Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 120 of 226
Found at i:40796453 original size:23 final size:23
Alignment explanation
Indices: 40796423--40796472 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
40796413 GTTTTTAGTC
* *
40796423 TATTTTATTAATTTTGTTAT-TAT
1 TATTTTATT-ATTATATTATATAT
40796446 TATTTTATTATTATATTATATAT
1 TATTTTATTATTATATTATATAT
40796469 TATT
1 TATT
40796473 ACCTACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TATTTTATTATTATATTATATAT
Found at i:40796552 original size:11 final size:11
Alignment explanation
Indices: 40796536--40796569 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
40796526 CGTTTTAATA
*
40796536 TATATACATAT
1 TATATACATAC
40796547 TATATACATAC
1 TATATACATAC
40796558 TATATACATAC
1 TATATACATAC
40796569 T
1 T
40796570 TTATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (11 bp):
TATATACATAC
Found at i:40796853 original size:51 final size:52
Alignment explanation
Indices: 40796739--40796854 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 52
40796729 ATTTTCCATG
**
40796739 TTTT-TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATA
1 TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
* * * * *
40796789 TTTTATATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATATATATATACTTATATATTTCATT-TTTTCATAAATGCATGAATATA
40796840 TTTTATATATATATA
1 TTTTATATATATATA
40796855 AGTTTTATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.07
51 28 0.51
52 23 0.42
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (52 bp):
TTTTATATATATATACTTATATATTTCATTTTTTCATAAATGCATGAATATA
Found at i:40799390 original size:5 final size:5
Alignment explanation
Indices: 40799368--40799401 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
40799358 TTTTATTAAA
*
40799368 TTTAT TATTAT TTGAT TTTAT TTTAT TTTAT TTT
1 TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTT
40799402 TTGTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:40801193 original size:21 final size:21
Alignment explanation
Indices: 40801156--40801195 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40801146 ACCTGCTGTT
*
40801156 GAGGAGGAAGTTATTGTTGGA
1 GAGGAGGAAGTCATTGTTGGA
*
40801177 GAGGAGGAAGTCCTTGTTG
1 GAGGAGGAAGTCATTGTTG
40801196 CAGATGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.05, G:0.42, T:0.28
Consensus pattern (21 bp):
GAGGAGGAAGTCATTGTTGGA
Found at i:40807666 original size:2 final size:2
Alignment explanation
Indices: 40807659--40807686 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40807649 TACCGTTCGT
40807659 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40807687 CATAATTCCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:40811935 original size:2 final size:2
Alignment explanation
Indices: 40811928--40811966 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
40811918 AAGATGTATT
40811928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40811967 GGTGTGCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40816384 original size:20 final size:21
Alignment explanation
Indices: 40816361--40816404 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
40816351 TTATGCTTTT
*
40816361 AAAATTAAGTTTT-GATCT-AG
1 AAAATCAA-TTTTCGATCTAAG
40816381 AAAATCAATTTTCGATCTAAG
1 AAAATCAATTTTCGATCTAAG
40816402 AAA
1 AAA
40816405 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (21 bp):
AAAATCAATTTTCGATCTAAG
Found at i:40817751 original size:11 final size:11
Alignment explanation
Indices: 40817711--40817751 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
40817701 GTCTTTTACA
40817711 AAAATAATA-C
1 AAAATAATATC
* *
40817721 AAAAAAAAAT-
1 AAAATAATATC
40817731 AAAATAATATC
1 AAAATAATATC
40817742 AAAATAATAT
1 AAAATAATAT
40817752 AAATATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAATAATATC
Found at i:40818149 original size:152 final size:150
Alignment explanation
Indices: 40817873--40818337 Score: 606
Period size: 153 Copynumber: 3.1 Consensus size: 150
40817863 CAATTGTTAA
* *
40817873 TATTTTGGCCATTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATAC-TA-TTT
1 TATTTCGGCCATTTGTTCGTA-TTTTTTCCCGGATTTTATTAC-TTTAAAAAA-ATACTTATTTT
* ** *
40817936 C-TATTTT-TTATTTTACATTATTTCGGTAGATTATGTTTGAAATGTATTCATTTAGTT-TGTTT
63 CGCATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTA-TTGTGTTT
40817998 TTTAAATAAA-TTAAAAAAACTCT
127 TTTAAATAAATTTAAAAAAACTCT
40818021 TATTTCGGCTC-TTTGTTCGTATTTTTTCCCGGATTTTATTACTTTCAATAAAAATACATTATTT
1 TATTTCGGC-CATTTGTTCGTATTTTTTCCCGGATTTTATTACTTT-AA-AAAAATAC-TTATTT
*
40818085 TCGCATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTATTGTGTTT
62 TCGCATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATTGTGTTT
40818150 TTTAAATAAAATTTTTAAAAAAA-TCCT
127 TTTAAAT-AAA--TTTAAAAAAACT-CT
* * * *
40818177 TATTTCGGCCATTTATTCGTATTTTTTCCCCAGAGTTTATTACTTTAAAAAAAT-GTTATTTTCG
1 TATTTCGGCCATTTGTTCGTATTTTTT-CCCGGATTTTATTACTTTAAAAAAATACTTATTTTCG
*
40818241 CATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTT
65 CATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATTGTGTTTTTT
*
40818306 AAATAAATTTTAAAAAAAACCCCT
130 AAATAAA-TTT-AAAAAAA-CTCT
40818330 TATTTCGG
1 TATTTCGG
40818338 NNNNNNNNNN
Statistics
Matches: 284, Mismatches: 14, Indels: 33
0.86 0.04 0.10
Matches are distributed among these distances:
146 3 0.01
147 26 0.09
148 22 0.08
149 3 0.01
150 4 0.01
151 11 0.04
152 65 0.23
153 89 0.31
155 8 0.03
156 37 0.13
157 16 0.06
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.51
Consensus pattern (150 bp):
TATTTCGGCCATTTGTTCGTATTTTTTCCCGGATTTTATTACTTTAAAAAAATACTTATTTTCGC
ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTATTGTGTTTTTTA
AATAAATTTAAAAAAACTCT
Found at i:40818633 original size:155 final size:155
Alignment explanation
Indices: 40818438--40818845 Score: 587
Period size: 153 Copynumber: 2.6 Consensus size: 155
40818428 NNNNNNNNNN
40818438 TGTATTCATTTAGTGTGTTTTTTAAATAAA-TTTAAAAAAAAACCCCTTATTTCGGCCCTTTGTT
1 TGTATTCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAAA--CCTTATTTCGGCCCTTTGTT
*
40818502 CGTATTTTTTTCCCGGATTTTATTAATTTCAATAAAAATATATTATTTTCGT-ATTTTATTATTT
64 CGTATTTTTTTCCCGGATTTTATTACTTT-AATAAAAATATATTATTTTC-TAATTTTATTATTT
40818566 TACATTATTTTAGTACATTATGTTTGAAA
127 TACATTATTTTAGTACATTATGTTTGAAA
* * * * * *
40818595 TGTATTAATTTACTGTG-TTTTTAAATAAATTTTTAAAAAAATCCTTTTTTCGGCCCTTTGTTTG
1 TGTATTCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAAACCTTATTTCGGCCCTTTGTTCG
* *
40818659 TATTTTTTTCCAGGATTTTATTACTTTTA-AAAAATATATTATTTTCTAATTTTATTATTTTACA
66 TATTTTTTTCCCGGATTTTATTACTTTAATAAAAATATATTATTTTCTAATTTTATTATTTTACA
40818723 TTATTTTAGTACATTATGTTTGAAA
131 TTATTTTAGTACATTATGTTTGAAA
* * * *
40818748 TGTATTCA-TTAGTGTGTTTTTTAAATAAA-TTTAAAAAAAAATCTTATTTCAGCCATTTGTTCT
1 TGTATTCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAAACCTTATTTCGGCCCTTTGTTCG
* *
40818811 TA-TTTTTTCTCGAATTTTATTACTTTTAATAAAAA
66 TATTTTTTTCCCGGATTTTATTAC-TTTAATAAAAA
40818846 CACACTAAAT
Statistics
Matches: 223, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
151 18 0.08
152 40 0.18
153 82 0.37
154 1 0.00
155 45 0.20
156 12 0.05
157 25 0.11
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.52
Consensus pattern (155 bp):
TGTATTCATTTAGTGTGTTTTTTAAATAAATTTTAAAAAAAAACCTTATTTCGGCCCTTTGTTCG
TATTTTTTTCCCGGATTTTATTACTTTAATAAAAATATATTATTTTCTAATTTTATTATTTTACA
TTATTTTAGTACATTATGTTTGAAA
Found at i:40822002 original size:9 final size:9
Alignment explanation
Indices: 40821988--40822053 Score: 89
Period size: 9 Copynumber: 7.2 Consensus size: 9
40821978 TTTGGTTAAA
40821988 AATTACCCG
1 AATTACCCG
40821997 AATTACCCG
1 AATTACCCG
40822006 AATTACCCG
1 AATTACCCG
*
40822015 -ATTAACCG
1 AATTACCCG
*
40822023 AATTAACCG
1 AATTACCCG
40822032 AAAATTACCCG
1 --AATTACCCG
40822043 AATTACCCG
1 AATTACCCG
40822052 AA
1 AA
40822054 AATTACCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
8 7 0.13
9 37 0.71
11 8 0.15
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:40822043 original size:20 final size:20
Alignment explanation
Indices: 40821988--40822061 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
40821978 TTTGGTTAAA
40821988 AATTACCCG--AATTACCCG
1 AATTACCCGAAAATTACCCG
*
40822006 AATTACCCG---ATTAACCG
1 AATTACCCGAAAATTACCCG
*
40822023 AATTAACCGAAAATTACCCG
1 AATTACCCGAAAATTACCCG
40822043 AATTACCCGAAAATTACCC
1 AATTACCCGAAAATTACCC
40822062 AAAAAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.31
18 9 0.18
20 25 0.51
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.22
Consensus pattern (20 bp):
AATTACCCGAAAATTACCCG
Found at i:40825539 original size:21 final size:18
Alignment explanation
Indices: 40825506--40825545 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
40825496 TTCGTTTTGT
40825506 TCATTTTTTATTCACATTA
1 TCATTTTTTATTC-CATTA
40825525 TCATGTTTATTATTCCATTA
1 TCAT-TTT-TTATTCCATTA
40825545 T
1 T
40825546 GCATCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (18 bp):
TCATTTTTTATTCCATTA
Found at i:40834466 original size:41 final size:41
Alignment explanation
Indices: 40834409--40834517 Score: 155
Period size: 41 Copynumber: 2.7 Consensus size: 41
40834399 NNNNNNNTCG
*
40834409 GGTTATAAACCTAGCAGGCTACGTGCCGGTGATTTGAATCA
1 GGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAATCA
40834450 GGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAATCA
1 GGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAATCA
* * ** * *
40834491 AGCTATAAGTCTAGCAGTCTATGTGCC
1 GGTTATAAACCTAGCAGGCTACGTGCC
40834518 ATTGAATCTG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (41 bp):
GGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAATCA
Found at i:40839319 original size:16 final size:16
Alignment explanation
Indices: 40839293--40839335 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
40839283 AGAAATATTT
*
40839293 CACTTAAAAAAAGGGG
1 CACTCAAAAAAAGGGG
*
40839309 CATTC-AAAAAAGGGG
1 CACTCAAAAAAAGGGG
40839324 CACTCAAAAAAA
1 CACTCAAAAAAA
40839336 AACAAACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (16 bp):
CACTCAAAAAAAGGGG
Found at i:40839332 original size:14 final size:15
Alignment explanation
Indices: 40839299--40839334 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
40839289 ATTTCACTTA
*
40839299 AAAAAAGGGGCATTC
1 AAAAAAGGGGCACTC
40839314 AAAAAAGGGGCACTC
1 AAAAAAGGGGCACTC
40839329 AAAAAA
1 AAAAAA
40839335 AAACAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.14, G:0.22, T:0.08
Consensus pattern (15 bp):
AAAAAAGGGGCACTC
Found at i:40840727 original size:50 final size:50
Alignment explanation
Indices: 40840673--40841065 Score: 526
Period size: 50 Copynumber: 7.9 Consensus size: 50
40840663 GCAATTAAGA
*
40840673 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* * * * *
40840723 AGATTGAAGCTACAATAGCGGATCTTACTTCCCT-GACATTGCAAT-TAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGGAA-C
*
40840773 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTACAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* * *
40840823 AGATTGAAGCTACAACAGCAGATCTTACTTCCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* *
40840873 AGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* * * * *
40840923 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGTAAT-TAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGGAA-C
*
40840973 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGTAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* *
40841023 AGATTGAAGCTACAACAACGGATCTTACTTCCCT-GACATTGCA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCA
40841066 ATTAAGAAGA
Statistics
Matches: 301, Mismatches: 33, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
49 7 0.02
50 288 0.96
51 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
Found at i:40840944 original size:150 final size:150
Alignment explanation
Indices: 40840664--40841398 Score: 604
Period size: 150 Copynumber: 4.9 Consensus size: 150
40840654 CCATAGTTTG
*
40840664 CAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTG
1 CAATGAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTG
* *
40840729 AAGCTACAATAGCGGATCTTACTTCCCTGACATTGCAATTAAGAAGATTGAAGCTACAACAGCGG
66 AAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAAGAAGATTGAAGCTACAACAGCGG
*
40840794 ATCTTACTTTCCT-AGCATTA
131 ATCTTACTTCCCTGA-CATTA
* * * *
40840814 CAGTGGAA-CAGATTGAAGCTACAACAGCAGATCTTACTTCCCTAGCGTTGCAGTGGAACAGATT
1 CAAT-GAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATT
* * * * *
40840878 GAAGCTACAACAGTGGATCTTACTTTCCT-AGCGTTGCAGTGGAA-CAGATTGAAGCTACAACAG
65 GAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAAT-GAAGAAGATTGAAGCTACAACAG
*
40840941 CGGATCTTACTTCCCTGACATTG
128 CGGATCTTACTTCCCTGACATTA
* * * *
40840964 TAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGTAGTGGAACAGATTG
1 CAATGAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTG
* * * * * * *
40841029 AAGCTACAACAACGGATCTTACTTCCCTGACATTGCAATTAAGAAGATCGAAGCCACAGCGGCGA
66 AAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAAGAAGATTGAAGCTACAACAGCGG
* *
40841094 ATCTTACTT--CTGGCGA-TG
131 ATCTTACTTCCCTGAC-ATTA
** * * * *** * ** * * **
40841112 CAGCGGAGCAGATTAAAGCTACAACAGTAAATCTCAC-TTCCCCGACATTGCAATTTAA-AGGAT
1 CAATGAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CGTTGCAGTGGAACA-GAT
* * * * ** * *
40841175 CGAAGCCACAAC-GACGAATCTTACTT--CTGGCGA-TGCAGCGGAGCAGATTGAAGCTACAACA
64 TGAAGCTACAACAG-CGGATCTTACTTCCCTGAC-ATTGCAATGAAGAAGATTGAAGCTACAACA
* * * * *
40841236 ACGAATCTCACTTCCCCGACATTG
127 GCGGATCTTACTTCCCTGACATTA
* * * * * * *
40841260 CAATTTAA-AAGATCGAAGCTACAACGGTGAATCTTAC-TT-CTGGCGATGCAGTGGAACAGATT
1 CAA-TGAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATT
* * * * * * * * *
40841322 GAAGCTACAACAGTGAATCTCACTTCCCCGACATTGCAATTTAA-AAGATCGAAGCCACAACGGT
65 GAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAA-TGAAGAAGATTGAAGCTACAACAGC
*
40841386 GAATCTTACTTCC
129 GGATCTTACTTCC
40841399 AGGCGATGCA
Statistics
Matches: 459, Mismatches: 104, Indels: 46
0.75 0.17 0.08
Matches are distributed among these distances:
146 65 0.14
147 13 0.03
148 130 0.28
149 8 0.02
150 237 0.52
151 6 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (150 bp):
CAATGAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGATTG
AAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAAGAAGATTGAAGCTACAACAGCGG
ATCTTACTTCCCTGACATTA
Found at i:40841082 original size:50 final size:49
Alignment explanation
Indices: 40840673--40841359 Score: 506
Period size: 50 Copynumber: 13.9 Consensus size: 49
40840663 GCAATTAAGA
* *
40840673 AGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAGT-GAAC
* * * *
40840723 AGATTGAAGCTACAATAGCGGATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGAA-C
* *
40840773 AGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCATTACAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAGT-GAAC
* *
40840823 AGATTGAAGCTACAACAGCAGATCTTACTTCCCT-AGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAGT-GAAC
* * *
40840873 AGATTGAAGCTACAACAGTGGATCTTACTTTCCT-AGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAGT-GAAC
* * * *
40840923 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGTAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGAA-C
* *
40840973 AGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCATTGTAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAGT-GAAC
* * * *
40841023 AGATTGAAGCTACAACAACGGATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGAA-C
* * * * * * * *
40841073 AGATCGAAGCCACAGCGGCGAATCTTACTT--CTGGCGA-TGCAGCGGAGC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGAC-ATTGCAG-TGAAC
* *** * * * *
40841121 AGATTAAAGCTACAACAGTAAATCTCACTTCCCCGACATTGCAATTTAA-
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGC-AGTGAAC
* * * * * *
40841170 AGGATCGAAGCCACAAC-GACGAATCTTACTT--CTGGCGA-TGCAGCGGAGC
1 A-GATTGAAGCTACAACAG-CGGATCTTACTTCCCTGAC-ATTGCAG-TGAAC
* * * * * * *
40841219 AGATTGAAGCTACAACAACGAATCTCACTTCCCCGACATTGCAATTTAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGC-AGTGAAC
* * * * *
40841269 AGATCGAAGCTACAACGGTGAATCTTACTT--CTGGCGA-TGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGAC-ATTGCAGT-GAAC
* * * *
40841317 AGATTGAAGCTACAACAGTGAATCTCACTTCCCCGACATTGCA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCA
40841360 ATTTAAAAGA
Statistics
Matches: 506, Mismatches: 100, Indels: 62
0.76 0.15 0.09
Matches are distributed among these distances:
47 3 0.01
48 96 0.19
49 18 0.04
50 380 0.75
51 9 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (49 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGAAC
Found at i:40841163 original size:98 final size:99
Alignment explanation
Indices: 40840661--40841447 Score: 833
Period size: 100 Copynumber: 7.9 Consensus size: 99
40840651 AAACCATAGT
* * *
40840661 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAA-AAGATCGAAGCTACAACAGCGAATCTTACTTTCCTAGCGATGCAGTGGAACAGA
* *
40840726 TTGAAGCTACAATAGCGGATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
* * *
40840761 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC-ATTACAGTGGAACAG
1 TTGCAATTAA-AAGATCGAAGCTACAACAGCGAATCTTACTTTCCTAGCGA-TGCAGTGGAACAG
* * *
40840825 ATTGAAGCTACAACAGCAGATCTTACTT-CCCTAGCG
64 ATTGAAGCTACAACAGCGGATCTTACTTCCCCGA-CA
* * * * * * *
40840861 TTGCAGTGGAACAGATTGAAGCTACAACAGTGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAAT-TAAAAGATCGAAGCTACAACAGCGAATCTTACTTTCCTAGCGATGCAGTGGAACAGA
*
40840926 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
* * * *
40840961 TTGTAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC-ATTGTAGTGGAACAG
1 TTGCAATTAA-AAGATCGAAGCTACAACAGCGAATCTTACTTTCCTAGCGA-TGCAGTGGAACAG
* *
40841025 ATTGAAGCTACAACAACGGATCTTACTTCCCTGACA
64 ATTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
* * * * * *
40841061 TTGCAATTAAGAAGATCGAAGCCACAGCGGCGAATCTTAC-TT-CTGGCGATGCAGCGGAGCAGA
1 TTGCAATTAA-AAGATCGAAGCTACAACAGCGAATCTTACTTTCCTAGCGATGCAGTGGAACAGA
* *** *
40841124 TTAAAGCTACAACAGTAAATCTCACTTCCCCGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
* * * * *
40841159 TTGCAATTTAAAGGATCGAAGCCACAAC-GACGAATCTTAC-TT-CTGGCGATGCAGCGGAGCAG
1 TTGCAA-TTAAAAGATCGAAGCTACAACAG-CGAATCTTACTTTCCTAGCGATGCAGTGGAACAG
* * *
40841221 ATTGAAGCTACAACAACGAATCTCACTTCCCCGACA
64 ATTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
* * *
40841257 TTGCAATTTAAAAGATCGAAGCTACAACGGTGAATCTTAC-TT-CTGGCGATGCAGTGGAACAGA
1 TTGCAA-TTAAAAGATCGAAGCTACAACAGCGAATCTTACTTTCCTAGCGATGCAGTGGAACAGA
* * *
40841320 TTGAAGCTACAACAGTGAATCTCACTTCCCCGACA
65 TTGAAGCTACAACAGCGGATCTTACTTCCCCGACA
* * * ** *
40841355 TTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTAC-TTCC-AGGCGATGCAACGGAATAG
1 TTGCAA-TTAAAAGATCGAAGCTACAACAGCGAATCTTACTTTCCTA-GCGATGCAGTGGAACAG
* * * *
40841418 ATTGAAGCTGCAACGGCGAATCTTATTTCC
64 ATTGAAGCTACAACAGCGGATCTTACTTCC
40841448 TCGGCAAGAC
Statistics
Matches: 609, Mismatches: 65, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
97 1 0.00
98 258 0.42
99 53 0.09
100 292 0.48
101 5 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (99 bp):
TTGCAATTAAAAGATCGAAGCTACAACAGCGAATCTTACTTTCCTAGCGATGCAGTGGAACAGAT
TGAAGCTACAACAGCGGATCTTACTTCCCCGACA
Found at i:40841388 original size:50 final size:50
Alignment explanation
Indices: 40841127--40841398 Score: 216
Period size: 50 Copynumber: 5.5 Consensus size: 50
40841117 GAGCAGATTA
* *
40841127 AAGCTACAACAGTAAATCTCACTTCCCCGACATTGCAATTTAAAGGATCG
1 AAGCTACAACAGTGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCG
* * * * * **** ** *
40841177 AAGCCACAAC-GACGAATCTTACTT--CTGGCGA-TGCAGCGGAGCAGATTG
1 AAGCTACAACAG-TGAATCTCACTTCCCCGAC-ATTGCAATTTAAAAGATCG
**
40841225 AAGCTACAACAACGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCG
1 AAGCTACAACAGTGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCG
* * * * * ** * *
40841275 AAGCTACAACGGTGAATCTTACTT--CTGGCGA-TGCAGTGGAACAGATTG
1 AAGCTACAACAGTGAATCTCACTTCCCCGAC-ATTGCAATTTAAAAGATCG
40841323 AAGCTACAACAGTGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCG
1 AAGCTACAACAGTGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCG
* * *
40841373 AAGCCACAACGGTGAATCTTACTTCC
1 AAGCTACAACAGTGAATCTCACTTCC
40841399 AGGCGATGCA
Statistics
Matches: 163, Mismatches: 49, Indels: 20
0.70 0.21 0.09
Matches are distributed among these distances:
48 69 0.42
49 5 0.03
50 89 0.55
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (50 bp):
AAGCTACAACAGTGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCG
Found at i:40843172 original size:21 final size:18
Alignment explanation
Indices: 40843139--40843178 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
40843129 TTTGTTTTGT
40843139 TCATTTTTTATTCACATTA
1 TCATTTTTTATTC-CATTA
40843158 TCATGTTTATTATTCCATTA
1 TCAT-TTT-TTATTCCATTA
40843178 T
1 T
40843179 GCATCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (18 bp):
TCATTTTTTATTCCATTA
Found at i:40843964 original size:2 final size:2
Alignment explanation
Indices: 40843957--40843981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40843947 TTATAGAACA
40843957 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
40843982 AAATATAAAA
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:40843994 original size:20 final size:18
Alignment explanation
Indices: 40843973--40844011 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40843963 ATATATATAT
*
40843973 ATATATATAA-AATATAAA
1 ATATAAATAAGAA-ATAAA
40843991 ATATAAATAAGAAATAAA
1 ATATAAATAAGAAATAAA
40844009 ATA
1 ATA
40844012 ATTCAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
ATATAAATAAGAAATAAA
Found at i:40844961 original size:89 final size:87
Alignment explanation
Indices: 40844804--40845016 Score: 234
Period size: 89 Copynumber: 2.5 Consensus size: 87
40844794 TTAAAGATGT
** * ** *
40844804 AAAAAG-CCCTCAAAC-TTTAAAAAAAAAAAATTAAGTCCC-TATTTTTTTATACTCAATTGAGC
1 AAAAAGACCCTCAAACTTTTAAAAAAAAGCAATTAAGCCCCGGCTTTTTCTATACTCAATTGAGC
40844866 ACTTGAACTTTCAAAATACATC
66 ACTTGAACTTTCAAAATACATC
* * * *
40844888 AGAAAGGCCTTCAAACTTCTTAAAAAAAAGCAATTAAGCCCCGGCTTTTTCTATCACTCAATTGG
1 AAAAAGACCCTCAAACTT-TTAAAAAAAAGCAATTAAGCCCCGGCTTTTTCTAT-ACTCAATTGA
* * *
40844953 GTACTTGAACTTTTAAAATGCATC
64 GCACTTGAACTTTCAAAATACATC
* * **
40844977 AAAAAGACCCTCCAAGTTTTTCAAAAAAGCAATTAAGCCC
1 AAAAAGACCCTCAAACTTTTAAAAAAAAGCAATTAAGCCC
40845017 ATGCTCTTAT
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
84 5 0.05
85 8 0.08
86 1 0.01
87 20 0.19
88 28 0.27
89 43 0.41
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (87 bp):
AAAAAGACCCTCAAACTTTTAAAAAAAAGCAATTAAGCCCCGGCTTTTTCTATACTCAATTGAGC
ACTTGAACTTTCAAAATACATC
Found at i:40845359 original size:19 final size:18
Alignment explanation
Indices: 40845328--40845363 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40845318 ACTTTATAAA
40845328 ATTTTATAATTTTTTTAT
1 ATTTTATAATTTTTTTAT
*
40845346 ATTTCTATATTTTTTTTA
1 ATTT-TATAATTTTTTTA
40845364 CGATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTATAATTTTTTTAT
Found at i:40845365 original size:48 final size:48
Alignment explanation
Indices: 40845303--40845397 Score: 129
Period size: 48 Copynumber: 2.0 Consensus size: 48
40845293 TTACATTTTG
* *
40845303 TATAATTTTCTTACGA-CTTTATAAAATTTTATAATTTTTTTATATTTC
1 TATAATTTTCTTACGATCTTTATAAAATTTTACAA-ATTTTTATATTTC
* * *
40845351 TATATTTTTTTTACGATTTTTATAAAATTTTACAAATTTTTATATTT
1 TATAATTTTCTTACGATCTTTATAAAATTTTACAAATTTTTATATTT
40845398 TTTATGATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
48 25 0.61
49 16 0.39
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (48 bp):
TATAATTTTCTTACGATCTTTATAAAATTTTACAAATTTTTATATTTC
Found at i:40845399 original size:8 final size:9
Alignment explanation
Indices: 40845329--40845427 Score: 65
Period size: 9 Copynumber: 10.6 Consensus size: 9
40845319 CTTTATAAAA
40845329 TTTTATAAT
1 TTTTATAAT
*
40845338 TTTTTTATAT
1 TTTTATA-AT
* *
40845348 TTCTATATT
1 TTTTATAAT
*
40845357 TTTTTTACGAT
1 TTTTATA--AT
*
40845368 TTTTATAAAA
1 TTTTAT-AAT
*
40845378 TTTTACAAAT
1 TTTTA-TAAT
*
40845388 TTTTATATT
1 TTTTATAAT
*
40845397 TTTTATGAT
1 TTTTATAAT
40845406 TTTTAT-AT
1 TTTTATAAT
*
40845414 TTTTCTAAT
1 TTTTATAAT
40845423 TTTTA
1 TTTTA
40845428 ATAAATTTCT
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
8 7 0.10
9 33 0.49
10 20 0.30
11 6 0.09
12 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40845409 original size:48 final size:47
Alignment explanation
Indices: 40845292--40845409 Score: 121
Period size: 49 Copynumber: 2.4 Consensus size: 47
40845282 ATTATATTTC
* * * *
40845292 TTTACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATAATTTT
1 TTTATATTTTATAT-ATTTT-TTACGACTTTATAAAATTTTACAATATT
* *
40845341 TTTATATTTCTATATTTTTTTTACGATTTTTATAAAATTTTACAA-ATT
1 TTTATATTT-TATATATTTTTTACGA-CTTTATAAAATTTTACAATATT
*
40845389 TTTATATTTTTTATGATTTTT
1 TTTATATTTTATAT-ATTTTT
40845410 ATATTTTTCT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
47 4 0.07
48 22 0.38
49 28 0.48
50 4 0.07
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (47 bp):
TTTATATTTTATATATTTTTTACGACTTTATAAAATTTTACAATATT
Found at i:40845426 original size:18 final size:19
Alignment explanation
Indices: 40845386--40845444 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
40845376 AATTTTACAA
40845386 ATTTTTATATTTTT-T-AT
1 ATTTTTATATTTTTCTAAT
40845403 GATTTTTATATTTTTCTAAT
1 -ATTTTTATATTTTTCTAAT
* **
40845423 -TTTTAATAAATTTCTAAT
1 ATTTTTATATTTTTCTAAT
40845441 ATTT
1 ATTT
40845445 AAATTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 29 0.83
19 4 0.11
20 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTTTATATTTTTCTAAT
Found at i:40845632 original size:89 final size:91
Alignment explanation
Indices: 40845535--40845731 Score: 254
Period size: 89 Copynumber: 2.2 Consensus size: 91
40845525 TTTTTTTTTT
* * * **
40845535 AAGTTTGAGGGTTTTTTTAATACATTTTGAAAGTTCAAGTACCTAATTGGGTGC-AAAA-AAAGG
1 AAGTTTGAGGGTTTTTTTAATACATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAGAAAAA
* *
40845598 TAGGGGCTTAATTGCTTTTTTTGAAA
66 CAAGGGCTTAATTGCTTTTTTTGAAA
* * * * *
40845624 AGGTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAGAAAAA
1 AAGTTTGAGGGTTTTTTTAATACATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAGAAAAA
*
40845689 CAAGGTCTTAATTGCTTTTTTTGAAA
66 CAAGGGCTTAATTGCTTTTTTTGAAA
*
40845715 AAGTTTGAGGGCTTTTT
1 AAGTTTGAGGGTTTTTT
40845732 GCACCCTTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
89 46 0.52
90 4 0.04
91 39 0.44
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (91 bp):
AAGTTTGAGGGTTTTTTTAATACATTTTGAAAGTTCAAGTACCCAAATGAGTGCAAAAAGAAAAA
CAAGGGCTTAATTGCTTTTTTTGAAA
Found at i:40847940 original size:13 final size:12
Alignment explanation
Indices: 40847918--40847995 Score: 60
Period size: 11 Copynumber: 6.8 Consensus size: 12
40847908 AAAACCCTAA
40847918 TTTT-TTTCTCCT
1 TTTTCTTTCT-CT
40847930 TTTTCTTTCTCT
1 TTTTCTTTCTCT
40847942 TTTTC-TTCTCT
1 TTTTCTTTCTCT
* *
40847953 GTTTCGTTCTACT
1 TTTTCTTTCT-CT
40847966 TTGTTC--T-TCT
1 TT-TTCTTTCTCT
*
40847976 TTTTCTAT-TCT
1 TTTTCTTTCTCT
40847987 TTTTCTTTC
1 TTTTCTTTC
40847996 ATTTATTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
9 3 0.05
10 4 0.07
11 22 0.39
12 16 0.29
13 8 0.14
14 3 0.05
ACGTcount: A:0.03, C:0.23, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTTCTTTCTCT
Found at i:40849587 original size:18 final size:18
Alignment explanation
Indices: 40849563--40849822 Score: 124
Period size: 18 Copynumber: 14.1 Consensus size: 18
40849553 ACACAATAAT
40849563 AATTTTTGAAAACAC-AA
1 AATTTTTGAAAACACGAA
40849580 AGATTTTTG-AAACACGAA
1 A-ATTTTTGAAAACACGAA
40849598 AATTTTTTGAAAACACGGAA
1 AA-TTTTTGAAAACAC-GAA
** * *
40849618 TTTTTTTGAAAACAAGGA
1 AATTTTTGAAAACACGAA
* * *
40849636 AATTTTCG-ATACATGAGA
1 AATTTTTGAAAACACGA-A
*
40849654 ATTTTTTG---ACACGAA
1 AATTTTTGAAAACACGAA
* *
40849669 AAATTTTGAAAATACGAA
1 AATTTTTGAAAACACGAA
* *
40849687 AA-TTTCGAAAACATG-A
1 AATTTTTGAAAACACGAA
* * * *
40849703 ATTTTTTTAAAATACGAT
1 AATTTTTGAAAACACGAA
** *
40849721 TTTTTTTAAAAAACACGAGA
1 AATTTTT-GAAAACACGA-A
**
40849741 TTTTTTTTGAAAACACGAAA
1 -AATTTTTGAAAACACG-AA
40849761 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
40849785 AATTTTT-AAAACACGAGA
1 AATTTTTGAAAACACGA-A
*
40849803 ATTTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
40849821 AA
1 AA
40849823 CACGAAAAAA
Statistics
Matches: 186, Mismatches: 34, Indels: 45
0.70 0.13 0.17
Matches are distributed among these distances:
15 7 0.04
16 7 0.04
17 41 0.22
18 57 0.31
19 35 0.19
20 13 0.07
21 8 0.04
23 2 0.01
24 3 0.02
25 13 0.07
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:40849605 original size:19 final size:17
Alignment explanation
Indices: 40849565--40849628 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 17
40849555 ACAATAATAA
*
40849565 TTTTTGAAAACAC-AAAGA
1 TTTTTG-AAACACGAAA-T
40849583 TTTTTGAAACACGAAAAT
1 TTTTTGAAACACG-AAAT
*
40849601 TTTTTGAAAACACGGAATT
1 TTTTTG-AAACAC-GAAAT
40849620 TTTTTGAAA
1 TTTTTGAAA
40849629 ACAAGGAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 6 0.15
18 15 0.38
19 18 0.45
20 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (17 bp):
TTTTTGAAACACGAAAT
Found at i:40849714 original size:17 final size:17
Alignment explanation
Indices: 40849694--40849759 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
40849684 GAAAATTTCG
*
40849694 AAAACATGAATTTTTTT
1 AAAACACGAATTTTTTT
* *
40849711 AAAATACGATTTTTTTT
1 AAAACACGAATTTTTTT
40849728 AAAAAACACGAGATTTTTTTT
1 --AAAACACGA-A-TTTTTTT
40849749 GAAAACACGAA
1 -AAAACACGAA
40849760 AACATGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 14 0.36
19 9 0.23
20 9 0.23
21 7 0.18
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (17 bp):
AAAACACGAATTTTTTT
Found at i:40849744 original size:20 final size:20
Alignment explanation
Indices: 40849721--40849758 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40849711 AAAATACGAT
40849721 TTTTTTTAAAAAACACGAGA
1 TTTTTTTAAAAAACACGAGA
**
40849741 TTTTTTTTGAAAACACGA
1 TTTTTTTAAAAAACACGA
40849759 AAACATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
TTTTTTTAAAAAACACGAGA
Found at i:40849779 original size:17 final size:17
Alignment explanation
Indices: 40849757--40849822 Score: 87
Period size: 17 Copynumber: 3.8 Consensus size: 17
40849747 TTGAAAACAC
*
40849757 GAAAACATGAAAATTTT
1 GAAAACACGAAAATTTT
40849774 GAAAACACGAAAATTTT
1 GAAAACACGAAAATTTT
* *
40849791 TAAAACACGAGAATTTTTT
1 GAAAACACGA-AA-ATTTT
40849810 GAAAACACGAAAA
1 GAAAACACGAAAA
40849823 CACGAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 25 0.60
18 4 0.10
19 13 0.31
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (17 bp):
GAAAACACGAAAATTTT
Found at i:40849901 original size:16 final size:16
Alignment explanation
Indices: 40849836--40849905 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
40849826 GAAAAAAAAA
40849836 TTTT-AAACACGGGAAT
1 TTTTGAAACAC-GGAAT
*
40849852 TTTTGAAAACACGAAAT
1 TTTTG-AAACACGGAAT
* **
40849869 TTTTTATTCACGAGAAT
1 TTTTGAAACACG-GAAT
40849886 TTTTGAAACACGGAAT
1 TTTTGAAACACGGAAT
40849902 TTTT
1 TTTT
40849906 TTTAAAGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
16 17 0.40
17 20 0.47
18 6 0.14
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (16 bp):
TTTTGAAACACGGAAT
Found at i:40849906 original size:17 final size:15
Alignment explanation
Indices: 40849836--40849905 Score: 59
Period size: 16 Copynumber: 4.3 Consensus size: 15
40849826 GAAAAAAAAA
40849836 TTTTAAACACGGGAAT
1 TTTTAAACAC-GGAAT
*
40849852 TTTTGAAAACACGAAATT
1 TTTT--AAACACGGAA-T
**
40849870 TTTTATTCACGAGAAT
1 TTTTAAACACG-GAAT
40849886 TTTTGAAACACGGAAT
1 TTTT-AAACACGGAAT
40849902 TTTT
1 TTTT
40849906 TTTAAAGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 22 0.51
17 10 0.23
18 11 0.26
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (15 bp):
TTTTAAACACGGAAT
Found at i:40849907 original size:34 final size:34
Alignment explanation
Indices: 40849843--40849906 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
40849833 AAATTTTAAA
*
40849843 CACGGGAATTTTTGAAAACACGAAATTTTTTATT
1 CACGAGAATTTTTGAAAACACGAAATTTTTTATT
*
40849877 CACGAGAATTTTTG-AAACACGGAATTTTTT
1 CACGAGAATTTTTGAAAACACGAAATTTTTT
40849907 TTAAAGAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (34 bp):
CACGAGAATTTTTGAAAACACGAAATTTTTTATT
Found at i:40849958 original size:27 final size:28
Alignment explanation
Indices: 40849928--40849980 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
40849918 AACACGAATA
*
40849928 TATT-TTTTGAAACACGGGAAATTTTAT
1 TATTATTTTGAAACACGAGAAATTTTAT
40849955 TATTATTTTGAAACACGAGAAATTTT
1 TATTATTTTGAAACACGAGAAATTTT
40849981 GAAGACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (28 bp):
TATTATTTTGAAACACGAGAAATTTTAT
Found at i:40850000 original size:18 final size:17
Alignment explanation
Indices: 40849959--40850007 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
40849949 TTTTATTATT
40849959 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
40849976 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
40849993 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
40850008 TTTTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:40851416 original size:30 final size:28
Alignment explanation
Indices: 40851315--40851481 Score: 131
Period size: 29 Copynumber: 5.7 Consensus size: 28
40851305 GCTTCTGGGG
* *
40851315 CAAAAGTGTAATTTTAGGAAAATATAGGG-
1 CAAAA-TGTAATTTTA-GAAAGTTTAGGGT
**
40851344 CTAAAGCGTAATTTCTAGAAAGTTTAGGGT
1 C-AAAATGTAATTT-TAGAAAGTTTAGGGT
* * * *
40851374 TAAAGTGCAATTTTGAGAAAGTCTAAGGGT
1 CAAAATGTAATTTT-AGAAAGT-TTAGGGT
*
40851404 CAAAATGTAATTTTAGAAAGTTTTGGGGT
1 CAAAATGTAATTTTAGAAAG-TTTAGGGT
*
40851433 CAAAATGTAAATTTTAGAAAAGTTTGGGGT
1 CAAAATGT-AATTTTAG-AAAGTTTAGGGT
*
40851463 CAAAATATAAATTTT-GAAA
1 CAAAATGT-AATTTTAGAAA
40851482 AGTACAGGGG
Statistics
Matches: 116, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
28 4 0.03
29 55 0.47
30 53 0.46
31 4 0.03
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.32
Consensus pattern (28 bp):
CAAAATGTAATTTTAGAAAGTTTAGGGT
Found at i:40851492 original size:30 final size:30
Alignment explanation
Indices: 40851382--40851498 Score: 98
Period size: 30 Copynumber: 3.9 Consensus size: 30
40851372 GTTAAAGTGC
* *
40851382 AATTTT-GAGAAAGTCTAAGGGTCAAAATGT-
1 AATTTTAGA-AAAGTC-AGGGGTCAAAATATA
** *
40851412 AATTTTAG-AAAGTTTTGGGGTCAAAATGTA
1 AATTTTAGAAAAG-TCAGGGGTCAAAATATA
**
40851442 AATTTTAGAAAAGTTTGGGGTCAAAATATA
1 AATTTTAGAAAAGTCAGGGGTCAAAATATA
*
40851472 AATTTT-GAAAAGTACAGGGGTTAAAAT
1 AATTTTAGAAAAGT-CAGGGGTCAAAAT
40851499 GCAAAAAATA
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
29 23 0.31
30 47 0.63
31 5 0.07
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.32
Consensus pattern (30 bp):
AATTTTAGAAAAGTCAGGGGTCAAAATATA
Found at i:40851785 original size:75 final size:72
Alignment explanation
Indices: 40851693--40852050 Score: 321
Period size: 75 Copynumber: 4.7 Consensus size: 72
40851683 CTCGGCGTGC
* * * **
40851693 GACCCGAGACTCAACTCACCTCTAGAATTATGAGTTGATCTTCGAAAAACAAAAATCGAAAATAC
1 GACCCGAGGCTCAACTCACCTCTAGAATTATGAGTTGATTTTTGAAAAA-AAAAATTAAAAATAC
40851758 CTC-GACATGT
65 CTCAG-C--GT
* * * **
40851768 GCCCCGAGGTTCAACTCACCTCTCGCAA-TATGAGTTGATTTTTGAAAAACATGAATTGAAAAGA
1 GACCCGAGGCTCAACTCACCTCTAG-AATTATGAGTTGATTTTTGAAAAA-AAAAATT---AA-A
40851832 AATACCTC-GACGT
60 AATACCTCAG-CGT
* *
40851845 GCGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAGACCGAAATTAA
1 --GACCCGAGGCTCAACTCACCTCTAGAATTATGAGTTGA-TTTTTGAAAAAA-A---AAATTAA
40851910 AAATACCTCAGCGT
59 AAATACCTCAGCGT
* * **
40851924 GACCCAAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTAAAAAAAAGACCGAAATTAAAAA
1 GACCCGAGGCTCAACTCACCTCTAGAATTATGAGTTGATTTTTGAAAAAA-A---AAATTAAAAA
40851987 TACCTCAGCGT
62 TACCTCAGCGT
* *
40851998 GACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATATTTGAAAAAAAAA
1 GACCCGAGGCTCAACTCACCTCTAGAATTATGAGTTGATTTTTGAAAAAAAAA
40852051 CAGAAAGTGA
Statistics
Matches: 244, Mismatches: 23, Indels: 35
0.81 0.08 0.12
Matches are distributed among these distances:
72 2 0.01
74 57 0.23
75 60 0.25
76 23 0.09
77 24 0.10
78 2 0.01
79 58 0.24
80 14 0.06
83 4 0.02
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.25
Consensus pattern (72 bp):
GACCCGAGGCTCAACTCACCTCTAGAATTATGAGTTGATTTTTGAAAAAAAAAATTAAAAATACC
TCAGCGT
Found at i:40851865 original size:79 final size:75
Alignment explanation
Indices: 40851693--40852047 Score: 350
Period size: 79 Copynumber: 4.7 Consensus size: 75
40851683 CTCGGCGTGC
* * * * * *
40851693 GACCCGAGACTCAACTCACCTCTAGAATTATGAGTTGATCTTCGAAAAACA-A---AAATCGAAA
1 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAA-AGACCGAAAT-AAAA
40851754 ATACCTC-GACATGT
64 ATACCTCAG-C--GT
* * * ** *
40851768 GCCCCGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATGAATTGAAA-AGA
1 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAA-A-G-ACCGAAATAAA
40851832 AATACCTC-GACGT
63 AATACCTCAG-CGT
40851845 GCGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTGAAAAAAGACCGAAATTAA
1 --GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTGAAAAAAGACCGAAA-TAA
40851910 AAATACCTCAGCGT
62 AAATACCTCAGCGT
* * **
40851924 GACCCAAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTAAAAAAAAGACCGAAATTAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAAGACCGAAA-TAAAAA
40851987 TACCTCAGCGT
65 TACCTCAGCGT
* * *
40851998 GACCCGAGGCTCAACTCACCTCTAGTATTATGAGTTGATATTTGAAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAA
40852048 AAACAGAAAG
Statistics
Matches: 242, Mismatches: 24, Indels: 27
0.83 0.08 0.09
Matches are distributed among these distances:
74 57 0.24
75 57 0.24
76 21 0.09
77 29 0.12
78 2 0.01
79 61 0.25
80 12 0.05
81 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (75 bp):
GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAAAGACCGAAATAAAAAT
ACCTCAGCGT
Found at i:40852951 original size:15 final size:14
Alignment explanation
Indices: 40852923--40852981 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
40852913 TTCGTCTTGA
* *
40852923 TTTTTCTTTCTTTTC
1 TTTTTGTTT-TTTTT
40852938 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
*
40852952 TTGTTTG-TTTTTTG
1 TT-TTTGTTTTTTTT
40852966 TTTTTGTTTTTTTT
1 TTTTTGTTTTTTTT
40852980 TT
1 TT
40852982 GTGTGTTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
13 4 0.11
14 22 0.58
15 12 0.32
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (14 bp):
TTTTTGTTTTTTTT
Found at i:40852964 original size:17 final size:16
Alignment explanation
Indices: 40852923--40852981 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
40852913 TTCGTCTTGA
* * *
40852923 TTTTTCTTTCTTTTCT
1 TTTTTTTTTTTTTTGT
40852939 TTTTGTTTTTTTTTTGT
1 TTTT-TTTTTTTTTTGT
*
40852956 TTGTTTTTTGTTTTTGT
1 TT-TTTTTTTTTTTTGT
40852973 TTTTTTTTT
1 TTTTTTTTT
40852982 GTGTGTTGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 10 0.28
17 24 0.67
18 2 0.06
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTTTTTGT
Found at i:40852964 original size:28 final size:28
Alignment explanation
Indices: 40852933--40852988 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
40852923 TTTTTCTTTC
*
40852933 TTTTCTTTTTGTTTTTTTTTTGTTTGTT
1 TTTTCTTTTTGTTTTTTTTTTGTGTGTT
*
40852961 TTTTGTTTTTGTTTTTTTTTTGTGTGTT
1 TTTTCTTTTTGTTTTTTTTTTGTGTGTT
40852989 GGCATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (28 bp):
TTTTCTTTTTGTTTTTTTTTTGTGTGTT
Found at i:40852982 original size:17 final size:17
Alignment explanation
Indices: 40852933--40852983 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
40852923 TTTTTCTTTC
*
40852933 TTTTCTTTTTGTTTTT-T
1 TTTTGTTTTT-TTTTTGT
*
40852950 TTTTGTTTGTTTTTTGT
1 TTTTGTTTTTTTTTTGT
40852967 TTTTGTTTTTTTTTTGT
1 TTTTGTTTTTTTTTTGT
40852984 GTGTTGGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (17 bp):
TTTTGTTTTTTTTTTGT
Found at i:40852983 original size:11 final size:11
Alignment explanation
Indices: 40852923--40852981 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
40852913 TTCGTCTTGA
* *
40852923 TTTTTCTTTCT
1 TTTTTTTTTGT
*
40852934 TTTCTTTTTGT
1 TTTTTTTTTGT
40852945 TTTTTTTTTGT
1 TTTTTTTTTGT
*
40852956 TTGTTTTTTGT
1 TTTTTTTTTGT
40852967 TTTTGTTTTT-T
1 TTTT-TTTTTGT
40852978 TTTT
1 TTTT
40852982 GTGTGTTGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 36 0.88
12 5 0.12
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:40858721 original size:17 final size:17
Alignment explanation
Indices: 40858692--40858828 Score: 104
Period size: 18 Copynumber: 7.8 Consensus size: 17
40858682 ACACAATAAT
40858692 AATTTTTGAAAACACGA
1 AATTTTTGAAAACACGA
40858709 AGATTTTTG-AAACACGA
1 A-ATTTTTGAAAACACGA
40858726 AATTTTTTTGAAAACACGGA
1 AA--TTTTTGAAAACAC-GA
*
40858746 ATATTTTTGAAAACAAGGA
1 A-ATTTTTGAAAAC-ACGA
* *
40858765 AATTTTTG-ATACATGA
1 AATTTTTGAAAACACGA
40858781 GAATTTTTTG---ACACGAA
1 -AA-TTTTTGAAAACACG-A
* *
40858798 AAATTTTGAAAATACGA
1 AATTTTTGAAAACACGA
*
40858815 AATTTTCGAAAACA
1 AATTTTTGAAAACA
40858829 TGATTTTTTT
Statistics
Matches: 98, Mismatches: 9, Indels: 26
0.74 0.07 0.20
Matches are distributed among these distances:
15 5 0.05
16 10 0.10
17 28 0.29
18 30 0.31
19 20 0.20
20 4 0.04
21 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (17 bp):
AATTTTTGAAAACACGA
Found at i:40858734 original size:19 final size:19
Alignment explanation
Indices: 40858694--40858954 Score: 97
Period size: 18 Copynumber: 13.9 Consensus size: 19
40858684 ACAATAATAA
40858694 TTTTTGAAAACACGAAGA--
1 TTTTTGAAAACACGAA-ATT
40858712 TTTTTG-AAACACGAAATT
1 TTTTTGAAAACACGAAATT
* *
40858730 TTTTTGAAAACACGGAATA
1 TTTTTGAAAACACGAAATT
*
40858749 TTTTTGAAAACAAGGAAA--
1 TTTTTGAAAAC-ACGAAATT
* *
40858767 TTTTTG-ATACATGAGAA-T
1 TTTTTGAAAACACGA-AATT
*
40858785 TTTTTG---ACACGAAA-A
1 TTTTTGAAAACACGAAATT
* *
40858800 ATTTTGAAAATACGAAA--
1 TTTTTGAAAACACGAAATT
* * *
40858817 TTTTCGAAAACATG-ATTT
1 TTTTTGAAAACACGAAATT
* * *
40858835 TTTTTTAAAATACG-ATTT
1 TTTTTGAAAACACGAAATT
*
40858853 TTTTTAAAAAACACGAGAATTTT
1 TTTTT-GAAAACACGA-AA--TT
* *
40858876 TTTTTGAAAACCCGAAAACATGAAA
1 TTTTTGAAAACACG--AA-AT---T
* *
40858901 ATTTTGAAAACACGAAA-A
1 TTTTTGAAAACACGAAATT
*
40858919 TTTTTG-AAACACGAGAAAT
1 TTTTTGAAAACACGA-AATT
40858938 TTTTTGAAAACACGAAA
1 TTTTTGAAAACACGAAA
40858955 ACACGAAATT
Statistics
Matches: 189, Mismatches: 29, Indels: 49
0.71 0.11 0.18
Matches are distributed among these distances:
15 7 0.04
16 10 0.05
17 32 0.17
18 58 0.31
19 36 0.19
20 12 0.06
21 1 0.01
22 9 0.05
23 10 0.05
24 2 0.01
25 12 0.06
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:40858739 original size:36 final size:37
Alignment explanation
Indices: 40858676--40858771 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 37
40858666 ACACGAGAAC
* *
40858676 TTTGAAACACAATAATAATTTTTGAAAACAC-GAAGATT
1 TTTGAAACACGA-AAT-TTTTTTGAAAACACGGAAGATT
*
40858714 TTTGAAACACGAAATTTTTTTGAAAACACGGAATATT
1 TTTGAAACACGAAATTTTTTTGAAAACACGGAAGATT
*
40858751 TTTGAAAACAAGGAAATTTTT
1 TTTG-AAAC-ACGAAATTTTT
40858772 GATACATGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
36 13 0.25
37 13 0.25
38 15 0.29
39 10 0.20
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (37 bp):
TTTGAAACACGAAATTTTTTTGAAAACACGGAAGATT
Found at i:40858771 original size:37 final size:34
Alignment explanation
Indices: 40858692--40858773 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 34
40858682 ACACAATAAT
40858692 AATTTTTGAAAACACGAAGATTTTTGAAACACGA
1 AATTTTTGAAAACACGAAGATTTTTGAAACACGA
* *
40858726 AATTTTTTTGAAAACACGGAATATTTTTGAAAACAAGGA
1 AA--TTTTTGAAAACAC-GAAGATTTTTG-AAAC-ACGA
40858765 AATTTTTGA
1 AATTTTTGA
40858774 TACATGAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
34 2 0.05
36 13 0.32
37 17 0.41
38 4 0.10
39 5 0.12
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (34 bp):
AATTTTTGAAAACACGAAGATTTTTGAAACACGA
Found at i:40858844 original size:18 final size:17
Alignment explanation
Indices: 40858823--40858861 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40858813 GAAATTTTCG
*
40858823 AAAACATGATTTTTTTTT
1 AAAACACGA-TTTTTTTT
*
40858841 AAAATACGATTTTTTTT
1 AAAACACGATTTTTTTT
40858858 AAAA
1 AAAA
40858862 AACACGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (17 bp):
AAAACACGATTTTTTTT
Found at i:40858925 original size:18 final size:18
Alignment explanation
Indices: 40858889--40858955 Score: 93
Period size: 17 Copynumber: 3.7 Consensus size: 18
40858879 TTGAAAACCC
*
40858889 GAAAACATGAAAA-TTTT
1 GAAAACACGAAAATTTTT
40858906 GAAAACACGAAAATTTTT
1 GAAAACACGAAAATTTTT
40858924 G-AAACACGAGAAATTTTTT
1 GAAAACACGA-AAA-TTTTT
40858943 GAAAACACGAAAA
1 GAAAACACGAAAA
40858956 CACGAAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
17 20 0.44
18 8 0.18
19 9 0.20
20 8 0.18
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.24
Consensus pattern (18 bp):
GAAAACACGAAAATTTTT
Found at i:40858957 original size:45 final size:44
Alignment explanation
Indices: 40858906--40858999 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 44
40858896 TGAAAATTTT
40858906 GAAAACACGAAA-ATTTTTGAAACACGAGAAATTTTTTGAAAACAC
1 GAAAACACGAAATATTTTTGAAACACG-GAAA-TTTTTGAAAACAC
* * *
40858951 GAAAACACGAAATTTTTTTTTAAACACGGGAATTTTTGAAAACAC
1 GAAAACACGAAA-TATTTTTGAAACACGGAAATTTTTGAAAACAC
40858996 -AAAA
1 GAAAA
40859000 TTTTTTATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
44 4 0.09
45 25 0.57
46 3 0.07
47 12 0.27
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.27
Consensus pattern (44 bp):
GAAAACACGAAATATTTTTGAAACACGGAAATTTTTGAAAACAC
Found at i:40858960 original size:28 final size:27
Alignment explanation
Indices: 40858925--40858978 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40858915 AAAATTTTTG
40858925 AAACACGAGAAATTTTTTGAAAACACGA
1 AAACACGA-AAATTTTTTGAAAACACGA
* **
40858953 AAACACGAAATTTTTTTTTAAACACG
1 AAACACGAAAATTTTTTGAAAACACG
40858979 GGAATTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (27 bp):
AAACACGAAAATTTTTTGAAAACACGA
Found at i:40858976 original size:64 final size:63
Alignment explanation
Indices: 40858860--40859005 Score: 163
Period size: 64 Copynumber: 2.3 Consensus size: 63
40858850 TTTTTTTTAA
* * *
40858860 AAAACACGAGAATTTTTTTTTGAAAACCCGAAAACATGAAAATTTTGAAAACACGAAAATTTTTG
1 AAAACACGAGAA--ATTTTTTGAAAACACGAAAACACGAAAATTTTGAAAACACGAAAATTTTTG
* ** **
40858925 -AAACACGAGAAATTTTTTGAAAACACGAAAACACGAAATTTTTTTTTAAACACGGGAATTTTTG
1 AAAACACGAGAAATTTTTTGAAAACACGAAAACACGAAA--ATTTTGAAAACACGAAAATTTTTG
40858989 AAAACAC-A-AAATTTTTT
1 AAAACACGAGAAATTTTTT
40859006 ATTCACGAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
62 24 0.34
63 9 0.13
64 31 0.44
65 6 0.09
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (63 bp):
AAAACACGAGAAATTTTTTGAAAACACGAAAACACGAAAATTTTGAAAACACGAAAATTTTTG
Found at i:40859029 original size:17 final size:17
Alignment explanation
Indices: 40858966--40859037 Score: 67
Period size: 17 Copynumber: 4.3 Consensus size: 17
40858956 CACGAAATTT
* *
40858966 TTTTTTAAACACGGGAA
1 TTTTTGAAACACGAGAA
*
40858983 TTTTTGAAAACAC-AAAA
1 TTTTTG-AAACACGAGAA
* **
40859000 TTTTTTATTCACGAGAA
1 TTTTTGAAACACGAGAA
40859017 TTTTTGAAACACGA-AA
1 TTTTTGAAACACGAGAA
40859033 TTTTT
1 TTTTT
40859038 TTTAAAAGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
16 11 0.26
17 26 0.60
18 6 0.14
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:40859038 original size:17 final size:17
Alignment explanation
Indices: 40858953--40859038 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 17
40858943 GAAAACACGA
*
40858953 AAACACGAAATTTTTTTTT
1 AAACACGAAA--TTTTTTG
*
40858972 AAACACGGGAA-TTTTTG
1 AAACAC-GAAATTTTTTG
*
40858989 AAAACACAAAATTTTTT-
1 -AAACACGAAATTTTTTG
**
40859006 ATTCACGAGAA-TTTTTG
1 AAACACGA-AATTTTTTG
40859023 AAACACGAAATTTTTT
1 AAACACGAAATTTTTT
40859039 TTAAAAGAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
16 12 0.23
17 20 0.38
18 11 0.21
19 6 0.12
20 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (17 bp):
AAACACGAAATTTTTTG
Found at i:40859039 original size:34 final size:35
Alignment explanation
Indices: 40858951--40859040 Score: 121
Period size: 37 Copynumber: 2.6 Consensus size: 35
40858941 TTGAAAACAC
*
40858951 GAAAACACGAAATTTTTTTTTAAACACGGGAATTTTT
1 GAAAACACGAAATTTTTTTTT--ACACGAGAATTTTT
* *
40858988 GAAAACACAAAATTTTTTATT-CACGAGAATTTTT
1 GAAAACACGAAATTTTTTTTTACACGAGAATTTTT
40859022 G-AAACACGAAATTTTTTTT
1 GAAAACACGAAATTTTTTTT
40859041 AAAAGAAAGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 16 0.33
34 13 0.27
37 19 0.40
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (35 bp):
GAAAACACGAAATTTTTTTTTACACGAGAATTTTT
Found at i:40859136 original size:18 final size:17
Alignment explanation
Indices: 40859095--40859140 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
40859085 TATTATTATT
40859095 ATTTTGAAACAGGAGAA
1 ATTTTGAAACAGGAGAA
*
40859112 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACAGGAGAA
40859129 ATTTTTGAAACA
1 A-TTTTGAAACA
40859141 CGATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (17 bp):
ATTTTGAAACAGGAGAA
Found at i:40859535 original size:15 final size:16
Alignment explanation
Indices: 40859506--40859535 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40859496 TGCTAATTAA
40859506 ATTTAAATGAAATAAT
1 ATTTAAATGAAATAAT
40859522 ATTTAAAT-AAATAA
1 ATTTAAATGAAATAA
40859536 AACTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTTAAATGAAATAAT
Found at i:40859545 original size:20 final size:20
Alignment explanation
Indices: 40859509--40859552 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40859499 TAATTAAATT
*
40859509 TAAATGAAATAATATTTAAA
1 TAAATAAAATAATATTTAAA
40859529 TAAATAAAACTAA-ATTTAAA
1 TAAATAAAA-TAATATTTAAA
40859549 -AAAT
1 TAAAT
40859553 TTAAGGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 15 0.68
21 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAATAAAATAATATTTAAA
Found at i:40859950 original size:13 final size:13
Alignment explanation
Indices: 40859932--40859957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40859922 CTGCAGTTTG
40859932 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
40859945 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
40859958 TGACCCGACT
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:0.00, C:0.15, G:0.62, T:0.23
Consensus pattern (13 bp):
GGTCGGGTCGGGT
Found at i:40859994 original size:14 final size:15
Alignment explanation
Indices: 40859975--40860006 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
40859965 ACTGTTGATT
40859975 TTTCTTTTTT-TCTC
1 TTTCTTTTTTCTCTC
40859989 TTTCTTTTTTCTCTC
1 TTTCTTTTTTCTCTC
40860004 TTT
1 TTT
40860007 TTCTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTTCTCTC
Found at i:40859998 original size:21 final size:21
Alignment explanation
Indices: 40859973--40860020 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
40859963 CGACTGTTGA
* * *
40859973 TTTTTCTTTTTTTCTCTTTCT
1 TTTTTCTCTCTTTTTCTTTCT
40859994 TTTTTCTCTCTTTTTCTTTCT
1 TTTTTCTCTCTTTTTCTTTCT
40860015 TTTTTC
1 TTTTTC
40860021 CTTCTTCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTCTCTCTTTTTCTTTCT
Found at i:40860005 original size:11 final size:11
Alignment explanation
Indices: 40859973--40860026 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
40859963 CGACTGTTGA
40859973 TTTTTCTTT-T
1 TTTTTCTTTCT
*
40859983 TTTCTCTTTCT
1 TTTTTCTTTCT
*
40859994 TTTTTCTCTC-
1 TTTTTCTTTCT
40860004 TTTTTCTTTCT
1 TTTTTCTTTCT
*
40860015 TTTTTCCTTCT
1 TTTTTCTTTCT
40860026 T
1 T
40860027 CTTCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
10 17 0.46
11 20 0.54
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:40860026 original size:21 final size:21
Alignment explanation
Indices: 40859973--40860032 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
40859963 CGACTGTTGA
* * *
40859973 TTTTTCTTTTTTTCTCTTTCT
1 TTTTTCCTTCTTTTTCTTTCT
40859994 TTTTT-CTCTCTTTTTCTTTCT
1 TTTTTCCT-TCTTTTTCTTTCT
*
40860015 TTTTTCCTTCTTCTTCTT
1 TTTTTCCTTCTTTTTCTT
40860033 CGGGTCACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.91
22 2 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTTCCTTCTTTTTCTTTCT
Found at i:40860345 original size:24 final size:26
Alignment explanation
Indices: 40860291--40860347 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
40860281 GAGGCTTTGC
40860291 TTGCTGCTATTTTTTTTGAATTTTCT
1 TTGCTGCTATTTTTTTTGAATTTTCT
* ** *
40860317 CTGCTG-T-TTTTTTTTGTTTTTTTT
1 TTGCTGCTATTTTTTTTGAATTTTCT
40860341 TTGCTGC
1 TTGCTGC
40860348 CTAAAATCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 19 0.76
25 1 0.04
26 5 0.20
ACGTcount: A:0.05, C:0.12, G:0.14, T:0.68
Consensus pattern (26 bp):
TTGCTGCTATTTTTTTTGAATTTTCT
Found at i:40860619 original size:30 final size:30
Alignment explanation
Indices: 40860557--40860695 Score: 144
Period size: 30 Copynumber: 4.7 Consensus size: 30
40860547 TTCTGGGGCA
* * *
40860557 AAAGTGTAATTTTAGAAAAATATA-GGGCT
1 AAAGTGTAATTTTAGAAAAGTTTAGGGGTT
40860586 AAAGTGTAATTTCTAG-AAAGTTTAGGGGTT
1 AAAGTGTAATTT-TAGAAAAGTTTAGGGGTT
* *
40860616 AAAGTGAAATTTT-GAGAAAGTTTAAGGGTT
1 AAAGTGTAATTTTAGA-AAAGTTTAGGGGTT
* *
40860646 AAAATGTAATTTTAGAAAAGTTT-GGGGTC
1 AAAGTGTAATTTTAGAAAAGTTTAGGGGTT
*
40860675 AAAATGTAAATTTT-GAAAAGT
1 AAAGTGT-AATTTTAGAAAAGT
40860696 ACAGGGGTCA
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.01
29 37 0.39
30 55 0.58
31 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAGTGTAATTTTAGAAAAGTTTAGGGGTT
Found at i:40860709 original size:59 final size:57
Alignment explanation
Indices: 40860550--40860717 Score: 162
Period size: 59 Copynumber: 2.9 Consensus size: 57
40860540 GCAAAGCTTC
* * *
40860550 TGGGG-CAAAAGTGT-AATTTTAGAAAAATATAGGGCTAAAGTGTAATTTCTAGAAAGTT
1 TGGGGTCAAAA-TGTAAATTTT-GAAAAGTATAGGGGTAAAATGTAATTT-TAGAAAGTT
* * * *
40860608 TAGGGGTTAAAGTG-AAATTTTGAGAAAGTTTAAGGGTTAAAATGTAATTTTAGAAAAGTT
1 T-GGGGTCAAAATGTAAATTTTGA-AAAGTAT-AGGGGTAAAATGTAATTTTAG-AAAGTT
* *
40860668 TGGGGTCAAAATGTAAATTTTGAAAAGTACAGGGGTCAAAATGCAATTTT
1 TGGGGTCAAAATGTAAATTTTGAAAAGTATAGGGGT-AAAATGTAATTTT
40860718 TTAATTTTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
58 8 0.09
59 47 0.52
60 35 0.39
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (57 bp):
TGGGGTCAAAATGTAAATTTTGAAAAGTATAGGGGTAAAATGTAATTTTAGAAAGTT
Found at i:40860715 original size:29 final size:28
Alignment explanation
Indices: 40860602--40860717 Score: 106
Period size: 30 Copynumber: 3.9 Consensus size: 28
40860592 TAATTTCTAG
* *
40860602 AAAGTTTAGGGGTTAAAGTGAAATTTTGA
1 AAAG-TTAGGGGTCAAAATGAAATTTTGA
* * *
40860631 GAAAGTTTAAGGGTTAAAATGTAATTTTAGA
1 -AAAG-TTAGGGGTCAAAATGAAATTTT-GA
*
40860662 AAAGTTTGGGGTCAAAATGTAAATTTTGA
1 AAAGTTAGGGGTCAAAATG-AAATTTTGA
* *
40860691 AAAGTACAGGGGTCAAAATGCAATTTT
1 AAAGT-TAGGGGTCAAAATGAAATTTT
40860718 TTAATTTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 25 0.34
30 46 0.63
31 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (28 bp):
AAAGTTAGGGGTCAAAATGAAATTTTGA
Found at i:40867212 original size:6 final size:6
Alignment explanation
Indices: 40867193--40867230 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
40867183 TTTCATCTTC
40867193 TTTATT TTCT-TT TTTATT TTTATT TTTATT TTTCATT T
1 TTTATT TT-TATT TTTATT TTTATT TTTATT TTT-ATT T
40867231 ACTTGTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.03
6 23 0.79
7 5 0.17
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:40873895 original size:12 final size:12
Alignment explanation
Indices: 40873878--40873902 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40873868 CAAGGCAGGA
40873878 GCCCAACACAAG
1 GCCCAACACAAG
40873890 GCCCAACACAAG
1 GCCCAACACAAG
40873902 G
1 G
40873903 ACTAACACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (12 bp):
GCCCAACACAAG
Found at i:40886414 original size:106 final size:106
Alignment explanation
Indices: 40886229--40886442 Score: 428
Period size: 106 Copynumber: 2.0 Consensus size: 106
40886219 CGAACATATG
40886229 TGGTGAATAGTAGTTGAAGGAGGATAATAAAATGATCCAAAATACATATTTGTACTTTTATAGAG
1 TGGTGAATAGTAGTTGAAGGAGGATAATAAAATGATCCAAAATACATATTTGTACTTTTATAGAG
40886294 GAATTATGATTAAAGTTTGCTATGATTATTGTTGAAACTCT
66 GAATTATGATTAAAGTTTGCTATGATTATTGTTGAAACTCT
40886335 TGGTGAATAGTAGTTGAAGGAGGATAATAAAATGATCCAAAATACATATTTGTACTTTTATAGAG
1 TGGTGAATAGTAGTTGAAGGAGGATAATAAAATGATCCAAAATACATATTTGTACTTTTATAGAG
40886400 GAATTATGATTAAAGTTTGCTATGATTATTGTTGAAACTCT
66 GAATTATGATTAAAGTTTGCTATGATTATTGTTGAAACTCT
40886441 TG
1 TG
40886443 AAGAGGTCAA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 108 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (106 bp):
TGGTGAATAGTAGTTGAAGGAGGATAATAAAATGATCCAAAATACATATTTGTACTTTTATAGAG
GAATTATGATTAAAGTTTGCTATGATTATTGTTGAAACTCT
Found at i:40889608 original size:25 final size:26
Alignment explanation
Indices: 40889555--40889625 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
40889545 AGTCATATCG
40889555 GGAAGCTC-CGAAGAGCCATTAATCA
1 GGAAGCTCACGAAGAGCCATTAATCA
* * *
40889580 GGAAGCTCACAAAGAGCCTTTAAT-T
1 GGAAGCTCACGAAGAGCCATTAATCA
40889605 GGAAAGCTCACGAAGAGCCAT
1 GG-AAGCTCACGAAGAGCCAT
40889626 ATATCGGGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.26
26 29 0.74
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCA
Found at i:40889639 original size:26 final size:27
Alignment explanation
Indices: 40889396--40889640 Score: 102
Period size: 25 Copynumber: 9.9 Consensus size: 27
40889386 ACCCTCTATC
* * *
40889396 GAGCCATATAA-CAGGAAGCTCATG-T
1 GAGCCATATAATCGGGAAGCTCACGAA
** *
40889421 GAGCTGTATAA-CGGGAAGCTCA-TAA
1 GAGCCATATAATCGGGAAGCTCACGAA
* * *
40889446 GAGTC--ATAATCGGGAAGCTCATG-C
1 GAGCCATATAATCGGGAAGCTCACGAA
* *
40889470 GAGCCA-ATAAT-GGGTAGCT-TCGAA
1 GAGCCATATAATCGGGAAGCTCACGAA
* *
40889494 GAGTCAT-TAATCAGGAAGCTCTA-G-A
1 GAGCCATATAATCGGGAAGCTC-ACGAA
* * * * *
40889519 TAGCCATAT-ATAGGGAAGTTCATG-C
1 GAGCCATATAATCGGGAAGCTCACGAA
*
40889544 GAGTC--AT-ATCGGGAAGCTC-CGAA
1 GAGCCATATAATCGGGAAGCTCACGAA
* *
40889567 GAGCCAT-TAATCAGGAAGCTCACAAA
1 GAGCCATATAATCGGGAAGCTCACGAA
* * *
40889593 GAGCC-TTTAATTGGAAAGCTCACGAA
1 GAGCCATATAATCGGGAAGCTCACGAA
*
40889619 GAGCCATAT-ATCGGGATGCTCA
1 GAGCCATATAATCGGGAAGCTCA
40889641 TAAGAGCTAT
Statistics
Matches: 161, Mismatches: 41, Indels: 35
0.68 0.17 0.15
Matches are distributed among these distances:
22 1 0.01
23 21 0.13
24 33 0.20
25 64 0.40
26 40 0.25
27 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (27 bp):
GAGCCATATAATCGGGAAGCTCACGAA
Found at i:40895343 original size:20 final size:20
Alignment explanation
Indices: 40895292--40895344 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
40895282 TATGAACTTC
40895292 TTCC-TTTACTTAGTTACCA
1 TTCCATTTACTTAGTTACCA
* *
40895311 TTCCATCTT-CTTATTTTCCA
1 TTCCAT-TTACTTAGTTACCA
*
40895331 TTTCATTTACTTAG
1 TTCCATTTACTTAG
40895345 CATTAACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 6 0.22
20 19 0.70
21 2 0.07
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.53
Consensus pattern (20 bp):
TTCCATTTACTTAGTTACCA
Found at i:40896088 original size:20 final size:20
Alignment explanation
Indices: 40896040--40896164 Score: 65
Period size: 20 Copynumber: 6.3 Consensus size: 20
40896030 AGATGCATAA
40896040 CAGGGGCACCAAAGTGCAAT
1 CAGGGGCACCAAAGTGCAAT
* * * * *
40896060 CAAGAGCACGAATGTGCGAT
1 CAGGGGCACCAAAGTGCAAT
* * *
40896080 CAGGGGCACCGAAGTGAAAA
1 CAGGGGCACCAAAGTGCAAT
* * *
40896100 CAAGGG-AACAAATGTGCATT
1 CAGGGGCACCAAA-GTGCAAT
* * * *
40896120 CAGGGGTACCGAAGTACAAA
1 CAGGGGCACCAAAGTGCAAT
* **
40896140 CAAGGG-AGGAAAGTGCAAT
1 CAGGGGCACCAAAGTGCAAT
40896159 CAGGGG
1 CAGGGG
40896165 TATTGAAGTA
Statistics
Matches: 71, Mismatches: 32, Indels: 5
0.66 0.30 0.05
Matches are distributed among these distances:
19 17 0.24
20 50 0.70
21 4 0.06
ACGTcount: A:0.38, C:0.18, G:0.33, T:0.11
Consensus pattern (20 bp):
CAGGGGCACCAAAGTGCAAT
Found at i:40896182 original size:20 final size:19
Alignment explanation
Indices: 40896120--40896357 Score: 102
Period size: 20 Copynumber: 11.9 Consensus size: 19
40896110 AATGTGCATT
40896120 CAGGGGTACCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
* * * *
40896140 CAAGGG-AGGAAAGTGCAAT
1 CAGGGGTACG-AAGTACAAA
*
40896159 CAGGGGTATTGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
* * *
40896179 CAGGGGCACGTAAGTGCAAT
1 CAGGGGTACG-AAGTACAAA
* **
40896199 CAAGGGTAAAAAAGTACAAA
1 CAGGGGT-ACGAAGTACAAA
* * *
40896219 CAGGGGCACAGATGTA-AATT
1 CAGGGGTAC-GAAGTACAA-A
40896239 CAGGGGTACTGAAGTACAAA
1 CAGGGGTAC-GAAGTACAAA
* * * *
40896259 AAAGGGCACGCAAGTACAAT
1 CAGGGGTACG-AAGTACAAA
* *
40896279 CAGGGGTACCAGAGTATAAA
1 CAGGGGTACGA-AGTACAAA
* * * *
40896299 CAAGGGCACGTAAGTGCAAT
1 CAGGGGTACG-AAGTACAAA
* *
40896319 TAGAGGTACAGAAGTACAAA
1 CAGGGGTAC-GAAGTACAAA
*
40896339 CAGGGGCACGTAAGTACAA
1 CAGGGGTACG-AAGTACAA
40896358 TCATTCAATA
Statistics
Matches: 152, Mismatches: 53, Indels: 26
0.66 0.23 0.11
Matches are distributed among these distances:
18 1 0.01
19 20 0.13
20 125 0.82
21 6 0.04
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (19 bp):
CAGGGGTACGAAGTACAAA
Found at i:40896206 original size:40 final size:40
Alignment explanation
Indices: 40896051--40896360 Score: 247
Period size: 40 Copynumber: 7.8 Consensus size: 40
40896041 AGGGGCACCA
* * * * * *
40896051 AAGTGCAATCAAGAGCACG-AATGTGCGATCAGGGGCACCG
1 AAGTACAAACAAGGGCACGTAA-GTGCAATCAGGGGTACAG
* * * *
40896091 AAGTGA-AAACAAGGGAAC-AAATGTGCATTCAGGGGTACCG
1 AAGT-ACAAACAAGGGCACGTAA-GTGCAATCAGGGGTACAG
* * **
40896131 AAGTACAAACAAGGG-AGGAAAGTGCAATCAGGGGTATTG
1 AAGTACAAACAAGGGCACGTAAGTGCAATCAGGGGTACAG
* * * *
40896170 AAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAAAA
1 AAGTACAAACAAGGGCACGTAAGTGCAATCAGGGGTACAG
* * * *
40896210 AAGTACAAACAGGGGCACAG-ATGT-AAATTCAGGGGTACTG
1 AAGTACAAACAAGGGCAC-GTAAGTGCAA-TCAGGGGTACAG
* * *
40896250 AAGTACAAAAAAGGGCACGCAAGTACAATCAGGGGTACCAG
1 AAGTACAAACAAGGGCACGTAAGTGCAATCAGGGGTA-CAG
* * *
40896291 -AGTATAAACAAGGGCACGTAAGTGCAATTAGAGGTACAG
1 AAGTACAAACAAGGGCACGTAAGTGCAATCAGGGGTACAG
* *
40896330 AAGTACAAACAGGGGCACGTAAGTACAATCA
1 AAGTACAAACAAGGGCACGTAAGTGCAATCA
40896361 TTCAATAATT
Statistics
Matches: 220, Mismatches: 39, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
39 37 0.17
40 178 0.81
41 5 0.02
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (40 bp):
AAGTACAAACAAGGGCACGTAAGTGCAATCAGGGGTACAG
Found at i:40896243 original size:60 final size:58
Alignment explanation
Indices: 40896171--40896347 Score: 151
Period size: 60 Copynumber: 3.0 Consensus size: 58
40896161 GGGGTATTGA
* *
40896171 AGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAAAAAAGTACAAACAGGGGCACAG
1 AGTATAAACAGGGGCACGTAAGTGCAAT-AAGGGTACAAAAGTACAAACAGGGGCACAG
* * * * * ** * *
40896230 ATGTA-AATTCAGGGGTAC-TGAAGTACAAAAAAGGGCACGCAAGTACAATCAGGGGTACCAG
1 A-GTATAA-ACAGGGGCACGT-AAGTGC-AATAAGGGTACAAAAGTACAAACAGGGGCA-CAG
* * *
40896291 AGTATAAACAAGGGCACGTAAGTGCAATTAGAGGTACAGAAGTACAAACAGGGGCAC
1 AGTATAAACAGGGGCACGTAAGTGCAATAAG-GGTACAAAAGTACAAACAGGGGCAC
40896348 GTAAGTACAA
Statistics
Matches: 89, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
59 9 0.10
60 71 0.80
61 9 0.10
ACGTcount: A:0.42, C:0.16, G:0.28, T:0.14
Consensus pattern (58 bp):
AGTATAAACAGGGGCACGTAAGTGCAATAAGGGTACAAAAGTACAAACAGGGGCACAG
Found at i:40908976 original size:20 final size:20
Alignment explanation
Indices: 40908927--40908977 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 20
40908917 TCCTGTATCA
*
40908927 TGTCTCAAATCAGTATGGCC
1 TGTCTTAAATCAGTATGGCC
40908947 --TCTT---TCAGTATGGCC
1 TGTCTTAAATCAGTATGGCC
40908962 TGTCTTAAATCAGTAT
1 TGTCTTAAATCAGTAT
40908978 CATGCAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 10
0.69 0.03 0.28
Matches are distributed among these distances:
15 11 0.44
17 4 0.16
18 3 0.12
20 7 0.28
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (20 bp):
TGTCTTAAATCAGTATGGCC
Found at i:40912958 original size:12 final size:12
Alignment explanation
Indices: 40912933--40912971 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40912923 ACTCGCTTCT
* *
40912933 TTACTTACTCAC
1 TTACTTGCTTAC
*
40912945 TTACTTGTTTAC
1 TTACTTGCTTAC
40912957 TTACTTGCTTAC
1 TTACTTGCTTAC
40912969 TTA
1 TTA
40912972 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:40913288 original size:50 final size:55
Alignment explanation
Indices: 40913220--40913360 Score: 168
Period size: 50 Copynumber: 2.6 Consensus size: 55
40913210 TTTTCTGTAC
* *
40913220 TGCCAATGCCATATCCCAGATATGGTCTTACATAGGAG-TTCTCAT-A-C-CAAT-
1 TGCCAATGCCATGTCCCAGATATGGTCTTACAT-GGAGCCTCTCATAATCTCAATA
* * *
40913271 T-CCCATGCCATGTCCCAGACATGGTCTTACATGGGGCCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGAGCCTCTCATAATCTCAAT-A
*
40913326 TGCCAATGCCATGTCTCAGATATGGTCTTACATGG
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGG
40913361 GATCTCTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
49 3 0.04
50 34 0.45
51 2 0.03
52 1 0.01
53 4 0.05
55 1 0.01
56 30 0.40
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (55 bp):
TGCCAATGCCATGTCCCAGATATGGTCTTACATGGAGCCTCTCATAATCTCAATA
Found at i:40918718 original size:25 final size:25
Alignment explanation
Indices: 40918687--40918835 Score: 104
Period size: 25 Copynumber: 6.0 Consensus size: 25
40918677 GTCCTGATAC
*
40918687 TTGGCTCTCATGAGCTGCCCATTAT
1 TTGGCTCTCATGAGCTTCCCATTAT
* * * * *
40918712 TTAGCTCTTAGGAGCATCCCAATAT
1 TTGGCTCTCATGAGCTTCCCATTAT
* ***
40918737 ATGGCTCT-ATTGAGCTTCATGTTAT
1 TTGGCTCTCA-TGAGCTTCCCATTAT
** * * *
40918762 TTGGCTCTCCGGAGCTCCCCGTTAA
1 TTGGCTCTCATGAGCTTCCCATTAT
*
40918787 TTAGCTCTCATGAGCTTCCCAATTA-
1 TTGGCTCTCATGAGCTTCCC-ATTAT
* *
40918812 ATGGCTCTCTTGAGCTTCCCATTA
1 TTGGCTCTCATGAGCTTCCCATTA
40918836 CGGCCCGTAT
Statistics
Matches: 92, Mismatches: 29, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
24 5 0.05
25 84 0.91
26 3 0.03
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36
Consensus pattern (25 bp):
TTGGCTCTCATGAGCTTCCCATTAT
Found at i:40918791 original size:75 final size:75
Alignment explanation
Indices: 40918687--40918829 Score: 189
Period size: 75 Copynumber: 1.9 Consensus size: 75
40918677 GTCCTGATAC
* * * *
40918687 TTGGCTCTCATGAGCTGCCCATTATTTAGCTCTTAGGAGCATCCCAA-TATATGGCTCTATTGAG
1 TTGGCTCTCAGGAGCTCCCCATTAATTAGCTCTCAGGAGCATCCCAATTA-ATGGCTCTATTGAG
40918751 CTTCATGTTAT
65 CTTCATGTTAT
* * * * *
40918762 TTGGCTCTCCGGAGCTCCCCGTTAATTAGCTCTCATGAGCTTCCCAATTAATGGCTCTCTTGAGC
1 TTGGCTCTCAGGAGCTCCCCATTAATTAGCTCTCAGGAGCATCCCAATTAATGGCTCTATTGAGC
40918827 TTC
66 TTC
40918830 CCATTACGGC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 56 0.97
76 2 0.03
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.36
Consensus pattern (75 bp):
TTGGCTCTCAGGAGCTCCCCATTAATTAGCTCTCAGGAGCATCCCAATTAATGGCTCTATTGAGC
TTCATGTTAT
Found at i:40918932 original size:25 final size:24
Alignment explanation
Indices: 40918846--40918932 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
40918836 CGGCCCGTAT
* * *
40918846 GAGCTTCCCGATAATTGGCTCGTAA
1 GAGCTTCCCGTTAA-TGGCTTGAAA
* * *
40918871 GAGCTTCTCGTTACATGGC-TCACAT
1 GAGCTTCCCGTTA-ATGGCTTGA-AA
40918896 GAGCTTCCCGTTATATGGCTTGAAA
1 GAGCTTCCCGTTA-ATGGCTTGAAA
40918921 GAGCTTCCCGTT
1 GAGCTTCCCGTT
40918933 TACATGCCCA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
25 46 0.94
26 3 0.06
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTTGAAA
Found at i:40923466 original size:22 final size:22
Alignment explanation
Indices: 40923424--40923469 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40923414 GGGCAGAAGA
*
40923424 ATTTTGTTCATAATAAGATAAT
1 ATTTTATTCATAATAAGATAAT
*
40923446 ATTTTATT-ATAATTAATATAAT
1 ATTTTATTCATAA-TAAGATAAT
40923468 AT
1 AT
40923470 ATAAACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTTATTCATAATAAGATAAT
Found at i:40923742 original size:20 final size:21
Alignment explanation
Indices: 40923717--40923761 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
40923707 CGATAATATA
40923717 TTAAGAATATTATT-TAAAAT
1 TTAAGAATATTATTCTAAAAT
*
40923737 TTAAGATTATTATTGCTAAAAT
1 TTAAGAATATTATT-CTAAAAT
40923759 TTA
1 TTA
40923762 TTATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
22 9 0.41
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TTAAGAATATTATTCTAAAAT
Found at i:40923775 original size:17 final size:18
Alignment explanation
Indices: 40923753--40923790 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40923743 TTATTATTGC
*
40923753 TAAAATT-TATTATTAAA
1 TAAAATTGTAATATTAAA
*
40923770 TAAAATTGTAATATTACA
1 TAAAATTGTAATATTAAA
40923788 TAA
1 TAA
40923791 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
TAAAATTGTAATATTAAA
Found at i:40930265 original size:18 final size:18
Alignment explanation
Indices: 40930232--40930325 Score: 106
Period size: 18 Copynumber: 5.4 Consensus size: 18
40930222 AAGGTTTTCT
40930232 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
40930247 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
*
40930265 TATTGATGCTAGTGACGA
1 TATTGATGATAGTGACGA
* *
40930283 TATTGAT-ACTAATGACGC
1 TATTGATGA-TAGTGACGA
* *
40930301 TATTGATGATAGTGATGC
1 TATTGATGATAGTGACGA
40930319 TATTGAT
1 TATTGAT
40930326 CGTGACCTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
15 11 0.16
16 1 0.01
18 55 0.81
19 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:40930325 original size:9 final size:9
Alignment explanation
Indices: 40930265--40930325 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
40930255 ATAGTGACGA
40930265 TATTGATGC
1 TATTGATGC
* * *
40930274 TAGTGACGA
1 TATTGATGC
*
40930283 TATTGATAC
1 TATTGATGC
* *
40930292 TAATGACGC
1 TATTGATGC
*
40930301 TATTGATGA
1 TATTGATGC
*
40930310 TAGTGATGC
1 TATTGATGC
40930319 TATTGAT
1 TATTGAT
40930326 CGTGACCTTG
Statistics
Matches: 36, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (9 bp):
TATTGATGC
Found at i:40933031 original size:22 final size:22
Alignment explanation
Indices: 40933003--40933045 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
40932993 TTTATTGTTC
40933003 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
40933025 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
40933046 TAGCCATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:40935849 original size:22 final size:23
Alignment explanation
Indices: 40935819--40935866 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40935809 CGTCTCAGAT
*
40935819 ATACGAACAGA-TATCAGAATTC
1 ATACAAACAGATTATCAGAATTC
* *
40935841 ATACAAACAGATTATCGGATTTC
1 ATACAAACAGATTATCAGAATTC
40935864 ATA
1 ATA
40935867 TTTTACAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (23 bp):
ATACAAACAGATTATCAGAATTC
Found at i:40938189 original size:5 final size:5
Alignment explanation
Indices: 40938179--40938210 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
40938169 TATGTTTTTT
40938179 ATAAA ATAAA ATAAA ATATAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATA-AA ATAAA ATAAA A
40938211 ATAATTAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:40938203 original size:16 final size:15
Alignment explanation
Indices: 40938182--40938214 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
40938172 GTTTTTTATA
40938182 AAATAAAATAAAATAT
1 AAATAAAATAAAA-AT
40938198 AAATAAAATAAAAAT
1 AAATAAAATAAAAAT
40938213 AA
1 AA
40938215 TTAGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAAAATAAAAAT
Found at i:40938212 original size:11 final size:11
Alignment explanation
Indices: 40938179--40938214 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
40938169 TATGTTTTTT
40938179 ATAAAAT-AAA
1 ATAAAATAAAA
*
40938189 ATAAAATATAA
1 ATAAAATAAAA
40938200 ATAAAATAAAA
1 ATAAAATAAAA
40938211 ATAA
1 ATAA
40938215 TTAGATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:40938495 original size:29 final size:30
Alignment explanation
Indices: 40938461--40938519 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
40938451 TTTGGTATAA
* * *
40938461 TGTACAATTTTATATATAAACTTTT-ATTT
1 TGTACAACTTTATACATAAAATTTTGATTT
40938490 TGTACAACTTTATACATAAAATTTTGATTT
1 TGTACAACTTTATACATAAAATTTTGATTT
40938520 GATCTCGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (30 bp):
TGTACAACTTTATACATAAAATTTTGATTT
Found at i:40942800 original size:30 final size:30
Alignment explanation
Indices: 40942764--40942826 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
40942754 AATTATTTTA
40942764 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
40942794 TTGTTAATTTTGTTATTGTTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
40942824 TTG
1 TTG
40942827 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:40943497 original size:18 final size:18
Alignment explanation
Indices: 40943470--40943513 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40943460 CGCCTTCTTC
*
40943470 TCCCCTTTCCCCTTTCCCT
1 TCCCC-TTCCACTTTCCCT
*
40943489 TCCCCTTCCATTTTCCCT
1 TCCCCTTCCACTTTCCCT
40943507 TCCCCTT
1 TCCCCTT
40943514 GGGTTGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.02, C:0.55, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCCCTTCCACTTTCCCT
Found at i:40943825 original size:11 final size:11
Alignment explanation
Indices: 40943809--40943834 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40943799 TTGCTGGATG
40943809 ATATTTTGGTT
1 ATATTTTGGTT
40943820 ATATTTTGGTT
1 ATATTTTGGTT
40943831 ATAT
1 ATAT
40943835 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:40946181 original size:22 final size:20
Alignment explanation
Indices: 40946138--40946176 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40946128 TAATTTAAAA
40946138 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
40946158 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
40946177 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:40946281 original size:14 final size:15
Alignment explanation
Indices: 40946259--40946335 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
40946249 CAATCAAACA
40946259 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
40946273 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
40946288 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
40946308 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
40946322 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
40946336 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:40946300 original size:20 final size:20
Alignment explanation
Indices: 40946275--40946314 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40946265 AATATTTTCC
*
40946275 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40946295 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40946315 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40946320 original size:34 final size:35
Alignment explanation
Indices: 40946263--40946329 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40946253 CAAACACCAG
*
40946263 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
40946298 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40946330 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40946336 original size:14 final size:14
Alignment explanation
Indices: 40946298--40946337 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
40946288 ACAGAAAAGT
*
40946298 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
40946312 AAATCATTTTACGG
1 AAAACATTTTACAG
40946326 AAAACATTTTAC
1 AAAACATTTTAC
40946338 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:40949096 original size:9 final size:9
Alignment explanation
Indices: 40949079--40949115 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40949069 TGAGTTTTCG
40949079 AATTCGAAT
1 AATTCGAAT
*
40949088 AACTCGAAT
1 AATTCGAAT
40949097 AATTCGAAT
1 AATTCGAAT
40949106 AATTCGAAT
1 AATTCGAAT
40949115 A
1 A
40949116 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40949684 original size:13 final size:13
Alignment explanation
Indices: 40949666--40949691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40949656 AGTAGTAATA
40949666 ATACTATTTATAT
1 ATACTATTTATAT
40949679 ATACTATTTATAT
1 ATACTATTTATAT
40949692 TATTAAATTA
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:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ATACTATTTATAT
Found at i:40950220 original size:5 final size:5
Alignment explanation
Indices: 40950210--40950235 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40950200 CTCGAAAATT
40950210 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
40950236 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:40951045 original size:20 final size:20
Alignment explanation
Indices: 40951008--40951045 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40950998 TTATTTAATA
*
40951008 AATTCATTTTTAATAAATTT
1 AATTCATTTTTAAAAAATTT
40951028 AATT-ATTTTTCAAAAAAT
1 AATTCATTTTT-AAAAAAT
40951046 GTTATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTCATTTTTAAAAAATTT
Found at i:40954000 original size:30 final size:30
Alignment explanation
Indices: 40953964--40954021 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
40953954 TAGGTACAAC
40953964 TGATGATAATGG-AAAATAATGTTATGAATG
1 TGATGATAATGGAAAAAT-ATGTTATGAATG
40953994 TGATGATAATGGAAAAATATGTTATGAA
1 TGATGATAATGGAAAAATATGTTATGAA
40954022 ACATGTGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.33
Consensus pattern (30 bp):
TGATGATAATGGAAAAATATGTTATGAATG
Found at i:40956524 original size:26 final size:25
Alignment explanation
Indices: 40956488--40956558 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
40956478 AAAAAATAAA
*
40956488 ATTTACCAAAATATTATAATTTTTTT
1 ATTTACCAAAATATTATAA-ATTTTT
* *
40956514 ATTTATCAAAAAATATATAAATTTTT
1 ATTTACCAAAATAT-TATAAATTTTT
40956540 ATTTACCAAAATA-TATAAA
1 ATTTACCAAAATATTATAAA
40956559 AAAAACCTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
24 6 0.15
26 28 0.72
27 5 0.13
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTACCAAAATATTATAAATTTTT
Found at i:40956572 original size:13 final size:13
Alignment explanation
Indices: 40956556--40956588 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
40956546 CAAAATATAT
40956556 AAAAAAAACCTGC
1 AAAAAAAACCTGC
40956569 AAAAAAAACCTGC
1 AAAAAAAACCTGC
40956582 AAAAAAA
1 AAAAAAA
40956589 GAAATCTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.70, C:0.18, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAAAAACCTGC
Found at i:40956660 original size:27 final size:27
Alignment explanation
Indices: 40956630--40956696 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
40956620 CGCCAATGGG
40956630 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
** *
40956657 ATTGGCGGCACCAATTGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
40956684 ATTGGCGGCACCA
1 ATTGGCGGCACCA
40956697 CTTAATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:40956749 original size:4 final size:4
Alignment explanation
Indices: 40956740--40956884 Score: 101
Period size: 4 Copynumber: 36.0 Consensus size: 4
40956730 GAAGGAGAGG
* *
40956740 GAAA GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG
1 GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA
*
40956788 GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GAAA GAAA G-AA G-AA
1 GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
40956834 G-AA GAAAA GGAAAA GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAAA
1 GAAA G-AAA -G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
40956881 GAAA
1 GAAA
40956885 AGAAGAAGAG
Statistics
Matches: 118, Mismatches: 8, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
3 24 0.20
4 62 0.53
5 25 0.21
6 7 0.06
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Done.