Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 85 of 93
Found at i:33025727 original size:19 final size:20
Alignment explanation
Indices: 33025705--33025745 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
33025695 TTTTAGTATA
33025705 ATTTA-AATATTAATATT-TT
1 ATTTATAAT-TTAATATTATT
33025724 ATTTATAATTTAATATTATT
1 ATTTATAATTTAATATTATT
33025744 AT
1 AT
33025746 GATTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTATAATTTAATATTATT
Found at i:33025815 original size:17 final size:16
Alignment explanation
Indices: 33025795--33025826 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
33025785 TCATTAAAAA
33025795 TTTAATATATTATTAAT
1 TTTAATATATT-TTAAT
33025812 TTTAATATATTTTAA
1 TTTAATATATTTTAA
33025827 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAATATATTTTAAT
Found at i:33031789 original size:30 final size:30
Alignment explanation
Indices: 33031755--33031819 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
33031745 AAAATGTAAT
* *
33031755 TATAAATATTTATTT-GATTTAAAATAAAAA
1 TATAAAAATTTATTTAG-CTTAAAATAAAAA
33031785 TATAAAAATTTATTTAGCTTAAAATAAAAA
1 TATAAAAATTTATTTAGCTTAAAATAAAAA
33031815 TATAA
1 TATAA
33031820 GAGTTTGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (30 bp):
TATAAAAATTTATTTAGCTTAAAATAAAAA
Found at i:33032177 original size:17 final size:17
Alignment explanation
Indices: 33032155--33032193 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
33032145 TTATTAGTTT
33032155 TTAAAATAAACA-TTTTG
1 TTAAAA-AAACATTTTTG
*
33032172 TTAAAAAAATATTTTTG
1 TTAAAAAAACATTTTTG
33032189 TTAAA
1 TTAAA
33032194 CAAATAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (17 bp):
TTAAAAAAACATTTTTG
Found at i:33032198 original size:17 final size:17
Alignment explanation
Indices: 33032167--33032199 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33032157 AAAATAAACA
33032167 TTTTGTTAAAAAAATAT
1 TTTTGTTAAAAAAATAT
*
33032184 TTTTGTTAAACAAATA
1 TTTTGTTAAAAAAATA
33032200 AGATGATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTTGTTAAAAAAATAT
Found at i:33033532 original size:2 final size:2
Alignment explanation
Indices: 33033519--33033572 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
33033509 TCCAAAGCCA
* *
33033519 AT AT AT AA AT AT AT AA AT AT -T 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
*
33033560 AT A- AT AT TT AT AT
1 AT AT AT AT AT AT AT
33033573 TCTCCCAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33033545 original size:23 final size:23
Alignment explanation
Indices: 33033519--33033571 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
33033509 TCCAAAGCCA
*
33033519 ATATATAAATATATAAATATTAT
1 ATATATAAATATATAAATATAAT
* *
33033542 ATATATATATATATATATATAAT
1 ATATATAAATATATAAATATAAT
*
33033565 ATTTATA
1 ATATATA
33033572 TTCTCCCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATAAATATATAAATATAAT
Found at i:33035817 original size:3 final size:3
Alignment explanation
Indices: 33035809--33035858 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
33035799 CACCCTCAAT
* *
33035809 AAG AAG AAG AAG AAG GAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
33035857 AA
1 AA
33035859 TAACCTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33050349 original size:95 final size:95
Alignment explanation
Indices: 33050186--33050378 Score: 359
Period size: 95 Copynumber: 2.0 Consensus size: 95
33050176 GGCTCATCTC
*
33050186 TTAGAAAAGATGGTTGTATAATACTAACTCTTTTAAGACTTTGTACAAAGATGGTTGTGTTTGAA
1 TTAGAAAAGATGGCTGTATAATACTAACTCTTTTAAGACTTTGTACAAAGATGGTTGTGTTTGAA
33050251 CATTTTGAGCTTCTGACTGAATCTTTTAGA
66 CATTTTGAGCTTCTGACTGAATCTTTTAGA
* *
33050281 TTAGAAAAGATGGCTGTGTCATACTAACTCTTTTAAGACTTTGTACAAAGATGGTTGTGTTTGAA
1 TTAGAAAAGATGGCTGTATAATACTAACTCTTTTAAGACTTTGTACAAAGATGGTTGTGTTTGAA
33050346 CATTTTGAGCTTCTGACTGAATCTTTTAGA
66 CATTTTGAGCTTCTGACTGAATCTTTTAGA
33050376 TTA
1 TTA
33050379 TATTACTTGT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (95 bp):
TTAGAAAAGATGGCTGTATAATACTAACTCTTTTAAGACTTTGTACAAAGATGGTTGTGTTTGAA
CATTTTGAGCTTCTGACTGAATCTTTTAGA
Found at i:33053550 original size:2 final size:2
Alignment explanation
Indices: 33053543--33053585 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
33053533 CCTAATTAGA
33053543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
33053586 TCCAATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33063229 original size:6 final size:6
Alignment explanation
Indices: 33063221--33063253 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
33063211 TTTAGTCCAT
*
33063221 AGACAT AGACAC AGACAC AGACAC AGACAC AGA
1 AGACAC AGACAC AGACAC AGACAC AGACAC AGA
33063254 GGTAAGGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.52, C:0.27, G:0.18, T:0.03
Consensus pattern (6 bp):
AGACAC
Found at i:33066327 original size:2 final size:2
Alignment explanation
Indices: 33066320--33066345 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33066310 ACATTGGCAA
33066320 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
33066346 GACACGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33072694 original size:19 final size:19
Alignment explanation
Indices: 33072670--33072707 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
33072660 TGGTAAAGAT
33072670 TGCTAATTTTCTTTCACAG
1 TGCTAATTTTCTTTCACAG
33072689 TGCTAATTTTCTTTCACAG
1 TGCTAATTTTCTTTCACAG
33072708 CATGATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (19 bp):
TGCTAATTTTCTTTCACAG
Found at i:33077823 original size:18 final size:19
Alignment explanation
Indices: 33077788--33077824 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
33077778 GTATTGATAT
33077788 TTAATGAATGTTTTTCTTTA
1 TTAATGAATG-TTTTCTTTA
33077808 TTAATGAATG-TTTCTTT
1 TTAATGAATGTTTTCTTT
33077825 TATCTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.59
Consensus pattern (19 bp):
TTAATGAATGTTTTCTTTA
Found at i:33078376 original size:1 final size:1
Alignment explanation
Indices: 33078370--33078401 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
33078360 ATTTGTGGAG
33078370 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33078402 AAGCTTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:33079533 original size:2 final size:2
Alignment explanation
Indices: 33079526--33079560 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
33079516 ACGTTCAGAG
*
33079526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33079561 GGCTTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:33079944 original size:2 final size:2
Alignment explanation
Indices: 33079939--33079965 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33079929 ATATATAATA
33079939 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
33079966 ATGGTTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33081082 original size:35 final size:35
Alignment explanation
Indices: 33081017--33081084 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
33081007 AAAGTAACGT
* *
33081017 TTCACTTATTTTAACTATTTCGTGTGAAATAGTAC
1 TTCACTTATTTTAACTATTTCGTATAAAATAGTAC
* *
33081052 TTCACTTGTTTTAATTA-TTCTGTATAAAATAGT
1 TTCACTTATTTTAACTATTTC-GTATAAAATAGT
33081085 GTTTTACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.11
35 25 0.89
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (35 bp):
TTCACTTATTTTAACTATTTCGTATAAAATAGTAC
Found at i:33081231 original size:15 final size:15
Alignment explanation
Indices: 33081213--33081242 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33081203 AAAGCCTCCA
*
33081213 ATAGTACCACCTTAG
1 ATAGTAACACCTTAG
33081228 ATAGTAACACCTTAG
1 ATAGTAACACCTTAG
33081243 CCAATAATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (15 bp):
ATAGTAACACCTTAG
Found at i:33081920 original size:54 final size:55
Alignment explanation
Indices: 33081838--33081948 Score: 188
Period size: 54 Copynumber: 2.0 Consensus size: 55
33081828 AATTTATAGC
* *
33081838 ATAAAGTAAATTGCAAAAGCAAAAGTGAAAAAAAAGA-GGTGAACACAAGAAAGA
1 ATAAAGTAAATTGCAAAAGCAAAAGTGAAAAAAAAAAGGGTAAACACAAGAAAGA
*
33081892 ATAAAGTAAATTGCAAAAGCAAAAGTGAAAAAAAAAAGGGTAAACACAAGGAAGA
1 ATAAAGTAAATTGCAAAAGCAAAAGTGAAAAAAAAAAGGGTAAACACAAGAAAGA
33081947 AT
1 AT
33081949 TTTTTTTTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.61, C:0.07, G:0.20, T:0.12
Consensus pattern (55 bp):
ATAAAGTAAATTGCAAAAGCAAAAGTGAAAAAAAAAAGGGTAAACACAAGAAAGA
Found at i:33082438 original size:14 final size:14
Alignment explanation
Indices: 33082419--33082452 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
33082409 GTTTGCTTGT
*
33082419 CTTTTACACTTTTA
1 CTTTTACAATTTTA
*
33082433 CTTTTATAATTTTA
1 CTTTTACAATTTTA
33082447 CTTTTA
1 CTTTTA
33082453 ACTACAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTTTACAATTTTA
Found at i:33083406 original size:34 final size:35
Alignment explanation
Indices: 33083336--33083423 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
33083326 GTAGAATAAG
* *
33083336 TAAAACAAGTGAAGTACTGCCTCACGTAAAACAAC
1 TAAAACAAGTGAAGTACTACCTCACGCAAAACAAC
* * *
33083371 TAAAACAAGTTAA-TACTACTTCATGCAAAACAAC
1 TAAAACAAGTGAAGTACTACCTCACGCAAAACAAC
* * *
33083405 TAGAATAAGTGGAGTACTA
1 TAAAACAAGTGAAGTACTA
33083424 TTTTATGTGG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
34 26 0.60
35 17 0.40
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (35 bp):
TAAAACAAGTGAAGTACTACCTCACGCAAAACAAC
Found at i:33084698 original size:29 final size:29
Alignment explanation
Indices: 33084652--33084712 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
33084642 GAGAAAAGGC
*
33084652 ACAAGAGAAAAAATTGTACATGAACAGGT
1 ACAAGAGAAAAAATTGTACATGAACAAGT
* *
33084681 ACAAGAGAAGAAGA-TGTATATGAACAAGT
1 ACAAGAGAA-AAAATTGTACATGAACAAGT
33084710 ACA
1 ACA
33084713 TAAGAACAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.16
Consensus pattern (29 bp):
ACAAGAGAAAAAATTGTACATGAACAAGT
Found at i:33087563 original size:3 final size:3
Alignment explanation
Indices: 33087555--33087598 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
33087545 AAAAAGAAAT
* * *
33087555 GAA GAA GAA GAA GAA GAA GAA GAA -TA GAA GAT GAA CAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
33087599 AAAGGCCCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:33087583 original size:20 final size:20
Alignment explanation
Indices: 33087560--33087598 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33087550 GAAATGAAGA
*
33087560 AGAAGAAGAAGAAGAAGAAT
1 AGAAGAAGAACAAGAAGAAT
*
33087580 AGAAGATGAACAAGAAGAA
1 AGAAGAAGAACAAGAAGAA
33087599 AAAGGCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.28, T:0.05
Consensus pattern (20 bp):
AGAAGAAGAACAAGAAGAAT
Found at i:33093786 original size:44 final size:44
Alignment explanation
Indices: 33093736--33093825 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
33093726 CTCACATAGC
33093736 ATTGCATGATGAATACAAGACTTCTCGTAGATTGTGATATCAGT
1 ATTGCATGATGAATACAAGACTTCTCGTAGATTGTGATATCAGT
33093780 ATTGCATGATGAATACAAGACTTCTCGTAGATTGTGATATCAGT
1 ATTGCATGATGAATACAAGACTTCTCGTAGATTGTGATATCAGT
33093824 AT
1 AT
33093826 GGCCCCAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.34
Consensus pattern (44 bp):
ATTGCATGATGAATACAAGACTTCTCGTAGATTGTGATATCAGT
Found at i:33104751 original size:24 final size:24
Alignment explanation
Indices: 33104698--33104751 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
33104688 TTATAATTAA
* *
33104698 AATAAATAAAATTTAATTTTAATT
1 AATAAATAAAAATTAATATTAATT
**
33104722 TTTAAATAAAAAATT-ATATTAATT
1 AATAAAT-AAAAATTAATATTAATT
33104746 AATAAA
1 AATAAA
33104752 CCAAATACTC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AATAAATAAAAATTAATATTAATT
Found at i:33107326 original size:2 final size:2
Alignment explanation
Indices: 33107313--33107397 Score: 116
Period size: 2 Copynumber: 42.5 Consensus size: 2
33107303 TGCTTCATGG
* * *
33107313 TA TA TA TG TA TA TA TT TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
33107355 TA TT TA TA TA TA TA TA TA TA TA TG TA TA TA TT 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
33107397 T
1 T
33107398 TAAAAAAAAG
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (2 bp):
TA
Found at i:33107354 original size:28 final size:28
Alignment explanation
Indices: 33107313--33107397 Score: 152
Period size: 28 Copynumber: 3.0 Consensus size: 28
33107303 TGCTTCATGG
33107313 TATATATGTATATATTTATATATATATATA
1 TATATATGTATATA-TT-TATATATATATA
33107343 TATATATGTATATATTTATATATATATA
1 TATATATGTATATATTTATATATATATA
33107371 TATATATGTATATATTTATATATATAT
1 TATATATGTATATATTTATATATATAT
33107398 TAAAAAAAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 39 0.71
29 2 0.04
30 14 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TATATATGTATATATTTATATATATATA
Found at i:33117701 original size:3 final size:3
Alignment explanation
Indices: 33117686--33117721 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
33117676 AACAACTACC
*
33117686 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33117722 TCTTTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:33126049 original size:24 final size:21
Alignment explanation
Indices: 33126017--33126067 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 21
33126007 TTTCTATCTG
*
33126017 TTTTTTTCTTTCTCTTTTTACCTC
1 TTTTTTTCTTTC-ATTTTT--CTC
33126041 TTTTTTTCTTTCATTTTTCTC
1 TTTTTTTCTTTCATTTTTCTC
33126062 TTTTTT
1 TTTTTT
33126068 CCTATGTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.35
23 5 0.19
24 12 0.46
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTTCTTTCATTTTTCTC
Found at i:33126292 original size:19 final size:18
Alignment explanation
Indices: 33126257--33126292 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
33126247 CTGAATTCCA
*
33126257 AAACCCTAAATCGATTTG
1 AAACCCTAAATCAATTTG
33126275 AAACCCTAAAATCAATTT
1 AAACCCT-AAATCAATTT
33126293 CCATTAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (18 bp):
AAACCCTAAATCAATTTG
Found at i:33130080 original size:3 final size:3
Alignment explanation
Indices: 33130074--33130107 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
33130064 CACCACCCCA
*
33130074 GTT GTT GTT GTT ATT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G
33130108 CTGCTGGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.32, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:33139996 original size:14 final size:14
Alignment explanation
Indices: 33139934--33139999 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 14
33139924 CCCGCTCACC
*
33139934 TCTTCTTCTTTCTT
1 TCTTCTTCTCTCTT
33139948 TCTTCTTCTCTCTT
1 TCTTCTTCTCTCTT
33139962 CCTCCTTCTTTCTCTCCCTT
1 --T-CTTC-TTCTCT--CTT
*
33139982 TTTTCTTCTCTCTT
1 TCTTCTTCTCTCTT
33139996 TCTT
1 TCTT
33140000 GGGCCGCCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 19 0.44
16 7 0.16
17 7 0.16
18 7 0.16
20 3 0.07
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TCTTCTTCTCTCTT
Found at i:33142467 original size:25 final size:25
Alignment explanation
Indices: 33142433--33142480 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
33142423 CAAGCCATTG
33142433 CAATTTGGGAATTTGAGCTTTGACC
1 CAATTTGGGAATTTGAGCTTTGACC
*
33142458 CAATTTGGGAATTTGAGTTTTGA
1 CAATTTGGGAATTTGAGCTTTGA
33142481 AGAAAAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (25 bp):
CAATTTGGGAATTTGAGCTTTGACC
Found at i:33142501 original size:32 final size:32
Alignment explanation
Indices: 33142465--33142525 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
33142455 ACCCAATTTG
33142465 GGAATTTGAGTTTTGAAGAAAAAGGATGAATT
1 GGAATTTGAGTTTTGAAGAAAAAGGATGAATT
*
33142497 GGAATTTGAGTTTTGAAGAAAAGGGATGA
1 GGAATTTGAGTTTTGAAGAAAAAGGATGA
33142526 GAGACATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.30
Consensus pattern (32 bp):
GGAATTTGAGTTTTGAAGAAAAAGGATGAATT
Found at i:33142831 original size:38 final size:38
Alignment explanation
Indices: 33142789--33142865 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
33142779 TCTTAGACTT
*
33142789 GTGGGTGATTTTCTTTCTTAAACTTTGAGTGTGGGTTG
1 GTGGGTGATTTTCTTTCTTAAACTTTGAATGTGGGTTG
33142827 GTGGGTGATTTTCTTTCTTAAACTTTGAATGTGGGTTG
1 GTGGGTGATTTTCTTTCTTAAACTTTGAATGTGGGTTG
33142865 G
1 G
33142866 AGGTTCTTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.14, C:0.08, G:0.31, T:0.47
Consensus pattern (38 bp):
GTGGGTGATTTTCTTTCTTAAACTTTGAATGTGGGTTG
Found at i:33159150 original size:4 final size:4
Alignment explanation
Indices: 33159131--33159194 Score: 55
Period size: 4 Copynumber: 16.2 Consensus size: 4
33159121 CTGTAGACAC
* *
33159131 ATAA ATTA A-AA A-AA ATAA ATAA ATAA ATTAAA ATAA ATAAA ATAA AAAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A-T-AA ATAA AT-AA ATAA ATAA
33159180 ATAA A-AA A-AA ATAA A
1 ATAA ATAA ATAA ATAA A
33159195 AAAAAAATCG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
3 11 0.22
4 31 0.61
5 6 0.12
6 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:33159154 original size:18 final size:18
Alignment explanation
Indices: 33159131--33159199 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
33159121 CTGTAGACAC
*
33159131 ATAAATTAAAAAAAATAA
1 ATAAAATAAAAAAAATAA
*
33159149 AT-AAATAAATTAAAATAA
1 ATAAAATAAA-AAAAATAA
33159167 ATAAAAT-AAAAAAATAAA
1 ATAAAATAAAAAAAAT-AA
*
33159185 AAAAAATAAAAAAAA
1 ATAAAATAAAAAAAA
33159200 AATCGGGATG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 11 0.26
18 21 0.49
19 11 0.26
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
ATAAAATAAAAAAAATAA
Found at i:33159159 original size:22 final size:22
Alignment explanation
Indices: 33159133--33159202 Score: 97
Period size: 23 Copynumber: 3.2 Consensus size: 22
33159123 GTAGACACAT
*
33159133 AAATTAAAAAAAATAAATAAAT
1 AAATTAAAAAAAATAAATAAAA
*
33159155 AAATTAAAATAAATAAAATAAAA
1 AAATTAAAAAAAAT-AAATAAAA
*
33159178 AAATAAAAAAAAATAAA-AAAA
1 AAATTAAAAAAAATAAATAAAA
33159199 AAAT
1 AAAT
33159203 CGGGATGGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 8 0.19
22 16 0.37
23 19 0.44
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (22 bp):
AAATTAAAAAAAATAAATAAAA
Found at i:33159172 original size:27 final size:26
Alignment explanation
Indices: 33159139--33159202 Score: 85
Period size: 27 Copynumber: 2.5 Consensus size: 26
33159129 ACATAAATTA
*
33159139 AAAAAAATAAATAAATAAATTAAAAT
1 AAAAAAATAAATAAATAAAATAAAAT
* *
33159165 AAATAAAATAAAAAAATAAAAAAAAAT
1 AAA-AAAATAAATAAATAAAATAAAAT
33159192 AAAAAAA-AAAT
1 AAAAAAATAAAT
33159203 CGGGATGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 3 0.09
26 7 0.21
27 23 0.70
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (26 bp):
AAAAAAATAAATAAATAAAATAAAAT
Found at i:33159186 original size:9 final size:9
Alignment explanation
Indices: 33159137--33159199 Score: 67
Period size: 9 Copynumber: 7.0 Consensus size: 9
33159127 ACACATAAAT
33159137 TAAAAAAAA
1 TAAAAAAAA
*
33159146 T-AAATAAA
1 TAAAAAAAA
*
33159154 TAAATTAAAA
1 TAAA-AAAAA
*
33159164 TAAATAAAA
1 TAAAAAAAA
33159173 T-AAAAAAA
1 TAAAAAAAA
33159181 TAAAAAAAAA
1 T-AAAAAAAA
33159191 TAAAAAAAA
1 TAAAAAAAA
33159200 AATCGGGATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 14 0.30
9 17 0.37
10 15 0.33
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:33159741 original size:30 final size:30
Alignment explanation
Indices: 33159705--33159768 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
33159695 CTTTTATACC
*
33159705 CAGAGGAAAGAGGGCAAAACGGTGTCGTTT
1 CAGAGGAAAGAGGGCAAAACGGCGTCGTTT
*
33159735 CAGAGGAAGGAGGGCAAAACGGCGTCGTTT
1 CAGAGGAAAGAGGGCAAAACGGCGTCGTTT
33159765 CAGA
1 CAGA
33159769 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.38, T:0.14
Consensus pattern (30 bp):
CAGAGGAAAGAGGGCAAAACGGCGTCGTTT
Found at i:33161662 original size:16 final size:16
Alignment explanation
Indices: 33161641--33161671 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33161631 TTATTTATAT
33161641 ATTTATTTAATAATTA
1 ATTTATTTAATAATTA
*
33161657 ATTTATTTATTAATT
1 ATTTATTTAATAATT
33161672 TTAATAAATA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTAATAATTA
Found at i:33173748 original size:13 final size:13
Alignment explanation
Indices: 33173730--33173755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33173720 TTTCCAAGGC
33173730 AATATATATATAT
1 AATATATATATAT
33173743 AATATATATATAT
1 AATATATATATAT
33173756 TGCTGGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATATATATAT
Found at i:33174204 original size:2 final size:2
Alignment explanation
Indices: 33174197--33174224 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33174187 TGTTTTCTTC
33174197 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
33174225 GTGGAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33179206 original size:26 final size:26
Alignment explanation
Indices: 33179177--33179226 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
33179167 TAGATTAATT
33179177 TTTTATTAATTAATATATAAATTATG
1 TTTTATTAATTAATATATAAATTATG
*
33179203 TTTTATTAATTAATGTATAAATTA
1 TTTTATTAATTAATATATAAATTA
33179227 ATAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TTTTATTAATTAATATATAAATTATG
Found at i:33179735 original size:31 final size:32
Alignment explanation
Indices: 33179697--33179796 Score: 107
Period size: 31 Copynumber: 3.1 Consensus size: 32
33179687 AGTGACTGTC
* * *
33179697 AATAAAATTTATATTTTTAAAAA-AAAATTAA
1 AATAAAATTTATAATATTAAAAATAAAAATAA
33179728 AATAAAATTTATAATATTAAAAATAAAAATAA
1 AATAAAATTTATAATATTAAAAATAAAAATAA
* *
33179760 AATATATAAGATTATAATA--AGAAATAAAAATAA
1 AATA-A-AA-TTTATAATATTAAAAATAAAAATAA
33179793 AATA
1 AATA
33179797 TATGATATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
31 21 0.35
32 11 0.18
33 18 0.30
34 2 0.03
35 8 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (32 bp):
AATAAAATTTATAATATTAAAAATAAAAATAA
Found at i:33179756 original size:27 final size:27
Alignment explanation
Indices: 33179719--33179808 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 27
33179709 ATTTTTAAAA
* *
33179719 AAAAATTAAAATAAAATTTATAATATT
1 AAAAATAAAAATAAAATATATAATATT
33179746 AAAAATAAAAATAAAATATATAAGATTATAAT
1 AAAAATAAAAATAAAATATAT-A-A-TAT--T
*
33179778 AAGAAATAAAAATAAAATATATGATATT
1 AA-AAATAAAAATAAAATATATAATATT
33179806 AAA
1 AAA
33179809 TTTATATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
27 20 0.37
28 4 0.07
29 1 0.02
30 6 0.11
31 1 0.02
32 3 0.06
33 19 0.35
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
AAAAATAAAAATAAAATATATAATATT
Found at i:33182933 original size:2 final size:2
Alignment explanation
Indices: 33182926--33182952 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33182916 CATCTTAAAC
33182926 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
33182953 CAATTGATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33183094 original size:23 final size:24
Alignment explanation
Indices: 33183060--33183117 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
33183050 TCATATATGG
*
33183060 ATTTGA-ACTTTTGTTTAT-TTTGAC
1 ATTTGAGA-TTTT-TTTATGTTGGAC
33183084 -TTTGAGATTTTTTTATGTTGGAC
1 ATTTGAGATTTTTTTATGTTGGAC
*
33183107 ATTTTAGATTT
1 ATTTGAGATTT
33183118 AATTTTTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 5 0.17
23 14 0.48
24 10 0.34
ACGTcount: A:0.21, C:0.05, G:0.16, T:0.59
Consensus pattern (24 bp):
ATTTGAGATTTTTTTATGTTGGAC
Found at i:33185295 original size:29 final size:30
Alignment explanation
Indices: 33185263--33185320 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
33185253 CGTGCAACAA
* **
33185263 TAATA-TTTTTTCAATATGGTGTGTAATAC
1 TAATATTTTTTTCAACATGACGTGTAATAC
33185292 TAATATTTTTTTCAACATGACGTGTAATA
1 TAATATTTTTTTCAACATGACGTGTAATA
33185321 ACCTTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.47
Consensus pattern (30 bp):
TAATATTTTTTTCAACATGACGTGTAATAC
Found at i:33185505 original size:76 final size:76
Alignment explanation
Indices: 33185338--33185508 Score: 236
Period size: 76 Copynumber: 2.2 Consensus size: 76
33185328 TTAGCTATGA
* *
33185338 CATGTAACATGTTTTTGTATATAGCGTGTAACAATAGTAATTTTTTTCAATATGACATGTAACAA
1 CATGTAACATGTTTTTGTACATAGCGTGTAACAATAATAATTTTTTTCAATATGACATGTAACAA
33185403 CCTAATCATAT
66 CCTAATCATAT
* * * * *
33185414 TATGTAACATATTTTTGTACAT-GACGTGTAATAATAATATTTTTTTTCAATATGACTTGTAACA
1 CATGTAACATGTTTTTGTACATAG-CGTGTAACAATAATAATTTTTTTCAATATGACATGTAACA
*
33185478 ACCTAATCATGT
65 ACCTAATCATAT
* *
33185490 CGTGTCACATGTTTTTGTA
1 CATGTAACATGTTTTTGTA
33185509 AACGGTGTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
75 1 0.01
76 81 0.99
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (76 bp):
CATGTAACATGTTTTTGTACATAGCGTGTAACAATAATAATTTTTTTCAATATGACATGTAACAA
CCTAATCATAT
Found at i:33189561 original size:19 final size:19
Alignment explanation
Indices: 33189525--33189562 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
33189515 AAAGAAATTA
*
33189525 TTAAAATAAAAAATTATAT
1 TTAAAATAAAAAAATATAT
33189544 TTAAAA-AAAAAACATATAT
1 TTAAAATAAAAAA-ATATAT
33189563 AATAGATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAATAAAAAAATATAT
Found at i:33191608 original size:30 final size:30
Alignment explanation
Indices: 33191574--33191630 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
33191564 TCATAAAGGT
* *
33191574 TTATTTGATTTAAAATAAAAGTATAAGAAC
1 TTATTTAATTTAAAATAAAAATATAAGAAC
33191604 TTATTTAATTTAAAATAAAAATATAAG
1 TTATTTAATTTAAAATAAAAATATAAG
33191631 GATTTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (30 bp):
TTATTTAATTTAAAATAAAAATATAAGAAC
Found at i:33191874 original size:18 final size:18
Alignment explanation
Indices: 33191851--33191887 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
33191841 TTTATACCCT
33191851 TAAATTTGTAAATTTAGA
1 TAAATTTGTAAATTTAGA
33191869 TAAATTTGTAAATTTAGA
1 TAAATTTGTAAATTTAGA
33191887 T
1 T
33191888 TTTTATAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (18 bp):
TAAATTTGTAAATTTAGA
Found at i:33198903 original size:75 final size:75
Alignment explanation
Indices: 33198823--33198981 Score: 318
Period size: 75 Copynumber: 2.1 Consensus size: 75
33198813 TCGTCTTCTG
33198823 GGCGGCTGCTCTCTGCAGAGCCCAAAGCACATCTGACCCACTTATCTCCTTTCCCTCTTCTTGCT
1 GGCGGCTGCTCTCTGCAGAGCCCAAAGCACATCTGACCCACTTATCTCCTTTCCCTCTTCTTGCT
33198888 TGGCGTTGGA
66 TGGCGTTGGA
33198898 GGCGGCTGCTCTCTGCAGAGCCCAAAGCACATCTGACCCACTTATCTCCTTTCCCTCTTCTTGCT
1 GGCGGCTGCTCTCTGCAGAGCCCAAAGCACATCTGACCCACTTATCTCCTTTCCCTCTTCTTGCT
33198963 TGGCGTTGGA
66 TGGCGTTGGA
33198973 GGCGGCTGC
1 GGCGGCTGC
33198982 CTTACGAGAC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.14, C:0.35, G:0.23, T:0.28
Consensus pattern (75 bp):
GGCGGCTGCTCTCTGCAGAGCCCAAAGCACATCTGACCCACTTATCTCCTTTCCCTCTTCTTGCT
TGGCGTTGGA
Found at i:33201244 original size:21 final size:22
Alignment explanation
Indices: 33201220--33201263 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
33201210 AAACCTAAAC
33201220 TCAAAGAGAGT-AACTTT-ACAT
1 TCAAA-AGAGTCAACTTTCACAT
*
33201241 TCAAAAGATTCAACTTTCACAT
1 TCAAAAGAGTCAACTTTCACAT
33201263 T
1 T
33201264 TATGTTGCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (22 bp):
TCAAAAGAGTCAACTTTCACAT
Found at i:33202049 original size:41 final size:43
Alignment explanation
Indices: 33201966--33202049 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 43
33201956 CTTACGGGCA
* *
33201966 GTGAGTGAAGAAGGCAGGAAAGAAGAAGAAAAGAACATAAAATG
1 GTGAGAGAAGAAGGCAGGAAAGAAGAAGAAAAG-ACAGAAAATG
* *
33202010 GTGAGAGAAGCAGGCAGGAAAGAAGAA-AAAAG-TAGAAAAT
1 GTGAGAGAAGAAGGCAGGAAAGAAGAAGAAAAGACAGAAAAT
33202050 AAAATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 6 0.17
43 5 0.14
44 25 0.69
ACGTcount: A:0.55, C:0.05, G:0.32, T:0.08
Consensus pattern (43 bp):
GTGAGAGAAGAAGGCAGGAAAGAAGAAGAAAAGACAGAAAATG
Found at i:33202532 original size:2 final size:2
Alignment explanation
Indices: 33202525--33202563 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
33202515 TAAGCAGGGG
33202525 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
33202564 GCGACATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33203563 original size:59 final size:59
Alignment explanation
Indices: 33203433--33203549 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
33203423 AATTAAGAAG
*
33203433 AAGAAGACGAATGTATGGAAAGTAATACTTTGTCAAGTATGACATCAAGAGGAAGATGC
1 AAGAAGACGAATGTATGGAAAGTAATACTTTCTCAAGTATGACATCAAGAGGAAGATGC
*
33203492 AAGAAGACGAATGTATGGAAAGTAATGCTTTCTCAAGTATGACATCAAGAGGAAGATG
1 AAGAAGACGAATGTATGGAAAGTAATACTTTCTCAAGTATGACATCAAGAGGAAGATG
33203550 TTGTTGAATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (59 bp):
AAGAAGACGAATGTATGGAAAGTAATACTTTCTCAAGTATGACATCAAGAGGAAGATGC
Found at i:33207586 original size:219 final size:211
Alignment explanation
Indices: 33207042--33207675 Score: 840
Period size: 216 Copynumber: 2.9 Consensus size: 211
33207032 GTGTAAATAC
* * * * *
33207042 TATATATATATTTAATTTATACATAAGCGTTACTATAACTTATAGTAAACTTTATTTATATTATT
1 TATACATATAGTTAATTTATACATAAGCATTACTATAACTTATA--ATACTTTATTTATATGATT
* * *
33207107 ACACTTAATAACCTTATTAATTATCACCTTAATTTTTATAACATATTGCTTATAATTAGTTATTA
64 ACACTTAATAA-TTTATTAGTTATCACCTTAATTTTTATAACATATTGTTTATAATTAGTTATTA
** * *
33207172 TTTATACAAACTTTGATATAAAACATTATAACATATAAACTGTGTCATTAATTTCATATATACAT
128 TTTATACAAACTTTGATATAAAACATTATAACATATAAGTTATGTCATTAATTT--TATATATAT
33207237 AATAAAGTAATATATTATATA
191 AATAAAGTAATATATTATATA
* * * *
33207258 TATACGTATATTTAATTTATACATAAGCATTACTGTAACTTATAATAGACTTTAGTTATATGATT
1 TATACATATAGTTAATTTATACATAAGCATTACTATAACTTATAAT--ACTTTATTTATATGATT
** *
33207323 ACACTTAATAATTTCATTAGTTATGGCCTTAATTTTTATAACATATTGTTTGTAATTAGTTATTA
64 ACACTTAATAATTT-ATTAGTTATCACCTTAATTTTTATAACATATTGTTTATAATTAGTTATTA
* *
33207388 TTTATACGAACTTTGATATAAATATTAAAATATTATAACATATAAGTTATGTCATTAATTTTATA
128 TTTATACAAACTTTG------ATA-TAAAACATTATAACATATAAGTTATGTCATTAATTTTATA
33207453 TATATAATAAAGTAATATATTATATA
186 TATATAATAAAGTAATATATTATATA
* *
33207479 TATACATATACGTNAATTTATCCATAAGCATTACTATAACTTATAATA-TTTATTTATATGATTA
1 TATACATATA-GTTAATTTATACATAAGCATTACTATAACTTATAATACTTTATTTATATGATTA
*
33207543 CACTTAATAAGTTTATTAGCTATCACCTTAGA-TTTTATAACATATTGTTTATAATTAGTTATTA
65 CACTTAATAA-TTTATTAGTTATCACCTTA-ATTTTTATAACATATTGTTTATAATTAGTTATTA
* * *
33207607 TTTACACAAACTTTGATATAAAACATTATAACATATAAGTTATATCATTAATTTCATATATATAT
128 TTTATACAAACTTTGATATAAAACATTATAACATATAAGTTATGTCATTAATTTTATATATATA-
33207672 ATAA
192 ATAA
33207676 TTATGGATGG
Statistics
Matches: 370, Mismatches: 34, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
212 43 0.12
213 7 0.02
214 1 0.00
215 2 0.01
216 125 0.34
219 82 0.22
220 5 0.01
221 38 0.10
222 35 0.09
223 32 0.09
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (211 bp):
TATACATATAGTTAATTTATACATAAGCATTACTATAACTTATAATACTTTATTTATATGATTAC
ACTTAATAATTTATTAGTTATCACCTTAATTTTTATAACATATTGTTTATAATTAGTTATTATTT
ATACAAACTTTGATATAAAACATTATAACATATAAGTTATGTCATTAATTTTATATATATAATAA
AGTAATATATTATATA
Found at i:33210230 original size:23 final size:23
Alignment explanation
Indices: 33210208--33210255 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
33210198 TAATAATATA
33210208 AATAAAATTTAT-TATAAATTAT
1 AATAAAATTTATGTATAAATTAT
**
33210230 AATAATGTTTATGTATAAATTA-
1 AATAAAATTTATGTATAAATTAT
33210252 AATA
1 AATA
33210256 TATGTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AATAAAATTTATGTATAAATTAT
Found at i:33210260 original size:23 final size:22
Alignment explanation
Indices: 33210215--33210269 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
33210205 ATAAATAAAA
33210215 TTTATTATAAATTATAATAATG
1 TTTATTATAAATTATAATAATG
33210237 TTTATGTATAAATTA-AATATATG
1 TTTAT-TATAAATTATAATA-ATG
* *
33210260 TATAATATAA
1 TTTATTATAA
33210270 GTTTATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
TTTATTATAAATTATAATAATG
Found at i:33212681 original size:2 final size:2
Alignment explanation
Indices: 33212676--33212704 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
33212666 ATAAAAAAAT
33212676 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33212705 AATTAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33219063 original size:2 final size:2
Alignment explanation
Indices: 33219052--33219084 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
33219042 TGTCACATAA
33219052 AT AT -T 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
33219085 TTTTTATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:33219138 original size:2 final size:2
Alignment explanation
Indices: 33219127--33219160 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
33219117 ACTGNACATA
33219127 AT AT -T AT AT AT AT AT AT AT AGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
33219161 TTTTTATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33219167 original size:76 final size:75
Alignment explanation
Indices: 33219046--33219197 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 75
33219036 CACTAATGTC
33219046 ACATAAATATTATATATATATATATATATATATATATATTTTTTATTGTAAGTAATGATTGATTG
1 ACATAAATATTATATATATATATATATATATATATATATTTTTTATTGTAAGTAATGATTGATTG
33219111 TTTTAAACTG
66 TTTTAAACTG
33219121 NACAT-AATATTATATATATATATATAGTATATATATATATTTTTTATTGTAAGTAATGATTGAT
1 -ACATAAATATTATATATATATATATA-TATATATATATATTTTTTATTGTAAGTAATGATTGAT
33219185 TGTTTTAAACTG
64 TGTTTTAAACTG
33219197 A
1 A
33219198 TCTCCCATGA
Statistics
Matches: 75, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
75 22 0.29
76 53 0.71
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (75 bp):
ACATAAATATTATATATATATATATATATATATATATATTTTTTATTGTAAGTAATGATTGATTG
TTTTAAACTG
Found at i:33223147 original size:42 final size:43
Alignment explanation
Indices: 33223048--33223150 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 43
33223038 ATCCTACCTA
*
33223048 TATT-ATATTTGTAAATAAAATATTAATATATGAAAGTATTAAT
1 TATTAATATTT-TAAATAAAATATTAATATATGAAAGTATCAAT
* * *
33223091 AATTAA-ATTATAAATAAAATATTAATAT-T-TAAGTAATCAAT
1 TATTAATATTTTAAATAAAATATTAATATATGAAAGT-ATCAAT
33223132 TATTAATATTTTAAATAAA
1 TATTAATATTTTAAATAAA
33223151 TTATAAATCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.08
41 11 0.22
42 29 0.57
43 6 0.12
44 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (43 bp):
TATTAATATTTTAAATAAAATATTAATATATGAAAGTATCAAT
Found at i:33223465 original size:148 final size:150
Alignment explanation
Indices: 33223193--33223703 Score: 490
Period size: 148 Copynumber: 3.4 Consensus size: 150
33223183 GTAATAATAT
* * * * * *
33223193 TTAAATTATAAATAAAATATTAATATGT-AAATTATTACTTATTAATATTTTAAATAAATTATAA
1 TTAAATTATTAATAAAATATTAATAT-TAAAATGATAAATTATTAATATTATAAATATATTAT--
* * * * *
33223257 ATTATTACTATTTAAAAGATAAAACATAAAT-AAATAAATAATCAGAATAACATTTAAATTATAT
63 A-T-CTAC-ATTTAAAAAATAAAATA-AAATAAAATAAATAATCATAATAACATTTAAATTATAA
* *
33223321 ATGAAATATTAGTATTTTTTAAAATGA
124 ATAAAATATTAGTATTTTATAAAATGA
** *
33223348 TTAAATTATTAATAAAATATTAATATT-AAATGATCTATTATTAATATTTTAAATA-AGTTAT-T
1 TTAAATTATTAATAAAATATTAATATTAAAATGATAAATTATTAATATTATAAATATA-TTATAT
*
33223410 C-ACATTTAAACAATAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTATAAATAAA
65 CTACATTTAAAAAATAAAATAAAAT-AAAATAAATAATCATAATAACATTTAAATTATAAATAAA
*
33223474 ATATTAGTATTTTAAAAAATAATGA
129 ATATTAGTATTTT--ATAA-AATGA
* *
33223499 TTAAATTATAAATAACATATTAATATTAAAATGATAAATTATTAATATTATAAATATATTATAAA
1 TTAAATTATTAATAAAATATTAATATTAAAATGATAAATTATTAATATTATAAATATATTAT---
* * * * *
33223564 ATCTTAATATTTAAAAAATAAAATAAAATAAAATAAAAAATTATAATATCATTAAAATTATAAAT
63 ATC-T-ACATTTAAAAAATAAAATAAAATAAAATAAATAATCATAATAACATTTAAATTATAAAT
* * *
33223629 AAAATAATAATATTTTATAAAA-CA
126 AAAATATTAGTATTTTATAAAATGA
* *
33223653 TTTAAATTA-T-A-AAAATATTAATATTTAAAAAG-TAAA-GATTAA-ATTATAAAT
1 -TTAAATTATTAATAAAATATTAATA-TTAAAATGATAAATTATTAATATTATAAAT
33223704 GAAATATTAA
Statistics
Matches: 306, Mismatches: 33, Indels: 39
0.81 0.09 0.10
Matches are distributed among these distances:
146 4 0.01
147 14 0.05
148 50 0.16
150 12 0.04
151 35 0.11
152 44 0.14
153 10 0.03
154 30 0.10
155 35 0.11
156 5 0.02
158 46 0.15
159 21 0.07
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (150 bp):
TTAAATTATTAATAAAATATTAATATTAAAATGATAAATTATTAATATTATAAATATATTATATC
TACATTTAAAAAATAAAATAAAATAAAATAAATAATCATAATAACATTTAAATTATAAATAAAAT
ATTAGTATTTTATAAAATGA
Found at i:33223530 original size:19 final size:20
Alignment explanation
Indices: 33223059--33223748 Score: 125
Period size: 20 Copynumber: 35.4 Consensus size: 20
33223049 ATTATATTTG
33223059 TAAATAAAATATTAATA-TA
1 TAAATAAAATATTAATATTA
*
33223078 TGAAAGTATTAATAATTAA-ATTA
1 T-AAA-TA-AAAT-ATTAATATTA
33223101 TAAATAAAATATTAATATT-
1 TAAATAAAATATTAATATTA
* *
33223120 TAAGTAATCAATTATTAATATTT
1 TAAATAA--AA-TATTAATATTA
* * * *
33223143 TAAATAAATTATAAATCTTT
1 TAAATAAAATATTAATATTA
* * * *
33223163 TGAA-AAAATA-AAAAATAA
1 TAAATAAAATATTAATATTA
**
33223181 T-CGTAATAATATTTAA-ATTA
1 TAAATAA-AATA-TTAATATTA
33223201 TAAATAAAATATTAATATGTA
1 TAAATAAAATATTAATAT-TA
* ** *
33223222 -AATTATTACTTATTAATATTT
1 TAA--ATAAAATATTAATATTA
* *
33223243 TAAATAAATTATAAATTATTA
1 TAAATAAAATATTAA-TATTA
** * **
33223264 CTATTTAAAAGA-TAA-AACA
1 -TAAATAAAATATTAATATTA
33223283 TAAAT-AAATA--AATA--A
1 TAAATAAAATATTAATATTA
*
33223298 TCAGAATAACAT-TTAA-ATTA
1 T-A-AATAAAATATTAATATTA
* * *
33223318 TATATGAAATATTAGTATT-
1 TAAATAAAATATTAATATTA
**
33223337 T-TTTAAAATGATTAA-ATTA
1 TAAATAAAAT-ATTAATATTA
*
33223356 TTAATAAAATATTAATATTA
1 TAAATAAAATATTAATATTA
** * *
33223376 -AATGATCTATTATTAATATTT
1 TAA--ATAAAATATTAATATTA
** * *
33223397 TAAATAAGTTATTCACATT-
1 TAAATAAAATATTAATATTA
*
33223416 T-AA-ACAATA--AA-A-TA
1 TAAATAAAATATTAATATTA
* *
33223430 -AAATAAAA-ATAAATAATCA
1 TAAATAAAATATTAAT-ATTA
*
33223449 T-AATAACAT-TTAA-ATTA
1 TAAATAAAATATTAATATTA
* *
33223466 TAAATAAAATATTAGTATTT
1 TAAATAAAATATTAATATTA
*
33223486 TAAAAAATAATGATTAA-ATTA
1 TAAATAA-AAT-ATTAATATTA
*
33223507 TAAATAACATATTAATATTA
1 TAAATAAAATATTAATATTA
33223527 -AAATGATAAATTATTAATATTA
1 TAAAT-A-AAA-TATTAATATTA
* * * *
33223549 TAAATATATTATAAAATCTTAA
1 TAAATAAAATAT-TAATATT-A
** * *
33223571 TATTTAAAA-AATAA-AATA
1 TAAATAAAATATTAATATTA
* *
33223589 -AAATAAAATA-AAAAATTA
1 TAAATAAAATATTAATATTA
*
33223607 T-AAT---ATCATTAAAATTA
1 TAAATAAAAT-ATTAATATTA
*
33223624 TAAATAAAATAATAATATT-
1 TAAATAAAATATTAATATTA
* *
33223643 T-TATAAAACATTTAA-ATTA
1 TAAATAAAATA-TTAATATTA
33223662 T--A-AAAATATTAATATT-
1 TAAATAAAATATTAATATTA
* *
33223678 TAAAAAGTAAAGATTAA-ATTA
1 TAAATA--AAATATTAATATTA
*
33223699 TAAATGAAATATTAATATT-
1 TAAATAAAATATTAATATTA
33223718 TAAATGATAAATTATTAATATTA
1 TAAAT-A-AAA-TATTAATATTA
*
33223741 TAACTAAA
1 TAAATAAA
33223749 TTATCAATTA
Statistics
Matches: 483, Mismatches: 104, Indels: 166
0.64 0.14 0.22
Matches are distributed among these distances:
13 1 0.00
14 4 0.01
15 8 0.02
16 11 0.02
17 39 0.08
18 61 0.13
19 88 0.18
20 102 0.21
21 74 0.15
22 73 0.15
23 22 0.05
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
TAAATAAAATATTAATATTA
Found at i:33223543 original size:16 final size:17
Alignment explanation
Indices: 33223521--33223559 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
33223511 TAACATATTA
33223521 ATATTAAAATGATAAAT
1 ATATTAAAATGATAAAT
* *
33223538 -TATTAATATTATAAAT
1 ATATTAAAATGATAAAT
33223554 ATATTA
1 ATATTA
33223560 TAAAATCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATTAAAATGATAAAT
Found at i:33223626 original size:158 final size:152
Alignment explanation
Indices: 33223188--33223677 Score: 518
Period size: 158 Copynumber: 3.2 Consensus size: 152
33223178 TAATCGTAAT
* * * *
33223188 AATATTTAAATTATAAATAAAATATTAATATGTAAATTATTACTTATTAATATTTTAAATAAATT
1 AATA-TTAAATTATAAATAAAATATTAATAT-TAAATGATAAATTATTAATATTATAAAT-AATT
* * * * *
33223253 ATAAATTATTACTATTTAAAAGATAAAACATAAAT-AAATAAATAATCAGAATAACATTTAAATT
63 ATAAA-TCTTAATATTTAAAAAATAAAATA-AAATAAAATAAATAATCATAATAACATTTAAATT
* * **
33223317 ATATATGAAATATTAGTATTTT-TTAA
126 ATAAATAAAATATTAGTATTTTAAAAA
* ** *
33223343 AATGATTAAATTATTAATAAAATATTAATATTAAATGATCTATTATTAATATTTTAAATAAGTTA
1 AAT-ATTAAATTATAAATAAAATATTAATATTAAATGATAAATTATTAATATTATAAATAA-TTA
* *
33223408 T---TC---ACATTTAAACAATAAAATAAAATAAAAATAAATAATCATAATAACATTTAAATTAT
64 TAAATCTTAATATTTAAAAAATAAAATAAAAT-AAAATAAATAATCATAATAACATTTAAATTAT
33223467 AAATAAAATATTAGTATTTTAAAAAA
128 AAATAAAATATTAGTATTTT-AAAAA
*
33223493 TAATGATTAAATTATAAATAACATATTAATATTAAAATGATAAATTATTAATATTATAAATATAT
1 -AAT-ATTAAATTATAAATAAAATATTAATATT-AAATGATAAATTATTAATATTATAAATA-AT
* * * *
33223558 TATAAAATCTTAATATTTAAAAAATAAAATAAAATAAAATAAAAAATTATAATATCATTAAAATT
62 TAT-AAATCTTAATATTTAAAAAATAAAATAAAATAAAATAAATAATCATAATAACATTTAAATT
* *
33223623 ATAAATAAAATAATAATATTTTATAAAA
126 ATAAATAAAATATTAGTATTTTA-AAAA
*
33223651 CAT-TTAAATTAT--A-AAAATATTAATATT
1 AATATTAAATTATAAATAAAATATTAATATT
33223678 TAAAAAGTAA
Statistics
Matches: 287, Mismatches: 31, Indels: 37
0.81 0.09 0.10
Matches are distributed among these distances:
146 4 0.01
147 14 0.05
148 48 0.17
150 3 0.01
151 30 0.10
152 42 0.15
153 4 0.01
154 28 0.10
155 37 0.13
156 3 0.01
157 3 0.01
158 50 0.17
159 21 0.07
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (152 bp):
AATATTAAATTATAAATAAAATATTAATATTAAATGATAAATTATTAATATTATAAATAATTATA
AATCTTAATATTTAAAAAATAAAATAAAATAAAATAAATAATCATAATAACATTTAAATTATAAA
TAAAATATTAGTATTTTAAAAA
Found at i:33223683 original size:17 final size:18
Alignment explanation
Indices: 33223629--33223683 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
33223619 AATTATAAAT
*
33223629 AAAATAATAATATTTTATA
1 AAAATATTAATA-TTTATA
33223648 AAACAT-TTAA-A-TTATA
1 AAA-ATATTAATATTTATA
33223664 AAAATATTAATATTTA-A
1 AAAATATTAATATTTATA
33223681 AAA
1 AAA
33223684 GTAAAGATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
15 2 0.06
16 12 0.39
17 5 0.16
18 4 0.13
19 6 0.19
20 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTAATATTTATA
Found at i:33223947 original size:28 final size:28
Alignment explanation
Indices: 33223888--33224056 Score: 72
Period size: 28 Copynumber: 6.2 Consensus size: 28
33223878 TGATCAATTA
* * * *
33223888 TTAATATTTTAAAA-AAACTATCAATTT
1 TTAATATTTAAAAATAAAATATTAATAT
33223915 ATTAATATTTAAAAATAAAATATTAATAT
1 -TTAATATTTAAAAATAAAATATTAATAT
* *
33223944 TTAA-ATTT-----TTAATTATTAATAT
1 TTAATATTTAAAAATAAAATATTAATAT
* *** *
33223966 TCAA-AAAAATAAAATAAAAAATTAATCAT
1 TTAATATTTA-AAAATAAAATATTAAT-AT
* *
33223995 AATAATATTT-AAATTAAAAATATTAATATT
1 -TTAATATTTAAAAAT-AAAATATTAATA-T
*
33224025 TTAA-A-TTATAAATAAAATATTTAATAT
1 TTAATATTTAAAAATAAAATA-TTAATAT
33224052 TTAAT
1 TTAAT
33224057 TTATTAATAA
Statistics
Matches: 103, Mismatches: 23, Indels: 30
0.66 0.15 0.19
Matches are distributed among these distances:
22 16 0.16
27 17 0.17
28 36 0.35
29 20 0.19
30 13 0.13
31 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAATATTTAAAAATAAAATATTAATAT
Found at i:33224007 original size:156 final size:155
Alignment explanation
Indices: 33223689--33224016 Score: 340
Period size: 156 Copynumber: 2.1 Consensus size: 155
33223679 AAAAAGTAAA
* * * ** *
33223689 GATTAAATTATAAATGAAATATTAATATTTAAATGATAAATTATTAATATTATAACTAAATTATC
1 GATTAAATTATAAATAAAATATCAATATTGAAATGATAAATTATTAATATTATAAAAAAACTATC
* * *
33223754 AATTATTAATATTTAAAAATAAAATAAAATAACATAATTGATCATAATAATATTTAAATTAAATA
66 AATTATTAATATTTAAAAATAAAATAAAATAACATAATTGATAATAATAATATTCAAATAAAATA
* * * * *
33223819 AAATATTCATATTTTACCACATTAAT
131 AAATA-TAAAAATTAACCACAATAAT
* * *
33223845 GATTAAATTATAAATAAAATATCAGTATTGAAATGATCAATTATTAATATTTTAAAAAAACTATC
1 GATTAAATTATAAATAAAATATCAATATTGAAATGATAAATTATTAATATTATAAAAAAACTATC
* ** ** *
33223910 AATTTATTAATATTTAAAAATAAAATATTAAT-ATTTAAATTTTTAATTATTAATATTCAAA-AA
66 AA-TTATTAATATTTAAAAATAAAATA-AAATAACAT-AATTGATAA-TAATAATATTCAAATAA
* *
33223973 AATAAAATA-AAAAATTAATCATAATAAT
127 AATAAAATATAAAAATTAACCACAATAAT
*
33224001 -ATTTAAATTAAAAATA
1 GA-TTAAATTATAAATA
33224017 TTAATATTTT
Statistics
Matches: 141, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
155 1 0.01
156 83 0.59
157 26 0.18
158 19 0.13
159 12 0.09
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (155 bp):
GATTAAATTATAAATAAAATATCAATATTGAAATGATAAATTATTAATATTATAAAAAAACTATC
AATTATTAATATTTAAAAATAAAATAAAATAACATAATTGATAATAATAATATTCAAATAAAATA
AAATATAAAAATTAACCACAATAAT
Found at i:33224009 original size:21 final size:21
Alignment explanation
Indices: 33223917--33224048 Score: 73
Period size: 21 Copynumber: 6.5 Consensus size: 21
33223907 ATCAATTTAT
* *
33223917 TAATATTTAAAAATAA-AATAT
1 TAATATTT-AAATTAATAATAA
** *
33223938 TAATATTTAAATTTTTAATTAT
1 TAATATTTAAATTAATAA-TAA
*
33223960 TAATATTCAAA--AA-AATAA
1 TAATATTTAAATTAATAATAA
** *
33223978 -AATA-AAAAATTAATCATAA
1 TAATATTTAAATTAATAATAA
* *
33223997 TAATATTTAAATTAAAAATAT
1 TAATATTTAAATTAATAATAA
33224018 TAATATTTTAAATT-ATAAATAA
1 TAATA-TTTAAATTAAT-AATAA
33224040 -AATATTTAA
1 TAATATTTAA
33224049 TATTTAATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 19
0.70 0.14 0.16
Matches are distributed among these distances:
16 3 0.04
17 4 0.05
18 4 0.05
19 6 0.07
20 13 0.15
21 30 0.35
22 25 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATATTTAAATTAATAATAA
Found at i:33224030 original size:22 final size:21
Alignment explanation
Indices: 33223996--33224046 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
33223986 ATTAATCATA
33223996 ATAATA-TTTAAATTAAAAAT
1 ATAATATTTTAAATTAAAAAT
*
33224016 ATTAATATTTTAAATTATAAAT
1 A-TAATATTTTAAATTAAAAAT
*
33224038 AAAATATTT
1 ATAATATTT
33224047 AATATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
22 14 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAATATTTTAAATTAAAAAT
Found at i:33224060 original size:27 final size:28
Alignment explanation
Indices: 33224011--33224075 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
33224001 ATTTAAATTA
33224011 AAAATA-TTAATATTTTAAATTATAAAT
1 AAAATATTTAATATTTTAAATTATAAAT
* *
33224038 AAAATATTTAATA-TTTAATTTATTAAT
1 AAAATATTTAATATTTTAAATTATAAAT
33224065 AATTAATATTT
1 AA--AATATTT
33224076 TAATTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 20 0.61
28 6 0.18
29 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAATATTTAATATTTTAAATTATAAAT
Found at i:33253244 original size:92 final size:93
Alignment explanation
Indices: 33253084--33253269 Score: 340
Period size: 92 Copynumber: 2.0 Consensus size: 93
33253074 GACAAAACTA
33253084 GATTGGGTTTGTCTATATATATATATATATATTAATTTCTTGTGTCCAAATTAACGAAAAGCACA
1 GATTGGGTTTGTCTATATATATATATATATATTAATTTCTTGTGTCCAAATTAACGAAAAGCACA
33253149 CCGAGCTAGAGTAATAATCATGTTCATG
66 CCGAGCTAGAGTAATAATCATGTTCATG
*
33253177 GNATTGGGTTT-T-TTTATATATATATATATATTAATTTCTTGTGTCCAAATTAACGAAAAGCAC
1 G-ATTGGGTTTGTCTATATATATATATATATATTAATTTCTTGTGTCCAAATTAACGAAAAGCAC
33253240 ACCGAGCTAGAGTAATAATCATGTTCATG
65 ACCGAGCTAGAGTAATAATCATGTTCATG
33253269 G
1 G
33253270 CATATCTATA
Statistics
Matches: 91, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
92 80 0.88
93 2 0.02
94 9 0.10
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (93 bp):
GATTGGGTTTGTCTATATATATATATATATATTAATTTCTTGTGTCCAAATTAACGAAAAGCACA
CCGAGCTAGAGTAATAATCATGTTCATG
Found at i:33253283 original size:2 final size:2
Alignment explanation
Indices: 33253271--33253319 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
33253261 TGTTCATGGC
* *
33253271 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33253312 AT AT -T AT A
1 AT AT AT AT A
33253320 CATCAGGTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33258263 original size:2 final size:2
Alignment explanation
Indices: 33258256--33258297 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
33258246 GCATGTGCAA
33258256 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
33258298 TGAGTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33264621 original size:12 final size:12
Alignment explanation
Indices: 33264606--33264634 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
33264596 TTCTTCAAAC
33264606 TCTTCCTCCTCT
1 TCTTCCTCCTCT
33264618 TCTTCCTCCTCT
1 TCTTCCTCCTCT
33264630 TCTTC
1 TCTTC
33264635 TTCATTGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (12 bp):
TCTTCCTCCTCT
Found at i:33267823 original size:12 final size:12
Alignment explanation
Indices: 33267808--33267832 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33267798 ATATATATAT
33267808 TGTGGGTAATGA
1 TGTGGGTAATGA
33267820 TGTGGGTAATGA
1 TGTGGGTAATGA
33267832 T
1 T
33267833 ATGATCTTAA
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:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (12 bp):
TGTGGGTAATGA
Found at i:33270666 original size:2 final size:2
Alignment explanation
Indices: 33270659--33270690 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33270649 CGATTCAATA
33270659 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
33270691 GTGNCATTGT
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:33270782 original size:2 final size:2
Alignment explanation
Indices: 33270767--33270806 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
33270757 ATTCTAATTC
33270767 AT AT A- AT A- 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
33270807 GTGTGTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33273529 original size:2 final size:2
Alignment explanation
Indices: 33273522--33273549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33273512 AGGTACAATA
33273522 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
33273550 TCTTCTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33280240 original size:2 final size:2
Alignment explanation
Indices: 33280233--33280291 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
33280223 TCAGCCATTG
*
33280233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
33280275 AT AT AT CT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
33280292 GTTTCTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33282216 original size:21 final size:21
Alignment explanation
Indices: 33282167--33282217 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
33282157 AGTGATCCTC
33282167 ATGCAAAAAAAAAAAAAAAGG
1 ATGCAAAAAAAAAAAAAAAGG
* *
33282188 AT-TAAAAAAAAGAGAAAAAGG
1 ATGCAAAAAAAA-AAAAAAAGG
*
33282209 GTGCAAAAA
1 ATGCAAAAA
33282218 TTGCAACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.33
21 11 0.46
22 5 0.21
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.08
Consensus pattern (21 bp):
ATGCAAAAAAAAAAAAAAAGG
Found at i:33289841 original size:30 final size:30
Alignment explanation
Indices: 33289805--33289866 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
33289795 TTTAAAAAAT
33289805 TATTTTT-TATT-ACATTAAATTAAATTTTTA
1 TATTTTTATATTGA-ATTAAA-TAAATTTTTA
*
33289835 TATTTTTATTTTGAATTAAATAAATTTTTA
1 TATTTTTATATTGAATTAAATAAATTTTTA
33289865 TA
1 TA
33289867 ATTAATAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 19 0.66
31 9 0.31
32 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (30 bp):
TATTTTTATATTGAATTAAATAAATTTTTA
Found at i:33291054 original size:2 final size:2
Alignment explanation
Indices: 33291047--33291080 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
33291037 AGAAAAGAAC
33291047 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33291081 GTAGATGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:33291476 original size:2 final size:2
Alignment explanation
Indices: 33291469--33291493 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33291459 ATACTCTACA
33291469 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
33291494 AAATCTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33297411 original size:18 final size:18
Alignment explanation
Indices: 33297390--33297429 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33297380 GACAGTGAGC
* *
33297390 GAGACAGAGATAGGGAAA
1 GAGACAGAGAGAGAGAAA
*
33297408 GAGAGAGAGAGAGAGAAA
1 GAGACAGAGAGAGAGAAA
33297426 GAGA
1 GAGA
33297430 TGGGAGAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.42, T:0.03
Consensus pattern (18 bp):
GAGACAGAGAGAGAGAAA
Found at i:33300134 original size:2 final size:2
Alignment explanation
Indices: 33300114--33300154 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
33300104 ATTGTGTCAA
*
33300114 AG AG GG AG AG AG -G AG -G AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
33300154 A
1 A
33300155 AAGTGGGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33308805 original size:22 final size:20
Alignment explanation
Indices: 33308775--33308819 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
33308765 AATAAATGAA
* *
33308775 AAAATTAAATTATAATAAAAT
1 AAAATTAAAGTAAAAT-AAAT
33308796 AAAATATAAAGTAAAATAAAT
1 AAAAT-TAAAGTAAAATAAAT
33308817 AAA
1 AAA
33308820 TAAAAAGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAATTAAAGTAAAATAAAT
Found at i:33309867 original size:24 final size:21
Alignment explanation
Indices: 33309840--33309900 Score: 52
Period size: 24 Copynumber: 2.6 Consensus size: 21
33309830 TGCTTATATT
33309840 TAATATTAGAAAATCAAAAAATAA
1 TAATA-TAGAAAAT-AAAAAA-AA
33309864 TAATGATAGTAATAATAAAAAAAA
1 TAAT-ATAG-AA-AATAAAAAAAA
33309888 TAATAGTA-AAAAT
1 TAATA-TAGAAAAT
33309901 GCATAGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 1 0.03
24 15 0.45
25 9 0.27
26 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.26
Consensus pattern (21 bp):
TAATATAGAAAATAAAAAAAA
Found at i:33313623 original size:22 final size:21
Alignment explanation
Indices: 33313594--33313637 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
33313584 CAAAAAATTT
*
33313594 AAATTATAATAA-AACCAAATA
1 AAATTATAA-AATAAACAAATA
33313615 AAATATATAAAATAAACAAATA
1 AAAT-TATAAAATAAACAAATA
33313637 A
1 A
33313638 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATTATAAAATAAACAAATA
Found at i:33322419 original size:16 final size:17
Alignment explanation
Indices: 33322388--33322421 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33322378 TAAATAAAAT
*
33322388 TATTTTATAATTTTTTA
1 TATTTTATAATCTTTTA
33322405 TATTTT-TAATCTTTTA
1 TATTTTATAATCTTTTA
33322421 T
1 T
33322422 TCTAACAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTATAATCTTTTA
Found at i:33330750 original size:15 final size:15
Alignment explanation
Indices: 33330730--33330759 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33330720 TATCATATAA
33330730 ATTATTAGAACACAT
1 ATTATTAGAACACAT
33330745 ATTATTAGAACACAT
1 ATTATTAGAACACAT
33330760 GGTTTTAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
ATTATTAGAACACAT
Found at i:33343063 original size:27 final size:27
Alignment explanation
Indices: 33343027--33343078 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
33343017 TAAATTGTAA
* *
33343027 AAATTATAAATTATAAATGTTTTAAAT
1 AAATTATAAAATATAAATATTTTAAAT
*
33343054 AAATTATAAAATATTAATATTTTAA
1 AAATTATAAAATATAAATATTTTAA
33343079 TTTTATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
AAATTATAAAATATAAATATTTTAAAT
Found at i:33343396 original size:26 final size:27
Alignment explanation
Indices: 33343366--33343416 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
33343356 TTAAAGTTTT
* *
33343366 AATTATACATT-TTAGTACTTTAAATA
1 AATTATAAATTATTAATACTTTAAATA
*
33343392 AATTATAAATTATTAATATTTTAAA
1 AATTATAAATTATTAATACTTTAAA
33343417 AATAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (27 bp):
AATTATAAATTATTAATACTTTAAATA
Found at i:33343449 original size:81 final size:83
Alignment explanation
Indices: 33343344--33343495 Score: 213
Period size: 81 Copynumber: 1.9 Consensus size: 83
33343334 AATTTCAAGT
* * * *
33343344 TAAAAAATCAAATTAAAGTTTTAATTATACA-TT-TTAGTACTT-TAAATAAATTATA-AATTAT
1 TAAAAAATAAAATTAAAGTTTTAATTA-AAATTTATTAATACTTCT-AATAAATTATAGAAATAT
33343405 TAATATTTTAAAAATAAAAA
64 TAATATTTTAAAAATAAAAA
*
33343425 TAAATAATAAAATTAAAGTTTTAATTAAAATTTATTAATACTTCTAATAAATTATAGAAATATTA
1 TAAAAAATAAAATTAAAGTTTTAATTAAAATTTATTAATACTTCTAATAAATTATAGAAATATTA
33343490 ATATTT
66 ATATTT
33343496 CATATTAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
80 2 0.03
81 27 0.44
82 19 0.31
83 14 0.23
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (83 bp):
TAAAAAATAAAATTAAAGTTTTAATTAAAATTTATTAATACTTCTAATAAATTATAGAAATATTA
ATATTTTAAAAATAAAAA
Found at i:33349066 original size:23 final size:23
Alignment explanation
Indices: 33349035--33349090 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
33349025 TCGAGAGTCT
*
33349035 AAATTCATGGGAACAAGGCACTC
1 AAATCCATGGGAACAAGGCACTC
33349058 AAATCCATGGGAACAAGGCACTC
1 AAATCCATGGGAACAAGGCACTC
33349081 AAATCCATGG
1 AAATCCATGG
33349091 CATTGGCGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.16
Consensus pattern (23 bp):
AAATCCATGGGAACAAGGCACTC
Found at i:33358392 original size:42 final size:42
Alignment explanation
Indices: 33358231--33358386 Score: 258
Period size: 42 Copynumber: 3.7 Consensus size: 42
33358221 TTGGGGCTGT
*
33358231 CTTGGCTGGAGAACTTGGCACAGAAGCAATAGTCACGACCGG
1 CTTGGCTGGAGAAGTTGGCACAGAAGCAATAGTCACGACCGG
33358273 CTTGGCTGGAGAAGTTGGCACAGAAGCAATAGTCACGACCGG
1 CTTGGCTGGAGAAGTTGGCACAGAAGCAATAGTCACGACCGG
* *
33358315 CTTGGCTGGAGAAGTTGGCACAGAAGCAGTAGTCGCGACCGG
1 CTTGGCTGGAGAAGTTGGCACAGAAGCAATAGTCACGACCGG
* * *
33358357 CTTGGCTGGAGAAGATGGCACTGACGCAAT
1 CTTGGCTGGAGAAGTTGGCACAGAAGCAAT
33358387 TGTCGCTGAT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 107 1.00
ACGTcount: A:0.27, C:0.22, G:0.34, T:0.17
Consensus pattern (42 bp):
CTTGGCTGGAGAAGTTGGCACAGAAGCAATAGTCACGACCGG
Found at i:33367135 original size:2 final size:2
Alignment explanation
Indices: 33367128--33367155 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33367118 AAATCACTTT
33367128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33367156 AAGAATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33381293 original size:2 final size:2
Alignment explanation
Indices: 33381286--33381333 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
33381276 AGGGCTTCAA
33381286 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
33381328 AT AT AT
1 AT AT AT
33381334 TTAAATTCAA
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:33401839 original size:47 final size:47
Alignment explanation
Indices: 33401767--33401873 Score: 187
Period size: 47 Copynumber: 2.3 Consensus size: 47
33401757 TATCAAATTA
* * *
33401767 TCATGTCATGCCTACTACCATTGACTATAGAGGATCTCTGGATTCTG
1 TCATGCCATGCCTACTACCACTGACTATAGAGGATCTCTGAATTCTG
33401814 TCATGCCATGCCTACTACCACTGACTATAGAGGATCTCTGAATTCTG
1 TCATGCCATGCCTACTACCACTGACTATAGAGGATCTCTGAATTCTG
33401861 TCATGCCATGCCT
1 TCATGCCATGCCT
33401874 TCCATTTCTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (47 bp):
TCATGCCATGCCTACTACCACTGACTATAGAGGATCTCTGAATTCTG
Found at i:33407662 original size:125 final size:125
Alignment explanation
Indices: 33407440--33407685 Score: 347
Period size: 125 Copynumber: 2.0 Consensus size: 125
33407430 TACAAAATTT
* * * *
33407440 AAAATCTAAGTTCAAGAAATTTACCTTACACATTTTTTAAAAATATTACCTTAATCTGTTCCATA
1 AAAATCTAAATTCAAGAAATTTACCTGACACATTTTTTAAAAACATTACCTTAATCCGTTCCATA
* *
33407505 ACCGAATATAACGTATCCAAACTTTACTTTATCAAGTTGAG-TA-CTTACGAGTACCTATAC
66 ACCGAATATAACGTATCCAAACCTTACATTATCAAGTTG-GTTATC-TACGAGTACCTATAC
*
33407565 AAAATCTAAATTCAAGAAATTTACCTGACACGTTTTTTAAAAACATTATCC-TAATCCG-TCTCA
1 AAAATCTAAATTCAAGAAATTTACCTGACACATTTTTTAAAAACATTA-CCTTAATCCGTTC-CA
* *
33407628 TAACCGAATATAATGTATTCAAACCTTACATTATCAAGTTGGTTATCTACGAGTACCT
64 TAACCGAATATAACGTATCCAAACCTTACATTATCAAGTTGGTTATCTACGAGTACCT
33407686 GTATAATCAT
Statistics
Matches: 108, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
124 3 0.03
125 102 0.94
126 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.35
Consensus pattern (125 bp):
AAAATCTAAATTCAAGAAATTTACCTGACACATTTTTTAAAAACATTACCTTAATCCGTTCCATA
ACCGAATATAACGTATCCAAACCTTACATTATCAAGTTGGTTATCTACGAGTACCTATAC
Found at i:33417390 original size:8 final size:8
Alignment explanation
Indices: 33417377--33417408 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
33417367 TTTAAAATCA
33417377 TAATATTT
1 TAATATTT
33417385 TAATATTT
1 TAATATTT
33417393 TAAT-TTT
1 TAATATTT
33417400 TAATATTT
1 TAATATTT
33417408 T
1 T
33417409 TTAAATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TAATATTT
Found at i:33417400 original size:15 final size:16
Alignment explanation
Indices: 33417377--33417408 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
33417367 TTTAAAATCA
33417377 TAATATTTTAATATTT
1 TAATATTTTAATATTT
33417393 TAAT-TTTTAATATTT
1 TAATATTTTAATATTT
33417408 T
1 T
33417409 TTAAATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATATTTTAATATTT
Found at i:33418766 original size:74 final size:74
Alignment explanation
Indices: 33418669--33418809 Score: 228
Period size: 74 Copynumber: 1.9 Consensus size: 74
33418659 AAACTTATAC
* *
33418669 TTATAAATATGTATTCATTAAATGACGATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATATATTCATCAAATGACGATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
33418734 TTAAACTTA
66 TTAAACTTA
* * * *
33418743 TTATAAATGTATATTCATCAAATGATGATTATTAAAATATTTTTTATTATAGTTATTAGTAAGAT
1 TTATAAATATATATTCATCAAATGACGATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
33418808 TT
66 TT
33418810 GTTCCATTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (74 bp):
TTATAAATATATATTCATCAAATGACGATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
TTAAACTTA
Found at i:33426442 original size:2 final size:2
Alignment explanation
Indices: 33426435--33426462 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33426425 AAATATTAGA
33426435 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
33426463 CCCTCTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:33432406 original size:9 final size:9
Alignment explanation
Indices: 33432392--33432448 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
33432382 ATACGATTAA
*
33432392 TAACACGCT
1 TAACACGAT
*
33432401 TAACACGTT
1 TAACACGAT
*
33432410 TAACACAAT
1 TAACACGAT
*
33432419 TAATACGAT
1 TAACACGAT
* *
33432428 TAATACGTT
1 TAACACGAT
33432437 TAACACGAT
1 TAACACGAT
33432446 TAA
1 TAA
33432449 ATAAAAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (9 bp):
TAACACGAT
Found at i:33432527 original size:14 final size:14
Alignment explanation
Indices: 33432499--33432536 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
33432489 TTTAAAACCT
33432499 ATAATTAT-A-AAA
1 ATAATTATAACAAA
33432511 ATAATTATAACAAA
1 ATAATTATAACAAA
*
33432525 ATAATAATAACA
1 ATAATTATAACA
33432537 TCAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
13 1 0.04
14 14 0.61
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAATTATAACAAA
Found at i:33436091 original size:2 final size:2
Alignment explanation
Indices: 33436042--33436072 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
33436032 TAATTACTAT
33436042 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33436073 CAATATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33444756 original size:18 final size:19
Alignment explanation
Indices: 33444728--33444766 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
33444718 AAATTATTTG
* *
33444728 ATAATTTTTTTTACAAATT
1 ATAATTTTTTTAAAAAATT
33444747 ATAA-TTTTTTAAAAAATT
1 ATAATTTTTTTAAAAAATT
33444765 AT
1 AT
33444767 CATAAAAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAATTTTTTTAAAAAATT
Found at i:33444926 original size:15 final size:15
Alignment explanation
Indices: 33444908--33444938 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33444898 TTTAAATTTT
33444908 ATTTTTTTAAAAAAA
1 ATTTTTTTAAAAAAA
33444923 ATTTTTTTAAAAAAA
1 ATTTTTTTAAAAAAA
33444938 A
1 A
33444939 AATTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTTTTAAAAAAA
Found at i:33444929 original size:17 final size:17
Alignment explanation
Indices: 33444908--33444943 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
33444898 TTTAAATTTT
33444908 ATTTTTTT--AAAAAAA
1 ATTTTTTTAAAAAAAAA
33444923 ATTTTTTTAAAAAAAAA
1 ATTTTTTTAAAAAAAAA
33444940 ATTT
1 ATTT
33444944 AAAATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
17 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTTTTAAAAAAAAA
Found at i:33444991 original size:30 final size:31
Alignment explanation
Indices: 33444941--33445006 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
33444931 AAAAAAAAAA
33444941 TTTAAAATTTATATTTGATATAATTTTTATT
1 TTTAAAATTTATATTTGATATAATTTTTATT
33444972 TTTANAAA-TTATA-TTGATATAATTTTTATT
1 TTTA-AAATTTATATTTGATATAATTTTTATT
33445002 TTTAA
1 TTTAA
33445007 GAGATAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 1 0.03
30 21 0.62
31 9 0.26
32 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTAAAATTTATATTTGATATAATTTTTATT
Found at i:33447106 original size:50 final size:49
Alignment explanation
Indices: 33447044--33447151 Score: 128
Period size: 50 Copynumber: 2.2 Consensus size: 49
33447034 TTGATGTATT
* * *
33447044 AATAATGAATAATTTTTATATATTA-TCAAATTATTAAATTTTGATATCTC
1 AATAAT-AATAATTTTTATATAATACT-AAACTATCAAATTTTGATATCTC
* *
33447094 AATAATATATAATTTCTATATAATACTAGACTATCAAATTTTGATATCTC
1 AATAATA-ATAATTTTTATATAATACTAAACTATCAAATTTTGATATCTC
*
33447144 ATTAATAA
1 AATAATAA
33447152 ATTATTTTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 2 0.04
50 47 0.94
51 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (49 bp):
AATAATAATAATTTTTATATAATACTAAACTATCAAATTTTGATATCTC
Done.