Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 123 of 216
Found at i:39064352 original size:23 final size:26
Alignment explanation
Indices: 39064324--39064379 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 26
39064314 AAAGTTATTC
*
39064324 AAAAAATTATAT-AAATTAGAAA-A-
1 AAAAAATTATATAAAATTAAAAATAT
39064347 AAAAAATTATATAAAATTAAAAATAT
1 AAAAAATTATATAAAATTAAAAATAT
39064373 AAAAAAT
1 AAAAAAT
39064380 CTTTACAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 12 0.41
24 9 0.31
25 1 0.03
26 7 0.24
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (26 bp):
AAAAAATTATATAAAATTAAAAATAT
Found at i:39064739 original size:48 final size:44
Alignment explanation
Indices: 39064653--39064767 Score: 124
Period size: 47 Copynumber: 2.5 Consensus size: 44
39064643 TCTTAATTTA
* * *
39064653 TTTTTATAATTTTTATGCTTCTTATAATATTTTTAAAATTTATTAAT
1 TTTTTACAATTTTTAT-ATT-TTATAATATTTTTAAAATTCA-TAAT
*
39064700 TTTATTAATAATTTTATATATTTTAT-ATATTTTTAAAAATTCATAAT
1 TTT-TT-ACAATTTT-TATATTTTATAATATTTTT-AAAATTCATAAT
39064747 TTTTTACAATTTTTATATTTT
1 TTTTTACAATTTTTATATTTT
39064768 TCCTAATTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
44 8 0.13
45 7 0.11
46 2 0.03
47 18 0.30
48 13 0.21
49 10 0.16
50 3 0.05
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (44 bp):
TTTTTACAATTTTTATATTTTATAATATTTTTAAAATTCATAAT
Found at i:39064785 original size:18 final size:17
Alignment explanation
Indices: 39064711--39064847 Score: 66
Period size: 18 Copynumber: 8.0 Consensus size: 17
39064701 TTATTAATAA
* *
39064711 TTTTATATATTTTATAT
1 TTTTTTATAATTTATAT
* * * *
39064728 ATTTTTAAAAATTCATAA
1 -TTTTTTATAATTTATAT
* *
39064746 TTTTTTACAATTTTTAT
1 TTTTTTATAATTTATAT
**
39064763 ATTTTTCCTAATTTATA-
1 -TTTTTTATAATTTATAT
*
39064780 TTTTTTATAAATTATAT
1 TTTTTTATAATTTATAT
*
39064797 TTTTTTAT-TTTTA-AT
1 TTTTTTATAATTTATAT
**
39064812 GTTTTTTGGAACTATT-TAT
1 -TTTTTTATAA-T-TTATAT
*
39064831 TTTTTTACAATTTATAT
1 TTTTTTATAATTTATAT
39064848 AATTTCTTGT
Statistics
Matches: 86, Mismatches: 25, Indels: 17
0.67 0.20 0.13
Matches are distributed among these distances:
15 2 0.02
16 24 0.28
17 24 0.28
18 32 0.37
19 4 0.05
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTTTATAATTTATAT
Found at i:39064801 original size:16 final size:16
Alignment explanation
Indices: 39064722--39064801 Score: 61
Period size: 16 Copynumber: 4.7 Consensus size: 16
39064712 TTTATATATT
*
39064722 TTATATATTTTTAAAAA
1 TTATAT-TTTTTATAAA
* *
39064739 TTCATAATTTTTTACAATTT
1 TT-AT-ATTTTTTATAA--A
** *
39064759 TTATATTTTTCCTAAT
1 TTATATTTTTTATAAA
39064775 TTATATTTTTTATAAA
1 TTATATTTTTTATAAA
39064791 TTATATTTTTT
1 TTATATTTTTT
39064802 TATTTTTAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
16 25 0.49
17 2 0.04
18 18 0.35
19 4 0.08
20 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATTTTTTATAAA
Found at i:39067333 original size:109 final size:108
Alignment explanation
Indices: 39067185--39067399 Score: 279
Period size: 109 Copynumber: 2.0 Consensus size: 108
39067175 AGTAATAAAC
* * * *
39067185 TCAACTTCACATGTCGGTGAATTCATCAAGTTCGTCTCAATAGGACCACTCAAATCCTAGGATAT
1 TCAACCTCACATGTCAGTGAATACATCAAGTTCGTCTCAATAGGACCACCCAAATCCTAGGATAT
39067250 GAATTCATTAAAAGTGAGAACTCAACCTTATGCATGTACATCAT
66 GAATTCATTAAAAGTGAGAACTCAACCTTATGC-TGTACATCAT
* * * * *
39067294 TCAACCTCACTTGTCAGTGAATACATCAAG-TCTGTCTCAATTGGACCACCCAAATCTTGGGGTA
1 TCAACCTCACATGTCAGTGAATACATCAAGTTC-GTCTCAATAGGACCACCCAAATCCTAGGATA
* * * * *
39067358 TTATTTTATTAAGAGTGAGAACTCAACCTTATGCTTTACATC
65 TGAATTCATTAAAAGTGAGAACTCAACCTTATGCTGTACATC
39067400 GTTTTCCATA
Statistics
Matches: 91, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
108 9 0.10
109 82 0.90
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (108 bp):
TCAACCTCACATGTCAGTGAATACATCAAGTTCGTCTCAATAGGACCACCCAAATCCTAGGATAT
GAATTCATTAAAAGTGAGAACTCAACCTTATGCTGTACATCAT
Found at i:39072460 original size:17 final size:17
Alignment explanation
Indices: 39072438--39072477 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
39072428 GTTATACAAA
39072438 CTTACTAAGATTAATTG
1 CTTACTAAGATTAATTG
** *
39072455 CTTACTCTGTTTAATTG
1 CTTACTAAGATTAATTG
39072472 CTTACT
1 CTTACT
39072478 CTCATTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (17 bp):
CTTACTAAGATTAATTG
Found at i:39072991 original size:55 final size:55
Alignment explanation
Indices: 39072907--39073033 Score: 182
Period size: 55 Copynumber: 2.3 Consensus size: 55
39072897 CTAATGGAAG
* * *** *
39072907 CAAGTCATTGAGTTACATGGGCTAGTCACATTGGCGTGTGGCTGGCCATGTGACC
1 CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGCTGACCATGTGACC
* *
39072962 CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGTTGACCGTGTGACC
1 CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGCTGACCATGTGACC
39073017 CAAGTCAGTGAGTTACA
1 CAAGTCAGTGAGTTACA
39073034 TGGCCTAAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (55 bp):
CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGCTGACCATGTGACC
Found at i:39073062 original size:55 final size:54
Alignment explanation
Indices: 39072907--39073069 Score: 177
Period size: 55 Copynumber: 3.0 Consensus size: 54
39072897 CTAATGGAAG
* * * *
39072907 CAAGTCATTGAGTTACATGGGCTAGTCACATTGGCGTGTGGC-TGGCCATGTGACC
1 CAAGTCAGTGAGTTACATGGGCTAG-CACATAGGCGTGT-GCTTGACCGTGTGACC
* * * *
39072962 CAAGTCAGTGAGTTACACGGGCTAGTCACACAAGCGTGTGGTTGACCGTGTGACC
1 CAAGTCAGTGAGTTACATGGGCTAG-CACATAGGCGTGTGCTTGACCGTGTGACC
* *
39073017 CAAGTCAGTGAGTTACATGGCCTAAG-ACATAGGCGTGTCTCTTGACCGTGTGA
1 CAAGTCAGTGAGTTACATGGGCT-AGCACATAGGCGTGT-GCTTGACCGTGTGA
39073070 GACACACGGC
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
54 11 0.12
55 78 0.86
56 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACATGGGCTAGCACATAGGCGTGTGCTTGACCGTGTGACC
Found at i:39075153 original size:16 final size:16
Alignment explanation
Indices: 39075132--39075162 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39075122 AAGCCTATAC
39075132 ATATACATCAAACAAT
1 ATATACATCAAACAAT
39075148 ATATACATCAAACAA
1 ATATACATCAAACAA
39075163 GTTAGCCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (16 bp):
ATATACATCAAACAAT
Found at i:39082729 original size:370 final size:370
Alignment explanation
Indices: 39082011--39082753 Score: 1012
Period size: 370 Copynumber: 2.0 Consensus size: 370
39082001 TTAAGCAAGC
* * *
39082011 ATCCTGCTCATGGAATCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGAACAAAATGTAG
1 ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGAACAAAATATAG
* * * **
39082076 ATGAACATTGTGTTTACAAATATTTAGGGGATCAAAAGGTGGTCTTTCTTGTTCTATATGTCGAT
66 ATGAACATTGTGTTTACAAACATTTAGGAGATCAAAAGGTGATCTTTCTCATTCTATATGTCGAT
* * ** *
39082141 GACATTCAACTCATTAGAAATTATGTAGGGACATTGTCATCAGTTAAACTGTGGTTAACCCAACA
131 GACATTCAACTCATTAGAAATTATGTAGAGACATTGTCATCAGTTAAACTATGACTAACCCAAAA
* * ** ** * * * *
39082206 GTTTAGCATGAAGGACTCGAGAGAATTTAATTTTTTTCTAGGTATTCGAATCTTAATGGATCGAA
196 ATTTAGCATGAAGGACTCGAGAAAAGCTAATTTCATTCTAGGTATTCAAAACCTAAGGGATCGAA
* *
39082271 AGAACAAAGTGATAGCACTGTCTCATGCTTCATAAATAGATAAGATATTGGAACATTATACAATG
261 AGAACAAAGTGATAGCACTGTCTCAGGCTTCATAAATAGATAAGATATTGGAACATTATACAATA
* *
39082336 ACTGATTCAATAAAGGGAAATCAACC-TTCTGTATCGGGATTTCAT
326 ACTGATTCAATAAAGGAAAATCAACCTTTC-GTATCGAGATTTCAT
*
39082381 ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGACTTTTGGATTTGAGA-AAAATATA
1 ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGA-ACAAAATATA
*
39082445 GATGAACCTTGTGTTTACAAACATTTAGGAGAT-AGAAAGGTGATCTTTCTCATTCTATATGTCG
65 GATGAACATTGTGTTTACAAACATTTAGGAGATCA-AAAGGTGATCTTTCTCATTCTATATGTCG
* * **
39082509 ATGACATTCTACTCATT-GAAAATGT-TGTAGAGACATTGTTATTGGTTAAACTATGACTAACCC
129 ATGACATTCAACTCATTAG-AAAT-TATGTAGAGACATTGTCATCAGTTAAACTATGACTAACCC
* * *
39082572 AAAAATTTAGCATGAATGACTTGGGAAAAGCTAATTTCATTCTAGGTATTCAAAACCTAAGGGAT
192 AAAAATTTAGCATGAAGGACTCGAGAAAAGCTAATTTCATTCTAGGTATTCAAAACCTAAGGGAT
* * * *
39082637 CGAAAGAACAAAGTGATAGCACTGTCTCAGGCTTCATACATAGATAAGATATTGGAGCGTTATGC
257 CGAAAGAACAAAGTGATAGCACTGTCTCAGGCTTCATAAATAGATAAGATATTGGAACATTATAC
* *
39082702 AATAATTGATTCGAA-AAAGGAAAATCAACCTTTCGTATCGAGATTTCGT
322 AATAACTGATTC-AATAAAGGAAAATCAACCTTTCGTATCGAGATTTCAT
39082751 ATC
1 ATC
39082754 TCTTTATAGG
Statistics
Matches: 325, Mismatches: 42, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
369 2 0.01
370 316 0.97
371 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (370 bp):
ATCCCGCTCATGGAACCAAAGATTTGATCAAGCAATCAAGAATTTTGGATTTGAACAAAATATAG
ATGAACATTGTGTTTACAAACATTTAGGAGATCAAAAGGTGATCTTTCTCATTCTATATGTCGAT
GACATTCAACTCATTAGAAATTATGTAGAGACATTGTCATCAGTTAAACTATGACTAACCCAAAA
ATTTAGCATGAAGGACTCGAGAAAAGCTAATTTCATTCTAGGTATTCAAAACCTAAGGGATCGAA
AGAACAAAGTGATAGCACTGTCTCAGGCTTCATAAATAGATAAGATATTGGAACATTATACAATA
ACTGATTCAATAAAGGAAAATCAACCTTTCGTATCGAGATTTCAT
Found at i:39083416 original size:25 final size:25
Alignment explanation
Indices: 39083360--39083420 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
39083350 ACATATTTTT
*
39083360 TCAAAATTTTACAAGGGAAAAATCA
1 TCAAAATTTTACAAGGCAAAAATCA
* *
39083385 TCAAAATTTTACAAGAGCTAAAATCG
1 TCAAAATTTTACAAG-GCAAAAATCA
*
39083411 TCAAATTTTT
1 TCAAAATTTT
39083421 GTTAAGGGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTACAAGGCAAAAATCA
Found at i:39084748 original size:26 final size:27
Alignment explanation
Indices: 39084710--39084778 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
39084700 CTCTGACCAG
* * * *
39084710 CTCATACTAAAGGGTCTTCGAACCCA-
1 CTCAAACTCAAGGGTCATCCAACCCAT
*
39084736 CTCAAACTCAAGGGACATCCAACCCAT
1 CTCAAACTCAAGGGTCATCCAACCCAT
*
39084763 TTCAAACTCAAGGGTC
1 CTCAAACTCAAGGGTC
39084779 CTTGAGCCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 21 0.60
27 14 0.40
ACGTcount: A:0.33, C:0.32, G:0.14, T:0.20
Consensus pattern (27 bp):
CTCAAACTCAAGGGTCATCCAACCCAT
Found at i:39086611 original size:27 final size:26
Alignment explanation
Indices: 39086581--39086670 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 26
39086571 AGGAATAACA
*
39086581 GTCATTTTACCCTATAGGGGTATCTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
*
39086608 GTCATTTTACCATATGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
* *
39086635 GTCATTTTATCCTATGAAGGTATTTCG
1 GTCATTTTACCCTATG-GGGTATTTCG
39086662 GTCATTTTA
1 GTCATTTTA
39086671 TTTATTTTAG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 1 0.02
27 55 0.98
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGTATTTCG
Found at i:39089022 original size:30 final size:31
Alignment explanation
Indices: 39088988--39089056 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
39088978 AACTTTTAAC
39088988 TCAGTCACTCAA-ATT-TTAAAAAATAACAAA
1 TCAGTCACT-AACATTATTAAAAAATAACAAA
* * *
39089018 TCAGTCACTAACATTATTGAAAAGTGACAAA
1 TCAGTCACTAACATTATTAAAAAATAACAAA
39089049 TCAGTCAC
1 TCAGTCAC
39089057 CCACTAACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 12 0.35
31 20 0.59
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (31 bp):
TCAGTCACTAACATTATTAAAAAATAACAAA
Found at i:39090573 original size:23 final size:23
Alignment explanation
Indices: 39090547--39090623 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
39090537 CCTTCAATTA
39090547 TTTTTCGATTTGGAATTAGGGTG
1 TTTTTCGATTTGGAATTAGGGTG
* *
39090570 TTTTTCGATTAT--AATCTTAGTTTGAG
1 TTTTTCGATT-TGGAA--TTAG--GGTG
*
39090596 TTTTTTGATTTGGAATTAGGGTG
1 TTTTTCGATTTGGAATTAGGGTG
39090619 TTTTT
1 TTTTT
39090624 AGTGTTGTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 2 0.05
23 17 0.40
24 5 0.12
25 5 0.12
26 11 0.26
27 2 0.05
ACGTcount: A:0.18, C:0.04, G:0.23, T:0.55
Consensus pattern (23 bp):
TTTTTCGATTTGGAATTAGGGTG
Found at i:39092329 original size:41 final size:41
Alignment explanation
Indices: 39092247--39092330 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 41
39092237 AGTCATAACA
* *
39092247 TATTTTAGATATTTTCTGATATAATAAAATATCATATTTTG
1 TATTTTAGATATTTTCTGATATAATAAAATATAATAATTTG
* * *
39092288 TATTTTAGATATTTTCTGAT-TTATCATATATAATAAATTTG
1 TATTTTAGATATTTTCTGATATAATAAAATATAAT-AATTTG
39092329 TA
1 TA
39092331 AAGGTTTCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 10 0.27
41 27 0.73
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (41 bp):
TATTTTAGATATTTTCTGATATAATAAAATATAATAATTTG
Found at i:39096454 original size:44 final size:44
Alignment explanation
Indices: 39096406--39096546 Score: 153
Period size: 44 Copynumber: 3.1 Consensus size: 44
39096396 AATATTAATT
39096406 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
* * * * * *
39096450 ATTTTATGAAAT-TATATA-TCATTAGTAA-ATTATATTTAATATTAATA
1 ATTTTA--AATTGTATAAATTCA-TA-TAAGA--AAATTTATTATCAAGA
39096497 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
39096541 ATTTTA
1 ATTTTA
39096547 TGAAATTATA
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
44 27 0.36
45 14 0.18
46 14 0.18
47 21 0.28
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (44 bp):
ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
Found at i:39096487 original size:47 final size:45
Alignment explanation
Indices: 39096335--39096564 Score: 170
Period size: 47 Copynumber: 5.0 Consensus size: 45
39096325 AGTAAATTCA
*
39096335 TATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCAT
1 TATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATCAT
* * ** * *
39096381 TATTAA-ATTATATTTAATATTAATTATTTTA--AATTGTATAAATTCA-
1 TA-TAAGA--AAATTTATTATTAAGAATTTTATGAAAT-TATATA-TCAT
*
39096427 TATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCAT
1 TATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCAT
* * * * *
39096472 TAGTAA-ATTATATTTAATATTAATAATTTTA--AATTGTATAAATTCA-
1 TA-TAAGA--AAATTTATTATTAAGAATTTTATGAAAT-TATATA-TCAT
* *
39096518 TATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTAT
1 TATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCAT
39096563 TA
1 TA
39096565 AATTATATGT
Statistics
Matches: 139, Mismatches: 27, Indels: 37
0.68 0.13 0.18
Matches are distributed among these distances:
44 40 0.29
45 27 0.19
46 28 0.20
47 43 0.31
48 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (45 bp):
TATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCAT
Found at i:39096568 original size:25 final size:24
Alignment explanation
Indices: 39096540--39096597 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
39096530 TATTATCAAG
* *
39096540 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
39096565 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
39096591 AATTATA
1 AATTATA
39096598 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:39096637 original size:91 final size:91
Alignment explanation
Indices: 39096327--39096618 Score: 482
Period size: 91 Copynumber: 3.2 Consensus size: 91
39096317 TGGATTTTAG
* *
39096327 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
39096392 ATTTAATATTAATTATTTTAAATTGTA
65 ATTTAATATTAATTATTTTAAATTGTA
*
39096419 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTAGTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
39096484 TTTAATATTAATAATTTTAAATTGTA
66 TTTAATATTAATTATTTTAAATTGTA
39096510 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAA-T-TATAT-ATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* * *
39096572 TGTAATAATAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTGTA
*
39096598 CAAATTCATATAAGAAAATTT
1 TAAATTCATATAAGAAAATTT
39096619 GTTAGTTATA
Statistics
Matches: 190, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
88 55 0.29
89 5 0.03
90 1 0.01
91 113 0.59
92 16 0.08
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTGTA
Found at i:39096762 original size:120 final size:120
Alignment explanation
Indices: 39096638--39097049 Score: 772
Period size: 120 Copynumber: 3.4 Consensus size: 120
39096628 AATTATTTTA
*
39096638 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
39096703 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
39096758 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
39096823 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
39096878 AATTTTATTAAATTATATATTTTAATT-AAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
39096942 ATAGTATCATATATTATGATTCGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
39096997 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
39097050 TAAATATAAT
Statistics
Matches: 286, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
119 116 0.41
120 170 0.59
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:39096787 original size:18 final size:17
Alignment explanation
Indices: 39096759--39096793 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39096749 ATTATTAAGA
*
39096759 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39096776 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39096794 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39096836 original size:43 final size:42
Alignment explanation
Indices: 39096768--39096956 Score: 103
Period size: 43 Copynumber: 4.6 Consensus size: 42
39096758 AATTTTATTA
* **
39096768 AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATT-TATATTTTAAGTATCATATATTTAATAATAATTATGTT
* *
39096811 AATTTATATTTTATAGTATCATATA-TT-ATGAT--TTGA-GTA
1 AATTTATATTTTA-AGTATCATATATTTAATAATAATT-ATGTT
* * * * * * *
39096850 AATTCATA---TAAGAAT-AT-TAATTATTAAGAATTTTATT
1 AATTTATATTTTAAGTATCATATATTTAATAATAATTATGTT
* *
39096887 AAATTATATATTTTAATTA-AATATATTTAATAATAATTATGTT
1 -AATT-TATATTTTAAGTATCATATATTTAATAATAATTATGTT
* *
39096930 AAATTATCTTTTATAGTATCATATATT
1 AATTTATATTTTA-AGTATCATATATT
39096957 ATGATTCGAG
Statistics
Matches: 105, Mismatches: 25, Indels: 32
0.65 0.15 0.20
Matches are distributed among these distances:
33 2 0.02
34 4 0.04
35 6 0.06
36 2 0.02
37 3 0.03
38 4 0.04
39 14 0.13
40 1 0.01
41 12 0.11
42 23 0.22
43 34 0.32
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (42 bp):
AATTTATATTTTAAGTATCATATATTTAATAATAATTATGTT
Found at i:39096899 original size:17 final size:17
Alignment explanation
Indices: 39096879--39096912 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
39096869 ATTATTAAGA
39096879 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-TATAT
39096896 ATTTTAATTAAATATAT
1 ATTTTAATTAAATATAT
39096913 TTAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATTAAATATAT
Found at i:39097032 original size:16 final size:16
Alignment explanation
Indices: 39097011--39097059 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
39097001 TTATTAAATT
39097011 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
39097027 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
39097042 AT-TATGTTTAAATATA
1 ATATAT-TTTAATTATA
39097058 AT
1 AT
39097060 TAAATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
16 15 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:39097278 original size:45 final size:44
Alignment explanation
Indices: 39097197--39097287 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 44
39097187 ACCTCTATTT
*
39097197 CATTCAACCAAACACAATATTACTATTACGCTTCTATTCCATTA
1 CATTCAACCAAACACAATATTACTATTACGCCTCTATTCCATTA
* * *
39097241 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCTATTA
1 CATTCAACCAAACACAAT-A-TTACTATTACGCCTCTATTCCATTA
39097286 CA
1 CA
39097288 CATTTATTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
43 2 0.05
44 15 0.37
45 24 0.59
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.35
Consensus pattern (44 bp):
CATTCAACCAAACACAATATTACTATTACGCCTCTATTCCATTA
Found at i:39097285 original size:16 final size:16
Alignment explanation
Indices: 39097264--39097328 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
39097254 AATTGATTTG
39097264 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
* * *
39097280 CTATTACACATTTATT
1 CTATTACGCCTCTATT
39097296 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
39097312 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
39097328 C
1 C
39097329 CAATACAGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.22, C:0.29, G:0.05, T:0.45
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:39101295 original size:6 final size:6
Alignment explanation
Indices: 39101284--39101317 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
39101274 AAATATTCAT
39101284 TGTTAA TGTTAA TGTTAA TGTTAA TGTTAA TGTT
1 TGTTAA TGTTAA TGTTAA TGTTAA TGTTAA TGTT
39101318 CTATTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (6 bp):
TGTTAA
Found at i:39101497 original size:91 final size:91
Alignment explanation
Indices: 39101342--39101548 Score: 369
Period size: 91 Copynumber: 2.3 Consensus size: 91
39101332 GTTAAGATTC
39101342 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
** *
39101407 TTTAATATTAATTATTTTAAATTATA
66 TGAAATAATAATTATTTTAAATTATA
*
39101433 TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
39101498 TGAAATAATAATTATTTTAAATTATA
66 TGAAATAATAATTATTTTAAATTATA
*
39101524 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
39101549 GTTATAATTA
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 110 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGAAATAATAATTATTTTAAATTATA
Found at i:39101515 original size:47 final size:46
Alignment explanation
Indices: 39101373--39101516 Score: 127
Period size: 47 Copynumber: 3.1 Consensus size: 46
39101363 ATTATCAAGA
*
39101373 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATCATTATTAAATTATA-TTAATAATAATT
* * * * * **
39101420 A-TTT-T-AAATTATATA-AATTCA-TATAATAAAATTTATTATCAAGA
1 ATTTTATGAAATTATATATCATT-ATTA-AATTATATTAATAAT-AATT
*
39101464 ATTTTATGAAATTATATATCATTATTAAATTATATGAAATAATAATT
1 ATTTTATGAAATTATATATCATTATTAAATTATAT-TAATAATAATT
39101511 ATTTTA
1 ATTTTA
39101517 AATTATACAA
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
43 10 0.14
44 19 0.26
45 4 0.06
46 4 0.06
47 26 0.36
48 9 0.12
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (46 bp):
ATTTTATGAAATTATATATCATTATTAAATTATATTAATAATAATT
Found at i:39101517 original size:26 final size:28
Alignment explanation
Indices: 39101463--39101523 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
39101453 TATTATCAAG
* *
39101463 AATTTTATGAAATTATATATCATTATTA
1 AATTATATGAAATAATATATCATTATTA
*
39101491 AATTATATGAAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATCATTATTA
39101517 AATTATA
1 AATTATA
39101524 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 5 0.17
28 15 0.50
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
AATTATATGAAATAATATATCATTATTA
Found at i:39101674 original size:117 final size:118
Alignment explanation
Indices: 39101553--39101858 Score: 422
Period size: 117 Copynumber: 2.6 Consensus size: 118
39101543 TTATTAGTTA
* * *
39101553 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTC
1 TAATTA-TTTAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-
* * *
39101617 AAATTATATTTTATAG-ATCATATATTATGATTTTAGTAAATTC-ATAAGACTAT
64 AAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAATAAAAATAT
*
39101670 TAATTA-CTAAGGATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TAATTATTTAA--ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
39101734 AAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATAT
64 AAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCA-ATAAAAATAT
* * * *
39101790 TGATTATTAAGAATTTTATTAAATTATATATTTCAATTATATTATATTTAATAATAATTATGTTT
1 TAATTATTTA-AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TT
39101855 AAAT
64 AAAT
39101859 ATGATTAAAT
Statistics
Matches: 168, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
115 3 0.02
117 68 0.40
118 28 0.17
120 61 0.36
121 7 0.04
122 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (118 bp):
TAATTATTTAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAA
ATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAATAAAAATAT
Found at i:39101716 original size:16 final size:16
Alignment explanation
Indices: 39101695--39101741 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
39101685 TTATTAAATT
39101695 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
39101711 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
39101726 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
39101742 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:39101836 original size:120 final size:117
Alignment explanation
Indices: 39101564--39101858 Score: 439
Period size: 120 Copynumber: 2.5 Consensus size: 117
39101554 AATTATTTTA
* * *
39101564 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
* * *
39101628 TATAGATCATATATTATGATTTTAGTAAATTCATAAGACTATTAATTACTAAG
65 TATAGATCATATATTATGATTTGAGTAAATTCATAAAAATATTAATTACTAAG
*
39101681 GATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
39101746 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTGATTATTAAG
66 ATAG-ATCATATATTATGATTTGAGTAAATTC--ATAAAAATATTAATTACTAAG
* *
39101801 AATTTTATTAAATTATATATTTCAATTATATTATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
39101859 ATGATTAAAT
Statistics
Matches: 161, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
117 62 0.39
118 28 0.17
120 65 0.40
121 6 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (117 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGATCATATATTATGATTTGAGTAAATTCATAAAAATATTAATTACTAAG
Found at i:39103707 original size:20 final size:20
Alignment explanation
Indices: 39103682--39103722 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
39103672 TATTATAACT
*
39103682 TTTTTTTATTTATCAAAATA
1 TTTTTTTATTTACCAAAATA
39103702 TTTTTTTATTTACCAAAATA
1 TTTTTTTATTTACCAAAATA
39103722 T
1 T
39103723 ATCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTTATTTACCAAAATA
Found at i:39103838 original size:27 final size:27
Alignment explanation
Indices: 39103781--39103851 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
39103771 ACGCCAATGG
* *
39103781 CATTGGCGGTACCAAAGGTGCCAAAGC
1 CATTGGCGGCACCAATGGTGCCAAAGC
* *
39103808 CATTGACGGCACCAATGGTGCCAATA-T
1 CATTGGCGGCACCAATGGTGCCAA-AGC
*
39103835 CATTGGCAGCACCAATG
1 CATTGGCGGCACCAATG
39103852 TATAATAGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAGC
Found at i:39103973 original size:16 final size:15
Alignment explanation
Indices: 39103951--39104051 Score: 71
Period size: 16 Copynumber: 6.5 Consensus size: 15
39103941 GAGAAAAAAC
39103951 AAAGAAAGAAGAAGA
1 AAAGAAAGAAGAAGA
**
39103966 AAAGGAAAGGGGAAG-
1 AAA-GAAAGAAGAAGA
39103981 AAA-AAAGAAGGAAAGA
1 AAAGAAAGAA-G-AAGA
*
39103997 AAAGGAAAGGAGAAGA
1 AAA-GAAAGAAGAAGA
* *
39104013 GAAAAAAAAAAGAAGA
1 -AAAGAAAGAAGAAGA
* *
39104029 AGAAGAAAAAAAAAGA
1 A-AAGAAAGAAGAAGA
39104045 AAAGAAA
1 AAAGAAA
39104052 AAGGTAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
13 4 0.06
14 1 0.01
15 16 0.24
16 38 0.56
17 4 0.06
18 5 0.07
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAAGA
Found at i:39103981 original size:26 final size:26
Alignment explanation
Indices: 39103952--39104052 Score: 78
Period size: 26 Copynumber: 3.8 Consensus size: 26
39103942 AGAAAAAACA
* *
39103952 AAGAAAGAAGAAGAAAAGGAAAGGGG
1 AAGAAAAAAGAAGAAAAGAAAAGGGG
* *
39103978 AAGAAAAAAGAAGGAAAGAAAA-GGA
1 AAGAAAAAAGAAGAAAAGAAAAGGGG
* * * * **
39104003 AAGGAGAAGAGAAAAAAAAAAGAAGAAG
1 AA-GAAAAAAGAAGAAAAGAA-AAGGGG
*
39104031 AAGAAAAAAAAAGAAAAGAAAA
1 AAGAAAAAAGAAGAAAAGAAAA
39104053 AGGTAATTTT
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
25 4 0.07
26 34 0.62
27 15 0.27
28 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAGAAGAAAAGAAAAGGGG
Found at i:39104000 original size:31 final size:30
Alignment explanation
Indices: 39103955--39104026 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
39103945 AAAAACAAAG
*
39103955 AAAGAAGAAGAAAAGGAAAGGGGAAGA-AA
1 AAAGAAGAAGAAAAGGAAAGGAGAAGAGAA
39103984 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAA
1 AAAGAA-G-AAGAAAAGGAAAGGAGAAGAGAA
*
39104016 AAA-AAAAAGAA
1 AAAGAAGAAGAA
39104027 GAAGAAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 11 0.29
30 1 0.03
31 21 0.55
32 5 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (30 bp):
AAAGAAGAAGAAAAGGAAAGGAGAAGAGAA
Found at i:39104024 original size:19 final size:20
Alignment explanation
Indices: 39103981--39104050 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 20
39103971 AAAGGGGAAG
*
39103981 AAAAAAGAAGGA-AAG-AAA
1 AAAAAAGAAGAAGAAGAAAA
** *
39103999 AGGAAAGGAGAAG-AGAAAA
1 AAAAAAGAAGAAGAAGAAAA
39104018 AAAAAAGAAGAAGAAG-AAA
1 AAAAAAGAAGAAGAAGAAAA
39104037 AAAAAAGAA-AAGAA
1 AAAAAAGAAGAAGAA
39104051 AAAGGTAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 15 0.36
19 25 0.60
20 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAGAAGAAGAAAA
Found at i:39109816 original size:18 final size:18
Alignment explanation
Indices: 39109795--39109837 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
39109785 CCCAATGATT
*
39109795 GCCACCATCTTCTTCTTC
1 GCCACCACCTTCTTCTTC
39109813 GCCACCACCTTCTTCTTC
1 GCCACCACCTTCTTCTTC
*
39109831 ACCACCA
1 GCCACCA
39109838 ACCATATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.49, G:0.05, T:0.30
Consensus pattern (18 bp):
GCCACCACCTTCTTCTTC
Found at i:39110860 original size:21 final size:20
Alignment explanation
Indices: 39110836--39110874 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39110826 AAAAATACCT
*
39110836 TCTTTTTTTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
39110857 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
39110875 CGCAACACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:39111003 original size:27 final size:27
Alignment explanation
Indices: 39110963--39111022 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
39110953 GAGTAATGTT
*
39110963 GCCAATGCCTTTGGCACCATTGGTGCC
1 GCCAATGCCATTGGCACCATTGGTGCC
* *
39110990 GCCAATGGCATTGGCACCTTTGGTGCC
1 GCCAATGCCATTGGCACCATTGGTGCC
39111017 GCCAAT
1 GCCAAT
39111023 CGTTTTGGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.25
Consensus pattern (27 bp):
GCCAATGCCATTGGCACCATTGGTGCC
Found at i:39111030 original size:27 final size:27
Alignment explanation
Indices: 39110963--39111033 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
39110953 GAGTAATGTT
39110963 GCCAAT-GCCTTTGGCACCATTGGTGCC
1 GCCAATCG-CTTTGGCACCATTGGTGCC
* * *
39110990 GCCAATGGCATTGGCACCTTTGGTGCC
1 GCCAATCGCTTTGGCACCATTGGTGCC
*
39111017 GCCAATCGTTTTGGCAC
1 GCCAATCGCTTTGGCAC
39111034 GGTGCAGACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.15, C:0.31, G:0.27, T:0.27
Consensus pattern (27 bp):
GCCAATCGCTTTGGCACCATTGGTGCC
Found at i:39111197 original size:22 final size:22
Alignment explanation
Indices: 39111172--39111214 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39111162 ATTTCTATGG
*
39111172 TTTTGTTTTTCTATTCTTTCAA
1 TTTTCTTTTTCTATTCTTTCAA
* *
39111194 TTTTCTTTTTTTTTTCTTTCA
1 TTTTCTTTTTCTATTCTTTCA
39111215 TTTCATTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTTTTTCTATTCTTTCAA
Found at i:39112326 original size:3 final size:3
Alignment explanation
Indices: 39112320--39112354 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39112310 ATTATTATTA
39112320 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
39112355 TTCTTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:39113356 original size:12 final size:12
Alignment explanation
Indices: 39113339--39113363 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39113329 GGTGTTCATT
39113339 CGGTTAACCGAC
1 CGGTTAACCGAC
39113351 CGGTTAACCGAC
1 CGGTTAACCGAC
39113363 C
1 C
39113364 CGAAATAACA
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:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:39113544 original size:9 final size:9
Alignment explanation
Indices: 39113526--39113583 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
39113516 TTTGGTTAAA
39113526 AATTAACCG
1 AATTAACCG
*
39113535 AATTACCCG
1 AATTAACCG
39113544 AATTAACCG
1 AATTAACCG
*
39113553 AATTACCCG
1 AATTAACCG
*
39113562 AATTAACCA
1 AATTAACCG
*
39113571 AATTAACCA
1 AATTAACCG
39113580 AATT
1 AATT
39113584 GAATCACTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:39113549 original size:18 final size:18
Alignment explanation
Indices: 39113526--39113575 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
39113516 TTTGGTTAAA
39113526 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
39113544 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
39113562 AATTAACCAAATTA
1 AATTAACCGAATTA
39113576 ACCAAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:39113713 original size:13 final size:13
Alignment explanation
Indices: 39113695--39113719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39113685 TTATGATTGG
39113695 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
39113708 ATTGGGTTGGGT
1 ATTGGGTTGGGT
39113720 TGGGTTGGGT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:39113717 original size:18 final size:18
Alignment explanation
Indices: 39113690--39113724 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39113680 TAATTTTATG
39113690 ATTGGATTGGGTTGGGTA
1 ATTGGATTGGGTTGGGTA
*
39113708 ATTGGGTTGGGTTGGGT
1 ATTGGATTGGGTTGGGT
39113725 TGGGTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.49, T:0.40
Consensus pattern (18 bp):
ATTGGATTGGGTTGGGTA
Found at i:39115104 original size:41 final size:41
Alignment explanation
Indices: 39115059--39115150 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
39115049 TTATACTATA
39115059 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATT
1 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATT
39115100 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATT
1 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATT
*
39115141 AT-TATTATTA
1 ATGTAATATTA
39115151 TTATTATAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 7 0.14
41 43 0.86
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (41 bp):
ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATT
Found at i:39115135 original size:3 final size:3
Alignment explanation
Indices: 39115127--39115157 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
39115117 CTAACTGTAT
39115127 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
39115158 AGAATCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39117781 original size:1 final size:1
Alignment explanation
Indices: 39117775--39117801 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
39117765 AACTTGGATG
39117775 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
39117802 CTAATTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39119940 original size:13 final size:13
Alignment explanation
Indices: 39119908--39119941 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
39119898 TCTTAATAAT
39119908 AATATTA-TATTA
1 AATATTATTATTA
39119920 AA-ATTATTATTA
1 AATATTATTATTA
39119932 AATATTATTA
1 AATATTATTA
39119942 ATAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATTATTATTA
Found at i:39119951 original size:34 final size:35
Alignment explanation
Indices: 39119907--39119977 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
39119897 TTCTTAATAA
39119907 TAATATTATATTAA-AATTATTATTAAA-TAT-TAT
1 TAATATTATATTAAGAA-TATTATTAAATTATATAT
*
39119940 TAATAATTATATTAAGAATGTTATTAAATTATATAT
1 TAAT-ATTATATTAAGAATATTATTAAATTATATAT
39119976 TA
1 TA
39119978 TTTTATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 4 0.12
34 19 0.58
35 5 0.15
36 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (35 bp):
TAATATTATATTAAGAATATTATTAAATTATATAT
Found at i:39120058 original size:61 final size:57
Alignment explanation
Indices: 39119940--39120076 Score: 157
Period size: 61 Copynumber: 2.3 Consensus size: 57
39119930 TAAATATTAT
* * * *
39119940 TAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTATTTTTAA
1 TAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
* *
39119998 TAATAATTATGTTAAAATATGATTAAATTATTTATTTTTATTTTTATTAAAATATATTTAA
1 TAATAATTATATTAAAATATGATTAAATTA--TA-TATTA-TTTTATTAAAATATATTTAA
* *
39120059 CAATAATTTTATTAAAAT
1 TAATAATTATATTAAAAT
39120077 TTAATAACAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
57 13 0.20
58 14 0.21
59 2 0.03
60 4 0.06
61 33 0.50
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
TAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
Found at i:39120090 original size:25 final size:26
Alignment explanation
Indices: 39120039--39120090 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
39120029 TTATTTTTAT
*
39120039 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATATATAACAATAA
*
39120065 TTTTATTAAAATTTA-ATAACAATAA
1 TTTTATTAAAATATATATAACAATAA
39120090 T
1 T
39120091 CAACTACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTATTAAAATATATATAACAATAA
Found at i:39120996 original size:27 final size:27
Alignment explanation
Indices: 39120957--39121034 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
39120947 TAGTATTGGC
*
39120957 GCCTATCTCAGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
* *
39120984 GCCTATCTGAGAGGCGCCATTAGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
* *
39121011 GTC-ATGTTGAGAGGCGCCAATGGT
1 GCCTAT-CTGAGAGGCGCCAATGGT
39121035 TTGATTTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.05
27 41 0.95
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.24
Consensus pattern (27 bp):
GCCTATCTGAGAGGCGCCAATGGTGGT
Found at i:39125979 original size:16 final size:15
Alignment explanation
Indices: 39125948--39125991 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
39125938 GCAAAATCAA
39125948 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
39125963 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
39125979 ATAAAAATTAAAT
1 AT-AAAATTAAAT
39125992 GAGTCAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:39126165 original size:60 final size:60
Alignment explanation
Indices: 39126101--39126222 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
39126091 ATACTAAACT
* * * * *
39126101 AAACACAACAACTTATAGCTTAATCCTAAATTACAAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACAAACAAATT-AATTATAAAATAATTAC
* *
39126161 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACAAACAAATTAATTATAAAATAATTAC
39126221 AA
1 AA
39126223 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACAAACAAATTAATTATAAAATAATTAC
Found at i:39126241 original size:21 final size:21
Alignment explanation
Indices: 39126210--39126472 Score: 154
Period size: 21 Copynumber: 12.2 Consensus size: 21
39126200 AATTAATTAT
39126210 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
39126232 AAAAAATTACAATATTACAATATATC
1 AAAAAATTACAATATT-C---ATA-C
***
39126258 CCGAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
39126279 --AAAATTACAAAATTACAATATTC
1 AAAAAATTACAATATT-C-ATA--C
39126302 ATACCAAAAAATTACAATATTCATAC
1 A-A--AAAA--TTACAATATTCATAC
39126328 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
39126349 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * *
39126367 TATAAA-TACAA-ATTTAATTAT
1 AAAAAATTACAATA-TTCA-TAC
39126388 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
39126410 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
39126429 --AAAATTATAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
39126448 AAAAAATTAGAATATTCATAC
1 AAAAAATTACAATATTCATAC
39126469 AAAA
1 AAAA
39126473 TACTAACCCA
Statistics
Matches: 194, Mismatches: 21, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
17 3 0.02
18 7 0.04
19 51 0.26
20 12 0.06
21 57 0.29
22 12 0.06
23 13 0.07
24 1 0.01
25 5 0.03
26 16 0.08
28 7 0.04
29 1 0.01
30 9 0.05
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:39126285 original size:19 final size:19
Alignment explanation
Indices: 39126284--39126473 Score: 163
Period size: 19 Copynumber: 9.4 Consensus size: 19
39126274 CATACAAAAT
39126284 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
39126303 TACCAAAAAATTACAATATTCA
1 TA-C--AAAATTACAATATTCA
39126325 TACAAAAAATTACAATATTCA
1 TAC--AAAATTACAATATTCA
* *
39126346 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
*
39126364 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
*
39126387 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
39126407 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
39126426 TACAAAATTATAATATTCA
1 TACAAAATTACAATATTCA
*
39126445 TACAAAAAATTAGAATATTCA
1 TAC--AAAATTACAATATTCA
39126466 TACAAAAT
1 TACAAAAT
39126474 ACTAACCCAA
Statistics
Matches: 145, Mismatches: 10, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
17 3 0.02
18 7 0.05
19 50 0.34
20 13 0.09
21 42 0.29
22 23 0.16
23 5 0.03
25 2 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:39126517 original size:120 final size:122
Alignment explanation
Indices: 39126284--39126508 Score: 348
Period size: 120 Copynumber: 1.8 Consensus size: 122
39126274 CATACAAAAT
39126284 TACAAAATTACAATATTCATACCAAAAAATTACAATATTCATACAAAAAATTACAATATTCATAC
1 TACAAAATTACAATATTCATACC-AAAAATTACAATATTCATACAAAAAATTACAATATTCATAC
* * *
39126349 AAAATACTAATCCAAAACTATAAATACAAATTTAATTATAAAATAATTACAATATTCA
65 AAAATACTAATCCAAAACTATAAACACAAATATAATAATAAAATAATTACAATATTCA
* *
39126407 TACAAAATTACAATATTCATA-C-AAAATTATAATATTCATACAAAAAATTAGAATATTCATACA
1 TACAAAATTACAATATTCATACCAAAAATTACAATATTCATACAAAAAATTACAATATTCATACA
*
39126470 AAATACTAA-CCCAAACTATAAACACTAAATATAGATAAT
66 AAATACTAATCCAAAACTATAAACAC-AAATATA-ATAAT
39126509 TTATAATTAA
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
119 14 0.15
120 54 0.57
121 4 0.04
122 1 0.01
123 21 0.22
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (122 bp):
TACAAAATTACAATATTCATACCAAAAATTACAATATTCATACAAAAAATTACAATATTCATACA
AAATACTAATCCAAAACTATAAACACAAATATAATAATAAAATAATTACAATATTCA
Found at i:39126649 original size:17 final size:17
Alignment explanation
Indices: 39126608--39126651 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
39126598 TACCTTTTTT
* *
39126608 TTTCTTTCTTCTTCTTC
1 TTTCTCTCTTCTTCTCC
39126625 -TTCTTCTCTTCTTCTCC
1 TTTC-TCTCTTCTTCTCC
39126642 TTTCTCTCTT
1 TTTCTCTCTT
39126652 TTTTTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 3 0.13
17 17 0.74
18 3 0.13
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTCTCTCTTCTTCTCC
Found at i:39126789 original size:27 final size:27
Alignment explanation
Indices: 39126759--39126828 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
39126749 AGAAGGCCAC
39126759 CATTGGCGCCTCCCTATGAGGCACATT
1 CATTGGCGCCTCCCTATGAGGCACATT
* *
39126786 CATTGGCACCTCTCTATGAGGCACATT
1 CATTGGCGCCTCCCTATGAGGCACATT
*
39126813 CATTGGCGCCTACCTA
1 CATTGGCGCCTCCCTA
39126829 ATATGCGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (27 bp):
CATTGGCGCCTCCCTATGAGGCACATT
Found at i:39128734 original size:58 final size:60
Alignment explanation
Indices: 39128664--39128817 Score: 163
Period size: 58 Copynumber: 2.6 Consensus size: 60
39128654 GTTCAACTAT
* *
39128664 GATTAAACTTAATCACTTTAATAGTAAATTAATATAATACTTATC-C-AGATAAATATTA
1 GATTAAACTTAATCACTTTAATATTAAATTAATAGAATACTTATCACAAGATAAATATTA
* * *
39128722 GATTAAATTTAAT-A-TTAAATATATTAAATTAATAGAATATTTATCTACAAGATAAATATTA
1 GATTAAACTTAATCACTT-TA-ATATTAAATTAATAGAATACTTATC-ACAAGATAAATATTA
* * **
39128783 AATATTAAGATAATCACTTTAATATTAAATTAATA
1 GAT-TAAACTTAATCACTTTAATATTAAATTAATA
39128818 AAATGCTATC
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
56 2 0.03
57 2 0.03
58 34 0.44
60 1 0.01
61 14 0.18
62 21 0.27
63 2 0.03
64 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (60 bp):
GATTAAACTTAATCACTTTAATATTAAATTAATAGAATACTTATCACAAGATAAATATTA
Found at i:39128857 original size:16 final size:16
Alignment explanation
Indices: 39128836--39128867 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39128826 TCAGGATAAG
39128836 TATTAAATTAATTAAA
1 TATTAAATTAATTAAA
*
39128852 TATTAAATTTATTAAA
1 TATTAAATTAATTAAA
39128868 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTAAATTAATTAAA
Found at i:39132367 original size:43 final size:42
Alignment explanation
Indices: 39132301--39132428 Score: 138
Period size: 42 Copynumber: 3.0 Consensus size: 42
39132291 ATAGGATTTC
* *
39132301 TGATATGTG-TCATCGTGTAAGACCACGTCGGGGACGTTGGCA
1 TGATATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
*
39132343 TCGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCA
1 T-GA-TATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* *
39132386 TGATATGTGATTGCATGTAAGACCACGTCTGGGACGTTGGCA
1 TGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
39132428 T
1 T
39132429 TGTATGAGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
41 2 0.03
42 35 0.48
43 32 0.44
44 4 0.05
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (42 bp):
TGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:39140550 original size:44 final size:46
Alignment explanation
Indices: 39140493--39140585 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 46
39140483 TACAACATCT
* *
39140493 ATTCTATTCAACCAAACAAAAGAA-CGTT-ATTACAACTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATCATTGATTACAACTCTATTCC
** *
39140537 ATTCCATTCAACCAAACAATTGAATTATTGATTACAACTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATCATTGATTACAACTCTATTCC
39140583 ATT
1 ATT
39140586 ACAGCTCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 21 0.50
45 2 0.05
46 19 0.45
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATCATTGATTACAACTCTATTCC
Found at i:39140588 original size:16 final size:16
Alignment explanation
Indices: 39140567--39140637 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
39140557 TGAATTATTG
*
39140567 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
39140583 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
39140599 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
39140615 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
39140631 ATTACAG
1 ATTACAG
39140638 TAAACCAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.37
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:39163540 original size:167 final size:167
Alignment explanation
Indices: 39163257--39163700 Score: 755
Period size: 167 Copynumber: 2.7 Consensus size: 167
39163247 GCAACTGGTA
* *
39163257 GAATTCTAGTCACACCATATATTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
1 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
*
39163322 TTTTAGATTATCAAATAGTATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
66 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
39163387 TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
131 TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
* *
39163424 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAAATAATTTCGGTGAATACAATG
1 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
* * *
39163489 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTTAACATGAGAACTTTCACCTATAAT
66 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
*
39163554 TTTCGGTGAAAACATGAGAACTTATTTCAGTGTTGTT
131 TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
* * * *
39163591 GAATTCCAGTCACACCATATCTTCAAGTTGATCCCAACAATGAACTTATTTCGTTGAATACAATG
1 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
*
39163656 TTTTA-ATTATCAAATAGAATCCCAAATGAATTTGATACTCAACAT
66 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACAT
39163701 AAGACTTACA
Statistics
Matches: 260, Mismatches: 17, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
166 38 0.15
167 222 0.85
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (167 bp):
GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
Found at i:39164120 original size:18 final size:18
Alignment explanation
Indices: 39164097--39164133 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
39164087 AATTAAATCC
*
39164097 TTAGATACCGCCAATGGG
1 TTAGATACCGCCAACGGG
39164115 TTAGATACCGCCAACGGG
1 TTAGATACCGCCAACGGG
39164133 T
1 T
39164134 GGATACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (18 bp):
TTAGATACCGCCAACGGG
Found at i:39172102 original size:29 final size:29
Alignment explanation
Indices: 39172062--39172135 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
39172052 GTGTACTCTG
* **
39172062 TATATGTTGCCTTTGTGGCATACTTTATA
1 TATATGTAGCCTTTGTGGCATACACTATA
39172091 TATATGTAGCCTTTGTGGCATACACTATA
1 TATATGTAGCCTTTGTGGCATACACTATA
39172120 TATA--TAGCCTTTGTGG
1 TATATGTAGCCTTTGTGG
39172136 TGTACTCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 12 0.29
29 30 0.71
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (29 bp):
TATATGTAGCCTTTGTGGCATACACTATA
Found at i:39175440 original size:48 final size:48
Alignment explanation
Indices: 39175366--39175604 Score: 282
Period size: 48 Copynumber: 5.0 Consensus size: 48
39175356 ATAAGTACTG
* * *
39175366 ATATTCTATTGAGATAC-AAGGTTGGCACGGACTGTGTACAGGCCACCA
1 ATATTCTGTTAAGATACAAAGG-TGGCACGGACTGTGTGCAGGCCACCA
* *
39175414 ATATTCTGTTAAGATACAAAGGTGGCACGGACTGTTTGCAGACCACCA
1 ATATTCTGTTAAGATACAAAGGTGGCACGGACTGTGTGCAGGCCACCA
* * *
39175462 ATATTCTGTTAAGATACAAGGGTGGCACGTACTGTGTGTAGGCCACCA
1 ATATTCTGTTAAGATACAAAGGTGGCACGGACTGTGTGCAGGCCACCA
** * **
39175510 ATATTCTGTTAAGATACAGGGGTGGCACGGACTATGTAAAGGCCACCA
1 ATATTCTGTTAAGATACAAAGGTGGCACGGACTGTGTGCAGGCCACCA
* * ** * * *
39175558 AGAGTCTGTTATTACACAAAGGTGGTACGGACTGTGTGTAGGCCACC
1 ATATTCTGTTAAGATACAAAGGTGGCACGGACTGTGTGCAGGCCACC
39175605 GAGAAATCTA
Statistics
Matches: 164, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
48 160 0.98
49 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (48 bp):
ATATTCTGTTAAGATACAAAGGTGGCACGGACTGTGTGCAGGCCACCA
Found at i:39177569 original size:56 final size:50
Alignment explanation
Indices: 39177304--39177599 Score: 258
Period size: 50 Copynumber: 5.8 Consensus size: 50
39177294 GATAATAACA
* * ** * * *
39177304 TGCCAAAGCCATGTCCCGGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCT-CGG
* * * ** * * *
39177353 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
* * * *
39177403 TGCCCATGCCATGTCCCAGACATGGTCTT--ATGGGGGCCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCGTCTCGG
* * *
39177452 TGTCAGCGCTATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
*
39177502 TGCCAACGCCATGTCCGAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--G-TCTC--GG
* * *
39177557 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39177600 TTACCCAAAT
Statistics
Matches: 204, Mismatches: 32, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
48 2 0.01
49 75 0.37
50 80 0.39
51 2 0.01
52 1 0.00
53 4 0.02
55 2 0.01
56 38 0.19
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
Found at i:39183678 original size:12 final size:12
Alignment explanation
Indices: 39183661--39183686 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39183651 AAGTATCTTG
39183661 TTATTAGAATCA
1 TTATTAGAATCA
39183673 TTATTAGAATCA
1 TTATTAGAATCA
39183685 TT
1 TT
39183687 TGGTTATGAG
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:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTATTAGAATCA
Found at i:39184969 original size:16 final size:16
Alignment explanation
Indices: 39184945--39184980 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39184935 ATTGCAAATT
*
39184945 TTTTTTATACTATCTA
1 TTTTATATACTATCTA
*
39184961 TTTTATATACTATTTA
1 TTTTATATACTATCTA
39184977 TTTT
1 TTTT
39184981 TAAGATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATATACTATCTA
Found at i:39199303 original size:19 final size:20
Alignment explanation
Indices: 39199265--39199314 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
39199255 GTGTCCCTTG
39199265 TTTTTGAAATTTCTCATATT
1 TTTTTGAAATTTCTCATATT
*
39199285 TTTTTGAAATTT-TCTTATT
1 TTTTTGAAATTTCTCATATT
* *
39199304 TATTTCAAATT
1 TTTTTGAAATT
39199315 AGTCCCTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTGAAATTTCTCATATT
Found at i:39208652 original size:77 final size:76
Alignment explanation
Indices: 39208457--39208685 Score: 440
Period size: 76 Copynumber: 3.0 Consensus size: 76
39208447 AACAACAAGC
39208457 AATTTGATAGATGACCCAATAATTAAACCAATTCCAGAAAAAAAAAATTGACAAGAGTGATGCGA
1 AATTTGATAGATGACCCAATAATTAAACCAATTCCAG-AAAAAAAAATTGACAAGAGTGATGCGA
39208522 AGGAACTTAGAT
65 AGGAACTTAGAT
39208534 AATTTGATAGATGACCCAATAATTAAACCAATTCCAGAAAAAAAAATTGACAAGAGTGATGCGAA
1 AATTTGATAGATGACCCAATAATTAAACCAATTCCAGAAAAAAAAATTGACAAGAGTGATGCGAA
39208599 GGAACTTAGAT
66 GGAACTTAGAT
*
39208610 AATTTGATAGATGACCCACTAATTAAACCAATTCCAGAAAAAAAAATTGACAAGAGTGATGCGAA
1 AATTTGATAGATGACCCAATAATTAAACCAATTCCAGAAAAAAAAATTGACAAGAGTGATGCGAA
39208675 GGAACTTAGAT
66 GGAACTTAGAT
39208686 CTTACTTACT
Statistics
Matches: 151, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
76 114 0.75
77 37 0.25
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (76 bp):
AATTTGATAGATGACCCAATAATTAAACCAATTCCAGAAAAAAAAATTGACAAGAGTGATGCGAA
GGAACTTAGAT
Found at i:39209540 original size:9 final size:9
Alignment explanation
Indices: 39209528--39209553 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39209518 TCTCCTCCCT
39209528 AATTTCACA
1 AATTTCACA
39209537 AATTTCACA
1 AATTTCACA
39209546 AATTTCAC
1 AATTTCAC
39209554 TTTCACACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTTCACA
Found at i:39209691 original size:16 final size:17
Alignment explanation
Indices: 39209670--39209701 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39209660 TAGAATCGGG
39209670 AGTCGCCG-AGTCACCA
1 AGTCGCCGAAGTCACCA
39209686 AGTCGCCGAAGTCACC
1 AGTCGCCGAAGTCACC
39209702 GAGTACCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (17 bp):
AGTCGCCGAAGTCACCA
Found at i:39213374 original size:24 final size:24
Alignment explanation
Indices: 39213317--39213375 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
39213307 GGTTTAATGC
* *
39213317 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
*
39213341 AAATGAATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
39213365 AAATGGATATA
1 AAATGGATATA
39213376 AATGGAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:39213467 original size:20 final size:19
Alignment explanation
Indices: 39213441--39213505 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
39213431 AATATTTTTA
39213441 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
39213460 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
39213478 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
39213497 ATTTATGTA
1 A-TTATGTA
39213506 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:39213470 original size:37 final size:37
Alignment explanation
Indices: 39213416--39213528 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
39213406 TTATGTTTTA
*
39213416 ATTC-AAGACTTGTGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
39213452 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* *
39213489 ATTCAAAGATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
39213526 ATT
1 ATT
39213529 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:39213484 original size:17 final size:17
Alignment explanation
Indices: 39213428--39213522 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 17
39213418 TCAAGACTTG
39213428 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
39213445 TGTAGTGATTCAAAGACTTA
1 TGTAAT-ATTTTTA-A-TTA
39213465 TGTAATATTTTTAATTA
1 TGTAATATTTTTAATTA
* ***
39213482 TGTAGTGATTCAAAGATTTA
1 TGTAAT-ATTTTTA-A-TTA
*
39213502 TGTAATGTTTTTAATTA
1 TGTAATATTTTTAATTA
39213519 TGTA
1 TGTA
39213523 GTGATTTAAT
Statistics
Matches: 55, Mismatches: 17, Indels: 12
0.65 0.20 0.14
Matches are distributed among these distances:
17 20 0.36
18 10 0.18
19 9 0.16
20 16 0.29
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (17 bp):
TGTAATATTTTTAATTA
Found at i:39213547 original size:9 final size:9
Alignment explanation
Indices: 39213529--39213625 Score: 140
Period size: 9 Copynumber: 10.6 Consensus size: 9
39213519 TGTAGTGATT
39213529 TAATTCGGG
1 TAATTCGGG
*
39213538 TAATTTGGG
1 TAATTCGGG
*
39213547 TAATTTTCAGG
1 TAA--TTCGGG
39213558 TAATTCGGG
1 TAATTCGGG
39213567 TAATTCGGG
1 TAATTCGGG
39213576 TAATTCGGG
1 TAATTCGGG
*
39213585 TAAGTCGGG
1 TAATTCGGG
39213594 TAATTCGGG
1 TAATTCGGG
*
39213603 TAAGTCGGG
1 TAATTCGGG
39213612 TAATTCGGG
1 TAATTCGGG
39213621 TAATT
1 TAATT
39213626 TTTAACCAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
9 71 0.91
11 7 0.09
ACGTcount: A:0.24, C:0.09, G:0.32, T:0.35
Consensus pattern (9 bp):
TAATTCGGG
Found at i:39213763 original size:28 final size:27
Alignment explanation
Indices: 39213731--39213796 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
39213721 AAAATTCGGT
39213731 TCGGTTAACGGTTA-AAAAATTTGAGAGG
1 TCGGTTAACGGTTACAAAAATTT-AG-GG
* *
39213759 TCGGTTAATTCGGTTACAAGAATTTCGGG
1 TCGGTTAA--CGGTTACAAAAATTTAGGG
39213788 TCGGTTAAC
1 TCGGTTAAC
39213797 CGGTCGGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 10 0.30
30 7 0.21
31 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TCGGTTAACGGTTACAAAAATTTAGGG
Found at i:39213803 original size:12 final size:12
Alignment explanation
Indices: 39213786--39213810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39213776 AAGAATTTCG
39213786 GGTCGGTTAACC
1 GGTCGGTTAACC
39213798 GGTCGGTTAACC
1 GGTCGGTTAACC
39213810 G
1 G
39213811 ACTGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:39214818 original size:21 final size:21
Alignment explanation
Indices: 39214789--39214844 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
39214779 CGAGGAAGCA
* *
39214789 AAGTTGCAACATTGGACTA-TG
1 AAGTCGCAACATT-CACTATTG
*
39214810 AAGTCGCAACATTCAGTATTG
1 AAGTCGCAACATTCACTATTG
39214831 AAGGTCGCAACATT
1 AA-GTCGCAACATT
39214845 TGAGCGAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 11 0.37
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (21 bp):
AAGTCGCAACATTCACTATTG
Found at i:39229450 original size:15 final size:16
Alignment explanation
Indices: 39229419--39229458 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
39229409 ATAGTAAAAA
39229419 TATAATTTTATTATTTT
1 TATAA-TTTATTATTTT
39229436 TATAATTTA-TATTTT
1 TATAATTTATTATTTT
39229451 TATAATTT
1 TATAATTT
39229459 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.61
16 4 0.17
17 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATAATTTATTATTTT
Found at i:39229478 original size:28 final size:30
Alignment explanation
Indices: 39229446--39229516 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 30
39229436 TATAATTTAT
*
39229446 ATTTTTATAATTTTTAAAAAATT-AAT-TA
1 ATTTTTATAATTTGTAAAAAATTAAATGTA
* *
39229474 ATTTTTATCATTTGTAAAAGATTAAAATGTA
1 ATTTTTATAATTTGTAAAAAATT-AAATGTA
39229505 A-TTTTATAATTT
1 ATTTTTATAATTT
39229517 AAAAATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 20 0.56
30 13 0.36
31 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
ATTTTTATAATTTGTAAAAAATTAAATGTA
Found at i:39230344 original size:4 final size:4
Alignment explanation
Indices: 39230335--39230369 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
39230325 TATTATTTGT
39230335 TTAA TTAA TTAA TTAA TTAA TTTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA -TTAA TTAA TTAA TT
39230370 TCTTTAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:39230377 original size:13 final size:13
Alignment explanation
Indices: 39230335--39230370 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
39230325 TATTATTTGT
39230335 TTAATTAA-TTAA
1 TTAATTAATTTAA
39230347 TTAATTAATTTAA
1 TTAATTAATTTAA
39230360 TTAATTAATTT
1 TTAATTAATTT
39230371 CTTTAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTAATTTAA
Found at i:39230377 original size:17 final size:17
Alignment explanation
Indices: 39230335--39230369 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
39230325 TATTATTTGT
39230335 TTAA-TTAATTAATTAA
1 TTAATTTAATTAATTAA
39230351 TTAATTTAATTAATTAA
1 TTAATTTAATTAATTAA
39230368 TT
1 TT
39230370 TCTTTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTTAATTAATTAA
Found at i:39230387 original size:17 final size:18
Alignment explanation
Indices: 39230362--39230400 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
39230352 TAATTTAATT
39230362 AATTAATTTCTTT-AATCA
1 AATTAATTT-TTTCAATCA
39230380 AATT-ATTTTTTCAATCA
1 AATTAATTTTTTCAATCA
39230397 AATT
1 AATT
39230401 CTAATTCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 13 0.65
18 4 0.20
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTAATTTTTTCAATCA
Found at i:39231112 original size:19 final size:19
Alignment explanation
Indices: 39231083--39231125 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
39231073 GTATCAAAAG
*
39231083 AATAAGTCAAACTAGAT-A
1 AATAAGTCAAAATAGATCA
39231101 AATAATGTCAAAATAGATCA
1 AATAA-GTCAAAATAGATCA
39231121 AATAA
1 AATAA
39231126 CCACATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAGTCAAAATAGATCA
Found at i:39233277 original size:11 final size:13
Alignment explanation
Indices: 39233253--39233284 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39233243 TAGTTTATTA
39233253 ATATTTTAATATG
1 ATATTTTAATATG
39233266 AT-TTTTAA-ATG
1 ATATTTTAATATG
39233277 ATATTTTA
1 ATATTTTA
39233285 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:39235389 original size:26 final size:25
Alignment explanation
Indices: 39235336--39235396 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
39235326 CCATAATTAT
* **
39235336 ATATATTATATAATAAGACCTATGC
1 ATATATTATATAATAAGACCCACAC
*
39235361 ATATATGTATATAGTAAGACCCACAC
1 ATATAT-TATATAATAAGACCCACAC
39235387 ATAATATTAT
1 AT-ATATTAT
39235397 TTATGTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 6 0.20
26 20 0.67
27 4 0.13
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (25 bp):
ATATATTATATAATAAGACCCACAC
Found at i:39242118 original size:71 final size:71
Alignment explanation
Indices: 39241922--39242247 Score: 340
Period size: 71 Copynumber: 4.6 Consensus size: 71
39241912 ATAATCGAAA
* * * * * * * *
39241922 AATAAATACGTCCTACACTGGTCAGTAAAAC-CAACAAATAAGTGTGCCTAGCACTAGTCGGTAT
1 AATAAATGCGTCCTGCGCTGGTCAATAGAACTGAA-AAATAAGTGTGCCCAGCACTGGTCGGTAT
*
39241986 AACTGAT
65 AACTGAC
* * * *
39241993 AATAAATGTGTCCTGCGCT-GTCTATAGAACCGAAAAATAAGTATGCCCAGCACTGGTCGGTATA
1 AATAAATGCGTCCTGCGCTGGTCAATAGAACTGAAAAATAAGTGTGCCCAGCACTGGTCGGTATA
39242057 ACTGAC
66 ACTGAC
* * *
39242063 AATAAATGCATCCTACGCTGGTCAATAGAACTGAAAAATAAGTGTGCCCATCACTGGTCGGTATA
1 AATAAATGCGTCCTGCGCTGGTCAATAGAACTGAAAAATAAGTGTGCCCAGCACTGGTCGGTATA
* *
39242128 ACCGAA
66 ACTGAC
* ** * *
39242134 AATAAATGTGCGT--TGCGCTAGTTGATAGAACTGAAGAATAAATGTGCCCAGCACTGGTCGGTA
1 AATAAA--TGCGTCCTGCGCTGGTCAATAGAACTGAAAAATAAGTGTGCCCAGCACTGGTCGGTA
39242197 TAA-TCGAC
64 TAACT-GAC
* * *
39242205 AATAAATGTGTCCTGCGCTGGTCAGTAGAACTG-ACAATAAGTG
1 AATAAATGCGTCCTGCGCTGGTCAATAGAACTGAAAAATAAGTG
39242248 GCCATTCAAT
Statistics
Matches: 210, Mismatches: 38, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
69 4 0.02
70 64 0.30
71 138 0.66
73 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (71 bp):
AATAAATGCGTCCTGCGCTGGTCAATAGAACTGAAAAATAAGTGTGCCCAGCACTGGTCGGTATA
ACTGAC
Found at i:39242144 original size:35 final size:35
Alignment explanation
Indices: 39241937--39242214 Score: 148
Period size: 35 Copynumber: 7.9 Consensus size: 35
39241927 ATACGTCCTA
* * * * *
39241937 CACTGGTCAGTAAAACCAACAAATAAGTGTGCCTAG
1 CACTGGTCGGTATAACCGA-AAATAAATGTGCCCAG
* * * * *
39241973 CACTAGTCGGTATAACTGATAATAAATGTGTCCTG
1 CACTGGTCGGTATAACCGAAAATAAATGTGCCCAG
* ** * * *
39242008 CGCT-GTCTATAGAACCGAAAAATAAGTATGCCCAG
1 CACTGGTCGGTATAACCG-AAAATAAATGTGCCCAG
* * *
39242043 CACTGGTCGGTATAACTGACAATAAATGCAT-CCTA-
1 CACTGGTCGGTATAACCGAAAATAAATG--TGCCCAG
* ** * * * *
39242078 CGCTGGTCAATAGAACTGAAAAATAAGTGTGCCCAT
1 CACTGGTCGGTATAACCG-AAAATAAATGTGCCCAG
***
39242114 CACTGGTCGGTATAACCGAAAATAAATGTGCGTTG
1 CACTGGTCGGTATAACCGAAAATAAATGTGCCCAG
* * * * * *
39242149 CGCTAGTTGATAGAACTGAAGAATAAATGTGCCCAG
1 CACTGGTCGGTATAACCGAA-AATAAATGTGCCCAG
* *
39242185 CACTGGTCGGTATAATCGACAATAAATGTG
1 CACTGGTCGGTATAACCGAAAATAAATGTG
39242215 TCCTGCGCTG
Statistics
Matches: 171, Mismatches: 63, Indels: 17
0.68 0.25 0.07
Matches are distributed among these distances:
34 10 0.06
35 89 0.52
36 71 0.42
37 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (35 bp):
CACTGGTCGGTATAACCGAAAATAAATGTGCCCAG
Found at i:39242224 original size:142 final size:140
Alignment explanation
Indices: 39241957--39242247 Score: 381
Period size: 142 Copynumber: 2.1 Consensus size: 140
39241947 TAAAACCAAC
* * *
39241957 AAATAAGTGTGCCTAGCACTAGTCGGTATAACTGATAATAAATGTGTCCTGCGCTGTCTATAGAA
1 AAATAAGTGTGCCCAGCACTAGTCGGTATAACCGAAAATAAATGTGTCCTGCGCTGTCTATAGAA
*
39242022 CCGAAAAATAAGTATGCCCAGCACTGGTCGGTATAACTGACAATAAATGCATCCTACGCTGGTCA
66 CCGAAAAATAAATATGCCCAGCACTGGTCGGTATAACTGACAATAAATGCATCCTACGCTGGTCA
39242087 ATAGAACTGAA
131 ATAGAACTG-A
* * *
39242098 AAATAAGTGTGCCCATCACTGGTCGGTATAACCGAAAATAAATGTG-CGTTGCGCTAGT-TGATA
1 AAATAAGTGTGCCCAGCACTAGTCGGTATAACCGAAAATAAATGTGTC-CTGCGCT-GTCT-ATA
* * * ** *
39242161 GAACTGAAGAATAAATGTGCCCAGCACTGGTCGGTATAA-TCGACAATAAATGTGTCCTGCGCTG
63 GAACCGAAAAATAAATATGCCCAGCACTGGTCGGTATAACT-GACAATAAATGCATCCTACGCTG
*
39242225 GTCAGTAGAACTGA
127 GTCAATAGAACTGA
*
39242239 CAATAAGTG
1 AAATAAGTG
39242248 GCCATTCAAT
Statistics
Matches: 131, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
140 1 0.01
141 58 0.44
142 72 0.55
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (140 bp):
AAATAAGTGTGCCCAGCACTAGTCGGTATAACCGAAAATAAATGTGTCCTGCGCTGTCTATAGAA
CCGAAAAATAAATATGCCCAGCACTGGTCGGTATAACTGACAATAAATGCATCCTACGCTGGTCA
ATAGAACTGA
Found at i:39242896 original size:15 final size:15
Alignment explanation
Indices: 39242876--39242909 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39242866 ACATTTCTAA
39242876 TATTTTATCTTT-TAT
1 TATTTTAT-TTTATAT
39242891 TATTTTATTTTATAT
1 TATTTTATTTTATAT
39242906 TATT
1 TATT
39242910 ATTAACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTATTTTATAT
Found at i:39251696 original size:16 final size:16
Alignment explanation
Indices: 39251675--39251705 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39251665 TTCATCACAA
39251675 CATAGATACATTTATG
1 CATAGATACATTTATG
*
39251691 CATAGATTCATTTAT
1 CATAGATACATTTAT
39251706 ATTAAAACAA
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:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (16 bp):
CATAGATACATTTATG
Found at i:39252712 original size:18 final size:17
Alignment explanation
Indices: 39252670--39252713 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
39252660 TGTCATTCGT
*
39252670 TTTCAAAACATTATTCA
1 TTTCAAATCATTATTCA
*
39252687 TTTACAAATCTTTATTCAA
1 TTT-CAAATCATTATTC-A
39252706 TTTCAAAT
1 TTTCAAAT
39252714 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 16 0.70
19 4 0.17
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTCAAATCATTATTCA
Found at i:39260660 original size:21 final size:21
Alignment explanation
Indices: 39260631--39260678 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
39260621 AAGCTCATAA
* *
39260631 AGCTTAACATAAGCTCGAAAG
1 AGCTGAACAGAAGCTCGAAAG
**
39260652 AGCTGAACAGAAGCTCGTGAG
1 AGCTGAACAGAAGCTCGAAAG
39260673 AGCTGA
1 AGCTGA
39260679 TCCACCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.17
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCGAAAG
Found at i:39261885 original size:14 final size:16
Alignment explanation
Indices: 39261848--39261886 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
39261838 TATCTAAATG
39261848 ATAATATTTTAAACAA
1 ATAATATTTTAAACAA
*
39261864 AAAATATTTT-AA-AA
1 ATAATATTTTAAACAA
39261878 ATAATATTT
1 ATAATATTT
39261887 ACGAGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 10 0.48
15 2 0.10
16 9 0.43
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAATATTTTAAACAA
Found at i:39268696 original size:9 final size:9
Alignment explanation
Indices: 39268680--39268721 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
39268670 GAGTTAAACG
39268680 AATCGAGTT
1 AATCGAGTT
*
39268689 ATTCGAGTT
1 AATCGAGTT
39268698 AATCGAGTT
1 AATCGAGTT
39268707 AATCGAGTT
1 AATCGAGTT
*
39268716 ATTCGA
1 AATCGA
39268722 ATCAACTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (9 bp):
AATCGAGTT
Found at i:39269049 original size:30 final size:31
Alignment explanation
Indices: 39269015--39269074 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
39269005 AAACCTTTTA
*
39269015 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
39269045 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
39269075 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:39269723 original size:5 final size:5
Alignment explanation
Indices: 39269713--39269738 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39269703 GAACAAATAT
39269713 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
39269739 ATTCCATCTC
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:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:39273642 original size:10 final size:9
Alignment explanation
Indices: 39273613--39273642 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39273603 GGGTTTAAGG
*
39273613 TTTAGAGTT
1 TTTAGGGTT
39273622 TTTAGGGTT
1 TTTAGGGTT
39273631 TTTAGGGTT
1 TTTAGGGTT
39273640 TTT
1 TTT
39273643 GAGAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (9 bp):
TTTAGGGTT
Found at i:39274175 original size:124 final size:124
Alignment explanation
Indices: 39273759--39274201 Score: 602
Period size: 127 Copynumber: 3.5 Consensus size: 124
39273749 GATAAAATCA
* * * * * * **
39273759 AAGCAGGATGCTTTATCAGAAGGATTTCTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTATGGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
39273824 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTATAAAAAATGCTCC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTA-AAAAAATGCTTC
* * *
39273884 AAGTAGGATACTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGC
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
39273949 AGGTCCTGGAAGAAATAGTTTCGAGTTGACGTTTCTGTGCAAATAGTTTAAAAAAATGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTTTGAGCAAATAG--TAAAAAAATGCTTC
* *
39274011 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATTGCGCCCTCGTGGACGCACTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
39274075 TAGGTCCTGGAAAAATAATTTTGAGTTGACGTTTTTGAGCAAATAGTACAAAAACGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTAAAAAAATGCTTC
* * * *
39274135 TAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCACGCCCTCGTAGACGTGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
39274199 TAG
65 TAG
39274202 CATGTTTGGG
Statistics
Matches: 282, Mismatches: 32, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
124 73 0.26
125 65 0.23
126 61 0.22
127 79 0.28
128 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTAAAAAAATGCTTC
Found at i:39277399 original size:114 final size:114
Alignment explanation
Indices: 39277212--39277585 Score: 694
Period size: 114 Copynumber: 3.3 Consensus size: 114
39277202 TTTTTTCAAT
* *
39277212 TATTAATTGTTAGTAAAATTATCAAATTATATCAAATTATTAATTATTAGTACCAGTCAAAACAT
1 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
* *
39277277 ATTGTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
66 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
39277326 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
1 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
39277391 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
66 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
*
39277440 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTGCCAGTCAAAACAT
1 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
*
39277505 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAAGTGATAATTG
66 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
39277554 TATTAATGGTTAGTAAAATTATCAAATTATAT
1 TATTAATGGTTAGTAAAATTATCAAATTATAT
39277586 TTAAGTTAAG
Statistics
Matches: 254, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 254 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (114 bp):
TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
Found at i:39277611 original size:21 final size:21
Alignment explanation
Indices: 39277585--39277863 Score: 319
Period size: 21 Copynumber: 13.0 Consensus size: 21
39277575 TCAAATTATA
*
39277585 TTTAAGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTT
39277606 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
39277627 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * * *
39277649 TTTTATTTAAAGATTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
****
39277670 TAGGGGTT-AGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
39277690 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * * *
39277712 TTAAAGTCAATGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
39277733 TTTAAGTTAAGAGTTTAGGG-T
1 TTTAAGTTAAG-GGTTAGGGTT
*
39277754 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
39277776 TTTAAGTTAAAAGTTTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTT
39277798 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
39277819 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
39277840 TTTAAGTTAAGGGGTTTAGGGTT
1 TTTAAGTTAA-GGG-TTAGGGTT
39277863 T
1 T
39277864 GTCAATTAAA
Statistics
Matches: 215, Mismatches: 34, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
20 15 0.07
21 121 0.56
22 67 0.31
23 12 0.06
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:39277646 original size:28 final size:28
Alignment explanation
Indices: 39277615--39277711 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 28
39277605 TTTTAAGTTA
39277615 AGGGTTAGGGTTTTAAAGTTAAGGGTTT
1 AGGGTTAGGGTTTTAAAGTTAAGGGTTT
*** *
39277643 AGGGTT-TTTTATTTAAAGATTAGGGTTTAGGGGTT
1 AGGGTTAGGGT-TTTAAAG-TTA------AGGGTTT
*
39277678 AGGGTTAGGGTTTTTAAGTTAAGGGTTT
1 AGGGTTAGGGTTTTAAAGTTAAGGGTTT
39277706 AGGGTT
1 AGGGTT
39277712 TTAAAGTCAA
Statistics
Matches: 51, Mismatches: 9, Indels: 18
0.65 0.12 0.23
Matches are distributed among these distances:
27 1 0.02
28 25 0.49
29 3 0.06
34 3 0.06
35 18 0.35
36 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (28 bp):
AGGGTTAGGGTTTTAAAGTTAAGGGTTT
Found at i:39277666 original size:43 final size:42
Alignment explanation
Indices: 39277588--39277863 Score: 306
Period size: 43 Copynumber: 6.5 Consensus size: 42
39277578 AATTATATTT
* * *
39277588 AAGTTAAGGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTA
1 AAGTTAAGGGTTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTA
* * *
39277630 AAGTTAAGGGTTTAGGGTTTTTTATTTAAAGATTAGGG-TTTA
1 AAGTTAAGGG-TTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTA
** *
39277672 GGGGTT-AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTA
1 -AAGTTAAGGGTTAGGGTTTTTAAGTTAA-AGTTTAGGGTTTTA
* * *
39277715 AAGTCAATGGTTATGGTTTTTAAGTTAAGAGTTTAGGGTTTT-
1 AAGTTAAGGGTTAGGGTTTTTAAGTTAA-AGTTTAGGGTTTTA
* *
39277757 AGGTTAAGGGTTTAGGGTTTTTAAGTTAAAAGTTTAGGGTTTTT
1 AAGTTAAGGG-TTAGGGTTTTTAAGTT-AAAGTTTAGGGTTTTA
* * *
39277801 AAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTT
1 AAGTTAAGGGTTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTA
39277843 AAGTTAAGGGGTTTAGGGTTT
1 AAGTTAA-GGG-TTAGGGTTT
39277864 GTCAATTAAA
Statistics
Matches: 200, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
41 16 0.08
42 55 0.28
43 109 0.55
44 20 0.10
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (42 bp):
AAGTTAAGGGTTAGGGTTTTTAAGTTAAAGTTTAGGGTTTTA
Found at i:39277815 original size:64 final size:65
Alignment explanation
Indices: 39277585--39277863 Score: 327
Period size: 64 Copynumber: 4.4 Consensus size: 65
39277575 TCAAATTATA
* * *
39277585 TTTAAGTT-AAGGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAAAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * ****
39277649 TTTTA-TTTAAAGATTAGGGTTTAGGGGTT-AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAAAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * * *
39277712 TTAAAG-TCAATGGTTATGGTTTTTAAGTTAAGAGTTTAGGG-TTTTAGGTTAAGGGTTTAGGGT
1 TTTAAGTTAAAAGGTTAGGGTTTTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
39277775 T
65 T
*
39277776 TTTAAGTTAAAAGTTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAAAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
**
39277840 TTTAAGTTAAGGGGTTTAGGGTTT
1 TTTAAGTTAAAAGG-TTAGGGTTT
39277864 GTCAATTAAA
Statistics
Matches: 177, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
63 53 0.30
64 73 0.41
65 51 0.29
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (65 bp):
TTTAAGTTAAAAGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:39278429 original size:18 final size:18
Alignment explanation
Indices: 39278403--39278445 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39278393 GACTCGAAAA
* *
39278403 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
39278421 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
39278439 AGGAAAC
1 AGGAAAC
39278446 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:39279103 original size:7 final size:7
Alignment explanation
Indices: 39279093--39279118 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39279083 TTATATACAT
39279093 AATACTA
1 AATACTA
39279100 AATACTA
1 AATACTA
39279107 AATACTA
1 AATACTA
39279114 AATAC
1 AATAC
39279119 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:39279324 original size:20 final size:20
Alignment explanation
Indices: 39279287--39279324 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39279277 TTTATTTTTA
*
39279287 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
39279307 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
39279325 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Done.