Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 118 of 210
Found at i:35203841 original size:27 final size:27
Alignment explanation
Indices: 35203811--35204010 Score: 219
Period size: 27 Copynumber: 7.4 Consensus size: 27
35203801 GGTATAACAC
*
35203811 TCATTTTACCCAATGGAGGTATTTCGG
1 TCATTTTACCCTATGGAGGTATTTCGG
* *
35203838 TCATTTTATCTTATAGG-GGTATTTCGG
1 TCATTTTACCCTAT-GGAGGTATTTCGG
* *
35203865 TCATTTTACCCTAT-TAGGGTATTTTGG
1 TCATTTTACCCTATGGA-GGTATTTCGG
* *
35203892 TCATTGTACCCTA-GCG-GGTATTTCGA
1 TCATTTTACCCTATG-GAGGTATTTCGG
*
35203918 TCATTTTACCCTATGGAGGTATTTTGG
1 TCATTTTACCCTATGGAGGTATTTCGG
*
35203945 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGAGGTATTTCGG
* * **
35203972 TCAATTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGGAGGTATTTCGG
*
35203999 TCAATTTACCCT
1 TCATTTTACCCT
35204011 CTGGGGGCTT
Statistics
Matches: 147, Mismatches: 19, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
26 21 0.14
27 124 0.84
28 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (27 bp):
TCATTTTACCCTATGGAGGTATTTCGG
Found at i:35203940 original size:80 final size:81
Alignment explanation
Indices: 35203815--35204010 Score: 238
Period size: 80 Copynumber: 2.4 Consensus size: 81
35203805 TAACACTCAT
* * * *
35203815 TTTACCCAATG-GAGGTATTTCGGTCATTTTATCTTATAGGGGTATTTCGGTCATTTTACCCTAT
1 TTTACCCTATGCG-GGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTAT
* *
35203879 TAGGGTATTTTGGTC-A
65 GAGGGTATTTCGGTCAA
*
35203895 TTGTACCCTA-GCGGGTATTTCGATCATTTTACCCTAT-GGAGGTATTTTGGTCATTTTACCCTA
1 TT-TACCCTATGCGGGTATTTCGATCATTTTACCCTATAGG-GGTATTTCGGTCATTTTACCCTA
*
35203958 TGGGGGTATTTCGGTCAA
64 TGAGGGTATTTCGGTCAA
* * *
35203976 TTTACCCTATGGGGGTATTTCAATCAATTTACCCT
1 TTTACCCTATGCGGGTATTTCGATCATTTTACCCT
35204011 CTGGGGGCTT
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
79 2 0.02
80 66 0.66
81 32 0.32
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (81 bp):
TTTACCCTATGCGGGTATTTCGATCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCTATG
AGGGTATTTCGGTCAA
Found at i:35204009 original size:107 final size:107
Alignment explanation
Indices: 35203811--35204010 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 107
35203801 GGTATAACAC
* * *
35203811 TCATTTTACCCAATGGAGGTATTTCGGTCATTTTATCTTATAGGGGTATTTCGGTCATTTTACCC
1 TCATTTTACCCAATGGAGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCAATTTACCC
* ***
35203876 TATTAGGGTATTTTGGTCATTGTACCCTAGCGGGTATTTCGA
66 TATGAGGGTATTTCAATCATTGTACCCTAGCGGGTATTTCGA
* * *
35203918 TCATTTTACCCTATGGAGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGTCAATTTACCC
1 TCATTTTACCCAATGGAGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCAATTTACCC
*
35203983 TATGGGGGTATTTCAATCAATT-TACCCT
66 TATGAGGGTATTTCAATC-ATTGTACCCT
35204011 CTGGGGGCTT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 78 0.96
108 3 0.04
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (107 bp):
TCATTTTACCCAATGGAGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCAATTTACCC
TATGAGGGTATTTCAATCATTGTACCCTAGCGGGTATTTCGA
Found at i:35207722 original size:156 final size:156
Alignment explanation
Indices: 35207532--35207838 Score: 587
Period size: 156 Copynumber: 2.0 Consensus size: 156
35207522 ATGAAAAGAA
*
35207532 GTTTATATAGGAAAAATTAGGGGAACATGTAGCAAAAAATTAGCTACATTAGGGTTATTTGGGCG
1 GTTTATATAGGAAAAATTAGGGCAACATGTAGCAAAAAATTAGCTACATTAGGGTTATTTGGGCG
35207597 GCAAGCAATGGGTGTGACGGCAAGGCATGAATTTTTCCCTCCTTTTTGCTGTCTTGGGCCTCAAA
66 GCAAGCAATGGGTGTGACGGCAAGGCATGAATTTTTCCCTCCTTTTTGCTGTCTTGGGCCTCAAA
*
35207662 CTCATACTATATCTTACTAAACAGAG
131 CTCAGACTATATCTTACTAAACAGAG
35207688 GTTTATATAGGAAAAATTAGGGCAACATGTAGCAAAAAATTAGCTACATTAGGGTTATTTGGGCG
1 GTTTATATAGGAAAAATTAGGGCAACATGTAGCAAAAAATTAGCTACATTAGGGTTATTTGGGCG
*
35207753 GCAAGCAATGGGTGTGATGGCAAGGCATGAATTTTTCCCTCCTTTTTGCTGTCTTGGGCCTCAAA
66 GCAAGCAATGGGTGTGACGGCAAGGCATGAATTTTTCCCTCCTTTTTGCTGTCTTGGGCCTCAAA
35207818 CTCAGACTATATCTTACTAAA
131 CTCAGACTATATCTTACTAAA
35207839 AAAACTGATT
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
156 148 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (156 bp):
GTTTATATAGGAAAAATTAGGGCAACATGTAGCAAAAAATTAGCTACATTAGGGTTATTTGGGCG
GCAAGCAATGGGTGTGACGGCAAGGCATGAATTTTTCCCTCCTTTTTGCTGTCTTGGGCCTCAAA
CTCAGACTATATCTTACTAAACAGAG
Found at i:35208406 original size:24 final size:24
Alignment explanation
Indices: 35208374--35208422 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
35208364 TCGTACCATC
35208374 TCTTTGATCTTTCTTTACACATTT
1 TCTTTGATCTTTCTTTACACATTT
35208398 TCTTTGATCTTTCTTTACACATTT
1 TCTTTGATCTTTCTTTACACATTT
35208422 T
1 T
35208423 GGCATTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.04, T:0.59
Consensus pattern (24 bp):
TCTTTGATCTTTCTTTACACATTT
Found at i:35216329 original size:11 final size:11
Alignment explanation
Indices: 35216304--35216335 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
35216294 AGAGAATGAT
35216304 GAATGA-TGA-
1 GAATGATTGAG
35216313 GAATGATTGAG
1 GAATGATTGAG
35216324 GAATGATTGAG
1 GAATGATTGAG
35216335 G
1 G
35216336 GATGCGTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 6 0.29
10 3 0.14
11 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (11 bp):
GAATGATTGAG
Found at i:35216498 original size:13 final size:14
Alignment explanation
Indices: 35216470--35216499 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35216460 GCTTCGTGGC
35216470 TTTTGACTTGATTT
1 TTTTGACTTGATTT
*
35216484 TTTTGGCTTGATTT
1 TTTTGACTTGATTT
35216498 TT
1 TT
35216500 AAGCAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.67
Consensus pattern (14 bp):
TTTTGACTTGATTT
Found at i:35234114 original size:13 final size:13
Alignment explanation
Indices: 35234096--35234128 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
35234086 CGTGTGTGAC
35234096 ACACGGCCAGGCG
1 ACACGGCCAGGCG
35234109 ACACGGCCAGGCG
1 ACACGGCCAGGCG
35234122 ACACGGC
1 ACACGGC
35234129 TGTGTGTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.39, G:0.36, T:0.00
Consensus pattern (13 bp):
ACACGGCCAGGCG
Found at i:35241934 original size:558 final size:544
Alignment explanation
Indices: 35240883--35241984 Score: 1654
Period size: 558 Copynumber: 2.0 Consensus size: 544
35240873 TCACCTTGGC
35240883 TGTCTTCTACGCTCAAAAGTGCCTGACTATTCAGAATTTCCCCAGGTACTTTGGTCATTAAGTTT
1 TGTCTTCTACGCTCAAAAGTGCCTGACTATTCAGAATTTCCCCAGGTACTTTGGTCATTAAGTTT
* *
35240948 TCCTCTTTATCTAGACTTTGGGGCTGCTCATGCTGGTGACCAATTCAATTTACGTTTGTGCTCAT
66 TCCTCTTTATCTAGACTTTGGGGCTGCTCATACGGGTGACCAATTCAATTTACGTTTGTGCTCAT
* * * * *
35241013 GTAACCATCTTGTAGATTCGCAAGAGTTTCACCTCTAAGTTGACTTAGTTCTAGCCTTAATAGTC
131 GCAACCATCCTGTAGATTCGCAAAAGTTTCACCTCTAAGATGACTTAGTTCTAGCATTAATAGTC
*
35241078 TTTGGTTCTCCTAAATCTCCCACTCTTCATAGAGTCCTTCTTCATAAATTTCATCACCATCATCT
196 TTTGGTTCTCCTAAATCTCCCACTCTTCATAGACTCCTTCTTCATAAATTTCATCACCATCATCT
*
35241143 GACCATATGTAATCAAAGTTTCCCATGATGCTTGCTAAACTAATTTCAATAGTCACTGCTGCAGT
261 GACCATATATAATCAAAGTTTCCCATGATGCTTGCTAAACTAATTTCAATAGTCACTGCTGCAGT
* *
35241208 TCTTTTTACAGGGGGTGTATCGAGATTTCTTGAAGAGCAAAGAAGTATTGGTAATGTTAAGAAAA
326 TCTTTTTACAGGGGGTGTATCGAGATTTCTTAAAGAGCAAAGAAGTATTAGTAATGTTAAGAAAA
* * *
35241273 TAAGAATAAACTAAATATAGTATCTATAATTTAGATATTTCTTAATTATTCTATTAGAATGCAAA
391 TAAGAATAAACTAAAGATAGTATCTATAATTTAGATATTTCCTAACTATTCTATTAGAATGCAAA
* *
35241338 AATCAAAATCAATTTAGTGACACTACCTCCCTGGCAATGATACCAACAACTTCACCGCCTCCAAA
456 AATCAAAATCAATTTAGTGACACTACCTCCCTGGCAATGACACCAACAACTTCACCACCTCCAAA
*
35241403 CGTACCAATATCCAAAGTAGAAAT
521 CGTACCAATATCCAAAGTAAAAAT
* * *
35241427 TGTCTTCTATGCTCAGAAGTGCCTGACTATTTAGAATTTCCCCAGGTACTTTGGTCATTAAGTTT
1 TGTCTTCTACGCTCAAAAGTGCCTGACTATTCAGAATTTCCCCAGGTACTTTGGTCATTAAGTTT
* *
35241492 TCCTCTTTATCTAGACTTTTGGGTTGCTCATACGGGTGACCAATTCAATTTACGTTTGTGCTCAT
66 TCCTCTTTATCTAGACTTTGGGGCTGCTCATACGGGTGACCAATTCAATTTACGTTTGTGCTCAT
*
35241557 GCAACCCGTCCTGTAGA-TCTGCAAAAGTTTCACCTCTAAGATGACTTAGTTCTAGCATTAATAG
131 GCAA-CCATCCTGTAGATTC-GCAAAAGTTTCACCTCTAAGATGACTTAGTTCTAGCATTAATAG
*
35241621 TCTTTGGTTCTCCTAAATCTCCCACTCTTCATAGACTCCTTCTTCTTAAATTTCATCATCATAAT
194 TCTTTGGTTCTCCTAAATCTCCCACTCTTCATAGACTCCTTCTTCATAAA-TT--TCATC---A-
*
35241686 CTATTTCATCATCTGACCATATATAATCAAAGTTGT-CTATGATGCTTGCTAAACTAATTTCAAT
252 C-----CATCATCTGACCATATATAATCAAAGTT-TCCCATGATGCTTGCTAAACTAATTTCAAT
* * * * *
35241750 GGTCACTGTTGCAGTTCTTTTTGCAGAGGGGTGTATTGAGATTTCTTAAAGAGCAAAGAAGTGTT
311 AGTCACTGCTGCAGTTCTTTTTACAG-GGGGTGTATCGAGATTTCTTAAAGAGCAAAGAAGTATT
* *
35241815 ATTAATGTTAA-ACAAATAAGAATAAACTAAAGATCGTATCTATAATTTAGATATTTCCTAACTA
375 AGTAATGTTAAGA-AAATAAGAATAAACTAAAGATAGTATCTATAATTTAGATATTTCCTAACTA
* * * *
35241879 TTTTATTAGAATGCAAAAATCAAAATCAATTTAGTGACATTGCCTCACC-GGCAATGACACTAAC
439 TTCTATTAGAATGCAAAAATCAAAATCAATTTAGTGACACTACCTC-CCTGGCAATGACACCAAC
* * * *
35241943 AACTTGACCACCTCCAGACGTACCGATATCCAGAGTAAAAAT
503 AACTTCACCACCTCCAAACGTACCAATATCCAAAGTAAAAAT
35241985 CCTACAAAAA
Statistics
Matches: 500, Mismatches: 40, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
544 128 0.26
545 99 0.20
546 2 0.00
548 5 0.01
551 1 0.00
552 1 0.00
557 78 0.16
558 184 0.37
559 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (544 bp):
TGTCTTCTACGCTCAAAAGTGCCTGACTATTCAGAATTTCCCCAGGTACTTTGGTCATTAAGTTT
TCCTCTTTATCTAGACTTTGGGGCTGCTCATACGGGTGACCAATTCAATTTACGTTTGTGCTCAT
GCAACCATCCTGTAGATTCGCAAAAGTTTCACCTCTAAGATGACTTAGTTCTAGCATTAATAGTC
TTTGGTTCTCCTAAATCTCCCACTCTTCATAGACTCCTTCTTCATAAATTTCATCACCATCATCT
GACCATATATAATCAAAGTTTCCCATGATGCTTGCTAAACTAATTTCAATAGTCACTGCTGCAGT
TCTTTTTACAGGGGGTGTATCGAGATTTCTTAAAGAGCAAAGAAGTATTAGTAATGTTAAGAAAA
TAAGAATAAACTAAAGATAGTATCTATAATTTAGATATTTCCTAACTATTCTATTAGAATGCAAA
AATCAAAATCAATTTAGTGACACTACCTCCCTGGCAATGACACCAACAACTTCACCACCTCCAAA
CGTACCAATATCCAAAGTAAAAAT
Found at i:35247656 original size:23 final size:20
Alignment explanation
Indices: 35247630--35247685 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
35247620 AGCAAACGAT
35247630 CCTCAAGTCATGTTTTAATCCAC
1 CCTCAA-TCATG--TTAATCCAC
*
35247653 CCTCAATGATGTTAATCCAC
1 CCTCAATCATGTTAATCCAC
*
35247673 CCTCAATGATGTT
1 CCTCAATCATGTT
35247686 GATTGAATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 22 0.69
22 4 0.12
23 6 0.19
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.34
Consensus pattern (20 bp):
CCTCAATCATGTTAATCCAC
Found at i:35247669 original size:20 final size:20
Alignment explanation
Indices: 35247644--35247685 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
35247634 AAGTCATGTT
35247644 TTAATCCACCCTCAATGATG
1 TTAATCCACCCTCAATGATG
35247664 TTAATCCACCCTCAATGATG
1 TTAATCCACCCTCAATGATG
35247684 TT
1 TT
35247686 GATTGAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (20 bp):
TTAATCCACCCTCAATGATG
Found at i:35253162 original size:14 final size:15
Alignment explanation
Indices: 35253135--35253163 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35253125 ACTTCTTTAC
35253135 CAAGGAAGAAATCTA
1 CAAGGAAGAAATCTA
35253150 CAAGGAA-AAATCTA
1 CAAGGAAGAAATCTA
35253164 TAGAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (15 bp):
CAAGGAAGAAATCTA
Found at i:35256268 original size:27 final size:26
Alignment explanation
Indices: 35256231--35256316 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
35256221 CCAGAATAGC
*
35256231 AAACACAGGATAGTCCGTCAGGACAGT
1 AAACACGGGATAGTCCGTC-GGACAGT
* * *
35256258 GATCACGGGATAGTCCGTCGAAACAGT
1 AAACACGGGATAGTCCGTCG-GACAGT
* *
35256285 AAACACGGGATAGCCCGTCGGGACAAT
1 AAACACGGGATAGTCCGTC-GGACAGT
35256312 AAACA
1 AAACA
35256317 TGCGGTAGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
26 1 0.02
27 46 0.96
28 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.27, T:0.14
Consensus pattern (26 bp):
AAACACGGGATAGTCCGTCGGACAGT
Found at i:35262348 original size:18 final size:19
Alignment explanation
Indices: 35262325--35262360 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35262315 TATAATTTGA
*
35262325 TTTATTTGGTT-TTAATAG
1 TTTATTCGGTTCTTAATAG
35262343 TTTATTCGGTTCTTAATA
1 TTTATTCGGTTCTTAATA
35262361 TATAAATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.58
Consensus pattern (19 bp):
TTTATTCGGTTCTTAATAG
Found at i:35275255 original size:28 final size:28
Alignment explanation
Indices: 35275215--35275270 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
35275205 GGACATAATG
35275215 CCAACAAGGGTAAATCCACCCACTTAAA
1 CCAACAAGGGTAAATCCACCCACTTAAA
35275243 CCAACAAGGGTAAATCCACCCACTTAAA
1 CCAACAAGGGTAAATCCACCCACTTAAA
35275271 TGATGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.14
Consensus pattern (28 bp):
CCAACAAGGGTAAATCCACCCACTTAAA
Found at i:35277905 original size:2 final size:2
Alignment explanation
Indices: 35277900--35277925 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35277890 GCTTTTTTTG
35277900 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
35277926 ATGTATCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35278068 original size:34 final size:35
Alignment explanation
Indices: 35278024--35278090 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
35278014 CAGTAAAATG
35278024 TTTTCCGTAAAATGATTT-CTAGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
35278058 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
35278091 CTAATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:35280530 original size:24 final size:24
Alignment explanation
Indices: 35280503--35280549 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35280493 GCATATACTC
35280503 CAAACAAAAAGAGTAAA-AAAAAAT
1 CAAACAAAAAGAG-AAACAAAAAAT
*
35280527 CAAACAAATAGAGAAACAAAAAA
1 CAAACAAAAAGAGAAACAAAAAA
35280550 GAAAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.74, C:0.11, G:0.09, T:0.06
Consensus pattern (24 bp):
CAAACAAAAAGAGAAACAAAAAAT
Found at i:35282653 original size:16 final size:16
Alignment explanation
Indices: 35282632--35282664 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35282622 TTCGCTGTAT
35282632 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
35282648 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
35282664 T
1 T
35282665 AGCAAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:35282873 original size:19 final size:20
Alignment explanation
Indices: 35282836--35282873 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
35282826 ATTTAAATTT
* *
35282836 TAATAAGATTATTTTATCAA
1 TAATAAGATAATTTAATCAA
35282856 TAATAA-ATAATTTAATCA
1 TAATAAGATAATTTAATCA
35282874 TATTTAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TAATAAGATAATTTAATCAA
Found at i:35283035 original size:120 final size:120
Alignment explanation
Indices: 35282880--35283199 Score: 597
Period size: 120 Copynumber: 2.7 Consensus size: 120
35282870 ATCATATTTA
* *
35282880 AACAGAATTATTATTAAATATATTATAATTTAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
35282945 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
35283000 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
35283065 TATTCTTATATGAATTTACTCAAATCATATTATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
35283120 AACATAATTATTATTAAATATATTATTATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
35283185 TATTCTTATAT-AATT
66 TATTCTTATATGAATT
35283200 ANNNNNNNNN
Statistics
Matches: 196, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
119 4 0.02
120 192 0.98
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:35283045 original size:14 final size:15
Alignment explanation
Indices: 35282996--35283047 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
35282986 ATAAAATATA
35282996 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
35283011 TATTAAATATATTAT
1 AATTAAATATATTAT
35283026 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
35283039 AATTTAATA
1 AATTAAATA
35283048 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:35283149 original size:18 final size:16
Alignment explanation
Indices: 35283117--35283158 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
35283107 TAAAATATAA
*
35283117 ATTAACATA-ATTATT
1 ATTAAAATATATTATT
35283132 ATT-AAATATATTATT
1 ATTAAAATATATTATT
35283147 ATTAAAATATAT
1 ATTAAAATATAT
35283159 AATTTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 12 0.50
16 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAAATATATTATT
Found at i:35284702 original size:50 final size:51
Alignment explanation
Indices: 35284648--35284745 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 51
35284638 TTTTTTTAAT
* * *
35284648 ATCATGAATCAAAAGGTGAA-A-AATTTATAAAATTATATCGTTAGTTCAAA
1 ATCATGAATCAAAAGCTCAATAGAAATT-TAAAATTATATCGTTAGTTCAAA
35284698 ATCATGAATCAAAAGCTCAATAGTAAATTTAAAATTATATCGTTAGTT
1 ATCATGAATCAAAAGCTCAATAG-AAATTTAAAATTATATCGTTAGTT
35284746 GCAATTACAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 18 0.43
51 1 0.02
52 19 0.45
53 4 0.10
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (51 bp):
ATCATGAATCAAAAGCTCAATAGAAATTTAAAATTATATCGTTAGTTCAAA
Found at i:35312123 original size:12 final size:12
Alignment explanation
Indices: 35312106--35312130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35312096 GATGAGCAAA
35312106 ATTTGGCTTTTT
1 ATTTGGCTTTTT
35312118 ATTTGGCTTTTT
1 ATTTGGCTTTTT
35312130 A
1 A
35312131 ATTCATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.12, C:0.08, G:0.16, T:0.64
Consensus pattern (12 bp):
ATTTGGCTTTTT
Found at i:35338142 original size:42 final size:42
Alignment explanation
Indices: 35338093--35338186 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
35338083 CTCGGTATCG
* *
35338093 CACACTTAGTGCCCGTTATACAACATCATCATTTTAATTTCA
1 CACACTTAGTGCCCATTATACAACATCATCATTTTAATTCCA
* * *
35338135 CACACTTAGTGCCCATTATCCAACATCATTATTTTAATTCCG
1 CACACTTAGTGCCCATTATACAACATCATCATTTTAATTCCA
35338177 CACACTTAGT
1 CACACTTAGT
35338187 TCCATTCATA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (42 bp):
CACACTTAGTGCCCATTATACAACATCATCATTTTAATTCCA
Found at i:35339077 original size:17 final size:16
Alignment explanation
Indices: 35339055--35339093 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
35339045 TATTATAAAG
*
35339055 TTACTATATTTACCTT
1 TTACTATATTAACCTT
35339071 ATTACTATATTAACCTT
1 -TTACTATATTAACCTT
35339088 TTACTA
1 TTACTA
35339094 ATAATTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (16 bp):
TTACTATATTAACCTT
Found at i:35340226 original size:67 final size:67
Alignment explanation
Indices: 35340098--35340225 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 67
35340088 TGAAATGAGC
* *
35340098 CAACCATATGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAGAATGAGTGAAAAAAATGGC
1 CAACCATATGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAAAAAAATGGC
35340163 AG
66 AG
*
35340165 CAACCATGTGTTTTGAAGAA-AAATAAGTGGTGTTTGGCAAGAGAGAAAATGAGAGAAAAAA
1 CAACCATATGTTTTGAAGAAGAAA-AA-TGGTGTTTGGCAAGAGAGAAAATGAGAGAAAAAA
35340226 TTTTGTTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
66 3 0.05
67 21 0.38
68 32 0.57
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.21
Consensus pattern (67 bp):
CAACCATATGTTTTGAAGAAGAAAAATGGTGTTTGGCAAGAGAGAAAATGAGAGAAAAAAATGGC
AG
Found at i:35367755 original size:34 final size:34
Alignment explanation
Indices: 35367712--35367779 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
35367702 TTGAAATCGA
* *
35367712 ACACTGTATCTTTCTCTAACAATAAACATAGCGG
1 ACACTGTATCTTTCTCTAACAACAAACACAGCGG
35367746 ACACTGTATCTTTCTCTAACAACAAACACAGCGG
1 ACACTGTATCTTTCTCTAACAACAAACACAGCGG
35367780 CTTAGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (34 bp):
ACACTGTATCTTTCTCTAACAACAAACACAGCGG
Found at i:35372893 original size:21 final size:20
Alignment explanation
Indices: 35372860--35372899 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
35372850 AAGGACATTG
35372860 TATAATTAATATTTCATTAA
1 TATAATTAATATTTCATTAA
* *
35372880 TATAACTTTATATTTTATTA
1 TATAA-TTAATATTTCATTA
35372900 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTAATATTTCATTAA
Found at i:35381072 original size:17 final size:16
Alignment explanation
Indices: 35381047--35381096 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
35381037 TTATTTTCTG
*
35381047 AAAAAATTAATTAATAT
1 AAAAAATTAATAAAT-T
*
35381064 AAAATATTAATAAATT
1 AAAAAATTAATAAATT
*
35381080 AAAAAATTAAAAAATT
1 AAAAAATTAATAAATT
35381096 A
1 A
35381097 GATAATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAAATTAATAAATT
Found at i:35381086 original size:8 final size:8
Alignment explanation
Indices: 35381047--35381106 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
35381037 TTATTTTCTG
35381047 AAAAAATT
1 AAAAAATT
**
35381055 AATTAATAT
1 AAAAAAT-T
*
35381064 AAAATATT
1 AAAAAATT
*
35381072 AATAAATT
1 AAAAAATT
35381080 AAAAAATT
1 AAAAAATT
35381088 AAAAAATT
1 AAAAAATT
* *
35381096 AGATAATT
1 AAAAAATT
35381104 AAA
1 AAA
35381107 TTAAAATTTA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
8 35 0.88
9 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (8 bp):
AAAAAATT
Found at i:35381837 original size:30 final size:30
Alignment explanation
Indices: 35381779--35381840 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
35381769 GCTTCCTGAA
* *
35381779 AATATTTACAAAAAAAGGCATCTAATTTTT
1 AATATTTACAAAAAAAGGCAACCAATTTTT
*
35381809 AATATTTACAAAAAGA-GCAACCAGATTTTT
1 AATATTTACAAAAAAAGGCAACCA-ATTTTT
35381839 AA
1 AA
35381841 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAAAGGCAACCAATTTTT
Found at i:35390469 original size:322 final size:322
Alignment explanation
Indices: 35389884--35390855 Score: 1800
Period size: 322 Copynumber: 3.0 Consensus size: 322
35389874 TTCTCAAAAA
*
35389884 TAAAAATGAAAATGGCCTGGAAATGAATTTATGGTTTTCAAAATAAATGAAGTTTGAGGATGGAA
1 TAAAAATGAAAATGGCCTGGAAATGAATTTATGGTTTTCAAAATAAATGAAGTTTGAGAATGGAA
* *
35389949 ATAAATCATTTGGTCATAGTAAACTCGTTGAGTGTAGAAATATGAAATATAATTTCTATTAGGTT
66 ATAAATCATTTGGTCATAGTAAACTCGTTGAATGTAGAAATATTAAATATAATTTCTATTAGGTT
*
35390014 AGTTCTATTAGGTTTATAACTTTGTTATTCGAATTTAAACTAACCACTGGCGTTTGTTTAGTTTA
131 AGTTTTATTAGGTTTATAACTTTGTTATTCGAATTTAAACTAACCACTGGCGTTTGTTTAGTTTA
35390079 GTTCTATTAGGTTTATAACTTTTTAACCCTCTACTAAGTAGGATTAAATTATAACTCTTCATTAT
196 GTTCTATTAGGTTTATAACTTTTTAACCCTCTACTAAGTAGGATTAAATTATAACTCTTCATTAT
* *
35390144 GTATTATTTTATTTATAAATAGATTATTTATCATCTGTAACAAGTGAAAAACTCATTAATTT
261 GTATTATTTGATTTCTAAATAGATTATTTATCATCTGTAACAAGTGAAAAACTCATTAATTT
35390206 TAAAAATGAAAATGGCCTGGAAATGAATTTATGGTTTTCAAAATAAATGAAGTTTGAGAATGGAA
1 TAAAAATGAAAATGGCCTGGAAATGAATTTATGGTTTTCAAAATAAATGAAGTTTGAGAATGGAA
*
35390271 ATAAATCATTTGGTCATATTAAACTCGTTGAATGTAGAAATATTAAATATAATTTCTATTAGGTT
66 ATAAATCATTTGGTCATAGTAAACTCGTTGAATGTAGAAATATTAAATATAATTTCTATTAGGTT
* *
35390336 AGTTTTATTAGGTTTATAACTTTTTTATTCGAATTTAAACTAACCACTGGCGTTTGTTTCGTTTA
131 AGTTTTATTAGGTTTATAACTTTGTTATTCGAATTTAAACTAACCACTGGCGTTTGTTTAGTTTA
35390401 GTTCTATTAGGTTTATAACTTTTTAACCCTCTACTAAGTAGGATTAAATTATAACTCTTCATTAT
196 GTTCTATTAGGTTTATAACTTTTTAACCCTCTACTAAGTAGGATTAAATTATAACTCTTCATTAT
*
35390466 GTATTATTTGATTTCTAAATAGATTATTTATCATCTGTAACAAGTGAAAAACTCATAAATTT
261 GTATTATTTGATTTCTAAATAGATTATTTATCATCTGTAACAAGTGAAAAACTCATTAATTT
* *
35390528 TTAAAATGAAAATGACCTGGAAATGAATTTATGGTTTTCAAAATAAATGAAGTTTGAGAATGGAA
1 TAAAAATGAAAATGGCCTGGAAATGAATTTATGGTTTTCAAAATAAATGAAGTTTGAGAATGGAA
*
35390593 ATAAATCATTTGGTCATAGTAATCTCGTTGAATGTAGAAATATTAAATATAATTTCTATTAGGTT
66 ATAAATCATTTGGTCATAGTAAACTCGTTGAATGTAGAAATATTAAATATAATTTCTATTAGGTT
* *
35390658 AGTTTTATTAGGTTTATAACTTTGTTATTCGAATTTAAACTACCCATTGGCGTTTGTTTAGTTTA
131 AGTTTTATTAGGTTTATAACTTTGTTATTCGAATTTAAACTAACCACTGGCGTTTGTTTAGTTTA
35390723 GTTCTATTAGGTTTATAACTTTTTAACCCTCTACTAAGTAGGATTAAATTATAACTCTTCATTAT
196 GTTCTATTAGGTTTATAACTTTTTAACCCTCTACTAAGTAGGATTAAATTATAACTCTTCATTAT
35390788 GTATTATTTGATTTCTAAATAGATTATTTATCATCTGTAACAAGTGAAAAACTCATTAATTT
261 GTATTATTTGATTTCTAAATAGATTATTTATCATCTGTAACAAGTGAAAAACTCATTAATTT
*
35390850 TTAAAA
1 TAAAAA
35390856 CAAAAGATTG
Statistics
Matches: 631, Mismatches: 19, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
322 631 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (322 bp):
TAAAAATGAAAATGGCCTGGAAATGAATTTATGGTTTTCAAAATAAATGAAGTTTGAGAATGGAA
ATAAATCATTTGGTCATAGTAAACTCGTTGAATGTAGAAATATTAAATATAATTTCTATTAGGTT
AGTTTTATTAGGTTTATAACTTTGTTATTCGAATTTAAACTAACCACTGGCGTTTGTTTAGTTTA
GTTCTATTAGGTTTATAACTTTTTAACCCTCTACTAAGTAGGATTAAATTATAACTCTTCATTAT
GTATTATTTGATTTCTAAATAGATTATTTATCATCTGTAACAAGTGAAAAACTCATTAATTT
Found at i:35393192 original size:20 final size:22
Alignment explanation
Indices: 35393153--35393193 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35393143 TCAATATAAG
*
35393153 CATTTTAGTTGTGCTTTAATTA
1 CATTTTAGCTGTGCTTTAATTA
35393175 CATTTTAGCTG-G-TTTAATT
1 CATTTTAGCTGTGCTTTAATT
35393194 CAGTGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.54
Consensus pattern (22 bp):
CATTTTAGCTGTGCTTTAATTA
Found at i:35397229 original size:12 final size:12
Alignment explanation
Indices: 35397212--35397241 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
35397202 CCTGAAACGC
35397212 CCGTGTGCTAGG
1 CCGTGTGCTAGG
35397224 CCGTGTGCTAGG
1 CCGTGTGCTAGG
35397236 CCGTGT
1 CCGTGT
35397242 AACAACTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.27, G:0.40, T:0.27
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:35408737 original size:11 final size:11
Alignment explanation
Indices: 35408721--35408746 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35408711 ACCTACTCAA
35408721 AGTTCAATTCT
1 AGTTCAATTCT
35408732 AGTTCAATTCT
1 AGTTCAATTCT
35408743 AGTT
1 AGTT
35408747 TTCTTTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (11 bp):
AGTTCAATTCT
Found at i:35412285 original size:26 final size:27
Alignment explanation
Indices: 35412226--35412290 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
35412216 CAAGTGAGAG
*
35412226 CAAAAGAGCAAAAAGAAAAGATTGAAAAA
1 CAAAAGAG--AAAAGAAAAGATGGAAAAA
*
35412255 -TAAAGAGAAAAGAAAAG-TGGAAAAA
1 CAAAAGAGAAAAGAAAAGATGGAAAAA
35412280 CAAAAG-GAAAA
1 CAAAAGAGAAAA
35412291 CAAGAGGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 12 0.38
26 14 0.44
28 6 0.19
ACGTcount: A:0.69, C:0.05, G:0.20, T:0.06
Consensus pattern (27 bp):
CAAAAGAGAAAAGAAAAGATGGAAAAA
Found at i:35413948 original size:19 final size:19
Alignment explanation
Indices: 35413924--35413963 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
35413914 CACTTGTAAG
35413924 AAAGCCAAATCGAGGATCA
1 AAAGCCAAATCGAGGATCA
35413943 AAAGCCAAATCGAGGATCA
1 AAAGCCAAATCGAGGATCA
35413962 AA
1 AA
35413964 CCACATGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.10
Consensus pattern (19 bp):
AAAGCCAAATCGAGGATCA
Found at i:35419843 original size:21 final size:20
Alignment explanation
Indices: 35419799--35419843 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
35419789 CAAATTCTTT
*
35419799 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
35419819 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
35419840 TTTC
1 TTTC
35419844 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:35420770 original size:28 final size:30
Alignment explanation
Indices: 35420730--35420789 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
35420720 CAATCACTCT
**
35420730 TTTTTTTTCAATTTTGA-TTTTTTTTCTTC
1 TTTTTTTTCAATTCCGATTTTTTTTTCTTC
35420759 TTTTTTTT-AATTCCGATTTTTTTTTCTTC
1 TTTTTTTTCAATTCCGATTTTTTTTTCTTC
35420788 TT
1 TT
35420790 CTTCTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.10, C:0.12, G:0.03, T:0.75
Consensus pattern (30 bp):
TTTTTTTTCAATTCCGATTTTTTTTTCTTC
Found at i:35420864 original size:12 final size:11
Alignment explanation
Indices: 35420847--35420899 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 11
35420837 ATACAAACTC
*
35420847 TTTTTTTTGAA
1 TTTTTTTTTAA
35420858 TTTTTTTTTCAAA
1 TTTTTTTTT--AA
35420871 TTTTTTTTTCAA
1 TTTTTTTTT-AA
*
35420883 GTTTTTTTT-A
1 TTTTTTTTTAA
35420893 TTTTTTT
1 TTTTTTT
35420900 ACAATACCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 7 0.19
11 8 0.22
12 10 0.28
13 11 0.31
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:35420865 original size:13 final size:13
Alignment explanation
Indices: 35420847--35420891 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
35420837 ATACAAACTC
*
35420847 TTTTTTTT-GAAT
1 TTTTTTTTCAAAT
35420859 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
*
35420872 TTTTTTTTCAAGT
1 TTTTTTTTCAAAT
35420885 TTTTTTT
1 TTTTTTT
35420892 ATTTTTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 8 0.27
13 22 0.73
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:35428493 original size:36 final size:36
Alignment explanation
Indices: 35428446--35428517 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
35428436 TGCGACATCG
35428446 ATCATCCGCTGTTGCAACATAGCGACAAGTATCAGT
1 ATCATCCGCTGTTGCAACATAGCGACAAGTATCAGT
35428482 ATCATCCGCTGTTGCAACATAGCGACAAGTATCAGT
1 ATCATCCGCTGTTGCAACATAGCGACAAGTATCAGT
35428518 TTAGTGATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (36 bp):
ATCATCCGCTGTTGCAACATAGCGACAAGTATCAGT
Found at i:35444313 original size:19 final size:19
Alignment explanation
Indices: 35444286--35444324 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35444276 CAACTGTCGG
*
35444286 TAATCAATGCATAACCTCA
1 TAATAAATGCATAACCTCA
*
35444305 TAATAAATGCATACCCTCA
1 TAATAAATGCATAACCTCA
35444324 T
1 T
35444325 GGTTTCATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (19 bp):
TAATAAATGCATAACCTCA
Found at i:35453007 original size:25 final size:25
Alignment explanation
Indices: 35452933--35453044 Score: 93
Period size: 25 Copynumber: 4.5 Consensus size: 25
35452923 GTACATGTAT
* *
35452933 GCTCATACGAGCTGTA-AACGGTAA
1 GCTCATACGAGCTGAATAACAGTAA
* * *
35452957 GCTCTTTCGAGCTGAATAA-TGATAA
1 GCTCATACGAGCTGAATAACAG-TAA
* *
35452982 GCTCCTCCGAGCTGAATAACAGTAA
1 GCTCATACGAGCTGAATAACAGTAA
* ** *
35453007 GCTCATACGAGCTGAGTGTCGGTAA
1 GCTCATACGAGCTGAATAACAGTAA
*
35453032 GCTCATAAGAGCT
1 GCTCATACGAGCT
35453045 AAAATTAGTA
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
24 14 0.20
25 56 0.79
26 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACAGTAA
Found at i:35458105 original size:19 final size:19
Alignment explanation
Indices: 35458083--35458129 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
35458073 GTATAAGATA
35458083 TATTTTCCTTTTTTATTTT
1 TATTTTCCTTTTTTATTTT
* *
35458102 TATTTTTC-TCTTTATTTT
1 TATTTTCCTTTTTTATTTT
*
35458120 T-TCTTCCTTT
1 TATTTTCCTTT
35458130 CGAAACTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 7 0.32
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (19 bp):
TATTTTCCTTTTTTATTTT
Found at i:35458766 original size:3 final size:3
Alignment explanation
Indices: 35458758--35458812 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
35458748 TAATTTAGTG
*
35458758 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
35458804 TTA TTA TTA
1 TTA TTA TTA
35458813 GTTTCATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:35462715 original size:23 final size:22
Alignment explanation
Indices: 35462664--35462715 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
35462654 CCTCGTTTTT
*
35462664 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
35462686 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
35462709 TTCTTTT
1 TTCTTTT
35462716 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:35478016 original size:22 final size:22
Alignment explanation
Indices: 35477990--35478034 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
35477980 AGATCAACAC
35477990 AAATAT-AATCACATACATATCA
1 AAATATCAATCACAT-CATATCA
*
35478012 AAATATCAATCTCATCATATCA
1 AAATATCAATCACATCATATCA
35478034 A
1 A
35478035 TCATCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATCAATCACATCATATCA
Found at i:35481819 original size:18 final size:19
Alignment explanation
Indices: 35481791--35481827 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
35481781 GCACTCACAT
35481791 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
35481810 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
35481828 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:35488755 original size:17 final size:18
Alignment explanation
Indices: 35488730--35488776 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
35488720 AATGCTCGTG
35488730 ATAAAAAAAGAGAAAAGA
1 ATAAAAAAAGAGAAAAGA
* *
35488748 A-AAGAAAAGA-AACAGA
1 ATAAAAAAAGAGAAAAGA
35488764 ATAAAAAAAGAGA
1 ATAAAAAAAGAGA
35488777 GAGAGCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.25
17 16 0.67
18 2 0.08
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (18 bp):
ATAAAAAAAGAGAAAAGA
Found at i:35489518 original size:10 final size:10
Alignment explanation
Indices: 35489471--35489518 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
35489461 GAAGATTTTG
*
35489471 AATTTTAATT
1 AATTTTTATT
*
35489481 AATTTTATATCA
1 AATTTT-TAT-T
35489493 AATTTTTATT
1 AATTTTTATT
35489503 AATTTTTATT
1 AATTTTTATT
35489513 -ATTTTT
1 AATTTTT
35489519 GACAGATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
9 6 0.18
10 16 0.48
11 5 0.15
12 6 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
AATTTTTATT
Found at i:35492116 original size:21 final size:21
Alignment explanation
Indices: 35492090--35492144 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
35492080 GTTCTAGGCG
*
35492090 TGTTTAATGTGTCCTAATGCA
1 TGTTTAATATGTCCTAATGCA
* * *
35492111 TGTTTAATAAGTTCTAATGTA
1 TGTTTAATATGTCCTAATGCA
*
35492132 TGTTTAATTTGTC
1 TGTTTAATATGTC
35492145 TTAGGAGAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.49
Consensus pattern (21 bp):
TGTTTAATATGTCCTAATGCA
Found at i:35503929 original size:23 final size:23
Alignment explanation
Indices: 35503899--35503944 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
35503889 CCATCTCATC
35503899 TCATTCA-TTGCATTTAGATTAAT
1 TCATTCATTTGCATTTAG-TTAAT
*
35503922 TCATTCATTTGTATTTAGTTAAT
1 TCATTCATTTGCATTTAGTTAAT
35503945 ATTAATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (23 bp):
TCATTCATTTGCATTTAGTTAAT
Found at i:35511194 original size:12 final size:11
Alignment explanation
Indices: 35511164--35511198 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
35511154 CAGGAACTTC
35511164 TCTGTGATATT
1 TCTGTGATATT
*
35511175 TTTGTGATATT
1 TCTGTGATATT
35511186 ATCTGTGATATT
1 -TCTGTGATATT
35511198 T
1 T
35511199 GTGTTTGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (11 bp):
TCTGTGATATT
Found at i:35518248 original size:23 final size:23
Alignment explanation
Indices: 35518222--35518265 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
35518212 AAATTCATTG
*
35518222 CATAACAT-TATAGCTTTTATGAA
1 CATAACATATA-AGCATTTATGAA
35518245 CATAACATATAAGCATTTATG
1 CATAACATATAAGCATTTATG
35518266 TTTTCATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (23 bp):
CATAACATATAAGCATTTATGAA
Found at i:35522467 original size:22 final size:23
Alignment explanation
Indices: 35522442--35522489 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
35522432 TAGGGAATTA
*
35522442 AGAGTTAA-TAGGTGTTTTCA-TT
1 AGAGGTAAGTAGG-GTTTTCAGTT
*
35522464 AGAGGTAAGTATGGTTTTCAGTT
1 AGAGGTAAGTAGGGTTTTCAGTT
35522487 AGA
1 AGA
35522490 AAATAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.40
Consensus pattern (23 bp):
AGAGGTAAGTAGGGTTTTCAGTT
Found at i:35526100 original size:22 final size:22
Alignment explanation
Indices: 35526072--35526131 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
35526062 TATTTAGGAA
35526072 TTGGTACGAAATGGTATAGAAG
1 TTGGTACGAAATGGTATAGAAG
* * *
35526094 TTGGTACGAAATGGTATGGTAT
1 TTGGTACGAAATGGTATAGAAG
*
35526116 TTGGTACGAATTGGTA
1 TTGGTACGAAATGGTA
35526132 ATGGTTCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (22 bp):
TTGGTACGAAATGGTATAGAAG
Found at i:35532094 original size:51 final size:54
Alignment explanation
Indices: 35532034--35532154 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 54
35532024 CATGTCCAAC
*
35532034 CCCGTGTAACTCACTCACTTGGGTCACACGGCC-AC-ACGC-CCGTGTGACTAG
1 CCCGTGTAACTCACTCACTTGGGTCACACGGCCAACTACACACCGTGTGACTAG
* * * *
35532085 CCCGTGTAACTCACTTACTTGGGTCATACGGCCAACTACACATTCGTTTGACTAG
1 CCCGTGTAACTCACTCACTTGGGTCACACGGCCAACTACACA-CCGTGTGACTAG
*
35532140 CCCGTTTAACTCACT
1 CCCGTGTAACTCACT
35532155 GACCTGGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
51 31 0.52
52 2 0.03
53 3 0.05
55 24 0.40
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (54 bp):
CCCGTGTAACTCACTCACTTGGGTCACACGGCCAACTACACACCGTGTGACTAG
Found at i:35535227 original size:24 final size:24
Alignment explanation
Indices: 35535185--35535230 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
35535175 CATATCAGTA
*
35535185 AGTAAGTAAGTAAACAAGTAAAAG
1 AGTAAGTAAGTAAAAAAGTAAAAG
35535209 AGTAAGTACAG-AAAAAAGTAAA
1 AGTAAGTA-AGTAAAAAAGTAAA
35535231 GGTCATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.61, C:0.04, G:0.20, T:0.15
Consensus pattern (24 bp):
AGTAAGTAAGTAAAAAAGTAAAAG
Found at i:35541762 original size:30 final size:29
Alignment explanation
Indices: 35541719--35541776 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
35541709 TCCGAGCTTT
35541719 GGGGAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGAAAAGTGTAAATATGCAAAAGTTTA
* * * *
35541748 GGGGCAAAATTGTAATTTTGCCAAAGTTT
1 GGGG-AAAAGTGTAAATATGCAAAAGTTT
35541777 GAGTCAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.38, C:0.07, G:0.26, T:0.29
Consensus pattern (29 bp):
GGGGAAAAGTGTAAATATGCAAAAGTTTA
Found at i:35542138 original size:50 final size:51
Alignment explanation
Indices: 35542033--35542165 Score: 164
Period size: 50 Copynumber: 2.7 Consensus size: 51
35542023 TTATTGAGGC
* *
35542033 TATGAGAGGTCC-CACGTAAGACCATGTCTGGGACATGGCGTTGGTACCGA
1 TATGAGAGGTCCTCACGTAAGACCATGTCTGGGACATGGCGTGGGAACCGA
* **
35542083 GATGAGAGGTCCTC-CGTAAGACCATGTCTGGGACATGGCGTGGGAATTGA
1 TATGAGAGGTCCTCACGTAAGACCATGTCTGGGACATGGCGTGGGAACCGA
** * *
35542133 TATGAGAACT-CTCATGTAAGACCATATCTGGGA
1 TATGAGAGGTCCTCACGTAAGACCATGTCTGGGA
35542166 TATAGTATCT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
49 3 0.04
50 67 0.94
51 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (51 bp):
TATGAGAGGTCCTCACGTAAGACCATGTCTGGGACATGGCGTGGGAACCGA
Found at i:35543967 original size:20 final size:20
Alignment explanation
Indices: 35543935--35543973 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35543925 TGAGTTATTT
*
35543935 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAACTAAAC
35543955 AAGTAAG-AGAGTAACTAAA
1 AAGTAAGCA-AGTAACTAAA
35543974 GAAGAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (20 bp):
AAGTAAGCAAGTAACTAAAC
Found at i:35549590 original size:10 final size:10
Alignment explanation
Indices: 35549575--35549613 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
35549565 ACGAGCTCAA
35549575 TGAGCTGAAT
1 TGAGCTGAAT
*
35549585 TGAGCTGACT
1 TGAGCTGAAT
* *
35549595 TGAGCTCAAG
1 TGAGCTGAAT
35549605 TGAGCTGAA
1 TGAGCTGAA
35549614 CCACATGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (10 bp):
TGAGCTGAAT
Found at i:35549598 original size:20 final size:20
Alignment explanation
Indices: 35549575--35549612 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35549565 ACGAGCTCAA
* *
35549575 TGAGCTGAATTGAGCTGACT
1 TGAGCTCAAGTGAGCTGACT
35549595 TGAGCTCAAGTGAGCTGA
1 TGAGCTCAAGTGAGCTGA
35549613 ACCACATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTCAAGTGAGCTGACT
Found at i:35558022 original size:16 final size:17
Alignment explanation
Indices: 35558001--35558036 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
35557991 TCAATTATCC
35558001 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
35558017 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
35558034 CTC
1 CTC
35558037 TCAACTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:35563963 original size:32 final size:32
Alignment explanation
Indices: 35563920--35564000 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 32
35563910 ATGTGATTGG
35563920 CACAAAGCCATCAGTAGTAGT-GATATGATCGGTA
1 CACAAAGCCATCAGTAGTAGTAG-TATGATC-G-A
* *
35563954 CAC-AA-CCATCAGTAATGGTAGTATGATCGA
1 CACAAAGCCATCAGTAGTAGTAGTATGATCGA
35563984 CACAAAGCCATCAGTAG
1 CACAAAGCCATCAGTAG
35564001 CATCGCAGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.10
31 3 0.07
32 28 0.68
33 3 0.07
34 3 0.07
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (32 bp):
CACAAAGCCATCAGTAGTAGTAGTATGATCGA
Found at i:35564226 original size:24 final size:24
Alignment explanation
Indices: 35564170--35564226 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
35564160 GCCATACTCA
*
35564170 AAATCAGTCATGCAAATCACAAAC
1 AAATCAGTCATACAAATCACAAAC
* * *
35564194 AGATCAGTCATACCAATCACAGAC
1 AAATCAGTCATACAAATCACAAAC
*
35564218 AAATGAGTC
1 AAATCAGTC
35564227 GTTTACATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.46, C:0.25, G:0.12, T:0.18
Consensus pattern (24 bp):
AAATCAGTCATACAAATCACAAAC
Found at i:35564375 original size:81 final size:80
Alignment explanation
Indices: 35564290--35564471 Score: 240
Period size: 81 Copynumber: 2.2 Consensus size: 80
35564280 GACCCTCTAG
* **
35564290 GGGCATTACGATCATTTTACCT-TACAGGAGTATTTTGATCATTTAACCCTATGAGGGTATTACG
1 GGGCATTACGGTCATTTTACCTATA-AGGA-TATTTTGATCATTTAACCCTACAAGGGTATTACG
35564354 ATCATTTTACCCTACAA
64 ATCATTTTACCCTACAA
* * *
35564371 GGGCATTACGGTCATTTGACCCTATAAGGATTTTTTGATCATTTTACCCTACAAGGGTATTACGA
1 GGGCATTACGGTCATTTTA-CCTATAAGGATATTTTGATCATTTAACCCTACAAGGGTATTACGA
* * *
35564436 TCATTTTACCTTATAG
65 TCATTTTACCCTACAA
*
35564452 GGGCATTATGGTCATTTTAC
1 GGGCATTACGGTCATTTTAC
35564472 AAATATTGGG
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
80 1 0.01
81 78 0.89
82 7 0.08
83 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (80 bp):
GGGCATTACGGTCATTTTACCTATAAGGATATTTTGATCATTTAACCCTACAAGGGTATTACGAT
CATTTTACCCTACAA
Found at i:35564459 original size:27 final size:27
Alignment explanation
Indices: 35564281--35564471 Score: 150
Period size: 27 Copynumber: 7.1 Consensus size: 27
35564271 ATAGTCATTG
* *
35564281 ACCCTCTAGGGGCATTACGATCATTTT
1 ACCCTATAGGGGTATTACGATCATTTT
* * * ** *
35564308 ACCTTACAGGAGTATTTTGATCATTTA
1 ACCCTATAGGGGTATTACGATCATTTT
35564335 ACCCTAT-GAGGGTATTACGATCATTTT
1 ACCCTATAG-GGGTATTACGATCATTTT
* * * * *
35564362 ACCCTACAAGGGCATTACGGTCATTTG
1 ACCCTATAGGGGTATTACGATCATTTT
* * * **
35564389 ACCCTATAAGGATTTTTTGATCATTTT
1 ACCCTATAGGGGTATTACGATCATTTT
* *
35564416 ACCCTACAAGGGTATTACGATCATTTT
1 ACCCTATAGGGGTATTACGATCATTTT
* * * *
35564443 ACCTTATAGGGGCATTATGGTCATTTT
1 ACCCTATAGGGGTATTACGATCATTTT
35564470 AC
1 AC
35564472 AAATATTGGG
Statistics
Matches: 124, Mismatches: 38, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
26 1 0.01
27 123 0.99
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
ACCCTATAGGGGTATTACGATCATTTT
Found at i:35564467 original size:54 final size:54
Alignment explanation
Indices: 35564281--35564471 Score: 188
Period size: 54 Copynumber: 3.5 Consensus size: 54
35564271 ATAGTCATTG
* * **
35564281 ACCCTCTAGGGGCATTACGATCATTTTACCTTAC-AGGAGTATTTTGATCATTTA
1 ACCCTATAGGGGCATTACGATCATTTTACCCTACAAGG-GTATTACGATCATTTA
* * * *
35564335 ACCCTAT-GAGGGTATTACGATCATTTTACCCTACAAGGGCATTACGGTCATTTG
1 ACCCTATAG-GGGCATTACGATCATTTTACCCTACAAGGGTATTACGATCATTTA
* *** ** *
35564389 ACCCTATAAGGATTTTTTGATCATTTTACCCTACAAGGGTATTACGATCATTTT
1 ACCCTATAGGGGCATTACGATCATTTTACCCTACAAGGGTATTACGATCATTTA
* * *
35564443 ACCTTATAGGGGCATTATGGTCATTTTAC
1 ACCCTATAGGGGCATTACGATCATTTTAC
35564472 AAATATTGGG
Statistics
Matches: 111, Mismatches: 23, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
53 1 0.01
54 107 0.96
55 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (54 bp):
ACCCTATAGGGGCATTACGATCATTTTACCCTACAAGGGTATTACGATCATTTA
Found at i:35573832 original size:42 final size:41
Alignment explanation
Indices: 35573775--35573928 Score: 161
Period size: 41 Copynumber: 3.7 Consensus size: 41
35573765 TATGTTATCT
35573775 TGTAAGACCACGTCTGGGACGTTGGCATAGACTTGTGTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATAGA-TTGTGTTACG
* * * * *
35573817 TGTAAGACCATGTCTGGGACATTGGAATCGTATT-TGTTTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATAG-ATTGTGTTACG
*
35573858 TGTAAGACC-CTGTCTGGGACAG-TGGCATAGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATAGAT-TGTG-TTACG
* *
35573901 TGTAAGACCACGTCCGAGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
35573929 TGTACGAGCT
Statistics
Matches: 91, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
40 2 0.02
41 31 0.34
42 31 0.34
43 26 0.29
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATAGATTGTGTTACG
Found at i:35575149 original size:50 final size:49
Alignment explanation
Indices: 35575025--35575154 Score: 145
Period size: 49 Copynumber: 2.6 Consensus size: 49
35575015 GATAATAACA
* * *
35575025 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTATAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCATATAC
* ** * *
35575074 TGCAAATGCCATAACCCAGATATGGTCTTACATGAGA-GTTCTCATATCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGATGTT-TCATAT-AC
**
35575124 TGCCAATGCCATGTCTTAGACATGGTCTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC
35575155 GGGGGACCTC
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
48 3 0.05
49 36 0.55
50 26 0.40
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCATATAC
Found at i:35575167 original size:50 final size:50
Alignment explanation
Indices: 35575025--35575260 Score: 136
Period size: 50 Copynumber: 4.6 Consensus size: 50
35575015 GATAATAACA
* * * ** * * *
35575025 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGG-GATGTTTCCTAT-AC
1 TGCCAATGCCATGTCCTAGACATGGTCTTAC-GGGAGACCTCTCATATCAG
* ** * * ** **
35575074 TGCAAATGCCATAACCCAGATATGGTCTTACATGAGAGTTCTCATATCAG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGGGAGACCTCTCATATCAG
* * *
35575124 TGCCAATGCCATGTCTTAGACATGGTCTTACGGGGGACCTCTCATCTC-G
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGGGAGACCTCTCATATCAG
* ** * * *
35575173 ATACCAACACCATGTCCCAGACATGGTCTTACGTGAGACCTCTCATAACCTCAATAA
1 -TGCCAATGCCATGTCCTAGACATGGTCTTACGGGAGACCTCTCAT-A--TC---AG
*
35575230 TGCCAATGCCATGTCCTAGACATAGTCTTAC
1 TGCCAATGCCATGTCCTAGACATGGTCTTAC
35575261 ATGGGGTCTC
Statistics
Matches: 139, Mismatches: 38, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
48 1 0.01
49 35 0.25
50 75 0.54
53 2 0.01
56 26 0.19
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACGGGAGACCTCTCATATCAG
Found at i:35575251 original size:56 final size:52
Alignment explanation
Indices: 35575124--35575260 Score: 152
Period size: 50 Copynumber: 2.6 Consensus size: 52
35575114 CTCATATCAG
* * *
35575124 TGCCAATGCCATGTCTTAGACATGGTCTTACGGGGGACCTCTCATCTCGATA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGGGAGACCTCTCATCTCAATA
** * *
35575176 --CCAACACCATGTCCCAGACATGGTCTTACGTGAGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACGGGAGACCTCTCAT---CTCAAT-A
*
35575230 TGCCAATGCCATGTCCTAGACATAGTCTTAC
1 TGCCAATGCCATGTCCTAGACATGGTCTTAC
35575261 ATGGGGTCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
50 37 0.54
53 5 0.07
54 1 0.01
56 25 0.37
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (52 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACGGGAGACCTCTCATCTCAATA
Found at i:35581368 original size:17 final size:16
Alignment explanation
Indices: 35581334--35581369 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
35581324 TCCCTTATCC
*
35581334 CTCATCCTTCTCATCT
1 CTCATCCTTCTCAACT
35581350 CTCATCCTCTCTCAACT
1 CTCATCCT-TCTCAACT
35581367 CTC
1 CTC
35581370 TTAGCTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.14, C:0.47, G:0.00, T:0.39
Consensus pattern (16 bp):
CTCATCCTTCTCAACT
Found at i:35586868 original size:51 final size:51
Alignment explanation
Indices: 35586748--35586930 Score: 219
Period size: 51 Copynumber: 3.6 Consensus size: 51
35586738 AAAGTGATGG
* * * *
35586748 TCACCTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT-ATCGA
* * * *
35586798 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATCGA
* * * *
35586849 TCACATGTGTAGTACTATGTGCAGGCTACTGCGTGTATCGGATGGTAAC-A
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATCGA
35586899 GTCACATGTGTAGTACTATGTGCAGGCTACTA
1 -TCACATGTGTAGTACTATGTGCAGGCTACTA
35586931 TGTGAACCAA
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
50 38 0.34
51 74 0.65
52 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTATCGA
Found at i:35586875 original size:101 final size:102
Alignment explanation
Indices: 35586748--35586932 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
35586738 AAAGTGATGG
* * * *
35586748 TCACCTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGATAACAGTCACATGTGTAGT
35586811 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* * *
35586849 TCACATGTGTAGTACTATGTGCAGGCTACTGCGTGTATCGGATGGTAACAGTCACATGTGTAGTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAACAGTCACATGTGTAGTA
35586914 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
35586933 TGAACCAAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.51
102 33 0.44
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAACAGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:35586992 original size:45 final size:45
Alignment explanation
Indices: 35586941--35587029 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
35586931 TGTGAACCAA
* *
35586941 ACATCATTGATTAGTAAGGTGGTTGCTATGTGATGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG
*
35586986 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCG
35587030 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGATGAATCCACCGG
Found at i:35595235 original size:3 final size:3
Alignment explanation
Indices: 35595219--35595295 Score: 136
Period size: 3 Copynumber: 25.0 Consensus size: 3
35595209 AAAATTTTAG
35595219 AAT AAT AAGCT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AA--T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35595266 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35595296 TGGGAAGAGC
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
3 69 0.96
5 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35601020 original size:22 final size:22
Alignment explanation
Indices: 35600992--35601039 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
35600982 TATAGGCTTA
35600992 AGAATATTCCTTCACTTCCTTC
1 AGAATATTCCTTCACTTCCTTC
*
35601014 AGAATATTCCTTCACTTCCTTT
1 AGAATATTCCTTCACTTCCTTC
35601036 AGAA
1 AGAA
35601040 GTGATTGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (22 bp):
AGAATATTCCTTCACTTCCTTC
Found at i:35604663 original size:12 final size:14
Alignment explanation
Indices: 35604643--35604678 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
35604633 TCCAAGTTAG
35604643 ATAAAATAATT-AA
1 ATAAAATAATTAAA
35604656 AT-AAATAATTAAA
1 ATAAAATAATTAAA
35604669 ATAAAATAAT
1 ATAAAATAAT
35604679 ATATCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.38
13 6 0.29
14 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAATAATTAAA
Found at i:35610380 original size:292 final size:283
Alignment explanation
Indices: 35609865--35610386 Score: 647
Period size: 292 Copynumber: 1.8 Consensus size: 283
35609855 TTAAAATAAT
* * * * *
35609865 AATAAATAATGAGATGTATGATTTGAAACTAATTAATAATAACACAAGAAATATGTATGATATCA
1 AATAAATAATAAAACGTATGATTTGAAACTAATTAATAATAACACAAGAAATATATACGATATCA
* * *
35609930 AAACAAAAATTAGATTAAACTATAAATAAAATGAAATTTAAACATATGAATACATCATATTAAGG
66 AAACAAAAATTAGATTAAACTATAAATAAAAAGAAATTCAAACATAAGAATACATCATATTAAGG
* * * * *
35609995 TTACTAAATGAATATAATTATTTATCATGGTGTTGTCATCAGTCCTAAATTGGTGTCAAGTTAAT
131 TAACTAAATGAATATAATGATTTATCATGGTGTTGTCATCACTCCTAAATTAGTATCAAGTTAAT
* *
35610060 TTGTGACATAATCTCAATCAATAACATTATTAATATGGAAACTCTATCAAATATTTAGAATACAA
196 TTGTGACACAATCTCAATCAACAACATTATTAATATGGAAACTCTATCAAATATTTAGAATACAA
35610125 ATTTGTATTCCAAAATAAGATAC
261 ATTTGTATTCCAAAATAAGATAC
* * *
35610148 AATAAATAATAAAACGTATGGTTTGAAACTAATTAATAATAACACATGAAATATATACGATATTA
1 AATAAATAATAAAACGTATGATTTGAAACTAATTAATAATAACACAAGAAATATATACGATATCA
* * * *
35610213 AAATAAAAA-TAGATT-AATTGTAAGTAAAAAGAAATTCAAACATAAGAATACATCATATTAAAA
66 AAACAAAAATTAGATTAAACTATAAATAAAAAGAAATTCAAACATAAGAATACATCATATT---A
* * * *
35610276 AGGCTAATTGAATAT-AATTATTTTTAATGATATTGTCATGGTGTTGTCATCAACT-TTAAGTTA
128 AGG-TAACT-AA-ATGAA-TA----TAATGAT-TTATCATGGTGTTGTCATC-ACTCCTAAATTA
* *
35610339 GTATTAAGTTAATTTGTGACACCATCTCAATCAACAACATTATTAATA
183 GTATCAAGTTAATTTGTGACACAATCTCAATCAACAACATTATTAATA
35610387 CTAGAAATCC
Statistics
Matches: 198, Mismatches: 28, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
281 38 0.19
282 6 0.03
283 65 0.33
284 4 0.02
285 3 0.02
286 4 0.02
287 4 0.02
291 6 0.03
292 66 0.33
293 2 0.01
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.34
Consensus pattern (283 bp):
AATAAATAATAAAACGTATGATTTGAAACTAATTAATAATAACACAAGAAATATATACGATATCA
AAACAAAAATTAGATTAAACTATAAATAAAAAGAAATTCAAACATAAGAATACATCATATTAAGG
TAACTAAATGAATATAATGATTTATCATGGTGTTGTCATCACTCCTAAATTAGTATCAAGTTAAT
TTGTGACACAATCTCAATCAACAACATTATTAATATGGAAACTCTATCAAATATTTAGAATACAA
ATTTGTATTCCAAAATAAGATAC
Found at i:35610861 original size:15 final size:15
Alignment explanation
Indices: 35610841--35610876 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
35610831 TAACCAAGTT
35610841 GGTGACCC-AGTTGAA
1 GGTGACCCGA-TTGAA
35610856 GGTGACCCGATTGAA
1 GGTGACCCGATTGAA
35610871 GGTGAC
1 GGTGAC
35610877 ACCAACTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.19
Consensus pattern (15 bp):
GGTGACCCGATTGAA
Found at i:35611477 original size:298 final size:293
Alignment explanation
Indices: 35610891--35611602 Score: 758
Period size: 298 Copynumber: 2.4 Consensus size: 293
35610881 ACTCCATCAA
* * *
35610891 GAGCTTAAATAATAGTA-AGTGTATATATACAAATGATGGAAGTAATAAAGTGTACATAGTAAAA
1 GAGCTTAAATAATA-TATAG-ATAGATATACAAATGATGGAAGTAATAAAGTGTACATAATAAAA
* * * * * **
35610955 TTAAGATGTATAAAAATCAAAATAAAGTTTTAGTTGAGTGGTAAATTAAAAATTTTATTAATGTA
64 TTAAAATGTTTAAAAATTAAAATAAA--TTTAGTTGAGTGGTAAATTAAAGATTTTACTAATACA
* * * *
35611020 AATAGTTTGGGTTCGAATCTCACAATATGCATTTTTTATTAGTTTTTTAAAATAAAAAGACTAAA
127 AATAGTTTGGGTCCAAATCCCACAATATGCATTTTTTATTAGTTTTTTAAAATAAAAAAACTAAA
* * * ** * *
35611085 ATAGCCTTGAATAATATAGCTTATTTTAATTATGGAATGGTATGTCCTTAATTTTCCTAACCGAG
192 ATACCCTCGAATAATATAACTTATTTTAATTACAGAAGGGTATGTCCTTAATTTTCCTAACCAAG
* * *
35611150 TTGGTAACTCGATTGAGGGTGACATCAACTCAGTAAG
257 TTGGTAACTCGATTGAGAGTAACATCAACTCAATAAG
* *
35611187 TAGCTTAAATAATACTATAGATAGATATACAAATGATGAAAGTAATAAAGTGT-CATAATAAAAT
1 GAGCTTAAATAATA-TATAGATAGATATACAAATGATGGAAGTAATAAAGTGTACATAATAAAAT
35611251 TAAAATGTTTAAATATATTAAAATAACATGTTAGTTGAGTGGTAAATTAAAGATTTTACTAATAC
65 TAAAATGTTTAAA-A-ATTAAAATAA-AT-TTAGTTGAGTGGTAAATTAAAGATTTTACTAATAC
* ** *
35611316 AATTAGTTTGGGTCCAAATCCCACCGTATGC-TTATTTGTATTGGTTTTTT-AAATAAAAAAAAC
126 AAATAGTTTGGGTCCAAATCCCACAATATGCATT-TTT-TATTAGTTTTTTAAAAT-AAAAAAAC
* *
35611379 TAAAGTACCCTCGAATAATATAATTTATTTTAATTACAGAAGGGTATG-CCTATAATTTTCCTAA
188 TAAAATACCCTCGAATAATATAACTTATTTTAATTACAGAAGGGTATGTCCT-TAATTTTCCTAA
*** * * * * *
35611443 CCAAGTTGGTGGTTTGGTTGTGAGTAATATCAACTCAATCAG
252 CCAAGTTGGTAACTCGATTGAGAGTAACATCAACTCAATAAG
* * * * *
35611485 GAGCTTAAATAATA-AT--ATAGATATACAATTCATGGAGGTAA-AAAGTGTGCATAATAAAACT
1 GAGCTTAAATAATATATAGATAGATATACAAATGATGGAAGTAATAAAGTGTACATAATAAAATT
* * * * *
35611546 AAAATGTATTAAAAAAGTAAAATAAAATTTTGATTGAGTAGTAAATTTAAGGTTTTA
66 AAAATGT-TT-AAAAATTAAAAT-AAATTTAG-TTGAGTGGTAAATTAAAGATTTTA
35611603 TGCAAAATGT
Statistics
Matches: 350, Mismatches: 52, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
293 10 0.03
294 69 0.20
295 26 0.07
296 54 0.15
297 77 0.22
298 114 0.33
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (293 bp):
GAGCTTAAATAATATATAGATAGATATACAAATGATGGAAGTAATAAAGTGTACATAATAAAATT
AAAATGTTTAAAAATTAAAATAAATTTAGTTGAGTGGTAAATTAAAGATTTTACTAATACAAATA
GTTTGGGTCCAAATCCCACAATATGCATTTTTTATTAGTTTTTTAAAATAAAAAAACTAAAATAC
CCTCGAATAATATAACTTATTTTAATTACAGAAGGGTATGTCCTTAATTTTCCTAACCAAGTTGG
TAACTCGATTGAGAGTAACATCAACTCAATAAG
Found at i:35618620 original size:50 final size:52
Alignment explanation
Indices: 35618566--35618683 Score: 143
Period size: 50 Copynumber: 2.3 Consensus size: 52
35618556 TAATAAAGTT
35618566 ATGCATTATGTAACTTCCATGCTAG-TTAAGTATGCATCA-TAAA-TAATGAC
1 ATGCATTATGTAACTTCCATGCTAGTTTAAGTATGCATCATTAAATTAA-GAC
* * * * *
35618616 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGTATCATTAAATTAAGTC
1 ATGCATTATGTAACTTCCATGCTAGTTTAAGTATGCATCATTAAATTAAGAC
* *
35618668 TTGCATTAAGTAACTT
1 ATGCATTATGTAACTT
35618684 ATTTGTTCAT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
50 23 0.40
51 12 0.21
52 19 0.33
53 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (52 bp):
ATGCATTATGTAACTTCCATGCTAGTTTAAGTATGCATCATTAAATTAAGAC
Found at i:35623557 original size:95 final size:94
Alignment explanation
Indices: 35623417--35623602 Score: 219
Period size: 95 Copynumber: 2.0 Consensus size: 94
35623407 GTACCGGTGG
** * * *
35623417 TGGATACCTTACCGATGGTTAAGATTTTGTATATATTGTGTATTCTTCACAGCTCATGTGAGAAA
1 TGGATACCTTACCGATGACTAAAATTTTGCATATATTGTGGATTCTTCACAGCTCATGTGAGAAA
*
35623482 CATTATGTAATGATTAATGTCTCGATTTAC
66 CACTATGTAATGATTAATGTCT-GATTTAC
* * * * * * * *
35623512 TGGATACCTTACTGATGACTAAAATTTTGCATGTGTTGTGGATTCTTCATATCTCGTGTGAGTAG
1 TGGATACCTTACCGATGACTAAAATTTTGCATATATTGTGGATTCTTCACAGCTCATGTGAGAAA
* *
35623577 CACTGTGTAATGGTTAATGTCTGATT
66 CACTATGTAATGATTAATGTCTGATT
35623603 CACAGGTCAT
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
94 4 0.05
95 71 0.95
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (94 bp):
TGGATACCTTACCGATGACTAAAATTTTGCATATATTGTGGATTCTTCACAGCTCATGTGAGAAA
CACTATGTAATGATTAATGTCTGATTTAC
Found at i:35630973 original size:4 final size:4
Alignment explanation
Indices: 35630959--35631035 Score: 145
Period size: 4 Copynumber: 19.2 Consensus size: 4
35630949 AGTACCTTGT
*
35630959 CATA TATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
35631007 CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA C
35631036 CTTTTAAAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:35635182 original size:18 final size:18
Alignment explanation
Indices: 35635152--35635206 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
35635142 GTGCAAAAAC
*
35635152 AAGAAGAAAAAAATGAAA
1 AAGAAGAAAAAAAAGAAA
35635170 AAGAA-AAAGAAAAAG-AA
1 AAGAAGAAA-AAAAAGAAA
*
35635187 AAGAGTGAGAAAAAAAGAAA
1 AAGA-AGA-AAAAAAAGAAA
35635207 TTGAGTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 9 0.30
18 10 0.33
19 7 0.23
20 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (18 bp):
AAGAAGAAAAAAAAGAAA
Found at i:35646740 original size:43 final size:42
Alignment explanation
Indices: 35646631--35646743 Score: 156
Period size: 41 Copynumber: 2.7 Consensus size: 42
35646621 TCTTCCTAAG
* * *
35646631 AAAGAGGAGATGATAATTTTGGGTTTTTGAAAAAAGAATTTA
1 AAAGAGGAGAAGATAATCTTGGGTTGTTGAAAAAAGAATTTA
*
35646673 AAA-AGGAGAAGATAATCTTAGGTTGTTGAAAAAAGAATTTAA
1 AAAGAGGAGAAGATAATCTTGGGTTGTTGAAAAAAGAATTT-A
* *
35646715 AAAGAGGAGAAGATAAACATGGGTTGTTG
1 AAAGAGGAGAAGATAATCTTGGGTTGTTG
35646744 GATTTACCGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 33 0.53
42 7 0.11
43 22 0.35
ACGTcount: A:0.45, C:0.02, G:0.26, T:0.27
Consensus pattern (42 bp):
AAAGAGGAGAAGATAATCTTGGGTTGTTGAAAAAAGAATTTA
Found at i:35648621 original size:11 final size:11
Alignment explanation
Indices: 35648597--35648702 Score: 67
Period size: 11 Copynumber: 9.7 Consensus size: 11
35648587 TATTGGATTA
**
35648597 AAAAAAAAAAG
1 AAAAAAAATTG
*
35648608 AAAGAAAATTG
1 AAAAAAAATTG
*
35648619 AAAAAAAATTC
1 AAAAAAAATTG
*
35648630 AAAAAAAAGTG
1 AAAAAAAATTG
*
35648641 -AAAAAAATCG
1 AAAAAAAATTG
**
35648651 AACAAAAAAAAAG
1 -A-AAAAAAATTG
* *
35648664 AGAGAGAAA--G
1 A-AAAAAAATTG
35648674 -AAAAAAATTG
1 AAAAAAAATTG
35648684 AAAAAAAATTG
1 AAAAAAAATTG
35648695 AAAAAAAA
1 AAAAAAAA
35648703 GAAGAAGAGG
Statistics
Matches: 73, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
8 5 0.07
10 10 0.14
11 44 0.60
12 6 0.08
13 8 0.11
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.09
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:35648678 original size:44 final size:42
Alignment explanation
Indices: 35648631--35648711 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
35648621 AAAAAATTCA
35648631 AAAAAAAGTG-AAAAAAATCGAACAAAAAAAAAGAGAGAGAAAG
1 AAAAAAAGTGAAAAAAAATCGAA-AAAAAAAAAGA-AGAGAAAG
* * *
35648674 AAAAAAATTGAAAAAAAATTGAAAAAAAAGAAGAAGAG
1 AAAAAAAGTGAAAAAAAATCGAAAAAAAAAAAGAAGAG
35648712 GATTTCGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 4 0.12
43 19 0.56
44 11 0.32
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.07
Consensus pattern (42 bp):
AAAAAAAGTGAAAAAAAATCGAAAAAAAAAAAGAAGAGAAAG
Found at i:35648800 original size:16 final size:16
Alignment explanation
Indices: 35648758--35648800 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
35648748 AATTGTATTT
**
35648758 GAAGTGAAAAAAAATC
1 GAAGTGAAAAAAAAAA
*
35648774 GAAGTATAAAAAAAAAA
1 GAAGT-GAAAAAAAAAA
35648791 GAAGTGAAAA
1 GAAGTGAAAA
35648801 GTCTTGTGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.12
Consensus pattern (16 bp):
GAAGTGAAAAAAAAAA
Found at i:35654360 original size:40 final size:40
Alignment explanation
Indices: 35654315--35654393 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
35654305 AAAGAACGAG
35654315 AAAAATGGCTAGAAACAAGAATGATCTTGGTCCTAATGAA
1 AAAAATGGCTAGAAACAAGAATGATCTTGGTCCTAATGAA
35654355 AAAAATGGCTAGAAACAAGAATGATCTTGGTCCTAATGA
1 AAAAATGGCTAGAAACAAGAATGATCTTGGTCCTAATGA
35654394 CAATCCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAAATGGCTAGAAACAAGAATGATCTTGGTCCTAATGAA
Found at i:35667763 original size:27 final size:27
Alignment explanation
Indices: 35667731--35667801 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
35667721 CCAACTTGCA
35667731 CCCGAAGGGTAAAATGACCAAAATACC
1 CCCGAAGGGTAAAATGACCAAAATACC
* * **
35667758 CTCGAAGGGTAAAATAACTGAAATACC
1 CCCGAAGGGTAAAATGACCAAAATACC
*
35667785 CCCAAAGGGTAAAATGA
1 CCCGAAGGGTAAAATGA
35667802 TTGTTAAACC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (27 bp):
CCCGAAGGGTAAAATGACCAAAATACC
Found at i:35668018 original size:26 final size:26
Alignment explanation
Indices: 35667989--35668043 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
35667979 TTTGCCACAT
35667989 ATACTGTTACTGGCAGCTTCGCTACG
1 ATACTGTTACTGGCAGCTTCGCTACG
* * * *
35668015 ATACTTTTACTGGTAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTCGCTACG
35668041 ATA
1 ATA
35668044 TTGGTGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTCGCTACG
Found at i:35668179 original size:28 final size:28
Alignment explanation
Indices: 35668138--35668351 Score: 230
Period size: 28 Copynumber: 7.5 Consensus size: 28
35668128 GTTGCATTAT
* *
35668138 CACACTGTTACTGTATTAGGCTAAGGCC
1 CACACTATTACTGTATTGGGCTAAGGCC
*
35668166 CACACTATTTCTGTATTGGGCTAAGGCC
1 CACACTATTACTGTATTGGGCTAAGGCC
* *
35668194 CACACTCTTACTGTATTGGACTAAGGCC
1 CACACTATTACTGTATTGGGCTAAGGCC
* * *
35668222 CACACTTTTACTATATTGGGTTAAGGCC
1 CACACTATTACTGTATTGGGCTAAGGCC
* * *
35668250 CACACTATTACGGTATCGGGCTAAGGCT
1 CACACTATTACTGTATTGGGCTAAGGCC
* * *
35668278 CACATTGTTACTGTATCGGGCTAAGGCC
1 CACACTATTACTGTATTGGGCTAAGGCC
* *
35668306 CACACTGTACTGTTACTGCATAGGGCTAAGGCC
1 CACAC--TA---TTACTGTATTGGGCTAAGGCC
*
35668339 CAGACTATTACTG
1 CACACTATTACTG
35668352 CATGTTGTAG
Statistics
Matches: 156, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
28 130 0.83
30 1 0.01
31 2 0.01
33 23 0.15
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.29
Consensus pattern (28 bp):
CACACTATTACTGTATTGGGCTAAGGCC
Found at i:35670042 original size:21 final size:21
Alignment explanation
Indices: 35670000--35670039 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35669990 AAACTTGGAT
**
35670000 CAAAATTGACCATTTGATTTG
1 CAAAATTGAAAATTTGATTTG
35670021 CAAAATTGAAAATTT-ATTT
1 CAAAATTGAAAATTTGATTT
35670040 TGCCATTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (21 bp):
CAAAATTGAAAATTTGATTTG
Found at i:35678068 original size:25 final size:25
Alignment explanation
Indices: 35678007--35678068 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
35677997 ACGAGTTGTA
*
35678007 AACGGTAAGCTACTCTAAGCTGAAT
1 AACGGTAAGCTTCTCTAAGCTGAAT
* *
35678032 AACGGTAAGCTTCTCTTATCTGAAT
1 AACGGTAAGCTTCTCTAAGCTGAAT
*
35678057 AATGGTAAGCTT
1 AACGGTAAGCTT
35678069 GTACGGGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (25 bp):
AACGGTAAGCTTCTCTAAGCTGAAT
Found at i:35683651 original size:15 final size:14
Alignment explanation
Indices: 35683631--35683660 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35683621 TGAAAGAGGT
35683631 AAGAAGAAGGAAAAG
1 AAGAAG-AGGAAAAG
35683646 AAGAAGAGGAAAAG
1 AAGAAGAGGAAAAG
35683660 A
1 A
35683661 GAACGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAGAAGAGGAAAAG
Found at i:35684437 original size:19 final size:19
Alignment explanation
Indices: 35684404--35684453 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
35684394 AATTTTTGAC
* *
35684404 ATATGAATTATTATTTTATA
1 ATATTAATTAATA-TTTATA
35684424 AT-TTAATTAATATTTATA
1 ATATTAATTAATATTTATA
35684442 ATATTATATTAA
1 ATATTA-ATTAA
35684454 GGTCGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.31
19 11 0.42
20 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTAATTAATATTTATA
Found at i:35687385 original size:96 final size:96
Alignment explanation
Indices: 35687194--35687373 Score: 342
Period size: 96 Copynumber: 1.9 Consensus size: 96
35687184 AAAATTAAGG
*
35687194 GTTTTTAGAACACTTTTCCAAAAATTGATTAACAGTTAAGATGCCAAAGTCGAAAACATTATCGA
1 GTTTTTAGAACACTTTTCCAAAAATTGATTAACAGTTAAGATGCCAAAGTCAAAAACATTATCGA
35687259 GTACTAACCATAAGAAATCAAGCTCATCTAC
66 GTACTAACCATAAGAAATCAAGCTCATCTAC
35687290 GTTTTTAGAACACTTTTCCAAAAATTGATTAACAGTTAAGATGCCAAAGTCAAAAACATTATCGA
1 GTTTTTAGAACACTTTTCCAAAAATTGATTAACAGTTAAGATGCCAAAGTCAAAAACATTATCGA
*
35687355 GTACTAACCTTAAGAAATC
66 GTACTAACCATAAGAAATC
35687374 GAGTTCGTCT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 82 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (96 bp):
GTTTTTAGAACACTTTTCCAAAAATTGATTAACAGTTAAGATGCCAAAGTCAAAAACATTATCGA
GTACTAACCATAAGAAATCAAGCTCATCTAC
Found at i:35694336 original size:16 final size:16
Alignment explanation
Indices: 35694315--35694345 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35694305 AGTTTATGCT
35694315 AAGTAAATGCAATGGA
1 AAGTAAATGCAATGGA
*
35694331 AAGTAAATGGAATGG
1 AAGTAAATGCAATGG
35694346 TAAGAAAGTA
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:0.48, C:0.03, G:0.29, T:0.19
Consensus pattern (16 bp):
AAGTAAATGCAATGGA
Found at i:35694354 original size:20 final size:20
Alignment explanation
Indices: 35694329--35694366 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35694319 AAATGCAATG
35694329 GAAAGTAAATGGAATGGTAA
1 GAAAGTAAATGGAATGGTAA
*
35694349 GAAAGTAAATGGAGTGGT
1 GAAAGTAAATGGAATGGT
35694367 TCATAGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (20 bp):
GAAAGTAAATGGAATGGTAA
Found at i:35695680 original size:37 final size:36
Alignment explanation
Indices: 35695630--35695706 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 36
35695620 GATAGATACG
35695630 GGTTAGGGGTGTTACATTTAGTGGTATACGAGCTAC
1 GGTTAGGGGTGTTACATTTAGTGGTATACGAGCTAC
35695666 AGGTTAGGGGTGTTACATTTAGTGGTATACGAGCTAC
1 -GGTTAGGGGTGTTACATTTAGTGGTATACGAGCTAC
35695703 GGTT
1 GGTT
35695707 TAGTCAGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 4 0.10
37 36 0.90
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.34
Consensus pattern (36 bp):
GGTTAGGGGTGTTACATTTAGTGGTATACGAGCTAC
Found at i:35698406 original size:21 final size:22
Alignment explanation
Indices: 35698365--35698406 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
35698355 TTTAAAGATT
*
35698365 TTAATTTTATATATTTTATAAG
1 TTAATTTTATATATTTAATAAG
35698387 TTAA-TTTAT-TATTATAATAA
1 TTAATTTTATATATT-TAATAA
35698407 AGAAAAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAATTTTATATATTTAATAAG
Found at i:35701519 original size:55 final size:55
Alignment explanation
Indices: 35701427--35701555 Score: 188
Period size: 55 Copynumber: 2.3 Consensus size: 55
35701417 TAACGAAAGA
35701427 AAGTCAATGAGTTACACGGGCTAGTCACACGAGCGTGTGGTTGGCCGTGTGACCC
1 AAGTCAATGAGTTACACGGGCTAGTCACACGAGCGTGTGGTTGGCCGTGTGACCC
* * * * *
35701482 AAGTCAGTGAGTTACACGGGCTAGTTATACG-GACGTGTGGTTGGCTGTGTGGCCC
1 AAGTCAATGAGTTACACGGGCTAGTCACACGAG-CGTGTGGTTGGCCGTGTGACCC
*
35701537 AAGTTAATGAGTTACACGG
1 AAGTCAATGAGTTACACGG
35701556 CGTCGACCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 1 0.02
55 65 0.98
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (55 bp):
AAGTCAATGAGTTACACGGGCTAGTCACACGAGCGTGTGGTTGGCCGTGTGACCC
Found at i:35702409 original size:33 final size:33
Alignment explanation
Indices: 35702371--35702437 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
35702361 GGCATGAAAA
35702371 GGAAATGAATGGTAATTGTTTAAAAGAAACTAT
1 GGAAATGAATGGTAATTGTTTAAAAGAAACTAT
35702404 GGAAATGAATGGTAATTGTTTAAAAGAAACTAT
1 GGAAATGAATGGTAATTGTTTAAAAGAAACTAT
35702437 G
1 G
35702438 TCATGTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (33 bp):
GGAAATGAATGGTAATTGTTTAAAAGAAACTAT
Found at i:35704718 original size:28 final size:30
Alignment explanation
Indices: 35704647--35704735 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
35704637 TAGCGGTATA
*
35704647 GTGTGGGCCTTAGCCCATTACAGTAACAGT
1 GTGTGGGCCTTAGCCCAATACAGTAACAGT
35704677 GTGTGGGCCTTAGCCCAATACAGTAACA-T
1 GTGTGGGCCTTAGCCCAATACAGTAACAGT
*
35704706 -TGTGGGCCTTAGCCCAATATAGTAATCAGT
1 GTGTGGGCCTTAGCCCAATACAGTAA-CAGT
35704736 ACAATGTAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 24 0.44
29 3 0.05
30 28 0.51
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (30 bp):
GTGTGGGCCTTAGCCCAATACAGTAACAGT
Found at i:35704902 original size:26 final size:27
Alignment explanation
Indices: 35704846--35704917 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
35704836 AATATCGCAG
* * *
35704846 CAAAGCTGCCAGTAACA-AAGACGCAG
1 CAAAGCTGCCAGTAACAGTAGACACAA
35704872 CAAAGCTGCCAGTAACAGTA-ACACAA
1 CAAAGCTGCCAGTAACAGTAGACACAA
* *
35704898 TAAAGCTTCCAGTAACAGTA
1 CAAAGCTGCCAGTAACAGTA
35704918 TATGTGGCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 39 0.98
27 1 0.03
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14
Consensus pattern (27 bp):
CAAAGCTGCCAGTAACAGTAGACACAA
Found at i:35705126 original size:27 final size:26
Alignment explanation
Indices: 35705094--35705366 Score: 273
Period size: 27 Copynumber: 10.2 Consensus size: 26
35705084 TATAATAGTA
35705094 ATTTTACCCTATTAGGGTATTTCGGTC
1 ATTTTACCC-ATTAGGGTATTTCGGTC
*
35705121 ATTTTACCC-TTCAGGAGTATTTCGATC
1 ATTTTACCCATT-AGG-GTATTTCGGTC
*
35705148 ATTTTACCCTTTGAGGGTATTTCGGTC
1 ATTTTACCCATT-AGGGTATTTCGGTC
*
35705175 ATTTTACCCATTGAGGGTAATTCGGTC
1 ATTTTACCCATT-AGGGTATTTCGGTC
* *
35705202 ATTTTACCCATTGACGGTA-TTCGGTT
1 ATTTTACCCATT-AGGGTATTTCGGTC
*
35705228 ATTTTACCCTTTGAGGGTATTTCGGTC
1 ATTTTACCCATT-AGGGTATTTCGGTC
* *
35705255 AGTTTACCC-TTCAAGGGTATTTCGATC
1 ATTTTACCCATT--AGGGTATTTCGGTC
* * *
35705282 ATTTTACCCATCGAGGGTATTTCGATT
1 ATTTTACCCAT-TAGGGTATTTCGGTC
* * *
35705309 AGTTTATCCATCGAGGGTATTTCGGTC
1 ATTTTACCCAT-TAGGGTATTTCGGTC
* *
35705336 ATTTTAGCCATCGAGGGTATTTCGGTC
1 ATTTTACCCAT-TAGGGTATTTCGGTC
35705363 ATTT
1 ATTT
35705367 GCCCACGAAT
Statistics
Matches: 217, Mismatches: 22, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
25 2 0.01
26 28 0.13
27 181 0.83
28 6 0.03
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (26 bp):
ATTTTACCCATTAGGGTATTTCGGTC
Found at i:35705334 original size:134 final size:135
Alignment explanation
Indices: 35705094--35705366 Score: 390
Period size: 134 Copynumber: 2.0 Consensus size: 135
35705084 TATAATAGTA
* *
35705094 ATTTTACCCTATTAGGGTATTTCGGTCATTTTACCCTTCAGGAGTATTTCGATCATTTTACCCTT
1 ATTTTACCCTATTAGGGTATTTCGGTCAGTTTACCCTTCAGGAGTATTTCGATCATTTTACCCAT
* * * * *
35705159 TGAGGGTATTTCGGTCATTTTACCCATTGAGGGTAATTCGGTCATTTTACCCATTGACGGTA-TT
66 CGAGGGTATTTCGATCAGTTTACCCATCGAGGGTAATTCGGTCATTTTACCCATCGACGGTATTT
*
35705223 CGGTT
131 CGGTC
35705228 ATTTTACCCT-TTGAGGGTATTTCGGTCAGTTTACCCTTCAAGG-GTATTTCGATCATTTTACCC
1 ATTTTACCCTATT-AGGGTATTTCGGTCAGTTTACCCTTC-AGGAGTATTTCGATCATTTTACCC
* * * * *
35705291 ATCGAGGGTATTTCGATTAGTTTATCCATCGAGGGTATTTCGGTCATTTTAGCCATCGAGGGTAT
64 ATCGAGGGTATTTCGATCAGTTTACCCATCGAGGGTAATTCGGTCATTTTACCCATCGACGGTAT
35705356 TTCGGTC
129 TTCGGTC
35705363 ATTT
1 ATTT
35705367 GCCCACGAAT
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
133 2 0.02
134 108 0.88
135 13 0.11
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (135 bp):
ATTTTACCCTATTAGGGTATTTCGGTCAGTTTACCCTTCAGGAGTATTTCGATCATTTTACCCAT
CGAGGGTATTTCGATCAGTTTACCCATCGAGGGTAATTCGGTCATTTTACCCATCGACGGTATTT
CGGTC
Found at i:35711897 original size:28 final size:28
Alignment explanation
Indices: 35711826--35711910 Score: 134
Period size: 28 Copynumber: 3.0 Consensus size: 28
35711816 GTAGCAGTAT
*
35711826 AGTGTGGGCCTTAGCCCATTACAGTAAC
1 AGTGTGGGCCTTAGCCCAATACAGTAAC
*
35711854 AGTGTGTAGGCCTTAGCCCAATATAGTAAC
1 AGTGTG--GGCCTTAGCCCAATACAGTAAC
35711884 AGTGTGGGCCTTAGCCCAATACAGTAA
1 AGTGTGGGCCTTAGCCCAATACAGTAA
35711911 TTGGTACAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
28 26 0.50
30 26 0.50
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAGTAAC
Found at i:35712116 original size:27 final size:27
Alignment explanation
Indices: 35712050--35712126 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 27
35712040 ATAATGATGA
*
35712050 AGCAAAGCTACCAATAACAGTA-ACGT
1 AGCAAAGCTACCAGTAACAGTATACGT
* * *
35712076 AGTAAAGCTGCCAGTAACAGTATATGT
1 AGCAAAGCTACCAGTAACAGTATACGT
* *
35712103 GGCAAAGCCACCAGT-ACAGTATAC
1 AGCAAAGCTACCAGTAACAGTATAC
35712127 TTCCCCTATC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 27 0.66
27 14 0.34
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.18
Consensus pattern (27 bp):
AGCAAAGCTACCAGTAACAGTATACGT
Found at i:35712321 original size:27 final size:27
Alignment explanation
Indices: 35712270--35712413 Score: 159
Period size: 27 Copynumber: 5.3 Consensus size: 27
35712260 AGGAGTATAA
*
35712270 CAGTCATTTTACCCTAT-GGGGGTATTT
1 CAGTCATTTTACCCT-TCGAGGGTATTT
35712297 CAGTCATTTTACCCTTC-AGGAGTATTT
1 CAGTCATTTTACCCTTCGAGG-GTATTT
* *
35712324 C-GATCATTTTACCCATCGAGGGTAGTT
1 CAG-TCATTTTACCCTTCGAGGGTATTT
* *
35712351 CAGTCATTTTACCCATCGAGGGTAGTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
* *
35712378 CAATCATTTTACCTTTCGAGGGTATTT
1 CAGTCATTTTACCCTTCGAGGGTATTT
**
35712405 TGGTCATTT
1 CAGTCATTT
35712414 CCCCACGAAT
Statistics
Matches: 102, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.04
27 94 0.92
28 4 0.04
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (27 bp):
CAGTCATTTTACCCTTCGAGGGTATTT
Found at i:35722977 original size:52 final size:51
Alignment explanation
Indices: 35722846--35722977 Score: 169
Period size: 50 Copynumber: 2.6 Consensus size: 51
35722836 ATGTGTTTTG
** *
35722846 CATTAAAGAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCAT
* * * *
35722897 -AATAAATTATGGCATGCTTTATA-TAACTCTCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTA-AGTAACTCTCATGTTAGTT-AAGTTTGCAT
35722948 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTAAGTAACTC
35722978 ATTTGTTTAT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
50 32 0.48
51 11 0.17
52 23 0.35
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAGTTAAGTTTGCAT
Found at i:35722979 original size:50 final size:50
Alignment explanation
Indices: 35722846--35723017 Score: 149
Period size: 50 Copynumber: 3.4 Consensus size: 50
35722836 ATGTGTTTTG
** *
35722846 CATTAAAGAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTAAGTAAC-CTCATGTTAGTTAAGTTTGCAT
* * * *
35722897 -AATAAATTATGGCATGCTTTATA-TAACTCTCATGTTAGTTAAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTA-AGTAAC-CTCATGTTAGTT-AAGTTTGCAT
* *
35722948 CATTAAATTAAGTCATGCATTAAGTAA-CTCATTTGTTTATTTAA-TTTACAT
1 CATTAAATTAAGTCATGCATTAAGTAACCTCA--TG-TTAGTTAAGTTTGCAT
*
35722999 C-TT-AATTAAGTCTTGCATT
1 CATTAAATTAAGTCATGCATT
35723018 TAAGCATATT
Statistics
Matches: 100, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
49 15 0.15
50 38 0.38
51 18 0.18
52 24 0.24
53 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (50 bp):
CATTAAATTAAGTCATGCATTAAGTAACCTCATGTTAGTTAAGTTTGCAT
Found at i:35736077 original size:23 final size:23
Alignment explanation
Indices: 35736049--35736094 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35736039 TCTTTGTAAT
* * *
35736049 TTTAGATTTTAGTTTTCCTTTCA
1 TTTAGACTTTAGGTTTACTTTCA
35736072 TTTAGACTTTAGGTTTACTTTCA
1 TTTAGACTTTAGGTTTACTTTCA
35736095 GTTCAATTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.57
Consensus pattern (23 bp):
TTTAGACTTTAGGTTTACTTTCA
Found at i:35741437 original size:28 final size:28
Alignment explanation
Indices: 35741397--35741458 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
35741387 TCTATCAAAA
*
35741397 CTTGGATGAGTCCTTCAATTTTCATTAT
1 CTTGGATGAGTCCTTCAATTGTCATTAT
35741425 CTTGGATGAGTCCTTCAATTGTCATTAT
1 CTTGGATGAGTCCTTCAATTGTCATTAT
35741453 CTTGGA
1 CTTGGA
35741459 AAAGGGAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (28 bp):
CTTGGATGAGTCCTTCAATTGTCATTAT
Done.