Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 409 of 410
Found at i:123412057 original size:3 final size:3
Alignment explanation
Indices: 123412049--123412101 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
123412039 TTAGTGTTCT
123412049 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
123412097 TAA TA
1 TAA TA
123412102 GGCACCGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:123416618 original size:237 final size:236
Alignment explanation
Indices: 123416204--123416684 Score: 689
Period size: 237 Copynumber: 2.0 Consensus size: 236
123416194 ATCAGGTTAG
* *
123416204 AAACTTAAGCCATGTGACCCCAATACAATGCAAACACCATTCCCTACAGAAATCACTTCAAATAA
1 AAACTTAAGCCATGCGACCCCAATACAATGCAAACACCATTCCCTACAGAAATCACTTAAAATAA
* * *
123416269 GTTCCAATTAACCACCTCTAATGACATATTCCAAGAGGGTGGTAATAGTTACACGTATTATACCC
66 GTTCCAATTAACCACCTCTAATGACATATTCCAAGAGGGTGCTAATAGTTACACGTATCAAACCC
* *
123416334 AAACCAAATTCATAAAGGAATTGAACAAACCACGAATGCAAACAATAACCAT-AGCAACCTAAAG
131 AAACCAAATTCATAAAAGAATTGAACAAACCACGAATGCAAACAATAACC-TGAGCAACCCAAAG
*
123416398 ATACAATACTACAAACTATATAACAACTAAGCTAAGAATACA
195 ATAAAATACTACAAACTATATAACAACTAAGCTAAGAATACA
* * * * * *
123416440 AAACTTAAGCCATGCGACTCCAATACCATTGGAAACACCATTGCCTACGGAAATTACTTAAAATA
1 AAACTTAAGCCATGCGACCCCAATA-CAATGCAAACACCATTCCCTACAGAAATCACTTAAAATA
* * *
123416505 AGTTCCGATTAACCGCCTCTAATGACATATTCGAAGAGGGTGCTAATAGTTAGC-CGTA-CAAAC
65 AGTTCCAATTAACCACCTCTAATGACATATTCCAAGAGGGTGCTAATAGTTA-CACGTATCAAAC
* **
123416568 CCAAACCAAGTTCATAAAAGAATTGAAACAAACCATTAATGCAAACAATAACCTGAGCAACCCAA
129 CCAAACCAAATTCATAAAAGAATTG-AACAAACCACGAATGCAAACAATAACCTGAGCAACCCAA
* * *
123416633 AGATAAAATGCTATAAACTATATAACAACTAAGCTAAGAATATA
193 AGATAAAATACTACAAACTATATAACAACTAAGCTAAGAATACA
*
123416677 AAAGTTAA
1 AAACTTAA
123416685 AACTTCAATA
Statistics
Matches: 217, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
236 50 0.23
237 166 0.76
238 1 0.00
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (236 bp):
AAACTTAAGCCATGCGACCCCAATACAATGCAAACACCATTCCCTACAGAAATCACTTAAAATAA
GTTCCAATTAACCACCTCTAATGACATATTCCAAGAGGGTGCTAATAGTTACACGTATCAAACCC
AAACCAAATTCATAAAAGAATTGAACAAACCACGAATGCAAACAATAACCTGAGCAACCCAAAGA
TAAAATACTACAAACTATATAACAACTAAGCTAAGAATACA
Found at i:123419204 original size:21 final size:20
Alignment explanation
Indices: 123419165--123419204 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
123419155 ATGTTGGGGA
*
123419165 TTTTGAAGGTGCTTTGAAGG
1 TTTTGAAGGTGATTTGAAGG
*
123419185 TTTTGAATGTGATGTTGAAG
1 TTTTGAAGGTGAT-TTGAAG
123419205 AGTCGGCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.42
Consensus pattern (20 bp):
TTTTGAAGGTGATTTGAAGG
Found at i:123433611 original size:88 final size:88
Alignment explanation
Indices: 123433497--123433678 Score: 337
Period size: 88 Copynumber: 2.1 Consensus size: 88
123433487 ATAATAACTC
*
123433497 AACATTGGTACCAATTTAATAGTAAATATTCTAAATTTGGACAAATCTAATAGCCAATATATTAT
1 AACATTGGTACCAATTCAATAGTAAATATTCTAAATTTGGACAAATCTAATAGCCAATATATTAT
123433562 CTTAATGAAGACAAATTAACGCA
66 CTTAATGAAGACAAATTAACGCA
* *
123433585 AACATTGGTACCAATTCAATAGTAAATATTCTAAATTTGGACAAATCTAATAGCCGATATATTGT
1 AACATTGGTACCAATTCAATAGTAAATATTCTAAATTTGGACAAATCTAATAGCCAATATATTAT
123433650 CTTAATGAAGACAAATTAACGCA
66 CTTAATGAAGACAAATTAACGCA
123433673 AACATT
1 AACATT
123433679 CATGTAAGAG
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (88 bp):
AACATTGGTACCAATTCAATAGTAAATATTCTAAATTTGGACAAATCTAATAGCCAATATATTAT
CTTAATGAAGACAAATTAACGCA
Found at i:123434526 original size:14 final size:14
Alignment explanation
Indices: 123434507--123434533 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
123434497 TCAACGGTGG
123434507 AGGTATTGTGTCCA
1 AGGTATTGTGTCCA
123434521 AGGTATTGTGTCC
1 AGGTATTGTGTCC
123434534 GAGGAGAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (14 bp):
AGGTATTGTGTCCA
Found at i:123438810 original size:16 final size:18
Alignment explanation
Indices: 123438784--123438816 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
123438774 TACACCATAA
123438784 TAAATTTTTAAA-AAATC
1 TAAATTTTTAAATAAATC
123438801 TAAA-TTTTAAATAAAT
1 TAAATTTTTAAATAAAT
123438817 AAAATTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTTTTAAATAAATC
Found at i:123442483 original size:2 final size:2
Alignment explanation
Indices: 123442476--123442508 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
123442466 AGAGCTAGAT
123442476 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 T
123442509 TACTTAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123446868 original size:29 final size:30
Alignment explanation
Indices: 123446810--123446869 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
123446800 AAGTTAATAT
*
123446810 AATGATAAAATTGTATTTTAACCCTTTAAA
1 AATGATAAAATTGTATTTTAACCCTCTAAA
* *
123446840 AATG-TAAAATT-TATTATTCATCCTCTAAA
1 AATGATAAAATTGTATT-TTAACCCTCTAAA
123446869 A
1 A
123446870 TAATTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 4 0.15
29 18 0.69
30 4 0.15
ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40
Consensus pattern (30 bp):
AATGATAAAATTGTATTTTAACCCTCTAAA
Found at i:123447839 original size:6 final size:6
Alignment explanation
Indices: 123447828--123447863 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
123447818 TATTATGCTA
*
123447828 AATATT AATATT AATATT AATATT AATATA AATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT
123447864 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AATATT
Found at i:123448082 original size:2 final size:2
Alignment explanation
Indices: 123448075--123448103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
123448065 GTAAAATGCA
123448075 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 A
123448104 AAGGAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123449883 original size:13 final size:13
Alignment explanation
Indices: 123449857--123449926 Score: 70
Period size: 13 Copynumber: 5.2 Consensus size: 13
123449847 TATATACATA
*
123449857 TTCAT-TTTATAG
1 TTCATATTTAAAG
123449869 TTCATATTTAAAG
1 TTCATATTTAAAG
*
123449882 TTTATAATTCTAAAG
1 TTCAT-ATT-TAAAG
123449897 TTCATATTTAAAG
1 TTCATATTTAAAG
*
123449910 TTTATAGTTCTAAAG
1 TTCATA-TT-TAAAG
123449925 TT
1 TT
123449927 TACTTGTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
12 5 0.10
13 20 0.41
14 8 0.16
15 16 0.33
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (13 bp):
TTCATATTTAAAG
Found at i:123449897 original size:15 final size:15
Alignment explanation
Indices: 123449877--123449928 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
123449867 AGTTCATATT
123449877 TAAAGTTTATAATTC
1 TAAAGTTTATAATTC
*
123449892 TAAAGTTCAT-ATT-
1 TAAAGTTTATAATTC
*
123449905 TAAAGTTTATAGTTC
1 TAAAGTTTATAATTC
123449920 TAAAGTTTA
1 TAAAGTTTA
123449929 CTTGTGTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 9 0.28
14 5 0.16
15 18 0.56
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (15 bp):
TAAAGTTTATAATTC
Found at i:123449907 original size:28 final size:28
Alignment explanation
Indices: 123449867--123449926 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
123449857 TTCATTTTAT
123449867 AGTTCATATTTAAAGTTTATAATTCTAA
1 AGTTCATATTTAAAGTTTATAATTCTAA
*
123449895 AGTTCATATTTAAAGTTTATAGTTCTAA
1 AGTTCATATTTAAAGTTTATAATTCTAA
123449923 AGTT
1 AGTT
123449927 TACTTGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (28 bp):
AGTTCATATTTAAAGTTTATAATTCTAA
Found at i:123459737 original size:14 final size:14
Alignment explanation
Indices: 123459718--123459750 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
123459708 TGTTTCGTTG
123459718 AAAAT-AATTTTCGA
1 AAAATAAATTTT-GA
123459732 AAAATAAATTTTGA
1 AAAATAAATTTTGA
123459746 AAAAT
1 AAAAT
123459751 GACTTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (14 bp):
AAAATAAATTTTGA
Found at i:123460533 original size:15 final size:15
Alignment explanation
Indices: 123460513--123460593 Score: 60
Period size: 15 Copynumber: 5.3 Consensus size: 15
123460503 TTACTACAAA
123460513 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
123460528 ATATTTATAATTTTAAT
1 ATATTTAT--TATTAAT
*
123460545 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
123460562 ATA-TTAATATTGAAT
1 ATATTTATTATT-AAT
*
123460577 A-ATTT-TTAATAAT
1 ATATTTATTATTAAT
123460590 ATAT
1 ATAT
123460594 GAACAACATT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
13 4 0.08
14 13 0.25
15 16 0.31
17 11 0.21
19 8 0.15
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:123460564 original size:19 final size:17
Alignment explanation
Indices: 123460511--123460560 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
123460501 TTTTACTACA
123460511 AAATATTTATTATTAAT
1 AAATATTTATTATTAAT
*
123460528 --ATATTTATAATTTTAAT
1 AAATATTTAT--TATTAAT
123460545 AAATATTTATTATTAA
1 AAATATTTATTATTAA
123460561 AATATTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 8 0.30
17 11 0.41
19 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATTTATTATTAAT
Found at i:123460572 original size:14 final size:15
Alignment explanation
Indices: 123460510--123460587 Score: 50
Period size: 17 Copynumber: 4.9 Consensus size: 15
123460500 TTTTTACTAC
*
123460510 AAAATATTTATTATT
1 AAAATATTTAATATT
* *
123460525 AATATATTTATAATTTT
1 AAAATA-TT-TAATATT
*
123460542 AATAAATATTTATTATT
1 -A-AAATATTTAATATT
123460559 AAAATA-TTAATATT
1 AAAATATTTAATATT
*
123460573 GAATAATTTTTAATA
1 -AA-AATATTTAATA
123460588 ATATATGAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
14 7 0.15
15 12 0.25
16 6 0.12
17 16 0.33
18 3 0.06
19 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
AAAATATTTAATATT
Found at i:123460625 original size:15 final size:16
Alignment explanation
Indices: 123460605--123460635 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
123460595 AACAACATTA
123460605 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
123460620 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
123460636 AAAATAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:123461165 original size:21 final size:22
Alignment explanation
Indices: 123461139--123461197 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
123461129 GTTTTAAGAA
*
123461139 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
123461160 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
123461182 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
123461198 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:123461212 original size:26 final size:24
Alignment explanation
Indices: 123461168--123461217 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
123461158 ATTTGTTTTA
*
123461168 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
123461192 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
123461218 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:123480031 original size:142 final size:139
Alignment explanation
Indices: 123479836--123480091 Score: 338
Period size: 142 Copynumber: 1.8 Consensus size: 139
123479826 CGTTTTAGCC
* *
123479836 GTTACTCGGAATTCCAGTGTAAATGTCGGAAATGAGTATACCAACAAGGATATATCCATATCCGA
1 GTTACACGGAATTCCAGTGTAAACGTCGGAAATGAGTATACCAACAAGGATATAT-C-TAT---A
* *
123479901 TAACGG-AAAA-AACAGTCAGAGTAACACAGACCATAGCTCCTAAACCCTAAACAAAGTTCAGCT
61 T-ACGGAAAAATAACAGTCAGAGTAACACAAACCATAGCTCATAAACCCTAAACAAAGTTCAGCT
123479964 TTCTCCGCCGTCTAT
125 TTCTCCGCCGTCTAT
* * *
123479979 GTTACACGGAA-TCCGGTGTAAACGTCGGAAATGAGTATACCAACACGTATATATCTATATACGG
1 GTTACACGGAATTCCAGTGTAAACGTCGGAAATGAGTATACCAACAAGGATATATCTATATACGG
* * * *
123480043 AAAAATAAGAGTCGGAGTAACATAAACCATAGCTCATATACCCTAAACA
66 AAAAATAACAGTCAGAGTAACACAAACCATAGCTCATAAACCCTAAACA
123480092 TTAAATACAA
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
136 4 0.04
137 6 0.06
138 37 0.37
140 3 0.03
141 1 0.01
142 39 0.39
143 10 0.10
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (139 bp):
GTTACACGGAATTCCAGTGTAAACGTCGGAAATGAGTATACCAACAAGGATATATCTATATACGG
AAAAATAACAGTCAGAGTAACACAAACCATAGCTCATAAACCCTAAACAAAGTTCAGCTTTCTCC
GCCGTCTAT
Found at i:123480252 original size:14 final size:14
Alignment explanation
Indices: 123480233--123480265 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
123480223 TACAACAAGG
123480233 ATATCAACTTTATC
1 ATATCAACTTTATC
123480247 ATATCAACTTTATC
1 ATATCAACTTTATC
123480261 A-ATCA
1 ATATCA
123480266 TTATCAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATCAACTTTATC
Found at i:123484770 original size:105 final size:105
Alignment explanation
Indices: 123484582--123484771 Score: 299
Period size: 105 Copynumber: 1.8 Consensus size: 105
123484572 CCGTCAGCAA
123484582 AGTTTGCCACACCAATTCAGATTGTCACCTACACCATCTATTGGTACATTATCGGATACACCTAT
1 AGTTTGCCACACCAATTCAGATTGTCACCTACACCATCTATTGGTACATTATCGGATACACCTAT
* *
123484647 GACGGGGCAGAAACGAGATGTATTTGAGAAGAGTATTGAG
66 GACGGGACAGAAAAGAGATGTATTTGAGAAGAGTATTGAG
* ** * * *
123484687 AGTTTGCCACAGCAATTTGGGTTGTCACCTACCCCATCTATTGGTACGTTATCGGATACACCTAT
1 AGTTTGCCACACCAATTCAGATTGTCACCTACACCATCTATTGGTACATTATCGGATACACCTAT
*
123484752 GACGGGACGGAAAAGAGATG
66 GACGGGACAGAAAAGAGATG
123484772 CTCAAGATGC
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 76 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (105 bp):
AGTTTGCCACACCAATTCAGATTGTCACCTACACCATCTATTGGTACATTATCGGATACACCTAT
GACGGGACAGAAAAGAGATGTATTTGAGAAGAGTATTGAG
Found at i:123499287 original size:15 final size:17
Alignment explanation
Indices: 123499259--123499291 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
123499249 AAGTGTTTTT
123499259 ATTTTTTATATTAAATA
1 ATTTTTTATATTAAATA
123499276 ATTTTTT-T-TTAAATA
1 ATTTTTTATATTAAATA
123499291 A
1 A
123499292 CCATACACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTTATATTAAATA
Found at i:123523569 original size:115 final size:108
Alignment explanation
Indices: 123523400--123523625 Score: 303
Period size: 115 Copynumber: 2.0 Consensus size: 108
123523390 CCTTGGCGGT
* *
123523400 AAATTCATGGCTGGATCAAATTGTTGATTAGGATATTTTGCTGGGATTCTTTATATAAAATTTAT
1 AAATGCATGGCTGGATCAAATTGTTGATTAGGATATTTAGCTGGGATTCTTTATATAAAATTTA-
* * *
123523465 TTATTTATTTATGAATTTTCTGACTCAAGCTCATATATTTTATATAAGG
65 TT-TTT-TGTA--AATTTGCTGACTCAAGCTCATATATTCTATAT-AGG
123523514 AAATGCATGGCTGGATC-AATATGTTGAATTAGGATATTTAGCTGGGATTAC-TTATATAAAATT
1 AAATGCATGGCTGGATCAAAT-TGTTG-ATTAGGATATTTAGCTGGGATT-CTTTATATAAAATT
*
123523577 TATTTTTTGTAAATTTGCTGACTCAAGTTCATATATTCTATATAGG
63 TATTTTTTGTAAATTTGCTGACTCAAGCTCATATATTCTATATAGG
123523623 AAA
1 AAA
123523626 ATAGCGAGTG
Statistics
Matches: 103, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
109 6 0.06
110 29 0.28
112 3 0.03
113 6 0.06
114 23 0.22
115 35 0.34
116 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (108 bp):
AAATGCATGGCTGGATCAAATTGTTGATTAGGATATTTAGCTGGGATTCTTTATATAAAATTTAT
TTTTTGTAAATTTGCTGACTCAAGCTCATATATTCTATATAGG
Found at i:123524949 original size:213 final size:204
Alignment explanation
Indices: 123524569--123525139 Score: 605
Period size: 213 Copynumber: 2.7 Consensus size: 204
123524559 CATTTTTGTG
* * * * * *
123524569 GATACGAGGACAAACCTCCAAAGATG---CAAATGCATAGAAAACCTTTAAAAAAAGTTATCTAT
1 GATATGAGGACATACCTCCAAAGATGCTCCGAATGCATAGAAAACCTTTAAAAAAAATGATCCAT
* * *
123524631 ATCTGTGTCTGACACACACACTTGAGTCTGAGTCAGAGGTTCACGAACCACCAATTA-TGTTATT
66 ATCTGTGTCTGACACTCACACTTGAGTC-----C-GAGGTTCATGAACCACCAATTAGTGTAATT
* ** *
123524695 GTATATTGTATATT-GTTGTTCATTACTCATTGTTCATGTTGCTCCAACTTTTCATTTTTCTGGA
125 -T-TATTGT-TGTTCGTTACTCATTACTCATTGTCCATGTTGCTCCAACTTTTCATTTTTCTGGA
* *
123524759 TATACCTGTGTTTTTAACAAATG
187 TATACCTATG---TTAA-AAA-C
* *
123524782 GATATGAGGCCGTACCTCCAAAGATGCTCCGAATGCATAGAAAACCTTTAAAGAAAAATGATCCA
1 GATATGAGGACATACCTCCAAAGATGCTCCGAATGCATAGAAAACCTTTAAA-AAAAATGATCCA
* *
123524847 TATCTATGTTTGACACTCACACTTGAGTCCGAGGTTCATGAACCACCAATTAGTGTAATTTTATT
65 TATCTGTGTCTGACACTCACACTTGAGTCCGAGGTTCATGAACCACCAATTAGTGTAATTTTATT
* * * *
123524912 GTTGTTCGTAACTCATTGATTGTCATTGTCCATGTTGCTCTAACTTTTCATTTTTGTGGATATAC
130 GTTGTTCGTTACTCATT-A--CTCATTGTCCATGTTGCTCCAACTTTTCATTTTTCTGGATATAC
* *
123524977 CTATGTTGAATAC
192 CTATGTTAAAAAC
*
123524990 GATATGAGGACATACCTCCAAAGATGCTCCGAATGCATAGAAAACCTTAAAAAAGAATATGATCT
1 GATATGAGGACATACCTCCAAAGATGCTCCGAATGCATAGAAAACCTTTAAAAA-AA-ATGATC-
* * * *
123525055 C-TATCTGTGTCTGACACTCACGTGAGTCCGAGTCAGAGGTTCATGAACCACCAATTAGTGTATT
63 CATATCTGTGTCTGACACTCAC---ACT-TGAGTCCGAGGTTCATGAACCACCAATTAGTGTAAT
123525119 TTTATTGTTGTTCGTTACTCA
124 TTTATTGTTGTTCGTTACTCA
123525140 CTGTTCATGT
Statistics
Matches: 307, Mismatches: 35, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
207 2 0.01
208 51 0.17
209 29 0.09
210 17 0.06
211 23 0.07
212 9 0.03
213 119 0.39
216 22 0.07
217 35 0.11
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (204 bp):
GATATGAGGACATACCTCCAAAGATGCTCCGAATGCATAGAAAACCTTTAAAAAAAATGATCCAT
ATCTGTGTCTGACACTCACACTTGAGTCCGAGGTTCATGAACCACCAATTAGTGTAATTTTATTG
TTGTTCGTTACTCATTACTCATTGTCCATGTTGCTCCAACTTTTCATTTTTCTGGATATACCTAT
GTTAAAAAC
Found at i:123526384 original size:3 final size:3
Alignment explanation
Indices: 123526376--123526415 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
123526366 GAACATATAT
123526376 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
123526416 CGTATTGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:123528252 original size:4 final size:4
Alignment explanation
Indices: 123528243--123528271 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
123528233 CTTGGGTTAT
123528243 TTAA TTAA TTAA TTAA TTAA TT-A TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
123528272 GTTCACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (4 bp):
TTAA
Found at i:123532465 original size:19 final size:19
Alignment explanation
Indices: 123532441--123532477 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
123532431 TCACTCTGAC
*
123532441 ATACTCTTAATGATGATAT
1 ATACTCTTAACGATGATAT
123532460 ATACTCTTAACGATGATA
1 ATACTCTTAACGATGATA
123532478 AAGATGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
ATACTCTTAACGATGATAT
Found at i:123535899 original size:2 final size:2
Alignment explanation
Indices: 123535892--123535923 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
123535882 TAGAAGATGC
123535892 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
123535924 GACCTGGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:123537323 original size:39 final size:37
Alignment explanation
Indices: 123537266--123537340 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 37
123537256 GAGATTTCTC
123537266 AAATTTGGTCACTCCCTGAAAGAAATTTATGTTATTT
1 AAATTTGGTCACTCCCTGAAAGAAATTTATGTTATTT
* *
123537303 AAATTTAGAGTCACTTCCTGAAATAAATTTATGTTATT
1 AAATTT-G-GTCACTCCCTGAAAGAAATTTATGTTATT
123537341 CGAATTCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 6 0.18
38 1 0.03
39 27 0.79
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (37 bp):
AAATTTGGTCACTCCCTGAAAGAAATTTATGTTATTT
Found at i:123538615 original size:31 final size:31
Alignment explanation
Indices: 123538577--123538636 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
123538567 CTAATGGCCG
* *
123538577 AAAAAGAAAAA-TTCTAATATTTGGGTGACCA
1 AAAAAGAAAAAGTT-AAATAGTTGGGTGACCA
123538608 AAAAAGAAAAAGTTAAATAGTTGGGTGAC
1 AAAAAGAAAAAGTTAAATAGTTGGGTGAC
123538637 TACCGGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (31 bp):
AAAAAGAAAAAGTTAAATAGTTGGGTGACCA
Found at i:123539740 original size:2 final size:2
Alignment explanation
Indices: 123539735--123539766 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
123539725 ATATATATAT
123539735 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
123539767 CATACGCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:123548731 original size:60 final size:60
Alignment explanation
Indices: 123548597--123548732 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 60
123548587 GTTAAAATTG
* * *
123548597 AATAGTTGAGTGA-TCATTTTGTAACTTTTCATAGTAAGGTAACCAAAAAAGAAGTTTACT
1 AATAGTTGGGTGACT-ATTTTGTAACTTTTCATAGTAAGATAACCAAAAAAGAAATTTACT
** * ** * * *
123548657 AATAACTGGATGACTATTTTGTAACTTTTCATAGTTTGATGACTAAAAAAGAAATTTATT
1 AATAGTTGGGTGACTATTTTGTAACTTTTCATAGTAAGATAACCAAAAAAGAAATTTACT
123548717 AATAGTTGGGTGACTA
1 AATAGTTGGGTGACTA
123548733 CTAGTGTAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 60 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (60 bp):
AATAGTTGGGTGACTATTTTGTAACTTTTCATAGTAAGATAACCAAAAAAGAAATTTACT
Found at i:123555916 original size:2 final size:2
Alignment explanation
Indices: 123555909--123555935 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
123555899 CACTCCCTTT
123555909 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
123555936 GCTTCATTGA
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:123557001 original size:2 final size:2
Alignment explanation
Indices: 123556994--123557034 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
123556984 GTTTTAGTGT
* *
123556994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA 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
123557035 GTTGTTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:123557427 original size:3 final size:3
Alignment explanation
Indices: 123557419--123557477 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
123557409 CATTTAACCC
*
123557419 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
123557467 TAT TAT TAT TA
1 TAT TAT TAT TA
123557478 ACAACAACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:123560074 original size:13 final size:12
Alignment explanation
Indices: 123560044--123560082 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
123560034 ATTAATTAAG
123560044 ATTTA-AATAAT
1 ATTTATAATAAT
*
123560055 TTTTATAATATAT
1 ATTTATAATA-AT
123560068 ATTTATAATAAT
1 ATTTATAATAAT
123560080 ATT
1 ATT
123560083 CGTCCCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.17
12 9 0.38
13 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTATAATAAT
Found at i:123560487 original size:2 final size:2
Alignment explanation
Indices: 123560480--123560514 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
123560470 ATTGCACATT
123560480 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 T
123560515 TAATGTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:123563388 original size:30 final size:30
Alignment explanation
Indices: 123563354--123563485 Score: 228
Period size: 30 Copynumber: 4.4 Consensus size: 30
123563344 CCTTCTTGGT
*
123563354 GGTGGAGGTGGTCGTTTCCTTGGTGGCGGA
1 GGTGGAGGTGGTCGTCTCCTTGGTGGCGGA
* *
123563384 GGTGGAGGTGGTTGTCTCCTTGGTGGGGGA
1 GGTGGAGGTGGTCGTCTCCTTGGTGGCGGA
123563414 GGTGGAGGTGGTCGTCTCCTTGGTGGCGGA
1 GGTGGAGGTGGTCGTCTCCTTGGTGGCGGA
*
123563444 GGTGGAGGTGGTCGTCTCCTTGGTGACGGA
1 GGTGGAGGTGGTCGTCTCCTTGGTGGCGGA
123563474 GGTGGAGGTGGT
1 GGTGGAGGTGGT
123563486 GATGATGGAG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 96 1.00
ACGTcount: A:0.08, C:0.13, G:0.52, T:0.28
Consensus pattern (30 bp):
GGTGGAGGTGGTCGTCTCCTTGGTGGCGGA
Found at i:123563502 original size:51 final size:51
Alignment explanation
Indices: 123563441--123563537 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
123563431 CCTTGGTGGC
*
123563441 GGAGGTGGAGGTGGTCGT-CTCCTTGGTGACGGAGGTGGAGGTGGTGATGAT
1 GGAGGTGGAGGTGGTCGTCCT-CGTGGTGACGGAGGTGGAGGTGGTGATGAT
* *
123563492 GGAGGTGGAGGTGGTGGTCCTCGTGGTGATGGAGGTGGAGGTGGTG
1 GGAGGTGGAGGTGGTCGTCCTCGTGGTGACGGAGGTGGAGGTGGTG
123563538 GTCCCCTAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
51 40 0.95
52 2 0.05
ACGTcount: A:0.12, C:0.08, G:0.55, T:0.25
Consensus pattern (51 bp):
GGAGGTGGAGGTGGTCGTCCTCGTGGTGACGGAGGTGGAGGTGGTGATGAT
Found at i:123563508 original size:30 final size:30
Alignment explanation
Indices: 123563484--123563563 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
123563474 GGTGGAGGTG
*
123563484 GTGATGATGGAGGTGGAGGTGGTGGTCCTC
1 GTGATGATGGAGGTGGAGGTGGTGGACCTC
* *
123563514 GTGGTGATGGAGGTGGAGGTGGTGGTCC-C
1 GTGATGATGGAGGTGGAGGTGGTGGACCTC
* *
123563543 CTAGGTGATGGAGGTGGAGGT
1 GT-GATGATGGAGGTGGAGGT
123563564 CTTCTTATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 2 0.04
30 45 0.96
ACGTcount: A:0.14, C:0.09, G:0.53, T:0.25
Consensus pattern (30 bp):
GTGATGATGGAGGTGGAGGTGGTGGACCTC
Found at i:123563526 original size:81 final size:81
Alignment explanation
Indices: 123563411--123563563 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 81
123563401 CCTTGGTGGG
* * * *
123563411 GGAGGTGGAGGTGGTCGTCTCCTTGGTGGCGGAGGTGGAGGTGGTCGTCTCCTTGGTGACGGAGG
1 GGAGGTGGAGGTGGTCGTCTCCGTGGTGACGGAGGTGGAGGTGGTCGTCCCCTAGGTGACGGAGG
123563476 TGGAGGTGGTGATGAT
66 TGGAGGTGGTGATGAT
* * * *
123563492 GGAGGTGGAGGTGGTGGTC-CTCGTGGTGATGGAGGTGGAGGTGGTGGTCCCCTAGGTGATGGAG
1 GGAGGTGGAGGTGGTCGTCTC-CGTGGTGACGGAGGTGGAGGTGGTCGTCCCCTAGGTGACGGAG
123563556 GTGGAGGT
65 GTGGAGGT
123563564 CTTCTTATCA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.02
81 62 0.98
ACGTcount: A:0.12, C:0.11, G:0.52, T:0.25
Consensus pattern (81 bp):
GGAGGTGGAGGTGGTCGTCTCCGTGGTGACGGAGGTGGAGGTGGTCGTCCCCTAGGTGACGGAGG
TGGAGGTGGTGATGAT
Found at i:123564317 original size:22 final size:23
Alignment explanation
Indices: 123564285--123564346 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
123564275 TGTTTTTTTT
123564285 TTATTCAAATAATA-GATTATATA
1 TTATT-AAATAATATGATTATATA
*
123564308 TTATTAAATACAAATGATTATATA
1 TTATTAAATA-ATATGATTATATA
*
123564332 TGTATTTAATAATAT
1 T-TATTAAATAATAT
123564347 TGAAAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 5 0.15
23 7 0.21
24 13 0.39
25 8 0.24
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (23 bp):
TTATTAAATAATATGATTATATA
Found at i:123565501 original size:3 final size:3
Alignment explanation
Indices: 123565493--123565522 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
123565483 GCCCATTCAT
123565493 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
123565523 GGGTTAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:123566567 original size:31 final size:31
Alignment explanation
Indices: 123566527--123566588 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
123566517 TTTATTTTTT
* *
123566527 GAGTTAAATTTGACTC-TCAACTTTTTAAAAA
1 GAGTCAAATTTGA-TCATCAACATTTTAAAAA
123566558 GAGTCAAATTTGATCATCAACATTTTAAAAA
1 GAGTCAAATTTGATCATCAACATTTTAAAAA
123566589 ATAGTTGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (31 bp):
GAGTCAAATTTGATCATCAACATTTTAAAAA
Found at i:123566744 original size:17 final size:18
Alignment explanation
Indices: 123566717--123566754 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
123566707 TTTGATTTTG
123566717 ATTTATTATAAATTATAA
1 ATTTATTATAAATTATAA
* *
123566735 ATTT-TTATAATTTTTAA
1 ATTTATTATAAATTATAA
123566752 ATT
1 ATT
123566755 ATTTGTTAAC
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTATTATAAATTATAA
Found at i:123569405 original size:187 final size:192
Alignment explanation
Indices: 123568982--123569723 Score: 809
Period size: 208 Copynumber: 3.8 Consensus size: 192
123568972 TTTCTTGTCC
* * * *
123568982 AGTCGATATTGTTGTCTTTTGAATGTTTGCCGGCTCTTCAGATTTGAATAATGTCGATTTGTGCT
1 AGTCGATATTGTTGTCTTTTGAATGCTTGCCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
* * * *
123569047 CACGAAGCTGCGCTTAGAAAAGTAGTAGCTTATTTTTAGTTCTAAATTCAGCTTTTGAATTACTA
66 CACGAAGCTGCGCTTAGAAAAATTGTAGTTTATTTTTAGTTCTAAATTCAGCTTTTGAATTACTG
* *
123569112 AT-C-TACGTTCTAATTTCTCTAAATTTTTTTGAATTTTTTCCTTTTTTACAATGATCCGTCACC
131 ATGCGTACGTTCTAATTTCTC---ATCTTTTT---TTTCTTCCTTTTTTACAATGATCCGTCACC
123569175 GCA
190 GCA
* * * *
123569178 AGTCGATATTATTCTCTTTTGAATGCTTGCCGGATCTTCAGATTCGAACAATATCGA-CT-T-CT
1 AGTCGATATTGTTGTCTTTTGAATGCTTGCCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
* *
123569240 CACGAAGGTTCGCTTAGAAAAATTTGTAGTTTATTTTTAGTTCTAAATTCAGCTTTTGAATTACT
66 CACGAAGCTGCGCTTAGAAAAA-TTGTAGTTTATTTTTAGTTCTAAATTCAGCTTTTGAATTACT
* * * *
123569305 GATGCGTACGTTTTGATTTCTC-TGTTTTTTTTCTT-CTTTTTT-TAATGATCCGTCACCGCA
130 GATGCGTACGTTCTAATTTCTCATCTTTTTTTTCTTCCTTTTTTACAATGATCCGTCACCGCA
* * * *
123569365 AGTCGATATTGTTGTCTTTTGAATACTTACCGGCTCTTCAGATTCGAAGAATATCGATTTGTGTT
1 AGTCGATATTGTTGTCTTTTGAATGCTTGCCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
* ** * * *
123569430 CACGAAGCTGCGCTTAGAAATATTGTAGTTTATTTTTTCTTGTACATTCAGCTTTTGCATTACTG
66 CACGAAGCTGCGCTTAGAAAAATTGTAGTTTATTTTTAGTTCTAAATTCAGCTTTTGAATTACTG
* * * * **
123569495 ATGTGTACGTTCTAATTTCTCTTCTTTTTTTTTTTTTGAAATATTTTTCTTTTTCTTTTTTAATG
131 ATGCGTACGTTCTAATTTCTCATC--------TTTTT----T-TTCTTC--CTT-TTTTACAATG
*
123569560 ATCCGTCACTGCA
180 ATCCGTCACCGCA
*
123569573 AGTCGATATTGTTGTCTTTTGAATGCTTGCCGGCTCTTCAGATTCGAACAATACCGATTTGTGCT
1 AGTCGATATTGTTGTCTTTTGAATGCTTGCCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
* * * * * *
123569638 CACGAAACTGCGCCTCGAAAAGTTGTAGTTTA-TTTTAGTTGTAAATTCAGCTTTTAAATTACTG
66 CACGAAGCTGCGCTTAGAAAAATTGTAGTTTATTTTTAGTTCTAAATTCAGCTTTTGAATTACTG
*
123569702 ATGCGTACGTTGTAATTTCTCA
131 ATGCGTACGTTCTAATTTCTCA
123569724 GTTTTTTATT
Statistics
Matches: 461, Mismatches: 60, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
187 68 0.15
188 8 0.02
189 62 0.13
190 21 0.05
192 6 0.01
193 21 0.05
194 43 0.09
195 2 0.00
196 64 0.14
198 5 0.01
202 1 0.00
203 4 0.01
206 2 0.00
207 50 0.11
208 104 0.23
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (192 bp):
AGTCGATATTGTTGTCTTTTGAATGCTTGCCGGCTCTTCAGATTCGAACAATATCGATTTGTGCT
CACGAAGCTGCGCTTAGAAAAATTGTAGTTTATTTTTAGTTCTAAATTCAGCTTTTGAATTACTG
ATGCGTACGTTCTAATTTCTCATCTTTTTTTTCTTCCTTTTTTACAATGATCCGTCACCGCA
Found at i:123576202 original size:22 final size:22
Alignment explanation
Indices: 123576180--123576222 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
123576170 TGGAAAAATA
123576180 AAAT-AATAATTAAAAATTTAT
1 AAATAAATAATTAAAAATTTAT
* *
123576201 AAATAAATATTTATAAATTTAT
1 AAATAAATAATTAAAAATTTAT
123576223 TTAAGATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAAATAATTAAAAATTTAT
Found at i:123576207 original size:14 final size:14
Alignment explanation
Indices: 123576185--123576218 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
123576175 AAATAAAATA
*
123576185 ATAATTAAAAATTT
1 ATAAATAAAAATTT
*
123576199 ATAAATAAATATTT
1 ATAAATAAAAATTT
123576213 ATAAAT
1 ATAAAT
123576219 TTATTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATAAAAATTT
Found at i:123586198 original size:43 final size:43
Alignment explanation
Indices: 123586137--123586222 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
123586127 CCATAAAAAG
123586137 TTGGTTTCTTCTCCTAGTTAAACTATGCTATCTTTTCTCGATC
1 TTGGTTTCTTCTCCTAGTTAAACTATGCTATCTTTTCTCGATC
123586180 TTGGTTTCTTCTCCTAGTTAAACTATGCTATCTTTTCTCGATC
1 TTGGTTTCTTCTCCTAGTTAAACTATGCTATCTTTTCTCGATC
123586223 GAACTCTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.16, C:0.23, G:0.12, T:0.49
Consensus pattern (43 bp):
TTGGTTTCTTCTCCTAGTTAAACTATGCTATCTTTTCTCGATC
Found at i:123587908 original size:46 final size:46
Alignment explanation
Indices: 123587858--123588033 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
123587848 TGGTTGAGCA
123587858 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
123587904 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
123587949 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
123587997 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
123588034 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:123588014 original size:93 final size:93
Alignment explanation
Indices: 123587855--123588026 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
123587845 GGATGGTTGA
* *
123587855 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
123587920 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
123587948 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
123588013 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
123588027 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:123594955 original size:46 final size:46
Alignment explanation
Indices: 123594905--123595080 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
123594895 TGGTTGAGCA
123594905 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
123594951 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
123594996 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
123595044 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
123595081 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:123595061 original size:93 final size:93
Alignment explanation
Indices: 123594902--123595073 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
123594892 GGATGGTTGA
* *
123594902 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
123594967 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
123594995 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
123595060 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
123595074 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:123597191 original size:22 final size:24
Alignment explanation
Indices: 123597149--123597192 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
123597139 TAACTAAGTT
123597149 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
123597173 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
123597193 TCTTGGCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:123598177 original size:15 final size:16
Alignment explanation
Indices: 123598159--123598191 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
123598149 ATTACAATTG
123598159 TACAAATATA-ATTTT
1 TACAAATATATATTTT
*
123598174 TACACATATATATTTT
1 TACAAATATATATTTT
123598190 TA
1 TA
123598192 TTACCATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TACAAATATATATTTT
Found at i:123600088 original size:31 final size:31
Alignment explanation
Indices: 123600053--123600130 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
123600043 AAGTACATAA
*
123600053 TATTTATTATTCATTAATGATAACAAAAAAG
1 TATTTATTATTAATTAATGATAACAAAAAAG
123600084 TATTTATTATTAATTAATGATAACAAAAAAG
1 TATTTATTATTAATTAATGATAACAAAAAAG
123600115 TATTTATTATTAATTA
1 TATTTATTATTAATTA
123600131 CAAAGCGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (31 bp):
TATTTATTATTAATTAATGATAACAAAAAAG
Found at i:123603291 original size:66 final size:66
Alignment explanation
Indices: 123603190--123603327 Score: 204
Period size: 66 Copynumber: 2.1 Consensus size: 66
123603180 AAGGAGTCCT
* * **
123603190 CCACCACCACCACCACGTCCAAAAACACCTCCGCCAATTTCACATCCACCTTTGAGGGCGTCTCC
1 CCACCGCCACCACCACGTCCAAAAACACCTCCGCCAATCTCACATCCACCTTTGAGGGCACCTCC
123603255 A
66 A
* * * *
123603256 CCACCGCCACCATCACGTCCAAATACACCTCCGCCAGTCTCACTTCCACCTTTGAGGGCACCTCC
1 CCACCGCCACCACCACGTCCAAAAACACCTCCGCCAATCTCACATCCACCTTTGAGGGCACCTCC
123603321 A
66 A
123603322 CCACCG
1 CCACCG
123603328 TCACTGTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.25, C:0.47, G:0.12, T:0.17
Consensus pattern (66 bp):
CCACCGCCACCACCACGTCCAAAAACACCTCCGCCAATCTCACATCCACCTTTGAGGGCACCTCC
A
Found at i:123603443 original size:78 final size:77
Alignment explanation
Indices: 123603335--123603655 Score: 508
Period size: 78 Copynumber: 4.2 Consensus size: 77
123603325 CCGTCACTGT
123603335 CACCACCATCA-C-CACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
1 CACCACCATCACCACACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
123603398 TGAGGACGCCTC
66 TGAGGACGCCTC
* *
123603410 CACCACCATCACCATCACCACCACCACCACGTCCAAACATACCTCCGCCAGTCTCACTTCCACCT
1 CACCACCATCACCA-CACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCT
**
123603475 TTGAGGGTGCCTC
65 TTGAGGACGCCTC
*
123603488 CACCACCATCACCACCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCT
1 CACCACCATCACCA-CACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCT
123603553 TTGAGGACGCCTC
65 TTGAGGACGCCTC
* *
123603566 CACCACTATCA-C-CACCGCCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
1 CACCACCATCACCACACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
123603629 TGAGTG-CGCCTC
66 TGAG-GACGCCTC
*
123603641 CACCACCACCACCAC
1 CACCACCATCACCAC
123603656 GCTCAAACAC
Statistics
Matches: 227, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
75 79 0.35
76 3 0.01
77 2 0.01
78 143 0.63
ACGTcount: A:0.26, C:0.50, G:0.09, T:0.15
Consensus pattern (77 bp):
CACCACCATCACCACACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
TGAGGACGCCTC
Found at i:123603495 original size:3 final size:3
Alignment explanation
Indices: 123603487--123603517 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
123603477 GAGGGTGCCT
*
123603487 CCA CCA CCA TCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
123603518 GTCCAAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.65, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:123603647 original size:156 final size:158
Alignment explanation
Indices: 123603190--123603655 Score: 591
Period size: 156 Copynumber: 3.0 Consensus size: 158
123603180 AAGGAGTCCT
* * * * *
123603190 CCACCACCACCACCACGTCCAAAAACACCTCCGCCAATTTCACATCCACCTTTGAGG--GCGT--
1 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
* * *
123603251 ----CT-CCACCACCGCCACCATCACGTCCAAATACACCTCCGCCAGTCTCACTTCCACCTTTGA
66 ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGA
*
123603311 GGGCACCTCCACCACCGTCACTGTCACCACCATCA
131 GGGCGCCTCCACCA-C--CAC---CACCACCA-CA
*
123603346 CCACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGACGCCTCC
1 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
* * *
123603411 ACCACCATCACCATCACCACCACCACCACGTCCAAACATACCTCCGCCAGTCTCACTTCCACCTT
66 ACCACTATCA-C--CACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTT
* *
123603476 TGAGGGTGCCT---CCACCACCATCA-C-CA
128 TGAGGGCGCCTCCACCACCACCACCACCACA
123603502 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
1 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
*
123603567 ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTTTGA
66 ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGA
*
123603632 GTGCGCCTCCACCACCACCACCAC
131 GGGCGCCTCCACCACCACCACCAC
123603656 GCTCAAACAC
Statistics
Matches: 271, Mismatches: 23, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
153 57 0.21
155 1 0.00
156 138 0.51
158 4 0.01
159 4 0.01
162 3 0.01
164 2 0.01
165 5 0.02
166 1 0.00
168 56 0.21
ACGTcount: A:0.25, C:0.49, G:0.10, T:0.16
Consensus pattern (158 bp):
CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGA
GGGCGCCTCCACCACCACCACCACCACA
Found at i:123603656 original size:63 final size:63
Alignment explanation
Indices: 123603577--123603710 Score: 207
Period size: 63 Copynumber: 2.1 Consensus size: 63
123603567 ACCACTATCA
* * *
123603577 CCACCGCCACCACCACG-TCCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGTGCGCCT
1 CCACCACCACCACCACGCT-CAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGGCACCT
*
123603640 CCACCACCACCACCACGCTCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGGCACCT
1 CCACCACCACCACCACGCTCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGGCACCT
*
123603703 TCACCACC
1 CCACCACC
123603711 TCCAATTCCC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 64 0.98
64 1 0.02
ACGTcount: A:0.23, C:0.50, G:0.10, T:0.16
Consensus pattern (63 bp):
CCACCACCACCACCACGCTCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGGCACCT
Found at i:123603857 original size:36 final size:36
Alignment explanation
Indices: 123603722--123604239 Score: 455
Period size: 36 Copynumber: 14.8 Consensus size: 36
123603712 CCAATTCCCC
* * *
123603722 CACCTTCAATGAACCAACCTTTACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * *
123603758 CACCTCCAATGAACCAACCATCACTTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * *
123603794 CACCTCCAACGAACCAACCTTTACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * *
123603830 CACCTCCAGTGAACCAACCGTCTCCTCCA---C-CT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * ** *
123603862 -A-ATTCAAT-AA-C-ACCTTCACCT--TTCTCAC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
*
123603890 C---TCCAATGAACCAACCTTCACCTCTACCTCTGC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCT-CT
* * * * *
123603923 CACCTTCGATAAACCAACCGTCACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
123603959 CACCTCCAATGAACCAACCTTCACCTCCACC-CT-T
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
123603993 GCCACCACCAATGAACCAACCTTCACCTCCACCTTTCT
1 --CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * *
123604031 CACCACCAATGAACGAA-CTATCACCTCCACCCCTAT
1 CACCTCCAATGAACCAACCT-TCACCTCCACCTCTCT
* *
123604067 CACCTCCAATGAACCAACCTACACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
123604103 TACCTCCAATGAACCAACCTTCACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * * *
123604139 CACCACCAATGAACGAACCATCACCTCCACCCCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
123604175 CACCTCCAATGAAACAACCTTCATCTCCACCAT-TCT
1 CACCTCCAATGAACCAACCTTCACCTCCACC-TCTCT
* ** *
123604211 CACCACCAATGAATGAACCATCACCTCCA
1 CACCTCCAATGAACCAACCTTCACCTCCA
123604240 ATGAACCAAC
Statistics
Matches: 388, Mismatches: 72, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.03
28 4 0.01
29 4 0.01
30 14 0.04
31 1 0.00
32 4 0.01
33 3 0.01
34 1 0.00
35 4 0.01
36 336 0.87
37 3 0.01
38 1 0.00
ACGTcount: A:0.28, C:0.45, G:0.05, T:0.22
Consensus pattern (36 bp):
CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
Found at i:123603890 original size:93 final size:93
Alignment explanation
Indices: 123603785--123603954 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
123603775 CCATCACTTC
* * *
123603785 CACCTTTCTCACCTCCAACGAACCAACCTTTACCTCCACCTCTGTCACCTCC-AGTGAACCAACC
1 CACCTTTCTCACCTCCAACGAACCAACCTTCACCTCCACCTCTGCCACCTCCGA-TAAACCAACC
*
123603849 GTCTCCTCCACCTAATTCAATAACACCTT
65 GTCACCTCCACCTAATTCAATAACACCTT
* * *
123603878 CACCTTTCTCACCTCCAATGAACCAACCTTCACCTCTACCTCTGCCACCTTCGATAAACCAACCG
1 CACCTTTCTCACCTCCAACGAACCAACCTTCACCTCCACCTCTGCCACCTCCGATAAACCAACCG
123603943 TCACCTCCACCT
66 TCACCTCCACCT
123603955 TTCTCACCTC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
93 68 0.99
94 1 0.01
ACGTcount: A:0.25, C:0.45, G:0.05, T:0.24
Consensus pattern (93 bp):
CACCTTTCTCACCTCCAACGAACCAACCTTCACCTCCACCTCTGCCACCTCCGATAAACCAACCG
TCACCTCCACCTAATTCAATAACACCTT
Found at i:123604241 original size:57 final size:57
Alignment explanation
Indices: 123604174--123604296 Score: 192
Period size: 57 Copynumber: 2.2 Consensus size: 57
123604164 TCCACCCCTG
* *
123604174 TCACCTCCAATGAAACAACCTTCATCTCCACCATTCTCACCACCAATGAATGAACCA
1 TCACCTCCAATGAAACAACCTTCACCTCCACCATTCTCACCACCAATGAACGAACCA
* * *
123604231 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTTTCACCACCAATGAACGAACCA
1 TCACCTCCAATGAAACAACCTTCACCTCCACCATTCTCACCACCAATGAACGAACCA
*
123604288 TCACATCCA
1 TCACCTCCA
123604297 CCCCTGTCAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.33, C:0.41, G:0.05, T:0.21
Consensus pattern (57 bp):
TCACCTCCAATGAAACAACCTTCACCTCCACCATTCTCACCACCAATGAACGAACCA
Found at i:123604241 original size:93 final size:93
Alignment explanation
Indices: 123604138--123604332 Score: 223
Period size: 93 Copynumber: 2.1 Consensus size: 93
123604128 TCCACCTTTC
* * * *
123604138 TCACCACCAATGAACGAACCATCACCTCCACCCCTGTCACCTCCAATGAAAC-AACCTTCATC-T
1 TCACCTCCAATGAACCAACCATCACCTCCACCCCTGTCACCACCAATG-AACGAACCATCA-CAT
* **
123604201 CCACCATTCTCACCACCAATGAATGAACCA
64 CCACCACTCTCACCACCAATGAACCAACCA
* ** *
123604231 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTTTCACCACCAATGAACGAACCATCACATCC
1 TCACCTCCAATGAACCAACCATCACCTCCACCCCTGTCACCACCAATGAACGAACCATCACATCC
* * * *
123604296 ACCCCTGTCACCTCCAATGAACCAACCT
66 ACCACTCTCACCACCAATGAACCAACCA
123604324 TCACCTCCA
1 TCACCTCCA
123604333 CCTTACTCAC
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
92 4 0.05
93 81 0.95
ACGTcount: A:0.31, C:0.44, G:0.06, T:0.19
Consensus pattern (93 bp):
TCACCTCCAATGAACCAACCATCACCTCCACCCCTGTCACCACCAATGAACGAACCATCACATCC
ACCACTCTCACCACCAATGAACCAACCA
Found at i:123604250 original size:21 final size:21
Alignment explanation
Indices: 123604210--123604260 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
123604200 TCCACCATTC
* **
123604210 TCACCACCAATGAATGAACCA
1 TCACCTCCAATGAACCAACCA
*
123604231 TCACCTCCAATGAACCAACCT
1 TCACCTCCAATGAACCAACCA
123604252 TCACCTCCA
1 TCACCTCCA
123604261 CCTTTTTCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.41, G:0.06, T:0.18
Consensus pattern (21 bp):
TCACCTCCAATGAACCAACCA
Found at i:123604250 original size:129 final size:129
Alignment explanation
Indices: 123604104--123604366 Score: 465
Period size: 129 Copynumber: 2.0 Consensus size: 129
123604094 CACCTTTCTT
*
123604104 ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACCTCCAC
1 ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACATCCAC
* *
123604169 CCCTGTCACCTCCAATGAAACAACCTTCATCTCCACCATT-CTCACCACCAATGAATGAACCATC
66 CCCTGTCACCTCCAATGAAACAACCTTCACCTCCACC-TTACTCACCACCAATGAACGAACCATC
*
123604233 ACCTCCAATGAACCAACCTTCACCTCCACCTTTTTCACCACCAATGAACGAACCATCACATCCAC
1 ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACATCCAC
*
123604298 CCCTGTCACCTCCAATGAACCAACCTTCACCTCCACCTTACTCACCACCAATGAACGAACCATC
66 CCCTGTCACCTCCAATGAAACAACCTTCACCTCCACCTTACTCACCACCAATGAACGAACCATC
123604362 ACCTC
1 ACCTC
123604367 AACCTTTCTC
Statistics
Matches: 128, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
128 2 0.02
129 126 0.98
ACGTcount: A:0.31, C:0.44, G:0.05, T:0.20
Consensus pattern (129 bp):
ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACATCCAC
CCCTGTCACCTCCAATGAAACAACCTTCACCTCCACCTTACTCACCACCAATGAACGAACCATC
Found at i:123604271 original size:36 final size:36
Alignment explanation
Indices: 123604231--123604515 Score: 347
Period size: 36 Copynumber: 7.9 Consensus size: 36
123604221 GAATGAACCA
*
123604231 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTT
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
* * * * ** *
123604267 TCACCACCAATGAACGAACCATCACATCCACCCCTG
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
*
123604303 TCACCTCCAATGAACCAACCTTCACCTCCACCTTAC
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
* * * *
123604339 TCACCACCAATGAACGAACCATCACCTCAACCTTTC
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
* * *
123604375 TCATCTCCAATGGACCAACCTTTACCTCCACCTTTC
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
*
123604411 TCACCTCCAAT-AGACCAACCTTCACCTCCATCTTTC
1 TCACCTCCAATGA-ACCAACCTTCACCTCCACCTTTC
* * * * * *
123604447 TCACCACCAAAGAACGAACCATCACCTCCACCCTTG
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
123604483 TCACCTCCAATGAACCAACCTTCACCTCCACCT
1 TCACCTCCAATGAACCAACCTTCACCTCCACCT
123604516 CCACCTTCAG
Statistics
Matches: 204, Mismatches: 43, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
36 203 1.00
37 1 0.00
ACGTcount: A:0.28, C:0.45, G:0.05, T:0.22
Consensus pattern (36 bp):
TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
Found at i:123604568 original size:45 final size:45
Alignment explanation
Indices: 123604513--123604829 Score: 406
Period size: 45 Copynumber: 6.8 Consensus size: 45
123604503 TTCACCTCCA
*
123604513 CCTCCACCTTCAGCTCTATCACCAAGGAGGACACCACCCCCACCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
*
123604558 CCTCCGCCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
*
123604603 CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCGCCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCA-C-CC-CCA---CCG
* * *
123604654 CCTCCACCTTCAGCTCCATCACCAATGAAGACACCA---CCGCCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
* * *
123604696 CCACCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCACCA
1 CCTCCACCTTCAGCTCCATCACCAAGGAGG--A-CACCA-C-CC-CCACCG
*
123604747 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCACCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
*
123604792 CCTCCACCTTCAACTCCATCACCAAGGAGGACACCACC
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACC
123604830 ACCTCCACCA
Statistics
Matches: 238, Mismatches: 19, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
42 29 0.12
44 1 0.00
45 126 0.53
46 2 0.01
47 3 0.01
48 8 0.03
49 1 0.00
51 68 0.29
ACGTcount: A:0.27, C:0.50, G:0.12, T:0.11
Consensus pattern (45 bp):
CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
Found at i:123604839 original size:93 final size:93
Alignment explanation
Indices: 123604513--123604841 Score: 445
Period size: 93 Copynumber: 3.5 Consensus size: 93
123604503 TTCACCTCCA
* * * *
123604513 CCTCCACCTTCAGCTCTATCACCAAGGAGGACACCA-C-CC-CCACCGCCTCCGCCTTCAGCTCC
1 CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCACCTCCACCTTCAGCTCC
*
123604575 ATCACCAAGGAGGACACCACCCCCACCG
66 ATCACCAAGGAGGACACCACCACCACCG
*
123604603 CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCGCCGCCTCCACCTTCAGC
1 CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCA---CCACCTCCACCTTCAGC
* * *
123604668 TCCATCACCAATGA--AGA-CACCACCGCCG
63 TCCATCACCAAGGAGGACACCACCACCACCG
*
123604696 CCACCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCACCACCTCCACCTTCAGC
1 CCTCCACCTTCAGCTCCATCACCAAGAAGG--A-CACCACCACCACCACCACCTCCACCTTCAGC
123604761 TCCATCACCAAGGAGGACACCACCACCACCG
63 TCCATCACCAAGGAGGACACCACCACCACCG
* * *
123604792 CCTCCACCTTCAACTCCATCACCAAGGAGGACACCACCACCTCCACCACC
1 CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCACC
123604842 AAGGACACAT
Statistics
Matches: 211, Mismatches: 16, Indels: 21
0.85 0.06 0.08
Matches are distributed among these distances:
90 34 0.16
91 1 0.00
92 2 0.01
93 88 0.42
94 3 0.01
95 3 0.01
96 80 0.38
ACGTcount: A:0.27, C:0.50, G:0.12, T:0.11
Consensus pattern (93 bp):
CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCACCTCCACCTTCAGCTCC
ATCACCAAGGAGGACACCACCACCACCG
Found at i:123605459 original size:30 final size:29
Alignment explanation
Indices: 123605419--123605487 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
123605409 ATTAATAATT
** *
123605419 TATAAGAATTGGATTAAATCAAAATTTCATG
1 TATAA-AATTGGACAAAATC-AAAGTTCATG
*
123605450 TATAAAATTGTACAAAATCAAAGTTCATG
1 TATAAAATTGGACAAAATCAAAGTTCATG
*
123605479 TATATAATT
1 TATAAAATT
123605488 ACACGTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 17 0.52
30 11 0.33
31 5 0.15
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (29 bp):
TATAAAATTGGACAAAATCAAAGTTCATG
Found at i:123607791 original size:20 final size:20
Alignment explanation
Indices: 123607739--123607791 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
123607729 AAAATATTGA
* *
123607739 TTTATCGATATTTATAATAC
1 TTTATCAATATTTATAAGAC
* *
123607759 TTTA-CAAAAATTTATAAGAT
1 TTTATC-AATATTTATAAGAC
123607779 TTTATCAATATTT
1 TTTATCAATATTT
123607792 TTAAAATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTATCAATATTTATAAGAC
Found at i:123607895 original size:20 final size:19
Alignment explanation
Indices: 123607866--123607918 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
123607856 TATTTAACAG
* *
123607866 TTTATTAAAATTTCTAAGGA
1 TTTATCAAAATTT-TAACGA
123607886 TTTATCAAAATATTTAACGA
1 TTTATCAAAAT-TTTAACGA
* *
123607906 ATTATCAATATTT
1 TTTATCAAAATTT
123607919 ATGAGACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (19 bp):
TTTATCAAAATTTTAACGA
Found at i:123608066 original size:20 final size:19
Alignment explanation
Indices: 123608009--123608064 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
123607999 CAAAAGTTCA
*
123608009 AAAATATCTAATGATTTACC
1 AAAATTTCTAAT-ATTTACC
* * *
123608029 AACATTTATAAGAATTTACC
1 AAAATTTCTAA-TATTTACC
123608049 AAAATTTCTAATATTT
1 AAAATTTCTAATATTT
123608065 TATCAATATT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (19 bp):
AAAATTTCTAATATTTACC
Found at i:123619309 original size:225 final size:228
Alignment explanation
Indices: 123618906--123619600 Score: 712
Period size: 231 Copynumber: 3.0 Consensus size: 228
123618896 GGCTCTTGCA
* * *
123618906 TTTTACTATGTTCAATGGTTTCAGTCACAGT-CGCAACTGCATCAATTCCGA-CCTTATTCTTCC
1 TTTTACTATGTTCAAGGGTTTCAGTCACAGTAC-CAACTGCATCAA-TCCCATCCTT-GTC-TCC
* * * *
123618969 -TCTTGTGTTTATCTTCCCCAA-CCTTTTCTGCTTCCCCATTGTTCCCCAAATTCACCACCTTGC
62 TTCTTGTGTTTATCTTTCCCAACCCTTTT-TGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGC
* *
123619032 TACTTTCTTTTTCTGCATTATCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTACA
126 TACTTTCTTGTTCTGCATTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACT-CA
* *
123619097 TCTTT-TTTT-T-T-C-TTACGCGCCTT-TGGAGATTCCT
190 TCTTTATTTTCTATGCTTTACGAGCCTTCT-CAGATTCCT
* * * *
123619131 TTTTACTATGTTCAAGGGTTCCGGTCACAATACCAACTGCATTAATCCCATCCTTGTCGTCCTTC
1 TTTTACTATGTTCAAGGGTTTCAGTCACAGTACCAACTGCATCAATCCCATCCTTGTC-TCCTTC
* * *
123619196 TTGTGTTTATCTTTCCCGACCCTTTTTGCTTCCCCTTTGTTCTCCAAGTTCATCGCCTTGCTACT
65 TTGTGTTTATCTTTCCCAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACT
** * * * * * *
123619261 TTCTTGTTCTGTGTTCTTTTTTCCACCTAAATAATTTTCTACTGAAATCTCTTTAACCTCATCTT
130 TTCTTGTTCTGCATTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAA-CTCATCTT
*
123619326 TACTTTTCTCATGCTTTTTATGAGCCTTCTCAGATTCCT
194 TA-TTTTCT-ATGC--TTTACGAGCCTTCTCAGATTCCT
** * * ** * * *
123619365 TTTTACTATGTTTGAGGGTTTCAGTCACAGTAGCAACTACATCGGTCTCGTCCCTGT-T-CTTCT
1 TTTTACTATGTTCAAGGGTTTCAGTCACAGTACCAACTGCATCAATCCCATCCTTGTCTCCTTCT
* * ** *
123619428 TATGTTTGTCTTTCTTAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCGACTT
66 TGTGTTTATCTTTCCCAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTT
* *
123619493 TCTTGTTCTGCATTCTCTTTTCCACCCAAACAAGTTTCCATTGGAATCTCTTCAACTGCATCTTT
131 TCTTGTTCTGCATTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACT-CATCTTT
* * ** *
123619558 ACTTGTCTTATGCTTTTTATGAGTGTTCTTAGATTCCT
195 A-TTTTC-TATGC--TTTACGAGCCTTCTCAGATTCCT
123619596 TTTTA
1 TTTTA
123619601 TCTGTATCAA
Statistics
Matches: 390, Mismatches: 63, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
224 9 0.02
225 148 0.38
226 9 0.02
227 4 0.01
228 1 0.00
230 3 0.01
231 152 0.39
232 2 0.01
234 61 0.16
235 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.44
Consensus pattern (228 bp):
TTTTACTATGTTCAAGGGTTTCAGTCACAGTACCAACTGCATCAATCCCATCCTTGTCTCCTTCT
TGTGTTTATCTTTCCCAACCCTTTTTGCTTCCCCATTGTTCTCCAAGTTCATCACCTTGCTACTT
TCTTGTTCTGCATTCTCTTTTCCACCTAAACAAGTTTCCATTGAAATCTCTTCAACTCATCTTTA
TTTTCTATGCTTTACGAGCCTTCTCAGATTCCT
Found at i:123630139 original size:25 final size:23
Alignment explanation
Indices: 123630108--123630169 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
123630098 TCGATCATTC
*
123630108 TATTAAAAATTTTATTCATTTATA
1 TATTAAAAATTTTATCCA-TTATA
*
123630132 TTATTAAAAA-TTAATCCATTATA
1 -TATTAAAAATTTTATCCATTATA
123630155 TATTATAAAATTTTA
1 TATTA-AAAATTTTA
123630170 ATAATAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 5 0.16
23 9 0.28
24 9 0.28
25 9 0.28
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAAAAATTTTATCCATTATA
Found at i:123630151 original size:24 final size:26
Alignment explanation
Indices: 123630108--123630171 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 26
123630098 TCGATCATTC
* *
123630108 TATTAAAAATTTTATTCATT-TATAT
1 TATTAAAAATTTAATCCATTATATAT
123630133 TATTAAAAA-TTAATCCATTATATAT
1 TATTAAAAATTTAATCCATTATATAT
*
123630158 TA-TAAAATTTTAAT
1 TATTAAAAATTTAAT
123630172 AATAAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTAAAAATTTAATCCATTATATAT
Found at i:123630170 original size:25 final size:24
Alignment explanation
Indices: 123630108--123630171 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
123630098 TCGATCATTC
*
123630108 TATTA-AAAATTTT-ATTCATTTA
1 TATTATAAAATTTTAATCCATTTA
*
123630130 TATTATTAAAA-ATTAATCCATTATA
1 TATTA-TAAAATTTTAATCCATT-TA
123630155 TATTATAAAATTTTAAT
1 TATTATAAAATTTTAAT
123630172 AATAAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 5 0.15
23 2 0.06
24 15 0.44
25 12 0.35
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTATAAAATTTTAATCCATTTA
Found at i:123639257 original size:59 final size:60
Alignment explanation
Indices: 123639188--123639322 Score: 166
Period size: 60 Copynumber: 2.3 Consensus size: 60
123639178 ATTACATTAG
* * * *
123639188 TAGTTATCCAATTATTAGTAAATTTT-TTTTTAGTCACTCAATTATAAAAAGTTATAAAA
1 TAGTCATCCAACTATTAGTAAATTTTCTTTTTAGTCACCCAACTATAAAAAGTTATAAAA
* * * *
123639247 TAGTCATCCAACTATTAGTAAATTTTCTTTTTGGTCACCCAACTATGAAAATTTATAAAG
1 TAGTCATCCAACTATTAGTAAATTTTCTTTTTAGTCACCCAACTATAAAAAGTTATAAAA
*
123639307 T-GAACATCCAACTATT
1 TAG-TCATCCAACTATT
123639323 CAACTTTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 25 0.38
60 40 0.62
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (60 bp):
TAGTCATCCAACTATTAGTAAATTTTCTTTTTAGTCACCCAACTATAAAAAGTTATAAAA
Found at i:123643473 original size:2 final size:2
Alignment explanation
Indices: 123643466--123643493 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
123643456 AACTCAGGTA
123643466 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
123643494 ACACACACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:123645433 original size:6 final size:6
Alignment explanation
Indices: 123645423--123645462 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
123645413 CAATTTGAAT
* * *
123645423 TTGAGT TTGAGT TTAAGC TTGAGC TTGAGC TTGAGC TTGA
1 TTGAGC TTGAGC TTGAGC TTGAGC TTGAGC TTGAGC TTGA
123645463 ACTTAAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.20, C:0.10, G:0.30, T:0.40
Consensus pattern (6 bp):
TTGAGC
Found at i:123646544 original size:2 final size:2
Alignment explanation
Indices: 123646537--123646568 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
123646527 CTTTTAAAGC
123646537 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
123646569 GACAATTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123647441 original size:2 final size:2
Alignment explanation
Indices: 123647434--123647475 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
123647424 CATAAGATAC
123647434 AT AT AT AT A- 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
123647475 A
1 A
123647476 ACAGTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123649407 original size:15 final size:14
Alignment explanation
Indices: 123649363--123649421 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
123649353 CGACATATTA
*
123649363 TTTTATTAATA-AT
1 TTTTATTATTATAT
*
123649376 TTTT-TT-TTAAAT
1 TTTTATTATTATAT
123649388 ATTTTATTATTATTAT
1 -TTTTATTATTA-TAT
123649404 TTTTATTATTATAT
1 TTTTATTATTATAT
123649418 TTTT
1 TTTT
123649422 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 2 0.05
12 4 0.10
13 8 0.21
14 9 0.23
15 14 0.36
16 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTATTATAT
Found at i:123649563 original size:16 final size:17
Alignment explanation
Indices: 123649542--123649573 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
123649532 CCTTTCTCTT
123649542 TTCTTTG-TTTGTTTTC
1 TTCTTTGTTTTGTTTTC
123649558 TTCTTTGTTTTGTTTT
1 TTCTTTGTTTTGTTTT
123649574 TGGTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.78
Consensus pattern (17 bp):
TTCTTTGTTTTGTTTTC
Found at i:123649563 original size:21 final size:20
Alignment explanation
Indices: 123649534--123649572 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
123649524 TGACTGGTCC
123649534 TTTCTCTTT-TCTTTGTTTGT
1 TTTCTCTTTGT-TTTGTTTGT
123649554 TTTCTTCTTTGTTTTGTTT
1 TTTC-TCTTTGTTTTGTTT
123649573 TTGGTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (20 bp):
TTTCTCTTTGTTTTGTTTGT
Found at i:123651214 original size:14 final size:14
Alignment explanation
Indices: 123651197--123651231 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
123651187 GTTTGCTAGG
*
123651197 TTTTGAATGAAAAA
1 TTTTGAATCAAAAA
*
123651211 TTTTGCATCAAAAA
1 TTTTGAATCAAAAA
123651225 TTTTGAA
1 TTTTGAA
123651232 AATTGTGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (14 bp):
TTTTGAATCAAAAA
Found at i:123654138 original size:20 final size:21
Alignment explanation
Indices: 123654113--123654162 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
123654103 ATGCAAAAAA
123654113 TAATTTACAT-AAAAATAAAG
1 TAATTTACATAAAAAATAAAG
123654133 TAATTTACATAAAAAATAAAG
1 TAATTTACATAAAAAATAAAG
123654154 TAATTTACA
1 TAATTTACA
123654163 ATACAAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (21 bp):
TAATTTACATAAAAAATAAAG
Found at i:123654365 original size:33 final size:33
Alignment explanation
Indices: 123654325--123654417 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
123654315 AACTCGAGCC
*
123654325 GGGGGAGTAGAGAACGGCGCTGGATACGGGCCG
1 GGGGGAGTAGAGAACGGCGCTGGATACGGGCCA
* *
123654358 GGGGGAGTAGAGAACGACGCTGGATATGGGCCA
1 GGGGGAGTAGAGAACGGCGCTGGATACGGGCCA
*
123654391 GGGGGAGAAGAGAACGGCGAC-GGATAC
1 GGGGGAGTAGAGAACGGCG-CTGGATAC
123654418 TGCTCTGGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.48, T:0.09
Consensus pattern (33 bp):
GGGGGAGTAGAGAACGGCGCTGGATACGGGCCA
Found at i:123654448 original size:66 final size:66
Alignment explanation
Indices: 123654320--123654457 Score: 156
Period size: 66 Copynumber: 2.1 Consensus size: 66
123654310 TGATGAACTC
* * *
123654320 GAGCC-GGGGGAGTAGAGAACGGCGCTGGATACGGGCCGGGGGGAGTAGAGAACGACGCTGGATA
1 GAGCCAGGGGGAGAAGAGAACGGCGCTGGATACGGGCCGGGAGGAGCAGAGAACGACGCTGGATA
123654384 T
66 T
* * * * * *
123654385 GGGCCAGGGGGAGAAGAGAACGGCGAC-GGATAC-TGCTCTGGAGGAGCAGAGTACGATGGTGGA
1 GAGCCAGGGGGAGAAGAGAACGGCG-CTGGATACGGGC-CGGGAGGAGCAGAGAACGACGCTGGA
123654448 TAT
64 TAT
123654451 GAGCCAG
1 GAGCCAG
123654458 CAGGAGTAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
65 6 0.10
66 53 0.88
67 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.46, T:0.12
Consensus pattern (66 bp):
GAGCCAGGGGGAGAAGAGAACGGCGCTGGATACGGGCCGGGAGGAGCAGAGAACGACGCTGGATA
T
Found at i:123654463 original size:33 final size:33
Alignment explanation
Indices: 123654426--123654548 Score: 174
Period size: 33 Copynumber: 3.7 Consensus size: 33
123654416 ACTGCTCTGG
* * *
123654426 AGGAGCAGAGTACGATGGTGGATATGAGCCAGC
1 AGGAGCAGAGTACGGTGGTGGATATGAGCCGGA
*
123654459 AGGAGTAGAGTACGGTGGTGGATATGAGCCGGA
1 AGGAGCAGAGTACGGTGGTGGATATGAGCCGGA
* * *
123654492 AGGAGCGGAGTACGGTGGTGGATAGGAACCGGA
1 AGGAGCAGAGTACGGTGGTGGATATGAGCCGGA
*
123654525 AGGAGCGGAGTACGGTGGTGGATA
1 AGGAGCAGAGTACGGTGGTGGATA
123654549 GGAGGTAGAA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.28, C:0.11, G:0.46, T:0.15
Consensus pattern (33 bp):
AGGAGCAGAGTACGGTGGTGGATATGAGCCGGA
Found at i:123654569 original size:33 final size:33
Alignment explanation
Indices: 123654426--123654570 Score: 164
Period size: 33 Copynumber: 4.4 Consensus size: 33
123654416 ACTGCTCTGG
* * *
123654426 AGGAGCAGAGTACGATGGTGGATATGAGCCAGC
1 AGGAGCAGAGTACGGTGGTGGATAGGAGCCAGA
* * *
123654459 AGGAGTAGAGTACGGTGGTGGATATGAGCCGGA
1 AGGAGCAGAGTACGGTGGTGGATAGGAGCCAGA
* * *
123654492 AGGAGCGGAGTACGGTGGTGGATAGGAACCGGA
1 AGGAGCAGAGTACGGTGGTGGATAGGAGCCAGA
* **
123654525 AGGAGCGGAGTACGGTGGTGGATAGGAGGTAGA
1 AGGAGCAGAGTACGGTGGTGGATAGGAGCCAGA
* *
123654558 AGTAGTAGAGTAC
1 AGGAGCAGAGTAC
123654571 TGATGTGGTA
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 97 1.00
ACGTcount: A:0.29, C:0.10, G:0.45, T:0.16
Consensus pattern (33 bp):
AGGAGCAGAGTACGGTGGTGGATAGGAGCCAGA
Found at i:123654708 original size:6 final size:6
Alignment explanation
Indices: 123654686--123654725 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
123654676 CCGGAGTGTA
* *
123654686 GCTCCG GATCTG GCTCCG GCTCCG GCTCCG GCTCCG GCTC
1 GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTCCG GCTC
123654726 TACCTCCGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.45, G:0.33, T:0.20
Consensus pattern (6 bp):
GCTCCG
Found at i:123654732 original size:18 final size:18
Alignment explanation
Indices: 123654697--123654735 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
123654687 CTCCGGATCT
**
123654697 GGCTCCGGCTCCGGCTCC
1 GGCTCCGGCTCCACCTCC
*
123654715 GGCTCCGGCTCTACCTCC
1 GGCTCCGGCTCCACCTCC
123654733 GGC
1 GGC
123654736 GCTGGTGCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.49, G:0.31, T:0.18
Consensus pattern (18 bp):
GGCTCCGGCTCCACCTCC
Found at i:123656788 original size:296 final size:297
Alignment explanation
Indices: 123656309--123657030 Score: 1153
Period size: 297 Copynumber: 2.4 Consensus size: 297
123656299 TGCAATTAAT
*
123656309 ATTATATAACAACAAATTTAATCAAAATTTTAATCAATCAATAAAAATTATCAAATAAATAATTC
1 ATTATATAACAACAAATTTAATCAAAATTTTAATCAATCAATAAAAATTATCAAATAAATAATTA
* * * * * *
123656374 AATAAATTTATATAACCTAATCATTTTTTTAAAA-TACCTTATCCAAAATATCACAATACACTAA
66 AATAAA--T-TA-AA-TTTA-CATTATATAAAAATTACATTA---AAAA-ATCACAATACACTAA
* * *
123656438 TACACTACTAAAAAATAATTTTATTGCACAACCATTTTGAAAATTAATTTTATAATTCCCCATCA
121 TACACTAATAAAAAATAAATTTATTGCACAACCATTTTAAAAATTAATTTTATAATTCCCCATCA
123656503 TTTATATACAATAAAAAATAAATATAAATTATCTAAAGATT-AAAAACATATGAATTAAAAATAA
186 TTTATATACAATAAAAAATAAATATAAATTATCTAAAGATTAAAAAACATATGAATTAAAAATAA
123656567 TTGAAATTGAAACATACCTGAA-TAGTTTCTTTCACACAACCTATAAA
251 TTGAAATTGAAACATACCT-AAGTAGTTTCTTTCACACAACCTATAAA
* *
123656614 ATTATATAATAATAAATTTAATCAAAATTTTAATCAATCAATAAAAATTATCAAATAAATAATTA
1 ATTATATAACAACAAATTTAATCAAAATTTTAATCAATCAATAAAAATTATCAAATAAATAATTA
*
123656679 AATAAATTAAATTTACATTATATAAAAATTACATTAAAAAATCACACTACACTAATACACTAATA
66 AATAAATTAAATTTACATTATATAAAAATTACATTAAAAAATCACAATACACTAATACACTAATA
123656744 AAAAATAAATTTATTGCACAACCATTTTAAAAATTAATTTTATAATTCCCCATCATTTATATACA
131 AAAAATAAATTTATTGCACAACCATTTTAAAAATTAATTTTATAATTCCCCATCATTTATATACA
123656809 ATAAAAAATAAATATAAATTATCTAAAGATTAAAAAACATATGAATTAAAAATAATTGAAATTGA
196 ATAAAAAATAAATATAAATTATCTAAAGATTAAAAAACATATGAATTAAAAATAATTGAAATTGA
* **
123656874 AACATTCCTAAGTAGTTTCTTTCACGTAACCTATAAA
261 AACATACCTAAGTAGTTTCTTTCACACAACCTATAAA
*
123656911 ATTATATAACAACAAATTTAATCAAAATTTTAATCAATCAATAAAAATTATCAAATAAATAATTT
1 ATTATATAACAACAAATTTAATCAAAATTTTAATCAATCAATAAAAATTATCAAATAAATAATTA
* *
123656976 AATAAATTAAATTTACATTATATAAAAATTACATTAAAAAATCATAAAACACTAA
66 AATAAATTAAATTTACATTATATAAAAATTACATTAAAAAATCACAATACACTAA
123657031 ACTATAAACA
Statistics
Matches: 392, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
296 119 0.30
297 182 0.46
299 10 0.03
300 8 0.02
301 2 0.01
302 2 0.01
303 1 0.00
305 68 0.17
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (297 bp):
ATTATATAACAACAAATTTAATCAAAATTTTAATCAATCAATAAAAATTATCAAATAAATAATTA
AATAAATTAAATTTACATTATATAAAAATTACATTAAAAAATCACAATACACTAATACACTAATA
AAAAATAAATTTATTGCACAACCATTTTAAAAATTAATTTTATAATTCCCCATCATTTATATACA
ATAAAAAATAAATATAAATTATCTAAAGATTAAAAAACATATGAATTAAAAATAATTGAAATTGA
AACATACCTAAGTAGTTTCTTTCACACAACCTATAAA
Found at i:123657466 original size:13 final size:14
Alignment explanation
Indices: 123657448--123657476 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
123657438 CTTTTTTTAT
123657448 TTCTTCTTCTT-TC
1 TTCTTCTTCTTCTC
123657461 TTCTTCTTCTTCTC
1 TTCTTCTTCTTCTC
123657475 TT
1 TT
123657477 TTTTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTCTTCTTCTTCTC
Found at i:123657486 original size:16 final size:17
Alignment explanation
Indices: 123657438--123657486 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
123657428 TTTAACTAAC
123657438 CTTTTTTTATTTCTTCTT
1 CTTTTTTT-TTTCTTCTT
*
123657456 CTTTCTTCTTCTTCTTC-T
1 CTTT-TT-TTTTTCTTCTT
123657474 CTTTTTTTTTTCT
1 CTTTTTTTTTTCT
123657487 ACCTTTGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 6 0.22
17 2 0.07
18 9 0.33
19 8 0.30
20 2 0.07
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTTTTTTTTCTTCTT
Found at i:123657747 original size:15 final size:14
Alignment explanation
Indices: 123657723--123657781 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 14
123657713 TTTTTTTAAA
123657723 AAAAATATAATAAT
1 AAAAATATAATAAT
123657737 AAAAATAATAATAAT
1 AAAAAT-ATAATAAT
**
123657752 -AAAATATTTTAA-
1 AAAAATATAATAAT
* *
123657764 AAAAATTTATTAAT
1 AAAAATATAATAAT
123657778 AAAA
1 AAAA
123657782 TAATATGTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
13 15 0.39
14 15 0.39
15 8 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAAATATAATAAT
Found at i:123669557 original size:29 final size:29
Alignment explanation
Indices: 123669524--123669580 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
123669514 TAATCAGACT
*
123669524 GTTTTGTTCATGATTGGGTAGTGCTGCCG
1 GTTTTGTGCATGATTGGGTAGTGCTGCCG
123669553 GTTTTGTGCATGATTGGGTAGTGCTGCC
1 GTTTTGTGCATGATTGGGTAGTGCTGCC
123669581 ACTTGCCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.11, C:0.14, G:0.35, T:0.40
Consensus pattern (29 bp):
GTTTTGTGCATGATTGGGTAGTGCTGCCG
Found at i:123676359 original size:4 final size:4
Alignment explanation
Indices: 123676350--123676376 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
123676340 GACATATAAG
123676350 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
123676377 GATGCATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:123678489 original size:2 final size:2
Alignment explanation
Indices: 123678482--123678510 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
123678472 ATAAATATTA
123678482 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123678511 TTTAAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123680332 original size:22 final size:23
Alignment explanation
Indices: 123680291--123680333 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
123680281 AATATTTTAA
*
123680291 CATGTTAATAATTTTTATTAGCT
1 CATGTTAATAATTTTAATTAGCT
123680314 CATGTTAAT-ATTTTAATTAG
1 CATGTTAATAATTTTAATTAG
123680334 AAAGTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (23 bp):
CATGTTAATAATTTTAATTAGCT
Found at i:123680397 original size:13 final size:14
Alignment explanation
Indices: 123680368--123680401 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
123680358 GTATCAAATT
123680368 ATATCAAAAATTAAA
1 ATAT-AAAAATTAAA
123680383 ATATAAAAATT-AA
1 ATATAAAAATTAAA
123680396 ATATAA
1 ATATAA
123680402 TATAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 7 0.37
15 4 0.21
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (14 bp):
ATATAAAAATTAAA
Found at i:123688826 original size:106 final size:105
Alignment explanation
Indices: 123688610--123689101 Score: 556
Period size: 107 Copynumber: 4.4 Consensus size: 105
123688600 ATTGGTATAC
* ** * * *
123688610 AAAATACTAGTTTTAAAAAAAAAAATTTTGGGTGCTGAACTATCAATGGCCAGTACCCAGTACCA
1 AAAATACGAGTTTTAAAAAAAAAAA--TTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTA-CA
**
123688675 AAAAAAAATTCAAATTTTTTTTCAAAAAATTTTTTTGCTCTCTA
63 AAAAAAAATTCAAATTTTTTTTCAAAAAA-AATTTTGCTCTCTA
*
123688719 AAAATACGAGTTTTAAAAAAAAAAATTGGGTGCTGGACTGTCAATGGCCGGCACCCAGTACCAAA
1 AAAATACGAGTTTTAAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTA-CAAA
123688784 AAAAAATTCAAATTTTTTTTCAAAAAAAATTTTGCTCTCTA
65 AAAAAATTCAAATTTTTTTTCAAAAAAAATTTTGCTCTCTA
*
123688825 AAAATACGAGTTTT-AAAAAAAAAATTAGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAAA
1 AAAATACGAGTTTTAAAAAAAAAAATT-GGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAA
123688889 AAAAAATTC-AATTTTTTTTCAAAAAAATTTAAATTTTTTTTGCTCTCTA
65 AAAAAATTCAAATTTTTTTTC--AAAAA---AAA----TTTTGCTCTCTA
** ** *
123688938 AAAATACGAGTTTTAAAAAAACAATTTTTTTTTGTGCTGGCCTGTCAATGGCTGGCACCCAGTAC
1 AAAATACGAGTTTTAAAAAAA-AA---AATTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTAC
****
123689003 AAAAAAAAATTCAAATTTTTTTTCAAAATTTTTTTTTTTGCTCTCTA
62 AAAAAAAAATTCAAATTTTTTTTCAAAA---AAAATTTTGCTCTCTA
123689050 AAAATACGAGTTTTTTTAAAAAAAAAAATTTGGGGTGCTGGCCTGTCAATGG
1 AAAATACGAG---TTTTAAAAAAAAAAA-TT-GGGTGCTGGCCTGTCAATGG
123689102 GAAACCAACA
Statistics
Matches: 336, Mismatches: 23, Indels: 44
0.83 0.06 0.11
Matches are distributed among these distances:
104 11 0.03
105 25 0.07
106 62 0.18
107 63 0.19
109 27 0.08
112 24 0.07
113 44 0.13
114 8 0.02
115 13 0.04
116 4 0.01
117 42 0.12
118 13 0.04
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34
Consensus pattern (105 bp):
AAAATACGAGTTTTAAAAAAAAAAATTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAAAA
AAAAATTCAAATTTTTTTTCAAAAAAAATTTTGCTCTCTA
Found at i:123688914 original size:22 final size:22
Alignment explanation
Indices: 123688887--123688929 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
123688877 ACCCAGTACA
*
123688887 AAAAAAAATTCAATTTTTTTTC
1 AAAAAAAATTAAATTTTTTTTC
*
123688909 AAAAAAATTTAAATTTTTTTT
1 AAAAAAAATTAAATTTTTTTT
123688930 GCTCTCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (22 bp):
AAAAAAAATTAAATTTTTTTTC
Found at i:123691246 original size:47 final size:47
Alignment explanation
Indices: 123691182--123691292 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
123691172 GACATTGAGT
*
123691182 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
123691229 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
123691276 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
123691293 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:123698502 original size:47 final size:47
Alignment explanation
Indices: 123698438--123698548 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
123698428 GACATTGAGT
*
123698438 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
123698485 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
123698532 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
123698549 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:123700271 original size:46 final size:46
Alignment explanation
Indices: 123700208--123700332 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
123700198 AACTAGGCAT
*
123700208 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGC
123700254 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGC
* *
123700300 CCGAGCTCGTTG-GTTGTGTCCGAGTTCATTTAT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT
123700333 AGGCGGGTTA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 19 0.25
46 57 0.75
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGC
Found at i:123703380 original size:108 final size:107
Alignment explanation
Indices: 123703219--123703479 Score: 373
Period size: 108 Copynumber: 2.4 Consensus size: 107
123703209 ATGATTGTGT
* * *
123703219 CAGGCCAGCACCCAAATTTTTTTTTAAAAAACTCGTTTTTTTAGAGTGCAAAAAATTTTTTTTGA
1 CAGGCCAGCACCCAAATTTTTTTTT--AAAACTCGTATTTTTAGAGAGCAAAAAA-ATTTTTTGA
* *
123703284 AAAAAAATTTG-ATTTTTTTTTTGGTATTGGGTGCCGGCCATTGA
63 AAAAAAATTTGAATTTATTTTTTGGTACTGGGTGCCGGCCATTGA
123703328 CAGGCCAGCA-CCAAATTTTTTTTTAAAACTCGTATTTTTAGAGAGCAAAAAAAAATTTTTTGAA
1 CAGGCCAGCACCCAAATTTTTTTTTAAAACTCGTATTTTTAGAGAGC--AAAAAAATTTTTTGAA
123703392 AAAAAATTTGAATTTATTTTTTGGTACTGGGTGCCGGCCATTGA
64 AAAAAATTTGAATTTATTTTTTGGTACTGGGTGCCGGCCATTGA
123703436 CAGGCCAGCACCCAAAAAATTTTTTTTTTTAAAACTCGTATTTT
1 CAGGCCAGCACCC---AAA--TTTTTTTTTAAAACTCGTATTTT
123703480 GTATACTAAT
Statistics
Matches: 138, Mismatches: 5, Indels: 13
0.88 0.03 0.08
Matches are distributed among these distances:
106 20 0.14
107 19 0.14
108 61 0.44
109 12 0.09
112 3 0.02
114 23 0.17
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (107 bp):
CAGGCCAGCACCCAAATTTTTTTTTAAAACTCGTATTTTTAGAGAGCAAAAAAATTTTTTGAAAA
AAAATTTGAATTTATTTTTTGGTACTGGGTGCCGGCCATTGA
Found at i:123711013 original size:42 final size:42
Alignment explanation
Indices: 123710954--123711039 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
123710944 CATTACAACA
123710954 ACCGCAAAACCAAAAACCAAAACAAACAAAACCCAAAATCTT
1 ACCGCAAAACCAAAAACCAAAACAAACAAAACCCAAAATCTT
123710996 ACCGCAAAACCAAAAACCAAAACAAACAAAACCCAAAATCTT
1 ACCGCAAAACCAAAAACCAAAACAAACAAAACCCAAAATCTT
123711038 AC
1 AC
123711040 GTTGTAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.59, C:0.31, G:0.02, T:0.07
Consensus pattern (42 bp):
ACCGCAAAACCAAAAACCAAAACAAACAAAACCCAAAATCTT
Found at i:123715244 original size:22 final size:23
Alignment explanation
Indices: 123715199--123715244 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
123715189 AAAAAATTAT
* *
123715199 AAATTTGTCACTTAATTATTTAA
1 AAATTTGTCACTTAAATATCTAA
*
123715222 AAATTT-TCATTTAAATATCTAA
1 AAATTTGTCACTTAAATATCTAA
123715244 A
1 A
123715245 CTATTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTTGTCACTTAAATATCTAA
Found at i:123715906 original size:1 final size:1
Alignment explanation
Indices: 123715900--123715924 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
123715890 AGAATCATTG
123715900 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
123715925 AACAAACAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:123719905 original size:30 final size:30
Alignment explanation
Indices: 123719869--123719968 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 30
123719859 ATTTTTACAG
* * *
123719869 ATCTTTTAAAAATATATGAATATATTATAT
1 ATCTTTTAAATATTTAAGAATATATTATAT
123719899 ATCTTTTAGGCATATATTTAAGAATATATTATAT
1 ATCTTTTA---A-ATATTTAAGAATATATTATAT
** *
123719933 AT-TTTTCTGATATTTAGGAATATATTATAT
1 ATCTTTT-AAATATTTAAGAATATATTATAT
123719963 ATCTTT
1 ATCTTT
123719969 CTTATTTCTG
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
30 30 0.52
31 3 0.05
33 5 0.09
34 20 0.34
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (30 bp):
ATCTTTTAAATATTTAAGAATATATTATAT
Found at i:123719970 original size:30 final size:32
Alignment explanation
Indices: 123719886--123719970 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 32
123719876 AAAAATATAT
123719886 GAATATATTATATATCTTT-TAGGCATATATTTAA
1 GAATATATTATATATCTTTCTA-G-A-ATATTTAA
* *
123719920 GAATATATTATATATTTTTCT-G-ATATTTAG
1 GAATATATTATATATCTTTCTAGAATATTTAA
123719950 GAATATATTATATATCTTTCT
1 GAATATATTATATATCTTTCT
123719971 TATTTCTGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 27 0.57
33 1 0.02
34 18 0.38
35 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (32 bp):
GAATATATTATATATCTTTCTAGAATATTTAA
Found at i:123721721 original size:44 final size:45
Alignment explanation
Indices: 123721626--123721740 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 45
123721616 ACAGGACAGA
*
123721626 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCTTTGGAG
* *
123721672 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGG-TATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCT-TTGGAG
* **
123721716 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
123721741 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 34 0.56
46 26 0.43
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCTTTGGAG
Found at i:123727221 original size:48 final size:50
Alignment explanation
Indices: 123727163--123727262 Score: 150
Period size: 48 Copynumber: 2.0 Consensus size: 50
123727153 GTATATATTA
*
123727163 ATTTTTAATTTTGATTCAATTTTATATCTT-TA-TTTTATATTAGATAGT
1 ATTTTTAATTTTGATTCAATTATATATCTTATATTTTTATATTAGATAGT
* * *
123727211 ATTTTTAATTTTGATTTAATTATATATTTTATATTTTTATATTGGATAGT
1 ATTTTTAATTTTGATTCAATTATATATCTTATATTTTTATATTAGATAGT
123727261 AT
1 AT
123727263 GATGTAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 27 0.59
49 2 0.04
50 17 0.37
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (50 bp):
ATTTTTAATTTTGATTCAATTATATATCTTATATTTTTATATTAGATAGT
Found at i:123731960 original size:28 final size:27
Alignment explanation
Indices: 123731929--123732010 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 27
123731919 AAAAAATTAA
123731929 TATGAAAAAATCGAGAATCAAATCAAAT
1 TATGAAAAAATCGAGAA-CAAATCAAAT
* * *
123731957 TATG-AAGAA-C-A-AA-AAGT-TAA-
1 TATGAAAAAATCGAGAACAAATCAAAT
123731977 TATGAAAAAATCGAGAACCAAATCAAAT
1 TATGAAAAAATCGAGAA-CAAATCAAAT
123732005 TATGAA
1 TATGAA
123732011 GAACAGTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
20 4 0.10
21 6 0.15
22 4 0.10
23 1 0.03
24 4 0.10
25 1 0.03
26 4 0.10
27 6 0.15
28 10 0.25
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (27 bp):
TATGAAAAAATCGAGAACAAATCAAAT
Found at i:123731977 original size:48 final size:48
Alignment explanation
Indices: 123731916--123732015 Score: 182
Period size: 48 Copynumber: 2.1 Consensus size: 48
123731906 AAAAATCTAA
*
123731916 AACAAAAAATTAATATGAAAAAATCGAGAATCAAATCAAATTATGAAG
1 AACAAAAAATTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
*
123731964 AACAAAAAGTTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
1 AACAAAAAATTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
123732012 AACA
1 AACA
123732016 GTTCAAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (48 bp):
AACAAAAAATTAATATGAAAAAATCGAGAACCAAATCAAATTATGAAG
Done.