Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 12 of 34
Found at i:1777354 original size:21 final size:22
Alignment explanation
Indices: 1777321--1777443 Score: 82
Period size: 23 Copynumber: 5.7 Consensus size: 22
1777311 ATATGAATAT
1777321 TATATATATATATATAATATAAAA
1 TATATATATA-ATATAATA-AAAA
*
1777345 CATATAATATAATATAATAAAAA
1 TATAT-ATATAATATAATAAAAA
* * *
1777368 TATATAT-TAAAATTTATAGAAA
1 TATATATATAATA-TAATAAAAA
* *
1777390 TATA-A-AT-AT-T-TTAAATA
1 TATATATATAATATAATAAAAA
1777407 TA-AT-TATAATATAATAAAATA
1 TATATATATAATATAATAAAA-A
*
1777428 TATAAATATAATATAA
1 TATATATATAATATAA
1777444 ATTTATAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
16 1 0.01
17 8 0.11
18 3 0.04
19 1 0.01
20 5 0.07
21 9 0.12
22 14 0.18
23 18 0.24
24 12 0.16
25 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
TATATATATAATATAATAAAAA
Found at i:1777682 original size:2 final size:2
Alignment explanation
Indices: 1777675--1777700 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1777665 AACATAATTC
1777675 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1777701 TTGGTTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1784759 original size:16 final size:16
Alignment explanation
Indices: 1784738--1784771 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1784728 TACACTTTAA
1784738 CACATAAATAGGTGAT
1 CACATAAATAGGTGAT
1784754 CACATAAATAGGTGAT
1 CACATAAATAGGTGAT
1784770 CA
1 CA
1784772 AACTAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.24
Consensus pattern (16 bp):
CACATAAATAGGTGAT
Found at i:1788431 original size:21 final size:20
Alignment explanation
Indices: 1788402--1788444 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1788392 CATCTCTGCA
1788402 TTTTTTTTTTC-TTTCTTCTT
1 TTTTTTTTTTCATTT-TTCTT
1788422 TTTTTGTTTTTCATTTTTCTT
1 TTTTT-TTTTTCATTTTTCTT
1788443 TT
1 TT
1788445 ATCTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 13 0.62
22 3 0.14
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTTCATTTTTCTT
Found at i:1788997 original size:18 final size:17
Alignment explanation
Indices: 1788966--1789002 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1788956 TAAACTATTT
1788966 AATTTTTTAAAAAAATA
1 AATTTTTTAAAAAAATA
*
1788983 AATTTATTTATAAAAATA
1 AATTT-TTTAAAAAAATA
1789001 AA
1 AA
1789003 AAATAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTTTTAAAAAAATA
Found at i:1789719 original size:25 final size:25
Alignment explanation
Indices: 1789689--1789747 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1789679 AGTAATATAG
* *
1789689 ATTATATA-TATGAT-TACTAA-AT
1 ATTATATATTATAATATAATAACAT
1789711 ATTTATATATTATAATATAATAACAT
1 A-TTATATATTATAATATAATAACAT
1789737 ATTATATATTA
1 ATTATATATTA
1789748 CAATGTCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.03
23 7 0.23
24 5 0.16
25 15 0.48
26 3 0.10
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (25 bp):
ATTATATATTATAATATAATAACAT
Found at i:1790142 original size:20 final size:20
Alignment explanation
Indices: 1790100--1790153 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1790090 CTGAACAATT
*
1790100 TGTATCAATACAATAAGGTAA
1 TGTATCGATAC-ATAAGGTAA
1790121 TGTATCGATACATAA-GTAAA
1 TGTATCGATACATAAGGT-AA
1790141 TGTATCGATACAT
1 TGTATCGATACAT
1790154 GCTTGAGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 2 0.06
20 19 0.61
21 10 0.32
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATAAGGTAA
Found at i:1790271 original size:52 final size:52
Alignment explanation
Indices: 1790209--1790400 Score: 224
Period size: 52 Copynumber: 3.7 Consensus size: 52
1790199 TCTGGAAAGA
* * * * *
1790209 AAATATATCGATGCATTTTTTATTGTATCGATACATTTTAGGTTTTTGACCC
1 AAATATATCGATACATTATTCATTGTATCAATACATTCTAGGTTTTTGACCC
*
1790261 AAATATATCGATACATTATTCATTGTATTAATACATTCTAGGCTTTTT-ACCC
1 AAATATATCGATACATTATTCATTGTATCAATACATTCTAGG-TTTTTGACCC
* * **
1790313 AAATGTATCGATACATTATTCATTGTATCAATACATTCTGGGTTTTTGACTT
1 AAATATATCGATACATTATTCATTGTATCAATACATTCTAGGTTTTTGACCC
* * * ** *
1790365 AAATGTATTGATACATTCTTCAAAGTATCGATACAT
1 AAATATATCGATACATTATTCATTGTATCAATACAT
1790401 GCAGGCAATT
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
51 5 0.04
52 112 0.92
53 5 0.04
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (52 bp):
AAATATATCGATACATTATTCATTGTATCAATACATTCTAGGTTTTTGACCC
Found at i:1795969 original size:51 final size:51
Alignment explanation
Indices: 1795913--1796021 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
1795903 ATCTCGAGAT
*
1795913 GCATCAGAAACATTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATC
1 GCATCACAAACATTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATC
***** *
1795964 GCATCACCTTTTTTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATT
1 GCATCACAAACATTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATC
1796015 GCATCAC
1 GCATCAC
1796022 CTTTTTGGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (51 bp):
GCATCACAAACATTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATC
Found at i:1796022 original size:51 final size:51
Alignment explanation
Indices: 1795925--1796027 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
1795915 ATCAGAAACA
1795925 TTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATCGCATCACCTTTT
1 TTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATCGCATCACCTTTT
*
1795976 TTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATTGCATCACCTTTT
1 TTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATCGCATCACCTTTT
1796027 T
1 T
1796028 GGTCGTCAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (51 bp):
TTTGTGTCATGATTATGCAGGGTAGCAATAGCCTAAATCGCATCACCTTTT
Found at i:1799884 original size:20 final size:20
Alignment explanation
Indices: 1799811--1799890 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
1799801 CAAAAACCCA
* * *
1799811 TAATGTATCGATGCAATGAG
1 TAATGTATCGATACATTTAG
*
1799831 AAATGTATCGATACAATTGTAAG
1 TAATGTATCGATAC-ATT-T-AG
* *
1799854 -CATGCATCGATACATTTAG
1 TAATGTATCGATACATTTAG
*
1799873 TAATGTATCGATATATTT
1 TAATGTATCGATACATTT
1799891 CCTTGGTAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
19 2 0.04
20 27 0.57
21 5 0.11
22 11 0.23
23 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (20 bp):
TAATGTATCGATACATTTAG
Found at i:1800435 original size:34 final size:34
Alignment explanation
Indices: 1800367--1800499 Score: 109
Period size: 34 Copynumber: 4.0 Consensus size: 34
1800357 TTCTCCAAAT
*
1800367 CTTTTTCCTTCTTCAAAGTCCACGACTCTA-TGGCAC
1 CTTTTTTCTT-TTC-AAGTCCACGACTC-AGTGGCAC
*
1800403 CTTTTTTCTTTTCAAGTCCATGACTCAGTGGCA-
1 CTTTTTTCTTTTCAAGTCCACGACTCAGTGGCAC
* * *
1800436 -TCTCTTC--TTAAAGTCCACGACTTC-GTGGCAAC
1 CTTTTTTCTTTTCAAGTCCACGAC-TCAGTGGC-AC
* *
1800468 C-TTTTTCATTTCAAGTCCAAGACTCAGTGGCA
1 CTTTTTTCTTTTCAAGTCCACGACTCAGTGGCA
1800500 TCTCTTCTCA
Statistics
Matches: 79, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
30 17 0.22
31 3 0.04
32 9 0.11
33 4 0.05
34 34 0.43
35 3 0.04
36 9 0.11
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (34 bp):
CTTTTTTCTTTTCAAGTCCACGACTCAGTGGCAC
Found at i:1800450 original size:30 final size:30
Alignment explanation
Indices: 1800416--1800523 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
1800406 TTTTCTTTTC
1800416 AAGTCCATGACTCAGTGGCATCTCTTCTTA
1 AAGTCCATGACTCAGTGGCATCTCTTCTTA
* * * *
1800446 AAGTCCACGACTTC-GTGGCAACCTTTTTCATTTC
1 AAGTCCATGAC-TCAGTGGC-ATC-TCTTC--TTA
* *
1800480 AAGTCCAAGACTCAGTGGCATCTCTTCTCA
1 AAGTCCATGACTCAGTGGCATCTCTTCTTA
*
1800510 AAGTCAATGACTCA
1 AAGTCCATGACTCA
1800524 ATGGTACCCT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
30 28 0.46
31 4 0.07
32 8 0.13
33 4 0.07
34 17 0.28
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (30 bp):
AAGTCCATGACTCAGTGGCATCTCTTCTTA
Found at i:1800480 original size:64 final size:64
Alignment explanation
Indices: 1800374--1800602 Score: 205
Period size: 64 Copynumber: 3.6 Consensus size: 64
1800364 AATCTTTTTC
* *
1800374 CTTCTTCAAAGTCCACGACTCTATGGCACCTTTTTTCTTTTCAAGTCCATGACTCAGTGGCATCT
1 CTTCTT-AAAGTCCACGACTCTATGGCACCTTTTTTCATTTCAAGTCCAAGACTCAGTGGCATCT
*
1800439 CTTCTTAAAGTCCACGACT-TCGTGGCAACC-TTTTTCATTTCAAGTCCAAGACTCAGTGGCATC
1 CTTCTTAAAGTCCACGACTCT-ATGGC-ACCTTTTTTCATTTCAAGTCCAAGACTCAGTGGCATC
1800502 T
64 T
* * * * * * * * * * * *
1800503 CTTCTCAAAGTCAATGACTCAATGGTACCCTTTTCCTTTTTAAGTCTACA-CCTCCGTGGCA-CG
1 CTTCTTAAAGTCCACGACTCTATGGCACCTTTTTTCATTTCAAGTCCA-AGACTCAGTGGCATC-
1800566 T
64 T
* * * * *
1800567 TTTTTTTAAGTCTACAACTCTATGGCACCTTTTTTC
1 CTTCTTAAAGTCCACGACTCTATGGCACCTTTTTTC
1800603 TTTTAAAATT
Statistics
Matches: 132, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
63 5 0.04
64 117 0.89
65 10 0.08
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.37
Consensus pattern (64 bp):
CTTCTTAAAGTCCACGACTCTATGGCACCTTTTTTCATTTCAAGTCCAAGACTCAGTGGCATCT
Found at i:1800573 original size:30 final size:30
Alignment explanation
Indices: 1800539--1800601 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1800529 ACCCTTTTCC
* * *
1800539 TTTTTAAGTCTACACCTCCGTGGCACGTTT
1 TTTTTAAGTCTACAACTCCATGGCACCTTT
*
1800569 TTTTTAAGTCTACAACTCTATGGCACCTTT
1 TTTTTAAGTCTACAACTCCATGGCACCTTT
1800599 TTT
1 TTT
1800602 CTTTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTTTAAGTCTACAACTCCATGGCACCTTT
Found at i:1800676 original size:32 final size:31
Alignment explanation
Indices: 1800636--1801390 Score: 712
Period size: 32 Copynumber: 23.6 Consensus size: 31
1800626 CACCTTTTCC
* *
1800636 TTCAAAGCCCACACAAGTCGGT-ACTAGCCCT
1 TTCAAAGCCCACACAAGTCGGTGGC-AACCCT
* * *
1800667 TTCAAAAGCCTATACAAGTCTGTGGCAACCCT
1 TTC-AAAGCCCACACAAGTCGGTGGCAACCCT
* * * *
1800699 CTCAAATTCCCACACAAGTCGATGGCAACCTT
1 TTCAAA-GCCCACACAAGTCGGTGGCAACCCT
* *
1800731 TTCAAAGCCCACAAAAGTCAGTGGCAACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
* *
1800762 TT-AAAGACCACACAAGTCAGTGGCAACCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCC-T
*
1800793 TTAAAAGCCCACACAAGTCGGTGGCAACCC-
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
* ** *
1800823 TTCAAAGCCTACACAAGTCAATGGAAACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
* *
1800854 TATCAAAGCCCACACAAGTCGATGGAAACCCT
1 T-TCAAAGCCCACACAAGTCGGTGGCAACCCT
* * * *
1800886 TTGAAAAGCCTACACAAGTCGATGGCAACCCC
1 TT-CAAAGCCCACACAAGTCGGTGGCAACCCT
*
1800918 TTCTAAAGCCCACACAAGTCGGTGGCAACTC-
1 TTC-AAAGCCCACACAAGTCGGTGGCAACCCT
*
1800949 TTCTAAAGCCCACATAAGTCGGTGGCAACCCT
1 TTC-AAAGCCCACACAAGTCGGTGGCAACCCT
*
1800981 TCTCAAAGCTCACACAAGTCGGTGGCAACCCT
1 T-TCAAAGCCCACACAAGTCGGTGGCAACCCT
** * *
1801013 TCTCTAAAGTTCGCACAAGTCAGTGGCAACCCT
1 T-TC-AAAGCCCACACAAGTCGGTGGCAACCCT
* *
1801046 TCCCTAAAGCCCACACAAGTAGGTGGCAACCCT
1 T-TC-AAAGCCCACACAAGTCGGTGGCAACCCT
* * * *
1801079 TCCCTAAAGCCTACACAAGTCGGTGGTAACCCC
1 T-TC-AAAGCCCACACAAGTCGGTGGCAACCCT
* ** *
1801112 TTCTAAAGCCCACCCAAGTTAGTGGCAACCATT
1 TTC-AAAGCCCACACAAGTCGGTGGCAACC-CT
*
1801145 TTCAAAGCCCACACAAGTCGGTGGTAACCCT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1801176 TCTAAAAGCCCACACAAGTTGGTGGCAACTC-
1 T-TCAAAGCCCACACAAGTCGGTGGCAACCCT
*
1801207 TTCTAAAGCCCACACAAGTTGGTGGCAACCCT
1 TTC-AAAGCCCACACAAGTCGGTGGCAACCCT
*
1801239 TCTCTAAAGTCCACACAAGTCGGTGGCAA-CCT
1 T-TC-AAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1801271 CTTCTAAAGCCCATACAAGCCGGTGGTAACCCTT
1 -TTC-AAAGCCCACACAAGTCGGTGGCAACCC-T
** *
1801305 TTCTAAAGCTTACACAAGTCGGTGGCAACCCCC
1 TTC-AAAGCCCACACAAGTCGGTGGCAA-CCCT
* *
1801338 TTCAATAGCCTACATAAGTCGGTGGCAACCCT
1 TTCAA-AGCCCACACAAGTCGGTGGCAACCCT
*
1801370 CTCAAATGCCCACACAAGTCG
1 TTCAAA-GCCCACACAAGTCG
1801391 TGGTATCTCC
Statistics
Matches: 610, Mismatches: 91, Indels: 45
0.82 0.12 0.06
Matches are distributed among these distances:
30 51 0.08
31 92 0.15
32 301 0.49
33 162 0.27
34 4 0.01
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (31 bp):
TTCAAAGCCCACACAAGTCGGTGGCAACCCT
Found at i:1801163 original size:258 final size:255
Alignment explanation
Indices: 1800636--1801388 Score: 811
Period size: 258 Copynumber: 2.9 Consensus size: 255
1800626 CACCTTTTCC
* * * * * * * *
1800636 TTCAAAGCCCACACAAGTCGGT-ACTAGCCCTTTCAAAAGCCTATACAAGTCTGTGGCAAC-CCT
1 TTCAAAGCCCACACAAGTCGGTGGC-AACCCCTTCTAAAGCCCACACAAGTCGGTGGCAACTCTT
* * * * * *
1800699 CTCAAATTCCCACACAAGTCGATGGCAA-CCTTTTCAAAGCCCACAAAAGTCAGTGGCAACCCT-
65 CT-AAA-GCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCTCACACAAGTCGGTGGCAACCCTC
*
1800762 T-TAAAGACCACACAAGTCAGTGGCAACCCTTTTAAAAGCCCACACAAGTCGGTGGCAACCCTT-
128 TCTAAAGACCACACAAGTCAGTGGCAACCCTTCT-AAAGCCCACACAAGTCGGTGGCAACCCTTC
** * * *
1800825 -C-AAAGCCTACACAAGTCAATGGAAACCCTTATCAAAGCCCACACAAGTCGATGGAAACCCTT
192 CCTAAAGCCTACACAAGTCGGTGGAACCCCTTATCAAAGCCCACACAAGTAGATGGAAACCATT
** * *
1800887 TGAAAAGCCTACACAAGTCGATGGCAACCCCTTCTAAAGCCCACACAAGTCGGTGGCAACTCTTC
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCCTTCTAAAGCCCACACAAGTCGGTGGCAACTCTTC
*
1800952 TAAAGCCCACATAAGTCGGTGGCAACCCTTCTCAAAGCTCACACAAGTCGGTGGCAACCCTTCTC
66 TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCTCACACAAGTCGGTGGCAACCC-TCTC
** * *
1801017 TAAAGTTCGCACAAGTCAGTGGCAACCCTTCCCTAAAGCCCACACAAGTAGGTGGCAACCCTTCC
130 TAAAGACCACACAAGTCAGTGGCAACCCTT--CTAAAGCCCACACAAGTCGGTGGCAACCCTTCC
* * *
1801082 CTAAAGCCTACACAAGTCGGTGGTAACCCCTTCT-AAAGCCCACCCAAGTTAG-TGGCAACCATT
193 CTAAAGCCTACACAAGTCGGTGG-AACCCCTTATCAAAGCCCACACAAG-TAGATGGAAACCATT
* *
1801145 TTCAAAGCCCACACAAGTCGGTGGTAA-CCCTTCTAAAAGCCCACACAAGTTGGTGGCAACTCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCCTTCT-AAAGCCCACACAAGTCGGTGGCAACTCTT
*
1801209 CTAAAGCCCACACAAGTTGGTGGCAACCCTTCTCTAAAG-TCCACACAAGTCGGTGGCAA-CCTC
65 CTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-AAAGCT-CACACAAGTCGGTGGCAACCCTC
* * * * * **
1801272 TTCTAAAGCCCATACAAGCCGGTGGTAACCCTTTTCTAAAGCTTACACAAGTCGGTGGCAACCC-
128 -TCTAAAGACCACACAAGTCAGTGGCAACCC--TTCTAAAGCCCACACAAGTCGGTGGCAACCCT
* * *
1801336 -CCTTCAATAGCCTACATAAGTCGGTGGCAA-CCC-TCTCAAATGCCCACACAAGT
190 TCCCT-AA-AGCCTACACAAGTCGGTGG-AACCCCTTATCAAA-GCCCACACAAGT
1801389 CGTGGTATCT
Statistics
Matches: 425, Mismatches: 54, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
250 18 0.04
251 80 0.19
252 6 0.01
253 1 0.00
254 27 0.06
255 28 0.07
256 7 0.02
257 19 0.04
258 205 0.48
259 32 0.08
260 2 0.00
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (255 bp):
TTCAAAGCCCACACAAGTCGGTGGCAACCCCTTCTAAAGCCCACACAAGTCGGTGGCAACTCTTC
TAAAGCCCACACAAGTCGGTGGCAACCCTTCTCAAAGCTCACACAAGTCGGTGGCAACCCTCTCT
AAAGACCACACAAGTCAGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCCCTA
AAGCCTACACAAGTCGGTGGAACCCCTTATCAAAGCCCACACAAGTAGATGGAAACCATT
Found at i:1801405 original size:226 final size:223
Alignment explanation
Indices: 1800639--1801406 Score: 840
Period size: 226 Copynumber: 3.4 Consensus size: 223
1800629 CTTTTCCTTC
* ** * * * *
1800639 AAAGCCCACACAAGTCGGTACTAGCCCTTTCAAAAGCCTATACAAGTCTGTGGCAACCCTCTCAA
1 AAAGCCTACACAAGTCGGT-GGAACCCCTTCAAAAGCCTACACAAGTCGGTGGCAACCCTCTCAA
* * * * *
1800704 ATTCCCACACAAGTCGATGGCAA--CCTTTTCAAAGCCCACAAAAGTCAGTGGCAACCCTT-TAA
65 A-GCCCACACAAGTCGGTGGCAACTCCTTCTAAAAGCCCACAAAAGTCGGTGGCAACCCTTCTAA
* * *
1800766 AGACCACACAAGTCAGTGGCAACCCTT-T-TAAAAGCCCACACAAGTCGGTGGCAACCCTTC-AA
129 AGCCCACACAAGTCGGTGGCAACCCTTCTCT-AAAGTCCACACAAGTCGGTGGCAACCCTTCTAA
* **
1800828 AGCCTACACAAGTCAATGGAAACCCTTATC-
193 AGCCCACACAAGTCGGTGGAAACCCTTATCT
* * * * *
1800858 AAAGCCCACACAAGTCGATGGAAACCCTTTGAAAAGCCTACACAAGTCGATGGCAACCC-CTTCT
1 AAAGCCTACACAAGTCGGTGG-AACCCCTTCAAAAGCCTACACAAGTCGGTGGCAACCCTC-TC-
*
1800922 AAAGCCCACACAAGTCGGTGGCAACT-CTTCT-AAAGCCCACATAAGTCGGTGGCAACCCTTCTC
63 AAAGCCCACACAAGTCGGTGGCAACTCCTTCTAAAAGCCCACAAAAGTCGGTGGCAACCCTTCT-
* * * *
1800985 AAAGCTCACACAAGTCGGTGGCAACCCTTCTCTAAAGTTCGCACAAGTCAGTGGCAACCCTTCCC
127 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGTCCACACAAGTCGGTGGCAACCCTT--C
* * **
1801050 TAAAGCCCACACAAGTAGGTGGCAACCCTTCCCT
190 TAAAGCCCACACAAGTCGGTGGAAACCCTTATCT
* * * ** * *
1801084 AAAGCCTACACAAGTCGGTGGTAACCCCTTCTAAAGCCCACCCAAGTTAGTGGCAACCATTTTCA
1 AAAGCCTACACAAGTCGGTGG-AACCCCTTCAAAAGCCTACACAAGTCGGTGGCAACC-CTCTCA
* * * *
1801149 AAGCCCACACAAGTCGGTGGTAAC-CCTTCTAAAAGCCCACACAAGTTGGTGGCAACTCTTCTAA
64 AAGCCCACACAAGTCGGTGGCAACTCCTTCTAAAAGCCCACAAAAGTCGGTGGCAACCCTTCTAA
*
1801213 AGCCCACACAAGTTGGTGGCAACCCTTCTCTAAAGTCCACACAAGTCGGTGGCAACCTCTTCTAA
129 AGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGTCCACACAAGTCGGTGGCAACC-CTTCTAA
* * * *
1801278 AGCCCATACAAGCCGGTGGTAACCCTTTTCT
193 AGCCCACACAAGTCGGTGGAAACCCTTATCT
* * *
1801309 AAAGCTTACACAAGTCGGTGGCAACCCCCTTCAATAGCCTACATAAGTCGGTGGCAACCCTCTCA
1 AAAGCCTACACAAGTCGGTGG-AA-CCCCTTCAAAAGCCTACACAAGTCGGTGGCAACCCTCTCA
* *
1801374 AATGCCCACACAAGTC-GTGGTATCTCCTTCTAA
64 AA-GCCCACACAAGTCGGTGGCAACTCCTTCTAA
1801407 GCTCAATATT
Statistics
Matches: 461, Mismatches: 67, Indels: 35
0.82 0.12 0.06
Matches are distributed among these distances:
218 1 0.00
219 98 0.21
220 8 0.02
221 26 0.06
222 26 0.06
223 1 0.00
224 1 0.00
225 89 0.19
226 178 0.39
227 33 0.07
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (223 bp):
AAAGCCTACACAAGTCGGTGGAACCCCTTCAAAAGCCTACACAAGTCGGTGGCAACCCTCTCAAA
GCCCACACAAGTCGGTGGCAACTCCTTCTAAAAGCCCACAAAAGTCGGTGGCAACCCTTCTAAAG
CCCACACAAGTCGGTGGCAACCCTTCTCTAAAGTCCACACAAGTCGGTGGCAACCCTTCTAAAGC
CCACACAAGTCGGTGGAAACCCTTATCT
Found at i:1801537 original size:50 final size:51
Alignment explanation
Indices: 1801459--1801598 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 51
1801449 AAGCCATTAC
* * *
1801459 TTTC-TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTATCACCTTT-T
1 TTTCTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTAGCACCTTTGT
* * *
1801508 TTTCTTAAGTCCAATATCGTTGGCATTGAATTAGCATATTGGCACCTTTGT
1 TTTCTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTAGCACCTTTGT
** * *
1801559 CATCTTTAAGTCTAATATCACTGGCCTTGAATTAGCATAT
1 TTTC-TTAAGTCCAATATCGCTGGCCTTGAATTAGCATAT
1801599 CGACACCTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 4 0.05
50 38 0.50
51 3 0.04
52 31 0.41
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (51 bp):
TTTCTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTAGCACCTTTGT
Found at i:1801589 original size:52 final size:52
Alignment explanation
Indices: 1801463--1801726 Score: 217
Period size: 52 Copynumber: 4.9 Consensus size: 52
1801453 CATTACTTTC
* ** **
1801463 TAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTATCACCTTT-TTTTC-T
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * *
1801513 TAAGTCCAATATCGTTGGCATTGAATTAGCATATTGGCACCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
* * * * * *
1801565 TAAGTCTAATATCACTGGCCTTGAATTAGCATATCGACACCTTTATCATTCTTCTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C-----C--T-TTGTCATCTT
* * * * *
1801626 TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTGTCATTTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
** * * *
1801678 TAAACCCAATATTGTTGGCCTTGAATCAGCATATTGGCACCTTTATCAT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
1801727 TCTTATCATC
Statistics
Matches: 170, Mismatches: 33, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
50 38 0.22
51 3 0.02
52 84 0.49
53 2 0.01
55 1 0.01
58 1 0.01
60 1 0.01
61 40 0.24
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (52 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTT
Found at i:1801675 original size:61 final size:60
Alignment explanation
Indices: 1801558--1801887 Score: 266
Period size: 61 Copynumber: 5.6 Consensus size: 60
1801548 GGCACCTTTG
* * * * * *
1801558 TCATCTTTAAGTCTAATATCACTGGCCTTGAATTAGCATATCGACACCTTTATCATTCTT
1 TCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* * * *
1801618 CTCATCTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTGTCATT-TT
1 -TCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* *
1801678 T-A-----AA-CCCAATATTGTTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
1 TCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* *
1801731 ATCATCTTCAAGCCCAATATCCCTGG-CTATGAATCAGCATATTGGCACCTTTATCATTCGTT
1 -TCATCTTTAAGCCCAATATCGCTGGCCT-TGAATCAGCATATTGGCACCTTTATCATTC-TT
* * * * * * ** * * *
1801793 GCATCTTGAAGTCTAATGTTGCTAACCTTGAATCAGCACATTAGCACTCTTT-TCATCCTT
1 TCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC-CTTTATCATTCTT
* * * * *
1801853 ATCATCTTTAAGTCTAATGTTGCAGGCCTTGAATC
1 -TCATCTTTAAGCCCAATATCGCTGGCCTTGAATC
1801888 TGCGTACTAG
Statistics
Matches: 219, Mismatches: 36, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
52 40 0.18
53 4 0.02
54 1 0.00
55 1 0.00
58 1 0.00
59 1 0.00
60 8 0.04
61 155 0.71
62 8 0.04
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (60 bp):
TCATCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
Found at i:1801710 original size:113 final size:113
Alignment explanation
Indices: 1801512--1801788 Score: 349
Period size: 113 Copynumber: 2.5 Consensus size: 113
1801502 CCTTTTTTTC
* * * * * ** *
1801512 TTAAGTCCAATATCGTTGGCATTGAATTAGCATATTGGCACCTTTGTCATCTTTAAGTCTAATAT
1 TTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAACCCAATAT
* *
1801577 CACTGGCCTTGAATTAGCATATCGACACCTTTATCATTCTTCTCATCT
66 CACTGGCCTTGAATCAGCATATCGACACCTTTATCATTCTTATCATCT
* * *
1801625 TTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTGTCATTTTTAAACCCAATAT
1 TTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAACCCAATAT
*** * *
1801690 TGTTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTATCATCT
66 CACTGGCCTTGAATCAGCATATCGACACCTTTATCATTCTTATCATCT
* * *
1801738 TCAAGCCCAATATCCCTGG-CTATGAATCAGCATATTGGCACCTTTATCATT
1 TTAAGCCCAATATCGCTGGCCT-TGAATCAGCATATTGGCACCTTTGTCATT
1801789 CGTTGCATCT
Statistics
Matches: 139, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
112 2 0.01
113 137 0.99
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (113 bp):
TTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATTTTTAAACCCAATAT
CACTGGCCTTGAATCAGCATATCGACACCTTTATCATTCTTATCATCT
Found at i:1802508 original size:20 final size:20
Alignment explanation
Indices: 1802466--1802519 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1802456 TTCAGTAATT
1802466 TGTATCGATACAATAAGGCAA
1 TGTATCGATAC-ATAAGGCAA
1802487 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAAG-GCAA
*
1802507 TGTATCAATACAT
1 TGTATCGATACAT
1802520 GCCTAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGGCAA
Found at i:1808094 original size:57 final size:58
Alignment explanation
Indices: 1808033--1808474 Score: 300
Period size: 58 Copynumber: 7.7 Consensus size: 58
1808023 AAAATGTTTT
* * *
1808033 AATGGTGCTAAAATACATGAAATTACATAGTAGTCCCTAAATCATA-AAAATGACTAA
1 AATGGTCCTAAAATGCATGAAATTACATAATAGTCCCTAAATCATAGAAAATGACTAA
*
1808090 AATGG-CCTGAAAATGCATGAAATTGA-ATAATAGTCCTTAAAAT-ATAGAAAATGACTAA
1 AATGGTCCT-AAAATGCATGAAATT-ACATAATAGTCCCT-AAATCATAGAAAATGACTAA
* * * * * * *
1808148 AATGGTCCTAAAATACATGAAATTGCATTATAATCCTTTAATGCA-AGAAAAATGACTTA
1 AATGGTCCTAAAATGCATGAAATTACATAATAGTCCCTAAAT-CATAG-AAAATGACTAA
* * * * *
1808207 AAT-GACCTAAGATGTATGAAATTGCATAATAGTCCCTAAAACATAGAAAATGACTAA
1 AATGGTCCTAAAATGCATGAAATTACATAATAGTCCCTAAATCATAGAAAATGACTAA
* * * * * * * *
1808264 AATGGTCCT-AAATGCATGAAATTACACAATGGT-CCTAAGTCATGGCAAATTATTAG
1 AATGGTCCTAAAATGCATGAAATTACATAATAGTCCCTAAATCATAGAAAATGACTAA
* * * * * * * *
1808320 AAT-GACCTTAAAATGCATGAAATTGCATAA-ATGTTCTTAAATCAT-GTCAAATTATTAG
1 AATGGTCC-TAAAATGCATGAAATTACATAATA-GTCCCTAAATCATAG-AAAATGACTAA
* * * * **
1808378 AA-GGACCTTAAAATGCATAAAATGAAATAA-AGGTCTTTAAATCAT-GAAAATGACTAA
1 AATGGTCC-TAAAATGCATGAAATTACATAATA-GTCCCTAAATCATAGAAAATGACTAA
* * * * * *
1808435 AATAGTGCTAGAATGCATAAAATCACATAATAGTACCTAA
1 AATGGTCCTAAAATGCATGAAATTACATAATAGTCCCTAA
1808475 GATGCATGAA
Statistics
Matches: 307, Mismatches: 59, Indels: 38
0.76 0.15 0.09
Matches are distributed among these distances:
55 3 0.01
56 22 0.07
57 123 0.40
58 142 0.46
59 17 0.06
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (58 bp):
AATGGTCCTAAAATGCATGAAATTACATAATAGTCCCTAAATCATAGAAAATGACTAA
Found at i:1808159 original size:29 final size:30
Alignment explanation
Indices: 1808071--1808169 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 30
1808061 AGTAGTCCCT
1808071 AAATCATA-AAAATGACTAAAATGG-CCTGA
1 AAATCATAGAAAATGACTAAAATGGTCCT-A
* * *
1808100 AAATGCAT-GAAATTGA--ATAATAGTCCTTA
1 AAAT-CATAGAAAATGACTAAAATGGTCC-TA
1808129 AAAT-ATAGAAAATGACTAAAATGGTCCTA
1 AAATCATAGAAAATGACTAAAATGGTCCTA
1808158 AAATACAT-GAAA
1 AAAT-CATAGAAA
1808170 TTGCATTATA
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
27 2 0.04
28 12 0.22
29 17 0.31
30 22 0.40
31 2 0.04
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (30 bp):
AAATCATAGAAAATGACTAAAATGGTCCTA
Found at i:1808170 original size:29 final size:28
Alignment explanation
Indices: 1808033--1808170 Score: 79
Period size: 29 Copynumber: 4.8 Consensus size: 28
1808023 AAAATGTTTT
* * *
1808033 AATGGTGCTAAAATACATGAAATTACAT
1 AATGGTCCTAAAATACATGAAATGACAA
* * *
1808061 AGTAGTCCCT-AAAT-CATAAAAATGACTAA
1 AATGGT-CCTAAAATACAT-GAAATGAC-AA
* *
1808090 AATGG-CCTGAAAATGCATGAAATTGA-AT
1 AATGGTCCT-AAAATACATGAAA-TGACAA
* *
1808118 AATAGTCCTTAAAATATA-GAAAATGACTAA
1 AATGGTCC-TAAAATACATG-AAATGAC-AA
1808148 AATGGTCCTAAAATACATGAAAT
1 AATGGTCCTAAAATACATGAAAT
1808171 TGCATTATAA
Statistics
Matches: 81, Mismatches: 16, Indels: 25
0.66 0.13 0.20
Matches are distributed among these distances:
27 6 0.07
28 23 0.28
29 36 0.44
30 16 0.20
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (28 bp):
AATGGTCCTAAAATACATGAAATGACAA
Found at i:1808247 original size:116 final size:115
Alignment explanation
Indices: 1808033--1808289 Score: 340
Period size: 116 Copynumber: 2.2 Consensus size: 115
1808023 AAAATGTTTT
* * * *
1808033 AATGGTGCTAAAATACATGAAATTACATAGTAGTCCCTAAATCATAAAAATGACTAAAATGGCCT
1 AATGGTCCTAAAATACATGAAATTACATAGTAATCCCTAAATCAGAAAAATGACTAAAATGACCT
* *
1808098 GAAAATGCATGAAATTGAATAATAGTCCTTAAAATATAGAAAATGACTAA
66 GAAAATGCATGAAATTGAATAATAGTCCCTAAAACATAGAAAATGACTAA
* * * *
1808148 AATGGTCCTAAAATACATGAAATTGCATTA-TAATCCTTTAATGCAAGAAAAATGACTTAAATGA
1 AATGGTCCTAAAATACATGAAATTACA-TAGTAATCCCTAAAT-C-AGAAAAATGACTAAAATGA
* * *
1808212 CCT-AAGATGTATGAAATTGCATAATAGTCCCTAAAACATAGAAAATGACTAA
63 CCTGAAAATGCATGAAATTGAATAATAGTCCCTAAAACATAGAAAATGACTAA
*
1808264 AATGGTCCT-AAATGCATGAAATTACA
1 AATGGTCCTAAAATACATGAAATTACA
1808290 CAATGGTCCT
Statistics
Matches: 124, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
115 49 0.40
116 56 0.45
117 19 0.15
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (115 bp):
AATGGTCCTAAAATACATGAAATTACATAGTAATCCCTAAATCAGAAAAATGACTAAAATGACCT
GAAAATGCATGAAATTGAATAATAGTCCCTAAAACATAGAAAATGACTAA
Found at i:1808284 original size:29 final size:29
Alignment explanation
Indices: 1808068--1808301 Score: 84
Period size: 29 Copynumber: 8.2 Consensus size: 29
1808058 CATAGTAGTC
*
1808068 CCTAAAT-CATAAAAATGACTAAAATGG-
1 CCTAAATGCATGAAAATGACTAAAATGGT
* * *
1808095 CCTGAAAATGCATGAAATTGA--ATAATAGT
1 CCT--AAATGCATGAAAATGACTAAAATGGT
1808124 CCTTAAAAT--ATAGAAAATGACTAAAATGGT
1 CC-T-AAATGCAT-GAAAATGACTAAAATGGT
* * * *
1808154 CCTAAAATACATGAAATTGCATTATAA---T
1 CCT-AAATGCATGAAAATG-ACTAAAATGGT
* * * *
1808182 CCTTTAATGCAAGAAAAATGACTTAAAT-GA
1 CC-TAAATGCATG-AAAATGACTAAAATGGT
* * * *
1808212 CCTAAGATGTATGAAATTG-C-ATAATAGT
1 CCTAA-ATGCATGAAAATGACTAAAATGGT
*
1808240 CCCTAAA-ACATAGAAAATGACTAAAATGGT
1 -CCTAAATGCAT-GAAAATGACTAAAATGGT
* *
1808270 CCTAAATGCATG-AAATTAC-ACAATGGT
1 CCTAAATGCATGAAAATGACTAAAATGGT
1808297 CCTAA
1 CCTAA
1808302 GTCATGGCAA
Statistics
Matches: 152, Mismatches: 33, Indels: 44
0.66 0.14 0.19
Matches are distributed among these distances:
27 22 0.14
28 40 0.26
29 43 0.28
30 40 0.26
31 7 0.05
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (29 bp):
CCTAAATGCATGAAAATGACTAAAATGGT
Found at i:1808342 original size:29 final size:29
Alignment explanation
Indices: 1808310--1808400 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
1808300 AAGTCATGGC
1808310 AAATTATTAGAATGACCTTAAAATGCATG
1 AAATTATTAGAATGACCTTAAAATGCATG
**
1808339 AAATTGCA-TA-AATGTTCTT-AAAT-CATG
1 AAATT--ATTAGAATGACCTTAAAATGCATG
* *
1808366 TCAAATTATTAGAAGGACCTTAAAATGCATA
1 --AAATTATTAGAATGACCTTAAAATGCATG
1808397 AAAT
1 AAAT
1808401 GAAATAAAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
27 5 0.10
28 6 0.12
29 27 0.56
30 6 0.12
31 4 0.08
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (29 bp):
AAATTATTAGAATGACCTTAAAATGCATG
Found at i:1812054 original size:20 final size:21
Alignment explanation
Indices: 1812015--1812058 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
1812005 AACAATTTGC
1812015 ATCGATACAATAAGGTAATGT
1 ATCGATACAATAAGGTAATGT
1812036 ATCGATAC-ATAA-GTGAATGT
1 ATCGATACAATAAGGT-AATGT
1812056 ATC
1 ATC
1812059 AACACATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.09
20 12 0.55
21 8 0.36
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (21 bp):
ATCGATACAATAAGGTAATGT
Found at i:1813176 original size:79 final size:78
Alignment explanation
Indices: 1813033--1813422 Score: 405
Period size: 79 Copynumber: 5.0 Consensus size: 78
1813023 TATTTTGAAG
* * * * * * *
1813033 AAAA-AATAGGGTTGGGGAATCCCCGATGGTGAAAAGTC-GATATTTTGGAAACAAAATC-GAGG
1 AAAATAATAGGGTTGGAGTATCCCCGATGGTGAAAAATCAG-TGTTTTAGAAATAAAACCAG-GG
*
1813095 TTGGAGTATGCCCTC
64 TTGGAGTATCCCCTC
*
1813110 GAAAATAATAGGGTTGGAGCATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCAGGGT
1 -AAAATAATAGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCAGGGT
* *
1813175 TGAAGTATCCCTTC
65 TGGAGTATCCCCTC
** * * * **
1813189 AAAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAATC-GATGTTTTAGAAATAAAGCTGGGG
1 -AAAATAATAGGGTTGGAGTATCCCCGATGGTGAAAAATCAG-TGTTTTAGAAATAAAACCAGGG
1813253 TTGGAGTATCCCCTC
64 TTGGAGTATCCCCTC
* * ** * *
1813268 AGAAATAACAGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTT-GCAAATAAAACCAGGG
1 A-AAATAATAGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAG-AAATAAAACCAGGG
*
1813332 TTAGAGTATCCCCTC
64 TTGGAGTATCCCCTC
* * * *
1813347 AAAACAAT-GAGGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGT
1 AAAATAATAG-GGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCAGGGT
1813411 TGGAGTATCCCC
65 TGGAGTATCCCC
1813423 GATGATGGAA
Statistics
Matches: 261, Mismatches: 42, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
77 1 0.00
78 67 0.26
79 191 0.73
80 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (78 bp):
AAAATAATAGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCAGGGTT
GGAGTATCCCCTC
Found at i:1813329 original size:158 final size:157
Alignment explanation
Indices: 1813042--1813422 Score: 450
Period size: 158 Copynumber: 2.4 Consensus size: 157
1813032 GAAAAAATAG
* * * * * * * *
1813042 GGTTGGGGAATCCCCGATGGTGAAAAGTCGA-TATTTTGGAAACAAAATCGAGGTTGGAGTATGC
1 GGTTGGAGTATCCCCGATGGTGAAAAAT-GAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
* * * * *
1813106 CCTCGAAAATAATAGGGTTGGAGCATCCCCGATGGTGAAAAATCAGTGTTTTAGAAATAAAACCA
65 CCTCGAAAATAACAGGGTTAGAGCATCCCCGATGATGAAAAATCAATATTTTAGAAATAAAACCA
* * *
1813171 GGGTT-GAAGTATCCCTTCAAAAATAACGG
130 GGGTTAG-AGTATCCCCTC-AAAACAACGA
* * *
1813200 GGTTGGAGTATCCCTGATTGTGAAAAATCGA-TGTTTTAGAAAT-AAAGCTGGGGTTGGAGTATC
1 GGTTGGAGTATCCCCGATGGTGAAAAAT-GAGTGTTTTAGAAATAAAATC-GGGGTTGGAGTATC
* *
1813263 CCCTC-AGAAATAACAGGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTT-GCAAATAAAA
64 CCCTCGA-AAATAACAGGGTTAGAGCATCCCCGATGATGAAAAATCAATATTTTAG-AAATAAAA
*
1813326 CCAGGGTTAGAGTATCCCCTCAAAACAATGA
127 CCAGGGTTAGAGTATCCCCTCAAAACAACGA
*
1813357 GGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATGGTGAAAAATGAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1813422 C
66 C
1813423 GATGATGGAA
Statistics
Matches: 191, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
156 1 0.01
157 68 0.36
158 121 0.63
159 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (157 bp):
GGTTGGAGTATCCCCGATGGTGAAAAATGAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
CTCGAAAATAACAGGGTTAGAGCATCCCCGATGATGAAAAATCAATATTTTAGAAATAAAACCAG
GGTTAGAGTATCCCCTCAAAACAACGA
Found at i:1813445 original size:51 final size:51
Alignment explanation
Indices: 1813357--1813454 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
1813347 AAAACAATGA
* * * *
1813357 GGTTGGAGTATCCCCGATGGTGAAAAATTAGTGTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATGATGAAAAATGAGTATTTTAAAAATAAAATCGG
*
1813408 GGTTGGAGTATCCCCGATGATGGAAAATCGA-TATTTTAAAAATAAAA
1 GGTTGGAGTATCCCCGATGATGAAAAAT-GAGTATTTTAAAAATAAAA
1813455 ACATGAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATGATGAAAAATGAGTATTTTAAAAATAAAATCGG
Found at i:1816385 original size:242 final size:240
Alignment explanation
Indices: 1815959--1816540 Score: 781
Period size: 242 Copynumber: 2.4 Consensus size: 240
1815949 TGAAGTAGAT
* * * * * *
1815959 AGGTGCCAACAACTTGTGTGGGCTTTAAGAGGAAAGCGTCCTACTCTTTAAAGACTGGAAGGTGC
1 AGGTGCCAACAACTTGTGTGGGCTTTAA-AGAAAAG-GTCTTGCTCTTTGAGGACTGAAAGGTGC
* * *
1816024 CACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTTGAAGACTAAAAGGTGCCACC
64 CACCAACTTGTGTGGGCTTTAAAAGGAGAAGACAGCCTGCTCTTTGAAGACTAAAAGATGCCACC
* * **
1816089 AACTTGTATGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGATTGAAAGGTGACACCAACT
129 AACTTGTATGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGCACCGAAAGGTGACACCAACT
* * ** *
1816154 TGTGTGGGCTTTAAAAGGAAAAGACATCTTGCTTTTTGAGGA-CTGAA
194 TGTGTGGGCTTTAAAAGGAAAAGACATCCTACACTTTGAGCATC-GAA
*
1816201 AGGTGCCAACAACTTGTGTGGGCTTTGAAAGAAAAGTGTCTTGCTCTTTGAGGACTGAAAAGTGC
1 AGGTGCCAACAACTTGTGTGGGCTTT-AAAGAAAAG-GTCTTGCTCTTTGAGGACTGAAAGGTGC
*
1816266 CACCAACTTGTGTGGGCTTTAAAAGGAGAAGAC-GCCTTGCTCTTTGAGGACTAAAAGATGCCAC
64 CACCAACTTGTGTGGGCTTTAAAAGGAGAAGACAGCC-TGCTCTTTGAAGACTAAAAGATGCCAC
* * *
1816330 CAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGAGCACCGAAAGGTGCCACCAAC
128 CAACTTGTATGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGCACCGAAAGGTGACACCAAC
* * *
1816395 TTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTACACTTTGAGCATCGAA
193 TTGTGTGGGCTTTAAAAGGAAAAGACATCCTACACTTTGAGCATCGAA
* *
1816443 AGGTACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTGCTCTTTGAGGACTGAAAGGT
1 AGGTGCCAACAACTTGTGTGGGCTTT-AAA-GAAAAGG--TCTTGCTCTTTGAGGACTGAAAGGT
* **
1816508 GCCACCAACTTGTATAAGCTTTAAAAGGAGAAG
62 GCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1816541 GCATTCTTCT
Statistics
Matches: 300, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
241 2 0.01
242 235 0.78
243 9 0.03
244 54 0.18
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (240 bp):
AGGTGCCAACAACTTGTGTGGGCTTTAAAGAAAAGGTCTTGCTCTTTGAGGACTGAAAGGTGCCA
CCAACTTGTGTGGGCTTTAAAAGGAGAAGACAGCCTGCTCTTTGAAGACTAAAAGATGCCACCAA
CTTGTATGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGCACCGAAAGGTGACACCAACTTG
TGTGGGCTTTAAAAGGAAAAGACATCCTACACTTTGAGCATCGAA
Found at i:1816544 original size:61 final size:61
Alignment explanation
Indices: 1815959--1816542 Score: 739
Period size: 61 Copynumber: 9.6 Consensus size: 61
1815949 TGAAGTAGAT
* * * * * *
1815959 AGGTGCCAACAACTTGTGTGGGCTTTAAGAGG-AAA-GCGTCCTACTCTTTAAAGACTGGA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * *
1816018 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTGCTCTTTGAAGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * *
1816079 AGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTGAGGATTGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * * *
1816140 AGGTGACACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCTTGCTTTTTGAGGACTGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * *
1816201 AGGTGCCAACAACTTGTGTGGGCTTTGAAA-GAAAA-GTGTCTTGCTCTTTGAGGACTGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * *
1816260 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGACG-CCTTGCTCTTTGAGGACTAAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCC-TGCTCTTTGAGGACTGAA
* * * *
1816321 AGATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGAGCACCGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* * * *
1816382 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTACACTTTGAGCA-TCGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAA
* * *
1816443 AGGTACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCTTGCTCTTTGAGGACTGAA
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
* ** *
1816504 AGGTGCCACCAACTTGTATAAGCTTTAAAAGGAGAAGGC
1 AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1816543 ATTCTTCTTT
Statistics
Matches: 457, Mismatches: 60, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
59 77 0.17
60 13 0.03
61 364 0.80
62 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (61 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAA
Found at i:1817566 original size:23 final size:23
Alignment explanation
Indices: 1817539--1817583 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1817529 AGCAGGTTCT
* *
1817539 TTTTTTTTTCTTTTTTTATTTTAG
1 TTTTTTTTT-GTTTGTTATTTTAG
1817563 TTTTTTTTTGTTTGTTATTTT
1 TTTTTTTTTGTTTGTTATTTT
1817584 TTTTAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (23 bp):
TTTTTTTTTGTTTGTTATTTTAG
Found at i:1817584 original size:24 final size:24
Alignment explanation
Indices: 1817539--1817585 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1817529 AGCAGGTTCT
*
1817539 TTTTTTTTTCTTTTTTTATTTTAG
1 TTTTTTTTTCTTTTTATATTTTAG
* *
1817563 TTTTTTTTTGTTTGTTATTTTTT
1 TTTTTTTTTCTTT-TTATATTTT
1817586 TTAGAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.85
Consensus pattern (24 bp):
TTTTTTTTTCTTTTTATATTTTAG
Found at i:1817587 original size:27 final size:27
Alignment explanation
Indices: 1817538--1817589 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1817528 AAGCAGGTTC
*
1817538 TTTTTTTTTTCTTTTTTTATTTTAGTT
1 TTTTTTTTTTCTTATTTTATTTTAGTT
*
1817565 TTTTTTTGTTTGTTATTTT-TTTTAG
1 TTTTTTT-TTTCTTATTTTATTTTAG
1817590 AAAAAAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.08, C:0.02, G:0.08, T:0.83
Consensus pattern (27 bp):
TTTTTTTTTTCTTATTTTATTTTAGTT
Found at i:1819364 original size:79 final size:78
Alignment explanation
Indices: 1819182--1819434 Score: 256
Period size: 79 Copynumber: 3.2 Consensus size: 78
1819172 TACATCTCCC
* * * * *
1819182 GGTTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCTGATTATG-GAAAATCGATGCT
1 GGTTAGAGTATCCCATC-AAAATAACGGGGTTGGAGTATCCCC-GATTGTGAG-AAATCGATGTT
**
1819246 TTAGAAATAAGGCCGG
63 TTAGAAATAAAACCGG
* * * *
1819262 GGTTAGAGTATCCCCGTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTT
1 GGTTAGAGTAT-CCCATCAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCGATGTTTT
1819327 AGAAATAAAACCGG
65 AGAAATAAAACCGG
* * * * * * *
1819341 GGTTAGAGTATCTCATCAGAAATAACGAGATTGGAGTATCCTCGATTGTGAAAAGATTGGTGTTT
1 GGTTAGAGTATCCCATCA-AAATAACGGGGTTGGAGTATCCCCGATTGTGAGAA-ATCGATGTTT
**
1819406 TAGAAATAAAATTGG
64 TAGAAATAAAACCGG
*
1819421 GGTTGGAGTATCCC
1 GGTTAGAGTATCCC
1819435 TGATTGTGAG
Statistics
Matches: 144, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
78 4 0.03
79 70 0.49
80 66 0.46
81 4 0.03
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (78 bp):
GGTTAGAGTATCCCATCAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCGATGTTTTA
GAAATAAAACCGG
Found at i:1819433 original size:52 final size:52
Alignment explanation
Indices: 1819371--1819487 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 52
1819361 AATAACGAGA
*** * *
1819371 TTGGAGTATCCTC-GATTGTGAAAAGATTGGTGTTTTAGAAATAAAATTGGGG
1 TTGGAGTATCCTCTGATTGTGAAAA-ATCAATATTTTAGAAATAAAACTGGGG
* *
1819423 TTGGAGTATCC-CTGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGG
1 TTGGAGTATCCTCTGATTGTGAAAAATCAATATTTTAGAAATAAAACTGGGG
*
1819474 TTAGAGTATCCTCT
1 TTGGAGTATCCTCT
1819488 CGAAAATAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
51 32 0.58
52 23 0.42
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (52 bp):
TTGGAGTATCCTCTGATTGTGAAAAATCAATATTTTAGAAATAAAACTGGGG
Found at i:1819443 original size:131 final size:130
Alignment explanation
Indices: 1819288--1819604 Score: 417
Period size: 131 Copynumber: 2.4 Consensus size: 130
1819278 TGAAAATAAC
* * *
1819288 GGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGGGGTTAGAGTAT-
1 GGGGTTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTAGAGTATC
* * * * *
1819352 CTCATC-AGAAATAACGAGATTGGAGTATCCTCGATTGTGAAAAGATTGGTGTTTTAGAAATAAA
66 CTC-TCGA-AAATAACGAGATTGGAGTATCCCCAATTATGAAAA-ATTGATATTTTAGAAATAAA
*
1819416 ATT
128 ACT
1819419 GGGGTTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTAGAGTATC
1 GGGGTTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTAGAGTATC
* * * *
1819484 CTCTCGAAAATAAGGGGATTGGATTATCCCCAATTATGAAAAATTGATATTTTGGAAATAAAACT
66 CTCTCGAAAATAACGAGATTGGAGTATCCCCAATTATGAAAAATTGATATTTTAGAAATAAAACT
* * * *
1819549 GGGGTTAGAGTATCCTTGA--GATGAAAAATCAATTTTTTAGAAATAAAGCTGGGGTT
1 GGGGTTGGAGTATCCCTGATTG-TGAGAAATCAATATTTTAGAAATAAAGCTGGGGTT
1819605 GAAGTACCCC
Statistics
Matches: 166, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
128 1 0.01
129 33 0.20
130 36 0.22
131 92 0.55
132 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (130 bp):
GGGGTTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTAGAGTATC
CTCTCGAAAATAACGAGATTGGAGTATCCCCAATTATGAAAAATTGATATTTTAGAAATAAAACT
Found at i:1819513 original size:79 final size:78
Alignment explanation
Indices: 1819419--1819564 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 78
1819409 AAATAAAATT
** * * *
1819419 GGGGTTGGAGTATCCCTGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTAGAGTATC
1 GGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACTGGGGTTAGAGTATC
1819484 CTCTCGAAAATAA
66 CTCTCGAAAATAA
* ** *
1819497 GGGGATTGGATTATCCCCAATTATGAAAAATTGATATTTTGGAAATAAAACTGGGGTTAGAGTAT
1 GGGG-TTGGAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACTGGGGTTAGAGTAT
1819562 CCT
65 CCT
1819565 TGAGATGAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
78 4 0.07
79 54 0.93
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.31
Consensus pattern (78 bp):
GGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAACTGGGGTTAGAGTATC
CTCTCGAAAATAA
Found at i:1819574 original size:50 final size:50
Alignment explanation
Indices: 1819519--1819628 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
1819509 ATCCCCAATT
** * * **
1819519 ATGAAAAATTGATATTTTGGAAATAAAACTGGGGTT-AGAGTATCCTTGAG
1 ATGAAAAATCAATATTTTAGAAATAAAACTGGGGTTGA-AGTACCCCCGAG
* *
1819569 ATGAAAAATCAATTTTTTAGAAATAAAGCTGGGGTTGAAGTACCCCCGAG
1 ATGAAAAATCAATATTTTAGAAATAAAACTGGGGTTGAAGTACCCCCGAG
1819619 ATGAAAAATC
1 ATGAAAAATC
1819629 TAGAAATTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 50 0.98
51 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (50 bp):
ATGAAAAATCAATATTTTAGAAATAAAACTGGGGTTGAAGTACCCCCGAG
Found at i:1823217 original size:51 final size:52
Alignment explanation
Indices: 1823162--1823300 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 52
1823152 TCTGGAAAGA
* * * * * *
1823162 AAATGTATCGATACATTTTTCATTGTATCGATGCATTATGGGTTTTGGTCC-
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTATAGGTATTCGACCT
* * *
1823213 AAATGTATCAATACATTCTTCATTGTATCGAAACATTCTAGGTATTCGACCT
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTATAGGTATTCGACCT
*
1823265 AAATGTATCGATACATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTCTTCATTGTATCGATACAT
1823301 CCAGTTAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 42 0.56
52 33 0.44
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTATAGGTATTCGACCT
Found at i:1827306 original size:22 final size:21
Alignment explanation
Indices: 1827276--1827316 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1827266 CTTTGAATAT
*
1827276 TAAATTTGAGAAATTCAAGAAA
1 TAAACTTGA-AAATTCAAGAAA
*
1827298 TAAACTTGAAATTTCAAGA
1 TAAACTTGAAAATTCAAGA
1827317 TAGAGAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
TAAACTTGAAAATTCAAGAAA
Found at i:1828751 original size:21 final size:21
Alignment explanation
Indices: 1828727--1828768 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1828717 TCTTTGCATA
*
1828727 AAAATTTTATT-TTAATTCTTT
1 AAAATTTT-TTCTAAATTCTTT
1828748 AAAATTTTTTCTAAATTCTTT
1 AAAATTTTTTCTAAATTCTTT
1828769 TATCAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
AAAATTTTTTCTAAATTCTTT
Found at i:1828898 original size:27 final size:28
Alignment explanation
Indices: 1828834--1828900 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
1828824 TTTCTAATGG
* * *
1828834 AATTTTTATTGGAATTATTACATGAATA
1 AATTTTAATTAGAATTATCACATGAATA
* *
1828862 AATTGTTAATTAGACTTATCACATGTA-A
1 AATT-TTAATTAGAATTATCACATGAATA
1828890 AATTTTAATTA
1 AATTTTAATTA
1828901 ACCCCTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 7 0.21
28 9 0.27
29 17 0.52
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (28 bp):
AATTTTAATTAGAATTATCACATGAATA
Found at i:1832675 original size:20 final size:20
Alignment explanation
Indices: 1832650--1832699 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1832640 GACAGAATGC
* *
1832650 ATCGATACATTCATACATAT
1 ATCGATACATTCAAAAATAT
*
1832670 ATCGATACATTGAAAAATAT
1 ATCGATACATTCAAAAATAT
*
1832690 ATTGATACAT
1 ATCGATACAT
1832700 CTAGGTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (20 bp):
ATCGATACATTCAAAAATAT
Found at i:1832679 original size:71 final size:71
Alignment explanation
Indices: 1832614--1832852 Score: 379
Period size: 71 Copynumber: 3.4 Consensus size: 71
1832604 TACATTATTC
* * *
1832614 AATATATCGATACATCTGGGTAAAAAGACAGAATGCATCGATACATTCATACATATATCGATACA
1 AATATATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACATGTATCGATACA
1832679 TTGAAA
66 TTGAAA
* * * *
1832685 AATATATTGATACATCTAGGTAAAAAGACATAATGTATCGATACATTCATACATGTATCAATACA
1 AATATATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACATGTATCGATACA
1832750 TTGAAA
66 TTGAAA
* *
1832756 AATGTATCGATACATCTGGGTAAAATGACAAAATGTATCGATACATTCATACATGTATCGATACA
1 AATATATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACATGTATCGATACA
1832821 TTGAAA
66 TTGAAA
* *
1832827 AATGTATCGATACATTTGGGTAAAAA
1 AATATATCGATACATCTGGGTAAAAA
1832853 AGTGACTATT
Statistics
Matches: 154, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 154 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (71 bp):
AATATATCGATACATCTGGGTAAAAAGACAAAATGTATCGATACATTCATACATGTATCGATACA
TTGAAA
Found at i:1832729 original size:31 final size:31
Alignment explanation
Indices: 1832683--1832801 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 31
1832673 GATACATTGA
* *
1832683 AAAATATATTGATACATCTAGGTAAAAAGAC
1 AAAATGTATCGATACATCTAGGTAAAAAGAC
* *
1832714 ATAATGTATCGATACATTCATACATGTATCAATACATTGA-
1 AAAATGTATCGATACA-TC-T--AGGTA--AA-A-A--GAC
* *
1832754 AAAATGTATCGATACATCTGGGTAAAATGAC
1 AAAATGTATCGATACATCTAGGTAAAAAGAC
1832785 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
1832802 TCATACATGT
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
30 2 0.03
31 30 0.43
32 2 0.03
33 2 0.03
34 2 0.03
35 4 0.06
36 3 0.04
37 2 0.03
38 2 0.03
39 3 0.04
40 15 0.22
41 2 0.03
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
AAAATGTATCGATACATCTAGGTAAAAAGAC
Found at i:1832742 original size:20 final size:20
Alignment explanation
Indices: 1832713--1832842 Score: 82
Period size: 20 Copynumber: 6.0 Consensus size: 20
1832703 GGTAAAAAGA
1832713 CATA-ATGTATCGATACATT
1 CATACATGTATCGATACATT
*
1832732 CATACATGTATCAATACATT
1 CATACATGTATCGATACATT
* * *
1832752 GAAAAATGTATCGATACATCTGGGT
1 CATACATGTATCGATACA--T---T
*
1832777 AAAATGACAAAATGTATCGATACATT
1 --CAT-AC--A-TGTATCGATACATT
1832803 CATACATGTATCGATACATT
1 CATACATGTATCGATACATT
* * *
1832823 GAAAAATGTATCGATACATT
1 CATACATGTATCGATACATT
1832843 TGGGTAAAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
19 4 0.05
20 59 0.68
21 1 0.01
22 1 0.01
23 2 0.02
24 2 0.02
25 1 0.01
26 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 12 0.14
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Consensus pattern (20 bp):
CATACATGTATCGATACATT
Found at i:1832761 original size:40 final size:40
Alignment explanation
Indices: 1832716--1832842 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
1832706 AAAAAGACAT
1832716 AATGTATCGATACATTCATACATGTATCAATACATTGAAA
1 AATGTATCGATACATTCATACATGTATCAATACATTGAAA
**
1832756 AATGTATCGAT--A--CAT-C-TGGGT-AA-A-A-TGACAA
1 AATGTATCGATACATTCATACATGTATCAATACATTGA-AA
*
1832787 AATGTATCGATACATTCATACATGTATCGATACATTGAAA
1 AATGTATCGATACATTCATACATGTATCAATACATTGAAA
1832827 AATGTATCGATACATT
1 AATGTATCGATACATT
1832843 TGGGTAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
30 3 0.04
31 14 0.20
32 1 0.01
33 3 0.04
34 3 0.04
35 4 0.06
36 4 0.06
37 3 0.04
38 2 0.03
39 1 0.01
40 30 0.42
41 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (40 bp):
AATGTATCGATACATTCATACATGTATCAATACATTGAAA
Found at i:1840320 original size:40 final size:40
Alignment explanation
Indices: 1840268--1840393 Score: 116
Period size: 40 Copynumber: 3.1 Consensus size: 40
1840258 TTTCGAGTGT
1840268 TTTG-TGGAGTTGCTATTC-GTGCTTGTTGTGGAGTTGCTG
1 TTTGTTGGAGTTGCTATTCGGTGC-TGTTGTGGAGTTGCTG
* ** * * *
1840307 TTTGTTGGAGTTGCT-GTCATTGCTGCTGTGGAAGCTACTG
1 TTTGTTGGAGTTGCTATTCGGTGCTGTTGTGG-AGTTGCTG
*
1840347 CTTGTTGGAGTTGCTAGTTTCGGGTGCT-TTGTGGAGTTGCTG
1 TTTGTTGGAGTTGCTA--TTC-GGTGCTGTTGTGGAGTTGCTG
1840389 TTTGT
1 TTTGT
1840394 GCTTGTTGGA
Statistics
Matches: 67, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
39 13 0.19
40 33 0.49
42 10 0.15
43 7 0.10
44 4 0.06
ACGTcount: A:0.09, C:0.12, G:0.35, T:0.44
Consensus pattern (40 bp):
TTTGTTGGAGTTGCTATTCGGTGCTGTTGTGGAGTTGCTG
Found at i:1840374 original size:26 final size:22
Alignment explanation
Indices: 1840345--1840404 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 22
1840335 TGGAAGCTAC
1840345 TGCTTGTTGGAGTTGCTAGTTTCGGG
1 TGCTTGTTGGAGTTGCT-GTTT---G
1840371 TGCTT-TGTGGAGTTGCTGTTTG
1 TGCTTGT-TGGAGTTGCTGTTTG
1840393 TGCTTGTTGGAG
1 TGCTTGTTGGAG
1840405 CTTTCGATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
22 11 0.34
23 1 0.03
25 5 0.16
26 15 0.47
ACGTcount: A:0.07, C:0.10, G:0.38, T:0.45
Consensus pattern (22 bp):
TGCTTGTTGGAGTTGCTGTTTG
Found at i:1840387 original size:106 final size:106
Alignment explanation
Indices: 1840202--1840401 Score: 276
Period size: 106 Copynumber: 1.9 Consensus size: 106
1840192 TTGTTCGTGC
* * * *
1840202 TTGTTGGAGCTACTGTCATTGTTGTCTTGGAAGCTGCTGCTTGTTGGAGCTATTGGTTTCGAGTG
1 TTGTTGGAGCTACTGTCATTGCTGTCTTGGAAGCTACTGCTTGTTGGAGCTACTAGTTTCGAGTG
*
1840267 TTTTGTGGAGTTGCTATTCGTGCTTGTTGTGGAGTTGCTGT
66 CTTTGTGGAGTTGCTATTCGTGCTTGTTGTGGAGTTGCTGT
* * * * *
1840308 TTGTTGGAGTTGCTGTCATTGCTG-CTGTGGAAGCTACTGCTTGTTGGAGTTGCTAGTTTCGGGT
1 TTGTTGGAGCTACTGTCATTGCTGTCT-TGGAAGCTACTGCTTGTTGGAGCTACTAGTTTCGAGT
* *
1840372 GCTTTGTGGAGTTGCTGTTTGTGCTTGTTG
65 GCTTTGTGGAGTTGCTATTCGTGCTTGTTG
1840402 GAGCTTTCGA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 2 0.02
106 79 0.98
ACGTcount: A:0.10, C:0.12, G:0.34, T:0.44
Consensus pattern (106 bp):
TTGTTGGAGCTACTGTCATTGCTGTCTTGGAAGCTACTGCTTGTTGGAGCTACTAGTTTCGAGTG
CTTTGTGGAGTTGCTATTCGTGCTTGTTGTGGAGTTGCTGT
Found at i:1841062 original size:4 final size:4
Alignment explanation
Indices: 1841055--1841089 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1841045 TTTCATGATG
*
1841055 ATTT ATTT ATTT ATTT ATTT -TTT ATTT TTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1841090 TGATTTCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (4 bp):
ATTT
Found at i:1841078 original size:15 final size:15
Alignment explanation
Indices: 1841055--1841090 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1841045 TTTCATGATG
1841055 ATTTATTTATTTATTT
1 ATTT-TTTATTTATTT
*
1841071 ATTTTTTATTTTTTT
1 ATTTTTTATTTATTT
1841086 ATTTT
1 ATTTT
1841091 GATTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
ATTTTTTATTTATTT
Found at i:1846051 original size:52 final size:52
Alignment explanation
Indices: 1845971--1846090 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
1845961 AAAAGTTACT
* *
1845971 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
1846023 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
1846075 TGCATGTATCGATACA
1 TGCATGTATCGATACA
1846091 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:1846103 original size:52 final size:52
Alignment explanation
Indices: 1845971--1846110 Score: 185
Period size: 52 Copynumber: 2.7 Consensus size: 52
1845961 AAAAGTTACT
* *
1845971 TGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*** *
1846023 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*
1846075 TGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TGCATGTATCGATACATAAGAT-AGTGTATCGATACA
1846111 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 74 0.95
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:1846117 original size:13 final size:13
Alignment explanation
Indices: 1846099--1846123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1846089 CAAAGATCGG
1846099 TGTATCGATACAA
1 TGTATCGATACAA
1846112 TGTATCGATACA
1 TGTATCGATACA
1846124 TTTAAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1846205 original size:13 final size:13
Alignment explanation
Indices: 1846187--1846211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1846177 AAAAAAAATA
1846187 TGTATCGATACAT
1 TGTATCGATACAT
1846200 TGTATCGATACA
1 TGTATCGATACA
1846212 ACATTTTATG
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:1849444 original size:31 final size:33
Alignment explanation
Indices: 1849406--1849481 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
1849396 CTCGAATTTG
**
1849406 AAATGACCCGAA-TCCGAATGATCCAAACCC-A
1 AAATGACCCGAACTCAAAATGATCCAAACCCAA
**
1849437 AAATGACCCGAACTCAAAATGATCTGAACCCAA
1 AAATGACCCGAACTCAAAATGATCCAAACCCAA
*
1849470 AAATGATCCGAA
1 AAATGACCCGAA
1849482 AATTTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
31 12 0.32
32 14 0.37
33 12 0.32
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.14
Consensus pattern (33 bp):
AAATGACCCGAACTCAAAATGATCCAAACCCAA
Found at i:1849474 original size:17 final size:16
Alignment explanation
Indices: 1849422--1849481 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
1849412 CCCGAATCCG
*
1849422 AATGATCCAAACCCAA
1 AATGATCCGAACCCAA
* *
1849438 AATGACCCGAACTCAA
1 AATGATCCGAACCCAA
*
1849454 AATGATCTGAACCCAAA
1 AATGATCCGAACCC-AA
1849471 AATGATCCGAA
1 AATGATCCGAA
1849482 AATTTTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
16 24 0.67
17 12 0.33
ACGTcount: A:0.47, C:0.27, G:0.12, T:0.15
Consensus pattern (16 bp):
AATGATCCGAACCCAA
Found at i:1851869 original size:2 final size:2
Alignment explanation
Indices: 1851862--1851889 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1851852 ATTTACTTTG
1851862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1851890 GTTAAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1853889 original size:13 final size:13
Alignment explanation
Indices: 1853871--1853896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1853861 TACACAAAGT
1853871 ATGTATCGATACA
1 ATGTATCGATACA
1853884 ATGTATCGATACA
1 ATGTATCGATACA
1853897 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:1853894 original size:32 final size:33
Alignment explanation
Indices: 1853853--1853916 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1853843 TAGCCAAACT
**
1853853 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1853885 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1853917 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1856744 original size:21 final size:21
Alignment explanation
Indices: 1856720--1856776 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1856710 TATTTATCCA
1856720 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1856741 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1856762 AATGTATCGATACAT
1 AATGTATCGATACAT
1856777 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1856856 original size:19 final size:19
Alignment explanation
Indices: 1856832--1856899 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1856822 AATTCAACAA
1856832 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1856851 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1856866 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1856883 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1856900 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1856871 original size:13 final size:13
Alignment explanation
Indices: 1856853--1856877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1856843 ACATAAGTTT
1856853 TGTATCGATACAA
1 TGTATCGATACAA
1856866 TGTATCGATACA
1 TGTATCGATACA
1856878 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1856875 original size:32 final size:32
Alignment explanation
Indices: 1856834--1856896 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1856824 TTCAACAATT
*
1856834 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1856866 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1856897 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1856957 original size:13 final size:13
Alignment explanation
Indices: 1856939--1856964 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1856929 CATTTTTCTG
1856939 TGTATCGATACAT
1 TGTATCGATACAT
1856952 TGTATCGATACAT
1 TGTATCGATACAT
1856965 GGATCTTTGT
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:1856961 original size:33 final size:33
Alignment explanation
Indices: 1856919--1856985 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1856909 GCCAAGGAAA
***
1856919 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1856952 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1856985 T
1 T
1856986 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1859524 original size:31 final size:28
Alignment explanation
Indices: 1859442--1859513 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
1859432 TTCACAATCA
*
1859442 GGGATACTCCAACCCCGTTGATCAT-C--G
1 GGGATACTCCAACCCCGTT-AT-TTCCGAG
1859469 GGGATACTCCAACCCCGTTATTTCCGAG
1 GGGATACTCCAACCCCGTTATTTCCGAG
1859497 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
1859514 ACTTTATTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
27 19 0.46
28 18 0.44
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTCCGAG
Found at i:1859633 original size:52 final size:51
Alignment explanation
Indices: 1859496--1859717 Score: 180
Period size: 52 Copynumber: 4.3 Consensus size: 51
1859486 TTATTTCCGA
* * * *** *
1859496 GGGGATACTCCAACCCCGACTTTA-TTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCG-TTTTATTTTCAAAAACACCAATTTTTCACAATC
* * * * *
1859547 GGGGATATTCCAATCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAA-CCCCGTTTTATTTTCAAAAACACCAATTTTT-CACAATC
* * * **
1859599 GGGGATACTTCAACCCCAGTTTTATTTTC-GAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCC-GTTTTATTTTCAAAAACACCAATTTTTC-ACAATC
* * *
1859651 GGGGATACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTTCACAGTC
1 GGGGATACTCCAACCCCG-TTTTATTTTCAAAAACACCAATTTTTCACAATC
*
1859703 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1859718 TTGTTATTTC
Statistics
Matches: 136, Mismatches: 28, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
51 36 0.26
52 84 0.62
53 16 0.12
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGTTTTATTTTCAAAAACACCAATTTTTCACAATC
Found at i:1859737 original size:28 final size:28
Alignment explanation
Indices: 1859705--1859776 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1859695 TCACAGTCGA
** * **
1859705 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1859733 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
1859761 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1859777 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:1859794 original size:263 final size:263
Alignment explanation
Indices: 1859327--1859827 Score: 744
Period size: 263 Copynumber: 1.9 Consensus size: 263
1859317 TTCTCAATTC
* * *
1859327 TCCACAATCGGGGACATTCGAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGT
1 TCCACAATCGGGGACATTCGAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
1859392 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGATACTCCAACCC
*
1859457 CGTTGATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* * * *
1859522 TCCAAAATATTGATTTTTCATAATCGGGGATATTCCAATCCCGGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
1859587 TTT
261 TTT
* * *
1859590 TCCACAATCGGGGATACTTC-AACCCC-AGTTTTATTTTCGAAACACCAATTTTCCTTTAATCGG
1 TCCACAATCGGGGACA-TTCGAACCCCGA-TTTTATTTTCAAAACACCAATTTT-CTATAATCGG
* * *
1859653 GGATACTCCAACTCCGATTTTATTTTC-AAAAATACCAATTT-TTCACAGTC-GAGGATACTCCA
63 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAG-GGATACTCCA
** *
1859715 ACCTTGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGC
127 ACCCCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGAC
*
1859779 TTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
190 TTTATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
1859828 TTATTTTCGA
Statistics
Matches: 214, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 150 0.70
264 37 0.17
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (263 bp):
TCCACAATCGGGGACATTCGAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGATACTCCAACCC
CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:1859909 original size:77 final size:78
Alignment explanation
Indices: 1859730--1859932 Score: 230
Period size: 77 Copynumber: 2.6 Consensus size: 78
1859720 GTTATTTCAT
* * *
1859730 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
1859795 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* * ****
1859809 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTT-TT-TTTTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
1859872 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* * * *
1859886 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
1859933 TTATTATCTC
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
76 3 0.03
77 56 0.53
78 4 0.04
79 42 0.40
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:1872352 original size:15 final size:15
Alignment explanation
Indices: 1872332--1872398 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
1872322 TCTTCTTCTT
1872332 AAAAAAAAAAGAGCA
1 AAAAAAAAAAGAGCA
* *
1872347 AAAAAAAAACAAAACA
1 AAAAAAAAA-AGAGCA
*
1872363 AAAAAACAAA-A-CA
1 AAAAAAAAAAGAGCA
* *
1872376 AAGAAAAAGAGAG-A
1 AAAAAAAAAAGAGCA
1872390 AAAGAAAAA
1 AAA-AAAAA
1872399 GAACCTGCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
13 9 0.22
14 5 0.12
15 15 0.37
16 12 0.29
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAGCA
Found at i:1872355 original size:18 final size:17
Alignment explanation
Indices: 1872332--1872383 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
1872322 TCTTCTTCTT
1872332 AAAAAAAAAAGAGCAAAA
1 AAAAAAAAAAGA-CAAAA
*
1872350 AAAAAACAAA-ACAAAA
1 AAAAAAAAAAGACAAAA
1872366 AAACAAAACAAAGA-AAAA
1 AAA-AAAA-AAAGACAAAA
1872384 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 8 0.28
17 4 0.14
18 16 0.55
19 1 0.03
ACGTcount: A:0.85, C:0.10, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGACAAAA
Found at i:1872374 original size:13 final size:13
Alignment explanation
Indices: 1872349--1872382 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
1872339 AAAGAGCAAA
1872349 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1872362 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1872375 AAAGAAAA
1 AAA-AAAA
1872383 AGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:1873744 original size:59 final size:59
Alignment explanation
Indices: 1873366--1874087 Score: 975
Period size: 59 Copynumber: 12.2 Consensus size: 59
1873356 TCCGCTTTTT
* * * * **
1873366 AGTCCTCAAAGAGCAGGATGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCGGGACGCCTTTT-CTTCTAAAGCCCACACAAGTTGGTGGCACCTT-C
*
1873427 AGTCCTCAAAGAGTGGGACGCCTTTTCTT-TCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTCT-AAAGCCCACACAAGTTGGTGGCACC-TT-C
* * **
1873488 A-TCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCTACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTT-C
* *
1873547 AGTCCTCAAAGAGCGGGACACCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1873606 AGTCCTCAAAGAGCAGGACACC---T-TT-TAAAGCCCACACAAGTTGGTGGCA-CTTCCC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTT--C
*
1873661 AGTCCTCAAAGAGCAGGACGCCTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTTC
*
1873720 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1873779 AGTCCTCAAAGAGCGAGACGCTTTTTC-TCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTC-TAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1873838 AGTCCTCAAAGAGCAGGACACCTTTTC-TCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTC-TAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1873897 AGTCCTCAAAGAGCGGGACGCTTTTTC-TCTTAAAGCCCACACAAGTTGGTGGCACCTTT
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTC-TAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1873956 AGTCCTCAAAGAGCAGGACACCTTTTC-TCTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTC-TAAAGCCCACACAAGTTGGTGGCACCTTC
* *
1874015 GGTCCTCAAAGAGCGGGACGCTTTTTC-TCTCAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCGGGACGCCTTTTCTTCT-AAAGCCCACACAAGTTGGTGGCACCTTC
* *
1874074 AGTCTTCAAGGAGC
1 AGTCCTCAAAGAGC
1874088 AAGACCCTTT
Statistics
Matches: 607, Mismatches: 40, Indels: 30
0.90 0.06 0.04
Matches are distributed among these distances:
53 3 0.00
54 24 0.04
55 24 0.04
56 1 0.00
58 3 0.00
59 371 0.61
60 150 0.25
61 31 0.05
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (59 bp):
AGTCCTCAAAGAGCGGGACGCCTTTTCTTCTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:1874586 original size:19 final size:19
Alignment explanation
Indices: 1874562--1874629 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
1874552 ACTTCAACAA
1874562 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1874581 TTTGTATCTATAC--AA--
1 TTTGTATCGATACATAAGT
1874596 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1874613 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1874630 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1874600 original size:32 final size:32
Alignment explanation
Indices: 1874564--1874626 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1874554 TTCAACAATT
* *
1874564 TGTATCGATACATAAGTTTTGTATCTATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1874596 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1874627 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1874687 original size:13 final size:13
Alignment explanation
Indices: 1874669--1874694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1874659 CATTTTTCTG
1874669 TGTATCGATACAT
1 TGTATCGATACAT
1874682 TGTATCGATACAT
1 TGTATCGATACAT
1874695 GGATCTTTGT
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:1874691 original size:33 final size:33
Alignment explanation
Indices: 1874649--1874715 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1874639 GCTAAGGAAA
***
1874649 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1874682 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1874715 T
1 T
1874716 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1877127 original size:51 final size:53
Alignment explanation
Indices: 1877049--1877441 Score: 174
Period size: 52 Copynumber: 7.5 Consensus size: 53
1877039 AGTTTCTCAA
* * * * * *
1877049 TTCTCCACAATCGGGGACATTCGAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1877100 TT-TTCTATAATCGGGGTTACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
1877154 TTCTTCACAATCGGGGATACTCCAACCCCG--TTGATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * * ***
1877212 TAT-TTC-CGA--GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * * * * * *
1877261 TT-TTCATAATCAGGGATATTCCAA-TCCCGGTTTTA-TTGCTAAAACACTAAT
1 TTCTTCACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAAT
* * * ***
1877312 TT-TTCCACAATCGGGGATACTTCAACCCCGGTTTTATTT-TTGAAACACCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-T
* *
1877365 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1877417 TT-TTCACAGTCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
1877442 CTTGTTATTT
Statistics
Matches: 254, Mismatches: 59, Indels: 57
0.69 0.16 0.15
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 7 0.03
51 61 0.24
52 85 0.33
53 31 0.12
54 26 0.10
55 23 0.09
56 2 0.01
57 6 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:1877233 original size:28 final size:27
Alignment explanation
Indices: 1877163--1877238 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
1877153 TTTCTTCACA
1877163 ATCGGGGATACTCCAACCCCGTTGATC
1 ATCGGGGATACTCCAACCCCGTTGATC
1877190 ATCGGGGATACTCCAACCCCGTT-AT-
1 ATCGGGGATACTCCAACCCCGTTGATC
*
1877215 TTCCGAGGGGATACTCCAACCCCG
1 AT-C--GGGGATACTCCAACCCCG
1877239 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
27 23 0.51
28 18 0.40
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTGATC
Found at i:1877462 original size:28 final size:28
Alignment explanation
Indices: 1877430--1877501 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1877420 TCACAGTCGA
** * **
1877430 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1877458 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
1877486 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1877502 GCTTTTTGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:1879655 original size:15 final size:15
Alignment explanation
Indices: 1879635--1879665 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1879625 TAAATATGTC
*
1879635 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1879650 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1879665 C
1 C
1879666 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1881438 original size:102 final size:101
Alignment explanation
Indices: 1881202--1881468 Score: 319
Period size: 102 Copynumber: 2.6 Consensus size: 101
1881192 AAGATTTTGT
** * *
1881202 TTATTTAAATTTAAATAAGCTAATAAAAATTAAATATATAAATAGGGAATATTTATTAATTTTAA
1 TTATTTAAATTTAAATAAATTAAT-AAAATTACATAT-TAAATA-GGAAAATTTATTAATTTTAA
* * *
1881267 AGTTGTTTAATATTATGTGGACTCTATTTTTAAATATTA
63 AGTAGATTAATATCATGTGGACTCTATTTTTAAATATTA
* *
1881306 TTA---AAATTTAAATAAATTAATACAATTACATAATTAAATAGGAAAATTTATTAATTTTGAAG
1 TTATTTAAATTTAAATAAATTAATAAAATTACAT-ATTAAATAGGAAAATTTATTAATTTTAAAG
1881368 TAGATTAATATCATGTGG-CTCTA-TTTTAAATATTTA
65 TAGATTAATATCATGTGGACTCTATTTTTAAATA-TTA
* * * *
1881404 TTAATTTAAATTTATATAAATTAATAAAATTACATTTTAAATAAGATAATCTTATTAATTTTAAA
1 TT-ATTTAAATTTAAATAAATTAATAAAATTACATATTAAATAGGAAAAT-TTATTAATTTTAAA
1881469 ATTTTAAAAA
Statistics
Matches: 141, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
97 9 0.06
98 10 0.07
99 36 0.26
100 14 0.10
101 30 0.21
102 39 0.28
104 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (101 bp):
TTATTTAAATTTAAATAAATTAATAAAATTACATATTAAATAGGAAAATTTATTAATTTTAAAGT
AGATTAATATCATGTGGACTCTATTTTTAAATATTA
Found at i:1882599 original size:15 final size:16
Alignment explanation
Indices: 1882573--1882620 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
1882563 CTTGGTAAGT
1882573 AGAAAGAAAATTGAAA-
1 AGAAA-AAAATTGAAAG
*
1882589 AGATAAAAATTGAAAG
1 AGAAAAAAATTGAAAG
1882605 AGAAAAAAAGTTGAAA
1 AGAAAAAAA-TTGAAA
1882621 CGTAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 12 0.43
17 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
AGAAAAAAATTGAAAG
Found at i:1882604 original size:14 final size:15
Alignment explanation
Indices: 1882579--1882611 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1882569 AAGTAGAAAG
*
1882579 AAAATTGAAAAGATA
1 AAAATTGAAAAGAGA
1882594 AAAATTG-AAAGAGA
1 AAAATTGAAAAGAGA
1882608 AAAA
1 AAAA
1882612 AAGTTGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAAATTGAAAAGAGA
Found at i:1882631 original size:2 final size:2
Alignment explanation
Indices: 1882626--1882661 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1882616 TGAAACGTAA
1882626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1882662 TTTCTTGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1883555 original size:16 final size:17
Alignment explanation
Indices: 1883513--1883576 Score: 64
Period size: 16 Copynumber: 4.0 Consensus size: 17
1883503 GACAACATAA
*
1883513 TATTA-AATTTATTATT
1 TATTATAATTAATTATT
* * *
1883529 TATGAT-TTTAATTTTT
1 TATTATAATTAATTATT
1883545 TA-TATAATTAA-TATT
1 TATTATAATTAATTATT
1883560 TATTATAATTAATTATT
1 TATTATAATTAATTATT
1883577 ATAATATTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
15 7 0.19
16 26 0.70
17 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTATAATTAATTATT
Found at i:1884234 original size:6 final size:6
Alignment explanation
Indices: 1884217--1884262 Score: 74
Period size: 6 Copynumber: 7.3 Consensus size: 6
1884207 TGTGGTGGTC
1884217 TTTCTAT TTTCTT TTTCTT TTTCTTT TTTCTT TTTCTT TTTCTT TT
1 TTTCT-T TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TT
1884263 CCCTTCTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 27 0.71
7 11 0.29
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:1884244 original size:13 final size:12
Alignment explanation
Indices: 1884217--1884262 Score: 74
Period size: 13 Copynumber: 3.7 Consensus size: 12
1884207 TGTGGTGGTC
1884217 TTTCTATTTTCTT
1 TTTCT-TTTTCTT
1884230 TTTCTTTTTCTTT
1 TTTCTTTTTC-TT
1884243 TTTCTTTTTCTT
1 TTTCTTTTTCTT
1884255 TTTCTTTT
1 TTTCTTTT
1884263 CCCTTCTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 15 0.47
13 17 0.53
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTCTTTTTCTT
Found at i:1884245 original size:19 final size:19
Alignment explanation
Indices: 1884217--1884262 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1884207 TGTGGTGGTC
*
1884217 TTTCTATTTTCTTTTTCTT
1 TTTCTTTTTTCTTTTTCTT
1884236 TTTCTTTTTTCTTTTTCTT
1 TTTCTTTTTTCTTTTTCTT
1884255 TTTCTTTT
1 TTTCTTTT
1884263 CCCTTCTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTCTTTTTTCTTTTTCTT
Found at i:1886200 original size:37 final size:38
Alignment explanation
Indices: 1886098--1886215 Score: 116
Period size: 37 Copynumber: 3.0 Consensus size: 38
1886088 TTATTAGAGA
* *
1886098 TATTATATTAAAATGTACATATATAATAAATAATTAAAAAT
1 TATTATATTAAAAT-TATAT-TATATTAAATAA-TAAAAAT
* *
1886139 TATTAAATT-ATATTATATTCATATTAAATAATAAAAA-
1 TATTATATTAAAATTATATT-ATATTAAATAATAAAAAT
*
1886176 TA-TATATTAAAATTATATCTATATTAAACAATAAATAAT
1 TATTATATTAAAATTATAT-TATATTAAATAATAAA-AAT
1886215 T
1 T
1886216 TAAATTGTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
36 5 0.08
37 24 0.37
38 10 0.15
39 15 0.23
40 3 0.05
41 8 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (38 bp):
TATTATATTAAAATTATATTATATTAAATAATAAAAAT
Found at i:1886285 original size:15 final size:14
Alignment explanation
Indices: 1886265--1886324 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 14
1886255 ATAAAAGAAG
1886265 AATAAAAGAATTAAA
1 AATAAAA-AATTAAA
*
1886280 AATAAATAATTTAAA
1 AATAAA-AAATTAAA
*
1886295 AAT-AAAAATAAAA
1 AATAAAAAATTAAA
1886308 AATGTAAAAACATTAAA
1 AA--TAAAAA-ATTAAA
1886325 GGGAGATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.22
14 2 0.06
15 16 0.44
16 5 0.14
17 5 0.14
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (14 bp):
AATAAAAAATTAAA
Found at i:1886300 original size:21 final size:21
Alignment explanation
Indices: 1886276--1886317 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1886266 ATAAAAGAAT
* *
1886276 TAAAAATAAATAATTTAAAAA
1 TAAAAATAAAAAATGTAAAAA
1886297 TAAAAATAAAAAATGTAAAAA
1 TAAAAATAAAAAATGTAAAAA
1886318 CATTAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAAAATAAAAAATGTAAAAA
Found at i:1887819 original size:13 final size:14
Alignment explanation
Indices: 1887786--1887828 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1887776 TACATTAATT
1887786 TTAAAATATATTTA
1 TTAAAATATATTTA
1887800 TTAAAATAT-TTTA
1 TTAAAATATATTTA
*
1887813 CTT-AAATAAATTTA
1 -TTAAAATATATTTA
1887827 TT
1 TT
1887829 TAAGTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAAATATATTTA
Found at i:1896171 original size:20 final size:20
Alignment explanation
Indices: 1896146--1896211 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1896136 GTTATAAGCT
1896146 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
1896166 ATGTATCGATACA-------
1 ATGTATCGATACATTTCTTC
1896179 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTCTTC
1896199 ATGTATCGATACA
1 ATGTATCGATACA
1896212 ATGTATCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTCTTC
Found at i:1896184 original size:13 final size:12
Alignment explanation
Indices: 1896146--1896230 Score: 69
Period size: 13 Copynumber: 7.6 Consensus size: 12
1896136 GTTATAAGCT
1896146 ATGTATCGATAC
1 ATGTATCGATAC
*
1896158 AT-T-TC--TTC
1 ATGTATCGATAC
1896166 ATGTATCGATAC
1 ATGTATCGATAC
1896178 AATGTATCGATAC
1 -ATGTATCGATAC
*
1896191 AT-T-TC--TTC
1 ATGTATCGATAC
1896199 ATGTATCGATAC
1 ATGTATCGATAC
1896211 AATGTATCGATAC
1 -ATGTATCGATAC
*
1896224 TTGTATC
1 ATGTATC
1896231 ATGTATCGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
8 8 0.14
9 2 0.03
10 8 0.14
11 2 0.03
12 14 0.24
13 24 0.41
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:1896188 original size:33 final size:33
Alignment explanation
Indices: 1896146--1896244 Score: 166
Period size: 33 Copynumber: 3.0 Consensus size: 33
1896136 GTTATAAGCT
1896146 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
1896179 ATGTATCGATACATTTCTTCATGTATCGATACA
1 ATGTATCGATACATTTCTTCATGTATCGATACA
*
1896212 ATGTATCGATAC-TTGT-ATCATGTATCGATACA
1 ATGTATCGATACATT-TCTTCATGTATCGATACA
1896244 A
1 A
1896245 ATAATGATAG
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
32 18 0.28
33 46 0.72
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (33 bp):
ATGTATCGATACATTTCTTCATGTATCGATACA
Found at i:1896333 original size:13 final size:13
Alignment explanation
Indices: 1896315--1896339 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1896305 ACATTAAACA
1896315 TGTATCGATACAT
1 TGTATCGATACAT
1896328 TGTATCGATACA
1 TGTATCGATACA
1896340 AGGTAGCATG
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:1897160 original size:19 final size:18
Alignment explanation
Indices: 1897136--1897198 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
1897126 AAACCGTAAC
1897136 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1897155 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1897168 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
*
1897187 TGTATTGATACA
1 TGTATCGATACA
1897199 ATGTATCACT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1897173 original size:13 final size:13
Alignment explanation
Indices: 1897155--1897179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1897145 ACATAAGTGT
1897155 TGTATCGATACAA
1 TGTATCGATACAA
1897168 TGTATCGATACA
1 TGTATCGATACA
1897180 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1897177 original size:32 final size:32
Alignment explanation
Indices: 1897136--1897205 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
1897126 AAACCGTAAC
1897136 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1897168 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1897200 TGTATC
1 TGTATC
1897206 ACTACGAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1907308 original size:13 final size:13
Alignment explanation
Indices: 1907290--1907314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1907280 AGAATGCACA
1907290 GTATCGATACATT
1 GTATCGATACATT
1907303 GTATCGATACAT
1 GTATCGATACAT
1907315 GACAAAATGT
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):
GTATCGATACATT
Found at i:1907327 original size:20 final size:21
Alignment explanation
Indices: 1907302--1907354 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1907292 ATCGATACAT
1907302 TGTATCGATACATG-ACAA-AA
1 TGTATCGATACATGTA-AAGAA
*
1907322 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
*
1907343 TATATCGATACA
1 TGTATCGATACA
1907355 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:1913568 original size:27 final size:30
Alignment explanation
Indices: 1913514--1913571 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 30
1913504 TAGGGTCAAA
*
1913514 ATCTGGAAAAATTCCAGAATGTATCGATAC
1 ATCTGGAAAAACTCCAGAATGTATCGATAC
1913544 ATCTGG-AAAACT-CAG-ATGTATCGATAC
1 ATCTGGAAAAACTCCAGAATGTATCGATAC
1913571 A
1 A
1913572 GCATTCTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.48
28 3 0.11
29 5 0.19
30 6 0.22
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (30 bp):
ATCTGGAAAAACTCCAGAATGTATCGATAC
Found at i:1913602 original size:33 final size:33
Alignment explanation
Indices: 1913560--1913637 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
1913550 AAAACTCAGA
1913560 TGTATCGATACAGCATTCTCTATATCGATACAT
1 TGTATCGATACAGCATTCTCTATATCGATACAT
*
1913593 TGTATCGATACAGCATTCTCTGTATCGATACAT
1 TGTATCGATACAGCATTCTCTATATCGATACAT
1913626 TGTATCGATACA
1 TGTATCGATACA
1913638 AAGGGTTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAGCATTCTCTATATCGATACAT
Found at i:1913618 original size:20 final size:20
Alignment explanation
Indices: 1913560--1913624 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
1913550 AAAACTCAGA
1913560 TGTATCGATACAGCATTCTC
1 TGTATCGATACAGCATTCTC
*
1913580 TATATCGAT--A-CA---T-
1 TGTATCGATACAGCATTCTC
1913593 TGTATCGATACAGCATTCTC
1 TGTATCGATACAGCATTCTC
1913613 TGTATCGATACA
1 TGTATCGATACA
1913625 TTGTATCGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 1 0.03
20 20 0.56
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAGCATTCTC
Found at i:1916107 original size:13 final size:13
Alignment explanation
Indices: 1916089--1916113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1916079 AGAATGCACA
1916089 GTATCGATACATT
1 GTATCGATACATT
1916102 GTATCGATACAT
1 GTATCGATACAT
1916114 GACCAAATGT
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):
GTATCGATACATT
Found at i:1916126 original size:20 final size:21
Alignment explanation
Indices: 1916101--1916153 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1916091 ATCGATACAT
*
1916101 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
1916121 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
1916142 TGTATCGATACA
1 TGTATCGATACA
1916154 AGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:1916231 original size:13 final size:13
Alignment explanation
Indices: 1916213--1916238 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1916203 TACACACAAG
1916213 ATGTATCGATACA
1 ATGTATCGATACA
1916226 ATGTATCGATACA
1 ATGTATCGATACA
1916239 TCCCAAAATG
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:1918481 original size:20 final size:19
Alignment explanation
Indices: 1918439--1918489 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1918429 GTTACAAGCT
1918439 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTC-TC
1918459 ATGTATCGATACATTGTAC-C
1 ATGTATCGATACATT-T-CTC
1918479 ATGTATCGATA
1 ATGTATCGATA
1918490 TAAATAGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 27 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTTCTC
Found at i:1918566 original size:19 final size:19
Alignment explanation
Indices: 1918521--1918576 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
1918511 CTGCCAGCTT
**
1918521 CATGTATCGATACAATTTGTC
1 CATGTATCGATAC-A-TTGAA
1918542 CATGTATCGATACATTGAA
1 CATGTATCGATACATTGAA
*
1918561 CATGTATCGATGCATT
1 CATGTATCGATACATT
1918577 ATATCGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 18 0.56
20 1 0.03
21 13 0.41
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:1919503 original size:19 final size:19
Alignment explanation
Indices: 1919479--1919526 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1919469 ATTCGTTGTG
*
1919479 TATCGATACCAAG-ATCATA
1 TATCGATACAAAGAAT-ATA
1919498 TATCGATACAAAGCAATATA
1 TATCGATACAAAG-AATATA
1919518 TATCGATAC
1 TATCGATAC
1919527 TTCTGGATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 12 0.46
21 2 0.08
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (19 bp):
TATCGATACAAAGAATATA
Found at i:1920041 original size:109 final size:110
Alignment explanation
Indices: 1919925--1920149 Score: 355
Period size: 109 Copynumber: 2.1 Consensus size: 110
1919915 TTTCAACTTA
* * * *
1919925 TTGATTTTATATTTTATTTTAATTATGAAAACATTGGTTTTTTATGGTTTATTTGTTCTAAGAAA
1 TTGATTTTATATTTTATTTTAATTATAAAAACATTGGTTCTTTATGATTTATTTGTTCCAA-AAA
* *
1919990 AATTAAAGTCAAGCACA-TTTCGTTGTTTGAAAGTTTTT-TATTAT
65 AATTAAAATCAAGCACATTTTCATTGTTTGAAAGTTTTTCTATTAT
*
1920034 TTGATTTTATATTTTATTTTAATTATAAAAATATTGGTTCTTTATGATTTATTTGTTCCAAAAAA
1 TTGATTTTATATTTTATTTTAATTATAAAAACATTGGTTCTTTATGATTTATTTGTTCCAAAAAA
*
1920099 ATTAAAATCAAGCATATTTTCATTGTTTGAAAGTTTTTCTATTAT
66 ATTAAAATCAAGCACATTTTCATTGTTTGAAAGTTTTTCTATTAT
1920144 TTGATT
1 TTGATT
1920150 CATACTTGTC
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
108 18 0.17
109 76 0.72
110 12 0.11
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.52
Consensus pattern (110 bp):
TTGATTTTATATTTTATTTTAATTATAAAAACATTGGTTCTTTATGATTTATTTGTTCCAAAAAA
ATTAAAATCAAGCACATTTTCATTGTTTGAAAGTTTTTCTATTAT
Done.