Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 94 of 186
Found at i:30844566 original size:12 final size:12
Alignment explanation
Indices: 30844549--30844581 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
30844539 TAGATAAATA
30844549 TAAGTGATTTTT
1 TAAGTGATTTTT
30844561 TAAGTGA-TTTT
1 TAAGTGATTTTT
30844572 TAA-TGATTTT
1 TAAGTGATTTT
30844582 ATTGTTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 10 0.50
12 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (12 bp):
TAAGTGATTTTT
Found at i:30844578 original size:10 final size:11
Alignment explanation
Indices: 30844549--30844581 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
30844539 TAGATAAATA
30844549 TAAGTGATTTTT
1 TAAGTGA-TTTT
30844561 TAAGTGATTTT
1 TAAGTGATTTT
30844572 TAA-TGATTTT
1 TAAGTGATTTT
30844582 ATTGTTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 7 0.33
12 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (11 bp):
TAAGTGATTTT
Found at i:30853502 original size:193 final size:193
Alignment explanation
Indices: 30853167--30853554 Score: 767
Period size: 193 Copynumber: 2.0 Consensus size: 193
30853157 TTTCGATGAA
*
30853167 TGAAATTTAATAAATTTCATCCCATCTGTGCACGTATCATCCCCCCTTTCCTCGAAAAGATTCGT
1 TGAAACTTAATAAATTTCATCCCATCTGTGCACGTATCATCCCCCCTTTCCTCGAAAAGATTCGT
30853232 CCTCAAATCTTGTCTTTAATCGAATGTTGGTTTGATTTGTTTGGTTTTTGACATTGTTGTTGGGC
66 CCTCAAATCTTGTCTTTAATCGAATGTTGGTTTGATTTGTTTGGTTTTTGACATTGTTGTTGGGC
30853297 CTTGAGGTAGTGTGAGCTCATCACATCCATGGGTCTGAAATTAGGCTTTGAGGCTCACATCAT
131 CTTGAGGTAGTGTGAGCTCATCACATCCATGGGTCTGAAATTAGGCTTTGAGGCTCACATCAT
30853360 TGAAACTTAATAAATTTCATCCCATCTGTGCACGTATCATCCCCCCTTTCCTCGAAAAGATTCGT
1 TGAAACTTAATAAATTTCATCCCATCTGTGCACGTATCATCCCCCCTTTCCTCGAAAAGATTCGT
30853425 CCTCAAATCTTGTCTTTAATCGAATGTTGGTTTGATTTGTTTGGTTTTTGACATTGTTGTTGGGC
66 CCTCAAATCTTGTCTTTAATCGAATGTTGGTTTGATTTGTTTGGTTTTTGACATTGTTGTTGGGC
30853490 CTTGAGGTAGTGTGAGCTCATCACATCCATGGGTCTGAAATTAGGCTTTGAGGCTCACATCAT
131 CTTGAGGTAGTGTGAGCTCATCACATCCATGGGTCTGAAATTAGGCTTTGAGGCTCACATCAT
30853553 TG
1 TG
30853555 CAAAAAAATA
Statistics
Matches: 194, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 194 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (193 bp):
TGAAACTTAATAAATTTCATCCCATCTGTGCACGTATCATCCCCCCTTTCCTCGAAAAGATTCGT
CCTCAAATCTTGTCTTTAATCGAATGTTGGTTTGATTTGTTTGGTTTTTGACATTGTTGTTGGGC
CTTGAGGTAGTGTGAGCTCATCACATCCATGGGTCTGAAATTAGGCTTTGAGGCTCACATCAT
Found at i:30856848 original size:26 final size:26
Alignment explanation
Indices: 30856818--30856872 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
30856808 TTCATGACTC
30856818 CTTAAAGAAAATAAAGAAGAAAACTA
1 CTTAAAGAAAATAAAGAAGAAAACTA
30856844 CTTAAAGAAAATAAAGAAGAAAACTA
1 CTTAAAGAAAATAAAGAAGAAAACTA
30856870 CTT
1 CTT
30856873 CTAAAGAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (26 bp):
CTTAAAGAAAATAAAGAAGAAAACTA
Found at i:30866659 original size:74 final size:74
Alignment explanation
Indices: 30866534--30866677 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
30866524 CGTGTCCTCG
*
30866534 GCCGTGTGGAAATAGGGCTAAAAATTCCCAAGTATTGACATACACATGGCCATAAACTCGAGCCA
1 GCCGTGTGGAAATAGGGCTAAAAATTCCCAAGTATTGACATACACACGGCCATAAACTCGAGCCA
30866599 CACGATCCT
66 CACGATCCT
*
30866608 GCCGTGTGGAAATAGGGCTAAAAATTCCTAAGTATTGACATACACACGGCCATAAACTCGAGCCA
1 GCCGTGTGGAAATAGGGCTAAAAATTCCCAAGTATTGACATACACACGGCCATAAACTCGAGCCA
30866673 CACGA
66 CACGA
30866678 CCGTGTGACA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (74 bp):
GCCGTGTGGAAATAGGGCTAAAAATTCCCAAGTATTGACATACACACGGCCATAAACTCGAGCCA
CACGATCCT
Found at i:30869997 original size:30 final size:30
Alignment explanation
Indices: 30869961--30870018 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
30869951 TAGGCAGTTC
* *
30869961 CACATGGGTAATCCACATGCCCATGTGTGA
1 CACATGGGTAAGCCACACGCCCATGTGTGA
*
30869991 CACATGGGTAGGCCACACGCCCATGTGT
1 CACATGGGTAAGCCACACGCCCATGTGT
30870019 AATGACCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (30 bp):
CACATGGGTAAGCCACACGCCCATGTGTGA
Found at i:30877621 original size:17 final size:17
Alignment explanation
Indices: 30877599--30877633 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
30877589 AGGATATGTA
30877599 TGGCATGCCATTAGGTT
1 TGGCATGCCATTAGGTT
*
30877616 TGGCATGCCATTTGGTT
1 TGGCATGCCATTAGGTT
30877633 T
1 T
30877634 ACATGCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.29, T:0.40
Consensus pattern (17 bp):
TGGCATGCCATTAGGTT
Found at i:30879596 original size:46 final size:45
Alignment explanation
Indices: 30879461--30879732 Score: 192
Period size: 46 Copynumber: 5.8 Consensus size: 45
30879451 AGTGGTATGT
* *
30879461 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCAT-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-TGA-GATGA
* * *
30879507 AAGCTAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGC-CTGAGATGA
* *
30879553 GAGATAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-GAGAT-GA
* * * ** * * * *
30879600 CAAGGTAGTGTAAGACCTGTCTAAGACATGGCATCAG-CT-TGTTGT
1 -GAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCCTGAGATGA
* * * *
30879645 GTG-TCAGTGTAAGACCTGTCTGGGACATGGCATTGACACTGATAGATGA
1 GAGCT-AGTGTAAGACATGTCTGGGACAT-GCATCGGC-CTG--AGATGA
* * *
30879694 GAGCTAGTGTAAGTCCTGTCTGGGACACGGCATCGGCCT
1 GAGCTAGTGTAAGACATGTCTGGGACA-TGCATCGGCCT
30879733 CGATATATGA
Statistics
Matches: 177, Mismatches: 35, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
43 1 0.01
44 27 0.15
45 1 0.01
46 80 0.45
47 2 0.01
48 27 0.15
49 38 0.21
50 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTGAGATGA
Found at i:30879712 original size:49 final size:49
Alignment explanation
Indices: 30879503--30879779 Score: 170
Period size: 49 Copynumber: 5.8 Consensus size: 49
30879493 CGGCCATATT
* * * *
30879503 ATGAAAG-CTAGTGTAAGACATGTCTGGGACA-TGCATCGACATTG--AG
1 ATGAAAGTC-AGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATAG
* * * * * *
30879549 ATGAGAGAT-AGTGTAAGACATGTCTGGGACA-TGCATCGGCCTCGAGAT
1 ATGAAAG-TCAGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATAG
** * * * *
30879597 AT-ACAAGGT-AGTGTAAGACCTGTCTAAGACATGGCATC-AGCTTG-TTG
1 ATGA-AA-GTCAGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATAG
* * *
30879644 -TG--TGTCAGTGTAAGACCTGTCTGGGACATGGCATTGACACT-GATAG
1 ATGAAAGTCAGTGTAAGACCTGTCTGGGACACGGCATCGAC-CTCGATAG
* * * *
30879690 ATGAGAG-CTAGTGTAAGTCCTGTCTGGGACACGGCATCGGCCTCGATAT
1 ATGAAAGTC-AGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATAG
* *
30879739 ATGAAAGTCAGTGTAAGACCTGTCTTGGACACAGCATCGAC
1 ATGAAAGTCAGTGTAAGACCTGTCTGGGACACGGCATCGAC
30879780 TTTAATGTGC
Statistics
Matches: 180, Mismatches: 33, Indels: 33
0.73 0.13 0.13
Matches are distributed among these distances:
43 2 0.01
44 26 0.14
45 2 0.01
46 43 0.24
47 3 0.02
48 30 0.17
49 73 0.41
50 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (49 bp):
ATGAAAGTCAGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATAG
Found at i:30879776 original size:142 final size:138
Alignment explanation
Indices: 30879512--30879776 Score: 354
Period size: 142 Copynumber: 1.9 Consensus size: 138
30879502 TATGAAAGCT
*
30879512 AGTGTAAGACATGTCTGGGACATGCATCGACATTGAGATGAGAGATAGTGTAAGACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCGACACTGAGATGAGAGATAGTGTAAGACATGTCTGGG
* **
30879577 ACATGCATCGGCCTCGAGATATACAAGGTAGTGTAAGACCTGTCTAAGACATGGCATCAGCTTGT
66 ACAGGCATCGGCCTCGAGATATACAAGGTAGTGTAAGACCTGTCTAAGACACAGCATCAGCTTGT
30879642 TGTGTGTC
131 TGTGTGTC
* * * * *
30879650 AGTGTAAGACCTGTCTGGGACATGGCATTGACACTGATAGATGAGAGCTAGTGTAAGTCCTGTCT
1 AGTGTAAGACATGTCTGGGACAT-GCATCGACACTG--AGATGAGAGATAGTGTAAGACATGTCT
* **
30879715 GGGACACGGCATCGGCCTCGATATATGA-AA-GTCAGTGTAAGACCTGTCTTGGACACAGCATC
63 GGGACA-GGCATCGGCCTCGAGATAT-ACAAGGT-AGTGTAAGACCTGTCTAAGACACAGCATC
30879777 GACTTTAATG
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
138 22 0.20
139 10 0.09
141 32 0.29
142 44 0.40
143 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (138 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACACTGAGATGAGAGATAGTGTAAGACATGTCTGGG
ACAGGCATCGGCCTCGAGATATACAAGGTAGTGTAAGACCTGTCTAAGACACAGCATCAGCTTGT
TGTGTGTC
Found at i:30892022 original size:46 final size:46
Alignment explanation
Indices: 30891969--30892138 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
30891959 TTGAGCATCT
* *
30891969 GAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* * * *
30892015 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CGTCC
* * * *
30892062 GAACTCGTTGAATTGAGTCCGAGTTCATTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* *
30892108 GAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
30892139 GGGGTGGGTT
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 55 0.55
47 28 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:30892122 original size:93 final size:93
Alignment explanation
Indices: 30891963--30892133 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
30891953 GGATGGTTGA
* * * * * *
30891963 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
30892028 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
30892056 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
30892121 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
30892134 ACTTAGGGGT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:30896497 original size:35 final size:35
Alignment explanation
Indices: 30896451--30896521 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
30896441 ATATAAATGG
30896451 TAAAATTAAAATTTAAATCCCTTAACCATTTAATT
1 TAAAATTAAAATTTAAATCCCTTAACCATTTAATT
30896486 TAAAATTAAAATTTAAATCCCTTAACCATTTAATT
1 TAAAATTAAAATTTAAATCCCTTAACCATTTAATT
30896521 T
1 T
30896522 CATAGCCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAAATTAAAATTTAAATCCCTTAACCATTTAATT
Found at i:30898138 original size:22 final size:21
Alignment explanation
Indices: 30898104--30898147 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
30898094 TGACAATGTA
30898104 AATGCAAAATTTTTCAGAAATC
1 AATGCAAAA-TTTTCAGAAATC
* *
30898126 AATGCATAGTTTTCAGAAATC
1 AATGCAAAATTTTCAGAAATC
30898147 A
1 A
30898148 TTCGTACCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (21 bp):
AATGCAAAATTTTCAGAAATC
Found at i:30900041 original size:27 final size:29
Alignment explanation
Indices: 30899988--30900041 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
30899978 GAGATTGGCA
* * *
30899988 ATTTTATCGTATTATATGTTATCCGGTAG
1 ATTTTATCGCATTATATGATATACGGTAG
30900017 ATTTTAT-GCATT-TATGATATACGGT
1 ATTTTATCGCATTATATGATATACGGT
30900042 GGTTTTTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 4 0.18
29 7 0.32
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (29 bp):
ATTTTATCGCATTATATGATATACGGTAG
Found at i:30900636 original size:122 final size:122
Alignment explanation
Indices: 30900499--30900744 Score: 431
Period size: 122 Copynumber: 2.0 Consensus size: 122
30900489 CTTGATTTAT
30900499 ATTATAAAAAAATTATTTAATTAAAACATTATAAATTATATTAATTAAAATTAAGATATTATATT
1 ATTATAAAAAAATTATTTAATTAAAACATTATAAATTATATTAATTAAAATTAAGATATTATATT
* *
30900564 AAAGAAAATAAGTAAAATAAAGA-AGATTGTATGGTAATAAAATATAAATGTGTAATA
66 AAAGAAAATAAATAAAATAAAGACA-ATTGTATGGAAATAAAATATAAATGTGTAATA
*
30900621 ATTATAAAAATATTATTTAATTAAAACATTATAAATTATATTAATTAAAATTAAGATATTATATT
1 ATTATAAAAAAATTATTTAATTAAAACATTATAAATTATATTAATTAAAATTAAGATATTATATT
* *
30900686 AAAGGAAATAAATAAAATAAAGACAATTGTATGGAAATAAAATATACATGTGTAATA
66 AAAGAAAATAAATAAAATAAAGACAATTGTATGGAAATAAAATATAAATGTGTAATA
30900743 AT
1 AT
30900745 CATATTTGTA
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
122 117 0.99
123 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (122 bp):
ATTATAAAAAAATTATTTAATTAAAACATTATAAATTATATTAATTAAAATTAAGATATTATATT
AAAGAAAATAAATAAAATAAAGACAATTGTATGGAAATAAAATATAAATGTGTAATA
Found at i:30900681 original size:23 final size:25
Alignment explanation
Indices: 30900629--30900687 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
30900619 TAATTATAAA
30900629 AATATTAT-TTAATTAAAACATTAT
1 AATATTATATTAATTAAAACATTAT
30900653 AA-ATTATATTAATT-AAA-ATTA-
1 AATATTATATTAATTAAAACATTAT
30900674 AGATATTATATTAA
1 A-ATATTATATTAA
30900688 AGGAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 1 0.03
22 5 0.16
23 18 0.56
24 8 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
AATATTATATTAATTAAAACATTAT
Found at i:30901232 original size:18 final size:17
Alignment explanation
Indices: 30901209--30901260 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
30901199 AAATAGATAT
30901209 TTATTTTATTTATTATCA
1 TTATTTTATTTATTAT-A
* *
30901227 TTATTTAATTAATTGATA
1 TTATTTTATTTATT-ATA
*
30901245 TTATATTATTATATTA
1 TTATTTTATT-TATTA
30901261 ATGAATAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATTTTATTTATTATA
Found at i:30901635 original size:98 final size:98
Alignment explanation
Indices: 30901523--30901863 Score: 675
Period size: 98 Copynumber: 3.5 Consensus size: 98
30901513 GGTTTTAAGG
30901523 TTTG-AAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTTTGATGTTTTGGAAGCTT
1 TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTTTGATGTTTTGGAAGCTT
30901587 TAGAACAAAGTTTTGTTGAAATTAAGTTGAAGT
66 TAGAACAAAGTTTTGTTGAAATTAAGTTGAAGT
30901620 TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTTTGATGTTTTGGAAGCTT
1 TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTTTGATGTTTTGGAAGCTT
30901685 TAGAACAAAGTTTTGTTGAAATTAAGTTGAAGT
66 TAGAACAAAGTTTTGTTGAAATTAAGTTGAAGT
30901718 TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTTTGATGTTTTGGAAGCTT
1 TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTTTGATGTTTTGGAAGCTT
30901783 TAGAACAAAGTTTTGTTGAAATTAAGTTGAAGT
66 TAGAACAAAGTTTTGTTGAAATTAAGTTGAAGT
30901816 TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTT
1 TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTT
30901864 AATATGTTCA
Statistics
Matches: 243, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
97 4 0.02
98 239 0.98
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (98 bp):
TTTGAAAGCTTTAAAAGGTGAGTCAATTAAGTCATTTTCTCTTAATTTTGATGTTTTGGAAGCTT
TAGAACAAAGTTTTGTTGAAATTAAGTTGAAGT
Found at i:30906410 original size:27 final size:28
Alignment explanation
Indices: 30906335--30906411 Score: 70
Period size: 27 Copynumber: 2.8 Consensus size: 28
30906325 GAGATATTTT
* ** *
30906335 GATATTTTATAATTATTTAATTAGATAA
1 GATATTTTATTATTATTTTTTTAGAAAA
* *
30906363 -ATATTATT-TTATTAATATTTTA-AAAA
1 GATATT-TTATTATTATTTTTTTAGAAAA
30906389 GATATTTTATTATTATTTTTTTA
1 GATATTTTATTATTATTTTTTTA
30906412 TTACTTTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
26 5 0.13
27 31 0.82
28 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
GATATTTTATTATTATTTTTTTAGAAAA
Found at i:30908573 original size:46 final size:46
Alignment explanation
Indices: 30908506--30908722 Score: 256
Period size: 46 Copynumber: 4.7 Consensus size: 46
30908496 GTGTGCTTAC
**
30908506 TGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACA
1 TGAAATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAACA
** *
30908552 TGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATCG-CAACG
1 TGAAATGAAATGAATAAGACCATGGTTGAAAGATACCAT-GACAACA
* * * *
30908598 TGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGAAATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAACA
*** *
30908644 TGACGGGAAATGAATAATACCATGGTTGAAAGATACCATGACAACA
1 TGAAATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAACA
*** * *
30908690 TGACGGGAAACGAATAAGACCATAGTTGAAAGA
1 TGAAATGAAATGAATAAGACCATGGTTGAAAGA
30908723 CACTATGGCA
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
45 1 0.01
46 153 0.99
47 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (46 bp):
TGAAATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAACA
Found at i:30908841 original size:13 final size:13
Alignment explanation
Indices: 30908820--30908889 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
30908810 ACCAGATGAC
30908820 AAATGGTTATATG
1 AAATGGTTATATG
* **
30908833 AATTGGTTATACA
1 AAATGGTTATATG
* *
30908846 AAATGGTTGTGTG
1 AAATGGTTATATG
* *
30908859 AAATGTTTATAGG
1 AAATGGTTATATG
* *
30908872 AATTGGTCATATGG
1 AAATGGTTATAT-G
30908886 AAAT
1 AAAT
30908890 ATATGTACAA
Statistics
Matches: 39, Mismatches: 17, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
13 35 0.90
14 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (13 bp):
AAATGGTTATATG
Found at i:30908860 original size:26 final size:26
Alignment explanation
Indices: 30908820--30908869 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
30908810 ACCAGATGAC
*
30908820 AAATGGTTATATGAATTGGTTATACA
1 AAATGGTTATATGAAATGGTTATACA
* * *
30908846 AAATGGTTGTGTGAAATGTTTATA
1 AAATGGTTATATGAAATGGTTATA
30908870 GGAATTGGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40
Consensus pattern (26 bp):
AAATGGTTATATGAAATGGTTATACA
Found at i:30919821 original size:28 final size:31
Alignment explanation
Indices: 30919790--30919847 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 31
30919780 ACATCAAAAA
*
30919790 AAATCAATAAA-A-CTAATAATAA-AATAAT
1 AAATAAATAAAGATCTAATAATAATAATAAT
*
30919818 AAATAAATAAAGATTTAATAATAATAATAA
1 AAATAAATAAAGATCTAATAATAATAATAA
30919848 AATGAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
29 1 0.04
30 9 0.36
31 5 0.20
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (31 bp):
AAATAAATAAAGATCTAATAATAATAATAAT
Found at i:30923185 original size:32 final size:32
Alignment explanation
Indices: 30923149--30923217 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
30923139 ACGAGAGAAT
30923149 AGAAACGACAAACAGAGGGAATTTTTATAAAA
1 AGAAACGACAAACAGAGGGAATTTTTATAAAA
30923181 AGAAACGACAAACAGAGGGAATTTTTATAAAA
1 AGAAACGACAAACAGAGGGAATTTTTATAAAA
30923213 AGAAA
1 AGAAA
30923218 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.55, C:0.09, G:0.19, T:0.17
Consensus pattern (32 bp):
AGAAACGACAAACAGAGGGAATTTTTATAAAA
Found at i:30937983 original size:40 final size:40
Alignment explanation
Indices: 30937902--30937988 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 40
30937892 TGACGACATA
* * * **
30937902 TCAGCTAAATTTGACACTTAGTGTGCGGTTCAATATGGCT
1 TCAGCTAAATTTGACACTTAGTATGCGATTCAAGAAAGCT
* * *
30937942 TCGGCTAAATTTGGCACTTAGTATGCGATTCGAGAAAGCT
1 TCAGCTAAATTTGACACTTAGTATGCGATTCAAGAAAGCT
30937982 TCAGCTA
1 TCAGCTA
30937989 TGTACGACAC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (40 bp):
TCAGCTAAATTTGACACTTAGTATGCGATTCAAGAAAGCT
Found at i:30938035 original size:28 final size:28
Alignment explanation
Indices: 30937994--30938106 Score: 127
Period size: 28 Copynumber: 4.0 Consensus size: 28
30937984 AGCTATGTAC
*
30937994 GACACTTAGTGTGCGAGATATCGAGTAT
1 GACACTTAGTGTGCGAGACATCGAGTAT
* * * *
30938022 GACACTTAGAGTGCGAAACATTGAGAAT
1 GACACTTAGTGTGCGAGACATCGAGTAT
** * *
30938050 GACACTTAGTGTGCGAGTTATTGATTAT
1 GACACTTAGTGTGCGAGACATCGAGTAT
* *
30938078 GGCACTTAGTGTGTGAGACATCGAGTAT
1 GACACTTAGTGTGCGAGACATCGAGTAT
30938106 G
1 G
30938107 CAACGACATT
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 68 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.29
Consensus pattern (28 bp):
GACACTTAGTGTGCGAGACATCGAGTAT
Found at i:30943131 original size:19 final size:19
Alignment explanation
Indices: 30943107--30943149 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
30943097 CTCGCTAAAT
30943107 AATCTCATAAGGTCTGATG
1 AATCTCATAAGGTCTGATG
30943126 AATCTCATAAGGTCTGATG
1 AATCTCATAAGGTCTGATG
30943145 AATCT
1 AATCT
30943150 TAGGTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (19 bp):
AATCTCATAAGGTCTGATG
Found at i:30950886 original size:55 final size:55
Alignment explanation
Indices: 30950802--30950913 Score: 208
Period size: 55 Copynumber: 2.0 Consensus size: 55
30950792 GTCTCAAATT
30950802 CAAGTCTTTTTGTGACATCAAGTATTTAAGACTTTTGTGAAT-GGTATATACTCGG
1 CAAGTCTTTTTGTGACATCAAGTATTTAAGACTTTTGTG-ATCGGTATATACTCGG
30950857 CAAGTCTTTTTGTGACATCAAGTATTTAAGACTTTTGTGATCGGTATATACTCGG
1 CAAGTCTTTTTGTGACATCAAGTATTTAAGACTTTTGTGATCGGTATATACTCGG
30950912 CA
1 CA
30950914 CTTTTCACCA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
54 2 0.04
55 54 0.96
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (55 bp):
CAAGTCTTTTTGTGACATCAAGTATTTAAGACTTTTGTGATCGGTATATACTCGG
Found at i:30953276 original size:66 final size:66
Alignment explanation
Indices: 30953170--30953301 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
30953160 ATACCTTAAT
*
30953170 GTCTTTGTTGAGCCCGTCTTCAAATCGTCGGCACATCTTGGCTTCTATAGGAACATATTCCCTGG
1 GTCTTCGTTGAGCCCGTCTTCAAATCGTCGGCACATCTTGGCTTCTATAGGAACATATTCCCTGG
30953235 C
66 C
* *
30953236 GTCTTCGTTGAGCCCGTCTTCAAATCGTCGGCACATCTTGGTTTCTGTAGGAACATATTCCCTGG
1 GTCTTCGTTGAGCCCGTCTTCAAATCGTCGGCACATCTTGGCTTCTATAGGAACATATTCCCTGG
30953301 C
66 C
30953302 ATACTTACTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.33
Consensus pattern (66 bp):
GTCTTCGTTGAGCCCGTCTTCAAATCGTCGGCACATCTTGGCTTCTATAGGAACATATTCCCTGG
C
Found at i:30955442 original size:46 final size:45
Alignment explanation
Indices: 30955375--30955542 Score: 153
Period size: 46 Copynumber: 3.6 Consensus size: 45
30955365 TGCCCCTAAG
*
30955375 TGAACTCAGACTCAACTCAACGAGCTCGGTCGTTCACATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGCTCGGTCGTT-ACATCCATAAA
* *
30955421 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGCTCGG-T--C--GTTACATCCATAAA
* * * * * *
30955468 CGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGCTCGGTC-GTTACATCCATAAA
* *
30955514 TGAAGTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGCTCGG
30955543 ATGCTCAACC
Statistics
Matches: 99, Mismatches: 15, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 52 0.53
47 28 0.28
48 1 0.01
49 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGCTCGGTCGTTACATCCATAAA
Found at i:30955492 original size:93 final size:93
Alignment explanation
Indices: 30955376--30955546 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
30955366 GCCCCTAAGT
* * *
30955376 GAACTCAGACTCAACTCAACGAGCTCGGTCGTTCACATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
30955441 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* ** * *
30955469 GAACTCGGACTCAACTCAACGAGCTCAGACATTTGCATCCATAAGTGAAGTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
30955534 CGAGTTCGGATGC
66 CGAGTTCGGATGC
30955547 TCAACCATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCACATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:30957333 original size:64 final size:64
Alignment explanation
Indices: 30957232--30957358 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 64
30957222 AGAGTATAGG
* * * *
30957232 AGAGCGAAAGGAACGAGAAACGGGCCAAAAATAGAGAAAATTGGCCAAAGTACGAAATCAACAT
1 AGAGCGAAAAGAACAAGAAACGGGCCAAAAACAGAGAAAATGGGCCAAAGTACGAAATCAACAT
30957296 AGAGCGAAAAGAACAAGAAACGGGCCAAAAACAGAGAAAATGGGCCAAAGTACGAAATCAACA
1 AGAGCGAAAAGAACAAGAAACGGGCCAAAAACAGAGAAAATGGGCCAAAGTACGAAATCAACA
30957359 CGGCCTGGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.52, C:0.17, G:0.24, T:0.07
Consensus pattern (64 bp):
AGAGCGAAAAGAACAAGAAACGGGCCAAAAACAGAGAAAATGGGCCAAAGTACGAAATCAACAT
Found at i:30957781 original size:19 final size:19
Alignment explanation
Indices: 30957757--30957799 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
30957747 TAAATACCTC
30957757 AGATTCATCAGACCTTATG
1 AGATTCATCAGACCTTATG
*
30957776 AGATTCATCGGACCTTATG
1 AGATTCATCAGACCTTATG
30957795 AGATT
1 AGATT
30957800 ATTTAGCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (19 bp):
AGATTCATCAGACCTTATG
Found at i:30958563 original size:40 final size:40
Alignment explanation
Indices: 30958505--30958586 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
30958495 TGACGACATA
*
30958505 TCGGCTAAATTAGACACTTAGTGTACGGTTCGAGATAGCT
1 TCGGCTAAATTAGACACTTAGTGTACGATTCGAGATAGCT
* * *
30958545 TCGGCTAAATTTGGCACTTAGTGTGCGATTCGAGATAGCT
1 TCGGCTAAATTAGACACTTAGTGTACGATTCGAGATAGCT
30958585 TC
1 TC
30958587 AGGTATATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (40 bp):
TCGGCTAAATTAGACACTTAGTGTACGATTCGAGATAGCT
Found at i:30958604 original size:40 final size:40
Alignment explanation
Indices: 30958505--30958612 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
30958495 TGACGACATA
* * * *
30958505 TCGGCTAAATTAGACACTTAGTGTACGGTTCGAGATAGCT
1 TCGGCTAAATCAGGCACTTAGTGTGCGATTCGAGATAGCT
**
30958545 TCGGCTAAATTTGGCACTTAGTGTGCGATTCGAGATAGCT
1 TCGGCTAAATCAGGCACTTAGTGTGCGATTCGAGATAGCT
*
30958585 TCAGG-TATATACAGG-ACTTAGTGTGCGA
1 TC-GGCTAAAT-CAGGCACTTAGTGTGCGA
30958613 GATATCGAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 55 0.93
41 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (40 bp):
TCGGCTAAATCAGGCACTTAGTGTGCGATTCGAGATAGCT
Found at i:30958640 original size:28 final size:28
Alignment explanation
Indices: 30958600--30958681 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
30958590 TATATACAGG
30958600 ACTTAGTGTGCGAGATATCGAGTATGGC
1 ACTTAGTGTGCGAGATATCGAGTATGGC
* * *
30958628 ACTTAGTGTGCGAGTTATTGATTATGGC
1 ACTTAGTGTGCGAGATATCGAGTATGGC
*
30958656 ACTTAGTGTGCG-GTACATCGAGTATG
1 ACTTAGTGTGCGAG-ATATCGAGTATG
30958682 CAGCAGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.98
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.33
Consensus pattern (28 bp):
ACTTAGTGTGCGAGATATCGAGTATGGC
Found at i:30964673 original size:40 final size:40
Alignment explanation
Indices: 30964626--30964809 Score: 192
Period size: 40 Copynumber: 4.6 Consensus size: 40
30964616 CTCGCACAAG
* * *
30964626 GCCTTCGGGTCTTAGCCCGGATATGGTCACCAGTATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACCAGCACAAAT
* * *
30964666 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACCAGCACAAAT
*
30964706 GCCTTTGGGTCTTAGCCCGGATATAG-CAACTC-GCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-AC-CAGCACAAAT
** * * * * * *
30964746 GCCTTCGAATCTTAGTCCTGATATAGTTACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACCAGCACAAAT
*
30964786 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
30964810 CATTCGAATA
Statistics
Matches: 116, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 115 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACCAGCACAAAT
Found at i:30964721 original size:80 final size:80
Alignment explanation
Indices: 30964590--30964809 Score: 218
Period size: 80 Copynumber: 2.8 Consensus size: 80
30964580 ACCCAAGCAT
** * * *
30964590 CTTCGGAAT-TTAG-CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAGCCCGGATATGG
1 CTTC-GAATCTTAGCCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAG
* *
30964652 TC-AC-CAGTATAAATGC
65 -CAACTC-GCACAAATGC
* * * *
30964668 CTTCGGGA-CTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTTGGGTCTTAGCCCGGATATAG
1 CTTC-GAATCTTAGCCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAG
30964732 CAACTCGCACAAATGC
65 CAACTCGCACAAATGC
* * * * *
30964748 CTTCGAATCTTAGTCCTGATATAGTTACTAGCATAAAAGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGAATCTTAGCCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATAT
30964810 CATTCGAATA
Statistics
Matches: 117, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
78 11 0.09
79 19 0.16
80 86 0.74
81 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
CTTCGAATCTTAGCCCGGATATAGTCACTAGCACAAAAGCCTTCGGGTCTTAGCCCGGATATAGC
AACTCGCACAAATGC
Found at i:30971598 original size:8 final size:9
Alignment explanation
Indices: 30971574--30971609 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
30971564 GGGTTTACCC
30971574 ACAATTAAA
1 ACAATTAAA
30971583 ACAATTAAA
1 ACAATTAAA
30971592 A-AATTAAA
1 ACAATTAAA
30971600 ACAAGTTAAA
1 ACAA-TTAAA
30971610 CACTAACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 12 0.48
10 5 0.20
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.22
Consensus pattern (9 bp):
ACAATTAAA
Found at i:30971598 original size:17 final size:18
Alignment explanation
Indices: 30971576--30971609 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
30971566 GTTTACCCAC
30971576 AATTAAAACAA-TTAAAA
1 AATTAAAACAAGTTAAAA
30971593 AATTAAAACAAGTTAAA
1 AATTAAAACAAGTTAAA
30971610 CACTAACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTAAAACAAGTTAAAA
Found at i:30973401 original size:61 final size:61
Alignment explanation
Indices: 30973306--30973428 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
30973296 AACATGTCCT
30973306 TTTCAAAGAAGAAGCTTTATGTTTAATATGTCTATTGGTTGTTGTTTCTATTTGTTATTGC
1 TTTCAAAGAAGAAGCTTTATGTTTAATATGTCTATTGGTTGTTGTTTCTATTTGTTATTGC
*
30973367 TTTCAAAGAAGAAGCTTTATGTTTAATATGTCTATTGGTTGTTGTTTCTATTTGTTGTTGC
1 TTTCAAAGAAGAAGCTTTATGTTTAATATGTCTATTGGTTGTTGTTTCTATTTGTTATTGC
30973428 T
1 T
30973429 GATAACTTTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (61 bp):
TTTCAAAGAAGAAGCTTTATGTTTAATATGTCTATTGGTTGTTGTTTCTATTTGTTATTGC
Found at i:30974185 original size:51 final size:51
Alignment explanation
Indices: 30974104--30974203 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
30974094 AAGGTGGTGA
* * * *
30974104 GGGTGGTGAGGTTGTTGGTAGTAAATGTGGTAAGAGTGAGGGTGAGGGTAG
1 GGGTGGTAAGGTTGTTGGCAGTAAATGTGGTAAGAGCGAGGGAGAGGGTAG
* *
30974155 GGGTGGTAAGGTTGTTGGCAGT-AATAGTGGTGAGGGCGAGGGAGAGGGT
1 GGGTGGTAAGGTTGTTGGCAGTAAAT-GTGGTAAGAGCGAGGGAGAGGGT
30974204 GAAGGTAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 3 0.07
51 39 0.93
ACGTcount: A:0.21, C:0.02, G:0.52, T:0.25
Consensus pattern (51 bp):
GGGTGGTAAGGTTGTTGGCAGTAAATGTGGTAAGAGCGAGGGAGAGGGTAG
Found at i:30977658 original size:28 final size:29
Alignment explanation
Indices: 30977604--30977662 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
30977594 GTCTAGCCAA
30977604 CACAATAATTAAATAAAATAAAATTTACC
1 CACAATAATTAAATAAAATAAAATTTACC
30977633 CACAATAATTAAA-AAAATAAAATTTACC
1 CACAATAATTAAATAAAATAAAATTTACC
30977661 CA
1 CA
30977663 TATACAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.25
Consensus pattern (29 bp):
CACAATAATTAAATAAAATAAAATTTACC
Found at i:30977671 original size:29 final size:29
Alignment explanation
Indices: 30977604--30977671 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
30977594 GTCTAGCCAA
*
30977604 CACAATAATTAAATAAAATAAAATTTACC
1 CACAACAATTAAATAAAATAAAATTTACC
*
30977633 CACAATAATTAAA-AAAATAAAATTTACC
1 CACAACAATTAAATAAAATAAAATTTACC
*
30977661 CATATACAATT
1 CACA-ACAATT
30977672 TTGTATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 18 0.50
29 18 0.50
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (29 bp):
CACAACAATTAAATAAAATAAAATTTACC
Found at i:30977706 original size:163 final size:163
Alignment explanation
Indices: 30977518--30977844 Score: 654
Period size: 163 Copynumber: 2.0 Consensus size: 163
30977508 ACTTAAAAAT
30977518 TTCGTATCCACCAACCTACATTTCACACAAAAAAATCAACTTTTTTATTATATAAACTCTATGAT
1 TTCGTATCCACCAACCTACATTTCACACAAAAAAATCAACTTTTTTATTATATAAACTCTATGAT
30977583 TCCCTAATTTAGTCTAGCCAACACAATAATTAAATAAAATAAAATTTACCCACAATAATTAAAAA
66 TCCCTAATTTAGTCTAGCCAACACAATAATTAAATAAAATAAAATTTACCCACAATAATTAAAAA
30977648 AATAAAATTTACCCATATACAATTTTGTATATG
131 AATAAAATTTACCCATATACAATTTTGTATATG
30977681 TTCGTATCCACCAACCTACATTTCACACAAAAAAATCAACTTTTTTATTATATAAACTCTATGAT
1 TTCGTATCCACCAACCTACATTTCACACAAAAAAATCAACTTTTTTATTATATAAACTCTATGAT
30977746 TCCCTAATTTAGTCTAGCCAACACAATAATTAAATAAAATAAAATTTACCCACAATAATTAAAAA
66 TCCCTAATTTAGTCTAGCCAACACAATAATTAAATAAAATAAAATTTACCCACAATAATTAAAAA
30977811 AATAAAATTTACCCATATACAATTTTGTATATG
131 AATAAAATTTACCCATATACAATTTTGTATATG
30977844 T
1 T
30977845 AGAAAAGCTC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (163 bp):
TTCGTATCCACCAACCTACATTTCACACAAAAAAATCAACTTTTTTATTATATAAACTCTATGAT
TCCCTAATTTAGTCTAGCCAACACAATAATTAAATAAAATAAAATTTACCCACAATAATTAAAAA
AATAAAATTTACCCATATACAATTTTGTATATG
Found at i:30977821 original size:28 final size:29
Alignment explanation
Indices: 30977767--30977825 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
30977757 GTCTAGCCAA
30977767 CACAATAATTAAATAAAATAAAATTTACC
1 CACAATAATTAAATAAAATAAAATTTACC
30977796 CACAATAATTAAA-AAAATAAAATTTACC
1 CACAATAATTAAATAAAATAAAATTTACC
30977824 CA
1 CA
30977826 TATACAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.57
29 13 0.43
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.25
Consensus pattern (29 bp):
CACAATAATTAAATAAAATAAAATTTACC
Found at i:30977834 original size:29 final size:29
Alignment explanation
Indices: 30977767--30977834 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 29
30977757 GTCTAGCCAA
*
30977767 CACAATAATTAAATAAAATAAAATTTACC
1 CACAACAATTAAATAAAATAAAATTTACC
*
30977796 CACAATAATTAAA-AAAATAAAATTTACC
1 CACAACAATTAAATAAAATAAAATTTACC
*
30977824 CATATACAATT
1 CACA-ACAATT
30977835 TTGTATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 18 0.50
29 18 0.50
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (29 bp):
CACAACAATTAAATAAAATAAAATTTACC
Found at i:30978341 original size:113 final size:113
Alignment explanation
Indices: 30978175--30978384 Score: 300
Period size: 113 Copynumber: 1.9 Consensus size: 113
30978165 TACTCTATTA
**
30978175 TTCACGCATGGAAAAGAAATATTTCATCAATATCTAATTTAAAAAAATAAAAAAATC-CTTAATT
1 TTCACGCATGGAAAAGAAATATTTCATCAATATCTAATTTAAAAAAAT-AAAAAATCACACAATT
* * **
30978239 TCTTATTAACCCTAAAATAAATTGGCTAAATATGCTTATCCGAATACAT
65 TCTTATGAACCCTAAAACAAATCAGCTAAATATGCTTATCCGAATACAT
* *
30978288 TTCACGCATGGGAAAGAAATGTTTCATCAATAT-TCAA-TTAAAAAATATAAAAAATCACACAAT
1 TTCACGCATGGAAAAGAAATATTTCATCAATATCT-AATTTAAAAAA-ATAAAAAATCACACAAT
30978351 TTCTTATGAACCCTAAAACAAATCAGCTAAATAT
64 TTCTTATGAACCCTAAAACAAATCAGCTAAATAT
30978385 ACAGTGACTA
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
112 17 0.20
113 69 0.80
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (113 bp):
TTCACGCATGGAAAAGAAATATTTCATCAATATCTAATTTAAAAAAATAAAAAATCACACAATTT
CTTATGAACCCTAAAACAAATCAGCTAAATATGCTTATCCGAATACAT
Found at i:30978889 original size:17 final size:17
Alignment explanation
Indices: 30978867--30978900 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30978857 TAGTTAAGGG
30978867 TTTTAAATT-TTTTTTAA
1 TTTT-AATTATTTTTTAA
30978884 TTTTAATTATTTTTTAA
1 TTTTAATTATTTTTTAA
30978901 GTTCAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTAATTATTTTTTAA
Found at i:30980907 original size:15 final size:16
Alignment explanation
Indices: 30980855--30980925 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 16
30980845 CTACATACTC
*
30980855 GAATTTTTTTGGGTTT
1 GAATTTTTTTGAGTTT
30980871 GAATTTTTTTGAG-TT
1 GAATTTTTTTGAGTTT
*
30980886 CATATTTTTTT-AGTTT
1 GA-ATTTTTTTGAGTTT
* * *
30980902 GGATTTTTTAGA-CTT
1 GAATTTTTTTGAGTTT
30980917 GAATTTTTT
1 GAATTTTTT
30980926 GAGATTCGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
15 22 0.49
16 23 0.51
ACGTcount: A:0.18, C:0.03, G:0.17, T:0.62
Consensus pattern (16 bp):
GAATTTTTTTGAGTTT
Found at i:30980925 original size:31 final size:31
Alignment explanation
Indices: 30980855--30980925 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
30980845 CTACATACTC
* * *
30980855 GAATTTTTTTGGGTTTGAATTTTTTTGAGTT
1 GAATTTTTTTGAGTTTGAATTTTTTAGACTT
* *
30980886 CATATTTTTTT-AGTTTGGATTTTTTAGACTT
1 GA-ATTTTTTTGAGTTTGAATTTTTTAGACTT
30980917 GAATTTTTT
1 GAATTTTTT
30980926 GAGATTCGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 7 0.21
31 18 0.55
32 8 0.24
ACGTcount: A:0.18, C:0.03, G:0.17, T:0.62
Consensus pattern (31 bp):
GAATTTTTTTGAGTTTGAATTTTTTAGACTT
Found at i:30981919 original size:10 final size:10
Alignment explanation
Indices: 30981906--30981932 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30981896 ATTATATTAA
30981906 TTATTATTTT
1 TTATTATTTT
30981916 TTATTATTTT
1 TTATTATTTT
30981926 TTATTAT
1 TTATTAT
30981933 ACTGGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTATTTT
Found at i:30983097 original size:20 final size:20
Alignment explanation
Indices: 30983054--30983102 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
30983044 AGGGGCAATT
*
30983054 AAATCAATTTGATTAAAATA
1 AAATCAAATTGATTAAAATA
* *
30983074 AAATCAAATTGATTATAATC
1 AAATCAAATTGATTAAAATA
*
30983094 AAATAAAAT
1 AAATCAAAT
30983103 CAGGATACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATA
Found at i:30989708 original size:184 final size:184
Alignment explanation
Indices: 30989399--30989741 Score: 659
Period size: 184 Copynumber: 1.9 Consensus size: 184
30989389 ATCCAATTTT
30989399 ACTGAAAACTAGTTGTTACACTTACAGCAGCTGCCACCGGTAACACTAAGTTTTGGATCGAAGAT
1 ACTGAAAACTAGTTGTTACACTTACAGCAGCTGCCACCGGTAACACTAAGTTTTGGATCGAAGAT
*
30989464 TGCGCTTGAACCAAAGCTTCAAATTGCGAATTGATTGAATTGGTGGGAGTTTCCATTTTCTGTTA
66 TGCGCTTGAACCAAAGCTTCAAATTGCGAATTGATTGAATTGGTAGGAGTTTCCATTTTCTGTTA
30989529 AGAAACAAAACTAGAATTAGAAAACTTATATCTATTTCTAAAAGTGAACCACAA
131 AGAAACAAAACTAGAATTAGAAAACTTATATCTATTTCTAAAAGTGAACCACAA
*
30989583 ACTGAAAACTAGTTGTTACACTTACAGCAGCTGCCACCGGTAACACTGAGTTTTGGATCGAAGAT
1 ACTGAAAACTAGTTGTTACACTTACAGCAGCTGCCACCGGTAACACTAAGTTTTGGATCGAAGAT
*
30989648 TGCGCTTGAACCAAAGCTTCAAATTGCGAATTGATTGAATTGTTAGGAGTTTCCATTTTCTGTTA
66 TGCGCTTGAACCAAAGCTTCAAATTGCGAATTGATTGAATTGGTAGGAGTTTCCATTTTCTGTTA
30989713 AGAAACAAAACTAGAATTAGAAAACTTAT
131 AGAAACAAAACTAGAATTAGAAAACTTAT
30989742 CAACTTTTGT
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 156 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (184 bp):
ACTGAAAACTAGTTGTTACACTTACAGCAGCTGCCACCGGTAACACTAAGTTTTGGATCGAAGAT
TGCGCTTGAACCAAAGCTTCAAATTGCGAATTGATTGAATTGGTAGGAGTTTCCATTTTCTGTTA
AGAAACAAAACTAGAATTAGAAAACTTATATCTATTTCTAAAAGTGAACCACAA
Found at i:30990286 original size:82 final size:81
Alignment explanation
Indices: 30990054--30990732 Score: 465
Period size: 82 Copynumber: 8.2 Consensus size: 81
30990044 ATGACAAGAT
* *
30990054 TAAATCCCGAAACAAAATTATTTAATTAAATCT-TGTTTGGAAACAAAA-T--CA-A-AATAAAA
1 TAAATCCCGAAAC-AAATTATTTAATTAATTCTAT-TTTGGAAACAAAATTAAAATAGAATAAAA
* *
30990113 TCTGTTAAGCGACGGGAA
64 TCTGTTAAACGACTGGAA
* * ** * * *
30990131 TAAATCTCGAAACATAATTATTTGATTAAGCCTTCTCGTTTAGAAACAAAATCAAAATCGAATAA
1 TAAATCCCGAAACA-AATTATTTAATTAA---TTCTATTTTGGAAACAAAATTAAAATAGAATAA
* *
30990196 AATTTGTTAAATGACTGGAA
62 AATCTGTTAAACGACTGGAA
* *
30990216 TAAATCCCGAAACAGATTATTCAATTTAATTCTATTTTGGAAACAAAATTAAAATAGAATAAAAT
1 TAAATCCCGAAACAAATTATTTAA-TTAATTCTATTTTGGAAACAAAATTAAAATAGAATAAAAT
*
30990281 CTGTTAAACGGC-GTGAA
65 CTGTTAAACGACTG-GAA
* * * * * ** * * *
30990298 TAAATCCCAAAATAGATTATTCAATGTAATTTTA-TTTAAAAATTAAAATTATGAAACAAAATCA
1 TAAATCCCGAAACAAATTATTTAAT-TAATTCTATTTTGGAAA-CAAAATTA--AAATAGAAT-A
* * ** *
30990362 AAATCAAGTTTGTTGAATGACAAGAT
61 AAATC-----TGTTAAACGACTGGAA
* *
30990388 TAAATCCCGAAACAAAATTATTTAATTAAATCT-TGTTTGGAAACAAAA-T--CA-A-AATAAAA
1 TAAATCCCGAAAC-AAATTATTTAATTAATTCTAT-TTTGGAAACAAAATTAAAATAGAATAAAA
* *
30990447 TCTGTTAAGCGACGGGAA
64 TCTGTTAAACGACTGGAA
* * ** * * *
30990465 TAAATCTCGAAACATAATTATTTGATTAAGCCTTCTCGTTTAGAAACAAAATCAAAATCGAATAA
1 TAAATCCCGAAACA-AATTATTTAATTAA---TTCTATTTTGGAAACAAAATTAAAATAGAATAA
* *
30990530 AATTTGTTAAATGACTGGAA
62 AATCTGTTAAACGACTGGAA
* *
30990550 TAAATCCCGAAACAGATTATTCAATTTAATTCTATTTTGGAAACAAAATTAAAATAGAATAAAAT
1 TAAATCCCGAAACAAATTATTTAA-TTAATTCTATTTTGGAAACAAAATTAAAATAGAATAAAAT
*
30990615 CTGTTAAACGGC-GTGAA
65 CTGTTAAACGACTG-GAA
* * *
30990632 TAAATCTCGAAACAAATTTTATTTAATTTTAATTTCTCA-TTTGGAAACAAAATAAAAAATGGAA
1 TAAATCCCGAAACAAA--TTATTTAA--TTAA-TTCT-ATTTTGGAAACAAAAT-TAAAATAGAA
* *
30990696 TAAAATCTGTTGATCG-CTGGGAA
59 TAAAATCTGTTAAACGACT-GGAA
30990719 TAAATCCCGAAACA
1 TAAATCCCGAAACA
30990733 GATTTTATTC
Statistics
Matches: 471, Mismatches: 85, Indels: 82
0.74 0.13 0.13
Matches are distributed among these distances:
76 2 0.00
77 60 0.13
80 30 0.06
81 9 0.02
82 142 0.30
83 5 0.01
84 29 0.06
85 88 0.19
86 19 0.04
87 39 0.08
88 1 0.00
89 1 0.00
90 30 0.06
91 16 0.03
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (81 bp):
TAAATCCCGAAACAAATTATTTAATTAATTCTATTTTGGAAACAAAATTAAAATAGAATAAAATC
TGTTAAACGACTGGAA
Found at i:30990594 original size:162 final size:164
Alignment explanation
Indices: 30990036--30990736 Score: 657
Period size: 167 Copynumber: 4.2 Consensus size: 164
30990026 CAAAATCAAG
* ** * * *
30990036 TTTGTTGAATGACAAGATTAAATCCCGAAACAAAATTATTTAATTAAATCTTGTTTGGAAACAAA
1 TTTGTTAAATGACTGGAATAAATCCCGAAAC-AGATTATTCAATTAAATCTTGTTTGGAAACAAA
* * *
30990101 A-T-CA-A-AATAAAATCTGTTAAGCGACGGGAATAAATCTCGAAACATAATTATTTGATTAAGC
65 ATTAAATAGAATAAAATCTGTTAAACGACGGGAATAAATCTCGAAACATAATTATTTAATTAA--
*
30990162 CTTCTCGTTTAGAAACAAAAT-CAAAATCGAATAAAA
128 CTTCTCATTTAGAAACAAAATACAAAATCGAATAAAA
*
30990198 TTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTTAATTCTAT-TTTGGAAACAA
1 TTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAA-TTAAATCT-TGTTTGGAAACAA
* * * *
30990262 AATTAAAATAGAATAAAATCTGTTAAACGGCGTGAATAAATC-CCAAA-ATAGATTATTCAATGT
64 AATT-AAATAGAATAAAATCTGTTAAACGACGGGAATAAATCTCGAAACATA-ATTATTTAAT-T
* * * * * *
30990325 AA-TT-TTATTTAAAAATTAAAATTATGAAACAAAATCAAAATCAAG
126 AACTTCTCATTTAGAAA--CAAA--AT---ACAAAATC-GAATAAAA
* ** * * *
30990370 TTTGTTGAATGACAAGATTAAATCCCGAAACAAAATTATTTAATTAAATCTTGTTTGGAAACAAA
1 TTTGTTAAATGACTGGAATAAATCCCGAAAC-AGATTATTCAATTAAATCTTGTTTGGAAACAAA
* * *
30990435 A-T-CA-A-AATAAAATCTGTTAAGCGACGGGAATAAATCTCGAAACATAATTATTTGATTAAGC
65 ATTAAATAGAATAAAATCTGTTAAACGACGGGAATAAATCTCGAAACATAATTATTTAATTAA--
*
30990496 CTTCTCGTTTAGAAACAAAAT-CAAAATCGAATAAAA
128 CTTCTCATTTAGAAACAAAATACAAAATCGAATAAAA
*
30990532 TTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTTAATTCTAT-TTTGGAAACAA
1 TTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAA-TTAAATCT-TGTTTGGAAACAA
* *
30990596 AATTAAAATAGAATAAAATCTGTTAAACGGCGTGAATAAATCTCGAAACA-AATTTTATTTAATT
64 AATT-AAATAGAATAAAATCTGTTAAACGACGGGAATAAATCTCGAAACATAA--TTATTTAA--
* * * *
30990660 TTAATTTCTCATTTGGAAACAAAATAAAAAATGGAATAAAA
124 TTAACTTCTCATTTAGAAACAAAATACAAAATCGAATAAAA
* *
30990701 TCTGTT-GATCG-CTGGGAATAAATCCCGAAACAGATT
1 TTTGTTAAAT-GACT-GGAATAAATCCCGAAACAGATT
30990737 TTATTCAAAG
Statistics
Matches: 438, Mismatches: 61, Indels: 73
0.77 0.11 0.13
Matches are distributed among these distances:
161 18 0.04
162 99 0.23
163 19 0.04
164 2 0.00
165 8 0.02
166 16 0.04
167 102 0.23
168 42 0.10
169 48 0.11
170 6 0.01
171 17 0.04
172 52 0.12
173 9 0.02
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (164 bp):
TTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTAAATCTTGTTTGGAAACAAAA
TTAAATAGAATAAAATCTGTTAAACGACGGGAATAAATCTCGAAACATAATTATTTAATTAACTT
CTCATTTAGAAACAAAATACAAAATCGAATAAAA
Found at i:30990611 original size:334 final size:334
Alignment explanation
Indices: 30990002--30990637 Score: 1272
Period size: 334 Copynumber: 1.9 Consensus size: 334
30989992 GTTAAATGAC
30990002 AAAATTAAAATTATGAAACAAAATCAAAATCAAGTTTGTTGAATGACAAGATTAAATCCCGAAAC
1 AAAATTAAAATTATGAAACAAAATCAAAATCAAGTTTGTTGAATGACAAGATTAAATCCCGAAAC
30990067 AAAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTTAAGCGACGGGAAT
66 AAAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTTAAGCGACGGGAAT
30990132 AAATCTCGAAACATAATTATTTGATTAAGCCTTCTCGTTTAGAAACAAAATCAAAATCGAATAAA
131 AAATCTCGAAACATAATTATTTGATTAAGCCTTCTCGTTTAGAAACAAAATCAAAATCGAATAAA
30990197 ATTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTTAATTCTATTTTGGAAACAA
196 ATTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTTAATTCTATTTTGGAAACAA
30990262 AATTAAAATAGAATAAAATCTGTTAAACGGCGTGAATAAATCCCAAAATAGATTATTCAATGTAA
261 AATTAAAATAGAATAAAATCTGTTAAACGGCGTGAATAAATCCCAAAATAGATTATTCAATGTAA
30990327 TTTTATTTA
326 TTTTATTTA
30990336 AAAATTAAAATTATGAAACAAAATCAAAATCAAGTTTGTTGAATGACAAGATTAAATCCCGAAAC
1 AAAATTAAAATTATGAAACAAAATCAAAATCAAGTTTGTTGAATGACAAGATTAAATCCCGAAAC
30990401 AAAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTTAAGCGACGGGAAT
66 AAAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTTAAGCGACGGGAAT
30990466 AAATCTCGAAACATAATTATTTGATTAAGCCTTCTCGTTTAGAAACAAAATCAAAATCGAATAAA
131 AAATCTCGAAACATAATTATTTGATTAAGCCTTCTCGTTTAGAAACAAAATCAAAATCGAATAAA
30990531 ATTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTTAATTCTATTTTGGAAACAA
196 ATTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTTAATTCTATTTTGGAAACAA
30990596 AATTAAAATAGAATAAAATCTGTTAAACGGCGTGAATAAATC
261 AATTAAAATAGAATAAAATCTGTTAAACGGCGTGAATAAATC
30990638 TCGAAACAAA
Statistics
Matches: 302, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 302 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (334 bp):
AAAATTAAAATTATGAAACAAAATCAAAATCAAGTTTGTTGAATGACAAGATTAAATCCCGAAAC
AAAATTATTTAATTAAATCTTGTTTGGAAACAAAATCAAAATAAAATCTGTTAAGCGACGGGAAT
AAATCTCGAAACATAATTATTTGATTAAGCCTTCTCGTTTAGAAACAAAATCAAAATCGAATAAA
ATTTGTTAAATGACTGGAATAAATCCCGAAACAGATTATTCAATTTAATTCTATTTTGGAAACAA
AATTAAAATAGAATAAAATCTGTTAAACGGCGTGAATAAATCCCAAAATAGATTATTCAATGTAA
TTTTATTTA
Found at i:30990913 original size:20 final size:20
Alignment explanation
Indices: 30990884--30990925 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30990874 AAACAAAAAT
30990884 ATATAAATATAA-ATAAATAA
1 ATATAAATATAATA-AAATAA
*
30990904 ATATATATATAATAAAATAA
1 ATATAAATATAATAAAATAA
30990924 AT
1 AT
30990926 TGAATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAATATAATAAAATAA
Found at i:30990921 original size:16 final size:14
Alignment explanation
Indices: 30990880--30990925 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
30990870 CAGCAAACAA
*
30990880 AAATATATAAATAT
1 AAATAAATAAATAT
30990894 AAATAAATAAATAT
1 AAATAAATAAATAT
*
30990908 ATATATAATAAA-AT
1 AAATA-AATAAATAT
30990922 AAAT
1 AAAT
30990926 TGAATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 22 0.79
15 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATAAATAAATAT
Found at i:30992747 original size:24 final size:24
Alignment explanation
Indices: 30992720--30992768 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
30992710 TTAATAGATA
*
30992720 TTGCATGTTTTATTATTATTATTT
1 TTGCATGTGTTATTATTATTATTT
30992744 TTGCATGTGTTATTATTATTATTT
1 TTGCATGTGTTATTATTATTATTT
30992768 T
1 T
30992769 CAAATCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.65
Consensus pattern (24 bp):
TTGCATGTGTTATTATTATTATTT
Found at i:31008765 original size:17 final size:17
Alignment explanation
Indices: 31008743--31008795 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
31008733 TAGTTGAAGA
31008743 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
*
31008760 ATCTGTTT-G--TTT-A
1 ATCTGTTTGGATTTTGC
31008773 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
31008790 ATCTGT
1 ATCTGT
31008796 CTGTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
16 4 0.13
17 14 0.47
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (17 bp):
ATCTGTTTGGATTTTGC
Found at i:31008776 original size:30 final size:30
Alignment explanation
Indices: 31008742--31008800 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
31008732 TTAGTTGAAG
*
31008742 AATCTGTTTGGATTTTGCATCTGTTTGTTT
1 AATCTGTTTGGATTTTGCATCTGTCTGTTT
31008772 AATCTGTTTGGATTTTGCATCTGTCTGTT
1 AATCTGTTTGGATTTTGCATCTGTCTGTT
31008801 GAAGAATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (30 bp):
AATCTGTTTGGATTTTGCATCTGTCTGTTT
Found at i:31012863 original size:27 final size:27
Alignment explanation
Indices: 31012833--31012951 Score: 78
Period size: 32 Copynumber: 4.0 Consensus size: 27
31012823 TTTTGAAATT
*
31012833 ATTATGTCTTGAA-TTTGTTAGATATTG
1 ATTATGT-TTGAAGCTTGTTAGATATTG
*
31012860 ATTATGTTTTAAGCTTGTTAGATATTG
1 ATTATGTTTGAAGCTTGTTAGATATTG
* *
31012887 AATTTATTATGTTTTAAGCTTGTTGGATATTG
1 -----ATTATGTTTGAAGCTTGTTAGATATTG
* *
31012919 ACTTTATTATGTTTTAAGCTTGTTGGATATTG
1 -----ATTATGTTTGAAGCTTGTTAGATATTG
31012951 A
1 A
31012952 AATGATTGAC
Statistics
Matches: 82, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
26 4 0.05
27 21 0.26
32 57 0.70
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.52
Consensus pattern (27 bp):
ATTATGTTTGAAGCTTGTTAGATATTG
Found at i:31012899 original size:32 final size:32
Alignment explanation
Indices: 31012860--31012952 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
31012850 TTAGATATTG
*
31012860 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
31012892 ATTATGTTTTAAGCTTGTTGGATATTGACTTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
31012924 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTGGATATTGAA
31012953 ATGATTGACA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:31014328 original size:14 final size:14
Alignment explanation
Indices: 31014309--31014344 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31014299 CCAAAAAAGT
31014309 AAATCATTTTCCAG
1 AAATCATTTTCCAG
31014323 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
31014337 AAAACATT
1 AAATCATT
31014345 ACTGTCAAAC
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:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:31015430 original size:13 final size:14
Alignment explanation
Indices: 31015412--31015444 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
31015402 TTCAATATTT
31015412 CTTTTTTC-TTTTC
1 CTTTTTTCTTTTTC
31015425 C-TTTTTCTTTTTC
1 CTTTTTTCTTTTTC
31015438 CTTTTTT
1 CTTTTTT
31015445 TACACTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 7 0.39
14 5 0.28
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTCTTTTTC
Found at i:31021626 original size:14 final size:16
Alignment explanation
Indices: 31021607--31021650 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
31021597 GGCAACCCAT
31021607 ATTTATTT-ATTTT-A
1 ATTTATTTAATTTTGA
31021621 ATTTATTTAATTTTGA
1 ATTTATTTAATTTTGA
*
31021637 ATTTGGTTTAATTT
1 ATTT-ATTTAATTT
31021651 ATGTTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 5 0.19
17 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (16 bp):
ATTTATTTAATTTTGA
Found at i:31022340 original size:17 final size:17
Alignment explanation
Indices: 31022318--31022351 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31022308 TTATGTTACT
31022318 ATAAAAAATAAATAAAA
1 ATAAAAAATAAATAAAA
*
31022335 ATAAAAAATAAGTAAAA
1 ATAAAAAATAAATAAAA
31022352 GAGAGAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
ATAAAAAATAAATAAAA
Found at i:31022399 original size:18 final size:18
Alignment explanation
Indices: 31022367--31022401 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31022357 AGAGAGAGAC
*
31022367 TATATATATAGAAAAATA
1 TATATATAAAGAAAAATA
*
31022385 TATATATAAATAAAAAT
1 TATATATAAAGAAAAAT
31022402 TGCATGTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
TATATATAAAGAAAAATA
Found at i:31026458 original size:51 final size:50
Alignment explanation
Indices: 31026362--31026458 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
31026352 ATGTTACTTT
* *
31026362 AATTTTTTTAAAAAATTCACATTAATCTCATAAAAATTAATTAGACCCCA
1 AATTTTTTTAAAAAATTCACATTAAACTCATAAAAATTAACTAGACCCCA
* * *
31026412 AATTTTTTTAAAAAAATTCTCATTAAACT-TTAAAAATTTTACTAGAC
1 AATTTTTTT-AAAAAATTCACATTAAACTCATAAAAA-TTAACTAGAC
31026459 ATTTCTCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
50 15 0.38
51 25 0.62
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.39
Consensus pattern (50 bp):
AATTTTTTTAAAAAATTCACATTAAACTCATAAAAATTAACTAGACCCCA
Found at i:31038597 original size:28 final size:27
Alignment explanation
Indices: 31038556--31038609 Score: 99
Period size: 28 Copynumber: 2.0 Consensus size: 27
31038546 CGAGAAGTCC
31038556 AAAATTTTTTTCATATTAAAAACAGGT
1 AAAATTTTTTTCATATTAAAAACAGGT
31038583 AAAAGTTTTTTTCATATTAAAAACAGG
1 AAAA-TTTTTTTCATATTAAAAACAGG
31038610 GCTAGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (27 bp):
AAAATTTTTTTCATATTAAAAACAGGT
Found at i:31039294 original size:27 final size:28
Alignment explanation
Indices: 31039248--31039302 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
31039238 CTCCCTTGAA
*
31039248 TGCGAACCCCCTATAGGTGAGCCCCTGT
1 TGCGAACCCCCTATAAGTGAGCCCCTGT
* *
31039276 TGCGAA-CCTCTATAAGTGAGTCCCTGT
1 TGCGAACCCCCTATAAGTGAGCCCCTGT
31039303 ATTCAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.25
Consensus pattern (28 bp):
TGCGAACCCCCTATAAGTGAGCCCCTGT
Found at i:31039322 original size:28 final size:26
Alignment explanation
Indices: 31039256--31039322 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
31039246 AATGCGAACC
*
31039256 CCCTATAGGTGAGCCCCTGTTGCGAA
1 CCCTATAGGTGAGCCCCTGTTGCAAA
* * *
31039282 CCTCTATAAGTGAGTCCCTGTATTCAAA
1 CC-CTATAGGTGAGCCCCTGT-TGCAAA
31039310 CACCTATAGGTGA
1 C-CCTATAGGTGA
31039323 ACCTTGAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 2 0.06
27 16 0.48
28 14 0.42
29 1 0.03
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (26 bp):
CCCTATAGGTGAGCCCCTGTTGCAAA
Found at i:31044637 original size:11 final size:12
Alignment explanation
Indices: 31044621--31044660 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
31044611 GAAAATGTAG
31044621 AAAAATTAT-TA
1 AAAAATTATATA
*
31044632 AAAAATTATAAA
1 AAAAATTATATA
31044644 AAGAAATTATATA
1 AA-AAATTATATA
31044657 AAAA
1 AAAA
31044661 TAATAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.36
12 5 0.20
13 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AAAAATTATATA
Found at i:31044659 original size:24 final size:24
Alignment explanation
Indices: 31044623--31044668 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
31044613 AAATGTAGAA
*
31044623 AAATTATTAAAAAATTATAAAAAG
1 AAATTATTAAAAAATAATAAAAAG
31044647 AAATTA-TATAAAAATAATAAAA
1 AAATTATTA-AAAAATAATAAAA
31044669 TGATAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATTATTAAAAAATAATAAAAAG
Found at i:31045083 original size:17 final size:18
Alignment explanation
Indices: 31045061--31045094 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
31045051 TAAATTTAAT
31045061 TATTTTTTTA-AATTTTC
1 TATTTTTTTATAATTTTC
31045078 TATTTTTTTATAATTTT
1 TATTTTTTTATAATTTT
31045095 TTACAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTTTATAATTTTC
Found at i:31045104 original size:27 final size:26
Alignment explanation
Indices: 31045064--31045123 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
31045054 ATTTAATTAT
* *
31045064 TTTTTTAAATTTTCTATTTTTTTATAA
1 TTTTTTAAATTTTCTA-ATATTTATAA
31045091 TTTTTTACAA-TTTCTAATATTTATAA
1 TTTTTTA-AATTTTCTAATATTTATAA
*
31045117 TGTTTTA
1 TTTTTTA
31045124 TTATTTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 14 0.48
27 13 0.45
28 2 0.07
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTTAAATTTTCTAATATTTATAA
Found at i:31045184 original size:9 final size:9
Alignment explanation
Indices: 31045158--31045216 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
31045148 TATACAAAAA
31045158 TTATAATTT
1 TTATAATTT
31045167 TT-TAATTT
1 TTATAATTT
*
31045175 TTATAGTTT
1 TTATAATTT
*
31045184 TTAATAATTC
1 TT-ATAATTT
31045194 TTATAATATT
1 TTATAAT-TT
31045204 TTAATAATTT
1 TT-ATAATTT
31045214 TTA
1 TTA
31045217 GACTTAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 8 0.19
9 15 0.36
10 14 0.33
11 5 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:31045197 original size:19 final size:20
Alignment explanation
Indices: 31045158--31045212 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
31045148 TATACAAAAA
*
31045158 TTATAAT-TTTT--TAATTT
1 TTATAATATTTTAATAATTC
*
31045175 TTATAGT-TTTTAATAATTC
1 TTATAATATTTTAATAATTC
31045194 TTATAATATTTTAATAATT
1 TTATAATATTTTAATAATT
31045213 TTTAGACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.31
19 11 0.34
20 11 0.34
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATAATATTTTAATAATTC
Found at i:31047228 original size:12 final size:12
Alignment explanation
Indices: 31047211--31047244 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31047201 TAAAACTGTT
31047211 ATCTGAATCTAA
1 ATCTGAATCTAA
*
31047223 ATCTGAAACTAA
1 ATCTGAATCTAA
*
31047235 ATCTGTATCT
1 ATCTGAATCT
31047245 GTATCTGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (12 bp):
ATCTGAATCTAA
Found at i:31047232 original size:31 final size:30
Alignment explanation
Indices: 31047192--31047250 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
31047182 AATTCTGCAT
31047192 ATCTAAAACTAAAACTGTTATCTGAATCTAA
1 ATCTAAAACTAAAACTG-TATCTGAATCTAA
* * *
31047223 ATCTGAAACTAAATCTGTATCTGTATCT
1 ATCTAAAACTAAAACTGTATCTGAATCT
31047251 GACTGTGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (30 bp):
ATCTAAAACTAAAACTGTATCTGAATCTAA
Found at i:31054149 original size:20 final size:20
Alignment explanation
Indices: 31054117--31054154 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31054107 TGTTTCACAT
31054117 TCATATAACTAATATTTATA
1 TCATATAACTAATATTTATA
*
31054137 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
31054155 ACTTAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATA
Found at i:31064697 original size:29 final size:28
Alignment explanation
Indices: 31064615--31064698 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
31064605 AACACACTAG
* * *
31064615 TATAATCCTCCAAAACACGCCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
31064643 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
31064671 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
31064699 GCACAGAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 32 0.64
29 18 0.36
ACGTcount: A:0.45, C:0.31, G:0.05, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:31064762 original size:13 final size:14
Alignment explanation
Indices: 31064739--31064768 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31064729 GGATATAAAC
31064739 ATCAGCATCTCCAA
1 ATCAGCATCTCCAA
31064753 ATCA-CATCTCCAA
1 ATCAGCATCTCCAA
31064766 ATC
1 ATC
31064769 CCTTCTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.23
Consensus pattern (14 bp):
ATCAGCATCTCCAA
Found at i:31064775 original size:13 final size:13
Alignment explanation
Indices: 31064744--31064782 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
31064734 TAAACATCAG
*
31064744 CATCTCCAAATCA
1 CATCTCCAAATCC
31064757 CATCTCCAAATCC
1 CATCTCCAAATCC
* *
31064770 CTTCTCAAAATCC
1 CATCTCCAAATCC
31064783 TATGGCATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (13 bp):
CATCTCCAAATCC
Found at i:31066931 original size:55 final size:54
Alignment explanation
Indices: 31066823--31067061 Score: 215
Period size: 55 Copynumber: 4.5 Consensus size: 54
31066813 ATTAGGGTTT
* * **
31066823 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACA-GGGCATTGGTAA-GTTTCATAAGGC
* * * *
31066878 AAGGATATCATTTAAGACCATGTCAAGATAGGGCATTGATAAGTTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACAGGGCATTGGTAAGTTTC-ATAAGGC
* * * * *
31066933 AATGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 AA-GGATACCATGTAAGACCATGTCAAGACAGGGCATTGGTAAGTTTCATAAGGC
* * * *
31066986 AAGTATACCATGTAAGACCATGTCGAGACAGGGTAATGGTAAGTTTC--AA---
1 AAGGATACCATGTAAGACCATGTCAAGACAGGGCATTGGTAAGTTTCATAAGGC
* *
31067035 AAGGATACCACGTAAGACCATGACAAG
1 AAGGATACCATGTAAGACCATGTCAAG
31067062 TCATGGAAAT
Statistics
Matches: 149, Mismatches: 30, Indels: 16
0.76 0.15 0.08
Matches are distributed among these distances:
49 23 0.15
52 3 0.02
53 44 0.30
54 15 0.10
55 62 0.42
56 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACAGGGCATTGGTAAGTTTCATAAGGC
Found at i:31067029 original size:108 final size:110
Alignment explanation
Indices: 31066830--31067079 Score: 286
Period size: 108 Copynumber: 2.4 Consensus size: 110
31066820 TTTAAGGATA
* *
31066830 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATATCATTTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
* *
31066895 CCATGTCAAGATAGGGCATTGATAAGTTTCTATAAGGCAATGGTC
66 CCATGTCAAGACAGGGCAATGATAAGTTTCTATAAGGCAATGGTC
* * *
31066940 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGTATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAG
* * * * *
31067002 ACCATGTCGAGACAGGGTAATGGTAAGTTTC-AAAAGG--A---TA
65 ACCATGTCAAGACAGGGCAATGATAAGTTTCTATAAGGCAATGGTC
* * *
31067042 CCACGTAAGACCATGACAAGTCATGGAAA-TGGTAAGGT
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGT
31067080 ACCCGTGTAT
Statistics
Matches: 119, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
102 29 0.24
103 2 0.02
105 1 0.01
107 8 0.07
108 46 0.39
109 7 0.06
110 26 0.22
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAGA
CCATGTCAAGACAGGGCAATGATAAGTTTCTATAAGGCAATGGTC
Found at i:31067290 original size:16 final size:16
Alignment explanation
Indices: 31067269--31067299 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31067259 ATAAATTTGA
31067269 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
31067285 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
31067300 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:31069130 original size:11 final size:13
Alignment explanation
Indices: 31069105--31069135 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
31069095 GGTTAATAAT
31069105 TATAATAATTATA
1 TATAATAATTATA
*
31069118 TATAATATTTATA
1 TATAATAATTATA
31069131 TATAA
1 TATAA
31069136 CTTAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATAATTATA
Found at i:31072387 original size:25 final size:25
Alignment explanation
Indices: 31072346--31072397 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
31072336 TCCCAAAATC
* **
31072346 ACATCAAATTCATCAAATGGCAATA
1 ACATCAAATTCACCAAAAAGCAATA
31072371 ACATCAAA-TCAGCCAAAAAGCAATA
1 ACATCAAATTCA-CCAAAAAGCAATA
31072396 AC
1 AC
31072398 CCTTTACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.52, C:0.23, G:0.08, T:0.17
Consensus pattern (25 bp):
ACATCAAATTCACCAAAAAGCAATA
Found at i:31077439 original size:42 final size:43
Alignment explanation
Indices: 31077376--31077493 Score: 125
Period size: 43 Copynumber: 2.8 Consensus size: 43
31077366 TTATATGTGT
* *
31077376 TTTCGTGTAAGACCAC-ATCTGGGATGTTGGCATC-ATATTTGA
1 TTTCGTGTAAGACC-CTGTCTGGGAAGTTGGCATCGATATTTGA
*
31077418 TTTCGTGTAAGACCCTGTCTGGGACAG-TGGCGTCGATATTTGA
1 TTTCGTGTAAGACCCTGTCTGGGA-AGTTGGCATCGATATTTGA
* * * * *
31077461 TTACATGTAAGACCATGTCTGAGACGTTGGCAT
1 TTTCGTGTAAGACCCTGTCTGGGAAGTTGGCAT
31077494 TGTACGAGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 28 0.44
43 34 0.54
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (43 bp):
TTTCGTGTAAGACCCTGTCTGGGAAGTTGGCATCGATATTTGA
Found at i:31081773 original size:24 final size:24
Alignment explanation
Indices: 31081722--31081866 Score: 195
Period size: 24 Copynumber: 6.0 Consensus size: 24
31081712 ACTTTATCAT
*
31081722 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
31081747 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31081771 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
31081795 ATAACTAGGGCAGAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
31081818 ATAATTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
31081843 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
31081867 CACTTCCTCC
Statistics
Matches: 106, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
23 20 0.19
24 52 0.49
25 34 0.32
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31081940 original size:20 final size:20
Alignment explanation
Indices: 31081915--31081981 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
31081905 TTATGATTAC
31081915 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
31081935 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31081955 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31081975 ACCATGT
1 ATCATGT
31081982 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31081946 original size:11 final size:11
Alignment explanation
Indices: 31081915--31081970 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
31081905 TTATGATTAC
31081915 ATCATGTGCAT
1 ATCATGTGCAT
*
31081926 ATCA--TACAT
1 ATCATGTGCAT
31081935 ATCATGTGCAT
1 ATCATGTGCAT
*
31081946 ATCA--TACAT
1 ATCATGTGCAT
*
31081955 GTCATGTGCAT
1 ATCATGTGCAT
31081966 ATCAT
1 ATCAT
31081971 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:31088427 original size:31 final size:31
Alignment explanation
Indices: 31088389--31088452 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
31088379 CCTTTTCATA
31088389 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
31088420 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
31088451 TT
1 TT
31088453 ACTGTAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:31088688 original size:25 final size:24
Alignment explanation
Indices: 31088646--31088715 Score: 90
Period size: 23 Copynumber: 2.9 Consensus size: 24
31088636 GCTTTATCAT
*
31088646 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
31088671 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
31088694 ATAACTAGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTT
31088716 ACCATATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
23 22 0.54
24 7 0.17
25 12 0.29
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:31088697 original size:23 final size:23
Alignment explanation
Indices: 31088667--31088716 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
31088657 CCTAGCCTCT
*
31088667 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTAGGGCATAAGCCC
31088690 TTTAATAACTAGGGCATAAGCCC
1 TTTAATAACTAGGGCATAAGCCC
31088713 TTTA
1 TTTA
31088717 CCATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (23 bp):
TTTAATAACTAGGGCATAAGCCC
Found at i:31088778 original size:20 final size:20
Alignment explanation
Indices: 31088753--31088819 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
31088743 TTATGATTAC
31088753 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
31088773 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31088793 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
31088813 ACCATGT
1 ATCATGT
31088820 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:31088784 original size:11 final size:11
Alignment explanation
Indices: 31088753--31088808 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
31088743 TTATGATTAC
31088753 ATCATGTGCAT
1 ATCATGTGCAT
*
31088764 ATCA--TACAT
1 ATCATGTGCAT
31088773 ATCATGTGCAT
1 ATCATGTGCAT
*
31088784 ATCA--TACAT
1 ATCATGTGCAT
*
31088793 GTCATGTGCAT
1 ATCATGTGCAT
31088804 ATCAT
1 ATCAT
31088809 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:31094915 original size:341 final size:344
Alignment explanation
Indices: 31094286--31094973 Score: 1112
Period size: 341 Copynumber: 2.0 Consensus size: 344
31094276 TACAAGTGAC
* * *
31094286 ATGTCACCAAGGTTTTATGTTATGTTATCCGAGTGCTGGTCCTGTACGTCCTACCGGTGACTGAG
1 ATGTCACCAAGGTTTTATGTTATGTGATCCGAGTGCTGGTCCTGTACATCCTACCAGTGACTGAG
*
31094351 AATACCGACATATGTTGTGGTTACTTGACAGCTTGTGTGAGCAGCACCGAGTAGCTACATCTTGA
66 AATACCGACATATGTTGTGGTTACTTGACAGCTTGTGTGAGCAGCACCGAGTAACTACATCTTGA
*
31094416 CTGACAGCTTGTATGAGCAGGCCCGTTAATGGCTCGAGAGCGAGCATGTATGTGATATGAAATAG
131 CTGACAGCTTGTATGAGCAGGCCCGTTAATGGCTCGAGAGCGAGCATATATGTGATATGAAATAG
* *
31094481 AGGTAGCAGCGGCTACATATGTGGCACCTTGTGCGCAAGATTCCCCGAGTATCCGAGATTATTAT
196 AGGTAGCAACGGCTACATATGTGGCACCTTGTGCGCAAGATTCCCCGAGTATCCAAGATTATTAT
*
31094546 TCCGAGTGGTTCATTGGGTATCACAAAAGAT-G-A-GAGTATGAAACCATTATGAGTGGTACAGG
261 TCCGAGTGGTTAATTGGGTATCACAAAAGATAGAATGAGTATGAAACCATTATGAGTGGTACAGG
*
31094608 TATGTGCAGAAAACTTACG
326 TATGTGCACAAAACTTACG
* * * * *
31094627 ATGTCACCAGGGTTTTATGTTATGTGATCCGGGTGCTGGTCCTGTATATCCTAGCAGTGGCTGAG
1 ATGTCACCAAGGTTTTATGTTATGTGATCCGAGTGCTGGTCCTGTACATCCTACCAGTGACTGAG
* * * * *
31094692 TATACCGGCATATGTTGTGGTTACTTGACAGCTTGTGTGAGCAGTACTGAGTAACTACGTCTTGA
66 AATACCGACATATGTTGTGGTTACTTGACAGCTTGTGTGAGCAGCACCGAGTAACTACATCTTGA
* * *
31094757 CTGACAGCTTGTGTGAGTAGGCCCGTTAATGGCTCGAGAGCGAGCATATATGTGATATGAGATAG
131 CTGACAGCTTGTATGAGCAGGCCCGTTAATGGCTCGAGAGCGAGCATATATGTGATATGAAATAG
* *
31094822 AGGTAGCAATGGCTACATATGTGGCACCTTGTGTGCAAGATTCCCCGAGTATCCAAGATTATTAT
196 AGGTAGCAACGGCTACATATGTGGCACCTTGTGCGCAAGATTCCCCGAGTATCCAAGATTATTAT
* *
31094887 TCCGAGTGGTTAATTGGGTATGACAAAAGATGAGAATGAGTATGAAACCATTATGAGTGGTACTG
261 TCCGAGTGGTTAATTGGGTATCACAAAAGAT-AGAATGAGTATGAAACCATTATGAGTGGTACAG
31094952 GTATGTGCACAAAACTTACG
325 GTATGTGCACAAAACTTACG
31094972 AT
1 AT
31094974 TATTAAATTC
Statistics
Matches: 317, Mismatches: 26, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
341 267 0.84
343 1 0.00
344 1 0.00
345 48 0.15
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (344 bp):
ATGTCACCAAGGTTTTATGTTATGTGATCCGAGTGCTGGTCCTGTACATCCTACCAGTGACTGAG
AATACCGACATATGTTGTGGTTACTTGACAGCTTGTGTGAGCAGCACCGAGTAACTACATCTTGA
CTGACAGCTTGTATGAGCAGGCCCGTTAATGGCTCGAGAGCGAGCATATATGTGATATGAAATAG
AGGTAGCAACGGCTACATATGTGGCACCTTGTGCGCAAGATTCCCCGAGTATCCAAGATTATTAT
TCCGAGTGGTTAATTGGGTATCACAAAAGATAGAATGAGTATGAAACCATTATGAGTGGTACAGG
TATGTGCACAAAACTTACG
Found at i:31107706 original size:57 final size:57
Alignment explanation
Indices: 31107607--31107715 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
31107597 TATGCACTGT
* * *
31107607 TCAATCCTCCCACCACCAAACAAGTCGGAGGCTCTACCTCTGTTCCCATAGAACCCA
1 TCAATCCTCCCACCACCAAACAAGTCGAAGACTATACCTCTGTTCCCATAGAACCCA
* * * *
31107664 TCAATCCTTCCATCACCAAACAAGTCGAAGACTATACTTCTGTTCCTATAGA
1 TCAATCCTCCCACCACCAAACAAGTCGAAGACTATACCTCTGTTCCCATAGA
31107716 TCCCGATGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.30, C:0.35, G:0.11, T:0.24
Consensus pattern (57 bp):
TCAATCCTCCCACCACCAAACAAGTCGAAGACTATACCTCTGTTCCCATAGAACCCA
Found at i:31115656 original size:91 final size:90
Alignment explanation
Indices: 31115484--31115674 Score: 249
Period size: 91 Copynumber: 2.1 Consensus size: 90
31115474 ATGACCTCCG
* *
31115484 TGCTCTTAATGAGTTCATAGCCTAGAGTTTGGGTGCTCTTACTAAGACAGACTTGATGAATTCAC
1 TGCTCTTAATGAGTTCATAGCCTAGAGTTTGGATGCTCTTACTAAGACAGACTTGATGAAGTCAC
* *
31115549 CGAACTTATAGGATGAACTACTAGA
66 CGAACTTATAGGATGAACCACTAAA
* * * * * *
31115574 TGCTCTTAATGAGTTCATAGCCTAGGGTTTTGATGGTCTTATTTGAGATAGACTTGATGAACGT-
1 TGCTCTTAATGAGTTCATAGCCTAGAGTTTGGATGCTCTTA-CTAAGACAGACTTGATGAA-GTC
*
31115638 ACCGAATTTATAGGATGAACCACTAAA
64 ACCGAACTTATAGGATGAACCACTAAA
*
31115665 TGTTCTTAAT
1 TGCTCTTAAT
31115675 AAATTGATAT
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
90 37 0.43
91 49 0.56
92 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (90 bp):
TGCTCTTAATGAGTTCATAGCCTAGAGTTTGGATGCTCTTACTAAGACAGACTTGATGAAGTCAC
CGAACTTATAGGATGAACCACTAAA
Found at i:31124818 original size:19 final size:20
Alignment explanation
Indices: 31124787--31124824 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31124777 AAAAAATGGG
31124787 TAAATAATATTCT-GAAAAA
1 TAAATAATATTCTAGAAAAA
31124806 TAAA-AATATTTCTAGAAAA
1 TAAATAATA-TTCTAGAAAA
31124825 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAATAATATTCTAGAAAAA
Found at i:31125166 original size:2 final size:2
Alignment explanation
Indices: 31125159--31125200 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31125149 GAATTAAGAA
31125159 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31125201 TTGCTTGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:31128012 original size:16 final size:16
Alignment explanation
Indices: 31127991--31128023 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31127981 TCAACTCCGC
31127991 TTAATTATGACAAAAG
1 TTAATTATGACAAAAG
31128007 TTAATTATGACAAAAG
1 TTAATTATGACAAAAG
31128023 T
1 T
31128024 AATCTTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (16 bp):
TTAATTATGACAAAAG
Found at i:31128899 original size:21 final size:20
Alignment explanation
Indices: 31128867--31128915 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
31128857 AGTCGATTTT
*
31128867 CACACAGGCATGTGCCTTGGC
1 CACAC-GGCATGTCCCTTGGC
31128888 CACACGGCCATGTCCCTTGGC
1 CACACGG-CATGTCCCTTGGC
31128909 CACACGG
1 CACACGG
31128916 GCGTGTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.18, C:0.39, G:0.27, T:0.16
Consensus pattern (20 bp):
CACACGGCATGTCCCTTGGC
Found at i:31132393 original size:12 final size:12
Alignment explanation
Indices: 31132372--31132401 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31132362 ATTCCAAGTG
31132372 TTCAACGGGAAA
1 TTCAACGGGAAA
*
31132384 TTCAATGGGAAA
1 TTCAACGGGAAA
31132396 TTCAAC
1 TTCAAC
31132402 AGGTATGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (12 bp):
TTCAACGGGAAA
Found at i:31134014 original size:24 final size:23
Alignment explanation
Indices: 31133973--31134049 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
31133963 AAGCTCCTCC
* *
31133973 TGAGCTGATAAACAGTAAGTTCTAT
1 TGAGCT-AAAAAC-GTAAGCTCTAT
31133998 TGAGCTAAAAACTGTAAGCTCTAT
1 TGAGCTAAAAAC-GTAAGCTCTAT
* * *
31134022 TAAGCTGAATA-GTAAGCTCTAT
1 TGAGCTAAAAACGTAAGCTCTAT
31134044 TGAGCT
1 TGAGCT
31134050 GAATCGGTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 16 0.36
24 23 0.51
25 6 0.13
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (23 bp):
TGAGCTAAAAACGTAAGCTCTAT
Found at i:31134082 original size:46 final size:47
Alignment explanation
Indices: 31133958--31134108 Score: 139
Period size: 46 Copynumber: 3.2 Consensus size: 47
31133948 CGAGTCATGG
* ** * *
31133958 TCGGTAAGCTCCTCCTGAGCTGATAAACAGTAAGTTCTATTGAGCTAAAA
1 TCGGTAAGCTTCTAATGAGCTG--AAACAGTAAGCTCTATTGAGCT-GAA
* * * * *
31134008 ACTGTAAGC-TCTATTAAGCTG-AATAGTAAGCTCTATTGAGCTGAA
1 TCGGTAAGCTTCTAATGAGCTGAAACAGTAAGCTCTATTGAGCTGAA
*
31134053 TCGGTAAGCTTC-AATGAGCTGAAACAGTAAGCTCT-TACGAGCTGAA
1 TCGGTAAGCTTCTAATGAGCTGAAACAGTAAGCTCTAT-TGAGCTGAA
31134099 TCGGTAAGCT
1 TCGGTAAGCT
31134109 CATACAAGCG
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
45 17 0.20
46 51 0.61
49 8 0.10
50 7 0.08
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (47 bp):
TCGGTAAGCTTCTAATGAGCTGAAACAGTAAGCTCTATTGAGCTGAA
Found at i:31134109 original size:23 final size:23
Alignment explanation
Indices: 31134011--31134109 Score: 89
Period size: 23 Copynumber: 4.3 Consensus size: 23
31134001 GCTAAAAACT
*
31134011 GTAAGCTC-TATTAAGCTGAAT-A
1 GTAAGCTCTTA-TGAGCTGAATCA
*
31134033 GTAAGCTC-TATTGAGCTGAATCG
1 GTAAGCTCTTA-TGAGCTGAATCA
* *
31134056 GTAAGCT-TCAATGAGCTGAAACA
1 GTAAGCTCT-TATGAGCTGAATCA
* *
31134079 GTAAGCTCTTACGAGCTGAATCG
1 GTAAGCTCTTATGAGCTGAATCA
31134102 GTAAGCTC
1 GTAAGCTC
31134110 ATACAAGCGG
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
22 20 0.31
23 42 0.66
24 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (23 bp):
GTAAGCTCTTATGAGCTGAATCA
Found at i:31141193 original size:26 final size:25
Alignment explanation
Indices: 31141164--31141243 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 25
31141154 GTTATGGTCG
*
31141164 GTAAGCTCCTCCTGAGCTAATAAACA
1 GTAAGCTCCTACTGAGCTAA-AAACA
* *
31141190 GTAAGCT-CTATTGAGCTGAAAACA
1 GTAAGCTCCTACTGAGCTAAAAACA
* *
31141214 GTAAGCT-CTATTGAGCT--GAACA
1 GTAAGCTCCTACTGAGCTAAAAACA
31141236 GTAAGCTC
1 GTAAGCTC
31141244 TATCGAACAG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 11 0.22
24 22 0.45
25 9 0.18
26 7 0.14
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (25 bp):
GTAAGCTCCTACTGAGCTAAAAACA
Found at i:31141216 original size:24 final size:24
Alignment explanation
Indices: 31141176--31141246 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
31141166 AAGCTCCTCC
*
31141176 TGAGCTAATAAACAGTAAGCTCTAT
1 TGAGCTGA-AAACAGTAAGCTCTAT
31141201 TGAGCTGAAAACAGTAAGCTCTAT
1 TGAGCTGAAAACAGTAAGCTCTAT
31141225 TGAGCTG--AACAGTAAGCTCTAT
1 TGAGCTGAAAACAGTAAGCTCTAT
31141247 CGAACAGAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
22 15 0.33
24 23 0.51
25 7 0.16
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (24 bp):
TGAGCTGAAAACAGTAAGCTCTAT
Found at i:31141301 original size:23 final size:22
Alignment explanation
Indices: 31141185--31141344 Score: 124
Period size: 23 Copynumber: 7.0 Consensus size: 22
31141175 CTGAGCTAAT
*
31141185 AAACAGTAAGCTCTATTGAGCTG
1 AAACAGTAAGCTCTA-CGAGCTG
*
31141208 AAAACAGTAAGCTCTATTGAGCTG
1 -AAACAGTAAGCTCTA-CGAGCTG
* *
31141232 -AACAGTAAGCTCTATCGAACAG
1 AAACAGTAAGCTCTA-CGAGCTG
* * * * *
31141254 AATCGGTAAGCTTCAATGAGTTG
1 AAACAGTAAGC-TCTACGAGCTG
31141277 AAACAGTAAGCTCTTACGAGCTG
1 AAACAGTAAGCTC-TACGAGCTG
* *
31141300 AATCGGTAAGCTCTTACGAGCTG
1 AAACAGTAAGCTC-TACGAGCTG
**
31141323 AATTAGTAAGCTCATACGAGCT
1 AAACAGTAAGCTC-TACGAGCT
31141345 ATGGCGAGTT
Statistics
Matches: 113, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
22 21 0.19
23 66 0.58
24 26 0.23
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (22 bp):
AAACAGTAAGCTCTACGAGCTG
Found at i:31146873 original size:29 final size:29
Alignment explanation
Indices: 31146836--31146919 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 29
31146826 TGACACCAGC
*
31146836 GTGTCTTTGGTCGTGTGAGACACATGAGT
1 GTGTCTTTGGCCGTGTGAGACACATGAGT
* *
31146865 GTGTCTTTGGCCGTGTGAGACACACGGGT
1 GTGTCTTTGGCCGTGTGAGACACATGAGT
* *
31146894 GTGTTTTTGGCCATGTGAGACACATG
1 GTGTCTTTGGCCGTGTGAGACACATG
31146920 GTAGGGCCAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.32
Consensus pattern (29 bp):
GTGTCTTTGGCCGTGTGAGACACATGAGT
Found at i:31147938 original size:23 final size:23
Alignment explanation
Indices: 31147912--31147980 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
31147902 TTTGAACTTG
31147912 GGTTTCAAGAAACGTTACACTAA
1 GGTTTCAAGAAACGTTACACTAA
31147935 GGTTTCAAGAAACGTTACACTAA
1 GGTTTCAAGAAACGTTACACTAA
31147958 GGTTTCAAGAAACGTTACACTAA
1 GGTTTCAAGAAACGTTACACTAA
31147981 CACTTAACCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (23 bp):
GGTTTCAAGAAACGTTACACTAA
Found at i:31171888 original size:31 final size:31
Alignment explanation
Indices: 31171853--31172018 Score: 153
Period size: 31 Copynumber: 5.4 Consensus size: 31
31171843 GATATTAAAT
31171853 TTAATTTAATATTTAGATAGATAATATTTTA
1 TTAATTTAATATTTAGATAGATAATATTTTA
* * **
31171884 TTAATTTAAT-GTTA-ATATG-TGATATTAAA
1 TTAATTTAATATTTAGATA-GATAATATTTTA
*
31171913 TTTAATTTAATATTTAGATAGATAGTATTTTA
1 -TTAATTTAATATTTAGATAGATAATATTTTA
* * * * *
31171945 TTAATTAAATATTAATATA-AT-ATACTTAA
1 TTAATTTAATATTTAGATAGATAATATTTTA
** *
31171974 TTTAATTTAATATTTATCTAGATAATATTTTG
1 -TTAATTTAATATTTAGATAGATAATATTTTA
31172006 TTAATTTAATATT
1 TTAATTTAATATT
31172019 AATATGATTA
Statistics
Matches: 106, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
29 15 0.14
30 32 0.30
31 45 0.42
32 14 0.13
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (31 bp):
TTAATTTAATATTTAGATAGATAATATTTTA
Found at i:31171902 original size:61 final size:61
Alignment explanation
Indices: 31171831--31172025 Score: 293
Period size: 61 Copynumber: 3.2 Consensus size: 61
31171821 ATTTATCTAG
31171831 ATATTAATATGAGATATTAAATTTAATTTAATATTTAGATAGATAATATTTTATTAATTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTAGATAGATAATATTTTATTAATTTA
* * * *
31171892 ATGTTAATATGTGATATTAAATTTAATTTAATATTTAGATAGATAGTATTTTATTAATTAA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTAGATAGATAATATTTTATTAATTTA
* * ** *
31171953 ATATTAATATAATATACTT-AATTTAATTTAATATTTATCTAGATAATATTTTGTTAATTTA
1 ATATTAATATGAGATA-TTAAATTTAATTTAATATTTAGATAGATAATATTTTATTAATTTA
31172014 ATATTAATATGA
1 ATATTAATATGA
31172026 TTAATTCTAA
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
61 117 0.98
62 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.50
Consensus pattern (61 bp):
ATATTAATATGAGATATTAAATTTAATTTAATATTTAGATAGATAATATTTTATTAATTTA
Found at i:31173847 original size:31 final size:31
Alignment explanation
Indices: 31173806--31173879 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
31173796 TTTGTCCATG
* * *
31173806 TTAATTTTTAAAAATATATATAGTTTTTAAT
1 TTAATATTTAAAAATATAGATAATTTTTAAT
* *
31173837 TTAATATTTAATATTATAGATAATTTTTAAT
1 TTAATATTTAAAAATATAGATAATTTTTAAT
* *
31173868 TAAAAATTTAAA
1 TTAATATTTAAA
31173880 TTTAGATATC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
TTAATATTTAAAAATATAGATAATTTTTAAT
Found at i:31173895 original size:31 final size:31
Alignment explanation
Indices: 31173820--31173887 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
31173810 TTTTTAAAAA
* * * *
31173820 TATATATAGTTTTTAATTTAATATTTAATAT
1 TATAGATAATTTTTAATTAAAAATTTAATAT
31173851 TATAGATAATTTTTAATTAAAAATTTAA-AT
1 TATAGATAATTTTTAATTAAAAATTTAATAT
31173881 T-TAGATA
1 TATAGATA
31173888 TCATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 6 0.18
30 3 0.09
31 24 0.73
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (31 bp):
TATAGATAATTTTTAATTAAAAATTTAATAT
Done.