Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 10 of 144
Found at i:2281919 original size:24 final size:25
Alignment explanation
Indices: 2281892--2281939 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2281882 GAGCAAATCG
*
2281892 ATTTTT-CTGTTAAAAATTTTACTC
1 ATTTTTACTGTTAAAAATTGTACTC
*
2281916 ATTTTTATTGTTAAAAATTGTACT
1 ATTTTTACTGTTAAAAATTGTACT
2281940 GTATGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.54
Consensus pattern (25 bp):
ATTTTTACTGTTAAAAATTGTACTC
Found at i:2284851 original size:25 final size:25
Alignment explanation
Indices: 2284777--2284852 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
2284767 AGATAGGTTC
* * *
2284777 TCCAGAT-GACTTGTCACCAAGGCTC
1 TCCAGATAGA-TTGCCACAAAGGCTT
*
2284802 TCCAGATA-ATATACCACAAAGGCTT
1 TCCAGATAGAT-TGCCACAAAGGCTT
2284827 TCCAGATAGATTGCCACAAAGGCTT
1 TCCAGATAGATTGCCACAAAGGCTT
2284852 T
1 T
2284853 TTAGAGAGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 1 0.02
25 40 0.93
26 2 0.05
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (25 bp):
TCCAGATAGATTGCCACAAAGGCTT
Found at i:2284862 original size:25 final size:25
Alignment explanation
Indices: 2284815--2284872 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
2284805 AGATAATATA
* *
2284815 CCACAAAGGCTTTCCAGATAGATTG
1 CCACAAAGGCTTTCCAGAGAGATCG
**
2284840 CCACAAAGGCTTTTTAGAGAGATCG
1 CCACAAAGGCTTTCCAGAGAGATCG
*
2284865 CCATAAAG
1 CCACAAAG
2284873 AATTTATAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (25 bp):
CCACAAAGGCTTTCCAGAGAGATCG
Found at i:2300694 original size:18 final size:17
Alignment explanation
Indices: 2300661--2300699 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2300651 TTTTATAAAT
2300661 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2300679 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2300696 TGTG
1 TGTG
2300700 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2300956 original size:23 final size:23
Alignment explanation
Indices: 2300925--2300977 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2300915 AGTGTTATTG
2300925 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2300948 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2300971 ATCAGTG
1 ATCAGTG
2300978 TGACACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2304348 original size:28 final size:28
Alignment explanation
Indices: 2304285--2304407 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
2304275 ATATTAAGTC
*
2304285 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
2304312 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
2304340 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
2304368 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
2304397 CGCACACTTAG
1 CGCACACTTAG
2304408 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 49 0.56
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:2310872 original size:103 final size:104
Alignment explanation
Indices: 2310693--2310957 Score: 415
Period size: 103 Copynumber: 2.6 Consensus size: 104
2310683 AACCGTTATT
* * * *
2310693 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
2310758 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
*
2310796 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
2310861 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* * **
2310900 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAACACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
2310958 TTATGTACAA
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 83 0.56
104 65 0.44
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:2311319 original size:30 final size:29
Alignment explanation
Indices: 2311285--2311349 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
2311275 TAATCCACCA
2311285 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
2311315 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
2311345 CCCAA
1 CCCAA
2311350 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:2311323 original size:31 final size:30
Alignment explanation
Indices: 2311292--2311349 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2311282 CCACCCAACT
2311292 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
2311322 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
2311350 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:2314529 original size:30 final size:30
Alignment explanation
Indices: 2314483--2314576 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
2314473 TTTTATTATG
*
2314483 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
2314514 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * * *
2314544 CTATTATTTGATACTCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
2314574 CCA
1 CCA
2314577 TAAATATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 50 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:2314538 original size:15 final size:15
Alignment explanation
Indices: 2314493--2314570 Score: 52
Period size: 15 Copynumber: 5.2 Consensus size: 15
2314483 CCAATATCTC
2314493 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
2314508 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
2314523 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
2314538 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
*
2314553 GATACTCATATCTTT
1 GATACCCATATCTTT
2314568 GAT
1 GAT
2314571 TTTCCATAAA
Statistics
Matches: 44, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
14 7 0.16
15 29 0.66
16 8 0.18
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:2318421 original size:19 final size:19
Alignment explanation
Indices: 2318381--2318424 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2318371 TAATGAAACT
* *
2318381 ATAATTGATAATTAACAAA
1 ATAATTGATAACTAAAAAA
2318400 ATAATTGA-AACTAAAAAGA
1 ATAATTGATAACTAAAAA-A
2318419 ATAATT
1 ATAATT
2318425 ATTATAGAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (19 bp):
ATAATTGATAACTAAAAAA
Found at i:2320815 original size:10 final size:10
Alignment explanation
Indices: 2320796--2320845 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
2320786 TTAAATTCTA
2320796 AAAGATAAAT
1 AAAGATAAAT
2320806 ACAA-ATAAAT
1 A-AAGATAAAT
*
2320816 AAAGATAATT
1 AAAGATAAAT
2320826 AAAGATAAAT
1 AAAGATAAAT
*
2320836 AAAAATAAAT
1 AAAGATAAAT
2320846 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:2321190 original size:16 final size:16
Alignment explanation
Indices: 2321169--2321203 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2321159 TGAAGTTATA
*
2321169 AATTACAAAGAATCGT
1 AATTACAAAGAATCAT
2321185 AATTACAAAGAATCAT
1 AATTACAAAGAATCAT
2321201 AAT
1 AAT
2321204 ATGAAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTACAAAGAATCAT
Found at i:2321218 original size:12 final size:12
Alignment explanation
Indices: 2321201--2321251 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
2321191 AAAGAATCAT
2321201 AATATGAAGTTA
1 AATATGAAGTTA
2321213 AATATGAAGTTA
1 AATATGAAGTTA
* **
2321225 TATATGTCG-T-
1 AATATGAAGTTA
2321235 AATATGAAGTTA
1 AATATGAAGTTA
2321247 AATAT
1 AATAT
2321252 CTTTCCATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 6 0.19
11 2 0.06
12 23 0.74
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (12 bp):
AATATGAAGTTA
Found at i:2323133 original size:3 final size:3
Alignment explanation
Indices: 2323108--2323156 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
2323098 AAAAAATGAT
** * *
2323108 TTA TT- TTA TTA TCG TTA TCA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2323155 TT
1 TT
2323157 TCGTCTTTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2323136 original size:18 final size:18
Alignment explanation
Indices: 2323113--2323155 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2323103 ATGATTTATT
*
2323113 TTATTATCGTTATCATTA
1 TTATTATCATTATCATTA
*
2323131 TTATTATTATTATCATTA
1 TTATTATCATTATCATTA
2323149 TTATTAT
1 TTATTAT
2323156 TTCGTCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTATCATTATCATTA
Found at i:2328644 original size:13 final size:13
Alignment explanation
Indices: 2328626--2328678 Score: 78
Period size: 13 Copynumber: 4.4 Consensus size: 13
2328616 TCTTCACTCC
2328626 AACCACCCCACTA
1 AACCACCCCACTA
2328639 AACCA-CCC-C--
1 AACCACCCCACTA
2328648 AACCACCCCACTA
1 AACCACCCCACTA
2328661 AACCACCCCACTA
1 AACCACCCCACTA
2328674 AACCA
1 AACCA
2328679 TCCTAACCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.14
10 3 0.08
11 2 0.06
12 3 0.08
13 23 0.64
ACGTcount: A:0.40, C:0.55, G:0.00, T:0.06
Consensus pattern (13 bp):
AACCACCCCACTA
Found at i:2328652 original size:22 final size:22
Alignment explanation
Indices: 2328624--2328670 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2328614 TATCTTCACT
2328624 CCAACCACCCCACTAAACCACC
1 CCAACCACCCCACTAAACCACC
2328646 CCAACCACCCCACTAAACCACC
1 CCAACCACCCCACTAAACCACC
2328668 CCA
1 CCA
2328671 CTAAACCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.60, G:0.00, T:0.04
Consensus pattern (22 bp):
CCAACCACCCCACTAAACCACC
Found at i:2328672 original size:35 final size:35
Alignment explanation
Indices: 2328626--2328694 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
2328616 TCTTCACTCC
2328626 AACCACCCCACTAAACCACCCCAACCACCCCACTA
1 AACCACCCCACTAAACCACCCCAACCACCCCACTA
* * *
2328661 AACCACCCCACTAAACCATCCTAACCACTCCACT
1 AACCACCCCACTAAACCACCCCAACCACCCCACT
2328695 TGCCTACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.54, G:0.00, T:0.10
Consensus pattern (35 bp):
AACCACCCCACTAAACCACCCCAACCACCCCACTA
Found at i:2329096 original size:19 final size:18
Alignment explanation
Indices: 2329059--2329100 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
2329049 GGAGAGAGTG
*
2329059 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
2329077 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
2329096 TTATT
1 TTATT
2329101 ACTAATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:2329159 original size:33 final size:39
Alignment explanation
Indices: 2329085--2329166 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 39
2329075 TATTATTTTC
*
2329085 TATTATTATTATTATTACTAATACCACTATTATCATCAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
*
2329124 TATTACTATTA-TATTA-TAATA-C-CT-TT-TCATTAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
2329157 TATTACTATT
1 TATTACTATT
2329167 GTGTTTTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 16 0.39
34 2 0.05
35 2 0.05
36 1 0.02
37 5 0.12
38 5 0.12
39 10 0.24
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTACTATTATTATTACTAATACCACTATTATCATCAT
Found at i:2329196 original size:23 final size:23
Alignment explanation
Indices: 2329112--2329197 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
2329102 CTAATACCAC
* *
2329112 TATTATCATCATTATTACTATTA-
1 TATTATTAT-ATTTTTACTATTAT
* * *
2329135 TATTATAATACCTTTTCATTATTAT
1 TATTATTATA--TTTTTACTATTAT
* * *
2329160 TACTATTGTGTTTTTACTATTAT
1 TATTATTATATTTTTACTATTAT
2329183 TATTATTATATTTTT
1 TATTATTATATTTTT
2329198 TTTTTGTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
22 1 0.02
23 31 0.66
24 9 0.19
25 6 0.13
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTATTATATTTTTACTATTAT
Found at i:2366986 original size:69 final size:69
Alignment explanation
Indices: 2366901--2367037 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 69
2366891 TTTGTTGGTT
*
2366901 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
2366966 AAAC
66 AAAC
* * * * * * *
2366970 TGTTCTGGCAGTTGTTTTGATTGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAATATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
2367035 AAA
66 AAA
2367038 ATGGAAATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (69 bp):
TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
AAAC
Found at i:2368231 original size:37 final size:37
Alignment explanation
Indices: 2368184--2368272 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
2368174 ATCATAAATA
* *
2368184 AATAATCTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
2368221 ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
2368258 AATGAACTAATCAAT
1 AATAAACTAATCAAT
2368273 ATATTTATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.36
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:2368352 original size:33 final size:33
Alignment explanation
Indices: 2368315--2368390 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
2368305 TTAAAACTTG
*
2368315 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
2368348 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
2368381 AATTATACAT
1 AATTATACAT
2368391 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:2381643 original size:42 final size:42
Alignment explanation
Indices: 2381531--2381628 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 42
2381521 NNNNNNNNNC
*
2381531 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAATAG
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAAGAG
* * *
2381573 GTGTAAGACTATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAAGAG
2381615 GTGTAAGACCATAG
1 GTGTAAGACCATAG
2381629 TTGAACTGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATATATGAAGAG
Found at i:2386165 original size:7 final size:7
Alignment explanation
Indices: 2386164--2386190 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2386154 AAAAAAAGAA
2386164 AAAAAAT
1 AAAAAAT
2386171 AAAAAAT
1 AAAAAAT
2386178 AAAAAAT
1 AAAAAAT
2386185 AAAAAA
1 AAAAAA
2386191 CAGCAGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:2386174 original size:14 final size:14
Alignment explanation
Indices: 2386147--2386188 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
2386137 AATGAATTAG
2386147 GAAAAAGAAA-AAAA
1 GAAAAA-AAATAAAA
2386161 GAAAAAAAATAAAA
1 GAAAAAAAATAAAA
2386175 -AATAAAAAATAAAA
1 GAA-AAAAAATAAAA
2386189 AACAGCAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAAAAAATAAAA
Found at i:2386890 original size:18 final size:18
Alignment explanation
Indices: 2386856--2386890 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2386846 AATTTTTGAC
*
2386856 TTTTCGCGTTTTCAAAAG
1 TTTTCGCGTTTTAAAAAG
*
2386874 TTTTCGTGTTTTAAAAA
1 TTTTCGCGTTTTAAAAA
2386891 AAAAATTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTTCGCGTTTTAAAAAG
Found at i:2386916 original size:23 final size:23
Alignment explanation
Indices: 2386875--2386964 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
2386865 TTTCAAAAGT
2386875 TTTCGTGTTTTAAAA--AAAAAA
1 TTTCGTGTTTTAAAATGAAAAAA
* * *
2386896 TTCCGCGTTTTAAAATGAAAAAT
1 TTTCGTGTTTTAAAATGAAAAAA
* *
2386919 TTTCGTGTTTTCAAATGAAAAAT
1 TTTCGTGTTTTAAAATGAAAAAA
2386942 TTTCGTGTTTTAAAATGAAAAAA
1 TTTCGTGTTTTAAAATGAAAAAA
2386965 AAACAAAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
21 13 0.22
23 46 0.78
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (23 bp):
TTTCGTGTTTTAAAATGAAAAAA
Found at i:2387100 original size:20 final size:19
Alignment explanation
Indices: 2387073--2387115 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2387063 GTATTTTATC
2387073 AAAAAAA-TTTATGTTTTCA
1 AAAAAAATTTTATGTTTT-A
*
2387092 AAAACAAATTTTCTGTTTTA
1 AAAA-AAATTTTATGTTTTA
2387112 AAAA
1 AAAA
2387116 TTTTCGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAAAAATTTTATGTTTTA
Found at i:2387115 original size:37 final size:37
Alignment explanation
Indices: 2387075--2387154 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
2387065 ATTTTATCAA
*
2387075 AAAAATTTAT-GT-TTTCAAAAACAAATTTTC-TGTTTT
1 AAAAATTT-TCGTGTTTCAAAAACAAA-ATTCGTGTTTT
*
2387111 AAAAATTTTCGTGTTTCAAAAATAAAATTCGTGTTTT
1 AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
2387148 CAAAAAT
1 -AAAAAT
2387155 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 1 0.03
36 13 0.34
37 18 0.47
38 6 0.16
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (37 bp):
AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
Found at i:2387118 original size:16 final size:17
Alignment explanation
Indices: 2387097--2387133 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2387087 TTTCAAAAAC
*
2387097 AAATTTTC-TGTTTTAA
1 AAATTTTCGTGTTTCAA
2387113 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
2387130 AAAT
1 AAAT
2387134 AAAATTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:2387143 original size:20 final size:21
Alignment explanation
Indices: 2387118--2387158 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2387108 TTTAAAAATT
2387118 TTCGTG-TTTCAAAAATAAAA
1 TTCGTGTTTTCAAAAATAAAA
2387138 TTCGTGTTTTCAAAAATAAAA
1 TTCGTGTTTTCAAAAATAAAA
2387159 ATAAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
TTCGTGTTTTCAAAAATAAAA
Found at i:2387183 original size:15 final size:16
Alignment explanation
Indices: 2387163--2387193 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2387153 ATAAAAATAA
2387163 AAAATC-TCATGTTTT
1 AAAATCTTCATGTTTT
2387178 AAAATCTTCATGTTTT
1 AAAATCTTCATGTTTT
2387194 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (16 bp):
AAAATCTTCATGTTTT
Found at i:2387249 original size:16 final size:15
Alignment explanation
Indices: 2387201--2387254 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
2387191 TTTTTTAAAA
2387201 AAAAGTTTTGTGTTTCT
1 AAAA-TTTTGTGTTT-T
*
2387218 AAAATTCTTGTATTTT
1 AAAATT-TTGTGTTTT
2387234 AAAATTTTCGTGTTTT
1 AAAATTTT-GTGTTTT
2387250 CAAAA
1 -AAAA
2387255 AAGGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 15 0.47
17 15 0.47
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (15 bp):
AAAATTTTGTGTTTT
Found at i:2394624 original size:1 final size:1
Alignment explanation
Indices: 2394620--2394725 Score: 68
Period size: 1 Copynumber: 106.0 Consensus size: 1
2394610 AAAAGTAAAC
* * * * * * * * *
2394620 AAAAAACAAAAAAAAACAACAAAAAAAACAACAAAAAAACAAAACAAAAAAACAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
2394685 CAAAACAAAAAAAGAAAAAACAAAGAAAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2394726 TCAAGATGAA
Statistics
Matches: 73, Mismatches: 32, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:2394625 original size:13 final size:13
Alignment explanation
Indices: 2394622--2394702 Score: 121
Period size: 13 Copynumber: 6.3 Consensus size: 13
2394612 AAGTAAACAA
2394622 AAAACAAAAAAA-
1 AAAACAAAAAAAC
2394634 AACAACAAAAAAA-
1 AA-AACAAAAAAAC
*
2394647 ACAACAAAAAAAC
1 AAAACAAAAAAAC
2394660 AAAACAAAAAAAC
1 AAAACAAAAAAAC
2394673 AAAACAAAAAAAC
1 AAAACAAAAAAAC
*
2394686 AAAACAAAAAAAG
1 AAAACAAAAAAAC
2394699 AAAA
1 AAAA
2394703 AACAAAGAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.19
13 52 0.81
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAC
Found at i:2394657 original size:33 final size:34
Alignment explanation
Indices: 2394616--2394707 Score: 118
Period size: 33 Copynumber: 2.7 Consensus size: 34
2394606 GAAAAAAAGT
2394616 AAAC-AAAAAACAAAAAAAAACAACAAAA-AAAA
1 AAACAAAAAAACAAAAAAAAACAACAAAACAAAA
*
2394648 CAACAAAAAAACAAAACAAAAA-AACAAAACAAAA
1 AAACAAAAAAACAAAA-AAAAACAACAAAACAAAA
*
2394682 AAACAAAACAAAAAAAGAAAAAACAA
1 AAACAAAA-AAACAAA-AAAAAACAA
2394708 AGAAAAGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
32 3 0.06
33 18 0.35
34 16 0.31
35 11 0.22
36 3 0.06
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (34 bp):
AAACAAAAAAACAAAAAAAAACAACAAAACAAAA
Found at i:2394674 original size:46 final size:44
Alignment explanation
Indices: 2394607--2394708 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 44
2394597 ATTATGCCTG
**
2394607 AAAAAAAGTAAACAAAAAACAAAA-AAAAACAACAAAA-AAAACAA
1 AAAAAAACAAAACAAAAAACAAAACAAAAA-AACAAAACAAAA-AA
2394651 CAAAAAAACAAAACAAAAAAACAAAACAAAAAAACAAAACAAAAAA
1 -AAAAAAACAAAAC-AAAAAACAAAACAAAAAAACAAAACAAAAAA
2394697 AGAAAAAACAAA
1 A-AAAAAACAAA
2394709 GAAAAGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
45 12 0.24
46 30 0.59
47 9 0.18
ACGTcount: A:0.84, C:0.13, G:0.02, T:0.01
Consensus pattern (44 bp):
AAAAAAACAAAACAAAAAACAAAACAAAAAAACAAAACAAAAAA
Found at i:2394679 original size:38 final size:39
Alignment explanation
Indices: 2394622--2394702 Score: 121
Period size: 38 Copynumber: 2.1 Consensus size: 39
2394612 AAGTAAACAA
*
2394622 AAAACAAAAAAAAACAACAAAAAAA-ACAACAAAAAAAC
1 AAAACAAAAAAAAACAACAAAAAAACAAAACAAAAAAAC
*
2394660 AAAACAAAAAAACAA-AACAAAAAAACAAAACAAAAAAAG
1 AAAACAAAAAAA-AACAACAAAAAAACAAAACAAAAAAAC
2394699 AAAA
1 AAAA
2394703 AACAAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
38 22 0.56
39 17 0.44
ACGTcount: A:0.85, C:0.14, G:0.01, T:0.00
Consensus pattern (39 bp):
AAAACAAAAAAAAACAACAAAAAAACAAAACAAAAAAAC
Found at i:2394702 original size:26 final size:25
Alignment explanation
Indices: 2394620--2394725 Score: 126
Period size: 25 Copynumber: 4.2 Consensus size: 25
2394610 AAAAGTAAAC
2394620 AAAAAACAAAAAAA-AACAACAAAAA
1 AAAAAACAAAAAAACAA-AACAAAAA
*
2394645 AAACAACAAAAAAACAAAACAAAAA
1 AAAAAACAAAAAAACAAAACAAAAA
2394670 AACAAAACAAAAAAACAAAACAAAAA
1 AA-AAAACAAAAAAACAAAACAAAAA
* * * *
2394696 AAGAAA-AAACAAAGAAAAGAAAAA
1 AAAAAACAAAAAAACAAAACAAAAA
*
2394720 GAAAAA
1 AAAAAA
2394726 TCAAGATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
24 19 0.27
25 26 0.37
26 26 0.37
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (25 bp):
AAAAAACAAAAAAACAAAACAAAAA
Found at i:2395705 original size:76 final size:77
Alignment explanation
Indices: 2395580--2397519 Score: 2513
Period size: 76 Copynumber: 24.7 Consensus size: 77
2395570 TCAAGAAATA
* *
2395580 TTTTTAAAATTCTGTTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTGCTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
2395645 CACGCTGAGGTA-
65 CACGCTGAGGTAT
*
2395657 TTTTTAAATTTATGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
2395722 ACGCTGAGGTATTT
66 ACGCTGAGGTA--T
** *
2395736 TTTTTAAATTTCTATTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCTGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
2395801 ACGTTGAGGTAT
66 ACGCTGAGGTAT
*
2395813 TTTTTTAA-TTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
2395877 ACGCTGAAGTA-
66 ACGCTGAGGTAT
*
2395888 TTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
2395953 ACGCTGAAGTA-
66 ACGCTGAGGTAT
*
2395964 TTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
2396029 ACGCTGAGGTATTTTT
66 ACGCTGAGGTA----T
* *
2396045 TTTTTAAATTTATGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTT
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
2396110 ACGCTGAGGTAT
66 ACGCTGAGGTAT
2396122 TTTTTAATTTAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 TTTTT-A---AATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
2396186 GGTCACGCTGAGGTATTT
62 GGTCACGCTGAGGTA--T
** *
2396204 TTTTTAAATTTCTATTTTTTTCAAAAAAGCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
2396269 ACGCTGAGGTATT
66 ACGCTGAGGTA-T
* *
2396282 TTTTTAATTTAATTTCTG-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTAAGCATCG
1 TTTTT-A---AATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
2396346 GGTCACGCTGAGGTA-
62 GGTCACGCTGAGGTAT
*
2396361 TTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
* *
2396426 ATGCTAAGGTATTT
66 ACGCTGAGGTA--T
2396440 TTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTGC-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* *
2396505 CATGCTAAGGTATTT
65 CACGCTGAGGTA--T
*
2396520 TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTGC-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
2396585 TACGCTGAGGTATT
65 CACGCTGAGGTA-T
*
2396599 TTTTTAATTTAATTTCTG-TTTTTTCAAAAACTCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 TTTTT-A---AATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
2396663 GGTCACGCTGAGGTA-
62 GGTCACGCTGAGGTAT
*
2396678 TTTTTAAATTTCTGCTTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
2396742 ACGCTGAGGTA-
66 ACGCTGAGGTAT
2396753 TTTTTAAATTTCTGCTTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
2396817 ACGCTGAGGTATTTT
66 ACGCTGAGGTA---T
2396832 TTTTTAAATTTCTGCTTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TTTTTAAATTTCTGC---TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
*
2396897 GTCACACTGAGGTA-
63 GTCACGCTGAGGTAT
*
2396911 TTTTTAAATTTCTGCTTTTTTCAAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGAG
1 TTTTTAAATTTCTGCTTTTTTC--AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
2396976 TCACGCTGAGGTA-
64 TCACGCTGAGGTAT
2396989 TTTTTAAATTTCTGCTTTTTTCAAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 TTTTTAAATTTCTGCTTTTTTC--AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
2397054 TCACGCTGAGGTA-
64 TCACGCTGAGGTAT
* *
2397067 TTTTT-AATTTATGTCTTTTTT---TAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTAAATTTCTG-CTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
2397128 TCACGCTGAGGTA-
64 TCACGCTGAGGTAT
* * *
2397141 TTTTT-AATTTCTGTTTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTAAATTTCTG-CTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
*
2397204 TTACGCTGAGGTATTATTATT
64 TCACGCTGAGG------TA-T
* * * * *
2397225 ATATTTTAAATTTCTG-TTTTTCATAAAAAAAACTCAACTCATATTGCGAGAGGTGAGTTGATCT
1 -T-TTTTAAATTTCTGCTTTTT--T-CAAAAAA-TCAACTCATAATAC-AGAGGTGAGTTGAGCC
** ** *
2397289 TCGGACCATACCGAGGTATT
59 TCGGGTCACGCTGAGGTA-T
* * * * *
2397309 TCTTTTAAATTTCT--ATTTTTC-AAAAATCAACTCATACTGCGAGGGGTGAGTTGATCCTCGGG
1 T-TTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
* *
2397371 TCGTAGGCCGAGGTATT
64 TC--ACGCTGAGGTA-T
* * * *
2397388 TCTTTTCAATTTAT--ATTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGT
1 T-TTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
2397450 CATGCTGAGGTATT
65 CACGCTGAGGTA-T
* *
2397464 TCTTTTAAATTTCTG--TTTTTC-AAAAATCAACTCATATTTCGAGAGGTGAGTTGAGC
1 T-TTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGC
2397520 TTTGAGTCGC
Statistics
Matches: 1710, Mismatches: 89, Indels: 128
0.89 0.05 0.07
Matches are distributed among these distances:
73 17 0.01
74 53 0.03
75 148 0.09
76 420 0.25
77 87 0.05
78 183 0.11
79 240 0.14
80 199 0.12
81 198 0.12
82 25 0.01
83 73 0.04
84 4 0.00
85 6 0.00
86 4 0.00
87 9 0.01
89 5 0.00
90 39 0.02
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (77 bp):
TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGGTAT
Found at i:2396283 original size:316 final size:309
Alignment explanation
Indices: 2395580--2397519 Score: 2524
Period size: 316 Copynumber: 6.2 Consensus size: 309
2395570 TCAAGAAATA
* *
2395580 TTTTTAAAATTCTGTTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTATTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
2395645 CACGCTGAGGTA-TTTTTAAATTTATGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGT
65 CACGCTGAGGTATTTTTTAAATTTCT-CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGT
**
2395709 TGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTCTATTTTTTTCAAAAAATCAACTCATA
129 TGAGCCTCGGGTCACGCTGAGGTA---TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATA
* *
2395774 ATACAGAGGTGAGTTGAGCCTCTGGTCACGTTGAGGTA-TTTTTTTAA-TTCTGCTTTTTTCAAA
191 ATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAA
*
2395837 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTA---
256 AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
2395888 TTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTATTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
2395953 ACGCTGAAGTA-TTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTT
66 ACGCTGAGGTATTTTTTAAATTTCT-CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTT
*
2396017 GAGCCTCGGGTCACGCTGAGGTATTTTTTTTTTAAATTTATGCTTTTTTCAAAAAATCAACTCAT
130 GAGCCTCGGGTCACGCTGAGGTA-----TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCAT
*
2396082 AATACAGAGGTGAGTTGAGCCTCGGGTTACGCTGAGGTATTTTTTAATTTAATTTCTG-TTTTTT
190 AATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTTT--TTTAATTTCTGCTTTTTT
2396146 CAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
252 CAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
2396204 TTTTTAAATTTCTATTTTTTTCAAAAAAGCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TTTTTAAATTTCTATTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
2396269 ACGCTGAGGTATTTTTTTAATTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTG
66 ACGCTGAGGTA-TTTTTT-A---AATTTCTCTTTTTTCAAAAAATCAACTCATAATACAGAGGTG
* * *
2396334 AGTTAAGCATCGGGTCACGCTGAGGTATTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATA
126 AGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATA
* *
2396399 ATACAGAGGTGAGTTGAGCCTCGGGTCATGCTAAGGTATTTTTTTTAAATTTCTGCTTTTTTTCA
191 ATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTT-AATTTCTGC-TTTTTTCA
* *
2396464 AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCTAAGGTATTT
254 AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
2396520 TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTC-TATTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* * *
2396585 TACGCTGAGGTATTTTTTTAATTTAATTTCTGTTTTTTCAAAAACTCAACTCATAATACAGAGGT
65 CACGCTGAGGTA-TTTTTT-A---AATTTCTCTTTTTTCAAAAAATCAACTCATAATACAGAGGT
2396650 GAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTT-AAAAAATCAACTCAT
125 GAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCAT
* *
2396714 AATACAGAGGTGAGTTGAGTCTCGGGTCACGCTGAGGTA--TTTTTAAATTTCTGCTTTTTT-AA
190 AATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAA
2396776 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
255 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTT
*
2396832 TTTTTAAATTTCTGCTTTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TTTTTAAA-TT-T-CTATTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
*
2396897 GTCACACTGAGGTA-TTTTTAAATTTCTGCTTTTTTCAAAAAAAATCAACTCATAATACAGAGGT
63 GTCACGCTGAGGTATTTTTTAAATTTCT-CTTTTTTC--AAAAAATCAACTCATAATACAGAGGT
*
2396961 GAGTTGAGCCTCGAGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTCAAAAAAAATCAACTC
125 GAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTC--AAAAAATCAACTC
*
2397026 ATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA---TTTTTAATTTATGTCTTTTTT
188 ATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTG-CTTTTTT
*
2397088 ---TAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA---
252 CAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
* * *
2397141 TTTTT-AATTTCTGTTTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TTTTTAAATTTCT-ATTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
* * * *
2397204 TTACGCTGAGGTATTATTATTATATTTTAAATTTCTGTTTTTCATAAAAAAAACTCAACTCATAT
64 TCACGCTGAGG------TA-T-T-TTTTAAATTTCTCTTTTT--T-CAAAAAA-TCAACTCATAA
* * * ** ** * *
2397269 TGCGAGAGGTGAGTTGATCTTCGGACCATACCGAGGTATTTCTTTTAAATTTCT--ATTTTTC-A
116 TAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTTAAATTTCTGCTTTTTTCAA
* * * * * * *
2397331 AAAATCAACTCATACTGCGAGGGGTGAGTTGATCCTCGGGTCGTAGGCCGAGGTATTTCTTTTCA
177 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC--ACGCTGAGGTATTT-TTTTTA
* * * *
2397396 ATTTAT--ATTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCATGCTGA
238 ATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGA
2397458 GGTATTT
303 GGTATTT
* * * *
2397465 CTTTTAAATTTC--TGTTTTTC-AAAAATCAACTCATATTTCGAGAGGTGAGTTGAGC
1 TTTTTAAATTTCTATTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGC
2397520 TTTGAGTCGC
Statistics
Matches: 1487, Mismatches: 80, Indels: 116
0.88 0.05 0.07
Matches are distributed among these distances:
305 19 0.01
306 40 0.03
307 129 0.09
308 28 0.02
309 85 0.06
311 130 0.09
312 41 0.03
313 124 0.08
314 140 0.09
315 12 0.01
316 304 0.20
317 193 0.13
318 31 0.02
319 16 0.01
320 6 0.00
321 103 0.07
322 65 0.04
323 11 0.01
324 4 0.00
325 6 0.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (309 bp):
TTTTTAAATTTCTATTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGGTATTTTTTAAATTTCTCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTG
AGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACA
GAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAATTTCTGCTTTTTTCAAAAAATC
AACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
Found at i:2396542 original size:236 final size:233
Alignment explanation
Indices: 2395580--2397519 Score: 2443
Period size: 236 Copynumber: 8.2 Consensus size: 233
2395570 TCAAGAAATA
* *
2395580 TTTTTAAAATTC-TGTTTTTTTCAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 TTTTTAAATTTCTTCTTTTTTTC-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
* *
2395644 TCACGCTGAGGTA-TTTTTAAATTTATGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAG
65 TCACGCTGAGGTATTTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAG
*
2395708 TTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTCT-ATTTTTTTCAAAAAATCAACTCA
130 TTGAGCCTCGGGTCACGCTGAGGTA---TTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCA
* *
2395772 TAATACAGAGGTGAGTTGAGCCTCTGGTCACGTTGAGGTATT
192 TAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
2395814 TTTTT-AA-TTCTGC-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
2395876 CACGCTGAAGTA-TTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGT
66 CACGCTGAGGTATTTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGT
* *
2395940 TGAGCCTCGGGTCACGCTGAAGTATTTTTAAATTTCTAC-TTTTTTCAAAAAATCAACTCATAAT
131 TGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCATAAT
2396004 ACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
196 ACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA---TT
* *
2396045 TTTTTAAATTTATGC-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* *
2396109 TACGCTGAGGTATTTTTTAATTTAATTTCT-GTTTTTTCAAAAAATCAACTCATAATACAGAGGT
66 CACGCTGAGGTATTTTTT-A---AATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGT
* *
2396173 GAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTTAAATTTCT-ATTTTTTTCAAAAAAGCAAC
127 GAGTTGAGCCTCGGGTCACGCTGAGGTA---TTTTTAAATTTCTGCTTTTTTTCAAAAAATCAAC
2396237 TCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
189 TCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
* * *
2396282 TTTTT-AATTTAATTTCTGTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTAAGCATCG
1 TTTTTAAATTT--CTTCT-TTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
2396346 GGTCACGCTGAGGTA-TTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTG
63 GGTCACGCTGAGGTATTTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTG
* *
2396410 AGTTGAGCCTCGGGTCATGCTAAGGTATTTTTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACT
128 AGTTGAGCCTCGGGTCACGCTGAGGTA---TTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACT
* *
2396475 CATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCTAAGGTATTT
190 CATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TT
2396520 TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
* * *
2396585 TACGCTGAGGTATTTTTTTAATTTAATTTCT-GTTTTTTCAAAAACTCAACTCATAATACAGAGG
66 CACGCTGAGGTA-TTTTTT-A---AATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGG
2396649 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGC-TTTTTT-AAAAAATCAACTC
126 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTC
*
2396712 ATAATACAGAGGTGAGTTGAGTCTCGGGTCACGCTGAGGTA--
191 ATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
2396753 TTTTTAAATTTCTGC-TTTTTT-AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
2396816 CACGCTGAGGTATTTTTTTTTAAATTTCTGCTTTTTTTTTCAAAAAATCAACTCATAATACAGAG
66 CACGCTGAGGTA---TTTTTTAAATTTCTAC---TTTTTTCAAAAAATCAACTCATAATACAGAG
*
2396881 GTGAGTTGAGCCTCGGGTCACACTGAGGTATTTTTAAATTTCTGC-TTTTTTCAAAAAAAATCAA
125 GTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTC--AAAAAATCAA
*
2396945 CTCATAATACAGAGGTGAGTTGAGCCTCGAGTCACGCTGAGGTA--
188 CTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
2396989 TTTTTAAATTTCTGC-TTTTTTCAAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TTTTTAAATTTCTTCTTTTTTTC--AAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
* * *
2397053 GTCACGCTGAGGTA-TTTTT-AATTTATGTCTTTTTT---TAAATCAACTCATAATACGAGAGGT
64 GTCACGCTGAGGTATTTTTTAAATTTCT-ACTTTTTTCAAAAAATCAACTCATAATAC-AGAGGT
*
2397113 GAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT-AATTTCTGTTTTTTTTC-AAAAATCAACTCA
127 GAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCA
* * *
2397176 TATTGCGAGAGGTGAGTTGAGCCTCGGGTTACGCTGAGGTATT
192 TAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
* * * * * *
2397219 ATTATTATATTTTAAATTTCTGTTTTTCATAAAAAAAACTCAACTCATATTGCGAGAGGTGAGTT
1 -TTTTTA-AATTT---CTTCT-TTTTT--T-CAAAAAA-TCAACTCATAATAC-AGAGGTGAGTT
* * ** ** * *
2397284 GATCTTCGGACCATACCGAGGTATTTCTTTTAAATTTCTA--TTTTTC-AAAAATCAACTCATAC
55 GAGCCTCGGGTCACGCTGAGGTA-TT-TTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAA
* * * * * * * *
2397346 TGCGAGGGGTGAGTTGATCCTCGGGTCGTAGGCCGAGGTATTTCTTTTCAA-TT-T-ATATTTTT
118 TAC-AGAGGTGAGTTGAGCCTCGGGTC--ACGCTGAGGTA--T-TTTTAAATTTCTGCTTTTTTT
* *
2397408 C-AAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTCGGGTCATGCTGAGGTATT
177 CAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
* * *
2397464 TCTTTTAAA--T-TTCTGTTTTTC-AAAAATCAACTCATATTTCGAGAGGTGAGTTGAGC
1 T-TTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGC
2397520 TTTGAGTCGC
Statistics
Matches: 1542, Mismatches: 91, Indels: 148
0.87 0.05 0.08
Matches are distributed among these distances:
227 17 0.01
228 104 0.07
229 32 0.02
230 45 0.03
231 191 0.12
232 57 0.04
233 172 0.11
234 16 0.01
235 17 0.01
236 262 0.17
237 145 0.09
238 47 0.03
239 78 0.05
240 158 0.10
241 63 0.04
242 9 0.01
243 41 0.03
244 8 0.01
245 46 0.03
246 24 0.02
247 2 0.00
248 6 0.00
249 2 0.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (233 bp):
TTTTTAAATTTCTTCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGGTATTTTTTAAATTTCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGT
TGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCATAAT
ACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
Found at i:2397761 original size:30 final size:29
Alignment explanation
Indices: 2397726--2397866 Score: 110
Period size: 30 Copynumber: 4.8 Consensus size: 29
2397716 TGACCCCTGT
* *
2397726 ACTTTTCGAAATTTACATTTTGACCATAA
1 ACTTTTCAAAATTTACATTTTGACCACAA
*
2397755 ACCTTTTTAAAATTTACATTTTGACCACAA
1 A-CTTTTCAAAATTTACATTTTGACCACAA
**
2397785 ACTTTTCTAAAA-TTACATTTCAACC-CTTAA
1 ACTTTTC-AAAATTTACATTTTGACCAC--AA
* * *
2397815 ACTTTTTCAAAATTT-CACTTTAACCCCTAA
1 AC-TTTTCAAAATTTACATTTTGACCAC-AA
*
2397845 AC-TTTCAAGAAATTACATTTTG
1 ACTTTTCAA-AATTTACATTTTG
2397867 GCCCATATTT
Statistics
Matches: 92, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
28 7 0.08
29 21 0.23
30 56 0.61
31 8 0.09
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (29 bp):
ACTTTTCAAAATTTACATTTTGACCACAA
Found at i:2397804 original size:59 final size:60
Alignment explanation
Indices: 2397726--2397873 Score: 151
Period size: 59 Copynumber: 2.5 Consensus size: 60
2397716 TGACCCCTGT
* * * *
2397726 ACTTTTCGAAATTTACATTTTGA-CCATAAACCTTTTT-AAAATTTACATTTTGACCAC-AA
1 ACTTTTCAAAAATTACATTTTGACCCATAAA-CTTTTTCAAAATTT-CACTTTAACCACTAA
* ** * *
2397785 ACTTTTCTAAAATTACATTTCAACCCTTAAACTTTTTCAAAATTTCACTTTAACCCCTAA
1 ACTTTTCAAAAATTACATTTTGACCCATAAACTTTTTCAAAATTTCACTTTAACCACTAA
*
2397845 AC-TTTCAAGAAATTACATTTTGGCCCATA
1 ACTTTTCAA-AAATTACATTTTGACCCATA
2397874 TTTTTGCTAA
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
59 39 0.54
60 33 0.46
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
ACTTTTCAAAAATTACATTTTGACCCATAAACTTTTTCAAAATTTCACTTTAACCACTAA
Found at i:2398270 original size:10 final size:10
Alignment explanation
Indices: 2398251--2398284 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2398241 CAAGCAAAGC
*
2398251 AACAAGCAAA
1 AACAAACAAA
2398261 AACAAACAAA
1 AACAAACAAA
*
2398271 AAGAAACAAA
1 AACAAACAAA
2398281 AACA
1 AACA
2398285 GCAACCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (10 bp):
AACAAACAAA
Found at i:2398302 original size:15 final size:15
Alignment explanation
Indices: 2398278--2398310 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2398268 AAAAAGAAAC
2398278 AAAAACAGCAACCAA
1 AAAAACAGCAACCAA
*
2398293 AAAAATAGCAACCAA
1 AAAAACAGCAACCAA
2398308 AAA
1 AAA
2398311 GAAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.21, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAACAGCAACCAA
Found at i:2398322 original size:13 final size:12
Alignment explanation
Indices: 2398306--2398353 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
2398296 AATAGCAACC
2398306 AAAAAGAAAGAAA
1 AAAAAGAAA-AAA
2398319 AAAAAGAAAAAA
1 AAAAAGAAAAAA
* *
2398331 AATAA-AAAATA
1 AAAAAGAAAAAA
*
2398342 AAAAATAAAAAA
1 AAAAAGAAAAAA
2398354 CAGCAGGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.30
12 12 0.40
13 9 0.30
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:2398337 original size:6 final size:7
Alignment explanation
Indices: 2398327--2398353 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2398317 AAAAAAAGAA
2398327 AAAAAAT
1 AAAAAAT
2398334 AAAAAAT
1 AAAAAAT
2398341 AAAAAAT
1 AAAAAAT
2398348 AAAAAA
1 AAAAAA
2398354 CAGCAGGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:2398353 original size:9 final size:9
Alignment explanation
Indices: 2398306--2398339 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
2398296 AATAGCAACC
2398306 AAAAAGAAAG
1 AAAAA-AAAG
2398316 AAAAAAAAG
1 AAAAAAAAG
*
2398325 AAAAAAAAT
1 AAAAAAAAG
2398334 AAAAAA
1 AAAAAA
2398340 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:2399053 original size:18 final size:18
Alignment explanation
Indices: 2399019--2399053 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2399009 AATTTTTGAC
*
2399019 TTTTCGCGTTTTCAAAAG
1 TTTTCGCGTTTTAAAAAG
*
2399037 TTTTCGTGTTTTAAAAA
1 TTTTCGCGTTTTAAAAA
2399054 AAAAATTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTTCGCGTTTTAAAAAG
Found at i:2399079 original size:23 final size:23
Alignment explanation
Indices: 2399038--2399127 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
2399028 TTTCAAAAGT
2399038 TTTCGTGTTTTAAAA--AAAAAA
1 TTTCGTGTTTTAAAATGAAAAAA
* * *
2399059 TTCCGCGTTTTAAAATGAAAAAT
1 TTTCGTGTTTTAAAATGAAAAAA
* * *
2399082 TTTCATGTTTTCAAATGAAAAAT
1 TTTCGTGTTTTAAAATGAAAAAA
2399105 TTTCGTGTTTTAAAATGAAAAAA
1 TTTCGTGTTTTAAAATGAAAAAA
2399128 AAACAAAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.23
23 44 0.77
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (23 bp):
TTTCGTGTTTTAAAATGAAAAAA
Found at i:2399262 original size:20 final size:19
Alignment explanation
Indices: 2399235--2399277 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2399225 GTATTTTATC
2399235 AAAAAAA-TTTATGTTTTCA
1 AAAAAAATTTTATGTTTT-A
*
2399254 AAAACAAATTTTCTGTTTTA
1 AAAA-AAATTTTATGTTTTA
2399274 AAAA
1 AAAA
2399278 TTTTCGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 8 0.38
21 9 0.43
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
AAAAAAATTTTATGTTTTA
Found at i:2399277 original size:37 final size:37
Alignment explanation
Indices: 2399237--2399316 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
2399227 ATTTTATCAA
*
2399237 AAAAATTTAT-GT-TTTCAAAAACAAATTTTC-TGTTTT
1 AAAAATTT-TCGTGTTTCAAAAACAAA-ATTCGTGTTTT
*
2399273 AAAAATTTTCGTGTTTCAAAAAGAAAATTCGTGTTTT
1 AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
2399310 CAAAAAT
1 -AAAAAT
2399317 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 1 0.03
36 13 0.34
37 18 0.47
38 6 0.16
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (37 bp):
AAAAATTTTCGTGTTTCAAAAACAAAATTCGTGTTTT
Found at i:2399280 original size:16 final size:17
Alignment explanation
Indices: 2399259--2399294 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2399249 TTTCAAAAAC
*
2399259 AAATTTTC-TGTTTTAA
1 AAATTTTCGTGTTTCAA
2399275 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
2399292 AAA
1 AAA
2399295 GAAAATTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:2399305 original size:20 final size:21
Alignment explanation
Indices: 2399280--2399320 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2399270 TTTAAAAATT
2399280 TTCGTG-TTTCAAAAAGAAAA
1 TTCGTGTTTTCAAAAAGAAAA
*
2399300 TTCGTGTTTTCAAAAATAAAA
1 TTCGTGTTTTCAAAAAGAAAA
2399321 ATAAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (21 bp):
TTCGTGTTTTCAAAAAGAAAA
Found at i:2399410 original size:16 final size:15
Alignment explanation
Indices: 2399362--2399415 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
2399352 TTTTTTTAAA
2399362 AAAAGTTTTGTGTTTCT
1 AAAA-TTTTGTGTTT-T
*
2399379 AAAATTCTTGTATTTT
1 AAAATT-TTGTGTTTT
2399395 AAAATTTTCGTGTTTT
1 AAAATTTT-GTGTTTT
2399411 CAAAA
1 -AAAA
2399416 AAGGAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.06
16 15 0.47
17 15 0.47
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (15 bp):
AAAATTTTGTGTTTT
Found at i:2401371 original size:35 final size:35
Alignment explanation
Indices: 2401325--2401395 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2401315 AATTGGGTCA
2401325 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
1 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
2401360 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
1 AAAACGAGGTATTGAGACCTCGATATTATAAACTG
2401395 A
1 A
2401396 GCCGTAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (35 bp):
AAAACGAGGTATTGAGACCTCGATATTATAAACTG
Found at i:2401830 original size:5 final size:5
Alignment explanation
Indices: 2401820--2401865 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
2401810 TATGTTTTTA
*
2401820 ATATT ATATT ATATT ATTAAT ATATT ATATT ATATT ACTA-T ATATT
1 ATATT ATATT ATATT A-TATT ATATT ATATT ATATT A-TATT ATATT
2401866 TATAAAACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:2401868 original size:16 final size:16
Alignment explanation
Indices: 2401817--2401869 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 16
2401807 AAGTATGTTT
2401817 TTAATATTATATTATATTA
1 TTAATA-TATATT-TA-TA
2401836 TTAATATATTATATTATA
1 TTAATATA-TAT-TTATA
*
2401854 TTACTATATATTTATA
1 TTAATATATATTTATA
2401870 AAACAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.16
17 3 0.10
18 11 0.35
19 11 0.35
20 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATATATATTTATA
Found at i:2401869 original size:21 final size:21
Alignment explanation
Indices: 2401820--2401865 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2401810 TATGTTTTTA
*
2401820 ATATTATATTATATTATTAAT
1 ATATTATATTATATTACTAAT
2401841 ATATTATATTATATTACT-AT
1 ATATTATATTATATTACTAAT
2401861 ATATT
1 ATATT
2401866 TATAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTATATTATATTACTAAT
Found at i:2401948 original size:35 final size:34
Alignment explanation
Indices: 2401891--2401957 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
2401881 AGAATAGATA
* *
2401891 TGAGAAAGAAAGAAACAGAGAAGCAAAACGAAATT
1 TGAGAAAGAAAGAAACAAAGAAG-AAAAAGAAATT
*
2401926 TGAGAAAGAAA-AAGAGAAAGAAGAAAAAGAAA
1 TGAGAAAGAAAGAA-ACAAAGAAGAAAAAGAAA
2401958 GAGAACCACG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.66, C:0.04, G:0.24, T:0.06
Consensus pattern (34 bp):
TGAGAAAGAAAGAAACAAAGAAGAAAAAGAAATT
Found at i:2409713 original size:41 final size:41
Alignment explanation
Indices: 2409696--2409849 Score: 281
Period size: 41 Copynumber: 3.8 Consensus size: 41
2409686 ACTTATAGCA
2409696 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
* * *
2409737 TGATTCAAATCATCGGCACATAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
2409778 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
2409819 TGATTCAGATCACCGGCACGTAGCCTGCTAG
1 TGATTCAGATCACCGGCACGTAGCCTGCTAG
2409850 ACTTAAAGTC
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (41 bp):
TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
Found at i:2409805 original size:82 final size:82
Alignment explanation
Indices: 2409668--2409854 Score: 293
Period size: 82 Copynumber: 2.3 Consensus size: 82
2409658 ACAGATTCAA
* * *
2409668 CGGCACATAACCTGCTAAACTTATAGCATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
1 CGGCACATAGCCTGCTAGACTTATAACATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
*
2409733 AACCTGATTCAAATCAT
66 AACCTGATTCAAATCAC
** *
2409750 CGGCACATAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
1 CGGCACATAGCCTGCTAGACTTATAACATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
*
2409815 AACCTGATTCAGATCAC
66 AACCTGATTCAAATCAC
*
2409832 CGGCACGTAGCCTGCTAGACTTA
1 CGGCACATAGCCTGCTAGACTTA
2409855 AAGTCTGAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 94 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (82 bp):
CGGCACATAGCCTGCTAGACTTATAACATGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTAT
AACCTGATTCAAATCAC
Found at i:2416609 original size:18 final size:18
Alignment explanation
Indices: 2416586--2416624 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2416576 TACTTTTCTC
2416586 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
2416604 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
2416622 TTT
1 TTT
2416625 TTTTTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:2416793 original size:39 final size:39
Alignment explanation
Indices: 2416750--2416862 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 39
2416740 TCGGATAGTT
2416750 CGAAGTAATAGTTGACACCCAGTGTCTCATCGACCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGACCTAGC
** ** * *
2416789 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-ACCTAGC
*
2416828 CGAAGAAATTTAG-TGACACCCAGTGTCTCATCGAC
1 CGAAGTAA--TAGTTGACACCCAGTGTCTCATCGAC
2416863 TCGAGGTCGA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
38 19 0.33
39 20 0.34
40 1 0.02
41 16 0.28
42 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (39 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGACCTAGC
Found at i:2416810 original size:38 final size:38
Alignment explanation
Indices: 2416723--2416862 Score: 115
Period size: 39 Copynumber: 3.6 Consensus size: 38
2416713 CACACCAATA
* *
2416723 TGGCACCCAGTGCCTCATCGGA--TAGTTCGAAGTAATAGT
1 TGGCACCCAGTGTCTCATC-GACCTAG-CCGAAGTAA-AGT
*
2416762 TGACACCCAGTGTCTCATCGACCTAGCCGAAGTAAAGT
1 TGGCACCCAGTGTCTCATCGACCTAGCCGAAGTAAAGT
* ** * * *
2416800 TGGTACCCAGTACCTCATCGAATCTATCCGAAG-AAATT
1 TGGCACCCAGTGTCTCATCG-ACCTAGCCGAAGTAAAGT
2416838 TAGTGACACCCAGTGTCTCATCGAC
1 T-G-G-CACCCAGTGTCTCATCGAC
2416863 TCGAGGTCGA
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
38 26 0.32
39 36 0.44
40 5 0.06
41 14 0.17
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (38 bp):
TGGCACCCAGTGTCTCATCGACCTAGCCGAAGTAAAGT
Found at i:2416858 original size:41 final size:41
Alignment explanation
Indices: 2416750--2416861 Score: 110
Period size: 38 Copynumber: 2.8 Consensus size: 41
2416740 TCGGATAGTT
2416750 CGAAGTAATAG-T-TGACACCCAGTGTCTCATCG-ACCTAGC
1 CGAAGTAA-AGTTGTGACACCCAGTGTCTCATCGAACCTAGC
* ** * *
2416789 CGAAGTAAAGTTG-G-TACCCAGTACCTCATCGAATCTATC
1 CGAAGTAAAGTTGTGACACCCAGTGTCTCATCGAACCTAGC
*
2416828 CGAAG-AAATTTAGTGACACCCAGTGTCTCATCGA
1 CGAAGTAAAGTT-GTGACACCCAGTGTCTCATCGA
2416862 CTCGAGGTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
38 21 0.36
39 21 0.36
40 1 0.02
41 15 0.26
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (41 bp):
CGAAGTAAAGTTGTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:2417883 original size:18 final size:17
Alignment explanation
Indices: 2417848--2417880 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2417838 CTTTTTATTC
2417848 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
2417865 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
2417881 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:2422088 original size:24 final size:24
Alignment explanation
Indices: 2422060--2422108 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2422050 ATCATACACA
*
2422060 TTTAAATAAATATAT-TAATTTATT
1 TTTAAATAAATAAATATAA-TTATT
*
2422084 TTTAATTAAATAAATATAATTATT
1 TTTAAATAAATAAATATAATTATT
2422108 T
1 T
2422109 ATATATACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAAATAAATAAATATAATTATT
Found at i:2447174 original size:28 final size:28
Alignment explanation
Indices: 2447119--2447202 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 28
2447109 TTAAATTTTA
* * *
2447119 TCCACGTGTTATTCAACATCCTATGTTG
1 TCCACATGTCATTCGACATCCTATGTTG
* *
2447147 TTCACATGTCGTTCGACATCCTATGTTG
1 TCCACATGTCATTCGACATCCTATGTTG
*
2447175 TCCACGTGTCATTCGACATCCTATGTTG
1 TCCACATGTCATTCGACATCCTATGTTG
2447203 AAAGCTTAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (28 bp):
TCCACATGTCATTCGACATCCTATGTTG
Found at i:2451619 original size:44 final size:44
Alignment explanation
Indices: 2451556--2451642 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
2451546 TCTGCTAGTG
2451556 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCATGAATTTT
1 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCATGAATTTT
*
2451600 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCGTGAATTT
1 TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCATGAATTT
2451643 GCACATCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.40
Consensus pattern (44 bp):
TTAATATTCCTTGGTCGCCCAGCTCCTTCCAATTCATGAATTTT
Found at i:2453637 original size:14 final size:14
Alignment explanation
Indices: 2453618--2453645 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2453608 ACTCACTGTT
2453618 TATCCGTGCATATG
1 TATCCGTGCATATG
2453632 TATCCGTGCATATG
1 TATCCGTGCATATG
2453646 CAGATCATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
TATCCGTGCATATG
Found at i:2463810 original size:33 final size:33
Alignment explanation
Indices: 2463772--2463837 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2463762 GACTGAGTGG
* *
2463772 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTAGACAGGAGCTAGAATGT
*
2463805 GAGTGTTTGGTTGCTAGATAGGAGCTAGAATGT
1 GAGTGTTTGGTTGCTAGACAGGAGCTAGAATGT
2463838 CAAGAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.08, G:0.39, T:0.32
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTAGACAGGAGCTAGAATGT
Found at i:2472906 original size:22 final size:23
Alignment explanation
Indices: 2472880--2472924 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
2472870 ACCTGATCAG
2472880 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
2472902 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
2472925 TAGTAAAGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:2473124 original size:23 final size:23
Alignment explanation
Indices: 2473094--2473149 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2473084 GATTCCATCC
*
2473094 AAACACACCAAAAT-GTCCAACCA
1 AAACACACCAAAATAATCC-ACCA
* *
2473117 AAACACACCAATATAATCCTCCA
1 AAACACACCAAAATAATCCACCA
2473140 AAACACACCA
1 AAACACACCA
2473150 GTATCATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.52, C:0.36, G:0.02, T:0.11
Consensus pattern (23 bp):
AAACACACCAAAATAATCCACCA
Found at i:2473159 original size:28 final size:28
Alignment explanation
Indices: 2473126--2473211 Score: 109
Period size: 28 Copynumber: 3.0 Consensus size: 28
2473116 AAAACACACC
*
2473126 AATATAATCCTCCAAAACACACCAGTAT
1 AATATAATCCTCCAAAACACACCAGAAT
* * * *
2473154 CATATAATCCTCCCAAACAAACTAGAAT
1 AATATAATCCTCCAAAACACACCAGAAT
*
2473182 AATATAATCCACCCAAAACACACCAGAAT
1 AATATAATCC-TCCAAAACACACCAGAAT
2473211 A
1 A
2473212 GCACAAAGTG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 32 0.68
29 15 0.32
ACGTcount: A:0.49, C:0.29, G:0.03, T:0.19
Consensus pattern (28 bp):
AATATAATCCTCCAAAACACACCAGAAT
Found at i:2476187 original size:26 final size:26
Alignment explanation
Indices: 2476147--2476198 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2476137 GAGCTGGTCC
*
2476147 CTACACGAGTCCAGAATGGATGGAGG
1 CTACACGAGTACAGAATGGATGGAGG
2476173 CTACACGAGTACAGAATGGATGGAGG
1 CTACACGAGTACAGAATGGATGGAGG
2476199 GTTTGCATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.35, T:0.15
Consensus pattern (26 bp):
CTACACGAGTACAGAATGGATGGAGG
Found at i:2479596 original size:11 final size:11
Alignment explanation
Indices: 2479580--2479604 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2479570 CCAACCCCCA
2479580 TTTTTCCTTTC
1 TTTTTCCTTTC
2479591 TTTTTCCTTTC
1 TTTTTCCTTTC
2479602 TTT
1 TTT
2479605 GAAACACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTCCTTTC
Found at i:2481835 original size:27 final size:27
Alignment explanation
Indices: 2481787--2481945 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
2481777 GCGAGGCTGC
* *
2481787 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
2481814 CAAATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
2481840 CAGATATATGTGGTAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
2481867 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
2481894 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
2481921 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
2481946 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 9 0.08
27 99 0.88
28 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:2481946 original size:54 final size:54
Alignment explanation
Indices: 2481805--2481948 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
2481795 GTGACGAAGT
* * * *
2481805 CACCAGATACAAAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGTAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
2481859 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
2481913 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
2481949 GCTTCCTCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 4 0.05
54 81 0.95
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:2483569 original size:26 final size:26
Alignment explanation
Indices: 2483538--2483645 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
2483528 TGAAATGCCC
*
2483538 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2483564 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2483590 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
2483616 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2483642 ATCA
1 ATCA
2483646 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2488726 original size:18 final size:19
Alignment explanation
Indices: 2488703--2488742 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2488693 TTCCTTTAAA
2488703 TTATTTCAT-TATTTA-TTT
1 TTATTTCATCT-TTTACTTT
2488721 TTATTTCATCTTTTACTTT
1 TTATTTCATCTTTTACTTT
2488740 TTA
1 TTA
2488743 CTTTTTACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTCATCTTTTACTTT
Found at i:2491687 original size:18 final size:19
Alignment explanation
Indices: 2491649--2491688 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2491639 CCCATCTTTC
2491649 TCTTCTAATTGGAATTTTA
1 TCTTCTAATTGGAATTTTA
2491668 TCTTCTAATTGGAA-TTTA
1 TCTTCTAATTGGAATTTTA
2491686 TCT
1 TCT
2491689 GATTTTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (19 bp):
TCTTCTAATTGGAATTTTA
Found at i:2500381 original size:31 final size:31
Alignment explanation
Indices: 2500346--2500405 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2500336 ATGATTGAAT
*
2500346 TATTCAAAAAATTTTATTCAAGTCCCTAAAC
1 TATTCAAAAAATTTTATTCAAGTCACTAAAC
* *
2500377 TATTCAAAAATTTTTATTTAAGTCACTAA
1 TATTCAAAAAATTTTATTCAAGTCACTAA
2500406 GCGGTTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (31 bp):
TATTCAAAAAATTTTATTCAAGTCACTAAAC
Found at i:2503311 original size:15 final size:15
Alignment explanation
Indices: 2503293--2503335 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
2503283 ATTCAATGTT
*
2503293 TAATAATTTAAAAAG
1 TAATAATTTAAAAAA
*
2503308 TAATTATTTGAAAAAA
1 TAATAATTT-AAAAAA
*
2503324 TATTAATTTAAA
1 TAATAATTTAAA
2503336 TTGAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
TAATAATTTAAAAAA
Found at i:2503497 original size:22 final size:23
Alignment explanation
Indices: 2503457--2503501 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2503447 AATATAGTTG
2503457 TTTGATAAAAGTAAATATTATTT
1 TTTGATAAAAGTAAATATTATTT
* *
2503480 TTTGA-AAAATTAATTATTATTT
1 TTTGATAAAAGTAAATATTATTT
2503502 AATTTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
TTTGATAAAAGTAAATATTATTT
Found at i:2514975 original size:58 final size:58
Alignment explanation
Indices: 2514905--2515021 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
2514895 GCTTATCGAT
2514905 TTGGGTGCTTTTAATTAACTCGGCACTCTAGCTTTGGGAATTTTATTCCCAAATTCCC
1 TTGGGTGCTTTTAATTAACTCGGCACTCTAGCTTTGGGAATTTTATTCCCAAATTCCC
* * *
2514963 TTGGGTGCTTTTAATTAACTCGGTATTCTAGCTTTGGGAATTTTATTCTCAAATTCCC
1 TTGGGTGCTTTTAATTAACTCGGCACTCTAGCTTTGGGAATTTTATTCCCAAATTCCC
2515021 T
1 T
2515022 GATTACATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.43
Consensus pattern (58 bp):
TTGGGTGCTTTTAATTAACTCGGCACTCTAGCTTTGGGAATTTTATTCCCAAATTCCC
Found at i:2521479 original size:13 final size:13
Alignment explanation
Indices: 2521458--2521492 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2521448 GAATTTTTCC
2521458 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
2521471 AAAGTACTTCTCA
1 AAAGCACTTCTCA
*
2521484 AAAACACTT
1 AAAGCACTT
2521493 TTTCACAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:2526205 original size:23 final size:23
Alignment explanation
Indices: 2526177--2526220 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2526167 TTTATACTAT
2526177 TCTCTGTCTTTTAACACGCTTTC
1 TCTCTGTCTTTTAACACGCTTTC
*
2526200 TCTCTGTCTTTTGACACGCTT
1 TCTCTGTCTTTTAACACGCTT
2526221 CTTTCTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.48
Consensus pattern (23 bp):
TCTCTGTCTTTTAACACGCTTTC
Found at i:2526865 original size:23 final size:23
Alignment explanation
Indices: 2526837--2526881 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2526827 AAGAGAAAGG
2526837 AGAAGATTGCGTTGAAAAATGGA
1 AGAAGATTGCGTTGAAAAATGGA
*
2526860 AGAAGATTGTGTTGAAAAATGG
1 AGAAGATTGCGTTGAAAAATGG
2526882 CAAATCTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (23 bp):
AGAAGATTGCGTTGAAAAATGGA
Found at i:2534501 original size:48 final size:48
Alignment explanation
Indices: 2534419--2534512 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
2534409 TTTCTTGGCT
* *
2534419 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
2534467 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
2534513 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:2536977 original size:48 final size:48
Alignment explanation
Indices: 2536895--2536988 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
2536885 TTTCTTGGCT
* *
2536895 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
2536943 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
2536989 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:2541041 original size:12 final size:12
Alignment explanation
Indices: 2541024--2541057 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2541014 AAAATCTTTA
*
2541024 TAAAAGTAAAAG
1 TAAAAGCAAAAG
2541036 TAAAAGCAAAAG
1 TAAAAGCAAAAG
*
2541048 CAAAAGCAAA
1 TAAAAGCAAA
2541058 TCAAGTGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.09, G:0.15, T:0.09
Consensus pattern (12 bp):
TAAAAGCAAAAG
Found at i:2542089 original size:58 final size:58
Alignment explanation
Indices: 2542009--2542120 Score: 215
Period size: 58 Copynumber: 1.9 Consensus size: 58
2541999 TCGAAGGGAA
*
2542009 AGACATAGATACTGATGTTATAACAGAAGCAGATGTGGGGTTGAATAAATCTTCGGAG
1 AGACATAGATACTGATGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCGGAG
2542067 AGACATAGATACTGATGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTC
1 AGACATAGATACTGATGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTC
2542121 TACATTCGAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (58 bp):
AGACATAGATACTGATGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCGGAG
Found at i:2542450 original size:42 final size:42
Alignment explanation
Indices: 2542394--2542486 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
2542384 ACAATGCTGA
*
2542394 AAGTTCAAAATCGGAAGAGTTTGAGAAGGACAGTAACATCAC
1 AAGTTTAAAATCGGAAGAGTTTGAGAAGGACAGTAACATCAC
*
2542436 AAGTTTAAANTCGGAAGAGTTTGAGAAGGACAGTAACATCAC
1 AAGTTTAAAATCGGAAGAGTTTGAGAAGGACAGTAACATCAC
2542478 AAGTTTAAA
1 AAGTTTAAA
2542487 TAATCTGAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (42 bp):
AAGTTTAAAATCGGAAGAGTTTGAGAAGGACAGTAACATCAC
Found at i:2545407 original size:32 final size:32
Alignment explanation
Indices: 2545357--2545422 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
2545347 GGGTCTTTTT
*
2545357 ACGCCCTTTTTCAGTTTACTAAATACAAATTA
1 ACGCCCTTTTTCAATTTACTAAATACAAATTA
* *
2545389 ACGCTCTTTTTTAATTTACTAAATACAAATTA
1 ACGCCCTTTTTCAATTTACTAAATACAAATTA
2545421 AC
1 AC
2545423 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (32 bp):
ACGCCCTTTTTCAATTTACTAAATACAAATTA
Found at i:2545634 original size:22 final size:22
Alignment explanation
Indices: 2545606--2545650 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2545596 TAAGATTATC
2545606 TAAATTAAGAAAATATCTTTAA
1 TAAATTAAGAAAATATCTTTAA
2545628 TAAATTAAGAAAATATCTTTAA
1 TAAATTAAGAAAATATCTTTAA
2545650 T
1 T
2545651 TTATCTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
TAAATTAAGAAAATATCTTTAA
Found at i:2546207 original size:10 final size:11
Alignment explanation
Indices: 2546175--2546209 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
2546165 CGGCCAGCCC
2546175 ATATTAATTTTT
1 ATATT-ATTTTT
2546187 ATATTATTTTT
1 ATATTATTTTT
2546198 ATATTATTTTT
1 ATATTATTTTT
2546209 A
1 A
2546210 AATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:2546367 original size:30 final size:30
Alignment explanation
Indices: 2546331--2546393 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
2546321 ACTTAACAAG
2546331 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
2546361 CAAATGCCTTTCAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
2546391 CAA
1 CAA
2546394 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:2552333 original size:29 final size:29
Alignment explanation
Indices: 2552255--2552400 Score: 170
Period size: 29 Copynumber: 5.1 Consensus size: 29
2552245 ACCCCCACAT
*
2552255 ACATGCATATGGCCCACTT-GGCCCAA-TC
1 ACATTCATATGGCCCA-TTAGGCCCAATTC
* *
2552283 TCATTTATATGGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* *
2552312 ACATTCATATGGCCTATCAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* *
2552341 ATATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAATTC
* * * *
2552370 ACCTTTATATGGCCCGTTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAATTC
2552399 AC
1 AC
2552401 CTTATATTCA
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
27 2 0.02
28 20 0.20
29 79 0.78
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAATTC
Found at i:2558490 original size:43 final size:43
Alignment explanation
Indices: 2558427--2558528 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 43
2558417 GCTGGTGAAT
* * *
2558427 AATATTATCGGGCTTCGGGCCTAGCAGGTTATAATGCCGGTGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGTGA
* * * *
2558470 GATAATATCAGGCTTTGGGCCTAGTAGGCTATAATGCCAGTGA
1 AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGTGA
*
2558513 AATGATATCGGGCTTC
1 AATAATATCGGGCTTC
2558529 AAGACTAGCA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
AATAATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGTGA
Found at i:2558591 original size:41 final size:40
Alignment explanation
Indices: 2558546--2558623 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
2558536 GCAGGTGAAA
* **
2558546 TGCCGGAGAATGAGTTCAGACTTAAAGTCTAGCAGGCTTTG
1 TGCCGGAG-ATGAATTCAGACTTAAAACCTAGCAGGCTTTG
* **
2558587 TGCCGGTGATGAATTCAGGTTTAAAACCTAGCAGGCT
1 TGCCGGAGATGAATTCAGACTTAAAACCTAGCAGGCT
2558624 AAATGTCGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
40 24 0.77
41 7 0.23
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (40 bp):
TGCCGGAGATGAATTCAGACTTAAAACCTAGCAGGCTTTG
Found at i:2565280 original size:29 final size:29
Alignment explanation
Indices: 2565214--2565366 Score: 152
Period size: 29 Copynumber: 5.4 Consensus size: 29
2565204 ACCCTTACAT
* *
2565214 ACATGCATATGGCCTACTTA-GCCC-AATC
1 ACATTCATATGGCCCA-TTAGGCCCAAATC
* * * *
2565242 TCATTTATATAGCCCATTAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* *
2565271 ACATTCATATGGCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
2565300 ATATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * *
2565329 ACCTTTATATGGCCCGTT-GGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
2565357 ACCTT-ATATG
1 ACATTCATATG
2565367 CATGCTCATA
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
27 8 0.08
28 30 0.28
29 68 0.64
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:2585659 original size:23 final size:22
Alignment explanation
Indices: 2585633--2585677 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2585623 TTGTAGTATA
2585633 AAATAAGAATATTTTAATTAAAT
1 AAATAAGAATA-TTTAATTAAAT
* * *
2585656 AAATACGAGTATTTATTTAAAT
1 AAATAAGAATATTTAATTAAAT
2585678 TATGTTTAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATAAGAATATTTAATTAAAT
Found at i:2589119 original size:3 final size:3
Alignment explanation
Indices: 2589113--2589153 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
2589103 GAGAGAAAGG
2589113 AGA AGA AG- AGA ATG- AGA AGA AGA AG- AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2589154 AGAAAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.15
3 28 0.82
4 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:2589129 original size:14 final size:13
Alignment explanation
Indices: 2589112--2589161 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
2589102 CGAGAGAAAG
2589112 GAGAAGAAGAGAA
1 GAGAAGAAGAGAA
2589125 TGAGAAG-A-AGAA
1 -GAGAAGAAGAGAA
2589137 GAGAAGAAGAAGAA
1 GAGAAGAAG-AGAA
2589151 GA-AAGAA-AGAA
1 GAGAAGAAGAGAA
2589162 AAAAGGTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 10 0.30
12 5 0.15
13 6 0.18
14 12 0.36
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (13 bp):
GAGAAGAAGAGAA
Found at i:2589133 original size:17 final size:17
Alignment explanation
Indices: 2589113--2589157 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
2589103 GAGAGAAAGG
2589113 AGAAGAAGAGAATG-AGA
1 AGAAGAAGAGAA-GAAGA
2589130 AGAAGAAGAGAAGAAGA
1 AGAAGAAGAGAAGAAGA
2589147 AGAAGAA-AGAA
1 AGAAGAAGAGAA
2589158 AGAAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (17 bp):
AGAAGAAGAGAAGAAGA
Found at i:2589308 original size:41 final size:41
Alignment explanation
Indices: 2589262--2589525 Score: 404
Period size: 41 Copynumber: 6.2 Consensus size: 41
2589252 TATTGTAATT
*
2589262 TTGTAAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATA
1 TTGT-AATTTTGTATGAATATTATAAATTTTTTGTATGAATA
** *
2589303 TTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATA
1 TTG--------TAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
2589352 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
2589393 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
2589434 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
2589475 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
2589516 TTGTAATTTT
1 TTGTAATTTT
2589526 TGTTAGTAAT
Statistics
Matches: 209, Mismatches: 5, Indels: 18
0.90 0.02 0.08
Matches are distributed among these distances:
41 171 0.82
48 17 0.08
49 21 0.10
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (41 bp):
TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATA
Found at i:2589328 original size:27 final size:24
Alignment explanation
Indices: 2589239--2589526 Score: 221
Period size: 22 Copynumber: 13.1 Consensus size: 24
2589229 TTTTAGGTAA
*
2589239 TTTTTTGTATGAATATTGTAATTT
1 TTTTTTGTATGAATATTGTAATAT
2589263 TGTAAATTTTGTATGAATA-T-T-ATAT
1 T-T---TTTTGTATGAATATTGTAATAT
2589288 TTTTTTGTATGAATATTGTAATAT
1 TTTTTTGTATGAATATTGTAATAT
*
2589312 TATAATTTTGTATGAATATTG-CA-AT
1 T-T--TTTTGTATGAATATTGTAATAT
2589337 TTTTTTGTATGAATATTGT-A-A-
1 TTTTTTGTATGAATATTGTAATAT
*
2589358 --TTTTGTATGAATATTATAA-A-
1 TTTTTTGTATGAATATTGTAATAT
2589378 TTTTTTGTATGAATATTGT-A-A-
1 TTTTTTGTATGAATATTGTAATAT
*
2589399 --TTTTGTATGAATATTATAA-A-
1 TTTTTTGTATGAATATTGTAATAT
2589419 TTTTTTGTATGAATATTGT-A-A-
1 TTTTTTGTATGAATATTGTAATAT
*
2589440 --TTTTGTATGAATATTATAA-A-
1 TTTTTTGTATGAATATTGTAATAT
2589460 TTTTTTGTATGAATATTGT-A-A-
1 TTTTTTGTATGAATATTGTAATAT
*
2589481 --TTTTGTATGAATATTATAA-A-
1 TTTTTTGTATGAATATTGTAATAT
2589501 TTTTTTGTATGAATATTGTAAT-T
1 TTTTTTGTATGAATATTGTAATAT
2589524 TTT
1 TTT
2589527 GTTAGTAATT
Statistics
Matches: 229, Mismatches: 10, Indels: 51
0.79 0.03 0.18
Matches are distributed among these distances:
19 64 0.28
20 8 0.03
21 19 0.08
22 85 0.37
23 4 0.02
24 8 0.03
25 9 0.04
26 2 0.01
27 17 0.07
28 13 0.06
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTTTTGTATGAATATTGTAATAT
Found at i:2589703 original size:38 final size:38
Alignment explanation
Indices: 2589658--2589739 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
2589648 CATATAAAGT
2589658 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
2589696 TTATAAAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
2589734 TTATAA
1 TTATAA
2589740 CTGACTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:2589817 original size:15 final size:15
Alignment explanation
Indices: 2589776--2589817 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2589766 GTTAATTCAT
*
2589776 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
2589791 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
2589807 TTAAATTTTAT
1 TTAAATTTTAT
2589818 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:2594839 original size:22 final size:21
Alignment explanation
Indices: 2594804--2594848 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
2594794 TACCTAATTT
*
2594804 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCCTTCCTTC
2594825 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCT-CTTCCTTCCTTC
2594847 TT
1 TT
2594849 ATTTCTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCCTTCCTTC
Found at i:2594952 original size:27 final size:26
Alignment explanation
Indices: 2594933--2594989 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 26
2594923 CTCTCATAAT
2594933 GGCACCACCATTGGCGCCTCCCAGGTA
1 GGCACCACCATTGGCGCCTCCCA-GTA
*
2594960 GGCACCACAATTGGCGCCTCCCAGATA
1 GGCACCACCATTGGCGCCTCCCAG-TA
2594987 GGC
1 GGC
2594990 GCCAATACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.14
Consensus pattern (26 bp):
GGCACCACCATTGGCGCCTCCCAGTA
Found at i:2597470 original size:43 final size:43
Alignment explanation
Indices: 2597365--2597570 Score: 166
Period size: 43 Copynumber: 4.8 Consensus size: 43
2597355 TTGGTTTATT
* * * * *
2597365 CGATGATGCA-TTATGTGTACCAATATGATTGCTTCGGTTTATC
1 CGATGATGCACCT-TGTGTGCCAGTATAATTGCTTCGGTTTGTC
* * * * *
2597408 CAATGAAGCA-CTATCTGTGCCAGTATGATTGCTTCGGTTTTTC
1 CGATGATGCACCT-TGTGTGCCAGTATAATTGCTTCGGTTTGTC
* * *
2597451 C-AGTGATGCACCTTGTGTGCTAGTATAATTGCCTCAGTTTGTC
1 CGA-TGATGCACCTTGTGTGCCAGTATAATTGCTTCGGTTTGTC
* * * * *
2597494 CGATGATGCACTTTCTGTGCTAGTATAATTGCTTCGATTCGTC
1 CGATGATGCACCTTGTGTGCCAGTATAATTGCTTCGGTTTGTC
* * * *
2597537 CGATGATGCACATCGTGTGCCAGTTTATTTGCTT
1 CGATGATGCACCTTGTGTGCCAGTATAATTGCTT
2597571 TGACTTGAAA
Statistics
Matches: 134, Mismatches: 26, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
42 1 0.01
43 130 0.97
44 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (43 bp):
CGATGATGCACCTTGTGTGCCAGTATAATTGCTTCGGTTTGTC
Found at i:2597544 original size:86 final size:86
Alignment explanation
Indices: 2597392--2597556 Score: 197
Period size: 86 Copynumber: 1.9 Consensus size: 86
2597382 TACCAATATG
* * * * **
2597392 ATTGCTTCGGTTTATCCAATGAAGCACTATCTGTGCCAGTATGATTGCTTCGGTTTTTCCAGTGA
1 ATTGCCTCAGTTTATCCAATGAAGCACTATCTGTGCCAGTATAATTGCTTCGATTCGTCCAGTGA
* *
2597457 TGCACCTTGTGTGCTAGTATA
66 TGCACATCGTGTGCTAGTATA
* * * * *
2597478 ATTGCCTCAGTTTGTCCGATGATGCACTTTCTGTGCTAGTATAATTGCTTCGATTCGTCC-GATG
1 ATTGCCTCAGTTTATCCAATGAAGCACTATCTGTGCCAGTATAATTGCTTCGATTCGTCCAG-TG
2597542 ATGCACATCGTGTGC
65 ATGCACATCGTGTGC
2597557 CAGTTTATTT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
85 1 0.02
86 64 0.98
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (86 bp):
ATTGCCTCAGTTTATCCAATGAAGCACTATCTGTGCCAGTATAATTGCTTCGATTCGTCCAGTGA
TGCACATCGTGTGCTAGTATA
Found at i:2599638 original size:12 final size:12
Alignment explanation
Indices: 2599623--2599660 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2599613 CAAAATCAAG
*
2599623 AATTTAACTTAA
1 AATTTAAATTAA
2599635 AATTTAGAATTAA
1 AATTTA-AATTAA
2599648 AA-TTAAATTAA
1 AATTTAAATTAA
2599659 AA
1 AA
2599661 ATTATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 8 0.33
12 9 0.38
13 7 0.29
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (12 bp):
AATTTAAATTAA
Done.