Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 17 of 150
Found at i:4612597 original size:25 final size:25
Alignment explanation
Indices: 4612527--4612598 Score: 65
Period size: 28 Copynumber: 2.7 Consensus size: 25
4612517 TTATACAACA
* *
4612527 TTTAGTTTCTAAAAATATTTTTTATT
1 TTTA-TTTTTAAAAAAATTTTTTATT
*
4612553 TTCATTTTTAGAAAATAAATTTATTT-TT
1 TTTATTTTT--AAAA-AAATTT-TTTATT
4612581 TTTATTTTTAAAAAAATT
1 TTTATTTTTAAAAAAATT
4612599 AAAAAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
25 9 0.24
26 7 0.18
27 4 0.11
28 15 0.39
29 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTATTTTTAAAAAAATTTTTTATT
Found at i:4613392 original size:126 final size:125
Alignment explanation
Indices: 4613137--4613581 Score: 662
Period size: 126 Copynumber: 3.6 Consensus size: 125
4613127 AGGATAAGGA
*
4613137 TTCTAGCAGGATGCTTTATAAGAAGAATTTGTGAAAT--CG-CCATCGTGGACGCGCTTTTGCTA
1 TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCA-CGTGGACGCGCTTTTGCTA
* * * **
4613199 CAGTTGGCCCCGGAAAAAAATAATTTCGAGTTGACGTTTCTGAGTGAATAGTATAAAAACGC
65 CAGTAGGTCCTGG-AAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGC
* * ** *
4613261 TTCTAGCAAGATGCGTTATGAGAAGAATTTGTGAAATCATGCCCATGTGGACGCGCTTTTGCTAC
1 TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
* *
4613326 AGTAGGTCTTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAAGGC
66 AGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAACGC
* * *
4613387 TTCTAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCGTCCACGTGGATGCGCTTTTGCTAC
1 TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
4613452 AGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGC
66 AGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGC
* * * *
4613512 TTCTAGCAGGATGTTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTAT
1 TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
4613577 AGTAG
66 AGTAG
4613582 CATGTTCTGT
Statistics
Matches: 290, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
124 34 0.12
125 108 0.37
126 145 0.50
127 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (125 bp):
TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
AGTAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAACGC
Found at i:4614756 original size:45 final size:45
Alignment explanation
Indices: 4614687--4614831 Score: 166
Period size: 45 Copynumber: 3.2 Consensus size: 45
4614677 TAACGGTAGC
* **
4614687 AGTAACAGTAACAGTATTCAACACACAAAGTGTTGAACCTG-TAAA
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACC-GATAAA
* * ** *
4614732 AGTAACGGTAATAGTATTCGACACACAAAGTGCCGAGTCGATAAC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACCGATAAA
* * * *
4614777 AGTAAAAGTAACAGTATTCGACACACAAAGTGCCGAATCAATAAC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACCGATAAA
4614822 AGTAACAGTA
1 AGTAACAGTA
4614832 GTCGGCACAT
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
44 1 0.01
45 84 0.99
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAACCGATAAA
Found at i:4617669 original size:20 final size:20
Alignment explanation
Indices: 4617644--4617681 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4617634 TTTTTTAAAA
4617644 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
4617664 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
4617682 TACCTCGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:4618677 original size:51 final size:51
Alignment explanation
Indices: 4618615--4618714 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
4618605 AAATTATTTA
*
4618615 AAATAGGGATTTACGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* *
4618666 AAATATGGATTTAAGAGAAATTTAGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
4618715 GAAAATTTAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 44 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.25, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:4618688 original size:11 final size:10
Alignment explanation
Indices: 4618674--4618750 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 10
4618664 TTAAATATGG
4618674 ATTTAAGAGAA
1 ATTT-AGAGAA
*
4618685 ATTTAGAAGGA
1 ATTTAG-AGAA
4618696 ATTTGAGAGCAA
1 ATTT-AGAG-AA
*
4618708 ATTGAGAGAAA
1 ATTTAGAG-AA
4618719 ATTTAGAGGAA
1 ATTTAGA-GAA
*
4618730 ATTGAGAGGAA
1 ATTTAGA-GAA
4618741 ATTT-GAGAA
1 ATTTAGAGAA
4618750 A
1 A
4618751 GGATTAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 40 0.73
12 7 0.13
ACGTcount: A:0.48, C:0.01, G:0.26, T:0.25
Consensus pattern (10 bp):
ATTTAGAGAA
Found at i:4618729 original size:33 final size:34
Alignment explanation
Indices: 4618674--4618748 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
4618664 TTAAATATGG
* *
4618674 ATTTAAGAGAAATTTAGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
*
4618708 A-TTGAGAGAAAATTTAG-AGGAAATTGAGAGGAA
1 ATTTGAGAG-AAATTTAGAAGGAAATTGAGAGCAA
4618741 ATTTGAGA
1 ATTTGAGA
4618749 AAGGATTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 21 0.58
34 15 0.42
ACGTcount: A:0.47, C:0.01, G:0.27, T:0.25
Consensus pattern (34 bp):
ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:4618731 original size:22 final size:23
Alignment explanation
Indices: 4618695--4618748 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
4618685 ATTTAGAAGG
4618695 AATTTGAGAGCAAATTGAGAGAA
1 AATTTGAGAGCAAATTGAGAGAA
* *
4618718 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGAA
4618740 AATTTGAGA
1 AATTTGAGA
4618749 AAGGATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGAA
Found at i:4622412 original size:39 final size:39
Alignment explanation
Indices: 4622367--4622444 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
4622357 ATGACATTAA
4622367 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
1 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
4622406 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
1 GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
4622445 TTATAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.31
Consensus pattern (39 bp):
GAATTAAATTGAATAAAGTGAAAGCTATTGGAAATTTGG
Found at i:4625382 original size:32 final size:31
Alignment explanation
Indices: 4625346--4625410 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
4625336 AAAATTTCAA
4625346 AATTCAAAAAAGTAGAAG-GACTAAAATTGATC
1 AATTCAAAAAA-TA-AAGAGACTAAAATTGATC
* *
4625378 AATTCAAAAAATACAGATACTAAAATTGATC
1 AATTCAAAAAATAAAGAGACTAAAATTGATC
4625409 AA
1 AA
4625411 ATTAAAGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 17 0.57
32 11 0.37
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (31 bp):
AATTCAAAAAATAAAGAGACTAAAATTGATC
Found at i:4625451 original size:30 final size:30
Alignment explanation
Indices: 4625417--4625481 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
4625407 TCAAATTAAA
4625417 GTACATAGACTAATCCTTAACTTTTGCATT
1 GTACATAGACTAATCCTTAACTTTTGCATT
4625447 GTACATAGACTAATCCTTAACTTTTGCATT
1 GTACATAGACTAATCCTTAACTTTTGCATT
4625477 GTACA
1 GTACA
4625482 AGAATTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (30 bp):
GTACATAGACTAATCCTTAACTTTTGCATT
Found at i:4627340 original size:309 final size:302
Alignment explanation
Indices: 4626697--4627355 Score: 722
Period size: 309 Copynumber: 2.1 Consensus size: 302
4626687 TCAAACTCAT
* *
4626697 GCCAAGTGCATTAGTAAAACATTTAATTTACCACTCACCTAAAGCTTCATTTTAATATTTTTATA
1 GCCAATTGCATTA-TAAAACATTTAATTTACCACTCAACTAAAGCTTCATTTTAATATTTTTATA
* * * *
4626762 CATTTTAGTTTTATTATGCACATTCTATTATCTCCATTAAATGTATATTTATATCTATTTATACT
65 AATTTTAATTTTATTATGCACATTCTATTATCACCATTAAATCTATATTTATATCTATTTATACT
* * ** * * * * *
4626827 ATTGTTTAAACTCTTGACTGAGTTGGTGTCGCAAGTTAACTGAGCACGAACTAATTGGTTAGGAA
130 ATTATTTAAACTCCTGACTGAGTTAATGTCACAACTCAACAGAGCACCAACTAA---GTTAGGAA
* * *
4626892 ATTACGGGAATGCACATCCTTAATTAAAATAAGTAATATTATTCGGGGTATTTTAGTCTTTTCAA
192 ATTACGGGAATGCACATCCATAATTAAAATAAATAATATTATTCGGGATATTTTAGTCTTTTCAA
** ** * * * *
4626957 TTCAAAAAAATGAATAAAAATATGTATATGGTGAGATTTGAATCTAC
257 TT-AAAAAAACCAATAAAAATATACATATGGTAAAATTTGAACCCAC
* * ** *
4627004 ACCATTTGCATTATAAAACCCTTAATTTACCACTCAAGTAAA-CATTCATTTTAATATTTTTATA
1 GCCAATTGCATTATAAAACATTTAATTTACCACTCAACTAAAGC-TTCATTTTAATATTTTTATA
4627068 AATTTTAATTTTATTATGCACATTCTATTACCTCCACCAGTTATATATCTATACTTGTATAT-TA
65 AATTTTAATTTTATTATGCACATTCTATTA--T-CACCA-TTA-A-ATCTATA-TT-TATATCTA
* * *
4627132 TTTATACTATTATTTCAGCTCCT-ACTGAGTTAATGTCAC-CCTCAACCAG-GTCACCAACTCAA
122 TTTATACTATTATTTAAACTCCTGACTGAGTTAATGTCACAACTCAA-CAGAG-CACCAACT-AA
* * * *
4627194 -TTAGGAAGTTACGGGAATGCACTTTCATAATTAAAATAAATAATATTATTCGAGTATATTTTAG
184 GTTAGGAAATTACGGGAATGCACATCCATAATTAAAATAAATAATATTATTCG-GGATATTTTAG
* *
4627258 TCTTTTCACTT-AAAAAACCAATAAAAATATACATATTGTAAAATTTGAACCCAC
248 TCTTTTCAATTAAAAAAACCAATAAAAATATACATATGGTAAAATTTGAACCCAC
4627312 GCCAATTGCATTGATAAAACATTTAATTTACCA-TGCAACTAAAG
1 GCCAATTGCATT-ATAAAACATTTAATTTACCACT-CAACTAAAG
4627356 TATATATATA
Statistics
Matches: 291, Mismatches: 45, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
305 1 0.00
306 73 0.25
307 10 0.03
308 46 0.16
309 76 0.26
310 22 0.08
311 5 0.02
312 28 0.10
313 25 0.09
314 5 0.02
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (302 bp):
GCCAATTGCATTATAAAACATTTAATTTACCACTCAACTAAAGCTTCATTTTAATATTTTTATAA
ATTTTAATTTTATTATGCACATTCTATTATCACCATTAAATCTATATTTATATCTATTTATACTA
TTATTTAAACTCCTGACTGAGTTAATGTCACAACTCAACAGAGCACCAACTAAGTTAGGAAATTA
CGGGAATGCACATCCATAATTAAAATAAATAATATTATTCGGGATATTTTAGTCTTTTCAATTAA
AAAAACCAATAAAAATATACATATGGTAAAATTTGAACCCAC
Found at i:4627363 original size:2 final size:2
Alignment explanation
Indices: 4627356--4627397 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4627346 GCAACTAAAG
*
4627356 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4627398 CATTTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4628515 original size:21 final size:21
Alignment explanation
Indices: 4628491--4628531 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4628481 GTCAATAACC
4628491 AAATGTTCACACAAACAGACA
1 AAATGTTCACACAAACAGACA
**
4628512 AAATGTTCTGACAAACAGAC
1 AAATGTTCACACAAACAGAC
4628532 GTATATTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (21 bp):
AAATGTTCACACAAACAGACA
Found at i:4638412 original size:18 final size:18
Alignment explanation
Indices: 4638389--4638428 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4638379 GTTTTAAAAT
*
4638389 TGAATAACGATTTGTAAA
1 TGAATAACGATTTGGAAA
* *
4638407 TGAATAATGTTTTGGAAA
1 TGAATAACGATTTGGAAA
4638425 TGAA
1 TGAA
4638429 CGACACAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (18 bp):
TGAATAACGATTTGGAAA
Found at i:4642803 original size:46 final size:46
Alignment explanation
Indices: 4642751--4642847 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 46
4642741 AATTTGTCTT
* *
4642751 TATAGGAAGAGATGTCAACTATCTTATATGAAGATAATACAGCATG
1 TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
* *
4642797 TATAGGAAGAGAAGTCAACTATCTTATCTGAAGATAATGCAACATG
1 TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
4642843 TATAG
1 TATAG
4642848 CTCAATTGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (46 bp):
TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
Found at i:4644393 original size:21 final size:21
Alignment explanation
Indices: 4644369--4644412 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4644359 ATATTTTTAA
*
4644369 ATTTGTTTAGATT-TATAATTT
1 ATTT-TTTAGATTATACAATTT
*
4644390 ATTTTTTATATTATACAATTT
1 ATTTTTTAGATTATACAATTT
4644411 AT
1 AT
4644413 ATAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTTTTAGATTATACAATTT
Found at i:4644736 original size:3 final size:3
Alignment explanation
Indices: 4644728--4644765 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4644718 GCAAAAACAA
4644728 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4644766 GCACGAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4646190 original size:28 final size:27
Alignment explanation
Indices: 4646151--4646216 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 27
4646141 TTTTTGCCCG
4646151 TTTATTATTATTGTCGTTATTATTTTATT-
1 TTTATT-TTATT-TC-TTATTATTTTATTA
*
4646180 TTTATTTTA-TTCTTGTTATTTTATTA
1 TTTATTTTATTTCTTATTATTTTATTA
*
4646206 TTTCTTTTATT
1 TTTATTTTATT
4646217 ATTCTCACGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 12 0.36
26 10 0.30
27 2 0.06
28 3 0.09
29 6 0.18
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.73
Consensus pattern (27 bp):
TTTATTTTATTTCTTATTATTTTATTA
Found at i:4658464 original size:24 final size:23
Alignment explanation
Indices: 4658432--4658502 Score: 61
Period size: 28 Copynumber: 2.8 Consensus size: 23
4658422 TCTGAGATAT
*
4658432 TTTAGTTAATATATATTATATTTA
1 TTTA-TTAATATATATTATATTAA
4658456 TTTACTTAATAAATAAGTATTATATTAA
1 TTTA-TTAAT--AT-A-TATTATATTAA
*
4658484 TTATATTATTATATATTAT
1 TT-TATTAATATATATTAT
4658503 TATATATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
24 15 0.38
25 1 0.03
26 4 0.10
27 1 0.03
28 16 0.41
29 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTATTAATATATATTATATTAA
Found at i:4658500 original size:10 final size:10
Alignment explanation
Indices: 4658476--4658509 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
4658466 AAATAAGTAT
*
4658476 TATATTAAT-
1 TATATTATTA
4658485 TATATTATTA
1 TATATTATTA
4658495 TATATTATTA
1 TATATTATTA
4658505 TATAT
1 TATAT
4658510 AAAAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATTATTA
Found at i:4659694 original size:25 final size:24
Alignment explanation
Indices: 4659633--4659692 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
4659623 AAGTGGAAAG
4659633 TGAATTTGAATTGAAATGTGATTAT
1 TGAA-TTGAATTGAAATGTGATTAT
*
4659658 TGAATAGAAATTGAAATG-G--T-T
1 TGAATTG-AATTGAAATGTGATTAT
4659679 TGAATTGAATTGAA
1 TGAATTGAATTGAA
4659693 TTATTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 7 0.22
21 7 0.22
22 1 0.03
24 3 0.09
25 14 0.44
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.38
Consensus pattern (24 bp):
TGAATTGAATTGAAATGTGATTAT
Found at i:4659701 original size:18 final size:19
Alignment explanation
Indices: 4659638--4659718 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
4659628 GAAAGTGAAT
4659638 TTGAATTGAAATGTG-ATTA
1 TTGAATTGAAAT-TGAATTA
*
4659657 TTGAATAGAAATTGAAATGGT-
1 TTGAATTGAAATTG-AAT--TA
4659678 TTGAATTG-AATTGAATTA
1 TTGAATTGAAATTGAATTA
* *
4659696 TTGAATTGAACTGGAA-TA
1 TTGAATTGAAATTGAATTA
4659714 TTGAA
1 TTGAA
4659719 ATTGGTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.02
18 17 0.33
19 19 0.37
20 7 0.13
21 7 0.13
22 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (19 bp):
TTGAATTGAAATTGAATTA
Found at i:4660124 original size:45 final size:45
Alignment explanation
Indices: 4660055--4660154 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
4660045 GCTGACTACT
* *
4660055 GTTACTGTTACTGATTCAATACTTTGTGTG-TCGAATACTGTTACC
1 GTTACTGTTACAGATTCAATACTTTGTGTGCT-GAATAATGTTACC
* *
4660100 GTTATTGTTACAGATTC-ATCACTTTGTGTGCTGAATAATGTTACT
1 GTTACTGTTACAGATTCAAT-ACTTTGTGTGCTGAATAATGTTACC
*
4660145 GCTACTGTTA
1 GTTACTGTTA
4660155 TTGTTTACTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 2 0.04
45 44 0.94
46 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGATTCAATACTTTGTGTGCTGAATAATGTTACC
Found at i:4667031 original size:21 final size:21
Alignment explanation
Indices: 4667007--4667084 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
4666997 AAACTGTTGC
*
4667007 TTTCCAAAAGAAAACGGAGGA
1 TTTCCAAAAGAAAACAGAGGA
* *
4667028 TTTCCAGAAGAAAACAAAGGA
1 TTTCCAAAAGAAAACAGAGGA
* *
4667049 TTTCCAAAAGAAGACAGAAGA
1 TTTCCAAAAGAAAACAGAGGA
* *
4667070 TTTTCAACAGAAAAC
1 TTTCCAAAAGAAAAC
4667085 TAAGGTGTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.17
Consensus pattern (21 bp):
TTTCCAAAAGAAAACAGAGGA
Found at i:4667072 original size:42 final size:42
Alignment explanation
Indices: 4667007--4667089 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
4666997 AAACTGTTGC
* *
4667007 TTTCCAAAAGAAAACGGAGGATTTCCAGA-AGAAAACAAAGGA
1 TTTCCAAAAGAAAACAGAAGATTTCCA-ACAGAAAACAAAGGA
* * *
4667049 TTTCCAAAAGAAGACAGAAGATTTTCAACAGAAAACTAAGG
1 TTTCCAAAAGAAAACAGAAGATTTCCAACAGAAAACAAAGG
4667090 TGTCTATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.17
Consensus pattern (42 bp):
TTTCCAAAAGAAAACAGAAGATTTCCAACAGAAAACAAAGGA
Found at i:4669116 original size:3 final size:3
Alignment explanation
Indices: 4669108--4669161 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
4669098 TTCCTCACTA
*
4669108 TAT TAT TA- TAT TAT GCTAT TAT TTT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4669153 TAT TAT TAT
1 TAT TAT TAT
4669162 ATTTCTATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
5 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4669117 original size:8 final size:8
Alignment explanation
Indices: 4669106--4669164 Score: 64
Period size: 8 Copynumber: 6.8 Consensus size: 8
4669096 TATTCCTCAC
4669106 TATATTAT
1 TATATTAT
4669114 TATATTAT
1 TATATTAT
*
4669122 GCTATTATTTT
1 --TA-TATTAT
4669133 TATATTAT
1 TATATTAT
4669141 TATTATTAT
1 TA-TATTAT
4669150 TATTATTAT
1 TA-TATTAT
4669159 TATATT
1 TATATT
4669165 TCTATTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
8 19 0.42
9 19 0.42
10 2 0.04
11 5 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (8 bp):
TATATTAT
Found at i:4669135 original size:45 final size:43
Alignment explanation
Indices: 4669086--4669182 Score: 99
Period size: 45 Copynumber: 2.2 Consensus size: 43
4669076 ATTAATTCAG
* *
4669086 TTTATTTATTTATTCCTCACTA-TATTATTATATTATGCTATTATT
1 TTTATTTATTTATT-ATCACTATTATTATTATATT-T-CTATTATA
* * *
4669131 TTTATATTA-TTATTATTATTATTATTATTATATTTCTATTCTA
1 TTTAT-TTATTTATTATCACTATTATTATTATATTTCTATTATA
4669174 TTTATTTAT
1 TTTATTTAT
4669183 CTAAGTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
42 3 0.07
43 11 0.25
44 5 0.11
45 22 0.50
46 3 0.07
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (43 bp):
TTTATTTATTTATTATCACTATTATTATTATATTTCTATTATA
Found at i:4669217 original size:3 final size:3
Alignment explanation
Indices: 4669209--4669248 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4669199 TTTAACCTTG
4669209 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4669249 TACTCATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4670857 original size:5 final size:6
Alignment explanation
Indices: 4670841--4670898 Score: 55
Period size: 6 Copynumber: 8.8 Consensus size: 6
4670831 GAGGCAACCC
4670841 ATTTTT ATTTTT ATTTTT ATTTGTTT ATATACTTT ATTTTT ATTTTCT
1 ATTTTT ATTTTT ATTTTT A-TT-TTT AT-T--TTT ATTTTT ATTTT-T
4670889 A-TTTT ATTTT
1 ATTTTT ATTTT
4670899 CTCGCATGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
5 2 0.04
6 27 0.60
7 5 0.11
8 6 0.13
9 5 0.11
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:4677079 original size:16 final size:16
Alignment explanation
Indices: 4677060--4677099 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
4677050 ATTATTTTAA
*
4677060 TTTA-ATATTTAATATT
1 TTTATATATTGAA-ATT
4677076 TTTATATATTGAAATT
1 TTTATATATTGAAATT
4677092 TTTATATA
1 TTTATATA
4677100 GTCATCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTATATATTGAAATT
Found at i:4685787 original size:17 final size:17
Alignment explanation
Indices: 4685765--4685798 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4685755 TGAAGAAGCC
4685765 CCTTGAATGTAAGAGCT
1 CCTTGAATGTAAGAGCT
4685782 CCTTGAATGTAAGAGCT
1 CCTTGAATGTAAGAGCT
4685799 TAGCCAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
CCTTGAATGTAAGAGCT
Found at i:4690196 original size:2 final size:2
Alignment explanation
Indices: 4690189--4690219 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4690179 TTGGTATGTT
4690189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4690220 TAAAATAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4693858 original size:2 final size:2
Alignment explanation
Indices: 4693853--4693933 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
4693843 ATATTATATA
4693853 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4693895 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4693934 TTTGAATTGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4697669 original size:20 final size:20
Alignment explanation
Indices: 4697628--4697664 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4697618 ACAGAAATAA
4697628 TGTCAAGTATATAATATTAT
1 TGTCAAGTATATAATATTAT
4697648 TGTCAAGTA-ATAA-ATTA
1 TGTCAAGTATATAATATTA
4697665 CATTGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (20 bp):
TGTCAAGTATATAATATTAT
Found at i:4700265 original size:57 final size:58
Alignment explanation
Indices: 4700197--4700315 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 58
4700187 TTTTTATTGA
* *
4700197 AATAGAATTAATATTAAATTAAATTTAATACTTATCTTAAT-AGTATTTTATTAATTT
1 AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
* * * *
4700254 AATAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTT
1 AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
4700312 AATA
1 AATA
4700316 TTAAAGTGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 36 0.65
58 19 0.35
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (58 bp):
AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
Found at i:4700328 original size:58 final size:56
Alignment explanation
Indices: 4700202--4700335 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 56
4700192 ATTGAAATAG
* *
4700202 AATT-AATATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 AATTAAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAAT
* * * *
4700257 AGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAAT
1 A-ATTAAATATTAAATTAAATCTAATACTTATCTTAAT-AGTATTATATTAATTTAAT
*
4700315 -ATTAAAGTGATTAAGTTAAAT
1 AATTAAA-T-ATTAAATTAAAT
4700336 TATAGTTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
55 1 0.02
56 8 0.12
57 29 0.44
58 28 0.42
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (56 bp):
AATTAAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAAT
Found at i:4706160 original size:15 final size:16
Alignment explanation
Indices: 4706135--4706164 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4706125 TTTATTATGG
4706135 TTTCAATTTAATCTTT
1 TTTCAATTTAATCTTT
4706151 TTTC-ATTTAATCTT
1 TTTCAATTTAATCTT
4706165 GCCTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCAATTTAATCTTT
Found at i:4706308 original size:14 final size:14
Alignment explanation
Indices: 4706281--4706314 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4706271 TTTTAGTTCA
* *
4706281 TTTTTGTTTTTATT
1 TTTTTATTTATATT
4706295 TTTTTATTTATATT
1 TTTTTATTTATATT
4706309 TTTTTA
1 TTTTTA
4706315 ATGTTGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:4710335 original size:17 final size:17
Alignment explanation
Indices: 4710297--4710352 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
4710287 GCAAAAAAAA
4710297 AAAAAAGGAG-AAGAAG
1 AAAAAAGGAGAAAGAAG
4710313 AGAGAAAAGAAGAGAAAGAAG
1 A-A-AAAAG--GAGAAAGAAG
*
4710334 AAAAAAGGAGGAAGAAG
1 AAAAAAGGAGAAAGAAG
4710351 AA
1 AA
4710353 TAGGGAGCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
16 1 0.03
17 12 0.35
18 5 0.15
19 5 0.15
20 4 0.12
21 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAGAAAGAAG
Found at i:4710442 original size:17 final size:16
Alignment explanation
Indices: 4710416--4710505 Score: 78
Period size: 17 Copynumber: 5.5 Consensus size: 16
4710406 CGGCCCGAAG
*
4710416 AAGAAGAAGAGAAAGGA
1 AAGAAAAAGA-AAAGGA
4710433 AAGAAAAAGAAGAA-GA
1 AAGAAAAAGAA-AAGGA
*
4710449 AAGGAAAA-AAAA-GA
1 AAGAAAAAGAAAAGGA
* *
4710463 AAAAAAAAGAAAAAGAAA
1 AAGAAAAAG-AAAAG-GA
4710481 AAGAAAAAGAAAAAGGA
1 AAGAAAAAG-AAAAGGA
4710498 AAGAAAAA
1 AAGAAAAA
4710506 ACAGTCAGGT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
14 10 0.16
15 2 0.03
16 14 0.23
17 20 0.33
18 15 0.25
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAGGA
Found at i:4710442 original size:20 final size:20
Alignment explanation
Indices: 4710413--4710479 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
4710403 GTTCGGCCCG
*
4710413 AAGAAGAAGAAGAGAAAGGA
1 AAGAAAAAGAAGAGAAAGGA
4710433 AAGAAAAAGAAGAAGAAAGGA
1 AAGAAAAAGAAG-AGAAAGGA
4710454 AA-AAAAAGAA-A-AAA--A
1 AAGAAAAAGAAGAGAAAGGA
4710469 AAGAAAAAGAA
1 AAGAAAAAGAA
4710480 AAAGAAAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
15 3 0.07
16 8 0.18
17 3 0.07
18 1 0.02
20 19 0.43
21 10 0.23
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAGAGAAAGGA
Found at i:4710449 original size:26 final size:26
Alignment explanation
Indices: 4710413--4710495 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
4710403 GTTCGGCCCG
*
4710413 AAGAAGAAGAAGAGAAAGGAAAGAAA
1 AAGAAGAAGAAGAGAAAGAAAAGAAA
*
4710439 AAGAAGAAGAA-AGGAAAAAAAAGAAAA
1 AAGAAGAAGAAGA-GAAAGAAAAG-AAA
* * *
4710466 AAAAAGAAAAAGAAAAAGAAAAAGAAA
1 AAGAAGAAGAAGAGAAAG-AAAAGAAA
4710493 AAG
1 AAG
4710496 GAAAGAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
25 1 0.02
26 19 0.41
27 20 0.43
28 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (26 bp):
AAGAAGAAGAAGAGAAAGAAAAGAAA
Found at i:4710465 original size:6 final size:6
Alignment explanation
Indices: 4710432--4710505 Score: 82
Period size: 6 Copynumber: 12.5 Consensus size: 6
4710422 AAGAGAAAGG
* *
4710432 AAAGAA AAAGAA GAAGAA AGGAAAAA AAAG-A AAA-AA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA A--AAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
4710480 AAAGAA AAAGAA AAAG-G AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
4710506 ACAGTCAGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.21
6 40 0.70
8 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:4710473 original size:36 final size:38
Alignment explanation
Indices: 4710432--4710506 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 38
4710422 AAGAGAAAGG
* *
4710432 AAAGAAAAAGAAGAAG-AAAGGAAAAA-AAAGAAAAAA
1 AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAGAAAAAA
4710468 AAAGAAAAAGAAAAAGAAAAAGAAAAAGGAAAGAAAAAA
1 AAAGAAAAAGAAAAAGAAAAAGAAAAA-GAAAGAAAAAA
4710507 CAGTCAGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 15 0.44
37 9 0.26
39 10 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (38 bp):
AAAGAAAAAGAAAAAGAAAAAGAAAAAGAAAGAAAAAA
Found at i:4710506 original size:12 final size:10
Alignment explanation
Indices: 4710431--4710506 Score: 66
Period size: 10 Copynumber: 7.7 Consensus size: 10
4710421 GAAGAGAAAG
*
4710431 GAAAGAAAAA
1 GAAAAAAAAA
* *
4710441 GAAGAAGAAA
1 GAAAAAAAAA
*
4710451 GGAAAAAAAA
1 GAAAAAAAAA
4710461 GAAAAAAAAA
1 GAAAAAAAAA
*
4710471 G-AAAAAGAA
1 GAAAAAAAAA
*
4710480 -AAAGAAAAA
1 GAAAAAAAAA
*
4710489 GAAAAAGGAAA
1 GAAAAA-AAAA
4710500 GAAAAAA
1 GAAAAAA
4710507 CAGTCAGGTC
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
9 13 0.26
10 28 0.56
11 9 0.18
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:4710597 original size:19 final size:20
Alignment explanation
Indices: 4710573--4710626 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
4710563 GTATCAGCCA
4710573 ACCCAGCAGGCCA-GCCAG-C
1 ACCCAGCAGG-CAGGCCAGAC
*
4710592 ACCCAGCAAGCAGGCCAGAC
1 ACCCAGCAGGCAGGCCAGAC
4710612 AGCCCAGCA-GCAGGC
1 A-CCCAGCAGGCAGGC
4710627 AGCCAAACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 8 0.26
21 7 0.23
ACGTcount: A:0.30, C:0.43, G:0.28, T:0.00
Consensus pattern (20 bp):
ACCCAGCAGGCAGGCCAGAC
Found at i:4710603 original size:23 final size:20
Alignment explanation
Indices: 4710576--4710631 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 20
4710566 TCAGCCAACC
4710576 CAGCAGGCCAGCCAGCACCCAG
1 CAGCAGGCCAGCCAG--CCCAG
*
4710598 CAAGCAGGCCAGACAGCCCAG
1 C-AGCAGGCCAGCCAGCCCAG
4710619 CAGCAGG-CAGCCA
1 CAGCAGGCCAGCCA
4710632 AACAGCAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 6 0.19
22 1 0.03
23 13 0.42
ACGTcount: A:0.30, C:0.41, G:0.29, T:0.00
Consensus pattern (20 bp):
CAGCAGGCCAGCCAGCCCAG
Found at i:4718461 original size:21 final size:21
Alignment explanation
Indices: 4718435--4718478 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
4718425 NNNNNTTCTC
4718435 ATGAAGCCATTCTGATAGTGG
1 ATGAAGCCATTCTGATAGTGG
*
4718456 ATGAAGCCATTGTGATAGTGG
1 ATGAAGCCATTCTGATAGTGG
4718477 AT
1 AT
4718479 CAACATCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (21 bp):
ATGAAGCCATTCTGATAGTGG
Found at i:4718752 original size:20 final size:20
Alignment explanation
Indices: 4718727--4718766 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4718717 ATGTGCCGTA
4718727 TATTATCCACCACTCAGCTG
1 TATTATCCACCACTCAGCTG
4718747 TATTATCCACCACTCAGCTG
1 TATTATCCACCACTCAGCTG
4718767 CATAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.35, G:0.10, T:0.30
Consensus pattern (20 bp):
TATTATCCACCACTCAGCTG
Found at i:4718831 original size:32 final size:32
Alignment explanation
Indices: 4718768--4718842 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
4718758 ACTCAGCTGC
* *
4718768 ATAATATTATT-TAAATTTCAAAATAACTTAA
1 ATAATATAATTATAAATTTCAAAATAAATTAA
*
4718799 ATAATATAATTATAAATTAT-AAATTAAATTAA
1 ATAATATAATTATAAATT-TCAAAATAAATTAA
*
4718831 ATAATTTAATTA
1 ATAATATAATTA
4718843 ACTGTTTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 10 0.26
32 27 0.71
33 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (32 bp):
ATAATATAATTATAAATTTCAAAATAAATTAA
Found at i:4718959 original size:5 final size:6
Alignment explanation
Indices: 4718934--4718973 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
4718924 ACAACTGTAT
*
4718934 AAATAA AAGAT-A AAGTAA AAATAA AAATAA AAATAA AAAT
1 AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAAT
4718974 TCTATTTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 1 0.03
6 27 0.90
7 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:4721557 original size:54 final size:54
Alignment explanation
Indices: 4721494--4721606 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
4721484 CTAATATGAG
4721494 TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
1 TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
* *
4721548 TTTATAAATATTTGGGTCATGCAAGATTCTTCTTTAAATTTTTGGGCTCTTTCA
1 TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
4721602 TTTAT
1 TTTAT
4721607 TGTTTCTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (54 bp):
TTTATAAATATTTAGGTCATGCAAGATGCTTCTTTAAATTTTTGGGCTCTTTCA
Found at i:4721592 original size:30 final size:30
Alignment explanation
Indices: 4721498--4721593 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 30
4721488 TATGAGTTTA
* *
4721498 TAAATATTTAGGTCATGCAAGATGCTTCTT
1 TAAATATTTGGGTCATGCAAGATTCTTCTT
* * *
4721528 TAAATTTTTGGG-C-T-C---TTTCATT-TA
1 TAAATATTTGGGTCATGCAAGATTC-TTCTT
4721552 TAAATATTTGGGTCATGCAAGATTCTTCTT
1 TAAATATTTGGGTCATGCAAGATTCTTCTT
*
4721582 TAAATTTTTGGG
1 TAAATATTTGGG
4721594 CTCTTTCATT
Statistics
Matches: 49, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
24 14 0.29
25 3 0.06
26 1 0.02
27 2 0.04
28 1 0.02
29 3 0.06
30 25 0.51
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (30 bp):
TAAATATTTGGGTCATGCAAGATTCTTCTT
Found at i:4724121 original size:19 final size:19
Alignment explanation
Indices: 4724084--4724121 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4724074 AAATGATTAT
*
4724084 ATAAGTAGAATGATAAATA
1 ATAAGTAGAATGAAAAATA
4724103 ATAAGTA-AATGAAAGAATA
1 ATAAGTAGAATGAAA-AATA
4724122 TTATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
ATAAGTAGAATGAAAAATA
Found at i:4724144 original size:15 final size:15
Alignment explanation
Indices: 4724124--4724167 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
4724114 AAAGAATATT
4724124 ATTATAATAATCATC
1 ATTATAATAATCATC
*
4724139 ATTATAATAA-CATT
1 ATTATAATAATCATC
*
4724153 AATATTAATAATCAT
1 ATTA-TAATAATCAT
4724168 ATCATGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 16 0.64
16 3 0.12
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTATAATAATCATC
Found at i:4724293 original size:15 final size:17
Alignment explanation
Indices: 4724256--4724297 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
4724246 TGAAAATATC
*
4724256 AAAAATAATAAGAAATA
1 AAAAATAACAAGAAATA
4724273 ATAAAATAACAAG-AATA
1 A-AAAATAACAAGAAATA
4724290 AAAAATAA
1 AAAAATAA
4724298 TAACGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 6 0.26
18 10 0.43
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAATAACAAGAAATA
Found at i:4724295 original size:24 final size:23
Alignment explanation
Indices: 4724257--4724317 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
4724247 GAAAATATCA
*
4724257 AAAATAATAAGAAATAATAA-AAT
1 AAAA-AATAAAAAATAATAACAAT
*
4724280 AACAAGAATAAAAAATAATAACGAT
1 AA-AA-AATAAAAAATAATAACAAT
4724305 AAAAAATAAAAAA
1 AAAAAATAAAAAA
4724318 AATTGTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 11 0.33
24 18 0.55
25 4 0.12
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAAAATAAAAAATAATAACAAT
Found at i:4724296 original size:16 final size:16
Alignment explanation
Indices: 4724256--4724313 Score: 73
Period size: 16 Copynumber: 3.5 Consensus size: 16
4724246 TGAAAATATC
4724256 AAAAATAATAAGAAATA
1 AAAAATAATAAG-AATA
*
4724273 ATAAAATAACAAGAATA
1 A-AAAATAATAAGAATA
4724290 AAAAATAATAACG-ATA
1 AAAAATAATAA-GAATA
4724306 AAAAATAA
1 AAAAATAA
4724314 AAAAAATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 20 0.54
17 7 0.19
18 10 0.27
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAAATAATAAGAATA
Found at i:4724313 original size:7 final size:7
Alignment explanation
Indices: 4724257--4724317 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 7
4724247 GAAAATATCA
4724257 AAAATAAT
1 AAAA-AAT
*
4724265 AAGAAAT
1 AAAAAAT
4724272 AATAAAAT
1 AA-AAAAT
4724280 AACAAGAAT
1 AA-AA-AAT
4724289 AAAAAAT
1 AAAAAAT
*
4724296 AATAACGAT
1 AA-AA-AAT
4724305 AAAAAAT
1 AAAAAAT
4724312 AAAAAA
1 AAAAAA
4724318 AATTGTGCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
7 18 0.41
8 17 0.39
9 9 0.20
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:4724552 original size:14 final size:14
Alignment explanation
Indices: 4724533--4724564 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4724523 GTAAATAAAT
4724533 AAAATAATACATAA
1 AAAATAATACATAA
*
4724547 AAAATAATATATAA
1 AAAATAATACATAA
4724561 AAAA
1 AAAA
4724565 ATCAATACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAATACATAA
Found at i:4731493 original size:4 final size:4
Alignment explanation
Indices: 4731484--4731518 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
4731474 TATTTTATCT
* *
4731484 TTTA TTTA TTTA TTTA TTTG TTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
4731519 GCTTATCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:4739513 original size:101 final size:99
Alignment explanation
Indices: 4739343--4739640 Score: 478
Period size: 101 Copynumber: 3.0 Consensus size: 99
4739333 CAACCACATA
4739343 GTTAATAGATGATGAAGTAGGCAACT-GC--GACACCTATCATTTCGAATATTGTGTGGTCAAAA
1 GTTAATAGATGATGAAGTAGGCAACTCGCATGACACCTATCATTTCGAATATTGTGTGGTCAAAA
4739405 ATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
66 ATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
4739439 GTTAATAGATGATGAAGTAGG-ATACTGCGACATGACACCTATCATTTCGAATATTGTGTGGTCA
1 GTTAATAGATGATGAAGTAGGCA-ACT-CG-CATGACACCTATCATTTCGAATATTGTGTGGTCA
4739503 AAAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
63 AAAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
* * * *
4739540 GTTAATAGATGATGAAGTAGGCAACTACGGCATGATACCTACCATTTTGAATATTGTATGGTCAA
1 GTTAATAGATGATGAAGTAGGCAACT-C-GCATGACACCTATCATTTCGAATATTGTGTGGTCAA
*
4739605 AAATGAAAGGTTAGGTGTGATAGAACATGAGGGCAT
64 AAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
4739641 ATATAGTTTT
Statistics
Matches: 188, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
95 1 0.01
96 24 0.13
98 1 0.01
99 1 0.01
101 159 0.85
102 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (99 bp):
GTTAATAGATGATGAAGTAGGCAACTCGCATGACACCTATCATTTCGAATATTGTGTGGTCAAAA
ATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
Found at i:4741433 original size:19 final size:19
Alignment explanation
Indices: 4741409--4741451 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4741399 TTTTATTTTT
*
4741409 TTATTA-ATTGATAATGTAA
1 TTATTATATTCAT-ATGTAA
*
4741428 TTATTATTTTCATATGTAA
1 TTATTATATTCATATGTAA
4741447 TTATT
1 TTATT
4741452 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (19 bp):
TTATTATATTCATATGTAA
Found at i:4741486 original size:18 final size:18
Alignment explanation
Indices: 4741459--4741517 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
4741449 ATTTTTTCTT
*
4741459 TTTATATATATATGTATA
1 TTTATGTATATATGTATA
4741477 TTTATGTATATAT-T-TA
1 TTTATGTATATATGTATA
4741493 TTTCCATGTATATATACGTATA
1 TTT--ATGTATATAT--GTATA
4741515 TTT
1 TTT
4741518 TTTAATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.15
17 1 0.03
18 22 0.65
21 1 0.03
22 5 0.15
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTATGTATATATGTATA
Found at i:4746988 original size:7 final size:7
Alignment explanation
Indices: 4746976--4747349 Score: 137
Period size: 7 Copynumber: 53.7 Consensus size: 7
4746966 ATATTACTGT
4746976 CTAAACC
1 CTAAACC
4746983 CTAAACC
1 CTAAACC
*
4746990 CTAAACT
1 CTAAACC
* *
4746997 ATAAACT
1 CTAAACC
* *
4747004 TTAAGCCC
1 CTAA-ACC
*
4747012 CTAACCC
1 CTAAACC
4747019 CTAAAACC
1 CT-AAACC
4747027 CT-AACC
1 CTAAACC
4747033 CT-AACC
1 CTAAACC
*
4747039 CTTAAACA
1 C-TAAACC
4747047 C-ACAACC
1 CTA-AACC
*
4747054 ATAAACC
1 CTAAACC
*
4747061 ATAAACC
1 CTAAACC
4747068 CTAAACC
1 CTAAACC
4747075 CTAAA-C
1 CTAAACC
*
4747081 CTACACC
1 CTAAACC
4747088 CTAAA--
1 CTAAACC
*
4747093 TTATAACC
1 CTA-AACC
* *
4747101 ATTAAACT
1 -CTAAACC
* *
4747109 CTTAACA
1 CTAAACC
4747116 CTAAACC
1 CTAAACC
4747123 CTAAACC
1 CTAAACC
*
4747130 TTAAACC
1 CTAAACC
*
4747137 CTAACCCC
1 CTAA-ACC
*
4747145 CTAAATC
1 CTAAACC
4747152 CTAAACC
1 CTAAACC
* *
4747159 TTAAA-A
1 CTAAACC
4747165 CTAAACC
1 CTAAACC
* **
4747172 ATAAAAT
1 CTAAACC
*
4747179 CTAAATC
1 CTAAACC
*
4747186 CTAAACT
1 CTAAACC
4747193 CT-AACC
1 CTAAACC
4747199 CTTAAACCC
1 C-TAAA-CC
4747208 CT-AACAC
1 CTAAAC-C
4747215 CTAAACC
1 CTAAACC
*
4747222 TTAAA-C
1 CTAAACC
*
4747228 ATAAAACC
1 CT-AAACC
4747236 CTAAACC
1 CTAAACC
*
4747243 ATAAA-C
1 CTAAACC
*
4747249 ATAAACC
1 CTAAACC
*
4747256 ATAAACC
1 CTAAACC
*
4747263 ATAAA-C
1 CTAAACC
* *
4747269 ATACACC
1 CTAAACC
*
4747276 CTAAATC
1 CTAAACC
*
4747283 GT-AACC
1 CTAAACC
* *
4747289 ATTAAACT
1 -CTAAACC
* *
4747297 CTTAACA
1 CTAAACC
*
4747304 CTAAATC
1 CTAAACC
4747311 CTAAACC
1 CTAAACC
*
4747318 TTAAACC
1 CTAAACC
*
4747325 CCAAACC
1 CTAAACC
* *
4747332 ATATA-C
1 CTAAACC
*
4747338 CTACACC
1 CTAAACC
4747345 CTAAA
1 CTAAA
4747350 TATATATATT
Statistics
Matches: 275, Mismatches: 67, Indels: 50
0.70 0.17 0.13
Matches are distributed among these distances:
5 2 0.01
6 48 0.17
7 184 0.67
8 35 0.13
9 6 0.02
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:4747081 original size:21 final size:21
Alignment explanation
Indices: 4746977--4747349 Score: 155
Period size: 21 Copynumber: 17.9 Consensus size: 21
4746967 TATTACTGTC
*
4746977 TAAACCCTAAACCCTAAACTA
1 TAAACCCTAAACCCTAAACCA
** * * *
4746998 TAAACTTTAAGCCCCTAACCCC
1 TAAACCCTAA-ACCCTAAACCA
* *
4747020 TAAAACCCT-AACCCTAACCCT
1 T-AAACCCTAAACCCTAAACCA
* *
4747041 TAAACAC-ACAACCATAAACCA
1 TAAACCCTA-AACCCTAAACCA
4747062 TAAACCCTAAACCCTAAACC-
1 TAAACCCTAAACCCTAAACCA
* *
4747082 TACACCCTAAA--TTATAACCA
1 TAAACCCTAAACCCTA-AACCA
* * * *
4747102 TTAAACTCTTAACACTAAACCC
1 -TAAACCCTAAACCCTAAACCA
* * *
4747124 TAAACCTTAAACCCTAACCCCC
1 TAAACCCTAAACCCTAA-ACCA
* * *
4747146 TAAATCCTAAACCTTAAAAC-
1 TAAACCCTAAACCCTAAACCA
* **
4747166 TAAACCATAAAATCTAAATCC-
1 TAAACCCTAAACCCTAAA-CCA
* *
4747187 TAAACTCT-AACCCTTAAACCCC
1 TAAACCCTAAACCC-TAAA-CCA
*
4747209 T-AACACCTAAACCTTAAA-CA
1 TAAAC-CCTAAACCCTAAACCA
*
4747229 TAAAACCCTAAACCATAAA-CA
1 T-AAACCCTAAACCCTAAACCA
* *
4747250 TAAACCATAAACCATAAA-CA
1 TAAACCCTAAACCCTAAACCA
* * *
4747270 TACACCCTAAATCGT-AACCA
1 TAAACCCTAAACCCTAAACCA
* * *
4747290 TTAAACTCTTAACACTAAATCC-
1 -TAAACCCTAAACCCTAAA-CCA
* *
4747312 TAAACCTTAAACCCCAAACCA
1 TAAACCCTAAACCCTAAACCA
* *
4747333 TATA-CCTACACCCTAAA
1 TAAACCCTAAACCCTAAA
4747350 TATATATATT
Statistics
Matches: 261, Mismatches: 68, Indels: 47
0.69 0.18 0.12
Matches are distributed among these distances:
18 2 0.01
19 6 0.02
20 76 0.29
21 121 0.46
22 43 0.16
23 13 0.05
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACCA
Found at i:4747218 original size:22 final size:22
Alignment explanation
Indices: 4747103--4747227 Score: 63
Period size: 22 Copynumber: 5.9 Consensus size: 22
4747093 TTATAACCAT
*
4747103 TAAACTCTTAACAC-TAAA-CCC
1 TAAACTCTAAAC-CTTAAACCCC
* *
4747124 TAAAC-CTTAAACCCTAACCCCC
1 TAAACTC-TAAACCTTAAACCCC
*
4747146 TAAA-TCCTAAACCTTAAA--AC
1 TAAACT-CTAAACCTTAAACCCC
* *
4747166 TAAAC-CATAAA-ATCTAAA-TCC
1 TAAACTC-TAAACCT-TAAACCCC
*
4747187 TAAACTCTAACCCTTAAACCCC
1 TAAACTCTAAACCTTAAACCCC
4747209 TAACAC-CTAAACCTTAAAC
1 TAA-ACTCTAAACCTTAAAC
4747228 ATAAAACCCT
Statistics
Matches: 80, Mismatches: 11, Indels: 25
0.69 0.09 0.22
Matches are distributed among these distances:
19 2 0.03
20 15 0.19
21 25 0.31
22 35 0.44
23 3 0.04
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACTCTAAACCTTAAACCCC
Found at i:4747280 original size:20 final size:20
Alignment explanation
Indices: 4747214--4747280 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
4747204 ACCCCTAACA
*
4747214 CCTAAACCTTAAACATAAAAC
1 CCTAAACCATAAACAT-AAAC
4747235 CCTAAACCATAAACATAAAC
1 CCTAAACCATAAACATAAAC
* *
4747255 CATAAACCATAAACATACAC
1 CCTAAACCATAAACATAAAC
4747275 CCTAAA
1 CCTAAA
4747281 TCGTAACCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (20 bp):
CCTAAACCATAAACATAAAC
Found at i:4747546 original size:21 final size:21
Alignment explanation
Indices: 4747514--4747555 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4747504 TATAAAATAA
4747514 TAAACCTCAAA-CCTCAAACTC
1 TAAACCTCAAACCCT-AAACTC
4747535 TAAACCAT-AAACCCTAAACTC
1 TAAACC-TCAAACCCTAAACTC
4747556 ACAGATACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCTCAAACCCTAAACTC
Found at i:4750349 original size:39 final size:37
Alignment explanation
Indices: 4750282--4750374 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
4750272 TCCAGTATGG
* *
4750282 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
4750321 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
4750358 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
4750375 AATCTGTAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:4750501 original size:12 final size:13
Alignment explanation
Indices: 4750486--4750514 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4750476 GTGTCAATTT
4750486 ATTT-GTGTGAAA
1 ATTTCGTGTGAAA
4750498 ATTTCGTGTGAAA
1 ATTTCGTGTGAAA
4750511 ATTT
1 ATTT
4750515 TATCGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (13 bp):
ATTTCGTGTGAAA
Found at i:4751774 original size:19 final size:19
Alignment explanation
Indices: 4751723--4751774 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
4751713 GTTAGCCGAA
*
4751723 TGTATATATATGTTTTGAAT
1 TGTATATATATG-TATGAAT
* *
4751743 TTTAT-TAAAATGTATGAAT
1 TGTATAT-ATATGTATGAAT
4751762 TGTATATATATGT
1 TGTATATATATGT
4751775 GTGTGTGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (19 bp):
TGTATATATATGTATGAAT
Found at i:4752306 original size:41 final size:41
Alignment explanation
Indices: 4752249--4752353 Score: 192
Period size: 41 Copynumber: 2.6 Consensus size: 41
4752239 GGCTCGATGC
*
4752249 CTAGCAGGCTTAATGCCGGTGAATTATTTTAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
4752290 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
*
4752331 CTAGCAGGCTTAAGGCCGGTGAA
1 CTAGCAGGCTTAATGCCGGTGAA
4752354 ATGATTTGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
Found at i:4754545 original size:5 final size:5
Alignment explanation
Indices: 4754535--4754594 Score: 102
Period size: 5 Copynumber: 11.6 Consensus size: 5
4754525 TGATTTTATA
4754535 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAATTT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA--T
4754587 ATAAT ATA
1 ATAAT ATA
4754595 CTTTTTAGCT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
5 48 0.91
7 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:4754777 original size:12 final size:12
Alignment explanation
Indices: 4754760--4754788 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4754750 TTTAATTTAT
4754760 TAATAATAATAG
1 TAATAATAATAG
4754772 TAATAATAATAG
1 TAATAATAATAG
4754784 TAATA
1 TAATA
4754789 CATATACCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:4760856 original size:15 final size:15
Alignment explanation
Indices: 4760836--4760869 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4760826 AGCAAAGTGT
4760836 TAGTAAGTAGGGATG
1 TAGTAAGTAGGGATG
4760851 TAGTAAGTAGGGATG
1 TAGTAAGTAGGGATG
4760866 TAGT
1 TAGT
4760870 GTTTGATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (15 bp):
TAGTAAGTAGGGATG
Found at i:4763850 original size:20 final size:20
Alignment explanation
Indices: 4763825--4763865 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
4763815 ACCAAATAAG
4763825 AACCTGGTTTGAATAAATTA
1 AACCTGGTTTGAATAAATTA
4763845 AACCTGGTTTGAATAAATTA
1 AACCTGGTTTGAATAAATTA
4763865 A
1 A
4763866 GGCATTGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (20 bp):
AACCTGGTTTGAATAAATTA
Found at i:4764698 original size:20 final size:18
Alignment explanation
Indices: 4764661--4764713 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
4764651 CAAAAGTTAT
*
4764661 AAAAATTATTAAATTTTA
1 AAAAATTATTAAAATTTA
4764679 AAAAATATATTTAAAATTTA
1 AAAAAT-TA-TTAAAATTTA
4764699 TTAAAAATT-TTAAAA
1 --AAAAATTATTAAAA
4764714 AATATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.20
19 8 0.27
20 9 0.30
21 1 0.03
22 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATTATTAAAATTTA
Found at i:4764700 original size:30 final size:31
Alignment explanation
Indices: 4764660--4764719 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
4764650 ACAAAAGTTA
4764660 TAAAAATTATT-AAATTTTAAAAAATATATT
1 TAAAAATTATTAAAATTTTAAAAAATATATT
*
4764690 TAAAATTTATTAAAAATTTTAAAAAATATA
1 TAAAAATTATT-AAAATTTTAAAAAATATA
4764720 AATATCGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 10 0.37
32 17 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TAAAAATTATTAAAATTTTAAAAAATATATT
Found at i:4764730 original size:18 final size:17
Alignment explanation
Indices: 4764709--4764760 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
4764699 TTAAAAATTT
*
4764709 TAAAAAATATAAATATCG
1 TAAAAAATATAAA-ATCA
**
4764727 TAAAATTTTATAAAATCA
1 TAAAA-AATATAAAATCA
4764745 TAAATAAATATAAAAT
1 TAAA-AAATATAAAAT
4764761 GTATCAAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAAAATATAAAATCA
Found at i:4764741 original size:37 final size:33
Alignment explanation
Indices: 4764660--4764758 Score: 89
Period size: 37 Copynumber: 2.9 Consensus size: 33
4764650 ACAAAAGTTA
*
4764660 TAAAAATTATT-AAATTTTAAAAAATAT--ATT
1 TAAAATTTATTAAAATTTTAAAAAATATAAATT
4764690 TAAAATTTATTAAAAATTTTAAAAAATATAAATAT
1 TAAAATTTATT-AAAATTTTAAAAAATATAAAT-T
**
4764725 CGTAAAATTT-TATAAAATCATAAATAAATATAAA
1 --TAAAATTTAT-TAAAATTTTAAA-AAATATAAA
4764759 ATGTATCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
30 10 0.18
32 16 0.28
34 2 0.04
35 1 0.02
36 10 0.18
37 18 0.32
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (33 bp):
TAAAATTTATTAAAATTTTAAAAAATATAAATT
Found at i:4765889 original size:30 final size:31
Alignment explanation
Indices: 4765841--4765903 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
4765831 TTTCTTATGT
4765841 CAATATTTCGAAACCCATATCTTTGACTTTC
1 CAATATTTCGAAACCCATATCTTTGACTTTC
*
4765872 CAATATTT-GATACCCATATCTTTGACTTTC
1 CAATATTTCGAAACCCATATCTTTGACTTTC
4765902 CA
1 CA
4765904 TAATATGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.40
Consensus pattern (31 bp):
CAATATTTCGAAACCCATATCTTTGACTTTC
Found at i:4765895 original size:15 final size:16
Alignment explanation
Indices: 4765853--4765898 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
4765843 ATATTTCGAA
4765853 ACCCATATCTTTGACT
1 ACCCATATCTTTGACT
** *
4765869 TTCCA-ATATTTGA-T
1 ACCCATATCTTTGACT
4765883 ACCCATATCTTTGACT
1 ACCCATATCTTTGACT
4765899 TTCCATAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 4
0.69 0.19 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (16 bp):
ACCCATATCTTTGACT
Found at i:4770244 original size:27 final size:27
Alignment explanation
Indices: 4770205--4770258 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4770195 GAGGTTCAGC
4770205 AAATTTTTCCTACGTCCTCAGGCACTA
1 AAATTTTTCCTACGTCCTCAGGCACTA
*
4770232 AAATTTTGT-CTACGTCCTCGGGCACTA
1 AAATTTT-TCCTACGTCCTCAGGCACTA
4770259 CCAAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (27 bp):
AAATTTTTCCTACGTCCTCAGGCACTA
Found at i:4770514 original size:30 final size:31
Alignment explanation
Indices: 4770459--4770518 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
4770449 TTTCTTATGC
* *
4770459 CAATATTTCGATACCCATTTTTTTGACTTTT
1 CAATATTTCGATACCCATATCTTTGACTTTT
*
4770490 CAATATTT-GATACCTATATCTTTGACTTT
1 CAATATTTCGATACCCATATCTTTGACTTT
4770519 CCATAATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (31 bp):
CAATATTTCGATACCCATATCTTTGACTTTT
Found at i:4774667 original size:45 final size:45
Alignment explanation
Indices: 4774598--4774714 Score: 153
Period size: 45 Copynumber: 2.6 Consensus size: 45
4774588 AAATGGCAAG
* * ***
4774598 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAGATAGTGAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTAAAGACAACAAA
** *
4774643 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTGAAGACAACAAA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTAAAGACAACAAA
*
4774688 TCTTATCTCCCTGAAGTTGTAGCGGAG
1 TCTTATCTCCCTGAAGTTGTAGTGGAG
4774715 TAGATTTAGG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGCAAACTAAAGACAACAAA
Found at i:4774947 original size:20 final size:21
Alignment explanation
Indices: 4774910--4774950 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4774900 TTTTGCCCGG
*
4774910 ACCCAAAACTAAATAAATAAA
1 ACCCAAAACTAAAAAAATAAA
4774931 ACCCAAAA-TAAAAAAATAAA
1 ACCCAAAACTAAAAAAATAAA
4774951 CAGTCCATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.71, C:0.17, G:0.00, T:0.12
Consensus pattern (21 bp):
ACCCAAAACTAAAAAAATAAA
Found at i:4779748 original size:62 final size:56
Alignment explanation
Indices: 4779672--4779819 Score: 161
Period size: 57 Copynumber: 2.5 Consensus size: 56
4779662 AATTGACGGT
4779672 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGAT-C--T--TGATATAGCCCTCCCGAAGAATATGTG-G
** *
4779735 AAAAAGATCTAGCCTAGACGGATGATCTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCTTGATATAGCCCTCCCGAAGAATATGTGG
* * * *
4779791 AAAATGGATTTAGCCCGAACGGGTAATCT
1 AAAA-AGATCTAGCCCGGACGGGTGATCT
4779820 GAATTAGGGT
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
56 5 0.07
57 44 0.59
59 1 0.01
61 1 0.01
62 18 0.24
63 5 0.07
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (56 bp):
AAAAAGATCTAGCCCGGACGGGTGATCTTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:4781575 original size:116 final size:116
Alignment explanation
Indices: 4781371--4781597 Score: 427
Period size: 116 Copynumber: 2.0 Consensus size: 116
4781361 TTATCCTTTT
* *
4781371 CCCATTATCTCCTTCCATTATCTCTTTAATAAGAGCCTCCACATTCTTACGCTTTACGTCAGGGT
1 CCCATTATCTCCTTCCATTATCTCTTTAACAAGAGCCTCCACATCCTTACGCTTTACGTCAGGGT
4781436 TGATTTCCATTCCATTGCCCCATGTGGTGCACGAATATCGACAATTCGTTG
66 TGATTTCCATTCCATTGCCCCATGTGGTGCACGAATATCGACAATTCGTTG
*
4781487 CCCATTATCTCCTTCCATTATCTCTTTAACAAGAGCCTCTACATCCTTACGCTTTACGTCAGGGT
1 CCCATTATCTCCTTCCATTATCTCTTTAACAAGAGCCTCCACATCCTTACGCTTTACGTCAGGGT
4781552 TGATTTCCATTCCATTGCCCCATGTGGTGCACGAATATCGACAATT
66 TGATTTCCATTCCATTGCCCCATGTGGTGCACGAATATCGACAATT
4781598 TGTTTGTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 108 1.00
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.35
Consensus pattern (116 bp):
CCCATTATCTCCTTCCATTATCTCTTTAACAAGAGCCTCCACATCCTTACGCTTTACGTCAGGGT
TGATTTCCATTCCATTGCCCCATGTGGTGCACGAATATCGACAATTCGTTG
Found at i:4784156 original size:3 final size:3
Alignment explanation
Indices: 4784143--4784172 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
4784133 CAATCCAGCT
*
4784143 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
4784173 TGTGGTGCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4784562 original size:37 final size:37
Alignment explanation
Indices: 4784441--4784578 Score: 111
Period size: 37 Copynumber: 3.7 Consensus size: 37
4784431 AACTAATATT
* **
4784441 ATTATTATGGTTAGTTATTAGGATTAGTAAAAACCCTA
1 ATTATTATTGTTAGTTATTATTATTAGT-AAAACCCTA
* *** * *
4784479 ATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTA-CATT
1 ATTATTATTGTTAGTTA-T-T-ATTATTAG-TAAAACCCTA
*
4784518 A-TATTATTGTTAGTTATTATTTTTAGTAAAACCCTA
1 ATTATTATTGTTAGTTATTATTATTAGTAAAACCCTA
*
4784554 ATTATTATTGTTAGTTAGTATTATT
1 ATTATTATTGTTAGTTATTATTATT
4784579 TTGCGTAAAA
Statistics
Matches: 76, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
35 2 0.03
36 10 0.13
37 29 0.38
38 17 0.22
39 11 0.14
40 6 0.08
41 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.51
Consensus pattern (37 bp):
ATTATTATTGTTAGTTATTATTATTAGTAAAACCCTA
Found at i:4784599 original size:76 final size:79
Alignment explanation
Indices: 4784394--4784622 Score: 245
Period size: 76 Copynumber: 2.9 Consensus size: 79
4784384 GTTTAGTTAT
* * *
4784394 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTGGTAAAAAAC---TATTATTATTAT-GTTAGTTAT
4784459 TAGGATTAGTAAAAACCC
62 TAGGATTAGTAAAAACCC
* * **** *
4784477 TAATTATTATT-TTAGTTAGTATGATTGTTAGT-TTTTAC-ATTA-TATTATTGTTAGTTATTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTGGTAAAAAACTATTATTATTA-TGTTAGTTATTAG
**
4784538 TTTTAGT-AAAACCC
65 GATTAGTAAAAACCC
*
4784552 TAATTATTATTGTTAGTTAGTATTATT-TTGCGTAAAAAACTATTATTATTGTGTTAGTTATTAG
1 TAATTATTATTGTTAGTTAGTATTATTGTTG-GTAAAAAACTATTATTATTATGTTAGTTATTAG
4784616 GATTAGT
65 GATTAGT
4784623 GGTTAAACGT
Statistics
Matches: 120, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
75 20 0.17
76 37 0.31
77 7 0.06
78 21 0.17
79 4 0.03
81 2 0.02
82 19 0.16
83 10 0.08
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (79 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTGGTAAAAAACTATTATTATTATGTTAGTTATTAGG
ATTAGTAAAAACCC
Found at i:4784607 original size:41 final size:41
Alignment explanation
Indices: 4784394--4784614 Score: 132
Period size: 40 Copynumber: 5.6 Consensus size: 41
4784384 GTTTAGTTAT
* *
4784394 TAATAATTATTGTTACTTAG-TATTATTGTT-AGTAAAAAAC
1 TAATTATTATTGTTAGTTAGTTATTATT-TTGAGTAAAAAAC
* ** *
4784434 TAA-TATTATTATTATGGTTAGTTATTAGGATT-AGTAAAAACCC
1 TAATTATTATTGTTA--GTTAGTTATTA-TTTTGAGTAAAAA-AC
* ****
4784477 TAATTATTATT-TTAGTTAG-TATGATTGTT-AGT-TTTTAC
1 TAATTATTATTGTTAGTTAGTTATTATT-TTGAGTAAAAAAC
* * **
4784515 --ATTA-TATTATT-GTTAGTTATTATTTTTAGTAAAACCC
1 TAATTATTATTGTTAGTTAGTTATTATTTTGAGTAAAAAAC
*
4784552 TAATTATTATTGTTAGTTAG-TATTATTTTGCGTAAAAAAC
1 TAATTATTATTGTTAGTTAGTTATTATTTTGAGTAAAAAAC
4784592 T-ATTATTATTG-T-GTTAGTTATTA
1 TAATTATTATTGTTAGTTAGTTATTA
4784615 GGATTAGTGG
Statistics
Matches: 140, Mismatches: 25, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
35 11 0.08
36 15 0.11
37 6 0.04
38 7 0.05
39 23 0.16
40 35 0.25
41 14 0.10
42 15 0.11
43 7 0.05
44 7 0.05
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (41 bp):
TAATTATTATTGTTAGTTAGTTATTATTTTGAGTAAAAAAC
Found at i:4787504 original size:15 final size:16
Alignment explanation
Indices: 4787486--4787521 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4787476 TGCTGTAAAA
*
4787486 TTGTTATG-TGTAATG
1 TTGTTATGTTGCAATG
4787501 TTGTTATGTTGCAATG
1 TTGTTATGTTGCAATG
4787517 TTGTT
1 TTGTT
4787522 GTAACACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (16 bp):
TTGTTATGTTGCAATG
Found at i:4790199 original size:156 final size:156
Alignment explanation
Indices: 4789769--4790430 Score: 1036
Period size: 156 Copynumber: 4.3 Consensus size: 156
4789759 ACTTCAAAAC
* * *
4789769 AAATTTATTAAAAAATCCTTATTTCGGCCTTTTGTTCGTA-TTTTTTCTCGGATTTTATTACTTT
1 AAATTTATTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
4789833 CAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
66 CAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
*
4789898 GTATTAATTTAGTGTG---TTTAAAA
131 GTATTAATTTAGTGTGTTTTTTAAAT
* *
4789921 AATATTTTTTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTCTTTTCCCGGATTTTATTACTT
1 AA-ATTTATTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTT
4789986 TCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
65 TCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
4790051 TGTATTAATTTAGTGTGTTTTTTAAAT
130 TGTATTAATTTAGTGTGTTTTTTAAAT
**
4790078 AAATTTAAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
1 AAATTTATTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
*
4790143 CAATAAAAATATATTATTTTCTAATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAAT
66 CAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
* *
4790208 GTATTAATTAATTGTGTTTTTTAAAT
131 GTATTAATTTAGTGTGTTTTTTAAAT
* * *
4790234 AAATTT-TTAAAAAACTCTTATTTCAGCCCTTTGTTCGTATTTTTTT-CCAGATTTTATTACTTT
1 AAATTTATTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
* *
4790297 C-A-AAAAATATTTTATTTTCGT-ATTTTATTATTTTACATTCTTTTAGTACATTATGTTTGAAA
66 CAATAAAAATATATTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
*
4790359 TGTATTAATTTAGTGTGTTTTTTATAT
130 TGTATTAATTTAGTGTGTTTTTTAAAT
* * * * **
4790386 AAACTTAGTAAAAAACCTTTATTTTGGCTATTTGTTCGTATTTTT
1 AAATTTATTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTT
4790431 CTTATTTTCA
Statistics
Matches: 471, Mismatches: 32, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
152 86 0.18
153 68 0.14
154 120 0.25
155 36 0.08
156 153 0.32
157 8 0.02
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (156 bp):
AAATTTATTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
CAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
GTATTAATTTAGTGTGTTTTTTAAAT
Found at i:4790483 original size:310 final size:309
Alignment explanation
Indices: 4789778--4790430 Score: 983
Period size: 310 Copynumber: 2.1 Consensus size: 309
4789768 CAAATTTATT
* * * *
4789778 AAAAAATCCTTATTTCGGCCTTTTGTTCGTA-TTTTTTCTCGGATTTTATTACTTTCAATAAAAA
1 AAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAAT-AAAA
* *
4789842 TATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATT
65 TATACTATTTTCTAATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATT
* * *
4789907 TAGTGTGTTTAAAAAATATTTTTTAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTCTTTTCCC
130 AAGTGTGTTTAAAAAATAATTTTTAAAAAACCCTTATTTCAGCCCTTTGTTCGTATTCTTTTCCC
*
4789972 GGATTTTATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTA
195 AGATTTTATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTA
*
4790037 CATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTAAA
260 CATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAACTTAAA
* *
4790087 AAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTTCAATAAAAA
1 AAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAAT-AAAA
*
4790152 TATATTATTTTCTAATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATT
65 TATACTATTTTCTAATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATT
* *** * *
4790217 AATTGTGTTTTTTAAATAAATTTTTAAAAAACTCTTATTTCAGCCCTTTGTTCGTATT-TTTTTC
130 AAGTGTGTTTAAAAAAT-AATTTTTAAAAAACCCTTATTTCAGCCCTTTGTTCGTATTCTTTTCC
* *
4790281 CAGATTTTATTACTTTC-A-AAAAATATTTTATTTTCGT-ATTTTATTATTTTACATTCTTTTAG
194 CAGATTTTATTACTTTCAATAAAAATATATTATTTTC-TAATTTTATTATTTTACATTATTTTAG
* **
4790343 TACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTATATAAACTTAGT
258 TACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAACTTAAA
* * *
4790395 AAAAAACCTTTATTTTGGCTATTTGTTCGTATTTTT
1 AAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTT
4790431 CTTATTTTCA
Statistics
Matches: 317, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
308 120 0.38
309 31 0.10
310 129 0.41
311 37 0.12
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (309 bp):
AAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAATAAAAT
ATACTATTTTCTAATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATTA
AGTGTGTTTAAAAAATAATTTTTAAAAAACCCTTATTTCAGCCCTTTGTTCGTATTCTTTTCCCA
GATTTTATTACTTTCAATAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTAC
ATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAACTTAAA
Found at i:4790819 original size:5 final size:5
Alignment explanation
Indices: 4790809--4790863 Score: 58
Period size: 5 Copynumber: 11.0 Consensus size: 5
4790799 CTTCTTCTTC
* * * *
4790809 TCCTT TCCTT TCCTT T-CTT CTCCTT TCCTT TTCTT TCTTT TTCTT TCTTT
1 TCCTT TCCTT TCCTT TCCTT -TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
4790859 TCCTT
1 TCCTT
4790864 CTTTCTTCTC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
4 3 0.08
5 34 0.85
6 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TCCTT
Found at i:4790828 original size:20 final size:20
Alignment explanation
Indices: 4790803--4790863 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
4790793 CTCCCTCTTC
4790803 TTCTTCTCCTTTCCTTTCCT
1 TTCTTCTCCTTTCCTTTCCT
*
4790823 TTCTTCTCCTTTCCTTTTCT
1 TTCTTCTCCTTTCCTTTCCT
* * *
4790843 TTCTTTTTCTTTCTTTTCCT
1 TTCTTCTCCTTTCCTTTCCT
4790863 T
1 T
4790864 CTTTCTTCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTTCTCCTTTCCTTTCCT
Found at i:4790872 original size:20 final size:20
Alignment explanation
Indices: 4790802--4790869 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
4790792 CCTCCCTCTT
*
4790802 CTTC-TTCTCCTTTCCTTTC
1 CTTCTTTCTCCTTTCTTTTC
4790821 CTT-TCTTCTCCTTTCCTTTTC
1 CTTCT-TTCTCCTTT-CTTTTC
* *
4790842 TTTCTTT-TTCTTTCTTTTC
1 CTTCTTTCTCCTTTCTTTTC
4790861 CTTCTTTCT
1 CTTCTTTCT
4790870 TCTCCTCCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 15 0.38
20 15 0.38
21 9 0.22
22 1 0.03
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (20 bp):
CTTCTTTCTCCTTTCTTTTC
Found at i:4791833 original size:96 final size:95
Alignment explanation
Indices: 4791589--4791868 Score: 336
Period size: 95 Copynumber: 2.9 Consensus size: 95
4791579 GTTTGTCAAT
* * * *
4791589 TAAATTAATTATAAATTTT-TCAAAATTGGATTA-GCTTTCGTGTTTATTA-TTTTTTAAGAAAA
1 TAAATTAATTATAAATTTTAT-AAAATTAGATTAGGGTTTAGTGTTTA--AGGTTTTTAAGAAAA
* *
4791651 AATTAATTAAATTAGGGTTTAGGGTTACTTGAG
63 AATCAATTAAATTAGGGTTTAGGGTTACTTAAG
* * * * *
4791684 TAATTTAATTAAAAAAATTTA-AAAATTAGATTAGGGTTTAGAG-TTAAGGGTTTTTAAGGAAAA
1 TAAATTAATT-ATAAATTTTATAAAATTAGATTAGGGTTTAGTGTTTAA-GGTTTTTAAGAAAAA
4791747 ATCAATTAAATTAGGGTTTAGGGTTACTTAAG
64 ATCAATTAAATTAGGGTTTAGGGTTACTTAAG
*
4791779 TAAATTAATTATGAAGTTTTATAAAATTAGATTAGGGTTTAGTGTTTAAGGTTTTTAAGTAAAAA
1 TAAATTAATTAT-AAATTTTATAAAATTAGATTAGGGTTTAGTGTTTAAGGTTTTTAAG-AAAAA
* *
4791844 ATCAAATAAATTAGGGTTTGGGGTT
64 ATCAATTAAATTAGGGTTTAGGGTT
4791869 TAGGGTTATT
Statistics
Matches: 157, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
93 1 0.01
94 1 0.01
95 80 0.51
96 44 0.28
97 31 0.20
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.41
Consensus pattern (95 bp):
TAAATTAATTATAAATTTTATAAAATTAGATTAGGGTTTAGTGTTTAAGGTTTTTAAGAAAAAAT
CAATTAAATTAGGGTTTAGGGTTACTTAAG
Found at i:4794265 original size:34 final size:33
Alignment explanation
Indices: 4794222--4794295 Score: 112
Period size: 34 Copynumber: 2.2 Consensus size: 33
4794212 ATGTAAAAGT
*
4794222 AAATTTCTATTTTAGTACATGAAATAATATAGAA
1 AAATTTCTATTTTAGTACATCAAATAATAT-GAA
*
4794256 AAATTTCTATTTTATTACATCAAATAATATGAA
1 AAATTTCTATTTTAGTACATCAAATAATATGAA
4794289 AATATTT
1 AA-ATTT
4794296 AAAATGTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (33 bp):
AAATTTCTATTTTAGTACATCAAATAATATGAA
Found at i:4794434 original size:20 final size:20
Alignment explanation
Indices: 4794411--4794462 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
4794401 GCAAAGGTTG
4794411 TGGTTGCTCGG-CGGGGATTC
1 TGGTTGCTCGGTCGGGGA-TC
* *
4794431 TGGTTCCTCCGGTTGGGGATC
1 TGGTTGCT-CGGTCGGGGATC
4794452 TGGTTG-TCGGT
1 TGGTTGCTCGGT
4794463 GTTGGGACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 10 0.37
22 5 0.19
ACGTcount: A:0.04, C:0.19, G:0.42, T:0.35
Consensus pattern (20 bp):
TGGTTGCTCGGTCGGGGATC
Found at i:4794738 original size:18 final size:18
Alignment explanation
Indices: 4794698--4794740 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
4794688 CACTAGAAGA
* * *
4794698 AGGAAACATATAAGAGTT
1 AGGATACATAAAAGAGCT
4794716 AGGATACATAAAAGAGCT
1 AGGATACATAAAAGAGCT
*
4794734 GGGATAC
1 AGGATAC
4794741 GCACCTGCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGAGCT
Found at i:4795400 original size:7 final size:7
Alignment explanation
Indices: 4795388--4795419 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
4795378 TATTAGTTAT
4795388 ATACTAA
1 ATACTAA
4795395 ATACTAA
1 ATACTAA
4795402 ATACTAA
1 ATACTAA
4795409 ATACTAA
1 ATACTAA
4795416 ATAC
1 ATAC
4795420 CAATCGACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTAA
Found at i:4796607 original size:11 final size:11
Alignment explanation
Indices: 4796593--4796646 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
4796583 TTTAAATAGA
4796593 AATTTGAGAGG
1 AATTTGAGAGG
*
4796604 AATTTGAAAGG
1 AATTTGAGAGG
4796615 AATTTGAGA-G
1 AATTTGAGAGG
4796625 AATATT-AGAGAG
1 AAT-TTGAGAG-G
*
4796637 AAATTGAGAG
1 AATTTGAGAG
4796647 AAAGGATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 7 0.19
11 22 0.61
12 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:4797797 original size:16 final size:16
Alignment explanation
Indices: 4797776--4797831 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
4797766 CGTTTGGTTC
4797776 ACTGTAATAGAATAGA
1 ACTGTAATAGAATAGA
4797792 ACTGTAATTA-AATAGA
1 ACTGTAA-TAGAATAGA
* *
4797808 ATTGTAATGGAATA-A
1 ACTGTAATAGAATAGA
4797823 ACTTGTAAT
1 AC-TGTAAT
4797832 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.09
16 29 0.85
17 2 0.06
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.32
Consensus pattern (16 bp):
ACTGTAATAGAATAGA
Found at i:4801597 original size:40 final size:40
Alignment explanation
Indices: 4801468--4801584 Score: 216
Period size: 40 Copynumber: 2.9 Consensus size: 40
4801458 GTTTGAATAA
*
4801468 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTATAT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
4801508 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
*
4801548 AAAACGCCGCTAAAGATCAAGCATTAGCGGCGCTTTA
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA
4801585 AGGAAAGCGC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTATAT
Found at i:4801692 original size:41 final size:41
Alignment explanation
Indices: 4801635--4801751 Score: 198
Period size: 41 Copynumber: 2.9 Consensus size: 41
4801625 TTTTGACCTT
* *
4801635 TCAGGCCTTTAGCGGCGTTTATGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
4801676 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
* *
4801717 TCAGGGCTTTAGCGGCGTTTTTGTAAAAGCGCCGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGC
4801752 AAAAACATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.26
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
Found at i:4802148 original size:7 final size:7
Alignment explanation
Indices: 4802059--4802188 Score: 66
Period size: 7 Copynumber: 18.4 Consensus size: 7
4802049 TATCTCTATA
*
4802059 GTTTAAG
1 GTTTATG
*
4802066 GTTTTTG
1 GTTTATG
*
4802073 GTTTAGG
1 GTTTATG
*
4802080 GTATATG
1 GTTTATG
*
4802087 GTATA-G
1 GTTTATG
*
4802093 AGTTTAAG
1 -GTTTATG
4802101 GTTTATG
1 GTTTATG
*
4802108 GATTATGG
1 GTTTAT-G
*
4802116 GTTTAGG
1 GTTTATG
*
4802123 GGTTATG
1 GTTTATG
**
4802130 GTTTACA
1 GTTTATG
*
4802137 ATTTATG
1 GTTTATG
*
4802144 GTTTAAG
1 GTTTATG
4802151 GTTTA-G
1 GTTTATG
*
4802157 GATTTAGG
1 G-TTTATG
*
4802165 GGTTATG
1 GTTTATG
*
4802172 GTTTATT
1 GTTTATG
*
4802179 GTTTAAG
1 GTTTATG
4802186 GTT
1 GTT
4802189 ATAGATTAAG
Statistics
Matches: 91, Mismatches: 27, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
6 3 0.03
7 80 0.88
8 8 0.09
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.47
Consensus pattern (7 bp):
GTTTATG
Found at i:4802177 original size:35 final size:34
Alignment explanation
Indices: 4802138--4802241 Score: 95
Period size: 35 Copynumber: 3.0 Consensus size: 34
4802128 TGGTTTACAA
*
4802138 TTTATGGTTTAAGGTTTAGGATTTAGGGGTT-ATGG
1 TTTATGGTTTAAGGTTTAGGA-TTAAGGGTTGA-GG
*
4802173 TTTATTGTTTAAGGTTATA-GATTAAGGGTTGAGG
1 TTTATGGTTTAAGGTT-TAGGATTAAGGGTTGAGG
* * * **
4802207 TTTAAGGTTTAGGGGTTAGGGGTAAGGGGTTGAGG
1 TTTATGGTTTAAGGTTTAGGATTAA-GGGTTGAGG
4802242 GTTAAGAGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
33 2 0.04
34 26 0.46
35 27 0.47
36 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (34 bp):
TTTATGGTTTAAGGTTTAGGATTAAGGGTTGAGG
Found at i:4805716 original size:107 final size:107
Alignment explanation
Indices: 4805518--4805717 Score: 285
Period size: 107 Copynumber: 1.9 Consensus size: 107
4805508 AAATAATAAG
* * * *
4805518 TAAGACAATGTTTTGCGTTTGGAAATTCGAAAAAACGTACCCTAATGTGTTGGGTTTCGATTTTT
1 TAAGACAATGTTTTGCATTTGGAAATTCGAAAAAACGTACCCTAATGTGCTAGGTTTCGATTTTC
4805583 TCGTTCAACCAAATAGCCAAAAATCCTTATAAAATTTCAAAA
66 TCGTTCAACCAAATAGCCAAAAATCCTTATAAAATTTCAAAA
* * **
4805625 TAAGGCAATGTTTTGCATTTGGAAAATTCGAGAAAACGTGTCCTAATGTGCTAGGTTTCGA-TTT
1 TAAGACAATGTTTTGCATTTGG-AAATTCGAAAAAACGTACCCTAATGTGCTAGGTTTCGATTTT
** *
4805689 CTCGTTGGACCAAATAGCCAAATATCCTT
65 CTCGTTCAACCAAATAGCCAAAAATCCTT
4805718 TTGAATCTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
107 48 0.59
108 33 0.41
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (107 bp):
TAAGACAATGTTTTGCATTTGGAAATTCGAAAAAACGTACCCTAATGTGCTAGGTTTCGATTTTC
TCGTTCAACCAAATAGCCAAAAATCCTTATAAAATTTCAAAA
Found at i:4810715 original size:44 final size:44
Alignment explanation
Indices: 4810652--4810739 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
4810642 CCCCCAACAT
*
4810652 GTTTCACAGTCCTACAAACATTGTATAAACCTAATAACCACCCA
1 GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
4810696 GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
1 GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
4810740 ACAAAAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.40, C:0.30, G:0.06, T:0.25
Consensus pattern (44 bp):
GTTTCACAGTCCTACAAACATTATATAAACCTAATAACCACCCA
Found at i:4811877 original size:20 final size:21
Alignment explanation
Indices: 4811848--4811889 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
4811838 CATTTACATA
4811848 TTTTGCAATTTTA-TTTTATT
1 TTTTGCAATTTTATTTTTATT
*
4811868 TTTTGTAATTTTATTTTTATT
1 TTTTGCAATTTTATTTTTATT
4811889 T
1 T
4811890 ATGACATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTGCAATTTTATTTTTATT
Found at i:4813967 original size:31 final size:33
Alignment explanation
Indices: 4813927--4813987 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 33
4813917 TTAAATTTTA
* *
4813927 AAAAGTATAAAAATTAAAATTGACC-AATTCAG
1 AAAAGTATAAAAAATAAAATTAACCGAATTCAG
4813959 AAAA-TATAAAAAATAAAATTAACCGAATT
1 AAAAGTATAAAAAATAAAATTAACCGAATT
4813988 AAAGTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.61, C:0.08, G:0.07, T:0.25
Consensus pattern (33 bp):
AAAAGTATAAAAAATAAAATTAACCGAATTCAG
Found at i:4817457 original size:336 final size:336
Alignment explanation
Indices: 4816844--4817621 Score: 1452
Period size: 336 Copynumber: 2.3 Consensus size: 336
4816834 CTACTCGTAA
* * * * **
4816844 CTAAGTATCATTCCCATTCAAAGCATGTTACGCAATCATTT-TCAAGTCCCACACGAGCTTATAA
1 CTAAGTATCATTCCCATTCAAAGTATGTTACACAATCATTTCT-GAGTTCCACACGAGCTTACGA
*
4816908 AATCTCTTTTGCTAACTCAGGCATGAATTAGGACCAAATTATGACTTCATAATTTCCTCAATGCA
65 AAGCTCTTTTGCTAACTCAGGCATGAATTAGGACCAAATTATGACTTCATAATTTCCTCAATGCA
4816973 ATCACATCACCTTATGAAAGCCTTTCCACATCGCGACACCACTTACTGTCAAACAAAGTTGCGAA
130 ATCACATCACCTTATGAAAGCCTTTCCACATCGCGACACCACTTACTGTCAAACAAAGTTGCGAA
4817038 GTCAAAATTTCTTGGTTGCAACGTTGCCCCTATTTTTGACAAAATACACTTTTTTTTTGTACCTA
195 GTCAAAATTTCTTGGTTGCAACGTTGCCCCTATTTTTGACAAAATACACTTTTTTTTTGTACCTA
4817103 TTCAATAATTTTCAACTAAATCATATGTTCACATTCAATCATTTACCAATCCTACTTATGCCAAA
260 TTCAATAATTTTCAACTAAATCATATGTTCACATTCAATCATTTACCAATCCTACTTATGCCAAA
4817168 TCATCACAAAAC
325 TCATCACAAAAC
4817180 CTAAGTATCATTCCCATTCAAAGTATGTTACACAATCATTTCTGAGTTCCACACGAGCTTACGAA
1 CTAAGTATCATTCCCATTCAAAGTATGTTACACAATCATTTCTGAGTTCCACACGAGCTTACGAA
4817245 AGCTCTTTTGCTAACTCAGGCATGAATTAGGACCAAATTATGACTTCATAATTTCCTCAATGCAA
66 AGCTCTTTTGCTAACTCAGGCATGAATTAGGACCAAATTATGACTTCATAATTTCCTCAATGCAA
4817310 TCACATCACCTTATGAAAGCCTTTCCACATCGCGACACCACTTACTGTCAAACAAAGTTGCGAAG
131 TCACATCACCTTATGAAAGCCTTTCCACATCGCGACACCACTTACTGTCAAACAAAGTTGCGAAG
4817375 TCAAAATTTCTTGGTTGCAACGTTGCCCCTATTTTTGACAAAATACACTTTTTTTTTGTACCTAT
196 TCAAAATTTCTTGGTTGCAACGTTGCCCCTATTTTTGACAAAATACACTTTTTTTTTGTACCTAT
4817440 TCAATAATTTTCAACTAAATCATATGTTCACATTCAATCATTTACCAATCCTACTTATGCCAAAT
261 TCAATAATTTTCAACTAAATCATATGTTCACATTCAATCATTTACCAATCCTACTTATGCCAAAT
4817505 CATCACAAAAC
326 CATCACAAAAC
4817516 CTAAGTATCATTCCCATTCAAAGTATGTTACACAATCATTTCTGAGTTCCACACGAGCTTACGAA
1 CTAAGTATCATTCCCATTCAAAGTATGTTACACAATCATTTCTGAGTTCCACACGAGCTTACGAA
*
4817581 AGCTCTTTTGCTAAC-CTGGGCATGAATTAGGACCAAATTAT
66 AGCTCTTTTGCTAACTC-AGGCATGAATTAGGACCAAATTAT
4817622 AAAGTTTTAA
Statistics
Matches: 432, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
335 1 0.00
336 430 1.00
337 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (336 bp):
CTAAGTATCATTCCCATTCAAAGTATGTTACACAATCATTTCTGAGTTCCACACGAGCTTACGAA
AGCTCTTTTGCTAACTCAGGCATGAATTAGGACCAAATTATGACTTCATAATTTCCTCAATGCAA
TCACATCACCTTATGAAAGCCTTTCCACATCGCGACACCACTTACTGTCAAACAAAGTTGCGAAG
TCAAAATTTCTTGGTTGCAACGTTGCCCCTATTTTTGACAAAATACACTTTTTTTTTGTACCTAT
TCAATAATTTTCAACTAAATCATATGTTCACATTCAATCATTTACCAATCCTACTTATGCCAAAT
CATCACAAAAC
Found at i:4823203 original size:2 final size:2
Alignment explanation
Indices: 4823196--4823246 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4823186 ATAAAACCAC
4823196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4823238 AT AT AT AT A
1 AT AT AT AT A
4823247 CCAAACACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4823694 original size:30 final size:30
Alignment explanation
Indices: 4823639--4823700 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
4823629 CACTAAGCAA
4823639 GTTTTATATACATGTATCATCCATTT-CAT
1 GTTTTATATACATGTATCATCCATTTCCAT
4823668 GTTTTAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTT-ATATA-CATGT-ATCATCCATTTCCAT
4823699 GT
1 GT
4823701 ATTTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (30 bp):
GTTTTATATACATGTATCATCCATTTCCAT
Found at i:4823936 original size:25 final size:24
Alignment explanation
Indices: 4823908--4823983 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 24
4823898 GTAATCTTAT
4823908 ACAAGCTAAGAATCAGTAAGCTCTC
1 ACAAGCTAAGAATC-GTAAGCTCTC
4823933 ACAAGCTATA-AATCGATAAGCTCAT-
1 ACAAGCTA-AGAATCG-TAAGCTC-TC
* *
4823958 ACGAGCTGAGAATCGGTAAGCTCTC
1 ACAAGCTAAGAATC-GTAAGCTCTC
4823983 A
1 A
4823984 TGAGTTGTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
24 3 0.07
25 37 0.86
26 3 0.07
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (24 bp):
ACAAGCTAAGAATCGTAAGCTCTC
Done.