Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 131 of 187
Found at i:38953582 original size:28 final size:28
Alignment explanation
Indices: 38953491--38953588 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
38953481 TTACAGAGTC
*
38953491 TCGCCACAAAAGC-ATCATTTAAGAGGT
1 TCGCCACAAAGGCTATCATTTAAGAGGT
* * * * *
38953518 TTGCCACGAAGGCTTAGCCTTCT-AGAGTT
1 TCGCCACAAAGGC-TATCATT-TAAGAGGT
* *
38953547 TTGCCACAAAGGCTATCATTTAACAGGT
1 TCGCCACAAAGGCTATCATTTAAGAGGT
38953575 TCGCCACAAAGGCT
1 TCGCCACAAAGGCT
38953589 TGCCTTTATA
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
27 11 0.20
28 22 0.40
29 21 0.38
30 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (28 bp):
TCGCCACAAAGGCTATCATTTAAGAGGT
Found at i:38953625 original size:29 final size:27
Alignment explanation
Indices: 38953491--38953626 Score: 78
Period size: 29 Copynumber: 4.8 Consensus size: 27
38953481 TTACAGAGTC
* * *
38953491 TCGCCACAAAAGCATCATTTAAGAGGT
1 TCGCCACAAAGGCTTCATTTAACAGGT
* * * * *
38953518 TTGCCACGAAGGCTTAGCCTTCT-AGAGTT
1 TCGCCACAAAGGCTT--CATT-TAACAGGT
*
38953547 TTGCCACAAAGGCTATCATTTAACAGGT
1 TCGCCACAAAGGCT-TCATTTAACAGGT
*
38953575 TCGCCACAAAGGCTTGCCTTTATACA-GT
1 TCGCCACAAAGGCTT-CATTTA-ACAGGT
* *
38953603 TCTGGCACAAAGACTGTCATTTAA
1 TC-GCCACAAAGGCT-TCATTTAA
38953627 TAGTTGTTTT
Statistics
Matches: 85, Mismatches: 15, Indels: 17
0.73 0.13 0.15
Matches are distributed among these distances:
27 13 0.15
28 30 0.35
29 39 0.46
30 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (27 bp):
TCGCCACAAAGGCTTCATTTAACAGGT
Found at i:38972022 original size:26 final size:26
Alignment explanation
Indices: 38971939--38972161 Score: 259
Period size: 26 Copynumber: 8.5 Consensus size: 26
38971929 TCATGGTTTT
* * *
38971939 CCACAAAGCCTTTCAATTCATTTTACG
1 CCACAAAGGCTTTC-TTTCATATTACG
* * * *
38971966 CCACAAACGTTGTTCTTTCATATTGCA
1 CCACAAAGGCT-TTCTTTCATATTACG
38971993 CCACAAAGGCTTTCATTT-ATATTACG
1 CCACAAAGGCTTTC-TTTCATATTACG
** *
38972019 CCACAAAGTTTTTCTTTCATACTACG
1 CCACAAAGGCTTTCTTTCATATTACG
* *
38972045 CCACAAAGGCTTTCTTCCATATTACA
1 CCACAAAGGCTTTCTTTCATATTACG
* *
38972071 CCACAAAGGCTTTTTTTCATACTACG
1 CCACAAAGGCTTTCTTTCATATTACG
* *
38972097 ACACAAAGGTTTTCTTTCATATTACG
1 CCACAAAGGCTTTCTTTCATATTACG
*
38972123 CCACAAAGGCTTCCTTTCATATTACG
1 CCACAAAGGCTTTCTTTCATATTACG
38972149 CCACAAAGGCTTT
1 CCACAAAGGCTTT
38972162 TCATTATTTT
Statistics
Matches: 162, Mismatches: 31, Indels: 7
0.81 0.16 0.04
Matches are distributed among these distances:
25 3 0.02
26 128 0.79
27 28 0.17
28 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (26 bp):
CCACAAAGGCTTTCTTTCATATTACG
Found at i:38972571 original size:26 final size:25
Alignment explanation
Indices: 38972520--38972788 Score: 252
Period size: 26 Copynumber: 10.3 Consensus size: 25
38972510 GTTTTCAACG
* *
38972520 AAGGCTTTCAATTCATTTTACTCCACA
1 AAGGCTTTC--TTCATATTACGCCACA
38972547 AAGGCTTTAGCTT-ATATTACGCCACA
1 AAGGCTTT--CTTCATATTACGCCACA
* *
38972573 AAGGCTTTCTTTCATACTATGCCACA
1 AAGGCTTTC-TTCATATTACGCCACA
*
38972599 AAAGCTTTCTTCCATATTACGCCACA
1 AAGGCTTTCTT-CATATTACGCCACA
* * *
38972625 AAGGCTTTCTTCCATACTACACCATA
1 AAGGCTTTCTT-CATATTACGCCACA
* * * *
38972651 AAGGCTTTTGTTCACACTACGCCATA
1 AAGGC-TTTCTTCATATTACGCCACA
* * *
38972677 AATGCTTTCTTCCATATTATGCCATA
1 AAGGCTTTCTT-CATATTACGCCACA
*
38972703 AAGGCTTTCTTCCATACTACGCCACA
1 AAGGCTTTCTT-CATATTACGCCACA
*
38972729 AAGGCTTTCTTTCATATTACGTCACA
1 AAGGCTTTC-TTCATATTACGCCACA
* *
38972755 AAGGTTTTCTTTCATATTACGCTACA
1 AAGGCTTTC-TTCATATTACGCCACA
38972781 AAGGCTTT
1 AAGGCTTT
38972789 TCATTATTTG
Statistics
Matches: 205, Mismatches: 29, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
24 1 0.00
25 9 0.04
26 177 0.86
27 17 0.08
29 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (25 bp):
AAGGCTTTCTTCATATTACGCCACA
Found at i:38972574 original size:575 final size:576
Alignment explanation
Indices: 38971630--38972736 Score: 1591
Period size: 575 Copynumber: 1.9 Consensus size: 576
38971620 AAAGGCTATT
* * *
38971630 CTTATGTGGGGTTTTCCCATCATCGTATGAGACACGCAAAAAAACCTCTTTAGGTAATAACCTTC
1 CTTATGTGAGGTTTTCCCATCATCGCATGAGACACACAAAAAAACCTCTTTAGGTAATAACCTTC
* * *
38971695 CTTTAAGTTCCTTTAAAGAGTTCCATGGCCATGGACTTTTCCTTTTAGAATTCATGTTTAAATTC
66 CTTTAAGTTCCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTCATGTTTAAAGTC
** * *
38971760 CCGATCGACCTCTGTTGACAATACACCAAATAAATTGATATAGAATCCGCCACAAAGGATATCTT
131 CCGAAAGACCTCTGTTGACAATACACCAAATAAATTGATATAGAACCCGCCAAAAAGGATATCTT
* * * * *
38971825 TTACAGTACACCATTAAGATTCTTATCATTACACATCAAGAGCATCTCCTTTTAGAGATAGCCAT
196 TTACAATACACCATTAAGATTCTTATCATTACACACCAAGAACATCTCCTTTCAGAGATAGCCAC
* *
38971890 AAAAGCTTTCATCTTGTGATTTACTACAAAGACTTTTTTTCATGGTTTTCCACAAAGCCTTTCAA
261 AAAAGCTTTCATCTTGTGATTTACCACAAAGACTTTTTTTCATGGTTTTCAACAAAGCCTTTCAA
* * *
38971955 TTCATTTTACGCCACAAACGTTGTTCTTTCATATTGCACCACAAAGGCTTTCATTT-ATATTACG
326 TTCATTTTACGCCACAAACGTTGTGCTTTCATATTACACCACAAAGGCTTTC-TTTCATACTACG
* * *
38972019 CCAC-AAAGTTTTTCTTTCATACTACGCCACAAAGGCTTTCTTCCATATTACACCACAAAGGCTT
390 CCACAAAAG-CTTTCTTCCATACTACGCCACAAAGGCTTTCTTCCATACTACACCACAAAGGCTT
* * * * * *
38972083 TTTTTCATACTACGACACAAAGGTTTTCTTTCATATTACGCCACAAAGGCTTCCTTTCATATTAC
454 TTGTTCACACTACGACACAAAGGCTTTCTTCCATATTACGCCACAAAGGCTTCCTTCCATACTAC
38972148 GCCACAAAGGCTTTTCATTATTTTTCGTGTTTTTCTGATATTGATTTTCCTAAACTCA
519 GCCACAAAGGCTTTTCATTATTTTTCGTGTTTTTCTGATATTGATTTTCCTAAACTCA
* *
38972206 CTTATGTGAGGTTTTCCCATCATCGCATGGGACACACAAAAAAACC-CTTTGGGTAATAACCTTC
1 CTTATGTGAGGTTTTCCCATCATCGCATGAGACACACAAAAAAACCTCTTTAGGTAATAACCTTC
* * **
38972270 TTTTAAGTTGCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTTGTGTTTAAAGTC
66 CTTTAAGTTCCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTCATGTTTAAAGTC
* *
38972335 CCGAAAGACCTCTTTTGACAATGCACCAAA-AAATTTGATATAGAACCCGCCAAAAAGGATATCT
131 CCGAAAGACCTCTGTTGACAATACACCAAATAAA-TTGATATAGAACCCGCCAAAAAGGATATCT
* ** *
38972399 TTTATAATATGCCATTAAGATTCTTATCATTACACGCCAAGAACATCTCCTTTCAGAGACT-GCC
195 TTTACAATACACCATTAAGATTCTTATCATTACACACCAAGAACATCTCCTTTCAGAGA-TAGCC
* * *
38972463 ACAAAAGCTTTCATCTTGTGATTTACCACAAAGGCTTTTTTTTCATGGTTTTCAACGAAGGCTTT
259 ACAAAAGCTTTCATCTTGTGATTTACCACAAAGAC-TTTTTTTCATGGTTTTCAACAAAGCCTTT
* * *
38972528 CAATTCATTTTACTCCACAAAGGCTT-TAGC-TT-ATATTACGCCACAAAGGCTTTCTTTCATAC
323 CAATTCATTTTACGCCACAAACG-TTGT-GCTTTCATATTACACCACAAAGGCTTTCTTTCATAC
* * *
38972590 TATGCCACAAAAGCTTTCTTCCATATTACGCCACAAAGGCTTTCTTCCATACTACACCATAAAGG
386 TACGCCACAAAAGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTCCATACTACACCACAAAGG
* * * * * *
38972655 CTTTTGTTCACACTACGCCATAAATGCTTTCTTCCATATTATGCCATAAAGGCTTTCTTCCATAC
451 CTTTTGTTCACACTACGACACAAAGGCTTTCTTCCATATTACGCCACAAAGGCTTCCTTCCATAC
38972720 TACGCCACAAAGGCTTT
516 TACGCCACAAAGGCTTT
38972737 CTTTCATATT
Statistics
Matches: 468, Mismatches: 56, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
574 6 0.01
575 362 0.77
576 97 0.21
577 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (576 bp):
CTTATGTGAGGTTTTCCCATCATCGCATGAGACACACAAAAAAACCTCTTTAGGTAATAACCTTC
CTTTAAGTTCCTTTAAAGAGTGCCATGGCCATGGACTTTTCCTTTCAGAATTCATGTTTAAAGTC
CCGAAAGACCTCTGTTGACAATACACCAAATAAATTGATATAGAACCCGCCAAAAAGGATATCTT
TTACAATACACCATTAAGATTCTTATCATTACACACCAAGAACATCTCCTTTCAGAGATAGCCAC
AAAAGCTTTCATCTTGTGATTTACCACAAAGACTTTTTTTCATGGTTTTCAACAAAGCCTTTCAA
TTCATTTTACGCCACAAACGTTGTGCTTTCATATTACACCACAAAGGCTTTCTTTCATACTACGC
CACAAAAGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTCCATACTACACCACAAAGGCTTTT
GTTCACACTACGACACAAAGGCTTTCTTCCATATTACGCCACAAAGGCTTCCTTCCATACTACGC
CACAAAGGCTTTTCATTATTTTTCGTGTTTTTCTGATATTGATTTTCCTAAACTCA
Found at i:38972632 original size:78 final size:77
Alignment explanation
Indices: 38972537--38972788 Score: 301
Period size: 78 Copynumber: 3.2 Consensus size: 77
38972527 TCAATTCATT
* * *
38972537 TTACTCCACAAAGGCTTTAGCTT-ATATTACGCCACAAAGGCTTTCTTTCATACTATGCCACAAA
1 TTACGCCACAAAGGCTTT--CTTCATACTACGCCACAAAGGCTTTCTTTCATACTACGCCACAAA
38972601 AGCTTTCTTCCATA
64 AGCTTTCTTCCATA
* * * *
38972615 TTACGCCACAAAGGCTTTCTTCCATACTACACCATAAAGGCTTT-TGTTCACACTACGCCATAAA
1 TTACGCCACAAAGGCTTTCTT-CATACTACGCCACAAAGGCTTTCT-TTCATACTACGCCACAAA
*
38972679 TGCTTTCTTCCATA
64 AGCTTTCTTCCATA
* * * * *
38972693 TTATGCCATAAAGGCTTTCTTCCATACTACGCCACAAAGGCTTTCTTTCATATTACGTCACAAAG
1 TTACGCCACAAAGGCTTTCTT-CATACTACGCCACAAAGGCTTTCTTTCATACTACGCCACAAAA
* *
38972758 GTTTTCTTTCATA
65 GCTTTCTTCCATA
*
38972771 TTACGCTACAAAGGCTTT
1 TTACGCCACAAAGGCTTT
38972789 TCATTATTTG
Statistics
Matches: 148, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
76 3 0.02
77 1 0.01
78 143 0.97
79 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (77 bp):
TTACGCCACAAAGGCTTTCTTCATACTACGCCACAAAGGCTTTCTTTCATACTACGCCACAAAAG
CTTTCTTCCATA
Found at i:38979089 original size:21 final size:21
Alignment explanation
Indices: 38979060--38979099 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
38979050 AAATTAAGTA
38979060 TTTTCATTAAGATTTAGTTATG
1 TTTTCATTAAG-TTTAGTTATG
*
38979082 TTTT-ATTAAGTTTTGTTA
1 TTTTCATTAAGTTTAGTTA
38979100 AATCCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60
Consensus pattern (21 bp):
TTTTCATTAAGTTTAGTTATG
Found at i:38982254 original size:27 final size:27
Alignment explanation
Indices: 38982224--38982401 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38982214 ATATTGAGTC
* * * *
38982224 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38982251 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38982278 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38982306 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38982333 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38982360 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38982387 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38982402 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38982363 original size:82 final size:81
Alignment explanation
Indices: 38982245--38982400 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38982235 TGCTATATAA
* *
38982245 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38982310 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38982327 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38982391 CACTTAGTGC
65 CACTTAGTGC
38982401 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38985443 original size:47 final size:47
Alignment explanation
Indices: 38985380--38985731 Score: 445
Period size: 47 Copynumber: 7.4 Consensus size: 47
38985370 CAGCCAAGAC
*
38985380 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
38985427 AGTGCATATATGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAA
1 AGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
38985474 AGTGCATATATGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAA
1 AGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * * *
38985521 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
38985568 AGTGCATATATGTGATAAGGCTTAATGGCCGATGTGATGAATGTGAA
1 AGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
38985615 AGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGGA
1 AGTG--CATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
38985664 AGTGTATATATATGTGA-CAGGGCTGAGTGGCCAACGTGATGGATGTGAA
1 AGTG--CATATATGTGATAAGGCCT-AATGGCCGATGTGATGAATGTGAA
*
38985713 AGTGCATAAATGTGATAAG
1 AGTGCATATATGTGATAAG
38985732 TCCCGAAGGG
Statistics
Matches: 266, Mismatches: 35, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
47 181 0.68
48 6 0.02
49 79 0.30
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.28
Consensus pattern (47 bp):
AGTGCATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:38985464 original size:22 final size:22
Alignment explanation
Indices: 38985436--38985511 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
38985426 AAGTGCATAT
38985436 ATGTGATAAGGCTTAATGGCCG
1 ATGTGATAAGGCTTAATGGCCG
* * * **
38985458 ATGTGATGAATG-TGAAAGTGCATAT
1 ATGTGAT-AAGGCTTAATG-GC--CG
38985483 ATGTGATAAGGCTTAATGGCCG
1 ATGTGATAAGGCTTAATGGCCG
38985505 ATGTGAT
1 ATGTGAT
38985512 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 18 0.46
23 5 0.13
24 5 0.13
25 11 0.28
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (22 bp):
ATGTGATAAGGCTTAATGGCCG
Found at i:38985672 original size:141 final size:140
Alignment explanation
Indices: 38985380--38985731 Score: 524
Period size: 141 Copynumber: 2.5 Consensus size: 140
38985370 CAGCCAAGAC
* * * * * * *
38985380 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTGATAA
1 AGTG-ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATATATGTGATAA
*
38985445 GGCTTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTGATAAGGCTTAATGGCCGATGTG
65 GGCTTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTGATAAGGCCTAATGGCCGATGTG
38985510 ATGAATGTGAA
130 ATGAATGTGAA
38985521 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATATATGTGATAA
1 AGTG-ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATATATGTGATAA
* *
38985586 GGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATG
65 GGCTTAATGGCCGATGTGATGAATGTGAAAGTG--CATATATGTGATAAGGCCTAATGGCCGATG
*
38985651 TGATGAATGTGGA
128 TGATGAATGTGAA
* *
38985664 AGTGTATATATATGTGACAGGGCTGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGAT
1 AGTG---ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATATATGTGAT
38985729 AAG
63 AAG
38985732 TCCCGAAGGG
Statistics
Matches: 194, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
141 91 0.47
143 43 0.22
145 60 0.31
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.28
Consensus pattern (140 bp):
AGTGATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATATATGTGATAAG
GCTTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTGATAAGGCCTAATGGCCGATGTGA
TGAATGTGAA
Found at i:38985906 original size:37 final size:37
Alignment explanation
Indices: 38985850--38985928 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
38985840 CCGAGCTCTA
* * *
38985850 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
38985887 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
38985924 AAGAC
1 AAGAC
38985929 TTCGCAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:38995431 original size:22 final size:22
Alignment explanation
Indices: 38995403--38995457 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
38995393 CAATAAGTCA
*
38995403 ACAGGACGGTTCAACATCGTAG
1 ACAGGACGGCTCAACATCGTAG
* *
38995425 AGAGGACGACTCAACATCGTAG
1 ACAGGACGGCTCAACATCGTAG
38995447 ACAGGACGGCT
1 ACAGGACGGCT
38995458 AAAAGCCGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.15
Consensus pattern (22 bp):
ACAGGACGGCTCAACATCGTAG
Found at i:38995667 original size:127 final size:127
Alignment explanation
Indices: 38995441--38995694 Score: 384
Period size: 127 Copynumber: 2.0 Consensus size: 127
38995431 CGACTCAACA
** * *
38995441 TCGTAGACAGGACGGCTAAAAGCCGTAAATATCGTAGCAACGCTGCCAGTTAACAGAACAGTTAT
1 TCGTAGACAGGACGGCTAAAAGCCGTAAATATCACAGCAACACTGCCAGTTAACAGAACAGCTAT
*
38995506 AAGCCATAAGTATCGTAGAAAGGCTGAAAGCCTTATACAGGACGACTACAAGCCGTACACTT
66 AAGCCATAAGTATCGCAGAAAGGCTGAAAGCCTTATACAGGACGACTACAAGCCGTACACTT
* * * *
38995568 TCGTAGACAGGACGGCTAAAGGCCGTAAATATCACAGCAATACTGTCTGTTAACAGAAC-GACTA
1 TCGTAGACAGGACGGCTAAAAGCCGTAAATATCACAGCAACACTGCCAGTTAACAGAACAG-CTA
* * *
38995632 TAAGCTATAAGTATCGCAGAAAGGCTGAAAGCCTTATACAGGACGGCTACAGGCCGTACACTT
65 TAAGCCATAAGTATCGCAGAAAGGCTGAAAGCCTTATACAGGACGACTACAAGCCGTACACTT
38995695 CCTCCGTCCA
Statistics
Matches: 114, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
126 1 0.01
127 113 0.99
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (127 bp):
TCGTAGACAGGACGGCTAAAAGCCGTAAATATCACAGCAACACTGCCAGTTAACAGAACAGCTAT
AAGCCATAAGTATCGCAGAAAGGCTGAAAGCCTTATACAGGACGACTACAAGCCGTACACTT
Found at i:38999966 original size:21 final size:22
Alignment explanation
Indices: 38999932--38999972 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
38999922 TCATGACCTT
* *
38999932 ATTATATAATGGTTTTATATTA
1 ATTATATAAAGGTTATATATTA
38999954 ATTA-ATAAAGGTTATATAT
1 ATTATATAAAGGTTATATAT
38999973 GTAAAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
ATTATATAAAGGTTATATATTA
Found at i:39000722 original size:17 final size:19
Alignment explanation
Indices: 39000686--39000723 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
39000676 GTTTATAAGC
39000686 AAATAGATATTGTTAATTTT
1 AAATAGATATTG-TAATTTT
39000706 AAATAGATA-TG-AATTTT
1 AAATAGATATTGTAATTTT
39000723 A
1 A
39000724 TATGCTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
AAATAGATATTGTAATTTT
Found at i:39004283 original size:40 final size:41
Alignment explanation
Indices: 39004085--39004269 Score: 204
Period size: 40 Copynumber: 4.6 Consensus size: 41
39004075 TCGAATGATG
* * * *
39004085 TCCGGGCTAAGTCCCGAAGGC-TTTGCGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
39004125 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTA-AT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39004165 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
39004204 TCCGGGTTAAGTCCCGAAGGAATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39004245 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39004270 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 34 0.28
40 79 0.65
41 9 0.07
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39009832 original size:16 final size:17
Alignment explanation
Indices: 39009811--39009846 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
39009801 CATAGCAGTC
39009811 GGTTATCTATTCACT-G
1 GGTTATCTATTCACTCG
39009827 GGTTATCTATTCACTCG
1 GGTTATCTATTCACTCG
39009844 GGT
1 GGT
39009847 AGTACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (17 bp):
GGTTATCTATTCACTCG
Found at i:39011412 original size:21 final size:22
Alignment explanation
Indices: 39011378--39011418 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39011368 TCATGACCTT
* *
39011378 ATTATATAATGGTTTTATATTA
1 ATTATATAAAGGTTATATATTA
39011400 ATTA-ATAAAGGTTATATAT
1 ATTATATAAAGGTTATATAT
39011419 GTAAAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
ATTATATAAAGGTTATATATTA
Found at i:39014592 original size:43 final size:43
Alignment explanation
Indices: 39014507--39014609 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
39014497 TTGAATTTGA
*
39014507 GGCACTAAGTGTGCGATAAATAAAATAGCTACGGCTAATTAATT
1 GGCACTAAGTGTGCGATAAAT-AAATAGCTACAGCTAATTAATT
* * *
39014551 GTCACTAAGTGTGCGATACAAT-TATAGCTTCAGCTAATTAATT
1 GGCACTAAGTGTGCGATA-AATAAATAGCTACAGCTAATTAATT
39014594 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
39014610 GTTCATTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 33 0.62
44 17 0.32
45 3 0.06
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (43 bp):
GGCACTAAGTGTGCGATAAATAAATAGCTACAGCTAATTAATT
Found at i:39017562 original size:51 final size:51
Alignment explanation
Indices: 39017503--39017605 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
39017493 GCCTTGAACA
* * *
39017503 CGGCCTTCAGTAATCGCACACGGGCTTGTCCTTGCCGAACCCAAGTTTAGT
1 CGGCCTTCAGTAATCGCACACGGGCGTGTCCCTGCCAAACCCAAGTTTAGT
*
39017554 CGGCCTTCAGTAATCGCACATGGGCGTGTCCCTGCCAAACCCAAGTTTAGT
1 CGGCCTTCAGTAATCGCACACGGGCGTGTCCCTGCCAAACCCAAGTTTAGT
39017605 C
1 C
39017606 CAATTCAGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.24
Consensus pattern (51 bp):
CGGCCTTCAGTAATCGCACACGGGCGTGTCCCTGCCAAACCCAAGTTTAGT
Found at i:39022310 original size:43 final size:43
Alignment explanation
Indices: 39022225--39022413 Score: 254
Period size: 43 Copynumber: 4.4 Consensus size: 43
39022215 TTGAATTTAG
* * * *
39022225 GGCACTAAGTGTCCGATA-AATGAAATAGCTACGGCTAATTAATT
1 GGCACTAAGTGTGCGATACAAT--TATAGCTTCAGCTAATTAATT
* * **
39022269 AGCACTAAGTGTGCGATACAGTTATAGCCCCAGCTAATTAATT
1 GGCACTAAGTGTGCGATACAATTATAGCTTCAGCTAATTAATT
*
39022312 GGCACTAAGTGTGCGATACAATTATAGCTTCAGCAAATTAATT
1 GGCACTAAGTGTGCGATACAATTATAGCTTCAGCTAATTAATT
*
39022355 GGCACTAAGTGTGCGATACAATTATATCTTCAGCTAATTAATT
1 GGCACTAAGTGTGCGATACAATTATAGCTTCAGCTAATTAATT
*
39022398 GGAACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
39022414 GTTCGTTGAA
Statistics
Matches: 129, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
43 111 0.86
44 16 0.12
45 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (43 bp):
GGCACTAAGTGTGCGATACAATTATAGCTTCAGCTAATTAATT
Found at i:39024418 original size:79 final size:82
Alignment explanation
Indices: 39024307--39024491 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
39024297 GCTACTCGTT
* *
39024307 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
39024370 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
39024387 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
39024450 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
39024467 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39024492 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:39024491 original size:40 final size:40
Alignment explanation
Indices: 39024288--39024491 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
39024278 CGGAATTTAA
** *
39024288 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39024328 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
39024368 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39024407 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
39024447 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
39024487 CCGGA
1 CCGGA
39024492 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:39032434 original size:79 final size:81
Alignment explanation
Indices: 39032325--39032507 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
39032315 TACTCGTTCA
* *
39032325 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
39032388 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
39032405 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
39032468 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
39032484 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39032508 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:39032507 original size:40 final size:40
Alignment explanation
Indices: 39032304--39032507 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
39032294 CGGAATTTAA
** *
39032304 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39032344 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39032384 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39032423 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
39032463 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
39032503 CCGGA
1 CCGGA
39032508 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:39041474 original size:34 final size:34
Alignment explanation
Indices: 39041387--39041488 Score: 100
Period size: 34 Copynumber: 3.0 Consensus size: 34
39041377 ATGCATTTTG
* * *
39041387 GATACTG-TACTGAAATGGGCTAAGGCCCACATT
1 GATACTGCGACTGATATGGGCTAAGGCCCACACT
** *
39041420 GATACTGTTACTG-TGTTGGGCTAAGGCCCACACT
1 GATACTGCGACTGAT-ATGGGCTAAGGCCCACACT
* * *
39041454 GATATTGCGACTGATATGGGCTTAGGCCCAGACT
1 GATACTGCGACTGATATGGGCTAAGGCCCACACT
39041488 G
1 G
39041489 TTCAACACTG
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
33 7 0.12
34 49 0.86
35 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (34 bp):
GATACTGCGACTGATATGGGCTAAGGCCCACACT
Found at i:39045937 original size:72 final size:72
Alignment explanation
Indices: 39045846--39045990 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
39045836 AAGAGGGAAT
39045846 ATGAATCGGCTAGGCTTGGGGATTAAGAAAAATGGATACATTTCATTTTACGAGCCTAGGGGTAA
1 ATGAATCGGCTAGGCTTGGGGATTAAGAAAAATGGATACATTTCATTTTACGAGCCTAGGGGTAA
39045911 ATTTGTA
66 ATTTGTA
*
39045918 ATGAATCGGCTAGGCTTGGGTATTAAGAAAAATGGATACATTTCATTTTACGAGCCTAGGGGTAA
1 ATGAATCGGCTAGGCTTGGGGATTAAGAAAAATGGATACATTTCATTTTACGAGCCTAGGGGTAA
39045983 ATTTGTA
66 ATTTGTA
39045990 A
1 A
39045991 ATACGTGAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (72 bp):
ATGAATCGGCTAGGCTTGGGGATTAAGAAAAATGGATACATTTCATTTTACGAGCCTAGGGGTAA
ATTTGTA
Found at i:39046447 original size:24 final size:24
Alignment explanation
Indices: 39046415--39046510 Score: 95
Period size: 24 Copynumber: 3.8 Consensus size: 24
39046405 TGACATTGTG
39046415 CTAAGTGAAATAAGACCATGACAT
1 CTAAGTGAAATAAGACCATGACAT
** *
39046439 CTAAGTGAAATAAGTTCATGGCAATGT
1 CTAAGTGAAATAAGACCATGAC-A--T
*
39046466 GCTAAGTGAAATAA-ATCCGTGACAT
1 -CTAAGTGAAATAAGA-CCATGACAT
*
39046491 CTAAGTGAAATAAGTCCATG
1 CTAAGTGAAATAAGACCATG
39046511 GCATTGTGCT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
24 36 0.63
25 2 0.04
27 2 0.04
28 17 0.30
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (24 bp):
CTAAGTGAAATAAGACCATGACAT
Found at i:39046489 original size:52 final size:52
Alignment explanation
Indices: 39046411--39046524 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 52
39046401 GATATGACAT
*
39046411 TGTGCTAAGTGAAATAAGACCATGACATCTAAGTGAAATAAGTTCATGGCAA
1 TGTGCTAAGTGAAATAAGACCATGACATCTAAGTGAAATAAGTCCATGGCAA
* *
39046463 TGTGCTAAGTGAAATAA-ATCCGTGACATCTAAGTGAAATAAGTCCATGGCAT
1 TGTGCTAAGTGAAATAAGA-CCATGACATCTAAGTGAAATAAGTCCATGGCAA
39046515 TGTGCTAAGT
1 TGTGCTAAGT
39046525 AAGAAATTTC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 1 0.02
52 57 0.98
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (52 bp):
TGTGCTAAGTGAAATAAGACCATGACATCTAAGTGAAATAAGTCCATGGCAA
Found at i:39046680 original size:52 final size:52
Alignment explanation
Indices: 39046554--39046704 Score: 200
Period size: 52 Copynumber: 3.0 Consensus size: 52
39046544 CCTTAGGAAT
* *
39046554 AAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCAC-TT-TGAGAA
1 AAAATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAAA
* * * ** * *
39046604 GAGATAAC-TTGGTCATGAGTGTGGTACCACGTGAAGGCCACTTTGTGAAAA
1 AAAATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAAA
39046655 AAAATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAA
1 AAAATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAA
39046705 GAAGGTAGCT
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
49 28 0.34
50 7 0.09
51 10 0.12
52 37 0.45
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (52 bp):
AAAATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAAA
Found at i:39046734 original size:51 final size:50
Alignment explanation
Indices: 39046557--39046736 Score: 200
Period size: 51 Copynumber: 3.5 Consensus size: 50
39046547 TAGGAATAAA
*
39046557 ATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AG
1 ATAGCTTT-GACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAG
* * * ** * * * *
39046607 ATAACTTGGTCATGAGTGTGGTACCACGTGAAGGCCACTTTGTGAAAAAAA
1 ATAGCTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTG-AAGAAG
*
39046658 ATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAG
1 ATAGCTTT-GACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAG
* *
39046709 GTAGCTTTGACTACAAGGGTGGTACTAT
1 ATAGCTTTGAC-ACAAGTGTGGTACTAT
39046737 TTGCATGCCG
Statistics
Matches: 105, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
49 30 0.29
50 10 0.10
51 33 0.31
52 32 0.30
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.28
Consensus pattern (50 bp):
ATAGCTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAG
Found at i:39047236 original size:280 final size:280
Alignment explanation
Indices: 39046735--39047297 Score: 1126
Period size: 280 Copynumber: 2.0 Consensus size: 280
39046725 GGGTGGTACT
39046735 ATTTGCATGCCGCCGGGTATCCGTTATTATTCCAATGTGTTCAATGGGAAATGACTAGGTGTAAT
1 ATTTGCATGCCGCCGGGTATCCGTTATTATTCCAATGTGTTCAATGGGAAATGACTAGGTGTAAT
39046800 TGAATATGACTATGTGGTGAATAAGTTCAGGTACATGTGTGTAAACTTATGAGCAATGTGCTCGA
66 TGAATATGACTATGTGGTGAATAAGTTCAGGTACATGTGTGTAAACTTATGAGCAATGTGCTCGA
39046865 TATGTGATTGAACTTTGGTAAGATTGATATGGAGTAAGTGTTACAATGAAAGTTACTGCAAAGAA
131 TATGTGATTGAACTTTGGTAAGATTGATATGGAGTAAGTGTTACAATGAAAGTTACTGCAAAGAA
39046930 AACATGAAAGAGTGAAATTTAGTAATAAAACAGTTTTGGCCAGCACTAGTTGTGTGAATTTGAAA
196 AACATGAAAGAGTGAAATTTAGTAATAAAACAGTTTTGGCCAGCACTAGTTGTGTGAATTTGAAA
39046995 AATCACCAAAAATGGTGAAA
261 AATCACCAAAAATGGTGAAA
39047015 ATTTGCATGCCGCCGGGTATCCGTTATTATTCCAATGTGTTCAATGGGAAATGACTAGGTGTAAT
1 ATTTGCATGCCGCCGGGTATCCGTTATTATTCCAATGTGTTCAATGGGAAATGACTAGGTGTAAT
39047080 TGAATATGACTATGTGGTGAATAAGTTCAGGTACATGTGTGTAAACTTATGAGCAATGTGCTCGA
66 TGAATATGACTATGTGGTGAATAAGTTCAGGTACATGTGTGTAAACTTATGAGCAATGTGCTCGA
39047145 TATGTGATTGAACTTTGGTAAGATTGATATGGAGTAAGTGTTACAATGAAAGTTACTGCAAAGAA
131 TATGTGATTGAACTTTGGTAAGATTGATATGGAGTAAGTGTTACAATGAAAGTTACTGCAAAGAA
39047210 AACATGAAAGAGTGAAATTTAGTAATAAAACAGTTTTGGCCAGCACTAGTTGTGTGAATTTGAAA
196 AACATGAAAGAGTGAAATTTAGTAATAAAACAGTTTTGGCCAGCACTAGTTGTGTGAATTTGAAA
39047275 AATCACCAAAAATGGTGAAA
261 AATCACCAAAAATGGTGAAA
39047295 ATT
1 ATT
39047298 AAATTAGAGG
Statistics
Matches: 283, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
280 283 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (280 bp):
ATTTGCATGCCGCCGGGTATCCGTTATTATTCCAATGTGTTCAATGGGAAATGACTAGGTGTAAT
TGAATATGACTATGTGGTGAATAAGTTCAGGTACATGTGTGTAAACTTATGAGCAATGTGCTCGA
TATGTGATTGAACTTTGGTAAGATTGATATGGAGTAAGTGTTACAATGAAAGTTACTGCAAAGAA
AACATGAAAGAGTGAAATTTAGTAATAAAACAGTTTTGGCCAGCACTAGTTGTGTGAATTTGAAA
AATCACCAAAAATGGTGAAA
Found at i:39050367 original size:28 final size:28
Alignment explanation
Indices: 39050327--39050380 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
39050317 CAAGATTCCT
*
39050327 TAAATTTTTGTGAAAAAAATTACTATCG
1 TAAATATTTGTGAAAAAAATTACTATCG
* *
39050355 TAAATATTTGTGAAAAGAATTGCTAT
1 TAAATATTTGTGAAAAAAATTACTAT
39050381 TGGAAGAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (28 bp):
TAAATATTTGTGAAAAAAATTACTATCG
Found at i:39051996 original size:27 final size:27
Alignment explanation
Indices: 39051954--39052322 Score: 323
Period size: 27 Copynumber: 13.7 Consensus size: 27
39051944 AAATAAAGAG
* *
39051954 AAATTACCGAAATACCCCCGATTTATA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
39051981 AAATTATCGAAGTACCCTC-AGTTTGTA
1 AAATTACCGAAATACCCTCGA-TTTGTA
*
39052008 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
39052035 AAATTACCGGAATACCCCCAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
39052062 AAATTACCAAAACACCCTCAATTATG--
1 AAATTACCGAAATACCCTCGATT-TGTA
**
39052088 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
39052115 AAATTATCAAAATACCCCCGATTTGTG
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
39052142 AAATTACCAAAACATCCTTGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
39052169 AAATTATCGAAACACCCTAGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* **
39052196 AAATTACCGAAATATCCTTAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
**
39052223 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
39052250 AAATTACCAAAACACTCTCAATTTTGTA
1 AAATTACCGAAATACCCTCGA-TTTGTA
** * * *
39052278 AAATTATTGAAATACCAT-TATAGTGTA
1 AAATTACCGAAATACCCTCGAT-TTGTA
*
39052305 AAATTACTGAAATACCCT
1 AAATTACCGAAATACCCT
39052323 TATAATGTAA
Statistics
Matches: 279, Mismatches: 56, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
25 2 0.01
26 22 0.08
27 234 0.84
28 21 0.08
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:39055347 original size:28 final size:28
Alignment explanation
Indices: 39055315--39055416 Score: 150
Period size: 28 Copynumber: 3.6 Consensus size: 28
39055305 TGGGAAGTAG
* *
39055315 TTGGGCCTAATGGGCCATATAAATGTGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
**
39055343 TTGGGCCTGATGGGTGATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
*
39055371 TTGGGCTTGATGGGCCATATGAATGTGA
1 TTGGGCCTGATGGGCCATATGAATGTGA
*
39055399 TTGGGCCTGATTGGCCAT
1 TTGGGCCTGATGGGCCAT
39055417 GTGTCCGAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.22, C:0.13, G:0.34, T:0.31
Consensus pattern (28 bp):
TTGGGCCTGATGGGCCATATGAATGTGA
Found at i:39055806 original size:26 final size:27
Alignment explanation
Indices: 39055758--39056085 Score: 201
Period size: 27 Copynumber: 12.3 Consensus size: 27
39055748 AGAAATTATT
**
39055758 GAAATACCCCCGGTTTGTAAAATTACC
1 GAAATACCCCTAGTTTGTAAAATTACC
*
39055785 -AAAGTA-CCCTAGTTTCTAAAATTACC
1 GAAA-TACCCCTAGTTTGTAAAATTACC
*
39055811 GAAATACCCCTAGTTTGTAAAATCACC
1 GAAATACCCCTAGTTTGTAAAATTACC
*
39055838 GAAA-ACCCC-CGATTTGTAAAATTACC
1 GAAATACCCCTAG-TTTGTAAAATTACC
* * * * * * *
39055864 GAAATA-CCATCGATTATGAAATTTCT
1 GAAATACCCCTAGTTTGTAAAATTACC
* * *
39055890 GTAATA-CCCTTGATTTGTAAAATTATC
1 GAAATACCCCTAG-TTTGTAAAATTACC
* * *
39055917 G-AATACCCCCAATTTGTGAAATTACC
1 GAAATACCCCTAGTTTGTAAAATTACC
* * *
39055943 GAAACA-CCCTCGATTTTTAAAATTACC
1 GAAATACCCCTAG-TTTGTAAAATTACC
* * *
39055970 TAAACA-CCCTCGATTTGTAAAATTACC
1 GAAATACCCCTAG-TTTGTAAAATTACC
* * *
39055997 GAAATA-CCCTCGATTTGTAAATTTACT
1 GAAATACCCCTAG-TTTGTAAAATTACC
* * * *
39056024 AAAATA-TCCTTGATTTGTAAAATTATC
1 GAAATACCCCTAG-TTTGTAAAATTACC
* * * *
39056051 GAAACACCCCCAATTTGTAAAATTATC
1 GAAATACCCCTAGTTTGTAAAATTACC
39056078 GAAATACC
1 GAAATACC
39056086 ATTGTAGTGT
Statistics
Matches: 238, Mismatches: 52, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
25 1 0.00
26 84 0.35
27 151 0.63
28 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (27 bp):
GAAATACCCCTAGTTTGTAAAATTACC
Found at i:39055830 original size:53 final size:53
Alignment explanation
Indices: 39055758--39056085 Score: 152
Period size: 53 Copynumber: 6.2 Consensus size: 53
39055748 AGAAATTATT
* * *
39055758 GAAATACCCCCGGTTTGTAAAATTACC-AAAGTACCCTAG-TTTCTAAAATTACC
1 GAAATACCCCCAGTTTGTAAAATCACCGAAA--ACCCCAGATTTCTAAAATTACC
* * *
39055811 GAAATACCCCTAGTTTGTAAAATCACCGAAAACCCCCGATTTGTAAAATTACC
1 GAAATACCCCCAGTTTGTAAAATCACCGAAAACCCCAGATTTCTAAAATTACC
** * * * ** * * ** * *
39055864 GAAATACCATC-GATTATGAAATTTCTGTAATACCCTTGATTTGTAAAATTATC
1 GAAATACCCCCAGTTTGTAAAATCACCG-AAAACCCCAGATTTCTAAAATTACC
* * * *
39055917 G-AATACCCCCAATTTGTGAAATTACCGAAACACCCTC-GATTTTTAAAATTACC
1 GAAATACCCCCAGTTTGTAAAATCACCGAAA-ACCC-CAGATTTCTAAAATTACC
* * * * * * *
39055970 TAAACACCCTC-GATTTGTAAAATTACCGAAATACCCTC-GATTTGTAAATTTACT
1 GAAATACCCCCAG-TTTGTAAAATCACCGAAA-ACCC-CAGATTTCTAAAATTACC
* * ** * * * *
39056024 AAAATA-TCCTTGATTTGTAAAATTATCGAAACACCCCCA-ATTTGTAAAATTATC
1 GAAATACCCCCAG-TTTGTAAAATCACCGAAA-A-CCCCAGATTTCTAAAATTACC
39056078 GAAATACC
1 GAAATACC
39056086 ATTGTAGTGT
Statistics
Matches: 212, Mismatches: 51, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
52 24 0.11
53 97 0.46
54 88 0.42
55 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (53 bp):
GAAATACCCCCAGTTTGTAAAATCACCGAAAACCCCAGATTTCTAAAATTACC
Found at i:39056083 original size:54 final size:54
Alignment explanation
Indices: 39055758--39056085 Score: 310
Period size: 54 Copynumber: 6.1 Consensus size: 54
39055748 AGAAATTATT
* * * *
39055758 GAAATACCCCCGGTTTGTAAAATTACC-AAAGTACCCTAG-TTTCTAAAATTACC
1 GAAATACCCTCGATTTGTAAAATTACCGAAA-TACCCTCGATTTGTAAAATTACC
* * *
39055811 GAAATACCC-CTAGTTTGTAAAATCACCGAAA-ACCCCCGATTTGTAAAATTACC
1 GAAATACCCTCGA-TTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACC
* * * * * *
39055864 GAAATACCATCGATTATG--AAATTTCTGTAATACCCTTGATTTGTAAAATTATC
1 GAAATACCCTCGATT-TGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACC
* * * * *
39055917 G-AATACCCCCAATTTGTGAAATTACCGAAACACCCTCGATTTTTAAAATTACC
1 GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACC
* * * *
39055970 TAAACACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAATTTACT
1 GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACC
* * * * * * * *
39056024 AAAATATCCTTGATTTGTAAAATTATCGAAACACCCCCAATTTGTAAAATTATC
1 GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACC
39056078 GAAATACC
1 GAAATACC
39056086 ATTGTAGTGT
Statistics
Matches: 219, Mismatches: 47, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
51 2 0.01
52 24 0.11
53 93 0.42
54 100 0.46
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (54 bp):
GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCGATTTGTAAAATTACC
Found at i:39056096 original size:27 final size:27
Alignment explanation
Indices: 39056066--39056127 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
39056056 ACCCCCAATT
*
39056066 TGTAAAATTATCGAAATACCATTGTAG
1 TGTAAAATTATCAAAATACCATTGTAG
*
39056093 TGTAAAATTATCAAAATACCCTTGTAG
1 TGTAAAATTATCAAAATACCATTGTAG
39056120 TGTAAAAT
1 TGTAAAAT
39056128 AACTGACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (27 bp):
TGTAAAATTATCAAAATACCATTGTAG
Found at i:39056097 original size:81 final size:81
Alignment explanation
Indices: 39055773--39056116 Score: 225
Period size: 81 Copynumber: 4.3 Consensus size: 81
39055763 ACCCCCGGTT
* * * * * * * *
39055773 TGTAAAATTACCAAAGTACCCTAG-TTTCTAAAATTACCGAAATACCCCTAGTTTGTAAAATCAC
1 TGTAAAATTATCAAAATACCCTTGATTTGTAAAATTACCGAAACACCCCCAATTTGTAAAATTAC
** *
39055837 CGAAA-ACCCCCGATT
66 CGAAATACCATCGATG
* * * * * * * * ***
39055852 TGTAAAATTACCGAAATACCATCGATTATG--AAATTTCTGTAATACCCTTGATTTGTAAAATTA
1 TGTAAAATTATCAAAATACCCTTGATT-TGTAAAATTACCGAAACACCCCCAATTTGTAAAATTA
* ** * *
39055915 TCG-AATACCCCCAATT
65 CCGAAATACCATCGATG
* * * * * * * * *
39055931 TGTGAAATTACCGAAACACCCTCGATTTTTAAAATTACCTAAACACCCTCGATTTGTAAAATTAC
1 TGTAAAATTATCAAAATACCCTTGATTTGTAAAATTACCGAAACACCCCCAATTTGTAAAATTAC
* *
39055996 CGAAATACCCTCGATT
66 CGAAATACCATCGATG
* * *
39056012 TGTAAATTTA-CTAAAATATCCTTGATTTGTAAAATTATCGAAACACCCCCAATTTGTAAAATTA
1 TGTAAAATTATC-AAAATACCCTTGATTTGTAAAATTACCGAAACACCCCCAATTTGTAAAATTA
* *
39056076 TCGAAATACCATTG-TAG
65 CCGAAATACCATCGAT-G
39056093 TGTAAAATTATCAAAATACCCTTG
1 TGTAAAATTATCAAAATACCCTTG
39056117 TAGTGTAAAA
Statistics
Matches: 212, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
78 3 0.01
79 81 0.38
80 33 0.16
81 94 0.44
82 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (81 bp):
TGTAAAATTATCAAAATACCCTTGATTTGTAAAATTACCGAAACACCCCCAATTTGTAAAATTAC
CGAAATACCATCGATG
Found at i:39056631 original size:11 final size:11
Alignment explanation
Indices: 39056615--39056640 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39056605 ATTGCATGTA
39056615 TGATATTATTG
1 TGATATTATTG
39056626 TGATATTATTG
1 TGATATTATTG
39056637 TGAT
1 TGAT
39056641 GTGGGCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:39059983 original size:15 final size:14
Alignment explanation
Indices: 39059940--39059983 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
39059930 TAGGAAATTC
*
39059940 TATTTTAAGTTTAT
1 TATTTTAATTTTAT
*
39059954 TTTTTTAATTATTAT
1 TATTTTAATT-TTAT
39059969 TATTTTAGATTTTAT
1 TATTTTA-ATTTTAT
39059984 ATTAATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.32
15 14 0.56
16 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (14 bp):
TATTTTAATTTTAT
Found at i:39060890 original size:23 final size:24
Alignment explanation
Indices: 39060864--39060909 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
39060854 TTCCTTTAAA
39060864 TCAT-TTTGTTATTTAT-TTTCATT
1 TCATCTTT-TTATTTATATTTCATT
*
39060887 TCATCTTTTTATTTTTATTTCAT
1 TCATCTTTTTATTTATATTTCAT
39060910 CTTTTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (24 bp):
TCATCTTTTTATTTATATTTCATT
Found at i:39060920 original size:19 final size:19
Alignment explanation
Indices: 39060875--39060914 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39060865 CATTTTGTTA
39060875 TTTATTTTCATTTCATCTT
1 TTTATTTTCATTTCATCTT
*
39060894 TTTATTTTTATTTCATCTT
1 TTTATTTTCATTTCATCTT
39060913 TT
1 TT
39060915 ACTTTTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTTCATTTCATCTT
Found at i:39065166 original size:15 final size:14
Alignment explanation
Indices: 39065123--39065166 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
39065113 TAGGAAATTC
*
39065123 TATTTTAAGTTTAT
1 TATTTTAATTTTAT
*
39065137 TTTTTTAATTATTAT
1 TATTTTAATT-TTAT
39065152 TATTTTAGATTTTAT
1 TATTTTA-ATTTTAT
39065167 ATTAATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.32
15 14 0.56
16 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (14 bp):
TATTTTAATTTTAT
Found at i:39066072 original size:23 final size:24
Alignment explanation
Indices: 39066046--39066091 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
39066036 TTCCTTTAAA
39066046 TCAT-TTTGTTATTTAT-TTTCATT
1 TCATCTTT-TTATTTATATTTCATT
*
39066069 TCATCTTTTTATTTTTATTTCAT
1 TCATCTTTTTATTTATATTTCAT
39066092 CTTTTACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (24 bp):
TCATCTTTTTATTTATATTTCATT
Found at i:39066102 original size:19 final size:19
Alignment explanation
Indices: 39066057--39066096 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
39066047 CATTTTGTTA
39066057 TTTATTTTCATTTCATCTT
1 TTTATTTTCATTTCATCTT
*
39066076 TTTATTTTTATTTCATCTT
1 TTTATTTTCATTTCATCTT
39066095 TT
1 TT
39066097 ACTTTTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTTCATTTCATCTT
Found at i:39066809 original size:43 final size:42
Alignment explanation
Indices: 39066724--39066824 Score: 107
Period size: 43 Copynumber: 2.4 Consensus size: 42
39066714 TAGAAAGCTC
* * * *
39066724 ATACAATGCCAAC-GTCCCAGACGTGGTCTTACATGTATTCAA
1 ATACAATGCC-ACTGTCCCAAACGTGGTCTTACACGGAATCAA
39066766 ATATCAATGCCACTGTCCCAAACAG-GGTCTTACACGGAATCAA
1 ATA-CAATGCCACTGTCCCAAAC-GTGGTCTTACACGGAATCAA
*
39066809 ATACGATGCCATCTGT
1 ATACAATGCCA-CTGT
39066825 AACATCCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
42 12 0.24
43 37 0.74
44 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
ATACAATGCCACTGTCCCAAACGTGGTCTTACACGGAATCAA
Found at i:39072490 original size:39 final size:39
Alignment explanation
Indices: 39072445--39072565 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
39072435 ATGGAAGACA
*
39072445 CTGGAAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
39072484 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* * *
39072523 CTGGAAATGTGTCCAGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
39072562 CTGG
1 CTGG
39072566 TGCTGGTAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:39075964 original size:52 final size:51
Alignment explanation
Indices: 39075833--39076024 Score: 200
Period size: 52 Copynumber: 3.8 Consensus size: 51
39075823 TAGGAATGAA
* * * *
39075833 ATAGCTTTGGACACAAGTGTGGTATTATGTAAAGGCCAC-TTTG-AGAAGAG
1 ATAGCTTTGGTCAGAAGTGTGGTACTATGTGAAGGCCACTTTTGAAGAA-AG
39075883 ATAGC-TTGGTCACG-AGTGTGGTACTATGTGAAGGCCACTTTATGAAGAAAG
1 ATAGCTTTGGTCA-GAAGTGTGGTACTATGTGAAGGCCACTTT-TGAAGAAAG
* *
39075934 ATAGCTTTGGTCAGAACTGTGATACTATGTGAAGGCCACTTTGTGAAG-AAG
1 ATAGCTTTGGTCAGAAGTGTGGTACTATGTGAAGGCCACTTT-TGAAGAAAG
* * *
39075985 GTAGCTTTGACTACA-AAG-GTGGTACTATGTGCAGGCCACT
1 ATAGCTTTG-GT-CAGAAGTGTGGTACTATGTGAAGGCCACT
39076025 GGGTATTCGT
Statistics
Matches: 122, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
49 28 0.23
50 7 0.06
51 41 0.34
52 44 0.36
53 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (51 bp):
ATAGCTTTGGTCAGAAGTGTGGTACTATGTGAAGGCCACTTTTGAAGAAAG
Found at i:39076013 original size:51 final size:50
Alignment explanation
Indices: 39075833--39076024 Score: 208
Period size: 51 Copynumber: 3.8 Consensus size: 50
39075823 TAGGAATGAA
* * *
39075833 ATAGCTTTGGACACAAGTGTGGTATTATGTAAAGGCCACTTTGAGAAG-AG
1 ATAGCTTT-GACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAG
* * * *
39075883 ATAGCTTGGTCACGAGTGTGGTACTATGTGAAGGCCACTTTATGAAGAAAG
1 ATAGCTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAG
* * * *
39075934 ATAGCTTTGGTCAGAACTGTGATACTATGTGAAGGCCACTTTGTGAAGAAG
1 ATAGCTTT-GACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAG
* *
39075985 GTAGCTTTGACTACAAAG-GTGGTACTATGTGCAGGCCACT
1 ATAGCTTTGAC-AC-AAGTGTGGTACTATGTGAAGGCCACT
39076025 GGGTATTCGT
Statistics
Matches: 118, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
49 33 0.28
50 9 0.08
51 40 0.34
52 36 0.31
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (50 bp):
ATAGCTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAG
Found at i:39079976 original size:39 final size:40
Alignment explanation
Indices: 39079825--39079994 Score: 200
Period size: 40 Copynumber: 4.3 Consensus size: 40
39079815 GGACTAAGAT
* * *
39079825 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
* * *
39079865 CCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
**
39079905 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACA-TC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTA-AGTC
* * * * *
39079945 CCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
39079984 CCGAAGGCATT
1 CCGAAGGCATT
39079995 TGAACGAGGA
Statistics
Matches: 111, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 31 0.28
40 79 0.71
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTACTAAATCCGGGTTAAGTC
Found at i:39080014 original size:79 final size:79
Alignment explanation
Indices: 39079847--39080029 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 79
39079837 GTGCGAGATA
* * * *
39079847 CTAAATCCGGGTTAAGTCCCGAGGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAA-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
39079912 CATTCGTGCGAGTTG
65 CATTCGAACGAGGAG
* * * *
39079927 TTAAATCCGGGTTACATCCCGAAGGCA-TGGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTA-ATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
39079991 CATTTGAACGAGGAG
65 CATTCGAACGAGGAG
*
39080006 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTT-AATCCCGAAGG
39080030 TACGTGATTT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
78 14 0.16
79 48 0.56
80 23 0.27
81 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (79 bp):
CTAAATCCGGGTTAATCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAG
Found at i:39082041 original size:38 final size:37
Alignment explanation
Indices: 39081998--39082132 Score: 119
Period size: 37 Copynumber: 3.6 Consensus size: 37
39081988 ACAAGACTTG
* * *
39081998 CCTACATGGCGTGATCTAGGGTGATCCGCCCAAACTCA
1 CCTACATGGCATGATCCAGGGAGATCCG-CCAAACTCA
* * * *
39082036 CCTACATGTCATGATCCAGGGAGGTTCGCCAAACTCG
1 CCTACATGGCATGATCCAGGGAGATCCGCCAAACTCA
* * * *
39082073 CCTATATGGCATGATCCAGGGAGGTCCGTCAGACTCGA
1 CCTACATGGCATGATCCAGGGAGATCCGCCAAACTC-A
* * *
39082111 -CTATATGGCATAATCCATGGAG
1 CCTACATGGCATGATCCAGGGAG
39082133 GTTAGTGAGA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
37 59 0.73
38 22 0.27
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (37 bp):
CCTACATGGCATGATCCAGGGAGATCCGCCAAACTCA
Found at i:39082086 original size:37 final size:37
Alignment explanation
Indices: 39082027--39082135 Score: 137
Period size: 37 Copynumber: 2.9 Consensus size: 37
39082017 GGTGATCCGC
* * *
39082027 CCAAACTCACCTACATGTCATGATCCAGGGAGGTTCG
1 CCAAACTCGCCTATATGGCATGATCCAGGGAGGTTCG
*
39082064 CCAAACTCGCCTATATGGCATGATCCAGGGAGGTCCG
1 CCAAACTCGCCTATATGGCATGATCCAGGGAGGTTCG
* * * * *
39082101 TCAGACTCGACTATATGGCATAATCCATGGAGGTT
1 CCAAACTCGCCTATATGGCATGATCCAGGGAGGTT
39082136 AGTGAGATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.23
Consensus pattern (37 bp):
CCAAACTCGCCTATATGGCATGATCCAGGGAGGTTCG
Found at i:39089306 original size:88 final size:88
Alignment explanation
Indices: 39089157--39089332 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 88
39089147 GATCCTTTTA
*
39089157 GCTACTAGAACTCACCTTTTACATTTTATTCAATTTGGTCCTTTCCCTAATTAAACCCATAATCA
1 GCTACTAGAACTCACCTTTTACATTTTATTCAATTTGGTCCTTTCCCTAATTAAACACATAATCA
39089222 ATAAAATTTTCTTATCAGAATTT
66 ATAAAATTTTCTTATCAGAATTT
39089245 GCTACTAGAACTCACCTTTTACATTTTATTCAATTTGGTCCTTTCCCTAATTAAACACATAATCA
1 GCTACTAGAACTCACCTTTTACATTTTATTCAATTTGGTCCTTTCCCTAATTAAACACATAATCA
39089310 ATAAAATTTTCTTATCAGAATTT
66 ATAAAATTTTCTTATCAGAATTT
39089333 TCATATAGCA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (88 bp):
GCTACTAGAACTCACCTTTTACATTTTATTCAATTTGGTCCTTTCCCTAATTAAACACATAATCA
ATAAAATTTTCTTATCAGAATTT
Found at i:39090734 original size:21 final size:21
Alignment explanation
Indices: 39090708--39090754 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39090698 TGTGGGTGTC
39090708 CACACGCCCATGTGAAGGCCA
1 CACACGCCCATGTGAAGGCCA
** *
39090729 CACACGCCTGTGTGGAGGCCA
1 CACACGCCCATGTGAAGGCCA
*
39090750 TACAC
1 CACAC
39090755 TTCCGTGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.36, G:0.26, T:0.13
Consensus pattern (21 bp):
CACACGCCCATGTGAAGGCCA
Found at i:39091068 original size:63 final size:64
Alignment explanation
Indices: 39090991--39091111 Score: 217
Period size: 64 Copynumber: 1.9 Consensus size: 64
39090981 CACATGGCTG
39090991 TGTGGCACCAAAAATCA-CAAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGACCATCTA
1 TGTGGCACCAAAAATCACCAAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGACCATCTA
* *
39091054 TGTGGCACCAAAAATCACCCAAAAAGCCTAATTCCCAATTTCACATGGCCGTGTGGAC
1 TGTGGCACCAAAAATCACCAAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGAC
39091112 TGCCCATGTG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (64 bp):
TGTGGCACCAAAAATCACCAAAAAAGCCTAATTCCCAATTTCACATGACCGTGTGGACCATCTA
Found at i:39108861 original size:100 final size:100
Alignment explanation
Indices: 39108688--39108945 Score: 489
Period size: 100 Copynumber: 2.6 Consensus size: 100
39108678 AAGAACATGT
* *
39108688 TGGGCTGAGTAATCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAACAGGTTTGATGTG
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAACAGGTTTGATGTG
39108753 TTCTTAAGGAAAATTATAATAAATTAGGAGTTTGC
66 TTCTTAAGGAAAATTATAATAAATTAGGAGTTTGC
39108788 TGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAACAGGTTTGATGTG
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAACAGGTTTGATGTG
39108853 TTCTTAAGGAAAATTATAATAAATTAGGAGTTTGC
66 TTCTTAAGGAAAATTATAATAAATTAGGAGTTTGC
*
39108888 TGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAAAAGGTT
1 TGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAACAGGTT
39108946 CAGTATATTC
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 155 1.00
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.33
Consensus pattern (100 bp):
TGGGCTGAGTAACCGGGGTGGGGTGCTTAGCTGTCATCTCTCTTCGCGTCAACAGGTTTGATGTG
TTCTTAAGGAAAATTATAATAAATTAGGAGTTTGC
Found at i:39113450 original size:20 final size:19
Alignment explanation
Indices: 39113409--39113451 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
39113399 TTCGATCAAT
*
39113409 TTTTGGGTCTCGATCCTGA
1 TTTTGGGTCTCGATCCTAA
*
39113428 TTTTGGGTTCTCGATTCTAA
1 TTTTGGG-TCTCGATCCTAA
39113448 TTTT
1 TTTT
39113452 CGATCTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (19 bp):
TTTTGGGTCTCGATCCTAA
Found at i:39113473 original size:13 final size:13
Alignment explanation
Indices: 39113457--39113481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39113447 ATTTTCGATC
39113457 TAAAGTTCAATTT
1 TAAAGTTCAATTT
39113470 TAAAGTTCAATT
1 TAAAGTTCAATT
39113482 ACCTATTGGG
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TAAAGTTCAATTT
Found at i:39117842 original size:25 final size:26
Alignment explanation
Indices: 39117803--39117874 Score: 103
Period size: 25 Copynumber: 2.8 Consensus size: 26
39117793 CAAGCCCATT
39117803 TTCACAGCTCGTGTAAGCATACT-GA
1 TTCACAGCTCGTGTAAGCATACTCGA
* *
39117828 TTTACAGCTCATGTAAGCATA-TCGA
1 TTCACAGCTCGTGTAAGCATACTCGA
*
39117853 TTCACAGCTCGTGTGAGCATAC
1 TTCACAGCTCGTGTAAGCATAC
39117875 ATGTACAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (26 bp):
TTCACAGCTCGTGTAAGCATACTCGA
Found at i:39121970 original size:120 final size:120
Alignment explanation
Indices: 39121757--39121996 Score: 462
Period size: 120 Copynumber: 2.0 Consensus size: 120
39121747 CGATACTTCC
* *
39121757 GTTCCAAACCTAAAAAATTCAGCATACATTAGCAATTAATCCTTTCCAGTTTAGTTCCTAAACAT
1 GTTCCAAACCTAAAAAATTCAGCACACATTAGCAATTAATCCTTTCCAATTTAGTTCCTAAACAT
39121822 CATGCATAAATTACTTCAACAAATAATCATTCAACAGCCTAATTAAGAATTCAAT
66 CATGCATAAATTACTTCAACAAATAATCATTCAACAGCCTAATTAAGAATTCAAT
39121877 GTTCCAAACCTAAAAAATTCAGCACACATTAGCAATTAATCCTTTCCAATTTAGTTCCTAAACAT
1 GTTCCAAACCTAAAAAATTCAGCACACATTAGCAATTAATCCTTTCCAATTTAGTTCCTAAACAT
39121942 CATGCATAAATTACTTCAACAAATAATCATTCAACAGCCTAATTAAGAATTCAAT
66 CATGCATAAATTACTTCAACAAATAATCATTCAACAGCCTAATTAAGAATTCAAT
39121997 ATCGCATAGT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.30
Consensus pattern (120 bp):
GTTCCAAACCTAAAAAATTCAGCACACATTAGCAATTAATCCTTTCCAATTTAGTTCCTAAACAT
CATGCATAAATTACTTCAACAAATAATCATTCAACAGCCTAATTAAGAATTCAAT
Found at i:39128230 original size:30 final size:30
Alignment explanation
Indices: 39128189--39128457 Score: 153
Period size: 30 Copynumber: 9.1 Consensus size: 30
39128179 TCAACCAATA
* * *
39128189 AAAAGGAATAGCTTCGACTATCGAGTTATG
1 AAAAGGGATAGCTTCGACCATCGAATTATG
**
39128219 AAAAGGGATAGCTTCGACCATAAAATTATG
1 AAAAGGGATAGCTTCGACCATCGAATTATG
* * * *
39128249 ACAAGGGAT-GGTGACGACCATC-AATAATG
1 AAAAGGGATAGCT-TCGACCATCGAATTATG
* * *
39128278 AAAAGGGAT-G--ACGACCATAGAACTATG
1 AAAAGGGATAGCTTCGACCATCGAATTATG
* * * *
39128305 AAAAGGGATAGTTTTGACTATTGAATTATG
1 AAAAGGGATAGCTTCGACCATCGAATTATG
* * * *
39128335 AAAAGGGATAGCTTTGGCTATCAAATTATG
1 AAAAGGGATAGCTTCGACCATCGAATTATG
* * * *
39128365 AAAAGGAAT-GGTGAT-GAGCATC-AACTATG
1 AAAAGGGATAGCT--TCGACCATCGAATTATG
* * * *
39128394 AAAAGGGAT-GGTGACGA-CATCAAAATATG
1 AAAAGGGATAGCT-TCGACCATCGAATTATG
* *
39128423 AAAAGGGATAGCTTCAACTATCGAATTATGG
1 AAAAGGGATAGCTTCGACCATCGAATTAT-G
39128454 AAAA
1 AAAA
39128458 AGATGGTCAC
Statistics
Matches: 188, Mismatches: 39, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
26 8 0.04
27 14 0.07
28 5 0.03
29 55 0.29
30 100 0.53
31 6 0.03
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (30 bp):
AAAAGGGATAGCTTCGACCATCGAATTATG
Found at i:39128395 original size:116 final size:116
Alignment explanation
Indices: 39128189--39128457 Score: 328
Period size: 116 Copynumber: 2.3 Consensus size: 116
39128179 TCAACCAATA
* * *
39128189 AAAAGGAATAGCTTCGACTATCGAGTTATGAAAAGGGATAGCTTCGACCATAAAATTATGACAAG
1 AAAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCGACCATAAAATTATGAAAAG
* *
39128254 GGATGGTGACGACCATCAATAATGAAAAGGGA-TGACGACCAT-AGAACTATG
66 GAATGGTGACGACCATCAATAATGAAAAGGGAGTGACGA-CATCA-AAATATG
* * * * * * *
39128305 AAAAGGGATAGTTTTGACTATTGAATTATGAAAAGGGATAGCTTTGGCTATCAAATTATGAAAAG
1 AAAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCGACCATAAAATTATGAAAAG
* *
39128370 GAATGGTGATGAGCATCAACT-ATGAAAAGGGATGGTGACGACATCAAAATATG
66 GAATGGTGACGACCATCAA-TAATGAAAAGGGA--GTGACGACATCAAAATATG
*
39128423 AAAAGGGATAGCTTCAACTATCGAATTATGGAAAA
1 AAAAGGGATAGCTTCGACTATCGAATTAT-GAAAA
39128458 AGATGGTCAC
Statistics
Matches: 129, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
116 82 0.64
117 1 0.01
118 34 0.26
119 12 0.09
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.23
Consensus pattern (116 bp):
AAAAGGGATAGCTTCGACTATCGAATTATGAAAAGGGATAGCTTCGACCATAAAATTATGAAAAG
GAATGGTGACGACCATCAATAATGAAAAGGGAGTGACGACATCAAAATATG
Found at i:39130335 original size:156 final size:156
Alignment explanation
Indices: 39130090--39130403 Score: 628
Period size: 156 Copynumber: 2.0 Consensus size: 156
39130080 ATTGGATGGC
39130090 CTTATTGTGTAAATTAGCCATCCTAAAGATAATGGGACAGTTGGATGCTTTAATTTCTTTTAATT
1 CTTATTGTGTAAATTAGCCATCCTAAAGATAATGGGACAGTTGGATGCTTTAATTTCTTTTAATT
39130155 ATAATGTTTTATATGTTATTTTTTTAAGAAAATAAGTAAAAGGTTAATAAAATAAAGAAAACATG
66 ATAATGTTTTATATGTTATTTTTTTAAGAAAATAAGTAAAAGGTTAATAAAATAAAGAAAACATG
39130220 ATAGTTTTCTTCCCTAATTTGTTTTG
131 ATAGTTTTCTTCCCTAATTTGTTTTG
39130246 CTTATTGTGTAAATTAGCCATCCTAAAGATAATGGGACAGTTGGATGCTTTAATTTCTTTTAATT
1 CTTATTGTGTAAATTAGCCATCCTAAAGATAATGGGACAGTTGGATGCTTTAATTTCTTTTAATT
39130311 ATAATGTTTTATATGTTATTTTTTTAAGAAAATAAGTAAAAGGTTAATAAAATAAAGAAAACATG
66 ATAATGTTTTATATGTTATTTTTTTAAGAAAATAAGTAAAAGGTTAATAAAATAAAGAAAACATG
39130376 ATAGTTTTCTTCCCTAATTTGTTTTG
131 ATAGTTTTCTTCCCTAATTTGTTTTG
39130402 CT
1 CT
39130404 ATTCATCGAA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 158 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (156 bp):
CTTATTGTGTAAATTAGCCATCCTAAAGATAATGGGACAGTTGGATGCTTTAATTTCTTTTAATT
ATAATGTTTTATATGTTATTTTTTTAAGAAAATAAGTAAAAGGTTAATAAAATAAAGAAAACATG
ATAGTTTTCTTCCCTAATTTGTTTTG
Found at i:39131226 original size:20 final size:20
Alignment explanation
Indices: 39131173--39131230 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
39131163 ATGCCTCTGT
*
39131173 TTGCACTTTAGTGCCCCTGA
1 TTGCACTTTAGTGCTCCTGA
* *
39131193 TCGCA-TATTCGTGCTCCTGA
1 TTGCACT-TTAGTGCTCCTGA
*
39131213 TTGCACTTTGGTGCTCCT
1 TTGCACTTTAGTGCTCCT
39131231 ATTATGCATC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCACTTTAGTGCTCCTGA
Found at i:39132972 original size:30 final size:30
Alignment explanation
Indices: 39132938--39133001 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
39132928 TGTCTCAATT
*
39132938 GTGTGTGGCACACGGCCACGCGACATAGCC
1 GTGTGTGACACACGGCCACGCGACATAGCC
* *
39132968 GTGTGTGACACATGGCCATGCGACATAGCC
1 GTGTGTGACACACGGCCACGCGACATAGCC
39132998 GTGT
1 GTGT
39133002 CCCTTGTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.28, G:0.33, T:0.19
Consensus pattern (30 bp):
GTGTGTGACACACGGCCACGCGACATAGCC
Found at i:39144949 original size:15 final size:15
Alignment explanation
Indices: 39144929--39144957 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39144919 TTTAGGGGAG
39144929 AAAAAACTCCCTATA
1 AAAAAACTCCCTATA
39144944 AAAAAACTCCCTAT
1 AAAAAACTCCCTAT
39144958 CGTTAATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAACTCCCTATA
Found at i:39145173 original size:65 final size:65
Alignment explanation
Indices: 39145092--39145220 Score: 258
Period size: 65 Copynumber: 2.0 Consensus size: 65
39145082 CTTGACGTGG
39145092 AATATTGCAAGAAGAGAAAGCATATCCCACTATGATATATTCTTCTTTTTACATTGCATGAAAAA
1 AATATTGCAAGAAGAGAAAGCATATCCCACTATGATATATTCTTCTTTTTACATTGCATGAAAAA
39145157 AATATTGCAAGAAGAGAAAGCATATCCCACTATGATATATTCTTCTTTTTACATTGCATGAAAA
1 AATATTGCAAGAAGAGAAAGCATATCCCACTATGATATATTCTTCTTTTTACATTGCATGAAAA
39145221 CTTTTTCACG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (65 bp):
AATATTGCAAGAAGAGAAAGCATATCCCACTATGATATATTCTTCTTTTTACATTGCATGAAAAA
Found at i:39147952 original size:27 final size:27
Alignment explanation
Indices: 39147891--39147955 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
39147881 GTCGAATGAT
*
39147891 TGAAATACCCCCATAGGGTAAAATAAC
1 TGAAATACCCTCATAGGGTAAAATAAC
*
39147918 TGAAATACCCTCATAGGGTAAAATGAC
1 TGAAATACCCTCATAGGGTAAAATAAC
**
39147945 TGTTATACCCT
1 TGAAATACCCT
39147956 TCAGAGATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (27 bp):
TGAAATACCCTCATAGGGTAAAATAAC
Found at i:39148210 original size:26 final size:26
Alignment explanation
Indices: 39148178--39148258 Score: 108
Period size: 26 Copynumber: 3.1 Consensus size: 26
39148168 TTTGCCACAT
* *
39148178 ATACTATTACTGGTAGCTTTACTGCG
1 ATACTATTACTGGCAGCTTTACTACG
*
39148204 ATACTATTACTGGCAGCTTTACTACT
1 ATACTATTACTGGCAGCTTTACTACG
* **
39148230 ATACTATTACTGACAAATTTACTACG
1 ATACTATTACTGGCAGCTTTACTACG
39148256 ATA
1 ATA
39148259 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTACTACG
Found at i:39148408 original size:28 final size:28
Alignment explanation
Indices: 39148366--39148454 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
39148356 ACTGCATTGT
39148366 TACTGTATTGGGCTAAGGCCCACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
*
39148394 TTCTGTATTGGGCTAAGGCCCACACTGA
1 TACTGTATTGGGCTAAGGCCCACACTGA
* * *
39148422 TACTGTATTAGGATAAGGCTCACACT-A
1 TACTGTATTGGGCTAAGGCCCACACTGA
39148449 TACTGT
1 TACTGT
39148455 CACTGAGTAG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 7 0.12
28 49 0.88
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACACTGA
Found at i:39149342 original size:18 final size:18
Alignment explanation
Indices: 39149311--39149345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39149301 ATTCTCTTGA
39149311 AAGAACAAAAATTGCTGG
1 AAGAACAAAAATTGCTGG
* *
39149329 AAGAAGAAAGATTGCTG
1 AAGAACAAAAATTGCTG
39149346 CCGAATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.26, T:0.17
Consensus pattern (18 bp):
AAGAACAAAAATTGCTGG
Found at i:39153567 original size:7 final size:7
Alignment explanation
Indices: 39153557--39153581 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39153547 AAATATTTTT
39153557 AAATTGA
1 AAATTGA
39153564 AAATTGA
1 AAATTGA
39153571 AAATTGA
1 AAATTGA
39153578 AAAT
1 AAAT
39153582 AGTTACTTAT
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:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
AAATTGA
Found at i:39159448 original size:40 final size:40
Alignment explanation
Indices: 39159350--39159612 Score: 300
Period size: 40 Copynumber: 6.6 Consensus size: 40
39159340 TCCTCGTTCA
* * * ** *
39159350 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
39159389 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
39159429 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
39159469 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
39159509 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
39159549 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
39159589 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39159613 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:39167298 original size:27 final size:27
Alignment explanation
Indices: 39167268--39167445 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39167258 ATATTGAGTC
* * * *
39167268 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39167295 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39167322 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39167350 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39167377 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39167404 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39167431 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39167446 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39167407 original size:82 final size:81
Alignment explanation
Indices: 39167289--39167444 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39167279 TGCTATATAA
* *
39167289 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39167354 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39167371 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39167435 CACTTAGTGC
65 CACTTAGTGC
39167445 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39172867 original size:11 final size:11
Alignment explanation
Indices: 39172851--39172875 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39172841 TAGAAAACGA
39172851 ACAAATGCAAT
1 ACAAATGCAAT
39172862 ACAAATGCAAT
1 ACAAATGCAAT
39172873 ACA
1 ACA
39172876 TCCAGAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (11 bp):
ACAAATGCAAT
Found at i:39175796 original size:24 final size:24
Alignment explanation
Indices: 39175769--39175844 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
39175759 AAATGATTAT
*
39175769 TTTGCCTATGATGTAAATGAATGA
1 TTTGCCTATGATGTAAATGACTGA
*
39175793 TTTGTCCGA-GATGTAAATGACTGA
1 TTTG-CCTATGATGTAAATGACTGA
* * *
39175817 TTTGTCTGTGATTTAAATGACTGA
1 TTTGCCTATGATGTAAATGACTGA
39175841 TTTG
1 TTTG
39175845 TCTTTGATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.02
24 40 0.91
25 3 0.07
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (24 bp):
TTTGCCTATGATGTAAATGACTGA
Found at i:39175845 original size:24 final size:24
Alignment explanation
Indices: 39175777--39175866 Score: 108
Period size: 24 Copynumber: 3.8 Consensus size: 24
39175767 ATTTTGCCTA
* *
39175777 TGATGTAAATGAATGATTTGTCCG
1 TGATGTAAATGACTGATTTGTCTG
*
39175801 AGATGTAAATGACTGATTTGTCTG
1 TGATGTAAATGACTGATTTGTCTG
* *
39175825 TGATTTAAATGACTGATTTGTCTT
1 TGATGTAAATGACTGATTTGTCTG
* **
39175849 TGATTTGTATGACTGATT
1 TGATGTAAATGACTGATT
39175867 CCGTGTAGGG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (24 bp):
TGATGTAAATGACTGATTTGTCTG
Found at i:39176174 original size:63 final size:64
Alignment explanation
Indices: 39176082--39176220 Score: 190
Period size: 63 Copynumber: 2.2 Consensus size: 64
39176072 TTGGTGGCCG
* * * *
39176082 TGTGCCGATCATATTACCATTACTGATGGTTGTGTGCCGATCATATTACTTCTAC-AATTGCTT
1 TGTGCCGATCATACTAACATTACTGATGGTTGTGTGCCGATCATATTACTACTACTAATGGCTT
* * * *
39176145 TGTGCTGATCATACTAATATTATTGATGGTTGTGTGCCGATCATATTACTACTACTGATGGCTT
1 TGTGCCGATCATACTAACATTACTGATGGTTGTGTGCCGATCATATTACTACTACTAATGGCTT
*
39176209 TGTGCCAATCAT
1 TGTGCCGATCAT
39176221 TTTACTGTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
63 49 0.75
64 16 0.25
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (64 bp):
TGTGCCGATCATACTAACATTACTGATGGTTGTGTGCCGATCATATTACTACTACTAATGGCTT
Found at i:39176213 original size:95 final size:95
Alignment explanation
Indices: 39176048--39176226 Score: 243
Period size: 95 Copynumber: 1.9 Consensus size: 95
39176038 TATTGATGGA
* * * *
39176048 TTTGTGCAGATCATATTACCATTATTGGTGGCCGTGTGCCGATCATATTACCATTACTGATGGTT
1 TTTGTGCAGATCATACTAACATTATTGATGGCCGTGTGCCGATCATATTACCACTACTGATGGTT
*
39176113 GTGTGCCGATCATATTACTTCTACAATTGC
66 GTGTGCCAATCATATTACTTCTACAATTGC
* * ** *
39176143 TTTGTGCTGATCATACTAATATTATTGATGGTTGTGTGCCGATCATATTACTACTACTGATGGCT
1 TTTGTGCAGATCATACTAACATTATTGATGGCCGTGTGCCGATCATATTACCACTACTGATGG-T
*
39176208 T-TGTGCCAATCATTTTACT
65 TGTGTGCCAATCATATTACT
39176227 GTACTTATGG
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 70 0.97
96 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (95 bp):
TTTGTGCAGATCATACTAACATTATTGATGGCCGTGTGCCGATCATATTACCACTACTGATGGTT
GTGTGCCAATCATATTACTTCTACAATTGC
Found at i:39176226 original size:32 final size:33
Alignment explanation
Indices: 39176041--39176239 Score: 153
Period size: 32 Copynumber: 6.3 Consensus size: 33
39176031 GCGATGCTAT
* * * * *
39176041 TGATGGATT-TGTGCAGATCATATTACCATTAT
1 TGATGGCTTGTGTGCCGATCATATTACTACTAC
* * * *
39176073 TGGTGGC-CGTGTGCCGATCATATTACCATTAC
1 TGATGGCTTGTGTGCCGATCATATTACTACTAC
*
39176105 TGATGG-TTGTGTGCCGATCATATTACTTCTAC
1 TGATGGCTTGTGTGCCGATCATATTACTACTAC
* * * * * * *
39176137 -AATTGCTT-TGTGCTGATCATACTAATATTAT
1 TGATGGCTTGTGTGCCGATCATATTACTACTAC
39176168 TGATGG-TTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTTGTGTGCCGATCATATTACTACTAC
* * *
39176200 TGATGGCTT-TGTGCCAATCATTTTACT-GTAC
1 TGATGGCTTGTGTGCCGATCATATTACTACTAC
*
39176231 TTATGGCTT
1 TGATGGCTT
39176240 ATAGCCATTC
Statistics
Matches: 132, Mismatches: 29, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
31 33 0.25
32 97 0.73
33 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (33 bp):
TGATGGCTTGTGTGCCGATCATATTACTACTAC
Found at i:39176261 original size:22 final size:22
Alignment explanation
Indices: 39176231--39176277 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
39176221 TTTACTGTAC
* *
39176231 TTATGGCTTATAGCCATTCTAT
1 TTATAGCTTATAGCCATCCTAT
*
39176253 TTATAGCTTATAGCTATCCTAT
1 TTATAGCTTATAGCCATCCTAT
39176275 TTA
1 TTA
39176278 CGGCTCTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTAT
Found at i:39179222 original size:21 final size:23
Alignment explanation
Indices: 39179181--39179228 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
39179171 TATTAACCTT
*
39179181 TTAACTTTATAATAATAAT-AAA
1 TTAACTTTATAAAAATAATAAAA
39179203 TTAAC-TTATAAAACAT-ATAAAA
1 TTAACTTTATAAAA-ATAATAAAA
39179225 TTAA
1 TTAA
39179229 AATATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAACTTTATAAAAATAATAAAA
Found at i:39181944 original size:14 final size:15
Alignment explanation
Indices: 39181922--39181954 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
39181912 ATGATATTTC
*
39181922 TATTATTTTTAGTAT
1 TATTATTTTTACTAT
39181937 TATT-TTTTTACTAT
1 TATTATTTTTACTAT
39181951 TATT
1 TATT
39181955 CTTACTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (15 bp):
TATTATTTTTACTAT
Found at i:39181959 original size:12 final size:12
Alignment explanation
Indices: 39181921--39181964 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
39181911 TATGATATTT
39181921 CTATTATTTTTA
1 CTATTATTTTTA
*
39181933 GTATTATTTTTTTA
1 CTATTA--TTTTTA
*
39181947 CTATTATTCTTA
1 CTATTATTTTTA
39181959 CTATTA
1 CTATTA
39181965 CCTTTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (12 bp):
CTATTATTTTTA
Found at i:39182065 original size:6 final size:6
Alignment explanation
Indices: 39181998--39182064 Score: 86
Period size: 6 Copynumber: 11.5 Consensus size: 6
39181988 ATTGATTTTA
39181998 TTTC-T TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTC-T
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
* *
39182044 TTTTAT CTTT-AT TTTTAT TTT
1 TTTCAT -TTTCAT TTTCAT TTT
39182065 TGTTTTAGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
5 11 0.19
6 43 0.75
7 3 0.05
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTCAT
Found at i:39182070 original size:23 final size:25
Alignment explanation
Indices: 39182031--39182094 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 25
39182021 TTTCATTTTC
*
39182031 ATTTTCATTTTCTTTTTA-T-CTTT
1 ATTTTTATTTTCTTTTTAGTACTTT
39182054 ATTTTTATTTT-TGTTTTAGTTACTTT
1 ATTTTTATTTTCT-TTTTAG-TACTTT
*
39182080 ATTTTTTATCTTCTT
1 A-TTTTTATTTTCTT
39182095 AGGCTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
22 1 0.03
23 15 0.45
25 1 0.03
26 5 0.15
27 10 0.30
28 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.73
Consensus pattern (25 bp):
ATTTTTATTTTCTTTTTAGTACTTT
Found at i:39189543 original size:340 final size:341
Alignment explanation
Indices: 39188546--39189568 Score: 1913
Period size: 341 Copynumber: 3.0 Consensus size: 341
39188536 AACTACTTAT
*
39188546 ACAGTAAATCATTATCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
*
39188611 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATCTCCCACTATGATATATTCTTTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
*
39188676 GTTGCATGAAAACTTTTTTACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
* *
39188741 TAATCGAGTTATAAATATAAGAAAATTCACAACCGTGAGCTTAAAGGTTAGAAAAACAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
*
39188806 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGCAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
*
39188871 TAAACCTAAACATTAA
326 TAACCCTAAACATTAA
* *
39188887 ACAGTAAATCATTGTCAATCCATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
39188952 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
39189017 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
*
39189082 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAATAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
39189147 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
39189212 TAACCCTAAACATTAA
326 TAACCCTAAACATTAA
39189228 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
1 ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
*
39189293 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATGCCACTATGATATATTC-TTTTTTTAC
66 AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
*
39189357 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCTTGAATTGAAACT
131 GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
39189422 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
196 TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
* *
39189487 ACAATTTTATTAATCACTAGTTTACTAAAAGCAAATAGTTGAGAAGCTGATAATTGGAATGAAAA
261 ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
39189552 TAACCCTAAACATTAA
326 TAACCCTAAACATTAA
39189568 A
1 A
39189569 TAGTCAAGGC
Statistics
Matches: 665, Mismatches: 17, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
340 217 0.33
341 448 0.67
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (341 bp):
ACAGTAAATCATTGTCGATCAATCTTTCCAAGAAATTTCTATTAATTTTATATCATTTGGTTGCA
AAACTTGACGTGGAGTCTTGTAAGAAGAGAGAGCATATCCCACTATGATATATTCTTTTTTTTAC
GTTGCATGAAAACTTTTTAACTGAATCATGAAAGTGAAAAGTGTATCCATGCATGAATTGAAACT
TAATCGAGTTATAAATATAAGAAAATTCACAGCCTTGAGCTTAAAGGTTAGAAAAACAGGATGCA
ACAATTTTATTAATCACCAGTTTACTAAAAGCAAATAGTTGAGATGCTGATAATTGGAATGAAAA
TAACCCTAAACATTAA
Found at i:39190307 original size:23 final size:23
Alignment explanation
Indices: 39190281--39190327 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
39190271 TCATTTTCAT
*
39190281 TGATCTTAATCTTGATT-TTTTGC
1 TGATCTTAATCCTG-TTGTTTTGC
39190304 TGATCTTAATCCTGTTGTTTTGC
1 TGATCTTAATCCTGTTGTTTTGC
39190327 T
1 T
39190328 TTCCTCTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (23 bp):
TGATCTTAATCCTGTTGTTTTGC
Found at i:39191571 original size:7 final size:7
Alignment explanation
Indices: 39191559--39191587 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
39191549 AACATTTAAA
39191559 TAAATTT
1 TAAATTT
39191566 TAAATTT
1 TAAATTT
39191573 TAAATTT
1 TAAATTT
39191580 TAAATTT
1 TAAATTT
39191587 T
1 T
39191588 TTAGTTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAAATTT
Found at i:39192502 original size:12 final size:12
Alignment explanation
Indices: 39192484--39192526 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
39192474 TGTGTTATTT
39192484 CTATTATTTTTA
1 CTATTATTTTTA
*
39192496 GTATTATTTTTTA
1 CTATTA-TTTTTA
*
39192509 CTATTATTCTTA
1 CTATTATTTTTA
*
39192521 CAATTA
1 CTATTA
39192527 CATTTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (12 bp):
CTATTATTTTTA
Found at i:39192508 original size:13 final size:13
Alignment explanation
Indices: 39192484--39192516 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39192474 TGTGTTATTT
39192484 CTATTA-TTTTTA
1 CTATTATTTTTTA
*
39192496 GTATTATTTTTTA
1 CTATTATTTTTTA
39192509 CTATTATT
1 CTATTATT
39192517 CTTACAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (13 bp):
CTATTATTTTTTA
Found at i:39192572 original size:6 final size:6
Alignment explanation
Indices: 39192561--39192621 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
39192551 ATTTTATTTC
* * *
39192561 TTTTAT TTTTAT TTTTAT TTTTAT CTTTAT TTTTGT TTGTAGT TGCTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T T--TTTAT
39192612 TTTTAT TTTT
1 TTTTAT TTTT
39192622 TTAGACTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 39 0.85
7 2 0.04
8 2 0.04
9 3 0.07
ACGTcount: A:0.13, C:0.03, G:0.07, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:39203804 original size:42 final size:43
Alignment explanation
Indices: 39203738--39203858 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 43
39203728 ATCAAATATT
* * * *
39203738 GATGCCACTGTCCCAGATAGGGTCTTACACGAAAT-T-ATATAC
1 GATGCCAATGTCCCAGACATGGTCTTACACGAAATCTCAAAT-C
* *
39203780 GATGCCAATGTCCCTGACATGGTCTTACA-GTAAATCTCAAATT
1 GATGCCAATGTCCCAGACATGGTCTTACACG-AAATCTCAAATC
* *
39203823 GATTCCAATGTCCCAGACGTGGTCTTACACGAAATC
1 GATGCCAATGTCCCAGACATGGTCTTACACGAAATC
39203859 AGATATCAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 29 0.44
43 32 0.48
44 4 0.06
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (43 bp):
GATGCCAATGTCCCAGACATGGTCTTACACGAAATCTCAAATC
Found at i:39208875 original size:51 final size:51
Alignment explanation
Indices: 39208813--39208996 Score: 221
Period size: 51 Copynumber: 3.6 Consensus size: 51
39208803 GTTCACATAT
* * *
39208813 TAGCCTACACATAGTACTACACATGTGACCATCA-CTATCCGATACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCAT-AGCTATCCGGTACACGTAG
* ** *
39208864 TAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATCCGGTATGCATAG
1 TAGCCTGCACATAGTACTACACACGTGA-CCATAGCTATCCGGTACACGTAG
* * * * *
39208915 TAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCATAGCTATCCGGTACACGTAG
39208965 TAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGCCTGCACATAGTACTACACACGTGACCAT
39208997 CACTTTCACT
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 43 0.39
51 66 0.59
52 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGCCTGCACATAGTACTACACACGTGACCATAGCTATCCGGTACACGTAG
Found at i:39208977 original size:101 final size:101
Alignment explanation
Indices: 39208808--39208992 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
39208798 TACCGGTTCA
* *
39208808 CATATTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCGATACACGTAGTAGCCTGCA
39208873 CATAGTACTACACACGTGATCGAAGCTATCCGGTATG
65 CATAGTACTACACACGTGATCGAAGCTATCCGGTATG
* * * *
39208910 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCGATACACGTAGTAGCCTGCA
39208974 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
39208993 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 1 0.01
101 43 0.57
102 32 0.42
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTATG
Found at i:39209016 original size:101 final size:100
Alignment explanation
Indices: 39208803--39209026 Score: 249
Period size: 101 Copynumber: 2.2 Consensus size: 100
39208793 AATGATACCG
* * *
39208803 GTTCACATATTAGCCTACACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGC
1 GTTCATATAGTAGCCTACACATAGTACTACACATGCGACCAT-ACTATCCGATACACGTAGTAGC
*
39208868 CTGCACATAGTACTACACACGTGATCGAAGCTATCC
65 CTGCACATAGTACTACACACGTGATCCAAGCTATCC
* * * * *
39208904 GGT-ATGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCTTTCTGGTACACGTAGTA
1 GTTCAT--ATAGTAGCCTACACATAGTACTACACATGCGACCATA-CTATCCGATACACGTAGTA
*
39208967 GCCTGCACATAGTACTACACACGTGA-CCATCA-CTTTCAC
63 GCCTGCACATAGTACTACACACGTGATCCA--AGCTATC-C
* *
39209006 TTTCATATAGTGGCCTACACA
1 GTTCATATAGTAGCCTACACA
39209027 CAGTCTGTGC
Statistics
Matches: 102, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
100 4 0.04
101 62 0.61
102 34 0.33
103 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (100 bp):
GTTCATATAGTAGCCTACACATAGTACTACACATGCGACCATACTATCCGATACACGTAGTAGCC
TGCACATAGTACTACACACGTGATCCAAGCTATCC
Found at i:39211789 original size:29 final size:29
Alignment explanation
Indices: 39211522--39211776 Score: 270
Period size: 29 Copynumber: 8.8 Consensus size: 29
39211512 ACCTTAGATA
*
39211522 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* * *
39211551 ATGAAAAGGGAT--CATGACGACCATC-AACT
1 ATGAAAAGGGATAGC-T-TCGGCTATCGAA-T
* * *
39211580 ATGAAAAGGGATGGTGATTAC--C-ATAGAAT
1 ATGAAAAGGGAT--AGCTT-CGGCTATCGAAT
* *
39211609 ATGAAAAGGGATAGCTTCGACTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
39211638 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
*
39211667 ATGAAAAAGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* **
39211696 GTGAAAAGGGATAGCTTCTACTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
*
39211725 ATGAAAAGGGATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
39211754 GTGAAAAGGGATAGCTTTGGCTA
1 ATGAAAAGGGATAGCTTCGGCTA
39211777 GCGATTATAA
Statistics
Matches: 190, Mismatches: 24, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.01
27 4 0.02
28 3 0.02
29 177 0.93
30 3 0.02
32 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:39211884 original size:29 final size:29
Alignment explanation
Indices: 39211522--39211886 Score: 193
Period size: 29 Copynumber: 12.6 Consensus size: 29
39211512 ACCTTAGATA
* * * *
39211522 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATGGTTTCGACTATCGAAT
** ** *
39211551 ATGAAAAGGGATCATGACGACCATC-AACT
1 ATGAAAAGGGATGGTTTCGACTATCGAA-T
* *
39211580 ATGAAAAGGGATGGTGATT--ACCATAGAAT
1 ATGAAAAGGGATGGT--TTCGACTATCGAAT
* * *
39211609 ATGAAAAGGGATAGCTTCGACTATCAAAT
1 ATGAAAAGGGATGGTTTCGACTATCGAAT
* * *
39211638 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATGGTTTCGACTATCGAAT
* * * *
39211667 ATGAAAAAGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATGGTTTCGACTATCGAAT
* * * *
39211696 GTGAAAAGGGATAGCTTCTACTATCGAAT
1 ATGAAAAGGGATGGTTTCGACTATCGAAT
* * * *
39211725 ATGAAAAGGGATAGCTTCGGCTATCAAAT
1 ATGAAAAGGGATGGTTTCGACTATCGAAT
* * * * *
39211754 GTGAAAAGGGATAGCTTT-GGCTAGCGATT
1 ATGAAAAGGGAT-GGTTTCGACTATCGAAT
* ** * * *
39211783 ATAAAAAAAGATGGTGAT-GACCATC-AGCT
1 ATGAAAAGGGATGGT-TTCGACTATCGA-AT
* ** * * *
39211812 ATGAAAATGGATGGTGACGACCATTGATT
1 ATGAAAAGGGATGGTTTCGACTATCGAAT
* *
39211841 AATGAAAAGGGATGGTTTCGACCATTGAAT
1 -ATGAAAAGGGATGGTTTCGACTATCGAAT
39211871 ATGAAAAGGGATGGTT
1 ATGAAAAGGGATGGTT
39211887 ACAACCATCG
Statistics
Matches: 267, Mismatches: 57, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
27 2 0.01
28 4 0.01
29 231 0.87
30 30 0.11
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATGGTTTCGACTATCGAAT
Found at i:39211893 original size:29 final size:29
Alignment explanation
Indices: 39211811--39211894 Score: 114
Period size: 30 Copynumber: 2.9 Consensus size: 29
39211801 GACCATCAGC
* * *
39211811 TATGAAAATGGATGGTGACGACCATTGAT
1 TATGAAAAGGGATGGTTACGACCATTGAA
*
39211840 TAATGAAAAGGGATGGTTTCGACCATTGAA
1 T-ATGAAAAGGGATGGTTACGACCATTGAA
*
39211870 TATGAAAAGGGATGGTTACAACCAT
1 TATGAAAAGGGATGGTTACGACCAT
39211895 CGTTTAGCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (29 bp):
TATGAAAAGGGATGGTTACGACCATTGAA
Found at i:39215420 original size:22 final size:23
Alignment explanation
Indices: 39215386--39215429 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
39215376 TAATGATGTG
*
39215386 CAAACTATGAAATAATTAAAAACA
1 CAAACTA-GAAATAACTAAAAACA
39215410 CAAACTA-AAATAACTAAAAA
1 CAAACTAGAAATAACTAAAAA
39215430 TTAATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.66, C:0.14, G:0.02, T:0.18
Consensus pattern (23 bp):
CAAACTAGAAATAACTAAAAACA
Found at i:39217171 original size:27 final size:25
Alignment explanation
Indices: 39217141--39217190 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
39217131 TTTTGTTTAA
*
39217141 TCTCAATCTCGTTTTTCTTTTTCTCAC
1 TCTCAATCTC-TTTTT-TTCTTCTCAC
*
39217168 TCTCACTCTCTTTTTTTCTTCTC
1 TCTCAATCTCTTTTTTTCTTCTC
39217191 TCGAGTTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.08, C:0.32, G:0.02, T:0.58
Consensus pattern (25 bp):
TCTCAATCTCTTTTTTTCTTCTCAC
Found at i:39218218 original size:12 final size:12
Alignment explanation
Indices: 39218199--39218232 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39218189 AATGGAAACT
39218199 AATTTTTTTT-G
1 AATTTTTTTTCG
39218210 AATTTTTTTTCG
1 AATTTTTTTTCG
*
39218222 AGTTTTTTTTC
1 AATTTTTTTTC
39218233 AAGAAACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71
Consensus pattern (12 bp):
AATTTTTTTTCG
Found at i:39228198 original size:54 final size:54
Alignment explanation
Indices: 39228116--39228224 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
39228106 TAGAACAACC
*
39228116 AGTTACGGTGTACGTTTGACTGTATCAAAATATACAACTCACGATGTTGGGATA
1 AGTTACGGTGTACATTTGACTGTATCAAAATATACAACTCACGATGTTGGGATA
* *
39228170 AGTTATGGTGTACATTTGACTGTATCAAAATATACAACTCATGATGTTGGGATA
1 AGTTACGGTGTACATTTGACTGTATCAAAATATACAACTCACGATGTTGGGATA
39228224 A
1 A
39228225 TGATGATCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (54 bp):
AGTTACGGTGTACATTTGACTGTATCAAAATATACAACTCACGATGTTGGGATA
Found at i:39229118 original size:20 final size:20
Alignment explanation
Indices: 39229093--39229143 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
39229083 GTATTGATTT
*
39229093 GGTATCGATACT-TTTCTTAA
1 GGTATCGATA-TATTTCCTAA
39229113 GGTATCGATATATTTCCTAA
1 GGTATCGATATATTTCCTAA
39229133 GGTATCGATAT
1 GGTATCGATAT
39229144 TCCTGCTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (20 bp):
GGTATCGATATATTTCCTAA
Found at i:39240733 original size:19 final size:19
Alignment explanation
Indices: 39240709--39240747 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39240699 GGCCCTACGG
*
39240709 GCGTGTGGGCCCCACACGA
1 GCGTGTGGACCCCACACGA
39240728 GCGTGTGGACCCCACACGA
1 GCGTGTGGACCCCACACGA
39240747 G
1 G
39240748 TGAACCACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.36, G:0.36, T:0.10
Consensus pattern (19 bp):
GCGTGTGGACCCCACACGA
Found at i:39243143 original size:40 final size:40
Alignment explanation
Indices: 39242993--39243143 Score: 169
Period size: 40 Copynumber: 3.8 Consensus size: 40
39242983 TATAACCACA
* * ** * *
39242993 AGCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACT
* * *
39243033 CGCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACT
* *
39243073 CGCACAAATGCCTTCAGGTCTTAGCCCGGATAAAATC-ACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGAT-AAATCAACT
* *
39243113 AGCATAAATGCCTTCGGGACTTAGCCCGGAT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGAT
39243144 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 92 0.96
41 4 0.04
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAATCAACT
Found at i:39252469 original size:21 final size:19
Alignment explanation
Indices: 39252440--39252478 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
39252430 GTCCTAGTTT
39252440 ATTTATGTTATAATTGTTGCA
1 ATTTATGTT-TAATT-TTGCA
*
39252461 ATTTGTGTTTAATTTTGC
1 ATTTATGTTTAATTTTGC
39252479 TAAAATCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.56
Consensus pattern (19 bp):
ATTTATGTTTAATTTTGCA
Found at i:39257745 original size:61 final size:62
Alignment explanation
Indices: 39257668--39257791 Score: 198
Period size: 61 Copynumber: 2.0 Consensus size: 62
39257658 GACAATCAAA
* *
39257668 TGTTGAACATCAAATTTGATCACCTAATTTAATTAGTTTTAAC-TTTAATTTCTAGGGGTTT
1 TGTTGAACATCAAATTTCATCACCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
*
39257729 TGTTGAAC-TCCAAATTTCATCGCCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
1 TGTTGAACAT-CAAATTTCATCACCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
39257791 T
1 T
39257792 TTTTGCATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
60 1 0.02
61 39 0.67
62 18 0.31
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (62 bp):
TGTTGAACATCAAATTTCATCACCTAATTTAATTAGTTTTAACATTTAATTTCTAGGGCTTT
Found at i:39259615 original size:7 final size:7
Alignment explanation
Indices: 39259603--39259628 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39259593 GCTAAGCTAC
39259603 CACTTAT
1 CACTTAT
39259610 CACTTAT
1 CACTTAT
39259617 CACTTAT
1 CACTTAT
39259624 CACTT
1 CACTT
39259629 GCCACTTGTC
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:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (7 bp):
CACTTAT
Found at i:39259634 original size:14 final size:14
Alignment explanation
Indices: 39259600--39259635 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39259590 GTGGCTAAGC
39259600 TACCACTTATCACT
1 TACCACTTATCACT
*
39259614 TATCACTTATCACT
1 TACCACTTATCACT
*
39259628 TGCCACTT
1 TACCACTT
39259636 GTCATTGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.25, C:0.33, G:0.03, T:0.39
Consensus pattern (14 bp):
TACCACTTATCACT
Found at i:39259637 original size:64 final size:65
Alignment explanation
Indices: 39259551--39259683 Score: 187
Period size: 64 Copynumber: 2.1 Consensus size: 65
39259541 CTTACACGGA
* * * * * *
39259551 ATCACTTATCATTTATCTCTTGTCACTGGTCAGATAAGTGTGGCT-AAGCTACCACTTATCACTT
1 ATCACTTATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
* *
39259615 ATCACTTATCACTTGCCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
1 ATCACTTATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
39259680 ATCA
1 ATCA
39259684 GAAGTACTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 38 0.63
65 22 0.37
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (65 bp):
ATCACTTATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTG
Found at i:39262178 original size:29 final size:31
Alignment explanation
Indices: 39262144--39262203 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
39262134 GAATCAAAAT
39262144 AACCTATACACATTCGAAC-T-TAATCATCC
1 AACCTATACACATTCGAACATATAATCATCC
39262173 AACCTATACACATTCGAACATATAATCATCC
1 AACCTATACACATTCGAACATATAATCATCC
39262204 TTTTACTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 19 0.66
30 1 0.03
31 9 0.31
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.27
Consensus pattern (31 bp):
AACCTATACACATTCGAACATATAATCATCC
Found at i:39263064 original size:36 final size:36
Alignment explanation
Indices: 39263012--39263094 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
39263002 ATATATAATT
* * * *
39263012 ATCACTTTTAAATATTACAACTATATCATTATG-CCGA
1 ATCACTTAT-AATATTACAACTACACCAATA-GACCGA
*
39263049 ATCACTTATAATATTACAATTACACCAATAGACCGA
1 ATCACTTATAATATTACAACTACACCAATAGACCGA
39263085 ATCACTTATA
1 ATCACTTATA
39263095 TGCTCAATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
35 1 0.03
36 31 0.77
37 8 0.20
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (36 bp):
ATCACTTATAATATTACAACTACACCAATAGACCGA
Found at i:39266988 original size:26 final size:27
Alignment explanation
Indices: 39266952--39267062 Score: 95
Period size: 27 Copynumber: 4.1 Consensus size: 27
39266942 TATAACGGTC
*
39266952 ATTTTGCCC-TTCAGGGTTATTTCAGTA
1 ATTTTACCCTTTCAGGG-TATTTCAGTA
* ** *
39266979 ATTTTACCTTTTGGGGGTATTT-TGATA
1 ATTTTACCCTTTCAGGGTATTTCAG-TA
* **
39267006 ATTTTACCCTTTGAGGGTATTTTGGTA
1 ATTTTACCCTTTCAGGGTATTTCAGTA
39267033 ATTTTACCC-TTCGAGGGTA-TTCAGTA
1 ATTTTACCCTTTC-AGGGTATTTCAGTA
39267059 ATTT
1 ATTT
39267063 AACAACTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
26 12 0.17
27 51 0.74
28 6 0.09
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.47
Consensus pattern (27 bp):
ATTTTACCCTTTCAGGGTATTTCAGTA
Done.