-AA
* * * * *
40664687 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCAGGTACACA
*
40664752 TAGTAGCCTGCACTTAGTACTACACATGCGACCAA
64 TAGTAGCCTGCACTTAGTACTACACACGCGACCAA
* * * * * **
40664787 CAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAAGTGATCACAGTTTTCGGGTATGCA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-C-CAATTATCAGGTACACA
*
40664852 TAGTAGCCTGCACTTAGTACTACACATGCGACCAA
64 TAGTAGCCTGCACTTAGTACTACACACGCGACCAA
* *
40664887 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
40664934 TCACAATAGT
Statistics
Matches: 314, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
98 1 0.00
99 39 0.12
100 230 0.73
101 44 0.14
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (98 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACATA
GTAGCCTGCACTTAGTACTACACACGCGACCAA
Found at i:40666646 original size:70 final size:73
Alignment explanation
Indices: 40666514--40666647 Score: 159
Period size: 70 Copynumber: 1.9 Consensus size: 73
40666504 TAATGGTATT
* * * *
40666514 AAAATATATACATAATAATAGTATTACAAAGTGTACACATAGCATTAAAAATATATACATAATAT
1 AAAATACATACATAATAATAGTATTACAAAGTATACACATAGCATTAAAAATATAGAAATAATAT
40666579 GGCGTTGA
66 GGCGTTGA
** * *
40666587 AAAATACATACATAAT-ATAGTATTA-AAA-TATTTACATAGCATT-TACATATTAGAAATAATA
1 AAAATACATACATAATAATAGTATTACAAAGTATACACATAGCATTAAAAATA-TAGAAATAATA
40666648 ATGTTAAAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
69 4 0.08
70 21 0.40
71 3 0.06
72 9 0.17
73 15 0.29
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (73 bp):
AAAATACATACATAATAATAGTATTACAAAGTATACACATAGCATTAAAAATATAGAAATAATAT
GGCGTTGA
Found at i:40666874 original size:23 final size:23
Alignment explanation
Indices: 40666848--40666918 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 23
40666838 CATAAAGAGT
40666848 ATATATA-TACATATATAATAAAA
1 ATATATACTA-ATATATAATAAAA
*
40666871 ATATATACTAATAT-TTATAAATA
1 ATATATACTAATATATAATAAA-A
* *
40666894 ATA-ATAGTAA-ATATAATAATA
1 ATATATACTAATATATAATAAAA
40666915 ATAT
1 ATAT
40666919 TAAGTATAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 6 0.15
22 17 0.43
23 15 0.38
24 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (23 bp):
ATATATACTAATATATAATAAAA
Found at i:40667133 original size:17 final size:17
Alignment explanation
Indices: 40667097--40667135 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40667087 ACACTAATAT
*
40667097 AATAATAATGATAATCA
1 AATAATAATGAAAATCA
* *
40667114 AATAATAATTAAAATGA
1 AATAATAATGAAAATCA
40667131 AATAA
1 AATAA
40667136 AATAACGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (17 bp):
AATAATAATGAAAATCA
Found at i:40668899 original size:21 final size:21
Alignment explanation
Indices: 40668866--40668909 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
40668856 TCTGATATCC
*
40668866 TCGATCAGTTCCACTGCAACT
1 TCGATCAGCTCCACTGCAACT
* * *
40668887 TCGATTAGCTCCATTGTAACT
1 TCGATCAGCTCCACTGCAACT
40668908 TC
1 TC
40668910 AGGGCTCTGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (21 bp):
TCGATCAGCTCCACTGCAACT
Found at i:40669201 original size:87 final size:85
Alignment explanation
Indices: 40669066--40669851 Score: 530
Period size: 87 Copynumber: 9.0 Consensus size: 85
40669056 AACAGACATT
* * * * **
40669066 AAAAACAGAAATTGAATATAGCTTAGCACGTGAGCCAAGGCTCAACTCATTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAG--CGTG-CCCAAGGCTCAACTCACCTCTCGCAATATGAG
* *
40669131 TTGGTTTTTG-AAACTTAATTTG
63 TTGATTTTTGAAAACTTAAATTG
* ** * *
40669153 AAAAGCAGATTTTGAAAATACCTC-GACATCTGACCCAAGGCTCAACTCACCTCTCGCAATATAA
1 AAAAACAGAAATTGAAAATACCTCAG-C--GTG-CCCAAGGCTCAACTCACCTCTCGCAATATGA
*
40669217 GTTGATTTTTGAAAAATATAAATTG
62 GTTGATTTTTGAAAACT-TAAATTG
40669242 AAAAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGA
1 ---AAAAACAGAAATTGAAAATACCTCAGCGTGCCC-AAGGCTCAACTCACCTCTCGCAATATGA
* *
40669307 GTTGATTTTTGAAAAACATAACTTG
62 GTTGATTTTTG-AAAACTTAAATTG
* ** *
40669332 AAAAACGGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTG-CCCAAGGCTCAACTCACCTCTCGCAATATGAGTT
***
40669397 GATTTTTGAAAAACAGGAATTG
65 GATTTTTG-AAAACTTAAATTG
* ** * * *** * * * * * * *
40669419 ---CA-ATTAACTCAGCGTGCC-C-GAG-GCTCAA--CTCACCTCTCGCAACAT-G-AGT-TGA-
1 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCAAGGCTCAACTCAC-C-TC-TCGCAATATGAG
*
40669471 TT--TTTTTGAAAAATATAAATTG
63 TTGATTTTTGAAAACT-TAAATTG
* *
40669493 AAAGAACAGAAATTGAAAATACCTCAGCATGTGAGCCAAGGCTCAACTAACCTCTCGCAATATGA
1 AAA-AACAGAAATTGAAAATACCTCAGC--GTG-CCCAAGGCTCAACTCACCTCTCGCAATATGA
** *
40669558 GTTGATTTTTGAAAACAGAATTTG
62 GTTGATTTTTGAAAACTTAAATTG
* * ** *
40669582 CAAAAACAG-ATTCTGAAAATACCTCGGCATGTAAACCGAGGCTCAACTCACCTCTCGCAATATG
1 -AAAAACAGAAAT-TGAAAATACCTCAGC--GT-GCCCAAGGCTCAACTCACCTCTCGCAATATG
*
40669646 AGTTGATTTTTTTGAAAAATATAAATTG
61 AGTTGA--TTTTTGAAAACT-TAAATTG
* ** * *
40669674 AAAGAACAGAAATTGAAAATACATCAGCGTGTCCTGAGGCTCAATTCACTTCTCGCAATATGAGT
1 AAA-AACAGAAATTGAAAATACCTCAGCGTG-CCCAAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
40669739 TGCTTTTTGAAAAATATAAATTAA
64 TGATTTTTGAAAACT-TAAATT-G
* * **
40669763 AAAAACAGAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCATTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC--GTG-CCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
40669828 TTGATTTTTG-AAACATAAATTG
63 TTGATTTTTGAAAACTTAAATTG
40669850 AA
1 AA
40669852 TATACCTCAA
Statistics
Matches: 551, Mismatches: 102, Indels: 92
0.74 0.14 0.12
Matches are distributed among these distances:
73 4 0.01
74 11 0.02
76 2 0.00
77 11 0.02
78 4 0.01
79 12 0.02
80 3 0.01
81 3 0.01
82 1 0.00
83 8 0.01
84 3 0.01
85 7 0.01
86 4 0.01
87 147 0.27
88 58 0.11
89 76 0.14
90 132 0.24
91 17 0.03
92 45 0.08
93 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (85 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAACTTAAATTG
Found at i:40669476 original size:73 final size:74
Alignment explanation
Indices: 40669329--40669483 Score: 217
Period size: 72 Copynumber: 2.1 Consensus size: 74
40669319 AAAACATAAC
* * * *
40669329 TTGAAAAACGGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGA
1 TTGAAAAACGGAAATTGAAAATAACTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAACATGA
40669394 GTTGA-TTT
66 GTTGATTTT
* *
40669402 TTGAAAAACAGG-AATTGCAATTAACTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAACATG
1 TTGAAAAAC-GGAAATTGAAAATAACTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAACATG
40669465 AGTTGATTTTT
65 AGTTGA-TTTT
40669476 TTGAAAAA
1 TTGAAAAA
40669484 TATAAATTGA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
72 33 0.45
73 27 0.37
74 13 0.18
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (74 bp):
TTGAAAAACGGAAATTGAAAATAACTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAACATGA
GTTGATTTT
Found at i:40669874 original size:430 final size:423
Alignment explanation
Indices: 40669054--40669938 Score: 1174
Period size: 430 Copynumber: 2.1 Consensus size: 423
40669044 GACTCTTTAA
* * * * * **
40669054 AAAACAG-ACATT-AAAAACAGAAATTGAATATAGCTTAGCACGTGAGCCAAGGCTCAACTCATT
1 AAAACAGAAAATTGAAAAACAGAAATTGAAAATACCTCAGCACGTGAGCCAAGGCTCAACTAACC
* ** * *
40669117 TCTCGCAATATGAGTTGGTTTTTGAAACTTAATTTGAAAAGCAGATTTTGAAAATACCTCGACAT
66 TCTCGCAATATGAGTTGATTTTTGAAACAGAATTTGAAAAACAGATTCTGAAAATACCTCGACAT
* *
40669182 CTGACCCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAATATAAATTGAAAAA
131 CTAAACCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAATATAAATTG-AAAA
*
40669247 AAACAGAAATTGAAAATACCTCAGCGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
195 AAACAGAAATTGAAAATACATCAGCGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * * *
40669312 TTTTTGAAAAACATAACTTGAAAAACGGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACT
260 TTTTTGAAAAACATAAATTAAAAAACAGAAATTGAAAATACCTCAGCGTGGCCTGAGGCTCAACT
* * *
40669377 CACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGGAATTGCAATTAACTCAGCGTGCCCGAGG
325 CACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTGCAATTAACTCAACGTGCCCGAGG
* *
40669442 CTCAACTCACCTCTCGCAACATGAGTTGATTTTTTTG
389 CTCAACTCACCTCTCGCAACATAAGTTGA--TTTCTG
* *
40669479 AAAA-ATATAAATTGAAAGAACAGAAATTGAAAATACCTCAGCATGTGAGCCAAGGCTCAACTAA
1 AAAACAGA-AAATTGAAA-AACAGAAATTGAAAATACCTCAGCACGTGAGCCAAGGCTCAACTAA
40669543 CCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAACAGATTCTGAAAATACCTCG
64 CCTCTCGCAATATGAGTTGATTTTTG-AAACAGAATTTG-AAAAACAGATTCTGAAAATACCTCG
* * * *
40669608 GCATGTAAACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATATAAATT
127 ACATCTAAACCAAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TTTTTGAAAAATATAAATT
* * * * *
40669673 G-AAAGAACAGAAATTGAAAATACATCAGCGTGTCCTGAGGCTCAATTCACTTCTCGCAATATGA
190 GAAAAAAACAGAAATTGAAAATACATCAGCGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGA
* *
40669737 GTTGCTTTTTGAAAAATATAAATTAAAAAAACAGAAATTGAAAATACCTCAGCATGTGAGCC-GA
255 GTTGATTTTTGAAAAACATAAATT-AAAAAACAGAAATTGAAAATACCTCAGC--GTG-GCCTGA
** * *
40669801 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG-AAACATAAATTG-AATATACCTCAACG
316 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGCAAT-TAACTCAACG
** *
40669864 T-CTTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTCTG
380 TGCCCGAGGCTCAACTCACCTCTCGCAACATAAGTTGATTTCTG
*
40669907 AAAACAGAAATTTGAAAAACAGAAATTGAAAA
1 AAAACAGAAAATTGAAAAACAGAAATTGAAAA
40669939 AAATAGAAAT
Statistics
Matches: 400, Mismatches: 46, Indels: 26
0.85 0.10 0.06
Matches are distributed among these distances:
424 1 0.00
425 4 0.01
426 4 0.01
427 18 0.05
428 81 0.20
429 12 0.03
430 174 0.44
431 45 0.11
432 20 0.05
433 39 0.10
434 2 0.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (423 bp):
AAAACAGAAAATTGAAAAACAGAAATTGAAAATACCTCAGCACGTGAGCCAAGGCTCAACTAACC
TCTCGCAATATGAGTTGATTTTTGAAACAGAATTTGAAAAACAGATTCTGAAAATACCTCGACAT
CTAAACCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAAATATAAATTGAAAAA
AACAGAAATTGAAAATACATCAGCGTGCCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGAAAAACATAAATTAAAAAACAGAAATTGAAAATACCTCAGCGTGGCCTGAGGCTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGCAATTAACTCAACGTGCCCGAGGCT
CAACTCACCTCTCGCAACATAAGTTGATTTCTG
Found at i:40669939 original size:14 final size:15
Alignment explanation
Indices: 40669907--40669939 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40669897 TTGATTTCTG
40669907 AAAACAGAAATTTGA
1 AAAACAGAAATTTGA
40669922 AAAACAGAAA-TTGA
1 AAAACAGAAATTTGA
40669936 AAAA
1 AAAA
40669940 AATAGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (15 bp):
AAAACAGAAATTTGA
Found at i:40669946 original size:16 final size:16
Alignment explanation
Indices: 40669907--40669951 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
40669897 TTGATTTCTG
40669907 AAAACAGAAATTTG--A
1 AAAACAGAAA-TTGAAA
40669922 AAAACAGAAATTGAAA
1 AAAACAGAAATTGAAA
*
40669938 AAAATAGAAATTGA
1 AAAACAGAAATTGA
40669952 GATTACCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 14 0.52
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.18
Consensus pattern (16 bp):
AAAACAGAAATTGAAA
Found at i:40670846 original size:44 final size:43
Alignment explanation
Indices: 40670792--40670899 Score: 123
Period size: 43 Copynumber: 2.5 Consensus size: 43
40670782 TCATTAGAAT
* * *
40670792 GCCC-TTTCGGGTTTTCA-TTCTAAT-CTTTTGTGTTAATTAAGAC
1 GCCCTTTTCGGGTTTTCACCT-TAATCCTTTT-TATT-ATCAAGAC
* *
40670835 GCCCTTTTCGGGTCTTCACCTTGATCCTTTTTATTATCAAGAC
1 GCCCTTTTCGGGTTTTCACCTTAATCCTTTTTATTATCAAGAC
40670878 GCCCTTTTCGGGTTTTCACCTT
1 GCCCTTTTCGGGTTTTCACCTT
40670900 GATTCCCCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
43 32 0.57
44 18 0.32
45 6 0.11
ACGTcount: A:0.15, C:0.25, G:0.16, T:0.44
Consensus pattern (43 bp):
GCCCTTTTCGGGTTTTCACCTTAATCCTTTTTATTATCAAGAC
Found at i:40682723 original size:22 final size:22
Alignment explanation
Indices: 40682683--40682744 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
40682673 TAGTATAAAA
40682683 AAAATATA-AC-TAATA-ATATT
1 AAAATATATACATAATATATA-T
40682703 GAAAATATATACATAATATATAT
1 -AAAATATATACATAATATATAT
*
40682726 AAAACATATACGAT-ATATA
1 AAAATATATAC-ATAATATA
40682745 CACATACATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 8 0.22
22 17 0.47
23 8 0.22
24 3 0.08
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (22 bp):
AAAATATATACATAATATATAT
Found at i:40688793 original size:28 final size:29
Alignment explanation
Indices: 40688733--40688843 Score: 102
Period size: 30 Copynumber: 3.8 Consensus size: 29
40688723 AAGCTTGGGA
* * *
40688733 ATTTTGCTTTAGGATTTTTTATTTTTGGG
1 ATTTTGATTTAGGGTTTTTTATTTTTGAG
*
40688762 ATTTTGGA-TTAGGG-TTTTTATTTTTGAT
1 ATTTT-GATTTAGGGTTTTTTATTTTTGAG
*
40688790 ATTTTTATTTAGGGTTTTTTTATTTTTGAG
1 ATTTTGATTTAGGG-TTTTTTATTTTTGAG
* * *
40688820 ATATT-AGTTTAGAGTTTTTGATTT
1 ATTTTGA-TTTAGGGTTTTTTATTT
40688844 GATCACTACT
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
27 1 0.01
28 23 0.34
29 20 0.29
30 24 0.35
ACGTcount: A:0.18, C:0.01, G:0.19, T:0.62
Consensus pattern (29 bp):
ATTTTGATTTAGGGTTTTTTATTTTTGAG
Found at i:40692993 original size:12 final size:12
Alignment explanation
Indices: 40692976--40693000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40692966 GTGGTGAGCT
40692976 GACAAGTACTCA
1 GACAAGTACTCA
40692988 GACAAGTACTCA
1 GACAAGTACTCA
40693000 G
1 G
40693001 TCCCATTGTC
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:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (12 bp):
GACAAGTACTCA
Found at i:40704459 original size:20 final size:21
Alignment explanation
Indices: 40704434--40704478 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
40704424 AAAAATGAAA
40704434 TTTGAAATTTTT-ATAAA-TAT
1 TTTGAAATTTTTGA-AAATTAT
40704454 TTTG-AATTTTTGAAAATTAT
1 TTTGAAATTTTTGAAAATTAT
40704474 TTTGA
1 TTTGA
40704479 TTTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTGAAATTTTTGAAAATTAT
Found at i:40704461 original size:19 final size:20
Alignment explanation
Indices: 40704434--40704483 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
40704424 AAAAATGAAA
40704434 TTTGAAATTTTT-ATAAA-TAT
1 TTTG-AATTTTTGA-AAATTAT
40704454 TTTGAATTTTTGAAAATTAT
1 TTTGAATTTTTGAAAATTAT
40704474 TTTG-ATTTTT
1 TTTGAATTTTT
40704484 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTGAATTTTTGAAAATTAT
Found at i:40709701 original size:17 final size:17
Alignment explanation
Indices: 40709658--40709702 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
40709648 CTACAGTTTA
* * *
40709658 TTGGAAGCTCGATTGGG
1 TTGGAAACTTGATTAGG
40709675 TTGGAAACTTGATTAGG
1 TTGGAAACTTGATTAGG
40709692 TTGGAAACTTG
1 TTGGAAACTTG
40709703 TCGGAGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (17 bp):
TTGGAAACTTGATTAGG
Found at i:40724553 original size:73 final size:73
Alignment explanation
Indices: 40724433--40724579 Score: 195
Period size: 73 Copynumber: 2.0 Consensus size: 73
40724423 TTTTATCATC
* * * * *
40724433 TTAATTCGATTTAAAATTTTTTTGAGTTGAGTTAAACGAGATAAAATTCAAATTGAAGTGAATTG
1 TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
40724498 AATATATT
66 AATATATT
* * ** * *
40724506 TTAATTCGATTTAAATTTTTTTTGAATTCAGTCGAGTGAGATCAAATTTAAATCGAAGCGAATTG
1 TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
40724571 AATATATT
66 AATATATT
40724579 T
1 T
40724580 GTTTGAACTA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.41
Consensus pattern (73 bp):
TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
AATATATT
Found at i:40727590 original size:25 final size:25
Alignment explanation
Indices: 40727513--40727604 Score: 62
Period size: 25 Copynumber: 3.7 Consensus size: 25
40727503 TACACCACAA
* * *
40727513 CTCTCTTGAGCTTTCCAATACTTGG
1 CTCTCTTGAGCTTCCCGATATTTGG
* ***
40727538 CTCT-TATGAGCTTCTCGAT-TAACAG
1 CTCTCT-TGAGCTTCCCGATAT-TTGG
40727563 CTCTCTTGAGCTTCCCGATATTTGG
1 CTCTCTTGAGCTTCCCGATATTTGG
* **
40727588 CTCGCAAGAGCTTCCCG
1 CTCTCTTGAGCTTCCCG
40727605 TTTACATGCT
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
24 1 0.02
25 46 0.94
26 2 0.04
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (25 bp):
CTCTCTTGAGCTTCCCGATATTTGG
Found at i:40729780 original size:42 final size:42
Alignment explanation
Indices: 40729724--40729868 Score: 184
Period size: 42 Copynumber: 3.4 Consensus size: 42
40729714 TTACTAAGAT
40729724 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
1 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
*
40729766 GACCATATTTGGGATATGACATCGATATGAGAATTCGTGTAA
1 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
*** * * * *
40729808 GACCATGGATGGGTTATTGGCATCAATACGAG-ATTACATGTAA
1 GACCATATTTGGGATA-TGGCATCGATATGAGAATT-CGTGTAA
*
40729851 GACCATATCTGGGATATG
1 GACCATATTTGGGATATG
40729869 AAATTGTTAC
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 58 0.66
43 30 0.34
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (42 bp):
GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
Found at i:40743678 original size:40 final size:40
Alignment explanation
Indices: 40743634--40743725 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
40743624 ATCTAATGTT
* *
40743634 CCATTTCATATATCTATTTCCATATAACTGATTCATATCA
1 CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
* * * *
40743674 CCATTTCGTACATTTATTTCTATATAACCGATTCATATAA
1 CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
*
40743714 CTATTTCATATA
1 CCATTTCATATA
40743726 AACACTTCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (40 bp):
CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
Found at i:40743711 original size:13 final size:13
Alignment explanation
Indices: 40743695--40743742 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
40743685 ATTTATTTCT
40743695 ATATAACCGA-TTC
1 ATATAACC-ACTTC
* *
40743708 ATATAACTATTTC
1 ATATAACCACTTC
*
40743721 ATATAAACACTTC
1 ATATAACCACTTC
40743734 ATATAACCA
1 ATATAACCA
40743743 TTTCTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 1 0.03
13 28 0.97
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (13 bp):
ATATAACCACTTC
Found at i:40743726 original size:26 final size:27
Alignment explanation
Indices: 40743688--40743749 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
40743678 TTCGTACATT
*
40743688 TATTTCTATATAACCGA-TTCATATAAC
1 TATTTCTATATAAAC-ACTTCATATAAC
40743715 TATTTC-ATATAAACACTTCATATAAC
1 TATTTCTATATAAACACTTCATATAAC
*
40743741 CATTTCTAT
1 TATTTCTAT
40743750 TTACTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.03
26 22 0.71
27 8 0.26
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (27 bp):
TATTTCTATATAAACACTTCATATAAC
Found at i:40745120 original size:18 final size:18
Alignment explanation
Indices: 40745087--40745139 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
40745077 ATTCACCTAA
*
40745087 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
40745106 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
40745124 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
40745140 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:40745266 original size:18 final size:18
Alignment explanation
Indices: 40745243--40745309 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
40745233 GTAGTGATTC
40745243 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
40745261 AATTCGGTTAATTTGGGT
1 AATTCGGTTAATTCGGGT
*
40745279 AATCCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
40745297 AATTTGGTTAATT
1 AATTCGGTTAATT
40745310 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:40745310 original size:9 final size:9
Alignment explanation
Indices: 40745243--40745309 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
40745233 GTAGTGATTC
40745243 AATTCGGTT
1 AATTCGGTT
*
40745252 AATTCGGGT
1 AATTCGGTT
40745261 AATTCGGTT
1 AATTCGGTT
* *
40745270 AATTTGGGT
1 AATTCGGTT
*
40745279 AATCCGGTT
1 AATTCGGTT
*
40745288 AATTCGGGT
1 AATTCGGTT
*
40745297 AATTTGGTT
1 AATTCGGTT
40745306 AATT
1 AATT
40745310 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:40758716 original size:44 final size:45
Alignment explanation
Indices: 40758663--40758765 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
40758653 TGTCTTTAAC
* * * *
40758663 ATGGACTTACATGAATTATTCTTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
40758707 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
40758753 ATGGACTTACATG
1 ATGGACTTACATG
40758766 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 32 0.64
46 18 0.36
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:40758764 original size:46 final size:44
Alignment explanation
Indices: 40758685--40758770 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
40758675 GAATTATTCT
*
40758685 TGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAATCC
1 TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
*
40758729 TGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
40758771 TTTCTGTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 15 0.39
46 23 0.61
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (44 bp):
TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
Found at i:40761179 original size:32 final size:32
Alignment explanation
Indices: 40761132--40761210 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
40761122 GTTTGCCATT
*
40761132 TGAACTTGTTC-AAAAGTACCTAGTTGGTGCC
1 TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
40761163 T-ACACTTGTCCAAAAAGTACCTAGTTGGTGCT
1 TGA-ACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
40761195 TGAACTTATCCAAAAA
1 TGAACTTGTCCAAAAA
40761211 ATTATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.02
31 8 0.19
32 32 0.76
33 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
Found at i:40770368 original size:21 final size:21
Alignment explanation
Indices: 40770342--40770382 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40770332 AGACGAGCAA
* *
40770342 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
40770363 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
40770383 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:40774266 original size:38 final size:38
Alignment explanation
Indices: 40774222--40774299 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
40774212 AAAAACGAAT
40774222 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
40774260 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
1 AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
40774298 AA
1 AA
40774300 TAAATAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (38 bp):
AAAATTAATATATTCAATTAGAATAATAATAAAAATGA
Found at i:40780281 original size:17 final size:18
Alignment explanation
Indices: 40780247--40780282 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40780237 CAAGTTGTCG
*
40780247 GCCCGTGTGGGCCTACAC
1 GCCCGTGTGGGCCCACAC
40780265 GCCCGTGT-GGCCCACAC
1 GCCCGTGTGGGCCCACAC
40780282 G
1 G
40780283 GCTTAGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.11, C:0.42, G:0.33, T:0.14
Consensus pattern (18 bp):
GCCCGTGTGGGCCCACAC
Found at i:40780560 original size:24 final size:24
Alignment explanation
Indices: 40780505--40780553 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
40780495 TCGACAGCCC
40780505 CACTTTTTAACTTTTCGCCTCTTT
1 CACTTTTTAACTTTTCGCCTCTTT
40780529 CACTTTTTAACTTTTCGCCTCTTT
1 CACTTTTTAACTTTTCGCCTCTTT
40780553 C
1 C
40780554 CATTTTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.31, G:0.04, T:0.53
Consensus pattern (24 bp):
CACTTTTTAACTTTTCGCCTCTTT
Found at i:40812532 original size:18 final size:18
Alignment explanation
Indices: 40812509--40812551 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
40812499 TGATAATGTA
40812509 ACACTTTAAAATTGTATC
1 ACACTTTAAAATTGTATC
40812527 ACACTTTAAAATTGTATC
1 ACACTTTAAAATTGTATC
40812545 ACACTTT
1 ACACTTT
40812552 CACATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (18 bp):
ACACTTTAAAATTGTATC
Found at i:40821208 original size:34 final size:34
Alignment explanation
Indices: 40821172--40821238 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
40821162 TCTATTTCAA
* *
40821172 ATAAAAACATAAAAAGTATCATTTTTATTTAAAAAT
1 ATAAAAAAATAAAAA-T-TCAATTTTATTTAAAAAT
*
40821208 ATAAAAAAATTAAAATTCAATTTTATTTAAA
1 ATAAAAAAATAAAAATTCAATTTTATTTAAA
40821239 TCGAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 14 0.50
35 1 0.04
36 13 0.46
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
ATAAAAAAATAAAAATTCAATTTTATTTAAAAAT
Found at i:40824541 original size:2 final size:2
Alignment explanation
Indices: 40824534--40824566 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40824524 TTTAGACATC
40824534 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
40824567 CACCTGCTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:40827613 original size:3 final size:3
Alignment explanation
Indices: 40827607--40827632 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40827597 ATTGAAAAAT
40827607 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40827633 GGCAAGTAAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40831104 original size:41 final size:40
Alignment explanation
Indices: 40831059--40831196 Score: 195
Period size: 41 Copynumber: 3.4 Consensus size: 40
40831049 GATTCACCGG
* * *
40831059 CACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCATCGA
1 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA-CGA
*
40831100 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCA
1 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACGA
* *
40831140 GCACTTAGTCTGCTAGGTTTATAACCTGATTCAGATCACCGG
1 -CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA-CGA
40831182 CACTTAGCCTGCTAG
1 CACTTAGCCTGCTAG
40831197 ACGTATAGTC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.02
41 84 0.97
42 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (40 bp):
CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACGA
Found at i:40834760 original size:57 final size:58
Alignment explanation
Indices: 40834668--40834776 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
40834658 AATATAGATT
* * * *
40834668 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTT-GGAATGCGACTC
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAG-TTGGGAATGCGACTC
*
40834726 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAACAAGTTGGGAATG
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGTTGGGAATG
40834777 TGAAGTTGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 2 0.04
57 27 0.60
58 16 0.36
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (58 bp):
CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGTTGGGAATGCGACTC
Found at i:40834788 original size:57 final size:57
Alignment explanation
Indices: 40834668--40834799 Score: 144
Period size: 57 Copynumber: 2.3 Consensus size: 57
40834658 AATATAGATT
* * * *
40834668 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTTGGAATGCGACTC
1 CGCGAACT-TTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTTGGAATGCGACTC
* *
40834726 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAACAAG-TTGGGAATGTGAAGT-
1 CGCGAAC-TTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTT-GGAATGCG-ACTC
*
40834783 TGCGAACTTTTTATACT
1 CGCGAACTTTTTATACT
40834800 AGTAGAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 12 0.19
57 34 0.53
58 17 0.27
59 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (57 bp):
CGCGAACTTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTTGGAATGCGACTC
Found at i:40835095 original size:69 final size:69
Alignment explanation
Indices: 40835006--40835506 Score: 439
Period size: 69 Copynumber: 7.3 Consensus size: 69
40834996 TCTTTGCATA
* * * * * * *
40835006 CGAGCCTTAATATGACAGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGC-GACTTTTC
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAG-CTCTTC
*
40835070 GCTTG
65 GCCTG
* * * * ** ** *
40835075 TGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTACTGGAGACTGCGGCTCTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
40835140 CCTG
66 CCTG
* * * *
40835144 CGAGCCATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
40835209 CCTG
66 CCTG
* * * * *
40835213 CAAGCCATAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTAC-GACTCTTC
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAG-CTCTTC
40835277 GCCTG
65 GCCTG
* * * * * * * * * * *
40835282 CAAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
40835347 CCTG
66 CCTG
* * * * ** * *
40835351 CGAGCCTTAGTGTGACAGTTGAGAGCTTTGCTCTAGTTAATTGTGTTGGAGACTGTAGCTCTTCA
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
40835416 CCTG
66 CCTG
* * * * * * * * * *
40835420 TGAGCCTTAGTTTAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGCAGCTTTTCG
1 CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
* *
40835485 CTTA
66 CCTG
* *
40835489 CGAGCTTTAGTATGACAG
1 CGAGCCTTAGTGTGACAG
40835507 AAATGCTAGT
Statistics
Matches: 346, Mismatches: 83, Indels: 6
0.80 0.19 0.01
Matches are distributed among these distances:
68 1 0.00
69 343 0.99
70 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.35
Consensus pattern (69 bp):
CGAGCCTTAGTGTGACAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTCTTCG
CCTG
Found at i:40835224 original size:138 final size:138
Alignment explanation
Indices: 40835006--40835499 Score: 506
Period size: 138 Copynumber: 3.6 Consensus size: 138
40834996 TCTTTGCATA
* * * * * * *
40835006 CGAGCCTTAATATGACAGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGC-GACTTTTC
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAG-CTTTTC
* * **
40835070 GCTTGTGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTACTGGAGACTGCGGCT
65 GCCTGCGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCT
40835135 CTTCGCCTG
130 CTTCGCCTG
* * ** * *
40835144 CGAGCCATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTCG
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
* * * * * ** * *
40835209 CCTGCAAGCCATAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACGACTC
66 CCTGCGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCTC
40835274 TTCGCCTG
131 TTCGCCTG
* * * * *
40835282 CAAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCG
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
* * * **
40835347 CCTGCGAGCCTTAGTGTGACAGTT-GAGAGCTTTGCTCTAGTTAATTGTGTTGGAGACTGTAGCT
66 CCTGCGAGCCTTAGTGTGATAGTTGGA-AGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCT
*
40835411 CTTCACCTG
130 CTTCGCCTG
* * * * * * * * * *
40835420 TGAGCCTTAGTTTAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGCAGCTTTTCG
1 CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
* * *
40835485 CTTACGAGCTTTAGT
66 CCTGCGAGCCTTAGT
40835500 ATGACAGAAA
Statistics
Matches: 286, Mismatches: 68, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
137 1 0.00
138 284 0.99
139 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (138 bp):
CGAGCCTTAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCG
CCTGCGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGTTAACTGTGTTGGAGACTGCGGCTC
TTCGCCTG
Found at i:40835253 original size:207 final size:207
Alignment explanation
Indices: 40835022--40835506 Score: 535
Period size: 207 Copynumber: 2.3 Consensus size: 207
40835012 TTAATATGAC
* * * **
40835022 AGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGCGACTTTTCGCTTGTGAGCCTTAGTG
1 AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTTAGTG
* * * * *
40835087 TGATAGTTG-GAAGCTTTGCTCTCGTTAACTGTACTGGAGA-CTGCGGCTCTTCGCCTGCGAGCC
66 TGACAGCTGAGAA-CTTTGCTCTCGTTAACTAT-CTGGAAAGCTGCAGCTCTTCGCCTGCGAGCC
* ** *
40835150 ATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTCGCCTGCA
129 ATAGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGACTGCAGCTCTTCACCTGCA
*
40835215 AGCCATAGTGTGAT
194 AGCCATAGTGTAAT
* * * * * *
40835229 AGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACGACTCTTCGCCTGCAAGCCTTAGTG
1 AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTTAGTG
* * * * * *
40835294 TGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCGCCTGCGAGCCTT
66 TGACAGCTGAGAACTTTGCTCTCGTTAACTATCTGGAAAGCTGCAGCTCTTCGCCTGCGAGCCAT
* * * * * **
40835359 AGTGTGACAGTTGAGAGCTTTGCTCTAGTTAATTGTGTTGGAGACTGTAGCTCTTCACCTGTGAG
131 AGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGACTGCAGCTCTTCACCTGCAAG
* *
40835424 CCTTAGTTTAAT
196 CCATAGTGTAAT
* * * * * *
40835436 AGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGC-AGCTTTTCGCTTACGAGCTTTAGT
1 AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGA-CTTTTCGCTTGCAAGCCTTAGT
*
40835500 ATGACAG
65 GTGACAG
40835507 AAATGCTAGT
Statistics
Matches: 227, Mismatches: 48, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
206 5 0.02
207 219 0.96
208 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (207 bp):
AGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTTAGTG
TGACAGCTGAGAACTTTGCTCTCGTTAACTATCTGGAAAGCTGCAGCTCTTCGCCTGCGAGCCAT
AGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGACTGCAGCTCTTCACCTGCAAG
CCATAGTGTAAT
Found at i:40836473 original size:22 final size:20
Alignment explanation
Indices: 40836418--40836474 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
40836408 TTTTTTTAAA
* *
40836418 AAAAATTCAATAAAAATATT
1 AAAATTTCAAAAAAAATATT
*
40836438 AAAATTTTATAAAAAAATACTT
1 AAAATTTCA-AAAAAAATA-TT
*
40836460 AGAGATTTCAAAAAA
1 A-AAATTTCAAAAAA
40836475 TTATAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.24
21 8 0.28
22 8 0.28
23 6 0.21
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAATTTCAAAAAAAATATT
Found at i:40837385 original size:5 final size:5
Alignment explanation
Indices: 40837379--40837408 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
40837369 ATATATGGTA
*
40837379 TGATA TGATT TGATT TGATT TGATT TGATT
1 TGATT TGATT TGATT TGATT TGATT TGATT
40837409 AAATATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (5 bp):
TGATT
Found at i:40853206 original size:42 final size:42
Alignment explanation
Indices: 40853152--40853277 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
40853142 AAATATATAC
*
40853152 TCTCAATGTGGATTGAAA-TTTAGTTTAGTTAGCACGGTTGTT
1 TCTCAACGTGGATT-AAATTTTAGTTTAGTTAGCACGGTTGTT
* * * *
40853194 TCTTAACGTGGATTAAATTTTACTTTAGTTGGCACGGTTGAT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
* * *
40853236 TCTCAATGTGGATTAAATTTTAGTTTAGTTAACACGTTTGTT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
40853278 ATTATACTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 3 0.04
42 68 0.96
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (42 bp):
TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
Found at i:40855790 original size:22 final size:24
Alignment explanation
Indices: 40855765--40855808 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
40855755 CATAAAACTG
40855765 TTAAAG-ATTTTA-TGATTTTTCA
1 TTAAAGAATTTTAGTGATTTTTCA
* *
40855787 TTAATGAATTTTAGTTATTTTT
1 TTAAAGAATTTTAGTGATTTTT
40855809 TATGTTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 6 0.33
24 7 0.39
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (24 bp):
TTAAAGAATTTTAGTGATTTTTCA
Found at i:40856326 original size:25 final size:26
Alignment explanation
Indices: 40856293--40856341 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
40856283 TATGTTGTTT
40856293 TGAATTATTTTGA-ATTGAAATGTTGC
1 TGAATTA-TTTGACATTGAAATGTTGC
*
40856319 TGAA-TATTTGACATTGGAATGTT
1 TGAATTATTTGACATTGAAATGTT
40856342 AATTATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (26 bp):
TGAATTATTTGACATTGAAATGTTGC
Found at i:40859130 original size:21 final size:22
Alignment explanation
Indices: 40859106--40859151 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
40859096 TACAATCGTT
40859106 CTGT-GGCAAAGGATGAATTGA
1 CTGTAGGCAAAGGATGAATTGA
*
40859127 CTGTAAATGCAAAGGATGAATTGA
1 CTGT--AGGCAAAGGATGAATTGA
40859151 C
1 C
40859152 AACAAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
24 17 0.81
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (22 bp):
CTGTAGGCAAAGGATGAATTGA
Found at i:40859158 original size:24 final size:24
Alignment explanation
Indices: 40859111--40859158 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40859101 TCGTTCTGTG
***
40859111 GCAAAGGATGAATTGACTGTAAAT
1 GCAAAGGATGAATTGACAACAAAT
40859135 GCAAAGGATGAATTGACAACAAAT
1 GCAAAGGATGAATTGACAACAAAT
40859159 TACCCAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAACAAAT
Found at i:40859313 original size:42 final size:43
Alignment explanation
Indices: 40859254--40859377 Score: 162
Period size: 42 Copynumber: 2.9 Consensus size: 43
40859244 ATGAGTTCCT
* *
40859254 GTTTAACCCTAATGGGTTTTCGTTCAGCTCTTTTGAGC-TTCA
1 GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTTCA
*
40859296 GTTTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTTCA
1 GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTTCA
* * * * *
40859339 -TTCAACCCTTATGGGTTTTTGTTTAGCACTTATGTGCTT
1 GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTT
40859378 CTATTCAGCC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 68 0.94
43 4 0.06
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (43 bp):
GTTTAACCCTTATGGGTTTTCGTTCAGCTCTTATGAGCTTTCA
Found at i:40859330 original size:21 final size:21
Alignment explanation
Indices: 40859249--40859356 Score: 65
Period size: 21 Copynumber: 5.1 Consensus size: 21
40859239 CTCATATGAG
* *
40859249 TTCCTGTTTAACCCTAATGGGT
1 TTCC-GTTCAACCCTTATGGGT
* * * * * *
40859271 TTTCGTTCAGCTCTTTTGAGC
1 TTCCGTTCAACCCTTATGGGT
* *
40859292 TTCAGTTTAACCCTTATGGGT
1 TTCCGTTCAACCCTTATGGGT
* * *
40859313 TTCCGTTCAGCTCTTATGAGCT
1 TTCCGTTCAACCCTTATG-GGT
*
40859335 TT-CATTCAACCCTTATGGGT
1 TTCCGTTCAACCCTTATGGGT
40859355 TT
1 TT
40859357 TTGTTTAGCA
Statistics
Matches: 60, Mismatches: 25, Indels: 4
0.67 0.28 0.04
Matches are distributed among these distances:
20 4 0.07
21 49 0.82
22 7 0.12
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
TTCCGTTCAACCCTTATGGGT
Found at i:40866096 original size:57 final size:60
Alignment explanation
Indices: 40865999--40866146 Score: 196
Period size: 57 Copynumber: 2.5 Consensus size: 60
40865989 ACCCTAATTC
* * * *
40865999 GGATTACCCGTCCGGACTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
*
40866057 -GATCACCTGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
40866118 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
40866147 ACCGTCAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
56 6 0.08
57 43 0.56
60 1 0.01
61 1 0.01
62 20 0.26
63 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Done.