Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold107
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: 2327068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1246839 original size:18 final size:16
Alignment explanation
Indices: 1246801--1246842 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
1246791 TATTTTTCAA
*
1246801 AAAAATATTTTAAAAG
1 AAAAATAATTTAAAAG
1246817 AAAAATAATTTAAAAG
1 AAAAATAATTTAAAAG
1246833 TAGAAAATAA
1 -A-AAAATAA
1246843 AAAATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 1 0.04
18 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (16 bp):
AAAAATAATTTAAAAG
Found at i:1247140 original size:121 final size:123
Alignment explanation
Indices: 1246896--1247143 Score: 290
Period size: 121 Copynumber: 2.0 Consensus size: 123
1246886 AAATTAAAAA
*
1246896 AAATCAAATATCTTTAATTTATTTTATTAATATTATTATAATTTAAATTTAATATAATTTTTAAT
1 AAATCAAATATCTTTAATTTATTTTATTAATATAATTATAATTTAAATTTAATATAATTTTTAAT
* ** * ** *
1246961 TAAGTTAATATTATTAAACATGTAATATTAAAATTTAATTAAAATTTTATAATAATAT
66 TAAGATAATATTATTAAACACATAATATTAAAATTTAATAAAAAAATTATAAAAATAT
* * *
1247019 AAAT-AAATATTTTTAATTTATTTTATTATTATAATT-TAATTTAAATTTTATA-AATTTTTTAA
1 AAATCAAATATCTTTAATTTATTTTATTAATATAATTATAATTTAAATTTAATATAA-TTTTTAA
* * ** *
1247081 TTAA-ATACTTCTTATTTTACCCATAATATT-AAATTTAATAAAAAAATTATAAAATATAT
65 TTAAGATA-ATATTATTAAACACATAATATTAAAATTTAATAAAAAAATTATAAAA-ATAT
1247140 AAAT
1 AAAT
1247144 TTATAATATA
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
120 24 0.23
121 49 0.46
122 29 0.27
123 4 0.04
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (123 bp):
AAATCAAATATCTTTAATTTATTTTATTAATATAATTATAATTTAAATTTAATATAATTTTTAAT
TAAGATAATATTATTAAACACATAATATTAAAATTTAATAAAAAAATTATAAAAATAT
Found at i:1251933 original size:20 final size:21
Alignment explanation
Indices: 1251908--1251951 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1251898 AAAGAATTTG
1251908 AAATA-TTTTAATATT-ATTCA
1 AAATATTTTTAAT-TTAATTCA
1251928 AAATATTTTTAATTTAATTCA
1 AAATATTTTTAATTTAATTCA
1251949 AAA
1 AAA
1251952 AAATACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATATTTTTAATTTAATTCA
Found at i:1253918 original size:20 final size:21
Alignment explanation
Indices: 1253883--1253924 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1253873 CAATTTGTAG
1253883 CAATACAATAAGTGAATCTAT
1 CAATACAATAAGTGAATCTAT
* *
1253904 CAATAC-ATTAGTGAATGTAT
1 CAATACAATAAGTGAATCTAT
1253924 C
1 C
1253925 GATATATGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (21 bp):
CAATACAATAAGTGAATCTAT
Found at i:1254063 original size:51 final size:52
Alignment explanation
Indices: 1253997--1254097 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 52
1253987 AAAAATATCG
* *
1253997 ATACATTTTTTATTATATCGATACATTCTAGG-TTTTGACCCAAATGTATTA
1 ATACATTCTATATTATATCGATACATTCTAGGTTTTTGACCCAAATGTATTA
* *
1254048 ATACATTCTATATTATATTGATACATTCTGGGTTTTTGACCCAAATGTAT
1 ATACATTCTATATTATATCGATACATTCTAGGTTTTTGACCCAAATGTAT
1254098 CGATCCATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 28 0.62
52 17 0.38
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (52 bp):
ATACATTCTATATTATATCGATACATTCTAGGTTTTTGACCCAAATGTATTA
Found at i:1254117 original size:52 final size:50
Alignment explanation
Indices: 1253992--1254125 Score: 169
Period size: 52 Copynumber: 2.6 Consensus size: 50
1253982 AATGAAAAAA
1253992 TATCGATACATTTTTTATTATATCGATACATTCTAGGTTTTGACCCAAATG
1 TATCGATACA-TTTTTATTATATCGATACATTCTAGGTTTTGACCCAAATG
** * * *
1254043 TATTAATACATTCTATATTATATTGATACATTCTGGGTTTTTGACCCAAATG
1 TATCGATACATT-TTTATTATATCGATACATTCTAGG-TTTTGACCCAAATG
* *
1254095 TATCGATCCATTTTTCAATATATCGATACAT
1 TATCGATACATTTTT-ATTATATCGATACAT
1254126 GCAAGCAAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
50 2 0.03
51 31 0.45
52 36 0.52
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (50 bp):
TATCGATACATTTTTATTATATCGATACATTCTAGGTTTTGACCCAAATG
Found at i:1261329 original size:165 final size:165
Alignment explanation
Indices: 1261057--1261389 Score: 621
Period size: 165 Copynumber: 2.0 Consensus size: 165
1261047 AAGAGATAGT
*
1261057 TCTTCAGTTCATAAGGTGGTGATCGAAATGAGAAATAACCTTCTTTCATCATCCTTTCACAAATT
1 TCTTCAGTTCACAAGGTGGTGATCGAAATGAGAAATAACCTTCTTTCATCATCCTTTCACAAATT
1261122 AAAATTTCCTTTTGCCACCCCCTTTGAGCCTAATAAATTCATTCTTTTGAAATCCTGATCAAGGA
66 AAAATTTCCTTTTGCCACCCCCTTTGAGCCTAATAAATTCATTCTTTTGAAATCCTGATCAAGGA
*
1261187 TCACCTCCTACATTTGGGTGGTATGGGGGCAAATA
131 TCACCTCCTACATTTGGGGGGTATGGGGGCAAATA
*
1261222 TCTTCAGTTCACAAGGTGGTGATCGAAATGAGAAATAGCCTTCTTTCATCATCCTTTCACAAATT
1 TCTTCAGTTCACAAGGTGGTGATCGAAATGAGAAATAACCTTCTTTCATCATCCTTTCACAAATT
*
1261287 AAAATTTCCTTTTGCCACCCCCTTTGAGCTTAATAAATTCATTCTTTTGAAATCCTGATCAAGGA
66 AAAATTTCCTTTTGCCACCCCCTTTGAGCCTAATAAATTCATTCTTTTGAAATCCTGATCAAGGA
*
1261352 TCACCTCCTACATTTGGGGGGTATGGGGGCACATA
131 TCACCTCCTACATTTGGGGGGTATGGGGGCAAATA
1261387 TCT
1 TCT
1261390 CATCCTAAAA
Statistics
Matches: 163, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
165 163 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (165 bp):
TCTTCAGTTCACAAGGTGGTGATCGAAATGAGAAATAACCTTCTTTCATCATCCTTTCACAAATT
AAAATTTCCTTTTGCCACCCCCTTTGAGCCTAATAAATTCATTCTTTTGAAATCCTGATCAAGGA
TCACCTCCTACATTTGGGGGGTATGGGGGCAAATA
Found at i:1263043 original size:30 final size:29
Alignment explanation
Indices: 1262976--1263439 Score: 304
Period size: 30 Copynumber: 15.8 Consensus size: 29
1262966 TAACCTTTTC
* *
1262976 AAAGTCCACAACTCAGTAGCATCCCTTTTT
1 AAAGTCCACAACTCAGTGGCA-CCCTTCTT
** *
1263006 CAAAGTCCATGACTCAGTGGCATCTCTTCTT
1 -AAAGTCCACAACTCAGTGGCA-CCCTTCTT
*
1263037 AAAGTCCACAACTCAGTGGCATCTCTT-TT
1 AAAGTCCACAACTCAGTGGCA-CCCTTCTT
* ** * *
1263066 CAAAGTCTATGACTTAGCGGCATCCCTTCTT
1 -AAAGTCCACAACTCAGTGGCA-CCCTTCTT
* *
1263097 CAAAGTCCATAACTCTGTGGCACCCTTC-T
1 -AAAGTCCACAACTCAGTGGCACCCTTCTT
* * *
1263126 AAAGTCCACAACTCCGTGACACCCTTTTTT
1 AAAGTCCACAACTCAGTGGCACCC-TTCTT
* *
1263156 AAAGTCCATAACTCAGTAGCACCCTTC-T
1 AAAGTCCACAACTCAGTGGCACCCTTCTT
* *
1263184 AAAGTCCACAAATCAGTGGCACCCCTTTTT
1 AAAGTCCACAACTCAGTGGCA-CCCTTCTT
1263214 AAAGTCCACAACTCAGTGGCACCCTT-TT
1 AAAGTCCACAACTCAGTGGCACCCTTCTT
* * * * *
1263242 CAAAGTCCACAATTCTGTAGCACCATTTTT
1 -AAAGTCCACAACTCAGTGGCACCCTTCTT
* * *
1263272 AAAGTCCACAACTCAGTCGCA-TCTTTTT
1 AAAGTCCACAACTCAGTGGCACCCTTCTT
* **
1263300 CAAAGTTCACAACTCCA-TGGCACTTTTC-T
1 -AAAGTCCACAACT-CAGTGGCACCCTTCTT
* *
1263329 AAAGTCTA-AACTCTA-TAGCACCCTT-TT
1 AAAGTCCACAACTC-AGTGGCACCCTTCTT
* ** * *
1263356 -AAGTCTACAACTTTGTAGCACCCTCCTTTT
1 AAAGTCCACAACTCAGTGGCACCCT--TCTT
* *
1263386 TAAGTCCACAACTTC-GTGGCACCCTCCTTTT
1 AAAGTCCACAAC-TCAGTGGCACCCT--TCTT
* *
1263417 AAAGTCCATAACTCCGTGGCACC
1 AAAGTCCACAACTCAGTGGCACC
1263440 TTTTTTTTTA
Statistics
Matches: 355, Mismatches: 57, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
26 8 0.02
27 26 0.07
28 53 0.15
29 75 0.21
30 105 0.30
31 87 0.25
32 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.30
Consensus pattern (29 bp):
AAAGTCCACAACTCAGTGGCACCCTTCTT
Found at i:1263166 original size:58 final size:58
Alignment explanation
Indices: 1262971--1263523 Score: 311
Period size: 58 Copynumber: 9.3 Consensus size: 58
1262961 TAAAGTAACC
* * ** * * *
1262971 TTTTCAAAGTCCACAACTCAGTAGCATCCCTTTTTCAAAGTCCATGACTCAGTGGCA-TCT
1 TTTTTAAAGTCCACAACTCAGTGGCA-CCC-TTTT-AAAGTCCACAACTCCGTGACACCCT
* * * ** ** * *
1263031 CTTCTTAAAGTCCACAACTCAGTGGCATCTCTTTTCAAAGTCTATGACTTAGCGGCATCCCT
1 -TTTTTAAAGTCCACAACTCAGTGGCA-CCCTTTT-AAAGTCCACAACTCCGTGACA-CCCT
* * * * *
1263093 TCTTCAAAGTCCATAACTCTGTGGCACCCTTCTAAAGTCCACAACTCCGTGACACCCT
1 TTTTTAAAGTCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCCGTGACACCCT
* * * * * * *
1263151 TTTTTAAAGTCCATAACTCAGTAGCACCCTTCTAAAGTCCACAAATCAGTGGCACCCC
1 TTTTTAAAGTCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCCGTGACACCCT
* * *
1263209 TTTTTAAAGTCCACAACTCAGTGGCACCCTTTTCAAAGTCCACAATTCTGT-AGCA-CCA
1 TTTTTAAAGTCCACAACTCAGTGGCACCCTTTT-AAAGTCCACAACTCCGTGA-CACCCT
* * * * * *
1263267 TTTTTAAAGTCCACAACTCAGTCGCATCTTTTTCAAAGTTCACAACTCCATGGCA--CT
1 TTTTTAAAGTCCACAACTCAGTGGCACCCTTTT-AAAGTCCACAACTCCGTGACACCCT
* * * * **
1263324 TTTCTAAAGTCTA-AACTCTA-TAGCACCCTTTT-AAGTCTACAACTTTGT-AGCACCCT
1 TTTTTAAAGTCCACAACTC-AGTGGCACCCTTTTAAAGTCCACAACTCCGTGA-CACCCT
* * *
1263380 CCTTTTT-AAGTCCACAACTTC-GTGGCACCCTCCTTTTAAAGTCCATAACTCCGTGGCACCTTT
1 --TTTTTAAAGTCCACAAC-TCAGTGGCA--C-CCTTTTAAAGTCCACAACTCCGTGACACC-CT
* * * * * * * *
1263443 TTTTTTAAGTTCATAACTCCGTGGCACCCTCCTTTCTACAGTTCACAACTCTGTGGCACTCTCT
1 TTTTTAAAGTCCACAACTCAGTGGCA--C-CCTTT-TAAAGTCCACAACTCCGTGACAC-C-CT
1263507 TTTTT-AAGTCCACAACT
1 TTTTTAAAGTCCACAACT
1263524 TCGTGACACC
Statistics
Matches: 393, Mismatches: 75, Indels: 46
0.76 0.15 0.09
Matches are distributed among these distances:
54 13 0.03
56 16 0.04
57 19 0.05
58 143 0.36
59 33 0.08
60 29 0.07
61 60 0.15
62 42 0.11
63 30 0.08
64 8 0.02
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (58 bp):
TTTTTAAAGTCCACAACTCAGTGGCACCCTTTTAAAGTCCACAACTCCGTGACACCCT
Found at i:1263390 original size:31 final size:31
Alignment explanation
Indices: 1263352--1263533 Score: 184
Period size: 31 Copynumber: 5.8 Consensus size: 31
1263342 TATAGCACCC
* ** *
1263352 TTTTAAGTCTACAACTTTGTAGCACCCTCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCTCCT
*
1263383 TTTTAAGTCCACAACTTCGTGGCACCCTCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCTCCT
* * * **
1263414 TTTAAAGTCCATAACTCCGTGGCACCTTTTT
1 TTTTAAGTCCACAACTCCGTGGCACCCTCCT
* *
1263445 TTTTAAGTTCATAACTCCGTGGCACCCTCCT
1 TTTTAAGTCCACAACTCCGTGGCACCCTCCT
* * * * *
1263476 TTCTACAGTTCACAACTCTGTGGCACTCTCTT
1 TTTTA-AGTCCACAACTCCGTGGCACCCTCCT
* *
1263508 TTTTAAGTCCACAACTTCGTGACACC
1 TTTTAAGTCCACAACTCCGTGGCACC
1263534 ATTTCAAGTC
Statistics
Matches: 125, Mismatches: 25, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
31 99 0.79
32 26 0.21
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (31 bp):
TTTTAAGTCCACAACTCCGTGGCACCCTCCT
Found at i:1263617 original size:31 final size:33
Alignment explanation
Indices: 1263579--1263645 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1263569 AGTCAATGGC
1263579 ACCTTTTT-AAAA-CCCACACAAGTAGGTGGAA
1 ACCTTTTTCAAAAGCCCACACAAGTAGGTGGAA
* * *
1263610 ACCTTTTTCAAAAGCCCACATAAGTTGGTGGCA
1 ACCTTTTTCAAAAGCCCACACAAGTAGGTGGAA
1263643 ACC
1 ACC
1263646 CTCTCAAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 8 0.26
32 4 0.13
33 19 0.61
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (33 bp):
ACCTTTTTCAAAAGCCCACACAAGTAGGTGGAA
Found at i:1263640 original size:33 final size:33
Alignment explanation
Indices: 1263575--1263798 Score: 105
Period size: 31 Copynumber: 7.3 Consensus size: 33
1263565 CACAAGTCAA
*
1263575 TGGC-ACCTTTTT-AAAA-CCCACACAAGTAGG
1 TGGCAACCTTTTTCAAAAGCCCACATAAGTAGG
* *
1263605 TGGAAACCTTTTTCAAAAGCCCACATAAGTTGG
1 TGGCAACCTTTTTCAAAAGCCCACATAAGTAGG
* * *
1263638 TGGCAACC-CTCTC-AAAGCCTACATAAGTCA-G
1 TGGCAACCTTTTTCAAAAGCCCACATAAGT-AGG
*
1263669 TGGCAACC--TTTC-AAAGCTCAC--AAGTTA-G
1 TGGCAACCTTTTTCAAAAGCCCACATAAG-TAGG
* *
1263697 TGGC-ATCTTTTT--AAAG-CC-CATAAGTCA-T
1 TGGCAACCTTTTTCAAAAGCCCACATAAGT-AGG
** *
1263725 TGGCTTCC-CTTTC-AAAGCCCACATAAGTTA-G
1 TGGCAACCTTTTTCAAAAGCCCACATAAG-TAGG
* * * *
1263756 TGGTAACCCTTTTT-GAAAGCTCACATAAGTTGG
1 TGGCAA-CCTTTTTCAAAAGCCCACATAAGTAGG
1263789 TGGCAACCTT
1 TGGCAACCTT
1263799 CTCAAAGCCC
Statistics
Matches: 150, Mismatches: 25, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
26 1 0.01
27 4 0.03
28 24 0.16
29 9 0.06
30 15 0.10
31 41 0.27
32 15 0.10
33 41 0.27
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (33 bp):
TGGCAACCTTTTTCAAAAGCCCACATAAGTAGG
Found at i:1263662 original size:31 final size:31
Alignment explanation
Indices: 1263615--1263821 Score: 142
Period size: 31 Copynumber: 6.8 Consensus size: 31
1263605 TGGAAACCTT
* *
1263615 TTTCAAAAGCCCACATAAGTTGGTGGCAACCC
1 TTTC-AAAGCCTACATAAGTTAGTGGCAACCC
* *
1263647 TCTCAAAGCCTACATAAGTCAGTGGCAA-CC
1 TTTCAAAGCCTACATAAGTTAGTGGCAACCC
* * *
1263677 TTTCAAAG-CT-CACAAGTTAGTGGC-ATCT
1 TTTCAAAGCCTACATAAGTTAGTGGCAACCC
* * * **
1263705 TTTTAAAGCC--CATAAGTCATTGGCTTCCC
1 TTTCAAAGCCTACATAAGTTAGTGGCAACCC
* *
1263734 TTTCAAAGCCCACATAAGTTAGTGGTAACCC
1 TTTCAAAGCCTACATAAGTTAGTGGCAACCC
* *
1263765 TTTTTGAAAG-CTCACATAAGTTGGTGGCAA-CC
1 --TTTCAAAGCCT-ACATAAGTTAGTGGCAACCC
* * *
1263797 TTCTCAAAGCCCATACAAGTTAGTG
1 TT-TCAAAGCCTACATAAGTTAGTG
1263822 CATCTCGTTC
Statistics
Matches: 135, Mismatches: 30, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
27 1 0.01
28 31 0.23
29 13 0.10
30 11 0.08
31 50 0.37
32 7 0.05
33 22 0.16
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (31 bp):
TTTCAAAGCCTACATAAGTTAGTGGCAACCC
Found at i:1263804 original size:64 final size:60
Alignment explanation
Indices: 1263580--1263821 Score: 190
Period size: 64 Copynumber: 3.9 Consensus size: 60
1263570 GTCAATGGCA
* * * *
1263580 CCTTTTTAAAACCCACACAAGT-AGGTGGAAACCTTTTTCAAAAGCCCACATAAGTTGGTGGCAA
1 CCTTTTT-AAAGCCACATAAGTCA-GTGGCAACC--TTTC-AAAGCCCACATAAGTTAGTGG-AA
1263644 C
60 C
* * * *
1263645 CC-TCTCAAAGCCTACATAAGTCAGTGGCAACCTTTCAAAGCTCAC--AAGTTAGTGGCA-
1 CCTTTTTAAAGCC-ACATAAGTCAGTGGCAACCTTTCAAAGCCCACATAAGTTAGTGGAAC
* * **
1263702 TCTTTTTAAAGCC-CATAAGTCATTGGCTTCCCTTTCAAAGCCCACATAAGTTAGTGGTAAC
1 CCTTTTTAAAGCCACATAAGTCAGTGGC-AACCTTTCAAAGCCCACATAAGTTAGTGG-AAC
** * *
1263763 CCTTTTTGAAAGCTCACATAAGTTGGTGGCAACCTTCTCAAAGCCCATACAAGTTAGTG
1 CCTTTTT-AAAGC-CACATAAGTCAGTGGCAACCTT-TCAAAGCCCACATAAGTTAGTG
1263822 CATCTCGTTC
Statistics
Matches: 141, Mismatches: 24, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
56 13 0.09
57 15 0.11
58 9 0.06
59 19 0.13
60 1 0.01
61 14 0.10
62 9 0.06
63 10 0.07
64 48 0.34
65 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (60 bp):
CCTTTTTAAAGCCACATAAGTCAGTGGCAACCTTTCAAAGCCCACATAAGTTAGTGGAAC
Found at i:1263938 original size:52 final size:52
Alignment explanation
Indices: 1263839--1263940 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 52
1263829 TTCTAAGCCT
* *
1263839 AATGTCGTTGGCCTTACATCAACACATTAACACTCTTCTCATTTTTAAGTCC
1 AATGTCATTGGCCTTACATCAACACATTAACACTCTTCTCATCTTTAAGTCC
* * *
1263891 AATGTCATTGGCCTTGA-ATCAACATATTAGCAC-CTTTGTCATCTTTAAGT
1 AATGTCATTGGCCTT-ACATCAACACATTAACACTC-TTCTCATCTTTAAGT
1263941 TTAATATTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
51 1 0.02
52 41 0.95
53 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (52 bp):
AATGTCATTGGCCTTACATCAACACATTAACACTCTTCTCATCTTTAAGTCC
Found at i:1264003 original size:52 final size:52
Alignment explanation
Indices: 1263947--1264079 Score: 126
Period size: 52 Copynumber: 2.6 Consensus size: 52
1263937 AAGTTTAATA
*
1263947 TTGCTGGCCTTGAATTAGTATATTGGCA-CCTT-TATCATTCTTAAGCCCGATG
1 TTGCTGGCCTTGAATTAGTATATTGGCATCCTTCTA--ATTCTTAAGCCCAATG
* * * * * * *
1263999 TTGCTAGCTTTAAATTAGTACATTGGCATTCTTCTAATTTTTAAGTCCAATG
1 TTGCTGGCCTTGAATTAGTATATTGGCATCCTTCTAATTCTTAAGCCCAATG
** * *
1264051 TCACTGGCCTTGAATCAGCATATTGGCAT
1 TTGCTGGCCTTGAATTAGTATATTGGCAT
1264080 TTTTTTATCT
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
52 58 0.92
53 3 0.05
54 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (52 bp):
TTGCTGGCCTTGAATTAGTATATTGGCATCCTTCTAATTCTTAAGCCCAATG
Found at i:1264281 original size:52 final size:52
Alignment explanation
Indices: 1264203--1264452 Score: 236
Period size: 52 Copynumber: 4.8 Consensus size: 52
1264193 TTTATCTCCA
* * * * *
1264203 TTTAAGTCTAATGTTGCTGACCTTGAATCAGCACATAGGCACCTTTGTCATT
1 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATT
* * * *
1264255 TTTAAGCCCAATGTCGTTGGCTTTGAATTAGCACATTGGCACCCTTGTCATT
1 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATT
* * * * * *
1264307 TTTAAGTCTAATGTCGCTGGCCTTAAATCAGCACATTGGCA-TTCTTCTCATC
1 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCT-TTGTCATT
* * * * *
1264359 TTTAAGTCCAATGTCATTGGCCTTGAATCAACACATTAGCATTCTTCTG--ATC
1 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCA-CCTT-TGTCATT
* * * *
1264411 TTTAAGTCTAATATCATTGGCCTTGAATCAGCATATTGGCAC
1 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCAC
1264453 TTTTCTTATC
Statistics
Matches: 161, Mismatches: 33, Indels: 9
0.79 0.16 0.04
Matches are distributed among these distances:
52 158 0.98
53 1 0.01
54 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (52 bp):
TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATT
Found at i:1264336 original size:104 final size:105
Alignment explanation
Indices: 1264203--1264452 Score: 288
Period size: 104 Copynumber: 2.4 Consensus size: 105
1264193 TTTATCTCCA
* * * * *
1264203 TTTAAGTCTAATGTTGCTGACCTTGAATCAGCACATAGGCACCT-TTGTCATTTTTAAGCCCAAT
1 TTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCTTCTCATCTTTAAGCCCAAT
* * * * * * *
1264267 GTCGTTGGCTTTGAATTAGCACATTGGCACCCTTGTCATT
66 GTCATTGGCCTTGAATCAACACATTAGCACCCTTCTCATC
* * *
1264307 TTTAAGTCTAATGTCGCTGGCCTTAAATCAGCACATTGGCA-TTCTTCTCATCTTTAAGTCCAAT
1 TTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCTTCTCATCTTTAAGCCCAAT
** *
1264371 GTCATTGGCCTTGAATCAACACATTAGCATTCTTCTGATC
66 GTCATTGGCCTTGAATCAACACATTAGCACCCTTCTCATC
* ** *
1264411 TTTAAGTCTAATATCATTGGCCTTGAATCAGCATATTGGCAC
1 TTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1264453 TTTTCTTATC
Statistics
Matches: 121, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
103 1 0.01
104 120 0.99
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (105 bp):
TTTAAGTCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCTTCTCATCTTTAAGCCCAAT
GTCATTGGCCTTGAATCAACACATTAGCACCCTTCTCATC
Found at i:1265035 original size:23 final size:23
Alignment explanation
Indices: 1265009--1265053 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1264999 TTTATAAACT
*
1265009 TTTTAT-TTTTAGTTTTTGTTATA
1 TTTTATATTTTA-TTTTGGTTATA
*
1265032 TTTTCTATTTTATTTTGGTTAT
1 TTTTATATTTTATTTTGGTTAT
1265054 TTATGCCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (23 bp):
TTTTATATTTTATTTTGGTTATA
Found at i:1265502 original size:19 final size:19
Alignment explanation
Indices: 1265478--1265516 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1265468 CCAGCCAACA
1265478 TACCTAAGTTTTTTCTTTC
1 TACCTAAGTTTTTTCTTTC
1265497 TACCTAAGTTTTTTCTTTC
1 TACCTAAGTTTTTTCTTTC
1265516 T
1 T
1265517 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.21, G:0.05, T:0.59
Consensus pattern (19 bp):
TACCTAAGTTTTTTCTTTC
Found at i:1270380 original size:30 final size:30
Alignment explanation
Indices: 1270346--1270436 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
1270336 ATTTCCAATA
1270346 TTTAAATACTAGTTTAATAAATTAAGTCCT
1 TTTAAATACTAGTTTAATAAATTAAGTCCT
** ** * *
1270376 TTT-AA-ACTA---TAGGACCTTTAGT-AT
1 TTTAAATACTAGTTTAATAAATTAAGTCCT
1270400 ATTTAAATACTAGTTTAATAAATTAAGTCCT
1 -TTTAAATACTAGTTTAATAAATTAAGTCCT
1270431 TTTAAA
1 TTTAAA
1270437 CTATAGGACC
Statistics
Matches: 42, Mismatches: 12, Indels: 14
0.62 0.18 0.21
Matches are distributed among these distances:
24 1 0.02
25 11 0.26
26 2 0.05
27 4 0.10
28 4 0.10
29 2 0.05
30 17 0.40
31 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.43
Consensus pattern (30 bp):
TTTAAATACTAGTTTAATAAATTAAGTCCT
Found at i:1270427 original size:55 final size:55
Alignment explanation
Indices: 1270343--1270455 Score: 226
Period size: 55 Copynumber: 2.1 Consensus size: 55
1270333 AACATTTCCA
1270343 ATATTTAAATACTAGTTTAATAAATTAAGTCCTTTTAAACTATAGGACCTTTAGT
1 ATATTTAAATACTAGTTTAATAAATTAAGTCCTTTTAAACTATAGGACCTTTAGT
1270398 ATATTTAAATACTAGTTTAATAAATTAAGTCCTTTTAAACTATAGGACCTTTAGT
1 ATATTTAAATACTAGTTTAATAAATTAAGTCCTTTTAAACTATAGGACCTTTAGT
1270453 ATA
1 ATA
1270456 ACATAAGGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.42
Consensus pattern (55 bp):
ATATTTAAATACTAGTTTAATAAATTAAGTCCTTTTAAACTATAGGACCTTTAGT
Found at i:1276605 original size:6 final size:6
Alignment explanation
Indices: 1276596--1276621 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1276586 ATATTTATAT
1276596 AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
1276622 TTATTTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:1281089 original size:6 final size:6
Alignment explanation
Indices: 1281078--1281138 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
1281068 CCGAAATTTC
*
1281078 TCTTTT TCTTTT TCTTTT T-TTTCT T-TTTT T-TTTT CTCTTTT GCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTT-T TCTTTT TCTTTT -TCTTTT TCTTTT
*
1281125 TCCTTT TCTATTT T
1 TCTTTT TCT-TTT T
1281139 AGTTTTCTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
5 9 0.19
6 30 0.64
7 8 0.17
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:1281097 original size:14 final size:14
Alignment explanation
Indices: 1281074--1281125 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
1281064 TTTTCCGAAA
*
1281074 TTTCTCTTTTTCTT
1 TTTCTTTTTTTCTT
1281088 TTTCTTTTTTTTCTT
1 TTTC-TTTTTTTCTT
1281103 TTT-TTTTTTCTCTT
1 TTTCTTTTTT-TCTT
*
1281117 TTGCTTTTT
1 TTTCTTTTT
1281126 CCTTTTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 6 0.18
14 10 0.30
15 17 0.52
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:1281100 original size:15 final size:15
Alignment explanation
Indices: 1281080--1281125 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
1281070 GAAATTTCTC
1281080 TTTTTCTTTTTCTTT
1 TTTTTCTTTTTCTTT
1281095 TTTTTCTTTTT-TTT
1 TTTTTCTTTTTCTTT
* *
1281109 TTTCTCTTTTGCTTT
1 TTTTTCTTTTTCTTT
1281124 TT
1 TT
1281126 CCTTTTCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (15 bp):
TTTTTCTTTTTCTTT
Found at i:1281126 original size:14 final size:13
Alignment explanation
Indices: 1281078--1281138 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
1281068 CCGAAATTTC
1281078 TCTTTTTCT-TTT
1 TCTTTTTCTCTTT
*
1281090 TCTTTTTTTTCTTTT
1 TC-TTTTTCTC-TTT
*
1281105 TTTTTTTCTCTTT
1 TCTTTTTCTCTTT
1281118 TGCTTTTTC-CTTT
1 T-CTTTTTCTCTTT
1281131 TCTATTTT
1 TCT-TTTT
1281139 AGTTTTCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 4 0.10
13 19 0.47
14 13 0.32
15 4 0.10
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (13 bp):
TCTTTTTCTCTTT
Found at i:1285043 original size:56 final size:56
Alignment explanation
Indices: 1284957--1285196 Score: 178
Period size: 56 Copynumber: 4.3 Consensus size: 56
1284947 CTATACCAGT
* ** * *
1284957 TATACCTACTAGCTACTTTTAGGTTTTATCATCTTTGTGCCAATCTCAACTAGAGC
1 TATACCTACCAGCTACGGTTAGGCTTTATCATCTTGGTGCCAATCTCAACTAGAGC
* *
1285013 TATACCTACCAGCTACGGTTGGGCTTTATCATCTTGGTGCCAATTTCAACTAGAGC
1 TATACCTACCAGCTACGGTTAGGCTTTATCATCTTGGTGCCAATCTCAACTAGAGC
** *** * * * * * * *
1285069 TATACCTATTAGCTATTTTTGGGCTTTCTCATTTTGGTGCTAATTTCATA-TGGAGT
1 TATACCTACCAGCTACGGTTAGGCTTTATCATCTTGGTGCCAATCTCA-ACTAGAGC
** *** * * * * *
1285125 TATACCTATTAGCTATTCTCTA-ACTTTATCATCTTAGTGCCAATTTCAATTAGAGT
1 TATACCTACCAGCTACGGT-TAGGCTTTATCATCTTGGTGCCAATCTCAACTAGAGC
*
1285181 TATACCTACTAGCTAC
1 TATACCTACCAGCTAC
1285197 TTTTGGGCAT
Statistics
Matches: 154, Mismatches: 27, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
55 1 0.01
56 151 0.98
57 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (56 bp):
TATACCTACCAGCTACGGTTAGGCTTTATCATCTTGGTGCCAATCTCAACTAGAGC
Found at i:1290646 original size:30 final size:32
Alignment explanation
Indices: 1290623--1290688 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 32
1290613 AAATTTTATG
*
1290623 TATATTAAATAATA-AAATA-AAAATTATACT
1 TATATCAAATAATACAAATATAAAATTATACT
* *
1290653 TATGTCAAATAATACAAATATAAAATAATA-T
1 TATATCAAATAATACAAATATAAAATTATACT
1290684 TATAT
1 TATAT
1290689 TTATATTAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 12 0.40
31 10 0.33
32 8 0.27
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (32 bp):
TATATCAAATAATACAAATATAAAATTATACT
Found at i:1290678 original size:16 final size:16
Alignment explanation
Indices: 1290624--1290682 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
1290614 AATTTTATGT
*
1290624 ATATTAAATAATA-AA
1 ATATAAAATAATACAA
* **
1290639 ATA-AAAATTATACTT
1 ATATAAAATAATACAA
* *
1290654 ATGTCAAATAATACAA
1 ATATAAAATAATACAA
1290670 ATATAAAATAATA
1 ATATAAAATAATA
1290683 TTATATTTAT
Statistics
Matches: 31, Mismatches: 11, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
16 19 0.61
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (16 bp):
ATATAAAATAATACAA
Found at i:1295144 original size:20 final size:20
Alignment explanation
Indices: 1295121--1295169 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1295111 GCAAATTGTT
*
1295121 TCGATACATCTAGGAATGTA
1 TCGATACATCTACGAATGTA
* **
1295141 TCGATACATTTACTTATGTA
1 TCGATACATCTACGAATGTA
1295161 TCGATACAT
1 TCGATACAT
1295170 TTTGGTCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
TCGATACATCTACGAATGTA
Found at i:1296773 original size:23 final size:23
Alignment explanation
Indices: 1296746--1296789 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1296736 GCATTCAACC
*
1296746 TTGGGTTATAATCTCTT-AAGAAT
1 TTGGGGTATAAT-TCTTGAAGAAT
1296769 TTGGGGTATAATTCTTGAAGA
1 TTGGGGTATAATTCTTGAAGA
1296790 GATTGAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGGGGTATAATTCTTGAAGAAT
Found at i:1300015 original size:22 final size:23
Alignment explanation
Indices: 1299969--1300015 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1299959 TGGAAAATGT
*
1299969 GATAATCATACAATGAACTGATG
1 GATAATCATACAATGAAATGATG
* *
1299992 GATAA-CATTCAATGAAATGCTG
1 GATAATCATACAATGAAATGATG
1300014 GA
1 GA
1300016 CATATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (23 bp):
GATAATCATACAATGAAATGATG
Found at i:1300444 original size:10 final size:10
Alignment explanation
Indices: 1300431--1300455 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1300421 TGTTTCTTTT
1300431 GGGAGCTATA
1 GGGAGCTATA
1300441 GGGAGCTATA
1 GGGAGCTATA
1300451 GGGAG
1 GGGAG
1300456 ATATGGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.48, T:0.16
Consensus pattern (10 bp):
GGGAGCTATA
Found at i:1301955 original size:32 final size:29
Alignment explanation
Indices: 1301917--1302802 Score: 311
Period size: 28 Copynumber: 30.4 Consensus size: 29
1301907 CCTTAACTTG
*
1301917 TGTGGGCTTCAAAAAGAGTTGCCACCAACT
1 TGTGGGCTTTAAAAAGAG-TGCCACCAACT
*
1301947 CATGTGGGCTTTGAAAAGAGTGCCACCAACT
1 --TGTGGGCTTTAAAAAGAGTGCCACCAACT
* **
1301978 TGTGGGCTTT-AAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * **
1302006 TGTGGGCTTT-GAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * *
1302034 TGTGGGCTTTGAAAAGAGTTGTCACCGACT
1 TGTGGGCTTTAAAAAGAG-TGCCACCAACT
* * * *
1302064 CGTGGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* *** * * * ** *
1302092 TGTGGAC--TAACTTGTGGGCTTTGAAAAGAGTT
1 TGTGGGCTTTAAAAAGAGTGC---CACCA-A-CT
* * * *
1302124 GTCACCGACTTGTGGGCTTTGAAAGGAGTTGTCACCGACT
1 -T----G---TG--GGCTTTAAAAAGAG-TGCCACCAACT
* * **
1302164 TGTGGGCTTTGAAAGGA-TGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* ***
1302192 TGTGGGCTTTAAAAGGA-TGCCATTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * *
1302220 TGTGGGCTTTGAAAA-AGTGACACTAACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* **
1302248 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
** * **
1302277 TGTGGG-TTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * *
1302305 TGTGGGCTTTCAAAAGAGTTACCACCGACT
1 TGTGGGCTTTAAAAAGAG-TGCCACCAACT
* * * * **
1302335 CGTGGGCTTT-GACAGAATGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * **
1302363 TGTGGGCTTTGAAAGGA-TGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * * **
1302391 TGTGGGCTTT-GAATGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * **
1302419 TGTGGGCTTTGAAAAGAGTTCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * * *
1302448 TGTAGGCTTT-GAAAGGGTGCCACAAACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* *
1302476 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTAAAAAGAG-TGCCACCAACT
* * * * *
1302506 CGTAGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* **
1302534 TGTGGGCTTT-GAAAGAGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * **
1302562 TGTGGGCTTTGAAAAGAGCGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * * **
1302591 TGTGGGCTTT-GAAAGGGTGCTACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * * *
1302619 TGTGGGCTTTGAAAAGAGTTGGCATCGACT
1 TGTGGGCTTTAAAAAGAG-TGCCACCAACT
** * * * **
1302649 CATGGGCTTT-GAAAGAATGCGACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * **
1302677 TGTGGGCTTT-GAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* *
1302705 TGTGGGCTTTGAAAAGAGGTGCCACCGACT
1 TGTGGGCTTTAAAAAGA-GTGCCACCAACT
** * * ***
1302735 CAT-GGCTTTGAAAGGA-TGCCATTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
* * **
1302762 TATGGGCTTT-AAAAGGGTGCCACTGACT
1 TGTGGGCTTTAAAAAGAGTGCCACCAACT
1302790 TGTGGGCTTTAAA
1 TGTGGGCTTTAAA
1302803 GAGATGAAAG
Statistics
Matches: 680, Mismatches: 135, Indels: 81
0.76 0.15 0.09
Matches are distributed among these distances:
26 3 0.00
27 25 0.04
28 369 0.54
29 129 0.19
30 107 0.16
31 12 0.02
32 19 0.03
33 1 0.00
35 1 0.00
37 1 0.00
39 1 0.00
40 3 0.00
41 1 0.00
42 3 0.00
44 4 0.01
45 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTAAAAAGAGTGCCACCAACT
Found at i:1302174 original size:100 final size:98
Alignment explanation
Indices: 1302003--1302538 Score: 357
Period size: 85 Copynumber: 6.0 Consensus size: 98
1301993 GGTGCCACTG
*
1302003 ACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCGTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCGTG
1302068 GGCTTTGAAAGGATGCCACTAACTTGTGGACTA
66 GGCTTTGAAAGGATGCCACTAACTTGTGGACTA
* * * *
1302101 ACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTTGTGGGCTTTGAAAGGAGTTGTCACCGACTTG
1 ACTTGTGGGCTTTG-AAAG-GGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCG
1302166 TGGGCTTTGAAAGGATG-C-C--AC---T-G----
64 TGGGCTTTGAAAGGATGCCACTAACTTGTGGACTA
* * ** * ** *
1302189 ACTTGTGGGCTTTAAAAGGATGCCATTGACTTGTGGGCTTTGAAAA-AG-TGACACTAACTTGTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCGTG
*
1302252 GGCTTTGAAAAGAGTG-C-C--AC---T-G----
66 GGCTTTGAAAGGA-TGCCACTAACTTGTGGACTA
* * * **
1302274 ACTTGTGGGTTTTGAAAGGGTGCCACTGACTTGTGGGCTTTCAAAAGAGTTACCACCGACTCGTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCGTG
* *
1302339 GGCTTTGACAGAATG-C-C--AC---T-G----
66 GGCTTTGAAAGGATGCCACTAACTTGTGGACTA
* * * * * * *
1302360 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AATG-GGTGCCACTGACTTGTG
1 ACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCGTG
* *
1302423 GGCTTTGAAAAGA-GTTC-C--AC---T-G----
66 GGCTTTGAAAGGATG-CCACTAACTTGTGGACTA
* ** * *
1302445 ACTTGTAGGCTTTGAAAGGGTGCCACAAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTA
1 ACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCGTG
1302510 GGCTTTGAAAGGATGCCACTAACTTGTGG
66 GGCTTTGAAAGGATGCCACTAACTTGTGG
1302539 GCTTTGAAAG
Statistics
Matches: 371, Mismatches: 50, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
83 1 0.00
84 47 0.13
85 98 0.26
86 75 0.20
87 50 0.13
88 15 0.04
90 2 0.01
92 1 0.00
93 2 0.01
94 1 0.00
96 2 0.01
98 15 0.04
99 5 0.01
100 57 0.15
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (98 bp):
ACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTCGTG
GGCTTTGAAAGGATGCCACTAACTTGTGGACTA
Found at i:1302200 original size:28 final size:28
Alignment explanation
Indices: 1302101--1302808 Score: 742
Period size: 28 Copynumber: 24.8 Consensus size: 28
1302091 TTGTGGACTA
* * *
1302101 ACTTGTGGGCTTTGAAAAGAGTTGTCACCG
1 ACTTGTGGGCTTTG-AAAG-GATGCCACTG
* *
1302131 ACTTGTGGGCTTTGAAAGGAGTTGTCACCG
1 ACTTGTGGGCTTTGAAAGGA--TGCCACTG
1302161 ACTTGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
1302189 ACTTGTGGGCTTTAAAAGGATGCCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
1302217 ACTTGTGGGCTTTGAAA-AAGTGACACTA
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
*
1302245 ACTTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
* *
1302274 ACTTGTGGGTTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * * *
1302302 ACTTGTGGGCTTTCAAAAGAGTTACCACCG
1 ACTTGTGGGCTTT-GAAAG-GATGCCACTG
* * *
1302332 ACTCGTGGGCTTTGACAGAATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
1302360 ACTTGTGGGCTTTGAAAGGATGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
1302388 ACTTGTGGGCTTTGAATGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
1302416 ACTTGTGGGCTTTGAAAAGAGTTCCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
* * **
1302445 ACTTGTAGGCTTTGAAAGGGTGCCACAA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
1302473 ACTTGTGGGCTTTGAAAAGAGTTGCCACCG
1 ACTTGTGGGCTTTG-AAAG-GATGCCACTG
* * *
1302503 ACTCGTAGGCTTTGAAAGGATGCCACTA
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
1302531 ACTTGTGGGCTTTGAAA-GAGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
* *
1302559 ACTTGTGGGCTTTGAAAAGAGCGCCACTG
1 ACTTGTGGGCTTTGAAAGGA-TGCCACTG
* *
1302588 ACTTGTGGGCTTTGAAAGGGTGCTACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
1302616 ACTTGTGGGCTTTGAAAAGAGTTGGCA-TCG
1 ACTTGTGGGCTTTG-AAAG-GATGCCACT-G
** * *
1302646 ACTCATGGGCTTTGAAAGAATGCGACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
*
1302674 ACTTGTGGGCTTTGAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* *
1302702 ACTTGTGGGCTTTGAAAAGAGGTGCCACCG
1 ACTTGTGGGCTTTG-AAAG-GATGCCACTG
** *
1302732 ACTCAT-GGCTTTGAAAGGATGCCATTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
* * *
1302759 ACTTATGGGCTTTAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGAAAGGATGCCACTG
1302787 ACTTGTGGGCTTT-AAAGAGATG
1 ACTTGTGGGCTTTGAAAG-GATG
1302809 AAAGTTCTAG
Statistics
Matches: 573, Mismatches: 86, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.03
28 327 0.57
29 117 0.20
30 110 0.19
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
ACTTGTGGGCTTTGAAAGGATGCCACTG
Found at i:1302356 original size:143 final size:143
Alignment explanation
Indices: 1302097--1302808 Score: 800
Period size: 143 Copynumber: 5.0 Consensus size: 143
1302087 TAACTTGTGG
* * * *
1302097 ACTAACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTTGTGGGCTTTG-AAAGGAGTTGTCACCG
1 ACTAACTTGTGGGCTTTG-AAAGAG-TGCCACTGACTTGTGGGCTTTGAAAAGG-G-TGCCACTG
* ** *
1302161 ACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-AAAAG-GATGCCATTGACTTGTG
62 ACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGATGCCACCGACTCGTG
*
1302224 GGCTTTGAAAA-AGTGAC
127 GGCTTTGAAAAGA-TGCC
*
1302241 ACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGTTTTG-AAAGGGTGCCACTGACT
1 ACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
* * * * * * * *
1302305 TGTGGGCTTTCAAAAGAGTTACCACCGACTCGTGGGCTTTG-ACAGA-ATGCCACTGACTTGTGG
65 TGTGGGCTTT-GAAAG-GGTGCCACTGACTTGTGGGCTTTGAAAAGAGATGCCACCGACTCGTGG
*
1302368 GCTTTGAAAGGATGCC
128 GCTTTGAAAAGATGCC
* * * * *
1302384 ACTGACTTGTGGGCTTTGAATGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTCCACTGACTT
1 ACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTT
* ** * *
1302449 GTAGGCTTTGAAAGGGTGCCACAAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTAGGCT
66 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGATGCCACCGACTCGTGGGCT
*
1302514 TTGAAAGGATGCC
131 TTGAAAAGATGCC
* *
1302527 ACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGCGCCACTGACTT
1 ACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTT
* * * * *
1302592 GTGGGCTTTGAAAGGGTGCTACTGACTTGTGGGCTTTGAAAAGAGTTGGCATCGACTCATGGGCT
66 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGATGCCACCGACTCGTGGGCT
*
1302657 TTG-AAAGAATGCG
131 TTGAAAAG-ATGCC
* * *
1302670 ACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGGTGCCACCGACT
1 ACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAG-GGTGCCACTGACT
** * * * * * *
1302735 CAT-GGCTTTGAAAGGATGCCATTGACTTATGGGCTTT-AAAAG-GGTGCCACTGACTTGTGGGC
65 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGATGCCACCGACTCGTGGGC
1302797 TTT-AAAGAGATG
130 TTTGAAA-AGATG
1302809 AAAGTTCTAG
Statistics
Matches: 492, Mismatches: 64, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
141 60 0.12
142 48 0.10
143 347 0.71
144 37 0.08
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (143 bp):
ACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACTT
GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGATGCCACCGACTCGTGGGCT
TTGAAAAGATGCC
Found at i:1302392 original size:171 final size:172
Alignment explanation
Indices: 1302101--1302805 Score: 865
Period size: 171 Copynumber: 4.1 Consensus size: 172
1302091 TTGTGGACTA
* * * * * *
1302101 ACTTGTGGGCTTTGAAAAGAGTTGTCACCGACTTGTGGGCTTTGAAAGGAGTTGTCACCGACTTG
1 ACTTGTGGGCTTTG-AAAGAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCG
* *
1302166 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTAAAAGGATGCCATTGACTTGTGGGCTTTG
65 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
* *
1302231 AAAAAGTGACACTAACTTGTGGGCTTTGAAAAGAGTGCCACTG
130 AAAAAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
* * *
1302274 ACTTGTGGGTTTTGAAAG-GGTGCCACTGACTTGTGGGCTTTCAAAAGAGTTACCACCGACTCGT
1 ACTTGTGGGCTTTGAAAGAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGT
* *
1302338 GGGCTTTGACAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGA
66 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGA
*** *
1302403 ATGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTCCACTG
131 AAAAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
* **
1302445 ACTTGTAGGCTTTGAAAG-GGTGCCACAAACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGT
1 ACTTGTGGGCTTTGAAAGAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGT
* *
1302509 AGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTG
66 GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG
* * *
1302573 AAAAGAGCGCCACTGACTTGTGGGCTTTG-AAAGGGTGCTACTG
130 AAAA-AGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
* * ** * * * *
1302616 ACTTGTGGGCTTTGAAAAGAGTTGGCA-TCGACTCATGGGCTTTG-AAAGA-ATGCGACTGACTT
1 ACTTGTGGGCTTTG-AAAGAGGTGCCACT-GACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTC
* * * **
1302678 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGGTGCCACCGACTCAT-GGCT
64 GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAG-GATGCCACTGACTTGTGGGCT
* * * *
1302742 TTG-AAAGGATGCCATTGACTTATGGGCTTT-AAAAGGGTGCCACTG
127 TTGAAAAAG-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
1302787 ACTTGTGGGCTTT-AAAGAG
1 ACTTGTGGGCTTTGAAAGAG
1302806 ATGAAAGTTC
Statistics
Matches: 463, Mismatches: 59, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
169 6 0.01
170 3 0.01
171 367 0.79
172 45 0.10
173 41 0.09
174 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (172 bp):
ACTTGTGGGCTTTGAAAGAGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGT
GGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGA
AAAAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTG
Found at i:1304045 original size:17 final size:15
Alignment explanation
Indices: 1304011--1304079 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
1304001 TCCCTTTCTA
1304011 TTTTTTTGT-TATTTT
1 TTTTTTTGTGT-TTTT
*
1304026 TTTCTTTGTGTTTTT
1 TTTTTTTGTGTTTTT
1304041 GTTTTTTT-TGTTTTT
1 -TTTTTTTGTGTTTTT
*
1304056 TCTATTTTT-TGGTTTT
1 T-T-TTTTTGTGTTTTT
1304072 TTTTTTTG
1 TTTTTTTG
1304080 GTATGAAGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 6 0.13
15 21 0.46
16 19 0.41
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.83
Consensus pattern (15 bp):
TTTTTTTGTGTTTTT
Found at i:1304047 original size:32 final size:31
Alignment explanation
Indices: 1304011--1304078 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
1304001 TCCCTTTCTA
1304011 TTTTTTTGTTATTTT-T-TTCTTTGTGTTTTTGT
1 TTTTTTTGTT-TTTTCTATTCTTTG-GTTTTT-T
*
1304043 TTTTTTTGTTTTTTCTATTTTTTGGTTTTTT
1 TTTTTTTGTTTTTTCTATTCTTTGGTTTTTT
1304074 TTTTT
1 TTTTT
1304079 GGTATGAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 10 0.30
32 17 0.52
33 6 0.18
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.84
Consensus pattern (31 bp):
TTTTTTTGTTTTTTCTATTCTTTGGTTTTTT
Found at i:1317967 original size:20 final size:20
Alignment explanation
Indices: 1317941--1317994 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1317931 AAAAGACAGA
* *
1317941 ATGTATCGATACATTGA-AG
1 ATGTATCGATACATTCATAC
*
1317960 AGTGTATCGATATATTCATAC
1 A-TGTATCGATACATTCATAC
1317981 ATGTATCGATACAT
1 ATGTATCGATACAT
1317995 CTGGGTACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTCATAC
Found at i:1324934 original size:16 final size:16
Alignment explanation
Indices: 1324913--1324948 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1324903 ACTTTTGGTT
**
1324913 CTTTGCTTGTTTTTAA
1 CTTTGCTTGTACTTAA
1324929 CTTTGCTTGTACTTAA
1 CTTTGCTTGTACTTAA
1324945 CTTT
1 CTTT
1324949 CCTTAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.58
Consensus pattern (16 bp):
CTTTGCTTGTACTTAA
Found at i:1325838 original size:20 final size:20
Alignment explanation
Indices: 1325815--1325865 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1325805 ACTCAAAGTA
*
1325815 TCGATGCATAAGTATTTGCG
1 TCGATACATAAGTATTTGCG
**
1325835 TCGATACATAAGTATTTGTA
1 TCGATACATAAGTATTTGCG
1325855 TCGATACATAA
1 TCGATACATAA
1325866 AAGGTTGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGATACATAAGTATTTGCG
Found at i:1326062 original size:20 final size:20
Alignment explanation
Indices: 1326037--1326075 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1326027 CTACCACTGT
1326037 TTGTATCGATACATGGTATA
1 TTGTATCGATACATGGTATA
*
1326057 TTGTATCGATACATTGTAT
1 TTGTATCGATACATGGTAT
1326076 TGATACATAG
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:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATGGTATA
Found at i:1328855 original size:56 final size:54
Alignment explanation
Indices: 1328795--1328988 Score: 156
Period size: 56 Copynumber: 3.4 Consensus size: 54
1328785 CAACATGGTC
*
1328795 AGTTATGTTTGGCTTAATGCACTATGGGCCAACTTCACTAGGCTTATCACTTGGCT
1 AGTTATGTTAGGCTTAAT-CACTATGGGCCAACTTCACTAGGCTTA-CACTTGGCT
* * * * * * *
1328851 AGTTATCTTAGGCTTTTATCTCTTTGTGAGCTAACTTCACTAAGCTTACAACATAGGC-
1 AGTTATGTTAGGC-TTAATCACTATG-G-GCCAACTTCACTAGGCTTAC-AC-TTGGCT
*** * * *
1328909 AGTTACAATAGGTTTAATACACTATAGGCCAACTTCACTAGGCTTACAATATGGCT
1 AGTTATGTTAGGCTTAAT-CACTATGGGCCAACTTCACTAGGCTTACACT-TGGCT
*
1328965 AGCTATGTTAGGCTTAAATCACTA
1 AGTTATGTTAGGCTT-AATCACTA
1328989 CAAAAAAAAC
Statistics
Matches: 104, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
54 1 0.01
55 4 0.04
56 49 0.47
57 14 0.13
58 32 0.31
59 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (54 bp):
AGTTATGTTAGGCTTAATCACTATGGGCCAACTTCACTAGGCTTACACTTGGCT
Found at i:1332433 original size:13 final size:13
Alignment explanation
Indices: 1332415--1332440 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1332405 TACAGCAAGT
1332415 ATGTATCGATACA
1 ATGTATCGATACA
1332428 ATGTATCGATACA
1 ATGTATCGATACA
1332441 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1333574 original size:13 final size:13
Alignment explanation
Indices: 1333553--1333585 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1333543 CCGTTTGAAG
1333553 CAATGTATCGATA
1 CAATGTATCGATA
*
1333566 CATTGTATCGATA
1 CAATGTATCGATA
1333579 CAATGTA
1 CAATGTA
1333586 CCATGTATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1333674 original size:19 final size:20
Alignment explanation
Indices: 1333630--1333675 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1333620 GGGCTAGTTT
**
1333630 CATGTATCAATACAATTGTC
1 CATGTATCAATACAATTGAA
*
1333650 CATGTATCGATACAA-TGAA
1 CATGTATCAATACAATTGAA
1333669 CATGTAT
1 CATGTAT
1333676 AAGTTGAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCAATACAATTGAA
Found at i:1334919 original size:36 final size:34
Alignment explanation
Indices: 1334836--1334933 Score: 116
Period size: 36 Copynumber: 3.0 Consensus size: 34
1334826 CCTTACAGCA
*
1334836 CTATC-TTTC-AAGGCTAAGATAGAA-AC-CTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACTCTCTCC
**
1334866 CTATCTTTTCACGGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAA-CTCTCTCC
1334901 CTATCTTTTTCAAAGGCTAAGATAGAACT-TCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACTCTCTC
1334934 AATCACTTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
30 5 0.09
31 4 0.07
32 13 0.23
34 5 0.09
35 11 0.19
36 19 0.33
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (34 bp):
CTATCTTTTCAAAGGCTAAGATAGAACTCTCTCC
Found at i:1335446 original size:10 final size:10
Alignment explanation
Indices: 1335427--1335457 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1335417 GTATCAATAC
1335427 ATGAACAGTG
1 ATGAACAGTG
*
1335437 ATGAATAGTG
1 ATGAACAGTG
1335447 ATGAACAGTG
1 ATGAACAGTG
1335457 A
1 A
1335458 AAAATGAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1335621 original size:21 final size:21
Alignment explanation
Indices: 1335591--1335631 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1335581 GTCAACCTTG
*
1335591 TGTATTGATACCATTA-GTATA
1 TGTATCGATA-CATTACGTATA
1335612 TGTATCGATACATTACGTAT
1 TGTATCGATACATTACGTAT
1335632 TTTTACTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATTACGTATA
Found at i:1336577 original size:25 final size:25
Alignment explanation
Indices: 1336543--1336594 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1336533 CAGAAGGAGG
1336543 TGGGGTGAACTTAATCAATAAAATA
1 TGGGGTGAACTTAATCAATAAAATA
1336568 TGGGGTGAACTTAATCAATAAAATA
1 TGGGGTGAACTTAATCAATAAAATA
1336593 TG
1 TG
1336595 CAAATATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (25 bp):
TGGGGTGAACTTAATCAATAAAATA
Found at i:1337304 original size:13 final size:13
Alignment explanation
Indices: 1337286--1337311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1337276 CATTAAAATT
1337286 ATATCGATATAAA
1 ATATCGATATAAA
1337299 ATATCGATATAAA
1 ATATCGATATAAA
1337312 TTTGATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
ATATCGATATAAA
Found at i:1338856 original size:21 final size:21
Alignment explanation
Indices: 1338832--1338886 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1338822 CACTTGCAAC
*
1338832 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
1338853 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
* *
1338874 TCACTTAATTTCT
1 TCATTTATTTTCT
1338887 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:1338887 original size:21 final size:21
Alignment explanation
Indices: 1338847--1338890 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1338837 TCTTTTCTCC
* *
1338847 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
1338868 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
1338889 TC
1 TC
1338891 AAGAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:1340489 original size:32 final size:33
Alignment explanation
Indices: 1340444--1340534 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 33
1340434 CAACACTATC
1340444 TTTC-AAGGCTAAGATAGAAACCTCCCTATC-T
1 TTTCAAAGGCTAAGATAGAAACCTCCCTATCTT
** *
1340475 TTTCACGGGCTAAGATAGAACCTCTCTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAA--AC-CTCCCTATCTT
*
1340511 TTTCAAAAGCTAAGATAG-AACCTC
1 TTTCAAAGGCTAAGATAGAAACCTC
1340535 TCAATCATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 4 0.08
32 16 0.33
33 1 0.02
34 1 0.02
35 10 0.21
36 16 0.33
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (33 bp):
TTTCAAAGGCTAAGATAGAAACCTCCCTATCTT
Found at i:1340523 original size:36 final size:35
Alignment explanation
Indices: 1340465--1340536 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
1340455 AGATAGAAAC
***
1340465 CTCCCTATCTTTTCACGGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTCAAAAGCTAAGATAGAACCTCT
1340500 CTCCCTATCTTTTTCAAAAGCTAAGATAGAACCTCT
1 CTCCCTATC-TTTTCAAAAGCTAAGATAGAACCTCT
1340536 C
1 C
1340537 AATCATTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.32
Consensus pattern (35 bp):
CTCCCTATCTTTTCAAAAGCTAAGATAGAACCTCT
Found at i:1341691 original size:21 final size:21
Alignment explanation
Indices: 1341665--1341742 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
1341655 AAAATTATCC
1341665 GAATGTATCGATACATTTGTA
1 GAATGTATCGATACATTTGTA
*
1341686 GAATGTATCGATACATTTGTG
1 GAATGTATCGATACATTTGTA
*
1341707 GAATGTATCGATACA-TTCTA
1 GAATGTATCGATACATTTGTA
*
1341727 CAAATGTATCGATACA
1 -GAATGTATCGATACA
1341743 GGGTCCCAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 3 0.06
21 49 0.94
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (21 bp):
GAATGTATCGATACATTTGTA
Found at i:1341803 original size:19 final size:19
Alignment explanation
Indices: 1341779--1341883 Score: 114
Period size: 19 Copynumber: 5.8 Consensus size: 19
1341769 TTTCAGCAAT
*
1341779 TTGTATCGATACATAAATG
1 TTGTATCGATACATAAATA
*
1341798 TTGTATCGATACATAAATG
1 TTGTATCGATACATAAATA
*
1341817 TTGTATTGATAC----A-A
1 TTGTATCGATACATAAATA
*
1341831 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAATA
*
1341849 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAATA
*
1341868 TTGTGTCGATACATAA
1 TTGTATCGATACATAA
1341884 TTAGCTACTG
Statistics
Matches: 75, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.13
15 1 0.01
18 1 0.01
19 63 0.84
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAATA
Found at i:1341838 original size:32 final size:32
Alignment explanation
Indices: 1341799--1341861 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1341789 ACATAAATGT
* *
1341799 TGTATCGATACATAAATGTTGTATTGATACAA
1 TGTATCGATACATAAATATTGTATCGATACAA
*
1341831 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAATATTGTATCGATACA
1341862 TAAGTATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCGATACAA
Found at i:1341879 original size:51 final size:51
Alignment explanation
Indices: 1341780--1341880 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
1341770 TTCAGCAATT
* * *
1341780 TGTATCGATACATAAATGTTGTATCGATACATAAATGTTGTATTGATACAA
1 TGTATCGATACATAAATATTGTATCGATACATAAATATTGTATCGATACAA
* * *
1341831 TGTATCGATACATAAGTATTGTATCGATACATAAGTATTGTGTCGATACA
1 TGTATCGATACATAAATATTGTATCGATACATAAATATTGTATCGATACA
1341881 TAATTAGCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (51 bp):
TGTATCGATACATAAATATTGTATCGATACATAAATATTGTATCGATACAA
Found at i:1341941 original size:13 final size:13
Alignment explanation
Indices: 1341923--1341948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1341913 CATTTTTCTG
1341923 TGTATCGATACAT
1 TGTATCGATACAT
1341936 TGTATCGATACAT
1 TGTATCGATACAT
1341949 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1341966 original size:34 final size:33
Alignment explanation
Indices: 1341904--1341969 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
1341894 CCAAGGGAAC
*
1341904 GTATCGATACATTTTTCTGTGTATCGATACATT
1 GTATCGATACATTATTCTGTGTATCGATACATT
*
1341937 GTATCGATACATCTATTCTTTGTATCGATACAT
1 GTATCGATACAT-TATTCTGTGTATCGATACAT
1341970 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.44
Consensus pattern (33 bp):
GTATCGATACATTATTCTGTGTATCGATACATT
Found at i:1344377 original size:51 final size:51
Alignment explanation
Indices: 1344321--1344703 Score: 215
Period size: 52 Copynumber: 7.3 Consensus size: 51
1344311 CTCCACAATT
* *
1344321 GGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATC
** * * * *
1344372 GGGGATACTCCAACTTCGATTTTATTTCCAAAA-AATACCAATTTCTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACTA--ATTTTC-T-ATAATC
* ** * * * * *** *
1344426 GGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAA-CCCCGT-TATTTCC
1 GGGGATACTCCAACCCCGATTTTATTTTC---AAAACACTAATTTTC-TATA-AT-C
* * * * * *
1344479 GAGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTTATAATC
1 --GGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATC
* * *
1344532 GGGGATACTCCAACCCCGGTTTTATTGCTT--AAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATT--TTCAAAACACTAA-TTTTCTATAATC
* *
1344584 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT--CTATAATC
* * * * *
1344637 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTT-TCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACTAATTTTCT-ATAATC
*
1344689 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1344704 TCGTTATTTC
Statistics
Matches: 247, Mismatches: 60, Indels: 49
0.69 0.17 0.14
Matches are distributed among these distances:
50 5 0.02
51 66 0.27
52 72 0.29
53 37 0.15
54 39 0.16
55 22 0.09
56 1 0.00
57 5 0.02
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATC
Found at i:1344437 original size:54 final size:51
Alignment explanation
Indices: 1344306--1344702 Score: 214
Period size: 51 Copynumber: 7.6 Consensus size: 51
1344296 TTGAGTTTCT
* * * *
1344306 CAATTCTCCACAATTGGGGATATTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * * *
1344357 TAATT-TTCTATAATCGGGGATACTCCAACTTCGATTTTATTTCCAAAAAATAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACAC
* * * ** * *
1344410 CAATTTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAA-TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACAC
* * * * * *
1344463 CAACCCCGTTATTTC-CGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATAT
1 CAA-----TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
** * * * * * * **
1344517 TGATTTTTTATAATCGGGGATACTCCAACCCCGGTTTTATTGCTTAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * * * *
1344568 TAATTTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTCTT-CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * *
1344620 TAATT-TTCCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC
1 CAATTCTTCAC---AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC
* *
1344674 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTCTTCACAATCGGGGATACTCCAAC
1344703 CTCGTTATTT
Statistics
Matches: 265, Mismatches: 57, Indels: 47
0.72 0.15 0.13
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 4 0.02
51 72 0.27
52 63 0.24
53 46 0.17
54 36 0.14
55 25 0.09
56 2 0.01
57 8 0.03
58 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:1344457 original size:27 final size:28
Alignment explanation
Indices: 1344423--1344498 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1344413 TTTCTTCACA
1344423 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1344450 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
1344478 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1344499 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1344695 original size:105 final size:103
Alignment explanation
Indices: 1344483--1344703 Score: 266
Period size: 105 Copynumber: 2.1 Consensus size: 103
1344473 ATTTCCGAGG
* * *
1344483 GGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTTATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTTTTATAATCGGGGATACTCCAACCC
* * ** * *
1344548 CGGTTTTATTGCTTAAACACTAATTTTTCCACAATCGG
66 CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
** *
1344586 GGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCCTT-TAATCGGGGATACTCCAA
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTT---TTATAATCGGGGATACTCCAA
* *
1344650 CTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
63 CCCCGATTTTA-TTCCAAAAACACCAATTTTTCCACAATCGA
1344691 GGATACTCCAACC
1 GGATACTCCAACC
1344704 TCGTTATTTC
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
103 35 0.35
105 48 0.48
106 17 0.17
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.33
Consensus pattern (103 bp):
GGATACTCCAACCCCGACTTTATTTCCAAAACACTAATTTTTTATAATCGGGGATACTCCAACCC
CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
Found at i:1344718 original size:28 final size:28
Alignment explanation
Indices: 1344686--1344759 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
1344676 ATTTTTCACA
*
1344686 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCTCGTTACTTC
1344714 ATCGAGGATACTCCAACCTCGTTACTTC
1 ATCGAGGATACTCCAACCTCGTTACTTC
1344742 --CGAGGGGATACTCCAACC
1 ATCGA--GGATACTCCAACC
1344760 CCGGCTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 3 0.07
28 40 0.93
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCTCGTTACTTC
Found at i:1344781 original size:264 final size:263
Alignment explanation
Indices: 1344312--1344813 Score: 810
Period size: 264 Copynumber: 1.9 Consensus size: 263
1344302 TTCTCAATTC
* * *
1344312 TCCACAATTGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
* *
1344377 TACTCCAACTTCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
* *
1344442 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* * *
1344507 TCCAAAATATTGATTTTTTATAATCGGGGATACTCCAACCCCGGTTTTATTGCTTAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTTAAACACTAAT
1344572 TTT
261 TTT
* *
1344575 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT--CTATAATCGGG
1344640 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * *
1344703 CTCGTTATTTCATCGAGGATACTCCAACCTCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTT
*
1344768 ATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
193 ATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
1344814 TTATTTTCGA
Statistics
Matches: 219, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
263 76 0.35
264 108 0.49
265 35 0.16
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (263 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTTAAACACTAAT
TTT
Found at i:1344830 original size:107 final size:107
Alignment explanation
Indices: 1344637--1344836 Score: 251
Period size: 107 Copynumber: 1.9 Consensus size: 107
1344627 CCCTTTAATC
* * *
1344637 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
1344702 CCTCGTTATTTCATCGAGGATACTCCAACCTCGTTACTTCCGA
66 CCCCGTTATTT-ATCGAGGATACTCCAACCTCGTTACTTCCGA
* * *** * * *
1344745 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
1344809 CCCCGTTATTT-TCGAGGGGATACTCCAA
66 CCCCGTTATTTATCGA--GGATACTCCAA
1344837 TCCCGATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
105 4 0.05
107 53 0.68
108 21 0.27
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGAGGATACTCCAACCTCGTTACTTCCGA
Found at i:1346997 original size:4 final size:4
Alignment explanation
Indices: 1346988--1347012 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1346978 TCTTGAGGTG
1346988 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1347013 ATATCTGTCT
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:1357336 original size:7 final size:7
Alignment explanation
Indices: 1357326--1357388 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
1357316 AAAAGGCAAA
1357326 AAAAAAG
1 AAAAAAG
1357333 AAAAAAG
1 AAAAAAG
1357340 AAAAAA-
1 AAAAAAG
* *
1357346 ACAAAAC
1 AAAAAAG
*
1357353 AAAAAACA
1 AAAAAA-G
1357361 AAACAAAG
1 AAA-AAAG
1357369 AAAAAGAG
1 AAAAA-AG
*
1357377 AGAAAAG
1 AAAAAAG
1357384 AAAAA
1 AAAAA
1357389 GAACCTGCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
6 5 0.11
7 26 0.57
8 12 0.26
9 3 0.07
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1357338 original size:12 final size:12
Alignment explanation
Indices: 1357309--1357388 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
1357299 CCTTCTCTTC
1357309 AAAAAAAAAAAG
1 AAAAAAAAAAAG
**
1357321 GCAAAAAAAAAG
1 AAAAAAAAAAAG
1357333 AAAAAAGAAAAA-
1 AAAAAA-AAAAAG
*
1357345 AACAAAACAAAA-
1 AA-AAAAAAAAAG
* *
1357357 AACAAAACAAAG
1 AAAAAAAAAAAG
1357369 AAAAAGAGAGAAAAG
1 AAAAA-A-A-AAAAG
1357384 AAAAA
1 AAAAA
1357389 GAACCTGCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
11 6 0.12
12 26 0.50
13 10 0.19
14 1 0.02
15 9 0.17
ACGTcount: A:0.82, C:0.06, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1357343 original size:15 final size:15
Alignment explanation
Indices: 1357325--1357388 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
1357315 AAAAAGGCAA
1357325 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
1357340 AAAAAAACAAAACAA-
1 AAAAAAAGAAAA-AAG
* *
1357355 AAAACAA-AACAAAG
1 AAAAAAAGAAAAAAG
* *
1357369 AAAAAGAGAGAAAAG
1 AAAAAAAGAAAAAAG
1357384 AAAAA
1 AAAAA
1357389 GAACCTGCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
13 2 0.05
14 8 0.21
15 27 0.69
16 2 0.05
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:1358605 original size:59 final size:59
Alignment explanation
Indices: 1358350--1359273 Score: 882
Period size: 55 Copynumber: 16.2 Consensus size: 59
1358340 GCTTTTTAGC
* *
1358350 CCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
* * *
1358410 CCTCAAAGAGCAGGAC-AC----CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAAT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCT-CCAGT
* **
1358465 CCTCAAAGAGCAGGACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTC-TTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGT
*
1358526 CCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
* *
1358585 CCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC-GT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC--TCCAGT
* * * *
1358645 CCCCAAAGAGAAGGAC-CC----CTTTTAAAGCCCACACAAGTTGGTGGTACTTCCTAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCC-AGT
* * * **
1358700 CCTTAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGT
* * * * *
1358761 CTTCAAAGAGCGGGACGTCTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
* * * * *
1358820 CCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGTACCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
* * * *
1358879 CCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGA
1 CCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TCCAGT
* ** ** *
1358940 CCCCAAAGAGCAGGAC-CC----CTTTCGAAGCCCACACAAGTTGGTGGCATTTTCTAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGT
*
1358995 CCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGG------CA-T
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
* * *
1359042 CCTCAAAGAGCAGGACACC---TC--TTAAAGCCTACACAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TCCAGT
* * **
1359097 CCCCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTCCAGT
* *
1359152 CCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TCCAGT
* * **
1359207 CCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTTAGT
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTCCAGT
1359262 CCTCAAAGAGCA
1 CCTCAAAGAGCA
1359274 AGATACACTT
Statistics
Matches: 746, Mismatches: 73, Indels: 95
0.82 0.08 0.10
Matches are distributed among these distances:
45 2 0.00
47 40 0.05
48 1 0.00
53 5 0.01
54 32 0.04
55 270 0.36
56 9 0.01
57 4 0.01
59 146 0.20
60 110 0.15
61 121 0.16
62 6 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (59 bp):
CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
Found at i:1358761 original size:235 final size:225
Alignment explanation
Indices: 1358350--1359273 Score: 1069
Period size: 235 Copynumber: 4.1 Consensus size: 225
1358340 GCTTTTTAGC
* *
1358350 CCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCA
1 CCTCAAAGAGCAGGACGCCTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCCA
*
1358415 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAATCCTCAAAGAGCAGG
65 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAGCAGG
*
1358479 ACGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGACGC
129 AC-CC-TC-C-TTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
*
1358544 CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCAGT
190 C-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * *
1358585 CCTCAAAGAGCGGGACGCCTTTTCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCGTCCCCA
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCCCA
* * * *
1358650 AAGAGAAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGTA-CTTCCTAGTCCTTAAAGAGCAGG
65 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGG
* *
1358714 ATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTTCAAAGAGCGGGACGT
129 A--CC--CTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG-
* *
1358779 CTTTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
189 C----CTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* * * * *
1358820 CCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGTACCTTCAGTCCTCAA
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCCAA
** * * *
1358885 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGACCCCAAAGAG
66 AGAGCAGGA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAG
** * *
1358950 CAGGA-CC-CCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACAC
125 CAGGACCCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGC
1359013 CTTTCAAAGCCCACACAAGTTGGTGG------CA-T
190 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGT
* *
1359042 CCTCAAAGAGCAGGACACC---TC--TTAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCCCA
1 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCCCA
* **
1359102 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
65 AAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGA
*
1359167 CACCT-C--TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTT
130 C-CCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTT
* * *
1359228 TCAAAGCCCACACGAGTTGGTGGCACTTTTTAGT
193 TCAAAGCCCACACAAGTTGGTGGCAC-CTTCAGT
1359262 CCTCAAAGAGCA
1 CCTCAAAGAGCA
1359274 AGATACACTT
Statistics
Matches: 600, Mismatches: 58, Indels: 77
0.82 0.08 0.10
Matches are distributed among these distances:
212 110 0.18
213 7 0.01
214 3 0.00
216 1 0.00
217 24 0.04
218 20 0.03
219 3 0.00
220 13 0.02
222 17 0.03
223 2 0.00
229 24 0.04
233 1 0.00
234 98 0.16
235 219 0.37
236 4 0.01
237 4 0.01
238 1 0.00
239 8 0.01
240 37 0.06
241 4 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (225 bp):
CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCCAA
AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGAC
CCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCA
AAGCCCACACAAGTTGGTGGCACCTTCAGT
Found at i:1358946 original size:295 final size:283
Alignment explanation
Indices: 1358373--1359273 Score: 1113
Period size: 295 Copynumber: 3.2 Consensus size: 283
1358363 GATGCCTTTT
* *
1358373 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACACCTTTTAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACCTTTTAAAG
* *
1358437 CCCACACAAGTTGGTGGCACTTCCCAATCCTCAAAGAGCAGGACGCCTTCTCTTTTTAAAGCCCA
66 CCCACACAAGTTGGTGGCA-TTTCC-AT-CTCAAAGAGCAGGACGACTT-T-TTTTTAAAGCCCA
**
1358502 CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAA
126 CACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAA
* *
1358567 GTTGGTGGCACCTCCAGTCCTCAAAGAGCGGGACGCCTTTTC-TTTCAAAGCCCACACAAGTTGG
190 GTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGA-G-CTTTTCTTTTCAAAGCCCACACAAGTTGG
* *
1358631 TGGCACCTTTCCGTCCCCAAAGAGAAGGACC
253 TGGCACCTTTCAGTCCCCAAAGAGCAGGACC
* * * * *
1358662 CCTTTTAAAGCCCACACAAGTTGGTGGTACTTCCTAGTCCTTAAAGAGCAGGATGCCTTCTCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGA------CACCTT
* *
1358727 TTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTTCAAAGAGCGGGACGTCTTTTTTTTTAAA
60 TTAAAGCCCACACAAGTTGGTGGCA-TTTCCA-TC-TCAAAGAGCAGGACGAC-TTTTTTTTAAA
*
1358792 GCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCAC
121 GCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCAC
* *
1358857 CCAAGTTGGTGGTACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAG
186 ACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGA-GC-TTTTCTTTTCAAAGCCCACACAAG
*
1358922 TTGGTGGCACCTTTCAGACCCCAAAGAGCAGGACC
249 TTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACC
* * *
1358957 CCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGACACCTTTCAAAG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACCTTTTAAAG
* * *
1359022 CCCACACAAGTTGGTGGCA--T-C--CTCAAAGAGCAGGAC-AC---CTCTTAAAGCCTACACAA
66 CCCACACAAGTTGGTGGCATTTCCATCTCAAAGAGCAGGACGACTTTTTTTTAAAGCCCACACAA
* * *
1359078 GTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGG
131 GTTGGTGGCACC-TTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGG
** ** *
1359138 TGGCATTTTCCAGTCCTCAAAGAGCAGGA-C--ACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
195 TGGCACCTT-CAGTCCTCAAAGAGCAGGAGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
1359199 CTTTCAGTCCTCAAAGAGCAGGACG
259 CTTTCAGTCCCCAAAGAGCAGGACC
* *
1359224 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCA
1359274 AGATACACTT
Statistics
Matches: 547, Mismatches: 51, Indels: 50
0.84 0.08 0.08
Matches are distributed among these distances:
267 92 0.17
268 4 0.01
271 1 0.00
272 23 0.04
273 19 0.03
276 31 0.06
277 21 0.04
280 1 0.00
281 13 0.02
282 1 0.00
285 1 0.00
286 1 0.00
289 60 0.11
290 17 0.03
293 1 0.00
294 79 0.14
295 129 0.24
296 51 0.09
297 2 0.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (283 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACACCTTTTAAAG
CCCACACAAGTTGGTGGCATTTCCATCTCAAAGAGCAGGACGACTTTTTTTTAAAGCCCACACAA
GTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGT
GGCACCTTCAGTCCTCAAAGAGCAGGAGCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
TTCAGTCCCCAAAGAGCAGGACC
Found at i:1359417 original size:25 final size:25
Alignment explanation
Indices: 1359387--1359435 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1359377 TTGTCCTCAA
1359387 GAAGCAGGACACTTTCCTTTTCTTC
1 GAAGCAGGACACTTTCCTTTTCTTC
1359412 GAAGCAGGACACTTTCCTTTTCTT
1 GAAGCAGGACACTTTCCTTTTCTT
1359436 TTCTTCCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.37
Consensus pattern (25 bp):
GAAGCAGGACACTTTCCTTTTCTTC
Found at i:1360152 original size:13 final size:13
Alignment explanation
Indices: 1360134--1360190 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1360124 ACATAAATGT
1360134 TGTATCGATACAA
1 TGTATCGATACAA
1360147 TGTATCGATACATAAGTA
1 TGTATCGATAC---A--A
1360165 TTGTATCGATACAA
1 -TGTATCGATACAA
1360179 TGTATCGATACA
1 TGTATCGATACA
1360191 TAAGTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1360158 original size:32 final size:32
Alignment explanation
Indices: 1360122--1360209 Score: 158
Period size: 32 Copynumber: 2.8 Consensus size: 32
1360112 AGCGATTTGT
* *
1360122 ATACATAAATGTTGTATCGATACAATGTATCG
1 ATACATAAGTATTGTATCGATACAATGTATCG
1360154 ATACATAAGTATTGTATCGATACAATGTATCG
1 ATACATAAGTATTGTATCGATACAATGTATCG
1360186 ATACATAAGTATTGTATCGATACA
1 ATACATAAGTATTGTATCGATACA
1360210 TAATTAGCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (32 bp):
ATACATAAGTATTGTATCGATACAATGTATCG
Found at i:1360171 original size:19 final size:19
Alignment explanation
Indices: 1360147--1360212 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
1360137 ATCGATACAA
1360147 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGTAT
1360166 TGTATCGATAC---A--A-
1 TGTATCGATACATAAGTAT
1360179 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGTAT
1360198 TGTATCGATACATAA
1 TGTATCGATACATAA
1360213 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
16 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTAT
Found at i:1360270 original size:13 final size:13
Alignment explanation
Indices: 1360252--1360277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1360242 CATTTTTCTG
1360252 TGTATCGATACAT
1 TGTATCGATACAT
1360265 TGTATCGATACAT
1 TGTATCGATACAT
1360278 CTATTCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1360298 original size:34 final size:33
Alignment explanation
Indices: 1360232--1360298 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1360222 GCCAAGGCAA
* *
1360232 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGCATCGATACAT
*
1360265 TGTATCGATACATCTATTCTTTGCATCGATACAT
1 TGTATCGATACAT-TATTCTGTGCATCGATACAT
1360299 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGCATCGATACAT
Found at i:1362612 original size:51 final size:51
Alignment explanation
Indices: 1362556--1362942 Score: 237
Period size: 52 Copynumber: 7.4 Consensus size: 51
1362546 AATTCTCCAC
* * * *
1362556 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTAT
** *
1362607 AATCGGGGATACTCCAACTTCGATTTTATTTCCAAAAAACACCAA-TTTCTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACCAATTTTC-T-AT
* * ** * * ***
1362661 AATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAA-GCCCGTTAT
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAATTTTC--TAT
** * * ***
1362714 TTTCGAGGAGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTT-TCAT
1 AATCG-GG-GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCT-AT
* * * * * * * *
1362767 AATCGGGGATACTCAAACCCTGGTTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTTCTAT
* * *
1362819 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTT--CTAT
* * *
1362872 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTT-TCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCT-AT
*
1362924 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
1362943 TCGTTATTTC
Statistics
Matches: 254, Mismatches: 62, Indels: 39
0.72 0.17 0.11
Matches are distributed among these distances:
51 62 0.24
52 70 0.28
53 60 0.24
54 41 0.16
55 15 0.06
56 2 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCTAT
Found at i:1362676 original size:54 final size:51
Alignment explanation
Indices: 1362545--1362941 Score: 248
Period size: 51 Copynumber: 7.6 Consensus size: 51
1362535 TTGAGTTTCT
* * *
1362545 CAATTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* * *
1362596 TAATT-TTCTATAATCGGGGATACTCCAACTTCGATTTTATTTCCAAAAAACAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACAC
* * * ** * *
1362649 CAATTTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAA-TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACAC
** *** * * * *
1362702 CAAGCCCGTT-ATTTTCGAGGAGATACTCCAACCCCGACTTTATTTCCAAAATAT
1 CAA-TTC-TTCACAATCG-GG-GATACTCCAACTCCGATTTTATTTCCAAAACAC
** * * * * * *
1362756 TGATTTTTCATAATCGGGGATACTCAAAC-CCTGGTTTTATTGCTAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACAC
* * * * *
1362807 TAATTTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
1 CAATTCTT-CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
* *
1362859 CAATT-TTCCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATAC
1 CAATTCTTCAC---AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC
* *
1362913 CAATTTTTCACAATCGAGGATACTCCAAC
1 CAATTCTTCACAATCGGGGATACTCCAAC
1362942 CTCGTTATTT
Statistics
Matches: 266, Mismatches: 58, Indels: 43
0.72 0.16 0.12
Matches are distributed among these distances:
50 6 0.02
51 67 0.25
52 64 0.24
53 60 0.23
54 41 0.15
55 22 0.08
56 2 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
Found at i:1362731 original size:28 final size:27
Alignment explanation
Indices: 1362662--1362737 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
1362652 TTTCTTCACA
1362662 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
1362689 ATCGGGGATACTCCAAGCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
1362715 TTCGAGGAGATACTCCAACCCCG
1 ATCG-GG-GATACTCCAACCCCG
1362738 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 24 0.56
28 14 0.33
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:1362957 original size:28 final size:28
Alignment explanation
Indices: 1362925--1362999 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
1362915 ATTTTTCACA
* *
1362925 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
1362953 ATCGAGGATACTCCAACCCCGTTACTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
1362981 --CGAGGGGATACTCCAACCC
1 ATCGA--GGATACTCCAACCC
1363000 TGGCTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.07
28 40 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.24
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTACTTC
Found at i:1363033 original size:264 final size:263
Alignment explanation
Indices: 1362551--1363052 Score: 765
Period size: 264 Copynumber: 1.9 Consensus size: 263
1362541 TTCTCAATTC
* * *
1362551 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
1362616 TACTCCAACTTCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * *
1362681 CGTTAATCATCGGGGATACTCCAAGCCCGTTATTTTCGAGGAGATACTCCAACCCCGACTTTATT
131 CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGAGATACTCCAACCCCGACTTTATT
* *
1362746 TCCAAAATATTGATTTTTCATAATCGGGGATACTCAAACCCTGGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATCGGGGATACTCAAACCCTGGTTTTATTGCTAAAACACTAAT
1362811 TTT
261 TTT
* *
1362814 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT--CTATAATCGGG
*
1362879 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * * *
1362942 CTCGTTATTTCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCTGGCTTT
129 CCCGTTA-ATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGAGATACTCCAACCCCGACTTT
** *
1363007 ATTCCCAAAATATTGATTTCTCATAATTTGGGATACTCCAACCCTG
193 ATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCAAACCCTG
1363053 TTATTTTCGA
Statistics
Matches: 214, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
263 76 0.36
264 103 0.48
265 35 0.16
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (263 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGAGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATCGGGGATACTCAAACCCTGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:1364943 original size:13 final size:13
Alignment explanation
Indices: 1364925--1364950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1364915 ACAATATTCT
1364925 TTGTATCGATACA
1 TTGTATCGATACA
1364938 TTGTATCGATACA
1 TTGTATCGATACA
1364951 AAGGTTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1365083 original size:21 final size:22
Alignment explanation
Indices: 1365059--1365108 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1365049 ATCAAATCTT
* *
1365059 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1365080 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1365102 --TCAAAAT
1 CTTCAAAAT
1365109 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1367579 original size:52 final size:51
Alignment explanation
Indices: 1367509--1367691 Score: 181
Period size: 52 Copynumber: 3.5 Consensus size: 51
1367499 GAAATAATAA
*
1367509 AGTTGGAGTATCCTCGATTGTGAAAAATTTGTGTTTTTAGAAATAAAATCGG
1 AGTTGGAGTATCC-CGATTGTGAAAAATTAGTGTTTTTAGAAATAAAATCGG
** * *
1367561 AGTTGGAGTATCTCCGATTAAAGAAAAATTGGTGTTTTGA-AAATAAAATCGG
1 AGTTGGAGTATC-CCGATT-GTGAAAAATTAGTGTTTTTAGAAATAAAATCGG
* * * * * *
1367613 GGTTGCAATATCCCCGATTGTGGAAAATTAATG-TTTTAGAAATAAAACCGG
1 AGTTGGAGTAT-CCCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAATCGG
* * *
1367664 GGTTGGAGTATCCCTGATTATGAGAAAT
1 AGTTGGAGTATCCC-GATTGTGAAAAAT
1367692 CAATATTTTG
Statistics
Matches: 107, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
50 7 0.07
51 39 0.36
52 43 0.40
53 18 0.17
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.32
Consensus pattern (51 bp):
AGTTGGAGTATCCCGATTGTGAAAAATTAGTGTTTTTAGAAATAAAATCGG
Found at i:1367665 original size:51 final size:51
Alignment explanation
Indices: 1367510--1367729 Score: 208
Period size: 51 Copynumber: 4.3 Consensus size: 51
1367500 AAATAATAAA
* * ** * *
1367510 GTTGGAGTATCCTCGATTGTGAAAAATTTGTGTTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAATG-TTTTAGAAATAAAACCGGG
* * ** *
1367562 GTTGGAGTATCTCCGATTAAAGAAAAATTGGTGTTTT-GAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTAATGTTTTAG-AAATAAAACCGGG
* * * *
1367614 GTTGCAATATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGG
* * * * * * *
1367665 GTTGGAGTATCCCTGATTATGAGAAATCAATATTTTGGAAATAAAGCCAGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGG
1367716 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1367730 TAGGAAATAA
Statistics
Matches: 138, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
51 79 0.57
52 48 0.35
53 11 0.08
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAACCGGG
Found at i:1367747 original size:28 final size:27
Alignment explanation
Indices: 1367712--1367785 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
1367702 GAAATAAAGC
1367712 CAGGGTTGGAGTATCCCCTAGG-AAATAA
1 CAGGGTTGGAGTATCCCC--GGTAAATAA
* *
1367740 CAGGGTTGGAGTATCCCCGGTGATTAA
1 CAGGGTTGGAGTATCCCCGGTAAATAA
*
1367767 CGGGGTTGGAGTATCCCCG
1 CAGGGTTGGAGTATCCCCG
1367786 ATTGTGAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.05
27 22 0.52
28 18 0.43
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (27 bp):
CAGGGTTGGAGTATCCCCGGTAAATAA
Found at i:1367853 original size:54 final size:51
Alignment explanation
Indices: 1367771--1367893 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
1367761 GATTAACGGG
* * *
1367771 GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAGAAATTAGTG---TTTTGAAAATAAAATCGAA
1367825 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTATGAG-AAATTAGTGTTTTGAAAATAAAATCGAA
* *
1367876 GTGGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1367894 GCGCAGAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 33 0.52
53 2 0.03
54 28 0.44
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAGAAATTAGTGTTTTGAAAATAAAATCGAA
Found at i:1370293 original size:33 final size:33
Alignment explanation
Indices: 1370254--1370332 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
1370244 CAAAGAATAG
1370254 ATGTATCGATACAATGTATCAATACACAGAAAA
1 ATGTATCGATACAATGTATCAATACACAGAAAA
*
1370287 ATGTATCGATACAATGTATCGATACACAGAAAA
1 ATGTATCGATACAATGTATCAATACACAGAAAA
1370320 ATGTATCGATACA
1 ATGTATCGATACA
1370333 TTTCCTTGGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAATGTATCAATACACAGAAAA
Found at i:1370304 original size:13 final size:13
Alignment explanation
Indices: 1370286--1370312 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1370276 TACACAGAAA
1370286 AATGTATCGATAC
1 AATGTATCGATAC
1370299 AATGTATCGATAC
1 AATGTATCGATAC
1370312 A
1 A
1370313 CAGAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1370324 original size:20 final size:20
Alignment explanation
Indices: 1370266--1370332 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
1370256 GTATCGATAC
*
1370266 AATGTATCAATACACAGAAA
1 AATGTATCGATACACAGAAA
1370286 AATGTATCGAT--AC-----
1 AATGTATCGATACACAGAAA
1370299 AATGTATCGATACACAGAAA
1 AATGTATCGATACACAGAAA
1370319 AATGTATCGATACA
1 AATGTATCGATACA
1370333 TTTCCTTGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
18 2 0.05
20 24 0.62
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACACAGAAA
Found at i:1370374 original size:13 final size:13
Alignment explanation
Indices: 1370356--1370406 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 13
1370346 AGCTTCCTAG
1370356 CGATACATTGTAT
1 CGATACATTGTAT
1370369 CGATACAAAATTATGTAT
1 CGATAC---A-T-TGTAT
1370387 CGATACATTGTAT
1 CGATACATTGTAT
1370400 CGATACA
1 CGATACA
1370407 ACACTTACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
13 18 0.55
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.33
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1370394 original size:31 final size:32
Alignment explanation
Indices: 1370356--1370427 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 32
1370346 AGCTTCCTAG
*
1370356 CGATACATTGTATCGATACAA-AATTATGTAT
1 CGATACATTGTATCGATACAACAATTACGTAT
*
1370387 CGATACATTGTATCGATACAACACTTACGTAT
1 CGATACATTGTATCGATACAACAATTACGTAT
1370419 CGATACATT
1 CGATACATT
1370428 TACTGAATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 21 0.55
32 17 0.45
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACAATTACGTAT
Found at i:1371350 original size:55 final size:54
Alignment explanation
Indices: 1371266--1371950 Score: 681
Period size: 55 Copynumber: 12.0 Consensus size: 54
1371256 ATAAAGTGTA
* * * *
1371266 TCCTGCTCTTTGAGGACTAAAAAGTGCCACTAACTCGTGTAGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
1371321 TCCTGTTCTTTGAGGACTGAAAGGTGCCACCAACTTCTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
1371376 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
1371431 TCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
*
1371492 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* *
1371547 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
1371602 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* *
1371663 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * ** *
1371718 TCATGCTCTTTGAGGACTGGAAAATGCCACCAACCTACGTGGGCTTTGAAAGGAGAAGATG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTG-AA--AG--G-CG
* *
1371779 TCCTGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * *
1371838 TCCTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * *
1371899 TCCTACTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGG
1371951 AAAAGGCATC
Statistics
Matches: 539, Mismatches: 52, Indels: 79
0.80 0.08 0.12
Matches are distributed among these distances:
54 11 0.02
55 262 0.49
56 28 0.05
58 2 0.00
59 24 0.04
60 84 0.16
61 118 0.22
62 6 0.01
64 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:1371538 original size:116 final size:113
Alignment explanation
Indices: 1371265--1371976 Score: 700
Period size: 116 Copynumber: 6.2 Consensus size: 113
1371255 AATAAAGTGT
* * * * *
1371265 ATCCTGCTCTTTGAGGACT-AAAAAGTGCCACTAACTCGTGTAGGCTTTG-AAAG-GCGTCCTGT
1 ATCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAGAGCGTCCTGC
* * *
1371327 TCTTTGAGGACTGAAAGGTGCCACCAACTTCTGTGGGCTTT-AAGAGGT
65 TCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGC
* * *
1371375 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-GTGTCCTGCT
1 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAGCGTCCTGCT
* * * *
1371438 CTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGC
66 CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT--AAAG---AGGC
* * *
1371491 ATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAG-GTGTCCTGC
1 ATCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGAGCGTCCTGC
* *
1371553 TCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGT
65 TCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGC
* * * *
1371601 GTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATC
1 ATCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAG----AGCGTC
*
1371665 CTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGC
61 CTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGC
* * ** *
1371717 ATCATGCTCTTTGAGGACTGGAAAATGCCACCAACCTACGTGGGCTTTGAAAGGAGAAGATGTCC
1 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAA--AG-AG-CGTCC
* *
1371782 TGCTCTTTGAGGACTG-AAGGTGCCACTAACTTGTGTGGGCTTTAAAAGAAAAGGC
62 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAG---AGGC
* * *
1371837 GTCCTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG----AGCGTCC
* *
1371902 TACTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
62 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAA-G---AGGC
1371958 ATCCTGCTCTTTGAGGACT
1 ATCCTGCTCTTTGAGGACT
1371977 AAAAAGTGGG
Statistics
Matches: 519, Mismatches: 53, Indels: 49
0.84 0.09 0.08
Matches are distributed among these distances:
110 134 0.26
111 8 0.02
113 3 0.01
114 4 0.01
115 30 0.06
116 201 0.39
117 9 0.02
118 4 0.01
120 98 0.19
121 28 0.05
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.27
Consensus pattern (113 bp):
ATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAGCGTCCTGCT
CTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAGAGGC
Found at i:1371545 original size:171 final size:172
Alignment explanation
Indices: 1371266--1371950 Score: 833
Period size: 171 Copynumber: 4.0 Consensus size: 172
1371256 ATAAAGTGTA
* * *
1371266 TCCTGCTCTTTGAGGACTAAAAAGTGCCACTAACTCGTGT-AGGCTTTG-AAAG-----GCGTCC
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGA-GCTTTGAAAAGAAAAAGCATCC
* * * **
1371324 TGTTCTTTGAGGACT-GAAAGGTGCCACCAACTTCTGTGGGCTTT-AAGAGGTGTCCTGCTCTTT
65 TGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAGAGGCATCCTGCTCTTT
*
1371387 GAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
129 GAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1371431 TCCTGCTCTTTGGGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGCATCCT
* **
1371496 GCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTG
66 GCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAGAGGCATCCTGCTCTTTG
1371559 AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
130 AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
1371602 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGCATCCT
* *
1371667 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCATCATGCTCTTTGA
66 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCATCCTGCTCTTTGA
* **
1371731 GGACTGGAAAATGCCACCAACCTACGTGGGCTTTGAAAGGAGAAGATG
131 GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AA--AG--G-TG
* * * * * *
1371779 TCCTGCTCTTTGAGGACTG-AAGGTGCCACTAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCT
1 TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGCATCCT
* * *
1371842 GCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTACTC
66 GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--AAAG---AGGCATCCTGCTC
** *
1371907 TTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG
126 TTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
1371951 AAAAGGCATC
Statistics
Matches: 467, Mismatches: 32, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
165 43 0.09
166 5 0.01
171 255 0.55
172 8 0.02
174 2 0.00
175 58 0.12
176 27 0.06
177 24 0.05
179 2 0.00
180 23 0.05
181 20 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (172 bp):
TCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTCGTGTGAGCTTTGAAAAGAAAAAGCATCCT
GCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAGAGGCATCCTGCTCTTTGA
GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:1371652 original size:29 final size:29
Alignment explanation
Indices: 1371509--1371652 Score: 92
Period size: 28 Copynumber: 5.2 Consensus size: 29
1371499 CTTTGAGGAC
1371509 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** * * *
1371538 T-AAGAGGTGTCCTGC-TCTT-TGAGGAC-T
1 TGAA-AGGTG-CCACCAACTTGTGTGGGCTT
* *
1371565 GGAAA-ATGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
** *
1371593 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC--
1 TGAAAGGTG-CCACCAACTTGTGTGGG-CTT
1371619 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1 TGAAAGGTGCCACCAACTTGTGTGGGCTT
1371648 TGAAA
1 TGAAA
1371653 AGAAAAAGCA
Statistics
Matches: 81, Mismatches: 20, Indels: 28
0.63 0.16 0.22
Matches are distributed among these distances:
25 6 0.07
26 17 0.21
27 13 0.16
28 20 0.25
29 19 0.23
30 6 0.07
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:1372978 original size:20 final size:18
Alignment explanation
Indices: 1372948--1372987 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
1372938 CAGATTCTTC
1372948 TTTTGTTTTGTTGTTTTTT
1 TTTTGTTTTGTT-TTTTTT
1372967 TTTTGCTTTTGTTTTTTTT
1 TTTTG-TTTTGTTTTTTTT
1372986 TT
1 TT
1372988 AGAAAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (18 bp):
TTTTGTTTTGTTTTTTTT
Found at i:1383812 original size:28 final size:29
Alignment explanation
Indices: 1383752--1383833 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
1383742 TTTTGGAGAT
*
1383752 AATAACGGGGTTAGAGTATCCCC--TCGA
1 AATAACGGGGTTGGAGTATCCCCGATCGA
1383779 AGATAACGGGGTTGGAGTATCCCCGAT-GA
1 A-ATAACGGGGTTGGAGTATCCCCGATCGA
* *
1383808 AATAATGAGGTTGGAGTA-CCCTCGAT
1 AATAACGGGGTTGGAGTATCCC-CGAT
1383834 TGTGAAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
27 4 0.08
28 40 0.83
29 3 0.06
30 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (29 bp):
AATAACGGGGTTGGAGTATCCCCGATCGA
Found at i:1383875 original size:52 final size:51
Alignment explanation
Indices: 1383816--1383997 Score: 208
Period size: 51 Copynumber: 3.5 Consensus size: 51
1383806 GAAATAATGA
*
1383816 GGTTGGAGTA-CCCTCGATTGTGAAAAATTGATGTTTTTAGAAATAAAATCG
1 GGTTGGAGTATCCC-CGATTATGAAAAATTGATGTTTTTAGAAATAAAATCG
* * * *
1383867 GAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGA-AAATAAAATCG
1 G-GTTGGAGTATCCCCGATT-ATGAAAAATTGATGTTTTTAGAAATAAAATCG
* * * * *
1383919 GGTTGCAGTATCCTCGATTATGGAAAATTAATG-TTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTTAGAAATAAAATC-G
*
1383970 GGTTGGAGTATCCCCGATTATGAGAAAT
1 GGTTGGAGTATCCCCGATTATGAAAAAT
1383998 CAATATTTCG
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 4 0.04
50 20 0.18
51 42 0.38
52 26 0.24
53 18 0.16
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTTAGAAATAAAATCG
Found at i:1384013 original size:51 final size:51
Alignment explanation
Indices: 1383816--1384035 Score: 191
Period size: 51 Copynumber: 4.3 Consensus size: 51
1383806 GAAATAATGA
* * * *
1383816 GGTTGGAGTA-CCCTCGATTGTGA-AAAATTGATGTTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCC-CGATTATGAGAAAATTAATG-TTTGA-AAATAAAACCGG
* * ** *
1383868 AGTTGGAGTATCCCCGATTA-AAGGAAAATTGGTGTTTTGAAAATAAAATC-G
1 GGTTGGAGTATCCCCGATTATGA-GAAAATTAATG-TTTGAAAATAAAACCGG
* * *
1383919 GGTTGCAGTATCCTCGATTATG-GAAAATTAATGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAGAAAATTAATGTTTGA-AAATAAAACCGG
* * * *
1383970 GGTTGGAGTATCCCCGATTATGAG-AAATCAATATTTCGAAAATAAAGCCGA
1 GGTTGGAGTATCCCCGATTATGAGAAAATTAATGTTT-GAAAATAAAACCGG
1384021 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1384036 TCGAAAATAA
Statistics
Matches: 140, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
49 4 0.03
50 18 0.13
51 75 0.54
52 26 0.19
53 17 0.12
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAGAAAATTAATGTTTGAAAATAAAACCGG
Found at i:1384025 original size:102 final size:104
Alignment explanation
Indices: 1383814--1384033 Score: 268
Period size: 102 Copynumber: 2.1 Consensus size: 104
1383804 ATGAAATAAT
* * * *
1383814 GAGGTTGGAGTACCCTCGATTGTGAAAAATTGATGTTTTTAGAAATAAAATCGGAGTTGGAGTAT
1 GAGGTTGGAGTATCCTCGATTATGAAAAATTAATGTTTTTAGAAATAAAACCGGAGTTGGAGTAT
*** * * *
1383879 CCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATC
66 CCCCGATTAAAGGAAAATCAATATTTCGAAAATAAAACC
* * *
1383918 G-GGTTGCAGTATCCTCGATTATGGAAAATTAATG-TTTTAGAAATAAAACCGGGGTTGGAGTAT
1 GAGGTTGGAGTATCCTCGATTATGAAAAATTAATGTTTTTAGAAATAAAACCGGAGTTGGAGTAT
* *
1383981 CCCCGATT--ATGAGAAATCAATATTTCGAAAATAAAGCC
66 CCCCGATTAAAGGA-AAATCAATATTTCGAAAATAAAACC
1384019 GAGGTTGGAGTATCC
1 GAGGTTGGAGTATCC
1384034 CCTCGAAAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
100 3 0.03
101 19 0.19
102 47 0.48
103 28 0.29
104 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (104 bp):
GAGGTTGGAGTATCCTCGATTATGAAAAATTAATGTTTTTAGAAATAAAACCGGAGTTGGAGTAT
CCCCGATTAAAGGAAAATCAATATTTCGAAAATAAAACC
Found at i:1384058 original size:28 final size:28
Alignment explanation
Indices: 1384021--1384090 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
1384011 ATAAAGCCGA
1384021 GGTTGGAGTATCCCCTCGA-AAATAACGG
1 GGTTGGAGTATCCCC-CGATAAATAACGG
* * *
1384049 GGTTGGAGTAT-CTCCGATGATTAACGG
1 GGTTGGAGTATCCCCCGATAAATAACGG
1384076 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1384091 GATTGTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 20 0.56
28 13 0.36
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCCGATAAATAACGG
Found at i:1384144 original size:53 final size:51
Alignment explanation
Indices: 1384077--1384199 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
1384067 GATTAACGGG
* * *
1384077 GTTGGAGTATCCCCGATTGT-GAAAATTGGTGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAGAAAATT--AGTA-TTTTGAAAATAAAATCGAA
*
1384130 GTTGGAGTATCCCCGATTATAGAAAATTAGTATTTTGAAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTAGAAAATTAGTATTTTGAAAATAAAATCGAA
* *
1384181 GTGGGAATATCCCCGATTG
1 GTTGGAGTATCCCCGATTG
1384200 CGGAGAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
51 33 0.53
52 3 0.05
53 19 0.31
54 7 0.11
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAGAAAATTAGTATTTTGAAAATAAAATCGAA
Found at i:1386567 original size:13 final size:13
Alignment explanation
Indices: 1386549--1386574 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1386539 CAAAGAATAG
1386549 ATGTATCGATACA
1 ATGTATCGATACA
1386562 ATGTATCGATACA
1 ATGTATCGATACA
1386575 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1386571 original size:34 final size:33
Alignment explanation
Indices: 1386528--1386594 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
1386518 AACTTCCTAG
*
1386528 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
1386562 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
1386595 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:1386659 original size:32 final size:32
Alignment explanation
Indices: 1386618--1386690 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
1386608 AGCTTCCTAG
*
1386618 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGCATCGATACAAAACTTATGTAT
* *
1386650 CGATACATTGCATCGATACAACATTTATGTAT
1 CGATACATTGCATCGATACAAAACTTATGTAT
1386682 CGATACATT
1 CGATACATT
1386691 TACTGAATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGCATCGATACAAAACTTATGTAT
Found at i:1386685 original size:19 final size:18
Alignment explanation
Indices: 1386626--1386688 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
1386616 AGCGATACAT
*
1386626 TGTATCGATACAAAACTTA
1 TGTATCGATACAACA-TTA
1386645 TGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
*
1386658 TGCATCGATACAACATTTA
1 TGTATCGATACAACA-TTA
1386677 TGTATCGATACA
1 TGTATCGATACA
1386689 TTTACTGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
16 5 0.14
18 1 0.03
19 20 0.57
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:1386773 original size:21 final size:21
Alignment explanation
Indices: 1386749--1386823 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
1386739 TGGGACCTTT
* *
1386749 TATCGATACATTTGTA-GAATG
1 TATCGATACA-TTCTACAAATG
*
1386770 TATCGATACATTCCACAAATG
1 TATCGATACATTCTACAAATG
1386791 TATCGATACATTCTACAAATG
1 TATCGATACATTCTACAAATG
1386812 TATCGATACATT
1 TATCGATACATT
1386824 TGGATAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (21 bp):
TATCGATACATTCTACAAATG
Found at i:1392170 original size:12 final size:12
Alignment explanation
Indices: 1392153--1392178 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1392143 TAGATGTTAT
1392153 TCTAATACTTTG
1 TCTAATACTTTG
1392165 TCTAATACTTTG
1 TCTAATACTTTG
1392177 TC
1 TC
1392179 AGCTTAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (12 bp):
TCTAATACTTTG
Found at i:1393226 original size:13 final size:13
Alignment explanation
Indices: 1393208--1393232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1393198 ACAATAAGCA
1393208 TGTATCGATACAT
1 TGTATCGATACAT
1393221 TGTATCGATACA
1 TGTATCGATACA
1393233 ATGAGCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1393232 original size:32 final size:32
Alignment explanation
Indices: 1393189--1393253 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1393179 CAATTGAGTA
1393189 TGTATCAATACAATAAGCATGTATCGATACAT
1 TGTATCAATACAATAAGCATGTATCGATACAT
* * *
1393221 TGTATCGATACAATGAGCATGTGTCGATACAT
1 TGTATCAATACAATAAGCATGTATCGATACAT
1393253 T
1 T
1393254 ATCTAGATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTATCAATACAATAAGCATGTATCGATACAT
Found at i:1395906 original size:20 final size:20
Alignment explanation
Indices: 1395881--1395931 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1395871 CTTCCAGATA
1395881 TATCGATACATCATTCAATG
1 TATCGATACATCATTCAATG
1395901 TATCGATACATCATTCAATG
1 TATCGATACATCATTCAATG
1395921 TATCGATACAT
1 TATCGATACAT
1395932 TCTGAAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
TATCGATACATCATTCAATG
Done.