Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 137 of 150
Found at i:41291904 original size:4 final size:4
Alignment explanation
Indices: 41291895--41291920 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41291885 TATATCACCA
41291895 AATC AATC AATC AATC AATC AATC AA
1 AATC AATC AATC AATC AATC AATC AA
41291921 ACCAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
AATC
Found at i:41295107 original size:11 final size:11
Alignment explanation
Indices: 41295088--41295121 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
41295078 AAAAAGTTTA
41295088 TATTATTTTGG
1 TATTATTTTGG
*
41295099 TATT-TTTTTG
1 TATTATTTTGG
41295109 TATTATTTTGG
1 TATTATTTTGG
41295120 TA
1 TA
41295122 AAAACCCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (11 bp):
TATTATTTTGG
Found at i:41297109 original size:27 final size:26
Alignment explanation
Indices: 41297059--41297119 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
41297049 ACCAAAAATT
*
41297059 TATTTTAAAAATAAAAAACAAAAAAG
1 TATTTTAAAAATAAAAAACAAAAAAA
*
41297085 TATTTTAAAATTAAAAAA-ATTAAAAAA
1 TATTTTAAAAATAAAAAACA--AAAAAA
41297112 TATATTTA
1 TAT-TTTA
41297120 TTTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 17 0.57
27 8 0.27
28 4 0.13
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
TATTTTAAAAATAAAAAACAAAAAAA
Found at i:41298409 original size:31 final size:31
Alignment explanation
Indices: 41298374--41298438 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
41298364 TTAAAAACAT
41298374 AGTAACTTAAATAAAAACTTCCAAATAGTTC
1 AGTAACTTAAATAAAAACTTCCAAATAGTTC
* **
41298405 AGTAACTTAAATGAAAACTTTTAAATAGTTC
1 AGTAACTTAAATAAAAACTTCCAAATAGTTC
41298436 AGT
1 AGT
41298439 GACTACTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
AGTAACTTAAATAAAAACTTCCAAATAGTTC
Found at i:41299889 original size:4 final size:4
Alignment explanation
Indices: 41299880--41299904 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41299870 AAACAAGGGT
41299880 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
41299905 CCCAATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:41300668 original size:24 final size:24
Alignment explanation
Indices: 41300641--41300716 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
41300631 TCAAATATGG
*
41300641 AAAAAGAAAGAAAATAGAATATAT
1 AAAAAGAAAGAAAATAGAATATAA
* **
41300665 AAAAA-ATAGAAAATCA-AATATGG
1 AAAAAGAAAGAAAAT-AGAATATAA
*
41300688 AAAAAGAAACAAAATAGAATATAA
1 AAAAAGAAAGAAAATAGAATATAA
41300712 AAAAA
1 AAAAA
41300717 ATAAAGAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 19 0.45
24 23 0.55
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.14
Consensus pattern (24 bp):
AAAAAGAAAGAAAATAGAATATAA
Found at i:41300673 original size:47 final size:47
Alignment explanation
Indices: 41300621--41300768 Score: 226
Period size: 47 Copynumber: 3.1 Consensus size: 47
41300611 ATTTAATGGG
41300621 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
1 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
* * *
41300668 AAATAGAAAATCAAATATGGAAAAAGAAACAAAATAGAATATAAAAA
1 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
* * *
41300715 AAATAAAGAATCAAATATGGGAAAGGAAAGAAAATA-ACATATATAAA
1 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGA-ATATATAAA
41300762 AAATAGA
1 AAATAGA
41300769 TCATATTAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 1 0.01
47 89 0.99
ACGTcount: A:0.67, C:0.03, G:0.14, T:0.16
Consensus pattern (47 bp):
AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
Found at i:41300675 original size:23 final size:23
Alignment explanation
Indices: 41300641--41300719 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
41300631 TCAAATATGG
*
41300641 AAAAAGAA-AGAAAATAGAATAT
1 AAAAAAAATAGAAAATAGAATAT
*
41300663 ATAAAAAATAGAAAATCA-AATAT
1 AAAAAAAATAGAAAAT-AGAATAT
* *
41300686 GGAAAAAGAA-ACAAAATAGAATAT
1 --AAAAAAAATAGAAAATAGAATAT
41300710 AAAAAAAATA
1 AAAAAAAATA
41300720 AAGAATCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
22 13 0.29
23 14 0.31
24 12 0.27
25 6 0.13
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (23 bp):
AAAAAAAATAGAAAATAGAATAT
Found at i:41300731 original size:23 final size:22
Alignment explanation
Indices: 41300658--41300732 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 22
41300648 AAGAAAATAG
*
41300658 AATATATAAAAAATAGAAAATCA
1 AATATAAAAAAAATA-AAAATCA
*
41300681 AATATGGAAAAAGAAA-CAAAAT-A
1 AATAT--AAAAA-AAATAAAAATCA
41300704 GAATATAAAAAAAATAAAGAATCA
1 -AATATAAAAAAAATAAA-AATCA
41300728 AATAT
1 AATAT
41300733 GGGAAAGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
21 3 0.07
22 7 0.17
23 14 0.33
24 11 0.26
25 4 0.10
26 3 0.07
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (22 bp):
AATATAAAAAAAATAAAAATCA
Found at i:41312459 original size:18 final size:18
Alignment explanation
Indices: 41312433--41312472 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
41312423 ATAATTTGTG
*
41312433 ATAATTATACATTTAAAA-
1 ATAACTATA-ATTTAAAAT
41312451 ATAACTATAATTTAAAAT
1 ATAACTATAATTTAAAAT
41312469 ATAA
1 ATAA
41312473 GAAAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAACTATAATTTAAAAT
Found at i:41313473 original size:243 final size:240
Alignment explanation
Indices: 41313032--41313556 Score: 560
Period size: 243 Copynumber: 2.2 Consensus size: 240
41313022 TTAAAATATT
* *
41313032 AATGTGGGTTTAAAAATAACAT-TCAATAAATAATAAAACGTATGATTTGAAACTAATTAATAAT
1 AATGTGTGTTTAAAAATAACATAT-AATAAATAATAAAACGTATGACTTGAAACTAATTAATAAT
* * * *
41313096 AACGCATGAAATATGTACGTTATTAAAATGAAAAAAATTAGACTGAAATGTTTATTTTAGTGTTG
65 AACCCATAAAATATGTACGATATTAAAATGAAAAAAATTAGACTGAAATGTTTATATTAGTGTTG
* * *
41313161 TCATCATGAGTCAGTGTAAAGTTAACTTGTGACACCAGCTCAATCAAATGCATTATTAATACTAG
130 TCATCATAAGTCAGTGTAAAGTTAACTTGTGACACAAGCTCAATCAAATACATTATTAATAC-AG
* *
41313226 AAATCCTATCACACACGTATGCGCGTGGAAACTAAAAATATGGAAAATA
194 AAATCCTATCACACACGTATGCGCGTGGAAACCAAAAATA--GAAAACA
* ** * *
41313275 AATGTGTGTTTAAAAATAACATATATTAAATAATTGAATGTATGGCTTGAAACTAATTAATAATA
1 AATGTGTGTTTAAAAATAACATATAATAAATAATAAAACGTATGACTTGAAACTAATTAATAATA
* * ** *
41313340 ACCCATAAAATATGTATGATATTAAAAT-TAAAATTTTA-A-TTAAATTGTTTATCATT-GTGTT
66 ACCCATAAAATATGTACGATATTAAAATGAAAAAAATTAGACTGAAA-TGTTTAT-ATTAGTGTT
* * ** * *
41313401 GTTATCAATATTAAGTTAGTGTCGAGTTAACTTGTGACACAA-ATCCAATCAAGTACATTATTAA
129 GTCATC---A-TAAGTCAGTGTAAAGTTAACTTGTGACACAAGCT-CAATCAAATACATTATTAA
* ** * * * * *
41313465 TA-AGAAATCTTATCACAGGCGTATGTGTGTGGCAACCACAAATAGAACACA
189 TACAGAAATCCTATCACACACGTATGCGCGTGGAAACCAAAAATAGAAAACA
* *
41313516 AATGTGTGTTTAAAAATAATATATAATAAAAAATGAAAACG
1 AATGTGTGTTTAAAAATAACATATAATAAATAAT-AAAACG
41313557 AGAAACCACG
Statistics
Matches: 232, Mismatches: 41, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
240 4 0.02
241 54 0.23
242 12 0.05
243 114 0.49
244 3 0.01
245 45 0.19
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (240 bp):
AATGTGTGTTTAAAAATAACATATAATAAATAATAAAACGTATGACTTGAAACTAATTAATAATA
ACCCATAAAATATGTACGATATTAAAATGAAAAAAATTAGACTGAAATGTTTATATTAGTGTTGT
CATCATAAGTCAGTGTAAAGTTAACTTGTGACACAAGCTCAATCAAATACATTATTAATACAGAA
ATCCTATCACACACGTATGCGCGTGGAAACCAAAAATAGAAAACA
Found at i:41316817 original size:66 final size:66
Alignment explanation
Indices: 41316735--41316863 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
41316725 GAATCGGAAA
* * * *
41316735 GAATAAAACAAGCCGAAAAAGAATGATAAAGAT-GGGTGAATAAATCAAAACAGATAAAAAATAG
1 GAATAAAACAAACCGAAAAAGAAT-AAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATAG
41316799 AT
65 AT
41316801 GAATAAAACAAACCGAAAAAGAATAAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATA
1 GAATAAAACAAACCGAAAAAGAATAAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATA
41316864 TGGAGGAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 6 0.10
66 52 0.90
ACGTcount: A:0.63, C:0.08, G:0.16, T:0.13
Consensus pattern (66 bp):
GAATAAAACAAACCGAAAAAGAATAAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATAGA
T
Found at i:41318514 original size:18 final size:19
Alignment explanation
Indices: 41318491--41318526 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41318481 GTTTATTCAA
*
41318491 AATTTT-ATGTCAAACAAT
1 AATTTTCATGCCAAACAAT
41318509 AATTTTCATGCCAAACAA
1 AATTTTCATGCCAAACAA
41318527 GTTCCACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (19 bp):
AATTTTCATGCCAAACAAT
Found at i:41319726 original size:30 final size:30
Alignment explanation
Indices: 41319671--41319729 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
41319661 CTTAACAAAC
* *
41319671 AAATGTCTCTAAAATATTAGCAAAATTAAT
1 AAATGTCTCTAAAATAATAACAAAATTAAT
* *
41319701 AAATGTCTTTAAAATAATAATAAAATTAA
1 AAATGTCTCTAAAATAATAACAAAATTAA
41319730 CAATAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATGTCTCTAAAATAATAACAAAATTAAT
Found at i:41321852 original size:17 final size:17
Alignment explanation
Indices: 41321799--41321854 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
41321789 AATCAGATAT
41321799 ATATATATACAAAACAA
1 ATATATATACAAAACAA
* *
41321816 AAATGTA-ACAAAATAGCAA
1 ATATATATAC-AAA-A-CAA
41321835 ATATATATACAAAACAA
1 ATATATATACAAAACAA
41321852 ATA
1 ATA
41321855 CGTAAGAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 2 0.06
17 14 0.45
18 2 0.06
19 11 0.35
20 2 0.06
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.21
Consensus pattern (17 bp):
ATATATATACAAAACAA
Found at i:41324384 original size:44 final size:45
Alignment explanation
Indices: 41324327--41324416 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 45
41324317 TTAAAAATTT
* * *
41324327 TTTTTTTGTCAGAATTAGATATCA-ATATACGAAA-AAATAAAAAA
1 TTTTCTTGTCAGAATCAAATATCAGA-ATACGAAACAAATAAAAAA
*
41324371 TTTTCTTGTCAGAATCAAATATCAGAATACGAAACAAGTAAAAAA
1 TTTTCTTGTCAGAATCAAATATCAGAATACGAAACAAATAAAAAA
41324416 T
1 T
41324417 ATTTTTTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 29 0.73
45 11 0.28
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (45 bp):
TTTTCTTGTCAGAATCAAATATCAGAATACGAAACAAATAAAAAA
Found at i:41324480 original size:96 final size:96
Alignment explanation
Indices: 41324371--41324569 Score: 238
Period size: 96 Copynumber: 2.1 Consensus size: 96
41324361 AAATAAAAAA
* * * ** * * *
41324371 TTTTCTTGTCAGAATCAAATATCAGAATACGAAACAAGTAAAAAATATTTTTTTTGGTGTTGGTC
1 TTTT-TTGTCAGAATCAAATATCAGAATACGAAAAAAATAAAAAA-AATTTTTGAGGTGCTAGCC
*
41324436 TGTCAATGGCCGACACCTAGTACAA-TTAATTG
64 TGTCAATGGCCGACACCCAGTACAATTTAATTG
** *
41324468 TTTTTTGTCAGAATCAGGTATTAGAATACGAAAAAAATAAAAAAAATTTTTGAGGTGCTAGCCTG
1 TTTTTTGTCAGAATCAAATATCAGAATACGAAAAAAATAAAAAAAATTTTTGAGGTGCTAGCCTG
* * *
41324533 TCAATGGTCGGCACCCAGTACAATTTAATTT
66 TCAATGGCCGACACCCAGTACAATTTAATTG
41324564 TTTTTT
1 TTTTTT
41324570 TCGTGTCAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
95 35 0.41
96 47 0.55
97 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (96 bp):
TTTTTTGTCAGAATCAAATATCAGAATACGAAAAAAATAAAAAAAATTTTTGAGGTGCTAGCCTG
TCAATGGCCGACACCCAGTACAATTTAATTG
Found at i:41324969 original size:100 final size:100
Alignment explanation
Indices: 41324816--41325194 Score: 373
Period size: 100 Copynumber: 3.7 Consensus size: 100
41324806 CACGAAATTT
* * * *
41324816 TTTTTTTAAATTGTACTGGGTGTCGACTATTGACAGGCCAGCACCAAATTTTTTTA-TTTTTTCG
1 TTTTTTTAAATTGTACTGGATGCCGGCCATTGACAGGCCAGCACCAAATTTTTTTACTTTTTTCG
* *
41324880 TATTCTGATATCTAATTTTGACACGAAAAAAAAGAA
66 TATACTGATATCTAATTCTGACACGAAAAAAAA-AA
* * *
41324916 TTTTTTTAAATTGTATTGGATGCCGGCCATTGATAGGCCTGCACTCAAATTTTTTTTTTTTACTT
1 TTTTTTTAAATTGTACTGGATGCCGGCCATTGACAGGCCAGCAC-CAAA-----TTTTTTTACTT
41324981 TTTTCGTATACTGATATCTAATTCTGACACG-------AAA
60 TTTTCGTATACTGATATCTAATTCTGACACGAAAAAAAAAA
*
41325015 TTTTTTTAAAATTGTACTAGG-TGCCGGCCATTGAAAGGCCAGCACCAAAAATTTTTTTATTACT
1 TTTTTTT-AAATTGTACT-GGATGCCGGCCATTGACAGGCCAGCACC--AAA--TTTTT-TTACT
*
41325079 TTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAATAAA
59 TTTTTCGTATACTGATATCTAATTCTGACACG-AAAAAAA-AAA
* * * *
41325123 TTTTTTTTAAATTGTACT-GAGTGTCTGCCATTGACAGGCCAGCACCTAATTTTTTTTTCCTTTT
1 -TTTTTTTAAATTGTACTGGA-TGCCGGCCATTGACAGGCCAGCACC-AA-ATTTTTTTACTTTT
41325187 TTCGTATA
62 TTCGTATA
41325195 TCAATATTAT
Statistics
Matches: 235, Mismatches: 19, Indels: 45
0.79 0.06 0.15
Matches are distributed among these distances:
98 7 0.03
99 46 0.20
100 69 0.29
101 9 0.04
105 15 0.06
106 14 0.06
107 33 0.14
108 35 0.15
109 7 0.03
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (100 bp):
TTTTTTTAAATTGTACTGGATGCCGGCCATTGACAGGCCAGCACCAAATTTTTTTACTTTTTTCG
TATACTGATATCTAATTCTGACACGAAAAAAAAAA
Found at i:41325092 original size:99 final size:99
Alignment explanation
Indices: 41324914--41325113 Score: 305
Period size: 99 Copynumber: 2.0 Consensus size: 99
41324904 GAAAAAAAAG
* * * ** *
41324914 AATTTTTTTAAATTGTATTGGATGCCGGCCATTGATAGGCCTGCACTCAAATTTTTTTTTTTTAC
1 AATTTTTTTAAATTGTATAGGATGCCGGCCATTGAAAGGCCAGCACTCAAAAATTTTTTTATTAC
41324979 TTTTTTCGTATACTGATATCTAATTCTGACACGA
66 TTTTTTCGTATACTGATATCTAATTCTGACACGA
41325013 AATTTTTTTAAAATTGTACTAGG-TGCCGGCCATTGAAAGGCCAGCAC-CAAAAATTTTTTTATT
1 AATTTTTTT-AAATTGTA-TAGGATGCCGGCCATTGAAAGGCCAGCACTCAAAAATTTTTTTATT
*
41325076 ACTTTTTTCGTATACTGATATCTGATTCTGACACGA
64 ACTTTTTTCGTATACTGATATCTAATTCTGACACGA
41325112 AA
1 AA
41325114 AAAAATAAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
99 59 0.64
100 30 0.33
101 3 0.03
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (99 bp):
AATTTTTTTAAATTGTATAGGATGCCGGCCATTGAAAGGCCAGCACTCAAAAATTTTTTTATTAC
TTTTTTCGTATACTGATATCTAATTCTGACACGA
Found at i:41330687 original size:19 final size:20
Alignment explanation
Indices: 41330653--41330693 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
41330643 TTACAAAATT
*
41330653 TAAAATAATTTTTTAATAAA
1 TAAAATAATATTTTAATAAA
*
41330673 TAAAAT-ATATTTTAATTAA
1 TAAAATAATATTTTAATAAA
41330692 TA
1 TA
41330694 TATACAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATAATATTTTAATAAA
Found at i:41344697 original size:7 final size:7
Alignment explanation
Indices: 41344682--41344716 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
41344672 AATAATAGAA
41344682 AAATTAT
1 AAATTAT
*
41344689 AAATGAT
1 AAATTAT
41344696 AAATTAT
1 AAATTAT
41344703 AAATTAT
1 AAATTAT
41344710 AAATTAT
1 AAATTAT
41344717 TAAAAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (7 bp):
AAATTAT
Found at i:41357318 original size:12 final size:12
Alignment explanation
Indices: 41357301--41357334 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
41357291 TGACTCAGCC
41357301 ATATTAATTTTT
1 ATATTAATTTTT
*
41357313 ATATTATTTTTT
1 ATATTAATTTTT
41357325 ATA-TAATTTT
1 ATATTAATTTT
41357335 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:41357575 original size:3 final size:3
Alignment explanation
Indices: 41357558--41357629 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
41357548 ATAAGGAGAA
* *
41357558 AAT AAT AAG AA- AAT AAT ATT AA- AA- ACAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
41357601 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41357630 ACAAAAAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
2 5 0.08
3 57 0.90
4 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:41368320 original size:31 final size:31
Alignment explanation
Indices: 41368284--41368344 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
41368274 ATTTGGCCCA
41368284 TGAACTATTCGAA-AGTTTTCATTTAAGTCAT
1 TGAACTATTC-AAGAGTTTTCATTTAAGTCAT
*
41368315 TGAACTATTCAAGAGTTTTTATTTAAGTCA
1 TGAACTATTCAAGAGTTTTCATTTAAGTCA
41368345 CTGGGCTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (31 bp):
TGAACTATTCAAGAGTTTTCATTTAAGTCAT
Found at i:41368947 original size:16 final size:15
Alignment explanation
Indices: 41368909--41368952 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
41368899 TGATTCAAAC
41368909 TCGAAATAATTTGAA
1 TCGAAATAATTTGAA
* *
41368924 TCCAAAATCAATTTTAA
1 T-CGAAAT-AATTTGAA
41368941 TCGAAATAATTT
1 TCGAAATAATTT
41368953 AAAAACTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.25
16 10 0.42
17 8 0.33
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (15 bp):
TCGAAATAATTTGAA
Found at i:41377519 original size:16 final size:16
Alignment explanation
Indices: 41377500--41377538 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
41377490 GGTTGCAATA
*
41377500 GAATAGGACTGTAATG
1 GAATAGAACTGTAATG
*
41377516 GAATAAAACTGTAATG
1 GAATAGAACTGTAATG
41377532 GAATAGA
1 GAATAGA
41377539 GTTGTAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (16 bp):
GAATAGAACTGTAATG
Found at i:41377627 original size:34 final size:35
Alignment explanation
Indices: 41377583--41377649 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41377573 CAATAAAATA
*
41377583 TTTTCCATAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCATAAAATGATTTACTGGAAAATATTTTAC
*
41377617 TTTTCTATAAAATGATTTACTGGAAAATATTTT
1 TTTTCCATAAAATGATTTACTGGAAAATATTTT
41377650 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCATAAAATGATTTACTGGAAAATATTTTAC
Found at i:41377761 original size:20 final size:20
Alignment explanation
Indices: 41377736--41377774 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41377726 GTTTTTACAT
41377736 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
41377756 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
41377775 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:41384194 original size:19 final size:19
Alignment explanation
Indices: 41384172--41384290 Score: 67
Period size: 19 Copynumber: 6.5 Consensus size: 19
41384162 TGGTACCTAC
41384172 TATTATTTTATTCTTATAT
1 TATTATTTTATTCTTATAT
* *
41384191 TATTATTTTACAATACTCAT-T
1 TATTATTTT---ATTCTTATAT
* *
41384212 TCA-AATTTTA-TC-TATGT
1 T-ATTATTTTATTCTTATAT
* *
41384229 T-TTA-TTTATTTTTATGT
1 TATTATTTTATTCTTATAT
*
41384246 AATTATTTTA-T-TT-TAT
1 TATTATTTTATTCTTATAT
*
41384262 TATTATTTTGTTCTTATAT
1 TATTATTTTATTCTTATAT
41384281 TATTATTTTA
1 TATTATTTTA
41384291 ACCATTTTGC
Statistics
Matches: 75, Mismatches: 12, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
15 4 0.05
16 14 0.19
17 11 0.15
18 7 0.09
19 25 0.33
21 7 0.09
22 7 0.09
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.65
Consensus pattern (19 bp):
TATTATTTTATTCTTATAT
Found at i:41385578 original size:30 final size:31
Alignment explanation
Indices: 41385510--41385578 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 31
41385500 CTTAACAACC
* *
41385510 TAATGACTTAAATAAAAACTTTTGAATAGTT
1 TAATGACTTAAATAAAAACGTTTGAATAATT
* * * *
41385541 CAGTGACTTCAATGAAAA-GTTTGAATAATT
1 TAATGACTTAAATAAAAACGTTTGAATAATT
41385571 TAATGACT
1 TAATGACT
41385579 ATTTTGTAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (31 bp):
TAATGACTTAAATAAAAACGTTTGAATAATT
Found at i:41387653 original size:20 final size:21
Alignment explanation
Indices: 41387604--41387654 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
41387594 TTAAAAGAAT
41387604 ATATAAAAATATTAAATAAAA
1 ATATAAAAATATTAAATAAAA
** *
41387625 A-ATGTAAAT-TTTAATAAAA
1 ATATAAAAATATTAAATAAAA
41387644 ATATAAAAATA
1 ATATAAAAATA
41387655 CTCTGATCCA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
19 10 0.43
20 12 0.52
21 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
ATATAAAAATATTAAATAAAA
Found at i:41388906 original size:43 final size:43
Alignment explanation
Indices: 41388750--41388905 Score: 226
Period size: 43 Copynumber: 3.6 Consensus size: 43
41388740 AAAAATGCCA
*
41388750 CTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAATAAACTCCG
1 CTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAATAAACGCCG
* *
41388793 CTAAAGATCATGTTCTTTAGCGGCACTAAGGAAATAAACGCTG
1 CTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAATAAACGCCG
*
41388836 CTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA-AAACGCCG
1 CTAAAGATCATGTTCTTTAGCGGCGCTAAGGAA-ATAAACGCCG
* *
41388879 CTAAA-AGTAATGTTCTATAGCGGCGCT
1 CTAAAGA-TCATGTTCTTTAGCGGCGCT
41388906 TGGTCACAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
42 1 0.01
43 101 0.98
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (43 bp):
CTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAATAAACGCCG
Found at i:41389381 original size:21 final size:21
Alignment explanation
Indices: 41389357--41389422 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
41389347 TCTATCGCTA
*
41389357 CTTCTCTCGCTGCGGCCTCTG
1 CTTCTCTCGCTGCAGCCTCTG
*
41389378 CTTCTCTCGCTGTAGCCTCTG
1 CTTCTCTCGCTGCAGCCTCTG
* *
41389399 CTTCCCTCGCTATCA-CCTCTG
1 CTTCTCTCGCT-GCAGCCTCTG
41389420 CTT
1 CTT
41389423 TAAGTTGTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 38 0.97
22 1 0.03
ACGTcount: A:0.05, C:0.42, G:0.17, T:0.36
Consensus pattern (21 bp):
CTTCTCTCGCTGCAGCCTCTG
Found at i:41397046 original size:5 final size:5
Alignment explanation
Indices: 41397021--41397092 Score: 53
Period size: 5 Copynumber: 14.4 Consensus size: 5
41397011 TTACTTTATT
*
41397021 TAATA T-ATA TATATAA TAATA TAATA TAAT- TAATA TATTATA TTATA
1 TAATA TAATA TA-AT-A TAATA TAATA TAATA TAATA TA--ATA TAATA
* *
41397068 TTATA TTATA TAATA -AA-A TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
41397093 CATAACATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
3 1 0.02
4 12 0.21
5 33 0.58
6 4 0.07
7 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
TAATA
Found at i:41397067 original size:24 final size:22
Alignment explanation
Indices: 41397021--41397092 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 22
41397011 TTACTTTATT
41397021 TAATATA-TATATATAATAATA
1 TAATATATTATATATAATAATA
* *
41397042 TAATATAATTAATATATTATATTA
1 TAATAT-ATT-ATATATAATAATA
* *
41397066 TATTATA-T-TATATAATAAAA
1 TAATATATTATATATAATAATA
41397086 TAATATA
1 TAATATA
41397093 CATAACATAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
20 15 0.37
21 6 0.15
22 2 0.05
23 2 0.05
24 16 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATATTATATATAATAATA
Found at i:41397402 original size:9 final size:9
Alignment explanation
Indices: 41397388--41397998 Score: 192
Period size: 9 Copynumber: 68.2 Consensus size: 9
41397378 GGTCATTACA
41397388 TAAGTTATG
1 TAAGTTATG
41397397 TAAG-T-TG
1 TAAGTTATG
41397404 TAAGTTATG
1 TAAGTTATG
41397413 TAAGTTATG
1 TAAGTTATG
*
41397422 TATA-ATAT-
1 TA-AGTTATG
41397430 TAA-TTAAT-
1 TAAGTT-ATG
41397438 TAAGTTATG
1 TAAGTTATG
*
41397447 TAATTTATG
1 TAAGTTATG
*
41397456 TATAATATTAATG
1 --TAA-GTT-ATG
41397469 TAAGTTATG
1 TAAGTTATG
*
41397478 TAATTTATG
1 TAAGTTATG
*
41397487 -AA-TAAT-
1 TAAGTTATG
***
41397493 TAAAAAAATG
1 T-AAGTTATG
41397503 TAAGTTATG
1 TAAGTTATG
41397512 TAAG-T-TG
1 TAAGTTATG
41397519 TAAGTTATG
1 TAAGTTATG
* *
41397528 TAATTTAAG
1 TAAGTTATG
*
41397537 -AA-TAAT-
1 TAAGTTATG
***
41397543 TAAAAAAATG
1 T-AAGTTATG
41397553 TAAGTTATG
1 TAAGTTATG
41397562 TAAG-T-TG
1 TAAGTTATG
41397569 TAAGTTATG
1 TAAGTTATG
41397578 TAAGTTATG
1 TAAGTTATG
*
41397587 TATA-ATAT-
1 TA-AGTTATG
41397595 TAA-TTAAT-
1 TAAGTT-ATG
41397603 TAAGTTATG
1 TAAGTTATG
*
41397612 TAATTTATG
1 TAAGTTATG
*
41397621 TATTGCATTAATG
1 TA-AG--TT-ATG
41397634 TAAGTTATG
1 TAAGTTATG
*
41397643 TAATTTATG
1 TAAGTTATG
*
41397652 -AA-TAAT-
1 TAAGTTATG
***
41397658 TAAAAAAATG
1 T-AAGTTATG
41397668 TAAGTTATG
1 TAAGTTATG
41397677 TAAG-T-TG
1 TAAGTTATG
41397684 TAAGTTATG
1 TAAGTTATG
41397693 TAAGTTATG
1 TAAGTTATG
*
41397702 TATA-ATAT-
1 TA-AGTTATG
41397710 TAA-TTAAT-
1 TAAGTT-ATG
41397718 TAAGTTATG
1 TAAGTTATG
*
41397727 TAATTTATG
1 TAAGTTATG
*
41397736 TATAATATTAATG
1 --TAA-GTT-ATG
41397749 TAAGTTATG
1 TAAGTTATG
*
41397758 TAATTTATG
1 TAAGTTATG
*
41397767 -AA-TAAT-
1 TAAGTTATG
***
41397773 TAAAAAATG
1 TAAGTTATG
41397782 TAAGTTATG
1 TAAGTTATG
41397791 TAAG-T-TG
1 TAAGTTATG
41397798 TAAGTTATG
1 TAAGTTATG
41397807 TAAGTTATG
1 TAAGTTATG
*
41397816 TATA-ATAT-
1 TA-AGTTATG
41397824 TAA-TTAAT-
1 TAAGTT-ATG
*
41397832 TAGGTTATG
1 TAAGTTATG
*
41397841 TAATTTATG
1 TAAGTTATG
*
41397850 TATAATATTAATG
1 --TAA-GTT-ATG
41397863 TAAGTTATG
1 TAAGTTATG
*
41397872 TATA-ATAT-
1 TA-AGTTATG
41397880 TAA-TTAAT-
1 TAAGTT-ATG
41397888 TAAGTTATG
1 TAAGTTATG
*
41397897 TAATTTATG
1 TAAGTTATG
*
41397906 TATAATATTAATG
1 --TAA-GTT-ATG
41397919 TAAGTTATG
1 TAAGTTATG
*
41397928 TAATTTATG
1 TAAGTTATG
*
41397937 TATTAATTAAT-
1 TA--AGTT-ATG
41397948 TAAGTTATG
1 TAAGTTATG
*
41397957 TAATTTATG
1 TAAGTTATG
*
41397966 TATAATATTAATG
1 --TAA-GTT-ATG
41397979 TAAGTTATG
1 TAAGTTATG
41397988 TAAGTTATG
1 TAAGTTATG
41397997 TA
1 TA
41397999 TAATATTAAT
Statistics
Matches: 469, Mismatches: 60, Indels: 146
0.69 0.09 0.22
Matches are distributed among these distances:
7 53 0.11
8 73 0.16
9 253 0.54
10 20 0.04
11 35 0.07
12 15 0.03
13 20 0.04
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:41397409 original size:16 final size:16
Alignment explanation
Indices: 41397388--41397418 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41397378 GGTCATTACA
41397388 TAAGTTATGTAAGTTG
1 TAAGTTATGTAAGTTG
41397404 TAAGTTATGTAAGTT
1 TAAGTTATGTAAGTT
41397419 ATGTATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (16 bp):
TAAGTTATGTAAGTTG
Found at i:41397447 original size:34 final size:34
Alignment explanation
Indices: 41397404--41398023 Score: 219
Period size: 34 Copynumber: 18.3 Consensus size: 34
41397394 ATGTAAGTTG
41397404 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* *
41397438 TAAGTTATGTAATTTATGTATAATATTAA-T--G
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* * * **
41397469 TAAGTTATGTAATTTATGAATAAT-TAAAAAAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
*
41397502 GTAAGTTATGTAAG-T-TGTA-AGTTATGTAATTTAA-
1 -TAAGTTATGTAAGTTATGTATA-ATAT-TAA-TTAAT
* * *** * *
41397536 GAA-TAAT-TAAAAAAATGTA-AGTTATGTAAGTT--G
1 TAAGTTATGT-AAGTTATGTATA-ATAT-TAA-TTAAT
41397569 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* **
41397603 TAAGTTATGTAATTTATG--T-AT-TGCATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* * * **
41397633 GTAAGTTATGTAATTTATGAATAAT-TAAAAAAAT
1 -TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* *
41397667 GTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGT-ATAATAT
1 -TAAGTTATGTAAG-T-TATG-TA--TAA--TAT-TAATTA-AT
* *
41397710 TAA-TTAAT-TAAGTTATGTAATTTATGTATAATATTAAT
1 TAAGTT-ATGTAAGTTATGT-A--TA-ATATTA-ATTAAT
* * **
41397748 GTAAGTTATGTAATTTATGAAT-A-ATTAAAAAAT
1 -TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* *
41397781 GTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGT-ATAATAT
1 -TAAGTTATGTAAG-T-TATG-TA--TAA--TAT-TAATTA-AT
*
41397824 TAA-TTAAT-TAGGTTATG--TAAT-TT-ATGT-A-
1 TAAGTT-ATGTAAGTTATGTATAATATTAAT-TAAT
*
41397852 TAATATTAATGTAAGTTATGTATAATATTAATTAAT
1 TAA-GTT-ATGTAAGTTATGTATAATATTAATTAAT
* *
41397888 TAAGTTATGTAATTTATGTATAATATTAA-T--G
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
*
41397919 TAAGTTATGTAA--T-T-TAT-GTATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* *
41397948 TAAGTTATGTAATTTATGTATAATATTAA-T--G
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
41397979 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
41398013 TAAGTTATGTA
1 TAAGTTATGTA
41398024 TAATACTAAT
Statistics
Matches: 450, Mismatches: 64, Indels: 144
0.68 0.10 0.22
Matches are distributed among these distances:
26 6 0.01
27 4 0.01
28 4 0.01
29 14 0.03
30 18 0.04
31 95 0.21
32 15 0.03
33 37 0.08
34 157 0.35
35 13 0.03
36 7 0.02
37 2 0.00
38 7 0.02
39 23 0.05
40 12 0.03
41 12 0.03
42 19 0.04
43 5 0.01
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (34 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAAT
Found at i:41397472 original size:56 final size:56
Alignment explanation
Indices: 41397410--41398051 Score: 532
Period size: 56 Copynumber: 11.4 Consensus size: 56
41397400 GTTGTAAGTT
41397410 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* * *** * **
41397466 ATGTAAGTTATGTA-ATTTATGAA-TAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTT-
1 ATGTAAGTTATGTATA-ATATTAATTAATT-AAGTTATGTAATTTATGT-A-TAAT-A-TTA
* * * * ** * *
41397525 ATGTAATTTAAGAATAAT-TAAAAAAATGTAAGTTATGTAA-GT-TG--TAA-GTT-
1 ATGTAAGTTATGTATAATATTAATTAAT-TAAGTTATGTAATTTATGTATAATATTA
***
41397575 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* * *** * **
41397631 ATGTAAGTTATGTA-ATTTATGAA-TAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTT-
1 ATGTAAGTTATGTATA-ATATTAATTAATT-AAGTTATGTAATTTATGT-A-TAAT-A-TTA
41397690 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* * *** * **
41397746 ATGTAAGTTATGTA-ATTTATGAA-TAATTAAAAAATGTAAGTTATGTAAGTTGTAAGTT-
1 ATGTAAGTTATGTATA-ATATTAATTAATTAAGTTATGTAATTTATGT-A-TAAT-A-TTA
*
41397804 ATGTAAGTTATGTATAATATTAATTAATTAGGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
41397860 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
*
41397916 ATGTAAGTTATGTAATTTATGTATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGT-A--TA-ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
* * * *
41397976 ATGTAAGTTATGTA-AGTTATGT-ATAATATTAA-TTAAT-TAAGTTATGTATAATACTA
1 ATGTAAGTTATGTATA-ATAT-TAATTA-ATTAAGTT-ATGTAATTTATGTATAATATTA
*
41398032 ATGTAAGTTATGTATTATAT
1 ATGTAAGTTATGTATAATAT
41398052 AATAACAACG
Statistics
Matches: 473, Mismatches: 72, Indels: 82
0.75 0.11 0.13
Matches are distributed among these distances:
50 29 0.06
51 7 0.01
52 2 0.00
53 1 0.00
54 1 0.00
55 38 0.08
56 199 0.42
57 19 0.04
58 31 0.07
59 82 0.17
60 64 0.14
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (56 bp):
ATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTA
Found at i:41397522 original size:16 final size:16
Alignment explanation
Indices: 41397501--41397583 Score: 73
Period size: 16 Copynumber: 5.1 Consensus size: 16
41397491 ATTAAAAAAA
41397501 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41397517 TGTAAGTTATGTAA-T
1 TGTAAGTTATGTAAGT
* **
41397532 T-TAAGAATAAT-TAAAAAAA
1 TGTAAG--TTATGT---AAGT
41397551 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41397567 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41397583 T
1 T
41397584 ATGTATAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
14 4 0.07
15 3 0.06
16 36 0.67
18 5 0.09
19 2 0.04
20 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.41
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:41397564 original size:165 final size:165
Alignment explanation
Indices: 41397388--41397695 Score: 589
Period size: 165 Copynumber: 1.9 Consensus size: 165
41397378 GGTCATTACA
41397388 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTT
*
41397453 ATGTATAATATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
66 ATGTATAACATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
41397518 GTAAGTTATGTAATTTAAGAATAATTAAAAAAATG
131 GTAAGTTATGTAATTTAAGAATAATTAAAAAAATG
41397553 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTT
1 TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTT
**
41397618 ATGTATTGCATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
66 ATGTATAACATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
41397683 GTAAGTTATGTAA
131 GTAAGTTATGTAA
41397696 GTTATGTATA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 140 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.43
Consensus pattern (165 bp):
TAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTT
ATGTATAACATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
GTAAGTTATGTAATTTAAGAATAATTAAAAAAATG
Found at i:41397636 original size:115 final size:114
Alignment explanation
Indices: 41397517--41397990 Score: 690
Period size: 115 Copynumber: 4.1 Consensus size: 114
41397507 TTATGTAAGT
41397517 TGTAAGTTATGTAATTTAAGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAG
1 TGTAAGTTATGTAATTTAAGAATAATT-AAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAG
***
41397582 TTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAA
65 TTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
41397632 TGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAG
1 TGTAAGTTATGTAATTTAAGAATAATT-AAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAG
41397697 TTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
65 TTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
41397747 TGTAAGTTATGTAATTTATGAATAATTAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 TGTAAGTTATGTAATTTAAGAATAATTAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
*
41397812 TATGTATAATATTAATTAATTAGGTTATGTAATTTATGTATAATATTAA
66 TATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
* *** * **
41397861 TGTAAGTTATGTATAATATT-A-ATTAATTAAGTTATGTAATTTATGT-A-TAAT-A-TTAATGT
1 TGTAAGTTATG--TAAT-TTAAGAATAATTAAAAAATGTAAGTTATGTAAGTTGTAAGTT-ATGT
*
41397920 AAGTTATGTAATTTATGTATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
62 AAGTTATGT-A--TA-ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
41397977 TGTAAGTTATGTAA
1 TGTAAGTTATGTAA
41397991 GTTATGTATA
Statistics
Matches: 336, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
111 2 0.01
112 14 0.04
113 3 0.01
114 101 0.30
115 160 0.48
116 54 0.16
117 2 0.01
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (114 bp):
TGTAAGTTATGTAATTTAAGAATAATTAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
TATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
Found at i:41397687 original size:16 final size:16
Alignment explanation
Indices: 41397666--41397698 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41397656 ATTAAAAAAA
41397666 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41397682 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41397698 T
1 T
41397699 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:41397801 original size:16 final size:16
Alignment explanation
Indices: 41397780--41397812 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41397770 AATTAAAAAA
41397780 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41397796 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
41397812 T
1 T
41397813 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:41397870 original size:22 final size:22
Alignment explanation
Indices: 41397838--41397883 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
41397828 TAATTAGGTT
*
41397838 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
41397860 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
41397882 AT
1 AT
41397884 TAATTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:41397919 original size:22 final size:21
Alignment explanation
Indices: 41397892--41397989 Score: 82
Period size: 22 Copynumber: 4.8 Consensus size: 21
41397882 ATTAATTAAG
41397892 TTATGTAATTTATGTATAATA
1 TTATGTAATTTATGTATAATA
*
41397913 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAATTTATGTATAATA
* *
41397932 TTATGT-ATTAAT-TAATTAA-G
1 TTATGTAATTTATGT-A-TAATA
41397952 TTATGTAATTTATGTATAATA
1 TTATGTAATTTATGTATAATA
*
41397973 TTAATGTAAGTTATGTA
1 TT-ATGTAATTTATGTA
41397990 AGTTATGTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
17 4 0.07
18 4 0.07
19 2 0.03
20 16 0.26
21 10 0.16
22 25 0.41
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
TTATGTAATTTATGTATAATA
Found at i:41397976 original size:116 final size:116
Alignment explanation
Indices: 41397592--41398045 Score: 434
Period size: 114 Copynumber: 3.9 Consensus size: 116
41397582 TTATGTATAA
*** ** *
41397592 TATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAATGTAAGTTATGTAATTTATGAATAA
1 TATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGATATGTATAA
* ** ** * * *
41397657 T-TAAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGT-A--TA-A
66 TATTAATTAAT-TAAGTTATGT-A-TAAT-ACTAATGTAAGTTATGTAATTTATG
** *
41397707 TATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGAAT-A
1 TATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGATATGTATAA
** ** * * *
41397771 -ATTAAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGT-A--TA-A
66 TATTAATTAAT-TAAGTTATGT-A-TAAT-ACTAATGTAAGTTATGTAATTTATG
*
41397821 TATTAATTAATTAGGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTATA-ATAT-TA-A
1 TATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTA-AGATATGTATA
* * *
41397883 TTAATTAAGTT-ATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATG
65 AT-ATTAA-TTAAT-TAAGTTATGTATAATACTAATGTAAGTTATGTAATTTATG
*
41397937 TATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGTTATGTATAA
1 TATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGATATGTATAA
41398002 TATTAATTAATTAAGTTATGTATAATACTAATGTAAGTTATGTA
66 TATTAATTAATTAAGTTATGTATAATACTAATGTAAGTTATGTA
41398046 TTATATAATA
Statistics
Matches: 304, Mismatches: 21, Indels: 27
0.86 0.06 0.08
Matches are distributed among these distances:
112 15 0.05
113 4 0.01
114 105 0.35
115 81 0.27
116 88 0.29
117 9 0.03
118 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (116 bp):
TATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAAGATATGTATAA
TATTAATTAATTAAGTTATGTATAATACTAATGTAAGTTATGTAATTTATG
Found at i:41398016 original size:25 final size:29
Alignment explanation
Indices: 41397409--41398037 Score: 211
Period size: 25 Copynumber: 22.0 Consensus size: 29
41397399 AGTTGTAAGT
*
41397409 TATGTAAGTTATGTATAATATTAATTAATTAA
1 TATGTAAGTTATGTATAATATTAA-T--GTAA
*
41397441 GTTATGTAATTTATGTATAATATTAATGTAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
* * *
41397472 GTTATGTAATTTATGAAT-A-ATTAA--AAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
* *
41397499 AATGTAAGTTATGTA-AGT-TGTAA-GT--
1 TATGTAAGTTATGTATAATAT-TAATGTAA
* * * *
41397524 TATGTAATTTAAGAAT-A-ATTAA--AAA
1 TATGTAAGTTATGTATAATATTAATGTAA
* *
41397549 AATGTAAGTTATGTA-AGT-TGTAA-GT--
1 TATGTAAGTTATGTATAATAT-TAATGTAA
*
41397574 TATGTAAGTTATGTATAATATTAATTAATTAA
1 TATGTAAGTTATGTATAATATTAA-T--GTAA
* ***
41397606 GTTATGTAATTTATGTATTGCATTAATGTAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
* * *
41397637 GTTATGTAATTTATGAAT-A-ATTAA--AAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
* *
41397664 AATGTAAGTTATGTA-AGT-TGTAA-GT--
1 TATGTAAGTTATGTATAATAT-TAATGTAA
*
41397689 TATGTAAGTTATGTATAATATTAATTAATTAA
1 TATGTAAGTTATGTATAATATTAA-T--GTAA
*
41397721 GTTATGTAATTTATGTATAATATTAATGTAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
* *
41397752 GTTATGTAATTTATGAAT-A-ATTAA---AA
1 --TATGTAAGTTATGTATAATATTAATGTAA
* *
41397778 AATGTAAGTTATGTA-AGT-TGTAA-GT--
1 TATGTAAGTTATGTATAATAT-TAATGTAA
41397803 TATGTAAGTTATGTATAATATTAAT-T-A
1 TATGTAAGTTATGTATAATATTAATGTAA
* * * * *
41397830 -AT-TAGGTTATGTAATTTATGTATAATATTA
1 TATGTAAGTTATGT-A-TAATAT-TAATGTAA
*
41397860 -ATGTAAGTTATGTATAATATTAATTAATTAA
1 TATGTAAGTTATGTATAATATTAA-T--GTAA
*
41397891 GTTATGTAATTTATGTATAATATTAATGTAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
* *
41397922 GTTATGTAATTTATGTATTA-ATTAAT-TAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
*
41397951 GTTATGTAATTTATGTATAATATTAATGTAA
1 --TATGTAAGTTATGTATAATATTAATGTAA
41397982 GTTATGTAAGTTATGTATAATATTAAT-T-A
1 --TATGTAAGTTATGTATAATATTAATGTAA
*
41398011 -AT-TAAGTTATGTATAATACTAATGTAA
1 TATGTAAGTTATGTATAATATTAATGTAA
41398038 GTTATGTATT
Statistics
Matches: 471, Mismatches: 63, Indels: 129
0.71 0.10 0.19
Matches are distributed among these distances:
24 16 0.03
25 124 0.26
26 33 0.07
27 12 0.03
28 7 0.01
29 44 0.09
30 21 0.04
31 122 0.26
33 4 0.01
34 88 0.19
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (29 bp):
TATGTAAGTTATGTATAATATTAATGTAA
Found at i:41398041 original size:22 final size:21
Alignment explanation
Indices: 41397985--41398054 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 21
41397975 AATGTAAGTT
41397985 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATA-TA
*
41398007 ATTAATTAAGTTATGTATAATACTA
1 A-T--GTAAGTTATGTATAATA-TA
*
41398032 ATGTAAGTTATGTATTATATA
1 ATGTAAGTTATGTATAATATA
41398053 AT
1 AT
41398055 AACAACGTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.10
22 16 0.39
23 1 0.02
24 1 0.02
25 19 0.46
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.46
Consensus pattern (21 bp):
ATGTAAGTTATGTATAATATA
Found at i:41398050 original size:25 final size:26
Alignment explanation
Indices: 41397985--41398050 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 26
41397975 AATGTAAGTT
* * *
41397985 ATGTAAGTTATGTATAATATTAATTA
1 ATGTAAGTTATGTATTATAATAACTA
41398011 AT-TAAGTTATG---TATAAT-ACTA
1 ATGTAAGTTATGTATTATAATAACTA
41398032 ATGTAAGTTATGTATTATA
1 ATGTAAGTTATGTATTATA
41398051 TAATAACAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 5 0.15
22 13 0.39
25 13 0.39
26 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (26 bp):
ATGTAAGTTATGTATTATAATAACTA
Found at i:41400716 original size:16 final size:16
Alignment explanation
Indices: 41400671--41400726 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
41400661 TAAATCTCAC
*
41400671 ATCTTTTATTTATT-T
1 ATCTTTTATTAATTGT
* *
41400686 ATTTATTTCTTAATTGT
1 ATCT-TTTATTAATTGT
41400703 ATCTTTTATTAATTGT
1 ATCTTTTATTAATTGT
41400719 ATCTTTTA
1 ATCTTTTA
41400727 ATTACTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.66
Consensus pattern (16 bp):
ATCTTTTATTAATTGT
Found at i:41401253 original size:8 final size:8
Alignment explanation
Indices: 41401240--41401266 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41401230 GACCATAAAA
41401240 CACCAAAC
1 CACCAAAC
41401248 CACCAAAC
1 CACCAAAC
41401256 CACCAAAC
1 CACCAAAC
41401264 CAC
1 CAC
41401267 AAAATCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (8 bp):
CACCAAAC
Found at i:41401415 original size:13 final size:14
Alignment explanation
Indices: 41401380--41401420 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
41401370 CAAACCCCTA
*
41401380 AAGT-CTAAACCGT
1 AAGTCCTAAACCAT
*
41401393 AAGTCATAAACCAT
1 AAGTCCTAAACCAT
41401407 AA-TCCTAAACCAT
1 AAGTCCTAAACCAT
41401420 A
1 A
41401421 TCTTTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (14 bp):
AAGTCCTAAACCAT
Found at i:41405660 original size:36 final size:37
Alignment explanation
Indices: 41405531--41405702 Score: 287
Period size: 37 Copynumber: 4.7 Consensus size: 37
41405521 TTTGAGTACT
*
41405531 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
41405568 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
41405605 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
41405642 TCTGATC-AGAAACAAAGTGATAGGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
**
41405678 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGAAACAAAGTGATAAGTG
41405703 ATCATACGTA
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
35 11 0.08
36 39 0.30
37 80 0.62
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:41419473 original size:31 final size:31
Alignment explanation
Indices: 41419426--41419484 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
41419416 CAGCGTAATA
*
41419426 ACTTAAATAAAAACTTTCAAATAGTTTAGTG
1 ACTTAAATAAAAACTTTCAAATAATTTAGTG
* * *
41419457 ACTTGAATGAAAACTTTCGAATAATTTA
1 ACTTAAATAAAAACTTTCAAATAATTTA
41419485 ATGATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTTAGTG
Found at i:41429345 original size:29 final size:29
Alignment explanation
Indices: 41429292--41429349 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
41429282 TTTAGTTTTC
*
41429292 TTTAATAGTACAATGATTAAATTAATTCA
1 TTTAATAGTACAATGACTAAATTAATTCA
*
41429321 TTTAATAGTA-AATGGACTAATTTAATTCA
1 TTTAATAGTACAAT-GACTAAATTAATTCA
41429350 GTCCCTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (29 bp):
TTTAATAGTACAATGACTAAATTAATTCA
Found at i:41430159 original size:17 final size:17
Alignment explanation
Indices: 41430112--41430159 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
41430102 AATTCATTAA
41430112 AAAAATTTAAACAAAAATT
1 AAAAA-TTAAA-AAAAATT
*
41430131 -AATATTATAAAAAAATT
1 AAAAATTA-AAAAAAATT
41430148 AAAAATTAAAAA
1 AAAAATTAAAAA
41430160 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATTAAAAAAAATT
Found at i:41430261 original size:24 final size:25
Alignment explanation
Indices: 41430234--41430286 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
41430224 CACCATATGA
41430234 ATAAAAA-AAAAATCCAAAATAAAT
1 ATAAAAATAAAAATCCAAAATAAAT
* * *
41430258 ATAAAAATAAAATTCCAAATTTAAT
1 ATAAAAATAAAAATCCAAAATAAAT
41430283 ATAA
1 ATAA
41430287 TGCAATGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.25
Consensus pattern (25 bp):
ATAAAAATAAAAATCCAAAATAAAT
Found at i:41432935 original size:14 final size:14
Alignment explanation
Indices: 41432916--41432962 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
41432906 AATTAGTTGA
*
41432916 AATATTTTGTTATT
1 AATATTTTATTATT
*
41432930 AATATTTTATTTTT
1 AATATTTTATTATT
41432944 AAATATTTTATTAATT
1 -AATATTTTATT-ATT
41432960 AAT
1 AAT
41432963 TAATAGTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.43
15 14 0.50
16 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
AATATTTTATTATT
Found at i:41432950 original size:15 final size:15
Alignment explanation
Indices: 41432901--41432961 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 15
41432891 TTGGTGTTGA
41432901 ATTTTAATTAGTTGAAAT
1 ATTTT-ATTA-TT-AAAT
*
41432919 ATTTTGTTATT-AAT
1 ATTTTATTATTAAAT
*
41432933 ATTTTATTTTTAAAT
1 ATTTTATTATTAAAT
41432948 ATTTTATTAATTAA
1 ATTTTATT-ATTAA
41432962 TTAATAGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 12 0.32
15 11 0.30
16 6 0.16
17 3 0.08
18 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (15 bp):
ATTTTATTATTAAAT
Found at i:41434460 original size:20 final size:21
Alignment explanation
Indices: 41434435--41434474 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
41434425 ATATAATGAA
*
41434435 GTACCAGAAAT-TACGAGGGG
1 GTACCAAAAATATACGAGGGG
41434455 GTACCAAAAATATACGAGGG
1 GTACCAAAAATATACGAGGG
41434475 AGAGGGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (21 bp):
GTACCAAAAATATACGAGGGG
Found at i:41434647 original size:20 final size:20
Alignment explanation
Indices: 41434592--41434649 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
41434582 AAACAGGTAG
* *
41434592 AGTACCAAAAATCATGAGGA
1 AGTACAAAAAATTATGAGGA
* *
41434612 AATACTACAAAA-TATGAGGA
1 AGTAC-AAAAAATTATGAGGA
41434632 AGTACAAAAAATTATGAG
1 AGTACAAAAAATTATGAG
41434650 AGGATATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 5 0.17
20 21 0.70
21 4 0.13
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.19
Consensus pattern (20 bp):
AGTACAAAAAATTATGAGGA
Found at i:41436618 original size:3 final size:3
Alignment explanation
Indices: 41436612--41436682 Score: 99
Period size: 3 Copynumber: 23.3 Consensus size: 3
41436602 TTATGTTTTC
* *
41436612 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT T-T TTT TACA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T
41436658 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
41436683 TATTTATTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
2 2 0.03
3 55 0.89
4 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41437014 original size:8 final size:8
Alignment explanation
Indices: 41437003--41437027 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41436993 CCAAATATCC
41437003 TTTTAAAA
1 TTTTAAAA
41437011 TTTTAAAA
1 TTTTAAAA
41437019 TTTTAAAA
1 TTTTAAAA
41437027 T
1 T
41437028 AAGACAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:41437119 original size:115 final size:108
Alignment explanation
Indices: 41436912--41437224 Score: 459
Period size: 115 Copynumber: 2.9 Consensus size: 108
41436902 TTTAATTTTT
*
41436912 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAAACGTGCCTTAATGTGCTGGGTTTCGATTTTC
1 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATTTTC
*
41436977 TCGTTTGACCAAATAGCCAAATATCCTTTTAAAATTTTAAAATTTTAAAA
66 TCGTTCGACCAAATAGCCAAATATCC---T----TTTTAAAATTTTAAAA
* * * *
41437027 TAAGACAATGTTTTGCATTTGGAAATTCGAGAAAATGTGCCCTAATGTGCTGGGTTTCGATTTTC
1 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATTTTC
41437092 TCGTTCGACCAAATAGCCAAATATCC-TTTTAAAATTTTAAAA
66 TCGTTCGACCAAATAGCCAAATATCCTTTTTAAAATTTTAAAA
41437134 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGA-TTTC
1 TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATTTTC
* * * *
41437198 TCGTTGGACCGAATGGCTAAATATCCT
66 TCGTTCGACCAAATAGCCAAATATCCT
41437225 CTTACATCTT
Statistics
Matches: 183, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
106 26 0.14
107 72 0.39
115 85 0.46
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (108 bp):
TAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATTTTC
TCGTTCGACCAAATAGCCAAATATCCTTTTTAAAATTTTAAAA
Found at i:41437122 original size:107 final size:106
Alignment explanation
Indices: 41437011--41437224 Score: 347
Period size: 107 Copynumber: 2.0 Consensus size: 106
41437001 CCTTTTAAAA
*
41437011 TTTTAAAATTTTAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGAAAATGTGCCCTAATGTG
1 TTTTAAAATTTTAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTG
41437076 CTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCC
66 CTGGGTTTCGA-TTTCTCGTTCGACCAAATAGCCAAATATCC
* * *
41437118 TTTTAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTG
1 TTTTAAAATTTTAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTG
* * * *
41437183 CTGGGTTTCGATTTCTCGTTGGACCGAATGGCTAAATATCC
66 CTGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCC
41437224 T
1 T
41437225 CTTACATCTT
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
106 27 0.27
107 72 0.73
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (106 bp):
TTTTAAAATTTTAAAATAAGACAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTG
CTGGGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCC
Found at i:41437708 original size:20 final size:21
Alignment explanation
Indices: 41437633--41437702 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 21
41437623 ACAGCACGCC
*
41437633 AAAAATTATGAGGGAATA-CA
1 AAAAATTATGAGGGAGTACCA
* *
41437653 AAAAATTATGA-GAAGATGCCA
1 AAAAATTATGAGGGAG-TACCA
*
41437674 AAAAA-TATTAGGGAGTACCA
1 AAAAATTATGAGGGAGTACCA
41437694 AAAAATTAT
1 AAAAATTAT
41437703 CAGGAGAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 2 0.05
20 25 0.62
21 13 0.32
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAAATTATGAGGGAGTACCA
Found at i:41437766 original size:22 final size:23
Alignment explanation
Indices: 41437726--41437772 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
41437716 AAGGAAGAAT
*
41437726 AAAATATTACGAGGGAATACCAAA
1 AAAATATTAC-AGGAAATACCAAA
41437750 AAAATATTA-AGGAAATACCAAA
1 AAAATATTACAGGAAATACCAAA
41437772 A
1 A
41437773 GACTTGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
24 9 0.41
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.17
Consensus pattern (23 bp):
AAAATATTACAGGAAATACCAAA
Found at i:41438515 original size:31 final size:31
Alignment explanation
Indices: 41438471--41438535 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
41438461 CATACAAATA
41438471 ATTATGAAGTAATACTAAAAATTATGAGAAT
1 ATTATGAAGTAATACTAAAAATTATGAGAAT
* *
41438502 ATTATG-AGATAATACTAAAATTTATGAGATT
1 ATTATGAAG-TAATACTAAAAATTATGAGAAT
41438533 ATT
1 ATT
41438536 TTATCTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (31 bp):
ATTATGAAGTAATACTAAAAATTATGAGAAT
Found at i:41440809 original size:18 final size:18
Alignment explanation
Indices: 41440777--41440825 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
41440767 ATAAACTGGT
41440777 ATTAGAGAAAA-GGTTACA
1 ATTAGA-AAAAGGGTTACA
*
41440795 GTTAGAAAAAGGGTTACA
1 ATTAGAAAAAGGGTTACA
*
41440813 ATCAGAAAAAGGG
1 ATTAGAAAAAGGG
41440826 GATTGAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.49, C:0.06, G:0.27, T:0.18
Consensus pattern (18 bp):
ATTAGAAAAAGGGTTACA
Found at i:41446175 original size:10 final size:10
Alignment explanation
Indices: 41446130--41446175 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
41446120 TAAATATTTG
41446130 TTTATATTA-A
1 TTTAT-TTATA
41446140 TTTATTT-TA
1 TTTATTTATA
41446149 TTTATTTATA
1 TTTATTTATA
41446159 TAATTATTTATA
1 T--TTATTTATA
41446171 TTTAT
1 TTTAT
41446176 ATTTGTTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 10 0.31
10 12 0.38
12 10 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTATTTATA
Found at i:41452948 original size:27 final size:26
Alignment explanation
Indices: 41452892--41452957 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 26
41452882 TGATTTCATT
* * *
41452892 AAAGAAA-AA-TTAGTAGAACTAGAA
1 AAAGAAAGAAGTTTGTAGAAATACAA
*
41452916 AAAGAAGAGAATTTTGTAGAAATACAA
1 AAAGAA-AGAAGTTTGTAGAAATACAA
*
41452943 ATAGAAAGAAGTTTG
1 AAAGAAAGAAGTTTG
41452958 ATTCAAAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 6 0.18
25 1 0.03
26 10 0.29
27 17 0.50
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.21
Consensus pattern (26 bp):
AAAGAAAGAAGTTTGTAGAAATACAA
Found at i:41454960 original size:19 final size:22
Alignment explanation
Indices: 41454912--41454958 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
41454902 CCCAAAGGAC
41454912 TTGTTGACATTCCCGTATGGTG
1 TTGTTGACATTCCCGTATGGTG
*
41454934 TTGTTGACATTCCTGTATGGTG
1 TTGTTGACATTCCCGTATGGTG
41454956 TTG
1 TTG
41454959 ACCTTTAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.45
Consensus pattern (22 bp):
TTGTTGACATTCCCGTATGGTG
Found at i:41455527 original size:27 final size:28
Alignment explanation
Indices: 41455488--41455562 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
41455478 ATTTCTCTCG
** * *
41455488 TCCCAACAAACTTGCCCT-TGTTTACTG
1 TCCCAACGGACTTACCCTGTGTTTACTA
* *
41455515 TCCCAGCGGACTTACCTTGTGTTTACTA
1 TCCCAACGGACTTACCCTGTGTTTACTA
*
41455543 TCCCAACGGACTTACTCTGT
1 TCCCAACGGACTTACCCTGT
41455563 TTTGTATTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.20, C:0.32, G:0.15, T:0.33
Consensus pattern (28 bp):
TCCCAACGGACTTACCCTGTGTTTACTA
Found at i:41456894 original size:2 final size:2
Alignment explanation
Indices: 41456887--41456918 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41456877 CCATTGAATA
41456887 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
41456919 GGTTGTTCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41457197 original size:124 final size:123
Alignment explanation
Indices: 41456978--41457224 Score: 413
Period size: 124 Copynumber: 2.0 Consensus size: 123
41456968 TACACTTTCA
* *
41456978 TTCTTCCATTGTCTTATGACATCTCCTAAAGAAAGTTCTCATCATATTATAAAACATTATGTACC
1 TTCTTCCATTGTCTCATGACATCTCCTAAAGAAAGTTCTCATCATAGTATAAAACATTATGTACC
* *
41457043 TTTCTTAGCAACTTACATTGCAAATTTTTCCACAACTTTACGAATGTATGAATATTGT
66 TTTCTTAGCAACTTACATTGCAAATTTTTCCACAAATTTACCAATGTATGAATATTGT
* * *
41457101 TTCTTCCATTGTCTCATGACAATCTCTTAAAGAAAGTTCTCATCATAGTATAAATCTTTATGTAC
1 TTCTTCCATTGTCTCATGAC-ATCTCCTAAAGAAAGTTCTCATCATAGTATAAAACATTATGTAC
*
41457166 CTTTCTTAGCAACTTGCATTGCAAATTTTTCCACAAATTTACCAATGTATGAATATTGT
65 CTTTCTTAGCAACTTACATTGCAAATTTTTCCACAAATTTACCAATGTATGAATATTGT
41457225 GACAAACTAT
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
123 19 0.17
124 96 0.83
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (123 bp):
TTCTTCCATTGTCTCATGACATCTCCTAAAGAAAGTTCTCATCATAGTATAAAACATTATGTACC
TTTCTTAGCAACTTACATTGCAAATTTTTCCACAAATTTACCAATGTATGAATATTGT
Found at i:41463198 original size:5 final size:6
Alignment explanation
Indices: 41463173--41463197 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41463163 GGTTATCTAA
41463173 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
41463198 AGTCACTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:41464044 original size:51 final size:51
Alignment explanation
Indices: 41463930--41464037 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
41463920 TCTATCTAAG
* * * * *
41463930 GTGTCACAACACCACAAGTTAGTGTCGTGACATTGAAGTATTTTGCCCTCA
1 GTGTCACAACACCAAAAGTTAGTATCATGACATTGAAGTATTCTACCCTCA
*
41463981 GTGTCACAACACCAAAAGTTAGTATCATGACATTGGAGTATTCTACCCTCA
1 GTGTCACAACACCAAAAGTTAGTATCATGACATTGAAGTATTCTACCCTCA
41464032 GTGTCA
1 GTGTCA
41464038 TGACACCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (51 bp):
GTGTCACAACACCAAAAGTTAGTATCATGACATTGAAGTATTCTACCCTCA
Found at i:41468052 original size:18 final size:18
Alignment explanation
Indices: 41468029--41468074 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
41468019 GATGTTCATC
41468029 ATATTTTTTATTATTGTT
1 ATATTTTTTATTATTGTT
* *
41468047 ATATTTTTT-TCATTTTT
1 ATATTTTTTATTATTGTT
41468064 AT-TTTTTTATT
1 ATATTTTTTATT
41468075 TTTATAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (18 bp):
ATATTTTTTATTATTGTT
Found at i:41468068 original size:15 final size:14
Alignment explanation
Indices: 41468033--41468079 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
41468023 TTCATCATAT
41468033 TTTTTATTATTGTTATA
1 TTTTT-TTATT-TT-TA
41468050 TTTTTTTCATTTTTA
1 TTTTTTT-ATTTTTA
41468065 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
41468079 T
1 T
41468080 AAATGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 4 0.14
17 8 0.28
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:41468427 original size:18 final size:18
Alignment explanation
Indices: 41468406--41468440 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41468396 TTTTGAAGGA
* *
41468406 TTTTTTGTTTTTGTTTTT
1 TTTTTTATTTTGGTTTTT
41468424 TTTTTTATTTTGGTTTT
1 TTTTTTATTTTGGTTTT
41468441 GAAAATGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (18 bp):
TTTTTTATTTTGGTTTTT
Found at i:41469517 original size:98 final size:98
Alignment explanation
Indices: 41469410--41469606 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
41469400 TTTAAAATAA
* * *
41469410 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGCGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGCGATTTC
*
41469475 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGATCTTTTAAAG
*
41469508 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGCGATTTC
41469573 TTAAATCTTGGATAAGTGGATGATCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGATCTTTTAAAG
41469606 T
1 T
41469607 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (98 bp):
TAAAGGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGCGATTTC
TTAAATCTTGGATAAGTGGATGATCTTTTAAAG
Found at i:41470441 original size:19 final size:19
Alignment explanation
Indices: 41470409--41470470 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 19
41470399 GTGTTCAGAA
*
41470409 TTTTA-AATTTTTTTATAG
1 TTTTAGAATTATTTTATAG
41470427 TTTTAGAATTATTTTATAAG
1 TTTTAGAATTATTTTAT-AG
*
41470447 TTGTTTAGAATTATCATTATAG
1 -T-TTTAGAATTAT-TTTATAG
41470469 TT
1 TT
41470471 CAAATTAGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.14
19 10 0.27
20 3 0.08
21 2 0.05
22 13 0.35
23 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (19 bp):
TTTTAGAATTATTTTATAG
Found at i:41473599 original size:155 final size:155
Alignment explanation
Indices: 41473323--41473968 Score: 786
Period size: 154 Copynumber: 4.3 Consensus size: 155
41473313 CTGCACCAAT
41473323 ATTTGTTCGTATTTTTTT-CCAGAATTTTATTACTTT-AA-AAAATATATATTATTTTC------
1 ATTTGTTCGTATTTTTTTCCCAG-ATTTTATTACTTTCAATAAAA-ATATATTATTTTCGTATTT
* * * * * *
41473379 TA--ATTTT--ATTATTTTAGTACATTATTTTTGAAATGTATTCATTTAGTTTGATTTATAAATA
64 TATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATA
41473440 AATTTAAAAAAAACTCTTATTTCGGCC
129 AATTTAAAAAAAACTCTTATTTCGGCC
* * *
41473467 ATTTGTTTGTATTTTTTCCCCGGATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTA
1 ATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTA
41473532 TTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA
66 TTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA
*
41473597 TTT---AAAAACCCTTATTTCGGCC
131 TTTAAAAAAAACTCTTATTTCGGCC
* * * *
41473619 ATTTGTTCAT-TTTTTTTCCTAAATTTTATT-CTTT--A-AAAAATATACTATTTTC-TAATTTT
1 ATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAATAAAAATATATTATTTTCGT-ATTTT
* * *
41473678 ATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTCGTGTTTTTTAAACT
65 ATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACT-GTGTTTTTTAAA-T
* * *
41473743 -AATTTTAAAAAATC-CTTATTTCGATCC
128 AAATTTAAAAAAAACTCTTATTTCG-GCC
* *
41473770 -TTTGTTCGTA-TTTTTTCCCATATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTA
1 ATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTA
* *
41473833 TTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTATGTTTTTAAAATAAA
66 TTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA
*
41473898 TTTAGTAAAAAACTCTTATTTCGGCC
131 TTTA-AAAAAAACTCTTATTTCGGCC
* * * *
41473924 CTCTGTTCGTATTTTTTTACCGGATTTTATTACTTTCAATAAAAA
1 ATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAATAAAAA
41473969 ACACACTAAA
Statistics
Matches: 431, Mismatches: 40, Indels: 50
0.83 0.08 0.10
Matches are distributed among these distances:
144 29 0.07
145 18 0.04
146 5 0.01
147 68 0.16
148 18 0.04
149 1 0.00
150 38 0.09
151 29 0.07
152 27 0.06
153 21 0.05
154 75 0.17
155 72 0.17
156 30 0.07
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (155 bp):
ATTTGTTCGTATTTTTTTCCCAGATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTA
TTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA
TTTAAAAAAAACTCTTATTTCGGCC
Found at i:41473719 original size:302 final size:295
Alignment explanation
Indices: 41473323--41473959 Score: 874
Period size: 301 Copynumber: 2.1 Consensus size: 295
41473313 CTGCACCAAT
* *
41473323 ATTTGTTCGTATTTTTTTCCAGAATTTTATTACTTTAAAAAATATATATTATTTTCTAATTTTAT
1 ATTTGTTCATATTTTTTTCCAGAATTTTATTACTTTAAAAAATATATATTATTTTATAATTTTAT
* *
41473388 TATTTTAGTACATTATTTTTGAAATGTATTCATTTAGT-TTGATTTATAAA-TAAATTTAAAAAA
66 TATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTCGTGATTTATAAACT-AATTTAAAAAA
* *
41473451 AACTCTTATTTCG-GCCATTTGTTTGTATTTTTTCCCCGGATTTTATTACTTTCAATAAAAATAT
130 AAC-CTTATTTCGAGCC-TTTGTTCGTATTTTTT-CCCAGATTTTATTACTTTCAATAAAAATAT
41473515 ATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAC
192 ATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAC
* *
41473580 TGTGTTTTTTAAATAAATTTAAAAACCCTTATTTCGGCC
257 TATGTTTTTAAAATAAATTTAAAAACCCTTATTTCGGCC
*
41473619 ATTTGTTCAT-TTTTTTTCCTA-AATTTTATT-CTTTAAAAAATATACTATTTTCTAATTTTATT
1 ATTTGTTCATATTTTTTTCC-AGAATTTTATTACTTTAAAAAATATA-TA---T-T-ATTTTATA
* *
41473681 ATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTCGTGTTTTTTAAACTAAT
59 ATTTT--ATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTCGTGATTTATAAACTAAT
* * * *
41473746 TTTAAAAAATCCTTATTTCGATCCTTTGTTCGTATTTTTTCCCATATTTTATTACTTTCAATAAA
122 TTAAAAAAAACCTTATTTCGAGCCTTTGTTCGTATTTTTTCCCAGATTTTATTACTTTCAATAAA
*
41473811 AATATATTATTTTTGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA
187 AATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAA
*
41473876 TTTACTATGTTTTTAAAATAAATTTAGTAAAAAACTCTTATTTCGGCC
252 TTTACTATGTTTTTAAAATAAA-TT--T-AAAAACCCTTATTTCGGCC
* * * *
41473924 CTCTGTTCGTATTTTTTTACC-GGATTTTATTACTTT
1 ATTTGTTCATATTTTTTT-CCAGAATTTTATTACTTT
41473960 CAATAAAAAA
Statistics
Matches: 300, Mismatches: 21, Indels: 29
0.86 0.06 0.08
Matches are distributed among these distances:
294 14 0.05
295 20 0.07
296 10 0.03
298 1 0.00
299 1 0.00
300 11 0.04
301 107 0.36
302 65 0.22
303 23 0.08
304 2 0.01
305 25 0.08
306 15 0.05
307 6 0.02
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (295 bp):
ATTTGTTCATATTTTTTTCCAGAATTTTATTACTTTAAAAAATATATATTATTTTATAATTTTAT
TATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTCGTGATTTATAAACTAATTTAAAAAAA
ACCTTATTTCGAGCCTTTGTTCGTATTTTTTCCCAGATTTTATTACTTTCAATAAAAATATATTA
TTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTATG
TTTTTAAAATAAATTTAAAAACCCTTATTTCGGCC
Found at i:41475559 original size:307 final size:305
Alignment explanation
Indices: 41474959--41475640 Score: 1132
Period size: 306 Copynumber: 2.2 Consensus size: 305
41474949 NNNNNNNNNN
41474959 AATAATATAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATCCGGGAAAAAAATACGAAC
1 AATAATA-AAA-TAGAAAATAGTATA-TTTTTTAAAGTAATAAAATCCGGGAAAAAAATACGAAC
*
41475024 AAATGGCAGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAA
63 AAAGGGCAGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAA
41475089 CATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAAT
128 CATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAAT
* * *
41475154 AAAATCTGGAAAAAAGTACAAACAAAGGGCCGAAATAAGAGTTTTTTTTTAAATTTATTTAAAAA
193 AAAATCAGGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAAATTTATTTAAAAA
41475219 TCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAA
258 TCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAA
* *
41475267 AATAATAAAATACGAAAATAATATATTTTTTAAAGTAATAAAATCTGGGAAAAAAATACGAACAA
1 AATAATAAAATA-GAAAATAGTATATTTTTTAAAGTAATAAAATCCGGGAAAAAAATACGAACAA
* *
41475332 AGGGCCGGAATAAGGG-TTTTTTTAATTTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
65 AGGGCAGAAATAAGGGTTTTTTTTAA-TTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
41475396 ATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATA
129 ATAATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATA
** * *
41475461 AAATCCAGGAAAAAAATATGAATAAAGGGCCGAAATAAGGGTTTTTTTTAAAATTTATTTAAAAA
194 AAAT-CAGGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAAATTTATTTAAAAA
41475526 TCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAA
258 TCAAACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAA
* * * * *
41475574 AATAATAAATTTAAAAAATAGTATATTTTTTAAAAATAATAAAATCCAGAAAAAAAATACGAACA
1 AATAATAAA-ATAGAAAATAGTATATTTTTT-AAAGTAATAAAATCCGGGAAAAAAATACGAACA
41475639 AA
64 AA
41475641 TGGTCGAAAT
Statistics
Matches: 350, Mismatches: 19, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
305 9 0.03
306 161 0.46
307 140 0.40
308 40 0.11
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (305 bp):
AATAATAAAATAGAAAATAGTATATTTTTTAAAGTAATAAAATCCGGGAAAAAAATACGAACAAA
GGGCAGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACAT
AATGTACTAAAATAATGTAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAA
ATCAGGAAAAAAATACAAACAAAGGGCCGAAATAAGAGTTTTTTTTAAAATTTATTTAAAAATCA
AACTAAATGAATACATTTCAAAAATAATGTACTAAAATAATGTAA
Found at i:41478944 original size:21 final size:21
Alignment explanation
Indices: 41478918--41478958 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
41478908 TTCTAATTTG
*
41478918 TATATTATTTTAATATTTTAA
1 TATATTAATTTAATATTTTAA
41478939 TATATTAATTTAATATTTTA
1 TATATTAATTTAATATTTTA
41478959 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTAATTTAATATTTTAA
Found at i:41479270 original size:25 final size:26
Alignment explanation
Indices: 41479223--41479279 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
41479213 AAAATTATAT
** *
41479223 TTAAAAATAGTAAGTTAT-TTTTTAA
1 TTAAAAATAGTAAACTATATTTTAAA
*
41479248 TTAAAAATATTAAACTATATTTTAAA
1 TTAAAAATAGTAAACTATATTTTAAA
41479274 TTAAAA
1 TTAAAA
41479280 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (26 bp):
TTAAAAATAGTAAACTATATTTTAAA
Found at i:41487133 original size:22 final size:24
Alignment explanation
Indices: 41487107--41487150 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41487097 GAAAAATATT
41487107 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
41487129 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
41487151 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:41487256 original size:68 final size:67
Alignment explanation
Indices: 41487188--41487392 Score: 224
Period size: 68 Copynumber: 3.0 Consensus size: 67
41487178 TAGTGTTACA
*
41487188 AAATAATAATAAAACATCAAGTTTG-T-TTTACTAATCAAATGTTAGATTTTGTTACAACAATTA
1 AAATAATAATAAAA-AT-AAGTTTGATATTTACTAATCAAATGTTAGATTTTATTACAACAATTA
41487251 ATAC
64 ATAC
* **
41487255 AATTAATACA-ATTAAT-AGTTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 AAATAATA-ATAAAAATAAGTTTGAT--ATTTACTAATCAAATGTTAGATTTTATTACAACAATT
41487318 AATAC
63 AATAC
* ** *
41487323 AATTAATACA-ATTAATAA-TTTGATAAATTTACTAATCAAATGTTAGATTTTATTACATCAATT
1 AAATAATA-ATAAAAATAAGTTTGAT--ATTTACTAATCAAATGTTAGATTTTATTACAACAATT
41487386 AATAC
63 AATAC
41487391 AA
1 AA
41487393 TTAACAATTA
Statistics
Matches: 127, Mismatches: 5, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
64 6 0.05
65 1 0.01
66 2 0.02
67 9 0.07
68 108 0.85
69 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (67 bp):
AAATAATAATAAAAATAAGTTTGATATTTACTAATCAAATGTTAGATTTTATTACAACAATTAAT
AC
Found at i:41487258 original size:9 final size:9
Alignment explanation
Indices: 41487244--41487271 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41487234 TTTTGTTACA
41487244 ACAATTAAT
1 ACAATTAAT
41487253 ACAATTAAT
1 ACAATTAAT
41487262 ACAATTAAT
1 ACAATTAAT
41487271 A
1 A
41487272 GTTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41487324 original size:9 final size:9
Alignment explanation
Indices: 41487312--41487339 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41487302 TTTTATTACA
41487312 ACAATTAAT
1 ACAATTAAT
41487321 ACAATTAAT
1 ACAATTAAT
41487330 ACAATTAAT
1 ACAATTAAT
41487339 A
1 A
41487340 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41487393 original size:68 final size:68
Alignment explanation
Indices: 41487214--41487423 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
41487204 TCAAGTTTGT
* *
41487214 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAGTTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41487279 AAA
66 AAA
41487282 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41487347 AAA
66 AAA
*
41487350 TTTACTAATCAAATGTTAGATTTTATTACATCAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
41487413 AAT
66 AAA
41487416 TTTACTAA
1 TTTACTAA
41487424 CAATTAATTT
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 27 0.20
67 1 0.01
68 110 0.80
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:41487433 original size:16 final size:16
Alignment explanation
Indices: 41487412--41487453 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41487402 AATAATTTGA
*
41487412 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41487428 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41487444 TAGTTTTAAT
1 TAATTTTAAT
41487454 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41487437 original size:22 final size:23
Alignment explanation
Indices: 41487427--41487482 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
41487417 TTACTAACAA
* * *
41487427 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
41487449 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
41487472 TTAATTTTAAT
1 TTAATTTTAAT
41487483 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:41493111 original size:33 final size:34
Alignment explanation
Indices: 41493040--41493122 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 34
41493030 ACAAAAATAC
* * **
41493040 TTTTACTAACAATTAACAATTAATAATTGGTTGG
1 TTTTAATAACAATTAACAATTAATAATTGGATAA
*
41493074 TTTTAAT-ACAATTAACAATTAATAATTTGATAA
1 TTTTAATAACAATTAACAATTAATAATTGGATAA
*
41493107 TTTTACTAACAATTAA
1 TTTTAATAACAATTAA
41493123 TTTTAATAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 28 0.67
34 14 0.33
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.42
Consensus pattern (34 bp):
TTTTAATAACAATTAACAATTAATAATTGGATAA
Found at i:41493125 original size:16 final size:16
Alignment explanation
Indices: 41493104--41493145 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41493094 AATAATTTGA
*
41493104 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41493120 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41493136 TAGTTTTAAT
1 TAATTTTAAT
41493146 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41494387 original size:21 final size:22
Alignment explanation
Indices: 41494362--41494411 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
41494352 CTAAAAGGGG
*
41494362 AATAAATGA-GTAAATAAAAAT
1 AATAAATAAGGTAAATAAAAAT
* *
41494383 AAT-AATAAGGTAAGTAATAAT
1 AATAAATAAGGTAAATAAAAAT
41494404 AATAAATA
1 AATAAATA
41494412 CAATAACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 16 0.67
22 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (22 bp):
AATAAATAAGGTAAATAAAAAT
Found at i:41498673 original size:44 final size:44
Alignment explanation
Indices: 41498558--41498898 Score: 164
Period size: 44 Copynumber: 7.8 Consensus size: 44
41498548 ATTATCGACT
* * *
41498558 TCAATCTACTCCACTGCAACCTCAGGGAGATAAGA-TT-TACTTC
1 TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-TTTC
** ** * *
41498601 TTCGGTCTGC-CTCACTGTGATTTTAGGGAGATAAGACTTGTTTTC
1 -TCAATCTGCTC-CACTGCAACTTCAGGGAGATAAGACTTGTTTTC
* ** *
41498646 TCAATCTGCTCCACTGCAACTTCAGGGAGATGAGAC--CCTAT-
1 TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTC
* * ** ** * *
41498687 GCGATCCACTCTGCTGCAACTTCAGAGAGAAAAGATCTAT-TTCTT-
1 TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGTT-TTC
* * * * ***
41498732 T-AATCCGCTCCACTACAACTTCAGGGAGATAGGA-TTATCCGC
1 TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTC
* *
41498774 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTG-TTTC
1 -TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTC
* * * ** * * *
41498818 TTCAGTCTGCCCCGCTGTGACTTCAGGGGGATAAAACCTGTTTTC
1 -TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTC
* * *
41498863 TCAGTCTGCTCCGCTGCAACCTCAGGGAGATAAGAC
1 TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
41498899 CTGATGCGAT
Statistics
Matches: 218, Mismatches: 64, Indels: 30
0.70 0.21 0.10
Matches are distributed among these distances:
41 27 0.12
42 5 0.02
43 2 0.01
44 170 0.78
45 13 0.06
46 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (44 bp):
TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTTTC
Found at i:41498864 original size:217 final size:217
Alignment explanation
Indices: 41498541--41499027 Score: 653
Period size: 217 Copynumber: 2.2 Consensus size: 217
41498531 AACGTCGGGA
* * * *
41498541 AGATAGGATTATCGACTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTACTTCTTCGG
1 AGATAGGATTATCGACTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTACTTCTTCAG
* * * * * *
41498606 TCTGCCTCACTGTGATTTTAGGGAGATAAGACTTGTTTTCTCAATCTGCTCCACTGCAACTTCAG
66 TCTGCCCCACTGTGACTTCAGGGAGATAAAACCTGTTTTCTCAATCTGCTCCACTGCAACCTCAG
* *
41498671 GGAGATGAGACCCT-ATGCGATCCACTCTGCTGCAACTTCAGAGAGAAAAGATCTATT-TCTTTA
131 GGAGATAAGA-CCTGATGCGATCCACTCTACTGCAACTTCAGAGAGAAAAGATCTATTAT-TTTA
*
41498734 ATCCGCTCCACTACAACTTCAGGG
194 ATCCGCCCCACTACAACTTCAGGG
**
41498758 AGATAGGATTATCCG-CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGTTTCTTCA
1 AGATAGGATTAT-CGACTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTACTTCTTCA
* * * *
41498822 GTCTGCCCCGCTGTGACTTCAGGGGGATAAAACCTGTTTTCTCAGTCTGCTCCGCTGCAACCTCA
65 GTCTGCCCCACTGTGACTTCAGGGAGATAAAACCTGTTTTCTCAATCTGCTCCACTGCAACCTCA
* *
41498887 GGGAGATAAGACCTGATGCGATCCACTCTACTGTAACTTCAGAGAGATAAGATCTATTATTTTAA
130 GGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGAAAAGATCTATTATTTTAA
**
41498952 TCCGCCCCACTGTAACTTCAGGG
195 TCCGCCCCACTACAACTTCAGGG
* * *
41498975 AGATAGGA-TAGT-GTCTTCGATCTGCTCCACTGTAA-TCTCAGGGAGATAGGATT
1 AGATAGGATTA-TCGACTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATT
41499028 ACTGGCTTCA
Statistics
Matches: 239, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
215 2 0.01
216 40 0.17
217 194 0.81
218 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (217 bp):
AGATAGGATTATCGACTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTACTTCTTCAG
TCTGCCCCACTGTGACTTCAGGGAGATAAAACCTGTTTTCTCAATCTGCTCCACTGCAACCTCAG
GGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGAAAAGATCTATTATTTTAAT
CCGCCCCACTACAACTTCAGGG
Found at i:41499158 original size:141 final size:142
Alignment explanation
Indices: 41498899--41499531 Score: 902
Period size: 141 Copynumber: 4.5 Consensus size: 142
41498889 GAGATAAGAC
* * *
41498899 CTGATGCGATCCACTCTACTGTAACTTCAGAGAGATAAGAT-CTATTATTTTAATCCGCCCCACT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTGTTTTAATCCGCTCCACT
* *
41498963 GTAACTTCAGGGAGATAGGATAGT-GTCTTCGATCTGCTCCACTGTAATCTCAGGGAGATAGGAT
65 GTAACTTCAGGGAGATAGGATAGTAGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
*
41499027 TACTGGCTTCAAT
130 TTCTGGCTTCAAT
41499040 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTG
** * *
41499105 TAACTTCAGGGAGATAGGATAGT-GTCTTCGATCTATTCCGCTGTAATCACAGGGAGATAAGATC
66 TAACTTCAGGGAGATAGGATAGTAGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
41499169 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* * * ** *
41499181 CGGATGTGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTGTTTTAATCAACTCCACTT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTG
* * * *
41499246 TAACTTCAGGGAGATAGGATACTAGT-TTCCATCTGCTTCGTTGTAATCTCAGGGAGATAAGATT
66 TAACTTCAGGGAGATAGGATAGTAGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
41499310 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* ** * * *
41499322 CTGATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTACTTTAATTCGTTTCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTG
* *
41499387 TAA-TCTCAGGGAGATAGGATTA-TCAG-CTTCAATCTGCTCCGCTGTAATCTTAGGGAGATAAG
66 TAACT-TCAGGGAGATAGGA-TAGT-AGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
*
41499449 ATTTCAGGCTTCAAT
128 ATTTCTGGCTTCAAT
* *
41499464 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTGTTTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTG
41499529 TAA
66 TAA
41499532 TCTCGGGAGG
Statistics
Matches: 437, Mismatches: 49, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
140 1 0.00
141 323 0.74
142 113 0.26
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTG
TAACTTCAGGGAGATAGGATAGTAGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:41499565 original size:44 final size:44
Alignment explanation
Indices: 41499481--41499615 Score: 107
Period size: 44 Copynumber: 3.1 Consensus size: 44
41499471 GATCTACTCT
* * * * * *
41499481 ACTGTAACTTCAGAGAGATAAGA-TCATTTGTTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTGATTT-CTTCAGTCTGCTCC
* *
41499525 ACTGTAA-TCTC-GGGAGGATAAGACTTGTTTTC-TCAGTCTGCTCC
1 ACTGCAACT-TCAGGGA-GATAAGA-TTGATTTCTTCAGTCTGCTCC
* * *
41499569 GCTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTGATTTCTTCAGTCTGCTCC
41499613 ACT
1 ACT
41499616 ACTGCTTAGG
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
43 11 0.15
44 52 0.72
45 5 0.07
46 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGATTGATTTCTTCAGTCTGCTCC
Found at i:41501040 original size:13 final size:14
Alignment explanation
Indices: 41501022--41501074 Score: 67
Period size: 13 Copynumber: 4.0 Consensus size: 14
41501012 TTAGCCTCTC
41501022 CATTTTT-ATTTTT
1 CATTTTTCATTTTT
*
41501035 CATTTTT-ATTCTT
1 CATTTTTCATTTTT
*
41501048 CATTTTTCA-TTCT
1 CATTTTTCATTTTT
41501061 CATTTTTCATTTTT
1 CATTTTTCATTTTT
41501075 TTCATTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 30 0.88
14 4 0.12
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:41501054 original size:20 final size:20
Alignment explanation
Indices: 41501029--41501074 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
41501019 CTCCATTTTT
* *
41501029 ATTTTTCATTTTTATTCTTC
1 ATTTTTCATTCTCATTCTTC
*
41501049 ATTTTTCATTCTCATTTTTC
1 ATTTTTCATTCTCATTCTTC
41501069 ATTTTT
1 ATTTTT
41501075 TTCATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTTCATTCTCATTCTTC
Found at i:41501083 original size:7 final size:7
Alignment explanation
Indices: 41501022--41501074 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
41501012 TTAGCCTCTC
41501022 CATTTTT
1 CATTTTT
41501029 -ATTTTT
1 CATTTTT
41501035 CATTTTT
1 CATTTTT
*
41501042 -ATTCTT
1 CATTTTT
41501048 CATTTTT
1 CATTTTT
*
41501055 CA-TTCT
1 CATTTTT
41501061 CATTTTT
1 CATTTTT
41501068 CATTTTT
1 CATTTTT
41501075 TTCATTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 16 0.41
7 23 0.59
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:41501086 original size:20 final size:18
Alignment explanation
Indices: 41501024--41501086 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 18
41501014 AGCCTCTCCA
41501024 TTTTT-ATTTTTCATTTT
1 TTTTTCATTTTTCATTTT
*
41501041 TATTCTTCATTTTTCATTCTCA
1 T-TT-TTCATTTTTCATT-T-T
41501063 TTTTTCATTTTTTTCATTTT
1 TTTTTCA--TTTTTCATTTT
41501083 TTTT
1 TTTT
41501087 GACTCAGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
17 1 0.03
18 2 0.05
19 2 0.05
20 18 0.49
21 4 0.11
22 10 0.27
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTCATTTTTCATTTT
Found at i:41501993 original size:6 final size:6
Alignment explanation
Indices: 41501984--41502012 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
41501974 TCTTTTTCTT
41501984 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT
41502013 TTCCCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
ATTTTG
Found at i:41506225 original size:21 final size:22
Alignment explanation
Indices: 41506200--41506249 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
41506190 CTAAAAGGGG
*
41506200 AATAAAT-GGGTAAATAAAAAT
1 AATAAATAAGGTAAATAAAAAT
* *
41506221 AAT-AATAAGGTAAGTAATAAT
1 AATAAATAAGGTAAATAAAAAT
41506242 AATAAATA
1 AATAAATA
41506250 CAATAACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (22 bp):
AATAAATAAGGTAAATAAAAAT
Found at i:41529198 original size:12 final size:12
Alignment explanation
Indices: 41529181--41529205 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41529171 AGATAAAGAC
41529181 ACACACACACAT
1 ACACACACACAT
41529193 ACACACACACAT
1 ACACACACACAT
41529205 A
1 A
41529206 TATATATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
ACACACACACAT
Found at i:41529850 original size:2 final size:2
Alignment explanation
Indices: 41529809--41529837 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41529799 CAAATATTAT
41529809 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 T
41529838 TAGAGTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41531916 original size:2 final size:2
Alignment explanation
Indices: 41531909--41531945 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41531899 TCTTATTTAG
41531909 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
41531946 GGAAGAAAAG
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:41536909 original size:56 final size:56
Alignment explanation
Indices: 41536842--41536954 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
41536832 ATCTTTACTT
41536842 GATTTACTTGAAGTAATAGTAGAGACTGCGTCATCATGGTCATCAGCAGTGGTAGG
1 GATTTACTTGAAGTAATAGTAGAGACTGCGTCATCATGGTCATCAGCAGTGGTAGG
41536898 GATTTACTTGAAGTAATAGTAGAGACTGCGTCATCATGGTCATCAGCAGTGGTAGG
1 GATTTACTTGAAGTAATAGTAGAGACTGCGTCATCATGGTCATCAGCAGTGGTAGG
41536954 G
1 G
41536955 TGACCAGTGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.28
Consensus pattern (56 bp):
GATTTACTTGAAGTAATAGTAGAGACTGCGTCATCATGGTCATCAGCAGTGGTAGG
Found at i:41540027 original size:16 final size:16
Alignment explanation
Indices: 41540006--41540104 Score: 77
Period size: 16 Copynumber: 6.6 Consensus size: 16
41539996 AAGTATTTTA
41540006 AAAATATTTTAAAATT
1 AAAATATTTTAAAATT
41540022 AAAATATTTTAAAATT
1 AAAATATTTTAAAATT
* **
41540038 AAAAAATAATAAAA--
1 AAAATATTTTAAAATT
*
41540052 AAAGTA-TTT----TT
1 AAAATATTTTAAAATT
41540063 AAAATATTTTAAAATT
1 AAAATATTTTAAAATT
* * *
41540079 AAAAAAATTTAAAAAT
1 AAAATATTTTAAAATT
41540095 AAATATATTT
1 AAA-ATATTT
41540105 ATTATATCAG
Statistics
Matches: 62, Mismatches: 13, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
11 5 0.08
12 3 0.05
13 1 0.02
14 4 0.06
16 45 0.73
17 4 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
AAAATATTTTAAAATT
Found at i:41540051 original size:57 final size:57
Alignment explanation
Indices: 41539990--41540097 Score: 180
Period size: 57 Copynumber: 1.9 Consensus size: 57
41539980 TTTTAAAATT
* * *
41539990 TAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAATATTTTAAAATTAAAAAATAA
1 TAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAATAAAAAATAA
*
41540047 TAAAAAAAGTATTTTTAAAATATTTTAAAATTAAAAAAATTTAAAAATAAA
1 TAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAATAAA
41540098 TATATTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (57 bp):
TAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAATAAAAAATAA
Found at i:41547816 original size:21 final size:21
Alignment explanation
Indices: 41547792--41547834 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41547782 GAGTCGATGG
*
41547792 GTGA-TATGAAGTCAGCTCTCT
1 GTGATTATGAAG-CAGCACTCT
*
41547813 GTGATTGTGAAGCAGCACTCT
1 GTGATTATGAAGCAGCACTCT
41547834 G
1 G
41547835 CTTGGAACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGATTATGAAGCAGCACTCT
Found at i:41556992 original size:29 final size:30
Alignment explanation
Indices: 41556935--41556992 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
41556925 TATTATTTAA
* *
41556935 TTTTTTAAAAATATTTGTAATACATAATTT
1 TTTTTTAAAAATATTTGTAATAAAAAATTT
* *
41556965 TTTTTTGATAATA-TTGTAATAAAAAATT
1 TTTTTTAAAAATATTTGTAATAAAAAATT
41556993 AAAAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTTTTAAAAATATTTGTAATAAAAAATTT
Found at i:41577098 original size:14 final size:13
Alignment explanation
Indices: 41577068--41577104 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
41577058 ATTTCCAAAA
*
41577068 TTTCAAATTAAGT
1 TTTCAAATTAAGC
41577081 TTTCAAACTTAAGC
1 TTTCAAA-TTAAGC
41577095 TTTCAAATTA
1 TTTCAAATTA
41577105 CAAATATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (13 bp):
TTTCAAATTAAGC
Found at i:41581430 original size:21 final size:21
Alignment explanation
Indices: 41581406--41581461 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
41581396 ATGAACAATT
*
41581406 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
41581427 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
41581447 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
41581462 CGATTTGCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:41581447 original size:20 final size:23
Alignment explanation
Indices: 41581417--41581461 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
41581407 AGAAAAAGAG
41581417 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
41581438 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
41581460 AA
1 AA
41581462 CGATTTGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:41584293 original size:35 final size:35
Alignment explanation
Indices: 41584247--41584396 Score: 225
Period size: 35 Copynumber: 4.4 Consensus size: 35
41584237 GGTAACCATC
*
41584247 AGATTCTCTGCAACAAAATAATGCGTGAACAGGAG
1 AGATTCCCTGCAACAAAATAATGCGTGAACAGGAG
* *
41584282 AGATTCCCTGCAA-GAAATGAT--GTGAACAGGAG
1 AGATTCCCTGCAACAAAATAATGCGTGAACAGGAG
* *
41584314 AGATTCCCTGCAACAAAATAATGTGTGAACAAGAG
1 AGATTCCCTGCAACAAAATAATGCGTGAACAGGAG
*
41584349 AGATTCCCTGCAACAAAATAATACGTGAACAGGAG
1 AGATTCCCTGCAACAAAATAATGCGTGAACAGGAG
41584384 AGATTCCCTGCAA
1 AGATTCCCTGCAA
41584397 GAAATTTGTA
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
32 24 0.23
33 6 0.06
34 6 0.06
35 67 0.65
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (35 bp):
AGATTCCCTGCAACAAAATAATGCGTGAACAGGAG
Done.