Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 37 of 97
Found at i:15216899 original size:75 final size:72
Alignment explanation
Indices: 15216664--15216891 Score: 201
Period size: 72 Copynumber: 3.2 Consensus size: 72
15216654 TTAATCATAA
* * *
15216664 TAATATTT--AAATTAAATAAAATATTAATATTTAAATTATCTATTATTAATATTTTAAATAAAT
1 TAATATTTAAAAAATAAAT-AAATATTAATATTTAAATTAT-TATTAATAATATTTTAATTAAAT
15216727 AATC-AATTAT
64 --TCTAATTAT
* * *
15216737 TAAT-TTTCAAAAATAAAATAAA-A-TAA-A-AT-AATTGATTA-TAATAATATTTAAATTAAA-
1 TAATATTTAAAAAAT-AAATAAATATTAATATTTAAATT-ATTATTAATAATATTTTAATTAAAT
* *
15216794 T-AAAGTAT
64 TCTAATTAT
* *
15216802 TAATATTTTAAAATATAAATAAATATTAATATTTAAATTATTAATTAGTAATATTTTAATTAAAT
1 TAATA-TTTAAAAAATAAATAAATATTAATATTTAAATTATT-ATTAATAATATTTTAATTAAAT
15216867 TCTAGATTAT
64 TCTA-ATTAT
15216877 TAATATTTAAAAAAT
1 TAATATTTAAAAAAT
15216892 CTAATAAAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 33
0.73 0.08 0.19
Matches are distributed among these distances:
65 10 0.08
66 7 0.06
67 9 0.07
68 19 0.15
69 7 0.06
70 7 0.06
71 6 0.05
72 23 0.19
73 6 0.05
74 17 0.14
75 13 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (72 bp):
TAATATTTAAAAAATAAATAAATATTAATATTTAAATTATTATTAATAATATTTTAATTAAATTC
TAATTAT
Found at i:15220362 original size:23 final size:23
Alignment explanation
Indices: 15220335--15220414 Score: 142
Period size: 23 Copynumber: 3.5 Consensus size: 23
15220325 TCAAGTCAAA
*
15220335 TGTCGTGACATGCCATGCATCAC
1 TGTCGTGACACGCCATGCATCAC
15220358 TGTCGTGACACGCCATGCATCAC
1 TGTCGTGACACGCCATGCATCAC
*
15220381 TGTCATGACACGCCATGCATCAC
1 TGTCGTGACACGCCATGCATCAC
15220404 TGTCGTGACAC
1 TGTCGTGACAC
15220415 ACCAATCACT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.24
Consensus pattern (23 bp):
TGTCGTGACACGCCATGCATCAC
Found at i:15220523 original size:55 final size:55
Alignment explanation
Indices: 15220447--15220632 Score: 176
Period size: 55 Copynumber: 3.4 Consensus size: 55
15220437 TAGTTACACC
* * * * *
15220447 AACATCCATGACACGCTAAAAACCCAAAAAACTGGTTAGCCCACGACACACCAGG
1 AACAGCCATGACACGCTAAAAACCCAAAAAACTAGTTAACCCACAACACACCAGA
* * * * *
15220502 AACAGCCATGACACGCCAAAAACCC-ATAAATTCAGTTAACCCACCACACCCCAGA
1 AACAGCCATGACACGCTAAAAACCCAAAAAACT-AGTTAACCCACAACACACCAGA
* * * * * * *
15220557 AACAGTCGTGACACGCTAACAACCCAAATAACTAGTTAACCCACAACACGCTAGT
1 AACAGCCATGACACGCTAAAAACCCAAAAAACTAGTTAACCCACAACACACCAGA
***
15220612 AACAGTTGTGACACGCTAAAA
1 AACAGCCATGACACGCTAAAA
15220633 TAACAGTTCA
Statistics
Matches: 107, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
54 5 0.05
55 98 0.92
56 4 0.04
ACGTcount: A:0.41, C:0.32, G:0.13, T:0.13
Consensus pattern (55 bp):
AACAGCCATGACACGCTAAAAACCCAAAAAACTAGTTAACCCACAACACACCAGA
Found at i:15221733 original size:161 final size:161
Alignment explanation
Indices: 15221465--15221960 Score: 548
Period size: 161 Copynumber: 3.0 Consensus size: 161
15221455 TTATCACATG
* * * * * * * *
15221465 TTATCTCTACTCTTCTCCGTTTTCACTCACTTCACTGACTTAGCTATTGGACCGGCCTGCATCGA
1 TTATCTCTACTCTTTTCCGTTTTCACTCACTTCAATGACTTATCCATTGAACGGGCCTTCATTGA
* * *
15221530 CGCTCTCCAG-TCACCCTAAACCTTATTTCTTGCTAATGTTTCACTACTTAGCTCCATAGATTAA
66 CGCTCTCCAGCT-ACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTACTTAGCTCCATAGATTAA
* *
15221594 TAAACAAGGTAGAGCATATATATACATATATA
130 TAAACAAGGTAGAACATATATATATATATATA
* *
15221626 TTATCTCTACTCTTTTCCGTTTTCACTCACTTTAATGACTTATCCATTGAACGGGCCTTCCTTGA
1 TTATCTCTACTCTTTTCCGTTTTCACTCACTTCAATGACTTATCCATTGAACGGGCCTTCATTGA
* *
15221691 TGCTCTCTAGCTACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTACTTAGCTCCATAGATTAAT
66 CGCTCTCCAGCTACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTACTTAGCTCCATAGATTAAT
* *
15221756 AAACAAGGGAGAATATATATATATATATATATATATATGTATA
131 AAACAA--G-G------TAGA-ACATATATATATATA--TATA
* * ** * * * *
15221799 TTATCTTTACTTTTTTTTGTTTTCACTTACTTCATTGACTTATCCA-TCAGACGGGCTTTCATTG
1 TTATCTCTACTCTTTTCCGTTTTCACTCACTTCAATGACTTATCCATTGA-ACGGGCCTTCATTG
* * **
15221863 ACACTTTCCAGCCGCCTTAAGCCTTATTTCTTGCTAGTGTTTCACT-CTTTAGCTCCATAGATTA
65 ACGCTCTCCAGCTACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTAC-TTAGCTCCATAGATTA
*
15221927 ATAAACAAGGGAGAACATATATATATATATATA
129 ATAAACAAGGTAGAACATATATATATATATATA
15221960 T
1 T
15221961 ATATNNNNNN
Statistics
Matches: 282, Mismatches: 38, Indels: 30
0.81 0.11 0.09
Matches are distributed among these distances:
161 124 0.44
162 1 0.00
163 15 0.05
164 3 0.01
170 4 0.01
171 13 0.05
172 3 0.01
173 119 0.42
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (161 bp):
TTATCTCTACTCTTTTCCGTTTTCACTCACTTCAATGACTTATCCATTGAACGGGCCTTCATTGA
CGCTCTCCAGCTACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTACTTAGCTCCATAGATTAAT
AAACAAGGTAGAACATATATATATATATATA
Found at i:15221775 original size:2 final size:2
Alignment explanation
Indices: 15221768--15221799 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
15221758 ACAAGGGAGA
*
15221768 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15221800 TATCTTTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15221890 original size:173 final size:173
Alignment explanation
Indices: 15221609--15221964 Score: 509
Period size: 173 Copynumber: 2.1 Consensus size: 173
15221599 AAGGTAGAGC
* * *
15221609 ATATATATACATATATATTATCTCTACTCTTTTCCGTTTTCACTCACTTTAATGACTTATCCATT
1 ATATATATATATATATATTATCTCTACTCTTTTCCGTTTTCACTCACTTCAATGACTTATCCATA
* ** * *
15221674 GAACGGGCCTTCCTTGATGCTCTCTAGCTACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTAC-
66 GAACGGGCCTTCATTGACACTCTCCAGCCACCTTAAGCCTTATTTCTTGCTAGTGTTTCACT-CT
*
15221738 TTAGCTCCATAGATTAATAAACAAGGGAGAATATATATATATAT
130 TTAGCTCCATAGATTAATAAACAAGGGAGAACATATATATATAT
* * * ** * *
15221782 ATATATATATATGTATATTATCTTTACTTTTTTTTGTTTTCACTTACTTCATTGACTTATCCATC
1 ATATATATATATATATATTATCTCTACTCTTTTCCGTTTTCACTCACTTCAATGACTTATCCAT-
* * *
15221847 AG-ACGGGCTTTCATTGACACTTTCCAGCCGCCTTAAGCCTTATTTCTTGCTAGTGTTTCACTCT
65 AGAACGGGCCTTCATTGACACTCTCCAGCCACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTCT
15221911 TTAGCTCCATAGATTAATAAACAAGGGAGAACATATATATATAT
130 TTAGCTCCATAGATTAATAAACAAGGGAGAACATATATATATAT
15221955 ATATATATAT
1 ATATATATAT
15221965 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
172 1 0.01
173 160 0.99
174 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (173 bp):
ATATATATATATATATATTATCTCTACTCTTTTCCGTTTTCACTCACTTCAATGACTTATCCATA
GAACGGGCCTTCATTGACACTCTCCAGCCACCTTAAGCCTTATTTCTTGCTAGTGTTTCACTCTT
TAGCTCCATAGATTAATAAACAAGGGAGAACATATATATATAT
Found at i:15222108 original size:2 final size:2
Alignment explanation
Indices: 15222101--15222153 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
15222091 CAAGGGGAGA
15222101 AT AT AT AT AT AT AT AT AGT AT AT AT AT AT AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
15222142 AT -T A- AT AT AT AT
1 AT AT AT AT AT AT AT
15222154 CTTTACTCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.09
2 40 0.87
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15222124 original size:15 final size:14
Alignment explanation
Indices: 15222101--15222153 Score: 69
Period size: 15 Copynumber: 4.0 Consensus size: 14
15222091 CAAGGGGAGA
15222101 ATATATATATATAT
1 ATATATATATATAT
15222115 ATAGTATATATATAT
1 ATA-TATATATATAT
15222130 ATATA-ATATA-AT
1 ATATATATATATAT
15222142 AT-TA-ATATATAT
1 ATATATATATATAT
15222154 CTTTACTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.19
12 6 0.16
13 5 0.14
14 5 0.14
15 14 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:15222124 original size:17 final size:17
Alignment explanation
Indices: 15222100--15222143 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
15222090 ACAAGGGGAG
15222100 AATATATATATATATAT
1 AATATATATATATATAT
*
15222117 AGTATATATATATATAT
1 AATATATATATATATAT
15222134 AATATA-ATAT
1 AATATATATAT
15222144 TAATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:15222147 original size:11 final size:13
Alignment explanation
Indices: 15222101--15222153 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
15222091 CAAGGGGAGA
15222101 ATATATAT-ATAT
1 ATATATATAATAT
15222113 ATATAGTAT-ATAT
1 ATATA-TATAATAT
15222126 ATATATATAATAT
1 ATATATATAATAT
15222139 A-ATAT-TAATAT
1 ATATATATAATAT
15222150 ATAT
1 ATAT
15222154 CTTTACTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.18
12 14 0.37
13 17 0.45
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:15223043 original size:74 final size:74
Alignment explanation
Indices: 15222915--15223056 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 74
15222905 ATAAATGGAA
* * *
15222915 TAAATCTTACTAATAGTTATAATAAAAAATATTTCAATTATCATCATTTGATGAATACACATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
15222980 TAATAAGTT
66 TAATAAGTT
* ** * **
15222989 TAAATCTTACTGATAATTATAAT-AAAAATATTTTCAATAATTGTTATTTAATGAATACGTATTT
1 TAAATCTTACTAATAATTATAATAAAAAATA-TTTCAATAATCATCATTTAATGAATACACATTT
15223053 ATAA
65 ATAA
15223057 GTATAGGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
73 7 0.12
74 51 0.88
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (74 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATGAATACACATTTA
TAATAAGTT
Found at i:15229110 original size:42 final size:42
Alignment explanation
Indices: 15229051--15229192 Score: 212
Period size: 42 Copynumber: 3.4 Consensus size: 42
15229041 TGTTGATTTG
* *
15229051 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGTT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
15229093 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* * * * *
15229135 GACCCGGCTATGTGTGAGTGGGATTGCACATAAGCCATTGCT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
*
15229177 GACCCGACTATATGCG
1 GACCCGACTATGTGCG
15229193 CATAAGCCGT
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (42 bp):
GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:15230708 original size:3 final size:3
Alignment explanation
Indices: 15230702--15230729 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15230692 CCAGCAGCTT
15230702 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
15230730 CTTTCACGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:15231548 original size:42 final size:42
Alignment explanation
Indices: 15231502--15231631 Score: 179
Period size: 42 Copynumber: 3.1 Consensus size: 42
15231492 TGTTGATGTG
***
15231502 GACCCAGCTATGTGCGAGTAAGAGTGTATATAAGCCGATGAT
1 GACCCAGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
*
15231544 GACCCAACTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
1 GACCCAGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
** * **
15231586 GACCGGGCTATGTGAGAGTGGGAGTGCGCATAAGCCGATGAT
1 GACCCAGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
15231628 GACC
1 GACC
15231632 TAACCATGTG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.20
Consensus pattern (42 bp):
GACCCAGCTATGTGCGAGTAAGAGTGCGCATAAGCCGATGAT
Found at i:15231703 original size:2 final size:2
Alignment explanation
Indices: 15231696--15231732 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
15231686 ACGATGATGA
15231696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15231733 CATGNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15241685 original size:68 final size:68
Alignment explanation
Indices: 15241540--15241845 Score: 336
Period size: 68 Copynumber: 4.5 Consensus size: 68
15241530 GATAAGATTT
* * * *
15241540 TGTATATGATGTAAATTCCATATCCCATATGAGATGATCAAGTATGCATGATGT-ATACTAT-AG
1 TGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGAT-TAATGCCATGAG
* *
15241603 GATGG
65 AAT-A
* * * *
15241608 TGTATATGATGTAAATTTCATATACCATATGAGGTGATTACGTATGCATGATTAATGCCGTGAGA
1 TGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGATTAATGCCATGAGA
15241673 ATA
66 ATA
* * * * *
15241676 TGTAAATGATGTATATTCCATATACTACATGAGATGATTAAGTATGTATGATTAATGCCATGAGA
1 TGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGATTAATGCCATGAGA
15241741 ATA
66 ATA
* * * * *
15241744 TGTATATGATGTATATTCCATATACTACATGAGATGATTGAGT-TAGCAT-A--AATGTCATGAG
1 TGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTAT-GCATGATTAATGCCATGAG
*
15241805 ATTA
65 AATA
* *
15241809 TGTATACGATGTAAATTCCATATACCTTATGAGATGA
1 TGTATATGATGTAAATTCCATATACCATATGAGATGA
15241846 GTAAACATGT
Statistics
Matches: 206, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
65 45 0.22
67 3 0.01
68 154 0.75
69 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (68 bp):
TGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGATTAATGCCATGAGA
ATA
Found at i:15242018 original size:29 final size:29
Alignment explanation
Indices: 15241972--15242046 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
15241962 ATCATAAAAT
*
15241972 GCCCAAGGGCAATAGGGATATATGTTGCCA
1 GCCCAA-GGCAATAGGGATATATATTGCCA
*
15242002 GCCCAAGGCAATGGGGATATATATTGCCA
1 GCCCAAGGCAATAGGGATATATATTGCCA
*
15242031 ACCCAAGATGCAATAG
1 GCCCAAG--GCAATAG
15242047 AGATGTACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
29 27 0.69
30 6 0.15
31 6 0.15
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (29 bp):
GCCCAAGGCAATAGGGATATATATTGCCA
Found at i:15248988 original size:35 final size:35
Alignment explanation
Indices: 15248949--15249025 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
15248939 AAGGTCGAGT
* *
15248949 GTAACCTTTACAACATGTCTTTTGCAGAATCAAGA
1 GTAACCTTTACAACATGCCTTTTCCAGAATCAAGA
* * * * *
15248984 GTAACCTTTATAGCATGCCTTTTCCAGGATCAGGT
1 GTAACCTTTACAACATGCCTTTTCCAGAATCAAGA
15249019 GTAACCT
1 GTAACCT
15249026 CTATCAAGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (35 bp):
GTAACCTTTACAACATGCCTTTTCCAGAATCAAGA
Found at i:15249972 original size:21 final size:20
Alignment explanation
Indices: 15249935--15249982 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
15249925 AATCTTGAAG
*
15249935 CTTCTATCTTTCAAGAATCGA
1 CTTCT-TCTTTCAAGAATCCA
*
15249956 CTTCTTCTTTCTCAGAATCCA
1 CTTCTTCTTTC-AAGAATCCA
15249977 -TTCTTC
1 CTTCTTC
15249983 ACTGTTGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.21, C:0.29, G:0.06, T:0.44
Consensus pattern (20 bp):
CTTCTTCTTTCAAGAATCCA
Found at i:15255168 original size:43 final size:42
Alignment explanation
Indices: 15255120--15255328 Score: 249
Period size: 43 Copynumber: 4.9 Consensus size: 42
15255110 TGTGATAATT
* * *
15255120 ATGACCCAACTATGTGCGGTGTAGGAGTGCACATGAGTTGGTG
1 ATGACCCAGCTATGTGCGGTGT-GGAGTGCACATGAGCTGATG
*
15255163 ATGACCCAGCTATGTGCGGTGTGGTAGTGCAAATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTGG-AGTGCACATGAGCTGATG
* * *
15255206 ATGACCCAACTATGTGCGCTATGGTA-TGGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGTGG-AGT-GCACATGAGCTGATG
* *
15255249 ATGACTCAGCTATGTGTGGTGTGGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTGT-GGAGTGCACATGAGCTGATG
* * *
15255292 ATGACCCAGTTATGTACGGTGTGGGAGTGCACGTGAG
1 ATGACCCAGCTATGTGCGGTGT-GGAGTGCACATGAG
15255329 TTGAGGGAGA
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
42 3 0.02
43 138 0.96
44 3 0.02
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (42 bp):
ATGACCCAGCTATGTGCGGTGTGGAGTGCACATGAGCTGATG
Found at i:15255216 original size:86 final size:85
Alignment explanation
Indices: 15255120--15255332 Score: 275
Period size: 86 Copynumber: 2.5 Consensus size: 85
15255110 TGTGATAATT
*
15255120 ATGACCCAACTATGTGCGGTGTAGGAGTGCACATGAGTTGGTGATGACCCAGCTATGTGCGGTGT
1 ATGACCCAACTATGTGCGGTGT-GGAGTGCACATGAGTTGATGATGACCCAGCTATGTGCGGTGT
*
15255185 GGTAGTGCAAATGAGCTGATG
65 GGGAGTGCAAATGAGCTGATG
* * * * *
15255206 ATGACCCAACTATGTGCGCTATGGTA-TGGCACATGAGCTGATGATGACTCAGCTATGTGTGGTG
1 ATGACCCAACTATGTGCGGTGTGG-AGT-GCACATGAGTTGATGATGACCCAGCTATGTGCGGTG
*
15255270 TGGGAGTGCACATGAGCTGATG
64 TGGGAGTGCAAATGAGCTGATG
** * *
15255292 ATGACCCAGTTATGTACGGTGTGGGAGTGCACGTGAGTTGA
1 ATGACCCAACTATGTGCGGTGT-GGAGTGCACATGAGTTGA
15255333 GGGAGAGTTA
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
85 3 0.03
86 102 0.94
87 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.26
Consensus pattern (85 bp):
ATGACCCAACTATGTGCGGTGTGGAGTGCACATGAGTTGATGATGACCCAGCTATGTGCGGTGTG
GGAGTGCAAATGAGCTGATG
Found at i:15258672 original size:15 final size:15
Alignment explanation
Indices: 15258624--15258675 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
15258614 CTATGTTTTC
15258624 ATAACTGAATTATAAA
1 ATAA-TGAATTATAAA
* *
15258640 ATAAAGATGTTGATAAA
1 ATAATGA-ATT-ATAAA
*
15258657 ATGATGAATTATAAA
1 ATAATGAATTATAAA
15258672 ATAA
1 ATAA
15258676 AGCTCAAGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
15 10 0.36
16 8 0.29
17 10 0.36
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.31
Consensus pattern (15 bp):
ATAATGAATTATAAA
Found at i:15265510 original size:13 final size:13
Alignment explanation
Indices: 15265492--15265516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15265482 GGAGAAATTG
15265492 TGATTTTATAAAA
1 TGATTTTATAAAA
15265505 TGATTTTATAAA
1 TGATTTTATAAA
15265517 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:15269795 original size:19 final size:19
Alignment explanation
Indices: 15269771--15269808 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
15269761 CCATTTGACT
*
15269771 TATTGGAGTATGATTTGAG
1 TATTGGAGCATGATTTGAG
*
15269790 TATTGGAGCATGGTTTGAG
1 TATTGGAGCATGATTTGAG
15269809 GTTTAGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.34, T:0.39
Consensus pattern (19 bp):
TATTGGAGCATGATTTGAG
Found at i:15273466 original size:129 final size:129
Alignment explanation
Indices: 15273236--15273496 Score: 416
Period size: 129 Copynumber: 2.0 Consensus size: 129
15273226 GGTATATTAA
* * * * *
15273236 ACGGTCACTACAGTGGTGGGGGTTTCCGTGGACTGCCTATGAGAGGGGCATGGTAACCCAATTAT
1 ACGGTAACTACAGTGGTGGGAGTTTCCGTGGACTGCCTATGAGAAGAGCACGGTAACCCAATTAT
*
15273301 ATATTTACCTCCGGGGGGAGATGTTGGATGAAGTATCTCCTGAGGTAAGATTTGAATGCACCTC
66 ATACTTACCTCCGGGGGGAGATGTTGGATGAAGTATCTCCTGAGGTAAGATTTGAATGCACCTC
* *
15273365 ACGGTAACTACAGTGGTGGGAGTTTCCGTGGACTGCCTATGAGAATAGCACGGTAACTCAATTAT
1 ACGGTAACTACAGTGGTGGGAGTTTCCGTGGACTGCCTATGAGAAGAGCACGGTAACCCAATTAT
* *
15273430 ATACTTACCTCCGGGGGGAGATGTTAGG-TGAAGTATCTCCTGAGGTATGATTTGAGTGCACCTC
66 ATACTTACCTCCGGGGGGAGATGTT-GGATGAAGTATCTCCTGAGGTAAGATTTGAATGCACCTC
15273494 ACG
1 ACG
15273497 TTCGGGCCAC
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
129 119 0.98
130 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (129 bp):
ACGGTAACTACAGTGGTGGGAGTTTCCGTGGACTGCCTATGAGAAGAGCACGGTAACCCAATTAT
ATACTTACCTCCGGGGGGAGATGTTGGATGAAGTATCTCCTGAGGTAAGATTTGAATGCACCTC
Found at i:15287046 original size:14 final size:14
Alignment explanation
Indices: 15287027--15287054 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
15287017 ATCACGTACC
15287027 ATTTTCTTCTAGTA
1 ATTTTCTTCTAGTA
15287041 ATTTTCTTCTAGTA
1 ATTTTCTTCTAGTA
15287055 TAAGGCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
ATTTTCTTCTAGTA
Found at i:15288134 original size:21 final size:20
Alignment explanation
Indices: 15288090--15288136 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
15288080 ATTAAATATT
*
15288090 AATTAATTTAATAAAACCTT
1 AATTAATTTAATAAAACCTA
**
15288110 AATTAATTTAAATAATTCCTA
1 AATTAATTT-AATAAAACCTA
15288131 AATTAA
1 AATTAA
15288137 CTAATTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTAATTTAATAAAACCTA
Found at i:15291969 original size:67 final size:66
Alignment explanation
Indices: 15291896--15292090 Score: 241
Period size: 67 Copynumber: 2.9 Consensus size: 66
15291886 AAGTTAGTTG
*
15291896 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTATTGTAGGTTGTGGTTGAGTCTTTGAAAAACCA
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATT-TTGAAGGTTGTGGTTGAGTCTTTGAAAAACCA
15291961 CT
65 CT
* ** * *
15291963 TTGGGTTTTGGTTGAGCCTATGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCA
1 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTTTG-AAGGTTGTGGTTGAGTCTTTGAAAAACCA
15292028 CT
65 CT
* * * *
15292030 TTGGGTTTTAGTTGATCTCG-GTAAAAACCATTGTTAAAGGTTGTGGCTGAGT-TTGTGAAAA
1 TTGGGTTTTGGTTGATCCCGTG-AAAAACCATT-TTGAAGGTTGTGGTTGAGTCTT-TGAAAA
15292091 GCCATTGTAA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
66 5 0.05
67 103 0.94
68 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.36
Consensus pattern (66 bp):
TTGGGTTTTGGTTGATCCCGTGAAAAACCATTTTGAAGGTTGTGGTTGAGTCTTTGAAAAACCAC
T
Found at i:15291987 original size:32 final size:32
Alignment explanation
Indices: 15291896--15292044 Score: 147
Period size: 35 Copynumber: 4.5 Consensus size: 32
15291886 AAGTTAGTTG
* ** *
15291896 TTGGGTTTTGGTTGATCCCGTGAAAAACCATT
1 TTGGGTTTTGGTTGAGCCTTTGAAAAACCACT
* *
15291928 ATTGTAGGTTGTGGTTGAGTCTTTGAAAAACCACT
1 -TTG--GGTTTTGGTTGAGCCTTTGAAAAACCACT
*
15291963 TTGGGTTTTGGTTGAGCCTATGAAAAACCA-T
1 TTGGGTTTTGGTTGAGCCTTTGAAAAACCACT
*
15291994 TGTGAAAGGTTGTGGTTGAGCCTTTGAAAAACCACT
1 T-TG---GGTTTTGGTTGAGCCTTTGAAAAACCACT
*
15292030 TTGGGTTTTAGTTGA
1 TTGGGTTTTGGTTGA
15292045 TCTCGGTAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
31 2 0.02
32 36 0.38
33 3 0.03
34 3 0.03
35 50 0.52
36 2 0.02
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (32 bp):
TTGGGTTTTGGTTGAGCCTTTGAAAAACCACT
Found at i:15297610 original size:17 final size:17
Alignment explanation
Indices: 15297588--15297622 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
15297578 TGAGCTTAAG
15297588 GACAATTTCTTAAATTT
1 GACAATTTCTTAAATTT
15297605 GACAATTTCTTAAATTT
1 GACAATTTCTTAAATTT
15297622 G
1 G
15297623 TTTTCACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (17 bp):
GACAATTTCTTAAATTT
Found at i:15298237 original size:28 final size:28
Alignment explanation
Indices: 15298198--15298279 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
15298188 CAAAAAACTG
*
15298198 CTTTTCATGGATCAAGGATAACCTCTGC
1 CTTTTCAAGGATCAAGGATAACCTCTGC
* * *
15298226 CTTTTCAAGGATCATGAATAACCTCTGG
1 CTTTTCAAGGATCAAGGATAACCTCTGC
*
15298254 ATTTTCAAGGATCAAGCG-TAACCTCT
1 CTTTTCAAGGATCAAG-GATAACCTCT
15298280 CTTTTTTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (28 bp):
CTTTTCAAGGATCAAGGATAACCTCTGC
Found at i:15302652 original size:24 final size:25
Alignment explanation
Indices: 15302606--15302652 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
15302596 TCACCAAAGC
**
15302606 TTTTCTCTCTAATTTCTCTTTCTAA
1 TTTTCTCTCTAATTTCTAATTCTAA
*
15302631 TTTTCT-TCTACTTTCTAATTCT
1 TTTTCTCTCTAATTTCTAATTCT
15302653 CTATCTATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTCTCTCTAATTTCTAATTCTAA
Found at i:15305046 original size:2 final size:2
Alignment explanation
Indices: 15305039--15305079 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
15305029 TCCTTTTTAT
15305039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15305080 TCAATAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15313339 original size:23 final size:23
Alignment explanation
Indices: 15313309--15313363 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
15313299 AATTTTACTC
15313309 TATCTTTGGCACAACCAAAACAT
1 TATCTTTGGCACAACCAAAACAT
15313332 TATCTTTGGCACAACCAAAACAT
1 TATCTTTGGCACAACCAAAACAT
15313355 TATCTTTGG
1 TATCTTTGG
15313364 TAGAACTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.31
Consensus pattern (23 bp):
TATCTTTGGCACAACCAAAACAT
Found at i:15315401 original size:26 final size:27
Alignment explanation
Indices: 15315359--15315417 Score: 102
Period size: 26 Copynumber: 2.2 Consensus size: 27
15315349 CTCAGTTTCC
*
15315359 TGATTCGATTTTGCTGTCTTTTGTCTT
1 TGATTCGATATTGCTGTCTTTTGTCTT
15315386 TGATTCG-TATTGCTGTCTTTTGTCTT
1 TGATTCGATATTGCTGTCTTTTGTCTT
15315412 TGATTC
1 TGATTC
15315418 AATGTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 24 0.77
27 7 0.23
ACGTcount: A:0.08, C:0.15, G:0.19, T:0.58
Consensus pattern (27 bp):
TGATTCGATATTGCTGTCTTTTGTCTT
Found at i:15318272 original size:25 final size:25
Alignment explanation
Indices: 15318238--15318286 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
15318228 TCAGTTAAAG
15318238 TTAAAGGAAGATAAGCCTCAATCAA
1 TTAAAGGAAGATAAGCCTCAATCAA
15318263 TTAAAGGAAGATAAGCCTCAATCA
1 TTAAAGGAAGATAAGCCTCAATCA
15318287 GTCAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.20
Consensus pattern (25 bp):
TTAAAGGAAGATAAGCCTCAATCAA
Found at i:15318293 original size:25 final size:25
Alignment explanation
Indices: 15318240--15318293 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
15318230 AGTTAAAGTT
*
15318240 AAAGGAAGATAAGCCTCAATCAATT
1 AAAGGAAGATAAGCCTCAATCAATC
*
15318265 AAAGGAAGATAAGCCTCAATCAGTC
1 AAAGGAAGATAAGCCTCAATCAATC
15318290 AAAG
1 AAAG
15318294 AAAGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (25 bp):
AAAGGAAGATAAGCCTCAATCAATC
Found at i:15340688 original size:36 final size:36
Alignment explanation
Indices: 15340621--15340727 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 36
15340611 AAAAGCAATT
** * *
15340621 TATTGGTAAAGGTTACGCTCAATTTTG-TAAAAGTCA
1 TATT-GTAAAGGTTACGCTTGATCTTGTTAAAAGGCA
*
15340657 TATTGTGAAGGTTACGCTTGATCTTGTTAAAAGGCA
1 TATTGTAAAGGTTACGCTTGATCTTGTTAAAAGGCA
* * *
15340693 TGTTTTAAAGGTTATGCTTGATCTTGTTGAAAAGG
1 TATTGTAAAGGTTACGCTTGATCTTGTT-AAAAGG
15340728 AAAGTTGATA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
35 18 0.30
36 36 0.60
37 6 0.10
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.38
Consensus pattern (36 bp):
TATTGTAAAGGTTACGCTTGATCTTGTTAAAAGGCA
Found at i:15348016 original size:11 final size:11
Alignment explanation
Indices: 15348002--15348031 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
15347992 TGAAAATTGA
15348002 GAAAAAAAAAG
1 GAAAAAAAAAG
*
15348013 GAAAGAAAAAG
1 GAAAAAAAAAG
15348024 GAAAAAAA
1 GAAAAAAA
15348032 GAATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAG
Found at i:15350285 original size:6 final size:6
Alignment explanation
Indices: 15350274--15350324 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
15350264 TCCATATATC
* *
15350274 TAGATT TAGA-T TAGA-T TAGA-T TAGATT CAGATT CAGATT TAGATT
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT
15350319 TA-ATT T
1 TAGATT T
15350325 GAATAATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
5 19 0.45
6 23 0.55
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (6 bp):
TAGATT
Found at i:15350289 original size:5 final size:5
Alignment explanation
Indices: 15350274--15350318 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
15350264 TCCATATATC
15350274 TAGATT TAGAT TAGAT TAGAT TAGAT TCAGAT TCAGATT TAGAT T
1 TAGA-T TAGAT TAGAT TAGAT TAGAT T-AGAT T-AGA-T TAGAT T
15350319 TAATTTGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 19 0.51
6 16 0.43
7 2 0.05
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (5 bp):
TAGAT
Found at i:15354818 original size:42 final size:41
Alignment explanation
Indices: 15354759--15354841 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 41
15354749 TTCAACTGTA
15354759 AGTATATATATATATATATATATATAT-TATTTATATAAGANT
1 AGTATATATATATATATATATATATATAT-TTTATATAAGA-T
15354801 AGTATATATATATATATATATATATATATTTTATATAAGAT
1 AGTATATATATATATATATATATATATATTTTATATAAGAT
15354842 TATGTCTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
41 1 0.03
42 38 0.95
43 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (41 bp):
AGTATATATATATATATATATATATATATTTTATATAAGAT
Found at i:15354837 original size:2 final size:2
Alignment explanation
Indices: 15354761--15354829 Score: 88
Period size: 2 Copynumber: 34.5 Consensus size: 2
15354751 CAACTGTAAG
* *
15354761 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA TA TA -A GA NTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
15354802 GTA TA TA TA TA TA TA TA TA TA TA TA TA T
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA T
15354830 TTTATATAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
1 2 0.03
2 55 0.92
3 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:15358424 original size:2 final size:2
Alignment explanation
Indices: 15358417--15358470 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
15358407 GGTAAGCAAC
*
15358417 AT AT AT AT CAA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15358460 AT AT AT AT AT A
1 AT AT AT AT AT A
15358471 AACACATGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 48 0.98
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15361950 original size:400 final size:401
Alignment explanation
Indices: 15361159--15362359 Score: 1647
Period size: 400 Copynumber: 3.0 Consensus size: 401
15361149 GAATTATTTA
* *
15361159 ATTGTTTAACTACTAAAA-TATTTTTTCATTTGATTACTTAAATTATTTAATTAATTTAATAAAA
1 ATTGCTTAACTACTAAAACT-TTTTTTCATTTGATTAGTTAAATTATTTAATTAATTTAATAAAA
* * * **
15361223 CTTCAATTAATGTAAATACTTTTAAATTTTACTAAATTTATTAATACATTTTAAATTGATTAACA
65 CTTTAATTAATGTAAATACTTTTAAATTTTACTAAATTTACTAATACATTTTGAATTGATTAATT
*
15361288 ACTATCATTTGATTTGTTAAATTACTAATTTAATTAATTGATTAATTACTAATACATAATTCTTC
130 ACTATCATTTGATTTGTTAAATTACTAATTTAATTAATTGATTAATTACTAATACATGATTCTTC
15361353 AGAATTAGTTAAATTTTGTAATTAATTCCCTAAATCCCTTAATTAATTTAAA-TAAAAAATAATA
195 AGAATTAGTTAAATTTTGTAATTAATTCCCT-AAT-CCTTAATTAATTTAAATTAAAAAATAATA
* * *
15361417 ATATATAATGTTACTAATTTAATTGATTCCTTAATTACTTATAACACCCTAACACTTAATTAACT
258 TTATATAATATTACTAATTTAATTAATTCCTTAATTACTTATAACACCCTAACACTTAATTAACT
* * * * *
15361482 AAATTATTTAATTACCTTACTAAACACCATAGTTTATTTAAATGTTTTTAAAATTAAATAATATT
323 AAATTATTTAATTACCTTACTAAACTCCTTAATTTATTTAAATATTTTTAAAATAAAATAATATT
15361547 ACTAATTTAGTTTC
388 ACTAATTTAGTTTC
* *
15361561 -TTGCTTAACTACTAAAACTTTTTTTCATTTCATTAGTTAAATT-TTTAACTAATTTAATAAAAC
1 ATTGCTTAACTACTAAAACTTTTTTTCATTTGATTAGTTAAATTATTTAATTAATTTAATAAAAC
* *
15361624 TTTAATTAATGTAAATCCTTTTAAATTGTACTAAATTTACTAATACATTTTGAATTGATTAATTA
66 TTTAATTAATGTAAATACTTTTAAATTTTACTAAATTTACTAATACATTTTGAATTGATTAATTA
* *
15361689 CTATCATTTGATTTGTTAAATTACTAATTTAACTAATTGATTAATTACTAATACATGATTCTTTA
131 CTATCATTTGATTTGTTAAATTACTAATTTAATTAATTGATTAATTACTAATACATGATTCTTCA
* * * * *
15361754 GAGTTAGTTAAATTTTATAATTAATTTCGTGAAGTCCTTAATTAATTTAAATTAAAAAA-ACTAT
196 GAATTAGTTAAATTTTGTAATTAATTCCCT-AA-TCCTTAATTAATTTAAATTAAAAAATAATAT
15361818 TATATAATATTACTAATTTAATTAATTCCTTAATTACTTATAACACCCTAACACTTAATTAACTA
259 TATATAATATTACTAATTTAATTAATTCCTTAATTACTTATAACACCCTAACACTTAATTAACTA
*
15361883 AATTATTTAATTACCTTACTAAACTCCTTAATTTATTTAAATATTTTTAAAATCAAATAATATTA
324 AATTATTTAATTACCTTACTAAACTCCTTAATTTATTTAAATATTTTTAAAATAAAATAATATTA
15361948 CTAATTTAG-TTC
389 CTAATTTAGTTTC
* * * *
15361960 ATTGCTTAACTACTAAAACTATTTTTCTTTTGATTAGTTAAATTATTTAATTAATTTCATAAGAC
1 ATTGCTTAACTACTAAAACTTTTTTTCATTTGATTAGTTAAATTATTTAATTAATTTAATAAAAC
* *
15362025 CTT-ATTATATGTAAATACTTTTAAATTTTACTAAATTTACTAATACATTTTGTATTGATTAATT
66 TTTAATTA-ATGTAAATACTTTTAAATTTTACTAAATTTACTAATACATTTTGAATTGATTAATT
* * * *
15362089 ACAAACAATTGATTT-TTAAAATTACTAATTTAATTAATTGATTGATTACTAATACATGATTCTT
130 ACTATCATTTGATTTGTT-AAATTACTAATTTAATTAATTGATTAATTACTAATACATGATTCTT
* * * * *
15362153 CAAAATTAATTAAATTTTGTAATT-ATAACCCTAAACACTTAATTAATTTAAATAAAAAAAGTAA
194 CAGAATTAGTTAAATTTTGTAATTAAT-TCCCTAATC-CTTAATTAATTTAAATTAAAAAA-TAA
* * ** * * ** ** *
15362217 TATTATATAATATTACTCATTTAATTTATTGTTTAATTACTTAGAATACATTGCATTACGTAATT
256 TATTATATAATATTACTAATTTAATTAATTCCTTAATTACTTATAACACCCT--AACACTTAATT
* * * *
15362282 AAC-ATAATTATTTAATTAACTCATTAACACT--TTAATTAATTTAAATA-TTTT-AAATAAAAT
319 AACTA-AATTATTTAATTACCTTACTAA-ACTCCTTAATTTATTTAAATATTTTTAAAATAAAAT
*
15362342 AATATTACAAATTTAGTT
382 AATATTACTAATTTAGTT
15362360 AATTACTTAT
Statistics
Matches: 712, Mismatches: 71, Indels: 32
0.87 0.09 0.04
Matches are distributed among these distances:
399 4 0.01
400 390 0.55
401 218 0.31
402 51 0.07
403 16 0.02
404 30 0.04
405 3 0.00
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.45
Consensus pattern (401 bp):
ATTGCTTAACTACTAAAACTTTTTTTCATTTGATTAGTTAAATTATTTAATTAATTTAATAAAAC
TTTAATTAATGTAAATACTTTTAAATTTTACTAAATTTACTAATACATTTTGAATTGATTAATTA
CTATCATTTGATTTGTTAAATTACTAATTTAATTAATTGATTAATTACTAATACATGATTCTTCA
GAATTAGTTAAATTTTGTAATTAATTCCCTAATCCTTAATTAATTTAAATTAAAAAATAATATTA
TATAATATTACTAATTTAATTAATTCCTTAATTACTTATAACACCCTAACACTTAATTAACTAAA
TTATTTAATTACCTTACTAAACTCCTTAATTTATTTAAATATTTTTAAAATAAAATAATATTACT
AATTTAGTTTC
Found at i:15364291 original size:20 final size:21
Alignment explanation
Indices: 15364266--15364312 Score: 78
Period size: 20 Copynumber: 2.3 Consensus size: 21
15364256 AGCTACAATA
*
15364266 TGAAAAGATAACTTTTTA-TT
1 TGAAAAGATAACCTTTTATTT
15364286 TGAAAAGATAACCTTTTATTT
1 TGAAAAGATAACCTTTTATTT
15364307 TGAAAA
1 TGAAAA
15364313 TACACCAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (21 bp):
TGAAAAGATAACCTTTTATTT
Found at i:15364486 original size:30 final size:30
Alignment explanation
Indices: 15364452--15364513 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
15364442 ATATGAGAAG
*
15364452 ATAACTTTTCATTTGAAGGGACAACCTTTT
1 ATAACTTTTCATTTGAAGAGACAACCTTTT
15364482 ATAACTTTTCATTTGAAGAGACAACCTTTT
1 ATAACTTTTCATTTGAAGAGACAACCTTTT
15364512 AT
1 AT
15364514 TTTGAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.40
Consensus pattern (30 bp):
ATAACTTTTCATTTGAAGAGACAACCTTTT
Found at i:15372080 original size:29 final size:28
Alignment explanation
Indices: 15371991--15372080 Score: 85
Period size: 31 Copynumber: 3.1 Consensus size: 28
15371981 TTGTTGAAAT
*
15371991 GTTATACCTCCTTG-AAAAGTTAGATAG
1 GTTATACCTCCTTGAAAAAGGTAGATAG
* * *
15372018 GTTATACTTGAGCCTTGAAAAA-GTAAACTTG
1 GTTATACCT---CCTTGAAAAAGGTAGA-TAG
15372049 GTTATACCTCCATTGAAAAAGGTAGATAG
1 GTTATACCTCC-TTGAAAAAGGTAGATAG
15372078 GTT
1 GTT
15372081 GTGCTTTAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
27 8 0.16
28 2 0.04
29 13 0.27
30 12 0.24
31 14 0.29
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.32
Consensus pattern (28 bp):
GTTATACCTCCTTGAAAAAGGTAGATAG
Found at i:15376599 original size:43 final size:43
Alignment explanation
Indices: 15376525--15376643 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
15376515 TCACTAGCTC
* * * * **
15376525 ATGCGCACTCCTTACTCTCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATC-CTCGACTT
* *
15376568 ATGCGTACTCCCTACTCGCACATAACCGGGTCATCCTCGACTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCCTCGACTT
*
15376611 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCA
15376644 ATATAATTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCCTCGACTT
Found at i:15381586 original size:20 final size:21
Alignment explanation
Indices: 15381561--15381607 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
15381551 AGTTATAATA
15381561 TGAAAAGATAA-CTTTTCA-TT
1 TGAAAAGATAACCTTTT-ATTT
15381581 TGAAAAGATAACCTTTTATTT
1 TGAAAAGATAACCTTTTATTT
15381602 TGAAAA
1 TGAAAA
15381608 TACTCCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (21 bp):
TGAAAAGATAACCTTTTATTT
Found at i:15383637 original size:9 final size:9
Alignment explanation
Indices: 15383623--15383656 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
15383613 ACATGATTAA
15383623 TAACACGTT
1 TAACACGTT
**
15383632 TAACACAAT
1 TAACACGTT
15383641 TAACACGTT
1 TAACACGTT
15383650 TAACACG
1 TAACACG
15383657 ATTCAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (9 bp):
TAACACGTT
Found at i:15389500 original size:90 final size:90
Alignment explanation
Indices: 15389380--15389544 Score: 201
Period size: 90 Copynumber: 1.8 Consensus size: 90
15389370 GTTTCTAAGG
* * * *
15389380 GAGATGTTCCCTTTTTCAAACATTATAATGGC-ACTTGGTGACAT-TTGTAGAAATTCTTGTTAA
1 GAGATGTTCCCTATCTCAAACATTATAATGGCTA-TTGGTGAAATATTGTA-AAA-TCTTGTAAA
*
15389443 GTCTTTAAAGGGAAAACCCTTTAGGAAA
63 CTCTTTAAAGGGAAAACCCTTTAGGAAA
* *
15389471 GAGATG-TCCCTATCTCAAGCATTGTAATGGCTATTGGTGAAATACTTGTAAAATCTTGTAAACT
1 GAGATGTTCCCTATCTCAAACATTATAATGGCTATTGGTGAAATA-TTGTAAAATCTTGTAAACT
*
15389535 CTTTATAGGG
65 CTTTAAAGGG
15389545 GTGAACAATC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
90 48 0.76
91 10 0.16
92 5 0.08
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (90 bp):
GAGATGTTCCCTATCTCAAACATTATAATGGCTATTGGTGAAATATTGTAAAATCTTGTAAACTC
TTTAAAGGGAAAACCCTTTAGGAAA
Found at i:15391201 original size:22 final size:22
Alignment explanation
Indices: 15391170--15391213 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
15391160 TTCAATTCCC
* *
15391170 TAAGAGAGAAGAGAAAAGAGAA
1 TAAGAAAGAAGAAAAAAGAGAA
15391192 TAAGAAAGAAGAAAAAAGAGAA
1 TAAGAAAGAAGAAAAAAGAGAA
15391214 AACTATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (22 bp):
TAAGAAAGAAGAAAAAAGAGAA
Found at i:15403370 original size:35 final size:35
Alignment explanation
Indices: 15403324--15403394 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
15403314 TTAGTTGTTG
* * *
15403324 GGTTTTGGTTGATCCCGGTAAAATCCATTGTGAAA
1 GGTTTTGGTTGAGCCCGGTAAAAGCCATTGTAAAA
*
15403359 GGTTTTGGTTGAGCCTGGTAAAAGCCATTGTAAAA
1 GGTTTTGGTTGAGCCCGGTAAAAGCCATTGTAAAA
15403394 G
1 G
15403395 CTTGGTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.32
Consensus pattern (35 bp):
GGTTTTGGTTGAGCCCGGTAAAAGCCATTGTAAAA
Found at i:15403983 original size:22 final size:22
Alignment explanation
Indices: 15403957--15403999 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
15403947 AATGTGGTAT
15403957 ACAAAA-TACCAATGGAATGTCG
1 ACAAAATTACCAAT-GAATGTCG
15403979 ACAAAATTTACCAATGAATGT
1 ACAAAA-TTACCAATGAATGT
15404000 ATTTCTGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 6 0.32
24 7 0.37
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (22 bp):
ACAAAATTACCAATGAATGTCG
Found at i:15404852 original size:20 final size:20
Alignment explanation
Indices: 15404825--15404877 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
15404815 GTAGTAAAGA
* *
15404825 ACATCTATGGATAGATGGTC
1 ACATCTATCGATAGATGGAC
* *
15404845 AGATCTATCAATAGATGGAC
1 ACATCTATCGATAGATGGAC
15404865 ACATCTATCGATA
1 ACATCTATCGATA
15404878 AATAGCAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (20 bp):
ACATCTATCGATAGATGGAC
Found at i:15409473 original size:36 final size:37
Alignment explanation
Indices: 15409407--15409492 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 37
15409397 AATCCACCAT
* * *
15409407 CAGCTTGCCTTTTCAACAAGATTAGGCGTAA-CTTTTA
1 CAGCATGCCTTTTCAACAAGATCAGGCGTAATC-TTCA
* *
15409444 CAGCATGCCTTTT-AATAGGATCAGGCGTAATCTTCA
1 CAGCATGCCTTTTCAACAAGATCAGGCGTAATCTTCA
*
15409480 CAACATGCCTTTT
1 CAGCATGCCTTTT
15409493 GCAGGATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 29 0.69
37 13 0.31
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (37 bp):
CAGCATGCCTTTTCAACAAGATCAGGCGTAATCTTCA
Found at i:15411280 original size:22 final size:23
Alignment explanation
Indices: 15411252--15411298 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
15411242 ATTTCTATGC
15411252 ATTACTA-CAAGAACTAAGCT-AA
1 ATTACTATCAA-AACTAAGCTCAA
*
15411274 ATTACTATCAAAATTAAGCTCAA
1 ATTACTATCAAAACTAAGCTCAA
15411297 AT
1 AT
15411299 AACTCTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGCTCAA
Found at i:15422195 original size:24 final size:26
Alignment explanation
Indices: 15422167--15422226 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 26
15422157 AACCATAAAA
15422167 TCTTTTTCAGCAT-T-TTTTTCAAAT
1 TCTTTTTCAGCATGTCTTTTTCAAAT
*
15422191 TCTTTTTCA--ATGTCTTTTTCAATT
1 TCTTTTTCAGCATGTCTTTTTCAAAT
*
15422215 TCTTTTTTAGCA
1 TCTTTTTCAGCA
15422227 ACCATTACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 2 0.07
23 1 0.03
24 26 0.87
26 1 0.03
ACGTcount: A:0.18, C:0.17, G:0.05, T:0.60
Consensus pattern (26 bp):
TCTTTTTCAGCATGTCTTTTTCAAAT
Found at i:15422196 original size:12 final size:12
Alignment explanation
Indices: 15422167--15422221 Score: 60
Period size: 12 Copynumber: 4.6 Consensus size: 12
15422157 AACCATAAAA
*
15422167 TCTTTTTCAGCAT
1 TCTTTTTCA-AAT
15422180 T-TTTTTCAAAT
1 TCTTTTTCAAAT
15422191 TCTTTTTC-AAT
1 TCTTTTTCAAAT
*
15422202 GTCTTTTTCAATT
1 -TCTTTTTCAAAT
15422215 TCTTTTT
1 TCTTTTT
15422222 TAGCAACCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 6 0.16
12 28 0.76
13 3 0.08
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (12 bp):
TCTTTTTCAAAT
Found at i:15423334 original size:73 final size:72
Alignment explanation
Indices: 15423230--15423432 Score: 241
Period size: 72 Copynumber: 2.8 Consensus size: 72
15423220 AAATTGCAGA
* * * * *
15423230 CAAAGAGC-TCTTAGTCGACTAACT-TTCTTCTTAGTCGACTAAGTTGGTTCTGTCTTCTGGTCG
1 CAAAGAGCAT-TTAGTCAACTAACTCAT-TTCTTGGTCGACTAAGTTGGTTTTGTCTTCTAGTC-
15423293 CAGATTCTAG
63 CAGATTCTAG
* **
15423303 CAGAGAGCATTTAGTCAACTAACTCATTTCTTGGTCGACTAAGTTGGTTTTGTCTTGAAGTCCAG
1 CAAAGAGCATTTAGTCAACTAACTCATTTCTTGGTCGACTAAGTTGGTTTTGTCTTCTAGTCCAG
* *
15423368 ATTTTGG
66 ATTCTAG
** *
15423375 CAAAGAGCATTTAGTCAACTAACTCACATCTTGGTCGACTAAGTCGGTTTTGT-TTCTA
1 CAAAGAGCATTTAGTCAACTAACTCATTTCTTGGTCGACTAAGTTGGTTTTGTCTTCTA
15423433 AATATTCTCC
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
71 3 0.03
72 57 0.51
73 50 0.45
74 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (72 bp):
CAAAGAGCATTTAGTCAACTAACTCATTTCTTGGTCGACTAAGTTGGTTTTGTCTTCTAGTCCAG
ATTCTAG
Found at i:15432699 original size:2 final size:2
Alignment explanation
Indices: 15432692--15432722 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15432682 CATTTGTTGG
*
15432692 TA TA TA TA TA GA 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
15432723 GTTGTGCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:15432930 original size:40 final size:38
Alignment explanation
Indices: 15432838--15432940 Score: 134
Period size: 38 Copynumber: 2.7 Consensus size: 38
15432828 ATAGTGCTCA
* * * *
15432838 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCATGATGTGGGGGGATGCACACGATGACACGGAT
* *
15432876 TGTGCATGATGTGGGGGGATGCACACGATGACTCCGGCTT
1 TGTGCATGATGTGGGGGGATGCACACGATGAC-ACGG-AT
15432916 TGTGCATGATGTGGGGGGATGCACA
1 TGTGCATGATGTGGGGGGATGCACA
15432941 TGAGCTGGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 29 0.51
39 2 0.04
40 26 0.46
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.24
Consensus pattern (38 bp):
TGTGCATGATGTGGGGGGATGCACACGATGACACGGAT
Found at i:15437654 original size:73 final size:72
Alignment explanation
Indices: 15437550--15437747 Score: 213
Period size: 72 Copynumber: 2.7 Consensus size: 72
15437540 AAATTGCAGA
* * **
15437550 CAGAGAGC-TCTTAGTCGACTAACT-TTCTTCTTGGTCAACTAAGTTGATTT-TGTCTTCTGGCT
1 CAGAGAGCAT-TTAGTCGACTAACTCAT-TTCTTGGTCGACTAAGTTG-TTTCTGTCTTCAAGC-
**
15437612 GTAGATTTTGG
62 ACAGATTTTGG
* * *
15437623 TAGAGAGCATTTAGTCGACTAACTCATTTCTTAGTCGACTAAGTTGTTTCTGTCTTGAAGCACAG
1 CAGAGAGCATTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGTTTCTGTCTTCAAGCACAG
15437688 ATTTTGG
66 ATTTTGG
** * * *
15437695 CAGAGAGCATTTAGTCGACTAACTCAGATCTTGGTTGACTAAGTCGGTTCTGT
1 CAGAGAGCATTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGTTTCTGT
15437748 TTCTCAATAT
Statistics
Matches: 106, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
72 58 0.55
73 46 0.43
74 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (72 bp):
CAGAGAGCATTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGTTTCTGTCTTCAAGCACAG
ATTTTGG
Found at i:15441193 original size:11 final size:11
Alignment explanation
Indices: 15441174--15441208 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
15441164 TCCTAATAAA
*
15441174 TTTTTTTTTTC
1 TTTTCTTTTTC
15441185 TTTTCTTTTTC
1 TTTTCTTTTTC
15441196 TTTTC-TTTTC
1 TTTTCTTTTTC
15441206 TTT
1 TTT
15441209 CTTCTTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:15441199 original size:16 final size:16
Alignment explanation
Indices: 15441174--15441214 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
15441164 TCCTAATAAA
*
15441174 TTTTTTTTTTCTTTTC
1 TTTTTCTTTTCTTTTC
15441190 TTTTTCTTTTCTTTTC
1 TTTTTCTTTTCTTTTC
15441206 TTTCTTCTT
1 TTT-TTCTT
15441215 CCTCTTCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTC
Found at i:15441211 original size:4 final size:5
Alignment explanation
Indices: 15441175--15441208 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
15441165 CCTAATAAAT
*
15441175 TTTTT TTTTC TTTTC TTTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTT
15441209 CTTCTTCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:15441255 original size:30 final size:30
Alignment explanation
Indices: 15441203--15441281 Score: 113
Period size: 30 Copynumber: 2.5 Consensus size: 30
15441193 TTCTTTTCTT
15441203 TTCTTTCTTCTTCCTCTTCTCCTCCCGTCGGCC
1 TTCTTTC-TC-TCCT-TTCTCCTCCCGTCGGCC
*
15441236 TTCTTTCTCTCCTTTCTCCTCTCGTCGGCC
1 TTCTTTCTCTCCTTTCTCCTCCCGTCGGCC
*
15441266 TTCTTTCTCTTCTTTC
1 TTCTTTCTCTCCTTTC
15441282 CTTTCCTTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
30 31 0.70
31 4 0.09
32 2 0.05
33 7 0.16
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.51
Consensus pattern (30 bp):
TTCTTTCTCTCCTTTCTCCTCCCGTCGGCC
Found at i:15441304 original size:49 final size:44
Alignment explanation
Indices: 15441250--15441344 Score: 118
Period size: 49 Copynumber: 2.0 Consensus size: 44
15441240 TTCTCTCCTT
* *
15441250 TCTCCTCTCGTCGGCCTTCTTTCTCTTCTTTCCTTTCCTTTCTTCTTTC
1 TCTCCTCCCGTCGGCCTTCCTTCTC-TC--TCCTTTCC-TTCTT-TTTC
*
15441299 TCTCCTCCCGTCGGCTTTCCTTCTCTCTCCTTTCCTTCTTTTTC
1 TCTCCTCCCGTCGGCCTTCCTTCTCTCTCCTTTCCTTCTTTTTC
15441343 TC
1 TC
15441345 ATTCTTTACC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
44 6 0.14
45 5 0.12
46 8 0.19
48 2 0.05
49 22 0.51
ACGTcount: A:0.00, C:0.41, G:0.06, T:0.53
Consensus pattern (44 bp):
TCTCCTCCCGTCGGCCTTCCTTCTCTCTCCTTTCCTTCTTTTTC
Found at i:15441454 original size:15 final size:16
Alignment explanation
Indices: 15441436--15441469 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15441426 TTCATTACTA
15441436 TTATT-ATTATTTATT
1 TTATTAATTATTTATT
*
15441451 TTATTAATTTTTTATT
1 TTATTAATTATTTATT
15441467 TTA
1 TTA
15441470 CTTCCTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTAATTATTTATT
Found at i:15443968 original size:43 final size:43
Alignment explanation
Indices: 15443897--15444311 Score: 432
Period size: 43 Copynumber: 10.0 Consensus size: 43
15443887 CAACTCTCTC
* * *
15443897 TCAGCTTATGTGCACTCCAAC-ACT-GCACATAACTAGGTCATCA
1 TCAGCTCATGTGCACTCC--CTACTCGCACATAGCTGGGTCATCA
*
15443940 TCAGCTCATGTGCACTCCCTACTCGCACATAACTGGGTCATCA
1 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
* * * *
15443983 TCAGCTCATGTGTACT-CCT-C-CACACATGGCTGGGCCATCA
1 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
15444023 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATC-
1 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
* * * *
15444065 TGCAGCTCATGTGTACT-TCT-CT-ACACATAGCTGGGCCATCA
1 T-CAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
*
15444106 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCAACA
1 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
* ** *
15444149 TCAGCTCATGTGTACT-CCT-C-CATACATGGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
*
15444189 TCAGCTCATGTGCACTCCCTACTCGCACATAGGTGGGTCATCA
1 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
* * * * * *
15444232 TCAGCTCATGTGTACT-CCT-C-CACGCATGGTTGGGTCAGCA
1 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
* * *
15444272 -CAACTCATGTGCACT-CCTACACCGCACATGGCTGGGTCAT
1 TCAGCTCATGTGCACTCCCTAC-TCGCACATAGCTGGGTCAT
15444312 AATTATCAAG
Statistics
Matches: 314, Mismatches: 42, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
39 16 0.05
40 108 0.34
41 15 0.05
42 33 0.11
43 142 0.45
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.26
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCA
Found at i:15444039 original size:83 final size:83
Alignment explanation
Indices: 15443935--15444311 Score: 580
Period size: 83 Copynumber: 4.6 Consensus size: 83
15443925 ATAACTAGGT
*
15443935 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAACTGGGTCATCATCAGCTCATGTGTACTC
1 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCATCAGCTCATGTGTACTC
15444000 CTCCACACATGGCTGGGC
66 CTCCACACATGGCTGGGC
15444018 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATC-TGCAGCTCATGTGTACT
1 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCAT-CAGCTCATGTGTACT
* * *
15444082 TCTCTACACATAGCTGGGC
65 CCTCCACACATGGCTGGGC
*
15444101 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCAACATCAGCTCATGTGTACTC
1 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCATCAGCTCATGTGTACTC
* *
15444166 CTCCATACATGGCTGGGT
66 CTCCACACATGGCTGGGC
*
15444184 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGGTGGGTCATCATCAGCTCATGTGTACTC
1 CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCATCAGCTCATGTGTACTC
* * *
15444249 CTCCACGCATGGTTGGGT
66 CTCCACACATGGCTGGGC
* * * *
15444267 CAGCA-CAACTCATGTGCACT-CCTACACCGCACATGGCTGGGTCAT
1 CATCATCAGCTCATGTGCACTCCCTAC-TCGCACATAGCTGGGTCAT
15444312 AATTATCAAG
Statistics
Matches: 271, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
81 5 0.02
82 31 0.11
83 234 0.86
84 1 0.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (83 bp):
CATCATCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGTCATCATCAGCTCATGTGTACTC
CTCCACACATGGCTGGGC
Found at i:15447642 original size:17 final size:18
Alignment explanation
Indices: 15447616--15447652 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
15447606 CAAAAGCATG
*
15447616 AAACTTAACTT-AAATAA
1 AAACTAAACTTAAAATAA
15447633 AAACTAAACTTAAAATAA
1 AAACTAAACTTAAAATAA
15447651 AA
1 AA
15447653 CATCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (18 bp):
AAACTAAACTTAAAATAA
Found at i:15458851 original size:29 final size:30
Alignment explanation
Indices: 15458815--15458891 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
15458805 AAATATTTAT
* *
15458815 AATATCCATAGTAGCTAAACAAGATATA-C
1 AATATCCATAATAACTAAACAAGATATATC
* *
15458844 AATATCCACAATAACTAAGCAAGATATATTC
1 AATATCCATAATAACTAAACAAGATATA-TC
15458875 AATATCCATAATAACTA
1 AATATCCATAATAACTA
15458892 GCACATGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 24 0.59
31 17 0.41
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.26
Consensus pattern (30 bp):
AATATCCATAATAACTAAACAAGATATATC
Found at i:15460123 original size:187 final size:175
Alignment explanation
Indices: 15459774--15460139 Score: 516
Period size: 187 Copynumber: 2.0 Consensus size: 175
15459764 CTAATTCATA
* * *
15459774 GATATAAGTAAAATCTCTCTCTTTGTAAAAGCACAATACCAATCACAAGAGATGGATTTTAAAGC
1 GATATAAGTAAAATCTCCCTCATTGTAAAAGCACAATACCAATCACAAGAGATGGATTTTAAAAC
15459839 TCATTATATCAATTGGTAAAACACTAGTAAAGACTTCCCCTATCATTAAGCATATCAACTTCAAG
66 TCATTATATCAATTGGTAAAACACTAGTAAAGACTTCCCCTATCATTAAGCATATCAACTTCAAG
* * *
15459904 GCTCAAATAGATTTAAGAAAGATATGATCAATTTAAAGCTCAAGT
131 GCTCAAACACATTTAAGAAAGATATGATCAATTTAAAACTCAAGT
* * * *
15459949 GATATATGTAAAATCTCCCTCATTGTAAAAGCACAATATCAATTACGAGAGATGGAATCATTTAA
1 GATATAAGTAAAATCTCCCTCATTGTAAAAGCACAATACCAATCACAAGAGATGG-AT--TTTAA
15460014 AACTCATTATATCAATTGGTAAAACACTAGTAAAGACTTCCCCTATCATTAAGCATTACAAGCAT
63 AACTCATTATATCAATTGGTAAAACACTAGTAAAGACTTCCCC--T-A-T---CATT--AAGCAT
* *
15460079 ATCAACTTCAAGGCTTAAACACATTTAAGAAAGATGTGATCAATTTAAAACTCAAGT
119 ATCAACTTCAAGGCTCAAACACATTTAAGAAAGATATGATCAATTTAAAACTCAAGT
15460136 GATA
1 GATA
15460140 AGGGACAATT
Statistics
Matches: 167, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
175 49 0.29
176 2 0.01
178 47 0.28
180 1 0.01
181 1 0.01
182 1 0.01
185 4 0.02
187 62 0.37
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (175 bp):
GATATAAGTAAAATCTCCCTCATTGTAAAAGCACAATACCAATCACAAGAGATGGATTTTAAAAC
TCATTATATCAATTGGTAAAACACTAGTAAAGACTTCCCCTATCATTAAGCATATCAACTTCAAG
GCTCAAACACATTTAAGAAAGATATGATCAATTTAAAACTCAAGT
Found at i:15462336 original size:19 final size:17
Alignment explanation
Indices: 15462312--15462357 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
15462302 GTAAATAAAC
*
15462312 ATAAAATTAAAATAACTTT
1 ATAAAAATAAAATAA--TT
*
15462331 ATAAAAATAAACTAATT
1 ATAAAAATAAAATAATT
15462348 ATAAAAATAA
1 ATAAAAATAA
15462358 CTAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.48
19 13 0.52
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAAATAAAATAATT
Found at i:15462359 original size:16 final size:16
Alignment explanation
Indices: 15462320--15462361 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
15462310 ACATAAAATT
15462320 AAAATAACT--TTATA
1 AAAATAACTAATTATA
15462334 AAAATAAACTAATTATA
1 AAAAT-AACTAATTATA
15462351 AAAATAACTAA
1 AAAATAACTAA
15462362 AAATAACTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 6 0.24
17 10 0.40
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAACTAATTATA
Found at i:15471419 original size:15 final size:15
Alignment explanation
Indices: 15471399--15471433 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
15471389 ATATTTTGAT
15471399 TTTAAAGCTTTGGAA
1 TTTAAAGCTTTGGAA
* *
15471414 TTTAAAGTTTTTGAA
1 TTTAAAGCTTTGGAA
15471429 TTTAA
1 TTTAA
15471434 GGTTGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (15 bp):
TTTAAAGCTTTGGAA
Found at i:15477758 original size:25 final size:26
Alignment explanation
Indices: 15477725--15477784 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
15477715 CGTGAATATC
15477725 ACCAGTGGCCTCGCCA-CATATAACAA
1 ACCA-TGGCCTCGCCAGCATATAACAA
* * *
15477751 CCCATGGCCTTGCCATGTATATAACAA
1 ACCATGGCCTCGCCA-GCATATAACAA
15477778 ACCATGG
1 ACCATGG
15477785 ACCCAGCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 10 0.36
26 3 0.11
27 15 0.54
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (26 bp):
ACCATGGCCTCGCCAGCATATAACAA
Found at i:15477794 original size:28 final size:27
Alignment explanation
Indices: 15477742--15477796 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
15477732 GCCTCGCCAC
* **
15477742 ATATAACAACCCATGGCCTTGCCATGT
1 ATATAACAAACCATGGCCCAGCCATGT
15477769 ATATAACAAACCATGGACCCAGCCATGT
1 ATATAACAAACCATGG-CCCAGCCATGT
15477797 CTAACAGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.22
Consensus pattern (27 bp):
ATATAACAAACCATGGCCCAGCCATGT
Found at i:15478306 original size:2 final size:2
Alignment explanation
Indices: 15478299--15478323 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15478289 AAGTAAACCA
15478299 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
15478324 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:15479089 original size:4 final size:4
Alignment explanation
Indices: 15479080--15479146 Score: 57
Period size: 4 Copynumber: 16.5 Consensus size: 4
15479070 GAGCCTTTTC
* * *
15479080 CTTT CTTT CTCT CTTTT CTTC CTTT CTTT CTTT CCTTT CCTTT C-TC CTTT
1 CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT -CTTT -CTTT CTTT CTTT
*
15479130 C-TT CTTC CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CT
15479147 CCTTTCTCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
3 5 0.10
4 34 0.67
5 12 0.24
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:15479097 original size:18 final size:18
Alignment explanation
Indices: 15479074--15479151 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 18
15479064 AAACTCGAGC
15479074 CTTTTCCTTTCTTTCTCT
1 CTTTTCCTTTCTTTCTCT
* *
15479092 CTTTT-CTTCCTTTCTTT
1 CTTTTCCTTTCTTTCTCT
15479109 C-TTTCCTTTCCTTTCTCCTTT
1 CTTTTCCTTT-CTTTCT-C--T
15479130 CTTCTTCCTTTCTTTCTC-
1 CTT-TTCCTTTCTTTCTCT
15479148 CTTT
1 CTTT
15479152 CTCTTTCCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
16 3 0.06
17 15 0.31
18 14 0.29
21 3 0.06
22 7 0.14
23 7 0.14
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
CTTTTCCTTTCTTTCTCT
Found at i:15479099 original size:13 final size:12
Alignment explanation
Indices: 15479081--15479158 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 12
15479071 AGCCTTTTCC
15479081 TTTCTTTCTCTCT
1 TTTCTTTCTC-CT
15479094 TTTC--T-TCC-
1 TTTCTTTCTCCT
15479102 TTTCTTTCTTTCCT
1 TTTCTTTC--TCCT
*
15479116 TTCCTTTCTCC-
1 TTTCTTTCTCCT
15479127 TTTC-TTCTTCC-
1 TTTCTTTC-TCCT
15479138 TTTCTTTCTCCT
1 TTTCTTTCTCCT
15479150 TTCTCTTTC
1 TT-TCTTTC
15479159 CTTCTTGGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
8 4 0.08
9 1 0.02
10 6 0.11
11 14 0.26
12 8 0.15
13 13 0.25
14 7 0.13
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTCTTTCTCCT
Found at i:15479118 original size:21 final size:21
Alignment explanation
Indices: 15479077--15479143 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
15479067 CTCGAGCCTT
* *
15479077 TTCCTTTCTTTCTCTCTTTTC
1 TTCCTTTCTTTCTTTCCTTTC
15479098 TTCCTTTCTTTCTTTCCTTTCC
1 TTCCTTTCTTTCTTTCCTTT-C
15479120 TTTCTCCTTTC-TTC-TTCCTTTC
1 --T-TCCTTTCTTTCTTTCCTTTC
15479142 TT
1 TT
15479144 TCTCCTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 18 0.45
22 2 0.05
23 7 0.17
24 4 0.10
25 7 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (21 bp):
TTCCTTTCTTTCTTTCCTTTC
Found at i:15479147 original size:22 final size:24
Alignment explanation
Indices: 15479094--15479161 Score: 97
Period size: 22 Copynumber: 2.9 Consensus size: 24
15479084 CTTTCTCTCT
15479094 TTTCTTCCTTTCTTTCTTTCCTTTCC
1 TTTC-TCCTTTC-TTCTTTCCTTTCC
15479120 TTTCTCCTTTCTTC-TTCCTTT-C
1 TTTCTCCTTTCTTCTTTCCTTTCC
15479142 TTTCTCCTTTC-TCTTTCCTT
1 TTTCTCCTTTCTTCTTTCCTT
15479162 CTTGGTTGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.05
22 18 0.44
23 7 0.17
24 3 0.07
25 7 0.17
26 4 0.10
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTCTCCTTTCTTCTTTCCTTTCC
Found at i:15482778 original size:17 final size:16
Alignment explanation
Indices: 15482767--15482806 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
15482757 TATAATAACT
15482767 TTATAAAAATAAAGTAA
1 TTATAAAAAT-AAGTAA
*
15482784 TTATAAAAATAACTAAA
1 TTATAAAAATAAGT-AA
15482801 TTATAA
1 TTATAA
15482807 TTAAAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
TTATAAAAATAAGTAA
Found at i:15495560 original size:43 final size:43
Alignment explanation
Indices: 15495479--15495590 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 43
15495469 TATTGACTCG
*
15495479 GCTATGTGCGAGTAGGGAGTGCGCATAAGTCAAGGATGACCCGA
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCCAAGGATGA-CCGA
* * * *
15495523 -TTATGTGTGAGTAGGGAGTGCGCATAA-CCTAGTGATGACCTA
1 GCTATGTGCGAGTAGGGAGTGCGCATAAGCCAAG-GATGACCGA
*
15495565 GCCATGTGCGAGTAGGGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
15495591 GAGCTGGTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 6 0.10
43 52 0.90
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAAGCCAAGGATGACCGA
Found at i:15496057 original size:60 final size:60
Alignment explanation
Indices: 15495984--15496114 Score: 190
Period size: 60 Copynumber: 2.2 Consensus size: 60
15495974 TGAAATACAT
* *
15495984 TCTCGCTACAGCGAGAAACTTTCTGTTTCTAGGTGACAATTTCGCTGCAGCGAGATTGAA
1 TCTCGCTGCAGCGAGAAACATTCTGTTTCTAGGTGACAATTTCGCTGCAGCGAGATTGAA
* * * * *
15496044 TTTCGCTGCAGCGAGAAACATTCTGTTTTTGGGTTACAATTTCGCTGTAGCGAGATTGAA
1 TCTCGCTGCAGCGAGAAACATTCTGTTTCTAGGTGACAATTTCGCTGCAGCGAGATTGAA
*
15496104 TCTCACTGCAG
1 TCTCGCTGCAG
15496115 TGCAAAATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (60 bp):
TCTCGCTGCAGCGAGAAACATTCTGTTTCTAGGTGACAATTTCGCTGCAGCGAGATTGAA
Found at i:15499265 original size:15 final size:14
Alignment explanation
Indices: 15499243--15499286 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
15499233 GCTTGGAAGC
15499243 AAAAAAGAGAAAGG
1 AAAAAAGAGAAAGG
15499257 AAGAAAAGAGAAA-G
1 AA-AAAAGAGAAAGG
15499271 AAAAGAAGAGAAAGG
1 AAAA-AAGAGAAAGG
15499286 A
1 A
15499287 GAAGGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.07
14 13 0.48
15 12 0.44
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAAAGG
Found at i:15499271 original size:21 final size:20
Alignment explanation
Indices: 15499250--15499300 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
15499240 AGCAAAAAAG
*
15499250 AGAAAGGAAGAAAA-GAGAA
1 AGAAAAGAAGAAAAGGAGAA
15499269 AGAAAAGAAGAGAAAGGAGAA
1 AGAAAAGAAGA-AAAGGAGAA
*
15499290 GGAAAA-AAGAA
1 AGAAAAGAAGAA
15499301 GAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 11 0.39
20 7 0.25
21 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAGAAAAGGAGAA
Found at i:15499303 original size:21 final size:22
Alignment explanation
Indices: 15499256--15499305 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
15499246 AAAGAGAAAG
15499256 GAAGAAAAGAGAAAGAAAAGAA
1 GAAGAAAAGAGAAAGAAAAGAA
* *
15499278 G-AGAAAGGAGAAGGAAAA-AA
1 GAAGAAAAGAGAAAGAAAAGAA
15499298 GAAGAAAA
1 GAAGAAAA
15499306 TAAAAAAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
GAAGAAAAGAGAAAGAAAAGAA
Found at i:15500383 original size:15 final size:16
Alignment explanation
Indices: 15500356--15500385 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15500346 CTAAGCCTCA
15500356 TGCAAAGGTTTTACAT
1 TGCAAAGGTTTTACAT
15500372 TGCAAA-GTTTTACA
1 TGCAAAGGTTTTACA
15500386 AAAAAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (16 bp):
TGCAAAGGTTTTACAT
Found at i:15502744 original size:35 final size:35
Alignment explanation
Indices: 15502705--15502777 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
15502695 GGAGTACGTG
* *
15502705 TGATGATATTGAAATGTGCGTGTAGGGAGTGTACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGAGCACA
***
15502740 TGATGATATTGCCTTGTGCGTGTAGGGAGAGCACA
1 TGATGATATTGAAATGTGCGTGTAGGGAGAGCACA
15502775 TGA
1 TGA
15502778 GCTAAGTAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.10, G:0.34, T:0.30
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGTAGGGAGAGCACA
Found at i:15502813 original size:2 final size:2
Alignment explanation
Indices: 15502806--15502832 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15502796 GGTGTACATG
15502806 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
15502833 GCTATAGGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15505185 original size:32 final size:32
Alignment explanation
Indices: 15505144--15505209 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
15505134 ATAATTTGGT
15505144 ACAAATATAGACCAATGGAGGCAAAATATGGA
1 ACAAATATAGACCAATGGAGGCAAAATATGGA
15505176 ACAAATATAGACCAATGGAGGCAAAATATGGA
1 ACAAATATAGACCAATGGAGGCAAAATATGGA
15505208 AC
1 AC
15505210 TTGGAAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.15
Consensus pattern (32 bp):
ACAAATATAGACCAATGGAGGCAAAATATGGA
Found at i:15514163 original size:80 final size:81
Alignment explanation
Indices: 15514072--15514229 Score: 219
Period size: 80 Copynumber: 2.0 Consensus size: 81
15514062 TTATTTTCCC
* * * * *
15514072 ATATATATAAGGTTATTAGGAGCCGAACGGGAGGTAATTG-CTCTATTCCCTCACCTTGGATACG
1 ATATATATAAGGTTATTAAGAGCCGAACGGGAGGTAATTGCCCCCATTCCCTCACCTTAGATACA
*
15514136 TCTCTGATGTCGATGT
66 TCTCTAATGTCGATGT
** **
15514152 ATATATATAAGGTTATTAAGAGTTGAGTGGGAGGTAATTGCCCCCATTCCCTCACCTTAGATACA
1 ATATATATAAGGTTATTAAGAGCCGAACGGGAGGTAATTGCCCCCATTCCCTCACCTTAGATACA
15514217 TCTCTAATGTCGA
66 TCTCTAATGTCGA
15514230 CATAGTTATT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 35 0.52
81 32 0.48
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (81 bp):
ATATATATAAGGTTATTAAGAGCCGAACGGGAGGTAATTGCCCCCATTCCCTCACCTTAGATACA
TCTCTAATGTCGATGT
Found at i:15514788 original size:92 final size:92
Alignment explanation
Indices: 15514692--15515008 Score: 214
Period size: 92 Copynumber: 3.3 Consensus size: 92
15514682 TTTCACTTAT
15514692 AATTTAATCATTAATATTTTTAAATATAAATATCTTATTTAAAATTTAAATGTTATTATGATTAA
1 AATTTAATCATTAATATTTTTAAATATAAATATCTTATTTAAAATTTAAATGTTATTATGATTAA
*
15514757 AATATTAATAATTTTAATTAACATTTA
66 AATATTAATAATTTTAATTAATATTTA
* * * * * * ** *** * **
15514784 AATTTAA-AATATCAT-TTTTATAACATATAATTAAC-AATTCAAGCGTTTTTCT-TTTTTACAA
1 AATTTAATCAT-TAATATTTT-TAA-ATATAAATATCTTATTTAA-AATTTAAATGTTATTATGA
* * *
15514845 TAATATTAATAATTGATAATTTAAATATTAATATTTTATTGA
62 T--TA-AAAT-ATTAATAATTT-TA-ATTAATA---T-TT-A
* * * *
15514887 TAATTTAATCATTAATATTTTAAAATATTAATATTTTATTTATAATTTAAATGTTATTATGATTA
1 -AATTTAATCATTAATATTTTTAAATATAAATATCTTATTTAAAATTTAAATGTTATTATGATTA
*
15514952 AAATATTAATAATTTTAATTAATTTTTA
65 AAATATTAATAATTTTAATTAATATTTA
15514980 AATTTAAAAT-ATT-ATATTTTTATAATATA
1 AATTT--AATCATTAATATTTTTA-AATATA
15515009 TATTTAAAAT
Statistics
Matches: 160, Mismatches: 42, Indels: 45
0.65 0.17 0.18
Matches are distributed among these distances:
91 6 0.04
92 38 0.24
93 22 0.14
94 7 0.04
95 4 0.03
96 10 0.06
97 1 0.01
98 12 0.08
99 1 0.01
100 10 0.06
101 4 0.03
102 4 0.03
103 12 0.08
104 23 0.14
105 6 0.04
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (92 bp):
AATTTAATCATTAATATTTTTAAATATAAATATCTTATTTAAAATTTAAATGTTATTATGATTAA
AATATTAATAATTTTAATTAATATTTA
Found at i:15514804 original size:196 final size:194
Alignment explanation
Indices: 15514458--15515140 Score: 942
Period size: 196 Copynumber: 3.5 Consensus size: 194
15514448 ATTAATTTAA
* * * *
15514458 AATATTAATAGTTGATCATTTAAATATTAATATTTTA-GATAAATTTAATCATTAATATTTT-AT
1 AATATTAATAATTGATAATTTAAATATTAATATTTTATTAT-AATTTAATCATTAATATTTTAAA
*
15514521 ATATTAATATTTTATTTATAATTGAAATGTTATTATGATT-AAATATTAATAA-TTTAATTAATT
65 ATATTAATATTTTATTTATAATTTAAATGTTATTATGATTAAAATATTAATAATTTTAATTAATT
* *
15514584 TTTAAATTTAAAATATTTTTTTTATTAAAAATAATTAAAAATTTAAACATTTCTCTTTTTTATAA
130 TTTAAATTTAAAATATTATTTTTATTAAATATAATTAAAAATTTAAACATTT-TCTTTTTTATAA
15514649 T
194 T
* * * * *
15514650 AATATTAATAATTAATAATCTGAATATTAATATTTCACTTATAATTTAATCATTAATATTTTTAA
1 AATATTAATAATTGATAATTTAAATATTAATATTTTA-TTATAATTTAATCATTAATATTTTAAA
* * * **
15514715 ATATAAATATCTTATTTAAAATTTAAATGTTATTATGATTAAAATATTAATAATTTTAATTAACA
65 ATATTAATATTTTATTTATAATTTAAATGTTATTATGATTAAAATATTAATAATTTTAATTAATT
* * * * * *
15514780 TTTAAATTTAAAATATCATTTTTA-TAACATATAATTAACAATTCAAGCGTTTTTCTTTTTTACA
130 TTTAAATTTAAAATATTATTTTTATTAA-ATATAATTAAAAATTTAAAC-ATTTTCTTTTTTATA
15514844 AT
193 AT
15514846 AATATTAATAATTGATAATTTAAATATTAATATTTTATTGATAATTTAATCATTAATATTTTAAA
1 AATATTAATAATTGATAATTTAAATATTAATATTTTATT-ATAATTTAATCATTAATATTTTAAA
15514911 ATATTAATATTTTATTTATAATTTAAATGTTATTATGATTAAAATATTAATAATTTTAATTAATT
65 ATATTAATATTTTATTTATAATTTAAATGTTATTATGATTAAAATATTAATAATTTTAATTAATT
* *
15514976 TTTAAATTTAAAATATTATATTT-TTATAATATATATTTAAAATTTAAA-A-----TTTTTTATA
130 TTTAAATTTAAAATATTATTTTTATTA-AATATA-ATTAAAAATTTAAACATTTTCTTTTTTATA
15515034 AT
193 AT
*
15515036 AATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCA-TAACATTTTAAA
1 AATATTAATAATTGATAATTTAAATATTAATATTTTA-TTATAATTTAATCATTAATATTTTAAA
* *
15515100 ATATTAACATTTTATTTATAATTTAAATATTATTATGATTA
65 ATATTAATATTTTATTTATAATTTAAATGTTATTATGATTA
15515141 TTTGATTCTA
Statistics
Matches: 436, Mismatches: 43, Indels: 27
0.86 0.08 0.05
Matches are distributed among these distances:
189 50 0.11
190 59 0.14
191 2 0.00
192 31 0.07
193 20 0.05
194 39 0.09
195 17 0.04
196 204 0.47
197 14 0.03
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (194 bp):
AATATTAATAATTGATAATTTAAATATTAATATTTTATTATAATTTAATCATTAATATTTTAAAA
TATTAATATTTTATTTATAATTTAAATGTTATTATGATTAAAATATTAATAATTTTAATTAATTT
TTAAATTTAAAATATTATTTTTATTAAATATAATTAAAAATTTAAACATTTTCTTTTTTATAAT
Found at i:15514885 original size:26 final size:26
Alignment explanation
Indices: 15514856--15514908 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
15514846 AATATTAATA
15514856 ATTGATAATTTAAAT-ATTAATATTTT
1 ATTGATAATTT-AATCATTAATATTTT
15514882 ATTGATAATTTAATCATTAATATTTT
1 ATTGATAATTTAATCATTAATATTTT
15514908 A
1 A
15514909 AAATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTGATAATTTAATCATTAATATTTT
Found at i:15514914 original size:42 final size:41
Alignment explanation
Indices: 15514844--15514968 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 41
15514834 CTTTTTTACA
* *
15514844 ATAATATTAATAATTGATAATTT-AAATATTAATATTTTATTG
1 ATAAT-TTAAT-ATTAATATTTTAAAATATTAATATTTTATTG
*
15514886 ATAATTTAATCATTAATATTTTAAAATATTAATATTTTATTT
1 ATAATTTAAT-ATTAATATTTTAAAATATTAATATTTTATTG
* * *
15514928 ATAATTTAAATGTTATTATGATTAAAATATTAATAATTTTA
1 ATAATTT-AATATTAATAT-TTTAAAATATTAAT-ATTTTA
15514969 ATTAATTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 14 0.19
42 36 0.50
43 16 0.22
44 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (41 bp):
ATAATTTAATATTAATATTTTAAAATATTAATATTTTATTG
Found at i:15514969 original size:17 final size:16
Alignment explanation
Indices: 15514949--15515028 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
15514939 GTTATTATGA
15514949 TTAAAATATTAATAATT
1 TTAAAATATT-ATAATT
* *
15514966 TTAATTAAT-TTTTAAAT
1 TTAA--AATATTATAATT
*
15514983 TTAAAATATTATATTT
1 TTAAAATATTATAATT
*
15514999 TTATAATA-TAT-A-T
1 TTAAAATATTATAATT
*
15515012 TTAAAAT-TTAAAATT
1 TTAAAATATTATAATT
15515027 TT
1 TT
15515029 TTATAATAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
13 9 0.19
14 1 0.02
15 9 0.19
16 12 0.25
17 12 0.25
18 2 0.04
19 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAAAATATTATAATT
Found at i:15514989 original size:34 final size:36
Alignment explanation
Indices: 15514949--15515025 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
15514939 GTTATTATGA
* *
15514949 TTAAAATATTAATAATTTTA-ATTA-AT-TTTTAAAT
1 TTAAAATATT-ATAATTTTATAATATATATTTAAAAT
*
15514983 TTAAAATATTATATTTTTATAATATATATTTAAAAT
1 TTAAAATATTATAATTTTATAATATATATTTAAAAT
15515019 TTAAAAT
1 TTAAAAT
15515026 TTTTTATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 8 0.22
34 13 0.35
35 2 0.05
36 14 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TTAAAATATTATAATTTTATAATATATATTTAAAAT
Found at i:15515055 original size:29 final size:30
Alignment explanation
Indices: 15514996--15515056 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
15514986 AAATATTATA
*
15514996 TTTTTATAATATATATTTAAAATTTAAAAT
1 TTTTTATAATATATATTTAAAATTGAAAAT
*
15515026 TTTTTATAATA-ATA-TTAATAATTGATAAT
1 TTTTTATAATATATATTTAA-AATTGAAAAT
15515055 TT
1 TT
15515057 AAATATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 13 0.46
30 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTTTATAATATATATTTAAAATTGAAAAT
Found at i:15515085 original size:41 final size:41
Alignment explanation
Indices: 15515010--15515125 Score: 121
Period size: 41 Copynumber: 2.8 Consensus size: 41
15515000 TATAATATAT
* * *
15515010 ATTTAAAAT-TTAAAATTTT-TTATAATAATATTAATAATTGATA
1 ATTTAAAATATTAACATTTTATT-T-ATAAT-TTAATAA-TAACA
* *
15515053 ATTT-AAATATTAATATTTTATTTATAATTTAATCATAACA
1 ATTTAAAATATTAACATTTTATTTATAATTTAATAATAACA
*
15515093 TTTTAAAATATTAACATTTTATTTATAATTTAA
1 ATTTAAAATATTAACATTTTATTTATAATTTAA
15515126 ATATTATTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.09
41 33 0.52
42 9 0.14
43 14 0.22
44 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (41 bp):
ATTTAAAATATTAACATTTTATTTATAATTTAATAATAACA
Found at i:15523687 original size:22 final size:23
Alignment explanation
Indices: 15523655--15523704 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
15523645 GCGCGTTGTC
*
15523655 ATTCGCGTATGTATG-TGTGTGT
1 ATTCGCATATGTATGATGTGTGT
15523677 ATTCGCATATGTATGTATGTGTGT
1 ATTCGCATATGTATG-ATGTGTGT
15523701 ATTC
1 ATTC
15523705 ATCTCTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 14 0.56
24 11 0.44
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (23 bp):
ATTCGCATATGTATGATGTGTGT
Found at i:15524635 original size:23 final size:23
Alignment explanation
Indices: 15524609--15524652 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
15524599 TATTAAAAAA
*
15524609 ATAAATA-ATAATCTATTTATCAC
1 ATAAATATATAA-ATATTTATCAC
15524632 ATAAATATATAAATATTTATC
1 ATAAATATATAAATATTTATC
15524653 TTATTAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAAATATATAAATATTTATCAC
Found at i:15525226 original size:3 final size:3
Alignment explanation
Indices: 15525218--15525245 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15525208 TGTGCAGATG
15525218 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
15525246 GGGATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15531053 original size:15 final size:15
Alignment explanation
Indices: 15531009--15531054 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
15530999 AGATTAGAGA
*
15531009 TTTTGATTTTAAAGC
1 TTTTGATTTTAAAGT
*
15531024 TTTGGATTTTAAAGT
1 TTTTGATTTTAAAGT
15531039 TTTTGATTTTAAAGT
1 TTTTGATTTTAAAGT
15531054 T
1 T
15531055 GTTTTAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (15 bp):
TTTTGATTTTAAAGT
Found at i:15539286 original size:38 final size:40
Alignment explanation
Indices: 15539197--15539302 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 40
15539187 CACACTCGGC
* *
15539197 TCATGTACATCCCCTCACATCGTGCACATAGCCGGCGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
* * * *
15539237 TCATGTGCATCCCCCCACATCATGCACA-A-TCAGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
*
15539275 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
15539303 CGAGCACTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 31 0.54
39 1 0.02
40 25 0.44
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.21
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCCAGCGCCA
Found at i:15539426 original size:2 final size:2
Alignment explanation
Indices: 15539419--15539458 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
15539409 CATGCACAAC
15539419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15539459 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15543298 original size:2 final size:2
Alignment explanation
Indices: 15543291--15543332 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
15543281 GGTGAATGAA
15543291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15543333 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15545042 original size:39 final size:41
Alignment explanation
Indices: 15544989--15545072 Score: 109
Period size: 42 Copynumber: 2.1 Consensus size: 41
15544979 ATGTATACGT
15544989 ATACGTTTAATAAACATGT-A-ACACGACACGACACGATTA
1 ATACGTTTAATAAACATGTAATACACGACACGACACGATTA
* * * *
15545028 ATACGTTTATTAAACGTGTCAATATACGACATGACACGATTA
1 ATACGTTTAATAAACATGT-AATACACGACACGACACGATTA
15545070 ATA
1 ATA
15545073 ACACGTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 17 0.45
41 1 0.03
42 20 0.53
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (41 bp):
ATACGTTTAATAAACATGTAATACACGACACGACACGATTA
Found at i:15554551 original size:22 final size:22
Alignment explanation
Indices: 15554526--15554577 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
15554516 ATGCACCTTA
15554526 ATTTATATATGTATAAT-ATAAT
1 ATTTATATATGT-TAATCATAAT
15554548 A-TT-TATA-GTTAATCATAAT
1 ATTTATATATGTTAATCATAAT
15554567 ATATTATATAT
1 AT-TTATATAT
15554578 TAATGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 4 0.16
21 4 0.16
22 5 0.20
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTATATATGTTAATCATAAT
Found at i:15554886 original size:21 final size:21
Alignment explanation
Indices: 15554845--15554884 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
15554835 ACTTACTTAT
15554845 ATATCAATATCTATAAGTTTC
1 ATATCAATATCTATAAGTTTC
*
15554866 ATATTAATAT-TATAAGTTT
1 ATATCAATATCTATAAGTTT
15554885 TCTCTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATCAATATCTATAAGTTTC
Found at i:15562136 original size:19 final size:20
Alignment explanation
Indices: 15562109--15562154 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
15562099 AGGAGACAAG
*
15562109 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
15562128 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
15562147 ATAATATT
1 ATAATATT
15562155 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:15563990 original size:13 final size:13
Alignment explanation
Indices: 15563972--15563996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15563962 AGGGAAATTG
15563972 TGATTTTATAAAA
1 TGATTTTATAAAA
15563985 TGATTTTATAAA
1 TGATTTTATAAA
15563997 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:15566721 original size:11 final size:11
Alignment explanation
Indices: 15566705--15566745 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
15566695 AATATGATTG
15566705 ATACGATTAAT
1 ATACGATTAAT
15566716 ATACGATTAAT
1 ATACGATTAAT
15566727 ATACGA-TAA-
1 ATACGATTAAT
*
15566736 ACACGATTAA
1 ATACGATTAA
15566746 AATGATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 5 0.18
10 6 0.21
11 17 0.61
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (11 bp):
ATACGATTAAT
Found at i:15567553 original size:40 final size:40
Alignment explanation
Indices: 15567494--15567582 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
15567484 TTATATAATA
* *
15567494 TCATCTCTTAAATATATTTT-TAATATCATATCTTTTATTT
1 TCATTTCTTAAATATATTTTCT-ATATCATATATTTTATTT
*
15567534 TCATTTCTT-AATATAATTTTCTATATTATATATTTTATTT
1 TCATTTCTTAAATAT-ATTTTCTATATCATATATTTTATTT
*
15567574 TAATTTCTT
1 TCATTTCTT
15567583 TTTTCTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 5 0.12
40 37 0.86
41 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (40 bp):
TCATTTCTTAAATATATTTTCTATATCATATATTTTATTT
Found at i:15568195 original size:25 final size:25
Alignment explanation
Indices: 15568161--15568217 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
15568151 TGAAAGAGGT
*
15568161 TTTTGTTTGGATTCATACTAAATTC
1 TTTTGTTTGGATTCATACTAAAGTC
15568186 TTTTGTTTGGATTCATACTAAAGTC
1 TTTTGTTTGGATTCATACTAAAGTC
*
15568211 TCTTGTT
1 TTTTGTT
15568218 AAGTATCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (25 bp):
TTTTGTTTGGATTCATACTAAAGTC
Done.