Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008591.1 Hibiscus syriacus cultivar Beakdansim tig00111540_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1730314
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:387503 original size:66 final size:66
Alignment explanation
Indices: 387433--387579 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
387423 ACAAAATCAT
*
387433 CTTTGAG-TCTATTTCTTCAAAAACAAATTTTGTCTCTCTTGAGACAG-TTTCTAATGAAAAATA
1 CTTTGAGAT-TATTTCTTCAAAAACAAATTTTGTCTCTCTTGAGA-AGATTTCTAATGAAAAACA
387496 AAC
64 AAC
* ** * * *
387499 CTTTGAGATTGTTTCTTTGAAAACAAATTTTGTCTCTCTTGAGATGATTTTTAATGAAAAACCAA
1 CTTTGAGATTATTTCTTCAAAAACAAATTTTGTCTCTCTTGAGAAGATTTCTAATGAAAAACAAA
387564 C
66 C
*
387565 CTTTGAGATTGTTTC
1 CTTTGAGATTATTTC
387580 ATTTGAAACA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 70 0.97
67 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (66 bp):
CTTTGAGATTATTTCTTCAAAAACAAATTTTGTCTCTCTTGAGAAGATTTCTAATGAAAAACAAA
C
Found at i:387589 original size:66 final size:66
Alignment explanation
Indices: 387452--387600 Score: 221
Period size: 66 Copynumber: 2.3 Consensus size: 66
387442 TATTTCTTCA
*
387452 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAATAAACCTTTGAGATTGTTTCTTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAACAAACCTTTGAGATTGTTTCTTT
387517 G
66 G
* * *
387518 AAAACAAATTTTGTCTCTCTTGAGA-TGATTTTTAATGAAAAACCAACCTTTGAGATTGTTTCAT
1 AAAACAAATTTTGTCTCTCTTGAGACAG-TTTCTAATGAAAAACAAACCTTTGAGATTGTTTC-T
387582 TTG
64 TTG
*
387585 -AAACAAATTTCGTCTC
1 AAAACAAATTTTGTCTC
387601 ACTTAAAACG
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
65 1 0.01
66 71 0.93
67 4 0.05
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (66 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAACAAACCTTTGAGATTGTTTCTTT
G
Found at i:387729 original size:36 final size:32
Alignment explanation
Indices: 387682--387814 Score: 97
Period size: 32 Copynumber: 3.8 Consensus size: 32
387672 TTGAGAAAAA
*
387682 ATCTTTAAGTTTGTTTCTTTGAAAACAAAATTTACC
1 ATCTTTGAGTTTGTTTCTTTG-AAACAAAA---ACC
* *
387718 ATCTTTGAGTTTGTTTCCCTTGAAACAAAACAAACAAA
1 ATCTTTGAGTTTGTTT-CTTTGAAAC--AA-AAAC--C
* *
387756 ATCTTTGAGTGTGTTTTTCTTGAAACAAAAA-C
1 ATCTTTGAGTTTGTTTCT-TTGAAACAAAAACC
*
387788 ATCTTTGAGTTTGTTTCTCTCGAAACA
1 ATCTTTGAGTTTGTTTCT-TTGAAACA
387815 CCGATCTTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
32 24 0.30
35 3 0.04
36 23 0.29
37 4 0.05
38 24 0.30
39 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (32 bp):
ATCTTTGAGTTTGTTTCTTTGAAACAAAAACC
Found at i:387926 original size:63 final size:65
Alignment explanation
Indices: 387818--387983 Score: 174
Period size: 63 Copynumber: 2.5 Consensus size: 65
387808 CGAAACACCG
* * * *
387818 ATCTTTGAGAACGTTTCCCTTAAACACAAATTTTGTTTCGCTTGAGACAGTTTCCTTT-AA-ACG
1 ATCTTTGAG-TCGTTTCCCTTGAA-ACAAATTTTGTCTCGCTTGAGACAGTTACCTTTAAACACG
387881 TC
64 TC
** *
387883 ATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCTTTTGAGACAGTTACTTTTGAAACACGT
1 ATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTACCTTT-AAACACGT
387948 C
65 C
* * **
387949 ACCTTTGAGTATGTTTTTCTTGAAACAAATCTTTG
1 ATCTTTGAGT-CGTTTCCCTTGAAACAAAT-TTTG
387984 AGTCTGTTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
63 28 0.33
64 12 0.14
65 11 0.13
66 14 0.16
67 16 0.19
68 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (65 bp):
ATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTACCTTTAAACACGTC
Found at i:387983 original size:28 final size:28
Alignment explanation
Indices: 387951--388013 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
387941 AACACGTCAC
387951 CTTTGAGTATGTTT-TTCTTGAAACAAAT
1 CTTTGAGTATGTTTCTT-TTGAAACAAAT
*
387979 CTTTGAGTCTGTTTCTTTTGAAACAAAT
1 CTTTGAGTATGTTTCTTTTGAAACAAAT
388007 CTTTGAG
1 CTTTGAG
388014 CCGGTTTCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (28 bp):
CTTTGAGTATGTTTCTTTTGAAACAAAT
Found at i:388020 original size:28 final size:28
Alignment explanation
Indices: 387967--388030 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
387957 GTATGTTTTT
* * *
387967 CTTGAAACAAATCTTTGAGTCTGTTTCT
1 CTTGAAACAAATCTTTGAGCCGGTTTCC
*
387995 TTTGAAACAAATCTTTGAGCCGGTTTCC
1 CTTGAAACAAATCTTTGAGCCGGTTTCC
388023 CTTGAAAC
1 CTTGAAAC
388031 CACAATCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (28 bp):
CTTGAAACAAATCTTTGAGCCGGTTTCC
Found at i:388279 original size:134 final size:134
Alignment explanation
Indices: 388059--388419 Score: 445
Period size: 134 Copynumber: 2.7 Consensus size: 134
388049 CCAGTCGTCC
* * * * * *
388059 TCATCACGTAGGAGCAGTGTCATCCCCTGACTAGATCTCTTCATCGCGTAGGAGTCATCTTACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACTAGATCTCTTCATCACGTAGGAGCCATGTCACCC
* * * * * *
388124 CTAGATAACCAGACGTCCTCATCATGTAGGAACCGTGTTATCGCCCTTTCTAAA-AAAGACCAGA
66 ATAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAGAAAG-CCAGA
388188 ACTCT
130 ACTCT
* * *
388193 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCTTCATCATGTAGGAGCCATGTCACCT
1 TCATCACGTATGAGCCGTGTCATCCCCTGACTAGATCTCTTCATCACGTAGGAGCCATGTCACCC
* ** * *
388258 ATAGATAATCAGTTGTCCTCATCGCGTAGGAACCGAGTTATCACCATTCCTAAAGATAGCCAGAA
66 ATAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAGAAAGCCAGAA
388323 CTCT
131 CTCT
* * * *
388327 TCATCACGTATGAGCCGTGTCATCCCCTGACTAGATTTCCTCATCACGTAGGAACCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACTAGATCTCTTCATCACGTAGGAGCCATGTCACCC
* ** * *
388392 TTAGACGACCAGACCTCTTCATCACGTA
66 ATAGATAACCAGACGTCCTCATCACGTA
388420 TGAGCAGTGT
Statistics
Matches: 190, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
134 187 0.98
135 3 0.02
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (134 bp):
TCATCACGTATGAGCCGTGTCATCCCCTGACTAGATCTCTTCATCACGTAGGAGCCATGTCACCC
ATAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCACCATTCCTAAAGAAAGCCAGAA
CTCT
Found at i:388430 original size:43 final size:40
Alignment explanation
Indices: 388317--388436 Score: 116
Period size: 43 Copynumber: 2.9 Consensus size: 40
388307 CTAAAGATAG
388317 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGA
* ** * * * *
388357 CTAGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGA
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCT----GA
* *
388400 CCAGACCTCTTCATCACGTATGAGCAGTGTCATCCCC
1 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC
388437 AACAACCAAC
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
39 4 0.07
40 26 0.43
43 27 0.45
44 3 0.05
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.25
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGA
Found at i:391112 original size:21 final size:22
Alignment explanation
Indices: 391087--391127 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
391077 ATAAAGAGTC
391087 ATATGAGAA-CAAATATAAGTA
1 ATATGAGAATCAAATATAAGTA
* *
391108 ATATGATAATGAAATATAAG
1 ATATGAGAATCAAATATAAG
391128 GCTATGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.02, G:0.15, T:0.27
Consensus pattern (22 bp):
ATATGAGAATCAAATATAAGTA
Found at i:392246 original size:149 final size:149
Alignment explanation
Indices: 391977--392428 Score: 762
Period size: 149 Copynumber: 3.0 Consensus size: 149
391967 GAGTCGAGGG
* * * * * * *
391977 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTT-TGAGGCACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATTTGTGAAGTCTTGTAAGACACAT
* * *
392041 ACTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
392106 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
392125 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGAAACATTTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATTTGTGAAGTCTTGTAAGACACAT
392190 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
392255 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
392274 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATTTGTGAAGTCTTGTAAGACACAT
*
392339 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGGATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
* *
392404 TATGACACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
392423 TCTACG
1 TCTACG
392429 TGCACTTCGG
Statistics
Matches: 287, Mismatches: 16, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
148 48 0.17
149 239 0.83
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATTTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:392664 original size:21 final size:21
Alignment explanation
Indices: 392640--392700 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
392630 ATAAATAATT
*
392640 TGATGATAATGATAGA-GATAA
1 TGATAATAAT-ATAGATGATAA
*
392661 TGATAATAATATATATGATAA
1 TGATAATAATATAGATGATAA
* * *
392682 TGCTAAGAAAATAGATGAT
1 TGATAATAATATAGATGAT
392701 GATATATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (21 bp):
TGATAATAATATAGATGATAA
Found at i:392706 original size:33 final size:33
Alignment explanation
Indices: 392642--392707 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
392632 AAATAATTTG
*
392642 ATGATAATGATAGAGATAATGATAATAATATAT
1 ATGATAATGATAGAGAAAATGATAATAATATAT
* * *
392675 ATGATAATGCTA-AGAAAATAGATGATGATATAT
1 ATGATAATGATAGAGAAAAT-GATAATAATATAT
392708 GTACATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGATAATGATAGAGAAAATGATAATAATATAT
Found at i:397464 original size:149 final size:149
Alignment explanation
Indices: 397195--397646 Score: 780
Period size: 149 Copynumber: 3.0 Consensus size: 149
397185 GAGTCGAGGG
* * * * * * * *
397195 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTT-TGAGGCACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
* * *
397259 ACTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
397324 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
397343 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGAAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
397408 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
397473 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
397492 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
397557 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
397622 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
397641 TCTACG
1 TCTACG
397647 TGCACTTCGG
Statistics
Matches: 289, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
148 47 0.16
149 242 0.84
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:403257 original size:13 final size:13
Alignment explanation
Indices: 403241--403282 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
403231 TACGTTAGAA
*
403241 AAATTATAGATTT
1 AAATTATAGATCT
403254 AAATTATAGATCT
1 AAATTATAGATCT
403267 AAATTATAGATCT
1 AAATTATAGATCT
403280 AAA
1 AAA
403283 GTGTTGTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (13 bp):
AAATTATAGATCT
Found at i:418601 original size:21 final size:21
Alignment explanation
Indices: 418559--418607 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
418549 GATGATGGTC
* *
418559 CAGTTTTTTAAGAAGATGATT
1 CAGTTTTGTAAGAAGATAATT
418580 CAGTTTTGTAAGATAGA-AATT
1 CAGTTTTGTAAGA-AGATAATT
418601 CATGTTT
1 CA-GTTT
418608 ATGCATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (21 bp):
CAGTTTTGTAAGAAGATAATT
Found at i:427836 original size:3 final size:3
Alignment explanation
Indices: 427828--427915 Score: 95
Period size: 3 Copynumber: 28.3 Consensus size: 3
427818 ATTTTTAAAA
* * * **
427828 ATT ATT ATT ATT ATT ATT AAAT ATT AGT ATT ATT ATT ATT ATA AAA
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
427874 ATT ATT ATT ATT ATT AAT ATT ATAT ATT ATAT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT A
427916 AAAAAAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
3 64 0.89
4 8 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:430835 original size:3 final size:3
Alignment explanation
Indices: 430827--430854 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
430817 AAATCTCTCT
430827 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
430855 CCTGGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:436857 original size:23 final size:23
Alignment explanation
Indices: 436819--436907 Score: 88
Period size: 23 Copynumber: 3.9 Consensus size: 23
436809 GAGTCGAGGG
*
436819 TTCTACGCGGTTATTCGGGACAA
1 TTCTACGCGGTCATTCGGGACAA
* *
436842 TTCTACGTGGTCATTCGGGACAT
1 TTCTACGCGGTCATTCGGGACAA
* * *
436865 TTTTACGCGGTCCTTTGGGACAA
1 TTCTACGCGGTCATTCGGGACAA
* ***
436888 TACTATATGGTCATTCGGGA
1 TTCTACGCGGTCATTCGGGA
436908 TATTTCTATG
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCATTCGGGACAA
Found at i:436928 original size:46 final size:46
Alignment explanation
Indices: 436819--436915 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
436809 GAGTCGAGGG
** * * *
436819 TTCTACGCGGTTATTCGGGACAATTCTACGTGGTCATTCGGGACAT
1 TTCTACGCGGTCCTTTGGGACAATACTACATGGTCATTCGGGACAT
* * *
436865 TTTTACGCGGTCCTTTGGGACAATACTATATGGTCATTCGGGATAT
1 TTCTACGCGGTCCTTTGGGACAATACTACATGGTCATTCGGGACAT
436911 TTCTA
1 TTCTA
436916 TGTGGCACTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (46 bp):
TTCTACGCGGTCCTTTGGGACAATACTACATGGTCATTCGGGACAT
Found at i:436936 original size:24 final size:24
Alignment explanation
Indices: 436919--436965 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
436909 ATTTCTATGT
*
436919 GGCACTTTGGTGCAATTTATACGC
1 GGCACTTTGATGCAATTTATACGC
436943 GGCACTTTGATGCAATTTATACG
1 GGCACTTTGATGCAATTTATACG
436966 AGCTGTGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (24 bp):
GGCACTTTGATGCAATTTATACGC
Found at i:437547 original size:17 final size:19
Alignment explanation
Indices: 437507--437547 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
437497 CCTTATCATA
**
437507 CAAATATATGTTTAAATTT
1 CAAATATATGTTTAAAAGT
437526 CAAATATAT-TTTAAAAGT
1 CAAATATATGTTTAAAAGT
437544 -AAAT
1 CAAAT
437548 GTTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
CAAATATATGTTTAAAAGT
Found at i:438966 original size:65 final size:64
Alignment explanation
Indices: 438855--439055 Score: 194
Period size: 65 Copynumber: 3.1 Consensus size: 64
438845 GTAAGTATAC
* * * * * * *
438855 CGATGCATAAATCAATGTATCGATGCACTCT-TGTTTTAATT-GAACATCGAATGGCTTTTGTGT
1 CGATGCAT-AAGCTATGCATCGATGCACTCTATGTATT-ATTAAAACATCGAATGG-TTTTATGC
438918 AT
63 AT
*
438920 CGATGCATATA-CTATGCATCGATGCACTCTATGTATTATTAAAACATCGAATTGATTTTATGCA
1 CGATGCATA-AGCTATGCATCGATGCACTCTATGTATTATTAAAACATCGAA-TGGTTTTATGCA
*
438984 C
64 T
* * * **
438985 CGATGCACAAGCTATGCATCGATGCACCCCAACTATT-TTAAAACATCGAATGTGTTTTATGCAT
1 CGATGCATAAGCTATGCATCGATGCACTCTATGTATTATTAAAACATCGAATG-GTTTTATGCAT
439049 CGATGCA
1 CGATGCA
439056 CCCTCAATGT
Statistics
Matches: 115, Mismatches: 15, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
63 2 0.02
64 51 0.44
65 60 0.52
66 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (64 bp):
CGATGCATAAGCTATGCATCGATGCACTCTATGTATTATTAAAACATCGAATGGTTTTATGCAT
Found at i:439047 original size:64 final size:66
Alignment explanation
Indices: 438897--439056 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 66
438887 GTTTTAATTG
* * * * * * **
438897 AACATCGAATG-GCTTTTGTGTATCGATGCATATACTATGCATCGATGCACTCTATGTATTATTA
1 AACATCGAATGTGATTTTATGCATCGATGCACATACTATGCATCGATGCACCCCAACTATTATTA
438961 A
66 A
*
438962 AACATCGAAT-TGATTTTATGCACCGATGCACA-AGCTATGCATCGATGCACCCCAACTATT-TT
1 AACATCGAATGTGATTTTATGCATCGATGCACATA-CTATGCATCGATGCACCCCAACTATTATT
439024 AA
65 AA
439026 AACATCGAATGTG-TTTTATGCATCGATGCAC
1 AACATCGAATGTGATTTTATGCATCGATGCAC
439057 CCTCAATGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
64 32 0.39
65 50 0.61
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (66 bp):
AACATCGAATGTGATTTTATGCATCGATGCACATACTATGCATCGATGCACCCCAACTATTATTA
A
Found at i:439074 original size:64 final size:65
Alignment explanation
Indices: 438953--439075 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 65
438943 GCACTCTATG
* * *
438953 TATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAGCTATGCATCGATGCACCCCAAC
1 TATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAGCAATGCACCAATGCACCCCAAC
* *** *
439018 TATT-TTAAAACATCGAATGTG-TTTTATGCATCGATGCACCCTCAATGTACCAATGCAC
1 TATTATTAAAACATCGAAT-TGATTTTATGCACCGATGCACAAGCAATGCACCAATGCAC
439076 TAAGTCTTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
64 43 0.88
65 6 0.12
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (65 bp):
TATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAGCAATGCACCAATGCACCCCAAC
Found at i:444294 original size:21 final size:22
Alignment explanation
Indices: 444270--444324 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
444260 TTATGCATAA
444270 TGCATCGATAT-ACTATGAAGG
1 TGCATCGATATCACTATGAAGG
* *
444291 TGCATCGATGCATCCCTATGAATG
1 TGCATCGAT--ATCACTATGAAGG
444315 TGCATCGATA
1 TGCATCGATA
444325 CATCATGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 9 0.31
22 1 0.03
23 2 0.07
24 17 0.59
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (22 bp):
TGCATCGATATCACTATGAAGG
Found at i:444317 original size:24 final size:24
Alignment explanation
Indices: 444282--444328 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
444272 CATCGATATA
*
444282 CTATGAAGGTGCATCGATGCATCC
1 CTATGAAGGTGCATCGATACATCC
*
444306 CTATGAATGTGCATCGATACATC
1 CTATGAAGGTGCATCGATACATC
444329 ATGATGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (24 bp):
CTATGAAGGTGCATCGATACATCC
Found at i:446606 original size:16 final size:16
Alignment explanation
Indices: 446585--446634 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
446575 ATTTAACAAA
446585 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
446601 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
446617 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
446633 AA
1 AA
446635 AGTAAGGGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.18
Consensus pattern (16 bp):
AAGGGGGAGAAGTGTT
Found at i:447082 original size:65 final size:63
Alignment explanation
Indices: 446983--447170 Score: 213
Period size: 65 Copynumber: 2.9 Consensus size: 63
446973 GCTTGAATCA
* * * * *
446983 ATGCATCGATGCACCCTTGTTTTAATT-AAACATCGAATGGCTTTTGTGTACCGATGCATATA-C
1 ATGCATCGATGCACCC-TGTATT-ATTAAAACATCGAATGGATTTTATGCACCGATGCACA-AGC
447046 T
63 T
*
447047 ATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAGCT
1 ATGCATCGATGCAC-CC-TGTATTATTAAAACATCGAATGGATTTTATGCACCGATGCACAAGCT
*
447112 ATGCATCGATGCACCCTGACTATT-TTAAAACATCGAATGTG-TTTTATGCATCGATGCAC
1 ATGCATCGATGCACCCTG--TATTATTAAAACATCGAATG-GATTTTATGCACCGATGCAC
447171 TCTCAATGTA
Statistics
Matches: 109, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
63 2 0.02
64 51 0.47
65 56 0.51
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACCCTGTATTATTAAAACATCGAATGGATTTTATGCACCGATGCACAAGCT
Found at i:447186 original size:64 final size:65
Alignment explanation
Indices: 446981--447189 Score: 164
Period size: 64 Copynumber: 3.2 Consensus size: 65
446971 ATGCTTGAAT
* * * * * * *
446981 CAATGCATCGATGCACCCTTG--TTTTAATT-AAACATCGAATGGCTTTTGTGTACCGATGCATA
1 CAATGCACCGATGCACCC-TGACTATT-ATTAAAACATCGAATTGATTTTATGCACCGATGCACA
447043 TA-
64 -AG
* *
447045 CTATGCATCGATGCACTCCATG--TATTATTAAAACATCGAATTGATTTTATGCACCGATGCACA
1 CAATGCACCGATGCAC-CC-TGACTATTATTAAAACATCGAATTGATTTTATGCACCGATGCACA
447108 AG
64 AG
* * * **
447110 CTATGCATCGATGCACCCTGACTATT-TTAAAACATCGAATGTG-TTTTATGCATCGATGCACTC
1 CAATGCACCGATGCACCCTGACTATTATTAAAACATCGAAT-TGATTTTATGCACCGATGCACAA
*
447173 T
65 G
*
447174 CAATGTACCGATGCAC
1 CAATGCACCGATGCAC
447190 TAAGTCTTCC
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
63 2 0.02
64 65 0.52
65 57 0.46
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (65 bp):
CAATGCACCGATGCACCCTGACTATTATTAAAACATCGAATTGATTTTATGCACCGATGCACAAG
Found at i:448002 original size:35 final size:35
Alignment explanation
Indices: 447963--448042 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
447953 AACACATTCA
447963 TCAATTACATTCTAAACC-CTAAAATCCAAAATACT
1 TCAATTACATTCTAAACCTC-AAAATCCAAAATACT
** *
447998 TCAATTGTATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTCAAAATCCAAAATACT
*
448033 TTAATTACAT
1 TCAATTACAT
448043 ACCAACCCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 37 0.97
36 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAAATCCAAAATACT
Found at i:448422 original size:149 final size:151
Alignment explanation
Indices: 448217--448515 Score: 478
Period size: 154 Copynumber: 2.0 Consensus size: 151
448207 AAATACTCAA
*
448217 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAATC
1 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTATATAAAATTTAAATCAAATC
* * * *
448282 AAACTGAATTGAA-T-TTTT-GAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAA
66 AAACTGAATTGAATTATTTTCAAATTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAA
448344 TATTATTTGATTCTAATTCAG
131 TATTATTTGATTCTAATTCAG
*
448365 TTCAGTTTATAAAATAGTTGACTCGAAACTTTTTTCGATTTGAGTATATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAGTTGACTCGAAA-TTTTTTCGATTTGAGTATATAAAATTTAAATCAAAT
* *
448430 CGAATTGAATTGAATTAAATTTTCAAATTTCTGTTTAAATTTAATTATAAATATTTATAATACTA
65 CAAACTGAATTGAATT--ATTTTCAAATTTCTGTTTAAATTTAATTATAAATATTTATAATACTA
448495 TAATATTATTTGATTCTAATT
128 TAATATTATTTGATTCTAATT
448516 TATATAGTTT
Statistics
Matches: 137, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
148 28 0.20
149 46 0.34
150 1 0.01
153 4 0.03
154 58 0.42
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.46
Consensus pattern (151 bp):
TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTATATAAAATTTAAATCAAATC
AAACTGAATTGAATTATTTTCAAATTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAA
TATTATTTGATTCTAATTCAG
Found at i:448948 original size:21 final size:22
Alignment explanation
Indices: 448924--448964 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
448914 AAATTTAGCA
*
448924 TTTAGGGTTA-TGTTTTAAGGG
1 TTTAGGGTTATTGCTTTAAGGG
448945 TTTAGGGTTATTGCTTTAAG
1 TTTAGGGTTATTGCTTTAAG
448965 TTCAGTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (22 bp):
TTTAGGGTTATTGCTTTAAGGG
Found at i:449096 original size:35 final size:35
Alignment explanation
Indices: 449021--449096 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
449011 GTTGGGCATA
*
449021 TAATTAAAATATTTTGGAATTTGAGGTTTAGAATG
1 TAATTGAAATATTTTGGAATTTGAGGTTTAGAATG
*
449056 TAATTGAAGTATTTTGGAATTTG-GGATTTAGAATG
1 TAATTGAAATATTTTGGAATTTGAGG-TTTAGAATG
449091 TAATTG
1 TAATTG
449097 TTGACTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.05
35 36 0.95
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.43
Consensus pattern (35 bp):
TAATTGAAATATTTTGGAATTTGAGGTTTAGAATG
Found at i:449218 original size:15 final size:15
Alignment explanation
Indices: 449195--449226 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
449185 ACAGTGAAAC
*
449195 GACCGTTACGTTGGG
1 GACCATTACGTTGGG
449210 GACCATTACGTTGGG
1 GACCATTACGTTGGG
449225 GA
1 GA
449227 ACATATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.25
Consensus pattern (15 bp):
GACCATTACGTTGGG
Found at i:449620 original size:40 final size:40
Alignment explanation
Indices: 449576--449653 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
449566 ACTCGTTTGA
*
449576 TGGATATATCGGCGTCTTCAACACAATTTACATGCAAAAT
1 TGGATATATAGGCGTCTTCAACACAATTTACATGCAAAAT
* * * * *
449616 TGGATCTCTAGGCGTCTTTAACACAATTTGCATTCAAA
1 TGGATATATAGGCGTCTTCAACACAATTTACATGCAAA
449654 CATGGAGGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (40 bp):
TGGATATATAGGCGTCTTCAACACAATTTACATGCAAAAT
Found at i:453274 original size:14 final size:14
Alignment explanation
Indices: 453254--453323 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 14
453244 AATTTAGTAA
453254 AATTTAATAATAAT
1 AATTTAATAATAAT
* * *
453268 GATTTAATCATTATT
1 AATTTAAT-AATAAT
*
453283 AAATTTTAACTACTAAT
1 -AA-TTTAA-TAATAAT
*
453300 GATTTAATAATAAT
1 AATTTAATAATAAT
453314 AATTTAATAA
1 AATTTAATAA
453324 GTTGATACAA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
14 22 0.51
15 9 0.21
16 2 0.05
17 9 0.21
18 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (14 bp):
AATTTAATAATAAT
Found at i:453837 original size:2 final size:2
Alignment explanation
Indices: 453825--453853 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
453815 TTCTCTAACC
453825 AT AT A- 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
453854 TTCTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454864 original size:16 final size:15
Alignment explanation
Indices: 454828--454875 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
454818 TAAAAAAAAT
454828 TAAATTTTATAAT-A
1 TAAATTTTATAATAA
454842 TATAATTTTATTAATAA
1 TA-AATTTTA-TAATAA
454859 TAAATTTTA-AATAA
1 TAAATTTTATAATAA
454873 TAA
1 TAA
454876 TGAGCTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 10 0.32
15 7 0.23
16 11 0.35
17 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATTTTATAATAA
Found at i:454875 original size:17 final size:16
Alignment explanation
Indices: 454814--454876 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
454804 CATTTTAAAT
* *
454814 ATTTTAAAAAAAATTAA
1 ATTTTAATAATAA-TAA
454831 ATTTT-ATAAT-ATATA
1 ATTTTAATAATAATA-A
*
454846 ATTTTATTAATAATAA
1 ATTTTAATAATAATAA
454862 ATTTTAAATAATAAT
1 ATTTT-AATAATAAT
454877 GAGCTAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.05
15 7 0.18
16 13 0.34
17 16 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTTAATAATAATAA
Found at i:455984 original size:28 final size:28
Alignment explanation
Indices: 455952--456009 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
455942 GATGTCGACA
* *
455952 ATGAACCTTAAATTGAATATGGCTCAGG
1 ATGAACCTTAAATTAAATAAGGCTCAGG
455980 ATGAACCTTAAATTAAATAAGGCTCAGG
1 ATGAACCTTAAATTAAATAAGGCTCAGG
456008 AT
1 AT
456010 TTAGCTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (28 bp):
ATGAACCTTAAATTAAATAAGGCTCAGG
Found at i:460988 original size:21 final size:21
Alignment explanation
Indices: 460964--461004 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
460954 ATCAATACAT
460964 TTAAAAAAAATAAAAACTAAA
1 TTAAAAAAAATAAAAACTAAA
* * *
460985 TTAATATAAGTAAAAACTAA
1 TTAAAAAAAATAAAAACTAA
461005 TTTTATTAAT
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:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TTAAAAAAAATAAAAACTAAA
Found at i:465778 original size:28 final size:28
Alignment explanation
Indices: 465746--465800 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
465736 CTATGCTTGT
*
465746 ATATCTATGCTACTGATAGGATGATATC
1 ATATCTATGCTACCGATAGGATGATATC
* *
465774 ATATCTCTGCTGCCGATAGGATGATAT
1 ATATCTATGCTACCGATAGGATGATAT
465801 TTCAAGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (28 bp):
ATATCTATGCTACCGATAGGATGATATC
Found at i:471771 original size:23 final size:23
Alignment explanation
Indices: 471741--471808 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
471731 GAGTCGAGGG
*
471741 TTCTACGCGGTCTTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
*
471764 TTCTACGCTGTCCTTCGGGACA-
1 TTCTACGCGGTCCTTCGGGACAT
* * *
471786 -TCTATGTGGTCCTTTGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
471808 T
1 T
471809 CTATGTGGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 17 0.46
23 20 0.54
ACGTcount: A:0.13, C:0.25, G:0.25, T:0.37
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:471797 original size:21 final size:22
Alignment explanation
Indices: 471749--471816 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 22
471739 GGTTCTACGC
* *
471749 GGTCTTTCGGGACATTTCTACGCT
1 GGTCCTTCGGGACA-TTCTATG-T
471773 -GTCCTTCGGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTATGT
*
471793 GGTCCTTTGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
471815 GG
1 GG
471817 AACTTCAGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.03
21 17 0.44
22 9 0.23
23 12 0.31
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:472072 original size:15 final size:15
Alignment explanation
Indices: 472048--472086 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
472038 TATAGGGACA
* *
472048 ATGATAATAATATTG
1 ATGATGATAATACTG
*
472063 ATGATGATAATGCTG
1 ATGATGATAATACTG
472078 ATGATGATA
1 ATGATGATA
472087 TATGTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.36
Consensus pattern (15 bp):
ATGATGATAATACTG
Found at i:473829 original size:33 final size:33
Alignment explanation
Indices: 473787--473858 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
473777 CATAATATGA
*
473787 AGCAATCAACTAATAG-CTCATCCAAAAATCTCG
1 AGCAATCAACCAA-AGACTCATCCAAAAATCTCG
* * *
473820 AGCAATCAACCAACGACTCATCGAAAAATCTTG
1 AGCAATCAACCAAAGACTCATCCAAAAATCTCG
473853 AGCAAT
1 AGCAAT
473859 AAACAAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.19
Consensus pattern (33 bp):
AGCAATCAACCAAAGACTCATCCAAAAATCTCG
Found at i:475318 original size:15 final size:17
Alignment explanation
Indices: 475295--475328 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
475285 TTAATATATG
475295 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
475311 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
475327 TT
1 TT
475329 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:481046 original size:23 final size:22
Alignment explanation
Indices: 481020--481062 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
481010 ACATGTGACT
*
481020 TACATAGTAAATATTCTATTTCA
1 TACATAGTAAAGATTC-ATTTCA
481043 TACATAGTAAAGATTCATTT
1 TACATAGTAAAGATTCATTT
481063 TTTAGGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (22 bp):
TACATAGTAAAGATTCATTTCA
Found at i:489344 original size:24 final size:23
Alignment explanation
Indices: 489306--489351 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
489296 CCCTAATTAA
* *
489306 ATAAATAATATAAAAATTAAAAT
1 ATAAATAATAAAAAAAATAAAAT
489329 ATAAATTAATAAAAAAAATAAAA
1 ATAAA-TAATAAAAAAAATAAAA
489352 ATATTCACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAAATAATAAAAAAAATAAAAT
Found at i:501004 original size:9 final size:9
Alignment explanation
Indices: 500990--501024 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
500980 GAAATCGGTT
500990 AATTAACCG
1 AATTAACCG
*
500999 AATTAATCG
1 AATTAACCG
501008 AATTAACCG
1 AATTAACCG
501017 AATTAACC
1 AATTAACC
501025 CTTAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:502915 original size:20 final size:20
Alignment explanation
Indices: 502892--502951 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
502882 TGTATTGTAT
502892 TGTATGAATAGTACTGATAC
1 TGTATGAATAGTACTGATAC
*
502912 TGTATGAATAGTACTAATA-
1 TGTATGAATAGTACTGATAC
* *
502931 TGTGTGAACAGTACTGATAC
1 TGTATGAATAGTACTGATAC
502951 T
1 T
502952 CAAAAACTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (20 bp):
TGTATGAATAGTACTGATAC
Found at i:505141 original size:23 final size:24
Alignment explanation
Indices: 505090--505164 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
505080 GTCATACTAA
* **
505090 TAAATTAAAATAAATTATATATTT
1 TAAATGAAAATAAAAAATATATTT
505114 TAAATGAAAATAAAAAATAT-TTT
1 TAAATGAAAATAAAAAATATATTT
*
505137 TAAATTAAGTTAATAATAAAATATATTT
1 TAAATGAA---AATAA-AAAATATATTT
505165 AATAAGTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
23 10 0.24
24 17 0.40
26 5 0.12
27 7 0.17
28 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAATGAAAATAAAAAATATATTT
Found at i:505182 original size:25 final size:26
Alignment explanation
Indices: 505126--505213 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 26
505116 AATGAAAATA
* *
505126 AAAAATATTTTTAAATTAAGTTAATA-
1 AAAAATATATTT-AATTAAGTTGATAT
505152 ATAAAATATATTTAA-TAAGTTGATAT
1 A-AAAATATATTTAATTAAGTTGATAT
* *
505178 AAAAATGT-TTTAAGTTAA-TAGATAT
1 AAAAATATATTTAA-TTAAGTTGATAT
*
505203 AAAATTATATT
1 AAAAATATATT
505214 ATATATAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 5 0.10
25 27 0.53
26 9 0.18
27 10 0.20
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (26 bp):
AAAAATATATTTAATTAAGTTGATAT
Found at i:505343 original size:23 final size:22
Alignment explanation
Indices: 505317--505397 Score: 57
Period size: 23 Copynumber: 3.8 Consensus size: 22
505307 AAATATTAAA
505317 AAATAATTTAGAATGTTAATGTG
1 AAATAATTTAGAA-GTTAATGTG
* *
505340 AAATATTTTA-AA--AAAT-T-
1 AAATAATTTAGAAGTTAATGTG
*
505357 -AAGAATTTAGAACGTTAATGTG
1 AAATAATTTAGAA-GTTAATGTG
*
505379 AAATAATTTAAGAAATTAA
1 AAATAATTT-AGAAGTTAA
505398 GAATTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
16 7 0.16
17 2 0.05
18 1 0.02
19 3 0.07
20 3 0.07
21 1 0.02
22 2 0.05
23 20 0.47
24 4 0.09
ACGTcount: A:0.51, C:0.01, G:0.12, T:0.36
Consensus pattern (22 bp):
AAATAATTTAGAAGTTAATGTG
Found at i:505368 original size:39 final size:39
Alignment explanation
Indices: 505321--505462 Score: 166
Period size: 39 Copynumber: 3.7 Consensus size: 39
505311 ATTAAAAAAT
*
505321 AATTTAGAATGTTAATGTGAAATATTTTAAAAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAAAAATTAAG
* *
505360 AATTTAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAAAAATTAAG
* * *
505399 AATTTAGAATGTT-ATGTTGTCAA-AATTTAAGAAATT-GG
1 AATTTAGAATGTTAATG-TG-AAATAATTTAAAAAATTAAG
*
505437 ATTTTAGAATGTTAGA-GTGAAATAAT
1 AATTTAGAATGTTA-ATGTGAAATAAT
505463 GAGGATTATG
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
37 2 0.02
38 21 0.23
39 64 0.71
40 3 0.03
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAAAAATTAAG
Found at i:505496 original size:18 final size:20
Alignment explanation
Indices: 505473--505510 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
505463 GAGGATTATG
505473 AATAAAAT-T-TAATATAAA
1 AATAAAATGTATAATATAAA
505491 AATAAAATGTATAATATAAA
1 AATAAAATGTATAATATAAA
505511 TCGGGTACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AATAAAATGTATAATATAAA
Found at i:507657 original size:32 final size:32
Alignment explanation
Indices: 507616--507680 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
507606 CAAGTTCAAC
507616 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
1 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
507648 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
1 GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
507680 G
1 G
507681 TCAGAGGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.48, T:0.09
Consensus pattern (32 bp):
GGGGAAGGGGTCGTGCTGAAAGCAGCAAGAAG
Found at i:511396 original size:13 final size:15
Alignment explanation
Indices: 511368--511399 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
511358 AATCACAGAA
511368 GAAATAAGATAGGGG
1 GAAATAAGATAGGGG
511383 GAAATAA-A-AGGGG
1 GAAATAAGATAGGGG
511396 GAAA
1 GAAA
511400 AGGGTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.38, T:0.09
Consensus pattern (15 bp):
GAAATAAGATAGGGG
Found at i:513991 original size:10 final size:10
Alignment explanation
Indices: 513976--514007 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
513966 ATTGTCTTAT
513976 TATATAACAA
1 TATATAACAA
513986 TATATAACAA
1 TATATAACAA
513996 TATATAACAA
1 TATATAACAA
514006 TA
1 TA
514008 ATTATTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (10 bp):
TATATAACAA
Found at i:514094 original size:14 final size:14
Alignment explanation
Indices: 514072--514103 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
514062 AGAGAGCATT
514072 GTTAATTTTTAAAA
1 GTTAATTTTTAAAA
*
514086 GTTATTTTTTAAAA
1 GTTAATTTTTAAAA
514100 GTTA
1 GTTA
514104 GGATTTAAAC
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:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
GTTAATTTTTAAAA
Found at i:516471 original size:20 final size:21
Alignment explanation
Indices: 516428--516471 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
516418 TAATAAAAAA
* *
516428 TTATCTAAAATATTATTATTT
1 TTATCTAAAACATTAATATTT
516449 TTATCTAAAACATTAAT-TTT
1 TTATCTAAAACATTAATATTT
516469 TTA
1 TTA
516472 ATATTTTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATCTAAAACATTAATATTT
Found at i:519238 original size:159 final size:161
Alignment explanation
Indices: 518948--519267 Score: 610
Period size: 159 Copynumber: 2.0 Consensus size: 161
518938 TTCTATGGTT
518948 TTCTCGATCATAGGGAAACCATCATTGCAACTATAAGCATTTGGATCTGACACCCTCACCTGCAT
1 TTCTCGATCATAGGGAAACCATCATTGCAACTATAAGCATTTGGATCTGACACCCTCACCTGCAT
519013 AAATCACAATCAATCTTATTAAAAGGCCAGAAACAATCACTTATCAATAACACAGATTTCTTTGC
66 AAATCACAATCAATCTTATTAAAAGGCCAGAAACAATCACTTATCAATAACACAGATTTCTTTGC
519078 TTTTGCAACTCACTTCTTC-TGAACTGGTGC
131 TTTTGCAACTCACTTCTTCATGAACTGGTGC
519108 TTCTCGATCATAGGGAAACCATCATTGCAACTATAAGCATTTGGATCTGACA-CCTCACCTGCAT
1 TTCTCGATCATAGGGAAACCATCATTGCAACTATAAGCATTTGGATCTGACACCCTCACCTGCAT
519172 AAATCACAATC-ATCTTATTAAAAGGCCAGAAACACATCACTTATCAATAACACAGATTTCTTTG
66 AAATCACAATCAATCTTATTAAAAGGCCAGAAACA-ATCACTTATCAATAACACAGATTTCTTTG
519236 CTTTTGCAACTCACTTCTTCATGAACTGGTGC
130 CTTTTGCAACTCACTTCTTCATGAACTGGTGC
519268 CAAACAAGAA
Statistics
Matches: 158, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
158 23 0.15
159 72 0.46
160 63 0.40
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (161 bp):
TTCTCGATCATAGGGAAACCATCATTGCAACTATAAGCATTTGGATCTGACACCCTCACCTGCAT
AAATCACAATCAATCTTATTAAAAGGCCAGAAACAATCACTTATCAATAACACAGATTTCTTTGC
TTTTGCAACTCACTTCTTCATGAACTGGTGC
Found at i:520576 original size:14 final size:14
Alignment explanation
Indices: 520557--520585 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
520547 ATGGTATTTT
520557 TTAATGTCGTCAAA
1 TTAATGTCGTCAAA
520571 TTAATGTCGTCAAA
1 TTAATGTCGTCAAA
520585 T
1 T
520586 ATCAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (14 bp):
TTAATGTCGTCAAA
Found at i:525500 original size:27 final size:28
Alignment explanation
Indices: 525438--525510 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 28
525428 GTTAAACTAA
525438 TTAAAA-TC-TTGCTCGACTCATGCTCG
1 TTAAAACTCGTTGCTCGACTCATGCTCG
* *
525464 TTAAAAAAACTTGTTGCTCTACTCATGCTCG
1 TT---AAAACTCGTTGCTCGACTCATGCTCG
525495 TT-AAACTCGTTGCTCG
1 TTAAAACTCGTTGCTCG
525511 TTTAGCCCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 2 0.05
27 12 0.32
29 4 0.11
30 1 0.03
31 19 0.50
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (28 bp):
TTAAAACTCGTTGCTCGACTCATGCTCG
Found at i:525510 original size:16 final size:16
Alignment explanation
Indices: 525489--525530 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
525479 GCTCTACTCA
*
525489 TGCTCGTTAAACTCGT
1 TGCTCGTTAAACCCGT
* *
525505 TGCTCGTTTAGCCCGT
1 TGCTCGTTAAACCCGT
525521 TGCTCGTTAA
1 TGCTCGTTAA
525531 TCTCATTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.38
Consensus pattern (16 bp):
TGCTCGTTAAACCCGT
Found at i:525956 original size:13 final size:13
Alignment explanation
Indices: 525938--525963 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
525928 ACTTTAAATA
525938 ATTACCCTTAATT
1 ATTACCCTTAATT
525951 ATTACCCTTAATT
1 ATTACCCTTAATT
525964 TTAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTACCCTTAATT
Found at i:527631 original size:82 final size:81
Alignment explanation
Indices: 527494--527657 Score: 310
Period size: 82 Copynumber: 2.0 Consensus size: 81
527484 GCTGATCCGC
527494 ACCATCCAACTCTATGAGTAACTGAAAACGTGACCAATTCTTTCATGCCATTATTTGCAATTGGT
1 ACCATCCAACTCTATGAGTAACTGAAAACGTGACCAATTCTTTCATGCCATTATTTGCAATTGGT
*
527559 TATTTTTTTTATATGGA
66 TA-ATTTTTTATATGGA
527576 ACCATCCAACTCTATGAGTAACTGAAAACGTGACCAATTCTTTCATGCCATTATTTGCAATTGGT
1 ACCATCCAACTCTATGAGTAACTGAAAACGTGACCAATTCTTTCATGCCATTATTTGCAATTGGT
527641 TAATTTTTTATATGGA
66 TAATTTTTTATATGGA
527657 A
1 A
527658 AGATGGTAAG
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 14 0.17
82 67 0.83
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (81 bp):
ACCATCCAACTCTATGAGTAACTGAAAACGTGACCAATTCTTTCATGCCATTATTTGCAATTGGT
TAATTTTTTATATGGA
Found at i:528084 original size:31 final size:31
Alignment explanation
Indices: 528049--528120 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
528039 TGTTTCGTAG
528049 AACCAGTTAACATCATCTTTACCAAAGAGAA
1 AACCAGTTAACATCATCTTTACCAAAGAGAA
528080 AACCAGTTAACATCATCTTTACCAAAGAGAA
1 AACCAGTTAACATCATCTTTACCAAAGAGAA
528111 AACCAGTTAA
1 AACCAGTTAA
528121 ATACATGCCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (31 bp):
AACCAGTTAACATCATCTTTACCAAAGAGAA
Found at i:533315 original size:151 final size:145
Alignment explanation
Indices: 533028--533323 Score: 506
Period size: 151 Copynumber: 2.0 Consensus size: 145
533018 GGTTTGGGGC
533028 CAACTGGTTGTTTGTAACTGGGCCGATCCAGTTTCCATTGGGCCTGTAATTTTTTTTTAATATAA
1 CAACTGGTTGTTTGTAACTGGGCCGATCCAGTTTCCATTGGGCCTGTAATTTTTTTTTAATATAA
533093 TAATAATAAATAATATTATTATTATATTATTATTAATTTATAATTTATAATAATAAATAAATAAG
66 TAATAATAAATAATATTATTATTATATTATTATTAATTTATAATTTATAATAATAAATAAATAAG
533158 TAAAATGGGTAAAAA
131 TAAAATGGGTAAAAA
533173 CAACTGGTTGTTTGTAACTGGGCCGATCCCAGTTTCCATTGGGCCTGTAATTTATTTTTTAATAA
1 CAACTGGTTGTTTGTAACTGGGCCGAT-CCAGTTTCCATTGGGCCTGTAATTT-TTTTTTAAT-A
533238 TAAT-ATAATATAATAATAATTATTATTATTATTATTA-TAATTATAATAATTTATAATAATAAA
63 TAATAATAATA-AATAAT-ATTATTATTA-TATTATTATTAATT-T-ATAATTTATAATAATAAA
533301 TAAATAAGTAAAATGGGTAAAAA
123 TAAATAAGTAAAATGGGTAAAAA
533324 ATTAGTATTT
Statistics
Matches: 143, Mismatches: 0, Indels: 10
0.93 0.00 0.07
Matches are distributed among these distances:
145 27 0.19
146 25 0.17
147 15 0.10
148 11 0.08
149 15 0.10
150 9 0.06
151 41 0.29
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (145 bp):
CAACTGGTTGTTTGTAACTGGGCCGATCCAGTTTCCATTGGGCCTGTAATTTTTTTTTAATATAA
TAATAATAAATAATATTATTATTATATTATTATTAATTTATAATTTATAATAATAAATAAATAAG
TAAAATGGGTAAAAA
Found at i:533758 original size:113 final size:112
Alignment explanation
Indices: 533572--533821 Score: 439
Period size: 113 Copynumber: 2.2 Consensus size: 112
533562 ATAGAATCAT
* *
533572 GCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATTAGTTCTTCTC
1 GCAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
533637 ATTTTGAACTCGAACTGGAACTGCTGTTCCACCGAGTGATGAATTTAA
65 ATTATGAACTCGAACTGGAACTGCTGTTCCACCGAGTGATGAATTTAA
*
533685 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTC
1 GC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
533750 ATTATGAACTCGAACTGGAACTGCTGTTCCACCGAGTGATGAATTTAA
65 ATTATGAACTCGAACTGGAACTGCTGTTCCACCGAGTGATGAATTTAA
533798 GCAAAAGTTGAACAAGTTC-TCTCA
1 GCAAAAGTTGAACAAGTTCTTCTCA
533822 GTGATGAATT
Statistics
Matches: 132, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
111 5 0.04
112 17 0.13
113 105 0.80
114 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (112 bp):
GCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAACTGCTGTTCCACCGAGTGATGAATTTAA
Found at i:533825 original size:37 final size:39
Alignment explanation
Indices: 533784--533860 Score: 140
Period size: 38 Copynumber: 2.0 Consensus size: 39
533774 TGTTCCACCG
533784 AGTGATGAATTTAAGC-AAAAGTTGAACAAGTTC-TCTC
1 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTC
533821 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTC
1 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTC
533860 A
1 A
533861 TTATGAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 16 0.42
38 17 0.45
39 5 0.13
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (39 bp):
AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTC
Found at i:533874 original size:17 final size:17
Alignment explanation
Indices: 533852--533903 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
533842 GTTGAACAAG
533852 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
533869 TTCTTCTTCCA-GATG-AG
1 TTCTTC-T-CATTATGAAC
533886 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
533903 T
1 T
533904 CTAACTGGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
15 2 0.07
16 4 0.15
17 15 0.56
18 4 0.15
19 2 0.07
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.46
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:533941 original size:144 final size:149
Alignment explanation
Indices: 533671--533967 Score: 498
Period size: 144 Copynumber: 2.0 Consensus size: 149
533661 TGTTCCACCG
533671 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTA
1 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TC--TA
*
533736 GATGAGTTCTTCTCATTATGAACTCGAACTGGAACTGCTGTTCCACCGAGTGATGAATTTAAGC-
63 GATGAGTTCTTCTCATTATGAACTCGAACTGGAACTGCTGATCCACCGAGTGATGAATTTAAGCA
533800 AAAAGTTGAACAAGTTC-TCTC
128 AAAAGTTGAACAAGTTCTTCTC
533821 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-C-C-AGAT
1 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTAGAT
*
533883 GAGTTCTTCTCATTATGAACTCTAACTGGCAA-TGCTGATCCACCGAGTGATGAATTTAAGCAAA
66 GAGTTCTTCTCATTATGAACTCGAACTGG-AACTGCTGATCCACCGAGTGATGAATTTAAGCAAA
533947 AAGTTGAACAAGTTCTTCTC
130 AAGTTGAACAAGTTCTTCTC
533967 A
1 A
533968 TTATGAACTT
Statistics
Matches: 142, Mismatches: 2, Indels: 10
0.92 0.01 0.06
Matches are distributed among these distances:
144 60 0.42
145 19 0.13
146 5 0.04
147 1 0.01
149 1 0.01
150 56 0.39
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (149 bp):
AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTAGAT
GAGTTCTTCTCATTATGAACTCGAACTGGAACTGCTGATCCACCGAGTGATGAATTTAAGCAAAA
AGTTGAACAAGTTCTTCTC
Found at i:533947 original size:107 final size:110
Alignment explanation
Indices: 533821--534037 Score: 368
Period size: 107 Copynumber: 2.0 Consensus size: 110
533811 AAGTTCTCTC
533821 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA-CTTCTT-CTTC-CAGAT
1 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCCTTCTCAGAT
533883 GAGTTCTTCTCATTATGAACTCTAACTGGCAATGCTGATCCACCG
66 GAGTTCTTCTCATTATGAACTCTAACTGGCAATGCTGATCCACCG
533928 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA--TCTTCTTCCTTC-TCA
* *
533993 GATGAGTTCTTCTCATTATGAACTCTAACTGGCACTGTTGATCCA
63 GATGAGTTCTTCTCATTATGAACTCTAACTGGCAATGCTGATCCA
534038 TTGAATGATG
Statistics
Matches: 102, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
107 47 0.46
110 6 0.06
111 4 0.04
113 45 0.44
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.35
Consensus pattern (110 bp):
AGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCCTTCTCAGAT
GAGTTCTTCTCATTATGAACTCTAACTGGCAATGCTGATCCACCG
Found at i:534940 original size:114 final size:114
Alignment explanation
Indices: 534740--535191 Score: 742
Period size: 114 Copynumber: 4.0 Consensus size: 114
534730 GATCATGCAG
* * * * * * * * * *
534740 TTCATCTTTTAATTCCAATAATTGGTTCTGTGGTTCCTACCGAACCAGATCAAATGACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* * *
534805 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTATACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCAAA
*
534854 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
534919 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTATTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCAAA
534968 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
535033 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTATTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCAAA
*
535082 TTCATCTTTCAAATCTAATGATTGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
535147 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAG
535192 AACGTAGCAC
Statistics
Matches: 319, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 319 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCGTATTTCTACTATGAGCAAA
Found at i:535904 original size:13 final size:13
Alignment explanation
Indices: 535884--535959 Score: 68
Period size: 13 Copynumber: 5.8 Consensus size: 13
535874 TGACCCCCTC
535884 TTTTTTCTTCT-T
1 TTTTTTCTTCTCT
535896 TTCTTTTCTTCTCT
1 TT-TTTTCTTCTCT
*
535910 TTTTTTCTTTTCAT
1 TTTTTTCTTCTC-T
*
535924 TTTTTTATT-T-T
1 TTTTTTCTTCTCT
*
535935 TTTTATTTTTCTTCT
1 TTTT-TTCTTC-TCT
535950 TTTTTTCTTC
1 TTTTTTCTTC
535960 AAGCATAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
11 5 0.09
12 6 0.11
13 19 0.36
14 18 0.34
15 5 0.09
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTCTTCTCT
Found at i:535917 original size:23 final size:23
Alignment explanation
Indices: 535884--535943 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
535874 TGACCCCCTC
*
535884 TTTTTTCTTCTTTTC-TTTTCTTC
1 TTTTTT-TTCTTTTCATTTTCTTA
*
535907 TCTTTTTTTCTTTTCATTTTTTTA
1 T-TTTTTTTCTTTTCATTTTCTTA
*
535931 TTTTTTTTATTTT
1 TTTTTTTTCTTTT
535944 TCTTCTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTTTTCTTTTCATTTTCTTA
Found at i:535938 original size:18 final size:18
Alignment explanation
Indices: 535885--535955 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
535875 GACCCCCTCT
*
535885 TTTTTCTTCTTTTCTTTT-
1 TTTTTCTTATTTT-TTTTA
* * *
535903 CTTCTCTTTTTTTCTTTTCA
1 TTTTTCTTATTTT-TTTT-A
535923 TTTTT-TTATTTTTTTTA
1 TTTTTCTTATTTTTTTTA
*
535940 TTTTTCTTCTTTTTTT
1 TTTTTCTTATTTTTTT
535956 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 6 0.14
18 28 0.65
19 6 0.14
20 3 0.07
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTATTTTTTTTA
Found at i:535952 original size:23 final size:23
Alignment explanation
Indices: 535884--535952 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 23
535874 TGACCCCCTC
*
535884 TTTTTTCTTCTTTTC-TT-TTCTTC
1 TTTTTT-TTCTTTTCATTCTT-TTA
*
535907 TCTTTTTTTCTTTTCATTTTTTTA
1 T-TTTTTTTCTTTTCATTCTTTTA
*
535931 TTTTTTTTATTTTTC-TTCTTTT
1 TTTTTTTT-CTTTTCATTCTTTT
535953 TTTCTTCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 22 0.56
24 15 0.38
25 2 0.05
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTTTTCTTTTCATTCTTTTA
Found at i:546609 original size:15 final size:16
Alignment explanation
Indices: 546584--546613 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
546574 ATAAAATGAA
546584 ATAATAATATAAAAAT
1 ATAATAATATAAAAAT
546600 ATAA-AATATAAAAA
1 ATAATAATATAAAAA
546614 ATTTGAAAAC
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAATAATATAAAAAT
Found at i:548844 original size:3 final size:3
Alignment explanation
Indices: 548836--548892 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
548826 ATTTATTTTT
* *
548836 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
548881 TTA TAA TAA TAA
1 TAA TAA TAA TAA
548893 ATAAATAAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:548860 original size:21 final size:21
Alignment explanation
Indices: 548836--548900 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
548826 ATTTATTTTT
548836 TAATAATAATAATAATATATA
1 TAATAATAATAATAATATATA
548857 TAATAATAATAATAAT-TATTA
1 TAATAATAATAATAATATA-TA
* *
548878 TAATTATAATAATAA-ATAAA
1 TAATAATAATAATAATATATA
548898 TAA
1 TAA
548901 GTAAAATGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.15
21 34 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAATAATAATAATATATA
Found at i:549371 original size:26 final size:26
Alignment explanation
Indices: 549334--549386 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
549324 GCCATCTTGA
549334 ATTATTAGATATCCCTGTCGCTGTTG
1 ATTATTAGATATCCCTGTCGCTGTTG
*
549360 ATTATTATATATCCCTGTCGCTGTTG
1 ATTATTAGATATCCCTGTCGCTGTTG
549386 A
1 A
549387 GTGTCCGTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (26 bp):
ATTATTAGATATCCCTGTCGCTGTTG
Found at i:549833 original size:30 final size:30
Alignment explanation
Indices: 549798--549863 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
549788 AACCGGTAAA
549798 GAACCGACTGAAAACCGAG-AAAACCGGGGT
1 GAACCGACTGAAAACCG-GCAAAACCGGGGT
* **
549828 GAACCGGCTGAAAACCGGCAAAACCGGTTT
1 GAACCGACTGAAAACCGGCAAAACCGGGGT
549858 GAACCG
1 GAACCG
549864 CTGGTTCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.36, C:0.26, G:0.29, T:0.09
Consensus pattern (30 bp):
GAACCGACTGAAAACCGGCAAAACCGGGGT
Found at i:550111 original size:24 final size:24
Alignment explanation
Indices: 550078--550133 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
550068 TAGAAGTTTG
*
550078 ATTGAGGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
550102 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
550126 ATTGAAGC
1 ATTGAAGC
550134 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:557408 original size:2 final size:2
Alignment explanation
Indices: 557401--557429 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
557391 GGAAGGAAAC
557401 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
557430 GAAAACACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:561515 original size:14 final size:14
Alignment explanation
Indices: 561496--561523 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
561486 TATGCATCAC
561496 ATAGAAGCCAACAA
1 ATAGAAGCCAACAA
561510 ATAGAAGCCAACAA
1 ATAGAAGCCAACAA
561524 CATCAAATCC
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:0.57, C:0.21, G:0.14, T:0.07
Consensus pattern (14 bp):
ATAGAAGCCAACAA
Found at i:570988 original size:20 final size:20
Alignment explanation
Indices: 570965--571004 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
570955 TTATGCTTAT
570965 GAAAA-GAGAATATAAAAAAA
1 GAAAAGGAGAATA-AAAAAAA
*
570985 GAAAAGGAGGATAAAAAAAA
1 GAAAAGGAGAATAAAAAAAA
571005 TGAGTGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
GAAAAGGAGAATAAAAAAAA
Found at i:571004 original size:21 final size:20
Alignment explanation
Indices: 570965--571004 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
570955 TTATGCTTAT
*
570965 GAAAAGAGAATATAAAAAAA
1 GAAAAGAGAATAAAAAAAAA
*
570985 GAAAAGGAGGATAAAAAAAA
1 GAAAA-GAGAATAAAAAAAA
571005 TGAGTGAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
GAAAAGAGAATAAAAAAAAA
Found at i:575315 original size:24 final size:24
Alignment explanation
Indices: 575271--575316 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
575261 GAAGAAACAC
**
575271 CATCTTTATCAGCCTTGAACTCTA
1 CATCTTTATCAGCCTCAAACTCTA
*
575295 CATCTTTATCATCCTCAAACTC
1 CATCTTTATCAGCCTCAAACTC
575317 CTTTATCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (24 bp):
CATCTTTATCAGCCTCAAACTCTA
Found at i:577776 original size:30 final size:31
Alignment explanation
Indices: 577711--577793 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
577701 ACCAAAATGT
* *
577711 AACTTTGAAAATTTTACATTTTTAGTCCCTA
1 AACTTTTAAAATTTTACATTTTGAGTCCCTA
* *
577742 AACTTTTAAAACTTTACATTTTGA-TCCTTA
1 AACTTTTAAAATTTTACATTTTGAGTCCCTA
577772 AACTTTT-AAATTTTACATTTTG
1 AACTTTTAAAATTTTACATTTTG
577794 GTCACTAGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 14 0.30
30 12 0.26
31 21 0.45
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (31 bp):
AACTTTTAAAATTTTACATTTTGAGTCCCTA
Found at i:579519 original size:10 final size:10
Alignment explanation
Indices: 579504--579568 Score: 57
Period size: 10 Copynumber: 6.6 Consensus size: 10
579494 CGCCTAAGAA
579504 AGAAAAAAAG
1 AGAAAAAAAG
579514 AGAAAAAAA-
1 AGAAAAAAAG
579523 A-AAAAAAAG
1 AGAAAAAAAG
579532 A-AAGAAAAAG
1 AGAA-AAAAAG
* *
579542 AAAAAGAAAAA
1 AGAAA-AAAAG
579553 AGAAAAGAAA-
1 AGAAAA-AAAG
579563 AGAAAA
1 AGAAAA
579569 TGAGAGGTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
8 7 0.15
9 4 0.08
10 24 0.50
11 13 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:579529 original size:18 final size:18
Alignment explanation
Indices: 579506--579573 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
579496 CCTAAGAAAG
579506 AAAAAAAGAGAAAAAAAA
1 AAAAAAAGAGAAAAAAAA
579524 AAAAAAAGAAAGAAAAAGAAA
1 AAAAAAAG--AGAAAAA-AAA
*
579545 AAGAAAAA-AGAAAAGAAA
1 AA-AAAAAGAGAAAAAAAA
* *
579563 AGAAAATGAGA
1 AAAAAAAGAGA
579574 GGTTCAAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
17 4 0.10
18 15 0.36
19 6 0.14
20 7 0.17
21 5 0.12
22 5 0.12
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (18 bp):
AAAAAAAGAGAAAAAAAA
Found at i:579568 original size:16 final size:16
Alignment explanation
Indices: 579502--579568 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
579492 TACGCCTAAG
*
579502 AAAG-AAAAAAAGAGA
1 AAAGAAAAAAAAAAGA
*
579517 AAAAAAAAAAAAAAG-
1 AAAGAAAAAAAAAAGA
579532 AAAGAAAAAGAAAAAGA
1 AAAGAAAAA-AAAAAGA
579549 AAA-AAGAAAAGAAAAGA
1 AAAGAA-AAAA-AAAAGA
579566 AAA
1 AAA
579569 TGAGAGGTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
15 11 0.25
16 18 0.41
17 15 0.34
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAAAGA
Found at i:580832 original size:134 final size:135
Alignment explanation
Indices: 580585--581290 Score: 801
Period size: 134 Copynumber: 5.3 Consensus size: 135
580575 AGATAAACCA
* * *
580585 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAGATGGAGAA-AACGTTC
1 ATTAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAA-GTTC
* * *
580649 GTAATGAGAAGAACTTGTCCAACATTTGCTCGATTCACGATATTT-GAATCAGCAAAACCTTATT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGATATTTCGAATCAGCAAAACCTTACT
*
580713 TAAGGG
130 TGAGGG
* * * *
580719 ATT-ACAATTTCTAATGAAGAGTTCATAATGAGAAGAACTCATTCGATAGAGGGAGAAGAATTTT
1 ATTAAC-ATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * * * * *
580783 TTAATGATAATAA-TTGTTCAACCTTTGCTCGATTCACGACATTTCGAATCAGC-GAACCTCACT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGATATTTCGAATCAGCAAAACCTTACT
*
580846 TGAGTG
130 TGAGGG
* * * *
580852 ATTAATATTTCCAAT-AGATAGTTCATAATGAGAAGAATTTATCCGATAGAGGGAGAAGAAGTTC
1 ATTAACATTTCCAATGA-AGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * * * * * *
580916 GTAATAAAAAGAATTTGTTCAACCTTTGCTCGATTCACGGTATTTTGAATCAGCGAAACC-TATT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGATATTTCGAATCAGCAAAACCTTACT
580980 TGAGGG
130 TGAGGG
* * *
580986 ATTAAAATTTCCAAT-AGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGTAGTTC
1 ATTAACATTTCCAATGA-AGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * *
581050 GTAATGAGAAGAACTTGTTCAACCTTTGTTCGATTCAC-ATCATTTTGAATCAGCGAAACCTTAC
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGAT-ATTTCGAATCAGCAAAACCTTAC
581114 TTGAGGG
129 TTGAGGG
* * * * *
581121 ATTAACACTTCCAATGGAA-AGAT-ATAATGAGAAGAACTCATCCGAT-GAGGAAGAAAAAGTTT
1 ATTAACATTTCCAAT-GAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * ** *
581183 GTAATGAGAATAACTTGTTCAACCTTTGCTCGATTCACG-TATTTCAAATCAGCAATGCCTCACT
65 GTAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGATATTTCGAATCAGCAAAACCTTACT
* *
581247 CGAAGG
130 TGAGGG
* * *
581253 ATTAACATTTTCAGTAGAA-AGTTCATGATGAGAAGAAC
1 ATTAACATTTCCAAT-GAAGAGTTCATAATGAGAAGAAC
581291 CGTAGCTTGA
Statistics
Matches: 488, Mismatches: 71, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
132 41 0.08
133 165 0.34
134 249 0.51
135 31 0.06
136 1 0.00
137 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (135 bp):
ATTAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGATATTTCGAATCAGCAAAACCTTACTT
GAGGG
Found at i:581203 original size:267 final size:267
Alignment explanation
Indices: 580585--581237 Score: 861
Period size: 267 Copynumber: 2.4 Consensus size: 267
580575 AGATAAACCA
* * *
580585 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATTCGATAGATGGAGAAAACGTTCG
1 ATTAACATTTCCAATGGAAAGTTCATAATGAGAAGAACTCATCCGATAGA-GGAGAAAAAGTTCG
* * *
580650 TAATGAGAAGAACTTGTCCAACATTTGCTCGATTCACGATA-TTTGAATCAGCAAAACCTTATTT
65 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGGTATTTTGAATCAGCAAAACCTTATTT
* * * *
580714 AAGGGATTACAATTTCTAATGAAGAGTTCATAATGAGAAGAACTCATTCGATAGAGGGAGAAGAA
130 AAGGGATTAAAATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGAA
* ** * *
580779 TTTTTTAATGATAATAATTGTTCAACCTTTGCTCGATTCACGACATTTCGAATCAGCGAACCTCA
195 GTTCGTAATGAGAAGAATTGTTCAACCTTTGCTCGATTCACGACATTTCGAATCAGCGAACCTCA
*
580844 CTTGAGTG
260 CTTGAGGG
* * * * * *
580852 ATTAATATTTCCAATAGATAGTTCATAATGAGAAGAATTTATCCGATAGAGGGAGAAGAAGTTCG
1 ATTAACATTTCCAATGGAAAGTTCATAATGAGAAGAACTCATCCGATAGA-GGAGAAAAAGTTCG
* * * *
580917 TAATAAAAAGAATTTGTTCAACCTTTGCTCGATTCACGGTATTTTGAATCAGCGAAACC-TATTT
65 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGGTATTTTGAATCAGCAAAACCTTATTT
* *
580981 GAGGGATTAAAATTTCCAAT-AGAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGT
130 AAGGGATTAAAATTTCCAATGA-AGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGA
* *
581045 AGTTCGTAATGAGAAGAACTTGTTCAACCTTTGTTCGATTCAC-ATCATTTTGAATCAGCGAAAC
194 AGTTCGTAATGAGAAGAA-TTGTTCAACCTTTGCTCGATTCACGA-CATTTCGAATCAGCG-AAC
*
581109 CTTACTTGAGGG
256 CTCACTTGAGGG
* * *
581121 ATTAACACTTCCAATGGAAAGAT-ATAATGAGAAGAACTCATCCGAT-GAGGAAGAAAAAGTTTG
1 ATTAACATTTCCAATGGAAAGTTCATAATGAGAAGAACTCATCCGATAGAGG-AGAAAAAGTTCG
* **
581184 TAATGAGAATAACTTGTTCAACCTTTGCTCGATTCAC-GTATTTCAAATCAGCAA
65 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGGTATTTTGAATCAGCAA
581238 TGCCTCACTC
Statistics
Matches: 333, Mismatches: 47, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
266 17 0.05
267 211 0.63
268 74 0.22
269 31 0.09
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (267 bp):
ATTAACATTTCCAATGGAAAGTTCATAATGAGAAGAACTCATCCGATAGAGGAGAAAAAGTTCGT
AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGGTATTTTGAATCAGCAAAACCTTATTTA
AGGGATTAAAATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCGATAGAGGGAGAAGAAG
TTCGTAATGAGAAGAATTGTTCAACCTTTGCTCGATTCACGACATTTCGAATCAGCGAACCTCAC
TTGAGGG
Found at i:581468 original size:25 final size:24
Alignment explanation
Indices: 581436--581487 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
581426 GCCCAACCCA
* *
581436 AAACAACCTCAACCT-AACCTAACC
1 AAACAACCCCAAACTAAACC-AACC
581460 AAACTAACCCCAAACTAAACCAACC
1 AAAC-AACCCCAAACTAAACCAACC
581485 AAA
1 AAA
581488 TACCCAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.52, C:0.38, G:0.00, T:0.10
Consensus pattern (24 bp):
AAACAACCCCAAACTAAACCAACC
Found at i:582947 original size:19 final size:20
Alignment explanation
Indices: 582918--582962 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
582908 GATATTTATG
*
582918 TTTATTTTG-TTT-TATTTT
1 TTTATTATGTTTTCTATTTT
582936 TTCTATTATGTTTTCTATTTT
1 TT-TATTATGTTTTCTATTTT
582957 TTTATT
1 TTTATT
582963 TAATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 6 0.26
20 7 0.30
21 8 0.35
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTATTATGTTTTCTATTTT
Found at i:586198 original size:12 final size:12
Alignment explanation
Indices: 586181--586231 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
586171 TTCAAAGAGG
586181 TTTTATATTTAA
1 TTTTATATTTAA
586193 TTTTATA-TTATA
1 TTTTATATTTA-A
*
586205 TTTGAT-TTTAA
1 TTTTATATTTAA
586216 TTTTA-ATATTAA
1 TTTTATAT-TTAA
586228 TTTT
1 TTTT
586232 TTAAATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:586247 original size:24 final size:27
Alignment explanation
Indices: 586214--586345 Score: 92
Period size: 29 Copynumber: 4.7 Consensus size: 27
586204 ATTTGATTTT
*
586214 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
586239 AATTA-AATATT-ATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
* * *
586264 TATTATAGATATTAATTTTAATATTATTTTTA
1 AATTATA-ATATTAA-TTT--T-TTAATATTA
*
586296 AATAAATTAAATATTAATTTTTTAATATTA
1 AAT-TA-T-AATATTAATTTTTTAATATTA
*
586326 TATTATAGATATTTAATTTT
1 AATTATA-ATA-TTAATTTT
586346 ATATCATATA
Statistics
Matches: 83, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
23 9 0.11
24 7 0.08
25 10 0.12
26 1 0.01
27 6 0.07
28 5 0.06
29 12 0.14
30 9 0.11
31 2 0.02
32 9 0.11
33 4 0.05
34 8 0.10
35 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:586260 original size:13 final size:13
Alignment explanation
Indices: 586192--586329 Score: 82
Period size: 12 Copynumber: 11.2 Consensus size: 13
586182 TTTATATTTA
586192 ATTTT-ATATTAT
1 ATTTTAATATTAT
* *
586204 A-TTTGATTTTA-
1 ATTTTAATATTAT
586215 ATTTTAATATTAAT
1 ATTTTAATATT-AT
*
586229 TTTTTAA-A-TA-
1 ATTTTAATATTAT
* *
586239 AATTAAATATTAT
1 ATTTTAATATTAT
*
586252 TTTTTAATATTAT
1 ATTTTAATATTAT
*
586265 ATTATAGATATTA-
1 ATTTTA-ATATTAT
586278 ATTTTAATATTAT
1 ATTTTAATATTAT
586291 -TTTTAA-A-TA-
1 ATTTTAATATTAT
* *
586300 AATTAAATATTAAT
1 ATTTTAATATT-AT
*
586314 TTTTTAATATTAT
1 ATTTTAATATTAT
586327 ATT
1 ATT
586330 ATAGATATTT
Statistics
Matches: 93, Mismatches: 19, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
10 10 0.11
11 8 0.09
12 29 0.31
13 26 0.28
14 20 0.22
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
ATTTTAATATTAT
Found at i:586275 original size:27 final size:25
Alignment explanation
Indices: 586220--586299 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
586210 TTTTAATTTT
*
586220 AATATTAATTTTTTAA-A-TAAATTA
1 AATATT-ATTTTTTAATATTATATTA
586244 AATATTATTTTTTAATATTATATTA
1 AATATTATTTTTTAATATTATATTA
* *
586269 TAGATATTA-ATTTTAATATTATTTTTA
1 -A-ATATTATTTTTTAATATTA-TATTA
586296 AATA
1 AATA
586300 AATTAAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
23 9 0.19
24 7 0.15
25 9 0.19
26 13 0.27
27 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (25 bp):
AATATTATTTTTTAATATTATATTA
Found at i:586299 original size:61 final size:64
Alignment explanation
Indices: 586193--586346 Score: 248
Period size: 61 Copynumber: 2.5 Consensus size: 64
586183 TTATATTTAA
*
586193 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATT-ATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
586253 TTTTAATATTATATTATAGATATTAATTTTAATATT-A-TTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
586315 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATTATAGATA-TTAATTTTA
586347 TATCATATAA
Statistics
Matches: 88, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
60 4 0.05
61 31 0.35
62 27 0.31
63 26 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (64 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATT
Found at i:586326 original size:36 final size:38
Alignment explanation
Indices: 586244--586326 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 38
586234 AAATAAATTA
*
586244 AATATTATTTTTTAATATTATATTATAGATATTAATTTT
1 AATATTA-TTTTTAATATTAAATTATAGATATTAATTTT
586283 AATATTATTTTTAA-A-TAAATTA-A-ATATTAATTTTTT
1 AATATTATTTTTAATATTAAATTATAGATATTAA--TTTT
586319 AATATTAT
1 AATATTAT
586327 ATTATAGATA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
34 7 0.17
35 1 0.02
36 18 0.44
37 1 0.02
38 7 0.17
39 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (38 bp):
AATATTATTTTTAATATTAAATTATAGATATTAATTTT
Found at i:586340 original size:21 final size:23
Alignment explanation
Indices: 586306--586372 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 23
586296 AATAAATTAA
* *
586306 ATATTAATTTTTTAATATTATAT
1 ATATAAATTATTTAATATTATAT
* *
586329 -TATAGA-TATTTAATTTTATAT
1 ATATAAATTATTTAATATTATAT
586350 CATATAAATTATTTATATATTAT
1 -ATATAAATTATTTA-ATATTAT
586373 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 13 0.38
22 4 0.12
23 5 0.15
24 6 0.18
25 6 0.18
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
ATATAAATTATTTAATATTATAT
Found at i:586378 original size:20 final size:19
Alignment explanation
Indices: 586355--586400 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
586345 TATATCATAT
586355 AAATTATTTATATATTATTA
1 AAATTATTTATAT-TTATTA
*
586375 AAA-T-TTTATATTTATTT
1 AAATTATTTATATTTATTA
*
586392 TAATTATTT
1 AAATTATTT
586401 TGATTTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.32
18 8 0.36
19 4 0.18
20 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AAATTATTTATATTTATTA
Found at i:586386 original size:62 final size:61
Alignment explanation
Indices: 586191--586390 Score: 173
Period size: 62 Copynumber: 3.3 Consensus size: 61
586181 TTTTATATTT
* * *
586191 AATTTT-ATATTATATT-T-GATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATT-A
1 AATTTTAATATTATATTATAGATATTAATTTTAATA-TCA--TTATAAATAAATTAAATATTAA
** * *
586251 TTTTTTAATATTATATTATAGATATTAATTTTAATATTATTTTTAAATAAATTAAATATTAA
1 AATTTTAATATTATATTATAGATATTAATTTTAATATCA-TTATAAATAAATTAAATATTAA
** * *
586313 TTTTTTAATATTATATTATAGATATTTAATTTT-ATATCA-TATAAATTATTTATATATTATTAA
1 AATTTTAATATTATATTATAGATA-TTAATTTTAATATCATTATAAATAAATTA-A-A-TATTAA
586376 AATTTT-ATATT-TATT
1 AATTTTAATATTATATT
586391 TTAATTATTT
Statistics
Matches: 122, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
60 14 0.11
61 36 0.30
62 39 0.32
63 33 0.27
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (61 bp):
AATTTTAATATTATATTATAGATATTAATTTTAATATCATTATAAATAAATTAAATATTAA
Found at i:586396 original size:17 final size:18
Alignment explanation
Indices: 586340--586390 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
586330 ATAGATATTT
586340 AATTTTATATCA-TA-TAA
1 AATTTTATAT-ATTATTAA
*
586357 ATTATTTATATATTATTAA
1 AAT-TTTATATATTATTAA
586376 AATTTTATAT-TTATT
1 AATTTTATATATTATT
586391 TTAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 8 0.28
18 16 0.55
19 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTATATATTATTAA
Found at i:586898 original size:31 final size:31
Alignment explanation
Indices: 586861--586920 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
586851 TAGTTGTATG
*
586861 AATTATTTAAATTTCAGTATTGT-AAAACTAA
1 AATTATTTAAATCTCAGTATT-TCAAAACTAA
586892 AATTATTTAAATCTCAGTATTTCAAAACT
1 AATTATTTAAATCTCAGTATTTCAAAACT
586921 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTTCAAAACTAA
Found at i:587012 original size:18 final size:18
Alignment explanation
Indices: 586989--587029 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
586979 CGTTAAAAAA
586989 CAAACAGTCTTCTTCTTG
1 CAAACAGTCTTCTTCTTG
587007 CAAACAGTCTTCTTCTTG
1 CAAACAGTCTTCTTCTTG
587025 CAAAC
1 CAAAC
587030 TGCAGACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (18 bp):
CAAACAGTCTTCTTCTTG
Found at i:587253 original size:2 final size:2
Alignment explanation
Indices: 587246--587272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
587236 AAAACAAAAT
587246 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
587273 TCTTATACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:603935 original size:21 final size:20
Alignment explanation
Indices: 603894--603932 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
603884 GAGAAAGTGG
603894 AAAATATATTAAATTTATTT
1 AAAATATATTAAATTTATTT
603914 AAAA-ATATTAAATTTATTT
1 AAAATATATTAAATTTATTT
603933 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATATATTAAATTTATTT
Found at i:603972 original size:2 final size:2
Alignment explanation
Indices: 603965--603989 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
603955 TACACTTTAA
603965 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
603990 ATGTATTCTA
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:605367 original size:18 final size:18
Alignment explanation
Indices: 605346--605384 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
605336 ATTTATCAAA
*
605346 TTATTTTATGATTATTTT
1 TTATTTTATGATTATATT
*
605364 TTATTTTGTGATTATATT
1 TTATTTTATGATTATATT
605382 TTA
1 TTA
605385 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (18 bp):
TTATTTTATGATTATATT
Found at i:605573 original size:20 final size:20
Alignment explanation
Indices: 605550--605611 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
605540 AACTTAAATC
605550 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-AAATAATATAT
*
605570 AAAAT--TTTAATAATATAT
1 AAAATAATTAAATAATATAT
* *
605588 AAAATAATT-TATATTATAT
1 AAAATAATTAAATAATATAT
605607 AAAAT
1 AAAAT
605612 TAAATATCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 5 0.14
18 11 0.31
19 13 0.36
20 7 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATAATTAAATAATATAT
Found at i:605607 original size:19 final size:18
Alignment explanation
Indices: 605561--605612 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
605551 AAATAATTAA
605561 AATAA-ATATAAAATTTT
1 AATAATATATAAAATTTT
605578 AATAATATATAAAATAATTT
1 AATAATATATAAAAT--TTT
*
605598 -ATATTATATAAAATT
1 AATAATATATAAAATT
605613 AAATATCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 6 0.19
18 9 0.29
19 13 0.42
20 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATATATAAAATTTT
Found at i:605700 original size:24 final size:23
Alignment explanation
Indices: 605630--605694 Score: 103
Period size: 24 Copynumber: 2.8 Consensus size: 23
605620 TATAATATAA
* *
605630 TATTAAAAAATTAATATTTATTT
1 TATTTAAAAATTAATATTTAATT
605653 TATTTTAAAAATTAATATTTAATT
1 TA-TTTAAAAATTAATATTTAATT
605677 TATTTAAAAATTAATATT
1 TATTTAAAAATTAATATT
605695 AAAATTAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 18 0.46
24 21 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTAAAAATTAATATTTAATT
Found at i:605729 original size:39 final size:35
Alignment explanation
Indices: 605660--605733 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 35
605650 TTTTATTTTA
*
605660 AAAATTAATATTTAATTTATTTAAAAATTAATATT
1 AAAATTAATATTTAATTAATTTAAAAATTAATATT
605695 AAAATTAATATCTATAATATAATATTAAAAATTAATATT
1 AAAATTAATAT-T-TAAT-TAAT-TTAAAAATTAATATT
605734 TAATTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
35 11 0.32
36 1 0.03
37 4 0.12
38 3 0.09
39 15 0.44
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (35 bp):
AAAATTAATATTTAATTAATTTAAAAATTAATATT
Found at i:605729 original size:62 final size:61
Alignment explanation
Indices: 605657--605784 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 61
605647 TTATTTTATT
* *
605657 TTAAAAATTAATATTTAATTTATTT-AAAAATTAATATTAAAATTAATATCTATAATATAATA
1 TTAAAAATTAATATTTAATTTATTTAAAAAAATAATATTAAAATTAAAATC-A-AATATAATA
605719 TTAAAAATTAATATTTAATTTATTTAAAAAAATAATATTAAAATTAAAATCAAATATAATA
1 TTAAAAATTAATATTTAATTTATTTAAAAAAATAATATTAAAATTAAAATCAAATATAATA
605780 -TAAAA
1 TTAAAA
605785 TCAAATATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
60 5 0.08
61 9 0.14
62 26 0.41
63 23 0.37
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (61 bp):
TTAAAAATTAATATTTAATTTATTTAAAAAAATAATATTAAAATTAAAATCAAATATAATA
Found at i:605784 original size:86 final size:87
Alignment explanation
Indices: 605598--605792 Score: 254
Period size: 86 Copynumber: 2.2 Consensus size: 87
605588 AAAATAATTT
* * *
605598 ATATTATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTATTTTATTTTAAAA
1 ATATAATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAA
* * * *
605663 ATTAATATTTAATTTATTTAAAA
66 AATAATATTAAAATTA-TAAAAA
605686 AT-TAATATTAAAATT-AATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAA
1 ATATAATA-TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAA
605748 AAATAATATTAAAATTA-AAATCAA
65 AAATAATATTAAAATTATAAA--AA
*
605772 ATATAATATAAAATCAAATAT
1 ATATAATATAAAATTAAATAT
605793 AAAAACCTCT
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
84 2 0.02
86 49 0.52
87 34 0.36
88 9 0.10
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (87 bp):
ATATAATATAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAA
AATAATATTAAAATTATAAAAA
Done.