Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold186
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: 1043505
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.30
Warning! 56388 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:334062 original size:166 final size:164
Alignment explanation
Indices: 333719--334277 Score: 622
Period size: 165 Copynumber: 3.4 Consensus size: 164
333709 AATTCAAATG
* * * * * * * *
333719 AAATAAATTAAATTTTTCAAAACTGAATTAATAGGAGTTCAATGATAATATTAGATGAATTCTAA
1 AAATGAATT-AATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTTAA
* *** *** * * ** *
333784 AAACTTTAAATTGAGAAACCCCCCT-GAAAACTTTTGTGGAA-TAGAAAACTCAATTTTTCAAAA
65 AAA-TTAAAACCAAGAAAAATCCTTCGAAAACATTT-ACGAAGTAGAAAACTCAATATTTCAAAA
*
333847 AAAATGGAACTTT-AA-GAAACAAATTCAAAAACTCACGA
128 AAAA-GGAA-TTTCAAGGAAA-AAATTCAAAAACTCATGA
* * * *
333885 AGATTAATTAATTTTTCAAAACTGATTTAATATGAAATAAATTATAATATTTGATTAATTTTAAA
1 AAATGAATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTTAAA
* * *
333950 AATTAAAAACTAAGAAAAATCCCTTCGAAAATATTTACGAAGTAGAAAACTCCATATTTCAAAAA
66 AATT-AAAACCAAGAAAAAT-CCTTCGAAAACATTTACGAAGTAGAAAACTCAATATTTCAAAAA
* *
334015 AAAAGAATTTCAAGGAAAAAATTCAAAAACTTATGA
129 AAAGGAATTTCAAGGAAAAAATTCAAAAACTCATGA
*
334051 AAATGAATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGGTGAATTTTAAA
1 AAATGAATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTTAAA
* * * **
334116 AATTAAAACCAAGAAAAATCCTTCGAAAACATTTATGGAGTGGAAAACTTTATATTTCAAAACAA
66 AATTAAAACCAAGAAAAATCCTTCGAAAACATTTACGAAGTAGAAAACTCAATATTTCAAAA-AA
* * *
334181 AGGGAATTTCAAGGAAAAAATTTAAGAACTCATGA
130 AAGGAATTTCAAGGAAAAAATTCAAAAACTCATGA
* * * *
334216 AAATGAATTAATTTTGCAAAACTAATTTCATATGAATTAAATAATAATATTTGATGAATTTT
1 AAATGAATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTT
334278 TCAAATTTTA
Statistics
Matches: 337, Mismatches: 49, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
164 39 0.12
165 164 0.49
166 98 0.29
167 36 0.11
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.32
Consensus pattern (164 bp):
AAATGAATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTTAAA
AATTAAAACCAAGAAAAATCCTTCGAAAACATTTACGAAGTAGAAAACTCAATATTTCAAAAAAA
AGGAATTTCAAGGAAAAAATTCAAAAACTCATGA
Found at i:334238 original size:165 final size:166
Alignment explanation
Indices: 333825--334277 Score: 626
Period size: 165 Copynumber: 2.7 Consensus size: 166
333815 TTTTGTGGAA
* * * *
333825 TAGAAAACTCAATTTTTCAAAAAAAATGGAACTTT-AA-GAAACAAATTCAAAAACTCACGAAGA
1 TAGAAAACTCCATATTTCAAAAAAAA-GGAA-TTTCAAGGAAA-AAATTCAAAAACTCATGAAAA
* * *
333888 TTAATTAATTTTTCAAAACTGATTTAATATGAAATAAATTATAATATTTGATTAATTTTAAAAAT
63 TGAATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTTAAAAAT
* *
333953 TAAAAACTAAGAAAAATCCCTTCGAAAATATTTACGAAG
128 TAAAAACCAAGAAAAATCCCTTCGAAAACATTTACGAAG
* *
333992 TAGAAAACTCCATATTTCAAAAAAAAAGAATTTCAAGGAAAAAATTCAAAAACTTATGAAAATGA
1 TAGAAAACTCCATATTTCAAAAAAAAGGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGA
*
334057 ATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGGTGAATTTTAAAAATT-A
66 ATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTTAAAAATTAA
* *
334121 AAACCAAGAAAAAT-CCTTCGAAAACATTTATGGAG
131 AAACCAAGAAAAATCCCTTCGAAAACATTTACGAAG
* ** * * *
334156 TGGAAAACTTTATATTTCAAAACAAAGGGAATTTCAAGGAAAAAATTTAAGAACTCATGAAAATG
1 TAGAAAACTCCATATTTCAAAA-AAAAGGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATG
* * * *
334221 AATTAATTTTGCAAAACTAATTTCATATGAATTAAATAATAATATTTGATGAATTTT
65 AATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTT
334278 TCAAATTTTA
Statistics
Matches: 256, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
164 37 0.14
165 106 0.41
166 85 0.33
167 28 0.11
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (166 bp):
TAGAAAACTCCATATTTCAAAAAAAAGGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGA
ATTAATTTTTCAAAACTGATTTAATATGAATTAAATTATAATATTTGATGAATTTTAAAAATTAA
AAACCAAGAAAAATCCCTTCGAAAACATTTACGAAG
Found at i:340786 original size:51 final size:52
Alignment explanation
Indices: 340650--340787 Score: 172
Period size: 51 Copynumber: 2.7 Consensus size: 52
340640 AATTGCCTAC
* * * *
340650 ATGTAT-GATACATTGAAGAATATATCGATTCATTTAGGTCAAAAACCCAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
* * * * * *
340701 ATGTATCGATACAATGAATAATGCATTGACACATTTGGGT-TAAAACCCAGA
1 ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
340752 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAAAAATGTATCGATACATTT
340788 TCTTTCTAGA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 48 0.66
52 25 0.34
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCGATACATTTAGGTCAAAAACCCAGA
Found at i:341584 original size:52 final size:52
Alignment explanation
Indices: 341516--341700 Score: 237
Period size: 52 Copynumber: 3.6 Consensus size: 52
341506 CTTAATGATA
* * *
341516 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAAATAAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAT
* * * *
341568 AAAGGTGCCACTGTGCTGATTCATGGCCAGCGACATTGGA-TATAAAGATAAC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT-TAAAGATAAT
* * * * * *
341620 AAAGGTGCTAATATGCTAATTCAAAGCCAACGACATTGGGCTTAAAGATGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAT
341672 AAAGGTGCCAATATGCTGATTCAAGGCCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCA
341701 CCAATATCAG
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
51 1 0.01
52 111 0.98
53 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAT
Found at i:342302 original size:28 final size:30
Alignment explanation
Indices: 342249--342312 Score: 105
Period size: 28 Copynumber: 2.2 Consensus size: 30
342239 GAATACAAAA
*
342249 TTGTGGACTTAAAAAAGGGGTGCCACGGAG
1 TTGTGGACTTAAAAAAGGGGTACCACGGAG
342279 TTGTGGACTT-AAAAA-GGGTACCACGGAG
1 TTGTGGACTTAAAAAAGGGGTACCACGGAG
342307 TTGTGG
1 TTGTGG
342313 CCTTTGAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 18 0.55
29 5 0.15
30 10 0.30
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.23
Consensus pattern (30 bp):
TTGTGGACTTAAAAAAGGGGTACCACGGAG
Found at i:343101 original size:13 final size:13
Alignment explanation
Indices: 343083--343108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343073 TACAGCAAGT
343083 ATGTATCGATACA
1 ATGTATCGATACA
343096 ATGTATCGATACA
1 ATGTATCGATACA
343109 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:344553 original size:28 final size:28
Alignment explanation
Indices: 344521--344582 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
344511 ATTTTAGGTG
344521 GATTTTCATGCATGGAA-TTTCCAACTAA
1 GATTTTCATGCATGGAATTTTCC-ACTAA
*
344549 GATTTTCATGCATGGAATTTTCCACTAG
1 GATTTTCATGCATGGAATTTTCCACTAA
344577 GATTTT
1 GATTTT
344583 TTAATATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (28 bp):
GATTTTCATGCATGGAATTTTCCACTAA
Found at i:345203 original size:7 final size:7
Alignment explanation
Indices: 345191--345217 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
345181 AATTATAATT
345191 AATTTCA
1 AATTTCA
345198 AATTTCA
1 AATTTCA
345205 AATTTCA
1 AATTTCA
345212 AATTTC
1 AATTTC
345218 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTCA
Found at i:352283 original size:14 final size:15
Alignment explanation
Indices: 352255--352292 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
352245 TGTAAAATTC
*
352255 AATTTATTT-TTTTT
1 AATTTTTTTATTTTT
352269 -ATTTTTTTATTTTT
1 AATTTTTTTATTTTT
352283 AATTTTTTTA
1 AATTTTTTTA
352293 CATATGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 5 0.24
15 9 0.43
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
AATTTTTTTATTTTT
Found at i:352775 original size:12 final size:12
Alignment explanation
Indices: 352753--352787 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
352743 AGAAACTTGG
352753 AGAAA-AAAAAA
1 AGAAAGAAAAAA
352764 AGAAAGAAAAAA
1 AGAAAGAAAAAA
352776 AGAAAGATAAAA
1 AGAAAGA-AAAA
352788 TTTTAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 5 0.23
12 13 0.59
13 4 0.18
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:354591 original size:155 final size:154
Alignment explanation
Indices: 354389--354901 Score: 446
Period size: 156 Copynumber: 3.3 Consensus size: 154
354379 GTTACCATAA
* * ** * * *
354389 TACTTTTATGTCGAAGGTATACCTATAAGGGTATTTTTTTTAATTTTTCAAAATCGAGTCCTAGG
1 TACTTTTACGTCAAAGGTAT-CCCCTAAGGGCA-TTTTTGTAATTTTTTAAAATCGAGTCCTAGG
* * * * * *
354454 TTGTCA-AGAGGTCCGCTTTTACGTGGAAGGTGGGTATTTAGGATAAGTTTATCCTTTCTATGAT
64 TTGTCATCGAGGTCCGCTTTTATGT-GAAAGTGGGTATTTAGGATAGGTTCATCCTTTCTATAAT
* **
354518 CCTTTTAAGTCCTTTAGGGGTGCCAGG
128 CCTTTTAAGTCCTTTAAGGGTATCAGG
* * * *
354545 TACTTTTATGTCAAAGGTATCCCCTAAGGGCATTTTTGTAATTTTTTAAAACCAAGTCTTAGGTT
1 TACTTTTACGTCAAAGGTATCCCCTAAGGGCATTTTTGTAATTTTTTAAAATCGAGTCCTAGGTT
* * ** * * *
354610 GTTATCGA-GTCCGCTTTAATGCCAAATGTGGATATTTATGATAGGTTCATCCCATTT-TGTAAT
66 GTCATCGAGGTCCGCTTTTATGTGAAA-GTGGGTATTTAGGATAGGTTCAT-CC-TTTCTATAAT
* * * *
354673 CTTTTTTAAGTCTTTTAAGGATATCGGG
128 C-CTTTTAAGTCCTTTAAGGGTATCAGG
* * *** * * *
354701 TACTTCTACGTCAAAGATATCTTTTAAGGGTA-TTTTGATAATTTTTTAGAATCGAGTTCTAGGT
1 TACTTTTACGTCAAAGGTATCCCCTAAGGGCATTTTTG-TAATTTTTTAAAATCGAGTCCTAGGT
* **
354765 TGTCATCG-GGTCTGCTTTTATGCTGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTATAATC
65 TGTCATCGAGGTCCGCTTTTATG-TGAAAGTGGGTATTTAGGATAGGTTCATCCTTTCTATAATC
*
354829 CTTTTGAAGTCCTTTAAGGGTATCAAG
129 CTTTT-AAGTCCTTTAAGGGTATCAGG
* * **
354856 TA-TTTCTGCGTCGAAGGTATCCCCT-AGAGGCATTTTCATAATTTTT
1 TACTTT-TACGTCAAAGGTATCCCCTAAG-GGCATTTTTGTAATTTTT
354902 CTTGAGCTTA
Statistics
Matches: 278, Mismatches: 66, Indels: 27
0.75 0.18 0.07
Matches are distributed among these distances:
153 2 0.01
154 70 0.25
155 74 0.27
156 129 0.46
157 3 0.01
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (154 bp):
TACTTTTACGTCAAAGGTATCCCCTAAGGGCATTTTTGTAATTTTTTAAAATCGAGTCCTAGGTT
GTCATCGAGGTCCGCTTTTATGTGAAAGTGGGTATTTAGGATAGGTTCATCCTTTCTATAATCCT
TTTAAGTCCTTTAAGGGTATCAGG
Found at i:359353 original size:153 final size:153
Alignment explanation
Indices: 359082--359521 Score: 432
Period size: 153 Copynumber: 2.9 Consensus size: 153
359072 AAAAATTCAG
* *
359082 AACTCATTAAAA-AAATTAAAATTTTCAAAACTGATTTAATATGAATTAGAAAATAATATTTGAT
1 AACTCA-TAAAATAAATT-AAATTTTTAAAACTGATTTAATATGAATTA-AAAATAATATTTGAA
* * * * * **
359146 GAATTTTAAAAATTTTAAACTGAGAAAAATCCAACTG-AAAAAACTTACAAAGTAAAAAACTCCG
63 GAATTTTAAAAATTATAAACTCAGAAAAAT--TATTGCAAAAAATTTACGGAGTAAAAAACTCCG
* *
359210 TATTTTGGA-AACA-TAAAAA-TTCTAA
126 TATTTTCGATAACAGAAAAAATTTCTAA
* *
359235 AACTCATAAAAT-TATGTAAATTTTATAAAACTGATTTAATATAAATTAAACAATAATATTTGAA
1 AACTCATAAAATAAAT-TAAATTTT-TAAAACTGATTTAATATGAATTAAA-AATAATATTTGAA
* * * *
359299 GAATTTTAAAAATTACAAGCAT-AGAAAAATTTTTGCCAAAAAATTTACGGAGTAAAAAACTCCA
63 GAATTTTAAAAATTATAAAC-TCAGAAAAATTATTG-CAAAAAATTTACGGAGTAAAAAACTCCG
*
359363 TA-TTTCGATACCAGAAAAAATTTCTAA
126 TATTTTCGATAACAGAAAAAATTTCTAA
* ** * * *
359390 AACTCATAAAATAAATTGAATTTTTTAAAGTTGCTTCAATATGAATT-AAAATAATATTTGAAAA
1 AACTCATAAAATAAATT-AAATTTTTAAAACTGATTTAATATGAATTAAAAATAATATTTGAAGA
** * * *
359454 ATTTTAAAAAACATAAACTCAGAAAAA-TATTACTAGAGAAATTTACGGAGTCAAAAACTCCGTA
65 ATTTTAAAAATTATAAACTCAGAAAAATTATTGC-A-AAAAATTTACGGAGTAAAAAACTCCGTA
359518 TTTT
128 TTTT
359522 AAAAAAGGAA
Statistics
Matches: 237, Mismatches: 34, Indels: 31
0.78 0.11 0.10
Matches are distributed among these distances:
151 3 0.01
152 26 0.11
153 153 0.65
154 11 0.05
155 36 0.15
156 8 0.03
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (153 bp):
AACTCATAAAATAAATTAAATTTTTAAAACTGATTTAATATGAATTAAAAATAATATTTGAAGAA
TTTTAAAAATTATAAACTCAGAAAAATTATTGCAAAAAATTTACGGAGTAAAAAACTCCGTATTT
TCGATAACAGAAAAAATTTCTAA
Found at i:366673 original size:41 final size:41
Alignment explanation
Indices: 366626--366705 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
366616 CGTGCATTTG
* *
366626 TACCATTAGAAGACATTTGCATTTGCATCATTTCACATGTA
1 TACCATTAGAAGACACTGGCATTTGCATCATTTCACATGTA
* **
366667 TACCATTAGATGACACTGGCATTTGCATTGTTTCACATG
1 TACCATTAGAAGACACTGGCATTTGCATCATTTCACATG
366706 CATTTATCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (41 bp):
TACCATTAGAAGACACTGGCATTTGCATCATTTCACATGTA
Found at i:367336 original size:30 final size:30
Alignment explanation
Indices: 367296--367372 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 30
367286 TTTTACCCTA
* *
367296 ATCATCTTTTGGACTGAAGGTTTTGCCTCG
1 ATCATTTTTTGGACTGAAAGTTTTGCCTCG
* *
367326 ATCATTTTTTGG-CTGAAAGTTTTTCCTTG
1 ATCATTTTTTGGACTGAAAGTTTTGCCTCG
*
367355 A-CAATTTTTGGACT-AAAG
1 ATCATTTTTTGGACTGAAAG
367373 ATTTCACCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 13 0.32
29 17 0.41
30 11 0.27
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (30 bp):
ATCATTTTTTGGACTGAAAGTTTTGCCTCG
Found at i:367528 original size:59 final size:60
Alignment explanation
Indices: 367441--367597 Score: 158
Period size: 59 Copynumber: 2.6 Consensus size: 60
367431 AGGTTTTGCC
* * *
367441 TTGGTCATTTTTTTAACTACAAGTTTCACTTTGGTCAT-TTTTCTAACTACAAG-TTTCACT
1 TTGGTCATTTTTTCAACTAAAAGTTTCACCTTGGTCATCTTTTC-AACTA-AAGATTTCACT
* * *
367501 TTGGTCA-TTTTTCGACTAAAAGTTTCACCTTGGTTATCTTTTCAACTAAAGATTTCACC
1 TTGGTCATTTTTTCAACTAAAAGTTTCACCTTGGTCATCTTTTCAACTAAAGATTTCACT
* * * * * * *
367560 CTAGTCATCTTTTCAATTGAAGGTTTCATCTTGGTCAT
1 TTGGTCATTTTTTCAACTAAAAGTTTCACCTTGGTCAT
367598 TTATTTGATT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
58 3 0.04
59 41 0.52
60 35 0.44
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (60 bp):
TTGGTCATTTTTTCAACTAAAAGTTTCACCTTGGTCATCTTTTCAACTAAAGATTTCACT
Found at i:367559 original size:30 final size:28
Alignment explanation
Indices: 367439--367849 Score: 171
Period size: 30 Copynumber: 14.0 Consensus size: 28
367429 GAAGGTTTTG
*
367439 CCTTGGTCATTTTTTTAACTACAAGTTTCA
1 CCTTGGTCA-TTTTTCAACTA-AAGTTTCA
*
367469 CTTTGGTCATTTTTCTAACTACAAGTTTCA
1 CCTTGGTCATTTTTC-AACTA-AAGTTTCA
* *
367499 CTTTGGTCATTTTTCGACTAAAAGTTTCA
1 CCTTGGTCATTTTTCAACT-AAAGTTTCA
*
367528 CCTTGGTTATCTTTTCAACTAAAGATTTCA
1 CCTTGGTCAT-TTTTCAACTAAAG-TTTCA
* * * *
367558 CCCTAGTCATCTTTTCAATTGAAGGTTTCA
1 CCTTGGTCAT-TTTTCAACT-AAAGTTTCA
* ** * * **
367588 TCTTGGTCATTTATTTGATTAATGGTTTTT
1 CCTTGGTCATTT-TTCAACTAA-AGTTTCA
** * **
367618 CCTTGGTCATTTTTTTATTGAAAGTTTTG
1 CCTTGGTCATTTTTCAACT-AAAGTTTCA
*
367647 CCTTGATCATCTTTTCAACTAAATGTTTC-
1 CCTTGGTCAT-TTTTCAACTAAA-GTTTCA
* * ** *
367676 TCTCTAGTCATTTTTTTGACTGAAGGTTTCA
1 CCT-TGGTCA-TTTTTCAACT-AAAGTTTCA
** ** **
367707 CCTT--TTTTTTTTTTACTAAAGGTTTTG
1 CCTTGGTCATTTTTCAACTAAA-GTTTCA
* * * *
367734 CCATGGTTATCTTTCAACTAAATATTTCA
1 CCTTGGTCATTTTTCAACTAAA-GTTTCA
* * * *
367763 TCTTAGTCATCTTTTCAATTGAAGGTTTCA
1 CCTTGGTCAT-TTTTCAACT-AAAGTTTCA
* * *
367793 CCTTAGTCATATTTCAACTAAAGGTTTCT
1 CCTTGGTCATTTTTCAACTAAA-GTTTCA
* **
367822 CTTTGGTCATATTTTTTACTAAAGTTTC
1 CCTTGGTCAT-TTTTCAACTAAAGTTTC
367850 CATTTTAGTT
Statistics
Matches: 293, Mismatches: 67, Indels: 43
0.73 0.17 0.11
Matches are distributed among these distances:
26 2 0.01
27 16 0.05
28 3 0.01
29 103 0.35
30 159 0.54
31 10 0.03
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (28 bp):
CCTTGGTCATTTTTCAACTAAAGTTTCA
Found at i:367770 original size:86 final size:87
Alignment explanation
Indices: 367627--367796 Score: 220
Period size: 86 Copynumber: 2.0 Consensus size: 87
367617 TCCTTGGTCA
* * * *
367627 TTTTTTTATTGAAAGTTTTGCCTTGATCATCTTTTCAACTAAATGTTTCTCTCTAGTCATTTTTT
1 TTTTTTTACTGAAAGTTTTGCCATGATCATCTTTTCAACTAAATATTTCTCTCTAGTCATCTTTT
**
367692 TGACTGAAGGTTTCACCTTTTT
66 CAACTGAAGGTTTCACCTTTTT
* *
367714 TTTTTTTACT-AAAGGTTTTGCCATGGTTATC-TTTCAACTAAATATTTCATCT-TAGTCATCTT
1 TTTTTTTACTGAAA-GTTTTGCCATGATCATCTTTTCAACTAAATATTTC-TCTCTAGTCATCTT
*
367776 TTCAATTGAAGGTTTCACCTT
64 TTCAACTGAAGGTTTCACCTT
367797 AGTCATATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 46 0.64
87 26 0.36
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (87 bp):
TTTTTTTACTGAAAGTTTTGCCATGATCATCTTTTCAACTAAATATTTCTCTCTAGTCATCTTTT
CAACTGAAGGTTTCACCTTTTT
Found at i:367830 original size:29 final size:29
Alignment explanation
Indices: 367745--367835 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 29
367735 CATGGTTATC
** * *
367745 TTTCAACTAAATATTTCATCTTAGTCATCT
1 TTTCAACTAAAGGTTTCACCTTAGTCAT-A
* *
367775 TTTCAATTGAAGGTTTCACCTTAGTCATA
1 TTTCAACTAAAGGTTTCACCTTAGTCATA
* * *
367804 TTTCAACTAAAGGTTTCTCTTTGGTCATA
1 TTTCAACTAAAGGTTTCACCTTAGTCATA
367833 TTT
1 TTT
367836 TTTACTAAAG
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
29 27 0.54
30 23 0.46
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (29 bp):
TTTCAACTAAAGGTTTCACCTTAGTCATA
Found at i:369059 original size:28 final size:28
Alignment explanation
Indices: 368990--369063 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
368980 ATAAAGCCGG
* *
368990 GGTTGGAGTATCCCCTCG--GAGGTAACGG
1 GGTTGGAGTAT--CCTCGATGAGATAACGA
369018 GGTTGGAGTATCCTCGATGAGATAACGA
1 GGTTGGAGTATCCTCGATGAGATAACGA
369046 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCTCGAT
369064 TGTGAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.12
28 37 0.88
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCTCGATGAGATAACGA
Found at i:369165 original size:52 final size:51
Alignment explanation
Indices: 369046--369538 Score: 305
Period size: 52 Copynumber: 9.4 Consensus size: 51
369036 GAGATAACGA
* ** * * *
369046 GGTTGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAG-GAAAATTGGTG-TTTTAGAAATAAAACCGG
* * * * *
369099 AGCTGAAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGA
1 GGTTGGAGTATCCCCGATT-AAGGAAAATTGGTGTTTTAGAAATAAAACCGG
** * *
369151 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAGG-AAAATTGGTGTTTTAGAAATAAAACCGG
* *** * * *
369203 GGTTGGAGTATCCCCGATT-ATGAGAAATCAATATTTTA-AGAATAAAGCAGG
1 GGTTGGAGTATCCCCGATTAAGGA-AAATTGGTGTTTTAGA-AATAAAACCGG
* ** * *** * *
369254 GGTTGGAGTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTAT-CCC-C-G-ATTAA-GGAAAATTGGTGT-T-TTAGA-AATAAAACCGG
** * * *
369309 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTGGTG---TTTTAGAAATAAAACCGG
* * * *
369363 AGCTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTAAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-AAGGAAAATTGGTGTTTTAGAAATAAAACCGG
* ** * * *
369415 GGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGA
1 GGTTGGAGTATCCCCGATTAAGG-AAAATTGGTGTTTTAGAAATAAAACCGG
* ** * *
369467 GGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAAGG-AAAATTGGTGTTTTAGAAATAAAACCGG
369519 GGTTGGAGTATCCCCGATTA
1 GGTTGGAGTATCCCCGATTA
369539 TGAGAAATCA
Statistics
Matches: 341, Mismatches: 77, Indels: 45
0.74 0.17 0.10
Matches are distributed among these distances:
50 2 0.01
51 37 0.11
52 208 0.61
53 31 0.09
54 28 0.08
55 29 0.09
56 2 0.01
57 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTAAGGAAAATTGGTGTTTTAGAAATAAAACCGG
Found at i:369259 original size:51 final size:52
Alignment explanation
Indices: 369133--369584 Score: 237
Period size: 52 Copynumber: 8.6 Consensus size: 52
369123 AAAATTGGTG
* * * * * *
369133 TTTTAAAAATAAAACCGAGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTG
1 TTTTAAGAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
*
369185 TTTT-AGCAATAAAACCGGGGTTGGAGTATCCCCGATTAT-GAGAAATCAATA
1 TTTTAAG-AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
* * * ***
369236 TTTTAAGAATAAAGCAGGGGTTGGAGTATCCCC---T-CGGAAATAA-C-GGG
1 TTTTAAGAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAA-AATCAATA
* ** * * *** *
369283 GTTGGAGTATCCCCGATGATTAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTT
1 TTTTAAG-A------AT-A-AAACCGGGGTTGGAGTATCCCCGATTATGGAAAAA-T-CAATA
** * * * ** *** *
369344 TTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGAAAAATTGGTG
1 TTTTAAG-AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
* * * * * *
369397 TTTTAAAAATAAAACCGGGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTG
1 TTTTAAGAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
* * * * * *
369449 TTTT-AGCAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTG
1 TTTTAAG-AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
*
369501 TTTT-AGCAATAAAACCGGGGTTGGAGTATCCCCGATTAT-GAGAAATCAATA
1 TTTTAAG-AATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
* *
369552 TTTTAAGAATAAAGCAGGGGTTGGAGTATCCCC
1 TTTTAAGAATAAAACCGGGGTTGGAGTATCCCC
369585 TCGGAAATAA
Statistics
Matches: 316, Mismatches: 59, Indels: 51
0.74 0.14 0.12
Matches are distributed among these distances:
47 4 0.01
48 6 0.02
49 2 0.01
51 74 0.23
52 159 0.50
53 8 0.03
54 24 0.08
55 26 0.08
56 1 0.00
57 2 0.01
58 5 0.02
61 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (52 bp):
TTTTAAGAATAAAACCGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
Found at i:369314 original size:27 final size:28
Alignment explanation
Indices: 369252--369326 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
369242 GAATAAAGCA
***
369252 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
369280 GGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
369307 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
369327 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:369408 original size:264 final size:263
Alignment explanation
Indices: 368938--369533 Score: 944
Period size: 264 Copynumber: 2.3 Consensus size: 263
368928 CAGAAATAAC
*
368938 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTT-AGAATAAAGCCGGGGTTGGAGTATCC
** * *
369003 CCTCGGAGGTAACGGGGTTGGAGTATCCTCGATGAGATAACGAGGTTGGAGTATCCTCGATTGTG
65 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAGATAACGAGGTTGGAGTATCCCCGATTGTG
*
369068 AAAAAATTGGTGTTTTTGGAAATAAAATCGGAGCTGAAGTATCCCCGATTAAAGGAAAATTGGTG
130 AAAAAATTGGTGTTTTTGGAAATAAAATCGGAGCTGAAGTATCCCCGATTAAAGAAAAATTGGTG
*
369133 TTTTAAAAATAAAACCGAGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
195 TTTTAAAAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAA
369198 ACCG
260 ACCG
* *
369202 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTT-AGAATAAAGCCGGGGTTGGAGTATCC
* *
369267 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATGA-TTAACGGGGTTGGAGTATCCCCGATTGTG
65 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAGATAACGAGGTTGGAGTATCCCCGATTGTG
*
369331 -AAAAATTGGTGTTTTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAGAAAAATTGG
130 AAAAAATTGGTG--TTTTTGGAAATAAAATCGGAGCTGAAGTATCCCCGATTAAAGAAAAATTGG
*
369395 TGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATA
193 TGTTTTAAAAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATA
369460 AAACCG
258 AAACCG
* * * * * * *
369466 AGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCAATTAT-GAGAAATCAATATTTTAG-AATAAAGCCGGGGTTGGAGTATC
369531 CCC
64 CCC
369534 GATTATGAGA
Statistics
Matches: 305, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
262 11 0.04
263 26 0.09
264 232 0.76
265 36 0.12
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (263 bp):
GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAATAAAGCCGGGGTTGGAGTATCCC
CTCGGAAATAACGGGGTTGGAGTATCCCCGATGAGATAACGAGGTTGGAGTATCCCCGATTGTGA
AAAAATTGGTGTTTTTGGAAATAAAATCGGAGCTGAAGTATCCCCGATTAAAGAAAAATTGGTGT
TTTAAAAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAA
CCG
Found at i:369465 original size:316 final size:315
Alignment explanation
Indices: 369069--369752 Score: 1165
Period size: 316 Copynumber: 2.2 Consensus size: 315
369059 TCGATTGTGA
* * * ** *
369069 AAAAATTGGTGTTTTTGGAAATAAAATCGGAGCTGAAGTATCCCCGATTAAAGG-AAAATTGGTG
1 AAAAATTGGTG-TTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATT-GTGGAAAAATTAGTG
*
369133 TTTTAAAAATAAAACCGAGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
64 TTTTAAAAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAA
369198 ACCGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGT
129 ACCGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGT
369263 ATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATT
194 ATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATT
369328 GTGAAAAATTGGTGTTTTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAG
259 GTGAAAAATTGGTG-TTTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAG
* * * * *
369386 AAAAATTGGTGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTT
1 AAAAATTGGTGTTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATTGTGGAAAAATTAGTGTT
**
369451 TTAGCAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
66 TTAAAAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
369516 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
131 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
369581 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGT
196 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGT
* *
369646 GAAAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAG
261 GAAAAATTGGTGTTTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAG
* *
369701 -AAAATTAGTGTTTTGAAAATAAAATCGGAGATGGAATATCCCCGATTGTGGA
1 AAAAATTGGTGTTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATTGTGGA
369753 GAATTGAGAA
Statistics
Matches: 344, Mismatches: 22, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
314 45 0.13
315 43 0.12
316 245 0.71
317 11 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (315 bp):
AAAAATTGGTGTTTTGAAAATAAAATCGGAGATGGAGTATCCCCGATTGTGGAAAAATTAGTGTT
TTAAAAATAAAACCGAGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAAGAATAAAGCAGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGT
GAAAAATTGGTGTTTTTTGGAAATAAAATCGGAGCTGGAGTATCCCCGATTAAAG
Found at i:369630 original size:27 final size:28
Alignment explanation
Indices: 369568--369642 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
369558 GAATAAAGCA
***
369568 GGGGTTGGAGTATCCCCTCGGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
369596 GGGGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
369623 GGGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
369643 TGTGAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:369706 original size:53 final size:51
Alignment explanation
Indices: 369626--369747 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
369616 GATTAACGGG
* * *
369626 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG--TTTTGAAAATAAAATCGGA
369679 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGAAAATAAAATCGGA
* *
369730 GATGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
369748 GTGGAGAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
51 34 0.54
52 1 0.02
53 28 0.44
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:369741 original size:51 final size:52
Alignment explanation
Indices: 369312--369747 Score: 189
Period size: 52 Copynumber: 8.3 Consensus size: 52
369302 TTAACGGGGT
* * * *
369312 TGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTTGGAAATAAAATCGGAGC
1 TGGAGTATCCCCGATTATGAAAAATTAGTG--TTTTTGAAAATAAAATCGGAGA
* * * * * *
369366 TGGAGTATCCCCGATTAAAGAAAAATTGGTG-TTTTAAAAATAAAACCGGGGT
1 TGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTTGAAAATAAAATCGGAGA
* * * * * *
369418 TGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAG-CAATAAAA-CCGAGGT
1 TGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTTGAAAATAAAATCGGA-GA
* * * * * * *
369470 TGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAG-CAATAAAACCGGGGT
1 TGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTTGAAAATAAAATCGGAGA
* * * * * * *
369522 TGGAGTATCCCCGATTATGAGAAATCAAT-ATTTT-AAGAAT-AAAGCAGGGGT
1 TGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAA-AATAAAATC-GGAGA
** * **** ** * * *
369573 TGGAGTATCCCC---TCGGAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGGGT
1 TGGAGTATCCCCGATTATGAAA-AA-----TT--AGTGTTTTTGAAAATAAAATCGGAGA
* * * *
369628 TGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTGGAAATAAAATCGGAGT
1 TGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTTGAAAATAAAATCGGAGA
369681 TGGAGTATCCCCGATTAT-AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGA
1 TGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTTGAAAATAAAATCGGAGA
*
369732 TGGAATATCCCCGATT
1 TGGAGTATCCCCGATT
369748 GTGGAGAATT
Statistics
Matches: 299, Mismatches: 58, Indels: 53
0.73 0.14 0.13
Matches are distributed among these distances:
48 4 0.01
49 2 0.01
50 9 0.03
51 68 0.23
52 119 0.40
53 36 0.12
54 17 0.06
55 29 0.10
56 3 0.01
57 6 0.02
58 6 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
TGGAGTATCCCCGATTATGAAAAATTAGTGTTTTTGAAAATAAAATCGGAGA
Found at i:372116 original size:13 final size:13
Alignment explanation
Indices: 372098--372123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
372088 CAAAGGATAG
372098 ATGTATCGATACA
1 ATGTATCGATACA
372111 ATGTATCGATACA
1 ATGTATCGATACA
372124 CAAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:372199 original size:19 final size:18
Alignment explanation
Indices: 372175--372303 Score: 108
Period size: 19 Copynumber: 7.8 Consensus size: 18
372165 AGCAATACAT
372175 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
372194 TGTATCGATAC---C-T-
1 TGTATCGATACAAACTTA
372207 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
372226 TGTATCGATAC---C-T-
1 TGTATCGATACAAACTTA
372239 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
372258 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
372271 TGTATCGATACAACATTTA
1 TGTATCGATACAA-ACTTA
372290 TGTATCGATACAAA
1 TGTATCGATACAAA
372304 TCGCTGAAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 37
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
14 3 0.03
15 2 0.02
16 2 0.02
17 2 0.02
18 4 0.04
19 46 0.50
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:372212 original size:13 final size:13
Alignment explanation
Indices: 372194--372281 Score: 59
Period size: 13 Copynumber: 5.8 Consensus size: 13
372184 ACAAAACTTA
372194 TGTATCGATACCT
1 TGTATCGATACCT
372207 TGTATCGATACAAAACTT
1 TGTATCGATAC----C-T
372225 ATGTATCGATACCT
1 -TGTATCGATACCT
372239 TGTATCGATACAACACTT
1 TGTATCGAT---AC-C-T
*
372257 ATGTATCGATACAT
1 -TGTATCGATACCT
372271 TGTATCGATAC
1 TGTATCGATAC
372282 AACATTTATG
Statistics
Matches: 62, Mismatches: 1, Indels: 24
0.71 0.01 0.28
Matches are distributed among these distances:
13 31 0.50
14 2 0.03
15 1 0.02
16 4 0.06
17 2 0.03
18 2 0.03
19 20 0.32
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACCT
Found at i:372215 original size:32 final size:32
Alignment explanation
Indices: 372169--372301 Score: 221
Period size: 32 Copynumber: 4.2 Consensus size: 32
372159 CTTCCTAGCA
372169 ATACATTGTATCGATACAAAACTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
*
372201 ATACCTTGTATCGATACAAAACTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
* *
372233 ATACCTTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
* *
372265 ATACATTGTATCGATACAACATTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
372297 ATACA
1 ATACA
372302 AATCGCTGAA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 97 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTTATGTATCG
Found at i:372365 original size:21 final size:19
Alignment explanation
Indices: 372339--372415 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 19
372329 GTTGGGACCC
372339 TGTATCGATACATTAGTAGAA
1 TGTATCGATACATTA-TA-AA
*
372360 TGTATCGATACATTCCACAAA
1 TGTATCGATACATT--ATAAA
*
372381 TGTATCGATACATTCTACAAA
1 TGTATCGATACA-T-TATAAA
372402 TGTATCGATACATT
1 TGTATCGATACATT
372416 TGGATAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 45 0.88
22 2 0.04
23 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACATTATAAA
Found at i:374795 original size:13 final size:12
Alignment explanation
Indices: 374746--374796 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 12
374736 ATTTAACATG
374746 AATAATAAA-A-
1 AATAATAAATAT
*
374756 AATAATAAA-AA
1 AATAATAAATAT
374767 AATAA-AAATAT
1 AATAATAAATAT
374778 AATAATAAATAGT
1 AATAATAAATA-T
374791 AATAAT
1 AATAAT
374797 TGATTAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 13 0.36
11 11 0.31
12 5 0.14
13 7 0.19
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:378413 original size:84 final size:86
Alignment explanation
Indices: 378299--379028 Score: 554
Period size: 84 Copynumber: 8.7 Consensus size: 86
378289 CTATGGAAAC
* * * *
378299 TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACTTTAAGTTTGTCTAT
1 TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCTGT
378364 C-ATCTTTGACCCTAGAGA-T
66 CGATCTTTGACCCTAGAGACT
* * * * * *
378383 TTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTCCCTCATCTCAAGTCTGCCTGT
1 TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCTGT
* * * *
378448 CG-CCTTTTACCTTGGAGACT
66 CGATCTTTGACCCTAGAGACT
* * * * ** * * * *
378468 TTT-TTACCCTTAGTCTGCCTATCGACTTTGACCTTGGAGACTTTCTTACCCTCAGTCTACCTGT
1 TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCTGT
378532 CGA-CTTTGACCCTAGAGAC-
66 CGATCTTTGACCCTAGAGACT
** * * ** * * *
378551 TGCCTCA-CCTCAAATCTGCCTGTC-AGCTTTGACCCTAGAGACTTTCTTACCTTTAGTCTGCTT
1 TTTCTTACCCTC-AGTCTGCCTGTCGA-CTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCT
* *
378614 GTC-AGCTTTGACCCTGGAGACT
64 GTCGATCTTTGACCCTAGAGACT
* * * * ** * * *
378636 ACTTCTT---CTCAAGTCTGCCTATCG-GTTGTGACCCTGGAGACTTTCTTACCCCT-AGTTTGC
1 -TTTCTTACCCTC-AGTCTGCCTGTCGACTT-TGACCCTAGAGACTGCCTCA-CCTTAAGTCTGC
* *
378696 CTGTCGAT-TTTGACCTTGGAGAC-
62 CTGTCGATCTTTGACCCTAGAGACT
* * * * * * ** * *
378719 TGTCTCA-TCTCAAGTTTGCCTGTCGACTTTGACCTTAGAGACTACCTCTTCTCAAGTCTGCTTG
1 TTTCTTACCCTC-AGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCTG
* *
378783 TCGGT-TTTGACCCTTGAGAC-
65 TCGATCTTTGACCCTAGAGACT
* * * * * * *
378803 TTTCTTACCTTCATTCTACTTGTCGACTTTGACCTTAGAGACTGCCTCACCTCAAATCTGCCTGT
1 TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCTGT
*
378868 CGAT-TTTCACCCTAGAGACT
66 CGATCTTTGACCCTAGAGACT
* * * * * *
378888 TTT-TTACCCTCAATCTACTTGTCGACTTTGACTCTAGAGACTGCCTCACCTCAAGTCTGCCTAT
1 TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCTGT
*
378952 CG-GCTTTGACCCT-GAAGACT
66 CGATCTTTGACCCTAG-AGACT
*
378972 TTT-TTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTC
1 TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTC
379029 CGTCTCAATT
Statistics
Matches: 523, Mismatches: 102, Indels: 42
0.78 0.15 0.06
Matches are distributed among these distances:
82 3 0.01
83 10 0.02
84 493 0.94
85 15 0.03
86 2 0.00
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (86 bp):
TTTCTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTTAAGTCTGCCTGT
CGATCTTTGACCCTAGAGACT
Found at i:378513 original size:126 final size:127
Alignment explanation
Indices: 378367--379823 Score: 843
Period size: 126 Copynumber: 11.5 Consensus size: 127
378357 TGTCTATCAT
* * *
378367 CTTTGACCCTAGAGATTTTCTTACCCTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTCCCTC
1 CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTC
* * * * * *
378431 ATCTCAAGTCTGCCTGTCGCCTTTTACCTTGGAGACTTTTTTACCCTTAGTCTGCCTATCGA
66 ACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTAAGTCTGCCTGTCGA
* * * * *
378493 CTTTGACCTTGGAGACTTTCTTACCCTC-AGTCTACCTGTCGACTTTGACCCTAGAGACTGCCTC
1 CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTC
* * * * * * *
378557 ACCTCAAATCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTTTAGTCTGCTTGTC-A
66 ACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTAAGTCTGCCTGTCGA
* * * * *
378618 GCTTTGACCCTGGAGACTACTTCTT---CTCAAGTCTGCCTATCGG-TTGTGACCCTGGAGACTT
1 -CTTTGACCCTAGAGACT--TTCTTACCCTCAAGTCTGCCTGTCGGCTT-TGACCTTAGAGACTG
* * * * * ** * * * *
378679 TCTTACCCCTAGTTTGCCTGTCGATTTTGACCTTGGAGACTGTCTCA-TCTCAAGTTTGCCTGTC
62 CCTCACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCT-AAGTCTGCCTGTC
378743 GA
126 GA
* * * * **
378745 CTTTGACCTTAGAGACTACCTCTT---CTCAAGTCTGCTTGTCGGTTTTGACCCTT-GAGACTTT
1 CTTTGACCCTAGAGACT--TTCTTACCCTCAAGTCTGCCTGTCGGCTTTGA-CCTTAGAGACTGC
* * * * * * ** * *
378806 CTTACCTTC-ATTCTACTTGTCGACTTTGACCTTAGAGACTGCCTCA-CCTCAAATCTGCCTGTC
63 CTCACC-TCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCT-AAGTCTGCCTGTC
378869 GA
126 GA
* * * * * *
378871 TTTTCACCCTAGAGACTTTTTTACCCTCAA-TCTACTTGTCGACTTTGA-CTCTAGAGACTGCCT
1 CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCT-TAGAGACTGCCT
* * * * *
378934 CACCTCAAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTTTTACCCTCAGTCTGCCTGTCGA
65 CACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTAAGTCTGCCTGTCGA
** * * *
378997 CTTTGACCCTAGAGACTGCCTCA-CCTCAAGTCCGTCTCAATTTGCTTATCAGCTTTGACCTTAG
1 CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTG-C-C----TG----TCGGCTTTGACCTTAG
* * * * * *
379061 AGACTGCCTCACCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCCTCAGTTTAC
56 AGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTAAGTCTGC
379126 CTGTC-A
121 CTGTCGA
* * * * * * ***
379132 CCTATGACCCTAGAGAC-TGCTT-CACCTCAAGCCTGCCTATCGGTTTTGACCTTGGAGACTTTT
1 -CTTTGACCCTAGAGACTTTCTTAC-CCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCC
* * * * * ** * *
379195 TTACTCTCAA-TTTGCCTGTCGCCTATGACCTTGGAAACTGCCTCA-CCTCAAGTCTACCTGTCG
64 TCAC-CTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCT-AAGTCTGCCTGTCG
*
379258 G
127 A
*
379259 CTTTGACCCT-GAAGAC-TTCTTACCCTC-AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCT
1 CTTTGACCCTAG-AGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCT
* * ** * *
379321 CACCTCAAGTCTGCCTGTCGGCTTTAACCTTGGAGATTTTCTTATGCTTAGTGTGCCTGTCGA
65 CACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTAAGTCTGCCTGTCGA
** * * * * * *** *
379384 CTTTGACCCTAGAGACTGCCTCA-CGTCAAGTCTGCCTGTCGGCTTTAACTTTGGAGACTTTTTT
1 CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTC
* * * * ** * *
379448 ACCCTC-AGTCTGCTTGTCAGCTTTGACCCTAGA-AGCTGCCTCA-CCTCAAGTCTGCTTGTC-A
66 A-CCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGA-CTTTCTTACCCT-AAGTCTGCCTGTCGA
* ** * *
379509 GCTTTGACCCTAGAGACTTTCCTA-CCTTTAGTCTACCTGTCAGCTTCAGCTTTGACCCTAGAGA
1 -CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTC-G-----GCTTTGACCTTAGAGA
** * * * * ** * * *
379573 CTG-CTGCTTCTCAAGTGTACTTATCGATTTTGACCCTAGAGACTTTCTTACCCCT-AGTCTGCT
59 CTGCCT-CACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTA-CCCTAAGTCTGCC
379636 TGTCGA
122 TGTCGA
** * * * * * * *
379642 CTTTGACTTTAGAGACTGTCTCA-CCTCAAATCTGTCTGTCTGCTTTGACTTTAGAGACT--TTC
1 CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTC
** * * ** * * * *
379704 -TTTC-AGTCTGCCTATCGACTTTGACCTTGGAGACTGCCTCA-TCTCAAGTCTGCCTATCGG
66 ACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCT-AAGTCTGCCTGTCGA
* * * *
379764 TTTTGACCCTATAGAC-TTCTTTACCCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACT
1 CTTTGACCCTAGAGACTTTC-TTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACT
379824 TTTTCACCTT
Statistics
Matches: 1025, Mismatches: 244, Indels: 127
0.73 0.17 0.09
Matches are distributed among these distances:
120 2 0.00
121 2 0.00
122 53 0.05
123 33 0.03
124 11 0.01
125 108 0.11
126 585 0.57
127 27 0.03
128 5 0.00
130 1 0.00
131 4 0.00
132 84 0.08
133 2 0.00
134 4 0.00
135 4 0.00
136 98 0.10
137 2 0.00
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (127 bp):
CTTTGACCCTAGAGACTTTCTTACCCTCAAGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCCTC
ACCTCAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTAAGTCTGCCTGTCGA
Found at i:379004 original size:42 final size:42
Alignment explanation
Indices: 378263--379549 Score: 449
Period size: 42 Copynumber: 30.5 Consensus size: 42
378253 ACCCACCTTC
* * **
378263 TACCCTCAGT-TGTCTGTCGGCTTTGACTATGGAA-ACTTTCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCT-GAAGACTTTCT
**
378304 TACCCTCAGTCTGCCTGTCGACTTTGACCCT-AGAGACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* ** * * * * *
378346 CACTTTAAGTTTGTCTATC-ATCTTTGACCCT-AGAGATTTTCT
1 TACCCTCAGTCTGCCTGTCGA-CTTTGACCCTGA-AGACTTTCT
* * * **
378388 TACCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTCCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
* * * * * * *
378430 CA-TCTCAAGTCTGCCTGTCGCCTTTTACCTTGGAGACTTTTT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
* * * *
378472 TACCCTTAGTCTGCCTATCGACTTTGACCTTGGAGACTTTCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
* **
378514 TACCCTCAGTCTACCTGTCGACTTTGACCCT-AGAGACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* *
378556 CA-CCTCAAATCTGCCTGTC-AGCTTTGACCCT-AGAGACTTTCT
1 TACCCTC-AGTCTGCCTGTCGA-CTTTGACCCTGA-AGACTTTCT
* * * *
378598 TACCTTTAGTCTGCTTGTC-AGCTTTGACCCTGGAGACTACTTCT
1 TACCCTCAGTCTGCCTGTCGA-CTTTGACCCTGAAGACT--TTCT
* * *
378642 T---CTCAAGTCTGCCTATCG-GTTGTGACCCTGGAGACTTTCT
1 TACCCTC-AGTCTGCCTGTCGACTT-TGACCCTGAAGACTTTCT
* * * * *
378682 TACCC-CTAGTTTGCCTGTCGATTTTGACCTTGGAGACTGTCT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
* * * * *
378724 CA-TCTCAAGTTTGCCTGTCGACTTTGA-CCTTAGAGACTACCTCT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGA-AGACT--TTCT
* **
378768 T---CTCAAGTCTGCTTGTCGGTTTTGACCCTTG-AGACTTTCT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCC-TGAAGACTTTCT
* * * * * **
378808 TACCTTCATTCTACTTGTCGACTTTGA-CCTTAGAGACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* * * * *
378850 CA-CCTCAAATCTGCCTGTCGATTTTCACCCT-AGAGACTTTTT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* * * * **
378892 TACCCTCAATCTACTTGTCGACTTTGACTCT-AGAGACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* * * *
378934 CA-CCTCAAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTTT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
**
378976 TACCCTCAGTCTGCCTGTCGACTTTGACCCT-AGAGACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* * * **
379018 CA-CCTCAAGTCCGTCTCAATTTGCTTATC-AGCTTTGA-CCTTAGAGACTGCCT
1 TACCCTC-AGTCTG-C-C----TG----TCGA-CTTTGACCCTGA-AGACTTTCT
* * *
379070 CA-CCTCAAGTTTGCCTGTCGGCTTTGACCCT-AGAGACTTTCT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* * * *
379112 TACCCTCAGTTTACCTGTC-ACCTATGACCCT-AGAGAC-TGCT
1 TACCCTCAGTCTGCCTGTCGA-CTTTGACCCTGA-AGACTTTCT
* * ** * * *
379153 T-CACCTCAAGCCTGCCTATCGGTTTTGACCTTGGAGACTTTTT
1 TAC-CCTC-AGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
* * * * * * **
379196 TACTCTCAATTTGCCTGTCGCCTATGACCTTGGAA-ACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCT-GAAGACTTTCT
* * *
379238 CA-CCTCAAGTCTACCTGTCGGCTTTGACCCTGAAGAC-TTCT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
* **
379279 TACCCTCAGTCTGCCTGTCGGCTTTGACCCT-AGAGACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* * * * * *
379321 CA-CCTCAAGTCTGCCTGTCGGCTTTAACCTTGGAGATTTTCT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
** * * **
379363 TATGCTTAGTGTGCCTGTCGACTTTGACCCT-AGAGACTGCCT
1 TACCCTCAGTCTGCCTGTCGACTTTGACCCTGA-AGACTTTCT
* * * * ** * *
379405 CA-CGTCAAGTCTGCCTGTCGGCTTTAACTTTGGAGACTTTTT
1 TACCCTC-AGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
* **
379447 TACCCTCAGTCTGCTTGTC-AGCTTTGACCCTAGAAG-CTGCCT
1 TACCCTCAGTCTGCCTGTCGA-CTTTGACCCT-GAAGACTTTCT
* * *
379489 CA-CCTCAAGTCTGCTTGTC-AGCTTTGACCCT-AGAGACTTTCC
1 TACCCTC-AGTCTGCCTGTCGA-CTTTGACCCTGA-AGACTTTCT
* * *
379531 TACCTTTAGTCTACCTGTC
1 TACCCTCAGTCTGCCTGTC
379550 AGCTTCAGCT
Statistics
Matches: 934, Mismatches: 230, Indels: 163
0.70 0.17 0.12
Matches are distributed among these distances:
40 14 0.01
41 95 0.10
42 725 0.78
43 49 0.05
44 11 0.01
46 2 0.00
48 2 0.00
50 1 0.00
51 5 0.01
52 30 0.03
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (42 bp):
TACCCTCAGTCTGCCTGTCGACTTTGACCCTGAAGACTTTCT
Found at i:379102 original size:220 final size:220
Alignment explanation
Indices: 378829--379248 Score: 608
Period size: 220 Copynumber: 1.9 Consensus size: 220
378819 TACTTGTCGA
* *
378829 CTTTGACCTTAGAGACTGCCTCACCTCAAATCTGCCTGTCGATTTTCACCCTAGAGACTTTTTTA
1 CTTTGACCTTAGAGACTGCCTCACCTCAAATCTGCCTGTCGACTTTCACCCTAGAGACTTTCTTA
* * * *
378894 CCCTCAATCTACTTGTCGA-CTTTGACTCTAGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTT
66 CCCTCAATCTACCTGTC-ACCTATGACCCTAGAGACTGCCTCACCTCAAGCCTGCCTATCGGCTT
* * *
378958 TGACCCTGAAGACTTTTTTACCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCT
130 TGACCCTGAAGACTTTTTTACCCTCAATCTGCCTGTCGACTATGACCCTAGAAACTGCCTCACCT
379023 CAAGTCCGTCTCAATTTGCTTATCAG
195 CAAGTCCGTCTCAATTTGCTTATCAG
* * * *
379049 CTTTGACCTTAGAGACTGCCTCACCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTA
1 CTTTGACCTTAGAGACTGCCTCACCTCAAATCTGCCTGTCGACTTTCACCCTAGAGACTTTCTTA
* * * *
379114 CCCTCAGTTTACCTGTCACCTATGACCCTAGAGACTGCTTCACCTCAAGCCTGCCTATCGGTTTT
66 CCCTCAATCTACCTGTCACCTATGACCCTAGAGACTGCCTCACCTCAAGCCTGCCTATCGGCTTT
* * * * * * *
379179 GACCTTGGAGACTTTTTTACTCTCAATTTGCCTGTCGCCTATGACCTTGGAAACTGCCTCACCTC
131 GACCCTGAAGACTTTTTTACCCTCAATCTGCCTGTCGACTATGACCCTAGAAACTGCCTCACCTC
379244 AAGTC
196 AAGTC
379249 TACCTGTCGG
Statistics
Matches: 175, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
219 1 0.01
220 174 0.99
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.33
Consensus pattern (220 bp):
CTTTGACCTTAGAGACTGCCTCACCTCAAATCTGCCTGTCGACTTTCACCCTAGAGACTTTCTTA
CCCTCAATCTACCTGTCACCTATGACCCTAGAGACTGCCTCACCTCAAGCCTGCCTATCGGCTTT
GACCCTGAAGACTTTTTTACCCTCAATCTGCCTGTCGACTATGACCCTAGAAACTGCCTCACCTC
AAGTCCGTCTCAATTTGCTTATCAG
Found at i:379140 original size:136 final size:136
Alignment explanation
Indices: 378913--379162 Score: 389
Period size: 136 Copynumber: 1.8 Consensus size: 136
378903 TACTTGTCGA
*
378913 CTTTGACTCTAGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTTTTA
1 CTTTGACTCTAGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTCTTA
* *
378978 CCCTCAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCCTCACCTCAAGTCCGTCTCAATTTGCT
66 CCCTCAGTCTACCTGTCGACTATGACCCTAGAGACTGCCTCACCTCAAGTCCGTCTCAATTTGCT
379043 TATCAG
131 TATCAG
* *
379049 CTTTGAC-CTTAGAGACTGCCTCACCTCAAGTTTGCCTGTCGGCTTTGACCCT-AGAGACTTTCT
1 CTTTGACTC-TAGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTGA-AGACTTTCT
* *
379112 TACCCTCAGTTTACCTGTC-ACCTATGACCCTAGAGACTGCTTCACCTCAAG
64 TACCCTCAGTCTACCTGTCGA-CTATGACCCTAGAGACTGCCTCACCTCAAG
379163 CCTGCCTATC
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
135 3 0.03
136 101 0.97
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.31
Consensus pattern (136 bp):
CTTTGACTCTAGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCCTGAAGACTTTCTTA
CCCTCAGTCTACCTGTCGACTATGACCCTAGAGACTGCCTCACCTCAAGTCCGTCTCAATTTGCT
TATCAG
Found at i:379193 original size:84 final size:84
Alignment explanation
Indices: 379049--379823 Score: 658
Period size: 84 Copynumber: 9.2 Consensus size: 84
379039 TGCTTATCAG
* * *
379049 CTTTGACCTTAGAGACTGCCTCACCTCAAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTA
1 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTA
* *
379114 CCCTCAGTTTACCTGTCAC
66 CCCTCAGTCTGCCTGTCAC
* * * * * * *
379133 CTATGACCCTAGAGACTGCTTCACCTCAAGCCTGCCTATCGGTTTTGACCTTGGAGACTTTTTTA
1 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTA
* * * *
379198 CTCTCAATTTGCCTGTCGC
66 CCCTCAGTCTGCCTGTCAC
* * * * * *
379217 CTATGACCTTGGAAACTGCCTCACCTCAAGTCTACCTGTCGGCTTTGACCCTGAAGAC-TTCTTA
1 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTA
**
379281 CCCTCAGTCTGCCTGTCGG
66 CCCTCAGTCTGCCTGTCAC
* * *
379300 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTAACCTTGGAGATTTTCTTA
1 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTA
** * *
379365 TGCTTAGTGTGCCTGTCGA-
66 CCCTCAGTCTGCCTGTC-AC
* * ** *
379384 CTTTGACCCTAGAGACTGCCTCACGTCAAGTCTGCCTGTCGGCTTTAACTTTGGAGACTTTTTTA
1 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTA
* *
379449 CCCTCAGTCTGCTTGTCAG
66 CCCTCAGTCTGCCTGTCAC
* * * *
379468 CTTTGACCCTAGA-AGCTGCCTCACCTCAAGTCTGCTTGTCAGCTTTGACCCTAGAGACTTTCCT
1 CTTTGACCCTAGAGA-CTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTT
* * *
379532 ACCTTTAGTCTACCTGTCAGCTTC
65 ACCCTCAGTCTGCCTGTCA----C
** * * * * ** *
379556 AGCTTTGACCCTAGAGACTG-CTGCTTCTCAAGTGTACTTATCGATTTTGACCCTAGAGACTTTC
1 --CTTTGACCCTAGAGACTGCCT-CACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC
*
379620 TTACCC-CTAGTCTGCTTGTCGA-
63 TTACCCTC-AGTCTGCCTGTC-AC
** * * * * ** *
379642 CTTTGACTTTAGAGACTGTCTCACCTCAAATCTGTCTGTCTGCTTTGACTTTAGAGACTTTCTT-
1 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTA
*
379706 ---TCAGTCTGCCTATCGA-
66 CCCTCAGTCTGCCTGTC-AC
* * * * * **
379722 CTTTGACCTTGGAGACTGCCTCATCTCAAGTCTGCCTATCGGTTTTGACCCTATAGAC-TTCTTT
1 CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC-TT
*
379786 ACCCTCAAGTCTGCCTATCGA-
65 ACCCTC-AGTCTGCCTGTC-AC
*
379807 CTTTGACCTTAGAGACT
1 CTTTGACCCTAGAGACT
379824 TTTTCACCTT
Statistics
Matches: 560, Mismatches: 109, Indels: 43
0.79 0.15 0.06
Matches are distributed among these distances:
79 3 0.01
80 60 0.11
81 1 0.00
83 71 0.13
84 326 0.58
85 32 0.06
89 2 0.00
90 63 0.11
91 2 0.00
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (84 bp):
CTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTA
CCCTCAGTCTGCCTGTCAC
Found at i:379491 original size:251 final size:250
Alignment explanation
Indices: 378259--379823 Score: 968
Period size: 252 Copynumber: 6.2 Consensus size: 250
378249 GCCTACCCAC
* ** * * ** *
378259 CTTC-TACCCTCAGT-TGTCTGTCGGCTTTGACTATGGAAACTTTCTTACCCTC-AGTCTGCCTG
1 CTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCA-CCTCAAGTCTGCCTG
* ** * * * * * *
378321 TCGACTTTGACCCTAGAGACTGCCTCA-CTTTAAGTTTGTCTATC-ATCTTTGACCCTAGAGATT
65 TCGGCTTTGACCCTAGAGACTTTCTTACCCTT-AGTCTGCCTGTCGA-CTTTGACCCTAGAGACT
** * * *** * *
378384 TTCTTACCCTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTCCCTCATCTCAAGTCTGCCTGT
128 GCCTCA-CCTCAAGTCTGCCTGTCGGCTTTGACTTTGGAGACTTTTTTACCTC-AGTCTGCCTGT
* * * * *** * * * * * *
378448 CGCCTTTTA-CCTTGGAGACTTTTTTACC-CTTAGTCTGCCTATCGACTTTGACCTTGGAGA
191 CGACTTTGACCCTAGAAG-CTGCCTCACCTC-AAGTCTGCCTGTCGGCTTTGACCCTAGAGA
* * *
378508 CTTTCTTACCCTCAGTCTACCTGTCGACTTTGACCCTAGAGACTGCCTCACCTCAAATCTGCCTG
1 C-TTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTG
* * * * *
378573 TCAGCTTTGACCCTAGAGACTTTCTTACCTTTAGTCTGCTTGTC-AGCTTTGACCCTGGAGACTA
65 TCGGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTGTCGA-CTTTGACCCTAGAGACTG
* ** * ** * * *
378637 CTTCTTCTCAAGTCTGCCTATCGG-TTGTGACCCTGGAGACTTTCTTACCCCTAGTTTGCCTGTC
129 CCTCACCTCAAGTCTGCCTGTCGGCTT-TGACTTTGGAGACTTTTTTACCTC-AGTCTGCCTGTC
* * * * * * * *
378701 GATTTTGA-CCTTGGAGACTGTCTCATCTCAAGTTTGCCTGTCGACTTTGACCTTAGAGA
192 GACTTTGACCCTAGAAG-CTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGA
* * * * * * ** * * * *
378760 CTACCT-CTTCTCAAGTCTGCTTGTCGGTTTTGACCCTTGAGACTTTCTTACCTTC-ATTCTACT
1 CTTCTTAC-CCTC-AGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACC-TCAAGTCTGCC
* * ** * * * * *
378823 TGTCGACTTTGACCTTAGAGACTGCCTCA-CCTCAAATCTGCCTGTCGATTTTCACCCTAGAGAC
63 TGTCGGCTTTGACCCTAGAGACTTTCTTACCCT-TAGTCTGCCTGTCGACTTTGACCCTAGAGAC
*** * * * * * * *** * *
378887 TTTTTTACCCTCAA-TCTACTTGTCGACTTTGACTCTAGAGACTGCCTCACCTCAAGTCTGCCTA
127 TGCCTCA-CCTCAAGTCTGCCTGTCGGCTTTGACTTTGGAGACTTTTTTACCTC-AGTCTGCCTG
* *** * *
378951 TCGGCTTTGACCCT-GAAGACTTTTTTACCCTC-AGTCTGCCTGTCGACTTTGACCCTAGAGA
190 TCGACTTTGACCCTAGAAG-CTGCCTCA-CCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGA
* * * * *
379012 CTGCCT-CACCTCAAGTCCGTCTCAATTTGCTTATCAGCTTTGACCTTAGAGACTGCCTCACCTC
1 CTTCTTAC-CCTC-AGTCTG-C-C----TG----TCGGCTTTGACCCTAGAGACTGCCTCACCTC
* * * * *
379076 AAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCCTCAGTTTACCTGTC-ACCTATGAC
54 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTGTCGA-CTTTGAC
* * * * * *
379140 CCTAGAGACTGCTTCACCTCAAGCCTGCCTATCGGTTTTGACCTTGGAGACTTTTTTACTCTCAA
118 CCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACTTTGGAGACTTTTTTAC-CTCAG
* * * * * * *
379205 TTTGCCTGTCGCCTATGACCTTGGAAACTGCCTCACCTCAAGTCTACCTGTCGGCTTTGACCCT-
182 TCTGCCTGTCGACTTTGACCCTAGAAGCTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTA
379269 GAAGA
247 G-AGA
379274 CTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGT
1 CTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGT
* * * * ** *
379339 CGGCTTTAACCTTGGAGATTTTCTTATGCTTAGTGTGCCTGTCGACTTTGACCCTAGAGACTGCC
66 CGGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCC
* * *
379404 TCACGTCAAGTCTGCCTGTCGGCTTTAACTTTGGAGACTTTTTTACCCTCAGTCTGCTTGTC-AG
131 TCACCTCAAGTCTGCCTGTCGGCTTTGACTTTGGAGACTTTTTTA-CCTCAGTCTGCCTGTCGA-
* *
379468 CTTTGACCCTAGAAGCTGCCTCACCTCAAGTCTGCTTGTCAGCTTTGACCCTAGAGA
194 CTTTGACCCTAGAAGCTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGA
* * * * **
379525 CTTTCCTACCTTTAGTCTACCTGTCAGCTTCAGCTTTGACCCTAGAGACTG-CTGCTTCTCAAGT
1 C-TTCTTACCCTCAGTCTGCCTGTC-G-----GCTTTGACCCTAGAGACTGCCT-CACCTCAAGT
* * * * ** * * **
379589 GTACTTATCGATTTTGACCCTAGAGACTTTCTTACCCCTAGTCTGCTTGTCGACTTTGACTTTAG
58 CTGCCTGTCGGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTGTCGACTTTGACCCTAG
* * * * * *
379654 AGACTGTCTCACCTCAAATCTGTCTGTCTGCTTTGACTTTAGAGACTTTCTT---TCAGTCTGCC
123 AGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACTTTGGAGACTTTTTTACCTCAGTCTGCC
* * * * * * *
379716 TATCGACTTTGA-CCTTGGAGACTGCCTCATCTCAAGTCTGCCTATCGGTTTTGACCCTATAGA
188 TGTCGACTTTGACCCTAGAAG-CTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGA
* * *
379779 CTTCTTTACCCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACT
1 CTTC-TTACCCTC-AGTCTGCCTGTCGGCTTTGACCCTAGAGACT
379824 TTTTCACCTT
Statistics
Matches: 1022, Mismatches: 242, Indels: 104
0.75 0.18 0.08
Matches are distributed among these distances:
249 17 0.02
250 4 0.00
251 219 0.21
252 368 0.36
253 32 0.03
254 61 0.06
255 13 0.01
257 2 0.00
258 121 0.12
259 1 0.00
260 1 0.00
261 19 0.02
262 154 0.15
263 10 0.01
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.35
Consensus pattern (250 bp):
CTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGT
CGGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTGCC
TCACCTCAAGTCTGCCTGTCGGCTTTGACTTTGGAGACTTTTTTACCTCAGTCTGCCTGTCGACT
TTGACCCTAGAAGCTGCCTCACCTCAAGTCTGCCTGTCGGCTTTGACCCTAGAGA
Found at i:379550 original size:42 final size:41
Alignment explanation
Indices: 379048--379824 Score: 296
Period size: 42 Copynumber: 18.5 Consensus size: 41
379038 TTGCTTATCA
* * * *
379048 GCTTTGACCTTAGAGACTGCCTCACCTCAAGTTTGCCTGTCG
1 GCTTTGACCCTAGAGACTTCCT-ACCTTAAGTCTGCCTGTCG
* * * * * *
379090 GCTTTGACCCTAGAGACTTTCTTACCCTCAGTTTACCTGTCA
1 GCTTTGACCCTAGAGAC-TTCCTACCTTAAGTCTGCCTGTCG
* * * * * * *
379132 CCTATGACCCTAGAGACTGCTTCACCTCAAGCCTGCCTATCG
1 GCTTTGACCCTAGAGACTTCCT-ACCTTAAGTCTGCCTGTCG
* * * ** * *
379174 GTTTTGACCTTGGAGACTTTTTTACTCTCAA-TTTGCCTGTCG
1 GCTTTGACCCTAGAGAC-TTCCTAC-CTTAAGTCTGCCTGTCG
* * * * * * * *
379216 CCTATGACCTTGGAAACTGCCTCACCTCAAGTCTACCTGTCG
1 GCTTTGACCCTAGAGACTTCCT-ACCTTAAGTCTGCCTGTCG
* * *
379258 GCTTTGACCCT-GAAGACTTCTTACCCTCAGTCTGCCTGTCG
1 GCTTTGACCCTAG-AGACTTCCTACCTTAAGTCTGCCTGTCG
* *
379299 GCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCG
1 GCTTTGACCCTAGAGACTTCCT-ACCTTAAGTCTGCCTGTCG
* * * * * * *
379341 GCTTTAACCTTGGAGATTTTCTTATGCTT-AGTGTGCCTGTCG
1 GCTTTGACCCTAGAGA-CTTCCTA-CCTTAAGTCTGCCTGTCG
* * * *
379383 ACTTTGACCCTAGAGACTGCCTCACGTCAAGTCTGCCTGTCG
1 GCTTTGACCCTAGAGACTTCCT-ACCTTAAGTCTGCCTGTCG
* ** * ** * * * *
379425 GCTTTAACTTTGGAGACTTTTTTACCCTCAGTCTGCTTGTCA
1 GCTTTGACCCTAGAGAC-TTCCTACCTTAAGTCTGCCTGTCG
* * * *
379467 GCTTTGACCCTAGA-AGCTGCCTCACCTCAAGTCTGCTTGTCA
1 GCTTTGACCCTAGAGA-CTTCCT-ACCTTAAGTCTGCCTGTCG
* *
379509 GCTTTGACCCTAGAGACTTTCCTACCTTTAGTCTACCTGTCAG
1 GCTTTGACCCTAGAGAC-TTCCTACCTTAAGTCTGCCTGTC-G
* * * * * * *
379552 CTTCAGCTTTGACCCTAGAGACTGCTGCT-TCTCAAGTGTACTTATCG
1 -----GCTTTGACCCTAGAGACT--TCCTACCTTAAGTCTGCCTGTCG
** * * *
379599 ATTTTGACCCTAGAGACTTTCTTACCCCT-AGTCTGCTTGTCG
1 GCTTTGACCCTAGAGAC-TTCCTA-CCTTAAGTCTGCCTGTCG
* ** * * * *
379641 ACTTTGACTTTAGAGACTGT-CTCACCTCAAATCTGTCTGTCT
1 GCTTTGACCCTAGAGACT-TCCT-ACCTTAAGTCTGCCTGTCG
** * * *
379683 GCTTTGACTTTAGAGACTT--T-CTTTCAGTCTGCCTATCG
1 GCTTTGACCCTAGAGACTTCCTACCTTAAGTCTGCCTGTCG
* * * * * * *
379721 ACTTTGACCTTGGAGACTGCCTCATCTCAAGTCTGCCTATCG
1 GCTTTGACCCTAGAGACTTCCT-ACCTTAAGTCTGCCTGTCG
* * * * *
379763 GTTTTGACCCTATAGACTTCTTTACCCTCAAGTCTGCCTATCG
1 GCTTTGACCCTAGAGACTTC-CTA-CCTTAAGTCTGCCTGTCG
* *
379806 ACTTTGACCTTAGAGACTT
1 GCTTTGACCCTAGAGACTT
379825 TTTCACCTTT
Statistics
Matches: 539, Mismatches: 158, Indels: 75
0.70 0.20 0.10
Matches are distributed among these distances:
38 26 0.05
40 2 0.00
41 59 0.11
42 361 0.67
43 58 0.11
47 2 0.00
48 28 0.05
49 3 0.01
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.34
Consensus pattern (41 bp):
GCTTTGACCCTAGAGACTTCCTACCTTAAGTCTGCCTGTCG
Found at i:379750 original size:80 final size:82
Alignment explanation
Indices: 379601--379823 Score: 218
Period size: 80 Copynumber: 2.7 Consensus size: 82
379591 ACTTATCGAT
* * * * * * *
379601 TTTGACCCTAGAGACTTTCTTACCCCTAGTCTGCTTGTCGACTTTGACTTTAGAGACTGTCTCAC
1 TTTGACCCTAGAGAC-TTCTT-TCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACTGCCTCAC
* * *
379666 CTCAAATCTGTCTGTCTGC
64 CTCAAATCTGCCTATCGGC
** * *
379685 TTTGACTTTAGAGACTT-TCTT-TC-AGTCTGCCTATCGACTTTGACCTTGGAGACTGCCTCATC
1 TTTGACCCTAGAGACTTCT-TTCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACTGCCTCACC
* *
379747 TCAAGTCTGCCTATCGGT
65 TCAAATCTGCCTATCGGC
*
379765 TTTGACCCTATAGACTTCTTTACCCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACT
1 TTTGACCCTAGAGACTTCTTT---CTCAAGTCTGCCTATCGACTTTGACCTTAGAGACT
379824 TTTTCACCTT
Statistics
Matches: 113, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
80 62 0.55
81 2 0.02
82 1 0.01
83 3 0.03
84 15 0.13
85 30 0.27
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (82 bp):
TTTGACCCTAGAGACTTCTTTCTCAAGTCTGCCTATCGACTTTGACCTTAGAGACTGCCTCACCT
CAAATCTGCCTATCGGC
Found at i:380391 original size:3 final size:3
Alignment explanation
Indices: 380375--380426 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
380365 ATTTAACATG
* *
380375 AAT AAT AA- AA- AAT AAT AA- AAT AAT AAA AAT -AT AAT AAT AA- AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
380418 AAT AAT AAT
1 AAT AAT AAT
380427 TGATTAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 10 0.24
3 32 0.76
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:380396 original size:8 final size:8
Alignment explanation
Indices: 380378--380422 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
380368 TAACATGAAT
380378 AATAA-AA
1 AATAATAA
380385 AATAATAA
1 AATAATAA
380393 AATAAT-A
1 AATAATAA
*
380400 AA-AATAT
1 AATAATAA
380407 AATAATAA
1 AATAATAA
*
380415 AACAATAA
1 AATAATAA
380423 TAATTGATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
6 3 0.09
7 10 0.31
8 19 0.59
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
AATAATAA
Found at i:380398 original size:18 final size:19
Alignment explanation
Indices: 380375--380411 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
380365 ATTTAACATG
380375 AATAATAAAAA-ATAATAA
1 AATAATAAAAATATAATAA
380393 AATAATAAAAATATAATAA
1 AATAATAAAAATATAATAA
380412 TAAAACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AATAATAAAAATATAATAA
Found at i:380408 original size:11 final size:10
Alignment explanation
Indices: 380375--380425 Score: 59
Period size: 11 Copynumber: 4.8 Consensus size: 10
380365 ATTTAACATG
380375 AATAATAAAA
1 AATAATAAAA
380385 AATAATAAAA
1 AATAATAAAA
380395 TAATAA-AAATA
1 -AATAATAAA-A
380406 TAATAATAAAA
1 -AATAATAAAA
380417 CAATAATAA
1 -AATAATAA
380426 TTGATTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
10 13 0.35
11 21 0.57
12 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (10 bp):
AATAATAAAA
Found at i:380410 original size:14 final size:14
Alignment explanation
Indices: 380376--380426 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
380366 TTTAACATGA
*
380376 ATAATAAAAAATAAT
1 ATAATAATAAA-AAT
*
380391 AAAATAATAAAAAT
1 ATAATAATAAAAAT
380405 ATAATAATAAAACA-
1 ATAATAATAAAA-AT
380419 ATAATAAT
1 ATAATAAT
380427 TGATTAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 22 0.69
15 10 0.31
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
ATAATAATAAAAAT
Found at i:380931 original size:13 final size:13
Alignment explanation
Indices: 380913--380938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
380903 TACAGCAAGT
380913 ATGTATCGATACA
1 ATGTATCGATACA
380926 ATGTATCGATACA
1 ATGTATCGATACA
380939 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:383187 original size:21 final size:21
Alignment explanation
Indices: 383154--383198 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
383144 TTGCAAGTTG
*
383154 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
383176 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
383196 AAA
1 AAA
383199 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:385022 original size:15 final size:15
Alignment explanation
Indices: 385002--385032 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
384992 TAAAAATGTC
*
385002 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
385017 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
385032 C
1 C
385033 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:387131 original size:13 final size:13
Alignment explanation
Indices: 387113--387138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387103 ACATTTTTCC
387113 TTGTATCGATACA
1 TTGTATCGATACA
387126 TTGTATCGATACA
1 TTGTATCGATACA
387139 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:387283 original size:21 final size:21
Alignment explanation
Indices: 387259--387305 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
387249 AAATCTTTTG
387259 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
387280 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
387300 CAAAAT
1 CAAAAT
387306 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:387302 original size:20 final size:19
Alignment explanation
Indices: 387261--387303 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
387251 ATCTTTTGCA
387261 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
387281 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
387301 AAA
1 AAA
387304 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:389698 original size:13 final size:13
Alignment explanation
Indices: 389680--389705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
389670 TACAGCAAGT
389680 ATGTATCGATACA
1 ATGTATCGATACA
389693 ATGTATCGATACA
1 ATGTATCGATACA
389706 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:391305 original size:23 final size:22
Alignment explanation
Indices: 391263--391306 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
391253 AGGGAGCCAA
* *
391263 AATAAAAAAAAGCAAGAAAAAG
1 AATAAAAAAAAGAAACAAAAAG
391285 AATAAAAAAACAGAAACAAAAA
1 AATAAAAAAA-AGAAACAAAAA
391307 AAACAGCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.80, C:0.07, G:0.09, T:0.05
Consensus pattern (22 bp):
AATAAAAAAAAGAAACAAAAAG
Found at i:391416 original size:20 final size:21
Alignment explanation
Indices: 391391--391429 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
391381 AAAAAAGACA
391391 ACAGC-AAACATCAAGCAAAG
1 ACAGCAAAACATCAAGCAAAG
391411 ACAGCAAAACATCAAGCAA
1 ACAGCAAAACATCAAGCAA
391430 TAGTAGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.26, G:0.13, T:0.05
Consensus pattern (21 bp):
ACAGCAAAACATCAAGCAAAG
Found at i:393976 original size:2 final size:2
Alignment explanation
Indices: 393969--393995 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
393959 AAAACACTAA
393969 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
393996 CATCAATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:396906 original size:2 final size:2
Alignment explanation
Indices: 396901--396935 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
396891 TCTCTCTCTC
396901 TA TA TA TA 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 TA TA TA TA T
396936 TTCTTTTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:401794 original size:3 final size:3
Alignment explanation
Indices: 401786--401817 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
401776 ATTAGATTTG
401786 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
401818 TGGGTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:404703 original size:2 final size:2
Alignment explanation
Indices: 404696--404720 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
404686 AGCGACTGTG
404696 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
404721 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:404725 original size:2 final size:2
Alignment explanation
Indices: 404720--404760 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
404710 ATATATATAT
*
404720 AC AC AC AC AC AC AC AG AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
404761 TATGCAGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.46, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:410580 original size:79 final size:79
Alignment explanation
Indices: 410412--410583 Score: 263
Period size: 79 Copynumber: 2.2 Consensus size: 79
410402 TGTTTCGATT
410412 CCTCTCTTTTTTTATTTCGATTGCTTTTTCTCTTCGCTTGATTCAATTCTTTTTTTTCTTCTTTC
1 CCTC-CTTTTTTTATTTCGATTGCTTTTTCTCTTCGCTTGATTCAATTCTTTTTTTTCTTCTTTC
*
410477 TATTCCTCTTTTCCC
65 TATTCCTCTCTTCCC
* ** * * * *
410492 CATTTTTTTTTTATTTTGATTGCTTTTTCTCTTTGCTTGATTCAATTCTTTTTTTTCTTTTTTTT
1 CCTCCTTTTTTTATTTCGATTGCTTTTTCTCTTCGCTTGATTCAATTCTTTTTTTTCTTCTTTCT
410557 ATTCCTCTCTTCCC
66 ATTCCTCTCTTCCC
410571 CCTCCTTTTTTTA
1 CCTCCTTTTTTTA
410584 GCAGCTGTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 79 0.98
80 2 0.02
ACGTcount: A:0.08, C:0.23, G:0.05, T:0.64
Consensus pattern (79 bp):
CCTCCTTTTTTTATTTCGATTGCTTTTTCTCTTCGCTTGATTCAATTCTTTTTTTTCTTCTTTCT
ATTCCTCTCTTCCC
Found at i:411240 original size:3 final size:3
Alignment explanation
Indices: 411234--411311 Score: 62
Period size: 3 Copynumber: 27.0 Consensus size: 3
411224 TAATTAATTA
411234 ATT ATT ATT ATT ATT -TT ATGT A-T ATAT ATT -TT -TT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT
*
411277 -TT -TT ATT ATT -TA ATT ATTT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT A-TT ATT ATT
411312 CTTTTATTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
2 13 0.20
3 40 0.62
4 11 0.17
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:411273 original size:31 final size:28
Alignment explanation
Indices: 411228--411311 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
411218 TTTTTTTAAT
*
411228 TAATTAATTATTATTATTATTTTATGTATA
1 TAATTATTTATTATTATT-TTTTAT-TATA
* *
411258 TATATTTTTTATTATTATTTTTTATTATT
1 TA-ATTATTTATTATTATTTTTTATTATA
*
411287 TAATTATTTATTATTATTTATTATT
1 TAATTATTTATTATTATTTTTTATT
411312 CTTTTATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 21 0.44
29 5 0.10
30 8 0.17
31 14 0.29
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (28 bp):
TAATTATTTATTATTATTTTTTATTATA
Found at i:411282 original size:7 final size:7
Alignment explanation
Indices: 411260--411343 Score: 57
Period size: 7 Copynumber: 12.0 Consensus size: 7
411250 TATGTATATA
411260 TATTTTT
1 TATTTTT
*
411267 TA-TTAT
1 TATTTTT
411273 TATTTTT
1 TATTTTT
411280 TATTATTT
1 TATT-TTT
* *
411288 AATTATT
1 TATTTTT
*
411295 TA-TTAT
1 TATTTTT
*
411301 TATTTAT
1 TATTTTT
411308 TATTCTTT
1 TATT-TTT
411316 TA-TTTT
1 TATTTTT
*
411322 AATTTTT
1 TATTTTT
*
411329 AATTTTTT
1 TA-TTTTT
411337 TATTTTT
1 TATTTTT
411344 AAATTATCCC
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
6 13 0.21
7 32 0.52
8 16 0.26
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (7 bp):
TATTTTT
Found at i:411282 original size:10 final size:10
Alignment explanation
Indices: 411260--411340 Score: 60
Period size: 10 Copynumber: 8.1 Consensus size: 10
411250 TATGTATATA
411260 TATTTTTTAT
1 TATTTTTTAT
411270 TATTATTTT-T
1 TATT-TTTTAT
*
411280 TATTATTTAAT
1 TATT-TTTTAT
*
411291 TATTTATTAT
1 TATTTTTTAT
*
411301 TATTTATTAT
1 TATTTTTTAT
*
411311 TCTTTTATT-T
1 TATTTT-TTAT
* *
411321 TAATTTTTAA
1 TATTTTTTAT
411331 T-TTTTTTAT
1 TATTTTTTAT
411340 T
1 T
411341 TTTAAATTAT
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
9 9 0.16
10 37 0.65
11 11 0.19
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:411287 original size:38 final size:38
Alignment explanation
Indices: 411241--411316 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
411231 TTAATTATTA
* *
411241 TTATTATTTTATGTATATA-TATTTTTTATTATTATTTT
1 TTATTATTTAAT-TATATATTATTATTTATTATTATTTT
* *
411279 TTATTATTTAATTATTTATTATTATTTATTATTCTTTT
1 TTATTATTTAATTATATATTATTATTTATTATTATTTT
411317 ATTTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 5 0.15
38 28 0.85
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (38 bp):
TTATTATTTAATTATATATTATTATTTATTATTATTTT
Found at i:411297 original size:25 final size:25
Alignment explanation
Indices: 411219--411311 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 25
411209 TCGATCTTCT
*
411219 TTTTTTAATTAATTAATTA-TTATTA
1 TTTTTT-ATTATTTAATTATTTATTA
* *
411244 TTATTTTATGTATATATATTTTTTATTATTA
1 TT-TTTTAT-TAT-T-TA-ATTAT-TTATTA
411275 TTTTTTATTATTTAATTATTTATTA
1 TTTTTTATTATTTAATTATTTATTA
*
411300 TTATTTATTATT
1 TTTTTTATTATT
411312 CTTTTATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
25 21 0.38
26 9 0.16
27 3 0.05
28 3 0.05
29 5 0.09
30 6 0.11
31 8 0.15
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTTTTATTATTTAATTATTTATTA
Found at i:411840 original size:5 final size:5
Alignment explanation
Indices: 411830--411873 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
411820 GACATTTGAA
* *
411830 AATTT AATTT AATTT ATTTT AATTTT AATTTT AATTT TATTT AA
1 AATTT AATTT AATTT AATTT AA-TTT AA-TTT AATTT AATTT AA
411874 AATATTGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 23 0.68
6 11 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
AATTT
Found at i:411856 original size:6 final size:6
Alignment explanation
Indices: 411832--411868 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
411822 CATTTGAAAA
411832 TTTAA- TTTAA- TTT-AT TTTAAT TTTAAT TTTAAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
411869 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 1 0.03
5 11 0.37
6 18 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:412415 original size:18 final size:17
Alignment explanation
Indices: 412387--412421 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
412377 TATTTATTTA
*
412387 TTTATTTAAATTTAAAT
1 TTTATTTAAATATAAAT
412404 TTTATTTAAAATATAAAT
1 TTTATTT-AAATATAAAT
412422 AAGTAACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTATTTAAATATAAAT
Found at i:412724 original size:155 final size:156
Alignment explanation
Indices: 412525--412884 Score: 440
Period size: 155 Copynumber: 2.3 Consensus size: 156
412515 GTTTTAATGC
* * * * ** * * *
412525 AAAATTACCAAAATCCCCATAAGATATACCATCGACATGGAAGTATCTTAGTAATCC-TAAAGGA
1 AAAATTACAAAAATACCCTTAAGGTATACTTTCGATATGAAAGTATCTCAGTAA-CCTTAAAGGA
* * *
412589 CTTAAAAATGATAATAAATAGGATGAACCTATTCTAAATACACACATTTGACATAA-ATGCATC-
65 CTCAAAAATGATAATAAATAGGATGAACCTATCCTAAATACACACATTCGACATAAGA-GCATCT
* * *
412652 C-AGTGATAACCTAGGATTTGATTTTAAA
129 CGA-TGACAACCTAAGACTTGATTTTAAA
* *
412680 AAAATTACAAAAATGCCCTTAAGGTATACTTTCGATATGAAAGTATCTCGGTAACCTTAAAGGAC
1 AAAATTACAAAAATACCCTTAAGGTATACTTTCGATATGAAAGTATCTCAGTAACCTTAAAGGAC
* * * * *
412745 TCAAAAATGATAGTAAATGGGATGAACCTATCCTAAATGCATACCTTCGACATAAGAGCATCTCG
66 TCAAAAATGATAATAAATAGGATGAACCTATCCTAAATACACACATTCGACATAAGAGCATCTCG
*
412810 ATGACAACCTAAGACTTGGTTTTAAA
131 ATGACAACCTAAGACTTGATTTTAAA
* *
412836 AAAATTACAAAAATACTCTTAGGGTATACTTTCGATATGAAAGTATCTC
1 AAAATTACAAAAATACCCTTAAGGTATACTTTCGATATGAAAGTATCTC
412885 GATATCTCTA
Statistics
Matches: 176, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
154 2 0.01
155 104 0.59
156 69 0.39
157 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (156 bp):
AAAATTACAAAAATACCCTTAAGGTATACTTTCGATATGAAAGTATCTCAGTAACCTTAAAGGAC
TCAAAAATGATAATAAATAGGATGAACCTATCCTAAATACACACATTCGACATAAGAGCATCTCG
ATGACAACCTAAGACTTGATTTTAAA
Found at i:414570 original size:19 final size:19
Alignment explanation
Indices: 414525--414613 Score: 100
Period size: 19 Copynumber: 4.9 Consensus size: 19
414515 CTGCCAGTTT
**
414525 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
414546 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
414565 CATGTATCGATAC-----A
1 CATGTATCGATACAATGAA
414579 -ATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
414597 CATGTATCGATACAATG
1 CATGTATCGATACAATG
414614 TATCAAAACA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.20
14 1 0.02
18 1 0.02
19 31 0.52
21 15 0.25
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:414588 original size:32 final size:32
Alignment explanation
Indices: 414547--414643 Score: 149
Period size: 32 Copynumber: 3.0 Consensus size: 32
414537 CAATTTGTCC
414547 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAATGAACATGTATCGATACA
414579 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAATGAACATGTATCGATACA
* * * *
414611 ATGTATCAAAACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAATG-AACATGTATCGATACA
414644 TCTGGGTGTG
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 45 0.75
33 15 0.25
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAATGAACATGTATCGATACA
Found at i:414617 original size:13 final size:13
Alignment explanation
Indices: 414566--414594 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
414556 TACAATGAAC
414566 ATGTATCGATACA
1 ATGTATCGATACA
414579 ATGTATCGATACA
1 ATGTATCGATACA
414592 ATG
1 ATG
414595 AACATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:415406 original size:29 final size:29
Alignment explanation
Indices: 415344--415408 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
415334 ACAAATTTTG
* *
415344 CAAAAATTATAAATTAGTCCTTAAATTCT
1 CAAAAATTATAAATAAGTCCTTAAAATCT
*
415373 CAAAAATTATAAA-AAGGTCCTTAAAATGT
1 CAAAAATTATAAATAA-GTCCTTAAAATCT
*
415402 GAAAAAT
1 CAAAAAT
415409 GTCTAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.31
Consensus pattern (29 bp):
CAAAAATTATAAATAAGTCCTTAAAATCT
Found at i:416172 original size:10 final size:10
Alignment explanation
Indices: 416140--416172 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
416130 GTTATTTCCA
416140 TTTTTTTCTT
1 TTTTTTTCTT
*
416150 TTCTTTTCTT
1 TTTTTTTCTT
416160 TTTTTTTCTT
1 TTTTTTTCTT
416170 TTT
1 TTT
416173 ATTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:416895 original size:155 final size:154
Alignment explanation
Indices: 416714--417027 Score: 368
Period size: 155 Copynumber: 2.0 Consensus size: 154
416704 AATATGGGTT
* * *
416714 AAACTCTGTATCTCGGTAGCAGAAAAAATGTTTAAA-CTCATAAAATAAATTAAACTTTT-TAAA
1 AAACTCCGTATCTCGGTAACAGAAAAAAT-TCTAAAGCTCATAAAATAAATTAAA-TTTTGTAAA
* * *
416777 ATTGATTTAATATGAATTATAA-AATAATATTTG-AAGAATTTTAAAAATTATAAACTTAAAAAA
64 ACTAATTTAATATGAATTA-AACAATAATA-TCGAAAGAATTTTAAAAATTATAAA-TTAAAAAA
416840 AATCATAAC-GAAAAAATTTACAGAGTAGA
126 AATCAT-ACTGAAAAAATTTACAGAGTAGA
* * * *
416869 AAACTCCGTATCTTGGTAATAGAAAAAATTCTAAAGCTCATAAAATAAATTTAATTTTGTTAAAC
1 AAACTCCGTATCTCGGTAACAGAAAAAATTCTAAAGCTCATAAAATAAATTAAATTTTGTAAAAC
* * * ** *
416934 TAATTTAATGTGAATTAAACAATAATATCGAAATAATTTTGAAAATTATAAATTTTAAAAAATCC
66 TAATTTAATATGAATTAAACAATAATATCGAAAGAATTTTAAAAATTATAAATTAAAAAAAATCA
* * *
416999 TACTGGAGAAATTTACGGAGTAGA
131 TACTGAAAAAATTTACAGAGTAGA
417023 AAACT
1 AAACT
417028 TCATATTTTG
Statistics
Matches: 135, Mismatches: 19, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
153 2 0.01
154 46 0.34
155 87 0.64
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.33
Consensus pattern (154 bp):
AAACTCCGTATCTCGGTAACAGAAAAAATTCTAAAGCTCATAAAATAAATTAAATTTTGTAAAAC
TAATTTAATATGAATTAAACAATAATATCGAAAGAATTTTAAAAATTATAAATTAAAAAAAATCA
TACTGAAAAAATTTACAGAGTAGA
Found at i:418290 original size:43 final size:42
Alignment explanation
Indices: 418132--418306 Score: 147
Period size: 43 Copynumber: 4.0 Consensus size: 42
418122 AACAAAGGGT
* *
418132 AAGATGTTGGCCAAGGCGAAACCATACGAACCAACAAGTTAGTTAGAA
1 AAGATGTTGGCC-GGGCGAAACCATACGTACCAAC-A---AGTTAG-A
** * ** *
418180 AAGA-GTTGGCCGGAATGAAACCATACATACCAATGAGTTAAA
1 AAGATGTTGGCCGG-GCGAAACCATACGTACCAACAAGTTAGA
*
418222 AAGATGTTGGCTGGGAC-AAAGCCATACGTACCAACAAGTTAGA
1 AAGATGTTGGCCGGG-CGAAA-CCATACGTACCAACAAGTTAGA
* *
418265 AAGATGTTGGTCGAGGCGAAACCATACCTACCAACAAGTTAG
1 AAGATGTTGGCCG-GGCGAAACCATACGTACCAACAAGTTAG
418307 GAGGGTTGAC
Statistics
Matches: 103, Mismatches: 18, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
42 8 0.08
43 63 0.61
44 5 0.05
46 1 0.01
47 22 0.21
48 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.18
Consensus pattern (42 bp):
AAGATGTTGGCCGGGCGAAACCATACGTACCAACAAGTTAGA
Found at i:418372 original size:40 final size:40
Alignment explanation
Indices: 418310--418691 Score: 243
Period size: 40 Copynumber: 9.5 Consensus size: 40
418300 AAGTTAGGAG
* * * * *
418310 GGTTGACCATGGCAAAGCCGATAAAGTCAACTAGTTAGAA
1 GGTTGGCCAAGGCAAAACCGATAAAGTCAACGAGTTAAAA
* * * *
418350 GGTTGGCCAAGACAAAAACGATAAAGCCAACGGGTTAGAAA
1 GGTTGGCCAAGGCAAAACCGATAAAGTCAACGAGTTA-AAA
** ** * *
418391 GGTTGATC-AGGTGAAATCGATAAAGCCAAC-AGGTTAAAAA
1 GGTTGGCCAAGGCAAAACCGATAAAGTCAACGA-GTT-AAAA
* * * * * *
418431 GGTTGACC-AGAGCGAAACCAATAAAGTCGACCAATTAAAA
1 GGTTGGCCAAG-GCAAAACCGATAAAGTCAACGAGTTAAAA
* * * *
418471 GGTTGGCTATGGCAAAACCGATAAAGTCAACCAATTAAAA
1 GGTTGGCCAAGGCAAAACCGATAAAGTCAACGAGTTAAAA
* * * * * *
418511 AGTTGGCCAGGGCGAAACCAATAAAGCCAACGGGTTATAAA
1 GGTTGGCCAAGGCAAAACCGATAAAGTCAACGAGTTA-AAA
** ** * * *
418552 GGTTAACCAAGATAAAATCGATAAAGTCAACTAATTAAAA
1 GGTTGGCCAAGGCAAAACCGATAAAGTCAACGAGTTAAAA
* * *
418592 GGTTGGCCAAGGTAAAACCGATAAAGAT-AACGGGTTAGAAG
1 GGTTGGCCAAGGCAAAACCGATAAAG-TCAACGAGTTA-AAA
* * * *
418633 GGTTGACCAGGGCAAAACCGATAAAGTCACCGAATT-AAA
1 GGTTGGCCAAGGCAAAACCGATAAAGTCAACGAGTTAAAA
* *
418672 GGTTGGCTAGGGCAAAACCG
1 GGTTGGCCAAGGCAAAACCG
418692 GGTTGACTAG
Statistics
Matches: 264, Mismatches: 68, Indels: 21
0.75 0.19 0.06
Matches are distributed among these distances:
39 20 0.08
40 158 0.60
41 85 0.32
42 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (40 bp):
GGTTGGCCAAGGCAAAACCGATAAAGTCAACGAGTTAAAA
Found at i:418387 original size:81 final size:81
Alignment explanation
Indices: 418310--418678 Score: 316
Period size: 81 Copynumber: 4.6 Consensus size: 81
418300 AAGTTAGGAG
* * * * *
418310 GGTTGACCATGGCAAAGCCGATAAAGTCAACTAGTTAGAAGGTTGGCCAAGACAAAAACGATAAA
1 GGTTGACCATGGCAAAACCGATAAAGTCAACTAATTAAAAGGTTGGCCAAGACAAAACCAATAAA
418375 GCCAACGGGTTAGAAA
66 GCCAACGGGTTAGAAA
* ** * * * * *
418391 GGTTGATCA-GGTGAAATCGATAAAGCCAAC-AGGTTAAAAAGGTTGACC-AGAGCGAAACCAAT
1 GGTTGACCATGGCAAAACCGATAAAGTCAACTA-ATT-AAAAGGTTGGCCAAGA-CAAAACCAAT
* * ***
418453 AAAGTCGACCAATTA-AAA
63 AAAGCCAACGGGTTAGAAA
* * * * * * *
418471 GGTTGGCTATGGCAAAACCGATAAAGTCAACCAATTAAAAAGTTGGCCAGGGCGAAACCAATAAA
1 GGTTGACCATGGCAAAACCGATAAAGTCAACTAATTAAAAGGTTGGCCAAGACAAAACCAATAAA
*
418536 GCCAACGGGTTATAAA
66 GCCAACGGGTTAGAAA
* * ** * ** *
418552 GGTTAACCAAGATAAAATCGATAAAGTCAACTAATTAAAAGGTTGGCCAAGGTAAAACCGATAAA
1 GGTTGACCATGGCAAAACCGATAAAGTCAACTAATTAAAAGGTTGGCCAAGACAAAACCAATAAA
** *
418617 GATAACGGGTTAGAAG
66 GCCAACGGGTTAGAAA
* * *
418633 GGTTGACCAGGGCAAAACCGATAAAGTCACCGAATT-AAAGGTTGGC
1 GGTTGACCATGGCAAAACCGATAAAGTCAACTAATTAAAAGGTTGGC
418679 TAGGGCAAAA
Statistics
Matches: 224, Mismatches: 57, Indels: 15
0.76 0.19 0.05
Matches are distributed among these distances:
79 1 0.00
80 71 0.32
81 151 0.67
82 1 0.00
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18
Consensus pattern (81 bp):
GGTTGACCATGGCAAAACCGATAAAGTCAACTAATTAAAAGGTTGGCCAAGACAAAACCAATAAA
GCCAACGGGTTAGAAA
Found at i:418473 original size:121 final size:121
Alignment explanation
Indices: 418330--418658 Score: 338
Period size: 121 Copynumber: 2.7 Consensus size: 121
418320 GGCAAAGCCG
* * * * *
418330 ATAAAGTCAACTAGTTAGAAGGTTGGCCAAGACAAAAACGATAAAGCCAACGGGTTAGAAAGGTT
1 ATAAAGTCAACTAATTAAAAGGTTGGCCAAGGCAAAACCGATAAAGACAACGGGTTAGAAAGGTT
* * * * * *
418395 GATCAGGTGAAATCGATAAAGCCAACAGGTTAAAAAGGTTGACC-AGAGCGAAACCA
66 GACCAGGCGAAACCAATAAAGCCAACAGGTTAAAAAGGTTAACCAAGA-CAAAACCA
* * * * * *** *
418451 ATAAAGTCGACCAATTAAAAGGTTGGCTATGGCAAAACCGATAAAGTCAACCAATTA-AAAAGTT
1 ATAAAGTCAACTAATTAAAAGGTTGGCCAAGGCAAAACCGATAAAGACAACGGGTTAGAAAGGTT
* * * * * *
418515 GGCCAGGGCGAAACCAATAAAGCCAACGGGTTATAAAGGTTAACCAAGATAAAATCG
66 GACCA-GGCGAAACCAATAAAGCCAACAGGTTAAAAAGGTTAACCAAGACAAAACCA
* * *
418572 ATAAAGTCAACTAATTAAAAGGTTGGCCAAGGTAAAACCGATAAAGATAACGGGTTAGAAGGGTT
1 ATAAAGTCAACTAATTAAAAGGTTGGCCAAGGCAAAACCGATAAAGACAACGGGTTAGAAAGGTT
* *
418637 GACCAGGGCAAAACCGATAAAG
66 GACCA-GGCGAAACCAATAAAG
418659 TCACCGAATT
Statistics
Matches: 165, Mismatches: 40, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
120 9 0.05
121 129 0.78
122 27 0.16
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (121 bp):
ATAAAGTCAACTAATTAAAAGGTTGGCCAAGGCAAAACCGATAAAGACAACGGGTTAGAAAGGTT
GACCAGGCGAAACCAATAAAGCCAACAGGTTAAAAAGGTTAACCAAGACAAAACCA
Found at i:419368 original size:92 final size:88
Alignment explanation
Indices: 419229--419486 Score: 243
Period size: 90 Copynumber: 2.9 Consensus size: 88
419219 ACTAATGTCA
*
419229 TCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGTGGCAAAAATGCATA
1 TCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGTGGC--AAACGCATA
*
419294 TGAAACGATGCAAATGCCAATATAG
64 TGAAACAATGCAAATGCCAATATAG
* * *
419319 TCTAATGGTGT-GATGTGCATGAAACGATATGCAAATGCAAGCATCAATAAAGTGGCAAACGCCT
1 TCTAAT-GTGTAGATATACATGAAAC-A-ATGCAAATGCAAGCATCAATAAAGTGGCAAACGCAT
* * *
419383 ATGAAACAATGCAAATACTAATGTCATG
63 ATGAAACAATGCAAATGCCAATAT-A-G
* * * ** * * * ** *
419411 TATAA--TGCAAATGCACATGAAACGATGTAAATGTAAGCATCTGTAAAGTGGCAAATGCATATG
1 TCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGTGGCAAACGCATATG
* *
419474 GAATAATGCAAAT
66 AAACAATGCAAAT
419487 ACTAATGTCA
Statistics
Matches: 140, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
88 44 0.31
89 2 0.01
90 55 0.39
91 6 0.04
92 33 0.24
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (88 bp):
TCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGTGGCAAACGCATATG
AAACAATGCAAATGCCAATATAG
Found at i:419398 original size:90 final size:89
Alignment explanation
Indices: 419229--419398 Score: 245
Period size: 90 Copynumber: 1.9 Consensus size: 89
419219 ACTAATGTCA
*
419229 TCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGTGGCAAAAATGCATA
1 TCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGTGGC-AAAACGCATA
*
419294 TGAAACGATGCAAATGCCAATATAG
65 TGAAACAATGCAAATGCCAATATAG
* * *
419319 TCTAATGGTGT-GATGTGCATGAAACGATATGCAAATGCAAGCATCAATAAAGTGGC-AAACGCC
1 TCTAAT-GTGTAGATATACATGAAAC-A-ATGCAAATGCAAGCATCAATAAAGTGGCAAAACGCA
419382 TATGAAACAATGCAAAT
63 TATGAAACAATGCAAAT
419399 ACTAATGTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
90 39 0.54
91 5 0.07
92 28 0.39
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.22
Consensus pattern (89 bp):
TCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGTGGCAAAACGCATAT
GAAACAATGCAAATGCCAATATAG
Found at i:419421 original size:44 final size:45
Alignment explanation
Indices: 419366--419497 Score: 123
Period size: 44 Copynumber: 3.0 Consensus size: 45
419356 CAAGCATCAA
*
419366 TAAAGTGGCAAACGCCTATGAAACAATGCAAATACTAATGTCATG
1 TAAAGTGGCAAATGCCTATGAAACAATGCAAATACTAATGTCATG
* * *
419411 TATAA-T-GCAAATGCAC-ATGAAACGATGTAAAT-GTAA-G-CATCTG
1 TA-AAGTGGCAAATGC-CTATGAAACAATGCAAATACTAATGTCA--TG
* * *
419454 TAAAGTGGCAAATGCATATGGAATAATGCAAATACTAATGTCAT
1 TAAAGTGGCAAATGCCTATGAAACAATGCAAATACTAATGTCAT
419498 CTAACATGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
41 2 0.03
42 3 0.04
43 8 0.12
44 41 0.61
45 8 0.12
46 3 0.04
47 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (45 bp):
TAAAGTGGCAAATGCCTATGAAACAATGCAAATACTAATGTCATG
Found at i:419537 original size:88 final size:87
Alignment explanation
Indices: 419215--419721 Score: 369
Period size: 88 Copynumber: 5.7 Consensus size: 87
419205 AAAACAAGAT
* * *
419215 AAATACTAATGTCATCTAATGTGTAGATATACATGAAACAATGCAAATGCAAGCATCAATAAAGT
1 AAATACTAATGTCATCTAA-ATGTAGATATGCATGAAACGATGCAAATGCAAGCATCAATAAAGT
*
419280 GGCAAAAATGCATATGAAACGATGC
65 GGC--AAATGCATATGAAACAATGC
* * * * *
419305 AAATGCCAATAT-AGTCT-AATGGTGTGATGTGCATGAAACGATATGCAAATGCAAGCATCAATA
1 AAATACTAATGTCA-TCTAAAT-GT-AGATATGCATGAAACG--ATGCAAATGCAAGCATCAATA
* *
419368 AAGTGGCAAACGCCTATGAAACAATGC
61 AAGTGGCAAATGCATATGAAACAATGC
* * * * **
419395 AAATACTAATGTCATGTATAATGCA-A-ATGCACATGAAACGATGTAAATGTAAGCATCTGTAAA
1 AAATACTAATGTCATCTA-AATGTAGATATG--CATGAAACGATGCAAATGCAAGCATCAATAAA
* *
419458 GTGGCAAATGCATATGGAATAATGC
63 GTGGCAAATGCATATGAAACAATGC
* * ** * *
419483 AAATACTAATGTCATCTAACATGTAGATATGCATGGAATGATGCAACCGCAAGCAGCAATCAAGT
1 AAATACTAATGTCATCTAA-ATGTAGATATGCATGAAACGATGCAAATGCAAGCATCAATAAAGT
* * * ** *
419548 AGCAAATGCTTATAAAATGATGT
65 GGCAAATGCATATGAAACAATGC
* * * * * * * * * * *
419571 ATATGCTAATGCCATCTAAAGTGCAAATGTGCATGAAACGATGCAAAGGTAGGCATCCATAAAGG
1 AAATACTAATGTCATCTAAA-TGTAGATATGCATGAAACGATGCAAATGCAAGCATCAATAAAGT
* ** *
419636 GGCAAATGCATATGCAATGATAC
65 GGCAAATGCATATGAAACAATGC
* * * * *
419659 AAATACCATTGTCATCTAAGATGCA-A-ATGTAAGTGAAACGATGCAAACGCAAGCATCAATAAA
1 AAATACTAATGTCATCTAA-ATGTAGATATG-CA-TGAAACGATGCAAATGCAAGCATCAATAAA
419722 ATAGAAAATG
Statistics
Matches: 323, Mismatches: 77, Indels: 36
0.74 0.18 0.08
Matches are distributed among these distances:
86 2 0.01
87 4 0.01
88 213 0.66
89 7 0.02
90 64 0.20
91 2 0.01
92 31 0.10
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (87 bp):
AAATACTAATGTCATCTAAATGTAGATATGCATGAAACGATGCAAATGCAAGCATCAATAAAGTG
GCAAATGCATATGAAACAATGC
Found at i:423274 original size:19 final size:19
Alignment explanation
Indices: 423250--423310 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
423240 TTGGGTTAAA
*
423250 ATTCAAAATGTATCAATAC
1 ATTCAAAATGTATCGATAC
423269 ATTCAAAATGTATCGATAC
1 ATTCAAAATGTATCGATAC
**
423288 AATGAAAAATGTATCGATAC
1 -ATTCAAAATGTATCGATAC
423308 ATT
1 ATT
423311 TTCATTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (19 bp):
ATTCAAAATGTATCGATAC
Found at i:423298 original size:20 final size:20
Alignment explanation
Indices: 423254--423308 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
423244 GTTAAAATTC
* **
423254 AAAATGTATCAATAC-ATTC
1 AAAATGTATCGATACAATGA
423273 AAAATGTATCGATACAATGA
1 AAAATGTATCGATACAATGA
423293 AAAATGTATCGATACA
1 AAAATGTATCGATACA
423309 TTTTCATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (20 bp):
AAAATGTATCGATACAATGA
Found at i:423377 original size:21 final size:20
Alignment explanation
Indices: 423347--423399 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
423337 GAGATGGTCT
*
423347 TGTATTGATACATTTCAAACA
1 TGTATCGATACA-TTCAAACA
***
423368 TGTATCGATACATTCATTTA
1 TGTATCGATACATTCAAACA
423388 TGTATCGATACA
1 TGTATCGATACA
423400 GTACCTATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCAAACA
Found at i:425001 original size:27 final size:27
Alignment explanation
Indices: 424962--425031 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
424952 TTTAAAAACG
*
424962 GGGTTGAAGTATCCCCTCGAAAGAAT-
1 GGGTTGGAGTATCCCCTCGAAAGAATA
**
424988 GTGGTTGGAGTATCGTCTCGAAAGAATA
1 G-GGTTGGAGTATCCCCTCGAAAGAATA
425016 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
425032 GATGAATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 35 0.95
28 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCGAAAGAATA
Found at i:427973 original size:61 final size:61
Alignment explanation
Indices: 427908--428347 Score: 233
Period size: 61 Copynumber: 7.6 Consensus size: 61
427898 GATGAGAAGA
* * *
427908 GTGCCAA-AGTGTTGATTCAAGGTCAACGACGTTGGACTT-AAGGATGTGAAGAATGATAAAG
1 GTGCCAATA-TGTTGATTCAAGGCCAACGACATTGGACTTGAA-GATGAGAAGAATGATAAAG
* * * * * *
427969 GTGCCAATATATTGATTCATA-GCCAGCAATATTGGGCTTGAAGATGAGAAGAATGATAAGG
1 GTGCCAATATGTTGATTCA-AGGCCAACGACATTGGACTTGAAGATGAGAAGAATGATAAAG
* * * *
428030 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGAT-ACGAA-AA--AT----
1 GTGCCAATATGTTGATTCAAGGCCAACGACATTGGACTTGAAGATGA-GAAGAATGATAAAG
* * * *
428084 GT--CAATGTGCTGATTCACGGCCAACGATATTAGG-CTTGAAGAT--G-AGAA-G---AA-
1 GTGCCAATATGTTGATTCAAGGCCAACGACATT-GGACTTGAAGATGAGAAGAATGATAAAG
* * * * *
428135 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTT----A-G-G--G-ATGTTAAAG
1 GTGCCAATATGTTGATTCAAGGCCAACGACATTGGACTTGAAGATGAGAAGAATGATAAAG
* * * * * * *
428186 ATGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGAAGGATGATAAAG
1 GTGCCAATATGTTGATTCAAGGCCAACGACATTGGACTTGAAGATG-AGAAGAATGATAAAG
* * * * * * * *
428248 GTGCCAATATGCTAATTCAAGGCTAGCGATATTGGACTTAAAGGTGAGAAGGATGATAAAG
1 GTGCCAATATGTTGATTCAAGGCCAACGACATTGGACTTGAAGATGAGAAGAATGATAAAG
* * * *
428309 GTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTT
1 GTGCCAATATGTTGATTCAAGGCCAACGACATTGGACTT
428348 AAAGGTGCCA
Statistics
Matches: 318, Mismatches: 31, Indels: 60
0.78 0.08 0.15
Matches are distributed among these distances:
46 1 0.00
47 2 0.01
48 2 0.01
49 1 0.00
50 6 0.02
51 2 0.01
52 98 0.31
53 2 0.01
54 2 0.01
56 1 0.00
57 1 0.00
58 2 0.01
59 1 0.00
60 4 0.01
61 140 0.44
62 53 0.17
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (61 bp):
GTGCCAATATGTTGATTCAAGGCCAACGACATTGGACTTGAAGATGAGAAGAATGATAAAG
Found at i:428120 original size:52 final size:52
Alignment explanation
Indices: 428031--428232 Score: 235
Period size: 52 Copynumber: 3.9 Consensus size: 52
428021 ATGATAAGGG
*
428031 TGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGAT-ACGAAAAA
1 TGCCAATGTGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGA-GAAAAA
* * * * *
428083 TGTCAATGTGCTGATTCACGGCCAACGATATTAGGCTTGAAGATGAGAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAA
* * ** ** *
428135 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAGGGATGTTAAAGA
1 TGCCAATGTGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAA
* * * *
428187 TGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATGA
1 TGCCAATGTGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGA
428233 AGAAGGATGA
Statistics
Matches: 124, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
52 123 0.99
53 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (52 bp):
TGCCAATGTGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAA
Found at i:428348 original size:61 final size:62
Alignment explanation
Indices: 428175--428354 Score: 299
Period size: 61 Copynumber: 2.9 Consensus size: 62
428165 TTGGGCTTAG
* * * * *
428175 GGATGTTAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGATGAAGAA
1 GGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGAAGAA
*
428237 GGATGATAAAGGTGCCAATATGCTAATTCAAGGCTAGCGATATTGGACTTAAAGGTG-AGAA
1 GGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGAAGAA
428298 GGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTG
1 GGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTG
428355 CCAATGTGCT
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
61 60 0.54
62 51 0.46
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (62 bp):
GGATGATAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGAAGAA
Found at i:428365 original size:43 final size:43
Alignment explanation
Indices: 428304--428391 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
428294 AGAAGGATGA
* * *
428304 TAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGACT
*
428347 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACACTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGACT
428390 TA
1 TA
428392 GAAAGAGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGACT
Found at i:428373 original size:21 final size:20
Alignment explanation
Indices: 428306--428373 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
428296 AAGGATGATA
428306 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
* *
428327 AAGGCTAGCGATATTG--GACTTA
1 AAGG-T-GCCA-ATTGCTGA-TTC
428349 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
428370 AAGG
1 AAGG
428374 CCAGCGACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
AAGGTGCCAATTGCTGATTC
Found at i:428495 original size:32 final size:32
Alignment explanation
Indices: 428459--428655 Score: 168
Period size: 32 Copynumber: 6.2 Consensus size: 32
428449 TAGAAGGAGA
428459 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* * * *
428491 TGCCACCGACATATGTGGGC-TTT-AAAGAAGAT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAG--GGT
* ** * *
428523 TGCCACCGACTTGTGT-GGCCCTTAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* ** * **
428554 TGCCACCAGCTCATGCGGGCTTCAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
428586 TGCCACTAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
428618 CGCCACCAACTTGTGTGGGC-TTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTG-AAAGGGT
428650 TGCCAC
1 TGCCAC
428656 TAGCTTCTAT
Statistics
Matches: 128, Mismatches: 31, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
30 4 0.03
31 22 0.17
32 99 0.77
33 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
Found at i:428615 original size:63 final size:65
Alignment explanation
Indices: 428459--428625 Score: 182
Period size: 63 Copynumber: 2.6 Consensus size: 65
428449 TAGAAGGAGA
* * *
428459 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACC-GACATATGTGGGCTTTAAAGAAGAT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAGACATATGCGGGCTTCAAAGAAGAT
* * * * *
428523 TGCCACCGACTTGTGTGGCCCTTA-AAAAGGTTGCCACCAG-C-TCATGCGGGCTTCAGAA-AGG
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAGACAT-ATGCGGGCTTCA-AAGAAG
*
428584 GT
64 AT
* *
428586 TGCCACTAACTTGTGTGGGCTTTAGAAAGGGTCGCCACCA
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCA
428626 ACTTGTGTGG
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
62 1 0.01
63 47 0.56
64 36 0.43
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (65 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAGACATATGCGGGCTTCAAAGAAGAT
Found at i:428623 original size:95 final size:96
Alignment explanation
Indices: 428483--428660 Score: 234
Period size: 95 Copynumber: 1.9 Consensus size: 96
428473 GTGGGCTTTT
* * *
428483 GAAAGGGTTGCCACCGACATATGTGGGCTTTAAAGAAGATTGCCACCGACTTGTGTGGCCCTT-A
1 GAAAGGGTTGCCACCAACATATGTGGGCTTTAAAGAAGATCGCCACCAACTTGTGTGGCCCTTGA
428547 AAAAGGTTGCCACCAGCTCATGCGGGCTTCA
66 AAAAGGTTGCCACCAGCTCATGCGGGCTTCA
* * * * * * *
428578 GAAAGGGTTGCCACTAACTTGTGTGGGCTTTAGAA-AGGGTCGCCACCAACTTGTGTGGGCTTTG
1 GAAAGGGTTGCCACCAACATATGTGGGCTTTA-AAGAAGATCGCCACCAACTTGTGTGGCCCTTG
*
428642 AAAAAGGTTGCCACTAGCT
65 AAAAAGGTTGCCACCAGCT
428661 TCTATGAGCT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
95 50 0.71
96 20 0.29
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (96 bp):
GAAAGGGTTGCCACCAACATATGTGGGCTTTAAAGAAGATCGCCACCAACTTGTGTGGCCCTTGA
AAAAGGTTGCCACCAGCTCATGCGGGCTTCA
Found at i:428657 original size:64 final size:63
Alignment explanation
Indices: 428459--428655 Score: 216
Period size: 64 Copynumber: 3.1 Consensus size: 63
428449 TAGAAGGAGA
* * * *
428459 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGTTGCCACCGACATATGTGGGCTTTAAAGAAGAT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTATGTGGGCTTTAAA-AAGGT
* * * * * * * * *
428523 TGCCACCGACTTGTGTGGCCCTTA-AAAAGGTTGCCACCAGCTCATGCGGGCTTCAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTATGTGGGCTTTA-AAAAGGT
* * *
428586 TGCCACTAACTTGTGTGGGCTTTAGAAAGGGTCGCCACCAACTTGTGTGGGCTTTGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTATGTGGGCTTT-AAAAAGGT
428650 TGCCAC
1 TGCCAC
428656 TAGCTTCTAT
Statistics
Matches: 105, Mismatches: 25, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
63 47 0.45
64 57 0.54
65 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (63 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAGGGTTGCCACCAACTTATGTGGGCTTTAAAAAGGT
Found at i:428915 original size:28 final size:28
Alignment explanation
Indices: 428855--428926 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
428845 TATACAACAA
* * *
428855 GTGCCACTGA-TTATGGACTTTGAAAAT
1 GTGCCACTGACTTGTGGACTTCGAAAAG
* *
428882 GAGCCACTGACTTGTGGACTTCGAAGAG
1 GTGCCACTGACTTGTGGACTTCGAAAAG
* *
428910 GTGCCACTAACTAGTGG
1 GTGCCACTGACTTGTGG
428927 GCTTTGAGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGACTTCGAAAAG
Found at i:430264 original size:10 final size:9
Alignment explanation
Indices: 430259--430298 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
430249 TCTTTTCTTG
430259 TTTTTTGTT
1 TTTTTTGTT
430268 TTTTTATGTT
1 TTTTT-TGTT
430278 TTTTTTGTT
1 TTTTTTGTT
*
430287 TGTTTTGTT
1 TTTTTTGTT
430296 TTT
1 TTT
430299 ACGAAAGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:430295 original size:18 final size:19
Alignment explanation
Indices: 430259--430298 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
430249 TCTTTTCTTG
*
430259 TTTTTTGTTTTTTTATGTT
1 TTTTTTGTTTGTTTATGTT
430278 TTTTTTGTTTGTTT-TGTT
1 TTTTTTGTTTGTTTATGTT
430296 TTT
1 TTT
430299 ACGAAAGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (19 bp):
TTTTTTGTTTGTTTATGTT
Found at i:442948 original size:5 final size:5
Alignment explanation
Indices: 442932--442977 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
442922 GTCTACAGTA
*
442932 TTCTT TTTTT TTCTT TT-TT CTTCTT TTCTT TTCTT TTCTT TT-TT TT
1 TTCTT TTCTT TTCTT TTCTT -TTCTT TTCTT TTCTT TTCTT TTCTT TT
442978 AAACCTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 6 0.16
5 29 0.78
6 2 0.05
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTCTT
Found at i:444279 original size:13 final size:13
Alignment explanation
Indices: 444261--444286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
444251 AATTTGGTCA
444261 TGTATCGATACAT
1 TGTATCGATACAT
444274 TGTATCGATACAT
1 TGTATCGATACAT
444287 CTTTTATGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:444390 original size:20 final size:21
Alignment explanation
Indices: 444346--444398 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
444336 GCCAATCACC
*
444346 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
444367 TGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
444387 TGTATCGATACA
1 TGTATCGATACA
444399 ATGTATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.50
21 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:444404 original size:13 final size:13
Alignment explanation
Indices: 444386--444411 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
444376 ACATTTGGTC
444386 ATGTATCGATACA
1 ATGTATCGATACA
444399 ATGTATCGATACA
1 ATGTATCGATACA
444412 TCTAAAGTTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:447080 original size:8 final size:8
Alignment explanation
Indices: 447067--447092 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
447057 AACATCAATC
447067 ATCACAAA
1 ATCACAAA
447075 ATCACAAA
1 ATCACAAA
447083 ATCACAAA
1 ATCACAAA
447091 AT
1 AT
447093 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:453154 original size:20 final size:21
Alignment explanation
Indices: 453107--453159 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
453097 GCCAATCACC
*
453107 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
453128 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
453148 TGTATCGATACA
1 TGTATCGATACA
453160 ATGTATCGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:453677 original size:18 final size:17
Alignment explanation
Indices: 453645--453693 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
453635 TAAAGCTTCA
*
453645 TTCTTTCC-ATTTTTCAT
1 TTCTTTCCTTTTTTTC-T
453662 TT-TTTCTCTTTTTTTCT
1 TTCTTTC-CTTTTTTTCT
453679 TTCTTTCCTTTTTTT
1 TTCTTTCCTTTTTTT
453694 TAATTGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.14
17 14 0.50
18 10 0.36
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTCCTTTTTTTCT
Found at i:453692 original size:16 final size:17
Alignment explanation
Indices: 453641--453692 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
453631 ACCCTAAAGC
*
453641 TTCA-TTCTTTCCATTT
1 TTCATTTCTTTCCTTTT
453657 TTCATTT-TTTCTCTTTTT
1 TTCATTTCTTTC-C-TTTT
453675 TTC-TTTCTTTCCTTTT
1 TTCATTTCTTTCCTTTT
453691 TT
1 TT
453693 TTAATTGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (17 bp):
TTCATTTCTTTCCTTTT
Found at i:453923 original size:33 final size:33
Alignment explanation
Indices: 453881--453946 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
453871 ATTTAAAGGT
453881 GATTAGATTAAGGATCATTTTA-TTCTACATTAG
1 GATTAGATTAAGGATCATTTTATTTC-ACATTAG
453914 GATTAGATTAAGGATCATTTTATTTCACATTAG
1 GATTAGATTAAGGATCATTTTATTTCACATTAG
453947 TTTTGTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (33 bp):
GATTAGATTAAGGATCATTTTATTTCACATTAG
Found at i:454063 original size:22 final size:22
Alignment explanation
Indices: 454032--454080 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
454022 CTATCCACAC
* *
454032 TTTTCTTTTTTATTTTATTCTTT
1 TTTTGTTTTTT-TTCTATTCTTT
*
454055 TTTTGTTTTTTTTCTTTTCTTT
1 TTTTGTTTTTTTTCTATTCTTT
454077 TTTT
1 TTTT
454081 TTAATCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.04, C:0.08, G:0.02, T:0.86
Consensus pattern (22 bp):
TTTTGTTTTTTTTCTATTCTTT
Found at i:454064 original size:17 final size:17
Alignment explanation
Indices: 454044--454098 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
454034 TTCTTTTTTA
454044 TTTTATTCTTTTTTTGT
1 TTTTATTCTTTTTTTGT
* *
454061 TTTTTTTCTTTTCTTTTT
1 TTTTATTCTTTT-TTTGT
*
454079 TTTTAATCTTTTTTTTGT
1 TTTTATTC-TTTTTTTGT
454097 TT
1 TT
454099 ATTTTTGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 11 0.35
18 16 0.52
19 4 0.13
ACGTcount: A:0.05, C:0.07, G:0.04, T:0.84
Consensus pattern (17 bp):
TTTTATTCTTTTTTTGT
Found at i:454090 original size:25 final size:25
Alignment explanation
Indices: 454035--454101 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
454025 TCCACACTTT
*
454035 TCTTTTTTATTTTATTCTTTTTTTG
1 TCTTTTTTATTTTATTCTTTTTTTA
* * *
454060 TTTTTTTTCTTTTCTT-TTTTTTTAA
1 TCTTTTTTATTTTATTCTTTTTTT-A
*
454085 TCTTTTTTTTGTTTATT
1 TCTTTTTTAT-TTTATT
454102 TTTGTTTCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 7 0.21
25 21 0.64
26 5 0.15
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.82
Consensus pattern (25 bp):
TCTTTTTTATTTTATTCTTTTTTTA
Found at i:454092 original size:36 final size:38
Alignment explanation
Indices: 454031--454104 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
454021 ACTATCCACA
*
454031 CTTTTCTTTTTTATTTTATTCTTTTTTTGTTT-TTTTT
1 CTTTTCTTTTTTATTTAATTCTTTTTTTGTTTATTTTT
454068 CTTTTCTTTTTT-TTTAA-TCTTTTTTTTGTTTATTTTT
1 CTTTTCTTTTTTATTTAATTC-TTTTTTTGTTTATTTTT
454105 GTTTCTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
35 2 0.06
36 15 0.44
37 17 0.50
ACGTcount: A:0.07, C:0.08, G:0.03, T:0.82
Consensus pattern (38 bp):
CTTTTCTTTTTTATTTAATTCTTTTTTTGTTTATTTTT
Found at i:454110 original size:36 final size:37
Alignment explanation
Indices: 454033--454116 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
454023 TATCCACACT
* *
454033 TTTCTTTTTTATTTTATTCTTTTTTTGTTTTTTTTCT
1 TTTCTTTTTTATTTAATTCTTTTTTTGTTTTTTTTCG
454070 TTTCTTTTTT-TTTAA-TCTTTTTTTTGTTTATTTTT-G
1 TTTCTTTTTTATTTAATTC-TTTTTTTGTTT-TTTTTCG
*
454106 TTTCTTATTTA
1 TTTCTTTTTTA
454117 GAGGAAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 2 0.05
36 24 0.59
37 15 0.37
ACGTcount: A:0.08, C:0.07, G:0.04, T:0.81
Consensus pattern (37 bp):
TTTCTTTTTTATTTAATTCTTTTTTTGTTTTTTTTCG
Found at i:454452 original size:6 final size:6
Alignment explanation
Indices: 454441--454479 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
454431 TGCAACTAAA
454441 TTTTCT TTTTCT TTTTCT TTTT-T TTTTCCT ATTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT -TTTTCT TT
454480 CCATCTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 18 0.60
7 3 0.10
8 4 0.13
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:455263 original size:12 final size:12
Alignment explanation
Indices: 455246--455270 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
455236 GATGAAAGTA
455246 ATGCATATATGT
1 ATGCATATATGT
455258 ATGCATATATGT
1 ATGCATATATGT
455270 A
1 A
455271 ATATAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGCATATATGT
Found at i:455811 original size:77 final size:77
Alignment explanation
Indices: 455684--455840 Score: 287
Period size: 77 Copynumber: 2.0 Consensus size: 77
455674 ATGTAATATC
*
455684 AAAGAAACGTTATAACAAAATAATAGAAACAAATACATATAAAAGGGCTTATCATTAAGACATTG
1 AAAGAAAAGTTATAACAAAATAATAGAAACAAATACATATAAAAGGGCTTATCATTAAGACATTG
455749 CCCTCATAAAGG
66 CCCTCATAAAGG
*
455761 AAAGAAAAGTTATAACAAAATAATAGAAACAAATACATATAAAAGGGCTTATCGTTAAGACATTG
1 AAAGAAAAGTTATAACAAAATAATAGAAACAAATACATATAAAAGGGCTTATCATTAAGACATTG
*
455826 CCCTTATAAAGG
66 CCCTCATAAAGG
455838 AAA
1 AAA
455841 ATTAGAGCAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (77 bp):
AAAGAAAAGTTATAACAAAATAATAGAAACAAATACATATAAAAGGGCTTATCATTAAGACATTG
CCCTCATAAAGG
Found at i:456712 original size:18 final size:18
Alignment explanation
Indices: 456691--456725 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
456681 AATGGGATGG
456691 AACAAA-ATTAATAAAATT
1 AACAAATATTAA-AAAATT
456709 AACAAATATTAAAAAAT
1 AACAAATATTAAAAAAT
456726 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AACAAATATTAAAAAATT
Done.