Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 129 of 132
Found at i:39982981 original size:23 final size:23
Alignment explanation
Indices: 39982955--39983000 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
39982945 TATTCCTTTT
39982955 TTAAATTAAATAAATTTAATTTA
1 TTAAATTAAATAAATTTAATTTA
*
39982978 TTAAATTAAATGAATTTAATTTA
1 TTAAATTAAATAAATTTAATTTA
39983001 AAATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAAATTAAATAAATTTAATTTA
Found at i:39985155 original size:24 final size:25
Alignment explanation
Indices: 39985086--39985162 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
39985076 ATTGTATAAT
39985086 TTTTAATAATCTATATAATTT-TTA
1 TTTTAATAATCTATATAATTTATTA
** **
39985110 TCATAATAA-AAATATAATTTTATTA
1 TTTTAATAATCTATATAA-TTTATTA
*
39985135 TTTTAATAATCTATAT-ATTTATAA
1 TTTTAATAATCTATATAATTTATTA
39985159 TTTT
1 TTTT
39985163 TAGAAAATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
23 6 0.15
24 20 0.49
25 11 0.27
26 4 0.10
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTAATAATCTATATAATTTATTA
Found at i:39985163 original size:25 final size:25
Alignment explanation
Indices: 39985082--39985164 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
39985072 TTAAATTGTA
39985082 TAATTTTTAATAATCTATATAATTT
1 TAATTTTTAATAATCTATATAATTT
* ** **
39985107 TTA-TCATAATAA-AAATATAATTT
1 TAATTTTTAATAATCTATATAATTT
*
39985130 TATTATTTTAATAATCTATAT-ATTT
1 TAAT-TTTTAATAATCTATATAATTT
39985155 ATAATTTTTA
1 -TAATTTTTA
39985165 GAAAATTAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
23 10 0.24
24 7 0.17
25 18 0.43
26 7 0.17
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TAATTTTTAATAATCTATATAATTT
Found at i:39986059 original size:36 final size:36
Alignment explanation
Indices: 39986005--39986195 Score: 242
Period size: 36 Copynumber: 5.4 Consensus size: 36
39985995 ATTTTTATTG
* *
39986005 ATATTA-GT-TTGAACATGCTGTTTAGGTGATGTCT
1 ATATTACGTGTTGAAGACGCTGTTTAGGTGATGTCT
* *
39986039 ATATTACCTGTTGAAGATGCTGTTTAGGTGATGTCT
1 ATATTACGTGTTGAAGACGCTGTTTAGGTGATGTCT
* * * ** *
39986075 ATATTTCTTGTTGAAGACGTTGTTTAGGTGAAATTT
1 ATATTACGTGTTGAAGACGCTGTTTAGGTGATGTCT
* *
39986111 ATATTACGTGTTGAAGACGCTATTTAGATGATGTCT
1 ATATTACGTGTTGAAGACGCTGTTTAGGTGATGTCT
* *
39986147 ATATTACTTGTTGAAGACGCTGTTTAGGTGATGTTT
1 ATATTACGTGTTGAAGACGCTGTTTAGGTGATGTCT
39986183 ATATTACGTGTTG
1 ATATTACGTGTTG
39986196 GCCAAATTAA
Statistics
Matches: 133, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
34 6 0.05
35 1 0.01
36 126 0.95
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (36 bp):
ATATTACGTGTTGAAGACGCTGTTTAGGTGATGTCT
Found at i:39986137 original size:72 final size:72
Alignment explanation
Indices: 39986021--39986195 Score: 269
Period size: 72 Copynumber: 2.4 Consensus size: 72
39986011 GTTTGAACAT
* * * * * *
39986021 GCTGTTTAGGTGATGTCTATATTACCTGTTGAAGATGCTGTTTAGGTGATGTCTATATTTCTTGT
1 GCTGTTTAGGTGATGTTTATATTACGTGTTGAAGACGCTATTTAGATGATGTCTATATTACTTGT
39986086 TGAAGAC
66 TGAAGAC
* **
39986093 GTTGTTTAGGTGAAATTTATATTACGTGTTGAAGACGCTATTTAGATGATGTCTATATTACTTGT
1 GCTGTTTAGGTGATGTTTATATTACGTGTTGAAGACGCTATTTAGATGATGTCTATATTACTTGT
39986158 TGAAGAC
66 TGAAGAC
39986165 GCTGTTTAGGTGATGTTTATATTACGTGTTG
1 GCTGTTTAGGTGATGTTTATATTACGTGTTG
39986196 GCCAAATTAA
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 91 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (72 bp):
GCTGTTTAGGTGATGTTTATATTACGTGTTGAAGACGCTATTTAGATGATGTCTATATTACTTGT
TGAAGAC
Found at i:39986328 original size:2 final size:2
Alignment explanation
Indices: 39986321--39986348 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39986311 TTTGCCATTC
39986321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39986349 GTGTGTGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39998609 original size:6 final size:6
Alignment explanation
Indices: 39998598--39998654 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
39998588 TAGAATAATC
* * * * *
39998598 TTAAAT TTAAAT TTAAAT TTTAA- CT-AAT TCAAAT TTAAAA ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
39998644 TTAAAT TTAAA
1 TTAAAT TTAAA
39998655 ATAAATCTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
4 2 0.05
5 1 0.03
6 37 0.93
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:39998657 original size:17 final size:17
Alignment explanation
Indices: 39998605--39998660 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
39998595 ATCTTAAATT
* *
39998605 TAAATTTAAATTTTAAC
1 TAAATTTAAATTTAAAA
*
39998622 T-AATTCAAATTTAAAAA
1 TAAATTTAAATTT-AAAA
39998639 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
39998656 TAAAT
1 TAAAT
39998661 CTCAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 10 0.30
17 13 0.39
18 10 0.30
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:40000592 original size:21 final size:21
Alignment explanation
Indices: 40000547--40000592 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
40000537 GAAATTTTTA
*
40000547 CGAA-TCGAGTCGAATGAGAT
1 CGAATTCGAATCGAATGAGAT
*
40000567 AGAATTCGAATCGAATTGA-AT
1 CGAATTCGAATCGAA-TGAGAT
40000588 CGAAT
1 CGAAT
40000593 ATATTTGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.14
21 15 0.71
22 3 0.14
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (21 bp):
CGAATTCGAATCGAATGAGAT
Found at i:40006225 original size:14 final size:15
Alignment explanation
Indices: 40006187--40006231 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
40006177 GCAATTAATT
40006187 AACTTTATAAAATAA
1 AACTTTATAAAATAA
* *
40006202 AAATAT-TAAAA-AA
1 AACTTTATAAAATAA
40006215 AACTTTATAAAATAA
1 AACTTTATAAAATAA
40006230 AA
1 AA
40006232 AGAAAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (15 bp):
AACTTTATAAAATAA
Found at i:40006431 original size:30 final size:30
Alignment explanation
Indices: 40006358--40006435 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 30
40006348 AATATAAAAC
* *
40006358 TAAATAATTTTATT-TATTTTTTTGAATTTT
1 TAAATAATTTT-TTATAATTTTTTGAATGTT
**
40006388 TAAA-AA-TAATTATAATTTTTTGAATGTT
1 TAAATAATTTTTTATAATTTTTTGAATGTT
40006416 TAAATAATTTTTTATAATTT
1 TAAATAATTTTTTATAATTT
40006436 CTAACAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 2 0.05
28 19 0.49
29 4 0.10
30 14 0.36
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (30 bp):
TAAATAATTTTTTATAATTTTTTGAATGTT
Found at i:40010595 original size:22 final size:22
Alignment explanation
Indices: 40010570--40010611 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40010560 TTGCCGATGA
* *
40010570 TGACTCATTTTTCTCGAGTCAT
1 TGACTCAGTCTTCTCGAGTCAT
*
40010592 TGACTCGGTCTTCTCGAGTC
1 TGACTCAGTCTTCTCGAGTC
40010612 GTAATCCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.40
Consensus pattern (22 bp):
TGACTCAGTCTTCTCGAGTCAT
Found at i:40014787 original size:140 final size:140
Alignment explanation
Indices: 40014534--40015098 Score: 1022
Period size: 140 Copynumber: 4.0 Consensus size: 140
40014524 TTTTCTTGCT
* *
40014534 CTCATGCCATTTCTGGATTCCCCCACGAATTCCTTGAAGGAAAACACCAAGACTTAAATACACCC
1 CTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
*
40014599 TACATCTGAAAATTGGAACAAAAAGAAAAACACAAGAGAAAAGCAGTCACCTTCTTGGCCGAGTC
66 TACATCTGAGAATTGGAACAAAAAGAAAAACACAAGAGAAAAGCAGTCACCTTCTTGGCCGAGTC
40014664 TCTATTTGGG
131 TCTATTTGGG
*
40014674 TTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
1 CTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
40014739 TACATCTGAGAATTGGAACAAAAAGAAAAACACAAGAGAAAAGCAGTCACCTTCTTGGCCGAGTC
66 TACATCTGAGAATTGGAACAAAAAGAAAAACACAAGAGAAAAGCAGTCACCTTCTTGGCCGAGTC
40014804 TCTATTTGGG
131 TCTATTTGGG
*
40014814 TTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
1 CTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
* *
40014879 TACATCTGAGAATTGGAACAAAAAGAAAAACACAAGAGAAAAGTAGTCACCTTCTTGGCCGAGTT
66 TACATCTGAGAATTGGAACAAAAAGAAAAACACAAGAGAAAAGCAGTCACCTTCTTGGCCGAGTC
40014944 TCTATTTGGG
131 TCTATTTGGG
40014954 CTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
1 CTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
* * * * *
40015019 TGCATCTGAGAATTGGAACAAAAATAAAATCACAAGAGAAAAGTAGTCACCTTCTTAGCCGAGTC
66 TACATCTGAGAATTGGAACAAAAAGAAAAACACAAGAGAAAAGCAGTCACCTTCTTGGCCGAGTC
40015084 TCTATTTGGG
131 TCTATTTGGG
40015094 CTCAT
1 CTCAT
40015099 CTGAGATTTT
Statistics
Matches: 413, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 413 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (140 bp):
CTCATGCCATTGCTGGATTCCCCCACGAATACCTTGAAGGAAAACACCAAGACTTAAATACACCC
TACATCTGAGAATTGGAACAAAAAGAAAAACACAAGAGAAAAGCAGTCACCTTCTTGGCCGAGTC
TCTATTTGGG
Found at i:40022552 original size:30 final size:30
Alignment explanation
Indices: 40022518--40022661 Score: 204
Period size: 30 Copynumber: 4.8 Consensus size: 30
40022508 ATTTTATTCC
* *
40022518 AAAATTGCATTTTAACCCCTAAATTTTTCA
1 AAAATTACATTTTAACCCTTAAATTTTTCA
* *
40022548 AAAATTACATTTTAACCCTTTAATTTTTCT
1 AAAATTACATTTTAACCCTTAAATTTTTCA
*
40022578 AAAATTACATTTTAGCCCTTAAACTTTTT-A
1 AAAATTACATTTTAACCCTTAAA-TTTTTCA
40022608 AAAATTACATTTTAACCCTTAAATTCTTTC-
1 AAAATTACATTTTAACCCTTAAATT-TTTCA
40022638 AAAATTACATTTTAACCC-TAAATT
1 AAAATTACATTTTAACCCTTAAATT
40022662 CTCTAAAACT
Statistics
Matches: 103, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
29 8 0.08
30 90 0.87
31 5 0.05
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAATTTTTCA
Found at i:40026176 original size:45 final size:45
Alignment explanation
Indices: 40026048--40026179 Score: 147
Period size: 46 Copynumber: 2.9 Consensus size: 45
40026038 TGAGGACACG
* * *
40026048 CCAATCTCTTACCCCTAATTATGGGGCAAATTGCAGTCATTATCAT
1 CCAATCTCTTACCCC-AATTATGGGGCAGATTGCAGCCATCATCAT
* ** * *
40026094 CCAATCTCTTAGTCTTAATTATGGGGCAGATTACAGCCATCATTAT
1 CCAATCTCTTA-CCCCAATTATGGGGCAGATTGCAGCCATCATCAT
* * *
40026140 CCAATCTCTTACCCCGATTATAGGGTAGATTGCAGCCATC
1 CCAATCTCTTACCCCAATTATGGGGCAGATTGCAGCCATC
40026180 CAATCTCTTA
Statistics
Matches: 70, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
45 22 0.31
46 47 0.67
47 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (45 bp):
CCAATCTCTTACCCCAATTATGGGGCAGATTGCAGCCATCATCAT
Found at i:40026591 original size:209 final size:208
Alignment explanation
Indices: 40026225--40026758 Score: 692
Period size: 209 Copynumber: 2.6 Consensus size: 208
40026215 CATCCGAAAT
** *
40026225 AATAAAGTGGTCATCTTCCTGATGAGATGCAGAGAAGTTCATCAAATCCGTCTTCTTGATGAGAT
1 AATAAAGTGGTCATCTTCCTGATGAGATGCAGAGAAGTAAACCAAATCCGTCTTCTTGATGAGAT
* * * ** * * * *
40026290 ACAGAGAAGTGGATTAAAATATTGAAACGGTCATCTTCCTAATGAGATACAGAGAAGTAGACCAA
66 ACAAAGAAGTGGATTAAAACAATGAGGC-GACATCTTCCTGATGAGATACAGAAAAGTACACCAA
*
40026355 TTCAATGAAGCGAAGCTCAAGGTGAGTGAAACTTCAAAACCCCATCTTCCTGATAAGATACAAAA
130 ATCAATGAAGCGAAGCTCAAGGTGAGTGAAACTTCAAAACCCCATCTTCCTGATAAGATACAAAA
*
40026420 AAGTGGGTCGAAGC
195 AAGTGGGTCAAAGC
* * ** * *
40026434 AATAAAGTGGTAATTTTCCTGACAAGATGCAGAGAAGTAAACCAAATCCATCTTCCTGATGAGAT
1 AATAAAGTGGTCATCTTCCTGATGAGATGCAGAGAAGTAAACCAAATCCGTCTTCTTGATGAGAT
* *
40026499 ACAAAGAAGTGGATTAAAACAATGAGGCGACCATTTTCCTGATGAGATACAGAAAAGTACACTAA
66 ACAAAGAAGTGGATTAAAACAATGAGGCGA-CATCTTCCTGATGAGATACAGAAAAGTACACCAA
* * * * * * * *
40026564 ATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCTAACCCCCATCTTCTTGATGAGATACAGAG
130 ATCAATGAAGCGAAGCTCAAGGTGAGTGAAACTTCAAAACCCCATCTTCCTGATAAGATACAAAA
40026629 AAGTGGGTCAAAGC
195 AAGTGGGTCAAAGC
* * * * * * *
40026643 AATAAAGCGATCATCTTCTTGATGAGATACAAAGAAGTAGACCAAATCTGTCTTCTTGATGAGAT
1 AATAAAGTGGTCATCTTCCTGATGAGATGCAGAGAAGTAAACCAAATCCGTCTTCTTGATGAGAT
40026708 ACAAAGAAGTGGATTAAAACAATGAAGTG-GACATCTTCCTGATGAGATACA
66 ACAAAGAAGTGGATTAAAACAATG-AG-GCGACATCTTCCTGATGAGATACA
40026759 AAGAAGTGGA
Statistics
Matches: 278, Mismatches: 44, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
208 1 0.00
209 272 0.98
210 4 0.01
211 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (208 bp):
AATAAAGTGGTCATCTTCCTGATGAGATGCAGAGAAGTAAACCAAATCCGTCTTCTTGATGAGAT
ACAAAGAAGTGGATTAAAACAATGAGGCGACATCTTCCTGATGAGATACAGAAAAGTACACCAAA
TCAATGAAGCGAAGCTCAAGGTGAGTGAAACTTCAAAACCCCATCTTCCTGATAAGATACAAAAA
AGTGGGTCAAAGC
Found at i:40026751 original size:85 final size:85
Alignment explanation
Indices: 40026608--40026765 Score: 237
Period size: 85 Copynumber: 1.9 Consensus size: 85
40026598 CTAACCCCCA
* * * *
40026608 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCTTCTTGATGAGATAC
1 TCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTGATGAGATAC
40026673 AAAGAAGTAGACCAAATCTG
66 AAAGAAGTAGACCAAATCTG
* * *
40026693 TCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGA-CATCTTCCTGATGAGATA
1 TCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATAAAG-CGATCATCTTCCTGATGAGATA
40026757 CAAAGAAGT
65 CAAAGAAGT
40026766 GGATTAAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 63 0.97
86 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (85 bp):
TCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGATCATCTTCCTGATGAGATAC
AAAGAAGTAGACCAAATCTG
Found at i:40026764 original size:48 final size:48
Alignment explanation
Indices: 40026693--40026813 Score: 206
Period size: 48 Copynumber: 2.5 Consensus size: 48
40026683 ACCAAATCTG
*
40026693 TCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGACA
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGACA
*
40026741 TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGCCA
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGACA
* *
40026789 TCTTCCTGATGAGATATAGAGAAGT
1 TCTTCCTGATGAGATACAAAGAAGT
40026814 AAACCAATTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGACA
Found at i:40026798 original size:257 final size:258
Alignment explanation
Indices: 40026482--40027023 Score: 687
Period size: 257 Copynumber: 2.1 Consensus size: 258
40026472 AAACCAAATC
* *
40026482 CATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAGGCGACCATTTTCCTGATGAGAT
1 CATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGACCATCTTCCTGATGAGAT
* * * * * * *
40026547 ACAGAAAAGTACACTAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCTAACCCCCATC-T
66 ACAGAAAAGTAAACCAAATCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACCCCATCTT
* * * * * * * * *
40026611 TCTTGATGAGATA-CAGAGAAGTGGGTCAAAGCAATAAAGCGATC-ATCTTCTTGATGAGATACA
131 TC-TAATAAGATATAAAAAAAGTGGGTCAAAGCAATAAAGCG-GCAATCTTCCTAACGAGATACA
* * *
40026674 AAGAAGTAGACCAAA-TCTGTCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGG
194 AAGAAGTAAACCAAATTC-GTCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGG
40026738 A
258 A
* *
40026739 CATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGCCATCTTCCTGATGAGAT
1 CATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGACCATCTTCCTGATGAGAT
* * * *
40026804 ATAGAGAAGTAAACCAATTCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACCTCATCTT
66 ACAGAAAAGTAAACCAAATCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACCCCATCTT
* * * *
40026869 TCTAATAAGATATAAAAAAAGTGGGTCGAAGCAATAAAGTGGCAATCTTCCTAACGAGATGCAGA
131 TCTAATAAGATATAAAAAAAGTGGGTCAAAGCAATAAAGCGGCAATCTTCCTAACGAGATACAAA
*** * *
40026934 GAAGTAAACCAAATTCGTCTTCCTGATGAGATATGGAGAAGTGGATTAAAACAATGAGGCGGT
196 GAAGTAAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGGA
* *
40026997 CATCTTCCTAATGAGATACAGAGAAGT
1 CATCTTCCTGATGAGATACAAAGAAGT
40027024 AGACCAAATC
Statistics
Matches: 243, Mismatches: 38, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
257 122 0.50
258 119 0.49
259 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (258 bp):
CATCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGACCATCTTCCTGATGAGAT
ACAGAAAAGTAAACCAAATCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACCCCATCTT
TCTAATAAGATATAAAAAAAGTGGGTCAAAGCAATAAAGCGGCAATCTTCCTAACGAGATACAAA
GAAGTAAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGGA
Found at i:40026827 original size:48 final size:48
Alignment explanation
Indices: 40026693--40026830 Score: 150
Period size: 48 Copynumber: 2.9 Consensus size: 48
40026683 ACCAAATCTG
* ** **
40026693 TCTTCTTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGACA
1 TCTTCCTGATGAGATACAAAGAAGTAAACCAAAACAATGAAGTGGACA
** ** *
40026741 TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGCCA
1 TCTTCCTGATGAGATACAAAGAAGTAAACCAAAACAATGAAGTGGACA
* * **
40026789 TCTTCCTGATGAGATATAGAGAAGTAAACCAATTCAATGAAG
1 TCTTCCTGATGAGATACAAAGAAGTAAACCAAAACAATGAAG
40026831 CAAAGCTCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.25
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAAAGAAGTAAACCAAAACAATGAAGTGGACA
Found at i:40027120 original size:210 final size:210
Alignment explanation
Indices: 40026741--40027128 Score: 557
Period size: 210 Copynumber: 1.8 Consensus size: 210
40026731 GAAGTGGACA
* * *
40026741 TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGCCATCTTCCTGATGAGATAT
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGGCCATCTTCCTAATGAGATAC
* *
40026806 AGAGAAGTAAACCAATTCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACCTCATCTTTC
66 AGAGAAGTAAACCAAATCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACCTCATCTTCC
* *
40026871 TAATAAGATATAAAAAAAGTGGGTCGAAGCAATAAAGTGG-CAATCTTCCTAACGAGATGCAGAG
131 TAATAAGATATAAAAAAAGTGGGTCAAAGCAAAAAAGTGGTC-ATCTTCCTAACGAGATGCAGAG
40026935 AAGTAAACCAAATTCG
195 AAGTAAACCAAATTCG
*** * *
40026951 TCTTCCTGATGAGATATGGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGGCCATCTTCCTAATGAGATAC
* * * *
40027016 AGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTT-CAAACCATCATCTTC
66 AGAGAAGTAAACCAAATCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACC-TCATCTTC
* * *
40027080 CTAATGAGATA-CAAAGAAGTGGGTCAAAGCAAAAAAAGTGGTCATCTTC
130 CTAATAAGATATAAAAAAAGTGGGTCAAAGC-AAAAAAGTGGTCATCTTC
40027129 TTGATGAGAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
209 22 0.14
210 133 0.85
211 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (210 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAATGAAGCGGCCATCTTCCTAATGAGATAC
AGAGAAGTAAACCAAATCAATGAAGCAAAGCTCAAGGTGAGTGAAACTTCCAAACCTCATCTTCC
TAATAAGATATAAAAAAAGTGGGTCAAAGCAAAAAAGTGGTCATCTTCCTAACGAGATGCAGAGA
AGTAAACCAAATTCG
Found at i:40027147 original size:49 final size:49
Alignment explanation
Indices: 40027072--40027197 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 49
40027062 CTTCAAACCA
* * * * *
40027072 TCATCTTCCTAATGAGATACAAAGAAGTGGGTCAAAGCAAAAAAAGTGG
1 TCATCTTCTTGATGAGATATAAAGAAGTGGATCAAAACAAAAAAAGTGG
* * ** *
40027121 TCATCTTCTTGATGAGATATAGAGAAGTGGATTAAAACAAATGAGGTGG
1 TCATCTTCTTGATGAGATATAAAGAAGTGGATCAAAACAAAAAAAGTGG
40027170 TCATCTTCTTGATGAGATATAAAGAAGT
1 TCATCTTCTTGATGAGATATAAAGAAGT
40027198 AGCCAAATCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (49 bp):
TCATCTTCTTGATGAGATATAAAGAAGTGGATCAAAACAAAAAAAGTGG
Found at i:40027252 original size:173 final size:171
Alignment explanation
Indices: 40026951--40027323 Score: 514
Period size: 173 Copynumber: 2.2 Consensus size: 171
40026941 ACCAAATTCG
*
40026951 TCTTCCTGATGAGATATGGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATAC
1 TCTT-CTGATGAGATATAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATAC
* * * *
40027016 AGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCATCATCTTCC
65 AAAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGCGAATGAAACTTCAAACCACCATCTTCC
* * * *
40027081 TAATGAGATACAAAGAAGTGGGTCAAAGCAAAAAAAGTGGTCA
130 TAATGAGATACAAAGAAATGGGTCAAAGC-AAAAAAGCGATAA
* * *
40027124 TCTTCTTGATGAGATATAGAGAAGTGGATTAAAACAAATGAGGTGGTCATCTTCTTGATGAGATA
1 TCTTC-TGATGAGATATAGAGAAGTGGATTAAAAC-AATGAGGCGGTCATCTTCCTAATGAGATA
* * *
40027189 TAAAGAAGTAG-CCAAATCGATGAAGCGAAGCTCAATGCGAATGAGACTTCAAACCCCCATCTTC
64 CAAAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGCGAATGAAACTTCAAACCACCATCTTC
* * *
40027253 TTGATGAGATACAAAGAAATGGGTCAAAGCAATAAAGCGATAA
129 CTAATGAGATACAAAGAAATGGGTCAAAGCAAAAAAGCGATAA
* *
40027296 ACTTACTGATAAGATATAGAGAAGTGGA
1 TCTT-CTGATGAGATATAGAGAAGTGGA
40027324 CCAAATCCAT
Statistics
Matches: 177, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
172 34 0.19
173 108 0.61
174 35 0.20
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (171 bp):
TCTTCTGATGAGATATAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATACA
AAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGCGAATGAAACTTCAAACCACCATCTTCCT
AATGAGATACAAAGAAATGGGTCAAAGCAAAAAAGCGATAA
Found at i:40027344 original size:382 final size:382
Alignment explanation
Indices: 40026701--40027429 Score: 917
Period size: 382 Copynumber: 1.9 Consensus size: 382
40026691 TGTCTTCTTG
* **
40026701 ATGAGATACAAAGAAGTGGATTAAAACAATGAAGTGGACATCTTCCTGATGAGATACAAAGAAGT
1 ATGAGATACAAAGAAGTGGATCAAAACAAAAAAGTGGACATCTTCCTGATGAGATACAAAGAAGT
* *
40026766 GGATTAAAACAATGAAGTGGCCATCTTCCTGATGAGATATAGAGAAGTAAACCAATTCAATGAAG
66 GGATTAAAACAATGAAGTGGCCATCTTCCTGATGAGATATAAAGAAGTAAACCAAATCAATGAAG
* * * *
40026831 CAAAGCTCAAGGTGAGTGAAACTTCCAAACCTCATCTTTCTAATAAGATATAAAAAAAGTGGGTC
131 CAAAGCTCAAGGCGAATGAAACTTCCAAACCCCATCTTTCTAATAAGATACAAAAAAAGTGGGTC
* * * * * * * * *
40026896 GAAGCAATAAAGTGGCAATCTTCCTAACGAGATGCAGAGAAGTAAACCAAATTCGTCTTCCTGAT
196 AAAGCAATAAAGCGACAAACTTACTAACAAGATACAGAGAAGTAAACCAAATCCATCTTCCTGAT
**
40026961 GAGATATGGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTAG
261 GAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTAG
* *
40027026 ACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAACCATCATCTTCCTA
326 ACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCATCATCTTCCTA
* * * * * *
40027083 ATGAGATACAAAGAAGTGGGTCAAAGCAAAAAAAGTGGTCATCTTCTTGATGAGATATAGAGAAG
1 ATGAGATACAAAGAAGTGGATCAAAAC-AAAAAAGTGGACATCTTCCTGATGAGATACAAAGAAG
* * * * *
40027148 TGGATTAAAACAAATGAGGTGGTCATCTTCTTGATGAGATATAAAGAAGT-AGCCAAATCGATGA
65 TGGATTAAAAC-AATGAAGTGGCCATCTTCCTGATGAGATATAAAGAAGTAAACCAAATCAATGA
* * * * * *
40027212 AGCGAAGCTCAATGCGAATGAGACTT-CAAACCCCCATC-TTCTTGATGAGATACAAAGAAA-TG
129 AGCAAAGCTCAAGGCGAATGAAACTTCCAAA-CCCCATCTTTC-TAATAAGATACAAAAAAAGTG
* * * * ** *
40027274 GGTCAAAGCAATAAAGCGATAAACTTACTGATAAGATATAGAGAAGTGGACCAAATCCATCTTTC
192 GGTCAAAGCAATAAAGCGACAAACTTACTAACAAGATACAGAGAAGTAAACCAAATCCATCTTCC
* * * * **
40027339 TGATGAGATACAGAGAAGTGGATTGAAACAATGAGGTGGTCATCTTCCTGATGAGGTACATTGAA
257 TGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATACAGAGAA
*
40027404 GTAGATCAAATCAATGAAGCAAAGCT
322 GTAGACCAAATCAATGAAGCAAAGCT
40027430 TAATATAAGT
Statistics
Matches: 290, Mismatches: 53, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
382 162 0.56
383 94 0.32
384 34 0.12
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (382 bp):
ATGAGATACAAAGAAGTGGATCAAAACAAAAAAGTGGACATCTTCCTGATGAGATACAAAGAAGT
GGATTAAAACAATGAAGTGGCCATCTTCCTGATGAGATATAAAGAAGTAAACCAAATCAATGAAG
CAAAGCTCAAGGCGAATGAAACTTCCAAACCCCATCTTTCTAATAAGATACAAAAAAAGTGGGTC
AAAGCAATAAAGCGACAAACTTACTAACAAGATACAGAGAAGTAAACCAAATCCATCTTCCTGAT
GAGATACAGAGAAGTGGATTAAAACAATGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTAG
ACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCATCATCTTCCTA
Found at i:40027414 original size:85 final size:84
Alignment explanation
Indices: 40027301--40027577 Score: 245
Period size: 85 Copynumber: 3.3 Consensus size: 84
40027291 GATAAACTTA
* * * * * * * *
40027301 CTGATAAGATATAGAGAAGTGGACCAAATCCATCTTTCTGATGAGATACAGAGAAGTGGATTGAA
1 CTGATGAGATACAAAGAAGTAGACCAAATCAATCTTCCT-ATAAGATACAGAGAAGTGGATCGAA
*
40027366 ACAATGAGGTGGTCATCTTC
65 ACAATGAAGTGGTCATCTTC
* ** * **** * * * *
40027386 CTGATGAGGTACATTGAAGTAGATCAAATCAATGAAGC-A-AAGCTTA-ATATAAGTGGGTCGAA
1 CTGATGAGATACAAAGAAGTAGACCAAATCAATCTTCCTATAAG-ATACAGAGAAGTGGATCGAA
* *
40027448 ACAATAAAGTGGTCATCTTG
65 ACAATGAAGTGGTCATCTTC
* ** *
40027468 CTGATGAGATACAAAGAAGTAGAGCAAATCTGTCTTCCTTATAAGATACAGAGAAGTGGATCAAA
1 CTGATGAGATACAAAGAAGTAGACCAAATCAATCTTCC-TATAAGATACAGAGAAGTGGATCGAA
40027533 ACAATGAAGTGGTCATCTTC
65 ACAATGAAGTGGTCATCTTC
* *
40027553 CTGATGAGATACAAAAAAGTGGACC
1 CTGATGAGATACAAAGAAGTAGACC
40027578 CAAAAGATAA
Statistics
Matches: 146, Mismatches: 41, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
82 59 0.40
83 3 0.02
84 3 0.02
85 81 0.55
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (84 bp):
CTGATGAGATACAAAGAAGTAGACCAAATCAATCTTCCTATAAGATACAGAGAAGTGGATCGAAA
CAATGAAGTGGTCATCTTC
Found at i:40029660 original size:30 final size:31
Alignment explanation
Indices: 40029594--40029694 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 31
40029584 TCTAAAATTG
* *
40029594 CATTTTAACCCCCAAA-CTTTCTCAAAATCA
1 CATTTTGACCCCTAAACCTTTCTCAAAATCA
*
40029624 TATTTTGACCCCTAAACCTTTC-CAAAATCA
1 CATTTTGACCCCTAAACCTTTCTCAAAATCA
* * * * **
40029654 CATTTTGATCCTTAAA-CTTCCTTAAAATTG
1 CATTTTGACCCCTAAACCTTTCTCAAAATCA
40029684 CATTTTGACCC
1 CATTTTGACCC
40029695 TCAAATTCTT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
29 4 0.07
30 49 0.84
31 5 0.09
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (31 bp):
CATTTTGACCCCTAAACCTTTCTCAAAATCA
Found at i:40029711 original size:30 final size:29
Alignment explanation
Indices: 40029587--40029712 Score: 78
Period size: 30 Copynumber: 4.2 Consensus size: 29
40029577 ATTTTTTTCT
* *
40029587 AAAATTGCATTTTAACCCCCAAA-CTTTCTC
1 AAAATTGCATTTTGACCCTCAAATC-TTC-C
*** *
40029617 AAAATCATATTTTGACCC-CTAAACCTTTCC
1 AAAATTGCATTTTGACCCTC-AAATC-TTCC
** * *
40029647 AAAATCACATTTTGATCCTTAAA-CTTCC
1 AAAATTGCATTTTGACCCTCAAATCTTCC
40029675 TTAAAATTGCATTTTGACCCTCAAATTCTTCC
1 --AAAATTGCATTTTGACCCTCAAA-TCTTCC
40029707 AAAATT
1 AAAATT
40029713 AGATTTTAAC
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
28 4 0.05
29 2 0.03
30 62 0.79
31 5 0.06
32 5 0.06
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
AAAATTGCATTTTGACCCTCAAATCTTCC
Found at i:40029719 original size:30 final size:30
Alignment explanation
Indices: 40029643--40029732 Score: 71
Period size: 30 Copynumber: 3.0 Consensus size: 30
40029633 CCCTAAACCT
* * * *
40029643 TTCCAAAATCACATTTTGATCCTTAAA--C
1 TTCCAAAATTAGATTTTGAACCTCAAATTC
*
40029671 TTCCTTAAAATT-GCATTTTGACCCTCAAATTC
1 TTCC--AAAATTAG-ATTTTGAACCTCAAATTC
*
40029703 TTCCAAAATTAGATTTT-AACTTCAAATTC
1 TTCCAAAATTAGATTTTGAACCTCAAATTC
40029732 T
1 T
40029733 CCGAAACTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
28 4 0.08
29 11 0.22
30 29 0.58
31 1 0.02
32 5 0.10
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (30 bp):
TTCCAAAATTAGATTTTGAACCTCAAATTC
Found at i:40032955 original size:23 final size:26
Alignment explanation
Indices: 40032925--40032971 Score: 73
Period size: 23 Copynumber: 1.9 Consensus size: 26
40032915 TAAAAAATAT
40032925 ATATTAC-AAA-TTTT-GTATAAAAA
1 ATATTACAAAATTTTTAGTATAAAAA
40032948 ATATTACAAAATTTTTAGTATAAA
1 ATATTACAAAATTTTTAGTATAAA
40032972 TTAAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 3 0.14
25 4 0.19
26 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
ATATTACAAAATTTTTAGTATAAAAA
Found at i:40042293 original size:18 final size:18
Alignment explanation
Indices: 40042262--40042311 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
40042252 TTTTATTCGT
40042262 TAATTTTTAGATTTTTTAA
1 TAATTTTTA-ATTTTTTAA
40042281 TAATTTTTAATTTTTTAA
1 TAATTTTTAATTTTTTAA
40042299 -ATATTTTT-ATTTT
1 TA-ATTTTTAATTTT
40042312 GATATTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.20
18 15 0.50
19 9 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TAATTTTTAATTTTTTAA
Found at i:40044883 original size:31 final size:29
Alignment explanation
Indices: 40044834--40044896 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
40044824 AACAGTGTCA
*
40044834 TAATTTGAATAAATTTTTAATATGTAAAGAT
1 TAATTTGAACAAATTTTTAATA-G-AAAGAT
*
40044865 TAATTTGAAGCAAA-TTTTAGTAGAAAGAT
1 TAATTTGAA-CAAATTTTTAATAGAAAGAT
40044894 TAA
1 TAA
40044897 AATGAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.31
30 1 0.03
31 16 0.55
32 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.40
Consensus pattern (29 bp):
TAATTTGAACAAATTTTTAATAGAAAGAT
Found at i:40047962 original size:42 final size:42
Alignment explanation
Indices: 40047916--40048006 Score: 155
Period size: 42 Copynumber: 2.1 Consensus size: 42
40047906 GCTTCTGTCG
* *
40047916 GTTTTCTTTTAACTCAGCTTCGCCTTTCTCCACCTTCAGTTT
1 GTTTTCTTTTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTT
40047958 GTTTTCTTTTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTT
1 GTTTTCTTTTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTT
40048000 GTGTTTC
1 GT-TTTC
40048007 GTAATATTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.12, C:0.30, G:0.11, T:0.47
Consensus pattern (42 bp):
GTTTTCTTTTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTT
Found at i:40048028 original size:42 final size:41
Alignment explanation
Indices: 40047929--40048019 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
40047919 TTCTTTTAAC
* *
40047929 TCAGCTTCGCCTTTCTCCACCTTCAGTTTGTTTTCTTTTAAA
1 TCAGCTTCGCCCTTCTCCACCTTCAGTTTGTTTTC-TGTAAA
40047971 TCAGCTTCGCCCTTCTCCACCTTCAGTTTGTGTTTC-GTAATA
1 TCAGCTTCGCCCTTCTCCACCTTCAGTTTGT-TTTCTGTAA-A
*
40048013 TTAGCTT
1 TCAGCTT
40048020 TGTTCTTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 37 0.84
43 4 0.09
ACGTcount: A:0.14, C:0.29, G:0.12, T:0.45
Consensus pattern (41 bp):
TCAGCTTCGCCCTTCTCCACCTTCAGTTTGTTTTCTGTAAA
Found at i:40051920 original size:4 final size:4
Alignment explanation
Indices: 40051911--40051959 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
40051901 AAATAAACGG
*
40051911 GAAA GAAA GAAA GAAAA GAAA GAAA GGAAA -AAA G-AA GAAT GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA
40051959 G
1 G
40051960 GTAATGTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 6 0.15
4 25 0.64
5 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:40056761 original size:20 final size:21
Alignment explanation
Indices: 40056736--40056778 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
40056726 TACTTACTAC
40056736 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
40056756 TACTAACTAATAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
40056777 TA
1 TA
40056779 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:40056948 original size:12 final size:12
Alignment explanation
Indices: 40056931--40056956 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40056921 AAATTACAAT
40056931 ATTTTAAAATTA
1 ATTTTAAAATTA
40056943 ATTTTAAAATTA
1 ATTTTAAAATTA
40056955 AT
1 AT
40056957 CAAACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:40057155 original size:4 final size:4
Alignment explanation
Indices: 40057148--40057195 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
40057138 TTCTTCCTTC
* * *
40057148 TTCT TTCT TTCT TTTT TTCT TTCT CTTTT TTCT TTCT TT-T TTCC TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT
40057196 ATTTTCGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 3 0.08
4 30 0.83
5 3 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:40057168 original size:12 final size:12
Alignment explanation
Indices: 40057151--40057189 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
40057141 TTCCTTCTTC
40057151 TTTCTTTCTTTT
1 TTTCTTTCTTTT
40057163 TTTCTTTCTCTTT
1 TTTCTTTCT-TTT
40057176 TTTCTTTCTTTT
1 TTTCTTTCTTTT
40057188 TT
1 TT
40057190 CCTTCTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTTCTTTT
Found at i:40057172 original size:36 final size:36
Alignment explanation
Indices: 40057123--40057200 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
40057113 ACACATTACT
*
40057123 TTTTTTTCCTTCTCCTTCTTCCTTCTTCTTTCTTTC
1 TTTTTTTCCTTCTCCTTCTTCCTTCTTCTTTCCTTC
* * * * *
40057159 TTTTTTTCTTTCTCTTTTTTCTTTCTTTTTTCCTTC
1 TTTTTTTCCTTCTCCTTCTTCCTTCTTCTTTCCTTC
*
40057195 TATTTT
1 TTTTTT
40057201 CGTTGGTCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (36 bp):
TTTTTTTCCTTCTCCTTCTTCCTTCTTCTTTCCTTC
Found at i:40057176 original size:11 final size:11
Alignment explanation
Indices: 40057145--40057201 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
40057135 TCCTTCTTCC
*
40057145 TTCTTCTTTCT
1 TTCTTTTTTCT
40057156 TTCTTTTTTTCTT
1 TTC-TTTTTTC-T
40057169 TCTCTTTTTTCT
1 T-TCTTTTTTCT
*
40057181 TTCTTTTTTCC
1 TTCTTTTTTCT
*
40057192 TTCTATTTTC
1 TTCTTTTTTC
40057202 GTTGGTCCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 21 0.52
12 8 0.20
13 9 0.22
14 2 0.05
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:40057200 original size:13 final size:13
Alignment explanation
Indices: 40057124--40057200 Score: 65
Period size: 12 Copynumber: 6.3 Consensus size: 13
40057114 CACATTACTT
40057124 TTTTTTCCTTCTC
1 TTTTTTCCTTCTC
* *
40057137 CTTCTTCC-T-TC
1 TTTTTTCCTTCTC
* *
40057148 TTCTTTCTTTCT-
1 TTTTTTCCTTCTC
*
40057160 TTTTTTCTTTCTC
1 TTTTTTCCTTCTC
40057173 TTTTTT-CTT-TC
1 TTTTTTCCTTCTC
*
40057184 TTTTTTCCTTCTA
1 TTTTTTCCTTCTC
40057197 TTTT
1 TTTT
40057201 CGTTGGTCCC
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
11 14 0.28
12 18 0.36
13 18 0.36
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTCCTTCTC
Found at i:40057990 original size:35 final size:35
Alignment explanation
Indices: 40057944--40058013 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
40057934 ACAACCTCTC
* *
40057944 TAATTCGTTTCGATGACAAATAAATTTCTGTCGTT
1 TAATTCGTTTCGACGACAAATAAATTTCCGTCGTT
40057979 TAATTCGTTTCGACGACAAATAAATTTCCGTCGTT
1 TAATTCGTTTCGACGACAAATAAATTTCCGTCGTT
40058014 CAAGTAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (35 bp):
TAATTCGTTTCGACGACAAATAAATTTCCGTCGTT
Found at i:40058109 original size:37 final size:37
Alignment explanation
Indices: 40058065--40058141 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
40058055 TTCAATTAAG
*
40058065 TTAATTTTTTAAATATTTTCAAATAATTTTTTTGTCA
1 TTAATTTTTTAAATATTTTAAAATAATTTTTTTGTCA
*
40058102 TTAATTTTTTTAATATTTTAAAATAATTTTTTTGTCA
1 TTAATTTTTTAAATATTTTAAAATAATTTTTTTGTCA
40058139 TTA
1 TTA
40058142 TAAATAAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (37 bp):
TTAATTTTTTAAATATTTTAAAATAATTTTTTTGTCA
Found at i:40058428 original size:17 final size:16
Alignment explanation
Indices: 40058406--40058447 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
40058396 AACTTGTTTA
40058406 ATTTAATTTAATTTATT
1 ATTTAATTTAATTT-TT
*
40058423 ATTTAATTTCATTTTT
1 ATTTAATTTAATTTTT
*
40058439 ATTTCATTT
1 ATTTAATTT
40058448 GATGCTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTAATTTAATTTTT
Found at i:40058857 original size:25 final size:25
Alignment explanation
Indices: 40058826--40058877 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
40058816 AGTTTGACTC
* *
40058826 AAACAAATAAACAGAGTTTAATTGA
1 AAACAAATAAACAAAGTTTAACTGA
40058851 AAACAAATAAACAAAGTTTAACTGA
1 AAACAAATAAACAAAGTTTAACTGA
40058876 AA
1 AA
40058878 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (25 bp):
AAACAAATAAACAAAGTTTAACTGA
Found at i:40061365 original size:38 final size:39
Alignment explanation
Indices: 40061312--40061388 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
40061302 AAGATACACC
* *
40061312 CTGAATTATAAGTAACAGGTGAATATTTCCT-AAATATT
1 CTGAATTATAAGTAACAGGTAAATATCTCCTAAAATATT
*
40061350 CTGAATTATATGTAACAGGTAAATATCTCCTAAAATATT
1 CTGAATTATAAGTAACAGGTAAATATCTCCTAAAATATT
40061389 TGAGTAGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 28 0.80
39 7 0.20
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (39 bp):
CTGAATTATAAGTAACAGGTAAATATCTCCTAAAATATT
Found at i:40063280 original size:18 final size:18
Alignment explanation
Indices: 40063246--40063287 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
40063236 AAAAAAAAAC
*
40063246 TAATTAACAAAATAGATT
1 TAATTAACAAAAAAGATT
40063264 TAATTAA-AAACAAAGATT
1 TAATTAACAAA-AAAGATT
*
40063282 AAATTA
1 TAATTA
40063288 CCAACAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (18 bp):
TAATTAACAAAAAAGATT
Found at i:40064481 original size:76 final size:76
Alignment explanation
Indices: 40064216--40064720 Score: 684
Period size: 76 Copynumber: 6.7 Consensus size: 76
40064206 TGAAAATAAC
* * *
40064216 CACAAAACACATGCTATCTGTATCTTCAGTTCATAAACATCCCAAT-AACCATAGAGATTCAAAC
1 CACAAAA-ACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAAC
40064280 ACAAAACCA-CA
65 ACAAAACCATCA
*** * * *
40064291 CACAACAGGTATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAGACCATTGAGATGCCAAC
1 CACAA-AAACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAAC
40064356 AC-AAA-CATCA
65 ACAAAACCATCA
* * * *
40064366 TACGAACACATAC--TCTGTATCTTCGGTTCATAAACATCCCAATAAACCATTGAGATTCAAACA
1 CACAAAAACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACA
40064429 CAAAACCATCA
66 CAAAACCATCA
*
40064440 CACAAAAACATACTGTCTGTACCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACA
1 CACAAAAACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACA
*
40064505 TAAAACCATCA
66 CAAAACCATCA
* * *
40064516 CACAAAAACATACTGTCTGTACCTTCAGTTCATAAACATCCCCATAAACCATTGAGATTTAAACA
1 CACAAAAACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACA
*
40064581 CAAAAACATCA
66 CAAAACCATCA
* *
40064592 CACAAAAGCATACCTGTCTGTATCTTTAGTTCATAAACATCCCAATAAACCATTGAGATTCAAAC
1 CACAAAAACATA-CTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAAC
40064657 ACAAAACCAT--
65 ACAAAACCATCA
* * * *
40064667 CACATAGACAGTACTGTTTGTATCTTCAGTTCATCAACATCCTCAATAAACCAT
1 CACAAAAACA-TACTGTCTGTATCTTCAGTTCATAAACATCC-CAATAAACCAT
40064721 GTACAATGTA
Statistics
Matches: 380, Mismatches: 40, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
72 47 0.12
73 3 0.01
74 22 0.06
75 80 0.21
76 171 0.45
77 57 0.15
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (76 bp):
CACAAAAACATACTGTCTGTATCTTCAGTTCATAAACATCCCAATAAACCATTGAGATTCAAACA
CAAAACCATCA
Found at i:40064839 original size:42 final size:42
Alignment explanation
Indices: 40064782--40064915 Score: 164
Period size: 42 Copynumber: 3.2 Consensus size: 42
40064772 ACCTGGCTAG
* * * *
40064782 CTTCAGTAGGTTTTCTTCTAACTGAGCTTTGTCCTTCTCCAG
1 CTTCAGTTGGTTTTCTTTTAACTGAGCTTTGCCCTTCTCCAC
*
40064824 CTTCAGTTGGTTTTCTTTTAACTCG-GCTTCGCCCTTCTCCAC
1 CTTCAGTTGGTTTTCTTTTAACT-GAGCTTTGCCCTTCTCCAC
* * *
40064866 CTTCAGTTTGTTTTCTTTTAAATCAGCTTCT-CCCTTCTCCAC
1 CTTCAGTTGGTTTTCTTTTAACTGAGCTT-TGCCCTTCTCCAC
40064908 CTTCAGTT
1 CTTCAGTT
40064916 CGCCTTCTCT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
42 79 0.99
43 1 0.01
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.45
Consensus pattern (42 bp):
CTTCAGTTGGTTTTCTTTTAACTGAGCTTTGCCCTTCTCCAC
Found at i:40064936 original size:42 final size:42
Alignment explanation
Indices: 40064794--40064936 Score: 117
Period size: 42 Copynumber: 3.4 Consensus size: 42
40064784 TCAGTAGGTT
* * * * * * **
40064794 TTCTTCTAACTGAGCTTTGTCCTTCTCCAGCTTCAGTTGGTT
1 TTCTTCTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTCGCC
* * * * **
40064836 TTCTTTTAACTCGGCTTCGCCCTTCTCCACCTTCAGTTTGTT
1 TTCTTCTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTCGCC
* *
40064878 TTCTTTTAAATCAGCTTCTCCCTTCTCCACCTTCAGTTCGCC
1 TTCTTCTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTCGCC
*
40064920 TTC-TCTAATATTAGCTT
1 TTCTTCTAA-ATCAGCTT
40064937 TGTTCTTCTT
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 4 0.05
42 81 0.95
ACGTcount: A:0.13, C:0.31, G:0.11, T:0.45
Consensus pattern (42 bp):
TTCTTCTAAATCAGCTTCGCCCTTCTCCACCTTCAGTTCGCC
Found at i:40065425 original size:17 final size:17
Alignment explanation
Indices: 40065403--40065436 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40065393 ATTAAATAAT
40065403 TTTTTTATAA-ATGTTTA
1 TTTTTTA-AATATGTTTA
40065420 TTTTTTAAATATGTTTA
1 TTTTTTAAATATGTTTA
40065437 GGGTTTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTTAAATATGTTTA
Found at i:40070499 original size:11 final size:11
Alignment explanation
Indices: 40070483--40070514 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
40070473 ACAATCATAC
40070483 ATTTACAATTT
1 ATTTACAATTT
40070494 ATTTACAATTT
1 ATTTACAATTT
40070505 ATTTACAATT
1 ATTTACAATT
40070515 AAATTGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTACAATTT
Found at i:40072274 original size:4 final size:4
Alignment explanation
Indices: 40072267--40072335 Score: 92
Period size: 4 Copynumber: 18.2 Consensus size: 4
40072257 TGCAATATAT
*
40072267 ATAG ATAG ATAG ATAG ATAG ATAG AT-- ATAG ATAG ATGG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
*
40072313 ATAG AT-- ATAG ATAG ATGG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG A
40072336 AACAAATTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
4 53 0.93
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:40072299 original size:22 final size:22
Alignment explanation
Indices: 40072271--40072335 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
40072261 ATATATATAG
40072271 ATAGATAGATAGATAGATAGAT
1 ATAGATAGATAGATAGATAGAT
*
40072293 ATAGATAGATGGATAGATAGAT
1 ATAGATAGATAGATAGATAGAT
* * *
40072315 AGATATAGATAGATGGATAGA
1 ATAGATAGATAGATAGATAGA
40072336 AACAAATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (22 bp):
ATAGATAGATAGATAGATAGAT
Found at i:40072301 original size:26 final size:26
Alignment explanation
Indices: 40072265--40072335 Score: 133
Period size: 26 Copynumber: 2.7 Consensus size: 26
40072255 ACTGCAATAT
*
40072265 ATATAGATAGATAGATAGATAGATAG
1 ATATAGATAGATGGATAGATAGATAG
40072291 ATATAGATAGATGGATAGATAGATAG
1 ATATAGATAGATGGATAGATAGATAG
40072317 ATATAGATAGATGGATAGA
1 ATATAGATAGATGGATAGA
40072336 AACAAATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (26 bp):
ATATAGATAGATGGATAGATAGATAG
Found at i:40072334 original size:34 final size:33
Alignment explanation
Indices: 40072267--40072369 Score: 90
Period size: 34 Copynumber: 3.2 Consensus size: 33
40072257 TGCAATATAT
*
40072267 ATAGATAGATAGATAGATAG--ATAGAT--ATAG
1 ATAGAT-GATAGATAGATAGATATAGATAGATGG
40072297 ATAGATGGATAGATAGATAGATATAGATAGATGG
1 ATAGAT-GATAGATAGATAGATATAGATAGATGG
* * * *
40072331 ATAGA-AACAAATTAATATAGATATAGATAGATGG
1 ATAGATGATAGA-T-AGATAGATATAGATAGATGG
40072365 ATAGA
1 ATAGA
40072370 AACAAATTAG
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
30 19 0.31
32 9 0.15
33 1 0.02
34 32 0.52
ACGTcount: A:0.50, C:0.01, G:0.23, T:0.26
Consensus pattern (33 bp):
ATAGATGATAGATAGATAGATATAGATAGATGG
Found at i:40072370 original size:34 final size:34
Alignment explanation
Indices: 40072313--40072378 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
40072303 GGATAGATAG
40072313 ATAGATATAGATAGATGGATAGAAACAAATTAAT
1 ATAGATATAGATAGATGGATAGAAACAAATTAAT
40072347 ATAGATATAGATAGATGGATAGAAACAAATTA
1 ATAGATATAGATAGATGGATAGAAACAAATTA
40072379 GAACAGATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (34 bp):
ATAGATATAGATAGATGGATAGAAACAAATTAAT
Found at i:40074386 original size:23 final size:24
Alignment explanation
Indices: 40074324--40074405 Score: 89
Period size: 23 Copynumber: 3.5 Consensus size: 24
40074314 TTAATGTTCA
* *
40074324 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCAATGAACATTAAT
*
40074347 CGAACATGTTC-ACGAACATTAAT
1 CGAACATGTTCAATGAACATTAAT
40074370 CGAACATG-TCAATGAACATATAAT
1 CGAACATGTTCAATGAACAT-TAAT
* *
40074394 TGAACACGTTCA
1 CGAACATGTTCA
40074406 CGAACAATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.10
23 31 0.63
24 10 0.20
25 3 0.06
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (24 bp):
CGAACATGTTCAATGAACATTAAT
Found at i:40075215 original size:13 final size:14
Alignment explanation
Indices: 40075186--40075218 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40075176 TAAATCATCT
40075186 TCTTCTTTCTTGATC
1 TCTTCTTTC-TGATC
40075201 TCTTCTTTC-GATC
1 TCTTCTTTCTGATC
40075214 TCTTC
1 TCTTC
40075219 ATCTCTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
15 9 0.50
ACGTcount: A:0.06, C:0.30, G:0.06, T:0.58
Consensus pattern (14 bp):
TCTTCTTTCTGATC
Found at i:40083729 original size:35 final size:34
Alignment explanation
Indices: 40083641--40083716 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
40083631 TAAACTAAAA
* *
40083641 CCAAATATTTTTAATTTTTTACCTTTTACTTGAC
1 CCAAATATTTTTAATTTTTTACCTTTTACCTAAC
* *
40083675 CAAAATATTTTTAATTTTTTACTTTTTACCTAAC
1 CCAAATATTTTTAATTTTTTACCTTTTACCTAAC
40083709 CCAAATAT
1 CCAAATAT
40083717 AATTTCATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.01, T:0.50
Consensus pattern (34 bp):
CCAAATATTTTTAATTTTTTACCTTTTACCTAAC
Found at i:40088347 original size:78 final size:77
Alignment explanation
Indices: 40088203--40088366 Score: 294
Period size: 76 Copynumber: 2.1 Consensus size: 77
40088193 ATGCTTGTTA
40088203 CACACAAAACAACTTCTAAATACCAAAAGTATAAAGCACATGAGTCTTAACACTCTCCTTATTCA
1 CACACAAAACAACTTCTAAATACCAAAAGTATAAAGCACATGAGTCTTAACACTCTCCTTATTCA
40088268 AACACAAA-CCT
66 AACACAAACCCT
*
40088279 CACACAAAACAACTTTTAAATACCAAAAGTATCAAAGCACATGAGTTCTTAACACTCTCCTTATT
1 CACACAAAACAACTTCTAAATACCAAAAGTAT-AAAGCACATGAG-TCTTAACACTCTCCTTATT
40088344 CAAACACAAACCCT
64 CAAACACAAACCCT
40088358 CACACAAAA
1 CACACAAAA
40088367 GCATACATTA
Statistics
Matches: 84, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
76 31 0.37
77 12 0.14
78 29 0.35
79 12 0.14
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.22
Consensus pattern (77 bp):
CACACAAAACAACTTCTAAATACCAAAAGTATAAAGCACATGAGTCTTAACACTCTCCTTATTCA
AACACAAACCCT
Found at i:40091402 original size:16 final size:17
Alignment explanation
Indices: 40091372--40091408 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
40091362 TTTTAAAATT
40091372 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATTTA
40091390 TTTAATTAA-AAATTTA
1 TTTAATTAATAAATTTA
40091406 TTT
1 TTT
40091409 TCATTCTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAATTAATAAATTTA
Found at i:40092301 original size:15 final size:14
Alignment explanation
Indices: 40092262--40092302 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40092252 ATGTTAATTT
*
40092262 TTTTTGTATTGTAA
1 TTTTTGTATTATAA
*
40092276 TTTTTTTATTATAA
1 TTTTTGTATTATAA
40092290 TTTTTGTCATTAT
1 TTTTTGT-ATTAT
40092303 GATTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.68
Consensus pattern (14 bp):
TTTTTGTATTATAA
Found at i:40092793 original size:22 final size:22
Alignment explanation
Indices: 40092767--40092825 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
40092757 AAAAATAATT
* * *
40092767 AAATTTTAATTTAATTTTTTAA
1 AAATTATAATTTAATATTATAA
* *
40092789 AAATTATATTTTTACTATTATAA
1 AAATTATA-ATTTAATATTATAA
40092812 AAATTATAATTTAA
1 AAATTATAATTTAA
40092826 CTTCAATCTC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATTATAATTTAATATTATAA
Found at i:40097734 original size:2 final size:2
Alignment explanation
Indices: 40097727--40097752 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40097717 TAAAATTAAA
40097727 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
40097753 TATTTTAATT
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:40103328 original size:18 final size:19
Alignment explanation
Indices: 40103296--40103333 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
40103286 TCTAACATAT
* *
40103296 TATATTATGTTATTT-TTA
1 TATATTATATAATTTATTA
40103314 TATATTATATAATTTATTA
1 TATATTATATAATTTATTA
40103333 T
1 T
40103334 GAAAATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TATATTATATAATTTATTA
Found at i:40111802 original size:31 final size:31
Alignment explanation
Indices: 40111761--40111820 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
40111751 AATGTAAATA
*
40111761 TTTATCAAAATAATATAGTTTTATTTTTTAG
1 TTTATCAAAATAATATAATTTTATTTTTTAG
* * *
40111792 TTTATTAAAATGATATAATTTTGTTTTTT
1 TTTATCAAAATAATATAATTTTATTTTTT
40111821 TTATTCGGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (31 bp):
TTTATCAAAATAATATAATTTTATTTTTTAG
Found at i:40112583 original size:18 final size:19
Alignment explanation
Indices: 40112560--40112597 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
40112550 TTTAACATAT
*
40112560 TATATTATGTTATTT-TTA
1 TATATTATGTGATTTATTA
40112578 TATATTATGTGATTTATTA
1 TATATTATGTGATTTATTA
40112597 T
1 T
40112598 GAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TATATTATGTGATTTATTA
Found at i:40113124 original size:25 final size:27
Alignment explanation
Indices: 40113091--40113146 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
40113081 TTTACATTTA
40113091 TAAACATAATAGC-TATATTTATTTTT
1 TAAACATAATAGCATATATTTATTTTT
* * *
40113117 TAAA-ATAATTGCATTTATTTGTTTTT
1 TAAACATAATAGCATATATTTATTTTT
40113143 TAAA
1 TAAA
40113147 TACTACAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (27 bp):
TAAACATAATAGCATATATTTATTTTT
Found at i:40114351 original size:16 final size:16
Alignment explanation
Indices: 40114320--40114353 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40114310 CTTTTTTAAA
* *
40114320 ATGATTTTTTTTATTT
1 ATGATTTTTATAATTT
40114336 ATGATTTTTATAATTT
1 ATGATTTTTATAATTT
40114352 AT
1 AT
40114354 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
ATGATTTTTATAATTT
Found at i:40115064 original size:32 final size:32
Alignment explanation
Indices: 40115019--40115083 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
40115009 TAACCCTCCG
* * *
40115019 TTGGAATGGCTTTTTTACTTTCGTATTCTCAC
1 TTGGAATGCCTTTTTGACTTCCGTATTCTCAC
*
40115051 TTGGAATGCCTTTTTGACTTCCGTATTTTCAC
1 TTGGAATGCCTTTTTGACTTCCGTATTCTCAC
40115083 T
1 T
40115084 AACATTCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.49
Consensus pattern (32 bp):
TTGGAATGCCTTTTTGACTTCCGTATTCTCAC
Found at i:40121439 original size:22 final size:22
Alignment explanation
Indices: 40121408--40121456 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
40121398 CTAAATCTTC
*
40121408 AAAAATAAAG-GAAAAGAAAAAG
1 AAAAAAAAAGTGAAAA-AAAAAG
*
40121430 AAAAAAAAAGTGAAAAAAAATG
1 AAAAAAAAAGTGAAAAAAAAAG
40121452 AAAAA
1 AAAAA
40121457 GATGACATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (22 bp):
AAAAAAAAAGTGAAAAAAAAAG
Found at i:40121444 original size:12 final size:11
Alignment explanation
Indices: 40121408--40121449 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
40121398 CTAAATCTTC
*
40121408 AAAAATAAAGG
1 AAAAAAAAAGG
40121419 AAAAGAAAAA-G
1 AAAA-AAAAAGG
40121430 AAAAAAAAAGTG
1 AAAAAAAAAG-G
40121442 AAAAAAAA
1 AAAAAAAA
40121450 TGAAAAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 5 0.19
11 9 0.33
12 13 0.48
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:40130441 original size:24 final size:23
Alignment explanation
Indices: 40130406--40130473 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
40130396 AATCAATTAT
*
40130406 ATTCAACT-AATACTAAATTTAC
1 ATTCAATTAAATACTAAATTTAC
* **
40130428 ATTGCAATTAAATACTTAAAATTGT
1 ATT-CAATTAAATAC-TAAATTTAC
40130453 ATTCAATTAAATACTAAATTT
1 ATTCAATTAAATACTAAATTT
40130474 GGAGTTACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 3 0.08
23 10 0.26
24 16 0.42
25 9 0.24
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
ATTCAATTAAATACTAAATTTAC
Found at i:40131087 original size:27 final size:25
Alignment explanation
Indices: 40131056--40131105 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
40131046 TATTTATCTA
40131056 TTATAAAATATAAAATATAAATATATT
1 TTATAAAATATAAAAT-T-AATATATT
* *
40131083 TTATATAATTTAAAATTAATATA
1 TTATAAAATATAAAATTAATATA
40131106 AAAAAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 1 0.05
27 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATAAAATATAAAATTAATATATT
Found at i:40134151 original size:29 final size:28
Alignment explanation
Indices: 40134119--40134180 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
40134109 TTATGTGCAT
*
40134119 AATTG-CATCAAATTAAAGTTCATGTATAC
1 AATTGACATCAAATCAAAGTTCA--TATAC
*
40134148 AATTGCACATTAAATCAAAGTTCATATAC
1 AATTG-ACATCAAATCAAAGTTCATATAC
40134177 AATT
1 AATT
40134181 TTGAGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 14 0.48
31 15 0.52
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (28 bp):
AATTGACATCAAATCAAAGTTCATATAC
Found at i:40163042 original size:364 final size:363
Alignment explanation
Indices: 40162374--40163090 Score: 1204
Period size: 364 Copynumber: 2.0 Consensus size: 363
40162364 AGGGGCTTAA
40162374 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
1 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
* *
40162439 ATCTGATTCTCTTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATGTGGGAAACTTTG
66 ATCTGATTCTCTTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATATGGAAAACTTTG
* **
40162504 GTGATTTTGGACTCTGTGGTCTGTCAGGTAATGGCTGCAAGTTGATAGTCTATTATGTTATTCTA
131 GTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATAGTCTACCATGTTATTCTA
* * * * *
40162569 CGGTTATAATTTGGTCTCTACGTTCTTAAATCGTCAGTATAACAATCTCACTTGTAAATGTTAAT
196 CAGTTATAATTTGGTCTCTACATTCTTAAATCGTCAGTATAACAATCTCACTCGTAAATATCAAT
* *
40162634 TATGTTTTCTAGACAACAAGATACCCGATGATTTGGGTGAAGGCACCAGTGATGCTAGAGCAAAT
261 TATGTTTTCTAGACAACAAGATACCCGACGATTTGGGTGAAGGCACCAGCGATGCTAGAGCAAAT
40162699 CAACACAACATGAAACTGTCACAAGAGAACACTTTTGC
326 CAACACAACATGAAACTGTCACAAGAGAACACTTTTGC
*
40162737 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGATCAG
1 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
*
40162802 ATCTGATTCTCTTTTGCATATAGGTTCTTCTGTCACCGCTGTGGTTTTCTGATATGGAAAACTTT
66 ATCTGATTCTC-TTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATATGGAAAACTTT
*
40162867 GGTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATATTCTACCATGTTAATT-
130 GGTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATAGTCTACCATGTT-ATTC
*
40162931 TACAGTTATAATTTGGTCTCTACATTCTTAAA-CTGTCAGTATAACAATCTTACTCGTAAATATC
194 TACAGTTATAATTTGGTCTCTACATTCTTAAATC-GTCAGTATAACAATCTCACTCGTAAATATC
* * *
40162995 AATTATGTTTTCTAGACAACAAGATACCCGGCGGTTTGGGTGAAGGCACCGGCGATGCTAGAGCA
258 AATTATGTTTTCTAGACAACAAGATACCCGACGATTTGGGTGAAGGCACCAGCGATGCTAGAGCA
* *
40163060 AATCAACACAATATGGAACTGTCACAAGAGA
323 AATCAACACAACATGAAACTGTCACAAGAGA
40163091 GCGCCTTTAC
Statistics
Matches: 330, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
363 76 0.23
364 251 0.76
365 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (363 bp):
TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
ATCTGATTCTCTTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATATGGAAAACTTTG
GTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATAGTCTACCATGTTATTCTA
CAGTTATAATTTGGTCTCTACATTCTTAAATCGTCAGTATAACAATCTCACTCGTAAATATCAAT
TATGTTTTCTAGACAACAAGATACCCGACGATTTGGGTGAAGGCACCAGCGATGCTAGAGCAAAT
CAACACAACATGAAACTGTCACAAGAGAACACTTTTGC
Found at i:40168243 original size:364 final size:363
Alignment explanation
Indices: 40167575--40168291 Score: 1204
Period size: 364 Copynumber: 2.0 Consensus size: 363
40167565 AGGGGCTTAA
40167575 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
1 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
* *
40167640 ATCTGATTCTCTTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATGTGGGAAACTTTG
66 ATCTGATTCTCTTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATATGGAAAACTTTG
* **
40167705 GTGATTTTGGACTCTGTGGTCTGTCAGGTAATGGCTGCAAGTTGATAGTCTATTATGTTATTCTA
131 GTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATAGTCTACCATGTTATTCTA
* * * * *
40167770 CGGTTATAATTTGGTCTCTACGTTCTTAAATCGTCAGTATAACAATCTCACTTGTAAATGTTAAT
196 CAGTTATAATTTGGTCTCTACATTCTTAAATCGTCAGTATAACAATCTCACTCGTAAATATCAAT
* *
40167835 TATGTTTTCTAGACAACAAGATACCCGATGATTTGGGTGAAGGCACCAGTGATGCTAGAGCAAAT
261 TATGTTTTCTAGACAACAAGATACCCGACGATTTGGGTGAAGGCACCAGCGATGCTAGAGCAAAT
40167900 CAACACAACATGAAACTGTCACAAGAGAACACTTTTGC
326 CAACACAACATGAAACTGTCACAAGAGAACACTTTTGC
*
40167938 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGATCAG
1 TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
*
40168003 ATCTGATTCTCTTTTGCATATAGGTTCTTCTGTCACCGCTGTGGTTTTCTGATATGGAAAACTTT
66 ATCTGATTCTC-TTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATATGGAAAACTTT
*
40168068 GGTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATATTCTACCATGTTAATT-
130 GGTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATAGTCTACCATGTT-ATTC
*
40168132 TACAGTTATAATTTGGTCTCTACATTCTTAAA-CTGTCAGTATAACAATCTTACTCGTAAATATC
194 TACAGTTATAATTTGGTCTCTACATTCTTAAATC-GTCAGTATAACAATCTCACTCGTAAATATC
* * *
40168196 AATTATGTTTTCTAGACAACAAGATACCCGGCGGTTTGGGTGAAGGCACCGGCGATGCTAGAGCA
258 AATTATGTTTTCTAGACAACAAGATACCCGACGATTTGGGTGAAGGCACCAGCGATGCTAGAGCA
* *
40168261 AATCAACACAATATGGAACTGTCACAAGAGA
323 AATCAACACAACATGAAACTGTCACAAGAGA
40168292 GCGCCTTTAC
Statistics
Matches: 330, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
363 76 0.23
364 251 0.76
365 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (363 bp):
TGTTGATCCTGTAAGTTTTGGCGTGTATATATATTTTAAATTCAATTTGCTTAGTTTTGGAACAG
ATCTGATTCTCTTTGCATATAGGTTCTTCCGTCACCGCTGTGGTTTTCTGATATGGAAAACTTTG
GTGATTTTGGACTCTGTGATCTGTCAGGTAATGGCTGCAAGTTGATAGTCTACCATGTTATTCTA
CAGTTATAATTTGGTCTCTACATTCTTAAATCGTCAGTATAACAATCTCACTCGTAAATATCAAT
TATGTTTTCTAGACAACAAGATACCCGACGATTTGGGTGAAGGCACCAGCGATGCTAGAGCAAAT
CAACACAACATGAAACTGTCACAAGAGAACACTTTTGC
Found at i:40169373 original size:23 final size:23
Alignment explanation
Indices: 40169347--40169392 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40169337 TTTATTTAAT
*
40169347 TTAATTGAACAAGTTCATGAACA
1 TTAATCGAACAAGTTCATGAACA
* *
40169370 TTAATCGAATATGTTCATGAACA
1 TTAATCGAACAAGTTCATGAACA
40169393 ATGTTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (23 bp):
TTAATCGAACAAGTTCATGAACA
Found at i:40171616 original size:13 final size:13
Alignment explanation
Indices: 40171600--40171624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40171590 TTATATGTTT
40171600 TTTTATTTTTAAA
1 TTTTATTTTTAAA
40171613 TTTTATTTTTAA
1 TTTTATTTTTAA
40171625 TATAAAGCAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATTTTTAAA
Found at i:40183384 original size:29 final size:29
Alignment explanation
Indices: 40183326--40183380 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40183316 GAACTATTTC
*
40183326 GTCATGATTCAAGATTAAAGATTTGAAGT
1 GTCATGATTCAAGATTAAAAATTTGAAGT
40183355 GTCATGATTC-A-ATTAAACAATTTGAA
1 GTCATGATTCAAGATTAAA-AATTTGAA
40183381 AGTGGTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 8 0.33
29 10 0.42
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (29 bp):
GTCATGATTCAAGATTAAAAATTTGAAGT
Found at i:40184230 original size:2 final size:2
Alignment explanation
Indices: 40184225--40184257 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40184215 TATATATATA
*
40184225 TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
40184258 TCTGTGATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40189007 original size:31 final size:31
Alignment explanation
Indices: 40188964--40189027 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
40188954 CTTAACAACC
* * *
40188964 CATTGACTTAAATAAAAATTTTCGAATAGTT
1 CATTAACTTAAATAAAAATTTCCAAATAGTT
*
40188995 CATTAACTTAAATGAAAATTTCCAAATAGTT
1 CATTAACTTAAATAAAAATTTCCAAATAGTT
40189026 CA
1 CA
40189028 GTGATCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (31 bp):
CATTAACTTAAATAAAAATTTCCAAATAGTT
Found at i:40189604 original size:15 final size:17
Alignment explanation
Indices: 40189574--40189615 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
40189564 GATATCACAA
40189574 ATTGAATTT-AATTAAT
1 ATTGAATTTGAATTAAT
40189590 -TTGAATTTGAA-TAAT
1 ATTGAATTTGAATTAAT
*
40189605 ATTTAATTTGA
1 ATTGAATTTGA
40189616 TTTTATAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (17 bp):
ATTGAATTTGAATTAAT
Found at i:40190037 original size:15 final size:15
Alignment explanation
Indices: 40190019--40190052 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40190009 ACTTTAGTGA
*
40190019 CAAACCTAAATACTT
1 CAAACCTAAATAATT
*
40190034 CAAACCTGAATAATT
1 CAAACCTAAATAATT
40190049 CAAA
1 CAAA
40190053 TTCAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.03, T:0.24
Consensus pattern (15 bp):
CAAACCTAAATAATT
Found at i:40195362 original size:16 final size:16
Alignment explanation
Indices: 40195332--40195381 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
40195322 TAGCAATTAA
*
40195332 TTATTTTTTCGTAAATT
1 TTATTTTTT-TTAAATT
**
40195349 TTATTTTTTTTAAAAA
1 TTATTTTTTTTAAATT
*
40195365 ATATTTTTTTTAAATT
1 TTATTTTTTTTAAATT
40195381 T
1 T
40195382 AAATTTTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATTTTTTTTAAATT
Found at i:40199291 original size:11 final size:11
Alignment explanation
Indices: 40199269--40199326 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
40199259 CACTTTTGTC
40199269 TTCTTCTTTTTT
1 TTCTT-TTTTTT
40199281 TTCTTTTTTTT
1 TTCTTTTTTTT
* **
40199292 CTCAATTTTTT
1 TTCTTTTTTTT
40199303 TTCAATTCTTTTTT
1 TTC--TT-TTTTTT
40199317 TTCTTTTTTT
1 TTCTTTTTTT
40199327 CGACTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
11 21 0.57
12 7 0.19
14 9 0.24
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:40199317 original size:13 final size:11
Alignment explanation
Indices: 40199275--40199316 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
40199265 TGTCTTCTTC
*
40199275 TTTTTTTTC-T
1 TTTTTTTTCAA
40199285 TTTTTTTCTCAA
1 TTTTTTT-TCAA
40199297 TTTTTTTTCAA
1 TTTTTTTTCAA
40199308 TTCTTTTTT
1 TT-TTTTTT
40199317 TTCTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 7 0.25
11 8 0.29
12 13 0.46
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:40204167 original size:21 final size:23
Alignment explanation
Indices: 40204142--40204184 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40204132 TCTTTAATAT
40204142 TCAATTT-ATATTCAAG-TTTTG
1 TCAATTTAATATTCAAGATTTTG
*
40204163 TCAATTTAATATTTAAGATTTT
1 TCAATTTAATATTCAAGATTTT
40204185 TTTTGTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (23 bp):
TCAATTTAATATTCAAGATTTTG
Found at i:40213127 original size:59 final size:60
Alignment explanation
Indices: 40212994--40213128 Score: 141
Period size: 59 Copynumber: 2.2 Consensus size: 60
40212984 AAAATGGGAT
* * *
40212994 CAATTGTCAAATTCAAAGATTAACTTGAACAAAAAAAAAATTTCAAGCCCTAATGTAAAAA
1 CAATTGCCAAGTTC-AAGATTAACTTGAACAAAAAAAAAAGTTCAAGCCCTAATGTAAAAA
* * * *
40213055 CAATTGCTAAGTTCAAGACTTAACTT-AGAC-AAAAAAAAAGTTCAA-CTCTTATGTAGAAA
1 CAATTGCCAAGTTCAAGA-TTAACTTGA-ACAAAAAAAAAAGTTCAAGCCCTAATGTAAAAA
* *
40213114 TAGTTGCCAAGTTCA
1 CAATTGCCAAGTTCA
40213129 CACCCCAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
59 23 0.37
60 19 0.31
61 20 0.32
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (60 bp):
CAATTGCCAAGTTCAAGATTAACTTGAACAAAAAAAAAAGTTCAAGCCCTAATGTAAAAA
Found at i:40219646 original size:20 final size:20
Alignment explanation
Indices: 40219623--40219660 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40219613 AAATATTAAA
40219623 AAAAACATAATAATAAATTT
1 AAAAACATAATAATAAATTT
*
40219643 AAAAATATAATAATAAAT
1 AAAAACATAATAATAAAT
40219661 ATTTATGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAACATAATAATAAATTT
Found at i:40225434 original size:3 final size:3
Alignment explanation
Indices: 40225428--40225452 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40225418 AAACAAATTA
40225428 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
40225453 CTGCTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40246046 original size:69 final size:69
Alignment explanation
Indices: 40245941--40246104 Score: 265
Period size: 69 Copynumber: 2.4 Consensus size: 69
40245931 AGTTGAATAA
* *
40245941 TTTACTAAAGAGAGGACCTTTTCACCCAATTTTTATTAGATGGTTGAGTCATTTGATGACAGAGC
1 TTTACTAAAGAGAGGACC-TTTCACCCAATTGTTATTAGATGGTTGAGTCATTTGATGAAAGAGC
*
40246006 TTGAC
65 TTAAC
*
40246011 TTTATTAAAGAGAGGACCTTTCACCCAATTGTTATTAGATGGTTGAGTCATTTGATGAAAGAGCT
1 TTTACTAAAGAGAGGACCTTTCACCCAATTGTTATTAGATGGTTGAGTCATTTGATGAAAGAGCT
40246076 TAAC
66 TAAC
* *
40246080 TTTACTAAAGATAGGATCTTTCACC
1 TTTACTAAAGAGAGGACCTTTCACC
40246105 TGATGTGCCC
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 70 0.80
70 17 0.20
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (69 bp):
TTTACTAAAGAGAGGACCTTTCACCCAATTGTTATTAGATGGTTGAGTCATTTGATGAAAGAGCT
TAAC
Found at i:40248504 original size:28 final size:28
Alignment explanation
Indices: 40248472--40248529 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
40248462 TAAAAGCTAA
*
40248472 TATTCAATTATTATTGTTATTATTATAT
1 TATTCAAGTATTATTGTTATTATTATAT
40248500 TATTCAAGTATTATTGTTATTATTATAT
1 TATTCAAGTATTATTGTTATTATTATAT
40248528 TA
1 TA
40248530 AAATCCTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (28 bp):
TATTCAAGTATTATTGTTATTATTATAT
Found at i:40256334 original size:16 final size:18
Alignment explanation
Indices: 40256302--40256334 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40256292 ATTCACCCAT
40256302 TAATATAATAAATGACAA
1 TAATATAATAAATGACAA
40256320 TAATA-AATAAA-GACA
1 TAATATAATAAATGACA
40256335 TGGCCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (18 bp):
TAATATAATAAATGACAA
Found at i:40258110 original size:136 final size:136
Alignment explanation
Indices: 40257947--40258218 Score: 508
Period size: 136 Copynumber: 2.0 Consensus size: 136
40257937 AGAGGAAAAA
* *
40257947 CATGATTTTAGTTGTTGTAATAATAATACTAATTAAGGATCCTCTTGAATTGACGTTTATTTTCA
1 CATGATTTTAGTTGTTGTAATAATAATACTAATTAAGGATCCCCTTGAATTGAAGTTTATTTTCA
*
40258012 GTGTGATGCGTTTAGTTTTTTTTTTATTTTATGTTACAGTATTATTACAATATCAAATTTCACTA
66 GTGTGATGCGTTTAGTTTTTATTTTATTTTATGTTACAGTATTATTACAATATCAAATTTCACTA
40258077 TCACTG
131 TCACTG
40258083 CATGATTTTAGTTGTTGTAATAATAATACTAATTAAGGATCCCCTTGAATTGAAGTTTATTTTCA
1 CATGATTTTAGTTGTTGTAATAATAATACTAATTAAGGATCCCCTTGAATTGAAGTTTATTTTCA
*
40258148 GTGTGATGCGTTTAGTTTTTATTTTATTTTATGTTACATTATTATTACAATATCAAATTTCACTA
66 GTGTGATGCGTTTAGTTTTTATTTTATTTTATGTTACAGTATTATTACAATATCAAATTTCACTA
40258213 TCACTG
131 TCACTG
40258219 TTATTTTTAT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 132 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (136 bp):
CATGATTTTAGTTGTTGTAATAATAATACTAATTAAGGATCCCCTTGAATTGAAGTTTATTTTCA
GTGTGATGCGTTTAGTTTTTATTTTATTTTATGTTACAGTATTATTACAATATCAAATTTCACTA
TCACTG
Found at i:40268532 original size:2 final size:2
Alignment explanation
Indices: 40268525--40268574 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
40268515 TTTGATCACC
40268525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40268567 AT AT AT AT
1 AT AT AT AT
40268575 TATTACATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40301378 original size:2 final size:2
Alignment explanation
Indices: 40301371--40301429 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
40301361 ACTAAACTTT
40301371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40301413 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
40301430 GATACATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40306357 original size:98 final size:98
Alignment explanation
Indices: 40306162--40306347 Score: 300
Period size: 98 Copynumber: 1.9 Consensus size: 98
40306152 TTTCACAATA
* * * *
40306162 ACTTTTTTTTTCATCATTTATTAAGGGACCAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGT
1 ACTTTTATTTTCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGC
40306227 CCTTACCTACTCCCTCTAAATTCCCCGTGCGTG
66 CCTTACCTACTCCCTCTAAATTCCCCGTGCGTG
* *
40306260 ACTTTTATTTTCATCATTTATTAAGAGACAAAAATATAAATTTTCATTTGAGAGGGGGCCAAGGC
1 ACTTTTATTTTCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGC
* *
40306325 CCTTACTTACTCCCTTTAAATTC
66 CCTTACCTACTCCCTCTAAATTC
40306348 GTCCTGCGTG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 80 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (98 bp):
ACTTTTATTTTCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGC
CCTTACCTACTCCCTCTAAATTCCCCGTGCGTG
Found at i:40306490 original size:129 final size:129
Alignment explanation
Indices: 40306260--40306495 Score: 316
Period size: 129 Copynumber: 1.8 Consensus size: 129
40306250 CCCGTGCGTG
* * * * * *
40306260 ACTTTTATTTTCATCATTTATTAAGAGACAAAAATATAAATTTTCATTTGAGAGGGGGCCAAGGC
1 ACTTTTATTTCCATCATTTATTAAGAGACAAAAACATAAATTTTCAGTTGAAAGAGGGCCAAGAC
* ** * *
40306325 CCTTACTTACTCCCTTTAAATTCGTCCTGCGTGTGTGAGTGTCAAAATGTAATTTTTCACAATA
66 CCTCACCCACTCCCTCTAAATTCGTCCTACGTGTGTGAGTGTCAAAATGTAATTTTTCACAATA
40306389 ACTTTTATTTCCATCATTTATTAAG-GA-ATCAAAACATAAATTTTCAGTTGAAAGAGGGCCAAG
1 ACTTTTATTTCCATCATTTATTAAGAGACA--AAAACATAAATTTTCAGTTGAAAGAGGGCCAAG
*
40306452 ACCCTCACCCACTCCCTCTAAATTCG-CCTTACGTGTGTGGGTGT
64 ACCCTCACCCACTCCCTCTAAATTCGTCC-TACGTGTGTGAGTGT
40306496 GGATGTGTGA
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
127 1 0.01
128 4 0.04
129 87 0.95
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (129 bp):
ACTTTTATTTCCATCATTTATTAAGAGACAAAAACATAAATTTTCAGTTGAAAGAGGGCCAAGAC
CCTCACCCACTCCCTCTAAATTCGTCCTACGTGTGTGAGTGTCAAAATGTAATTTTTCACAATA
Found at i:40306920 original size:28 final size:30
Alignment explanation
Indices: 40306887--40306949 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
40306877 TTGAGAATCA
* *
40306887 AAATTAACTCAAAA-ATAAA-ATT-AAAGTT
1 AAATTAAC-AAAAATATAAATATTAAAAATT
40306915 AAATTAACAAAAATATAAATATTAAAAATT
1 AAATTAACAAAAATATAAATATTAAAAATT
40306945 AAATT
1 AAATT
40306950 TGATATTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 4 0.13
28 13 0.43
29 3 0.10
30 10 0.33
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATTAACAAAAATATAAATATTAAAAATT
Found at i:40309446 original size:98 final size:98
Alignment explanation
Indices: 40309251--40309436 Score: 300
Period size: 98 Copynumber: 1.9 Consensus size: 98
40309241 TTTCACAATA
* * *
40309251 ACTTTTATTTCCATCATTTATTAAGGGACTAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGT
1 ACTTTTATTTCCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGC
40309316 CCTTACCTACTCCCTCTAAATTCCCCGTGCGTG
66 CCTTACCTACTCCCTCTAAATTCCCCGTGCGTG
* * *
40309349 ACTTTTATTTTCATCATTTATTAAGAGACAAAAATATAAATTTTCATTTGAGAGGGGGCCAAGGC
1 ACTTTTATTTCCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGC
* *
40309414 CCTTACTTACTCCCTTTAAATTC
66 CCTTACCTACTCCCTCTAAATTC
40309437 GTCCTGCGTG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 80 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
ACTTTTATTTCCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAGAGGGGCCCAAGGC
CCTTACCTACTCCCTCTAAATTCCCCGTGCGTG
Found at i:40309579 original size:129 final size:129
Alignment explanation
Indices: 40309349--40309584 Score: 350
Period size: 129 Copynumber: 1.8 Consensus size: 129
40309339 CCCGTGCGTG
* * * * *
40309349 ACTTTTATTTTCATCATTTATTAAGAGACAAAAATATAAATTTTCATTTGAGAGGGGGCCAAGGC
1 ACTTTTATTTCCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAAAGAGGGCCAAGAC
** * *
40309414 CCTTACTTACTCCCTTTAAATTCGTCCTGCGTGTGTGGGTGTCAAAATGCAATTTTTCACAATA
66 CCTTACCCACTCCCTCTAAATTCGTCCTACGTGTGTGGGTGTCAAAATGCAATTTTTCACAATA
*
40309478 ACTTTTATTTCCATCATTTATTAAGGGATC-AAAACATAAATTTTCATTTGAAAGAGGGCCAAGA
1 ACTTTTATTTCCATCATTTATTAAGAGA-CAAAAACATAAATTTTCATTTGAAAGAGGGCCAAGA
40309542 CCCTTACCCACTCCCTCTAAATTCG-CCTTACGTGTGTGGGTGT
65 CCCTTACCCACTCCCTCTAAATTCGTCC-TACGTGTGTGGGTGT
40309585 GGATGTGTGA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
128 2 0.02
129 92 0.97
130 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (129 bp):
ACTTTTATTTCCATCATTTATTAAGAGACAAAAACATAAATTTTCATTTGAAAGAGGGCCAAGAC
CCTTACCCACTCCCTCTAAATTCGTCCTACGTGTGTGGGTGTCAAAATGCAATTTTTCACAATA
Found at i:40317584 original size:201 final size:201
Alignment explanation
Indices: 40317189--40317707 Score: 625
Period size: 201 Copynumber: 2.6 Consensus size: 201
40317179 TTCCTTCTTA
* * ** *
40317189 TTATGATGTTAACGTATGTTTAACATTAAATCAATTATTTGAAATTTAGTTTCTCTATACCTTTT
1 TTATGATATTAACGTATGTTTGATGTTAAATCAATTATTTGAAATTTAGTTTCTCTATACCTTTC
* * * * * * *
40317254 ATCATTTATCTTTAAAGAGTATATAACTTTTTATTGACACCTTCATATATATATATAATGTTTAT
66 ATAATTTATGTTTAAAGAATATAT-A-TTTTTATGGACACCTTCATATATATATATAATGCTCAC
* * *
40317319 CTCATCCATTTTAATAATTTTCTTTCTTTTGACATGCGTCAGTCAATAACTTTTCTCTTTTTATA
129 CTCATCCATTTTAATAATTTTCTTGC-TTTGACACGCGTAAGTCAATAACTTTTCTCTTTTTATA
*
40317384 AAACCACTT
193 AAACAACTT
*
40317393 TTATGATATTAACAG-ATGTTTGATGTTAAATCAATTATTTGGAATTTAGTTTCTCTATACCTTT
1 TTATGATATTAAC-GTATGTTTGATGTTAAATCAATTATTTGAAATTTAGTTTCTCTATACCTTT
* * * *
40317457 CATAATTTATGTTTAAA-AATATATATTTTTATGGACACCTTCATATGTGTATGTTATGCTCACC
65 CATAATTTATGTTTAAAGAATATATATTTTTATGGACACCTTCATATATATATATAATGCTCACC
* * * *
40317521 TCATTCATTTTAATAATTTTTCTTGGC-TTGACACGTGTAAG-CTAATATCTTTTTTCTTTTTAT
130 TCATCCATTTTAATAA-TTTTCTT-GCTTTGACACGCGTAAGTC-AATAACTTTTCTCTTTTTAT
40317584 AAAACAACTT
192 AAAACAACTT
* * * *
40317594 TTATGATGTTAACGTATGTTTGATGTTAAATCAATCATTTGAAATTTAGTTTTTCTATACTTTTC
1 TTATGATATTAACGTATGTTTGATGTTAAATCAATTATTTGAAATTTAGTTTCTCTATACCTTTC
* * * *
40317659 ATATTTTATGTTTAAAGAGA-ATATATTTTTTATAGACAACTTCGTATAT
66 ATAATTTATGTTTAAAGA-ATATATA-TTTTTATGGACACCTTCATATAT
40317708 GTACATGTCA
Statistics
Matches: 272, Mismatches: 35, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
200 2 0.01
201 157 0.58
202 14 0.05
203 27 0.10
204 71 0.26
205 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (201 bp):
TTATGATATTAACGTATGTTTGATGTTAAATCAATTATTTGAAATTTAGTTTCTCTATACCTTTC
ATAATTTATGTTTAAAGAATATATATTTTTATGGACACCTTCATATATATATATAATGCTCACCT
CATCCATTTTAATAATTTTCTTGCTTTGACACGCGTAAGTCAATAACTTTTCTCTTTTTATAAAA
CAACTT
Found at i:40317807 original size:6 final size:6
Alignment explanation
Indices: 40317791--40317859 Score: 54
Period size: 6 Copynumber: 11.8 Consensus size: 6
40317781 AATCTTACAT
* * * **
40317791 TTTAAA ATTAAA TTTAAA -TT-GA TTCAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
40317837 TTT-AC TTTAAA TTTTAAA TTTAA
1 TTTAAA TTTAAA -TTTAAA TTTAA
40317860 TCAAATTTGA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
4 1 0.02
5 7 0.15
6 33 0.70
7 6 0.13
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:40317839 original size:18 final size:18
Alignment explanation
Indices: 40317825--40317858 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40317815 CAAATTTATT
40317825 TTTAAA-TTTAAATTTAC
1 TTTAAATTTTAAATTTAC
40317842 TTTAAATTTTAAATTTA
1 TTTAAATTTTAAATTTA
40317859 ATCAAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATTTTAAATTTAC
Found at i:40318556 original size:21 final size:20
Alignment explanation
Indices: 40318526--40318566 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
40318516 TAATAGTAGT
*
40318526 TAATAATATTATTTATAATA
1 TAATAATATTATTAATAATA
40318546 TAATAAATATTATTAATAATA
1 TAAT-AATATTATTAATAATA
40318567 ATATTAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATAATATTATTAATAATA
Found at i:40318564 original size:13 final size:13
Alignment explanation
Indices: 40318546--40318637 Score: 57
Period size: 13 Copynumber: 7.2 Consensus size: 13
40318536 ATTTATAATA
40318546 TAATAAATATTAT
1 TAATAAATATTAT
*
40318559 TAAT-AATAATAT
1 TAATAAATATTAT
* **
40318571 TAGTGAAACGTTAT
1 TAAT-AAATATTAT
* * *
40318585 TAATAAACAGTAG
1 TAATAAATATTAT
*
40318598 TAATAAATA-AATT
1 TAATAAATATTA-T
40318611 TAATAAATA-T-T
1 TAATAAATATTAT
40318622 TAATAAATATTTAT
1 TAATAAATA-TTAT
40318636 TA
1 TA
40318638 TTAATAATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
11 10 0.17
12 11 0.18
13 28 0.47
14 11 0.18
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (13 bp):
TAATAAATATTAT
Found at i:40318572 original size:12 final size:12
Alignment explanation
Indices: 40318526--40318572 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
40318516 TAATAGTAGT
*
40318526 TAATAATATTAT
1 TAATAATATTAA
*
40318538 TTATAATA-TAA
1 TAATAATATTAA
*
40318549 TAAATATTATTAA
1 T-AATAATATTAA
40318562 TAATAATATTA
1 TAATAATATTA
40318573 GTGAAACGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
11 3 0.11
12 21 0.75
13 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:40318624 original size:11 final size:11
Alignment explanation
Indices: 40318598--40318634 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
40318588 TAAACAGTAG
40318598 TAATAAATAAATT
1 TAATAAAT--ATT
40318611 TAATAAATATT
1 TAATAAATATT
40318622 TAATAAATATT
1 TAATAAATATT
40318633 TA
1 TA
40318635 TTATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 16 0.67
13 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATAAATATT
Found at i:40319784 original size:29 final size:29
Alignment explanation
Indices: 40319696--40319905 Score: 98
Period size: 29 Copynumber: 7.1 Consensus size: 29
40319686 TTCCTTGGAA
* * **
40319696 ACCCCTGAACTTCTCCAAAATTATATTTTT
1 ACCCCTAAACTT-TCTAAAATTCCATTTTT
* * *
40319726 A-CCCTAAAACTTTTTGAAAATTACAATTTT
1 ACCCCT-AAACTTTCT-AAAATTCCATTTTT
*
40319756 ACCCCTAAACTTTCTAAAATTTCATTTTT
1 ACCCCTAAACTTTCTAAAATTCCATTTTT
* *
40319785 AATCCCT--A-TTTCACCAAAATTACCA-TTTT
1 -ACCCCTAAACTTT--CTAAAATT-CCATTTTT
* *
40319814 ACCCCTAAAATTTCTAAAATTCCATTTTG
1 ACCCCTAAACTTTCTAAAATTCCATTTTT
* *
40319843 ACCCC--AATTTTACCAAAAATTACCA-TTTT
1 ACCCCTAAACTTT--CTAAAATT-CCATTTTT
*
40319872 A-CCCTCAAACTTTCCAAAA-TCTCATTTTT
1 ACCCCT-AAACTTTCTAAAATTC-CATTTTT
40319901 GACCC
1 -ACCC
40319906 AATTTCGACC
Statistics
Matches: 140, Mismatches: 19, Indels: 41
0.70 0.09 0.20
Matches are distributed among these distances:
27 9 0.06
28 15 0.11
29 63 0.45
30 39 0.28
31 14 0.10
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (29 bp):
ACCCCTAAACTTTCTAAAATTCCATTTTT
Found at i:40319813 original size:58 final size:57
Alignment explanation
Indices: 40319742--40319929 Score: 236
Period size: 58 Copynumber: 3.2 Consensus size: 57
40319732 AAACTTTTTG
* * *
40319742 AAAATTACAATTTTACCCCTAAACTTTCTAAAATTTCATTTTTAATCCCTATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTTGA-CCCAATTTCACC
* * *
40319800 AAAATTACCATTTTACCCCTAAAATTTCTAAAATTCCA-TTTTGACCCCAATTTTACC
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTTGA-CCCAATTTCACC
* *
40319857 AAAAATTACCATTTTA-CCCTCAAACTTTCCAAAATCTCATTTTTGACCCAATTTCGACC
1 -AAAATTACCATTTTACCCCT-AAACTTTCTAAAATTTCATTTTTGACCCAATTTC-ACC
*
40319916 AAAATTACTATTTT
1 AAAATTACCATTTT
40319930 GCCCTCGGGT
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
57 19 0.17
58 85 0.75
59 9 0.08
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTTGACCCAATTTCACC
Found at i:40326682 original size:15 final size:15
Alignment explanation
Indices: 40326641--40326716 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
40326631 TTCAATGAAT
*
40326641 AAAAGAAAAAGAAGAA
1 AAAAGCAAAA-AAGAA
*
40326657 GAAAAAC-AAAAAGAA
1 -AAAAGCAAAAAAGAA
*
40326672 AAAAGCAAAAAATAA
1 AAAAGCAAAAAAGAA
*
40326687 AAAA-CAACAAAATAA
1 AAAAGCAA-AAAAGAA
40326702 AAAAG--AAAAAGAA
1 AAAAGCAAAAAAGAA
40326715 AA
1 AA
40326717 GGAGAGGTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
13 8 0.16
14 9 0.18
15 27 0.53
16 3 0.06
17 4 0.08
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.03
Consensus pattern (15 bp):
AAAAGCAAAAAAGAA
Found at i:40326717 original size:5 final size:6
Alignment explanation
Indices: 40326641--40326716 Score: 59
Period size: 6 Copynumber: 12.5 Consensus size: 6
40326631 TTCAATGAAT
* *
40326641 AAAAGA AAAAGA AGAAGA AAAACA AAAAGAA AAAAGCA AAAA-A TAAAA-A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAG-A AAAAG-A AAAAGA -AAAAGA
* *
40326690 ACAACA AAATA-A AAAAGA AAAAGA AAA
1 AAAAGA AAA-AGA AAAAGA AAAAGA AAA
40326717 GGAGAGGTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
5 5 0.09
6 41 0.71
7 12 0.21
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:40327649 original size:51 final size:51
Alignment explanation
Indices: 40327557--40327976 Score: 268
Period size: 51 Copynumber: 8.3 Consensus size: 51
40327547 ATACAACGGG
* * * *
40327557 AAGATCTAAGACCGCAACGGCAGATCC-TGTACCGCAAAAACACAAAAGGGA
1 AAGATCTAAGACCGCAACGGCGGA-CCGTGTACCTCAGAAACACAGAAGGGA
* * **
40327608 AAGGTCTAAGACCGCAACGGCGGACCGTGCACCTCAGAAACATGGAAGGGA
1 AAGATCTAAGACCGCAACGGCGGACCGTGTACCTCAGAAACACAGAAGGGA
* * * * *
40327659 AAGATCTAAGACTGCAATGGCAGATCC-AGTACCGT-A-AAACACACAAGGGA
1 AAGATCTAAGACCGCAACGGCGGA-CCGTGTACC-TCAGAAACACAGAAGGGA
* * * * * * ** *
40327709 AAGGTCTAAG-TCACAACGACGGACCATGTACCTCAGAAGCATGGAAGGGG
1 AAGATCTAAGACCGCAACGGCGGACCGTGTACCTCAGAAACACAGAAGGGA
* * ** * * * *
40327759 AAGATCTAAGACCGCAATGGCAG-CTCCAGTACCACAAAAACACAAAAGGGG
1 AAGATCTAAGACCGCAACGGCGGAC-CGTGTACCTCAGAAACACAGAAGGGA
* ** * * **
40327810 AAGGTCTAA-TTCGCAACGGTGGACCGTGTACCTCAGAAGCATGGAAGGGA
1 AAGATCTAAGACCGCAACGGCGGACCGTGTACCTCAGAAACACAGAAGGGA
* * * * * * * *
40327860 AAGATCTAAGACCACAATGGCAGATCC-AGTACCGCAAAAACAAAAAAGGGA
1 AAGATCTAAGACCGCAACGGCGGA-CCGTGTACCTCAGAAACACAGAAGGGA
* * *
40327911 AATG-TCTAAG-TCGCAACGGCGGACCGTGTACCTCAGAAGCA-TGAAGGGA
1 AA-GATCTAAGACCGCAACGGCGGACCGTGTACCTCAGAAACACAGAAGGGA
*
40327960 AAGATCTAAGATCGCAA
1 AAGATCTAAGACCGCAA
40327977 TGGCAGATCC
Statistics
Matches: 271, Mismatches: 83, Indels: 31
0.70 0.22 0.08
Matches are distributed among these distances:
48 4 0.01
49 29 0.11
50 100 0.37
51 132 0.49
52 6 0.02
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.13
Consensus pattern (51 bp):
AAGATCTAAGACCGCAACGGCGGACCGTGTACCTCAGAAACACAGAAGGGA
Found at i:40327756 original size:100 final size:101
Alignment explanation
Indices: 40327557--40328028 Score: 669
Period size: 101 Copynumber: 4.7 Consensus size: 101
40327547 ATACAACGGG
* * *
40327557 AAGATCTAAGACCGCAACGGCAGATCCTGTACCGCAAAAACACAAAAGGGAAAGGTCTAAGACCG
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTAAG-TCG
* *
40327622 CAACGGCGGACCGTGCACCTCAGAAACATGGAAGGGA
65 CAACGGCGGACCGTGTACCTCAGAAGCATGGAAGGGA
* * * *
40327659 AAGATCTAAGACTGCAATGGCAGATCCAGTACCG-TAAAACACACAAGGGAAAGGTCTAAGTCAC
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTAAGTCGC
* * *
40327723 AACGACGGACCATGTACCTCAGAAGCATGGAAGGGG
66 AACGGCGGACCGTGTACCTCAGAAGCATGGAAGGGA
* * * *
40327759 AAGATCTAAGACCGCAATGGCAGCTCCAGTACCACAAAAACACAAAAGGGGAAGGTCTAATTCGC
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTAAGTCGC
*
40327824 AACGGTGGACCGTGTACCTCAGAAGCATGGAAGGGA
66 AACGGCGGACCGTGTACCTCAGAAGCATGGAAGGGA
* * *
40327860 AAGATCTAAGACCACAATGGCAGATCCAGTACCGCAAAAACAAAAAAGGGAAATGTCTAAGTCGC
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTAAGTCGC
40327925 AACGGCGGACCGTGTACCTCAGAAGCAT-GAAGGGA
66 AACGGCGGACCGTGTACCTCAGAAGCATGGAAGGGA
* * * * * * * *
40327960 AAGATCTAAGATCGCAATGGCAGATCCAGTACCACAAAGATACAAAAAGGAGAGGTTTAAGTCGT
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTAAGTCGC
40328025 AACG
66 AACG
40328029 ACGAACCCGG
Statistics
Matches: 326, Mismatches: 43, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
100 129 0.40
101 166 0.51
102 31 0.10
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (101 bp):
AAGATCTAAGACCGCAATGGCAGATCCAGTACCGCAAAAACACAAAAGGGAAAGGTCTAAGTCGC
AACGGCGGACCGTGTACCTCAGAAGCATGGAAGGGA
Found at i:40327966 original size:201 final size:202
Alignment explanation
Indices: 40327557--40328020 Score: 671
Period size: 201 Copynumber: 2.3 Consensus size: 202
40327547 ATACAACGGG
* * *
40327557 AAGATCTAAGACCGCAACGGCAGATCCTGTACCGCAAAAACACAAAAGGGAAAGGTCTAAGACCG
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCACAAAAACACAAAAGGGAAAGGTCTAAGACCG
**
40327622 CAACGGCGGACCGTGCACCTCAGAAACATGGAAGGGAAAGATCTAAGACTGCAATGGCAGATCCA
66 CAACGGCGGACCGTGCACCTCAGAAACATGGAAGGGAAAGATCTAAGACCACAATGGCAGATCCA
* * *
40327687 GTACCGTAAAACACACAAGGGAAAGGTCTAAGTCACAACGACGGACCATGTACCTCAGAAGCATG
131 GTACCGAAAAACAAAAAAGGGAAAGGTCTAAGTCACAACGACGGACCATGTACCTCAGAAGCATG
*
40327752 GAAGGGG
196 GAAGGGA
* * **
40327759 AAGATCTAAGACCGCAATGGCAGCTCCAGTACCACAAAAACACAAAAGGGGAAGGTCTAA-TTCG
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCACAAAAACACAAAAGGGAAAGGTCTAAGACCG
* * *
40327823 CAACGGTGGACCGTGTACCTCAGAAGCATGGAAGGGAAAGATCTAAGACCACAATGGCAGATCCA
66 CAACGGCGGACCGTGCACCTCAGAAACATGGAAGGGAAAGATCTAAGACCACAATGGCAGATCCA
* * * *
40327888 GTACCGCAAAAACAAAAAAGGGAAATGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGCAT
131 GTACCG-AAAAACAAAAAAGGGAAAGGTCTAAGTCACAACGACGGACCATGTACCTCAGAAGCAT
40327953 -GAAGGGA
195 GGAAGGGA
* * * * * *
40327960 AAGATCTAAGATCGCAATGGCAGATCCAGTACCACAAAGATACAAAAAGGAGAGGTTTAAG
1 AAGATCTAAGACCGCAATGGCAGATCCAGTACCACAAAAACACAAAAGGGAAAGGTCTAAG
40328021 TCGTAACGAC
Statistics
Matches: 232, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
201 126 0.54
202 106 0.46
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (202 bp):
AAGATCTAAGACCGCAATGGCAGATCCAGTACCACAAAAACACAAAAGGGAAAGGTCTAAGACCG
CAACGGCGGACCGTGCACCTCAGAAACATGGAAGGGAAAGATCTAAGACCACAATGGCAGATCCA
GTACCGAAAAACAAAAAAGGGAAAGGTCTAAGTCACAACGACGGACCATGTACCTCAGAAGCATG
GAAGGGA
Found at i:40328466 original size:17 final size:17
Alignment explanation
Indices: 40328444--40328503 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 17
40328434 AAATTGATTC
*
40328444 AAATTTATTTTAACTTT
1 AAATTTATTTTAAATTT
40328461 AAATTTATCTTTTTAAATTT
1 AAATTTA---TTTTAAATTT
*
40328481 AAATTTGTTTTAAATTTT
1 AAATTTATTTTAAA-TTT
40328499 AAATT
1 AAATT
40328504 CAATCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 14 0.38
18 8 0.22
20 15 0.41
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:40341607 original size:10 final size:10
Alignment explanation
Indices: 40341592--40341624 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
40341582 GTTGATTGTT
40341592 TTAAACTAAA
1 TTAAACTAAA
40341602 TTAAACTAAA
1 TTAAACTAAA
40341612 TT-AA-TAAA
1 TTAAACTAAA
40341620 TTAAA
1 TTAAA
40341625 AGTGCGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.27
9 4 0.18
10 12 0.55
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAAACTAAA
Found at i:40344432 original size:21 final size:21
Alignment explanation
Indices: 40344406--40344491 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 21
40344396 ATCACACACA
40344406 ATTATTTTTAAAAAAAATTAC
1 ATTATTTTTAAAAAAAATTAC
*
40344427 ATTATTTTTAAAAAAAATTAT
1 ATTATTTTTAAAAAAAATTAC
*
40344448 ATCT-TTCTTAAATTTTAATCAAATTAC
1 AT-TATTTTTAAA----AA--AAATTAC
40344475 ATTATTTTTAAAAAAAA
1 ATTATTTTTAAAAAAAA
40344492 AAATATGTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
21 32 0.60
22 1 0.02
23 2 0.04
25 2 0.04
26 1 0.02
27 15 0.28
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAAAAAAAATTAC
Done.