Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 105 of 106
Found at i:40482862 original size:13 final size:12
Alignment explanation
Indices: 40482839--40482869 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
40482829 TGAAAATCCA
40482839 AAATAAATAAAT
1 AAATAAATAAAT
40482851 AAATACAATAAAT
1 AAATA-AATAAAT
40482864 AAATAA
1 AAATAA
40482870 CGCTGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:40482965 original size:8 final size:9
Alignment explanation
Indices: 40482947--40482984 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
40482937 GCAACCATAT
40482947 TTTTAATTA
1 TTTTAATTA
40482956 TTTT-ATTA
1 TTTTAATTA
40482964 TTTTAATT-
1 TTTTAATTA
*
40482972 TTTTTATTA
1 TTTTAATTA
40482981 TTTT
1 TTTT
40482985 TTAACAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 15 0.58
9 11 0.42
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTAATTA
Found at i:40482969 original size:17 final size:17
Alignment explanation
Indices: 40482947--40482984 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
40482937 GCAACCATAT
40482947 TTTTAATTATTTTATTA
1 TTTTAATTATTTTATTA
*
40482964 TTTTAATTTTTTTATTA
1 TTTTAATTATTTTATTA
40482981 TTTT
1 TTTT
40482985 TTAACAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTAATTATTTTATTA
Found at i:40485515 original size:2 final size:2
Alignment explanation
Indices: 40485504--40485535 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
40485494 CACATTTCAA
40485504 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40485536 CATAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40489701 original size:2 final size:2
Alignment explanation
Indices: 40489688--40489745 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
40489678 TATTGAAACC
*
40489688 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40489730 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
40489746 TTTGTTTGAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40495610 original size:6 final size:6
Alignment explanation
Indices: 40495599--40495631 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
40495589 CCGTTTGTGA
40495599 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAG
40495632 GGAAACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:40495897 original size:29 final size:30
Alignment explanation
Indices: 40495841--40495899 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
40495831 ATCTTATCAA
** *
40495841 ATATAATTTATTTTTATTTGCATCAAATAT
1 ATATAATTTATTTTTATTACCATAAAATAT
40495871 ATATAATTT-TTTTTATTACCATAAAATAT
1 ATATAATTTATTTTTATTACCATAAAATAT
40495900 TATTAGATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATAATTTATTTTTATTACCATAAAATAT
Found at i:40498844 original size:19 final size:22
Alignment explanation
Indices: 40498820--40498865 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
40498810 AGCAATTGTG
40498820 TTAATT-TCAAA-T-TTTTATT
1 TTAATTATCAAACTATTTTATT
40498839 TTAATTATCAAACTAATTTTATT
1 TTAATTATCAAACT-ATTTTATT
40498862 TTAA
1 TTAA
40498866 AAATTTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 1 0.04
23 11 0.48
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAATTATCAAACTATTTTATT
Found at i:40499087 original size:32 final size:32
Alignment explanation
Indices: 40499027--40499087 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
40499017 ATCTTACCAA
*** *
40499027 ATATAATTTATTTTTATTTTTATCAAATATAT
1 ATATAATTTATTTTTATTACAATAAAATATAT
*
40499059 ATATAATTTGTTTTTATTACAATAAAATA
1 ATATAATTTATTTTTATTACAATAAAATA
40499088 CTATTAGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (32 bp):
ATATAATTTATTTTTATTACAATAAAATATAT
Found at i:40505607 original size:36 final size:35
Alignment explanation
Indices: 40505536--40505612 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
40505526 ATTGAAGCAT
* *
40505536 TACTTT-ACATAAACAATTAAAAGAAGTGAATTAC
1 TACTTTCACATAAACAATTAAAAGAAGTAAAGTAC
* * *
40505570 TACTTTCACATAAAATAATTAGAATAAGTAAAGTAC
1 TACTTTCACAT-AAACAATTAAAAGAAGTAAAGTAC
40505606 TA-TTTCA
1 TACTTTCA
40505613 TGTAGAACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 6 0.17
35 9 0.25
36 21 0.58
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (35 bp):
TACTTTCACATAAACAATTAAAAGAAGTAAAGTAC
Found at i:40507553 original size:22 final size:22
Alignment explanation
Indices: 40507525--40507579 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
40507515 CAATGAACAA
40507525 CGATTTTGCTCTTTGTAGGCAG
1 CGATTTTGCTCTTTGTAGGCAG
*
40507547 CGATTTTGCTCTTTGTAGGTAG
1 CGATTTTGCTCTTTGTAGGCAG
40507569 CGATTTTGCTC
1 CGATTTTGCTC
40507580 AGGGAGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.13, C:0.18, G:0.25, T:0.44
Consensus pattern (22 bp):
CGATTTTGCTCTTTGTAGGCAG
Found at i:40508000 original size:22 final size:22
Alignment explanation
Indices: 40507952--40508000 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40507942 GAAATTGAAT
* **
40507952 AGACTGGTTTTTAAGTATTGTG
1 AGACTGATTTTTAAGTATTACG
40507974 AGACTGATTTTTAAGTATTACG
1 AGACTGATTTTTAAGTATTACG
*
40507996 TGACT
1 AGACT
40508001 TAATCACTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (22 bp):
AGACTGATTTTTAAGTATTACG
Found at i:40508043 original size:22 final size:22
Alignment explanation
Indices: 40508011--40508068 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
40508001 TAATCACTGT
* *
40508011 GTGACTAGTTTTTAGGTATTAC
1 GTGACTGGTTTTTAGGTATGAC
*
40508033 GTGATTGG-TTTTAGGTATGAC
1 GTGACTGGTTTTTAGGTATGAC
40508054 GTGACTGGTTTTTAG
1 GTGACTGGTTTTTAG
40508069 ACATTGCGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.19, C:0.07, G:0.29, T:0.45
Consensus pattern (22 bp):
GTGACTGGTTTTTAGGTATGAC
Found at i:40508127 original size:23 final size:24
Alignment explanation
Indices: 40508101--40508207 Score: 94
Period size: 23 Copynumber: 4.4 Consensus size: 24
40508091 GCAATGCTTA
*
40508101 AGTCACACAATGCCTTAT-TAACT
1 AGTCACACAATGCCTTATAAAACT
* *
40508124 AGTCATACAATGCCTTACT--AACA
1 AGTCACACAATGCCTTA-TAAAACT
* *
40508147 AGTCACGCAATGTCTTATCAGAAACT
1 AGTCACACAATGCCTTAT-A-AAACT
* *
40508173 AGTCACGCAATACCTTATCAAAACT
1 AGTCACACAATGCCTTAT-AAAACT
40508198 AGTCACACAA
1 AGTCACACAA
40508208 GGCTCAAAGT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
22 1 0.01
23 33 0.47
24 1 0.01
25 14 0.20
26 21 0.30
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.25
Consensus pattern (24 bp):
AGTCACACAATGCCTTATAAAACT
Found at i:40508181 original size:26 final size:26
Alignment explanation
Indices: 40508147--40508402 Score: 179
Period size: 26 Copynumber: 10.4 Consensus size: 26
40508137 CTTACTAACA
*
40508147 AGTCACGCAATGTCTTATCAGAAACT
1 AGTCACGCAATGACTTATCAGAAACT
40508173 AGTCACGCAAT-ACCTTATCA-AAACT
1 AGTCACGCAATGA-CTTATCAGAAACT
* * **
40508198 AGTCACACAA-GGC---TCA-AAGTT
1 AGTCACGCAATGACTTATCAGAAACT
* * *
40508219 AGTCATGCAAT-ACCTATC---CACT
1 AGTCACGCAATGACTTATCAGAAACT
40508241 AGTCACGCAAT-ACTTTATCAGAAACT
1 AGTCACGCAATGAC-TTATCAGAAACT
* *
40508267 AATCACGCAAT-ATCTTATCAAAAACT
1 AGTCACGCAATGA-CTTATCAGAAACT
* * **
40508293 AGTCACGTAAT-AC---CCA-AAGTT
1 AGTCACGCAATGACTTATCAGAAACT
* * *
40508314 AGTCACGCGATGCCTTATTAGAAACT
1 AGTCACGCAATGACTTATCAGAAACT
* *
40508340 AATCACGCAATGTCTTATCAGAAACT
1 AGTCACGCAATGACTTATCAGAAACT
*
40508366 AGTCACGCAATGCCTTATCAGAAACT
1 AGTCACGCAATGACTTATCAGAAACT
40508392 AGTCACGCAAT
1 AGTCACGCAAT
40508403 ACCTAAAGTC
Statistics
Matches: 180, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
21 27 0.15
22 16 0.09
23 4 0.02
24 3 0.02
25 16 0.09
26 113 0.63
27 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (26 bp):
AGTCACGCAATGACTTATCAGAAACT
Found at i:40508372 original size:99 final size:95
Alignment explanation
Indices: 40508149--40508424 Score: 331
Period size: 99 Copynumber: 2.9 Consensus size: 95
40508139 TACTAACAAG
* ** *
40508149 TCACGCAATGTCTTATCAGAAACTAGTCACGCAATACCTTATC-AAAACTAGTCACACAAGGCTC
1 TCACGCAATGTCTTATCAGAAACTAGTCACGCAATACCTTATCAAAAACTAGTCACGCAATACCC
* ** *
40508213 AAAGTTAGTCATGCAATACCTATCCACTAG
66 AAAGTTAGTCACGCAATACCTATAAACTAA
* * * *
40508243 TCACGCAAT-ACTTTATCAGAAACTAATCACGCAATATCTTATCAAAAACTAGTCACGTAATACC
1 TCACGCAATGTC-TTATCAGAAACTAGTCACGCAATACCTTATCAAAAACTAGTCACGCAATACC
* *
40508307 CAAAGTTAGTCACGCGATGCCTTATTAGAAACTAA
65 CAAAGTTAGTCACGCAATACC-TA-T--AAACTAA
* * *
40508342 TCACGCAATGTCTTATCAGAAACTAGTCACGCAATGCCTTATCAGAAACTAGTCACGCAATACCT
1 TCACGCAATGTCTTATCAGAAACTAGTCACGCAATACCTTATCAAAAACTAGTCACGCAATACCC
*
40508407 AAAGTCAGTCACGCAATA
66 AAAGTTAGTCACGCAATA
40508425 TCCAAAGTCA
Statistics
Matches: 151, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
93 1 0.01
94 38 0.25
95 33 0.22
96 2 0.01
97 1 0.01
99 75 0.50
100 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (95 bp):
TCACGCAATGTCTTATCAGAAACTAGTCACGCAATACCTTATCAAAAACTAGTCACGCAATACCC
AAAGTTAGTCACGCAATACCTATAAACTAA
Found at i:40508418 original size:21 final size:21
Alignment explanation
Indices: 40508392--40508451 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
40508382 ATCAGAAACT
40508392 AGTCACGCAATACCTAAAGTC
1 AGTCACGCAATACCTAAAGTC
40508413 AGTCACGCAATATCC-AAAGTC
1 AGTCACGCAATA-CCTAAAGTC
*
40508434 AGTCACGCAATGCCTAAA
1 AGTCACGCAATACCTAAA
40508452 AACTAGTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (21 bp):
AGTCACGCAATACCTAAAGTC
Found at i:40509074 original size:15 final size:14
Alignment explanation
Indices: 40509051--40509084 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
40509041 TCTGGTTATG
40509051 AGAAAGCTGGAAAA
1 AGAAAGCTGGAAAA
*
40509065 GGAAAGGCTGGAAAA
1 AGAAA-GCTGGAAAA
40509080 AGAAA
1 AGAAA
40509085 TTTTGAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.56, C:0.06, G:0.32, T:0.06
Consensus pattern (14 bp):
AGAAAGCTGGAAAA
Found at i:40516695 original size:14 final size:14
Alignment explanation
Indices: 40516676--40516706 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40516666 AAAGAATTTT
40516676 TAACCAATTTCGAC
1 TAACCAATTTCGAC
40516690 TAACCAATTTCGAC
1 TAACCAATTTCGAC
40516704 TAA
1 TAA
40516707 GTAACTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.26, G:0.06, T:0.29
Consensus pattern (14 bp):
TAACCAATTTCGAC
Found at i:40525159 original size:2 final size:2
Alignment explanation
Indices: 40525152--40525188 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40525142 GCTAATTAAA
40525152 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40525189 CACAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40525535 original size:144 final size:145
Alignment explanation
Indices: 40525265--40525551 Score: 382
Period size: 144 Copynumber: 2.0 Consensus size: 145
40525255 AAGTGTACTT
* *
40525265 TACCCATTTAATCAAATATTCAAACAAAATTAATTATTTTGAAATGATTGTAATTTTAATGTGAC
1 TACCCATTCAATCAAATATTCAAACAAAATTAATTATTTTGAAATGATTGTAAATTTAATGTGAC
* * * ** ** * *
40525330 TTGTTTAGAAAGATGCCATGGAAGGATTTTTAGTGTAAAATTTAACGTGGTAGTTCCATTTAATT
66 TTGTTTAGAAAGATGCCACGAAAGGACTTTTAGTACAAAACCTAACGTGGTAATTACATTTAATT
*
40525395 CTATAAATTCTTATA
131 CTATAAAGTCTTATA
* * *
40525410 TACCCATTCAATCAAATATTCAAA-TAAATTAATTATTTT-AAATTATTGTAAATTTAATGTGGC
1 TACCCATTCAATCAAATATTCAAACAAAATTAATTATTTTGAAATGATTGTAAATTTAATGTGAC
*
40525473 TTGTTTA-ACAAGATGCCACGAAAGGAACTTTTAGTACAAAACCTAATGTGGTAATTACATTTAA
66 TTGTTTAGA-AAGATGCCACGAAAGG-ACTTTTAGTACAAAACCTAACGTGGTAATTACATTTAA
*
40525537 TTTTATAAAGTCTTA
129 TTCTATAAAGTCTTA
40525552 GATTTAATAG
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
142 1 0.01
143 42 0.34
144 57 0.46
145 23 0.19
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (145 bp):
TACCCATTCAATCAAATATTCAAACAAAATTAATTATTTTGAAATGATTGTAAATTTAATGTGAC
TTGTTTAGAAAGATGCCACGAAAGGACTTTTAGTACAAAACCTAACGTGGTAATTACATTTAATT
CTATAAAGTCTTATA
Found at i:40542552 original size:15 final size:15
Alignment explanation
Indices: 40542515--40542545 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40542505 AAATAAGCAT
40542515 CACAACTTGAAAGTG
1 CACAACTTGAAAGTG
40542530 CACAACTTGAAAGTG
1 CACAACTTGAAAGTG
40542545 C
1 C
40542546 TGAACTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (15 bp):
CACAACTTGAAAGTG
Found at i:40549952 original size:44 final size:44
Alignment explanation
Indices: 40549867--40549955 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
40549857 TATTCGTACC
*
40549867 TAAATATTATTATTTACGTATAATTTGATAGTATTACATATATA
1 TAAATATTATTATTTACGTATAATGTGATAGTATTACATATATA
* * *
40549911 TAAATATTGTTATTTAGGTATATATGT-ATA-TATATATATATATA
1 TAAATATTATTATTTACGTATA-ATGTGATAGTAT-TACATATATA
40549955 T
1 T
40549956 CTTTTTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 3 0.08
44 33 0.85
45 3 0.08
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.49
Consensus pattern (44 bp):
TAAATATTATTATTTACGTATAATGTGATAGTATTACATATATA
Found at i:40560447 original size:22 final size:22
Alignment explanation
Indices: 40560417--40560462 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
40560407 TTAACTACTC
40560417 TTTAATACTCTTTAAATTGCAT
1 TTTAATACTCTTTAAATTGCAT
* *
40560439 TTTACTACTTTTTAAATTGCAT
1 TTTAATACTCTTTAAATTGCAT
40560461 TT
1 TT
40560463 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTAATACTCTTTAAATTGCAT
Found at i:40601184 original size:7 final size:7
Alignment explanation
Indices: 40601172--40601208 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
40601162 ACCACCATTA
40601172 AAAAAAG
1 AAAAAAG
40601179 AAAAAAG
1 AAAAAAG
*
40601186 AAATAAAA
1 AAA-AAAG
40601194 AAAAAAG
1 AAAAAAG
40601201 AAAAAAG
1 AAAAAAG
40601208 A
1 A
40601209 GAGACACCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:40601195 original size:11 final size:11
Alignment explanation
Indices: 40601171--40601208 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40601161 TACCACCATT
40601171 AAAA-AAAGAA
1 AAAAGAAAGAA
*
40601181 AAAAGAAATAA
1 AAAAGAAAGAA
*
40601192 AAAAAAAAGAA
1 AAAAGAAAGAA
40601203 AAAAGA
1 AAAAGA
40601209 GAGACACCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:40601199 original size:15 final size:16
Alignment explanation
Indices: 40601174--40601203 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40601164 CACCATTAAA
40601174 AAAAGAAAAAAGAAAT
1 AAAAGAAAAAAGAAAT
40601190 AAAA-AAAAAAGAAA
1 AAAAGAAAAAAGAAA
40601204 AAAGAGAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAT
Found at i:40625001 original size:31 final size:30
Alignment explanation
Indices: 40624966--40625052 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 30
40624956 TTAAAGGTAA
*
40624966 AATTTTTAAGATAAAATACATTCATTTATT
1 AATTTTTAAAATAAAATACATTCATTTATT
** * * **
40624996 CAATTTTTATTATAATTATATATAAATTTATT
1 -AATTTTTAAAATAA-AATACATTCATTTATT
40625028 AATTTTTAAAAT-AAATAC-TTCATTT
1 AATTTTTAAAATAAAATACATTCATTT
40625053 CAAATATATA
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 1 0.02
31 22 0.51
32 12 0.28
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.51
Consensus pattern (30 bp):
AATTTTTAAAATAAAATACATTCATTTATT
Found at i:40655790 original size:2 final size:2
Alignment explanation
Indices: 40655783--40655807 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40655773 TTAGTGACGA
40655783 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40655808 GCTAGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40676796 original size:38 final size:38
Alignment explanation
Indices: 40676743--40676817 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
40676733 ATAAACTTCT
* * * * *
40676743 TGTGTAGTTGTTCAACTTGACGAATCTGTTTCATGATC
1 TGTGTAATTGCTCAACTGGACAAATCTATTTCATGATC
40676781 TGTGTAATTGCTCAACTGGACAAATCTATTTCATGAT
1 TGTGTAATTGCTCAACTGGACAAATCTATTTCATGAT
40676818 GGGAATGGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (38 bp):
TGTGTAATTGCTCAACTGGACAAATCTATTTCATGATC
Found at i:40678120 original size:15 final size:14
Alignment explanation
Indices: 40678100--40678143 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
40678090 TCCTTACTCA
40678100 CTCTCTTTCTGCTCT
1 CTCTCTTTCT-CTCT
40678115 CTCTCTTTCTCTCT
1 CTCTCTTTCTCTCT
*
40678129 C-CACTTTCTCTCT
1 CTCTCTTTCTCTCT
40678142 CT
1 CT
40678144 ACTTTGGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 12 0.44
14 5 0.19
15 10 0.37
ACGTcount: A:0.02, C:0.43, G:0.02, T:0.52
Consensus pattern (14 bp):
CTCTCTTTCTCTCT
Found at i:40680293 original size:22 final size:24
Alignment explanation
Indices: 40680268--40680324 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
40680258 CTTTTTATTT
* *
40680268 TTTAATTTT-TTAT-TATTATATG
1 TTTAATTTTAATATATATAATATG
40680290 TTTAAATTTTAATATATATAATATG
1 TTT-AATTTTAATATATATAATATG
*
40680315 ATTAATTTTA
1 TTTAATTTTA
40680325 TAATTATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 3 0.10
23 6 0.21
24 10 0.34
25 10 0.34
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTAATTTTAATATATATAATATG
Found at i:40693299 original size:5 final size:5
Alignment explanation
Indices: 40693289--40693316 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40693279 CAATGACCCA
40693289 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
40693317 GAAGACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:40696313 original size:54 final size:49
Alignment explanation
Indices: 40696249--40696356 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 49
40696239 GTCACCTATA
*
40696249 TATACGTATCCCATCCTAAATTGGATATGAATGTGTGAATAGAAGATTAAGACG
1 TATACGTATCCCATCCTAAATTGAATATGAA--TGTG--TA-AAGATTAAGACG
*
40696303 TATACGTATCCCATCCTAGATTGAATATGAATGTGTAAAGATTAAGACG
1 TATACGTATCCCATCCTAAATTGAATATGAATGTGTAAAGATTAAGACG
40696352 TATAC
1 TATAC
40696357 TTGAACCTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
49 17 0.33
50 2 0.04
52 4 0.08
54 29 0.56
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (49 bp):
TATACGTATCCCATCCTAAATTGAATATGAATGTGTAAAGATTAAGACG
Found at i:40703302 original size:14 final size:15
Alignment explanation
Indices: 40703278--40703308 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
40703268 TTCGAAACCA
40703278 CTCTGTTTTTTCTTT
1 CTCTGTTTTTTCTTT
40703293 CTCT-TTTTTTCTTT
1 CTCTGTTTTTTCTTT
40703307 CT
1 CT
40703309 ATTAATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (15 bp):
CTCTGTTTTTTCTTT
Found at i:40710198 original size:19 final size:20
Alignment explanation
Indices: 40710174--40710214 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40710164 GAAAGAAATG
40710174 GATGGGA-GAAGACGA-GGAA
1 GATGGGAGGAAGA-GAGGGAA
40710193 GATGGGAGGAAGAGAGGGAA
1 GATGGGAGGAAGAGAGGGAA
40710213 GA
1 GA
40710215 AGAGAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.41, C:0.02, G:0.51, T:0.05
Consensus pattern (20 bp):
GATGGGAGGAAGAGAGGGAA
Found at i:40712884 original size:16 final size:18
Alignment explanation
Indices: 40712846--40712883 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
40712836 ATATATTTAC
40712846 ATTTTGTATTCAATATTT
1 ATTTTGTATTCAATATTT
40712864 ATTTTG-ATT-AATATTT
1 ATTTTGTATTCAATATTT
40712880 -TTTT
1 ATTTT
40712884 TTGGCATGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 3 0.15
18 6 0.30
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
ATTTTGTATTCAATATTT
Found at i:40714558 original size:18 final size:18
Alignment explanation
Indices: 40714535--40714574 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
40714525 TTAGGTATCG
40714535 GATTCAGGGGTTTTTGGA
1 GATTCAGGGGTTTTTGGA
40714553 GATTCAGGGGTTTTTGGA
1 GATTCAGGGGTTTTTGGA
40714571 GATT
1 GATT
40714575 GCGGCGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.38, T:0.40
Consensus pattern (18 bp):
GATTCAGGGGTTTTTGGA
Found at i:40722174 original size:16 final size:16
Alignment explanation
Indices: 40722155--40722190 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
40722145 ATAATATATG
40722155 TATTAAATAAATTACA
1 TATTAAATAAATTACA
40722171 TATTAAATAAATTACA
1 TATTAAATAAATTACA
40722187 TATT
1 TATT
40722191 TATTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAAATAAATTACA
Found at i:40722194 original size:20 final size:19
Alignment explanation
Indices: 40722150--40722190 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 19
40722140 CATTAATAAT
40722150 ATATGTATTAAATAAATTAC
1 ATAT-TATTAAATAAATTAC
40722170 --A-TATTAAATAAATTAC
1 ATATTATTAAATAAATTAC
40722186 ATATT
1 ATATT
40722191 TATTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 7
0.72 0.00 0.28
Matches are distributed among these distances:
16 15 0.83
18 2 0.11
19 1 0.06
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATTATTAAATAAATTAC
Found at i:40722299 original size:17 final size:19
Alignment explanation
Indices: 40722271--40722322 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
40722261 AAGTAAATCG
*
40722271 ATTTCAATTATTTTTAATT
1 ATTTTAATTATTTTTAATT
* *
40722290 -TTTT-ATTATTATAAATT
1 ATTTTAATTATTTTTAATT
40722307 GATTTTAATTATTTTT
1 -ATTTTAATTATTTTT
40722323 TTTATAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
17 11 0.44
18 3 0.12
19 4 0.16
20 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTAATTATTTTTAATT
Found at i:40724603 original size:54 final size:55
Alignment explanation
Indices: 40724545--40724681 Score: 199
Period size: 54 Copynumber: 2.5 Consensus size: 55
40724535 GAGATATTGA
* * *
40724545 TGGTGAGAGGAGAAGGGAGAAAGAGCGAGCAAGGAGCAGAGATAGAG-ACAT-GAG
1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGCAGAGATAGAGAAC-TGGAG
* *
40724599 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGTAGGGATAGAGAACTGGAG
1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGCAGAGATAGAGAACTGGAG
40724654 -GGTGAAAGGAGAAGGGAGAAGGAGCGAG
1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAG
40724682 GGAAAAGCAG
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
54 71 0.93
55 5 0.07
ACGTcount: A:0.40, C:0.05, G:0.47, T:0.07
Consensus pattern (55 bp):
TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAAAGGAGCAGAGATAGAGAACTGGAG
Found at i:40724630 original size:24 final size:24
Alignment explanation
Indices: 40724603--40724681 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 24
40724593 CATGAGTGGT
40724603 GAAAGGAGAAGGGAGAAGGAGCGA
1 GAAAGGAGAAGGGAGAAGGAGCGA
* * *
40724627 GAAAGGAGTAGGGATAGAGAACTGGAGGGT
1 GAAAGGAG-AAGG---GAGAA--GGAGCGA
40724657 GAAAGGAGAAGGGAGAAGGAGCGA
1 GAAAGGAGAAGGGAGAAGGAGCGA
40724681 G
1 G
40724682 GGAAAAGCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
24 14 0.33
25 3 0.07
26 5 0.12
28 5 0.12
29 3 0.07
30 13 0.30
ACGTcount: A:0.42, C:0.04, G:0.49, T:0.05
Consensus pattern (24 bp):
GAAAGGAGAAGGGAGAAGGAGCGA
Found at i:40724694 original size:54 final size:52
Alignment explanation
Indices: 40724546--40724729 Score: 176
Period size: 54 Copynumber: 3.4 Consensus size: 52
40724536 AGATATTGAT
* * * * *
40724546 GGTGAGAGGAGAAGGGAGAAAGAGCGAGCAAGGAGCAGAGATAGAG-ACATGAG
1 GGTGAAAGGAGAAGGGAGAAGGAGCGAGGAA-AAGCAGGGATAGAGAAC-TGAG
*
40724599 TGGTGAAAGGAGAAGGGAGAAGGAGCGA-GAAAGGAGTAGGGATAGAGAACTGGAG
1 -GGTGAAAGGAGAAGGGAGAAGGAGCGAGGAAA--AGCAGGGATAGAGAACT-GAG
* *
40724654 GGTGAAAGGAGAAGGGAGAAGGAGCGAGGGAAAAGCAGGGATAGGGATCTAGAG
1 GGTGAAAGGAGAAGGGAGAAGGAGCGA-GGAAAAGCAGGGATAGAGAACT-GAG
* *
40724708 AGTGGAAGG-GTAAGGGAGAAGG
1 GGTGAAAGGAG-AAGGGAGAAGG
40724730 TGCTTGATAG
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
53 3 0.03
54 99 0.89
55 5 0.05
56 4 0.04
ACGTcount: A:0.40, C:0.05, G:0.48, T:0.08
Consensus pattern (52 bp):
GGTGAAAGGAGAAGGGAGAAGGAGCGAGGAAAAGCAGGGATAGAGAACTGAG
Found at i:40746695 original size:21 final size:20
Alignment explanation
Indices: 40746657--40746695 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40746647 AAAACTCAGT
*
40746657 TATTTTTCTATGTAAATACA
1 TATTTTTCTAGGTAAATACA
*
40746677 TATTTTTTTAGGTATAATA
1 TATTTTTCTAGGTA-AATA
40746696 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (20 bp):
TATTTTTCTAGGTAAATACA
Found at i:40752969 original size:30 final size:29
Alignment explanation
Indices: 40752935--40753007 Score: 69
Period size: 31 Copynumber: 2.4 Consensus size: 29
40752925 ATCATTAATC
* *
40752935 ATAAATATTTATTTGACTCAA-AATAAAAAT
1 ATAAA-ATTTATTTAACACAATAA-AAAAAT
*
40752965 ATAAAAATTTGATTCAACACAATAAAAAAAT
1 AT-AAAATTT-ATTTAACACAATAAAAAAAT
40752996 A-AAAATTTATTT
1 ATAAAATTTATTT
40753008 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
28 3 0.08
29 7 0.19
30 6 0.17
31 18 0.50
32 2 0.06
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (29 bp):
ATAAAATTTATTTAACACAATAAAAAAAT
Found at i:40754986 original size:23 final size:24
Alignment explanation
Indices: 40754950--40755001 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
40754940 TGCTAATGTG
*
40754950 AAGGACAATTTAAACAATAATACT
1 AAGGACAATTTAAACAATAATAAT
*
40754974 AAGGA-AATTTAAATAATAATAAT
1 AAGGACAATTTAAACAATAATAAT
40754997 AAGGA
1 AAGGA
40755002 GTAACATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.25
Consensus pattern (24 bp):
AAGGACAATTTAAACAATAATAAT
Found at i:40765439 original size:22 final size:22
Alignment explanation
Indices: 40765411--40765455 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
40765401 CCCCGAGCAA
* *
40765411 AGATGTCATGTAAGAGAAATAC
1 AGATGTCATGTAAAAAAAATAC
40765433 AGATGTCATGTAAAAAAAATAC
1 AGATGTCATGTAAAAAAAATAC
40765455 A
1 A
40765456 AATCTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (22 bp):
AGATGTCATGTAAAAAAAATAC
Found at i:40773373 original size:23 final size:24
Alignment explanation
Indices: 40773329--40773386 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
40773319 ATCTAGTTAG
* * *
40773329 ATTAGAATAACAATTCCTAATTCT
1 ATTAGGATAAGAATTCCTAATTAT
40773353 ATTAGGATAAGAA-TCCTAATTAT
1 ATTAGGATAAGAATTCCTAATTAT
40773376 ATTAGGATAAG
1 ATTAGGATAAG
40773387 GTTATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (24 bp):
ATTAGGATAAGAATTCCTAATTAT
Found at i:40788347 original size:2 final size:2
Alignment explanation
Indices: 40788302--40788328 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40788292 CCTTCAAACG
40788302 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
40788329 ACTTCAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:40805268 original size:2 final size:2
Alignment explanation
Indices: 40805261--40805286 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40805251 TAGCGTTCTT
40805261 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
40805287 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:40814409 original size:27 final size:27
Alignment explanation
Indices: 40814378--40814568 Score: 151
Period size: 27 Copynumber: 7.2 Consensus size: 27
40814368 CTGAGGTAAT
*
40814378 TGCTGTTGCTGCAGCTGGGGAAGCTGC
1 TGCTGTTGCTGCATCTGGGGAAGCTGC
* * * *
40814405 GGCTGTTGCTGCATTTGTGGAAGTTGC
1 TGCTGTTGCTGCATCTGGGGAAGCTGC
*
40814432 TGTTGTTGCTGCATCTGGGGCAA-CTGC
1 TGCTGTTGCTGCATCTGGGG-AAGCTGC
* * *
40814459 TGTTGTTGTTGCAGCT-GGGATAGCTGC
1 TGCTGTTGCTGCATCTGGGGA-AGCTGC
* *
40814486 TGC---TGCTGTATCTGCGGAAGCTGC
1 TGCTGTTGCTGCATCTGGGGAAGCTGC
* * * *
40814510 TGCTGCTGCTGTATCTGTGGATGCTGC
1 TGCTGTTGCTGCATCTGGGGAAGCTGC
* * *
40814537 TGCTGCTGTTGCAGCTGAGGG-AGCTGC
1 TGCTGTTGCTGCATCTG-GGGAAGCTGC
40814564 TGCTG
1 TGCTG
40814569 CTGCAAGTGA
Statistics
Matches: 132, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
24 16 0.12
25 4 0.03
26 4 0.03
27 104 0.79
28 4 0.03
ACGTcount: A:0.10, C:0.20, G:0.37, T:0.32
Consensus pattern (27 bp):
TGCTGTTGCTGCATCTGGGGAAGCTGC
Found at i:40814520 original size:78 final size:78
Alignment explanation
Indices: 40814423--40814571 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 78
40814413 CTGCATTTGT
* * * * * *
40814423 GGAAGTTGCTGTTGTTGCTGCATCTGGGGCA-ACTGCTGTTGTTGTTGCAGCTG-GGATAGCTGC
1 GGAAGCTGCTGCTGCTGCTGCATCTGGGG-ATACTGCTGCTGCTGTTGCAGCTGAGG-GAGCTGC
40814486 TGCTGCTGTATCTGC
64 TGCTGCTGTATCTGC
* * *
40814501 GGAAGCTGCTGCTGCTGCTGTATCTGTGGATGCTGCTGCTGCTGTTGCAGCTGAGGGAGCTGCTG
1 GGAAGCTGCTGCTGCTGCTGCATCTGGGGATACTGCTGCTGCTGTTGCAGCTGAGGGAGCTGCTG
40814566 CTGCTG
66 CTGCTG
40814572 CAAGTGAGGG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
77 1 0.02
78 57 0.95
79 2 0.03
ACGTcount: A:0.11, C:0.21, G:0.36, T:0.32
Consensus pattern (78 bp):
GGAAGCTGCTGCTGCTGCTGCATCTGGGGATACTGCTGCTGCTGTTGCAGCTGAGGGAGCTGCTG
CTGCTGTATCTGC
Found at i:40814626 original size:24 final size:24
Alignment explanation
Indices: 40814468--40814626 Score: 106
Period size: 24 Copynumber: 6.4 Consensus size: 24
40814458 CTGTTGTTGT
40814468 TGCAGCTG-GGATAGCTGCTGCTGC
1 TGCAGCTGTGGA-AGCTGCTGCTGC
* * *
40814492 TGTATCTGCGGAAGCTGCTGCTGC
1 TGCAGCTGTGGAAGCTGCTGCTGC
* *
40814516 TGCTGTATCTGTGGATGCTGCTGCTGC
1 TGC---AGCTGTGGAAGCTGCTGCTGC
* *
40814543 TGTTGCAGCTGAGGGAGCTGCTGCTGC
1 ---TGCAGCTGTGGAAGCTGCTGCTGC
* * * * *
40814570 TGCAAG-TGAGGGAGCTGTTGTTGT
1 TGC-AGCTGTGGAAGCTGCTGCTGC
*
40814594 TGCAACTGTGGAAGCTGCTGCTGC
1 TGCAGCTGTGGAAGCTGCTGCTGC
*
40814618 TGCTGCTGT
1 TGCAGCTGT
40814627 TGTTGCAGCT
Statistics
Matches: 106, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
23 1 0.01
24 61 0.58
25 5 0.05
27 36 0.34
30 3 0.03
ACGTcount: A:0.12, C:0.21, G:0.36, T:0.30
Consensus pattern (24 bp):
TGCAGCTGTGGAAGCTGCTGCTGC
Found at i:40814639 original size:36 final size:35
Alignment explanation
Indices: 40814583--40814702 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 35
40814573 AAGTGAGGGA
* *
40814583 GCTGTTGTTGTTGCAACTGTGGAAGCTGCTGCTGCT
1 GCTGCTGTTGTTGCAGCTGTGGAAGCTG-TGCTGCT
40814619 GCTGCTGTTGTTGCAGCTGTGGAAG-TG-GCTGCT
1 GCTGCTGTTGTTGCAGCTGTGGAAGCTGTGCTGCT
* * * * *
40814652 GCTGTTGTTGTTGTAGTTGCGGCAGCTGTTGCTGCT
1 GCTGCTGTTGTTGCAGCTGTGGAAGCTG-TGCTGCT
*
40814688 G-TAGCTGTGGTTGCA
1 GCT-GCTGTTGTTGCA
40814703 TCTGCTGGTG
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
33 26 0.37
34 2 0.03
35 3 0.04
36 39 0.56
ACGTcount: A:0.09, C:0.17, G:0.37, T:0.37
Consensus pattern (35 bp):
GCTGCTGTTGTTGCAGCTGTGGAAGCTGTGCTGCT
Found at i:40814708 original size:24 final size:24
Alignment explanation
Indices: 40814681--40814726 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40814671 CGGCAGCTGT
40814681 TGCTGCTGTAGCTG-TGGTTGCATC
1 TGCTGCTGTAGCTGCT-GTTGCATC
* *
40814705 TGCTGGTGTTGCTGCTGTTGCA
1 TGCTGCTGTAGCTGCTGTTGCA
40814727 ATTGTTGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.07, C:0.20, G:0.35, T:0.39
Consensus pattern (24 bp):
TGCTGCTGTAGCTGCTGTTGCATC
Found at i:40816035 original size:2 final size:2
Alignment explanation
Indices: 40816028--40816064 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40816018 ATGTTATTGT
*
40816028 GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
40816065 CAGTCTAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40817859 original size:17 final size:19
Alignment explanation
Indices: 40817837--40817871 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
40817827 CCCGTTTGAT
40817837 TCAAGG-AGGA-CAAAAGG
1 TCAAGGAAGGATCAAAAGG
40817854 TCAAGGAAGGATCAAAAG
1 TCAAGGAAGGATCAAAAG
40817872 ATTACAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.49, C:0.11, G:0.31, T:0.09
Consensus pattern (19 bp):
TCAAGGAAGGATCAAAAGG
Found at i:40822948 original size:36 final size:36
Alignment explanation
Indices: 40822899--40822970 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
40822889 GGCTTTTACG
40822899 AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
1 AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
* *
40822935 AGTCAATTCCTCATTCATCAAGTAGTAAGTGCAAAT
1 AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
40822971 GATCATAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (36 bp):
AGTCAATTACTCATTCATCAAGCAGTAAGTGCAAAT
Found at i:40832486 original size:2 final size:2
Alignment explanation
Indices: 40832479--40832507 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40832469 CGAATTAAGG
40832479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40832508 AAAGAATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40844873 original size:2 final size:2
Alignment explanation
Indices: 40844866--40844894 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40844856 CCTCCACGTA
40844866 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
40844895 CCTCCTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:40846616 original size:2 final size:2
Alignment explanation
Indices: 40846609--40846642 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40846599 ACTAACAATA
40846609 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
40846643 TGAATCATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40850324 original size:31 final size:31
Alignment explanation
Indices: 40850289--40850362 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
40850279 AACAAAGCAT
*
40850289 TAAAATTTTGGTTTCAGCACAAATCTTACAG
1 TAAAATTTTGGTGTCAGCACAAATCTTACAG
*
40850320 TAAAACTTTGGTGTCAGCACAAATCTTACAG
1 TAAAATTTTGGTGTCAGCACAAATCTTACAG
*
40850351 TAAAATTATGGT
1 TAAAATTTTGGT
40850363 CAAAAGTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (31 bp):
TAAAATTTTGGTGTCAGCACAAATCTTACAG
Found at i:40856886 original size:2 final size:2
Alignment explanation
Indices: 40856873--40856913 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
40856863 AAATAACATC
*
40856873 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40856914 AAGGTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:40866619 original size:2 final size:2
Alignment explanation
Indices: 40866612--40866644 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40866602 GATTCACAGC
40866612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
40866645 ATGGGGACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40903258 original size:5 final size:5
Alignment explanation
Indices: 40903250--40903275 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40903240 TAATAAAGTG
40903250 AGAAT AGAAT AGAAT AGAAT AGAAT A
1 AGAAT AGAAT AGAAT AGAAT AGAAT A
40903276 ACTATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (5 bp):
AGAAT
Found at i:40923216 original size:16 final size:16
Alignment explanation
Indices: 40923195--40923225 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40923185 GCATTAAAGC
40923195 AAAAGACAAAAATTTT
1 AAAAGACAAAAATTTT
*
40923211 AAAAGATAAAAATTT
1 AAAAGACAAAAATTT
40923226 ATAAGTAGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAAGACAAAAATTTT
Found at i:40923460 original size:2 final size:2
Alignment explanation
Indices: 40923453--40923496 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
40923443 CAAGTGGGAT
*
40923453 TA TA TA TA CA T- 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
40923494 TA T
1 TA T
40923497 GTCATGGGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40938622 original size:6 final size:6
Alignment explanation
Indices: 40938611--40938637 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40938601 CAAGGATGGG
40938611 GGAGAT GGAGAT GGAGAT GGAGAT GGA
1 GGAGAT GGAGAT GGAGAT GGAGAT GGA
40938638 CATTGTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GGAGAT
Found at i:40939820 original size:2 final size:2
Alignment explanation
Indices: 40939813--40939843 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
40939803 AACATACAGA
*
40939813 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40939844 GTTGGGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40944284 original size:5 final size:5
Alignment explanation
Indices: 40944274--40944306 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
40944264 CTTTCTCTTT
*
40944274 CTCTC CTCTC CTCTC CTCTC CTCTC ATCTC CTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTC
40944307 CCTAGCTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.58, G:0.00, T:0.39
Consensus pattern (5 bp):
CTCTC
Found at i:40949315 original size:2 final size:2
Alignment explanation
Indices: 40949308--40949376 Score: 84
Period size: 2 Copynumber: 34.5 Consensus size: 2
40949298 CACATGCAGC
* * * *
40949308 TA TA TA TA TG TA TA CA TA TA TA TA TA TG TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
40949350 TA TG TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
40949377 CTAGCTCATT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40949326 original size:10 final size:10
Alignment explanation
Indices: 40949308--40949372 Score: 93
Period size: 10 Copynumber: 6.9 Consensus size: 10
40949298 CACATGCAGC
40949308 TATATATATG
1 TATATATATG
*
40949318 TATACATA--
1 TATATATATG
40949326 TATATATATG
1 TATATATATG
40949336 TATATATATG
1 TATATATATG
40949346 --TATATATG
1 TATATATATG
40949354 TATATATATG
1 TATATATATG
40949364 TATATATAT
1 TATATATAT
40949373 ATATCTAGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
8 15 0.31
10 34 0.69
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (10 bp):
TATATATATG
Found at i:40949331 original size:18 final size:18
Alignment explanation
Indices: 40949308--40949376 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
40949298 CACATGCAGC
*
40949308 TATATATATGTATACATA
1 TATATATATGTATATATA
40949326 TATATATATGTATATATA
1 TATATATATGTATATATA
*
40949344 TGTATATATGTATATATA
1 TATATATATGTATATATA
* *
40949362 TGTATATATATATAT
1 TATATATATGTATAT
40949377 CTAGCTCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (18 bp):
TATATATATGTATATATA
Found at i:40949339 original size:28 final size:28
Alignment explanation
Indices: 40949308--40949372 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
40949298 CACATGCAGC
40949308 TATATATATGTATACATATATATATATG
1 TATATATATGTATACATATATATATATG
* *
40949336 TATATATATGTATATATGTATATATATG
1 TATATATATGTATACATATATATATATG
40949364 TATATATAT
1 TATATATAT
40949373 ATATCTAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.49
Consensus pattern (28 bp):
TATATATATGTATACATATATATATATG
Found at i:40951890 original size:2 final size:2
Alignment explanation
Indices: 40951885--40951909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40951875 TTTTTTTTTT
40951885 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
40951910 TATGGTATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40955461 original size:2 final size:2
Alignment explanation
Indices: 40955454--40955519 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
40955444 ACCACCCTCA
*
40955454 AT AT AT AT AC 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
40955496 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
40955520 CTTGAAGATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40956982 original size:13 final size:13
Alignment explanation
Indices: 40956943--40956984 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
40956933 TTTCTTTAAA
*
40956943 AACAAAAATTAAT
1 AACAAAAAATAAT
40956956 -ACAAAAGGAATAAT
1 AACAAAA--AATAAT
40956970 AACAAAAAATAAT
1 AACAAAAAATAAT
40956983 AA
1 AA
40956985 TAAATCATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 6 0.24
13 8 0.32
14 5 0.20
15 6 0.24
ACGTcount: A:0.71, C:0.07, G:0.05, T:0.17
Consensus pattern (13 bp):
AACAAAAAATAAT
Found at i:40957810 original size:2 final size:2
Alignment explanation
Indices: 40957803--40957838 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
40957793 TCATCTTCAC
40957803 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40957839 CTCTGTCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:40957825 original size:17 final size:17
Alignment explanation
Indices: 40957803--40957836 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40957793 TCATCTTCAC
40957803 TATATATATATATATAT
1 TATATATATATATATAT
40957820 TATATATATATATATAT
1 TATATATATATATATAT
40957837 ATCTCTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:40958032 original size:2 final size:2
Alignment explanation
Indices: 40958025--40958054 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40958015 GGATAGATAG
40958025 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
40958055 TTCTAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40964787 original size:15 final size:15
Alignment explanation
Indices: 40964758--40964800 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
40964748 ATCTGTTCCC
40964758 CCCCTTCCCCTCCCCCG
1 CCCC-TCCCC-CCCCCG
*
40964775 CGCCTCCCCCCCCCG
1 CCCCTCCCCCCCCCG
*
40964790 CCCCGCCCCCC
1 CCCCTCCCCCC
40964801 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.65
16 5 0.22
17 3 0.13
ACGTcount: A:0.00, C:0.81, G:0.09, T:0.09
Consensus pattern (15 bp):
CCCCTCCCCCCCCCG
Found at i:40966673 original size:13 final size:13
Alignment explanation
Indices: 40966655--40966679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40966645 AAACCAAACC
40966655 TTTTAATTCATAG
1 TTTTAATTCATAG
40966668 TTTTAATTCATA
1 TTTTAATTCATA
40966680 CCTTTCCAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTTAATTCATAG
Found at i:40967015 original size:22 final size:23
Alignment explanation
Indices: 40966990--40967032 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
40966980 ATCCAAACTG
40966990 ACATACTT-TTCA-AGCAACTTGT
1 ACAT-CTTCTTCAGAGCAACTTGT
40967012 ACATCTTCTTCAGAGCAACTT
1 ACATCTTCTTCAGAGCAACTT
40967033 CACAAGGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 8 0.42
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (23 bp):
ACATCTTCTTCAGAGCAACTTGT
Found at i:40997945 original size:26 final size:26
Alignment explanation
Indices: 40997910--40997976 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
40997900 TGAACCATAA
*
40997910 TAATGTTTAAATTATAAATAAAATAT
1 TAATATTTAAATTATAAATAAAATAT
* *
40997936 TACTGA-TTAAATTATATATAAAATAT
1 TAAT-ATTTAAATTATAAATAAAATAT
40997962 TAATATTTAAATTAT
1 TAATATTTAAATTAT
40997977 CAATTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 34 0.97
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (26 bp):
TAATATTTAAATTATAAATAAAATAT
Found at i:40997994 original size:19 final size:19
Alignment explanation
Indices: 40997941--40997999 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 19
40997931 AATATTACTG
40997941 ATTAA-ATTATATATAAAAT
1 ATTAATATTAT-TATAAAAT
* *
40997960 ATTAATATTTAAATTATCAATT
1 ATTAATA-TT--ATTATAAAAT
40997982 ATTAATATTATTATAAAA
1 ATTAATATTATTATAAAA
40998000 AAGAAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 12 0.38
20 1 0.03
21 4 0.12
22 13 0.41
23 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAATATTATTATAAAAT
Found at i:40998148 original size:22 final size:23
Alignment explanation
Indices: 40998096--40998153 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 23
40998086 TTTTCAAATG
*
40998096 TTAATGATTAA-ATTATAAATAA
1 TTAATTATTAATATTATAAATAA
40998118 --AA-TATTAATATT-TAAATAA
1 TTAATTATTAATATTATAAATAA
40998137 TTAATTATTAATATTAT
1 TTAATTATTAATATTAT
40998154 TATGAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 2 0.07
22 10 0.33
23 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAATTATTAATATTATAAATAA
Found at i:40998151 original size:161 final size:157
Alignment explanation
Indices: 40997930--40998297 Score: 437
Period size: 161 Copynumber: 2.4 Consensus size: 157
40997920 ATTATAAATA
* * *
40997930 AAATATTACTGATTAAATTATATATAAAATATTAATATTTAAATTATCAATTATTAATATTATTA
1 AAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTAATATTATTA
* * **
40997995 TAAAAAAGAAAAAAGTTTAAA-TGATCAATTATATATTATGAAAAATAACATTTTAATTTTAAAA
66 T-AAAAAGAAAAAAATTTAAATTGAT-AATAATATATTAT-AAAAAT-ACATTTTAAAATTAAAA
*
40998059 ATTAATTAAAATATTTATATTTNAATATTTTC
127 ATTAATTAAAATATTAATATTT-AATATTTTC
* *
40998091 AAATGTTAATGATTAAATTATAAATAAAATATTAATATTTAAATAATTAATTATTAATATTATTA
1 AAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTAATATTATTA
* * * *
40998156 TGAAAAGAAAAAAATTTAAATTTATAATAATATATTATAAATATATATTTTAAAATTAAAAATTA
66 TAAAAAGAAAAAAATTTAAATTGATAATAATATATTATAAAAATACATTTTAAAATTAAAAATTA
* *
40998221 ATTAAAGTATTAATATTT--TA--ATC
131 ATTAAAATATTAATATTTAATATTTTC
* * * * *
40998244 ATAATA-TCAT--CTAAATTATAAATAAAATATTAATATTTAACTGATCGATTATTA
1 A-AATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTA
40998298 GGATTTCAAA
Statistics
Matches: 182, Mismatches: 23, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
151 39 0.21
153 6 0.03
154 3 0.02
155 2 0.01
158 34 0.19
159 5 0.03
160 29 0.16
161 64 0.35
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.42
Consensus pattern (157 bp):
AAATATTAATGATTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTAATATTATTA
TAAAAAGAAAAAAATTTAAATTGATAATAATATATTATAAAAATACATTTTAAAATTAAAAATTA
ATTAAAATATTAATATTTAATATTTTC
Found at i:40998416 original size:30 final size:29
Alignment explanation
Indices: 40998382--40998450 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
40998372 TAAATTATCA
* *
40998382 ATTAAATATTACTATTTGAAAATATTAATT
1 ATTAAATATTAATATTT-AAAATATAAATT
**
40998412 ATTAAAATATTAATATTTAAGTTATAAATT
1 ATT-AAATATTAATATTTAAAATATAAATT
40998442 A-TAAATATT
1 ATTAAATATT
40998451 TTAAATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 7 0.21
29 1 0.03
30 13 0.38
31 13 0.38
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (29 bp):
ATTAAATATTAATATTTAAAATATAAATT
Found at i:40998431 original size:15 final size:15
Alignment explanation
Indices: 40998385--40998431 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
40998375 ATTATCAATT
*
40998385 AAATATTACTATTTGA
1 AAATATTAATATTT-A
40998401 AAATATTAAT-TATTA
1 AAATATTAATAT-TTA
40998416 AAATATTAATATTTA
1 AAATATTAATATTTA
40998431 A
1 A
40998432 GTTATAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
AAATATTAATATTTA
Found at i:40998439 original size:22 final size:22
Alignment explanation
Indices: 40998401--40998451 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
40998391 TACTATTTGA
40998401 AAATA-TTAATTATTAAAATAT
1 AAATATTTAATTATTAAAATAT
* *
40998422 TAATATTTAAGTTA-TAAATTAT
1 AAATATTTAA-TTATTAAAATAT
40998444 AAATATTT
1 AAATATTT
40998452 TAAATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 18 0.72
23 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATATTTAATTATTAAAATAT
Found at i:40998473 original size:16 final size:16
Alignment explanation
Indices: 40998454--40998487 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40998444 AAATATTTTA
40998454 AATAATT-AATTATAAT
1 AATAATTAAATT-TAAT
40998470 AATAATTAAATTTAAT
1 AATAATTAAATTTAAT
40998486 AA
1 AA
40998488 ATTATTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAATTAAATTTAAT
Found at i:40998485 original size:26 final size:25
Alignment explanation
Indices: 40998455--40998532 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 25
40998445 AATATTTTAA
40998455 ATAATTAATTATAATAATAATTAAATT
1 ATAATTAATTAT-ATAAT-ATTAAATT
*
40998482 -TAATAAATTAT-TAATGATTAAATT
1 ATAATTAATTATATAAT-ATTAAATT
* *
40998506 ATAAATAA-AATATTAATATTAAATT
1 ATAATTAATTATA-TAATATTAAATT
40998531 AT
1 AT
40998533 TAATATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
24 14 0.33
25 15 0.35
26 14 0.33
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
ATAATTAATTATATAATATTAAATT
Found at i:40998528 original size:14 final size:14
Alignment explanation
Indices: 40998485--40998539 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
40998475 TTAAATTTAA
40998485 TAAATTATTAATGAT
1 TAAATTATTAAT-AT
40998500 TAAATTA-TAA-A-
1 TAAATTATTAATAT
*
40998511 TAAAATATTAATAT
1 TAAATTATTAATAT
40998525 TAAATTATTAATAT
1 TAAATTATTAATAT
40998539 T
1 T
40998540 TTAATTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 1 0.03
14 17 0.49
15 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATTATTAATAT
Found at i:40998532 original size:25 final size:25
Alignment explanation
Indices: 40998469--40998537 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
40998459 TTAATTATAA
*
40998469 TAATAATTAAATT-TAATAAATTAT
1 TAATAATTAAATTATAATAAAATAT
*
40998493 TAATGATTAAATTATAAATAAAATAT
1 TAATAATTAAATTAT-AATAAAATAT
40998519 TAAT-ATTAAATTATTAATA
1 TAATAATTAAATTA-TAATA
40998538 TTTTAATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.30
25 14 0.35
26 14 0.35
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TAATAATTAAATTATAATAAAATAT
Found at i:41039607 original size:2 final size:2
Alignment explanation
Indices: 41039600--41039631 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41039590 AGAGGGTAGA
41039600 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
41039632 TAGTTAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41039888 original size:2 final size:2
Alignment explanation
Indices: 41039881--41039912 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41039871 TCCCTANGTA
41039881 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
41039913 TTAGTTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41040101 original size:280 final size:279
Alignment explanation
Indices: 41039599--41040156 Score: 1082
Period size: 280 Copynumber: 2.0 Consensus size: 279
41039589 AAGAGGGTAG
41039599 AATATATATATATATATATATATATATATATATTAGTTAAGTTGTTAAATTAAATTTTAATTAAA
1 AATATATATATATATATATATATATATATATATTAGTTAAG-TGTTAAATTAAATTTTAATTAAA
41039664 GCAAATGCTCGAACTTGATCACACTTTTAAAATAGGATAAGTTTGAACATATATAATAATAATAA
65 GCAAATGCTCGAACTTGATCACACTTTTAAAATAGGATAAGTTTGAACATATATAATAATAATAA
41039729 TGCGGTCTCACCAATAGCTAGGAACGTACTTGACTTTCAAGTTATGGAGCACTATATATCAACTT
130 TGCGGTCTCACCAATAGCTAGGAACGTACTTGACTTTCAAGTTATGGAGCACTATATATCAACTT
41039794 ATTGTATTGGCAATTTATACTAAGAATTCCATTAAAATAAAACACTACTTACACAATCTTACTTC
195 ATTGTATTGGCAATTTATACTAAGAATTCCATTAAAATAAAACACTACTTACACAATCTTACTTC
41039859 ATCAAGCTCCATTCCCTANGT
260 ATCAAGCTCCATTCCCTA-GT
41039880 AATATATATATATATATATATATATATATATATTTAGTTAAG-GTTAAATTAAATTTTAATTAAA
1 AATATATATATATATATATATATATATATATA-TTAGTTAAGTGTTAAATTAAATTTTAATTAAA
41039944 GCAAATGCTCGAACTTGATCACACTTTTAAAATAGGATAAGTTTGAACATATATAATAATAATAA
65 GCAAATGCTCGAACTTGATCACACTTTTAAAATAGGATAAGTTTGAACATATATAATAATAATAA
41040009 TGCGGTCTCACCAATAGCTAGGAACGTACTTGACTTTCAAGTTATGGAGCACTATATATCAACTT
130 TGCGGTCTCACCAATAGCTAGGAACGTACTTGACTTTCAAGTTATGGAGCACTATATATCAACTT
41040074 ATTGTATTGGCAATTTATACTAAGAATTCCATTAAAATAAAACACTACTTACACAATCTTACTTC
195 ATTGTATTGGCAATTTATACTAAGAATTCCATTAAAATAAAACACTACTTACACAATCTTACTTC
41040139 ATCAAGCTCCATTCCCTA
260 ATCAAGCTCCATTCCCTA
41040157 ATGATCTCTT
Statistics
Matches: 276, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
280 235 0.85
281 32 0.12
282 9 0.03
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (279 bp):
AATATATATATATATATATATATATATATATATTAGTTAAGTGTTAAATTAAATTTTAATTAAAG
CAAATGCTCGAACTTGATCACACTTTTAAAATAGGATAAGTTTGAACATATATAATAATAATAAT
GCGGTCTCACCAATAGCTAGGAACGTACTTGACTTTCAAGTTATGGAGCACTATATATCAACTTA
TTGTATTGGCAATTTATACTAAGAATTCCATTAAAATAAAACACTACTTACACAATCTTACTTCA
TCAAGCTCCATTCCCTAGT
Found at i:41049817 original size:2 final size:2
Alignment explanation
Indices: 41049810--41049851 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41049800 AAGTTATTCC
41049810 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
41049852 TAAATTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41050051 original size:84 final size:84
Alignment explanation
Indices: 41049909--41050068 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 84
41049899 GAATTTGACA
*
41049909 TTCAATTTTATTAAAACTATAATTATTCATAACTAGAAAGATTTAATTGAATCATTGAAAATATC
1 TTCAATTTTATTAAAACTATAATTATTCATAACTAGAAACATTTAATTGAATCATTGAAAATATC
41049974 TACAAAAGCAATAAAAAACG
66 TA-AAAAGCAATAAAAAACG
* *
41049994 TTCAATTTTATTAAAATTATAATTATT-TTAACTAGAAACATTTAATTGAATCATTGAAAATATC
1 TTCAATTTTATTAAAACTATAATTATTCATAACTAGAAACATTTAATTGAATCATTGAAAATATC
*
41050058 TATAAAGCAAT
66 TAAAAAGCAAT
41050069 CAAGAAAGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
83 8 0.11
84 37 0.52
85 26 0.37
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (84 bp):
TTCAATTTTATTAAAACTATAATTATTCATAACTAGAAACATTTAATTGAATCATTGAAAATATC
TAAAAAGCAATAAAAAACG
Found at i:41050821 original size:3 final size:3
Alignment explanation
Indices: 41050813--41050843 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41050803 TAGGTCTACA
41050813 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41050844 GCTTTAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41059204 original size:18 final size:18
Alignment explanation
Indices: 41059175--41059223 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
41059165 CTCTTCCCTG
**
41059175 TTAAAT-AAATTATTTTA
1 TTAAATAAAATTATAATA
*
41059192 TTAAATAAAATTAAAATA
1 TTAAATAAAATTATAATA
*
41059210 TTAAATATAATTAT
1 TTAAATAAAATTAT
41059224 GACGAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAATAAAATTATAATA
Found at i:41059662 original size:17 final size:16
Alignment explanation
Indices: 41059642--41059687 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
41059632 AAAGTTTGTT
*
41059642 TTATTTTTTAATTTATA
1 TTATTATTT-ATTTATA
41059659 TTATTATTTATTTAT-
1 TTATTATTTATTTATA
41059674 TT-TTATTTTATTTA
1 TTATTA-TTTATTTA
41059688 CTTATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 6 0.22
17 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTATTTATTTATA
Found at i:41059667 original size:20 final size:19
Alignment explanation
Indices: 41059640--41059692 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
41059630 TTAAAGTTTG
41059640 TTTTATTT-TTTAATTTATA
1 TTTTATTTATTT-ATTTATA
*
41059659 TTATTATTTATTTATTTTTA
1 TT-TTATTTATTTATTTATA
*
41059679 TTTTATTTACTTAT
1 TTTTATTTATTTAT
41059693 ATATTCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 13 0.43
20 14 0.47
21 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATTTATTTATTTATA
Found at i:41059683 original size:27 final size:28
Alignment explanation
Indices: 41059641--41059697 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
41059631 TAAAGTTTGT
*
41059641 TTTATTTTTTAATTTATATTA-TTATTTA
1 TTTATTTTTTAATTTAT-TTACTTATATA
*
41059669 TTTA-TTTTTATTTTATTTACTTATATA
1 TTTATTTTTTAATTTATTTACTTATATA
41059696 TT
1 TT
41059698 CTAAATCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.12
27 19 0.73
28 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTATTTTTTAATTTATTTACTTATATA
Found at i:41064257 original size:14 final size:15
Alignment explanation
Indices: 41064231--41064263 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
41064221 CTGCAAACAA
41064231 AGAAAGTAAAGAGAG
1 AGAAAGTAAAGAGAG
41064246 AGAAAG-AAAGAGAG
1 AGAAAGTAAAGAGAG
41064260 AGAA
1 AGAA
41064264 GAATGGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (15 bp):
AGAAAGTAAAGAGAG
Found at i:41074124 original size:14 final size:14
Alignment explanation
Indices: 41074105--41074131 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41074095 AGATATGACA
41074105 GAGAAAAAGGAAAT
1 GAGAAAAAGGAAAT
41074119 GAGAAAAAGGAAA
1 GAGAAAAAGGAAA
41074132 AGTATGACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.04
Consensus pattern (14 bp):
GAGAAAAAGGAAAT
Found at i:41074899 original size:39 final size:39
Alignment explanation
Indices: 41074856--41074943 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
41074846 TGGTGTGGTA
* * * *
41074856 GAAGGTGGGGGTGTTG-TGGTTGGTGGAGGTGTTGCAGTT
1 GAAGGTGGAGGTGTTGCT-GTTGGAGGAGGTGGTGAAGTT
* *
41074895 GAAGGCGGAGGTGTTGCTGTTGGAGGTGGTGGTGAAGTT
1 GAAGGTGGAGGTGTTGCTGTTGGAGGAGGTGGTGAAGTT
41074934 GAAGGTGGAG
1 GAAGGTGGAG
41074944 TTATGGTGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 40 0.98
40 1 0.02
ACGTcount: A:0.15, C:0.03, G:0.53, T:0.28
Consensus pattern (39 bp):
GAAGGTGGAGGTGTTGCTGTTGGAGGAGGTGGTGAAGTT
Found at i:41074928 original size:21 final size:21
Alignment explanation
Indices: 41074877--41074943 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
41074867 TGTTGTGGTT
41074877 GGTGGAGGTGTTGCAGTTGAA
1 GGTGGAGGTGTTGCAGTTGAA
* * *
41074898 GGCGGAGGTGTTGCTGTTGGA
1 GGTGGAGGTGTTGCAGTTGAA
* *
41074919 GGT---GGTGGTGAAGTTGAA
1 GGTGGAGGTGTTGCAGTTGAA
41074937 GGTGGAG
1 GGTGGAG
41074944 TTATGGTGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
18 14 0.40
21 21 0.60
ACGTcount: A:0.16, C:0.04, G:0.52, T:0.27
Consensus pattern (21 bp):
GGTGGAGGTGTTGCAGTTGAA
Found at i:41080135 original size:54 final size:54
Alignment explanation
Indices: 41080065--41080168 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
41080055 GCTGGAATGA
* * *
41080065 ACTCTGAGCCATGGTTGTATCTTCCTCC-CAAATCTTCTTTCTAGATTCAGACCG
1 ACTCTGAACCAGGGTTGTATCTTCCTCCTC-AATCTTCATTCTAGATTCAGACCG
*
41080119 ACTCTGAACCAGGGTTGTATCTTCTTCCTCAATCTTCATTCTAGATTCAG
1 ACTCTGAACCAGGGTTGTATCTTCCTCCTCAATCTTCATTCTAGATTCAG
41080169 TCAGCCTCTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 44 0.98
55 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.37
Consensus pattern (54 bp):
ACTCTGAACCAGGGTTGTATCTTCCTCCTCAATCTTCATTCTAGATTCAGACCG
Found at i:41102046 original size:3 final size:3
Alignment explanation
Indices: 41102040--41102106 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
41102030 TGAATTCGTA
* * * * *
41102040 GGT GGT GGA GGT GAT GGT GGT TGT CGA GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * *
41102088 GAT GGT TGT GGT GAT GGT G
1 GGT GGT GGT GGT GGT GGT G
41102107 AAGCGTCAGG
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.07, C:0.01, G:0.58, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:41102059 original size:12 final size:12
Alignment explanation
Indices: 41102042--41102106 Score: 78
Period size: 12 Copynumber: 5.4 Consensus size: 12
41102032 AATTCGTAGG
*
41102042 TGGTGGAGGTGA
1 TGGTGGTGGTGA
*
41102054 TGGTGGTTGTCGA
1 TGGTGGTGGT-GA
*
41102067 -GGTGGTGGTGG
1 TGGTGGTGGTGA
41102078 TGGTGGTGGTGA
1 TGGTGGTGGTGA
*
41102090 TGGTTGTGGTGA
1 TGGTGGTGGTGA
41102102 TGGTG
1 TGGTG
41102107 AAGCGTCAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.08, C:0.02, G:0.57, T:0.34
Consensus pattern (12 bp):
TGGTGGTGGTGA
Found at i:41105694 original size:10 final size:10
Alignment explanation
Indices: 41105679--41105706 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41105669 TATTTTATAA
41105679 TTTTATTATT
1 TTTTATTATT
41105689 TTTTATTATT
1 TTTTATTATT
41105699 TTTTATTA
1 TTTTATTA
41105707 ATTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTATTATT
Found at i:41105694 original size:18 final size:17
Alignment explanation
Indices: 41105671--41105705 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41105661 AAAATTACTA
41105671 TTTTATAATTTTATTATT
1 TTTTATAATTTT-TTATT
*
41105689 TTTTATTATTTTTTATT
1 TTTTATAATTTTTTATT
41105706 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATAATTTTTTATT
Found at i:41119099 original size:2 final size:2
Alignment explanation
Indices: 41119092--41119144 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
41119082 ATGAAACAAG
41119092 TA TA TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41119135 TA TA TA TA TA
1 TA TA TA TA TA
41119145 CAACATTAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41122313 original size:2 final size:2
Alignment explanation
Indices: 41122306--41122345 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
41122296 GTGTAGATTT
*
41122306 AG AG AG AG AA AG AG AG AG ATG TAG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG A-G -AG AG AG AG AG AG AG AG AG
41122346 GTGTGGGGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 31 0.91
3 2 0.06
4 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (2 bp):
AG
Found at i:41122330 original size:22 final size:22
Alignment explanation
Indices: 41122300--41122345 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
41122290 AAGAAAGTGT
*
41122300 AGATTTAGAGAGAGAAAGAGAG
1 AGATGTAGAGAGAGAAAGAGAG
*
41122322 AGATGTAGAGAGAGAGAGAGAG
1 AGATGTAGAGAGAGAAAGAGAG
41122344 AG
1 AG
41122346 GTGTGGGGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.41, T:0.11
Consensus pattern (22 bp):
AGATGTAGAGAGAGAAAGAGAG
Found at i:41137829 original size:13 final size:13
Alignment explanation
Indices: 41137811--41137835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41137801 GAAGAAATTG
41137811 TGATTTTATAAAA
1 TGATTTTATAAAA
41137824 TGATTTTATAAA
1 TGATTTTATAAA
41137836 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:41140360 original size:1 final size:1
Alignment explanation
Indices: 41140354--41140381 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
41140344 CATTTTAGTC
41140354 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
41140382 GCTCGTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41140882 original size:12 final size:12
Alignment explanation
Indices: 41140859--41140908 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
41140849 AGCGCCAGCA
*
41140859 CCAACACCAACT
1 CCAACTCCAACT
*
41140871 CTAACTCCAACT
1 CCAACTCCAACT
* *
41140883 CCAACACCAATT
1 CCAACTCCAACT
*
41140895 CCAATTCCAACT
1 CCAACTCCAACT
41140907 CC
1 CC
41140909 GAATCCTCCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.18
Consensus pattern (12 bp):
CCAACTCCAACT
Done.