Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 150 of 163
Found at i:41190184 original size:25 final size:23
Alignment explanation
Indices: 41190150--41190200 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
41190140 AAAATAAAAA
41190150 AAAATCAAATACTAAATAAAATATT
1 AAAATCAAATA-TAAATAAAAT-TT
*
41190175 AAAATCAAATATAAATAATATTT
1 AAAATCAAATATAAATAAAATTT
41190198 AAA
1 AAA
41190201 CCAGTTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 9 0.36
25 11 0.44
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAATCAAATATAAATAAAATTT
Found at i:41191039 original size:9 final size:9
Alignment explanation
Indices: 41191015--41191075 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 9
41191005 AAAAAATAAT
41191015 TAAAATTTA
1 TAAAATTTA
41191024 TATAAATTTA
1 TA-AAATTTA
41191034 TAAAATTTA
1 TAAAATTTA
*
41191043 TTAAAAGTTA
1 -TAAAATTTA
*
41191053 TGAAAA-CTA
1 T-AAAATTTA
*
41191062 TAAAACTTA
1 TAAAATTTA
41191071 TAAAA
1 TAAAA
41191076 AATAATAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
8 4 0.09
9 20 0.44
10 21 0.47
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (9 bp):
TAAAATTTA
Found at i:41191053 original size:19 final size:18
Alignment explanation
Indices: 41191015--41191075 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
41191005 AAAAAATAAT
*
41191015 TAAAATTTATATAAATTTA
1 TAAAATTTATA-AAACTTA
*
41191034 TAAAATTTATTAAAAGTTA
1 TAAAATTTA-TAAAACTTA
*
41191053 TGAAAA-CTATAAAACTTA
1 T-AAAATTTATAAAACTTA
41191071 TAAAA
1 TAAAA
41191076 AATAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 4 0.11
18 9 0.24
19 18 0.49
20 6 0.16
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATTTATAAAACTTA
Found at i:41191202 original size:25 final size:24
Alignment explanation
Indices: 41191165--41191211 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
41191155 TTAATGTAAC
41191165 ATTTGATACTTAAACTCTTTTTTTA
1 ATTTGATACTT-AACTCTTTTTTTA
* * *
41191190 ATTTGGTATTTAATTCTTTTTT
1 ATTTGATACTTAACTCTTTTTT
41191212 GATTCAATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.62
Consensus pattern (24 bp):
ATTTGATACTTAACTCTTTTTTTA
Found at i:41192406 original size:120 final size:120
Alignment explanation
Indices: 41192277--41192519 Score: 459
Period size: 120 Copynumber: 2.0 Consensus size: 120
41192267 AAAAAAATGG
* *
41192277 GAAAAATATAAAATTTAAGTATGGTTGGTTCAAAAGAAAATAGAAAGGGTGATCATTTTTCATAT
1 GAAAAATATAAAATTTAAGTATGGTTAGTTCAAAAGAAAATAGAAAAGGTGATCATTTTTCATAT
41192342 TAATATATAAAAATCAATCATTCCAACACGAATGAAACCTCAAAAACACTTAAAA
66 TAATATATAAAAATCAATCATTCCAACACGAATGAAACCTCAAAAACACTTAAAA
41192397 GAAAAATATAAAATTTAAGTATGGTTAGTTCAAAAGAAAATAGAAAAGGTGATCATTTTTCATAT
1 GAAAAATATAAAATTTAAGTATGGTTAGTTCAAAAGAAAATAGAAAAGGTGATCATTTTTCATAT
*
41192462 TAATATATAAAAATCAATCATTCCAACACGAATGAAACCTCGAAAACACTTAAAA
66 TAATATATAAAAATCAATCATTCCAACACGAATGAAACCTCAAAAACACTTAAAA
41192517 GAA
1 GAA
41192520 TCAAAACTTA
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (120 bp):
GAAAAATATAAAATTTAAGTATGGTTAGTTCAAAAGAAAATAGAAAAGGTGATCATTTTTCATAT
TAATATATAAAAATCAATCATTCCAACACGAATGAAACCTCAAAAACACTTAAAA
Found at i:41203223 original size:30 final size:30
Alignment explanation
Indices: 41203168--41203229 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
41203158 TATAACTTGC
* *
41203168 TTCAATTGATTCATGCAGTAGGATTCAAAT
1 TTCAATTGATTCATGCAGCAAGATTCAAAT
* *
41203198 TTCAATTGATTCATGCCGCAAGATTCGAAT
1 TTCAATTGATTCATGCAGCAAGATTCAAAT
41203228 TT
1 TT
41203230 GAGATGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (30 bp):
TTCAATTGATTCATGCAGCAAGATTCAAAT
Found at i:41206295 original size:22 final size:22
Alignment explanation
Indices: 41206270--41206388 Score: 89
Period size: 22 Copynumber: 5.4 Consensus size: 22
41206260 TACATAAACT
*
41206270 AAAAAATTTGAATTATAGGGAC
1 AAAAAATTTGAATTACAGGGAC
* * *
41206292 AAAAAATTTGATTTACAGAGAT
1 AAAAAATTTGAATTACAGGGAC
** *
41206314 AAAAAAAATGAATTACAGGGAGGG
1 AAAAAATTTGAATTACAGGGA--C
**
41206338 AAAAAA--TGAACCACAGGGAC
1 AAAAAATTTGAATTACAGGGAC
* *
41206358 AAAAAAATTCGAATTATAGGGAC
1 -AAAAAATTTGAATTACAGGGAC
*
41206381 CAAAAATT
1 AAAAAATT
41206389 CAAATTATAG
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
21 6 0.08
22 53 0.71
23 10 0.13
24 6 0.08
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.20
Consensus pattern (22 bp):
AAAAAATTTGAATTACAGGGAC
Found at i:41206386 original size:44 final size:43
Alignment explanation
Indices: 41206270--41206388 Score: 105
Period size: 44 Copynumber: 2.7 Consensus size: 43
41206260 TACATAAACT
* *** *
41206270 AAAAAATTTGAATTATAGGGACAAAAAATTTGATTTACAGAGAT
1 AAAAAAATTGAATTATAGGGACAAAAAA-TTGAACCACAGAGAC
* * * *
41206314 AAAAAAAATGAATTACAGGGAGGGAAAAAA-TGAACCACAGGGAC
1 AAAAAAATTGAATTATAGGGA--CAAAAAATTGAACCACAGAGAC
*
41206358 AAAAAAATTCGAATTATAGGGACCAAAAATT
1 AAAAAAATT-GAATTATAGGGACAAAAAATT
41206389 CAAATTATAG
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
43 5 0.09
44 36 0.62
45 11 0.19
46 6 0.10
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.20
Consensus pattern (43 bp):
AAAAAAATTGAATTATAGGGACAAAAAATTGAACCACAGAGAC
Found at i:41206409 original size:24 final size:23
Alignment explanation
Indices: 41206352--41206410 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
41206342 AATGAACCAC
*
41206352 AGGGACAAAAAAATTCGAATTAT
1 AGGGACAAAAAAATTCAAATTAT
*
41206375 AGGGAC-CAAAAATTCAAATTAT
1 AGGGACAAAAAAATTCAAATTAT
*
41206397 AGGTACAATAAAAA
1 AGGGACAA-AAAAA
41206411 AGACAAGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 19 0.63
23 6 0.20
24 5 0.17
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.20
Consensus pattern (23 bp):
AGGGACAAAAAAATTCAAATTAT
Found at i:41212281 original size:41 final size:41
Alignment explanation
Indices: 41212236--41212325 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
41212226 ACACGATCTG
* *
41212236 GGCACACGGGCGTGTACATGACTGTGTGATACACACGGGTT
1 GGCACACGGGCATGTACATGACTGTGTGACACACACGGGTT
* * *
41212277 GGCACACGGGCATGTACATGATTGTGTGACATACATGGGTT
1 GGCACACGGGCATGTACATGACTGTGTGACACACACGGGTT
41212318 GGCACACG
1 GGCACACG
41212326 ACCGTGTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.22
Consensus pattern (41 bp):
GGCACACGGGCATGTACATGACTGTGTGACACACACGGGTT
Found at i:41219020 original size:54 final size:56
Alignment explanation
Indices: 41218858--41219022 Score: 165
Period size: 56 Copynumber: 3.0 Consensus size: 56
41218848 GTTTTTTGAA
* * * * * *
41218858 GGCACACGGGGGTGTATCCAGAGTGTGTGTCTATACTG-TTGAGAGGTATACGGGCT
1 GGCACACGGAGGTGTGTCCAGGGTGTGTGTCTATACTGTTTG-GAGGCACACGAGCT
* * * * * * *
41218914 GGCATACGGGGGTGTGTTCAGGGCGTGTGTCTATACTGTTTGAAGACTCACGAGCT
1 GGCACACGGAGGTGTGTCCAGGGTGTGTGTCTATACTGTTTGGAGGCACACGAGCT
* *
41218970 GGCACA-TGAGG-GTGTCCAGGGTGTGTGTTTATACTGTTTGGAGGCACACGAGC
1 GGCACACGGAGGTGTGTCCAGGGTGTGTGTCTATACTGTTTGGAGGCACACGAGC
41219023 ATGGGTCAAG
Statistics
Matches: 88, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
54 36 0.41
55 3 0.03
56 46 0.52
57 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.37, T:0.27
Consensus pattern (56 bp):
GGCACACGGAGGTGTGTCCAGGGTGTGTGTCTATACTGTTTGGAGGCACACGAGCT
Found at i:41219577 original size:40 final size:40
Alignment explanation
Indices: 41219533--41219630 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
41219523 CTGAGTTGGT
* * *
41219533 AGTGACACTGTAAACACTACAATATTATAACTGAACCGGC
1 AGTGACACTGTAAACACTACAAGATTACAACTAAACCGGC
* * * *
41219573 AGTGACACTGTAAATACTACAAGGTTACCACTAAACTGGC
1 AGTGACACTGTAAACACTACAAGATTACAACTAAACCGGC
41219613 AGTGACACTGTAAACACT
1 AGTGACACTGTAAACACT
41219631 GCAACGTGTC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
AGTGACACTGTAAACACTACAAGATTACAACTAAACCGGC
Found at i:41219739 original size:29 final size:27
Alignment explanation
Indices: 41219706--41219841 Score: 85
Period size: 29 Copynumber: 4.7 Consensus size: 27
41219696 AGTATCACGT
41219706 TTGCATCTGTAACTGTATTTGTATCATG
1 TTGCATCTGTAACTGTATTTGTA-CATG
* *
41219734 TCTGCAT-TCGTAACTATATTTGTGACATAA
1 T-TGCATCT-GTAACTGTATTTGT-ACAT-G
* * ** *
41219764 CTGCATTTGTAACTACATCTGTAACATG
1 TTGCATCTGTAACTGTATTTGT-ACATG
* *
41219792 ATTGTATCTGTAACTGTATGTGTGACATG
1 -TTGCATCTGTAACTGTATTTGT-ACATG
* *
41219821 ATTGTATCTGTAATTGTATTT
1 -TTGCATCTGTAACTGTATTT
41219842 ACATTATTTC
Statistics
Matches: 86, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.02
29 82 0.95
30 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (27 bp):
TTGCATCTGTAACTGTATTTGTACATG
Found at i:41219802 original size:17 final size:17
Alignment explanation
Indices: 41219780--41219833 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
41219770 TTGTAACTAC
41219780 ATCTGTAACATGATTGT
1 ATCTGTAACATGATTGT
41219797 ATCTGTAAC-----TGT
1 ATCTGTAACATGATTGT
* *
41219809 ATGTGTGACATGATTGT
1 ATCTGTAACATGATTGT
41219826 ATCTGTAA
1 ATCTGTAA
41219834 TTGTATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
12 10 0.36
17 18 0.64
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (17 bp):
ATCTGTAACATGATTGT
Found at i:41222673 original size:2 final size:2
Alignment explanation
Indices: 41222666--41222690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41222656 GTAAAAAGTA
41222666 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
41222691 GCTGAAACTA
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:41228006 original size:23 final size:23
Alignment explanation
Indices: 41227975--41228021 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
41227965 AGATTGAAAT
*
41227975 AATATTCATATTTATATTAT-TAA
1 AATAGTCATATTT-TATTATATAA
41227998 AATAGTCATATTTTATTATATAA
1 AATAGTCATATTTTATTATATAA
41228021 A
1 A
41228022 GTGTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
AATAGTCATATTTTATTATATAA
Found at i:41238042 original size:596 final size:580
Alignment explanation
Indices: 41236926--41238108 Score: 2159
Period size: 596 Copynumber: 2.0 Consensus size: 580
41236916 TTGTGAAGTG
41236926 TCAACCAGAGCTAACCAATTTTCTTATAACAAGTTTCGTATTGAGTTAAGCCCACGTTTGATTTA
1 TCAACCAGAGCTAACCAATTTTCTTATAACAAGTTTCGTATTGAGTTAAGCCCACGTTTGATTTA
*
41236991 TTAAAATTGAATAAAATTATAATGAAATAAAATTGTAATTAATAATTCAATTATTGTTTTGTTGA
66 TTAAAATTGAATAAAATTATAATGAAATAAAATTGTAATCAATAATTCAATTATTGTTTTGTTGA
*
41237056 ATGTAATGAAATAGAACTGTAATAATACTCTAGTATTTGATTGAATGTAATAGATGATATGATAA
131 ATGTAATGAAATAGAACTGTAACAATACTCTAGTATTTGATTGAATGTAATAGATGATATGATAA
*
41237121 TATAGGGGAAAAAACTAAAATAATCAGAGCACCCTTAGCAAATTATTTTTAGATAGATGATTATT
196 TATAGGGAAAAAAACTAAAATAATCAGAGCACCCTTAGCAAATTATTTTTAGATAGATGATTATT
41237186 GTTGTTATTATTATTGTTATTAAATTTTAATAGGATTATTATTAAATATAATTTAATCATATTCT
261 GTTGTTATTATTATTGTTATTAAATTTTAATAGGATTATTATTAAATATAATTTAATCATATTCT
41237251 TAATTAATTATTTTTATATTAAAATATTTTATTTAAATTATATTTTGAAATAATTTATTTTATAT
326 TAATTAATTATTTTTATATTAAAATATTTTATTTAAATTATATTTTGAAATAATTTATTTTATAT
41237316 TAAATTATATTACATATTTTATTTTTATATTTTTCATATCCAAATTTCAAAAGACTAATTTGAAA
391 TAAATTATATTACATATTTTATTTTTATATTTTTCATATCCAAATTTCAAAAGACTAATTTGAAA
41237381 ATTAATTTTATTTTGCTATTCAATGTTGCATGGAATAACTATTCTTCGGTATCACTAAAAAATAG
456 ATTAATTTTATTTTGCTATTCAATGTTGCATGGAATAACTATTCTTCGGTATCACTAAAAAATAG
41237446 CTATTACGAGAGTGTCAGTAATAGGAAAGTAATAACTATTCCATTGAATGAATATTATAT
521 CTATTACGAGAGTGTCAGTAATAGGAAAGTAATAACTATTCCATTGAATGAATATTATAT
*
41237506 TCAACCAGAGCTAACCAATTTTCTTATAACAAGTTTGGTATTGAGTTAAGCCCACGTTTGATTTA
1 TCAACCAGAGCTAACCAATTTTCTTATAACAAGTTTCGTATTGAGTTAAGCCCACGTTTGATTTA
*
41237571 TTGAAATTGAATAAAATTATAATTGAATAGAATCGTAATAAAATAAAGTTGTAATCAATAATTCA
66 TTAAAATTGAATAAAA-T-T-A-T-AAT-G-A----AAT---A-AAA-TTGTAATCAATAATTCA
41237636 ATTATTGTTTTGTTGAATGTAATGAAATAGAACTGTAACAATACTCTAGTATTTGATTGAATGTA
115 ATTATTGTTTTGTTGAATGTAATGAAATAGAACTGTAACAATACTCTAGTATTTGATTGAATGTA
*
41237701 ATAGATGATATGATAATATAGGGAAAAAAACTAAAATGATCAGAGCACCCTTAGCAAATTATTTT
180 ATAGATGATATGATAATATAGGGAAAAAAACTAAAATAATCAGAGCACCCTTAGCAAATTATTTT
41237766 TAGATAGATGATTATTGTTGTTATTATTATTGTTATTAAATTTTAATAGGATTATTATTAAATAT
245 TAGATAGATGATTATTGTTGTTATTATTATTGTTATTAAATTTTAATAGGATTATTATTAAATAT
41237831 AATTTAATCATATTCTTAATTAATTATTTTTATATTAAAATATTTTATTTAAATTATATTTTGAA
310 AATTTAATCATATTCTTAATTAATTATTTTTATATTAAAATATTTTATTTAAATTATATTTTGAA
*
41237896 ATAATTTATTTTATATTAAATTATATTGCATATTTTATTTTTATATTTTTCATATCCAAATTTCA
375 ATAATTTATTTTATATTAAATTATATTACATATTTTATTTTTATATTTTTCATATCCAAATTTCA
41237961 AAAGACTAATTTGAAAATTAATTTTATTTTGCTATTCAATGTTGCATGGAATAACTATTCTTCGG
440 AAAGACTAATTTGAAAATTAATTTTATTTTGCTATTCAATGTTGCATGGAATAACTATTCTTCGG
41238026 TATCACTAAAAAATAGCTATTACGAGAGTGTCAGTAATAGGAAAGTAATAACTATTCCATTGAAT
505 TATCACTAAAAAATAGCTATTACGAGAGTGTCAGTAATAGGAAAGTAATAACTATTCCATTGAAT
41238091 GAATATTATAT
570 GAATATTATAT
41238102 TCAACCA
1 TCAACCA
41238109 AACAAAGAAA
Statistics
Matches: 580, Mismatches: 7, Indels: 16
0.96 0.01 0.03
Matches are distributed among these distances:
580 79 0.14
581 1 0.00
582 1 0.00
583 1 0.00
584 1 0.00
585 3 0.01
586 1 0.00
587 1 0.00
591 3 0.01
594 1 0.00
595 3 0.01
596 485 0.84
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (580 bp):
TCAACCAGAGCTAACCAATTTTCTTATAACAAGTTTCGTATTGAGTTAAGCCCACGTTTGATTTA
TTAAAATTGAATAAAATTATAATGAAATAAAATTGTAATCAATAATTCAATTATTGTTTTGTTGA
ATGTAATGAAATAGAACTGTAACAATACTCTAGTATTTGATTGAATGTAATAGATGATATGATAA
TATAGGGAAAAAAACTAAAATAATCAGAGCACCCTTAGCAAATTATTTTTAGATAGATGATTATT
GTTGTTATTATTATTGTTATTAAATTTTAATAGGATTATTATTAAATATAATTTAATCATATTCT
TAATTAATTATTTTTATATTAAAATATTTTATTTAAATTATATTTTGAAATAATTTATTTTATAT
TAAATTATATTACATATTTTATTTTTATATTTTTCATATCCAAATTTCAAAAGACTAATTTGAAA
ATTAATTTTATTTTGCTATTCAATGTTGCATGGAATAACTATTCTTCGGTATCACTAAAAAATAG
CTATTACGAGAGTGTCAGTAATAGGAAAGTAATAACTATTCCATTGAATGAATATTATAT
Found at i:41238685 original size:11 final size:11
Alignment explanation
Indices: 41238669--41238695 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41238659 ATTAAATTAA
41238669 AAAATATTATT
1 AAAATATTATT
41238680 AAAATATTATT
1 AAAATATTATT
41238691 AAAAT
1 AAAAT
41238696 TTTGTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATATTATT
Found at i:41244628 original size:21 final size:19
Alignment explanation
Indices: 41244592--41244643 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
41244582 TGACTTGAAA
41244592 ATTAATTTTCAA-TAATATCG
1 ATTAATTTT-AATTAAT-TCG
*
41244612 TATTAATTTTAATTAATTTG
1 -ATTAATTTTAATTAATTCG
41244632 ATTAA-TTTAATT
1 ATTAATTTTAATT
41244644 TTACTTTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.24
19 5 0.17
20 4 0.14
21 13 0.45
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (19 bp):
ATTAATTTTAATTAATTCG
Found at i:41246280 original size:30 final size:28
Alignment explanation
Indices: 41246239--41246539 Score: 137
Period size: 30 Copynumber: 10.2 Consensus size: 28
41246229 TGTTTTATTT
* *
41246239 AAAAATCATATTTTAACCCTCAAACTTTTC
1 AAAAATTATATTTT-ACCC-CAAACTTTCC
* *
41246269 AAAAATTATA-TTTCCCCCGAACTTTCC
1 AAAAATTATATTTTACCCCAAACTTTCC
*
41246296 AAAAATTATGTTTTGACTCCCAAAC-TTCC
1 AAAAATTATATTTT-AC-CCCAAACTTTCC
* * ** *
41246325 TAAAAATTTAGATTTGATTCCAAACTTCCC
1 -AAAAA-TTATATTTTACCCCAAACTTTCC
* * *
41246355 TAAAATTCAAATTTTACCCCCAAACTTTCA
1 AAAAATT-ATATTTTA-CCCCAAACTTTCC
* **
41246385 AAAAATT-TGGATTTGACCAGTAAACTTTCC
1 AAAAATTAT--ATTTTACC-CCAAACTTTCC
* *
41246415 AAAAATT-TGAATTTAACCCTTAAAC-TTCC
1 AAAAATTAT--ATTTTACCC-CAAACTTTCC
* * * *
41246444 TAAAATTTTGGATTTGACCCCAAACTTCCC
1 AAAAATTAT--ATTTTACCCCAAACTTTCC
* * *
41246474 AAAAATTTAGATTTGACCCCTAAACTTCCC
1 AAAAA-TTATATTTTACCCC-AAACTTTCC
* *
41246504 AAAAATTTATATTTGACCCTCAAA-TTCCC
1 AAAAA-TTATATTTTACCC-CAAACTTTCC
41246533 AAAAATT
1 AAAAATT
41246540 TAGATTTGAC
Statistics
Matches: 216, Mismatches: 38, Indels: 36
0.74 0.13 0.12
Matches are distributed among these distances:
27 17 0.08
28 10 0.05
29 60 0.28
30 120 0.56
31 9 0.04
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAAATTATATTTTACCCCAAACTTTCC
Found at i:41246347 original size:29 final size:29
Alignment explanation
Indices: 41246283--41246596 Score: 256
Period size: 30 Copynumber: 10.6 Consensus size: 29
41246273 ATTATATTTC
* * *
41246283 CCCCGAACTTTCCAAAAA-TTATGTTTTGA
1 CCCCAAACTTCCCAAAAATTTA-GATTTGA
*
41246312 CTCCCAAACTTCCTAAAAATTTAGATTTGA
1 C-CCCAAACTTCCCAAAAATTTAGATTTGA
** * * * *
41246342 TTCCAAACTTCCCTAAAATTCAAATTTTA
1 CCCCAAACTTCCCAAAAATTTAGATTTGA
* * *
41246371 CCCCCAAACTTTCAAAAAATTTGGATTTGA
1 -CCCCAAACTTCCCAAAAATTTAGATTTGA
** * *
41246401 CCAGTAAACTTTCCAAAAATTT-GAATTTAA
1 CC-CCAAACTTCCCAAAAATTTAG-ATTTGA
* * * *
41246431 CCCTTAAACTTCCTAAAATTTTGGATTTGA
1 CCC-CAAACTTCCCAAAAATTTAGATTTGA
41246461 CCCCAAACTTCCCAAAAATTTAGATTTGA
1 CCCCAAACTTCCCAAAAATTTAGATTTGA
*
41246490 CCCCTAAACTTCCCAAAAATTTATATTTGA
1 CCCC-AAACTTCCCAAAAATTTAGATTTGA
41246520 CCCTCAAA-TTCCCAAAAATTTAGATTTGA
1 CCC-CAAACTTCCCAAAAATTTAGATTTGA
** * * * *
41246549 CCCTTGAACTTCCCTAAAATTCAAATTTAGC
1 CCC-CAAACTTCCCAAAAATTTAGATTT-GA
*
41246580 CCCCAAACTTTCCAAAA
1 CCCCAAACTTCCCAAAA
41246597 TTTCATTTTG
Statistics
Matches: 229, Mismatches: 45, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
29 78 0.34
30 142 0.62
31 9 0.04
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (29 bp):
CCCCAAACTTCCCAAAAATTTAGATTTGA
Found at i:41246559 original size:59 final size:59
Alignment explanation
Indices: 41246283--41246596 Score: 267
Period size: 59 Copynumber: 5.3 Consensus size: 59
41246273 ATTATATTTC
* * * * *
41246283 CCCCGAACTTTCCAAAAA-TTATGTTTTGACTCC-CAAACTTCCTAAAAATTTAGATTTGA
1 CCCCAAACTTCCCAAAAATTTA-GATTTGAC-CCTTAAACTTCCCAAAAATTTAGATTTGA
** * * * * ** * * *
41246342 TTCCAAACTTCCCTAAAATTCAAATTTTACCCCCAAACTTTCAAAAAATTTGGATTTGA
1 CCCCAAACTTCCCAAAAATTTAGATTTGACCCTTAAACTTCCCAAAAATTTAGATTTGA
** * * * * *
41246401 CCAGTAAACTTTCCAAAAATTT-GAATTTAACCCTTAAACTTCCTAAAATTTTGGATTTGA
1 CC-CCAAACTTCCCAAAAATTTAG-ATTTGACCCTTAAACTTCCCAAAAATTTAGATTTGA
* *
41246461 CCCCAAACTTCCCAAAAATTTAGATTTGACCCCTAAACTTCCCAAAAATTTATATTTGA
1 CCCCAAACTTCCCAAAAATTTAGATTTGACCCTTAAACTTCCCAAAAATTTAGATTTGA
* * * * *
41246520 CCCTCAAA-TTCCCAAAAATTTAGATTTGACCCTTGAACTTCCCTAAAATTCAAATTTAGC
1 CCC-CAAACTTCCCAAAAATTTAGATTTGACCCTTAAACTTCCCAAAAATTTAGATTT-GA
*
41246580 CCCCAAACTTTCCAAAA
1 CCCCAAACTTCCCAAAA
41246597 TTTCATTTTG
Statistics
Matches: 205, Mismatches: 42, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
58 2 0.01
59 138 0.67
60 65 0.32
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (59 bp):
CCCCAAACTTCCCAAAAATTTAGATTTGACCCTTAAACTTCCCAAAAATTTAGATTTGA
Found at i:41246559 original size:89 final size:90
Alignment explanation
Indices: 41246244--41246610 Score: 281
Period size: 89 Copynumber: 4.1 Consensus size: 90
41246234 TATTTAAAAA
* ** * * * *
41246244 TCATATTTTAACCCTCAAACTTTTCAAAAA-TTATATTT-CCCCCGAACTTTCCAAAAA-TTATG
1 TCATA-TTTGACCCTCAAACTTCCCAAAAATTTAGATTTGACCCCAAACTTCCCAAAAATTTA-G
* *
41246306 TTTTGACTCCC-AAACTTCCTAAAAATT
64 ATTTGAC-CCCTAAACTTCCCAAAAATT
* ** * * * * * * *
41246333 T-AGATTTGATTC-CAAACTTCCCTAAAATTCAAATTTTACCCCCAAACTTTCAAAAAATTTGGA
1 TCATATTTGACCCTCAAACTTCCCAAAAATTTAGATTTGA-CCCCAAACTTCCCAAAAATTTAGA
** *
41246396 TTTGACCAGTAAACTTTCCAAAAATT
65 TTTGACCCCTAAACTTCCCAAAAATT
* * * * * *
41246422 TGA-ATTTAACCCTTAAACTTCCTAAAATTTTGGATTTGACCCCAAACTTCCCAAAAATTTAGAT
1 TCATATTTGACCCTCAAACTTCCCAAAAATTTAGATTTGACCCCAAACTTCCCAAAAATTTAGAT
41246486 TTGACCCCTAAACTTCCCAAAAATT
66 TTGACCCCTAAACTTCCCAAAAATT
** * * *
41246511 T-ATATTTGACCCTCAAA-TTCCCAAAAATTTAGATTTGACCCTTGAACTTCCCTAAAATTCAAA
1 TCATATTTGACCCTCAAACTTCCCAAAAATTTAGATTTGACCC-CAAACTTCCCAAAAATTTAGA
* *
41246574 TTT-AGCCCCCAAACTTTCC-AAAATT
65 TTTGA-CCCCTAAACTTCCCAAAAATT
41246599 TCAT-TTTGACCC
1 TCATATTTGACCC
41246611 CTTTTTCCTT
Statistics
Matches: 220, Mismatches: 47, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
86 12 0.05
87 11 0.05
88 41 0.19
89 135 0.61
90 21 0.10
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (90 bp):
TCATATTTGACCCTCAAACTTCCCAAAAATTTAGATTTGACCCCAAACTTCCCAAAAATTTAGAT
TTGACCCCTAAACTTCCCAAAAATT
Found at i:41248559 original size:16 final size:17
Alignment explanation
Indices: 41248531--41248574 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
41248521 CAAAAATAGT
41248531 AAATTTT-TAATTTA-A
1 AAATTTTATAATTTATA
*
41248546 AACTTTTATAATTTATA
1 AAATTTTATAATTTATA
41248563 AAATTTTA-AATT
1 AAATTTTATAATT
41248575 AATACAGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 11 0.44
17 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTTTATAATTTATA
Found at i:41254093 original size:3 final size:3
Alignment explanation
Indices: 41254085--41254124 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41254075 ATTCATACCT
41254085 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41254125 ATATGTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41262140 original size:28 final size:28
Alignment explanation
Indices: 41262108--41262170 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
41262098 GTTTAAACTA
** * **
41262108 AAAAAATTAATTTTATTTGTTTCAATTT
1 AAAAAATTAAACTTATTTGCTTCAAAAT
41262136 AAAAAATTAAACTTATTTGCTTCAAAAT
1 AAAAAATTAAACTTATTTGCTTCAAAAT
41262164 AAAAAAT
1 AAAAAAT
41262171 AAAAAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (28 bp):
AAAAAATTAAACTTATTTGCTTCAAAAT
Found at i:41262605 original size:2 final size:2
Alignment explanation
Indices: 41262598--41262628 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41262588 AATAGAACTT
41262598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41262629 GTGTCGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41264547 original size:39 final size:40
Alignment explanation
Indices: 41264477--41264557 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
41264467 GAAGCTGAGA
*
41264477 AAAAGGGAATATAAATTTGTTTTTGTAACTAAAACACCATG
1 AAAAGGGAATATAAA-TTGTTTTTGTAACTAAAACACAATG
* *
41264518 AAAAGGGATTATAAA-TGTTTTTGTAACTAAATCACAATG
1 AAAAGGGAATATAAATTGTTTTTGTAACTAAAACACAATG
41264557 A
1 A
41264558 CACATTGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 23 0.62
41 14 0.38
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (40 bp):
AAAAGGGAATATAAATTGTTTTTGTAACTAAAACACAATG
Found at i:41265302 original size:12 final size:12
Alignment explanation
Indices: 41265285--41265310 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41265275 TTAGTGTATC
41265285 ATGTAGATATAT
1 ATGTAGATATAT
41265297 ATGTAGATATAT
1 ATGTAGATATAT
41265309 AT
1 AT
41265311 ATATATTATT
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:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGTAGATATAT
Found at i:41267074 original size:37 final size:38
Alignment explanation
Indices: 41267032--41267108 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 38
41267022 TGGACAAGTT
* *
41267032 TTTTTATTTTTCATAAAGTTGAA-ATTTAATT-TTTATA
1 TTTTTATTTTT-AAAAAGTTAAAGATTTAATTATTTATA
*
41267069 TTTTTATTTTTAAAAATTTAAAGATTTAATTATTTATA
1 TTTTTATTTTTAAAAAGTTAAAGATTTAATTATTTATA
41267107 TT
1 TT
41267109 ATTTTACTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 8 0.23
37 19 0.54
38 8 0.23
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (38 bp):
TTTTTATTTTTAAAAAGTTAAAGATTTAATTATTTATA
Found at i:41274208 original size:3 final size:3
Alignment explanation
Indices: 41274200--41274229 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41274190 TTAGTGGTTG
41274200 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41274230 TAAAAGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41276135 original size:379 final size:379
Alignment explanation
Indices: 41275434--41276140 Score: 1137
Period size: 379 Copynumber: 1.9 Consensus size: 379
41275424 GAAATGTTAT
* *
41275434 GTTTTAGTCACTTATGCTATCGTGTTGTAACATTTTAATCACTGAGCATTAGTTGTTGTTAACAA
1 GTTTTAGTCACTTATGCTATCGTGTTGTAACATTTTAATCACTGAGCATTAATTGTAGTTAACAA
* *
41275499 TGTAATGATAAGCTGACATGGCACGTTAAATCATCATTTCAAACGAAAATTTTAAGTTAAATTTT
66 TGTAACGATAAGCTGACATGACACGTTAAATCATCATTTCAAACGAAAATTTTAAGTTAAATTTT
* *
41275564 AGCTTCAAACGAAAAAATATGGGGATCAAGTGTGTAATCTAACCTAAATTTTTTGTTTGAAATGA
131 AGCTTCAAACAAAAAAATATGGGGATAAAGTGTGTAATCTAACCTAAATTTTTTGTTTGAAATGA
* * ** * * *
41275629 TTATCTAACGTGTCACGTCAGCTTATCGTTACATTGTTAACGACAATTAATGCTCAGTGATTAAA
196 TTATCTAACGTGTCACGTAAGCTTATCGCTACACCGTTAACGACAATTAAGGCTCAATGACTAAA
* ** * *
41275694 ATGTTACAACACGATAGCATAAGTGACTTAAACGCAATATTTCAAACATAAATGATTAAAATGTA
261 ATGTTACAACACGATAACATAAGTGACGAAAACGCAACATTTCAAACATAAATGACTAAAATGTA
41275759 ACATGAGACAAAATAGTTTACCCTTTTTTTATACAATACATTTTTTTTAAGTGA
326 ACATGAGACAAAATAGTTTACCCTTTTTTTATACAATACATTTTTTTTAAGTGA
*
41275813 GTTTTAGTCACTTATGCTATTGTGTTGTAACATTTTAATCACTGAGCATTAATTGTAGTTAACAA
1 GTTTTAGTCACTTATGCTATCGTGTTGTAACATTTTAATCACTGAGCATTAATTGTAGTTAACAA
* * * *
41275878 TGTAACGATAAGCTGACGTGACATGTTAAATCATCATTTCAAACGGAAATTTTAGGTTAAATTTT
66 TGTAACGATAAGCTGACATGACACGTTAAATCATCATTTCAAACGAAAATTTTAAGTTAAATTTT
41275943 AGCTTCAAACAAAAAAATATGGGGATAAAGTGTGTAATCTAACCTAAA-TTTTTGTTTGAAATGA
131 AGCTTCAAACAAAAAAATATGGGGATAAAGTGTGTAATCTAACCTAAATTTTTTGTTTGAAATGA
* *
41276007 TTATCTAACGTGTCACGTAAGCTTATTGCTACACCGTTAACGATAATTAACGGCTCAATGACTAA
196 TTATCTAACGTGTCACGTAAGCTTATCGCTACACCGTTAACGACAATTAA-GGCTCAATGACTAA
* * * *
41276072 AATGTTACAACACGTTAACATAAGTGACGAAAATGTAACATTTCAAACATAAGTGACTAAAATGT
260 AATGTTACAACACGATAACATAAGTGACGAAAACGCAACATTTCAAACATAAATGACTAAAATGT
41276137 AACA
325 AACA
41276141 CAAGGTAAAC
Statistics
Matches: 298, Mismatches: 29, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
378 60 0.20
379 238 0.80
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (379 bp):
GTTTTAGTCACTTATGCTATCGTGTTGTAACATTTTAATCACTGAGCATTAATTGTAGTTAACAA
TGTAACGATAAGCTGACATGACACGTTAAATCATCATTTCAAACGAAAATTTTAAGTTAAATTTT
AGCTTCAAACAAAAAAATATGGGGATAAAGTGTGTAATCTAACCTAAATTTTTTGTTTGAAATGA
TTATCTAACGTGTCACGTAAGCTTATCGCTACACCGTTAACGACAATTAAGGCTCAATGACTAAA
ATGTTACAACACGATAACATAAGTGACGAAAACGCAACATTTCAAACATAAATGACTAAAATGTA
ACATGAGACAAAATAGTTTACCCTTTTTTTATACAATACATTTTTTTTAAGTGA
Found at i:41279115 original size:27 final size:25
Alignment explanation
Indices: 41279084--41279140 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
41279074 ATTTTTGAAT
*
41279084 TTATATATATCTTATAACTTTATATA
1 TTATATATATATTAT-ACTTTATATA
*
41279110 TATATATATATATTATAGTTTATATA
1 T-TATATATATATTATACTTTATATA
41279136 TTATA
1 TTATA
41279141 ATAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.14
26 11 0.39
27 13 0.46
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
TTATATATATATTATACTTTATATA
Found at i:41279121 original size:14 final size:14
Alignment explanation
Indices: 41279104--41279140 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41279094 CTTATAACTT
41279104 TATATA-TATA-TA
1 TATATATTATAGTA
*
41279116 TATATATTATAGTT
1 TATATATTATAGTA
41279130 TATATATTATA
1 TATATATTATA
41279141 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
TATATATTATAGTA
Found at i:41284126 original size:70 final size:67
Alignment explanation
Indices: 41284004--41284136 Score: 169
Period size: 70 Copynumber: 1.9 Consensus size: 67
41283994 ATAAACAATA
* * ** *
41284004 TAATGATTTTACATTTTAACTTAATAGATAAATATTTATCAAAATGACATAATTTTATTTTTTAA
1 TAATGATTTTACATTTTAACTTAAAAGATAAACATTTATCAAAACAACATAATTTTATCTTTTAA
41284069 CT
66 CT
*
41284071 TAATGATTTTGAC-TTTTAACTTTAGAAAAGATAAACATTTATCAAAACAATATAATTTTATCTT
1 TAATGATTTT-ACATTTTAAC-TT--AAAAGATAAACATTTATCAAAACAACATAATTTTATCTT
41284135 TT
62 TT
41284137 CTTATTCGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
67 17 0.30
68 4 0.07
70 35 0.62
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (67 bp):
TAATGATTTTACATTTTAACTTAAAAGATAAACATTTATCAAAACAACATAATTTTATCTTTTAA
CT
Found at i:41284572 original size:143 final size:142
Alignment explanation
Indices: 41284326--41284609 Score: 541
Period size: 143 Copynumber: 2.0 Consensus size: 142
41284316 TTATTTGCAT
*
41284326 AAAAAAAAATACATAAACACAGATATAATCAAATCTACATAGATTCATTCAAAACAAGTGTCTAT
1 AAAAAAAAATACATAAACACAGATATAATCAAATCTACATAGATTCATTCAAAACAAGTATCTAT
41284391 TCAACTCATTTTGGGGACTTACATTTCAAACAAGGACTGAGATGAACTCATGAAAACCCAGTTTT
66 TCAACTCATTTTGGGGACTTACATTTCAAACAAGGACTGAGATGAACTCATGAAAACCCAGTTTT
41284456 TCTTTACATAAG
131 TCTTTACATAAG
*
41284468 AAAAAAAAGATACATAAACACAGATATAATCAAATCTACATAGATTCATTCAGAACAAGTATCTA
1 AAAAAAAA-ATACATAAACACAGATATAATCAAATCTACATAGATTCATTCAAAACAAGTATCTA
41284533 TTCAACTCATTTTGGGGACTTACATTTCAAACAAGGACTGAGATGAACTCATGAAAACCCAGTTT
65 TTCAACTCATTTTGGGGACTTACATTTCAAACAAGGACTGAGATGAACTCATGAAAACCCAGTTT
41284598 TTCTTTACATAA
130 TTCTTTACATAA
41284610 TTGGTCAATC
Statistics
Matches: 139, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
142 8 0.06
143 131 0.94
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (142 bp):
AAAAAAAAATACATAAACACAGATATAATCAAATCTACATAGATTCATTCAAAACAAGTATCTAT
TCAACTCATTTTGGGGACTTACATTTCAAACAAGGACTGAGATGAACTCATGAAAACCCAGTTTT
TCTTTACATAAG
Found at i:41288643 original size:33 final size:34
Alignment explanation
Indices: 41288606--41288687 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 34
41288596 ATATAAAAAA
* *
41288606 TAAATTAATTT-TATATTTTATATATCATTATAT
1 TAAATTAATTTAAATATTTCATATATCATTATAT
*
41288639 TAAATT-ATTTAAATATTTCATATATTATTATAT
1 TAAATTAATTTAAATATTTCATATATCATTATAT
41288672 TAAATT-ATTTAAATAT
1 TAAATTAATTTAAATAT
41288688 AATTTATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 4 0.09
33 41 0.91
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (34 bp):
TAAATTAATTTAAATATTTCATATATCATTATAT
Found at i:41288662 original size:25 final size:25
Alignment explanation
Indices: 41288609--41288681 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
41288599 TAAAAAATAA
** *
41288609 ATTA-ATT-TTATATTTTATATATC
1 ATTATATTATTATATTAAATATTTC
41288632 ATTATATTAAATTAT-TTAAATATTTC
1 ATTATATT--ATTATATTAAATATTTC
41288658 A-TATATTATTATATTAAATTATTT
1 ATTATATTATTATATTAAA-TATTT
41288682 AAATATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
23 9 0.22
24 8 0.20
25 11 0.27
26 9 0.22
27 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATATTATTATATTAAATATTTC
Found at i:41288671 original size:17 final size:17
Alignment explanation
Indices: 41288616--41288709 Score: 63
Period size: 17 Copynumber: 5.8 Consensus size: 17
41288606 TAAATTAATT
* *
41288616 TTATATTTTATATATCA
1 TTATATTTAATATATTA
*
41288633 TTATATTAAAT-TATT-
1 TTATATTTAATATATTA
* *
41288648 TAAATATTTCATATATTA
1 T-TATATTTAATATATTA
*
41288666 TTATATTAAAT-TA-T-
1 TTATATTTAATATATTA
* * *
41288680 TTAAATATAATTTATTA
1 TTATATTTAATATATTA
41288697 TTATATTTAATAT
1 TTATATTTAATAT
41288710 TTTAAAATAT
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
14 8 0.14
15 4 0.07
16 13 0.23
17 30 0.54
18 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTAATATATTA
Found at i:41288699 original size:31 final size:32
Alignment explanation
Indices: 41288625--41288720 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 32
41288615 TTTATATTTT
* *
41288625 ATATATCATTATATTAAATTATTTAAATATTTC
1 ATATATTATTATATTAAATTATTTAAATA-TTA
41288658 ATATATTATTATATTAAATTATTTAAATA-TA
1 ATATATTATTATATTAAATTATTTAAATATTA
* *
41288689 ATTTATTATTATATTTAATATT-TTAAAATATT
1 ATATATTATTATA-TTAA-ATTATTTAAATATT
41288721 TTGTAAATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
31 13 0.23
32 11 0.20
33 32 0.57
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (32 bp):
ATATATTATTATATTAAATTATTTAAATATTA
Found at i:41295038 original size:21 final size:20
Alignment explanation
Indices: 41294998--41295044 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
41294988 AATATTGAAT
41294998 TAAAAATTGGTTTTAAATAAA
1 TAAAAATTGGTTTTAAAT-AA
41295019 TAAAAA-T-GTTTCTAATATAA
1 TAAAAATTGGTTT-TAA-ATAA
41295039 TAAAAA
1 TAAAAA
41295045 CAACTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.17
20 12 0.50
21 8 0.33
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (20 bp):
TAAAAATTGGTTTTAAATAA
Found at i:41303712 original size:30 final size:30
Alignment explanation
Indices: 41303660--41303720 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41303650 CTAAATTGTA
* *** *
41303660 TAACTCATTGACTTGGGTCACACGGCTGTG
1 TAACTCACTGACTTGAAACACACGACTGTG
41303690 TAACTCACTGACTTGAAACACACGACTGTG
1 TAACTCACTGACTTGAAACACACGACTGTG
41303720 T
1 T
41303721 TACAGGCCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (30 bp):
TAACTCACTGACTTGAAACACACGACTGTG
Found at i:41305814 original size:5 final size:5
Alignment explanation
Indices: 41305804--41305867 Score: 128
Period size: 5 Copynumber: 12.8 Consensus size: 5
41305794 GTTATCACAC
41305804 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
41305854 AATAA AATAA AATA
1 AATAA AATAA AATA
41305868 TTTATATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 59 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:41314195 original size:12 final size:12
Alignment explanation
Indices: 41314174--41314281 Score: 64
Period size: 12 Copynumber: 9.3 Consensus size: 12
41314164 ATAACATCCA
*
41314174 AACAACAAAAAT
1 AACAATAAAAAT
*
41314186 AACAATAAAAAC
1 AACAATAAAAAT
* **
41314198 AGCAGCAAAAAT
1 AACAATAAAAAT
* *
41314210 AACAGT-AAAAC
1 AACAATAAAAAT
*
41314221 AAC-AT-TAAA-
1 AACAATAAAAAT
41314230 AACAATAAAAAT
1 AACAATAAAAAT
* *
41314242 AGCAATAAAAAC
1 AACAATAAAAAT
* *
41314254 AGCAACAAAAAT
1 AACAATAAAAAT
41314266 AACAGA-AAAAAT
1 AACA-ATAAAAAT
41314278 AACA
1 AACA
41314282 CGAAAATAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
9 3 0.04
10 6 0.08
11 10 0.13
12 55 0.73
13 1 0.01
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.10
Consensus pattern (12 bp):
AACAATAAAAAT
Found at i:41314213 original size:44 final size:44
Alignment explanation
Indices: 41314160--41314245 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
41314150 AAAACGCATA
*
41314160 AAAAATAACA-TCCAAACAACA-AAAATAACAATAAAAACAGCAGC
1 AAAAATAACAGT-AAAACAACATAAAA-AACAATAAAAACAGCAGC
* *
41314204 AAAAATAACAGTAAAACAACATTAAAAACAATAAAAATAGCA
1 AAAAATAACAGTAAAACAACATAAAAAACAATAAAAACAGCA
41314246 ATAAAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 33 0.89
45 4 0.11
ACGTcount: A:0.67, C:0.16, G:0.05, T:0.12
Consensus pattern (44 bp):
AAAAATAACAGTAAAACAACATAAAAAACAATAAAAACAGCAGC
Found at i:41314252 original size:44 final size:44
Alignment explanation
Indices: 41314148--41314252 Score: 110
Period size: 44 Copynumber: 2.4 Consensus size: 44
41314138 GAAACAATAG
*
41314148 TAAAAAC-GCATA-AAAAATAACATCCAAACAACAAAAATAACAA
1 TAAAAACAGCA-ACAAAAATAACATCAAAACAACAAAAATAACAA
* *
41314191 TAAAAACAGCAGCAAAAATAACAGT-AAAACAACATTAAA-AACAA
1 TAAAAACAGCAACAAAAATAACA-TCAAAACAACA-AAAATAACAA
* *
41314235 TAAAAATAGCAATAAAAA
1 TAAAAACAGCAACAAAAA
41314253 CAGCAACAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
43 7 0.13
44 41 0.79
45 4 0.08
ACGTcount: A:0.68, C:0.15, G:0.05, T:0.12
Consensus pattern (44 bp):
TAAAAACAGCAACAAAAATAACATCAAAACAACAAAAATAACAA
Found at i:41314304 original size:56 final size:54
Alignment explanation
Indices: 41314177--41314308 Score: 135
Period size: 56 Copynumber: 2.4 Consensus size: 54
41314167 ACATCCAAAC
* * * **
41314177 AACAA-AAATAACAATAAAAACAGCAGCAAAAATAACAGTAAAACAACATTAAA
1 AACAATAAAAAACAATAAAAACAGCAACAAAAATAACAGAAAAACAACACGAAA
*
41314230 AACAATAAAAATAGCAATAAAAACAGCAACAAAAATAACAGAAAAAATAACACGAAA
1 AACAATAAAAA-A-CAATAAAAACAGCAACAAAAATAACAG-AAAAACAACACGAAA
41314287 ATA-AA-AATCAAAACAATAAAAA
1 A-ACAATAA--AAAACAATAAAAA
41314309 ACAACTCAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
53 5 0.08
54 4 0.06
55 1 0.02
56 37 0.56
57 15 0.23
58 4 0.06
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.11
Consensus pattern (54 bp):
AACAATAAAAAACAATAAAAACAGCAACAAAAATAACAGAAAAACAACACGAAA
Found at i:41314329 original size:22 final size:21
Alignment explanation
Indices: 41314295--41314364 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
41314285 AAATAAAAAT
*
41314295 CAAAACAAT-AAAAAA-CAAC
1 CAAAACAGTAAAAAAATCAAC
41314314 TCAAAAACAGTAAAAAAAATCAAC
1 -C-AAAACAGT-AAAAAAATCAAC
*
41314338 CAAAACAGTAAAAAAAGC-AC
1 CAAAACAGTAAAAAAATCAAC
41314358 CAAAACA
1 CAAAACA
41314365 ATAATATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.23
21 15 0.34
22 8 0.18
23 7 0.16
24 4 0.09
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (21 bp):
CAAAACAGTAAAAAAATCAAC
Found at i:41314341 original size:23 final size:22
Alignment explanation
Indices: 41314304--41314353 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 22
41314294 TCAAAACAAT
41314304 AAAAAACAACTCAAAAACAGTAA
1 AAAAAACAACTC-AAAACAGTAA
41314327 AAAAAATCAAC-CAAAACAGTAA
1 AAAAAA-CAACTCAAAACAGTAA
41314349 AAAAA
1 AAAAA
41314354 GCACCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.58
23 7 0.27
24 4 0.15
ACGTcount: A:0.72, C:0.16, G:0.04, T:0.08
Consensus pattern (22 bp):
AAAAAACAACTCAAAACAGTAA
Found at i:41314359 original size:20 final size:22
Alignment explanation
Indices: 41314304--41314364 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
41314294 TCAAAACAAT
41314304 AAAAAA-CAACTCAAAAACAGTAA
1 AAAAAAGCAAC-C-AAAACAGTAA
*
41314327 AAAAAATCAACCAAAACAGT-A
1 AAAAAAGCAACCAAAACAGTAA
41314348 AAAAAAGC-ACCAAAACA
1 AAAAAAGCAACCAAAACA
41314365 ATAATATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 9 0.25
21 8 0.22
22 8 0.22
23 7 0.19
24 4 0.11
ACGTcount: A:0.69, C:0.20, G:0.05, T:0.07
Consensus pattern (22 bp):
AAAAAAGCAACCAAAACAGTAA
Found at i:41315008 original size:18 final size:20
Alignment explanation
Indices: 41314977--41315013 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
41314967 ACCTAGAAAT
*
41314977 TTTAGAAAATATCA-AAAAG
1 TTTAGAAAAAATCATAAAAG
41314996 TTTA-AAAAAATCATAAAA
1 TTTAGAAAAAATCATAAAA
41315014 ATGTAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (20 bp):
TTTAGAAAAAATCATAAAAG
Found at i:41315223 original size:23 final size:23
Alignment explanation
Indices: 41315186--41315240 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
41315176 TGGAATTTTT
*
41315186 TATTTTTTTCAGAAAAATTTATGG
1 TATTTTTTTCAG-AAAATTTAAGG
*
41315210 TATTTTTTT-GGAAAATTTAAGG
1 TATTTTTTTCAGAAAATTTAAGG
*
41315232 AATTTTTTT
1 TATTTTTTT
41315241 TGCATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 18 0.64
23 1 0.04
24 9 0.32
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.55
Consensus pattern (23 bp):
TATTTTTTTCAGAAAATTTAAGG
Found at i:41323923 original size:2 final size:2
Alignment explanation
Indices: 41323916--41323940 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41323906 TGAATTGTTA
41323916 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
41323941 ATTTAAGCTT
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:41325156 original size:50 final size:50
Alignment explanation
Indices: 41325080--41325187 Score: 189
Period size: 50 Copynumber: 2.1 Consensus size: 50
41325070 AGTATATCAA
41325080 CAGTCACTCAACCTTGATTTCGATGACAAAACAGTCACTCAACTTTCAATT
1 CAGTCA-TCAACCTTGATTTCGATGACAAAACAGTCACTCAACTTTCAATT
* *
41325131 CAGTCATCAACTTTGATTTCGATGACAAAATAGTCACTCAACTTTCAATT
1 CAGTCATCAACCTTGATTTCGATGACAAAACAGTCACTCAACTTTCAATT
41325181 CAGTCAT
1 CAGTCAT
41325188 TTAACTTTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 49 0.89
51 6 0.11
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (50 bp):
CAGTCATCAACCTTGATTTCGATGACAAAACAGTCACTCAACTTTCAATT
Found at i:41325209 original size:50 final size:50
Alignment explanation
Indices: 41325105--41325215 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
41325095 GATTTCGATG
***** *
41325105 ACAAAACAGTCACTCAACTTTCAATTCAGTCATCAACTTTGATTTCGATG
1 ACAAAACAGTCACTCAACTTTCAATTCAGTCATCAACTTTGAAAAAAATA
* *
41325155 ACAAAATAGTCACTCAACTTTCAATTCAGTCATTTAACTTT-AAAAAAATA
1 ACAAAACAGTCACTCAACTTTCAATTCAGTCA-TCAACTTTGAAAAAAATA
*
41325205 ACAAATCAGTC
1 ACAAAACAGTC
41325216 CTACTAATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 43 0.86
51 7 0.14
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.31
Consensus pattern (50 bp):
ACAAAACAGTCACTCAACTTTCAATTCAGTCATCAACTTTGAAAAAAATA
Found at i:41326110 original size:20 final size:21
Alignment explanation
Indices: 41326069--41326111 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41326059 TCATGGTAAA
41326069 TTAACTGATAACGTCAATTTG
1 TTAACTGATAACGTCAATTTG
* *
41326090 TTAACTGGTCACGTC-ATTTG
1 TTAACTGATAACGTCAATTTG
41326110 TT
1 TT
41326112 CCGTTAGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (21 bp):
TTAACTGATAACGTCAATTTG
Found at i:41328485 original size:33 final size:36
Alignment explanation
Indices: 41328443--41328508 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
41328433 TGTTTATGTG
* *
41328443 AAATTGAAGAGAAA-GAGAAGAG-AG-GCAAGGATC
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
41328476 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
41328509 GGTAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 2 0.07
36 6 0.21
ACGTcount: A:0.53, C:0.06, G:0.32, T:0.09
Consensus pattern (36 bp):
AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
Found at i:41329560 original size:23 final size:22
Alignment explanation
Indices: 41329534--41329606 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 22
41329524 ACACTAGCGC
41329534 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TGTGT
*
41329557 GCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTT-GTGT
41329580 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
41329603 GCTC
1 GCTC
41329607 AGTACTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.02
23 43 0.93
24 2 0.04
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.38
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTGTGT
Found at i:41329635 original size:39 final size:39
Alignment explanation
Indices: 41329571--41329645 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
41329561 TCCGATTAGC
*
41329571 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
41329610 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
41329646 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:41329640 original size:23 final size:23
Alignment explanation
Indices: 41329605--41329698 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
41329595 CTTTGTGTGC
*
41329605 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
41329628 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
41329651 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
41329676 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
41329698 T
1 T
41329699 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:41330577 original size:28 final size:28
Alignment explanation
Indices: 41330546--41330638 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
41330536 AAATGGTAAT
41330546 TTTTGGTGAAATCGAGGTTAAAATGGGA
1 TTTTGGTGAAATCGAGGTTAAAATGGGA
*
41330574 TTTT-G-GAAAGTTCGATGG-TAAAATGGTAA
1 TTTTGGTGAAA--TCGA-GGTTAAAATGG-GA
* *
41330603 TTTTTGGTGAAATTGGGGTTAAAAATGGGA
1 -TTTTGGTGAAATCGAGGTT-AAAATGGGA
41330633 TTTTGG
1 TTTTGG
41330639 AAAGTTTGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
26 4 0.08
27 1 0.02
28 16 0.31
29 11 0.21
30 8 0.15
31 8 0.15
32 4 0.08
ACGTcount: A:0.30, C:0.02, G:0.31, T:0.37
Consensus pattern (28 bp):
TTTTGGTGAAATCGAGGTTAAAATGGGA
Found at i:41330598 original size:58 final size:59
Alignment explanation
Indices: 41330526--41330655 Score: 208
Period size: 58 Copynumber: 2.2 Consensus size: 59
41330516 ATTTTTGACT
*
41330526 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGGATTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG
* * *
41330584 TTCGATGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG
*
41330643 TTTGAGGGTAAAA
1 TTCGAGGGTAAAA
41330656 ATATAATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
58 35 0.54
59 30 0.46
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (59 bp):
TTCGAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG
Found at i:41330636 original size:30 final size:30
Alignment explanation
Indices: 41330534--41330626 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
41330524 CTTTCGGGGG
*
41330534 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGGTAATTTTTGGTGAAATTGAGGT
*
41330564 TAAAATGG-GA-TTTT-G-GAAAGTTCGATGG-
1 TAAAATGGTAATTTTTGGTGAAA-TT-GA-GGT
*
41330592 TAAAATGGTAATTTTTGGTGAAATTGGGGT
1 TAAAATGGTAATTTTTGGTGAAATTGAGGT
41330622 TAAAA
1 TAAAA
41330627 ATGGGATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 14 0.27
29 6 0.12
30 18 0.35
31 3 0.06
32 4 0.08
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.35
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGTGAAATTGAGGT
Found at i:41330654 original size:29 final size:29
Alignment explanation
Indices: 41330565--41330657 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
41330555 AATCGAGGTT
* *
41330565 AAAATGGGATTTTGGAAAGTTCGATGGT-
1 AAAATGGGATTTTGGAAAGTTTGAGGGTA
*
41330593 AAAATGGTAATTTTTGGTGAAA--TTG-GGGTTA
1 AAAATGG-GA-TTTT-G-GAAAGTTTGAGGG-TA
41330624 AAAATGGGATTTTGGAAAGTTTGAGGGTA
1 AAAATGGGATTTTGGAAAGTTTGAGGGTA
41330653 AAAAT
1 AAAAT
41330658 ATAATTTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
27 4 0.08
28 8 0.15
29 17 0.33
30 11 0.21
31 8 0.15
32 4 0.08
ACGTcount: A:0.35, C:0.01, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGGGATTTTGGAAAGTTTGAGGGTA
Found at i:41331789 original size:15 final size:16
Alignment explanation
Indices: 41331751--41331859 Score: 71
Period size: 15 Copynumber: 6.7 Consensus size: 16
41331741 ATTACGTCAT
41331751 TTATTATTATTAATAA
1 TTATTATTATTAATAA
* *
41331767 TT-TCATTATTAAT-G
1 TTATTATTATTAATAA
41331781 TTATTATTATTAATATCA
1 TTATTATTATTAATA--A
* ** *
41331799 TTGTTATCGTTAATAT
1 TTATTATTATTAATAA
* *
41331815 TTATTGGTATTATTTATTA
1 TTA-T--TATTATTAATAA
*
41331834 TTATAATTATTAATAA
1 TTATTATTATTAATAA
41331850 -TATTATTATT
1 TTATTATTATT
41331860 TGTAGCATTT
Statistics
Matches: 68, Mismatches: 18, Indels: 15
0.67 0.18 0.15
Matches are distributed among these distances:
14 2 0.03
15 29 0.43
16 13 0.19
17 1 0.01
18 13 0.19
19 10 0.15
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.58
Consensus pattern (16 bp):
TTATTATTATTAATAA
Found at i:41331815 original size:27 final size:27
Alignment explanation
Indices: 41331758--41331815 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
41331748 CATTTATTAT
* *
41331758 TATTAATAATTTCATTATTAATGTTAT
1 TATTAATAATATCATTATTAATGTTAA
* *
41331785 TATTATTAATATCATTGTT-ATCGTTAA
1 TATTAATAATATCATTATTAAT-GTTAA
41331812 TATT
1 TATT
41331816 TATTGGTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (27 bp):
TATTAATAATATCATTATTAATGTTAA
Found at i:41334004 original size:13 final size:13
Alignment explanation
Indices: 41333986--41334010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41333976 ATTACATCAA
41333986 TTAAATAATTTTG
1 TTAAATAATTTTG
41333999 TTAAATAATTTT
1 TTAAATAATTTT
41334011 ATTTTAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTG
Found at i:41338006 original size:23 final size:23
Alignment explanation
Indices: 41337958--41338006 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
41337948 TGATCTAAGG
* *
41337958 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATGAACTAA
41337981 AAAAATAAAAGAAAATAGAACTAA
1 AAAAATAAAAGAAAAT-GAACTAA
41338005 AA
1 AA
41338007 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAAATGAACTAA
Found at i:41338846 original size:19 final size:19
Alignment explanation
Indices: 41338822--41338864 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41338812 AAATATAAAT
41338822 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
41338841 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
41338860 TAAAT
1 TAAAT
41338865 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:41339594 original size:103 final size:103
Alignment explanation
Indices: 41339427--41339613 Score: 288
Period size: 103 Copynumber: 1.8 Consensus size: 103
41339417 ATTTTGTGAA
* *
41339427 TTTTTTCCTTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATGAAATGACACCCAAGCA
1 TTTTTTCCTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGCA
*
41339492 CTCCATCCCGGTTACTCAGCCCAACATGCTCTCAATTT
66 CTCCACCCCGGTTACTCAGCCCAACATGCTCTCAATTT
* * *
41339530 TTTTCTTCTCTTTTTT-TTT-AGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACAACCAAG
1 TTTT-TTC-CTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAG
41339593 CACTCCACCCCGGTTACTCAG
64 CACTCCACCCCGGTTACTCAG
41339614 TCTAACACAT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
103 63 0.83
104 6 0.08
105 7 0.09
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (103 bp):
TTTTTTCCTTTTTTCTTTAAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGCA
CTCCACCCCGGTTACTCAGCCCAACATGCTCTCAATTT
Found at i:41339632 original size:103 final size:104
Alignment explanation
Indices: 41339427--41339655 Score: 275
Period size: 103 Copynumber: 2.2 Consensus size: 104
41339417 ATTTTGTGAA
* *
41339427 TTTTTTC-CTTTTTTCTTTAAGAATACATTGGACCTTTTGACGCGAAATGAAATGACACCCAAGC
1 TTTTTTCTCTTTTTT-TTT-AGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGC
* **
41339491 ACTCCATCCCGGTTACTCAGCCCAACATGCTCTCAATTT-T
64 ACTCCACCCCGGTTACTCAGCCCAACACACTCTCAATTTAT
* * * *
41339531 TTTCTTCTCTTTTTTTTTAGAATGCATTAGCCCTTTTGACGCGAAGTGAAATGACAACCAAGCAC
1 TTTTTTCTCTTTTTTTTTAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGCAC
* * *
41339596 TCCACCCCGGTTACTCAGTCTAACACATTC-CGAATTTAT
66 TCCACCCCGGTTACTCAGCCCAACACACTCTC-AATTTAT
*
41339635 TTATTATTTTCTTTTTTTTTA
1 TT-TT-TTCTCTTTTTTTTTA
41339656 TTCGGGTTAG
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
102 1 0.01
103 71 0.67
104 12 0.11
105 8 0.08
106 14 0.13
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (104 bp):
TTTTTTCTCTTTTTTTTTAGAATACATTAGACCTTTTGACGCGAAATGAAATGACAACCAAGCAC
TCCACCCCGGTTACTCAGCCCAACACACTCTCAATTTAT
Found at i:41340312 original size:4 final size:4
Alignment explanation
Indices: 41340303--41340347 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
41340293 TCCTGGACAA
41340303 AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAGAT AGAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAA
41340348 AAAAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.05
4 26 0.70
5 8 0.22
6 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:41340357 original size:8 final size:8
Alignment explanation
Indices: 41340302--41340358 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
41340292 TTCCTGGACA
41340302 AAAATAAAT
1 AAAA-AAAT
*
41340311 AAATAAAT
1 AAAAAAAT
*
41340319 AAATAAAT
1 AAAAAAAT
41340327 AAAATAAGAT
1 AAAA-AA-AT
*
41340337 AGAAAAAT
1 AAAAAAAT
41340345 AAAAAAAAT
1 -AAAAAAAT
41340354 AAAAA
1 AAAAA
41340359 TAATTGGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 22 0.54
9 14 0.34
10 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (8 bp):
AAAAAAAT
Found at i:41343245 original size:21 final size:21
Alignment explanation
Indices: 41343203--41343246 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41343193 CCTCGATTTT
*
41343203 CTTTTGAAAATCCACAGTTTG
1 CTTTTGAAAATCCACAGATTG
* * *
41343224 CTTTTGGAAATCTATAGATTG
1 CTTTTGAAAATCCACAGATTG
41343245 CT
1 CT
41343247 GCTGAAATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
CTTTTGAAAATCCACAGATTG
Found at i:41344824 original size:23 final size:23
Alignment explanation
Indices: 41344776--41344824 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41344766 TGATCTAAGG
* * *
41344776 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATAAACTAA
41344799 AAAAATAAAAGAAAATAAAACTAA
1 AAAAATAAAAGAAAAT-AAACTAA
41344823 AA
1 AA
41344825 GAAGTAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAAATAAACTAA
Found at i:41345664 original size:19 final size:19
Alignment explanation
Indices: 41345640--41345682 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
41345630 AAATATAAAT
41345640 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
41345659 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
41345678 TAAAT
1 TAAAT
41345683 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:41368973 original size:18 final size:18
Alignment explanation
Indices: 41368942--41368976 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41368932 TTTTATATAT
*
41368942 AAATAAAATAAGAAATTG
1 AAATAAAAGAAGAAATTG
*
41368960 AAATAAAAGGAGAAATT
1 AAATAAAAGAAGAAATT
41368977 AGAGTTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (18 bp):
AAATAAAAGAAGAAATTG
Found at i:41369113 original size:22 final size:23
Alignment explanation
Indices: 41369083--41369125 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
41369073 CAGGAATTTA
* *
41369083 ATTATAAATTACTTTTTTTATGC
1 ATTATAAATTACATTTGTTATGC
41369106 ATTA-AAATTACATTTGTTAT
1 ATTATAAATTACATTTGTTAT
41369126 AAAATGAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (23 bp):
ATTATAAATTACATTTGTTATGC
Found at i:41373353 original size:56 final size:56
Alignment explanation
Indices: 41373287--41373440 Score: 191
Period size: 56 Copynumber: 2.8 Consensus size: 56
41373277 ATGCTGTTAG
* * * * *
41373287 GATATTATTATGCGATATTATCTTTTAATAATTTAATTTTTAATGAGGTATTTTAA
1 GATATTATTATGAGATATTATCTTTTAACAATTTGATTTTTAATGAGATATTATAA
* * * * * *
41373343 GATATTATTATGTGATACTATCTTTTAGCAATTCGATTCTTAATGAGATATTATAG
1 GATATTATTATGAGATATTATCTTTTAACAATTTGATTTTTAATGAGATATTATAA
* *
41373399 GATATTATTTTGAGATTTTATCTTTTAACAATTTGATTTTTA
1 GATATTATTATGAGATATTATCTTTTAACAATTTGATTTTTA
41373441 CGTAACTACT
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 81 1.00
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.51
Consensus pattern (56 bp):
GATATTATTATGAGATATTATCTTTTAACAATTTGATTTTTAATGAGATATTATAA
Found at i:41380062 original size:21 final size:21
Alignment explanation
Indices: 41380036--41380077 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41380026 GATACCTGAT
*
41380036 AAAAGGTATCAATACTTTTTG
1 AAAAGGTATCAATACCTTTTG
*
41380057 AAAAGGTATCGATACCTTTTG
1 AAAAGGTATCAATACCTTTTG
41380078 TCATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
AAAAGGTATCAATACCTTTTG
Found at i:41382915 original size:129 final size:129
Alignment explanation
Indices: 41382685--41382943 Score: 518
Period size: 129 Copynumber: 2.0 Consensus size: 129
41382675 GGTTGAAAAG
41382685 TGATTGCAATGAGATATTCTCTCCAAAGTTTTTGGTTATGCTGATACTGCAGAACGTACAATGCA
1 TGATTGCAATGAGATATTCTCTCCAAAGTTTTTGGTTATGCTGATACTGCAGAACGTACAATGCA
41382750 CTCTTTGAGATGCCTCTTATTTTTATTTTGGGGAGATTGGTTGGGTTTAGAGTTTAGTAGCGAA
66 CTCTTTGAGATGCCTCTTATTTTTATTTTGGGGAGATTGGTTGGGTTTAGAGTTTAGTAGCGAA
41382814 TGATTGCAATGAGATATTCTCTCCAAAGTTTTTGGTTATGCTGATACTGCAGAACGTACAATGCA
1 TGATTGCAATGAGATATTCTCTCCAAAGTTTTTGGTTATGCTGATACTGCAGAACGTACAATGCA
41382879 CTCTTTGAGATGCCTCTTATTTTTATTTTGGGGAGATTGGTTGGGTTTAGAGTTTAGTAGCGAA
66 CTCTTTGAGATGCCTCTTATTTTTATTTTGGGGAGATTGGTTGGGTTTAGAGTTTAGTAGCGAA
41382943 T
1 T
41382944 TTCCGTTGAC
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 130 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (129 bp):
TGATTGCAATGAGATATTCTCTCCAAAGTTTTTGGTTATGCTGATACTGCAGAACGTACAATGCA
CTCTTTGAGATGCCTCTTATTTTTATTTTGGGGAGATTGGTTGGGTTTAGAGTTTAGTAGCGAA
Found at i:41384808 original size:22 final size:22
Alignment explanation
Indices: 41384782--41384824 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
41384772 ATTTTGGTTT
41384782 AATTAGGGTTTAGGAAAATTTA
1 AATTAGGGTTTAGGAAAATTTA
*
41384804 AATTAGGGTTTTGGAAAATTT
1 AATTAGGGTTTAGGAAAATTT
41384825 TATGATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (22 bp):
AATTAGGGTTTAGGAAAATTTA
Found at i:41389972 original size:14 final size:14
Alignment explanation
Indices: 41389938--41389973 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
41389928 GTGGATGTAG
41389938 ATATATATATACAC
1 ATATATATATACAC
**
41389952 ACGTATATATACAC
1 ATATATATATACAC
41389966 ATATATAT
1 ATATATAT
41389974 TAAACTTCAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (14 bp):
ATATATATATACAC
Found at i:41390031 original size:32 final size:32
Alignment explanation
Indices: 41389990--41390054 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
41389980 TCATAGCTTG
41389990 TAGGTATCTCTCAACTAGTTTAGATTATATGT
1 TAGGTATCTCTCAACTAGTTTAGATTATATGT
41390022 TAGGTATCTCTCAACTAGTTTAGATTATATGT
1 TAGGTATCTCTCAACTAGTTTAGATTATATGT
41390054 T
1 T
41390055 TGGCATGATA
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:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (32 bp):
TAGGTATCTCTCAACTAGTTTAGATTATATGT
Found at i:41395750 original size:2 final size:2
Alignment explanation
Indices: 41395738--41395767 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
41395728 CATGAGATGC
41395738 AT AT A- 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 AT AT A
41395768 GGGCTGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41399161 original size:17 final size:18
Alignment explanation
Indices: 41399139--41399179 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41399129 TGTTTAGCAT
*
41399139 TGCTTTCGAT-TCAAAAG
1 TGCTTTCGATGTCAAAAA
*
41399156 TGCTTTCTATGTCAAAAA
1 TGCTTTCGATGTCAAAAA
41399174 TGCTTT
1 TGCTTT
41399180 TAAAAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (18 bp):
TGCTTTCGATGTCAAAAA
Found at i:41399362 original size:24 final size:23
Alignment explanation
Indices: 41399335--41399384 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
41399325 GAATGGTGAC
41399335 ATATGTTATCAAAATAA-TAAAAAA
1 ATAT-TTATCAAAA-AATTAAAAAA
* *
41399359 ATATTTTTTAAAAAATTAAAAAA
1 ATATTTATCAAAAAATTAAAAAA
41399382 ATA
1 ATA
41399385 AGAAATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 2 0.09
23 17 0.74
24 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
ATATTTATCAAAAAATTAAAAAA
Found at i:41399825 original size:16 final size:16
Alignment explanation
Indices: 41399804--41399842 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41399794 CGGACTCGGG
* **
41399804 TTTTCTTGAGCTTGGA
1 TTTTCTCGAGCTCAGA
41399820 TTTTCTCGAGCTCAGA
1 TTTTCTCGAGCTCAGA
41399836 TTTTCTC
1 TTTTCTC
41399843 AGGCTTGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (16 bp):
TTTTCTCGAGCTCAGA
Found at i:41400912 original size:35 final size:35
Alignment explanation
Indices: 41400873--41400944 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
41400863 CATTTAAAAA
*
41400873 AAAATAAAGAACTAACATTTAGTTATATTTTAAGT
1 AAAATAAAGAACTAACATATAGTTATATTTTAAGT
41400908 AAAATAAAGAACTAACATATAGTTATATTTTAAGT
1 AAAATAAAGAACTAACATATAGTTATATTTTAAGT
41400943 AA
1 AA
41400945 TAACATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (35 bp):
AAAATAAAGAACTAACATATAGTTATATTTTAAGT
Found at i:41407724 original size:29 final size:30
Alignment explanation
Indices: 41407692--41407763 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
41407682 GTAATTAGAT
41407692 TTGAATTTTAAATTAA-AAAAATAGAAAAA
1 TTGAATTTTAAATTAATAAAAATAGAAAAA
*
41407721 TTGAATTTTTAAA--AATAAAAATATAAAAA
1 TTGAA-TTTTAAATTAATAAAAATAGAAAAA
*
41407750 TTAAATTTTAAATT
1 TTGAATTTTAAATT
41407764 TGAGAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
28 9 0.24
29 21 0.57
30 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (30 bp):
TTGAATTTTAAATTAATAAAAATAGAAAAA
Found at i:41410510 original size:15 final size:15
Alignment explanation
Indices: 41410492--41410533 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
41410482 TAATTATAAT
41410492 TATAATAATAATTAA
1 TATAATAATAATTAA
* *
41410507 TATATTAATAAATAA
1 TATAATAATAATTAA
*
41410522 AAT-ATAATAATT
1 TATAATAATAATT
41410534 TTAATTGTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAATAATAATTAA
Found at i:41410641 original size:29 final size:31
Alignment explanation
Indices: 41410608--41410674 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
41410598 CTTAAATTTT
*
41410608 ATTTAAGAAAAAAAG-TTAAATT-AACTAAA
1 ATTTAAGAAAAAAAGAATAAATTGAACTAAA
* * *
41410637 TTTTAA-AAATAAAGAATAAATTGATCTAAA
1 ATTTAAGAAAAAAAGAATAAATTGAACTAAA
41410667 ATTTAAGA
1 ATTTAAGA
41410675 TTACGTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 7 0.23
29 11 0.37
30 11 0.37
31 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.31
Consensus pattern (31 bp):
ATTTAAGAAAAAAAGAATAAATTGAACTAAA
Found at i:41410705 original size:19 final size:19
Alignment explanation
Indices: 41410677--41410715 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41410667 ATTTAAGATT
*
41410677 ACGTTTGTAATCTAAAATA
1 ACGTTCGTAATCTAAAATA
41410696 ACGTTCGTAATCTAAAATA
1 ACGTTCGTAATCTAAAATA
41410715 A
1 A
41410716 TTTAAGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (19 bp):
ACGTTCGTAATCTAAAATA
Found at i:41414745 original size:9 final size:10
Alignment explanation
Indices: 41414727--41414758 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
41414717 ATTTTTAAAA
41414727 ATTAAAAATT
1 ATTAAAAATT
41414737 ATT-AAAATT
1 ATTAAAAATT
41414746 ATTAAAAATT
1 ATTAAAAATT
41414756 ATT
1 ATT
41414759 TATTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:41414775 original size:33 final size:31
Alignment explanation
Indices: 41414727--41414787 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 31
41414717 ATTTTTAAAA
41414727 ATTAAAAATTATTAAAATTATTAAAAATTATTT
1 ATTAAAAATTATT-AAATT-TTAAAAATTATTT
* *
41414760 ATTAATAATTTTTAAATTTTAAAAATTA
1 ATTAAAAATTATTAAATTTTAAAAATTA
41414788 ATTAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 10 0.38
32 5 0.19
33 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTAAAAATTATTAAATTTTAAAAATTATTT
Found at i:41429268 original size:14 final size:14
Alignment explanation
Indices: 41429237--41429274 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41429227 AGGTTTAGGG
*
41429237 TTTAA-TAATTTTA
1 TTTAATTAAATTTA
*
41429250 ATTAATTAAATTTA
1 TTTAATTAAATTTA
41429264 TTTAATTAAAT
1 TTTAATTAAAT
41429275 ATTTATTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAAATTTA
Found at i:41437536 original size:16 final size:15
Alignment explanation
Indices: 41437515--41437550 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
41437505 TAAATTGATT
41437515 ATTTTAAAAAATTAAA
1 ATTTTAAAAAATT-AA
41437531 ATTTT-AAAAATTAA
1 ATTTTAAAAAATTAA
41437545 ATTTTA
1 ATTTTA
41437551 CTCTTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.37
15 7 0.37
16 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTTAAAAAATTAA
Found at i:41455200 original size:55 final size:55
Alignment explanation
Indices: 41455134--41455245 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
41455124 CATCATAGTG
*
41455134 TTAAATGAGAGATTTTCATGATTTCGAATTGTTGAAGATCAACCAACAATAATGC
1 TTAAATGAGAGATTTTCATGATTTCGAATTGCTGAAGATCAACCAACAATAATGC
41455189 TTAAATGAGAGATTTTCATGATTTCGAATTGCTGAAGATCAACCAACAATAATGC
1 TTAAATGAGAGATTTTCATGATTTCGAATTGCTGAAGATCAACCAACAATAATGC
41455244 TT
1 TT
41455246 TAACATTCGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (55 bp):
TTAAATGAGAGATTTTCATGATTTCGAATTGCTGAAGATCAACCAACAATAATGC
Found at i:41458992 original size:10 final size:10
Alignment explanation
Indices: 41458977--41459004 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41458967 TATTAACTTA
41458977 CTTCTTTCTT
1 CTTCTTTCTT
41458987 CTTCTTTCTT
1 CTTCTTTCTT
41458997 CTTCTTTC
1 CTTCTTTC
41459005 ATTCATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:41463583 original size:88 final size:87
Alignment explanation
Indices: 41463432--41463595 Score: 240
Period size: 88 Copynumber: 1.9 Consensus size: 87
41463422 CTCATGGAGT
* * * *
41463432 AATATGAATATCGTTAAGTATCAATTAGTTGGGCAAAGCAGTTTCTTAACATTCAAATGTGAGAT
1 AATATAAATATCATTAAGTATCAATTAGTTGGGCAAAGCAGTTTCATAACACTCAAATGTGAGAT
*
41463497 CTATCGAAAGACCACAAGTTTA
66 CTATCAAAAGACCACAAGTTTA
*
41463519 AATATAAATATCATTCAAGTATCAATTAGTTGGGCAAAGCAGTTTCATAACACTCGAA-GATGAG
1 AATATAAATATCATT-AAGTATCAATTAGTTGGGCAAAGCAGTTTCATAACACTCAAATG-TGAG
*
41463583 ATTTATCAAAAGA
64 ATCTATCAAAAGA
41463596 TCGCAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
87 14 0.21
88 54 0.79
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (87 bp):
AATATAAATATCATTAAGTATCAATTAGTTGGGCAAAGCAGTTTCATAACACTCAAATGTGAGAT
CTATCAAAAGACCACAAGTTTA
Found at i:41466093 original size:22 final size:22
Alignment explanation
Indices: 41466070--41466113 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41466060 ATTATTCGAA
41466070 TTATTTAAAATTAAAAATTAAAT
1 TTATTT-AAATTAAAAATTAAAT
* *
41466093 TTATTTGAATTTAAAATTAAA
1 TTATTTAAATTAAAAATTAAA
41466114 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTATTTAAATTAAAAATTAAAT
Found at i:41473089 original size:2 final size:2
Alignment explanation
Indices: 41473082--41473117 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
41473072 ATACATATAA
41473082 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41473118 AAATATTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:41478660 original size:17 final size:17
Alignment explanation
Indices: 41478585--41478663 Score: 56
Period size: 17 Copynumber: 4.5 Consensus size: 17
41478575 ATAAAAATAA
*
41478585 AAATTTAATTATAAATT
1 AAATTAAATTATAAATT
41478602 AAATATAAA--AT-AATT
1 AAAT-TAAATTATAAATT
* * *
41478617 ATATTTATATCATAAAAATT
1 A-AATTAAAT--TATAAATT
41478637 CAAATTAAATTATAAATT
1 -AAATTAAATTATAAATT
41478655 AAATTAAAT
1 AAATTAAAT
41478664 AAAAAGTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
15 8 0.17
16 4 0.09
17 13 0.28
18 10 0.21
19 1 0.02
20 10 0.21
21 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAAATTATAAATT
Found at i:41482363 original size:6 final size:6
Alignment explanation
Indices: 41482352--41482376 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41482342 CCTGCAAATT
41482352 ATAAAC ATAAAC ATAAAC ATAAAC A
1 ATAAAC ATAAAC ATAAAC ATAAAC A
41482377 AATGAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAC
Found at i:41483005 original size:2 final size:2
Alignment explanation
Indices: 41482998--41483046 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
41482988 TAATGAGTTG
41482998 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41483040 TC TC TC T
1 TC TC TC T
41483047 GTTTTTCTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:41489943 original size:26 final size:26
Alignment explanation
Indices: 41489885--41489947 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
41489875 TATAATGACA
*
41489885 AAATAAAA-AATATATAATTAA-AAT
1 AAATAAAATAATATATAATTAATAAC
*
41489909 AAATTAAATAA-ATATAATTAATAAC
1 AAATAAAATAATATATAATTAATAAC
41489934 ACAATAAAATAATA
1 A-AATAAAATAATA
41489948 AATAGAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 17 0.53
25 5 0.16
26 9 0.28
27 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (26 bp):
AAATAAAATAATATATAATTAATAAC
Found at i:41489962 original size:30 final size:30
Alignment explanation
Indices: 41489906--41489962 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
41489896 ATATAATTAA
* * *
41489906 AATAAATTAAATAAATATAATTAATAACAC
1 AATAAAATAAATAAATAGAATAAATAACAC
41489936 AATAAAAT-AATAAATAGAAGTAAATAA
1 AATAAAATAAATAAATAGAA-TAAATAA
41489963 AATCACAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 10 0.43
30 13 0.57
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (30 bp):
AATAAAATAAATAAATAGAATAAATAACAC
Found at i:41490218 original size:21 final size:22
Alignment explanation
Indices: 41490184--41490233 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
41490174 ATAGCATAAA
*
41490184 AAATAACA-AATAAATAAAA-T
1 AAATAAAATAATAAATAAAATT
*
41490204 ACATAAAATAATAAATAAAATT
1 AAATAAAATAATAAATAAAATT
41490226 AAATAAAA
1 AAATAAAA
41490234 GCGAGAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.24
21 11 0.44
22 8 0.32
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (22 bp):
AAATAAAATAATAAATAAAATT
Found at i:41490296 original size:13 final size:15
Alignment explanation
Indices: 41490267--41490337 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
41490257 ATGAATAACC
41490267 AATAAATAAATCAAT
1 AATAAATAAATCAAT
41490282 AATAAA-AAA-CAAT
1 AATAAATAAATCAAT
*
41490295 AAATATATGAAATACAAT
1 -AATAAAT-AAAT-CAAT
*
41490313 CATAAA-AAATCTAAT
1 AATAAATAAATC-AAT
*
41490328 -ATAATTAAAT
1 AATAAATAAAT
41490338 TAAGGATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
13 4 0.09
14 13 0.29
15 17 0.38
16 3 0.07
17 4 0.09
18 4 0.09
ACGTcount: A:0.65, C:0.07, G:0.01, T:0.27
Consensus pattern (15 bp):
AATAAATAAATCAAT
Found at i:41490510 original size:14 final size:15
Alignment explanation
Indices: 41490491--41490524 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41490481 AACAACTAGA
*
41490491 TAAATAAA-CAAAAT
1 TAAATAAATAAAAAT
41490505 TAAATAAATAAAAAT
1 TAAATAAATAAAAAT
41490520 TAAAT
1 TAAAT
41490525 GTTAAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATAAATAAAAAT
Found at i:41493399 original size:19 final size:19
Alignment explanation
Indices: 41493377--41493422 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
41493367 AAATTTAAAT
41493377 AATTTTTTTGAAT-TTTTAA
1 AATTTTTTT-AATGTTTTAA
* *
41493396 AATTTTATTAATGTTTTAG
1 AATTTTTTTAATGTTTTAA
41493415 AATTTTTT
1 AATTTTTT
41493423 ATAAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (19 bp):
AATTTTTTTAATGTTTTAA
Found at i:41493407 original size:28 final size:28
Alignment explanation
Indices: 41493366--41493421 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
41493356 CCAATACTTA
* *
41493366 AAAATTTAAATAATTTTTTTGAATTTTT
1 AAAATTTAAATAATGTTTTAGAATTTTT
* *
41493394 AAAATTTTATTAATGTTTTAGAATTTTT
1 AAAATTTAAATAATGTTTTAGAATTTTT
41493422 TATAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (28 bp):
AAAATTTAAATAATGTTTTAGAATTTTT
Found at i:41497979 original size:11 final size:11
Alignment explanation
Indices: 41497965--41498010 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
41497955 TTTGATGTTG
*
41497965 TTTTGTTATCA
1 TTTTGTTATTA
41497976 TTTTGTTATTA
1 TTTTGTTATTA
* *
41497987 TATTGCTATTA
1 TTTTGTTATTA
*
41497998 TTTTGTTGTTA
1 TTTTGTTATTA
41498009 TT
1 TT
41498011 GTTTGGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.17, C:0.04, G:0.11, T:0.67
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:41498618 original size:21 final size:21
Alignment explanation
Indices: 41498565--41498623 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
41498555 TTGAACTTTG
* *
41498565 AAACCCTAGACCATGAACCCT
1 AAACCTTAGATCATGAACCCT
* * * *
41498586 ATACGTTGGATCATGGACCCT
1 AAACCTTAGATCATGAACCCT
*
41498607 AAACCTTAGATCTTGAA
1 AAACCTTAGATCATGAA
41498624 TCTTAGGTCC
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (21 bp):
AAACCTTAGATCATGAACCCT
Found at i:41506508 original size:13 final size:15
Alignment explanation
Indices: 41506490--41506529 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
41506480 TTTTTTTTCT
41506490 AAAATAATATA-A-A
1 AAAATAATATATATA
*
41506503 AAAATAATATATATC
1 AAAATAATATATATA
41506518 AAAATAATATAT
1 AAAATAATATAT
41506530 TCTTTTCGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 1 0.04
15 12 0.50
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAATATATATA
Found at i:41507010 original size:27 final size:27
Alignment explanation
Indices: 41506969--41507020 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
41506959 ATTCGGGTTG
*
41506969 GTGTCGCTTGACAGGTAGGCACCACTA
1 GTGTCGCCTGACAGGTAGGCACCACTA
*
41506996 GTGTCGCCTGTCAGGTAGGCACCAC
1 GTGTCGCCTGACAGGTAGGCACCAC
41507021 CCCCATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.31, T:0.21
Consensus pattern (27 bp):
GTGTCGCCTGACAGGTAGGCACCACTA
Found at i:41511088 original size:21 final size:19
Alignment explanation
Indices: 41511052--41511090 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
41511042 TATCCTTAAT
41511052 TTTTAAAAAATTAAATTTA
1 TTTTAAAAAATTAAATTTA
41511071 TTTTAAATAAAGTTAAATTT
1 TTTTAAA-AAA-TTAAATTT
41511091 TAAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTTAAAAAATTAAATTTA
Found at i:41519518 original size:188 final size:187
Alignment explanation
Indices: 41519177--41519522 Score: 498
Period size: 188 Copynumber: 1.8 Consensus size: 187
41519167 CACAAAATCA
* * *
41519177 TAACAATCTTGTGCTACCTCAACCAAGGAAATGTTAGGACAATACTATACATGAAGAAAACCAGC
1 TAACAATCTCGTACTACCTCAACCAAGGAAATGTTAGAACAATACTATACATGAAGAAAACCAGC
* * *
41519242 AATCACAACCCATGTATTTATGTACAAGCAATGAATTCAGGTTATAAGAAAGGTTTGAAATTATA
66 AATCACAACCCATGGATTTATGTACAAGCAACGAATTCAGGTTATAAAAAAGGTTTGAAATTATA
* *
41519307 CCTTCTTAATTTGAGCAAGAAAATCGATGGGGAAATCACTAAGGGACTATAGAGGCG
131 CCTTCCTAATCTGAGCAAGAAAATCGATGGGGAAATCACTAAGGGACTATAGAGGCG
* * * * **
41519364 TAACAATCTCGTACTACCTTAGCCTAAGGAAATGTTAGAACAATACTATGCATGAAGACAA-TTG
1 TAACAATCTCGTACTACCTCAACC-AAGGAAATGTTAGAACAATACTATACATGAAGAAAACCAG
* * *
41519428 ACAATCACAACCCATGGATTTATGTACGAGGAACGAA-TCCGGATTATAAAAAAGGTTTGAAATT
65 -CAATCACAACCCATGGATTTATGTACAAGCAACGAATTCAGG-TTATAAAAAAGGTTTGAAATT
41519492 ATACCTTCCTAATCTGAGCAAGAAAATCGAT
128 ATACCTTCCTAATCTGAGCAAGAAAATCGAT
41519523 TTTGGAAGTT
Statistics
Matches: 139, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
187 25 0.18
188 114 0.82
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (187 bp):
TAACAATCTCGTACTACCTCAACCAAGGAAATGTTAGAACAATACTATACATGAAGAAAACCAGC
AATCACAACCCATGGATTTATGTACAAGCAACGAATTCAGGTTATAAAAAAGGTTTGAAATTATA
CCTTCCTAATCTGAGCAAGAAAATCGATGGGGAAATCACTAAGGGACTATAGAGGCG
Found at i:41521099 original size:16 final size:17
Alignment explanation
Indices: 41521075--41521112 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41521065 TTTCTTGATT
41521075 TTAAT-TTATAAT-TAA
1 TTAATATTATAATATAA
41521090 TTAATATTATAATATAA
1 TTAATATTATAATATAA
41521107 -TAATAT
1 TTAATAT
41521113 AAATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 13 0.62
17 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATTATAATATAA
Found at i:41521525 original size:16 final size:17
Alignment explanation
Indices: 41521501--41521538 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
41521491 TTTCTTGATT
41521501 TTAAT-TTATAAT-TAA
1 TTAATATTATAATATAA
41521516 TTAATATTATAATATAA
1 TTAATATTATAATATAA
41521533 -TAATAT
1 TTAATAT
41521539 AAATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 13 0.62
17 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATATTATAATATAA
Done.