Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 29 of 30
Found at i:4557268 original size:30 final size:30
Alignment explanation
Indices: 4557232--4557292 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
4557222 ATTAGAAGCA
*
4557232 ATGTATCGATACAAT-TCATCATGTATCGAT
1 ATGTATCGATACAATGT-ACCATGTATCGAT
4557262 ATGTATCGATACAATGTACCATGTATCGAT
1 ATGTATCGATACAATGTACCATGTATCGAT
4557292 A
1 A
4557293 CAAATAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (30 bp):
ATGTATCGATACAATGTACCATGTATCGAT
Found at i:4562291 original size:162 final size:160
Alignment explanation
Indices: 4562108--4562397 Score: 411
Period size: 162 Copynumber: 1.8 Consensus size: 160
4562098 ATTCAATTTT
* ** *
4562108 ATTTTATTTATTCTCGAAAATAGTATTTCATACCCTAATGGAACCCCGAAAGGATACAAAAGATT
1 ATTTTATTTATTCTAGAAAATACCATTTCATACCCTAATGGAACCCCGAAAGAATACAAAAGATT
* * * * *
4562173 TTTGAAATTTTTTATATCTCTACAGATGCCAATAGGAATATAAAAGATTAGAAAAAAT-AAATAT
66 TTTAAAATCTTTTATACCCCTAC--A-GCCAATAAGAATATAAAAGATTAGAAAAAATAAAATAT
4562237 TAGAATTTATCCAAATAATACCAATTTAAGTTA
128 TAGAATTTATCCAAATAATACCAATTTAAGTTA
* * * *
4562270 ATTTTATTTATTTTAGAAAATACCATTTCATACCCTAATGGAAGCCCGAAAGAATATAAAAGGTT
1 ATTTTATTTATTCTAGAAAATACCATTTCATACCCTAATGGAACCCCGAAAGAATACAAAAGATT
* *
4562335 TTTAAAATCTTTTATACCCCTACAGCCTATAAGAATATGAAAGATTAGAAAAAATAAAATATT
66 TTTAAAATCTTTTATACCCCTACAGCCAATAAGAATATAAAAGATTAGAAAAAATAAAATATT
4562398 TTTTAATTTT
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
159 28 0.25
160 8 0.07
162 76 0.68
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (160 bp):
ATTTTATTTATTCTAGAAAATACCATTTCATACCCTAATGGAACCCCGAAAGAATACAAAAGATT
TTTAAAATCTTTTATACCCCTACAGCCAATAAGAATATAAAAGATTAGAAAAAATAAAATATTAG
AATTTATCCAAATAATACCAATTTAAGTTA
Found at i:4564452 original size:164 final size:166
Alignment explanation
Indices: 4563872--4564608 Score: 816
Period size: 165 Copynumber: 4.5 Consensus size: 166
4563862 ACCATATTAG
** * * * * *
4563872 ATGAATTTTAAAAATTTTAAACCAAGAGAAATCC-CCCCAAAAAAAATTTACGAAGAAGAAAATT
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTC-AAAAAAA-TTACGGAGTAGAAAACT
** * ** * ** * * * *
4563936 CAATTTTTCGAAAAAAAAGGGATTTTCAAATAAAAAATTCAAAACTCATGAAAAGGAATTAATTT
64 CCGTATTTCGAAAAAAAA-AAAATTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTT
* * * *
4564001 TTTAAAACTGATTTAATGTAAAATAAATAATAATATTTT
128 TTGAAAACTGAATTAATATAAAATAAATAATAATATTTC
* * * *
4564040 ATGAATTTTAAAAATCAAAAACCAAGAAAAATCAC-CCTGAAAAAATTTATGGAGTAGAAAACTC
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAATC-CTCCTCAAAAAAATTACGGAGTAGAAAACTC
* * * * *
4564104 TGTATTTCGAAAAAAAAAGAATTCCAAGGAAAAAA-TAAAAATTTATGGAAATGAATGAATTTTT
65 CGTATTTCGAAAAAAAAAAAATTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTT
* * *
4564168 GAAAATTAAATTAATGTAAAATAAATAATAATATTTC
130 GAAAACTGAATTAATATAAAATAAATAATAATATTTC
* * * *
4564205 ATAAATTTTAAAAATTAAAAACCAAGAAAAAT-CTTCTCAAAAAAATTAACGGAGTAGAAAATTT
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTCAAAAAAATT-ACGGAGTAGAAAACTC
*
4564269 CGTATTTCG--AAAAAAAAAATTTCAAGGAAAAAATT-AAACATTCATGGAAATGAATGTATTTT
65 CGTATTTCGAAAAAAAAAAAATTTCAAGGAAAAAATTCAAA-ATTCATGGAAATGAATGAATTTT
*
4564331 TGAAAACTGAATTAATATGAAATAAATAATAATATTT-
129 TGAAAACTGAATTAATATAAAATAAATAATAATATTTC
* * * *
4564368 TTTAATTTT-AAAATTAAAAATCAAGAAAAATCCTCCT-AAAAAAATTATGGAGTAGAAAACTCC
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTCAAAAAAATTACGGAGTAGAAAACTCC
* * *
4564431 ATATTTCGAAAAAAGAAAAAATTT-AAGGAAAAAATTCAAAATTCATGGAAACGAAAGAATTTTT
66 GTATTTCGAAAAAA-AAAAAATTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTT
* *
4564495 GAAAACTGAATTAATATAAAATAAATAATGATATTTG
130 GAAAACTGAATTAATATAAAATAAATAATAATATTTC
* * * *
4564532 ATGAATTTTAAAAATTATAAACCATGAAAAATCCTCC-CAAAAAAATTTACGGAGAAGAAAACTT
1 ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTCAAAAAAA-TTACGGAGTAGAAAACTC
4564596 CGTAATTT-GAAAA
65 CGT-ATTTCGAAAA
4564609 TATGAGGAAT
Statistics
Matches: 485, Mismatches: 69, Indels: 32
0.83 0.12 0.05
Matches are distributed among these distances:
161 21 0.04
162 30 0.06
163 108 0.22
164 84 0.17
165 137 0.28
166 35 0.07
167 32 0.07
168 35 0.07
169 3 0.01
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (166 bp):
ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCTCAAAAAAATTACGGAGTAGAAAACTCC
GTATTTCGAAAAAAAAAAAATTTCAAGGAAAAAATTCAAAATTCATGGAAATGAATGAATTTTTG
AAAACTGAATTAATATAAAATAAATAATAATATTTC
Found at i:4564517 original size:327 final size:329
Alignment explanation
Indices: 4563875--4564608 Score: 937
Period size: 327 Copynumber: 2.2 Consensus size: 329
4563865 ATATTAGATG
* * * * *
4563875 AATTTTAAAAATTTTAAACCAAGAGAAATCCCCCCAAAAAAAATTTACGAAGAAGAAAATTCAAT
1 AATTTTAAAAATTATAAACCAAGAAAAATCCTCCC-AAAAAAATTTACGGAGAAGAAAATTC-GT
* * * *
4563940 TTTTCGAAAAAAAAGGGATTTTCAAATAAAAAATTCAAAACTCATGAAAAGGAATTAATTTTTTA
64 ATTTCGAAAAAAAA--GAATTTCAAAGAAAAAATTCAAAACTCATGAAAAGGAATTAATTTTTGA
* *
4564005 AAACTGATTTAATGTAAAATAAATAATAATATTTTATGAATTTTAAAAATCAAAAACCAAGAAAA
127 AAACTGAATTAATATAAAATAAATAATAATATTTTATGAATTTTAAAAATCAAAAACCAAGAAAA
* ** *
4564070 ATCACCCTGAAAAAATTTATGGAGTAGAAAACTCTGTATTTCGAAAAAAAAAGAATTCCAAGGAA
192 ATCACCCTGAAAAAAATTATGGAGTAGAAAACTCCATATTTCGAAAAAAAAAAAATTCCAAGGAA
* * * * *
4564135 AAAATAAAAATTTATGGAAATGAATGAATTTTTGAAAATTAAATTAATGTAAAATAAATAATAAT
257 AAAATAAAAATTCATGGAAACGAAAGAATTTTTGAAAACTAAATTAATATAAAATAAATAATAAT
4564200 ATTTCATA
322 ATTTCATA
* * * * *
4564208 AATTTTAAAAATTAAAAACCAAGAAAAATCTTCTCAAAAAAATTAACGGAGTAGAAAATTTCGTA
1 AATTTTAAAAATTATAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGAAGAAAA-TTCGTA
* * * *
4564273 TTTCGAAAAAAAA-AATTTCAAGGAAAAAATT-AAACATTCATGGAAATGAATGT-ATTTTTGAA
65 TTTCGAAAAAAAAGAATTTCAAAGAAAAAATTCAAA-ACTCATGAAAAGGAAT-TAATTTTTGAA
* * * *
4564335 AACTGAATTAATATGAAATAAATAATAATATTTT-TTAATTTT-AAAATTAAAAATCAAGAAAAA
128 AACTGAATTAATATAAAATAAATAATAATATTTTATGAATTTTAAAAATCAAAAACCAAGAAAAA
*
4564398 TC-CTCCT-AAAAAAATTATGGAGTAGAAAACTCCATATTTCGAAAAAAGAAAAAATT-TAAGGA
193 TCAC-CCTGAAAAAAATTATGGAGTAGAAAACTCCATATTTCGAAAAAA-AAAAAATTCCAAGGA
* * *
4564460 AAAAATTCAAAATTCATGGAAACGAAAGAATTTTTGAAAACTGAATTAATATAAAATAAATAATG
256 AAAAA-TAAAAATTCATGGAAACGAAAGAATTTTTGAAAACTAAATTAATATAAAATAAATAATA
* *
4564525 ATATTTGATG
320 ATATTTCATA
*
4564535 AATTTTAAAAATTATAAACCATGAAAAATCCTCCCAAAAAAATTTACGGAGAAGAAAACTTCGTA
1 AATTTTAAAAATTATAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGAAGAAAA-TTCGT-
4564600 ATTT-GAAAA
64 ATTTCGAAAA
4564609 TATGAGGAAT
Statistics
Matches: 348, Mismatches: 46, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
326 48 0.14
327 152 0.44
328 14 0.04
329 67 0.19
330 1 0.00
332 34 0.10
333 32 0.09
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (329 bp):
AATTTTAAAAATTATAAACCAAGAAAAATCCTCCCAAAAAAATTTACGGAGAAGAAAATTCGTAT
TTCGAAAAAAAAGAATTTCAAAGAAAAAATTCAAAACTCATGAAAAGGAATTAATTTTTGAAAAC
TGAATTAATATAAAATAAATAATAATATTTTATGAATTTTAAAAATCAAAAACCAAGAAAAATCA
CCCTGAAAAAAATTATGGAGTAGAAAACTCCATATTTCGAAAAAAAAAAAATTCCAAGGAAAAAA
TAAAAATTCATGGAAACGAAAGAATTTTTGAAAACTAAATTAATATAAAATAAATAATAATATTT
CATA
Found at i:4565582 original size:27 final size:27
Alignment explanation
Indices: 4565533--4565617 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
4565523 CTTTTTTTCT
* * *
4565533 TTTTAAATCCATAACTTCGTGGCACCC
1 TTTTAAGTCCACAACTTCATGGCACCC
* **
4565560 TTTTAAGTCCACAACTTTATGGCACTT
1 TTTTAAGTCCACAACTTCATGGCACCC
* * *
4565587 TTTTAAGTTCACAA-TTCCGTGGCACCT
1 TTTTAAGTCCACAACTT-CATGGCACCC
4565614 TTTT
1 TTTT
4565618 CTTTTTAAGT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
26 2 0.04
27 45 0.96
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.40
Consensus pattern (27 bp):
TTTTAAGTCCACAACTTCATGGCACCC
Found at i:4565623 original size:33 final size:33
Alignment explanation
Indices: 4565415--4565648 Score: 145
Period size: 34 Copynumber: 7.3 Consensus size: 33
4565405 CAACAATTTT
* * *
4565415 GTGGCACTTTTTTCTTTTAAAGTCTACAAC-TC
1 GTGGCACCTTTTTCTTTTTAAGTCCACAACTTC
* * *
4565447 TGTGGTACCATTTTTCTTTTTATGTCTACAACTTC
1 -GTGGCACC-TTTTTCTTTTTAAGTCCACAACTTC
* * * * * *
4565482 ATGGTACCATTTTTCTTTTAAAGTCTATAACTCC
1 GTGGCACC-TTTTTCTTTTTAAGTCCACAACTTC
* * *
4565516 ATGGCACCTTTTTTTCTTTTTAAATCCATAACTTC
1 GTGGCACC--TTTTTCTTTTTAAGTCCACAACTTC
*
4565551 GTGGCACC-----C-TTTTAAGTCCACAACTTT
1 GTGGCACCTTTTTCTTTTTAAGTCCACAACTTC
* *
4565578 ATGGCA-C----T-TTTTTAAGTTCACAA-TTCC
1 GTGGCACCTTTTTCTTTTTAAGTCCACAACTT-C
*
4565605 GTGGCACCTTTTTCTTTTTAAGTCCATAACTTC
1 GTGGCACCTTTTTCTTTTTAAGTCCACAACTTC
4565638 GTGGCACCTTT
1 GTGGCACCTTT
4565649 CCCTTTTAAA
Statistics
Matches: 163, Mismatches: 25, Indels: 26
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.02
27 38 0.23
28 2 0.01
32 1 0.01
33 31 0.19
34 58 0.36
35 30 0.18
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (33 bp):
GTGGCACCTTTTTCTTTTTAAGTCCACAACTTC
Found at i:4565655 original size:33 final size:33
Alignment explanation
Indices: 4565586--4565655 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
4565576 TTATGGCACT
* **
4565586 TTTTTAAGTTCACAATTCCGTGGCACCTTTTTC
1 TTTTTAAGTCCACAATTCCGTGGCACCTTTCCC
*
4565619 TTTTTAAGTCCATAACTT-CGTGGCACCTTTCCC
1 TTTTTAAGTCCACAA-TTCCGTGGCACCTTTCCC
4565652 TTTT
1 TTTT
4565656 AAAACCCGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (33 bp):
TTTTTAAGTCCACAATTCCGTGGCACCTTTCCC
Found at i:4565685 original size:32 final size:33
Alignment explanation
Indices: 4565649--4566018 Score: 292
Period size: 31 Copynumber: 11.7 Consensus size: 33
4565639 TGGCACCTTT
*
4565649 CCCTTTTAAAA-CCCGCACAAGTCGATGGCAAC
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
* *
4565681 CCC-TTT-AAAGCCCACACAAGTTGGTGGCAAC
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
* ** * * *
4565712 CTC-TTCCAAAGCCTACACAAGTTGGTGGCAAC
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
* * * *
4565744 CCC--TCAAAAGCCTATACAAGTTGATGGCAAC
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
* * * * *
4565775 CTCTTCT-AAAGCCCACACAAGTTGGTAGCAAC
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
4565807 CCC-TTTAAAAGCCCACACAAGTC-AGTGGCAA-
1 CCCTTTTAAAAGCCCACACAAGTCGA-TGGCAAC
*
4565838 CCCTTTTAAAAGCCCACACAAGTCGGTGGCAAC
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
* *
4565871 CCC--TCAAAAGCCCACACAAGTCGGTGGCAA-
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
* * *
4565901 -CTTTTTAAAAGTCCACACAAGT-TAGTGGCAAC
1 CCCTTTTAAAAGCCCACACAAGTCGA-TGGCAAC
** *
4565933 CCC--TCCAAAGCCCATACAAGTCGATGGCAA-
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
* * *
4565963 CCC-TTTCAAAGCCCACACAAGTCAATGGTAAC
1 CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
**
4565995 CTTTTTTCAAAAGCCCACACAAGT
1 CCCTTTT-AAAAGCCCACACAAGT
4566019 TGGTGACAAT
Statistics
Matches: 277, Mismatches: 42, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
29 1 0.00
30 6 0.02
31 148 0.53
32 100 0.36
33 7 0.03
34 15 0.05
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.19
Consensus pattern (33 bp):
CCCTTTTAAAAGCCCACACAAGTCGATGGCAAC
Found at i:4565731 original size:63 final size:63
Alignment explanation
Indices: 4565664--4566058 Score: 359
Period size: 63 Copynumber: 6.2 Consensus size: 63
4565654 TTAAAACCCG
* * * *
4565664 CACAAGTCGATGGCAACCCCTTTAAAGCCCACACAAGTTGGTGGCAACCTCTTCCAAAGCCTA
1 CACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTCCAAAGCCCA
* * * * * * *
4565727 CACAAGTTGGTGGCAACCCCTCAAAAGCCTATACAAGTTGATGGCAACCTCTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTCCAAAGCCCA
* * * * **
4565790 CACAAGTTGGTAGCAACCCCTTTAAAAGCCCACACAAGTCAGTGGCAACC-CTTTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCCTCT-AAAGCCCACACAAGTCGGTGGCAACCTC-TTCCAAAGCCCA
* * ** *
4565854 CACAAGTCGGTGGCAACCCCTCAAAAGCCCACACAAGTCGGTGGCAA-CTTTTTAAAAGTCCA
1 CACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTCCAAAGCCCA
** * * * *
4565916 CACAAGTTAGTGGCAACCCCTCCAAAGCCCATACAAGTCGATGGCAACC-CTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTCCAAAGCCCA
** * ** * * *
4565978 CACAAGTCAATGGTAACCTTTTTTCAAAAGCCCACACAAGTTGGTGACAA--TCTTCTCAAAAGC
1 CACAAGTCGGTGGCAACC---CCTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTC-C-AAAGC
*
4566041 CTA
61 CCA
4566044 CACAAGTCGGTGGCA
1 CACAAGTCGGTGGCA
4566059 TCTCTTCTAA
Statistics
Matches: 273, Mismatches: 49, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
62 79 0.29
63 99 0.36
64 53 0.19
65 23 0.08
66 19 0.07
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.19
Consensus pattern (63 bp):
CACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTCGGTGGCAACCTCTTCCAAAGCCCA
Found at i:4566047 original size:32 final size:31
Alignment explanation
Indices: 4565687--4566058 Score: 273
Period size: 32 Copynumber: 11.7 Consensus size: 31
4565677 CAACCCCTTT
* *
4565687 AAAGCCCACACAAGTTGGTGGCAACCTCTTCC
1 AAAGCCCACACAAGTTGGTGGCAACTTC-TCA
* **
4565719 AAAGCCTACACAAGTTGGTGGCAACCCCTCA
1 AAAGCCCACACAAGTTGGTGGCAACTTCTCA
* * * * *
4565750 AAAGCCTATACAAGTTGATGGCAACCTCTTCT
1 AAAGCCCACACAAGTTGGTGGCAACTTC-TCA
* ** *
4565782 AAAGCCCACACAAGTTGGTAGCAACCCCTTTA
1 AAAGCCCACACAAGTTGGTGGCAACTTC-TCA
** *
4565814 AAAGCCCACACAAGTCAGTGGCAACCCTT-TTA
1 AAAGCCCACACAAGTTGGTGGCAA--CTTCTCA
* **
4565846 AAAGCCCACACAAGTCGGTGGCAACCCCTCA
1 AAAGCCCACACAAGTTGGTGGCAACTTCTCA
* * *
4565877 AAAGCCCACACAAGTCGGTGGCAACTTTTTA
1 AAAGCCCACACAAGTTGGTGGCAACTTCTCA
* * ** *
4565908 AAAGTCCACACAAGTTAGTGGCAACCCCTCC
1 AAAGCCCACACAAGTTGGTGGCAACTTCTCA
* * *
4565939 AAAGCCCATACAAGTCGATGGCAACCCTT-TC-
1 AAAGCCCACACAAGTTGGTGGCAA--CTTCTCA
*** * *
4565970 AAAGCCCACACAAGTCAATGGTAACCTTTTTTCA
1 AAAGCCCACACAAGTTGGTGGCAA-C--TTCTCA
*
4566004 AAAGCCCACACAAGTTGGTGACAATCTTCTCA
1 AAAGCCCACACAAGTTGGTGGCAA-CTTCTCA
* *
4566036 AAAGCCTACACAAGTCGGTGGCA
1 AAAGCCCACACAAGTTGGTGGCA
4566059 TCTCTTCTAA
Statistics
Matches: 275, Mismatches: 55, Indels: 20
0.79 0.16 0.06
Matches are distributed among these distances:
30 3 0.01
31 119 0.43
32 129 0.47
33 3 0.01
34 21 0.08
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (31 bp):
AAAGCCCACACAAGTTGGTGGCAACTTCTCA
Found at i:4566199 original size:52 final size:52
Alignment explanation
Indices: 4566136--4566424 Score: 199
Period size: 52 Copynumber: 5.4 Consensus size: 52
4566126 AAGTTTAATG
* * * *
4566136 TCGCTGACCTTGAATCAGCACATCGGTACCTTTTTC-TTTCTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACATCGGTACATTTGTCATCT-TTAAGTCCAATA
* * * * *
4566188 TTGCTGGCCTTGAATTAGCATATTGGTGCATTTGTCATCTTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACATCGGTACATTTGTCATCTTTAAGTCCAATA
* * * *
4566240 TCGCTAGCCTTGAATCAGCATACTAGCG--CCTTTGTCATCTTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACA-TCG-GTACATTTGTCATCTTTAAGTCCAATA
* * * * * *
4566292 TCACTAGCCTTGAATCAGCATATCAGCACCTTTATCATTCT-TCTTATCTTCAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCACATC-G-----GTA-CATT-TGTC--ATCTTTAAGTCCAATA
* * * * * *
4566353 TCACTTGCCTTGAGTCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACATCGGTACATTTGTCATCTTTAAGTCCAATA
*
4566405 TCGCTAGCCTTGAATCAGCA
1 TCGCTGGCCTTGAATCAGCA
4566425 TATTGGTGCC
Statistics
Matches: 189, Mismatches: 33, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
51 1 0.01
52 135 0.71
53 5 0.03
54 6 0.03
55 1 0.01
59 5 0.03
60 2 0.01
61 34 0.18
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (52 bp):
TCGCTGGCCTTGAATCAGCACATCGGTACATTTGTCATCTTTAAGTCCAATA
Found at i:4566350 original size:61 final size:61
Alignment explanation
Indices: 4566274--4566584 Score: 268
Period size: 61 Copynumber: 5.2 Consensus size: 61
4566264 AGCGCCTTTG
*
4566274 TCATCTTTAAGTCCAATATCACTAGCCTTGAATCAGCATATCAGCACCTTTATCATTCTTC
1 TCATCTTTAAGTCCAATATCACTAGCCTTGAATCAGCATATTAGCACCTTTATCATTCTTC
* * * * * * * *
4566335 TTATCTTCAAGTCCAATGTCACTTGCCTTGAGTCAGCACATTGGCA-C-----C--T-TTG
1 TCATCTTTAAGTCCAATATCACTAGCCTTGAATCAGCATATTAGCACCTTTATCATTCTTC
* * ** *
4566387 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGTGCCCTTATCATTCTTC
1 TCATCTTTAAGTCCAATATCACTAGCCTTGAATCAGCATATTAGCACCTTTATCATTCTTC
* * * *
4566448 TCATCTTTAAGCCCGATATCACTCA-CCGTGAATTAGCATATTAGCACCTTTATCATTCTTC
1 TCATCTTTAAGTCCAATATCACT-AGCCTTGAATCAGCATATTAGCACCTTTATCATTCTTC
* * * * * * * *
4566509 GCATCTTTAAGTCCACTGTCACT-GACCTTGAATCAGCAAATTGGCA-CTCTTCTCATCCTTA
1 TCATCTTTAAGTCCAATATCACTAG-CCTTGAATCAGCATATTAGCACCT-TTATCATTCTTC
*
4566570 TCATCTTTGAGTCCA
1 TCATCTTTAAGTCCA
4566585 GTGTTGCAGG
Statistics
Matches: 195, Mismatches: 42, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
52 39 0.20
53 2 0.01
55 1 0.01
58 1 0.01
60 4 0.02
61 147 0.75
62 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (61 bp):
TCATCTTTAAGTCCAATATCACTAGCCTTGAATCAGCATATTAGCACCTTTATCATTCTTC
Found at i:4566422 original size:113 final size:113
Alignment explanation
Indices: 4566222--4566503 Score: 332
Period size: 113 Copynumber: 2.5 Consensus size: 113
4566212 GGTGCATTTG
* * * *
4566222 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATACTAGCGCCTTTGTCATCTTTAAGTC
1 TCATCTTCAAGTCCAATATCACTAGCCTTGAATCAGCACACTAGCACCTTTGTCATCTTTAAGTC
*
4566287 CAATATCACTAGCCTTGAATCAGCATATCAGCACCTTTATCATTCTTC
66 CAATATCACTAGCCTTGAATCAGCATATCAGCACCCTTATCATTCTTC
* * * * * *
4566335 TTATCTTCAAGTCCAATGTCACTTGCCTTGAGTCAGCACATTGGCACCTTTGTCATCTTTAAGTC
1 TCATCTTCAAGTCCAATATCACTAGCCTTGAATCAGCACACTAGCACCTTTGTCATCTTTAAGTC
* ** **
4566400 CAATATCGCTAGCCTTGAATCAGCATATTGGTGCCCTTATCATTCTTC
66 CAATATCACTAGCCTTGAATCAGCATATCAGCACCCTTATCATTCTTC
* * * * * * * *
4566448 TCATCTTTAAGCCCGATATCACTCA-CCGTGAATTAGCATATTAGCACCTTTATCAT
1 TCATCTTCAAGTCCAATATCACT-AGCCTTGAATCAGCACACTAGCACCTTTGTCAT
4566504 TCTTCGCATC
Statistics
Matches: 140, Mismatches: 28, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
113 140 1.00
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (113 bp):
TCATCTTCAAGTCCAATATCACTAGCCTTGAATCAGCACACTAGCACCTTTGTCATCTTTAAGTC
CAATATCACTAGCCTTGAATCAGCATATCAGCACCCTTATCATTCTTC
Found at i:4567183 original size:20 final size:20
Alignment explanation
Indices: 4567141--4567194 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
4567131 TTCAACAATT
4567141 TGTATCGATACAATAAGGCAA
1 TGTATCGATAC-ATAAGGCAA
4567162 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAG-GCAA
4567182 TGTATCGATACAT
1 TGTATCGATACAT
4567195 GCCTGAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGGCAA
Found at i:4567201 original size:20 final size:21
Alignment explanation
Indices: 4567141--4567214 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
4567131 TTCAACAATT
* *
4567141 TGTATCGATACAATAA-GGCAA
1 TGTATCGATAC-ATAACTGAAA
*
4567162 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAACTGAAA
**
4567182 TGTATCGATACATGCCTGAAA
1 TGTATCGATACATAACTGAAA
*
4567203 TGTATCGGTACA
1 TGTATCGATACA
4567215 AGACCATGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 21 0.46
21 25 0.54
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATAACTGAAA
Found at i:4567283 original size:40 final size:40
Alignment explanation
Indices: 4567237--4567314 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
4567227 ATTTTGAAAG
* * * *
4567237 GAAATTGTATCGATATATTTTTTAATGTATTGATACATAT
1 GAAATTGTATCGATACATTTCTCAATGTATCGATACATAT
*
4567277 GAAATTGTATCGATACATTTCTCATTGTATCGATACAT
1 GAAATTGTATCGATACATTTCTCAATGTATCGATACAT
4567315 TCTGGGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (40 bp):
GAAATTGTATCGATACATTTCTCAATGTATCGATACATAT
Found at i:4574509 original size:2 final size:2
Alignment explanation
Indices: 4574502--4574544 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4574492 TAAATGAGTC
4574502 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4574544 A
1 A
4574545 ATTCTTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4577145 original size:22 final size:21
Alignment explanation
Indices: 4577119--4577164 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4577109 GACAAATAGA
* *
4577119 TATTTTTTATTATATTTCAATT
1 TATTTTATATTATATGT-AATT
*
4577141 TATTTTATATTTTATGTAATT
1 TATTTTATATTATATGTAATT
4577162 TAT
1 TAT
4577165 CATAATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TATTTTATATTATATGTAATT
Found at i:4577533 original size:125 final size:126
Alignment explanation
Indices: 4577255--4577596 Score: 596
Period size: 125 Copynumber: 2.7 Consensus size: 126
4577245 ATTTATTTTA
4577255 CATAGATTTTAACATGTTCGTATATTATTAATTAAAGCACTAAATAACATAAAAAATTACATGAA
1 CATAGATTTTAACATGTTCGTATATTATTAATTAAAGCACTAAATAACATAAAAAATTACATGAA
*
4577320 CATATCATAAATATACGAACACATTATTTAGTTATATTAAATATGATATTTAGTTACATAT
66 CATATCATAAATATACGAACACGTTATTTAGTTATATTAAATATGATATTTAGTTACATAT
* * * *
4577381 CATAGATTTTAACGTGTTCGCATATTATTAATTAAAGTACTAAATAACATAAAAAATTACATAAA
1 CATAGATTTTAACATGTTCGTATATTATTAATTAAAGCACTAAATAACATAAAAAATTACATGAA
*
4577446 GATATCATAAATATACGAACACGTTATTTAGTTA-ATTAAATATGATATTTAGTTACATAT
66 CATATCATAAATATACGAACACGTTATTTAGTTATATTAAATATGATATTTAGTTACATAT
* *
4577506 CATAGATTTTAACATATTCGTATATTATTAATTAAAACACTAAATAACATAAAAAATTACATGAA
1 CATAGATTTTAACATGTTCGTATATTATTAATTAAAGCACTAAATAACATAAAAAATTACATGAA
*
4577571 CATATCATCAATATACGAACACGTTA
66 CATATCATAAATATACGAACACGTTA
4577597 AACTCTATAT
Statistics
Matches: 202, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
125 109 0.54
126 93 0.46
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (126 bp):
CATAGATTTTAACATGTTCGTATATTATTAATTAAAGCACTAAATAACATAAAAAATTACATGAA
CATATCATAAATATACGAACACGTTATTTAGTTATATTAAATATGATATTTAGTTACATAT
Found at i:4578062 original size:12 final size:12
Alignment explanation
Indices: 4578020--4578068 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
4578010 TATTCATGTA
4578020 ATTTTTTATATT
1 ATTTTTTATATT
*
4578032 ATTTAGTATTTTAATT
1 ATTT--T-TTAT-ATT
4578048 ATTTTTTATATT
1 ATTTTTTATATT
4578060 ATTTTTTAT
1 ATTTTTTAT
4578069 TAAATCTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 16 0.52
13 3 0.10
14 2 0.06
15 3 0.10
16 7 0.23
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (12 bp):
ATTTTTTATATT
Found at i:4579512 original size:120 final size:111
Alignment explanation
Indices: 4579291--4579677 Score: 450
Period size: 120 Copynumber: 3.4 Consensus size: 111
4579281 TATTTTTAAT
*
4579291 AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAACTAAAATATT-A--A-T-TA-T
1 AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATATT
* * * *
4579350 TTTTT-AAAATTAAAAGTGTTATTATTATTATTATTTTTAATAAAATA
66 TTTTTAAAAATAAAAAATATTTTTATTATTA--ATTTTTAATAAAATA
* * * *
4579397 AAAAATAATATTTAATTAAGTTTAAAAAAATTACATTAACAGATTAAATTATTAATTATTATGTT
1 AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTAT-AT
4579462 TTTATAAAATTCAAAAATAAAAAA-AGGTTTTT-TTATAATAATTTTTAATAAAATA
65 TTT-T----TT-AAAAATAAAAAATA--TTTTTATTAT--TAATTTTTAATAAAATA
* * *
4579517 AAAAATAATATTTAATTAAGTTTAAACAATTTATATTAACAAATTAAAATATTAGTTATTATATT
1 AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATATT
*
4579582 TTTTTAAAAATAAAAAATATTTTTATTATTATTTTTTAATAAAATA
66 TTTTTAAAAATAAAAAATATTTTTATTATTAATTTTTAATAAAATA
* *
4579628 AAAAATAATATTTAATTAAATTTTTAAAAATTTACATTAACAAATTAAAA
1 AAAAATAATATTTAATT-AAGTTTAAAAAATTTACATTAACAAATTAAAA
4579678 CATAATATTT
Statistics
Matches: 239, Mismatches: 21, Indels: 36
0.81 0.07 0.12
Matches are distributed among these distances:
106 49 0.21
107 1 0.00
109 1 0.00
110 1 0.00
111 34 0.14
112 33 0.14
113 19 0.08
114 4 0.02
118 3 0.01
119 4 0.02
120 84 0.35
121 4 0.02
122 2 0.01
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (111 bp):
AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATATT
TTTTTAAAAATAAAAAATATTTTTATTATTAATTTTTAATAAAATA
Found at i:4579601 original size:33 final size:34
Alignment explanation
Indices: 4579562--4579652 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 34
4579552 TTAACAAATT
* *
4579562 AAAATATTAGTTATTATATTTTTTTA-AAAATAA
1 AAAATATTATTTATTATATTTTTTAATAAAATAA
4579595 AAAATATT-TTTATTATTATTTTTTAATAAAATAA
1 AAAATATTATTTATTA-TATTTTTTAATAAAATAA
* *
4579629 AAAATAATATTTAATTAAATTTTT
1 AAAATATTATTT-ATTATATTTTT
4579653 AAAAATTTAC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 6 0.12
33 17 0.34
34 14 0.28
35 9 0.18
36 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
AAAATATTATTTATTATATTTTTTAATAAAATAA
Found at i:4579617 original size:32 final size:35
Alignment explanation
Indices: 4579562--4579652 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 35
4579552 TTAACAAATT
4579562 AAAATATTAGTTATTATATTTTTTT-A-AAAATAA
1 AAAATATTAGTTATTATATTTTTTTAATAAAATAA
*
4579595 AAAATATT-TTTATTAT-TATTTTTTAATAAAATAA
1 AAAATATTAGTTATTATAT-TTTTTTAATAAAATAA
* * *
4579629 AAAATAATATTTAATTAAATTTTT
1 AAAATATTAGTT-ATTATATTTTT
4579653 AAAAATTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
31 1 0.02
32 13 0.27
33 9 0.18
34 14 0.29
35 3 0.06
36 8 0.16
37 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
AAAATATTAGTTATTATATTTTTTTAATAAAATAA
Found at i:4579926 original size:15 final size:15
Alignment explanation
Indices: 4579906--4579935 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4579896 TTTAAAAATT
4579906 TTTTTTAATTTAAAA
1 TTTTTTAATTTAAAA
*
4579921 TTTTTTATTTTAAAA
1 TTTTTTAATTTAAAA
4579936 AAAATAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTAATTTAAAA
Found at i:4579982 original size:23 final size:24
Alignment explanation
Indices: 4579952--4580001 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
4579942 ATAATTAATA
4579952 TTTTAATTT-ATT-AATATAATTT
1 TTTTAATTTAATTAAATATAATTT
*
4579974 TTTTAAATTTAATTAAATATTATTT
1 TTTT-AATTTAATTAAATATAATTT
4579999 TTT
1 TTT
4580002 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 5 0.21
24 3 0.12
25 12 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTAATTTAATTAAATATAATTT
Found at i:4582178 original size:156 final size:155
Alignment explanation
Indices: 4581894--4582235 Score: 443
Period size: 156 Copynumber: 2.2 Consensus size: 155
4581884 TAAATTTAAG
* *
4581894 AAAAATTACAAAAATACCCCTAGAGGATACCTTCGACGTGAAAGTATCTCGGTACTCCTAAAAAA
1 AAAAATTACAAAAATACCCCTAGA-GATACCTTCGACGTGAAAATATCTCAGTACTCCTAAAAAA
* * *
4581959 CTTGAAAAGGACTATAAAAGGGATGAACATATCCTAAATATCCACTTTCGGTATAAAAGCAGACC
65 CTTAAAAAAGACTATAAAAGGGATGAACATATCCTAAATATCCACTTTCGGCATAAAAGCAGACC
*
4582024 CAATGATAACCTAGGACTCGATTCTA
130 CAATGATAACCTAGGACTCAATTCTA
* ** * **
4582050 AAAAATTATAAAAATACCCCTAGGAGATATTTTCGACGTGAAAATATCTTAGTAC-CCGTAAAGG
1 AAAAATTACAAAAATACCCCTA-GAGATACCTTCGACGTGAAAATATCTCAGTACTCC-TAAAAA
* *
4582114 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCTTAAATATCCACTTTCGGCATAAAAGCAGAC
64 ACTTAAAAAAGACTATAAAAGGGATGAACATATCCTAAATATCCACTTTCGGCATAAAAGCAGAC
** * * * * *
4582179 CCGGTTATAACTTAGGATTTAATTTTA
129 CCAATGATAACCTAGGACTCAATTCTA
*
4582206 AAAAATTACAAAAATACTCCTAAGAGATAC
1 AAAAATTACAAAAATACCCCT-AGAGATAC
4582236 ATTTAACGTA
Statistics
Matches: 159, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
155 2 0.01
156 154 0.97
157 3 0.02
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (155 bp):
AAAAATTACAAAAATACCCCTAGAGATACCTTCGACGTGAAAATATCTCAGTACTCCTAAAAAAC
TTAAAAAAGACTATAAAAGGGATGAACATATCCTAAATATCCACTTTCGGCATAAAAGCAGACCC
AATGATAACCTAGGACTCAATTCTA
Found at i:4584097 original size:58 final size:58
Alignment explanation
Indices: 4583976--4584098 Score: 192
Period size: 58 Copynumber: 2.1 Consensus size: 58
4583966 TTTGTTGTTG
* * * *
4583976 CTTGCTTCTTGTTTGTTTGTTGTTGCTGTTTTGTCTTGTCGTTGGTTCTTTCCTGCTG
1 CTTGCTTCTTGTTTGTTTGCTGTTGCTGTTTTGTCTTGCCGTTGGTTCTTTCCTACTA
* *
4584034 TTTGCTTCTTGTTTGTTTGCTGTTGCTGTTTTGTCTTGCCGTTGGTTCTTTCTTACTA
1 CTTGCTTCTTGTTTGTTTGCTGTTGCTGTTTTGTCTTGCCGTTGGTTCTTTCCTACTA
4584092 CTTGCTT
1 CTTGCTT
4584099 TTATTGGTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.02, C:0.18, G:0.22, T:0.59
Consensus pattern (58 bp):
CTTGCTTCTTGTTTGTTTGCTGTTGCTGTTTTGTCTTGCCGTTGGTTCTTTCCTACTA
Found at i:4584475 original size:17 final size:17
Alignment explanation
Indices: 4584443--4584476 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4584433 CCATTAGCTA
4584443 CTTGCATTGCTGTCTTT
1 CTTGCATTGCTGTCTTT
4584460 CTTGCCATTGCT-TCTTT
1 CTTG-CATTGCTGTCTTT
4584477 GCTATTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.26, G:0.15, T:0.53
Consensus pattern (17 bp):
CTTGCATTGCTGTCTTT
Found at i:4584927 original size:18 final size:17
Alignment explanation
Indices: 4584905--4584940 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 17
4584895 CACACATTAA
4584905 AAAAATCAAAAAATGAAAT
1 AAAAAT-AAAAAAT-AAAT
4584924 AAAAATAAAAAATAAAT
1 AAAAATAAAAAATAAAT
4584941 TGAGTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAAATAAAAAATAAAT
Found at i:4590609 original size:13 final size:13
Alignment explanation
Indices: 4590591--4590615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4590581 CATAAAGTGT
4590591 TGTATCGATACAA
1 TGTATCGATACAA
4590604 TGTATCGATACA
1 TGTATCGATACA
4590616 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4590613 original size:33 final size:33
Alignment explanation
Indices: 4590571--4590637 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4590561 TTCAACGATT
4590571 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
4590604 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
4590637 T
1 T
4590638 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:4590696 original size:13 final size:13
Alignment explanation
Indices: 4590678--4590702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4590668 ATCACTTAAA
4590678 TGTATCGATACAT
1 TGTATCGATACAT
4590691 TGTATCGATACA
1 TGTATCGATACA
4590703 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4590767 original size:52 final size:52
Alignment explanation
Indices: 4590711--4590839 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
4590701 CACTAATCTT
* *
4590711 TGTATCGATACATGCCGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
4590763 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
4590815 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
4590840 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:4595327 original size:13 final size:13
Alignment explanation
Indices: 4595309--4595333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4595299 TTCAACGATT
4595309 TGTATCGATACAA
1 TGTATCGATACAA
4595322 TGTATCGATACA
1 TGTATCGATACA
4595334 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4595369 original size:18 final size:19
Alignment explanation
Indices: 4595322--4595370 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
4595312 ATCGATACAA
*
4595322 TGTATCGATACATAAGTGT
1 TGTATCAATACATAAGTGT
* *
4595341 TGTATCGATACATAA-TTT
1 TGTATCAATACATAAGTGT
*
4595359 TGTATTAATACA
1 TGTATCAATACA
4595371 ATGTATCGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (19 bp):
TGTATCAATACATAAGTGT
Found at i:4595440 original size:13 final size:13
Alignment explanation
Indices: 4595422--4595446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4595412 ATTACTCAAA
4595422 TGTATCGATACAT
1 TGTATCGATACAT
4595435 TGTATCGATACA
1 TGTATCGATACA
4595447 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4597657 original size:24 final size:26
Alignment explanation
Indices: 4597630--4597683 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
4597620 TCAAAATTTT
4597630 ATTCAT-C-GGGGACACTCCAACCCC
1 ATTCATCCAGGGGACACTCCAACCCC
*
4597654 ATTCTTCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGGGACACTCCAACCCC
4597681 ATT
1 ATT
4597684 TTCAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 1 0.04
27 20 0.77
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCCC
Found at i:4598751 original size:34 final size:34
Alignment explanation
Indices: 4598707--4598774 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
4598697 TACGAAAGAT
* *
4598707 GGCCTGGTATGAGAAGGATAAGAAACTTCTCATC
1 GGCCTAGTATGAGAAGGATAAGAAACTTCGCATC
4598741 GGCCTAGTATGAGAAGGATAAGAAACTTCGCATC
1 GGCCTAGTATGAGAAGGATAAGAAACTTCGCATC
4598775 CATTGCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (34 bp):
GGCCTAGTATGAGAAGGATAAGAAACTTCGCATC
Found at i:4602549 original size:18 final size:18
Alignment explanation
Indices: 4602510--4602552 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4602500 TGTAATGAAG
*
4602510 AAAGCAATCGAAACAAAC
1 AAAGCAATCGAAACAAAA
*
4602528 AAAGCAAT-TAAACAAATA
1 AAAGCAATCGAAACAAA-A
4602546 AAAGCAA
1 AAAGCAA
4602553 ATGAAGTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.65, C:0.16, G:0.09, T:0.09
Consensus pattern (18 bp):
AAAGCAATCGAAACAAAA
Found at i:4602673 original size:20 final size:18
Alignment explanation
Indices: 4602639--4602694 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
4602629 AACATCGAGC
4602639 AAAAATAAAGAAAAGATGAG
1 AAAAA-AAAGAAAAGA-GAG
*
4602659 AGAAAAAAAGCAAAGAGAG
1 A-AAAAAAAGAAAAGAGAG
*
4602678 AAAAGAAAAGAAGAGAG
1 AAAA-AAAAGAAAAGAG
4602695 GAATCGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.10
19 14 0.45
20 10 0.32
21 4 0.13
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.04
Consensus pattern (18 bp):
AAAAAAAAGAAAAGAGAG
Found at i:4602691 original size:17 final size:16
Alignment explanation
Indices: 4602645--4602694 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
4602635 GAGCAAAAAT
*
4602645 AAAGAAAAGATGAGAG
1 AAAGAAAAGAAGAGAG
4602661 AAA-AAAAGCAAAGAGAG
1 AAAGAAAAG--AAGAGAG
4602678 AAAAGAAAAGAAGAGAG
1 -AAAGAAAAGAAGAGAG
4602695 GAATCGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.17
16 3 0.10
17 13 0.45
18 3 0.10
19 5 0.17
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (16 bp):
AAAGAAAAGAAGAGAG
Found at i:4602732 original size:24 final size:24
Alignment explanation
Indices: 4602705--4602751 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4602695 GAATCGAAAC
*
4602705 AAAAAAAAGAATTGAAACAGCAAA
1 AAAAAAAAGAACTGAAACAGCAAA
*
4602729 AAAAAACAGAACTGAAACAGCAA
1 AAAAAAAAGAACTGAAACAGCAA
4602752 GAAGAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.68, C:0.13, G:0.13, T:0.06
Consensus pattern (24 bp):
AAAAAAAAGAACTGAAACAGCAAA
Found at i:4602834 original size:16 final size:16
Alignment explanation
Indices: 4602815--4602849 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4602805 AGCAACCGAA
4602815 AGCAA-CAACAAGCAAT
1 AGCAAGCAACAA-CAAT
4602831 AGCAAGCAACAACAAT
1 AGCAAGCAACAACAAT
4602847 AGC
1 AGC
4602850 TTTGGTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.54, C:0.26, G:0.14, T:0.06
Consensus pattern (16 bp):
AGCAAGCAACAACAAT
Found at i:4602919 original size:25 final size:25
Alignment explanation
Indices: 4602872--4602919 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
4602862 TCAAAGAAAG
**
4602872 AAACCAGTAAATCAACTCCAGGATT
1 AAACCAGTAAATCAACAACAGGATT
* *
4602897 AAACCAGTAAGTCAACAAGAGGA
1 AAACCAGTAAATCAACAACAGGA
4602920 AGAAGAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.15
Consensus pattern (25 bp):
AAACCAGTAAATCAACAACAGGATT
Found at i:4609217 original size:13 final size:13
Alignment explanation
Indices: 4609199--4609223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4609189 TTCTACAATT
4609199 TGTATCGATACAA
1 TGTATCGATACAA
4609212 TGTATCGATACA
1 TGTATCGATACA
4609224 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4617181 original size:2 final size:2
Alignment explanation
Indices: 4617174--4617212 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4617164 GGTTTCAATG
4617174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4617213 ATTGAATTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4617262 original size:6 final size:7
Alignment explanation
Indices: 4617245--4617270 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4617235 CAAAACTATA
4617245 AAAAATC
1 AAAAATC
4617252 AAAAATC
1 AAAAATC
4617259 AAAAATC
1 AAAAATC
4617266 AAAAA
1 AAAAA
4617271 AATTGATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATC
Found at i:4617591 original size:18 final size:18
Alignment explanation
Indices: 4617536--4617591 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
4617526 TTTTTAAAAT
* *
4617536 TTTTTGAATTTTCCTTAT
1 TTTTTGAATTTTTCTTAG
*
4617554 TTTTATG-ATTTTT-TGAAG
1 TTTT-TGAATTTTTCT-TAG
4617572 TTTTTGAATTTTTCTTAG
1 TTTTTGAATTTTTCTTAG
4617590 TT
1 TT
4617592 ATTTTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
17 3 0.10
18 24 0.80
19 3 0.10
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (18 bp):
TTTTTGAATTTTTCTTAG
Found at i:4617603 original size:36 final size:36
Alignment explanation
Indices: 4617517--4617603 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
4617507 TTTATTTATT
*
4617517 TTATTTTAATTTTTAAAATTTTTTGAATTTTCCTTA
1 TTATTTTAATTTTTAAAAGTTTTTGAATTTTCCTTA
* ** *
4617553 TT-TTTATGATTTTTTGAAGTTTTTGAATTTTTCTTA
1 TTATTT-TAATTTTTAAAAGTTTTTGAATTTTCCTTA
*
4617589 GTTATTTTTATTTTT
1 -TTATTTTAATTTTT
4617604 TAATTCCTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
35 3 0.07
36 27 0.64
37 9 0.21
38 3 0.07
ACGTcount: A:0.22, C:0.03, G:0.07, T:0.68
Consensus pattern (36 bp):
TTATTTTAATTTTTAAAAGTTTTTGAATTTTCCTTA
Found at i:4619498 original size:44 final size:44
Alignment explanation
Indices: 4619438--4619522 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
4619428 TCTTTATTGA
4619438 AAAAAAATTAATGAAGTGACTTTCATATACTAGAAGCACACTTG
1 AAAAAAATTAATGAAGTGACTTTCATATACTAGAAGCACACTTG
*
4619482 AAAAAAATTAATGAAGTGACTTTCATATACTAGAAGTACAC
1 AAAAAAATTAATGAAGTGACTTTCATATACTAGAAGCACAC
4619523 CTATGGACTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (44 bp):
AAAAAAATTAATGAAGTGACTTTCATATACTAGAAGCACACTTG
Found at i:4619913 original size:58 final size:56
Alignment explanation
Indices: 4619804--4620003 Score: 163
Period size: 58 Copynumber: 3.5 Consensus size: 56
4619794 TATAAGTCTC
* * * * *
4619804 TAGAACATGGAAAATGATCTAAATGATCCTAATATACATGAAACT-CTATAAAAGTTCT
1 TAGATCATAGAAAATGACCTAAATGATCCTAAAATACAT-AAAATGC-ATAAAA-TTCT
* **
4619862 TAGATTATAGAAAATGACCTAAATGATCCTAAAATTTATAAAATTGCATAAAAATTCT
1 TAGATCATAGAAAATGACCTAAATGATCCTAAAATACATAAAA-TGCAT-AAAATTCT
* * * * * *
4619920 TAGATCAT-GAAAAATGACATAAATTAT-ATCAAAATGCATAAAATGACCTAAAAATCT
1 TAGATCATAG-AAAATGACCTAAATGATCCT-AAAATACATAAAATG-CATAAAATTCT
*
4619977 CTAGATCATAAAAAATGACCTAAATGA
1 -TAGATCATAGAAAATGACCTAAATGA
4620004 CTTCAAAATT
Statistics
Matches: 115, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
57 14 0.12
58 96 0.83
59 5 0.04
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.28
Consensus pattern (56 bp):
TAGATCATAGAAAATGACCTAAATGATCCTAAAATACATAAAATGCATAAAATTCT
Found at i:4620010 original size:58 final size:57
Alignment explanation
Indices: 4619872--4620172 Score: 206
Period size: 58 Copynumber: 5.2 Consensus size: 57
4619862 TAGATTATAG
* * * *
4619872 AAAATGACCTAAATGA-TCCTAAAATTTATAAAATTG-CATAAAAATTCTTAGATCATGA
1 AAAATGACCTAAATGACTTC-AAAATTCATAAAA-TGACCTAAAAA-TCCTAGATCATGA
* * * *
4619930 AAAATGACATAAATTA-TATCAAAATGCATAAAATGACCTAAAAATCTCTAGATCATAA
1 AAAATGACCTAAATGACT-TCAAAATTCATAAAATGACCTAAAAATC-CTAGATCATGA
* * * * *
4619988 AAAATGACCTAAATGACTTCAAAATTCACAAAATTACACT-TAAGTCCCTAGATCATGGT
1 AAAATGACCTAAATGACTTCAAAATTCATAAAATGAC-CTAAAAAT-CCTAGATCAT-GA
* * *
4620047 AAAA-GACCTAAATGACATT-AAAA-TCTATAAATTGCATCT--AAATCCTCAAATCATGA
1 AAAATGACCTAAATGAC-TTCAAAATTC-ATAAAATG-ACCTAAAAATCCT-AGATCATGA
* * * * ** * *
4620103 AAAATGACCTTAATGACGTCAAAATACATGAAATGATATAAAAGTCCATAGTTCATGA
1 AAAATGACCTAAATGACTTCAAAATTCATAAAATGACCTAAAAATCC-TAGATCATGA
4620161 AAAATGACCTAA
1 AAAATGACCTAA
4620173 CATACATAAA
Statistics
Matches: 192, Mismatches: 34, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
56 12 0.06
57 36 0.19
58 131 0.68
59 13 0.07
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (57 bp):
AAAATGACCTAAATGACTTCAAAATTCATAAAATGACCTAAAAATCCTAGATCATGA
Found at i:4620059 original size:116 final size:115
Alignment explanation
Indices: 4619920--4620127 Score: 244
Period size: 115 Copynumber: 1.8 Consensus size: 115
4619910 TAAAAATTCT
* * *
4619920 TAGATCATGAAAAATGACATAAATTATATCAAAATGC-ATAAAATG-ACCTAAAAAT-CTCTAGA
1 TAGATCATGAAAAATGACATAAATGACATCAAAAT-CTATAAAATGCACCT--AAATCCTC-AAA
*
4619982 TCATAAAAAATGACCTAAATGACTTCAAAATTCACAAAATTACACTTAAGTCCC
62 TCATAAAAAATGACCTAAATGACGTCAAAATTCACAAAATTACACTTAAGTCCC
* * * * *
4620036 TAGATCATGGTAAAA-GACCTAAATGACATTAAAATCTATAAATTGCATCTAAATCCTCAAATCA
1 TAGATCAT-GAAAAATGACATAAATGACATCAAAATCTATAAAATGCACCTAAATCCTCAAATCA
* *
4620100 TGAAAAATGACCTTAATGACGTCAAAAT
65 TAAAAAATGACCTAAATGACGTCAAAAT
4620128 ACATGAAATG
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
115 35 0.45
116 34 0.44
117 8 0.10
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (115 bp):
TAGATCATGAAAAATGACATAAATGACATCAAAATCTATAAAATGCACCTAAATCCTCAAATCAT
AAAAAATGACCTAAATGACGTCAAAATTCACAAAATTACACTTAAGTCCC
Found at i:4620224 original size:58 final size:58
Alignment explanation
Indices: 4620162--4620313 Score: 148
Period size: 58 Copynumber: 2.6 Consensus size: 58
4620152 AGTTCATGAA
* * *
4620162 AAATGACC-T-AACATACATAAAATTTTCAATAAAAGTCCCTAGATCATAAAAATGCCCT
1 AAATGACCTTGAAAATACATAAAA-TTAC-ATAAAAGTCCATAGATCATAAAAATGCCCT
* * * ***
4620220 AAATGACCTTGAAAATGCATGAAATTACATAAAAGTCCATAGATTATAAAAATTATCT
1 AAATGACCTTGAAAATACATAAAATTACATAAAAGTCCATAGATCATAAAAATGCCCT
* ** *
4620278 AAATAACCTT-AGCATATATAAAATTACATAAAAGTC
1 AAATGACCTTGAAAATACATAAAATTACATAAAAGTC
4620314 GTTAAGTCAT
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
57 21 0.27
58 42 0.55
59 4 0.05
60 10 0.13
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.28
Consensus pattern (58 bp):
AAATGACCTTGAAAATACATAAAATTACATAAAAGTCCATAGATCATAAAAATGCCCT
Found at i:4622652 original size:20 final size:19
Alignment explanation
Indices: 4622627--4622677 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
4622617 GTTACAAGCA
4622627 ATGTATCGATACAATTCAT-C
1 ATGTATCGATAC-ATT-ATAC
4622647 ATGTATCGATACATTATACC
1 ATGTATCGATACATTATA-C
4622667 ATGTATCGATA
1 ATGTATCGATA
4622678 TAAATAGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 24 0.83
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACATTATAC
Found at i:4623763 original size:62 final size:62
Alignment explanation
Indices: 4623642--4623763 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
4623632 TAGAAATTCT
* * * **
4623642 TAGTTTAATTGGTATATAACTCTAATACTAATTAAGAGAGAATTAATCTAAAATTATAACTC
1 TAGTTTAATTGGTATATAACTCTAAAAATAATAAAGAGAGAATTAATCTAAAACCATAACTC
*
4623704 TAGTTTAATTGGTATATAACTGC-AAAAATAATAAAGTGAGAATTAATCTAAAACCATAAC
1 TAGTTTAATTGGTATATAACT-CTAAAAATAATAAAGAGAGAATTAATCTAAAACCATAAC
4623764 AATTTAACTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 52 0.98
63 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.34
Consensus pattern (62 bp):
TAGTTTAATTGGTATATAACTCTAAAAATAATAAAGAGAGAATTAATCTAAAACCATAACTC
Found at i:4624017 original size:35 final size:35
Alignment explanation
Indices: 4623947--4624014 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
4623937 TATCTCATAG
*
4623947 AAATAAAATTCATATTTATTAATATCTATAATTTA
1 AAATAAAATCCATATTTATTAATATCTATAATTTA
4623982 AAATAAAATCCATTTATTT-TTAAT-TCT-TAATTT
1 AAATAAAATCCA--TATTTATTAATATCTATAATTT
4624015 TAATCTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 6 0.20
35 14 0.47
36 5 0.17
37 5 0.17
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (35 bp):
AAATAAAATCCATATTTATTAATATCTATAATTTA
Found at i:4624624 original size:6 final size:6
Alignment explanation
Indices: 4624613--4624647 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
4624603 AAAAGCTCCA
4624613 AAACCC AAACCC -AACCC AAACCC AAACCC AAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
4624648 TTCCCAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:4624630 original size:11 final size:12
Alignment explanation
Indices: 4624613--4624647 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
4624603 AAAAGCTCCA
4624613 AAACCCAAACCC
1 AAACCCAAACCC
4624625 -AACCCAAACCC
1 AAACCCAAACCC
4624636 AAACCCAAACCC
1 AAACCCAAACCC
4624648 TTCCCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACCCAAACCC
Found at i:4627007 original size:2 final size:2
Alignment explanation
Indices: 4627000--4627026 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4626990 CTTTTATTTG
4627000 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4627027 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4629352 original size:32 final size:32
Alignment explanation
Indices: 4629316--4629430 Score: 97
Period size: 32 Copynumber: 3.6 Consensus size: 32
4629306 ATAGGAGTTC
*
4629316 TTTTGAACATGAGTTGTTCTAAACAAAAGCTG
1 TTTTGAACATGAGCTGTTCTAAACAAAAGCTG
* * * *
4629348 TTTTGAATA-GAAGCTGTTCTAATCAAGAGCTA
1 TTTTGAACATG-AGCTGTTCTAAACAAAAGCTG
* * * * *
4629380 TTATGAACATGGGCTATTCTAAATATAAGCTG
1 TTTTGAACATGAGCTGTTCTAAACAAAAGCTG
* * *
4629412 TTCTGAATATGAGTTGTTC
1 TTTTGAACATGAGCTGTTC
4629431 AAAAAATAGG
Statistics
Matches: 62, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
31 1 0.02
32 60 0.97
33 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (32 bp):
TTTTGAACATGAGCTGTTCTAAACAAAAGCTG
Found at i:4639600 original size:16 final size:17
Alignment explanation
Indices: 4639568--4639607 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
4639558 CCATAATTCA
*
4639568 AGGAAATCTAGAAAATC
1 AGGAAATCTACAAAATC
4639585 AGGAAATCT-CAAAATC
1 AGGAAATCTACAAAATC
*
4639601 AGTAAAT
1 AGGAAAT
4639608 TTGCAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (17 bp):
AGGAAATCTACAAAATC
Found at i:4639633 original size:18 final size:19
Alignment explanation
Indices: 4639612--4639655 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
4639602 GTAAATTTGC
*
4639612 AAATCTGC-AGAAATCAGA
1 AAATCTGCTACAAATCAGA
*
4639630 AAATCTGCTACAAATCAGG
1 AAATCTGCTACAAATCAGA
4639649 AAATCTG
1 AAATCTG
4639656 GAAATCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.20
Consensus pattern (19 bp):
AAATCTGCTACAAATCAGA
Found at i:4643704 original size:31 final size:31
Alignment explanation
Indices: 4643669--4643764 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
4643659 TTAAGGAAGG
4643669 TTAATCTCCTTAAATCAAGGAATCCCATAAT
1 TTAATCTCCTTAAATCAAGGAATCCCATAAT
* *
4643700 TTAATCTCCCTAAATCAAGGAAACCCATAAT
1 TTAATCTCCTTAAATCAAGGAATCCCATAAT
*
4643731 TCAATCTCCTTAAATCAAGGAATCCCATAAT
1 TTAATCTCCTTAAATCAAGGAATCCCATAAT
4643762 TTA
1 TTA
4643765 GAAATTTTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (31 bp):
TTAATCTCCTTAAATCAAGGAATCCCATAAT
Found at i:4645788 original size:84 final size:84
Alignment explanation
Indices: 4645647--4645819 Score: 310
Period size: 84 Copynumber: 2.1 Consensus size: 84
4645637 GTATCATAAA
* * *
4645647 TAGGTTGTGATTGTGGTTAAGTTGGAGACACTATGGATGTAGGAGAAGGTTTAGATATAGATGTT
1 TAGGTTGTGACTGTGGTTAAGTTGGAGACACTATGGATGTAGGAGAAGGTCTAGATATAGATATT
4645712 TGGGTAGGCAGATCAAGAT
66 TGGGTAGGCAGATCAAGAT
*
4645731 TAGGTTGTGACTGTGGTTGAGTTGGAGACACTATGGATGTAGGAGAAGGTCTAGATATAGATATT
1 TAGGTTGTGACTGTGGTTAAGTTGGAGACACTATGGATGTAGGAGAAGGTCTAGATATAGATATT
4645796 TGGGTAGGCAGATCAAGAT
66 TGGGTAGGCAGATCAAGAT
4645815 TAGGT
1 TAGGT
4645820 AAAGGCTGCT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.28, C:0.06, G:0.35, T:0.31
Consensus pattern (84 bp):
TAGGTTGTGACTGTGGTTAAGTTGGAGACACTATGGATGTAGGAGAAGGTCTAGATATAGATATT
TGGGTAGGCAGATCAAGAT
Found at i:4648075 original size:31 final size:31
Alignment explanation
Indices: 4648014--4648109 Score: 147
Period size: 31 Copynumber: 3.1 Consensus size: 31
4648004 TAAGGAAGGC
4648014 TAATCTCCTTAAATCAAGGAATTCCCATAATT
1 TAATCTCCTTAAATCAAGGAA-TCCCATAATT
* *
4648046 TAATCTCCCTAAATCAAGGAAACCCATAATT
1 TAATCTCCTTAAATCAAGGAATCCCATAATT
* *
4648077 CAATCTCCTTAAATCAAGGAATCTCATAATT
1 TAATCTCCTTAAATCAAGGAATCCCATAATT
4648108 TA
1 TA
4648110 GAAATTCTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
31 37 0.65
32 20 0.35
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (31 bp):
TAATCTCCTTAAATCAAGGAATCCCATAATT
Found at i:4649370 original size:27 final size:27
Alignment explanation
Indices: 4649340--4649432 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
4649330 GAACCAATGA
4649340 AGAATTCTGGCTGAAAAGATTATTTGG
1 AGAATTCTGGCTGAAAAGATTATTTGG
* * * ** ** *
4649367 AGAATTCAGGATTTCAACAAGAGAACCAATGA
1 AGAATTCTGG--CTGAA-AAGATTA--TTTGG
4649399 AGAATTCTGGCTGAAAAGATTATTTGG
1 AGAATTCTGGCTGAAAAGATTATTTGG
4649426 AGAATTC
1 AGAATTC
4649433 AGGATTTCAA
Statistics
Matches: 45, Mismatches: 16, Indels: 10
0.63 0.23 0.14
Matches are distributed among these distances:
27 18 0.40
29 8 0.18
30 8 0.18
32 11 0.24
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (27 bp):
AGAATTCTGGCTGAAAAGATTATTTGG
Found at i:4649421 original size:59 final size:59
Alignment explanation
Indices: 4649329--4649459 Score: 253
Period size: 59 Copynumber: 2.2 Consensus size: 59
4649319 AGGCACAGTA
4649329 AGAACCAATGAAGAATTCTGGCTGAAAAGATTATTTGGAGAATTCAGGATTTCAACAAG
1 AGAACCAATGAAGAATTCTGGCTGAAAAGATTATTTGGAGAATTCAGGATTTCAACAAG
*
4649388 AGAACCAATGAAGAATTCTGGCTGAAAAGATTATTTGGAGAATTCAGGATTTCAATAAG
1 AGAACCAATGAAGAATTCTGGCTGAAAAGATTATTTGGAGAATTCAGGATTTCAACAAG
4649447 AGAACCAATGAAG
1 AGAACCAATGAAG
4649460 CTGTTTTGTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 71 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.24
Consensus pattern (59 bp):
AGAACCAATGAAGAATTCTGGCTGAAAAGATTATTTGGAGAATTCAGGATTTCAACAAG
Found at i:4650035 original size:2 final size:2
Alignment explanation
Indices: 4650028--4650064 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4650018 TTAGAAATTC
4650028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4650065 TTTATAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4650868 original size:16 final size:16
Alignment explanation
Indices: 4650849--4650892 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
4650839 TTCAGGCAGG
4650849 TTTGGGTTTGGGTTCA
1 TTTGGGTTTGGGTTCA
* **
4650865 TTTGGGTTCGGGTTTG
1 TTTGGGTTTGGGTTCA
4650881 TTTGGGTTTGGG
1 TTTGGGTTTGGG
4650893 CTTATTCGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.02, C:0.05, G:0.43, T:0.50
Consensus pattern (16 bp):
TTTGGGTTTGGGTTCA
Found at i:4650903 original size:16 final size:16
Alignment explanation
Indices: 4650868--4650952 Score: 91
Period size: 16 Copynumber: 5.4 Consensus size: 16
4650858 GGGTTCATTT
* * *
4650868 GGGTTCGGGTTTGTTT
1 GGGTTCGGGCTTATTC
*
4650884 GGGTTTGGGCTTATTC
1 GGGTTCGGGCTTATTC
*
4650900 GGGTTCAGGCTTATTC
1 GGGTTCGGGCTTATTC
* *
4650916 GGGTTCGAGCTTATAC
1 GGGTTCGGGCTTATTC
*
4650932 GGG-TCGGGCTTTTTC
1 GGGTTCGGGCTTATTC
4650947 GGGTTC
1 GGGTTC
4650953 AAGTTTGAGT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.21
16 44 0.79
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.40
Consensus pattern (16 bp):
GGGTTCGGGCTTATTC
Found at i:4650920 original size:32 final size:32
Alignment explanation
Indices: 4650852--4650951 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 32
4650842 AGGCAGGTTT
* * * *
4650852 GGGTTTGGG-TTCATTTGGGTTCGGGTTTGTTT
1 GGGTTTGGGCTT-ATTCGGGTTCGGGCTTATTC
*
4650884 GGGTTTGGGCTTATTCGGGTTCAGGCTTATTC
1 GGGTTTGGGCTTATTCGGGTTCGGGCTTATTC
* * * *
4650916 GGGTTCGAGCTTATACGGG-TCGGGCTTTTTC
1 GGGTTTGGGCTTATTCGGGTTCGGGCTTATTC
4650947 GGGTT
1 GGGTT
4650952 CAAGTTTGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
31 15 0.26
32 40 0.70
33 2 0.04
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (32 bp):
GGGTTTGGGCTTATTCGGGTTCGGGCTTATTC
Found at i:4650948 original size:31 final size:32
Alignment explanation
Indices: 4650892--4650952 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
4650882 TTGGGTTTGG
*
4650892 GCTTATTCGGGTTCAGGCTTATTCGGGTTCGA
1 GCTTATACGGGTTCAGGCTTATTCGGGTTCGA
* *
4650924 GCTTATACGGG-TCGGGCTTTTTCGGGTTC
1 GCTTATACGGGTTCAGGCTTATTCGGGTTC
4650953 AAGTTTGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.10, C:0.20, G:0.33, T:0.38
Consensus pattern (32 bp):
GCTTATACGGGTTCAGGCTTATTCGGGTTCGA
Found at i:4652559 original size:16 final size:16
Alignment explanation
Indices: 4652530--4652583 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
4652520 TCAGTCTCGG
*
4652530 GTTCGGGTTCTTTCGA
1 GTTCGGGTTTTTTCGA
*
4652546 GTTTGGGTTTTTTCGA
1 GTTCGGGTTTTTTCGA
4652562 GTTCGGGTTTTTTCGA
1 GTTCGGGTTTTTTCGA
4652578 GTTCGG
1 GTTCGG
4652584 ACTTAACTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.06, C:0.13, G:0.33, T:0.48
Consensus pattern (16 bp):
GTTCGGGTTTTTTCGA
Found at i:4652833 original size:12 final size:12
Alignment explanation
Indices: 4652816--4652848 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4652806 GCTGAAAAAT
4652816 TGTGTACAGCTA
1 TGTGTACAGCTA
4652828 TGTGTACAGCTA
1 TGTGTACAGCTA
*
4652840 GGTGTACAG
1 TGTGTACAG
4652849 TTAGATGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (12 bp):
TGTGTACAGCTA
Found at i:4652851 original size:61 final size:61
Alignment explanation
Indices: 4652767--4652888 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
4652757 TGCTAGGTGC
* *
4652767 TGTGAACAGCTATGTGTATAGTTAGATGCTATTATAAAAGCTGAAAAATTGTGTACAGCTA
1 TGTGAACAGCTAGGTGTACAGTTAGATGCTATTATAAAAGCTGAAAAATTGTGTACAGCTA
* *
4652828 TGTGTACAGCTAGGTGTACAGTTAGATGCTATTCTAAAAGCTGAAAAATTGTGTACAGCTA
1 TGTGAACAGCTAGGTGTACAGTTAGATGCTATTATAAAAGCTGAAAAATTGTGTACAGCTA
4652889 GGTGCTATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.32
Consensus pattern (61 bp):
TGTGAACAGCTAGGTGTACAGTTAGATGCTATTATAAAAGCTGAAAAATTGTGTACAGCTA
Found at i:4659502 original size:24 final size:22
Alignment explanation
Indices: 4659463--4659508 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
4659453 AGATAAAATG
*
4659463 AATATAAAAATGAATATATAAT
1 AATATAAAAATGAATAAATAAT
*
4659485 AATATACATAAATTAATAAATAAT
1 AATATA-A-AAATGAATAAATAAT
4659509 TGAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AATATAAAAATGAATAAATAAT
Found at i:4659787 original size:21 final size:21
Alignment explanation
Indices: 4659761--4659838 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
4659751 AATAAATATC
4659761 TTATTATTAATTTTAATTTTA
1 TTATTATTAATTTTAATTTTA
* ***
4659782 TTATTATAAAAACTAATTTTATA
1 TTATTATTAATTTTAA-TTT-TA
* *
4659805 TTTATTATTATTTTTAATTTCA
1 -TTATTATTAATTTTAATTTTA
**
4659827 TTAAAATTAATT
1 TTATTATTAATT
4659839 CTAGCACCTA
Statistics
Matches: 41, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
21 21 0.51
22 4 0.10
23 5 0.12
24 11 0.27
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTATTAATTTTAATTTTA
Found at i:4664373 original size:23 final size:22
Alignment explanation
Indices: 4664329--4664373 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4664319 ATTTGATGTT
* *
4664329 TTATATATTTTTAAATATATAA
1 TTATATATTTTCAAATAAATAA
4664351 TTATATATTTTACAAATAAATAA
1 TTATATATTTT-CAAATAAATAA
4664374 AATTACTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATATATTTTCAAATAAATAA
Found at i:4664705 original size:15 final size:14
Alignment explanation
Indices: 4664673--4664710 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
4664663 ATAAATTTTA
4664673 TTAAT-AAATATAT
1 TTAATGAAATATAT
*
4664686 TTAATGAAAGTATTT
1 TTAATGAAA-TATAT
4664701 TTAATGAAAT
1 TTAATGAAAT
4664711 TAAATTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 4 0.18
15 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (14 bp):
TTAATGAAATATAT
Found at i:4664711 original size:71 final size:70
Alignment explanation
Indices: 4664604--4664750 Score: 163
Period size: 70 Copynumber: 2.1 Consensus size: 70
4664594 TTTATTATCA
* * * * *
4664604 AATAAATTTATTTAACAAAATTTTTTTAAATTAAATTAAAATT-TTTACTTACAAATTAGATAAA
1 AATAAATATATTTAACAAAATATTTTTAAATGAAATT-AAATTGTTTA-ATACAAATGAGATAAA
* *
4664668 TTTTATT
64 TCTTATG
* * *
4664675 AATAAATATATTTAATGAAAGTATTTTT-AATGAAATTAAATTGTTTAATATAAATGAGATAAAT
1 AATAAATATATTTAA-CAAAATATTTTTAAATGAAATTAAATTGTTTAATACAAATGAGATAAAT
4664739 CTTATG
65 CTTATG
4664745 AATAAA
1 AATAAA
4664751 AAATATATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
70 29 0.45
71 26 0.41
72 9 0.14
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (70 bp):
AATAAATATATTTAACAAAATATTTTTAAATGAAATTAAATTGTTTAATACAAATGAGATAAATC
TTATG
Found at i:4665664 original size:3 final size:3
Alignment explanation
Indices: 4665656--4665687 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4665646 TATCATTTCT
4665656 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4665688 GCACATGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4666404 original size:13 final size:13
Alignment explanation
Indices: 4666386--4666414 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4666376 AGCTAATCCA
4666386 AATATATATGATT
1 AATATATATGATT
4666399 AATATATATGATT
1 AATATATATGATT
4666412 AAT
1 AAT
4666415 TAAGGCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (13 bp):
AATATATATGATT
Found at i:4674030 original size:36 final size:35
Alignment explanation
Indices: 4673950--4674030 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
4673940 TCAAAATGAC
* *
4673950 AAAAAAAAAAGTCAAAAGCAAAAGCACAAAAAATG
1 AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
* *
4673985 AAAAGAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGG
1 AAAACAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GG
4674020 AACAACAAAAA
1 AA-AACAAAAA
4674031 TAAAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 6 0.15
35 15 0.38
36 18 0.46
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.05
Consensus pattern (35 bp):
AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
Found at i:4674289 original size:1 final size:1
Alignment explanation
Indices: 4674283--4674316 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
4674273 ACCTAATCCT
**
4674283 AAAAAAAAAAAAAAAACCAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4674317 CCTTTTCACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4674304 original size:18 final size:18
Alignment explanation
Indices: 4674283--4674318 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4674273 ACCTAATCCT
4674283 AAAAAAAAAAAAAAAACC
1 AAAAAAAAAAAAAAAACC
4674301 AAAAAAAAAAAAAAAACC
1 AAAAAAAAAAAAAAAACC
4674319 TTTTCACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAACC
Found at i:4675412 original size:27 final size:27
Alignment explanation
Indices: 4675369--4676545 Score: 1850
Period size: 27 Copynumber: 43.0 Consensus size: 27
4675359 GTGGCATTTT
* *
4675369 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
4675397 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4675424 CTTTTAAAGTCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
4675452 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4675479 CTTTTAAAATCCACAACTCCGTGGCACCC
1 CTTTT-AAGTCCACAACTCCGTGGCA-CC
*
4675508 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4675535 CTTTTAAAATCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
4675563 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4675590 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
4675618 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4675645 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
4675673 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4675700 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4675727 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4675754 CTTTTAAAGACCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
4675782 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4675809 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4675836 CTTTTAAAGTCCACAATTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
4675864 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4675891 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
4675919 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4675946 CTTTTAAGTCCATAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4675973 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4676000 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676027 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676054 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4676081 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
4676109 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4676136 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676163 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4676190 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676217 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4676244 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
4676272 CTGTTTAAGACCACAACTCCGTGGCACC
1 CT-TTTAAGTCCACAACTCCGTGGCACC
* * **
4676300 CTTTTAAGTCCATAACTTCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676327 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4676354 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676381 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676408 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
4676436 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
4676464 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
4676491 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
4676518 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
4676545 C
1 C
4676546 ATTTCAAAGC
Statistics
Matches: 1062, Mismatches: 74, Indels: 27
0.91 0.06 0.02
Matches are distributed among these distances:
27 732 0.69
28 302 0.28
29 28 0.03
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:4676583 original size:32 final size:32
Alignment explanation
Indices: 4676528--4677001 Score: 745
Period size: 32 Copynumber: 14.8 Consensus size: 32
4676518 CTTTTAAATC
* *
4676528 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
4676559 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
4676591 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
4676623 CACAAGTCGGTGACAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
4676655 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
4676687 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
4676719 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
4676751 CACAAGTCGGTGGCAACCCATTTCAAAGCCTA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
4676783 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
4676815 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
4676847 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
4676879 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
4676911 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
4676943 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
4676975 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
4677002 TCACCATTTT
Statistics
Matches: 415, Mismatches: 25, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
31 15 0.04
32 397 0.96
33 3 0.01
ACGTcount: A:0.31, C:0.34, G:0.19, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:4678308 original size:23 final size:24
Alignment explanation
Indices: 4678264--4678309 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
4678254 AAATTTAGGT
*
4678264 AAAAAAGAAAGAAAGAAGATGAAG
1 AAAAAAGAAAGAAAAAAGATGAAG
*
4678288 AAAAAAGAAA-AAAAAATATGAA
1 AAAAAAGAAAGAAAAAAGATGAA
4678310 ATGGAGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (24 bp):
AAAAAAGAAAGAAAAAAGATGAAG
Found at i:4681103 original size:34 final size:34
Alignment explanation
Indices: 4681048--4681264 Score: 276
Period size: 34 Copynumber: 6.4 Consensus size: 34
4681038 AGGTTTTCCA
*
4681048 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * * *
4681081 TATTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
4681115 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* **
4681149 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
4681183 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
4681217 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
4681251 TGTTGATTAAATGG
1 TGTTGATTAAATGG
4681265 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
33 14 0.09
34 143 0.91
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:4681240 original size:102 final size:101
Alignment explanation
Indices: 4681048--4681264 Score: 353
Period size: 102 Copynumber: 2.1 Consensus size: 101
4681038 AGGTTTTCCA
** * * *
4681048 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
4681113 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
4681149 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
* * *
4681214 CATTGTTGACTAAATGGTAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
4681251 TGTTGATTAAATGG
1 TGTTGATTAAATGG
4681265 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 14 0.13
102 93 0.87
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:4685732 original size:34 final size:34
Alignment explanation
Indices: 4685675--4685893 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 34
4685665 AAGTGGGAGA
*
4685675 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
4685708 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
4685742 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
4685776 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
4685810 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
4685844 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
4685878 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
4685894 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 143 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:4685815 original size:102 final size:101
Alignment explanation
Indices: 4685675--4685893 Score: 357
Period size: 102 Copynumber: 2.2 Consensus size: 101
4685665 AAGTGGGAGA
** * * *
4685675 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
4685740 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
4685776 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
4685841 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
4685878 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
4685894 TGGTTTTTAC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:4686282 original size:3 final size:3
Alignment explanation
Indices: 4686274--4686299 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4686264 GACGGCGTGG
4686274 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4686300 TACCAAATGT
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:4689163 original size:23 final size:23
Alignment explanation
Indices: 4689133--4689177 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
4689123 GTACAATTGC
4689133 TAAAAGTTAAA-AAAAGAAAAAA
1 TAAAAGTTAAAGAAAAGAAAAAA
4689155 TAAACAGTTAAATGAAAAGAAAA
1 TAAA-AGTTAAA-GAAAAGAAAA
4689178 TAAGATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
25 9 0.45
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (23 bp):
TAAAAGTTAAAGAAAAGAAAAAA
Found at i:4691688 original size:3 final size:3
Alignment explanation
Indices: 4691680--4691711 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4691670 ACAAAGGTAA
4691680 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4691712 GAAGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4691716 original size:3 final size:3
Alignment explanation
Indices: 4691710--4691747 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4691700 TAATAATAAT
4691710 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
4691748 AAGTTTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4694598 original size:16 final size:16
Alignment explanation
Indices: 4694539--4694603 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
4694529 CTAATTAACT
*
4694539 TAAACTCAAAATGATT
1 TAAACTCAAAATGATC
* * * *
4694555 TAAATTTAGAATGATT
1 TAAACTCAAAATGATC
* *
4694571 TGAA-TACGAAATGATC
1 TAAACT-CAAAATGATC
4694587 TAAACTCAAAATGATC
1 TAAACTCAAAATGATC
4694603 T
1 T
4694604 GAATAAAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (16 bp):
TAAACTCAAAATGATC
Found at i:4694630 original size:32 final size:32
Alignment explanation
Indices: 4694546--4694630 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
4694536 ACTTAAACTC
* * * *
4694546 AAAATGATTTAAATTTAGAATGATTTGAATAC
1 AAAATGATTCAAATTTAAAATGATCTGAATAA
* * *
4694578 GAAATGA-TCTAAACTCAAAATGATCTGAATAA
1 AAAATGATTC-AAATTTAAAATGATCTGAATAA
4694610 AAAATGATTCAAATTTAAAAT
1 AAAATGATTCAAATTTAAAAT
4694631 CGCTCTAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
31 1 0.02
32 38 0.93
33 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.32
Consensus pattern (32 bp):
AAAATGATTCAAATTTAAAATGATCTGAATAA
Found at i:4698818 original size:21 final size:21
Alignment explanation
Indices: 4698792--4698839 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
4698782 AGCTGCATTG
*
4698792 TTTCATCGAACAAGTACATCT
1 TTTCATCCAACAAGTACATCT
* *
4698813 TTTCATCCAATAAGTGCATCT
1 TTTCATCCAACAAGTACATCT
4698834 TTTCAT
1 TTTCAT
4698840 TTAACGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (21 bp):
TTTCATCCAACAAGTACATCT
Found at i:4703889 original size:35 final size:35
Alignment explanation
Indices: 4703839--4703909 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
4703829 CCATCATATC
*
4703839 TTTTATTATGTATGGATATTCTTAGTCACTTTATT
1 TTTTATTATGCATGGATATTCTTAGTCACTTTATT
4703874 TTTTATTATGCATGGATATTCTTAGTCACTTTATT
1 TTTTATTATGCATGGATATTCTTAGTCACTTTATT
4703909 T
1 T
4703910 AAGTATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.56
Consensus pattern (35 bp):
TTTTATTATGCATGGATATTCTTAGTCACTTTATT
Found at i:4706017 original size:13 final size:13
Alignment explanation
Indices: 4705974--4706021 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
4705964 ACGAAAGGTA
4705974 TAAAAG-AATTCT
1 TAAAAGAAATTCT
* *
4705986 TAAAATAAAATTAT
1 TAAAA-GAAATTCT
*
4706000 CAAAAGAAATTCT
1 TAAAAGAAATTCT
4706013 TAAAAGAAA
1 TAAAAGAAA
4706022 ATAAAATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 5 0.18
13 14 0.50
14 9 0.32
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (13 bp):
TAAAAGAAATTCT
Found at i:4709063 original size:26 final size:27
Alignment explanation
Indices: 4709033--4709084 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
4709023 TTTTTAAAAT
4709033 AAAAT-CAAGGTTGGAGTATCCCCGCG
1 AAAATACAAGGTTGGAGTATCCCCGCG
*
4709059 AAAATAACGAGGTTGGAGTATCCCCG
1 AAAAT-ACAAGGTTGGAGTATCCCCG
4709085 ATTGTGAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (27 bp):
AAAATACAAGGTTGGAGTATCCCCGCG
Found at i:4709126 original size:51 final size:51
Alignment explanation
Indices: 4709070--4709185 Score: 169
Period size: 51 Copynumber: 2.3 Consensus size: 51
4709060 AAATAACGAG
* * *
4709070 GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGGAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTTAGAAATAAAATCGGA
* * * *
4709121 GTTGGAATATCCCCGATTGTGGGAAATTGGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTTAGAAATAAAATCGGA
4709172 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
4709186 TTGGAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.29, C:0.11, G:0.28, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTATTTTAGAAATAAAATCGGA
Found at i:4709133 original size:79 final size:79
Alignment explanation
Indices: 4708913--4709135 Score: 215
Period size: 78 Copynumber: 2.8 Consensus size: 79
4708903 ACAACTGGGC
**
4708913 TAGAGTATCCCCGATTATG-GAAAATCGGTGTTTCTAGAAATAAAAATTGG-GATTGGAGTATCC
1 TAGAGTATCCCCGATTATGAG-AAATTAGTGTTT-TAGAAAT-AAAATTGGAG-TTGGAGTATCC
* *
4708976 CCTCGAAAATAATAGGGT
62 CCGCGAAAATAAGAGGGT
** * * **
4708994 TAGAGTATCCCTAATTAT-AGAAAATAGTATTTTTA-AAATAAAA-TCAAGGTTGGAGTATCCCC
1 TAGAGTATCCCCGATTATGAGAAATTAGT-GTTTTAGAAATAAAATTGGA-GTTGGAGTATCCCC
4709056 GCGAAAATAACGA-GGT
64 GCGAAAATAA-GAGGGT
* * * *
4709072 TGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGGAAATAAAATTGGAGTTGGAATATCCCCG
1 TAGAGTATCCCCGATTATGAGAAATTAGTGTTTTAGAAATAAAATTGGAGTTGGAGTATCCCCG
4709136 ATTGTGGGAA
Statistics
Matches: 114, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
77 1 0.01
78 47 0.41
79 37 0.32
80 9 0.08
81 20 0.18
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (79 bp):
TAGAGTATCCCCGATTATGAGAAATTAGTGTTTTAGAAATAAAATTGGAGTTGGAGTATCCCCGC
GAAAATAAGAGGGT
Found at i:4709199 original size:28 final size:28
Alignment explanation
Indices: 4709168--4709243 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
4709158 GAAATAAAAT
*
4709168 CGGGGTTGGAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
*
4709196 CGGGATTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
4709224 CGGGGTTGGAGTA-CCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
4709244 TATGAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.16
28 36 0.82
29 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:4709347 original size:28 final size:27
Alignment explanation
Indices: 4709281--4709348 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 27
4709271 TAAAGCCGAT
*
4709281 GTTGGAGTATTCCCTCGGAAATAACGGG
1 GTTGGAGTA-TCCCTCGGAAATAACAGG
4709309 GTTGGAGTATCCC-CGATGAAATAACAGG
1 GTTGGAGTATCCCTCG--GAAATAACAGG
4709337 GTTGGAGTATCC
1 GTTGGAGTATCC
4709349 TCAATTGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.05
27 4 0.11
28 31 0.84
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCTCGGAAATAACAGG
Found at i:4709407 original size:51 final size:51
Alignment explanation
Indices: 4709341--4709480 Score: 149
Period size: 51 Copynumber: 2.7 Consensus size: 51
4709331 AACAGGGTTG
* *
4709341 GAGTATCCTCAATTGTGAAAAATT-AGTGTTTTGAAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTGAAAAATTGA-TGTTTTGAAAATAAAATCGGAGTTA
* ** * * *
4709392 GAGTATCTCCGATTGTGGTAAATCGATGCTTT-AGAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAAAAATTGATGTTTTGA-AAATAAAATCGGAGTTA
** *
4709443 GAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAAT
1 GAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAAT
4709481 GGAACCGGGA
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
50 1 0.01
51 68 0.97
52 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAATCGGAGTTA
Found at i:4711826 original size:20 final size:19
Alignment explanation
Indices: 4711801--4711874 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 19
4711791 AAAATGCTTG
*
4711801 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
4711821 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
4711841 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
4711861 AATGTATCGATACA
1 AATGTATCGATACA
4711875 TCTGAGTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:4711918 original size:20 final size:20
Alignment explanation
Indices: 4711893--4711943 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
4711883 AACTTCCTAG
4711893 ATGTATCGATACAAAG-ATCA
1 ATGTATCGATACAAAGAAT-A
**
4711913 ATGTATCGATACATTGAATA
1 ATGTATCGATACAAAGAATA
4711933 ATGTATCGATA
1 ATGTATCGATA
4711944 TATTTCCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAAGAATA
Found at i:4712574 original size:15 final size:15
Alignment explanation
Indices: 4712554--4712596 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4712544 TTAAAAAAAT
4712554 TGATGAAAAATAAAG
1 TGATGAAAAATAAAG
* *
4712569 TGATGAGAAATACAG
1 TGATGAAAAATAAAG
4712584 TGAT-ATAAAATAA
1 TGATGA-AAAATAA
4712597 TTATAGATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (15 bp):
TGATGAAAAATAAAG
Found at i:4712651 original size:4 final size:4
Alignment explanation
Indices: 4712642--4712671 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4712632 ATCAACACAA
4712642 AAAT AAAT AAAT AAAT AAAT -AAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
4712672 ACAATTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:4713467 original size:29 final size:28
Alignment explanation
Indices: 4713435--4713493 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
4713425 AATTTTTGTA
4713435 TTATAGTA-AAATAATATATATTTTAATTT
1 TTATAGTATAAAT-ATA-ATATTTTAATTT
* *
4713464 TTATATTATTAAATTTAATATTTTAATTT
1 TTATAGTA-TAAATATAATATTTTAATTT
4713493 T
1 T
4713494 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 20 0.77
30 2 0.08
31 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TTATAGTATAAATATAATATTTTAATTT
Found at i:4713470 original size:14 final size:14
Alignment explanation
Indices: 4713452--4713503 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
4713442 AAAATAATAT
*
4713452 ATATTTTAATTTTT
1 ATATTTTAATTTTA
*
4713466 ATATTATTAAATTTA
1 ATATT-TTAATTTTA
4713481 ATATTTTAATTTTA
1 ATATTTTAATTTTA
*
4713495 AAATTTTAA
1 ATATTTTAA
4713504 AATATTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATATTTTAATTTTA
Found at i:4713500 original size:21 final size:21
Alignment explanation
Indices: 4713456--4713496 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4713446 TAATATATAT
4713456 TTTAATTTTTATATTATTAAA
1 TTTAATTTTTATATTATTAAA
4713477 TTTAATATTTTA-ATT-TTAAA
1 TTTAAT-TTTTATATTATTAAA
4713497 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAATTTTTATATTATTAAA
Found at i:4713502 original size:22 final size:22
Alignment explanation
Indices: 4713454--4713512 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
4713444 AATAATATAT
4713454 ATTTTAAT-TTTTATATTATTAA
1 ATTTTAATATTTTA-ATTATTAA
4713476 A-TTTAATATTTTAATT-TTAAA
1 ATTTTAATATTTTAATTATT-AA
* *
4713497 ATTTTAAAATATTAAT
1 ATTTTAATATTTTAAT
4713513 AAATAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 12 0.38
22 18 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTAATATTTTAATTATTAA
Found at i:4713506 original size:29 final size:30
Alignment explanation
Indices: 4713443--4713513 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
4713433 TATTATAGTA
* * *
4713443 AAATAATATATATTTTAATTTTTATATTATT
1 AAATATTA-ATATTTTAATTTTAAAATTATT
4713474 AAAT-TTAATATTTTAATTTTAAAATT-TT
1 AAATATTAATATTTTAATTTTAAAATTATT
4713502 AAAATATTAATA
1 -AAATATTAATA
4713514 AATAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 21 0.60
30 8 0.23
31 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
AAATATTAATATTTTAATTTTAAAATTATT
Found at i:4713529 original size:17 final size:18
Alignment explanation
Indices: 4713502--4713544 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
4713492 TTAAAATTTT
4713502 AAAAT-ATTAATAA-ATA
1 AAAATAATTAATAATATA
*
4713518 AAAATAATTAATAATATT
1 AAAATAATTAATAATATA
4713536 AAAA-AATTA
1 AAAATAATTA
4713545 TTTAACTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 5 0.21
17 13 0.54
18 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAATTAATAATATA
Found at i:4713672 original size:22 final size:23
Alignment explanation
Indices: 4713624--4713670 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
4713614 ACAGGTTGGG
*
4713624 TTTAAATTATTTTTTATATAAAA
1 TTTAAAATATTTTTTATATAAAA
4713647 TTTAAAAT-TTTTTTAT-TAAAA
1 TTTAAAATATTTTTTATATAAAA
4713668 TTT
1 TTT
4713671 TATCGATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 8 0.35
23 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAAAATATTTTTTATATAAAA
Found at i:4713748 original size:15 final size:14
Alignment explanation
Indices: 4713730--4713780 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
4713720 TATTATAATT
4713730 TTAAAATTATAAAAA
1 TTAAAA-TATAAAAA
*
4713745 TTAAAATAT-TAAA
1 TTAAAATATAAAAA
4713758 TATAATAATATAAAAA
1 T-TAA-AATATAAAAA
*
4713774 TCAAAAT
1 TTAAAAT
4713781 GATACTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
13 4 0.13
14 9 0.30
15 13 0.43
16 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAATATAAAAA
Done.