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 18 of 150
Found at i:4824495 original size:9 final size:9
Alignment explanation
Indices: 4824481--4824511 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
4824471 AAGCCCATAT
4824481 ATTTCACAA
1 ATTTCACAA
4824490 ATTTCACAA
1 ATTTCACAA
4824499 ATTTCACAA
1 ATTTCACAA
4824508 ATTT
1 ATTT
4824512 TACCATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (9 bp):
ATTTCACAA
Found at i:4832563 original size:10 final size:11
Alignment explanation
Indices: 4832543--4832575 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4832533 ATTTTTCCTA
4832543 GGATGTGAATT
1 GGATGTGAATT
4832554 GGAT-TGAATT
1 GGATGTGAATT
*
4832564 GAATGTGAATT
1 GGATGTGAATT
4832575 G
1 G
4832576 TATTAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (11 bp):
GGATGTGAATT
Found at i:4832569 original size:21 final size:21
Alignment explanation
Indices: 4832545--4832586 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4832535 TTTTCCTAGG
*
4832545 ATGTGAATTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
4832566 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
4832587 GCTAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:4833002 original size:24 final size:25
Alignment explanation
Indices: 4832949--4832996 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4832939 TTGGCTCTCA
*
4832949 CGAGCTTCCCGTTATATAGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
4832974 CGAGCTTCCCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
4832997 CGGAGCATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:4835368 original size:22 final size:22
Alignment explanation
Indices: 4835327--4835377 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
4835317 AATTTTTAAT
4835327 TTTAAAAAATAGAGAAACTAAA
1 TTTAAAAAATAGAGAAACTAAA
4835349 TTTATAAAAATA-A-AAGACTAAA
1 TTTA-AAAAATAGAGAA-ACTAAA
4835371 TTCTAAA
1 TT-TAAA
4835378 TATACAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.08
22 15 0.58
23 9 0.35
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (22 bp):
TTTAAAAAATAGAGAAACTAAA
Found at i:4839159 original size:19 final size:19
Alignment explanation
Indices: 4839117--4839156 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
4839107 TCACTCCCCC
4839117 CTTCTCTTCTTTCACCTTT
1 CTTCTCTTCTTTCACCTTT
4839136 CTTCTC-TCTTT-ACCCTTT
1 CTTCTCTTCTTTCA-CCTTT
4839154 CTT
1 CTT
4839157 TCTGCCGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.05
18 13 0.65
19 6 0.30
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (19 bp):
CTTCTCTTCTTTCACCTTT
Found at i:4853530 original size:14 final size:13
Alignment explanation
Indices: 4853497--4853532 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
4853487 ATTAGGAGTC
4853497 AAATTGAGTTAAA
1 AAATTGAGTTAAA
4853510 AAATTGAGTTAAA
1 AAATTGAGTTAAA
4853523 AAATTTGAGT
1 AAA-TTGAGT
4853533 CGAGTTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (13 bp):
AAATTGAGTTAAA
Found at i:4854355 original size:18 final size:18
Alignment explanation
Indices: 4854313--4854355 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
4854303 TAAAGTTTGG
*
4854313 AAATTTAAAAATAATTAT
1 AAATTAAAAAATAATTAT
* * *
4854331 CATTTAAAAAATAATTTT
1 AAATTAAAAAATAATTAT
4854349 AAATTAA
1 AAATTAA
4854356 CTATTATAAC
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTAAAAAATAATTAT
Found at i:4854718 original size:6 final size:6
Alignment explanation
Indices: 4854702--4854735 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
4854692 ATAAAATAAA
4854702 TTTCATT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTT
4854736 AAGTGAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTCTT
Found at i:4859287 original size:16 final size:16
Alignment explanation
Indices: 4859266--4859299 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4859256 CTTCAACCTC
*
4859266 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
4859282 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
4859298 TC
1 TC
4859300 CTCTCCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:4861008 original size:321 final size:321
Alignment explanation
Indices: 4860426--4861068 Score: 1214
Period size: 321 Copynumber: 2.0 Consensus size: 321
4860416 TAACCTCAAG
4860426 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATATGTCATAAG
1 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATATGTCATAAG
* *
4860491 AAGTATTTTAAGTGTTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTAACA
66 AAGTATTTTAAATGCTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTAACA
4860556 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTCATGTATGAGGACTATC
131 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTCATGTATGAGGACTATC
*
4860621 TTTTCGTATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAGATA
196 TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAGATA
*
4860686 CATACTCAATGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
261 CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
*
4860747 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGTCTATGAGTAATACAAGATATGTCATAAG
1 AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATATGTCATAAG
* *
4860812 AAGTATTTTAAATGCTAGAATGAATTGCACCTATTATTATATATACTAGATGGATGTTTCTGACA
66 AAGTATTTTAAATGCTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTAACA
*
4860877 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTGATGTATGAGGACTATC
131 TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTCATGTATGAGGACTATC
4860942 TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAGATA
196 TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAGATA
4861007 CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
261 CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
4861068 A
1 A
4861069 CTGTGTCTGT
Statistics
Matches: 314, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
321 314 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (321 bp):
AGTTACCTTCATTCAGGGAGTGCTATGGTTGTTACGCCTATGAGTAATACAAGATATGTCATAAG
AAGTATTTTAAATGCTAGAATGAATTCCACCTATTATTATATATACTAGATGGATGTTTCTAACA
TCTGAAATTGCTTATTGTAAATCAATGACTCTTTTAAGTTTAGAATTTCATGTATGAGGACTATC
TTTTCATATCTATGTTTCTTTTGTTGTTTAAGTTGCAATATAGATCTTTCTCTCTGAGACAGATA
CATACTCAAGGAGAGGTGTATGCACACATGCATGTAATTACATGTTATTCTTGTTTACCAC
Found at i:4861740 original size:20 final size:20
Alignment explanation
Indices: 4861715--4861754 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
4861705 AATATTTTCC
* *
4861715 AGTAAATCATTTTACAGAAA
1 AGTAAAACACTTTACAGAAA
*
4861735 AGTAAAACACTTTCCAGAAA
1 AGTAAAACACTTTACAGAAA
4861755 TTATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTAAAACACTTTACAGAAA
Found at i:4862937 original size:28 final size:27
Alignment explanation
Indices: 4862899--4862961 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
4862889 ATATATATAA
* *
4862899 AATATATATTTT-TATTATATAATTACAT
1 AATAT-TATTTTAT-TTATATAAATAAAT
4862927 AATTATTATTTTATTTATATAAATAAAT
1 AA-TATTATTTTATTTATATAAATAAAT
4862955 AATATTA
1 AATATTA
4862962 ATTAAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 5 0.16
28 22 0.71
29 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTATTTTATTTATATAAATAAAT
Found at i:4863867 original size:2 final size:2
Alignment explanation
Indices: 4863860--4863911 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
4863850 GTTGATCGTG
4863860 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4863901 TA TA TA TA TA T
1 TA TA TA TA TA T
4863912 TACTTTAATG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4870129 original size:376 final size:376
Alignment explanation
Indices: 4869436--4870190 Score: 1467
Period size: 376 Copynumber: 2.0 Consensus size: 376
4869426 AATGGAAACC
4869436 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTTAGTATATGAAAAGCAACAAGAC
1 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTTAGTATATGAAAAGCAACAAGAC
4869501 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATAAAGTAAAATCTAGAAGACAT
66 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATAAAGTAAAATCTAGAAGACAT
*
4869566 TGAAATGTTGCAAATGCATCATATCAGTCTTCCTCTTTTGCTGAAATAGAAAAGATATAACCCAG
131 TGAAATGTTGAAAATGCATCATATCAGTCTTCCTCTTTTGCTGAAATAGAAAAGATATAACCCAG
4869631 ATAAGATAAGCATTAACTTATCTATACAAGTAAAATTCAAGAACATGCAAATAACTCAACCCGAC
196 ATAAGATAAGCATTAACTTATCTATACAAGTAAAATTCAAGAACATGCAAATAACTCAACCCGAC
*
4869696 GAGTAAGGCAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATGATCATGTAAAACGA
261 GAGTAAGACAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATGATCATGTAAAACGA
4869761 CTTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
326 CTTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
4869812 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTTAGTATATGAAAAGCAACAAGAC
1 ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTTAGTATATGAAAAGCAACAAGAC
4869877 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATACAAGTAAAATCTAGAAGACA
66 ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATA-AAGTAAAATCTAGAAGACA
4869942 TTGAAATGTTGAAAATGCATCATATCAGTCTTCCTC-TTTGCTGAAATAGAAAAGATATAACCCA
130 TTGAAATGTTGAAAATGCATCATATCAGTCTTCCTCTTTTGCTGAAATAGAAAAGATATAACCCA
4870006 GATAAGATAAGCATTAACTTATCTATACAAGTAAAATTCAAGAACATGCAAATAACTCAACCCGA
195 GATAAGATAAGCATTAACTTATCTATACAAGTAAAATTCAAGAACATGCAAATAACTCAACCCGA
*
4870071 CGAGTAAGACAATATTGACACTGTGTAATCACTTAGGATTGCCGAATACATGATCATGTAAAACG
260 CGAGTAAGACAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATGATCATGTAAAACG
4870136 ACTTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
325 ACTTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
4870188 ATT
1 ATT
4870191 GCCAAGCAAG
Statistics
Matches: 375, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
376 321 0.86
377 54 0.14
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (376 bp):
ATTTAAAATCATACTAGGCAGCTTGGACATAACATATATGCTTAGTATATGAAAAGCAACAAGAC
ATTAACATGACAAAACCAGCACTTGTAAATCACATAATTGATATAAAGTAAAATCTAGAAGACAT
TGAAATGTTGAAAATGCATCATATCAGTCTTCCTCTTTTGCTGAAATAGAAAAGATATAACCCAG
ATAAGATAAGCATTAACTTATCTATACAAGTAAAATTCAAGAACATGCAAATAACTCAACCCGAC
GAGTAAGACAATATTGACACTGTGTAATCACATAGGATTGCCGAATACATGATCATGTAAAACGA
CTTACCTCTCAAGAGTTTGGTTTTTCCTTAGCTGCATGCGTGAAAAATTCG
Found at i:4871383 original size:24 final size:25
Alignment explanation
Indices: 4871332--4871384 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4871322 TGGATACAAG
**
4871332 TTTAGTATTGATTTTGGAAAATGCT
1 TTTAGTATTGATTTTAAAAAATGCT
*
4871357 TTTAGTATTG-TTGTTAAAAAATGTT
1 TTTAGTATTGATT-TTAAAAAATGCT
4871382 TTT
1 TTT
4871385 GAAAAATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (25 bp):
TTTAGTATTGATTTTAAAAAATGCT
Found at i:4875382 original size:31 final size:32
Alignment explanation
Indices: 4875347--4875414 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
4875337 AAAATTAGAT
* *
4875347 TAAATTGTGATTAAAAT-AAAAT-TTAAATACA
1 TAAATTG-CATTAAAATAAAAATATTAAATAAA
*
4875378 TAAA-TGCATTAAATTAAAAATATTAAATAAA
1 TAAATTGCATTAAAATAAAAATATTAAATAAA
4875409 TAAATT
1 TAAATT
4875415 ATTTACTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 7 0.23
30 7 0.23
31 16 0.52
32 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (32 bp):
TAAATTGCATTAAAATAAAAATATTAAATAAA
Found at i:4875573 original size:2 final size:2
Alignment explanation
Indices: 4875566--4875590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4875556 TTAATATTTA
4875566 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4875591 CTCTGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4890403 original size:19 final size:19
Alignment explanation
Indices: 4890381--4890424 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
4890371 CGTAAATCTC
4890381 AAAAAATTATTTAAAATAA
1 AAAAAATTATTTAAAATAA
4890400 AAAAAA-TATTTAAAATAA
1 AAAAAATTATTTAAAATAA
4890418 AAAAAAT
1 AAAAAAT
4890425 CGAACAACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAATTATTTAAAATAA
Found at i:4895809 original size:26 final size:26
Alignment explanation
Indices: 4895779--4895836 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
4895769 CATCCTCAAA
*
4895779 CTATAATCTAGATATTAAATTGGTCT
1 CTATAATCAAGATATTAAATTGGTCT
*
4895805 CTATAATCAAGATTTTAAATTGGTCT
1 CTATAATCAAGATATTAAATTGGTCT
4895831 CTATAA
1 CTATAA
4895837 ATTTTGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (26 bp):
CTATAATCAAGATATTAAATTGGTCT
Found at i:4896335 original size:34 final size:34
Alignment explanation
Indices: 4896282--4896347 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
4896272 CAAACACCAG
*
4896282 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTAC-GAAAAGT
4896317 AAAATATTTTCCAG-AAATCATTTTACGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACGAAAA
4896348 ACATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (34 bp):
AAAATATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:4902320 original size:13 final size:13
Alignment explanation
Indices: 4902304--4902349 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
4902294 CGTAAAAACA
4902304 AAGATTAAACAAT
1 AAGATTAAACAAT
* *
4902317 AAGATTCATC-AT
1 AAGATTAAACAAT
4902329 -AGATTAAACAAT
1 AAGATTAAACAAT
*
4902341 GAGATTAAA
1 AAGATTAAA
4902350 ATATATTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 7 0.26
12 4 0.15
13 16 0.59
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (13 bp):
AAGATTAAACAAT
Found at i:4902924 original size:53 final size:53
Alignment explanation
Indices: 4902855--4902965 Score: 222
Period size: 53 Copynumber: 2.1 Consensus size: 53
4902845 ACTCATGGAT
4902855 TTGCACCTTAATGTTTTTGTCATCAATCACCTCCACCCTATAGTACTTCCCTA
1 TTGCACCTTAATGTTTTTGTCATCAATCACCTCCACCCTATAGTACTTCCCTA
4902908 TTGCACCTTAATGTTTTTGTCATCAATCACCTCCACCCTATAGTACTTCCCTA
1 TTGCACCTTAATGTTTTTGTCATCAATCACCTCCACCCTATAGTACTTCCCTA
4902961 TTGCA
1 TTGCA
4902966 ATTTTCTACT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.23, C:0.32, G:0.08, T:0.38
Consensus pattern (53 bp):
TTGCACCTTAATGTTTTTGTCATCAATCACCTCCACCCTATAGTACTTCCCTA
Found at i:4906527 original size:22 final size:21
Alignment explanation
Indices: 4906492--4906532 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
4906482 ACTTATACTT
4906492 TTAAATTCTACAAATATAAAGA
1 TTAAATTCTACAAA-ATAAAGA
4906514 TTAAATTCCT-CAAAATAAA
1 TTAAATT-CTACAAAATAAA
4906533 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 11 0.61
23 2 0.11
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (21 bp):
TTAAATTCTACAAAATAAAGA
Found at i:4909552 original size:13 final size:13
Alignment explanation
Indices: 4909534--4909558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4909524 TAATTTATAT
4909534 GTGTGAAAATTTC
1 GTGTGAAAATTTC
4909547 GTGTGAAAATTT
1 GTGTGAAAATTT
4909559 TATCGTTGGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:4911516 original size:41 final size:41
Alignment explanation
Indices: 4911346--4911497 Score: 268
Period size: 41 Copynumber: 3.7 Consensus size: 41
4911336 GACTATATGT
*
4911346 CTAGCAGGCTAAGTGCCGGTGAATTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
*
4911387 CTAGAAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
*
4911428 CTAGCAGGCTAAGTGCCGGTGAACTGAATTAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
*
4911469 CTAGTAGGCTAAGTGCCGGTGAACTGAAT
1 CTAGCAGGCTAAGTGCCGGTGAACTGAAT
4911498 TAGACTTTAA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:4911532 original size:41 final size:41
Alignment explanation
Indices: 4911346--4911516 Score: 153
Period size: 41 Copynumber: 4.2 Consensus size: 41
4911336 GACTATATGT
* * * * * * *
4911346 CTAGCAGGCTAAGTGCCGGTGAATTGAATCAGGCTATAAGC
1 CTAGTAGGATAAGTGCCAGTGAACTGAATTAGACTATAAAC
* * * * * *
4911387 CTAGAAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGTAGGATAAGTGCCAGTGAACTGAATTAGACTATAAAC
* * * * *
4911428 CTAGCAGGCTAAGTGCCGGTGAACTGAATTAGGCTATAAGC
1 CTAGTAGGATAAGTGCCAGTGAACTGAATTAGACTATAAAC
* * *
4911469 CTAGTAGGCTAAGTGCCGGTGAACTGAATTAGACTTTAAAC
1 CTAGTAGGATAAGTGCCAGTGAACTGAATTAGACTATAAAC
4911510 CTAGTAG
1 CTAGTAG
4911517 ATGAATTGCT
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 122 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
CTAGTAGGATAAGTGCCAGTGAACTGAATTAGACTATAAAC
Found at i:4914853 original size:8 final size:8
Alignment explanation
Indices: 4914840--4914902 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
4914830 GTGTTAAAAA
4914840 ATATTATT
1 ATATTATT
4914848 ATATTA-T
1 ATATTATT
*
4914855 AGTAATGATT
1 A-T-ATTATT
* *
4914865 ATGTTTTT
1 ATATTATT
4914873 ATATTATATT
1 ATA-T-TATT
4914883 ATATTATT
1 ATATTATT
4914891 ATATTATT
1 ATATTATT
4914899 ATAT
1 ATAT
4914903 ATATATGACA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
7 2 0.05
8 28 0.64
9 6 0.14
10 8 0.18
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (8 bp):
ATATTATT
Found at i:4914974 original size:40 final size:40
Alignment explanation
Indices: 4914918--4915011 Score: 170
Period size: 40 Copynumber: 2.3 Consensus size: 40
4914908 TGACAAAGAA
4914918 AGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
1 AGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
*
4914959 AGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGGG
1 AGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
4914999 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
4915012 GAAAGAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 46 0.88
41 6 0.12
ACGTcount: A:0.64, C:0.09, G:0.28, T:0.00
Consensus pattern (40 bp):
AGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGGG
Found at i:4916253 original size:39 final size:38
Alignment explanation
Indices: 4916133--4916266 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 38
4916123 GACCTTGAGT
*
4916133 CGATGAGACACTGGGTGTCATACTGTTACTTCGAA-TAGATT
1 CGATGAGACACTGGGTGTCA-ACT-TTACTTCGAACT--ATC
** ** * *
4916174 CGATGAGGTACTGGGTACCAAC-TTACTTCG-GCTTTGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGAACTAT-C
*
4916211 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACT-TTACTTCGAACTATC
*
4916250 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
4916267 CCATTCTGGT
Statistics
Matches: 73, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
36 1 0.01
37 18 0.25
38 9 0.12
39 24 0.33
40 5 0.07
41 16 0.22
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGAACTATC
Found at i:4916951 original size:17 final size:17
Alignment explanation
Indices: 4916929--4916962 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4916919 ATGTGGCATG
*
4916929 TACCTAGGTAATGTATA
1 TACCTAAGTAATGTATA
*
4916946 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
4916963 GGGATTAGTC
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:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:4920540 original size:13 final size:13
Alignment explanation
Indices: 4920522--4920546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4920512 TAATTTATAT
4920522 GTGTGAAAATTTC
1 GTGTGAAAATTTC
4920535 GTGTGAAAATTT
1 GTGTGAAAATTT
4920547 TATCGTTGGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:4922516 original size:41 final size:41
Alignment explanation
Indices: 4922349--4922500 Score: 295
Period size: 41 Copynumber: 3.7 Consensus size: 41
4922339 GACTATATGT
*
4922349 CTAGCAGGCTAAGTGCCGGTGAATTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
4922390 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
4922431 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
4922472 CTAGCAGGCTAAGTGCCGGTGAACTGAAT
1 CTAGCAGGCTAAGTGCCGGTGAACTGAAT
4922501 TAGACTTTAA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 110 1.00
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:4924528 original size:23 final size:24
Alignment explanation
Indices: 4924484--4924529 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
4924474 TTTCTCACAT
* **
4924484 TTTCAATTCAATCATTTTTCCACC
1 TTTCAATTCAATAATTAATCCACC
4924508 TTTCAA-TCAATAATTAATCCAC
1 TTTCAATTCAATAATTAATCCAC
4924530 AATTTCATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTCAATTCAATAATTAATCCACC
Found at i:4924683 original size:6 final size:6
Alignment explanation
Indices: 4924672--4924702 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
4924662 TTCCCACTAA
*
4924672 TAATAC TAATAC TAATAC TAATAT TAATAC T
1 TAATAC TAATAC TAATAC TAATAC TAATAC T
4924703 TACCTCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (6 bp):
TAATAC
Found at i:4925414 original size:20 final size:20
Alignment explanation
Indices: 4925386--4925431 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
4925376 GTTTCGTCAC
4925386 TTCTATTCTGTTT-CTTTCTT
1 TTCTATTCT-TTTGCTTTCTT
* *
4925406 TTCTTTTCTTTTGCTTTGTT
1 TTCTATTCTTTTGCTTTCTT
4925426 TT-TATT
1 TTCTATT
4925432 TCCTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.04, C:0.15, G:0.07, T:0.74
Consensus pattern (20 bp):
TTCTATTCTTTTGCTTTCTT
Found at i:4925595 original size:4 final size:4
Alignment explanation
Indices: 4925586--4925613 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
4925576 TCTCATGATA
4925586 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
4925614 ATCTTTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:4935833 original size:16 final size:17
Alignment explanation
Indices: 4935787--4935833 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
4935777 TAACATATAT
*
4935787 AATAAGAAGTTATAATAA
1 AATAA-AAGTTAAAATAA
* *
4935805 AATTAATGTTAAAATAA
1 AATAAAAGTTAAAATAA
4935822 AA-AAAAGTTAAA
1 AATAAAAGTTAAA
4935834 TTAATTACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 8 0.33
17 12 0.50
18 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (17 bp):
AATAAAAGTTAAAATAA
Found at i:4940084 original size:12 final size:12
Alignment explanation
Indices: 4940060--4940098 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
4940050 TTTTTTACTT
4940060 TTATCATTATTA
1 TTATCATTATTA
4940072 TTAT-ATTATTTA
1 TTATCATTA-TTA
4940084 TTATCACTTATTA
1 TTATCA-TTATTA
4940097 TT
1 TT
4940099 TCTATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.17
12 11 0.46
13 6 0.25
14 3 0.12
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATCATTATTA
Found at i:4940178 original size:18 final size:17
Alignment explanation
Indices: 4940152--4940185 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4940142 CTTTTATAAA
*
4940152 TACATACATATATTTTTG
1 TACAAACATAT-TTTTTG
4940170 TACAAACATATTTTTT
1 TACAAACATATTTTTT
4940186 ATAATATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (17 bp):
TACAAACATATTTTTTG
Found at i:4945142 original size:29 final size:29
Alignment explanation
Indices: 4945109--4945175 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
4945099 TTTTTAACCG
*
4945109 TTAACCGAACTGAAATTTTTTCAAAAAAA
1 TTAACCGAACTGAAATTTTTGCAAAAAAA
***
4945138 TTAACCGAACTGAAATTTTTGGTTAAAAA
1 TTAACCGAACTGAAATTTTTGCAAAAAAA
4945167 TTAACCGAA
1 TTAACCGAA
4945176 TTAACCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (29 bp):
TTAACCGAACTGAAATTTTTGCAAAAAAA
Found at i:4945179 original size:9 final size:9
Alignment explanation
Indices: 4945165--4945267 Score: 127
Period size: 9 Copynumber: 11.4 Consensus size: 9
4945155 TTTGGTTAAA
4945165 AATTAACCG
1 AATTAACCG
*
4945174 AATTAACCA
1 AATTAACCG
*
4945183 AATTACCCG
1 AATTAACCG
*
4945192 AATTAACTG
1 AATTAACCG
4945201 AATTATA-CG
1 AATTA-ACCG
4945210 AATTAACCG
1 AATTAACCG
4945219 AATTAACCG
1 AATTAACCG
4945228 AATTAACCG
1 AATTAACCG
* *
4945237 AATTACCCA
1 AATTAACCG
*
4945246 AATTACCCG
1 AATTAACCG
*
4945255 AATTTACCG
1 AATTAACCG
4945264 AATT
1 AATT
4945268 GAATCACTAC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
8 1 0.01
9 79 0.98
10 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:4945386 original size:18 final size:18
Alignment explanation
Indices: 4945363--4945416 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
4945353 AATTTTTATG
4945363 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
4945381 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
*
4945399 CTTGGGTTGGGATTGGGT
1 ATTGGGTTGGG-TTGGGT
4945417 TTAGGTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 27 0.84
19 5 0.16
ACGTcount: A:0.11, C:0.02, G:0.48, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:4946255 original size:20 final size:20
Alignment explanation
Indices: 4946227--4946280 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
4946217 ACTAGGGAGT
* *
4946227 ACCATAGTGCAAACATGGGC
1 ACCAAAGTGCAAACAGGGGC
*
4946247 ACCAAAGTGCAAAAAGGGGC
1 ACCAAAGTGCAAACAGGGGC
*
4946267 ACCAAAGTGAAAAC
1 ACCAAAGTGCAAAC
4946281 TATAAGTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (20 bp):
ACCAAAGTGCAAACAGGGGC
Found at i:4951190 original size:19 final size:19
Alignment explanation
Indices: 4951154--4951191 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
4951144 AAGAAGGACG
*
4951154 GGAAAAATAAGAGAAAAGA
1 GGAAAAATAAGAAAAAAGA
4951173 GGAAAAA-AAGAAAGAAAGA
1 GGAAAAATAAGAAA-AAAGA
4951192 AAAGATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (19 bp):
GGAAAAATAAGAAAAAAGA
Found at i:4951192 original size:24 final size:24
Alignment explanation
Indices: 4951165--4951214 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4951155 GAAAAATAAG
*
4951165 AGAAAAGAGGAAAAAAA-GAAAGAA
1 AGAAAAGA-GAAAAAAATGAAAAAA
*
4951189 AGAAAAGATAAAAAAATGAAAAAA
1 AGAAAAGAGAAAAAAATGAAAAAA
4951213 AG
1 AG
4951215 TTACACTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (24 bp):
AGAAAAGAGAAAAAAATGAAAAAA
Found at i:4952734 original size:24 final size:24
Alignment explanation
Indices: 4952704--4952762 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
4952694 TGCATCGATG
**
4952704 TATGAGAGCCCCTTGTGTGGGACA
1 TATGAGAGCCCCTTGTGCAGGACA
* * *
4952728 TTTGAGACCCCCTTGTGCAGGACG
1 TATGAGAGCCCCTTGTGCAGGACA
4952752 TATGAGAGCCC
1 TATGAGAGCCC
4952763 TTAGTGGGAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.24
Consensus pattern (24 bp):
TATGAGAGCCCCTTGTGCAGGACA
Found at i:4952881 original size:26 final size:26
Alignment explanation
Indices: 4952812--4952884 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 26
4952802 ATATTCGTGA
4952812 GAAGTTCGTCAAGACTATCTAGTGTGG
1 GAAG-TCGTCAAGACTATCTAGTGTGG
*
4952839 GAAGTCGATCAAAACTATCTAGTGT-G
1 GAAGTCG-TCAAGACTATCTAGTGTGG
*
4952865 GAAGTCCGTCAGGACTATCT
1 GAAGT-CGTCAAGACTATCT
4952885 TGTAAATGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 19 0.46
27 22 0.54
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (26 bp):
GAAGTCGTCAAGACTATCTAGTGTGG
Found at i:4953395 original size:28 final size:28
Alignment explanation
Indices: 4953355--4953422 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
4953345 AGGTGTTCCG
* *
4953355 TGTCACGACATCCCTGGCAGTTTACTGT
1 TGTCGCGACATCCCTGGCAGTTTACCGT
4953383 TGTCGCGACATCCCTGGCAGTTTACCGT
1 TGTCGCGACATCCCTGGCAGTTTACCGT
*
4953411 TGTCGTGACATC
1 TGTCGCGACATC
4953423 GAAAGAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (28 bp):
TGTCGCGACATCCCTGGCAGTTTACCGT
Found at i:4957877 original size:54 final size:54
Alignment explanation
Indices: 4957777--4957883 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
4957767 ATTGAAAACC
* *
4957777 TTGTTCTAGAAAACACCATTATTCAAAAGGAAGCTACTATTAAGGGGGAGACTG
1 TTGTTCTAGAAAACACAATTATTCAAAAGGAAGCTACTATTAAGGGGAAGACTG
* *
4957831 TTGTTCTAGAAAACACAATTGTTCAAAAGGAAGCTACTGA-TCAGGGGAAGACT
1 TTGTTCTAGAAAACACAATTATTCAAAAGGAAGCTACT-ATTAAGGGGAAGACT
4957884 ACTATTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 47 0.98
55 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (54 bp):
TTGTTCTAGAAAACACAATTATTCAAAAGGAAGCTACTATTAAGGGGAAGACTG
Found at i:4966677 original size:22 final size:23
Alignment explanation
Indices: 4966639--4966685 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
4966629 ATCGCGTTTA
*
4966639 TTCTATTTTCATTTTTATTTTTT
1 TTCTATTTTCATTTTTATTTGTT
*
4966662 TTCTCTTTT-ATTTTTATTTGTT
1 TTCTATTTTCATTTTTATTTGTT
4966684 TT
1 TT
4966686 GTGAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.79
Consensus pattern (23 bp):
TTCTATTTTCATTTTTATTTGTT
Found at i:4967325 original size:2 final size:2
Alignment explanation
Indices: 4967318--4967352 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4967308 ACATACGTTT
4967318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4967353 TAACTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4969571 original size:19 final size:19
Alignment explanation
Indices: 4969547--4969591 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4969537 AACGTCTCTT
*
4969547 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTACAT-CA
4969566 TTTGCATTACATTACATCA
1 TTTGCATTACATTACATCA
*
4969585 TATGCAT
1 TTTGCAT
4969592 AAAAAGTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (19 bp):
TTTGCATTACATTACATCA
Found at i:4973094 original size:21 final size:21
Alignment explanation
Indices: 4973070--4973112 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
4973060 AATCTGATAA
4973070 AGAAGAGTCTAAATTAAGACT
1 AGAAGAGTCTAAATTAAGACT
4973091 AGAAGAGTCTAAATTAAGACT
1 AGAAGAGTCTAAATTAAGACT
4973112 A
1 A
4973113 TCCCTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (21 bp):
AGAAGAGTCTAAATTAAGACT
Found at i:4973859 original size:89 final size:89
Alignment explanation
Indices: 4973756--4974856 Score: 1571
Period size: 89 Copynumber: 12.4 Consensus size: 89
4973746 GAAAGATAAT
* * * * *
4973756 AGATCTTGTTTTCATGTACTGGCGTGAAGTAGATTAGAGATACCAGATCTTGCCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
* * **
4973821 GTGGCGAAGCAGATCAAAGAAAGT
66 GTGGCGAAGTAGATCGAAGAAAAC
* * * * * * *
4973845 AGATATTGTCTTCATATACTGGCGTGGAGTAGATCAAAGATAACAGATCTTGCCTTCTCAGACTA
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
* * *
4973910 GTGGTGAAGCAGATC-AAAAAAAGC
66 GTGGCGAAGTAGATCGAAGAAAA-C
* * *
4973934 AGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCAAAGATAATAGATCTTGTCTTTCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
** * *
4973999 GTGGCGAAACAGATTGAAGAAAGC
66 GTGGCGAAGTAGATCGAAGAAAAC
* * *
4974023 AGATATTGCCTTCATGTACTGGTGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
**
4974088 GTGGCGAAACAGATCGAAGAAAAC
66 GTGGCGAAGTAGATCGAAGAAAAC
*
4974112 AGATCTTGTATTCATGTACTGGCGTGAAGTAGATCAAAGAT-ACTAGATCTTGTCTTCCCATACT
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAAC-AGATCTTGTCTTCCCATACT
* *
4974176 GGTGGCGAAATAGATCGAAGAAAAT
65 GGTGGCGAAGTAGATCGAAGAAAAC
* *
4974201 AGATCTTGTCTTCATGTACTGGAGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
*
4974266 GTGGCGAAGTAGATCGAAGAAAAT
66 GTGGCGAAGTAGATCGAAGAAAAC
* *
4974290 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATATTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
4974355 GTGGCGAAGTAGATCGAAGAAAAC
66 GTGGCGAAGTAGATCGAAGAAAAC
* * * *
4974379 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACATATATTGTTTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
*
4974444 GTGGCGAAGTAGATCAAAGAAAAC
66 GTGGCGAAGTAGATCGAAGAAAAC
* *
4974468 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCTATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
4974533 GTGGCGAAGTAGATCGAAGAAAAC
66 GTGGCGAAGTAGATCGAAGAAAAC
* *
4974557 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAATAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
*
4974622 GTGGCGAAGTAGATCGAAGAAGAC
66 GTGGCGAAGTAGATCGAAGAAAAC
* *
4974646 AGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
*
4974711 GTGGCGAAGTAGATCAAAGAAAAC
66 GTGGCGAAGTAGATCGAAGAAAAC
* * *** *
4974735 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAA-AAAATAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AAAGATAACAGATCTTGTCTTCCCATACT
* * *
4974799 GG-CGTGAAGTAGATCGAAGAAAGC
65 GGTGGCGAAGTAGATCGAAGAAAAC
* * *
4974823 AGATCTTATCTTCATGTATTGGCATGAAGTAGAT
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGAT
4974857 TGAAGATTAC
Statistics
Matches: 925, Mismatches: 82, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
88 56 0.06
89 860 0.93
90 9 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTG
GTGGCGAAGTAGATCGAAGAAAAC
Found at i:4974906 original size:44 final size:44
Alignment explanation
Indices: 4974853--4975039 Score: 121
Period size: 44 Copynumber: 4.2 Consensus size: 44
4974843 GGCATGAAGT
4974853 AGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGC
1 AGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGC
* ** * * * * *
4974897 AGATCGAAGATGGCAGATTTTACCTCCCTGAG--GTTACAGTGGAGT
1 AGATTGAAGATTACAAATCTTATCTCCCTAAGCAG-T--AGTGGAGC
* *** * * ** * **
4974942 ACATTGAAGCCAATAATTC-TATCTCCCTGGGCAGCAGTGGAAT
1 AGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGC
*
4974985 AGATTGAAGATTACAGATCTTATCAT-CCTAAGCAGTAGTGGAGC
1 AGATTGAAGATTACAAATCTTATC-TCCCTAAGCAGTAGTGGAGC
*
4975029 AGATCGAAGAT
1 AGATTGAAGAT
4975040 GGCGGATTTT
Statistics
Matches: 101, Mismatches: 35, Indels: 14
0.67 0.23 0.09
Matches are distributed among these distances:
42 1 0.01
43 20 0.20
44 62 0.61
45 17 0.17
46 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
AGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGC
Found at i:4975102 original size:44 final size:43
Alignment explanation
Indices: 4975052--4975248 Score: 111
Period size: 44 Copynumber: 4.5 Consensus size: 43
4975042 CGGATTTTAC
4975052 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTC-TAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAG--AGTAATTCTTAT
** * * *
4975096 CTCCCTG-GGCAACAGTGGCA-TAGATTGAAGATTACAAATCTTAT
1 CTCCCTGAGGTTACAGTGG-AGTACATTGAAGAGT--AATTCTTAT
* * * * * *
4975140 CTCCCT-AGG-CAGTAGTGGAGTAGATCGAAGATGACAGATT-TTAC
1 CTCCCTGAGGTTA-CAGTGGAGTACATTGAAGA-G-TA-ATTCTTAT
* *
4975184 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG-CAGTCTTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAG--AGTAATTCTTAT
* *
4975228 CTCCCTGAAGTTGCAGTGGAG
1 CTCCCTGAGGTTACAGTGGAG
4975249 CAGATTAAAG
Statistics
Matches: 117, Mismatches: 21, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
41 2 0.02
43 26 0.22
44 66 0.56
45 20 0.17
46 2 0.02
47 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (43 bp):
CTCCCTGAGGTTACAGTGGAGTACATTGAAGAGTAATTCTTAT
Found at i:4975190 original size:88 final size:88
Alignment explanation
Indices: 4974850--4975214 Score: 249
Period size: 88 Copynumber: 4.1 Consensus size: 88
4974840 ATTGGCATGA
* * * *
4974850 AGTAGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGAT
1 AGTAGATTGAAGATTACAAATCTTATCTCCCTAGGCAGCAGTGGAGTAGATCGAAGATGACAGAT
**
4974915 TTTACCTCCCTGAGGTTACAGTGG
66 TTTACCTCCCTG-GGCAACAGTGG
* *** * * * * * *
4974939 AGTACATTGAAGCCAATAATTC-TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGAT
1 AGTAGATTGAAGATTACAAATCTTATCTCCCTAGGCAGCAGTGGAGTAGATCGAAGATGACAGAT
* * ** **
4975003 CTTATCAT-CCTAAGCAGTAGTGG
66 TTTA-CCTCCCTGGGCAACAGTGG
* * ** ** * * * * * *
4975026 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTA-CAGTGGAGTACATTG-A-A-GCCAG
1 AGTAGATTGAAGATTACAAATCTTATCTCCCT-AGG-CAGCAGTGGAGTAGATCGAAGATGACAG
* *
4975087 TAATTCTATCTCCCTGGGCAACAGTGG
64 --ATTTTACCTCCCTGGGCAACAGTGG
*
4975114 CA-TAGATTGAAGATTACAAATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGACAGA
1 -AGTAGATTGAAGATTACAAATCTTATCTCCCTAGGCAGCAGTGGAGTAGATCGAAGATGACAGA
**
4975178 TTTTACCTCCCTGAGGTTACAGTGG
65 TTTTACCTCCCTG-GGCAACAGTGG
*
4975203 AGTACATTGAAG
1 AGTAGATTGAAG
4975215 CCAGCAGTCT
Statistics
Matches: 195, Mismatches: 67, Indels: 28
0.67 0.23 0.10
Matches are distributed among these distances:
86 4 0.02
87 33 0.17
88 100 0.51
89 53 0.27
90 5 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (88 bp):
AGTAGATTGAAGATTACAAATCTTATCTCCCTAGGCAGCAGTGGAGTAGATCGAAGATGACAGAT
TTTACCTCCCTGGGCAACAGTGG
Found at i:4975234 original size:132 final size:132
Alignment explanation
Indices: 4974852--4975218 Score: 646
Period size: 132 Copynumber: 2.8 Consensus size: 132
4974842 TGGCATGAAG
4974852 TAGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
1 TAGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
* *
4974917 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
4974982 AA
131 AA
* *
4974984 TAGATTGAAGATTACAGATCTTATCAT-CCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATT
1 TAGATTGAAGATTACAAATCTTATC-TCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATT
4975048 TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTG
65 TTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTG
*
4975113 GCA
130 GAA
* * *
4975116 TAGATTGAAGATTACAAATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAAGATGACAGATTT
1 TAGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
4975181 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
66 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAG
4975219 CAGTCTTATC
Statistics
Matches: 223, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
131 1 0.00
132 221 0.99
133 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (132 bp):
TAGATTGAAGATTACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTT
TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGG
AA
Found at i:4976457 original size:21 final size:21
Alignment explanation
Indices: 4976433--4976473 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4976423 TGCATTTTTT
4976433 TTTAAAATTATTACTATATTA
1 TTTAAAATTATTACTATATTA
** *
4976454 TTTATTATTATTCCTATATT
1 TTTAAAATTATTACTATATT
4976474 TATACACGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAAATTATTACTATATTA
Found at i:4976584 original size:2 final size:2
Alignment explanation
Indices: 4976577--4976625 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4976567 ACATACATTT
4976577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4976619 TA TA TA T
1 TA TA TA T
4976626 TAACTTTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4987546 original size:30 final size:30
Alignment explanation
Indices: 4987507--4987563 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
4987497 TTTTACAAAT
4987507 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
4987537 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
4987564 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:4988784 original size:35 final size:35
Alignment explanation
Indices: 4988718--4988784 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
4988708 CAAACACCAG
*
4988718 AAAATATTTTCCAGTAAATCATTTTACAAAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
* *
4988753 AAAACATTTTTCAG-AAATCATTTTACGAAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAA
4988785 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
Found at i:4989060 original size:21 final size:20
Alignment explanation
Indices: 4989010--4989060 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
4989000 ATTCAAAAAC
*
4989010 TAAATAAAATTATAAAAATTA
1 TAAAT-AAATTACAAAAATTA
*
4989031 -ATAACAAATTACAGAAAATTA
1 TA-AATAAATTACA-AAAATTA
4989052 TAAATAAAT
1 TAAATAAAT
4989061 ACCATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 8 0.33
21 15 0.62
22 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
TAAATAAATTACAAAAATTA
Found at i:4990566 original size:18 final size:18
Alignment explanation
Indices: 4990539--4990574 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4990529 AATTATTCCC
4990539 TTTTTCTTGAAATTTTTA
1 TTTTTCTTGAAATTTTTA
* *
4990557 TTTTTTTTGAGATTTTTA
1 TTTTTCTTGAAATTTTTA
4990575 CAAGTAGGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTTCTTGAAATTTTTA
Found at i:4991407 original size:42 final size:42
Alignment explanation
Indices: 4991334--4991485 Score: 121
Period size: 42 Copynumber: 3.6 Consensus size: 42
4991324 TCGTGTTTAC
*
4991334 TTTCCGTTTAGCTCTCACGAGCTTCTATTTAACTCA-TATGAG
1 TTTCCGTTCAGCTCTCACGAGCTTCTATTTAAC-CATTATGAG
* * * *
4991376 TTTCCGTTCAGCTCT-ATTGAGTTTCTGTTTAACCATTATGGG
1 TTTCCGTTCAGCTCTCA-CGAGCTTCTATTTAACCATTATGAG
* * * * * * *
4991418 TTTCCATTAAGCTTTTATGAGCTTCTATTCAACCCTTA-GAGG
1 TTTCCGTTCAGCTCTCACGAGCTTCTATTTAACCATTATGA-G
* * *
4991460 TTTCTGTTTAGCTCTCATGAGCTTCT
1 TTTCCGTTCAGCTCTCACGAGCTTCT
4991486 GTTCAGCCTT
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
41 4 0.05
42 83 0.94
43 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTCACGAGCTTCTATTTAACCATTATGAG
Found at i:4995448 original size:16 final size:14
Alignment explanation
Indices: 4995417--4995456 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
4995407 AAACATATTA
4995417 AATTAATTTTAATT
1 AATTAATTTTAATT
4995431 AATTAATTTCTCAATT
1 AATTAATTT-T-AATT
*
4995447 AAATAATTTT
1 AATTAATTTT
4995457 TTAAACCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 2 0.09
16 12 0.52
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTAATTTTAATT
Found at i:5000225 original size:18 final size:17
Alignment explanation
Indices: 5000199--5000237 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5000189 TATTTCCAGA
*
5000199 AACATATATCATATCAG
1 AACATATATCAGATCAG
*
5000216 AACATCATATCAGATTAG
1 AACAT-ATATCAGATCAG
5000234 AACA
1 AACA
5000238 AATCCTACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.26
Consensus pattern (17 bp):
AACATATATCAGATCAG
Found at i:5002153 original size:16 final size:16
Alignment explanation
Indices: 5002132--5002164 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5002122 CATTTTACCA
5002132 ATAAAAGCCCATTTCC
1 ATAAAAGCCCATTTCC
5002148 ATAAAAGCCCATTTCC
1 ATAAAAGCCCATTTCC
5002164 A
1 A
5002165 ACTTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.30, G:0.06, T:0.24
Consensus pattern (16 bp):
ATAAAAGCCCATTTCC
Found at i:5002713 original size:9 final size:10
Alignment explanation
Indices: 5002689--5002714 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5002679 GTTAATTTCA
5002689 ATTTTTGAAT
1 ATTTTTGAAT
5002699 ATTTTTGAAT
1 ATTTTTGAAT
5002709 ATTTTT
1 ATTTTT
5002715 TTCATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (10 bp):
ATTTTTGAAT
Found at i:5009248 original size:10 final size:11
Alignment explanation
Indices: 5009220--5009245 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5009210 TGTTTTTGTT
5009220 AAAAATTATAA
1 AAAAATTATAA
5009231 AAAAATTATAA
1 AAAAATTATAA
5009242 AAAA
1 AAAA
5009246 TTAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:5010021 original size:9 final size:9
Alignment explanation
Indices: 5010007--5010061 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
5009997 TCATCAATTG
5010007 TTTTATAAT
1 TTTTATAAT
*
5010016 TTTTATAAAG
1 TTTTAT-AAT
*
5010026 TTTTACAAT
1 TTTTATAAT
*
5010035 TTTTTTATAT
1 TTTTATA-AT
*
5010045 TTTTATGAT
1 TTTTATAAT
5010054 TTTTATAA
1 TTTTATAA
5010062 AAATAATTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 22 0.61
10 14 0.39
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:5010030 original size:19 final size:18
Alignment explanation
Indices: 5010007--5010131 Score: 80
Period size: 19 Copynumber: 6.8 Consensus size: 18
5009997 TCATCAATTG
5010007 TTTTATAATTTTTATAAA
1 TTTTATAATTTTTATAAA
* * *
5010025 GTTTTACAATTTTTTTATAT
1 -TTTTATAATTTTTATA-AA
*
5010045 TTTTATGATTTTTATAAA
1 TTTTATAATTTTTATAAA
*
5010063 ---AATAATTTTTCATAAA
1 TTTTATAATTTTT-ATAAA
5010079 TTTTA-AATTTTTATTAAAA
1 TTTTATAATTTTTA-T-AAA
*
5010098 TTTAATAA-TTTTATTAAA
1 TTTTATAATTTTTA-TAAA
* *
5010116 ATTTATTATTTATTAT
1 TTTTATAATTT-TTAT
5010132 GGTTTTTAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
15 8 0.10
16 5 0.06
17 1 0.01
18 17 0.21
19 45 0.55
20 6 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTATAATTTTTATAAA
Found at i:5010109 original size:53 final size:52
Alignment explanation
Indices: 5010011--5010117 Score: 128
Period size: 53 Copynumber: 2.0 Consensus size: 52
5010001 CAATTGTTTT
* * * *
5010011 ATAATTTTTATAAAGTTTTACAATTTTTTTATATTTTTATGATTTTTATAAAA
1 ATAATTTTTATAAAGTTTTACAATTTTTTTAAAATTTAAT-AATTTTATAAAA
*
5010064 ATAATTTTTCATAAA-TTTTA-AATTTTTATTAAAATTTAATAATTTTATTAAA
1 ATAATTTTT-ATAAAGTTTTACAATTTTT-TTAAAATTTAATAATTTTATAAAA
5010116 AT
1 AT
5010118 TTATTATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
52 19 0.40
53 23 0.49
54 5 0.11
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (52 bp):
ATAATTTTTATAAAGTTTTACAATTTTTTTAAAATTTAATAATTTTATAAAA
Found at i:5010744 original size:36 final size:37
Alignment explanation
Indices: 5010711--5010781 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
5010701 TATAAAATGT
5010711 TTAT-GAT-AATATAAAATATATTAATTAAAAAAATAA
1 TTATAGATCAATATAAAAT-TATTAATTAAAAAAATAA
* * *
5010747 TTATAGTTCAATTTATAATTATTAATTAAAAAAAT
1 TTATAGATCAATATAAAATTATTAATTAAAAAAAT
5010782 TATACTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 4 0.13
37 18 0.60
38 8 0.27
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (37 bp):
TTATAGATCAATATAAAATTATTAATTAAAAAAATAA
Found at i:5011192 original size:14 final size:13
Alignment explanation
Indices: 5011170--5011199 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
5011160 ATTTTTTTTC
5011170 ATTCATTATATCT
1 ATTCATTATATCT
5011183 ATTCACTTATATCT
1 ATTCA-TTATATCT
5011197 ATT
1 ATT
5011200 AATTTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTCATTATATCT
Found at i:5011626 original size:7 final size:7
Alignment explanation
Indices: 5011616--5011648 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5011606 ACTACATACG
5011616 ATATTAT
1 ATATTAT
*
5011623 ATATAAT
1 ATATTAT
5011630 ATATTAT
1 ATATTAT
5011637 ATATTAT
1 ATATTAT
5011644 ATATT
1 ATATT
5011649 TTGACCAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATATTAT
Found at i:5015383 original size:2 final size:2
Alignment explanation
Indices: 5015376--5015405 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5015366 TCTCAATCCA
5015376 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
5015406 TTCAATACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5016473 original size:36 final size:37
Alignment explanation
Indices: 5016405--5016475 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
5016395 TTTTCATAAT
* * *
5016405 TTCACTTTTTCACTTTTAATCACTATTGAATTCAAAA
1 TTCACTTTTTCACATTTAATCAATATTCAATTCAAAA
5016442 TTCAC-TTTTC-CATTTAAGTCAATATTCAATTCAA
1 TTCACTTTTTCACATTTAA-TCAATATTCAATTCAA
5016476 TTCCACACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 6 0.20
36 19 0.63
37 5 0.17
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (37 bp):
TTCACTTTTTCACATTTAATCAATATTCAATTCAAAA
Found at i:5016506 original size:23 final size:22
Alignment explanation
Indices: 5016463--5016506 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
5016453 ATTTAAGTCA
5016463 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
5016486 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
5016507 TTAATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:5016631 original size:23 final size:23
Alignment explanation
Indices: 5016605--5016703 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
5016595 ATAAGTGCCA
5016605 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
5016628 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5016651 CACTGAAATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5016674 CGCTGATATGTAGCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
5016697 CACTGAT
1 CACTGAT
5016704 CAATAACACT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5022598 original size:19 final size:17
Alignment explanation
Indices: 5022574--5022612 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
5022564 GTTTCCATCA
5022574 TTTTTCCTCTGTTTTCTAT
1 TTTTTCCTCT-TTTTC-AT
*
5022593 TTTTTCTTCTTTTTCAT
1 TTTTTCCTCTTTTTCAT
5022610 TTT
1 TTT
5022613 CTTCTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTCCTCTTTTTCAT
Found at i:5022606 original size:18 final size:18
Alignment explanation
Indices: 5022574--5022617 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5022564 GTTTCCATCA
*
5022574 TTTTTCCTCTGTTTTCTAT
1 TTTTTCTTCTGTTTTC-AT
5022593 TTTTTCTTCT-TTTTCAT
1 TTTTTCTTCTGTTTTCAT
5022610 TTTCTTCT
1 TTT-TTCT
5022618 ATTCTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 9 0.39
19 9 0.39
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTCTTCTGTTTTCAT
Found at i:5026597 original size:29 final size:29
Alignment explanation
Indices: 5026563--5026618 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
5026553 TTAGACACGG
5026563 GCTGGGACACGACCGTGTGAA-ACACACAA
1 GCTGGGACACGACCGTGT-AAGACACACAA
* *
5026592 GCTGGGACATGGCCGTGTAAGACACAC
1 GCTGGGACACGACCGTGTAAGACACAC
5026619 GGGCGTGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.30, C:0.27, G:0.30, T:0.12
Consensus pattern (29 bp):
GCTGGGACACGACCGTGTAAGACACACAA
Found at i:5027109 original size:26 final size:26
Alignment explanation
Indices: 5027073--5027317 Score: 202
Period size: 26 Copynumber: 9.4 Consensus size: 26
5027063 AATAAAGTAA
* *
5027073 TTATCTAGCAGGCTTTGAGTCGGTGT
1 TTATTTAGCAGGCTTTGAGCCGGTGT
* * **
5027099 TTATTTAGCAGGCCTAGAGCCGGTAA
1 TTATTTAGCAGGCTTTGAGCCGGTGT
* *
5027125 TTATTTAGCAGGCTTTGAGTCGGTTT
1 TTATTTAGCAGGCTTTGAGCCGGTGT
* * * *
5027151 TTATGTAGTAGGCTTTTAGCCGGTGA
1 TTATTTAGCAGGCTTTGAGCCGGTGT
* * * * * *
5027177 TTATTTAGTAAGCCTTAAGCCAGTGA
1 TTATTTAGCAGGCTTTGAGCCGGTGT
* * * *
5027203 TTATTTAACAGACTTTGAGCCGATGG
1 TTATTTAGCAGGCTTTGAGCCGGTGT
*
5027229 TCATTTAGCAGGCTTTGAGCCGGTGT
1 TTATTTAGCAGGCTTTGAGCCGGTGT
* * * * *
5027255 TTATTGAGTAGGCTTTAAGCTGGTGG
1 TTATTTAGCAGGCTTTGAGCCGGTGT
* * *
5027281 TTATTTATCAGGCTTTAAGCCGGTAAT
1 TTATTTAGCAGGCTTTGAGCCGGT-GT
5027308 TTATTTAGCA
1 TTATTTAGCA
5027318 AGTACCATGT
Statistics
Matches: 169, Mismatches: 49, Indels: 1
0.77 0.22 0.00
Matches are distributed among these distances:
26 160 0.95
27 9 0.05
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (26 bp):
TTATTTAGCAGGCTTTGAGCCGGTGT
Found at i:5027273 original size:78 final size:77
Alignment explanation
Indices: 5027078--5027302 Score: 225
Period size: 78 Copynumber: 2.9 Consensus size: 77
5027068 AGTAATTATC
* * * * *
5027078 TAGCAGGCTTTGAGTCGGTGTTTATTTAGCAGGCCTAGAGCCGGTAATTATTTAGCAGGCTTTGA
1 TAGCAGGCTTTGAGCCGGTGTTTATTTAGTAGGCTTA-AGCCGGTGATTATTTAACAGGCTTTGA
* * ** *
5027143 GTCGGTTTTTATG
65 GCCGATGGTCATG
* * * * * *
5027156 TAGTAGGCTTTTAGCCGGTGATTATTTAGTAAGCCTTAAGCCAGTGATTATTTAACAGACTTTGA
1 TAGCAGGCTTTGAGCCGGTGTTTATTTAGT-AGGCTTAAGCCGGTGATTATTTAACAGGCTTTGA
*
5027221 GCCGATGGTCATT
65 GCCGATGGTCATG
* * * * *
5027234 TAGCAGGCTTTGAGCCGGTGTTTATTGAGTAGGCTTTAAGCTGGTGGTTATTTATCAGGCTTTAA
1 TAGCAGGCTTTGAGCCGGTGTTTATTTAGTAGGC-TTAAGCCGGTGATTATTTAACAGGCTTTGA
5027299 GCCG
65 GCCG
5027303 GTAATTTATT
Statistics
Matches: 117, Mismatches: 28, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
77 3 0.03
78 109 0.93
79 5 0.04
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (77 bp):
TAGCAGGCTTTGAGCCGGTGTTTATTTAGTAGGCTTAAGCCGGTGATTATTTAACAGGCTTTGAG
CCGATGGTCATG
Found at i:5028414 original size:22 final size:22
Alignment explanation
Indices: 5028389--5028459 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
5028379 ACGGTTTCAA
* *
5028389 CACACGGGTGTGTGGGGGTAGC
1 CACACAGGCGTGTGGGGGTAGC
* *
5028411 CACATAGGCGTGTGGGTGTAGC
1 CACACAGGCGTGTGGGGGTAGC
*
5028433 CACACAGGCGTGT-GGGGTAGT
1 CACACAGGCGTGTGGGGGTAGC
5028454 CACACA
1 CACACA
5028460 CGGGCTAACC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
21 12 0.29
22 30 0.71
ACGTcount: A:0.20, C:0.21, G:0.41, T:0.18
Consensus pattern (22 bp):
CACACAGGCGTGTGGGGGTAGC
Found at i:5036559 original size:2 final size:2
Alignment explanation
Indices: 5036552--5036589 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5036542 ACTACAAGTA
5036552 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
5036590 TATTTTCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5036794 original size:18 final size:17
Alignment explanation
Indices: 5036758--5036805 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5036748 GTCTTTCAAA
* *
5036758 ATTTATATAATTTTTAT
1 ATTTAGATAATTTTCAT
5036775 ATTTAGATAACTTTTCAT
1 ATTTAGATAA-TTTTCAT
5036793 ATATTA-ATAATTT
1 AT-TTAGATAATTT
5036806 ATATTATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 12 0.44
18 12 0.44
19 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTAGATAATTTTCAT
Found at i:5043399 original size:6 final size:7
Alignment explanation
Indices: 5043382--5043406 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5043372 TTAAAAACCC
5043382 TTTTTAA
1 TTTTTAA
5043389 TTTTTAA
1 TTTTTAA
5043396 TTTTTAA
1 TTTTTAA
5043403 TTTT
1 TTTT
5043407 GCATTATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:5044819 original size:159 final size:158
Alignment explanation
Indices: 5044530--5044840 Score: 444
Period size: 159 Copynumber: 2.0 Consensus size: 158
5044520 AAATATTAAA
*
5044530 ATATTATATCAACAGATATAGATCGATACATATCAATATAAATCGATATTGATCAAAACATATCA
1 ATATTATATCAACAGATAAAGATCGATACATATCAATATAAATCGATATTGATCAAAACATATCA
* * ** *
5044595 ATAAATACATATCTCGAGATACAAAAGTAATTTTTGTTTGCCACATTTTCACAGCTTTTTTTTTT
66 ATAAATACATATATCAAGATACAAAAGTAATTTTTGTTCCCCACATTTTCACAGC-ATTTTTTTT
5044660 TTATTTTGAAAGATGTTTCGCATCATTTT
130 TTATTTTGAAAGATGTTTCGCATCATTTT
* ** * * *
5044689 ATATTGTATCAATGGATAAAGATCGATACTTATCTATATAACTCGATATTGATCAAAACATATCA
1 ATATTATATCAACAGATAAAGATCGATACATATCAATATAAATCGATATTGATCAAAACATATCA
* * * * *
5044754 ATAAATACATATATCAAGATACGAGAA-TGATTTTTGTTCCCCGCATTTTCCCATCATTTTTTTT
66 ATAAATACATATATCAAGATAC-AAAAGTAATTTTTGTTCCCCACATTTTCACAGCATTTTTTTT
5044818 TTATTTTGAAAGATGTTTCGCAT
130 TTATTTTGAAAGATGTTTCGCAT
5044841 ACAATAAGCT
Statistics
Matches: 134, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
158 31 0.23
159 100 0.75
160 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (158 bp):
ATATTATATCAACAGATAAAGATCGATACATATCAATATAAATCGATATTGATCAAAACATATCA
ATAAATACATATATCAAGATACAAAAGTAATTTTTGTTCCCCACATTTTCACAGCATTTTTTTTT
TATTTTGAAAGATGTTTCGCATCATTTT
Found at i:5045897 original size:310 final size:308
Alignment explanation
Indices: 5045223--5046044 Score: 1132
Period size: 310 Copynumber: 2.7 Consensus size: 308
5045213 AAATATTAAA
* ** *
5045223 ATATTGTATCAACGGATACATATCGATACATACATATATAAATCGATATTGATAAAAACATATCA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATAA
* **
5045288 ATAAATATATATCTCGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCACCA--TTTTTTT
66 ATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCTTCATTTTTTTTT
*
5045351 TATTTTGAAAGATATTTCGCATCATTTTATATTGTATCAATGGATACAGATCGATACATACCGAT
131 TATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATGGATACAGATCGATACATACCGAT
* *
5045416 AT---T-G--ATCAAAACATACTAATAAATATATATCTTGAGATACGAGAATGATTTTTGTTCCC
196 ATAAATCGATATCAAAACATACTAATAAATACATATCTTGAGATACGAGAATGAGTTTTGTTCCC
* * *
5045475 TGCATTTTCTCATGATTTTTTTTTAATTTTGAAAGATGTTTCGCATCATTTT
261 CGCATTTTCTCATCA---TTTTTT-ATTTTGAAAGATGTTTCGCATCATTTC
** *
5045527 ATATTGTATCAACGGATACAGATAAATACATACCGATATAAATCGATATTGATCAAAACATATAA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATAA
*
5045592 ATAAATACATATCTCGAGATATGAGAATGATTTTTGTTCCCCGCATTTTCTCTTCATTTTTTTTT
66 ATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCTTCATTTTTTTTT
*
5045657 TATTTTGAAAGATGTTTCGCATGATTTTATATTGTATCAATGGATACAGATC-AGTACATACCGA
131 TATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATGGATACAGATCGA-TACATACCGA
*
5045721 TATAAATCGATATTGATAAACACATA-TCAATAAATACATATCTTGAGATACGAGAATGAGTTTT
195 TATAAATCGATA-T--CAAA-ACATACT-AATAAATACATATCTTGAGATACGAGAATGAGTTTT
*
5045785 GTTCCCCGCATTTTCTCATCA-TTTTT-TTTTGAAAGATGTTTCGCATGATTTC
255 GTTCCCCGCATTTTCTCATCATTTTTTATTTTGAAAGATGTTTCGCATCATTTC
* *
5045837 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATTGATATTGATAAAAACATATTA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATAA
** * *
5045902 ATAAATACATATCTTAAGATACGAGAATAATTTTTGTTCCCTGCATTTT-TCTTATCAATTTTTT
66 ATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTC-T-TC-ATTTTTT
* * * *
5045966 TTTTATTTTAAAAGATGTTCCGCATCATTTTATATTATATCAA-GAGATACAGATCGATGCATAC
128 TTTTATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATG-GATACAGATCGATACATAC
* *
5046030 CAATATAAAACGATA
192 CGATATAAATCGATA
5046045 AATACATATA
Statistics
Matches: 462, Mismatches: 37, Indels: 30
0.87 0.07 0.06
Matches are distributed among these distances:
304 110 0.24
305 1 0.00
306 70 0.15
309 3 0.01
310 130 0.28
311 3 0.01
312 81 0.18
313 2 0.00
315 4 0.01
316 58 0.13
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (308 bp):
ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATAA
ATAAATACATATCTCGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCTTCATTTTTTTTT
TATTTTGAAAGATGTTTCGCATCATTTTATATTGTATCAATGGATACAGATCGATACATACCGAT
ATAAATCGATATCAAAACATACTAATAAATACATATCTTGAGATACGAGAATGAGTTTTGTTCCC
CGCATTTTCTCATCATTTTTTATTTTGAAAGATGTTTCGCATCATTTC
Found at i:5045898 original size:152 final size:154
Alignment explanation
Indices: 5045223--5046044 Score: 1035
Period size: 158 Copynumber: 5.3 Consensus size: 154
5045213 AAATATTAAA
* **
5045223 ATATTGTATCAACGGATACATATCGATACATACATATATAAATCGATATTGATAAAAACATATCA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
* * *
5045288 ATAAATATATATCTCGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCACCATTTTTTTTA
66 ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCA--TTTTTTA
*
5045353 TTTTGAAAGATATTTCGCATCATTTT
129 TTTTGAAAGATGTTTCGCATCATTTT
* *
5045379 ATATTGTATCAATGGATACAGATCGATACATA-C---------CGATATTGATCAAAACATA-CT
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATC-
* * *
5045433 AATAAATATATATCTTGAGATACGAGAATGATTTTTGTTCCCTGCATTTTCTCATGATTTTTTTT
65 AATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCA---TTTTT
5045498 TAATTTTGAAAGATGTTTCGCATCATTTT
127 T-ATTTTGAAAGATGTTTCGCATCATTTT
** * *
5045527 ATATTGTATCAACGGATACAGATAAATACATACCGATATAAATCGATATTGATCAAAACATATAA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
* * *
5045592 ATAAATACATATCTCGAGATATGAGAATGATTTTTGTTCCCCGCATTTTCTCTTCATTTTTTTTT
66 ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCA----TTTTT
*
5045657 TATTTTGAAAGATGTTTCGCATGATTTT
127 TATTTTGAAAGATGTTTCGCATCATTTT
* *
5045685 ATATTGTATCAATGGATACAGATC-AGTACATACCGATATAAATCGATATTGATAAACACATATC
1 ATATTGTATCAACGGATACAGATCGA-TACATACCGATATAAATCGATATTGATAAAAACATATC
*
5045749 AATAAATACATATCTTGAGATACGAGAATGAGTTTTGTTCCCCGCATTTTCTCATCA-TTTTT-T
65 AATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCATTTTTTAT
* *
5045812 TTTGAAAGATGTTTCGCATGATTTC
130 TTTGAAAGATGTTTCGCATCATTTT
* *
5045837 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATTGATATTGATAAAAACATATTA
1 ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
* * * *
5045902 ATAAATACATATCTTAAGATACGAGAATAATTTTTGTTCCCTGCATTTTTCTTATCAATTTTTTT
66 ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCA-TTTTCTCATC-A----TTT
* *
5045967 TTTATTTTAAAAGATGTTCCGCATCATTTT
125 TTTATTTTGAAAGATGTTTCGCATCATTTT
* * * *
5045997 ATATTATATCAA-GAGATACAGATCGATGCATACCAATATAAAACGATA
1 ATATTGTATCAACG-GATACAGATCGATACATACCGATATAAATCGATA
5046045 AATACATATA
Statistics
Matches: 592, Mismatches: 48, Indels: 48
0.86 0.07 0.07
Matches are distributed among these distances:
145 1 0.00
146 71 0.12
147 8 0.01
148 55 0.09
149 1 0.00
152 125 0.21
153 15 0.03
154 1 0.00
156 30 0.05
157 1 0.00
158 206 0.35
159 15 0.03
160 63 0.11
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (154 bp):
ATATTGTATCAACGGATACAGATCGATACATACCGATATAAATCGATATTGATAAAAACATATCA
ATAAATACATATCTTGAGATACGAGAATGATTTTTGTTCCCCGCATTTTCTCATCATTTTTTATT
TTGAAAGATGTTTCGCATCATTTT
Found at i:5059042 original size:13 final size:13
Alignment explanation
Indices: 5059024--5059048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5059014 GAATTAATAT
5059024 GTGTGAAAATTTC
1 GTGTGAAAATTTC
5059037 GTGTGAAAATTT
1 GTGTGAAAATTT
5059049 TATCGTTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:5064110 original size:14 final size:14
Alignment explanation
Indices: 5064091--5064118 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5064081 TTCCATGCCT
5064091 AATTCCTATTTGTC
1 AATTCCTATTTGTC
5064105 AATTCCTATTTGTC
1 AATTCCTATTTGTC
5064119 TAGCATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
AATTCCTATTTGTC
Found at i:5065024 original size:14 final size:13
Alignment explanation
Indices: 5065005--5065047 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
5064995 GAAGCTGAAC
5065005 CTAACTTAGCTAG
1 CTAACTTAGCTAG
5065018 TCTAACTTAGCTAG
1 -CTAACTTAGCTAG
*
5065032 CTAACTCAGCT-G
1 CTAACTTAGCTAG
5065044 CTAA
1 CTAA
5065048 GACATTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 13 0.46
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (13 bp):
CTAACTTAGCTAG
Found at i:5065553 original size:3 final size:3
Alignment explanation
Indices: 5065482--5065536 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
5065472 GTGTTTGATG
*
5065482 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5065530 TTA TTA T
1 TTA TTA T
5065537 GTTCCCCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5065768 original size:19 final size:18
Alignment explanation
Indices: 5065744--5065779 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5065734 ATTGTTTATG
*
5065744 GTTATTATTATTTATCGTC
1 GTTATTAATATTT-TCGTC
5065763 GTTATTAATATTTTCGT
1 GTTATTAATATTTTCGT
5065780 TTCTAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.58
Consensus pattern (18 bp):
GTTATTAATATTTTCGTC
Found at i:5068239 original size:16 final size:17
Alignment explanation
Indices: 5068207--5068239 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5068197 AAAAGTTTTC
5068207 TTTTTTCTAAAAGTTCA
1 TTTTTTCTAAAAGTTCA
5068224 TTTTTTCTAAAA-TTCA
1 TTTTTTCTAAAAGTTCA
5068240 AAAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTTTCTAAAAGTTCA
Found at i:5069299 original size:67 final size:67
Alignment explanation
Indices: 5069191--5069335 Score: 254
Period size: 67 Copynumber: 2.2 Consensus size: 67
5069181 TTTAACTTAG
* *
5069191 TAATTTAACGGTTGGTGACCAAAAAGCATAAAATCAAATAGTTAGTTAACTATTTTAAAACTTTT
1 TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTGAAAACTTTT
5069256 CA
66 CA
* *
5069258 TAATTTAACGGTTGGTGACTAAAAAACATAAAATTAAATAGTTAGTTAACTATTTGAAAACTTTT
1 TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTGAAAACTTTT
5069323 CA
66 CA
5069325 TAATTTAACGG
1 TAATTTAACGG
5069336 AAAAAGAAGT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 74 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (67 bp):
TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTGAAAACTTTT
CA
Found at i:5072303 original size:27 final size:29
Alignment explanation
Indices: 5072259--5072327 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
5072249 AATAAACACC
*
5072259 AAAAATTTATTTTCAAAA-TAAAAAAATA
1 AAAAAATTATTTTCAAAATTAAAAAAATA
*
5072287 AAAAAATTATTTT-AAAATTAAAAAATTA
1 AAAAAATTATTTTCAAAATTAAAAAAATA
5072315 AAAAAATATATTT
1 AAAAAAT-TATTT
5072328 ATTATATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 4 0.11
28 28 0.76
29 5 0.14
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAAATTATTTTCAAAATTAAAAAAATA
Found at i:5091733 original size:25 final size:24
Alignment explanation
Indices: 5091696--5091784 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 24
5091686 CAGATTCAAT
* *
5091696 AAAAAATATAAAAAAAGAGAAAAA
1 AAAAAAAAGAAAAAAAGAGAAAAA
*
5091720 AATAAAAAAGAAAAAAGAAAGAAAAA
1 AA-AAAAAAGAAAAAA-AGAGAAAAA
5091746 GAAAAAAAAGAAAGAAGAAGAG-AAAA
1 -AAAAAAAAGAAA-AA-AAGAGAAAAA
*
5091772 TAAAAAAAGAAAA
1 AAAAAAAAGAAAA
5091785 GGAGAGGCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 3 0.05
25 22 0.40
26 22 0.40
27 7 0.13
28 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAGAGAAAAA
Found at i:5091734 original size:26 final size:25
Alignment explanation
Indices: 5091696--5091784 Score: 92
Period size: 26 Copynumber: 3.4 Consensus size: 25
5091686 CAGATTCAAT
*
5091696 AAAAAATATAAAAAAAGAGAAAAAAA
1 AAAAAAGA-AAAAAAAGAGAAAAAAA
5091722 TAAAAAAGAAAAAAGAA-AGAAAAAGAA
1 -AAAAAAGAAAAAA-AAGAGAAAAA-AA
* *
5091749 AAAAAAGAAAGAAGAAGAG-AAAATA
1 AAAAAAGAAA-AAAAAGAGAAAAAAA
5091774 AAAAAAGAAAA
1 AAAAAAGAAAA
5091785 GGAGAGGCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
24 1 0.02
25 11 0.20
26 28 0.51
27 15 0.27
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.04
Consensus pattern (25 bp):
AAAAAAGAAAAAAAAGAGAAAAAAA
Found at i:5091736 original size:7 final size:7
Alignment explanation
Indices: 5091716--5091784 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
5091706 AAAAAAGAGA
*
5091716 AAAAAAT
1 AAAAAAG
5091723 AAAAAAG
1 AAAAAAG
5091730 AAAAAAG
1 AAAAAAG
5091737 AAAGAAAAAG
1 --A-AAAAAG
5091747 AAAAAA-
1 AAAAAAG
*
5091753 AAGAAAG
1 AAAAAAG
*
5091760 AAGAAGAG
1 AA-AAAAG
*
5091768 AAAATA-
1 AAAAAAG
5091774 AAAAAAG
1 AAAAAAG
5091781 AAAA
1 AAAA
5091785 GGAGAGGCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
6 10 0.20
7 27 0.54
8 6 0.12
9 1 0.02
10 6 0.12
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:5091745 original size:19 final size:19
Alignment explanation
Indices: 5091705--5091771 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
5091695 TAAAAAATAT
*
5091705 AAAAAAAGAGAAAA-AAA-
1 AAAAAAAGAAAAAAGAAAG
*
5091722 TAAAAAAGAAAAAAGAAAG
1 AAAAAAAGAAAAAAGAAAG
5091741 AAAAAGAA-AAAAAAGAAAG
1 AAAAA-AAGAAAAAAGAAAG
* *
5091760 AAGAAGAGAAAA
1 AAAAAAAGAAAA
5091772 TAAAAAAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
17 12 0.29
18 4 0.10
19 23 0.56
20 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (19 bp):
AAAAAAAGAAAAAAGAAAG
Found at i:5091785 original size:26 final size:25
Alignment explanation
Indices: 5091708--5091785 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 25
5091698 AAAATATAAA
5091708 AAAAG-AGAAA-AAAAT-AAAAAAG
1 AAAAGAAGAAAGAAAATAAAAAAAG
*
5091730 AAAA-AAGAAAGAAAA-AGAAAAAAA
1 AAAAGAAGAAAGAAAATA-AAAAAAG
5091754 AGAAAGAAGAAGAGAAAATAAAAAAAG
1 A-AAAGAAGAA-AGAAAATAAAAAAAG
5091781 AAAAG
1 AAAAG
5091786 GAGAGGCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
22 9 0.20
23 4 0.09
24 7 0.15
25 3 0.07
26 9 0.20
27 13 0.28
28 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (25 bp):
AAAAGAAGAAAGAAAATAAAAAAAG
Found at i:5092759 original size:24 final size:24
Alignment explanation
Indices: 5092725--5092776 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5092715 ATGTCCCAAA
*
5092725 ATTACAGTGGACTT-AACCTTGAAG
1 ATTACAATGGA-TTGAACCTTGAAG
**
5092749 ATTACAATGGATTGAAGTTTGAAG
1 ATTACAATGGATTGAACCTTGAAG
5092773 ATTA
1 ATTA
5092777 TAGTGGGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (24 bp):
ATTACAATGGATTGAACCTTGAAG
Found at i:5093238 original size:90 final size:89
Alignment explanation
Indices: 5093051--5093607 Score: 258
Period size: 89 Copynumber: 6.4 Consensus size: 89
5093041 CAATGAAGTT
* * * *
5093051 GCAGATCTTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTATAC
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
* *
5093116 TGACAGCGGAGCAGATTGAAGATA
66 TGACAGCGAAGCAGATCGAAGATA
* * * * * * * * * *
5093140 ACATATCTTGTCTTCCTGTATTTGCAGCAAAGTAGATCAAAGATAGCAGATCTTGTCTTCCAATA
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAG-CCTTGCCTTCCAATA
* * *
5093205 TTGGCAGCGAAGTAGATCGAAGATA
65 CTGACAGCGAAGCAGATCGAAGATA
* ** * * * **
5093230 GCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGATACCATAG-TTTGCAGT--AA-
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACC--AGCCTTGCCTTCCAAT
* * * * *
5093291 AGT-AGA-CTAA--AGATAGCAGAT-
64 ACTGACAGCGAAGCAGATCGAAGATA
* * * ** * * * **
5093312 -CTTG-CCTT-CCTGTACTG-ACAACGAAGCAAA-C----CGAAGACACCAGCCTTACCTTCCTG
1 GC-AGATCTTGCCT-TCCTGTAC-TGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAA
* *
5093368 TACTGACAACGGAGCAGA-CTGAAGATA
63 TACTGACAGCGAAGCAGATC-GAAGATA
* * * * **
5093395 GCAGATCTTGCCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTAC
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
* *
5093460 TGACAGCGGAGCCGA-CTGAAGATA
66 TGACAGCGAAGCAGATC-GAAGATA
* * * ** * ***
5093484 GCAGATCATACCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCTTGTAC
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
* * * *
5093549 CGGCAGTGAAGCAGATCGAAGACA
66 TGACAGCGAAGCAGATCGAAGATA
* * * *
5093573 CCAG-CCTTGCCTTCTTGTACTGACAG-AATAGCAGA
1 GCAGATCTTGCCTTCCTGTACTGGCAGCAA-AGCAGA
5093608 CTGAAGATAG
Statistics
Matches: 347, Mismatches: 94, Indels: 55
0.70 0.19 0.11
Matches are distributed among these distances:
74 2 0.01
75 4 0.01
76 9 0.03
78 2 0.01
79 2 0.01
80 8 0.02
81 12 0.03
82 9 0.03
83 10 0.03
84 14 0.04
85 9 0.03
86 1 0.00
87 3 0.01
88 24 0.07
89 163 0.47
90 73 0.21
92 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (89 bp):
GCAGATCTTGCCTTCCTGTACTGGCAGCAAAGCAGATCAAAGACACCAGCCTTGCCTTCCAATAC
TGACAGCGAAGCAGATCGAAGATA
Found at i:5093267 original size:45 final size:45
Alignment explanation
Indices: 5093051--5093274 Score: 236
Period size: 45 Copynumber: 5.0 Consensus size: 45
5093041 CAATGAAGTT
* *
5093051 GCAGATCTTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGACA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
* * * *
5093096 CCAG-CCTTGCCTTCCTATACTGACAGCGGAGCAGATTGAAGATA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
* * * * * * * *
5093140 ACATATCTTGTCTTCCTGTATTTG-CAGCAAAGTAGATCAAAGATA
1 GCAGATCTTGCCTTCCTATA-CTGACAGCGAAGCAGATCGAAGATA
* * * * *
5093185 GCAGATCTTGTCTTCCAATATTGGCAGCGAAGTAGATCGAAGATA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
* *
5093230 GCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGATA
1 GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
5093275 CCATAGTTTG
Statistics
Matches: 146, Mismatches: 30, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
44 40 0.27
45 104 0.71
46 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (45 bp):
GCAGATCTTGCCTTCCTATACTGACAGCGAAGCAGATCGAAGATA
Found at i:5093392 original size:44 final size:44
Alignment explanation
Indices: 5093312--5093664 Score: 295
Period size: 44 Copynumber: 8.0 Consensus size: 44
5093302 GATAGCAGAT
* * *
5093312 CTTGCCTTCCTGTACTGACAACGAAGCAAACCGAAGACACCAGC
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGACACCAGC
* * * * * *
5093356 CTTACCTTCCTGTACTGACAACGGAGCAGACTGAAGATAGCAGAT
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGACACCAG-C
*
5093401 CTTGCCTTCCTGTACT-AGCAGCGAAGCAGA-TCGAAGACACTAGC
1 CTTGCCTTCCTGTACTGA-CAGCGAAGCAGACT-GAAGACACCAGC
* * * * *
5093445 CTTGCCTTCCTGTACTGACAGCGGAGCCGACTGAAGATAGCAGAT
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGACACCAG-C
* * * * *
5093490 CATACCTTCCTGTACCGGCAGTGAAGCAGA-TCGAAGACACCAGC
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGACT-GAAGACACCAGC
* * * *
5093534 CTTGCCTTCTTGTACCGGCAGTGAAGCAGA-TCGAAGACACCAGC
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGACT-GAAGACACCAGC
* * * * *
5093578 CTTGCCTTCTTGTACTGACAG-AATAGCAGACTGAAGATAGCAGAT
1 CTTGCCTTCCTGTACTGACAGCGA-AGCAGACTGAAGACACCAG-C
* * *
5093623 CTTGCATTCCTGTACTGACAGTGAAGTAGA-TCGAAGACACCA
1 CTTGCCTTCCTGTACTGACAGCGAAGCAGACT-GAAGACACCA
5093665 TAATTTGCAG
Statistics
Matches: 252, Mismatches: 45, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.00
44 150 0.60
45 100 0.40
46 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (44 bp):
CTTGCCTTCCTGTACTGACAGCGAAGCAGACTGAAGACACCAGC
Found at i:5093560 original size:133 final size:133
Alignment explanation
Indices: 5093401--5093664 Score: 384
Period size: 133 Copynumber: 2.0 Consensus size: 133
5093391 GATAGCAGAT
* *
5093401 CTTGCCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACTAGCCTTGCCTTCCTGTACTGACAG
1 CTTGCCTTCCTGTACCAGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAG
** * * *
5093466 CGGAGCCGACTGAAGATAGCAGATCATACCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACACC
66 AAGAGCAGACTGAAGATAGCAGATCATACATTCCTGTACCGACAGTGAAGCAGATCGAAGACACC
5093531 AGC
131 AGC
* * * *
5093534 CTTGCCTTCTTGTACCGGCAGTGAAGCAGATCGAAGACACCAGCCTTGCCTTCTTGTACTGACAG
1 CTTGCCTTCCTGTACCAGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAG
* * * * *
5093599 AATAGCAGACTGAAGATAGCAGATCTTGCATTCCTGTACTGACAGTGAAGTAGATCGAAGACACC
66 AAGAGCAGACTGAAGATAGCAGATCATACATTCCTGTACCGACAGTGAAGCAGATCGAAGACACC
5093664 A
131 A
5093665 TAATTTGCAG
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
133 115 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (133 bp):
CTTGCCTTCCTGTACCAGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGTACTGACAG
AAGAGCAGACTGAAGATAGCAGATCATACATTCCTGTACCGACAGTGAAGCAGATCGAAGACACC
AGC
Found at i:5093570 original size:89 final size:89
Alignment explanation
Indices: 5093294--5093643 Score: 375
Period size: 89 Copynumber: 3.9 Consensus size: 89
5093284 GCAGTAAAGT
* * * * *
5093294 AGACTAAAGATAGCAGATCTTGCCTTCCTGTACTGACAACGAAGCAAACCGAAGACACCAGCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTT
* *
5093359 ACCTTCCTGTACTGACAACGGAGC
66 GCCTTCCTGTACTGACAGCGGAGC
* *
5093383 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACTAGCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTT
5093448 GCCTTCCTGTACTGACAGCGGAGC
66 GCCTTCCTGTACTGACAGCGGAGC
* * * * *
5093472 CGACTGAAGATAGCAGATCATACCTTCCTGTACCGGCAGTGAAGCAGATCGAAGACACCAGCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTT
* * * * *
5093537 GCCTTCTTGTACCGGCAGTGAAGC
66 GCCTTCCTGTACTGACAGCGGAGC
* * * * * * * *
5093561 AGA-TCGAAGACACCAG-CCTTGCCTTCTTGTACTGACAG-AATAGCAGA-CTGAAGATAGCAGA
1 AGACT-GAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGA-AGCAGATC-GAAGACACCAG-
* *
5093622 TCTTGCATTCCTGTACTGACAG
62 CCTTGCCTTCCTGTACTGACAG
5093644 TGAAGTAGAT
Statistics
Matches: 219, Mismatches: 38, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
87 2 0.01
88 32 0.15
89 185 0.84
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (89 bp):
AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGCCTT
GCCTTCCTGTACTGACAGCGGAGC
Found at i:5093921 original size:44 final size:43
Alignment explanation
Indices: 5093864--5094243 Score: 175
Period size: 44 Copynumber: 8.7 Consensus size: 43
5093854 GATCGCATCC
* *
5093864 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACT
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGC-ACT
* * ** * *
5093908 AGTCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCAC-
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATT-GAAGCACT
* * * * *
5093951 ATATCTTATCTCTCTAAAGTTGCAGTAGAGCAGA-T-CA-CATCC
1 A-ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCA-CT
* * * *
5093993 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAAAT
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCACT
* * *
5094036 CAATCCTATCTTCCTAAAGTTGCAGTGAAGC-GAATTAAAATG-AC-
1 -AATCCTATCTCCCTAAAGTTGCAGTGGAGCAG-ATT-GAA-GCACT
* * * * * * *
5094080 AGATCTTATCTCTCTAAAGTTGCAGTAGAGCGGA-TCACACCATGAT
1 A-ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGA-AGCA--CT
* * * * **
5094126 AAGTCTTATCTCCCTAAGGTTACAGTGGAGCAGACTGGAGATAAC-
1 AA-TCCTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTGA-AGCACT
* * * * *
5094171 AAACCTTATCTCCCTGAAGTTGAAATGGAGCAAATTGAAGCTACT
1 AATCC-TATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGC-ACT
* * *
5094216 AATCCTATCTCCTTGAAGTTGCAATGGA
1 AATCCTATCTCCCTAAAGTTGCAGTGGA
5094244 ACGGATTAAA
Statistics
Matches: 252, Mismatches: 60, Indels: 48
0.70 0.17 0.13
Matches are distributed among these distances:
40 2 0.01
41 31 0.12
42 3 0.01
43 9 0.04
44 140 0.56
45 36 0.14
46 28 0.11
48 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCACT
Found at i:5093972 original size:129 final size:129
Alignment explanation
Indices: 5093820--5094192 Score: 437
Period size: 129 Copynumber: 2.8 Consensus size: 129
5093810 ATCGAAGATG
* * *
5093820 ACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCAATCTTATCTCCCTAAAGTTG
1 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTG
* ** * * * * *
5093885 CAGTGGAGTAGATTGAAGCTA-CTAGTCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACC
66 CAGTGGAGCAGATTGAAGAAATC-AATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACC
* *
5093949 ACATATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTG
1 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTG
* **
5094014 CAGTGGAGCAGATTGAAGAAATCAATCCTATCTTCCTAAAGTTGCAGTGAAGCGAATTAAAATG
66 CAGTGGAGCAGATTGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACC
*
5094078 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCGGATCACA-CCATGATAAGTCTTATCTCCCTA
1 ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCC-----AA-TCTTATCTCCCTA
* * * * * *
5094142 AGGTTACAGTGGAGCAGACTGGAGATAA-CAAACCTTATCTCCCTGAAGTTG
60 AAGTTGCAGTGGAGCAGATTGAAGA-AATCAATCC-TATCTCCCTAAAGTTG
5094193 AAATGGAGCA
Statistics
Matches: 209, Mismatches: 26, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
128 2 0.01
129 150 0.72
130 1 0.00
133 2 0.01
134 38 0.18
135 16 0.08
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (129 bp):
ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTG
CAGTGGAGCAGATTGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACC
Found at i:5094911 original size:11 final size:11
Alignment explanation
Indices: 5094895--5094919 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5094885 TTCGGTATAA
5094895 AAACCGATTGT
1 AAACCGATTGT
5094906 AAACCGATTGT
1 AAACCGATTGT
5094917 AAA
1 AAA
5094920 GGGGAAATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (11 bp):
AAACCGATTGT
Found at i:5095065 original size:26 final size:26
Alignment explanation
Indices: 5095003--5095055 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5094993 TAAATAAAAA
5095003 GTAGAAGTTTTTAAGGTGATTTTTTG
1 GTAGAAGTTTTTAAGGTGATTTTTTG
5095029 GTAGAAGTTTTTAAGGTGATTTTTTG
1 GTAGAAGTTTTTAAGGTGATTTTTTG
5095055 G
1 G
5095056 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (26 bp):
GTAGAAGTTTTTAAGGTGATTTTTTG
Found at i:5096016 original size:13 final size:13
Alignment explanation
Indices: 5095986--5096010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5095976 TCTTCATATT
5095986 TTTTAGATATGTA
1 TTTTAGATATGTA
5095999 TTTTAGATATGT
1 TTTTAGATATGT
5096011 TCTTTATATT
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
TTTTAGATATGTA
Found at i:5098958 original size:14 final size:14
Alignment explanation
Indices: 5098939--5098966 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5098929 CTGATAGCGA
5098939 CAGCAAGACTCCGG
1 CAGCAAGACTCCGG
5098953 CAGCAAGACTCCGG
1 CAGCAAGACTCCGG
5098967 TATTCAGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (14 bp):
CAGCAAGACTCCGG
Found at i:5100507 original size:20 final size:21
Alignment explanation
Indices: 5100469--5100510 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5100459 ATTTCATAAT
*
5100469 TTTTATATACCTACATATATA
1 TTTTATATACATACATATATA
*
5100490 TTTTA-ATACATACTTATATA
1 TTTTATATACATACATATATA
5100510 T
1 T
5100511 ATTGTACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATATACATACATATATA
Found at i:5101240 original size:73 final size:72
Alignment explanation
Indices: 5101130--5101271 Score: 216
Period size: 73 Copynumber: 2.0 Consensus size: 72
5101120 TCTTTTCAAA
* *
5101130 CTCAAGTTTTAAACGATCTCGGGAAGTAAGAAGAGATCGTGTCCTAACTTACT-GCGCATGATCC
1 CTCAAGTTTTAAACGATCTCGGAAAGTAAGAAGAGATCGTGTCCTAACTTACTAG-GAATGATCC
5101194 CTTTTTTC
65 CTTTTTTC
*
5101202 CTCAAGTTTTTAAACGATCTCGGAAATTAAGGAA-AGATCGTGTCCTAACTTACTAGGAATGATC
1 CTCAAG-TTTTAAACGATCTCGGAAAGTAA-GAAGAGATCGTGTCCTAACTTACTAGGAATGATC
5101266 CCTTTT
64 CCTTTT
5101272 CTAAACCCGA
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
72 6 0.09
73 54 0.84
74 4 0.06
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (72 bp):
CTCAAGTTTTAAACGATCTCGGAAAGTAAGAAGAGATCGTGTCCTAACTTACTAGGAATGATCCC
TTTTTTC
Done.