Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 12 of 75
Found at i:3460526 original size:20 final size:20
Alignment explanation
Indices: 3460497--3460536 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3460487 TGAACAGAAT
* *
3460497 AGAACGGAACGGAGCAAAAC
1 AGAACAGAACAGAGCAAAAC
3460517 AGAACAGAACAGAGCAAAAC
1 AGAACAGAACAGAGCAAAAC
3460537 GAAGCATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.20, G:0.25, T:0.00
Consensus pattern (20 bp):
AGAACAGAACAGAGCAAAAC
Found at i:3460919 original size:104 final size:103
Alignment explanation
Indices: 3460731--3460964 Score: 263
Period size: 104 Copynumber: 2.3 Consensus size: 103
3460721 TTATCAACAT
* * * * * * *
3460731 GGCCTGGTCACACGCCCATGTTCTTACTTGTGTGTCTCACACGGCCTGGGCACACCCCCATGTCC
1 GGCCTGGACACACGCCCATGTCCTT-GTTGTGTGGCACACACAGCCTAGGCACACCCCCATGTCC
** * * *
3460796 CTAGCTGTATGGTTTTAAAGTGTAAACAGTGAGTTATAC
65 CTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTACAC
*
3460835 GGCCCT-GACACACGCCCATGTCCTTGTTCGTGTGGCACACACAGCCTAGGCACACGCCCATGTC
1 GG-CCTGGACACACGCCCATGTCCTTGTT-GTGTGGCACACACAGCCTAGGCACACCCCCATGTC
* * *
3460899 CCTGGCCATGTGGTTCTAAAGCGTAAATAGTGAGTTACAC
64 CCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTACAC
* **
3460939 GGCCTGGACACATGTTCATGTCCTTG
1 GGCCTGGACACACGCCCATGTCCTTG
3460965 CCCATGTGGC
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
103 5 0.05
104 100 0.93
105 3 0.03
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (103 bp):
GGCCTGGACACACGCCCATGTCCTTGTTGTGTGGCACACACAGCCTAGGCACACCCCCATGTCCC
TAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTACAC
Found at i:3460973 original size:104 final size:104
Alignment explanation
Indices: 3460768--3461003 Score: 249
Period size: 104 Copynumber: 2.3 Consensus size: 104
3460758 TTGTGTGTCT
* * * ** * * *
3460768 CACACGGCCTGGGCACACCCCCATGTCCCTAGCTGTATGGTTTTAAAGTGTAAACAGTGAGTTAT
1 CACACAGCCTAGGCACACACCCATGTCCCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTAC
** *
3460833 ACGGCCCTGACACACGCCCATGTCCTTGTTCGTGTGGCA
66 ACGGCCCTGACACACGCCCATGTCCTTGCCCATGTGGCA
* * * *
3460872 CACACAGCCTAGGCACACGCCCATGTCCCTGGCCATGTGGTTCTAAAGCGTAAATAGTGAGTTAC
1 CACACAGCCTAGGCACACACCCATGTCCCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTAC
* ** *
3460937 ACGG-CCTGGACACATGTTCATGTCCTTGCCCATGTGGCT
66 ACGGCCCT-GACACACGCCCATGTCCTTGCCCATGTGGCA
* * * *
3460976 TATACAGTCTAGGCACACACCTATGTCC
1 CACACAGCCTAGGCACACACCCATGTCC
3461004 TTGCCCGTGT
Statistics
Matches: 108, Mismatches: 23, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
103 3 0.03
104 105 0.97
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (104 bp):
CACACAGCCTAGGCACACACCCATGTCCCTAGCCATATGGTTCTAAAGCGTAAACAGTGAGTTAC
ACGGCCCTGACACACGCCCATGTCCTTGCCCATGTGGCA
Found at i:3461033 original size:42 final size:42
Alignment explanation
Indices: 3460955--3461048 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
3460945 GACACATGTT
* * *
3460955 CATGTCCTTGCCCATGTGGCTTATACAGTCTAGGCACAC-AC
1 CATGTCCTTGCCCATGTGGCTCACACAGCCTAGGCACACGAC
* * *
3460996 CTATGTCCTTGCCCGTGTGGCTCACAC-GACCTGGGCACACGTC
1 C-ATGTCCTTGCCCATGTGGCTCACACAG-CCTAGGCACACGAC
3461039 CATGTCCTTG
1 CATGTCCTTG
3461049 GTCGTATGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 2 0.05
42 40 0.91
43 2 0.05
ACGTcount: A:0.17, C:0.34, G:0.22, T:0.27
Consensus pattern (42 bp):
CATGTCCTTGCCCATGTGGCTCACACAGCCTAGGCACACGAC
Found at i:3461033 original size:146 final size:145
Alignment explanation
Indices: 3460843--3461195 Score: 440
Period size: 146 Copynumber: 2.4 Consensus size: 145
3460833 ACGGCCCTGA
** * *
3460843 CACACGCCCATGTCCTTGTTCGTGTGGCACACAC-AGCCTAGGCACACGCCCATGTCCCTGGCCA
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGA-CCTGGGCACACGCCCATGTCCCTGGCCA
* * * * * *
3460907 TGTGGTTCTAAAGCGTAAATAGTGAGTTACACGGCCTGGACACATGTTCATGTCCTTGCCCATGT
65 TATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCCATGT
* * *
3460972 GGCTTATACAGTCTAGG
130 GGCTCACAC-GGCTAGG
* * * * * *
3460989 CACACACCTATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGTCCATGTCCTTGGTCGT
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGCCCATGTCCCTGGCCAT
**
3461054 ATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCTGTGTG
66 ATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCCATGTG
*
3461119 GCTCACACGGCTGGG
131 GCTCACACGGCTAGG
* * * *
3461134 AACACGCCCATGTCCTTGCCC-TATGGCTCACACGGCCTGGGCACACGCTCATGTCCCTGGCC
1 CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGCCCATGTCCCTGGCC
3461196 GTGTAGCGTC
Statistics
Matches: 175, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
144 35 0.20
145 23 0.13
146 116 0.66
147 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (145 bp):
CACACGCCCATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGCCCATGTCCCTGGCCAT
ATGATTCTAAAGCATAAACAGTGAGTTACACGGCCTGGACACATGCTCATGTCCTTACCCATGTG
GCTCACACGGCTAGG
Found at i:3461148 original size:41 final size:41
Alignment explanation
Indices: 3461081--3461189 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 41
3461071 ACAGTGAGTT
* * * *
3461081 ACACGGCCT-GGACACATGCTCATGTCCTTACCTGTGTGGCTC
1 ACACGGCCTGGGA-ACACGCCCATGTCCTTACC-CTATGGCTC
*
3461123 ACACGG-CTGGGAACACGCCCATGTCCTTGCCCTATGGCTC
1 ACACGGCCTGGGAACACGCCCATGTCCTTACCCTATGGCTC
* *
3461163 ACACGGCCTGGGCACACGCTCATGTCC
1 ACACGGCCTGGGAACACGCCCATGTCC
3461190 CTGGCCGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 13 0.22
41 36 0.62
42 9 0.16
ACGTcount: A:0.17, C:0.37, G:0.25, T:0.21
Consensus pattern (41 bp):
ACACGGCCTGGGAACACGCCCATGTCCTTACCCTATGGCTC
Found at i:3464396 original size:6 final size:6
Alignment explanation
Indices: 3464385--3464410 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3464375 TTTTGGGTTT
3464385 TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TT
3464411 TAAGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:3464983 original size:124 final size:125
Alignment explanation
Indices: 3464593--3465000 Score: 638
Period size: 125 Copynumber: 3.3 Consensus size: 125
3464583 ATTTATTATG
* *
3464593 GAAATCGCCCCCACGTGGACGCGCTGTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
* * *
3464658 ATTTCTGAGCAAATAGTATAAAAAATGCTTCTAGCAGGATGCTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
* * * * *
3464718 GAAATCACTCCTACGTGGACTCGCTTTTGCTACAGTAGGTCTTGAAAAAATAATTTTGACTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
*
3464783 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGTTTTATCAGAAGAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
* * * *
3464843 GAAATCGCTCCTACGTGGACGCGTTTTTGCTACAGTAGATCCTGAAAAAATAATTTCGAGTTGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
* * *
3464908 GTTTTTGAGCAAATAGTAT-AAAAATGCTTCAAGTAGGATGCTTTATTAGAATAATTTCT
66 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
*
3464967 GAAATCGCTCCCACGTGGACGCGTTTTTGCTACA
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACA
3465001 ATAGCATGAG
Statistics
Matches: 260, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
124 70 0.27
125 190 0.73
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTTGAGTTGAC
GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGTAGGATGCTTTATCAGAAGAATTTCT
Found at i:3468178 original size:49 final size:49
Alignment explanation
Indices: 3468118--3468267 Score: 291
Period size: 49 Copynumber: 3.1 Consensus size: 49
3468108 AAACTATTTT
3468118 CATCAAATAATATCAAATTATTCAAAATAAACTATTTTGTATTTTATTA
1 CATCAAATAATATCAAATTATTCAAAATAAACTATTTTGTATTTTATTA
3468167 CATCAAATAATATCAAATTATTCAAAATAAACTATTTTGTATTTTATTA
1 CATCAAATAATATCAAATTATTCAAAATAAACTATTTTGTATTTTATTA
*
3468216 CATCAAATAATATCAAATTATTCAAAATAAACTATTTTGTATTATATTA
1 CATCAAATAATATCAAATTATTCAAAATAAACTATTTTGTATTTTATTA
3468265 CAT
1 CAT
3468268 TAATATAAAC
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 100 1.00
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (49 bp):
CATCAAATAATATCAAATTATTCAAAATAAACTATTTTGTATTTTATTA
Found at i:3468714 original size:18 final size:18
Alignment explanation
Indices: 3468688--3468730 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
3468678 GACTAGAAAA
* * *
3468688 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
3468706 AGGATACATAAAATGGCT
1 AGGATACATAAAAGGGCT
3468724 AGGATAC
1 AGGATAC
3468731 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:3470540 original size:22 final size:22
Alignment explanation
Indices: 3470498--3470546 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3470488 TCTTTTAAAT
* *
3470498 AGAAATTTGAGAGGAATTTGAG
1 AGAAATTAGAGAGGAAATTGAG
3470520 AGAATATTAGAGA-GAAATTGAG
1 AGAA-ATTAGAGAGGAAATTGAG
3470542 AGAAA
1 AGAAA
3470547 ATATTTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (22 bp):
AGAAATTAGAGAGGAAATTGAG
Found at i:3470542 original size:10 final size:10
Alignment explanation
Indices: 3470498--3470546 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 10
3470488 TCTTTTAAAT
3470498 AGAAATTTGAG
1 AGAAA-TTGAG
*
3470509 AGGAATTTGAG
1 A-GAAATTGAG
3470520 AGAATATTAGAG
1 AGAA-ATT-GAG
3470532 AGAAATTGAG
1 AGAAATTGAG
3470542 AGAAA
1 AGAAA
3470547 ATATTTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 11 0.33
11 12 0.36
12 10 0.30
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:3473080 original size:18 final size:19
Alignment explanation
Indices: 3473042--3473103 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
3473032 AAGAATTCTA
* * *
3473042 AAAAATATAAAAAAAACAT
1 AAAAATTTAAAAAATAGAT
* *
3473061 AAATATTTTAAAAATA-AT
1 AAAAATTTAAAAAATAGAT
3473079 AATAAATTTAAAAAATAGAT
1 AA-AAATTTAAAAAATAGAT
3473099 AAAAA
1 AAAAA
3473104 AAAGTATTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 4 0.11
19 27 0.77
20 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATTTAAAAAATAGAT
Found at i:3473426 original size:27 final size:27
Alignment explanation
Indices: 3473354--3473438 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
3473344 GTATGGGGTA
* * *
3473354 GGTGGCGCCTATCTGACAAGCGCGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
3473381 GGTGGAGCTTATCTGACAGGCGCGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
* *
3473408 GGTGGAGCTTATCTGACAGGTGTGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
3473435 GGTG
1 GGTG
3473439 CTTAATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.24
Consensus pattern (27 bp):
GGTGGAGCTTATCTGACAGGCGCGACT
Found at i:3473708 original size:18 final size:19
Alignment explanation
Indices: 3473670--3473731 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
3473660 AAGAATTCTA
* * *
3473670 AAAAATATAAAAAAAACAT
1 AAAAATTTAAAAAATAGAT
* *
3473689 AAATATTTTAAAAATA-AT
1 AAAAATTTAAAAAATAGAT
3473707 AATAAATTTAAAAAATAGAT
1 AA-AAATTTAAAAAATAGAT
3473727 AAAAA
1 AAAAA
3473732 AAAGTATTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 4 0.11
19 27 0.77
20 4 0.11
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATTTAAAAAATAGAT
Found at i:3474054 original size:27 final size:27
Alignment explanation
Indices: 3473982--3474066 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
3473972 GTATGGGGTA
* * *
3473982 GGTGGCGCCTATCTGACAAGCGCGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
3474009 GGTGGAGCTTATCTGACAGGCGCGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
* *
3474036 GGTGGAGCTTATCTGACAGGTGTGACT
1 GGTGGAGCTTATCTGACAGGCGCGACT
3474063 GGTG
1 GGTG
3474067 CTTAATTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.24
Consensus pattern (27 bp):
GGTGGAGCTTATCTGACAGGCGCGACT
Found at i:3474188 original size:628 final size:628
Alignment explanation
Indices: 3472992--3474247 Score: 2512
Period size: 628 Copynumber: 2.0 Consensus size: 628
3472982 AAAATCAACC
3472992 TTCAAATCTTAAAAATATTTTCAATTTGATCCTAATTCTAAAGAATTCTAAAAAATATAAAAAAA
1 TTCAAATCTTAAAAATATTTTCAATTTGATCCTAATTCTAAAGAATTCTAAAAAATATAAAAAAA
3473057 ACATAAATATTTTAAAAATAATAATAAATTTAAAAAATAGATAAAAAAAAGTATTCCCCTCGGTT
66 ACATAAATATTTTAAAAATAATAATAAATTTAAAAAATAGATAAAAAAAAGTATTCCCCTCGGTT
3473122 AATTTACCTAAATAATTTTAAAAAAATTTAAATATTAAATAGGTTGTCAGCTGGATTATATACGA
131 AATTTACCTAAATAATTTTAAAAAAATTTAAATATTAAATAGGTTGTCAGCTGGATTATATACGA
3473187 AAATGGTATTTTTTTTGGGTCGCGCCTATCACTTTTTTATTTTAAAATATTTTTTTGTTTTTTAA
196 AAATGGTATTTTTTTTGGGTCGCGCCTATCACTTTTTTATTTTAAAATATTTTTTTGTTTTTTAA
3473252 TTATTATTTTATTGGTGGTGCATTTCTCATAGGCGCCACTGCTTGTATTTTTTCCCGGATTAGTA
261 TTATTATTTTATTGGTGGTGCATTTCTCATAGGCGCCACTGCTTGTATTTTTTCCCGGATTAGTA
3473317 TATGACCCGTGTAGAGATACGAAAATGGTATGGGGTAGGTGGCGCCTATCTGACAAGCGCGACTG
326 TATGACCCGTGTAGAGATACGAAAATGGTATGGGGTAGGTGGCGCCTATCTGACAAGCGCGACTG
3473382 GTGGAGCTTATCTGACAGGCGCGACTGGTGGAGCTTATCTGACAGGTGTGACTGGTGCTTAATTT
391 GTGGAGCTTATCTGACAGGCGCGACTGGTGGAGCTTATCTGACAGGTGTGACTGGTGCTTAATTT
3473447 TTCCCCTATATATACTCTCTCAAAAATCAAATGAGCTAAAGATATACACAAAATTTAGCAGAACA
456 TTCCCCTATATATACTCTCTCAAAAATCAAATGAGCTAAAGATATACACAAAATTTAGCAGAACA
3473512 GAACTAAGAAGCTAAGGAGAAGAAAGAAAGAAAGGAAAACAAAAAGAATAATAAGGTATTTTAGT
521 GAACTAAGAAGCTAAGGAGAAGAAAGAAAGAAAGGAAAACAAAAAGAATAATAAGGTATTTTAGT
3473577 TTATTTCTTTTTAAATAGAATGTAGAGTTTTTTTAGTAATTTT
586 TTATTTCTTTTTAAATAGAATGTAGAGTTTTTTTAGTAATTTT
3473620 TTCAAATCTTAAAAATATTTTCAATTTGATCCTAATTCTAAAGAATTCTAAAAAATATAAAAAAA
1 TTCAAATCTTAAAAATATTTTCAATTTGATCCTAATTCTAAAGAATTCTAAAAAATATAAAAAAA
3473685 ACATAAATATTTTAAAAATAATAATAAATTTAAAAAATAGATAAAAAAAAGTATTCCCCTCGGTT
66 ACATAAATATTTTAAAAATAATAATAAATTTAAAAAATAGATAAAAAAAAGTATTCCCCTCGGTT
3473750 AATTTACCTAAATAATTTTAAAAAAATTTAAATATTAAATAGGTTGTCAGCTGGATTATATACGA
131 AATTTACCTAAATAATTTTAAAAAAATTTAAATATTAAATAGGTTGTCAGCTGGATTATATACGA
3473815 AAATGGTATTTTTTTTGGGTCGCGCCTATCACTTTTTTATTTTAAAATATTTTTTTGTTTTTTAA
196 AAATGGTATTTTTTTTGGGTCGCGCCTATCACTTTTTTATTTTAAAATATTTTTTTGTTTTTTAA
3473880 TTATTATTTTATTGGTGGTGCATTTCTCATAGGCGCCACTGCTTGTATTTTTTCCCGGATTAGTA
261 TTATTATTTTATTGGTGGTGCATTTCTCATAGGCGCCACTGCTTGTATTTTTTCCCGGATTAGTA
3473945 TATGACCCGTGTAGAGATACGAAAATGGTATGGGGTAGGTGGCGCCTATCTGACAAGCGCGACTG
326 TATGACCCGTGTAGAGATACGAAAATGGTATGGGGTAGGTGGCGCCTATCTGACAAGCGCGACTG
3474010 GTGGAGCTTATCTGACAGGCGCGACTGGTGGAGCTTATCTGACAGGTGTGACTGGTGCTTAATTT
391 GTGGAGCTTATCTGACAGGCGCGACTGGTGGAGCTTATCTGACAGGTGTGACTGGTGCTTAATTT
3474075 TTCCCCTATATATACTCTCTCAAAAATCAAATGAGCTAAAGATATACACAAAATTTAGCAGAACA
456 TTCCCCTATATATACTCTCTCAAAAATCAAATGAGCTAAAGATATACACAAAATTTAGCAGAACA
3474140 GAACTAAGAAGCTAAGGAGAAGAAAGAAAGAAAGGAAAACAAAAAGAATAATAAGGTATTTTAGT
521 GAACTAAGAAGCTAAGGAGAAGAAAGAAAGAAAGGAAAACAAAAAGAATAATAAGGTATTTTAGT
3474205 TTATTTCTTTTTAAATAGAATGTAGAGTTTTTTTAGTAATTTT
586 TTATTTCTTTTTAAATAGAATGTAGAGTTTTTTTAGTAATTTT
3474248 ATTATTGGAA
Statistics
Matches: 628, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
628 628 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (628 bp):
TTCAAATCTTAAAAATATTTTCAATTTGATCCTAATTCTAAAGAATTCTAAAAAATATAAAAAAA
ACATAAATATTTTAAAAATAATAATAAATTTAAAAAATAGATAAAAAAAAGTATTCCCCTCGGTT
AATTTACCTAAATAATTTTAAAAAAATTTAAATATTAAATAGGTTGTCAGCTGGATTATATACGA
AAATGGTATTTTTTTTGGGTCGCGCCTATCACTTTTTTATTTTAAAATATTTTTTTGTTTTTTAA
TTATTATTTTATTGGTGGTGCATTTCTCATAGGCGCCACTGCTTGTATTTTTTCCCGGATTAGTA
TATGACCCGTGTAGAGATACGAAAATGGTATGGGGTAGGTGGCGCCTATCTGACAAGCGCGACTG
GTGGAGCTTATCTGACAGGCGCGACTGGTGGAGCTTATCTGACAGGTGTGACTGGTGCTTAATTT
TTCCCCTATATATACTCTCTCAAAAATCAAATGAGCTAAAGATATACACAAAATTTAGCAGAACA
GAACTAAGAAGCTAAGGAGAAGAAAGAAAGAAAGGAAAACAAAAAGAATAATAAGGTATTTTAGT
TTATTTCTTTTTAAATAGAATGTAGAGTTTTTTTAGTAATTTT
Found at i:3477606 original size:33 final size:33
Alignment explanation
Indices: 3477508--3477632 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 33
3477498 AACTTGAGCC
* * *
3477508 GAGAGGAGTGGAGTACGGCAGTAGATACGGG-CT
1 GAGAGGAGTGGAGTACGAC-GTGGATACGGGCCA
* *
3477541 GAGAGGAGTGAAGTACGATGGTGGATACGGGCCA
1 GAGAGGAGTGGAGTACGA-CGTGGATACGGGCCA
*
3477575 G-GAGGAGTGGAGTACGACGTTGGATACGGGCCT
1 GAGAGGAGTGGAGTACGACG-TGGATACGGGCCA
* * *
3477608 GA-ATGAGCGGAGTACTGAGGTGGAT
1 GAGAGGAGTGGAGTAC-GACGTGGAT
3477633 GTGAGCTGGG
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
32 1 0.01
33 70 0.92
34 5 0.07
ACGTcount: A:0.26, C:0.12, G:0.45, T:0.17
Consensus pattern (33 bp):
GAGAGGAGTGGAGTACGACGTGGATACGGGCCA
Found at i:3478781 original size:15 final size:14
Alignment explanation
Indices: 3478756--3478797 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3478746 ACATTTTTAT
3478756 AAATC-AATAAAAA
1 AAATCAAATAAAAA
*
3478769 ATTATCAAATAAATAA
1 A-AATCAAATAAA-AA
3478785 AAATCAAATAAAA
1 AAATCAAATAAAA
3478798 TTACATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 4 0.17
15 16 0.67
16 3 0.12
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATCAAATAAAAA
Found at i:3478788 original size:18 final size:18
Alignment explanation
Indices: 3478752--3478787 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3478742 ATCAACATTT
*
3478752 TTATAAATCAATAAAAAA
1 TTATAAATAAATAAAAAA
3478770 TTATCAAATAAATAAAAA
1 TTAT-AAATAAATAAAAA
3478788 TCAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
TTATAAATAAATAAAAAA
Found at i:3478901 original size:104 final size:104
Alignment explanation
Indices: 3478793--3479085 Score: 527
Period size: 104 Copynumber: 2.8 Consensus size: 104
3478783 AAAAATCAAA
* *
3478793 TAAAATTACATTA-AAAAAAATCACAAAACAC-TAAACTAAACACTAACAATTTATATAACCTAA
1 TAAAA-TACATTACTAAAAAATCACAAAACACAT-AACTAAACCCTAACAATTTATATAACCTAA
*
3478856 TCATAAATTACTAACAAAATAACTATAAAATTATTATTTTT
64 TCATAAATTATTAACAAAATAACTATAAAATTATTATTTTT
3478897 TAAAATACATTACTAAAAAATCACAAAACACATAACTAAACCCTAACAATTTATATAACCTAATC
1 TAAAATACATTACTAAAAAATCACAAAACACATAACTAAACCCTAACAATTTATATAACCTAATC
3478962 ATAAATTATTAACAAAATAACTATAAAATTATTATTTTT
66 ATAAATTATTAACAAAATAACTATAAAATTATTATTTTT
3479001 TAAAATACATTACTAAAAAATCACAAAACACATAACTAAACCCTAACAATTTATATAACCTAATC
1 TAAAATACATTACTAAAAAATCACAAAACACATAACTAAACCCTAACAATTTATATAACCTAATC
3479066 ATAAATTATTAACAAAATAA
66 ATAAATTATTAACAAAATAA
3479086 ATAACTATAA
Statistics
Matches: 184, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
103 7 0.04
104 176 0.96
105 1 0.01
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (104 bp):
TAAAATACATTACTAAAAAATCACAAAACACATAACTAAACCCTAACAATTTATATAACCTAATC
ATAAATTATTAACAAAATAACTATAAAATTATTATTTTT
Found at i:3478923 original size:50 final size:50
Alignment explanation
Indices: 3478869--3479028 Score: 128
Period size: 50 Copynumber: 3.1 Consensus size: 50
3478859 TAAATTACTA
3478869 ACAAAATAACTATAAAATTATTATTTTTTAAAATACATTACTAAAAAATC
1 ACAAAATAACTATAAAATTATTATTTTTTAAAATACATTACTAAAAAATC
** * ** * ** * * * *
3478919 ACAAAACACATAACTA-AACCCTAACAATTTATATAACCTA-ATCA-TAAATTATTA
1 AC--AA-A-ATAACTATAA-AATTATTATTT-TTTAAAATACATTACTAAA-AAATC
3478973 ACAAAATAACTATAAAATTATTATTTTTTAAAATACATTACTAAAAAATC
1 ACAAAATAACTATAAAATTATTATTTTTTAAAATACATTACTAAAAAATC
3479023 ACAAAA
1 ACAAAA
3479029 CACATAACTA
Statistics
Matches: 76, Mismatches: 24, Indels: 20
0.63 0.20 0.17
Matches are distributed among these distances:
49 6 0.08
50 26 0.34
51 7 0.09
52 4 0.05
53 7 0.09
54 20 0.26
55 6 0.08
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (50 bp):
ACAAAATAACTATAAAATTATTATTTTTTAAAATACATTACTAAAAAATC
Found at i:3479695 original size:27 final size:27
Alignment explanation
Indices: 3479660--3479741 Score: 121
Period size: 27 Copynumber: 3.0 Consensus size: 27
3479650 AGGGGGTAGG
*
3479660 CAGTGGCGCCTACCT-ATCAGGCGCGAC
1 CAGTTGCGCCTACCTGA-CAGGCGCGAC
*
3479687 TAGTTGCGCCTACCTGACAGGCGCGAC
1 CAGTTGCGCCTACCTGACAGGCGCGAC
*
3479714 CAGTTGCGCCTATCTGACAGGCGCGAC
1 CAGTTGCGCCTACCTGACAGGCGCGAC
3479741 C
1 C
3479742 TGTCTCAGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.17
Consensus pattern (27 bp):
CAGTTGCGCCTACCTGACAGGCGCGAC
Found at i:3496295 original size:28 final size:28
Alignment explanation
Indices: 3496264--3496319 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3496254 AAAAGTTATA
*
3496264 AAAAGATTATAAAAATCGTAAAAAAAAT
1 AAAAGATTATAAAAATCATAAAAAAAAT
** *
3496292 AAAATTTTATAAAAATCATACAAAAAAT
1 AAAAGATTATAAAAATCATAAAAAAAAT
3496320 TATAAAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.25
Consensus pattern (28 bp):
AAAAGATTATAAAAATCATAAAAAAAAT
Found at i:3503902 original size:20 final size:19
Alignment explanation
Indices: 3503864--3503902 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3503854 TTAATTTCTT
*
3503864 TTAAAATTTAAAAACATTA
1 TTAAAATTAAAAAACATTA
*
3503883 TTAAAATTAATAAAATATTA
1 TTAAAATTAA-AAAACATTA
3503903 AATAAAGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAAAATTAAAAAACATTA
Found at i:3504858 original size:15 final size:15
Alignment explanation
Indices: 3504834--3504867 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3504824 ATTTATTTTT
3504834 AATTATTTAAAT-AA
1 AATTATTTAAATGAA
3504848 AATTAATTTAAATGAA
1 AATT-ATTTAAATGAA
3504864 AATT
1 AATT
3504868 GAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATGAA
Found at i:3507562 original size:54 final size:54
Alignment explanation
Indices: 3507480--3507600 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
3507470 TTTATATTGC
*
3507480 ATGCATGACATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
1 ATGCATGAAATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
* *
3507534 ATGCATGAGATTTAATTTGAATATAGGATATTGAAATATGAATATTAATTAATT
1 ATGCATGAAATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
3507588 ATGCATGAAATTT
1 ATGCATGAAATTT
3507601 TGGTCTTTAC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.40
Consensus pattern (54 bp):
ATGCATGAAATTTAATTTGAATATAGGATATTGAAATATAAATATTAATTAATT
Found at i:3519707 original size:72 final size:72
Alignment explanation
Indices: 3519617--3519788 Score: 231
Period size: 72 Copynumber: 2.4 Consensus size: 72
3519607 AAAATCACAT
* *
3519617 ATAAACAACTATTGATAAAACTAATTTA-ATAAAAAATAAGTAGAATATAAATTCAATATCTAAA
1 ATAAACAACTATTGATAAAACTAATTTACA-AAAAAATAAGTAGAACATAAATTCAATATCCAAA
*
3519681 GACCAAAC
65 AACCAAAC
* * * *
3519689 ATAAACAACTTTTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTA-ATTTACAAAAAAATAAGTAGAACATAAATTCAATATCCAAA
3519753 AACCAAAC
65 AACCAAAC
* *
3519761 ATAAATAACTATTGATAAAACTAGTTTA
1 ATAAACAACTATTGATAAAACTAATTTA
3519789 GCATTGTTGT
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
72 84 0.98
73 2 0.02
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAATTTACAAAAAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:3522882 original size:25 final size:25
Alignment explanation
Indices: 3522854--3522940 Score: 105
Period size: 25 Copynumber: 3.7 Consensus size: 25
3522844 AACAAAGAAG
*
3522854 CAGCAGAAGAACAAAGAACCAGCAC
1 CAGCAGAGGAACAAAGAACCAGCAC
*
3522879 CAGCAGAGGAAC--A-AA-TA--AC
1 CAGCAGAGGAACAAAGAACCAGCAC
*
3522898 CAGCAGAGGAACAAAGAACCAACAC
1 CAGCAGAGGAACAAAGAACCAGCAC
3522923 CAGCAGAGGAACAAAGAA
1 CAGCAGAGGAACAAAGAA
3522941 TAAGTAGAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
19 14 0.26
21 2 0.04
22 4 0.08
23 2 0.04
25 31 0.58
ACGTcount: A:0.53, C:0.24, G:0.22, T:0.01
Consensus pattern (25 bp):
CAGCAGAGGAACAAAGAACCAGCAC
Found at i:3522901 original size:19 final size:19
Alignment explanation
Indices: 3522839--3522964 Score: 90
Period size: 19 Copynumber: 6.0 Consensus size: 19
3522829 GTGGTGGAGA
*
3522839 AGAGGAACAAAGAAGCAGC
1 AGAGGAACAAAGAACCAGC
*
3522858 AGAAGAACAAAGAACCAGCACCAGC
1 AGAGGAACAAAG----A--ACCAGC
*
3522883 AGAGGAACAAATAACCAGC
1 AGAGGAACAAAGAACCAGC
3522902 AGAGGAACAAAGAACCAACACCAGC
1 AGAGGAACAAAG-----A-ACCAGC
** *
3522927 AGAGGAACAAAGAATAAGT
1 AGAGGAACAAAGAACCAGC
3522946 AGAGGAACAAAGAACCAGC
1 AGAGGAACAAAGAACCAGC
3522965 GATGGGAGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
19 47 0.56
20 1 0.01
21 1 0.01
23 1 0.01
24 1 0.01
25 33 0.39
ACGTcount: A:0.53, C:0.21, G:0.24, T:0.02
Consensus pattern (19 bp):
AGAGGAACAAAGAACCAGC
Found at i:3522902 original size:44 final size:44
Alignment explanation
Indices: 3522839--3522964 Score: 189
Period size: 44 Copynumber: 2.9 Consensus size: 44
3522829 GTGGTGGAGA
* *
3522839 AGAGGAACAAAGAAGCAGCAGAAGAACAAAGAACCAGCACCAGC
1 AGAGGAACAAAGAACCAGCAGAGGAACAAAGAACCAGCACCAGC
* *
3522883 AGAGGAACAAATAACCAGCAGAGGAACAAAGAACCAACACCAGC
1 AGAGGAACAAAGAACCAGCAGAGGAACAAAGAACCAGCACCAGC
** *
3522927 AGAGGAACAAAGAATAAGTAGAGGAACAAAGAACCAGC
1 AGAGGAACAAAGAACCAGCAGAGGAACAAAGAACCAGC
3522965 GATGGGAGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.53, C:0.21, G:0.24, T:0.02
Consensus pattern (44 bp):
AGAGGAACAAAGAACCAGCAGAGGAACAAAGAACCAGCACCAGC
Found at i:3528349 original size:3 final size:3
Alignment explanation
Indices: 3528341--3528371 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3528331 GTAATGTGCT
*
3528341 TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3528372 CCTTTTTTTT
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:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3535319 original size:72 final size:72
Alignment explanation
Indices: 3535235--3535374 Score: 271
Period size: 72 Copynumber: 1.9 Consensus size: 72
3535225 ATATATATTC
*
3535235 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGGATTTTTTTATACGAATCTATTTAATTATA
1 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGGATTTTTTCATACGAATCTATTTAATTATA
3535300 AATAAAG
66 AATAAAG
3535307 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGGATTTTTTCATACGAATCTATTTAATTATA
1 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGGATTTTTTCATACGAATCTATTTAATTATA
3535372 AAT
66 AAT
3535375 GCAGTTTTGG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.48
Consensus pattern (72 bp):
ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGGATTTTTTCATACGAATCTATTTAATTATA
AATAAAG
Found at i:3535346 original size:36 final size:36
Alignment explanation
Indices: 3535235--3535348 Score: 92
Period size: 35 Copynumber: 3.2 Consensus size: 36
3535225 ATATATATTC
3535235 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGG
1 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGG
* * * ** ** *
3535271 ATTTTTTTATACGAA-TCTA--TTTAATTATAAATAA-AG
1 A---TTTT-TAGGAATTTTATGTTTGAGAATATGTAATGG
3535307 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGG
1 ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGG
3535343 ATTTTT
1 ATTTTT
3535349 TCATACGAAT
Statistics
Matches: 54, Mismatches: 16, Indels: 16
0.63 0.19 0.19
Matches are distributed among these distances:
32 5 0.09
33 7 0.13
35 10 0.19
36 10 0.19
37 10 0.19
39 7 0.13
40 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (36 bp):
ATTTTTAGGAATTTTATGTTTGAGAATATGTAATGG
Found at i:3537645 original size:16 final size:16
Alignment explanation
Indices: 3537620--3537654 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3537610 ATTATTTTTT
3537620 CAAAAACAAAGGAAAA
1 CAAAAACAAAGGAAAA
* *
3537636 CAAAATCAAATGAAAA
1 CAAAAACAAAGGAAAA
3537652 CAA
1 CAA
3537655 TAAAAGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.14, G:0.09, T:0.06
Consensus pattern (16 bp):
CAAAAACAAAGGAAAA
Found at i:3538420 original size:13 final size:13
Alignment explanation
Indices: 3538402--3538437 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3538392 TTCTTTATTG
3538402 CTTTTGAGAAGTA
1 CTTTTGAGAAGTA
*
3538415 CTTTTGAGAAGTG
1 CTTTTGAGAAGTA
3538428 CTTTTGAGAA
1 CTTTTGAGAA
3538438 ATTTGAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (13 bp):
CTTTTGAGAAGTA
Found at i:3541814 original size:46 final size:46
Alignment explanation
Indices: 3541736--3542104 Score: 585
Period size: 46 Copynumber: 8.0 Consensus size: 46
3541726 ACAATGCTAT
* *
3541736 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCCACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * *
3541782 AACTCAGTATGGTTTTCTTTATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
3541828 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
3541874 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
3541920 AACTCAGTATGATTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
3541966 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
3542012 AACTCAATATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* *
3542058 AACTCAATATGGTTTTCTTCATTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
3542104 A
1 A
3542105 CTTTGCCATG
Statistics
Matches: 306, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 306 1.00
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:3548793 original size:78 final size:78
Alignment explanation
Indices: 3548659--3549036 Score: 493
Period size: 78 Copynumber: 4.9 Consensus size: 78
3548649 AACTAATAGT
* * * *
3548659 GGATAATATATGTATATACATGTATAAGTTCTTGAATTTAGTTAAAATTATGTATGTTATATTTA
1 GGAT-ATATATGTATATACATGAATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTTA
*
3548724 TATATATGAAGTTC
65 TATATATAAAGTTC
3548738 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTTAT
3548803 ATATATAAAGTTC
66 ATATATAAAGTTC
3548816 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTTAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTTAT
3548881 ATATATAAAGTTC
66 ATATATAAAGTTC
* * *
3548894 GGATATATGTGTATATACATGAATAAGTTC-TGAATTTAGTTAAT-GT-TGAATGTTATA--TAT
1 GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTTAT
* * *
3548954 GTTTACAAGAGGTTC
66 ATATATAA-A-GTTC
** * * * * *
3548969 GGATAGGTATGTATAT--ATGAGTATAAATTCTTGGATTTA-TTAAAAGTATGGATGTTACATAT
1 GGATATATATGTATATACATGA--ATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTT
3549031 ATATAT
64 ATATAT
3549037 GTATAATATA
Statistics
Matches: 269, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
73 12 0.04
74 1 0.00
75 38 0.14
76 11 0.04
77 23 0.09
78 175 0.65
79 9 0.03
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.44
Consensus pattern (78 bp):
GGATATATATGTATATACATGAATAAATTCTTGAATTTAGTTAATAGTATGTATGTTATATTTAT
ATATATAAAGTTC
Found at i:3549737 original size:41 final size:41
Alignment explanation
Indices: 3549634--3549890 Score: 338
Period size: 41 Copynumber: 6.2 Consensus size: 41
3549624 CATTTCGGAC
* ** **
3549634 TATAAGTCTAGCAGGCTAAAAGCCGGTG-TACTGAATAAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGAT-CTGAACCAGGT
* * *
3549675 TTTAAAACCTAGCAGGCTAAGTGTCGGTGATCTGAACCAGGT
1 TAT-AAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
* *
3549717 TATAAGCCTAGCAGGCTAAGTGCCAGTGATCTAAACCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
*
3549758 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGC
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
* *
3549799 TATAAGCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
* *
3549840 TATAAGCCTAGCATGCTAAGTGCCGGTGATCTGAATCAGGCT
1 TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGG-T
3549882 T-TAAGCCTA
1 TATAAGCCTA
3549891 ACAGATATGA
Statistics
Matches: 192, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
41 158 0.82
42 33 0.17
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (41 bp):
TATAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGT
Found at i:3560721 original size:4 final size:4
Alignment explanation
Indices: 3560712--3560739 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3560702 ATCTTTTATT
3560712 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
3560740 ATCCTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:3565200 original size:16 final size:16
Alignment explanation
Indices: 3565179--3565212 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3565169 GTTTGTTCCT
3565179 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
3565195 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
3565211 TT
1 TT
3565213 AAGGATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATATACTTA
Found at i:3565308 original size:16 final size:16
Alignment explanation
Indices: 3565287--3565320 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3565277 GTTTGATCCT
3565287 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
3565303 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
3565319 TT
1 TT
3565321 AAGGATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATATACTTA
Found at i:3565335 original size:108 final size:108
Alignment explanation
Indices: 3565146--3565454 Score: 609
Period size: 108 Copynumber: 2.9 Consensus size: 108
3565136 TATCTCCTTG
3565146 TACAAGATTCGGATGATGTTTTCGTTTGTTCCTTTTTAAAATATACTTATTTTAAAATATACTTA
1 TACAAGATTCGGATGATGTTTTCGTTTGTTCCTTTTTAAAATATACTTATTTTAAAATATACTTA
3565211 TTAAGGATTCTAATAATATAAATTATAACTCATAATAATTTTT
66 TTAAGGATTCTAATAATATAAATTATAACTCATAATAATTTTT
*
3565254 TACAAGATTCGGATGATGTTTTCGTTTGATCCTTTTTAAAATATACTTATTTTAAAATATACTTA
1 TACAAGATTCGGATGATGTTTTCGTTTGTTCCTTTTTAAAATATACTTATTTTAAAATATACTTA
3565319 TTAAGGATTCTAATAATATAAATTATAACTCATAATAATTTTT
66 TTAAGGATTCTAATAATATAAATTATAACTCATAATAATTTTT
3565362 TACAAGATTCGGATGATGTTTTCGTTTGTTCCTTTTTAAAATATACTTATTTTAAAATATACTTA
1 TACAAGATTCGGATGATGTTTTCGTTTGTTCCTTTTTAAAATATACTTATTTTAAAATATACTTA
3565427 TTAAGGATTCTAATAATATAAATTATAA
66 TTAAGGATTCTAATAATATAAATTATAA
3565455 TTGTACGAGA
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 199 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (108 bp):
TACAAGATTCGGATGATGTTTTCGTTTGTTCCTTTTTAAAATATACTTATTTTAAAATATACTTA
TTAAGGATTCTAATAATATAAATTATAACTCATAATAATTTTT
Found at i:3565416 original size:16 final size:16
Alignment explanation
Indices: 3565395--3565428 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3565385 GTTTGTTCCT
3565395 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
3565411 TTTTAAAATATACTTA
1 TTTTAAAATATACTTA
3565427 TT
1 TT
3565429 AAGGATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAATATACTTA
Found at i:3568060 original size:21 final size:21
Alignment explanation
Indices: 3568036--3568077 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3568026 TTGTTATTAA
3568036 TGTGTTACCCTCATACAATAT
1 TGTGTTACCCTCATACAATAT
3568057 TGTGTTACCCTCATACAATAT
1 TGTGTTACCCTCATACAATAT
3568078 CCTTAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (21 bp):
TGTGTTACCCTCATACAATAT
Found at i:3570748 original size:19 final size:18
Alignment explanation
Indices: 3570712--3570749 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3570702 TTGTTCGAAC
3570712 ATTTTAATATTTTGTAAA
1 ATTTTAATATTTTGTAAA
3570730 ATTTTAAATAATTTT-TAAA
1 ATTTT-AAT-ATTTTGTAAA
3570749 A
1 A
3570750 AAACTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 8 0.44
20 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTTAATATTTTGTAAA
Found at i:3575587 original size:31 final size:31
Alignment explanation
Indices: 3575549--3575623 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
3575539 ATGTTAATGG
*
3575549 GTGACTGATTTGTCACTTTTCGATAACGTTA
1 GTGACTGATTTGTCACTTTTCGATAACATTA
3575580 GTGACTGATTTGTCACTTTTCGATAACATTA
1 GTGACTGATTTGTCACTTTTCGATAACATTA
3575611 GTGACTGATTTGT
1 GTGACTGATTTGT
3575624 TATTTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (31 bp):
GTGACTGATTTGTCACTTTTCGATAACATTA
Found at i:3575701 original size:20 final size:20
Alignment explanation
Indices: 3575678--3575716 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3575668 CAACGTGGCA
3575678 AGTTAACTGG-CTACGTCACT
1 AGTTAACTGGTC-ACGTCACT
3575698 AGTTAACTGGTCACGTCAC
1 AGTTAACTGGTCACGTCAC
3575717 CTGTCCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
AGTTAACTGGTCACGTCACT
Found at i:3582990 original size:12 final size:12
Alignment explanation
Indices: 3582973--3582997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3582963 GGTGTTCATT
3582973 CGGTTAACCGAC
1 CGGTTAACCGAC
3582985 CGGTTAACCGAC
1 CGGTTAACCGAC
3582997 C
1 C
3582998 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:3583247 original size:12 final size:12
Alignment explanation
Indices: 3583230--3583254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3583220 AGTAATTTCG
3583230 GGTCGGTTAACC
1 GGTCGGTTAACC
3583242 GGTCGGTTAACC
1 GGTCGGTTAACC
3583254 G
1 G
3583255 AATTTTTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:3583257 original size:121 final size:121
Alignment explanation
Indices: 3583120--3583387 Score: 536
Period size: 121 Copynumber: 2.2 Consensus size: 121
3583110 TAACCGAATT
3583120 CGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCGGTTAATTTTTTTATGATTTTTCGGTTAACG
1 CGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCGGTTAATTTTTTTATGATTTTTCGGTTAACG
3583185 GTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTATAGTAATTTCGGGTCGGTTAAC
66 GTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTATAGTAATTTCGGGTCGGTTAAC
3583241 CGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCGGTTAATTTTTTTATGATTTTTCGGTTAACG
1 CGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCGGTTAATTTTTTTATGATTTTTCGGTTAACG
3583306 GTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTATAGTAATTTCGGGTCGGTTAAC
66 GTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTATAGTAATTTCGGGTCGGTTAAC
3583362 CGGTCGGTTAACCGAATTTTTTCGGT
1 CGGTCGGTTAACCGAATTTTTTCGGT
3583388 TTTACCCGAA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 147 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.41
Consensus pattern (121 bp):
CGGTCGGTTAACCGAATTTTTTCGGTCGGGGGTCGGTTAATTTTTTTATGATTTTTCGGTTAACG
GTTAAAATTTTTGGAAGGTCGGTTAATTCGGTTATAGTAATTTCGGGTCGGTTAAC
Found at i:3583368 original size:12 final size:12
Alignment explanation
Indices: 3583351--3583375 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3583341 AGTAATTTCG
3583351 GGTCGGTTAACC
1 GGTCGGTTAACC
3583363 GGTCGGTTAACC
1 GGTCGGTTAACC
3583375 G
1 G
3583376 AATTTTTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:3585945 original size:19 final size:19
Alignment explanation
Indices: 3585921--3585984 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
3585911 ATTAAGCTTA
3585921 AAAATTATTAAAATATTAT
1 AAAATTATTAAAATATTAT
*
3585940 AAAATT-TGTGTAAA-ATTAT
1 AAAATTAT-T-AAAATATTAT
*
3585959 AGAAATTTATTAAAATTTTATT
1 A-AAA-TTATTAAAATATTA-T
3585981 AAAA
1 AAAA
3585985 ATGATAGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
18 1 0.03
19 13 0.37
20 9 0.26
21 9 0.26
22 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAATTATTAAAATATTAT
Found at i:3586393 original size:19 final size:20
Alignment explanation
Indices: 3586347--3586394 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
3586337 ATAATATGCT
3586347 AATAATTTTCGACAACTTTC
1 AATAATTTTCGACAACTTTC
* *
3586367 AGTGATTTTC-ACAA-TTTGC
1 AATAATTTTCGACAACTTT-C
3586386 AATAATTTT
1 AATAATTTT
3586395 TTTAGAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.13
19 12 0.52
20 8 0.35
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (20 bp):
AATAATTTTCGACAACTTTC
Found at i:3586838 original size:3 final size:3
Alignment explanation
Indices: 3586830--3586855 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3586820 CTTTACTCTT
3586830 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3586856 TTCTTTCCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3589737 original size:3 final size:3
Alignment explanation
Indices: 3589729--3589777 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
3589719 AGTTTACCCT
3589729 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3589777 T
1 T
3589778 GTGGCATTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3590034 original size:17 final size:20
Alignment explanation
Indices: 3589994--3590034 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
3589984 TAATCAATAA
3589994 AAATTATATAAAATATCATT
1 AAATTATATAAAATATCATT
3590014 AAATT-TAT-AAATATC-TT
1 AAATTATATAAAATATCATT
3590031 AAAT
1 AAAT
3590035 ATACTTACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 3 0.14
20 5 0.24
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTATATAAAATATCATT
Found at i:3595634 original size:40 final size:40
Alignment explanation
Indices: 3595579--3595659 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3595569 TTACACACTT
3595579 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
1 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
3595619 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
1 AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
3595659 A
1 A
3595660 TACACACCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (40 bp):
AACATTTATCACATATGCTCATTCTTTTAAATGTACCTGC
Found at i:3595782 original size:23 final size:23
Alignment explanation
Indices: 3595756--3595824 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
3595746 ATAAGTGCCA
3595756 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
3595779 CACTGATATGTAGACGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3595802 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3595825 ACATGCTAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3602791 original size:51 final size:51
Alignment explanation
Indices: 3602665--3602852 Score: 245
Period size: 51 Copynumber: 3.7 Consensus size: 51
3602655 ACCATTCGAT
* * ** * **
3602665 ACACATAGTAGCCTTCACATAGTACTACACACGTGTTCA--AACTTTCCGGT
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TATCCGAA
* *
3602715 TCATGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
* * *
3602766 ACACGTAGTAGCCTGCACATTGTACTACACAAGTGACCATTAATATCCGAT
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
3602817 ACACGTAGTAGCCTGCACATAGTACTACACACGTGA
1 ACACGTAGTAGCCTGCACATAGTACTACACACGTGA
3602853 TCGAAGCTAT
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
50 33 0.28
51 85 0.71
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (51 bp):
ACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGAA
Found at i:3609512 original size:23 final size:23
Alignment explanation
Indices: 3609486--3609554 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3609476 ATAAGTGCCA
3609486 CACTAATATGTAGCCGAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
* * *
3609509 CACTGATATGTAGCCGTAGCCAC
1 CACTAATATGTAGCCGAAGCTAC
*
3609532 CACTAAAATGTAGCCGAAGCTAC
1 CACTAATATGTAGCCGAAGCTAC
3609555 TCATGCTAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (23 bp):
CACTAATATGTAGCCGAAGCTAC
Found at i:3611408 original size:10 final size:10
Alignment explanation
Indices: 3611395--3611451 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
3611385 TTAAAATTAA
*
3611395 TTTTTATAGTT
1 TTTTTATA-AT
*
3611406 TTTTTATAAG
1 TTTTTATAAT
*
3611416 TTTTTA-CAT
1 TTTTTATAAT
3611425 TATTTTATAAT
1 T-TTTTATAAT
*
3611436 TTTTTACAAT
1 TTTTTATAAT
3611446 TTTTTA
1 TTTTTA
3611452 AATCTATATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.05
10 25 0.66
11 11 0.29
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:3611450 original size:20 final size:19
Alignment explanation
Indices: 3611405--3611451 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
3611395 TTTTTATAGT
3611405 TTTTTTATAAGTTTTTACA
1 TTTTTTATAAGTTTTTACA
*
3611424 TTATTTTATAATTTTTTACAA
1 TT-TTTTATAAGTTTTTAC-A
3611445 TTTTTTA
1 TTTTTTA
3611452 AATCTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTTATAAGTTTTTACA
Found at i:3611768 original size:33 final size:33
Alignment explanation
Indices: 3611720--3611784 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
3611710 GACGCTCACG
* *
3611720 GTATCGGCTCGCAGGAATCGAAGGGAGCTTGCC
1 GTATCAGCTCACAGGAATCGAAGGGAGCTTGCC
*
3611753 GTATCAGCTCACAGGAATCGAAGGGAGTTTGC
1 GTATCAGCTCACAGGAATCGAAGGGAGCTTGC
3611785 AGTCCTAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.34, T:0.20
Consensus pattern (33 bp):
GTATCAGCTCACAGGAATCGAAGGGAGCTTGCC
Found at i:3613450 original size:163 final size:163
Alignment explanation
Indices: 3613180--3613508 Score: 550
Period size: 163 Copynumber: 2.0 Consensus size: 163
3613170 TTCAATGAAA
*
3613180 TAATGCTAGTCAAAATCAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
1 TAATGCTAGTCAAAATAAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
* * *
3613245 GTGTTGACAGATGTACTTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
66 GTGTTCACAGATATACCTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
3613310 TCATTAATTATTATTTTAAGAAATCGTTTTTAT
131 TCATTAATTATTATTTTAAGAAATCGTTTTTAT
* *
3613343 TAATGCTAGTCAAAATAAGCATCCCATTGATGACTCCAATTTTTGTTATTCATTTTCAACCTAAT
1 TAATGCTAGTCAAAATAAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
* * * *
3613408 GTGTTCACAGATATCCCTAGGATTCAATTCAATTAATTTGATGCATTGACGGTTTTTATCAGCAT
66 GTGTTCACAGATATACCTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
* *
3613473 TCATTAATTATTATTTTAAGAACTTGTTTTTAT
131 TCATTAATTATTATTTTAAGAAATCGTTTTTAT
3613506 TAA
1 TAA
3613509 ATTCAAATTT
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 154 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (163 bp):
TAATGCTAGTCAAAATAAGCATCCCATTCATGACTCCAAATTTTGTTATTCATTTTCAACCTAAT
GTGTTCACAGATATACCTAGGACTCAATTAAATTAATTTGATGCATTGAAGGTTTTTATCAGCAT
TCATTAATTATTATTTTAAGAAATCGTTTTTAT
Found at i:3614286 original size:122 final size:123
Alignment explanation
Indices: 3614124--3614369 Score: 467
Period size: 122 Copynumber: 2.0 Consensus size: 123
3614114 AATTAATATT
3614124 TTTAATGATTTAATTTTTTTAAACATATTTGATAATTTAAAATAAAACAATTTGATAAAAAATTC
1 TTTAATGATTTAATTTTTTTAAACATATTTGATAATTTAAAATAAAACAATTTGATAAAAAATTC
* *
3614189 TTTAAAAAATTTAAAAAATAATAAGTAGATAAGAGCTAGTTATCACTTAATGAAGAAA
66 TTTAAAAAATTTAAAAAATAATAAGTAAATAAGAGCCAGTTATCACTTAATGAAGAAA
3614247 TTTAATGATTT-ATTTTTTTAAACATATTTGATAATTTAAAATAAAACAATTTGATAAAAAATTC
1 TTTAATGATTTAATTTTTTTAAACATATTTGATAATTTAAAATAAAACAATTTGATAAAAAATTC
3614311 TTTAAAAAATTTAAAAAATAATAAGTAAATAAGAGCCAGTTATCACTTAATGAAGAAA
66 TTTAAAAAATTTAAAAAATAATAAGTAAATAAGAGCCAGTTATCACTTAATGAAGAAA
3614369 T
1 T
3614370 AGTTTTAATT
Statistics
Matches: 121, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
122 110 0.91
123 11 0.09
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (123 bp):
TTTAATGATTTAATTTTTTTAAACATATTTGATAATTTAAAATAAAACAATTTGATAAAAAATTC
TTTAAAAAATTTAAAAAATAATAAGTAAATAAGAGCCAGTTATCACTTAATGAAGAAA
Found at i:3614408 original size:16 final size:15
Alignment explanation
Indices: 3614378--3614411 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3614368 ATAGTTTTAA
3614378 TTAATTTAATTTATT
1 TTAATTTAATTTATT
*
3614393 TTAATATTATTTTATT
1 TTAAT-TTAATTTATT
3614409 TTA
1 TTA
3614412 TAAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTAATTTAATTTATT
Found at i:3616083 original size:14 final size:15
Alignment explanation
Indices: 3616051--3616084 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3616041 ATTTTATAAC
* *
3616051 TTTTCAATACTTAAT
1 TTTTCAACACCTAAT
3616066 TTTTCAACACCTAAT
1 TTTTCAACACCTAAT
3616081 TTTT
1 TTTT
3616085 TAATTTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTCAACACCTAAT
Found at i:3616150 original size:5 final size:5
Alignment explanation
Indices: 3616140--3616164 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3616130 AAGAAAAAGT
3616140 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
3616165 TAATTATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:3619558 original size:22 final size:21
Alignment explanation
Indices: 3619512--3619559 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3619502 GCCCGTTTTT
* * *
3619512 AATTAAAATTATTTTTTATAA
1 AATTAAAACTAATTGTTATAA
3619533 AATTAAAACTAATTGTTATTAA
1 AATTAAAACTAATTGTTA-TAA
3619555 AATTA
1 AATTA
3619560 GTTGTTACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AATTAAAACTAATTGTTATAA
Found at i:3619603 original size:9 final size:9
Alignment explanation
Indices: 3619589--3619621 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3619579 ATTATCAAAT
3619589 TATTAATTG
1 TATTAATTG
3619598 TATTAATTG
1 TATTAATTG
3619607 --TTAATTG
1 TATTAATTG
3619614 TATTAATT
1 TATTAATT
3619622 ATTATAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (9 bp):
TATTAATTG
Found at i:3619610 original size:16 final size:16
Alignment explanation
Indices: 3619586--3619625 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
3619576 AAAATTATCA
3619586 AATTATTAATTGTATT
1 AATTATTAATTGTATT
*
3619602 AATTGTTAATTGTATT
1 AATTATTAATTGTATT
3619618 AATTATTA
1 AATTATTA
3619626 TAACAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
AATTATTAATTGTATT
Found at i:3621432 original size:22 final size:22
Alignment explanation
Indices: 3621402--3621452 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
3621392 GGTATTTTGT
*
3621402 AATTTAAT-AAAA-TATAATAAA
1 AATTAAATAAAAATTATAA-AAA
3621423 ATATTAAATAAAAATTATAAAAA
1 A-ATTAAATAAAAATTATAAAAA
3621446 AATTAAA
1 AATTAAA
3621453 CATTAGTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.04
22 12 0.46
23 8 0.31
24 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTAAATAAAAATTATAAAAA
Found at i:3621446 original size:11 final size:12
Alignment explanation
Indices: 3621402--3621450 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
3621392 GGTATTTTGT
3621402 AATT-TAAT-AA
1 AATTATAATAAA
3621412 AA-TATAATAAA
1 AATTATAATAAA
3621423 ATATTA-AATAAA
1 A-ATTATAATAAA
3621435 AATTATAA-AAA
1 AATTATAATAAA
3621446 AATTA
1 AATTA
3621451 AACATTAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.03
10 6 0.18
11 15 0.44
12 10 0.29
13 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATTATAATAAA
Found at i:3623495 original size:21 final size:21
Alignment explanation
Indices: 3623455--3623496 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3623445 AATTTATTTT
3623455 AAAATAATAAAATTTATAAAA
1 AAAATAATAAAATTTATAAAA
*
3623476 AAAATTATACAAATTT-TAAAA
1 AAAATAATA-AAATTTATAAAA
3623497 CTATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAATAAAATTTATAAAA
Found at i:3625027 original size:27 final size:27
Alignment explanation
Indices: 3624989--3625040 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3624979 ATACAGGGGT
*
3624989 GTGGTGCCTATCTGATAGGCGGCACTG
1 GTGGTGCCTATCTGATAGGCAGCACTG
*
3625016 GTGGTGCTTATCTGATAGGCAGCAC
1 GTGGTGCCTATCTGATAGGCAGCAC
3625041 ACCTAGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (27 bp):
GTGGTGCCTATCTGATAGGCAGCACTG
Found at i:3626781 original size:2 final size:2
Alignment explanation
Indices: 3626774--3626801 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3626764 AGCTCTGCTT
3626774 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
3626802 AGTTCGAAAC
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:3628617 original size:2 final size:2
Alignment explanation
Indices: 3628610--3628635 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3628600 TTAAGGAGGA
3628610 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
3628636 GAAGGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3629381 original size:28 final size:29
Alignment explanation
Indices: 3629316--3629382 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
3629306 ATTGAACTTG
*
3629316 AATTTTAAAATTCAAAAATAGAGAGAATA
1 AATTTTAAAAATCAAAAATAGAGAGAATA
3629345 AATTCTTAAAAAT-AAAAATATG-G-GAATTA
1 AATT-TTAAAAATCAAAAATA-GAGAGAA-TA
3629374 AATTTTAAA
1 AATTTTAAA
3629383 TTTATAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 8 0.24
29 18 0.53
30 8 0.24
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (29 bp):
AATTTTAAAAATCAAAAATAGAGAGAATA
Found at i:3629654 original size:17 final size:17
Alignment explanation
Indices: 3629621--3629654 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3629611 ATTATTTTGA
*
3629621 TTAAATTTTGGTAAAGG
1 TTAAATTTTAGTAAAGG
*
3629638 TTAAATTTTAGTTAAGG
1 TTAAATTTTAGTAAAGG
3629655 AGCTATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TTAAATTTTAGTAAAGG
Found at i:3631249 original size:16 final size:16
Alignment explanation
Indices: 3631211--3631249 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3631201 ACTGCTGCTT
*
3631211 TGCTCTGCCTCTTTTG
1 TGCTGTGCCTCTTTTG
**
3631227 TTTTGTGCCTCTTTTG
1 TGCTGTGCCTCTTTTG
3631243 TGCTGTG
1 TGCTGTG
3631250 AATTGGTTTT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.23, T:0.54
Consensus pattern (16 bp):
TGCTGTGCCTCTTTTG
Found at i:3633065 original size:64 final size:64
Alignment explanation
Indices: 3632964--3633222 Score: 509
Period size: 64 Copynumber: 4.0 Consensus size: 64
3632954 CGGTAGACAC
3632964 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
1 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
3633028 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
1 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
3633092 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
1 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
*
3633156 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAGTGTTAATGATGTGGACTGTCCACTAA
1 TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
3633220 TTT
1 TTT
3633223 GGCATGTNNN
Statistics
Matches: 194, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 194 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (64 bp):
TTTAGTTCCATTCTTGTTCATCTTAAAACAGTATGCAATGTTAATGATGTGGACTGTCCACTAA
Found at i:3634688 original size:21 final size:21
Alignment explanation
Indices: 3634664--3634708 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
3634654 GCCATGCAAC
*
3634664 TTGTCGAAATCATTTTTAAAT
1 TTGTCGAAACCATTTTTAAAT
3634685 TTGTCGAAACCATTTTTAAAT
1 TTGTCGAAACCATTTTTAAAT
3634706 TTG
1 TTG
3634709 AAAAATGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (21 bp):
TTGTCGAAACCATTTTTAAAT
Found at i:3637215 original size:24 final size:24
Alignment explanation
Indices: 3637178--3637225 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3637168 GACTGTGGGC
3637178 ATTTTAAAATTTGGCTTTATTTTT
1 ATTTTAAAATTTGGCTTTATTTTT
*
3637202 ATTTATAAAA-TTGGGTTTATTTTT
1 ATTT-TAAAATTTGGCTTTATTTTT
3637226 GGTTTGCGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.60
Consensus pattern (24 bp):
ATTTTAAAATTTGGCTTTATTTTT
Found at i:3638054 original size:193 final size:194
Alignment explanation
Indices: 3637737--3638101 Score: 529
Period size: 193 Copynumber: 1.9 Consensus size: 194
3637727 AGTCCCGAGT
* * *
3637737 GAGAGAAGACATTTAGAAGAAATGAATTAAGAGACCTACATGCTTGAATAAAAGCATTAAAGAAA
1 GAGAGAAGACAGTTAGAAGAAATGAATTAAGAGACCTACATACTTGAACAAAAGCATTAAAGAAA
* * *
3637802 ATGTAGCAACCATAAACAGAAAGTATGAGATTAATGGGTGGAGCATTTCTCTAGATTTTAATACC
66 ATGTAGCAACCATAAACAAAAAGTAGGAGATTAATGGGTGGAGCATTTATCTAGATTTTAATACC
*
3637867 TCGTATGGAACCATTATGA-CCTACCACCAATTGTAGTGGTAGAAACTGATTTGAAGTATTGTGA
131 TCGTATGAAACCATTATGATCC-ACCACCAATTGTAGTGGTAGAAACTGATTTGAAGTATTGTGA
* * * *
3637931 GAGAGAAGACAGTTAGAAGAAATGATTTGAGAGACCT-CATACTTTAACAAAAGTATTAAAGAAA
1 GAGAGAAGACAGTTAGAAGAAATGAATTAAGAGACCTACATACTTGAACAAAAGCATTAAAGAAA
* * * * *
3637995 ATGTATCAACTATAAATAAAAAGTAGGTGATTAATGGGTGGAGCATTTAT-TGAGATTTTAATGC
66 ATGTAGCAACCATAAACAAAAAGTAGGAGATTAATGGGTGGAGCATTTATCT-AGATTTTAATAC
* *
3638059 CTTGTATGAAACCATTATGATCCACCGCCAATTGTAGTGGTAG
130 CTCGTATGAAACCATTATGATCCACCACCAATTGTAGTGGTAG
3638102 TTTAGGTACG
Statistics
Matches: 151, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
192 1 0.01
193 114 0.75
194 36 0.24
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (194 bp):
GAGAGAAGACAGTTAGAAGAAATGAATTAAGAGACCTACATACTTGAACAAAAGCATTAAAGAAA
ATGTAGCAACCATAAACAAAAAGTAGGAGATTAATGGGTGGAGCATTTATCTAGATTTTAATACC
TCGTATGAAACCATTATGATCCACCACCAATTGTAGTGGTAGAAACTGATTTGAAGTATTGTGA
Found at i:3644787 original size:19 final size:19
Alignment explanation
Indices: 3644738--3644792 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3644728 AATACAAAAT
*
3644738 AATTCAAAATAATTT-TCAA
1 AATTCAAAAT-ATTTATAAA
3644757 AATTCAAAATATTTATAAA
1 AATTCAAAATATTTATAAA
*
3644776 AATTCAAAATATATATA
1 AATTCAAAATATTTATA
3644793 TATATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCAAAATATTTATAAA
Found at i:3648108 original size:2 final size:2
Alignment explanation
Indices: 3648103--3648141 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3648093 TGTATATATA
3648103 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3648142 ATAGGGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:3656644 original size:23 final size:24
Alignment explanation
Indices: 3656603--3656650 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3656593 CAGTACAAAT
*
3656603 AACAAAAACAATAGCAAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
*
3656627 AACAAAAACTACAG-AAAAATAAC
1 AACAAAAACAACAGCAAAAATAAC
3656650 A
1 A
3656651 GCACCAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.17, G:0.04, T:0.08
Consensus pattern (24 bp):
AACAAAAACAACAGCAAAAATAAC
Found at i:3657312 original size:14 final size:11
Alignment explanation
Indices: 3657276--3657308 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
3657266 CTCAACACCA
3657276 AAATTGAGAGG
1 AAATTGAGAGG
3657287 AAATTGAGAGG
1 AAATTGAGAGG
3657298 AAATTTGAGAG
1 AAA-TTGAGAG
3657309 AGGATTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:3659376 original size:42 final size:42
Alignment explanation
Indices: 3659238--3659376 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
3659228 CATGTCAGCA
* ** * *
3659238 AAAGCTCA-TCCAGCTGGATGTCCTTTCTTGCCAATTGTGCAG
1 AAAGCTCACT-CAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
* ** **
3659280 AAAGCTCAC-CTAGCTGGACTAGCTTTCCTGAGAACTGTGTGG
1 AAAGCTCACTC-AGCTGGACGAGCTTTCCTGCCAACTGTGCAG
**
3659322 AAAGCTTGCTCAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
1 AAAGCTCACTCAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
* *
3659364 AAATCGCACTCAG
1 AAAGCTCACTCAG
3659377 TTGGGTGCGC
Statistics
Matches: 73, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
41 1 0.01
42 71 0.97
43 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (42 bp):
AAAGCTCACTCAGCTGGACGAGCTTTCCTGCCAACTGTGCAG
Found at i:3665967 original size:441 final size:441
Alignment explanation
Indices: 3665139--3666028 Score: 1719
Period size: 441 Copynumber: 2.0 Consensus size: 441
3665129 TTTATAATTT
* * *
3665139 TATTAGTTTATATGTTTATAAATTTTAAAAATTTAAATTAAAATTTTAGTATTTTAAGATTAAAG
1 TATTATTTTATATGTTTACAAATTTTAAAAATTTAAATTAAAATTTTAGCATTTTAAGATTAAAG
3665204 TATAATGTTATCATTTACTAAATTAAAATCGTATAAAATTTAGAGTGTCAAAAATTAAATTTTAC
66 TATAATGTTATCATTTACTAAATTAAAATCGTATAAAATTTAGAGTGTCAAAAATTAAATTTTAC
3665269 ATTTTACAGGGTCGTGGCCTTACAAGGTTCTCTTGGTGTTGTCCTTGGTAGTAAACATGGTTTTG
131 ATTTTACAGGGTCGTGGCCTTACAAGGTTCTCTTGGTGTTGTCCTTGGTAGTAAACATGGTTTTG
3665334 AGGACTGGATTAGTGATTGAACCAATCAAATCATCAATTCTTTTTTAAAACGAATTATCTAGTCT
196 AGGACTGGATTAGTGATTGAACCAATCAAATCATCAATTCTTTTTTAAAACGAATTATCTAGTCT
3665399 AATTGGTTCAAAACCAATTATTCAATTATAAAATAATATTACTTATTTTTTAAGATTAAAAGTAT
261 AATTGGTTCAAAACCAATTATTCAATTATAAAATAATATTACTTATTTTTTAAGATTAAAAGTAT
3665464 ATTTAAAATAAAATTAAAAAAATAGTGAGAAAACTTTGAAAAGTCAATGCATGCATGAGAAATAA
326 ATTTAAAATAAAATTAAAAAAATAGTGAGAAAACTTTGAAAAGTCAATGCATGCATGAGAAATAA
3665529 ATATAAAATATGTTTATTTATTCTCTTCATATCTTTTCATATCTAATAAAA
391 ATATAAAATATGTTTATTTATTCTCTTCATATCTTTTCATATCTAATAAAA
* *
3665580 TATTATTTTATATGTTTACAAATTTTAAAAATTTAAATTTAAATTTTAGCATTTTAGGATTAAAG
1 TATTATTTTATATGTTTACAAATTTTAAAAATTTAAATTAAAATTTTAGCATTTTAAGATTAAAG
3665645 TATAATGTTATCATTTACTAAATTAAAATCGTATAAAATTTAGAGTGTCAAAAATTAAATTTTAC
66 TATAATGTTATCATTTACTAAATTAAAATCGTATAAAATTTAGAGTGTCAAAAATTAAATTTTAC
3665710 ATTTTACAGGGTCGTGGCCTTACAAGGTTCTCTTGGTGTTGTCCTTGGTAGTAAACATGGTTTTG
131 ATTTTACAGGGTCGTGGCCTTACAAGGTTCTCTTGGTGTTGTCCTTGGTAGTAAACATGGTTTTG
3665775 AGGACTGGATTAGTGATTGAACCAATCAAATCATCAATTCTTTTTTAAAACGAATTATCTAGTCT
196 AGGACTGGATTAGTGATTGAACCAATCAAATCATCAATTCTTTTTTAAAACGAATTATCTAGTCT
3665840 AATTGGTTCAAAACCAATTATTCAATTTATAAAATAA-ATTACTTATTTTTTAAGATTAAAAGTA
261 AATTGGTTCAAAACCAATTATTCAA-TTATAAAATAATATTACTTATTTTTTAAGATTAAAAGTA
3665904 TATTTAAAATAAAATTAAAAAAATAGTGAGAAAACTTTGAAAAGTCAATGCATGCATGAGAAATA
325 TATTTAAAATAAAATTAAAAAAATAGTGAGAAAACTTTGAAAAGTCAATGCATGCATGAGAAATA
3665969 AATATAAAATATGTTTATTTATTCTCTTCATATCTTTTCATATCTAATAAAA
390 AATATAAAATATGTTTATTTATTCTCTTCATATCTTTTCATATCTAATAAAA
3666021 TATTATTT
1 TATTATTT
3666029 GTCTTCTTTT
Statistics
Matches: 443, Mismatches: 5, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
441 432 0.98
442 11 0.02
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.40
Consensus pattern (441 bp):
TATTATTTTATATGTTTACAAATTTTAAAAATTTAAATTAAAATTTTAGCATTTTAAGATTAAAG
TATAATGTTATCATTTACTAAATTAAAATCGTATAAAATTTAGAGTGTCAAAAATTAAATTTTAC
ATTTTACAGGGTCGTGGCCTTACAAGGTTCTCTTGGTGTTGTCCTTGGTAGTAAACATGGTTTTG
AGGACTGGATTAGTGATTGAACCAATCAAATCATCAATTCTTTTTTAAAACGAATTATCTAGTCT
AATTGGTTCAAAACCAATTATTCAATTATAAAATAATATTACTTATTTTTTAAGATTAAAAGTAT
ATTTAAAATAAAATTAAAAAAATAGTGAGAAAACTTTGAAAAGTCAATGCATGCATGAGAAATAA
ATATAAAATATGTTTATTTATTCTCTTCATATCTTTTCATATCTAATAAAA
Found at i:3667257 original size:53 final size:53
Alignment explanation
Indices: 3667177--3667286 Score: 211
Period size: 53 Copynumber: 2.1 Consensus size: 53
3667167 ACTGGACTTC
3667177 ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
1 ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
*
3667230 ACAAAGAGTGATGATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
1 ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
3667283 ACAA
1 ACAA
3667287 GGACGTATCT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (53 bp):
ACAAAGAGTGATAATGGTGTCCTTTTAACAACTCACTACAAGCTATAGCTAAT
Found at i:3668674 original size:32 final size:32
Alignment explanation
Indices: 3668629--3668692 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
3668619 TTTTTCGTCC
* *
3668629 TTTTTTTTGTTTTTA-ATAAATGGCCCAATAT
1 TTTTTTTTCTTTTTACATAAATGACCCAATAT
*
3668660 TTTTTTTTACTTTTTACGTAAATGACCCAATAT
1 TTTTTTTT-CTTTTTACATAAATGACCCAATAT
3668693 GTTTATACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.29
32 6 0.21
33 14 0.50
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (32 bp):
TTTTTTTTCTTTTTACATAAATGACCCAATAT
Found at i:3669447 original size:41 final size:41
Alignment explanation
Indices: 3669400--3669490 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
3669390 GTGGGTTTAA
3669400 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
1 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
3669441 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
1 GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
3669482 GGAGCTTTG
1 GGAGCTTTG
3669491 GAAAATTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.21, C:0.10, G:0.40, T:0.30
Consensus pattern (41 bp):
GGAGCTTTGAAGGTAATGGTGATACGCCGTTGGTGATGAGT
Found at i:3670787 original size:31 final size:31
Alignment explanation
Indices: 3670752--3671211 Score: 372
Period size: 31 Copynumber: 14.9 Consensus size: 31
3670742 ATCAAGTTCG
*
3670752 GCAATGTATAATCATATACAAATTAAATTCA
1 GCAATGTATAATCATATACAAATTAATTTCA
* * *
3670783 GCAATGTATAACCATATACAAATCAATTT-G
1 GCAATGTATAATCATATACAAATTAATTTCA
3670813 GCAACT-TAT-ATCCATATAC-AATTCAATTTCA
1 GCAA-TGTATAAT-CATATACAAATT-AATTTCA
* * *
3670844 ACAATGTATAACCATGTACAAATTAATTTCA
1 GCAATGTATAATCATATACAAATTAATTTCA
* * * *
3670875 GCAATATATAATAATATACAAATCAA-TTCG
1 GCAATGTATAATCATATACAAATTAATTTCA
*
3670905 GCAACT-TATATTCATATAC-AATTCAATTTCA
1 GCAA-TGTATAATCATATACAAATT-AATTTCA
* * * *
3670936 ACAATGTATAACCATGTACAAATTAATTTTA
1 GCAATGTATAATCATATACAAATTAATTTCA
** *
3670967 GCAATACACAA-CAATGTATACAAATTAATTTCA
1 GCAATGTATAATC-A--TATACAAATTAATTTCA
* * * * *
3671000 GCAATATATAATAATATACGAATCAA-TTCG
1 GCAATGTATAATCATATACAAATTAATTTCA
*
3671030 GCAACT-TATATTCATATAC-AATTCAATTTCA
1 GCAA-TGTATAATCATATACAAATT-AATTTCA
* * *
3671061 ACAATGTATAACCATGTACAAATTAATTTCA
1 GCAATGTATAATCATATACAAATTAATTTCA
* * * * *
3671092 GCAATGTACAACCATATACGAATCAA-TTCG
1 GCAATGTATAATCATATACAAATTAATTTCA
*
3671122 GCAACT-TATATTCATATAC-AATTCAATTTCA
1 GCAA-TGTATAATCATATACAAATT-AATTTCA
* *
3671153 ACAATGTATAACCATATACAAATTAATTTCA
1 GCAATGTATAATCATATACAAATTAATTTCA
* *
3671184 GCAATGTACAATCATATACAAATCAATT
1 GCAATGTATAATCATATACAAATTAATT
3671212 CGGGAACTTA
Statistics
Matches: 339, Mismatches: 64, Indels: 52
0.75 0.14 0.11
Matches are distributed among these distances:
29 13 0.04
30 83 0.24
31 201 0.59
32 17 0.05
33 25 0.07
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (31 bp):
GCAATGTATAATCATATACAAATTAATTTCA
Found at i:3670869 original size:92 final size:92
Alignment explanation
Indices: 3670753--3670996 Score: 362
Period size: 92 Copynumber: 2.6 Consensus size: 92
3670743 TCAAGTTCGG
* * * * * *
3670753 CAATGTATAATCATATACAAATTAAATTCAGCAATGTATAACCATATACAAATCAATTTGGCAAC
1 CAATGTATAACCATGTACAAATTAATTTCAGCAATATATAACAATATACAAATCAATTCGGCAAC
3670818 TTATATCCATATACAATTCAATTTCAA
66 TTATATCCATATACAATTCAATTTCAA
*
3670845 CAATGTATAACCATGTACAAATTAATTTCAGCAATATATAATAATATACAAATCAATTCGGCAAC
1 CAATGTATAACCATGTACAAATTAATTTCAGCAATATATAACAATATACAAATCAATTCGGCAAC
*
3670910 TTATATTCATATACAATTCAATTTCAA
66 TTATATCCATATACAATTCAATTTCAA
* * * *
3670937 CAATGTATAACCATGTACAAATTAATTTTAGCAATACACAACAATGTATACAAATTAATT
1 CAATGTATAACCATGTACAAATTAATTTCAGCAATATATAACAA--TATACAAATCAATT
3670997 TCAGCAATAT
Statistics
Matches: 137, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
92 124 0.91
94 13 0.09
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (92 bp):
CAATGTATAACCATGTACAAATTAATTTCAGCAATATATAACAATATACAAATCAATTCGGCAAC
TTATATCCATATACAATTCAATTTCAA
Found at i:3670997 original size:64 final size:60
Alignment explanation
Indices: 3670917--3671119 Score: 178
Period size: 61 Copynumber: 3.3 Consensus size: 60
3670907 AACTTATATT
*
3670917 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTTAGCAATACACAA
1 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATACA-AA
* * ** * * * * * *
3670978 CAATGTATACAAATT-AATTTCAGCAATATATAATAATATACGAATCAA-TTCGGCAACTTATAT
1 C-A--TATAC-AATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAA--TACAA
*
3671041 T
60 A
*
3671042 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATGTACAAC
1 CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAA--TACAAA
3671104 CATATACGAA-TCAATT
1 CATATAC-AATTCAATT
3671120 CGGCAACTTA
Statistics
Matches: 108, Mismatches: 25, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
60 4 0.04
61 32 0.30
62 24 0.22
63 9 0.08
64 32 0.30
65 7 0.06
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.32
Consensus pattern (60 bp):
CATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATACAAA
Found at i:3671035 original size:217 final size:217
Alignment explanation
Indices: 3670766--3671188 Score: 720
Period size: 217 Copynumber: 1.9 Consensus size: 217
3670756 TGTATAATCA
* * *
3670766 TATACAAATTAAATTCAGCAATGTATAACCATATACAAATCAATTTGGCAACTTATATCCATATA
1 TATACAAATTAAATTCAGCAATATATAACAATATACAAATCAATTCGGCAACTTATATCCATATA
* *
3670831 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATATAATAATATACAA
66 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATACAACAATATACAA
*
3670896 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATGTACAAATTA
131 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
*
3670961 ATTTTAGCAATACACAACAATG
196 ATTTCAGCAATACACAACAATG
* * * *
3670983 TATACAAATTAATTTCAGCAATATATAATAATATACGAATCAATTCGGCAACTTATATTCATATA
1 TATACAAATTAAATTCAGCAATATATAACAATATACAAATCAATTCGGCAACTTATATCCATATA
* * *
3671048 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATGTACAACCATATACGA
66 CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATACAACAATATACAA
3671113 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
131 ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
3671178 ATTTCAGCAAT
196 ATTTCAGCAAT
3671189 GTACAATCAT
Statistics
Matches: 192, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 192 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (217 bp):
TATACAAATTAAATTCAGCAATATATAACAATATACAAATCAATTCGGCAACTTATATCCATATA
CAATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCAGCAATATACAACAATATACAA
ATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTA
ATTTCAGCAATACACAACAATG
Found at i:3671091 original size:92 final size:92
Alignment explanation
Indices: 3670983--3671265 Score: 440
Period size: 92 Copynumber: 3.1 Consensus size: 92
3670973 CACAACAATG
* * *
3670983 TATACAAATTAATTTCAGCAATATATAATAATATACGAATCAATTCGGCAACTTATATTCATATA
1 TATACAAATTAATTTCAGCAATGTACAATCATATACGAATCAATTCGGCAACTTATATTCATATA
3671048 CAATTCAATTTCAACAATGTATAACCA
66 CAATTCAATTTCAACAATGTATAACCA
* *
3671075 TGTACAAATTAATTTCAGCAATGTACAACCATATACGAATCAATTCGGCAACTTATATTCATATA
1 TATACAAATTAATTTCAGCAATGTACAATCATATACGAATCAATTCGGCAACTTATATTCATATA
3671140 CAATTCAATTTCAACAATGTATAACCA
66 CAATTCAATTTCAACAATGTATAACCA
* * * *
3671167 TATACAAATTAATTTCAGCAATGTACAATCATATACAAATCAATTCGGGAACTTATATCCATATG
1 TATACAAATTAATTTCAGCAATGTACAATCATATACGAATCAATTCGGCAACTTATATTCATATA
* * * *
3671232 CAAATCAATTTCGACAACGTATAACTA
66 CAATTCAATTTCAACAATGTATAACCA
*
3671259 TAAACAA
1 TATACAA
3671266 TTCGAATTCT
Statistics
Matches: 175, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 175 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.31
Consensus pattern (92 bp):
TATACAAATTAATTTCAGCAATGTACAATCATATACGAATCAATTCGGCAACTTATATTCATATA
CAATTCAATTTCAACAATGTATAACCA
Found at i:3671103 original size:125 final size:123
Alignment explanation
Indices: 3670752--3671103 Score: 462
Period size: 125 Copynumber: 2.8 Consensus size: 123
3670742 ATCAAGTTCG
* * * * ** *
3670752 GCAATGTATAATCATATACAAATTAAATTCAGCAA-TGTATAACCATATACAAATCAATTTGGCA
1 GCAATATATAATAATATACAAA-TCAATTCGGCAACT-TATATTCATATACAATTCAATTT--CA
* * * * *
3670816 AC--T-TATATCCATATAC-AATTCAATTTCAACAATGTATAACCATGTACAAATTAATTTCA
62 ACAATGTATAACCATGTACAAATT-AATTTCAGCAATGTACAACAATGTACAAATTAATTTCA
3670875 GCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAA
1 GCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAA
* **
3670940 TGTATAACCATGTACAAATTAATTTTAGCAATACACAACAATGTATACAAATTAATTTCA
66 TGTATAACCATGTACAAATTAATTTCAGCAATGTACAACAATG--TACAAATTAATTTCA
*
3671000 GCAATATATAATAATATACGAATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAA
1 GCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAA
3671065 TGTATAACCATGTACAAATTAATTTCAGCAATGTACAAC
66 TGTATAACCATGTACAAATTAATTTCAGCAATGTACAAC
3671104 CATATACGAA
Statistics
Matches: 203, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
120 4 0.02
122 31 0.15
123 49 0.24
124 4 0.02
125 115 0.57
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (123 bp):
GCAATATATAATAATATACAAATCAATTCGGCAACTTATATTCATATACAATTCAATTTCAACAA
TGTATAACCATGTACAAATTAATTTCAGCAATGTACAACAATGTACAAATTAATTTCA
Found at i:3673826 original size:14 final size:15
Alignment explanation
Indices: 3673789--3673830 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
3673779 TGTGGCCGGT
*
3673789 TAAAATTTAGTATTA
1 TAAATTTTAGTATTA
3673804 TATATATTTTA-TATTA
1 TA-A-ATTTTAGTATTA
3673820 TAAATTTTAGT
1 TAAATTTTAGT
3673831 TAAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 8 0.35
17 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
TAAATTTTAGTATTA
Found at i:3682819 original size:23 final size:23
Alignment explanation
Indices: 3682789--3682967 Score: 201
Period size: 23 Copynumber: 7.9 Consensus size: 23
3682779 NNNNNNNNNN
3682789 GGTTAGGGTTTTTAAGTTAATTA
1 GGTTAGGGTTTTTAAGTTAATTA
***
3682812 GGTTAGGGTTTTTAAGTTAAGGG
1 GGTTAGGGTTTTTAAGTTAATTA
3682835 GGTTAGGGTTTTTAAGTTAATTA
1 GGTTAGGGTTTTTAAGTTAATTA
*
3682858 GGTTAGGGTTTTTAAGTT--TAA
1 GGTTAGGGTTTTTAAGTTAATTA
3682879 GGTTTAGGGTTTTTAA-TTAAATTA
1 GG-TTAGGGTTTTTAAGTT-AATTA
3682903 GGTTAGGGTTTTTAAG-T--TTA
1 GGTTAGGGTTTTTAAGTTAATTA
3682923 GGATTTAGGGTTTTTAA-TTAAATTA
1 GG--TTAGGGTTTTTAAGTT-AATTA
* * *
3682948 GATTAGAGTTTTTAATTTAA
1 GGTTAGGGTTTTTAAGTTAA
3682968 GGGTATTAAT
Statistics
Matches: 134, Mismatches: 10, Indels: 24
0.80 0.06 0.14
Matches are distributed among these distances:
20 5 0.04
21 6 0.04
22 27 0.20
23 86 0.64
24 6 0.04
25 4 0.03
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (23 bp):
GGTTAGGGTTTTTAAGTTAATTA
Found at i:3682902 original size:45 final size:45
Alignment explanation
Indices: 3682791--3682969 Score: 251
Period size: 45 Copynumber: 4.0 Consensus size: 45
3682781 NNNNNNNNGG
*
3682791 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAG-TTAAGGGGG
1 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTTAA--GGT
3682837 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTTAAGGT
1 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTTAAGGT
3682882 TTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTT-AGGAT
1 TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTTAAGG-T
* *
3682927 TTAGGGTTTTTAA-TTAAATTAGATTAGAGTTTTTAA-TTTAAGG
1 TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTTAAGG
3682970 GTATTAATGG
Statistics
Matches: 126, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
44 8 0.06
45 77 0.61
46 37 0.29
47 4 0.03
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (45 bp):
TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTTAAGGT
Found at i:3683513 original size:18 final size:18
Alignment explanation
Indices: 3683490--3683525 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3683480 CGAAAATGGG
*
3683490 TACATATAAGGGTTAGGA
1 TACATATAAGGGCTAGGA
3683508 TACATATAAGGGCTAGGA
1 TACATATAAGGGCTAGGA
3683526 AATGCACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
TACATATAAGGGCTAGGA
Found at i:3684181 original size:7 final size:7
Alignment explanation
Indices: 3684171--3684195 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3684161 TTATATACAT
3684171 AATACTA
1 AATACTA
3684178 AATACTA
1 AATACTA
3684185 AATACTA
1 AATACTA
3684192 AATA
1 AATA
3684196 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3684364 original size:51 final size:52
Alignment explanation
Indices: 3684287--3684389 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 52
3684277 GTATATCTTC
3684287 AAGAGAGGACGGTAATCGAGCATGACTTTCCGGATGGTTCCACCTAATTAAA
1 AAGAGAGGACGGTAATCGAGCATGACTTTCCGGATGGTTCCACCTAATTAAA
3684339 AAGAGAGGA-GGTAATCGAGCATGACTTTCCGGATGGTTCCACCTAATTAAA
1 AAGAGAGGACGGTAATCGAGCATGACTTTCCGGATGGTTCCACCTAATTAAA
3684390 TAAATTTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 42 0.82
52 9 0.18
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (52 bp):
AAGAGAGGACGGTAATCGAGCATGACTTTCCGGATGGTTCCACCTAATTAAA
Found at i:3685329 original size:11 final size:11
Alignment explanation
Indices: 3685313--3685354 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
3685303 GAAAAGGGAG
3685313 TTAAGAGAAAC
1 TTAAGAGAAAC
*
3685324 TTAAGAGGAAC
1 TTAAGAGAAAC
*
3685335 TTAAGAGGAAC
1 TTAAGAGAAAC
3685346 TTAAGAGAA
1 TTAAGAGAA
3685355 TTTTTGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.24, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:3686193 original size:18 final size:18
Alignment explanation
Indices: 3686160--3686212 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
3686150 AGTTCAAAAA
* *
3686160 ATAAATTTATTAAAAATT
1 ATAAAATTATAAAAAATT
*
3686178 ATAAAATTATAAAAAAAT
1 ATAAAATTATAAAAAATT
*
3686196 -TGAAATT-TAAAAAATT
1 ATAAAATTATAAAAAATT
3686212 A
1 A
3686213 ATTAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 15 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAAAATTATAAAAAATT
Found at i:3686706 original size:52 final size:52
Alignment explanation
Indices: 3686628--3686731 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
3686618 AGCTCATTAA
3686628 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
1 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
3686680 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
1 CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
3686732 GATGTCCATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (52 bp):
CCTGCTCTGGCAGTTGTTCTTGAACAAAGTGATTCCCTTCTGACATAAAAAT
Found at i:3687664 original size:2 final size:2
Alignment explanation
Indices: 3687657--3687684 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3687647 TTTCCTATTA
3687657 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
3687685 TTTGAGTTCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3689215 original size:759 final size:759
Alignment explanation
Indices: 3687757--3689274 Score: 3018
Period size: 759 Copynumber: 2.0 Consensus size: 759
3687747 GCTGTGCTGA
*
3687757 ATCTTTTCCATTGTTTAATCAAGGAAACTGAGAAAGGAAACAGAGAGAAGATGGGGTGGGAATTG
1 ATCTTTTCAATTGTTTAATCAAGGAAACTGAGAAAGGAAACAGAGAGAAGATGGGGTGGGAATTG
3687822 GATTGAGATTATTGGACTTCACAAAGAGTGATGATGATGTATATATCTCCTTTTTTTTAAGTCAC
66 GATTGAGATTATTGGACTTCACAAAGAGTGATGATGATGTATATATCTCCTTTTTTTTAAGTCAC
3687887 ATTGTACTGTTGAATCTTGGACATTATTGTTGAGAGGTACCTATTAGGGTGATTTTAGATGGGTG
131 ATTGTACTGTTGAATCTTGGACATTATTGTTGAGAGGTACCTATTAGGGTGATTTTAGATGGGTG
3687952 GTGGGGTATCGTGCAATGTGTTGAGTTTATTTTTTATGTTATGCTATAGTATCGTTACAATATTT
196 GTGGGGTATCGTGCAATGTGTTGAGTTTATTTTTTATGTTATGCTATAGTATCGTTACAATATTT
3688017 AATCTTATTGTCATCATTATTTTTACACTAATTGTAAATAAATACTTTACTCATCGAAATCTACC
261 AATCTTATTGTCATCATTATTTTTACACTAATTGTAAATAAATACTTTACTCATCGAAATCTACC
3688082 CTTAATCTTTGTAAAATTTACACGAAAAAGATAAATCGGTTCCCCAACACGCACAATAAAAGTTC
326 CTTAATCTTTGTAAAATTTACACGAAAAAGATAAATCGGTTCCCCAACACGCACAATAAAAGTTC
3688147 TGCTCACTATTAGACCGGTTATAGAAAAGATGGTGACAAATTTAATCCCTTTTAAGTAAAAGTTT
391 TGCTCACTATTAGACCGGTTATAGAAAAGATGGTGACAAATTTAATCCCTTTTAAGTAAAAGTTT
3688212 TAATAATTCTTTGACGTCGTTTTCACATCATGTTCAATATTATTAGCTATGATAAAAAGGGAAAA
456 TAATAATTCTTTGACGTCGTTTTCACATCATGTTCAATATTATTAGCTATGATAAAAAGGGAAAA
3688277 AAAATGAAAATTGGTAAACTATATTCCGTAAAAAGTAATATTTTATTAATTAAATGTAAAAAATA
521 AAAATGAAAATTGGTAAACTATATTCCGTAAAAAGTAATATTTTATTAATTAAATGTAAAAAATA
3688342 AAAAATAATTAAAACCTTCTAACGGAATAAATTGTATAGTAAGAAATAAAACGTTGATTTTTTTA
586 AAAAATAATTAAAACCTTCTAACGGAATAAATTGTATAGTAAGAAATAAAACGTTGATTTTTTTA
3688407 TGGGATAATGATTTATTTGTCCCTCTAATTTTATAAAAGAATTATTTTAGTCTTTTATTTAATTT
651 TGGGATAATGATTTATTTGTCCCTCTAATTTTATAAAAGAATTATTTTAGTCTTTTATTTAATTT
3688472 TTAATTTTTTAGCATTTAATCTTATATTTTTATTTCAAATCACT
716 TTAATTTTTTAGCATTTAATCTTATATTTTTATTTCAAATCACT
*
3688516 ATCTTTTTAATTGTTTAATCAAGGAAACTGAGAAAGGAAACAGAGAGAAGATGGGGTGGGAATTG
1 ATCTTTTCAATTGTTTAATCAAGGAAACTGAGAAAGGAAACAGAGAGAAGATGGGGTGGGAATTG
3688581 GATTGAGATTATTGGACTTCACAAAGAGTGATGATGATGTATATATCTCCTTTTTTTTAAGTCAC
66 GATTGAGATTATTGGACTTCACAAAGAGTGATGATGATGTATATATCTCCTTTTTTTTAAGTCAC
3688646 ATTGTACTGTTGAATCTTGGACATTATTGTTGAGAGGTACCTATTAGGGTGATTTTAGATGGGTG
131 ATTGTACTGTTGAATCTTGGACATTATTGTTGAGAGGTACCTATTAGGGTGATTTTAGATGGGTG
3688711 GTGGGGTATCGTGCAATGTGTTGAGTTTATTTTTTATGTTATGCTATAGTATCGTTACAATATTT
196 GTGGGGTATCGTGCAATGTGTTGAGTTTATTTTTTATGTTATGCTATAGTATCGTTACAATATTT
3688776 AATCTTATTGTCATCATTATTTTTACACTAATTGTAAATAAATACTTTACTCATCGAAATCTACC
261 AATCTTATTGTCATCATTATTTTTACACTAATTGTAAATAAATACTTTACTCATCGAAATCTACC
3688841 CTTAATCTTTGTAAAATTTACACGAAAAAGATAAATCGGTTCCCCAACACGCACAATAAAAGTTC
326 CTTAATCTTTGTAAAATTTACACGAAAAAGATAAATCGGTTCCCCAACACGCACAATAAAAGTTC
3688906 TGCTCACTATTAGACCGGTTATAGAAAAGATGGTGACAAATTTAATCCCTTTTAAGTAAAAGTTT
391 TGCTCACTATTAGACCGGTTATAGAAAAGATGGTGACAAATTTAATCCCTTTTAAGTAAAAGTTT
3688971 TAATAATTCTTTGACGTCGTTTTCACATCATGTTCAATATTATTAGCTATGATAAAAAGGGAAAA
456 TAATAATTCTTTGACGTCGTTTTCACATCATGTTCAATATTATTAGCTATGATAAAAAGGGAAAA
3689036 AAAATGAAAATTGGTAAACTATATTCCGTAAAAAGTAATATTTTATTAATTAAATGTAAAAAATA
521 AAAATGAAAATTGGTAAACTATATTCCGTAAAAAGTAATATTTTATTAATTAAATGTAAAAAATA
3689101 AAAAATAATTAAAACCTTCTAACGGAATAAATTGTATAGTAAGAAATAAAACGTTGATTTTTTTA
586 AAAAATAATTAAAACCTTCTAACGGAATAAATTGTATAGTAAGAAATAAAACGTTGATTTTTTTA
3689166 TGGGATAATGATTTATTTGTCCCTCTAATTTTATAAAAGAATTATTTTAGTCTTTTATTTAATTT
651 TGGGATAATGATTTATTTGTCCCTCTAATTTTATAAAAGAATTATTTTAGTCTTTTATTTAATTT
3689231 TTAATTTTTTAGCATTTAATCTTATATTTTTATTTCAAATCACT
716 TTAATTTTTTAGCATTTAATCTTATATTTTTATTTCAAATCACT
3689275 CCAAAATGAT
Statistics
Matches: 757, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
759 757 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (759 bp):
ATCTTTTCAATTGTTTAATCAAGGAAACTGAGAAAGGAAACAGAGAGAAGATGGGGTGGGAATTG
GATTGAGATTATTGGACTTCACAAAGAGTGATGATGATGTATATATCTCCTTTTTTTTAAGTCAC
ATTGTACTGTTGAATCTTGGACATTATTGTTGAGAGGTACCTATTAGGGTGATTTTAGATGGGTG
GTGGGGTATCGTGCAATGTGTTGAGTTTATTTTTTATGTTATGCTATAGTATCGTTACAATATTT
AATCTTATTGTCATCATTATTTTTACACTAATTGTAAATAAATACTTTACTCATCGAAATCTACC
CTTAATCTTTGTAAAATTTACACGAAAAAGATAAATCGGTTCCCCAACACGCACAATAAAAGTTC
TGCTCACTATTAGACCGGTTATAGAAAAGATGGTGACAAATTTAATCCCTTTTAAGTAAAAGTTT
TAATAATTCTTTGACGTCGTTTTCACATCATGTTCAATATTATTAGCTATGATAAAAAGGGAAAA
AAAATGAAAATTGGTAAACTATATTCCGTAAAAAGTAATATTTTATTAATTAAATGTAAAAAATA
AAAAATAATTAAAACCTTCTAACGGAATAAATTGTATAGTAAGAAATAAAACGTTGATTTTTTTA
TGGGATAATGATTTATTTGTCCCTCTAATTTTATAAAAGAATTATTTTAGTCTTTTATTTAATTT
TTAATTTTTTAGCATTTAATCTTATATTTTTATTTCAAATCACT
Found at i:3694757 original size:15 final size:15
Alignment explanation
Indices: 3694722--3694750 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3694712 AAATAAAAGC
3694722 AATAATGATAATAAT
1 AATAATGATAATAAT
3694737 AATAATGATAATAA
1 AATAATGATAATAA
3694751 AACTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AATAATGATAATAAT
Found at i:3696135 original size:98 final size:99
Alignment explanation
Indices: 3695955--3696148 Score: 318
Period size: 98 Copynumber: 2.0 Consensus size: 99
3695945 GTCTTGCCAA
* * * * *
3695955 GGAAATAAGATTCGCCGTTGCGGCTTCAATCTGTTCTGCTGCATCGCCTGGAAGTAAGATTCGCC
1 GGAAATAAGATTCGCCATTGCAGCTTCAATCTGCTCCGCTGCATCGCCTAGAAGTAAGATTCGCC
3696020 GTTGTGGCTTCGATCTTTTAAATTGCAATGTTGG
66 GTTGTGGCTTCGATCTTTTAAATTGCAATGTTGG
* *
3696054 GGAAGTAAGATTCGCCATTGTAGCTTCAATCTGCTCCGCTGCATCGCC-AGAAGTAAGATTCGCC
1 GGAAATAAGATTCGCCATTGCAGCTTCAATCTGCTCCGCTGCATCGCCTAGAAGTAAGATTCGCC
3696118 GTTGTGGCTTCGATCTTTTAAATTGCAATGT
66 GTTGTGGCTTCGATCTTTTAAATTGCAATGT
3696149 NNNNNNNNNN
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 46 0.52
99 42 0.48
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (99 bp):
GGAAATAAGATTCGCCATTGCAGCTTCAATCTGCTCCGCTGCATCGCCTAGAAGTAAGATTCGCC
GTTGTGGCTTCGATCTTTTAAATTGCAATGTTGG
Found at i:3705863 original size:48 final size:48
Alignment explanation
Indices: 3705690--3705966 Score: 216
Period size: 50 Copynumber: 5.7 Consensus size: 48
3705680 NNNNNGTCGG
* *
3705690 GGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCC
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCC
* * * *** **
3705738 TGGAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-GTTGG
1 -GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGC-ATCG--CC
* * *
3705789 GGAAGTAAGATTCGCCATTGTAGCTTCAATCTGCTCCGCTGCATCGCC
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCC
* * * * *** *
3705837 AGAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-GTCGG
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGC-ATCG-C-C
* * * * *
3705887 GGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCC
* * *
3705935 AGAAGTAAGATTCGCCGTTGTGGCTTCGATCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
3705967 TTTAAATTGC
Statistics
Matches: 171, Mismatches: 49, Indels: 17
0.72 0.21 0.07
Matches are distributed among these distances:
48 60 0.35
49 43 0.25
50 68 0.40
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (48 bp):
GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCGTTGCATCGCC
Found at i:3705878 original size:98 final size:98
Alignment explanation
Indices: 3705685--3705978 Score: 498
Period size: 98 Copynumber: 3.0 Consensus size: 98
3705675 NNNNNNNNNN
* * * *
3705685 GTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCGTTGCATCGCCTGGAAGTAAGAT
1 GTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCC-AGAAGTAAGAT
3705750 TCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
65 TCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
* **
3705784 GTTGGGGAAGTAAGATTCGCCATTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATT
1 GTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATT
3705849 CGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
66 CGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
* *
3705882 GTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCTAGAAGTAAGATT
1 GTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATT
3705947 CGCCGTTGTGGCTTCGATCTTTTAAATTGCAA
66 CGCCGTTGTGGCTTCGATCTTTTAAATTGCAA
3705979 ACTATGATTT
Statistics
Matches: 183, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 136 0.74
99 47 0.26
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (98 bp):
GTCGGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATT
CGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
Found at i:3714972 original size:22 final size:22
Alignment explanation
Indices: 3714944--3714996 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
3714934 TCTTTCATCT
3714944 CTTCAATTCTATTTAGGCTTGC
1 CTTCAATTCTATTTAGGCTTGC
3714966 CTTCAATTCTATTTAGGCTTGC
1 CTTCAATTCTATTTAGGCTTGC
3714988 CTTCAATTC
1 CTTCAATTC
3714997 CATCACAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.45
Consensus pattern (22 bp):
CTTCAATTCTATTTAGGCTTGC
Found at i:3718920 original size:15 final size:15
Alignment explanation
Indices: 3718885--3718913 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3718875 AAATAAAAGC
3718885 AATAATGATAATAAT
1 AATAATGATAATAAT
3718900 AATAATGATAATAA
1 AATAATGATAATAA
3718914 AACTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AATAATGATAATAAT
Found at i:3718963 original size:15 final size:16
Alignment explanation
Indices: 3718928--3718982 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 16
3718918 AATTAATTTT
*
3718928 TAAAAACAATAAATAAA
1 TAAAAA-AACAAATAAA
*
3718945 TAAAAAGACAAAT-AA
1 TAAAAAAACAAATAAA
3718960 TAAAAAAACAAAATAAAA
1 TAAAAAAAC-AAAT-AAA
3718978 TAAAA
1 TAAAA
3718983 CGGGACTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 10 0.31
16 9 0.28
17 6 0.19
18 7 0.22
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (16 bp):
TAAAAAAACAAATAAA
Found at i:3721562 original size:60 final size:62
Alignment explanation
Indices: 3721467--3721596 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 62
3721457 CTTTATTCAT
* *
3721467 AAAACAAGCCAAAAAAACAAGCAAAAAGTTAAACAAAAGT-AA-AAAAAACACTACAACCT-AA
1 AAAACAAGCCAAAAAAACAAGCAAAAAGTGAAACAAAAGTCAAGAAAAAA-A-AACAACCTAAA
* *
3721528 AAAACAAGCC-CAAAAACAAGTAGAAAA-TGAAACAAAAGTCAAGAAAAAAAAACAACCTAAA
1 AAAACAAGCCAAAAAAACAAGCA-AAAAGTGAAACAAAAGTCAAGAAAAAAAAACAACCTAAA
3721589 AAAACAAG
1 AAAACAAG
3721597 GATCCTGTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
60 28 0.46
61 27 0.44
62 6 0.10
ACGTcount: A:0.68, C:0.17, G:0.08, T:0.07
Consensus pattern (62 bp):
AAAACAAGCCAAAAAAACAAGCAAAAAGTGAAACAAAAGTCAAGAAAAAAAAACAACCTAAA
Found at i:3730552 original size:12 final size:11
Alignment explanation
Indices: 3730535--3730591 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
3730525 AACAAATCCT
3730535 CTCTCATATTTC
1 CTCTCA-ATTTC
3730547 CTCTCAA-TTC
1 CTCTCAATTTC
3730557 CTCTCAATTTC
1 CTCTCAATTTC
*
3730568 CT-TCCAAAATT-
1 CTCT-C-AATTTC
3730579 CTCTCAATTTC
1 CTCTCAATTTC
3730590 CT
1 CT
3730592 TCCAAAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 15 0.39
11 12 0.32
12 11 0.29
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Done.