Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 207 of 210
Found at i:61179804 original size:24 final size:23
Alignment explanation
Indices: 61179750--61179804 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
61179740 TGACTAACTG
*
61179750 TAAAACATATATTTGAATTTGTAA
1 TAAAA-ATATATTAGAATTTGTAA
* *
61179774 TATAAAATATATTAGTAATTTTTTA
1 TA-AAAATATATTAG-AATTTGTAA
61179799 TAAAAA
1 TAAAAA
61179805 ATAATTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
TAAAAATATATTAGAATTTGTAA
Found at i:61183378 original size:39 final size:39
Alignment explanation
Indices: 61183321--61183399 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
61183311 GAGATGATTA
61183321 TGTAATCTTAGAGCTCTAATTGTATACAGCTTTTAATTG
1 TGTAATCTTAGAGCTCTAATTGTATACAGCTTTTAATTG
* *
61183360 TGTAATCTTAGAGTTCTAATTGTATATAGCTTTTAATTG
1 TGTAATCTTAGAGCTCTAATTGTATACAGCTTTTAATTG
61183399 T
1 T
61183400 AGCCGTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (39 bp):
TGTAATCTTAGAGCTCTAATTGTATACAGCTTTTAATTG
Found at i:61188473 original size:39 final size:39
Alignment explanation
Indices: 61188419--61188497 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
61188409 GAGATGATTA
*
61188419 TGTAATCTTAGAGTTCTAATTGTATACAGCTTTTAGTTG
1 TGTAATCTTAGAGTTCTAATTGTATACAGCTTTTAATTG
61188458 TGTAATCTTAGAGTTCTAATTGTATACAGCTTTTAATTG
1 TGTAATCTTAGAGTTCTAATTGTATACAGCTTTTAATTG
61188497 T
1 T
61188498 AGCCATTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (39 bp):
TGTAATCTTAGAGTTCTAATTGTATACAGCTTTTAATTG
Found at i:61189686 original size:13 final size:13
Alignment explanation
Indices: 61189668--61189695 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
61189658 ATATACCCTC
61189668 CATGTGTCCCCAA
1 CATGTGTCCCCAA
61189681 CATGTGTCCCCAA
1 CATGTGTCCCCAA
61189694 CA
1 CA
61189696 AGTGAATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.21
Consensus pattern (13 bp):
CATGTGTCCCCAA
Found at i:61192644 original size:2 final size:2
Alignment explanation
Indices: 61192637--61192683 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
61192627 TAAATTTGTG
61192637 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
61192679 AT AT A
1 AT AT A
61192684 ATAGAGAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61193333 original size:6 final size:6
Alignment explanation
Indices: 61193322--61193351 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
61193312 AATAATTATA
61193322 TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
61193352 AAATCCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:61194589 original size:21 final size:22
Alignment explanation
Indices: 61194564--61194613 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
61194554 TTTTTCATTG
* *
61194564 TTTTGCTGTT-GTTTGTTGTCA
1 TTTTGCTGTTAGTTTGCTGCCA
* *
61194585 TTTTGATGTTATTTTGCTGCCA
1 TTTTGCTGTTAGTTTGCTGCCA
61194607 TTTTGCT
1 TTTTGCT
61194614 ATTATATTGC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.08, C:0.12, G:0.20, T:0.60
Consensus pattern (22 bp):
TTTTGCTGTTAGTTTGCTGCCA
Found at i:61194618 original size:22 final size:22
Alignment explanation
Indices: 61194583--61194624 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
61194573 TGTTTGTTGT
* *
61194583 CATTTTGATGTTATTTTGCTGC
1 CATTTTGATATTATATTGCTGC
*
61194605 CATTTTGCTATTATATTGCT
1 CATTTTGATATTATATTGCT
61194625 ACTATTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (22 bp):
CATTTTGATATTATATTGCTGC
Found at i:61197754 original size:38 final size:40
Alignment explanation
Indices: 61197709--61197797 Score: 137
Period size: 38 Copynumber: 2.2 Consensus size: 40
61197699 AACATTTATA
* *
61197709 TTTAATATAATAAAATATTTATTATATTTAT-TTGTG-TT
1 TTTAATATAATAAAAGATTTATTATATTTATGTAGTGTTT
61197747 TTTAATATAATAAAAGATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAAGATTTATTATATTTAT-GTAGTGTTT
61197788 TTTAATATAA
1 TTTAATATAA
61197798 ATACTTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 30 0.65
40 4 0.09
41 12 0.26
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (40 bp):
TTTAATATAATAAAAGATTTATTATATTTATGTAGTGTTT
Found at i:61201298 original size:32 final size:31
Alignment explanation
Indices: 61201262--61201341 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
61201252 CTTAATCCCA
61201262 AAATTTAAAATAATCAAACCCCAAAATCAAAT
1 AAATTTAAAATAATCAAA-CCCAAAATCAAAT
* * *
61201294 AAATTTAAAAGAATTCAAATCCAAATTCAAAT
1 AAATTTAAAATAA-TCAAACCCAAAATCAAAT
*
61201326 CAATTTAAAATTAATC
1 AAATTTAAAA-TAATC
61201342 TTATTCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 34 0.83
33 7 0.17
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (31 bp):
AAATTTAAAATAATCAAACCCAAAATCAAAT
Found at i:61205127 original size:83 final size:83
Alignment explanation
Indices: 61204988--61205150 Score: 308
Period size: 83 Copynumber: 2.0 Consensus size: 83
61204978 CGGCTCTAAG
*
61204988 TTAGAAATTCAATATGACAAAACCCTAGAGAAATTCAGTTTGTTCTATCTCAGGCATATCACACA
1 TTAGAAATTCAATACGACAAAACCCTAGAGAAATTCAGTTTGTTCTATCTCAGGCATATCACACA
61205053 CGAAACTACCAAGTACCA
66 CGAAACTACCAAGTACCA
*
61205071 TTAGAAATTCAATACGACAAAACCCTAGGGAAATTCAGTTTGTTCTATCTCAGGCATATCACACA
1 TTAGAAATTCAATACGACAAAACCCTAGAGAAATTCAGTTTGTTCTATCTCAGGCATATCACACA
61205136 CGAAACTACCAAGTA
66 CGAAACTACCAAGTA
61205151 ACATCTGCTA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (83 bp):
TTAGAAATTCAATACGACAAAACCCTAGAGAAATTCAGTTTGTTCTATCTCAGGCATATCACACA
CGAAACTACCAAGTACCA
Found at i:61206787 original size:17 final size:17
Alignment explanation
Indices: 61206767--61206802 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
61206757 TTTGATTGGA
61206767 CTAATGTGGAGATTCTT
1 CTAATGTGGAGATTCTT
61206784 CTAATGTGGAGATTCTT
1 CTAATGTGGAGATTCTT
61206801 CT
1 CT
61206803 TTCTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (17 bp):
CTAATGTGGAGATTCTT
Found at i:61214102 original size:2 final size:2
Alignment explanation
Indices: 61214095--61214121 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61214085 AGTTTCAAAT
61214095 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
61214122 GTAGCAATTC
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:61217065 original size:7 final size:7
Alignment explanation
Indices: 61217063--61217099 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
61217053 TATTTTAAGT
61217063 TTTTAAA
1 TTTTAAA
61217070 TTTTTAAA
1 -TTTTAAA
61217078 TTTTAAA
1 TTTTAAA
61217085 TTTTAAA
1 TTTTAAA
61217092 TTTTAAA
1 TTTTAAA
61217099 T
1 T
61217100 CCAATTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:61217068 original size:8 final size:8
Alignment explanation
Indices: 61217055--61217099 Score: 60
Period size: 7 Copynumber: 6.0 Consensus size: 8
61217045 TGCACTTTTA
*
61217055 TTTTAAGT
1 TTTTAAAT
61217063 TTTTAAAT
1 TTTTAAAT
61217071 TTTTAAA-
1 TTTTAAAT
61217078 TTTTAAA-
1 TTTTAAAT
61217085 TTTTAAA-
1 TTTTAAAT
61217092 TTTTAAAT
1 TTTTAAAT
61217100 CCAATTGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 21 0.60
8 14 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
TTTTAAAT
Found at i:61221950 original size:18 final size:19
Alignment explanation
Indices: 61221912--61221953 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
61221902 AGGACTTTAG
*
61221912 GAGAGGGAAAATGAAAGAAA
1 GAGAGGGAAAA-GAAAAAAA
61221932 GAGAGGGAAAA-AAAAAAA
1 GAGAGGGAAAAGAAAAAAA
61221950 GAGA
1 GAGA
61221954 AACAGCGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (19 bp):
GAGAGGGAAAAGAAAAAAA
Found at i:61222392 original size:18 final size:18
Alignment explanation
Indices: 61222369--61222408 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
61222359 TGTAACTTTT
61222369 TAAAGTAAAAATTAAAAA
1 TAAAGTAAAAATTAAAAA
61222387 TAAAGTAAAAATTAAAAA
1 TAAAGTAAAAATTAAAAA
61222405 -AAAG
1 TAAAG
61222409 AAATAATAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
TAAAGTAAAAATTAAAAA
Found at i:61223212 original size:24 final size:23
Alignment explanation
Indices: 61223158--61223212 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
61223148 TATATACGTA
**
61223158 TTTTTATTTAATATTTATTTAAT
1 TTTTTATTTAATATTTATACAAT
*
61223181 TTTATTATTTAATATTTGTACATAT
1 TTT-TTATTTAATATTTATACA-AT
61223206 TTTTTAT
1 TTTTTAT
61223213 ATACATATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 19 0.70
25 5 0.19
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATTTAATATTTATACAAT
Found at i:61225439 original size:40 final size:40
Alignment explanation
Indices: 61225372--61225448 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
61225362 AAGTCTGCTT
* * *
61225372 ATGTGTGAGCTTGCTTTTTGTTGTAATCTGTGATTTTCTC
1 ATGTGTGAGATTGCTTTGTGTTATAATCTGTGATTTTCTC
*
61225412 ATGTGTGAGATTGGTTTGTGTTATAATCTGTGATTTT
1 ATGTGTGAGATTGCTTTGTGTTATAATCTGTGATTTT
61225449 ATCTTGATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.16, C:0.08, G:0.25, T:0.52
Consensus pattern (40 bp):
ATGTGTGAGATTGCTTTGTGTTATAATCTGTGATTTTCTC
Found at i:61226790 original size:111 final size:111
Alignment explanation
Indices: 61226596--61226818 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
61226586 GTTGTTTCCC
61226596 AGGTATGTTTTTAACTGTTTAGCTGTCACATTGTCACAATTTGTTGTCTTAGGCTTTGCAATTTG
1 AGGTATGTTTTTAACTGTTTAGCTGTCACATTGTCACAATTTGTTGTCTTAGGCTTTGCAATTTG
61226661 TCCGGGGTGTTTGACATTACATTGAACTTTAGAACAAAAGAGAACT
66 TCCGGGGTGTTTGACATTACATTGAACTTTAGAACAAAAGAGAACT
61226707 AGGTATGTTTTTAACTGTTTAGCTGTCACATTGTCACAATTTGTTGTCTTAGGCTTTGCAATTTG
1 AGGTATGTTTTTAACTGTTTAGCTGTCACATTGTCACAATTTGTTGTCTTAGGCTTTGCAATTTG
61226772 TCCGGGGTGTTTGACATTACATTGAACTTTAGAACAAAAGAGAACT
66 TCCGGGGTGTTTGACATTACATTGAACTTTAGAACAAAAGAGAACT
61226818 A
1 A
61226819 TCTTTTTAGT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (111 bp):
AGGTATGTTTTTAACTGTTTAGCTGTCACATTGTCACAATTTGTTGTCTTAGGCTTTGCAATTTG
TCCGGGGTGTTTGACATTACATTGAACTTTAGAACAAAAGAGAACT
Found at i:61227177 original size:17 final size:17
Alignment explanation
Indices: 61227155--61227189 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
61227145 CTTGTTTTCA
*
61227155 AATATTTCTTATCATAT
1 AATATTTCATATCATAT
61227172 AATATTTCATATCATAT
1 AATATTTCATATCATAT
61227189 A
1 A
61227190 GAGTATTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTCATATCATAT
Found at i:61227710 original size:18 final size:19
Alignment explanation
Indices: 61227687--61227724 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
61227677 AATCATTCAT
61227687 TCAAAG-TTCAAAACATGA
1 TCAAAGATTCAAAACATGA
61227705 TCAAAGACATTCAAAACATG
1 TCAAAG--ATTCAAAACATG
61227725 CCAAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (19 bp):
TCAAAGATTCAAAACATGA
Found at i:61230979 original size:154 final size:154
Alignment explanation
Indices: 61230699--61231007 Score: 573
Period size: 154 Copynumber: 2.0 Consensus size: 154
61230689 CTAATTGGCT
* * *
61230699 AATTTCATGGGGTCCGCACGCACGTTAGTTACCGATCCACCTTTGTTGACTAAAAGATAATTGGC
1 AATTTCATGGGGTCCGCACGCACATTAATTACCCATCCACCTTTGTTGACTAAAAGATAATTGGC
*
61230764 TAAGCTCAAGTCGTCGCCTGTGCTTTTGCCTAAGCCTTCAATCTCTTTCCCATTTACACTTTTTC
66 TAAGCTCAAGTCGTCACCTGTGCTTTTGCCTAAGCCTTCAATCTCTTTCCCATTTACACTTTTTC
61230829 TTCTTACAATAATACCACAACCCA
131 TTCTTACAATAATACCACAACCCA
61230853 AATTTCATGGGGTCCGCACGCACATTAATTACCCATCCACCTTTGTTGACTAAAAGATAATTGGC
1 AATTTCATGGGGTCCGCACGCACATTAATTACCCATCCACCTTTGTTGACTAAAAGATAATTGGC
61230918 TAAGCTCAAGTCGTCACCTGTGCTTTTGCCTAAGCCTTCAATCTCTTTCCCATTTACACTTTTTC
66 TAAGCTCAAGTCGTCACCTGTGCTTTTGCCTAAGCCTTCAATCTCTTTCCCATTTACACTTTTTC
*
61230983 TTCTTACAATCATACCACAACCCA
131 TTCTTACAATAATACCACAACCCA
61231007 A
1 A
61231008 GCTAAACTCA
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 150 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (154 bp):
AATTTCATGGGGTCCGCACGCACATTAATTACCCATCCACCTTTGTTGACTAAAAGATAATTGGC
TAAGCTCAAGTCGTCACCTGTGCTTTTGCCTAAGCCTTCAATCTCTTTCCCATTTACACTTTTTC
TTCTTACAATAATACCACAACCCA
Found at i:61239780 original size:50 final size:51
Alignment explanation
Indices: 61239685--61239784 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 51
61239675 TTAGGGGGAA
* **
61239685 AAAAGTGAAAATTATTCTTCAAGAAAGTGGTAGGAAATTTAAGTTCAATTC
1 AAAAGTGAAAATTATTCTTCAAGAAAGTGATACAAAATTTAAGTTCAATTC
** * *
61239736 AAAAGTGGCAATTATTCTT-AAGAAAGTTATACAAAATTTCAGTTCAATT
1 AAAAGTGAAAATTATTCTTCAAGAAAGTGATACAAAATTTAAGTTCAATT
61239785 GACTCAAATG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 25 0.60
51 17 0.40
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (51 bp):
AAAAGTGAAAATTATTCTTCAAGAAAGTGATACAAAATTTAAGTTCAATTC
Found at i:61240696 original size:83 final size:82
Alignment explanation
Indices: 61240536--61240701 Score: 282
Period size: 83 Copynumber: 2.0 Consensus size: 82
61240526 GTTTTAGTCT
61240536 CCCATTGGAAGACCTTGACTTGGAAATTAACACTCCCTTCATCATCATCGTCATTTGGAACAAGT
1 CCCATTGGAAGACCTTGACTTGGAAATTAACACTCCCTTCATCATCATCGTCATTTGGAACAAGT
*
61240601 TTTCTTGTTGGTCAAAA
66 TTTCTTGCTGGTCAAAA
61240618 CCCATTGGAAGACCTTGACTTGGAAATTAACAC-CCATCATT-ATCATCATCGTCATTTGGAACA
1 CCCATTGGAAGACCTTGACTTGGAAATTAACACTCC--C-TTCATCATCATCGTCATTTGGAACA
61240681 AGTTTTCTTGCTGGTCAAAA
63 AGTTTTCTTGCTGGTCAAAA
61240701 C
1 C
61240702 TCCCTTTTAA
Statistics
Matches: 80, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
81 2 0.03
82 33 0.41
83 43 0.54
84 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (82 bp):
CCCATTGGAAGACCTTGACTTGGAAATTAACACTCCCTTCATCATCATCGTCATTTGGAACAAGT
TTTCTTGCTGGTCAAAA
Found at i:61244144 original size:138 final size:141
Alignment explanation
Indices: 61243888--61244175 Score: 465
Period size: 138 Copynumber: 2.0 Consensus size: 141
61243878 TTCCATTGGA
*
61243888 AGACCTTGACTTGGAAATTAACACAGCCATCATCATCACCATCGTCATTTGGAATAAGTACTTTT
1 AGACCTTGACTTGGAAATTAACACA-CCATCATCAT--CCATCGTCATTTGGAACAAG-A-TTTT
*
61243953 CTTGTTGGTCAAAACTCCCTTTTAATACTCTTTCATGCCTTCTTCTTCATCAAAGCCCACATCAC
61 CTTGTTGGTCAAAACTCCCTTTTAATACTCTTTCATACCTTCTTCTTCATCAAAGCCCACATCAC
61244018 CAGAAGGCTAATACAT
126 CAGAAGGCTAATACAT
*
61244034 AGACCTTGACTTGGAAATTAACAC-CCATCATCAT-CATCGTCGTTTGGAACAAG-TTTTCTTGT
1 AGACCTTGACTTGGAAATTAACACACCATCATCATCCATCGTCATTTGGAACAAGATTTTCTTGT
*
61244096 TGGTCAAAACTCCCTTTTAATACTCTTTCATACCTTCTTCTTCATCAAAGTCCACATCACCAGAA
66 TGGTCAAAACTCCCTTTTAATACTCTTTCATACCTTCTTCTTCATCAAAGCCCACATCACCAGAA
*
61244161 GGCTGATACAT
131 GGCTAATACAT
61244172 AGAC
1 AGAC
61244176 TTAAGGCTTA
Statistics
Matches: 137, Mismatches: 5, Indels: 8
0.91 0.03 0.05
Matches are distributed among these distances:
138 86 0.63
141 17 0.12
144 10 0.07
146 24 0.18
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (141 bp):
AGACCTTGACTTGGAAATTAACACACCATCATCATCCATCGTCATTTGGAACAAGATTTTCTTGT
TGGTCAAAACTCCCTTTTAATACTCTTTCATACCTTCTTCTTCATCAAAGCCCACATCACCAGAA
GGCTAATACAT
Found at i:61245418 original size:22 final size:22
Alignment explanation
Indices: 61245368--61245418 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
61245358 TCCAAACAAT
61245368 AACAATAAAATATTAACAATAC
1 AACAATAAAATATTAACAATAC
* *
61245390 GATAATAAAAT-TGTAACGAA-AC
1 AACAATAAAATAT-TAAC-AATAC
61245412 AACAATA
1 AACAATA
61245419 TAACAGCAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.22
Consensus pattern (22 bp):
AACAATAAAATATTAACAATAC
Found at i:61249086 original size:125 final size:125
Alignment explanation
Indices: 61248930--61249182 Score: 470
Period size: 125 Copynumber: 2.0 Consensus size: 125
61248920 GCTACTATGA
* *
61248930 AGGGAATGAAGATGGCAGTGATCGGTGTAAGAAAAACAGATGAGGAAACAGAGAGTCAAGAGGGA
1 AGGGAATGAAGATGGCAGTGATCGGCGTAAGAAAAACAGATGAGGAAACAGAAAGTCAAGAGGGA
*
61248995 ATTAATGGCAGATCTTTGGAAAGGCCATTATGCTTGGAATTTTAGCTATTCAAAAAAGAG
66 ATTAATGGCAGATCTTTGGAAAGGCCATTATGCTTGGAATTTTAGCTATACAAAAAAGAG
*
61249055 AGGGAATGAAGATGGCAGTGATCGGCGTAAGAAAAACAGATGAGGAAATAGAAAGTCAAGAGGGA
1 AGGGAATGAAGATGGCAGTGATCGGCGTAAGAAAAACAGATGAGGAAACAGAAAGTCAAGAGGGA
61249120 ATTAATGGCAGATCTTTGGAAAGGCCATTATGCTTGGAATTTTAGCTATACAAAAAAGAG
66 ATTAATGGCAGATCTTTGGAAAGGCCATTATGCTTGGAATTTTAGCTATACAAAAAAGAG
61249180 AGG
1 AGG
61249183 AATAAGTAAG
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (125 bp):
AGGGAATGAAGATGGCAGTGATCGGCGTAAGAAAAACAGATGAGGAAACAGAAAGTCAAGAGGGA
ATTAATGGCAGATCTTTGGAAAGGCCATTATGCTTGGAATTTTAGCTATACAAAAAAGAG
Found at i:61257508 original size:12 final size:12
Alignment explanation
Indices: 61257491--61257519 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
61257481 ATCATAAATC
61257491 TTCATGTTATTT
1 TTCATGTTATTT
61257503 TTCATGTTATTT
1 TTCATGTTATTT
61257515 TTCAT
1 TTCAT
61257520 ATTGCCATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.66
Consensus pattern (12 bp):
TTCATGTTATTT
Found at i:61264619 original size:189 final size:189
Alignment explanation
Indices: 61264287--61264805 Score: 813
Period size: 189 Copynumber: 2.7 Consensus size: 189
61264277 GTGGTTGCCC
* * * *
61264287 AATTGAAGAAGTGTCGTTGCCTTTCGACCCCCTATGTAATCTTCAGCACTTAAAAATGAGCGGCT
1 AATTGAAGAAGTGTCGTTGCCTTTCGACTCTCTATGTAATCTTCAGCACTTAAATATGAGTGGCT
* * *
61264352 CAGCGGTCAAAAATGTATCGATCCAGTTGGAATCCCTTCGCAAACTGAATCTTAGTGGATGCCCA
66 CAGCGGTCAAAAATGTATCGATCAAGTTGGAATCCCTTCGTAAACTGAATCTTAGTGGTTGCCCA
*
61264417 ATGGTCAAATTTCCAGAAATCCCAGGAAGCTTAATAAAATTAAACTTATCTGGCACTCA
131 ATGGTCGAATTTCCAGAAATCCCAGGAAGCTTAATAAAATTAAACTTATCTGGCACTCA
** *
61264476 AATTGAAGAAGTGTCGTTGCCTTTCGACTCTCTATGTAATCTTCAGCTTTTAAATATGAGTAGCT
1 AATTGAAGAAGTGTCGTTGCCTTTCGACTCTCTATGTAATCTTCAGCACTTAAATATGAGTGGCT
*
61264541 CAGCGGTCAAAAATGTATCGATCAAATTGGAATCCCTTCGTAAACTGAATCTTAGTGGTTGCCCA
66 CAGCGGTCAAAAATGTATCGATCAAGTTGGAATCCCTTCGTAAACTGAATCTTAGTGGTTGCCCA
* * *
61264606 CTGGTCGAATTTCCAGAAATCCCGGGAAGCTTAATAGAATTAAACTTATCTGGCACTCA
131 ATGGTCGAATTTCCAGAAATCCCAGGAAGCTTAATAAAATTAAACTTATCTGGCACTCA
*
61264665 AATTGAAGAAGTGTCGTTGCCTTTCGACTCTCTATGTAATCTTAAGCACTTAAATATGAGTGGCT
1 AATTGAAGAAGTGTCGTTGCCTTTCGACTCTCTATGTAATCTTCAGCACTTAAATATGAGTGGCT
* * * * * * * *
61264730 GAGCGGTCAAACATGTATCGATCAAGTTGGAATCTCTTCATTATCTGGATCATAGTGGTTGCCCA
66 CAGCGGTCAAAAATGTATCGATCAAGTTGGAATCCCTTCGTAAACTGAATCTTAGTGGTTGCCCA
*
61264795 AAGGTCGAATT
131 ATGGTCGAATT
61264806 ACTCTCAGAT
Statistics
Matches: 300, Mismatches: 30, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
189 300 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (189 bp):
AATTGAAGAAGTGTCGTTGCCTTTCGACTCTCTATGTAATCTTCAGCACTTAAATATGAGTGGCT
CAGCGGTCAAAAATGTATCGATCAAGTTGGAATCCCTTCGTAAACTGAATCTTAGTGGTTGCCCA
ATGGTCGAATTTCCAGAAATCCCAGGAAGCTTAATAAAATTAAACTTATCTGGCACTCA
Found at i:61267276 original size:3 final size:3
Alignment explanation
Indices: 61267268--61267312 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
61267258 GTCATTTTTG
61267268 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
61267313 ATTATTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:61267317 original size:3 final size:3
Alignment explanation
Indices: 61267311--61267342 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
61267301 CTTCTTCTTC
61267311 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
61267343 TTCTCATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:61272869 original size:12 final size:12
Alignment explanation
Indices: 61272852--61272878 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
61272842 CTCTTAAAGT
61272852 TTTGGGTTCTGA
1 TTTGGGTTCTGA
61272864 TTTGGGTTCTGA
1 TTTGGGTTCTGA
61272876 TTT
1 TTT
61272879 AAATAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.30, T:0.56
Consensus pattern (12 bp):
TTTGGGTTCTGA
Found at i:61275476 original size:9 final size:9
Alignment explanation
Indices: 61275458--61275511 Score: 81
Period size: 9 Copynumber: 6.0 Consensus size: 9
61275448 GGATGCAGAG
61275458 AGATGCTAC
1 AGATGCTAC
*
61275467 AGATGATAC
1 AGATGCTAC
61275476 AGATGCTAC
1 AGATGCTAC
*
61275485 AGATGGTAC
1 AGATGCTAC
*
61275494 AGATGGTAC
1 AGATGCTAC
61275503 AGATGCTAC
1 AGATGCTAC
61275512 TGAAAAGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (9 bp):
AGATGCTAC
Found at i:61275489 original size:27 final size:27
Alignment explanation
Indices: 61275458--61275511 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
61275448 GGATGCAGAG
61275458 AGATGCTACAGATGATACAGATGCTAC
1 AGATGCTACAGATGATACAGATGCTAC
* *
61275485 AGATGGTACAGATGGTACAGATGCTAC
1 AGATGCTACAGATGATACAGATGCTAC
61275512 TGAAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (27 bp):
AGATGCTACAGATGATACAGATGCTAC
Found at i:61277246 original size:2 final size:2
Alignment explanation
Indices: 61277239--61277271 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
61277229 AAGTTGGTAA
61277239 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 A
61277272 ATGTTTCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61282957 original size:26 final size:27
Alignment explanation
Indices: 61282916--61282967 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
61282906 ATTTGATAAA
* * *
61282916 TTTTAAATTCATTTTCATTTTTTTAAT
1 TTTTAAATTCACTTTCACTATTTTAAT
61282943 TTTTAAATT-ACTTTCACTATTTTAA
1 TTTTAAATTCACTTTCACTATTTTAA
61282968 ATATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTAAATTCACTTTCACTATTTTAAT
Found at i:61283525 original size:3 final size:3
Alignment explanation
Indices: 61283517--61283542 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61283507 TCTTCCATGG
61283517 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
61283543 ACTCTAATGA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:61287668 original size:430 final size:428
Alignment explanation
Indices: 61287218--61288157 Score: 1221
Period size: 429 Copynumber: 2.2 Consensus size: 428
61287208 ATGCAATAAT
* ** * * * *
61287218 TTAAGGAAGATATGTAATCTTTCGAGAGCCATCAACCTTGAATCCCTGGATTGCACTGACTGTCA
1 TTAAGGAAAATACCTAATCTTTCAAGAGCCATCAACCTTGAATACCTGGATTGCACTAACTGTAA
* *
61287283 AAGTTTGGTTGAACTTGGGAATGAAGGTGATCGTACGGTATGCGTTTTCATACTTTTCTTCGAAA
66 AAGTTTGGTTGAACTTGGGAATGAAGATGATCGTACGGTATGCATTTTCATACTTTTCTTCGAAA
** *
61287348 AATATGATTTATAATTTGATGTATCAAATATTCATATAATAACATTTTATTT-AGTCTTTAAAAA
131 AA-AAAAATTATAATTTGATGTAT-AAATATTCATATAATAACATTTTATTTAAGTCTTTAAAAA
*
61287412 ATAAATATAAAATAATTTATTTTATTTAGATAAGTGACATCGTTTAATTTATTACTTGTGGGAGA
194 ATAAATATAAAATAATTTATTTTATTTAGATAAGTGACATCGTTTAATTTATTAATTGTGGGAGA
* * *
61287477 ATTTTCACGCCGGATACATTAAATATAAATTTTTATTTTTGTATAGTATTATAATTATTTCTTTC
259 ATTTTCACACC-GATACATCAAATATAAATTTTTATTTTTGTATAGTATTATAATTATTTATTTC
* *
61287542 CTTTCCATTTTTTACTAAATAGTTGATGCTCAAAAGTAATACA-CTTATTTTTTCTGTACAGGAT
323 CTTTCCATTTTTTACCAAATAGCTGATGCTCAAAAGTAATACAGC-TATTTTTTCTGTACAGGAT
61287606 TTCGCTAATTTAAGGCAAATTGACTTCAATGGGTGCGTGAGC
387 TTCGCTAATTTAAGGCAAATTGACTTCAATGGGTGCGTGAGC
* * *
61287648 TTAAGGAAAATACCTAATCTTTCAATAGCCATCAACCTTGAATACCTTGATTGCTCTAACTGTAA
1 TTAAGGAAAATACCTAATCTTTCAAGAGCCATCAACCTTGAATACCTGGATTGCACTAACTGTAA
* * * * * * *
61287713 AAGTTTGGTTGAACTTTGGAATGGAGATGATTGTATGGTATGTATTTTCATACTTTTTTTTGAAA
66 AAGTTTGGTTGAACTTGGGAATGAAGATGATCGTACGGTATGCATTTTCATACTTTTCTTCGAAA
* * *
61287778 AAAAAAATTATATTTTGATGTATAAATATTCATATGATAACATTTTATTTAAAGTTTTTAAAAAA
131 AAAAAAATTATAATTTGATGTATAAATATTCATATAATAACATTTTATTT-AAGTCTTTAAAAAA
* * * * *
61287843 TAAATATAAAATATTTTATTTTATTTAGATGAGTGACATTGTTTGATTTATTAATTGTGGGTGAA
195 TAAATATAAAATAATTTATTTTATTTAGATAAGTGACATCGTTTAATTTATTAATTGTGGGAGAA
* *
61287908 TTTTCACACCGATACGTCAAATATAAATTTTTATTTTTTTATAGTATTATAATTATTTATTTCCT
260 TTTTCACACCGATACATCAAATATAAATTTTTATTTTTGTATAGTATTATAATTATTTATTTCCT
* * ** *
61287973 TTTCATTTTTTACCAAGTAGCTGATGCTTGAAAGTAATACAGCTATTTTTTCTGTACAGGACCTT
325 TTCCATTTTTTACCAAATAGCTGATGCTCAAAAGTAATACAGCTATTTTTTCTGTACAGGA-TTT
* * * * * **
61288038 -GATAATTTAACGG-TAATTAACGTTTCAAAT-TGT-AGT-AAT
389 CGCTAATTTAA-GGCAAATTGAC--TTC-AATGGGTGCGTGAGC
* * * * *
61288077 TTAA-GAAAGATGCCTGATCTTTCAAGAGCCATCAACCTTCAATTCCTTGATTGCACTAACTGTA
1 TTAAGGAAA-ATACCTAATCTTTCAAGAGCCATCAACCTTGAATACCTGGATTGCACTAACTGTA
*
61288141 AAAGTCTGGTTGAACTT
65 AAAGTTTGGTTGAACTT
61288158 CCTTGCCTCG
Statistics
Matches: 444, Mismatches: 57, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
428 30 0.07
429 206 0.46
430 200 0.45
431 5 0.01
432 3 0.01
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (428 bp):
TTAAGGAAAATACCTAATCTTTCAAGAGCCATCAACCTTGAATACCTGGATTGCACTAACTGTAA
AAGTTTGGTTGAACTTGGGAATGAAGATGATCGTACGGTATGCATTTTCATACTTTTCTTCGAAA
AAAAAAATTATAATTTGATGTATAAATATTCATATAATAACATTTTATTTAAGTCTTTAAAAAAT
AAATATAAAATAATTTATTTTATTTAGATAAGTGACATCGTTTAATTTATTAATTGTGGGAGAAT
TTTCACACCGATACATCAAATATAAATTTTTATTTTTGTATAGTATTATAATTATTTATTTCCTT
TCCATTTTTTACCAAATAGCTGATGCTCAAAAGTAATACAGCTATTTTTTCTGTACAGGATTTCG
CTAATTTAAGGCAAATTGACTTCAATGGGTGCGTGAGC
Found at i:61288100 original size:429 final size:426
Alignment explanation
Indices: 61286991--61288157 Score: 1306
Period size: 430 Copynumber: 2.7 Consensus size: 426
61286981 AATATGAAAG
* * * * * * * * * *
61286991 ATTTTATCTAAATTAGTGGCATCATTTGATCTATTAATTGTGAGTTAATTTTCACATCCAATACC
1 ATTTTATTTAGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTCACA-CCGATACA
** * *
61287056 TCAAATATGGATTTTTATTTTTCT-TAGTATTATAATTATTTATTTTCTTTTTCGTTTCTTGCTG
65 TCAAATATAAATTTTTATTTTTCTATAGTATTATAATTATTTA-TTTCCTTTTC--AT-TT--T-
* * * * * *
61287120 CTTAAAGTAAGTAGTTGATGCTTAAAAGTAATACAAATATTGTTTCTATGCAGGAGCTTGTTAAT
123 -TT--ACTAAGTAGTTGATGCTTAAAAGTAATAC-ACTATTTTTTCTGTACAGGA-CTTGATAAT
* * * * * ** *
61287185 TTAAGGGAAATTTACGTTGCAGAA-TGCAATAATTTAAGGAAGATATGTAATCTTTCGAGAGCCA
183 TTAA-GGAAATTAACGTTTCA-AATTGTAGTAATTTAAGAAAGATACCTAATCTTTCAAGAGCCA
* * * * *
61287249 TCAACCTTGAATCCCTGGATTGCACTGACTGTCAAAGTTTGGTTGAACTTGGGAATGAAGGTGAT
246 TCAACCTTGAATACCTTGATTGCACTAACTGTAAAAGTTTGGTTGAACTTGGGAATGAAGATGAT
* ** *
61287314 CGTACGGTATGCGTTTTCATACTTTTCTTCGAAAAATATGATTTATAATTTGATGTATCAAATAT
311 CGTACGGTATGCATTTTCATACTTTTCTTCGAAAAATAAAAATTATAATTTGATGTATCAAATAT
61287379 TCATATAATAACATTTTATTTAGTCTTTAAAAAATAAATATAAAATAATTT
376 TCATATAATAACATTTTATTTAGTCTTTAAAAAATAAATATAAAATAATTT
* * * *
61287430 ATTTTATTTAGATAAGTGACATCGTTTAATTTATTACTTGTGGGAGAATTTTCACGCCGGATACA
1 ATTTTATTTAGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTCACACC-GATACA
* * * *
61287495 TTAAATATAAATTTTTATTTTTGTATAGTATTATAATTATTTCTTTCCTTTCCATTTTTTACTAA
65 TCAAATATAAATTTTTATTTTTCTATAGTATTATAATTATTTATTTCCTTTTCATTTTTTACTAA
* * * *
61287560 ATAGTTGATGCTCAAAAGTAATACACTTATTTTTTCTGTACAGGATTTCGCTAATTTAAGGCAAA
130 GTAGTTGATGCTTAAAAGTAATACAC-TATTTTTTCTGTACAGGACTT-GATAATTTAAGG-AAA
* * * ** *
61287625 TTGAC--TTC-AATGGGTGCGTGAGCTTAAGGAAA-ATACCTAATCTTTCAATAGCCATCAACCT
192 TTAACGTTTCAAAT-TGT-AGT-AATTTAA-GAAAGATACCTAATCTTTCAAGAGCCATCAACCT
* * * * *
61287686 TGAATACCTTGATTGCTCTAACTGTAAAAGTTTGGTTGAACTTTGGAATGGAGATGATTGTATGG
253 TGAATACCTTGATTGCACTAACTGTAAAAGTTTGGTTGAACTTGGGAATGAAGATGATCGTACGG
* * * * *
61287751 TATGTATTTTCATACTTTTTTTTGAAAAA-AAAAATTATATTTTGATGTAT-AAATATTCATATG
318 TATGCATTTTCATACTTTTCTTCGAAAAATAAAAATTATAATTTGATGTATCAAATATTCATATA
* *
61287814 ATAACATTTTATTTAAAGTTTTTAAAAAATAAATATAAAATATTTT
383 ATAACATTTTATTT--AGTCTTTAAAAAATAAATATAAAATAATTT
* * *
61287860 ATTTTATTTAGATGAGTGACATTGTTTGATTTATTAATTGTGGGTGAATTTTCACACCGATACGT
1 ATTTTATTTAGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTCACACCGATACAT
* *
61287925 CAAATATAAATTTTTATTTTTTTATAGTATTATAATTATTTATTTCCTTTTCATTTTTTACCAAG
66 CAAATATAAATTTTTATTTTTCTATAGTATTATAATTATTTATTTCCTTTTCATTTTTTACTAAG
* * *
61287990 TAGCTGATGCTTGAAAGTAATACAGCTATTTTTTCTGTACAGGACCTTGATAATTTAACGGTAAT
131 TAGTTGATGCTTAAAAGTAATACA-CTATTTTTTCTGTACAGGA-CTTGATAATTTAA-GGAAAT
* * *
61288055 TAACGTTTCAAATTGTAGTAATTTAAGAAAGATGCCTGATCTTTCAAGAGCCATCAACCTTCAAT
193 TAACGTTTCAAATTGTAGTAATTTAAGAAAGATACCTAATCTTTCAAGAGCCATCAACCTTGAAT
* *
61288120 TCCTTGATTGCACTAACTGTAAAAGTCTGGTTGAACTT
258 ACCTTGATTGCACTAACTGTAAAAGTTTGGTTGAACTT
61288158 CCTTGCCTCG
Statistics
Matches: 613, Mismatches: 96, Indels: 48
0.81 0.13 0.06
Matches are distributed among these distances:
426 2 0.00
428 33 0.05
429 212 0.35
430 254 0.41
431 8 0.01
432 5 0.01
434 1 0.00
436 2 0.00
437 1 0.00
438 2 0.00
439 76 0.12
440 17 0.03
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (426 bp):
ATTTTATTTAGATAAGTGACATCGTTTGATTTATTAATTGTGGGTGAATTTTCACACCGATACAT
CAAATATAAATTTTTATTTTTCTATAGTATTATAATTATTTATTTCCTTTTCATTTTTTACTAAG
TAGTTGATGCTTAAAAGTAATACACTATTTTTTCTGTACAGGACTTGATAATTTAAGGAAATTAA
CGTTTCAAATTGTAGTAATTTAAGAAAGATACCTAATCTTTCAAGAGCCATCAACCTTGAATACC
TTGATTGCACTAACTGTAAAAGTTTGGTTGAACTTGGGAATGAAGATGATCGTACGGTATGCATT
TTCATACTTTTCTTCGAAAAATAAAAATTATAATTTGATGTATCAAATATTCATATAATAACATT
TTATTTAGTCTTTAAAAAATAAATATAAAATAATTT
Found at i:61290575 original size:16 final size:16
Alignment explanation
Indices: 61290554--61290586 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
61290544 TTGCAGTGAA
61290554 AGATATTAAGATTCAT
1 AGATATTAAGATTCAT
61290570 AGATATTAAGATTCAT
1 AGATATTAAGATTCAT
61290586 A
1 A
61290587 CTTGAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (16 bp):
AGATATTAAGATTCAT
Found at i:61296305 original size:27 final size:27
Alignment explanation
Indices: 61296266--61296322 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
61296256 TGTACTTTTG
*
61296266 AAAGAATATCAAACCAACAAATTTAAC
1 AAAGAATACCAAACCAACAAATTTAAC
61296293 AAAGAATACCAAACCAACAAATTTAAC
1 AAAGAATACCAAACCAACAAATTTAAC
61296320 AAA
1 AAA
61296323 AAATTTGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.61, C:0.19, G:0.04, T:0.16
Consensus pattern (27 bp):
AAAGAATACCAAACCAACAAATTTAAC
Found at i:61298135 original size:18 final size:18
Alignment explanation
Indices: 61298112--61298149 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
61298102 TTCCGTAAGT
*
61298112 TAGATCACGATCTTTTAG
1 TAGATCACAATCTTTTAG
61298130 TAGATCACAATCTTTTAG
1 TAGATCACAATCTTTTAG
61298148 TA
1 TA
61298150 ATTCTCGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (18 bp):
TAGATCACAATCTTTTAG
Found at i:61302009 original size:19 final size:19
Alignment explanation
Indices: 61301968--61302010 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
61301958 ATAAACTCAA
61301968 AAAATAAAAAAAAGCAAGT
1 AAAATAAAAAAAAGCAAGT
*
61301987 -AAATAAAAAAACGCAAGT
1 AAAATAAAAAAAAGCAAGT
61302005 AAAATA
1 AAAATA
61302011 GAACAGACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.72, C:0.07, G:0.09, T:0.12
Consensus pattern (19 bp):
AAAATAAAAAAAAGCAAGT
Found at i:61307747 original size:8 final size:8
Alignment explanation
Indices: 61307736--61307760 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61307726 AATGTCTAAT
61307736 GGGAAATG
1 GGGAAATG
61307744 GGGAAATG
1 GGGAAATG
61307752 GGGAAATG
1 GGGAAATG
61307760 G
1 G
61307761 AAAATGCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.12
Consensus pattern (8 bp):
GGGAAATG
Found at i:61309153 original size:20 final size:21
Alignment explanation
Indices: 61309122--61309181 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 21
61309112 TATGTATATA
61309122 TATATAACAAAATTATAATAAG
1 TATATAA-AAAATTATAATAAG
61309144 TATATAAAAAAATTATAATAAG
1 TATAT-AAAAAATTATAATAAG
61309166 TATAT-AAAAATTATAA
1 TATATAAAAAATTATAA
61309182 AAAAAACTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.30
22 24 0.65
23 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (21 bp):
TATATAAAAAATTATAATAAG
Found at i:61310766 original size:34 final size:34
Alignment explanation
Indices: 61310728--61310795 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
61310718 CCAGCGAGAG
61310728 ATGCATCAAATGAATACTAAATATGAAGAAGGAT
1 ATGCATCAAATGAATACTAAATATGAAGAAGGAT
* * * *
61310762 ATGCATGAAATGGATACTGAATATGAAGAGGGAT
1 ATGCATCAAATGAATACTAAATATGAAGAAGGAT
61310796 GTGGAGCTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.24
Consensus pattern (34 bp):
ATGCATCAAATGAATACTAAATATGAAGAAGGAT
Found at i:61315644 original size:2 final size:2
Alignment explanation
Indices: 61315637--61315672 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
61315627 GGTTAAGTTC
* *
61315637 AT AT AT AT AC AT AT AT AT AC 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
61315673 CAATTGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:61315651 original size:10 final size:10
Alignment explanation
Indices: 61315636--61315672 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
61315626 TGGTTAAGTT
61315636 CATATATATA
1 CATATATATA
61315646 CATATATATA
1 CATATATATA
61315656 CATATATATA
1 CATATATATA
*
61315666 TATATAT
1 CATATAT
61315673 CAATTGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (10 bp):
CATATATATA
Found at i:61317728 original size:19 final size:19
Alignment explanation
Indices: 61317704--61317742 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
61317694 TGAATTCAAA
61317704 ATACATGGAATTTGGGCGC
1 ATACATGGAATTTGGGCGC
61317723 ATACATGGAATTTGGGCGC
1 ATACATGGAATTTGGGCGC
61317742 A
1 A
61317743 AGACGCTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (19 bp):
ATACATGGAATTTGGGCGC
Found at i:61321284 original size:29 final size:29
Alignment explanation
Indices: 61321250--61321307 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
61321240 AATGAAAAAG
*
61321250 ATCAAAATTATATAGTAAAACAAAACATT
1 ATCAAAATTATAAAGTAAAACAAAACATT
61321279 ATCAAAATTATAAAGTAAAACAAAACATT
1 ATCAAAATTATAAAGTAAAACAAAACATT
61321308 CACCTGCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.26
Consensus pattern (29 bp):
ATCAAAATTATAAAGTAAAACAAAACATT
Found at i:61326405 original size:16 final size:16
Alignment explanation
Indices: 61326384--61326415 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
61326374 AAACAGTGAT
61326384 GGTTCTTTTGTGTATC
1 GGTTCTTTTGTGTATC
61326400 GGTTCTTTTGTGTATC
1 GGTTCTTTTGTGTATC
61326416 TACTCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
GGTTCTTTTGTGTATC
Found at i:61333381 original size:13 final size:13
Alignment explanation
Indices: 61333365--61333397 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
61333355 TTAAATTAAA
61333365 TATTTAATATCGT
1 TATTTAATATCGT
61333378 TATTTAATATCGT
1 TATTTAATATCGT
61333391 TAATTTA
1 T-ATTTA
61333398 GTAATGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (13 bp):
TATTTAATATCGT
Found at i:61348605 original size:16 final size:16
Alignment explanation
Indices: 61348584--61348621 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
61348574 AATTTTTTAG
61348584 ATTAATTTTATTTAAA
1 ATTAATTTTATTTAAA
61348600 ATTAATTTTATTTAAA
1 ATTAATTTTATTTAAA
*
61348616 AATAAT
1 ATTAAT
61348622 GTATTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATTTTATTTAAA
Found at i:61352278 original size:189 final size:189
Alignment explanation
Indices: 61352064--61352531 Score: 708
Period size: 189 Copynumber: 2.5 Consensus size: 189
61352054 GTGAATTGGT
* * *
61352064 TCTTAGTAATTGCCCAATGATCAAATTTCCAGAAATCCCAAAAAGCTTAACAAAATTAAACTTAT
1 TCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCCAAGAAGCTTAACAAAATTAAATTTAT
* * *
61352129 CTGGCACTCAAATTGAAGAAGTGTCGTTGCCTTTTGACTCTCTATGTAATCTTCAGGA-CTTAAA
66 CTGGCACTCAAATTGAAGAAGTGTCCTTACCTTTCGACTCTCTATGTAATCTTCA-GATCTTAAA
* *
61352193 TATGAGTGGCTCAGTAGTCAAAAATGTATCGATCAA-GTTGGAATCTCTTCATAAACTGAA
130 TATGAGTGGCTCAGCAGTCAAAAATGTATCGAT-AAGGTTGGAATCCCTTCATAAACTGAA
* *
61352253 TCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCCAAGAAGCTTAATAGAATTAAATTTAT
1 TCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCCAAGAAGCTTAACAAAATTAAATTTAT
61352318 CTGGCACTCAAATTGAAGAAGTGTCCTTACCTTTCGACTCTCTATGTAATCTTCAGATCTTAAAT
66 CTGGCACTCAAATTGAAGAAGTGTCCTTACCTTTCGACTCTCTATGTAATCTTCAGATCTTAAAT
* *
61352383 ATGAGTGGCTCAGCAGTCAAAAATGTATCGATAAGGTTGGAATCCCTTCGTAAACTGGA
131 ATGAGTGGCTCAGCAGTCAAAAATGTATCGATAAGGTTGGAATCCCTTCATAAACTGAA
* * * * * * *
61352442 TCTTAGTGGTTGCCCAATGGTCTAATTTCCA-AACGTCCCAAGAAGCTTAACACATTTAGATTTA
1 TCTTAGTGATTGCCCAATGATCAAATTTCCAGAA-ATCCCAAGAAGCTTAACAAAATTAAATTTA
*
61352506 TCTCGCACTCAAATTGAAGAAGTGTC
65 TCTGGCACTCAAATTGAAGAAGTGTC
61352532 ATTGTGATAA
Statistics
Matches: 255, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
188 6 0.02
189 249 0.98
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (189 bp):
TCTTAGTGATTGCCCAATGATCAAATTTCCAGAAATCCCAAGAAGCTTAACAAAATTAAATTTAT
CTGGCACTCAAATTGAAGAAGTGTCCTTACCTTTCGACTCTCTATGTAATCTTCAGATCTTAAAT
ATGAGTGGCTCAGCAGTCAAAAATGTATCGATAAGGTTGGAATCCCTTCATAAACTGAA
Found at i:61362295 original size:4 final size:4
Alignment explanation
Indices: 61362286--61362313 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
61362276 ATACAAGAGG
61362286 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
61362314 TTATAGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:61362393 original size:24 final size:24
Alignment explanation
Indices: 61362366--61362412 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
61362356 AAATAATACA
*
61362366 AAAATATATGTATATATAAATTAT
1 AAAATATATGTACATATAAATTAT
*
61362390 AAAATATATGTACATATATATTA
1 AAAATATATGTACATATAAATTA
61362413 CAAAGATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAATATATGTACATATAAATTAT
Found at i:61362493 original size:48 final size:43
Alignment explanation
Indices: 61362435--61362546 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 43
61362425 GATGTATGCG
* * *
61362435 TATATTTTAAGACTATAAAATATATAAA-AAGAATATATGTATGTATA
1 TATATTTTAAGA-TATAAAA-ACA-AAATAAAAACATATGT-T-TATA
*
61362482 TATAGTTTTAAGTTATAAAAACAAAATAAAAACATATGTTTATA
1 TATA-TTTTAAGATATAAAAACAAAATAAAAACATATGTTTATA
61362526 TATAATTTTAAGATATAAAAA
1 TAT-ATTTTAAGATATAAAAA
61362547 TCTATGAAGG
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
44 22 0.39
45 5 0.09
46 12 0.21
47 11 0.19
48 7 0.12
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (43 bp):
TATATTTTAAGATATAAAAACAAAATAAAAACATATGTTTATA
Found at i:61362760 original size:3 final size:3
Alignment explanation
Indices: 61362752--61362813 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
61362742 AGCTATTATG
* *
61362752 TAA TAA TAA TAA T-A TGA TAA GTAA CAA TAA T-A TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA
61362797 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
61362814 CTAAAAAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:61365295 original size:33 final size:33
Alignment explanation
Indices: 61365251--61365314 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
61365241 TTGTAGCAGA
*
61365251 CTTGCATCGTGGCTGC-ATCACACAGCTAATAGG
1 CTTGCAACGTGGCTGCGAT-ACACAGCTAATAGG
*
61365284 CTTGCAACGTGGCTGCGATATACAGCTAATA
1 CTTGCAACGTGGCTGCGATACACAGCTAATA
61365315 AAGCGAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (33 bp):
CTTGCAACGTGGCTGCGATACACAGCTAATAGG
Found at i:61371634 original size:21 final size:20
Alignment explanation
Indices: 61371587--61371641 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
61371577 ACCGCTGTTT
*
61371587 CTAATCTCACTGCTACAGTA
1 CTAATCTCACCGCTACAGTA
*
61371607 TTCAATCTCACCGCTACAGTAA
1 CT-AATCTCACCGCTACAGT-A
61371629 CTAATCTCACCGC
1 CTAATCTCACCGC
61371642 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.90
22 2 0.07
ACGTcount: A:0.29, C:0.35, G:0.09, T:0.27
Consensus pattern (20 bp):
CTAATCTCACCGCTACAGTA
Found at i:61371898 original size:19 final size:20
Alignment explanation
Indices: 61371871--61371911 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
61371861 TTTTCTACTG
61371871 TTTAGTTTTTT-TAATATTT
1 TTTAGTTTTTTGTAATATTT
* *
61371890 TTTATTTTTTTGTATTATTT
1 TTTAGTTTTTTGTAATATTT
61371910 TT
1 TT
61371912 GTAAAATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTAGTTTTTTGTAATATTT
Found at i:61372759 original size:7 final size:7
Alignment explanation
Indices: 61372747--61372851 Score: 53
Period size: 7 Copynumber: 15.4 Consensus size: 7
61372737 AACCCTGAAT
61372747 CCTTAAA
1 CCTTAAA
61372754 CCTTAAA
1 CCTTAAA
*
61372761 CC-TGAA
1 CCTTAAA
*
61372767 CCCTAAA
1 CCTTAAA
*
61372774 CCCTAAA
1 CCTTAAA
61372781 -CTCTAAA
1 CCT-TAAA
*
61372788 TCCTTGAA
1 -CCTTAAA
61372796 -CTCTAAA
1 CCT-TAAA
61372803 CC-TAAA
1 CCTTAAA
*
61372809 CTTTAAA
1 CCTTAAA
*
61372816 CC-TCAA
1 CCTTAAA
61372822 CAC-TAAA
1 C-CTTAAA
61372829 -CTTAAA
1 CCTTAAA
61372835 CCTTAAA
1 CCTTAAA
* *
61372842 TCTCAAA
1 CCTTAAA
61372849 CCT
1 CCT
61372852 AAATCCTAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
5 1 0.01
6 21 0.28
7 48 0.63
8 4 0.05
9 2 0.03
ACGTcount: A:0.41, C:0.31, G:0.02, T:0.26
Consensus pattern (7 bp):
CCTTAAA
Found at i:61372773 original size:13 final size:13
Alignment explanation
Indices: 61372757--61372861 Score: 70
Period size: 13 Copynumber: 7.8 Consensus size: 13
61372747 CCTTAAACCT
* *
61372757 TAAACCTGAACCC
1 TAAACCTAAACTC
61372770 TAAACCCTAAACTC
1 TAAA-CCTAAACTC
*
61372784 TAAATCCTTGAACTC
1 TAAA-CC-TAAACTC
*
61372799 TAAACCTAAACTT
1 TAAACCTAAACTC
* *
61372812 TAAACCTCAACAC
1 TAAACCTAAACTC
*
61372825 TAAACTTAAAC-C
1 TAAACCTAAACTC
*
61372837 TTAAATCTCAAAC-C
1 -TAAACCT-AAACTC
61372851 TAAATCCTAAA
1 TAAA-CCTAAA
61372862 TCTCGAGGTT
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
12 1 0.01
13 40 0.55
14 22 0.30
15 10 0.14
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.25
Consensus pattern (13 bp):
TAAACCTAAACTC
Found at i:61373075 original size:18 final size:18
Alignment explanation
Indices: 61373052--61373086 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61373042 TTGTTTATAA
61373052 TTTAAAAAAATTAATTAT
1 TTTAAAAAAATTAATTAT
* *
61373070 TTTAAATAATTTAATTA
1 TTTAAAAAAATTAATTA
61373087 AAATTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAAAAATTAATTAT
Found at i:61399819 original size:23 final size:24
Alignment explanation
Indices: 61399786--61399833 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
61399776 TTTATCTTTG
61399786 TTTTATATTTT-ATATATAATTATA
1 TTTTATATTTTGAT-TATAATTATA
*
61399810 TTTT-TATTTTGGTTATAATTATA
1 TTTTATATTTTGATTATAATTATA
61399833 T
1 T
61399834 ATAAATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTTATATTTTGATTATAATTATA
Found at i:61409695 original size:16 final size:17
Alignment explanation
Indices: 61409676--61409708 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
61409666 GTTTTTTAAA
61409676 TTTTAAATTT-TAATTT
1 TTTTAAATTTGTAATTT
61409692 TTTTAAATTTGTAATTT
1 TTTTAAATTTGTAATTT
61409709 GATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTAAATTTGTAATTT
Found at i:61409697 original size:23 final size:23
Alignment explanation
Indices: 61409667--61409718 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
61409657 TTAATGTTGG
*
61409667 TTTTTTAAATTT-TAAATTTTAAT
1 TTTTTTAAATTTGT-AATTTGAAT
*
61409690 TTTTTTAAATTTGTAATTTGATT
1 TTTTTTAAATTTGTAATTTGAAT
61409713 TTTTTT
1 TTTTTT
61409719 GTTTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTTTAAATTTGTAATTTGAAT
Found at i:61410265 original size:27 final size:25
Alignment explanation
Indices: 61410211--61410258 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
61410201 AAGTCTGTCT
* *
61410211 TTTGCCTCAGTCACACAATCTATCC
1 TTTGCCTCAATCACACAATCTAACC
*
61410236 TTTGCTTCAATCACACAATCTAA
1 TTTGCCTCAATCACACAATCTAA
61410259 ACTCTTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.33
Consensus pattern (25 bp):
TTTGCCTCAATCACACAATCTAACC
Found at i:61419753 original size:39 final size:39
Alignment explanation
Indices: 61419699--61419787 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
61419689 ATTTTATGTG
61419699 GATGAAGATCAGATTGATGAGACGAGCAGTGAGGCATCC
1 GATGAAGATCAGATTGATGAGACGAGCAGTGAGGCATCC
* *
61419738 GATGAAGATCAGATTGATGAGACGAGCAGTGATGCATCG
1 GATGAAGATCAGATTGATGAGACGAGCAGTGAGGCATCC
61419777 GATGAAGATCA
1 GATGAAGATCA
61419788 AGAAATGTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (39 bp):
GATGAAGATCAGATTGATGAGACGAGCAGTGAGGCATCC
Found at i:61457832 original size:14 final size:14
Alignment explanation
Indices: 61457813--61457861 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
61457803 TACTAAGGAA
61457813 GATTTTCTTAGCCT
1 GATTTTCTTAGCCT
*
61457827 GATTTTCTTTA---A
1 GATTTTC-TTAGCCT
*
61457839 GATTTTCTTGGCCT
1 GATTTTCTTAGCCT
61457853 GATTTTCTT
1 GATTTTCTT
61457862 TAAGCCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
11 2 0.07
12 7 0.25
14 16 0.57
15 3 0.11
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.55
Consensus pattern (14 bp):
GATTTTCTTAGCCT
Found at i:61457847 original size:26 final size:26
Alignment explanation
Indices: 61457811--61457865 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
61457801 CATACTAAGG
61457811 AAGATTTTCTTAGCCTGATTTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
*
61457837 AAGATTTTCTTGGCCTGATTTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
61457863 AAG
1 AAG
61457866 CCAAAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.51
Consensus pattern (26 bp):
AAGATTTTCTTAGCCTGATTTTCTTT
Found at i:61459419 original size:23 final size:23
Alignment explanation
Indices: 61459392--61459442 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
61459382 ATAAATCAAA
*
61459392 TTTAA-TACTTAATATTTTAATTT
1 TTTAATTACTTAACA-TTTAATTT
**
61459415 TTTAATTTTTTAACATTTAATTT
1 TTTAATTACTTAACATTTAATTT
61459438 TTTAA
1 TTTAA
61459443 CTTATCATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTAATTACTTAACATTTAATTT
Found at i:61459424 original size:15 final size:16
Alignment explanation
Indices: 61459400--61459442 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
61459390 AATTTAATAC
* **
61459400 TTAATATTTTAATTTT
1 TTAATTTTTTAATCAT
61459416 TTAATTTTTTAA-CAT
1 TTAATTTTTTAATCAT
61459431 TTAATTTTTTAA
1 TTAATTTTTTAA
61459443 CTTATCATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTTTTTAATCAT
Found at i:61459432 original size:10 final size:8
Alignment explanation
Indices: 61459400--61459442 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
61459390 AATTTAATAC
*
61459400 TTAATATT
1 TTAATTTT
61459408 TTAATTTT
1 TTAATTTT
61459416 TTAATTTT
1 TTAATTTT
**
61459424 TTAA-CAT
1 TTAATTTT
61459431 TTAATTTT
1 TTAATTTT
61459439 TTAA
1 TTAA
61459443 CTTATCATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
TTAATTTT
Found at i:61459443 original size:15 final size:15
Alignment explanation
Indices: 61459415--61459443 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61459405 ATTTTAATTT
61459415 TTTAATTTTTTAACA
1 TTTAATTTTTTAACA
61459430 TTTAATTTTTTAAC
1 TTTAATTTTTTAAC
61459444 TTATCATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATTTTTTAACA
Found at i:61461565 original size:25 final size:26
Alignment explanation
Indices: 61461535--61461586 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
61461525 AAACTCTTTT
* *
61461535 AAAAGAAA-CTACAGAGAATTTCTTA
1 AAAAGAAACCCACAGAGAATTTATTA
*
61461560 AAAAGAAACCCAGAGAGAATTTATTA
1 AAAAGAAACCCACAGAGAATTTATTA
61461586 A
1 A
61461587 CTCAAATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.54, C:0.12, G:0.13, T:0.21
Consensus pattern (26 bp):
AAAAGAAACCCACAGAGAATTTATTA
Found at i:61462938 original size:12 final size:12
Alignment explanation
Indices: 61462921--61462947 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
61462911 TCAGGTAGTG
61462921 TTGGGTTAGGTA
1 TTGGGTTAGGTA
61462933 TTGGGTTAGGTA
1 TTGGGTTAGGTA
61462945 TTG
1 TTG
61462948 AGTTGGGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (12 bp):
TTGGGTTAGGTA
Found at i:61468870 original size:20 final size:20
Alignment explanation
Indices: 61468845--61468886 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
61468835 CTCAAGACGT
61468845 TTCCCGTGGTCCCAAAACAC
1 TTCCCGTGGTCCCAAAACAC
61468865 TTCCCGTGGTCCCAAAACAC
1 TTCCCGTGGTCCCAAAACAC
61468885 TT
1 TT
61468887 TCCTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.38, G:0.14, T:0.24
Consensus pattern (20 bp):
TTCCCGTGGTCCCAAAACAC
Found at i:61469343 original size:190 final size:190
Alignment explanation
Indices: 61469036--61469562 Score: 627
Period size: 190 Copynumber: 2.8 Consensus size: 190
61469026 CATGATATGG
* * * * * *
61469036 ATCTTAGTCATTGCCCAATAGCCGAATTCCCAATAATCCCAAGAAGCTTGACAGAATTTAACTTA
1 ATCTTAGTCATTGCCCAATAGACAAATTCCCGA-AATCCCAAGAAGCTTAACAAAATTAAACTTA
* * * * *
61469101 TCTGAAACTCAAATTGAAGATGTGTGCTTGTCTCTCGACACTCCAAGTAATCTTCAGACGTTAGA
65 TCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTCTCGACTCTCTAAGTAATCTTCAGACGTTAGA
61469166 TATGAGTGGCTCAAGGGTAAAAAAATGTATCCATCAAGATGG-AAT-CCCTTCGTGACCTGA
130 TATGAGTGGCTCAAGGGT-AAAAAATGTATCCATCAAGATGGAAATCCCCTTCGTGACCTGA
* *
61469226 ATCTTAGTCATTGCCCAATAGTCAAATTTCCCGAAATCCCAAGAA-CTTTAATAAAATTAAACTT
1 ATCTTAGTCATTGCCCAATAGACAAA-TTCCCGAAATCCCAAGAAGC-TTAACAAAATTAAACTT
* * * *
61469290 ATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCTCTAGGTAATCTTCAAACATTAG
64 ATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTCTCGACTCTCTAAGTAATCTTCAGACGTTAG
* * *
61469355 ATATGAGTGGCTCAAGGGTAAAAACTGTATCGATCAAGATGGAAATCGCCCTTCGTGATCTGA
129 ATATGAGTGGCTCAAGGGTAAAAAATGTATCCATCAAGATGGAAATC-CCCTTCGTGACCTGA
* * *
61469418 ATCTTAGTCATTGCCCAAT-GACAGAATTCCCAGAAATCCCAAGAAGCTTAAGAAAATTGAATTT
1 ATCTTAGTCATTGCCCAATAGACA-AATTCCC-GAAATCCCAAGAAGCTTAACAAAATTAAACTT
* * * * * * *
61469482 ATTTAGG-ACTCAAATT-AAGGAAGTGACTTTGTCTTTAGACTCTCTAAATAATCTTCAGATGTT
64 ATCT-GGAACTCAAATTGAA-GAAGTGTCCTTGTCTCTCGACTCTCTAAGTAATCTTCAGACGTT
* *
61469545 AAAGATGAGCT-GCTCAAG
127 AGATATGAG-TGGCTCAAG
61469563 TATTCAAAAG
Statistics
Matches: 291, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
189 22 0.08
190 127 0.44
191 16 0.05
192 122 0.42
193 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (190 bp):
ATCTTAGTCATTGCCCAATAGACAAATTCCCGAAATCCCAAGAAGCTTAACAAAATTAAACTTAT
CTGGAACTCAAATTGAAGAAGTGTCCTTGTCTCTCGACTCTCTAAGTAATCTTCAGACGTTAGAT
ATGAGTGGCTCAAGGGTAAAAAATGTATCCATCAAGATGGAAATCCCCTTCGTGACCTGA
Found at i:61488805 original size:34 final size:34
Alignment explanation
Indices: 61488767--61488875 Score: 91
Period size: 34 Copynumber: 3.1 Consensus size: 34
61488757 ATGTAACTTA
61488767 GTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAG
1 GTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAG
* ** * *
61488801 GTTGTGATT-TATTTAAAG-TTGATGTAAT-GTCACTTA-
1 GTTGT-ATTCCAACT-AAGTTTG-T-TAGTGGT-A-GTAG
61488837 GTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAG
1 GTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAG
61488871 GTTGT
1 GTTGT
61488876 GATTAGGTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 2 0.04
34 19 0.35
35 18 0.33
36 14 0.25
37 2 0.04
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.44
Consensus pattern (34 bp):
GTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAG
Found at i:61488852 original size:70 final size:70
Alignment explanation
Indices: 61488739--61488879 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
61488729 TTTTTTATTA
61488739 TTATTTAAAGTTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTT
1 TTATTTAAAGTTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTT
61488804 GTGAT
66 GTGAT
*
61488809 TTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTT
1 TTATTTAAAGTTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTT
61488874 GTGAT
66 GTGAT
61488879 T
1 T
61488880 AGGTTAACCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (70 bp):
TTATTTAAAGTTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTT
GTGAT
Found at i:61488855 original size:35 final size:34
Alignment explanation
Indices: 61488746--61488855 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 34
61488736 TTATTATTTA
61488746 AAGTTGATGTAATGTAACTTAGTTGTATTCCAACT
1 AAGTTGATGTAATGT-ACTTAGTTGTATTCCAACT
* * * **
61488781 AAGTT--TGTTAGTGGTA-GTAGGTTGTGATT-TATTT
1 AAGTTGATG-TAAT-GTACTTA-GTTGT-ATTCCAACT
61488815 AAAGTTGATGTAATGTCACTTAGTTGTATTCCAACT
1 -AAGTTGATGTAATGT-ACTTAGTTGTATTCCAACT
61488851 AAGTT
1 AAGTT
61488856 TGTTAGTGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 4 0.07
34 11 0.20
35 25 0.45
36 11 0.20
37 4 0.07
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (34 bp):
AAGTTGATGTAATGTACTTAGTTGTATTCCAACT
Found at i:61493209 original size:35 final size:35
Alignment explanation
Indices: 61493170--61493279 Score: 86
Period size: 35 Copynumber: 3.1 Consensus size: 35
61493160 TATTCCAACT
61493170 AAGTTTGTTAGTGGTAGTAGGTTGTGATTTATTTA
1 AAGTTTGTTAGTGGTAGTAGGTTGTGATTTATTTA
* * * **
61493205 AAG-TTGATGTAAT-GTCACTTA-GTTGT-ATTCCAACT-
1 AAGTTTG-T-TAGTGGT-A-GTAGGTTGTGATT-TATTTA
*
61493240 AAGTTTGCTAGTGGTAGTAGGTTGTGATTTATTTA
1 AAGTTTGTTAGTGGTAGTAGGTTGTGATTTATTTA
61493275 AAGTT
1 AAGTT
61493280 GATGTAATGT
Statistics
Matches: 54, Mismatches: 11, Indels: 20
0.64 0.13 0.24
Matches are distributed among these distances:
33 2 0.04
34 14 0.26
35 22 0.41
36 14 0.26
37 2 0.04
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (35 bp):
AAGTTTGTTAGTGGTAGTAGGTTGTGATTTATTTA
Found at i:61493230 original size:36 final size:36
Alignment explanation
Indices: 61493190--61493300 Score: 99
Period size: 35 Copynumber: 3.1 Consensus size: 36
61493180 GTGGTAGTAG
61493190 GTTGTGATTTATTTAAAGTTGATGTAATGTCACTTA
1 GTTGTGATTTATTTAAAGTTGATGTAATGTCACTTA
* ** * *
61493226 GTTGT-ATTCCAACT-AAGTT--TGCTAGTGGT-A-GTA
1 GTTGTGATT-TATTTAAAGTTGATG-TAAT-GTCACTTA
61493259 GGTTGTGATTTATTTAAAGTTGATGTAATGTCACTTA
1 -GTTGTGATTTATTTAAAGTTGATGTAATGTCACTTA
61493296 GTTGT
1 GTTGT
61493301 ATTCCAACTA
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 4 0.07
34 11 0.20
35 20 0.36
36 16 0.29
37 4 0.07
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (36 bp):
GTTGTGATTTATTTAAAGTTGATGTAATGTCACTTA
Found at i:61493240 original size:70 final size:70
Alignment explanation
Indices: 61493127--61493338 Score: 399
Period size: 70 Copynumber: 3.0 Consensus size: 70
61493117 TGTTTTATTT
61493127 TTTATTTAAAGTTGATGTAATGT-AGCTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGG
1 TTTATTTAAAGTTGATGTAATGTCA-CTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGG
61493191 TTGTGA
65 TTGTGA
*
61493197 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCCAACTAAGTTTGCTAGTGGTAGTAGGT
1 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGT
61493262 TGTGA
66 TGTGA
61493267 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGT
1 TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGT
61493332 TGTGA
66 TGTGA
61493337 TT
1 TT
61493339 AGGTTAACCT
Statistics
Matches: 139, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
70 138 0.99
71 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.44
Consensus pattern (70 bp):
TTTATTTAAAGTTGATGTAATGTCACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGT
TGTGA
Found at i:61493314 original size:35 final size:35
Alignment explanation
Indices: 61493205--61493314 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 35
61493195 GATTTATTTA
61493205 AAGTTGATGTAATGTCACTTAGTTGTATTCCAACT
1 AAGTTGATGTAATGTCACTTAGTTGTATTCCAACT
* * * **
61493240 AAGTT--TGCTAGTGGT-A-GTAGGTTGTGATT-TATTT
1 AAGTTGATG-TAAT-GTCACTTA-GTTGT-ATTCCAACT
61493274 AAAGTTGATGTAATGTCACTTAGTTGTATTCCAACT
1 -AAGTTGATGTAATGTCACTTAGTTGTATTCCAACT
61493310 AAGTT
1 AAGTT
61493315 TGTTAGTGGT
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 4 0.07
34 11 0.20
35 25 0.45
36 11 0.20
37 4 0.07
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (35 bp):
AAGTTGATGTAATGTCACTTAGTTGTATTCCAACT
Found at i:61494143 original size:35 final size:34
Alignment explanation
Indices: 61494104--61494213 Score: 84
Period size: 35 Copynumber: 3.1 Consensus size: 34
61494094 ACCACTAACA
61494104 AACTTAGTTGGAATACAACTAAGTGACATTACATC
1 AACTTAGTT-GAATACAACTAAGTGACATTACATC
** * * *
61494139 AACTTTAAATAAATCACAACCT-ACT-ACCACTA-A-C
1 AAC-TTAGTTGAAT-ACAA-CTAAGTGA-CATTACATC
61494173 AAACTTAGTTAGAATACAACTAAGTGACATTACATC
1 -AACTTAGTT-GAATACAACTAAGTGACATTACATC
61494209 AACTT
1 AACTT
61494214 TAAATAAATC
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
33 2 0.04
34 15 0.27
35 21 0.38
36 15 0.27
37 2 0.04
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (34 bp):
AACTTAGTTGAATACAACTAAGTGACATTACATC
Found at i:61494158 original size:36 final size:36
Alignment explanation
Indices: 61494118--61494228 Score: 108
Period size: 36 Copynumber: 3.1 Consensus size: 36
61494108 TAGTTGGAAT
61494118 ACAACTAAGTGACATTACATCAACTTTAAATAAATC
1 ACAACTAAGTGACATTACATCAACTTTAAATAAATC
* * **
61494154 ACAACCT-ACT-ACCACTA-A-CAAAC-TTAGTTAGAAT-
1 ACAA-CTAAGTGA-CATTACATC-AACTTTAAATA-AATC
61494188 ACAACTAAGTGACATTACATCAACTTTAAATAAATC
1 ACAACTAAGTGACATTACATCAACTTTAAATAAATC
61494224 ACAAC
1 ACAAC
61494229 CTACTACCAC
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
33 2 0.04
34 16 0.28
35 16 0.28
36 21 0.37
37 2 0.04
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (36 bp):
ACAACTAAGTGACATTACATCAACTTTAAATAAATC
Found at i:61494161 original size:70 final size:70
Alignment explanation
Indices: 61494080--61494291 Score: 388
Period size: 70 Copynumber: 3.0 Consensus size: 70
61494070 AGGTTAACCT
61494080 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
61494145 AAATA
66 AAATA
*
61494150 AATCACAACCTACTACCACTAACAAACTTAGTTAGAATACAACTAAGTGACATTACATCAACTTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
61494215 AAATA
66 AAATA
* * *
61494220 AATCACAACCTACTACCACTAACAAACTTAGTTGAAATACAACTAAGTTATATTACATCAACTTT
1 AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
61494285 AAATA
66 AAATA
61494290 AA
1 AA
61494292 AAATAAAACA
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 137 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (70 bp):
AATCACAACCTACTACCACTAACAAACTTAGTTGGAATACAACTAAGTGACATTACATCAACTTT
AAATA
Found at i:61494192 original size:34 final size:34
Alignment explanation
Indices: 61494084--61494262 Score: 97
Period size: 34 Copynumber: 5.1 Consensus size: 34
61494074 TAACCTAATC
*
61494084 ACAACCTACTACCACTAACAAACTTAGTTGGAAT
1 ACAACCTACTACCACTAACAAACTTAGTTAGAAT
* * **
61494118 ACAA-CTAAGTGA-CA-TTACATCAACTTTAAATA-AAT
1 ACAACCT-ACT-ACCACTAACA--AAC-TTAGTTAGAAT
61494153 CACAACCTACTACCACTAACAAACTTAGTTAGAAT
1 -ACAACCTACTACCACTAACAAACTTAGTTAGAAT
* * **
61494188 ACAA-CTAAGTGA-CA-TTACATCAACTTTAAATA-AAT
1 ACAACCT-ACT-ACCACTAACA--AAC-TTAGTTAGAAT
61494223 CACAACCTACTACCACTAACAAACTTAGTT-GAAAT
1 -ACAACCTACTACCACTAACAAACTTAGTTAG-AAT
61494258 ACAAC
1 ACAAC
61494263 TAAGTTATAT
Statistics
Matches: 107, Mismatches: 17, Indels: 42
0.64 0.10 0.25
Matches are distributed among these distances:
33 12 0.11
34 30 0.28
35 28 0.26
36 25 0.23
37 12 0.11
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (34 bp):
ACAACCTACTACCACTAACAAACTTAGTTAGAAT
Found at i:61494248 original size:35 final size:35
Alignment explanation
Indices: 61494139--61494248 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 35
61494129 ACATTACATC
61494139 AACTTTAAATAAATCACAACCTACTACCACTAACA
1 AACTTTAAATAAATCACAACCTACTACCACTAACA
** * *
61494174 AAC-TTAGTTAGAAT-ACAA-CTAAGTGA-CA-TTACA
1 AACTTTAAATA-AATCACAACCT-ACT-ACCACTAACA
61494207 TCAACTTTAAATAAATCACAACCTACTACCACTAACA
1 --AACTTTAAATAAATCACAACCTACTACCACTAACA
61494244 AACTT
1 AACTT
61494249 AGTTGAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
33 6 0.11
34 13 0.23
35 19 0.33
36 13 0.23
37 6 0.11
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (35 bp):
AACTTTAAATAAATCACAACCTACTACCACTAACA
Found at i:61501422 original size:67 final size:67
Alignment explanation
Indices: 61501335--61501470 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
61501325 ACCTAATCAC
* * *
61501335 AACCTACTACCACTAGCAAACTTAGTTGGAATACAACTAAGTTACATTACATCAATTTAAAATAC
1 AACCTACTACCACTAACAAACTTAGTTGGAATACAACCAAGTTACATTACATCAACTTAAAATAC
61501400 AA
66 AA
61501402 AACCTACTACCACTAACAAACTTAGTTGGAATACAACCAAGTTACATTACATCAACTTAAAATAC
1 AACCTACTACCACTAACAAACTTAGTTGGAATACAACCAAGTTACATTACATCAACTTAAAATAC
61501467 AA
66 AA
61501469 AA
1 AA
61501471 TAAAATAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (67 bp):
AACCTACTACCACTAACAAACTTAGTTGGAATACAACCAAGTTACATTACATCAACTTAAAATAC
AA
Found at i:61501843 original size:54 final size:54
Alignment explanation
Indices: 61501781--61501890 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
61501771 GTTTAGGAGA
61501781 TTAGACGTTTTTAGTAGAGTACAAAGAAAGGAATCTTATTATAAATAATAATGT
1 TTAGACGTTTTTAGTAGAGTACAAAGAAAGGAATCTTATTATAAATAATAATGT
61501835 TTAGACGTTTTTAGTAGAGTACAAAGAAAGGAATCTTATTATAAATAATAATGT
1 TTAGACGTTTTTAGTAGAGTACAAAGAAAGGAATCTTATTATAAATAATAATGT
61501889 TT
1 TT
61501891 TTCTTGTTGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.36
Consensus pattern (54 bp):
TTAGACGTTTTTAGTAGAGTACAAAGAAAGGAATCTTATTATAAATAATAATGT
Found at i:61506547 original size:67 final size:67
Alignment explanation
Indices: 61506439--61506574 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
61506429 TTTTATTTTA
*
61506439 TTTTGTATTTTAAGTTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTA
1 TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTA
61506504 GG
66 GG
61506506 TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTA
1 TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTA
61506571 GG
66 GG
61506573 TT
1 TT
61506575 GTGATTAGGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (67 bp):
TTTTGTATTTTAAATTGATGTAATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTA
GG
Found at i:61510335 original size:17 final size:18
Alignment explanation
Indices: 61510301--61510338 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
61510291 ATTTGGTCCT
61510301 AAATCTAAAAATAGAAAA
1 AAATCTAAAAATAGAAAA
* *
61510319 AAAT-TAAAATTATAAAA
1 AAATCTAAAAATAGAAAA
61510336 AAA
1 AAA
61510339 AAATTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AAATCTAAAAATAGAAAA
Found at i:61515759 original size:2 final size:2
Alignment explanation
Indices: 61515752--61515778 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61515742 GACAGAACAA
61515752 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
61515779 GGCGATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61520914 original size:2 final size:2
Alignment explanation
Indices: 61520907--61520931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61520897 TTGAACCTAC
61520907 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 T
61520932 GACAATTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61521822 original size:21 final size:22
Alignment explanation
Indices: 61521798--61521841 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
61521788 TTATTTCGAA
61521798 TATATAACATAGGTTTA-GACT
1 TATATAACATAGGTTTACGACT
*
61521819 TATATAGCATAGGTTTACGACT
1 TATATAACATAGGTTTACGACT
61521841 T
1 T
61521842 TCATAAGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
TATATAACATAGGTTTACGACT
Found at i:61528356 original size:17 final size:18
Alignment explanation
Indices: 61528326--61528359 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61528316 GATGTGATTT
*
61528326 TTTTTAAAGGTATTTTTA
1 TTTTTAAAGATATTTTTA
61528344 TTTTTAAA-ATATTTTT
1 TTTTTAAAGATATTTTT
61528360 CGACATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
TTTTTAAAGATATTTTTA
Found at i:61531619 original size:28 final size:28
Alignment explanation
Indices: 61531579--61531680 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
61531569 ATACTTACTT
*
61531579 TGTGTTTACTGTCCCGACAAG-CTCTATC
1 TGTGTTTATTGTCCCGA-AAGACTCTATC
* **
61531607 TGTGTTTATTGTCGCGATGGACTCTATC
1 TGTGTTTATTGTCCCGAAAGACTCTATC
* * **
61531635 TGTATTTATTGTCGCGATGGACTATCTATTC
1 TGTGTTTATTGTCCCGAAAGAC--TCTA-TC
61531666 TGTGTTTATTGTCCC
1 TGTGTTTATTGTCCC
61531681 AATGAACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.02
28 43 0.68
30 4 0.06
31 15 0.24
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (28 bp):
TGTGTTTATTGTCCCGAAAGACTCTATC
Found at i:61531690 original size:31 final size:30
Alignment explanation
Indices: 61531601--61531678 Score: 124
Period size: 28 Copynumber: 2.6 Consensus size: 30
61531591 CCCGACAAGC
61531601 TCTATCTGTGTTTATTGTCGCGATGGAC--
1 TCTATCTGTGTTTATTGTCGCGATGGACTA
*
61531629 TCTATCTGTATTTATTGTCGCGATGGACTA
1 TCTATCTGTGTTTATTGTCGCGATGGACTA
61531659 TCTATTCTGTGTTTATTGTC
1 TCTA-TCTGTGTTTATTGTC
61531679 CCAATGAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 27 0.60
30 4 0.09
31 14 0.31
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (30 bp):
TCTATCTGTGTTTATTGTCGCGATGGACTA
Found at i:61538485 original size:21 final size:22
Alignment explanation
Indices: 61538455--61538504 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
61538445 AATAAAATTA
*
61538455 TTAAAAAATT-TATTTTTTAAC
1 TTAAATAATTGTATTTTTTAAC
* *
61538476 TTAAATAATTGTTTTTTTTTAC
1 TTAAATAATTGTATTTTTTAAC
61538498 TATAAAT
1 T-TAAAT
61538505 TTACCTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAAATAATTGTATTTTTTAAC
Found at i:61539937 original size:9 final size:9
Alignment explanation
Indices: 61539920--61539956 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
61539910 TGAGTTTTCG
61539920 AATTCGAAT
1 AATTCGAAT
*
61539929 AACTCGAAT
1 AATTCGAAT
61539938 AATTCGAAT
1 AATTCGAAT
61539947 AATTCGAAT
1 AATTCGAAT
61539956 A
1 A
61539957 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:61543757 original size:14 final size:14
Alignment explanation
Indices: 61543738--61543777 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
61543728 TTGATTGCCA
61543738 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
61543752 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
61543766 GGAAAATGTTTT
1 GTAAAATGTTTT
61543778 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:61543786 original size:20 final size:20
Alignment explanation
Indices: 61543761--61543800 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61543751 CGTAAAATGA
*
61543761 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
61543781 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
61543801 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:61543790 original size:34 final size:35
Alignment explanation
Indices: 61543746--61543812 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
61543736 CAGTAAAATG
*
61543746 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
61543780 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
61543813 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:61543816 original size:14 final size:15
Alignment explanation
Indices: 61543740--61543816 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
61543730 GATTGCCAGT
* *
61543740 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
61543754 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
61543768 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
61543788 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
61543803 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
61543817 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:61546342 original size:20 final size:21
Alignment explanation
Indices: 61546317--61546363 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
61546307 AAAAATATAA
61546317 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTGAAATTTTTGA-AAATT
61546337 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
61546357 ATTTTGA
1 ATTTTGA
61546364 TTATTTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:61549731 original size:21 final size:22
Alignment explanation
Indices: 61549707--61549750 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
61549697 GTCGAGTTGG
61549707 TTTTAT-TCAATTTTGGGTTTT
1 TTTTATATCAATTTTGGGTTTT
* * *
61549728 TTTTCTATGACTTTTGGGTTTT
1 TTTTATATCAATTTTGGGTTTT
61549750 T
1 T
61549751 GTCATTTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.11, C:0.07, G:0.16, T:0.66
Consensus pattern (22 bp):
TTTTATATCAATTTTGGGTTTT
Found at i:61549857 original size:16 final size:16
Alignment explanation
Indices: 61549836--61549878 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
61549826 CAAATTTAAG
61549836 TCATTT-TAAGTTCAAA
1 TCATTTCTAA-TTCAAA
61549852 TCATTTCTAATTCAAA
1 TCATTTCTAATTCAAA
*
61549868 TCATCTCTAAT
1 TCATTTCTAAT
61549879 ATGACCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (16 bp):
TCATTTCTAATTCAAA
Found at i:61549986 original size:2 final size:2
Alignment explanation
Indices: 61549979--61550029 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
61549969 ATAAGAACAA
61549979 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
61550021 AT AT AT AT A
1 AT AT AT AT A
61550030 ATGGGGATAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61581927 original size:31 final size:32
Alignment explanation
Indices: 61581892--61581968 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
61581882 TTTCAAAATT
61581892 TTTAGATTATTTTGAGTTG-A-TTAATTTTGAG
1 TTTAGATTATTTTGAGTTGAAGTT-ATTTTGAG
* *
61581923 TTTAGATTGTTTTAAGTTGAAGTTATTTTGAG
1 TTTAGATTATTTTGAGTTGAAGTTATTTTGAG
*
61581955 TTCAGATTATTTTG
1 TTTAGATTATTTTG
61581969 GTCGGGTCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 17 0.44
32 20 0.51
33 2 0.05
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.55
Consensus pattern (32 bp):
TTTAGATTATTTTGAGTTGAAGTTATTTTGAG
Found at i:61581964 original size:16 final size:15
Alignment explanation
Indices: 61581893--61581968 Score: 75
Period size: 16 Copynumber: 4.9 Consensus size: 15
61581883 TTCAAAATTT
61581893 TTAGATTATTTTGAG
1 TTAGATTATTTTGAG
61581908 TT-GATTAATTTTGAG
1 TTAGATT-ATTTTGAG
* *
61581923 TTTAGATTGTTTTAAG
1 -TTAGATTATTTTGAG
61581939 TT-GAAGTTATTTTGAG
1 TTAG-A-TTATTTTGAG
61581955 TTCAGATTATTTTG
1 TT-AGATTATTTTG
61581969 GTCGGGTCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.10
15 13 0.26
16 26 0.52
17 5 0.10
18 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.20, T:0.54
Consensus pattern (15 bp):
TTAGATTATTTTGAG
Found at i:61588593 original size:2 final size:2
Alignment explanation
Indices: 61588586--61588619 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61588576 TCAAAAGAGA
61588586 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
61588620 TGGATTTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61590417 original size:17 final size:17
Alignment explanation
Indices: 61590381--61590413 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
61590371 AAGAATTTTT
61590381 TAAGTAAAAATATAATA
1 TAAGTAAAAATATAATA
61590398 TAAGT-AAAATATAATA
1 TAAGTAAAAATATAATA
61590414 ATAATTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAGTAAAAATATAATA
Found at i:61591856 original size:2 final size:2
Alignment explanation
Indices: 61591849--61591878 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61591839 ATATGTTTGA
61591849 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
61591879 TTGTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61592017 original size:2 final size:2
Alignment explanation
Indices: 61592010--61592039 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
61592000 NNNGTTTGTA
61592010 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
61592040 TTGAATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61593953 original size:23 final size:23
Alignment explanation
Indices: 61593921--61594018 Score: 160
Period size: 23 Copynumber: 4.3 Consensus size: 23
61593911 ATAAGTGCAA
*
61593921 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
**
61593944 CACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
61593967 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
61593990 CACTGAAACGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
61594013 CACTGA
1 CACTGA
61594019 TCAATAACAC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:61599922 original size:12 final size:12
Alignment explanation
Indices: 61599889--61599924 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
61599879 TCATAATTAG
61599889 TTTAATTTAATAT
1 TTTAATTTAAT-T
61599902 TTTAA-TTAATT
1 TTTAATTTAATT
61599913 TTTAATTTAATT
1 TTTAATTTAATT
61599925 AATAAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.27
12 11 0.50
13 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAATTTAATT
Done.