Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold96
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: 1013983
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 499 characters in sequence are not A, C, G, or T
File 5 of 8
Found at i:553372 original size:21 final size:21
Alignment explanation
Indices: 553348--553446 Score: 180
Period size: 21 Copynumber: 4.7 Consensus size: 21
553338 TTATTATCCA
553348 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
553369 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
553390 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
553411 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
553432 AATGTATCGATACAT
1 AATGTATCGATACAT
553447 CCTACAAATG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:553457 original size:42 final size:42
Alignment explanation
Indices: 553348--553466 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 42
553338 TTATTATCCA
** *
553348 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTCCTAAAATGTATCGATACATTTGTGG
** *
553390 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGG
1 AATGTATCGATACATTCCTAAAATGTATCGATACATTTGTGG
553432 AATGTATCGATACA-TCCTACAAATGTATCGATACA
1 AATGTATCGATACATTCCTA-AAATGTATCGATACA
553467 GGGTCCCAAC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
41 3 0.04
42 70 0.96
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (42 bp):
AATGTATCGATACATTCCTAAAATGTATCGATACATTTGTGG
Found at i:553457 original size:63 final size:63
Alignment explanation
Indices: 553348--553466 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 63
553338 TTATTATCCA
* ***
553348 AATGTATCGATACATTTGTAGAATGTATCGATACATTTGTGGAATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAGAATGTATCGATACATCTGACAAATGTATCGATACATTTGTAG
*
553411 AATGTATCGATACATTTGTGGAATGTATCGATACATCCT-ACAAATGTATCGATACA
1 AATGTATCGATACATTTGTAGAATGTATCGATACAT-CTGACAAATGTATCGATACA
553467 GGGTCCCAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
63 49 0.98
64 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (63 bp):
AATGTATCGATACATTTGTAGAATGTATCGATACATCTGACAAATGTATCGATACATTTGTAG
Found at i:553526 original size:19 final size:19
Alignment explanation
Indices: 553502--553569 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 19
553492 AATTCAACAA
553502 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
553521 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
553536 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
553553 TTTGTATCGATACATAA
1 TTTGTATCGATACATAA
553570 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:553541 original size:13 final size:13
Alignment explanation
Indices: 553523--553547 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553513 ACATAAGTTT
553523 TGTATCGATACAA
1 TGTATCGATACAA
553536 TGTATCGATACA
1 TGTATCGATACA
553548 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:553545 original size:32 final size:32
Alignment explanation
Indices: 553504--553566 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
553494 TTCAACAATT
553504 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
553536 TGTATCGATACATAAGTTTTGTATCGATACA
1 TGTATCGATACATAAGTTTTGTATCGATACA
553567 TAATTAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:553627 original size:13 final size:13
Alignment explanation
Indices: 553609--553634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
553599 CATTTTTCTG
553609 TGTATCGATACAT
1 TGTATCGATACAT
553622 TGTATCGATACAT
1 TGTATCGATACAT
553635 GGATCTTTGT
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:553631 original size:33 final size:33
Alignment explanation
Indices: 553589--553655 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
553579 GCCAAGGAAA
***
553589 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
553622 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
553655 T
1 T
553656 TGGAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:555445 original size:54 final size:51
Alignment explanation
Indices: 555312--555707 Score: 182
Period size: 52 Copynumber: 7.6 Consensus size: 51
555302 TTGAGTTTCT
* * * * *
555312 CAATTCTCCACAATCGGGGATATTCCAAGTCCGATTTTATTTTCAAGACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * *
555363 TAATT-TTCTATAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACAC
* * * ** * *
555416 CAATTTCTTCACAATCGGGGATACTCCAACCCCG--TTGATCATCGGGGATACTC
1 CAA-TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACAC
* * * * *
555469 CAACCCCGTTATTTC-CAA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATAT
1 CAA-----TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
** * * * * * * *
555523 TGATTTTTCATAATCGAGGATATTCCAA-TCCCGGTTTTATTGCTAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACAC
* * * * * *
555574 TAATTTTTCCACAATCAGGGATACTCCAAC-CCTGGTTTTATTTTCGAAACAC
1 CAATTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACAC
*
555626 CAATT-TTC-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC
1 CAATTCTTCAC---AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC
* * * *
555679 TAATTTTTCACAGTCGAGGATACTCCAAC
1 CAATTCTTCACAATCGGGGATACTCCAAC
555708 CTTGTTATTT
Statistics
Matches: 258, Mismatches: 58, Indels: 57
0.69 0.16 0.15
Matches are distributed among these distances:
48 4 0.02
49 5 0.02
50 3 0.01
51 71 0.28
52 82 0.32
53 28 0.11
54 29 0.11
55 22 0.09
56 2 0.01
57 9 0.03
58 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:555459 original size:27 final size:28
Alignment explanation
Indices: 555429--555504 Score: 104
Period size: 27 Copynumber: 2.8 Consensus size: 28
555419 TTTCTTCACA
555429 ATCGGGGATACTCCAACCCCGTTGA-T-C
1 ATCGGGGATACTCCAACCCCGTT-ATTCC
555456 ATCGGGGATACTCCAACCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTA-TTCC
*
555485 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
555505 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 1 0.02
27 23 0.51
28 19 0.42
29 2 0.04
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTCC
Found at i:555562 original size:51 final size:50
Alignment explanation
Indices: 555489--555708 Score: 190
Period size: 52 Copynumber: 4.3 Consensus size: 50
555479 ATTTCCAAGG
* * * * *
555489 GGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATCGA
1 GGATACTCCAA-CCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGA
* * * *
555540 GGATATTCCAATCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC-A
1 GGATACTCCAA-CCCGATTTTATTTCCAAAACACTAATTTTT-CACAATCGA
* * * * * ** *
555591 GGGATACTCCAACCCTGGTTTTATTTTCGAAACACCAATTTTCCTTTAATCGG
1 -GGATACTCCAACCC-GATTTTATTTCCAAAACACTAATTTTTC-ACAATCGA
* *
555644 GGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTTCACAGTCGA
1 GGATACTCCAAC-CCGATTTTATTTCC-AAAACACTAATTTTTCACAATCGA
555696 GGATACTCCAACC
1 GGATACTCCAACC
555709 TTGTTATTTC
Statistics
Matches: 132, Mismatches: 30, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
51 39 0.30
52 79 0.60
53 14 0.11
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (50 bp):
GGATACTCCAACCCGATTTTATTTCCAAAACACTAATTTTTCACAATCGA
Found at i:555728 original size:28 final size:28
Alignment explanation
Indices: 555696--555767 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
555686 TCACAGTCGA
** * **
555696 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
555724 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
555752 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
555768 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:555785 original size:263 final size:263
Alignment explanation
Indices: 555318--555818 Score: 724
Period size: 263 Copynumber: 1.9 Consensus size: 263
555308 TTCTCAATTC
* * * *
555318 TCCACAATCGGGGATATTCCAAGTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCAGGGA
1 TCCACAATCAGGGATACTCCAAGCCCGATTTTATTTTCAAGACACCAATTTTCTATAATCAGGGA
*
555383 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
555448 CGTTGATCATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGACTTTATT
131 CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACTTTATT
* * * *
555513 TCCAAAATATTGATTTTTCATAATCGAGGATATTCCAATCCCGGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATCGAGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
555578 TTT
261 TTT
* * *
555581 TCCACAATCAGGGATACTCCAA-CCCTGGTTTTATTTTCGAA-ACACCAATTTTCCTTTAATCGG
1 TCCACAATCAGGGATACTCCAAGCCC-GATTTTATTTTC-AAGACACCAATTTT-CTATAATCAG
* * *
555644 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACTAATTT-TTCACAGTCGAGGATACTCCAA
63 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
** * *
555707 CCTTGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCT
128 CCCCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACT
* *
555771 TTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
191 TTATTCCCAAAATATTGATTTCTCATAATCGAGGATACTCCAACCCCG
555819 TTATTTTCGA
Statistics
Matches: 211, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
261 1 0.00
262 27 0.13
263 146 0.69
264 37 0.18
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (263 bp):
TCCACAATCAGGGATACTCCAAGCCCGATTTTATTTTCAAGACACCAATTTTCTATAATCAGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATCGAGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:555833 original size:107 final size:107
Alignment explanation
Indices: 555642--555846 Score: 243
Period size: 107 Copynumber: 1.9 Consensus size: 107
555632 TCCTTTAATC
* * * *
555642 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTTCACAGTCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACTAATTTCTCACAATCGAGGATACTCCAA
**
555707 CCTTGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTTCA-CGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * *
555750 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACTAATTTCTCACAATCGAGGATACTCCAA
*
555814 CCCCGTTATTTTCGA-GGGGATACTCCAATCCCG
66 CCCCGTTA-TTTC-ACGGGGATACTCCAACCCCG
555847 ATTTTTTTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
107 55 0.68
108 25 0.31
109 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACTAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTCACGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:555870 original size:79 final size:79
Alignment explanation
Indices: 555721--555925 Score: 241
Period size: 79 Copynumber: 2.6 Consensus size: 79
555711 GTTATTTCAT
* * *
555721 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
555786 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
555800 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
555864 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
555879 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
555926 TTATTATCTC
Statistics
Matches: 106, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 3 0.03
79 103 0.97
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:557339 original size:19 final size:19
Alignment explanation
Indices: 557315--557428 Score: 117
Period size: 19 Copynumber: 6.6 Consensus size: 19
557305 GCTTAAATTT
*
557315 TATCGATACAAAACTTATG
1 TATCGATACAACACTTATG
557334 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
557353 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
557366 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
557385 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
557398 TATCGATACAACACTTTATG
1 TATCGATACAACAC-TTATG
*
557418 TATCAATACAA
1 TATCGATACAA
557429 ATCGTTGAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 25
0.75 0.02 0.23
Matches are distributed among these distances:
13 18 0.22
14 2 0.03
16 12 0.15
18 1 0.01
19 35 0.44
20 12 0.15
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (19 bp):
TATCGATACAACACTTATG
Found at i:557369 original size:13 final size:13
Alignment explanation
Indices: 557351--557407 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
557341 ACAACACTTA
557351 TGTATCGATACAT
1 TGTATCGATACAT
557364 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
557382 ATGTATCGATACAT
1 -TGTATCGATACAT
557396 TGTATCGATACA
1 TGTATCGATACA
557408 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:557373 original size:32 final size:32
Alignment explanation
Indices: 557332--557427 Score: 174
Period size: 32 Copynumber: 3.0 Consensus size: 32
557322 ACAAAACTTA
557332 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
557364 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
557396 TGTATCGATACAACACTTTATGTATCAATACA
1 TGTATCGATACAACAC-TTATGTATCGATACA
557428 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 48 0.77
33 14 0.23
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:558418 original size:12 final size:13
Alignment explanation
Indices: 558380--558420 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
558370 AAATAGTACC
558380 CAATGTATCGATA
1 CAATGTATCGATA
*
558393 CAGTGTATCGATA
1 CAATGTATCGATA
558406 CAATGTA-CGATA
1 CAATGTATCGATA
558418 CAA
1 CAA
558421 GGAATATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:564601 original size:13 final size:13
Alignment explanation
Indices: 564583--564613 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
564573 GTTACAAGCT
564583 ATGTATCGATACA
1 ATGTATCGATACA
564596 ATGTATCGATACA
1 ATGTATCGATACA
*
564609 TTGTA
1 ATGTA
564614 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:567832 original size:29 final size:29
Alignment explanation
Indices: 567790--567852 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
567780 CAAAACATGA
* *
567790 TACTTATATAGTTATATTACTAATTTGTT
1 TACTTACATAGTTATATTACGAATTTGTT
567819 TACTTACATAGTTATATTACGAATTTGTT
1 TACTTACATAGTTATATTACGAATTTGTT
567848 TACTT
1 TACTT
567853 TTCTTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (29 bp):
TACTTACATAGTTATATTACGAATTTGTT
Found at i:570772 original size:93 final size:91
Alignment explanation
Indices: 570461--570961 Score: 406
Period size: 93 Copynumber: 5.4 Consensus size: 91
570451 AATGGTTAAT
* * * * *
570461 TATTTATGATTTTGTTAATATTTTGTAATTTAATTTGATGAATTAATTTTATTTTATTGTTAAAA
1 TATTTATGATTTTGTTAATATTTTGTAATTTAGTTTGATAAATTAAGTTTA-TTT-GTGTTGAAA
* * **
570526 GATGATGAATTTAGTAATTTATATTAAAA
64 GATTATGTATTTAGTAATTTA-AAGAAAA
* * * *
570555 TATTTATGATTTT-ATAATTTGGTTTGGTAAATTT-GTTTGATAAATTTAGTTTAATTGTTGTTG
1 TATTTATGATTTTGTTAATAT--TTT-GT-AATTTAGTTTGATAAATTAAGTTTATTTG-TGTTG
* * * *
570618 AAATATTAGGTA-ATGGTTAATTTAAATGAAAA
61 AAAGATTATGTATTTAG-TAATTTAAA-GAAAA
* *
570650 TATTTATGATTTTGTCAATATTTTATAATTTAGTTTGATAAATTAAGTTTATTTGTGTTGAAAGA
1 TATTTATGATTTTGTTAATATTTTGTAATTTAGTTTGATAAATTAAGTTTATTTGTGTTGAAAGA
*
570715 TTATGTATTTAGTAATTTACAAGAAAT
66 TTATGTATTTAGTAATTTA-AAGAAAA
** * * * * * *
570742 TATTTACAATTTTTTTTAATATTTTGTAATTTGGTTTGATAAATTTAGTTTAATT-TATTGGAAG
1 TATTTATGA-TTTTGTTAATATTTTGTAATTTAGTTTGATAAATTAAGTTTATTTGTGTTGAAAG
* * * *
570806 ATTAAGTGATGATGATTAACTTAAATGAAAA
65 ATTATGT-AT--TTAGTAATTTAAA-GAAAA
* * *
570837 TATTTATGATTTTGTAAATATTTTGTAATTTAGTTTGATAAATT---TTCT-TTTTTGTTGAAAT
1 TATTTATGATTTTGTTAATATTTTGTAATTTAGTTTGATAAATTAAGTT-TATTTGTGTTGAAAG
* * * * *
570898 ATTATGTATTCAATAATTCATATGAAAT
65 ATTATGTATTTAGTAATTTA-AAGAAAA
* *
570926 TATTTATGATTTTATCAATATTTTGTAATTTAGTTT
1 TATTTATGATTTTGTTAATATTTTGTAATTTAGTTT
570962 AATTGTTGTT
Statistics
Matches: 327, Mismatches: 61, Indels: 43
0.76 0.14 0.10
Matches are distributed among these distances:
89 45 0.14
90 1 0.00
91 6 0.02
92 64 0.20
93 72 0.22
94 53 0.16
95 60 0.18
96 21 0.06
97 5 0.02
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (91 bp):
TATTTATGATTTTGTTAATATTTTGTAATTTAGTTTGATAAATTAAGTTTATTTGTGTTGAAAGA
TTATGTATTTAGTAATTTAAAGAAAA
Found at i:570849 original size:187 final size:183
Alignment explanation
Indices: 570461--570961 Score: 564
Period size: 187 Copynumber: 2.7 Consensus size: 183
570451 AATGGTTAAT
* * * *
570461 TATTTATGATTTTGTTAATATTTTGTAATTTAATTTGATGAATTAATTTTATTTTATTGTTAAAA
1 TATTTATGATTTTGTAAATATTTTGTAATTTAGTTTGATAAATTAA-TTTA-TTT-TTGTTGAAA
* * * * * *
570526 GATGATGAATTTAGTAATTTATATTAAAATATTTATGA-TTTTATAATTTGGTTTGGTAAATTTG
63 GATTATGTATTTAGTAATTTATATGAAATTATTTATGATTTTTTTAATAT--TTT-GT-AATTTG
* * * *
570590 TTTGATAAATTTAGTTTAATTGTTGTTGAAATATTAGGTAATGGTTAATTTAAATGAAAA
124 TTTGATAAATTTAGTTTAATTGTTATTGAAAGATTAGGTAATGATTAACTTAAATGAAAA
* * *
570650 TATTTATGATTTTGTCAATATTTTATAATTTAGTTTGATAAATTAAGTTTATTTGTGTTGAAAGA
1 TATTTATGATTTTGTAAATATTTTGTAATTTAGTTTGATAAATTAA-TTTATTTTTGTTGAAAGA
* * **
570715 TTATGTATTTAGTAATTTACAAGAAATTATTTACAATTTTTTTTAATATTTTGTAATTTGGTTTG
65 TTATGTATTTAGTAATTTATATGAAATTATTTATGA-TTTTTTTAATATTTTGTAATTT-GTTTG
* *
570780 ATAAATTTAGTTTAA-T-TTATTGGAAGATTAAGTGATGATGATTAACTTAAATGAAAA
128 ATAAATTTAGTTTAATTGTTATTGAAAGATT-AG-G-TAATGATTAACTTAAATGAAAA
*
570837 TATTTATGATTTTGTAAATATTTTGTAATTTAGTTTGATAAATT--TTCT-TTTTTGTTGAAATA
1 TATTTATGATTTTGTAAATATTTTGTAATTTAGTTTGATAAATTAATT-TATTTTTGTTGAAAGA
* * * * *
570899 TTATGTATTCAATAATTCATATGAAATTATTTATGATTTTATCAATATTTTGTAATTTAGTTT
65 TTATGTATTTAGTAATTTATATGAAATTATTTATGATTTTTTTAATATTTTGTAATTT-GTTT
570962 AATTGTTGTT
Statistics
Matches: 268, Mismatches: 37, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
183 24 0.09
184 53 0.20
185 9 0.03
186 23 0.09
187 101 0.38
188 3 0.01
189 55 0.21
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (183 bp):
TATTTATGATTTTGTAAATATTTTGTAATTTAGTTTGATAAATTAATTTATTTTTGTTGAAAGAT
TATGTATTTAGTAATTTATATGAAATTATTTATGATTTTTTTAATATTTTGTAATTTGTTTGATA
AATTTAGTTTAATTGTTATTGAAAGATTAGGTAATGATTAACTTAAATGAAAA
Found at i:572213 original size:17 final size:17
Alignment explanation
Indices: 572187--572220 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
572177 TTTAATTTTA
* *
572187 ATTTTTATTATTTATTT
1 ATTTTCATTATATATTT
572204 ATTTTCATTATATATTT
1 ATTTTCATTATATATTT
572221 GTATATGTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTCATTATATATTT
Found at i:572236 original size:34 final size:29
Alignment explanation
Indices: 572168--572244 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
572158 ATCGTGATTT
* *
572168 TTTATTTATTTTAATTTTAATTTTTATTA
1 TTTATTTATTTTCATTATAATTTTTATTA
572197 TTTATTTATTTTCATTATATATTTGTATATGTGA
1 TTTATTTATTTTCATTATA-ATTT-T-TAT-T-A
*
572231 TTTATTTTTTTTCA
1 TTTATTTATTTTCA
572245 ATAATAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 17 0.43
30 4 0.10
31 1 0.03
32 3 0.08
33 1 0.03
34 14 0.35
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.69
Consensus pattern (29 bp):
TTTATTTATTTTCATTATAATTTTTATTA
Found at i:572430 original size:22 final size:22
Alignment explanation
Indices: 572380--572430 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
572370 ATAAAATAAA
572380 AATTATTTTTAAATTAATATTT
1 AATTATTTTTAAATTAATATTT
572402 -A-TATATTTTATAATTAA-ATTTT
1 AATTAT-TTTTA-AATTAATA-TTT
572424 AATTATT
1 AATTATT
572431 AACTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
20 3 0.12
21 7 0.29
22 9 0.38
23 2 0.08
24 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTATTTTTAAATTAATATTT
Found at i:588607 original size:15 final size:15
Alignment explanation
Indices: 588574--588632 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 15
588564 TAAGATTTTT
588574 TTTAAATTATTTTATA
1 TTTAAATTATTTTA-A
*
588590 TTTAATTTATTTTAA
1 TTTAAATTATTTTAA
588605 TTTAAATTATTTTAAA
1 TTTAAATTATTTT-AA
588621 TTTTAAATTATT
1 -TTTAAATTATT
588633 AATTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
15 13 0.33
16 15 0.38
17 11 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAAATTATTTTAA
Found at i:588634 original size:15 final size:16
Alignment explanation
Indices: 588573--588642 Score: 65
Period size: 15 Copynumber: 4.4 Consensus size: 16
588563 TTAAGATTTT
*
588573 TTTTAAATTATTT-TA
1 TTTTAAATTATTTAAA
* *
588588 TATTTAATTTATTTTAA
1 T-TTTAAATTATTTAAA
588605 -TTTAAATTATTTTAAA
1 TTTTAAATTA-TTTAAA
*
588621 TTTTAAATTA-TTAAT
1 TTTTAAATTATTTAAA
588636 TTTTAAA
1 TTTTAAA
588643 ATCAAATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
15 20 0.43
16 16 0.35
17 10 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATTATTTAAA
Found at i:589043 original size:15 final size:15
Alignment explanation
Indices: 589025--589064 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
589015 ATATGTTTGT
589025 ATTATATATTAATTC
1 ATTATATATTAATTC
**
589040 ATTACCTATTAATTC
1 ATTATATATTAATTC
589055 ATTATATATT
1 ATTATATATT
589065 TTGTGTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATATATTAATTC
Found at i:589150 original size:17 final size:18
Alignment explanation
Indices: 589128--589163 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
589118 TGTGTGCTCA
*
589128 AAATATT-ATAAATTTAT
1 AAATATTGACAAATTTAT
589145 AAATATTGACAAATTTAT
1 AAATATTGACAAATTTAT
589163 A
1 A
589164 TATTCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
AAATATTGACAAATTTAT
Found at i:597328 original size:21 final size:22
Alignment explanation
Indices: 597295--597338 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
597285 ATTAATTATA
597295 AAATATAATAATCAAATTAAAAT
1 AAATATAATAATC-AATTAAAAT
*
597318 AAATAT-A-AATCATTTAAAAT
1 AAATATAATAATCAATTAAAAT
597338 A
1 A
597339 TTTTAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 1 0.05
23 6 0.30
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATAATAATCAATTAAAAT
Found at i:597373 original size:20 final size:20
Alignment explanation
Indices: 597350--597390 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
597340 TTTAAAAACG
*
597350 TGTAAAATTAATTTTTTCAT
1 TGTAAAATTAACTTTTTCAT
*
597370 TGTAAAATTAGCTTTTTCAT
1 TGTAAAATTAACTTTTTCAT
597390 T
1 T
597391 AATTAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (20 bp):
TGTAAAATTAACTTTTTCAT
Found at i:597799 original size:30 final size:30
Alignment explanation
Indices: 597759--597828 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
597749 TTTGATTCTA
*
597759 CTTCTAGTTGATATGGCTATTGCCGATCTG
1 CTTCTGGTTGATATGGCTATTGCCGATCTG
* *
597789 CTTCTGGTTGATATTGCTGTTGCCGATCTG
1 CTTCTGGTTGATATGGCTATTGCCGATCTG
*
597819 CTTTTGGTTG
1 CTTCTGGTTG
597829 CTGATCTGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.44
Consensus pattern (30 bp):
CTTCTGGTTGATATGGCTATTGCCGATCTG
Found at i:597834 original size:18 final size:18
Alignment explanation
Indices: 597807--597842 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
597797 TGATATTGCT
597807 GTTGCCGATCTGCTTTTG
1 GTTGCCGATCTGCTTTTG
*
597825 GTTGCTGATCTGCTTTTG
1 GTTGCCGATCTGCTTTTG
597843 CCAATTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.19, G:0.28, T:0.47
Consensus pattern (18 bp):
GTTGCCGATCTGCTTTTG
Found at i:598050 original size:18 final size:18
Alignment explanation
Indices: 598001--598048 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
597991 TGTATTGTGA
598001 TTTTTTTATTTT-ACTTTG
1 TTTTTTT-TTTTAACTTTG
598019 TTTTTTTTTGTTAAGCTTTG
1 TTTTTTTTT-TTAA-CTTTG
598039 TTTTTTTTTT
1 TTTTTTTTTT
598049 AAATGAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 2 0.07
18 9 0.33
19 2 0.07
20 14 0.52
ACGTcount: A:0.08, C:0.04, G:0.08, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTTTAACTTTG
Found at i:598093 original size:45 final size:45
Alignment explanation
Indices: 598044--598139 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
598034 CTTTGTTTTT
598044 TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAAA
1 TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAAA
* * * *
598089 TTTTTAATTGGGTTTTAATTGTGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAAA
598134 TTTTTA
1 TTTTTA
598140 GTTTGTGTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (45 bp):
TTTTTAAATGAGTTTTAATTGGGTTTGGGTTTAAGTTTATATAAA
Found at i:600052 original size:23 final size:23
Alignment explanation
Indices: 600020--600066 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
600010 AAAAATATCT
*
600020 TGGTAGGTTATTTTCACAAAGCA
1 TGGTAAGTTATTTTCACAAAGCA
600043 TGGTAAGTTATTTTCACAAAGCA
1 TGGTAAGTTATTTTCACAAAGCA
600066 T
1 T
600067 AGTTCTAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (23 bp):
TGGTAAGTTATTTTCACAAAGCA
Found at i:603013 original size:23 final size:23
Alignment explanation
Indices: 602987--603053 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
602977 GTTTGATTAT
** *
602987 TTGCTGTTTGTTGTTGCTTTTGC
1 TTGCTGTTTACTGCTGCTTTTGC
*
603010 TTGCTGTTTACTGCTGCTTTTGT
1 TTGCTGTTTACTGCTGCTTTTGC
*
603033 TTGTTGTTTACTGCTGCTTTT
1 TTGCTGTTTACTGCTGCTTTT
603054 TACTTGTTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.03, C:0.15, G:0.22, T:0.60
Consensus pattern (23 bp):
TTGCTGTTTACTGCTGCTTTTGC
Found at i:603138 original size:13 final size:13
Alignment explanation
Indices: 603122--603191 Score: 52
Period size: 13 Copynumber: 5.1 Consensus size: 13
603112 GCTGCTGTTT
*
603122 TTGCTGTTCGTGC
1 TTGCTGCTCGTGC
603135 TTGCTGCTCGTGC
1 TTGCTGCTCGTGC
*
603148 TGTTGTTGCTAC-TGTC
1 --TTGCTGCT-CGTG-C
*
603164 TTTGCTGTTCGTGC
1 -TTGCTGCTCGTGC
*
603178 TTACTGCTCGTGC
1 TTGCTGCTCGTGC
603191 T
1 T
603192 GTTGTTGCTA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 24 0.53
14 2 0.04
15 17 0.38
16 2 0.04
ACGTcount: A:0.03, C:0.24, G:0.27, T:0.46
Consensus pattern (13 bp):
TTGCTGCTCGTGC
Found at i:603148 original size:22 final size:22
Alignment explanation
Indices: 603123--603194 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
603113 CTGCTGTTTT
*
603123 TGCTGTTCGTGCTTGCTGCTCG
1 TGCTGTTCGTGCTTACTGCTCG
*
603145 TGCTGTT-GTTGC-TACTG-TCTT
1 TGCTGTTCG-TGCTTACTGCTC-G
603166 TGCTGTTCGTGCTTACTGCTCG
1 TGCTGTTCGTGCTTACTGCTCG
603188 TGCTGTT
1 TGCTGTT
603195 GTTGCTACTG
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 2 0.05
21 15 0.36
22 23 0.55
23 2 0.05
ACGTcount: A:0.03, C:0.24, G:0.28, T:0.46
Consensus pattern (22 bp):
TGCTGTTCGTGCTTACTGCTCG
Found at i:603157 original size:43 final size:43
Alignment explanation
Indices: 603099--603245 Score: 197
Period size: 43 Copynumber: 3.4 Consensus size: 43
603089 TGCTGCTTGT
* * *
603099 TCGTGCTATTTTTGCTGCTGTTTTTGCTGTTCGTGCTTGCTGC
1 TCGTGCTGTTGTTGCTACTGTTTTTGCTGTTCGTGCTTGCTGC
* *
603142 TCGTGCTGTTGTTGCTACTGTCTTTGCTGTTCGTGCTTACTGC
1 TCGTGCTGTTGTTGCTACTGTTTTTGCTGTTCGTGCTTGCTGC
*
603185 TCGTGCTGTTGTTGCTACTGTTCTTCAT-ATGTTCGTGCTTGCTGC
1 TCGTGCTGTTGTTGCTACTGTT-TT--TGCTGTTCGTGCTTGCTGC
*
603230 TTGTGCTGTTGTTGCT
1 TCGTGCTGTTGTTGCT
603246 CTTGTTCTTC
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
43 59 0.64
44 2 0.02
45 30 0.33
46 1 0.01
ACGTcount: A:0.04, C:0.21, G:0.26, T:0.49
Consensus pattern (43 bp):
TCGTGCTGTTGTTGCTACTGTTTTTGCTGTTCGTGCTTGCTGC
Found at i:603200 original size:22 final size:21
Alignment explanation
Indices: 603123--603204 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 21
603113 CTGCTGTTTT
*
603123 TGCTGTTCGTGCTTGCTGCTCG
1 TGCTGTTCGTGC-TACTGCTCG
*
603145 TGCTGTT-GTTGCTACTG-TCTT
1 TGCTGTTCG-TGCTACTGCTC-G
603166 TGCTGTTCGTGCTTACTGCTCG
1 TGCTGTTCGTGC-TACTGCTCG
603188 TGCTGTT-GTTGCTACTG
1 TGCTGTTCG-TGCTACTG
603205 TTCTTCATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
20 2 0.04
21 21 0.41
22 26 0.51
23 2 0.04
ACGTcount: A:0.04, C:0.23, G:0.28, T:0.45
Consensus pattern (21 bp):
TGCTGTTCGTGCTACTGCTCG
Found at i:603236 original size:45 final size:45
Alignment explanation
Indices: 603126--603263 Score: 194
Period size: 45 Copynumber: 3.1 Consensus size: 45
603116 CTGTTTTTGC
*
603126 TGTTCGTGCTTGCTGCTCGTGCTGTTGTTGCTACTG-TCTT--TGC
1 TGTTCGTGCTTGCTGCTCGTGCTGTTGTTGCTACTGTTCTTCAT-A
*
603169 TGTTCGTGCTTACTGCTCGTGCTGTTGTTGCTACTGTTCTTCATA
1 TGTTCGTGCTTGCTGCTCGTGCTGTTGTTGCTACTGTTCTTCATA
* *
603214 TGTTCGTGCTTGCTGCTTGTGCTGTTGTTGCT-CTTGTTCTTCATT
1 TGTTCGTGCTTGCTGCTCGTGCTGTTGTTGCTAC-TGTTCTTCATA
603259 TGTTC
1 TGTTC
603264 ATCTTTGCTA
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
43 35 0.41
44 5 0.06
45 45 0.52
46 1 0.01
ACGTcount: A:0.04, C:0.22, G:0.25, T:0.49
Consensus pattern (45 bp):
TGTTCGTGCTTGCTGCTCGTGCTGTTGTTGCTACTGTTCTTCATA
Found at i:603354 original size:35 final size:35
Alignment explanation
Indices: 603305--603390 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
603295 ATGCTAGAGT
* *
603305 TTGCTACTGTTGTTGTTGTCTTCAACTACTGGAGC
1 TTGCTGCTATTGTTGTTGTCTTCAACTACTGGAGC
* * * * *
603340 TTGTTGCTATTGTTGTTGTTTTCAGCTGCTGGAGT
1 TTGCTGCTATTGTTGTTGTCTTCAACTACTGGAGC
603375 TTGCTGCTATTGTTGT
1 TTGCTGCTATTGTTGT
603391 CTTCTCTTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (35 bp):
TTGCTGCTATTGTTGTTGTCTTCAACTACTGGAGC
Found at i:604600 original size:19 final size:19
Alignment explanation
Indices: 604576--604640 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
604566 TAGCCAAACT
604576 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
604595 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
604608 TGTATCGATACACATAAAATA
1 TGTATCGATACAC--AAAATA
604629 TGTATCGATACA
1 TGTATCGATACA
604641 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:604612 original size:13 final size:13
Alignment explanation
Indices: 604594--604619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
604584 TACACAAAAT
604594 ATGTATCGATACA
1 ATGTATCGATACA
604607 ATGTATCGATACA
1 ATGTATCGATACA
604620 CATAAAATAT
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:604617 original size:32 final size:33
Alignment explanation
Indices: 604576--604640 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
604566 TAGCCAAACT
604576 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
604608 TGTATCGATACACATAAAATATGTATCGATACA
1 TGTATCGATACACA-AAAATATGTATCGATACA
604641 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:606283 original size:28 final size:28
Alignment explanation
Indices: 606243--606313 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
606233 GAATAAAGCT
** *
606243 GGGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
606271 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
606299 GAGGTTGGAGTATCC
1 GGGGTTGGAGTATCC
606314 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:606399 original size:52 final size:51
Alignment explanation
Indices: 606303--606419 Score: 128
Period size: 52 Copynumber: 2.3 Consensus size: 51
606293 AATAACGAGG
* * * *
606303 TTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCAGGA
1 TTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGG-AATAAAACCAGGA
* * * *
606355 TTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCG-ATAAAATCGGGG
1 TTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTAG-GAATAAAACCAGGA
606407 TTGGAGTATCCCC
1 TTGGAGTATCCCC
606420 TCGGAAATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
52 39 0.71
53 15 0.27
54 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.32
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGGAATAAAACCAGGA
Found at i:606503 original size:55 final size:52
Alignment explanation
Indices: 606438--606565 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 52
606428 AACGGGGTTG
**
606438 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAA-TAAAATCGGAGTTA
1 GAGTATCCCCGATTGTGAAGAAATTAATG---TTTT-GAAAGTAAAATCGGAGTTA
* * *
606493 GAGTATCCCCGATTAT-AGGAAATTAATGTTTTGAAAGTAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAAGAAATTAATGTTTTGAAAGTAAAATCGGAGTTA
* * *
606544 GAATATCCTCGATTGTGGAGAA
1 GAGTATCCCCGATTGTGAAGAA
606566 TTGAGCAACT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
50 4 0.07
51 30 0.49
52 3 0.05
54 9 0.15
55 15 0.25
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (52 bp):
GAGTATCCCCGATTGTGAAGAAATTAATGTTTTGAAAGTAAAATCGGAGTTA
Found at i:606551 original size:134 final size:131
Alignment explanation
Indices: 606291--606551 Score: 348
Period size: 135 Copynumber: 2.0 Consensus size: 131
606281 TATCCCCGAT
*
606291 GAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCAGGAT
1 GAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCAGGAT
* * ** * *
606356 TGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCGATAAAATCGGGGTTGGAGTATCCCCT
66 TAGAGTATCCCCGATTATGG-AAAATTAATGTTTTAAAGATAAAATCGGAGTTGGAATATCCCCT
606421 CG
130 CG
* * *
606423 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATC-G
1 GAAATAACGAGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAACCAG
606487 GAGTTAGAGTATCCCCGATTATAGG-AAATTAATGTTTTGAAAG-TAAAATCGGAGTTGGAATAT
63 GA-TTAGAGTATCCCCGATTAT-GGAAAATTAATGTTTT-AAAGATAAAATCGGAGTTGGAATAT
606550 CC
125 CC
606552 TCGATTGTGG
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
132 32 0.28
133 5 0.04
134 36 0.32
135 38 0.34
136 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (131 bp):
GAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCAGGAT
TAGAGTATCCCCGATTATGGAAAATTAATGTTTTAAAGATAAAATCGGAGTTGGAATATCCCCTC
G
Found at i:606554 original size:132 final size:130
Alignment explanation
Indices: 606274--606551 Score: 339
Period size: 132 Copynumber: 2.1 Consensus size: 130
606264 AAGTAACGGG
* *
606274 GTTGGAGTATCCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTT
1 GTTGGAATATCCCTCG--GAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTT
* * **
606338 TGGAAATAAAACCAGGATTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCGATAAAATC
64 TGGAAATAAAACCAGGATTAGAGTATCCCCGATTATGG-AAAATTAATGTTTTAAAGATAAAATC
*
606403 GGG
128 GGA
* * *
606406 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTT
1 GTTGGAATAT-CCCTCGGAAATAACGAGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATT
*
606471 TTTGGAAATAAAATC-GGAGTTAGAGTATCCCCGATTATAGG-AAATTAATGTTTTGAAAG-TAA
62 TTTGGAAATAAAACCAGGA-TTAGAGTATCCCCGATTAT-GGAAAATTAATGTTTT-AAAGATAA
606533 AATCGGA
124 AATCGGA
606540 GTTGGAATATCC
1 GTTGGAATATCC
606552 TCGATTGTGG
Statistics
Matches: 128, Mismatches: 10, Indels: 15
0.84 0.07 0.10
Matches are distributed among these distances:
132 42 0.33
133 10 0.08
134 36 0.28
135 38 0.30
136 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (130 bp):
GTTGGAATATCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTG
GAAATAAAACCAGGATTAGAGTATCCCCGATTATGGAAAATTAATGTTTTAAAGATAAAATCGGA
Found at i:608937 original size:13 final size:13
Alignment explanation
Indices: 608919--608944 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
608909 ACAAAGATCC
608919 ATGTATCGATACA
1 ATGTATCGATACA
608932 ATGTATCGATACA
1 ATGTATCGATACA
608945 TAGAAAAATG
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:608940 original size:33 final size:33
Alignment explanation
Indices: 608898--608964 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
608888 AAAATTTCCA
***
608898 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
608931 AATGTATCGATACATAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
608964 A
1 A
608965 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:609029 original size:13 final size:13
Alignment explanation
Indices: 609011--609035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
609001 TCAAAACTTA
609011 TGTATCGATACAT
1 TGTATCGATACAT
609024 TGTATCGATACA
1 TGTATCGATACA
609036 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:609048 original size:19 final size:19
Alignment explanation
Indices: 609002--609056 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
608992 CGATACAATT
609002 CAAAACTTATGTATCGATA
1 CAAAACTTATGTATCGATA
609021 C---A--T-TGTATCGATA
1 CAAAACTTATGTATCGATA
609034 CAAAACTTATGTATCGATA
1 CAAAACTTATGTATCGATA
609053 CAAA
1 CAAA
609057 TTGTTGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
16 2 0.07
18 1 0.03
19 15 0.50
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (19 bp):
CAAAACTTATGTATCGATA
Found at i:609136 original size:21 final size:21
Alignment explanation
Indices: 609112--609168 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
609102 CATTTGTAGG
609112 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
609133 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
609154 ATGTATCGATACATT
1 ATGTATCGATACATT
609169 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:609845 original size:55 final size:54
Alignment explanation
Indices: 609756--610390 Score: 827
Period size: 55 Copynumber: 11.4 Consensus size: 54
609746 ATAAATTGTA
* * * *
609756 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
609811 TCCTGCTCTTTGAGGACTAAAAGGTGCCATCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
609866 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
609921 TCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTA-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
609976 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
610031 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAGAGGCG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
610086 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGTA
1 TCCTGCTCTTTGAGGACTA-AAAGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
610147 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
610202 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
610257 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
610312 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
610367 TCCTGCTCTTTGAGGACTGAAAAG
1 TCCTGCTCTTTGAGGACT-AAAAG
610391 CGGAAGGAGA
Statistics
Matches: 536, Mismatches: 21, Indels: 46
0.89 0.03 0.08
Matches are distributed among these distances:
53 2 0.00
54 19 0.04
55 448 0.84
56 14 0.03
57 5 0.01
59 2 0.00
60 2 0.00
61 43 0.08
62 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:609949 original size:110 final size:110
Alignment explanation
Indices: 609756--610388 Score: 929
Period size: 110 Copynumber: 5.7 Consensus size: 110
609746 ATAAATTGTA
* * * * *
609756 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* * *
609820 TTGAGGACTAAAAGGTGCCATCAACTTGTGTGGGCTTTAAGAGGTG
65 TTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
609866 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
609931 TGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
66 TGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
609976 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
* *
610041 TGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAGAGGCG
66 TGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
610086 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGTATCTT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCT
*
610151 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
60 GCTCTTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
610202 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTC
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTC
* * *
610265 TTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTG
64 TTTGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
610312 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCT
610376 TTGAGGACTGAAA
65 TTGAGGACTGAAA
610389 AGCGGAAGGA
Statistics
Matches: 483, Mismatches: 26, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
109 1 0.00
110 364 0.75
111 17 0.04
114 2 0.00
115 10 0.02
116 89 0.18
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (110 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAGATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:609966 original size:165 final size:163
Alignment explanation
Indices: 609756--610389 Score: 936
Period size: 165 Copynumber: 3.8 Consensus size: 163
609746 ATAAATTGTA
* * * *
609756 TCCTGCTCATTGAGGAGTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
609820 TTGAGGACT-AAAAGGTGCCATCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
65 TTGAGGACTGAAAA--TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
609884 GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
128 -GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
609921 TCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
609986 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTG
66 TGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACT-
* *
610050 GAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGCG
128 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
610086 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGTATCTT
1 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCT
*
610151 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAG
60 GCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAG
*
610216 GACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
124 GACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
610257 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
610321 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTG
65 TTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTG
610386 AAAA
129 AAAA
610390 GCGGAAGGAG
Statistics
Matches: 431, Mismatches: 22, Indels: 33
0.89 0.05 0.07
Matches are distributed among these distances:
165 262 0.61
166 14 0.03
167 4 0.01
170 19 0.04
171 132 0.31
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (163 bp):
TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
TGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAA
AATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:609998 original size:27 final size:27
Alignment explanation
Indices: 609968--610053 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
609958 TGTGGGCTTT
609968 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
609995 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
610023 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
610050 GAAA
1 GAAA
610054 ATGCCACCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:610227 original size:26 final size:26
Alignment explanation
Indices: 610197--610282 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
610187 GGGCTTTAAG
610197 AGGTGTCCTGCTCTTTGAGGACTGAA
1 AGGTGTCCTGCTCTTTGAGGACTGAA
** * * * *
610223 AGGTG-CCACCAACTTGTGTGGGCTTTAA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TGAA
*
610251 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGAGGACTGAA
610278 AGGTG
1 AGGTG
610283 CCACCAACTT
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 8 0.19
28 8 0.19
29 8 0.19
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGAGGACTGAA
Found at i:611368 original size:1 final size:1
Alignment explanation
Indices: 611364--611430 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
611354 CTTTTCTCTC
* * * * * * ** *
611364 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTTGTTTTTTTTTTTGCTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
611429 TT
1 TT
611431 GAAGAGAATG
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:611383 original size:16 final size:15
Alignment explanation
Indices: 611364--611416 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
611354 CTTTTCTCTC
*
611364 TTTTTCTTTGTTTTG
1 TTTTTTTTTGTTTTG
*
611379 TTTTTTTGTTTTTTTG
1 TTTTTTT-TTGTTTTG
611395 TTTTTTTTTTGTTTT-
1 -TTTTTTTTTGTTTTG
611410 TTTTTTT
1 TTTTTTT
611417 GCTCTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 7 0.21
15 6 0.18
16 13 0.39
17 7 0.21
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTGTTTTG
Found at i:611400 original size:32 final size:30
Alignment explanation
Indices: 611364--611430 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
611354 CTTTTCTCTC
* *
611364 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTGT
1 TTTTTCTTTGTTTT-TTTTTTTGCTCTTTT-T
*
611396 TTTTTTTTTGTTTTTTTTTTTGCTCTTTTT
1 TTTTTCTTTGTTTTTTTTTTTGCTCTTTTT
611426 TTTTT
1 TTTTT
611431 GAAGAGAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 6 0.19
31 13 0.41
32 13 0.41
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (30 bp):
TTTTTCTTTGTTTTTTTTTTTGCTCTTTTT
Found at i:611404 original size:27 final size:26
Alignment explanation
Indices: 611374--611431 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
611364 TTTTTCTTTG
** *
611374 TTTTGTTTTTTTGTTTTTTTGTTTTTT
1 TTTTGTTTTTTT-TTTTGCTCTTTTTT
611401 TTTTGTTTTTTTTTTTGCTCTTTTTT
1 TTTTGTTTTTTTTTTTGCTCTTTTTT
611427 TTTTG
1 TTTTG
611432 AAGAGAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.86
Consensus pattern (26 bp):
TTTTGTTTTTTTTTTTGCTCTTTTTT
Found at i:611424 original size:14 final size:12
Alignment explanation
Indices: 611364--611431 Score: 68
Period size: 14 Copynumber: 5.5 Consensus size: 12
611354 CTTTTCTCTC
*
611364 TTTTTCTTTGTTT
1 TTTTTGTTT-TTT
*
611377 TGTTTT-TTTGTT
1 T-TTTTGTTTTTT
611389 TTTTTG-TTTTT
1 TTTTTGTTTTTT
611400 TTTTTGTTTTTT
1 TTTTTGTTTTTT
611412 TTTTTGCTCTTTTT
1 TTTTTG-T-TTTTT
611426 TTTTTG
1 TTTTTG
611432 AAGAGAATGT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
11 14 0.29
12 14 0.29
13 5 0.10
14 15 0.31
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:623958 original size:28 final size:28
Alignment explanation
Indices: 623918--623988 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
623908 GAATAAAGCT
** *
623918 GGGGTTGGAGTATCCCCTCGGAAGTAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
623946 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGAGGAAATAAC
*
623974 GAGGTTGGAGTATCC
1 GGGGTTGGAGTATCC
623989 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGAGGAAATAAC
Found at i:624046 original size:52 final size:52
Alignment explanation
Indices: 623978--624094 Score: 139
Period size: 52 Copynumber: 2.2 Consensus size: 52
623968 AATAACGAGG
* * * *
623978 TTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAACCAGGA
1 TTGGAGTATCCCCGATTATGGAAAAATTAGTATTTTAGCG--ATAAAACCAGGA
* * *
624030 TTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCGATAAAACCGGGG
1 TTGGAGTATCCCCGATTATGGAAAAATTAGTATTTTAGCGATAAAACCAGGA
624082 TTGGAGTATCCCC
1 TTGGAGTATCCCC
624095 TCGGAAATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
52 40 0.71
53 15 0.27
54 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (52 bp):
TTGGAGTATCCCCGATTATGGAAAAATTAGTATTTTAGCGATAAAACCAGGA
Found at i:624178 original size:55 final size:52
Alignment explanation
Indices: 624113--624240 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 52
624103 AACGGGGTTG
**
624113 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAA-TAAAATCGGAGTTA
1 GAGTATCCCCGATTGTGAAGAAATTAATG---TTTT-GAAAGTAAAATCGGAGTTA
* * *
624168 GAGTATCCCCGATTAT-AGGAAATTAATGTTTTGAAAGTAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAAGAAATTAATGTTTTGAAAGTAAAATCGGAGTTA
* * *
624219 GAATATCCTCGATTGTGGAGAA
1 GAGTATCCCCGATTGTGAAGAA
624241 TTGAGCAACT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
50 4 0.07
51 30 0.49
52 3 0.05
54 9 0.15
55 15 0.25
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (52 bp):
GAGTATCCCCGATTGTGAAGAAATTAATGTTTTGAAAGTAAAATCGGAGTTA
Found at i:624226 original size:134 final size:131
Alignment explanation
Indices: 623966--624226 Score: 339
Period size: 135 Copynumber: 2.0 Consensus size: 131
623956 TATCCCCGAT
*
623966 GAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCAGGAT
1 GAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCAGGAT
* * ** * *
624031 TGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCGATAAAACCGGGGTTGGAGTATCCCCT
66 TAGAGTATCCCCGATTATGG-AAAATTAATGTTTTAAAGATAAAACCGGAGTTGGAATATCCCCT
624096 CG
130 CG
* * *
624098 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATC-G
1 GAAATAACGAGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATTTTTGGAAATAAAACCAG
*
624162 GAGTTAGAGTATCCCCGATTATAGG-AAATTAATGTTTTGAAAG-TAAAATCGGAGTTGGAATAT
63 GA-TTAGAGTATCCCCGATTAT-GGAAAATTAATGTTTT-AAAGATAAAACCGGAGTTGGAATAT
624225 CC
125 CC
624227 TCGATTGTGG
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
132 32 0.29
133 5 0.04
134 35 0.31
135 38 0.34
136 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (131 bp):
GAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAACCAGGAT
TAGAGTATCCCCGATTATGGAAAATTAATGTTTTAAAGATAAAACCGGAGTTGGAATATCCCCTC
G
Found at i:624229 original size:132 final size:130
Alignment explanation
Indices: 623949--624226 Score: 330
Period size: 132 Copynumber: 2.1 Consensus size: 130
623939 AAGTAACGGG
* *
623949 GTTGGAGTATCCC-CGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTT
1 GTTGGAATATCCCTCG--GAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTT
* * **
624013 TGGAAATAAAACCAGGATTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCGATAAAACC
64 TGGAAATAAAACCAGGATTAGAGTATCCCCGATTATGG-AAAATTAATGTTTTAAAGATAAAACC
*
624078 GGG
128 GGA
* * *
624081 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTT
1 GTTGGAATAT-CCCTCGGAAATAACGAGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTATT
*
624146 TTTGGAAATAAAATC-GGAGTTAGAGTATCCCCGATTATAGG-AAATTAATGTTTTGAAAG-TAA
62 TTTGGAAATAAAACCAGGA-TTAGAGTATCCCCGATTAT-GGAAAATTAATGTTTT-AAAGATAA
*
624208 AATCGGA
124 AACCGGA
624215 GTTGGAATATCC
1 GTTGGAATATCC
624227 TCGATTGTGG
Statistics
Matches: 127, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
132 42 0.33
133 10 0.08
134 35 0.28
135 38 0.30
136 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (130 bp):
GTTGGAATATCCCTCGGAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTG
GAAATAAAACCAGGATTAGAGTATCCCCGATTATGGAAAATTAATGTTTTAAAGATAAAACCGGA
Found at i:626608 original size:13 final size:13
Alignment explanation
Indices: 626590--626615 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
626580 ACAAAGATCC
626590 ATGTATCGATACA
1 ATGTATCGATACA
626603 ATGTATCGATACA
1 ATGTATCGATACA
626616 CAGAAAAATG
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:626611 original size:33 final size:33
Alignment explanation
Indices: 626569--626635 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
626559 AAAATTTCCA
***
626569 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
626602 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
626635 A
1 A
626636 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:626679 original size:19 final size:18
Alignment explanation
Indices: 626655--626722 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
626645 CAGTAGCTAA
626655 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
626674 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
626689 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
626706 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
626723 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:626695 original size:13 final size:13
Alignment explanation
Indices: 626677--626701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
626667 ACAATACTTA
626677 TGTATCGATACAT
1 TGTATCGATACAT
626690 TGTATCGATACA
1 TGTATCGATACA
626702 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:626699 original size:32 final size:32
Alignment explanation
Indices: 626658--626720 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
626648 TAGCTAATTA
*
626658 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
626690 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
626721 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:626802 original size:21 final size:21
Alignment explanation
Indices: 626778--626834 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
626768 CATTTGTAGG
626778 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
626799 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
626820 ATGTATCGATACATT
1 ATGTATCGATACATT
626835 TAATTTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:628772 original size:21 final size:21
Alignment explanation
Indices: 628739--628788 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
628729 TTGCAAGTTG
*
628739 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
628761 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
628782 AAATAAA
1 AAATAAA
628789 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:630606 original size:15 final size:15
Alignment explanation
Indices: 630586--630624 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
630576 TAAAAATGTC
*
630586 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
630601 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
630616 CCAAATGAA
1 CAAAATGAA
630625 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:632716 original size:13 final size:13
Alignment explanation
Indices: 632698--632735 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
632688 CATTTTTCTT
632698 TGTATCGATACAA
1 TGTATCGATACAA
*
632711 TGTATCGATACAC
1 TGTATCGATACAA
632724 TGTATCGATACA
1 TGTATCGATACA
632736 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:632890 original size:20 final size:20
Alignment explanation
Indices: 632847--632892 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
632837 AAATCTTTTG
632847 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
632868 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
632888 CAAAA
1 CAAAA
632893 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:635294 original size:19 final size:19
Alignment explanation
Indices: 635270--635334 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
635260 TAGCCAAACT
635270 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
635289 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
635302 TGTATCGATACACATAAAATA
1 TGTATCGATACAC--AAAATA
635323 TGTATCGATACA
1 TGTATCGATACA
635335 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:635306 original size:13 final size:13
Alignment explanation
Indices: 635288--635313 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
635278 TACACAAAAT
635288 ATGTATCGATACA
1 ATGTATCGATACA
635301 ATGTATCGATACA
1 ATGTATCGATACA
635314 CATAAAATAT
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:635311 original size:32 final size:33
Alignment explanation
Indices: 635270--635334 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
635260 TAGCCAAACT
635270 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
635302 TGTATCGATACACATAAAATATGTATCGATACA
1 TGTATCGATACACA-AAAATATGTATCGATACA
635335 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:639375 original size:166 final size:165
Alignment explanation
Indices: 639180--639621 Score: 506
Period size: 165 Copynumber: 2.7 Consensus size: 165
639170 GGGGTTTTTT
*
639180 CTCCGTAAATTTTTTCGGGAGGATTTTTCTTAAGTTTT-AATTTTAAAAATTCATCAAATATGT-
1 CTCCGTAAATTTTTTCGGGA-GATTTTTCTT-AGTTTTCAATTTT-AAAATTCATCAAACAT-TA
* *
639243 TTATTTATTTCAGT-TTAATTCAGTTTTCAAAAGTTCTTTCATTTTCATGAGCTTTTGA-TTTTT
62 TTATTTATTTCA-TATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGCTTTTGATTTTTT
* * * * *
639306 CCTTGAAATTTTCTTTTTTT-TTGAAATATGGTGTTTTCTA
126 CCTTGAAACTTCCTTTTTTTCCT-AAATACGGTATTTTCTA
* * *
639346 CTTCGTAAATTTTTTCAGGGAGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAACATTATC
1 CTCCGTAAATTTTTTC-GGGAGATTTTTCTTAGTTTTCAA-TTTTAAAATTCATCAAACATTATT
* * * * *
639411 ATTTATTTCATATTAATTCAATTTTTAAAAATTGA-T-ATTTCCATGAGTTTTTGATTTTTTCCT
64 ATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGCTTTTGATTTTTTCCT
639474 TGAAACTTCCTTTTTTTCCTAAATACGGTATTTTCTA
129 TGAAACTTCCTTTTTTTCCTAAATACGGTATTTTCTA
* * * * * *
639511 CTCCATAAATTCTTTCGAGAGAATTTTTCTCAGTTTTCAATTTGTAGAATTCATCAAACATCATC
1 CTCCGTAAATTTTTTCGGGAG-ATTTTTCTTAGTTTTCAATTT-TAAAATTCATCAAACATTAT-
*
639576 T-TTTGA-TTCATATTAATTTAGTTTTCAAAAATTCATTCATTTTCAT
63 TATTT-ATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCAT
639622 TCATTTTTGA
Statistics
Matches: 233, Mismatches: 30, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
164 23 0.10
165 121 0.52
166 74 0.32
167 15 0.06
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.50
Consensus pattern (165 bp):
CTCCGTAAATTTTTTCGGGAGATTTTTCTTAGTTTTCAATTTTAAAATTCATCAAACATTATTAT
TTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATGAGCTTTTGATTTTTTCCTTG
AAACTTCCTTTTTTTCCTAAATACGGTATTTTCTA
Found at i:642429 original size:154 final size:154
Alignment explanation
Indices: 641999--642497 Score: 515
Period size: 153 Copynumber: 3.2 Consensus size: 154
641989 GGATACTTTC
* * *
641999 ACGTCGAAGGTATACTTAGGGGCATTTTCATAATTTTTTAAAATCGAGTCCTAAGTTGTCACTG-
1 ACGTCGAAGGTATCCTTAGGGGCATTTTCGTAATTTTTTAAAATCGAGTCCTAAGTTGTCACCGA
* * *
642063 GGCCTACTTTTATGCCGAAAGTGGGTATTTAGGATAGGTT--TGCCCTATCCATATCCTTGTTAA
66 GTCC-ACTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCAT-CCCTATCCATATCCTTTTTAA
* * *
642126 ATCCTTTAGGGGTATTGGGCACTGTT
129 ATCCTTTAGGGGTATCGAGCACTATT
* * ** * * * *
642152 ACGCCGAAGGTATCCTTAAGGATATTTTAGTAATTTTTTAAAATCGAGTCCTAGGTTGT-AACTA
1 ACGTCGAAGGTATCCTTAGGGGCATTTTCGTAATTTTTTAAAATCGAGTCCTAAGTTGTCACCGA
*** * *
642216 GGTTTGCTTTTATACCGAAGGTGGGTATTTAGGATAGGTTCA-CCCCATCCATATCCTTTTTAAA
66 -GTCCACTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCTATCCATATCCTTTTTAAA
642280 TCCTTTAGGGGTATCGAGCACTATT
130 TCCTTTAGGGGTATCGAGCACTATT
* * * * *
642305 ACATCGAAGGTATCCCCTAGGGGTATTTTCGTAATTTTTTAAAATCGAGTTCTACGTTGTCACCG
1 ACGTCGAAGGTAT-CCTTAGGGGCATTTTCGTAATTTTTTAAAATCGAGTCCTAAGTTGTCACCG
* * * * * ** * ***
642370 AGTCCACTTTTATGCCGAAGGTAGATATTTAGGATATGTTCATCCTTTTTAATATCTTTTTTTGG
65 AGTCCACTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCTATCCATATCCTTTTTAAA
* * *
642435 TCATTTAGGGGTATC-AGGTACTTTT
130 TCCTTTAGGGGTATCGA-GCACTATT
* *
642460 ACGTCGAAGGTATCCCTTAGAGGCATTTTTGTAATTTT
1 ACGTCGAAGGTAT-CCTTAGGGGCATTTTCGTAATTTT
642498 CCTTGAACTT
Statistics
Matches: 282, Mismatches: 56, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
152 1 0.00
153 136 0.48
154 76 0.27
155 69 0.24
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (154 bp):
ACGTCGAAGGTATCCTTAGGGGCATTTTCGTAATTTTTTAAAATCGAGTCCTAAGTTGTCACCGA
GTCCACTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCTATCCATATCCTTTTTAAAT
CCTTTAGGGGTATCGAGCACTATT
Found at i:645849 original size:27 final size:27
Alignment explanation
Indices: 645786--645850 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
645776 AGAAACACAA
*
645786 AAAAAAAAAAGAGAAAAAGAATAAACG
1 AAAAAGAAAAGAGAAAAAGAATAAACG
* * *
645813 AAAACTGAAAAG-GAAAAAGCATGAAATG
1 AAAA-AGAAAAGAGAAAAAGAAT-AAACG
645841 AAAAAGAAAA
1 AAAAAGAAAA
645851 TGTAGATAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 18 0.58
28 13 0.42
ACGTcount: A:0.72, C:0.05, G:0.17, T:0.06
Consensus pattern (27 bp):
AAAAAGAAAAGAGAAAAAGAATAAACG
Found at i:647497 original size:42 final size:42
Alignment explanation
Indices: 647368--647497 Score: 104
Period size: 41 Copynumber: 3.1 Consensus size: 42
647358 CGACAAGTTG
* * *
647368 ACAAAGGATAAAAAGATTTACCTAGGACTAAGCTGACAAGTAA
1 ACAAAGGAT-AAAAGATTTACTTGGGACTAAGCTGGCAAGTAA
* * * * * ** *
647411 ACAAGGGATGAAAGATTGA-TTGGGATTGAACCAAAG-AA-TCA
1 ACAAAGGATAAAAGATTTACTTGGGACT-AAGC-TGGCAAGTAA
*
647452 ACAACGGATAAAAGATTTACTTGGGACTAAGCTGGCAAGTAA
1 ACAAAGGATAAAAGATTTACTTGGGACTAAGCTGGCAAGTAA
647494 ACAA
1 ACAA
647498 GAGAAGAAAG
Statistics
Matches: 63, Mismatches: 19, Indels: 11
0.68 0.20 0.12
Matches are distributed among these distances:
40 1 0.02
41 28 0.44
42 26 0.41
43 8 0.13
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.19
Consensus pattern (42 bp):
ACAAAGGATAAAAGATTTACTTGGGACTAAGCTGGCAAGTAA
Found at i:647560 original size:82 final size:81
Alignment explanation
Indices: 647371--647577 Score: 247
Period size: 82 Copynumber: 2.5 Consensus size: 81
647361 CAAGTTGACA
* * * **
647371 AAGGATAAAAAGATTTACCTAGGACTAAGCTGACAAGTAAACAAGGGATGAAAGATTGATTGGGA
1 AAGGAT-AAAAGATTTACCTGGGACTAAGCTGACAAGTAAACAAGAGAAGAAAGATTGATTAAGA
647436 TTGAACCAAAGAATCAAC
65 TTGAACCAAAG-ATCAAC
* *
647454 AACGGATAAAAGATTTACTTGGGACTAAGCTGGCAAGTAAACAAGAGAAGAAAG-TTGATTAAGA
1 AA-GGATAAAAGATTTACCTGGGACTAAGCTGACAAGTAAACAAGAGAAGAAAGATTGATTAAGA
* *
647518 TTGAACTGACAAG-TCAAT
65 TTGAAC-CA-AAGATCAAC
* *
647536 AGAGGATAAAAGATTTACCCGGGACTAAGCTGACAGGTAAAC
1 A-AGGATAAAAGATTTACCTGGGACTAAGCTGACAAGTAAAC
647578 GATAGATAAA
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
82 54 0.50
83 46 0.43
84 7 0.07
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.20
Consensus pattern (81 bp):
AAGGATAAAAGATTTACCTGGGACTAAGCTGACAAGTAAACAAGAGAAGAAAGATTGATTAAGAT
TGAACCAAAGATCAAC
Found at i:647982 original size:42 final size:42
Alignment explanation
Indices: 647936--648279 Score: 243
Period size: 42 Copynumber: 8.2 Consensus size: 42
647926 CTCAACGAGC
* **
647936 AGACAAAAGATAAAGAAGTCTCCCAGGTCAAAGTTGACGGGT
1 AGACAAAAGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGT
* * * ** *
647978 AGACAAAAGGAAAAAAAGTCTCCC-GAGTCAAAGTCGATAGGC
1 AGACAAAAGGTAAAGAAGTCTCCCAG-GTCAAAGCCGACGGGT
* * * * *
648020 AAACAAAAGGTAAAGAAGTCTCCTAGGTCAAAACCAAC-AGT
1 AGACAAAAGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGT
* * *
648061 AGACAAAGGGTAAAGAAGTCTCCCAGGTCAAAGCCGATGGGC
1 AGACAAAAGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGT
* * *** * ** *
648103 AAACAAAGGGTAAAGAAGTCTCTTGGGTTAAAGCCGACAAGC
1 AGACAAAAGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGT
* * * *
648145 AGACAAAAGATGAAGAAGTCT-CCTGAGTCAAAGCCGACGAGCT
1 AGACAAAAGGTAAAGAAGTCTCCCAG-GTCAAAGCCGACG-GGT
* * * * *
648188 -GACAAAGGGTGAAAG-AGTCTCTCGGGTTAAAGCTGACGGGT
1 AGACAAAAGGT-AAAGAAGTCTCCCAGGTCAAAGCCGACGGGT
* * * *
648229 AGACAAAGGGTAAA-AGAGTCTCTCAGGTCAAAGCCAACGGAT
1 AGACAAAAGGTAAAGA-AGTCTCCCAGGTCAAAGCCGACGGGT
648271 AGA-AAAAGG
1 AGACAAAAGG
648280 ATCAAAGGTA
Statistics
Matches: 233, Mismatches: 59, Indels: 21
0.74 0.19 0.07
Matches are distributed among these distances:
41 45 0.19
42 182 0.78
43 6 0.03
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.15
Consensus pattern (42 bp):
AGACAAAAGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGT
Found at i:648104 original size:83 final size:84
Alignment explanation
Indices: 647938--648124 Score: 234
Period size: 83 Copynumber: 2.2 Consensus size: 84
647928 CAACGAGCAG
* **** *
647938 ACAAAAGATAAAGAAGTCTCCCAGGTCAAAGTTGACGGGTAGACAAAAGGAAAAAAAGTCTCCCG
1 ACAAAAGGTAAAGAAGTCTCCCAGGTCAAAACCAACGAGTAGACAAAAGGAAAAAAAGTCTCCCG
*
648003 AGTCAAAGTCGATAGGCAA
66 AGTCAAAGCCGATAGGCAA
* * * *
648022 ACAAAAGGTAAAGAAGTCTCCTAGGTCAAAACCAAC-AGTAGACAAAGGGTAAAGAAGTCTCCC-
1 ACAAAAGGTAAAGAAGTCTCCCAGGTCAAAACCAACGAGTAGACAAAAGGAAAAAAAGTCTCCCG
*
648085 AGGTCAAAGCCGATGGGCAA
66 A-GTCAAAGCCGATAGGCAA
*
648105 ACAAAGGGTAAAGAAGTCTC
1 ACAAAAGGTAAAGAAGTCTC
648125 TTGGGTTAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 1 0.01
83 58 0.65
84 30 0.34
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (84 bp):
ACAAAAGGTAAAGAAGTCTCCCAGGTCAAAACCAACGAGTAGACAAAAGGAAAAAAAGTCTCCCG
AGTCAAAGCCGATAGGCAA
Found at i:648109 original size:125 final size:127
Alignment explanation
Indices: 647928--648263 Score: 308
Period size: 125 Copynumber: 2.7 Consensus size: 127
647918 GAGATTGACT
* * ** * *
647928 CAACGAGC-AGACAAAAGATAAAGAAGTCTCCCAGGTCAAAGTTGACGGGTAGACAAAAGGAAAA
1 CAACGAGCTAGACAAAGGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGCAAACAAAAGGAAAA
* * * *
647992 AAAGTCTCCCGAGTCAAAGTCGATAGGCAAACAAAAGGTAAAGAAGTCTCCT-AGGTCAAAAC
66 AAAGTCTCCCGAGTCAAAGCCGACAAGCAAACAAAAGATAAAGAAGTCTCCTGA-GTCAAAAC
* * *
648054 CAAC-AG-TAGACAAAGGGTAAAGAAGTCTCCCAGGTCAAAGCCGATGGGCAAACAAAGGGTAAA
1 CAACGAGCTAGACAAAGGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGCAAACAAAAGGAAAA
* ** * * * * *
648117 GAAGTCTCTTGGGTTAAAGCCGACAAGCAGACAAAAGATGAAGAAGTCTCCTGAGTCAAAGC
66 AAAGTCTCCCGAGTCAAAGCCGACAAGCAAACAAAAGATAAAGAAGTCTCCTGAGTCAAAAC
* * * * * * * * *
648179 CGACGAGCT-GACAAAGGGTGAAAG-AGTCTCTCGGGTTAAAGCTGACGGGTAGACAAAGGGTAA
1 CAACGAGCTAGACAAAGGGT-AAAGAAGTCTCCCAGGTCAAAGCCGACGGGCAAACAAAAGGAAA
* *
648242 AAGAGTCTCTC-AGGTCAAAGCC
65 AAAAGTCTCCCGA-GTCAAAGCC
648264 AACGGATAGA
Statistics
Matches: 170, Mismatches: 34, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
125 100 0.59
126 65 0.38
127 5 0.03
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (127 bp):
CAACGAGCTAGACAAAGGGTAAAGAAGTCTCCCAGGTCAAAGCCGACGGGCAAACAAAAGGAAAA
AAAGTCTCCCGAGTCAAAGCCGACAAGCAAACAAAAGATAAAGAAGTCTCCTGAGTCAAAAC
Found at i:648176 original size:84 final size:82
Alignment explanation
Indices: 647978--648220 Score: 247
Period size: 83 Copynumber: 2.9 Consensus size: 82
647968 GTTGACGGGT
* * * *
647978 AGACAAAAGGA-AAAAAAGTCTCCCGAGTCAAAGTCGATAGGCAAACAAAAGGTAAAGAAGTCTC
1 AGACAAAA-GATAAAGAAGTCT-CCGAGTCAAAGCCGATGGGCAAACAAAGGGTAAAGAAGTCTC
* * * * *
648042 CTAGGTCAAAACCAACAGT
64 TTGGGTTAAAGCCAACAGC
* * *
648061 AGACAAAGGGTAAAGAAGTCTCCCAGGTCAAAGCCGATGGGCAAACAAAGGGTAAAGAAGTCTCT
1 AGACAAAAGATAAAGAAGTCTCCGA-GTCAAAGCCGATGGGCAAACAAAGGGTAAAGAAGTCTCT
*
648126 TGGGTTAAAGCCGACAAGC
65 TGGGTTAAAGCCAAC-AGC
* * * **
648145 AGACAAAAGATGAAGAAGTCTCCTGAGTCAAAGCCGACGAGCTGACAAAGGGTGAAAG-AGTCTC
1 AGACAAAAGATAAAGAAGTCTCC-GAGTCAAAGCCGATGGGCAAACAAAGGGT-AAAGAAGTCTC
*
648209 TCGGGTTAAAGC
64 TTGGGTTAAAGC
648221 TGACGGGTAG
Statistics
Matches: 133, Mismatches: 22, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
82 4 0.03
83 62 0.47
84 62 0.47
85 5 0.04
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.14
Consensus pattern (82 bp):
AGACAAAAGATAAAGAAGTCTCCGAGTCAAAGCCGATGGGCAAACAAAGGGTAAAGAAGTCTCTT
GGGTTAAAGCCAACAGC
Found at i:648543 original size:44 final size:44
Alignment explanation
Indices: 648409--648649 Score: 144
Period size: 44 Copynumber: 5.5 Consensus size: 44
648399 AGATTTGACC
* * * * * *
648409 AGGGTGGTAACCATATGTCAAATCAGAATGAAAAACAATCTATCC
1 AGGGTGGTAACCATACGTCAGATAAGAATG-AAAAGAATCTAACT
* * * ** * * *
648454 AGGGTGGTAACCATACGTTAGATAAAAAGGAAGTGGATTTGACT
1 AGGGTGGTAACCATACGTCAGATAAGAATGAAAAGAATCTAACT
**
648498 AGGGTGGTAACCATACGTCAGATTGGAATGAAAAGAATCTAACT
1 AGGGTGGTAACCATACGTCAGATAAGAATGAAAAGAATCTAACT
* * * * ** * * *
648542 AGGGTGGTAACCATGCATTAGATAAGAAAGATGTAGACT-TGACC
1 AGGGTGGTAACCATACGTCAGATAAGAATGA-AAAGAATCTAACT
* * * * * *
648586 AAGGTGGTAACCATACGTCAAAT-CGAAATAAAAAGAATCTGACC
1 AGGGTGGTAACCATACGTCAGATAAG-AATGAAAAGAATCTAACT
**
648630 AGGGTAATAACCATACGTCA
1 AGGGTGGTAACCATACGTCA
648650 TATAGGAAAG
Statistics
Matches: 144, Mismatches: 49, Indels: 7
0.72 0.25 0.04
Matches are distributed among these distances:
43 5 0.03
44 111 0.77
45 28 0.19
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (44 bp):
AGGGTGGTAACCATACGTCAGATAAGAATGAAAAGAATCTAACT
Found at i:648584 original size:88 final size:88
Alignment explanation
Indices: 648397--648645 Score: 302
Period size: 88 Copynumber: 2.8 Consensus size: 88
648387 CAGGAATGAG
* * * *
648397 GTAGATTTGACCAGGGTGGTAACCATATGTCAAATCAGAATGAAAAACAATCTATCCAGGGTGGT
1 GTAGATTTGACCAGGGTGGTAACCATACGTCAAATCGGAATG-AAAAGAATCTAACCAGGGTGGT
*
648462 AACCATACGTTAGATAAAAAGGAA
65 AACCATACATTAGATAAAAAGGAA
* * * * *
648486 GTGGATTTGACTAGGGTGGTAACCATACGTCAGATTGGAATGAAAAGAATCTAACTAGGGTGGTA
1 GTAGATTTGACCAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTAACCAGGGTGGTA
* *
648551 ACCATGCATTAGATAAGAAA-GAT
66 ACCATACATTAGATAA-AAAGGAA
* * * * * **
648574 GTAGACTTGACCAAGGTGGTAACCATACGTCAAATCGAAATAAAAAGAATCTGACCAGGGTAATA
1 GTAGATTTGACCAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTAACCAGGGTGGTA
648639 ACCATAC
66 ACCATAC
648646 GTCATATAGG
Statistics
Matches: 134, Mismatches: 25, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
88 95 0.71
89 39 0.29
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (88 bp):
GTAGATTTGACCAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTAACCAGGGTGGTA
ACCATACATTAGATAAAAAGGAA
Found at i:648659 original size:88 final size:87
Alignment explanation
Indices: 648361--648676 Score: 298
Period size: 88 Copynumber: 3.6 Consensus size: 87
648351 CAAATCGTTT
* * * * *
648361 TACCAAGGTGGTAACCATACGTCA-AGCAGGAATGAGGTAGATTTGACCAGGGTGGTAACCATAT
1 TACCAGGGTGGTAACCATACGTCAGA-TAGGAAAGAAGTAGATTTGACCAGGGTGGTAACCATAC
*
648425 GTCAAATC-AGAATGAAAAACAATC
65 GTCAAATCGA-AAT-AAAAAGAATC
* * * *
648449 TATCCAGGGTGGTAACCATACGTTAGATA-AAAAGGAAGTGGATTTGACTAGGGTGGTAACCATA
1 TA-CCAGGGTGGTAACCATACGTCAGATAGGAAA-GAAGTAGATTTGACCAGGGTGGTAACCATA
* * * *
648513 CGTCAGATTGGAATGAAAAGAATC
64 CGTCAAATCGAAATAAAAAGAATC
* * * * * * * *
648537 TAACTAGGGTGGTAACCATGCATTAGATAAGAAAGATGTAGACTTGACCAAGGTGGTAACCATAC
1 T-ACCAGGGTGGTAACCATACGTCAGATAGGAAAGAAGTAGATTTGACCAGGGTGGTAACCATAC
648602 GTCAAATCGAAATAAAAAGAATC
65 GTCAAATCGAAATAAAAAGAATC
** * *
648625 TGACCAGGGTAATAACCATACGTCATATAGGAAAG-AGGAGAGTTTGACCAGG
1 T-ACCAGGGTGGTAACCATACGTCAGATAGGAAAGAAGTAGA-TTTGACCAGG
648677 TCCTAACACC
Statistics
Matches: 181, Mismatches: 40, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
87 4 0.02
88 115 0.64
89 61 0.34
90 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (87 bp):
TACCAGGGTGGTAACCATACGTCAGATAGGAAAGAAGTAGATTTGACCAGGGTGGTAACCATACG
TCAAATCGAAATAAAAAGAATC
Found at i:648812 original size:48 final size:47
Alignment explanation
Indices: 648663--648819 Score: 154
Period size: 48 Copynumber: 3.3 Consensus size: 47
648653 AGGAAAGAGG
* ** * *
648663 AGAGTTTGACCAGGTCCTAACACCAATATAATCAAACGAAGGG-TAAAA
1 AGAGTTTGACCAGG-CCTAACACCAATACAGCCAAA-TAAGGGATGAAA
* * * * **
648711 AGAGTTTGACTAGGCCCTAAGACCAATACAGCCAAATGAGGGAAGATT
1 AGAGTTTGACCAGG-CCTAACACCAATACAGCCAAATAAGGGATGAAA
* *
648759 TGAGTTTGACCAGGCGCTAACACCAATACAGGCAAATAAGGGATGAAA
1 AGAGTTTGACCAGGC-CTAACACCAATACAGCCAAATAAGGGATGAAA
648807 AGAGTTTGACCAG
1 AGAGTTTGACCAG
648820 ATACAGTCAA
Statistics
Matches: 86, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
47 5 0.06
48 81 0.94
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (47 bp):
AGAGTTTGACCAGGCCTAACACCAATACAGCCAAATAAGGGATGAAA
Found at i:649435 original size:20 final size:20
Alignment explanation
Indices: 649412--649556 Score: 137
Period size: 20 Copynumber: 6.7 Consensus size: 20
649402 AAGTACCCAG
649412 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
649432 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
649452 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
649472 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
649492 AAGTATCGATACATTCTGTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
649522 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
649543 ATGTATCGATACAT
1 ATGTATCGATACAT
649557 CTAGTTAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
20 79 0.76
21 2 0.02
24 5 0.05
27 4 0.04
30 2 0.02
31 12 0.12
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:655002 original size:20 final size:20
Alignment explanation
Indices: 654938--655012 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
654928 AAAAAGACAT
* *
654938 AATGTATCAATACATTGAAG
1 AATGTATCGATACATTGAAA
* *
654958 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
654978 CATGTATCGATACAGTGAAA
1 AATGTATCGATACATTGAAA
*
654998 AATGTGTCGATACAT
1 AATGTATCGATACAT
655013 CTGGGTACTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:655002 original size:40 final size:39
Alignment explanation
Indices: 654935--655012 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
654925 GGTAAAAAGA
* *
654935 CATAATGTATCAATACATTGAAGAATGTATCGATACATT
1 CATAATGTATCAATACAGTGAAAAATGTATCGATACATT
* *
654974 CATACATGTATCGATACAGTGAAAAATGTGTCGATACAT
1 CATA-ATGTATCAATACAGTGAAAAATGTATCGATACAT
655013 CTGGGTACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (39 bp):
CATAATGTATCAATACAGTGAAAAATGTATCGATACATT
Found at i:656029 original size:28 final size:28
Alignment explanation
Indices: 655911--656412 Score: 576
Period size: 28 Copynumber: 17.5 Consensus size: 28
655901 CATTAACTTA
** *
655911 TGTGGGCTTTGAAAAGACTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
655941 CGTGTGGGCTTTGAAAAGAGTTACCACT-AGCT
1 --TGTGGGCTTTG-AAAG-GGTGCCACTGA-CT
* *
655973 TGTGGGCTTTGAAAAGAGTGCCACGGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
656002 TGTGGGCTTTGAAAGGGTGCTATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
656030 TCTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
656058 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
656087 TGTGGACTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
656115 TGTGGACTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
656144 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
656172 TGCATGGGCTTTGAAAGGGTGCCACTGACT
1 TG--TGGGCTTTGAAAGGGTGCCACTGACT
* *
656202 TGTGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
656230 TGTGGGCTTTGAAAGGGTACCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* ** *
656258 TGTGGGCTTTAAAAAAAGTGCCATTGACT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACT
656287 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
656315 TATGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
**
656344 TGTGGG-TTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
656372 TGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
656400 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
656413 GAGATGAACG
Statistics
Matches: 411, Mismatches: 50, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
28 227 0.55
29 113 0.27
30 45 0.11
31 1 0.00
32 25 0.06
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:656068 original size:85 final size:85
Alignment explanation
Indices: 655911--656412 Score: 600
Period size: 85 Copynumber: 5.8 Consensus size: 85
655901 CATTAACTTA
** * * *
655911 TGTGGGCTTTGAAAAGACTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTTACCACT-AGCTTG
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTG-AAAG-GATGCCACTGA-CTTG
*
655975 TGGGCTTTGAAAAGAGTGCCACGGACT
59 TGGGCTTTGAAAAGAGTGCCACTGACT
* * * *
656002 TGTGGGCTTTGAAAGGGTGCTATTGACTTCTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
656067 TGAAAAGAGTGCCACTGACT
66 TGAAAAGAGTGCCACTGACT
* * * *
656087 TGTGGACTTTGAAAGGGTGCCACTGACTTGTGGACTTTGAAAAGAGTGCCACTGATTTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCT
*
656152 TTG-AAAGGGTGCCACTGACT
65 TTGAAAAGAGTGCCACTGACT
*
656172 TGCATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGC
1 TG--TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
* * *
656237 TTTG-AAAGGGTACCACTAACT
64 TTTGAAAAGAGTGCCACTGACT
* ** * * *
656258 TGTGGGCTTTAAAAAAAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCT
1 TGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
*
656323 TTGAAAAGAGTGCCACTAACT
65 TTGAAAAGAGTGCCACTGACT
**
656344 TGTGGG-TTTGAAAAAAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGC
656407 TTTGAA
64 TTTGAA
656413 GAGATGAACG
Statistics
Matches: 367, Mismatches: 36, Indels: 22
0.86 0.08 0.05
Matches are distributed among these distances:
84 9 0.02
85 200 0.54
86 84 0.23
87 51 0.14
89 8 0.02
90 4 0.01
91 11 0.03
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
TGAAAAGAGTGCCACTGACT
Found at i:656087 original size:57 final size:58
Alignment explanation
Indices: 655911--656412 Score: 630
Period size: 57 Copynumber: 8.7 Consensus size: 58
655901 CATTAACTTA
* * *
655911 TGTGGGCTTTGAAAAGACTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTTACCACT-AGCT
1 TGTGGGCTTTGAAAAGA-GTGCCACTGACT--TGTGGGCTTTGAAAAGAG-TGCCACTGA-CT
* * * *
655973 TGTGGGCTTTGAAAAGAGTGCCACGGACTTGTGGGCTTTG-AAAGGGTGCTATTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
656030 TCTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * *
656087 TGTGGACTTTG-AAAGGGTGCCACTGACTTGTGGACTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
656144 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGCATGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTG--TGGGCTTTGAAAAGAGTGCCACTGACT
* * *
656202 TGTGGGCTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTG-AAAGGGTACCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * * *
656258 TGTGGGCTTTAAAAAAAGTGCCATTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
* * *
656315 TATGGGCTTTGAAAAGAGTGCCACTAACTTGTGGG-TTTGAAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
656372 TGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAA
656413 GAGATGAACG
Statistics
Matches: 390, Mismatches: 41, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
56 88 0.23
57 207 0.53
58 45 0.12
59 23 0.06
61 10 0.03
62 17 0.04
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (58 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:657679 original size:11 final size:11
Alignment explanation
Indices: 657631--657689 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
657621 CCCCTTTCTG
* *
657631 TTTTTTTGCTA
1 TTTTTTTGTTT
* *
657642 TTTTTTTCTTGG
1 TTTTTTTGTT-T
657654 TTTTTTT-TTT
1 TTTTTTTGTTT
*
657664 GTTTTTTGTTT
1 TTTTTTTGTTT
657675 TTTTTTTGTTT
1 TTTTTTTGTTT
657686 TTTT
1 TTTT
657690 GGGTGTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 6 0.15
11 27 0.68
12 7 0.17
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:657690 original size:19 final size:18
Alignment explanation
Indices: 657653--657688 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
657643 TTTTTTCTTG
657653 GTTTTTTTTTTGTTTTTT
1 GTTTTTTTTTTGTTTTTT
657671 GTTTTTTTTTTGTTTTTT
1 GTTTTTTTTTTGTTTTTT
657689 TGGGTGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (18 bp):
GTTTTTTTTTTGTTTTTT
Found at i:660028 original size:12 final size:12
Alignment explanation
Indices: 660011--660035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
660001 CCTGGATTTT
660011 GCTTTCGAAGGA
1 GCTTTCGAAGGA
660023 GCTTTCGAAGGA
1 GCTTTCGAAGGA
660035 G
1 G
660036 TCAAAAAATG
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:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (12 bp):
GCTTTCGAAGGA
Found at i:664665 original size:13 final size:13
Alignment explanation
Indices: 664647--664703 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
664637 CATAAAGTGT
664647 TGTATCGATACAA
1 TGTATCGATACAA
664660 TGTATCGATACATAA
1 TGTATCGATAC--AA
664675 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
664692 TGTATCGATACA
1 TGTATCGATACA
664704 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:664682 original size:32 final size:32
Alignment explanation
Indices: 664627--664727 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
664617 TTCAACGATT
664627 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
664660 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
664692 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
664724 TGTA
1 TGTA
664728 AGCTACTGCC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 54 0.81
33 13 0.19
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:664684 original size:19 final size:18
Alignment explanation
Indices: 664625--664722 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
664615 ATTTCAACGA
664625 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
664644 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
664660 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
664676 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
664692 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
664708 TTTTGTATCGATACA
1 -TTTGTATCGATACA
664723 ATGTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:664783 original size:13 final size:13
Alignment explanation
Indices: 664765--664789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
664755 ATTACTCAAA
664765 TGTATCGATACAT
1 TGTATCGATACAT
664778 TGTATCGATACA
1 TGTATCGATACA
664790 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:678891 original size:79 final size:79
Alignment explanation
Indices: 678703--679009 Score: 289
Period size: 79 Copynumber: 3.9 Consensus size: 79
678693 GGAGATGACC
* * * * *
678703 ACGGGGCTGGAGTATCCTCGATTATGGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTAGAGTA
1 ACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGAAAATAAAATCAGGGTTAGAGTA
* *
678768 TCCCCTCGAAAATA
66 TCCTCTTGAAAATA
* * ** * * *
678782 ACAGGATTGGAGTATCCCTAATTATAGAAAATCGGTATTTTGAAAATAAAATCAGGGTTGGAGTA
1 ACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGAAAATAAAATCAGGGTTAGAGTA
* *
678847 TCCTTTTAAAAATA
66 TCCTCTTGAAAATA
* * ** * ***
678861 ACGGGGTTAGAGTATCCCCGATTGTGGAAAATCAATGCTTT-AGAAATAAGGCCAGGGTTAGAGT
1 ACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGA-AAATAAAATCAGGGTTAGAGT
*
678925 ATCCTCGTGAAAATA
65 ATCCTCTTGAAAATA
* * * *
678940 ACGAGGTTGGAGTATCCCCGA-T-TGCGAGAAATTGGTGTTTTGGAAATAAAATC-GGAGTTGGA
1 ACGGGGTTGGAGTATCCCCGATTATG-GA-AAATCGGTGTTTTGAAAATAAAATCAGG-GTTAGA
679002 GTATCCTC
63 GTATCCTC
679010 GATTGTGAAA
Statistics
Matches: 178, Mismatches: 45, Indels: 10
0.76 0.19 0.04
Matches are distributed among these distances:
77 2 0.01
78 6 0.03
79 170 0.96
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (79 bp):
ACGGGGTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTGAAAATAAAATCAGGGTTAGAGTA
TCCTCTTGAAAATA
Found at i:679013 original size:51 final size:51
Alignment explanation
Indices: 678945--679060 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 51
678935 AAATAACGAG
* * *
678945 GTTGGAGTATCCCCGATTGCGAGAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGCGAAAAATTGGTATTTTAGAAATAAAATCGGA
* * *
678996 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGCGAAAAATTGGTATTTTAGAAATAAAATCGGA
*
679047 GTTAGAGTATCCCC
1 GTTGGAGTATCCCC
679061 TCAGAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGCGAAAAATTGGTATTTTAGAAATAAAATCGGA
Found at i:679126 original size:105 final size:107
Alignment explanation
Indices: 679017--679270 Score: 300
Period size: 105 Copynumber: 2.4 Consensus size: 107
679007 CTCGATTGTG
* *
679017 AAAAATTGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCAGAAATAA-TGGGATTGGA
1 AAAAATTGATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCAGAAATAACAGGG-TTGGA
* *
679081 GTATCC-CGATGACATAACAGGGTTGGAGTACCGT-TTA-TGAA
65 GTATCCTCGATGAAATAACAGGGTTGGAGTACC-TCTAATTGAA
* * ** * * **
679122 AAAAATCGATATTTTAGATATAAAGCCAGGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGAG
1 AAAAATTGATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCAGAAATAACAGGGTTGGAG
* **
679187 TATCCTCGATGAAATAACAGGGTTGGAGTATCTCTAATTGTG
66 TATCCTCGATGAAATAACAGGGTTGGAGTACCTCTAATTGAA
* * *
679229 AAAAATTGATGTTTTGGAAATAAAATCGGAGTTAGAGTATCC
1 AAAAATTGATATTTTAGAAATAAAATCGGGGTTAGAGTATCC
679271 TCGATTGTCG
Statistics
Matches: 121, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
105 57 0.47
106 29 0.24
107 35 0.29
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (107 bp):
AAAAATTGATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCAGAAATAACAGGGTTGGAG
TATCCTCGATGAAATAACAGGGTTGGAGTACCTCTAATTGAA
Found at i:679188 original size:28 final size:28
Alignment explanation
Indices: 679148--679218 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 28
679138 GATATAAAGC
*
679148 CAGGGTTGGAGTATCC-CCTTGGAAATAA
1 CAGGGTTGGAGTATCCTCCAT-GAAATAA
*
679176 CAGGGTTGGAGTATCCTCGATGAAATAA
1 CAGGGTTGGAGTATCCTCCATGAAATAA
679204 CAGGGTTGGAGTATC
1 CAGGGTTGGAGTATC
679219 TCTAATTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 38 0.95
29 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.25
Consensus pattern (28 bp):
CAGGGTTGGAGTATCCTCCATGAAATAA
Found at i:679278 original size:51 final size:51
Alignment explanation
Indices: 679223--679351 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
679213 AGTATCTCTA
* *
679223 ATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTAGAGTATCCTCG
1 ATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTCAGAGTATCCCCG
* * *
679274 ATTGTCG-AAAATTGATGCTTTAGAAATAAAATCGGAGTCGGAGTATCCCCG
1 ATTGT-GAAAAATTGATGTTTTGGAAATAAAATCGGAGTCAGAGTATCCCCG
* **
679325 TTTAAGAAAAATTGATGTTTTGGAAAT
1 ATTGTGAAAAATTGATGTTTTGGAAAT
679352 GGAACCGGGA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
50 1 0.02
51 64 0.97
52 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (51 bp):
ATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTCAGAGTATCCCCG
Found at i:681698 original size:20 final size:20
Alignment explanation
Indices: 681673--681748 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
681663 AAAATGCCTG
681673 AATGTATCGATACATTATAA
1 AATGTATCGATACATTATAA
*
681693 AATGTATCGATACA--ATGAGC
1 AATGTATCGATACATTAT-A-A
* * **
681713 AATGTATCGATATAATGCAA
1 AATGTATCGATACATTATAA
681733 AATGTATCGATACATT
1 AATGTATCGATACATT
681749 TGGGTAAACC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 41 0.91
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTATAA
Found at i:682526 original size:42 final size:42
Alignment explanation
Indices: 682477--682601 Score: 137
Period size: 45 Copynumber: 2.9 Consensus size: 42
682467 TGAAAAAGCA
682477 TGCGTCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAATAAAG
1 TGCGTCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAATAAAG
* *
682519 TGCGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAAGG-GAATGAAG
1 TGCGTCCTGCTCTTTGAGGACAAAA--G-AAAG-AGGAAAATAAAG
* **
682564 TGTGGGCTGCTCTTTGAGGACAAAGGAGAAA-AGGAAAA
1 TGCGTCCTGCTCTTTGAGGACAAA--AGAAAGAGGAAAA
682602 GGCGTCCTAC
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
42 28 0.40
43 2 0.03
44 4 0.06
45 32 0.46
46 3 0.04
47 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.31, T:0.18
Consensus pattern (42 bp):
TGCGTCCTGCTCTTTGAGGACAAAAGAAAGAGGAAAATAAAG
Found at i:682669 original size:61 final size:59
Alignment explanation
Indices: 682603--682888 Score: 284
Period size: 61 Copynumber: 4.9 Consensus size: 59
682593 AAAGGAAAAG
* * * *
682603 GCGTCCTACTCTTTGAGGACTAAAAAGTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAAA
1 GCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAG--AAA
* * * * * * *
682664 GCGTCCTGCTCTTTAAGGACTGGAAGGTGCCACCAACTCGAGTGGTCTTTAAAAGGAGAAA
1 GCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA--AGAAA
* * * *
682725 GCATCCTGCTTTTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG---
1 GCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAA
* *
682780 GTGTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTAGGCTTTG-AAAG---
1 GCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAA
* * *
682835 GCCTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAA
1 GCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAA
682889 GACGTTTTGC
Statistics
Matches: 190, Mismatches: 30, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
54 4 0.02
55 85 0.45
56 7 0.04
58 2 0.01
60 2 0.01
61 88 0.46
63 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (59 bp):
GCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAA
Found at i:682807 original size:55 final size:55
Alignment explanation
Indices: 682728--682910 Score: 251
Period size: 55 Copynumber: 3.3 Consensus size: 55
682718 GGAGAAAGCA
* * * *
682728 TCCTGCTTTTTGAGGATTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
682783 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTAGGCTTTGAAAGGCC
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
682838 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTATGTGGGCTTTGAAAGACG
1 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
**
682893 TTTTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
682911 AAAGGGTGAA
Statistics
Matches: 114, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
54 4 0.04
55 110 0.96
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.31
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Done.