Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 5 of 193
Found at i:1680630 original size:29 final size:30
Alignment explanation
Indices: 1680597--1680760 Score: 122
Period size: 29 Copynumber: 5.6 Consensus size: 30
1680587 CCCCAAACAG
1680597 TCCAAAAATTA-CATTTTGACCCCGAAAC-T
1 TCCAAAAATTACCATTTT-ACCCCGAAACTT
*
1680626 TCC-AAAATTACCATTTTACCCCTAAACTT
1 TCCAAAAATTACCATTTTACCCCGAAACTT
*
1680655 TCC-AAAATT-CTATTTTTAACCCCG--A-TT
1 TCCAAAAATTACCA-TTTT-ACCCCGAAACTT
1680682 TCACCAAAAATTACCATTTTACCCCCG-AACTT
1 T--CCAAAAATTACCATTTTA-CCCCGAAACTT
1680714 TCC-AAAATT-CCATTTTTAACCCCG--A-TT
1 TCCAAAAATTACCA-TTTT-ACCCCGAAACTT
1680741 TCACCAAAAATTACCATTTT
1 T--CCAAAAATTACCATTTT
1680761 GCCCTCGGGT
Statistics
Matches: 114, Mismatches: 4, Indels: 33
0.75 0.03 0.22
Matches are distributed among these distances:
27 6 0.05
28 23 0.20
29 43 0.38
30 33 0.29
31 6 0.05
32 3 0.03
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTACCCCGAAACTT
Found at i:1680646 original size:28 final size:30
Alignment explanation
Indices: 1680601--1680738 Score: 132
Period size: 29 Copynumber: 4.7 Consensus size: 30
1680591 AAACAGTCCA
*
1680601 AAAATTA-CATTTTGACCCCGAAAC-TTCC
1 AAAATTACCATTTTAACCCCGAAACTTTCC
*
1680629 AAAATTACCATTTT-ACCCCTAAACTTTCC
1 AAAATTACCATTTTAACCCCGAAACTTTCC
*
1680658 AAAATT-CTATTTTTAACCCCG--A-TTTCACC
1 AAAATTACCA-TTTTAACCCCGAAACTTT--CC
*
1680687 AAAAATTACCATTTTACCCCCG-AACTTTCC
1 -AAAATTACCATTTTAACCCCGAAACTTTCC
1680717 AAAATT-CCATTTTTAACCCCGA
1 AAAATTACCA-TTTTAACCCCGA
1680739 TTTCACCAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
27 3 0.03
28 22 0.24
29 38 0.41
30 23 0.25
31 3 0.03
32 3 0.03
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGAAACTTTCC
Found at i:1680692 original size:30 final size:30
Alignment explanation
Indices: 1680658--1680760 Score: 124
Period size: 30 Copynumber: 3.4 Consensus size: 30
1680648 TAAACTTTCC
*
1680658 AAAATTCTATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
*
1680688 AAAATTACCA-TTTTACCCCCGAACTTT--CC-
1 AAAATT-CCATTTTTAACCCCG-A-TTTCACCA
1680717 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTCACCA
1680747 AAAATTACCATTTT
1 AAAATT-CCATTTT
1680761 GCCCTCGGGT
Statistics
Matches: 62, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
27 3 0.05
28 4 0.06
29 18 0.29
30 24 0.39
31 10 0.16
32 3 0.05
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:1680713 original size:59 final size:59
Alignment explanation
Indices: 1680629--1680760 Score: 237
Period size: 59 Copynumber: 2.2 Consensus size: 59
1680619 CGAAACTTCC
* *
1680629 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
*
1680688 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1680747 AAAATTACCATTTT
1 AAAATTACCATTTT
1680761 GCCCTCGGGT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 70 1.00
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:1680794 original size:59 final size:59
Alignment explanation
Indices: 1680629--1680802 Score: 215
Period size: 59 Copynumber: 2.9 Consensus size: 59
1680619 CGAAACTTCC
** * * *
1680629 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCTATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTATCCAAAATCCCATTTTTAACCCCGATTTCACCA
* *
1680688 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTATCCAAAATCCCATTTTTAACCCCGATTTCACCA
* * ** * *
1680747 AAAATTACCATTTTGCCCTCG-GGTATCCAAAAGTCCCGTTTTCAACCCCGATTTCA
1 AAAATTACCATTTTACCCCCGAACTATCCAAAA-TCCCATTTTTAACCCCGATTTCA
1680803 TCATTCCTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 8 0.08
59 95 0.92
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAACTATCCAAAATCCCATTTTTAACCCCGATTTCACCA
Found at i:1695882 original size:29 final size:29
Alignment explanation
Indices: 1695840--1695908 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
1695830 ATTCGGCAGT
1695840 CACAAAGGCTCACATATAACAGATTCTA-C
1 CACAAAGGCTCACATATAACAGATTC-AGC
*
1695869 CACAAAGGCTCACATATAATAGATTCAGC
1 CACAAAGGCTCACATATAACAGATTCAGC
1695898 CACAAAGGCTC
1 CACAAAGGCTC
1695909 TTCACTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 1 0.03
29 37 0.97
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.19
Consensus pattern (29 bp):
CACAAAGGCTCACATATAACAGATTCAGC
Found at i:1703611 original size:22 final size:22
Alignment explanation
Indices: 1703586--1703629 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1703576 AATTATGATA
1703586 GTTTTAAATTACTTATTCAAGC
1 GTTTTAAATTACTTATTCAAGC
1703608 GTTTTAAATTACTTATTCAAGC
1 GTTTTAAATTACTTATTCAAGC
1703630 ATTCCAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
GTTTTAAATTACTTATTCAAGC
Found at i:1703638 original size:22 final size:22
Alignment explanation
Indices: 1703591--1703639 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1703581 TGATAGTTTT
* **
1703591 AAATTACTTATTCAAGCGTTTT
1 AAATTACTTATTCAAGCATTCC
1703613 AAATTACTTATTCAAGCATTCC
1 AAATTACTTATTCAAGCATTCC
1703635 AAATT
1 AAATT
1703640 TGAATTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (22 bp):
AAATTACTTATTCAAGCATTCC
Found at i:1707035 original size:13 final size:14
Alignment explanation
Indices: 1707013--1707048 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1707003 CATTTACAAA
1707013 TAATTAAAATTT-T
1 TAATTAAAATTTAT
*
1707026 TAATTTAAATTTAT
1 TAATTAAAATTTAT
1707040 TAATTAAAA
1 TAATTAAAA
1707049 ATTGATGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTAAAATTTAT
Found at i:1717909 original size:7 final size:7
Alignment explanation
Indices: 1717899--1717937 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
1717889 CTTAAACACG
*
1717899 AAACCTT
1 AAACCTC
*
1717906 AAACCTT
1 AAACCTC
*
1717913 AAATCTC
1 AAACCTC
1717920 AAACCTC
1 AAACCTC
1717927 AAACCTC
1 AAACCTC
1717934 AAAC
1 AAAC
1717938 ATTGAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCTC
Found at i:1717915 original size:21 final size:20
Alignment explanation
Indices: 1717884--1717938 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1717874 ACCTTAAATT
1717884 TCAAA-CTTAAACACGAAACC
1 TCAAACCTTAAACAC-AAACC
* *
1717904 TTAAACCTTAAATCTCAAACC
1 TCAAACCTTAAA-CACAAACC
*
1717925 TCAAACCTCAAACA
1 TCAAACCTTAAACA
1717939 TTGAAAACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 5 0.18
21 21 0.75
22 2 0.07
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (20 bp):
TCAAACCTTAAACACAAACC
Found at i:1722483 original size:22 final size:22
Alignment explanation
Indices: 1722454--1722496 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1722444 GCTTGTGAAT
1722454 TTTATAATTTT-TAAATTTTTA
1 TTTATAATTTTATAAATTTTTA
*
1722475 TTTATTAATTTTATGAATTTTT
1 TTTA-TAATTTTATAAATTTTT
1722497 TAAATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATAATTTTATAAATTTTTA
Found at i:1722500 original size:32 final size:30
Alignment explanation
Indices: 1722451--1722510 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 30
1722441 AAAGCTTGTG
*
1722451 AATTTTATAATTTTTAAATTTTTATTTATT
1 AATTTTATAATTTTTAAATATTTATTTATT
1722481 AATTTTATGAATTTTTTAAATATTTATTTA
1 AATTTTAT-AA-TTTTTAAATATTTATTTA
1722511 ATTATTAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 8 0.30
31 2 0.07
32 17 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
AATTTTATAATTTTTAAATATTTATTTATT
Found at i:1729309 original size:140 final size:141
Alignment explanation
Indices: 1729056--1729334 Score: 377
Period size: 140 Copynumber: 2.0 Consensus size: 141
1729046 TAAATAAGAA
** * *
1729056 TAAGTTTGCATAGGTCCACGACCCCTATCAGTTTCAACTATTAGTAATGGAAAGGGCCTTTCACC
1 TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCAACTATAAGTAATGGAAAGGGCCTGTCACC
* * * *
1729121 AAGTTTATCCTAACTCCGAGCTTGAGGAGAAGCTTTTTCTCTAGCAAGGGAGTAATATTATGGGC
66 AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
*
1729186 TGAATCTATAC
131 CGAATCTATAC
**
1729197 TAAGTTTGTC-TAGGTCCAAAACCCCTATCAGTTTTGACTATAAGTAAT-G-AAGGGACCTAGT-
1 TAAGTTTG-CATAGGTCCAAAACCCCTATCAGTTTCAACTATAAGTAATGGAAAGGG-CCT-GTC
* * *
1729258 GCCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTGATCTTATG
63 ACCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATG
1729323 GGCCGAATCTAT
128 GGCCGAATCTAT
1729335 GTTAGGAAAG
Statistics
Matches: 121, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
139 5 0.04
140 73 0.60
141 42 0.35
142 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (141 bp):
TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCAACTATAAGTAATGGAAAGGGCCTGTCACC
AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
CGAATCTATAC
Found at i:1729840 original size:141 final size:141
Alignment explanation
Indices: 1729533--1729912 Score: 393
Period size: 141 Copynumber: 2.6 Consensus size: 141
1729523 GTCGGTTTTG
* * * *
1729533 ACTATTAGTAATGAAAGGGACCTTTCACCAAGTTTATTATAACTCCAAGCTTGAGGACAAGCTCT
1 ACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCATAATTCCGAGCTTGAGGACAAGCTCT
* * *
1729598 TTCTCTAGCAAAGGGCTAGAGAGTAAAATTATAAGCCAAATCTATAATAAGTCTGTTTAAGTCTA
66 TTCTCTAG-AAA--G---G-GAGTAATATTATAAGCCAAATCTATAATAAGTCTGTGTAAGTCCA
*
1729663 CGACACCTATCGGTTTCA
124 CGACACCTATCAGTTTCA
* * * * *
1729681 ACTACTAGTAATGGAAGGGACCTTTCGCAAAGTATATCCTAATTCCGAGCTTGAGGACAAGCTCT
1 ACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCATAATTCCGAGCTTGAGGACAAGCTCT
* * * * * * * *
1729746 TTCTCTAGTAAGGGAGTAATATTATGAGTCGAATCTATAATAAGTTTGTGTATGTCCATGACCCC
66 TTCTCTAGAAAGGGAGTAATATTATAAGCCAAATCTATAATAAGTCTGTGTAAGTCCACGACACC
*
1729811 TATCAGTTTCG
131 TATCAGTTTCA
* * * * *
1729822 ATTATTAGTAACGAAAGGGACCTTTTTGCCAAGTTTATCTTAACTT-CGAGTTTGAGGACAAGCT
1 ACTATTAGTAATGAAAGGGACC-TTTCGCCAAGTTTATCATAA-TTCCGAGCTTGAGGACAAGCT
* * * *
1729886 CTATCTCTTGCAAGGTAGTAATATTAT
64 CTTTCTCTAGAAAGGGAGTAATATTAT
1729913 CGGCCGGATC
Statistics
Matches: 195, Mismatches: 35, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
141 69 0.35
142 57 0.29
143 2 0.01
145 1 0.01
147 2 0.01
148 64 0.33
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (141 bp):
ACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCATAATTCCGAGCTTGAGGACAAGCTCT
TTCTCTAGAAAGGGAGTAATATTATAAGCCAAATCTATAATAAGTCTGTGTAAGTCCACGACACC
TATCAGTTTCA
Found at i:1730669 original size:141 final size:141
Alignment explanation
Indices: 1730108--1730811 Score: 896
Period size: 141 Copynumber: 5.0 Consensus size: 141
1730098 GGTGCTAATG
* * * *
1730108 AATAAGTTTGCGTAGGTCCACGACTCCTATCAGTTTTAACTATTAGTAATGAAAGGGACCTTTCA
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
*
1730173 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
66 CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
**
1730238 GTTGAATCTAT
131 GCCGAATCTAT
* * * * * *
1730249 AACAAGTTTGTATAGGTCCACAATCTCTATCGGTTTCAACTATTAGTAATGGAAGGGACCTTTCA
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
* *
1730314 CCATG-TTATCCTAACTCTGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
66 CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
*
1730378 GCCTAATCTAT
131 GCCGAATCTAT
* * * * * * **** **
1730389 AACAAGTTTGTGTAAGTCCACGACCCCTATAAGTTTCGACTTAATATGGGGGGAGGGGGACCTTT
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAAC-TATTA-GTAATGAAAGGGACCTTT
* *
1730454 CTCCAAGTTTATCCTAGCTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTAT
64 CACCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTAT
*
1730519 GGGCTGAATCTAT
129 GGGCCGAATCTAT
* * *
1730532 AATAAGTTTGTG-ACGGTCCACAACCCCAATCGGTTTAAACTATTAGTAATGAAATGGGA-CTTT
1 AATAAGTTTGTGTA-GGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAA-GGGACCTTT
* *
1730595 CGCCAAGTTTACCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTAT
64 CACCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTAT
*
1730660 GAGCCGAATCTAT
129 GGGCCGAATCTAT
* * * * *
1730673 TATAAGTTTGTGTAGGTCCACAACCCTTATCTGTTTCGACTATTAGTAATG-ATGGGACCTTTCA
1 AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
* * * * * *
1730737 CCAAGTTTATCCTAACTCCAAGCTCGAGGACAAGTTTTTTCTCTAGCAAGGGAGTGA-CTTATGG
66 CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
*
1730801 GACGAATCTAT
131 GCCGAATCTAT
1730812 GTTAGGAAAG
Statistics
Matches: 481, Mismatches: 75, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
139 19 0.04
140 154 0.32
141 186 0.39
142 26 0.05
143 96 0.20
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (141 bp):
AATAAGTTTGTGTAGGTCCACAACCCCTATCAGTTTCAACTATTAGTAATGAAAGGGACCTTTCA
CCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGG
GCCGAATCTAT
Found at i:1735209 original size:23 final size:23
Alignment explanation
Indices: 1735183--1735226 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1735173 TATTAAAATA
*
1735183 TTCATTTAGT-TATTATTTTTACT
1 TTCATTT-GTATATGATTTTTACT
1735206 TTCATTTGTATATGATTTTTA
1 TTCATTTGTATATGATTTTTA
1735227 AGCATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.64
Consensus pattern (23 bp):
TTCATTTGTATATGATTTTTACT
Found at i:1740178 original size:247 final size:249
Alignment explanation
Indices: 1739672--1740727 Score: 1193
Period size: 247 Copynumber: 4.3 Consensus size: 249
1739662 ATGTAAATTA
* * * *
1739672 TTCATTTAATAATTTTCGTGTTATAATTATATTCCACATCATATTCAAAATAAAATTTAATACCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACATCACATTCAAAATAACATTTAATACCC
* * * * * **
1739737 AAACCAACTTTTGCATGCGATAAGT-TTAAACCTTCATCTTTACCGATCATGTCAAAACTTCATT
66 AAATCAACTTTTGCATGTGATAAGTCTCAAACCTTCTTCTTTACCAATCATACCAAAACTTCATT
* * *
1739801 AAATAATTTACGTGTTTTAATTATATTCCACGTCACATTCAAAGTAACGTTTAATACTCAAATTT
131 AAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACTCAAATTT
* * *
1739866 AACTTTTATATGTGGTAGGTCTCGATCCTTCTTCTTTACCTATCATTCCAAAAT
196 AACTTTTATATGTGGTAGGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAT
* ** * * *
1739920 TTCACTTAATAATTT-TTTGTTTTAATTGTATTCCACGTCACATTCAAAATAACATTTAATATCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACATCACATTCAAAATAACATTTAATACCC
* * * * * *
1739984 AAATCAACTTTTGCATTTTATAAGT-TTAAACCTTCCTCTTCACCAATCATGCCAAAACTTCATT
66 AAATCAACTTTTGCATGTGATAAGTCTCAAACCTTCTTCTTTACCAATCATACCAAAACTTCATT
* * *
1740048 AAATAATTTGCGTGTTTTAATTATATTCCACGTCATGTTCAAAATAACATTTAATACCCAAATTT
131 AAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACTCAAATTT
* * * * * *
1740113 AATTTTTATAAGTGGTAGGCCTCGAACCTTTTTCTCTACCAATCATACCAAAAC
196 AACTTTTATATGTGGTAGGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAT
* * * * *
1740167 TTCATTTAATAATTTGCGTGTTTTAATCATATTTCACATCACGTT-AAAA-AA-ATTTAATACAC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACATCACATTCAAAATAACATTTAATACCC
* * * *
1740229 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTTTTCTTTACCAATCATACCAAAACTTCAT
66 AAA-TCAACTTTTGCATGTGATAAGTCTCAAACCTTCTTCTTTACCAATCATACCAAAACTTCAT
* * * * *
1740294 TTAATAATTTACGTGTTTTAATCATATTCCACGCCACGTTTAAAATAATATTTAATACTCAAATT
130 TAAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACTCAAATT
* * **
1740359 TAACTTTTTTATGTAGTAGGTCTCGAACCTTCTTCTTTATTAATCATACCAAAAT
195 TAACTTTTATATGTGGTAGGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAT
* * * ** * * *
1740414 TTCATTTAATAATTTACTTATTTTGATTATATTCCATGTCACGTTTAAAATAACATTTAATGCCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACATCACATTCAAAATAACATTTAATACCC
* * * * * * *
1740479 AAGTTTAACTTTTGCATGTGGTAGGTCTCGAACATTCTTCCTTTACCAATCATACCAAAACTTTA
66 AA-ATCAACTTTTGCATGTGATAAGTCTCAAACCTTCTT-CTTTACCAATCATACCAAAACTTCA
* * * * * *
1740544 TTTAATAATTTACGTATTTTGATTATATTCTACGTCACGTTCAAAA-AATATTTAATACTCAAGT
129 TTAAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACTCAAAT
** ** * ** * *
1740608 TTAACTTTTGCATACGATAAATCTCGAA---TCTTCTTTATCAATCATACCACAAT
194 TTAACTTTTATATGTGGTAGGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAT
* *
1740661 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCA-AGTTC-AAA-AATATTTAATACC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACATCACA-TTCAAAATAACATTTAATACC
1740723 CAAAT
65 CAAAT
1740728 TTATGATTAA
Statistics
Matches: 688, Mismatches: 111, Indels: 22
0.84 0.14 0.03
Matches are distributed among these distances:
244 1 0.00
245 26 0.04
246 23 0.03
247 452 0.66
248 40 0.06
249 2 0.00
250 80 0.12
251 64 0.09
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (249 bp):
TTCATTTAATAATTTACGTGTTTTAATTATATTCCACATCACATTCAAAATAACATTTAATACCC
AAATCAACTTTTGCATGTGATAAGTCTCAAACCTTCTTCTTTACCAATCATACCAAAACTTCATT
AAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACTCAAATTT
AACTTTTATATGTGGTAGGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAT
Found at i:1740192 original size:125 final size:125
Alignment explanation
Indices: 1739672--1740730 Score: 1138
Period size: 125 Copynumber: 8.6 Consensus size: 125
1739662 ATGTAAATTA
* * * ** *
1739672 TTCATTTAATAATTTTCGTGTTATAATTATATTCCACATCATATTCAAAATAAAATTTAATACCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
** * * ** * * **
1739737 AAA-CCAACTTTTGCATGCGATAAGT-TTAAACCTTCATCTTTACCGATCATGTCAAAAC
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
* * * * *
1739795 TTCATTAAATAATTTACGTGTTTTAATTATATTCCACGTCACATTCAAAGTAACGTTTAATACTC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
** * * * * *
1739860 AAATTTAACTTTTATATGTGGTAGGTCTCGATCCTTCTTCTTTACCTATCATTCCAAAAT
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
* ** * * *
1739920 TTCACTTAATAATTT-TTTGTTTTAATTGTATTCCACGTCACATTCAAAATAACATTTAATATCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
* * ** ** * * *
1739984 AAA-TCAACTTTTGCATTTTATAAGT-TTAAACCTTCCTCTTCACCAATCATGCCAAAAC
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
* * *
1740042 TTCATTAAATAATTTGCGTGTTTTAATTATATTCCACGTCATGTTCAAAATAACATTTAATACCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
* ** * * * * *
1740107 AAATTTAATTTTTATAAGTGGTAGGCCTCGAACCTTTTTCTCTACCAATCATACCAAAAC
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
* * * * *
1740167 TTCATTTAATAATTTGCGTGTTTTAATCATATTTCACATCACGTT-AAAA-AA-ATTTAATACAC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
*
1740229 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTTTTCTTTACCAATCATACCAAAAC
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
* * * * *
1740289 TTCATTTAATAATTTACGTGTTTTAATCATATTCCACGCCACGTTTAAAATAATATTTAATACTC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
** * * ** *
1740354 AAATTTAACTTTTTTATGTAGTAGGTCTCGAACCTTCTTCTTTATTAATCATACCAAAAT
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
* * * * * *
1740414 TTCATTTAATAATTTACTTATTTTGATTATATTCCATGTCACGTTTAAAATAACATTTAATGCCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
* * *
1740479 AAGTTTAACTTTTGCATGTGGTAGGTCTCGAACATTCTTCCTTTACCAATCATACCAAAAC
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTT-CTTTACCAATCATACCAAAAC
* * * * * *
1740540 TTTATTTAATAATTTACGTATTTTGATTATATTCTACGTCACGTTCAAAA-AATATTTAATACTC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
* ** * * * * *
1740604 AAGTTTAACTTTTGCATACGATAAATCTCGAA---TCTTCTTTATCAATCATACCACAAT
66 AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
* *
1740661 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCAAGTTC-AAA-AATATTTAATACCC
1 TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
1740724 AAATTTA
66 AAATTTA
1740731 TGATTAAATT
Statistics
Matches: 788, Mismatches: 139, Indels: 21
0.83 0.15 0.02
Matches are distributed among these distances:
120 22 0.03
121 59 0.07
122 146 0.19
123 126 0.16
124 78 0.10
125 294 0.37
126 63 0.08
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (125 bp):
TTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCC
AAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAAC
Found at i:1740449 original size:372 final size:373
Alignment explanation
Indices: 1739789--1740730 Score: 1107
Period size: 372 Copynumber: 2.5 Consensus size: 373
1739779 CCGATCATGT
* * * **
1739789 CAAAACTTCATTAAATAATTTACGTGTTTTAATTATATTCCACGTCACATTCAAAGTAACGTTTA
1 CAAAACTTCATTTAATAATTTACGTGTTTTAATTATATTTCACGTCACGTTCAAA--AAAATTTA
** * * * *
1739854 ATACTCAAATTTAACTTTTATATGTGGTAGGTCTCGATCCTTCTTCTTTACCTATCATTCCAAAA
64 ATACTCAAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAA
* ** * * * *
1739919 TTTCACTTAATAATTT-TTTGTTTTAATTGTATTCCACGTCACATTCAAAATAACATTTAATA-T
129 TTTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTTAAAATAATATTTAATACT
* * * *
1739982 CCAAA-TCAACTTTTGCATTTTATAAGTTTAAACCTTCCTCTTCACCAATCATGCCAAAACTTCA
194 -CAAATTTAACTTTTGCATTGTATAAGTTCAAACCTTCCTCTTCACCAATCATACCAAAACTTCA
* * *
1740046 TTAAATAATTTGCGTGTTTTAATTATATTCCACGTCATGTTCAAAATAACATTTAATACCCAAAT
258 TTAAATAATTTACGTATTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCCAAAT
* * * *
1740111 TTAATTTTTATAAGTGGTAGGCCTCGAACCTT-TTTCTCTACCAATCATAC
323 TTAACTTTTACAAGTGGTAGGCCTCGAACATTCTTCCTCTACCAATCATAC
* * *
1740161 CAAAACTTCATTTAATAATTTGCGTGTTTTAATCATATTTCACATCACGTT-AAAAAAATTTAAT
1 CAAAACTTCATTTAATAATTTACGTGTTTTAATTATATTTCACGTCACGTTCAAAAAAATTTAAT
* * *
1740225 ACACAAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTTTTCTTTACCAATCATACCAAAACT
66 ACTCAAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAATT
* *
1740290 TCATTTAATAATTTACGTGTTTTAATCATATTCCACGCCACGTTTAAAATAATATTTAATACTCA
131 TCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTTAAAATAATATTTAATACTCA
** * * * * ** *
1740355 AATTTAACTTTTTTA-TGTAGTAGGTCTCGAACCTTCTTCTTTATTAATCATACCAAAATTTCAT
196 AATTTAACTTTTGCATTGTA-TAAGT-TCAAACCTTCCTCTTCACCAATCATACCAAAACTTCAT
* * * * * * *
1740419 TTAATAATTTACTTATTTTGATTATATTCCATGTCACGTTTAAAATAACATTTAATGCCCAAGTT
259 TAAATAATTTACGTATTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCCAAATT
* * * *
1740484 TAACTTTTGCATGTGGTAGGTCTCGAACATTCTTCCTTTACCAATCATAC
324 TAACTTTTACAAGTGGTAGGCCTCGAACATTCTTCCTCTACCAATCATAC
* * *
1740534 CAAAACTTTATTTAATAATTTACGTATTTTGATTATA-TTCTACGTCACGTTCAAAAAATATTTA
1 CAAAACTTCATTTAATAATTTACGTGTTTTAATTATATTTC-ACGTCACGTTCAAAAAA-ATTTA
* ** * * * *
1740598 ATACTCAAGTTTAACTTTTGCATACGATAAATCTCGAA---TCTTCTTTATCAATCATACCACAA
64 ATACTCAAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAA
* * *
1740660 TTTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCAAG-TTCAAA-AATATTTAATACC
129 TTTCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTTAAAATAATATTTAATACT
1740723 CAAATTTA
194 CAAATTTA
1740731 TGATTAAATT
Statistics
Matches: 483, Mismatches: 78, Indels: 20
0.83 0.13 0.03
Matches are distributed among these distances:
369 77 0.16
370 65 0.13
371 22 0.05
372 219 0.45
373 57 0.12
374 6 0.01
375 37 0.08
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (373 bp):
CAAAACTTCATTTAATAATTTACGTGTTTTAATTATATTTCACGTCACGTTCAAAAAAATTTAAT
ACTCAAATTTAACTTTTGCATGTGGTAAGTCTCGAACCTTCTTCTTTACCAATCATACCAAAATT
TCATTTAATAATTTACGTGTTTTAATTATATTCCACGTCACGTTTAAAATAATATTTAATACTCA
AATTTAACTTTTGCATTGTATAAGTTCAAACCTTCCTCTTCACCAATCATACCAAAACTTCATTA
AATAATTTACGTATTTTAATTATATTCCACGTCACGTTCAAAATAACATTTAATACCCAAATTTA
ACTTTTACAAGTGGTAGGCCTCGAACATTCTTCCTCTACCAATCATAC
Found at i:1741166 original size:17 final size:15
Alignment explanation
Indices: 1741136--1741169 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1741126 TTCGTATTTT
1741136 ATAAATTTATTAAAA
1 ATAAATTTATTAAAA
1741151 ATAAATATTAATTAAAA
1 ATAAAT-TT-ATTAAAA
1741168 AT
1 AT
1741170 TTTAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAATTTATTAAAA
Found at i:1750636 original size:15 final size:16
Alignment explanation
Indices: 1750616--1750649 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1750606 TGTAGAATAC
1750616 ATACATACATAT-TAT
1 ATACATACATATATAT
1750631 ATACATACATATATAT
1 ATACATACATATATAT
1750647 ATA
1 ATA
1750650 TATTCCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
ATACATACATATATAT
Found at i:1750636 original size:19 final size:18
Alignment explanation
Indices: 1750612--1750651 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1750602 TGAATGTAGA
1750612 ATACATACATACATATTAT
1 ATACATACATACATA-TAT
*
1750631 ATACATACATATATATAT
1 ATACATACATACATATAT
1750649 ATA
1 ATA
1750652 TTCCATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (18 bp):
ATACATACATACATATAT
Found at i:1750828 original size:2 final size:2
Alignment explanation
Indices: 1750821--1750845 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1750811 TTGCTGCATT
1750821 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1750846 TCCATGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1758841 original size:2 final size:2
Alignment explanation
Indices: 1758834--1758902 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
1758824 TCAAGTTTGG
1758834 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1758876 TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1758903 TGTTAAATAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1767294 original size:23 final size:21
Alignment explanation
Indices: 1767240--1767295 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
1767230 AAAGATATAT
* *
1767240 ATAAGATTAATTTTTAATAAAT
1 ATAA-ATTAAATTTTAATAAAA
*
1767262 ATAAAATAAATTTTATATAACAA
1 ATAAATTAAATTTTA-ATAA-AA
1767285 ATAAATTAAAT
1 ATAAATTAAAT
1767296 ACATCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 9 0.32
22 8 0.29
23 11 0.39
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAAATTAAATTTTAATAAAA
Found at i:1768495 original size:150 final size:150
Alignment explanation
Indices: 1768224--1768525 Score: 541
Period size: 150 Copynumber: 2.0 Consensus size: 150
1768214 TGTTCGAATA
* *
1768224 ATCACAAAGTAGATCATCATTAAAGCACAACCGGAATAAAAACTGGTTCACTTTAGACTAAAGCC
1 ATCACAAAGTAGATCATCATTAAAGCACAACCAGAATAAAAACTGGTGCACTTTAGACTAAAGCC
* *
1768289 AACACACTGAATTAACTTGACTAAAACCTACACATGACAATTGTACATGGTGAGACTTGAAGATC
66 AACACACTGAATTAACTTGACTAAAACCTACACATGACAATAGTACATGATGAGACTTGAAGATC
1768354 CACATATATAATTGCGTATG
131 CACATATATAATTGCGTATG
*
1768374 ATCACAAAGTAGATCATCATTAAAGCACAACCAGAATAAGAACTGGTGCACTTTAGACTAAAGCC
1 ATCACAAAGTAGATCATCATTAAAGCACAACCAGAATAAAAACTGGTGCACTTTAGACTAAAGCC
* *
1768439 AACACACTGAATTAACTTGACTAAAACCTACACATGACAATAGTATATTATGAGACTTGAAGATC
66 AACACACTGAATTAACTTGACTAAAACCTACACATGACAATAGTACATGATGAGACTTGAAGATC
1768504 CACATATATAATTGCGTATG
131 CACATATATAATTGCGTATG
1768524 AT
1 AT
1768526 GAATTTCAAA
Statistics
Matches: 145, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 145 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (150 bp):
ATCACAAAGTAGATCATCATTAAAGCACAACCAGAATAAAAACTGGTGCACTTTAGACTAAAGCC
AACACACTGAATTAACTTGACTAAAACCTACACATGACAATAGTACATGATGAGACTTGAAGATC
CACATATATAATTGCGTATG
Found at i:1769067 original size:18 final size:16
Alignment explanation
Indices: 1769025--1769074 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
1769015 ACTCTGCCCA
1769025 ATATATTATTTTAATTT
1 ATATATT-TTTTAATTT
*
1769042 A-ATATTTTATAATTT
1 ATATATTTTTTAATTT
1769057 CATATATTTTTT-ATTT
1 -ATATATTTTTTAATTT
1769073 AT
1 AT
1769075 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 10 0.34
16 10 0.34
17 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATATATTTTTTAATTT
Found at i:1778249 original size:52 final size:52
Alignment explanation
Indices: 1778163--1778272 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 52
1778153 TTATTTTGTA
* * * * *
1778163 TGTATTTAATCTATATTTCCTTATTGGGGTTATATGAAAGATCCAATCAACT
1 TGTATTCAATCTATATTTCCCTATTAGGGCTATATGAAAGATCCAATCAACC
1778215 TGTATTCAATCTATATTTCCCTATTAGGGCTATATGAAAGATCCAATCAACC
1 TGTATTCAATCTATATTTCCCTATTAGGGCTATATGAAAGATCCAATCAACC
1778267 TGTATT
1 TGTATT
1778273 TCCTCATCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (52 bp):
TGTATTCAATCTATATTTCCCTATTAGGGCTATATGAAAGATCCAATCAACC
Found at i:1787446 original size:16 final size:15
Alignment explanation
Indices: 1787422--1787472 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
1787412 GTTTGAGTTA
*
1787422 ATTTTAATTTGGATG
1 ATTTTAATTTGGATT
1787437 ATTTTAAATTTGGATT
1 ATTTT-AATTTGGATT
*
1787453 ATTTTTTATTTGGATT
1 A-TTTTAATTTGGATT
1787469 ATTT
1 ATTT
1787473 AAGTTTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 8 0.25
16 20 0.62
17 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (15 bp):
ATTTTAATTTGGATT
Found at i:1789982 original size:31 final size:32
Alignment explanation
Indices: 1789947--1790025 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
1789937 TTTTAAAAAA
* *
1789947 AAAATTTGAAATTTTATTATTT-TGACA-AATT
1 AAAATTGGAAATTTTATT-TTTCTGAAAGAATT
**
1789978 AAAATTGGAAATTTCCTTTTTCTGAAAGAATT
1 AAAATTGGAAATTTTATTTTTCTGAAAGAATT
1790010 AAAATTGGAAATTTTA
1 AAAATTGGAAATTTTA
1790026 ATCATGTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.08
31 19 0.47
32 18 0.45
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (32 bp):
AAAATTGGAAATTTTATTTTTCTGAAAGAATT
Found at i:1790381 original size:16 final size:15
Alignment explanation
Indices: 1790345--1790383 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1790335 ATTAAATATA
*
1790345 TTTTTTAATTTTGAG
1 TTTTTTAATTTTAAG
*
1790360 TTTTTTATATTTTAAT
1 TTTTTTA-ATTTTAAG
1790376 TTTTTTAA
1 TTTTTTAA
1790384 ATTATTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (15 bp):
TTTTTTAATTTTAAG
Found at i:1792865 original size:30 final size:31
Alignment explanation
Indices: 1792804--1792866 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1792794 TTTAATAACC
1792804 CAGTGACTTAAATAAAAATTTTCAGATAGTT
1 CAGTGACTTAAATAAAAATTTTCAGATAGTT
*
1792835 CAGTGACTTAAATCAAAACTTTT-A-ATAGTT
1 CAGTGACTTAAAT-AAAAATTTTCAGATAGTT
1792865 CA
1 CA
1792867 ATGATCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.27
31 14 0.47
32 8 0.27
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAATTTTCAGATAGTT
Found at i:1796014 original size:21 final size:21
Alignment explanation
Indices: 1795988--1796045 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 21
1795978 AAATATAATT
1795988 CATAAAAATTCAAAAAATTAA
1 CATAAAAATTCAAAAAATTAA
1796009 CAT-AAAA-T-AAACGTAAATTAA
1 CATAAAAATTCAAA---AAATTAA
1796030 CATAAAAAATTCAAAA
1 CAT-AAAAATTCAAAA
1796046 TATATTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 4 0.13
21 13 0.43
22 1 0.03
23 4 0.13
24 1 0.03
25 3 0.10
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (21 bp):
CATAAAAATTCAAAAAATTAA
Found at i:1797751 original size:99 final size:99
Alignment explanation
Indices: 1797574--1797886 Score: 452
Period size: 99 Copynumber: 3.2 Consensus size: 99
1797564 CACTAGTTTA
* *
1797574 GCACCCAATGCCTCATCAGATAAACCGAAGTAATAGTCGCGCCCAGCACTATAATGCAAGTGACA
1 GCACCCAGTGCCTCATCAGATAAACCGAAGTAATAGTCGCGCCCAGCGCTATAATGCAAGTGACA
* * *
1797639 CCCAATGTATCATCGGTTAAACCGAAGTAAATTG
66 CCCAGTGTCTCATCGGTTAAACCGAAGTAATTTG
* * * * *
1797673 GCACCCAGTGTCTCATCAGATAAACCGAAATAATAGTCGCGCCCAACGTTATAATGCAAGTAACA
1 GCACCCAGTGCCTCATCAGATAAACCGAAGTAATAGTCGCGCCCAGCGCTATAATGCAAGTGACA
*
1797738 CCCAGTGTCTCATCGGTTAAATCGAAGTAATTTG
66 CCCAGTGTCTCATCGGTTAAACCGAAGTAATTTG
* **
1797772 GCACCCAGTGCCTCATC-GAATAAACCGAAGTAATAGTCACAACCAGCGCTATATAT--AAGTGA
1 GCACCCAGTGCCTCATCAG-ATAAACCGAAGTAATAGTCGCGCCCAGCGCTATA-ATGCAAGTGA
*
1797834 CACCCAGTGTCTTATCGGTTAAACCGAAGTAATTTG
64 CACCCAGTGTCTCATCGGTTAAACCGAAGTAATTTG
1797870 GCACCCAGTGCCTCATC
1 GCACCCAGTGCCTCATC
1797887 GACTCGTGGT
Statistics
Matches: 191, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
98 57 0.30
99 132 0.69
100 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (99 bp):
GCACCCAGTGCCTCATCAGATAAACCGAAGTAATAGTCGCGCCCAGCGCTATAATGCAAGTGACA
CCCAGTGTCTCATCGGTTAAACCGAAGTAATTTG
Found at i:1797999 original size:2 final size:2
Alignment explanation
Indices: 1797992--1798019 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1797982 TAACTCAACA
1797992 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
1798020 TTTACATTTC
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:1806190 original size:17 final size:16
Alignment explanation
Indices: 1806150--1806194 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1806140 TAAAAAACTA
*
1806150 AAAAATA-TTTTATTT
1 AAAAATATTTTTATTC
*
1806165 AATAATATTTTTATCTC
1 AAAAATATTTTTAT-TC
1806182 AAAAATATTTTTA
1 AAAAATATTTTTA
1806195 AAAAGCAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 6 0.24
16 6 0.24
17 13 0.52
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
AAAAATATTTTTATTC
Found at i:1807585 original size:21 final size:21
Alignment explanation
Indices: 1807546--1807588 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1807536 ATTTTTCGAA
*
1807546 TCGAGTTGAGTAGAATGAAAT
1 TCGAGTTGAATAGAATGAAAT
* *
1807567 TCGAGTTGAATCGAGTGAAAT
1 TCGAGTTGAATAGAATGAAAT
1807588 T
1 T
1807589 GTTCGAGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGAGTTGAATAGAATGAAAT
Found at i:1807824 original size:22 final size:20
Alignment explanation
Indices: 1807801--1807840 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1807791 TATATATATA
* *
1807801 TATATAGATTTTGGATTTTT
1 TATAAAGATTTTGAATTTTT
*
1807821 TATAAATATTTTGAATTTTT
1 TATAAAGATTTTGAATTTTT
1807841 GAAAATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (20 bp):
TATAAAGATTTTGAATTTTT
Found at i:1807846 original size:19 final size:21
Alignment explanation
Indices: 1807808--1807852 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1807798 ATATATATAG
* *
1807808 ATTTTGGATTTTTTATAAA-T
1 ATTTTGAATTTTTGATAAATT
1807828 ATTTTGAATTTTTGA-AAATT
1 ATTTTGAATTTTTGATAAATT
1807848 ATTTT
1 ATTTT
1807853 CATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
ATTTTGAATTTTTGATAAATT
Found at i:1810076 original size:18 final size:19
Alignment explanation
Indices: 1810042--1810078 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1810032 CAGCTACACT
*
1810042 AATTTTTAACCGTAAATAA
1 AATTTTTAACAGTAAATAA
1810061 AATTTTTAACAG-AAATAA
1 AATTTTTAACAGTAAATAA
1810079 TCAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (19 bp):
AATTTTTAACAGTAAATAA
Found at i:1812674 original size:12 final size:13
Alignment explanation
Indices: 1812638--1812673 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
1812628 TAGCATTAAA
1812638 TTATTTGAAAATTT
1 TTATTT-AAAATTT
1812652 TTATTTAAAATTT
1 TTATTTAAAATTT
1812665 TTATTTAAA
1 TTATTTAAA
1812674 TCATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTATTTAAAATTT
Found at i:1820401 original size:57 final size:57
Alignment explanation
Indices: 1820336--1820533 Score: 299
Period size: 57 Copynumber: 3.5 Consensus size: 57
1820326 CACTAAACGA
* *
1820336 ATGACCTTTGCCTCCTTGACTTGGACCTGAATTGGGGTTGACAGCATCGGTAAATGC
1 ATGACCTTTGCCTCCTTGACTTGGACCTGAATTGGGTTTGACAGCATCAGTAAATGC
*
1820393 ATGACCTTTGCCTCCTTCACTTGGACCTGAATTGGGTTTGACAGCATCAGTAAATGC
1 ATGACCTTTGCCTCCTTGACTTGGACCTGAATTGGGTTTGACAGCATCAGTAAATGC
* * * *
1820450 ATGACCTTTGCCACC-AGAACTTGGACCTGAATTGGGTTTGACAGAATCACTAAATGC
1 ATGACCTTTGCCTCCTTG-ACTTGGACCTGAATTGGGTTTGACAGCATCAGTAAATGC
* *
1820507 ATGACCTTTGCCTCCTGGACTAGGACC
1 ATGACCTTTGCCTCCTTGACTTGGACC
1820534 ACCGGTCTTG
Statistics
Matches: 128, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
57 127 0.99
58 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (57 bp):
ATGACCTTTGCCTCCTTGACTTGGACCTGAATTGGGTTTGACAGCATCAGTAAATGC
Found at i:1822992 original size:4 final size:4
Alignment explanation
Indices: 1822976--1823024 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
1822966 AACGGGTATT
* * *
1822976 GAAA GAAA AAAA GAAA GAAA GAAA G-AA GGAA GAAT GAGAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
1823024 G
1 G
1823025 GAGAAGGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
3 3 0.08
4 32 0.84
5 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:1823017 original size:20 final size:20
Alignment explanation
Indices: 1822994--1823039 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1822984 AAAAGAAAGA
*
1822994 AAGAAAG-AAGGAAGAATGAG
1 AAGAAAGAAAGG-AGAAGGAG
1823014 AAGAAAGAAAGGAGAAGGAG
1 AAGAAAGAAAGGAGAAGGAG
1823034 -AGAAAG
1 AAGAAAG
1823040 TCAATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
21 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (20 bp):
AAGAAAGAAAGGAGAAGGAG
Found at i:1825534 original size:6 final size:6
Alignment explanation
Indices: 1825525--1825565 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1825515 AGCCAGATCC
* *
1825525 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA GGAAGA AGAGG
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGG
1825566 TATTGGATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:1825695 original size:45 final size:45
Alignment explanation
Indices: 1825628--1825718 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
1825618 CCCTAGCTCA
* * *
1825628 TCAAGCCAATGATATCAGCCTCAGTTTGACGAGCCATCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
*
1825673 TCAAGCCAAGGATATCATCCTCAGTTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
1825718 T
1 T
1825719 TTACTCCTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCACAATAC
Found at i:1828101 original size:12 final size:12
Alignment explanation
Indices: 1828084--1828114 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1828074 TGTGTAACTA
1828084 GATTTTCGACTG
1 GATTTTCGACTG
1828096 GATTTTCGACTG
1 GATTTTCGACTG
1828108 GATTTTC
1 GATTTTC
1828115 ATCGTCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (12 bp):
GATTTTCGACTG
Found at i:1828754 original size:19 final size:19
Alignment explanation
Indices: 1828708--1828755 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1828698 AATAAATCTG
1828708 TTTAAAAAT-AAATAAAAT
1 TTTAAAAATAAAATAAAAT
*
1828726 TTTAATAAATAAAATACGAA-
1 TTTAA-AAATAAAATA-AAAT
1828746 TTTAAAAATA
1 TTTAAAAATA
1828756 TATCATACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 10 0.38
21 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
TTTAAAAATAAAATAAAAT
Found at i:1828817 original size:4 final size:4
Alignment explanation
Indices: 1828810--1828851 Score: 75
Period size: 4 Copynumber: 10.2 Consensus size: 4
1828800 TCATTCTTCC
1828810 TTCT TTCT TTCT TTCT TTCT TTCTT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTCT T
1828852 CTTCTGCCCG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:1830642 original size:13 final size:13
Alignment explanation
Indices: 1830624--1830650 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1830614 GATTTGAAGG
1830624 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
1830637 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
1830650 A
1 A
1830651 GAAGGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:1835118 original size:16 final size:18
Alignment explanation
Indices: 1835097--1835133 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1835087 ACATATTGTT
*
1835097 AAAATATTAA-TT-TATA
1 AAAATATAAAGTTGTATA
1835113 AAAATATAAAGTTGTATA
1 AAAATATAAAGTTGTATA
1835131 AAA
1 AAA
1835134 TTACTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAATATAAAGTTGTATA
Found at i:1836713 original size:17 final size:18
Alignment explanation
Indices: 1836691--1836727 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1836681 CAGCAAATTT
*
1836691 TATTTTTT-ATTTAAAAG
1 TATTTTTTGATTCAAAAG
1836708 TATTTTTTGATTCAAAAG
1 TATTTTTTGATTCAAAAG
1836726 TA
1 TA
1836728 CTTCTGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (18 bp):
TATTTTTTGATTCAAAAG
Found at i:1839292 original size:18 final size:18
Alignment explanation
Indices: 1839269--1839305 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1839259 ACAATTCACA
1839269 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
1839287 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
1839305 T
1 T
1839306 TGCTCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:1842038 original size:22 final size:22
Alignment explanation
Indices: 1842013--1842063 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1842003 AGATAAGTAT
1842013 TTGTATTTGCAATTATATTATC
1 TTGTATTTGCAATTATATTATC
1842035 TTGTATTTGCAATTATATTATC
1 TTGTATTTGCAATTATATTATC
1842057 TTGTATT
1 TTGTATT
1842064 AGTAGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (22 bp):
TTGTATTTGCAATTATATTATC
Found at i:1850454 original size:24 final size:23
Alignment explanation
Indices: 1850427--1850471 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1850417 ATTGGGGGAT
*
1850427 AAGTAGGAGGCAAATTATGGTGAG
1 AAGT-GGAAGCAAATTATGGTGAG
* *
1850451 AAGTGGAAGCCAATTTTGGTG
1 AAGTGGAAGCAAATTATGGTG
1850472 TAAAACCCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.33, C:0.07, G:0.36, T:0.24
Consensus pattern (23 bp):
AAGTGGAAGCAAATTATGGTGAG
Found at i:1853614 original size:2 final size:2
Alignment explanation
Indices: 1853603--1853652 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1853593 AAGAACACAC
*
1853603 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1853645 AT AT AT AT
1 AT AT AT AT
1853653 GTAGACATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1857255 original size:215 final size:215
Alignment explanation
Indices: 1856884--1857327 Score: 856
Period size: 215 Copynumber: 2.1 Consensus size: 215
1856874 ATTGATCATG
*
1856884 TAATGCTACCAAGCAGTGAAATCAACTTGTCAACAATGTTTTACATCATTCAACCGTAAGAATTG
1 TAATGCTACCAAGCAGTGAAATCAACTTGTCAACAATGTTTTACATCATTCAACCATAAGAATTG
1856949 AAAAATCACTTAAAGAACATCTATTGACATAGCAAAAAGAACCACTTAAAATTGATTAGTCATAA
66 AAAAATCACTTAAAGAACATCTATTGACATAGCAAAAAGAACCACTTAAAATTGATTAGTCATAA
1857014 TTAAACATGGTTGTTCCAAGAATCACTAATATACTGAAGTTCTATCCATGTTAGTTGGTAGCACA
131 TTAAACATGGTTGTTCCAAGAATCACTAATATACTGAAGTTCTATCCATGTTAGTTGGTAGCACA
1857079 CCACCACCAGCAATGACATA
196 CCACCACCAGCAATGACATA
1857099 TAATGCTACCAAGCAGTGAAATCAACTTGTCAACAATGTTTTACATCATTCAACCATAAGAATTG
1 TAATGCTACCAAGCAGTGAAATCAACTTGTCAACAATGTTTTACATCATTCAACCATAAGAATTG
1857164 AAAAATCACTTAAAGAACATCTATTGACATAGCAAAAAGAACCACTTAAAATTGATTAGTCATAA
66 AAAAATCACTTAAAGAACATCTATTGACATAGCAAAAAGAACCACTTAAAATTGATTAGTCATAA
1857229 TTAAACATGGTTGTTCCAAGAATCACTAATATACTGAAGTTCTATCCATGTTAGTTGGTAGCACA
131 TTAAACATGGTTGTTCCAAGAATCACTAATATACTGAAGTTCTATCCATGTTAGTTGGTAGCACA
1857294 CCACCACCAGCAATGACATA
196 CCACCACCAGCAATGACATA
1857314 TACAT-CT-CCAAGCA
1 TA-ATGCTACCAAGCA
1857328 ACAACATGAA
Statistics
Matches: 227, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
214 7 0.03
215 218 0.96
216 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (215 bp):
TAATGCTACCAAGCAGTGAAATCAACTTGTCAACAATGTTTTACATCATTCAACCATAAGAATTG
AAAAATCACTTAAAGAACATCTATTGACATAGCAAAAAGAACCACTTAAAATTGATTAGTCATAA
TTAAACATGGTTGTTCCAAGAATCACTAATATACTGAAGTTCTATCCATGTTAGTTGGTAGCACA
CCACCACCAGCAATGACATA
Found at i:1861430 original size:2 final size:2
Alignment explanation
Indices: 1861423--1861452 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1861413 ATTATAAACT
1861423 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1861453 ACCAACAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1870775 original size:22 final size:22
Alignment explanation
Indices: 1870750--1870792 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1870740 TGACTCAAAC
1870750 TTAAAAC-AATAAAAAAATTAAA
1 TTAAAACGAAT-AAAAAATTAAA
* *
1870772 TTAACACGAATATAAAATTAA
1 TTAAAACGAATAAAAAATTAA
1870793 TCCAAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (22 bp):
TTAAAACGAATAAAAAATTAAA
Found at i:1876710 original size:15 final size:15
Alignment explanation
Indices: 1876673--1876718 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1876663 TTAGGTTTTT
*
1876673 TATTAAAATAATACA
1 TATTAAAATAATATA
* **
1876688 AAAAAAAATAATATA
1 TATTAAAATAATATA
1876703 TATTAAAATAATATA
1 TATTAAAATAATATA
1876718 T
1 T
1876719 TCCTCCCGTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TATTAAAATAATATA
Found at i:1876911 original size:27 final size:27
Alignment explanation
Indices: 1876873--1876935 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
1876863 GTATAAATGG
1876873 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
1876900 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
1876927 ATGGTGCCT
1 GTGGTGCCT
1876936 TTCTATCAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.16, C:0.32, G:0.33, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:1876944 original size:27 final size:27
Alignment explanation
Indices: 1876874--1876954 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
1876864 TATAAATGGG
*
1876874 TGGTGCCTACCTGA-CAGGCGGCACCAG
1 TGGTGCCTACCT-ATCAGGCGGCACCAA
*
1876901 TGGTGCCTACCTGTCAGGCGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
** *
1876928 TGGTGCCTTTCTATCAGGTGGCACCAA
1 TGGTGCCTACCTATCAGGCGGCACCAA
1876955 CTCGTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.19, C:0.31, G:0.30, T:0.21
Consensus pattern (27 bp):
TGGTGCCTACCTATCAGGCGGCACCAA
Found at i:1877100 original size:20 final size:23
Alignment explanation
Indices: 1877063--1877103 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
1877053 TTTTAATAAA
1877063 TATAAGAATTGTAGAAAAAATAT
1 TATAAGAATTGTAGAAAAAATAT
1877086 TATAA-AATT-TA-AAAAAAT
1 TATAAGAATTGTAGAAAAAAT
1877104 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 4 0.22
23 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (23 bp):
TATAAGAATTGTAGAAAAAATAT
Found at i:1877222 original size:57 final size:55
Alignment explanation
Indices: 1877108--1877238 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 55
1877098 AAAAATTAAA
* * *
1877108 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
** * *
1877163 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAA-AAAATAT
1877220 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
1877239 CACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 13 0.21
56 15 0.24
57 29 0.46
58 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
Found at i:1877343 original size:27 final size:27
Alignment explanation
Indices: 1877302--1877362 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
1877292 TTATACAAGA
1877302 GGTGCCTACCAGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
**
1877329 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
1877356 GGTGCCT
1 GGTGCCT
1877363 TTGTCAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.39, T:0.21
Consensus pattern (27 bp):
GGTGCCTACCAGGTAGGCGGCACTAGT
Found at i:1877432 original size:25 final size:25
Alignment explanation
Indices: 1877397--1877446 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1877387 CAGATCTGTT
1877397 TAACAGAAAATTTTTGAAGAAGGAA
1 TAACAGAAAATTTTTGAAGAAGGAA
*
1877422 TAACAGTAAATTTTTGAAGAAGGAA
1 TAACAGAAAATTTTTGAAGAAGGAA
1877447 AGGAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (25 bp):
TAACAGAAAATTTTTGAAGAAGGAA
Found at i:1877494 original size:26 final size:26
Alignment explanation
Indices: 1877437--1877494 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1877427 GTAAATTTTT
* * *
1877437 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
1877463 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
1877489 GCAGAA
1 GAAGAA
1877495 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:1880294 original size:28 final size:28
Alignment explanation
Indices: 1880241--1880298 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1880231 CATTTTTCTG
*
1880241 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
1880269 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
1880297 TT
1 TT
1880299 ATTTAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:1880339 original size:26 final size:26
Alignment explanation
Indices: 1880290--1880339 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1880280 TCTATTTAAA
* *
1880290 TTTGAATTTATTTAATAGTTTTTATG
1 TTTGAATTAATTTAATAGTGTTTATG
1880316 TTTGAATTAATTTAATTAG-GTTTA
1 TTTGAATTAATTTAA-TAGTGTTTA
1880340 GCAAATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAGTGTTTATG
Found at i:1880416 original size:6 final size:6
Alignment explanation
Indices: 1880405--1880463 Score: 93
Period size: 6 Copynumber: 9.8 Consensus size: 6
1880395 ATATTTGCAT
*
1880405 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATAA ACATAA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATAA
1880453 ACATAA ACATA
1 ACATAA ACATA
1880464 TTTAATGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
5 1 0.02
6 47 0.96
7 1 0.02
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:1880906 original size:6 final size:6
Alignment explanation
Indices: 1880896--1880932 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1880886 CTGCGACTGC
*
1880896 GGCTCA AGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA GGCTCA G
1880933 CCGGCTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:1882936 original size:17 final size:16
Alignment explanation
Indices: 1882904--1882935 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1882894 TTTTTTTAAA
1882904 AAAATATTTAATATAT
1 AAAATATTTAATATAT
1882920 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
1882935 A
1 A
1882936 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:1883942 original size:27 final size:27
Alignment explanation
Indices: 1883912--1883973 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1883902 CTGGTAGGTT
1883912 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
1883939 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
1883966 GGCACCAC
1 GGCACCAC
1883974 CCAAAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.10
Consensus pattern (27 bp):
GGCACCACTGGTGCCGCCTACCAGACA
Found at i:1888816 original size:25 final size:25
Alignment explanation
Indices: 1888785--1888838 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
1888775 ATTATAAGAT
1888785 TCATGATTTCATGCCATCATCATCA
1 TCATGATTTCATGCCATCATCATCA
1888810 TCATGATTTCATGCCATCATCATCA
1 TCATGATTTCATGCCATCATCATCA
1888835 TCAT
1 TCAT
1888839 CATATATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (25 bp):
TCATGATTTCATGCCATCATCATCA
Found at i:1897990 original size:18 final size:18
Alignment explanation
Indices: 1897967--1898012 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1897957 TTTGTTCACA
* * *
1897967 GGTTTTGGTGTTGGGTGT
1 GGTTTTGGAGTTGGATGG
1897985 GGTTTTGGAGTTGGATGG
1 GGTTTTGGAGTTGGATGG
1898003 GGTTTTGGAG
1 GGTTTTGGAG
1898013 GTCTGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (18 bp):
GGTTTTGGAGTTGGATGG
Found at i:1904041 original size:17 final size:18
Alignment explanation
Indices: 1904014--1904047 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1904004 TTTTTCAGTC
1904014 AAAATGAAAAACAAAACT
1 AAAATGAAAAACAAAACT
*
1904032 AAAA-GAAAAAGAAAAC
1 AAAATGAAAAACAAAAC
1904048 AAGCAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.09, G:0.09, T:0.06
Consensus pattern (18 bp):
AAAATGAAAAACAAAACT
Found at i:1906227 original size:29 final size:29
Alignment explanation
Indices: 1906175--1906232 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1906165 TCACAAATTG
* *
1906175 GACTTATTTGATTCTTTTTAATAATATAAA
1 GACTAATTTGATTCTATTTAATAA-ATAAA
1906205 GACTAATTTGATT-TATTTAATAAATAAA
1 GACTAATTTGATTCTATTTAATAAATAAA
1906233 TCATAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 9 0.35
30 12 0.46
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (29 bp):
GACTAATTTGATTCTATTTAATAAATAAA
Found at i:1907337 original size:59 final size:58
Alignment explanation
Indices: 1907267--1907388 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 58
1907257 TATATATTTT
* *** *
1907267 GGTACCTAAACTTTG-C-TTAAAGGTTTAATTTGATACCTAAGTTTTTTTGGGTCTAATTA
1 GGTACCTAAAC-TTGACATT-AAGGTTCAATTTGATACCTAAACGTTTTT-GGTCCAATTA
* *
1907326 GGTATCTAAACTTGACATTAAGGTTCAATTTGATATCTAAACGTTTTTGGTCCAATTA
1 GGTACCTAAACTTGACATTAAGGTTCAATTTGATACCTAAACGTTTTTGGTCCAATTA
1907384 GGTAC
1 GGTAC
1907389 TTGAATTTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
58 16 0.30
59 35 0.66
60 2 0.04
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (58 bp):
GGTACCTAAACTTGACATTAAGGTTCAATTTGATACCTAAACGTTTTTGGTCCAATTA
Found at i:1913304 original size:33 final size:32
Alignment explanation
Indices: 1913244--1913312 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
1913234 AATTCTCTAG
1913244 TTATTTTATATATTCTTCAAATAATATTTCAA
1 TTATTTTATATATTCTTCAAATAATATTTCAA
* *
1913276 TTATATTTATTTATT-TTCATATAGATATTT-AA
1 TTAT-TTTATATATTCTTCAAATA-ATATTTCAA
1913308 -TATTT
1 TTATTT
1913313 AATCTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 2 0.06
31 3 0.09
32 13 0.39
33 15 0.45
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (32 bp):
TTATTTTATATATTCTTCAAATAATATTTCAA
Found at i:1914756 original size:16 final size:15
Alignment explanation
Indices: 1914723--1914754 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1914713 AATTTAATCA
*
1914723 TTAATATTTATTTTT
1 TTAAAATTTATTTTT
1914738 TTAAAATTTATTTTT
1 TTAAAATTTATTTTT
1914753 TT
1 TT
1914755 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTAAAATTTATTTTT
Found at i:1917909 original size:57 final size:57
Alignment explanation
Indices: 1917840--1918007 Score: 205
Period size: 59 Copynumber: 2.9 Consensus size: 57
1917830 TTAATAGAAT
* * * *
1917840 ATTTGGTACTTGAATTTGACACCTTTTTTTAATTTAGTATCTAAATTTTTTT-ACTCA
1 ATTTGGTACTTGAACTTGACA-CTTTTTTTAATTTGGTACCTAAATTTTTTTAACCCA
* **
1917897 ATTTGGTACTTGAACTTGACACATTTCCTAATTTGGTACCTAAACTTTTTTTAGACCCA
1 ATTTGGTACTTGAACTTGACACTTTTTTTAATTTGGTACCTAAA-TTTTTTTA-ACCCA
*
1917956 ATTTGGTACTTGAACTTGACA-TTTTTTCCTAATTTGGTACCTAAGTTTTTTT
1 ATTTGGTACTTGAACTTGACACTTTTTT--TAATTTGGTACCTAAATTTTTTT
1918008 TAGATTCAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
56 18 0.19
57 27 0.28
58 3 0.03
59 32 0.34
60 15 0.16
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (57 bp):
ATTTGGTACTTGAACTTGACACTTTTTTTAATTTGGTACCTAAATTTTTTTAACCCA
Found at i:1917967 original size:59 final size:59
Alignment explanation
Indices: 1917840--1918024 Score: 232
Period size: 60 Copynumber: 3.2 Consensus size: 59
1917830 TTAATAGAAT
* ** * *
1917840 ATTTGGTACTTGAATTTGACACCTTTTTTTAATTTAGTATCTAAATTTTTTT--ACTCA
1 ATTTGGTACTTGAACTTGACACCTTTTCCTAATTTGGTACCTAAATTTTTTTAGACTCA
* *
1917897 ATTTGGTACTTGAACTTGACA-CATTTCCTAATTTGGTACCTAAACTTTTTTTAGACCCA
1 ATTTGGTACTTGAACTTGACACCTTTTCCTAATTTGGTACCTAAA-TTTTTTTAGACTCA
** * *
1917956 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAGTTTTTTTTAGATTCA
1 ATTTGGTACTTGAACTTGACACCTTTTCCTAATTTGGTACCTAA-ATTTTTTTAGACTCA
1918016 ATTTGGTAC
1 ATTTGGTAC
1918025 CTAAATTTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
56 18 0.16
57 27 0.24
59 25 0.23
60 41 0.37
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACCTTTTCCTAATTTGGTACCTAAATTTTTTTAGACTCA
Found at i:1918266 original size:32 final size:31
Alignment explanation
Indices: 1918230--1918310 Score: 108
Period size: 32 Copynumber: 2.6 Consensus size: 31
1918220 GGATCCCAAA
* *
1918230 AAGTTTAAGTACGAACTTAAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAA-TGTC
* *
1918262 AAGTTTAGGTACCAAATTAAGAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
*
1918293 AAGTTTGAGTACCAAATT
1 AAGTTTAAGTACCAAATT
1918311 GGACCAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 20 0.47
32 23 0.53
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAATGTC
Found at i:1918293 original size:31 final size:31
Alignment explanation
Indices: 1918230--1918368 Score: 103
Period size: 31 Copynumber: 4.5 Consensus size: 31
1918220 GGATCCCAAA
* * * *
1918230 AAGTTTAAGTACGAACTTAAAAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAAGAAAAAA-TGTC
1918262 AAGTTTAGGTACCAAATTAAGAAAAAATGTC
1 AAGTTTAGGTACCAAATTAAGAAAAAATGTC
*
1918293 AAGTTT-GAGTACCAAATT-GGACCAAAAA----
1 AAGTTTAG-GTACCAAATTAAGA--AAAAATGTC
* * *
1918321 AAGTTTAGGTATCAAATTAGGAAAAAATATC
1 AAGTTTAGGTACCAAATTAAGAAAAAATGTC
*
1918352 AAATTT-GAGTACCAAAT
1 AAGTTTAG-GTACCAAAT
1918369 ATTATATTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.06
28 15 0.17
29 4 0.04
30 4 0.04
31 33 0.37
32 28 0.31
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAAGAAAAAATGTC
Found at i:1918346 original size:91 final size:90
Alignment explanation
Indices: 1918175--1918368 Score: 200
Period size: 91 Copynumber: 2.1 Consensus size: 90
1918165 TAAAAAAAGA
* ** *
1918175 TTAGGTACCAAATTAGGAGAAAAAGTCAAGTTCAGGTATTAAATTGGATCCCAAAAAGTTTAAGT
1 TTAGGTACCAAATTAAGAGAAAAAGTCAAGTTCAGGTACCAAATTGGATCCAAAAAAGTTTAAGT
* * *
1918240 ACGAACTTAAAAAAAAAGTGTCAAGT
66 ACGAAATTAAAAAAAAA-TATCAAAT
*
1918266 TTAGGTACCAAATTAAGA-AAAAATGTCAAGTT-TGAGTACCAAATTGGA-CCAAAAAAAGTTTA
1 TTAGGTACCAAATTAAGAGAAAAA-GTCAAGTTCAG-GTACCAAATTGGATCC-AAAAAAGTTTA
* **
1918328 GGTATC-AAATTAGGAAAAAATATCAAAT
63 AGTA-CGAAATTAAAAAAAAATATCAAAT
1918356 TT-GAGTACCAAAT
1 TTAG-GTACCAAAT
1918369 ATTATATTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
89 1 0.01
90 25 0.29
91 60 0.69
92 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (90 bp):
TTAGGTACCAAATTAAGAGAAAAAGTCAAGTTCAGGTACCAAATTGGATCCAAAAAAGTTTAAGT
ACGAAATTAAAAAAAAATATCAAAT
Found at i:1918972 original size:24 final size:23
Alignment explanation
Indices: 1918919--1918962 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1918909 GCATAAACAT
* *
1918919 AAAAAAACTTTTAGGACCATAAC
1 AAAAAAACCTTTAGGACCACAAC
1918942 AAAAAAACCTTTAGGACCACA
1 AAAAAAACCTTTAGGACCACA
1918963 GGAGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.20, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAAAACCTTTAGGACCACAAC
Found at i:1922825 original size:6 final size:6
Alignment explanation
Indices: 1922814--1922846 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1922804 CAAAGCTAAA
1922814 CCATCT CCATCT CCATCT CCATCT CCATCT CCA
1 CCATCT CCATCT CCATCT CCATCT CCATCT CCA
1922847 ACCGCTACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (6 bp):
CCATCT
Found at i:1927569 original size:23 final size:24
Alignment explanation
Indices: 1927523--1927569 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1927513 GCCCAAATTA
*
1927523 GTCTTTAAATTTAACAAATTGTTT
1 GTCTTTAAACTTAACAAATTGTTT
*
1927547 GTCTTTAAACTTGAC-AATTGTTT
1 GTCTTTAAACTTAACAAATTGTTT
1927570 TTACATTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (24 bp):
GTCTTTAAACTTAACAAATTGTTT
Found at i:1936810 original size:142 final size:141
Alignment explanation
Indices: 1936632--1936966 Score: 435
Period size: 142 Copynumber: 2.4 Consensus size: 141
1936622 TAATGGTTGA
** * * **
1936632 ATTAATTATTAACTTTAATTTTTGGTGAATTACAAGAGGATGACAAAGCTTTAACAACAACAAAA
1 ATTAATTATTAACTTTTTTTTTTGGTGAATTACAAGAGGAGGACAAAACCCTAACAACAACAAAA
* *
1936697 CTAGCGCAACTCGAACCCAAATCACATCTGGGATGGTGAACACCCTGACCATCAGGGGGCCAACA
66 CTAGCGCAACTCGAACCCAAACCACATCTGGGATGGTGAACACCCTGACCATCAGAGGGCCAACA
1936762 CAAGGATTCAG
131 CAAGGATTCAG
* * * *
1936773 ATTAATTATTAACTTTTTTTCTTTGGTGAATTACAAGAGAAGGGCAAAACCCTAACAGCAACACA
1 ATTAATTATTAACTTTTTTT-TTTGGTGAATTACAAGAGGAGGACAAAACCCTAACAACAACAAA
** * * * *
1936838 ACTAGCGTGACTCGAACCCAGACCACATCTGGGATGGTGAATACCTTGCCCATCAGAGGGCCAAC
65 ACTAGCGCAACTCGAACCCAAACCACATCTGGGATGGTGAACACCCTGACCATCAGAGGGCCAAC
*
1936903 ACACGGATTCAG
130 ACAAGGATTCAG
* * *
1936915 ATT-ATTATTAAC--TTTTTTTT-GTGAATTACAAGAGGAAGATAAAATCCTAACA
1 ATTAATTATTAACTTTTTTTTTTGGTGAATTACAAGAGGAGGACAAAACCCTAACA
1936967 GTAACACGAG
Statistics
Matches: 169, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
137 27 0.16
138 3 0.02
139 5 0.03
141 27 0.16
142 107 0.63
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (141 bp):
ATTAATTATTAACTTTTTTTTTTGGTGAATTACAAGAGGAGGACAAAACCCTAACAACAACAAAA
CTAGCGCAACTCGAACCCAAACCACATCTGGGATGGTGAACACCCTGACCATCAGAGGGCCAACA
CAAGGATTCAG
Found at i:1937028 original size:137 final size:141
Alignment explanation
Indices: 1936632--1937029 Score: 358
Period size: 142 Copynumber: 2.8 Consensus size: 141
1936622 TAATGGTTGA
* * * * ** * *
1936632 ATTAATTATTAACTTTAATT-TTTGGTGAATTACAAGAGGATGACAAAGCTTTAACAACAACAAA
1 ATTAATTATTAACTTT-TTTCTTTGGTGAATTACAAGAGAAGGACAAAACCCTAACAGCAACACA
* * * * * *** * *
1936696 ACTAGCGCAACTCGAACCCAAATCACATCTGGGATGGTGAACACCCTGACCATCAGGGGGCCAAC
65 ACTAGCACGACTCAAACCCAAACCACACCCAAGATGGTGAATACCCTGACCATCAGAGGGCCAAC
1936761 ACAAGGATTCAG
130 ACAAGGATTCAG
*
1936773 ATTAATTATTAACTTTTTTTCTTTGGTGAATTACAAGAGAAGGGCAAAACCCTAACAGCAACACA
1 ATTAATTATTAAC-TTTTTTCTTTGGTGAATTACAAGAGAAGGACAAAACCCTAACAGCAACACA
** * * * *** * *
1936838 ACTAGCGTGACTCGAACCCAGACCACATCTGGGATGGTGAATACCTTGCCCATCAGAGGGCCAAC
65 ACTAGCACGACTCAAACCCAAACCACACCCAAGATGGTGAATACCCTGACCATCAGAGGGCCAAC
*
1936903 ACACGGATTCAG
130 ACAAGGATTCAG
* * * *
1936915 ATT-ATTATTAAC-TTTTT-TTT-GTGAATTACAAGAGGAA-GATAAAATCCTAACAGTAACACG
1 ATTAATTATTAACTTTTTTCTTTGGTGAATTACAAGA-GAAGGACAAAACCCTAACAGCAACACA
* * ** * * *
1936975 AGTAGTACGACTCAAACGTAAATCACACCCAAGATGATGAATACCCTAACCATCA
65 ACTAGCACGACTCAAACCCAAACCACACCCAAGATGGTGAATACCCTGACCATCA
1937030 AACTGAAACG
Statistics
Matches: 214, Mismatches: 40, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
137 69 0.32
138 6 0.03
139 5 0.02
141 24 0.11
142 110 0.51
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (141 bp):
ATTAATTATTAACTTTTTTCTTTGGTGAATTACAAGAGAAGGACAAAACCCTAACAGCAACACAA
CTAGCACGACTCAAACCCAAACCACACCCAAGATGGTGAATACCCTGACCATCAGAGGGCCAACA
CAAGGATTCAG
Found at i:1938855 original size:29 final size:29
Alignment explanation
Indices: 1938823--1938921 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
1938813 AAAAGGGTCT
*
1938823 AATTTTTTTTTTAATTTTTAAGGGGTCCA
1 AATTTTTTTTTTAACTTTTAAGGGGTCCA
**
1938852 AATTTTTTTTTTAACTTTTATA--GGTTAA
1 AATTTTTTTTTTAACTTTTA-AGGGGTCCA
* **
1938880 AATTTTTTTTATCAACTTTTAAGGGCCCCA
1 AATTTTTTTT-TTAACTTTTAAGGGGTCCA
*
1938910 ATTTTTTTTTTT
1 AATTTTTTTTTT
1938922 TTAGTTTTTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
28 15 0.27
29 29 0.52
30 12 0.21
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (29 bp):
AATTTTTTTTTTAACTTTTAAGGGGTCCA
Found at i:1940119 original size:2 final size:2
Alignment explanation
Indices: 1940112--1940146 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1940102 TTGACATTTT
1940112 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1940147 TGGATAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1952552 original size:21 final size:21
Alignment explanation
Indices: 1952528--1952567 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1952518 ATCTGACTTG
1952528 TTTTATATTT-TTGTAATATAT
1 TTTTAT-TTTATTGTAATATAT
*
1952549 TTTTATTTTATTGTTATAT
1 TTTTATTTTATTGTAATAT
1952568 GTTATGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTATTTTATTGTAATATAT
Found at i:1956249 original size:7 final size:8
Alignment explanation
Indices: 1956230--1956257 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1956220 TATTCAATTT
1956230 TTTTTCAC
1 TTTTTCAC
1956238 TTTTTCAC
1 TTTTTCAC
1956246 TTTTTCAC
1 TTTTTCAC
1956254 TTTT
1 TTTT
1956258 AACCCATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (8 bp):
TTTTTCAC
Found at i:1956844 original size:14 final size:15
Alignment explanation
Indices: 1956809--1956842 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1956799 CAAATCTTCT
1956809 AAAAATTTTTATTAA
1 AAAAATTTTTATTAA
1956824 AAAAATTATTT-TTAA
1 AAAAATT-TTTATTAA
1956839 AAAA
1 AAAA
1956843 TTCTTCGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAATTTTTATTAA
Found at i:1957465 original size:115 final size:116
Alignment explanation
Indices: 1957243--1957457 Score: 371
Period size: 115 Copynumber: 1.9 Consensus size: 116
1957233 CTTTGGATTA
*
1957243 TATTTCTTTCATTGGTCCTACACGCATTTGCTTTATTTTCATTGCTTTCTACTTTCTTTCACTTT
1 TATTTCTTTCATTGGTCCTACACGCATCTGCTTTATTTTCATTGCTTTCTACTTTCTTTCACTTT
*
1957308 TTCCACGTACTTTATTGCAATAGTCAAAAGTTTGGCGCATATGCACAATCG
66 TTCCACGTACTTTACTGCAATAGTCAAAAGTTTGGCGCATATGCACAATCG
1957359 TATTTC-TTCATTGGTCCTACACGCATCTGCTTTATTTTCATTGCTTTCTACTTTCTTTC-CTTC
1 TATTTCTTTCATTGGTCCTACACGCATCTGCTTTATTTTCATTGCTTTCTACTTTCTTTCACTT-
* *
1957422 TTTCCACGTACTTTACTGCCATTGTCAAAAGTTTGG
65 TTTCCACGTACTTTACTGCAATAGTCAAAAGTTTGG
1957458 TTCATATGAA
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
114 3 0.03
115 85 0.90
116 6 0.06
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.46
Consensus pattern (116 bp):
TATTTCTTTCATTGGTCCTACACGCATCTGCTTTATTTTCATTGCTTTCTACTTTCTTTCACTTT
TTCCACGTACTTTACTGCAATAGTCAAAAGTTTGGCGCATATGCACAATCG
Found at i:1968103 original size:25 final size:24
Alignment explanation
Indices: 1968068--1968123 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1968058 ACTAGCGCGC
1968068 TCTCTG-TTTAGCAC-GTCTCGTGA
1 TCTCTGTTTTAGCACTGTCT-GTGA
* *
1968091 TCTCTGTTATTAGCACTGTGTGTGC
1 TCTCTGTT-TTAGCACTGTCTGTGA
1968116 TCTCTGTT
1 TCTCTGTT
1968124 GCCCAGCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.21
24 1 0.04
25 18 0.64
26 3 0.11
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (24 bp):
TCTCTGTTTTAGCACTGTCTGTGA
Found at i:1969961 original size:3 final size:3
Alignment explanation
Indices: 1969953--1969995 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1969943 AAATTTGTCA
1969953 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1969996 TGAAAGTACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1974831 original size:2 final size:2
Alignment explanation
Indices: 1974824--1974862 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1974814 TGACAAATAC
1974824 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1974863 GATTTGAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1978651 original size:51 final size:51
Alignment explanation
Indices: 1978562--1978700 Score: 136
Period size: 51 Copynumber: 2.7 Consensus size: 51
1978552 ATGTAAATGA
* * *
1978562 TGACAGAATGTGTAAATATTAAAGGCTAAATTTGTTAAAT-AATGATCAATT
1 TGACAGAATGTGTAAATATTAAAGGCTAAATTTATTAAATCAAT-ACCAAAT
* ** * *
1978613 TGACAGAATGTGTAAATGTTATTGGTTAGATTTATTAAATCAATACCAAAT
1 TGACAGAATGTGTAAATATTAAAGGCTAAATTTATTAAATCAATACCAAAT
* * * * * *
1978664 TGATAAAATGTGTAAATTTTTAGGGTTAAATTTATTA
1 TGACAGAATGTGTAAATATTAAAGGCTAAATTTATTA
1978701 TTATATCAAT
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
51 69 0.96
52 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (51 bp):
TGACAGAATGTGTAAATATTAAAGGCTAAATTTATTAAATCAATACCAAAT
Found at i:1992927 original size:14 final size:14
Alignment explanation
Indices: 1992881--1992923 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1992871 GATTTAGCAG
1992881 TAAAAAATTCAAAAT
1 TAAAAAA-TCAAAAT
1992896 TAAAAAATCAAAAT
1 TAAAAAATCAAAAT
*
1992910 TAAAATAT-AAAAT
1 TAAAAAATCAAAAT
1992923 T
1 T
1992924 TAAAGATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 6 0.22
14 14 0.52
15 7 0.26
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAAAAATCAAAAT
Found at i:2016818 original size:17 final size:16
Alignment explanation
Indices: 2016785--2016832 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2016775 ATCGATTTAA
*
2016785 TTAATTTTTCTAAATT
1 TTAATTTTTTTAAATT
*
2016801 TTTATTTTTTTAATATT
1 TTAATTTTTTTAA-ATT
*
2016818 TTAATTATTTTAAAT
1 TTAATTTTTTTAAAT
2016833 CAGATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTAATTTTTTTAAATT
Found at i:2019610 original size:19 final size:19
Alignment explanation
Indices: 2019583--2019641 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2019573 TAGTTATTTC
*
2019583 TAGTCATTTATAAATTTTT
1 TAGTAATTTATAAATTTTT
* * *
2019602 TAGTTATTTTTATATTTTT
1 TAGTAATTTATAAATTTTT
*
2019621 TGGTAATTTTATAAATTTTT
1 TAGTAA-TTTATAAATTTTT
2019641 T
1 T
2019642 TCTATTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (19 bp):
TAGTAATTTATAAATTTTT
Found at i:2019648 original size:19 final size:17
Alignment explanation
Indices: 2019588--2019653 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 17
2019578 ATTTCTAGTC
*
2019588 ATTTATAAATTTTTTAGTT
1 ATTTTTAAATTTTTT--TT
* *
2019607 ATTTTTATATTTTTTGGTA
1 ATTTTTAAATTTTTT--TT
2019626 ATTTTATAAATTTTTTTCT
1 ATTTT-TAAATTTTTTT-T
2019645 ATTTTTAAA
1 ATTTTTAAA
2019654 ATAATTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 5 0.13
19 25 0.64
20 9 0.23
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (17 bp):
ATTTTTAAATTTTTTTT
Found at i:2019678 original size:19 final size:19
Alignment explanation
Indices: 2019656--2019692 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2019646 TTTTTAAAAT
2019656 AATTTTAATAATTTTTGTA
1 AATTTTAATAATTTTTGTA
2019675 AATTTTAATAATTTTTGT
1 AATTTTAATAATTTTTGT
2019693 CATCCAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTTTAATAATTTTTGTA
Found at i:2019796 original size:31 final size:31
Alignment explanation
Indices: 2019754--2019819 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2019744 GTAAAAAAAA
2019754 TTTAAGGACAAAAGTGAGAAAAAATATATAT
1 TTTAAGGACAAAAGTGAGAAAAAATATATAT
* * *
2019785 TTTAGGGACAAAAGTGGGTAAAAATATATAT
1 TTTAAGGACAAAAGTGAGAAAAAATATATAT
2019816 TTTA
1 TTTA
2019820 TAATATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (31 bp):
TTTAAGGACAAAAGTGAGAAAAAATATATAT
Found at i:2035204 original size:50 final size:50
Alignment explanation
Indices: 2035096--2035204 Score: 173
Period size: 50 Copynumber: 2.2 Consensus size: 50
2035086 ATGGAGGTAC
*
2035096 AGACTGAAACCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGA
1 AGACTGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGA
* * *
2035146 AGACTGAAGCCGTAATGGCAAATCTCATTCACCTAAAGCTGTAGAGGGGT
1 AGACTGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGA
*
2035196 AGATTGAAG
1 AGACTGAAG
2035205 TCACAAGGAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (50 bp):
AGACTGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGA
Found at i:2035311 original size:40 final size:40
Alignment explanation
Indices: 2035258--2035592 Score: 322
Period size: 40 Copynumber: 8.4 Consensus size: 40
2035248 AGTTGCAACC
* * * *
2035258 TCCAATATCTTACCCTAACCAGAGGGCAGATTGAAGATAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
**
2035298 TCCAATCTTTTACCCCGATCATG-GGGCAGATTGAA-AGCAA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGA-CAA
* * * *
2035338 TCCAATCTTTTACCCTAACCAAAGGGTAGATTGAACACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
** *
2035378 TCCAATCTTTTACCCCGATCATG-GGGCAAATTGAA-AGCAA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGA-CAA
* * *
2035418 TCTAATCTTTTACCCTAACCAGAGGGCAAATTGAAGATC-A
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGA-CAA
* * * * * *
2035458 TCCGATCTCTTACCCGAATCATG-GGGCAGATTAAAAACTA
1 TCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACAA
* * * *
2035498 CCCAATCTATTACCCTAATCAGAGGGCAGATTGAAGGCCA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
*
2035538 TTCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
1 TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
*
2035578 TCCAATATTTTACCC
1 TCCAATCTTTTACCC
2035593 CTAAAGTTAT
Statistics
Matches: 239, Mismatches: 45, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
39 5 0.02
40 229 0.96
41 5 0.02
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (40 bp):
TCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
Found at i:2035391 original size:80 final size:80
Alignment explanation
Indices: 2035258--2035592 Score: 399
Period size: 80 Copynumber: 4.2 Consensus size: 80
2035248 AGTTGCAACC
* * *
2035258 TCCAATATCTTACCCTAACCAGAGGGCAGATTGAAGATAATCCAATCTTTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
2035323 GCAGATTGAAAGCAA
66 GCAGATTGAAAGCAA
* * *
2035338 TCCAATCTTTTACCCTAACCAAAGGGTAGATTGAACACAATCCAATCTTTTACCCCGATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
*
2035403 GCAAATTGAAAGCAA
66 GCAGATTGAAAGCAA
* * * *
2035418 TCTAATCTTTTACCCTAACCAGAGGGCAAATTGAAGATC-ATCCGATCTCTTA-CCCGAATCATG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGA-CAATCCAATCTTTTACCCCG-ATCATG
* * *
2035481 GGGCAGATTAAAAACTA
64 GGGCAGATTGAAAGCAA
* * * * * * **
2035498 CCCAATCTATTACCCTAATCAGAGGGCAGATTGAAGGCCATTCAATCTTTTACCCTAATCA-GAG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATG-G
2035562 GGCAGATTG-AAGACAA
65 GGCAGATTGAAAG-CAA
*
2035578 TCCAATATTTTACCC
1 TCCAATCTTTTACCC
2035593 CTAAAGTTAT
Statistics
Matches: 214, Mismatches: 35, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
79 8 0.04
80 203 0.95
81 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCCAATCTTTTACCCCGATCATGGG
GCAGATTGAAAGCAA
Found at i:2039451 original size:2 final size:2
Alignment explanation
Indices: 2039444--2039472 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2039434 AGATGTATGC
2039444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2039473 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2046243 original size:184 final size:183
Alignment explanation
Indices: 2045725--2046245 Score: 706
Period size: 184 Copynumber: 2.8 Consensus size: 183
2045715 AGACAAGACC
* * * * **
2045725 TGATTGTACATAAAAAATATACATTAGATACCATACAACAATTGAACTGGAACTAGAGATATAAC
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATTGAACCGGAACTA-AGCCATAAC
* *
2045790 GACCATAATCACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAAATACTTCATTAAGT
65 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAAATACTGCA-TAAGT
* *
2045855 GTATCA-TCACTAAGATATTTAGGAAATATTTAACAGAACCGGAATCAAAGGTTCT
129 GCAT-AGTCACTAAGATCTTTAGGAAATATTTAACAGAACCGGAATCAAAGGTTCT
* ** *
2045910 TGATTGCACATGAAAAATATATATTAGATACCATACGACAATCAAACCGGAACTCAAGCCATAAT
1 TGATTGCACATGAAAAATATACATTAGATACCATACGACAATTGAACCGGAACT-AAGCCATAAC
* * * *
2045975 GACCATAAACACAATTTATATGCACTTTTGAATCCCACAACAATCCAGCAGATACTGCGTAAGTG
65 GACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAAATACTGCATAAGTG
* * * *
2046040 CATAGTAACAAAGATCTTTAGGAAATATTTAA-AGGAACCGGCATCTAAGGTTCT
130 CATAGTCACTAAGATCTTTAGGAAATATTTAACA-GAACCGGAATCAAAGGTTCT
*
2046094 TGATTGCACATGAAAAATATACATTAGATACCATAGGGA-AATTGAACCGGAACTATAGCCATAA
1 TGATTGCACATGAAAAATATACATTAGATACCATA-CGACAATTGAACCGGAACTA-AGCCATAA
* * *
2046158 CGACCATTAGCACAATTTATATGCACTTTTGTATCCCACAATAAACCAGCAAATACTGCATAAGT
64 CGACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAAATACTGCATAAGT
* *
2046223 GCATAGTCATTAACATCTTTAGG
129 GCATAGTCACTAAGATCTTTAGG
2046246 CCACTTATAC
Statistics
Matches: 293, Mismatches: 38, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
183 3 0.01
184 181 0.62
185 108 0.37
186 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (183 bp):
TGATTGCACATGAAAAATATACATTAGATACCATACGACAATTGAACCGGAACTAAGCCATAACG
ACCATAAACACAATTTATATGCACTTTTGTATCCCACAACAAACCAGCAAATACTGCATAAGTGC
ATAGTCACTAAGATCTTTAGGAAATATTTAACAGAACCGGAATCAAAGGTTCT
Found at i:2050622 original size:9 final size:9
Alignment explanation
Indices: 2050608--2050647 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
2050598 CGATTAGTAT
2050608 GAAAACAAC
1 GAAAACAAC
2050617 GAAAACAAC
1 GAAAACAAC
2050626 GAAAACAAC
1 GAAAACAAC
* *
2050635 GATAACAAT
1 GAAAACAAC
2050644 GAAA
1 GAAA
2050648 TTAAATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.65, C:0.17, G:0.12, T:0.05
Consensus pattern (9 bp):
GAAAACAAC
Found at i:2056549 original size:13 final size:14
Alignment explanation
Indices: 2056521--2056551 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2056511 TTTCTTTTAT
2056521 TAATTAAAAAACCA
1 TAATTAAAAAACCA
2056535 TAATTAAAAAA-CA
1 TAATTAAAAAACCA
2056548 TAAT
1 TAAT
2056552 AACTTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (14 bp):
TAATTAAAAAACCA
Found at i:2059818 original size:29 final size:29
Alignment explanation
Indices: 2059749--2059844 Score: 75
Period size: 31 Copynumber: 3.2 Consensus size: 29
2059739 AAAGTTTTAA
* * * *
2059749 GTATACATTTGAACCACAATTAGAGTTTCAC
1 GTATACAATTGCACCA-AATTAAAG-TTCAT
* *
2059780 GTGTATAATTGCACCAAATTAAAGTTCAT
1 GTATACAATTGCACCAAATTAAAGTTCAT
* * *
2059809 GTATACAATTACACCTTAAATCAAAGTTTAT
1 GTATACAATTGCACC--AAATTAAAGTTCAT
2059840 GTATA
1 GTATA
2059845 ATTTTGAGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 16 0.31
30 7 0.13
31 29 0.56
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (29 bp):
GTATACAATTGCACCAAATTAAAGTTCAT
Found at i:2066228 original size:2 final size:2
Alignment explanation
Indices: 2066221--2066245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2066211 GTCAACACCC
2066221 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2066246 CACTGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2069543 original size:17 final size:17
Alignment explanation
Indices: 2069521--2069564 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
2069511 ATGCTCGAAT
*
2069521 TTCAAATTTAATTTTCA
1 TTCAAATTAAATTTTCA
2069538 TTCAAA-TAAATTTTCA
1 TTCAAATTAAATTTTCA
2069554 TTCAAA-TAAAT
1 TTCAAATTAAAT
2069565 GTCCTAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCAAATTAAATTTTCA
Found at i:2069551 original size:16 final size:16
Alignment explanation
Indices: 2069530--2069564 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2069520 TTTCAAATTT
2069530 AATTTTCATTCAAATA
1 AATTTTCATTCAAATA
2069546 AATTTTCATTCAAATA
1 AATTTTCATTCAAATA
2069562 AAT
1 AAT
2069565 GTCCTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTTTCATTCAAATA
Found at i:2079953 original size:19 final size:19
Alignment explanation
Indices: 2079894--2079954 Score: 90
Period size: 18 Copynumber: 3.3 Consensus size: 19
2079884 TAAAATTATT
2079894 ATTTTAAATTTTTTTT-TAA
1 ATTTT-AATTTTTTTTATAA
2079913 ATTTTAATTTTTTTTA-AA
1 ATTTTAATTTTTTTTATAA
*
2079931 ATTTTAATTTTTTTTATAT
1 ATTTTAATTTTTTTTATAA
2079950 ATTTT
1 ATTTT
2079955 TAGAATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 28 0.72
19 11 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTAATTTTTTTTATAA
Found at i:2079971 original size:18 final size:17
Alignment explanation
Indices: 2079903--2079974 Score: 83
Period size: 18 Copynumber: 4.0 Consensus size: 17
2079893 TATTTTAAAT
2079903 TTTTTTTTAAATTTTAA
1 TTTTTTTTAAATTTTAA
2079920 TTTTTTTTAAAATTTTAA
1 TTTTTTTT-AAATTTTAA
2079938 TTTTTTTTATATATTTTTAGA
1 TTTTTTTTA-A-A-TTTTA-A
*
2079959 ATTTTTTT-AATTTTAA
1 TTTTTTTTAAATTTTAA
2079975 AAAATATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
16 1 0.02
17 14 0.29
18 19 0.39
19 2 0.04
20 5 0.10
21 8 0.16
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (17 bp):
TTTTTTTTAAATTTTAA
Done.