Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 5 of 255
Found at i:1386707 original size:14 final size:15
Alignment explanation
Indices: 1386684--1386817 Score: 64
Period size: 14 Copynumber: 8.9 Consensus size: 15
1386674 AAAAAAGGAT
*
1386684 ATATACATAATAA-A
1 ATATATATAATAAGA
1386698 ATATATATAA-AAGA
1 ATATATATAATAAGA
1386712 ATATATA-AGA-AA-A
1 ATATATATA-ATAAGA
* *
1386725 ATAAATATTATAAGGA
1 ATATATATAATAA-GA
*
1386741 ATGTTATATAATAAGA
1 AT-ATATATAATAAGA
*
1386757 TATAGTATGTAATAA-A
1 -ATA-TATATAATAAGA
* * *
1386773 ATATAAATAATTATA
1 ATATATATAATAAGA
* * *
1386788 ATGAAATATAATATGGT
1 AT-ATATATAATA-AGA
1386805 ATATATATAATAA
1 ATATATATAATAA
1386818 TAGTAATAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 23
0.68 0.15 0.18
Matches are distributed among these distances:
13 11 0.12
14 29 0.33
15 6 0.07
16 22 0.25
17 21 0.24
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (15 bp):
ATATATATAATAAGA
Found at i:1387186 original size:21 final size:22
Alignment explanation
Indices: 1387156--1387198 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1387146 CATTAAAGCT
1387156 AAATTAAAAAATA-AATAAAATG
1 AAATTAAAAAATATAA-AAAATG
1387178 AAATT-AAAAATATAAAAAATG
1 AAATTAAAAAATATAAAAAATG
1387199 CAAGAGGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
AAATTAAAAAATATAAAAAATG
Found at i:1396465 original size:20 final size:21
Alignment explanation
Indices: 1396438--1396478 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1396428 TTCTAATATA
1396438 ATTTTTTTGTAA-TTTTAAAAT
1 ATTTTTTTG-AATTTTTAAAAT
1396459 ATTTTTTTGAATTTTTAAAA
1 ATTTTTTTGAATTTTTAAAA
1396479 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
ATTTTTTTGAATTTTTAAAAT
Found at i:1396591 original size:34 final size:34
Alignment explanation
Indices: 1396548--1396616 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1396538 AACAAAAGTT
*
1396548 AACGAACATTAATTTTTCCATTTATGTTAGAGTG
1 AACGAACATTAACTTTTCCATTTATGTTAGAGTG
1396582 AACGAACATTAACTTTTCCATTTATGTTAGAGTG
1 AACGAACATTAACTTTTCCATTTATGTTAGAGTG
1396616 A
1 A
1396617 TTTGACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (34 bp):
AACGAACATTAACTTTTCCATTTATGTTAGAGTG
Found at i:1397255 original size:25 final size:25
Alignment explanation
Indices: 1397216--1397267 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
1397206 ATGACCCTAC
* *
1397216 CAAATCAAATTAAATTATGAGAACT
1 CAAATCAAATCAAATTATGAAAACT
*
1397241 CAAATCATATCAAATTATGAAAACT
1 CAAATCAAATCAAATTATGAAAACT
1397266 CA
1 CA
1397268 GAAGAGACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (25 bp):
CAAATCAAATCAAATTATGAAAACT
Found at i:1398614 original size:20 final size:20
Alignment explanation
Indices: 1398589--1398638 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1398579 TGGCTTAAAA
1398589 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1398609 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1398626 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1398639 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1403253 original size:20 final size:20
Alignment explanation
Indices: 1403228--1403277 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1403218 TGGCTTAAAA
1403228 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1403248 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1403265 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1403278 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1406781 original size:16 final size:14
Alignment explanation
Indices: 1406754--1406787 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
1406744 AGAATCTGAG
1406754 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
1406768 AAAAAAATACAAGAAA
1 AAAAAAA-A-AAGAAA
1406784 AAAA
1 AAAA
1406788 TTCAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 1 0.06
16 10 0.56
ACGTcount: A:0.88, C:0.03, G:0.06, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:1420325 original size:31 final size:32
Alignment explanation
Indices: 1420240--1420327 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
1420230 TTTTGTGAGA
* * *
1420240 TTAATGAGAATTTTC-AAAATTTTAAGAGTGC
1 TTAATGAAAATTTTCAAAAAATTTAAAAGTGC
*
1420271 TTAATTAAAATTTTCAAAAAAATTTAAAAG-G-
1 TTAATGAAAATTTTC-AAAAAATTTAAAAGTGC
1420302 TATAATGAAAATTTTCAAAAAATTTA
1 T-TAATGAAAATTTTCAAAAAATTTA
1420328 GGGGCTCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
31 24 0.49
32 14 0.29
33 11 0.22
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.38
Consensus pattern (32 bp):
TTAATGAAAATTTTCAAAAAATTTAAAAGTGC
Found at i:1420586 original size:62 final size:62
Alignment explanation
Indices: 1420470--1420588 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
1420460 GTATCATGAT
* * *
1420470 AAAACACATATTGATGGTTTAAGTACCACATTAAACATTTTCAAAATACATGTACCATAATA
1 AAAACACATATTGATAGTTCAAGTACCACATTAAACATTTTCAAAACACATGTACCATAATA
* * * *
1420532 AAAACACATATTGATAGTTCAAGTACCACATTATATATTTTCAAAGCACTTGTACCA
1 AAAACACATATTGATAGTTCAAGTACCACATTAAACATTTTCAAAACACATGTACCA
1420589 CTAGACATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (62 bp):
AAAACACATATTGATAGTTCAAGTACCACATTAAACATTTTCAAAACACATGTACCATAATA
Found at i:1420835 original size:22 final size:21
Alignment explanation
Indices: 1420809--1420860 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1420799 ACAACTAACA
* * *
1420809 TAAATTATTAAACTAAAATTTT
1 TAAATTATAAAAAT-AAACTTT
*
1420831 TAAATTAAAAAAATAAACTTT
1 TAAATTATAAAAATAAACTTT
1420852 TAAATTATA
1 TAAATTATA
1420861 GGGACTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTATAAAAATAAACTTT
Found at i:1421301 original size:61 final size:61
Alignment explanation
Indices: 1421179--1421294 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
1421169 TTTTTTTTCC
* ** * *
1421179 TAGAATTAGAACTAAATTGATAGTTTTTATAAATATTGAGGGCTAAATTTATTGAAGTTTT
1 TAGAATTAGAACTAAAATGATAAATTTTATAAACATTCAGGGCTAAATTTATTGAAGTTTT
* * *
1421240 TAGAATTTGAACTAAAATGATAAATTTTGTAAACATTCAGGGCTAAATTTGTTGA
1 TAGAATTAGAACTAAAATGATAAATTTTATAAACATTCAGGGCTAAATTTATTGA
1421295 TTTTTTTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (61 bp):
TAGAATTAGAACTAAAATGATAAATTTTATAAACATTCAGGGCTAAATTTATTGAAGTTTT
Found at i:1422509 original size:29 final size:29
Alignment explanation
Indices: 1422412--1422509 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
1422402 AACCCATAAA
* **
1422412 TTGGTACCTAGACTATGTCATTTTTC-CCATT
1 TTGGTACCTAAACTAT-T--TTTTTCTCCAAG
*
1422443 TTGGTACCTAAA-TATTTTTTTGGTCACAAG
1 TTGGTACCTAAACTATTTTTTT-CTC-CAAG
* *
1422473 -TAGAACCTAAACTATTTTTTTCTCCAAG
1 TTGGTACCTAAACTATTTTTTTCTCCAAG
1422501 TTGGTACCT
1 TTGGTACCT
1422510 CTGTTGTTAG
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
27 5 0.09
28 4 0.08
29 19 0.36
30 14 0.26
31 11 0.21
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.43
Consensus pattern (29 bp):
TTGGTACCTAAACTATTTTTTTCTCCAAG
Found at i:1423372 original size:31 final size:31
Alignment explanation
Indices: 1423337--1423396 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1423327 TTTAAACAGT
* *
1423337 ATAAAGACTTAGAATGAGCCAATTGAAAAAC
1 ATAAAAACTTAGAATGACCCAATTGAAAAAC
1423368 ATAAAAACTTAGAATGACCCAATTGAAAA
1 ATAAAAACTTAGAATGACCCAATTGAAAA
1423397 TTATGGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (31 bp):
ATAAAAACTTAGAATGACCCAATTGAAAAAC
Found at i:1429779 original size:39 final size:39
Alignment explanation
Indices: 1429696--1429782 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 39
1429686 AAGATGCCCT
* * *
1429696 CTAATACATATGTATGTGTTTGTGTGTATATATATATGTA
1 CTAA-ACATATGTATGTGTTTGTGTGCATACATATATGAA
1429736 -TAAACAGTATGTATGTG-TT-TGTGCATACATATATGAAA
1 CTAAACA-TATGTATGTGTTTGTGTGCATACATATATG-AA
1429774 CTAAACATA
1 CTAAACATA
1429783 AACTTACATC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
37 14 0.34
38 8 0.20
39 19 0.46
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (39 bp):
CTAAACATATGTATGTGTTTGTGTGCATACATATATGAA
Found at i:1430813 original size:477 final size:478
Alignment explanation
Indices: 1429899--1431019 Score: 1576
Period size: 477 Copynumber: 2.3 Consensus size: 478
1429889 TATAGGGAAT
* *
1429899 CATGGCAGGAGATGATAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATAACAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
*
1429964 TACTAAATCATGATGAAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
66 TACTAAATCACGATGAAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
* * * * *
1430029 AATAAGGTTCATTCAAGTTCGGAGTATACAACCATGGCAGGAGATGATAATCAAACAAAAGTTAA
131 GATAAGGTTCATTCAAGTTCAGAGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGAA
** *
1430094 CTTCCCTAATCTCTAGATGACAAACCAAACTATACTAAATCGCGATGAAAATCCAGGAATATCTG
196 CTTCCCTAATCTCTAGATGACAAACCAAACTATACTAAATCAAGATGAAAATACAGGAATATCTG
* * * *
1430159 AAGATCACCGTTCTCCCATCCAGACCACTAAGGTTCATTCAAGTTCAGAGTAAACAACAATGGCA
261 -AGATCACCGATCACCAATCCAAACCACTAAGGTTCATTCAAGTTCAGAGTAAACAACAATGGCA
*
1430224 AGAGATAACAATCAAACAAAAGTGAACTTCCTAGTCTCTAGAAGACAAACGAAGCTACACTAAAT
325 AGAGATAACAATCAAACAAAAGTGAACTTCCTAGTCTCTAGAAGACAAACCAAGCTACACTAAAT
* * * **
1430289 CACGATGAGAAATCAGGAATATCTGTTTCCAAGGATCACTGATCTCCTATCCAAATTGA-AAGGT
390 CACGATGAGAAATCAGGAATATCTGTTTCCAAGGAACACTAATCTCCTATCAAAATCAATAAGGT
1430353 TCATTCAAGCTT-AGAGTAAACAAC
455 TCATTCAA-CTTCAGAGTAAACAAC
* * *
1430377 CATGGCAGGATATGACAATCAAACAAAAGTGAATTTCCCTAGCCTCTAGATGACAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
*
1430442 TACTAAATCACGAT-AAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCAAAATC
66 TACTAAATCACGATGAAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
* *
1430506 GATAAGGTTTATTCAAGTTCAGTGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGAA
131 GATAAGGTTCATTCAAGTTCAGAGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGAA
** * * * **
1430571 CTTCCCTGGTCTCTAGATGATAAACCAAGCTATACTAACTCAAGATGAAAATATGGGAATAT-TG
196 CTTCCCTAATCTCTAGATGACAAACCAAACTATACTAAATCAAGATGAAAATACAGGAATATCTG
* * * *
1430635 -GTTTCTGA-GGATCACCAATCCAAATCGA-TAAGGTTCATTCAAGTTCAGAGTAAACAACCATG
261 AG-ATC--ACCGATCACCAATCCAAA-CCACTAAGGTTCATTCAAGTTCAGAGTAAACAACAATG
* * * * * *
1430697 GCAGGAGATCACAATCAAACAAAAGTGGACTTCCTTAGTCTCTAGATGATAAACCAAGCTATACT
322 GCAAGAGATAACAATCAAACAAAAGTGAACTTCC-TAGTCTCTAGAAGACAAACCAAGCTACACT
*
1430762 AAATCACGATGA-AAATCCAGGAATAT-TGGTTTCCGAGGAACACTAATCTCCTATCAAAATCAA
386 AAATCACGATGAGAAAT-CAGGAATATCT-GTTTCCAAGGAACACTAATCTCCTATCAAAATCAA
*
1430825 TAAGGTTCATTCAACTTCAGAGTAAACGAC
449 TAAGGTTCATTCAACTTCAGAGTAAACAAC
* * * * *
1430855 AATGGGAGGAGATGACAATCAAACAAAAGTGAACTTCCTTAGTCTCGAGATGAAAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* * * * * *
1430920 TACTAAATCACGATGAAAATCCGAGAACATCGGTTTCCGAGGAACACCGATCTCCTAACCAAATA
66 TACTAAATCACGATGAAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
*
1430985 GATAAGGTTCATTCCAGTTCAGAGTAAACAACCAT
131 GATAAGGTTCATTCAAGTTCAGAGTAAACAACCAT
1431020 AGCACAAAAA
Statistics
Matches: 569, Mismatches: 64, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
474 1 0.00
475 2 0.00
476 82 0.14
477 241 0.42
478 168 0.30
479 75 0.13
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (478 bp):
CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
TACTAAATCACGATGAAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
GATAAGGTTCATTCAAGTTCAGAGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGAA
CTTCCCTAATCTCTAGATGACAAACCAAACTATACTAAATCAAGATGAAAATACAGGAATATCTG
AGATCACCGATCACCAATCCAAACCACTAAGGTTCATTCAAGTTCAGAGTAAACAACAATGGCAA
GAGATAACAATCAAACAAAAGTGAACTTCCTAGTCTCTAGAAGACAAACCAAGCTACACTAAATC
ACGATGAGAAATCAGGAATATCTGTTTCCAAGGAACACTAATCTCCTATCAAAATCAATAAGGTT
CATTCAACTTCAGAGTAAACAAC
Found at i:1430893 original size:162 final size:162
Alignment explanation
Indices: 1429899--1431019 Score: 1454
Period size: 162 Copynumber: 7.0 Consensus size: 162
1429889 TATAGGGAAT
* *
1429899 CATGGCAGGAGATGATAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATAACAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* *
1429964 TACTAAATCATGATGAAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
66 TACTAAATCACGATGAAAATCCAGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
* *
1430029 AATAAGGTTCATTCAAGTTCGGAGTATACAAC
131 AATAAGGTTCATTCAAGTTCAGAGTAAACAAC
* * * *
1430061 CATGGCAGGAGATGATAATCAAACAAAAGTTAACTTCCCTAATCTCTAGATGACAAACCAAACTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* * ** * * *
1430126 TACTAAATCGCGATGAAAATCCAGGAATATC----T--GAAGATCACCGTTCTCCCATCCAGACC
66 TACTAAATCACGATGAAAATCCAGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
*
1430185 ACTAAGGTTCATTCAAGTTCAGAGTAAACAAC
131 AATAAGGTTCATTCAAGTTCAGAGTAAACAAC
* * * * *
1430217 AATGGCAAGAGATAACAATCAAACAAAAGTGAACTT-CCTAGTCTCTAGAAGACAAACGAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* * * **
1430281 CACTAAATCACGATGAGAAAT-CAGGAATATCTGTTTCCAAGGATCACTGATCTCCTATCCAAAT
66 TACTAAATCACGATGA-AAATCCAGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAAT
**
1430345 TGA-AAGGTTCATTCAAGCTT-AGAGTAAACAAC
130 CAATAAGGTTCATTCAAG-TTCAGAGTAAACAAC
* * *
1430377 CATGGCAGGATATGACAATCAAACAAAAGTGAATTTCCCTAGCCTCTAGATGACAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* *
1430442 TACTAAATCACGAT-AAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCAAAATC
66 TACTAAATCACGATGAAAATCCAGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
* * *
1430506 GATAAGGTTTATTCAAGTTCAGTGTAAACAAC
131 AATAAGGTTCATTCAAGTTCAGAGTAAACAAC
* *
1430538 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTGGTCTCTAGATGATAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* * *** * *
1430603 TACTAACTCAAGATGAAAATATGGGAATATTGGTTTCTGAGGATCACC-A------ATCCAAATC
66 TACTAAATCACGATGAAAATCCAGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
*
1430661 GATAAGGTTCATTCAAGTTCAGAGTAAACAAC
131 AATAAGGTTCATTCAAGTTCAGAGTAAACAAC
* * * *
1430693 CATGGCAGGAGATCACAATCAAACAAAAGTGGACTTCCTTAGTCTCTAGATGATAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* * * *
1430758 TACTAAATCACGATGAAAATCCAGGAATATTGGTTTCCGAGGAACACTAATCTCCTATCAAAATC
66 TACTAAATCACGATGAAAATCCAGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
* *
1430823 AATAAGGTTCATTCAACTTCAGAGTAAACGAC
131 AATAAGGTTCATTCAAGTTCAGAGTAAACAAC
* * * * *
1430855 AATGGGAGGAGATGACAATCAAACAAAAGTGAACTTCCTTAGTCTCGAGATGAAAAACCAAGCTA
1 CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
* * * *
1430920 TACTAAATCACGATGAAAATCC-GAGAACATCGGTTTCCGAGGAACACCGATCTCCTAACCAAAT
66 TACTAAATCACGATGAAAATCCAG-GAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAAT
*
1430984 -AGATAAGGTTCATTCCAGTTCAGAGTAAACAAC
130 CA-ATAAGGTTCATTCAAGTTCAGAGTAAACAAC
1431017 CAT
1 CAT
1431020 AGCACAAAAA
Statistics
Matches: 836, Mismatches: 101, Indels: 44
0.85 0.10 0.04
Matches are distributed among these distances:
155 187 0.22
156 86 0.10
158 1 0.00
159 5 0.01
160 99 0.12
161 158 0.19
162 300 0.36
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (162 bp):
CATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGACAAACCAAGCTA
TACTAAATCACGATGAAAATCCAGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
AATAAGGTTCATTCAAGTTCAGAGTAAACAAC
Found at i:1430922 original size:317 final size:318
Alignment explanation
Indices: 1429900--1431019 Score: 1375
Period size: 317 Copynumber: 3.5 Consensus size: 318
1429890 ATAGGGAATC
*
1429900 ATGGCAGGAGATGATAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGAT-AACAAACCAAGCTA
1 ATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGAA-AAACCAAGCTA
* *
1429964 TACTAAATCATGATGAAAATCCGGGAATATCGGTTTCCGAGGATCACCAATCTCCTATCCAAATC
65 TACTAAATCACGATGAAAATACGGGAATATCGGTTTCCGAGGATCACCAA----C-ATCCAAATC
* * * * *
1430029 AATAAGGTTCATTCAAGTTCGGAGTATACAACCATGGCAGGAGATGATAATCAAACAAAAGTTAA
125 GATAAGGTTCATTCAAGTTCAGAGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGAA
* * *
1430094 CTTCCCTAATCTCTAGATGACAAACCAAACTATACTAAATCGCGATGAAAATCCAGGAATA----
190 CTTCCCTAGTCTCTAGATGACAAACCAAGCTATACTAAATCACGATGAAAATCCAGGAATATGGT
* * ** * * * * *
1430155 -TCTGAAGATCACCGTTCTCCCATCCAGACCACTAAGGTTCATTCAAGTTCAGAGTAAACAACA
255 TTCCGAGGATCACCAATCTCCTATCAAAATCAATAAGGTTCATTCAAGTTCAGAGTAAACAACA
* * * * * *
1430218 ATGGCAAGAGATAACAATCAAACAAAAGTGAACTT-CCTAGTCTCTAGAAGACAAACGAAGCTAC
1 ATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGAAAAACCAAGCTAT
* * * ** *
1430282 ACTAAATCACGATGAGAAAT-CAGGAATATCTGTTTCCAAGGATCACTGATCTCCTATCCAAATT
66 ACTAAATCACGATGA-AAATACGGGAATATCGGTTTCCGAGGATCAC----CAAC-ATCCAAATC
*
1430346 GA-AAGGTTCATTCAAGCTT-AGAGTAAACAACCATGGCAGGATATGACAATCAAACAAAAGTGA
125 GATAAGGTTCATTCAAG-TTCAGAGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGA
* * *
1430409 ATTTCCCTAGCCTCTAGATGACAAACCAAGCTATACTAAATCACGAT-AAAATCCGGGAATATCG
189 ACTTCCCTAGTCTCTAGATGACAAACCAAGCTATACTAAATCACGATGAAAATCCAGGAATAT-G
* * *
1430473 GTTTCCGAGGATCACCAATCTCCTATCAAAATCGATAAGGTTTATTCAAGTTCAGTGTAAACAAC
253 GTTTCCGAGGATCACCAATCTCCTATCAAAATCAATAAGGTTCATTCAAGTTCAGAGTAAACAAC
*
1430538 C
318 A
* *
1430539 ATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTGGTCTCTAGATGATAAACCAAGCTAT
1 ATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGAAAAACCAAGCTAT
* * * * *
1430604 ACTAACTCAAGATGAAAATATGGGAATATTGGTTTCTGAGGATCACC-A-ATCCAAATCGATAAG
66 ACTAAATCACGATGAAAATACGGGAATATCGGTTTCCGAGGATCACCAACATCCAAATCGATAAG
* * *
1430667 GTTCATTCAAGTTCAGAGTAAACAACCATGGCAGGAGATCACAATCAAACAAAAGTGGACTTCCT
131 GTTCATTCAAGTTCAGAGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCC
*
1430732 TAGTCTCTAGATGATAAACCAAGCTATACTAAATCACGATGAAAATCCAGGAATATTGGTTTCCG
196 TAGTCTCTAGATGACAAACCAAGCTATACTAAATCACGATGAAAATCCAGGAATA-TGGTTTCCG
* * * *
1430797 AGGAACACTAATCTCCTATCAAAATCAATAAGGTTCATTCAACTTCAGAGTAAACGACA
260 AGGATCACCAATCTCCTATCAAAATCAATAAGGTTCATTCAAGTTCAGAGTAAACAACA
* * *
1430856 ATGGGAGGAGATGACAATCAAACAAAAGTGAACTTCCTTAGTCTCGAGATGAAAAACCAAGCTAT
1 ATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGAAAAACCAAGCTAT
* * * * * * *
1430921 ACTAAATCACGATGAAAATCCGAGAACATCGGTTTCCGAGGAACACCGATCTCCTAACCAAATAG
66 ACTAAATCACGATGAAAATACGGGAATATCGGTTTCCGAGGATCACC-A---AC-ATCCAAATCG
*
1430986 ATAAGGTTCATTCCAGTTCAGAGTAAACAACCAT
126 ATAAGGTTCATTCAAGTTCAGAGTAAACAACCAT
1431020 AGCACAAAAA
Statistics
Matches: 686, Mismatches: 90, Indels: 46
0.83 0.11 0.06
Matches are distributed among these distances:
315 25 0.04
316 193 0.28
317 243 0.35
318 39 0.06
321 88 0.13
322 57 0.08
324 41 0.06
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (318 bp):
ATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCCTAGTCTCTAGATGAAAAACCAAGCTAT
ACTAAATCACGATGAAAATACGGGAATATCGGTTTCCGAGGATCACCAACATCCAAATCGATAAG
GTTCATTCAAGTTCAGAGTAAACAACCATGGCAGGAGATGACAATCAAACAAAAGTGAACTTCCC
TAGTCTCTAGATGACAAACCAAGCTATACTAAATCACGATGAAAATCCAGGAATATGGTTTCCGA
GGATCACCAATCTCCTATCAAAATCAATAAGGTTCATTCAAGTTCAGAGTAAACAACA
Found at i:1431676 original size:25 final size:25
Alignment explanation
Indices: 1431629--1431677 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1431619 ACAAACATTT
*
1431629 AATTAAATAATTAATTTAATAACTG
1 AATTAAATAATTAATGTAATAACTG
*
1431654 AATTGAATAATTAA-GTAACTAACT
1 AATTAAATAATTAATGTAA-TAACT
1431678 AACTATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (25 bp):
AATTAAATAATTAATGTAATAACTG
Found at i:1442831 original size:29 final size:29
Alignment explanation
Indices: 1442799--1442868 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
1442789 GCAATGTCAG
1442799 AACAGAATAGCACTGAAGTGC-TTAATCAA
1 AACAGAATAGCACTGAAGTGCATTAA-CAA
* *
1442828 AACAGAGT-GACATTGAAGTGCATTAACAA
1 AACAGAATAG-CACTGAAGTGCATTAACAA
*
1442857 AACA-AAAAGCAC
1 AACAGAATAGCAC
1442869 GTTAAATGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
28 4 0.12
29 25 0.76
30 4 0.12
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (29 bp):
AACAGAATAGCACTGAAGTGCATTAACAA
Found at i:1444010 original size:32 final size:32
Alignment explanation
Indices: 1443969--1444032 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1443959 AGGGAACATA
1443969 TTCTCTCTCCTTAATCTCTCGACACAATTAAC
1 TTCTCTCTCCTTAATCTCTCGACACAATTAAC
1444001 TTCTCTCTCCTTAATCTCTCGACACAATTAAC
1 TTCTCTCTCCTTAATCTCTCGACACAATTAAC
1444033 CTTGTGTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.34, G:0.03, T:0.38
Consensus pattern (32 bp):
TTCTCTCTCCTTAATCTCTCGACACAATTAAC
Found at i:1445107 original size:63 final size:63
Alignment explanation
Indices: 1445029--1445147 Score: 229
Period size: 63 Copynumber: 1.9 Consensus size: 63
1445019 AGCTGACTGG
1445029 GGAGGATTGTAAGGAGTCTCAGAACCTTGATAGGATGATGGATAGTGAGACGGGGCCGATTGT
1 GGAGGATTGTAAGGAGTCTCAGAACCTTGATAGGATGATGGATAGTGAGACGGGGCCGATTGT
*
1445092 GGAGGATTGTAAGGAGTCTCGGAACCTTGATAGGATGATGGATAGTGAGACGGGGC
1 GGAGGATTGTAAGGAGTCTCAGAACCTTGATAGGATGATGGATAGTGAGACGGGGC
1445148 TGTAGGTAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.27, C:0.11, G:0.39, T:0.23
Consensus pattern (63 bp):
GGAGGATTGTAAGGAGTCTCAGAACCTTGATAGGATGATGGATAGTGAGACGGGGCCGATTGT
Found at i:1446676 original size:22 final size:22
Alignment explanation
Indices: 1446648--1446700 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1446638 CTTAAAGTTC
*
1446648 CCTAAACTATGA-CCCTGAGATT
1 CCTAAACTATGAGCCC-AAGATT
*
1446670 CCTAAACTATGAGCCCAAGTTT
1 CCTAAACTATGAGCCCAAGATT
1446692 CCTAAACTA
1 CCTAAACTA
1446701 CAAGCCTCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.26
Consensus pattern (22 bp):
CCTAAACTATGAGCCCAAGATT
Found at i:1449560 original size:21 final size:22
Alignment explanation
Indices: 1449521--1449561 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1449511 TAGAAAAAAT
**
1449521 AAAAATATATATATCAAATTTC
1 AAAAATATATATAAAAAATTTC
1449543 AAAAA-ATATATAAAAAATT
1 AAAAATATATATAAAAAATT
1449562 CATAAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAATATATATAAAAAATTTC
Found at i:1462729 original size:16 final size:16
Alignment explanation
Indices: 1462704--1462738 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1462694 GTTTAAATTC
*
1462704 TTTGAGTCATTACAAG
1 TTTGAATCATTACAAG
*
1462720 TTTGAATCATTCCAAG
1 TTTGAATCATTACAAG
1462736 TTT
1 TTT
1462739 AATGTATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (16 bp):
TTTGAATCATTACAAG
Found at i:1462786 original size:16 final size:16
Alignment explanation
Indices: 1462767--1462819 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1462757 GTCATTACAG
*
1462767 GTCATTTCGAGTTTGA
1 GTCATTTTGAGTTTGA
* *
1462783 GTCATTTTAAG-TAGA
1 GTCATTTTGAGTTTGA
1462798 -TCATTTTGAGTTTGA
1 GTCATTTTGAGTTTGA
*
1462813 ATCATTT
1 GTCATTT
1462820 ATAAATAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 9 0.30
15 6 0.20
16 15 0.50
ACGTcount: A:0.25, C:0.09, G:0.19, T:0.47
Consensus pattern (16 bp):
GTCATTTTGAGTTTGA
Found at i:1473918 original size:31 final size:31
Alignment explanation
Indices: 1473848--1473919 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
1473838 TTTGATAGTT
*
1473848 CATGTATCACATTGGATGTTCATTTCAAAGTA
1 CATGTATCACATTGGATATT-ATTTCAAAGTA
* * **
1473880 TAAGTATCACATTGGATATT-TTATGGAAGTA
1 CATGTATCACATTGGATATTATT-TCAAAGTA
1473911 CATGTATCA
1 CATGTATCA
1473920 AATGTGACAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
30 2 0.06
31 13 0.41
32 17 0.53
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (31 bp):
CATGTATCACATTGGATATTATTTCAAAGTA
Found at i:1474212 original size:22 final size:22
Alignment explanation
Indices: 1474174--1474216 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
1474164 ATAATTATTA
1474174 AATTTATACATCAAAATTTGTCT
1 AATTTATACAT-AAAATTTGTCT
1474197 AATTTAATACAT-AAATTTGT
1 AATTT-ATACATAAAATTTGT
1474217 TTTATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 5 0.26
24 6 0.32
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (22 bp):
AATTTATACATAAAATTTGTCT
Found at i:1485735 original size:20 final size:21
Alignment explanation
Indices: 1485704--1485742 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1485694 AGGCCTGCCC
1485704 ATATTATATTTTAAAATTTTT
1 ATATTATATTTTAAAATTTTT
*
1485725 ATATT-TATTTTAATATTT
1 ATATTATATTTTAAAATTT
1485743 ACATTAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTATATTTTAAAATTTTT
Found at i:1488051 original size:22 final size:22
Alignment explanation
Indices: 1488026--1488072 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1488016 GCCTTATGTA
*
1488026 GTGCTAATCAGTCTATTTGAGT
1 GTGCTAATCAGTCTATTTAAGT
1488048 GTGCTAATCAGTCTATTTAAGT
1 GTGCTAATCAGTCTATTTAAGT
1488070 GTG
1 GTG
1488073 TAGGATGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (22 bp):
GTGCTAATCAGTCTATTTAAGT
Found at i:1489926 original size:22 final size:21
Alignment explanation
Indices: 1489885--1489926 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1489875 GCATCTCATT
*
1489885 ATTTTTGTTAACTTATATATC
1 ATTTTTGTTAACTTAGATATC
1489906 ATTTTGTGTTAGA-TTAGATAT
1 ATTTT-TGTTA-ACTTAGATAT
1489927 TAATATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 12 0.67
23 1 0.06
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (21 bp):
ATTTTTGTTAACTTAGATATC
Found at i:1492565 original size:46 final size:46
Alignment explanation
Indices: 1492515--1492690 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
1492505 TGGTTGAGCA
1492515 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1492561 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
1492606 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
1492654 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1492691 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:1492671 original size:93 final size:93
Alignment explanation
Indices: 1492512--1492683 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
1492502 GGATGGTTGA
* *
1492512 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1492577 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
1492605 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1492670 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
1492684 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:1495167 original size:37 final size:37
Alignment explanation
Indices: 1495106--1495251 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
1495096 TACGTATGAT
*
1495106 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
1495141 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1495178 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1495215 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1495252 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 4 0.04
37 91 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:1495294 original size:52 final size:52
Alignment explanation
Indices: 1495215--1495483 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
1495205 TAAGTGTAGC
* * **
1495215 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1495268 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1495320 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
1495372 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
1495418 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1495470 CACTTTGTCACTTG
1 CACTTT-TCACTTG
1495484 ATCAGAAGTA
Statistics
Matches: 196, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
46 43 0.22
49 1 0.01
52 137 0.70
53 15 0.08
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:1495402 original size:98 final size:98
Alignment explanation
Indices: 1495215--1495489 Score: 415
Period size: 98 Copynumber: 2.7 Consensus size: 98
1495205 TAAGTGTAGC
* *
1495215 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC---T---TT
*
1495280 GTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
59 GTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
1495320 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
1495385 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
1495418 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
1495483 GATCAGA
66 GATCAGA
1495490 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
98 108 0.68
101 1 0.01
104 42 0.26
105 9 0.06
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:1498800 original size:22 final size:21
Alignment explanation
Indices: 1498775--1498827 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1498765 TTTTGAATAG
1498775 TTTAATAACTTAAATAAAAAAT
1 TTTAATAACTTAAAT-AAAAAT
* *
1498797 TTTAAATAA-TTAAATGACAAT
1 TTT-AATAACTTAAATAAAAAT
1498818 TTT-ATAACTT
1 TTTAATAACTT
1498828 TTTAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 4 0.15
20 2 0.07
21 7 0.26
22 9 0.33
23 5 0.19
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTAATAACTTAAATAAAAAT
Found at i:1500410 original size:127 final size:126
Alignment explanation
Indices: 1500184--1500453 Score: 348
Period size: 127 Copynumber: 2.1 Consensus size: 126
1500174 GGCCAAACAT
* *
1500184 GAACTACTGTAGAAAAAGAGCGTCCACGTGGAAGCTTTTTTCATCAATTTTGATGACAGCGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGCGGAAGCTTTTTTCATCAATTTTGATAACAGCGCATC
** * * *
1500249 CTGCTTGAAGTGTTTTTGACACTATTTTTTCAGAACCGTCTTCTTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCATTTTTGACACTATCTTTTCAGAACCATCTTC-TCAAAATTAATTTTTCAG
* * * *
1500311 GAACTACTGTAGAAAAAGAGTGTCTATGCCGG-AGCTTTTTTCAGT-AATTTT-ACTAACAGTGC
1 GAACTACTGTAGAAAAAGAGCGTCCACG-CGGAAGCTTTTTTCA-TCAATTTTGA-TAACAGCGC
* *
1500373 ATCCTGCTTGAAGCATTTTTGACATTATCTTTTCAGAACCATCTTCTCAAAATTAATTTTTCTG
63 ATCCTGCTTGAAGCATTTTTGACACTATCTTTTCAGAACCATCTTCTCAAAATTAATTTTTCAG
* *
1500437 AAACTACTGTAAAAAAA
1 GAACTACTGTAGAAAAA
1500454 ACAAAATCCT
Statistics
Matches: 125, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
126 32 0.26
127 90 0.72
128 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGCGGAAGCTTTTTTCATCAATTTTGATAACAGCGCATC
CTGCTTGAAGCATTTTTGACACTATCTTTTCAGAACCATCTTCTCAAAATTAATTTTTCAG
Found at i:1500571 original size:34 final size:34
Alignment explanation
Indices: 1500523--1500587 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1500513 TTTTTAAAAA
*
1500523 TAAACCCTAATTTAATTAATTTTCTTAAAACCCT
1 TAAAACCTAATTTAATTAATTTTCTTAAAACCCT
*
1500557 TAAAACCTAATTTAATTAATTTTTTTAAAAC
1 TAAAACCTAATTTAATTAATTTTCTTAAAAC
1500588 AAAAACTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (34 bp):
TAAAACCTAATTTAATTAATTTTCTTAAAACCCT
Found at i:1503514 original size:9 final size:9
Alignment explanation
Indices: 1503502--1503553 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
1503492 ATTTTATCAA
1503502 TTAAATAAT
1 TTAAATAAT
*
1503511 TTAAATAAA
1 TTAAATAAT
* **
1503520 TAAAATTTT
1 TTAAATAAT
1503529 TTAAATAAT
1 TTAAATAAT
1503538 TT-AATAAT
1 TTAAATAAT
1503546 TTAAATAA
1 TTAAATAA
1503554 AATTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
8 8 0.24
9 26 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAATAAT
Found at i:1503535 original size:14 final size:14
Alignment explanation
Indices: 1503516--1503567 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
1503506 ATAATTTAAA
1503516 TAAATAAAATTTTT
1 TAAATAAAATTTTT
**
1503530 TAAATAATTTAATAATT
1 TAAATAA---AATTTTT
1503547 TAAATAAAATTTTT
1 TAAATAAAATTTTT
1503561 TAAATAA
1 TAAATAA
1503568 TTCAATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 19 0.61
17 12 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAAATAAAATTTTT
Found at i:1503554 original size:31 final size:31
Alignment explanation
Indices: 1503502--1503577 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
1503492 ATTTTATCAA
1503502 TTAAATAATTT-A-AA--TAAATAAAATTTT
1 TTAAATAATTTAATAATTTAAATAAAATTTT
1503529 TTAAATAATTTAATAATTTAAATAAAATTTT
1 TTAAATAATTTAATAATTTAAATAAAATTTT
*
1503560 TTAAATAATTCAATAATT
1 TTAAATAATTTAATAATT
1503578 ATTTTTCAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
27 11 0.25
28 1 0.02
29 2 0.05
31 30 0.68
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
TTAAATAATTTAATAATTTAAATAAAATTTT
Found at i:1505076 original size:31 final size:30
Alignment explanation
Indices: 1505035--1505093 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
1505025 TATTTTATTA
1505035 TTAATTTGTTATTATTTTAAAGGCATTTTG
1 TTAATTTGTTATTATTTTAAAGGCATTTTG
* *
1505065 TTAATTTTGTTATTATTTTAGAGGTATTT
1 TTAA-TTTGTTATTATTTTAAAGGCATTT
1505094 GCTTGTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (30 bp):
TTAATTTGTTATTATTTTAAAGGCATTTTG
Found at i:1505162 original size:21 final size:23
Alignment explanation
Indices: 1505136--1505187 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1505126 TAAGTCTACA
1505136 TAATTTTTA-AAAAT-TTATTTT
1 TAATTTTTAGAAAATATTATTTT
*
1505157 TAATTTGTTAGAAAATATTTTTTT
1 TAATTT-TTAGAAAATATTATTTT
*
1505181 TGATTTT
1 TAATTTT
1505188 ATTAGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 6 0.23
24 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (23 bp):
TAATTTTTAGAAAATATTATTTT
Found at i:1508491 original size:3 final size:3
Alignment explanation
Indices: 1508483--1508516 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1508473 AAATGATTAC
1508483 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1508517 AATCAACCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1510256 original size:26 final size:26
Alignment explanation
Indices: 1510204--1510252 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1510194 AAAATATAAT
*
1510204 TAAATGACTATTTTATAACTATTTTA
1 TAAATAACTATTTTATAACTATTTTA
1510230 TAAATAACTATTTTA-AA-TATTTT
1 TAAATAACTATTTTATAACTATTTT
1510253 TTATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 2 0.09
26 14 0.64
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
TAAATAACTATTTTATAACTATTTTA
Found at i:1510475 original size:21 final size:21
Alignment explanation
Indices: 1510432--1510475 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1510422 TAACAAAATA
* **
1510432 TAAAAAATAGAAATTATTTTG
1 TAAAAAATAGAAAATATAGTG
*
1510453 TAAAAAATATAAAATATAGTG
1 TAAAAAATAGAAAATATAGTG
1510474 TA
1 TA
1510476 GCCTTTAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (21 bp):
TAAAAAATAGAAAATATAGTG
Found at i:1511021 original size:24 final size:23
Alignment explanation
Indices: 1510989--1511036 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1510979 ATAATGATGT
* *
1510989 TTTTCTTTTTCTTTTTCTTTATA
1 TTTTCTTTTACTATTTCTTTATA
*
1511012 TTTTCATTTTAGTATTTCTTTATA
1 TTTTC-TTTTACTATTTCTTTATA
1511036 T
1 T
1511037 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.15, C:0.10, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTCTTTTACTATTTCTTTATA
Found at i:1512389 original size:31 final size:31
Alignment explanation
Indices: 1512344--1512403 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1512334 ATGACTTAAA
*
1512344 TAAATAAAAGTTTTTAAATAATTTAATGATT
1 TAAATAAAAGTTTTTAAATAATTCAATGATT
1512375 TAAATGAAAA-TTTTTAAATAATTCAATGA
1 TAAAT-AAAAGTTTTTAAATAATTCAATGA
1512404 ATATTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.42
Consensus pattern (31 bp):
TAAATAAAAGTTTTTAAATAATTCAATGATT
Found at i:1512402 original size:22 final size:22
Alignment explanation
Indices: 1512377--1512419 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1512367 TAATGATTTA
1512377 AATGAAAATTTTT-AAATAATTC
1 AATGAAAATTTTTCAAA-AATTC
*
1512399 AATGAATATTTTTCAAAAATT
1 AATGAAAATTTTTCAAAAATT
1512420 AAAAAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (22 bp):
AATGAAAATTTTTCAAAAATTC
Found at i:1517184 original size:18 final size:18
Alignment explanation
Indices: 1517163--1517199 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1517153 CCCAAATTAG
1517163 ACAAAAAAAACAAACAAA
1 ACAAAAAAAACAAACAAA
* *
1517181 ACAAAAAAACCAATCAAA
1 ACAAAAAAAACAAACAAA
1517199 A
1 A
1517200 TTACAGCCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.78, C:0.19, G:0.00, T:0.03
Consensus pattern (18 bp):
ACAAAAAAAACAAACAAA
Found at i:1529041 original size:3 final size:3
Alignment explanation
Indices: 1528995--1529029 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1528985 AATAGGAAGA
*
1528995 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1529030 ACTCAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1536038 original size:43 final size:43
Alignment explanation
Indices: 1535991--1536081 Score: 173
Period size: 43 Copynumber: 2.1 Consensus size: 43
1535981 CCTACTTGTC
1535991 AAGTTCAAAAATGAAAAATTATATTATCCCTAAATTAAAGCTA
1 AAGTTCAAAAATGAAAAATTATATTATCCCTAAATTAAAGCTA
*
1536034 AAGTTCAAAAATGAAAAATTATATTATCCCTAAATTAAAGCTG
1 AAGTTCAAAAATGAAAAATTATATTATCCCTAAATTAAAGCTA
1536077 AAGTT
1 AAGTT
1536082 TGTTTTCCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (43 bp):
AAGTTCAAAAATGAAAAATTATATTATCCCTAAATTAAAGCTA
Found at i:1539140 original size:3 final size:3
Alignment explanation
Indices: 1539132--1539159 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1539122 TCCAGTACTA
1539132 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1539160 GAAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1540159 original size:18 final size:18
Alignment explanation
Indices: 1540136--1540171 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1540126 TGAATCATAC
*
1540136 TAAGATTTTTTTTTATAT
1 TAAGATATTTTTTTATAT
1540154 TAAGATATTTTTTTATAT
1 TAAGATATTTTTTTATAT
1540172 CATATGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TAAGATATTTTTTTATAT
Found at i:1542609 original size:25 final size:25
Alignment explanation
Indices: 1542580--1542630 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1542570 GAATAAAAAG
1542580 ATAAATTTTAAATACAGTAAACTTA
1 ATAAATTTTAAATACAGTAAACTTA
1542605 ATAAATTTTAAATACAGTAAACTTA
1 ATAAATTTTAAATACAGTAAACTTA
1542630 A
1 A
1542631 AGGTTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (25 bp):
ATAAATTTTAAATACAGTAAACTTA
Found at i:1554767 original size:44 final size:43
Alignment explanation
Indices: 1554665--1554955 Score: 145
Period size: 44 Copynumber: 6.8 Consensus size: 43
1554655 CCTTTATTTT
* * * * *
1554665 AATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTC
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATTACTGGCCTC
* *
1554708 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATTACTGGCCTC
* * *** *
1554752 GATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TTTTT
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGAT-T--ACTGGCCTC
* * * *
1554798 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGA--CCTGG--TGC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATTACTGGCCT-C
* * * * *
1554839 GATCTGCTCTACTGTAACTTCAGAGAGATAAGA-T-C---CTTT
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATTACTGGCCTC
* * ****
1554878 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACTATATTC
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATTACTGGCCTC
*
1554922 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGAT
1554956 CTGCAATTCT
Statistics
Matches: 189, Mismatches: 42, Indels: 33
0.72 0.16 0.12
Matches are distributed among these distances:
39 28 0.15
40 4 0.02
41 28 0.15
43 28 0.15
44 69 0.37
45 2 0.01
46 29 0.15
47 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
AATCTGCTCCACTGTAACTCAGGGAGATAAGATTACTGGCCTC
Found at i:1567699 original size:3 final size:3
Alignment explanation
Indices: 1567691--1567726 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1567681 AATAGGAAGA
*
1567691 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1567727 GAATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1573275 original size:39 final size:39
Alignment explanation
Indices: 1573217--1573385 Score: 230
Period size: 39 Copynumber: 4.3 Consensus size: 39
1573207 ATGGAATCCC
* * *
1573217 GATTATACTAAATGTTTGCTCAAACAAGCATTATCCATT
1 GATTATACTGAATGCTTGCTCAAACGAGCATTATCCATT
*
1573256 GATTATACTGAATGCTTGCTCAAACGAGCATTATCCACT
1 GATTATACTGAATGCTTGCTCAAACGAGCATTATCCATT
* * * *
1573295 GATTATATTGAATGCTTGCTCAAATGAGTATTGTCCATT
1 GATTATACTGAATGCTTGCTCAAACGAGCATTATCCATT
** * *
1573334 GGCTATGCTGAATGCTTGCTCAAACTAGCATTATCCATT
1 GATTATACTGAATGCTTGCTCAAACGAGCATTATCCATT
1573373 GATTATACTGAAT
1 GATTATACTGAAT
1573386 AAGATTTTAT
Statistics
Matches: 110, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (39 bp):
GATTATACTGAATGCTTGCTCAAACGAGCATTATCCATT
Found at i:1574147 original size:16 final size:17
Alignment explanation
Indices: 1574118--1574155 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1574108 AATTTAATAA
1574118 AATTTGTGTTAATTGTG
1 AATTTGTGTTAATTGTG
1574135 AATTTGT-TTAATTGTG
1 AATTTGTGTTAATTGTG
*
1574151 CATTT
1 AATTT
1574156 AAAATGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (17 bp):
AATTTGTGTTAATTGTG
Found at i:1574537 original size:22 final size:23
Alignment explanation
Indices: 1574512--1574554 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1574502 TAATGCAAAT
*
1574512 TTATTTT-AGCAGTTACAAACCA
1 TTATTTTCAACAGTTACAAACCA
1574534 TTATTTTCAACAGTTACAAAC
1 TTATTTTCAACAGTTACAAAC
1574555 TGTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (23 bp):
TTATTTTCAACAGTTACAAACCA
Found at i:1574563 original size:23 final size:21
Alignment explanation
Indices: 1574512--1574570 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
1574502 TAATGCAAAT
1574512 TTATTTTAGCAGTTACAAACCA
1 TTATTTTA-CAGTTACAAACCA
**
1574534 TTATTTTCAACAGTTACAAACTG
1 TTATTTT--ACAGTTACAAACCA
*
1574557 TTTTTTTACAGTTA
1 TTATTTTACAGTTA
1574571 TAAAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 7 0.22
22 7 0.22
23 17 0.53
24 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.44
Consensus pattern (21 bp):
TTATTTTACAGTTACAAACCA
Found at i:1575096 original size:15 final size:15
Alignment explanation
Indices: 1575076--1575117 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1575066 CTAACGAGTT
* *
1575076 TATTTTGCAATAGTA
1 TATTTTCCAACAGTA
1575091 TATTTTCCAACAGTA
1 TATTTTCCAACAGTA
1575106 TATTTTCCAACA
1 TATTTTCCAACA
1575118 CCACTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (15 bp):
TATTTTCCAACAGTA
Found at i:1581592 original size:30 final size:30
Alignment explanation
Indices: 1581552--1581726 Score: 122
Period size: 35 Copynumber: 5.4 Consensus size: 30
1581542 ACCACCAAAT
* *
1581552 ACCACCCCACTAATTCCAACAACCCACTAAA
1 ACCACTCCACTAACTCCAACAACCCACT-AA
* *
1581583 CCACTCCACTTGCCACTAACTCCATC-TCCCACTAA
1 --A--CCAC-T-CCACTAACTCCAACAACCCACTAA
1581618 ACCA-TCCTACTAACTCCAACAACCCACTAA
1 ACCACTCC-ACTAACTCCAACAACCCACTAA
* *
1581648 ACCA-TCCCACTAACTCCAACCACCCCACTTA
1 ACCACT-CCACTAACTCCAA-CAACCCACTAA
* *
1581679 ACCACTTCACTAAACCACTCCAACCACCCCACTAA
1 ACCACTCCACT--A--ACTCCAA-CAACCCACTAA
1581714 ACCACTCCACTAA
1 ACCACTCCACTAA
1581727 ACCACCCTAA
Statistics
Matches: 118, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
28 2 0.02
29 12 0.10
30 24 0.20
31 23 0.19
32 1 0.01
33 4 0.03
35 34 0.29
36 6 0.05
37 12 0.10
ACGTcount: A:0.35, C:0.47, G:0.01, T:0.17
Consensus pattern (30 bp):
ACCACTCCACTAACTCCAACAACCCACTAA
Found at i:1581681 original size:13 final size:13
Alignment explanation
Indices: 1581665--1581761 Score: 75
Period size: 13 Copynumber: 8.1 Consensus size: 13
1581655 CACTAACTCC
*
1581665 AACCACCCCACTT
1 AACCACCCCACTA
**
1581678 AACCACTTCACTA
1 AACCACCCCACTA
*
1581691 AACCA-CTC-C--
1 AACCACCCCACTA
1581700 AACCACCCCACTA
1 AACCACCCCACTA
*
1581713 AACCACTCCACTA
1 AACCACCCCACTA
1581726 AACCA--CC-CT-
1 AACCACCCCACTA
1581735 AACCACCCCACTA
1 AACCACCCCACTA
**
1581748 AATTACCCCACTA
1 AACCACCCCACTA
1581761 A
1 A
1581762 CTTCATCACC
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
9 10 0.15
10 4 0.06
11 6 0.09
12 4 0.06
13 44 0.65
ACGTcount: A:0.37, C:0.48, G:0.00, T:0.14
Consensus pattern (13 bp):
AACCACCCCACTA
Found at i:1581706 original size:35 final size:35
Alignment explanation
Indices: 1581630--1581749 Score: 146
Period size: 35 Copynumber: 3.6 Consensus size: 35
1581620 CATCCTACTA
*
1581630 ACTCCAA-CAACCCACTAAACCA-TCCCACT--A--
1 ACTCCAACCACCCCACTAAACCACT-CCACTAAACC
* *
1581660 ACTCCAACCACCCCACTTAACCACTTCACTAAACC
1 ACTCCAACCACCCCACTAAACCACTCCACTAAACC
1581695 ACTCCAACCACCCCACTAAACCACTCCACTAAACC
1 ACTCCAACCACCCCACTAAACCACTCCACTAAACC
1581730 AC-CCTAACCACCCCACTAAA
1 ACTCC-AACCACCCCACTAAA
1581750 TTACCCCACT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.09
31 17 0.22
32 1 0.01
33 1 0.01
34 2 0.03
35 50 0.64
ACGTcount: A:0.38, C:0.49, G:0.00, T:0.13
Consensus pattern (35 bp):
ACTCCAACCACCCCACTAAACCACTCCACTAAACC
Found at i:1582215 original size:19 final size:18
Alignment explanation
Indices: 1582178--1582219 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1582168 GGGGAGAGTG
*
1582178 TTATTTTTAATATTGTTA
1 TTATTTTTAATATTATTA
*
1582196 TTATTTTCTATTATTATTA
1 TTATTTT-TAATATTATTA
1582215 TTATT
1 TTATT
1582220 ACTAATACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTATTTTTAATATTATTA
Found at i:1582278 original size:33 final size:39
Alignment explanation
Indices: 1582204--1582285 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 39
1582194 TATTATTTTC
*
1582204 TATTATTATTATTATTACTAATACCACTATTATCATCAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
*
1582243 TATTACTATTA-TATTA-TAATA-C-CT-TT-TCATTAT
1 TATTACTATTATTATTACTAATACCACTATTATCATCAT
1582276 TATTACTATT
1 TATTACTATT
1582286 GTGTTTTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 16 0.39
34 2 0.05
35 2 0.05
36 1 0.02
37 5 0.12
38 5 0.12
39 10 0.24
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTACTATTATTATTACTAATACCACTATTATCATCAT
Found at i:1583608 original size:16 final size:15
Alignment explanation
Indices: 1583587--1583627 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1583577 CCAAGTGTTT
*
1583587 TAATTTTAAAACATAC
1 TAATTTTAAAA-AAAC
1583603 TAATTTTAAAAAAAC
1 TAATTTTAAAAAAAC
1583618 T-ATTTTAAAA
1 TAATTTTAAAA
1583628 TTGAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
15 4 0.17
16 11 0.46
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATTTTAAAAAAAC
Found at i:1586031 original size:28 final size:28
Alignment explanation
Indices: 1585999--1586068 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
1585989 TATGGTACTC
*
1585999 AGTGTACGAAATATTGAGAATGACACTT
1 AGTGTGCGAAATATTGAGAATGACACTT
* *
1586027 AGTGTGCGAGATATTGAGAATGACATTT
1 AGTGTGCGAAATATTGAGAATGACACTT
*
1586055 AGTGTGCAAAATAT
1 AGTGTGCGAAATAT
1586069 CGAATGATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGACACTT
Found at i:1590590 original size:315 final size:316
Alignment explanation
Indices: 1589996--1590619 Score: 1031
Period size: 315 Copynumber: 2.0 Consensus size: 316
1589986 TAACAGCTCA
* * **
1589996 ATTTTGGGCCTAGTCGGAACAGTGGTTTCGGGACCACTATTTTGAGGCCAGAGAAAATTATTTTA
1 ATTTTAGGCCTAGTCAGAACAGTGGTTTCGGGACCACTATTCCGAGGCCAGAGAAAATTATTTTA
* *
1590061 GTATTATTTTATGTGTTATAATGTGATTTTATAAGTGCATGTAAATTTTGGTAAGTTAATTTTAG
66 GTATTATTTTATGTGTTATAATATAATTTTATAAGTGCATGTAAATTTTGGTAAGTTAATTTTAG
** *
1590126 CAATTTCTAGTCCAATTTTGAAAAAGGACTAAATCGCGTAAAAGGTAAAAGTTGTGTTTTAATAC
131 CAATTTCTAGTCCAATTTCAAAAAAGGACTAAATCGCGTAAAAGGTAAAAGTTGTATTTTAATAC
* * * *
1590191 CTAAAGGTGTTAAATTGCCTTTTATCTTAAATTGGGGGTCTTTAAAGTGAAATTAGGCCATTGAA
196 CTAAAAGTATTAAATTGCCTTTTATATTAAATTGGGGGTATTTAAAGTGAAATTAGGCCATTGAA
1590256 AGTGTGATGGCAGGGCCATGGGAGAC-AAAATTGTTGAAAAGTCAAAATCAGCCCG
261 AGTGTGATGGCAGGGCCATGGGAGACAAAAATTGTTGAAAAGTCAAAATCAGCCCG
*
1590311 ATTTTAGGCCTAGTCAGAACAGTGGTTTCGGGACCACTATTCCGAGGCCAGATAAAATTATTTTA
1 ATTTTAGGCCTAGTCAGAACAGTGGTTTCGGGACCACTATTCCGAGGCCAGAGAAAATTATTTTA
1590376 GTATTATTTTATGTGTTATAATATAATTTTATAAGTGCATGTAAATTTTGGTAAGTTAATTTTAG
66 GTATTATTTTATGTGTTATAATATAATTTTATAAGTGCATGTAAATTTTGGTAAGTTAATTTTAG
* * *
1590441 CGATTTCTAGTCCAATTTCAAAAAATGG-CTAAATCGCGTAAAAGGTAAAAGTTGTATTTTGATG
131 CAATTTCTAGTCCAATTTCAAAAAA-GGACTAAATCGCGTAAAAGGTAAAAGTTGTATTTTAATA
*
1590505 CCTAAAAGTATTAAATTG-CTTTGTGTATTAAATTTGGGGGTATTTAAAGTGAAATTAGGCCATT
195 CCTAAAAGTATTAAATTGCCTTT-TATATTAAA-TTGGGGGTATTTAAAGTGAAATTAGGCCATT
1590569 GAAAGTGTGATGGCA-GGCCATGGGAGACAAAAATTGTTGAAAAGTCAAAAT
258 GAAAGTGTGATGGCAGGGCCATGGGAGACAAAAATTGTTGAAAAGTCAAAAT
1590620 TAGGTGAACT
Statistics
Matches: 287, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
314 4 0.01
315 214 0.75
316 69 0.24
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.35
Consensus pattern (316 bp):
ATTTTAGGCCTAGTCAGAACAGTGGTTTCGGGACCACTATTCCGAGGCCAGAGAAAATTATTTTA
GTATTATTTTATGTGTTATAATATAATTTTATAAGTGCATGTAAATTTTGGTAAGTTAATTTTAG
CAATTTCTAGTCCAATTTCAAAAAAGGACTAAATCGCGTAAAAGGTAAAAGTTGTATTTTAATAC
CTAAAAGTATTAAATTGCCTTTTATATTAAATTGGGGGTATTTAAAGTGAAATTAGGCCATTGAA
AGTGTGATGGCAGGGCCATGGGAGACAAAAATTGTTGAAAAGTCAAAATCAGCCCG
Found at i:1592893 original size:50 final size:50
Alignment explanation
Indices: 1592835--1592939 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
1592825 TTTTAATGTG
*
1592835 AGTA-TGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGTT
1 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
1592884 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
1 AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
1592934 AGTATT
1 AGTATT
1592940 AGTCATGTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 4 0.07
50 50 0.93
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (50 bp):
AGTATTGTAATATTATGATTTAGCCAAAGGCATTGGCTTGTTATTAAGGT
Found at i:1594458 original size:46 final size:46
Alignment explanation
Indices: 1594355--1594529 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 46
1594345 GAGACTTGAT
* * * * *
1594355 AGCCAGTGTAAGACCATGTTTGAGACATGGCATC-GGCATTGAGACGAG
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA-CGAGATGAG
* *
1594403 GGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAG
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAG-ATGAG
* * * * **
1594449 AGCCAGTGTAAGACATGTCTGGGTCATGAATCGGCCTCGAGATGTT
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAG
*
1594495 AGCCAGTGTAAGACATGTCTGGGACATGCGTCAGC
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCAGC
1594530 ACGGTTACAT
Statistics
Matches: 105, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
45 2 0.02
46 75 0.71
47 17 0.16
48 11 0.10
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (46 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACGAGATGAG
Found at i:1600552 original size:32 final size:32
Alignment explanation
Indices: 1600511--1600574 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1600501 AATTCTCTGC
*
1600511 ATAGCCTGGAGTTTTTCAGTACCTTAATCTTA
1 ATAGCCTGGAGTTTCTCAGTACCTTAATCTTA
1600543 ATAGCCTGGAGTTTCTCAGTACCTTAATCTTA
1 ATAGCCTGGAGTTTCTCAGTACCTTAATCTTA
1600575 CTCTGAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (32 bp):
ATAGCCTGGAGTTTCTCAGTACCTTAATCTTA
Found at i:1602251 original size:46 final size:45
Alignment explanation
Indices: 1602113--1602318 Score: 170
Period size: 46 Copynumber: 4.5 Consensus size: 45
1602103 GTCGATGCCG
* * * *
1602113 TGTCCCAGACAGGTCTTACACTAAC-ACATGTAACCGT-GCCTATGCA
1 TGTCCCAGACATGTCTTACACTAGCAACATCT---CGTAGCCGATGCA
* * *
1602159 TGTCCCAGACATGTCTTACACTAG-GACATCTCGTAGCTGACGCA
1 TGTCCCAGACATGTCTTACACTAGCAACATCTCGTAGCCGATGCA
* *
1602203 TGTTCCAGACATGTCTGACACTAGCTAACATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTAGC-AACATCTCGTA-GCCGATGCA
** * * *
1602249 TGTCCCAGACATGTCTTACACTAGCCCTCGTCTC-AATGTCGATGCTA
1 TGTCCCAGACATGTCTTACACTAG-CAACATCTCGTA-GCCGATGC-A
1602296 TGTCCCAGACATGGTCTTACACT
1 TGTCCCAGACAT-GTCTTACACT
1602319 GGCTCACAAT
Statistics
Matches: 133, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
43 3 0.02
44 28 0.21
45 1 0.01
46 77 0.58
47 14 0.11
48 10 0.08
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTAGCAACATCTCGTAGCCGATGCA
Found at i:1603795 original size:50 final size:49
Alignment explanation
Indices: 1603736--1603837 Score: 186
Period size: 50 Copynumber: 2.1 Consensus size: 49
1603726 CATGACTAAC
*
1603736 ACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATATTACAAT
1 ACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATACTAC-AT
1603786 ACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATACTACAT
1 ACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATACTACAT
1603835 ACT
1 ACT
1603838 CACATTAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 5 0.10
50 46 0.90
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (49 bp):
ACTACCTTAATAACAAGCCAATGCCTTTGGCTAAATCATAATACTACAT
Found at i:1605669 original size:19 final size:19
Alignment explanation
Indices: 1605633--1605670 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1605623 CTCATAATTT
1605633 CAACTATTTCACACACTTA
1 CAACTATTTCACACACTTA
*
1605652 CAACTCATTTTACA-ACTTA
1 CAACT-ATTTCACACACTTA
1605671 GCAATCTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (19 bp):
CAACTATTTCACACACTTA
Found at i:1606432 original size:8 final size:8
Alignment explanation
Indices: 1606419--1606448 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1606409 TTATTTTTAT
1606419 TTATTAAA
1 TTATTAAA
1606427 TTATTAAA
1 TTATTAAA
1606435 TTATTTAAA
1 TTA-TTAAA
1606444 TTATT
1 TTATT
1606449 TGTACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTATTAAA
Found at i:1606651 original size:14 final size:15
Alignment explanation
Indices: 1606632--1606670 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1606622 ACTAACTTTG
1606632 AACTGAATT-CGGTT
1 AACTGAATTACGGTT
*
1606646 AACTGAATTAACTGTT
1 AACTGAATT-ACGGTT
1606662 AACTGAATT
1 AACTGAATT
1606671 TTCAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (15 bp):
AACTGAATTACGGTT
Found at i:1607333 original size:32 final size:32
Alignment explanation
Indices: 1607297--1607388 Score: 78
Period size: 35 Copynumber: 2.8 Consensus size: 32
1607287 GATTGTATTT
1607297 TACCTTTTCTACTCACAAAATGACCAAATTAG
1 TACCTTTTCTACTCACAAAATGACCAAATTAG
* * * * * * *
1607329 TACCTATT-TATTAGATCAAAGTGTAAACGAGTTAG
1 TACCTTTTCTACT-CA-CAAAATG--ACCAAATTAG
1607364 TACCTTTTCTACTCACAAAATGACC
1 TACCTTTTCTACTCACAAAATGACC
1607389 CATGAGCACC
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
31 3 0.07
32 10 0.23
33 6 0.14
34 6 0.14
35 15 0.35
36 3 0.07
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (32 bp):
TACCTTTTCTACTCACAAAATGACCAAATTAG
Found at i:1609056 original size:31 final size:31
Alignment explanation
Indices: 1609021--1609080 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1609011 TTACAAAGTC
* *
1609021 AACATTGAAGCCGAACTCAGGTATCAAATTG
1 AACATTAAAGCCAAACTCAGGTATCAAATTG
* * *
1609052 AACATTAAAGTCAAATTTAGGTATCAAAT
1 AACATTAAAGCCAAACTCAGGTATCAAAT
1609081 AGTATATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (31 bp):
AACATTAAAGCCAAACTCAGGTATCAAATTG
Found at i:1620532 original size:13 final size:14
Alignment explanation
Indices: 1620500--1620531 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1620490 TTGTTTCACT
*
1620500 AAAAATAATTTTTG
1 AAAAATGATTTTTG
1620514 AAAAATGATTTTTG
1 AAAAATGATTTTTG
1620528 AAAA
1 AAAA
1620532 TAGATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AAAAATGATTTTTG
Found at i:1620537 original size:14 final size:14
Alignment explanation
Indices: 1620501--1620537 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1620491 TGTTTCACTA
1620501 AAAATA-ATTTTTG
1 AAAATAGATTTTTG
1620514 AAAA-ATGATTTTTG
1 AAAATA-GATTTTTG
1620528 AAAATAGATT
1 AAAATAGATT
1620538 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 4 0.19
14 15 0.71
15 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (14 bp):
AAAATAGATTTTTG
Found at i:1620796 original size:28 final size:28
Alignment explanation
Indices: 1620740--1620797 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1620730 ATAATATTTT
* *
1620740 ATAATAATTAATATAATATATAAAGTTA
1 ATAATAAATAATATAATATATAAACTTA
1620768 ATAATAAATAATATCTAAT-TA-AAACTTA
1 ATAATAAATAATA--TAATATATAAACTTA
1620796 AT
1 AT
1620798 TTAATTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 20 0.77
29 2 0.08
30 4 0.15
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (28 bp):
ATAATAAATAATATAATATATAAACTTA
Found at i:1621076 original size:13 final size:13
Alignment explanation
Indices: 1621060--1621098 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1621050 TTTTAAGATT
*
1621060 AAATAATTTATTA
1 AAATAATTAATTA
1621073 AAATAATTAATTA
1 AAATAATTAATTA
*
1621086 AATTAA-TAATTA
1 AAATAATTAATTA
1621098 A
1 A
1621099 TCATATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATAATTAATTA
Found at i:1630107 original size:16 final size:16
Alignment explanation
Indices: 1630088--1630118 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1630078 ATAAAAAATA
1630088 ATATAAGGTTTATAAT
1 ATATAAGGTTTATAAT
1630104 ATATAAGGTTTATAA
1 ATATAAGGTTTATAA
1630119 ATTTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (16 bp):
ATATAAGGTTTATAAT
Found at i:1630809 original size:30 final size:30
Alignment explanation
Indices: 1630775--1630837 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1630765 ACTTAATAAG
1630775 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
1630805 CAAATGCCTTTAAAATAATAGCAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
1630835 CAA
1 CAA
1630838 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:1630907 original size:22 final size:22
Alignment explanation
Indices: 1630866--1630914 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1630856 ATATCCAAAC
1630866 AATAACAATAAAATAATAGCAA
1 AATAACAATAAAATAATAGCAA
* * **
1630888 CATAATAATAAAATGGTAGCAA
1 AATAACAATAAAATAATAGCAA
1630910 AATAA
1 AATAA
1630915 AGAGAAAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (22 bp):
AATAACAATAAAATAATAGCAA
Found at i:1634751 original size:36 final size:36
Alignment explanation
Indices: 1634703--1634773 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1634693 GAGTGATACA
1634703 TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGTG
1 TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGTG
* * *
1634739 TTGAATGTGATGGGATAGGTGTAGTGGAGGTAGGT
1 TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGT
1634774 AGCGTATTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.46, T:0.28
Consensus pattern (36 bp):
TTGAATGGGATGGAAAAGGTGTAGTGGAGGTAGGTG
Found at i:1641441 original size:3 final size:3
Alignment explanation
Indices: 1641435--1641489 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
1641425 ATAGAAGAAT
*
1641435 AGA AGA AGA AGA ATA AG- AGA AGA A-A CAG- AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA
*
1641478 AAA AGA AGA AGA
1 AGA AGA AGA AGA
1641490 GGAGGAGGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.11
3 39 0.89
ACGTcount: A:0.67, C:0.02, G:0.29, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:1641446 original size:14 final size:14
Alignment explanation
Indices: 1641427--1641487 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
1641417 ACTGGGCAAT
1641427 AGAAGAATAGAAGA
1 AGAAGAATAGAAGA
1641441 AGAAGAATA-AGAGA
1 AGAAGAATAGA-AGA
*
1641455 AGAA-ACAGAGAAGA
1 AGAAGA-ATAGAAGA
*
1641469 AGAAG-A-AGAAAA
1 AGAAGAATAGAAGA
1641481 AGAAGAA
1 AGAAGAA
1641488 GAGGAGGAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
12 10 0.25
13 4 0.10
14 25 0.62
15 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.28, T:0.03
Consensus pattern (14 bp):
AGAAGAATAGAAGA
Found at i:1643339 original size:3 final size:3
Alignment explanation
Indices: 1643331--1643359 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1643321 ACTTTCCACC
1643331 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1643360 AAAAGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1646085 original size:13 final size:14
Alignment explanation
Indices: 1646059--1646087 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1646049 AATTATTGAA
1646059 TTACTAATTTAACC
1 TTACTAATTTAACC
1646073 TTACTAA-TTAACC
1 TTACTAATTTAACC
1646086 TT
1 TT
1646088 TAAATCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (14 bp):
TTACTAATTTAACC
Found at i:1652841 original size:17 final size:15
Alignment explanation
Indices: 1652799--1652841 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
1652789 AATGTTTTTC
1652799 TTTCTTTTCCTTCCT
1 TTTCTTTTCCTTCCT
1652814 TTTCCATTTTCCTTCGCT
1 TTT-C-TTTTCCTTC-CT
1652832 TTTCTGTTTC
1 TTTCT-TTTC
1652842 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 14 0.58
18 5 0.21
ACGTcount: A:0.02, C:0.30, G:0.05, T:0.63
Consensus pattern (15 bp):
TTTCTTTTCCTTCCT
Found at i:1655983 original size:36 final size:36
Alignment explanation
Indices: 1655932--1656005 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
1655922 TTTGGAAGAC
* * *
1655932 TTCATCTCCTCCTATCTCCTCCTCACTTGTATCTTG
1 TTCATCTCCTACTATCTCCTCCTCACTTATAACTTG
1655968 TTCATCTCCTACTATCTCCTCCTCACTTATAACTTG
1 TTCATCTCCTACTATCTCCTCCTCACTTATAACTTG
1656004 TT
1 TT
1656006 TCATAGACTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.36, G:0.04, T:0.45
Consensus pattern (36 bp):
TTCATCTCCTACTATCTCCTCCTCACTTATAACTTG
Found at i:1659466 original size:6 final size:6
Alignment explanation
Indices: 1659455--1659493 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1659445 GTATTTGGCA
* * *
1659455 TATTGT TATTGT TATTGT TATTAT TATTTT TATTAT TAT
1 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TAT
1659494 AAACTACACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (6 bp):
TATTGT
Found at i:1659472 original size:12 final size:12
Alignment explanation
Indices: 1659455--1659493 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1659445 GTATTTGGCA
*
1659455 TATTGTTATTGT
1 TATTGTTATTAT
1659467 TATTGTTATTAT
1 TATTGTTATTAT
*
1659479 TATTTTTATTAT
1 TATTGTTATTAT
1659491 TAT
1 TAT
1659494 AAACTACACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TATTGTTATTAT
Found at i:1660315 original size:17 final size:16
Alignment explanation
Indices: 1660273--1660315 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1660263 AATGTTTTTA
1660273 TTTCTTTTCCTTCCCT
1 TTTCTTTTCCTTCCCT
* *
1660289 TTCCATTTTCCTTCGCT
1 TTTC-TTTTCCTTCCCT
1660306 TTTCTGTTTC
1 TTTCT-TTTC
1660316 TTTTTTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.02, C:0.33, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTCTTTTCCTTCCCT
Found at i:1666289 original size:13 final size:13
Alignment explanation
Indices: 1666232--1666290 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
1666222 AATTTTATGT
*
1666232 ATATATAAAATAA
1 ATATTTAAAATAA
* *
1666245 ATAATTAAAATAT
1 ATATTTAAAATAA
*
1666258 ATATGTTGAAATAAA
1 ATAT-TTAAAAT-AA
*
1666273 ATATTTTAAATAA
1 ATATTTAAAATAA
1666286 ATATT
1 ATATT
1666291 ACAATTATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 20 0.54
14 12 0.32
15 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1666315 original size:15 final size:16
Alignment explanation
Indices: 1666295--1666325 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1666285 AATATTACAA
1666295 TTATTAA-AAATAATT
1 TTATTAATAAATAATT
1666310 TTATTAATAAATAATT
1 TTATTAATAAATAATT
1666326 AAAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATTAATAAATAATT
Found at i:1666321 original size:34 final size:33
Alignment explanation
Indices: 1666270--1666340 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 33
1666260 ATGTTGAAAT
*
1666270 AAAATATTTTAAATAAAT-ATTACAATTAT-TA
1 AAAATATTTTAAATAAATAATTAAAATTATATA
*
1666301 AAAATAATTTTATTAATAAATAATTAAAATTTTATA
1 AAAAT-ATTTTA--AATAAATAATTAAAATTATATA
1666337 AAAA
1 AAAA
1666341 ATCATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 5 0.15
32 6 0.18
34 7 0.21
35 9 0.27
36 6 0.18
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
AAAATATTTTAAATAAATAATTAAAATTATATA
Found at i:1666710 original size:28 final size:29
Alignment explanation
Indices: 1666678--1666738 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
1666668 AATTTACAAG
1666678 AATTGAATC-AAATAAAAATT-ATGTATAA
1 AATTGAA-CAAAATAAAAATTCATGTATAA
* * *
1666706 AATTGCACAAAATCAAAATTCATGTATAG
1 AATTGAACAAAATAAAAATTCATGTATAA
1666735 AATT
1 AATT
1666739 ACACATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 16 0.57
29 11 0.39
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (29 bp):
AATTGAACAAAATAAAAATTCATGTATAA
Found at i:1666733 original size:29 final size:28
Alignment explanation
Indices: 1666687--1666743 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
1666677 GAATTGAATC
*
1666687 AAATAAAAATTATGTATAAAATTGCACA
1 AAATAAAAATTATGTATAAAATTACACA
* *
1666715 AAATCAAAATTCATGTATAGAATTACACA
1 AAATAAAAATT-ATGTATAAAATTACACA
1666744 TTAAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (28 bp):
AAATAAAAATTATGTATAAAATTACACA
Found at i:1668714 original size:39 final size:40
Alignment explanation
Indices: 1668641--1668721 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
1668631 ATAAATTTTA
**
1668641 TTTTATTGTTAATTTTTTTTACTATTTTATAGGTATTTGC
1 TTTTATTGTTAATTTTTGCTACTATTTTATAGGTATTTGC
1668681 TTTTATTGTTAA-TTTTGCTACTATTTTATAGGTATTTGC
1 TTTTATTGTTAATTTTTGCTACTATTTTATAGGTATTTGC
1668720 TT
1 TT
1668722 GCTAAGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.69
40 12 0.31
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (40 bp):
TTTTATTGTTAATTTTTGCTACTATTTTATAGGTATTTGC
Found at i:1669051 original size:15 final size:15
Alignment explanation
Indices: 1669031--1669066 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1669021 CAATACTAAG
1669031 ATTTTTAAAATATAT
1 ATTTTTAAAATATAT
* *
1669046 ATTTTTACAATATTT
1 ATTTTTAAAATATAT
1669061 ATTTTT
1 ATTTTT
1669067 CTTAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTTAAAATATAT
Found at i:1669529 original size:27 final size:27
Alignment explanation
Indices: 1669499--1669552 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1669489 ACGAGTAAAA
*
1669499 TATTCAAACTCAACTATGTTATTATCG
1 TATTCAAACTCAACTATGTCATTATCG
1669526 TATTCAAACTCAACTATGTCATTATCG
1 TATTCAAACTCAACTATGTCATTATCG
1669553 AATCGAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.39
Consensus pattern (27 bp):
TATTCAAACTCAACTATGTCATTATCG
Found at i:1672895 original size:17 final size:17
Alignment explanation
Indices: 1672870--1672903 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1672860 GGGCTGAGAA
1672870 TCCTAAGAGAAAACATC
1 TCCTAAGAGAAAACATC
*
1672887 TCCTGAGAGAAAACATC
1 TCCTAAGAGAAAACATC
1672904 AGTACTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (17 bp):
TCCTAAGAGAAAACATC
Found at i:1673685 original size:14 final size:14
Alignment explanation
Indices: 1673666--1673694 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1673656 GTAATGGGAT
1673666 TATTTCTTGACTGA
1 TATTTCTTGACTGA
1673680 TATTTCTTGACTGA
1 TATTTCTTGACTGA
1673694 T
1 T
1673695 GTTTTGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TATTTCTTGACTGA
Found at i:1680283 original size:28 final size:28
Alignment explanation
Indices: 1680227--1680281 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1680217 TTACCACATT
*
1680227 TAAAAAATAAATTAATTTTTTCTCTAAA
1 TAAAAAATAAATTAATTTTTTATCTAAA
*
1680255 TAAAAAATAAATTAGTTTTTTAT-TAAA
1 TAAAAAATAAATTAATTTTTTATCTAAA
1680282 ATTTTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (28 bp):
TAAAAAATAAATTAATTTTTTATCTAAA
Found at i:1680315 original size:42 final size:42
Alignment explanation
Indices: 1680255--1680348 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 42
1680245 TTTCTCTAAA
*
1680255 TAAAA-AATAAATTAG-TTTTTTATTAAAATTTTATTCATTTT
1 TAAAATAA-AAATTAGTTTTTTTATTAAAATTTCATTCATTTT
* *
1680296 TAAAACTAAAAATTAGTTTTTTTATTAAAGTTTCATTTATTTT
1 TAAAA-TAAAAATTAGTTTTTTTATTAAAATTTCATTCATTTT
*
1680339 TACAATAAAA
1 TAAAATAAAA
1680349 TTGACATGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 5 0.11
42 12 0.26
43 29 0.63
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (42 bp):
TAAAATAAAAATTAGTTTTTTTATTAAAATTTCATTCATTTT
Found at i:1683276 original size:34 final size:34
Alignment explanation
Indices: 1683233--1683298 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
1683223 CAGCTTAGTT
* *
1683233 TGACTATTAAGTACATTATATTATAAAT-ATAAAA
1 TGACTATTAAG-ACATTAAATTAGAAATGATAAAA
1683267 TGACTATTAAGACATTAAATTAGAAATGATAA
1 TGACTATTAAGACATTAAATTAGAAATGATAA
1683299 TGTATTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (34 bp):
TGACTATTAAGACATTAAATTAGAAATGATAAAA
Found at i:1683461 original size:35 final size:35
Alignment explanation
Indices: 1683385--1683470 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
1683375 AATCATATAG
*
1683385 AATAAAAT--TAAAATATTTTTAAATTATATTCAT
1 AATAAAATAATAAAATATTTTCAAATTATATTCAT
*
1683418 AATAAAAT-ATCAAAATATTTTACAAATTATATTTA-
1 AATAAAATAAT-AAAATATTTT-CAAATTATATTCAT
*
1683453 AATCAAATAATAAAATAT
1 AATAAAATAATAAAATAT
1683471 AAATTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 8 0.17
34 1 0.02
35 24 0.52
36 13 0.28
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (35 bp):
AATAAAATAATAAAATATTTTCAAATTATATTCAT
Found at i:1684013 original size:25 final size:25
Alignment explanation
Indices: 1683979--1684029 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1683969 TTTTGAATAG
* * *
1683979 AAAACGTGCTATTAGAAGTAGACTA
1 AAAACATGCTATCAGAAGCAGACTA
1684004 AAAACATGCTATCAGAAGCAGACTA
1 AAAACATGCTATCAGAAGCAGACTA
1684029 A
1 A
1684030 TCAAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAACATGCTATCAGAAGCAGACTA
Found at i:1686702 original size:28 final size:28
Alignment explanation
Indices: 1686670--1686726 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1686660 TCTGTGTCAT
1686670 ACCCATTGAAACATTGATTCGATGCCCA
1 ACCCATTGAAACATTGATTCGATGCCCA
1686698 ACCCATTGAAACATTGATTCGATGCCCA
1 ACCCATTGAAACATTGATTCGATGCCCA
1686726 A
1 A
1686727 GAATTCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (28 bp):
ACCCATTGAAACATTGATTCGATGCCCA
Found at i:1690633 original size:39 final size:39
Alignment explanation
Indices: 1690579--1690657 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
1690569 GTAGTTATAC
*
1690579 ATGCAAATGTTGGATCAATCCAGCAGTCAACATAGACTA
1 ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
1690618 ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
1 ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
1690657 A
1 A
1690658 GGGTGAGTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (39 bp):
ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
Found at i:1692687 original size:28 final size:26
Alignment explanation
Indices: 1692635--1692687 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
1692625 TCCTTAGTTG
* * *
1692635 TTTTATAATTTTTTGTTTTTGAAAAT
1 TTTTATAATATTTTGTATTTCAAAAT
1692661 TTTTATAAATATTTTGATATTTCAAAA
1 TTTTAT-AATATTTTG-TATTTCAAAA
1692688 ATTATTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 6 0.27
27 8 0.36
28 8 0.36
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (26 bp):
TTTTATAATATTTTGTATTTCAAAAT
Found at i:1694551 original size:26 final size:26
Alignment explanation
Indices: 1694522--1694681 Score: 257
Period size: 26 Copynumber: 6.2 Consensus size: 26
1694512 TGGTACAAAT
1694522 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
1694548 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
1694574 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
**
1694600 TGATAATGAATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
1694626 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
1694652 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
1694678 TGAT
1 TGAT
1694682 GGGCATTTCA
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 124 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:1694579 original size:52 final size:52
Alignment explanation
Indices: 1694522--1694681 Score: 284
Period size: 52 Copynumber: 3.1 Consensus size: 52
1694512 TGGTACAAAT
*
1694522 TGATAATGGGTTAGGTAAATATTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
*
1694574 TGATAATGGGTTAGGTAAATGTTCCATGATAATGAATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* *
1694626 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1694678 TGAT
1 TGAT
1694682 GGGCATTTCA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:1696715 original size:137 final size:138
Alignment explanation
Indices: 1696469--1696756 Score: 524
Period size: 137 Copynumber: 2.1 Consensus size: 138
1696459 GAGTAGTCTC
1696469 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1696534 TGTTATATGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTG-AAAAGGGCTCTGGCCCAGTAC
66 TGTTATATGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAAGGGCTCTGGCCCAGTAC
*
1696598 CATTGTTA
131 CACTGTTA
1696606 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
1696671 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAAGGGCTTTGGCCCAGTAC
66 TGTTATATGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAAGGGCTCTGGCCCAGTAC
1696736 CACTGTTA
131 CACTGTTA
**
1696744 CCTGAATGGGCTT
1 CCCAAATGGGCTT
1696757 AGGCCCAATG
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
137 107 0.74
138 38 0.26
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (138 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATATGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAAGGGCTCTGGCCCAGTAC
CACTGTTA
Found at i:1698914 original size:30 final size:30
Alignment explanation
Indices: 1698880--1698939 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1698870 GAAACCTCCT
* * *
1698880 AACCCACTACCTCCGCCAGCTCCTCCACCA
1 AACCCACTACCGCCACCAGCTCCACCACCA
* *
1698910 AACCCATTACCGGCACCAGCTCCACCACCA
1 AACCCACTACCGCCACCAGCTCCACCACCA
1698940 CCAACGAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.53, G:0.08, T:0.12
Consensus pattern (30 bp):
AACCCACTACCGCCACCAGCTCCACCACCA
Done.