Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 207 of 240
Found at i:62831451 original size:11 final size:11
Alignment explanation
Indices: 62831410--62831494 Score: 60
Period size: 11 Copynumber: 8.4 Consensus size: 11
62831400 GAGCTTTGTT
*
62831410 TTATTATTTTA
1 TTATTATTATA
62831421 TTATT-TTA-A
1 TTATTATTATA
*
62831430 CTATTATT-TA
1 TTATTATTATA
62831440 -TATTA-T-TA
1 TTATTATTATA
*
62831448 TTATTATT-TC
1 TTATTATTATA
*
62831458 TCATGTA-TATA
1 TTAT-TATTATA
*
62831469 TTATTTTTATA
1 TTATTATTATA
62831480 TTATTATTATA
1 TTATTATTATA
62831491 TTAT
1 TTAT
62831495 ATATGCCCTC
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 3 0.05
9 15 0.25
10 12 0.20
11 29 0.49
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (11 bp):
TTATTATTATA
Found at i:62831452 original size:18 final size:18
Alignment explanation
Indices: 62831431--62831498 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
62831421 TTATTTTAAC
62831431 TATTATTTATATTATTAT
1 TATTATTTATATTATTAT
*
62831449 TATTATTTCTCATGTATATAT
1 TATTATTTAT-AT-TAT-TAT
62831470 TATT-TTTATATTATTAT
1 TATTATTTATATTATTAT
62831487 TA-TATTATATAT
1 TATTATT-TATAT
62831499 GCCCTCTCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.02
17 7 0.16
18 17 0.40
19 4 0.09
20 7 0.16
21 7 0.16
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (18 bp):
TATTATTTATATTATTAT
Found at i:62831736 original size:18 final size:19
Alignment explanation
Indices: 62831700--62831756 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
62831690 ACTATTACTA
*
62831700 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
62831720 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
62831737 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
62831755 TT
1 TT
62831757 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:62831860 original size:14 final size:14
Alignment explanation
Indices: 62831841--62831872 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
62831831 GTATTTCTAT
62831841 TATATACATATATA
1 TATATACATATATA
*
62831855 TATATACATTTATA
1 TATATACATATATA
62831869 TATA
1 TATA
62831873 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATACATATATA
Found at i:62844176 original size:44 final size:44
Alignment explanation
Indices: 62843999--62844546 Score: 330
Period size: 44 Copynumber: 12.5 Consensus size: 44
62843989 TCATTAAAGT
* * *
62843999 AGATCTTGTCTTCATGTATTGGCGTAAAGCAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTAAAGTAGATCGAAGATAGC
* * * * * * *
62844043 AGGTCCTATCTTCCTATATT-G-ATAGGAAGTGGATCCAGGAT-GC
1 AGATCTTGTCTTCCTATATTGGCGTA--AAGTAGATCGAAGATAGC
* * * ** * *
62844086 AGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGG-CGTAAAGTAGATCGAAGATAGC
* * *
62844131 AGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGGTAGC
1 AGATCTTGTCTTCCTATATTGGCGTAAAGTAGATCGAAGATAGC
* * * *
62844175 AGATCCTATCTTTCTATATT-G-GTAGGAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGCGTA--AAGTAGATCGAAGATAGC
* * ** * *
62844218 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGG-CGTAAAGTAGATCGAAGATAGC
* * *
62844263 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTAAAGTAGATCGAAGATAGC
* * * * * *
62844307 ATG-TCCTATCTTCCTATATT-G-ATAGGAAGTGGATCCAATAT-GC
1 A-GATCTTGTCTTCCTATATTGGCGTA--AAGTAGATCGAAGATAGC
* * ** * *
62844350 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGG-CGTAAAGTAGATCGAAGATAGC
* * *
62844395 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGGCGTAAAGTAGATCGAAGATAGC
* * * * * *
62844439 AGGTCCTATCTTCCTATATT-G-ATAGGAAGTGGATCCAAGAT-GC
1 AGATCTTGTCTTCCTATATTGGCGTA--AAGTAGATCGAAGATAGC
* * * * * *
62844482 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGATTGC
1 AGATCTTGTCTTCCTATATTGG-CGTAAAGTAGATCGAAGATAGC
* *
62844527 AGATCTTGCCTTCCTGTATT
1 AGATCTTGTCTTCCTATATT
62844547 TGGCAGCGAA
Statistics
Matches: 374, Mismatches: 104, Indels: 51
0.71 0.20 0.10
Matches are distributed among these distances:
42 8 0.02
43 75 0.20
44 208 0.56
45 81 0.22
46 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (44 bp):
AGATCTTGTCTTCCTATATTGGCGTAAAGTAGATCGAAGATAGC
Found at i:62844236 original size:132 final size:132
Alignment explanation
Indices: 62843994--62844546 Score: 917
Period size: 132 Copynumber: 4.2 Consensus size: 132
62843984 TGAAGTCATT
* *
62843994 AAAGTAGATCTTGTCTTCATGTATTGGCGTAAAGCAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
62844059 TATTGATAGGAAGTGGATCCAGGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
62844124 AG
131 AG
* * *
62844126 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* *
62844191 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
62844256 AG
131 AG
* *
62844258 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCATGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
*
62844323 TATTGATAGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
62844388 AG
131 AG
*
62844390 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
* * * *
62844455 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGA
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
62844520 AG
131 AG
** * *
62844522 ATTGCAGATCTTGCCTTCCTGTATT
1 AAAGCAGATCTTGTCTTCATGTATT
62844547 TGGCAGCGAA
Statistics
Matches: 394, Mismatches: 27, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 394 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
AG
Found at i:62844540 original size:88 final size:89
Alignment explanation
Indices: 62844084--62844576 Score: 385
Period size: 88 Copynumber: 5.6 Consensus size: 89
62844074 GATCCAGGAT
* * * * ***
62844084 GCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGC-AGAAAGCAGATCTTGTCTTCATGT
1 GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC-CAAG-ATGCAGATCTTGTCTTCCCAT
* * *
62844148 ATTGG-CGTAAAGTAGATCGAAGGTA
64 ATTGGTGGTGAAGTAGATCGAAGATA
* * * * *
62844173 GCAGATCCTATCTTTCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATAT
1 GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCCAAGATGCAGATCTTGTCTTCCCATAT
* * *
62844237 TGGTGGCGAAGTAGATCGCAGAAA
66 TGGTGGTGAAGTAGATCGAAGATA
* * * * * * * *
62844261 GCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCATG-TCCTATCTTCCTAT
1 GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCCAAGAT-GCA-GATCTTGTCTTCCCAT
* * * * *
62844324 ATTGATAG-GAAGTGGATCCAATAT-
64 ATTGGTGGTGAAGTAGATCGAAGATA
* * * ***
62844348 GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC-AGAAAGCAGATCTTGTCTTCATGT
1 GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC-CAAG-ATGCAGATCTTGTCTTCCCAT
*
62844412 ATTGG-CGTGAAGTAGATCGAAGATA
64 ATTGGTGGTGAAGTAGATCGAAGATA
* * * * * *
62844437 GCAGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATAC
1 GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCCAAGATGCAGATCTTGTCTTCCCATAT
* *
62844501 TGGTGGTGAAGTAGATTGAAGATT
66 TGGTGGTGAAGTAGATCGAAGATA
* * * * *
62844525 GCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGAT
1 GCAGATCTTGTCTTCCTATA-TTGGTAGCGAAGTAGATCCAAGAT-GCAGAT
62844577 TTTACCTCCC
Statistics
Matches: 314, Mismatches: 74, Indels: 30
0.75 0.18 0.07
Matches are distributed among these distances:
87 68 0.22
88 156 0.50
89 70 0.22
90 14 0.04
91 6 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (89 bp):
GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCCAAGATGCAGATCTTGTCTTCCCATAT
TGGTGGTGAAGTAGATCGAAGATA
Found at i:62844685 original size:46 final size:46
Alignment explanation
Indices: 62844628--62844947 Score: 157
Period size: 46 Copynumber: 7.0 Consensus size: 46
62844618 CTCTATCTCA
*
62844628 CTGTATCTGGCAGTGGAATAGATTGAAGATTACAGATCTTGCCTTC
1 CTGTATCTGGCAGTGGAATAGATTGAAGATGACAGATCTTGCCTTC
* * * * * * * *
62844674 CTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTCC
1 CTGTATCTGGCAGTGGAA-TAGATTGAAGATGACAGATCTTGCCTTC
* * * ** * *
62844720 CTGTGA-CT-ACAGTGGAGTACATTGAAGCCGATA-A-CTCTGTC-TC
1 CTGT-ATCTGGCAGTGGAATAGATTGAAGATGACAGATCT-TGCCTTC
62844763 ACTGTATCTGGCAGTGGAATAGATTGAAGATTG-CAGATCTTGCCTTC
1 -CTGTATCTGGCAGTGGAATAGATTGAAGA-TGACAGATCTTGCCTTC
* * * * * * *
62844810 CTGTAT-TAGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTCC
1 CTGTATCT-GGCAGTGGAA-TAGATTGAAGATGACAGATCTTGCCTTC
* * * ** * *
62844856 CTGTGA-CT-ACAGTGGAGTACATTGAAGCCGATA-ACTCTAT--CTCC
1 CTGT-ATCTGGCAGTGGAATAGATTGAAGATGACAGA-TCT-TGCCTTC
*
62844900 CTGTATCTGGCAGTGGAATAGATTGAAGATTG-CAGATCCTGCCTTC
1 CTGTATCTGGCAGTGGAATAGATTGAAGA-TGACAGATCTTGCCTTC
62844946 CT
1 CT
62844948 ATATTGGTAG
Statistics
Matches: 193, Mismatches: 56, Indels: 50
0.65 0.19 0.17
Matches are distributed among these distances:
43 4 0.02
44 21 0.11
45 71 0.37
46 90 0.47
47 7 0.04
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (46 bp):
CTGTATCTGGCAGTGGAATAGATTGAAGATGACAGATCTTGCCTTC
Found at i:62844794 original size:136 final size:136
Alignment explanation
Indices: 62844512--62844952 Score: 787
Period size: 136 Copynumber: 3.3 Consensus size: 136
62844502 GGTGGTGAAG
*
62844512 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGAT
* *
62844577 TTTACCTCCC--TGACCACAATGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
66 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
62844640 GTGGAA
131 GTGGAA
*
62844646 TAGATTGAAGATTACAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGAT
*
62844711 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTGTCTCACTGTATCTGGCA
66 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
62844776 GTGGAA
131 GTGGAA
*
62844782 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGAT
*
62844847 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCA
66 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
62844912 GTGGAA
131 GTGGAA
* *
62844918 TAGATTGAAGATTGCAGATCCTGCCTTCCTATATT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATT
62844953 GGTAGGAAGT
Statistics
Matches: 294, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
134 73 0.25
136 221 0.75
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (136 bp):
TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGAT
TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
GTGGAA
Found at i:62845137 original size:43 final size:40
Alignment explanation
Indices: 62845090--62845178 Score: 124
Period size: 40 Copynumber: 2.1 Consensus size: 40
62845080 CTTGGGCAAC
*
62845090 AGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCG--CATTA-AATCTTATCTCCCTAAGCAGT
* *
62845133 AGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
62845173 AGTGGA
1 AGTGGA
62845179 GCAGATAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 26 0.60
41 4 0.09
43 13 0.30
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (40 bp):
AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
Found at i:62845166 original size:40 final size:40
Alignment explanation
Indices: 62845114--62845240 Score: 155
Period size: 40 Copynumber: 3.1 Consensus size: 40
62845104 AAGATTACAA
* *
62845114 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*** *
62845154 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCA-AG
* * *
62845195 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
62845236 TCTTA
1 TCTTA
62845241 GTGGAGCAGA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 37 0.51
41 4 0.06
42 31 0.43
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
Found at i:62845616 original size:16 final size:16
Alignment explanation
Indices: 62845597--62845646 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
62845587 CCTTTGTTGG
62845597 CCACCCACCTTAGCCA
1 CCACCCACCTTAGCCA
*
62845613 CCACTCAACCTTA-CCA
1 CCAC-CCACCTTAGCCA
*
62845629 CCA-CCACCCTTGGCCA
1 CCACCCA-CCTTAGCCA
62845645 CC
1 CC
62845647 TAAACCACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 4 0.14
16 15 0.54
17 7 0.25
ACGTcount: A:0.24, C:0.56, G:0.06, T:0.14
Consensus pattern (16 bp):
CCACCCACCTTAGCCA
Found at i:62845774 original size:21 final size:21
Alignment explanation
Indices: 62845729--62845794 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
62845719 GTTTTTGGTT
* *
62845729 TTTTGGAGAAGGATTGTTCTTTG
1 TTTTGGAGGAGG-TT-TTTTTTG
62845752 TTTTGGAGGAGGTTTTTTTTG
1 TTTTGGAGGAGGTTTTTTTTG
**
62845773 TTTT-TTGGAGGTGTTTTTTTG
1 TTTTGGAGGAGGT-TTTTTTTG
62845794 T
1 T
62845795 AAAAAAGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 19 0.50
22 2 0.05
23 11 0.29
ACGTcount: A:0.11, C:0.02, G:0.30, T:0.58
Consensus pattern (21 bp):
TTTTGGAGGAGGTTTTTTTTG
Found at i:62845778 original size:23 final size:23
Alignment explanation
Indices: 62845720--62845792 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
62845710 TAGGGGTGGG
* *
62845720 TTTTTGGTTTTTTGGAGAAGGATT
1 TTTTTTGTTTTTTGGAGGAGG-TT
*
62845744 GTTCTTTG--TTTTGGAGGAGGTT
1 -TTTTTTGTTTTTTGGAGGAGGTT
*
62845766 TTTTTTGTTTTTTGGAGG-TGTT
1 TTTTTTGTTTTTTGGAGGAGGTT
62845788 TTTTT
1 TTTTT
62845793 GTAAAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
21 6 0.15
22 10 0.24
23 20 0.49
25 5 0.12
ACGTcount: A:0.10, C:0.01, G:0.29, T:0.60
Consensus pattern (23 bp):
TTTTTTGTTTTTTGGAGGAGGTT
Found at i:62846132 original size:8 final size:8
Alignment explanation
Indices: 62846119--62846202 Score: 55
Period size: 8 Copynumber: 9.8 Consensus size: 8
62846109 GAGAGCTTTG
62846119 TTTTATTA
1 TTTTATTA
62846127 TTTTATTA
1 TTTTATTA
62846135 TTTTACTATTA
1 -TTT--TATTA
62846146 TTTATATTA
1 TTT-TATTA
62846155 TTATTATTA
1 TT-TTATTA
62846164 TTTCTCATGTA
1 TTT-T-AT-TA
*
62846175 -TATATTA
1 TTTTATTA
62846182 TTTT-TTA
1 TTTTATTA
*
62846189 TATTATTA
1 TTTTATTA
*
62846197 TATTAT
1 TTTTAT
62846203 ATATGCCCTC
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
7 8 0.13
8 22 0.35
9 19 0.30
10 7 0.11
11 7 0.11
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.67
Consensus pattern (8 bp):
TTTTATTA
Found at i:62846135 original size:3 final size:3
Alignment explanation
Indices: 62846121--62846202 Score: 54
Period size: 3 Copynumber: 28.3 Consensus size: 3
62846111 GAGCTTTGTT
*
62846121 TTA TTA TT- TTA TTA TT- TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
62846164 TT- TCTCA TGTA TATA TTA TT- TT- TTA -TA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
62846203 ATATGCCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
2 14 0.22
3 43 0.66
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:62846444 original size:18 final size:19
Alignment explanation
Indices: 62846408--62846464 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
62846398 ACTATTACTA
*
62846408 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
62846428 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
62846445 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
62846463 TT
1 TT
62846465 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:62846566 original size:12 final size:12
Alignment explanation
Indices: 62846549--62846578 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
62846539 GTATTTCTAT
62846549 TATATACATATA
1 TATATACATATA
*
62846561 TATATACATTTA
1 TATATACATATA
62846573 TATATA
1 TATATA
62846579 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATACATATA
Found at i:62848927 original size:22 final size:22
Alignment explanation
Indices: 62848885--62848927 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
62848875 TGCCGTTGTT
*
62848885 TTGCTACCATTTTGCTATTTTA
1 TTGCTACCATTTTGATATTTTA
* *
62848907 TTGCTACTATTTTGATGTTTT
1 TTGCTACCATTTTGATATTTT
62848928 TGTTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (22 bp):
TTGCTACCATTTTGATATTTTA
Found at i:62849388 original size:30 final size:31
Alignment explanation
Indices: 62849336--62849395 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
62849326 TAAGTTTTTA
62849336 TACTTTTCATAAATTTAAAATTTA-GTCCATT
1 TACTTTTCA-AAATTTAAAATTTAGGTCCATT
62849367 TACTTTTC-AAATTTCAAAATTTAGGTCCA
1 TACTTTTCAAAATTT-AAAATTTAGGTCCA
62849396 ACTATTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 6 0.22
30 8 0.30
31 13 0.48
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (31 bp):
TACTTTTCAAAATTTAAAATTTAGGTCCATT
Found at i:62854348 original size:21 final size:22
Alignment explanation
Indices: 62854307--62854349 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
62854297 TAAATAAATG
62854307 TGTAATAAATATATGTATACATT
1 TGTAATAAATATATG-ATACATT
*
62854330 TGTAATTAATATATG-TACAT
1 TGTAATAAATATATGATACAT
62854350 ACTTATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (22 bp):
TGTAATAAATATATGATACATT
Found at i:62854440 original size:19 final size:19
Alignment explanation
Indices: 62854402--62854440 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
62854392 TTAATTAAAT
*
62854402 AAAAGAAATAAAAGATAGA
1 AAAAGAAATAAAAGACAGA
62854421 AAAAGAGAATAAAA-ACAGA
1 AAAAGA-AATAAAAGACAGA
62854440 A
1 A
62854441 TAGCAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAAGAAATAAAAGACAGA
Found at i:62856452 original size:46 final size:44
Alignment explanation
Indices: 62856348--62856455 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
62856338 TGTCTTTAAC
** * * *
62856348 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
62856392 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
62856438 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
62856456 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:62857359 original size:17 final size:16
Alignment explanation
Indices: 62857332--62857364 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
62857322 TTCTATTCTG
62857332 TTTCTTTCTTTCTTTT
1 TTTCTTTCTTTCTTTT
62857348 TTTCTATTCTTTCTTTT
1 TTTCT-TTCTTTCTTTT
62857365 GTTTATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTCTTTCTTTT
Found at i:62857397 original size:19 final size:19
Alignment explanation
Indices: 62857373--62857415 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
62857363 TTGTTTATGT
62857373 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
62857392 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
62857411 ATATA
1 ATATA
62857416 AAACATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:62857411 original size:24 final size:24
Alignment explanation
Indices: 62857379--62857443 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
62857369 ATGTATATAT
62857379 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATATA-TAATCA
* *
62857403 ATAATATAATATAAAACATAATCA
1 ATAATATAATATAATATATAATCA
* *
62857427 TTACTATAATATAATAT
1 ATAATATAATATAATAT
62857444 TTTTTTAACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 4 0.12
24 30 0.88
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAATATAATATAATATATAATCA
Found at i:62857443 original size:5 final size:5
Alignment explanation
Indices: 62857372--62857416 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
62857362 TTTGTTTATG
62857372 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA
62857417 AACATAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.11
5 23 0.64
6 8 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:62862596 original size:46 final size:44
Alignment explanation
Indices: 62862492--62862599 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
62862482 TGTCTTTAAC
** * * *
62862492 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
62862536 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
62862582 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
62862600 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:62863489 original size:9 final size:9
Alignment explanation
Indices: 62863475--62863509 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
62863465 TTCTATTCTG
62863475 TTTCTTTTC
1 TTTCTTTTC
*
62863484 TTTCTTTTT
1 TTTCTTTTC
*
62863493 TTTCTATTC
1 TTTCTTTTC
62863502 TTTCTTTT
1 TTTCTTTT
62863510 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:62863502 original size:18 final size:19
Alignment explanation
Indices: 62863475--62863514 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
62863465 TTCTATTCTG
*
62863475 TTTCTTTTCTTTCTTTT-T
1 TTTCTATTCTTTCTTTTGT
62863493 TTTCTATTCTTTCTTTTGT
1 TTTCTATTCTTTCTTTTGT
62863512 TTT
1 TTT
62863515 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTCTATTCTTTCTTTTGT
Found at i:62863531 original size:5 final size:5
Alignment explanation
Indices: 62863518--62863590 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
62863508 TTGTTTTATG
62863518 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
62863566 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
62863591 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:62863543 original size:19 final size:19
Alignment explanation
Indices: 62863519--62863561 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
62863509 TGTTTTATGT
62863519 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
62863538 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
62863557 ATATA
1 ATATA
62863562 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:62863571 original size:24 final size:25
Alignment explanation
Indices: 62863525--62863589 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
62863515 ATGTATATAT
* *
62863525 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
62863549 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
62863574 TTACTATAATATAATA
1 ATAATATAATATAATA
62863590 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:62864439 original size:41 final size:37
Alignment explanation
Indices: 62864391--62864493 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 37
62864381 TCGAACTTGA
62864391 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
62864431 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
*
62864469 GCCGATGAGACACTGGGTGTCAACT
1 GTCGATGAGACACTGGGTGTCAACT
62864494 ATTGCTTCGA
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
37 19 0.39
38 11 0.22
40 2 0.04
41 17 0.35
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:62867555 original size:21 final size:22
Alignment explanation
Indices: 62867531--62867579 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
62867521 TGAATGCTTA
*
62867531 ATTTATTT-TAAATAAAATTTT
1 ATTTATTTAAAAATAAAATTTT
62867552 ATTT-TTTAAAAATAAAATTTT
1 ATTTATTTAAAAATAAAATTTT
62867573 ATTTATT
1 ATTTATT
62867580 CATAGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATTTAAAAATAAAATTTT
Found at i:62869225 original size:38 final size:37
Alignment explanation
Indices: 62869153--62869225 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
62869143 AAGTAATAAT
* * * *
62869153 TTGACACCTAATGTCTCATCGGTTAAACCGAAGTAAA
1 TTGACACCCAATGCCTAATCGATTAAACCGAAGTAAA
*
62869190 TTGACACCCAATGCCTAATCGAATTAATCCGAAGTA
1 TTGACACCCAATGCCTAATCG-ATTAAACCGAAGTA
62869226 GTAAACTGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 18 0.60
38 12 0.40
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (37 bp):
TTGACACCCAATGCCTAATCGATTAAACCGAAGTAAA
Found at i:62869455 original size:24 final size:24
Alignment explanation
Indices: 62869410--62869456 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
62869400 TATATATACC
62869410 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
62869434 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
62869457 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:62870159 original size:25 final size:24
Alignment explanation
Indices: 62870130--62870199 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 24
62870120 TTTCTCCTTC
62870130 CTTTCTTTCCTTTTTCTTTTCT-TTT
1 CTTTCTTT-CTTTTTC-TTTCTGTTT
62870155 CTTTCTTTCTTTTTCTTTCTGTTT
1 CTTTCTTTCTTTTTCTTTCTGTTT
*
62870179 CGTTTCTATCTATCTTTCTTT
1 C-TTTCTTTCT-T-TTTCTTT
62870200 TTATTTATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 5 0.12
24 11 0.28
25 16 0.40
26 1 0.03
27 7 0.17
ACGTcount: A:0.03, C:0.23, G:0.03, T:0.71
Consensus pattern (24 bp):
CTTTCTTTCTTTTTCTTTCTGTTT
Found at i:62870161 original size:14 final size:14
Alignment explanation
Indices: 62870142--62870185 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
62870132 TTCTTTCCTT
62870142 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
62870156 TTTC-TTTCTTTTTC
1 TTTCTTTTC-TTTTC
*
62870170 TTTCTGTTTCGTTTC
1 TTTCT-TTTCTTTTC
62870185 T
1 T
62870186 ATCTATCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.15
14 13 0.50
15 5 0.19
16 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:62870162 original size:29 final size:29
Alignment explanation
Indices: 62870130--62870201 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
62870120 TTTCTCCTTC
* *
62870130 CTTTCTTTCCTTTTTCT-TTTCTTTTCTTT
1 CTTTCTTT-CTTTTTCTGTTTCGTTTCTAT
62870159 CTTTCTTT-TTCTTTCTGTTTCGTTTCTAT
1 CTTTCTTTCTT-TTTCTGTTTCGTTTCTAT
*
62870188 CTATCTTTCTTTTT
1 CTTTCTTTCTTTTT
62870202 ATTTATTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 2 0.05
28 5 0.14
29 28 0.76
30 2 0.05
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (29 bp):
CTTTCTTTCTTTTTCTGTTTCGTTTCTAT
Found at i:62870232 original size:5 final size:5
Alignment explanation
Indices: 62870222--62870284 Score: 119
Period size: 5 Copynumber: 12.8 Consensus size: 5
62870212 TATTTTTTAT
62870222 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
62870272 TATAA TA-AA TATA
1 TATAA TATAA TATA
62870285 CTTAATAATT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.07
5 53 0.93
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:62871431 original size:31 final size:31
Alignment explanation
Indices: 62871395--62871457 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
62871385 AAAGTTATTT
62871395 CTTGAAATACTTTTTTTCGAGAGTATTTCGA
1 CTTGAAATACTTTTTTTCGAGAGTATTTCGA
62871426 CTTGAAATACTTTTTTTCGAGAGTATTTCGA
1 CTTGAAATACTTTTTTTCGAGAGTATTTCGA
62871457 C
1 C
62871458 ATTCATGAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (31 bp):
CTTGAAATACTTTTTTTCGAGAGTATTTCGA
Found at i:62873885 original size:19 final size:19
Alignment explanation
Indices: 62873831--62873886 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
62873821 TCCAACAACA
* *
62873831 ATTTAAAATCTTATAAA-A
1 ATTTAAAATATTATAAATT
* *
62873849 AATTAAAA-AGTATAAAATT
1 ATTTAAAATATTAT-AAATT
62873868 ATTTAAAATATTATAAATT
1 ATTTAAAATATTATAAATT
62873887 CTAATATATG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 3 0.10
18 10 0.34
19 12 0.41
20 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTTAAAATATTATAAATT
Found at i:62875806 original size:25 final size:25
Alignment explanation
Indices: 62875778--62875880 Score: 95
Period size: 25 Copynumber: 4.1 Consensus size: 25
62875768 CTCATACAGA
*
62875778 CTTTTCACAAAATTAGCTACAAAGG
1 CTTTTCACAAAATTAGCCACAAAGG
* *
62875803 C-TTTC-CAAATAATACGCCACAAAGA
1 CTTTTCACAAA-ATTA-GCCACAAAGG
*
62875828 CTTTTCACAAGATTAGCCACAAAGG
1 CTTTTCACAAAATTAGCCACAAAGG
* * *
62875853 CTTTCCAGATAA-TACGCCACAAAGG
1 CTTTTCACAAAATTA-GCCACAAAGG
62875878 CTT
1 CTT
62875881 CCTAGGTAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
23 4 0.06
24 9 0.14
25 40 0.63
26 7 0.11
27 3 0.05
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (25 bp):
CTTTTCACAAAATTAGCCACAAAGG
Found at i:62875850 original size:50 final size:50
Alignment explanation
Indices: 62875775--62875876 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
62875765 TTCCTCATAC
*
62875775 AGACTTTTCACAAAATTAGCTACAAAGGCTTTCCAAATAATACGCCACAA
1 AGACTTTTCACAAAATTAGCCACAAAGGCTTTCCAAATAATACGCCACAA
* *
62875825 AGACTTTTCACAAGATTAGCCACAAAGGCTTTCCAGATAATACGCCACAA
1 AGACTTTTCACAAAATTAGCCACAAAGGCTTTCCAAATAATACGCCACAA
62875875 AG
1 AG
62875877 GCTTCCTAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.23
Consensus pattern (50 bp):
AGACTTTTCACAAAATTAGCCACAAAGGCTTTCCAAATAATACGCCACAA
Found at i:62879420 original size:6 final size:7
Alignment explanation
Indices: 62879408--62879438 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
62879398 TAAAAATATA
62879408 AATTTTT
1 AATTTTT
62879415 AATTTTT
1 AATTTTT
62879422 AATTTTT
1 AATTTTT
62879429 AATTTTT
1 AATTTTT
62879436 AAT
1 AAT
62879439 AAAATAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:62884119 original size:28 final size:28
Alignment explanation
Indices: 62884087--62884140 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
62884077 TTTTTTATCT
62884087 TAAACACCAAACCATAAATCTCAAATAA
1 TAAACACCAAACCATAAATCTCAAATAA
* * * *
62884115 TAAACTCTAAACCCTAAATCTTAAAT
1 TAAACACCAAACCATAAATCTCAAAT
62884141 TTAGAGTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (28 bp):
TAAACACCAAACCATAAATCTCAAATAA
Found at i:62890798 original size:3 final size:3
Alignment explanation
Indices: 62890790--62890829 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
62890780 TGCCAAAATC
62890790 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
62890830 TTTTGCATTG
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:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:62895030 original size:7 final size:7
Alignment explanation
Indices: 62895018--62895042 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62895008 AGATACACGA
62895018 GAAATGG
1 GAAATGG
62895025 GAAATGG
1 GAAATGG
62895032 GAAATGG
1 GAAATGG
62895039 GAAA
1 GAAA
62895043 CGCGAAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (7 bp):
GAAATGG
Found at i:62895049 original size:14 final size:14
Alignment explanation
Indices: 62895018--62895051 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
62895008 AGATACACGA
* *
62895018 GAAATGGGAAATGG
1 GAAATGGGAAACGC
62895032 GAAATGGGAAACGC
1 GAAATGGGAAACGC
62895046 GAAATG
1 GAAATG
62895052 TAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.38, T:0.12
Consensus pattern (14 bp):
GAAATGGGAAACGC
Found at i:62907805 original size:18 final size:18
Alignment explanation
Indices: 62907778--62907822 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
62907768 TTTTTTTTAT
*
62907778 AATG-TTTTTGTCTCAAA
1 AATGCTTTTTGTCCCAAA
*
62907795 AGTGCTTTTTGTCCCAAA
1 AATGCTTTTTGTCCCAAA
62907813 AATGCTTTTT
1 AATGCTTTTT
62907823 CGAAGCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (18 bp):
AATGCTTTTTGTCCCAAA
Found at i:62908229 original size:143 final size:140
Alignment explanation
Indices: 62907888--62908260 Score: 434
Period size: 139 Copynumber: 2.6 Consensus size: 140
62907878 TCCCATCTTT
* * * *
62907888 ACCAGGCATATATCCTGCCTCCTCCATATGTGGAATAAGCAACTCTACAACCCCATTTGATCATT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATA
* * * *
62907953 TTCAGTAATTCAATTCCGTTTCTT-ATGCTTCTCTTCTCTTCAAGTCCCACTTTCAAGATCATGT
66 TTCAGTAATTCACTTCAGTTTCTTCATGCTTCTCTCCTCTTCAAGGCCCACTTTCAAGATCATGT
**
62908017 ATCAATGTAA
131 ATCAATCAAA
* * * *
62908027 ACCAGGCATTTACCCTGTTTCTTCCATATGTAGAACAAGCAACT-TAACAACCCCATTTGATCAT
1 ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCT-ACAACCCCATTTGATCAT
* * * *
62908091 ATTCAGTACCTT-ACTTTAGTTTCTTCA-GCTTCTCTCCT-TTGAAGGCCTA-TCTTCAAGATCA
65 ATTCAGTA-ATTCACTTCAGTTTCTTCATGCTTCTCTCCTCTTCAAGGCCCACT-TTCAAGATCA
62908152 TGTATCAAACAATCAAA
128 TGTAT----CAATCAAA
* * *
62908169 ACCAGGCATGTATCCTAGCTTCTTCCATATTTAGAATAAGCAACTCTATAACCCCATTTGATCAT
1 ACCAGGCATATATCCT-GCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCAT
*
62908234 GTTCAGTAATTCACTTCAGTTTCTTCA
65 ATTCAGTAATTCACTTCAGTTTCTTCA
62908261 AATCCCAACT
Statistics
Matches: 196, Mismatches: 27, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
137 1 0.01
138 24 0.12
139 82 0.42
140 3 0.02
142 22 0.11
143 63 0.32
144 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (140 bp):
ACCAGGCATATATCCTGCTTCTTCCATATGTAGAATAAGCAACTCTACAACCCCATTTGATCATA
TTCAGTAATTCACTTCAGTTTCTTCATGCTTCTCTCCTCTTCAAGGCCCACTTTCAAGATCATGT
ATCAATCAAA
Found at i:62911829 original size:18 final size:18
Alignment explanation
Indices: 62911802--62911876 Score: 114
Period size: 18 Copynumber: 4.2 Consensus size: 18
62911792 TACGACCGTT
*
62911802 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
*
62911820 TACGGCACTATTCATGTA
1 TACGGCACTATTCACGTA
62911838 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
62911856 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
62911874 TAC
1 TAC
62911877 AGTAGTTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:62917313 original size:42 final size:42
Alignment explanation
Indices: 62917265--62917636 Score: 390
Period size: 42 Copynumber: 8.5 Consensus size: 42
62917255 AGCCGCACAG
62917265 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* * *
62917307 TTAATCCTACCTCAATTAGGATTTATCATTTTAGCTTTTCTT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* **
62917349 TTAATCCCACCTCCATTAGGATTTATATAAGCATATCTTTTTAAATTTTCAT
1 TTAATCCCACCTCAATTAGG----AT-T-----TATCTTTTTAGCTTTTCAT
* * *
62917401 TTAATCTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* *
62917443 TTAATCCCAACTCAATTAGGATTTATGTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
*
62917485 TTAATCCCA-C-C-ATTGAGGATTTATGTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATT-AGGATTTATCTTTTTAGCTTTTCAT
* * *
62917525 TTAATCCCACCTCAATTAGGAGGATTTATGTTTTTAGTTTTTCTT
1 TTAATCCCACCTCAATT---AGGATTTATCTTTTTAGCTTTTCAT
* * *
62917570 TTAATCCCACCTCAATTAGGAGGACTTATGTTTTTAGTTTTTCAT
1 TTAATCCCACCTCAATT---AGGATTTATCTTTTTAGCTTTTCAT
* *
62917615 TTAATCCCGCCTGAATTAGGAT
1 TTAATCCCACCTCAATTAGGAT
62917637 ACTTCTGTTC
Statistics
Matches: 288, Mismatches: 26, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
39 3 0.01
40 35 0.12
41 2 0.01
42 124 0.43
43 3 0.01
45 82 0.28
46 2 0.01
47 2 0.01
48 2 0.01
52 33 0.11
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.47
Consensus pattern (42 bp):
TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
Found at i:62917449 original size:94 final size:94
Alignment explanation
Indices: 62917288--62917468 Score: 274
Period size: 94 Copynumber: 1.9 Consensus size: 94
62917278 AATTAGGATT
** * *
62917288 TATCTTTTTAGCTTTTCATTTAATCCTACCTCAATTAGGATTTATCATTTTAGCTTTTCTTTTAA
1 TATCTTTTTAAATTTTCATTTAATCCTACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTAA
* *
62917353 TCCCACCTCCATTAGGATTTATATAAGCA
66 TCCCAACTCAATTAGGATTTATATAAGCA
* *
62917382 TATCTTTTTAAATTTTCATTTAAT-CTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCATTTA
1 TATCTTTTTAAATTTTCATTTAATCCT-ACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTA
62917446 ATCCCAACTCAATTAGGATTTAT
65 ATCCCAACTCAATTAGGATTTAT
62917469 GTTTTTAGCT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 2 0.03
94 76 0.97
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.48
Consensus pattern (94 bp):
TATCTTTTTAAATTTTCATTTAATCCTACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTAA
TCCCAACTCAATTAGGATTTATATAAGCA
Found at i:62917528 original size:136 final size:134
Alignment explanation
Indices: 62917265--62917622 Score: 378
Period size: 136 Copynumber: 2.7 Consensus size: 134
62917255 AGCCGCACAG
* * *
62917265 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCATTTAATCCTACCTCAATTAGGATT
1 TTAATCCCACCTCAATTAGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATTAGGATT
* *
62917330 TATCATTTTAGCTTTTCTTTTAATCCCACCTCCATTAGGATTTATATAAGCATATCTTTTTAAAT
66 TATCATTTTAGCTTTTCATTTAATCCCA-C-CCATTAGGATTTATATAAGCATATCTATTTAAAT
62917395 TTTCAT
129 TTTCAT
* *
62917401 TTAATCTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCATTTAATCCCAACTCAATTAGGATT
1 TTAATCCCACCTCAATTAGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATTAGGATT
** **
62917466 TATGTTTTTAGCTTTTCATTTAATCCCA-CCATTGAGGA-TT-TAT--G----T-T-TTTAGCTT
66 TATCATTTTAGCTTTTCATTTAATCCCACCCATT-AGGATTTATATAAGCATATCTATTTAAATT
62917520 TTCAT
130 TTCAT
** * * *
62917525 TTAATCCCACCTCAATTAGGAGGATTTATGTTTTTAGTTTTTCTTTTAATCCCACCTCAATTAGG
1 TTAATCCCACCTCAATT---AGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATT---
* ** *
62917590 AGGACTTATGTTTTTAGTTTTTCATTTAATCCC
60 AGGATTTATCATTTTAGCTTTTCATTTAATCCC
62917623 GCCTGAATTA
Statistics
Matches: 198, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
124 27 0.14
125 1 0.01
126 1 0.01
127 38 0.19
130 32 0.16
132 3 0.02
133 7 0.04
134 4 0.02
136 85 0.43
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (134 bp):
TTAATCCCACCTCAATTAGGATTTACCTTTTTAGCTTTTCATTTAATCCCAACTCAATTAGGATT
TATCATTTTAGCTTTTCATTTAATCCCACCCATTAGGATTTATATAAGCATATCTATTTAAATTT
TCAT
Found at i:62917567 original size:45 final size:43
Alignment explanation
Indices: 62917394--62917636 Score: 318
Period size: 45 Copynumber: 5.7 Consensus size: 43
62917384 TCTTTTTAAA
* **
62917394 TTTTCATTTAATCTCACCTCAATT-AGGATTTACCTTTTTAGT
1 TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
* *
62917436 TTTTCATTTAATCCCAACTCAATT-AGGATTTATGTTTTTAGC
1 TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
*
62917478 TTTTCATTTAATCCCA-C-C-ATTGAGGATTTATGTTTTTAGC
1 TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
62917518 TTTTCATTTAATCCCACCTCAATTAGGAGGATTTATGTTTTTAGT
1 TTTTCATTTAATCCCACCTCAATT--GAGGATTTATGTTTTTAGT
* *
62917563 TTTTCTTTTAATCCCACCTCAATTAGGAGGACTTATGTTTTTAGT
1 TTTTCATTTAATCCCACCTCAATT--GAGGATTTATGTTTTTAGT
* *
62917608 TTTTCATTTAATCCCGCCTGAATT-AGGAT
1 TTTTCATTTAATCCCACCTCAATTGAGGAT
62917637 ACTTCTGTTC
Statistics
Matches: 183, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
39 3 0.02
40 35 0.19
41 2 0.01
42 58 0.32
43 3 0.02
45 82 0.45
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (43 bp):
TTTTCATTTAATCCCACCTCAATTGAGGATTTATGTTTTTAGT
Found at i:62920107 original size:23 final size:22
Alignment explanation
Indices: 62920065--62920107 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
62920055 ATTTTAACAA
*
62920065 AAATTTAATTATTAAAATATAT
1 AAATTTAATTATAAAAATATAT
62920087 AAATATTAA-TATAAAAGATAT
1 AAAT-TTAATTATAAAA-ATAT
62920108 TCTTTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAT
Found at i:62923169 original size:42 final size:42
Alignment explanation
Indices: 62923117--62923285 Score: 239
Period size: 42 Copynumber: 4.0 Consensus size: 42
62923107 ATGTCACCCG
* *
62923117 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTC
1 AATTAAGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
*
62923159 AATTAAGATTTATCTTTTTAGCTTTTCATTTAATCCCACCTC
1 AATTAAGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
* * *
62923201 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTA
1 AATTAAGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
* *
62923243 AATTAGGAGGATTTATGTTTTTAGTTTTTCATTTAATCTCACC
1 AATTA--A-GATTTATCTTTTTAGTTTTTCATTTAATCCCACC
62923286 GAATCAATTT
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
42 82 0.73
45 31 0.27
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (42 bp):
AATTAAGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
Found at i:62923208 original size:84 final size:86
Alignment explanation
Indices: 62923117--62923285 Score: 279
Period size: 84 Copynumber: 2.0 Consensus size: 86
62923107 ATGTCACCCG
*
62923117 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTCAATTA-A-GATTTATCTTTTTAG
1 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTAGAGGATTTATCTTTTTAG
62923180 CTTTTCATTTAATCCCACCTC
66 CTTTTCATTTAATCCCACCTC
*
62923201 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTAGGAGGATTTATGTTTTTA
1 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTA-GAGGATTTATCTTTTTA
* *
62923266 GTTTTTCATTTAATCTCACC
65 GCTTTTCATTTAATCCCACC
62923286 GAATCAATTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
84 46 0.59
86 1 0.01
87 31 0.40
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (86 bp):
AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTAGAGGATTTATCTTTTTAG
CTTTTCATTTAATCCCACCTC
Found at i:62928777 original size:19 final size:18
Alignment explanation
Indices: 62928736--62928790 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 18
62928726 TTATACTACA
*
62928736 AAACATTTATTATT-AAT
1 AAACATTTATAATTAAAT
62928753 --ACATTTATAATTATAAT
1 AAACATTTATAATTA-AAT
*
62928770 AAACATTTATTATTAAAT
1 AAACATTTATAATTAAAT
62928788 AAA
1 AAA
62928791 ATTAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 11 0.34
17 3 0.09
18 6 0.19
19 12 0.38
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
AAACATTTATAATTAAAT
Found at i:62929032 original size:16 final size:17
Alignment explanation
Indices: 62929003--62929036 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
62928993 TAAATTTACC
62929003 AGGAACTCTTTTTGAAG
1 AGGAACTCTTTTTGAAG
62929020 AGGAACT-TTTTTGAAG
1 AGGAACTCTTTTTGAAG
62929036 A
1 A
62929037 ATAAGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (17 bp):
AGGAACTCTTTTTGAAG
Found at i:62940664 original size:9 final size:9
Alignment explanation
Indices: 62940645--62940674 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
62940635 TACTAAGAAA
62940645 AATTCAAAAT
1 AATT-AAAAT
62940655 AATTAAAAT
1 AATTAAAAT
62940664 AATTAAAAT
1 AATTAAAAT
62940673 AA
1 AA
62940675 ACAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
AATTAAAAT
Found at i:62940680 original size:18 final size:19
Alignment explanation
Indices: 62940645--62940682 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
62940635 TACTAAGAAA
**
62940645 AATTCAAAATAATTAAAAT
1 AATTCAAAATAAACAAAAT
62940664 AATT-AAAATAAACAAAAT
1 AATTCAAAATAAACAAAAT
62940682 A
1 A
62940683 TAAAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
AATTCAAAATAAACAAAAT
Found at i:62945611 original size:6 final size:6
Alignment explanation
Indices: 62945600--62945660 Score: 113
Period size: 6 Copynumber: 10.2 Consensus size: 6
62945590 TCTATTTATT
*
62945600 TATGTA TATGTA TATGCA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
62945648 TATGTA TATGTA T
1 TATGTA TATGTA T
62945661 CTATCCTGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (6 bp):
TATGTA
Found at i:62946155 original size:20 final size:20
Alignment explanation
Indices: 62946130--62946169 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
62946120 TGATGTAACA
62946130 GTGCGAAAACAATTAATGCT
1 GTGCGAAAACAATTAATGCT
62946150 GTGCGAAAACAATTAATGCT
1 GTGCGAAAACAATTAATGCT
62946170 ATGCATTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GTGCGAAAACAATTAATGCT
Found at i:62946730 original size:11 final size:11
Alignment explanation
Indices: 62946714--62946738 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62946704 AATAAAATAA
62946714 AATAATTATAT
1 AATAATTATAT
62946725 AATAATTATAT
1 AATAATTATAT
62946736 AAT
1 AAT
62946739 TAAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTATAT
Found at i:62948912 original size:17 final size:17
Alignment explanation
Indices: 62948873--62948912 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
62948863 CATGCACATT
*
62948873 TTTATATGTATATATTA
1 TTTATATGTATATAATA
* *
62948890 TATATATTTATATAATA
1 TTTATATGTATATAATA
62948907 TTTATA
1 TTTATA
62948913 CGCATTTGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTATATGTATATAATA
Found at i:62961095 original size:42 final size:42
Alignment explanation
Indices: 62961047--62961272 Score: 263
Period size: 42 Copynumber: 5.1 Consensus size: 42
62961037 AGCCGCACAG
62961047 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* * *
62961089 TTAATCCTACCTCAATTAGGATTTATCATTTTAGCTTTTCTT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* **
62961131 TTAATCCCACCTCCATTAGGATTTATATAAGCATATCTTTTTAAATTTTCAT
1 TTAATCCCACCTCAATTAGG----AT-T-----TATCTTTTTAGCTTTTCAT
* * *
62961183 TTAATCTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
* *
62961225 TTAATCCCAACTCAATTAGGATTTATGTTTTTAGCTTTTCAT
1 TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
62961267 TTAATC
1 TTAATC
62961273 GTTATGTTGA
Statistics
Matches: 155, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
42 116 0.75
46 2 0.01
47 2 0.01
48 2 0.01
52 33 0.21
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (42 bp):
TTAATCCCACCTCAATTAGGATTTATCTTTTTAGCTTTTCAT
Found at i:62961231 original size:94 final size:94
Alignment explanation
Indices: 62961070--62961250 Score: 274
Period size: 94 Copynumber: 1.9 Consensus size: 94
62961060 AATTAGGATT
** * *
62961070 TATCTTTTTAGCTTTTCATTTAATCCTACCTCAATTAGGATTTATCATTTTAGCTTTTCTTTTAA
1 TATCTTTTTAAATTTTCATTTAATCCTACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTAA
* *
62961135 TCCCACCTCCATTAGGATTTATATAAGCA
66 TCCCAACTCAATTAGGATTTATATAAGCA
* *
62961164 TATCTTTTTAAATTTTCATTTAAT-CTCACCTCAATTAGGATTTACCTTTTTAGTTTTTCATTTA
1 TATCTTTTTAAATTTTCATTTAATCCT-ACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTA
62961228 ATCCCAACTCAATTAGGATTTAT
65 ATCCCAACTCAATTAGGATTTAT
62961251 GTTTTTAGCT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 2 0.03
94 76 0.97
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.48
Consensus pattern (94 bp):
TATCTTTTTAAATTTTCATTTAATCCTACCTCAATTAGGATTTACCATTTTAGCTTTTCATTTAA
TCCCAACTCAATTAGGATTTATATAAGCA
Found at i:62963738 original size:23 final size:22
Alignment explanation
Indices: 62963696--62963738 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
62963686 ATTTTAACAA
*
62963696 AAATTTAATTATTAAAATATAT
1 AAATTTAATTATAAAAATATAT
62963718 AAATATTAA-TATAAAAGATAT
1 AAAT-TTAATTATAAAA-ATAT
62963739 TCTTTTGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAT
Found at i:62966856 original size:43 final size:42
Alignment explanation
Indices: 62966731--62966900 Score: 241
Period size: 42 Copynumber: 4.0 Consensus size: 42
62966721 ATGTCACCCG
*
62966731 AATTAGGATTTATCTTTTTATTTTTTCATTTAATCCCACCTC
1 AATTAGGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
* *
62966773 AATTAAGATTTATCTTTTTAGCTTTTCATTTAATCCCACCTC
1 AATTAGGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
* *
62966815 AATTAGGATTTATCTTTTTATTTTTTTCATTTAATCCCACCTA
1 AATTAGGATTTATCTTTTTA-GTTTTTCATTTAATCCCACCTC
* *
62966858 AATTAGGAGGATTTATGTTTTTAGTTTTTCATTTAATCTCACC
1 AATT---AGGATTTATCTTTTTAGTTTTTCATTTAATCCCACC
62966901 GAATCAATTT
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
42 58 0.51
43 23 0.20
45 18 0.16
46 15 0.13
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (42 bp):
AATTAGGATTTATCTTTTTAGTTTTTCATTTAATCCCACCTC
Found at i:62966911 original size:85 final size:83
Alignment explanation
Indices: 62966737--62966900 Score: 238
Period size: 88 Copynumber: 1.9 Consensus size: 83
62966727 CCCGAATTAG
*
62966737 GATTTATCTTTTTATTTTTTCATTTAATCCCACCTCAATTAAGATTTATCTTTTTAGCTTTTCAT
1 GATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTAAGATTTATCTTTTTAGCTTTTCAT
*
62966802 TTAATCCCACCTCAATTA
66 TTAATCCCACCTCAATCA
* *
62966820 GGATTTATCTTTTTATTTTTTTCATTTAATCCCACCTAAATTAGGAGGATTTATGTTTTTAGTTT
1 -GATTTATCTTTTTA-TTTTTTCATTTAATCCCACCTAAATTA--A-GATTTATCTTTTTAGCTT
*
62966885 TTCATTTAATCTCACC
61 TTCATTTAATCCCACC
62966901 GAATCAATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
84 14 0.19
85 26 0.36
87 1 0.01
88 31 0.43
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (83 bp):
GATTTATCTTTTTATTTTTTCATTTAATCCCACCTAAATTAAGATTTATCTTTTTAGCTTTTCAT
TTAATCCCACCTCAATCA
Found at i:62972405 original size:19 final size:19
Alignment explanation
Indices: 62972381--62972419 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
62972371 TATTATTAAT
*
62972381 ACATTTATAATTATAATAA
1 ACATTTATAATTAAAATAA
*
62972400 ACATTTATTATTAAAATAA
1 ACATTTATAATTAAAATAA
62972419 A
1 A
62972420 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ACATTTATAATTAAAATAA
Found at i:62972665 original size:17 final size:18
Alignment explanation
Indices: 62972635--62972670 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
62972625 TAAATTTACC
62972635 AGGAACTCTTTTTTGAAG
1 AGGAACTCTTTTTTGAAG
62972653 AGGAACT-TTTTTTGAAG
1 AGGAACTCTTTTTTGAAG
62972670 A
1 A
62972671 ATAAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (18 bp):
AGGAACTCTTTTTTGAAG
Found at i:62976602 original size:1 final size:1
Alignment explanation
Indices: 62976598--62976629 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
62976588 AAAAAAATTT
62976598 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
62976630 TTTAAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:63000216 original size:50 final size:50
Alignment explanation
Indices: 63000092--63000335 Score: 283
Period size: 50 Copynumber: 4.7 Consensus size: 50
63000082 GATAATAACA
* * ** * *
63000092 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
63000143 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
63000193 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
63000243 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
*
63000298 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
63000336 TCTTTTTACC
Statistics
Matches: 166, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.55
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:63000270 original size:100 final size:105
Alignment explanation
Indices: 63000091--63000337 Score: 362
Period size: 100 Copynumber: 2.4 Consensus size: 105
63000081 TGATAATAAC
**
63000091 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATGGTGCCCATGCCATG
* *
63000156 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
63000193 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGGTGCCCATGCCAT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGAT-GGTGCCCATGCCAT
63000255 GTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 GTCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
63000298 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATC
63000338 TTTTTACCCA
Statistics
Matches: 130, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 36 0.28
107 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATGGTGCCCATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:63000456 original size:13 final size:13
Alignment explanation
Indices: 63000435--63000466 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
63000425 GCTTGGATCA
*
63000435 TCATCAAATAAAT
1 TCATAAAATAAAT
63000448 TCATAAAATAAAT
1 TCATAAAATAAAT
63000461 TCATAA
1 TCATAA
63000467 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:63000712 original size:30 final size:30
Alignment explanation
Indices: 63000678--63000735 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
63000668 CCTCGACTCT
**
63000678 AACTTTTTGAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
63000708 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
63000736 AATGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:63001321 original size:16 final size:16
Alignment explanation
Indices: 63001302--63001334 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
63001292 TTCTATTCTG
*
63001302 TTTCTTTTCTTTCTTT
1 TTTCTATTCTTTCTTT
63001318 TTTCTATTCTTTCTTT
1 TTTCTATTCTTTCTTT
63001334 T
1 T
63001335 GTTTTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTATTCTTTCTTT
Found at i:63001356 original size:5 final size:5
Alignment explanation
Indices: 63001343--63001414 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
63001333 TTGTTTTATG
63001343 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
63001391 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
63001415 ATATTTTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:63001368 original size:19 final size:19
Alignment explanation
Indices: 63001344--63001386 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
63001334 TGTTTTATGT
63001344 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
63001363 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
63001382 ATATA
1 ATATA
63001387 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:63001396 original size:24 final size:24
Alignment explanation
Indices: 63001350--63001415 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
63001340 ATGTATATAT
* * *
63001350 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
63001374 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
63001398 ATTACTATAATATAATAA
1 A-TAATATAATATAATAA
63001416 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 12 0.34
26 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:63002127 original size:44 final size:44
Alignment explanation
Indices: 63001986--63002140 Score: 170
Period size: 44 Copynumber: 3.5 Consensus size: 44
63001976 ATTATACAGG
* * * *
63001986 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
* ** *
63002032 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAG-AGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGTAGA
63002076 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AGTAGA
* *
63002120 TCCTATCTCCTTGAGATTACA
1 TCTTATCTCCCTGAGATTACA
63002141 ATAGAGCGGA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
44 59 0.64
45 1 0.01
46 31 0.34
47 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
Found at i:63002386 original size:174 final size:170
Alignment explanation
Indices: 63002073--63002405 Score: 445
Period size: 174 Copynumber: 1.9 Consensus size: 170
63002063 TTGAAGCCAG
* * *
63002073 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
* * *
63002138 ACAATAGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACGGTAGAGAAGATCACATCAGGTCT
66 ACAATAGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
* * *
63002203 TATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTC
131 TATTTCCCTGAAGATACAGTGGAATAGACCGGAGAATTTC
* *
63002243 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGA-T
* * * * *
63002306 TACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATC
65 TACAATAGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATC
*
63002371 AAGTCTTATTTCCCTGAAGATGCAGTGGAATAGAC
125 AAGTCTTATTTCCCTGAAGATACAGTGGAATAGAC
63002406 TGAAAACAAC
Statistics
Matches: 140, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
168 1 0.01
169 27 0.19
170 42 0.30
174 70 0.50
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCCTGAGATT
ACAATAGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGAAGATCACATCAAGTCT
TATTTCCCTGAAGATACAGTGGAATAGACCGGAGAATTTC
Found at i:63002606 original size:44 final size:44
Alignment explanation
Indices: 63002517--63002608 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 44
63002507 AGATGGAAGC
* * * * * *
63002517 GAAGTCACAAACCTTGTCTCTCTGAAGTTGCAGTAGAGCAGGTT
1 GAAGTCACAAACCTTATCCCCCTAAAGTTGCAGTAGACCAAGTT
* * *
63002561 GAAGTCACAAATCTTATCCCCCTAAAGTTGCAGTGGCCCAAGTT
1 GAAGTCACAAACCTTATCCCCCTAAAGTTGCAGTAGACCAAGTT
63002605 GAAG
1 GAAG
63002609 ATATGAGTCC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (44 bp):
GAAGTCACAAACCTTATCCCCCTAAAGTTGCAGTAGACCAAGTT
Found at i:63003445 original size:11 final size:11
Alignment explanation
Indices: 63003429--63003458 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
63003419 TTGTATTTTC
63003429 TTTATTTTCCT
1 TTTATTTTCCT
63003440 TTTATTTTCCT
1 TTTATTTTCCT
63003451 TTTATTTT
1 TTTATTTT
63003459 TGTTGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTTTCCT
Found at i:63004218 original size:3 final size:3
Alignment explanation
Indices: 63004195--63004233 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
63004185 TTTAGCAATT
* *
63004195 TTA TT- TTA TTG TTA CTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
63004234 ATCATTGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:63004557 original size:17 final size:17
Alignment explanation
Indices: 63004518--63004557 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
63004508 CATGCACATT
*
63004518 TTTATATGTATATATTA
1 TTTATATGTATATAATA
* *
63004535 TATATATTTATATAATA
1 TTTATATGTATATAATA
63004552 TTTATA
1 TTTATA
63004558 CGCATTTGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTATATGTATATAATA
Found at i:63010581 original size:16 final size:17
Alignment explanation
Indices: 63010560--63010605 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
63010550 GGTAAAGAGT
63010560 TAAAATAATTTAAAT-A
1 TAAAATAATTTAAATCA
* *
63010576 TAAAATAATTAAAATCT
1 TAAAATAATTTAAATCA
*
63010593 TAAAATGATTTAA
1 TAAAATAATTTAA
63010606 TTATGAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAATAATTTAAATCA
Found at i:63018514 original size:21 final size:21
Alignment explanation
Indices: 63018490--63018533 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
63018480 CGAACCTAAT
63018490 TAAATAGAAAGGATA-AATAAA
1 TAAATA-AAAGGATACAATAAA
*
63018511 TAAATAAAATGATACAATAAA
1 TAAATAAAAGGATACAATAAA
63018532 TA
1 TA
63018534 CTAAAGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (21 bp):
TAAATAAAAGGATACAATAAA
Found at i:63019296 original size:7 final size:7
Alignment explanation
Indices: 63019268--63019309 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
63019258 ATTACATTTA
63019268 CATTTCC
1 CATTTCC
*
63019275 CAATTCC
1 CATTTCC
* *
63019282 C-CTCCC
1 CATTTCC
63019288 CATTTCC
1 CATTTCC
63019295 CATTTCC
1 CATTTCC
63019302 CATTTCC
1 CATTTCC
63019309 C
1 C
63019310 GACCCCGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (7 bp):
CATTTCC
Found at i:63020601 original size:23 final size:23
Alignment explanation
Indices: 63020575--63020629 Score: 92
Period size: 25 Copynumber: 2.3 Consensus size: 23
63020565 TTGATATATG
63020575 TATATGTTAGTTTCGAATATGTA
1 TATATGTTAGTTTCGAATATGTA
63020598 TATATGTATTAGTTTCGAATATGTA
1 TATATG--TTAGTTTCGAATATGTA
63020623 TATATGT
1 TATATGT
63020630 ACATGTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.23
25 23 0.77
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (23 bp):
TATATGTTAGTTTCGAATATGTA
Found at i:63020615 original size:25 final size:25
Alignment explanation
Indices: 63020581--63020630 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
63020571 TATGTATATG
63020581 TTAGTTTCGAATATGTATATATGTA
1 TTAGTTTCGAATATGTATATATGTA
63020606 TTAGTTTCGAATATGTATATATGTA
1 TTAGTTTCGAATATGTATATATGTA
63020631 CATGTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (25 bp):
TTAGTTTCGAATATGTATATATGTA
Found at i:63021407 original size:13 final size:13
Alignment explanation
Indices: 63021389--63021510 Score: 119
Period size: 13 Copynumber: 9.7 Consensus size: 13
63021379 ATTTTTAATG
63021389 TAATATACTGTTT
1 TAATATACTGTTT
*
63021402 TAATATACTGTTA
1 TAATATACTGTTT
*
63021415 TAA-A-A-T-TTG
1 TAATATACTGTTT
**
63021424 TAATATTTTGTTT
1 TAATATACTGTTT
63021437 TAATATACTGTTAT
1 TAATATACTGTT-T
* *
63021451 AAATATATTGTTT
1 TAATATACTGTTT
*
63021464 TAATATAATGTTT
1 TAATATACTGTTT
63021477 TAATATACTGTTT
1 TAATATACTGTTT
* *
63021490 TAATATATTGTTA
1 TAATATACTGTTT
63021503 TAA-ATACT
1 TAATATACT
63021511 ACACCTTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
9 5 0.06
10 2 0.02
11 1 0.01
12 6 0.07
13 65 0.72
14 11 0.12
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:63021426 original size:35 final size:37
Alignment explanation
Indices: 63021387--63021500 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 37
63021377 TAATTTTTAA
*
63021387 TGTAATATACTGTTTTAATATACTGTTATAAA-AT-T
1 TGTAATATAATGTTTTAATATACTGTTATAAATATAT
**
63021422 TGTAATATTTTGTTTTAATATACTGTTATAAATATAT
1 TGTAATATAATGTTTTAATATACTGTTATAAATATAT
*
63021459 TGTTTTAATATAATGTTTTAATATACTGTT-TTAATATAT
1 TG---TAATATAATGTTTTAATATACTGTTATAAATATAT
63021498 TGT
1 TGT
63021501 TATAAATACT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
35 30 0.43
36 3 0.04
37 3 0.04
39 10 0.14
40 23 0.33
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.54
Consensus pattern (37 bp):
TGTAATATAATGTTTTAATATACTGTTATAAATATAT
Found at i:63021598 original size:81 final size:81
Alignment explanation
Indices: 63021500--63021660 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 81
63021490 TAATATATTG
*
63021500 TTATAAATACTACACCTTAATTTTTGA-TATAATATACTGTTTTAATATACTATTATAAAATTTG
1 TTATAAATACTACACCTTAATTATT-ATTATAATATACTGTTTTAATATACTATTATAAAATTTG
*
63021564 TAATATACTGTTATAAC
65 TAATATAATGTTATAAC
* *
63021581 TTATAAATACTACACCTTAATTATTATTGTAATATACTGTTTTAATATACTGTTATAAAATTTGT
1 TTATAAATACTACACCTTAATTATTATTATAATATACTGTTTTAATATACTATTATAAAATTTGT
63021646 AATATAATGTTATAA
66 AATATAATGTTATAA
63021661 ATATAATATT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
80 1 0.01
81 74 0.99
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (81 bp):
TTATAAATACTACACCTTAATTATTATTATAATATACTGTTTTAATATACTATTATAAAATTTGT
AATATAATGTTATAAC
Found at i:63021628 original size:13 final size:13
Alignment explanation
Indices: 63021610--63021634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63021600 ATTATTATTG
63021610 TAATATACTGTTT
1 TAATATACTGTTT
63021623 TAATATACTGTT
1 TAATATACTGTT
63021635 ATAAAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:63022755 original size:26 final size:26
Alignment explanation
Indices: 63022716--63022781 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 26
63022706 GACCCATGTT
63022716 AAATATATATATTTGATTAAAAAATAA
1 AAATATATATATTTGATT-AAAAATAA
63022743 AAA-ATATATATTTGATTAAAAATAA
1 AAATATATATATTTGATTAAAAATAA
63022768 AAATATATATATTT
1 AAATATATATATTT
63022782 AATATATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.29
26 24 0.63
27 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
AAATATATATATTTGATTAAAAATAA
Found at i:63029043 original size:6 final size:6
Alignment explanation
Indices: 63029032--63029057 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
63029022 TCAATAAAAA
63029032 GCCTCG GCCTCG GCCTCG GCCTCG GC
1 GCCTCG GCCTCG GCCTCG GCCTCG GC
63029058 GTTGTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.35, T:0.15
Consensus pattern (6 bp):
GCCTCG
Found at i:63032941 original size:6 final size:7
Alignment explanation
Indices: 63032914--63032939 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
63032904 ATAAATATAT
63032914 ATTTTTA
1 ATTTTTA
63032921 ATTTTTA
1 ATTTTTA
63032928 ATTTTTA
1 ATTTTTA
63032935 ATTTT
1 ATTTT
63032940 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Found at i:63033002 original size:29 final size:29
Alignment explanation
Indices: 63032947--63033003 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
63032937 TTTAAAATAC
**
63032947 TTTTAAAATAATTTTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTAATATTTTTTTAT
*
63032976 TTTTAAAAT-ATTTTTAATGTTTATTTTA
1 TTTTAAAATAATTTTTAATATTT-TTTTA
63033004 AAATAGGCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTTAAAATAATTTTTAATATTTTTTTAT
Found at i:63034322 original size:36 final size:36
Alignment explanation
Indices: 63034273--63034344 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
63034263 CCAACTATAC
**
63034273 TCATTTTTGTAGGTTAATAGTAGAACAATGCTTTTA
1 TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
63034309 TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
1 TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
63034345 ACAAGTCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (36 bp):
TCATTTTCATAGGTTAATAGTAGAACAATGCTTTTA
Found at i:63055099 original size:28 final size:28
Alignment explanation
Indices: 63055063--63055117 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
63055053 AATTTATTGC
* *
63055063 ATTGTAGTGACATCTAATAATACATAAG
1 ATTGCAGTGACATCAAATAATACATAAG
* *
63055091 ATTGCAGTGGCATGAAATAATACATAA
1 ATTGCAGTGACATCAAATAATACATAA
63055118 AGTAGTGTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (28 bp):
ATTGCAGTGACATCAAATAATACATAAG
Found at i:63055298 original size:5 final size:6
Alignment explanation
Indices: 63055280--63055307 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
63055270 TTTGTCTATA
63055280 TTATTT TTATTT TTATTT TTATTT TTAT
1 TTATTT TTATTT TTATTT TTATTT TTAT
63055308 GTAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTATTT
Found at i:63057291 original size:3 final size:3
Alignment explanation
Indices: 63057283--63057308 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
63057273 TTTAGATTTG
63057283 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
63057309 CAACATTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:63057924 original size:16 final size:16
Alignment explanation
Indices: 63057891--63057924 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
63057881 CAAAGGGTAT
63057891 ATTAATCGATTAATTA
1 ATTAATCGATTAATTA
63057907 ATTAA-CGATTAATCTA
1 ATTAATCGATTAAT-TA
63057923 AT
1 AT
63057925 GAAGTTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTAATCGATTAATTA
Found at i:63060330 original size:3 final size:3
Alignment explanation
Indices: 63060318--63060353 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
63060308 TTAATTCTTC
*
63060318 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
63060354 AATATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:63061003 original size:25 final size:25
Alignment explanation
Indices: 63060968--63061025 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
63060958 TATATATTAA
*
63060968 ATATATATTTTATTTTTAATAAAAT
1 ATATATTTTTTATTTTTAATAAAAT
*
63060993 ATATATTTTTTATTTTTAGTAAAAT
1 ATATATTTTTTATTTTTAATAAAAT
63061018 ATATATTT
1 ATATATTT
63061026 AATATGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATATATTTTTTATTTTTAATAAAAT
Found at i:63062267 original size:25 final size:25
Alignment explanation
Indices: 63062239--63062304 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
63062229 CTGATATTTA
*
63062239 GCTCTCACGAGCTTCCCAATTAATG
1 GCTCTCATGAGCTTCCCAATTAATG
* * *
63062264 GCTCTCTTGAGCTTCCCGATTTATG
1 GCTCTCATGAGCTTCCCAATTAATG
*
63062289 GCTCGCATGAGCTTCC
1 GCTCTCATGAGCTTCC
63062305 TGATGTACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.17, C:0.32, G:0.20, T:0.32
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCAATTAATG
Found at i:63062338 original size:25 final size:24
Alignment explanation
Indices: 63062321--63062380 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
63062311 ACAACTCGGT
*
63062321 TGAGCTTCTCGTTATACAGCTCACA
1 TGAGCTTCTCGTT-TACAACTCACA
* *
63062346 TGAGCTTCTCGTTTACATGCTCATA
1 TGAGCTTCTCGTTTACA-ACTCACA
63062371 TGAGCATTCT
1 TGAGC-TTCT
63062381 TGAATATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 4 0.12
25 24 0.75
26 4 0.12
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (24 bp):
TGAGCTTCTCGTTTACAACTCACA
Found at i:63075006 original size:30 final size:31
Alignment explanation
Indices: 63074952--63075011 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
63074942 AAACCTTTTA
*
63074952 TTTTCCCCCAAAATTTTTACTCTC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCTCTTCCCAC
* **
63074982 TTTTCCCCTAAAACTTTTGTTCTCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCTCTTCCCA
63075012 TCCCACCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.37, G:0.02, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCTCTTCCCAC
Found at i:63075139 original size:15 final size:16
Alignment explanation
Indices: 63075104--63075142 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
63075094 CTTTCCCTCT
63075104 AACTTTTATTCCCCAA
1 AACTTTTATTCCCCAA
* *
63075120 AACTTTT-TTTCCCTA
1 AACTTTTATTCCCCAA
63075135 AACTTTTA
1 AACTTTTA
63075143 CTTCTCACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (16 bp):
AACTTTTATTCCCCAA
Found at i:63077691 original size:19 final size:18
Alignment explanation
Indices: 63077667--63077734 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
63077657 AAAATTATTA
*
63077667 TTTTATAAAATTTTAATT
1 TTTTTTAAAATTTTAATT
* * *
63077685 TTTTTATATATTTTTAGAAT
1 TTTTT-TAAAATTTTA-ATT
63077705 TTTTTT-AAATTTATAATT
1 TTTTTTAAAATTT-TAATT
63077723 TTTGTTTAAAAT
1 TTT-TTTAAAAT
63077735 AAAAATTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 13 0.34
19 14 0.37
20 11 0.29
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTTAAAATTTTAATT
Found at i:63077771 original size:18 final size:20
Alignment explanation
Indices: 63077733--63077770 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
63077723 TTTGTTTAAA
*
63077733 ATAAAAATTTTAGAATTTTT
1 ATAAATATTTTAGAATTTTT
63077753 ATAAATATTTT-GAATTTT
1 ATAAATATTTTAGAATTTT
63077771 AAAAATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAGAATTTTT
Found at i:63077776 original size:18 final size:18
Alignment explanation
Indices: 63077734--63077777 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
63077724 TTGTTTAAAA
63077734 TAAAAATTTTAGAATTTT
1 TAAAAATTTTAGAATTTT
63077752 TATAAATATTTT-GAA-TTT
1 TA-AAA-ATTTTAGAATTTT
63077770 TAAAAATT
1 TAAAAATT
63077778 ACTTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 7 0.29
19 6 0.25
20 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TAAAAATTTTAGAATTTT
Found at i:63077789 original size:19 final size:18
Alignment explanation
Indices: 63077747--63077789 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
63077737 AAATTTTAGA
* *
63077747 ATTTTTATAAATATTTTG
1 ATTTTTAAAAATACTTTG
*
63077765 AATTTTAAAAATTACTTTG
1 ATTTTTAAAAA-TACTTTG
63077784 ATTTTT
1 ATTTTT
63077790 TTTTTGTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTTTTAAAAATACTTTG
Found at i:63078130 original size:7 final size:7
Alignment explanation
Indices: 63078118--63078143 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
63078108 AAAATAACCA
63078118 TTAAATT
1 TTAAATT
63078125 TTAAATT
1 TTAAATT
63078132 TTAAATT
1 TTAAATT
63078139 TTAAA
1 TTAAA
63078144 AGGATAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:63082241 original size:24 final size:24
Alignment explanation
Indices: 63082209--63082255 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
63082199 GACAAAAAAA
63082209 AATGTTGTATGTAAATAAATGATG
1 AATGTTGTATGTAAATAAATGATG
*
63082233 AATGTTGTATTTAAATAAATGAT
1 AATGTTGTATGTAAATAAATGAT
63082256 CTCGGCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (24 bp):
AATGTTGTATGTAAATAAATGATG
Done.