Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 26
Found at i:540131 original size:10 final size:11
Alignment explanation
Indices: 540098--540146 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
540088 TTCTTTGGCT
540098 TTTCATT-TTC
1 TTTCATTATTC
540108 TTTC-TCTATT-
1 TTTCAT-TATTC
540118 TTTCATT-TTC
1 TTTCATTATTC
540128 TTTCATTATTC
1 TTTCATTATTC
540139 TTTTCATT
1 -TTTCATT
540147 CTCAACAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 3 0.09
10 17 0.52
11 6 0.18
12 7 0.21
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTCATTATTC
Found at i:540897 original size:14 final size:14
Alignment explanation
Indices: 540878--540912 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
540868 TAAGAGAGGT
540878 AGGTGAAAGCTCAA
1 AGGTGAAAGCTCAA
540892 AGGTGAAAGCTCAA
1 AGGTGAAAGCTCAA
540906 AGGTGAA
1 AGGTGAA
540913 TAGTAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.31, T:0.14
Consensus pattern (14 bp):
AGGTGAAAGCTCAA
Found at i:541606 original size:20 final size:22
Alignment explanation
Indices: 541561--541607 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
541551 TACTTAGAGA
*
541561 AGTATCAATACCACAAGAGGAG
1 AGTATCAATACCACAAGAGAAG
*
541583 AGTATCGATACC-CAAG-GAAG
1 AGTATCAATACCACAAGAGAAG
541603 AGTAT
1 AGTAT
541608 TAGTACCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 4 0.17
22 11 0.48
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (22 bp):
AGTATCAATACCACAAGAGAAG
Found at i:542929 original size:54 final size:54
Alignment explanation
Indices: 542792--543398 Score: 808
Period size: 54 Copynumber: 11.3 Consensus size: 54
542782 TTTATTAAGA
* * * * ** **
542792 TGCACA-TGTAGTGCCTAGACGGTCGTTCATCAACCTATGATGAATTATGTGGGT
1 TGCACACT-TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* *
542846 TGTACAC--AGTGCCTG-TACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCC-GAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* * * *
542898 TACACACTTAGTGCCGAAACAGTTGTTCATCAACATATGATAAATTCTGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
*
542952 TGCACACTTAGTGCCGAAACGGTTGTTCATTAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* * * *
543006 TGCACACATAGTGTCGAAACGATTGTTCATCAACATATGATGAATTCTGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* *
543060 TGCACACTTAGTGCCAAAATGGTTGTTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
** * * *
543114 TGTGCACTTAGTACCGAAACGGTTTTTCATCAACATATGATGAATTCTGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* * * *
543168 TGCACACATAGTGTCGAAACAGTTGTTCATCAACATATGATGAATTTCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* *
543222 TGCACACTTAGTGCCGAAATGGTTGTTCATCAACATATGATGAATTCCATGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* *
543276 TGCACACATAGTGCTGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* ** *
543330 TGCACACTTAGTGTCGAAATAGTTGTTCATCAACATATGATGAATTCCGTAAAT
1 TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
* *
543384 TGTACACATAGTGCC
1 TGCACACTTAGTGCC
543399 CATTTGGTAA
Statistics
Matches: 482, Mismatches: 66, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
52 41 0.09
53 1 0.00
54 440 0.91
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
Found at i:545222 original size:22 final size:22
Alignment explanation
Indices: 545197--545239 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
545187 TACTTAGAAA
*
545197 AGTATCGATACCACAA-GAAGAG
1 AGTACCGATACC-CAAGGAAGAG
545219 AGTACCGATACCCAAGGAAGA
1 AGTACCGATACCCAAGGAAGA
545240 ATATTAGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (22 bp):
AGTACCGATACCCAAGGAAGAG
Found at i:548313 original size:19 final size:19
Alignment explanation
Indices: 548289--548326 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
548279 TTTGTGTGGA
*
548289 AAATTTGGATTTTTTTATG
1 AAATTTGGAATTTTTTATG
*
548308 AAATTTTGAATTTTTTATG
1 AAATTTGGAATTTTTTATG
548327 CGCCATCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (19 bp):
AAATTTGGAATTTTTTATG
Found at i:548414 original size:15 final size:16
Alignment explanation
Indices: 548377--548414 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
548367 CCATCTTTTA
*
548377 AAATAA-TTTTAAGAT
1 AAATAATTTTTAAGAC
548392 AAATAATTTTTAAGAC
1 AAATAATTTTTAAGAC
548408 AAA-AATT
1 AAATAATT
548415 GGTCTGCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (16 bp):
AAATAATTTTTAAGAC
Found at i:548953 original size:2 final size:2
Alignment explanation
Indices: 548948--549002 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
548938 AAACAACCTG
548948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
548990 AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT
549003 GTAATGAAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:555391 original size:17 final size:18
Alignment explanation
Indices: 555355--555409 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
555345 TATATCTGCA
* *
555355 AAAATAATTAATTAAA-T
1 AAAATACTTAAATAAATT
555372 AAAATA-TTAAA-AACATT
1 AAAATACTTAAATAA-ATT
555389 -AAATACTTAAATAAATT
1 AAAATACTTAAATAAATT
555406 AAAA
1 AAAA
555410 ATAAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 2 0.06
16 10 0.31
17 15 0.47
18 5 0.16
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATACTTAAATAAATT
Found at i:557789 original size:30 final size:30
Alignment explanation
Indices: 557753--557852 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
557743 CTTGGTCACC
557753 ATACTATTTGAAATTGGTGGCTAAGTCCTT
1 ATACTATTTGAAATTGGTGGCTAAGTCCTT
*** * *
557783 ATACTATTTGGTGTTGGTGCCCAAGT-CTCT
1 ATACTATTTGAAATTGGTGGCTAAGTCCT-T
* * *
557813 ATACTATTT-AACCTTGATGGCTAAGTCCCT
1 ATACTATTTGAA-ATTGGTGGCTAAGTCCTT
*
557843 GTACTATTTG
1 ATACTATTTG
557853 GTGTTAGTGG
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
29 2 0.04
30 50 0.94
31 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (30 bp):
ATACTATTTGAAATTGGTGGCTAAGTCCTT
Found at i:557834 original size:60 final size:59
Alignment explanation
Indices: 557753--557882 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 59
557743 CTTGGTCACC
* * * *
557753 ATACTATTTGAAATTGGTGGCTAAGTCCTTATACTATTTGGTGTTGGTGCCCAAGTCTCT
1 ATACTATTT-AAATTGATGGCTAAGTCCCTATACTATTTGGTGTTAGTGCCCAAGTCCCT
* * *
557813 ATACTATTTAACCTTGATGGCTAAGTCCCTGTACTATTTGGTGTTAGTGGCCAAGTCCCT
1 ATACTATTTAA-ATTGATGGCTAAGTCCCTATACTATTTGGTGTTAGTGCCCAAGTCCCT
*
557873 ATATTATTTA
1 ATACTATTTA
557883 GTGTTGGTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.03
60 59 0.97
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (59 bp):
ATACTATTTAAATTGATGGCTAAGTCCCTATACTATTTGGTGTTAGTGCCCAAGTCCCT
Found at i:557869 original size:30 final size:30
Alignment explanation
Indices: 557766--557892 Score: 128
Period size: 30 Copynumber: 4.2 Consensus size: 30
557756 CTATTTGAAA
* * *
557766 TTGGTGGCTAAGTCCTTATACTATTTGGTG
1 TTGGTGGCCAAGTCCCTATACTATTTAGTG
* * ***
557796 TTGGTGCCCAAGTCTCTATACTATTTAACC
1 TTGGTGGCCAAGTCCCTATACTATTTAGTG
* * * *
557826 TTGATGGCTAAGTCCCTGTACTATTTGGTG
1 TTGGTGGCCAAGTCCCTATACTATTTAGTG
* *
557856 TTAGTGGCCAAGTCCCTATATTATTTAGTG
1 TTGGTGGCCAAGTCCCTATACTATTTAGTG
557886 TTGGTGG
1 TTGGTGG
557893 GGATCCCAGA
Statistics
Matches: 73, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (30 bp):
TTGGTGGCCAAGTCCCTATACTATTTAGTG
Found at i:559793 original size:21 final size:21
Alignment explanation
Indices: 559769--559813 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
559759 TGAAAATGTG
*
559769 AAATGAAAAGATGTAAATGCA
1 AAATGAAAAGATGCAAATGCA
*
559790 AAATGCAAAGATGCAAATGCA
1 AAATGAAAAGATGCAAATGCA
559811 AAA
1 AAA
559814 GGTGTTGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.09, G:0.18, T:0.16
Consensus pattern (21 bp):
AAATGAAAAGATGCAAATGCA
Found at i:560521 original size:16 final size:17
Alignment explanation
Indices: 560493--560524 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
560483 ATATAAATCT
560493 TACCCAGACATGCTTTC
1 TACCCAGACATGCTTTC
560510 TACCCA-ACATGCTTT
1 TACCCAGACATGCTTT
560525 ATTTCGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.25, C:0.34, G:0.09, T:0.31
Consensus pattern (17 bp):
TACCCAGACATGCTTTC
Found at i:561478 original size:15 final size:16
Alignment explanation
Indices: 561447--561478 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
561437 TTTAAAAGAA
561447 TTTTAAGATAAATCAT
1 TTTTAAGATAAATCAT
561463 TTTTAAGATAAA-CAT
1 TTTTAAGATAAATCAT
561478 T
1 T
561479 GATATGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
TTTTAAGATAAATCAT
Found at i:563294 original size:2 final size:2
Alignment explanation
Indices: 563287--563313 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
563277 AAAATTAATA
563287 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
563314 AATAAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:565641 original size:13 final size:13
Alignment explanation
Indices: 565618--565650 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
565608 GCACTAACGG
565618 AAAAT-ATTAAAT
1 AAAATAATTAAAT
565630 AAAATAATTAAAT
1 AAAATAATTAAAT
*
565643 GAAATAAT
1 AAAATAAT
565651 AACCGTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATAATTAAAT
Found at i:568298 original size:21 final size:21
Alignment explanation
Indices: 568257--568299 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
568247 AATGATGTAA
*
568257 ATGACAAGTGATAAATGAAAT
1 ATGACAAGTGATAAATAAAAT
*
568278 ATGATAAG-GATAAGATAAAAT
1 ATGACAAGTGATAA-ATAAAAT
568299 A
1 A
568300 AGAGTTGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (21 bp):
ATGACAAGTGATAAATAAAAT
Found at i:571198 original size:12 final size:12
Alignment explanation
Indices: 571183--571225 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
571173 GAAGATTCAA
*
571183 ATGAAGAGGCGG
1 ATGAAGAGGAGG
* *
571195 ATGAAGATGATG
1 ATGAAGAGGAGG
*
571207 ATGAAGAGGTGG
1 ATGAAGAGGAGG
571219 ATGAAGA
1 ATGAAGA
571226 CAACCAAACT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.42, T:0.16
Consensus pattern (12 bp):
ATGAAGAGGAGG
Found at i:571199 original size:24 final size:24
Alignment explanation
Indices: 571171--571225 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
571161 AATGAGAGCT
571171 ATGAAGATTCA-AATGAAGAGGCGG
1 ATGAAGA-TCATAATGAAGAGGCGG
* * *
571195 ATGAAGATGATGATGAAGAGGTGG
1 ATGAAGATCATAATGAAGAGGCGG
571219 ATGAAGA
1 ATGAAGA
571226 CAACCAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.42, C:0.04, G:0.36, T:0.18
Consensus pattern (24 bp):
ATGAAGATCATAATGAAGAGGCGG
Found at i:572748 original size:21 final size:20
Alignment explanation
Indices: 572702--572750 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
572692 AAGTATCGTT
572702 TGAAAAATTCAATTTCTTAA
1 TGAAAAATTCAATTTCTTAA
572722 TGAAAAATTCAATTTCTTAA
1 TGAAAAATTCAATTTCTTAA
572742 TGAAAAATT
1 TGAAAAATT
572751 GGGAGCTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (20 bp):
TGAAAAATTCAATTTCTTAA
Found at i:574302 original size:53 final size:53
Alignment explanation
Indices: 574222--574349 Score: 229
Period size: 53 Copynumber: 2.4 Consensus size: 53
574212 CTAGAAAAAT
*
574222 GGCAATCTCTCGAAGGCTCTTAAAAAGACTACGAATGTTTTGCTATGGCACCA
1 GGCAATCTCTCGAAGGCTCTTAAAAAGACTACGAATGTTTTGCCATGGCACCA
*
574275 GGCAATCTCTCGAAGGCTCTTAAAAAGACTACGAATGTTTTGCCATGTCACCA
1 GGCAATCTCTCGAAGGCTCTTAAAAAGACTACGAATGTTTTGCCATGGCACCA
*
574328 AGCAATCTCTCGAAGGCTCTTA
1 GGCAATCTCTCGAAGGCTCTTA
574350 CAGCGTCAAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 72 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (53 bp):
GGCAATCTCTCGAAGGCTCTTAAAAAGACTACGAATGTTTTGCCATGGCACCA
Found at i:577040 original size:54 final size:54
Alignment explanation
Indices: 576949--577397 Score: 630
Period size: 54 Copynumber: 8.3 Consensus size: 54
576939 TTACCGAATG
* * * *
576949 GGCACTATCTGTGCGACCTAAGAAATTCATAATAAGTTTATGAAATTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * *
577003 GGCATTATGTGTGCAACCTAAAAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
*
577057 GGCATTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTTCC-TATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAA-TTTCCGTATT
*
577111 GGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * * *
577165 GGCACTGTGTGTGTAACTTAAGAAATTCATAATGAGTTTATGAATTCCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* *
577219 GGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCAGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
* * *
577273 GGCACTATGTGTGTAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
** * * * * *
577327 GGCACTATGTGTGCAACCCCACATAATTCGTAATGAGTTTGTGAATTACCGTATC
1 GGCACTATGTGTGCAACCTAAGA-AATTCATAATGAGTTTATGAATTTCCGTATT
* *
577382 AGCACTACGTGTGCAA
1 GGCACTATGTGTGCAA
577398 AACCATAGAA
Statistics
Matches: 359, Mismatches: 33, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
53 5 0.01
54 310 0.86
55 44 0.12
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATT
Found at i:586488 original size:54 final size:54
Alignment explanation
Indices: 586401--586849 Score: 553
Period size: 54 Copynumber: 8.3 Consensus size: 54
586391 TTACCGAATG
*
586401 GGCATTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
586455 GACACTATGTGTGCAACCTAAAAAAATCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
586509 AGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTATGAA-TTTCTATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATT
* *
586563 GGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * * * *
586617 GACACTATATGTGCAACATAATAAATTCGTAATAAGTTTATGAATTTTCATATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
586671 GGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
586725 GGTACTATGTGTGCAACCTAAGAAATTCATAATATA-TATATGAA-TTTCTGTACT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATA-AGTTTATGAATTTTC-GTATT
* * * * * * * ** *
586779 GGCACTATGGGTGCAACCCCACGTAATTCATAATGAGTTTGTAAATTACCGTATC
1 GGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
*
586834 GGTACTATGTGTGCAA
1 GGCACTATGTGTGCAA
586850 AACTATAGAA
Statistics
Matches: 339, Mismatches: 49, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
53 7 0.02
54 289 0.85
55 41 0.12
56 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:588771 original size:31 final size:31
Alignment explanation
Indices: 588733--588854 Score: 92
Period size: 31 Copynumber: 3.9 Consensus size: 31
588723 CTAAGGGAAC
588733 ATCTTAGGGCCTG-AGAGCCTACCCAAGATAT
1 ATCTTAGGGCCTGCAGAGCCTACCCAAGA-AT
* * * *
588764 ATTTTAGGGCCGTG--GGGCCTACCTAAGAACAC
1 ATCTTAGGGCC-TGCAGAGCCTACCCAAG-A-AT
* *
588796 ATCTTAGGG-CTGTAGGGCCTACCCAAGAAT
1 ATCTTAGGGCCTGCAGAGCCTACCCAAGAAT
* *
588826 GATCTCAGGGCC-GCAGAGCCTACCTAAGA
1 -ATCTTAGGGCCTGCAGAGCCTACCCAAGA
588855 GTCACATTAG
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
30 3 0.04
31 45 0.62
32 25 0.34
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.20
Consensus pattern (31 bp):
ATCTTAGGGCCTGCAGAGCCTACCCAAGAAT
Found at i:588805 original size:32 final size:32
Alignment explanation
Indices: 588731--588824 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 32
588721 CCCTAAGGGA
* *
588731 ACATCTTAGGGCC-TGAGAGCCTACCCAAG-AT
1 ACATCTTAGGGCCGTG-GGGCCTACCCAAGAAC
* * *
588762 ATATTTTAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCGTGGGGCCTACCCAAGAAC
* *
588794 ACATCTTAGGGCTGTAGGGCCTACCCAAGAA
1 ACATCTTAGGGCCGTGGGGCCTACCCAAGAA
588825 TGATCTCAGG
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
31 22 0.43
32 29 0.57
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (32 bp):
ACATCTTAGGGCCGTGGGGCCTACCCAAGAAC
Found at i:588821 original size:63 final size:63
Alignment explanation
Indices: 588731--588854 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
588721 CCCTAAGGGA
* * ** *
588731 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAT-ATTTTAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
*
588794 ACATCTTAGGG-CTGTAGGGCCTACCCAAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGA
588855 GTCACATTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 5 0.09
63 48 0.91
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:589781 original size:29 final size:26
Alignment explanation
Indices: 589741--589896 Score: 118
Period size: 28 Copynumber: 5.6 Consensus size: 26
589731 GTCCACATTC
* *
589741 AAAAATTACCAAAATATCATAGTTTTA
1 AAAAATTCCCAAAATGTCATA-TTTTA
589768 CAAATAATTCCCAAAATGTCATCATTTTAA
1 -AAA-AATTCCCAAAATGTCAT-ATTTT-A
* * *
589798 AAATAATTACCAGAATGTTAATATTTTA
1 AAA-AATTCCCAAAATG-TCATATTTTA
*
589826 AAAAATTCCTAAAATGTCACCT-TTTTAA
1 AAAAATTCCCAAAATGTCA--TATTTT-A
*
589854 AAAAAATCCCAAAATGTCACCT-TTTTAA
1 AAAAATTCCCAAAATGTCA--TATTTT-A
589882 AAAAATTCCCAAAAT
1 AAAAATTCCCAAAAT
589897 ATCACTGGGT
Statistics
Matches: 109, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
26 2 0.02
27 14 0.13
28 49 0.45
29 39 0.36
30 5 0.05
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAAATTCCCAAAATGTCATATTTTA
Found at i:589867 original size:28 final size:28
Alignment explanation
Indices: 589763--589901 Score: 147
Period size: 28 Copynumber: 4.9 Consensus size: 28
589753 AATATCATAG
* * *
589763 TTTTACAAATAATTCCCAAAATGTCATCA
1 TTTTA-AAAAAATTCCCAAAATGTCACCT
* * * *
589792 TTTTAAAAATAATTACCAGAATGTTA-AT
1 TTTTAAAAA-AATTCCCAAAATGTCACCT
*
589820 ATTTT-AAAAAATTCCTAAAATGTCACCT
1 -TTTTAAAAAAATTCCCAAAATGTCACCT
*
589848 TTTTAAAAAAAATCCCAAAATGTCACCT
1 TTTTAAAAAAATTCCCAAAATGTCACCT
*
589876 TTTTAAAAAAATTCCCAAAATATCAC
1 TTTTAAAAAAATTCCCAAAATGTCAC
589902 TGGGTCGGGT
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
27 16 0.18
28 53 0.58
29 22 0.24
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTTAAAAAAATTCCCAAAATGTCACCT
Found at i:589885 original size:56 final size:57
Alignment explanation
Indices: 589747--589901 Score: 156
Period size: 56 Copynumber: 2.7 Consensus size: 57
589737 ATTCAAAAAT
* * * *
589747 TACCAAAATATC-ATAGTTTTACAAATAATTCCCAAAATGTCATCATTTTAAAAATAAT
1 TACCAAAATGTCAATA-TTTTA-AAAAAATTCCCAAAATGTCACCATTTTAAAAATAAA
* * * *
589805 TACCAGAATGTTAATATTTT-AAAAAATTCCTAAAATGTCACCTTTTTAAAAA-AAA
1 TACCAAAATGTCAATATTTTAAAAAAATTCCCAAAATGTCACCATTTTAAAAATAAA
* * *
589860 TCCCAAAATGTCACCT-TTTTAAAAAAATTCCCAAAATATCAC
1 TACCAAAATGTCA-ATATTTTAAAAAAATTCCCAAAATGTCAC
589902 TGGGTCGGGT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
55 16 0.20
56 48 0.60
58 13 0.16
59 3 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (57 bp):
TACCAAAATGTCAATATTTTAAAAAAATTCCCAAAATGTCACCATTTTAAAAATAAA
Found at i:590466 original size:7 final size:7
Alignment explanation
Indices: 590454--590492 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
590444 GGACTTGAAA
590454 GAAGGAT
1 GAAGGAT
590461 GAAGGAT
1 GAAGGAT
590468 GAAGGAT
1 GAAGGAT
590475 GAAGGAT
1 GAAGGAT
590482 GAAGGA-
1 GAAGGAT
590488 GAAGG
1 GAAGG
590493 GAAAATTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.44, C:0.00, G:0.46, T:0.10
Consensus pattern (7 bp):
GAAGGAT
Found at i:596184 original size:63 final size:63
Alignment explanation
Indices: 596094--596217 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
596084 CCCTAAGGGA
* * * ** *
596094 ACATCTTAGGGCCTGAGAGCCTACCCAAG-ATAGATTTTAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCGTAGGGCCTGAGAGCCTACCCAAGAAT-GATCTCAGGGCCGCAGAGCCTACCTAAGAAC
*
596157 ACATCGTAGGGCC-GTAGGGCCTACCCAAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCGTAGGGCCTG-AGAGCCTACCCAAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGA
596218 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCGTAGGGCCTGAGAGCCTACCCAAGAATGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:597143 original size:29 final size:26
Alignment explanation
Indices: 597104--597257 Score: 123
Period size: 29 Copynumber: 5.5 Consensus size: 26
597094 TCCACATTCG
*
597104 AAAATTACCAAAATATCATAGTTTTACA
1 AAAATTACCAAAATGTCATA-TTTTA-A
*
597132 AATAATTCCCAAAATGTCATCATTTTAAA
1 AA-AATTACCAAAATGTCAT-ATTTT-AA
* *
597161 AATAATTACCAGAATGTTAATATTTTAA
1 AA-AATTACCAAAATG-TCATATTTTAA
597189 AAAATT-CCTAAAATGTCACCT-TTTTAA
1 AAAATTACC-AAAATGTCA--TATTTTAA
* * *
597216 AAAAATCCCAAAATGTCACATTTTTAAA
1 AAAATTACCAAAATGTCATA-TTTT-AA
597244 AAAATTACCAAAAT
1 AAAATTACCAAAAT
597258 ATCACTGGGT
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
26 4 0.04
27 33 0.32
28 23 0.22
29 39 0.38
30 5 0.05
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAATTACCAAAATGTCATATTTTAA
Found at i:597240 original size:28 final size:28
Alignment explanation
Indices: 597104--597262 Score: 146
Period size: 27 Copynumber: 5.7 Consensus size: 28
597094 TCCACATTCG
* * * *
597104 AAAATTACCAAAATATCATAGTTTTACAA
1 AAAATTCCCAAAATGTCACATTTTTA-AA
*
597133 ATAATTCCCAAAATGTCATCA-TTTTAAA
1 AAAATTCCCAAAATGTCA-CATTTTTAAA
* * *
597161 AATAATTACCAGAATGTTA-ATATTTT-AA
1 AA-AATTCCCAAAATGTCACAT-TTTTAAA
* *
597189 AAAATTCCTAAAATGTCACCTTTTTAAA
1 AAAATTCCCAAAATGTCACATTTTTAAA
597217 AAAA-TCCCAAAATGTCACATTTTTAAA
1 AAAATTCCCAAAATGTCACATTTTTAAA
* *
597244 AAAATTACCAAAATATCAC
1 AAAATTCCCAAAATGTCAC
597263 TGGGTCGGGT
Statistics
Matches: 106, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
27 42 0.40
28 26 0.25
29 37 0.35
30 1 0.01
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.33
Consensus pattern (28 bp):
AAAATTCCCAAAATGTCACATTTTTAAA
Found at i:603561 original size:32 final size:31
Alignment explanation
Indices: 603523--603599 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
603513 CGGGGCCATG
* *
603523 GGGCCTACCTAAGAATACATCTTAGGACCGTA
1 GGGCCTACCTAAGAAT-CATCTCAGGACCGCA
** * *
603555 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATCATCTCAGGACCGCA
*
603586 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
603600 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 22 0.61
32 14 0.39
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (31 bp):
GGGCCTACCTAAGAATCATCTCAGGACCGCA
Found at i:604525 original size:29 final size:29
Alignment explanation
Indices: 604485--604618 Score: 132
Period size: 29 Copynumber: 4.7 Consensus size: 29
604475 GTCCACATTC
* * *
604485 AAAAATTACCAAAATATCACCGTTTTACA
1 AAAAATTCCCAAAATGTCACCTTTTTACA
* * *
604514 AATAATTCCCAAAATGTCATCATTTTA-A
1 AAAAATTCCCAAAATGTCACCTTTTTACA
* * *
604542 AAATAATTACCATAATATCA--TTATTTA-A
1 AAA-AATTCCCAAAATGTCACCTT-TTTACA
*
604570 AAAAATTCCCAAAATGTCACCTTTTTTCA
1 AAAAATTCCCAAAATGTCACCTTTTTACA
604599 AAAAATTCCCAAAATGTCAC
1 AAAAATTCCCAAAATGTCAC
604619 TGGGTCGGGT
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
27 14 0.16
28 14 0.16
29 58 0.67
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAAATTCCCAAAATGTCACCTTTTTACA
Found at i:605067 original size:7 final size:7
Alignment explanation
Indices: 605053--605182 Score: 244
Period size: 7 Copynumber: 18.7 Consensus size: 7
605043 GGACTTGAAA
605053 GAAGGAT
1 GAAGGAT
*
605060 GGAGGAT
1 GAAGGAT
605067 GAAGGAT
1 GAAGGAT
605074 GAAGGAT
1 GAAGGAT
605081 GAAGGAT
1 GAAGGAT
605088 GAAGGAT
1 GAAGGAT
605095 GAAGGAT
1 GAAGGAT
605102 GAAGGAT
1 GAAGGAT
605109 GAAGGAT
1 GAAGGAT
605116 GAAGGAT
1 GAAGGAT
605123 GAAGGAT
1 GAAGGAT
605130 GAAGGAT
1 GAAGGAT
605137 GAAGGAT
1 GAAGGAT
605144 GAAGGAT
1 GAAGGAT
605151 GAAGGAT
1 GAAGGAT
605158 GAAGGAT
1 GAAGGAT
605165 GAAGGAT
1 GAAGGAT
605172 GAAGGA-
1 GAAGGAT
605178 GAAGG
1 GAAGG
605183 GAAAATTGAG
Statistics
Matches: 121, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
6 5 0.04
7 116 0.96
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (7 bp):
GAAGGAT
Found at i:605336 original size:10 final size:10
Alignment explanation
Indices: 605321--605345 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
605311 TTTAATTTAG
605321 TCACCAAATT
1 TCACCAAATT
605331 TCACCAAATT
1 TCACCAAATT
605341 TCACC
1 TCACC
605346 TATTTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (10 bp):
TCACCAAATT
Found at i:616207 original size:43 final size:43
Alignment explanation
Indices: 616159--616243 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
616149 TATGCATGCC
* *
616159 TAAGTATGGATGGAATGTAATCTTATAATATAGGAATTATATG
1 TAAGTATGGATGAAATGCAATCTTATAATATAGGAATTATATG
616202 TAAGTATGGATGAAATGCAATCTTATAATATAGGAATTATAT
1 TAAGTATGGATGAAATGCAATCTTATAATATAGGAATTATAT
616244 ATATAACCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (43 bp):
TAAGTATGGATGAAATGCAATCTTATAATATAGGAATTATATG
Found at i:619826 original size:24 final size:23
Alignment explanation
Indices: 619799--619867 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 23
619789 GTTACCACTT
*
619799 CCACGTAGAATTTGCACCGAAGTG
1 CCACATAG-ATTTGCACCGAAGTG
* *
619823 CCACATAGGATATGCACCAAAGTG
1 CCACATA-GATTTGCACCGAAGTG
619847 CCACATAGATTTGTC-CCGAAG
1 CCACATAGATTTG-CACCGAAG
619868 GACTGTGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
23 10 0.26
24 27 0.71
25 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CCACATAGATTTGCACCGAAGTG
Found at i:619905 original size:24 final size:24
Alignment explanation
Indices: 619847--619927 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
619837 CACCAAAGTG
* *
619847 CCACATAG-ATTTGTCCCGAAGGA
1 CCACGTAGAATTTGTCCTGAAGGA
*** *
619870 CTGTGTAAAATTTGTCCTGAAGGA
1 CCACGTAGAATTTGTCCTGAAGGA
* *
619894 CCACGTAGAATTTATCCTAAAGGA
1 CCACGTAGAATTTGTCCTGAAGGA
619918 CCGA-GTAGAA
1 CC-ACGTAGAA
619928 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
23 3 0.07
24 40 0.91
25 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCTGAAGGA
Found at i:620053 original size:15 final size:15
Alignment explanation
Indices: 620033--620083 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
620023 GTCTTTTATC
620033 CACATAGAACACATT
1 CACATAGAACACATT
* **
620048 CACATAGAGCATTTT
1 CACATAGAACACATT
*
620063 CACGTAGAACACATT
1 CACATAGAACACATT
620078 CACATA
1 CACATA
620084 TAATATGTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (15 bp):
CACATAGAACACATT
Found at i:625691 original size:24 final size:24
Alignment explanation
Indices: 625664--625773 Score: 109
Period size: 24 Copynumber: 4.6 Consensus size: 24
625654 CAGTCACCAC
*
625664 TGCCACATAGAATTTATATAAAAG
1 TGCCACATAGAATTTATATCAAAG
* *
625688 TGCCACATAGAATTTGTACCAAAG
1 TGCCACATAGAATTTATATCAAAG
* * *
625712 TGCCACATAG-ATTTGTCTCGAAG
1 TGCCACATAGAATTTATATCAAAG
* *
625735 -GACCACATAGAATTTATCTCGAA-
1 TG-CCACATAGAATTTATATCAAAG
625758 TGACCACATAGAATTT
1 TG-CCACATAGAATTT
625774 GTCCCAAAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.01
23 18 0.24
24 57 0.75
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (24 bp):
TGCCACATAGAATTTATATCAAAG
Found at i:625747 original size:47 final size:48
Alignment explanation
Indices: 625690--625794 Score: 126
Period size: 47 Copynumber: 2.2 Consensus size: 48
625680 TATAAAAGTG
* * * *
625690 CCACATAGAATTTGTAC-CAAAGTG-CCACATAG-ATTTGTCTCGAAGGA
1 CCACATAGAATTTAT-CTCAAA-TGACCACATAGAATTTGTCCCAAAGAA
*
625737 CCACATAGAATTTATCTCGAATGACCACATAGAATTTGTCCCAAAGAA
1 CCACATAGAATTTATCTCAAATGACCACATAGAATTTGTCCCAAAGAA
625785 CCACATAGAA
1 CCACATAGAA
625795 CCCTTAAGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
46 3 0.06
47 25 0.50
48 22 0.44
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (48 bp):
CCACATAGAATTTATCTCAAATGACCACATAGAATTTGTCCCAAAGAA
Found at i:625787 original size:24 final size:23
Alignment explanation
Indices: 625690--625794 Score: 104
Period size: 24 Copynumber: 4.4 Consensus size: 23
625680 TATAAAAGTG
* *
625690 CCACATAGAATTTGTACCAAAGTG
1 CCACATAGAATTTGTCCCAAAG-A
* *
625714 CCACATAG-ATTTGTCTCGAAGGA
1 CCACATAGAATTTGTC-CCAAAGA
* * *
625737 CCACATAGAATTTATCTCGAATGA
1 CCACATAGAATTTGTC-CCAAAGA
625761 CCACATAGAATTTGTCCCAAAGAA
1 CCACATAGAATTTGTCCCAAAG-A
625785 CCACATAGAA
1 CCACATAGAA
625795 CCCTTAAGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.26
24 51 0.74
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (23 bp):
CCACATAGAATTTGTCCCAAAGA
Found at i:625948 original size:15 final size:15
Alignment explanation
Indices: 625928--625965 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
625918 TAAAGTATTT
625928 TTCACATAAAACACA-
1 TTCACATAAAACA-AG
*
625943 TTCACATATAACAAG
1 TTCACATAAAACAAG
625958 TTCACATA
1 TTCACATA
625966 CTAATCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (15 bp):
TTCACATAAAACAAG
Found at i:627913 original size:50 final size:49
Alignment explanation
Indices: 627613--627915 Score: 243
Period size: 49 Copynumber: 6.1 Consensus size: 49
627603 TGCCTAAAGA
* * * *
627613 TGCATTTTGGGGAGAAAGGTGCCATTAATGCAAGTTAGATGAAAAATTG
1 TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
* * * * ** * *
627662 TGCAATTTTGGTAGAAAGGTGCCACTAATACAAGCT-GAAT-ACCTAACGA
1 TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG-ATGA-AAAATGG
* * * *
627711 TGCA-TTTTGGTCAGAAATGAGCCACTAATGTATGTTAGATGAAAAATGG
1 TGCATTTTTGG-CAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
* * * * *
627760 TGCATTTTGGGCAAAAAGGTGCCATTAATGCACGTTAGATGAAAAAGGG
1 TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
* * ** * **** * *
627809 TGCATTTTTTTGCAAAAAACTGCCACTAATGCAAGTTAAATTCCCAACGA
1 TGCA-TTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
*
627859 TGCATTTTTTGGCAGAAAGGTGCCACTAATACAAGTTAGATGAAAAATGG
1 TGCA-TTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
627909 TGCATTT
1 TGCATTT
627916 CGGAAACAGG
Statistics
Matches: 192, Mismatches: 55, Indels: 14
0.74 0.21 0.05
Matches are distributed among these distances:
48 8 0.04
49 103 0.54
50 81 0.42
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (49 bp):
TGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAATGG
Found at i:634341 original size:22 final size:21
Alignment explanation
Indices: 634313--634355 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
634303 TGAGTGCATC
634313 TATTGTAATTTAATATATGTTT
1 TATTGT-ATTTAATATATGTTT
**
634335 TATTGTATTTGGTATATGTTT
1 TATTGTATTTAATATATGTTT
634356 ATAATGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
TATTGTATTTAATATATGTTT
Found at i:634684 original size:50 final size:49
Alignment explanation
Indices: 634434--634686 Score: 244
Period size: 50 Copynumber: 5.1 Consensus size: 49
634424 TGCTTAACAA
* *
634434 TGCA-TTTTGGGCAAAAAGATGCCACTAATGCAAGTTAGATGAAAAATGG
1 TGCATTTTTGGGCAGAAAGGTG-CACTAATGCAAGTTAGATGAAAAATGG
* * * * * *** * *
634483 TTCATTTTT-TGTAGAAAGGTGTCACTATTGCAAGTTAAATGTCTAACGA
1 TGCATTTTTGGGCAGAAAGGTG-CACTAATGCAAGTTAGATGAAAAATGG
*
634532 TGCATTTTTGGGCAGAAAGGTGCTACTAATGCAAGTTAGATGAAAAAGGG
1 TGCATTTTTGGGCAGAAAGGTGC-ACTAATGCAAGTTAGATGAAAAATGG
* * * *** *
634582 TGTATTTTT--GTAGAAAGGTGCACCTAATGCAAGTTAAATGCCTAATGA
1 TGCATTTTTGGGCAGAAAGGTGCA-CTAATGCAAGTTAGATGAAAAATGG
*
634630 TGCATTTTTGGGCAGAAAGGTGACACTAATACAAGTTAGATGAAAAATGG
1 TGCATTTTTGGGCAGAAAGGTG-CACTAATGCAAGTTAGATGAAAAATGG
634680 TGCATTT
1 TGCATTT
634687 CGGAAAAAGG
Statistics
Matches: 158, Mismatches: 39, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
47 1 0.01
48 38 0.24
49 40 0.25
50 77 0.49
51 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (49 bp):
TGCATTTTTGGGCAGAAAGGTGCACTAATGCAAGTTAGATGAAAAATGG
Found at i:634700 original size:98 final size:96
Alignment explanation
Indices: 634416--634686 Score: 382
Period size: 98 Copynumber: 2.8 Consensus size: 96
634406 TCTAAAAGGA
* * * *
634416 AAGTTAAATGCTTAACAATGCA-TTTTGGGCAAAAAGATGCCACTAATGCAAGTTAGATGAAAAA
1 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTG-CACTAATGCAAGTTAGATGAAAAA
* *
634480 TGGTTCATTTTTTGTAGAAAGGTGTCACTATTGC
65 TGGTGCA-TTTTTGTAGAAAGGTG-CACTAATGC
*
634514 AAGTTAAATGTCTAACGATGCATTTTTGGGCAGAAAGGTGCTACTAATGCAAGTTAGATGAAAAA
1 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGC-ACTAATGCAAGTTAGATGAAAAA
* *
634579 GGGTGTATTTTTGTAGAAAGGTGCACCTAATGC
65 TGGTGCATTTTTGTAGAAAGGTGCA-CTAATGC
* *
634612 AAGTTAAATGCCTAATGATGCATTTTTGGGCAGAAAGGTGACACTAATACAAGTTAGATGAAAAA
1 AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTG-CACTAATGCAAGTTAGATGAAAAA
634677 TGGTGCATTT
65 TGGTGCATTT
634687 CGGAAAAAGG
Statistics
Matches: 155, Mismatches: 14, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
97 2 0.01
98 110 0.71
99 43 0.28
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (96 bp):
AAGTTAAATGCCTAACGATGCATTTTTGGGCAGAAAGGTGCACTAATGCAAGTTAGATGAAAAAT
GGTGCATTTTTGTAGAAAGGTGCACTAATGC
Found at i:651589 original size:19 final size:18
Alignment explanation
Indices: 651565--651611 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
651555 AAATTGCATG
*
651565 AAATAAGATGACAAAATGT
1 AAATAAGATG-CAAAATAT
* *
651584 AAATAACATGTAAAATAT
1 AAATAAGATGCAAAATAT
651602 AAATAAGATG
1 AAATAAGATG
651612 TGAATATAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (18 bp):
AAATAAGATGCAAAATAT
Found at i:655271 original size:5 final size:5
Alignment explanation
Indices: 655261--655291 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
655251 TTACAAAGTG
655261 AAATA AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
655292 CAACGCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:656445 original size:23 final size:21
Alignment explanation
Indices: 656419--656466 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
656409 CCTCCAAAGG
*
656419 TGAGAAAGTTTCTTTTCAAATTT
1 TGAGAAA-TTTATTTT-AAATTT
* *
656442 TGAGCAATTTATTTTGAATTT
1 TGAGAAATTTATTTTAAATTT
656463 TGAG
1 TGAG
656467 TTATGCCGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 7 0.32
23 6 0.27
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (21 bp):
TGAGAAATTTATTTTAAATTT
Found at i:657520 original size:2 final size:2
Alignment explanation
Indices: 657513--657537 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
657503 AAATATTTTG
657513 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
657538 AAGTGTCAAG
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:666344 original size:19 final size:19
Alignment explanation
Indices: 666320--666582 Score: 232
Period size: 19 Copynumber: 13.6 Consensus size: 19
666310 AATCGAAAAC
*
666320 GGGTATCGATACCATGGAA
1 GGGTATCGATACCGTGGAA
666339 GGGTATCGATACCGTGGAA
1 GGGTATCGATACCGTGGAA
*
666358 GGGTATCGATACCGTTGAA
1 GGGTATCGATACCGTGGAA
*
666377 GGGTATCGATACCGTTGAA
1 GGGTATCGATACCGTGGAA
*
666396 GGGTATCGATACTGTGGAA
1 GGGTATCGATACCGTGGAA
** *
666415 GGGTATCGATACTACAAGCATGA
1 GGGTATCGATAC--CGTGGA--A
* * *
666438 GGGTATCGGTACTGT-AACA
1 GGGTATCGATACCGTGGA-A
* * * * *
666457 GTAGTACCAATATTAC-T-TAA
1 G-GGTATCGATA--CCGTGGAA
*
666477 --GT-TGGAATTACCGTGGAA
1 GGGTATCG-A-TACCGTGGAA
666495 GGGTATCGATACCGTGGAA
1 GGGTATCGATACCGTGGAA
666514 GGGTATCGATACCGTGGAA
1 GGGTATCGATACCGTGGAA
*
666533 GGGTATCGATACCGTGAAA
1 GGGTATCGATACCGTGGAA
666552 GGGTATCGATACCGTGGAA
1 GGGTATCGATACCGTGGAA
*
666571 GGGTATCAATAC
1 GGGTATCGATAC
666583 TACAAGCATG
Statistics
Matches: 200, Mismatches: 30, Indels: 28
0.78 0.12 0.11
Matches are distributed among these distances:
16 1 0.00
17 4 0.02
18 4 0.02
19 162 0.81
20 11 0.05
21 6 0.03
23 12 0.06
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.24
Consensus pattern (19 bp):
GGGTATCGATACCGTGGAA
Found at i:666618 original size:156 final size:156
Alignment explanation
Indices: 666329--666634 Score: 542
Period size: 156 Copynumber: 2.0 Consensus size: 156
666319 CGGGTATCGA
*
666329 TACCATGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTTGAAGGGTATCGATACCGTTG
1 TACCATGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTTG
* * *
666394 AAGGGTATCGATACTGTGGAAGGGTATCGATACTACAAGCATGAGGGTATCGGTACTGTAACAGT
66 AAGGGTATCGATACCGTGGAAGGGTATCAATACTACAAGCATGAGAGTATCGGTACTGTAACAGT
*
666459 AGTACCAATATTACTTAAGTTGGAAT
131 AGTACCAATACTACTTAAGTTGGAAT
*
666485 TACCGTGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCG-TG
1 TACCATGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTTG
666549 AAAGGGTATCGATACCGTGGAAGGGTATCAATACTACAAGCATGAGAGTATCGGTACTGTAACAG
66 -AAGGGTATCGATACCGTGGAAGGGTATCAATACTACAAGCATGAGAGTATCGGTACTGTAACAG
666614 TAGTACCAATACTACTTAAGT
130 TAGTACCAATACTACTTAAGT
666635 AGGGATTAAG
Statistics
Matches: 143, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
155 2 0.01
156 141 0.99
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (156 bp):
TACCATGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTGGAAGGGTATCGATACCGTTG
AAGGGTATCGATACCGTGGAAGGGTATCAATACTACAAGCATGAGAGTATCGGTACTGTAACAGT
AGTACCAATACTACTTAAGTTGGAAT
Found at i:676213 original size:13 final size:14
Alignment explanation
Indices: 676188--676234 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 14
676178 GAAATGGTAA
*
676188 GTATTATATGATAT
1 GTATAATATGATAT
*
676202 GTATAA-ATGATAA
1 GTATAATATGATAT
*
676215 GTATAATATTATAT
1 GTATAATATGATAT
676229 G-ATAAT
1 GTATAAT
676235 GAGGGATTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
GTATAATATGATAT
Found at i:676217 original size:27 final size:26
Alignment explanation
Indices: 676179--676233 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
676169 TTTATTGGTG
* *
676179 AAATGGTAAGTATTATATGATATGTAT
1 AAATGATAAGTATAATATGATATG-AT
*
676206 AAATGATAAGTATAATATTATATGAT
1 AAATGATAAGTATAATATGATATGAT
676232 AA
1 AA
676234 TGAGGGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (26 bp):
AAATGATAAGTATAATATGATATGAT
Found at i:680497 original size:27 final size:26
Alignment explanation
Indices: 680466--680521 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
680456 TTTATTGGTG
* * *
680466 AAATGGTATGTATTATATGATATGTAT
1 AAATGATAAGTATAATATGATATG-AT
*
680493 AAATGATAAGTATAATATTATATGAT
1 AAATGATAAGTATAATATGATATGAT
680519 AAA
1 AAA
680522 AAGGGATTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (26 bp):
AAATGATAAGTATAATATGATATGAT
Found at i:680500 original size:13 final size:13
Alignment explanation
Indices: 680466--680521 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
680456 TTTATTGGTG
*
680466 AAATGGTATGTATT
1 AAATGATATGTA-T
*
680480 ATATGATATGTAT
1 AAATGATATGTAT
*
680493 AAATGATAAGTAT
1 AAATGATATGTAT
*
680506 AATATTATATG-AT
1 AA-ATGATATGTAT
680519 AAA
1 AAA
680522 AAGGGATTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 1 0.03
13 18 0.51
14 16 0.46
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
AAATGATATGTAT
Found at i:681459 original size:18 final size:18
Alignment explanation
Indices: 681436--681473 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
681426 GAAAAATATT
681436 AAGTACATATTTTTAACG
1 AAGTACATATTTTTAACG
681454 AAGTACATATTTTTAACG
1 AAGTACATATTTTTAACG
681472 AA
1 AA
681474 AACATTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
AAGTACATATTTTTAACG
Found at i:681478 original size:17 final size:18
Alignment explanation
Indices: 681440--681478 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
681430 AATATTAAGT
*
681440 ACATATTTTTAACGAAGT
1 ACATATTTTTAACGAAGA
681458 ACATATTTTTAACGAA-A
1 ACATATTTTTAACGAAGA
681475 ACAT
1 ACAT
681479 TTTAGACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (18 bp):
ACATATTTTTAACGAAGA
Found at i:681797 original size:51 final size:51
Alignment explanation
Indices: 681742--681847 Score: 169
Period size: 51 Copynumber: 2.1 Consensus size: 51
681732 TATAAGAAGT
* * *
681742 AAAATTGATTTTAAATAGCG-TCACTGCTTTACTCATAACTGACACATTTAA
1 AAAATTGATTTTAAATAGAGCT-ACTACTTTAATCATAACTGACACATTTAA
681793 AAAATTGATTTTAAATAGAGCTACTACTTTAATCATAACTGACACATTTAA
1 AAAATTGATTTTAAATAGAGCTACTACTTTAATCATAACTGACACATTTAA
681844 AAAA
1 AAAA
681848 AATATGGATA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (51 bp):
AAAATTGATTTTAAATAGAGCTACTACTTTAATCATAACTGACACATTTAA
Found at i:682783 original size:18 final size:18
Alignment explanation
Indices: 682734--682789 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
682724 AATTCTTAAT
682734 ATTTTATATCTTAAATTA
1 ATTTTATATCTTAAATTA
* * * *
682752 AATTCACATATTAAATTA
1 ATTTTATATCTTAAATTA
682770 ATTTTATATCTTAACATTA
1 ATTTTATATCTTAA-ATTA
682789 A
1 A
682790 AAGAAATATA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTTATATCTTAAATTA
Found at i:682856 original size:28 final size:29
Alignment explanation
Indices: 682798--682936 Score: 124
Period size: 30 Copynumber: 4.7 Consensus size: 29
682788 AAAAGAAATA
* *
682798 TATT-TTTATCTTAACTTATTATATATATTT
1 TATTCTTT-TCTTAACTTA-AAAATATATTT
*
682828 TATTCTTTTCGTAACTTAAAAA-ATATTT
1 TATTCTTTTCTTAACTTAAAAATATATTT
*
682856 TATTCTTATT-TTAATTTTAAAAATATATTT
1 TATTCTT-TTCTTAA-CTTAAAAATATATTT
* *
682886 TAGTATTTATCTTAACTTAAAAAGTATATTT
1 TATTCTTT-TCTTAACTTAAAAA-TATATTT
*
682917 TATTCTAATT-TTAACTTAAA
1 TATTCT-TTTCTTAACTTAAA
682937 TATTTATATT
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
28 16 0.18
29 12 0.13
30 42 0.47
31 19 0.21
32 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (29 bp):
TATTCTTTTCTTAACTTAAAAATATATTT
Found at i:682917 original size:31 final size:28
Alignment explanation
Indices: 682776--682936 Score: 121
Period size: 30 Copynumber: 5.5 Consensus size: 28
682766 ATTAATTTTA
* *
682776 TATCTTAACATTAAAAGAAATA-TAT-TTT
1 TATCTTAAC-TTAAAA-ATATATTTTATTT
* *
682804 TATCTTAACTTATTATATATATTTTATTCT
1 TATCTTAACTTA-AAAATATATTTTATT-T
* *
682834 TTTCGTAACTTAAAAA-ATATTTTATTCT
1 TATCTTAACTTAAAAATATATTTTATT-T
* *
682862 TATTTTAATTTTAAAAATATATTTTAGTATT
1 TATCTTAA-CTTAAAAATATATTTTA-T-TT
682893 TATCTTAACTTAAAAAGTATATTTTATTCT
1 TATCTTAACTTAAAAA-TATATTTTATT-T
* *
682923 AATTTTAACTTAAA
1 TATCTTAACTTAAA
682937 TATTTATATT
Statistics
Matches: 107, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
27 7 0.07
28 29 0.27
29 12 0.11
30 40 0.37
31 18 0.17
32 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (28 bp):
TATCTTAACTTAAAAATATATTTTATTT
Found at i:682948 original size:31 final size:29
Alignment explanation
Indices: 682820--682936 Score: 132
Period size: 30 Copynumber: 4.0 Consensus size: 29
682810 AACTTATTAT
*
682820 ATATATTTTATTCTT-TTCGTAACTTAAAA
1 ATATATTTTATTCTTATT-TTAACTTAAAA
*
682849 A-ATATTTTATTCTTATTTTAATTTTAAAA
1 ATATATTTTATTCTTATTTTAA-CTTAAAA
*
682878 ATATATTTTAGTAT-TTATCTTAACTTAAAA
1 ATATATTTTA-T-TCTTATTTTAACTTAAAA
*
682908 AGTATATTTTATTCTAATTTTAACTTAAA
1 A-TATATTTTATTCTTATTTTAACTTAAA
682937 TATTTATATT
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
28 16 0.21
29 11 0.15
30 29 0.39
31 18 0.24
32 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (29 bp):
ATATATTTTATTCTTATTTTAACTTAAAA
Found at i:682989 original size:29 final size:30
Alignment explanation
Indices: 682957--683022 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
682947 TTTATGATAG
* *
682957 TATTTTA-AATTTAAGATAAAAATATAATA
1 TATTTTAGAAGTTAAGATAAAAATAAAATA
* *
682986 TATTTTATGTAGTTAGGATAAAAATAAAATA
1 TATTTTA-GAAGTTAAGATAAAAATAAAATA
683017 TATTTT
1 TATTTT
683023 TATTGTTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.23
31 24 0.77
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (30 bp):
TATTTTAGAAGTTAAGATAAAAATAAAATA
Found at i:683041 original size:31 final size:31
Alignment explanation
Indices: 682967--683034 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
682957 TATTTTAAAT
*
682967 TTAAGATAAAAATATAATATATTTTATGTAG
1 TTAAGATAAAAATAAAATATATTTTATGTAG
*
682998 TTAGGATAAAAATAAAATATATTTTTAT-T-G
1 TTAAGATAAAAATAAAATATA-TTTTATGTAG
683028 TTAAGAT
1 TTAAGAT
683035 GTAAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 7 0.21
31 20 0.61
32 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (31 bp):
TTAAGATAAAAATAAAATATATTTTATGTAG
Found at i:683481 original size:29 final size:31
Alignment explanation
Indices: 683412--683500 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 31
683402 TAACAAAGAC
* *
683412 CAAAAGTGTAATTATGCCAAATATTAATAGTGA
1 CAAATGTGTAATTATACCAAATATT-ATAGT-A
*
683445 CCGAATGTGTAATTATACCAAATATTATA-T-
1 -CAAATGTGTAATTATACCAAATATTATAGTA
* * *
683475 CAAATGTGTAACTATACTAGATATTA
1 CAAATGTGTAATTATACCAAATATTA
683501 ACAACAAGTG
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 22 0.46
32 1 0.02
33 3 0.06
34 22 0.46
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (31 bp):
CAAATGTGTAATTATACCAAATATTATAGTA
Found at i:684041 original size:13 final size:13
Alignment explanation
Indices: 684023--684051 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
684013 CAACACGTAT
684023 TTTTGATAATTAA
1 TTTTGATAATTAA
684036 TTTTGATAATTAA
1 TTTTGATAATTAA
684049 TTT
1 TTT
684052 AATAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (13 bp):
TTTTGATAATTAA
Found at i:689008 original size:12 final size:12
Alignment explanation
Indices: 688991--689036 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
688981 CGTCAGGGGA
688991 ATTGCGTGGCTG
1 ATTGCGTGGCTG
689003 ATTGCGTGGCTG
1 ATTGCGTGGCTG
*
689015 ATTGCTTGGCTG
1 ATTGCGTGGCTG
*
689027 ATTGCTTGGC
1 ATTGCGTGGC
689037 CAAGCACACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.09, C:0.17, G:0.37, T:0.37
Consensus pattern (12 bp):
ATTGCGTGGCTG
Found at i:689470 original size:20 final size:21
Alignment explanation
Indices: 689432--689471 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
689422 TAATTAGATT
* *
689432 TATTTTTATTTTTATTTTAAC
1 TATTTTTATTTATAGTTTAAC
689453 TATTTTTA-TTATAGTTTAA
1 TATTTTTATTTATAGTTTAA
689472 ATAGATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (21 bp):
TATTTTTATTTATAGTTTAAC
Found at i:691845 original size:46 final size:46
Alignment explanation
Indices: 691781--692406 Score: 838
Period size: 46 Copynumber: 13.6 Consensus size: 46
691771 AAATGAATGA
* * * * *
691781 ATAAATGAAAATGCATAACGTTACATTATTGGCATGAAAGAATGAC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
691827 ATAAATGAAAATGTATAACAGTGCATTATTGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
691873 ATAAATGAAAAGGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
691919 ATAAAAGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
691965 ATAAATGAAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
692011 ATAAATGAAAATGCATAACGGTGCATTATCTGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
692057 ATAAATGAAAATGCATAAGGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
692103 ATAAATGAAAATGCATAACGGTTCATTATCGGCATGAAATGATGCA
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
692149 ATAAATGAAAATGCATAACGGTTCATTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** * *
692195 ATAAATGTAAATGCATAACAATGCATTATCGACATGAAAGGATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
692241 ATAAATGAAAATGCACAACAGTGCATTATCCGCATGAAAGGATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
692287 ATAAATGAACATGAATAACGATGCATTATCAGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * * * * **
692333 ACAAATGAACATGAATAACAGTGCATAATTGACATGAAAAAATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * *
692379 ACAAATGAAATTACATAACGGTGTATTA
1 ATAAATGAAAATGCATAACGGTGCATTA
692407 ACGTCATATA
Statistics
Matches: 518, Mismatches: 62, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 518 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:694166 original size:12 final size:12
Alignment explanation
Indices: 694145--694178 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
694135 ACCACATTTC
*
694145 CAATACCAAACA
1 CAATATCAAACA
694157 CAATATCAAACA
1 CAATATCAAACA
*
694169 CAATCTCAAA
1 CAATATCAAA
694179 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:696898 original size:20 final size:20
Alignment explanation
Indices: 696875--696945 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
696865 TTCGCTACAT
*
696875 GAAAGTCAAATTCACGTTGC
1 GAAAGTCAAATTCACATTGC
*
696895 GAAAGTCAAATTCGCATTGC
1 GAAAGTCAAATTCACATTGC
* * **
696915 GAAAGACAAATTCGCAACGC
1 GAAAGTCAAATTCACATTGC
696935 GAAAGTCAAAT
1 GAAAGTCAAAT
696946 ATGTAATGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
GAAAGTCAAATTCACATTGC
Found at i:697008 original size:29 final size:29
Alignment explanation
Indices: 696966--697047 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
696956 AAAATCAAAT
696966 TCGCAACGCGAATTTGACTTTCGCAACAA
1 TCGCAACGCGAATTTGACTTTCGCAACAA
* *
696995 TCGCAATGCGAATTTGACTGTCGCAACAA
1 TCGCAACGCGAATTTGACTTTCGCAACAA
697024 TCGCAACGCGAATTTGACTTTCGC
1 TCGCAACGCGAATTTGACTTTCGC
697048 GTTGCGAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (29 bp):
TCGCAACGCGAATTTGACTTTCGCAACAA
Found at i:698516 original size:21 final size:21
Alignment explanation
Indices: 698486--698603 Score: 164
Period size: 21 Copynumber: 5.6 Consensus size: 21
698476 GTGAATCGGG
* * *
698486 CTCTTAAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
*
698507 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
698528 CTCTTGAACAATTGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
698549 CTCTTGAATGATGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
698570 CTCTTGAACGATAGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
698591 CTCTTGAACGATG
1 CTCTTGAACGATG
698604 ACAGGTGATT
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 84 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:700742 original size:20 final size:20
Alignment explanation
Indices: 700719--700771 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
700709 AAACTTAAAT
*
700719 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAAAGAAAA
**
700739 TCGCAAAACGAAAAAGAAAA
1 TCGCAACGCGAAAAAGAAAA
700759 TCGCAACGCGAAA
1 TCGCAACGCGAAA
700772 CTAAAATAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.21, G:0.19, T:0.08
Consensus pattern (20 bp):
TCGCAACGCGAAAAAGAAAA
Found at i:700817 original size:20 final size:20
Alignment explanation
Indices: 700788--700826 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
700778 TAGCGTTGCG
700788 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
700808 ATTTTTGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
700827 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:704257 original size:56 final size:56
Alignment explanation
Indices: 704104--704258 Score: 233
Period size: 56 Copynumber: 2.8 Consensus size: 56
704094 AATGGCACTA
** *
704104 TGTGTGC-AAAACTAAGAAATTCATAATGAGTTTATGAATTTATGTTTGGGAACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGAACTT
*
704159 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT-GGACATTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGA-ACTT
* *
704215 TGTGTGCAAAAACTAAGAAATTCATAATAAGTTTTTGAATTTCC
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCC
704259 CTATTGGTAG
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
55 10 0.11
56 82 0.89
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (56 bp):
TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGAACTT
Found at i:704507 original size:81 final size:81
Alignment explanation
Indices: 704409--705386 Score: 1357
Period size: 81 Copynumber: 12.1 Consensus size: 81
704399 AGTTCTAAAA
** *
704409 TAAAAGATTAATGGCCTAGAAGTGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
704474 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
704490 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCTAATTAGATTAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
704555 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
704571 TAAAAGATTAATGGTCTAGCTGTGTATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
704636 GTTAAATACCTTTAAG
66 GTTAAATACCTTTGAG
* * * * *
704652 TAAAAGATTAATGGCCTAGATGTGCATTTCGCAGAAAGGTGTCAATTATCCCAGTTAGATTAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
704717 ATT-AATACATTTGAG
66 GTTAAATACCTTTGAG
* * * * *
704732 AAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATGCAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
704797 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
704813 TAAACGTTTAATGGCCTAGTTGTGCATTTGGTAGAAATGTTTCAATTATGCCAGTTAGATGAAGG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
704878 GTTAAATACCTTTGAC
66 GTTAAATACCTTTGAG
* * ** *
704894 TAAAAGATTAATTGCCTAGTTGTGCATTTGGAAGAAATGTGAAAATTATTCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
704959 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
704975 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
705040 GTTAAATACCTTTAAG
66 GTTAAATACCTTTGAG
* * * * * * *
705056 TAAAAGATTAATGGCCTAGCTATTCATTTGGCAAAAAAGTTTCAATTATGCCAATTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
705121 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** ** * *
705137 TAAAATATTAATGGCCTAACTGTTTATTTAGCAGAAATGTGTCAATTATGCCAGTTAGATGGAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
705202 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
705218 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCTAGTCAAATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
705283 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
705299 TAAAAGATTAATGGTCTAGTTGTGCATTTGGCAGAAAAGTGTCAATCATG-TAGGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCA-GTTAGATGAAA
* * *
705363 GGCTAAATGCCTTTGGG
65 GGTTAAATACCTTTGAG
705380 TAAAAGA
1 TAAAAGA
705387 CTAAAGGAAT
Statistics
Matches: 799, Mismatches: 96, Indels: 4
0.89 0.11 0.00
Matches are distributed among these distances:
80 72 0.09
81 727 0.91
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:708263 original size:46 final size:46
Alignment explanation
Indices: 708196--708719 Score: 656
Period size: 46 Copynumber: 11.4 Consensus size: 46
708186 AAATGAATGA
* * *
708196 ATAAATGAAAATGCATAACGGTGCATTATTGGCATGAAAGGATACC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
708242 ATAAATGAAAATGCATAACGGTGCATTATCGGCATCAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
*
708288 ATAAATGAAAATGCATAACAGTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* *
708334 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
708380 ATAAATTAAAATACATAATGGTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
708426 ATAAATGAAAATGCATAACGGTGCATTATCAACATGAAATGATGCT
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* ** * *
708472 ATAAATCAAAATGCATAATAGTGCATTATTGACATGAAAGTATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * * *
708518 ATAAATGAAAATGTATAATGGTGCATTATC-AGCATGAAAGTATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGA-CATGAAAGGATGCC
* * *
708564 ATAAATGAAAATGTATAACGGTGCATTATCGACATGAAATGATGCT
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * * *
708610 ATAAATGAAAAAGCCTAATGGTGCATTATC-AGCATGAAAGGATGCT
1 ATAAATGAAAATGCATAACGGTGCATTATCGA-CATGAAAGGATGCC
* * * * * * *
708656 ATAAATGAACATGAATAATGATACATTATCAACATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* *
708702 ATAAATGAACATGAATAA
1 ATAAATGAAAATGCATAA
708720 TGATGCATAA
Statistics
Matches: 421, Mismatches: 53, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
45 2 0.00
46 417 0.99
47 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
Found at i:708742 original size:24 final size:25
Alignment explanation
Indices: 708650--708729 Score: 89
Period size: 23 Copynumber: 3.4 Consensus size: 25
708640 AGCATGAAAG
*
708650 GATGCTATAAATGAACATGAATAAT
1 GATGCCATAAATGAACATGAATAAT
* * *
708675 GAT-ACAT-TATCAACATG-A-AAT
1 GATGCCATAAATGAACATGAATAAT
708696 GATGCCATAAATGAACATGAATAAT
1 GATGCCATAAATGAACATGAATAAT
708721 GATG-CATAA
1 GATGCCATAA
708730 TTGGCATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
21 6 0.14
22 4 0.09
23 16 0.36
24 8 0.18
25 10 0.23
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.26
Consensus pattern (25 bp):
GATGCCATAAATGAACATGAATAAT
Found at i:710513 original size:17 final size:18
Alignment explanation
Indices: 710492--710538 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
710482 CGTAGTTAAT
*
710492 TAGCTAGGTAGCTTAGGG
1 TAGCTAGCTAGCTTAGGG
* *
710510 -AGCTAGTTAG-GTAGGG
1 TAGCTAGCTAGCTTAGGG
710526 TAGCTAGCTAGCT
1 TAGCTAGCTAGCT
710539 AGATACCTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (18 bp):
TAGCTAGCTAGCTTAGGG
Found at i:718509 original size:12 final size:12
Alignment explanation
Indices: 718494--718520 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
718484 AATATTTGAT
718494 AAAATAAAATAA
1 AAAATAAAATAA
718506 AAAATAAAATAA
1 AAAATAAAATAA
718518 AAA
1 AAA
718521 TAACAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:718528 original size:12 final size:11
Alignment explanation
Indices: 718494--718528 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
718484 AATATTTGAT
718494 AAAATAAAATAA
1 AAAATAAAAT-A
718506 AAAATAAAATA
1 AAAATAAAATA
718517 AAAATAACAATA
1 AAAATAA-AATA
718529 TATATATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:718678 original size:2 final size:2
Alignment explanation
Indices: 718640--718664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
718630 ACATACATAC
718640 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
718665 AAGTTAAAAT
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:718683 original size:18 final size:16
Alignment explanation
Indices: 718656--718699 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
718646 ATATATATAT
718656 ATATAT-ATAAAGTTAAA
1 ATATATCATAAAG--AAA
718673 ATATATCATAAAGAAA
1 ATATATCATAAAGAAA
718689 ATATATACATA
1 ATATAT-CATA
718700 TATATCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.36
17 10 0.40
18 6 0.24
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (16 bp):
ATATATCATAAAGAAA
Found at i:723170 original size:14 final size:14
Alignment explanation
Indices: 723151--723194 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
723141 CATTGTTTAA
723151 ATAATGATTCTTAG
1 ATAATGATTCTTAG
723165 ATAATGATTCTTAG
1 ATAATGATTCTTAG
723179 ATAATGATTCTTAG
1 ATAATGATTCTTAG
723193 AT
1 AT
723195 TAGAGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
ATAATGATTCTTAG
Found at i:729697 original size:12 final size:12
Alignment explanation
Indices: 729680--729705 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
729670 TCATTATCCA
729680 TTTTATTTTATT
1 TTTTATTTTATT
729692 TTTTATTTTATT
1 TTTTATTTTATT
729704 TT
1 TT
729706 ATTGTAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:734731 original size:56 final size:56
Alignment explanation
Indices: 734652--734797 Score: 283
Period size: 56 Copynumber: 2.6 Consensus size: 56
734642 TTTATTGAAC
*
734652 TTTTAGATTTGGTACTTTTTAGGACGATTGTCCTAAACATTGAGACATAATTGACT
1 TTTTAGATTTGGTACTTTTTAGGACGATTGTCCTAAACATTAAGACATAATTGACT
734708 TTTTAGATTTGGTACTTTTTAGGACGATTGTCCTAAACATTAAGACATAATTGACT
1 TTTTAGATTTGGTACTTTTTAGGACGATTGTCCTAAACATTAAGACATAATTGACT
734764 TTTTAGATTTGGTACTTTTTAGGACGATTGTCCT
1 TTTTAGATTTGGTACTTTTTAGGACGATTGTCCT
734798 TAAAACCTTA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 89 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (56 bp):
TTTTAGATTTGGTACTTTTTAGGACGATTGTCCTAAACATTAAGACATAATTGACT
Found at i:736727 original size:14 final size:15
Alignment explanation
Indices: 736688--736733 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
736678 AATGCATGAC
*
736688 ATGAGCTAAGTATATG
1 ATGAGCTAA-TATATA
736704 ATGATG-TAATAT-TA
1 ATGA-GCTAATATATA
736718 ATGAGCTAATATATA
1 ATGAGCTAATATATA
736733 A
1 A
736734 GCCTTAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
15 6 0.23
16 7 0.27
17 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.35
Consensus pattern (15 bp):
ATGAGCTAATATATA
Found at i:739826 original size:31 final size:31
Alignment explanation
Indices: 739791--739894 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 31
739781 CTGTTGGTGT
739791 TGAACCTATACAAGGAATTACCAGCAGCGAC
1 TGAACCTATACAAGGAATTACCAGCAGCGAC
* * * **
739822 TGAACCTGCCAGAGATAGGAATTACCAGTTAATG-C
1 TGAACCT---ATACA-AGGAATTACCAG-CAGCGAC
*
739857 TGAACCTATACAAGGAATTACCAGCAGCAAC
1 TGAACCTATACAAGGAATTACCAGCAGCGAC
739888 TGAACCT
1 TGAACCT
739895 GTTAAAGTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
30 1 0.02
31 27 0.48
32 3 0.05
34 3 0.05
35 20 0.36
36 2 0.04
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
TGAACCTATACAAGGAATTACCAGCAGCGAC
Found at i:742985 original size:20 final size:20
Alignment explanation
Indices: 742960--743002 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
742950 TATAAGAGCT
742960 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
742980 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
743000 CAT
1 CAT
743003 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:749441 original size:31 final size:31
Alignment explanation
Indices: 749403--749522 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 31
749393 GTTCATAAAA
749403 AATTACCAGTTGGTGCTGAACCTATACAAGG
1 AATTACCAGTTGGTGCTGAACCTATACAAGG
* * * *
749434 AATTACCAGTAGCG-ACTGAACCTGCCAGAGAAAGG
1 AATTACCAGTTG-GTGCTGAACCT---ATA-CAAGG
* * *
749469 AATTACCAGTCGATCCTGAACCTATACAAGG
1 AATTACCAGTTGGTGCTGAACCTATACAAGG
*
749500 AATTACCAG-TAGTGACTGAACCT
1 AATTACCAGTTGGTG-CTGAACCT
749523 GTCAGAGTCT
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
30 1 0.01
31 40 0.58
32 3 0.04
34 2 0.03
35 23 0.33
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (31 bp):
AATTACCAGTTGGTGCTGAACCTATACAAGG
Found at i:749474 original size:35 final size:34
Alignment explanation
Indices: 749430--749529 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 34
749420 GAACCTATAC
749430 AAGGAATTACCAGTAGCGACTGAACCTGCCAGAGA
1 AAGGAATTACCAGTAGCGACTGAACCTG-CAGAGA
* *
749465 AAGGAATTACCAGT--CGATCCTGAACCT--ATA-C
1 AAGGAATTACCAGTAGCGA--CTGAACCTGCAGAGA
*
749496 AAGGAATTACCAGTAGTGACTGAACCTGTCAGAG
1 AAGGAATTACCAGTAGCGACTGAACCTG-CAGAG
749530 TCTTCATACC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
31 22 0.42
32 2 0.04
33 5 0.09
34 2 0.04
35 22 0.42
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (34 bp):
AAGGAATTACCAGTAGCGACTGAACCTGCAGAGA
Found at i:749509 original size:66 final size:66
Alignment explanation
Indices: 749403--749529 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
749393 GTTCATAAAA
* * *
749403 AATTACCAGTTGGTGCTGAACCTATACAAGGAATTACCAGTAGCGACTGAACCTGCCAGAGAAAG
1 AATTACCAGTCGATCCTGAACCTATACAAGGAATTACCAGTAGCGACTGAACCTGCCAGAGAAAG
749468 G
66 G
* *
749469 AATTACCAGTCGATCCTGAACCTATACAAGGAATTACCAGTAGTGACTGAACCTGTCAGAG
1 AATTACCAGTCGATCCTGAACCTATACAAGGAATTACCAGTAGCGACTGAACCTGCCAGAG
749530 TCTTCATACC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (66 bp):
AATTACCAGTCGATCCTGAACCTATACAAGGAATTACCAGTAGCGACTGAACCTGCCAGAGAAAG
G
Found at i:755025 original size:22 final size:22
Alignment explanation
Indices: 755000--755044 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
754990 ATCCATAAAA
* *
755000 AATAAAAAATAAATAAAATAAT
1 AATAAAAAAGAAACAAAATAAT
* *
755022 AATAATAAAGAAACAAGATAAT
1 AATAAAAAAGAAACAAAATAAT
755044 A
1 A
755045 CTATAACAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (22 bp):
AATAAAAAAGAAACAAAATAAT
Found at i:759714 original size:24 final size:23
Alignment explanation
Indices: 759687--759731 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
759677 TTCATTGATT
759687 TTATTCTCTCAAAATTTAATTTCG
1 TTATT-TCTCAAAATTTAATTTCG
* *
759711 TTATTTTTCTAAATTTAATTT
1 TTATTTCTCAAAATTTAATTT
759732 TCAAATTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTTCTCAAAATTTAATTTCG
Found at i:775351 original size:40 final size:40
Alignment explanation
Indices: 775307--775504 Score: 227
Period size: 40 Copynumber: 5.0 Consensus size: 40
775297 ATTTCTATGC
**
775307 ATTTGTAAAGCCTTCAAGTCATTTGTAAAGCCTTTGGGTA
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGGGTA
* * **
775347 ATTTGTAAAGCTTTCGGGTCATTTGTAAAGACTTCAGGTA
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGGGTA
* * ** *
775387 ATTTGTAAAGCTTTTGGGTCATTTGTAAAGCCTTCAGGTC
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGGGTA
* * * *
775427 ATTTGTAAATCCTCCGGGTAATTTGTAAAG-CTTTGGGTT
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGGGTA
* * *
775466 GTTTGTAAAACCTTCGGGTCATTTGTAAATCCTTTGGGT
1 ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGGGT
775505 CATCTGTCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 31 0.23
40 104 0.77
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (40 bp):
ATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGGGTA
Found at i:775403 original size:60 final size:59
Alignment explanation
Indices: 775306--775499 Score: 253
Period size: 60 Copynumber: 3.3 Consensus size: 59
775296 TATTTCTATG
* * *
775306 CATTTGTAAAGCCTTCAAGTCATTTGTAAAGCCTTTGGGTAATTTGTAAAGCTTTCGGGT
1 CATTTGTAAAGCCTTCAGGTAATTTGTAAAG-CTTTGGGTAATTTGTAAAGCCTTCGGGT
* * *
775366 CATTTGTAAAGACTTCAGGTAATTTGTAAAGCTTTTGGGTCATTTGTAAAGCCTTCAGGT
1 CATTTGTAAAGCCTTCAGGTAATTTGTAAAGC-TTTGGGTAATTTGTAAAGCCTTCGGGT
* * * ** *
775426 CATTTGTAAATCCTCCGGGTAATTTGTAAAGCTTTGGGTTGTTTGTAAAACCTTCGGGT
1 CATTTGTAAAGCCTTCAGGTAATTTGTAAAGCTTTGGGTAATTTGTAAAGCCTTCGGGT
*
775485 CATTTGTAAATCCTT
1 CATTTGTAAAGCCTT
775500 TGGGTCATCT
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
59 38 0.32
60 80 0.68
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (59 bp):
CATTTGTAAAGCCTTCAGGTAATTTGTAAAGCTTTGGGTAATTTGTAAAGCCTTCGGGT
Found at i:775504 original size:20 final size:20
Alignment explanation
Indices: 775306--775507 Score: 201
Period size: 20 Copynumber: 10.2 Consensus size: 20
775296 TATTTCTATG
***
775306 CATTTGTAAAGCCTTCAAGT
1 CATTTGTAAAGCCTTTGGGT
775326 CATTTGTAAAGCCTTTGGGT
1 CATTTGTAAAGCCTTTGGGT
*
775346 AATTTGTAAAG-CTTTCGGGT
1 CATTTGTAAAGCCTTT-GGGT
* **
775366 CATTTGTAAAGACTTCAGGT
1 CATTTGTAAAGCCTTTGGGT
* *
775386 AATTTGTAAAGCTTTTGGGT
1 CATTTGTAAAGCCTTTGGGT
**
775406 CATTTGTAAAGCCTTCAGGT
1 CATTTGTAAAGCCTTTGGGT
* **
775426 CATTTGTAAATCCTCCGGGT
1 CATTTGTAAAGCCTTTGGGT
*
775446 AATTTGTAAAG-CTTTGGGT
1 CATTTGTAAAGCCTTTGGGT
** * *
775465 TGTTTGTAAAACCTTCGGGT
1 CATTTGTAAAGCCTTTGGGT
*
775485 CATTTGTAAATCCTTTGGGT
1 CATTTGTAAAGCCTTTGGGT
775505 CAT
1 CAT
775508 CTGTCAATCT
Statistics
Matches: 148, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
19 18 0.12
20 127 0.86
21 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (20 bp):
CATTTGTAAAGCCTTTGGGT
Found at i:777264 original size:25 final size:25
Alignment explanation
Indices: 777205--777282 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 25
777195 ATTATTTCGA
777205 ATTATGATAATTAATT-TTAA-TATT
1 ATTAT-ATAATTAATTATTAATTATT
**
777229 -TTAT-TCTTTAATTATTAATTATT
1 ATTATATAATTAATTATTAATTATT
*
777252 ATTATATAATTAATTATT-ATTAGT
1 ATTATATAATTAATTATTAATTATT
777276 ATT-TATA
1 ATTATATA
777283 CTTTAGGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
21 7 0.16
22 4 0.09
23 12 0.27
24 12 0.27
25 10 0.22
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (25 bp):
ATTATATAATTAATTATTAATTATT
Found at i:790110 original size:20 final size:20
Alignment explanation
Indices: 790084--790137 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
790074 ACAGTCACAA
*
790084 TGGTATCTATACTCCTTTTTG
1 TGGTATC-ATACTCCCTTTTG
790105 -GGTATCAGTACTCCCTTTTG
1 TGGTATCA-TACTCCCTTTTG
790125 TGGTATCGATACT
1 TGGTATC-ATACT
790138 TCCTCGAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 17 0.59
21 10 0.34
22 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (20 bp):
TGGTATCATACTCCCTTTTG
Found at i:790123 original size:21 final size:20
Alignment explanation
Indices: 790084--790137 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
790074 ACAGTCACAA
790084 TGGTATCTATACTCCTTTT-
1 TGGTATCTATACTCCTTTTG
790103 TGGGTATC-AGTACTCCCTTTTG
1 T-GGTATCTA-TACT-CCTTTTG
*
790125 TGGTATCGATACT
1 TGGTATCTATACT
790138 TCCTCGAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.07
20 10 0.33
21 16 0.53
22 2 0.07
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (20 bp):
TGGTATCTATACTCCTTTTG
Found at i:795145 original size:24 final size:25
Alignment explanation
Indices: 795099--795145 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
795089 TTAGCAAGTT
*
795099 TCATTAATGGTATTTTTAGAATTTC
1 TCATTAATGGAATTTTTAGAATTTC
*
795124 TCATTAATTGAATTTTTA-AATT
1 TCATTAATGGAATTTTTAGAATT
795146 CAATTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (25 bp):
TCATTAATGGAATTTTTAGAATTTC
Found at i:814881 original size:59 final size:59
Alignment explanation
Indices: 814754--814882 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 59
814744 CGTAATGCTA
* * ** *
814754 TCCCGAATAAGACACATAAGGTCGTGCCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAG
* * ** *
814813 TCCCAAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAG
814872 TCCCGAATATG
1 TCCCGAATATG
814883 CAGCCTGCTG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTTAAGTACAG
Found at i:821689 original size:59 final size:59
Alignment explanation
Indices: 821597--821726 Score: 188
Period size: 59 Copynumber: 2.2 Consensus size: 59
821587 CCGTAGTGCT
* **
821597 ATCCCGAATATGACACATAAGGTCGTGCCCACCATCTGTACTAGGTATCCTTAAGTACA
1 ATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACA
* * **
821656 ATCCCGAATATGACACATAAGGTCGTTCCCACCATATACACTAGGTATCCTTTAGTGTA
1 ATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACA
*
821715 TTCCCGAATATG
1 ATCCCGAATATG
821727 CAGCCTGCTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (59 bp):
ATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACA
Found at i:847823 original size:20 final size:19
Alignment explanation
Indices: 847795--847856 Score: 90
Period size: 20 Copynumber: 3.2 Consensus size: 19
847785 ATTAGGCTAA
847795 GAATCTGAAAGTAAAGTTAT
1 GAATCTGAAAGTAAA-TTAT
*
847815 GAATTTGAAAGTAAATTTAT
1 GAATCTGAAAGTAAA-TTAT
847835 GAATCTGAAA-TAAATTAT
1 GAATCTGAAAGTAAATTAT
847853 GAAT
1 GAAT
847857 TTGGAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
18 8 0.21
19 4 0.10
20 27 0.69
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (19 bp):
GAATCTGAAAGTAAATTAT
Found at i:868506 original size:20 final size:20
Alignment explanation
Indices: 868481--868519 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
868471 TGTCTGACTC
*
868481 TGAAAGCAAAGTTATGAATT
1 TGAAAGCAAAGCTATGAATT
*
868501 TGAAAGTAAAGCTATGAAT
1 TGAAAGCAAAGCTATGAAT
868520 CTAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (20 bp):
TGAAAGCAAAGCTATGAATT
Found at i:873085 original size:18 final size:18
Alignment explanation
Indices: 873061--873106 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
873051 CTTAGGATTA
873061 TCTTTAGGTTTTTTA-TT
1 TCTTTAGGTTTTTTACTT
*
873078 TCCTTTAGGTATTTTACTT
1 T-CTTTAGGTTTTTTACTT
873097 TCTTTAGGTT
1 TCTTTAGGTT
873107 ATCTCAATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.84
19 3 0.12
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (18 bp):
TCTTTAGGTTTTTTACTT
Found at i:878293 original size:13 final size:13
Alignment explanation
Indices: 878249--878295 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
878239 ATGTTCTTTG
*
878249 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
878263 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
878275 TTTATTTAAAATAA
1 -ATATTTAAAATAA
878289 ATATTTA
1 ATATTTA
878296 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:879675 original size:3 final size:3
Alignment explanation
Indices: 879669--879741 Score: 112
Period size: 3 Copynumber: 24.7 Consensus size: 3
879659 TTTATTTTTT
* *
879669 TAA TAA TAT TTA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
879716 TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
879742 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:880264 original size:113 final size:114
Alignment explanation
Indices: 880063--880702 Score: 1064
Period size: 113 Copynumber: 5.7 Consensus size: 114
880053 AGAATTATTA
* * * *
880063 AACAAGTTCTTCTTATTATGAACTTTTTCTTCTTTCTGCAGATGACGAGTTCTTCTCATTATGAA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAA
* * *
880128 CTCTTC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTG
63 CTCTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
880179 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
880243 TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
66 TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
880292 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
880356 TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
66 TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
*
880405 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** *
880469 TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTG
66 TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
* *
880518 AACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
880583 TT-TCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTG
66 TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
880631 AACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
880693 TT-TCTGGAAA
66 TTCTCTGGAAA
880703 ATCTAATTCA
Statistics
Matches: 505, Mismatches: 17, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
110 50 0.10
112 3 0.01
113 411 0.81
114 2 0.00
116 39 0.08
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (114 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAACAAAAAGTTG
Found at i:882006 original size:83 final size:83
Alignment explanation
Indices: 881450--881993 Score: 1052
Period size: 83 Copynumber: 6.6 Consensus size: 83
881440 GTAGTTCCTA
881450 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
881515 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
881533 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
*
881598 ATTCAATGATTGGTTTTG
66 ATTCAATGATTGGTTCTG
881616 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
881681 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
881699 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
881764 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
881782 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
881847 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
881865 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
*
881930 ATTCAATGATTGGTTCTA
66 ATTCAATGATTGGTTCTG
*
881948 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTAT
881994 TGGCCAATTC
Statistics
Matches: 455, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 455 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:883159 original size:10 final size:10
Alignment explanation
Indices: 883146--883197 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
883136 TTGACCCTCC
883146 TTTTTCTTTT
1 TTTTTCTTTT
*
883156 TTTTTCTCTCT
1 TTTTTCT-TTT
883167 TTTTTCTTTTT
1 TTTTTC-TTTT
883178 TTTTTCTTTT
1 TTTTTCTTTT
*
883188 TCTTTCTTTT
1 TTTTTCTTTT
883198 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 20 0.54
11 16 0.43
12 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:883172 original size:21 final size:20
Alignment explanation
Indices: 883146--883197 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
883136 TTGACCCTCC
883146 TTTTTCTTTTTTTTTCTCTCT
1 TTTTTCTTTTTTTTT-TCTCT
*
883167 TTTTTCTTTTTTTTTTCTTT
1 TTTTTCTTTTTTTTTTCTCT
883187 TTCTTTCTTTT
1 TT-TTTCTTTT
883198 CTTCAAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTCTCT
Found at i:883176 original size:26 final size:26
Alignment explanation
Indices: 883145--883200 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
883135 CTTGACCCTC
*
883145 CTTTTTCTTTTTTTTTCTCTCTT-TTTT
1 CTTTTT-TTTTTCTTTCTCT-TTCTTTT
*
883172 CTTTTTTTTTTCTTTTTCTTTCTTTT
1 CTTTTTTTTTTCTTTCTCTTTCTTTT
883198 CTT
1 CTT
883201 CAAGCATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 2 0.08
26 18 0.69
27 6 0.23
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (26 bp):
CTTTTTTTTTTCTTTCTCTTTCTTTT
Found at i:895859 original size:3 final size:3
Alignment explanation
Indices: 895853--895952 Score: 157
Period size: 3 Copynumber: 33.7 Consensus size: 3
895843 TTTATTTTTT
* * *
895853 TAA TAA TAT TTA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
895900 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
895948 TAA TA
1 TAA TA
895953 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 87 0.98
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Done.