Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 101 of 163
Found at i:28569281 original size:31 final size:30
Alignment explanation
Indices: 28569244--28569403 Score: 91
Period size: 31 Copynumber: 5.4 Consensus size: 30
28569234 AAAAAACTTT
28569244 AGGTACCAAATTAGAAAAAAATGTCAAGTTC
1 AGGTACCAAATTAGAAAAAAATG-CAAGTTC
*** *
28569275 AGGTACCAAATTGAGTCTAAAA---AAGTTT
1 AGGTACCAAATT-AGAAAAAAATGCAAGTTC
* * * *
28569303 AGGTGCCGAATTAGGAAAAAGTGCCAAGTTC
1 AGGTACCAAATTAGAAAAAAATG-CAAGTTC
* * *** *
28569334 AGGTATC-AATTTGGGCAAAA--CAAAGTTT
1 AGGTACCAAATTAGAAAAAAATGC-AAGTTC
28569362 AGGTACCAAATTA-AAAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGAAAAAAA-TG-CAAGTTC
28569393 AGGTACCAAAT
1 AGGTACCAAAT
28569404 GTTATATTAA
Statistics
Matches: 94, Mismatches: 24, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
27 6 0.06
28 30 0.32
29 4 0.04
30 9 0.10
31 38 0.40
32 7 0.07
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (30 bp):
AGGTACCAAATTAGAAAAAAATGCAAGTTC
Found at i:28569315 original size:59 final size:59
Alignment explanation
Indices: 28569220--28569403 Score: 228
Period size: 59 Copynumber: 3.1 Consensus size: 59
28569210 AATTTAAGTG
* *
28569220 CCAAATTGAATCTTAAAAAACTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTA
1 CCAAATTGAGTC-TAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTA
* * * * *
28569280 CCAAATTGAGTCTAAAAAAGTTTAGGTGCCGAATTAGGAAAAAGTGCCAAGTTCAGGTA
1 CCAAATTGAGTCTAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTA
* * * *
28569339 TCAATTTG-GGCAAAACAAAGTTTAGGTACCAAATTA-AAAAAAAGTGTCAAGTTCAGGTA
1 CCAAATTGAGTCTAAA-AAAGTTTAGGTACCAAATTAGAAAAAAA-TGTCAAGTTCAGGTA
28569398 CCAAAT
1 CCAAAT
28569404 GTTATATTAA
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
58 10 0.10
59 83 0.80
60 11 0.11
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (59 bp):
CCAAATTGAGTCTAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTA
Found at i:28578072 original size:27 final size:27
Alignment explanation
Indices: 28578042--28578116 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
28578032 ATTTAAAAAA
*
28578042 TTTAAAATATATAAAATACATATATAT
1 TTTAAAATATATAAAATACATAAATAT
* * *
28578069 TTTATAATATATTAAAATA-TTAAATTT
1 TTTAAAATATA-TAAAATACATAAATAT
28578096 TTTAAAAATATATAAAA-ACAT
1 TTT-AAAATATATAAAATACAT
28578117 TAAACTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.03
27 24 0.62
28 14 0.36
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAAAATATATAAAATACATAAATAT
Found at i:28578125 original size:27 final size:26
Alignment explanation
Indices: 28578045--28578127 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 26
28578035 TAAAAAATTT
*
28578045 AAAATATATAAAATACATATATATTTT-
1 AAAATATATAAAA-ACAT-TAAATTTTA
* * *
28578072 ATAATATATTAAAATATTAAATTTTTTA
1 AAAATATATAAAAACATTAAA--TTTTA
28578100 AAAATATATAAAAACATTAAACTTTTA
1 AAAATATATAAAAACATTAAA-TTTTA
28578127 A
1 A
28578128 CTTTTTCCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
25 3 0.07
26 3 0.07
27 21 0.47
28 18 0.40
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAATATATAAAAACATTAAATTTTA
Found at i:28585380 original size:594 final size:594
Alignment explanation
Indices: 28584252--28585439 Score: 2349
Period size: 594 Copynumber: 2.0 Consensus size: 594
28584242 AAATAATATG
28584252 CTTTTGTGCTTGTTGATGACTAGTCTAGGTTTACTTTAGTTCTTTTTTTTAAATACTAAAGATGA
1 CTTTTGTGCTTGTTGATGACTAGTCTAGGTTTACTTTAGTTCTTTTTTTTAAATACTAAAGATGA
28584317 AGCTTTAGAAAAATTCATCACATTTTCAAAATGAATCAAAATGAAAAGGTTATTCTTTCACTTGT
66 AGCTTTAGAAAAATTCATCACATTTTCAAAATGAATCAAAATGAAAAGGTTATTCTTTCACTTGT
*
28584382 GTTAGAAGTGACCATGGAACCGAATTTCAAATTCTTGGTTATGAAATTTTTTTCAACTTGAATGA
131 GTTAGAAGTGACCATGAAACCGAATTTCAAATTCTTGGTTATGAAATTTTTTTCAACTTGAATGA
28584447 AATTAGCCATAATTTTTCTGCACCTAGAACCCATCAACAAAATGAAGTTGTCAAGAGGAAAAATA
196 AATTAGCCATAATTTTTCTGCACCTAGAACCCATCAACAAAATGAAGTTGTCAAGAGGAAAAATA
28584512 AAACTTAAAAAAAAACGACTAGAACCAGGCATTGTAAAAATAATTTGCCAAAATATTTTTGGACG
261 AAACTTAAAAAAAAACGACTAGAACCAGGCATTGTAAAAATAATTTGCCAAAATATTTTTGGACG
28584577 GAAGCCACAAACACCTCATGCTATATTGTTAAAAGAGTGATGATTTATTGTTAAGAAAAATCCAT
326 GAAGCCACAAACACCTCATGCTATATTGTTAAAAGAGTGATGATTTATTGTTAAGAAAAATCCAT
28584642 AAGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTATTTTCATCCTTCTAGATGCAAGTGTTTT
391 AAGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTATTTTCATCCTTCTAGATGCAAGTGTTTT
28584707 GTTTAAATAATGGGCAAGGCAATATTTGTAAATTTGATGCAAAAAGTGATGAAGGAAATTTTCTT
456 GTTTAAATAATGGGCAAGGCAATATTTGTAAATTTGATGCAAAAAGTGATGAAGGAAATTTTCTT
28584772 GGTTACCTTTTAAAATCTAAAGCTTTTTGAGTGTGGGATAAATGACTTACCGGGTATAGGGTGTT
521 GGTTACCTTTTAAAATCTAAAGCTTTTTGAGTGTGGGATAAATGACTTACCGGGTATAGGGTGTT
28584837 ACACTTTAC
586 ACACTTTAC
28584846 CTTTTGTGCTTGTTGATGACTAGTCTAGGTTTACTTTAGTTCTTTTTTTTAAATACTAAAGATGA
1 CTTTTGTGCTTGTTGATGACTAGTCTAGGTTTACTTTAGTTCTTTTTTTTAAATACTAAAGATGA
28584911 AGCTTTAGAAAAATTCATCACATTTTCAAAATGAATCAAAATGAAAAGGTTATTCTTTCACTTGT
66 AGCTTTAGAAAAATTCATCACATTTTCAAAATGAATCAAAATGAAAAGGTTATTCTTTCACTTGT
28584976 GTTAGAAGTGACCATGAAACCGAATTTCAAATTCTTGGTTATGAAATTTTTTTCAACTTGAATGA
131 GTTAGAAGTGACCATGAAACCGAATTTCAAATTCTTGGTTATGAAATTTTTTTCAACTTGAATGA
28585041 AATTAGCCATAATTTTTCTGCACCTAGAACCCATCAACAAAATGAAGTTGTCAAGAGGAAAAATA
196 AATTAGCCATAATTTTTCTGCACCTAGAACCCATCAACAAAATGAAGTTGTCAAGAGGAAAAATA
*
28585106 AAACTTAAAAAAAAACGACTAGAACCAGGCATTGTAAAAATAATTTGCCAAAATATTTTTGGATG
261 AAACTTAAAAAAAAACGACTAGAACCAGGCATTGTAAAAATAATTTGCCAAAATATTTTTGGACG
28585171 GAAGCCACAAACACCTCATGCTATATTGTTAAAAGAGTGATGATTTATTGTTAAGAAAAATCCAT
326 GAAGCCACAAACACCTCATGCTATATTGTTAAAAGAGTGATGATTTATTGTTAAGAAAAATCCAT
*
28585236 ACGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTATTTTCATCCTTCTAGATGCAAGTGTTTT
391 AAGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTATTTTCATCCTTCTAGATGCAAGTGTTTT
28585301 GTTTAAATAATGGGCAAGGCAATATTTGTAAATTTGATGCAAAAAGTGATGAAGGAAATTTTCTT
456 GTTTAAATAATGGGCAAGGCAATATTTGTAAATTTGATGCAAAAAGTGATGAAGGAAATTTTCTT
28585366 GGTTACCTTTTAAAATCTAAAGCTTTTTGAGTGTGGGATAAATGACTTACCGGGTATAGGGTGTT
521 GGTTACCTTTTAAAATCTAAAGCTTTTTGAGTGTGGGATAAATGACTTACCGGGTATAGGGTGTT
28585431 ACACTTTAC
586 ACACTTTAC
28585440 TTCACTCAAA
Statistics
Matches: 591, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
594 591 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (594 bp):
CTTTTGTGCTTGTTGATGACTAGTCTAGGTTTACTTTAGTTCTTTTTTTTAAATACTAAAGATGA
AGCTTTAGAAAAATTCATCACATTTTCAAAATGAATCAAAATGAAAAGGTTATTCTTTCACTTGT
GTTAGAAGTGACCATGAAACCGAATTTCAAATTCTTGGTTATGAAATTTTTTTCAACTTGAATGA
AATTAGCCATAATTTTTCTGCACCTAGAACCCATCAACAAAATGAAGTTGTCAAGAGGAAAAATA
AAACTTAAAAAAAAACGACTAGAACCAGGCATTGTAAAAATAATTTGCCAAAATATTTTTGGACG
GAAGCCACAAACACCTCATGCTATATTGTTAAAAGAGTGATGATTTATTGTTAAGAAAAATCCAT
AAGAACTTTTCAAAAATAAAAAGCCTAACATTAGTTATTTTCATCCTTCTAGATGCAAGTGTTTT
GTTTAAATAATGGGCAAGGCAATATTTGTAAATTTGATGCAAAAAGTGATGAAGGAAATTTTCTT
GGTTACCTTTTAAAATCTAAAGCTTTTTGAGTGTGGGATAAATGACTTACCGGGTATAGGGTGTT
ACACTTTAC
Found at i:28586258 original size:15 final size:15
Alignment explanation
Indices: 28586238--28586266 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28586228 CAATAGTGAA
28586238 TATAGTAGTTAGTTG
1 TATAGTAGTTAGTTG
28586253 TATAGTAGTTAGTT
1 TATAGTAGTTAGTT
28586267 AGTTGTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (15 bp):
TATAGTAGTTAGTTG
Found at i:28587971 original size:237 final size:237
Alignment explanation
Indices: 28587587--28588063 Score: 954
Period size: 237 Copynumber: 2.0 Consensus size: 237
28587577 TATCCTAATT
28587587 TTTATTTTATTTTGCAAGATCCCTTCAATAGAAGGATGAAGGGGATTGGTAAACAAGTTGGAGGT
1 TTTATTTTATTTTGCAAGATCCCTTCAATAGAAGGATGAAGGGGATTGGTAAACAAGTTGGAGGT
28587652 CTTTATATTTTTGTGTCACCAGTTTCTGATTCTGGTTTGTTTTTTGCTTTTAGTTTTGATTCTTA
66 CTTTATATTTTTGTGTCACCAGTTTCTGATTCTGGTTTGTTTTTTGCTTTTAGTTTTGATTCTTA
28587717 GCCTGATTTGATTCGTGTTGTATGTCCTCTTTAAGTTCTACAAATACAGATGTCTAGCATGCTCG
131 GCCTGATTTGATTCGTGTTGTATGTCCTCTTTAAGTTCTACAAATACAGATGTCTAGCATGCTCG
28587782 ACTTGGACAAGCTTCACTTACTCAAATGAATAAAATTTCAAG
196 ACTTGGACAAGCTTCACTTACTCAAATGAATAAAATTTCAAG
28587824 TTTATTTTATTTTGCAAGATCCCTTCAATAGAAGGATGAAGGGGATTGGTAAACAAGTTGGAGGT
1 TTTATTTTATTTTGCAAGATCCCTTCAATAGAAGGATGAAGGGGATTGGTAAACAAGTTGGAGGT
28587889 CTTTATATTTTTGTGTCACCAGTTTCTGATTCTGGTTTGTTTTTTGCTTTTAGTTTTGATTCTTA
66 CTTTATATTTTTGTGTCACCAGTTTCTGATTCTGGTTTGTTTTTTGCTTTTAGTTTTGATTCTTA
28587954 GCCTGATTTGATTCGTGTTGTATGTCCTCTTTAAGTTCTACAAATACAGATGTCTAGCATGCTCG
131 GCCTGATTTGATTCGTGTTGTATGTCCTCTTTAAGTTCTACAAATACAGATGTCTAGCATGCTCG
28588019 ACTTGGACAAGCTTCACTTACTCAAATGAATAAAATTTCAAG
196 ACTTGGACAAGCTTCACTTACTCAAATGAATAAAATTTCAAG
28588061 TTT
1 TTT
28588064 TCCTTTTACT
Statistics
Matches: 240, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 240 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (237 bp):
TTTATTTTATTTTGCAAGATCCCTTCAATAGAAGGATGAAGGGGATTGGTAAACAAGTTGGAGGT
CTTTATATTTTTGTGTCACCAGTTTCTGATTCTGGTTTGTTTTTTGCTTTTAGTTTTGATTCTTA
GCCTGATTTGATTCGTGTTGTATGTCCTCTTTAAGTTCTACAAATACAGATGTCTAGCATGCTCG
ACTTGGACAAGCTTCACTTACTCAAATGAATAAAATTTCAAG
Found at i:28591219 original size:25 final size:25
Alignment explanation
Indices: 28591187--28591269 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
28591177 AGGGTATACT
* *
28591187 TGGTTGTGTTCGGAGGTTATAGATA
1 TGGTTGTGTTCAGAGGTTATACATA
* *
28591212 TGGTTGTGTTCAAAGG--GTACATA
1 TGGTTGTGTTCAGAGGTTATACATA
* *
28591235 TGGTTGTGTTTAGAGGTTATATATA
1 TGGTTGTGTTCAGAGGTTATACATA
28591260 TGGTTGTGTT
1 TGGTTGTGTT
28591270 TTGAGGGTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.40
25 29 0.60
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.43
Consensus pattern (25 bp):
TGGTTGTGTTCAGAGGTTATACATA
Found at i:28591219 original size:48 final size:47
Alignment explanation
Indices: 28591164--28591341 Score: 164
Period size: 48 Copynumber: 3.7 Consensus size: 47
28591154 AAGGGTATAT
*
28591164 TGGTTGTGTTTGAAGGGTATACTTGGTTGTGTTCGGAGGTTATAGATA
1 TGGTTGTGTTTGAAGGGTATA-TTGGTTGTGTTTGGAGGTTATAGATA
** * * *
28591212 TGGTTGTGTTCAAAGGGTACATATGGTTGTGTTTAGAGGTTATATATA
1 TGGTTGTGTTTGAAGGGTATAT-TGGTTGTGTTTGGAGGTTATAGATA
* * *
28591260 TGGTTGTGTTTTG-AGGGTATATTTTGTTGTGTTTGGAGG--GTACATA
1 TGGTTGTG-TTTGAAGGGTATA-TTGGTTGTGTTTGGAGGTTATAGATA
* * * * *
28591306 AGGTTATGTTTGGAGGTTATGATTGATTGTGTTTGG
1 TGGTTGTGTTTGAAGGGTAT-ATTGGTTGTGTTTGG
28591342 TGGGTGATAG
Statistics
Matches: 107, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
45 4 0.04
46 29 0.27
47 2 0.02
48 69 0.64
49 3 0.03
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (47 bp):
TGGTTGTGTTTGAAGGGTATATTGGTTGTGTTTGGAGGTTATAGATA
Found at i:28591280 original size:21 final size:22
Alignment explanation
Indices: 28591147--28591346 Score: 132
Period size: 23 Copynumber: 8.6 Consensus size: 22
28591137 TTTAAGTGGA
*
28591147 TGTG-TTGAAGGGTATATTGGT
1 TGTGTTTGGAGGGTATATTGGT
*
28591168 TGTGTTTGAAGGGTATACTTGGT
1 TGTGTTTGGAGGGTATA-TTGGT
* *
28591191 TGTGTTCGGAGGTTATAGATATGGT
1 TGTGTTTGGAGGGTAT--AT-TGGT
*** *
28591216 TGTGTTCAAAGGGTACATATGGT
1 TGTGTTTGGAGGGTATAT-TGGT
* *
28591239 TGTGTTTAGAGGTTATATATATGGT
1 TGTGTTTGGAGG--GTATAT-TGGT
* *
28591264 TGTGTTTTGAGGGTATATTTTGT
1 TGTGTTTGGAGGGTATA-TTGGT
* *
28591287 TGTGTTTGGAGGGTACATAAGGT
1 TGTGTTTGGAGGGTATAT-TGGT
* * *
28591310 TATGTTTGGAGGTTATGATTGAT
1 TGTGTTTGGAGGGTAT-ATTGGT
*
28591333 TGTGTTTGGTGGGT
1 TGTGTTTGGAGGGT
28591347 GATAGTTTTA
Statistics
Matches: 143, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
21 4 0.03
22 13 0.09
23 85 0.59
24 4 0.03
25 37 0.26
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.44
Consensus pattern (22 bp):
TGTGTTTGGAGGGTATATTGGT
Found at i:28597776 original size:23 final size:25
Alignment explanation
Indices: 28597727--28597776 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
28597717 GTCAAGAGTA
*
28597727 AAAATTGTCAGTGCAAATGTAATAT
1 AAAATTGTCAGAGCAAATGTAATAT
28597752 AAAA-TGTCAGAGCAAAT-TAATAT
1 AAAATTGTCAGAGCAAATGTAATAT
28597775 AA
1 AA
28597777 GATGAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.33
24 12 0.50
25 4 0.17
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (25 bp):
AAAATTGTCAGAGCAAATGTAATAT
Found at i:28600415 original size:3 final size:3
Alignment explanation
Indices: 28600407--28600464 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
28600397 CGGGGCAACA
* * * *
28600407 TCT TCT TCT TTT TCT TCCT TC- TCT TCT TCT TTT TCT TCAT TTT TTT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TC-T TCT TCT
28600453 TCT TCT TCT TCT
1 TCT TCT TCT TCT
28600465 GCCTCAATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:28603076 original size:56 final size:56
Alignment explanation
Indices: 28602990--28603097 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
28602980 CTTATTAATG
* *
28602990 CTCGAGATGTTTCTAATCGTGTAAGGATATATGTGTAAAAGAACTTTAACACCATC
1 CTCGAGATGTTCCGAATCGTGTAAGGATATATGTGTAAAAGAACTTTAACACCATC
* *
28603046 CTCGAGGTGTTCCGAATCGTGTAAGGATATATGTGTGAAAGAACTTTAACAC
1 CTCGAGATGTTCCGAATCGTGTAAGGATATATGTGTAAAAGAACTTTAACAC
28603098 TGTCCAAGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (56 bp):
CTCGAGATGTTCCGAATCGTGTAAGGATATATGTGTAAAAGAACTTTAACACCATC
Found at i:28615832 original size:183 final size:183
Alignment explanation
Indices: 28615522--28615889 Score: 682
Period size: 183 Copynumber: 2.0 Consensus size: 183
28615512 AATGAAACCC
*
28615522 AGTCGAAGTCTCCGCATCGATACAAAATTTCATCGGGAACAAACCAAGATGCTTGCCATTCTAAG
1 AGTCGAAGTCTCCGCATCGATACAAAATTTCATCGGGAACAAACCAAGATGCTCGCCATTCTAAG
* *
28615587 TCTTCGTCTCGGAGACTTTAGAGTATTGCCATCCATTTTTCTTCTGAAAAGTTTTCTTGTCTTTG
66 TCTTCGTCTCGGAGACTTTAGAGTATTGCCATCCATTTTTCTTCTGAAAAGTTTTATTGTCTTTA
28615652 CGTGGCTAAAAACTCTTTCAAATGAGAGTAATCCTTAGACAAGTACTGATAGG
131 CGTGGCTAAAAACTCTTTCAAATGAGAGTAATCCTTAGACAAGTACTGATAGG
*
28615705 AGTCGAAGTCTCCGCATCGATACAAAATTTCATCGGGACCAAACCAAGATGCTCGCCATTCTAAG
1 AGTCGAAGTCTCCGCATCGATACAAAATTTCATCGGGAACAAACCAAGATGCTCGCCATTCTAAG
* *
28615770 TCTTCGTCTCGGAGACTTTGGAGTATTTCCATCCATTTTTCTTCTGAAAAGTTTTATTGTCTTTA
66 TCTTCGTCTCGGAGACTTTAGAGTATTGCCATCCATTTTTCTTCTGAAAAGTTTTATTGTCTTTA
28615835 CGTGGCTAAAAACTCTTTCAAATGAGAGTAATCCTTAGACAAGTACTGATAGG
131 CGTGGCTAAAAACTCTTTCAAATGAGAGTAATCCTTAGACAAGTACTGATAGG
28615888 AG
1 AG
28615890 ACTTTTTCTG
Statistics
Matches: 179, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 179 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (183 bp):
AGTCGAAGTCTCCGCATCGATACAAAATTTCATCGGGAACAAACCAAGATGCTCGCCATTCTAAG
TCTTCGTCTCGGAGACTTTAGAGTATTGCCATCCATTTTTCTTCTGAAAAGTTTTATTGTCTTTA
CGTGGCTAAAAACTCTTTCAAATGAGAGTAATCCTTAGACAAGTACTGATAGG
Found at i:28617965 original size:94 final size:96
Alignment explanation
Indices: 28617794--28617983 Score: 253
Period size: 94 Copynumber: 2.0 Consensus size: 96
28617784 AACCTTGGAA
* * *
28617794 AAGGGTATTTGATTATCCCGATTTAAAAAAAAGTCGCGCTTAGTAAGTTAAGACACAAATTTCAA
1 AAGGGTATTCGATTATCCCGATTGAAAAAAAAGTCGCGCCTAGTAAGTTAAGACACAAATTTCAA
*
28617859 AACCAGATATAAAGAAACATTGCCTC-ATTT
66 AACCAGAAATAAAGAAACATTGCCTCGATTT
* * *
28617889 AAGGGTATTCGA-TATCCCGGTTGAAGAAAAA-TCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTGAAAAAAAAGTCGCGCCTAGTAAGTTAAGACACAAA-TTTCA
* *
28617952 AAACCCA-AAATAAAGGAATATTGCCTCGATTT
65 AAA-CCAGAAATAAAGAAACATTGCCTCGATTT
28617984 TAAATATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
93 24 0.29
94 41 0.49
95 18 0.22
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (96 bp):
AAGGGTATTCGATTATCCCGATTGAAAAAAAAGTCGCGCCTAGTAAGTTAAGACACAAATTTCAA
AACCAGAAATAAAGAAACATTGCCTCGATTT
Found at i:28618172 original size:18 final size:17
Alignment explanation
Indices: 28618116--28618173 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 17
28618106 AATATGAGAA
28618116 AAAAT-AAAATACAATTT
1 AAAATCAAAATA-AATTT
*
28618133 ATAAATCAAAATAAATGAT
1 A-AAATCAAAATAAAT-TT
*
28618152 AAAATACAAAATTAATTT
1 AAAAT-CAAAATAAATTT
28618170 AAAA
1 AAAA
28618174 AATTAAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 1 0.03
18 16 0.47
19 17 0.50
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (17 bp):
AAAATCAAAATAAATTT
Found at i:28618360 original size:29 final size:28
Alignment explanation
Indices: 28618311--28618715 Score: 143
Period size: 29 Copynumber: 13.8 Consensus size: 28
28618301 TTGGGGAAGA
* * *
28618311 TTCG-GGGTAAAAACATTATTTTGAAAG
1 TTCGAGGGAAAAAATATAATTTTGAAAG
* *
28618338 TTCGAGGGTAAAAAATATCATTTCTAAAAG
1 TTCGAGGG-AAAAAATATAATTT-TGAAAG
* ** * *
28618368 ATCG-GGGGCAAAATGTAATTTTGGAAG
1 TTCGAGGGAAAAAATATAATTTTGAAAG
*
28618395 TTTGAGGGAAAAAATATAAATTTTGAAAG
1 TTCGAGGGAAAAAATAT-AATTTTGAAAG
* * *
28618424 TTCAAGGGCAAAAATAGAATTTTGGAAAG
1 TTCGAGGGAAAAAATATAATTTT-GAAAG
* ** *
28618453 TTTGAGGGGTTAAAATGTAATTTTTGATAAG
1 TTCGA-GGGAAAAAATATAA-TTTTGA-AAG
* ** * *
28618484 TT-TAGGGGTTAAAATGTAAATTTTGGAAG
1 TTCGA-GGGAAAAAATAT-AATTTTGAAAG
* ***
28618513 TT-TAGGTTTAAAATATAATTTTTGGAAAG
1 TTCGAGGGAAAAAATATAA-TTTT-GAAAG
* * **
28618542 TTTGGGGGTTTAAAATATAATTTTGAGAAG
1 TTCGAGGG-AAAAAATATAATTTTGA-AAG
* ** *
28618572 TTTGAGGGTCAAAATGTAATTTTTAGAAAG
1 TTCGAGGGAAAAAATATAA-TTTT-GAAAG
* * ** *
28618602 TTTAGGGGGGTTAAAATACAATTTTTGGAAAG
1 -TT-CGAGGGAAAAAATATAA-TTTT-GAAAG
* ** *
28618634 TTCAAGGGTTAAAATATATTTTTGGAAAG
1 TTCGAGGGAAAAAATATAATTTT-GAAAG
**
28618663 TTCGAGGGTTAAAATATAATTTTTGAAAAG
1 TTCGAGGGAAAAAATATAA-TTTTG-AAAG
* **
28618693 TTTGAGGGTCAAAATATAATTTT
1 TTCGAGGGAAAAAATATAATTTT
28618716 TAAAAAAGTT
Statistics
Matches: 304, Mismatches: 53, Indels: 40
0.77 0.13 0.10
Matches are distributed among these distances:
27 12 0.04
28 42 0.14
29 101 0.33
30 99 0.33
31 28 0.09
32 22 0.07
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (28 bp):
TTCGAGGGAAAAAATATAATTTTGAAAG
Found at i:28618475 original size:30 final size:29
Alignment explanation
Indices: 28618377--28618715 Score: 303
Period size: 30 Copynumber: 11.4 Consensus size: 29
28618367 GATCGGGGGC
* **
28618377 AAAATGTAATTTTGG-AAGTTTGAGGGAA
1 AAAATATAATTTTGGAAAGTTTGAGGGTT
** **
28618405 AAAATATAAATTTT-GAAAGTTCAAGGGCA
1 AAAATAT-AATTTTGGAAAGTTTGAGGGTT
*
28618434 AAAATAGAATTTTGGAAAGTTTGAGGGGTT
1 AAAATATAATTTTGGAAAGTTTGA-GGGTT
* *
28618464 AAAATGTAATTTTTGATAAGTTT-AGGGGTT
1 AAAATATAATTTTGGA-AAGTTTGA-GGGTT
* *
28618494 AAAATGTAAATTTTGG-AAGTTT-AGGTTT
1 AAAATAT-AATTTTGGAAAGTTTGAGGGTT
*
28618522 AAAATATAATTTTTGGAAAGTTTGGGGGTTT
1 AAAATATAA-TTTTGGAAAGTTTGAGGG-TT
*
28618553 AAAATATAATTTT-GAGAAGTTTGAGGGTC
1 AAAATATAATTTTGGA-AAGTTTGAGGGTT
* * *
28618582 AAAATGTAATTTTTAGAAAGTTTAGGGGGGTT
1 AAAATATAA-TTTTGGAAAGTTT--GAGGGTT
* **
28618614 AAAATACAATTTTTGGAAAGTTCAAGGGTT
1 AAAATATAA-TTTTGGAAAGTTTGAGGGTT
* *
28618644 AAAATATATTTTTGGAAAGTTCGAGGGTT
1 AAAATATAATTTTGGAAAGTTTGAGGGTT
* *
28618673 AAAATATAATTTTTGAAAAGTTTGAGGGTC
1 AAAATATAA-TTTTGGAAAGTTTGAGGGTT
28618703 AAAATATAATTTT
1 AAAATATAATTTT
28618716 TAAAAAAGTT
Statistics
Matches: 260, Mismatches: 35, Indels: 31
0.80 0.11 0.10
Matches are distributed among these distances:
27 2 0.01
28 29 0.11
29 85 0.33
30 94 0.36
31 26 0.10
32 24 0.09
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATATAATTTTGGAAAGTTTGAGGGTT
Found at i:28618693 original size:59 final size:59
Alignment explanation
Indices: 28618405--28618742 Score: 269
Period size: 59 Copynumber: 5.7 Consensus size: 59
28618395 TTTGAGGGAA
* * ** * * *
28618405 AAAATATAAATTTTGAAAGTTCAAGGGCAAAAATAGAA-TTTTGGAAAGTTTGAGGGGTT
1 AAAATATAATTTTTGAAAGTTCGAGGGTTAAAATATAATTTTTGAAAAGTTT-AAGGGTT
* * * * * *
28618464 AAAATGTAATTTTTGATAAGTT-TAGGGGTTAAAATGTAAATTTTG-GAAGTTT-AGGTTT
1 AAAATATAATTTTTGA-AAGTTCGA-GGGTTAAAATATAATTTTTGAAAAGTTTAAGGGTT
* * * * *
28618522 AAAATATAATTTTTGGAAAGTTTGGGGGTTTAAAATATAA-TTTTGAGAAGTTTGAGGGTC
1 AAAATATAATTTTT-GAAAGTTCGAGGG-TTAAAATATAATTTTTGAAAAGTTTAAGGGTT
* * * * * *
28618582 AAAATGTAATTTTTAGAAAGTTTAGGGGGGTTAAAATACAATTTTTGGAAAGTTCAAGGGTT
1 AAAATATAATTTTT-GAAAG-TT-CGAGGGTTAAAATATAATTTTTGAAAAGTTTAAGGGTT
* *
28618644 AAAATAT-ATTTTTGGAAAGTTCGAGGGTTAAAATATAATTTTTGAAAAGTTTGAGGGTC
1 AAAATATAATTTTT-GAAAGTTCGAGGGTTAAAATATAATTTTTGAAAAGTTTAAGGGTT
*
28618703 AAAATATAATTTTTAAAAAAGTTC-AGAGGTT-AAATATAAT
1 AAAATATAATTTTT--GAAAGTTCGAG-GGTTAAAATATAAT
28618743 ATAATTTTGG
Statistics
Matches: 229, Mismatches: 36, Indels: 27
0.78 0.12 0.09
Matches are distributed among these distances:
58 30 0.13
59 72 0.31
60 62 0.27
61 39 0.17
62 26 0.11
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (59 bp):
AAAATATAATTTTTGAAAGTTCGAGGGTTAAAATATAATTTTTGAAAAGTTTAAGGGTT
Found at i:28620549 original size:17 final size:17
Alignment explanation
Indices: 28620529--28620606 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
28620519 ACTTAAATTT
28620529 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
*
28620546 TAAATTTAAACTCAAAAA
1 TAAATTTAAATTC-AAAA
* *
28620564 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
*
28620581 TAAAATTAAACTT-AAAA
1 TAAATTTAAA-TTCAAAA
28620598 T-AATTTAAA
1 TAAATTTAAA
28620607 AATTTAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
16 7 0.13
17 29 0.56
18 16 0.31
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:28620581 original size:35 final size:33
Alignment explanation
Indices: 28620531--28620616 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 33
28620521 TTAAATTTTA
* *
28620531 AATTTAAATTCAAAATAAATTTAAACTCAAAAAT
1 AATTTAAATTTAAAATAAAATTAAACT-AAAAAT
*
28620565 AAGTTTAAATTTAAAATAAAATTAAACTTAAAAT
1 AA-TTTAAATTTAAAATAAAATTAAACTAAAAAT
28620599 AATTTAAAAATTTAAAAT
1 AATTT--AAATTTAAAAT
28620617 TTCAAAATTG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
33 3 0.07
34 9 0.20
35 34 0.74
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (33 bp):
AATTTAAATTTAAAATAAAATTAAACTAAAAAT
Found at i:28621044 original size:17 final size:18
Alignment explanation
Indices: 28621010--28621057 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28621000 TTTATTTTTT
*
28621010 AATATTAAAAAATTTAAA
1 AATATTAAAAAATATAAA
28621028 AATATTAAAAAA-ATAAA
1 AATATTAAAAAATATAAA
*
28621045 ATTAATTAAAAAA
1 AAT-ATTAAAAAA
28621058 GCCAGTATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATTAAAAAATATAAA
Found at i:28624298 original size:27 final size:27
Alignment explanation
Indices: 28624268--28624329 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28624258 CGTTCCAGAG
* * *
28624268 TGGTCAGGCGATAGGA-ATCATACGGGT
1 TGGTCAGGCGAT-GCATATAATACGAGT
28624295 TGGTCAGGCGATGCATATAATACGAGT
1 TGGTCAGGCGATGCATATAATACGAGT
28624322 TGGTCAGG
1 TGGTCAGG
28624330 GCACGAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (27 bp):
TGGTCAGGCGATGCATATAATACGAGT
Found at i:28624894 original size:14 final size:13
Alignment explanation
Indices: 28624870--28624919 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
28624860 GGAGTTGTAA
28624870 TAAACCTTAAACTC
1 TAAA-CTTAAACTC
*
28624884 TAAACTCTAAACTA
1 TAAACT-TAAACTC
*
28624898 TAAACATTAAACCC
1 TAAAC-TTAAACTC
28624912 TAAACTTA
1 TAAACTTA
28624920 TTTACGTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 5 0.16
14 25 0.81
15 1 0.03
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAACTTAAACTC
Found at i:28624894 original size:21 final size:22
Alignment explanation
Indices: 28624870--28624916 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
28624860 GGAGTTGTAA
*
28624870 TAAACCT-TAAAC-TCTAAACTC
1 TAAACCTATAAACAT-TAAACCC
28624891 TAAA-CTATAAACATTAAACCC
1 TAAACCTATAAACATTAAACCC
28624912 TAAAC
1 TAAAC
28624917 TTATTTACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 2 0.09
21 19 0.86
22 1 0.05
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAACCTATAAACATTAAACCC
Found at i:28625013 original size:15 final size:14
Alignment explanation
Indices: 28624987--28625035 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
28624977 AACTTAAATC
28624987 CTCAAAACCTTAAA
1 CTCAAAACCTTAAA
28625001 CTCAAAACTCTTAAAA
1 CTCAAAAC-CTT-AAA
* *
28625017 ATCTAAAACCCTAAA
1 CTC-AAAACCTTAAA
28625032 CTCA
1 CTCA
28625036 TCACTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.31
15 8 0.28
16 7 0.24
17 5 0.17
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (14 bp):
CTCAAAACCTTAAA
Found at i:28625127 original size:26 final size:26
Alignment explanation
Indices: 28625080--28625163 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
28625070 CTAAACCATG
* ** *
28625080 AATACAAACATCAATTTAATTAATTA
1 AATACAAACATAAAAATCATTAATTA
* *
28625106 AATACAAATATAAACATCATTAATTA
1 AATACAAACATAAAAATCATTAATTA
*
28625132 AATACAAACATAAAAATTATTAATTA
1 AATACAAACATAAAAATCATTAATTA
*
28625158 CATACA
1 AATACA
28625164 TATTATTTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (26 bp):
AATACAAACATAAAAATCATTAATTA
Found at i:28625237 original size:18 final size:17
Alignment explanation
Indices: 28625216--28625263 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
28625206 TTAATCTCAA
28625216 ATAAATATGATATTATT
1 ATAAATATGATATTATT
28625233 GATAAAT-T-A-ATTA--
1 -ATAAATATGATATTATT
28625246 ATAAATATGATATTATT
1 ATAAATATGATATTATT
28625263 A
1 A
28625264 AACCCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 11
0.69 0.00 0.31
Matches are distributed among these distances:
12 6 0.24
13 1 0.04
14 1 0.04
15 8 0.32
16 1 0.04
17 2 0.08
18 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATAAATATGATATTATT
Found at i:28626880 original size:27 final size:27
Alignment explanation
Indices: 28626828--28626889 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
28626818 CCTAACCAGT
*
28626828 AGGCACCATTGATGCCGCCATTCCAAA
1 AGGCACCATTGATGCCGCCATCCCAAA
*
28626855 AGGCACCATTGGTGCCGCC-TACCCAAA
1 AGGCACCATTGATGCCGCCAT-CCCAAA
*
28626882 AGACACCA
1 AGGCACCA
28626890 CCCGTCCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.31, C:0.35, G:0.19, T:0.15
Consensus pattern (27 bp):
AGGCACCATTGATGCCGCCATCCCAAA
Found at i:28629406 original size:11 final size:11
Alignment explanation
Indices: 28629385--28629441 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
28629375 AAACTTATCT
28629385 TTTTAAAATTTA
1 TTTT-AAATTTA
28629397 TTTTAAATTTAA
1 TTTTAAATTT-A
* *
28629409 ATTTAAATTAA
1 TTTTAAATTTA
*
28629420 GTTTAAATTTA
1 TTTTAAATTTA
28629431 TTTTAAATTTA
1 TTTTAAATTTA
28629442 AAAGTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 26 0.67
12 13 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:28629412 original size:17 final size:17
Alignment explanation
Indices: 28629390--28629482 Score: 123
Period size: 17 Copynumber: 5.4 Consensus size: 17
28629380 TATCTTTTTA
28629390 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
** *
28629407 AAATTTAAATTAAGTTT
1 AAATTTATTTTAAATTT
28629424 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
*
28629441 AAAAGTTATTTTAAATTT
1 -AAATTTATTTTAAATTT
*
28629459 AAATTAATTTTAAATTT
1 AAATTTATTTTAAATTT
*
28629476 GAATTTA
1 AAATTTA
28629483 AATTTAAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 48 0.75
18 16 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:28629465 original size:11 final size:11
Alignment explanation
Indices: 28629398--28629486 Score: 70
Period size: 11 Copynumber: 7.7 Consensus size: 11
28629388 TAAAATTTAT
28629398 TTTAAATTTAAA
1 TTTAAA-TTAAA
*
28629410 TTTAAATTAAG
1 TTTAAATTAAA
* *
28629421 TTTAAATTTAT
1 TTTAAATTAAA
28629432 TTTAAATTTAAAA
1 TTTAAA-TT-AAA
* **
28629445 GTTATTTTAAA
1 TTTAAATTAAA
*
28629456 TTTAAATTAAT
1 TTTAAATTAAA
*
28629467 TTTAAATTTGAA
1 TTTAAA-TTAAA
28629479 TTTAAATT
1 TTTAAATT
28629487 TAAAATAAAT
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
11 37 0.62
12 19 0.32
13 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:28629492 original size:7 final size:6
Alignment explanation
Indices: 28629398--28629490 Score: 95
Period size: 6 Copynumber: 16.0 Consensus size: 6
28629388 TAAAATTTAT
* *
28629398 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA TTT-AT TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
* * * *
28629445 GTT-AT TTTAAA TTTAAA -TTAAT TTTAAA TTTGAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
28629491 ATAAATAAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
5 15 0.21
6 50 0.71
7 5 0.07
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:28631306 original size:29 final size:30
Alignment explanation
Indices: 28631232--28631637 Score: 364
Period size: 29 Copynumber: 14.0 Consensus size: 30
28631222 CTGAACTGTC
* * * * *
28631232 CAAAAATTATATTTTGACCCTTACACTTTT
1 CAAAAATTACATTTTTACCCCTAAACTTCT
* **
28631262 CCAAAATTACA-TTTTACCCCTAAAAATCT
1 CAAAAATTACATTTTTACCCCTAAACTTCT
*
28631291 -AAAAATTACATTTTTACCCTTAAACTT-T
1 CAAAAATTACATTTTTACCCCTAAACTTCT
* * * *
28631319 CAAAAATTACATTTTGACCTC-GAACTTTT
1 CAAAAATTACATTTTTACCCCTAAACTTCT
* *
28631348 CAAAAATTACATTTTTGCCCCCAAACTTCT
1 CAAAAATTACATTTTTACCCCTAAACTTCT
* *
28631378 -AAAAAATACATTTTTA-CCCTCGAACTT-T
1 CAAAAATTACATTTTTACCCCT-AAACTTCT
28631406 CAAAAATTACATTTTTA-CCCTCAAACTTCT
1 CAAAAATTACATTTTTACCCCT-AAACTTCT
* *
28631436 CAAAAATTACATTTTTATCCCTTAACTTCT
1 CAAAAATTACATTTTTACCCCTAAACTTCT
* *
28631466 -GAAAATTACATTTTTACCCTCGAAA-TTC-
1 CAAAAATTACATTTTTACCC-CTAAACTTCT
* *
28631494 C-AAAATTACATTTTTGCCTCTAAACTTCT
1 CAAAAATTACATTTTTACCCCTAAACTTCT
* * *
28631523 TAAAAAATACATTTTTACCCTTAAACTTC-
1 CAAAAATTACATTTTTACCCCTAAACTTCT
*
28631552 CAAAAATCACATTTTTA-CCCTCAAACTT-T
1 CAAAAATTACATTTTTACCCCT-AAACTTCT
*
28631581 CAAAAATTACA-TTTTACCCTTAAACTT-T
1 CAAAAATTACATTTTTACCCCTAAACTTCT
* **
28631609 CAAAAATAATGTTTTTACCCC-AAA-TTCT
1 CAAAAATTACATTTTTACCCCTAAACTTCT
28631637 C
1 C
28631638 TGGAACTTCA
Statistics
Matches: 308, Mismatches: 50, Indels: 38
0.78 0.13 0.10
Matches are distributed among these distances:
27 6 0.02
28 66 0.21
29 166 0.54
30 66 0.21
31 4 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
CAAAAATTACATTTTTACCCCTAAACTTCT
Found at i:28631379 original size:87 final size:88
Alignment explanation
Indices: 28631232--28631636 Score: 449
Period size: 87 Copynumber: 4.7 Consensus size: 88
28631222 CTGAACTGTC
* * * **
28631232 CAAAAATTATATTTTGACC-CTTACACTTTTCCAAAATTACA-TTTTACCCCTAAAAATCTAAAA
1 CAAAAATTACATTTTGACCTC-TAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTAAAA
*
28631295 ATTACATTTTTACCCTTAAACTTT
65 ATTACATTTTTACCCTCAAACTTT
* * *
28631319 CAAAAATTACATTTTGACCTC-GAACTTTTCAAAAATTACATTTTTGCCCCCAAACTTCTAAAAA
1 CAAAAATTACATTTTGACCTCTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTAAAAA
* *
28631383 ATACATTTTTACCCTCGAACTTT
66 TTACATTTTTACCCTCAAACTTT
* * * * *
28631406 CAAAAATTACATTTTTACC-CTCAAACTTCTCAAAAATTACATTTTTATCCCTTAACTTCTGAAA
1 CAAAAATTACATTTTGACCTCT-AAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTAAAA
28631470 ATTACATTTTTACCCTCGAAA--TT
65 ATTACATTTTTACCCTC-AAACTTT
* * * *
28631493 CCAAAATTACATTTTTG-CCTCTAAACTTCTT-AAAAAATACATTTTTACCCTTAAACTTCCAAA
1 CAAAAATTACA-TTTTGACCTCTAAACTT-TTCAAAAATTACATTTTTACCCCTAAACTTCTAAA
*
28631556 AATCACATTTTTACCCTCAAACTTT
64 AATTACATTTTTACCCTCAAACTTT
* **
28631581 CAAAAATTACATTTT-ACC-CTTAAAC-TTTCAAAAATAATGTTTTTACCCC-AAA-TTCT
1 CAAAAATTACATTTTGACCTC-TAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCT
28631637 CTGGAACTTC
Statistics
Matches: 267, Mismatches: 38, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
84 3 0.01
85 5 0.02
86 37 0.14
87 149 0.56
88 71 0.27
89 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (88 bp):
CAAAAATTACATTTTGACCTCTAAACTTTTCAAAAATTACATTTTTACCCCTAAACTTCTAAAAA
TTACATTTTTACCCTCAAACTTT
Found at i:28631732 original size:14 final size:14
Alignment explanation
Indices: 28631693--28631747 Score: 58
Period size: 16 Copynumber: 3.7 Consensus size: 14
28631683 TTTAAAATTA
28631693 ATTTTATATTTTCTC
1 ATTTTAT-TTTTCTC
*
28631708 A-TTTATTTTTTTC
1 ATTTTATTTTTCTC
28631721 GTATTTTATTTTTCTC
1 --ATTTTATTTTTCTC
28631737 ATATTTATTTT
1 AT-TTTATTTT
28631748 CGTATATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 6 0.18
14 7 0.21
15 10 0.29
16 11 0.32
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (14 bp):
ATTTTATTTTTCTC
Found at i:28631754 original size:14 final size:14
Alignment explanation
Indices: 28631711--28631756 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
28631701 TTTTCTCATT
28631711 TATTT-TTTTCGTA
1 TATTTATTTTCGTA
28631724 T-TTTATTTTTC-TCA
1 TATTTA-TTTTCGT-A
28631738 TATTTATTTTCGTA
1 TATTTATTTTCGTA
28631752 TATTT
1 TATTT
28631757 GTTCATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.11
13 2 0.07
14 18 0.64
15 5 0.18
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (14 bp):
TATTTATTTTCGTA
Found at i:28631756 original size:30 final size:29
Alignment explanation
Indices: 28631693--28631752 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
28631683 TTTAAAATTA
28631693 ATTTTATATTTTCTCATTTATTTTTTTCGT
1 ATTTTATATTTTCTCA-TTATTTTTTTCGT
28631723 ATTTTAT-TTTTCTCA-TATTTATTTTCGT
1 ATTTTATATTTTCTCATTATTT-TTTTCGT
28631751 AT
1 AT
28631753 ATTTGTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 5 0.17
28 9 0.31
29 8 0.28
30 7 0.24
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.68
Consensus pattern (29 bp):
ATTTTATATTTTCTCATTATTTTTTTCGT
Found at i:28641289 original size:3 final size:3
Alignment explanation
Indices: 28641281--28641307 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
28641271 TTATGATATT
28641281 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
28641308 AGGGATGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28643678 original size:39 final size:40
Alignment explanation
Indices: 28643563--28644447 Score: 258
Period size: 39 Copynumber: 22.7 Consensus size: 40
28643553 GATCTTTTGT
* *
28643563 CCCGAG-CCTGGGGCAGGTCATCATCAGTAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* * * ** *
28643602 CTCGAG-CTTGGGGCAGAT--TGCAGCCATTCGATTTCTTAC
1 CCCGAGTCTTGGGGCAGATCAT-CA-TCAGTAAATCTCTTAC
28643641 CCCGAGTC-TGGGGCAGATCATCATCAGTAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* * * ** *
28643680 CCCGA-TCATGGGGGTAGAT--TGCAGTCATTCGATCTCTTAT
1 CCCGAGTC-TTGGGGCAGATCAT-CA-TCAGTAAATCTCTTAC
* * *
28643720 CCCGAG-CCTAGGGCAGATCATCATCAGTTAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* ** * * * *
28643759 CCTGA-TAATAGGGCAGATTACAGCCATCCG---ATCTGTTAC
1 CCCGAGTCTTGGGGCAGA-T-CA-TCATCAGTAAATCTCTTAC
* * *
28643798 CCCGAG-CTTGGGGTAGATCATTATCAATAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* ** * * ** *
28643837 CCCGA-TCATGGGGCAGATTGT-AGCCATTTGACCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCA-TCAGTAAATCTCTTAC
** * *
28643876 CCTAAG-CTTGGGGTAGATCATCATCAGCAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
** * *
28643915 CTTGA-T-TATGAGGCAGATTGCAGTCATC--T-GATCTCTTAC
1 CCCGAGTCT-TGGGGCAGA-T-CA-TCATCAGTAAATCTCTTAC
* * * * *
28643954 CCCGAG-CCTCGGGAAGATCATTATCAGCAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* * * * * **
28643993 CTCGA-TCATGGGGTAGAT--TGCAACCATTCTATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCAT-C-ATCAGTAAATCTCTTAC
* * * * * *
28644032 CCCGA-ACCTGAGGCAAATCACCATCAGCAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* * **
28644071 CCCGA-TCATGGGGCAGAT--TGCAGTCATTTGATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCAT-CA-TCAGTAAATCTCTTAC
* * * * *
28644110 CCCGAG-CCTAGGGCAAATCACCATCAGCAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* ** * * *
28644149 CTCGAG-CTTGGGGCAGATTGTAACCA-TCTAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGT-AAATCTCTTAC
* ** *
28644188 CCCGAG-CCTAAGGCAGATCATCATCAGGAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* *** ** * * **
28644227 CCCGA-TCATAATGCAGATTGT-AGCCATTCGATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCA-TCAGTAAATCTCTTAC
* *
28644266 CCCGAG-CTTGGGGCAGATCACCATCAGCAAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* * * * * *
28644305 CCCGAG-CCTGAGGTAGAT--TGCAGCCATTCAATCTCTTAC
1 CCCGAGTCTTGGGGCAGATCAT-CA-TCAGTAAATCTCTTAC
* * *** *
28644344 CTCGAG-CTTGAGGCAGATCATCATCAACCAATCTCTCAC
1 CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
* * ** *
28644383 CCCGAG-CTTGGGGCAAAT--TGCAATCATTCGATCTTTTAC
1 CCCGAGTCTTGGGGCAGATCAT-C-ATCAGTAAATCTCTTAC
*
28644422 CCCGAG-CTTGGGGCAGATCACCATCA
1 CCCGAGTCTTGGGGCAGATCATCATCA
28644448 ACTAATCTCT
Statistics
Matches: 602, Mismatches: 186, Indels: 116
0.67 0.21 0.13
Matches are distributed among these distances:
36 7 0.01
37 7 0.01
38 15 0.02
39 515 0.86
40 41 0.07
41 7 0.01
42 10 0.02
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (40 bp):
CCCGAGTCTTGGGGCAGATCATCATCAGTAAATCTCTTAC
Found at i:28643692 original size:78 final size:78
Alignment explanation
Indices: 28643563--28644473 Score: 955
Period size: 78 Copynumber: 11.7 Consensus size: 78
28643553 GATCTTTTGT
* * * * *
28643563 CCCGAGCCTGGGGCAGGTCATCATCAGTAAATCTCTTACCTCGAGCTTGGGGCAGATTGCAGCCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
*
28643628 TTCGATTTCTTAC
66 TTCGATCTCTTAC
* * * *
28643641 CCCGAGTCTGGGGCAGATCATCATCAGTAAATCTCTTACCCCGATCATGGGGGTAGATTGCAGTC
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCAT-GGGGCAGATTGCAGCC
*
28643706 ATTCGATCTCTTAT
65 ATTCGATCTCTTAC
* ** * * * *
28643720 CCCGAGCCTAGGGCAGATCATCATCAGTTAATCTCTTACCCTGATAATAGGGCAGATTACAGCCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
* *
28643785 TCCGATCTGTTAC
66 TTCGATCTCTTAC
* * * ** *
28643798 CCCGAGCTTGGGGTAGATCATTATCAATAAATCTCTTACCCCGATCATGGGGCAGATTGTAGCCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
* *
28643863 TTTGACCTCTTAC
66 TTCGATCTCTTAC
** * * ** * * *
28643876 CCTAAGCTTGGGGTAGATCATCATCAGCAAATCTCTTACCTTGATTATGAGGCAGATTGCAGTCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
28643941 -TCTGATCTCTTAC
66 TTC-GATCTCTTAC
* * * * * *
28643954 CCCGAGCCTCGGGAAGATCATTATCAGCAAATCTCTTACCTCGATCATGGGGTAGATTGCAACCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
*
28644019 TTCTATCTCTTAC
66 TTCGATCTCTTAC
* * * * *
28644032 CCCGAACCTGAGGCAAATCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGTCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
*
28644097 TTTGATCTCTTAC
66 TTCGATCTCTTAC
* * * * * * * *
28644110 CCCGAGCCTAGGGCAAATCACCATCAGCAAATCTCTTACCTCGAGCTTGGGGCAGATTGTAACCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
*
28644175 -TCTAATCTCTTAC
66 TTC-GATCTCTTAC
** * *** *
28644188 CCCGAGCCTAAGGCAGATCATCATCAGGAAATCTCTTACCCCGATCATAATGCAGATTGTAGCCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
28644253 TTCGATCTCTTAC
66 TTCGATCTCTTAC
* * * * * *
28644266 CCCGAGCTTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTGAGGTAGATTGCAGCCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
*
28644331 TTCAATCTCTTAC
66 TTCGATCTCTTAC
* * * * * * * * * **
28644344 CTCGAGCTTGAGGCAGATCATCATCAACCAATCTCTCACCCCGAGCTTGGGGCAAATTGCAATCA
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
*
28644409 TTCGATCTTTTAC
66 TTCGATCTCTTAC
* * * * **
28644422 CCCGAGCTTGGGGCAGATCACCATCAACTAATCTCTTA-TTCGATCATGGGGC
1 CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGC
28644474 TGATAGCTGT
Statistics
Matches: 695, Mismatches: 133, Indels: 11
0.83 0.16 0.01
Matches are distributed among these distances:
77 12 0.02
78 610 0.88
79 73 0.11
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (78 bp):
CCCGAGCCTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
TTCGATCTCTTAC
Found at i:28646681 original size:30 final size:30
Alignment explanation
Indices: 28646628--28646819 Score: 176
Period size: 30 Copynumber: 6.5 Consensus size: 30
28646618 AAAAGGTCCC
* * *
28646628 TAAACTATC-CAAAAATCATATTTTGACCCA
1 TAAACT-TCTCAAAAATTACATTTTTACCCA
* * *
28646658 TACACTTTTCCAAAATTACATTTTTACCCA
1 TAAACTTCTCAAAAATTACATTTTTACCCA
* *
28646688 TAAACTT-TCAAAAATTACA-TTTTGCCCC
1 TAAACTTCTCAAAAATTACATTTTTACCCA
*
28646716 TAAACTTCTCAAAAATTACATTTTTACCCC
1 TAAACTTCTCAAAAATTACATTTTTACCCA
* *
28646746 CAAACTTCTCAAAAATTACATTTTTACCCC
1 TAAACTTCTCAAAAATTACATTTTTACCCA
* ** * * *
28646776 GAATTTTCTC-AAAATGACATTTCTACCCT
1 TAAACTTCTCAAAAATTACATTTTTACCCA
*
28646805 TAAAACTTTTCAAAA
1 T-AAACTTCTCAAAA
28646820 TTATGTTTTA
Statistics
Matches: 135, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
28 14 0.10
29 40 0.30
30 78 0.58
31 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
TAAACTTCTCAAAAATTACATTTTTACCCA
Found at i:28646790 original size:88 final size:88
Alignment explanation
Indices: 28646625--28646797 Score: 197
Period size: 88 Copynumber: 2.0 Consensus size: 88
28646615 TTTAAAAGGT
* * * * * *
28646625 CCCTAAACTATCCAAAAATCATATTTTGACCCATACACTTTTCCAAAATTACATTTTTACCCATA
1 CCCTAAACTATCCAAAAATCACATTTTGACCCACAAACTTCTCAAAAATTACATTTTTACCCACA
*
28646690 AACTTTCAAAAATTACATTTTGC
66 AACTTTCAAAAATGACATTTTGC
* * *
28646713 CCCTAAACT-TCTCAAAAATTACATTTTTACCCCCAAACTTCTCAAAAATTACATTTTTACCC-C
1 CCCTAAACTATC-CAAAAATCACATTTTGACCCACAAACTTCTCAAAAATTACATTTTTACCCAC
* * *
28646776 GAATTTTCTCAAAATGACATTT
65 AAACTTTC-AAAAATGACATTT
28646798 CTACCCTTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
87 8 0.11
88 62 0.89
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.35
Consensus pattern (88 bp):
CCCTAAACTATCCAAAAATCACATTTTGACCCACAAACTTCTCAAAAATTACATTTTTACCCACA
AACTTTCAAAAATGACATTTTGC
Found at i:28646822 original size:59 final size:57
Alignment explanation
Indices: 28646663--28646819 Score: 174
Period size: 59 Copynumber: 2.7 Consensus size: 57
28646653 ACCCATACAC
* *
28646663 TTTTC-CAAAATTACATTTTTACCCATAAAC-TTTCAAAAATTACATTTTGCCCCTAA
1 TTTTCTCAAAATTACATTTTTACCC-TAAACTTTTCAAAAATTACATTTTACCCCGAA
** * *
28646719 ACTTCTCAAAAATTACATTTTTACCCCCAAACTTCTCAAAAATTACATTTTTACCCCGAA
1 TTTTCTC-AAAATTACATTTTTA-CCCTAAACTTTTCAAAAATTACA-TTTTACCCCGAA
* *
28646779 TTTTCTCAAAATGACATTTCTACCCTTAAAACTTTTCAAAA
1 TTTTCTCAAAATTACATTTTTACCC-T-AAACTTTTCAAAA
28646820 TTATGTTTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
56 3 0.04
57 1 0.01
58 22 0.27
59 29 0.35
60 27 0.33
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (57 bp):
TTTTCTCAAAATTACATTTTTACCCTAAACTTTTCAAAAATTACATTTTACCCCGAA
Found at i:28648845 original size:554 final size:544
Alignment explanation
Indices: 28647703--28649363 Score: 1260
Period size: 554 Copynumber: 3.1 Consensus size: 544
28647693 CATTAACAAA
* * * * * * * *
28647703 TATGTGCTTAAGATTATATAAAGAAAATTGGTATAGACTTTTGAGCAATGTGTAATATCCAAGGG
1 TATGTGCATAAAATTATATAAAGAAAATTAGTATAGACTTCTAAGGAAAGTGTAATATCCAAGAG
* * **
28647768 CGCAATCATGATTAAACCAGTGACCTATTGACCTTAAATAAAATGTCCTACCATTGAGGTATAAA
66 CGCAATCATAATTAAACCAGTGACCTATTGACCTGAAATAAAATGTCCTACCATTGAACTATAAA
* * * **
28647833 TCCTTGAAAAGTAAATTCAAAAATGTTTTAGTTTTTTAGCATTATTGAAACAAGTTTTTATGTTC
131 TCCTTGAAAAGTAAATGCAAAAATGTTTTA-TTTTTTAGCATTAATGAAAAAAGTTTTTATGTAA
* * *
28647898 ATAAATTATAAGACACTGTTATAAATTTCTAAGAAAAAAGTTACTCCCAACGACTTAATTACATT
195 AAAAATTATAAAACACTGGTATAAATTTCTAAGAAAAAAGTTACTCCCAACGACTTAATTACATT
* * * * *
28647963 TGAATCAAGAGGTTAAAGGCTTTTCCATGGAGCTATAGACCGTTGATGAACAAATGGAAAAAATG
260 TGAATCAAGAGGTCAAAGGCTTTGCAATGGAGCTATAGACCCTTCATGAACAAATGGAAAAAATG
* * * *
28648028 TTTTCATTATTTGCGTATTAATGAAATAAATTTTTATGTACATAAATTATATAAAGCAACTAGGT
325 TTTTAATTATGTGAGTATTAATCAAATAAATTTTTATGTACATAAATTATATAAAGCAACTAGGT
* * * ** * * * *
28648093 ATAGACATTTGAGAAAAAAGAAATTTTTAAGTGCCTAACCATTTTCGATTCGGTGTCTTATTGAT
390 ACAGACATTTGAGAAAAAAGAAATTTTTAAGGGCCCAACCAAGTTCAAATCGGTGACCTATTGAT
*** * * * ** *
28648158 ATATGGTCAAATGCTTTACCACTGAGCTGTAGACCCTCGATAATTGAGTGGGTAAATGTTATTTT
455 ATACAATCAAATGCTTTACCACTAAGCTATAGACCCT--ATAATTGAGTGGATAAACATTATTAT
*
28648223 TATTTAAGTATTAACAGAACAAGTTTT
518 TATTTAAGCATTAACAGAACAAGTTTT
* * * * * * ** * * *
28648250 TAGGTGCAT-ATATTGTACATACG-AAATGAACATACACTTCTAAGGAAAGTTTAATATCTAAGA
1 TATGTGCATAAAATTATATA-AAGAAAATTAGTATAGACTTCTAAGGAAAGTGTAATATCCAAGA
* * * * * *
28648313 TCGCAATCA-AATTTGAACCAGTGACCTCTTGACCTGGAATTAAATGTTCTACCATTGAACTATA
65 GCGCAATCATAA-TTAAACCAGTGACCTATTGACCTGAAATAAAATGTCCTACCATTGAACTATA
* * *
28648377 AATCCTT-AATAAGTATATGGAATAAATGTTTT-TTTATTCTAGTATTAATGAAAAAAGTTTTTA
129 AATCCTTGAA-AAGTAAATGCAA-AAATGTTTTATTT-TT-TAGCATTAATGAAAAAAGTTTTTA
* *
28648440 TGTAAAAAAAATTATATTAAACAACTGAGTATAAATTTCTAAGGAAAAAAAG-TACCTTCTAACG
190 TGT-AAAAAAATTATA--AAAC-ACTG-GTATAAATTTCTAA-G-AAAAAAGTTA-CTCCCAACG
* ** * *
28648504 GCTTAATTAGGTTTGAATTAATG-GGTCAAATGCTCTTGCAAT-GAGCTATAGACCCTTCATGAA
247 ACTTAATTACATTTGAATCAA-GAGGTCAAAGGCT-TTGCAATGGAGCTATAGACCCTTCATGAA
* * * *
28648567 TAAATGGAAAAAATGTTTTAATTATGTGAGTGTTAATCAAACT-AGTTTTTATGTACATAAATTT
310 CAAATGGAAAAAATGTTTTAATTATGTGAGTATTAATCAAA-TAAATTTTTATGTACATAAATTA
* ** * * * *
28648631 TATAAAGCAACTAGGTGCAGATGTTTGAG-AAAATGTAATTTTTTAGGGCCCAATCAAGTTCAAA
374 TATAAAGCAACTAGGTACAGACATTTGAGAAAAAAGAAATTTTTAAGGGCCCAACCAAGTTCAAA
* * * *
28648695 TCGGTGACCTCTTGATCTCCAATCAAATGCTCTT-CCACTAAGTTATAGACCCT-TAATATGTAG
439 TCGGTGACCTATTGATATACAATCAAATGCT-TTACCACTAAGCTATAGACCCTATAAT-TG-A-
* *
28648758 GTGGATAAACCATT-TTATTATTTACGCATTAACATAACAAGTTTT
500 GTGGATAAA-CATTATTATTATTTAAGCATTAACAGAACAAGTTTT
* * * *
28648803 TATGTGCCTAAAATTATATAAAGAAAATTTGTATAGACTTCTAAGG---GCG--CTAT-C---A-
1 TATGTGCATAAAATTATATAAAGAAAATTAGTATAGACTTCTAAGGAAAGTGTAATATCCAAGAG
* * ** * * *
28648858 TG---TC----TT-AACCAATGACCTATTGACCTTCAATTAAATGTACTACCATTGAGCTATAAA
66 CGCAATCATAATTAAACCAGTGACCTATTGACCTGAAATAAAATGTCCTACCATTGAACTATAAA
* * * * * * * *
28648915 TTCTTGATATGTAAATTG--GAAATGTTTTATTATTTTAGCATTATTGGAATAAGTTTTTATATA
131 TCCTTGAAAAGTAAA-TGCAAAAATGTTTTATT-TTTTAGCATTAATGAAAAAAGTTTTTATGTA
* * * * ** * * *
28648978 CATAAATTATATAAAATAACTAGTATGGATATT-TAAAAAAAAAGTTACTTCCAATGACTTAATT
194 -AAAAAAT-TATAAAA-CACTGGTATAAAT-TTCTAAGAAAAAAGTTACTCCCAACGACTTAATT
** * * * * * *
28649042 AGGTTTGAATCAAGAGGTCAAATGCTCTTCCAAT-GAGCTATAGGCCATTGATGAAAAAATGGAA
255 ACATTTGAATCAAGAGGTCAAAGGCT-TTGCAATGGAGCTATAGACCCTTCATGAACAAATGG--
* * * * * *
28649106 AAAAAAAATTGTTTTCATTATTTGCGTATTAATGAAATAAGTTTTGATGTACATAAATTATATAA
317 --AAAAAA-TGTTTTAATTATGTGAGTATTAATCAAATAAATTTTTATGTACATAAATTATATAA
* * * * * * ** * *
28649171 AGCAACT-GGTATAGACGTTTGGGAAAAAAGAAATATCTAAGGGCCTAACCATTTTCAATTTGGT
379 AGCAACTAGGTACAGACATTTGAGAAAAAAGAAATTTTTAAGGGCCCAACCAAGTTCAAATCGGT
* * * ** * * * *
28649235 GACCTTTTTATTTACGGTCAAATGCTTGACCACTAAGCTGTAG--CCTTTAATGAGTGAGTGGGT
444 GACCTATTGATATACAATCAAATGCTTTACCACTAAGCTATAGACCCTATAAT---TGAGTGGAT
* *
28649298 AAATA-TAGTTATTATTTGAGCATTAACAGAACAAGTTTT
506 AAACATTA-TTATTATTTAAGCATTAACAGAACAAGTTTT
* *
28649337 TATGTGCAT-AAATTATACAAAGGAAAT
1 TATGTGCATAAAATTATATAAAGAAAAT
28649364 GGATCTACAT
Statistics
Matches: 888, Mismatches: 179, Indels: 108
0.76 0.15 0.09
Matches are distributed among these distances:
529 1 0.00
530 75 0.08
531 2 0.00
532 10 0.01
533 29 0.03
534 104 0.12
535 124 0.14
536 57 0.06
537 5 0.01
541 2 0.00
544 1 0.00
545 7 0.01
546 105 0.12
547 42 0.05
548 9 0.01
549 3 0.00
550 7 0.01
551 7 0.01
552 14 0.02
553 111 0.12
554 166 0.19
555 7 0.01
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (544 bp):
TATGTGCATAAAATTATATAAAGAAAATTAGTATAGACTTCTAAGGAAAGTGTAATATCCAAGAG
CGCAATCATAATTAAACCAGTGACCTATTGACCTGAAATAAAATGTCCTACCATTGAACTATAAA
TCCTTGAAAAGTAAATGCAAAAATGTTTTATTTTTTAGCATTAATGAAAAAAGTTTTTATGTAAA
AAAATTATAAAACACTGGTATAAATTTCTAAGAAAAAAGTTACTCCCAACGACTTAATTACATTT
GAATCAAGAGGTCAAAGGCTTTGCAATGGAGCTATAGACCCTTCATGAACAAATGGAAAAAATGT
TTTAATTATGTGAGTATTAATCAAATAAATTTTTATGTACATAAATTATATAAAGCAACTAGGTA
CAGACATTTGAGAAAAAAGAAATTTTTAAGGGCCCAACCAAGTTCAAATCGGTGACCTATTGATA
TACAATCAAATGCTTTACCACTAAGCTATAGACCCTATAATTGAGTGGATAAACATTATTATTAT
TTAAGCATTAACAGAACAAGTTTT
Found at i:28652146 original size:28 final size:28
Alignment explanation
Indices: 28652109--28652174 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
28652099 GGGTTTGAAG
* *
28652109 ATGTGATTTTTGGATACCCGGGGC-AAA
1 ATGTAATTTTTGGACACCCGGGGCAAAA
* *
28652136 ATGGTAA-TTTTGGACACTCGGGTCAAAA
1 AT-GTAATTTTTGGACACCCGGGGCAAAA
28652164 ATGTAATTTTT
1 ATGTAATTTTT
28652175 AGAAAAATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (28 bp):
ATGTAATTTTTGGACACCCGGGGCAAAA
Found at i:28652192 original size:30 final size:30
Alignment explanation
Indices: 28652156--28652293 Score: 113
Period size: 30 Copynumber: 4.6 Consensus size: 30
28652146 TGGACACTCG
28652156 GGTCAAAAATGTAATTTTTAGAAAAATCGA
1 GGTCAAAAATGTAATTTTTAGAAAAATCGA
* * ** *
28652186 GGTCAAAAATGGAATTTTAAG-AAGTTTGA
1 GGTCAAAAATGTAATTTTTAGAAAAATCGA
* * *
28652215 GGGT-AAAAATGTAATTTTTA-AAAAGTTTGG
1 -GGTCAAAAATGTAATTTTTAGAAAA-ATCGA
* *
28652245 GGAT-AAAAATGTAATATTTAGAAAAAATCGG
1 GG-TCAAAAATGTAATTTTTAG-AAAAATCGA
*
28652276 GGTCAAAAATATAATTTT
1 GGTCAAAAATGTAATTTT
28652294 GGAGAAGTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
29 23 0.26
30 43 0.49
31 17 0.20
32 4 0.05
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.32
Consensus pattern (30 bp):
GGTCAAAAATGTAATTTTTAGAAAAATCGA
Found at i:28652309 original size:31 final size:30
Alignment explanation
Indices: 28652207--28652337 Score: 97
Period size: 30 Copynumber: 4.3 Consensus size: 30
28652197 GAATTTTAAG
* **
28652207 AAGTTT-GAGGGTAAAAATGTAATTTTTAAA
1 AAGTTTAG-GGGTAAAAATATAATTTTTGGA
* * *
28652237 AAGTTT-GGGGATAAAAATGTAATATTTAGA
1 AAGTTTAGGGG-TAAAAATATAATTTTTGGA
*** *
28652267 AAAAATCGGGGTCAAAAATATAA-TTTTGGA
1 AAGTTTAGGGGT-AAAAATATAATTTTTGGA
*
28652297 GAAGTTTAGGGGTTAAAATATAATTTTTGGA
1 -AAGTTTAGGGGTAAAAATATAATTTTTGGA
*
28652328 CAGTTTAGGG
1 AAGTTTAGGG
28652338 ACCTCCAGGG
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
29 3 0.04
30 51 0.62
31 28 0.34
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (30 bp):
AAGTTTAGGGGTAAAAATATAATTTTTGGA
Found at i:28652333 original size:91 final size:89
Alignment explanation
Indices: 28652160--28652338 Score: 225
Period size: 91 Copynumber: 2.0 Consensus size: 89
28652150 CACTCGGGTC
* *
28652160 AAAAATGTAATTTTTAGAAAAATCGAGGTCAAAAATGGAATTTTAAGAAGTTTGAGGGTAAAAAT
1 AAAAATGTAATATTTAGAAAAATCGAGGTCAAAAATAGAATTTTAAGAAGTTTGAGGGTAAAAAT
* *
28652225 GTAATTTTTAAAAAGTTTGGGGAT
66 ATAATTTTTAAAAAGTTTAGGGAT
* * * *
28652249 AAAAATGTAATATTTAGAAAAAATCGGGGTCAAAAATATAATTTTGGAGAAGTTT-AGGGGTTAA
1 AAAAATGTAATATTTAG-AAAAATCGAGGTCAAAAATAGAATTTT-AAGAAGTTTGA-GGGTAAA
** *
28652313 AATATAATTTTTGGACAGTTTAGGGA
63 AATATAATTTTTAAAAAGTTTAGGGA
28652339 CCTCCAGGGC
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 16 0.21
90 25 0.33
91 35 0.46
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (89 bp):
AAAAATGTAATATTTAGAAAAATCGAGGTCAAAAATAGAATTTTAAGAAGTTTGAGGGTAAAAAT
ATAATTTTTAAAAAGTTTAGGGAT
Found at i:28654238 original size:18 final size:17
Alignment explanation
Indices: 28654217--28654306 Score: 90
Period size: 17 Copynumber: 5.2 Consensus size: 17
28654207 TTTTTGGAAT
*
28654217 TTTAATATTTATAATAAA
1 TTTAA-ATTTAAAATAAA
28654235 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* * * *
28654253 TCTAAACTTATATTAAA
1 TTTAAATTTAAAATAAA
*
28654270 TTTAAAATTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
28654287 TTTAGATTCAAAATAAA
1 TTTAAATTTAAAATAAA
28654304 TTT
1 TTT
28654307 TAAAATGAGC
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
17 40 0.68
18 19 0.32
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:28654242 original size:6 final size:6
Alignment explanation
Indices: 28654231--28654290 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
28654221 ATATTTATAA
* * * * *
28654231 TAAATT TAAATT TAAATA TAAATC TAAACT TATA-T TAAATT TAAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
28654278 TAAA-A TAAATT TA
1 TAAATT TAAATT TA
28654291 GATTCAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
5 8 0.19
6 35 0.81
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:28659982 original size:17 final size:19
Alignment explanation
Indices: 28659960--28659995 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
28659950 TGATCGTTTT
28659960 GAATATA-TTAATA-ATAG
1 GAATATATTTAATACATAG
28659977 GAATATATTTAATACATAG
1 GAATATATTTAATACATAG
28659996 TCATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (19 bp):
GAATATATTTAATACATAG
Found at i:28660683 original size:230 final size:230
Alignment explanation
Indices: 28660280--28660744 Score: 745
Period size: 230 Copynumber: 2.0 Consensus size: 230
28660270 GTAAAAAATA
* *
28660280 ATATAATCTTAAGTGAAACAGATAAAATAAAAGTGAACTGAATTTGTTAGTTCTTTATATATTAG
1 ATATAATCTTAAGTGAAAAAGATAAAATAAAAGTGAACTGAATTTGGTAGTTCTTTATATATTAG
* *
28660345 TTAAATAGATAATCCAATTAACATGGTTTTATGTACTTTTATCCATTTTTTGGTGAATTATAAAA
66 ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCCATTTTTTGGTGAATTATAAAA
**
28660410 GGAAGGCAAAGTCCTAACAACAAAGTGATTGACAGGACTCGAACTCAGATCACATCTG-GAAAAA
131 GGAAGGCAAAGTCCTAACAACAAAGCAATTGACAGGACTCGAACTCAGATCACATCTGAG-AAAA
*
28660474 TGAATATCTTTAACCATCAGGCCAACACACGGGTTC
195 TGAATATCTTTAACCATCAGGCCAACACACAGGTTC
* *
28660510 ATATAATCTTAAGTGAAAAAGATAAAATAAAAGTGAATTGAATTTGGTATTTCTTTATATATTAG
1 ATATAATCTTAAGTGAAAAAGATAAAATAAAAGTGAACTGAATTTGGTAGTTCTTTATATATTAG
* *
28660575 ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCTATTTTTTGGTGAATTATAAAG
66 ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCCATTTTTTGGTGAATTATAAAA
* * * * **
28660640 GGAGGGCAAAG-CTCTAACAACGACGCAATTGACGGGACTCGAACTCAGATCACATCTGAGGCAA
131 GGAAGGCAAAGTC-CTAACAACAAAGCAATTGACAGGACTCGAACTCAGATCACATCTGAGAAAA
28660704 TGAATATCTTTAACCATCAGGCCAACACACAGGTTC
195 TGAATATCTTTAACCATCAGGCCAACACACAGGTTC
28660740 ATATA
1 ATATA
28660745 TGATCCTTTA
Statistics
Matches: 216, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
229 1 0.00
230 214 0.99
231 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (230 bp):
ATATAATCTTAAGTGAAAAAGATAAAATAAAAGTGAACTGAATTTGGTAGTTCTTTATATATTAG
ATAAATAGATAATCCAATTAACATGGTTTTATGTACCTTTATCCATTTTTTGGTGAATTATAAAA
GGAAGGCAAAGTCCTAACAACAAAGCAATTGACAGGACTCGAACTCAGATCACATCTGAGAAAAT
GAATATCTTTAACCATCAGGCCAACACACAGGTTC
Found at i:28672725 original size:14 final size:13
Alignment explanation
Indices: 28672702--28672733 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
28672692 AAAGTCAACG
28672702 GGTCAAGGTCAAT
1 GGTCAAGGTCAAT
28672715 GGTCAACGGTCAAT
1 GGTCAA-GGTCAAT
28672729 GGTCA
1 GGTCA
28672734 GTCAACGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (13 bp):
GGTCAAGGTCAAT
Found at i:28679947 original size:15 final size:16
Alignment explanation
Indices: 28679927--28679961 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28679917 GGGTTTGAAC
28679927 TTGGTTCA-ATTGGGT
1 TTGGTTCACATTGGGT
*
28679942 TTGGTTCACTTTGGGT
1 TTGGTTCACATTGGGT
28679958 TTGG
1 TTGG
28679962 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (16 bp):
TTGGTTCACATTGGGT
Found at i:28681624 original size:24 final size:25
Alignment explanation
Indices: 28681566--28681703 Score: 121
Period size: 24 Copynumber: 5.8 Consensus size: 25
28681556 ATATCTGAAT
*
28681566 AGCTGA-CGAGCGTAAA-AGTACAGT
1 AGCTGATCGAGCGTAAACA-TACAGA
* *
28681590 AG-TCGAT-GAGCGTAAACGTACAAA
1 AGCT-GATCGAGCGTAAACATACAGA
28681614 AGCT-ATCGAGCGTAAACATACAGA
1 AGCTGATCGAGCGTAAACATACAGA
* * *
28681638 AGATGAT-GAGCATAAACATACATA
1 AGCTGATCGAGCGTAAACATACAGA
* * *
28681662 AGCT-AACGAGTGTAAACGTACAGA
1 AGCTGATCGAGCGTAAACATACAGA
28681686 AGCTGA-CGAGCGTAAACA
1 AGCTGATCGAGCGTAAACA
28681704 AATAATAGCT
Statistics
Matches: 90, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
23 4 0.04
24 82 0.91
25 4 0.04
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (25 bp):
AGCTGATCGAGCGTAAACATACAGA
Found at i:28681713 original size:24 final size:24
Alignment explanation
Indices: 28681673--28681827 Score: 125
Period size: 24 Copynumber: 6.5 Consensus size: 24
28681663 GCTAACGAGT
* *
28681673 GTAAACGTACAGA-AGCTGACGAGC
1 GTAAACGTATA-ATAGCTGACAAGC
** *
28681697 GTAAACAAATAATAGCTGCCAAGC
1 GTAAACGTATAATAGCTGACAAGC
* * *
28681721 GTAAACATATAAAAGTTGA-AGAGC
1 GTAAACGTATAATAGCTGACA-AGC
* *
28681745 GTAAACGTACAATAACTGACAAGC
1 GTAAACGTATAATAGCTGACAAGC
* * *
28681769 ATAAATGTATATTAGCTGACAAGC
1 GTAAACGTATAATAGCTGACAAGC
* *
28681793 GTAAACGTATATTAGCTGACGAGC
1 GTAAACGTATAATAGCTGACAAGC
* *
28681817 GTGAATGTATA
1 GTAAACGTATA
28681828 TTAGTTAGCG
Statistics
Matches: 104, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
23 2 0.02
24 101 0.97
25 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (24 bp):
GTAAACGTATAATAGCTGACAAGC
Found at i:28681768 original size:48 final size:49
Alignment explanation
Indices: 28681566--28681773 Score: 151
Period size: 48 Copynumber: 4.3 Consensus size: 49
28681556 ATATCTGAAT
* * * *
28681566 AGCTGACGAGCGTAAA-AGTACAGTAG-TCGATGAGCGTAAACGTACAA-A
1 AGCTGACAAGCGTAAACA-TACAGAAGAT-GAAGAGCGTAAACATACAATA
* * *
28681614 AGCT-ATCGAGCGTAAACATACAGAAGATGATGAGCATAAACATAC-ATA
1 AGCTGA-CAAGCGTAAACATACAGAAGATGAAGAGCGTAAACATACAATA
* * * * * * * *
28681662 AGCTAACGAGTGTAAACGTACAGAAGCTGACGAGCGTAAACAAATAAT-
1 AGCTGACAAGCGTAAACATACAGAAGATGAAGAGCGTAAACATACAATA
* * * * *
28681710 AGCTGCCAAGCGTAAACATATAAAAGTTGAAGAGCGTAAACGTACAATA
1 AGCTGACAAGCGTAAACATACAGAAGATGAAGAGCGTAAACATACAATA
*
28681759 A-CTGACAAGCATAAA
1 AGCTGACAAGCGTAAA
28681774 TGTATATTAG
Statistics
Matches: 129, Mismatches: 24, Indels: 14
0.77 0.14 0.08
Matches are distributed among these distances:
47 2 0.02
48 121 0.94
49 6 0.05
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (49 bp):
AGCTGACAAGCGTAAACATACAGAAGATGAAGAGCGTAAACATACAATA
Found at i:28688535 original size:22 final size:22
Alignment explanation
Indices: 28688507--28688552 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
28688497 AACTACATAT
28688507 TCCTCGAATCATCTCATCACTA
1 TCCTCGAATCATCTCATCACTA
* **
28688529 TCCTCGAGTCATCTTGTCACTA
1 TCCTCGAATCATCTCATCACTA
28688551 TC
1 TC
28688553 TGACTTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.09, T:0.35
Consensus pattern (22 bp):
TCCTCGAATCATCTCATCACTA
Found at i:28691109 original size:23 final size:23
Alignment explanation
Indices: 28691083--28691129 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
28691073 TTTTCGAGAA
28691083 TTTTGTGTTT-ACCTTTTGGGGTT
1 TTTTGTGTTTGA-CTTTTGGGGTT
* *
28691106 TTTTGTTTTTGAGTTTTGGGGTT
1 TTTTGTGTTTGACTTTTGGGGTT
28691129 T
1 T
28691130 AATTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.04, C:0.04, G:0.28, T:0.64
Consensus pattern (23 bp):
TTTTGTGTTTGACTTTTGGGGTT
Found at i:28697890 original size:2 final size:2
Alignment explanation
Indices: 28697879--28697946 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
28697869 AGACCAAATT
28697879 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28697920 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28697947 TAAAGTTAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28699503 original size:172 final size:174
Alignment explanation
Indices: 28699192--28699504 Score: 427
Period size: 172 Copynumber: 1.8 Consensus size: 174
28699182 TTAAGTTGTT
*
28699192 TAATAATATAAGGAGTTCAATCATTAAAATATTAAATTAAAATTTTAATAGAGAATTTTTATATA
1 TAATAATATAAGAAGTTCAATCATTAAAATATTAAATTAAAATTTTAATA-AGAATTTTTATATA
**** ** * * * *
28699257 ATTTTTTGAAATATTTTAATAAAATTATTTTTTTTTAAAAGAATATTTTAATCAATCACTTTTGA
65 AAAAATTGAAATATTTTAATAAAATTATTTTTTCATAAAAGAATATTTTAACCAACCACTCTTAA
28699322 TAATTTTAGAGTATGAAATAGATTATTTTAATTATTTTAATAATA
130 TAATTTTAGAGTATGAAATAGATTATTTTAATTATTTTAATAATA
**
28699367 TAATAATATAAGAAGTTCAATCATTACAAATATTAAATTAAAA-TTTAAT-A-TTTTTTTATATA
1 TAATAATATAAGAAGTTCAATCATTA-AAATATTAAATTAAAATTTTAATAAGAATTTTTATATA
* *
28699429 AAAAATTGAAATGTTTTAATAAAATTATTTTTTCATAAAA-ATATATTTTAGCCAACCACTCTTA
65 AAAAATTGAAATATTTTAATAAAATTATTTTTTCATAAAAGA-ATATTTTAACCAACCACTCTTA
*
28699493 ATAGTTTTAGAG
129 ATAATTTTAGAG
28699505 CTAAACTAGA
Statistics
Matches: 120, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
171 1 0.01
172 71 0.59
173 1 0.01
175 31 0.26
176 16 0.13
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (174 bp):
TAATAATATAAGAAGTTCAATCATTAAAATATTAAATTAAAATTTTAATAAGAATTTTTATATAA
AAAATTGAAATATTTTAATAAAATTATTTTTTCATAAAAGAATATTTTAACCAACCACTCTTAAT
AATTTTAGAGTATGAAATAGATTATTTTAATTATTTTAATAATA
Found at i:28723287 original size:18 final size:18
Alignment explanation
Indices: 28723254--28723317 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
28723244 GTCAACAAAT
*
28723254 AATTT-AAAAATTATAAA
1 AATTTCAAAAAATATAAA
28723271 AATATTCAAAAAA-ATAAA
1 AAT-TTCAAAAAATATAAA
28723289 TTCAATTTTCAAAAAATATAAA
1 ---AA-TTTCAAAAAATATAAA
28723311 AATTTCA
1 AATTTCA
28723318 TAATTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
17 3 0.08
18 12 0.31
19 7 0.18
21 11 0.28
22 6 0.15
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTTCAAAAAATATAAA
Found at i:28728123 original size:11 final size:11
Alignment explanation
Indices: 28728083--28728127 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
28728073 TAAAAAATGA
*
28728083 TTTTTTTTATT
1 TTTTTTTTCTT
28728094 TTTTTCTTTCCTT
1 TTTTT-TTT-CTT
*
28728107 TATTTTTTCTT
1 TTTTTTTTCTT
28728118 TTTTTTTTCT
1 TTTTTTTTCT
28728128 AATATCACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 17 0.59
12 6 0.21
13 6 0.21
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:28729111 original size:14 final size:15
Alignment explanation
Indices: 28729079--28729120 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
28729069 GAGAACGTGA
28729079 AAAAAATGAAAGGGT
1 AAAAAATGAAAGGGT
*
28729094 AAAAAATGAAATGG-
1 AAAAAATGAAAGGGT
*
28729108 AAAAAATGGAAGG
1 AAAAAATGAAAGG
28729121 AAAGAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (15 bp):
AAAAAATGAAAGGGT
Found at i:28729336 original size:18 final size:19
Alignment explanation
Indices: 28729303--28729339 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
28729293 TGTTAAAATT
28729303 AATTGTATGAAAATTTATTG
1 AATTGTAT-AAAATTTATTG
28729323 AATTGTAT-AAATTTATT
1 AATTGTATAAAATTTATT
28729340 TTAACTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (19 bp):
AATTGTATAAAATTTATTG
Found at i:28730409 original size:25 final size:25
Alignment explanation
Indices: 28730363--28730417 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
28730353 ACTGATTCAG
*
28730363 TAAAAATTCATAATTAAATAATTAAT
1 TAAAAATTCATAA-TAAATAATTAAA
28730389 TAAAAATTCATAA-AAATTAATTAAA
1 TAAAAATTCATAATAAA-TAATTAAA
28730414 TAAA
1 TAAA
28730418 TAAAGCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 3 0.11
25 11 0.41
26 13 0.48
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAAATTCATAATAAATAATTAAA
Found at i:28736855 original size:30 final size:30
Alignment explanation
Indices: 28736821--28736885 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
28736811 ATTTTTGAGG
28736821 AATTTGGGGATAAAAATTA-AAATTTGGGAA
1 AATTTGGGGATAAAAA-TAGAAATTTGGGAA
* * *
28736851 AATTT-GGGATTAAAATAGAACTTTTGGAA
1 AATTTGGGGATAAAAATAGAAATTTGGGAA
28736880 AATTTG
1 AATTTG
28736886 AAGTTGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.07
29 23 0.77
30 5 0.17
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.34
Consensus pattern (30 bp):
AATTTGGGGATAAAAATAGAAATTTGGGAA
Found at i:28736984 original size:30 final size:29
Alignment explanation
Indices: 28736893--28737199 Score: 244
Period size: 29 Copynumber: 10.4 Consensus size: 29
28736883 TTGAAGTTGG
* *
28736893 AAATGTGATTTTTGGAAA-TTTAGGGGT-A
1 AAATGT-AATTTTGGAAAGTTTGGGGGTAA
* * * *
28736921 AAATGGTAAATTTT-GAATGTTCGAGTGTAA
1 AAAT-GT-AATTTTGGAAAGTTTGGGGGTAA
* * *
28736951 AAATGTAGTTTTGGAAAGTTCGGGGGGTCA
1 AAATGTAATTTTGGAAAGTT-TGGGGGTAA
* * *
28736981 AAATGTATTTTTGGAAAGTTCGGAGGTAA
1 AAATGTAATTTTGGAAAGTTTGGGGGTAA
*
28737010 AAATGTAATTTTGGAAAGTTTGGGCGTCAA
1 AAATGTAATTTTGGAAAGTTTGGGGGT-AA
* * **
28737040 AACATG-ATTTTTGAAAAGTTTAAGGGTAA
1 AA-ATGTAATTTTGGAAAGTTTGGGGGTAA
* *
28737069 AAATGTAATTTTGGAAAGTTTAGGGGTCA
1 AAATGTAATTTTGGAAAGTTTGGGGGTAA
* * *
28737098 AAACGTGATTTTTGGAAAGTTCGGGGGTAA
1 AAATGT-AATTTTGGAAAGTTTGGGGGTAA
* *** * *
28737128 AAATATAATTCAAGAAAGTTTGAGGGTCA
1 AAATGTAATTTTGGAAAGTTTGGGGGTAA
* *
28737157 AAATGTGATTTTTGGAAAGTTTGGGTGTAA
1 AAATGT-AATTTTGGAAAGTTTGGGGGTAA
28737187 AAATGTAATTTTG
1 AAATGTAATTTTG
28737200 TGAAGTTCAA
Statistics
Matches: 216, Mismatches: 53, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
28 15 0.07
29 104 0.48
30 94 0.44
31 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
AAATGTAATTTTGGAAAGTTTGGGGGTAA
Found at i:28737010 original size:59 final size:59
Alignment explanation
Indices: 28736893--28737199 Score: 313
Period size: 59 Copynumber: 5.2 Consensus size: 59
28736883 TTGAAGTTGG
* * * * *
28736893 AAATGTGATTTTTGGAAA-TTTAGGGGT-AAAATGGTAAATTTT-GAATGTTC-GAGTGTAA
1 AAATGT-AATTTTGGAAAGTTTGGGGGTCAAAAT-GTGATTTTTGGAAAGTTCGGAG-GTAA
* *
28736951 AAATGTAGTTTTGGAAAGTTCGGGGGGTCAAAATGT-ATTTTTGGAAAGTTCGGAGGTAA
1 AAATGTAATTTTGGAAAGTT-TGGGGGTCAAAATGTGATTTTTGGAAAGTTCGGAGGTAA
* ** * **
28737010 AAATGTAATTTTGGAAAGTTTGGGCGTCAAAACATGATTTTTGAAAAGTT-TAAGGGTAA
1 AAATGTAATTTTGGAAAGTTTGGGGGTCAAAATGTGATTTTTGGAAAGTTCGGA-GGTAA
* * *
28737069 AAATGTAATTTTGGAAAGTTTAGGGGTCAAAACGTGATTTTTGGAAAGTTCGGGGGTAA
1 AAATGTAATTTTGGAAAGTTTGGGGGTCAAAATGTGATTTTTGGAAAGTTCGGAGGTAA
* *** * *
28737128 AAATATAATTCAAGAAAGTTTGAGGGTCAAAATGTGATTTTTGGAAAGTTTGG-GTGTAA
1 AAATGTAATTTTGGAAAGTTTGGGGGTCAAAATGTGATTTTTGGAAAGTTCGGAG-GTAA
28737187 AAATGTAATTTTG
1 AAATGTAATTTTG
28737200 TGAAGTTCAA
Statistics
Matches: 208, Mismatches: 32, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
57 10 0.05
58 26 0.12
59 164 0.79
60 8 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
AAATGTAATTTTGGAAAGTTTGGGGGTCAAAATGTGATTTTTGGAAAGTTCGGAGGTAA
Found at i:28737087 original size:118 final size:119
Alignment explanation
Indices: 28736945--28737238 Score: 357
Period size: 118 Copynumber: 2.5 Consensus size: 119
28736935 GAATGTTCGA
* * *
28736945 GTGTAAAAATGTAGTTTTGGAAAGTTCGGGGGGTCAAAATGT-ATTTTTGGAAAGTTCGGAGGTA
1 GTGTAAAAATGTAATTTTGGAAAGTTCGAGGGGTCAAAACGTGATTTTTGGAAAGTTCGGAGGTA
* ***
28737009 AAAATGTAATTTTGGAAAGTTTG-GGCGTCAAAACATGATTTTTGAAAAGTTTAAG
66 AAAATATAATTCAAGAAAGTTTGAGG-GTCAAAACATGATTTTTGAAAAGTTT-AG
* *
28737064 G-GTAAAAATGTAATTTTGGAAAGTT-TAGGGGTCAAAACGTGATTTTTGGAAAGTTCGGGGGTA
1 GTGTAAAAATGTAATTTTGGAAAGTTCGAGGGGTCAAAACGTGATTTTTGGAAAGTTCGGAGGTA
** * *
28737127 AAAATATAATTCAAGAAAGTTTGAGGGTCAAAATGTGATTTTTGGAAAGTTTGG
66 AAAATATAATTCAAGAAAGTTTGAGGGTCAAAACATGATTTTTGAAAAGTTTAG
* ** * *
28737181 GTGTAAAAATGTAATTTTGTG-AAGTTC-AAGGGTCAAAAAATGATTTTCGAAAAGTTCG
1 GTGTAAAAATGTAATTTTG-GAAAGTTCGAGGGGTCAAAACGTGATTTTTGGAAAGTTCG
28737239 AGAACCTTCT
Statistics
Matches: 152, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
117 14 0.09
118 134 0.88
119 4 0.03
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (119 bp):
GTGTAAAAATGTAATTTTGGAAAGTTCGAGGGGTCAAAACGTGATTTTTGGAAAGTTCGGAGGTA
AAAATATAATTCAAGAAAGTTTGAGGGTCAAAACATGATTTTTGAAAAGTTTAG
Found at i:28737206 original size:59 final size:58
Alignment explanation
Indices: 28736947--28737238 Score: 304
Period size: 59 Copynumber: 5.0 Consensus size: 58
28736937 ATGTTCGAGT
* * * *
28736947 GTAAAAATGTAGTTTTGGAAAGTTCGGGGGGTCAAAATGT-ATTTTTGGAAAGTTCGGAG
1 GTAAAAATGTAATTTTGGAAAGTT-TGAGGGTCAAAACGTGATTTTTGGAAAGTTCGG-G
* * **
28737006 GTAAAAATGTAATTTTGGAAAGTTTG-GGCGTCAAAACATGATTTTTGAAAAGTTTAAGG
1 GTAAAAATGTAATTTTGGAAAGTTTGAGG-GTCAAAACGTGATTTTTGGAAAG-TTCGGG
28737065 GTAAAAATGTAATTTTGGAAAGTTT-AGGGGTCAAAACGTGATTTTTGGAAAGTTCGGGG
1 GTAAAAATGTAATTTTGGAAAGTTTGA-GGGTCAAAACGTGATTTTTGGAAAGTTC-GGG
* *** * *
28737124 GTAAAAATATAATTCAAGAAAGTTTGAGGGTCAAAATGTGATTTTTGGAAAGTTTGGG
1 GTAAAAATGTAATTTTGGAAAGTTTGAGGGTCAAAACGTGATTTTTGGAAAGTTCGGG
** ** * *
28737182 TGTAAAAATGTAATTTTGTG-AAGTTCAAGGGTCAAAAAATGATTTTCGAAAAGTTCG
1 -GTAAAAATGTAATTTTG-GAAAGTTTGAGGGTCAAAACGTGATTTTTGGAAAGTTCG
28737239 AGAACCTTCT
Statistics
Matches: 196, Mismatches: 28, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
57 2 0.01
58 14 0.07
59 173 0.88
60 7 0.04
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (58 bp):
GTAAAAATGTAATTTTGGAAAGTTTGAGGGTCAAAACGTGATTTTTGGAAAGTTCGGG
Found at i:28738949 original size:6 final size:6
Alignment explanation
Indices: 28738938--28739006 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
28738928 GGACTCCTTT
* * *
28738938 TTTAAA TTTAAA TTTAGAA --TGAA TTTAAA TTCAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
28738984 TTTAAA -CTAAA TTTAAA CTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
28739007 ATAAAATAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
4 2 0.04
5 8 0.16
6 37 0.76
7 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:28739024 original size:17 final size:17
Alignment explanation
Indices: 28738940--28739025 Score: 109
Period size: 17 Copynumber: 5.1 Consensus size: 17
28738930 ACTCCTTTTT
*
28738940 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
28738957 TGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
28738974 TAAATTTAAATTTAAAC
1 TAAATTTAAATTTAAAA
*
28738991 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
* *
28739008 TAAAATAAAATTTAAAA
1 TAAATTTAAATTTAAAA
28739025 T
1 T
28739026 TAGGTCCAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 58 1.00
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28739586 original size:39 final size:39
Alignment explanation
Indices: 28739528--28740031 Score: 263
Period size: 39 Copynumber: 12.9 Consensus size: 39
28739518 ATCTGTCCTT
* *
28739528 GGCTCGTGGGTAAGAGATTGGCTGATGGTGATCTACCCCA
1 GGCTCG-GGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
* *
28739568 GGCTCGGGATAAAAGATTGACTGATGGTGATCTGCCCCA
1 GGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
* * *
28739607 AGCTCAGGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCCTA
1 GGCTCGGGGTAAAAGATTGGCTG-ATGG-TG--ATCTGCCCCA
* * * *
28739646 GGCTTGGGGTAAGAGATTGGCTAATGGTGATTTGCCCCA
1 GGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
* *
28739685 GGCTCGGGGTAAAAGATT-G--AATGGCTGCAATCTGCCCTA
1 GGCTCGGGGTAAAAGATTGGCTGATGG-TG--ATCTGCCCCA
* * * * * *
28739724 GGCTCGAGGTAAAACATTAGCTAATGGTGATTTGCCTCA
1 GGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
* ** *
28739763 GGCTCGGGGTGAAAGA-T--CAAATGGTTGCAATCTACCCCA
1 GGCTCGGGGTAAAAGATTGGCTGATGG-TG--ATCTGCCCCA
* *** * * * *
28739802 AGCTCGGGGTAAAAGATTTAATAATCGTGATCTACCCTA
1 GGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
* * * * *
28739841 GGCTTGAGGTAAGAGA-T--C-GAATGGCTGCAATATGCCCTA
1 GGCTCGGGGTAAAAGATTGGCTG-ATGG-TG--ATCTGCCCCA
* *
28739880 GGCTCGGGGTAAGAGATTAGCTGATGGTGATCTG-CCCA
1 GGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
* * *
28739918 GGCTCGAGGTAAGAGA-T--CGGATGGCTGCAATCTGCCCCA
1 GGCTCGGGGTAAAAGATTGGCTGATGG-TG--ATCTGCCCCA
* * * *
28739957 AGCTCGGGGTAAAAGGTTGGTTAATGGTGATCTGCCCCA
1 GGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
* * * *
28739996 AGCTTGGGGTAAAAGATCGGATGACT-GTGATCTGCC
1 GGCTCGGGGTAAAAGATTGGCTGA-TGGTGATCTGCC
28740032 TTAGAGTTAG
Statistics
Matches: 364, Mismatches: 64, Indels: 73
0.73 0.13 0.15
Matches are distributed among these distances:
35 7 0.02
36 21 0.06
37 9 0.02
38 27 0.07
39 254 0.70
40 12 0.03
41 10 0.03
42 23 0.06
43 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (39 bp):
GGCTCGGGGTAAAAGATTGGCTGATGGTGATCTGCCCCA
Found at i:28739663 original size:78 final size:78
Alignment explanation
Indices: 28739558--28740014 Score: 497
Period size: 78 Copynumber: 5.9 Consensus size: 78
28739548 GCTGATGGTG
* * * * * *
28739558 ATCTACCCCAGGCTCGGGATAAAAGATTGACTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATTGACTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAGA
28739623 TCGAATGGCTGCA
66 TCGAATGGCTGCA
* * * *
28739636 ATCTGCCCTAGGCTTGGGGTAAGAGATTGGCTAATGGTGATTTGCCCCAGGCTCGGGGTAAAAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATTGACTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAGA
*
28739701 TTGAATGGCTGCA
66 TCGAATGGCTGCA
* * * * *
28739714 ATCTGCCCTAGGCTCGAGGTAAAACATT-AGCTAATGGTGATTTGCCTCAGGCTCGGGGTGAAAG
1 ATCTGCCCTAGGCTCGGGGTAAAAGATTGA-CTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
* *
28739778 ATCAAATGGTTGCA
65 ATCGAATGGCTGCA
* * * * * * * * * * *
28739792 ATCTACCCCAAGCTCGGGGTAAAAGATTTAATAATCGTGATCTACCCTAGGCTTGAGGTAAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATTGACTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAGA
28739857 TCGAATGGCTGCA
66 TCGAATGGCTGCA
* * * * *
28739870 ATATGCCCTAGGCTCGGGGTAAGAGATT-AGCTGATGGTGATCTG-CCCAGGCTCGAGGTAAGAG
1 ATCTGCCCTAGGCTCGGGGTAAAAGATTGA-CTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAG
*
28739933 ATCGGATGGCTGCA
65 ATCGAATGGCTGCA
* * * ** * *
28739947 ATCTGCCCCAAGCTCGGGGTAAAAGGTTGGTTAATGGTGATCTGCCCCAAGCTTGGGGTAAAAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATTGACTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAGA
28740012 TCG
66 TCG
28740015 GATGACTGTG
Statistics
Matches: 312, Mismatches: 62, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
77 66 0.21
78 245 0.79
79 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
ATCTGCCCTAGGCTCGGGGTAAAAGATTGACTAATGGTGATCTGCCCCAGGCTCGGGGTAAAAGA
TCGAATGGCTGCA
Found at i:28752281 original size:30 final size:30
Alignment explanation
Indices: 28752247--28752311 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
28752237 ATTTTCGAGG
28752247 AATTTGGGGATCAAAATTGAAAT-TTAGGAA
1 AATTTGGGGATCAAAATTGAAATATT-GGAA
* *
28752277 AATTT-GGGATTAAAATTGAACTATTGGAA
1 AATTTGGGGATCAAAATTGAAATATTGGAA
28752306 AATTTG
1 AATTTG
28752312 AAGTTGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
AATTTGGGGATCAAAATTGAAATATTGGAA
Found at i:28752427 original size:59 final size:59
Alignment explanation
Indices: 28752356--28752607 Score: 221
Period size: 60 Copynumber: 4.3 Consensus size: 59
28752346 AAAATGGTAA
*
28752356 ATTTTTGG-ATGTTCGGGT-GTAAAAATGTAATTTTAGAAAGTTTATGGGTCAAAACGTG
1 ATTTTTGGAAAGTTCGGGTGGTAAAAATGTAATTTTAGAAAGTTTA-GGGTCAAAACGTG
* ** * * * *
28752414 ATTTTTGGAATGTTCAAGTGGTAAAAATATAATTTTGGAAAG-TTAGGGGGTTAAAATGTG
1 ATTTTTGGAAAGTTCGGGTGGTAAAAATGTAATTTTAGAAAGTTTA--GGGTCAAAACGTG
* * * * *
28752474 ATTTTTGAAAAGTTCAGGG-GTTAAAACATG-ATTTTTAAAAAGTTTGAGGGTCAAAATGTG
1 ATTTTTGGAAAGTTC-GGGTGGTAAAA-ATGTAATTTTAGAAAGTTT-AGGGTCAAAACGTG
* * * * *
28752534 ATTTTTGGAAAGTT-TGGTGGAAAAAATGAAATTTT-GTGAAGTTCGAGGGTCAAAACGTG
1 ATTTTTGGAAAGTTCGGGTGGTAAAAATGTAATTTTAG-AAAGTT-TAGGGTCAAAACGTG
28752593 ATTTTTGGAAAGTTC
1 ATTTTTGGAAAGTTC
28752608 AAAGACCTTC
Statistics
Matches: 156, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
58 13 0.08
59 53 0.34
60 84 0.54
61 5 0.03
62 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (59 bp):
ATTTTTGGAAAGTTCGGGTGGTAAAAATGTAATTTTAGAAAGTTTAGGGTCAAAACGTG
Found at i:28752536 original size:30 final size:30
Alignment explanation
Indices: 28752377--28752606 Score: 114
Period size: 30 Copynumber: 7.7 Consensus size: 30
28752367 TTCGGGTGTA
* * *
28752377 AAAATGTAATTTTAG-AAAGTTT-ATGGGTC
1 AAAATGTGATTTTTGAAAAGTTTGA-GGGTT
* * * ** *
28752406 AAAACGTGATTTTTGGAATGTTCAAGTGGTA
1 AAAATGTGATTTTTGAAAAGTTTGAG-GGTT
* * * * *
28752437 AAAATAT-AATTTTGGAAAGTTAGGGGGTT
1 AAAATGTGATTTTTGAAAAGTTTGAGGGTT
*
28752466 AAAATGTGATTTTTGAAAAG-TTCAGGGGTT
1 AAAATGTGATTTTTGAAAAGTTTGA-GGGTT
** * *
28752496 AAAACATGATTTTTAAAAAGTTTGAGGGTC
1 AAAATGTGATTTTTGAAAAGTTTGAGGGTT
* **
28752526 AAAATGTGATTTTTGGAAAGTTTG-GTGGAA
1 AAAATGTGATTTTTGAAAAGTTTGAG-GGTT
** * *
28752556 AAAATGAAATTTTGTG--AAGTTCGAGGGTC
1 AAAATGTGATTTT-TGAAAAGTTTGAGGGTT
* *
28752585 AAAACGTGATTTTTGGAAAGTT
1 AAAATGTGATTTTTGAAAAGTT
28752607 CAAAGACCTT
Statistics
Matches: 151, Mismatches: 39, Indels: 21
0.72 0.18 0.10
Matches are distributed among these distances:
28 2 0.01
29 41 0.27
30 94 0.62
31 14 0.09
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGTGATTTTTGAAAAGTTTGAGGGTT
Found at i:28752607 original size:30 final size:30
Alignment explanation
Indices: 28752401--28752607 Score: 138
Period size: 30 Copynumber: 6.9 Consensus size: 30
28752391 GAAAGTTTAT
* *
28752401 GGGTCAAAACGTGATTTTTGGAATGTTCAA
1 GGGTCAAAACGTGATTTTTGGAAAGTTCGA
* ** * * *
28752431 GTGGTAAAAATAT-AATTTTGGAAAGTTAGG
1 G-GGTCAAAACGTGATTTTTGGAAAGTTCGA
* * *
28752461 GGGTTAAAATGTGATTTTTGAAAAGTTC-A
1 GGGTCAAAACGTGATTTTTGGAAAGTTCGA
* * ** *
28752490 GGGGTTAAAACATGATTTTTAAAAAGTTTGA
1 -GGGTCAAAACGTGATTTTTGGAAAGTTCGA
* *
28752521 GGGTCAAAATGTGATTTTTGGAAAGTTTG-
1 GGGTCAAAACGTGATTTTTGGAAAGTTCGA
** *
28752550 GTGG--AAAAAATGAAATTTTGTG-AAGTTCGA
1 G-GGTCAAAACGTG-ATTTTTG-GAAAGTTCGA
28752580 GGGTCAAAACGTGATTTTTGGAAAGTTC
1 GGGTCAAAACGTGATTTTTGGAAAGTTC
28752608 AAAGACCTTC
Statistics
Matches: 136, Mismatches: 30, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
28 6 0.04
29 25 0.18
30 90 0.66
31 15 0.11
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (30 bp):
GGGTCAAAACGTGATTTTTGGAAAGTTCGA
Found at i:28754334 original size:6 final size:6
Alignment explanation
Indices: 28754323--28754407 Score: 72
Period size: 6 Copynumber: 14.8 Consensus size: 6
28754313 ACATTTGGAC
* *
28754323 TTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAGAA- -TGAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAAAT
* * * *
28754369 TCAAA- ATAAAT TTAAAT TTAAA- CTAAAT TTAAAC TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
28754408 ATAAAATAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
4 2 0.03
5 12 0.19
6 46 0.74
7 2 0.03
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:28754346 original size:17 final size:17
Alignment explanation
Indices: 28754324--28754426 Score: 143
Period size: 17 Copynumber: 6.1 Consensus size: 17
28754314 CATTTGGACT
28754324 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
28754341 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
28754358 TGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
28754375 TAAATTTAAATTTAAAC
1 TAAATTTAAATTTAAAA
*
28754392 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
* *
28754409 TAAAATAAAATTTAAAA
1 TAAATTTAAATTTAAAA
28754426 T
1 T
28754427 TGGATCCAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 74 1.00
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28766589 original size:24 final size:24
Alignment explanation
Indices: 28766569--28766648 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
28766559 TTTAGCTAGC
*
28766569 ACGAGCCCAGATTGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
28766593 ACGAACCCAGAATGATTA---CTT
1 ACGAGCCCAGAATGATTAGCTCTT
28766614 ACGAGCCCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
28766638 ACGAGCCCAGA
1 ACGAGCCCAGA
28766649 GAGAGTTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
21 20 0.40
24 30 0.60
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:28766616 original size:21 final size:21
Alignment explanation
Indices: 28766590--28766631 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28766580 TTGATTAGCT
28766590 CTTACGAACCCAGAATGATTA
1 CTTACGAACCCAGAATGATTA
*
28766611 CTTACGAGCCCAGAATGATTA
1 CTTACGAACCCAGAATGATTA
28766632 GCTCTTACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (21 bp):
CTTACGAACCCAGAATGATTA
Found at i:28775010 original size:2 final size:2
Alignment explanation
Indices: 28775003--28775027 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28774993 ATTTAAGGTA
28775003 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
28775028 ATAGCAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28778974 original size:12 final size:12
Alignment explanation
Indices: 28778741--28778977 Score: 208
Period size: 12 Copynumber: 19.6 Consensus size: 12
28778731 ATGCATAGCT
28778741 TATGTATATATA
1 TATGTATATATA
* *
28778753 TATATACATATA
1 TATGTATATATA
28778765 TATGTATATATA
1 TATGTATATATA
** *
28778777 CGTGTATACATA
1 TATGTATATATA
*
28778789 TATGTACATATA
1 TATGTATATATA
* * *
28778801 TATATGTACATA
1 TATGTATATATA
28778813 TATGTATATATA
1 TATGTATATATA
*
28778825 CATGTATACATATA
1 TATGTAT--ATATA
*
28778839 TATGTATACATA
1 TATGTATATATA
* *
28778851 AATGTACATATA
1 TATGTATATATA
* * * *
28778863 TGTATACACATA
1 TATGTATATATA
28778875 TATGTATATATA
1 TATGTATATATA
* * *
28778887 TA--CACACATA
1 TATGTATATATA
28778897 TATGTATATGTATA
1 TATGTATA--TATA
* *
28778911 TATATGTATATA
1 TATGTATATATA
*
28778923 TATGTGTATATA
1 TATGTATATATA
28778935 TATGTATATATA
1 TATGTATATATA
*
28778947 TATGTATGTATA
1 TATGTATATATA
28778959 TATGTATATATA
1 TATGTATATATA
28778971 TATGTAT
1 TATGTAT
28778978 GTATTTGGTA
Statistics
Matches: 175, Mismatches: 44, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
10 7 0.04
12 148 0.85
14 20 0.11
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (12 bp):
TATGTATATATA
Found at i:28779622 original size:14 final size:14
Alignment explanation
Indices: 28779603--28779636 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28779593 AAATCAATTA
*
28779603 AGAGAATGAGAAAG
1 AGAGAAAGAGAAAG
*
28779617 AGAGAAAGAGACAG
1 AGAGAAAGAGAAAG
28779631 AGAGAA
1 AGAGAA
28779637 CCTTTAAGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.35, T:0.03
Consensus pattern (14 bp):
AGAGAAAGAGAAAG
Found at i:28780199 original size:70 final size:70
Alignment explanation
Indices: 28780079--28780220 Score: 196
Period size: 70 Copynumber: 2.0 Consensus size: 70
28780069 CTTAATATAT
* *
28780079 CATCCTACAATTAAATACAAAAAGTTATATTACTTCAGCACCACACTCATTTACACATACA-AAA
1 CATCCTACAATTAAATACAAAAAATTAAATTACTTCAGCACCACACTCATTTACACATACACAAA
28780143 AGTGA
66 AGTGA
* * * * * *
28780148 CATCTTACAATTACATCCAAAAAAATTAAATTAGTTCATCACCACATTCATTTACACATACACAA
1 CATCCTACAATTAAATAC-AAAAAATTAAATTACTTCAGCACCACACTCATTTACACATACACAA
28780213 AAGTGA
65 AAGTGA
28780219 CA
1 CA
28780221 ACCCTCTATG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 15 0.24
70 38 0.60
71 10 0.16
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (70 bp):
CATCCTACAATTAAATACAAAAAATTAAATTACTTCAGCACCACACTCATTTACACATACACAAA
AGTGA
Found at i:28781524 original size:48 final size:48
Alignment explanation
Indices: 28781470--28781571 Score: 170
Period size: 48 Copynumber: 2.1 Consensus size: 48
28781460 TTTCTTCTTC
28781470 TAAAATTCTAATCTTTTTGTATAT-TAACTGCCCCTTTTAAAGCCAAAA
1 TAAAATTCTAATCTTTTTGTATATCT-ACTGCCCCTTTTAAAGCCAAAA
* *
28781518 TAAAATTCTAATCTTTTTGTATATCTGCTGCCCCTTTTAAAGCTAAAA
1 TAAAATTCTAATCTTTTTGTATATCTACTGCCCCTTTTAAAGCCAAAA
28781566 TAAAAT
1 TAAAAT
28781572 GTTGCCTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
48 50 0.98
49 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (48 bp):
TAAAATTCTAATCTTTTTGTATATCTACTGCCCCTTTTAAAGCCAAAA
Found at i:28786301 original size:48 final size:48
Alignment explanation
Indices: 28786246--28786347 Score: 195
Period size: 48 Copynumber: 2.1 Consensus size: 48
28786236 TTTCTTCTTT
28786246 TAAAATTCTAATCTTTTTGTATATCAACTGCCCCTTTTAAAGCCAAAA
1 TAAAATTCTAATCTTTTTGTATATCAACTGCCCCTTTTAAAGCCAAAA
*
28786294 TAAAATTCTAATCTTTTTGTATATCAGCTGCCCCTTTTAAAGCCAAAA
1 TAAAATTCTAATCTTTTTGTATATCAACTGCCCCTTTTAAAGCCAAAA
28786342 TAAAAT
1 TAAAAT
28786348 GTTGCCTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (48 bp):
TAAAATTCTAATCTTTTTGTATATCAACTGCCCCTTTTAAAGCCAAAA
Found at i:28797586 original size:7 final size:7
Alignment explanation
Indices: 28797574--28797599 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28797564 AGGAAAGAAA
28797574 GATGAGG
1 GATGAGG
28797581 GATGAGG
1 GATGAGG
28797588 GATGAGG
1 GATGAGG
28797595 GATGA
1 GATGA
28797600 TTAGGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (7 bp):
GATGAGG
Found at i:28797853 original size:23 final size:21
Alignment explanation
Indices: 28797822--28797863 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
28797812 AAAAAAATAA
*
28797822 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATT-ATTAATT
28797844 AATTCAACCCAAATTATTAA
1 AATT-AACCCAAATTATTAA
28797864 ATGAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTAACCCAAATTATTAATT
Found at i:28810181 original size:23 final size:22
Alignment explanation
Indices: 28810145--28810188 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28810135 TAAATATTTC
*
28810145 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
28810168 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
28810189 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:28811571 original size:32 final size:32
Alignment explanation
Indices: 28811535--28811597 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
28811525 TGCAGCCCAA
*
28811535 GCTTG-TTTCTGTTTGTCCTTTCACCTTTTTTT
1 GCTTGCTTT-TGTTTGTCCTTTCACCTATTTTT
28811567 GCTTGCTTTTGTTTGTCCTTTCACCTATTTT
1 GCTTGCTTTTGTTTGTCCTTTCACCTATTTT
28811598 GTTGTGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 26 0.90
33 3 0.10
ACGTcount: A:0.05, C:0.22, G:0.13, T:0.60
Consensus pattern (32 bp):
GCTTGCTTTTGTTTGTCCTTTCACCTATTTTT
Found at i:28838059 original size:23 final size:25
Alignment explanation
Indices: 28838033--28838078 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28838023 CCAATTAGGG
28838033 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
28838056 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
28838079 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:28842088 original size:17 final size:17
Alignment explanation
Indices: 28842066--28842108 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
28842056 AATTAATATA
*
28842066 TTTATTTTCA-TTTTCAT
1 TTTATTTT-ATTTTTAAT
28842083 TTTATTTTATTTTTAAT
1 TTTATTTTATTTTTAAT
28842100 TTTATTTTA
1 TTTATTTTA
28842109 ATTATGCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTATTTTTAAT
Found at i:28842091 original size:5 final size:5
Alignment explanation
Indices: 28842066--28842108 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 5
28842056 AATTAATATA
28842066 TTTAT TTTCAT TTTCAT TTTAT TTTATT TTTAAT TTTAT TTTA
1 TTTAT TTT-AT TTT-AT TTTAT TTTA-T TTT-AT TTTAT TTTA
28842109 ATTATGCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 15 0.43
6 19 0.54
7 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:28842108 original size:11 final size:11
Alignment explanation
Indices: 28842066--28842111 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
28842056 AATTAATATA
*
28842066 TTTATTTTCAT
1 TTTATTTTAAT
28842077 TTTCATTTT-AT
1 TTT-ATTTTAAT
28842088 TTTATTTTTAAT
1 TTTA-TTTTAAT
28842100 TTTATTTTAAT
1 TTTATTTTAAT
28842111 T
1 T
28842112 ATGCAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 20 0.62
12 11 0.34
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:28843064 original size:17 final size:18
Alignment explanation
Indices: 28843044--28843077 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28843034 GTCGAAAGCA
28843044 AAAATTGA-AAAAAAAAG
1 AAAATTGAGAAAAAAAAG
28843061 AAAATTGAGAAAAAAAA
1 AAAATTGAGAAAAAAAA
28843078 AAGAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (18 bp):
AAAATTGAGAAAAAAAAG
Found at i:28843090 original size:15 final size:16
Alignment explanation
Indices: 28843072--28843102 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
28843062 AAATTGAGAA
28843072 AAAAAAAAGA-AAAAG
1 AAAAAAAAGATAAAAG
28843087 AAAAAAAAGATAAAAG
1 AAAAAAAAGATAAAAG
28843103 TGTGTTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGATAAAAG
Found at i:28843093 original size:20 final size:20
Alignment explanation
Indices: 28843051--28843094 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28843041 GCAAAAATTG
* *
28843051 AAAAAAAAAGAAAATTGAGA
1 AAAAAAAAAGAAAATAGAAA
28843071 AAAAAAAAAGAAAA-AGAAA
1 AAAAAAAAAGAAAATAGAAA
28843090 AAAAA
1 AAAAA
28843095 GATAAAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAGAAAATAGAAA
Found at i:28843438 original size:9 final size:9
Alignment explanation
Indices: 28843424--28843450 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28843414 ACCTTAAACA
28843424 CTTTGAGTG
1 CTTTGAGTG
28843433 CTTTGAGTG
1 CTTTGAGTG
28843442 CTTTGAGTG
1 CTTTGAGTG
28843451 AATCTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.33, T:0.44
Consensus pattern (9 bp):
CTTTGAGTG
Found at i:28859369 original size:13 final size:14
Alignment explanation
Indices: 28859351--28859380 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
28859341 AGTAACCTCC
28859351 AAGGAAAAGG-AAA
1 AAGGAAAAGGTAAA
28859364 AAGGAAAAGGTAAA
1 AAGGAAAAGGTAAA
28859378 AAG
1 AAG
28859381 AAGGCTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (14 bp):
AAGGAAAAGGTAAA
Found at i:28859948 original size:15 final size:14
Alignment explanation
Indices: 28859927--28859967 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
28859917 TCATGCCGAG
28859927 AAGGATGAAGAACA
1 AAGGATGAAGAACA
28859941 AGAGGATGAAG--CA
1 A-AGGATGAAGAACA
*
28859954 AAGGATGACGAACA
1 AAGGATGAAGAACA
28859968 CATTGACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 3 0.13
15 9 0.39
ACGTcount: A:0.51, C:0.10, G:0.32, T:0.07
Consensus pattern (14 bp):
AAGGATGAAGAACA
Found at i:28860404 original size:17 final size:17
Alignment explanation
Indices: 28860378--28860416 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
28860368 TTAGCATTCT
28860378 TGCA-TTTTATTGTGC-C
1 TGCATTTTTATTGT-CAC
28860394 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
28860411 TGCATT
1 TGCATT
28860417 CATTTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:28868732 original size:12 final size:11
Alignment explanation
Indices: 28868711--28868748 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
28868701 TATTGAATTG
28868711 AAAAAAAAAGA
1 AAAAAAAAAGA
28868722 AAAAGAAAAAG-
1 AAAA-AAAAAGA
28868733 -AAAAAAAAGA
1 AAAAAAAAAGA
28868743 AAAAAA
1 AAAAAA
28868749 TGTTTTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
11 9 0.38
12 6 0.25
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:28876576 original size:51 final size:51
Alignment explanation
Indices: 28876518--28876763 Score: 366
Period size: 51 Copynumber: 4.8 Consensus size: 51
28876508 AATTTGTCAT
28876518 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAA
* * *
28876569 GGATTCATTTACTCACGATGACACTTAGTCATCGAACCTTTAATTCGTGAA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAA
* *
28876620 GGATTCATTTACTAACGATGACACTTAGTCATCGGACCCTTAATCCGTAAA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAA
* ** * **
28876671 GGATTCATTTACTCATGATGACACTTAGTCATCAAACCCTTAATTTGTAAA
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAA
* *
28876722 GGATTTATTTACTCACGATGACACTTAATCATCGGACTCTTT
1 GGATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
28876764 CGTTTATAGC
Statistics
Matches: 174, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 171 0.98
52 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
GGATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAA
Found at i:28876652 original size:102 final size:102
Alignment explanation
Indices: 28876475--28876763 Score: 427
Period size: 102 Copynumber: 2.8 Consensus size: 102
28876465 TTTTATTTAG
* * * *
28876475 TACTCACGATGACATATTA-TCGTCGAACCATTTAATTTGTCATGGATTCATTTACTCACGATGA
1 TACTCACGATGACA-CTTAGTCATCGAACC-TTTAATTTGTAAAGGATTCATTTACTCACGATGA
28876539 CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
64 CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
28876578 TACTCACGATGACACTTAGTCATCGAACCTTTAATTCGTGAAGGATTCATTTACTAACGATGACA
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATTTGTAAAGGATTCATTTACTCACGATGACA
*
28876643 CTTAGTCATCGGACCCTTAATCCGTAAAGGATTCATT
66 CTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * * *
28876680 TACTCATGATGACACTTAGTCATCAAACCCTTAATTTGTAAAGGATTTATTTACTCACGATGACA
1 TACTCACGATGACACTTAGTCATCGAACCTTTAATTTGTAAAGGATTCATTTACTCACGATGACA
*
28876745 CTTAATCATCGGACTCTTT
66 CTTAGTCATCGGAC-CTTT
28876764 CGTTTATAGC
Statistics
Matches: 168, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
102 142 0.85
103 26 0.15
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (102 bp):
TACTCACGATGACACTTAGTCATCGAACCTTTAATTTGTAAAGGATTCATTTACTCACGATGACA
CTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:28912410 original size:145 final size:145
Alignment explanation
Indices: 28912160--28912446 Score: 385
Period size: 145 Copynumber: 2.0 Consensus size: 145
28912150 TTCTAGTTCA
* * * * * * *
28912160 TAGAGCTCCCATGGGTTAAGCTGATTAATGGGAGTTTTCCACCAAAGAATATCCTCTCTCCCTTG
1 TAGAGCTCCCATGGATTAAGCTGATCAATGGGAGTATACCACAAAAGAAGATCCTCTCTCACTTG
** * *
28912225 TGACTGTCAGGCCAAAGAAATTTCCCATTGATTTTGTTTTCATGCATCTAGTTGGTCGTGGACCT
66 TGACTGTCAGGCCAAAGAAATTGACCATTGATTTTCTTTTCATACATCTAGTTGGTCGTGGACCT
28912290 CATTCAAATCTTTCT
131 CATTCAAATCTTTCT
* * * * *
28912305 TAGAGGTCCCATGGATTAAGTTGATCAATGGGAGTATACCATAAAAGAAGATCTTCTCTTACTTG
1 TAGAGCTCCCATGGATTAAGCTGATCAATGGGAGTATACCACAAAAGAAGATCCTCTCTCACTTG
* * * *
28912370 TGACTTTTATGCCAAAGAAATTGACCATTGATTTTCTTTTCATACATCTAGTTGGTCGTGGGCCT
66 TGACTGTCAGGCCAAAGAAATTGACCATTGATTTTCTTTTCATACATCTAGTTGGTCGTGGACCT
*
28912435 CATTGAAATCTT
131 CATTCAAATCTT
28912447 GGACAAGCAA
Statistics
Matches: 121, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
145 121 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (145 bp):
TAGAGCTCCCATGGATTAAGCTGATCAATGGGAGTATACCACAAAAGAAGATCCTCTCTCACTTG
TGACTGTCAGGCCAAAGAAATTGACCATTGATTTTCTTTTCATACATCTAGTTGGTCGTGGACCT
CATTCAAATCTTTCT
Found at i:28917404 original size:18 final size:18
Alignment explanation
Indices: 28917381--28917427 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
28917371 AGAAGCACTC
28917381 AAGAAGAAGGAGAAATGA
1 AAGAAGAAGGAGAAATGA
28917399 AAGAAGAAGGAGAAATGA
1 AAGAAGAAGGAGAAATGA
28917417 AAGAAGAAGGA
1 AAGAAGAAGGA
28917428 CAAACATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04
Consensus pattern (18 bp):
AAGAAGAAGGAGAAATGA
Found at i:28919122 original size:17 final size:15
Alignment explanation
Indices: 28919099--28919147 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
28919089 TCAGTCATTT
28919099 GAAAAAGAAAAAATAA
1 GAAAAAGAAAAAA-AA
*
28919115 GAAAAAAGGGAAAAAAAT
1 G-AAAAA--GAAAAAAAA
28919133 GAAAAAGAAAAAAAA
1 GAAAAAGAAAAAAAA
28919148 TTTTAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 10 0.36
18 2 0.07
19 7 0.25
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (15 bp):
GAAAAAGAAAAAAAA
Found at i:28927527 original size:22 final size:22
Alignment explanation
Indices: 28927495--28927543 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
28927485 GCGCAGGAGT
28927495 ATTACACGACTACTAAGAAGGA
1 ATTACACGACTACTAAGAAGGA
*
28927517 ATTACATGACTACTAAGAAGGA
1 ATTACACGACTACTAAGAAGGA
28927539 ATTAC
1 ATTAC
28927544 TAGTAGTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.22
Consensus pattern (22 bp):
ATTACACGACTACTAAGAAGGA
Found at i:28959268 original size:23 final size:22
Alignment explanation
Indices: 28959237--28959280 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28959227 AAAGAAATAA
*
28959237 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
28959259 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
28959281 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:28974976 original size:7 final size:7
Alignment explanation
Indices: 28974939--28975069 Score: 169
Period size: 6 Copynumber: 20.4 Consensus size: 7
28974929 TTTCTTTCTC
28974939 TTTTTCA
1 TTTTTCA
28974946 -TTTTCA
1 TTTTTCA
28974952 -TTTTC-
1 TTTTTCA
*
28974957 CTTTTCA
1 TTTTTCA
28974964 -TTTTCA
1 TTTTTCA
28974970 TTTTTCA
1 TTTTTCA
28974977 TTTTTCA
1 TTTTTCA
28974984 TTTTTCA
1 TTTTTCA
28974991 TTTTTCA
1 TTTTTCA
28974998 TTTTTCA
1 TTTTTCA
28975005 TTTTTCA
1 TTTTTCA
28975012 TTTTTCA
1 TTTTTCA
28975019 -TTTTCA
1 TTTTTCA
28975025 -TTTTCA
1 TTTTTCA
28975031 -TTTTCA
1 TTTTTCA
28975037 -TTTTCA
1 TTTTTCA
28975043 TTTTT-A
1 TTTTTCA
28975049 TTTTT-A
1 TTTTTCA
28975055 TTTTT-A
1 TTTTTCA
28975061 TTTTT-A
1 TTTTTCA
28975067 TTT
1 TTT
28975070 AATATTGTTT
Statistics
Matches: 120, Mismatches: 0, Indels: 9
0.93 0.00 0.07
Matches are distributed among these distances:
6 68 0.57
7 52 0.43
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:28975097 original size:6 final size:6
Alignment explanation
Indices: 28974939--28975204 Score: 162
Period size: 6 Copynumber: 41.2 Consensus size: 6
28974929 TTTCTTTCTC
* ** * *
28974939 TTTTTCA TTTTCA TTTTCC TTTTCA TTTTCA TTTTTCA TTTTTCA TTTTTCA
1 TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-A TTTTT-A TTTTT-A
* * * *
28974991 TTTTTCA TTTTTCA TTTTTCA TTTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
1 TTTTT-A TTTTT-A TTTTT-A TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA
*
28975043 TTTTTA TTTTTA TTTTTA TTTTTA TTTAATA TTGTTT- TTTTTA TTTTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TT-TTTA TTTTTA --TTTTTA
* ** *
28975094 TTTTTA GTTTTA -GATTA GTTTTTTA TTTTTTA TTTTTA TTTTTA GTTTTA
1 TTTTTA TTTTTA TTTTTA --TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA
*
28975144 GTTTTGT- TTTGTTT TTTTTA TTTTTTA TTTTTA -TTTTA TTATGTACTA
1 -TTTT-TA TTT-TTA TTTTTA -TTTTTA TTTTTA TTTTTA TT-T-T--TA
28975192 TTTTTA TTTTTA T
1 TTTTTA TTTTTA T
28975205 GGTTTTTTTT
Statistics
Matches: 224, Mismatches: 16, Indels: 39
0.80 0.06 0.14
Matches are distributed among these distances:
5 11 0.05
6 118 0.53
7 77 0.34
8 13 0.06
9 1 0.00
10 4 0.02
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:28975139 original size:38 final size:35
Alignment explanation
Indices: 28975043--28975181 Score: 156
Period size: 38 Copynumber: 3.8 Consensus size: 35
28975033 TTCATTTTCA
* * *
28975043 TTTTTATTTTTATTTTTATTTTTATTTAATATTG-
1 TTTTTTTTTTTATTTTTATTTTTATTTTAGATTGT
*
28975077 TTTTTTTTATT-TTTTTATTTTTAGTTTTAGATTAGT
1 TTTTTTTTTTTATTTTTATTTTTA-TTTTAGATT-GT
*
28975113 TTTTTATTTTTTATTTTTATTTTTAGTTTTAGTTTTGT
1 TTTTT-TTTTTTATTTTTATTTTTA-TTTTAG-ATTGT
28975151 TTTGTTTTTTTTATTTTTTATTTTTATTTTA
1 TTT-TTTTTTTTA-TTTTTATTTTTATTTTA
28975182 TTATGTACTA
Statistics
Matches: 91, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
33 12 0.13
34 16 0.18
35 1 0.01
36 5 0.05
37 5 0.05
38 36 0.40
39 16 0.18
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (35 bp):
TTTTTTTTTTTATTTTTATTTTTATTTTAGATTGT
Found at i:28975145 original size:33 final size:32
Alignment explanation
Indices: 28974958--28975203 Score: 141
Period size: 33 Copynumber: 7.6 Consensus size: 32
28974948 TTCATTTTCC
* * * *
28974958 TTTTCATTTTCATTTTTCATTTTTCATTTTTCAT
1 TTTTTATTTTTATTTTT-AGTTTT-ATTTTTTAT
* * *
28974992 TTTTCATTTTTCATTTTTCATTTTTCA-TTTTCA-
1 TTTTTATTTTT-ATTTTT-AGTTTT-ATTTTTTAT
* * * *
28975025 TTTTCATTTTCATTTTCATTTTTA-TTTTTA-
1 TTTTTATTTTTATTTTTAGTTTTATTTTTTAT
*
28975055 TTTTTATTTTTATTTAATA-TTGTT-TTTTTTATT
1 TTTTTATTTTTATTT-TTAGTT-TTATTTTTTA-T
* *
28975088 TTTTTATTTTTAGTTTTAG-ATTAGTTTTTTAT
1 TTTTTATTTTTATTTTTAGTTTTA-TTTTTTAT
28975120 TTTTTATTTTTATTTTTAGTTTTAGTTTTGTT-T
1 TTTTTATTTTTATTTTTAGTTTTA-TTTT-TTAT
* *
28975153 TGTTT-TTTTTATTTTTTATTTTTATTTTATTAT
1 TTTTTATTTTTA-TTTTTAGTTTTATTTT-TTAT
* **
28975186 GTACTATTTTTATTTTTA
1 TTTTTATTTTTATTTTTA
28975204 TGGTTTTTTT
Statistics
Matches: 178, Mismatches: 20, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
30 21 0.12
31 17 0.10
32 38 0.21
33 63 0.35
34 24 0.13
35 15 0.08
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (32 bp):
TTTTTATTTTTATTTTTAGTTTTATTTTTTAT
Found at i:28977099 original size:23 final size:25
Alignment explanation
Indices: 28977073--28977118 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28977063 CCAATTAAGG
28977073 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
28977096 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
28977119 TGGATCGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:28979452 original size:12 final size:12
Alignment explanation
Indices: 28979435--28979462 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28979425 GCATCTGAAA
28979435 TGACCTGAATTG
1 TGACCTGAATTG
28979447 TGACCTGAATTG
1 TGACCTGAATTG
28979459 TGAC
1 TGAC
28979463 AGAGAGCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (12 bp):
TGACCTGAATTG
Found at i:28989336 original size:14 final size:14
Alignment explanation
Indices: 28989319--28989354 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
28989309 TTGTTTGACT
*
28989319 GAAAATGTTTTCTG
1 GAAAATGATTTCTG
28989333 GAAAATGATTTCTG
1 GAAAATGATTTCTG
28989347 GAAAATGA
1 GAAAATGA
28989355 ATTCCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTG
Done.