Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 41 of 56
Found at i:9574111 original size:17 final size:17
Alignment explanation
Indices: 9574089--9574124 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
9574079 AACTGATCAC
9574089 ATATAGTATATAGTAGT
1 ATATAGTATATAGTAGT
9574106 ATATAGTAGTATA-TAGT
1 ATATAGTA-TATAGTAGT
9574123 AT
1 AT
9574125 TGATTGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (17 bp):
ATATAGTATATAGTAGT
Found at i:9575374 original size:140 final size:140
Alignment explanation
Indices: 9575207--9575469 Score: 340
Period size: 140 Copynumber: 1.9 Consensus size: 140
9575197 CTAATTTATA
* * * *
9575207 TATATAAATAAGATATTTATTTATTTAAAAATATCAAAAAATGG-CTTCTAGGTGCTTTAAGACA
1 TATATAAATAAGATATTTATTAATTTAAAAATATCAAAAAATGGACATCCAAGTGCTTTAAGA-A
* * *
9575271 -GCTCTTTTCTTAATATT-AAAAATAAATAAATATTAATAAA-ATATTTATCTAAAA-TAATTAA
65 TGCCCTTTT-ATAATATTGAAAAATAAATAAATATT--TAAATATAATTAT-TAAAAGTAATTAA
9575332 AATATATATATAATT
126 AATATATATATAATT
* *
9575347 TATA-AAAGTAAGATATTTATTAATTTAAAAATATCAGAAAATGGACATCCAATTGCTTTAAGAA
1 TATATAAA-TAAGATATTTATTAATTTAAAAATATCAAAAAATGGACATCCAAGTGCTTTAAGAA
*
9575411 TGCCCTTTTATAATATTGAAAAATAAATATATATTTAAATATAATTATTAAAAGTAATT
65 TGCCCTTTTATAATATTGAAAAATAAATAAATATTTAAATATAATTATTAAAAGTAATT
9575470 TATAAAATTA
Statistics
Matches: 107, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
139 12 0.11
140 58 0.54
141 37 0.35
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (140 bp):
TATATAAATAAGATATTTATTAATTTAAAAATATCAAAAAATGGACATCCAAGTGCTTTAAGAAT
GCCCTTTTATAATATTGAAAAATAAATAAATATTTAAATATAATTATTAAAAGTAATTAAAATAT
ATATATAATT
Found at i:9575518 original size:4 final size:4
Alignment explanation
Indices: 9575499--9575533 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
9575489 ATAGGATTTA
9575499 AAAT AAAAT AAAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT A
9575534 TTATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 21 0.70
5 9 0.30
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:9576570 original size:3 final size:3
Alignment explanation
Indices: 9576562--9576695 Score: 195
Period size: 3 Copynumber: 45.7 Consensus size: 3
9576552 ATGTAATGTA
9576562 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
9576610 AAT AAT AAT AAT AAT AAT -AT AAT TAT AA- AAT AAT AAT AGT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
9576656 AAT AAAT AA- AAT AAT AAT AAC AAT AAT AAT -AT AAT AAT AA
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9576696 AAACAAATGG
Statistics
Matches: 118, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
2 8 0.07
3 107 0.91
4 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9576957 original size:17 final size:17
Alignment explanation
Indices: 9576935--9576994 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
9576925 GTTGAACAAA
9576935 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
** *
9576952 TTCTTCTTTTTCA-GATGAG
1 TTCTTCTCATT-ATGA--AC
9576971 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
9576988 TCCTTCT
1 TTCTTCT
9576995 GAAAATGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
17 18 0.56
18 2 0.06
19 12 0.38
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:9577191 original size:121 final size:121
Alignment explanation
Indices: 9577056--9577478 Score: 530
Period size: 121 Copynumber: 3.6 Consensus size: 121
9577046 GAATTAAGGC
* *
9577056 AAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGAGGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
9577121 GAATACTTCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCA
66 GAATACTTCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCA
*
9577177 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCATATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
9577242 GAACACTTCTGGAAATGTTAATGTTGATTTATCTCTTTCTGTGATAGAGTCATGCA
66 GAATACTTCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCA
*
9577298 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *** * *
9577362 TGAACTTCCTCTGGAAA-----A-GTTGATCCA--T-C--GAATGAT-GAATTCAAGCAA
65 TGAA-TACTTCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAG-AGTCATGC-A
* *
9577410 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
9577475 TGAA
65 TGAA
9577479 CTCTTCTTCC
Statistics
Matches: 273, Mismatches: 24, Indels: 18
0.87 0.08 0.06
Matches are distributed among these distances:
110 1 0.00
111 10 0.04
112 39 0.14
113 27 0.10
114 1 0.00
116 7 0.03
117 1 0.00
121 175 0.64
122 12 0.04
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (121 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAATACTTCTGGAAATGTTGATGATGATCTATCTCCTTCTGTGATAGAGTCATGCA
Found at i:9577226 original size:23 final size:22
Alignment explanation
Indices: 9577192--9577236 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9577182 TGAACAAGTT
9577192 CTTCTCATTATGAACTTCTTCTC
1 CTTCTCATTATG-ACTTCTTCTC
*
9577215 CTTCTTCA-TATGAGTTCTTCTC
1 CTTC-TCATTATGACTTCTTCTC
9577237 ATTATGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 8 0.40
24 3 0.15
ACGTcount: A:0.16, C:0.29, G:0.07, T:0.49
Consensus pattern (22 bp):
CTTCTCATTATGACTTCTTCTC
Found at i:9577437 original size:73 final size:73
Alignment explanation
Indices: 9577350--9577593 Score: 211
Period size: 73 Copynumber: 3.3 Consensus size: 73
9577340 TTCAGATAAG
9577350 TTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGT
1 TTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGT
9577415 TGAACAAA
66 TGAACAAA
***** * * * ** * * ** **
9577423 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTC-TTCTT
1 TTCTTCTCATTATGAACTTC--C-TC-TGGAAAAGTTGA-TCCATCGAATGATGAATTCAAGCAA
**** * * *
9577487 CCTCTTCAGATAAG
61 AAGGTTGA-ACAAA
*
9577501 TTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGT
1 TTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGT
9577566 TGAACAAA
66 TGAACAAA
9577574 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
9577594 TTCTTTCTTC
Statistics
Matches: 117, Mismatches: 47, Indels: 14
0.66 0.26 0.08
Matches are distributed among these distances:
73 55 0.47
74 10 0.09
75 3 0.03
76 3 0.03
77 10 0.09
78 36 0.31
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (73 bp):
TTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGT
TGAACAAA
Found at i:9577503 original size:38 final size:39
Alignment explanation
Indices: 9577423--9577518 Score: 158
Period size: 38 Copynumber: 2.5 Consensus size: 39
9577413 GTTGAACAAA
* *
9577423 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAG
1 TTCTTCTCATTATGAAC-TCTTCTTCTCTCTTCAGATAAG
9577463 TTCTTCTCATTATGAACTCTTCTTC-CTCTTCAGATAAG
1 TTCTTCTCATTATGAACTCTTCTTCTCTCTTCAGATAAG
9577501 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
9577519 TCCTCTGGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
38 29 0.54
39 8 0.15
40 17 0.31
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (39 bp):
TTCTTCTCATTATGAACTCTTCTTCTCTCTTCAGATAAG
Found at i:9577605 original size:151 final size:151
Alignment explanation
Indices: 9577309--9577635 Score: 611
Period size: 151 Copynumber: 2.2 Consensus size: 151
9577299 AGGTTGAACA
9577309 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCT
1 AGTTCTTCTCATTATGAAC-TCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCT
9577374 GGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
65 GGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAA
9577439 CTTCTTCTTCTTTCTTCAGATG
130 CTTCTTCTTCTTTCTTCAGATG
9577461 AGTTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCTG
1 AGTTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCTG
*
9577526 GAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
9577591 TTCTTCTT-TCTTCTTCAGATG
131 TTCTTCTTCT-TTCTTCAGATG
*
9577612 AATTCTTCTCATTATGAACTCTTC
1 AGTTCTTCTCATTATGAACTCTTC
9577636 CGGAAATGTT
Statistics
Matches: 172, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
150 1 0.01
151 152 0.88
152 19 0.11
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (151 bp):
AGTTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCTG
GAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCTTTCTTCAGATG
Found at i:9577618 original size:113 final size:110
Alignment explanation
Indices: 9577463--9577666 Score: 302
Period size: 112 Copynumber: 1.8 Consensus size: 110
9577453 TTCAGATGAG
*
9577463 TTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTCCTCTGGA
1 TTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-TCCTCCGGA
*
9577528 AAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAACAAA
65 AAAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAA
* *
9577574 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAA-TTCTTCTCATTATGAACTCTTCCG
1 TTCTTCTCATTATGAAC-TCTTC-TTCCTCTTCAGAT-AAGTTCTTCTCATTATGAACTCCTCCG
* * *
9577638 GAAATGTTGATCCATTGAATGATGGATTC
63 GAAAAGTTGATCCATCGAATGATGAATTC
9577667 GAATCTTTGC
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
111 17 0.20
112 35 0.42
113 29 0.35
114 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (110 bp):
TTCTTCTCATTATGAACTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTCCTCCGGAA
AAGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:9578231 original size:20 final size:20
Alignment explanation
Indices: 9578206--9578251 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
9578196 ATCGCAACAT
9578206 TGGTTCAGCACCATAATTAC
1 TGGTTCAGCACCATAATTAC
* *
9578226 TGGTTCAGTACCATAATTAT
1 TGGTTCAGCACCATAATTAC
9578246 TGGTTC
1 TGGTTC
9578252 GTAAAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (20 bp):
TGGTTCAGCACCATAATTAC
Found at i:9578534 original size:18 final size:18
Alignment explanation
Indices: 9578511--9578547 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
9578501 TGTGAAAGTT
*
9578511 ATAAATTGAATTTCAAAA
1 ATAAATTGAACTTCAAAA
9578529 ATAAATTGAACTTCAAAA
1 ATAAATTGAACTTCAAAA
9578547 A
1 A
9578548 GATAAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAAATTGAACTTCAAAA
Found at i:9585639 original size:15 final size:15
Alignment explanation
Indices: 9585619--9585650 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
9585609 AAAATAATGC
9585619 AATGAATGTATGCAA
1 AATGAATGTATGCAA
9585634 AATGAATGTATGCAA
1 AATGAATGTATGCAA
9585649 AA
1 AA
9585651 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:9589490 original size:2 final size:2
Alignment explanation
Indices: 9589483--9589518 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9589473 TTTACTAATT
9589483 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9589519 AGATATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9589670 original size:141 final size:143
Alignment explanation
Indices: 9589492--9589748 Score: 362
Period size: 141 Copynumber: 1.8 Consensus size: 143
9589482 TTATATATAT
* ***
9589492 ATATATATATATATATATATATATATAAGATATTTATTTATTTAAAAATATCAG-AAA-AGGGTT
1 ATATATATATATATATATATATAAATAAGATATTTATTTATTTAAAAATATCAGAAAATAGACAT
*
9589555 TCTAGGTGCTTTAAGACAACTCTTTTCTTAATATT-AAAAATAAATAAATATTAATAAAACACTT
66 TC-AGGTGCTTTAAGAC-ACTCATTTCTTAATATTGAAAAATAAATAAATATTAATAAAACACTT
9589619 ATCTAAAATAATTAA
129 ATCTAAAATAATTAA
*
9589634 ATATATATATATA-ATTTATA-AAAGTAAGATATTTATTTATTTAAAAATATCAGAAAATAGACA
1 ATATATATATATATATATATATAAA-TAAGATATTTATTTATTTAAAAATATCAGAAAATAGACA
* ** *
9589697 TTCAGTTGCTTTAAGACTGTCATTTCTTAATATTGAAAAATAAATATATATT
65 TTCAGGTGCTTTAAGACACTCATTTCTTAATATTGAAAAATAAATAAATATT
9589749 TAAATATAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
140 2 0.02
141 49 0.49
142 45 0.45
143 5 0.05
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (143 bp):
ATATATATATATATATATATATAAATAAGATATTTATTTATTTAAAAATATCAGAAAATAGACAT
TCAGGTGCTTTAAGACACTCATTTCTTAATATTGAAAAATAAATAAATATTAATAAAACACTTAT
CTAAAATAATTAA
Found at i:9589794 original size:14 final size:15
Alignment explanation
Indices: 9589775--9589803 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9589765 TCTTAAAAGT
9589775 AATTTATAAA-ATTA
1 AATTTATAAATATTA
9589789 AATTTATAAATATTA
1 AATTTATAAATATTA
9589804 TTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTATAAATATTA
Found at i:9591230 original size:3 final size:3
Alignment explanation
Indices: 9591222--9591304 Score: 93
Period size: 3 Copynumber: 28.7 Consensus size: 3
9591212 ATGTAATGTA
* *
9591222 AAT AAT AAT AAT AAT ATT AAT AAT AAT -AT AA- AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
9591268 AAAT AA- AAT AAC AAT AAC AAT AAT AAT -AT AAT AAT AA
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9591305 AAACAAATGG
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 8 0.12
3 56 0.84
4 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9592717 original size:2 final size:2
Alignment explanation
Indices: 9592712--9592765 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
9592702 AAATTAAAAT
9592712 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9592754 TA TA TA TA TA TA
1 TA TA TA TA TA TA
9592766 AGAAAACACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9593717 original size:73 final size:73
Alignment explanation
Indices: 9593598--9593757 Score: 302
Period size: 73 Copynumber: 2.2 Consensus size: 73
9593588 CAAAACAAGC
*
9593598 AGTGAGGCGTAATCTAAAATAGCTGCTAGTATATGCCTTTATTTATTTGTATAGCAGATTAATGT
1 AGTGAGGCGTAATCTAAAATAGCTGCTAGTATAAGCCTTTATTTATTTGTATAGCAGATTAATGT
9593663 AACTTCGG
66 AACTTCGG
9593671 AGTGAGGCGTAATCTAAAATAGCTGCTAGTATAAGCCTTTATTTATTTGTATAGCAGATTAATGT
1 AGTGAGGCGTAATCTAAAATAGCTGCTAGTATAAGCCTTTATTTATTTGTATAGCAGATTAATGT
9593736 AACTTCGG
66 AACTTCGG
*
9593744 AGTGAGGCGCAATC
1 AGTGAGGCGTAATC
9593758 ATAGTTAAAA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 85 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (73 bp):
AGTGAGGCGTAATCTAAAATAGCTGCTAGTATAAGCCTTTATTTATTTGTATAGCAGATTAATGT
AACTTCGG
Found at i:9599022 original size:21 final size:21
Alignment explanation
Indices: 9598998--9599037 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9598988 GAATGTCTCA
*
9598998 AAGGACCACCTAGATGTCCTG
1 AAGGACCACATAGATGTCCTG
*
9599019 AAGGACCACATATATGTCC
1 AAGGACCACATAGATGTCC
9599038 CGAAATGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
AAGGACCACATAGATGTCCTG
Found at i:9601790 original size:18 final size:17
Alignment explanation
Indices: 9601764--9601797 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9601754 TAAAAATATG
*
9601764 TATTTAATATATATAATA
1 TATTAAATATAT-TAATA
9601782 TATTAAATATATTAAT
1 TATTAAATATATTAAT
9601798 TTTTGTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTAAATATATTAATA
Found at i:9603291 original size:23 final size:23
Alignment explanation
Indices: 9603265--9603308 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9603255 TTTATCATTT
*
9603265 ATTTTAAATAATTTATCATTAAA
1 ATTTTAAATAATTTATAATTAAA
* *
9603288 ATTTTAATTATTTTATAATTA
1 ATTTTAAATAATTTATAATTA
9603309 TACGTTGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTAAATAATTTATAATTAAA
Found at i:9607938 original size:30 final size:30
Alignment explanation
Indices: 9607895--9607954 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
9607885 TGAGATGAAC
* * *
9607895 TTAAATTTTTAAAATTTTAAGGGGACAAAT
1 TTAAACTTATAAAATTTTAAGAGGACAAAT
*
9607925 TTAAACTTATAAAATTTTAAGAGGAGAAAT
1 TTAAACTTATAAAATTTTAAGAGGACAAAT
9607955 CAGGTTTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (30 bp):
TTAAACTTATAAAATTTTAAGAGGACAAAT
Found at i:9610922 original size:84 final size:84
Alignment explanation
Indices: 9610788--9610975 Score: 268
Period size: 84 Copynumber: 2.2 Consensus size: 84
9610778 CTGAATGAAA
* * *
9610788 TCGAACTCGTCAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCG-AAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
9610853 TGCCTCGGAGCTGAGAGTAG
65 TGCCTCGGAGCTGAGAGTAG
* * * *
9610873 TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
9610938 GCCTTGGAGTTGAGCGTAG
66 GCCTCGGAGCTGAGAGTAG
*
9610957 TCGAACTCAAAGGTCTTTG
1 TCGAACTCGAAGGTCTTTG
9610976 TGTTTCAAGA
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 83 0.90
85 9 0.10
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTGGTTAGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
GCCTCGGAGCTGAGAGTAG
Found at i:9611045 original size:33 final size:33
Alignment explanation
Indices: 9610963--9611090 Score: 188
Period size: 33 Copynumber: 3.9 Consensus size: 33
9610953 GTAGTCGAAC
*
9610963 TCAAAGG-TCTTTGTGTTTCAAGAGAAAC-ATTT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGA-TT
*
9610995 TCAAAGGTTTTTTTGTGTTTCAAGAGGAACGATT
1 TCAAAGG-TTTTTTGTGTTTCAAGAGAAACGATT
9611029 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
* *
9611062 TCAAAGATTTTTTGTGTTTAAAGAGAAAC
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAAC
9611091 TGTCTCCATG
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
32 7 0.08
33 52 0.59
34 28 0.32
35 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (33 bp):
TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
Found at i:9611073 original size:67 final size:65
Alignment explanation
Indices: 9610963--9611086 Score: 187
Period size: 67 Copynumber: 1.9 Consensus size: 65
9610953 GTAGTCGAAC
* *
9610963 TCAAAGGTCTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTGTGTTTCAAGAGGAACGAT
1 TCAAAGGTCTTTGTGTTTCAAGAGAAACATTTTCAAA-GATTTTTTGTGTTTAAAGAGGAACGAT
9611028 T
65 T
*
9611029 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGA-TTTCAAAGATTTTTTGTGTTTAAAGAG
1 TCAAAGG-TCTTTGTGTTTCAAGAGAAAC-ATTTTCAAAGATTTTTTGTGTTTAAAGAG
9611087 AAACTGTCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
66 25 0.47
67 27 0.51
68 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (65 bp):
TCAAAGGTCTTTGTGTTTCAAGAGAAACATTTTCAAAGATTTTTTGTGTTTAAAGAGGAACGATT
Found at i:9611189 original size:36 final size:36
Alignment explanation
Indices: 9611139--9611245 Score: 178
Period size: 36 Copynumber: 3.0 Consensus size: 36
9611129 TATTGGTTGG
* *
9611139 TGTTTCAAGGGAAACTGTCTCGAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
9611175 TGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
9611211 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
9611246 CTTTAGTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:9611928 original size:106 final size:106
Alignment explanation
Indices: 9611626--9613140 Score: 2496
Period size: 106 Copynumber: 14.3 Consensus size: 106
9611616 TGTACGATTC
* * * * * *
9611626 CCTTCGTTGTGGAGTTGAAATTGGTTCTGGAACTG-GAAAATTGTTTGTTGACAACCAGCCGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAATTGTTTATTGACAACCAGCGGTCC
* *
9611690 CTTCGTTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
65 CTTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
9611733 CATTCGCTGTGAAGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCC
9611798 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
9611840 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* *
9611905 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATGT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
9611946 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTG-GAAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAATTGTTTATTGACAACCAGCGGTCC
9612010 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
9612052 CCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCC
9612117 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * * *
9612159 CCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGATAAACAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
*
9612224 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
9612265 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
9612330 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
9612371 CCTTCGCTGTGAAGTTGAAATTGGCTCTTAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
9612436 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
9612477 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* *
9612542 TTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * *
9612583 CCTTCGCTGTGAAGTTGAAATTGACTCTCAAATTCAGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
9612648 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
9612689 CCTTCGTTGTGAAGTTGAAATTGGATCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCC
9612754 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
9612796 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
*
9612861 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
9612902 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
* *
9612967 TTTGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
9613008 CCTTCGTTGTG-AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
*
9613072 TTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
9613113 CCTTCGTTGTGAAGTTGAAATTGGCTCT
1 CCTTCGTTGTGAAGTTGAAATTGGCTCT
9613141 CGAGCAAATT
Statistics
Matches: 1315, Mismatches: 86, Indels: 15
0.93 0.06 0.01
Matches are distributed among these distances:
105 100 0.08
106 889 0.68
107 288 0.22
108 37 0.03
109 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:9612220 original size:319 final size:319
Alignment explanation
Indices: 9611626--9613140 Score: 2705
Period size: 319 Copynumber: 4.8 Consensus size: 319
9611616 TGTACGATTC
* * ** * * * *
9611626 CCTTCGTTGTGGAGTTGAAATTGGTTCTGGAACTGGAAAATTGTTTGTTGACAACCAGCCGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCC
* * * *
9611691 TTCGTTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTG
66 TTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
9611756 GCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
130 GCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
9611821 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
195 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
*
9611886 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATGT
260 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
9611946 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCC
9612011 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
9612076 CTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
131 CTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
9612141 TTGTCTGGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTG
196 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
* *
9612206 TTGATAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
261 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
*
9612265 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCC
*
9612330 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
* *
9612395 CTCTT-AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
131 CTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
9612459 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
196 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
*
9612524 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATAT
261 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
* *
9612583 CCTTCGCTGTGAAGTTGAAATTGACTCTCAAATT-CAGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGA-AAATTGTTTATTGACAACCAGCGGTCC
9612647 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
65 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTG
*
9612712 GATCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
130 GCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
9612777 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
195 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
9612842 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
260 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
*
9612902 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCC
* *
9612967 TTTGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTG-AGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
* * *
9613031 CTC-TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCG
131 CTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
9613095 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
196 TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
9613141 CGAGCAAATT
Statistics
Matches: 1149, Mismatches: 43, Indels: 9
0.96 0.04 0.01
Matches are distributed among these distances:
317 104 0.09
318 319 0.28
319 665 0.58
320 61 0.05
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (319 bp):
CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
CTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
TTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
Found at i:9612996 original size:637 final size:637
Alignment explanation
Indices: 9611626--9613140 Score: 2737
Period size: 637 Copynumber: 2.4 Consensus size: 637
9611616 TGTACGATTC
* * ** * * * * *
9611626 CCTTCGTTGTGGAGTTGAAATTGGTTCTGGAACTGGAAAATTGTTTGTTGACAACCAGCCGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
* * *
9611691 TTCGTTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTG
66 TTCG-TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
* *
9611756 GCTCTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
130 GCTCTT-AAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
9611821 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
194 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
* *
9611886 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATGTCCTTC
259 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATATCCTTC
* *
9611951 GCTGTGAAGTTGAAATTGACTCTGAAATTGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
324 GCTGTGAAGTTGAAATTGACTCTCAAATTAGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
*
9612016 CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTT
389 CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTT
9612081 GAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
454 GAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
9612146 TGGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGAT
519 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGAC
9612211 AAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
584 AAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
9612265 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
9612330 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
9612395 CTCTTAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
131 CTCTTAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
9612460 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGT
196 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGT
9612525 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATATCCTTCGC
261 TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATATCCTTCGC
9612590 TGTGAAGTTGAAATTGACTCTCAAATTCAG-AAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
326 TGTGAAGTTGAAATTGACTCTCAAATT-AGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTC
9612654 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTTG
390 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTTG
9612719 AAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
455 AAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
9612784 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
520 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACA
*
9612849 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
585 AACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
9612902 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
* * *
9612967 TTTGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTG-AGTTGAAATTGG
66 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
* *
9613031 CTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGT
131 CTCTTAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
9613096 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
196 TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
9613141 CGAGCAAATT
Statistics
Matches: 847, Mismatches: 28, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
636 120 0.14
637 603 0.71
638 64 0.08
639 60 0.07
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (637 bp):
CCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCC
TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
CTCTTAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGT
TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGT
TGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATATCCTTCGC
TGTGAAGTTGAAATTGACTCTCAAATTAGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCG
TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTTGA
AATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
ACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
Found at i:9618199 original size:2 final size:2
Alignment explanation
Indices: 9618184--9618236 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
9618174 AATTAATTAT
9618184 TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9618224 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
9618237 TTTAAACCCG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9619412 original size:21 final size:21
Alignment explanation
Indices: 9619387--9619459 Score: 128
Period size: 21 Copynumber: 3.5 Consensus size: 21
9619377 AACTCAAAAG
*
9619387 AATGTTTGAAAAAGATTTGGA
1 AATGTATGAAAAAGATTTGGA
*
9619408 AATGTTTGAAAAAGATTTGGA
1 AATGTATGAAAAAGATTTGGA
9619429 AATGTATGAAAAAGATTTGGA
1 AATGTATGAAAAAGATTTGGA
9619450 AATGTATGAA
1 AATGTATGAA
9619460 GTCATCATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (21 bp):
AATGTATGAAAAAGATTTGGA
Found at i:9620433 original size:20 final size:20
Alignment explanation
Indices: 9620384--9620439 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
9620374 TATCGGAAGG
* *
9620384 GGGTATCGGTACCATAGTAT
1 GGGTATCGATACCATAGTAA
*
9620404 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
9620426 GGGTATCGATACCA
1 GGGTATCGATACCA
9620440 GGCAACATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:9620478 original size:95 final size:94
Alignment explanation
Indices: 9620314--9620510 Score: 274
Period size: 95 Copynumber: 2.1 Consensus size: 94
9620304 TTGAATCAGA
* * *
9620314 ATCGATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTAATTTTGGTATTGATATCG
1 ATCGATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTAATTTTGGTATCGATACCA
* *
9620379 GAAGGGGGTATCGGTACCATA-GTATGGTAGT
66 GAAGGAGATATCGGTACCA-AGGTA--GTAGT
* *
9620410 ATCGATACCATGGTAA-GGGTATCGATACCAGGCAACATCGAA-CTTAATTTTGGTATCGATACC
1 ATCGATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATC-TAATTTTGGTATCGATACC
9620473 AGAAGGAGATATCGGTACCAAGGTAGTAGT
65 AGAAGGAGATATCGGTACCAAGGTAGTAGT
9620503 ATCGATAC
1 ATCGATAC
9620511 TATGTAGAGA
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
93 13 0.14
94 2 0.02
95 62 0.67
96 15 0.16
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (94 bp):
ATCGATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTAATTTTGGTATCGATACCA
GAAGGAGATATCGGTACCAAGGTAGTAGT
Found at i:9620955 original size:54 final size:54
Alignment explanation
Indices: 9620859--9620963 Score: 153
Period size: 54 Copynumber: 1.9 Consensus size: 54
9620849 TGTGCATATT
*
9620859 CACGGAATTCATCATGAGTTGATGAATCACCGTACATGCACT-ATGTGTGCAGCC
1 CACGAAATTCATCATGAGTTGATGAATCACCGTACATGCACTAAT-TGTGCAGCC
9620913 CACGAAATTCATCATGAGTTGATGAATTC-CCGTACA-GACACTAATTGTGCA
1 CACGAAATTCATCATGAGTTGATGAA-TCACCGTACATG-CACTAATTGTGCA
9620964 TTCTAATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
53 1 0.02
54 42 0.89
55 4 0.09
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (54 bp):
CACGAAATTCATCATGAGTTGATGAATCACCGTACATGCACTAATTGTGCAGCC
Found at i:9635662 original size:41 final size:43
Alignment explanation
Indices: 9635624--9635759 Score: 163
Period size: 44 Copynumber: 3.2 Consensus size: 43
9635614 CACCTCCTCC
*
9635624 TGTGATGAAATCAAG-CAAA-GGTGATGTAGTCCAACTCCTTA
1 TGTGATGAAATCAAGTGAAATGGTGATGTAGTCCAACTCCTTA
*
9635665 TGTGATTAAATCAAGTGAAATGGTGGTTATG-AGT-CAACTCCTTA
1 TGTGATGAAATCAAGTGAAATGGT-G--ATGTAGTCCAACTCCTTA
* *
9635709 TGTGATGAAATCAAGTGAAATGGTGATGCTAATCAAACTCCTTA
1 TGTGATGAAATCAAGTGAAATGGTGATG-TAGTCCAACTCCTTA
*
9635753 CGTGATG
1 TGTGATG
9635760 TATGAGCCAA
Statistics
Matches: 81, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
41 17 0.21
42 3 0.04
43 6 0.07
44 49 0.60
45 3 0.04
46 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (43 bp):
TGTGATGAAATCAAGTGAAATGGTGATGTAGTCCAACTCCTTA
Found at i:9640037 original size:110 final size:109
Alignment explanation
Indices: 9639829--9640040 Score: 277
Period size: 110 Copynumber: 1.9 Consensus size: 109
9639819 GTACACTATT
* * * * * *
9639829 AGTGCCTATACGAGAATTCATCAACCCTTGATGAATTTCGTGGGTTGTACACATAGTGCATGTAT
1 AGTGCCTATACGAGAATTCATCAACCCATGATGAATTCCGTGAGTTGCACACAAAGTGCATGTAC
*
9639894 GCTGATTTATCAACTCATAATGAATTCCGTGAATATGTACACAA
66 GCTGATTCATCAACTCATAATGAATTCCGTGAATATGTACACAA
* *
9639938 AGTGCCTATACGACG-ATTCATCAACTCATGATGAATTCCGTGAGTATGCATACAAAGTGCATGT
1 AGTGCCTATACGA-GAATTCATCAACCCATGATGAATTCCGTGAGT-TGCACACAAAGTGCATGT
*
9640002 ACG-TCGATTCATCAACTCATGAA-GAATTCTGTGAATATG
64 ACGCT-GATTCATCAACTCAT-AATGAATTCCGTGAATATG
9640041 CAGCCTATAA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
109 40 0.45
110 47 0.53
111 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (109 bp):
AGTGCCTATACGAGAATTCATCAACCCATGATGAATTCCGTGAGTTGCACACAAAGTGCATGTAC
GCTGATTCATCAACTCATAATGAATTCCGTGAATATGTACACAA
Found at i:9640041 original size:55 final size:54
Alignment explanation
Indices: 9639877--9640042 Score: 199
Period size: 55 Copynumber: 3.0 Consensus size: 54
9639867 CGTGGGTTGT
* * * *
9639877 ACACATAGTGCATGTATGCTGATTTATCAACTCAT-AATGAATTCCGTGAATATGT
1 ACACAAAGTGCATGTACGC-GATTCATCAACTCATGAA-GAATTCCGTGAATATGC
* * * *
9639932 ACACAAAGTGCCTATACGACGATTCATCAACTCATGATGAATTCCGTGAGTATGC
1 ACACAAAGTGCATGTACG-CGATTCATCAACTCATGAAGAATTCCGTGAATATGC
* *
9639987 ATACAAAGTGCATGTACGTCGATTCATCAACTCATGAAGAATTCTGTGAATATGC
1 ACACAAAGTGCATGTACG-CGATTCATCAACTCATGAAGAATTCCGTGAATATGC
9640042 A
1 A
9640043 GCCTATAATA
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
55 92 0.98
56 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (54 bp):
ACACAAAGTGCATGTACGCGATTCATCAACTCATGAAGAATTCCGTGAATATGC
Found at i:9640491 original size:20 final size:20
Alignment explanation
Indices: 9640466--9640522 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
9640456 GGATGTTGCC
*
9640466 TGGTATCGATACCCTTACCA
1 TGGTATCGATACCCCTACCA
*
9640486 TGGTATCGATACTACCCTACTA
1 TGGTATCGATAC--CCCTACCA
*
9640508 TGGTACCGATACCCC
1 TGGTATCGATACCCC
9640523 CACTGATATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.47
22 17 0.53
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.28
Consensus pattern (20 bp):
TGGTATCGATACCCCTACCA
Found at i:9640572 original size:94 final size:96
Alignment explanation
Indices: 9640408--9640594 Score: 272
Period size: 95 Copynumber: 2.0 Consensus size: 96
9640398 GATACTTCTA
** * * *
9640408 TACTATGGTACCGATACCCCCTTTGGGTATCGATACCAAAAATAGGTTGGATGTTGCCTGGTATC
1 TACTATGGTACCGATACCCCCACTGGATATCGATACCAAAAATAGATTCGATGTTGCCTGGTATC
9640473 GATACC-CTTACCATGGTATCGATACTACCC
66 GATACCTCTTACCATGGTATCGATACTACCC
* *
9640503 TACTATGGTACCGATACCCCCACT-GATATCGATACCAAAATTAGATTCGATGTT-TCTAGGTAT
1 TACTATGGTACCGATACCCCCACTGGATATCGATACCAAAAATAGATTCGATGTTGCCT-GGTAT
*
9640566 CGATACCTCTTATCATGGTATCGATACTA
65 CGATACCTCTTACCATGGTATCGATACTA
9640595 TCTCATAGGT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
93 2 0.02
94 38 0.46
95 42 0.51
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (96 bp):
TACTATGGTACCGATACCCCCACTGGATATCGATACCAAAAATAGATTCGATGTTGCCTGGTATC
GATACCTCTTACCATGGTATCGATACTACCC
Found at i:9640607 original size:20 final size:19
Alignment explanation
Indices: 9640559--9640611 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
9640549 TCGATGTTTC
* *
9640559 TAGGTATCGATACCTCTTA
1 TAGGTATCGATACATCTCA
9640578 TCATGGTATCGATACTATCTCA
1 T-A-GGTATCGATAC-ATCTCA
9640600 TAGGTATCGATA
1 TAGGTATCGATA
9640612 TTGATTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
21 12 0.41
22 5 0.17
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (19 bp):
TAGGTATCGATACATCTCA
Found at i:9643892 original size:23 final size:23
Alignment explanation
Indices: 9643866--9643916 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
9643856 TAGGATCGCA
9643866 TAGAAATGTCCCAAAGGACCACG
1 TAGAAATGTCCCAAAGGACCACG
* * * * *
9643889 TAGAATTTTCCCGAATGACCGCG
1 TAGAAATGTCCCAAAGGACCACG
9643912 TAGAA
1 TAGAA
9643917 CACTCGACTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (23 bp):
TAGAAATGTCCCAAAGGACCACG
Found at i:9656254 original size:20 final size:20
Alignment explanation
Indices: 9656229--9656274 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
9656219 CAATCAAACC
*
9656229 ATTTTTTCTTTATTTTTTCG
1 ATTTTTTATTTATTTTTTCG
9656249 ATTTTTTATTTATTTTTTCG
1 ATTTTTTATTTATTTTTTCG
9656269 ATTTTT
1 ATTTTT
9656275 CTCTGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (20 bp):
ATTTTTTATTTATTTTTTCG
Found at i:9663947 original size:16 final size:15
Alignment explanation
Indices: 9663909--9663948 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
9663899 ATATTTTATG
*
9663909 AAAATGAAAAAGCGT
1 AAAATGAAAAAGCGA
*
9663924 AAAGTGAATAAAGCGA
1 AAAATGAA-AAAGCGA
9663940 AAAATGAAA
1 AAAATGAAA
9663949 GAAAAAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.05, G:0.20, T:0.12
Consensus pattern (15 bp):
AAAATGAAAAAGCGA
Found at i:9668905 original size:24 final size:24
Alignment explanation
Indices: 9668873--9668925 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
9668863 AATGGCATGC
9668873 CATGAGGTGGAGTGATCACTGATT
1 CATGAGGTGGAGTGATCACTGATT
9668897 CATGAGGTGGAGTGATCACTGATT
1 CATGAGGTGGAGTGATCACTGATT
*
9668921 AATGA
1 CATGA
9668926 TATTGATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.28
Consensus pattern (24 bp):
CATGAGGTGGAGTGATCACTGATT
Found at i:9672589 original size:306 final size:306
Alignment explanation
Indices: 9672102--9673020 Score: 1547
Period size: 306 Copynumber: 3.0 Consensus size: 306
9672092 AATTAAGTAC
* * * **
9672102 ATTTACGGGTTAAGGGAGTTATAACCTTGGTTTTCAAATAGTGATATAATCTACCGATGC-GAAG
1 ATTTACGGGTTAAGGGTGTTATACCCTTGGTTGTCACGTAGTGATATAATCTACCGATGCAG-AG
* ** * *
9672166 TTTCGAGCATAGTGATGTCACTCAGACTAT-GGCGACGAGTTGGTTACACTCAACTATTAGCCCT
65 ATTCGAGCATAGTGATGTCACTTGGATTATAGG-GACGAGTTGGTTACACTCAACTTTTAGCCCT
* * * * *
9672230 ACGATAGTTCGTTCCGGTTACTCTTGAGCTCTGGAAGTCTAAGTTCGCATATCTTGAGGACAACT
129 ACGATAGTTCGTTCCGATTACTCATGAGCTCTGGAAGTATGAGTTCACATATCTTGAGGACAACT
9672295 ACAAGAGGAAGGTTAAGGACATATCCGATTAGTAGAAGAAATATTTTTGAATCGATGTTGTAGGA
194 ACAAGAGGAAGGTTAAGGACATATCCGATTAGTAGAAGAAATATTTTTGAATCGATGTTGTAGGA
*
9672360 GCCCGGGAGATGCTCACACCAGACTATATTGAGTGGAGGAGAATAAGG
259 GCCCGGGAGATGCTCACACCAGACTATATTGAGTGGAGGAGACTAAGG
*
9672408 ATTTACAGGTTAAGGGTGTTATACCCTTGGTTGTCACGTAGTGATATAATCTACCGATGCAGAGA
1 ATTTACGGGTTAAGGGTGTTATACCCTTGGTTGTCACGTAGTGATATAATCTACCGATGCAGAGA
9672473 TTCGAGCATAGTGATGTCACTTGGATTATAGGGACGAGTTGGTTACACTCAACTTTTAGCCCTAC
66 TTCGAGCATAGTGATGTCACTTGGATTATAGGGACGAGTTGGTTACACTCAACTTTTAGCCCTAC
9672538 GATAGTTCGTTCCGATTACTCATGAGCTCTGGAAGTATGAGTTCACATATCTTGAGGACAACTAC
131 GATAGTTCGTTCCGATTACTCATGAGCTCTGGAAGTATGAGTTCACATATCTTGAGGACAACTAC
* *
9672603 AAGAGGAAGGTTAAGGACATATCCGATTAGTGGAAGAAATTTTTTTGAATCGATGTTGTAGGAGC
196 AAGAGGAAGGTTAAGGACATATCCGATTAGTAGAAGAAATATTTTTGAATCGATGTTGTAGGAGC
9672668 CCGGGAGATGCTCACACCAGACTATATTGAGTGGAGGAGACTAAGG
261 CCGGGAGATGCTCACACCAGACTATATTGAGTGGAGGAGACTAAGG
9672714 ATTTACGGGTTAAGGGTGTTATACCCTTGGTTGTCACGTAGTGATATAATCTACCGATGCAGAGA
1 ATTTACGGGTTAAGGGTGTTATACCCTTGGTTGTCACGTAGTGATATAATCTACCGATGCAGAGA
9672779 TTCGAGCATAGTGATGTCACTTGGATTATAGGGACGAGTTGGTTACACTCAACTTTTAGCCCTAC
66 TTCGAGCATAGTGATGTCACTTGGATTATAGGGACGAGTTGGTTACACTCAACTTTTAGCCCTAC
9672844 GATAGTTCGTTCCGATTACTCATGAGCTCTGGAAGTATGAGTTCACATATCTTGAGGACAACTAC
131 GATAGTTCGTTCCGATTACTCATGAGCTCTGGAAGTATGAGTTCACATATCTTGAGGACAACTAC
* * * *
9672909 AAGAGGAAGGTTAAGGACATATCCAAATAGTAGAAGAAA-ATATTTTGAACCCATGTTGTAGGAG
196 AAGAGGAAGGTTAAGGACATATCCGATTAGTAGAAGAAATAT-TTTTGAATCGATGTTGTAGGAG
* * * *
9672973 CCTGGGAGATGCCCACACCATACTATATTAAGTGGAGGAGACTAAGG
260 CCCGGGAGATGCTCACACCAGACTATATTGAGTGGAGGAGACTAAGG
9673020 A
1 A
9673021 AGAATGAAAA
Statistics
Matches: 580, Mismatches: 30, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
305 1 0.00
306 576 0.99
307 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (306 bp):
ATTTACGGGTTAAGGGTGTTATACCCTTGGTTGTCACGTAGTGATATAATCTACCGATGCAGAGA
TTCGAGCATAGTGATGTCACTTGGATTATAGGGACGAGTTGGTTACACTCAACTTTTAGCCCTAC
GATAGTTCGTTCCGATTACTCATGAGCTCTGGAAGTATGAGTTCACATATCTTGAGGACAACTAC
AAGAGGAAGGTTAAGGACATATCCGATTAGTAGAAGAAATATTTTTGAATCGATGTTGTAGGAGC
CCGGGAGATGCTCACACCAGACTATATTGAGTGGAGGAGACTAAGG
Found at i:9674133 original size:31 final size:31
Alignment explanation
Indices: 9674090--9674150 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
9674080 GATAATATAA
* *
9674090 TAATTATTTTATAGT-ATTTAGATAAATTTAT
1 TAATAATTTTATAATCATTTA-ATAAATTTAT
*
9674121 TAATAATTTTATAATCTTTTAATAAATTTA
1 TAATAATTTTATAATCATTTAATAAATTTA
9674151 ATATCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (31 bp):
TAATAATTTTATAATCATTTAATAAATTTAT
Found at i:9674144 original size:19 final size:20
Alignment explanation
Indices: 9674120--9674169 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
9674110 GATAAATTTA
9674120 TTAATAATTTT-ATAATCT-T
1 TTAATAATTTTAAT-ATCTAT
*
9674139 TTAATAAATTTAATATCTAT
1 TTAATAATTTTAATATCTAT
*
9674159 TTTATAATTTT
1 TTAATAATTTT
9674170 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAATAATTTTAATATCTAT
Found at i:9674936 original size:31 final size:29
Alignment explanation
Indices: 9674894--9674979 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 29
9674884 TCAATAAGGT
9674894 TTAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAATTATAAAATA-TTATTAAATTTA
* *
9674924 TTAAAAGATTATAAAGTTATTAATAAATTTA
1 TTAAAA-ATTATAAA-ATATTATTAAATTTA
* *
9674955 TCTAAATACTATAAAATAATTATTA
1 T-TAAAAATTATAAAAT-ATTATTA
9674980 TATTATCGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 7 0.15
31 33 0.72
32 6 0.13
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (29 bp):
TTAAAAATTATAAAATATTATTAAATTTA
Found at i:9675840 original size:18 final size:18
Alignment explanation
Indices: 9675817--9675865 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
9675807 AGATTATCAA
* *
9675817 TTAATTGCTTTTTTTATT
1 TTAATTCCTTTTTTTACT
*
9675835 TTAATTTCCTCTTTTTACT
1 TTAA-TTCCTTTTTTTACT
*
9675854 TTAATTTCTTTT
1 TTAATTCCTTTT
9675866 AGTTGGTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.69
Consensus pattern (18 bp):
TTAATTCCTTTTTTTACT
Found at i:9676639 original size:24 final size:24
Alignment explanation
Indices: 9676607--9676662 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
9676597 CTATTCTTTC
9676607 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
9676631 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
9676655 GCTTCAAT
1 GCTTCAAT
9676663 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:9676921 original size:11 final size:11
Alignment explanation
Indices: 9676905--9676942 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
9676895 AATCGATTTT
9676905 GCCGGTTTTCA
1 GCCGGTTTTCA
9676916 GCCGGTTTTC-
1 GCCGGTTTTCA
9676926 -CCGGTTTTCA
1 GCCGGTTTTCA
9676936 GCCGGTT
1 GCCGGTT
9676943 CTTCCGGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
11 16 0.64
ACGTcount: A:0.05, C:0.29, G:0.29, T:0.37
Consensus pattern (11 bp):
GCCGGTTTTCA
Found at i:9676929 original size:20 final size:19
Alignment explanation
Indices: 9676901--9676951 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 19
9676891 TTCAAATCGA
9676901 TTTTGCCGGTTTTCAGCCGG
1 TTTT-CCGGTTTTCAGCCGG
9676921 TTTTCCCGGTTTTCAGCCGG
1 TTTT-CCGGTTTTCAGCCGG
9676941 TTCTTCCGGTT
1 TT-TTCCGGTT
9676952 CTTTACCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.04, C:0.27, G:0.25, T:0.43
Consensus pattern (19 bp):
TTTTCCGGTTTTCAGCCGG
Found at i:9677379 original size:3 final size:3
Alignment explanation
Indices: 9677371--9677396 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9677361 TAAATAATCC
9677371 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
9677397 ATATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9687714 original size:20 final size:21
Alignment explanation
Indices: 9687668--9687720 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
9687658 TTAGATGAAG
*
9687668 TAGTACCGATACTGATTCAAT
1 TAGTATCGATACTGATTCAAT
*
9687689 TAGTATTGATACTGATT-AGA-
1 TAGTATCGATACTGATTCA-AT
9687709 TAGTATCGATAC
1 TAGTATCGATAC
9687721 CATGATAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (21 bp):
TAGTATCGATACTGATTCAAT
Found at i:9687811 original size:22 final size:23
Alignment explanation
Indices: 9687785--9687829 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
9687775 CTGATAGGGG
*
9687785 GTATCGGTACCATAG-AAGGGTA
1 GTATCGATACCATAGTAAGGGTA
*
9687807 GTATCGATACCATGGTAAGGGTA
1 GTATCGATACCATAGTAAGGGTA
9687830 TCGATACCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (23 bp):
GTATCGATACCATAGTAAGGGTA
Found at i:9687869 original size:95 final size:96
Alignment explanation
Indices: 9687709--9687894 Score: 270
Period size: 95 Copynumber: 1.9 Consensus size: 96
9687699 ACTGATTAGA
*
9687709 TAGTATCGATACCATGATAAGGGGTATCGATACTAAGAAACATCAAATCTAATTTTGGTATCGAT
1 TAGTATCGATACCATGATAAGGGGTATCGATACTAAGAAACATCAAACCTAATTTTGGTATCGAT
*
9687774 A-CTGATAGGGGGTATCGGTACCATAGAAGGG
66 ACCCGA-AGGGGGTATCGGTACCATAGAAGGG
* * * *
9687805 TAGTATCGATACCATGGTAA-GGGTATCGATAC-CAGACAACATCGAACCTATTTTTGGTATCGA
1 TAGTATCGATACCATGATAAGGGGTATCGATACTAAGA-AACATCAAACCTAATTTTGGTATCGA
*
9687868 TACCCGAAGGGGGTATCGGTACTATAG
65 TACCCGAAGGGGGTATCGGTACCATAG
9687895 TATAGAAGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
94 3 0.04
95 56 0.69
96 22 0.27
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (96 bp):
TAGTATCGATACCATGATAAGGGGTATCGATACTAAGAAACATCAAACCTAATTTTGGTATCGAT
ACCCGAAGGGGGTATCGGTACCATAGAAGGG
Found at i:9687913 original size:95 final size:96
Alignment explanation
Indices: 9687713--9687918 Score: 247
Period size: 95 Copynumber: 2.2 Consensus size: 96
9687703 ATTAGATAGT
* * *
9687713 ATCGATACCATGATAAGGGGTATCGATACTAAGAAACATCAAATCTAATTTTGGTATCGATACTG
1 ATCGATACCATGGTAAGGGGTATCGATACTAAGAAACATCAAACCTAATTTTGGTATCGATACCG
* * *
9687778 ATAGGGGGTATCGGTACCATAGAAGGGTAGT
66 ATAGGGGGTATCGGTACCATAGAAGAGAAGA
* * *
9687809 ATCGATACCATGGTAA-GGGTATCGATAC-CAGACAACATCGAACCTATTTTTGGTATCGATACC
1 ATCGATACCATGGTAAGGGGTATCGATACTAAGA-AACATCAAACCTAATTTTGGTATCGATA-C
* * *
9687872 CGA-AGGGGGTATCGGTACTATAGTATAGAAGA
64 CGATAGGGGGTATCGGTACCATAGAAGAGAAGA
* *
9687904 ATCGGTACCAGGGTA
1 ATCGATACCATGGTA
9687919 GTAGTATCGC
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
94 3 0.03
95 73 0.78
96 18 0.19
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (96 bp):
ATCGATACCATGGTAAGGGGTATCGATACTAAGAAACATCAAACCTAATTTTGGTATCGATACCG
ATAGGGGGTATCGGTACCATAGAAGAGAAGA
Found at i:9688647 original size:68 final size:68
Alignment explanation
Indices: 9688574--9688897 Score: 468
Period size: 68 Copynumber: 4.8 Consensus size: 68
9688564 AAAGATTAAT
* * * *
9688574 AGGCCTAACTGTGCATTTGATAGAAATGTGTCATTTATGCCAATTAGATGAAAGTCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
9688639 TTG
66 TTG
* * * * *
9688642 AGGCCTAACAGTGCATTTAACAGAAATGTGTCATTTATTCTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
9688707 TTG
66 TTG
*
9688710 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTTCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
9688775 TTG
66 TTG
9688778 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
9688843 TTC
66 TTG
* * * ** * * * *
9688846 TGGCCTAAATGTGCAATTGGTAGAAAGGTATCAATTATTCCAATTAGATGAA
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
9688898 TAGTTAAATA
Statistics
Matches: 232, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 232 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:9688985 original size:81 final size:80
Alignment explanation
Indices: 9688848--9689089 Score: 337
Period size: 81 Copynumber: 3.0 Consensus size: 80
9688838 TGCCTTTCTG
* * * *
9688848 GCCTAAATGTGCAATTGGTAGAAAGGTATCAATTATTCCAATTAGATGAATA-GTTAAATACCGT
1 GCCTAAATGTGCAATTGGTAGAAA-GTACCAATTATGCCAGTTAGATGAA-AGGTTAAATACCAT
9688912 TGAGTAAAAGAATAATA
64 TGAGTAAAAGAATAATA
* *
9688929 GCCTAATTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCATT
1 GCCTAAATGTGCAATTGGTAGAAA-GTACCAATTATGCCAGTTAGATGAAAGGTTAAATACCATT
*
9688994 GAGTAAAAGAATAA-C
65 GAGTAAAAGAATAATA
*
9689009 GACCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAAAGGTTAAATA-CAT
1 G-CCTAAATGTGCAATTGGTAGAAAG-TACCAATTATGCCAGTTAGATGAAAGGTTAAATACCAT
9689073 ATGAGTAAAAGAATAAT
64 -TGAGTAAAAGAATAAT
9689090 GGTTAAACAC
Statistics
Matches: 146, Mismatches: 10, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
80 5 0.03
81 141 0.97
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (80 bp):
GCCTAAATGTGCAATTGGTAGAAAGTACCAATTATGCCAGTTAGATGAAAGGTTAAATACCATTG
AGTAAAAGAATAATA
Found at i:9690748 original size:45 final size:46
Alignment explanation
Indices: 9690663--9690750 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
9690653 AAAAAGCATG
* * *
9690663 AGTGCATTGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
9690709 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
9690751 TTCGATGTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:9693458 original size:23 final size:23
Alignment explanation
Indices: 9693415--9693458 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9693405 GCATGACCAT
*
9693415 GTGCATCGATGATCATTCAAGGC
1 GTGCATCGATGATCATGCAAGGC
*
9693438 GTGCATCGGTGTATCA-GCAAG
1 GTGCATCGATG-ATCATGCAAG
9693459 ATGAATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (23 bp):
GTGCATCGATGATCATGCAAGGC
Found at i:9699791 original size:13 final size:13
Alignment explanation
Indices: 9699773--9699798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9699763 CCTATCTTAT
9699773 AGATAGAAATAAA
1 AGATAGAAATAAA
9699786 AGATAGAAATAAA
1 AGATAGAAATAAA
9699799 CATCCGCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AGATAGAAATAAA
Found at i:9700217 original size:62 final size:60
Alignment explanation
Indices: 9700108--9700556 Score: 427
Period size: 62 Copynumber: 7.3 Consensus size: 60
9700098 ATGACCAACA
* * * * * *
9700108 AAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAG
1 AAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTAAG
* *
9700166 AAGATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAA
1 AA-ATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA--TT--AA
9700231 G
60 G
*
9700232 -AATCGCAACGCGA-TT-CAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAG
1 AAATCGCAACGCGATTTCCA-AGAATCGCAACGCGATTCAGAAAATCGCAACGCGA--TT--AAG
*** * *
9700294 -AATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCCA-AGAATCGCAACGCGATTCAG
1 AAATCGCAACGCGATTTCCAAGAATCGCAACGCGATT-CAGAAAATCGCAACGCGATTAAG
*
9700352 AAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTAAG
1 -AAATCGCAACGCGATTTCCAAGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTAAG
* *
9700414 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAG
1 -AAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAG
*
9700476 TAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATCTTCCAA
1 -AAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGA--TT--AA
9700541 G
60 G
9700542 -AATCGCAACGCGATT
1 AAATCGCAACGCGATT
9700557 CAGAAAATGA
Statistics
Matches: 342, Mismatches: 24, Indels: 45
0.83 0.06 0.11
Matches are distributed among these distances:
58 4 0.01
59 16 0.05
60 29 0.08
61 8 0.02
62 225 0.66
63 5 0.01
64 49 0.14
65 1 0.00
66 5 0.01
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (60 bp):
AAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAG
Found at i:9700284 original size:104 final size:104
Alignment explanation
Indices: 9700107--9700564 Score: 723
Period size: 104 Copynumber: 4.5 Consensus size: 104
9700097 AATGACCAAC
* * * * * **
9700107 AAAATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAGAA
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACG-CGATTCAGAA
* * * *
9700168 GATCGCAACGCGATCTTCCAAGAATCGCAATGCGATTCAT
65 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
9700208 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAA
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAA
9700273 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
66 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
*
9700312 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCA-AG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATT-CAGAA
9700374 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
65 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
* *
9700414 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGTAA
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAA
9700479 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
66 ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
9700518 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAAT
9700565 GAGTAAATTC
Statistics
Matches: 333, Mismatches: 16, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
101 16 0.05
102 99 0.30
103 9 0.03
104 209 0.63
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (104 bp):
AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAA
ATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
Found at i:9700556 original size:42 final size:41
Alignment explanation
Indices: 9700107--9700564 Score: 419
Period size: 42 Copynumber: 11.1 Consensus size: 41
9700097 AATGACCAAC
* * *
9700107 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
* ***
9700146 AAAAGCGCAA--CG-TTGAAAAGAAGATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCAAG-A-ATCGCAACGCGA--TT-CAG
* * *
9700188 AGAATCGCAATGCGA-TT-CATAAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCA-AGAATCGCAACGCGA--TT-CAG
* *
9700230 AGAATCGCAACGCGA-TT-CAGAAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTCCA-AGAATCGCAACGCGATTCAG
*
9700270 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAG
9700312 AAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
9700352 AAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGA--TT-CAG
* ***
9700394 AGAATCGCAACGCGATTAAGAA-AATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGA--TT-CAG
* ***
9700436 AGAATCGCAACGCGATTAAGAA-AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
* *
9700476 TAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAG
9700518 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTCAG
9700560 AAAAT
1 AAAAT
9700565 GAGTAAATTC
Statistics
Matches: 368, Mismatches: 29, Indels: 41
0.84 0.07 0.09
Matches are distributed among these distances:
36 1 0.00
37 4 0.01
39 14 0.04
40 102 0.28
41 3 0.01
42 230 0.62
43 10 0.03
44 4 0.01
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTCAG
Found at i:9700671 original size:6 final size:6
Alignment explanation
Indices: 9700660--9700692 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
9700650 GACACGTATT
9700660 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
9700693 CGAGACAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:9701215 original size:6 final size:6
Alignment explanation
Indices: 9701189--9701248 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
9701179 TCTCGTCTCG
9701189 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
9701234 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
9701249 AATACGTGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.28
6 39 0.72
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:9701400 original size:20 final size:20
Alignment explanation
Indices: 9701344--9701553 Score: 153
Period size: 20 Copynumber: 10.2 Consensus size: 20
9701334 GAATTTACTC
*
9701344 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
9701364 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
9701386 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
9701406 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
9701426 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* *
9701448 ATTTTATGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
* *
9701468 ATTCTT-GGAAGATCGTGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* ** *
9701490 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
* *
9701510 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
9701530 -GTTT-TGATATCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
9701549 ATTTT
1 ATTTT
9701554 GTTGGTCATT
Statistics
Matches: 151, Mismatches: 23, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
18 2 0.01
19 16 0.11
20 73 0.48
21 19 0.13
22 41 0.27
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:9701403 original size:42 final size:40
Alignment explanation
Indices: 9701344--9701553 Score: 135
Period size: 42 Copynumber: 5.1 Consensus size: 40
9701334 GAATTTACTC
*
9701344 ATTTTCTTAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATT-TTCGG-A-ATCGCGTTGCG
*
9701386 ATTTTCTGAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTTTCGGAATCGCGTTGCG
* ** *
9701426 ATTCTT-GGAAGATCGCGTTGCGATTTTATGAATCGCATTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTTTCGGAATCGCGTTGCG
* * * *** *
9701468 ATTCTT-GGAAGATCGTGTTGCGATCTTC-TTTTCAACGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTTTCGGAATC-GCGTTGCG
* * *
9701510 CTTTTCTAAATCGCGTTGCGGTTTT--GATATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTTTCGGA-ATCGCGTTGCG
9701549 ATTTT
1 ATTTT
9701554 GTTGGTCATT
Statistics
Matches: 137, Mismatches: 24, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
39 11 0.08
40 30 0.22
41 11 0.08
42 85 0.62
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (40 bp):
ATTTTCTGAATCGCGTTGCGATTTTCGGAATCGCGTTGCG
Found at i:9701420 original size:62 final size:62
Alignment explanation
Indices: 9701344--9701470 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
9701334 GAATTTACTC
* * *
9701344 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCG
9701406 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCG
9701468 ATT
1 ATT
9701471 CTTGGAAGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (62 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCG
Found at i:9702834 original size:122 final size:115
Alignment explanation
Indices: 9702588--9702834 Score: 262
Period size: 116 Copynumber: 2.1 Consensus size: 115
9702578 TTTTCTGTAC
* * *
9702588 CAATTTTTTATATTTATAATTAGGTTTCCTAATTTTTATAATTTTGTCAAATTTTAATTTTTACT
1 CAATTTTTTATATTTATAATTAGG-TTCCTAATTTTTATAAATTCGTAAAATTTTAATTTTTACT
* * * *
9702653 TTCCTTTTATATTTATCTTATTAATTCATCTAATTTTAAATTAAATCTAAT
65 CTACTTTTACATTTATCTTATTAATTCATCTAATTTTAAATAAAATCTAAT
*
9702704 CAATTTTTTATATTTATAATTAGAG-TCCTGGATTTTTATAAATTCGTAAAATGTTTAATGTTTT
1 CAATTTTTTATATTTATAATTAG-GTTCCT-AATTTTTATAAATTCGTAAAAT-TTTAAT-TTTT
* * * * * * *
9702768 ACTCTATTTTTCCATTTCTCTTATTTATTTCTTCATTCAATTTTGAATAAAATTTAAT
62 ACTCTACTTTTACATTTATCTTA-TTAATTCATC--T-AATTTTAAATAAAATCTAAT
9702826 CATATTTTT
1 CA-ATTTTT
9702835 CTCTTTTTTC
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
115 4 0.04
116 41 0.38
117 7 0.07
118 21 0.20
119 8 0.07
121 1 0.01
122 19 0.18
123 6 0.06
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.55
Consensus pattern (115 bp):
CAATTTTTTATATTTATAATTAGGTTCCTAATTTTTATAAATTCGTAAAATTTTAATTTTTACTC
TACTTTTACATTTATCTTATTAATTCATCTAATTTTAAATAAAATCTAAT
Found at i:9703307 original size:2 final size:2
Alignment explanation
Indices: 9703300--9703331 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9703290 ACTGTTCCAT
9703300 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9703332 TTTTCCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:9707047 original size:15 final size:15
Alignment explanation
Indices: 9707027--9707056 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9707017 TATCACAATC
*
9707027 GCGCAGGATTTCGGG
1 GCGCAGGATTCCGGG
9707042 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
9707057 AGAACCGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:9713671 original size:101 final size:105
Alignment explanation
Indices: 9713461--9713708 Score: 254
Period size: 101 Copynumber: 2.4 Consensus size: 105
9713451 AAAATATATT
* * *
9713461 TTGTCACACCAAGTATTTTTTTAGTGA-TCAAATGTTCGACACTATTATCAACAGAAATTTTGAT
1 TTGTCACACTAAGTA-TATTTTAGTGACT-AAATGTTCGACACTATTATCAACAGAAATTGTGAT
* * * *
9713525 AAACTTTTTTTGACATTGAAAGTATATTTTGTGACCACCAATG
64 AAAC-TTTTTTGACACTAAAAGTATAATTAGTGACCACCAATG
* * * * *
9713568 TTGTCATACTAAGTA-ATTTTAGTGACTAAATGTTTGATACTATTATCAGCA-AAATTGTGATGA
1 TTGTCACACTAAGTATATTTTAGTGACTAAATGTTCGACACTATTATCAACAGAAATTGTGATAA
***
9713631 A-TTTTTT-ACACTAAAAGTATAATTAGTGACCATTGATG
66 ACTTTTTTGACACTAAAAGTATAATTAGTGACCACCAATG
* * * * *
9713669 TTGTCACACTAATTATTTTTTATTGACCAAATGTTAGACA
1 TTGTCACACTAAGTATATTTTAGTGACTAAATGTTCGACA
9713709 TTTTGTAATG
Statistics
Matches: 117, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
101 37 0.32
102 25 0.21
104 11 0.09
105 30 0.26
106 1 0.01
107 13 0.11
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (105 bp):
TTGTCACACTAAGTATATTTTAGTGACTAAATGTTCGACACTATTATCAACAGAAATTGTGATAA
ACTTTTTTGACACTAAAAGTATAATTAGTGACCACCAATG
Found at i:9731833 original size:6 final size:6
Alignment explanation
Indices: 9731822--9732256 Score: 690
Period size: 6 Copynumber: 72.2 Consensus size: 6
9731812 TTGATTAATA
9731822 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
9731870 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
9731918 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
9731966 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
9732014 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
9732062 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
* * *
9732110 TGTATG TGTATG TGTATG TGTATG TGTATG TGTGTG TGTGTG TGTGTG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
* * * * * * *
9732158 TGTCTG TGCATG TGCATG TGCATG TGCATG TGCATG TGTGTG TGTGCATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGT--ATG
* * * * * * * *
9732208 TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG TGCATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
9732256 T
1 T
9732257 ATGTATATTT
Statistics
Matches: 419, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
6 415 0.99
8 4 0.01
ACGTcount: A:0.15, C:0.03, G:0.34, T:0.47
Consensus pattern (6 bp):
TGTATG
Found at i:9732669 original size:2 final size:2
Alignment explanation
Indices: 9732662--9732688 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9732652 TTAATCGAAT
9732662 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9732689 TACGGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9735702 original size:29 final size:29
Alignment explanation
Indices: 9735660--9735743 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
9735650 TCATTACTGG
*
9735660 AATTTATAAAAAGTTTTGTACTTTATAGT
1 AATTTATCAAAAGTTTTGTACTTTATAGT
9735689 AATTTATCAAAAGTTTTGTACTTTATAGT
1 AATTTATCAAAAGTTTTGTACTTTATAGT
*
9735718 AATGTATCAAAAGTTTTGTACTTTAT
1 AATTTATCAAAAGTTTTGTACTTTAT
9735744 CATAAATAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.48
Consensus pattern (29 bp):
AATTTATCAAAAGTTTTGTACTTTATAGT
Found at i:9735791 original size:85 final size:87
Alignment explanation
Indices: 9735675--9735875 Score: 200
Period size: 85 Copynumber: 2.3 Consensus size: 87
9735665 ATAAAAAGTT
* * * *
9735675 TTGTACTTTATAGTAATTTATCAAAAGTTTTGTACTTTATAGT-AATGTATCA-AAAGTTTTGTA
1 TTGTCCTTTATTGTAATTTACCAAAAGTTTTGTACTTTATAGTAAAT-T-CCACAAAGTTTTGT-
*
9735738 C-TTTATCATAAATAACA-AA-ATA
63 CTTTTATAATAAATAACATAACATA
* ** * *
9735760 TTGTCCTTTATTGTAATTTCCCAAATTTTTTGTCCTTTATTGTAAATTCCACAAAGTTTTGTCTT
1 TTGTCCTTTATTGTAATTTACCAAAAGTTTTGTACTTTATAGTAAATTCCACAAAGTTTTGTCTT
** *
9735825 TTATAATAAATTTCATAACATT
66 TTATAATAAATAACATAACATA
9735847 TTGTCCTTTATTGTAAATTTA--AAAAGTTT
1 TTGTCCTTTATTGT-AATTTACCAAAAGTTT
9735876 AGAATTTTAT
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
84 3 0.03
85 59 0.63
86 11 0.12
87 16 0.17
88 5 0.05
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (87 bp):
TTGTCCTTTATTGTAATTTACCAAAAGTTTTGTACTTTATAGTAAATTCCACAAAGTTTTGTCTT
TTATAATAAATAACATAACATA
Found at i:9735863 original size:29 final size:27
Alignment explanation
Indices: 9735668--9735871 Score: 124
Period size: 29 Copynumber: 7.1 Consensus size: 27
9735658 GGAATTTATA
* * *
9735668 AAAAGTTTTGTACTTTATAGTAATTTATC
1 AAAA-TTTTGTCCTTTATTGTAAATT-TC
* *
9735697 AAAAGTTTTGTACTTTATAGT-AATGTATC
1 AAAA-TTTTGTCCTTTATTGTAAAT-T-TC
* ** **
9735726 AAAAGTTTTGTACTTTATCATAAATAAC
1 AAAA-TTTTGTCCTTTATTGTAAATTTC
*
9735754 AAAATATTGTCCTTTATTGT-AATTTCCC
1 AAAATTTTGTCCTTTATTGTAAATTT--C
* *
9735782 AAATTTTTTGTCCTTTATTGTAAATTCC
1 AAA-ATTTTGTCCTTTATTGTAAATTTC
* **
9735810 ACAAAGTTTTGTCTTTTATAATAAATTTC
1 A-AAA-TTTTGTCCTTTATTGTAAATTTC
*
9735839 ATAACATTTTGTCCTTTATTGTAAATTTA
1 A-AA-ATTTTGTCCTTTATTGTAAATTTC
9735868 AAAA
1 AAAA
9735872 GTTTAGAATT
Statistics
Matches: 142, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.02
27 13 0.09
28 15 0.11
29 103 0.73
30 8 0.06
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (27 bp):
AAAATTTTGTCCTTTATTGTAAATTTC
Found at i:9735909 original size:15 final size:16
Alignment explanation
Indices: 9735878--9735911 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9735868 AAAAGTTTAG
9735878 AATTTTATTATAATTT
1 AATTTTATTATAATTT
*
9735894 AATTTT-TTATATTTT
1 AATTTTATTATAATTT
9735909 AAT
1 AAT
9735912 AAAGAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTTTATTATAATTT
Found at i:9741796 original size:29 final size:29
Alignment explanation
Indices: 9741737--9741848 Score: 98
Period size: 29 Copynumber: 3.9 Consensus size: 29
9741727 TAAACTTTTA
*** **
9741737 TAAATTATAATAAATACCAATTTTTTTTG
1 TAAATTATAATAAATACCAAAACTTAATG
*
9741766 TAAATTATAATAAATATCAAAACTTAATG
1 TAAATTATAATAAATACCAAAACTTAATG
* * ** *
9741795 TAAATTACAATAAATACCAAAATTTTCTA
1 TAAATTATAATAAATACCAAAACTTAATG
* * *
9741824 AAAATTACAATAAACACCAAAACTT
1 TAAATTATAATAAATACCAAAACTT
9741849 TTTATATATT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (29 bp):
TAAATTATAATAAATACCAAAACTTAATG
Found at i:9741859 original size:29 final size:29
Alignment explanation
Indices: 9741796--9741863 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
9741786 AACTTAATGT
*
9741796 AAATTACAATAAATACCAAAATTTTCTAA
1 AAATTACAATAAACACCAAAATTTTCTAA
*
9741825 AAATTACAATAAACACCAAAACTTTT-TAT
1 AAATTACAATAAACACCAAAA-TTTTCTAA
*
9741854 ATATTACAAT
1 AAATTACAAT
9741864 CAAAGGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTACAATAAACACCAAAATTTTCTAA
Found at i:9741860 original size:58 final size:58
Alignment explanation
Indices: 9741728--9741863 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 58
9741718 AATCAAGACT
* ** * ** * * *
9741728 AAAC-TTTTATAAATTATAATAAATACCAATTTTTTTTGTAAATTATAATAAATATCA
1 AAACTTTTTATAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACACCA
** *
9741785 AAACTTAATGTAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACACCA
1 AAACTTTTTATAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACACCA
*
9741843 AAACTTTTTATATATTACAAT
1 AAACTTTTTATAAATTACAAT
9741864 CAAAGGAAAA
Statistics
Matches: 62, Mismatches: 16, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
57 4 0.06
58 58 0.94
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (58 bp):
AAACTTTTTATAAATTACAATAAATACCAAAATTTTCTAAAAATTACAATAAACACCA
Found at i:9742144 original size:21 final size:20
Alignment explanation
Indices: 9742118--9742255 Score: 111
Period size: 21 Copynumber: 6.7 Consensus size: 20
9742108 GCGAATTGCA
9742118 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
*
9742139 TTGCGATAGTCGAAGTTCACG
1 TTGCGATAGTCCAAGTTC-CG
* * * *
9742160 TTGCGATTTATTACAAATT-TG
1 TTGCGA--TAGTCCAAGTTCCG
9742181 TTGCGATAGTCCAAGTT-CG
1 TTGCGATAGTCCAAGTTCCG
*
9742200 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
* * *
9742221 TTGCGATTTATTCCAAATT-TG
1 TTGCGA--TAGTCCAAGTTCCG
9742242 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
9742256 AATCGCAACG
Statistics
Matches: 94, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
19 32 0.34
21 47 0.50
23 15 0.16
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCCG
Found at i:9742216 original size:61 final size:62
Alignment explanation
Indices: 9742118--9742255 Score: 242
Period size: 61 Copynumber: 2.2 Consensus size: 62
9742108 GCGAATTGCA
9742118 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTACAAATTTG
1 TTGCGATAGTCCAAGTTC-CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTACAAATTTG
* *
9742181 TTGCGATAGTCCAAGTT-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTTG
1 TTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTACAAATTTG
9742242 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
9742256 AATCGCAACG
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
61 56 0.77
63 17 0.23
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (62 bp):
TTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTACAAATTTG
Found at i:9742356 original size:6 final size:6
Alignment explanation
Indices: 9742345--9742369 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9742335 GACACGTATT
9742345 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
9742370 GACGAGACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:9743168 original size:21 final size:21
Alignment explanation
Indices: 9743144--9743402 Score: 241
Period size: 21 Copynumber: 12.4 Consensus size: 21
9743134 TTTGGAATAA
*
9743144 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
9743165 ATCGCAA--CGAACATGGAAT
1 ATCGCAACGCGAACTTGGACT
* **
9743184 AAATTGCAACGCGAACTTCAACT
1 --ATCGCAACGCGAACTTGGACT
*
9743207 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
9743226 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
9743249 ATCACAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
9743270 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
9743289 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
9743312 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
9743331 ATCACAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
9743352 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
9743371 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
9743394 ATCGCAACG
1 ATCGCAACG
9743403 AATTTGAAAA
Statistics
Matches: 191, Mismatches: 29, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
19 55 0.29
21 98 0.51
23 38 0.20
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:9743182 original size:42 final size:42
Alignment explanation
Indices: 9743119--9743267 Score: 226
Period size: 42 Copynumber: 3.5 Consensus size: 42
9743109 TGCGATTTTG
**
9743119 GACTATCGCAACGAGTTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
9743161 GACTATCGCAACGAACATGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
9743203 AACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
9743245 GACTATCACAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
9743268 CTATCGCAAC
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 86 0.90
44 10 0.10
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:9743343 original size:82 final size:82
Alignment explanation
Indices: 9743228--9743404 Score: 300
Period size: 82 Copynumber: 2.1 Consensus size: 82
9743218 CTTGGAATAA
* *
9743228 ATCGCAACGCGAACTTCGACTATCACAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAAT
1 ATCGCAA--CGAACTTCGACTATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAAT
9743293 CGCAACGCGAACTTCGACT
64 CGCAACGCGAACTTCGACT
*
9743312 ATCGCAACGAACTTGGACTATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
1 ATCGCAACGAACTTCGACTATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
*
9743377 CAACGCGAACTTGGACT
66 CAACGCGAACTTCGACT
9743394 ATCGCAACGAA
1 ATCGCAACGAA
9743405 TTTGAAAAAT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
82 82 0.92
84 7 0.08
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (82 bp):
ATCGCAACGAACTTCGACTATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCG
CAACGCGAACTTCGACT
Found at i:9743443 original size:21 final size:21
Alignment explanation
Indices: 9743419--9743469 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
9743409 AAAAATCACA
*
9743419 TTGCAATAATCGAAGTTCGTG
1 TTGCAATAATCGAAGTTCGCG
* * *
9743440 TTGCGATAGTCGATGTTCGCG
1 TTGCAATAATCGAAGTTCGCG
9743461 TTGCGAATA
1 TTGC-AATA
9743470 TGAAAACTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (21 bp):
TTGCAATAATCGAAGTTCGCG
Found at i:9745759 original size:3 final size:3
Alignment explanation
Indices: 9745751--9745809 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
9745741 TTTTGATGGA
9745751 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9745799 ATT ATT ATT AT
1 ATT ATT ATT AT
9745810 CATCATCTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9745904 original size:9 final size:9
Alignment explanation
Indices: 9745861--9745911 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
9745851 GGTTTCTTAC
9745861 AAATT-TTA
1 AAATTATTA
9745869 AAATTAATTTA
1 AAATT-A-TTA
*
9745880 AAAATATTA
1 AAATTATTA
9745889 AATATTATTA
1 AA-ATTATTA
*
9745899 AAATTATAA
1 AAATTATTA
9745908 AAAT
1 AAAT
9745912 ATGAAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
8 5 0.14
9 15 0.42
10 9 0.25
11 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAATTATTA
Found at i:9746158 original size:16 final size:17
Alignment explanation
Indices: 9746129--9746163 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
9746119 TTTCATAAAG
*
9746129 TTTTAATATTTTTATAT
1 TTTTAATATATTTATAT
9746146 TTTTAATA-ATTTATAT
1 TTTTAATATATTTATAT
9746162 TT
1 TT
9746164 AAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAATATATTTATAT
Found at i:9746383 original size:20 final size:21
Alignment explanation
Indices: 9746347--9746400 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
9746337 ATTTTCTACG
9746347 TATTTTAAT-TTTT-AAATAA
1 TATTTTAATATTTTAAAATAA
9746366 T-TTTTAATATTTTAAAATAA
1 TATTTTAATATTTTAAAATAA
* *
9746386 TATTGTAAGATTTTA
1 TATTTTAATATTTTA
9746401 TAATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 7 0.23
19 5 0.17
20 7 0.23
21 11 0.37
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
TATTTTAATATTTTAAAATAA
Found at i:9754252 original size:21 final size:21
Alignment explanation
Indices: 9754228--9754268 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9754218 TGAAGCAAGG
* *
9754228 GAAGTAGAGAGAGCAGCAGCA
1 GAAGCAGACAGAGCAGCAGCA
*
9754249 GAAGCAGCCAGAGCAGCAGC
1 GAAGCAGACAGAGCAGCAGC
9754269 GGTAGCACAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.22, G:0.37, T:0.02
Consensus pattern (21 bp):
GAAGCAGACAGAGCAGCAGCA
Found at i:9754282 original size:21 final size:22
Alignment explanation
Indices: 9754235--9754290 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
9754225 AGGGAAGTAG
9754235 AGAGAGCAGCAGCAGAAGCAGC
1 AGAGAGCAGCAGCAGAAGCAGC
* * *
9754257 -CAGAGCAGCAGCGGTAGCA-C
1 AGAGAGCAGCAGCAGAAGCAGC
*
9754277 AGAGAGAAGCAGCA
1 AGAGAGCAGCAGCA
9754291 TATCAGCAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.39, C:0.23, G:0.36, T:0.02
Consensus pattern (22 bp):
AGAGAGCAGCAGCAGAAGCAGC
Found at i:9754994 original size:41 final size:41
Alignment explanation
Indices: 9754759--9755131 Score: 245
Period size: 43 Copynumber: 8.8 Consensus size: 41
9754749 ACCGCAAAAC
* * * * *
9754759 ATCAACACCTACTACGGC-ATTTTAGCGAAAAAAGCCGCTAAA
1 ATCAACACCTATTGCGGCGTTTTTA-TGAAAAACGCCGCT-AA
* * * **
9754801 CATCATA-ACCTATTGCGGCGTTTGTCTGAAAAATGATGCTAAA
1 -ATCA-ACACCTATTGCGGCGTTTTTATGAAAAACGCCGCT-AA
* * *
9754844 TATTAACACCTATTGCGGCATTTTTATGACAAACGCCGCTAAA
1 -ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCT-AA
* *
9754887 TATCAACACCTATTACGGCGTTTTTAT-AACAAATGCCGCTAAA
1 -ATCAACACCTATTGCGGCGTTTTTATGAA-AAACGCCGCT-AA
* * * *
9754930 TATCAACACCTATTGCGACGTTTTTCTGAAAAACACTGCTAA
1 -ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAA
* * * *
9754972 ATCAACACATATTGCGGTGTTTTTATGACAAATGCCGCTAA
1 ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAA
* *
9755013 ATAAAAACACTTATTGCGGCGTTTTTAT-AACAAACGCCGCTAAA
1 AT--CAACACCTATTGCGGCGTTTTTATGAA-AAACGCCGCT-AA
* * * *
9755057 TATCAACACCTATTGC-G-GTGTTTGTCACAAACGCCGCTAAA
1 -ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCT-AA
* * *
9755098 TATCAATACCTATTGCGGCATTTTTTGTGAAAAA
1 -ATCAACACCTATTGCGGC-GTTTTTATGAAAAA
9755132 ATGCCACGAA
Statistics
Matches: 264, Mismatches: 52, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
41 69 0.26
42 8 0.03
43 167 0.63
44 18 0.07
45 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (41 bp):
ATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAA
Found at i:9755022 original size:84 final size:86
Alignment explanation
Indices: 9754750--9755131 Score: 373
Period size: 86 Copynumber: 4.5 Consensus size: 86
9754740 AAAAAAAACA
* * * * * * * *
9754750 CCGCAAAACATCAACACCTACTACGGC-ATTTTAGCGAAAAAAGCCGCTAAACATCATA-ACCTA
1 CCGCTAAATATCAACACCTATTGCGGCGTTTTTA-TGAAAAACGCCGCTAAATATCA-ACACCTA
* * *
9754813 TTGCGGCGTTTGTCTGAAAAATG
64 TTGCGGCGTTTTTATGACAAATG
** * * *
9754836 ATGCTAAATATTAACACCTATTGCGGCATTTTTATGACAAACGCCGCTAAATATCAACACCTATT
1 CCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAACACCTATT
* *
9754901 ACGGCGTTTTTATAACAAATG
66 GCGGCGTTTTTATGACAAATG
* * * * *
9754922 CCGCTAAATATCAACACCTATTGCGACGTTTTTCTGAAAAACACTGCT-AA-ATCAACACATATT
1 CCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAACACCTATT
*
9754985 GCGGTGTTTTTATGACAAATG
66 GCGGCGTTTTTATGACAAATG
** *
9755006 CCGCTAAATAAAAACACTTATTGCGGCGTTTTTAT-AACAAACGCCGCTAAATATCAACACCTAT
1 CCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA-AAACGCCGCTAAATATCAACACCTAT
* * * *
9755070 TGC-G-GTGTTTGTCACAAACG
65 TGCGGCGTTTTTATGACAAATG
* * *
9755090 CCGCTAAATATCAATACCTATTGCGGCATTTTTTGTGAAAAA
1 CCGCTAAATATCAACACCTATTGCGGC-GTTTTTATGAAAAA
9755132 ATGCCACGAA
Statistics
Matches: 241, Mismatches: 48, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
83 2 0.01
84 103 0.43
85 15 0.06
86 116 0.48
87 5 0.02
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Consensus pattern (86 bp):
CCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAAAACGCCGCTAAATATCAACACCTATT
GCGGCGTTTTTATGACAAATG
Found at i:9755033 original size:127 final size:129
Alignment explanation
Indices: 9754792--9755122 Score: 397
Period size: 127 Copynumber: 2.6 Consensus size: 129
9754782 AGCGAAAAAA
* * * * *
9754792 GCCGCTAAACATCATA-ACCTATTGCGGCGTTTGTCTGAAAAATGATGCTAAATATTAACACCTA
1 GCCGCTAAATATCA-ACACCTATTGCGACGTTTGTCTGAAAAATCATGCTAAATATCAACACATA
** *
9754856 TTGCGGCATTTTTATGACAAACGCCGCTAAATATCAACACCTATTACGGCGTTTTTATAACAAAT
65 TTGCGGCATTTTTATGACAAACGCCGCTAAATAAAAACACCTATTACGGCGTTTTTATAACAAAC
*
9754921 GCCGCTAAATATCAACACCTATTGCGACGTTTTTCTGAAAAA-CACTGCT-AA-ATCAACACATA
1 GCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGAAAAATCA-TGCTAAATATCAACACATA
** * * *
9754983 TTGCGGTGTTTTTATGACAAATGCCGCTAAATAAAAACACTTATTGCGGCGTTTTTATAACAAAC
65 TTGCGGCATTTTTATGACAAACGCCGCTAAATAAAAACACCTATTACGGCGTTTTTATAACAAAC
** * ** * *
9755048 GCCGCTAAATATCAACACCTATTGCGGTGTTTGTC--ACAAA-CGCCGCTAAATATCAATACCTA
1 GCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGAAAAATC-ATGCTAAATATCAACACATA
9755110 TTGCGGCATTTTT
65 TTGCGGCATTTTT
9755123 TGTGAAAAAA
Statistics
Matches: 173, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
125 8 0.05
126 2 0.01
127 118 0.68
128 4 0.02
129 41 0.24
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (129 bp):
GCCGCTAAATATCAACACCTATTGCGACGTTTGTCTGAAAAATCATGCTAAATATCAACACATAT
TGCGGCATTTTTATGACAAACGCCGCTAAATAAAAACACCTATTACGGCGTTTTTATAACAAAC
Found at i:9766550 original size:29 final size:30
Alignment explanation
Indices: 9766476--9766551 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 30
9766466 ATTTTAAATA
* *
9766476 TTACATTTTTGTCCCTAAACTTTTCAAAAT
1 TTACATTTTTGTCACTAAACTTTTCAAAAC
* * *
9766506 TTATATTTTGGCCACTAAAC-TTTCAAAAC
1 TTACATTTTTGTCACTAAACTTTTCAAAAC
9766535 TTACATTTTTGTCACTA
1 TTACATTTTTGTCACTA
9766552 CCCAAAATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (30 bp):
TTACATTTTTGTCACTAAACTTTTCAAAAC
Found at i:9768695 original size:55 final size:55
Alignment explanation
Indices: 9768630--9768739 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
9768620 CTGCTTATTG
9768630 CTATTTTAGTTATTGAATATAGATATATATGCTACTAATGTTATGGATTACGAAA
1 CTATTTTAGTTATTGAATATAGATATATATGCTACTAATGTTATGGATTACGAAA
* *
9768685 CTATTTTAGTTATTGAGTATAGATATGTATGCTACTAATGTTATGGATTACGAAA
1 CTATTTTAGTTATTGAATATAGATATATATGCTACTAATGTTATGGATTACGAAA
9768740 TATATTTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (55 bp):
CTATTTTAGTTATTGAATATAGATATATATGCTACTAATGTTATGGATTACGAAA
Found at i:9770478 original size:43 final size:43
Alignment explanation
Indices: 9770430--9770518 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
9770420 GAACATAGAC
9770430 TTTGTATTAAAGAAATATGAGATAACATTCTTTAAGGTTTATA
1 TTTGTATTAAAGAAATATGAGATAACATTCTTTAAGGTTTATA
*
9770473 TTTGTATTAAAGAAATATGAGATAACATTCTTTGAGGTTTATA
1 TTTGTATTAAAGAAATATGAGATAACATTCTTTAAGGTTTATA
9770516 TTT
1 TTT
9770519 ACATAATGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (43 bp):
TTTGTATTAAAGAAATATGAGATAACATTCTTTAAGGTTTATA
Found at i:9772566 original size:16 final size:16
Alignment explanation
Indices: 9772545--9772587 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
9772535 GATTAAGCGC
9772545 TGAATGATTCAAATGT
1 TGAATGATTCAAATGT
9772561 TGAATGATTCAAATGT
1 TGAATGATTCAAATGT
9772577 TGAATGATTCA
1 TGAATGATTCA
9772588 GAGGCTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (16 bp):
TGAATGATTCAAATGT
Found at i:9772795 original size:12 final size:12
Alignment explanation
Indices: 9772780--9772834 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
9772770 GTTATTTAAA
9772780 CGGGTATTGGGC
1 CGGGTATTGGGC
*
9772792 CGGGTATTGGGT
1 CGGGTATTGGGC
9772804 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
9772816 CGAGAATCGGGC
1 CGGGTATTGGGC
9772828 CGGGTAT
1 CGGGTAT
9772835 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:9772839 original size:2 final size:2
Alignment explanation
Indices: 9772832--9772873 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
9772822 TCGGGCCGGG
* * *
9772832 TA TA TA TA TA TA TA TA TA TA AA T- TA AA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9772873 T
1 T
9772874 TTTTTATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:9772968 original size:13 final size:13
Alignment explanation
Indices: 9772938--9772986 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
9772928 TTTAATATTT
*
9772938 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
9772950 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
9772963 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
9772976 ATCGGGGCGGG
1 ATCGGGGCGGG
9772987 GATTACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:9772986 original size:26 final size:25
Alignment explanation
Indices: 9772938--9772986 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
9772928 TTTAATATTT
*
9772938 ATCGGGTCGGGTATCGGGGCGGGTA
1 ATCGGGGCGGGTATCGGGGCGGGTA
9772963 ATCGGGGCGGGTAATCGGGGCGGG
1 ATCGGGGCGGGT-ATCGGGGCGGG
9772987 GATTACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.12, C:0.16, G:0.55, T:0.16
Consensus pattern (25 bp):
ATCGGGGCGGGTATCGGGGCGGGTA
Found at i:9774713 original size:29 final size:29
Alignment explanation
Indices: 9774671--9774731 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
9774661 ATAACGTTTG
9774671 TAACGTTAAATACATAGATGATTCAAAAA
1 TAACGTTAAATACATAGATGATTCAAAAA
* *
9774700 TAACGTTTAGTACATAGATGATTCAAAAA
1 TAACGTTAAATACATAGATGATTCAAAAA
9774729 TAA
1 TAA
9774732 GATTGGACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (29 bp):
TAACGTTAAATACATAGATGATTCAAAAA
Found at i:9776389 original size:7 final size:7
Alignment explanation
Indices: 9776377--9776402 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
9776367 CTTTTCCTTC
9776377 ATTTCTA
1 ATTTCTA
9776384 ATTTCTA
1 ATTTCTA
9776391 ATTTCTA
1 ATTTCTA
9776398 ATTTC
1 ATTTC
9776403 CATTTGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTCTA
Found at i:9777176 original size:16 final size:19
Alignment explanation
Indices: 9777155--9777199 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
9777145 GTTATTTATT
9777155 TTATATTTAT-TA-ATG-A
1 TTATATTTATATATATGAA
*
9777171 TTATATATATATATATGAAA
1 TTATATTTATATATATG-AA
9777191 TTATATTTA
1 TTATATTTA
9777200 AAATTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
18 3 0.13
20 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TTATATTTATATATATGAA
Found at i:9777306 original size:34 final size:34
Alignment explanation
Indices: 9777267--9777336 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
9777257 AAATAAAAAT
* *
9777267 TTATAATTTGAATTTTAAA-TATTTTTTCTTATGA
1 TTATAATTTGAATATTAAATTAATTTTT-TTATGA
9777301 TTATAATTTGAATATTAAATTAATTTTTTTATGA
1 TTATAATTTGAATATTAAATTAATTTTTTTATGA
9777335 TT
1 TT
9777337 TCATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 26 0.79
35 7 0.21
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (34 bp):
TTATAATTTGAATATTAAATTAATTTTTTTATGA
Found at i:9777698 original size:17 final size:17
Alignment explanation
Indices: 9777678--9777711 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9777668 ATAATATATG
9777678 TATTATCTCAATAACAA
1 TATTATCTCAATAACAA
9777695 TATTATCTCAATAACAA
1 TATTATCTCAATAACAA
9777712 GTGTGAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (17 bp):
TATTATCTCAATAACAA
Found at i:9781848 original size:20 final size:20
Alignment explanation
Indices: 9781823--9781861 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
9781813 ACCCTTGAGT
9781823 ATCGATACTC-AAAGAATGAA
1 ATCGATACTCGAAA-AATGAA
9781843 ATCGATACTCGAAAAATGA
1 ATCGATACTCGAAAAATGA
9781862 GTACTGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (20 bp):
ATCGATACTCGAAAAATGAA
Found at i:9785882 original size:12 final size:12
Alignment explanation
Indices: 9785867--9785895 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9785857 AATAAATTTG
9785867 AAAATCGAAATT
1 AAAATCGAAATT
9785879 AAAATCGAAATT
1 AAAATCGAAATT
9785891 AAAAT
1 AAAAT
9785896 TTTAGAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (12 bp):
AAAATCGAAATT
Found at i:9790265 original size:16 final size:18
Alignment explanation
Indices: 9790233--9790265 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9790223 AAGTAGAAAT
9790233 CATTTTTCTTGCATTTTA
1 CATTTTTCTTGCATTTTA
9790251 CATTTTT-TT-CATTTT
1 CATTTTTCTTGCATTTT
9790266 TCGCATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.67
Consensus pattern (18 bp):
CATTTTTCTTGCATTTTA
Found at i:9793310 original size:5 final size:5
Alignment explanation
Indices: 9793302--9793340 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
9793292 GAAAAAAAGA
* * *
9793302 AAAAT AAAAT AAAAG AAAAT AAAAT AAAAG AAAAG AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
9793341 AAGAAAGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (5 bp):
AAAAT
Found at i:9793320 original size:10 final size:10
Alignment explanation
Indices: 9793302--9793356 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
9793292 GAAAAAAAGA
*
9793302 AAAATAAAAT
1 AAAAGAAAAT
9793312 AAAAGAAAAT
1 AAAAGAAAAT
* *
9793322 AAAATAAAAG
1 AAAAGAAAAT
*
9793332 AAAAGAAAAA
1 AAAAGAAAAT
*
9793342 AGAAAGCAAAT
1 A-AAAGAAAAT
9793353 AAAA
1 AAAA
9793357 AGGGGGATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
10 29 0.78
11 8 0.22
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:9793334 original size:31 final size:31
Alignment explanation
Indices: 9793296--9793356 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
9793286 GAAGAAGAAA
9793296 AAAAGAAAA-ATAAAATA-AAAGAAAATAAAAT
1 AAAAGAAAAGA-AAAA-AGAAAGAAAATAAAAT
*
9793327 AAAAGAAAAGAAAAAAGAAAGCAAATAAAA
1 AAAAGAAAAGAAAAAAGAAAGAAAATAAAA
9793357 AGGGGGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 25 0.93
32 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (31 bp):
AAAAGAAAAGAAAAAAGAAAGAAAATAAAAT
Done.