Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 132 of 211
Found at i:41831771 original size:5 final size:5
Alignment explanation
Indices: 41831761--41831789 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
41831751 TACTACAATA
41831761 TTATT TTATT TTATT TTATT TTATT TTAT
1 TTATT TTATT TTATT TTATT TTATT TTAT
41831790 AAATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:41841560 original size:16 final size:16
Alignment explanation
Indices: 41841539--41841569 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41841529 ATCGGGTTGA
*
41841539 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
41841555 GAAAATTAATTAATT
1 GAAAATTAATTAATT
41841570 AATTAAAATT
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:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:41841565 original size:20 final size:18
Alignment explanation
Indices: 41841542--41841583 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
41841532 GGGTTGAGAA
*
41841542 AATTATTTAATTGGAAAATT
1 AATTAATTAATT--AAAATT
41841562 AATTAATTAATTAAAATT
1 AATTAATTAATTAAAATT
41841580 AATT
1 AATT
41841584 TATGATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTAAAATT
Found at i:41852952 original size:20 final size:21
Alignment explanation
Indices: 41852913--41852954 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41852903 AGTATATAAT
*
41852913 TATATTTTAAAGAATAAAATA
1 TATATCTTAAAGAATAAAATA
*
41852934 TATATCTTAAA-ATTAAAATA
1 TATATCTTAAAGAATAAAATA
41852954 T
1 T
41852955 TATTAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TATATCTTAAAGAATAAAATA
Found at i:41853811 original size:17 final size:16
Alignment explanation
Indices: 41853778--41853817 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
41853768 TAAGTTATCA
41853778 AATAAAA-ATCATCTC
1 AATAAAATATCATCTC
*
41853793 AATTAAAATATCATTTC
1 AA-TAAAATATCATCTC
41853810 AATAAAAT
1 AATAAAAT
41853818 GTTTAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 9 0.41
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATATCATCTC
Found at i:41854003 original size:4 final size:4
Alignment explanation
Indices: 41853994--41854029 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
41853984 ATAACTCACG
41853994 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TTA ATT
41854030 TGACAACTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
ATTA
Found at i:41854342 original size:29 final size:31
Alignment explanation
Indices: 41854287--41854354 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 31
41854277 TTTATTATGG
*
41854287 TGTACTTGTACTTTTGTAAAATGTTTAATGT
1 TGTACTTGTACTTTAGTAAAATGTTTAATGT
41854318 TGTACTTGTA-TTTAG-AAAATGTTTAATGT
1 TGTACTTGTACTTTAGTAAAATGTTTAATGT
*
41854347 AGTACTTG
1 TGTACTTG
41854355 AATTATCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 21 0.60
30 4 0.11
31 10 0.29
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.49
Consensus pattern (31 bp):
TGTACTTGTACTTTAGTAAAATGTTTAATGT
Found at i:41854365 original size:29 final size:29
Alignment explanation
Indices: 41854304--41854368 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
41854294 GTACTTTTGT
* * *
41854304 AAAATGTTTAATGTTGTACTTGTATTTAG
1 AAAATGTTTAATGTAGTACTTGAATTTAC
41854333 AAAATGTTTAATGTAGTACTTGAA-TTATC
1 AAAATGTTTAATGTAGTACTTGAATTTA-C
41854362 AAAATGT
1 AAAATGT
41854369 GTTTTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (29 bp):
AAAATGTTTAATGTAGTACTTGAATTTAC
Found at i:41862469 original size:56 final size:56
Alignment explanation
Indices: 41862319--41862472 Score: 213
Period size: 56 Copynumber: 2.8 Consensus size: 56
41862309 GGTGCCACAG
*
41862319 TAGGAATCAAATTGCTAAAAGATAATA-CCCAGTAATAATATCCTATACTATCCCAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCA-TAATAATATCCTATACTATCCAAT
* * *
41862375 TAGGAATCAAATTGCTAAGAGATCATATCTCATAATAATATCCTATAAC-ATCCAAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTAT-ACTATCCAAT
* * *
41862431 TAGGAATCAAATTGCTAAAAGTTAACATCCCATGATAATATC
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATC
41862473 TTAACAACTA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
56 81 0.94
57 5 0.06
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATACTATCCAAT
Found at i:41862856 original size:5 final size:5
Alignment explanation
Indices: 41862846--41862882 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
41862836 GTTATTTGTT
41862846 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
41862883 ATTTATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:41863318 original size:21 final size:22
Alignment explanation
Indices: 41863294--41863336 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
41863284 TTCCTAATAT
* *
41863294 AATTGGTTGGTATTT-AATTTA
1 AATTGATTGCTATTTAAATTTA
*
41863315 AATTTATTGCTATTTAAATTTA
1 AATTGATTGCTATTTAAATTTA
41863337 TATTTATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (22 bp):
AATTGATTGCTATTTAAATTTA
Found at i:41863341 original size:22 final size:21
Alignment explanation
Indices: 41863304--41863344 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
41863294 AATTGGTTGG
41863304 TATTTAATTTAAATTTATTGC
1 TATTTAATTTAAATTTATTGC
*
41863325 TATTTAAATTTATATTTATT
1 TATTT-AATTTAAATTTATT
41863345 AAATTAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TATTTAATTTAAATTTATTGC
Found at i:41863344 original size:16 final size:16
Alignment explanation
Indices: 41863304--41863349 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41863294 AATTGGTTGG
41863304 TATTTAATTTAAATTTA
1 TATTT-ATTTAAATTTA
*
41863321 T-TGCTATTTAAATTTA
1 TAT-TTATTTAAATTTA
41863337 TATTTA-TTAAATT
1 TATTTATTTAAATT
41863350 AGACTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.28
16 15 0.60
17 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTTATTTAAATTTA
Found at i:41883835 original size:31 final size:32
Alignment explanation
Indices: 41883786--41883856 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
41883776 AGATATTTTA
* *
41883786 AGCTTGAAATTATCCAAATCTAAAAA-AATGG
1 AGCTTGAGATTATCCAAATCCAAAAATAATGG
* * * *
41883817 AGCTTGAGTTTATTCAAATCCAAAAATATTTG
1 AGCTTGAGATTATCCAAATCCAAAAATAATGG
41883849 AGCTTGAG
1 AGCTTGAG
41883857 CTTAAGCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 22 0.67
32 11 0.33
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (32 bp):
AGCTTGAGATTATCCAAATCCAAAAATAATGG
Found at i:41887795 original size:51 final size:50
Alignment explanation
Indices: 41887719--41887858 Score: 212
Period size: 51 Copynumber: 2.8 Consensus size: 50
41887709 CTGGTTCAAA
41887719 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACT-TCCGATACACG
* * *
41887770 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCAC-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTTCCGATACACG
*
41887820 TAGTA-CCTGCACATAGTACTACACACGTGACCATCACTT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTT
41887859 TCACTTTCAC
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
48 5 0.06
49 26 0.32
50 14 0.17
51 32 0.39
52 5 0.06
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTTCCGATACACG
Found at i:41888102 original size:16 final size:16
Alignment explanation
Indices: 41888081--41888111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41888071 AATCCAGTCC
41888081 AAAAATCACATTTTGG
1 AAAAATCACATTTTGG
*
41888097 AAAAATTACATTTTG
1 AAAAATCACATTTTG
41888112 CCCCTAAAGT
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:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAATCACATTTTGG
Found at i:41889807 original size:19 final size:19
Alignment explanation
Indices: 41889783--41889820 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41889773 CAGGTGCGAT
41889783 ACCCTTACAGCACCCCGAG
1 ACCCTTACAGCACCCCGAG
**
41889802 ACCCTTATGGCACCCCGAG
1 ACCCTTACAGCACCCCGAG
41889821 CCAATTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (19 bp):
ACCCTTACAGCACCCCGAG
Found at i:41890073 original size:19 final size:19
Alignment explanation
Indices: 41890040--41890079 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
41890030 AAAATATCAT
*
41890040 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
41890059 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
41890078 AT
1 AT
41890080 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:41891074 original size:15 final size:15
Alignment explanation
Indices: 41891054--41891085 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41891044 TATGCATGCA
*
41891054 AAATATAATAGACAT
1 AAATATAAAAGACAT
41891069 AAATATAAAAGACAT
1 AAATATAAAAGACAT
41891084 AA
1 AA
41891086 TAATGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:41910032 original size:17 final size:16
Alignment explanation
Indices: 41910004--41910041 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
41909994 ATCTACAAAG
41910004 GAAAGGGAAAGAAAAT
1 GAAAGGGAAAGAAAAT
41910020 GAAAGGCGAAAGAAAAT
1 GAAAGG-GAAAGAAAAT
41910037 GAAAG
1 GAAAG
41910042 AAAGAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.61, C:0.03, G:0.32, T:0.05
Consensus pattern (16 bp):
GAAAGGGAAAGAAAAT
Found at i:41913434 original size:22 final size:22
Alignment explanation
Indices: 41913406--41913447 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
41913396 GCTTGTACGG
*
41913406 GTTTAACACTTCTGTGCTCTCT
1 GTTTAACACTTCGGTGCTCTCT
41913428 GTTTAACACTTCGGTGCTCT
1 GTTTAACACTTCGGTGCTCT
41913448 TTGGTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (22 bp):
GTTTAACACTTCGGTGCTCTCT
Found at i:41928021 original size:87 final size:87
Alignment explanation
Indices: 41927875--41928050 Score: 352
Period size: 87 Copynumber: 2.0 Consensus size: 87
41927865 CATGTTGTCT
41927875 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
1 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
41927940 AAATGACTATTTTGCTTCGACC
66 AAATGACTATTTTGCTTCGACC
41927962 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
1 CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
41928027 AAATGACTATTTTGCTTCGACC
66 AAATGACTATTTTGCTTCGACC
41928049 CA
1 CA
41928051 ATCTTAAGAC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (87 bp):
CATGTCTCGAGATAATCAACAAATTGTCTCGAGACAATTGGGGTTGTCTTGAGACAAAAGGCACC
AAATGACTATTTTGCTTCGACC
Found at i:41935084 original size:40 final size:40
Alignment explanation
Indices: 41935029--41935110 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
41935019 CACAGAAAAT
* ** *
41935029 TCAATCTAGAAAAATAAAGGAAGAACTGTAGGAAGTTAAC
1 TCAATCTAGAAAAATAAAGAAAGAACTACAGAAAGTTAAC
41935069 TCAATCTAGAAAAATAAAGAAAGAACTACAGAAAGTTAAC
1 TCAATCTAGAAAAATAAAGAAAGAACTACAGAAAGTTAAC
41935109 TC
1 TC
41935111 CACACTCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (40 bp):
TCAATCTAGAAAAATAAAGAAAGAACTACAGAAAGTTAAC
Found at i:41935322 original size:20 final size:21
Alignment explanation
Indices: 41935297--41935340 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
41935287 TCTCACACTG
41935297 ATTCTTCTCTCCCCTT-TTTT
1 ATTCTTCTCTCCCCTTCTTTT
*
41935317 ATTCTTCTCTCTCCTTCTTTT
1 ATTCTTCTCTCCCCTTCTTTT
41935338 ATT
1 ATT
41935341 GGGTAGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTCTTCTCTCCCCTTCTTTT
Found at i:41937311 original size:27 final size:25
Alignment explanation
Indices: 41937278--41937401 Score: 95
Period size: 27 Copynumber: 4.6 Consensus size: 25
41937268 AGCGATAATC
41937278 ATGAAAGAAAAACCTTTGTGGCAAAAT
1 ATGAAAGAAAAA-CTTTGTGGC-AAAT
* * *
41937305 ATAAAAGAAAATTCTTTGTGGCCAAT
1 ATGAAAGAAAA-ACTTTGTGGCAAAT
* *
41937331 CATGAAAGAAAATACTTTGTAGCGAAAC
1 -ATGAAAGAAAA-ACTTTGTGGC-AAAT
* * **
41937359 ATGAAAGAAAAATCGTTATAACGAAAT
1 ATGAAAGAAAAA-CTTTGTGGC-AAAT
41937386 ATGAAAGAAAAACTTT
1 ATGAAAGAAAAACTTT
41937402 TGTGATGAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.09
27 71 0.89
28 2 0.03
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (25 bp):
ATGAAAGAAAAACTTTGTGGCAAAT
Found at i:41939873 original size:21 final size:22
Alignment explanation
Indices: 41939847--41939887 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41939837 AAATAAAATA
*
41939847 ATAAATTTTAATTAT-TTGCAT
1 ATAAATTTAAATTATATTGCAT
41939868 ATAAATTTAAATTATATTGC
1 ATAAATTTAAATTATATTGC
41939888 TTTTCGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
ATAAATTTAAATTATATTGCAT
Found at i:41944718 original size:8 final size:8
Alignment explanation
Indices: 41944705--41944733 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
41944695 CAATAAATAA
41944705 AAAATATT
1 AAAATATT
41944713 AAAATATT
1 AAAATATT
41944721 -AAATATT
1 AAAATATT
41944728 AAAATA
1 AAAATA
41944734 AATCATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATATT
Found at i:41948730 original size:20 final size:20
Alignment explanation
Indices: 41948666--41948730 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
41948656 TCCTCTTATT
*
41948666 TAAACATTGAGGATTTATCA
1 TAAACGTTGAGGATTTATCA
* * *
41948686 TAAACGTCGAGTA-ATAT--
1 TAAACGTTGAGGATTTATCA
41948703 TCAAACGTTGAGGATTTATCA
1 T-AAACGTTGAGGATTTATCA
41948724 TAAACGT
1 TAAACGT
41948731 CGGTATTCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 6 0.18
20 16 0.47
21 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.32
Consensus pattern (20 bp):
TAAACGTTGAGGATTTATCA
Found at i:41954721 original size:5 final size:5
Alignment explanation
Indices: 41954711--41954736 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41954701 AATTGATTCT
41954711 CCACC CCACC CCACC CCACC CCACC C
1 CCACC CCACC CCACC CCACC CCACC C
41954737 TCTCCCTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (5 bp):
CCACC
Found at i:41957438 original size:13 final size:13
Alignment explanation
Indices: 41957420--41957448 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41957410 AACGTGATGT
41957420 ATTGGTAAGAACA
1 ATTGGTAAGAACA
41957433 ATTGGTAAGAACA
1 ATTGGTAAGAACA
41957446 ATT
1 ATT
41957449 CCATAAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.28
Consensus pattern (13 bp):
ATTGGTAAGAACA
Found at i:41958928 original size:50 final size:50
Alignment explanation
Indices: 41958836--41959021 Score: 257
Period size: 50 Copynumber: 3.7 Consensus size: 50
41958826 AAGTCCCTGT
* * *
41958836 CACAAAGGCTTTATA-GCGACTCGCCACAAAGGTTTCCCAAATAGATCGC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
* * * *
41958885 CACAAAGGCTTTATAGGGGACTTGCCACAGAGGCTTCCCAAATAAATCAC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
* *
41958935 CACAAAGGCTTTATAGGAGACTCGTCATAAAGGCTTCCCAAATAAATCGC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
* * *
41958985 CACAAAGGCTTTACAGGTGACTCGCCACAAAAGCTTC
1 CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTC
41959022 ACATAAACTT
Statistics
Matches: 119, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 15 0.13
50 104 0.87
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (50 bp):
CACAAAGGCTTTATAGGAGACTCGCCACAAAGGCTTCCCAAATAAATCGC
Found at i:41959009 original size:25 final size:25
Alignment explanation
Indices: 41958836--41959020 Score: 88
Period size: 25 Copynumber: 7.4 Consensus size: 25
41958826 AAGTCCCTGT
* *
41958836 CACAAAGGCTTTA-TAGCGACTCGC
1 CACAAAGGCTTTACAAGTGACTCGC
* *
41958860 CACAAAGG-TTTCCCAAATAGA-TCGC
1 CACAAAGGCTTT-ACAAGT-GACTCGC
* * * *
41958885 CACAAAGGCTTTATAGGGGACTTGC
1 CACAAAGGCTTTACAAGTGACTCGC
* ** * * * *
41958910 CACAGAGGCTTCCCAAATAAATCAC
1 CACAAAGGCTTTACAAGTGACTCGC
* * * *
41958935 CACAAAGGCTTTATAGGAGACTCGT
1 CACAAAGGCTTTACAAGTGACTCGC
* ** * * *
41958960 CATAAAGGCTTCCCAAATAAATCGC
1 CACAAAGGCTTTACAAGTGACTCGC
*
41958985 CACAAAGGCTTTACAGGTGACTCGC
1 CACAAAGGCTTTACAAGTGACTCGC
*
41959010 CACAAAAGCTT
1 CACAAAGGCTT
41959021 CACATAAACT
Statistics
Matches: 106, Mismatches: 50, Indels: 9
0.64 0.30 0.05
Matches are distributed among these distances:
23 3 0.03
24 10 0.09
25 88 0.83
26 5 0.05
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (25 bp):
CACAAAGGCTTTACAAGTGACTCGC
Found at i:41974609 original size:166 final size:166
Alignment explanation
Indices: 41974335--41974666 Score: 664
Period size: 166 Copynumber: 2.0 Consensus size: 166
41974325 GGCTCCAAGG
41974335 GCCTGGTACAGCAGAATCGATGGCTACTTGACTGATCTGGGATTCAATCGAAGCAAGAGTGAGCC
1 GCCTGGTACAGCAGAATCGATGGCTACTTGACTGATCTGGGATTCAATCGAAGCAAGAGTGAGCC
41974400 AACACTGTATGTCAAGAAGCAAGGGACACAAACACAACTCATTGTGTCCCTATATGTTGATGACC
66 AACACTGTATGTCAAGAAGCAAGGGACACAAACACAACTCATTGTGTCCCTATATGTTGATGACC
41974465 TGCTGGTGACAGGAGGAGATCAAGCAGTGCTGGTTA
131 TGCTGGTGACAGGAGGAGATCAAGCAGTGCTGGTTA
41974501 GCCTGGTACAGCAGAATCGATGGCTACTTGACTGATCTGGGATTCAATCGAAGCAAGAGTGAGCC
1 GCCTGGTACAGCAGAATCGATGGCTACTTGACTGATCTGGGATTCAATCGAAGCAAGAGTGAGCC
41974566 AACACTGTATGTCAAGAAGCAAGGGACACAAACACAACTCATTGTGTCCCTATATGTTGATGACC
66 AACACTGTATGTCAAGAAGCAAGGGACACAAACACAACTCATTGTGTCCCTATATGTTGATGACC
41974631 TGCTGGTGACAGGAGGAGATCAAGCAGTGCTGGTTA
131 TGCTGGTGACAGGAGGAGATCAAGCAGTGCTGGTTA
41974667 ATTTCAAGAC
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 166 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (166 bp):
GCCTGGTACAGCAGAATCGATGGCTACTTGACTGATCTGGGATTCAATCGAAGCAAGAGTGAGCC
AACACTGTATGTCAAGAAGCAAGGGACACAAACACAACTCATTGTGTCCCTATATGTTGATGACC
TGCTGGTGACAGGAGGAGATCAAGCAGTGCTGGTTA
Found at i:41978212 original size:34 final size:34
Alignment explanation
Indices: 41978155--41978221 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
41978145 AATAATAGAG
* * *
41978155 AAATAAACTAGGTGAATTGCTCAATCATGAAAAT
1 AAATAAACAACGTGAATTGCTCAACCATGAAAAT
*
41978189 AAATAAACAACGTGAATCT-CTCAACCTTGAAAA
1 AAATAAACAACGTGAAT-TGCTCAACCATGAAAA
41978222 GAAAAGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (34 bp):
AAATAAACAACGTGAATTGCTCAACCATGAAAAT
Found at i:41983359 original size:21 final size:22
Alignment explanation
Indices: 41983322--41983362 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41983312 AAATAGGTAG
*
41983322 AAAACAATAAGAAAATAACACT
1 AAAACAACAAGAAAATAACACT
41983344 AAAACAACAA-AAAATAACA
1 AAAACAACAAGAAAATAACA
41983363 TATTTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.73, C:0.15, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAACAACAAGAAAATAACACT
Found at i:41991020 original size:24 final size:25
Alignment explanation
Indices: 41990979--41991048 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
41990969 TAGTCACAGT
* *
41990979 ATTGCACCAAAAGTGCCACATTTT-G
1 ATTGCACC-GAAGTGCCACATTTTCA
41991004 ATTGCACCGAAGTGCCAC-TTTTCA
1 ATTGCACCGAAGTGCCACATTTTCA
* *
41991028 ATTGCATCGAAGTGTCACATT
1 ATTGCACCGAAGTGCCACATT
41991049 CATTGTGCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.10
24 25 0.64
25 10 0.26
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (25 bp):
ATTGCACCGAAGTGCCACATTTTCA
Found at i:41992153 original size:19 final size:20
Alignment explanation
Indices: 41992126--41992172 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
41992116 TAATATTTAT
*
41992126 TTTAA-TTTATTTGATT-AA
1 TTTAATTTTACTTGATTAAA
41992144 TTTAATTTTACTTGATTAAA
1 TTTAATTTTACTTGATTAAA
*
41992164 ATTAATTTT
1 TTTAATTTT
41992173 TGCAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.20
19 10 0.40
20 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAATTTTACTTGATTAAA
Found at i:42008041 original size:12 final size:12
Alignment explanation
Indices: 42008024--42008049 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42008014 AAATCCCTTC
42008024 TAGCAGATACAA
1 TAGCAGATACAA
42008036 TAGCAGATACAA
1 TAGCAGATACAA
42008048 TA
1 TA
42008050 TCAAGTTATT
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:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (12 bp):
TAGCAGATACAA
Found at i:42016655 original size:3 final size:3
Alignment explanation
Indices: 42016647--42016685 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
42016637 ACAAAAACAC
42016647 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42016686 TGTTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42021476 original size:26 final size:26
Alignment explanation
Indices: 42021442--42021491 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
42021432 AAATTGTTAA
*
42021442 ATTTTTATATTC-AAAATTTATTTTT
1 ATTTTTATATTCTAAAATTAATTTTT
42021467 ATTTCTTATATTCTAAAATTAATTT
1 ATTT-TTATATTCTAAAATTAATTT
42021492 AAATTCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
27 10 0.45
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTATATTCTAAAATTAATTTTT
Found at i:42021711 original size:14 final size:14
Alignment explanation
Indices: 42021690--42021729 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42021680 TATGAATACT
42021690 GGAAAATGTTTTCC
1 GGAAAATGTTTTCC
* * *
42021704 GTAAAATGATTTCT
1 GGAAAATGTTTTCC
42021718 GGAAAATGTTTT
1 GGAAAATGTTTT
42021730 ACTTTTCTGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
GGAAAATGTTTTCC
Found at i:42021738 original size:20 final size:20
Alignment explanation
Indices: 42021713--42021750 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42021703 CGTAAAATGA
*
42021713 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
42021733 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
42021751 TTAGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:42029560 original size:18 final size:17
Alignment explanation
Indices: 42029534--42029572 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
42029524 ATTTTCCTTC
42029534 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
42029551 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
42029569 CACA
1 CACA
42029573 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:42034193 original size:44 final size:44
Alignment explanation
Indices: 42034056--42034177 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 44
42034046 ACTTGACGCG
* ** * * * *
42034056 ATCTGCTCTACTACAACTTCAGAGAGATGAGATCTAT-AACTTTA
1 ATCTGCTCCACTACAACCCCAGGGAGATAAGAT-TATCGACTTCA
* * *
42034100 ATTTGCTCCACTACAACCTCAGGGAGATAGGATTATCGACTTCA
1 ATCTGCTCCACTACAACCCCAGGGAGATAAGATTATCGACTTCA
**
42034144 ATCTGCTCCACTGGAACCCCAGGGAGATAAGATT
1 ATCTGCTCCACTACAACCCCAGGGAGATAAGATT
42034178 TGCTTCTTCA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 3 0.05
44 61 0.95
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (44 bp):
ATCTGCTCCACTACAACCCCAGGGAGATAAGATTATCGACTTCA
Found at i:42048651 original size:45 final size:44
Alignment explanation
Indices: 42048597--42048771 Score: 156
Period size: 45 Copynumber: 3.9 Consensus size: 44
42048587 ACCGAAGATG
* * *
42048597 ACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-AA
** * *
42048642 ACAAGTCTTATCTCCCTGAAGTTGCAGAAGAGTAGACTGACTAA-AA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGAA
* * * * **
42048688 TCAA-TCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGTT
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAA
* * *
42048731 ACTAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
42048772 ATGATGAATC
Statistics
Matches: 103, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 32 0.31
45 59 0.57
46 6 0.06
48 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGAA
Found at i:42048787 original size:44 final size:43
Alignment explanation
Indices: 42048600--42048802 Score: 158
Period size: 44 Copynumber: 4.6 Consensus size: 43
42048590 GAAGATGACA
* ** *
42048600 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATATC
** * *
42048644 AAGTCTTATCTCCCTGAAGTTGCAGAAGAGTAGACTGACTAAA-ATC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAATATC
* * * *
42048690 AATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGT-TAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAT-C
* * * *
42048733 TAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATGATG
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-ATC
**
42048778 AATCTTATCTCTTTGAAGTTGCAGT
1 AATCTTATCTCCCTGAAGTTGCAGT
42048803 AAAGTAGATC
Statistics
Matches: 125, Mismatches: 25, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
42 3 0.02
43 1 0.01
44 57 0.46
45 55 0.44
46 7 0.06
48 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATATC
Found at i:42049078 original size:45 final size:44
Alignment explanation
Indices: 42049011--42049129 Score: 130
Period size: 45 Copynumber: 2.7 Consensus size: 44
42049001 TCCACCATAT
* * *
42049011 CCAACTTTATTTCCCTGAAGTTGCAGTGGAGCAAACTAAAGATAA
1 CCAACCTTATCTCCCCGAAGTTGCAGTGGAGCAAACTAAAGAT-A
* **** * *
42049056 CCAACCTTATCTCCCCGAAGTTGTAGTGGAGCCGGTTGAGGATA
1 CCAACCTTATCTCCCCGAAGTTGCAGTGGAGCAAACTAAAGATA
*
42049100 CCAATCTTATCTCCCCGAAGTTGCAGTGGA
1 CCAACCTTATCTCCCCGAAGTTGCAGTGGA
42049130 ATAGATTGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
44 29 0.47
45 33 0.53
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (44 bp):
CCAACCTTATCTCCCCGAAGTTGCAGTGGAGCAAACTAAAGATA
Found at i:42050014 original size:5 final size:5
Alignment explanation
Indices: 42050006--42050030 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42049996 TTATACATAC
42050006 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
42050031 CTTACCCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:42050889 original size:22 final size:20
Alignment explanation
Indices: 42050836--42050892 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
42050826 ATACACAAAT
*
42050836 ATATATACATACATTTTTATA
1 ATATATACATA-TTTTTTATA
42050857 ATATAGGTACATATTTTTTATA
1 ATATA--TACATATTTTTTATA
42050879 ACTTATATACATAT
1 A--TATATACATAT
42050893 ATACATACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.16
22 16 0.52
23 6 0.19
24 4 0.13
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (20 bp):
ATATATACATATTTTTTATA
Found at i:42051564 original size:72 final size:72
Alignment explanation
Indices: 42051424--42051564 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 72
42051414 CTTTTCAAAT
* *
42051424 TCAAGTTTTAAACGATCCCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATCCCT
1 TCAAGTTTTAAACGATCCCAGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATCCCT
42051489 TTTTTTC
66 TTTTTTC
*
42051496 TCAAGTTTTAAACGATCTCAGGAATTAAGAA-AAATCGTGTCCTAACTTACTGGGCATGATCCCT
1 TCAAGTTTTAAACGATCCCAGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATCCCT
42051560 TTTTT
66 TTTTT
42051565 AAATCCGAGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 37 0.56
72 29 0.44
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (72 bp):
TCAAGTTTTAAACGATCCCAGGAATTAAGAAGAAATCGTGTCCTAACTTACTGGGCATGATCCCT
TTTTTTC
Found at i:42054950 original size:3 final size:3
Alignment explanation
Indices: 42054935--42054974 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
42054925 ATGGCTTTAG
*
42054935 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42054975 GCGTAGTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:42068472 original size:56 final size:55
Alignment explanation
Indices: 42068412--42068517 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 55
42068402 TAATTTTCAT
* * * *
42068412 TCTATTATATTTTTTCCATCCATAATGTACTTATTCA-AATTATACAAAAAAATTTA
1 TCTATTATA--TTTTACATCAATAATATACTTATTCACAATTAAACAAAAAAATTTA
* *
42068468 TCTATTGTATTTTACATCAATAATATACTTATTTACAATTAAACAAAAAA
1 TCTATTATATTTTACATCAATAATATACTTATTCACAATTAAACAAAAAA
42068518 TTCAAAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
54 22 0.51
55 13 0.30
56 8 0.19
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.42
Consensus pattern (55 bp):
TCTATTATATTTTACATCAATAATATACTTATTCACAATTAAACAAAAAAATTTA
Found at i:42070025 original size:23 final size:23
Alignment explanation
Indices: 42069982--42070025 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
42069972 ATATCTCCTG
**
42069982 TACATGAATGTGTCATCAATTTT
1 TACATGAATGTGTCAAAAATTTT
42070005 TACATGAATGTGTCAAAAATT
1 TACATGAATGTGTCAAAAATT
42070026 GATGCATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (23 bp):
TACATGAATGTGTCAAAAATTTT
Found at i:42092663 original size:25 final size:25
Alignment explanation
Indices: 42092612--42092664 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
42092602 ATTTCTTGTC
* *
42092612 TTTATTTTTTATTTCATTTTAGGAT
1 TTTATTTTTTATTTCATGTTAGAAT
*
42092637 TTTA-TTTTTATTTCATAGTTATAAT
1 TTTATTTTTTATTTCAT-GTTAGAAT
42092662 TTT
1 TTT
42092665 TCTTTATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.68
Consensus pattern (25 bp):
TTTATTTTTTATTTCATGTTAGAAT
Found at i:42097238 original size:22 final size:23
Alignment explanation
Indices: 42097205--42097250 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
42097195 ACATCATGTA
42097205 AAATAAGTAAAAA-CTAAGAATG
1 AAATAAGTAAAAATCTAAGAATG
42097227 AAATAA-TAAAAAATCTAAGAATG
1 AAATAAGT-AAAAATCTAAGAATG
42097250 A
1 A
42097251 TCCTCTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 11 0.50
23 10 0.45
ACGTcount: A:0.65, C:0.04, G:0.11, T:0.20
Consensus pattern (23 bp):
AAATAAGTAAAAATCTAAGAATG
Found at i:42099997 original size:9 final size:9
Alignment explanation
Indices: 42099985--42100114 Score: 119
Period size: 9 Copynumber: 14.7 Consensus size: 9
42099975 AAATTAATCG
42099985 ATTTAACCT
1 ATTTAACCT
*
42099994 ATTTAACCG
1 ATTTAACCT
*
42100003 A-TTAACCG
1 ATTTAACCT
42100011 ATTTAA-CT
1 ATTTAACCT
* *
42100019 GACTTAACCG
1 -ATTTAACCT
42100029 ATTTAACCGT
1 ATTTAACC-T
42100039 -TTTAACCT
1 ATTTAACCT
*
42100047 ATTTAACCG
1 ATTTAACCT
42100056 A-TTAA-CT
1 ATTTAACCT
42100063 GATTTAA-CT
1 -ATTTAACCT
42100072 GATTTAACCT
1 -ATTTAACCT
42100082 ATTTAACCT
1 ATTTAACCT
*
42100091 ATTTAACCG
1 ATTTAACCT
*
42100100 ATTTAACCG
1 ATTTAACCT
42100109 ATTTAA
1 ATTTAA
42100115 ATCACTATAT
Statistics
Matches: 104, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
7 1 0.01
8 15 0.14
9 85 0.82
10 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (9 bp):
ATTTAACCT
Found at i:42100004 original size:18 final size:18
Alignment explanation
Indices: 42099978--42100114 Score: 163
Period size: 18 Copynumber: 7.7 Consensus size: 18
42099968 TTGGTTAAAA
*
42099978 TTAATCGATTTAACCTAT
1 TTAACCGATTTAACCTAT
*
42099996 TTAACCGA-TTAACCGAT
1 TTAACCGATTTAACCTAT
* * *
42100013 TTAACTGACTTAACCGAT
1 TTAACCGATTTAACCTAT
*
42100031 TTAACCGTTTTAACCTAT
1 TTAACCGATTTAACCTAT
42100049 TTAACCGA-TTAA-CTGAT
1 TTAACCGATTTAACCT-AT
*
42100066 TTAACTGATTTAACCTAT
1 TTAACCGATTTAACCTAT
* *
42100084 TTAACCTATTTAACCGAT
1 TTAACCGATTTAACCTAT
42100102 TTAACCGATTTAA
1 TTAACCGATTTAA
42100115 ATCACTATAT
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
16 2 0.02
17 28 0.27
18 70 0.69
19 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.39
Consensus pattern (18 bp):
TTAACCGATTTAACCTAT
Found at i:42100032 original size:44 final size:45
Alignment explanation
Indices: 42099978--42100106 Score: 192
Period size: 44 Copynumber: 2.9 Consensus size: 45
42099968 TTGGTTAAAA
* *
42099978 TTAATCGATTTAACCTATTTAACCGA-TTAACCGATTTAACTGAC
1 TTAACCGATTTAACCTATTTAACCTATTTAACCGATTTAACTGAC
*
42100022 TTAACCGATTTAACCGT-TTTAACCTATTTAACCGA-TTAACTGAT
1 TTAACCGATTTAACC-TATTTAACCTATTTAACCGATTTAACTGAC
*
42100066 TTAACTGATTTAACCTATTTAACCTATTTAACCGATTTAAC
1 TTAACCGATTTAACCTATTTAACCTATTTAACCGATTTAAC
42100107 CGATTTAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
43 1 0.01
44 62 0.81
45 14 0.18
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (45 bp):
TTAACCGATTTAACCTATTTAACCTATTTAACCGATTTAACTGAC
Found at i:42100043 original size:53 final size:53
Alignment explanation
Indices: 42099985--42100111 Score: 202
Period size: 53 Copynumber: 2.4 Consensus size: 53
42099975 AAATTAATCG
42099985 ATTTAACCTATTTAACCGATTAACCGATTTAACTGACTTAACCGATTTAACCGT
1 ATTTAACCTATTTAACCGATTAACCGATTTAACTGACTTAACCGATTTAACC-T
* * *
42100039 -TTTAACCTATTTAACCGATTAACTGATTTAACTGATTTAACCTATTTAACCT
1 ATTTAACCTATTTAACCGATTAACCGATTTAACTGACTTAACCGATTTAACCT
*
42100091 ATTTAACCGATTTAACCGATT
1 ATTTAACCTATTTAACCGATT
42100112 TAAATCACTA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 67 0.99
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (53 bp):
ATTTAACCTATTTAACCGATTAACCGATTTAACTGACTTAACCGATTTAACCT
Found at i:42100162 original size:20 final size:20
Alignment explanation
Indices: 42100137--42100274 Score: 89
Period size: 20 Copynumber: 7.3 Consensus size: 20
42100127 TTAAAAAAAT
42100137 TACATAAGTCTTTGAATCAC
1 TACATAAGTCTTTGAATCAC
* ** *
42100157 TACATAA----TTAAAAAATT
1 TACATAAGTCTTTGAATCA-C
42100174 TACATAAGTCTTTGAATCAC
1 TACATAAGTCTTTGAATCAC
** * *
42100194 TACATAA--C-TAAAAACAT
1 TACATAAGTCTTTGAATCAC
42100211 TACATAAGTCTTTGAATCAC
1 TACATAAGTCTTTGAATCAC
** * *
42100231 TACATAA---TTAAAAACAT
1 TACATAAGTCTTTGAATCAC
42100248 TACATAAGTCTTTGAATCAC
1 TACATAAGTCTTTGAATCAC
42100268 TACATAA
1 TACATAA
42100275 TTAAAAACAT
Statistics
Matches: 83, Mismatches: 24, Indels: 22
0.64 0.19 0.17
Matches are distributed among these distances:
16 5 0.06
17 32 0.39
18 1 0.01
19 1 0.01
20 39 0.47
21 5 0.06
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.33
Consensus pattern (20 bp):
TACATAAGTCTTTGAATCAC
Found at i:42100216 original size:17 final size:17
Alignment explanation
Indices: 42100194--42100254 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
42100184 TTTGAATCAC
42100194 TACATAACTAAAAACAT
1 TACATAACTAAAAACAT
** * *
42100211 TACATAAGTCTTTGAATCAC
1 TACATAA--C-TAAAAACAT
*
42100231 TACATAATTAAAAACAT
1 TACATAACTAAAAACAT
42100248 TACATAA
1 TACATAA
42100255 GTCTTTGAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 19 0.59
19 1 0.03
20 12 0.38
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (17 bp):
TACATAACTAAAAACAT
Found at i:42100313 original size:37 final size:37
Alignment explanation
Indices: 42100114--42100296 Score: 314
Period size: 37 Copynumber: 4.9 Consensus size: 37
42100104 AACCGATTTA
* *
42100114 AATCACTATATAATTAAAAAAATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
42100151 AATCACTACATAATTAAAAA-ATTTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACA-TTACATAAGTCTTTG
*
42100188 AATCACTACATAACTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
42100225 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
42100262 AATCACTACATAATTAAAAACATTATATAAGTCTT
1 AATCACTACATAATTAAAAACATTACATAAGTCTT
42100297 GAAATTAACA
Statistics
Matches: 140, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
36 1 0.01
37 138 0.99
38 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:42103154 original size:7 final size:7
Alignment explanation
Indices: 42103144--42103168 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42103134 TGCAGTATTG
42103144 CATGAAA
1 CATGAAA
42103151 CATGAAA
1 CATGAAA
42103158 CATGAAA
1 CATGAAA
42103165 CATG
1 CATG
42103169 CAGTATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (7 bp):
CATGAAA
Found at i:42104292 original size:25 final size:25
Alignment explanation
Indices: 42104264--42104314 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
42104254 ACTTTAACTT
**
42104264 AGCTCTTTGTGGGTGTTAATTTTCC
1 AGCTCTTTGCAGGTGTTAATTTTCC
42104289 AGCTCTTTGCAGGTGTTAATTTTCC
1 AGCTCTTTGCAGGTGTTAATTTTCC
42104314 A
1 A
42104315 AAGCCACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (25 bp):
AGCTCTTTGCAGGTGTTAATTTTCC
Found at i:42104327 original size:14 final size:14
Alignment explanation
Indices: 42104308--42104337 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42104298 CAGGTGTTAA
42104308 TTTTCCAAAGCCAC
1 TTTTCCAAAGCCAC
42104322 TTTTCCAAAGCCAC
1 TTTTCCAAAGCCAC
42104336 TT
1 TT
42104338 CAAAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (14 bp):
TTTTCCAAAGCCAC
Found at i:42104843 original size:18 final size:19
Alignment explanation
Indices: 42104820--42104869 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
42104810 AACCGACCGA
42104820 TTAACCGAATTTGGTCGG-
1 TTAACCGAATTTGGTCGGT
* **
42104838 TTAACCAAATTTTTTCGGTT
1 TTAACCGAATTTGGTCGG-T
42104858 TTAACCGAATTT
1 TTAACCGAATTT
42104870 TGCACACCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (19 bp):
TTAACCGAATTTGGTCGGT
Found at i:42111691 original size:26 final size:25
Alignment explanation
Indices: 42111647--42111744 Score: 90
Period size: 26 Copynumber: 3.8 Consensus size: 25
42111637 AATTTTCTCT
42111647 AAATTTTATCG-GGGATAAAATCGTCA
1 AAATTTTA-CGAGGG-TAAAATCGTCA
* * *
42111673 CAATTTTATCGAGGGTAAATTTGTCA
1 AAATTTTA-CGAGGGTAAAATCGTCA
* * *
42111699 AAATTATACCATGGGTAAAATCTTCA
1 AAATTTTACGA-GGGTAAAATCGTCA
*
42111725 AAATTTTACTAGGGTAAAAT
1 AAATTTTACGAGGGTAAAAT
42111745 TGGGATGAGA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
25 11 0.19
26 45 0.76
27 3 0.05
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (25 bp):
AAATTTTACGAGGGTAAAATCGTCA
Found at i:42115083 original size:20 final size:20
Alignment explanation
Indices: 42115055--42115092 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42115045 CTTTAAAATC
*
42115055 AAGTTAAAATTATTTTAATA
1 AAGTAAAAATTATTTTAATA
*
42115075 AAGTAAAAATTCTTTTAA
1 AAGTAAAAATTATTTTAA
42115093 CTAGTCAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
AAGTAAAAATTATTTTAATA
Found at i:42120192 original size:49 final size:49
Alignment explanation
Indices: 42120107--42120202 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 49
42120097 CTTGAACTCA
** ** *
42120107 TGATCGCATAACCATTGACAACTAGGCTCTCGAGTTATACTCCAACCTG
1 TGATCGCATAACCACCGACAACTAGGAGCCCGAGTTATACTCCAACCTG
* * *
42120156 TGATCGCATAACCACCGTCAACTAGGAGCCCTAGTTATACTTCAACC
1 TGATCGCATAACCACCGACAACTAGGAGCCCGAGTTATACTCCAACC
42120203 CATGACCGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (49 bp):
TGATCGCATAACCACCGACAACTAGGAGCCCGAGTTATACTCCAACCTG
Found at i:42120221 original size:49 final size:49
Alignment explanation
Indices: 42120139--42120232 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 49
42120129 TAGGCTCTCG
** *
42120139 AGTTATACTCCAACCTGTGATCGCATAACCACCGTCAACTAGGAGCCCT
1 AGTTATACTCCAACCCATGACCGCATAACCACCGTCAACTAGGAGCCCT
* * * * *
42120188 AGTTATACTTCAACCCATGACCGTATAAGCACCGTGAACTGGGAG
1 AGTTATACTCCAACCCATGACCGCATAACCACCGTCAACTAGGAG
42120233 TTTGACTTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 37 1.00
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (49 bp):
AGTTATACTCCAACCCATGACCGCATAACCACCGTCAACTAGGAGCCCT
Found at i:42125165 original size:9 final size:9
Alignment explanation
Indices: 42125149--42125325 Score: 58
Period size: 9 Copynumber: 19.1 Consensus size: 9
42125139 AATTAATAAT
42125149 ATTATAAAA
1 ATTATAAAA
*
42125158 ATTGTAAAA
1 ATTATAAAA
42125167 A-TATAAAA
1 ATTATAAAA
42125175 TATATATAAAA
1 -AT-TATAAAA
*
42125186 ATTGTAAAGA
1 ATTATAAA-A
*
42125196 TATTAATTTAAA
1 -ATT-A-TAAAA
42125208 ATT-TAAAA
1 ATTATAAAA
* *
42125216 TTTATTAAA
1 ATTATAAAA
42125225 A-TATAAAA
1 ATTATAAAA
*
42125233 ATATTTAAAA
1 AT-TATAAAA
* **
42125243 GTT-GCAAA
1 ATTATAAAA
*
42125251 ATTATTTAAA
1 ATTA-TAAAA
* * *
42125261 TTTTTTAAA
1 ATTATAAAA
*
42125270 ATTTTAAAA
1 ATTATAAAA
* *
42125279 ATTGTGAAA
1 ATTATAAAA
*
42125288 ATCATTAAAA
1 ATTA-TAAAA
42125298 ATT-TAAAA
1 ATTATAAAA
* *
42125306 ATGATTTAAA
1 ATTA-TAAAA
42125316 ATTATAAAA
1 ATTATAAAA
42125325 A
1 A
42125326 ATATTTAGAT
Statistics
Matches: 122, Mismatches: 31, Indels: 30
0.67 0.17 0.16
Matches are distributed among these distances:
8 31 0.25
9 46 0.38
10 28 0.23
11 13 0.11
12 1 0.01
13 3 0.02
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (9 bp):
ATTATAAAA
Found at i:42125331 original size:19 final size:17
Alignment explanation
Indices: 42125201--42125332 Score: 88
Period size: 18 Copynumber: 7.3 Consensus size: 17
42125191 AAAGATATTA
42125201 ATTTAAAATTT-AAAAT
1 ATTTAAAATTTAAAAAT
* *
42125217 TTATTAAAATATAAAAAT
1 AT-TTAAAATTTAAAAAT
* *
42125235 ATTTAAAAGTTGCAAAATT
1 ATTTAAAA-TT-TAAAAAT
* *
42125254 ATTTAAATTTTTTAAAAT
1 ATTTAAA-ATTTAAAAAT
*
42125272 -TTTAAAAATTGTGAAAAT
1 ATTT-AAAATT-TAAAAAT
*
42125290 CATTAAAAATTTAAAAAT
1 -ATTTAAAATTTAAAAAT
42125308 GATTTAAAATTATAAAAAAT
1 -ATTTAAAATT-T-AAAAAT
42125328 ATTTA
1 ATTTA
42125333 GATTTTGTGA
Statistics
Matches: 89, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
16 1 0.01
17 19 0.21
18 35 0.39
19 26 0.29
20 8 0.09
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (17 bp):
ATTTAAAATTTAAAAAT
Found at i:42131403 original size:62 final size:62
Alignment explanation
Indices: 42131337--42131542 Score: 143
Period size: 62 Copynumber: 3.3 Consensus size: 62
42131327 TTGTACATGG
42131337 TTATATATTGTCGATATTGAATTGTTTATGTATATAGGATGCCGAATTAGATTTGTATTTGA
1 TTATATATTGTCGATATTGAATTGTTTATGTATATAGGATGCCGAATTAGATTTGTATTTGA
* * * ** * * * ** ** *
42131399 TTATACAATATCGA-ACTTG-ATTCGTACAGGGT-TGTA-CATTGTTGAAATTA-ATTCATACTT
1 TTATATATTGTCGATA-TTGAATT-GTTTA-TGTATATAGGA-TGCCG-AATTAGATTTGTATTT
*
42131459 GG
61 GA
* * * * * *
42131461 TTATATATTGTTGATAGTGAATTGTTTATGAATATAGGATGCCGAATTTGATTTGTGTATGA
1 TTATATATTGTCGATATTGAATTGTTTATGTATATAGGATGCCGAATTAGATTTGTATTTGA
*
42131523 TTATATATTGTCGATCTTGA
1 TTATATATTGTCGATATTGA
42131543 TTCGTGAATG
Statistics
Matches: 97, Mismatches: 37, Indels: 20
0.63 0.24 0.13
Matches are distributed among these distances:
61 10 0.10
62 75 0.77
63 12 0.12
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.44
Consensus pattern (62 bp):
TTATATATTGTCGATATTGAATTGTTTATGTATATAGGATGCCGAATTAGATTTGTATTTGA
Found at i:42131542 original size:124 final size:124
Alignment explanation
Indices: 42131317--42131564 Score: 338
Period size: 124 Copynumber: 2.0 Consensus size: 124
42131307 TTTACCTTGC
* * *
42131317 TGAAATTAAATTGTACATGGTTATATATTGTCGATATTGAATTGTTTATGTATATAGGATGCCGA
1 TGAAATTAAATTATACATGGTTATATATTGTCGATAGTGAATTGTTTATGAATATAGGATGCCGA
* *
42131382 ATTAGATTTGTATTTGATTATACAATATCGAACTTGATTCGT-ACAGGGTTGTACATTGT
66 ATTAGATTTGTATATGATTATACAATATCGAACTTGATTCGTGA-AGGGTTATACATTGT
* *
42131441 TGAAATT-AATTCATACTTGGTTATATATTGTTGATAGTGAATTGTTTATGAATATAGGATGCCG
1 TGAAATTAAATT-ATACATGGTTATATATTGTCGATAGTGAATTGTTTATGAATATAGGATGCCG
* * * * * * *
42131505 AATTTGATTTGTGTATGATTATATATTGTCGATCTTGATTCGTGAATGGTTATACATTGT
65 AATTAGATTTGTATATGATTATACAATATCGAACTTGATTCGTGAAGGGTTATACATTGT
42131565 CAAATTGTTG
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
123 4 0.04
124 103 0.95
125 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (124 bp):
TGAAATTAAATTATACATGGTTATATATTGTCGATAGTGAATTGTTTATGAATATAGGATGCCGA
ATTAGATTTGTATATGATTATACAATATCGAACTTGATTCGTGAAGGGTTATACATTGT
Found at i:42133901 original size:43 final size:41
Alignment explanation
Indices: 42133805--42134040 Score: 199
Period size: 43 Copynumber: 5.6 Consensus size: 41
42133795 CCGTTACTCA
* * * * **
42133805 GTGGATTCAGCACTTAGCAATCACATTA-AATTCAGTGATAC
1 GTGGAATCAGCACTTAGCAACCCCTTTACAA-TCAAAGATAC
* *
42133846 GGGGAATCAGCACATAGCAACCCCTTTCACAATCAAAGATAC
1 GTGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAAGATAC
* * * * **
42133888 AGTGGAATTAGCACTTAGCAACCACCTTTATATTTAGTGATAC
1 -GTGGAATCAGCACTTAGCAACC-CCTTTACAATCAAAGATAC
* * *
42133931 GGGGAATCAGCACATAGCAACCCCTTTTACAATCAAATATAC
1 GTGGAATCAGCACTTAGCAACCCC-TTTACAATCAAAGATAC
* *
42133973 GGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATA-ATTC
1 -GTGGAATCAGCACTTAGCAACC-CCTTTACAATCAA-AGATAC
42134016 -TGGGAATCAGCACTTAGCAACCCCT
1 GT-GGAATCAGCACTTAGCAACCCCT
42134041 CAGGGAATCT
Statistics
Matches: 157, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
41 27 0.17
42 59 0.38
43 63 0.40
44 8 0.05
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
GTGGAATCAGCACTTAGCAACCCCTTTACAATCAAAGATAC
Found at i:42133945 original size:85 final size:85
Alignment explanation
Indices: 42133803--42134040 Score: 320
Period size: 85 Copynumber: 2.8 Consensus size: 85
42133793 ATCCGTTACT
* *
42133803 CAGTGG-ATTCAGCACTTAGCAATCA-CATTAAATTCAGTGATACGGGGAATCAGCACATAGCAA
1 CAGTGGAATT-AGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAA
42133866 CCCCTTTCACAATCAAAGATA
65 CCCCTTTCACAATCAAAGATA
* *
42133887 CAGTGGAATTAGCACTTAGCAACCACCTTTATATTTAGTGATACGGGGAATCAGCACATAGCAAC
1 CAGTGGAATTAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
* *
42133952 CCCTTTTACAATCAAATATA
66 CCCTTTCACAATCAAAGATA
* * * * * * *
42133972 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAA-TCAATAATTCTGGGAATCAGCACTTAGCAA
1 CAGTGGAATTAGCACTTAGCAACCACCTTTA-AATTCAGTGATACGGGGAATCAGCACATAGCAA
42134036 CCCCT
65 CCCCT
42134041 CAGGGAATCT
Statistics
Matches: 136, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
84 20 0.15
85 115 0.85
86 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (85 bp):
CAGTGGAATTAGCACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:42133949 original size:42 final size:42
Alignment explanation
Indices: 42133811--42134037 Score: 207
Period size: 42 Copynumber: 5.4 Consensus size: 42
42133801 CTCAGTGGAT
* * *
42133811 TCAGCACTTAGCAATCA-CATTAAATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAATGATACGGGGAA
* * *
42133852 TCAGCACATAGCAACC-CCTTTCACAA-TCAAAGATACAGTGGAA
1 TCAGCACTTAGCAACCACCTTT-A-AATTCAATGATAC-GGGGAA
* * * *
42133895 TTAGCACTTAGCAACCACCTTTATATTTAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAATTCAATGATACGGGGAA
*
42133937 TCAGCACATAGCAACC-CCTTTTACAA-TCAAAT-ATACGGTGGAA
1 TCAGCACTTAGCAACCACC-TTTA-AATTC-AATGATACGG-GGAA
* * *
42133980 TCAGCACTTAGCAACCACCTTTAGAA-TCAATAATTCTGGGAA
1 TCAGCACTTAGCAACCACCTTTA-AATTCAATGATACGGGGAA
42134022 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
42134038 CCTCAGGGAA
Statistics
Matches: 152, Mismatches: 22, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
41 19 0.12
42 63 0.41
43 63 0.41
44 7 0.05
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTAAATTCAATGATACGGGGAA
Found at i:42134046 original size:26 final size:26
Alignment explanation
Indices: 42134017--42134066 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
42134007 CAATAATTCT
*
42134017 GGGAATCAGCACTTAGCAACCCCTCA
1 GGGAATCAGCACTTAACAACCCCTCA
* *
42134043 GGGAATCTGCACTTAACGACCCCT
1 GGGAATCAGCACTTAACAACCCCT
42134067 TTTTATCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.34, G:0.20, T:0.18
Consensus pattern (26 bp):
GGGAATCAGCACTTAACAACCCCTCA
Found at i:42137355 original size:29 final size:29
Alignment explanation
Indices: 42137310--42137389 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 29
42137300 GTACTCTTTG
*
42137310 TAAA-TTTAAATTTTAGTCCATTTATTTT
1 TAAATTTTAAAATTTAGTCCATTTATTTT
*
42137338 T-ATTTTTAGAAATTTAGTCTC-TTTATTTT
1 TAAATTTTA-AAATTTAGTC-CATTTATTTT
42137367 TCAAATTTTAAAATTTAGATCCA
1 T-AAATTTTAAAATTTAG-TCCA
42137390 ACAGTTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
27 1 0.02
28 5 0.12
29 18 0.43
30 10 0.24
31 8 0.19
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.54
Consensus pattern (29 bp):
TAAATTTTAAAATTTAGTCCATTTATTTT
Found at i:42138189 original size:42 final size:42
Alignment explanation
Indices: 42138142--42138385 Score: 271
Period size: 42 Copynumber: 5.8 Consensus size: 42
42138132 GCGTTTACAG
*
42138142 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCAA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCAA
* * *
42138184 AAAAAA-GCCGCTAAAAATCATGTTCTTTAGCAGCGCTTC-G
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCAA
* *
42138224 AAAAAACGCCACTAAAGATCATGTTCTTTAGCAGCGCTT-AA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCAA
* * * *
42138265 AGAAAAACACTGCTAAAGATCATATTCTTTAGCGGCGCTT-AGT
1 A-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCA-A
* * *
42138308 AAAAAACGCCGCTATAGATTATGTTCTTTAGCGGCGCTTTCAT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTCAA
* * * * *
42138351 CACAAACGCCGCGAAAAATAATGTTCTTTAGCGGC
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
42138386 ACTTTTGTAA
Statistics
Matches: 172, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
40 6 0.03
41 61 0.35
42 71 0.41
43 33 0.19
44 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCAA
Found at i:42138375 original size:43 final size:41
Alignment explanation
Indices: 42138142--42138385 Score: 274
Period size: 41 Copynumber: 5.9 Consensus size: 41
42138132 GCGTTTACAG
*
42138142 AAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTCA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCA
* * * *
42138183 AAAAAAAGCCGCTAAAAATCATGTTCTTTAGCAGCGCTTCG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCA
* * *
42138224 AAAAAACGCCACTAAAGATCATGTTCTTTAGCAGCGCTTAA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCA
* * *
42138265 AGAAAAACACTGCTAAAGATCATATTCTTTAGCGGCGCTT-A
1 A-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCA
* *
42138306 GTAAAAAACGCCGCTATAGATTATGTTCTTTAGCGGCGCTTTCA
1 --AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTCA
* * * * *
42138350 TCACAAACGCCGCGAAAAATAATGTTCTTTAGCGGC
1 -AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
42138386 ACTTTTGTAA
Statistics
Matches: 172, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
41 74 0.43
42 64 0.37
43 33 0.19
44 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCA
Found at i:42138816 original size:21 final size:21
Alignment explanation
Indices: 42138792--42138881 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 21
42138782 GCTTCTTTCG
* *
42138792 CTGCTTCTCGCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
* * *
42138813 CTGCTTCTCTCACTGTAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
42138834 CTGCTTCCCTCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAGCCT
* * *
42138855 CTACTTCCCTCGTTGCTGCCT
1 CTGCTTCCCTCGCTGCAGCCT
42138876 CTGCTT
1 CTGCTT
42138882 TAAGTTGTAG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.06, C:0.42, G:0.18, T:0.34
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCT
Found at i:42144215 original size:9 final size:9
Alignment explanation
Indices: 42144198--42144534 Score: 289
Period size: 9 Copynumber: 38.8 Consensus size: 9
42144188 TCATAGATAA
*
42144198 GTAAATTAT
1 GTAAGTTAT
42144207 GTAAGTTAT
1 GTAAGTTAT
*
42144216 GTACGTGTA-
1 GTAAGT-TAT
42144225 -TAAGTTAT
1 GTAAGTTAT
42144233 GTAAGTTAT
1 GTAAGTTAT
*
42144242 GT-A-TTAA
1 GTAAGTTAT
*
42144249 GTAAGCTAT
1 GTAAGTTAT
*
42144258 GTAAGTTGT
1 GTAAGTTAT
42144267 GT-A-TTAT
1 GTAAGTTAT
42144274 GTAAGTTAT
1 GTAAGTTAT
42144283 GTAAGTTAT
1 GTAAGTTAT
** *
42144292 CAAAGTAAT
1 GTAAGTTAT
*
42144301 GTATGTTAT
1 GTAAGTTAT
42144310 GTAAG-T-T
1 GTAAGTTAT
42144317 GTAAGTTAT
1 GTAAGTTAT
*
42144326 -TATGTATTAT
1 GTAAG--TTAT
42144336 GTAAGTTAT
1 GTAAGTTAT
42144345 GTAAGTTAT
1 GTAAGTTAT
42144354 GTAAGTTAAAT
1 GTAAGTT--AT
42144365 GT-A-TTAT
1 GTAAGTTAT
*
42144372 GTACGTTAT
1 GTAAGTTAT
*
42144381 GTAAGTTGT
1 GTAAGTTAT
*
42144390 GTAAGATAT
1 GTAAGTTAT
*
42144399 TTAAGTTAT
1 GTAAGTTAT
*
42144408 GTAAGTTTT
1 GTAAGTTAT
42144417 GT-A-TTAT
1 GTAAGTTAT
42144424 GTAAGTTAT
1 GTAAGTTAT
42144433 GTAAGTTAT
1 GTAAGTTAT
42144442 GTAAGTTAAAT
1 GTAAGTT--AT
42144453 GT-A-TTAT
1 GTAAGTTAT
*
42144460 GTAGGTTAT
1 GTAAGTTAT
*
42144469 GTAAGTTGT
1 GTAAGTTAT
*
42144478 GTAAGATAT
1 GTAAGTTAT
*
42144487 TTAAGTTAT
1 GTAAGTTAT
*
42144496 GTAAGTTTT
1 GTAAGTTAT
42144505 GT-A-TTAT
1 GTAAGTTAT
*
42144512 GTAAGTTTT
1 GTAAGTTAT
42144521 GT-A-TTAT
1 GTAAGTTAT
42144528 GTAAGTT
1 GTAAGTT
42144535 GTTATGTTAT
Statistics
Matches: 261, Mismatches: 41, Indels: 52
0.74 0.12 0.15
Matches are distributed among these distances:
7 41 0.16
8 19 0.07
9 182 0.70
10 8 0.03
11 11 0.04
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42144575 original size:88 final size:88
Alignment explanation
Indices: 42144198--42144563 Score: 399
Period size: 88 Copynumber: 4.2 Consensus size: 88
42144188 TCATAGATAA
* * * * * * * *
42144198 GTAAATTATGTAAGTTATGTACG-TGTATAAGTTATGTAAGTTATGTATTAAGTAAGCTATGTAA
1 GTAAGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAAGTTATGTAA
*
42144262 GTTGTGT-A-TT--ATGTAAGTTAT
66 GTTATGTAAGTTAAATGT-A-TTAT
** ** * * *
42144283 GTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTATTATGTATTATGTAAGTTATG
1 GTAAGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAG-T-TT-TGTATTATGTAAGTTATG
42144346 TAAGTTATGTAAGTTAAATGTATTAT
63 TAAGTTATGTAAGTTAAATGTATTAT
*
42144372 GTACGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAAGTTATGTAA
1 GTAAGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAAGTTATGTAA
42144437 GTTATGTAAGTTAAATGTATTAT
66 GTTATGTAAGTTAAATGTATTAT
* *
42144460 GTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAAGTTTTGT-A
1 GTAAGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAAGTTATGTAA
** *
42144524 -TTATGTAAGTTGTTATGTTATTAC
66 GTTATGTAAGTT-AAATG-TATTAT
*
42144548 GTAAGTTATGCAAGTT
1 GTAAGTTATGTAAGTT
42144564 TATATATATA
Statistics
Matches: 243, Mismatches: 26, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
84 6 0.02
85 20 0.08
86 18 0.07
87 29 0.12
88 125 0.51
89 32 0.13
90 3 0.01
91 10 0.04
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (88 bp):
GTAAGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTAAGTTTTGTATTATGTAAGTTATGTAA
GTTATGTAAGTTAAATGTATTAT
Found at i:42144647 original size:13 final size:13
Alignment explanation
Indices: 42144629--42144653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42144619 TGACAAGTCA
42144629 TTATATAATCAAT
1 TTATATAATCAAT
42144642 TTATATAATCAA
1 TTATATAATCAA
42144654 GTAATAATTA
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTATATAATCAAT
Found at i:42147095 original size:365 final size:366
Alignment explanation
Indices: 42146425--42147136 Score: 1167
Period size: 365 Copynumber: 1.9 Consensus size: 366
42146415 CGACATTTAC
* *
42146425 GGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGTCGCCGTTTTATAAAA
1 GGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTATAAAA
* * *
42146490 ATATAAGGAAACATTCTGGCGTTTTCCCAAACACGCCACAATTAATATATTATCGAACCGGCATC
66 ATATAAGGAAACATTCTAGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGGCACC
* * *
42146555 GTTTTCAGTAAATTTTATACATCCTTGCGGCGTTTTTAATAAAACACCACTAAAAGATTCCATCC
131 GTTTTCAGAAAATTTTATACATCCTTGCGGCATTTATAATAAAACACCACTAAAAGATTCCATCC
* * * *
42146620 TTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTACGGCGCTTTTAGGGAACATG
196 TTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTAAGGCGCTTTTAGGAAAAACG
**
42146685 CCACAACTAAATTTTATTCCCTAAGCCAAAACAACGCCGTATCGGTAAATGCAATAAATATTTGT
261 CCACAACTAAAACTTATTCCCTAAGCCAAAACAACGCCGTATCGGTAAATGCAATAAATATTTGT
42146750 GGCG-TTTTTTATCAAAACGCTGGTAATGTCTACCTTTTGT
326 GGCGTTTTTTTATCAAAACGCTGGTAATGTCTACCTTTTGT
*
42146790 GGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAATGGCGCCATTTTATAAAA
1 GGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTATAAAA
* *
42146855 ATATAAGGAAACATTCTAGCGTTTTCCCAAAAATGCCACAATTAATATATTATCGAACCGGCGCC
66 ATATAAGGAAACATTCTAGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGGCACC
* *
42146920 GTTTTCAGAAAATTTTATACATCCTTGCGGCATTTATAATAAAACGCCACTAAAATATTCCATCC
131 GTTTTCAGAAAATTTTATACATCCTTGCGGCATTTATAATAAAACACCACTAAAAGATTCCATCC
* *
42146985 TTCAACTGAAACGGCGCCG-TTTCGGCAAAGTTTAAATATTATTTAAGGCGCTTTTCGGAAAAAC
196 TTCAACTGAAACGGCGCCGTTTTC-GCAAAGTTCAAATATTATTTAAGGCGCTTTTAGGAAAAAC
* * * *
42147049 GCCACAACTAAAACTTATTCCCTAAGCCGAAACGACGTCGTATCGGTAAATGCAATAAATTTTTG
260 GCCACAACTAAAACTTATTCCCTAAGCCAAAACAACGCCGTATCGGTAAATGCAATAAATATTTG
42147114 TGGCGTTTTTTTTATCAAAACGC
325 TGGCG-TTTTTTTATCAAAACGC
42147137 CGCTAAATCT
Statistics
Matches: 319, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
364 4 0.01
365 299 0.94
367 16 0.05
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (366 bp):
GGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTATAAAA
ATATAAGGAAACATTCTAGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAACCGGCACC
GTTTTCAGAAAATTTTATACATCCTTGCGGCATTTATAATAAAACACCACTAAAAGATTCCATCC
TTCAACTGAAACGGCGCCGTTTTCGCAAAGTTCAAATATTATTTAAGGCGCTTTTAGGAAAAACG
CCACAACTAAAACTTATTCCCTAAGCCAAAACAACGCCGTATCGGTAAATGCAATAAATATTTGT
GGCGTTTTTTTATCAAAACGCTGGTAATGTCTACCTTTTGT
Found at i:42147212 original size:24 final size:23
Alignment explanation
Indices: 42147185--42147265 Score: 81
Period size: 24 Copynumber: 3.2 Consensus size: 23
42147175 TGTATCATTC
42147185 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTAT-T
* *
42147209 ATTTAAACAATTAATTACTTAAAAATT
1 ATTTAAATAATTAATTACCT----ATT
42147236 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTA-TT
42147261 ATTTA
1 ATTTA
42147266 TTTGTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
24 24 0.51
25 2 0.04
27 1 0.02
28 20 0.43
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAATTAATTACCTATT
Found at i:42147268 original size:28 final size:26
Alignment explanation
Indices: 42147185--42147268 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 26
42147175 TGTATCATTC
*
42147185 ATTTAAATAATTAATTACC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * * *
42147209 ATTTAAACAATTAATTACTTAAAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
42147237 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
42147265 ATTT
1 ATTT
42147269 GTTTATTTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
24 17 0.38
26 1 0.02
28 27 0.60
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:42147845 original size:12 final size:12
Alignment explanation
Indices: 42147828--42147852 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42147818 CTCTTAACAT
42147828 CTAACCCCTAAC
1 CTAACCCCTAAC
42147840 CTAACCCCTAAC
1 CTAACCCCTAAC
42147852 C
1 C
42147853 CTTAACCCAT
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:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:42147858 original size:14 final size:13
Alignment explanation
Indices: 42147829--42147871 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
42147819 TCTTAACATC
42147829 TAACCCCTAACC-
1 TAACCCCTAACCT
42147841 TAACCCCTAACCCT
1 TAACCCCTAA-CCT
*
42147855 TAACCCATAAACCT
1 TAACCCCT-AACCT
42147869 TAA
1 TAA
42147872 ATCACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 10 0.37
13 2 0.07
14 13 0.48
15 2 0.07
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (13 bp):
TAACCCCTAACCT
Found at i:42147917 original size:14 final size:14
Alignment explanation
Indices: 42147852--42147926 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
42147842 AACCCCTAAC
* *
42147852 CCTTAACCCATAAA
1 CCTTAATCCATAAT
*
42147866 CCTTAAATCACATTAAC
1 CCTT-AATC-CA-TAAT
* *
42147883 CCTTAAACCAGAAT
1 CCTTAATCCATAAT
*
42147897 CCCTAATCCATAAT
1 CCTTAATCCATAAT
42147911 CCTTAATTCCATAAT
1 CCTTAA-TCCATAAT
42147926 C
1 C
42147927 TATAAAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
14 22 0.46
15 14 0.29
16 5 0.10
17 7 0.15
ACGTcount: A:0.39, C:0.32, G:0.01, T:0.28
Consensus pattern (14 bp):
CCTTAATCCATAAT
Found at i:42148000 original size:20 final size:21
Alignment explanation
Indices: 42147975--42148018 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42147965 ATCCTAAATT
*
42147975 AACCATATATA-TATACCCTA
1 AACCATATATATTAAACCCTA
*
42147995 AACCATATTTATTAAACCCTA
1 AACCATATATATTAAACCCTA
42148016 AAC
1 AAC
42148019 TATAATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (21 bp):
AACCATATATATTAAACCCTA
Found at i:42148564 original size:41 final size:41
Alignment explanation
Indices: 42148486--42148564 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
42148476 TTTTAAATCC
* *
42148486 CTGAGCATTAGCGGCGCATCCTAAAAAACGCCGCTAAAGCA
1 CTGAGCATTAGCGGCGCATCATAAAAAACGCCACTAAAGCA
* * * * *
42148527 CTGAGCATTAGCGGTGCTTTATTAAAAACGTCACTAAA
1 CTGAGCATTAGCGGCGCATCATAAAAAACGCCACTAAA
42148565 TCCACGAAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCATCATAAAAAACGCCACTAAAGCA
Found at i:42148716 original size:115 final size:114
Alignment explanation
Indices: 42148509--42148982 Score: 610
Period size: 115 Copynumber: 4.1 Consensus size: 114
42148499 GCGCATCCTA
* * * * *
42148509 AAAAACGCCGCTAAAGCACTGAGCATTAGCGGTGCTTTA-TTAAAAACGTCACTAAATCCACGAA
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTACTTAAAAACGCCGCTAAATCCCCGAA
* * * * * *
42148573 AGCTAAGAAAACGACGTCGTTGGGCTTAGGTTTCTTTGCGGCGCCTTCCC
65 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTACC
*
42148623 AAAAACGCCGCTAAAAG-CCTGAGCATTAGCGGCGCTTACTTAAAAAACGCCGCTACATCCCCGA
1 AAAAACGCCGCT-AAAGCCCTGAGCATTAGCGGCGCTTACTT-AAAAACGCCGCTAAATCCCCGA
* * * *
42148687 AAGCTCAGAAAACAGCGTTGTTGGGCTTAGGTTTTTTTGTGGCACTTTATC
64 AAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTACC
* *
42148738 AAAAATGCCGCTAAAGCCCTGAGCATTAGTGGCGCTTACTTAAAAAACGCCGCTAAATCCCCGAA
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTT-AAAAACGCCGCTAAATCCCCGAA
* * *
42148803 AGCTCAGAAAATGGTGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTAGC
65 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTACC
* * * * * *
42148853 AAAAACGTCGGTAAAGCCCCTGAGCAATAGTGGCGCTTAATTAAAAACGCCGCAAAATCCCCGAA
1 AAAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAA
* **
42148918 AGCTCAGAAAACGGCGTCATTGGGCTTAGGTTTTTTTGTGGCGCTTTAGT
65 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTACC
*
42148968 AAAAATGCCGCTAAA
1 AAAAACGCCGCTAAA
42148983 TCCCCGAAAG
Statistics
Matches: 317, Mismatches: 38, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
113 3 0.01
114 34 0.11
115 257 0.81
116 23 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (114 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACGCCGCTAAATCCCCGAAA
GCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTACC
Found at i:42149066 original size:72 final size:73
Alignment explanation
Indices: 42148882--42149109 Score: 332
Period size: 73 Copynumber: 3.1 Consensus size: 73
42148872 CTGAGCAATA
* * * *
42148882 GTGGCGCTTAATTAAAAACGCCGCAAAATCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAG
1 GTGGCGCTTTAGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
42148947 GTTTTTTT
66 GTTTTTTT
* * * * *
42148955 GTGGCGCTTTAGTAAAAATGCCGCTAAATCCCCGAAAGCTGAAAAAACGACGTCGTTGGGATTAG
1 GTGGCGCTTTAGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
*
42149020 GTTTTTCT
66 GTTTTTTT
* *
42149028 GTGGCGCTTTA-TCAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GTGGCGCTTTAGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
42149092 GTTTTTTT
66 GTTTTTTT
*
42149100 GTGGCACTTT
1 GTGGCGCTTT
42149110 CGCAAAATCG
Statistics
Matches: 136, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 62 0.46
73 74 0.54
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (73 bp):
GTGGCGCTTTAGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
GTTTTTTT
Found at i:42149116 original size:72 final size:72
Alignment explanation
Indices: 42148896--42149116 Score: 316
Period size: 72 Copynumber: 3.1 Consensus size: 72
42148886 CGCTTAATTA
* *
42148896 AAAACGCCGCAAAATCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAGGTTTTTTTGTGGCG
1 AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
*
42148961 CTTTAGTA
66 CTTTAG-C
* * * * * *
42148969 AAAATGCCGCTAAATCCCCGAAAGCTGAAAAAACGACGTCGTTGGGATTAGGTTTTTCTGTGGCG
1 AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
*
42149034 CTTTATC
66 CTTTAGC
* *
42149041 AAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCA
1 AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
*
42149106 CTTTCGC
66 CTTTAGC
42149113 AAAA
1 AAAA
42149117 TCGTCGTTAA
Statistics
Matches: 128, Mismatches: 20, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 66 0.52
73 62 0.48
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (72 bp):
AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
CTTTAGC
Found at i:42149204 original size:114 final size:114
Alignment explanation
Indices: 42149041--42149354 Score: 468
Period size: 114 Copynumber: 2.8 Consensus size: 114
42149031 GCGCTTTATC
* *
42149041 AAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCA
1 AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
* * ** * *
42149106 CTTTCGCAAAATCGTCGTTAAAGCCTTGGGCATTAGCGGCGCTTCCCCA
66 CTTTCGCAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCGCTTCCCCA
*
42149155 AAAAAGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
1 AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
**
42149220 CTTTCGCAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCGCTTCCTTA
66 CTTTCGCAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCGCTTCCCCA
* * * *
42149269 AAAACGTCGCTAAATCCCCCGAAAGCTCGGAAAACGGCGTCGTTGGGCTTA-GTTATTTTGCGGC
1 AAAACGCCGCTAAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGC
*
42149333 GCTTTCGCAAAAACGCCGCTAA
65 GCTTTCGCAAAAACGCCACTAA
42149355 TGCTTATTTT
Statistics
Matches: 182, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
114 148 0.81
115 34 0.19
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (114 bp):
AAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCG
CTTTCGCAAAAACGCCACTAAAGCCCTGAGCATTAGCGGCGCTTCCCCA
Found at i:42149609 original size:13 final size:13
Alignment explanation
Indices: 42149590--42149629 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
42149580 TATATTTTTA
42149590 TAATATTATTAAT
1 TAATATTATTAAT
* *
42149603 TAGTATTAATAAT
1 TAATATTATTAAT
*
42149616 TAATATAATTAAT
1 TAATATTATTAAT
42149629 T
1 T
42149630 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TAATATTATTAAT
Found at i:42150469 original size:19 final size:18
Alignment explanation
Indices: 42150445--42150496 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
42150435 ATAATACACC
*
42150445 AAATATATTAAAAATATTA
1 AAATATATTAAAAAT-TGA
* *
42150464 AAATATCTCAACAAATTGA
1 AAATATATTAA-AAATTGA
*
42150483 AAATAAATTAAAAA
1 AAATATATTAAAAA
42150497 AATTTCTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATATATTAAAAATTGA
Found at i:42158094 original size:29 final size:29
Alignment explanation
Indices: 42158052--42158107 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
42158042 TAGAGACCGC
42158052 CAACTTATGACTTCTATCAATTTAACCAT
1 CAACTTATGACTTCTATCAATTTAACCAT
* *
42158081 CAACTTATGGCTTCTTTCAATTTAACC
1 CAACTTATGACTTCTATCAATTTAACC
42158108 CCACTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.39
Consensus pattern (29 bp):
CAACTTATGACTTCTATCAATTTAACCAT
Found at i:42160642 original size:21 final size:21
Alignment explanation
Indices: 42160601--42160643 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42160591 TAATTTAACA
*
42160601 CAAAATTTTTAACTTTGATTT
1 CAAAATTTATAACTTTGATTT
*
42160622 CAAAATCTTATAA-TTTTATTT
1 CAAAAT-TTATAACTTTGATTT
42160643 C
1 C
42160644 TATTCTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
CAAAATTTATAACTTTGATTT
Found at i:42161191 original size:3 final size:3
Alignment explanation
Indices: 42161183--42161223 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42161173 CTACAAAAGC
42161183 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42161224 ATTTTGCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:42168463 original size:18 final size:17
Alignment explanation
Indices: 42168439--42168483 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
42168429 ATAAAATTTT
42168439 AAAATATAAAAAAGCAA
1 AAAATATAAAAAAGCAA
* *
42168456 AGAAATATATAAAAATCCA
1 A-AAATATA-AAAAAGCAA
42168475 AAAATATAA
1 AAAATATAA
42168484 CTTTAGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 8 0.33
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (17 bp):
AAAATATAAAAAAGCAA
Found at i:42173068 original size:20 final size:20
Alignment explanation
Indices: 42173020--42173068 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
42173010 TTTAAAGGGG
42173020 AAATTAAATCAATTTGATTT
1 AAATTAAATCAATTTGATTT
*
42173040 AAATCAAATCAATTTGA-TT
1 AAATTAAATCAATTTGATTT
42173059 AGAATTAAAT
1 A-AATTAAAT
42173069 AAAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (20 bp):
AAATTAAATCAATTTGATTT
Found at i:42173081 original size:30 final size:30
Alignment explanation
Indices: 42173040--42173103 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
42173030 AATTTGATTT
* *
42173040 AAATCAAATCAATTTGATTAGAATTAAATA
1 AAATAAAATCAAATTGATTAGAATTAAATA
42173070 AAATAAAATCAAATTGATTAGAATTAAATA
1 AAATAAAATCAAATTGATTAGAATTAAATA
42173100 AAAT
1 AAAT
42173104 CAGGATATAT
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:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (30 bp):
AAATAAAATCAAATTGATTAGAATTAAATA
Found at i:42174359 original size:15 final size:16
Alignment explanation
Indices: 42174327--42174358 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42174317 TCTTTTGTAT
42174327 TATATATTTTTAAAAAA
1 TATATATTTTT-AAAAA
42174344 TATATATTTTTAAAA
1 TATATATTTTTAAAA
42174359 TTTTTAGAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATATTTTTAAAAA
Found at i:42174374 original size:11 final size:9
Alignment explanation
Indices: 42174349--42174383 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
42174339 AAAAATATAT
42174349 ATTTTTAAA
1 ATTTTTAAA
42174358 ATTTTTAGAA
1 ATTTTTA-AA
42174368 TATTTTTAAA
1 -ATTTTTAAA
42174378 ATTTTT
1 ATTTTT
42174384 TGAGAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 13 0.54
10 4 0.17
11 7 0.29
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:42174789 original size:14 final size:15
Alignment explanation
Indices: 42174772--42174802 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42174762 CTAAAAGGTT
42174772 TAAAA-TAAATATTG
1 TAAAATTAAATATTG
42174786 TAAAATTAAATATTG
1 TAAAATTAAATATTG
42174801 TA
1 TA
42174803 TAAGAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
TAAAATTAAATATTG
Found at i:42174970 original size:20 final size:20
Alignment explanation
Indices: 42174945--42174986 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
42174935 ATTTGATTCT
42174945 TCTCTCCAGTTTGGTTTCGA
1 TCTCTCCAGTTTGGTTTCGA
*
42174965 TCTCTCCGGTTTGGTTTCGA
1 TCTCTCCAGTTTGGTTTCGA
42174985 TC
1 TC
42174987 CAAGAGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.26, G:0.21, T:0.45
Consensus pattern (20 bp):
TCTCTCCAGTTTGGTTTCGA
Found at i:42178453 original size:29 final size:28
Alignment explanation
Indices: 42178419--42178484 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
42178409 TTTTGCAAAA
* *
42178419 TCAACATGACATGAAGAACCCTTGCAACT
1 TCAACATGACAGGAAGAA-CCTTACAACT
**
42178448 TCAACATGATGGGAAGAACCTTACAACT
1 TCAACATGACAGGAAGAACCTTACAACT
42178476 TCAACATGA
1 TCAACATGA
42178485 TGAGAGGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (28 bp):
TCAACATGACAGGAAGAACCTTACAACT
Found at i:42178478 original size:28 final size:29
Alignment explanation
Indices: 42178431--42178486 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
42178421 AACATGACAT
*
42178431 GAAGAACCCTTGCAACTTCAACATGATGG
1 GAAGAACCCTTACAACTTCAACATGATGG
42178460 GAAGAA-CCTTACAACTTCAACATGATG
1 GAAGAACCCTTACAACTTCAACATGATG
42178487 AGAGGAGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (29 bp):
GAAGAACCCTTACAACTTCAACATGATGG
Found at i:42178803 original size:70 final size:70
Alignment explanation
Indices: 42178630--42178805 Score: 194
Period size: 70 Copynumber: 2.5 Consensus size: 70
42178620 CATGGTGATG
* * * * ** * * *
42178630 GGAGGACCCATTTTGGACTTTACAACATCAGTAGGGCGGGAAGAACCCTTACAACTTCAACATGA
1 GGAGGGCCCATTCTGAACTTTGCAACATCAACATGGCGGGAAGAACACTTACAACTTCAACAGGA
42178695 TGAGA
66 TGAGA
* * * *
42178700 GGAGGGCCCATTCTGAGCTTTGCATCATCAACATGGCGGGAAGAGCACTTGCAACTTCAACACGG
1 GGAGGGCCCATTCTGAACTTTGCAACATCAACATGGCGGGAAGAACACTTACAACTTCAACA-GG
42178765 A-GAGA
65 ATGAGA
*
42178770 GGAGGGCTCATT-TCGAACTTTGCAACATCAACATGG
1 GGAGGGCCCATTCT-GAACTTTGCAACATCAACATGG
42178806 TGAGAAAAGA
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
69 1 0.01
70 85 0.97
71 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (70 bp):
GGAGGGCCCATTCTGAACTTTGCAACATCAACATGGCGGGAAGAACACTTACAACTTCAACAGGA
TGAGA
Found at i:42182771 original size:14 final size:15
Alignment explanation
Indices: 42182735--42182771 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
42182725 TGTATTCATA
*
42182735 TTGTATCATATTATT
1 TTGTATAATATTATT
42182750 TT-TATAAT-TTATT
1 TTGTATAATATTATT
42182763 TTGTATAAT
1 TTGTATAAT
42182772 CTATCAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 11 0.55
15 2 0.10
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (15 bp):
TTGTATAATATTATT
Found at i:42188718 original size:13 final size:14
Alignment explanation
Indices: 42188693--42188725 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
42188683 AAATGTGTAA
42188693 AAAATGAAAAAATG
1 AAAATGAAAAAATG
42188707 AAAATG-AAAAATG
1 AAAATGAAAAAATG
42188720 AAAATG
1 AAAATG
42188726 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAATGAAAAAATG
Found at i:42190250 original size:128 final size:128
Alignment explanation
Indices: 42190018--42190354 Score: 541
Period size: 128 Copynumber: 2.6 Consensus size: 128
42190008 GCTCCCTGAC
* * *
42190018 CAGCAGTGGAAT-GGTTGGGAAATTACAAATCTTGTCTCCCTAAGCAGTAGCGGAGTAGATCAAA
1 CAGCAGTGGAATAGG-TGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAA
* *
42190082 GACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATCTCTGGT
65 GACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
*
42190146 CAGTAGTGGAATAGGTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAG
1 CAGCAGTGGAATAGGTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAG
*
42190211 ACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGT
66 ACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
* * *
42190274 CAGCAGTGGAATAGGTTGGAAATTACAGATCGTGTCTCCCTAAGCAGTAGCGGAGCAGATTGAAG
1 CAGCAGTGGAATAGGTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAG
* * *
42190339 ATGACAAATCTTATCT
66 ACGGCGAATCTTATCT
42190355 CCCTGAAGTT
Statistics
Matches: 194, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
128 192 0.99
129 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (128 bp):
CAGCAGTGGAATAGGTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAG
ACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
Found at i:42190398 original size:44 final size:44
Alignment explanation
Indices: 42190325--42190428 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
42190315 AAGCAGTAGC
* *
42190325 GGAGCAGATTGAAGATGACAAATCTTATCTCCCTGAAGTTACAGT
1 GGAGCAGATTGAAG-TGACAAATCCTATCTCCCTAAAGTTACAGT
* **
42190370 GGAGCAGATTGAAGTCGA-TAATCCTATCTCCCTAAAGTTGTAGT
1 GGAGCAGATTGAAGT-GACAAATCCTATCTCCCTAAAGTTACAGT
* *
42190414 GGAGCGGATTAAAGT
1 GGAGCAGATTGAAGT
42190429 AATAGATCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 35 0.69
45 16 0.31
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (44 bp):
GGAGCAGATTGAAGTGACAAATCCTATCTCCCTAAAGTTACAGT
Found at i:42190442 original size:44 final size:44
Alignment explanation
Indices: 42190345--42190443 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
42190335 GAAGATGACA
* * *
42190345 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCGAT
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGTCAAT
* ** *
42190389 AATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAGT-AAT
1 AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGTCAAT
42190432 AGATCTTATCTC
1 A-ATCTTATCTC
42190444 TCTGATGTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGTCAAT
Found at i:42190525 original size:44 final size:44
Alignment explanation
Indices: 42190475--42190583 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
42190465 ATCGCATCAG
*
42190475 GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGAA-AA-CAA
1 GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGAC-CA-AAGAAGCAA
* ** *
42190519 GTCTTATC-CCCATGAAGTCACAGTGGGGCAGACCAAAGAAGCAA
1 GTCTTATCTCCC-TGAGGTTGCAGTGGAGCAGACCAAAGAAGCAA
*
42190563 ATCTTATCTCCCTGAGGTTGC
1 GTCTTATCTCCCTGAGGTTGC
42190584 GGTGAAGTAG
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
42 2 0.04
43 6 0.12
44 41 0.79
45 3 0.06
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (44 bp):
GTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCAAAGAAGCAA
Found at i:42194126 original size:52 final size:52
Alignment explanation
Indices: 42194069--42194172 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
42194059 AGATAATGTT
42194069 AGCAGGCCGTTGTTGAAATAAGAGCATGTGTTAAGGTTATGAATGTTGGAAG
1 AGCAGGCCGTTGTTGAAATAAGAGCATGTGTTAAGGTTATGAATGTTGGAAG
*
42194121 AGCAGGCCGTTGTTGAAATAAGAGCATGTGTTAAGGTTATGAGTGTTGGAAG
1 AGCAGGCCGTTGTTGAAATAAGAGCATGTGTTAAGGTTATGAATGTTGGAAG
42194173 TCGTTTCTAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.08, G:0.34, T:0.29
Consensus pattern (52 bp):
AGCAGGCCGTTGTTGAAATAAGAGCATGTGTTAAGGTTATGAATGTTGGAAG
Found at i:42197026 original size:27 final size:27
Alignment explanation
Indices: 42196907--42197027 Score: 111
Period size: 27 Copynumber: 4.5 Consensus size: 27
42196897 TAGTCCTTTA
* * *
42196907 GGACATTAAACGC-GAGGTAGTCTACTG
1 GGACATTAAACACGGA-GTAGTCCACCG
*
42196934 GGACATTAAACGA-GGAGTAGTCTACCG
1 GGACATTAAAC-ACGGAGTAGTCCACCG
* *
42196961 GGACAATAAACACGGAATAGTCCACCG
1 GGACATTAAACACGGAGTAGTCCACCG
* * * *
42196988 GGATAATAAACACGGGGTAGTCCATCG
1 GGACATTAAACACGGAGTAGTCCACCG
*
42197015 AGACATTAAACAC
1 GGACATTAAACAC
42197028 AAACATTAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.01
27 76 0.96
28 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (27 bp):
GGACATTAAACACGGAGTAGTCCACCG
Done.