Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 216 of 425
Found at i:65880545 original size:9 final size:10
Alignment explanation
Indices: 65880521--65880558 Score: 51
Period size: 9 Copynumber: 3.7 Consensus size: 10
65880511 AAAAATTTGA
65880521 AAAAAAATTCG
1 AAAAAAA-TCG
65880532 AAAAAAAATC-
1 -AAAAAAATCG
65880542 AAAAAAATCG
1 AAAAAAATCG
65880552 AAAAAAA
1 AAAAAAA
65880559 AGTGATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.36
10 7 0.28
11 2 0.08
12 7 0.28
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:65880545 original size:20 final size:20
Alignment explanation
Indices: 65880521--65880559 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
65880511 AAAAATTTGA
65880521 AAAAAAATTCGAAAAAAAATC
1 AAAAAAA-TCGAAAAAAAATC
65880542 AAAAAAATCGAAAAAAAA
1 AAAAAAATCGAAAAAAAA
65880560 GTGATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (20 bp):
AAAAAAATCGAAAAAAAATC
Found at i:65883152 original size:30 final size:30
Alignment explanation
Indices: 65883118--65883214 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65883108 TAAACTAAAA
65883118 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65883148 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65883178 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65883208 TGAGCTA
1 TGAGCTA
65883215 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65885393 original size:30 final size:30
Alignment explanation
Indices: 65885322--65885404 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
65885312 CTTTTGTTTC
* *
65885322 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
65885353 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
65885382 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
65885405 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:65885404 original size:18 final size:18
Alignment explanation
Indices: 65885355--65885410 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
65885345 CACTCTCAAA
* *
65885355 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
65885372 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
65885390 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
65885409 TT
1 TT
65885411 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:65885411 original size:12 final size:12
Alignment explanation
Indices: 65885380--65885404 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65885370 TTTTTCAATC
65885380 TCATTTTCTTTT
1 TCATTTTCTTTT
65885392 TCATTTTCTTTT
1 TCATTTTCTTTT
65885404 T
1 T
65885405 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:65885422 original size:12 final size:12
Alignment explanation
Indices: 65885407--65885437 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65885397 TTCTTTTTGC
65885407 TTTTCAAAGGCT
1 TTTTCAAAGGCT
65885419 TTTTCAAAGGCT
1 TTTTCAAAGGCT
65885431 TTTTCAA
1 TTTTCAA
65885438 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:65885495 original size:5 final size:5
Alignment explanation
Indices: 65885485--65885541 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65885475 CTCTTGCCTC
*
65885485 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
65885532 TCTTT TCTTT
1 TCTTT TCTTT
65885542 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:65885525 original size:15 final size:14
Alignment explanation
Indices: 65885485--65885541 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65885475 CTCTTGCCTC
*
65885485 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
65885500 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
65885515 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
65885532 TCTTTTCTTT
1 TCTTTTCTTT
65885542 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:65885551 original size:21 final size:20
Alignment explanation
Indices: 65885483--65885552 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
65885473 GCCTCTTGCC
65885483 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
65885506 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
65885526 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
65885546 TCTCTTT
1 TCTCTTT
65885553 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:65886475 original size:12 final size:11
Alignment explanation
Indices: 65886458--65886508 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
65886448 CATTAAACAC
65886458 TTTTTTCAGATT
1 TTTTTTC-GATT
*
65886470 TTTTTT-GAAT
1 TTTTTTCGATT
65886480 TTTTTT-GAATT
1 TTTTTTCG-ATT
65886491 TTTTTTCGAATT
1 TTTTTTCG-ATT
65886503 TTTTTT
1 TTTTTT
65886509 GACTTGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 10 0.29
11 8 0.23
12 17 0.49
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTTTCGATT
Found at i:65886482 original size:10 final size:10
Alignment explanation
Indices: 65886469--65886507 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
65886459 TTTTTCAGAT
65886469 TTTTTTTGAA
1 TTTTTTTGAA
65886479 TTTTTTTGAA
1 TTTTTTTGAA
65886489 TTTTTTTTCGAA
1 -TTTTTTT-GAA
65886501 TTTTTTT
1 TTTTTTT
65886508 TGACTTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.37
11 14 0.52
12 3 0.11
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:65886496 original size:11 final size:11
Alignment explanation
Indices: 65886467--65886510 Score: 72
Period size: 12 Copynumber: 4.0 Consensus size: 11
65886457 CTTTTTTCAG
65886467 ATTTTTTTTGA
1 ATTTTTTTTGA
65886478 A-TTTTTTTGA
1 ATTTTTTTTGA
65886488 ATTTTTTTTCGA
1 ATTTTTTTT-GA
65886500 ATTTTTTTTGA
1 ATTTTTTTTGA
65886511 CTTGTATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.32
11 10 0.32
12 11 0.35
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.70
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:65888192 original size:30 final size:30
Alignment explanation
Indices: 65888158--65888254 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65888148 TAAACTAAAA
65888158 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65888188 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65888218 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65888248 TGAGCTA
1 TGAGCTA
65888255 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65890964 original size:19 final size:19
Alignment explanation
Indices: 65890940--65890979 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65890930 AGCTCCCATG
65890940 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
65890959 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
65890978 TA
1 TA
65890980 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:65892241 original size:14 final size:14
Alignment explanation
Indices: 65892219--65892266 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
65892209 ACCTAAACCG
* *
65892219 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
65892233 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
65892247 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
65892261 ACCATT
1 ACCATT
65892267 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:65894237 original size:19 final size:18
Alignment explanation
Indices: 65894213--65894251 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
65894203 AGCTCCCATG
65894213 TAGCTCCACACCAGCTCAT
1 TAGCT-CACACCAGCTCAT
**
65894232 TAGCTCGGACCAGCTCAT
1 TAGCTCACACCAGCTCAT
65894250 TA
1 TA
65894252 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (18 bp):
TAGCTCACACCAGCTCAT
Found at i:65895693 original size:17 final size:17
Alignment explanation
Indices: 65895671--65895703 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
65895661 GCTACAGCCG
65895671 TTTAACTTGTTTAATTA
1 TTTAACTTGTTTAATTA
65895688 TTTAACTTGTTTAATT
1 TTTAACTTGTTTAATT
65895704 GTGCTTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTAACTTGTTTAATTA
Found at i:65905028 original size:14 final size:14
Alignment explanation
Indices: 65905009--65905045 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
65904999 CATAAATCAC
*
65905009 TTTTTTTTT-TGAA
1 TTTTTTTTTCGGAA
65905022 TTTTTTTTTCGGAA
1 TTTTTTTTTCGGAA
65905036 TTTTTTTTTC
1 TTTTTTTTTC
65905046 AAACTTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.11, C:0.05, G:0.08, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTCGGAA
Found at i:65907957 original size:30 final size:31
Alignment explanation
Indices: 65907923--65907982 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
65907913 AGCTCCAATC
* *
65907923 AGCTCACTTGAGCTTGTTT-CAGCTCATTTG
1 AGCTCAATTGAGCTTCTTTCCAGCTCATTTG
*
65907953 AGCTCAATTTAGCTTCTTTCCAGCTCATTT
1 AGCTCAATTGAGCTTCTTTCCAGCTCATTT
65907983 CTTTTTCTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (31 bp):
AGCTCAATTGAGCTTCTTTCCAGCTCATTTG
Found at i:65910488 original size:49 final size:49
Alignment explanation
Indices: 65910410--65910655 Score: 285
Period size: 49 Copynumber: 5.0 Consensus size: 49
65910400 GTAGCTGAAG
* * *
65910410 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAA
* * *
65910459 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AA
* * * * *
65910509 CCATTTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA
* * * * * *
65910559 GTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAA
* * *
65910609 CAATTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC
65910656 TCACAATAGC
Statistics
Matches: 162, Mismatches: 32, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
49 79 0.49
50 47 0.29
51 36 0.22
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAA
Found at i:65910647 original size:100 final size:99
Alignment explanation
Indices: 65910415--65910654 Score: 338
Period size: 100 Copynumber: 2.4 Consensus size: 99
65910405 TGAAGCTATC
* * * * * * *
65910415 TGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACAAATTATCAGGTACACATAGTAGC
** *
65910480 CTGCACTTAGTACTACACACGTGACCTAACCATT
66 CTGCACTTAGTACTACACACGCAACCTAACAATT
* *
65910514 TGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCAGGTACGCATAGTA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CAAA-TTATCAGGTACACATAGTA
*
65910579 GCCTGCACTTAGTACTACACATGCAACC-AACAATT
64 GCCTGCACTTAGTACTACACACGCAACCTAACAATT
65910614 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
65910655 CTCACAATAG
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
99 36 0.29
100 48 0.38
101 41 0.33
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (99 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACAAATTATCAGGTACACATAGTAGC
CTGCACTTAGTACTACACACGCAACCTAACAATT
Found at i:65911028 original size:35 final size:35
Alignment explanation
Indices: 65910977--65911043 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
65910967 ATATTTCATA
*
65910977 ATAACAATCTTCATATCATATAAATAACATTAATG
1 ATAACAATCATCATATCATATAAATAACATTAATG
*
65911012 ATAATAATCATCATATCATATAAATAACATTA
1 ATAACAATCATCATATCATATAAATAACATTA
65911044 TATTACTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.34
Consensus pattern (35 bp):
ATAACAATCATCATATCATATAAATAACATTAATG
Found at i:65911046 original size:19 final size:19
Alignment explanation
Indices: 65910989--65911046 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
65910979 AACAATCTTC
65910989 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
* *
65911008 A-AT--GAT-AATAATCATC
1 ATATCATATAAATAA-CATT
65911024 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
65911043 ATAT
1 ATAT
65911047 TACTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 5 0.17
16 6 0.20
17 2 0.07
18 2 0.07
19 10 0.33
20 5 0.17
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATCATATAAATAACATT
Found at i:65911270 original size:30 final size:30
Alignment explanation
Indices: 65911236--65911293 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
65911226 CTTTAATACG
65911236 AACTTTGGCAAAATTAC-CATTTTGCCCCCA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCCA
* *
65911266 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGCAAAATTACACTTTTGCCCC
65911294 TAGGCTCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCCA
Found at i:65913369 original size:15 final size:15
Alignment explanation
Indices: 65913340--65913378 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
65913330 AACAGAGAAG
65913340 CCAAGAATAAAGAAAT
1 CCAAG-ATAAAGAAAT
65913356 CCAAGATAAAGAAAT
1 CCAAGATAAAGAAAT
*
65913371 CCATGATA
1 CCAAGATA
65913379 CGAGAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (15 bp):
CCAAGATAAAGAAAT
Found at i:65914907 original size:21 final size:20
Alignment explanation
Indices: 65914863--65914911 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
65914853 TCAGCTCCCA
* *
65914863 TCAGCTCACTTGAGCTCGAT
1 TCAGCTCGCTTGAGCTAGAT
*
65914883 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
65914904 TCAGCTCG
1 TCAGCTCG
65914912 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:65916404 original size:19 final size:19
Alignment explanation
Indices: 65916380--65916430 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
65916370 ATTGTGAAGT
65916380 ATTAAAAAAAATATACGAA
1 ATTAAAAAAAATATACGAA
65916399 ATTAAAAAAAATATATACGAA
1 ATT-AAAAAAA-ATATACGAA
65916420 ATTAAAAAAAA
1 ATTAAAAAAAA
65916431 AGTGTGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.13
20 14 0.47
21 12 0.40
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (19 bp):
ATTAAAAAAAATATACGAA
Found at i:65916409 original size:21 final size:21
Alignment explanation
Indices: 65916383--65916431 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
65916373 GTGAAGTATT
65916383 AAAAAAAATATACGAAATTAA
1 AAAAAAAATATACGAAATTAA
*
65916404 AAAAAATATATACGAAATTAA
1 AAAAAAAATATACGAAATTAA
65916425 AAAAAAA
1 AAAAAAA
65916432 GTGTGTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAAAAAATATACGAAATTAA
Found at i:65917397 original size:19 final size:20
Alignment explanation
Indices: 65917365--65917405 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
65917355 GAATGAAATC
65917365 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
65917385 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
65917404 GA
1 GA
65917406 AAATGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:65919709 original size:21 final size:20
Alignment explanation
Indices: 65919665--65919713 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
65919655 TCAGCTCCCA
* *
65919665 TCAGCTCACTTGAGCTCGAT
1 TCAGCTCGCTTGAGCTAGAT
*
65919685 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
65919706 TCAGCTCG
1 TCAGCTCG
65919714 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:65922637 original size:49 final size:49
Alignment explanation
Indices: 65922560--65922805 Score: 276
Period size: 49 Copynumber: 5.0 Consensus size: 49
65922550 GTAGCTGAAG
* * * *
65922560 CTATCTGTTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAA
* * * *
65922609 TTATCTGGTACATGTAGTAGCCTACACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC-AA
* * * * * *
65922659 CCATTTGATACACGTAGTAGCCTGCACTTAGTACTGCACACGTGATCGAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA
* * * * *
65922709 GTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAA
* *
65922759 CAATCTGGTACACGTAGTACCCTGCACTTAGTACTACACATGTGACC
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
65922806 TCACAATAGC
Statistics
Matches: 160, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 79 0.49
50 45 0.28
51 36 0.22
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCAA
Found at i:65922747 original size:101 final size:98
Alignment explanation
Indices: 65922574--65922805 Score: 302
Period size: 100 Copynumber: 2.3 Consensus size: 98
65922564 CTGTTACGCA
* * **
65922574 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACATGTAGTAGCCTACACTTA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACATAGTAGCCTACACTTA
* * *
65922639 GTACTACACACGTGACCTAACCATTTGATACACG
66 GTACTACACACGCGACC-AACAATCTGATACACG
* * * * *
65922673 TAGTAGCCTGCACTTAGTACTGCACACGTGATCGAAGTTATCAGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-TTATCAGGTACACATAGTAGCCTACACT
* *
65922738 TAGTACTACACATGCGACCAACAATCTGGTACACG
64 TAGTACTACACACGCGACCAACAATCTGATACACG
*
65922773 TAGTACCCTGCACTTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACC
65922806 TCACAATAGC
Statistics
Matches: 113, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
99 29 0.26
100 44 0.39
101 40 0.35
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCAGGTACACATAGTAGCCTACACTTA
GTACTACACACGCGACCAACAATCTGATACACG
Found at i:65923178 original size:35 final size:35
Alignment explanation
Indices: 65923127--65923193 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
65923117 ATATTTCATA
*
65923127 ATAACAATCTTCATATCATATAAATAACATTAATG
1 ATAACAATCATCATATCATATAAATAACATTAATG
*
65923162 ATAATAATCATCATATCATATAAATAACATTA
1 ATAACAATCATCATATCATATAAATAACATTA
65923194 TATTACTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.34
Consensus pattern (35 bp):
ATAACAATCATCATATCATATAAATAACATTAATG
Found at i:65923196 original size:19 final size:19
Alignment explanation
Indices: 65923139--65923196 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
65923129 AACAATCTTC
65923139 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
* *
65923158 A-AT--GAT-AATAATCATC
1 ATATCATATAAATAA-CATT
65923174 ATATCATATAAATAACATT
1 ATATCATATAAATAACATT
65923193 ATAT
1 ATAT
65923197 TACTTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
15 5 0.17
16 6 0.20
17 2 0.07
18 2 0.07
19 10 0.33
20 5 0.17
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATCATATAAATAACATT
Found at i:65923420 original size:30 final size:30
Alignment explanation
Indices: 65923386--65923443 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
65923376 CTTTAATACG
65923386 AACTTTGGCAAAATTAC-CATTTTGCCCCCA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCCA
* *
65923416 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGCAAAATTACACTTTTGCCCC
65923444 TAGGCTCAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCCA
Found at i:65926476 original size:37 final size:37
Alignment explanation
Indices: 65926426--65926500 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
65926416 AATTTTGTTC
65926426 ATTTTAATAGCATTATTTTGGAAGTAAAAACAAAGAA
1 ATTTTAATAGCATTATTTTGGAAGTAAAAACAAAGAA
65926463 ATTTTAATAGCATTATTTTGGAAGTAAAAACAAAGAA
1 ATTTTAATAGCATTATTTTGGAAGTAAAAACAAAGAA
65926500 A
1 A
65926501 AATAAGTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.32
Consensus pattern (37 bp):
ATTTTAATAGCATTATTTTGGAAGTAAAAACAAAGAA
Found at i:65927548 original size:12 final size:12
Alignment explanation
Indices: 65927492--65927560 Score: 59
Period size: 12 Copynumber: 5.6 Consensus size: 12
65927482 AAAGAGTGTG
65927492 AAAGAAAGT-AA
1 AAAGAAAGTGAA
*
65927503 AAAGAGAATGAGAA
1 AAAGA-AA-GTGAA
*
65927517 AAAGAAAAATGAA
1 AAAG-AAAGTGAA
** *
65927530 ATTGAAATTGAA
1 AAAGAAAGTGAA
65927542 AAAGAAAGTGAA
1 AAAGAAAGTGAA
65927554 AAAGAAA
1 AAAGAAA
65927561 AAGAAATTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
11 5 0.11
12 25 0.56
13 6 0.13
14 8 0.18
15 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.12
Consensus pattern (12 bp):
AAAGAAAGTGAA
Found at i:65927548 original size:18 final size:18
Alignment explanation
Indices: 65927514--65927570 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
65927504 AAGAGAATGA
65927514 GAAAAAGAAAAATGAAATT
1 GAAAAAGAAAAA-GAAATT
** *
65927533 GAAATTGAAAAAGAAAGT
1 GAAAAAGAAAAAGAAATT
65927551 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATT
65927569 GA
1 GA
65927571 GATCGAGAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 22 0.69
19 10 0.31
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATT
Found at i:65927569 original size:30 final size:30
Alignment explanation
Indices: 65927533--65927589 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
65927523 AAATGAAATT
65927533 GAAATTGAAAAAGAAAGTGAAAAAGAAAAA
1 GAAATTGAAAAAGAAAGTGAAAAAGAAAAA
* ** *
65927563 GAAATTGAGATCGAGAGTGAAAAAGAA
1 GAAATTGAAAAAGAAAGTGAAAAAGAA
65927590 TGTGAGAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.25, T:0.12
Consensus pattern (30 bp):
GAAATTGAAAAAGAAAGTGAAAAAGAAAAA
Found at i:65927610 original size:42 final size:43
Alignment explanation
Indices: 65927513--65927614 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 43
65927503 AAAGAGAATG
* * *
65927513 AGAAAAAGAAAAATGAAATTGAAATTGAAAAAGAAAGTGAAAA
1 AGAAAAAGAAAATTGAAATCGAAAGTGAAAAAGAAAGTGAAAA
* * * *
65927556 AGAAAAAG-AAATTGAGATCGAGAGTGAAAAAGAATGTG-AGA
1 AGAAAAAGAAAATTGAAATCGAAAGTGAAAAAGAAAGTGAAAA
65927597 AGAAAAAGAAAATTGAAA
1 AGAAAAAGAAAATTGAAA
65927615 ATTGAGTTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 10 0.20
42 32 0.64
43 8 0.16
ACGTcount: A:0.63, C:0.01, G:0.23, T:0.14
Consensus pattern (43 bp):
AGAAAAAGAAAATTGAAATCGAAAGTGAAAAAGAAAGTGAAAA
Found at i:65936294 original size:30 final size:30
Alignment explanation
Indices: 65936260--65936356 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65936250 TAAACTAAAA
65936260 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
65936290 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
65936320 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
65936350 TGAGCTA
1 TGAGCTA
65936357 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:65938540 original size:30 final size:30
Alignment explanation
Indices: 65938469--65938551 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
65938459 CTTTTGTTTC
* *
65938469 AATTTCTTTTTCA-TCTTTTTTTTCACTCTCA
1 AATTTC-TTTTCATTC-TCTTTTTCAATCTCA
*
65938500 AATTTCTTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTCATTCTCTTTTTCAATCTCA
* *
65938529 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTC-TTTTCATTCTCTTTTT
65938552 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.11
30 31 0.70
31 8 0.18
ACGTcount: A:0.13, C:0.20, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTCATTCTCTTTTTCAATCTCA
Found at i:65938551 original size:18 final size:18
Alignment explanation
Indices: 65938502--65938557 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
65938492 CACTCTCAAA
* *
65938502 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
65938519 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
65938537 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
65938556 TT
1 TT
65938558 CAAAGCCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:65938558 original size:12 final size:12
Alignment explanation
Indices: 65938527--65938551 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65938517 TTTTTCAATC
65938527 TCATTTTCTTTT
1 TCATTTTCTTTT
65938539 TCATTTTCTTTT
1 TCATTTTCTTTT
65938551 T
1 T
65938552 GCTTTTCAAA
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:65938642 original size:6 final size:5
Alignment explanation
Indices: 65938620--65938675 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65938610 CTCTTGCCTC
65938620 TCTTT TCTTT T-TATT TCGTTT TCTTT TC--T TCTTT TGGCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T--CTTT TCTTT
65938666 TCTTT TCTTT
1 TCTTT TCTTT
65938676 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
3 3 0.07
4 1 0.02
5 30 0.68
6 4 0.09
7 6 0.14
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:65938686 original size:21 final size:18
Alignment explanation
Indices: 65938620--65938682 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 18
65938610 CTCTTGCCTC
65938620 TCTTTTCTTTTTATTTCGTTT
1 TCTTTTC-TTTT-TTT-GTTT
*
65938641 TCTTTTCTTCTTTTGGCTTT
1 TCTTTTCTT-TTTTTG-TTT
65938661 TCTTTTCTTTTCTTTGTTT
1 TCTTTTCTTTT-TTTGTTT
65938680 TCT
1 TCT
65938683 CTTTACAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 9 0.24
20 19 0.51
21 9 0.24
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.75
Consensus pattern (18 bp):
TCTTTTCTTTTTTTGTTT
Found at i:65939628 original size:12 final size:11
Alignment explanation
Indices: 65939613--65939651 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
65939603 TTTTTTTTTC
65939613 TTTTCGAAATTT
1 TTTTC-AAATTT
*
65939625 TTTTTAAATTTT
1 TTTTCAAA-TTT
65939637 TTTTCAAATTT
1 TTTTCAAATTT
65939648 TTTT
1 TTTT
65939652 TGACTTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTCAAATTT
Found at i:65939652 original size:12 final size:12
Alignment explanation
Indices: 65939608--65939652 Score: 65
Period size: 11 Copynumber: 3.7 Consensus size: 12
65939598 TCAGATTTTT
65939608 TTTTCTTTTCGAAA
1 TTTT-TTTTC-AAA
65939622 TTTTTTTT-AAA
1 TTTTTTTTCAAA
65939633 TTTTTTTTCAAA
1 TTTTTTTTCAAA
65939645 TTTTTTTT
1 TTTTTTTT
65939653 GACTTGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.37
12 11 0.37
13 4 0.13
14 4 0.13
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:65946732 original size:21 final size:20
Alignment explanation
Indices: 65946689--65946763 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 20
65946679 AAGAAAAAAA
**
65946689 GAAATGAAAGAAAAAGAGTGT
1 GAAA-GAAAGAAAAAGAAAGT
65946710 GAAAGAAAGCAAAAAGAAAGT
1 GAAAGAAAG-AAAAAGAAAGT
*
65946731 GAGAA-AAAGAAAAACGAAATT
1 GA-AAGAAAGAAAAA-GAAAGT
65946752 G-AA-AAAGAAAAA
1 GAAAGAAAGAAAAA
65946764 AATTTGAGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
19 11 0.23
20 10 0.21
21 25 0.52
22 2 0.04
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (20 bp):
GAAAGAAAGAAAAAGAAAGT
Found at i:65948630 original size:20 final size:20
Alignment explanation
Indices: 65948607--65948654 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65948597 AGCTCCGTCT
65948607 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** * *
65948627 AGCTCGTTTCAGGTCGTTTG
1 AGCTCAACTCAGCTCATTTG
65948647 AGCTCAAC
1 AGCTCAAC
65948655 CGAGCTTATT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:65953059 original size:24 final size:24
Alignment explanation
Indices: 65953032--65953077 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
65953022 GTACAAGAAA
* *
65953032 AAGAAAATTGAAAAATAGAAAGTC
1 AAGAAAAATGAAAAAAAGAAAGTC
65953056 AAGAAAAATGAAAAAAAGAAAG
1 AAGAAAAATGAAAAAAAGAAAG
65953078 GAAAAAGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (24 bp):
AAGAAAAATGAAAAAAAGAAAGTC
Found at i:65953061 original size:30 final size:30
Alignment explanation
Indices: 65953006--65953069 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 30
65952996 ACGATCAACT
*
65953006 AAAATTGAAAGAAAAAGTACAAGAAAAA-G
1 AAAATTGAAAAAAAAAGTACAAGAAAAATG
65953035 AAAATTGAAAAATAGAAAGT-CAAGAAAAATG
1 AAAATTGAAAAA-A-AAAGTACAAGAAAAATG
65953066 AAAA
1 AAAA
65953070 AAAGAAAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.35
30 10 0.32
31 10 0.32
ACGTcount: A:0.69, C:0.03, G:0.16, T:0.12
Consensus pattern (30 bp):
AAAATTGAAAAAAAAAGTACAAGAAAAATG
Found at i:65957275 original size:48 final size:47
Alignment explanation
Indices: 65957203--65957300 Score: 151
Period size: 48 Copynumber: 2.1 Consensus size: 47
65957193 GCTGATCCTA
* * *
65957203 GCATGCTTTTTCTTTAATGCTTCAGCAGCTCATTTAATATCGTCCAT
1 GCATGCTTTCTCTTTAATGCTTCAGCAGATCATTTAATATCATCCAT
*
65957250 GCATGCTTTGCTCTTTAATGCTTCAGCAGATCATTTAATGTCATCCAT
1 GCATGCTTT-CTCTTTAATGCTTCAGCAGATCATTTAATATCATCCAT
65957298 GCA
1 GCA
65957301 CTAGCAGCTC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 9 0.20
48 37 0.80
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (47 bp):
GCATGCTTTCTCTTTAATGCTTCAGCAGATCATTTAATATCATCCAT
Found at i:65958598 original size:28 final size:28
Alignment explanation
Indices: 65958567--65958681 Score: 124
Period size: 29 Copynumber: 4.0 Consensus size: 28
65958557 TACTTGTATC
* *
65958567 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
*
65958595 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCC-AATCACAT-TCATA
* *
65958624 TGGCCCATTAGGCTCAAATCACATTTATA
1 TGGCCCATTAGGC-CCAATCACATTCATA
* * *
65958653 TAGCCCGTTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
65958681 T
1 T
65958682 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 28 0.38
29 43 0.59
30 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:65958854 original size:15 final size:15
Alignment explanation
Indices: 65958834--65958881 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65958824 TCAAAGATGG
65958834 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
65958849 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
65958863 GTTTATGGATATAAA
1 GTTTATGGATATGAA
65958878 GTTT
1 GTTT
65958882 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:65958868 original size:14 final size:14
Alignment explanation
Indices: 65958828--65958871 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
65958818 AAGGATTCAA
65958828 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
65958842 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
65958857 AGATGGGTTTATGG
1 AGATGGGTTTATGG
65958871 A
1 A
65958872 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:65958897 original size:29 final size:29
Alignment explanation
Indices: 65958828--65958887 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
65958818 AAGGATTCAA
*
65958828 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
65958857 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
65958886 AG
1 AG
65958888 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:65962168 original size:30 final size:28
Alignment explanation
Indices: 65962115--65962170 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
65962105 TTCTTCCACG
* *
65962115 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
65962143 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
65962171 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:65963499 original size:15 final size:15
Alignment explanation
Indices: 65963479--65963526 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65963469 TCAAAGATGG
65963479 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
65963494 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
65963508 GTTTATGGATATAAA
1 GTTTATGGATATGAA
65963523 GTTT
1 GTTT
65963527 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:65963513 original size:14 final size:14
Alignment explanation
Indices: 65963473--65963516 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
65963463 AAGGATTCAA
65963473 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
65963487 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
65963502 AGATGGGTTTATGG
1 AGATGGGTTTATGG
65963516 A
1 A
65963517 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:65963542 original size:29 final size:29
Alignment explanation
Indices: 65963473--65963532 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
65963463 AAGGATTCAA
*
65963473 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
65963502 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
65963531 AG
1 AG
65963533 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:65966038 original size:18 final size:18
Alignment explanation
Indices: 65966004--65966038 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65965994 TTGCTACTAG
* *
65966004 TTTTAATGTGCTGATTTT
1 TTTTAATGAGCTAATTTT
65966022 TTTTAATGAGCTAATTT
1 TTTTAATGAGCTAATTT
65966039 AATGTGCTTC
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:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (18 bp):
TTTTAATGAGCTAATTTT
Found at i:65969071 original size:30 final size:30
Alignment explanation
Indices: 65969037--65969093 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
65969027 TTCAACTCAC
*
65969037 GAGTTAAAACTTAGCTCAACTTCAGCTTAG
1 GAGTTAAAACTCAGCTCAACTTCAGCTTAG
* * *
65969067 GAGTTTAACCTCAGCTCAACTTTAGCT
1 GAGTTAAAACTCAGCTCAACTTCAGCT
65969094 CGAGGGCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (30 bp):
GAGTTAAAACTCAGCTCAACTTCAGCTTAG
Found at i:65975341 original size:20 final size:20
Alignment explanation
Indices: 65975295--65975342 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65975285 AGTAAGCTCG
65975295 GTTGAGCTCAAACAAGCTGA
1 GTTGAGCTCAAACAAGCTGA
*** **
65975315 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACAAGCTGA
65975335 GTTGAGCT
1 GTTGAGCT
65975343 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACAAGCTGA
Found at i:65976948 original size:29 final size:28
Alignment explanation
Indices: 65976897--65976967 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
65976887 TTCTTTTGTT
*
65976897 TCAATTTCTTTTTCATCT-TTTTTCACTC
1 TCAATTTC-TTTTCATCTCTTTTTCAATC
*
65976925 TCAAATTTCTTTTCGTTCTCTTTTTCAATC
1 TC-AATTTCTTTTC-ATCTCTTTTTCAATC
*
65976955 TCATTTTCTTTTC
1 TCAATTTCTTTTC
65976968 TCACTTGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.19
29 19 0.51
30 11 0.30
ACGTcount: A:0.14, C:0.24, G:0.01, T:0.61
Consensus pattern (28 bp):
TCAATTTCTTTTCATCTCTTTTTCAATC
Found at i:65977030 original size:21 final size:21
Alignment explanation
Indices: 65977006--65977058 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
65976996 TTTTGTATTC
65977006 TTTTTCTCGATT-TTCTTTTCT
1 TTTTTCTC-ATTATTCTTTTCT
*
65977027 TTTTTCACATTCATTCTTTTCT
1 TTTTTCTCATT-ATTCTTTTCT
65977049 TTTTCTCTCA
1 TTTT-TCTCA
65977059 ACTGATTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 7 0.26
22 13 0.48
23 4 0.15
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTTCTCATTATTCTTTTCT
Found at i:65981297 original size:18 final size:19
Alignment explanation
Indices: 65981274--65981312 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
65981264 TTTATCTCAA
*
65981274 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
65981292 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
65981311 TT
1 TT
65981313 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:65981354 original size:13 final size:12
Alignment explanation
Indices: 65981318--65981356 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
65981308 TTTTTCTCTC
*
65981318 TCAAACTCTTTT
1 TCAATCTCTTTT
*
65981330 TCATTCTCTTTT
1 TCAATCTCTTTT
*
65981342 TCAATCTCATTT
1 TCAATCTCTTTT
65981354 TCA
1 TCA
65981357 TTTTCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.54
Consensus pattern (12 bp):
TCAATCTCTTTT
Found at i:65981354 original size:24 final size:24
Alignment explanation
Indices: 65981318--65981367 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
65981308 TTTTTCTCTC
* *
65981318 TCAAACTCTTTTTCATTCTCTTTT
1 TCAAACTCATTTTCATTCTCATTT
* *
65981342 TCAATCTCATTTTCATTTTCATTT
1 TCAAACTCATTTTCATTCTCATTT
65981366 TC
1 TC
65981368 TTTTTGTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (24 bp):
TCAAACTCATTTTCATTCTCATTT
Found at i:65981363 original size:12 final size:12
Alignment explanation
Indices: 65981327--65981367 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
65981317 CTCAAACTCT
*
65981327 TTTTCATTCTCT
1 TTTTCATTCTCA
*
65981339 TTTTCAATCTCA
1 TTTTCATTCTCA
*
65981351 TTTTCATTTTCA
1 TTTTCATTCTCA
65981363 TTTTC
1 TTTTC
65981368 TTTTTGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTCATTCTCA
Found at i:65981372 original size:12 final size:12
Alignment explanation
Indices: 65981323--65981358 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
65981313 CTCTCTCAAA
65981323 CTCTTTTTCATT
1 CTCTTTTTCATT
*
65981335 CTCTTTTTCAAT
1 CTCTTTTTCATT
*
65981347 CTCATTTTCATT
1 CTCTTTTTCATT
65981359 TTCATTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:65981372 original size:18 final size:18
Alignment explanation
Indices: 65981327--65981380 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
65981317 CTCAAACTCT
*
65981327 TTTTCATTCTCTTTTTCA
1 TTTTCATTTTCTTTTTCA
* * *
65981345 ATCTCATTTTCATTTTCA
1 TTTTCATTTTCTTTTTCA
* *
65981363 TTTTCTTTTTGTTTTTCA
1 TTTTCATTTTCTTTTTCA
65981381 AAGGTTTTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTCATTTTCTTTTTCA
Found at i:65981449 original size:5 final size:5
Alignment explanation
Indices: 65981439--65981497 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
65981429 GCCTTTTGCC
* *
65981439 TTTCT TTTCT TTT-T ATTTCGT TTTCT TTT-T CTACT TTTGCTT TTTCT
1 TTTCT TTTCT TTTCT -TTTC-T TTTCT TTTCT TTTCT TTT-C-T TTTCT
65981486 TTTCT TTTCT TT
1 TTTCT TTTCT TT
65981498 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
4 3 0.07
5 30 0.68
6 6 0.14
7 5 0.11
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:65981462 original size:16 final size:15
Alignment explanation
Indices: 65981439--65981497 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
65981429 GCCTTTTGCC
65981439 TTTCTTTTCTTTTTA
1 TTTCTTTTCTTTTTA
65981454 TTTCGTTTTCTTTTT-
1 TTTC-TTTTCTTTTTA
* * *
65981469 CTACTTTTGCTTTTTCT
1 TTTCTTTT-CTTTTT-A
65981486 TTTCTTTTCTTT
1 TTTCTTTTCTTT
65981498 GTTTTCTCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 4 0.11
15 12 0.33
16 14 0.39
17 6 0.17
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCTTTTTA
Found at i:65981498 original size:21 final size:21
Alignment explanation
Indices: 65981439--65981502 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
65981429 GCCTTTTGCC
* *
65981439 TTTCTTTTCTTTT-TATTTCGT
1 TTTCTTTTCTTTTCT-TTGCTT
* *
65981460 TTTCTTTT-TCTACTTTTGCTT
1 TTTCTTTTCTTTTC-TTTGCTT
65981481 TTTCTTTTCTTTTCTTTG-TT
1 TTTCTTTTCTTTTCTTTGCTT
65981501 TT
1 TT
65981503 CTCGTTACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.18
21 24 0.71
22 4 0.12
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.77
Consensus pattern (21 bp):
TTTCTTTTCTTTTCTTTGCTT
Found at i:65983828 original size:11 final size:12
Alignment explanation
Indices: 65983801--65983826 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
65983791 AAGCTGTAGC
65983801 AAACTAAATTAA
1 AAACTAAATTAA
65983813 AAACTAAATTAA
1 AAACTAAATTAA
65983825 AA
1 AA
65983827 CTTAGTTTAT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAACTAAATTAA
Found at i:65985038 original size:10 final size:10
Alignment explanation
Indices: 65985025--65985073 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
65985015 AAGCTTGGTT
65985025 GAGCTCAAAC
1 GAGCTCAAAC
*
65985035 GAGCTAAAAC
1 GAGCTCAAAC
*
65985045 GAACTCAAAC
1 GAGCTCAAAC
*
65985055 GAGCTGAAAC
1 GAGCTCAAAC
65985065 GAGCTCAAA
1 GAGCTCAAA
65985074 TGAGTTGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.10
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:65985082 original size:20 final size:20
Alignment explanation
Indices: 65985025--65985073 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
65985015 AAGCTTGGTT
*
65985025 GAGCTCAAACGAGCTAAAAC
1 GAGCTCAAACGAGCTGAAAC
*
65985045 GAACTCAAACGAGCTGAAAC
1 GAGCTCAAACGAGCTGAAAC
65985065 GAGCTCAAA
1 GAGCTCAAA
65985074 TGAGTTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.10
Consensus pattern (20 bp):
GAGCTCAAACGAGCTGAAAC
Found at i:65986337 original size:14 final size:14
Alignment explanation
Indices: 65986318--65986362 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
65986308 AACTCATCTT
*
65986318 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
65986332 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
65986345 AATTTAATTTAATG
1 AGTTTAATTTAATG
65986359 AGTT
1 AGTT
65986363 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:65987368 original size:29 final size:29
Alignment explanation
Indices: 65987335--65987394 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
65987325 ATAACCAAAC
*
65987335 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
65987364 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
65987393 CT
1 CT
65987395 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:65987387 original size:15 final size:15
Alignment explanation
Indices: 65987341--65987388 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
65987331 AAACCTACAA
*
65987341 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
65987356 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
65987370 AAACTTCATATCCAT
1 AAACTTCATATCCAT
65987385 AAAC
1 AAAC
65987389 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:65989994 original size:15 final size:15
Alignment explanation
Indices: 65989974--65990030 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 15
65989964 TTTTCTTGCT
65989974 TCTCTTTTCTTTT-G
1 TCTCTTTTCTTTTCG
65989988 ATCTCTTTTTACTTTTCG
1 -TCTC-TTTT-CTTTTCG
65990006 TCT-TTTTCTTTTC-
1 TCTCTTTTCTTTTCG
*
65990019 T-TATTTTCTTTT
1 TCTCTTTTCTTTT
65990031 TACAAGAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
12 1 0.03
13 10 0.26
14 6 0.16
15 8 0.21
16 4 0.11
17 8 0.21
18 1 0.03
ACGTcount: A:0.05, C:0.19, G:0.04, T:0.72
Consensus pattern (15 bp):
TCTCTTTTCTTTTCG
Found at i:65993002 original size:595 final size:594
Alignment explanation
Indices: 65992185--65993376 Score: 2179
Period size: 595 Copynumber: 2.0 Consensus size: 594
65992175 GGACAAGTCG
* * *
65992185 TGATGTATGCACGCCTGGGGTTCCCTCAAGTGCATCTCAAGATTCAATTGAGCTTCCAAAAACAC
1 TGATGTATGCACGCCCGGGGCTCCCTCAAGTGCATATCAAGATTCAATTGAGCTTCCAAAAACAC
65992250 CCATAACTCGAGCTTGTGCTAACATTTCCTAGAAGCTGTTTTAGCTTCTAATGCAAAACCTTGGT
66 CCATAACTCGAGCTTGTGCTAACATTTCCTAGAAGCTGTTTTAGCTTCTAATGCAAAACCTTGGT
65992315 TTGAAACAAGGGCCAATGCTCACAAAATCAGCTCGAAGCAACTATCCAAAGAACTCGTGCATTGT
131 TTGAAACAAGGGCCAATGCTCACAAAATCAGCTCGAAGCAACTATCCAAAGAACTCGTGCATTGT
* *
65992380 TGGCAAGTTGATCCTAGCTCATTTCCTGCTCCTCGAGCTCCGTCTAGCTCAACTCAACTCATTTG
196 TGGCAAGCTAATCCTAGCTCATTTCCTGCTCCTCGAGCTCCGTCTAGCTCAACTCAACTCATTTG
* * *
65992445 AGCTCGTTTTATCTCATTTGAGCTCAACCGAGCTTACTTTCAGCTCGTTCTTTATTTGAATAAAT
261 AGCTCGTTTCAGCTCATTTGAGCTCAACCGAGCTTACTTTCAGCTCGTTCTTTATTTCAATAAAT
*
65992510 TAAACTAAGTTTTAGTTTTATACTAATTAGTTTGCTACAGCTCATTAATGAAAATCCTAGCTCAA
326 TAAACTAAGTTTTAGTTTTATACTAATTAGTTTGCTACAGCTCATTAACGAAAATCCTAGCTCAA
*
65992575 ATAAGTTCATTAAATGTTTTCACTTAGTTTGAGCTTGCCGAACTTAATGCTACTAGCTAGTCTTT
391 ATAAGTTCATTAAATGTTTTCACTTAGTTTGAGCTAGCCGAACTTAATGCTACTAGCTAGTCTTT
*
65992640 AATTAATGTGTTTAGTTTAGCTTAGCATGATGTTTATGATGCTTAGTTCATGCTCTTAACATGTT
456 AATTAATGTGTTTAATTTAGCTTAGCATGATGTTTATGATGCTTAGTTCATGCTCTTAACATGTT
* *
65992705 CAGCTGAATATACATTGGGATTTAACGTGTTCATGTTTCTTGTAGGTTCATCCGAATGTATTGAG
521 CAGCTGAATATACATTGGGATTTAACGTGTTCATGTTTCTTGTAGGTTCAGCCAAATGTATTGAG
65992770 TACATTTAA
586 TACATTTAA
*
65992779 TGATGTATGCATGCCCGGGGCTCCCTCAAGTGCATATCAAGATTCAATTGAGCTTCCAAAAACAC
1 TGATGTATGCACGCCCGGGGCTCCCTCAAGTGCATATCAAGATTCAATTGAGCTTCCAAAAACAC
65992844 CCATAACTCGAGCTTGTGCTAAGCATTTCCTAGAAGCTGTTTTAGCTTCTAATGCAAAACCTTGG
66 CCATAACTCGAGCTTGTGCTAA-CATTTCCTAGAAGCTGTTTTAGCTTCTAATGCAAAACCTTGG
65992909 TTTGAAACAAGGGCCAATGCTCACAAAATCAGCTCGAAGCAACTATCCAAAGAAC-CTGTGCATT
130 TTTGAAACAAGGGCCAATGCTCACAAAATCAGCTCGAAGCAACTATCCAAAGAACTC-GTGCATT
* * *
65992973 GTTGGCAAGCTAATCCTGGCTCATTTCCTGCTCCTCGAGCTCTGTCTAGCTCAACTCAGCTCATT
194 GTTGGCAAGCTAATCCTAGCTCATTTCCTGCTCCTCGAGCTCCGTCTAGCTCAACTCAACTCATT
* *
65993038 TGAGCTTGTTTCAGCTCGTTTGAGCTCAACCGAGCTTACTTTCAGCTCGTTCTTTATTTCAATAA
259 TGAGCTCGTTTCAGCTCATTTGAGCTCAACCGAGCTTACTTTCAGCTCGTTCTTTATTTCAATAA
65993103 ATTAAACTAAGTTTTAGTTTTATACTAATTAGTTTGCTACAGCTCATTAACGAAAATCCTAGCTC
324 ATTAAACTAAGTTTTAGTTTTATACTAATTAGTTTGCTACAGCTCATTAACGAAAATCCTAGCTC
65993168 AAATAAGTTCATTAAATGTTTTCACTTAGTTTGAGCTAGCCGAACTTAATGCTACTAGCTAGTCT
389 AAATAAGTTCATTAAATGTTTTCACTTAGTTTGAGCTAGCCGAACTTAATGCTACTAGCTAGTCT
65993233 TTAATTAATGTGTTTAATTTAGCTTAGCATGATGTTTATGATGCTTAGTTCATGCTCTTAACATG
454 TTAATTAATGTGTTTAATTTAGCTTAGCATGATGTTTATGATGCTTAGTTCATGCTCTTAACATG
*
65993298 TTTAGCTGAATATACATTGGGATTTAACGTGTTCATGTTTCTTGTAGGTTCAGCCAAATGTATTG
519 TTCAGCTGAATATACATTGGGATTTAACGTGTTCATGTTTCTTGTAGGTTCAGCCAAATGTATTG
65993363 AGTACATTTAA
584 AGTACATTTAA
65993374 TGA
1 TGA
65993377 GATTCATGCA
Statistics
Matches: 576, Mismatches: 20, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
594 84 0.15
595 492 0.85
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (594 bp):
TGATGTATGCACGCCCGGGGCTCCCTCAAGTGCATATCAAGATTCAATTGAGCTTCCAAAAACAC
CCATAACTCGAGCTTGTGCTAACATTTCCTAGAAGCTGTTTTAGCTTCTAATGCAAAACCTTGGT
TTGAAACAAGGGCCAATGCTCACAAAATCAGCTCGAAGCAACTATCCAAAGAACTCGTGCATTGT
TGGCAAGCTAATCCTAGCTCATTTCCTGCTCCTCGAGCTCCGTCTAGCTCAACTCAACTCATTTG
AGCTCGTTTCAGCTCATTTGAGCTCAACCGAGCTTACTTTCAGCTCGTTCTTTATTTCAATAAAT
TAAACTAAGTTTTAGTTTTATACTAATTAGTTTGCTACAGCTCATTAACGAAAATCCTAGCTCAA
ATAAGTTCATTAAATGTTTTCACTTAGTTTGAGCTAGCCGAACTTAATGCTACTAGCTAGTCTTT
AATTAATGTGTTTAATTTAGCTTAGCATGATGTTTATGATGCTTAGTTCATGCTCTTAACATGTT
CAGCTGAATATACATTGGGATTTAACGTGTTCATGTTTCTTGTAGGTTCAGCCAAATGTATTGAG
TACATTTAA
Found at i:65993043 original size:20 final size:20
Alignment explanation
Indices: 65993020--65993067 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
65993010 AGCTCTGTCT
65993020 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
**** *
65993040 AGCTTGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
65993060 AGCTCAAC
1 AGCTCAAC
65993068 CGAGCTTACT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:65995957 original size:13 final size:13
Alignment explanation
Indices: 65995939--65995966 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
65995929 ACACGAGCCT
65995939 TTGTGATCGGCCC
1 TTGTGATCGGCCC
65995952 TTGTGATCGGCCC
1 TTGTGATCGGCCC
65995965 TT
1 TT
65995967 AAGGTAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.29, G:0.29, T:0.36
Consensus pattern (13 bp):
TTGTGATCGGCCC
Found at i:65997497 original size:30 final size:30
Alignment explanation
Indices: 65997463--65997559 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
65997453 TAAACTAAAA
65997463 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
65997493 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* * *
65997523 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
65997553 TGAGCTA
1 TGAGCTA
65997560 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 2 0.04
30 43 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:65999232 original size:30 final size:29
Alignment explanation
Indices: 65999187--65999271 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 29
65999177 TTCTTTTGTT
*
65999187 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCAT-TTCTTTTTCAATC
65999217 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATT-TCTTTTTCAATC
* *
65999247 TCATTTTCTTTTTCTTTTCTTTTTC
1 TCAATTTCTTTTTCATTTCTTTTTC
65999272 TTTTGATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 14 0.29
30 29 0.59
31 6 0.12
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (29 bp):
TCAATTTCTTTTTCATTTCTTTTTCAATC
Found at i:65999281 original size:11 final size:11
Alignment explanation
Indices: 65999222--65999282 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
65999212 CACTCTCAAA
65999222 TTTCTTTTCAT
1 TTTCTTTTCAT
* *
65999233 TCTCTTTTTCAA
1 TTTC-TTTTCAT
* *
65999245 TCTCATTTTCTT
1 TTTC-TTTTCAT
*
65999257 TTTCTTTTCTT
1 TTTCTTTTCAT
*
65999268 TTTCTTTTGAT
1 TTTCTTTTCAT
65999279 TTTC
1 TTTC
65999283 AAAGGCTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 23 0.56
12 18 0.44
ACGTcount: A:0.08, C:0.20, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTCTTTTCAT
Found at i:65999354 original size:5 final size:5
Alignment explanation
Indices: 65999344--65999400 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
65999334 CTCTTGCCTC
*
65999344 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
65999391 TCTTT TCTTT
1 TCTTT TCTTT
65999401 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:65999384 original size:15 final size:14
Alignment explanation
Indices: 65999344--65999400 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
65999334 CTCTTGCCTC
*
65999344 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
65999359 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
65999374 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
65999391 TCTTTTCTTT
1 TCTTTTCTTT
65999401 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:65999401 original size:21 final size:21
Alignment explanation
Indices: 65999344--65999411 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
65999334 CTCTTGCCTC
* *
65999344 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
65999365 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
65999386 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
65999406 CTCTTT
1 -TCTTT
65999412 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:66002038 original size:30 final size:30
Alignment explanation
Indices: 66002004--66002100 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
66001994 TAAACTAAAA
66002004 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
* * * * *
66002034 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTAAGCTAAAGT
* * * *
66002064 TCAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTAAGCT-AAAGT
66002094 TGAGCTA
1 TGAGCTA
66002101 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTAAGCTAAAGT
Found at i:66010972 original size:14 final size:14
Alignment explanation
Indices: 66010950--66010997 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
66010940 ACCTATATCG
* *
66010950 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
66010964 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
66010978 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
66010992 ACCATT
1 ACCATT
66010998 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:66013742 original size:11 final size:11
Alignment explanation
Indices: 66013728--66013768 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
66013718 AAAAAAACCG
66013728 AAAAAAAATTC
1 AAAAAAAATTC
66013739 AAAAAAAATTC
1 AAAAAAAATTC
*
66013750 AAAAAAAATTG
1 AAAAAAAATTC
66013761 AAAAAAAA
1 AAAAAAAA
66013769 AGTGATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:66013742 original size:22 final size:22
Alignment explanation
Indices: 66013716--66013768 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
66013706 TACAAGTTTG
*
66013716 AAAAAAAAACCGAAAAAAAATTC
1 AAAAAAAATCC-AAAAAAAATTC
* *
66013739 AAAAAAAATTCAAAAAAAATTG
1 AAAAAAAATCCAAAAAAAATTC
66013761 AAAAAAAA
1 AAAAAAAA
66013769 AGTGATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.77, C:0.08, G:0.04, T:0.11
Consensus pattern (22 bp):
AAAAAAAATCCAAAAAAAATTC
Found at i:66014705 original size:21 final size:20
Alignment explanation
Indices: 66014671--66014738 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
66014661 ACATTCTTGT
66014671 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
66014692 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
66014713 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
66014734 AAAGA
1 AAAGA
66014739 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:66014706 original size:6 final size:5
Alignment explanation
Indices: 66014682--66014738 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66014672 AAGAGAAAAC
*
66014682 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
66014729 AAAGA AAAGA
1 AAAGA AAAGA
66014739 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:66014713 original size:15 final size:14
Alignment explanation
Indices: 66014682--66014738 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66014672 AAGAGAAAAC
66014682 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
66014698 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
66014713 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
66014729 AAAGAAAAGA
1 AAAGAAAAGA
66014739 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:66018308 original size:37 final size:38
Alignment explanation
Indices: 66018240--66018313 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
66018230 GCAACTCAGC
* *
66018240 ATACGACTCGACTCTCCCCGAGGCGGTTCGTATCACTA
1 ATACGACTCCACTCTCCCCGAGGCGGATCGTATCACTA
*
66018278 ATACGACTCCACTCT-TCCGAGGCGGATCGTATCACT
1 ATACGACTCCACTCTCCCCGAGGCGGATCGTATCACT
66018314 TTTCTTCTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (38 bp):
ATACGACTCCACTCTCCCCGAGGCGGATCGTATCACTA
Found at i:66020987 original size:10 final size:11
Alignment explanation
Indices: 66020968--66021071 Score: 81
Period size: 12 Copynumber: 9.2 Consensus size: 11
66020958 TCAAGTAAGT
66020968 TTCAAAAAAAA
1 TTCAAAAAAAA
66020979 TTCAAAAAAAA
1 TTCAAAAAAAA
66020990 TTCAAATAAAAA
1 TTCAAA-AAAAA
66021002 GTTTCAAATAAAAA
1 --TTCAAA-AAAAA
*
66021016 TATGAAAAAAAA
1 T-TCAAAAAAAA
*
66021028 TT--AAAAAAG
1 TTCAAAAAAAA
66021037 TT--AAAAAAA
1 TTCAAAAAAAA
*
66021046 TTTAGAAAAAAA
1 TTCA-AAAAAAA
*
66021058 TTAGAAAAAAAA
1 TT-CAAAAAAAA
66021070 TT
1 TT
66021072 TGAACATTGT
Statistics
Matches: 81, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
9 16 0.20
11 18 0.22
12 30 0.37
13 5 0.06
14 12 0.15
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:66021054 original size:12 final size:11
Alignment explanation
Indices: 66021021--66021068 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
66021011 AAAAATATGA
66021021 AAAAAAATT--
1 AAAAAAATTAG
*
66021030 AAAAAAGTTA-
1 AAAAAAATTAG
*
66021040 AAAAAATTTAG
1 AAAAAAATTAG
66021051 AAAAAAATTAG
1 AAAAAAATTAG
66021062 AAAAAAA
1 AAAAAAA
66021069 ATTTGAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
9 8 0.24
10 9 0.26
11 17 0.50
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAAAATTAG
Found at i:66023285 original size:10 final size:10
Alignment explanation
Indices: 66023270--66023307 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
66023260 TATACAAGTA
66023270 AAAAAAATTC
1 AAAAAAATTC
66023280 AAAAAAATTC
1 AAAAAAATTC
*
66023290 GAAAAAAATTG
1 -AAAAAAATTC
66023301 AAAAAAA
1 AAAAAAA
66023308 AAGGTGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:66023285 original size:11 final size:11
Alignment explanation
Indices: 66023269--66023308 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
66023259 TTATACAAGT
66023269 AAAAAAAATTC
1 AAAAAAAATTC
66023280 -AAAAAAATTC
1 AAAAAAAATTC
* *
66023290 GAAAAAAATTG
1 AAAAAAAATTC
66023301 AAAAAAAA
1 AAAAAAAA
66023309 AGGTGTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:66024218 original size:9 final size:10
Alignment explanation
Indices: 66024211--66024267 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
66024201 AAGAGAAAAC
66024211 AAAGAAAAGA
1 AAAGAAAAGA
66024221 AAAGAAAAAGTA
1 AAAG-AAAAG-A
*
66024233 AAAGAAGA-A
1 AAAGAAAAGA
66024242 AAAGAAAATGA
1 AAAGAAAA-GA
66024253 AATA-AAAAGA
1 AA-AGAAAAGA
66024263 AAAGA
1 AAAGA
66024268 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:66024235 original size:6 final size:5
Alignment explanation
Indices: 66024211--66024267 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
66024201 AAGAGAAAAC
*
66024211 AAAGA AAAGA AAAGAA AAAGTA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
66024258 AAAGA AAAGA
1 AAAGA AAAGA
66024268 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:66024242 original size:15 final size:14
Alignment explanation
Indices: 66024211--66024267 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
66024201 AAGAGAAAAC
66024211 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
66024227 AAAGTAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
66024242 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
66024258 AAAGAAAAGA
1 AAAGAAAAGA
66024268 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:66024399 original size:30 final size:31
Alignment explanation
Indices: 66024336--66024406 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
66024326 TTTGAAAAGC
* *
66024336 AAAAAGAAA-ATGAGATTGAAAAAGAGAACG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
*
66024366 -AAAAGAAATTTGAGAGTGAAAAAGA-AGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAGA-ACG
66024396 AAAAAGAAATT
1 AAAAAGAAATT
66024407 GAAACAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 9 0.26
30 16 0.46
31 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAGAACG
Found at i:66028651 original size:13 final size:14
Alignment explanation
Indices: 66028633--66028667 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
66028623 GGCTGAACCT
66028633 ACATAATTAAATA-
1 ACATAATTAAATAG
66028646 ACATAATTAAATAG
1 ACATAATTAAATAG
66028660 A-ATAATTA
1 ACATAATTA
66028668 TTCATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 20 0.95
14 1 0.05
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (14 bp):
ACATAATTAAATAG
Found at i:66028909 original size:21 final size:21
Alignment explanation
Indices: 66028885--66028925 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
66028875 GTAAAAGAAA
*
66028885 TGAGCTAAAACGAGCTAAATT
1 TGAGCTAAAACAAGCTAAATT
* *
66028906 TGAGCTCAAGCAAGCTAAAT
1 TGAGCTAAAACAAGCTAAAT
66028926 CGAGCTCAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (21 bp):
TGAGCTAAAACAAGCTAAATT
Found at i:66028932 original size:20 final size:21
Alignment explanation
Indices: 66028897--66028941 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
66028887 AGCTAAAACG
*
66028897 AGCTAAATTTGAGCTCAAGCA
1 AGCTAAATTCGAGCTCAAGCA
*
66028918 AGCTAAA-TCGAGCTCAAGCG
1 AGCTAAATTCGAGCTCAAGCA
66028938 AGCT
1 AGCT
66028942 GATTAGAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (21 bp):
AGCTAAATTCGAGCTCAAGCA
Found at i:66028950 original size:20 final size:20
Alignment explanation
Indices: 66028897--66028951 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
66028887 AGCTAAAACG
*
66028897 AGCTAAATTTGAGCTCAAGCA
1 AGCTAAA-TAGAGCTCAAGCA
* *
66028918 AGCTAAATCGAGCTCAAGCG
1 AGCTAAATAGAGCTCAAGCA
* *
66028938 AGCTGATTAGAGCT
1 AGCTAAATAGAGCT
66028952 GAATGACGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (20 bp):
AGCTAAATAGAGCTCAAGCA
Found at i:66031794 original size:30 final size:29
Alignment explanation
Indices: 66031694--66031796 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 29
66031684 CGAGTTTAAA
* * *
66031694 CTAAAATGACCTAAGCTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
66031723 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
66031753 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
66031783 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
66031797 GGAGTGAGCT
Statistics
Matches: 54, Mismatches: 17, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
29 8 0.15
30 44 0.81
31 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:66032517 original size:179 final size:177
Alignment explanation
Indices: 66032194--66032549 Score: 536
Period size: 179 Copynumber: 2.0 Consensus size: 177
66032184 CACAGAGTCT
* *
66032194 TCAAGGCAGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTGTCATCCCAAATGCGTAACACCAA
1 TCAAGGCAGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTATCATCCCAAATGCGCAACACCAA
* * *
66032259 TGCGGATAAAGCATCTTGAATTCGCTTGGTTTGAGCTCGAGTCATGGGGCCTTTTGGAAGCTCGA
66 GGCGGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGCTCAA
66032324 TTGATTCATGATTTGCATTCAAGGATGCCCCAGGCGTGCTCACATCA
131 TTGATTCATGATTTGCATTCAAGGATGCCCCAGGCGTGCTCACATCA
* *
66032371 TCAAGGCATTGTCCTTAGCTCGC-CCAACGTCTTGGACCTTGTTATCATCCCAAATGCGCAACAC
1 TCAAGGCA--GTCCTTAGCTC-CTCCAACGTCATGAACCTTGTTATCATCCCAAATGCGCAACAC
* *
66032435 CAAGGCTGATAAAGCATCTTGAATTTGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGCT
63 CAAGGCGGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGCT
* ** **
66032500 CAATT-AGTTCTTGATTTGCATTTGAGGATGCCCTGGGCGTGCTCACATCA
128 CAATTGA-TTCATGATTTGCATTCAAGGATGCCCCAGGCGTGCTCACATCA
66032550 CCTACCCAAT
Statistics
Matches: 161, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
177 8 0.05
178 1 0.01
179 151 0.94
180 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (177 bp):
TCAAGGCAGTCCTTAGCTCCTCCAACGTCATGAACCTTGTTATCATCCCAAATGCGCAACACCAA
GGCGGATAAAGCATCTTGAATTCGCTTGGTTCGAGCTCGAGTCATGGGGCCTTTTGGAAGCTCAA
TTGATTCATGATTTGCATTCAAGGATGCCCCAGGCGTGCTCACATCA
Found at i:66037114 original size:10 final size:10
Alignment explanation
Indices: 66037099--66037125 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
66037089 TAAGTTGAAG
66037099 TTGAGCTGAT
1 TTGAGCTGAT
66037109 TTGAGCTGAT
1 TTGAGCTGAT
66037119 TTGAGCT
1 TTGAGCT
66037126 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:66037450 original size:13 final size:13
Alignment explanation
Indices: 66037432--66037466 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
66037422 CGGCTAACCT
66037432 ACATAATTAAATA
1 ACATAATTAAATA
66037445 ACATAATTAAATA
1 ACATAATTAAATA
*
66037458 AAATAATTA
1 ACATAATTA
66037467 TTCATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:66037724 original size:20 final size:21
Alignment explanation
Indices: 66037691--66037729 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
66037681 AGCTGAAATG
66037691 AGCTAAATTCGAGCTCAAGCA
1 AGCTAAATTCGAGCTCAAGCA
66037712 AGCTAAA-TCGAGCTCAAG
1 AGCTAAATTCGAGCTCAAG
66037730 TGAGCTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (21 bp):
AGCTAAATTCGAGCTCAAGCA
Found at i:66037735 original size:20 final size:20
Alignment explanation
Indices: 66037676--66037735 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
66037666 AATGAAGAAG
* *
66037676 AAAT-GAGCTGAAATGAGCT
1 AAATCGAGCTCAAGTGAGCT
**
66037695 AAATTCGAGCTCAAGCAAGCT
1 AAA-TCGAGCTCAAGTGAGCT
66037716 AAATCGAGCTCAAGTGAGCT
1 AAATCGAGCTCAAGTGAGCT
66037736 GATGGAAGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.09
20 16 0.48
21 14 0.42
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.20
Consensus pattern (20 bp):
AAATCGAGCTCAAGTGAGCT
Found at i:66039515 original size:103 final size:103
Alignment explanation
Indices: 66039348--66039656 Score: 591
Period size: 103 Copynumber: 3.0 Consensus size: 103
66039338 GCATGACATT
66039348 AATGTGTTCACATCATGCCGAATTTATGAGTGTTCATGAGATGTCTTAATGACTTGTTTATTTCA
1 AATGTGTTCACATCATGCCGAATTTATGAGTGTTCATGAGATGTCTTAATGACTTGTTTATTTCA
66039413 CGTAGGTACATCCCTTTGGATGGCACATGCATGTAAGG
66 CGTAGGTACATCCCTTTGGATGGCACATGCATGTAAGG
66039451 AATGTGTTCACATCATGCCGAATTTATGAGTGTTCATGAGATGTCTTAATGACTTGTTTATTTCA
1 AATGTGTTCACATCATGCCGAATTTATGAGTGTTCATGAGATGTCTTAATGACTTGTTTATTTCA
66039516 CGTAGGTACATCCCTTTGGATGGCACATGCATGTAAGG
66 CGTAGGTACATCCCTTTGGATGGCACATGCATGTAAGG
66039554 AATGTGTTCACATCATGCCGAATTTATGAGTGTTCATGAGATGTCTTAATGACTTGTTTATTTCA
1 AATGTGTTCACATCATGCCGAATTTATGAGTGTTCATGAGATGTCTTAATGACTTGTTTATTTCA
* * *
66039619 TGTAGGTACATCCCTTTGGACGGCACATGCATGCAAGG
66 CGTAGGTACATCCCTTTGGATGGCACATGCATGTAAGG
66039657 TGCATGCATA
Statistics
Matches: 203, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 203 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (103 bp):
AATGTGTTCACATCATGCCGAATTTATGAGTGTTCATGAGATGTCTTAATGACTTGTTTATTTCA
CGTAGGTACATCCCTTTGGATGGCACATGCATGTAAGG
Found at i:66039807 original size:13 final size:13
Alignment explanation
Indices: 66039789--66039813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66039779 GTATTGATCA
66039789 TGTGTTCACACCT
1 TGTGTTCACACCT
66039802 TGTGTTCACACC
1 TGTGTTCACACC
66039814 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Done.