Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 108 of 120
Found at i:31634168 original size:32 final size:32
Alignment explanation
Indices: 31634124--31634213 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
31634114 AGATTAAGTA
*
31634124 CAAA-TATAAAAAAAAGTGTCAAGTTT-AGGTAT
1 CAAATTATAAAAAAAAGT-TCAAGTTTGA-ATAT
31634156 CAAATTATAAAAAAAA-TATCAAGTTTGAATAT
1 CAAATTATAAAAAAAAGT-TCAAGTTTGAATAT
*
31634188 CAAATTAGATGAAAAAAAGTTCAAGT
1 CAAATT--ATAAAAAAAAGTTCAAGT
31634214 AATAAATTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
32 22 0.44
33 12 0.24
34 15 0.30
35 1 0.02
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (32 bp):
CAAATTATAAAAAAAAGTTCAAGTTTGAATAT
Found at i:31636248 original size:23 final size:24
Alignment explanation
Indices: 31636221--31636268 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
31636211 TTTTCATCAC
31636221 TTAT-TTTTAAAAAA-TTTAA-TT
1 TTATATTTTAAAAAAGTTTAACTT
31636242 TTATATTTTAAAAAAGTTTAACTT
1 TTATATTTTAAAAAAGTTTAACTT
31636266 TTA
1 TTA
31636269 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 5 0.21
24 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATATTTTAAAAAAGTTTAACTT
Found at i:31640499 original size:14 final size:13
Alignment explanation
Indices: 31640474--31640498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31640464 AATGGGTGGA
31640474 TTTAATTTTTTTG
1 TTTAATTTTTTTG
31640487 TTTAATTTTTTT
1 TTTAATTTTTTT
31640499 TTGAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTAATTTTTTTG
Found at i:31640499 original size:15 final size:17
Alignment explanation
Indices: 31640479--31640515 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
31640469 GTGGATTTAA
31640479 TTTTTTTG-TTTAAT-T
1 TTTTTTTGATTTAATAT
31640494 TTTTTTTGAATTTAATAT
1 TTTTTTTG-ATTTAATAT
31640512 TTTT
1 TTTT
31640516 ATATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTTTTGATTTAATAT
Found at i:31640600 original size:31 final size:31
Alignment explanation
Indices: 31640558--31640619 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
31640548 GGTTTAGTTA
*
31640558 TGATGAAAGTAATTGAAGTATGGTGAAATAT
1 TGATGAAAGTAATTGAAGTATAGTGAAATAT
*
31640589 TGATGATAGTAATTGAAGTATAGTGAAATAT
1 TGATGAAAGTAATTGAAGTATAGTGAAATAT
31640620 GAATTATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (31 bp):
TGATGAAAGTAATTGAAGTATAGTGAAATAT
Found at i:31640829 original size:23 final size:23
Alignment explanation
Indices: 31640784--31640829 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
31640774 TTTTTATAGA
* *
31640784 TTTAAATTTTAATCTCTTTATTT
1 TTTAAATTTTAATATCTTAATTT
31640807 TTTAAATTTTAATGAT-TTAATTT
1 TTTAAATTTTAAT-ATCTTAATTT
31640830 AATGATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTAAATTTTAATATCTTAATTT
Found at i:31651848 original size:20 final size:23
Alignment explanation
Indices: 31651805--31651851 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
31651795 GACGAATTAA
31651805 AAATTATTTATAGAAATTAAAAAT
1 AAATTATTTATAGAAATT-AAAAT
31651829 AAATTATTTA-A-AAATT-AAAT
1 AAATTATTTATAGAAATTAAAAT
31651849 AAA
1 AAA
31651852 AAGTATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
22 5 0.22
23 1 0.04
24 10 0.43
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AAATTATTTATAGAAATTAAAAT
Found at i:31651858 original size:22 final size:24
Alignment explanation
Indices: 31651802--31651858 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
31651792 AATGACGAAT
31651802 TAAAAATTATTTATAGAAATTAAA
1 TAAAAATTATTTATAGAAATTAAA
31651826 -AATAAATTATTTA-A-AAATTAAA
1 TAA-AAATTATTTATAGAAATTAAA
*
31651848 TAAAAAGTATT
1 TAAAAATTATT
31651859 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 15 0.50
23 5 0.17
24 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAAAATTATTTATAGAAATTAAA
Found at i:31671342 original size:15 final size:15
Alignment explanation
Indices: 31671318--31671422 Score: 129
Period size: 15 Copynumber: 7.0 Consensus size: 15
31671308 CAGCATTTCT
*
31671318 GCCATAGCCACCACC
1 GCCATAGCCGCCACC
* * *
31671333 TCCGTAGCCACCACC
1 GCCATAGCCGCCACC
* *
31671348 TCCATAACCGCCACC
1 GCCATAGCCGCCACC
31671363 GCCATAGCCGCCACC
1 GCCATAGCCGCCACC
* *
31671378 GCCATAACCACCACC
1 GCCATAGCCGCCACC
*
31671393 ACCATAGCCGCCACC
1 GCCATAGCCGCCACC
31671408 GCCATAGCCGCCACC
1 GCCATAGCCGCCACC
31671423 TCCAAAGTTA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 77 1.00
ACGTcount: A:0.25, C:0.53, G:0.13, T:0.09
Consensus pattern (15 bp):
GCCATAGCCGCCACC
Found at i:31671368 original size:45 final size:45
Alignment explanation
Indices: 31671318--31671426 Score: 164
Period size: 45 Copynumber: 2.4 Consensus size: 45
31671308 CAGCATTTCT
* * * *
31671318 GCCATAGCCACCACCTCCGTAGCCACCACCTCCATAACCGCCACC
1 GCCATAGCCGCCACCTCCATAACCACCACCACCATAACCGCCACC
* *
31671363 GCCATAGCCGCCACCGCCATAACCACCACCACCATAGCCGCCACC
1 GCCATAGCCGCCACCTCCATAACCACCACCACCATAACCGCCACC
31671408 GCCATAGCCGCCACCTCCA
1 GCCATAGCCGCCACCTCCA
31671427 AAGTTACGAG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.25, C:0.53, G:0.13, T:0.09
Consensus pattern (45 bp):
GCCATAGCCGCCACCTCCATAACCACCACCACCATAACCGCCACC
Found at i:31676658 original size:23 final size:23
Alignment explanation
Indices: 31676632--31676676 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31676622 AAATTCGAAT
**
31676632 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
31676655 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
31676677 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:31680222 original size:29 final size:29
Alignment explanation
Indices: 31680161--31680231 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
31680151 TAAAATGGTA
* * *
31680161 AATTTTTTATTAATAATAAAATTATATTTT
1 AATTTTTTA-AAATAATAAAATTATAATAT
31680191 AATTTTTTAAAATAATAAAAATT-TAATAT
1 AATTTTTTAAAATAAT-AAAATTATAATAT
*
31680220 AATCTTTTAAAA
1 AATTTTTTAAAA
31680232 ATTATTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTTTTTAAAATAATAAAATTATAATAT
Found at i:31680233 original size:30 final size:29
Alignment explanation
Indices: 31680172--31680247 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
31680162 ATTTTTTATT
* * *
31680172 AATAATAAAATTATATTTTAATTTTTTAA
1 AATAATAAAATTATAATATAATTTTTAAA
31680201 AATAATAAAAATT-TAATATAATCTTTTAAA
1 AATAAT-AAAATTATAATATAAT-TTTTAAA
* *
31680231 AATTATTAAAATAATAA
1 AA-TAATAAAATTATAA
31680248 AATTACATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.34
30 19 0.50
31 6 0.16
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (29 bp):
AATAATAAAATTATAATATAATTTTTAAA
Found at i:31681015 original size:88 final size:88
Alignment explanation
Indices: 31680835--31681016 Score: 208
Period size: 88 Copynumber: 2.1 Consensus size: 88
31680825 AGAATAACTG
* * * *
31680835 CAAGTTCAAGCTTAATATAAGAGCAATTATCAAATTTAAGGCTTAACTTTGAGTAAAAAAAATTA
1 CAAGTTCAAGCCTAATATAAGAACAATTATCAAATTTAAGACTTAACTTTGAATAAAAAAAATTA
* * *
31680900 AGCCTCAATGTGAAAAAAGTTAT
66 AGCCTCAATATGAAAAAAATTAC
* * * *
31680923 CAAGTTCAAGCCTAATATGAGAACAATTGTCAAGTTTAAGACTTAA-TTTGAATAAAAAAAGTTG
1 CAAGTTCAAGCCTAATATAAGAACAATTATCAAATTTAAGACTTAACTTTGAATAAAAAAAATT-
*
31680987 AGATCCT-AATAT-AAGAAAAATTAC
65 A-AGCCTCAATATGAA-AAAAATTAC
31681011 CAAGTT
1 CAAGTT
31681017 TTAATCCCAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
87 17 0.22
88 58 0.73
89 4 0.05
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.29
Consensus pattern (88 bp):
CAAGTTCAAGCCTAATATAAGAACAATTATCAAATTTAAGACTTAACTTTGAATAAAAAAAATTA
AGCCTCAATATGAAAAAAATTAC
Found at i:31684071 original size:23 final size:23
Alignment explanation
Indices: 31684032--31684075 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
31684022 AGCTAGGTTT
31684032 TTATATGTTTGATAATTAATTTC
1 TTATATGTTTGATAATTAATTTC
*
31684055 TTATAT-TTTTATCAATTAATT
1 TTATATGTTTGAT-AATTAATT
31684076 ACTGGATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (23 bp):
TTATATGTTTGATAATTAATTTC
Found at i:31687644 original size:2 final size:2
Alignment explanation
Indices: 31687631--31687668 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
31687621 AATCTTGGTT
*
31687631 TA TA TG 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
31687669 CTCTGAGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31689386 original size:4 final size:4
Alignment explanation
Indices: 31689373--31689403 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
31689363 GTTTTTAGTA
31689373 TATG -ATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
31689404 CTTAGAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:31692323 original size:58 final size:58
Alignment explanation
Indices: 31692204--31692509 Score: 441
Period size: 59 Copynumber: 5.2 Consensus size: 58
31692194 ACTAAAGTAT
* * *
31692204 AATTTGATACTTGAACTTGACATTTTTTTTTAATTTGATACCTAAATTTTTTTTGATCC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTT-ATCC
* *
31692263 AATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
*
31692321 AATTTGATACCTGAACTTGACATTTTTTCCTAATTTGATACCTAAACTTTTTTTTATCC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAAC-TTTTTTTATCC
* * *
31692380 AATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTGATCC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
* * * * *
31692438 AATTCGATACCTGAACTTGACATTTTTTCTTAATTTGGTACTTAAGCTTTTTTTTTATTC
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAAC--TTTTTTTATCC
*
31692498 AATTTGGTACCT
1 AATTTGATACCT
31692510 AAATTTATTA
Statistics
Matches: 222, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
58 99 0.45
59 104 0.47
60 19 0.09
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (58 bp):
AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
Found at i:31692410 original size:117 final size:117
Alignment explanation
Indices: 31692204--31692509 Score: 506
Period size: 117 Copynumber: 2.6 Consensus size: 117
31692194 ACTAAAGTAT
* *
31692204 AATTTGATACTTGAACTTGACATTTTTTTTTAATTTGATACCTAAA-TTTTTTTTGATCCAATTT
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTT-ATCCAATTT
*
31692268 GGTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTATCC
65 GGTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTGATCC
*
31692321 AATTTGATACCTGAACTTGACATTTTTTCCTAATTTGATACCTAAACTTTTTTTTATCCAATTTG
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTTATCCAATTTG
31692386 GTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTGATCC
66 GTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTGATCC
* * * * *
31692438 AATTCGATACCTGAACTTGACATTTTTTCTTAATTTGGTACTTAAGCTTTTTTTTTATTCAATTT
1 AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAAC-TTTTTTTTATCCAATTT
31692503 GGTACCT
65 GGTACCT
31692510 AAATTTATTA
Statistics
Matches: 177, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
117 146 0.82
118 31 0.18
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (117 bp):
AATTTGATACCTGAACTTGACATTTTTTCTTAATTTGATACCTAAACTTTTTTTTATCCAATTTG
GTACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTGATCC
Found at i:31692815 original size:25 final size:24
Alignment explanation
Indices: 31692778--31692827 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
31692768 AAAAGTTGTC
* *
31692778 AAATTTTAGTACCAAATTAAATAAA
1 AAATTTAAATACCAAATTAAA-AAA
31692803 AAATTTAAATACCAAATTAAAAAA
1 AAATTTAAATACCAAATTAAAAAA
31692827 A
1 A
31692828 TATGTCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATTTAAATACCAAATTAAAAAA
Found at i:31692837 original size:25 final size:25
Alignment explanation
Indices: 31692787--31692837 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
31692777 CAAATTTTAG
*
31692787 TACCAAATTAAATAAAAAATTTAAA
1 TACCAAATTAAATAAAAAATTCAAA
*
31692812 TACCAAATTAAA-AAAATATGTCAAA
1 TACCAAATTAAATAAAAAAT-TCAAA
31692837 T
1 T
31692838 TTAAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (25 bp):
TACCAAATTAAATAAAAAATTCAAA
Found at i:31694656 original size:31 final size:30
Alignment explanation
Indices: 31694595--31694666 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
31694585 CCGGTATGTA
* *
31694595 ACAAAACAGTCACTCAACTTTGAAAAAGTG
1 ACAAAACAGTCACTAAAATTTGAAAAAGTG
31694625 ACAAAACAGTCACTAAAATTATCG-AAAAGTG
1 ACAAAACAGTCACTAAAATT-T-GAAAAAGTG
* *
31694656 ATAAAATAGTC
1 ACAAAACAGTC
31694667 TTCTTGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 18 0.50
31 17 0.47
32 1 0.03
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (30 bp):
ACAAAACAGTCACTAAAATTTGAAAAAGTG
Found at i:31695950 original size:29 final size:31
Alignment explanation
Indices: 31695889--31695952 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
31695879 ATGGAAAAGA
*
31695889 ACTGTTTTGTCACATTTTTAAAAGTTGAGGG
1 ACTGTTTTATCACATTTTTAAAAGTTGAGGG
*
31695920 ACTGTTTTATCATA-TTTT-AAAGTTGAGGG
1 ACTGTTTTATCACATTTTTAAAAGTTGAGGG
31695949 ACTG
1 ACTG
31695953 AAATATAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.48
30 4 0.13
31 12 0.39
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (31 bp):
ACTGTTTTATCACATTTTTAAAAGTTGAGGG
Found at i:31705409 original size:17 final size:19
Alignment explanation
Indices: 31705382--31705416 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31705372 AAAAGGAAAA
31705382 CAAAAATGAAAC-AAGCTC
1 CAAAAATGAAACTAAGCTC
31705400 CAAAAA-GAAACTAAGCT
1 CAAAAATGAAACTAAGCT
31705417 TAAGTAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (19 bp):
CAAAAATGAAACTAAGCTC
Found at i:31707529 original size:27 final size:25
Alignment explanation
Indices: 31707482--31707531 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
31707472 AAGTCTGCCC
31707482 ATATAATTTTTTAATTTTTTTAAAA
1 ATATAATTTTTTAATTTTTTTAAAA
* *
31707507 ATATATTTATTTTATTTTATTTTAA
1 ATATAATT-TTTTAATTT-TTTTAA
31707532 TATTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 8 0.38
27 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
ATATAATTTTTTAATTTTTTTAAAA
Found at i:31717543 original size:54 final size:54
Alignment explanation
Indices: 31717442--31717596 Score: 175
Period size: 54 Copynumber: 2.9 Consensus size: 54
31717432 TTACGACTTC
* ** * * * *
31717442 CAAGTTTGAAGGAGAAGCATTAGCTGCTAGTGTAACATTGTCGTTTGTGTCCGC
1 CAAGTTTGAAGGAGAAACATTAGCTGCTAGTGTAACATCATCTTTTGTGACAGA
* * * * *
31717496 CAGGTTTGAAGGAGAAACATTAGCTGTTCGTATAAAATCATCTTTTGTGACAGA
1 CAAGTTTGAAGGAGAAACATTAGCTGCTAGTGTAACATCATCTTTTGTGACAGA
* * *
31717550 CAAGTTCGAAGGACAGACATTAGCTGCTAGTGTAACATCATCTTTTG
1 CAAGTTTGAAGGAGAAACATTAGCTGCTAGTGTAACATCATCTTTTG
31717597 CAACAGCAAA
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (54 bp):
CAAGTTTGAAGGAGAAACATTAGCTGCTAGTGTAACATCATCTTTTGTGACAGA
Found at i:31717616 original size:54 final size:54
Alignment explanation
Indices: 31717512--31717616 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 54
31717502 TGAAGGAGAA
* * ** * *
31717512 ACATTAGCTGTTCGTATAAAATCATCTTTTGTGACAGACAAGTTCGAAGGACAG
1 ACATTAGCTGCTAGTATAAAATCATCTTTTGCAACAGACAAATTCAAAGGACAG
* *
31717566 ACATTAGCTGCTAGTGTAACATCATCTTTTGCAACAG-CAAAATTCAAAGGA
1 ACATTAGCTGCTAGTATAAAATCATCTTTTGCAACAGAC-AAATTCAAAGGA
31717617 GAAGGATTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.02
54 41 0.98
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (54 bp):
ACATTAGCTGCTAGTATAAAATCATCTTTTGCAACAGACAAATTCAAAGGACAG
Found at i:31722501 original size:23 final size:23
Alignment explanation
Indices: 31722475--31722595 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
31722465 ACACTAGCGC
31722475 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
31722498 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
31722521 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
31722546 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
31722569 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
31722592 GCTC
1 GCTC
31722596 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:31722544 original size:48 final size:46
Alignment explanation
Indices: 31722475--31722595 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
31722465 ACACTAGCGC
* *
31722475 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
31722521 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
31722569 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
31722596 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:31722624 original size:39 final size:39
Alignment explanation
Indices: 31722560--31722634 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
31722550 TCCGATTAGC
*
31722560 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
31722599 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
31722635 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:31722629 original size:23 final size:23
Alignment explanation
Indices: 31722594--31722687 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
31722584 CTTTGTGTGC
*
31722594 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
31722617 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
31722640 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
31722665 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
31722687 T
1 T
31722688 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:31724295 original size:20 final size:20
Alignment explanation
Indices: 31724248--31724296 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
31724238 AAAATTATAA
31724248 AAAAAAAAC-TAAAGAATAT
1 AAAAAAAACTTAAAGAATAT
* *
31724267 ATAATAAACTTAAAGAATAT
1 AAAAAAAACTTAAAGAATAT
31724287 AAAAAAAACT
1 AAAAAAAACT
31724297 CAAAACCCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAAAAAACTTAAAGAATAT
Found at i:31730599 original size:26 final size:25
Alignment explanation
Indices: 31730547--31730624 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
31730537 TAAGATGATT
* *
31730547 ATATAAAAAATTTTAATAAATAAAAA
1 ATATATAAAA-TTTATTAAATAAAAA
*
31730573 ATATATAAAATTTATTAAATATTAAA
1 ATATATAAAATTTATTAAATA-AAAA
* *
31730599 ATAAAATAAATATTTTTTAAA-AAAAA
1 AT-ATATAAA-ATTTATTAAATAAAAA
31730625 TCAAAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
25 10 0.23
26 17 0.40
27 7 0.16
28 9 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATATAAAATTTATTAAATAAAAA
Found at i:31731247 original size:28 final size:29
Alignment explanation
Indices: 31731203--31731259 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
31731193 GGCTCAATTT
* * *
31731203 TTTTTTTATCAATTTTTAAGGGATCTAAA
1 TTTTTTTATCAACTTTTAAAGAATCTAAA
31731232 TTTTTTT-TCAACTTTTAAAGAATCTAAA
1 TTTTTTTATCAACTTTTAAAGAATCTAAA
31731260 ACTTCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (29 bp):
TTTTTTTATCAACTTTTAAAGAATCTAAA
Found at i:31741015 original size:38 final size:38
Alignment explanation
Indices: 31740973--31741050 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
31740963 TTTTGTATTG
* * *
31740973 TATCAATTAAAATATGAAACGTTTTGAAGGATATGTTT
1 TATCAATTAAAAAATGAAACATTTTGAAGGATATGCTT
31741011 TATCAATTAAAAAATGAAACATTTTGAAGGATATGCTT
1 TATCAATTAAAAAATGAAACATTTTGAAGGATATGCTT
31741049 TA
1 TA
31741051 AATTACAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.37
Consensus pattern (38 bp):
TATCAATTAAAAAATGAAACATTTTGAAGGATATGCTT
Found at i:31741566 original size:27 final size:27
Alignment explanation
Indices: 31741523--31741578 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
31741513 TTTGATATGA
31741523 TTTTTTTGTTCCATGTAATATTCAATG
1 TTTTTTTGTTCCATGTAATATTCAATG
*
31741550 TTTTTTTGGTTCC-TGTAATGTTCAATG
1 TTTTTTT-GTTCCATGTAATATTCAATG
31741577 TT
1 TT
31741579 CAACATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.18, C:0.11, G:0.14, T:0.57
Consensus pattern (27 bp):
TTTTTTTGTTCCATGTAATATTCAATG
Found at i:31742176 original size:17 final size:17
Alignment explanation
Indices: 31742132--31742182 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
31742122 ATACATCTAT
*
31742132 ATATTAATATATTATAA
1 ATATTAATAAATTATAA
31742149 AT-TATAATAAATTATAA
1 ATAT-TAATAAATTATAA
*
31742166 ATATTATTAAA-TATAA
1 ATATTAATAAATTATAA
31742182 A
1 A
31742183 AAATAGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.23
17 22 0.73
18 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATTAATAAATTATAA
Found at i:31742872 original size:2 final size:2
Alignment explanation
Indices: 31742865--31742901 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31742855 AAATTAAACA
31742865 AT AT AT AT 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 AT AT AT AT A
31742902 ACAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31758615 original size:6 final size:6
Alignment explanation
Indices: 31758604--31758636 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
31758594 ATATCTCATT
*
31758604 ATCCGA ATCCGA ATCCGA ATCCGA ATCCAA ATC
1 ATCCGA ATCCGA ATCCGA ATCCGA ATCCGA ATC
31758637 TTGTTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.36, C:0.33, G:0.12, T:0.18
Consensus pattern (6 bp):
ATCCGA
Found at i:31761124 original size:18 final size:18
Alignment explanation
Indices: 31761093--31761137 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
31761083 AAAAAAAAAA
31761093 TTTTAAAATCCTAAATATT
1 TTTTAAAATCCTAAAT-TT
*
31761112 TTTTAAAAT-CTAACTTT
1 TTTTAAAATCCTAAATTT
*
31761129 TTTTCAAAT
1 TTTTAAAAT
31761138 TAGACGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.42
18 5 0.21
19 9 0.38
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAATCCTAAATTT
Found at i:31764235 original size:13 final size:13
Alignment explanation
Indices: 31764219--31764244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31764209 CTCAAAACTA
31764219 TAAACCTTGAACC
1 TAAACCTTGAACC
31764232 TAAACCTTGAACC
1 TAAACCTTGAACC
31764245 CTGAATCAAA
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:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
TAAACCTTGAACC
Found at i:31766965 original size:48 final size:48
Alignment explanation
Indices: 31766907--31767006 Score: 191
Period size: 48 Copynumber: 2.1 Consensus size: 48
31766897 ACTACGTCGT
*
31766907 TTTAATAAATGTTTACTCGTTAAGTTAAAAAGTAAAATCATTATATTG
1 TTTAATAAATGTTTACTCGTTAAGTTAAAAAGCAAAATCATTATATTG
31766955 TTTAATAAATGTTTACTCGTTAAGTTAAAAAGCAAAATCATTATATTG
1 TTTAATAAATGTTTACTCGTTAAGTTAAAAAGCAAAATCATTATATTG
31767003 TTTA
1 TTTA
31767007 TGTAGTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (48 bp):
TTTAATAAATGTTTACTCGTTAAGTTAAAAAGCAAAATCATTATATTG
Found at i:31771614 original size:2 final size:2
Alignment explanation
Indices: 31771607--31771632 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31771597 AAAGGGTTAA
31771607 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
31771633 TGATTAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31776462 original size:15 final size:14
Alignment explanation
Indices: 31776437--31776486 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
31776427 GTTGTTATAT
31776437 TTTATATTTTTAAAAA
1 TTTA-ATTTTT-AAAA
**
31776453 TTTAATTTTTTAATT
1 TTTAA-TTTTTAAAA
31776468 TTTAATTTTTAAAA
1 TTTAATTTTTAAAA
31776482 TTTAA
1 TTTAA
31776487 ATTTAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.41
15 8 0.28
16 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAATTTTTAAAA
Found at i:31776489 original size:15 final size:15
Alignment explanation
Indices: 31776437--31776490 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31776427 GTTGTTATAT
*
31776437 TTTATATTTTTAAAAA
1 TTTAAATTTTT-AAAA
* *
31776453 TTT-AATTTTTTAAT
1 TTTAAATTTTTAAAA
*
31776467 TTTTAATTTTTAAAA
1 TTTAAATTTTTAAAA
31776482 TTTAAATTT
1 TTTAAATTT
31776491 AATTATTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 5 0.16
15 23 0.74
16 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAAATTTTTAAAA
Found at i:31777720 original size:33 final size:35
Alignment explanation
Indices: 31777639--31777722 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 35
31777629 GAACTATATA
*
31777639 AAAAAATTTAATAAATAAAAGAATATATAAAATTATT
1 AAAAAA-TTAA-AAATAAAACAATATATAAAATTATT
*
31777676 -AAATATT-AAAATAAAACAAT-T-TAAAGATT-TT
1 AAAAAATTAAAAATAAAACAATATATAAA-ATTATT
31777707 AAAAAATTAAAAATAA
1 AAAAAATTAAAAATAA
31777723 TATGGGCGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
31 6 0.15
32 10 0.24
33 18 0.44
34 1 0.02
35 2 0.05
36 4 0.10
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (35 bp):
AAAAAATTAAAAATAAAACAATATATAAAATTATT
Found at i:31790192 original size:11 final size:11
Alignment explanation
Indices: 31790178--31790212 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
31790168 TATTTTTTAT
31790178 ATATTATGAAC
1 ATATTATGAAC
31790189 ATATTATGAAC
1 ATATTATGAAC
31790200 ATATTATGAAC
1 ATATTATGAAC
31790211 AT
1 AT
31790213 GTATATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (11 bp):
ATATTATGAAC
Found at i:31793392 original size:4 final size:4
Alignment explanation
Indices: 31793383--31793408 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
31793373 TTCCAAGTGC
31793383 AACA AACA AACA AACA AACA AACA AA
1 AACA AACA AACA AACA AACA AACA AA
31793409 AGAGCGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:31795048 original size:42 final size:42
Alignment explanation
Indices: 31794989--31795072 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
31794979 CAAATATTTT
* *
31794989 TAAACCCAAATATAATTTCATTCTTAAAAAACACTTATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
* *
31795031 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
31795073 AACTCTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
Found at i:31799426 original size:22 final size:21
Alignment explanation
Indices: 31799391--31799431 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
31799381 TTCTAGTTAC
31799391 TTTTAATTTAAATCCAACTTAA
1 TTTTAATTTAAAT-CAACTTAA
31799413 TTTTAATTCT-AATCAACTT
1 TTTTAATT-TAAATCAACTT
31799432 CTTGAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 11 0.61
23 1 0.06
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAATTTAAATCAACTTAA
Found at i:31800774 original size:29 final size:27
Alignment explanation
Indices: 31800742--31800818 Score: 66
Period size: 29 Copynumber: 2.7 Consensus size: 27
31800732 GTCAGTGGTA
31800742 AAAATTAATTAAATTTAAAGTTTAGTGAT
1 AAAATTAATTAAATTTAAA-TTTAGT-AT
*
31800771 AAAATTTAA-TAACATGTAAATTTAGTAT
1 AAAA-TTAATTAA-ATTTAAATTTAGTAT
* * *
31800799 CAAATTTATCTATATTTAAA
1 AAAATTAAT-TAAATTTAAA
31800819 AGTAGGCGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
27 3 0.08
28 11 0.28
29 15 0.38
30 10 0.26
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (27 bp):
AAAATTAATTAAATTTAAATTTAGTAT
Found at i:31800780 original size:30 final size:30
Alignment explanation
Indices: 31800704--31800806 Score: 79
Period size: 30 Copynumber: 3.5 Consensus size: 30
31800694 ATTAATATTG
* * * *
31800704 AGTGATAGAATTTAATTAAAAAATAAAAG-TC
1 AGTGATAAAATTTAATT--AAATTTAAAGTTT
* *
31800735 AGTGGTAAAAATTAATTAAATTTAAAGTTT
1 AGTGATAAAATTTAATTAAATTTAAAGTTT
*
31800765 AGTGATAAAATTTAA-TAACATGTAAA-TTT
1 AGTGATAAAATTTAATTAA-ATTTAAAGTTT
*
31800794 AGT-ATCAAATTTA
1 AGTGATAAAATTTA
31800807 TCTATATTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
28 9 0.15
29 17 0.28
30 20 0.33
31 14 0.23
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.36
Consensus pattern (30 bp):
AGTGATAAAATTTAATTAAATTTAAAGTTT
Found at i:31803578 original size:18 final size:17
Alignment explanation
Indices: 31803545--31803578 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31803535 TATTTTATTC
*
31803545 TTAAAAATAATGTAAAG
1 TTAAAAATAATATAAAG
31803562 TTAAAAATATATATAAA
1 TTAAAAATA-ATATAAA
31803579 ATTCTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAAAAATAATATAAAG
Found at i:31816191 original size:21 final size:23
Alignment explanation
Indices: 31816165--31816213 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
31816155 TGGTTTTACG
*
31816165 TATTTTTTTAAT-TAAATA-ATA
1 TATTTTTATAATATAAATATATA
31816186 TATTTTTATAATATAAATATATA
1 TATTTTTATAATATAAATATATA
31816209 TATTT
1 TATTT
31816214 GCTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.44
22 6 0.24
23 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTTTTATAATATAAATATATA
Found at i:31816223 original size:21 final size:21
Alignment explanation
Indices: 31816173--31816224 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
31816163 CGTATTTTTT
*
31816173 TAATTAAATAATATATTTTTA
1 TAATTAAATAATATATTTTGA
*
31816194 TAATATAAAT-ATATATATTTGC
1 TAAT-TAAATAATATAT-TTTGA
31816216 TAATTAAAT
1 TAATTAAAT
31816225 GAAGATTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATTAAATAATATATTTTGA
Found at i:31816806 original size:18 final size:20
Alignment explanation
Indices: 31816785--31816830 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
31816775 TTTTTATTGG
31816785 AATTTTAG-GTTTTTA-GAA
1 AATTTTAGAGTTTTTATGAA
*
31816803 AATTTTAGATTTTTTATGAA
1 AATTTTAGAGTTTTTATGAA
31816823 AACTTTTA
1 AA-TTTTA
31816831 AGAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 6 0.25
20 5 0.21
21 5 0.21
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (20 bp):
AATTTTAGAGTTTTTATGAA
Found at i:31816854 original size:18 final size:18
Alignment explanation
Indices: 31816832--31816884 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
31816822 AAACTTTTAA
31816832 GAATTTTATGGTTTTTTT
1 GAATTTTATGGTTTTTTT
* * *
31816850 TAATTTTAGGGAATTTTTT
1 GAATTTTATGG-TTTTTTT
*
31816869 GCATTTTAT-GTTTTTT
1 GAATTTTATGGTTTTTT
31816885 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
17 5 0.19
18 10 0.37
19 12 0.44
ACGTcount: A:0.19, C:0.02, G:0.15, T:0.64
Consensus pattern (18 bp):
GAATTTTATGGTTTTTTT
Found at i:31820454 original size:31 final size:31
Alignment explanation
Indices: 31820419--31820480 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
31820409 TTATATTTTG
31820419 ATCATTAAACTATTCAAAAGTTTTTATTTAA
1 ATCATTAAACTATTCAAAAGTTTTTATTTAA
* *
31820450 ATCATTGAATTATTCAAAAGTTTTTATTTAA
1 ATCATTAAACTATTCAAAAGTTTTTATTTAA
31820481 GTCACTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (31 bp):
ATCATTAAACTATTCAAAAGTTTTTATTTAA
Found at i:31821515 original size:54 final size:55
Alignment explanation
Indices: 31821402--31821515 Score: 142
Period size: 54 Copynumber: 2.1 Consensus size: 55
31821392 CGATAATTTG
* * * *
31821402 AAAAAAAAATTTGGTATTGGCCATTGCATGGTCGACACCCCTTTTTTTTTAAGAT
1 AAAAAAAAAATTGGTATTGACCATTGCATGGTCGACACCCCTCTTTTTGTAAGAT
* * * *
31821457 -AAAAAAAAATTGGTGTTGATCATTGCATGGTCGACA-CCCTCTTTTTGTCATAT
1 AAAAAAAAAATTGGTATTGACCATTGCATGGTCGACACCCCTCTTTTTGTAAGAT
31821510 AAAAAA
1 AAAAAA
31821516 TTCAAATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 13 0.26
54 37 0.74
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (55 bp):
AAAAAAAAAATTGGTATTGACCATTGCATGGTCGACACCCCTCTTTTTGTAAGAT
Found at i:31821595 original size:60 final size:60
Alignment explanation
Indices: 31821466--31821595 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 60
31821456 TAAAAAAAAA
* * * *
31821466 TTGGTGTTGATCATTGCATGGTCGACACCCTCTTTTTGTCATATAAAAAATTCAAATTTT
1 TTGGTGTTGGTCATTGCATGGCCGACACCCTCTTTTTATCAGATAAAAAATTCAAATTTT
* *
31821526 TTGGTGTTGGTCA-TGCCATGGCCGACACTCTTTTTTTATCAGATAAAAAATTCAAATTTT
1 TTGGTGTTGGTCATTG-CATGGCCGACACCCTCTTTTTATCAGATAAAAAATTCAAATTTT
*
31821586 TTTGTGTTGG
1 TTGGTGTTGG
31821596 CTGTAACACC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 2 0.03
60 60 0.97
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (60 bp):
TTGGTGTTGGTCATTGCATGGCCGACACCCTCTTTTTATCAGATAAAAAATTCAAATTTT
Found at i:31822855 original size:6 final size:6
Alignment explanation
Indices: 31822832--31822874 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
31822822 AATTCATATT
* * *
31822832 ACTTTC AATTCC AATTTC ACTTTC ACTTTC ACTTTC ACTTTC A
1 ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC A
31822875 ATTTTGATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (6 bp):
ACTTTC
Found at i:31822855 original size:18 final size:18
Alignment explanation
Indices: 31822832--31822877 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
31822822 AATTCATATT
31822832 ACTTTCAATTCCAATTTC
1 ACTTTCAATTCCAATTTC
* * *
31822850 ACTTTCACTTTCACTTTC
1 ACTTTCAATTCCAATTTC
31822868 ACTTTCAATT
1 ACTTTCAATT
31822878 TTGATCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (18 bp):
ACTTTCAATTCCAATTTC
Found at i:31824708 original size:44 final size:45
Alignment explanation
Indices: 31824644--31824733 Score: 148
Period size: 44 Copynumber: 2.0 Consensus size: 45
31824634 TGTCATGGTC
*
31824644 GACACCCCCTTTTTATCTGAT-AAAGAATTAAATTTTTTTTGTGTT
1 GACACCCCCTTTTTATCTGATAAAAAAATTAAA-TTTTTTTGTGTT
31824689 GACA-CCCCTTTTTATCTGATAAAAAAATTAAATTTTTTTGTGTT
1 GACACCCCCTTTTTATCTGATAAAAAAATTAAATTTTTTTGTGTT
31824733 G
1 G
31824734 GTCATTGCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
44 29 0.67
45 14 0.33
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (45 bp):
GACACCCCCTTTTTATCTGATAAAAAAATTAAATTTTTTTGTGTT
Found at i:31824783 original size:61 final size:59
Alignment explanation
Indices: 31824689--31824965 Score: 271
Period size: 60 Copynumber: 4.6 Consensus size: 59
31824679 TTTTTGTGTT
* *
31824689 GACACC-CCTTTTTATCTGATAAAAAAATTAAATTTTTTTGTGTTGGTCATTGCATGGCC
1 GACACCACCTTTTTATCTGA-CAAAAAATTAAATTTTTTTGTGTTGGCCATTGCATGGCC
* * *
31824748 GACACTC-TCTTTTTAATCTGACAAAAAATTCAAATTTTTTTATATTGGCCATTGCATGGCC
1 GACAC-CACCTTTTT-ATCTGACAAAAAATT-AAATTTTTTTGTGTTGGCCATTGCATGGCC
* * * * *
31824809 GATACCACCTTTTT-TTTGATAAAAAAATCAGATTTTTTTGGTGTTGGCCA-TGCCATGGCC
1 GACACCACCTTTTTATCTGA-CAAAAAATTAAATTTTTTT-GTGTTGGCCATTG-CATGGCC
* * * *
31824869 GACACCACCTATTTATCTGATAAAAAATTTAAA-TTTTTTGATGTTAGCCATTGCATGACC
1 GACACCACCTTTTTATCTGACAAAAAA-TTAAATTTTTTTG-TGTTGGCCATTGCATGGCC
* *
31824929 GATACTC-CCTTTTAATCTGACAAAAAATT-AATTTTTT
1 GACAC-CACCTTTTTATCTGACAAAAAATTAAATTTTTT
31824966 CCTTCATTTC
Statistics
Matches: 180, Mismatches: 25, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.01
59 28 0.16
60 97 0.54
61 53 0.29
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (59 bp):
GACACCACCTTTTTATCTGACAAAAAATTAAATTTTTTTGTGTTGGCCATTGCATGGCC
Found at i:31824919 original size:120 final size:121
Alignment explanation
Indices: 31824694--31824955 Score: 327
Period size: 120 Copynumber: 2.2 Consensus size: 121
31824684 GTGTTGACAC
* * * *
31824694 CCCTTTTTATCTGATAAAAAAATTAAATTTTTTTGTGTTGGTCATTGCATGGCCGACACTCTCTT
1 CCCTTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACTCCCTA
* * *
31824759 TTTAATCTGACAAAAAATTCAAATTTTTTTATATTGGCCATTGCATGGCCGATAC-
66 TTTAATCTGACAAAAAATTCAAATTTTTTGATATTAGCCATTGCATGACCGATACT
* *
31824814 CACCTTTTT-TTTGATAAAAAAATCAGATTTTTTTGGTGTTGGCCA-TGCCATGGCCGACAC-CA
1 C-CCTTTTTATCTGATAAAAAAATCAAATTTTTTT-GTGTTGGCCATTG-CATGGCCGACACTC-
* * *
31824876 CCTATTT-ATCTGATAAAAAATTTAAATTTTTTGATGTTAGCCATTGCATGACCGATACT
62 CCTATTTAATCTGACAAAAAATTCAAATTTTTTGATATTAGCCATTGCATGACCGATACT
* *
31824935 CCCTTTTAATCTGACAAAAAA
1 CCCTTTTTATCTGATAAAAAA
31824956 TTAATTTTTT
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
120 77 0.64
121 44 0.36
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (121 bp):
CCCTTTTTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACTCCCTA
TTTAATCTGACAAAAAATTCAAATTTTTTGATATTAGCCATTGCATGACCGATACT
Found at i:31825661 original size:30 final size:30
Alignment explanation
Indices: 31825627--31825727 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
31825617 ATTAGAAATG
*
31825627 AAATATAAACGAAATTAGAAATTAAAATTA
1 AAATATAAACGAAATTAGAAATTAAATTTA
* *
31825657 AAATATACAGGAAATTAGAAATTAAATTTA
1 AAATATAAACGAAATTAGAAATTAAATTTA
* * *
31825687 AAATAAAAATGAAATTACAAATTAAATTTA
1 AAATATAAACGAAATTAGAAATTAAATTTA
31825717 AAA-AGTAAACG
1 AAATA-TAAACG
31825728 GAAAAAAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.02
30 60 0.98
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (30 bp):
AAATATAAACGAAATTAGAAATTAAATTTA
Found at i:31826882 original size:13 final size:13
Alignment explanation
Indices: 31826864--31826888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31826854 ATTTCAAAAA
31826864 TGTAAAAAATATG
1 TGTAAAAAATATG
31826877 TGTAAAAAATAT
1 TGTAAAAAATAT
31826889 CAGATTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TGTAAAAAATATG
Found at i:31827420 original size:58 final size:58
Alignment explanation
Indices: 31827243--31827555 Score: 292
Period size: 60 Copynumber: 5.2 Consensus size: 58
31827233 ACTGGTGCAT
* * * *
31827243 TGGCCAACACCAAAAAAATTTAAACTTTTTTATCAGACAAAAAGATAGTGTCGGTCATGCAA
1 TGGCCAACACC-AAAAAATTT-AA-TTTTTTATCAGATAAAAAGGTGGTGTCGATCATG-AA
* * * *
31827305 TGGCCAACACAAAAAAAATTCAATTTTTTGTCAGATTAAAAAGAG-GGTGTCGGTCATGAA
1 TGGCCAACAC-CAAAAAATTTAATTTTTTATCAGA-TAAAAAG-GTGGTGTCGATCATGAA
* * *
31827365 TGGCCAACACCAAAAAATTTGATTTTTTATCAGATAAATAGGTGGTGTCGATCATGGCA
1 TGGCCAACACCAAAAAATTTAATTTTTTATCAGATAAAAAGGTGGTGTCGATCAT-GAA
* * * **
31827424 TGACCAATACCCAAAAAA-TTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATAGCT
1 TGGCCAACA-CCAAAAAATTTAA-TTTTTTATCAGATAAAAAGGTGGTGTCGATCAT-GAA
* * * * *
31827484 TGGCCAACA-CAAAAAATTTAAATTTTTATCTGACAAAAAGGGGGTGTC-AGCCATGCAA
1 TGGCCAACACCAAAAAATTTAATTTTTTATCAGATAAAAAGGTGGTGTCGA-TCATG-AA
31827542 TGGCCAACACCAAA
1 TGGCCAACACCAAA
31827556 TTTTTTTTCT
Statistics
Matches: 212, Mismatches: 28, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.01
58 60 0.28
59 40 0.19
60 71 0.33
61 20 0.09
62 18 0.08
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (58 bp):
TGGCCAACACCAAAAAATTTAATTTTTTATCAGATAAAAAGGTGGTGTCGATCATGAA
Found at i:31827440 original size:119 final size:119
Alignment explanation
Indices: 31827243--31827551 Score: 324
Period size: 119 Copynumber: 2.6 Consensus size: 119
31827233 ACTGGTGCAT
* * * *
31827243 TGGCCAACACCAAAAAAATTTAAACTTTTTTATCAGACAAAAAGATAGTGTCGGTCATGCAATGG
1 TGGCCAACACC-AAAAAATTT-AA-TTTTTTATCAGACAAAAAGGTGGTGTCGATCATGCAATGA
* **
31827308 CCAACACAAAAAAAATTCAA-TTTTTTGTCAGATTAAAAAGAG-GGTGTCGGTCAT-GAA
63 CCAACACAAAAAAAATT-AATTTTTTTATCAGA-TAAAAAG-GTGGTGTCGACCATAGAA
* * *
31827365 TGGCCAACACCAAAAAATTTGATTTTTTATCAGATAAATAGGTGGTGTCGATCATGGC-ATGACC
1 TGGCCAACACCAAAAAATTTAATTTTTTATCAGACAAAAAGGTGGTGTCGATCAT-GCAATGACC
* ** **
31827429 AATACCCAAAAAATTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATAGCT
65 AACACAAAAAAAATTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATAGAA
* * * * *
31827484 TGGCCAACA-CAAAAAATTTAAATTTTTATCTGACAAAAAGGGGGTGTC-AGCCATGCAATGGCC
1 TGGCCAACACCAAAAAATTTAATTTTTTATCAGACAAAAAGGTGGTGTCGA-TCATGCAATGACC
31827547 AACAC
65 AACAC
31827552 CAAATTTTTT
Statistics
Matches: 157, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
117 4 0.03
118 64 0.41
119 66 0.42
120 3 0.02
121 9 0.06
122 11 0.07
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (119 bp):
TGGCCAACACCAAAAAATTTAATTTTTTATCAGACAAAAAGGTGGTGTCGATCATGCAATGACCA
ACACAAAAAAAATTAATTTTTTTATCAGATAAAAAGGTGGTGTCGACCATAGAA
Found at i:31828482 original size:15 final size:14
Alignment explanation
Indices: 31828457--31828507 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 14
31828447 AAAAAATGAT
31828457 ATATTTATAT-ATA
1 ATATTTATATAATA
31828470 AGTATTGTATATAATA
1 A-TATT-TATATAATA
31828486 ATATTTATA-ACATAA
1 ATATTTATATA-AT-A
31828501 ATATTTA
1 ATATTTA
31828508 ACCAAAAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.06
14 10 0.30
15 17 0.52
16 4 0.12
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (14 bp):
ATATTTATATAATA
Found at i:31837194 original size:21 final size:21
Alignment explanation
Indices: 31837168--31837210 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31837158 TAAAGTATCA
*
31837168 TTTTTTTAA-TCTCTAAGATTT
1 TTTTTTTAACTCT-TAAAATTT
31837189 TTTTTTTAACTCTTAAAATTT
1 TTTTTTTAACTCTTAAAATTT
31837210 T
1 T
31837211 GAAATTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTTTAACTCTTAAAATTT
Found at i:31843784 original size:2 final size:2
Alignment explanation
Indices: 31843771--31843814 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
31843761 TGCATACATG
* * * *
31843771 CA CA CA CG CA CA CA CG CG CG CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31843813 CA
1 CA
31843815 TTATGTGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.41, C:0.50, G:0.09, T:0.00
Consensus pattern (2 bp):
CA
Found at i:31845532 original size:164 final size:164
Alignment explanation
Indices: 31845255--31845583 Score: 597
Period size: 164 Copynumber: 2.0 Consensus size: 164
31845245 TATGAAGATT
*
31845255 ACAATCGAGCCAAAATCTTTTACCATACGAAGTAAAGCCAATAAAAAATAATTATTGGACACGGA
1 ACAATCGAGCCAAAATCTTTTACCATACGAAGTAAAGCAAATAAAAAATAATTATTGGACACGGA
31845320 TTTAATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGGT
66 TTTAATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGGT
31845385 GCTACCTATGTTGCTCCAACTCTACTTTTCTTGA
131 GCTACCTATGTTGCTCCAACTCTACTTTTCTTGA
* *
31845419 ACAATTGAGCCAAAATCTTTTACCATACGAAGTAAAGCAAATAAAAAATAATTGTTGGACACAGG
1 ACAATCGAGCCAAAATCTTTTACCATACGAAGTAAAGCAAATAAAAAATAATTATTGGACAC-GG
31845484 -TTTAATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGG
65 ATTTAATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGG
**
31845548 TGCTACCTATGTTGCTCTGACTCTACTTTTCTTGA
130 TGCTACCTATGTTGCTCCAACTCTACTTTTCTTGA
31845583 A
1 A
31845584 GTATCCGTGT
Statistics
Matches: 159, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
164 157 0.99
165 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (164 bp):
ACAATCGAGCCAAAATCTTTTACCATACGAAGTAAAGCAAATAAAAAATAATTATTGGACACGGA
TTTAATTGCTTTCAATGGCTATTCATCATCTAAAACTTTGACATGATTGAACAGTTCAATCAGGT
GCTACCTATGTTGCTCCAACTCTACTTTTCTTGA
Found at i:31856372 original size:15 final size:15
Alignment explanation
Indices: 31856334--31856378 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
31856324 GTACAATTAT
*
31856334 GGGTCGGGTCGGGTC
1 GGGTCGGGTCGGATC
* * *
31856349 GAGTTGGGTTGGATC
1 GGGTCGGGTCGGATC
31856364 GGGTCGGGTCGGATC
1 GGGTCGGGTCGGATC
31856379 AGGTTTAAGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.53, T:0.24
Consensus pattern (15 bp):
GGGTCGGGTCGGATC
Found at i:31856660 original size:19 final size:18
Alignment explanation
Indices: 31856619--31856660 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
31856609 CTAGCATTAT
*
31856619 TTTA-ATATTTAGTGTAG
1 TTTATATATTTAGTATAG
31856636 TATTATATATTTAGTATAG
1 T-TTATATATTTAGTATAG
31856655 ATTTAT
1 -TTTAT
31856661 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 16 0.76
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TTTATATATTTAGTATAG
Found at i:31857065 original size:6 final size:6
Alignment explanation
Indices: 31857054--31857084 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
31857044 TACAGACAAG
31857054 CAGCTC CAGCTC CAGCTC CAGCTC CAGCTC C
1 CAGCTC CAGCTC CAGCTC CAGCTC CAGCTC C
31857085 GTGCATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (6 bp):
CAGCTC
Found at i:31864907 original size:14 final size:15
Alignment explanation
Indices: 31864885--31864923 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
31864875 ATCATTTAAT
31864885 TATTTATGTTTGAAA
1 TATTTATGTTTGAAA
* *
31864900 TA-TTATGTTTTAAT
1 TATTTATGTTTGAAA
31864914 TATTTATGTT
1 TATTTATGTT
31864924 AGTATTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (15 bp):
TATTTATGTTTGAAA
Found at i:31866278 original size:21 final size:21
Alignment explanation
Indices: 31866254--31866297 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
31866244 CTACCTGTAG
*
31866254 AAGTAAGAGTTCTACCGATAC
1 AAGTAAGAGTACTACCGATAC
* * *
31866275 AAGTATGGGTACTATCGATAC
1 AAGTAAGAGTACTACCGATAC
31866296 AA
1 AA
31866298 CCCATACTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (21 bp):
AAGTAAGAGTACTACCGATAC
Found at i:31869650 original size:14 final size:15
Alignment explanation
Indices: 31869624--31869652 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31869614 CATAATACAT
31869624 TTAAAAAAGATTAAA
1 TTAAAAAAGATTAAA
31869639 TTAAAAAA-ATTAAA
1 TTAAAAAAGATTAAA
31869653 CTTGAGAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
TTAAAAAAGATTAAA
Found at i:31871193 original size:30 final size:31
Alignment explanation
Indices: 31871123--31871193 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
31871113 TTTGTTAATC
* *
31871123 AGTGATTGTTTTGTCACTTTTCGATAACGTT
1 AGTGACTGTTTTATCACTTTTCGATAACGTT
*
31871154 AGTAACTGTTTTATCACATTTTC-A-AA-GTT
1 AGTGACTGTTTTATCAC-TTTTCGATAACGTT
31871183 AAGTGACTGTT
1 -AGTGACTGTT
31871194 GTATTAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 3 0.09
30 11 0.32
31 15 0.44
32 5 0.15
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (31 bp):
AGTGACTGTTTTATCACTTTTCGATAACGTT
Found at i:31871951 original size:20 final size:19
Alignment explanation
Indices: 31871928--31871965 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31871918 ACTAAAAAGA
*
31871928 CAAAATAAATATAAAAAAAT
1 CAAAAGAAAT-TAAAAAAAT
31871948 CAAAAGAAATTAAAAAAA
1 CAAAAGAAATTAAAAAAA
31871966 ATAAAACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (19 bp):
CAAAAGAAATTAAAAAAAT
Found at i:31876787 original size:3 final size:3
Alignment explanation
Indices: 31876779--31876810 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31876769 ACCCGAGACT
31876779 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31876811 GATTCGTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:31879045 original size:21 final size:22
Alignment explanation
Indices: 31879014--31879072 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
31879004 CATTTTATTA
31879014 AATTATCTTTATTATA-AAATTT
1 AATTAT-TTTATTATATAAATTT
*
31879036 ATTTATTTTATTA-ATAAATTT
1 AATTATTTTATTATATAAATTT
* *
31879057 AATTCTTTTAATATAT
1 AATTATTTTATTATAT
31879073 TTTGAACTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 23 0.74
22 7 0.23
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTATTTTATTATATAAATTT
Found at i:31881613 original size:3 final size:3
Alignment explanation
Indices: 31881605--31881630 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31881595 AGAGTAAAGT
31881605 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
31881631 TTCTTTCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31881673 original size:29 final size:29
Alignment explanation
Indices: 31881640--31881695 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
31881630 ATTCTTTCTG
31881640 TGAAGAGGTGAGCTTTGAAAGGGCTATGC
1 TGAAGAGGTGAGCTTTGAAAGGGCTATGC
31881669 TGAAGAGGTGAGCTTTGAAAGGGCTAT
1 TGAAGAGGTGAGCTTTGAAAGGGCTAT
31881696 ATGGGGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.38, T:0.25
Consensus pattern (29 bp):
TGAAGAGGTGAGCTTTGAAAGGGCTATGC
Found at i:31881753 original size:75 final size:75
Alignment explanation
Indices: 31881664--31881818 Score: 310
Period size: 75 Copynumber: 2.1 Consensus size: 75
31881654 TTGAAAGGGC
31881664 TATGCTGAAGAGGTGAGCTTTGAAAGGGCTATATGGGGCTTTCCTTGCCCACGGAGGTGTCTGGG
1 TATGCTGAAGAGGTGAGCTTTGAAAGGGCTATATGGGGCTTTCCTTGCCCACGGAGGTGTCTGGG
31881729 AAATTTCTTT
66 AAATTTCTTT
31881739 TATGCTGAAGAGGTGAGCTTTGAAAGGGCTATATGGGGCTTTCCTTGCCCACGGAGGTGTCTGGG
1 TATGCTGAAGAGGTGAGCTTTGAAAGGGCTATATGGGGCTTTCCTTGCCCACGGAGGTGTCTGGG
31881804 AAATTTCTTT
66 AAATTTCTTT
31881814 TATGC
1 TATGC
31881819 CCCTTTGCTC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (75 bp):
TATGCTGAAGAGGTGAGCTTTGAAAGGGCTATATGGGGCTTTCCTTGCCCACGGAGGTGTCTGGG
AAATTTCTTT
Found at i:31883173 original size:20 final size:22
Alignment explanation
Indices: 31883143--31883186 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
31883133 CAATATTGGT
*
31883143 TTCATTTATTG-TTTGAATCGA
1 TTCATTTATTGTTTTAAATCGA
31883164 TTCA-TTATTGTTTTAAATCGA
1 TTCATTTATTGTTTTAAATCGA
31883185 TT
1 TT
31883187 TTTTTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (22 bp):
TTCATTTATTGTTTTAAATCGA
Found at i:31887705 original size:26 final size:25
Alignment explanation
Indices: 31887676--31887727 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
31887666 AACTTAAATT
* *
31887676 TAACAAAATAATTTTATTAAGTCATG
1 TAACAAAATAATGTTAAT-AGTCATG
**
31887702 TAACTTAATAATGTTAATAGTCATG
1 TAACAAAATAATGTTAATAGTCATG
31887727 T
1 T
31887728 CAGGGTTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (25 bp):
TAACAAAATAATGTTAATAGTCATG
Found at i:31889538 original size:3 final size:3
Alignment explanation
Indices: 31889530--31889566 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
31889520 ATTCTATGTG
31889530 CTT CTT CTT -TAT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT C
31889567 AGCAATCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 30 0.94
4 1 0.03
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:31896088 original size:21 final size:22
Alignment explanation
Indices: 31896048--31896088 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
31896038 TTTTATAATT
31896048 TTCTCAAATTCTAACATGTTTA
1 TTCTCAAATTCTAACATGTTTA
31896070 TTCTC-AATT-TAACACTGTT
1 TTCTCAAATTCTAACA-TGTT
31896089 CCCAACTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (22 bp):
TTCTCAAATTCTAACATGTTTA
Found at i:31902733 original size:29 final size:31
Alignment explanation
Indices: 31902677--31902739 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
31902667 TGGACATGAA
31902677 TTTTGAAATATAAAAAATAAAAAGACTAAATT
1 TTTTGAAATATAAAAAATAAAAAGACT-AATT
*
31902709 TTTTGAAATA-AAAATAT-AAAA-ACTAATT
1 TTTTGAAATATAAAAAATAAAAAGACTAATT
31902737 TTT
1 TTT
31902740 AAATTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 7 0.23
29 3 0.10
30 4 0.13
31 6 0.20
32 10 0.33
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (31 bp):
TTTTGAAATATAAAAAATAAAAAGACTAATT
Found at i:31905017 original size:63 final size:63
Alignment explanation
Indices: 31904950--31905077 Score: 156
Period size: 63 Copynumber: 2.1 Consensus size: 63
31904940 ATATTACTAC
* *
31904950 AAAAAAATATAAAATAC-T-TGTAAAAATTT-T-AAAAATAATAAAAGGTTTAAAATTATTTTTT
1 AAAAAAATATAAAATACATAAGTAAAAATTTCTAAAAAATAA-AAAAGGTTT-AAATTTTTTTTT
* * * *
31905011 ATAAAAATTTAAATTACATAAGTATAAATTTCTAAAAAATAAAAAAGGTTTAAATTTTTTTTT
1 AAAAAAATATAAAATACATAAGTAAAAATTTCTAAAAAATAAAAAAGGTTTAAATTTTTTTTT
31905074 AAAA
1 AAAA
31905078 TTTAAAGTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
61 14 0.25
62 1 0.02
63 23 0.41
64 10 0.18
65 8 0.14
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (63 bp):
AAAAAAATATAAAATACATAAGTAAAAATTTCTAAAAAATAAAAAAGGTTTAAATTTTTTTTT
Found at i:31905095 original size:60 final size:65
Alignment explanation
Indices: 31904973--31905108 Score: 196
Period size: 60 Copynumber: 2.2 Consensus size: 65
31904963 ATACTTGTAA
* *
31904973 AAATTT-T-AAAAATAATAAAAGGTTTAAAATTATTTTTTATAAAAATTTAAATTACATAAGTAT
1 AAATTTCTAAAAAATAATAAAAGGTTTAAAATTATTTTTTATAAAAATTTAAAGTACACAAGTAT
31905036 AAATTTCTAAAAAATAA-AAAAGGTTT-AAATT-TTTTTT-T-AAAATTTAAAGTACACAAGTAT
1 AAATTTCTAAAAAATAATAAAAGGTTTAAAATTATTTTTTATAAAAATTTAAAGTACACAAGTAT
*
31905096 AAAATTCTAAAAA
1 AAATTTCTAAAAA
31905109 GGTATTTAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
60 32 0.47
61 1 0.01
62 6 0.09
63 11 0.16
64 10 0.15
65 8 0.12
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (65 bp):
AAATTTCTAAAAAATAATAAAAGGTTTAAAATTATTTTTTATAAAAATTTAAAGTACACAAGTAT
Found at i:31905199 original size:19 final size:19
Alignment explanation
Indices: 31905167--31905214 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
31905157 ATTTTTAATT
*
31905167 TTTTTATAA-CATTTTCAA
1 TTTTTATAATTATTTTCAA
* *
31905185 TTTTTATAATTATTTTTAT
1 TTTTTATAATTATTTTCAA
*
31905204 TTTTTAAAATT
1 TTTTTATAATT
31905215 TCTAATTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATAATTATTTTCAA
Found at i:31905334 original size:5 final size:5
Alignment explanation
Indices: 31905324--31905353 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
31905314 GAACACTAAA
31905324 AAAAT AAAAT AAAAT AAAAT AAAA- AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
31905354 CACATGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:31910845 original size:1 final size:1
Alignment explanation
Indices: 31910839--31910863 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
31910829 CCTCACCCAA
31910839 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
31910864 GAAGCTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:31913550 original size:34 final size:35
Alignment explanation
Indices: 31913511--31913576 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
31913501 TATAGAATTT
**
31913511 AAATTTATTATTTTA-TTTTTTGAAAATATTTTTA
1 AAATTTATTATTACATTTTTTTGAAAATATTTTTA
31913545 AAATTTATTATTACATTTTTTTGAAAATATTT
1 AAATTTATTATTACATTTTTTTGAAAATATTT
31913577 ATGTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (35 bp):
AAATTTATTATTACATTTTTTTGAAAATATTTTTA
Found at i:31919621 original size:15 final size:16
Alignment explanation
Indices: 31919601--31919632 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
31919591 AATATTATAT
31919601 AATAAATAATA-AAAA
1 AATAAATAATATAAAA
31919616 AATAAATAATATAAAA
1 AATAAATAATATAAAA
31919632 A
1 A
31919633 GTCAATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAATAATATAAAA
Found at i:31934861 original size:26 final size:25
Alignment explanation
Indices: 31934805--31934861 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
31934795 ATTAGAAGAT
* * *
31934805 ACAAAAGTAAATTATTTCCCTTAAA
1 ACAAAAGTAAATTAATTCACTGAAA
* *
31934830 AAAAAATGTAAATTAATTCACTGCAA
1 ACAAAA-GTAAATTAATTCACTGAAA
31934856 ACAAAA
1 ACAAAA
31934862 AAAAGTTTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.26
Consensus pattern (25 bp):
ACAAAAGTAAATTAATTCACTGAAA
Found at i:31942888 original size:90 final size:91
Alignment explanation
Indices: 31942730--31942895 Score: 237
Period size: 91 Copynumber: 1.8 Consensus size: 91
31942720 TCAATGTAGG
* * * * * **
31942730 AACAATTGCCTAATTCAAGGATTAACTTGGACCAAAAGAAAGTTCAAACCCTAATATGTGAACAA
1 AACAATTGCCAAACTCAAGGATTAACCTGAACAAAAAGAAAGTTCAAACCCTAATATGAAAACAA
31942795 TTGGTTAGTTCGGACTCCAATATGAA
66 TTGGTTAGTTCGGACTCCAATATGAA
31942821 AACAATTGCCAAACTCAAGGATTAACCTGAACAAAAAG-AAGTTCAAA-CCTCAATATGAAAACA
1 AACAATTGCCAAACTCAAGGATTAACCTGAACAAAAAGAAAGTTCAAACCCT-AATATGAAAACA
*
31942884 ATTGGTTGGTTC
65 ATTGGTTAGTTC
31942896 AGGCCCCAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
89 3 0.05
90 30 0.45
91 33 0.50
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (91 bp):
AACAATTGCCAAACTCAAGGATTAACCTGAACAAAAAGAAAGTTCAAACCCTAATATGAAAACAA
TTGGTTAGTTCGGACTCCAATATGAA
Found at i:31942915 original size:90 final size:90
Alignment explanation
Indices: 31942721--31942966 Score: 266
Period size: 90 Copynumber: 2.7 Consensus size: 90
31942711 GCTCAAACCT
* *
31942721 CAATGTAGGAACAATTGCCTAATTCAAGGATTAACTTGGACCAAAAGAAAGTTCAAACC-CTAAT
1 CAATGTAGGAACAATTGCCAAATTCAAGGATTAACTTGGACAAAAAG-AAGTTCAAACCTC-AAT
** *
31942785 ATGTGAACAATTGGTTAGTTCGGACTC
64 ATGAAAACAATTGGTTAGTTCGGACCC
* * * * *
31942812 CAATAT-GAAAACAATTGCCAAACTCAAGGATTAACCTGAACAAAAAGAAGTTCAAACCTCAATA
1 CAATGTAG-GAACAATTGCCAAATTCAAGGATTAACTTGGACAAAAAGAAGTTCAAACCTCAATA
*
31942876 TGAAAACAATTGGTTGGTTCAGG-CCC
65 TGAAAACAATTGGTTAGTTC-GGACCC
* * * * * *
31942902 CAATGTAGGAACAATCGTCAAATTTAAGAATTAACTTGGACAAAAAAAAGTT-ATAATCTCAATA
1 CAATGTAGGAACAATTGCCAAATTCAAGGATTAACTTGGACAAAAAGAAGTTCA-AACCTCAATA
31942966 T
65 T
31942967 AGGAGTAGTT
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
89 1 0.01
90 85 0.66
91 42 0.33
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (90 bp):
CAATGTAGGAACAATTGCCAAATTCAAGGATTAACTTGGACAAAAAGAAGTTCAAACCTCAATAT
GAAAACAATTGGTTAGTTCGGACCC
Found at i:31951153 original size:29 final size:29
Alignment explanation
Indices: 31951119--31951178 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
31951109 TTTTTAATAT
31951119 ATTTTTTTTAATTTTT-T-AAAAAATTATA
1 ATTTTTTTT-ATTTTTATAAAAAAATTATA
31951147 A-TTTTTTTATTTTTAGTAAAAAAATTATA
1 ATTTTTTTTATTTTTA-TAAAAAAATTATA
31951176 ATT
1 ATT
31951179 ATAATTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 6 0.21
27 7 0.25
28 2 0.07
29 12 0.43
30 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTTTTTTTATTTTTATAAAAAAATTATA
Found at i:31951154 original size:27 final size:28
Alignment explanation
Indices: 31951116--31951178 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
31951106 TATTTTTTAA
* * *
31951116 TATATTTTTTTTAATTTT-TTAAAAAAT
1 TATAATTTTTTTATTTTTATAAAAAAAT
31951143 TATAATTTTTTTATTTTTAGTAAAAAAAT
1 TATAATTTTTTTATTTTTA-TAAAAAAAT
31951172 TATAATT
1 TATAATT
31951179 ATAATTAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 16 0.52
29 15 0.48
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TATAATTTTTTTATTTTTATAAAAAAAT
Found at i:31956839 original size:6 final size:7
Alignment explanation
Indices: 31956823--31956848 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31956813 GTATTAATTG
31956823 AAAAATA
1 AAAAATA
31956830 AAAAATA
1 AAAAATA
31956837 AAAAATA
1 AAAAATA
31956844 AAAAA
1 AAAAA
31956849 GGGAGGAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:31959125 original size:17 final size:16
Alignment explanation
Indices: 31959103--31959134 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
31959093 TATTTTTCGC
31959103 TTATTATTTTTCAATTA
1 TTATTATTTTT-AATTA
31959120 TTATTATTTTTAATT
1 TTATTATTTTTAATT
31959135 TTTTACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATTTTTAATTA
Found at i:31960425 original size:13 final size:14
Alignment explanation
Indices: 31960409--31960462 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 14
31960399 TATTTTTGAG
31960409 AAGTGCTTTT-AAA
1 AAGTGCTTTTGAAA
*
31960422 AAGTG-TTTTGGAA
1 AAGTGCTTTTGAAA
*
31960435 AAGTGATTTTGAAA
1 AAGTGCTTTTGAAA
*
31960449 AA-TACTTTTGAAA
1 AAGTGCTTTTGAAA
31960462 A
1 A
31960463 GTTTGGTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 4 0.11
13 22 0.63
14 9 0.26
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.37
Consensus pattern (14 bp):
AAGTGCTTTTGAAA
Found at i:31960461 original size:26 final size:25
Alignment explanation
Indices: 31960402--31960464 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
31960392 TTAGTATTAT
* * *
31960402 TTTTGAGAAGTGCTTTTAAAAAGTG
1 TTTTGAAAAGTGATTTTAAAAAGTC
31960427 TTTTGGAAAAGTGATTTTGAAAAA-TAC
1 TTTT-GAAAAGTGATTTT-AAAAAGT-C
31960454 TTTTGAAAAGT
1 TTTTGAAAAGT
31960465 TTGGTTTGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 4 0.12
26 19 0.59
27 9 0.28
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.40
Consensus pattern (25 bp):
TTTTGAAAAGTGATTTTAAAAAGTC
Found at i:31965765 original size:21 final size:22
Alignment explanation
Indices: 31965718--31965768 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
31965708 TATTAGTTTT
*
31965718 TAATTTT-TTTAAATATTTATG
1 TAATTTTATTTAAATATTTATA
* *
31965739 TTATTTTATTTTAATATTTA-A
1 TAATTTTATTTAAATATTTATA
31965760 TAATTTTAT
1 TAATTTTAT
31965769 AAGTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATTTTATTTAAATATTTATA
Found at i:31965916 original size:16 final size:16
Alignment explanation
Indices: 31965895--31965927 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31965885 TTATATTAAT
31965895 ATATAAAAATAATATA
1 ATATAAAAATAATATA
*
31965911 ATATAAAAATATTATA
1 ATATAAAAATAATATA
31965927 A
1 A
31965928 ACTTAAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAAAAATAATATA
Found at i:31966308 original size:9 final size:9
Alignment explanation
Indices: 31966252--31966309 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
31966242 TTTAATCCAA
*
31966252 TTTTAGAAT
1 TTTTAAAAT
31966261 TTTTATAAAT
1 TTTTA-AAAT
31966271 ATTTT-AAAT
1 -TTTTAAAAT
31966280 TTTTAAAATT
1 TTTTAAAA-T
*
31966290 ATTTTGAAAT
1 -TTTTAAAAT
31966300 TTTTAAAAT
1 TTTTAAAAT
31966309 T
1 T
31966310 ACTTATGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 21 0.51
10 5 0.12
11 11 0.27
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:31966309 original size:20 final size:19
Alignment explanation
Indices: 31966251--31966310 Score: 86
Period size: 20 Copynumber: 3.1 Consensus size: 19
31966241 ATTTAATCCA
31966251 ATTTTAGAATTTTTATAAA-T
1 ATTTTA-AATTTTTA-AAATT
31966271 ATTTTAAATTTTTAAAATT
1 ATTTTAAATTTTTAAAATT
31966290 ATTTTGAAATTTTTAAAATT
1 ATTTT-AAATTTTTAAAATT
31966310 A
1 A
31966311 CTTATGTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.08
19 14 0.37
20 21 0.55
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTTAAATTTTTAAAATT
Found at i:31966843 original size:110 final size:110
Alignment explanation
Indices: 31966632--31966849 Score: 287
Period size: 110 Copynumber: 2.0 Consensus size: 110
31966622 ACTTTTACAT
* * *
31966632 GGAGGTTGATAATGAGAGAGTTTGGGACTCGAAATTTCGTCCAGCTAGATGCGCTTTCTTGTTGA
1 GGAGGTTGATAATGAGAGAGTTTAGGACTCGAAATTTCGTCCAGCTAGACGCGCTTTCCTGTTGA
* * * **
31966697 GTCCCGAGATATCTAATCAATTTCGAGGTGCTGGATAATTTTATA
66 GTCCCAAGATATCTAACCAATTCCGAGGTGAAGGATAATTTTATA
* * *
31966742 GGAGGTTGATAATCG-GAGAGTTTAGGATTCGAAATTTCGTCTAGCTAGACGCTCTTTCCTGTTG
1 GGAGGTTGATAAT-GAGAGAGTTTAGGACTCGAAATTTCGTCCAGCTAGACGCGCTTTCCTGTTG
* *
31966806 AGTCGCAAGATATTTAACCAATTCCG-GGTTGAAGGATAATTTTA
65 AGTCCCAAGATATCTAACCAATTCCGAGG-TGAAGGATAATTTTA
31966850 CAGGGAGAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
109 2 0.02
110 90 0.97
111 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (110 bp):
GGAGGTTGATAATGAGAGAGTTTAGGACTCGAAATTTCGTCCAGCTAGACGCGCTTTCCTGTTGA
GTCCCAAGATATCTAACCAATTCCGAGGTGAAGGATAATTTTATA
Found at i:31967649 original size:2 final size:2
Alignment explanation
Indices: 31967642--31967668 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31967632 AGATGAGGTT
31967642 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 T
31967669 GATAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31969590 original size:3 final size:3
Alignment explanation
Indices: 31969578--31969618 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
31969568 GTTATCGTCG
* * *
31969578 TCA TCT TCA TCA TCA TCA TCA TCA TCA TCC TCG TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
31969619 TCTTCCCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.24, C:0.37, G:0.02, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:31975377 original size:22 final size:22
Alignment explanation
Indices: 31975323--31975377 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
31975313 TTCGAGCTTG
*
31975323 GTGTTGCAACACAACACACCTA
1 GTGTTGCGACACAACACACCTA
* * *
31975345 GTGTCGTGACACAACACA-TTGA
1 GTGTTGCGACACAACACACCT-A
31975367 GTGTTGCGACA
1 GTGTTGCGACA
31975378 TCCTCGACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (22 bp):
GTGTTGCGACACAACACACCTA
Found at i:31979085 original size:18 final size:18
Alignment explanation
Indices: 31979062--31979141 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
31979052 GATTTTTAGG
31979062 TTTAAATTTATTATTAAA
1 TTTAAATTTATTATTAAA
*
31979080 TTTAAATTCATT-TTAAA
1 TTTAAATTTATTATTAAA
* * *
31979097 TTAAAATATT-TGAAATAAA
1 TTTAAAT-TTAT-TATTAAA
*
31979116 TTTAAATTTAATTA-AAAA
1 TTTAAATTT-ATTATTAAA
31979134 TTTAAATT
1 TTTAAATT
31979142 AAAAAGTTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
17 12 0.24
18 25 0.51
19 11 0.22
20 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TTTAAATTTATTATTAAA
Found at i:31979097 original size:17 final size:18
Alignment explanation
Indices: 31979062--31979103 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
31979052 GATTTTTAGG
*
31979062 TTTAAATTTATTATTAAA
1 TTTAAATTCATTATTAAA
31979080 TTTAAATTCATT-TTAAA
1 TTTAAATTCATTATTAAA
*
31979097 TTAAAAT
1 TTTAAAT
31979104 ATTTGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTAAATTCATTATTAAA
Found at i:31979136 original size:12 final size:13
Alignment explanation
Indices: 31979091--31979146 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 13
31979081 TTAAATTCAT
31979091 TTTAAATTAAAATA
1 TTTAAATTAAAA-A
*
31979105 TTTGAAATAAATTTAAA
1 TTT-AAATTAA---AAA
31979122 TTT-AATTAAAAA
1 TTTAAATTAAAAA
31979134 TTTAAATTAAAAA
1 TTTAAATTAAAAA
31979147 GTTCAAGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
12 6 0.17
13 9 0.26
14 3 0.09
15 11 0.31
17 4 0.11
18 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
TTTAAATTAAAAA
Found at i:31981158 original size:29 final size:28
Alignment explanation
Indices: 31981126--31981274 Score: 126
Period size: 29 Copynumber: 5.1 Consensus size: 28
31981116 AAAATTACCA
31981126 TTTTACCCCCGAACTTTCCAAAATCCCAT
1 TTTTACCCCCGAA-TTTCCAAAATCCCAT
* *
31981155 TTTTAACCCCG-ATTTCACCAAAAATTACCA-
1 TTTTACCCCCGAATTT--CC-AAAA-TCCCAT
*
31981185 TTTTACCCTCGAACTTTCCAAAATCCCAT
1 TTTTACCCCCGAA-TTTCCAAAATCCCAT
* * *
31981214 TTTTAACCCC-AGTTTCACCAAAATTACCA-
1 TTTTACCCCCGAATTT--CCAAAA-TCCCAT
31981243 TTTTACCCCCGAATTTCCTAAAATCCCAT
1 TTTTACCCCCGAATTTCC-AAAATCCCAT
31981272 TTT
1 TTT
31981275 CGGCTCCGAT
Statistics
Matches: 95, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
27 6 0.06
28 12 0.13
29 46 0.48
30 23 0.24
31 5 0.05
32 3 0.03
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.34
Consensus pattern (28 bp):
TTTTACCCCCGAATTTCCAAAATCCCAT
Found at i:31981266 original size:58 final size:59
Alignment explanation
Indices: 31981113--31981311 Score: 298
Period size: 59 Copynumber: 3.4 Consensus size: 59
31981103 CCTAAACTAT
31981113 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
*
31981172 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATCCCATTTTTAACCCC-AGTTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGA-TTTCA
*** *
31981231 CC-AAAATTACCATTTTACCCCCGAA-TTTCCTAAAATCCCATTTTCGGCTCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCC-AAAATCCCATTTTTAACCCCGATTTCA
31981289 CCAAAAATTA-CATTTTTACCCCC
1 CCAAAAATTACCA-TTTTACCCCC
31981312 AAAAGTTAAA
Statistics
Matches: 129, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
57 5 0.04
58 48 0.37
59 76 0.59
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.32
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
Done.