Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 43 of 190
Found at i:11958936 original size:55 final size:55
Alignment explanation
Indices: 11958867--11959083 Score: 310
Period size: 55 Copynumber: 3.9 Consensus size: 55
11958857 ATTTCCCAAA
* * *
11958867 AATATTGCTTCTTTTGGATATATTGTTTTTATGTTTAAATCGATTGTTATGTTGG
1 AATACTGCTTCTTTTGAATATATTGTTTATATGTTTAAATCGATTGTTATGTTGG
* * *
11958922 AATACTGCTTCTTTTGAATAAATTGTTTATATGTTTAAATCGATTATCATGTTGG
1 AATACTGCTTCTTTTGAATATATTGTTTATATGTTTAAATCGATTGTTATGTTGG
* ** * * *
11958977 AATACTGTTTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTTATATTAG
1 AATACTGCTTCTTTTGAATATATTGTTTATATGTTTAAATCGATTGTTATGTTGG
11959032 AATACTGCTTCTTTTGAAT-TGATTGTTTATATGTTTAAATCGATTGTTATGT
1 AATACTGCTTCTTTTGAATAT-ATTGTTTATATGTTTAAATCGATTGTTATGT
11959084 AGCACGTCTA
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
55 143 1.00
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.51
Consensus pattern (55 bp):
AATACTGCTTCTTTTGAATATATTGTTTATATGTTTAAATCGATTGTTATGTTGG
Found at i:11960306 original size:62 final size:62
Alignment explanation
Indices: 11960236--11960359 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
11960226 TAAAATGAGC
*
11960236 ATCATAGTTTGAGAATATTTAGTGTAATTAACTCTTAAAAGTAATACAAACTATAGAAGATT
1 ATCATAGTTTGAGAATATTTACTGTAATTAACTCTTAAAAGTAATACAAACTATAGAAGATT
*
11960298 ATCATAGTTTGAGAATGTTTACTGTAATTAACTCTTAAAAGTAATACAAACTATAGAAGATT
1 ATCATAGTTTGAGAATATTTACTGTAATTAACTCTTAAAAGTAATACAAACTATAGAAGATT
11960360 GTAATTGATA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (62 bp):
ATCATAGTTTGAGAATATTTACTGTAATTAACTCTTAAAAGTAATACAAACTATAGAAGATT
Found at i:11966393 original size:30 final size:29
Alignment explanation
Indices: 11966357--11966472 Score: 81
Period size: 30 Copynumber: 3.7 Consensus size: 29
11966347 CTTATGAGGA
11966357 CGTTCAGGTACTTGAGAAGACCTGATATCT
1 CGTTCAGG-ACTTGAGAAGACCTGATATCT
* * *
11966387 CGTTCAGGGGCTTGGGAAGA-CTCAATATCT
1 CGTTCA-GGACTTGAGAAGACCT-GATATCT
*
11966417 CATTCAGGATCTTGGGATTGAGAAGACCTGATATCT
1 CGTTCAGGA-C------TTGAGAAGACCTGATATCT
*
11966453 CGTTCAGGAGCTTGTGAAGA
1 CGTTCAGGA-CTTGAGAAGA
11966473 TCGGGTGTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
29 4 0.06
30 35 0.53
31 2 0.03
36 23 0.35
37 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (29 bp):
CGTTCAGGACTTGAGAAGACCTGATATCT
Found at i:11967838 original size:26 final size:25
Alignment explanation
Indices: 11967803--11967856 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 25
11967793 ACTTTTAAAT
11967803 AAATAGTTAATAGAA-CTAGTTGGTC
1 AAATAGTTAATAGAATC-AGTTGGTC
11967828 AAATAAGTTAATAGAATCAGTTGGTC
1 AAAT-AGTTAATAGAATCAGTTGGTC
11967854 AAA
1 AAA
11967857 CCAGTCACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 4 0.15
26 22 0.81
27 1 0.04
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (25 bp):
AAATAGTTAATAGAATCAGTTGGTC
Found at i:11973228 original size:51 final size:50
Alignment explanation
Indices: 11973103--11973287 Score: 178
Period size: 51 Copynumber: 3.7 Consensus size: 50
11973093 AAAGTGATGG
* * * * * *
11973103 TCACGTGTGTTGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCAGATAGT-AT-GA
*
11973153 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATCAGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCAGATAG-TAT-GA
* *** * *
11973204 TCACTTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCAGATAGT-ATGA
*
11973255 TCACATATGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
11973288 TGAACCGGTA
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
50 37 0.33
51 72 0.65
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCAGATAGTATGA
Found at i:11973229 original size:101 final size:102
Alignment explanation
Indices: 11973103--11973287 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
11973093 AAAGTGATGG
* * * *
11973103 TCACGTGTGTTGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGAT-GGTCACATATGTAGT
11973166 ACTATGTGCAGGCTACTATGCGTATCAGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTATCAGATAGCTTCGA
* * *
11973204 TCACTTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATAGTGATGGTCACATATGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACATATGTAGTA
11973269 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
11973288 TGAACCGGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 37 0.49
102 34 0.45
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACATATGTAGTA
CTATGTGCAGGCTACTATGCGTATCAGATAGCTTCGA
Found at i:11973534 original size:16 final size:16
Alignment explanation
Indices: 11973513--11973544 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11973503 TGATTGAAAG
*
11973513 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
11973529 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
11973545 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:11976603 original size:65 final size:65
Alignment explanation
Indices: 11976526--11976672 Score: 215
Period size: 65 Copynumber: 2.3 Consensus size: 65
11976516 AGTTTTTGGA
* * *
11976526 GTTGCGATATTAAATCAGCTAACTCAAATAAAATTTTTCATGATATGAAAT-TGAATAAATTTTA
1 GTTGCGATATTAAATCAGCTAACTCAAATAAAATTGTTCATGATATGAAATCT-AACAAACTTTA
11976590 G
65 G
* * * *
11976591 GTTGCGATATTAAATCAGCTAACTTAAATTAAATTGTTCATGATTTGAAATCTAACGAACTTTAG
1 GTTGCGATATTAAATCAGCTAACTCAAATAAAATTGTTCATGATATGAAATCTAACAAACTTTAG
11976656 GTTGCGATATTAAATCA
1 GTTGCGATATTAAATCA
11976673 ACGAACCTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
65 73 0.99
66 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (65 bp):
GTTGCGATATTAAATCAGCTAACTCAAATAAAATTGTTCATGATATGAAATCTAACAAACTTTAG
Found at i:11976766 original size:132 final size:132
Alignment explanation
Indices: 11976591--11977531 Score: 994
Period size: 132 Copynumber: 7.1 Consensus size: 132
11976581 TAAATTTTAG
* * * * * * * *
11976591 GTTGCGATATTAAATCAGCTAACTTAAATTAAATTGTTCATGATTTGAAATCTAACGAACTTTAG
1 GTTGCAATCTTAAATCAACTAACTCAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTAG
* * *
11976656 GTTGCGATATTAAATCAACGAACCTTGATAATACCAGCTGCGATATTAAATCAATGAGTTGTTCG
66 GTTGCGATCTTAAATCAACGAACCTTGATAATACCAGCTGCGATCTTAAATCAACGAGTTGTTCG
11976721 GA
131 GA
** * * *
11976723 GTTGTGATCTTAAATCAACAAACTCAATTAAAATTGTTCATGATTTGAAAT-GAAATGAACTTTA
1 GTTGCAATCTTAAATCAACTAACTCAAATAAAATTGTTCATGATCTGAAATCG-AATGAACTTTA
* * * * * *
11976787 GGTTGCAAT-TTAAATCAATGAACCTTGATAATTCCAACTGCGATCTTAAATCAATGAGTTGTTT
65 GGTTGCGATCTTAAATCAACGAACCTTGATAATACCAGCTGCGATCTTAAATCAACGAGTTGTTC
11976851 GGA
130 GGA
* * *
11976854 GTTGCGATATTAAAT-AAGCTAACTTAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTA
1 GTTGCAATCTTAAATCAA-CTAACTCAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTA
* * * ** * * *
11976918 GGTTGTGATCTTAACTAAAAAAACCTTGATAATACTAG-TGATGATCTTAAATCAATGAGTTGTT
65 GGTTGCGATCTTAAATCAACGAACCTTGATAATACCAGCTG-CGATCTTAAATCAACGAGTTGTT
11976982 CGGA
129 CGGA
** * * * * * *
11976986 GTTGTGATATTAAATCAGCTAACTTAAATAAAATTGTTAATGATTTGAAATCGAATGAACTCTAG
1 GTTGCAATCTTAAATCAACTAACTCAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTAG
* * * * * * *
11977051 GTTGAGATCTTAAATCAACGAACCTTGATGATACCAGCTACGATCTTAAATCAGCGAGCTATTCA
66 GTTGCGATCTTAAATCAACGAACCTTGATAATACCAGCTGCGATCTTAAATCAACGAGTTGTTCG
11977116 GA
131 GA
* * * * * *
11977118 GTTGCAATCTGAAATTAGCTAACTCAACTAAAATTTTTCATGATCTAAAATCGAATGAACTTTAG
1 GTTGCAATCTTAAATCAACTAACTCAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTAG
* * * * * * * *
11977183 GTTGAGATCTTAAATCAACGAACCTTGATGATACAAGGTACGATCTTAAATCAGCGAGCTGTTCA
66 GTTGCGATCTTAAATCAACGAACCTTGATAATACCAGCTGCGATCTTAAATCAACGAGTTGTTCG
11977248 GA
131 GA
* * *
11977250 GTTGCAATCTTAAATTAGCTAACTCAAATAAAACTGTTCATGATCTGAAATCGAATGAACTTTAG
1 GTTGCAATCTTAAATCAACTAACTCAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTAG
** * * * *
11977315 GTTGCGATCTTAAATCAGTGAACCTAGATCATACCAGCTGTGATCTTAAATCAA-GAAGTTGTTT
66 GTTGCGATCTTAAATCAACGAACCTTGATAATACCAGCTGCGATCTTAAATCAACG-AGTTGTTC
11977379 GGA
130 GGA
* * * * * * * * *
11977382 GCTACTATATTAAATCAACTAACTTAAATAGAATTGTTCATGATCTCAAATAGAATGAACATTAG
1 GTTGCAATCTTAAATCAACTAACTCAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTAG
* * * * ** * *
11977447 GTTGCAATCTTAAAT-AGGCTAACCTTGATGATACCAATTGCGATATTAAATCAGCGAGTTGTTC
66 GTTGCGATCTTAAATCA-ACGAACCTTGATAATACCAGCTGCGATCTTAAATCAACGAGTTGTTC
*
11977511 GAA
130 GGA
11977514 GTTGCAATCTTAAATCAA
1 GTTGCAATCTTAAATCAA
11977532 TAAACCTTGA
Statistics
Matches: 687, Mismatches: 112, Indels: 20
0.84 0.14 0.02
Matches are distributed among these distances:
130 2 0.00
131 117 0.17
132 565 0.82
133 3 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (132 bp):
GTTGCAATCTTAAATCAACTAACTCAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTAG
GTTGCGATCTTAAATCAACGAACCTTGATAATACCAGCTGCGATCTTAAATCAACGAGTTGTTCG
GA
Found at i:11976899 original size:67 final size:68
Alignment explanation
Indices: 11976828--11977043 Score: 196
Period size: 67 Copynumber: 3.2 Consensus size: 68
11976818 TTCCAACTGC
*
11976828 GATCTTAAATC-AATGAGTTGTTTGGAGTTGCGATATTAAATAAGCTAACTTAAATAAAATTGTT
1 GATCTTAAATCGAATGAGTTGTTTGGAGTTGTGATATTAAATAAGCTAACTTAAATAAAATTGTT
*
11976892 CAT
66 AAT
* ** * * * *** * * *
11976895 GATCTGAAATCGAATGA--ACTTTAG-GTTGTGATCTTAACTAAAAAAACCTT-GATAATACTAG
1 GATCTTAAATCGAATGAGTTGTTTGGAGTTGTGATATTAAATAAGCTAA-CTTAAATAA-AATTG
*
11976956 -TGAT
64 TTAAT
* *
11976960 GATCTTAAATC-AATGAGTTGTTCGGAGTTGTGATATTAAATCAGCTAACTTAAATAAAATTGTT
1 GATCTTAAATCGAATGAGTTGTTTGGAGTTGTGATATTAAATAAGCTAACTTAAATAAAATTGTT
11977024 AAT
66 AAT
11977027 GAT-TTGAAATCGAATGA
1 GATCTT-AAATCGAATGA
11977044 ACTCTAGGTT
Statistics
Matches: 110, Mismatches: 29, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
64 5 0.05
65 33 0.30
66 21 0.19
67 41 0.37
68 10 0.09
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (68 bp):
GATCTTAAATCGAATGAGTTGTTTGGAGTTGTGATATTAAATAAGCTAACTTAAATAAAATTGTT
AAT
Found at i:11977395 original size:396 final size:393
Alignment explanation
Indices: 11976596--11977536 Score: 1151
Period size: 396 Copynumber: 2.4 Consensus size: 393
11976586 TTTAGGTTGC
* * * *
11976596 GATATTAAATCAGCTAACTTAAATTAAATTGTTCATGATTTGAAATCTAACGAACTTTAGGTTGC
1 GATATTAAATCAGCTAACTTAAATAAAATTGTTCATGATTTGAAATCGAATGAAC-TTAGGTTGA
* * **
11976661 GATATTAAATCAACGAACCTTGATAATACCAGCTGCGATATTAAATCAATGAGTTGTTCGGAGTT
65 GATCTTAAATCAACGAACCTTGATGATACCAGCTGCGATATTAAATCAGCGAGTTGTTC-GAGTT
** * * *
11976726 GTGATCTTAAATCAACAAACTCAATTAAAATTGTTCATGATTTGAAATGAAATGAACTTTAGGTT
129 GCAATCTTAAATCAACAAACTCAACTAAAATTGTTCATGATCTAAAATGAAATGAACTTTAGGTT
* * * * * **
11976791 GCAATTTAAATCAATGAACCTTGATAATTCCAACTGCGATCTTAAATCAATGAGTTGTTTGGAGT
194 GCAATTTAAATCAACGAACCTTGATAATTACAACTACGATCTTAAATCAACGAGCTGTTCAGAGT
* * *
11976856 TGCGATATTAAATAAGCTAACTTAAATAAAATTGTTCATGATCTGAAATCGAATGAACTTTAGGT
259 TGCAATATTAAATAAGCTAACTCAAATAAAACTGTTCATGATCTGAAATCGAATGAACTTTAGGT
* * * *
11976921 TGTGATCTTAACTAAAAAAACCTTGATAATACTAGTGATGATCTTAAATCAATGAGTTGTTCGGA
324 TGCGATCTTAAATAAAAAAACCTAGATAATACCAGTGATGATCTTAAATCAATGAGTTGTTCGGA
**
11976986 GTTGT
389 GTACT
*
11976991 GATATTAAATCAGCTAACTTAAATAAAATTGTTAATGATTTGAAATCGAATGAACTCTAGGTTGA
1 GATATTAAATCAGCTAACTTAAATAAAATTGTTCATGATTTGAAATCGAATGAACT-TAGGTTGA
* * * *
11977056 GATCTTAAATCAACGAACCTTGATGATACCAGCTACGATCTTAAATCAGCGAGCTATTCAGAGTT
65 GATCTTAAATCAACGAACCTTGATGATACCAGCTGCGATATTAAATCAGCGAGTTGTTC-GAGTT
* * * * *
11977121 GCAATCTGAAATTAGCTAACTCAACTAAAATTTTTCATGATCTAAAATCG-AATGAACTTTAGGT
129 GCAATCTTAAATCAACAAACTCAACTAAAATTGTTCATGATCTAAAAT-GAAATGAACTTTAGGT
* * *
11977185 TG-AGATCTTAAATCAACGAACCTTGATGA-TACAAGGTACGATCTTAAATCAGCGAGCTGTTCA
193 TGCA-AT-TTAAATCAACGAACCTTGATAATTACAA-CTACGATCTTAAATCAACGAGCTGTTCA
* *
11977248 GAGTTGCAATCTTAAATTAGCTAACTCAAATAAAACTGTTCATGATCTGAAATCGAATGAACTTT
255 GAGTTGCAATATTAAATAAGCTAACTCAAATAAAACTGTTCATGATCTGAAATCGAATGAACTTT
* *** *
11977313 AGGTTGCGATCTTAAATCAGTGAACCTAGATCATACCAGCTG-TGATCTTAAATCAA-GAAGTTG
320 AGGTTGCGATCTTAAATAAAAAAACCTAGATAATACCAG-TGATGATCTTAAATCAATG-AGTTG
*
11977376 TTTGGAGCTACT
383 TTCGGAG-TACT
* * * * *
11977388 -ATATTAAATCAACTAACTTAAATAGAATTGTTCATGATCTCAAATAGAATGAACATTAGGTTGC
1 GATATTAAATCAGCTAACTTAAATAAAATTGTTCATGATTTGAAATCGAATGAAC-TTAGGTTG-
* * **
11977452 A-ATCTTAAAT-AGGCTAACCTTGATGATACCAATTGCGATATTAAATCAGCGAGTTGTTCGAAG
64 AGATCTTAAATCA-ACGAACCTTGATGATACCAGCTGCGATATTAAATCAGCGAGTTGTTCG-AG
*
11977515 TTGCAATCTTAAATCAATAAAC
127 TTGCAATCTTAAATCAACAAAC
11977537 CTTGATGATA
Statistics
Matches: 464, Mismatches: 70, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
394 2 0.00
395 177 0.38
396 279 0.60
397 6 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (393 bp):
GATATTAAATCAGCTAACTTAAATAAAATTGTTCATGATTTGAAATCGAATGAACTTAGGTTGAG
ATCTTAAATCAACGAACCTTGATGATACCAGCTGCGATATTAAATCAGCGAGTTGTTCGAGTTGC
AATCTTAAATCAACAAACTCAACTAAAATTGTTCATGATCTAAAATGAAATGAACTTTAGGTTGC
AATTTAAATCAACGAACCTTGATAATTACAACTACGATCTTAAATCAACGAGCTGTTCAGAGTTG
CAATATTAAATAAGCTAACTCAAATAAAACTGTTCATGATCTGAAATCGAATGAACTTTAGGTTG
CGATCTTAAATAAAAAAACCTAGATAATACCAGTGATGATCTTAAATCAATGAGTTGTTCGGAGT
ACT
Found at i:11977584 original size:67 final size:67
Alignment explanation
Indices: 11977467--11977597 Score: 165
Period size: 67 Copynumber: 2.0 Consensus size: 67
11977457 TAAATAGGCT
* * * *
11977467 AACCTTGATGATACCAATTGCGATATTAAATCAGCGAGTTGTTCGAAGTTGCAATCTTAAATCAA
1 AACCTTGATGATACCAATTGCAATATTAAATCAACGAGCTATTCGAAGTTGCAATCTTAAATCAA
11977532 TA
66 TA
* ** **
11977534 AACCTTGATGATACCAATTGCAATCTTTGATCAACGAGCTATTC-ATAGTTGTGATCTTAAATCA
1 AACCTTGATGATACCAATTGCAATATTAAATCAACGAGCTATTCGA-AGTTGCAATCTTAAATCA
11977598 TCTAACTCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 1 0.02
67 53 0.98
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (67 bp):
AACCTTGATGATACCAATTGCAATATTAAATCAACGAGCTATTCGAAGTTGCAATCTTAAATCAA
TA
Found at i:11985173 original size:13 final size:13
Alignment explanation
Indices: 11985155--11985190 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
11985145 ATATATCCCT
11985155 AAGTGGTGGGAAA
1 AAGTGGTGGGAAA
*
11985168 AAGTGGTGGGAGA
1 AAGTGGTGGGAAA
11985181 AAGTGCGTGG
1 AAGTG-GTGG
11985191 TCGATTTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.31, C:0.03, G:0.50, T:0.17
Consensus pattern (13 bp):
AAGTGGTGGGAAA
Found at i:11986508 original size:13 final size:13
Alignment explanation
Indices: 11986490--11986516 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11986480 TCAATACTGG
11986490 ATCGATACCTACT
1 ATCGATACCTACT
11986503 ATCGATACCTACT
1 ATCGATACCTACT
11986516 A
1 A
11986517 GGTTTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (13 bp):
ATCGATACCTACT
Found at i:11991978 original size:58 final size:58
Alignment explanation
Indices: 11991916--11992031 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
11991906 TAGAGAACAT
11991916 AGTTAAAATTAATATATGAATTTGATTCATTTAAAAATATTAACTAAATATAGTTTAC
1 AGTTAAAATTAATATATGAATTTGATTCATTTAAAAATATTAACTAAATATAGTTTAC
11991974 AGTTAAAATTAATATATGAATTTGATTCATTTAAAAATATTAACTAAATATAGTTTAC
1 AGTTAAAATTAATATATGAATTTGATTCATTTAAAAATATTAACTAAATATAGTTTAC
11992032 CAAAATTATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (58 bp):
AGTTAAAATTAATATATGAATTTGATTCATTTAAAAATATTAACTAAATATAGTTTAC
Found at i:11991980 original size:30 final size:30
Alignment explanation
Indices: 11991946--11992031 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 30
11991936 TTTGATTCAT
11991946 TTAAAAATATTAACTAAATATAGTTTACAG
1 TTAAAAATATTAACTAAATATAGTTTACAG
* * * * * *
11991976 TTAAAATTAATATA-TGAAT-TTGATT-CAT
1 TTAAAAATATTA-ACTAAATATAGTTTACAG
11992004 TTAAAAATATTAACTAAATATAGTTTAC
1 TTAAAAATATTAACTAAATATAGTTTAC
11992032 CAAAATTATT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
27 1 0.02
28 16 0.39
29 8 0.20
30 15 0.37
31 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.41
Consensus pattern (30 bp):
TTAAAAATATTAACTAAATATAGTTTACAG
Found at i:11992009 original size:28 final size:28
Alignment explanation
Indices: 11991918--11992009 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
11991908 GAGAACATAG
11991918 TTAAAATTAATATATGAATTTGATTCAT
1 TTAAAATTAATATATGAATTTGATTCAT
* * * * * *
11991946 TTAAAAATATTA-ACTAAATATAGTTTACAG
1 TTAAAATTAATATA-TGAAT-TTGATT-CAT
11991976 TTAAAATTAATATATGAATTTGATTCAT
1 TTAAAATTAATATATGAATTTGATTCAT
11992004 TTAAAA
1 TTAAAA
11992010 ATATTAACTA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
27 1 0.02
28 22 0.46
29 8 0.17
30 16 0.33
31 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (28 bp):
TTAAAATTAATATATGAATTTGATTCAT
Found at i:11999763 original size:31 final size:32
Alignment explanation
Indices: 11999718--11999796 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 32
11999708 AAGGTATGTG
* * *
11999718 TATATAGAATATATATATGCGTGGGT-TTTCT
1 TATATATAATATATATATGCATGGGTCTTGCT
* *
11999749 TATATATAAAATATATATGCATGGGTCTTGGT
1 TATATATAATATATATATGCATGGGTCTTGCT
11999781 TATATATAATATATAT
1 TATATATAATATATAT
11999797 GCATATATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 23 0.56
32 18 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.44
Consensus pattern (32 bp):
TATATATAATATATATATGCATGGGTCTTGCT
Found at i:12000819 original size:34 final size:34
Alignment explanation
Indices: 12000780--12000861 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
12000770 ATGTGGTATG
* *
12000780 AATGAATTATTA-TATTGTATGAACTATTAATTT-A
1 AATGAATTGTTATTA-TGCATGAACTATT-ATTTCA
*
12000814 AATGAACTGTTATTATGCATGAACTATTATTTCA
1 AATGAATTGTTATTATGCATGAACTATTATTTCA
*
12000848 TATGAATTGTTATT
1 AATGAATTGTTATT
12000862 TTATGCAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 4 0.10
34 35 0.85
35 2 0.05
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (34 bp):
AATGAATTGTTATTATGCATGAACTATTATTTCA
Found at i:12000852 original size:17 final size:16
Alignment explanation
Indices: 12000781--12000884 Score: 61
Period size: 17 Copynumber: 6.2 Consensus size: 16
12000771 TGTGGTATGA
* *
12000781 ATGAATTATTATATTGT
1 ATGAACTATTAT-TTAT
*
12000798 ATGAACTATTAATTTAA
1 ATGAACTATT-ATTTAT
*
12000815 ATGAACTGTTA-TTAT
1 ATGAACTATTATTTAT
12000830 GCATGAACTATTATTTCAT
1 --ATGAACTATTATTT-AT
* *
12000849 ATGAATTGTTATTT-T
1 ATGAACTATTATTTAT
12000864 ATGCAAACTATCTATTT-T
1 ATG--AACTAT-TATTTAT
12000882 ATG
1 ATG
12000885 TGAACCATTT
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
15 7 0.10
16 1 0.01
17 46 0.67
18 13 0.19
19 2 0.03
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.47
Consensus pattern (16 bp):
ATGAACTATTATTTAT
Found at i:12000873 original size:34 final size:32
Alignment explanation
Indices: 12000800--12000880 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 32
12000790 TATATTGTAT
12000800 GAACTATTAATTTAAATGAACTGTTATTATGCA
1 GAACTATT-ATTTAAATGAACTGTTATTATGCA
* *
12000833 TGAACTATTATTTCATATGAATTGTTATTTTATGCA
1 -GAACTATTATTT-AAATGAACTGTTA--TTATGCA
12000869 -AACTATCTATTT
1 GAACTAT-TATTT
12000881 TATGTGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 4 0.10
34 25 0.61
35 5 0.12
36 7 0.17
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (32 bp):
GAACTATTATTTAAATGAACTGTTATTATGCA
Found at i:12006870 original size:17 final size:17
Alignment explanation
Indices: 12006848--12006880 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12006838 CACTAACATT
12006848 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
12006865 AAAATGCAATGACAAT
1 AAAATGCAATGACAAT
12006881 GTACACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:12017755 original size:32 final size:32
Alignment explanation
Indices: 12017714--12017782 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
12017704 TTGAAAATCT
12017714 AAACTAACAATCTGCACCATTTTT-ATATAACA
1 AAACTAACAATCT-CACCATTTTTGATATAACA
* * *
12017746 AAACTAACAATCTCCCCCTTTTTGATATAACG
1 AAACTAACAATCTCACCATTTTTGATATAACA
12017778 AAACT
1 AAACT
12017783 TTTTGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (32 bp):
AAACTAACAATCTCACCATTTTTGATATAACA
Found at i:12017893 original size:17 final size:16
Alignment explanation
Indices: 12017871--12017902 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12017861 TTATGAAGAC
12017871 ATCATTTATACAAAAAA
1 ATCATTTATA-AAAAAA
12017888 ATCATTTATAAAAAA
1 ATCATTTATAAAAAA
12017903 GCTTGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
ATCATTTATAAAAAAA
Found at i:12019366 original size:49 final size:50
Alignment explanation
Indices: 12019262--12019367 Score: 142
Period size: 49 Copynumber: 2.1 Consensus size: 50
12019252 TTATTGAAAT
* * * *
12019262 TATGAGTGGTCCCACATAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 TATGAGAGGTCCCACATAAGACCATGTCTAGGACATGGCATGGGCACCGA
* * *
12019312 GATGAGAGGTCCCCCGTAAGACCAT-TCTAGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCACATAAGACCATGTCTAGGACATGGCATGGGCACCGA
12019361 TATGAGA
1 TATGAGA
12019368 ACTTCCATGT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 27 0.56
50 21 0.44
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
TATGAGAGGTCCCACATAAGACCATGTCTAGGACATGGCATGGGCACCGA
Found at i:12019380 original size:49 final size:50
Alignment explanation
Indices: 12019271--12019385 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 50
12019261 TTATGAGTGG
* * * * **
12019271 TCCCACATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATGAGAAC
* *
12019321 TCCCCCGTAAGACCAT-TCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATGAGAAC
* *
12019370 TTCCATGTAAGACCAT
1 TCCCACGTAAGACCAT
12019386 ATCCGGGATA
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
49 40 0.74
50 14 0.26
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:12019673 original size:12 final size:12
Alignment explanation
Indices: 12019656--12019694 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
12019646 ATGAGTTATT
12019656 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
12019668 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
12019680 TAAGAAAGTAAG
1 TAAGTAAGCAAG
12019692 TAA
1 TAA
12019695 AGAAGAAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:12028960 original size:59 final size:59
Alignment explanation
Indices: 12028893--12029013 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
12028883 TGATATCATG
12028893 ATGGTATACAAAGGTTATATGCATAGTTGATTTGGTAGGATTTGATCAAGTGGTTGGAA
1 ATGGTATACAAAGGTTATATGCATAGTTGATTTGGTAGGATTTGATCAAGTGGTTGGAA
12028952 ATGGTATACAAAGGTTATATGCATAGTTGATTTGGTAGGATTTGATCAAGTGGTTGGAA
1 ATGGTATACAAAGGTTATATGCATAGTTGATTTGGTAGGATTTGATCAAGTGGTTGGAA
12029011 ATG
1 ATG
12029014 ATTTGAGTGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36
Consensus pattern (59 bp):
ATGGTATACAAAGGTTATATGCATAGTTGATTTGGTAGGATTTGATCAAGTGGTTGGAA
Found at i:12031747 original size:19 final size:18
Alignment explanation
Indices: 12031713--12031758 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
12031703 AACTGAACAC
*
12031713 AAATAATATTAATAAAAATA
1 AAATAA-ATGAAT-AAAATA
12031733 AAATAAATGAATAAAATA
1 AAATAAATGAATAAAATA
12031751 ATAATAAA
1 A-AATAAA
12031759 CTATGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 11 0.46
20 6 0.25
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATAAATGAATAAAATA
Found at i:12036998 original size:114 final size:114
Alignment explanation
Indices: 12036798--12037024 Score: 409
Period size: 114 Copynumber: 2.0 Consensus size: 114
12036788 GACCCATGAC
* *
12036798 TCTTTTTATATAGGGAGAGTTTAGAGAGTTCAACTACGATTAAACTTAATTATTTTAATAATAAA
1 TCTTTTTATATAGGCAGAGTTTAGAGAGTTCAACTACGATTAAACTTAATCATTTTAATAATAAA
*
12036863 TTAATATAATGTTTATCAAGATAAATATTAGATTAAATTTAAAATTAAG
66 TTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAAAATTAAG
*
12036912 TCTTTTTATATAGGCAGAGTTTAGAGAGTTCAACTATGATTAAACTTAATCATTTTAATAATAAA
1 TCTTTTTATATAGGCAGAGTTTAGAGAGTTCAACTACGATTAAACTTAATCATTTTAATAATAAA
*
12036977 TTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATATTAA
66 TTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAAAATTAA
12037025 ACCTATTAAA
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (114 bp):
TCTTTTTATATAGGCAGAGTTTAGAGAGTTCAACTACGATTAAACTTAATCATTTTAATAATAAA
TTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAAAATTAAG
Found at i:12037035 original size:58 final size:60
Alignment explanation
Indices: 12036973--12037085 Score: 185
Period size: 61 Copynumber: 1.9 Consensus size: 60
12036963 ATTTTAATAA
* *
12036973 TAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAACCTAT
1 TAAATTAATAGAATATTTACTACAAGATAAATATTAAATTAAATTTAATATTAAACCTAT
12037031 TAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATTAA
1 TAAATTAATAGAATATTTA-CTACAAGATAAATATTAAATTAAATTTAATATTAA
12037086 GATAATCACT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
58 18 0.36
60 1 0.02
61 31 0.62
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (60 bp):
TAAATTAATAGAATATTTACTACAAGATAAATATTAAATTAAATTTAATATTAAACCTAT
Found at i:12038336 original size:41 final size:41
Alignment explanation
Indices: 12038279--12038361 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
12038269 ATTGGAATTG
12038279 TAGACGACATAATTATCCATCAAAGGATTTGAATTAAATGC
1 TAGACGACATAATTATCCATCAAAGGATTTGAATTAAATGC
*
12038320 TAGACGACATAATTATCCATCGAAGGATTTGAATTAAATGC
1 TAGACGACATAATTATCCATCAAAGGATTTGAATTAAATGC
12038361 T
1 T
12038362 CACTTTGATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (41 bp):
TAGACGACATAATTATCCATCAAAGGATTTGAATTAAATGC
Found at i:12047409 original size:18 final size:18
Alignment explanation
Indices: 12047386--12047420 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12047376 AGATTAGCCT
*
12047386 AAAAATGCAAAACGAAAG
1 AAAAATGCAAAAAGAAAG
*
12047404 AAAAATTCAAAAAGAAA
1 AAAAATGCAAAAAGAAA
12047421 AAGTAATACA
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:0.71, C:0.09, G:0.11, T:0.09
Consensus pattern (18 bp):
AAAAATGCAAAAAGAAAG
Found at i:12048873 original size:26 final size:27
Alignment explanation
Indices: 12048700--12048870 Score: 182
Period size: 27 Copynumber: 6.4 Consensus size: 27
12048690 GGTATAACAT
* **
12048700 TCATTTTACCCAATATGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
12048727 TCATTTTACCTTATGGGAGAATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
12048754 TCATTCTACCCTACGGAGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
12048781 TCATTTTACCTTATAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
** *
12048808 TCATTTTACCCTAACGGGGTATTT-TG
1 TCATTTTACCCTATGGGGGTATTTCGG
*
12048834 TCATTTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
12048861 TCATTTTACC
1 TCATTTTACC
12048871 TATTTTAGGG
Statistics
Matches: 118, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
26 23 0.19
27 95 0.81
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:12057216 original size:13 final size:13
Alignment explanation
Indices: 12057190--12057231 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
12057180 GAAGATTAAT
12057190 AAAATAAACTAGTAA
1 AAAATAAA--AGTAA
12057205 AAAATAAAAGT-A
1 AAAATAAAAGTAA
*
12057217 AAAATAAAAATAA
1 AAAATAAAAGTAA
12057230 AA
1 AA
12057232 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 11 0.44
13 6 0.24
15 8 0.32
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (13 bp):
AAAATAAAAGTAA
Found at i:12063720 original size:44 final size:45
Alignment explanation
Indices: 12063670--12063786 Score: 164
Period size: 44 Copynumber: 2.6 Consensus size: 45
12063660 AGAAACGAGA
* * *
12063670 AAGACCATAGTTGAAAGATACTATGGCATTAAACC-GGAATGTAT
1 AAGACCATAGTTGAAAGATACTATGGCATTAAACCAGAAATGAAC
*** *
12063714 AAGACCATAGTTGAAAGATACTATAAAATTATACCAGAAATGAAC
1 AAGACCATAGTTGAAAGATACTATGGCATTAAACCAGAAATGAAC
12063759 AAGACCATAGTTGAAAGATACTATGGCA
1 AAGACCATAGTTGAAAGATACTATGGCA
12063787 ATACATCGGA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 31 0.50
45 31 0.50
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (45 bp):
AAGACCATAGTTGAAAGATACTATGGCATTAAACCAGAAATGAAC
Found at i:12066295 original size:20 final size:19
Alignment explanation
Indices: 12066246--12066282 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12066236 TACGGGATTG
*
12066246 CACTTCACTGCCTCTGTTA
1 CACTTCAGTGCCTCTGTTA
12066265 CACTTCAGTGCCTCTGTT
1 CACTTCAGTGCCTCTGTT
12066283 TGCACTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.35, G:0.14, T:0.38
Consensus pattern (19 bp):
CACTTCAGTGCCTCTGTTA
Found at i:12069684 original size:50 final size:49
Alignment explanation
Indices: 12069630--12069725 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 49
12069620 TATTGAGGTT
* * * * *
12069630 ATGAGAGGTCCCACGTCAGACCATGTTTGGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCACATAAGACCATGTCT-GGACATGGCATGGGCACCAAG
*
12069680 ATGAGAGGTCCCCCATAAGACCATGTCTGGACATGGCATGGGCACC
1 ATGAGAGGTCCCACATAAGACCATGTCTGGACATGGCATGGGCACC
12069726 GATATAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 16 0.40
50 24 0.60
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.19
Consensus pattern (49 bp):
ATGAGAGGTCCCACATAAGACCATGTCTGGACATGGCATGGGCACCAAG
Found at i:12070039 original size:12 final size:12
Alignment explanation
Indices: 12070022--12070060 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
12070012 ATGAGTTATT
12070022 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
12070034 TAAGTAAACAAG
1 TAAGTAAGCAAG
*
12070046 TAAGAAAGCAAG
1 TAAGTAAGCAAG
12070058 TAA
1 TAA
12070061 AGAAAAAGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:12077158 original size:50 final size:50
Alignment explanation
Indices: 12077035--12077160 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 50
12077025 GAGGTCCTAC
* * * **
12077035 GTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCA
1 GTAAGACCATGTTTGGGACATGGCATGGGAACCGAGATGAGAACTCCCCA
* *
12077085 GTAAGACCATGTTGGGGACATGGCATGGGAACCGATATGAGAACT-CCCA
1 GTAAGACCATGTTTGGGACATGGCATGGGAACCGAGATGAGAACTCCCCA
* * *
12077134 TGTAAGACCATATTTGGTATATGGCAT
1 -GTAAGACCATGTTTGGGACATGGCAT
12077161 TGGCAGTACA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 4 0.06
50 60 0.94
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (50 bp):
GTAAGACCATGTTTGGGACATGGCATGGGAACCGAGATGAGAACTCCCCA
Found at i:12084701 original size:25 final size:24
Alignment explanation
Indices: 12084671--12084734 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
12084661 TCTTAATCCA
**
12084671 TATAACAGGAAGCTCATGTGAGCTG
1 TATAAC-GGAAGCTCATCCGAGCTG
* *
12084696 TATAACGGAAAGCTTATCCGGGCTG
1 TATAACGG-AAGCTCATCCGAGCTG
12084721 TATAACGGGAAGCT
1 TATAAC-GGAAGCT
12084735 TATAAGAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 29 0.88
26 2 0.06
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (24 bp):
TATAACGGAAGCTCATCCGAGCTG
Found at i:12084913 original size:26 final size:26
Alignment explanation
Indices: 12084837--12084918 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
12084827 AAGTTCAAGC
* *
12084837 GAGCCA-T-ATCGGGAAGC-TTTGGA
1 GAGCCATTAATCGGGAAGCGTATGAA
* * *
12084860 GAGCCATTAATCAGGAAG-GTCTCAAA
1 GAGCCATTAATCGGGAAGCGTAT-GAA
*
12084886 GAGCCTTTAATCGGGAAGCGTATGAA
1 GAGCCATTAATCGGGAAGCGTATGAA
12084912 GAGCCAT
1 GAGCCAT
12084919 ATATTGGGAC
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
23 6 0.13
24 1 0.02
25 10 0.22
26 25 0.56
27 3 0.07
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (26 bp):
GAGCCATTAATCGGGAAGCGTATGAA
Found at i:12096788 original size:42 final size:42
Alignment explanation
Indices: 12096715--12096981 Score: 405
Period size: 42 Copynumber: 6.4 Consensus size: 42
12096705 TAGTGCCTAT
* * *
12096715 CAGGTTTATTGCCAGTGAAAC-ATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
* *
12096756 CAGGCTTAATGCCGGTGAAATAATTTTAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
*
12096798 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
*
12096840 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
* *
12096882 CAGGCTTAATGCCGGTGAAACAATATCAGACATTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
* *
12096924 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
12096965 CAGGC-TAAGTGCCGGTG
1 CAGGCTTAA-TGCCGGTG
12096982 TACTGAATCA
Statistics
Matches: 207, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.01
41 46 0.22
42 158 0.76
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATTTCAGACTTTACGTCTAG
Found at i:12096837 original size:84 final size:84
Alignment explanation
Indices: 12096715--12097024 Score: 425
Period size: 84 Copynumber: 3.7 Consensus size: 84
12096705 TAGTGCCTAT
* * * *
12096715 CAGGTTTATTGCCAGTGAAAC-ATTTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
*
12096779 TTTTAGACTTTACGTCTAG
66 TTTCAGACTTTACGTCTAG
12096798 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
12096863 TTTCAGACTTTACGTCTAG
66 TTTCAGACTTTACGTCTAG
* *
12096882 CAGGCTTAATGCCGGTGAAACAATATCAGACATTACGTCTAGCAGGCTTAATGCCGGTGAAA-CA
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
* *
12096946 TTTCAGACTATATGTCTAG
66 TTTCAGACTTTACGTCTAG
* * * * *
12096965 CAGGC-TAAGTGCCGGTG-TACTGA-ATCAGGCTTTAAGTCTAGCAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAA-TGCCGGTGAAAC-AATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAA
12097025 TCTGTTTAAA
Statistics
Matches: 208, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
81 3 0.01
82 34 0.16
83 50 0.24
84 121 0.58
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (84 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAA
TTTCAGACTTTACGTCTAG
Found at i:12097004 original size:41 final size:41
Alignment explanation
Indices: 12096715--12097024 Score: 367
Period size: 42 Copynumber: 7.5 Consensus size: 41
12096705 TAGTGCCTAT
* * * *
12096715 CAGGTTTATTGCCAGTGAAACATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACATATCAGACTTTACGTCTAG
* * *
12096756 CAGGCTTAATGCCGGTGAAATAATTTTAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAA-CATATCAGACTTTACGTCTAG
12096798 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAAC-ATATCAGACTTTACGTCTAG
* *
12096840 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAA-CATATCAGACTTTACGTCTAG
*
12096882 CAGGCTTAATGCCGGTGAAACAATATCAGACATTACGTCTAG
1 CAGGCTTAATGCCGGTGAAAC-ATATCAGACTTTACGTCTAG
* * *
12096924 CAGGCTTAATGCCGGTGAAACATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACATATCAGACTTTACGTCTAG
* * *
12096965 CAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAAGTCTAG
1 CAGGCTTAA-TGCCGGTGAAACAT--ATCAGACTTTACGTCTAG
*
12097006 CAGGC-TAAGTGCCAGTGAA
1 CAGGCTTAA-TGCCGGTGAA
12097025 TCTGTTTAAA
Statistics
Matches: 237, Mismatches: 24, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 76 0.32
42 155 0.65
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (41 bp):
CAGGCTTAATGCCGGTGAAACATATCAGACTTTACGTCTAG
Found at i:12098347 original size:23 final size:22
Alignment explanation
Indices: 12098304--12098347 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
12098294 TTCTAAGCCG
12098304 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
12098327 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
12098348 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:12098596 original size:51 final size:51
Alignment explanation
Indices: 12098489--12098617 Score: 147
Period size: 51 Copynumber: 2.5 Consensus size: 51
12098479 TTCAGTTTAC
* * *
12098489 ATAGTAGCCTACACATAGTACTACACATGTGACCATTACCATCCGATATACG
1 ATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCC-ATATACG
* * *
12098541 -TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATCC-TGTACG
1 ATAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACCATCCATATACG
*
12098590 AATAGTAGTCTGCACATAGTACTACACA
1 -ATAGTAGCCTGCACATAGTACTACACA
12098618 TGCGACCTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
49 5 0.07
51 60 0.90
52 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (51 bp):
ATAGTAGCCTGCACATAGTACTACACACGTGACCATAACCATCCATATACG
Found at i:12102642 original size:32 final size:32
Alignment explanation
Indices: 12102601--12102667 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
12102591 AGTGGCACTG
12102601 AATTAATCTTTGATACAGACACTTTAGTATAC
1 AATTAATCTTTGATACAGACACTTTAGTATAC
*
12102633 AATTAATCTTTGATTCAGACACTTTAGTATAC
1 AATTAATCTTTGATACAGACACTTTAGTATAC
12102665 AAT
1 AAT
12102668 AGAAAAGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (32 bp):
AATTAATCTTTGATACAGACACTTTAGTATAC
Found at i:12106024 original size:25 final size:25
Alignment explanation
Indices: 12105996--12106086 Score: 60
Period size: 25 Copynumber: 3.7 Consensus size: 25
12105986 TCTTGAGCCA
*
12105996 TATAATAGGAAGCTCATATGAGCTG
1 TATAATAGGAAGCTCATAAGAGCTG
** * ** *
12106021 TATAACGGGAAGCTTATCCGGGCTG
1 TATAATAGGAAGCTCATAAGAGCTG
* **
12106046 TATAA-CGAGAAGCTCATAAGAGCCA
1 TATAATAG-GAAGCTCATAAGAGCTG
*
12106071 TAT-TTAGGAAGCTCAT
1 TATAATAGGAAGCTCAT
12106087 GCAAGCCAAT
Statistics
Matches: 49, Mismatches: 15, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
24 10 0.20
25 39 0.80
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (25 bp):
TATAATAGGAAGCTCATAAGAGCTG
Found at i:12106227 original size:26 final size:25
Alignment explanation
Indices: 12106162--12106228 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 25
12106152 CAGTTCAAGT
12106162 GAGCCA-T-ATCGGGAAGCTCTAAA
1 GAGCCATTAATCGGGAAGCTCTAAA
* **
12106185 GATCCATTAATTAGGAAGCTCATAAA
1 GAGCCATTAATCGGGAAGCTC-TAAA
*
12106211 GAGCCTTTAATCGGGAAG
1 GAGCCATTAATCGGGAAG
12106229 TTCACGAAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 5 0.15
24 1 0.03
25 10 0.29
26 18 0.53
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCTAAA
Found at i:12107718 original size:11 final size:11
Alignment explanation
Indices: 12107702--12107756 Score: 78
Period size: 11 Copynumber: 5.2 Consensus size: 11
12107692 TTTTCAAAAC
12107702 TTTTAAACTAT
1 TTTTAAACTAT
12107713 TTTTAAACTAT
1 TTTTAAACTAT
12107724 TTTTAAA-TAT
1 TTTTAAACTAT
*
12107734 TTCTAAACTA-
1 TTTTAAACTAT
*
12107744 TTTTAAAATAT
1 TTTTAAACTAT
12107755 TT
1 TT
12107757 AAGGCTTGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
10 17 0.44
11 22 0.56
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAACTAT
Found at i:12107726 original size:21 final size:21
Alignment explanation
Indices: 12107702--12107756 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
12107692 TTTTCAAAAC
*
12107702 TTTTAAACTATTTTTAAACTAT
1 TTTTAAA-TATTTCTAAACTAT
12107724 TTTTAAATATTTCTAAACTAT
1 TTTTAAATATTTCTAAACTAT
*
12107745 TTTAAAATATTT
1 TTTTAAATATTT
12107757 AAGGCTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 24 0.77
22 7 0.23
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAATATTTCTAAACTAT
Found at i:12112036 original size:37 final size:37
Alignment explanation
Indices: 12111986--12112060 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
12111976 AATGTGGACT
12111986 TTAACTATCGTCGGTACTCCACGAAACTCCTCTGTCA
1 TTAACTATCGTCGGTACTCCACGAAACTCCTCTGTCA
*
12112023 TTAACTATTGTCGGTACTCCACGAAACTCCTCTGTCA
1 TTAACTATCGTCGGTACTCCACGAAACTCCTCTGTCA
12112060 T
1 T
12112061 CCAACAAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (37 bp):
TTAACTATCGTCGGTACTCCACGAAACTCCTCTGTCA
Found at i:12120143 original size:237 final size:237
Alignment explanation
Indices: 12119706--12120166 Score: 649
Period size: 237 Copynumber: 1.9 Consensus size: 237
12119696 CGTGTGGCCC
* * * **
12119706 AAAATCCACACTCGGTTCGTCATCTTTGGGATAGAACACACACCTAAAATCTGTTATTTCGAGGC
1 AAAATCCACACTCGCTTCATCATCTTTGGGATAGAACAAACACCTAAAATCCATTATTTCGAGGC
* *
12119771 AAGATTACAAATTCGAAACTTCAACAACCTAGATCTGACTAGATCTAGTACAGATCTGTACCTAA
66 AAGATTACAAATTCGAAACTTCAACAACCTAGATCTGACTAGATCTAGTACAAATCTATACCTAA
* *** *
12119836 CAATAAGAACAATCGTTTAGCAATAACCCTTACAAGAAATAACTAATCGAATCTGGTTAGATCGG
131 CAATAAGAACAATCGTTTAGCAATAACCCTTACAAGAAATAACTAATCAAATCCAATTAGATCAG
12119901 AGAAACTACTTACTCTATCAACCTACGACAGATATTTCAAAA
196 AGAAACTACTTACTCTATCAACCTACGACAGATATTTCAAAA
* * * * *
12119943 AAAATCCACACTCAGCTT-ATCATCTTTGGGCTAGCACAAACACTTGAAATCCATTATTTTGAGG
1 AAAATCCACACTC-GCTTCATCATCTTTGGGATAGAACAAACACCTAAAATCCATTATTTCGAGG
** * * *
12120007 CAAGATT-GTAATTCGCAGCTTCAACAATCC-AGATCTGACTAGATGTAGTACAAATCTATACCT
65 CAAGATTACAAATTCGAAACTTCAACAA-CCTAGATCTGACTAGATCTAGTACAAATCTATACCT
*
12120070 AACAATAAGAACAATCGTTTAGCAATAACCCCTTACAAGAAATAACTGATCAAATCCAATTAGAT
129 AACAATAAGAACAATCGTTTAGCAATAA-CCCTTACAAGAAATAACTAATCAAATCCAATTAGAT
* *
12120135 CAGAGAAACTACTTACTCTATTAGCCTACGAC
193 CAGAGAAACTACTTACTCTATCAACCTACGAC
12120167 GGATCCCGAC
Statistics
Matches: 196, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
236 74 0.38
237 119 0.61
238 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (237 bp):
AAAATCCACACTCGCTTCATCATCTTTGGGATAGAACAAACACCTAAAATCCATTATTTCGAGGC
AAGATTACAAATTCGAAACTTCAACAACCTAGATCTGACTAGATCTAGTACAAATCTATACCTAA
CAATAAGAACAATCGTTTAGCAATAACCCTTACAAGAAATAACTAATCAAATCCAATTAGATCAG
AGAAACTACTTACTCTATCAACCTACGACAGATATTTCAAAA
Found at i:12123976 original size:26 final size:25
Alignment explanation
Indices: 12123940--12124034 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 25
12123930 GGCTTTTTGA
* ** *
12123940 ATAATACCCCACTTAGGCTTTTCCAG
1 ATAATTCCCCACAAAGGC-TTTACAG
12123966 ATAATTCCCCACAAAGGCTTTACAG
1 ATAATTCCCCACAAAGGCTTTACAG
** * * *
12123991 ATAATTTACCATAAAGGCCTTACAA
1 ATAATTCCCCACAAAGGCTTTACAG
* *
12124016 ATAACTCGCCACAAAGGCT
1 ATAATTCCCCACAAAGGCT
12124035 AAGTTTAGTT
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
25 40 0.73
26 15 0.27
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (25 bp):
ATAATTCCCCACAAAGGCTTTACAG
Found at i:12130215 original size:21 final size:24
Alignment explanation
Indices: 12130191--12130233 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12130181 TTAGGGGTGT
12130191 TACAG-TTAGT-G-TTATCAGAGC
1 TACAGTTTAGTCGATTATCAGAGC
12130212 TACAGTTTAGTCGATTATCAGA
1 TACAGTTTAGTCGATTATCAGA
12130234 CTTAACATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 1 0.05
24 8 0.42
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (24 bp):
TACAGTTTAGTCGATTATCAGAGC
Found at i:12130674 original size:17 final size:17
Alignment explanation
Indices: 12130654--12130687 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12130644 TTCTGTGCCT
12130654 TTTCTTCTTCTTT-TTTA
1 TTTCTT-TTCTTTCTTTA
12130671 TTTCTTTTCTTTCTTTA
1 TTTCTTTTCTTTCTTTA
12130688 ATTTATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTTCTTTCTTTA
Found at i:12130680 original size:22 final size:21
Alignment explanation
Indices: 12130652--12130699 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
12130642 CGTTCTGTGC
12130652 CTTTTCTTCTTCTTT-TTTATTT
1 CTTTTC-T-TTCTTTATTTATTT
12130674 CTTTTCTTTCTTTAATTTATTT
1 CTTTTCTTTCTTT-ATTTATTT
12130696 CTTT
1 CTTT
12130700 GATTTCTCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (21 bp):
CTTTTCTTTCTTTATTTATTT
Found at i:12137255 original size:62 final size:61
Alignment explanation
Indices: 12137159--12137311 Score: 171
Period size: 62 Copynumber: 2.5 Consensus size: 61
12137149 AACGGACAAG
* * * * * * *
12137159 GGCCAAGGACATGGCGTGTGTCTGGGTCGTGTAACTCACTGTTTGTGGTATAATACCACAT
1 GGCCAAGGACACGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTATAGTATAAAACCACAC
* *
12137220 GGCCAAGGACACGAGCGTGTGTCTAGGCCGTGTAACTCACTTTTTATAGTATAAAATCACAC
1 GGCCAAGGACACG-GCGTGTGTCTAGGCCGTGTAACTCACTGTTTATAGTATAAAACCACAC
* * * *
12137282 GGCCAGGGACATAGGTGTGTGTCCAGGCCG
1 GGCCAAGGACA-CGGCGTGTGTCTAGGCCG
12137312 AGTGAACCAC
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
61 12 0.16
62 64 0.83
63 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (61 bp):
GGCCAAGGACACGGCGTGTGTCTAGGCCGTGTAACTCACTGTTTATAGTATAAAACCACAC
Found at i:12138629 original size:14 final size:13
Alignment explanation
Indices: 12138602--12138639 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
12138592 AGTTTCTAAA
12138602 TTTTCAAATTAAG
1 TTTTCAAATTAAG
12138615 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
12138629 TTTTCAAATTA
1 TTTTCAAATTA
12138640 CAAATATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:12138881 original size:69 final size:68
Alignment explanation
Indices: 12138804--12139010 Score: 243
Period size: 69 Copynumber: 3.0 Consensus size: 68
12138794 TGTCTTTTTT
* * * * * *
12138804 TTGCAGGGAATATTTCTTCTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTATTCACACATCA
1 TTGCAGGGAATCTTTCCTGTTCACGCATCA-TTTCTTGCAGGGAATCTCTCCTGTTCACACATCA
12138869 TTTC
65 TTTC
* * * * *
12138873 TTGCAGGGAATCTTTCCTGTTCACGCATCATTTCTTACAAGGAATCTTTCCTGTTCACGCATTAT
1 TTGCAGGGAATCTTTCCTGTTCACGCATCATTTCTTGCAGGGAATCTCTCCTGTTCACACATCA-
*
12138938 TTTG
65 TTTC
* ** * *
12138942 TTGGAGGGAATCTTTCCTGTTCATACATCATTTCTTGTAGGGAATCTCTCCTGTTCATACATCAT
1 TTGCAGGGAATCTTTCCTGTTCACGCATCATTTCTTGCAGGGAATCTCTCCTGTTCACACATCAT
12139007 TTC
66 TTC
12139010 T
1 T
12139011 GGTATTATTT
Statistics
Matches: 114, Mismatches: 23, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
68 31 0.27
69 83 0.73
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (68 bp):
TTGCAGGGAATCTTTCCTGTTCACGCATCATTTCTTGCAGGGAATCTCTCCTGTTCACACATCAT
TTC
Found at i:12138882 original size:34 final size:34
Alignment explanation
Indices: 12138804--12139010 Score: 225
Period size: 34 Copynumber: 6.0 Consensus size: 34
12138794 TGTCTTTTTT
* * * * * *
12138804 TTGCAGGGAATATTTCTTCTTCACGCATTATTTTG
1 TTGCAGGGAATCTTTCCTGTTCACACATCA-TTTC
* *
12138839 TTGCAGGGAATCTCTCCTATTCACACATCATTTC
1 TTGCAGGGAATCTTTCCTGTTCACACATCATTTC
*
12138873 TTGCAGGGAATCTTTCCTGTTCACGCATCATTTC
1 TTGCAGGGAATCTTTCCTGTTCACACATCATTTC
* * * * *
12138907 TTACAAGGAATCTTTCCTGTTCACGCATTATTTTG
1 TTGCAGGGAATCTTTCCTGTTCACACATCA-TTTC
* *
12138942 TTGGAGGGAATCTTTCCTGTTCATACATCATTTC
1 TTGCAGGGAATCTTTCCTGTTCACACATCATTTC
* * *
12138976 TTGTAGGGAATCTCTCCTGTTCATACATCATTTC
1 TTGCAGGGAATCTTTCCTGTTCACACATCATTTC
12139010 T
1 T
12139011 GGTATTATTT
Statistics
Matches: 148, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
34 97 0.66
35 51 0.34
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (34 bp):
TTGCAGGGAATCTTTCCTGTTCACACATCATTTC
Found at i:12138994 original size:103 final size:103
Alignment explanation
Indices: 12138823--12139010 Score: 304
Period size: 103 Copynumber: 1.8 Consensus size: 103
12138813 ATATTTCTTC
*
12138823 TTCACGCATTATTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTGCAGGGAATCTTT
1 TTCACGCATTATTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTGCAGGGAATCTCT
*
12138888 CCTGTTCACGCATCATTTCTTACAAGGAATCTTTCCTG
66 CCTGTTCACACATCATTTCTTACAAGGAATCTTTCCTG
* * * * *
12138926 TTCACGCATTATTTTGTTGGAGGGAATCTTTCCTGTTCATACATCATTTCTTGTAGGGAATCTCT
1 TTCACGCATTATTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTGCAGGGAATCTCT
*
12138991 CCTGTTCATACATCATTTCT
66 CCTGTTCACACATCATTTCT
12139011 GGTATTATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 77 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (103 bp):
TTCACGCATTATTTTGTTGCAGGGAATCTCTCCTATTCACACATCATTTCTTGCAGGGAATCTCT
CCTGTTCACACATCATTTCTTACAAGGAATCTTTCCTG
Found at i:12141844 original size:21 final size:22
Alignment explanation
Indices: 12141814--12141858 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12141804 GAACAAATTG
*
12141814 TTGATTCTATT-TATTTTTTTAT
1 TTGATTCTATTCT-TTTTTGTAT
12141836 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTTTTGTAT
12141857 TT
1 TT
12141859 CTTTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (22 bp):
TTGATTCTATTCTTTTTTGTAT
Found at i:12141914 original size:21 final size:23
Alignment explanation
Indices: 12141890--12141932 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
12141880 TTAATTTTTT
*
12141890 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
*
12141911 AAAAGAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
12141933 TAATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:12142698 original size:7 final size:6
Alignment explanation
Indices: 12142657--12142685 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12142647 CTAGAAATGA
12142657 TTTCTT TTTCTT TTTCTT TTTCTT TTTCT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCT
12142686 GGTTTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:12144249 original size:20 final size:20
Alignment explanation
Indices: 12144220--12144257 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12144210 CCAGATTCCC
*
12144220 GATTTGATAAACTATGTTTT
1 GATTTCATAAACTATGTTTT
*
12144240 GATTTCATAAATTATGTT
1 GATTTCATAAACTATGTT
12144258 ATTTGAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (20 bp):
GATTTCATAAACTATGTTTT
Found at i:12145491 original size:41 final size:41
Alignment explanation
Indices: 12145434--12145583 Score: 201
Period size: 41 Copynumber: 3.7 Consensus size: 41
12145424 TGGAGATAGC
* ** *
12145434 GATTCATGCTTTGTGCCTAGCAATCTTAGTGTTGGTGTGTT
1 GATTCATGCTTTGTGCCTAGCAAGCTTAGTGCCGGTGTATT
* *
12145475 GATTCAAGCTTTGTGCCTAGCAGGCTTAGTGCCGGTGTATT
1 GATTCATGCTTTGTGCCTAGCAAGCTTAGTGCCGGTGTATT
* * * *
12145516 GATTCAGGCTTTGTGCCTAGCAAGCTTAATGCCAGTGTACT
1 GATTCATGCTTTGTGCCTAGCAAGCTTAGTGCCGGTGTATT
*
12145557 GATTCATGCTTTGTGCCTAGCAGGCTT
1 GATTCATGCTTTGTGCCTAGCAAGCTT
12145584 TGTAACACCT
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (41 bp):
GATTCATGCTTTGTGCCTAGCAAGCTTAGTGCCGGTGTATT
Found at i:12160971 original size:7 final size:8
Alignment explanation
Indices: 12160950--12160979 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
12160940 TTTAGTTTCT
12160950 TATTTTTG
1 TATTTTTG
12160958 TATTTTTG
1 TATTTTTG
12160966 TATTTTTG
1 TATTTTTG
12160974 -ATTTTT
1 TATTTTT
12160980 TTTCTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (8 bp):
TATTTTTG
Found at i:12161141 original size:21 final size:21
Alignment explanation
Indices: 12161098--12161141 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
12161088 TTATAAAATT
* * *
12161098 ATTTAAAAAATATTTCATAAA
1 ATTTAAAAAAAATATAATAAA
*
12161119 ATTTAAAAAAAATATAATGAA
1 ATTTAAAAAAAATATAATAAA
12161140 AT
1 AT
12161142 ACAGATTTAT
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:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTAAAAAAAATATAATAAA
Found at i:12161780 original size:10 final size:11
Alignment explanation
Indices: 12161763--12161799 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
12161753 AAAGAGCAAC
12161763 AAAGAGGAAAG
1 AAAGAGGAAAG
*
12161774 AAA-AGGAGAG
1 AAAGAGGAAAG
12161784 AAAGAGG-AAG
1 AAAGAGGAAAG
12161794 AAAGAG
1 AAAGAG
12161800 ACGACACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (11 bp):
AAAGAGGAAAG
Found at i:12182531 original size:19 final size:19
Alignment explanation
Indices: 12182507--12182550 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12182497 GTGAAGGCAT
*
12182507 CGCGCGTGGAGGAG-ACGCA
1 CGCGCGCGGAGGAGCA-GCA
*
12182526 CGCGCGCGGAGGCGCAGCA
1 CGCGCGCGGAGGAGCAGCA
12182545 CGCGCG
1 CGCGCG
12182551 AAAGAGGCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.16, C:0.34, G:0.48, T:0.02
Consensus pattern (19 bp):
CGCGCGCGGAGGAGCAGCA
Found at i:12186232 original size:2 final size:2
Alignment explanation
Indices: 12186225--12186273 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
12186215 GAGTATGGAA
12186225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12186267 AT AT AT A
1 AT AT AT A
12186274 AATTATAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12186500 original size:15 final size:14
Alignment explanation
Indices: 12186465--12186503 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12186455 TTAGTTTTTA
12186465 AAAAAATATATAAT
1 AAAAAATATATAAT
* *
12186479 AATAAATATGTACAT
1 AAAAAATATATA-AT
12186494 AAAAAATATA
1 AAAAAATATA
12186504 CATGTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAAATATATAAT
Found at i:12186516 original size:30 final size:29
Alignment explanation
Indices: 12186465--12186524 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
12186455 TTAGTTTTTA
* *
12186465 AAAAAATATATAATAATAAAT-ATGTACAT
1 AAAAAATATACAATAAAAAATAAT-TACAT
*
12186494 AAAAAATATACATGTAAAAAATAATTACAT
1 AAAAAATATACA-ATAAAAAATAATTACAT
12186524 A
1 A
12186525 TGAAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAAATATACAATAAAAAATAATTACAT
Found at i:12190051 original size:12 final size:12
Alignment explanation
Indices: 12190034--12190060 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12190024 CTCTCGGTCT
12190034 CCCATTTCTTTA
1 CCCATTTCTTTA
12190046 CCCATTTCTTTA
1 CCCATTTCTTTA
12190058 CCC
1 CCC
12190061 GAAATCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (12 bp):
CCCATTTCTTTA
Found at i:12192500 original size:91 final size:91
Alignment explanation
Indices: 12192353--12192560 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 91
12192343 TTGATTTTAG
* *
12192353 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
12192418 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
* *
12192445 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATTAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
12192510 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
12192536 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
12192561 GTTATAATTA
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 91 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:12192535 original size:44 final size:43
Alignment explanation
Indices: 12192393--12192535 Score: 130
Period size: 44 Copynumber: 3.2 Consensus size: 43
12192383 GAATTTTATG
* *
12192393 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** *
12192437 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATT
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
12192484 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
12192528 AAATTATA
1 AAATTATA
12192536 CAAATTCATA
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 22 0.28
45 12 0.15
46 11 0.14
47 14 0.18
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:12192707 original size:18 final size:18
Alignment explanation
Indices: 12192666--12192712 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
12192656 ATGATTTGAG
12192666 TAAATTCATATAAGAATAT
1 TAAATT-ATATAAGAATAT
12192685 T-AATTAT-TAAGAATTAT
1 TAAATTATATAAGAA-TAT
12192702 TAAATTATATA
1 TAAATTATATA
12192713 TTTTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
17 6 0.24
18 10 0.40
19 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (18 bp):
TAAATTATATAAGAATAT
Found at i:12192854 original size:15 final size:15
Alignment explanation
Indices: 12192819--12192870 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12192809 TTAAGAATTT
*
12192819 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12192833 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12192847 TATTTAATAATAAT-
1 TATTTAATTATAATA
12192861 TATGTTAATT
1 TAT-TTAATT
12192871 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12192883 original size:120 final size:119
Alignment explanation
Indices: 12192579--12192981 Score: 656
Period size: 120 Copynumber: 3.4 Consensus size: 119
12192569 TATTTTAAAT
* * * * * *
12192579 TTTATTAAATCACATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTTTAT
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTTTAT
* *
12192643 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAA
65 AGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTGATTATTAAGAA
*
12192698 -TTATTAAATTATATATTTTAAATATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
*
12192762 GTATCATATATTATGATTTCAGTAAATTTATATAAGAATATTGATTATTAAGAA
66 GTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTGATTATTAAGAA
12192816 TTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTAT
1 -TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTAT
12192881 AGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTGATTATTAAGAA
65 AGTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTGATTATTAAGAA
12192936 TTTATT-AA--AT-TATTTTAATTATAATATATTTAATAATAATTATGTT
1 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
12192982 TAAATATGAT
Statistics
Matches: 269, Mismatches: 12, Indels: 10
0.92 0.04 0.03
Matches are distributed among these distances:
115 36 0.13
116 2 0.01
118 107 0.40
119 8 0.03
120 116 0.43
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (119 bp):
TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATA
GTATCATATATTATGATTTCAGTAAATTCATATAAGAATATTGATTATTAAGAA
Found at i:12192965 original size:16 final size:15
Alignment explanation
Indices: 12192943--12192984 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
12192933 GAATTTATTA
*
12192943 AATTATTTTAATTAT
1 AATTATTTTAATAAT
12192958 AA-TATATTTAATAAT
1 AATTAT-TTTAATAAT
12192973 AATTATGTTTAA
1 AATTAT-TTTAA
12192985 ATATGATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 3 0.13
15 12 0.52
16 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
AATTATTTTAATAAT
Found at i:12193219 original size:16 final size:16
Alignment explanation
Indices: 12193198--12193251 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
12193188 TTGATTTGCT
*
12193198 ATTACACCTCTATTTC
1 ATTACACCTCTATTCC
12193214 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
12193230 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
12193246 AATACA
1 ATTACA
12193252 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:12193994 original size:26 final size:26
Alignment explanation
Indices: 12193961--12194022 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
12193951 ATAAAAAATA
12193961 ACCAAAATATTATAACTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
*
12193987 ACCAAAATATTATAATTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTATTT
12194013 ACCAAAATAT
1 ACCAAAATAT
12194023 ACCCAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (26 bp):
ACCAAAATATTATAACTTTTTTATTT
Found at i:12194041 original size:11 final size:11
Alignment explanation
Indices: 12194027--12194057 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12194017 AAATATACCC
12194027 AAAAAAAACAA
1 AAAAAAAACAA
*
12194038 AAAACAAACAA
1 AAAAAAAACAA
12194049 AAAAAAAAC
1 AAAAAAAAC
12194058 CTGCACCGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:12194115 original size:27 final size:27
Alignment explanation
Indices: 12194085--12194144 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
12194075 CACCCTGGTC
*
12194085 GTGCCAAGGTAATTGGCGGCACCAAAG
1 GTGCCAAAGTAATTGGCGGCACCAAAG
* *
12194112 GTGCCAAAGTGATTGGCGGCACCAATG
1 GTGCCAAAGTAATTGGCGGCACCAAAG
12194139 GTGCCA
1 GTGCCA
12194145 TACTGCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (27 bp):
GTGCCAAAGTAATTGGCGGCACCAAAG
Found at i:12194154 original size:27 final size:27
Alignment explanation
Indices: 12194096--12194160 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
12194086 TGCCAAGGTA
*
12194096 ATTGGCGGCACCAAAGGTGCCAAAGTG
1 ATTGGCGGCACCAAAGGTGCCAAACTG
* *
12194123 ATTGGCGGCACCAATGGTGCCATACTG
1 ATTGGCGGCACCAAAGGTGCCAAACTG
*
12194150 CTTGGCGGCAC
1 ATTGGCGGCAC
12194161 TACTCGTGTT
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:0.23, C:0.26, G:0.32, T:0.18
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAACTG
Found at i:12194274 original size:11 final size:11
Alignment explanation
Indices: 12194241--12194282 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
12194231 GAGGTGCTGC
*
12194241 GAAAAAAAAGA
1 GAAAAAGAAGA
*
12194252 GAAAAAG-TGA
1 GAAAAAGAAGA
*
12194262 GAAAGAGAAGA
1 GAAAAAGAAGA
12194273 GAAAAAGAAG
1 GAAAAAGAAG
12194283 GTATTTTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (11 bp):
GAAAAAGAAGA
Found at i:12194344 original size:19 final size:21
Alignment explanation
Indices: 12194306--12194344 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
12194296 AATAATTGAT
*
12194306 TATATTGTTGTTATTGTTTTG
1 TATATTGTTGTTATTATTTTG
12194327 TATATT-TTG-TATTATTTT
1 TATATTGTTGTTATTATTTT
12194345 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (21 bp):
TATATTGTTGTTATTATTTTG
Found at i:12194408 original size:3 final size:3
Alignment explanation
Indices: 12194400--12194491 Score: 166
Period size: 3 Copynumber: 30.7 Consensus size: 3
12194390 TTTTAGTTAG
12194400 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
12194448 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12194492 AGATGTTATT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:12195297 original size:18 final size:18
Alignment explanation
Indices: 12195274--12195318 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
12195264 TTGATATGGT
*
12195274 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
12195292 TGGTGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
12195310 TGGTGGCGA
1 TGGTGGCGA
12195319 TCATTGGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.04, G:0.51, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:12199195 original size:12 final size:12
Alignment explanation
Indices: 12199178--12199202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12199168 GGTGTTCATT
12199178 CGGTTAACCGAC
1 CGGTTAACCGAC
12199190 CGGTTAACCGAC
1 CGGTTAACCGAC
12199202 C
1 C
12199203 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:12199371 original size:9 final size:9
Alignment explanation
Indices: 12199357--12199423 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
12199347 TTTGGTTAAA
12199357 AATTACCCG
1 AATTACCCG
12199366 AATTACCCG
1 AATTACCCG
*
12199375 AATTAACCG
1 AATTACCCG
*
12199384 AATTAACCG
1 AATTACCCG
**
12199393 AATTACCAA
1 AATTACCCG
* *
12199402 AAATACCAG
1 AATTACCCG
12199411 AATTACCCG
1 AATTACCCG
12199420 AATT
1 AATT
12199424 TTTTTATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:12199535 original size:34 final size:36
Alignment explanation
Indices: 12199496--12199573 Score: 88
Period size: 39 Copynumber: 2.1 Consensus size: 36
12199486 GACTTTAGTA
12199496 AATTGGGT-TGT-CTTTTAGTTTTATTGGATTGGGT
1 AATTGGGTATGTACTTTTAGTTTTATTGGATTGGGT
* * *
12199530 AATTGGGTAAACTTTAGTTTTAGTTTTATTGGGTTGGGT
1 AATTGGGT--A-TGTACTTTTAGTTTTATTGGATTGGGT
12199569 AATTG
1 AATTG
12199574 AGTTTGGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 8 0.22
38 2 0.06
39 26 0.72
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (36 bp):
AATTGGGTATGTACTTTTAGTTTTATTGGATTGGGT
Found at i:12200907 original size:160 final size:154
Alignment explanation
Indices: 12200421--12200894 Score: 373
Period size: 160 Copynumber: 3.0 Consensus size: 154
12200411 GCAAGTTGAA
* * * *
12200421 AAAAAAGTTAGTAAAAAAATCTTACTTCGGCCATTTATTCGTATTTTTTTCTCCGCATTTTATTC
1 AAAAAAGTTAGT--AATAATCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* ** *
12200486 CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
64 TTTTAAAAAATATCATAATTAGT-ATTTTATAATTTTACATTATTTCAGTGCATAATGTTTAAAA
* **
12200551 TTTATTAATTTAGTATGTTGTTTAAATT
128 TTTTTTAATTTAGTATGTTGAATAAA-T
**** * * * * *
12200579 AATTTGGTGTAAGAAAATAATCCTTA-TCCCTGCCCTTTGCTCGTATTATTTTC-CCG-ATTTTT
1 AAAAAAGT-T-AG-TAATAAT-CTTACTTCC-GCCATTTGTTCGTATTTTTTTCTCCGCA-TTTT
* * * * * * * **
12200641 TTTACTTTCAATAAAAATAT-ATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTT
60 ATTA-TTT-TA-AAAAATATCA-TA-ATTAGTATTTTATAATTTTACATTATTTCAGTGCATAAT
* * * * ***
12200705 GTTTGAAATATTTTGT-ATTAATTATTTCTGAATTTTT
120 GTTT-AAA-ATTTTTTAATTTAGTATGT-TGAATAAAT
12200742 AAAAAAGTTAGTAATACACTCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAATA-A-TCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
*
12200807 TTTTAAAAAATATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTAAA
64 TTTTAAAAAATATCAT-AA-TTAGTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTAAA
*
12200872 ATTTTTTAATTTAGTGTGTTGAA
127 ATTTTTTAATTTAGTATGTTGAA
12200895 GGGGAATAAA
Statistics
Matches: 234, Mismatches: 59, Indels: 46
0.69 0.17 0.14
Matches are distributed among these distances:
158 15 0.06
159 36 0.15
160 68 0.29
161 31 0.13
162 57 0.24
163 19 0.08
164 8 0.03
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.49
Consensus pattern (154 bp):
AAAAAAGTTAGTAATAATCTTACTTCCGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATT
TTAAAAAATATCATAATTAGTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTAAAATTT
TTTAATTTAGTATGTTGAATAAAT
Found at i:12200987 original size:27 final size:27
Alignment explanation
Indices: 12200949--12201004 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
12200939 TTAGCCACAT
*
12200949 ATTGGTGCCGCCTTTTTATTCCTCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
*
12200976 ATTGGTGTCGCCTTTTTATTCCCCTCC
1 ATTGGTGCCGCCTTTTTATTCCCCTCC
12201003 AT
1 AT
12201005 CACCCTCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.09, C:0.32, G:0.14, T:0.45
Consensus pattern (27 bp):
ATTGGTGCCGCCTTTTTATTCCCCTCC
Found at i:12201193 original size:16 final size:15
Alignment explanation
Indices: 12201172--12201201 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12201162 AATAAAAATA
12201172 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
12201188 TATTATTTTATATT
1 TATTATTTTATATT
12201202 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:12201776 original size:36 final size:37
Alignment explanation
Indices: 12201721--12201895 Score: 146
Period size: 39 Copynumber: 4.7 Consensus size: 37
12201711 TAAAAATTAC
* * *
12201721 TCTTTTTTTCTTTTTTCC-TTCCTTCCCTCTTCTTCT
1 TCTTTTTTTCTCTTCTCCTTTCCTTCCTTCTTCTTCT
* *
12201757 TCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
1 TCTTTTTTTCTCTTCTCCTTTCC--TTCCTT-CTTCTTCT
* *
12201797 TCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTCTTCTTTCT
1 TCTTT-TTTTCTCTTCTCCTTTCCT-TCCTTCTTC-TTCT
* * *
12201837 TTTTTTTTTCCCTTCTCCTTTCCTT--TTCTT-TCCT
1 TCTTTTTTTCTCTTCTCCTTTCCTTCCTTCTTCTTCT
*
12201871 TCTTTTTCTT-TCTT-TCCTCTCCTTC
1 TCTTTTT-TTCTCTTCTCCTTTCCTTC
12201896 ATTTCTTTCT
Statistics
Matches: 114, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
33 9 0.08
34 12 0.11
35 2 0.02
36 21 0.18
37 4 0.04
38 1 0.01
39 26 0.23
40 22 0.19
41 17 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (37 bp):
TCTTTTTTTCTCTTCTCCTTTCCTTCCTTCTTCTTCT
Found at i:12201793 original size:26 final size:26
Alignment explanation
Indices: 12201734--12201873 Score: 89
Period size: 26 Copynumber: 5.3 Consensus size: 26
12201724 TTTTTTCTTT
12201734 TTTCCTTC-CTTC-CCTCTT-CTTCTTC
1 TTTCCTTCTCTTCTCCT-TTCCTT-TTC
**
12201759 TTTTTTTCTCTTCTCCTTTCCTTTTC
1 TTTCCTTCTCTTCTCCTTTCCTTTTC
* *
12201785 TTTCCTTCT-TT-TTCTTTCTTTTTTC
1 TTTCCTTCTCTTCTCCTTTC-CTTTTC
12201810 TTCTCCTTTCCTCTTCTTCTTCTTT-CTTTT-
1 TT-TCC-TT-CTCTTC-TC--CTTTCCTTTTC
* *
12201840 TTT-TTTCCCTTCTCCTTTCCTTTTC
1 TTTCCTTCTCTTCTCCTTTCCTTTTC
12201865 TTTCCTTCT
1 TTTCCTTCT
12201874 TTTTCTTTCT
Statistics
Matches: 88, Mismatches: 12, Indels: 29
0.68 0.09 0.22
Matches are distributed among these distances:
23 4 0.05
24 11 0.12
25 20 0.23
26 27 0.31
27 10 0.11
28 2 0.02
29 3 0.03
30 2 0.02
31 5 0.06
33 4 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTCCTTCTCTTCTCCTTTCCTTTTC
Found at i:12201802 original size:4 final size:4
Alignment explanation
Indices: 12201781--12201932 Score: 97
Period size: 4 Copynumber: 38.0 Consensus size: 4
12201771 CTCCTTTCCT
*
12201781 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC
* * * *
12201826 -TTC -TTC TTTC TTT- TTTT TTTCC CTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTT-C -TTTC TTTC TTTC
* *
12201873 -TT- TTTC TTTC TTTCC TCTC CTTC ATTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC
12201921 TTTC TTTC TTTC
1 TTTC TTTC TTTC
12201933 CCTCTCCTTC
Statistics
Matches: 122, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
3 22 0.18
4 76 0.62
5 16 0.13
6 8 0.07
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:12201826 original size:33 final size:32
Alignment explanation
Indices: 12201789--12201927 Score: 126
Period size: 33 Copynumber: 4.2 Consensus size: 32
12201779 CTTTTCTTTC
12201789 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCT
1 CTTCTTTTTCTTTCTTTTTTCTT-TCCTTTCCT
* *
12201822 CTTCTTCTTCTTTCTTTTTTTTTTCCCTTCTCCT
1 CTTCTTTTTCTTTCTTTTTTCTTT-CCTT-TCCT
*
12201856 -TTCCTTTTCTTTCCTTCTTTTTCTTT-CTTTCCT
1 CTTCTTTTTCTTT-C-T-TTTTTCTTTCCTTTCCT
*
12201889 CTCCTTCATTTCTTTCTTTCTTTCTTT-CTTT-CT
1 CTTCTT--TTTCTTTCTTT-TTTCTTTCCTTTCCT
12201922 -TTCTTT
1 CTTCTTT
12201928 CTTTCCCTCT
Statistics
Matches: 89, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
30 1 0.01
32 5 0.06
33 43 0.48
34 23 0.26
35 2 0.02
36 15 0.17
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (32 bp):
CTTCTTTTTCTTTCTTTTTTCTTTCCTTTCCT
Found at i:12201830 original size:44 final size:40
Alignment explanation
Indices: 12201749--12201929 Score: 196
Period size: 39 Copynumber: 4.6 Consensus size: 40
12201739 TTCCTTCCCT
*
12201749 CTTCTTCTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
12201789 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTC-TT-
1 CTTCTTTTTCTTT-TTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
12201828 CTTCTTTCTTTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTT-TTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
12201869 CTTCTTTTTCTTTCTTTC-C-TCTCC-TT-CATTTCTTTC
1 CTTCTTTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
* *
12201905 TTTCTTTCTTTCTTTCTTTCT-TTCT
1 CTTC-TT-TTTCTTTTTTTCTCTTCT
12201930 TTCCCTCTCC
Statistics
Matches: 122, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
36 12 0.10
37 4 0.03
38 17 0.14
39 31 0.25
40 30 0.25
41 28 0.23
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.69
Consensus pattern (40 bp):
CTTCTTTTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:12201869 original size:10 final size:10
Alignment explanation
Indices: 12201774--12201888 Score: 52
Period size: 10 Copynumber: 11.7 Consensus size: 10
12201764 TTCTCTTCTC
12201774 CTTTCCTTTT
1 CTTTCCTTTT
12201784 CTTTCCTTCTT
1 CTTTCCTT-TT
12201795 -TTT-C-TTT
1 CTTTCCTTTT
12201802 C-TT--TTTT
1 CTTTCCTTTT
*
12201809 CTTCTCCTTTC
1 CTT-TCCTTTT
12201820 CTCTT-CTTCTT
1 CT-TTCCTT-TT
*
12201831 CTTTCTTTTTT
1 CTTTC-CTTTT
* *
12201842 TTTTCCCTTCTC
1 CTTT-CCTT-TT
12201854 CTTTCCTTTT
1 CTTTCCTTTT
12201864 CTTTCCTTCTT
1 CTTTCCTT-TT
12201875 -TTT-C-TTT
1 CTTTCCTTTT
12201882 CTTTCCT
1 CTTTCCT
12201889 CTCCTTCATT
Statistics
Matches: 80, Mismatches: 8, Indels: 34
0.66 0.07 0.28
Matches are distributed among these distances:
7 10 0.12
8 6 0.08
9 4 0.05
10 28 0.35
11 24 0.30
12 8 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:12201910 original size:80 final size:80
Alignment explanation
Indices: 12201748--12201941 Score: 248
Period size: 80 Copynumber: 2.4 Consensus size: 80
12201738 CTTCCTTCCC
* * ** *
12201748 TCTTC-TTCTTCTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTT
1 TCTTCTTTCTTTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
*
12201812 CTCCTTTCCTCTTCT
66 CTCATTTCCTCTTCT
12201827 TCTTCTTTCTTTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
1 TCTTCTTTCTTTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
*
12201892 CTTCATTTCTTTCTTTCTT
66 C-TCATTTC-CTC-TTC-T
*
12201911 TCTTTCTTTCTTTCTTTCTTTCCC-TCTCCTT
1 TC-TTCTTTCTTT-TTTTTTTCCCTTCTCCTT
12201942 CTCCCCCCCA
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
79 5 0.05
80 55 0.55
81 6 0.06
82 2 0.02
83 3 0.03
84 3 0.03
85 17 0.17
86 9 0.09
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.68
Consensus pattern (80 bp):
TCTTCTTTCTTTTTTTTTTCCCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
CTCATTTCCTCTTCT
Found at i:12202023 original size:27 final size:27
Alignment explanation
Indices: 12201977--12202055 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
12201967 TATTATAACA
**
12201977 TTGGTGCCGCCAATGTCTTTGGCACCT
1 TTGGTGCCGCCAATCACTTTGGCACCT
*
12202004 TTGGTGCCGCTAATCACTTTGGCACCT
1 TTGGTGCCGCCAATCACTTTGGCACCT
* * *
12202031 TCGGTACCGCCAATCACCTTGGCAC
1 TTGGTGCCGCCAATCACTTTGGCAC
12202056 GACCACGATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.29
Consensus pattern (27 bp):
TTGGTGCCGCCAATCACTTTGGCACCT
Found at i:12202141 original size:26 final size:28
Alignment explanation
Indices: 12202112--12202175 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
12202102 TTTTTTTGGT
12202112 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
12202138 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
12202166 ATATTTTGGT
1 ATATTTTGGT
12202176 TATTTTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:12203441 original size:15 final size:15
Alignment explanation
Indices: 12203421--12203452 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12203411 ATGAAGAGAG
12203421 CTATAGCAAGTCTAT
1 CTATAGCAAGTCTAT
12203436 CTATAGCAAGTCTAT
1 CTATAGCAAGTCTAT
12203451 CT
1 CT
12203453 TTTTAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.34
Consensus pattern (15 bp):
CTATAGCAAGTCTAT
Found at i:12205702 original size:103 final size:103
Alignment explanation
Indices: 12205523--12205728 Score: 385
Period size: 103 Copynumber: 2.0 Consensus size: 103
12205513 TTTTTTTTAC
* * *
12205523 ATTGTCTATTCGGCTGGTAATATTTCAGCCTATAAATAGTTTATCTTGTAAAAATTTGAAGGTTA
1 ATTGTCTATTCAGCTAGTAATAGTTCAGCCTATAAATAGTTTATCTTGTAAAAATTTGAAGGTTA
12205588 CATTACTTTTGACATATATAAACTTTGTGAGTTATTCA
66 CATTACTTTTGACATATATAAACTTTGTGAGTTATTCA
12205626 ATTGTCTATTCAGCTAGTAATAGTTCAGCCTATAAATAGTTTATCTTGTAAAAATTTGAAGGTTA
1 ATTGTCTATTCAGCTAGTAATAGTTCAGCCTATAAATAGTTTATCTTGTAAAAATTTGAAGGTTA
12205691 CATTACTTTTGACATATATAAACTTTGTGAGTTATTCA
66 CATTACTTTTGACATATATAAACTTTGTGAGTTATTCA
12205729 CTCTCAATTT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (103 bp):
ATTGTCTATTCAGCTAGTAATAGTTCAGCCTATAAATAGTTTATCTTGTAAAAATTTGAAGGTTA
CATTACTTTTGACATATATAAACTTTGTGAGTTATTCA
Found at i:12211136 original size:16 final size:16
Alignment explanation
Indices: 12211092--12211137 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12211082 TTACTTTATG
*
12211092 TAATTAATGCAAAATAA
1 TAATTAAT-TAAAATAA
12211109 -AATT-ATTCAAAATAA
1 TAATTAATT-AAAATAA
12211124 TAATTAATTAAAAT
1 TAATTAATTAAAAT
12211138 CATTAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 9 0.36
16 13 0.52
17 3 0.12
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
TAATTAATTAAAATAA
Found at i:12217057 original size:42 final size:43
Alignment explanation
Indices: 12216992--12217103 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 43
12216982 TTTCGCCTGC
* *
12216992 TAAAAGGGATGAAAGGTTAAAAACACCTA-T-ACATACCCCTAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTAGTAAC-TACACCAAG
** *
12217034 TGTAAGGGATGAAAGGTTGAAAACACC-AGTAACTACACCAAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTAGTAACTACACCAAG
*
12217076 TAAAAAGGATGAAAGGTTAAAAACACCT
1 TAAAAGGGATGAAAGGTTAAAAACACCT
12217104 GTGCATACTC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 55 0.95
43 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (43 bp):
TAAAAGGGATGAAAGGTTAAAAACACCTAGTAACTACACCAAG
Found at i:12217117 original size:42 final size:41
Alignment explanation
Indices: 12216992--12217118 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 41
12216982 TTTCGCCTGC
* * *
12216992 TAAAAGGGATGAAAGGTTAAAAACACCTATACATACCCCTAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTGT-CATACACCAAG
** * * *
12217034 TGTAAGGGATGAAAGGTTGAAAACACCAGTAACTACACCAAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTGTCA-TACACCAAG
* *
12217076 TAAAAAGGATGAAAGGTTAAAAACACCTGTGCATACTCCAAG
1 TAAAAGGGATGAAAGGTTAAAAACACCTGT-CATACACCAAG
12217118 T
1 T
12217119 GGGCGATTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 1 0.01
42 66 0.97
43 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (41 bp):
TAAAAGGGATGAAAGGTTAAAAACACCTGTCATACACCAAG
Found at i:12223058 original size:51 final size:51
Alignment explanation
Indices: 12222962--12223071 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
12222952 GTATAATAAT
* *
12222962 AAATTTAGTCCTCAAAGTTTACATATTTTGTGAAGTTAGCTTTGATTTAAC
1 AAATTTAGTCCACAAAGTTTACATATTTTATGAAGTTAGCTTTGATTTAAC
* * *
12223013 AAATTTAGTCCACAACA-TTTACATGTTTTATGAA-TTTGATCTTGATTTAAC
1 AAATTTAGTCCACAA-AGTTTACATATTTTATGAAGTTAGCT-TTGATTTAAC
12223064 AAATTTAG
1 AAATTTAG
12223072 CTGTAACGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
50 4 0.08
51 47 0.90
52 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (51 bp):
AAATTTAGTCCACAAAGTTTACATATTTTATGAAGTTAGCTTTGATTTAAC
Found at i:12232819 original size:17 final size:17
Alignment explanation
Indices: 12232797--12232830 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12232787 ACAAATGTTT
12232797 ATATAATTTTTTAATAA
1 ATATAATTTTTTAATAA
*
12232814 ATATAATTTTTTCATAA
1 ATATAATTTTTTAATAA
12232831 TTTTTTCAAG
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:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATAATTTTTTAATAA
Found at i:12233355 original size:28 final size:29
Alignment explanation
Indices: 12233316--12233385 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 29
12233306 TAAAATATTT
*
12233316 TTTTATAAATTTTATATTTTT-CAAAT-AA
1 TTTTATAAATTTTA-ATTTTTAAAAATAAA
12233344 TTTTA-ACAATTTTAATTTTTAAAAATAAA
1 TTTTATA-AATTTTAATTTTTAAAAATAAA
12233373 TTTTATAAATTTT
1 TTTTATAAATTTT
12233386 TGAATTCTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 7 0.19
28 16 0.43
29 13 0.35
30 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTATAAATTTTAATTTTTAAAAATAAA
Found at i:12235182 original size:34 final size:35
Alignment explanation
Indices: 12235125--12235191 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
12235115 AGAAAACAAT
* * * *
12235125 TTATTTTTTAATTTAACATATAAAATTTAATTTAA
1 TTATTTTTTAATATAAAAAATAAAATATAATTTAA
12235160 TTATTTTTTAA-ATAAAAAATAAAATATAATTT
1 TTATTTTTTAATATAAAAAATAAAATATAATTT
12235192 TACTCTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (35 bp):
TTATTTTTTAATATAAAAAATAAAATATAATTTAA
Found at i:12240414 original size:168 final size:166
Alignment explanation
Indices: 12240130--12240629 Score: 660
Period size: 168 Copynumber: 3.0 Consensus size: 166
12240120 ATCAGAGATT
** * *
12240130 GAATATCCATGCAAGAGCCATATTGAAGATCAGGAGAGTGATGATCAAATGTGTCTAAAACCTGT
1 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATC-AGTGTGTCTAAAACCCGT
* * * * *
12240195 CAAGGAAGAACCTAAAGATGACGTTTGTGATAAACCCTTGCATGGGACTCCTTCATGCAAGGAAA
65 CAAGGAAGAAGCTAAAGATGATGTTTGTGATAAA-CCTTGTATGAGACTCCTCCATGCAAGGAAA
* * * **
12240260 CTAAGAGGAAGAAATCACGATCACTATGTTCTAACGCA
129 CTAGGAGGAAGAAATCACAATCACAATGTTCTAAAACA
* * * *
12240298 GAATATCTATGCAAGAGCTATATTGATGATCATAAGAGTGATGATCAGTTGTGTCTAAAACCCGT
1 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAG-TGTGTCTAAAACCCGT
* *
12240363 CAAGGAAGAAGCTAAAGATGGTGTTTATGATGAAACCTTGTATGAGACTCCTCCATGCAA-GAAA
65 CAAGGAAGAAGCTAAAGATGATGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAAA
** **
12240427 GCTAGGAGGACTAAATCACAATCACAATGTTCTAAAATT
129 -CTAGGAGGAAGAAATCACAATCACAATGTTCTAAAACA
* *
12240466 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGAAGATCAAGTGAGTCTAAAACCCGT
1 GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATC-AGTGTGTCTAAAACCCGT
*
12240531 CAAAGAAGAAGCTAAAGATGATGTTTGTGATAAAACCTTGTATGAGACTCCTCCATGCAAGGAAA
65 CAAGGAAGAAGCTAAAGATGATGTTTGTGAT-AAACCTTGTATGAGACTCCTCCATGCAAGGAAA
* * *
12240596 CTAGGAAGAAGAAACCGCAATCACAATGTTCTAA
129 CTAGGAGGAAGAAATCACAATCACAATGTTCTAA
12240630 GCCTCGAAAG
Statistics
Matches: 289, Mismatches: 38, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
167 5 0.02
168 275 0.95
169 9 0.03
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (166 bp):
GAATATCCATGCAAGAGCCATATTGAAGATCACAAGAGTGATGATCAGTGTGTCTAAAACCCGTC
AAGGAAGAAGCTAAAGATGATGTTTGTGATAAACCTTGTATGAGACTCCTCCATGCAAGGAAACT
AGGAGGAAGAAATCACAATCACAATGTTCTAAAACA
Found at i:12244073 original size:21 final size:20
Alignment explanation
Indices: 12244049--12244088 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
12244039 AAAAAAAAAG
12244049 AAATAGCAACAAAACATTAAA
1 AAATAGCAACAAAAC-TTAAA
*
12244070 AAATAGCAACCAAACTTAA
1 AAATAGCAACAAAACTTAA
12244089 TTTAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.62, C:0.17, G:0.05, T:0.15
Consensus pattern (20 bp):
AAATAGCAACAAAACTTAAA
Found at i:12245952 original size:63 final size:63
Alignment explanation
Indices: 12245816--12245942 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 63
12245806 GCCTAAACAT
* * * *
12245816 ACGCCCGTGTCTCTGGCTCGTATGACTCTAATGCACAAAAAATGAGTTATACGGTTTGGACAC
1 ACGCTCGTGTCTCTGGCCCGTATGACTCTAATGCACAAAAAATGAGTTACACGGTCTGGACAC
* * * * *
12245879 ACGCTCGTGTCTTTGGCCCGTATGACTCTAATGTACAAATAGTGAGTTACATGGTCTGGACAC
1 ACGCTCGTGTCTCTGGCCCGTATGACTCTAATGCACAAAAAATGAGTTACACGGTCTGGACAC
12245942 A
1 A
12245943 TGTCTGTGTC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (63 bp):
ACGCTCGTGTCTCTGGCCCGTATGACTCTAATGCACAAAAAATGAGTTACACGGTCTGGACAC
Found at i:12249171 original size:18 final size:18
Alignment explanation
Indices: 12249138--12249188 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
12249128 ATTCACCTAA
*
12249138 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
12249157 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
12249175 ACCCAACCCAACCC
1 ACCCAACCCAACCC
12249189 TCATAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.39, C:0.47, G:0.02, T:0.12
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:12249305 original size:9 final size:9
Alignment explanation
Indices: 12249291--12249366 Score: 84
Period size: 9 Copynumber: 8.4 Consensus size: 9
12249281 GTAGAGATTC
12249291 AATTCGGTT
1 AATTCGGTT
12249300 AATTCGGTT
1 AATTCGGTT
12249309 AATTCGAG-T
1 AATTCG-GTT
* *
12249318 AACTCAGTT
1 AATTCGGTT
12249327 AATTCGAG-T
1 AATTCG-GTT
*
12249336 AATCCGGTT
1 AATTCGGTT
*
12249345 AATTCGGGT
1 AATTCGGTT
12249354 AATTCGGTT
1 AATTCGGTT
12249363 AATT
1 AATT
12249367 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.04
9 51 0.93
10 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Done.