Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
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: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 61 of 65
Found at i:12032783 original size:3 final size:3
Alignment explanation
Indices: 12032772--12032835 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
12032762 TTTTTTTTCG
** *
12032772 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12032817 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
12032836 CAAATTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12032813 original size:32 final size:32
Alignment explanation
Indices: 12032769--12032833 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
12032759 GGTTTTTTTT
*
12032769 TCGTTATTTTATTATTATTATTATTA-TTATTA
1 TCGTTATCTTATTATT-TTATTATTATTTATTA
12032801 TCGTTATCTTATTATTTTATTATTATTTATTA
1 TCGTTATCTTATTATTTTATTATTATTTATTA
12032833 T
1 T
12032834 TACAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
TCGTTATCTTATTATTTTATTATTATTTATTA
Found at i:12035951 original size:29 final size:30
Alignment explanation
Indices: 12035909--12035977 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 30
12035899 TTATTGAAAT
12035909 TTTTAATTGCTTTG-TTTTTTCGTACTAACA
1 TTTT-ATTGCTTTGTTTTTTTCGTACTAACA
12035939 TTTTATTGCTTTGTTTTTTTTTCGTACTAACA
1 TTTTATTGCTTTG--TTTTTTTCGTACTAACA
12035971 TTTTATT
1 TTTTATT
12035978 TTTGGCTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 9 0.25
30 4 0.11
32 23 0.64
ACGTcount: A:0.17, C:0.12, G:0.09, T:0.62
Consensus pattern (30 bp):
TTTTATTGCTTTGTTTTTTTCGTACTAACA
Found at i:12038191 original size:26 final size:25
Alignment explanation
Indices: 12038160--12038239 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
12038150 CCAATTTTTG
12038160 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
12038185 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
12038206 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
12038232 ACATTCTT
1 ACATTCTT
12038240 TCCACTTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.14
26 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:12038905 original size:11 final size:11
Alignment explanation
Indices: 12038877--12038914 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
12038867 AAGAGCAAAG
12038877 AGAAAAATCAA
1 AGAAAAATCAA
12038888 AGCAAAAATCAA
1 AG-AAAAATCAA
*
12038900 AGAAAAAGCAA
1 AGAAAAATCAA
12038911 AGAA
1 AGAA
12038915 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:12040101 original size:4 final size:4
Alignment explanation
Indices: 12040092--12040133 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
12040082 AAAAGTATAC
12040092 ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
12040134 GATACATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:12040737 original size:36 final size:36
Alignment explanation
Indices: 12040685--12040802 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
12040675 TGAGAATTTT
* *
12040685 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGATTGAGACAATTTCTTTA
* *
12040722 AAAGCAAATTTTGTCTCGATTGAGACAGCTTTC--TA
1 AAAACAAATTTTGTCTCGATTGAGACA-ATTTCTTTA
* *
12040757 AAAACAAATTTTGTCTCGTTTGAGACAATTTCTTGA
1 AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
12040793 AAAACAAATT
1 AAAACAAATT
12040803 CCGCCTCACT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
34 4 0.06
35 26 0.37
36 29 0.41
37 11 0.16
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGATTGAGACAATTTCTTTA
Found at i:12040818 original size:71 final size:72
Alignment explanation
Indices: 12040685--12040819 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 72
12040675 TGAGAATTTT
** * ** * *
12040685 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTCAAAGCAAATTTTGTCTCGATTGAGACAG
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
12040750 CTTTCTA
66 CTTTCTA
*
12040757 AAAACAAA-TTTTGTCTCGTTTGAGACAATTTCTTGAAAAACAAATTCCGCCTC-ACTGGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGA-TGGAGACA
12040820 TTTTTCATTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.02
71 45 0.83
72 8 0.15
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTGAAAAACAAATTCCGCCTCGATGGAGACAG
CTTTCTA
Found at i:12041262 original size:29 final size:28
Alignment explanation
Indices: 12041192--12041412 Score: 272
Period size: 28 Copynumber: 7.9 Consensus size: 28
12041182 TCTTGAGACA
12041192 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
*
12041220 GTTTCTCTTGAAAAAAATCTTTGAGTTA
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
12041248 GTTTCTCTTGAAAAAAAAATCTTTGAGTTT
1 GTTTCTCTTG--AAAAAAATCTTTGAGTTT
*
12041278 GTTTCTC-TGGAAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
*
12041305 GTTCCTCTTG-AAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
* * * *
12041332 GCTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTCTTGAA-AAAAATCTTTGAGTTT
* * *
12041361 GTTCCTTTTGAATAAATATCTTTGAG-TT
1 GTTTCTCTTGAA-AAAAATCTTTGAGTTT
*
12041389 GTTTCTTTTG--AAAAATCTTTGAGT
1 GTTTCTCTTGAAAAAAATCTTTGAGT
12041413 CTATTTATTT
Statistics
Matches: 175, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
25 12 0.07
27 48 0.27
28 51 0.29
29 40 0.23
30 24 0.14
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (28 bp):
GTTTCTCTTGAAAAAAATCTTTGAGTTT
Found at i:12041434 original size:25 final size:25
Alignment explanation
Indices: 12041378--12041428 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
12041368 TTGAATAAAT
* *
12041378 ATCTTTGAGTTGTTTCTTTTGAAAA
1 ATCTTTGAGTTATTTATTTTGAAAA
12041403 ATCTTTGAGTCTATTTATTTTGAAAA
1 ATCTTTGAGT-TATTTATTTTGAAAA
12041429 GTTTTGTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (25 bp):
ATCTTTGAGTTATTTATTTTGAAAA
Found at i:12041542 original size:28 final size:28
Alignment explanation
Indices: 12041511--12041579 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
12041501 ATTTTGTGAA
*
12041511 AAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
12041539 AAAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
12041567 AAACAAAAT-TTTG
1 AAA-AAAATCTTTG
12041580 TCTCTCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (28 bp):
AAAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:12041616 original size:67 final size:65
Alignment explanation
Indices: 12041524--12041694 Score: 270
Period size: 67 Copynumber: 2.6 Consensus size: 65
12041514 AAAATCTTTG
* *
12041524 AGATTGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTATCTTA
*
12041589 AGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTATCT
1 AGATAGTTTCTTTT-GAA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTATCT
12041654 TA
64 TA
* * *
12041656 AGATAATTTCTTTTGAAAAAAATCTTTGAATCTGTTTCT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCT
12041695 CTTAAAATGA
Statistics
Matches: 97, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
65 33 0.34
66 4 0.04
67 60 0.62
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (65 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTATCTTA
Found at i:12041628 original size:95 final size:93
Alignment explanation
Indices: 12041473--12041646 Score: 242
Period size: 95 Copynumber: 1.8 Consensus size: 93
12041463 CTTTGAGTCT
* * *
12041473 GAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTG
12041538 GAAA-AAAATCTTTGAGTTTGTTTCTTTG
66 GAAACAAAAT-TTTGAGTTTGTTTCTTTG
* * * * *
12041566 GAAACAAAATTTTGTCTCTCTTAAGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTT-TGTGAAAA-AAAAATCTTTGAGATTGTTTCTT
12041631 TGGAAACAAAATTTTG
64 TGGAAACAAAATTTTG
12041647 TCTATCTTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 28 0.40
94 6 0.09
95 31 0.44
96 5 0.07
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (93 bp):
GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTTG
GAAACAAAATTTTGAGTTTGTTTCTTTG
Found at i:12041736 original size:64 final size:64
Alignment explanation
Indices: 12041524--12041755 Score: 261
Period size: 67 Copynumber: 3.6 Consensus size: 64
12041514 AAAATCTTTG
* *
12041524 AGATTGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAATTTGTTTCTTT-GAAACAAAATTTTGTCTCTCTTA
* * *
12041589 AGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTATCT
1 AGATAGTTTCTTTT-GAA-AAAAATCTTTGAATTTGTTTCTTT-GAAACAAAATTTTGTCTCTCT
12041654 TA
63 TA
* * * *
12041656 AGATAATTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTATCTCTT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAATTTGTTTCT-TTGAAACA-AAATTTTGTCTCTCTT
*
12041719 G
64 A
* * ** *
12041720 AGACAGTTTCTCTTGAAGTAAATCTTTGAATATGTT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAATTTGTT
12041756 CATTTTGAAA
Statistics
Matches: 146, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
63 1 0.01
64 46 0.32
65 33 0.23
66 6 0.04
67 60 0.41
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.46
Consensus pattern (64 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAATTTGTTTCTTTGAAACAAAATTTTGTCTCTCTTA
Found at i:12042019 original size:120 final size:120
Alignment explanation
Indices: 12041795--12042009 Score: 276
Period size: 120 Copynumber: 1.8 Consensus size: 120
12041785 TTAACAAAAT
* * *
12041795 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATGAAAAAC
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAAC
*
12041860 TAACTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
66 AAACTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
* ** **
12041915 CATCTTTGAGTCTGTTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTTTTGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATGAAAA
* *
12041978 A-AAA-TCTTTGAGTTTGTTTCCTTTGAAACAAA
64 ACAAACT-TTTGAGATTGTTTCATTTGAAACAAA
12042010 ATATTGTCTC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 1 0.01
119 33 0.41
120 43 0.53
121 4 0.05
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (120 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATGAAAAAC
AAACTTTTGAGATTGTTTCATTTGAAACAAATTTGGTCTCACTTAAGATGTGATC
Found at i:12042709 original size:27 final size:28
Alignment explanation
Indices: 12042679--12042759 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
12042669 GAAACACATT
12042679 ATCTTTGAG-CTTGTTT-TCTTGAAACAA
1 ATCTTTGAGTC-TGTTTCTCTTGAAACAA
*
12042706 ATCTTTGAGTCTGTTTCTTTTGAAACAA
1 ATCTTTGAGTCTGTTTCTCTTGAAACAA
* *
12042734 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAGTCT-GTTTCTCTTGAAAC
12042760 CATAACTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 17 0.36
28 30 0.64
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (28 bp):
ATCTTTGAGTCTGTTTCTCTTGAAACAA
Found at i:12042737 original size:28 final size:28
Alignment explanation
Indices: 12042664--12042739 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
12042654 GAGACAGTTG
12042664 CTTTTGAAACACATTATCTTTGAGCTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGCTTGTTT
*
12042695 -TCTTGAAACAAATCTTTGAG-TCTGTTT
1 CTTTTGAAACAAATCTTTGAGCT-TGTTT
12042722 CTTTTGAAACAAATCTTT
1 CTTTTGAAACAAATCTTT
12042740 AATTTGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.02
27 14 0.34
28 16 0.39
29 1 0.02
30 9 0.22
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGCTTGTTT
Found at i:12042846 original size:40 final size:40
Alignment explanation
Indices: 12042788--12043101 Score: 195
Period size: 40 Copynumber: 7.4 Consensus size: 40
12042778 CCATCCGTCT
*
12042788 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* * * * *
12042828 TCATCACGTAGGAGCCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCC
* * * *
12042874 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATTTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* * *
12042914 TCATCACGTAGGAACCGGGTCA-CCCTTAGATAACCAG-CCATCC
1 TCATCACGTAGGAACCGTGTCATCCC-CAG---ACCAGATC-TCC
* * * *
12042957 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACCTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCC
* * * *
12043003 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATTTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* *
12043043 TCATCACGTAGGAACCGGGTCA-CCCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCCC-AG---ACCAGATC-TCC
12043086 TCATCACGTAGGAACC
1 TCATCACGTAGGAACC
12043102 TAGTTATCAC
Statistics
Matches: 214, Mismatches: 37, Indels: 43
0.73 0.13 0.15
Matches are distributed among these distances:
39 7 0.03
40 75 0.35
41 2 0.01
43 60 0.28
44 1 0.00
45 6 0.03
46 61 0.29
47 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (40 bp):
TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
Found at i:12042889 original size:46 final size:46
Alignment explanation
Indices: 12042818--12043022 Score: 187
Period size: 46 Copynumber: 4.7 Consensus size: 46
12042808 CATCCCCAGA
*
12042818 CCAGATCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
* * * * *
12042864 CCAGAACTCTTCATCACGTATGAGCCGTGTCATC-CC-CT-GA---
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
** * * * **
12042904 CCAGATTTCCTCATCACGTAGGAACCG-G--GTCACCCTTAGATAA
1 CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
*
12042947 CCAG-CCATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGG
1 CCAGACC-TCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
* *
12042993 CCAGACCTCTTCATCACGTATGAGCCGTGT
1 CCAGACCTCCTCATCACGTAGGAGCCGTGT
12043023 CATCCCCTGA
Statistics
Matches: 127, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
37 2 0.02
38 2 0.02
39 2 0.02
40 24 0.19
43 26 0.20
44 2 0.02
45 2 0.02
46 65 0.51
47 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (46 bp):
CCAGACCTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGG
Found at i:12042958 original size:43 final size:42
Alignment explanation
Indices: 12042911--12043101 Score: 174
Period size: 43 Copynumber: 4.5 Consensus size: 42
12042901 TGACCAGATT
*
12042911 TCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCC
1 TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCC
* ** **
12042953 ATCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACC
1 -TCCTCATCACGTAGGAACCG-G--GTCACCCCTAGATAACCAG-CC
* * * * **
12043000 TCTTCATCACGTATGAGCCGTGTCATCCCCT-G---ACCAGATT
1 TCCTCATCACGTAGGAACCGGGTCA-CCCCTAGATAACCAG-CC
12043040 TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCC
1 TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCC
12043082 GTCCTCATCACGTAGGAACC
1 -TCCTCATCACGTAGGAACC
12043102 TAGTTATCAC
Statistics
Matches: 118, Mismatches: 20, Indels: 20
0.75 0.13 0.13
Matches are distributed among these distances:
39 5 0.04
40 27 0.23
43 48 0.41
44 4 0.03
46 32 0.27
47 2 0.02
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.23
Consensus pattern (42 bp):
TCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCC
Found at i:12043047 original size:129 final size:129
Alignment explanation
Indices: 12042825--12043213 Score: 584
Period size: 129 Copynumber: 3.0 Consensus size: 129
12042815 AGACCAGATC
*
12042825 TCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
12042890 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCCA
66 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCCA
*
12042954 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGACCTCTTCATCACGTATGAGCC
1 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
* *
12043019 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCCTAGATAACCAGCCG
66 GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCCA
* *
12043083 TCCTCATCACGTAGGAACC-TAGTTATCACCCTTCCTAAAGATGACCAGAACTCTTCGTCACGTA
1 TCCTCATCACGTAGGAACCGT-GTTATCA-CCTT--T--AGATGGCCAGAACTCTTCATCACGTA
* ** * * * *
12043147 TGAGACGTGTCAT-CCCTCGACCAGATTTTTTCATCACGTAGGAGCCGTGTCGCCCTTAGATGAC
60 TGAGCCGTGTCATCCCCT-GACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAAC
12043211 CAG
124 CAG
12043214 ACCTCTTCAT
Statistics
Matches: 238, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
128 1 0.00
129 151 0.63
130 4 0.02
132 1 0.00
133 4 0.02
134 77 0.32
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (129 bp):
TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCC
GTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGCCA
Found at i:12043409 original size:3 final size:3
Alignment explanation
Indices: 12043398--12043464 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
12043388 TTTTTTTTCG
** *
12043398 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12043444 TT- TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
12043465 CAAATTTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 5 0.09
3 46 0.85
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12043442 original size:35 final size:35
Alignment explanation
Indices: 12043395--12043464 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
12043385 GGTTTTTTTT
*
12043395 TCGTTATTTTATTATTATTATTATTA-TTATTATTA
1 TCGTTATCTTATTATT-TTATTATTATTTATTATTA
12043430 TCGTTATCTTATTATTTTATTATTATTTATTATTA
1 TCGTTATCTTATTATTTTATTATTATTTATTATTA
12043465 CAAATTTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 9 0.27
35 24 0.73
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.66
Consensus pattern (35 bp):
TCGTTATCTTATTATTTTATTATTATTTATTATTA
Found at i:12049124 original size:16 final size:16
Alignment explanation
Indices: 12049103--12049134 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12049093 CTCATTTGAC
12049103 CATTAATCTTGTAACA
1 CATTAATCTTGTAACA
12049119 CATTAATCTTGTAACA
1 CATTAATCTTGTAACA
12049135 GTTTGATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
CATTAATCTTGTAACA
Found at i:12059484 original size:13 final size:14
Alignment explanation
Indices: 12059451--12059492 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
12059441 TAATTTAAAT
12059451 TTTTATTATCTTTAA
1 TTTTA-TATCTTTAA
*
12059466 TATTATATC-TTAA
1 TTTTATATCTTTAA
12059479 TTTTATA-CTTTAA
1 TTTTATATCTTTAA
12059492 T
1 T
12059493 ATGCAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 1 0.04
13 15 0.62
14 4 0.17
15 4 0.17
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTATATCTTTAA
Found at i:12071502 original size:111 final size:111
Alignment explanation
Indices: 12071170--12071494 Score: 587
Period size: 111 Copynumber: 2.9 Consensus size: 111
12071160 ATTACAAAAA
*
12071170 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
12071235 AATTAAAACGTTAAAATGTTACAGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
12071281 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
12071346 AATTAAAATGTTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
12071392 TTAATTCTTAATCTAATAATCATCCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
12071457 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGT
12071495 ATAGATATAT
Statistics
Matches: 205, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 205 1.00
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:12071674 original size:10 final size:10
Alignment explanation
Indices: 12071628--12071677 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
12071618 ATTAAAAAAT
* *
12071628 AGAGTATTTA
1 AGAGAATTTG
12071638 AGAGAAATTT-
1 AGAG-AATTTG
12071648 AGAGAATTTG
1 AGAGAATTTG
12071658 AGAGAATTTG
1 AGAGAATTTG
12071668 AGAGAATTTG
1 AGAGAATTTG
12071678 GTGTGATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
9 5 0.14
10 28 0.76
11 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:12071721 original size:21 final size:22
Alignment explanation
Indices: 12071695--12071742 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
12071685 AAAAGTGATT
* *
12071695 GAGGATTG-AGGTATTTATAGG
1 GAGGATTGAAAGTATTTATAAG
12071716 GAGGA-TGAAAGTATTTATAAG
1 GAGGATTGAAAGTATTTATAAG
12071737 GAGGAT
1 GAGGAT
12071743 GGGGACGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (22 bp):
GAGGATTGAAAGTATTTATAAG
Found at i:12073695 original size:21 final size:21
Alignment explanation
Indices: 12073653--12073695 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12073643 TTTAAGGGGT
*
12073653 TTTTTAAATAATAATTTTATA
1 TTTTTAAATAATAATTTAATA
12073674 TTTTTAAATAA-AATTTCAATA
1 TTTTTAAATAATAATTT-AATA
12073695 T
1 T
12073696 ATATATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTAAATAATAATTTAATA
Found at i:12074227 original size:14 final size:15
Alignment explanation
Indices: 12074199--12074229 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12074189 AACCATGACA
12074199 AAATAAAATATGAAC
1 AAATAAAATATGAAC
12074214 AAATAAAA-ATGAAC
1 AAATAAAATATGAAC
12074228 AA
1 AA
12074230 TTTGATCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATAAAATATGAAC
Found at i:12074822 original size:6 final size:6
Alignment explanation
Indices: 12074808--12074848 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
12074798 CGGGGATCAA
12074808 AACCC- AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
1 AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG AACCCG
12074849 GCCCGTTGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.34, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
AACCCG
Found at i:12075113 original size:24 final size:24
Alignment explanation
Indices: 12075086--12075136 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
12075076 TAAATCTAAC
* *
12075086 AATTATCTCACATTATTCAAAA-AA
1 AATTATATAACATTATT-AAAAGAA
12075110 AATTATATAACATTATTAAAAGAA
1 AATTATATAACATTATTAAAAGAA
12075134 AAT
1 AAT
12075137 CATAGTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AATTATATAACATTATTAAAAGAA
Found at i:12076454 original size:2 final size:2
Alignment explanation
Indices: 12076447--12076478 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12076437 TTTACTATTA
*
12076447 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12076479 TCACTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12077319 original size:74 final size:74
Alignment explanation
Indices: 12077227--12077661 Score: 584
Period size: 74 Copynumber: 5.9 Consensus size: 74
12077217 CAAAGATCGG
* * * *
12077227 AAATTGTATCTCATTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTTGTTTGAGATAGTTTTCA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCA
* *
12077292 CTCAAAACG
66 CTCGAAACA
* * *
12077301 AAATCTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGACAATTTTCA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCA
12077366 CTCGAAACA
66 CTCGAAACA
12077375 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCA
*
12077440 CTTGAAACA
66 CTCGAAACA
* * * * * *
12077449 AAATTTTATCTCACTTGATATTGTTTTTCTTAAAACAAATTTCGTCTCGCTTGAGTTATTTTTCA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCA
*
12077514 CTCGAAACC
66 CTCGAAACA
* * * * * * *
12077523 AAATTTTATCTCACTTGAGATTGTTTTTCTTAAAATAAACTTTGTCTCGCTCGAGACA-TTTTTA
1 AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCA
12077587 CTCGAAACAA
66 CTCGAAAC-A
* * * * *
12077597 GAAATTTTATCTCACTCGAGATTGTATTTCTTAAAACAAATTTCATCTCGCTTGAGAAAGTTTTC
1 -AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTC
12077662 CTTGAAATAT
Statistics
Matches: 319, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
73 13 0.04
74 252 0.79
75 50 0.16
76 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (74 bp):
AAATTTTATCTCACTCGAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTTGAGATAGTTTTCA
CTCGAAACA
Found at i:12077433 original size:36 final size:36
Alignment explanation
Indices: 12077243--12077660 Score: 268
Period size: 36 Copynumber: 11.3 Consensus size: 36
12077233 TATCTCATTC
* * * *
12077243 GAGATAGTTTTTCTTAAAACAAACTTCGTCTTGTTT
1 GAGATAGTTTTTCTTAAAACAAATTTCATCTCGCTT
* * * *
12077279 GAGATAGTTTTCACTCAAAACGAAATCTT-ATCTCACTC
1 GAGATAGTTTT-TCTTAAAAC-AAAT-TTCATCTCGCTT
* *
12077317 GAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTT
1 GAGATAGTTTTTCTTAAAACAAATTTCATCTCGCTT
* * * ** * * *
12077353 GAGACAATTTTCACTCGAAACAAAATTTTATCTCACTC
1 GAGATAGTTTT-TCTTAAAAC-AAATTTCATCTCGCTT
* *
12077391 GAGATAGTTTTTCTTAAAACAAACTTCGTCTCGCTT
1 GAGATAGTTTTTCTTAAAACAAATTTCATCTCGCTT
* * * *
12077427 GAGATAGTTTTCACTTGAAACAAAATTTTATCTCACTT
1 GAGATAGTTTT-TCTTAAAAC-AAATTTCATCTCGCTT
* * *
12077465 GATATTGTTTTTCTTAAAACAAATTTCGTCTCGCTT
1 GAGATAGTTTTTCTTAAAACAAATTTCATCTCGCTT
* * * * *
12077501 GAGTTA-TTTTTCACTCGAAACCAAATTTTATCTCACTT
1 GAGATAGTTTTT--CT-TAAAACAAATTTCATCTCGCTT
* * * *
12077539 GAGATTGTTTTTCTTAAAATAAACTTT-GTCTCGCTC
1 GAGATAGTTTTTCTTAAAACAAA-TTTCATCTCGCTT
* * * * * *
12077575 GAGACA-TTTTTACTCGAAACAAGAAATTTTATCTCACTC
1 GAGATAGTTTTT-CT--TAA-AACAAATTTCATCTCGCTT
* *
12077614 GAGATTGTATTTCTTAAAACAAATTTCATCTCGCTT
1 GAGATAGTTTTTCTTAAAACAAATTTCATCTCGCTT
*
12077650 GAGAAAGTTTT
1 GAGATAGTTTT
12077661 CCTTGAAATA
Statistics
Matches: 283, Mismatches: 80, Indels: 38
0.71 0.20 0.09
Matches are distributed among these distances:
35 12 0.04
36 108 0.38
37 49 0.17
38 85 0.30
39 25 0.09
40 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (36 bp):
GAGATAGTTTTTCTTAAAACAAATTTCATCTCGCTT
Found at i:12077635 original size:39 final size:37
Alignment explanation
Indices: 12077523--12077631 Score: 89
Period size: 39 Copynumber: 2.9 Consensus size: 37
12077513 ACTCGAAACC
* *
12077523 AAATTTTATCTCACTTGAGATTGTTTTTCTT-AA-AAT
1 AAATTTTATCTCACTCGAGATTG-TTTTCTTAAACAAG
* * * * *
12077559 AAACTTTGTCTCGCTCGAGACATT-TTTACTCGAAACAAG
1 AAATTTTATCTCACTCGAG--ATTGTTTTCT-TAAACAAG
12077598 AAATTTTATCTCACTCGAGATTGTATTTCTTAAA
1 AAATTTTATCTCACTCGAGATTGT-TTTCTTAAA
12077632 ACAAATTTCA
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
36 20 0.37
37 3 0.06
38 9 0.17
39 22 0.41
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (37 bp):
AAATTTTATCTCACTCGAGATTGTTTTCTTAAACAAG
Found at i:12081668 original size:30 final size:30
Alignment explanation
Indices: 12081632--12081691 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
12081622 ATGATTAAAG
12081632 ATATCCTTTTTATCTTCTATTGGGCTCACT
1 ATATCCTTTTTATCTTCTATTGGGCTCACT
12081662 ATATCCTTTTTATCTTCTATTGGGCTCACT
1 ATATCCTTTTTATCTTCTATTGGGCTCACT
12081692 CAAGCCCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.10, T:0.50
Consensus pattern (30 bp):
ATATCCTTTTTATCTTCTATTGGGCTCACT
Found at i:12082817 original size:20 final size:19
Alignment explanation
Indices: 12082792--12082845 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
12082782 GCGAAATAAA
12082792 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
12082812 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
12082832 AATCGCAACGCGAT
1 AATCGCAACGCGAT
12082846 TTTGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:12082856 original size:21 final size:20
Alignment explanation
Indices: 12082832--12082927 Score: 68
Period size: 21 Copynumber: 4.7 Consensus size: 20
12082822 CAGTTCCCAG
12082832 AATCGCAACGCGATTTTGAA
1 AATCGCAACGCGATTTTGAA
* **
12082852 GAATCGCAATGCGATAGT-ACA
1 -AATCGCAACGCGATTTTGA-A
** * *
12082873 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTTT-GAA
* *
12082895 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTTTGAA
12082915 AATCGCAACGCGA
1 AATCGCAACGCGA
12082928 ACATATAAAT
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
20 17 0.29
21 38 0.66
22 2 0.03
23 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGATTTTGAA
Found at i:12082920 original size:20 final size:20
Alignment explanation
Indices: 12082895--12083090 Score: 126
Period size: 20 Copynumber: 9.7 Consensus size: 20
12082885 GATTTTCCAT
**
12082895 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
**
12082915 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATCCGA-A
* * * *
12082935 AATCGCTACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * * *
12082955 TATCGCAATGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* *
12082976 AATTGCAACGCGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
12082997 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * *
12083017 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
12083037 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCG-AA
* *
12083058 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
12083078 AATCGCAACGCGA
1 AATCGCAACGCGA
12083091 TTTTTAAAGC
Statistics
Matches: 133, Mismatches: 37, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.01
20 82 0.62
21 50 0.38
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:12082990 original size:21 final size:20
Alignment explanation
Indices: 12082956--12083089 Score: 144
Period size: 21 Copynumber: 6.5 Consensus size: 20
12082946 GATTCTGACT
* *
12082956 ATCGCAATGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
12082977 ATTGCAACGCGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
* * *
12082998 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
12083018 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
12083038 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
12083059 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
12083079 ATCGCAACGCG
1 ATCGCAACGCG
12083090 ATTTTTAAAG
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
20 45 0.48
21 49 0.52
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:12082999 original size:82 final size:82
Alignment explanation
Indices: 12082895--12083090 Score: 202
Period size: 82 Copynumber: 2.4 Consensus size: 82
12082885 GATTTTCCAT
* ** * * * *
12082895 AATCGCAACGCGAATATG-AAAATCGCAACGCGAACATATAAATCGCTACGCG-ATTC-TGACTA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT-A-AA
* ** *
12082957 TCGCAATGAGTATCCGTAA
64 TCGCAACGACAATACGTAA
* * * * *
12082976 AATTGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATC
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATC
12083041 GCAACGACAATACGTAA
66 GCAACGACAATACGTAA
12083058 AATCGCAACGCGTATCCGT-AAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAAATCGCAACGCGA
12083091 TTTTTAAAGC
Statistics
Matches: 94, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
81 27 0.29
82 62 0.66
83 4 0.04
84 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (82 bp):
AATCGCAACGCGTATCCGTAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATC
GCAACGACAATACGTAA
Found at i:12083038 original size:41 final size:41
Alignment explanation
Indices: 12082956--12083087 Score: 194
Period size: 41 Copynumber: 3.2 Consensus size: 41
12082946 GATTCTGACT
* * * *
12082956 ATCGCAATGAGTATCCGTAAAATTGCAACGCGTATCCGTAAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-AA
*
12082998 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
12083038 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
12083079 ATCGCAACG
1 ATCGCAACG
12083088 CGATTTTTAA
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 19 0.23
41 48 0.59
42 15 0.18
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:12083066 original size:61 final size:62
Alignment explanation
Indices: 12082956--12083085 Score: 174
Period size: 61 Copynumber: 2.1 Consensus size: 62
12082946 GATTCTGACT
* * *
12082956 ATCGCAATGAGTATCCGTAAAATTGCAACGCGTATCCGTAAAATCGCAACGAGAATACGTAA
1 ATCGCAATGAGTATCCGTAAAATCGCAACGCGAATACGTAAAATCGCAACGAGAATACGTAA
* * * *
12083018 ATCGCAATGCGTATCCGT-AAATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAATGAGTATCCGTAAAATCGCAACG-CGAATACGTAAAATCGCAACGAGAATACGTAA
12083079 ATCGCAA
1 ATCGCAA
12083086 CGCGATTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
61 42 0.70
62 18 0.30
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (62 bp):
ATCGCAATGAGTATCCGTAAAATCGCAACGCGAATACGTAAAATCGCAACGAGAATACGTAA
Found at i:12083676 original size:20 final size:20
Alignment explanation
Indices: 12083651--12083722 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
12083641 TTCTAAACTT
12083651 AAAATCGCAACATC-AAAATG
1 AAAATCGCAACA-CGAAAATG
12083671 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
12083691 ACTATCGCAACGA-GATAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
12083712 AAAATCACAAC
1 AAAATCGCAAC
12083723 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 29 0.66
21 14 0.32
ACGTcount: A:0.53, C:0.21, G:0.12, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:12083748 original size:33 final size:33
Alignment explanation
Indices: 12083707--12083775 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
12083697 GCAACGAGAT
12083707 AAATGAAAATCACAACGAGAGAATCGCAACGCG
1 AAATGAAAATCACAACGAGAGAATCGCAACGCG
** *
12083740 AAATGAAAATCGTAACGAGATAATCGCAACGCG
1 AAATGAAAATCACAACGAGAGAATCGCAACGCG
12083773 AAA
1 AAA
12083776 CCAAAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.19, G:0.20, T:0.12
Consensus pattern (33 bp):
AAATGAAAATCACAACGAGAGAATCGCAACGCG
Found at i:12083782 original size:33 final size:33
Alignment explanation
Indices: 12083720--12083784 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
12083710 TGAAAATCAC
**
12083720 AACGAGAGAATCGCAACGCGAAATGAAAATCGT
1 AACGAGAGAATCGCAACGCGAAACCAAAATCGT
*
12083753 AACGAGATAATCGCAACGCGAAACCAAAATCG
1 AACGAGAGAATCGCAACGCGAAACCAAAATCG
12083785 CATTGCGATT
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:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AACGAGAGAATCGCAACGCGAAACCAAAATCGT
Found at i:12083804 original size:19 final size:19
Alignment explanation
Indices: 12083782--12083907 Score: 101
Period size: 19 Copynumber: 7.1 Consensus size: 19
12083772 GAAACCAAAA
* *
12083782 TCGCATTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
*
12083801 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
12083820 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
12083834 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
12083853 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
12083867 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
12083886 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
12083906 TC
1 TC
12083908 AACCAAAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
14 19 0.23
16 5 0.06
17 5 0.06
19 38 0.46
20 16 0.19
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:12083846 original size:33 final size:33
Alignment explanation
Indices: 12083804--12083878 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
12083794 TTTCTTTTCG
12083804 CGTTGCGATTTTAATTTCGCGTTACGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTACGATTCTCT
* *
12083837 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCGTTACGATTCTCT
12083870 CGTTGCGAT
1 CGTTGCGAT
12083879 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCGTTACGATTCTCT
Found at i:12083885 original size:33 final size:33
Alignment explanation
Indices: 12083817--12083899 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
12083807 TGCGATTTTA
* **
12083817 ATTTCGCGTTACGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
12083850 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
12083883 ATTTCCGCGTTGCGATT
1 ATTT-CGCGTTGCGATT
12083900 TTCATTTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.74
34 12 0.26
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
Found at i:12087351 original size:14 final size:14
Alignment explanation
Indices: 12087332--12087367 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
12087322 ATTGTTTAAT
*
12087332 TGATTTGTAAATGA
1 TGATTTGTAAAAGA
*
12087346 TGATTTGTAAAAGC
1 TGATTTGTAAAAGA
12087360 TGATTTGT
1 TGATTTGT
12087368 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:12087496 original size:19 final size:19
Alignment explanation
Indices: 12087474--12087532 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
12087464 AAAGATGACT
12087474 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
12087493 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
12087507 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
12087526 ATCGCAA
1 ATCGCAA
12087533 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:12087516 original size:33 final size:33
Alignment explanation
Indices: 12087474--12087553 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
12087464 AAAGATGACT
* *
12087474 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
12087507 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
12087540 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
12087554 CTAAATTCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:12087607 original size:33 final size:33
Alignment explanation
Indices: 12087565--12087642 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
12087555 TAAATTCACG
*
12087565 TTGCGATTTTCATTTCGCATTGTGATTCCCTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
* *
12087598 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
12087631 TTGCGATTTTCA
1 TTGCGATTTTCA
12087643 CGTTGCGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCA
Found at i:12087620 original size:19 final size:19
Alignment explanation
Indices: 12087596--12087671 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 19
12087586 GTGATTCCCT
12087596 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
12087615 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
12087631 --TTGCGATTTTCA---CG
1 CATTGCGATTTTCATTTCG
*
12087645 --TTGCGATTTTCATTTCA
1 CATTGCGATTTTCATTTCG
12087662 CATTGCGATT
1 CATTGCGATT
12087672 CTCTTGTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
14 20 0.43
16 7 0.15
17 4 0.09
19 16 0.34
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:12087876 original size:33 final size:32
Alignment explanation
Indices: 12087830--12087923 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 32
12087820 AAAAATGACT
* *
12087830 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACAAA
* * *
12087863 ATCGCAATACGAAATTAAAATCTCAATGACAAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACAAA
*
12087896 ATCGCAACGCGAAACTAAAATCGCAACG
1 ATCGCAATGCGAAA-TAAAATCGCAACG
12087924 CGAAACTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 49 0.98
34 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACAAA
Found at i:12087945 original size:19 final size:19
Alignment explanation
Indices: 12087893--12087938 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
12087883 TCTCAATGAC
12087893 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
12087912 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
12087931 AAATTCGC
1 AAAATCGC
12087939 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:12087985 original size:33 final size:33
Alignment explanation
Indices: 12087938--12088060 Score: 138
Period size: 33 Copynumber: 3.5 Consensus size: 33
12087928 ACTAAATTCG
12087938 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
* *
12087971 CGTTACGATTTTCATTTCGTATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGTATTGCGAT--TC---T-CT
* *
12088010 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
**
12088043 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
12088061 CGCGTTGCGA
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
33 44 0.58
34 1 0.01
35 2 0.03
37 2 0.03
38 1 0.01
39 26 0.34
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
Found at i:12088017 original size:20 final size:19
Alignment explanation
Indices: 12087982--12088072 Score: 66
Period size: 20 Copynumber: 4.9 Consensus size: 19
12087972 GTTACGATTT
**
12087982 TCATTTCGTATTGCGATAG
1 TCATTTCGCGTTGCGATAG
**
12088001 TCATTTCCGCGTTGCGATTT
1 TCATTT-CGCGTTGCGATAG
* *
12088021 TCATTTCGCATTACGAT--
1 TCATTTCGCGTTGCGATAG
*
12088038 TC---TCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATAG
12088054 TCATTTCCGCGTTGCGATA
1 TCATTT-CGCGTTGCGATA
12088073 TACATTAAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
14 9 0.16
16 2 0.04
17 2 0.04
19 16 0.29
20 26 0.47
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:12091526 original size:20 final size:20
Alignment explanation
Indices: 12091503--12091648 Score: 151
Period size: 20 Copynumber: 7.6 Consensus size: 20
12091493 CAGAATCTCG
12091503 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
12091523 TTGCGATTTTCGTATTCACA
1 TTGCGATTTACGTATTCGCA
* *
12091543 TTACGATTTACGTATTCGTA
1 TTGCGATTTACGTATTCGCA
* *
12091563 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATTCGCA
* *
12091583 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCA
*
12091603 TTGCGATTT-C-CA--CG--
1 TTGCGATTTACGTATTCGCA
* *
12091617 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCA
12091637 TTGCGATTTACG
1 TTGCGATTTACG
12091649 GATACACGTA
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
18 2 0.02
19 1 0.01
20 87 0.85
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:12091529 original size:40 final size:40
Alignment explanation
Indices: 12091482--12091569 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
12091472 GAAATTCAGT
* * *
12091482 ATTGCGATAGTCAG-AATCTCGTTGCGATTTACGTATTCGC
1 ATTGCGATAGTC-GTAATCACATTACGATTTACGTATTCGC
** * *
12091522 ATTGCGATTTTCGTATTCACATTACGATTTACGTATTCGT
1 ATTGCGATAGTCGTAATCACATTACGATTTACGTATTCGC
12091562 ATTGCGAT
1 ATTGCGAT
12091570 TTACGGATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTGCGATAGTCGTAATCACATTACGATTTACGTATTCGC
Found at i:12091649 original size:74 final size:75
Alignment explanation
Indices: 12091546--12091684 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 75
12091536 ATTCACATTA
* * * *
12091546 CGATTTACGTATTCGTATTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTCGTTGCGAT
1 CGATTTACGTATTCGTATTGCGATTTACGGATACACATAGCGATTTTACGGATACTCGTTGCGAT
12091610 TTCCACGTTG
66 TTCCACGTTG
* *
12091620 CGATTTACGTATTC-TCGTTGCGATTTACGGATACACGTAGCGATTTTACGGATACTCGTTGCGA
1 CGATTTACGTATTCGT-ATTGCGATTTACGGATACACATAGCGATTTTACGGATACTCGTTGCGA
12091684 T
65 T
12091685 AGTCAGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
73 1 0.02
74 37 0.65
75 19 0.33
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (75 bp):
CGATTTACGTATTCGTATTGCGATTTACGGATACACATAGCGATTTTACGGATACTCGTTGCGAT
TTCCACGTTG
Found at i:12091663 original size:54 final size:54
Alignment explanation
Indices: 12091563--12091665 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
12091553 CGTATTCGTA
* * * *
12091563 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTCCACG
1 TTGCGATTTACGGATACGCATTGCGATTTACGGATACACGTAGCGATTTCCACG
* * * *
12091617 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACACGTAGCGATTT
1 TTGCGATTTACGGATACGCATTGCGATTTACGGATACACGTAGCGATTT
12091666 TACGGATACT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (54 bp):
TTGCGATTTACGGATACGCATTGCGATTTACGGATACACGTAGCGATTTCCACG
Found at i:12091669 original size:21 final size:20
Alignment explanation
Indices: 12091563--12091684 Score: 103
Period size: 20 Copynumber: 6.3 Consensus size: 20
12091553 CGTATTCGTA
* *
12091563 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACACG
* * *
12091583 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACACG
12091603 TTGCGATTT-C-----CACG
1 TTGCGATTTACGGATACACG
* * *
12091617 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACACG
12091637 TTGCGATTTACGGATACACG
1 TTGCGATTTACGGATACACG
* *
12091657 TAGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACACG
12091678 TTGCGAT
1 TTGCGAT
12091685 AGTCAGAATC
Statistics
Matches: 83, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
14 12 0.14
15 1 0.01
19 1 0.01
20 51 0.61
21 18 0.22
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGGATACACG
Found at i:12091716 original size:20 final size:20
Alignment explanation
Indices: 12091693--12091745 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
12091683 ATAGTCAGAA
*
12091693 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
12091713 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
12091733 TCGCATTGCGATT
1 TCGCGTTGCGATT
12091746 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:12091763 original size:21 final size:21
Alignment explanation
Indices: 12091733--12091848 Score: 87
Period size: 21 Copynumber: 5.6 Consensus size: 21
12091723 ATTTTCATAT
12091733 TCGCATTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGGAAAA
* * **
12091754 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGAAAA
**
12091775 TCGCATTGCGATTCTTCAAAA
1 TCGCATTGCGATTCTGGAAAA
* * *
12091796 TCGCGTTGCGATTCTGGGAAC
1 TCGCATTGCGATTCTGGAAAA
*
12091817 T-G-ATTTGCGATTCTGG-AGA
1 TCGCA-TTGCGATTCTGGAAAA
*
12091836 TCGCGTTGCGATT
1 TCGCATTGCGATT
12091849 TTTATTTCGC
Statistics
Matches: 72, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.03
20 25 0.35
21 42 0.58
22 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTCTGGAAAA
Found at i:12091806 original size:42 final size:42
Alignment explanation
Indices: 12091713--12091806 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
12091703 ATTTATATGT
*
12091713 TCGCGTTGCG-ATTTTCATATTCGCATTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** *
12091754 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCAAAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
12091796 TCGCGTTGCGA
1 TCGCGTTGCGA
12091807 TTCTGGGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 8 0.18
42 33 0.75
43 3 0.07
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:12091844 original size:20 final size:19
Alignment explanation
Indices: 12091795--12091848 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
12091785 ATTCTTCAAA
12091795 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
12091814 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
12091835 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
12091849 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:12097850 original size:24 final size:24
Alignment explanation
Indices: 12097823--12097894 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
12097813 AAACGGAGAT
12097823 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
12097847 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
12097871 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
12097895 GCAATGTATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:12097852 original size:12 final size:12
Alignment explanation
Indices: 12097825--12097894 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
12097815 ACGGAGATAT
* *
12097825 CAGAAATCAAAA
1 CAGAATTCAGAA
*
12097837 CAGAATTCAGAT
1 CAGAATTCAGAA
*
12097849 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
12097861 CAGAATCCAGAT
1 CAGAATTCAGAA
*
12097873 CAGAAATCAGAA
1 CAGAATTCAGAA
*
12097885 CATAATTCAG
1 CAGAATTCAG
12097895 GCAATGTATC
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:12101085 original size:20 final size:20
Alignment explanation
Indices: 12101060--12101100 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12101050 ATCCAGAAGC
12101060 GATGTTGGAAGAATAAACAA
1 GATGTTGGAAGAATAAACAA
12101080 GATGTTGGAAGAATAAACAA
1 GATGTTGGAAGAATAAACAA
12101100 G
1 G
12101101 TCGTGGGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.27, T:0.20
Consensus pattern (20 bp):
GATGTTGGAAGAATAAACAA
Found at i:12101109 original size:20 final size:20
Alignment explanation
Indices: 12101060--12101109 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
12101050 ATCCAGAAGC
*
12101060 GATGTTGGAAGAATAAACAA
1 GATGTGGGAAGAATAAACAA
*
12101080 GATGTTGGAAGAATAAACAA
1 GATGTGGGAAGAATAAACAA
12101100 G-TCGTGGGAA
1 GAT-GTGGGAA
12101110 CTGGGTGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.44, C:0.06, G:0.30, T:0.20
Consensus pattern (20 bp):
GATGTGGGAAGAATAAACAA
Found at i:12101267 original size:3 final size:3
Alignment explanation
Indices: 12101261--12101292 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12101251 TATACATATT
12101261 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12101293 TGCAGTGGTT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12116849 original size:17 final size:17
Alignment explanation
Indices: 12116807--12116850 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
12116797 TTTTTTTATT
12116807 TGGGTTTAAAAATTAAC
1 TGGGTTTAAAAATTAAC
*
12116824 TAGGTTTTAAAATATTAA-
1 T-GGGTTTAAAA-ATTAAC
12116842 TGGGTTTAA
1 TGGGTTTAA
12116851 GGTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (17 bp):
TGGGTTTAAAAATTAAC
Found at i:12123909 original size:2 final size:2
Alignment explanation
Indices: 12123904--12123947 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12123894 TCTGTTATTA
12123904 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
12123946 AT
1 AT
12123948 TCATCCTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12124297 original size:16 final size:16
Alignment explanation
Indices: 12124276--12124310 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12124266 CTCAAACAAA
12124276 AAATCAA-CCTGAACCG
1 AAATCAATCC-GAACCG
12124292 AAATCAATCCGAACCG
1 AAATCAATCCGAACCG
12124308 AAA
1 AAA
12124311 ATAACTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.49, C:0.29, G:0.11, T:0.11
Consensus pattern (16 bp):
AAATCAATCCGAACCG
Found at i:12124382 original size:3 final size:3
Alignment explanation
Indices: 12124374--12124415 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
12124364 AACAAATAAT
12124374 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
12124416 TTTAGCAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12124827 original size:46 final size:46
Alignment explanation
Indices: 12124759--12124917 Score: 223
Period size: 46 Copynumber: 3.5 Consensus size: 46
12124749 GTGAAGACGG
*
12124759 TTGACCT-AAACAGAAA-CAACCTGAATTAACTCAAAAATCTAAAGT
1 TTGACCTGAACCA-AAACCAACCTGAATTAACTCAAAAATCTAAAGT
* *
12124804 TTGACCTGAACCAAAACCAACCTGAATTAACTCAAAAACCTAAAGG
1 TTGACCTGAACCAAAACCAACCTGAATTAACTCAAAAATCTAAAGT
* *
12124850 TTGACCTGAACCAAAACCAACCTGAATTGACCCAAAAATCTAAAGT
1 TTGACCTGAACCAAAACCAACCTGAATTAACTCAAAAATCTAAAGT
* * *
12124896 TTGACCCGAACCGAAACTAACC
1 TTGACCTGAACCAAAACCAACC
12124918 GATCCGATAT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
45 10 0.10
46 92 0.90
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.19
Consensus pattern (46 bp):
TTGACCTGAACCAAAACCAACCTGAATTAACTCAAAAATCTAAAGT
Found at i:12126112 original size:17 final size:17
Alignment explanation
Indices: 12126090--12126140 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
12126080 TCAGTTTGGG
12126090 TTATTTTCTGTTCGAAT
1 TTATTTTCTGTTCGAAT
* *
12126107 TTA-TTTCAGTTCGAGT
1 TTATTTTCTGTTCGAAT
*
12126123 TAATTTT-TGGTTCGAAT
1 TTATTTTCT-GTTCGAAT
12126140 T
1 T
12126141 CCTTTCAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.55
Consensus pattern (17 bp):
TTATTTTCTGTTCGAAT
Found at i:12126113 original size:32 final size:33
Alignment explanation
Indices: 12126077--12126161 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
12126067 ATTTGGGTTG
* *
12126077 ATTTCAGTTTGGGTT-ATTTTCT-GTTCGAATTT
1 ATTTCAGTTCGGGTTAATTTT-TGGTTCGAATTC
*
12126109 ATTTCAGTTCGAGTTAATTTTTGGTTCGAATTC
1 ATTTCAGTTCGGGTTAATTTTTGGTTCGAATTC
* *
12126142 CTTTCAGTTCGGGTTGATTT
1 ATTTCAGTTCGGGTTAATTT
12126162 CGGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 14 0.31
33 31 0.69
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (33 bp):
ATTTCAGTTCGGGTTAATTTTTGGTTCGAATTC
Found at i:12126736 original size:35 final size:35
Alignment explanation
Indices: 12126665--12126738 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
12126655 AGATCACTAT
* *
12126665 AAAAAGAATTTATTAGTATAAGGAAATTATTGTCC
1 AAAAAGAATTTATTAGTATAAGGAAATTAATATCC
* * **
12126700 AAAAAGAATTTATTATTCTAAGGGTATTAATATCC
1 AAAAAGAATTTATTAGTATAAGGAAATTAATATCC
12126735 AAAA
1 AAAA
12126739 TGGTGGAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (35 bp):
AAAAAGAATTTATTAGTATAAGGAAATTAATATCC
Found at i:12127800 original size:15 final size:15
Alignment explanation
Indices: 12127777--12127810 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12127767 TTTTTTATTT
*
12127777 TTTTTAATAAAATAA
1 TTTTGAATAAAATAA
12127792 TTTTGAATAAAATAA
1 TTTTGAATAAAATAA
12127807 TTTT
1 TTTT
12127811 AAAAACAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTTGAATAAAATAA
Found at i:12128396 original size:29 final size:25
Alignment explanation
Indices: 12128348--12128414 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 25
12128338 ATTTATATAT
*
12128348 TTTATTAATTTTTTTCATAATTTAATAAA
1 TTTATTAA--TTTTTAATAA-TTAA-AAA
12128377 TTTAATTTAATTTTTAATAATTAAAAA
1 TTT-A-TTAATTTTTAATAATTAAAAA
12128404 TTTATTAATTT
1 TTTATTAATTT
12128415 GATATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 7 0.20
26 1 0.03
27 6 0.17
28 4 0.11
29 12 0.34
30 1 0.03
31 4 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTATTAATTTTTAATAATTAAAAA
Found at i:12131736 original size:23 final size:23
Alignment explanation
Indices: 12131709--12131765 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
12131699 GTAAACGGAT
*
12131709 ATAAACGAACACAATAAATGAAC
1 ATAAACGAACACAATAAATAAAC
*
12131732 GTAAACGAACACAATAAATAAAC
1 ATAAACGAACACAATAAATAAAC
12131755 ATAAACGAACA
1 ATAAACGAACA
12131766 TAATTGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (23 bp):
ATAAACGAACACAATAAATAAAC
Found at i:12131973 original size:24 final size:24
Alignment explanation
Indices: 12131937--12131983 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
12131927 GATTGAGAGA
*
12131937 AACATAAATGAACACACATAAACT
1 AACATAAACGAACACACATAAACT
* * *
12131961 AACATGAACGAACAGATATAAAC
1 AACATAAACGAACACACATAAAC
12131984 GAACGAACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.19, G:0.09, T:0.15
Consensus pattern (24 bp):
AACATAAACGAACACACATAAACT
Found at i:12133094 original size:19 final size:18
Alignment explanation
Indices: 12133042--12133095 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
12133032 ACCCTTAAAA
12133042 TAATATAATTTTATATATT
1 TAATATAATTTTA-ATATT
* * *
12133061 TAATATTAGTATAATACTT
1 TAATATAATTTTAATA-TT
*
12133080 TAATATCATTTTAATA
1 TAATATAATTTTAATA
12133096 AAAATATTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATATAATTTTAATATT
Found at i:12133139 original size:12 final size:12
Alignment explanation
Indices: 12133116--12133150 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12133106 TCATTGAAAA
12133116 TTTTAA-AATAT
1 TTTTAATAATAT
*
12133127 TTTTATTAATAT
1 TTTTAATAATAT
12133139 TTTTAATAATAT
1 TTTTAATAATAT
12133151 AATATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTAATAATAT
Found at i:12133163 original size:23 final size:23
Alignment explanation
Indices: 12133133--12133179 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
12133123 ATATTTTTAT
12133133 TAATATTTTTAATA-ATATAATA
1 TAATATTTTTAATATATATAATA
12133155 TAATAATTTTTAATATTATATAATA
1 TAAT-ATTTTTAATA-TATATAATA
12133180 CCTTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
25 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTTTTAATATATATAATA
Found at i:12133170 original size:20 final size:20
Alignment explanation
Indices: 12133145--12133201 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
12133135 ATATTTTTAA
*
12133145 TAATATAATATAATAATTTT
1 TAATATAATATAATAATCTT
* *
12133165 TAATATTATATAAT-ACCTT
1 TAATATAATATAATAATCTT
*
12133184 TAATTATATTATAATAAT
1 TAA-TATAATATAATAAT
12133202 ATATGATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 6 0.21
20 22 0.76
21 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATAATATAATAATCTT
Found at i:12138597 original size:13 final size:13
Alignment explanation
Indices: 12138579--12138603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12138569 CAACATTTTC
12138579 AAAATTTAAACAT
1 AAAATTTAAACAT
12138592 AAAATTTAAACA
1 AAAATTTAAACA
12138604 AAATAAATTG
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTTAAACAT
Found at i:12139000 original size:7 final size:7
Alignment explanation
Indices: 12138988--12139032 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
12138978 GCTAAGATTC
*
12138988 GAAAGGG
1 GAAACGG
*
12138995 GAAAGGG
1 GAAACGG
*
12139002 GAAAGGG
1 GAAACGG
12139009 GAAACGG
1 GAAACGG
12139016 GAAACGG
1 GAAACGG
12139023 GAAACGG
1 GAAACGG
12139030 GAA
1 GAA
12139033 TTTGCCCTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.44, C:0.07, G:0.49, T:0.00
Consensus pattern (7 bp):
GAAACGG
Found at i:12139007 original size:14 final size:14
Alignment explanation
Indices: 12138988--12139032 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
12138978 GCTAAGATTC
*
12138988 GAAAGGGGAAAGGG
1 GAAAGGGGAAACGG
12139002 GAAAGGGGAAACGG
1 GAAAGGGGAAACGG
*
12139016 GAAACGGGAAACGG
1 GAAAGGGGAAACGG
12139030 GAA
1 GAA
12139033 TTTGCCCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.49, T:0.00
Consensus pattern (14 bp):
GAAAGGGGAAACGG
Found at i:12141585 original size:30 final size:28
Alignment explanation
Indices: 12141520--12141592 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
12141510 GCACTATACG
*
12141520 AACGAACACT-AACACCTTAAAAAAAATA
1 AACGAACA-TAAATACCTTAAAAAAAATA
**
12141548 AGTGAACATAAATACCTTCAAAAATAAATA
1 AACGAACATAAATACCTT-AAAAA-AAATA
*
12141578 AACGAACACAAATAC
1 AACGAACATAAATAC
12141593 AACACTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.03
28 13 0.36
29 5 0.14
30 17 0.47
ACGTcount: A:0.59, C:0.19, G:0.05, T:0.16
Consensus pattern (28 bp):
AACGAACATAAATACCTTAAAAAAAATA
Found at i:12142511 original size:15 final size:16
Alignment explanation
Indices: 12142485--12142520 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
12142475 TATTATCAAC
12142485 AAATAGATTTTTATAT
1 AAATAGATTTTTATAT
*
12142501 AAATA-ATTTTTATTT
1 AAATAGATTTTTATAT
12142516 AAATA
1 AAATA
12142521 TTTAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AAATAGATTTTTATAT
Found at i:12143196 original size:60 final size:59
Alignment explanation
Indices: 12143084--12143197 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 59
12143074 ATAGTCGGGT
* * * *
12143084 GACCATTTTTAACTTTTAATAGTCAACGGACATAACAAAGTAACATTATATAGTTAGAA
1 GACCATTTTCAACTTTTAATAGTCAACGAACATAACAAAGCAACACTATATAGTTAGAA
* * * *
12143143 GACCATTTTGCAACTTTTAATAGTCGATGAAC-TCAATAAAGCAACACTCTATAGT
1 GACCATTTT-CAACTTTTAATAGTCAACGAACAT-AACAAAGCAACACTATATAGT
12143198 CGGTAACCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
59 10 0.22
60 35 0.78
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (59 bp):
GACCATTTTCAACTTTTAATAGTCAACGAACATAACAAAGCAACACTATATAGTTAGAA
Found at i:12143663 original size:60 final size:60
Alignment explanation
Indices: 12143589--12143701 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
12143579 ATAAATGGGT
** * * *
12143589 GACCATTTTGTAACTTTTAATAGTCGAT-GGACTCAACAAAGCGA-TACCCTATAGTCAAGG
1 GACCATTTCATAACTTGTAATAGTAG-TGGGACTCAACAAAAC-ATTACCCTATAGTCAAGG
*
12143649 GACCATTTCATAACTTGTATTAGTAGTGGGACTCAACAAAACATTACCCTATA
1 GACCATTTCATAACTTGTAATAGTAGTGGGACTCAACAAAACATTACCCTATA
12143702 ATTGAGGGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.04
60 43 0.96
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (60 bp):
GACCATTTCATAACTTGTAATAGTAGTGGGACTCAACAAAACATTACCCTATAGTCAAGG
Found at i:12144245 original size:3 final size:3
Alignment explanation
Indices: 12144232--12144267 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
12144222 AATAGAGTGA
12144232 ATT ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12144268 ATATATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12144705 original size:5 final size:5
Alignment explanation
Indices: 12144695--12144726 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
12144685 GTAATTACTT
12144695 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TT
12144727 CTTTCTCAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:12145630 original size:40 final size:38
Alignment explanation
Indices: 12145545--12145619 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 38
12145535 AATATTTGTA
* *
12145545 AACATTTTCAATTGAACCGAAAATGTTATGAACAATGT
1 AACATTTTCAATTGAACCGAAAATGTTAAGAAAAATGT
* *
12145583 AACATTTTCGATTGACAATCGAAAATGTTAAGAAAAA
1 AACATTTTCAATTG--AACCGAAAATGTTAAGAAAAA
12145620 GTTGACATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 13 0.42
40 18 0.58
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.29
Consensus pattern (38 bp):
AACATTTTCAATTGAACCGAAAATGTTAAGAAAAATGT
Found at i:12146692 original size:87 final size:87
Alignment explanation
Indices: 12146569--12146743 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
12146559 TACAACAACG
12146569 GCTCTATTGACTTCATGATCATCCCCAACATTCAGAATTCATTCAAGGGATATTTAAACAAGTCT
1 GCTCTATTGACTTCATGATCATCCCCAACATTCAGAATTCATTCAAGGGATATTTAAACAAGTCT
12146634 TGAAGCCATTGATGAATAACAA
66 TGAAGCCATTGATGAATAACAA
12146656 GCTCTATTGACTTCATGATCATCCCCAACATTCAGAATTCATTCAAGGGATATTTAAACAAGTCT
1 GCTCTATTGACTTCATGATCATCCCCAACATTCAGAATTCATTCAAGGGATATTTAAACAAGTCT
12146721 TGAAGCCATTGATGAATAACAA
66 TGAAGCCATTGATGAATAACAA
12146743 G
1 G
12146744 AAACAAGTTT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (87 bp):
GCTCTATTGACTTCATGATCATCCCCAACATTCAGAATTCATTCAAGGGATATTTAAACAAGTCT
TGAAGCCATTGATGAATAACAA
Found at i:12147804 original size:23 final size:22
Alignment explanation
Indices: 12147776--12147819 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
12147766 CATTTCATAT
12147776 TTTTATAAAATTTTGAATTTTTA
1 TTTTATAAAATTTTG-ATTTTTA
**
12147799 TTTTATAGTATTTTGATTTTT
1 TTTTATAAAATTTTGATTTTT
12147820 GAAGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (22 bp):
TTTTATAAAATTTTGATTTTTA
Found at i:12149891 original size:16 final size:16
Alignment explanation
Indices: 12149870--12149920 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
12149860 TTTTAAATGG
12149870 GAAAGAAAAGTTACTA
1 GAAAGAAAAGTTACTA
* *
12149886 GAAAGATAAGATA--A
1 GAAAGAAAAGTTACTA
12149900 GAAAGAAAAGTTACTA
1 GAAAGAAAAGTTACTA
12149916 GAAAG
1 GAAAG
12149921 TTAAGATAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.41
16 17 0.59
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.16
Consensus pattern (16 bp):
GAAAGAAAAGTTACTA
Found at i:12149904 original size:14 final size:14
Alignment explanation
Indices: 12149885--12149932 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
12149875 AAAAGTTACT
12149885 AGAAAGATAAGATA
1 AGAAAGATAAGATA
* *
12149899 AGAAAGAAAAGTTA
1 AGAAAGATAAGATA
*
12149913 CTAGAAAGTTAAGATA
1 --AGAAAGATAAGATA
12149929 AGAA
1 AGAA
12149933 CAACATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 16 0.59
16 11 0.41
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (14 bp):
AGAAAGATAAGATA
Found at i:12149906 original size:30 final size:30
Alignment explanation
Indices: 12149870--12149932 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
12149860 TTTTAAATGG
12149870 GAAAGAAAAGTTACTAGAAAGATAAGATAA
1 GAAAGAAAAGTTACTAGAAAGATAAGATAA
*
12149900 GAAAGAAAAGTTACTAGAAAGTTAAGATAA
1 GAAAGAAAAGTTACTAGAAAGATAAGATAA
12149930 GAA
1 GAA
12149933 CAACATATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.17
Consensus pattern (30 bp):
GAAAGAAAAGTTACTAGAAAGATAAGATAA
Found at i:12150440 original size:51 final size:51
Alignment explanation
Indices: 12150361--12150475 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
12150351 GTAAATATTG
* ** * * **
12150361 AATAAAATAATAATAAATTAAAGGTAATGTTTTGATTTTAT-TCTAATTTTT
1 AATAAAATAATAATAAACTAAAAATAATGTTTTAACTTTATCT-TAATTCCT
12150412 AATAAAATAATAATAAACTAAAAATAATGTTTTAACTTTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAAATAATGTTTTAACTTTATCTTAATTCCT
12150463 AATAAAATAATAA
1 AATAAAATAATAA
12150476 ATCTAATTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 55 0.98
52 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAAATAATGTTTTAACTTTATCTTAATTCCT
Found at i:12151169 original size:31 final size:30
Alignment explanation
Indices: 12151095--12151186 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
12151085 TTCGATAATA
* * *
12151095 TAATAATTATTTTATAGTATTTAGATAAATT
1 TAATAATAATTTTATATTTTTTA-ATAAATT
* *
12151126 TATTAATAATTTTTTAATTTTTTAATAAATT
1 TAATAATAATTTTAT-ATTTTTTAATAAATT
*
12151157 TAATAAGT-ATTTTATATTTTTT-TTAAATT
1 TAATAA-TAATTTTATATTTTTTAATAAATT
12151186 T
1 T
12151187 TATTGAAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
29 7 0.14
30 7 0.14
31 30 0.59
32 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (30 bp):
TAATAATAATTTTATATTTTTTAATAAATT
Found at i:12151933 original size:31 final size:30
Alignment explanation
Indices: 12151898--12151984 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
12151888 TCAATGAAGT
12151898 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
12151929 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
12151960 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
12151985 TATTATCGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:12152368 original size:2 final size:2
Alignment explanation
Indices: 12152323--12152357 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12152313 ATCATAAACT
12152323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12152358 GAAAGATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12159001 original size:17 final size:18
Alignment explanation
Indices: 12158968--12159001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12158958 CCGCTATTAG
12158968 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
12158986 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
12159002 GACCGGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:12172878 original size:18 final size:18
Alignment explanation
Indices: 12172846--12172886 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12172836 CAAATATTTA
12172846 TAAAATTATAAGAAATTC
1 TAAAATTATAAGAAATTC
*
12172864 -AAAATATATACGAAATTC
1 TAAAAT-TATAAGAAATTC
12172882 TAAAA
1 TAAAA
12172887 AAATAGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (18 bp):
TAAAATTATAAGAAATTC
Found at i:12187519 original size:22 final size:22
Alignment explanation
Indices: 12187487--12187539 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
12187477 TTGAAAATCG
*
12187487 CGTTGCGATAGTCTACAGTTGT
1 CGTTACGATAGTCTACAGTTGT
*
12187509 TGTTACGATAGTCTACAGTTGT
1 CGTTACGATAGTCTACAGTTGT
*
12187531 CGTTGCGAT
1 CGTTACGAT
12187540 TTTTCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTACGATAGTCTACAGTTGT
Found at i:12187648 original size:20 final size:20
Alignment explanation
Indices: 12187623--12187698 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
12187613 ATTTTCAACT
*
12187623 ATCGCAACGTGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
12187643 ATCGCAACGCGAATTGAAAA
1 ATCGCAACGCGAAATGAAAA
12187663 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
**
12187683 ATCAAAACGCGAAATG
1 ATCGCAACGCGAAATG
12187699 CAACGCGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:12194474 original size:30 final size:29
Alignment explanation
Indices: 12194402--12194475 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
12194392 AAAAGAATAA
*
12194402 TTTATATAAATGAATTACTTGAAAATTAT
1 TTTATATAAATGAATTACATGAAAATTAT
*
12194431 TTT-TCAAAAAATGAATTACATGAAAATTAT
1 TTTAT--ATAAATGAATTACATGAAAATTAT
*
12194461 TTTATGTACAATGAA
1 TTTATATA-AATGAA
12194476 GTATCTAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.03
29 4 0.11
30 31 0.84
31 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (29 bp):
TTTATATAAATGAATTACATGAAAATTAT
Found at i:12194767 original size:17 final size:18
Alignment explanation
Indices: 12194745--12194792 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
12194735 TTAATATAAA
12194745 ATTAAAAATATAATAT-T
1 ATTAAAAATATAATATGT
*
12194762 ATTAAAATTATATTATATGT
1 ATTAAAA--ATATAATATGT
*
12194782 ATAAAAAATAT
1 ATTAAAAATAT
12194793 TTTAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 8 0.31
20 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTAAAAATATAATATGT
Found at i:12195672 original size:23 final size:23
Alignment explanation
Indices: 12195643--12195695 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
12195633 TTAATAAGTA
*
12195643 TGCCTTTGTTTCACGTTTTCATC
1 TGCCTTTGTTGCACGTTTTCATC
* *
12195666 TGTCTTTGTTGCACGTTTTTATC
1 TGCCTTTGTTGCACGTTTTCATC
12195689 TGCCTTT
1 TGCCTTT
12195696 ATGGTACGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.55
Consensus pattern (23 bp):
TGCCTTTGTTGCACGTTTTCATC
Found at i:12195704 original size:23 final size:23
Alignment explanation
Indices: 12195654--12195708 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
12195644 GCCTTTGTTT
* * *
12195654 CACGTTTTCATCTGTCTTTGTTG
1 CACGTTTTCATCTGCCTTTATGG
*
12195677 CACGTTTTTATCTGCCTTTATGG
1 CACGTTTTCATCTGCCTTTATGG
*
12195700 TACGTTTTC
1 CACGTTTTC
12195709 TTATGCTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (23 bp):
CACGTTTTCATCTGCCTTTATGG
Found at i:12196555 original size:20 final size:21
Alignment explanation
Indices: 12196530--12196601 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
12196520 TCCTAATTTA
* *
12196530 CAATGCGAA-TACGTAAATCG
1 CAATGCGAATTAGGAAAATCG
*
12196550 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAGGAAAATCG
*
12196571 CAATGCGAATTTGGAAAATCG
1 CAATGCGAATTAGGAAAATCG
12196592 CAATGCGAAT
1 CAATGCGAAT
12196602 ATCTATTCTG
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 9 0.19
21 39 0.81
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
CAATGCGAATTAGGAAAATCG
Found at i:12196570 original size:21 final size:21
Alignment explanation
Indices: 12196544--12196601 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
12196534 GCGAATACGT
12196544 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
12196565 AAATCGCAATGCGAATTTGGA
1 AAATCGCAATGCGAATTTGGA
12196586 AAATCGCAATGCGAAT
1 AAATCGCAATGCGAAT
12196602 ATCTATTCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTGGA
Found at i:12198876 original size:20 final size:20
Alignment explanation
Indices: 12198846--12198900 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
12198836 AGACATTCAT
12198846 TTGACTATCGCAACGC-GAA
1 TTGACTATCGCAACGCGGAA
* *
12198865 TATGATTATCGCAACACGGAA
1 T-TGACTATCGCAACGCGGAA
12198886 TTGACTATCGCAACG
1 TTGACTATCGCAACG
12198901 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 25 0.83
21 4 0.13
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:12198931 original size:33 final size:34
Alignment explanation
Indices: 12198892--12198967 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
12198882 GGAATTGACT
*
12198892 ATCGCAACGAGAGAATCGCAATGTG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
12198925 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
12198959 ATCACAACG
1 ATCGCAACG
12198968 CGAACTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Done.