Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 94 of 208
Found at i:28065449 original size:2 final size:2
Alignment explanation
Indices: 28065442--28065494 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
28065432 NNNNNNNNNC
* * *
28065442 TA TA TA TA TA TA TA TA TA AA CA -A TA CA 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
28065483 TA TA TA TA TA TA
1 TA TA TA TA TA TA
28065495 GAGTTTGTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:28065606 original size:2 final size:2
Alignment explanation
Indices: 28065601--28065648 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
28065591 CCACACATAC
28065601 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
28065643 AT AT AT
1 AT AT AT
28065649 TAACAAGTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28067501 original size:2 final size:2
Alignment explanation
Indices: 28067494--28067525 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28067484 GTTTTATGAA
28067494 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
28067526 GCCTCTTATA
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:28075429 original size:15 final size:16
Alignment explanation
Indices: 28075409--28075438 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28075399 ATATATAATT
28075409 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
28075424 TAATAAATATTCTTA
1 TAATAAATATTCTTA
28075439 TATTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:28075500 original size:120 final size:122
Alignment explanation
Indices: 28075363--28075587 Score: 373
Period size: 120 Copynumber: 1.9 Consensus size: 122
28075353 TTAATCATAT
*
28075363 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATA-AAAT-TCTTAATA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAAATGTCTTAATA
* *
28075426 ATAAATATTCTTATATTAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 ATAAATATTCTTATATGAATATACTAAAATCATAATATATAATACTATAAAATATAA
* * *
28075483 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATGATTTAATAGCTATTGTCTTAAT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATA-CAAATGTCTTAAT
28075548 AATAAATATTCTTATATGAATATACTAAAATCATAATATA
65 AATAAATATTCTTATATGAATATACTAAAATCATAATATA
28075588 ACTTGAGAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
120 49 0.51
122 2 0.02
123 45 0.47
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (122 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATACAAATGTCTTAATA
ATAAATATTCTTATATGAATATACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:28075520 original size:16 final size:17
Alignment explanation
Indices: 28075501--28075533 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28075491 AATTATTATT
28075501 AAATATA-ATTTAATAA
1 AAATATAGATTTAATAA
28075517 AAATATATGATTTAATA
1 AAATATA-GATTTAATA
28075534 GCTATTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATATAGATTTAATAA
Found at i:28078455 original size:49 final size:49
Alignment explanation
Indices: 28078383--28078487 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
28078373 TTAAGAAAAA
* * * *
28078383 AAAATTAAAATTAAGTTGAATATCATGAATCAAAAGGTGAACACTTTAT
1 AAAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTAT
28078432 AAAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTAT
1 AAAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTAT
28078481 AAAATTA
1 AAAATTA
28078488 TAACACATGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (49 bp):
AAAATTAAAATTAAGTTAAATATCATGAATCAAAAGCTCAACACTGTAT
Found at i:28080353 original size:33 final size:33
Alignment explanation
Indices: 28080309--28080374 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
28080299 GAATTAAAAT
28080309 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
*
28080342 TTGTTGGTATATGTATAATTGAGCTAAAATTAA
1 TTGTAGGTATATGTATAATTGAGCTAAAATTAA
28080375 AATTCCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (33 bp):
TTGTAGGTATATGTATAATTGAGCTAAAATTAA
Found at i:28080614 original size:19 final size:19
Alignment explanation
Indices: 28080587--28080623 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28080577 AACAAATTAA
*
28080587 TTGTTGGTATATGTAAAAT
1 TTGTAGGTATATGTAAAAT
28080606 TTGTAGGTATATGTAAAA
1 TTGTAGGTATATGTAAAA
28080624 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGTAGGTATATGTAAAAT
Found at i:28080946 original size:18 final size:18
Alignment explanation
Indices: 28080925--28080959 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28080915 TTAAATATAT
*
28080925 AATTTAATTAGTTTTATG
1 AATTTAAATAGTTTTATG
*
28080943 AATTTAAATATTTTTAT
1 AATTTAAATAGTTTTAT
28080960 TTTAACCAAT
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:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
AATTTAAATAGTTTTATG
Found at i:28081200 original size:13 final size:13
Alignment explanation
Indices: 28081182--28081210 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28081172 TAACCATTAC
28081182 AATAGTCACTCAA
1 AATAGTCACTCAA
28081195 AATAGTCACTCAA
1 AATAGTCACTCAA
28081208 AAT
1 AAT
28081211 TGATTTGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (13 bp):
AATAGTCACTCAA
Found at i:28084148 original size:26 final size:26
Alignment explanation
Indices: 28084097--28084150 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
28084087 TTAGAAATAA
*
28084097 TTAAATAGGATTTAAAAATTTTAATT
1 TTAAATAGGACTTAAAAATTTTAATT
* *
28084123 TTAAATA-GACTTAAAATTTTTAAAT
1 TTAAATAGGACTTAAAAATTTTAATT
28084148 TTA
1 TTA
28084151 GAACAAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (26 bp):
TTAAATAGGACTTAAAAATTTTAATT
Found at i:28091214 original size:39 final size:39
Alignment explanation
Indices: 28091169--28091248 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
28091159 ACTTATATTA
*
28091169 TATATATTTGATTAATATATTAATTAACTTAATTAATCT
1 TATATATATGATTAATATATTAATTAACTTAATTAATCT
28091208 TATATATATGATTAATATATTAATTAACTTAATTAATCT
1 TATATATATGATTAATATATTAATTAACTTAATTAATCT
28091247 TA
1 TA
28091249 CTTAAGTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (39 bp):
TATATATATGATTAATATATTAATTAACTTAATTAATCT
Found at i:28092181 original size:21 final size:21
Alignment explanation
Indices: 28092136--28092181 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28092126 TTATTGACAT
*
28092136 TTTATAATTAAAAATTATTTT
1 TTTATAATTAAAAATTATTTA
*
28092157 TTTATAATTAAACTATTA-TTA
1 TTTATAATTAAA-AATTATTTA
28092178 TTTA
1 TTTA
28092182 ATTTAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATAATTAAAAATTATTTA
Found at i:28093928 original size:23 final size:23
Alignment explanation
Indices: 28093902--28093948 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28093892 TTTGGTGCAG
28093902 TGCAGTTGTACTGCCTAGGGTCT
1 TGCAGTTGTACTGCCTAGGGTCT
28093925 TGCAGTTGTACTGCCTAGGGTCT
1 TGCAGTTGTACTGCCTAGGGTCT
28093948 T
1 T
28093949 TTTTCTCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.21, G:0.30, T:0.36
Consensus pattern (23 bp):
TGCAGTTGTACTGCCTAGGGTCT
Found at i:28094854 original size:24 final size:24
Alignment explanation
Indices: 28094817--28094873 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
28094807 CTGTTGTTGA
28094817 AGTTTTCAATTGAAAATGGTTTCTGT
1 AGTTTTC--TTGAAAATGGTTTCTGT
*
28094843 ATTTTTCTTGAAAATGGTTTCTGT
1 AGTTTTCTTGAAAATGGTTTCTGT
28094867 AGTTTTC
1 AGTTTTC
28094874 AATTTGTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 23 0.79
26 6 0.21
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.51
Consensus pattern (24 bp):
AGTTTTCTTGAAAATGGTTTCTGT
Found at i:28095914 original size:24 final size:24
Alignment explanation
Indices: 28095882--28095931 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
28095872 GTATAATTTG
*
28095882 AACCCAAATCACATTTGATGTGAT
1 AACCCAAATCACATTTGAGGTGAT
28095906 AACCCAAATCACATTTGAGGTGAT
1 AACCCAAATCACATTTGAGGTGAT
28095930 AA
1 AA
28095932 ATACTTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
AACCCAAATCACATTTGAGGTGAT
Found at i:28096598 original size:16 final size:16
Alignment explanation
Indices: 28096579--28096609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28096569 CTATTACGCA
28096579 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
*
28096595 TCTATTCCGTTACAG
1 TCTATTCCATTACAG
28096610 TGAACCAAAC
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:0.23, C:0.29, G:0.10, T:0.39
Consensus pattern (16 bp):
TCTATTCCATTACAGC
Found at i:28099960 original size:43 final size:42
Alignment explanation
Indices: 28099863--28100027 Score: 163
Period size: 43 Copynumber: 3.9 Consensus size: 42
28099853 TATGAGACTG
* * *
28099863 TGTAAGACCATATCTGGGATATGGCATCGATATATATGATTACG
1 TGTAAGACCATATCTGGGACATGGCATCG-T-TATGTGATTACA
* *
28099907 TGTAAGACCATGTCTGGGACATTGGCATCGTTATGTGATTTCA
1 TGTAAGACCATATCTGGGACA-TGGCATCGTTATGTGATTACA
* * * *
28099950 TGTAAGACCATAGCTGGG-CTATTGACATCGATATGTGATAACA
1 TGTAAGACCATATCTGGGAC-A-TGGCATCGTTATGTGATTACA
* * *
28099993 TGTAAGGCCATATCTGGGATATGGCATTG-TATGTG
1 TGTAAGACCATATCTGGGACATGGCATCGTTATGTG
28100028 TTATACGAGA
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
41 6 0.06
42 7 0.07
43 61 0.60
44 20 0.20
45 8 0.08
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACATGGCATCGTTATGTGATTACA
Found at i:28101375 original size:145 final size:145
Alignment explanation
Indices: 28101170--28101460 Score: 573
Period size: 145 Copynumber: 2.0 Consensus size: 145
28101160 CATGATGGAA
28101170 ACGGTATGAATTTTTGGAGGCTAATTTGATGACCAAATATAGGATTAAATGATTTGGTTGTGTAT
1 ACGGTATGAATTTTTGGAGGCTAATTTGATGACCAAATATAGGATTAAATGATTTGGTTGTGTAT
28101235 GTAAAATTTTGGCATGGTACATAGTATATGAAATTGGCATGTTTAAATTCGGTTATTTTACTTAG
66 GTAAAATTTTGGCATGGTACATAGTATATGAAATTGGCATGTTTAAATTCGGTTATTTTACTTAG
28101300 AAAATTACTAAAGTT
131 AAAATTACTAAAGTT
28101315 ACGGTATGAATTTTTGGAGGCTAATTTGATGACCAAATATAGGATTAAATGATTTGGTTGTGTAT
1 ACGGTATGAATTTTTGGAGGCTAATTTGATGACCAAATATAGGATTAAATGATTTGGTTGTGTAT
*
28101380 GTGAAATTTTGGCATGGTACATAGTATATGAAATTGGCATGTTTAAATTCGGTTATTTTACTTAG
66 GTAAAATTTTGGCATGGTACATAGTATATGAAATTGGCATGTTTAAATTCGGTTATTTTACTTAG
28101445 AAAATTACTAAAGTT
131 AAAATTACTAAAGTT
28101460 A
1 A
28101461 GTTGAGTAAG
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (145 bp):
ACGGTATGAATTTTTGGAGGCTAATTTGATGACCAAATATAGGATTAAATGATTTGGTTGTGTAT
GTAAAATTTTGGCATGGTACATAGTATATGAAATTGGCATGTTTAAATTCGGTTATTTTACTTAG
AAAATTACTAAAGTT
Found at i:28104425 original size:15 final size:16
Alignment explanation
Indices: 28104393--28104423 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28104383 AAAAAGGAAT
28104393 TTCGAATTAAAAAAAA
1 TTCGAATTAAAAAAAA
28104409 TTCGAATTAAAAAAA
1 TTCGAATTAAAAAAA
28104424 TTGCAAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
TTCGAATTAAAAAAAA
Found at i:28106603 original size:29 final size:29
Alignment explanation
Indices: 28106569--28106632 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
28106559 AATGAGTGAT
*
28106569 AAAAAAAGATA-GAGTGATTCAAAA-GAAA
1 AAAAAAAGAAACGAGTGA-TCAAAATGAAA
*
28106597 AAGAAAAAGAAACGAGTGATGAAAATGAAA
1 AA-AAAAAGAAACGAGTGATCAAAATGAAA
28106627 AAAAAA
1 AAAAAA
28106633 GAGTTTGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 2 0.06
29 17 0.55
30 12 0.39
ACGTcount: A:0.67, C:0.03, G:0.19, T:0.11
Consensus pattern (29 bp):
AAAAAAAGAAACGAGTGATCAAAATGAAA
Found at i:28112965 original size:43 final size:43
Alignment explanation
Indices: 28112904--28113156 Score: 278
Period size: 43 Copynumber: 5.9 Consensus size: 43
28112894 TTTTGGAAAT
* *
28112904 AAACGCCGCTATAGACCATGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
** * *
28112947 AAACGCCGCTAAAGACCATGACCTTTAATGGCGTTTTTTCCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* ** * *
28112990 AAATGCCGCTAAA-AGTTATAACCTTTAGCGGCACTTTT-CCAC
1 AAACGCCGCTAAAGA-CCATGACCTTTAGCGGCGCTTTTCCCAC
* * *
28113032 AAACGCCGCTAAAGACCACGAGCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
* *
28113075 AAACGCCGCTAAAGACCATGA-CTTATAGCGGCGCTTTTTCGCAA
1 AAACGCCGCTAAAGACCATGACCTT-TAGCGGCGC-TTTTCCCAC
* * **
28113119 AAACGCCGCTAAAAAGCATGACCTTTAGCAACGCTTTT
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT
28113157 TTGGAGGACG
Statistics
Matches: 175, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
42 37 0.21
43 102 0.58
44 33 0.19
45 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:28113104 original size:85 final size:85
Alignment explanation
Indices: 28112904--28113145 Score: 265
Period size: 85 Copynumber: 2.8 Consensus size: 85
28112894 TTTTGGAAAT
* * *
28112904 AAACGCCGCTATAGACCATGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT-CCACAAACGCCGCTAAAGACCACGAC
* *
28112969 CTTTAATGGCGTTTTTTCCAC
65 CTTTAACGGCGTTTTCTCCAC
* ** * * *
28112990 AAATGCCGCTAAA-AGTTATAACCTTTAGCGGCACTTTTCCACAAACGCCGCTAAAGACCACGAG
1 AAACGCCGCTAAAGA-CCATGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTAAAGACCACGAC
*
28113054 CTTTAGCGGCGCTTTTCT-CAC
65 CTTTAACGGCG-TTTTCTCCAC
* * * *
28113075 AAACGCCGCTAAAGACCATGA-CTTATAGCGGCGCTTTTTCGCAAAAACGCCGCTAAAAAGCATG
1 AAACGCCGCTAAAGACCATGACCTT-TAGCGGCGC-TTTTC-CACAAACGCCGCTAAAGACCACG
28113139 ACCTTTA
63 ACCTTTA
28113146 GCAACGCTTT
Statistics
Matches: 128, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
84 3 0.02
85 60 0.47
86 40 0.31
87 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (85 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCACAAACGCCGCTAAAGACCACGACC
TTTAACGGCGTTTTCTCCAC
Found at i:28118724 original size:35 final size:37
Alignment explanation
Indices: 28118648--28118733 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 37
28118638 CCCCTGAATC
* * *
28118648 CCTAAACCTTAAATCCCTACCTCTTAAACCCTAACAT
1 CCTAACCCTTAAACCCCTACCTCCTAAACCCTAACAT
* *
28118685 -CTAACCCCTAAACCCCTACC-CCTAAACCTTAA-AT
1 CCTAACCCTTAAACCCCTACCTCCTAAACCCTAACAT
28118719 CCTAACCCTTAAACC
1 CCTAACCCTTAAACC
28118734 ATAATCACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
34 2 0.05
35 23 0.55
36 17 0.40
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (37 bp):
CCTAACCCTTAAACCCCTACCTCCTAAACCCTAACAT
Found at i:28119382 original size:41 final size:41
Alignment explanation
Indices: 28119325--28119437 Score: 199
Period size: 41 Copynumber: 2.8 Consensus size: 41
28119315 GAATATGTTT
*
28119325 TTAGCGGCGCTTCTTCAAAAACACCGCTAAAGAACAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGAACAGAGCA
*
28119366 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGAACAGAGCA
*
28119407 TTAGCGGCGCTTCTTCAAAAATGCCGCTAAA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAA
28119438 TCCCCTAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.19
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGAACAGAGCA
Found at i:28119581 original size:40 final size:40
Alignment explanation
Indices: 28119537--28119613 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
28119527 TTTTCAGAAA
*
28119537 AGCGCCGCTAAT-ACTCGATCTTTAGCGGCGTTTTTTAGGT
1 AGCGCCGCTAATGA-TCGATCTTTAGCGGCATTTTTTAGGT
* *
28119577 AGCGCCGCTAATGATTGATTTTTAGCGGCATTTTTTA
1 AGCGCCGCTAATGATCGATCTTTAGCGGCATTTTTTA
28119614 TCCAAACGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
AGCGCCGCTAATGATCGATCTTTAGCGGCATTTTTTAGGT
Found at i:28119634 original size:12 final size:12
Alignment explanation
Indices: 28119617--28119642 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28119607 TTTTTTATCC
28119617 AAACGCCACTAA
1 AAACGCCACTAA
28119629 AAACGCCACTAA
1 AAACGCCACTAA
28119641 AA
1 AA
28119643 GTCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (12 bp):
AAACGCCACTAA
Found at i:28120198 original size:7 final size:7
Alignment explanation
Indices: 28120186--28120211 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28120176 CTCCCTCTTC
28120186 TTTTTCT
1 TTTTTCT
28120193 TTTTTCT
1 TTTTTCT
28120200 TTTTTCT
1 TTTTTCT
28120207 TTTTT
1 TTTTT
28120212 GTCTTTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:28120970 original size:45 final size:47
Alignment explanation
Indices: 28120917--28121017 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 47
28120907 TTCATATAGA
* *
28120917 ACTACACTTCTTTTATTT-TATT-TTAGAATAATG-TTTTTCAACCTT
1 ACTACACTTCATTTATTTATATTATTAGAATAA-GATGTTTCAACCTT
*
28120962 ATTACACTTCATTTATTTGATATTGATTAGAATAAGATGTTTCAACCTT
1 ACTACACTTCATTTATTT-ATATT-ATTAGAATAAGATGTTTCAACCTT
28121011 ACTACAC
1 ACTACAC
28121018 CATTCTATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
45 16 0.34
47 4 0.09
48 1 0.02
49 26 0.55
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (47 bp):
ACTACACTTCATTTATTTATATTATTAGAATAAGATGTTTCAACCTT
Found at i:28123860 original size:9 final size:9
Alignment explanation
Indices: 28123846--28123876 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28123836 GCTAAACGAA
28123846 TCGAGTTAT
1 TCGAGTTAT
*
28123855 TCGAGTTAA
1 TCGAGTTAT
28123864 TCGAGTTAT
1 TCGAGTTAT
28123873 TCGA
1 TCGA
28123877 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:28123959 original size:9 final size:9
Alignment explanation
Indices: 28123930--28123966 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
28123920 TGAGTTTTCG
28123930 AATTCGAAT
1 AATTCGAAT
*
28123939 AACTCGAAT
1 AATTCGAAT
28123948 AATTCGAAT
1 AATTCGAAT
*
28123957 AATTTGAAT
1 AATTCGAAT
28123966 A
1 A
28123967 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28124059 original size:30 final size:30
Alignment explanation
Indices: 28124015--28124099 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
28124005 AAACCTTTTT
* *
28124015 ACTTTTCCCTCAAAACTTTTACTCCTCCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCCCC
28124045 ACTTTCCCCCCAAAACTTTTACTCCTCCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCCCC
28124075 ACTTTCCCCCCAAAACTTTTACTCC
1 ACTTTCCCCCCAAAACTTTTACTCC
28124100 CCTCCCAACC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.21, C:0.46, G:0.00, T:0.33
Consensus pattern (30 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCCCC
Found at i:28126787 original size:49 final size:49
Alignment explanation
Indices: 28126688--28126787 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 49
28126678 TTATTTTATT
* * * ** *
28126688 TTAGAATAAGGTTTTTCAACCTTATTATACTTCATCTATTTGATATTGA
1 TTAGAATAAGGTGTTTCAACCTTACTACACCCCATCTATTAGATATTGA
*
28126737 TTAGAATAAGGTGTTTCAACCTTACTACACCCCTTCTATTAGA-ATATGA
1 TTAGAATAAGGTGTTTCAACCTTACTACACCCCATCTATTAGATAT-TGA
28126786 TT
1 TT
28126788 TTACAAGCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 2 0.05
49 41 0.95
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (49 bp):
TTAGAATAAGGTGTTTCAACCTTACTACACCCCATCTATTAGATATTGA
Found at i:28133051 original size:12 final size:12
Alignment explanation
Indices: 28133034--28133058 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28133024 AGCAACAATG
28133034 ATTTTAGTTTTT
1 ATTTTAGTTTTT
28133046 ATTTTAGTTTTT
1 ATTTTAGTTTTT
28133058 A
1 A
28133059 GTTTCTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (12 bp):
ATTTTAGTTTTT
Found at i:28141339 original size:16 final size:16
Alignment explanation
Indices: 28141318--28141358 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
28141308 AAATATTATT
28141318 ATTAAATTCAAATGAA
1 ATTAAATTCAAATGAA
* *
28141334 ATTAAACTGAAATGAA
1 ATTAAATTCAAATGAA
*
28141350 ATGAAATTC
1 ATTAAATTC
28141359 CAAAGACTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (16 bp):
ATTAAATTCAAATGAA
Found at i:28141720 original size:13 final size:13
Alignment explanation
Indices: 28141696--28141732 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
28141686 ATGAATAAGT
28141696 AATTTAAAAAAATA
1 AATTTAAAAAAA-A
*
28141710 GATTTAAAAAAAA
1 AATTTAAAAAAAA
28141723 AATTTAAAAA
1 AATTTAAAAA
28141733 CTACACTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AATTTAAAAAAAA
Found at i:28142109 original size:19 final size:19
Alignment explanation
Indices: 28142085--28142121 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28142075 TGAAACAAGT
*
28142085 TATAATTTTTTTAAAAATA
1 TATAATATTTTTAAAAATA
*
28142104 TATAATATTTTTAGAAAT
1 TATAATATTTTTAAAAAT
28142122 TACTTTCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATAATATTTTTAAAAATA
Found at i:28157550 original size:45 final size:45
Alignment explanation
Indices: 28157468--28157553 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
28157458 AGATACTCAA
* * *
28157468 TGGATTCAACACATAGCAACCACCTTATTAATCAATGATGTCCGG
1 TGGAATCAACACATAGCAACCACCTTACTAATAAATGATGTCCGG
* *
28157513 TGGAATCACCACATAGCAACTACCTTACTAATAAATGATGT
1 TGGAATCAACACATAGCAACCACCTTACTAATAAATGATGT
28157554 TCAGTTCACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (45 bp):
TGGAATCAACACATAGCAACCACCTTACTAATAAATGATGTCCGG
Found at i:28157619 original size:51 final size:49
Alignment explanation
Indices: 28157564--28157750 Score: 198
Period size: 51 Copynumber: 3.7 Consensus size: 49
28157554 TCAGTTCACA
* * *
28157564 TAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATTCGATCCATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGGT-CATG
* * * *
28157615 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGT-ATG
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATTCGGTCATG
* * * *
28157664 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 --TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATT-CGGT-CATG
28157716 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
28157751 CACTTTCACT
Statistics
Matches: 112, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
49 6 0.05
50 36 0.32
51 66 0.59
52 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGGTCATG
Found at i:28157743 original size:101 final size:101
Alignment explanation
Indices: 28157562--28157746 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
28157552 GTTCAGTTCA
* * * *
28157562 CATAGTAGCTTGCACATAGTACTACACATGTGACCATTACCATTCGATCCATGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTAGCCTGCA
28157627 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTATG
* *
28157664 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATT-CGATACACGTAGTAGCCTGCA
28157728 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
28157747 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 6 0.08
101 37 0.49
102 33 0.43
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTATG
Found at i:28180798 original size:140 final size:137
Alignment explanation
Indices: 28180479--28180871 Score: 599
Period size: 140 Copynumber: 2.8 Consensus size: 137
28180469 TAGAAAAATG
* *
28180479 AATTATATTCTTTCCAAAAG-ATATTAATTTCCATGCCTTTTATATTTTAACCGAAGTTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAA-TTAATTAA
*
28180543 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAAATAATATTTTGTATGAATCAAATT
28180608 CATATATT
130 CATATATT
* * *
28180616 AATTATATTCTTTCCAAAAAAATAATAATTTCAATGTCTTTTATATTTTGACCGATATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGA-ATTAATTAA
* * *
28180681 TATAACTATTTATATTAATAAATTTGGTAAAATATAAATATAAATAATATTTTGTATGAATCAAA
65 TATAACTGTTTATATTAATAAATTCGGTAAAATAT--ATACAAATAATATTTTGTATGAATCAAA
28180746 TTCATATATT
128 TTCATATATT
* * *
28180756 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATATTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACC-GAATTAATTAA
* * *
28180821 TATATCTGTTTATATTAATAAATTCGGTAAAATGTATACAATTAATATTTT
65 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAAATAATATTTT
28180872 ATATTTTGAT
Statistics
Matches: 230, Mismatches: 21, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
137 19 0.08
138 85 0.37
139 1 0.00
140 124 0.54
141 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.45
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAATTAATTAAT
ATAACTGTTTATATTAATAAATTCGGTAAAATATATACAAATAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:28180803 original size:71 final size:70
Alignment explanation
Indices: 28180587--28180805 Score: 166
Period size: 71 Copynumber: 3.1 Consensus size: 70
28180577 TATACAATTA
* *
28180587 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAAAATAATAATTTCAATG
1 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCC-AAAAAATATTAATTTCAATA
*
28180652 TCTTTT
65 TATTTT
* * * * * * *
28180658 ATATTTTG-ACCGATAT-TAATT-A-ATA-TAACTAT-TTATATT--AATAAATTTGGTAAAATA
1 ATATTTTGTA-TGA-ATCAAATTCATATATTAATTATATTCT-TTCCAAAAAATAT--T--AATT
* ** *
28180715 TAAATATAAATA
59 TCAATATATTTT
*
28180727 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATA
1 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAA-AATATTAATTTCAATA
28180792 TATTTT
65 TATTTT
28180798 ATATTTTG
1 ATATTTTG
28180806 ACCAAAATTA
Statistics
Matches: 106, Mismatches: 26, Indels: 32
0.65 0.16 0.20
Matches are distributed among these distances:
65 6 0.06
67 4 0.04
68 10 0.09
69 26 0.25
70 4 0.04
71 35 0.33
72 10 0.09
73 4 0.04
74 3 0.03
75 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (70 bp):
ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAAATATTAATTTCAATAT
ATTTT
Found at i:28184298 original size:18 final size:17
Alignment explanation
Indices: 28184246--28184295 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
28184236 ATTGGGCTTG
*
28184246 GCCTTTCCATTGTCCTTA
1 GCCTTTCCTTTG-CCTTA
* *
28184264 GGCTTTGCCTTAGCCTTA
1 GCCTTT-CCTTTGCCTTA
28184282 GCCTTTCCTTTGCC
1 GCCTTTCCTTTGCC
28184296 CTTGTTCTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.08, C:0.34, G:0.16, T:0.42
Consensus pattern (17 bp):
GCCTTTCCTTTGCCTTA
Found at i:28187675 original size:34 final size:34
Alignment explanation
Indices: 28187599--28187675 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
28187589 ATCACAATGC
* **
28187599 CAGTAATCAATAGGGCCTTTGCCCAATTTCAGTAA
1 CAGT-ATCAATAGGGCCTTGGCCCAATAACAGTAA
* *
28187634 TAGTATCAATGGGGCCTTGGCCC-ATAACAGTAA
1 CAGTATCAATAGGGCCTTGGCCCAATAACAGTAA
28187667 CAGATATCA
1 CAG-TATCA
28187676 GTCATGCAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
33 10 0.29
34 22 0.63
35 3 0.09
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.26
Consensus pattern (34 bp):
CAGTATCAATAGGGCCTTGGCCCAATAACAGTAA
Found at i:28187735 original size:29 final size:32
Alignment explanation
Indices: 28187679--28187738 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 32
28187669 GATATCAGTC
*
28187679 ATGCAGTGAATAGTATATAATATCATTAATCG
1 ATGCAGTGAATAGTACATAATATCATTAATCG
28187711 ATGCAGT-AATAGTACA-AA-ATCATTAATC
1 ATGCAGTGAATAGTACATAATATCATTAATC
28187739 AGTCTAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.37
30 2 0.07
31 8 0.30
32 7 0.26
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (32 bp):
ATGCAGTGAATAGTACATAATATCATTAATCG
Found at i:28188158 original size:27 final size:27
Alignment explanation
Indices: 28188128--28188472 Score: 345
Period size: 27 Copynumber: 12.8 Consensus size: 27
28188118 TCATCTCTTA
**
28188128 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
28188155 GGGGTATTTC-GATCATTTTACCTTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* * *
28188182 AGGGTATTTCGGTCATATTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
28188209 AGGATATTTCAGTCATTCTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
28188236 GGGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* * * * *
28188263 GTGGTATTTCGGTCATCTTACCCTGTA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
28188290 GGGATATTTTAGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
28188317 AGGGTATTTCAATTATTCTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
28188343 AGGGTATTTCAGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
28188370 GGGGTATTTCAATCATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
28188397 AGGGTATTTCAGTAATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
**
28188424 GGGGTATTTTGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* **
28188451 AGGGTATTTTGGTCATTTTACC
1 GGGGTATTTCAGTCATTTTACC
28188473 TATTTTGGGG
Statistics
Matches: 265, Mismatches: 48, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
26 24 0.09
27 239 0.90
28 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:28188247 original size:81 final size:80
Alignment explanation
Indices: 28188137--28188472 Score: 388
Period size: 81 Copynumber: 4.2 Consensus size: 80
28188127 AGGGGTATAA
* * *
28188137 CAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTATGAGGGTATTTCGGTCATATTA
1 CAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTAT-AGGGTATTTCGGTCATTTTA
28188202 CCCTATGAGGATATTT
65 CCCTATGAGGATATTT
* * * *
28188218 CAGTCATTCTACCCTATGGGGGTATTTCGATCATTTTACCCTATGGTGGTATTTCGGTCATCTTA
1 CAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATAG-GGTATTTCGGTCATTTTA
*
28188283 CCCTGT-AGGGATATTT
65 CCCTATGA-GGATATTT
* * * * * * *
28188299 TAGTCATTTTACCCTATAAGGGTATTTCAATTATTCTACCCTATAGGGTATTTCAGTCATTTTAT
1 CAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATAGGGTATTTCGGTCATTTTAC
* *
28188364 CCTATGGGGGTATTT
66 CCTATGAGGATATTT
* * * * *
28188379 CAATCATTTTATCTTATGAGGGTATTTC-AGTAATTTTACCCTATAGGGGTATTTTGGTCATTTT
1 CAGTCATTTTACCCTATGAGGGTATTTCGA-TCATTTTACCCTATA-GGGTATTTCGGTCATTTT
*
28188443 ACCCTATGAGGGTATTT
64 ACCCTATGAGGATATTT
**
28188460 TGGTCATTTTACC
1 CAGTCATTTTACC
28188473 TATTTTGGGG
Statistics
Matches: 216, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
79 1 0.00
80 65 0.30
81 150 0.69
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (80 bp):
CAGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCCTATAGGGTATTTCGGTCATTTTAC
CCTATGAGGATATTT
Found at i:28196450 original size:6 final size:6
Alignment explanation
Indices: 28196439--28196531 Score: 107
Period size: 6 Copynumber: 15.5 Consensus size: 6
28196429 AAAAAAGAAC
* * *
28196439 AAAGAG AAAGAG AAAGAC AAATAC AAAGAG AAAGAG AAAGAG AAAGAG
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG
* * * *
28196487 AAATAG AAAGAG AAAGAG AAAGA- AACGAC AAAGAGG AAAAAG AAA
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAGA-G AAAGAG AAA
28196532 ATAAAAGAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
5 4 0.05
6 67 0.89
7 4 0.05
ACGTcount: A:0.68, C:0.04, G:0.26, T:0.02
Consensus pattern (6 bp):
AAAGAG
Found at i:28196531 original size:30 final size:30
Alignment explanation
Indices: 28196439--28196518 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
28196429 AAAAAAGAAC
*
28196439 AAAGAGAAAGAGAAAGACAAATACAAAGAG
1 AAAGAGAAAGAGAAAGACAAATAGAAAGAG
*
28196469 AAAGAGAAAGAGAAAGAGAAATAGAAAGAG
1 AAAGAGAAAGAGAAAGACAAATAGAAAGAG
*
28196499 AAAGAGAAAGA-AACGACAAA
1 AAAGAGAAAGAGAAAGACAAA
28196519 GAGGAAAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 7 0.15
30 39 0.85
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.03
Consensus pattern (30 bp):
AAAGAGAAAGAGAAAGACAAATAGAAAGAG
Found at i:28200998 original size:21 final size:21
Alignment explanation
Indices: 28200974--28201015 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
28200964 CATTTTTTTT
*
28200974 ATCTTTTAGTCCCAGAATCAA
1 ATCTTTTAGTCCCAAAATCAA
28200995 ATCTTTTAGTCCCAAAATCAA
1 ATCTTTTAGTCCCAAAATCAA
28201016 GCTATGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (21 bp):
ATCTTTTAGTCCCAAAATCAA
Found at i:28217618 original size:138 final size:136
Alignment explanation
Indices: 28217271--28217688 Score: 590
Period size: 140 Copynumber: 3.0 Consensus size: 136
28217261 TAGAAAAATA
* ** *
28217271 AATTATATTCTTTCTAAAAGAATATTAATTTGTATATCTTTTATATTTTGACCGAAATTAATTTA
1 AATTATATTCTTTC-CAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTTA
* * * *
28217336 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATTAAATT
65 TATAACTTTTTATATTAATAAATTCGGTAAAATAT-TACAATTAATATTTTGTATGAATCAAAAT
28217401 CATATATATT
129 C--ATATATT
* *
28217411 AATTATATTCTTTCCAAACTAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAA-TTA
1 AATTATATTCTTTCCAAA-GAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTTA
*
28217475 GTATAACTTTTTATATTAATAAATCCGGTAAAATATTGACAATTAATATTTTGTATGAATCAAAA
65 -TATAACTTTTTATATTAATAAATTCGGTAAAATATT-ACAATTAATATTTTGTATGAATCAAAA
28217540 TCATATATT
128 TCATATATT
* *
28217549 AATTATATTCTTTCCAACAGAATATTAATTTCCATGTCTTCTATATCTTGACCGAAATTAATTTA
1 AATTATATTCTTTCCAA-AGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTTA
* * *
28217614 TATAA-TTGTTTATATTAATAAATTCGGTAATATA-TATAATTAATATTTTGTATGAATCAAACT
65 TATAACTT-TTTATATTAATAAATTCGGTAAAATATTACAATTAATATTTTGTATGAATCAAAAT
28217677 CATATATT
129 CATATATT
28217685 AATT
1 AATT
28217689 TTATCTACGT
Statistics
Matches: 254, Mismatches: 18, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
136 38 0.15
137 3 0.01
138 91 0.36
139 11 0.04
140 111 0.44
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (136 bp):
AATTATATTCTTTCCAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTTAT
ATAACTTTTTATATTAATAAATTCGGTAAAATATTACAATTAATATTTTGTATGAATCAAAATCA
TATATT
Found at i:28222108 original size:26 final size:26
Alignment explanation
Indices: 28222079--28222147 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
28222069 TGTTCCGACC
*
28222079 CACAGCTCATGTGAGCAGACTCATTT
1 CACAGCTCGTGTGAGCAGACTCATTT
* * *
28222105 CACAGCCCGTGTAAGCATACTCATTT
1 CACAGCTCGTGTGAGCAGACTCATTT
* *
28222131 CATAACTCGTGTGAGCA
1 CACAGCTCGTGTGAGCA
28222148 TATAGGTACA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAGACTCATTT
Found at i:28227825 original size:20 final size:20
Alignment explanation
Indices: 28227802--28227841 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28227792 AGTTAGAAAG
28227802 ATTACCAATTTACTAAATTC
1 ATTACCAATTTACTAAATTC
28227822 ATTACCAATTTACTAAATTC
1 ATTACCAATTTACTAAATTC
28227842 TCAATTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTACCAATTTACTAAATTC
Found at i:28230409 original size:23 final size:25
Alignment explanation
Indices: 28230362--28230419 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
28230352 GGCTAAGGCT
28230362 ATGTTTGGTATGATAGCTTAGCTTA
1 ATGTTTGGTATGATAGCTTAGCTTA
*
28230387 ATGTTTGGTATG-T-GTTTAGCTTA
1 ATGTTTGGTATGATAGCTTAGCTTA
* *
28230410 AAGCTTGGTA
1 ATGTTTGGTA
28230420 GCCTAAGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 17 0.57
24 1 0.03
25 12 0.40
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.45
Consensus pattern (25 bp):
ATGTTTGGTATGATAGCTTAGCTTA
Found at i:28232205 original size:16 final size:17
Alignment explanation
Indices: 28232158--28232211 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
28232148 TCTGTATTAT
*
28232158 TATTTAA-AAATCAATA
1 TATTTAATAAATAAATA
*
28232174 TATTTAAT-TATAAA-A
1 TATTTAATAAATAAATA
28232189 TATTTTAATAAATAAATA
1 TA-TTTAATAAATAAATA
*
28232207 AATTT
1 TATTT
28232212 GAATTTAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 3 0.10
16 17 0.57
17 8 0.27
18 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTAATAAATAAATA
Found at i:28232732 original size:35 final size:33
Alignment explanation
Indices: 28232635--28232745 Score: 106
Period size: 35 Copynumber: 3.4 Consensus size: 33
28232625 AATGAATAAG
*
28232635 ATTTA-TATTTGTGTT-TATATTTGT-TTTTGA
1 ATTTATTATTTGTGTTATATATTTGTATTTTTA
* * * *
28232665 ATTTATAATTTTTTTTATATATTTATGA-TTTTA
1 ATTTATTATTTGTGTTATATATTTGT-ATTTTTA
28232698 ATTGTATTATTTCGTGTTATATATTTGTATTTTTA
1 ATT-TATTATTT-GTGTTATATATTTGTATTTTTA
28232733 ATATTATT-TTTGT
1 AT-TTATTATTTGT
28232746 ACTGCTTTCG
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
30 5 0.08
31 7 0.11
32 8 0.12
33 9 0.14
34 11 0.17
35 23 0.36
36 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (33 bp):
ATTTATTATTTGTGTTATATATTTGTATTTTTA
Found at i:28232804 original size:2 final size:2
Alignment explanation
Indices: 28232797--28232833 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28232787 ATTCTAATGA
28232797 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
28232834 ATGATGATGT
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:28236874 original size:106 final size:106
Alignment explanation
Indices: 28236689--28237000 Score: 525
Period size: 107 Copynumber: 2.9 Consensus size: 106
28236679 TAAAAAAAGG
*
28236689 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTTGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* *
28236754 CGATTTCTCGTTTGACCAAATAGCTTAGTATCCTTCTAAAA
66 CGATTTCTCGTTTGACCAAATAGCTAAATATCCTTCTAAAA
28236795 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * *
28236860 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
66 CGATTTCTCGTTTGA-CCAAATAGCTAAATATCCTTCTAAAA
* * *
28236902 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTACCGTCCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
*
28236967 CGATTTCTCATTTGACCAAATAGCTAAATATCCT
66 CGATTTCTCGTTTGACCAAATAGCTAAATATCCT
28237001 CTTAAGTTTT
Statistics
Matches: 193, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
106 96 0.50
107 97 0.50
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (106 bp):
TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTTGACCAAATAGCTAAATATCCTTCTAAAA
Found at i:28236935 original size:107 final size:106
Alignment explanation
Indices: 28236689--28237005 Score: 526
Period size: 106 Copynumber: 3.0 Consensus size: 106
28236679 TAAAAAAAGG
*
28236689 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTTGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * *
28236754 CGATTTCTCGTTTGACCAAATAGCTTAGTATCCTTCTAAAA
66 CGATTTCTCGTTTGACCAAATAGCTAAATATCCTTTTAAAA
28236795 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* *
28236860 CGATTTCTCGTTTGACCCAAATAGCCAAATACCCTTTTAAAA
66 CGATTTCTCGTTTGA-CCAAATAGCTAAATATCCTTTTAAAA
* * *
28236902 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTACCGTCCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* *
28236967 CGATTTCTCATTTGACCAAATAGCTAAATATCCTCTTAA
66 CGATTTCTCGTTTGACCAAATAGCTAAATATCCTTTTAA
28237006 GTTTTAAGCC
Statistics
Matches: 197, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
106 100 0.51
107 97 0.49
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (106 bp):
TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCGTTTGACCAAATAGCTAAATATCCTTTTAAAA
Found at i:28248344 original size:84 final size:82
Alignment explanation
Indices: 28248246--28248610 Score: 216
Period size: 84 Copynumber: 4.3 Consensus size: 82
28248236 CCATAGATTT
* * * * *
28248246 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATAGAATCAAGTCTTATCTCCCAAAGCAGCAGTGGAGC
28248311 AGATGAAAGAAAAGAATCC
66 AGATGAAA-AAAAG-ATCC
* * * * * ** ** *
28248330 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TAGAATCA-AG-TCTTATCTC-CCAAAGCAGCAGTG
* * ** *
28248395 GAGTAGATCG-CATCAAG-TCT
62 GAGCAGAT-GAAAAAAAGATCC
** * * **
28248415 TATCTCCCT-AAGCAGTAGTGGAGCAGATGAAAGAAATCAA-TCTCATCTCCCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT---AG-AATCAAGTCTTATCTCCC-AAAGCAGCAGT
* * * * *
28248478 GGAACGGATTAAAACCACAGATCT
61 GGAGCAGATGAAAA--AAAGATCC
* * * ** *
28248502 TATCTCTCTGAAGTTGCAGTAGAGCAGATCGCGTCAAGTCTTATCTCCCAAAGCAGTAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATAGAATCAAGTCTTATCTCCCAAAGCAGCAGTGGAGC
*
28248567 AGACGAAAGAAAAGAATCC
66 AGATGAAA-AAAAG-ATCC
28248586 TATCTCCCTGAAGTTGCAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
28248611 GGATTAAAAC
Statistics
Matches: 206, Mismatches: 57, Indels: 36
0.69 0.19 0.12
Matches are distributed among these distances:
83 5 0.02
84 109 0.53
85 27 0.13
86 6 0.03
87 27 0.13
88 31 0.15
89 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (82 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATAGAATCAAGTCTTATCTCCCAAAGCAGCAGTGGAGC
AGATGAAAAAAAGATCC
Found at i:28248352 original size:44 final size:42
Alignment explanation
Indices: 28248202--28248658 Score: 196
Period size: 44 Copynumber: 10.7 Consensus size: 42
28248192 AAGCCAATCC
* ** ** * *
28248202 TATCTCCCTAAAGTTGTAGTGGAATAGATTAGAACCATAGATTT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGA-T-GAAAAAAAGATCT
* * * * **
28248246 TATCTCTCTGAAGTTGCAGTAGAGCAGATCG-CATCAAG-TCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGAT-GAAAAAAAGATCT
** * *
28248287 TATCTCCC-AAAGCAGTAGTGGAGCAGATGAAAGAAAAGAATCC
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATGAAA-AAAAG-ATCT
* * * *
28248330 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATGAAAA--AAAGATCT
* * * * * **
28248374 TATCTCTCTGAAGTTGCAGTAGAGTAGATCG-CATCAAG-TCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGAT-GAAAAAAAGATCT
** *
28248415 TATCTCCCT-AAGCAGTAGTGGAGCAGATGAAAGAAATCA-ATCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATGAAA-AAA--AGATCT
* * * * *
28248458 CATCTCCCTAAAGTTGCAGTGGAACGGATTAAAACCACAGATCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATGAAAA--AAAGATCT
* * * ****
28248502 TATCTCTCTGAAGTTGCAGTAGAGCAGATCG-CGTCAAG-TCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGAT-GAAAAAAAGATCT
** * * *
28248543 TATCTCCC-AAAGCAGTAGTGGAGCAGACGAAAGAAAAGAATCC
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATGAAA-AAAAG-ATCT
* * * *
28248586 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATGAAAA--AAAGATCT
* *
28248630 TATCTCTCTAAAGTTGCAGTAGAGCAGAT
1 TATCTCCCTAAAGTTGCAGTGGAGCAGAT
28248659 CGCATCAAGT
Statistics
Matches: 294, Mismatches: 94, Indels: 50
0.67 0.21 0.11
Matches are distributed among these distances:
39 3 0.01
40 45 0.15
41 37 0.13
42 6 0.02
43 38 0.13
44 158 0.54
45 7 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (42 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGATGAAAAAAAGATCT
Found at i:28248410 original size:128 final size:128
Alignment explanation
Indices: 28248197--28248697 Score: 824
Period size: 128 Copynumber: 3.9 Consensus size: 128
28248187 CAAAGAAGCC
* ** * * *
28248197 AATCCTATCTCCCTAAAGTTGTAGTGGAATAGATTAGAACCATAGATTTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
28248262 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGATGAAAGAAAAG
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGATGAAAGAAAAG
* *
28248325 AATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * **
28248390 CAGTAGAGTAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAGAAATC
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGATGAAAGAAAAG
28248453 AAT-CTCATCTCCCTAAAGTTGCAGTGGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
1 AATCCT-ATCTCCCTAAAGTTGCAGTGGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
* *
28248517 GCAGTAGAGCAGATCGCGTCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGACGAAAGAAAAG
65 GCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGATGAAAGAAAAG
* * *
28248581 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
*
28248646 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
66 CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGA
28248698 CAAAAACCAC
Statistics
Matches: 348, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
127 2 0.01
128 344 0.99
129 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (128 bp):
AATCCTATCTCCCTAAAGTTGCAGTGGAACGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
CAGTAGAGCAGATCGCATCAAGTCTTATCTCCCAAAGCAGTAGTGGAGCAGATGAAAGAAAAG
Found at i:28248704 original size:84 final size:86
Alignment explanation
Indices: 28248330--28248713 Score: 227
Period size: 84 Copynumber: 4.5 Consensus size: 86
28248320 AAAAGAATCC
* * ** *
28248330 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACAAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
* *
28248395 GAGTAGATCGCATCAAG-TCT
66 GAGCAGATCGAATCAAGATCT
** * * *
28248415 TATCTCCCT-AAGCAGTAGTGGAGCAGATGAAAGAA--ATCA-ATCTCATCTCCCTAAAGTTGCA
1 TATCTCCCTGAAGTTGTAGTGGAGCAGA-CAAA-AACCA-CAGATCTTATCTCTCTAAAGTTGCA
* * * ** *
28248476 GTGGAACGGATTAAAACCACAGATCT
63 GTAGAGCAGA-TCGAATCA-AGATCT
* * * **** * ** *
28248502 TATCTCTCTGAAGTTGCAGTAGAGCAGATC--GCGTCA-AG-TCTTATCTC-CCAAAGCAGTAGT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGA-CAAAAACCACAGATCTTATCTCTCTAAAGTTGCAGT
* ** *
28248562 GGAGCAGA-CGAAAGAAAAGAATCC
65 AGAGCAGATCG-AA-TCAAG-ATCT
* * **
28248586 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACAAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
*
28248651 GAGCAGATCGCATCAAG-TCT
66 GAGCAGATCGAATCAAGATCT
** *
28248671 TATCTCCCT-AAGCAGTAGTGGAGCAGACAAAAACCACAAATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACAAAAACCACAGATCT
28248714 CATCCCCATG
Statistics
Matches: 219, Mismatches: 61, Indels: 39
0.69 0.19 0.12
Matches are distributed among these distances:
83 4 0.02
84 112 0.51
85 39 0.18
86 6 0.03
87 24 0.11
88 32 0.15
89 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (86 bp):
TATCTCCCTGAAGTTGTAGTGGAGCAGACAAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
GAGCAGATCGAATCAAGATCT
Found at i:28249088 original size:4 final size:4
Alignment explanation
Indices: 28249079--28249121 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
28249069 TTTTTCGATC
* * *
28249079 TATT TATT TATT TGTTT TATT TATT TATT TCTT TATT TTTT TA
1 TATT TATT TATT T-ATT TATT TATT TATT TATT TATT TATT TA
28249122 CGGATCTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:28249101 original size:17 final size:16
Alignment explanation
Indices: 28249079--28249121 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
28249069 TTTTTCGATC
*
28249079 TATTTATTTATTTGTTT
1 TATTTATTTATTT-CTT
28249096 TATTTATTTATTTCTT
1 TATTTATTTATTTCTT
*
28249112 TATTTTTTTA
1 TATTTATTTA
28249122 CGGATCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (16 bp):
TATTTATTTATTTCTT
Found at i:28250592 original size:107 final size:106
Alignment explanation
Indices: 28250342--28250658 Score: 501
Period size: 107 Copynumber: 3.0 Consensus size: 106
28250332 TAAAGAAAGG
* *
28250342 TTTTAAAATAATGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * *
28250407 CGATTTCT-TGTTTGATCAAATAGCCAAGTATCCTTCTAAAA
66 CGATTTCTCT-TTTGACCAAATAGCCAAATATCCTTTTAAAA
*
28250448 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTAGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
*
28250513 CGATTTCTCTTTTGACCCAAATAGCCAAATACCCTTTTAAAA
66 CGATTTCTCTTTTGA-CCAAATAGCCAAATATCCTTTTAAAA
*
28250555 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACCTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * * *
28250620 TGATTTCTCATTTGACCAAATAGCTAAATATCCTCTTAA
66 CGATTTCTCTTTTGACCAAATAGCCAAATATCCTTTTAA
28250659 GTTTTAATCC
Statistics
Matches: 195, Mismatches: 14, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
106 96 0.49
107 99 0.51
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (106 bp):
TTTTAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGATTTCTCTTTTGACCAAATAGCCAAATATCCTTTTAAAA
Found at i:28258291 original size:16 final size:16
Alignment explanation
Indices: 28258270--28258301 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28258260 TTATGTAACT
28258270 CCCATGTTAGTTTAAG
1 CCCATGTTAGTTTAAG
28258286 CCCATGTTAGTTTAAG
1 CCCATGTTAGTTTAAG
28258302 TGTACATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
CCCATGTTAGTTTAAG
Found at i:28259690 original size:11 final size:10
Alignment explanation
Indices: 28259664--28259706 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
28259654 AGTAGGTTCG
28259664 TAAAAAAATT
1 TAAAAAAATT
28259674 TGAAAAATAATT
1 T-AAAAA-AATT
*
28259686 TAAAAAAATC
1 TAAAAAAATT
*
28259696 GAAAAAAATT
1 TAAAAAAATT
28259706 T
1 T
28259707 GAGAAAAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 12 0.44
11 10 0.37
12 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:28260866 original size:16 final size:17
Alignment explanation
Indices: 28260840--28260871 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28260830 GAGAATAAAC
28260840 AAAAATGTGAAAAAGAA
1 AAAAATGTGAAAAAGAA
28260857 AAAAAT-TGAAAAAGA
1 AAAAATGTGAAAAAGA
28260872 GATTGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (17 bp):
AAAAATGTGAAAAAGAA
Found at i:28263026 original size:52 final size:50
Alignment explanation
Indices: 28262911--28263028 Score: 139
Period size: 50 Copynumber: 2.3 Consensus size: 50
28262901 TAATAAAGTT
* *
28262911 ATGCATTATGTAACTTCCATGCTAGTTAAGTATGCATCATAAATAATGAC
1 ATGCATTATGTAACTCCCATGCTAGTTAAGTATACATCATAAATAATGAC
* * *
28262961 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTACATCATTAAATTAA-GTC
1 ATGCATTATGTAACTCCCATGCTAG-TTAAGTATACATCA-TAAA-TAATGAC
* *
28263013 TTGCATTAAGTAACTC
1 ATGCATTATGTAACTC
28263029 ATTTGTTCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 23 0.40
51 12 0.21
52 20 0.34
53 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (50 bp):
ATGCATTATGTAACTCCCATGCTAGTTAAGTATACATCATAAATAATGAC
Found at i:28266455 original size:22 final size:22
Alignment explanation
Indices: 28266427--28266470 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28266417 ATTGTCTTAA
28266427 GTTGCTACCATTTTACTATTAT
1 GTTGCTACCATTTTACTATTAT
* *
28266449 GTTGCTACTATTTTATTATTAT
1 GTTGCTACCATTTTACTATTAT
28266471 TGTTTGGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (22 bp):
GTTGCTACCATTTTACTATTAT
Found at i:28266539 original size:30 final size:30
Alignment explanation
Indices: 28266503--28266559 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
28266493 TATTTTATTG
28266503 TTAATTTTGTTATTATTTTAAAGGCATTTC
1 TTAATTTTGTTATTATTTTAAAGGCATTTC
*
28266533 TTAATTTTGTTATTATTTTAGAGGCAT
1 TTAATTTTGTTATTATTTTAAAGGCAT
28266560 CTAATTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTC
Found at i:28266865 original size:3 final size:3
Alignment explanation
Indices: 28266857--28266894 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28266847 TAATTTTCCT
28266857 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28266895 GTATTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28273832 original size:38 final size:38
Alignment explanation
Indices: 28273790--28273866 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
28273780 GTATGAGTTG
28273790 ATGGAAATTTGATGACTGAGATGATAAAACATTTATCT
1 ATGGAAATTTGATGACTGAGATGATAAAACATTTATCT
* *
28273828 ATGGAAGTTTGATGATTGAGATGATAAAACATTTATCT
1 ATGGAAATTTGATGACTGAGATGATAAAACATTTATCT
28273866 A
1 A
28273867 CACAAGTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (38 bp):
ATGGAAATTTGATGACTGAGATGATAAAACATTTATCT
Found at i:28273874 original size:38 final size:38
Alignment explanation
Indices: 28273797--28273878 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
28273787 TTGATGGAAA
***
28273797 TTTGATGACTGAGATGATAAAACATTTATCTATGGAAG
1 TTTGATGACTGAGATGATAAAACATTTATCTACACAAG
*
28273835 TTTGATGATTGAGATGATAAAACATTTATCTACACAAG
1 TTTGATGACTGAGATGATAAAACATTTATCTACACAAG
28273873 -TTGATG
1 TTTGATG
28273879 GAAGCTTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 6 0.15
38 34 0.85
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (38 bp):
TTTGATGACTGAGATGATAAAACATTTATCTACACAAG
Found at i:28273881 original size:48 final size:50
Alignment explanation
Indices: 28273828--28273940 Score: 140
Period size: 50 Copynumber: 2.3 Consensus size: 50
28273818 ACATTTATCT
* * *
28273828 ATGGAAGTTTGATGATTGAGATGAT-AAA-ACATTTATCTACACAAGTTG
1 ATGGAAGTTTGATGATTGAAATGATGAAACAAATCTATCTACACAAGTTG
* * * * *
28273876 ATGGAAGCTTGATGATTGAAATGATGAAACAAATCTCTTTGCATAAGTTG
1 ATGGAAGTTTGATGATTGAAATGATGAAACAAATCTATCTACACAAGTTG
28273926 ATGGAAGTTTGATGA
1 ATGGAAGTTTGATGA
28273941 CTAAAATGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 23 0.43
49 3 0.06
50 28 0.52
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (50 bp):
ATGGAAGTTTGATGATTGAAATGATGAAACAAATCTATCTACACAAGTTG
Found at i:28279271 original size:5 final size:5
Alignment explanation
Indices: 28279261--28279289 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
28279251 GAAAACAAAG
28279261 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
28279290 GTTCTATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:28280266 original size:14 final size:14
Alignment explanation
Indices: 28280247--28280276 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28280237 AGTGAGAGAG
*
28280247 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
28280261 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
28280275 GA
1 GA
28280277 ATGAGTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:28300209 original size:20 final size:21
Alignment explanation
Indices: 28300184--28300222 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28300174 TTCGAAAGTG
*
28300184 AAAAG-AAGGAAAATGAGAGC
1 AAAAGAAAAGAAAATGAGAGC
28300204 AAAAGAAAAGAAAATGAGA
1 AAAAGAAAAGAAAATGAGA
28300223 AAAGTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.05
Consensus pattern (21 bp):
AAAAGAAAAGAAAATGAGAGC
Found at i:28307503 original size:30 final size:30
Alignment explanation
Indices: 28307468--28307533 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
28307458 ACGGCTTGAG
* * *
28307468 ACACGGGCGTGTCACTTGGCCGTGTTAGAC
1 ACACGGACGGGTCACTTGGCCGTGTGAGAC
* *
28307498 ACACGGATGGGTCACTTGGCTGTGTGAGAC
1 ACACGGACGGGTCACTTGGCCGTGTGAGAC
28307528 ACACGG
1 ACACGG
28307534 CCTGGCCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.21
Consensus pattern (30 bp):
ACACGGACGGGTCACTTGGCCGTGTGAGAC
Found at i:28308411 original size:23 final size:23
Alignment explanation
Indices: 28308381--28308434 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
28308371 AATAGGAAAC
28308381 TTAAATTTCCAATTTGTTTTGTT
1 TTAAATTTCCAATTTGTTTTGTT
28308404 TTAAATTTCCAATTTGTTTTGTT
1 TTAAATTTCCAATTTGTTTTGTT
28308427 TT-AATTTC
1 TTAAATTTC
28308435 AAATAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.19
23 25 0.81
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.61
Consensus pattern (23 bp):
TTAAATTTCCAATTTGTTTTGTT
Found at i:28312220 original size:20 final size:20
Alignment explanation
Indices: 28312195--28312235 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28312185 ACCTAAAGAA
28312195 CATATTTTTAAGTTTATGTT
1 CATATTTTTAAGTTTATGTT
28312215 CATATTTTTAAGTTTATGTT
1 CATATTTTTAAGTTTATGTT
28312235 C
1 C
28312236 CTGAGCCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (20 bp):
CATATTTTTAAGTTTATGTT
Found at i:28314414 original size:17 final size:18
Alignment explanation
Indices: 28314383--28314416 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28314373 TAGTTAATTC
*
28314383 ATCAAATTAACTAATTTT
1 ATCAAATCAACTAATTTT
28314401 ATCAAATCAA-TAATTT
1 ATCAAATCAACTAATTT
28314417 ATCCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
ATCAAATCAACTAATTTT
Found at i:28317806 original size:20 final size:21
Alignment explanation
Indices: 28317765--28317832 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
28317755 CACGCTATCT
*
28317765 AATTTAATTAAATTAGATAAA
1 AATTTAATTAAATTAAATAAA
*
28317786 AATTTATTTAAA-TAAATAAA
1 AATTTAATTAAATTAAATAAA
*
28317806 AATAATTAATT-AATAAAGATAAA
1 AAT--TTAATTAAATTAA-ATAAA
28317829 AATT
1 AATT
28317833 AGCACGCTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 10 0.26
21 14 0.36
22 7 0.18
23 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
AATTTAATTAAATTAAATAAA
Found at i:28319082 original size:17 final size:16
Alignment explanation
Indices: 28319042--28319083 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
28319032 TTGAATGAGT
*
28319042 AAACAAATAAATTATA
1 AAACAAATAAATAATA
28319058 AAAC--ATAAATAATTA
1 AAACAAATAAATAA-TA
28319073 AAACAAATAAA
1 AAACAAATAAA
28319084 ACTTAGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 7 0.32
15 6 0.27
16 4 0.18
17 5 0.23
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACAAATAAATAATA
Found at i:28322079 original size:22 final size:22
Alignment explanation
Indices: 28322038--28322093 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
28322028 GGTTTATCGA
*
28322038 TTTATTTCATTTGTTTATTT-TT
1 TTTATTTC-TTTATTTATTTCTT
28322060 CTTTATTTCTTTATTTATTTCTT
1 -TTTATTTCTTTATTTATTTCTT
*
28322083 TTTATTCCTTT
1 TTTATTTCTTT
28322094 TATTCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.12, C:0.11, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTATTTCTTTATTTATTTCTT
Found at i:28322096 original size:9 final size:9
Alignment explanation
Indices: 28322082--28322106 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28322072 ATTTATTTCT
28322082 TTTTATTCC
1 TTTTATTCC
28322091 TTTTATTCC
1 TTTTATTCC
28322100 TTTTATT
1 TTTTATT
28322107 TATTTTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATTCC
Found at i:28324044 original size:6 final size:6
Alignment explanation
Indices: 28324026--28324063 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
28324016 TGCAAATGGA
28324026 TCATTT CTCATTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCATTT T
28324064 TGAGAAACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (6 bp):
TCATTT
Found at i:28324991 original size:23 final size:23
Alignment explanation
Indices: 28324961--28325004 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
28324951 AATTGGCCTT
28324961 GATTAGACTAAGGACATGTTTTC
1 GATTAGACTAAGGACATGTTTTC
28324984 GATTAGACTAAGGACATGTTT
1 GATTAGACTAAGGACATGTTT
28325005 AGGTTCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (23 bp):
GATTAGACTAAGGACATGTTTTC
Found at i:28328497 original size:26 final size:27
Alignment explanation
Indices: 28328459--28328528 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
28328449 AATATAAAAT
* *
28328459 ATTTAAAACAAATGATAAG-T-AGGAAA
1 ATTT-AAATAAATGATAAGATGAAGAAA
*
28328485 ATTTGAAATAAATCA-AAGATGAAGAAA
1 ATTT-AAATAAATGATAAGATGAAGAAA
28328512 ATTTAGAATAAATGATA
1 ATTTA-AATAAATGATA
28328529 GAAAATAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.09
26 14 0.40
27 17 0.49
28 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26
Consensus pattern (27 bp):
ATTTAAATAAATGATAAGATGAAGAAA
Found at i:28328702 original size:23 final size:24
Alignment explanation
Indices: 28328648--28328702 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
28328638 CTAAAATAAG
**
28328648 ATATGAAAAATTATTTAAATAGGT
1 ATATGAAAAATTAAATAAATAGGT
* *
28328672 AT-TAAAAAATTAAATAAATA-TT
1 ATATGAAAAATTAAATAAATAGGT
28328694 ATATGAAAA
1 ATATGAAAA
28328703 TGAGCCTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 3 0.12
23 20 0.80
24 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (24 bp):
ATATGAAAAATTAAATAAATAGGT
Found at i:28328736 original size:24 final size:25
Alignment explanation
Indices: 28328709--28328765 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
28328699 AAAATGAGCC
*
28328709 TAAAATAACTAATATA-AATTGA-TT
1 TAAAATAAATAATATAGAA-TGATTT
* *
28328733 TAAAGTAAATAGTATAGAATGATTT
1 TAAAATAAATAATATAGAATGATTT
28328758 TAAAATAA
1 TAAAATAA
28328766 TTATTACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (25 bp):
TAAAATAAATAATATAGAATGATTT
Found at i:28329728 original size:42 final size:42
Alignment explanation
Indices: 28329682--28329771 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
28329672 ACAGAACAAC
*
28329682 AAAAAGAAAAAAGAAAGAAAAACTTTTAAAATCACCTTCGAA
1 AAAAACAAAAAAGAAAGAAAAACTTTTAAAATCACCTTCGAA
********
28329724 AAAAACTTGGTCTTAAGAAAAACTTTTAAAATCACCTTCGAA
1 AAAAACAAAAAAGAAAGAAAAACTTTTAAAATCACCTTCGAA
28329766 AAAAAC
1 AAAAAC
28329772 TTGGTCTTCC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (42 bp):
AAAAACAAAAAAGAAAGAAAAACTTTTAAAATCACCTTCGAA
Found at i:28329772 original size:42 final size:42
Alignment explanation
Indices: 28329696--28329779 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
28329686 AGAAAAAAGA
28329696 AAGAAAAACTTTTAAAATCACCTTCGAAAAAAACTTGGTCTT
1 AAGAAAAACTTTTAAAATCACCTTCGAAAAAAACTTGGTCTT
28329738 AAGAAAAACTTTTAAAATCACCTTCGAAAAAAACTTGGTCTT
1 AAGAAAAACTTTTAAAATCACCTTCGAAAAAAACTTGGTCTT
28329780 CCCTTTTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (42 bp):
AAGAAAAACTTTTAAAATCACCTTCGAAAAAAACTTGGTCTT
Found at i:28330666 original size:132 final size:131
Alignment explanation
Indices: 28330530--28330775 Score: 368
Period size: 131 Copynumber: 1.9 Consensus size: 131
28330520 AATCTAGTTT
* * *
28330530 CCTACTACCTTGGGAAAATAAGATTCGCCATCTTCGATCTGCTACACTACTGCTTAGGGAGATAT
1 CCTACTACCTTGGGAAAATAAAATTCGCCATCTTCGATCTGC-ACACTACTGCTTAGGGAAACA-
* **
28330595 G-GTCTACAATGTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTTC
64 GAATCTACAAACTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTTC
28330659 TTC
129 TTC
* * * *
28330662 CCTACTACCTTGGGAAGATAAAATTTGCCGTCTTCGATCTGCCCACTACTGCTTAGGGAAACAGA
1 CCTACTACCTTGGGAAAATAAAATTCGCCATCTTCGATCTGCACACTACTGCTTAGGGAAACAGA
*
28330727 ATCTACAAACTTCAACCTACTCCACTGCTTCTCAGGGAGATAGGACTGG
66 ATCTACAAACTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGG
28330776 AGTCTTCGAT
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
130 1 0.01
131 63 0.62
132 38 0.37
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (131 bp):
CCTACTACCTTGGGAAAATAAAATTCGCCATCTTCGATCTGCACACTACTGCTTAGGGAAACAGA
ATCTACAAACTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTTCTT
C
Found at i:28330761 original size:131 final size:132
Alignment explanation
Indices: 28330479--28330775 Score: 375
Period size: 132 Copynumber: 2.2 Consensus size: 132
28330469 CATCCTCAGT
* * * * *
28330479 CTACTCCACTGCAATT-TCAGGGAGATAAGACTTGTAACTTCAATCTAGTTTCCTACTACCTTGG
1 CTACTCCACTGC--TTCTCAGGGAGATAGGACTGGTAACTTAAATCTACTTCCCTACTACCTTGG
* * * * **
28330543 GAAAATAAGATTCGCCATCTTCGATCTGCTACACTACTGCTTAGGGAGATATGGTCTACAATGTT
64 GAAAATAAAATTCGCCATCTTCGATCTGCTACACTACTGCTTAGGGAAACATGATCTACAAACTT
28330608 CAAC
129 CAAC
* ** *
28330612 CTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTTCTTCCCTACTACCTTGGGA
1 CTACTCCACTGCTTCTCAGGGAGATAGGACTGGTAACTTAAATCTACTTCCCTACTACCTTGGGA
* * * *
28330677 AGATAAAATTTGCCGTCTTCGATCTGC-CCACTACTGCTTAGGGAAACA-GAATCTACAAACTTC
66 AAATAAAATTCGCCATCTTCGATCTGCTACACTACTGCTTAGGGAAACATG-ATCTACAAACTTC
28330740 AAC
130 AAC
28330743 CTACTCCACTGCTTCTCAGGGAGATAGGACTGG
1 CTACTCCACTGCTTCTCAGGGAGATAGGACTGG
28330776 AGTCTTCGAT
Statistics
Matches: 142, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
130 1 0.01
131 64 0.45
132 65 0.46
133 12 0.08
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (132 bp):
CTACTCCACTGCTTCTCAGGGAGATAGGACTGGTAACTTAAATCTACTTCCCTACTACCTTGGGA
AAATAAAATTCGCCATCTTCGATCTGCTACACTACTGCTTAGGGAAACATGATCTACAAACTTCA
AC
Found at i:28330829 original size:45 final size:45
Alignment explanation
Indices: 28330778--28331271 Score: 708
Period size: 45 Copynumber: 11.0 Consensus size: 45
28330768 AGGACTGGAG
* * * *
28330778 TCTTCGATCTACTTTGATGCCAGTACAAGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* *
28330823 TCTTCGATCTACTTCGCTGCCAATACATGAAGACAAGATCGGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
28330868 TCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
28330913 TCTTCGATCTACTTCACTACCAATACAGGAAGAGAAGAGT-TGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGA-TCTGCTA
* *
28330958 TCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
** *
28331003 TCTTCGATCTACTTCATTGCCAATACAGGAAGACAAGATCTACTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* * *
28331048 TCTTTGATC-ACTTCGCTGCCAATACAGGAAGACAAAATCTGTTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
28331092 TCTTCGATCTACTTCGCTGCCAATGCAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
28331137 TCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
* ** *
28331182 TCTTCGATCTACTTTGCTGCCAATACAGGAAGATGAGATCCGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
*
28331227 TCTTCGATCTACTTCGCTGCC-A-ACAGGAAGACAAAATCTGCTA
1 TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
28331270 TC
1 TC
28331272 CTTTCTTTTC
Statistics
Matches: 400, Mismatches: 46, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
43 19 0.05
44 40 0.10
45 340 0.85
46 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
TCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA
Found at i:28331169 original size:224 final size:224
Alignment explanation
Indices: 28330778--28331271 Score: 717
Period size: 224 Copynumber: 2.2 Consensus size: 224
28330768 AGGACTGGAG
* * *
28330778 TCTTCGATCTACTTTGATGCCAGTACAAGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGC
1 TCTTCGATCTAC-TTCATGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGC
* * * *
28330843 CAATACATGAAGACAAGATCGGCTATCTTTGATCTACTTCGCTGCCAATATAGGAAGACAAGATC
65 CAATACAGGAAGACAAAATCGGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
*
28330908 TACTATCTTCGATCTACTTCACTACCAATACAGGAAGAGAAGAGT-TGCTATCTTCGATCTACTT
130 TACTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGA-TCTGCTATCTTCGATCTACTT
* *
28330972 CGCTACCAATATAGGAAGACAAGATCTGCTA
194 CGCTACCAATACAGGAAGACAAGATCCGCTA
* *
28331003 TCTTCGATCTACTTCATTGCCAATACAGGAAGACAAGATCTACTATCTTTGATC-ACTTCGCTGC
1 TCTTCGATCTACTTCA-TGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGC
* * *
28331067 CAATACAGGAAGACAAAATCTGTTATCTTCGATCTACTTCGCTGCCAATGCAGGAAGACAAGATC
65 CAATACAGGAAGACAAAATCGGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATC
* * *
28331132 TGCTATCTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTT
130 TACTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTC
* **
28331197 GCTGCCAATACAGGAAGATGAGATCCGCTA
195 GCTACCAATACAGGAAGACAAGATCCGCTA
* *
28331227 TCTTCGATCTACTTCGCTGCC-A-ACAGGAAGACAAAATCTGCTATC
1 TCTTCGATCTACTTC-ATGCCAATACAGGAAGACAAGATCTGCTATC
28331272 CTTTCTTTTC
Statistics
Matches: 242, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
222 21 0.09
223 2 0.01
224 174 0.72
225 45 0.19
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (224 bp):
TCTTCGATCTACTTCATGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGCTGCC
AATACAGGAAGACAAAATCGGCTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCT
ACTATCTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTTCG
CTACCAATACAGGAAGACAAGATCCGCTA
Found at i:28332549 original size:10 final size:10
Alignment explanation
Indices: 28332536--28332561 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28332526 TTAATTTTTC
28332536 TTTTTTTTAT
1 TTTTTTTTAT
28332546 TTTTTTTTAT
1 TTTTTTTTAT
28332556 TTTTTT
1 TTTTTT
28332562 GGACTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:28332559 original size:16 final size:17
Alignment explanation
Indices: 28332522--28332559 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
28332512 TAGCCTCTCC
28332522 ATTTTTAATTTTTCTTT
1 ATTTTTAATTTTTCTTT
*
28332539 -TTTTT-ATTTTTTTTT
1 ATTTTTAATTTTTCTTT
28332554 ATTTTT
1 ATTTTT
28332560 TTGGACTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (17 bp):
ATTTTTAATTTTTCTTT
Found at i:28332606 original size:46 final size:46
Alignment explanation
Indices: 28332555--28332644 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
28332545 TTTTTTTTTA
* * *
28332555 TTTTTTT-GGACTCAAAGCGCCCTTTGCGGGTTTTTACCTTGGTCT
1 TTTTTTTAGGACTCAAAGCGCCCTTTACGAGTTTTCACCTTGGTCT
*
28332600 TTTTTTTAGGACTCAAAGTGCCCTTTACGAGTTTTCACCTTGGTC
1 TTTTTTTAGGACTCAAAGCGCCCTTTACGAGTTTTCACCTTGGTC
28332645 CCTTCTCCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 7 0.17
46 33 0.82
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (46 bp):
TTTTTTTAGGACTCAAAGCGCCCTTTACGAGTTTTCACCTTGGTCT
Found at i:28333406 original size:22 final size:22
Alignment explanation
Indices: 28333378--28333419 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
28333368 ATTAATGATC
28333378 TAAAAAATGAAGCAATGCCCAT
1 TAAAAAATGAAGCAATGCCCAT
28333400 TAAAAAATGAAGCAATGCCC
1 TAAAAAATGAAGCAATGCCC
28333420 TTTGCTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (22 bp):
TAAAAAATGAAGCAATGCCCAT
Found at i:28333460 original size:11 final size:11
Alignment explanation
Indices: 28333446--28333485 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
28333436 TTGGCCTCTC
28333446 CTTTTTCTTTT
1 CTTTTTCTTTT
28333457 CTTTTAT-TTTT
1 CTTTT-TCTTTT
*
28333468 CCTTTTCTTTT
1 CTTTTTCTTTT
28333479 CTTTTTC
1 CTTTTTC
28333486 CATCATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 1 0.04
11 23 0.92
12 1 0.04
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:28333472 original size:17 final size:17
Alignment explanation
Indices: 28333447--28333486 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
28333437 TGGCCTCTCC
28333447 TTTTT-CTTTTCTTTTA
1 TTTTTCCTTTTCTTTTA
*
28333463 TTTTTCCTTTTCTTTTC
1 TTTTTCCTTTTCTTTTA
28333480 TTTTTCC
1 TTTTTCC
28333487 ATCATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCCTTTTCTTTTA
Found at i:28336171 original size:16 final size:16
Alignment explanation
Indices: 28336146--28336178 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28336136 TTCTATGATG
28336146 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTCA
*
28336162 AAATGTCATGCAGTCA
1 AAATGCCATGCAGTCA
28336178 A
1 A
28336179 GACAAAACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (16 bp):
AAATGCCATGCAGTCA
Found at i:28337276 original size:24 final size:25
Alignment explanation
Indices: 28337249--28337306 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
28337239 GAAAATGAGC
*
28337249 TTAAAATAACTAATATA-AATTGA-T
1 TTAAAATAAATAATATAGAA-TGATT
* *
28337273 TTAAAGTAAATAGTATAGAATGATT
1 TTAAAATAAATAATATAGAATGATT
28337298 TTAAAATAA
1 TTAAAATAA
28337307 TTATTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (25 bp):
TTAAAATAAATAATATAGAATGATT
Found at i:28339007 original size:72 final size:72
Alignment explanation
Indices: 28338926--28339070 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
28338916 TACATGCTCC
* *
28338926 TAACCAATCACTTGTATTTCTATAAGCTCAAGCACATAAAACACAAGAAAAATCAAAGAAAATGT
1 TAACCAATCACTTGTATTTCTACAAGCTCAAGCACACAAAACACAAGAAAAATCAAAGAAAATGT
28338991 AAAAATT
66 AAAAATT
* *
28338998 TAACCAATCACTTGTATTTCTACAAGCTCAAGCACACAAAAGACAAGAAAAATCAATGAAAATGT
1 TAACCAATCACTTGTATTTCTACAAGCTCAAGCACACAAAACACAAGAAAAATCAAAGAAAATGT
28339063 AAAAATT
66 AAAAATT
28339070 T
1 T
28339071 GAAGCAAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.23
Consensus pattern (72 bp):
TAACCAATCACTTGTATTTCTACAAGCTCAAGCACACAAAACACAAGAAAAATCAAAGAAAATGT
AAAAATT
Found at i:28344751 original size:129 final size:128
Alignment explanation
Indices: 28344514--28344754 Score: 313
Period size: 129 Copynumber: 1.9 Consensus size: 128
28344504 CTCAAAAATC
* *
28344514 TCGATATCAGAATTTACGACGTTTCAAAATATTATATCAAGAGGTTTTCTAAGAAAAAGTATCAA
1 TCGATATCAGAATTTACGAAGTTTCAAAATATTATATCAAAAGGTTTTCTAAGAAAAAGTATCAA
* * * *
28344579 ATTATTCATATATTTTAGTAAAAGAGCATTCTCATCAGAAAATCTCCATTGAGATAAAGAATT
66 ATTATTCATATAATTTAGTAAAAGAGAATTCCCACCAGAAAATCTCCATTGAGATAAAGAATT
** * * * * * *
28344642 TCGATATCAGAATTTGTGAAGTTTTAAAATGTTATA-CTAAAAGGTTTTTTGATAAATGAGTATC
1 TCGATATCAGAATTTACGAAGTTTCAAAATATTATATC-AAAAGGTTTTCTAAGAAA-AAGTATC
* *
28344706 AAATTATTCATATAATTTCGTAAAAGAGAATTCCCACCAGGAAATCTCC
64 AAATTATTCATATAATTTAGTAAAAGAGAATTCCCACCAGAAAATCTCC
28344755 TTTAGTTAGT
Statistics
Matches: 95, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
127 1 0.01
128 45 0.47
129 49 0.52
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (128 bp):
TCGATATCAGAATTTACGAAGTTTCAAAATATTATATCAAAAGGTTTTCTAAGAAAAAGTATCAA
ATTATTCATATAATTTAGTAAAAGAGAATTCCCACCAGAAAATCTCCATTGAGATAAAGAATT
Found at i:28344939 original size:120 final size:120
Alignment explanation
Indices: 28344776--28345016 Score: 365
Period size: 120 Copynumber: 2.0 Consensus size: 120
28344766 GAGATGAAGG
* **
28344776 ATTTCATTAAATTAGGCTATAGACTATATTGCAAGAAAATTCAAATTGTGTGGTTAATTGTATAA
1 ATTTCATTAAATTAGGCTATAGACTATATTGAAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
* * * *
28344841 AGTATTGATTTTTAGTAAGGAAAGAAGGAAAGGGTTTATGATGTTATTTTACCCA
66 AGTATTGATTTTTAGTAAGAAAAGAAAGAAAGGGTTTATGAGGTAATTTTACCCA
* * *
28344896 ATTTTATTAAATTAGGCTATGGACTATTTTGAAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
1 ATTTCATTAAATTAGGCTATAGACTATATTGAAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
* * *
28344961 AGTATTGGTTTTTTGTAAGAAAAGAAAGAAAGGGTTTATGGGGTAATTTTACCCA
66 AGTATTGATTTTTAGTAAGAAAAGAAAGAAAGGGTTTATGAGGTAATTTTACCCA
28345016 A
1 A
28345017 GGTCTATTGT
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (120 bp):
ATTTCATTAAATTAGGCTATAGACTATATTGAAAGAAAATTCAAATTAAGTGGTTAATTGTATAA
AGTATTGATTTTTAGTAAGAAAAGAAAGAAAGGGTTTATGAGGTAATTTTACCCA
Found at i:28345049 original size:120 final size:118
Alignment explanation
Indices: 28344808--28345041 Score: 292
Period size: 120 Copynumber: 2.0 Consensus size: 118
28344798 ACTATATTGC
** * *
28344808 AAGAAAATTCAAATTGTGTGGTTAATTGTATAAAGTATTGATTTTTAGTAAGGAAAGAAGGAAAG
1 AAGAAAATTCAAATTAAGTGGTTAATTGTATAAAGTATTGATTTTTAGTAAGAAAAGAAAGAAAG
* * * * * * **
28344873 GGTTTATGATGTTATTTTACCCAATTTTATTAAATTAGGCTATGGACTATTTTGA
66 GGTTTATGAGGTAATTTTACCCAAGTCTATT--AGTAGGCTAGGGAAAATTTTGA
* *
28344928 AAGAAAATTCAAATTAAGTGGTTAATTGTATAAAGTATTGGTTTTTTGTAAGAAAAGAAAGAAAG
1 AAGAAAATTCAAATTAAGTGGTTAATTGTATAAAGTATTGATTTTTAGTAAGAAAAGAAAGAAAG
*
28344993 GGTTTATGGGGTAATTTTACCCAAGGTCTATT-GTA-GCTAGGGAAAATTT
66 GGTTTATGAGGTAATTTTACCCAA-GTCTATTAGTAGGCTAGGGAAAATTT
28345042 ATGTGAAAAA
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
117 11 0.11
118 2 0.02
120 80 0.82
121 5 0.05
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (118 bp):
AAGAAAATTCAAATTAAGTGGTTAATTGTATAAAGTATTGATTTTTAGTAAGAAAAGAAAGAAAG
GGTTTATGAGGTAATTTTACCCAAGTCTATTAGTAGGCTAGGGAAAATTTTGA
Found at i:28351171 original size:13 final size:13
Alignment explanation
Indices: 28351133--28351174 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
28351123 TGGACATAGA
* *
28351133 TATATGAAACAGT
1 TATATGAAATATT
*
28351146 TATATGAAGTATT
1 TATATGAAATATT
28351159 TATATGAAATATT
1 TATATGAAATATT
28351172 TAT
1 TAT
28351175 TGGAATATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (13 bp):
TATATGAAATATT
Found at i:28357403 original size:20 final size:21
Alignment explanation
Indices: 28357374--28357417 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28357364 AAAATAAAGG
28357374 AAAAAAATTTTAA-AAT-TTAT
1 AAAAAAA-TTTAATAATATTAT
*
28357394 AAAAACATTTAATAATATTAT
1 AAAAAAATTTAATAATATTAT
28357415 AAA
1 AAA
28357418 CATTAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAAATTTAATAATATTAT
Found at i:28360256 original size:13 final size:12
Alignment explanation
Indices: 28360234--28360263 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
28360224 ATGTTAAGTT
28360234 ATTTGTGTGAAA
1 ATTTGTGTGAAA
28360246 ATTTCGTGTGAAA
1 ATTT-GTGTGAAA
28360259 ATTTG
1 ATTTG
28360264 ATCGTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.43
Consensus pattern (12 bp):
ATTTGTGTGAAA
Found at i:28361309 original size:20 final size:20
Alignment explanation
Indices: 28361284--28361323 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
28361274 AATATTTTCC
*
28361284 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
28361304 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
28361324 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:28361325 original size:34 final size:35
Alignment explanation
Indices: 28361272--28361338 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28361262 CAAACACCAG
*
28361272 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
28361307 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28361339 CATTATACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28362206 original size:33 final size:33
Alignment explanation
Indices: 28362165--28362231 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28362155 AAGATCTAAG
28362165 TAAGAGAAGCAACTAAAGTAAGTATACAAATGC
1 TAAGAGAAGCAACTAAAGTAAGTATACAAATGC
28362198 TAAGAGAAGCAACTAAAGTAAGTATACAAATGC
1 TAAGAGAAGCAACTAAAGTAAGTATACAAATGC
28362231 T
1 T
28362232 TAGTAAGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.19
Consensus pattern (33 bp):
TAAGAGAAGCAACTAAAGTAAGTATACAAATGC
Found at i:28363882 original size:34 final size:34
Alignment explanation
Indices: 28363844--28363924 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
28363834 TTAAGTTTAC
28363844 ATATATATATATGGGTAGTATT-GAATACGT-ACAA
1 ATATATATATATGGGTAGT-TTCGAATACGTGA-AA
* * * * *
28363878 ATATATATGTATAGTTAGTTTCGAATAGGTGAAT
1 ATATATATATATGGGTAGTTTCGAATACGTGAAA
28363912 ATATATATATATG
1 ATATATATATATG
28363925 TAAAATTCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
33 2 0.05
34 35 0.92
35 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.40
Consensus pattern (34 bp):
ATATATATATATGGGTAGTTTCGAATACGTGAAA
Found at i:28372516 original size:17 final size:17
Alignment explanation
Indices: 28372455--28372517 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
28372445 CGAGCAAGAT
28372455 AAAAAATAATATAAATGAA
1 AAAAAATAA-ATAAAT-AA
* *
28372474 AACACAAATTAATAAACAA
1 AA-A-AAATAAATAAATAA
**
28372493 ATGAAATAAATAAATAA
1 AAAAAATAAATAAATAA
28372510 AAAAAATA
1 AAAAAATA
28372518 CAGAATAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 18 0.53
19 5 0.15
20 6 0.18
21 5 0.15
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAAAATAAATAAATAA
Found at i:28372774 original size:16 final size:16
Alignment explanation
Indices: 28372755--28372827 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 16
28372745 ACGTGTATAT
28372755 ATATAAATATAAAAAA
1 ATATAAATATAAAAAA
**
28372771 ATATTCAT-T-AAAAA
1 ATATAAATATAAAAAA
*
28372785 ATATAAATATAGAAAA
1 ATATAAATATAAAAAA
***
28372801 ATATTCGT-TAGAAAAA
1 ATATAAATATA-AAAAA
28372817 ATATAAATATA
1 ATATAAATATA
28372828 TATACATATA
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
14 11 0.27
15 4 0.10
16 24 0.59
17 2 0.05
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (16 bp):
ATATAAATATAAAAAA
Done.