Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 36 of 311
Found at i:10303282 original size:97 final size:97
Alignment explanation
Indices: 10303115--10303297 Score: 312
Period size: 97 Copynumber: 1.9 Consensus size: 97
10303105 CCAAAAACAA
* * *
10303115 GCCATTTCCAAGACCATTTCATATATAAACATTTACACTAATAATGCACACTTTCAAAGCGTCAA
1 GCCATTTCCAAGACCATTTCATACATAAACATTTACACCAATAATGCACACTTTCAAAGCATCAA
*
10303180 GACCTTACCTAAACACACACACACACACACAT
66 AACCTTACCTAAACACACACACACACACACAT
*
10303212 GCCATTTCCAAGACCATTTCATACATAAACATTTAGACCAATAATGCACACTTTCAAAGCATCAA
1 GCCATTTCCAAGACCATTTCATACATAAACATTTACACCAATAATGCACACTTTCAAAGCATCAA
*
10303277 AACCTTACTTAAACACACACA
66 AACCTTACCTAAACACACACA
10303298 TGTATATGCC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 80 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (97 bp):
GCCATTTCCAAGACCATTTCATACATAAACATTTACACCAATAATGCACACTTTCAAAGCATCAA
AACCTTACCTAAACACACACACACACACACAT
Found at i:10306357 original size:26 final size:26
Alignment explanation
Indices: 10306326--10306433 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
10306316 TGAAATGCCC
*
10306326 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
10306352 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
10306378 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
10306404 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
10306430 ATCA
1 ATCA
10306434 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:10310598 original size:27 final size:27
Alignment explanation
Indices: 10310545--10310598 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
10310535 TTAAACCACA
**
10310545 TATCTATTCTGGTGGCTTGACCACACT
1 TATCTATTCTGGCAGCTTGACCACACT
*
10310572 TATCTGATTCTGGCAGCTT-ACCGCACT
1 TATCT-ATTCTGGCAGCTTGACCACACT
10310599 ATTTTTGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (27 bp):
TATCTATTCTGGCAGCTTGACCACACT
Found at i:10312371 original size:34 final size:35
Alignment explanation
Indices: 10312326--10312392 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
10312316 TCTTTTTTTA
*
10312326 GTGTGTTTCGGATGGA-TAGATCTTATGAGCATTG
1 GTGTGTCTCGGATGGATTAGATCTTATGAGCATTG
*
10312360 GTGTGTCTCGGATGGATTAGCTCTTATGAGCAT
1 GTGTGTCTCGGATGGATTAGATCTTATGAGCAT
10312393 CTAAAGTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 15 0.50
35 15 0.50
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.37
Consensus pattern (35 bp):
GTGTGTCTCGGATGGATTAGATCTTATGAGCATTG
Found at i:10317629 original size:20 final size:17
Alignment explanation
Indices: 10317589--10317624 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10317579 TTAGTAAGTT
10317589 CATATGTAAATAATAAA
1 CATATGTAAATAATAAA
10317606 CATATGTAAATAATAAA
1 CATATGTAAATAATAAA
10317623 CA
1 CA
10317625 ACATAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (17 bp):
CATATGTAAATAATAAA
Found at i:10317996 original size:46 final size:46
Alignment explanation
Indices: 10317929--10318100 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
10317919 TGTAACCCGC
*
10317929 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
10317975 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
10318025 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
10318068 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTT
10318101 GGGACGCTCA
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.55
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:10331550 original size:13 final size:13
Alignment explanation
Indices: 10331532--10331557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10331522 TGTTCTGGTA
10331532 GTGTATCCATCCT
1 GTGTATCCATCCT
10331545 GTGTATCCATCCT
1 GTGTATCCATCCT
10331558 TATCGAACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (13 bp):
GTGTATCCATCCT
Found at i:10332861 original size:35 final size:34
Alignment explanation
Indices: 10332822--10332892 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 34
10332812 AGTTCACTCA
*
10332822 AAATCACAATATCTAAGAGCTTACAATAAAATTCG
1 AAATCACAATATCTAAGAGCCTACAATAAAA-TCG
*
10332857 AAATCACAATATTTAAGAGCCTACAATAAAATCG
1 AAATCACAATATCTAAGAGCCTACAATAAAATCG
10332891 AA
1 AA
10332893 GCTAGTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 5 0.15
35 29 0.85
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (34 bp):
AAATCACAATATCTAAGAGCCTACAATAAAATCG
Found at i:10335509 original size:17 final size:17
Alignment explanation
Indices: 10335489--10335539 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
10335479 TGGGTATCAA
10335489 ATATTGGAAAGTCAAAG
1 ATATTGGAAAGTCAAAG
**
10335506 ATA-TGGGTA-TC-AA-
1 ATATTGGAAAGTCAAAG
10335519 ATATTGGAAAGTCAAAG
1 ATATTGGAAAGTCAAAG
10335536 ATAT
1 ATAT
10335540 GGGTATCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 3 0.12
14 6 0.23
15 4 0.15
16 6 0.23
17 7 0.27
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (17 bp):
ATATTGGAAAGTCAAAG
Found at i:10335512 original size:30 final size:30
Alignment explanation
Indices: 10335478--10335556 Score: 140
Period size: 30 Copynumber: 2.6 Consensus size: 30
10335468 AGCATTATTC
10335478 ATGGGTATCAAATATTGGAAAGTCAAAGAT
1 ATGGGTATCAAATATTGGAAAGTCAAAGAT
10335508 ATGGGTATCAAATATTGGAAAGTCAAAGAT
1 ATGGGTATCAAATATTGGAAAGTCAAAGAT
*
10335538 ATGGGTATCGAGATATTGG
1 ATGGGTATC-AAATATTGG
10335557 CATAATAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 39 0.83
31 8 0.17
ACGTcount: A:0.39, C:0.06, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGGGTATCAAATATTGGAAAGTCAAAGAT
Found at i:10335518 original size:15 final size:15
Alignment explanation
Indices: 10335478--10335546 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
10335468 AGCATTATTC
*
10335478 ATGGGTATCAAATAT
1 ATGGGTATCAAAGAT
**
10335493 -TGGAAAGTCAAAGAT
1 ATGGGTA-TCAAAGAT
*
10335508 ATGGGTATCAAATAT
1 ATGGGTATCAAAGAT
**
10335523 -TGGAAAGTCAAAGAT
1 ATGGGTA-TCAAAGAT
10335538 ATGGGTATC
1 ATGGGTATC
10335547 GAGATATTGG
Statistics
Matches: 39, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
14 8 0.21
15 23 0.59
16 8 0.21
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.28
Consensus pattern (15 bp):
ATGGGTATCAAAGAT
Found at i:10343278 original size:21 final size:19
Alignment explanation
Indices: 10343240--10343285 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
10343230 ATGGGGGTAA
10343240 AGGGTGAGAAATAAAAGTTT
1 AGGG-GAGAAATAAAAGTTT
10343260 AGGGGAGAAAATAAAAAGTTT
1 AGGGGAG-AAAT-AAAAGTTT
*
10343281 TGGGG
1 AGGGG
10343286 GTTTGGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 3 0.13
20 8 0.35
21 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (19 bp):
AGGGGAGAAATAAAAGTTT
Found at i:10344266 original size:20 final size:19
Alignment explanation
Indices: 10344224--10344266 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
10344214 GATTACCTAA
* * *
10344224 TAAAACATTTTGTTTCATT
1 TAAAACATTTTGGTCCATG
10344243 TAAAACAATTTTGGTCCATG
1 TAAAAC-ATTTTGGTCCATG
10344263 TAAA
1 TAAA
10344267 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (19 bp):
TAAAACATTTTGGTCCATG
Found at i:10345092 original size:23 final size:22
Alignment explanation
Indices: 10345052--10345095 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
10345042 AACAGATTTA
10345052 ACATAATGATGAACTGATGAAC
1 ACATAATGATGAACTGATGAAC
* *
10345074 ACATAATATATGAATTGATGAA
1 ACATAAT-GATGAACTGATGAA
10345096 TTTAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (22 bp):
ACATAATGATGAACTGATGAAC
Found at i:10345459 original size:19 final size:19
Alignment explanation
Indices: 10345418--10345459 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
10345408 CAAATTTTTT
10345418 AAAAAAAAGTTATGTATGCA
1 AAAAAAAAGTTATGTAT-CA
*
10345438 AAAAAAAATTATATGTAT-A
1 AAAAAAAAGT-TATGTATCA
10345457 AAA
1 AAA
10345460 TACATGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (19 bp):
AAAAAAAAGTTATGTATCA
Found at i:10345948 original size:17 final size:17
Alignment explanation
Indices: 10345926--10345960 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10345916 TTGAAATTAA
*
10345926 AATGAGGACCAATGCAC
1 AATGAGGACAAATGCAC
*
10345943 AATGAGTACAAATGCAC
1 AATGAGGACAAATGCAC
10345960 A
1 A
10345961 GGGGTTAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (17 bp):
AATGAGGACAAATGCAC
Found at i:10346876 original size:21 final size:22
Alignment explanation
Indices: 10346851--10346897 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
10346841 TTTTTTGTTA
*
10346851 TTGGGCCAT-TTAATTTGTATT
1 TTGGGCCATGTTAATTTGAATT
* *
10346872 TTGGGCCTTGTTATTTTGAATT
1 TTGGGCCATGTTAATTTGAATT
10346894 TTGG
1 TTGG
10346898 ACTTGGGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.15, C:0.09, G:0.23, T:0.53
Consensus pattern (22 bp):
TTGGGCCATGTTAATTTGAATT
Found at i:10350793 original size:15 final size:15
Alignment explanation
Indices: 10350773--10350803 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10350763 ACCACTGTTG
10350773 TTATCCAAACTATTT
1 TTATCCAAACTATTT
10350788 TTATCCAAACTATTT
1 TTATCCAAACTATTT
10350803 T
1 T
10350804 GATGAATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATCCAAACTATTT
Found at i:10371055 original size:21 final size:20
Alignment explanation
Indices: 10371031--10371069 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
10371021 TTTTGTGATG
10371031 AAACAATATAAATGATATACA
1 AAACAATATAAAT-ATATACA
*
10371052 AAACAATATATATATATA
1 AAACAATATAAATATATA
10371070 TATGTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (20 bp):
AAACAATATAAATATATACA
Found at i:10372586 original size:20 final size:20
Alignment explanation
Indices: 10372546--10372583 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
10372536 AATTTGGGAC
10372546 TTTTTTATATATATTTTGGT
1 TTTTTTATATATATTTTGGT
*
10372566 TTTTTTAT-TATCTTTTGG
1 TTTTTTATATATATTTTGG
10372584 GTTCATAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.71
Consensus pattern (20 bp):
TTTTTTATATATATTTTGGT
Found at i:10384145 original size:49 final size:49
Alignment explanation
Indices: 10384084--10384183 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
10384074 ATGGAAAAAG
10384084 AAACAGAATAAGCTTTATAGCTTAGTAGGCCCATATAATTCAGATTTTA
1 AAACAGAATAAGCTTTATAGCTTAGTAGGCCCATATAATTCAGATTTTA
*
10384133 AAACAGAGTAAGCTTTATAGCTTAGTAGGCCCATATAATTCAGATTTTA
1 AAACAGAATAAGCTTTATAGCTTAGTAGGCCCATATAATTCAGATTTTA
10384182 AA
1 AA
10384184 TTCAGATTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (49 bp):
AAACAGAATAAGCTTTATAGCTTAGTAGGCCCATATAATTCAGATTTTA
Found at i:10384187 original size:13 final size:13
Alignment explanation
Indices: 10384169--10384195 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10384159 AGGCCCATAT
10384169 AATTCAGATTTTA
1 AATTCAGATTTTA
10384182 AATTCAGATTTTA
1 AATTCAGATTTTA
10384195 A
1 A
10384196 CTTACCTTTT
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:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
AATTCAGATTTTA
Found at i:10384439 original size:19 final size:19
Alignment explanation
Indices: 10384401--10384480 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
10384391 TAATCATATA
* *
10384401 AACAGTAATTCATTCG-AT
1 AACAGTAACTCATCCGTAT
10384419 AACAGTAACTCATCCGTAT
1 AACAGTAACTCATCCGTAT
* * *
10384438 AAATAGTACCTCATCCATAT
1 -AACAGTAACTCATCCGTAT
* * *
10384458 AACAATAATTCATCTGTAT
1 AACAGTAACTCATCCGTAT
10384477 AACA
1 AACA
10384481 CATAGCTTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
18 14 0.29
19 19 0.39
20 16 0.33
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.30
Consensus pattern (19 bp):
AACAGTAACTCATCCGTAT
Found at i:10384450 original size:20 final size:20
Alignment explanation
Indices: 10384422--10384459 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10384412 ATTCGATAAC
*
10384422 AGTAACTCATCCGTATAAAT
1 AGTAACTCATCCATATAAAT
*
10384442 AGTACCTCATCCATATAA
1 AGTAACTCATCCATATAA
10384460 CAATAATTCA
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:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (20 bp):
AGTAACTCATCCATATAAAT
Found at i:10384736 original size:26 final size:24
Alignment explanation
Indices: 10384626--10384740 Score: 103
Period size: 24 Copynumber: 4.7 Consensus size: 24
10384616 TCTATGATCG
*
10384626 GTAAGCTCCTT-CTGAGCTGATGGACA
1 GTAAGCT-CTTAC-GAGCTGA-GAACA
*
10384652 GTAAGCTCATT--GAGCT-AAAACA
1 GTAAGCTC-TTACGAGCTGAGAACA
*
10384674 GTAAGCTCTTACAAGCTGAGAACA
1 GTAAGCTCTTACGAGCTGAGAACA
*
10384698 GTAAGCTCTTACGAGCTGATATATCA
1 GTAAGCTCTTACGAGCTGAGA-A-CA
*
10384724 GTAAGCTCATACGAGCT
1 GTAAGCTCTTACGAGCT
10384741 ACAGTGAGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.03
22 11 0.14
23 5 0.07
24 29 0.38
25 2 0.03
26 27 0.36
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (24 bp):
GTAAGCTCTTACGAGCTGAGAACA
Found at i:10389493 original size:19 final size:19
Alignment explanation
Indices: 10389471--10389595 Score: 67
Period size: 19 Copynumber: 6.4 Consensus size: 19
10389461 AAAAAATAAA
*
10389471 AATATATATAATAAAATGT
1 AATATATATAATAAAATAT
*
10389490 AATATAAATATATAAGAATAT
1 AATATATATA-ATAA-AATAT
* *
10389511 AATAGATATAATATAA-AT
1 AATATATATAATAAAATAT
* * *
10389529 AACATGTA-AA-ACAATAT
1 AATATATATAATAAAATAT
*
10389546 ATATAAATAATTAATAAATATAT
1 A-ATATAT-A-TAATAAA-ATAT
* * * *
10389569 AATATATGTGAGAATATAT
1 AATATATATAATAAAATAT
10389588 AATATATA
1 AATATATA
10389596 AAAATAATAA
Statistics
Matches: 78, Mismatches: 19, Indels: 18
0.68 0.17 0.16
Matches are distributed among these distances:
16 3 0.04
17 5 0.06
18 10 0.13
19 23 0.29
20 11 0.14
21 14 0.18
22 7 0.09
23 5 0.06
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (19 bp):
AATATATATAATAAAATAT
Found at i:10389561 original size:47 final size:47
Alignment explanation
Indices: 10389465--10389567 Score: 113
Period size: 46 Copynumber: 2.2 Consensus size: 47
10389455 AAAAATAAAA
* * *
10389465 AATAAAAAT-ATATATAATAAAATGTAATATAAATATATAAGAATAT
1 AATAAATATAATATATAATAAAATGTAAAACAAATATATAAGAATAT
* * *
10389511 AATAGATATAATATA-AATAACATGTAAAACAATATATATAAATAAT-T
1 AATAAATATAATATATAATAAAATGTAAAACAA-ATATAT-AAGAATAT
10389558 AATAAATATA
1 AATAAATATA
10389568 TAATATATGT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
46 21 0.45
47 21 0.45
48 5 0.11
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (47 bp):
AATAAATATAATATATAATAAAATGTAAAACAAATATATAAGAATAT
Found at i:10389565 original size:21 final size:22
Alignment explanation
Indices: 10389470--10389569 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 22
10389460 TAAAAAATAA
*
10389470 AAATATATATAATAAAATGTAAT
1 AAATATATATAA-ATAATGTAAT
* *
10389493 ATAA-ATATAT-AAGAATATAAT
1 A-AATATATATAAATAATGTAAT
* *
10389514 AGATATAATATAAATAACATGTAAA
1 AAATAT-ATATAAAT-A-ATGTAAT
10389539 ACAATATATATAAATAAT-TAAT
1 A-AATATATATAAATAATGTAAT
10389561 AAATATATA
1 AAATATATA
10389570 ATATATGTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.02
21 19 0.31
22 9 0.15
23 11 0.18
24 4 0.06
25 14 0.23
26 4 0.06
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
AAATATATATAAATAATGTAAT
Found at i:10390210 original size:8 final size:8
Alignment explanation
Indices: 10390197--10390224 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
10390187 GGCCACACAC
10390197 CGCCCACG
1 CGCCCACG
10390205 CGCCCACG
1 CGCCCACG
10390213 CGCCCACG
1 CGCCCACG
10390221 CGCC
1 CGCC
10390225 ACCCTAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.64, G:0.25, T:0.00
Consensus pattern (8 bp):
CGCCCACG
Found at i:10395412 original size:28 final size:28
Alignment explanation
Indices: 10395349--10395474 Score: 227
Period size: 28 Copynumber: 4.5 Consensus size: 28
10395339 ATATTAAGTC
*
10395349 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
10395376 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
10395404 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
10395432 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
10395460 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10395475 GTACAATTTA
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.23
28 73 0.77
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:10400957 original size:29 final size:28
Alignment explanation
Indices: 10400921--10400998 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
10400911 TCATGAGATT
10400921 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
10400951 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
10400978 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
10400999 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:10401272 original size:173 final size:174
Alignment explanation
Indices: 10400951--10401277 Score: 566
Period size: 173 Copynumber: 1.9 Consensus size: 174
10400941 AAATTGTACA
* *
10400951 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
10401016 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
10401081 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
10401125 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
10401190 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
10401254 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
10401278 ACCTTGAGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
173 80 0.56
174 64 0.44
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:10405139 original size:16 final size:16
Alignment explanation
Indices: 10405102--10405140 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
10405092 TCAAAAATAA
*
10405102 AATTTTAAAAATTATG
1 AATTTTAAAAAATATG
10405118 AA-TTTAAAAAATATG
1 AATTTTAAAAAATATG
10405133 AATTTTAA
1 AATTTTAA
10405141 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
AATTTTAAAAAATATG
Found at i:10410621 original size:27 final size:27
Alignment explanation
Indices: 10410583--10410637 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
10410573 CCAATGAAGG
10410583 AACTCACTCCTTTTTCTCTGGACTTAT
1 AACTCACTCCTTTTTCTCTGGACTTAT
10410610 AACTCACTCCTTTTTCTCTGGACTTAT
1 AACTCACTCCTTTTTCTCTGGACTTAT
10410637 A
1 A
10410638 TTTATCTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.29, G:0.07, T:0.44
Consensus pattern (27 bp):
AACTCACTCCTTTTTCTCTGGACTTAT
Found at i:10411750 original size:33 final size:35
Alignment explanation
Indices: 10411713--10411810 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 35
10411703 ATTGTTATAT
10411713 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTACTTAA
* *
10411746 TTAAAT-TTTATAA-ATAATTCATATTTATTACTTAA
1 TTAAATATTTAAAATATAATT--TATATATTACTTAA
*
10411781 --AAATATTTAAAATTTATATTTCATATATTA
1 TTAAATATTTAAAATATA-ATTT-ATATATTA
10411811 AAATATTAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.15
35 12 0.23
36 3 0.06
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTACTTAA
Found at i:10411800 original size:30 final size:30
Alignment explanation
Indices: 10411761--10411817 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
10411751 TTTTATAAAT
10411761 AATTCATATTT-AT-TACTTAAAAATATTTAA
1 AATTCATATTTCATATA-TT-AAAATATTTAA
*
10411791 AATTTATATTTCATATATTAAAATATT
1 AATTCATATTTCATATATTAAAATATT
10411818 AACAAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTCATATTTCATATATTAAAATATTTAA
Found at i:10412064 original size:34 final size:34
Alignment explanation
Indices: 10412021--10412088 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
10412011 AGCATTTTTT
10412021 CACTATACTTCTCAAAAGCACTGTCAAATTAGCC
1 CACTATACTTCTCAAAAGCACTGTCAAATTAGCC
10412055 CACTATACTTCTCAAAAGCACTGTCAAATTAGCC
1 CACTATACTTCTCAAAAGCACTGTCAAATTAGCC
10412089 TTCACATCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.26
Consensus pattern (34 bp):
CACTATACTTCTCAAAAGCACTGTCAAATTAGCC
Found at i:10415141 original size:13 final size:13
Alignment explanation
Indices: 10415123--10415148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10415113 GACCCTAAAG
10415123 TTAGTGTGTTGAA
1 TTAGTGTGTTGAA
10415136 TTAGTGTGTTGAA
1 TTAGTGTGTTGAA
10415149 AAATGAGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
TTAGTGTGTTGAA
Found at i:10424817 original size:22 final size:22
Alignment explanation
Indices: 10424789--10424835 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
10424779 CGACACCTCG
*
10424789 AAAGAGGTTTATTAATTTTTCA
1 AAAGAGGTTTATTAATTCTTCA
*
10424811 AAAGAGGTTTATTGATTCTTCA
1 AAAGAGGTTTATTAATTCTTCA
10424833 AAA
1 AAA
10424836 TCGAGAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
AAAGAGGTTTATTAATTCTTCA
Found at i:10428455 original size:21 final size:21
Alignment explanation
Indices: 10428431--10428567 Score: 132
Period size: 21 Copynumber: 6.6 Consensus size: 21
10428421 GTGTTTTACT
*
10428431 TTCTGTTTAGCTCTTTTGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * *
10428452 TTCTGTTTAACTCATATGAGT
1 TTCTGTTTAGCTCTTATGAGC
* *
10428473 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTTAGCTCTTATGAGC
* * * * *
10428494 TTCTGTTAAACCCTTATGGGT
1 TTCTGTTTAGCTCTTATGAGC
*
10428515 TTTTG-TTAGCTCTTATGAGC
1 TTCTGTTTAGCTCTTATGAGC
* *
10428535 TTCTATTTAGCTCTCATGAGC
1 TTCTGTTTAGCTCTTATGAGC
*
10428556 TTCTGTTCAGCT
1 TTCTGTTTAGCT
10428568 TTCAGGCTTC
Statistics
Matches: 89, Mismatches: 26, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
20 13 0.15
21 76 0.85
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTATGAGC
Found at i:10428477 original size:42 final size:41
Alignment explanation
Indices: 10428430--10428567 Score: 152
Period size: 42 Copynumber: 3.3 Consensus size: 41
10428420 CGTGTTTTAC
* *
10428430 TTTCTGTTTAGCTCTTTTGAGCTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTC-TATGAG
* * * *
10428472 TTTCTGTTCAGCTCTTACGAGCTTCTGTTAAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTC-TATGAG
* * *
10428514 TTTTTGTT-AGCTCTTATGAGCTTCTATTTAGCTCTCATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCT-ATGAG
*
10428555 CTTCTGTTCAGCT
1 TTTCTGTTCAGCT
10428568 TTCAGGCTTC
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 31 0.40
42 46 0.59
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.46
Consensus pattern (41 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTTAACTCTATGAG
Found at i:10435074 original size:20 final size:19
Alignment explanation
Indices: 10435038--10435082 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
10435028 CCTTTATTTC
10435038 TTTTTATAAAAAGATATAA
1 TTTTTATAAAAAGATATAA
* *
10435057 TTTTTATTAAATGTATATAA
1 TTTTTATAAAAAG-ATATAA
*
10435077 ATTTTA
1 TTTTTA
10435083 AATTTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTTTATAAAAAGATATAA
Found at i:10435136 original size:21 final size:21
Alignment explanation
Indices: 10435082--10435139 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
10435072 TATAAATTTT
10435082 AAAT-TTTTATAAAAAT-AAAA
1 AAATATTTTA-AAAAATAAAAA
* * *
10435102 AAATAATCTCAAAAATAAAAA
1 AAATATTTTAAAAAATAAAAA
10435123 AAATATTTTAAAAAATA
1 AAATATTTTAAAAAATA
10435140 TAATTAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATATTTTAAAAAATAAAAA
Found at i:10449155 original size:22 final size:22
Alignment explanation
Indices: 10449130--10449171 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10449120 TTAAAAGAAA
* *
10449130 CATAATTATTCAATTAATATCT
1 CATAACTATTCAAGTAATATCT
10449152 CATAACTATTCAAGTAATAT
1 CATAACTATTCAAGTAATAT
10449172 TACTTTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (22 bp):
CATAACTATTCAAGTAATATCT
Found at i:10456612 original size:17 final size:17
Alignment explanation
Indices: 10456585--10456625 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
10456575 TAGCTGTCAC
*
10456585 ATGATTTAAATTAAT-T
1 ATGAATTAAATTAATAT
10456601 ATTGAATTAAATTAATAT
1 A-TGAATTAAATTAATAT
10456619 ATGAATT
1 ATGAATT
10456626 TGATTCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.86
18 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
ATGAATTAAATTAATAT
Found at i:10457650 original size:34 final size:34
Alignment explanation
Indices: 10457607--10457675 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
10457597 TGTGTTAAAG
10457607 TTAGTGCAGGATCATATCATCATGACCAAATAAT
1 TTAGTGCAGGATCATATCATCATGACCAAATAAT
10457641 TTAGTGCAGGATCATATCATCATGACCAAATAAT
1 TTAGTGCAGGATCATATCATCATGACCAAATAAT
10457675 T
1 T
10457676 GTCGTTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.30
Consensus pattern (34 bp):
TTAGTGCAGGATCATATCATCATGACCAAATAAT
Found at i:10463091 original size:16 final size:17
Alignment explanation
Indices: 10463067--10463101 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
10463057 ATATAAAAAT
*
10463067 ATGGTAATAATT-TATA
1 ATGGCAATAATTGTATA
10463083 ATGGCAATAATTGTATA
1 ATGGCAATAATTGTATA
10463100 AT
1 AT
10463102 TTTACGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (17 bp):
ATGGCAATAATTGTATA
Found at i:10464107 original size:6 final size:6
Alignment explanation
Indices: 10464095--10464155 Score: 79
Period size: 6 Copynumber: 10.2 Consensus size: 6
10464085 TGCAAATGGA
* * *
10464095 TCATTT CCATTT CCA-TT TCAATTT CCATTT TCATTT TCATTT TCATTT
1 TCATTT TCATTT TCATTT TC-ATTT TCATTT TCATTT TCATTT TCATTT
10464143 TCATTT TCATTT T
1 TCATTT TCATTT T
10464156 TGGAAACCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
5 3 0.06
6 43 0.88
7 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (6 bp):
TCATTT
Found at i:10466531 original size:18 final size:18
Alignment explanation
Indices: 10466508--10466542 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10466498 AAGTTAAACG
10466508 AATCGAATTATTCGAGTT
1 AATCGAATTATTCGAGTT
*
10466526 AATCGAGTTATTCGAGT
1 AATCGAATTATTCGAGT
10466543 CAACTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (18 bp):
AATCGAATTATTCGAGTT
Found at i:10469045 original size:84 final size:85
Alignment explanation
Indices: 10468894--10469072 Score: 211
Period size: 84 Copynumber: 2.1 Consensus size: 85
10468884 ATAAATTGTC
* * *
10468894 ATGTTATTATTCACCTATGGTGCATGAGACTTTACACCGATAGTACATCAAACATTTTCCA-TTT
1 ATGTTATTATTCACCTATGGTGCATGAGACTTTACACCGACAGTACATCAAACATTCTCCACCTT
*
10468958 TTTTAATGCATGTCATATTT
66 TTTTAATGCATGCCATATTT
* * * * **
10468978 ATGTTATTATTCACTTATGGTGCATTAGAC-TTACACACTGACCGTATATCAAGTATTCTCC-CC
1 ATGTTATTATTCACCTATGGTGCATGAGACTTTACAC-C-GACAGTACATCAAACATTCTCCACC
10469041 TTTTTTTTAATGCATGCCATATTT
64 --TTTTTTAATGCATGCCATATTT
10469065 ATGTTATT
1 ATGTTATT
10469073 TTTGTATCAT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
83 6 0.08
84 29 0.36
85 16 0.20
87 29 0.36
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (85 bp):
ATGTTATTATTCACCTATGGTGCATGAGACTTTACACCGACAGTACATCAAACATTCTCCACCTT
TTTTAATGCATGCCATATTT
Found at i:10469069 original size:87 final size:84
Alignment explanation
Indices: 10468894--10469072 Score: 225
Period size: 87 Copynumber: 2.1 Consensus size: 84
10468884 ATAAATTGTC
* *
10468894 ATGTTATTATTCACCTATGGTGCATGAGACTTTACACCGATAGTACATCAAACATTTTCCATTTT
1 ATGTTATTATTCACCTATGGTGCATGAGACTTTACACCGACAGTACATCAAACATTTCCCATTTT
*
10468959 TTTAATGCATGTCATATTT
66 TTTAATGCATGCCATATTT
* * * * ** *
10468978 ATGTTATTATTCACTTATGGTGCATTAGAC-TTACACACTGACCGTATATCAAGTATTCTCCCCT
1 ATGTTATTATTCACCTATGGTGCATGAGACTTTACAC-C-GACAGTACATCAAACATT-T-CCCA
10469042 TTTTTTTAATGCATGCCATATTT
62 TTTTTTTAATGCATGCCATATTT
10469065 ATGTTATT
1 ATGTTATT
10469073 TTTGTATCAT
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
83 6 0.07
84 29 0.36
85 13 0.16
86 1 0.01
87 32 0.40
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (84 bp):
ATGTTATTATTCACCTATGGTGCATGAGACTTTACACCGACAGTACATCAAACATTTCCCATTTT
TTTAATGCATGCCATATTT
Found at i:10480421 original size:53 final size:53
Alignment explanation
Indices: 10480353--10480458 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 53
10480343 ACAAGTAAGC
* *
10480353 TTTACTAAAGTTTAGTAAGTTCAACGGTTAAAACGATAACCTTACCATATAAA
1 TTTACTAAAGTTTAGTAAGCTCAACGGTTAAAACGATAAACTTACCATATAAA
* *
10480406 TTTACTAAA-TCTTAGTAAGCTCAATGGTTAAAATGATAAACTTACCATATAAA
1 TTTACTAAAGT-TTAGTAAGCTCAACGGTTAAAACGATAAACTTACCATATAAA
10480459 CACATAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.02
53 47 0.98
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.33
Consensus pattern (53 bp):
TTTACTAAAGTTTAGTAAGCTCAACGGTTAAAACGATAAACTTACCATATAAA
Found at i:10482104 original size:53 final size:53
Alignment explanation
Indices: 10481925--10482128 Score: 183
Period size: 53 Copynumber: 3.8 Consensus size: 53
10481915 AGGGTTTAAG
* * * * * * *
10481925 GATACCAAGTAGGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGCAAA
* * * * * * * *
10481979 GAAATCATGTAAGACCATGTCAATACATGGCATTGATAAACTACTATAAGGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGCAAA
* * * *
10482034 GATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGCAAT
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAA
* * *
10482087 GATACCACGTAAGACCATGTCAAGACATGGTAATGGTAAGTT
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
10482129 TAATAAAGAA
Statistics
Matches: 117, Mismatches: 31, Indels: 5
0.76 0.20 0.03
Matches are distributed among these distances:
53 45 0.38
54 33 0.28
55 39 0.33
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (53 bp):
GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAA
Found at i:10486533 original size:91 final size:90
Alignment explanation
Indices: 10486378--10486558 Score: 326
Period size: 91 Copynumber: 2.0 Consensus size: 90
10486368 TCCTCGTTTG
*
10486378 GCACAATTTCACAAGCATACTTGCTAAGATTTACAAACTCTCTTTCATACTCAGCTACTAATTTA
1 GCACAATTTCACAAGCATACTTGCTAAGATGTACAAACTCTCTTTCATACTCAGCTACTAATTTA
*
10486443 TTTCTTTTTTTTTAGTTCAAGAAATT
66 TTTC-TTTTCTTTAGTTCAAGAAATT
10486469 GCACAATTTCACAAGCATACTTGCTAAGATGTACAAACTCTCTTTCATACTCAGCTACTAATTTA
1 GCACAATTTCACAAGCATACTTGCTAAGATGTACAAACTCTCTTTCATACTCAGCTACTAATTTA
*
10486534 TTTCTTTTCTTTAGTTTAAGAAATT
66 TTTCTTTTCTTTAGTTCAAGAAATT
10486559 TTTTTTTCGA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 19 0.22
91 68 0.78
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (90 bp):
GCACAATTTCACAAGCATACTTGCTAAGATGTACAAACTCTCTTTCATACTCAGCTACTAATTTA
TTTCTTTTCTTTAGTTCAAGAAATT
Found at i:10493423 original size:22 final size:21
Alignment explanation
Indices: 10493395--10493435 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
10493385 CCTTGGATGT
10493395 TTTTAA-GTTGTTTGTAAGATTC
1 TTTTAAGGTT-TTTG-AAGATTC
10493417 TTTTAAGGTTTTTGAAGAT
1 TTTTAAGGTTTTTGAAGAT
10493436 GGGTAGTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.54
Consensus pattern (21 bp):
TTTTAAGGTTTTTGAAGATTC
Found at i:10498707 original size:30 final size:30
Alignment explanation
Indices: 10498671--10498733 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
10498661 ACTTAACAAT
* *
10498671 CAAATGTCTCTACAATAATAATAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
10498701 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
10498731 CAA
1 CAA
10498734 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:10498788 original size:22 final size:22
Alignment explanation
Indices: 10498763--10498805 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10498753 TATCCAAACA
10498763 ATAATAACAAAATAGTAGCAAT
1 ATAATAACAAAATAGTAGCAAT
** *
10498785 ATAATAGTAAAATGGTAGCAA
1 ATAATAACAAAATAGTAGCAA
10498806 AATTGAGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAT
Found at i:10499679 original size:18 final size:18
Alignment explanation
Indices: 10499656--10499703 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
10499646 ACATTTAATT
*
10499656 AATTTTTTAAAATTTAAA
1 AATTTTTTAAAATATAAA
**
10499674 AATTTTAAAAAATATAAA
1 AATTTTTTAAAATATAAA
*
10499692 AATATTTTAAAA
1 AATTTTTTAAAA
10499704 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTTTTAAAATATAAA
Found at i:10499700 original size:20 final size:18
Alignment explanation
Indices: 10499664--10499713 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 18
10499654 TTAATTTTTT
*
10499664 AAAATTTAAAAATTTTAA
1 AAAATTAAAAAATTTTAA
10499682 AAAATATAAAAATATTTTAA
1 AAAAT-TAAAAA-ATTTTAA
10499702 AAAATTAAAAAA
1 AAAATTAAAAAA
10499714 ATCATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 6 0.21
19 11 0.38
20 12 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATTAAAAAATTTTAA
Found at i:10499712 original size:9 final size:9
Alignment explanation
Indices: 10499664--10499715 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
10499654 TTAATTTTTT
10499664 AAAATTTAA
1 AAAATTTAA
*
10499673 AAATTTTAA
1 AAAATTTAA
*
10499682 AAAATATAA
1 AAAATTTAA
10499691 AAATATTTTAA
1 AAA-A-TTTAA
*
10499702 AAAATTAAA
1 AAAATTTAA
10499711 AAAAT
1 AAAAT
10499716 CATTAAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 27 0.75
10 2 0.06
11 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATTTAA
Found at i:10499721 original size:20 final size:20
Alignment explanation
Indices: 10499671--10499723 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
10499661 TTTAAAATTT
*
10499671 AAAAATTTTAAAAAATATAA
1 AAAAATATTAAAAAATATAA
* *
10499691 AAATATTTTAAAAAAT-TAA
1 AAAAATATTAAAAAATATAA
10499710 AAAAATCATTAAAA
1 AAAAAT-ATTAAAA
10499724 TCATTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATATTAAAAAATATAA
Found at i:10506928 original size:8 final size:8
Alignment explanation
Indices: 10506915--10506940 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
10506905 AGAAATTAAA
10506915 AAAAAAAG
1 AAAAAAAG
10506923 AAAAAAAG
1 AAAAAAAG
10506931 AAAAAAAG
1 AAAAAAAG
10506939 AA
1 AA
10506941 GAGAAGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:10507018 original size:100 final size:99
Alignment explanation
Indices: 10506844--10507120 Score: 429
Period size: 96 Copynumber: 2.8 Consensus size: 99
10506834 AAGACTATAA
* * * *
10506844 AAGTTGATGGCTTCTGAAAGGGCATTGATGAATCAAAAGTTTTATTTCTTATATATGTGGGAG-A
1 AAGTTGATGGCTTCTTAAAGGACATTGATGAATCAAAAATTTTATTTCTTATATATGTGGGGGAA
*
10506908 AATTAAAAAAAAAAGAAAAAAAGAAAAAAAGAAGAG
66 AATT-GAAAAAAAAGAAAAAAAG-AAAAAAGAAGAG
*
10506944 AAGTTGATGGCTTCTTAAAGGACATTGATGAATCAAAAATTTTATTTTTTATATATGTGGGGGAA
1 AAGTTGATGGCTTCTTAAAGGACATTGATGAATCAAAAATTTTATTTCTTATATATGTGGGGGAA
10507009 AATTG--AAAAAA-AAAAAAAGAAAAAAGAAGAG
66 AATTGAAAAAAAAGAAAAAAAGAAAAAAGAAGAG
*
10507040 AAGTTGATGGCTTCTTAAAGGATATTGATGAATCAAAAATTTTATTTCTTATATATGT-GGGGAA
1 AAGTTGATGGCTTCTTAAAGGACATTGATGAATCAAAAATTTTATTTCTTATATATGTGGGGGAA
*
10507104 AATTGAAAAAAGAGAAA
66 AATTGAAAAAAAAGAAA
10507121 GGAGGATATG
Statistics
Matches: 164, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
95 11 0.07
96 68 0.41
97 13 0.08
98 9 0.05
100 58 0.35
101 5 0.03
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.29
Consensus pattern (99 bp):
AAGTTGATGGCTTCTTAAAGGACATTGATGAATCAAAAATTTTATTTCTTATATATGTGGGGGAA
AATTGAAAAAAAAGAAAAAAAGAAAAAAGAAGAG
Found at i:10511543 original size:24 final size:24
Alignment explanation
Indices: 10511498--10511544 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10511488 ATAAAAACTA
*
10511498 AACCCCCAAAACCTGAAAACAAAG
1 AACCCCCAAAACATGAAAACAAAG
*
10511522 AACCCTCAAAACAT-AAACACAAA
1 AACCCCCAAAACATGAAA-ACAAA
10511545 ATTATCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.57, C:0.32, G:0.04, T:0.06
Consensus pattern (24 bp):
AACCCCCAAAACATGAAAACAAAG
Found at i:10517854 original size:46 final size:46
Alignment explanation
Indices: 10517787--10517915 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
10517777 TGTAACTCGC
* * * *
10517787 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
10517833 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
10517879 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
10517916 TGCTCAACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:10517934 original size:46 final size:45
Alignment explanation
Indices: 10517795--10517934 Score: 131
Period size: 46 Copynumber: 3.0 Consensus size: 45
10517785 GCCCATAAGC
* ** * *
10517795 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
*** *
10517841 GAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T-AGT
*
10517887 GAACTCGGACTCAACTCAATGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCTAGT
10517933 GA
1 GA
10517935 CATGTCACTT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
46 78 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCTAGT
Found at i:10533048 original size:2 final size:2
Alignment explanation
Indices: 10533041--10533072 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10533031 AAAATTGAAA
10533041 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10533073 GAGGATATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10545565 original size:38 final size:38
Alignment explanation
Indices: 10545509--10545631 Score: 203
Period size: 38 Copynumber: 3.3 Consensus size: 38
10545499 AGGCCTAGAT
* *
10545509 ATAT-TTCCAGCACATAGCCTGCGGACCTCAAGTTCGG
1 ATATGTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGG
*
10545546 ATATGTTCCATCACGTAGCCTGCGGACCTCAAGTCCGG
1 ATATGTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGG
*
10545584 ATATGTTCCAGCACGTAGCCTGCGGACCTCAAGTCCAG
1 ATATGTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGG
10545622 ATATGTTCCA
1 ATATGTTCCA
10545632 AATACCATGC
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
37 4 0.05
38 76 0.95
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (38 bp):
ATATGTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGG
Found at i:10546703 original size:4 final size:4
Alignment explanation
Indices: 10546694--10546720 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10546684 CAAACACAAA
10546694 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
10546721 AACCTTGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:10546801 original size:22 final size:22
Alignment explanation
Indices: 10546761--10546802 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10546751 TGGCCACCCA
*
10546761 CCTTGGCCACCAACTCCACCAC
1 CCTTGGCCACCAACACCACCAC
10546783 CCTTGGCCACCTAA-ACCACC
1 CCTTGGCCACC-AACACCACC
10546803 CCAACCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.52, G:0.10, T:0.14
Consensus pattern (22 bp):
CCTTGGCCACCAACACCACCAC
Found at i:10546907 original size:23 final size:22
Alignment explanation
Indices: 10546881--10546924 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
10546871 TTGGTTTTTT
10546881 GGAGAAGGATTGTTCTTTGTTTC
1 GGAGAAGG-TTGTTCTTTGTTTC
* * *
10546904 GGAGGAGGTTTTTTTTTGTTT
1 GGAGAAGGTTGTTCTTTGTTT
10546925 TTTGGAGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.14, C:0.05, G:0.32, T:0.50
Consensus pattern (22 bp):
GGAGAAGGTTGTTCTTTGTTTC
Found at i:10546933 original size:21 final size:20
Alignment explanation
Indices: 10546907--10546946 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
10546897 TTGTTTCGGA
*
10546907 GGAGGTTTTTTTTTGTTTTTT
1 GGAGGTGTTTTTTT-TTTTTT
10546928 GGAGGTGTTTTTTTTTTTT
1 GGAGGTGTTTTTTTTTTTT
10546947 GGAAAGAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.05, C:0.00, G:0.25, T:0.70
Consensus pattern (20 bp):
GGAGGTGTTTTTTTTTTTTT
Found at i:10547081 original size:20 final size:20
Alignment explanation
Indices: 10547056--10547103 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
10547046 TCTTTGTTTG
10547056 TTTATTGTT-TTCCTTTCAAT
1 TTTATT-TTCTTCCTTTCAAT
10547076 TTTATTTTCTTCCTTTCAAT
1 TTTATTTTCTTCCTTTCAAT
10547096 TTTATTTT
1 TTTATTTT
10547104 GTTTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTATTTTCTTCCTTTCAAT
Found at i:10547311 original size:3 final size:3
Alignment explanation
Indices: 10547297--10547379 Score: 59
Period size: 3 Copynumber: 27.3 Consensus size: 3
10547287 GAGCTTTGTT
* *
10547297 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
10547341 TT- TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA T
10547380 ATATGCCCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 7 0.11
3 49 0.75
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:10547357 original size:21 final size:18
Alignment explanation
Indices: 10547297--10547379 Score: 87
Period size: 18 Copynumber: 4.4 Consensus size: 18
10547287 GAGCTTTGTT
*
10547297 TTATTATTTTATTATTTTTA
1 TTATTA-TTTA-TATTATTA
*
10547317 CTATTATTTATATTATTA
1 TTATTATTTATATTATTA
*
10547335 TTATTATTTCTCATGTATATA
1 TTATTATTTAT-AT-TAT-TA
10547356 TTATTATTTATATTATTA
1 TTATTATTTATATTATTA
10547374 -TATTAT
1 TTATTAT
10547380 ATATGCCCTC
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.11
18 18 0.33
19 9 0.16
20 10 0.18
21 12 0.22
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (18 bp):
TTATTATTTATATTATTA
Found at i:10547382 original size:27 final size:26
Alignment explanation
Indices: 10547296--10547383 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 26
10547286 AGAGCTTTGT
* * *
10547296 TTTATTATTTTATTATTTTTACTATTA
1 TTTA-TATATTATTATTTATATTATTA
* *
10547323 TTTATATTATTATTA-TTAT-TTCTCA
1 TTTATA-TATTATTATTTATATTATTA
*
10547348 TGTATATATTATTATTTATATTATTA
1 TTTATATATTATTATTTATATTATTA
10547374 TATTATATAT
1 T-TTATATAT
10547384 GCCCTCTCCA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
24 8 0.17
25 12 0.25
26 10 0.21
27 18 0.38
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTATATATTATTATTTATATTATTA
Found at i:10550205 original size:19 final size:19
Alignment explanation
Indices: 10550183--10550229 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
10550173 CTTCCTTTCT
10550183 TTTGCATT-CATTCCATACA
1 TTTGCATTACATTCCA-ACA
* *
10550202 TTTGCATTATATTGCAACA
1 TTTGCATTACATTCCAACA
10550221 TTTGCATTA
1 TTTGCATTA
10550230 AACTTTCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTCCAACA
Found at i:10553032 original size:6 final size:6
Alignment explanation
Indices: 10553021--10553053 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
10553011 GTTATATGGA
10553021 AAAGGC AAAGGC AAAGGC AAAGGC AAAGGC AAA
1 AAAGGC AAAGGC AAAGGC AAAGGC AAAGGC AAA
10553054 AAAAAAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAGGC
Found at i:10554337 original size:66 final size:66
Alignment explanation
Indices: 10554237--10554363 Score: 236
Period size: 66 Copynumber: 1.9 Consensus size: 66
10554227 CATTCATATA
*
10554237 ATAACACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACACATT
1 ATAACACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATCATTTGACACATT
10554302 C
66 C
*
10554303 ATAACACATCTAGTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATCATTTGACA
1 ATAACACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATCATTTGACA
10554364 TAAGCATAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (66 bp):
ATAACACATCTAGTTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATCATTTGACACATT
C
Found at i:10554811 original size:218 final size:218
Alignment explanation
Indices: 10554428--10554933 Score: 847
Period size: 218 Copynumber: 2.3 Consensus size: 218
10554418 TTCACAAGCC
* * *
10554428 TTAAGCCCCTAAGCAATAGGGTAACAGGCTAAAGATTTACAGATCTTAACCCCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAGATTTACAGATCTTAACCCCCTAAGCAGTAGG
**
10554493 GAAACAGATCGAAGACGAAGGGTCTTAAACCCCTAATCGGTAGGGTAACAGACCGAATTGTAGAT
66 GAAACAGATCGAAGACGAAGGGTCTTAAACCCCTAATCGGTAGGGTAACAGACCGAATTACAGAT
* *
10554558 CTTATCTCCCTAAGCAGTAGGGAAACAGATCGAAGATGAAGGTCTTAACCCCCTAAGCAGTAGGG
131 CTTATCTCCCTAAGCAGTAGGAAAACAGATCGAAGATGAAGATCTTAACCCCCTAAGCAGTAGGG
*
10554623 AAACAGATCGAAGATGATGGGCT
196 AAACAGATCAAAGATGATGGGCT
*
10554646 TTAACCCCCTAAGCAGTAGGGTAACATGCTAAAGATTTACAGATCTTAACCCCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAGATTTACAGATCTTAACCCCCTAAGCAGTAGG
**
10554711 GAAACAGATCGAAGACGAAGGGTCTTAAACCTGTAATCGGTAGGGTAACAGACCGAATTACAGAT
66 GAAACAGATCGAAGACGAAGGGTCTTAAACCCCTAATCGGTAGGGTAACAGACCGAATTACAGAT
10554776 CTTATCTCCCTAAGCAGTAGGAAAACAGATCGAAGATGAAGATCTTAACCCCCTAAGCAGTAGGG
131 CTTATCTCCCTAAGCAGTAGGAAAACAGATCGAAGATGAAGATCTTAACCCCCTAAGCAGTAGGG
10554841 AAACAGATCAAAGATGATGGGCT
196 AAACAGATCAAAGATGATGGGCT
* * *
10554864 TTAACCCCCTAAGCAGTAGAGTAACAAGC-CAA-ATTTACA-AGCCTTAACCCCCTAAGCAGTAG
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAGATTTACAGA-TCTTAACCCCCTAAGCAGTAG
*
10554926 GGTAACAG
65 GGAAACAG
10554934 GCTGAAGATT
Statistics
Matches: 272, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
215 1 0.00
216 34 0.12
217 2 0.01
218 235 0.86
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (218 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCTAAAGATTTACAGATCTTAACCCCCTAAGCAGTAGG
GAAACAGATCGAAGACGAAGGGTCTTAAACCCCTAATCGGTAGGGTAACAGACCGAATTACAGAT
CTTATCTCCCTAAGCAGTAGGAAAACAGATCGAAGATGAAGATCTTAACCCCCTAAGCAGTAGGG
AAACAGATCAAAGATGATGGGCT
Found at i:10554872 original size:44 final size:44
Alignment explanation
Indices: 10554473--10555153 Score: 396
Period size: 44 Copynumber: 15.6 Consensus size: 44
10554463 TTTACAGATC
* * *
10554473 TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAG-GGT
1 TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* * * * * * *
10554516 CTTAAACCCCTAATCGGTAGGGTAACAGACCGAA-TTG-T-AGAT
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* * *
10554558 CTTATCTCCCTAAGCAGTAGGGAAACAGATCGAAGATGA--AGGT
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
*
10554601 CTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCT
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* * * * * *
10554646 TTAACCCCCTAAGCAGTAGGGTAACATGCT-AAAGAT-TTACAGAT
1 TTAACCCCCTAAGCAGTAGGGAAACA-GATCGAAGATGAT-GAGCT
* * *
10554690 CTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAG-GGT
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* ** * * * * * * *
10554734 CTTAAACCTGTAATCGGTAGGGTAACAGACCG-A-ATTA-CAGAT
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* * * * *
10554776 CTTATCTCCCTAAGCAGTAGGAAAACAGATCGAAGATGAAGATC-
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* *
10554820 TTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATGATGGGCT
1 TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* * * * * ** *
10554864 TTAACCCCCTAAGCAGTAGAGTAACA-AGCCAA-ATTTACAAGCC
1 TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATGAGCT
* * * *
10554907 TTAACCCCCTAAGCAGTAGGGTAACAG-GCTGAAGATTTAT-AGAT
1 TTAACCCCCTAAGCAGTAGGGAAACAGATC-GAAGA-TGATGAGCT
* * *
10554951 CTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGGGCT
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
* * * * ** *
10554996 TTAACCCCCTAAGCAGTAGGGTAACA-AGCCAA-ATTTACAAGCC
1 TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGA-TGATGAGCT
* * * * * * *
10555039 TTAAACCCCTAAGCAGTAGGGTAACTG-GCTGAAGAT-TTACAGAT
1 TTAACCCCCTAAGCAGTAGGGAAACAGATC-GAAGATGAT-GAGCT
** * * *
10555083 CTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAAATTATGGGCT
1 -TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
*
10555128 TTAACCCCCTAAGCAGTAGGGTAACA
1 TTAACCCCCTAAGCAGTAGGGAAACA
10555154 AGCCGAATTT
Statistics
Matches: 490, Mismatches: 117, Indels: 60
0.73 0.18 0.09
Matches are distributed among these distances:
42 57 0.12
43 151 0.31
44 178 0.36
45 102 0.21
46 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (44 bp):
TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGAGCT
Found at i:10555003 original size:132 final size:132
Alignment explanation
Indices: 10554554--10555241 Score: 840
Period size: 132 Copynumber: 5.2 Consensus size: 132
10554544 ACCGAATTGT
* * * *
10554554 AGATCTTATCTCCCTAAGCAGTAGGGAAACAGATCGAAGATGAA-GGTC-TTAACCCCCTAAGCA
1 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGAT-AATGGGCTTTAACCCCCTAAGCA
* * * * *** * * *
10554617 GTAGGGAAACAGATCGAAGA-TGATGGGCTTTAACCCCCTAAGCAGTAGGGTAACATGCTAAAGA
65 GTAGGGTAACA-AGCCAA-ATTTACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGA
10554681 TTTAC
128 TTTAC
* * * ** *
10554686 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAA-GGG-TCTTAAACCTGTAATC
1 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGA-TAATGGGCT-TTAACCCCCTAAGC
* * * * * ** *
10554749 GGTAGGGTAAC-AGACCGAA-TTAC-AGATCTTATCTCCCTAAGCAGTAGGAAAACA-GATCGAA
64 AGTAGGGTAACAAG-CCAAATTTACAAG-CCTTAACCCCCTAAGCAGTAGGGTAACAGGCT-GAA
*
10554810 GA-TGA-
126 GATTTAC
*
10554815 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATGATGGGCTTTAACCCCCTAAGCAG
1 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGGGCTTTAACCCCCTAAGCAG
*
10554880 TAGAGTAACAAGCCAAATTTACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTT
66 TAGGGTAACAAGCCAAATTTACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTT
*
10554945 AT
131 AC
10554947 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGGGCTTTAACCCCCTAAGCAG
1 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGGGCTTTAACCCCCTAAGCAG
* *
10555012 TAGGGTAACAAGCCAAATTTACAAGCCTTAAACCCCTAAGCAGTAGGGTAACTGGCTGAAGATTT
66 TAGGGTAACAAGCCAAATTTACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTT
10555077 AC
131 AC
* * *
10555079 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAAATTATGGGCTTTAACCCCCTAAGCAG
1 AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGGGCTTTAACCCCCTAAGCAG
* * *
10555144 TAGGGTAACAAGCCGAATTTACAAACCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTT
66 TAGGGTAACAAGCCAAATTTACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTT
10555209 AC
131 AC
* * *
10555211 AAATCTTAACCCCCTAACCAGTAGGGTAACA
1 AGATCTTAACCCCCTAAGCAGTAGGGAAACA
10555242 AGCTGAATTT
Statistics
Matches: 486, Mismatches: 56, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
128 1 0.00
129 65 0.13
130 40 0.08
131 36 0.07
132 325 0.67
133 19 0.04
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (132 bp):
AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATAATGGGCTTTAACCCCCTAAGCAG
TAGGGTAACAAGCCAAATTTACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTT
AC
Found at i:10555192 original size:175 final size:175
Alignment explanation
Indices: 10554996--10555326 Score: 459
Period size: 175 Copynumber: 1.9 Consensus size: 175
10554986 ATAATGGGCT
* * *
10554996 TTAACCCCCTAAGCAGTAGGGTAACAAGC-CAA-ATTTACAAGCCTTAAACCCCTAAGCAGTAGG
1 TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAGATTTACAAACCTTAAACCCCTAACCAGTAGG
** *
10555059 GTAACTGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAAATTATG
66 GTAACAAGCTG-A-ATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAAATGATG
* *
10555124 GGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAAACC
129 GGCCTTAAACCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAAACC
* * * *
10555171 TTAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTACAAATCTTAACCCCCTAACCAGTAGG
1 TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAGATTTACAAACCTTAAACCCCTAACCAGTAGG
* * * ** *
10555236 GTAACAAGCTGAATTTACAGATCTTAACCCCTTAAGCAGTTGGGAAATAGATCGAAGATGATGGG
66 GTAACAAGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAAATGATGGG
*
10555301 CCTTAAACCCCTAAGTAGTAGGGTAA
131 CCTTAAACCCCTAAGCAGTAGGGTAA
10555327 TAGGCTGGAA
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
175 96 0.71
176 3 0.02
177 36 0.27
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (175 bp):
TTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAGATTTACAAACCTTAAACCCCTAACCAGTAGG
GTAACAAGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAAATGATGGG
CCTTAAACCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAAACC
Found at i:10555305 original size:132 final size:130
Alignment explanation
Indices: 10554473--10555345 Score: 669
Period size: 132 Copynumber: 6.7 Consensus size: 130
10554463 TTTACAGATC
* * * * *
10554473 TTAACCCCCTAAGCAGTAGGGAAACAGATCG-AA-GACGAAGGGTCTTAAACCCCTAATCGGTAG
1 TTAACCCCCTAAGCAGTAGGGAAA-AGACCGAAATTAC-AA--GCCTTAAACCCCTAAGCAGTAG
* * * * * * * *
10554536 GGTAACAGACCG-A-ATTGT--AGATCTTATCTCCCTAAGCAGTAGGGAAACAGATCGAAGATGA
62 GGTAACAGGCTGAAGATT-TACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGAT-AAAAATTA
*
10554597 AGGTC-
125 AGGGCT
* * *** * *
10554602 TTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGATGATGGGCTTTAACCCCCTAAGCAGTAGGG
1 TTAACCCCCTAAGCAGTAGGGAAA-AGACCGAA-ATTACAAGCCTTAAACCCCTAAGCAGTAGGG
* * * * * **
10554667 TAACATGCTAAAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGACGAAGG
64 TAACAGGCTGAAGATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGAT-AAAAATTAAGG
10554732 G-T
128 GCT
* ** * * * * *
10554734 CTTAAACCTGTAATCGGTAGGGTAACAGACCG-AATTAC-AGATCTT-ATCTCCCTAAGCAGTAG
1 -TTAACCCCCTAAGCAGTAGGG-AAAAGACCGAAATTACAAG-CCTTAAAC-CCCTAAGCAGTAG
** * * * * *
10554796 GAAAACA-GATCGAAGA-TGA-AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGATGA
62 GGTAACAGGCT-GAAGATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGAT-AAAAATTA
*
10554858 TGGGCT
125 AGGGCT
* *
10554864 TTAACCCCCTAAGCAGTAGAGTAACAAG-CC-AAATTTACAAGCCTTAACCCCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAG-GGAA-AAGACCGAAA-TTACAAGCCTTAAACCCCTAAGCAGTAGG
* * *
10554927 GTAACAGGCTGAAGATTTATAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGA-TAAT
63 GTAACAGGCTGAAGATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGAT-AAAAATTAA-
10554991 GGGCT
126 GGGCT
10554996 TTAACCCCCTAAGCAGTAGGGTAACAAG-CC-AAATTTACAAGCCTTAAACCCCTAAGCAGTAGG
1 TTAACCCCCTAAGCAGTAGGG-AA-AAGACCGAAA-TTACAAGCCTTAAACCCCTAAGCAGTAGG
* * *
10555059 GTAACTGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAAATTATG
63 GTAACAGGCTGAAGATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGAT-AAAAATTAAG
10555124 GGCT
127 GGCT
* *
10555128 TTAACCCCCTAAGCAGTAGGGTAACAAG-CCGAATTTACAAACCTTAAACCCCTAAGCAGTAGGG
1 TTAACCCCCTAAGCAGTAGGG-AA-AAGACCGAAATTACAAGCCTTAAACCCCTAAGCAGTAGGG
* * * * *
10555192 TAACAGGCTGAAGATTTACAAATCTTAACCCCCTAACCAGTAGGGTAACAAGCT-GAATTTACAG
64 TAACAGGCTGAAGATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAAC-AGATAAAAATTA-AG
**
10555256 ATC-
127 GGCT
* * * * *** *
10555259 TTAACCCCTTAAGCAGTTGGGAAATAGATCGAAGATGATGGGCCTTAAACCCCTAAGTAGTAGGG
1 TTAACCCCCTAAGCAGTAGGGAAA-AGACCGAA-ATTACAAGCCTTAAACCCCTAAGCAGTAGGG
*
10555324 TAATAGGCTGGAA-A-TTACAAAT
64 TAACAGGCT-GAAGATTTACAAAT
10555346 TTCTTTTTCC
Statistics
Matches: 629, Mismatches: 82, Indels: 64
0.81 0.11 0.08
Matches are distributed among these distances:
129 121 0.19
130 48 0.08
131 77 0.12
132 350 0.56
133 31 0.05
134 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (130 bp):
TTAACCCCCTAAGCAGTAGGGAAAAGACCGAAATTACAAGCCTTAAACCCCTAAGCAGTAGGGTA
ACAGGCTGAAGATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATAAAAATTAAGGGCT
Found at i:10555342 original size:88 final size:86
Alignment explanation
Indices: 10554425--10555342 Score: 420
Period size: 87 Copynumber: 10.5 Consensus size: 86
10554415 GAATTCACAA
* * * *
10554425 GCCTTAAGCCCCTAAGCAATAGGGTAACAGGCTAAAGATTTACAGATCTTAACCCCCTAAGCAGT
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCTGAA-A-TTACAGATCTTAA-CCCCTAAGCAGT
** *
10554490 AGGGAAACAGATCGAAGACGAAGG
63 AGGGAAACAGATCGAAGATTATGG
* * * * ** *
10554514 GTCTTAAACCCCTAATCGGTAGGGTAAC-AGACCG-AATTGTAGATCTTATCTCCCTAAGCAGTA
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAG-CTGAAATTACAGATCTTAAC-CCCTAAGCAGTA
* *
10554577 GGGAAACAGATCGAAGATGA-AG
64 GGGAAACAGATCGAAGATTATGG
* * * * * * **
10554599 GTCTTAACCCCCTAAGCAGTAGGGAAAC-AGATCGAAGATGA-TGGGCTTTAACCCCCTAAGCAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCT-GAA-ATTACAGATC-TTAA-CCCCTAAGCAG
* * * **
10554662 TAGGGTAACATGCT-AAAGATTTACAG
62 TAGGGAAACA-GATCGAAGA-TTATGG
** * * * ** * ** * *
10554688 ATCTTAACCCCCTAAGCAGTAGGGAAAC-AGATCGAAGACGA-AGGGTCTTAAACCTGTAATCGG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCT-GAA-ATTACA-GATCTT-AACCCCTAAGCAG
* * **
10554751 TAGGGTAACAGACCG-A-ATTACAG
62 TAGGGAAACAGATCGAAGATTATGG
** * ** * *
10554774 ATCTT-ATCTCCCTAAGCAGTAGGAAAAC-AGATCGAAGATGA-AGATCTTAACCCCCTAAGCAG
1 GCCTTAAAC-CCCTAAGCAGTAGGGTAACAAGCT-GAA-ATTACAGATCTTAA-CCCCTAAGCAG
* *
10554836 TAGGGAAACAGATCAAAGATGATGG
62 TAGGGAAACAGATCGAAGATTATGG
* * * * *
10554861 GCTTTAACCCCCTAAGCAGTAGAGTAACAAGC-CAAATTTACA-AGCCTTAACCCCCTAAGCAGT
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCTGAAA-TTACAGA-TCTTAA-CCCCTAAGCAGT
* * *
10554924 AGGGTAACAG-GCTGAAGATTTATAG
63 AGGGAAACAGATC-GAAGA-TTATGG
** * * * * * **
10554949 ATCTTAACCCCCTAAGCAGTAGGGAAAC-AGATCAAAGATA-ATGGGCTTTAACCCCCTAAGCAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCTGAAA-TTACA-GATC-TTAA-CCCCTAAGCAG
* * * ***
10555012 TAGGGTAACA-AGCCAA-ATTTACAA
62 TAGGGAAACAGATCGAAGA-TTATGG
**
10555036 GCCTTAAACCCCTAAGCAGTAGGGTAACTGGCTGAAGATTTACAGATCTTAACCCCCTAAGCAGT
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCTGAA-A-TTACAGATCTTAA-CCCCTAAGCAGT
** *
10555101 AGGGAAACAGATAAAAAATTATGG
63 AGGGAAACAGATCGAAGATTATGG
* * * * * *
10555125 GCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCGAATTTACAAACCTTAAACCCCTAAGCAGTAG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCTGAAATTACAGATCTT-AACCCCTAAGCAGTAG
* * ***
10555190 GGTAACAG-GCTGAAGATTTACAA
65 GGAAACAGATC-GAAGA-TTATGG
** * * * *
10555213 ATCTTAACCCCCTAACCAGTAGGGTAACAAGCTGAATTTACAGATCTTAACCCCTTAAGCAGTTG
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCTGAAATTACAGATCTTAACCCC-TAAGCAGTAG
* *
10555278 GGAAATAGATCGAAGATGATGG
65 GGAAACAGATCGAAGATTATGG
* * *
10555300 GCCTTAAACCCCTAAGTAGTAGGGTAATAGGCTGGAAATTACA
1 GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCT-GAAATTACA
10555343 AATTTCTTTT
Statistics
Matches: 649, Mismatches: 140, Indels: 81
0.75 0.16 0.09
Matches are distributed among these distances:
84 2 0.00
85 56 0.09
86 93 0.14
87 184 0.28
88 152 0.23
89 155 0.24
90 7 0.01
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (86 bp):
GCCTTAAACCCCTAAGCAGTAGGGTAACAAGCTGAAATTACAGATCTTAACCCCTAAGCAGTAGG
GAAACAGATCGAAGATTATGG
Found at i:10555464 original size:68 final size:68
Alignment explanation
Indices: 10555347--10555545 Score: 285
Period size: 68 Copynumber: 2.9 Consensus size: 68
10555337 ATTACAAATT
*
10555347 TCTTTT-TCCCTGAAATGGCATTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAG-
1 TCTTTTCTTCCTGAAATGGCATTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGC
*
10555410 AGGA
66 A-AA
* *
10555414 TCTTTTCTTCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGC
1 TCTTTTCTTCCTGAAATGGCATTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGC
10555479 AAA
66 AAA
* * * * * *
10555482 CCTCTTCTTCCAGAAAGGGCATTGGAGAGGCTAAAAGCCATAGCAGATCTCCTTGAAGTTTCAG
1 TCTTTTCTTCCTGAAATGGCATTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAG
10555546 TGGAAGAAGA
Statistics
Matches: 118, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
67 6 0.05
68 111 0.94
69 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (68 bp):
TCTTTTCTTCCTGAAATGGCATTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGC
AAA
Found at i:10555762 original size:44 final size:44
Alignment explanation
Indices: 10555657--10556120 Score: 399
Period size: 44 Copynumber: 10.6 Consensus size: 44
10555647 GATTTCAGCA
* * **
10555657 TGGCATCCCTGTGCTTATAGAGAACAAGTTGAAGATTTCAGCA--
1 TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAG-ATT
10555700 TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
1 TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
**
10555744 TGGCATCTTTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
1 TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
* * * * * *
10555788 TGGCATCCCTGTGCTTATAGGGAAC-GGATCGAAGATAGCAGATC
1 TGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAAACATCAGATT
* * * * * * **
10555832 TGACATTCCTGTGCTTACAGTGAAGC-AGATCAAAGATTTCAGCA--
1 TGGCATCCCTGTGCTTATAGGGAA-CAAGTTGAAA-ACATCAG-ATT
10555876 TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
1 TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
* *
10555920 TGGCATCCCTGTTCTTATAGGGAACAAGTTGAAAAAAAT-AGATT
1 TGGCATCCCTGTGCTTATAGGGAACAAGTTG-AAAACATCAGATT
* * * * * *
10555964 TGGCATCCCTGTGCTTATAGGGAAC-GGATCGAAGATAGCAGATC
1 TGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAAACATCAGATT
* * * ** ** * * **
10556008 TGACATTCCTGTGCTTACAATGAAGTAGATCGAAGATTTCAGCA--
1 TGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAAACATCAG-ATT
* *
10556052 TGACATCCCTGTGCTTATAGGGAACAAGTTGAAAACAACAGATT
1 TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
*
10556096 TGGCTTCCCTGTGCTTATAGGGAAC
1 TGGCATCCCTGTGCTTATAGGGAAC
10556121 GGATCGAAGA
Statistics
Matches: 341, Mismatches: 64, Indels: 31
0.78 0.15 0.07
Matches are distributed among these distances:
42 3 0.01
43 57 0.17
44 253 0.74
45 26 0.08
46 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATT
Found at i:10555913 original size:176 final size:176
Alignment explanation
Indices: 10555688--10556120 Score: 760
Period size: 176 Copynumber: 2.5 Consensus size: 176
10555678 GAACAAGTTG
**
10555688 AAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATTTGGCATCTT
1 AAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATTTGGCATCCC
*
10555753 TGTGCTTATAGGGAACAAGTTG-AAAACATCAGATTTGGCATCCCTGTGCTTATAGGGAACGGAT
66 TGTGCTTATAGGGAACAAGTTGAAAAAAAT-AGATTTGGCATCCCTGTGCTTATAGGGAACGGAT
*
10555817 CGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCA
130 CGAAGATAGCAGATCTGACATTCCTGTGCTTACAATGAAGCAGATCA
10555864 AAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATTTGGCATCCC
1 AAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATTTGGCATCCC
*
10555929 TGTTCTTATAGGGAACAAGTTGAAAAAAATAGATTTGGCATCCCTGTGCTTATAGGGAACGGATC
66 TGTGCTTATAGGGAACAAGTTGAAAAAAATAGATTTGGCATCCCTGTGCTTATAGGGAACGGATC
* *
10555994 GAAGATAGCAGATCTGACATTCCTGTGCTTACAATGAAGTAGATCG
131 GAAGATAGCAGATCTGACATTCCTGTGCTTACAATGAAGCAGATCA
* * *
10556040 AAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAAACAACAGATTTGGCTTCCC
1 AAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATTTGGCATCCC
10556105 TGTGCTTATAGGGAAC
66 TGTGCTTATAGGGAAC
10556121 GGATCGAAGA
Statistics
Matches: 245, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
176 239 0.98
177 6 0.02
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (176 bp):
AAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACATCAGATTTGGCATCCC
TGTGCTTATAGGGAACAAGTTGAAAAAAATAGATTTGGCATCCCTGTGCTTATAGGGAACGGATC
GAAGATAGCAGATCTGACATTCCTGTGCTTACAATGAAGCAGATCA
Found at i:10556151 original size:44 final size:44
Alignment explanation
Indices: 10555598--10556153 Score: 251
Period size: 44 Copynumber: 12.7 Consensus size: 44
10555588 AGGAGCAGAC
* * * *
10555598 CGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGAT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAA-CGGAT
* ** * * *
10555643 CCAAGATTTCAG--CATGGCATCCCTGTGCTTATAGAGAAC-AAGT
1 CGAAGATAGCAGATC-TGACATCCCTGTGCTTATAGGGAACGGA-T
* ** * *
10555686 TGAAGATTTCAG--CATGGCATCCCTGTGCTTATAGGGAAC-AAGT
1 CGAAGATAGCAGATC-TGACATCCCTGTGCTTATAGGGAACGGA-T
* * * * * * ** *
10555729 TGAAAACATCAGATTTGGCATCTTTGTGCTTATAGGGAAC-AAGT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGA-T
* * * * * *
10555773 TGAAAACATCAGATTTGGCATCCCTGTGCTTATAGGGAACGGAT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGAT
* * * *
10555817 CGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGAT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAA-CGGAT
* ** * *
10555862 CAAAGATTTCAG--CATGGCATCCCTGTGCTTATAGGGAAC-AAGT
1 CGAAGATAGCAGATC-TGACATCCCTGTGCTTATAGGGAACGGA-T
* * * * * * * *
10555905 TGAAAACATCAGATTTGGCATCCCTGTTCTTATAGGGAAC-AAGT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGA-T
* * * ** * *
10555949 TGAAAAAAATAGATTTGGCATCCCTGTGCTTATAGGGAACGGAT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGAT
* * **
10555993 CGAAGATAGCAGATCTGACATTCCTGTGCTTACAATGAA-GTAGAT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAACG--GAT
** *
10556038 CGAAGATTTCAG--CATGACATCCCTGTGCTTATAGGGAAC-AAGT
1 CGAAGATAGCAGATC-TGACATCCCTGTGCTTATAGGGAACGGA-T
* * * * * * *
10556081 TGAAAACAACAGATTTGGCTTCCCTGTGCTTATAGGGAACGGAT
1 CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGAT
* *
10556125 CGAAGATAGCAAATCTGACATTCCTGTGC
1 CGAAGATAGCAGATCTGACATCCCTGTGC
10556154 ATACAGTGAA
Statistics
Matches: 406, Mismatches: 86, Indels: 39
0.76 0.16 0.07
Matches are distributed among these distances:
42 3 0.01
43 72 0.18
44 293 0.72
45 38 0.09
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
CGAAGATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGAT
Found at i:10556153 original size:176 final size:176
Alignment explanation
Indices: 10555598--10556153 Score: 699
Period size: 176 Copynumber: 3.2 Consensus size: 176
10555588 AGGAGCAGAC
* * * * * * ** *
10555598 CGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCCAAGATTTCAG--CATGGC
1 CGAAAATAGCAGATCTGACATCCCTGTGCTTATAGGGAA-CGGATCGAAGATAGCAGATC-TGAC
* * * *
10555661 ATCCCTGTGCTTATAGA-GAACAAG-TTGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAA
64 ATTCCTGTGCTTACA-ATGAAGAAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAA
**
10555724 CAAGTTGAAAACATCAGATTTGGCATCTTTGTGCTTATAGGGAACAAGT
128 CAAGTTGAAAACATCAGATTTGGCATCCCTGTGCTTATAGGGAACAAGT
* * * * *
10555773 TGAAAACATCAGATTTGGCATCCCTGTGCTTATAGGGAACGGATCGAAGATAGCAGATCTGACAT
1 CGAAAATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGATCGAAGATAGCAGATCTGACAT
* * *
10555838 TCCTGTGCTTACAGTGAAGCAGATCAAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAA
66 TCCTGTGCTTACAATGAAGAAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAA
*
10555903 GTTGAAAACATCAGATTTGGCATCCCTGTTCTTATAGGGAACAAGT
131 GTTGAAAACATCAGATTTGGCATCCCTGTGCTTATAGGGAACAAGT
* * ** * *
10555949 TGAAAAAAATAGATTTGGCATCCCTGTGCTTATAGGGAACGGATCGAAGATAGCAGATCTGACAT
1 CGAAAATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGATCGAAGATAGCAGATCTGACAT
* *
10556014 TCCTGTGCTTACAATGAAGTAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAA
66 TCCTGTGCTTACAATGAAGAAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAA
* * *
10556079 GTTGAAAACAACAGATTTGGCTTCCCTGTGCTTATAGGGAAC-GGAT
131 GTTGAAAACATCAGATTTGGCATCCCTGTGCTTATAGGGAACAAG-T
* * *
10556125 CGAAGATAGCAAATCTGACATTCCTGTGC
1 CGAAAATAGCAGATCTGACATCCCTGTGC
10556154 ATACAGTGAA
Statistics
Matches: 332, Mismatches: 44, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
174 13 0.04
175 52 0.16
176 267 0.80
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (176 bp):
CGAAAATAGCAGATCTGACATCCCTGTGCTTATAGGGAACGGATCGAAGATAGCAGATCTGACAT
TCCTGTGCTTACAATGAAGAAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAA
GTTGAAAACATCAGATTTGGCATCCCTGTGCTTATAGGGAACAAGT
Found at i:10556164 original size:132 final size:132
Alignment explanation
Indices: 10555923--10556176 Score: 427
Period size: 132 Copynumber: 1.9 Consensus size: 132
10555913 TCAGATTTGG
* *
10555923 CATCCCTGTTCTTATAGGGAACAAGTTGAAAAAAATAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CATCCCTGTGCTTATAGGGAACAAGTTGAAAAAAACAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * *
10555988 CGGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAATGAAGTAGATCGAAGATTTCAGCAT
66 CGGATCGAAGATAGCAAATCTGACATTCCTGTGCATACAATGAAGCAGATCAAAGATTTCAGCAT
10556053 GA
131 GA
* *
10556055 CATCCCTGTGCTTATAGGGAACAAGTTGAAAACAACAGATTTGGCTTCCCTGTGCTTATAGGGAA
1 CATCCCTGTGCTTATAGGGAACAAGTTGAAAAAAACAGATTTGGCATCCCTGTGCTTATAGGGAA
*
10556120 CGGATCGAAGATAGCAAATCTGACATTCCTGTGCATACAGTGAAGCAGATCAAAGAT
66 CGGATCGAAGATAGCAAATCTGACATTCCTGTGCATACAATGAAGCAGATCAAAGAT
10556177 AGCGGATATC
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 113 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (132 bp):
CATCCCTGTGCTTATAGGGAACAAGTTGAAAAAAACAGATTTGGCATCCCTGTGCTTATAGGGAA
CGGATCGAAGATAGCAAATCTGACATTCCTGTGCATACAATGAAGCAGATCAAAGATTTCAGCAT
GA
Found at i:10556563 original size:22 final size:22
Alignment explanation
Indices: 10556523--10556564 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10556513 TGGCCACCCA
*
10556523 CCTTGGCCACCAACTCCACCAC
1 CCTTGGCCACCAACACCACCAC
10556545 CCTTGGCCACCTAA-ACCACC
1 CCTTGGCCACC-AACACCACC
10556565 CCAACCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.52, G:0.10, T:0.14
Consensus pattern (22 bp):
CCTTGGCCACCAACACCACCAC
Found at i:10556682 original size:21 final size:22
Alignment explanation
Indices: 10556637--10556714 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
10556627 GGGTTTTTGG
* * *
10556637 TTTTTTGGAGAAGGATTGTTCTT
1 TTTTTTGGAGGAGG-TTTTTTTT
10556660 TTTTTTGGAGGAGGTTTTTTTTT
1 TTTTTTGGAGGAGG-TTTTTTTT
*
10556683 GTTTTTTGGAGG-TGTTTTTTTGT
1 -TTTTTTGGAGGAGGTTTTTTT-T
10556706 TTTTTTGGA
1 TTTTTTGGA
10556715 AAGAAGGCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.33
23 21 0.44
24 11 0.23
ACGTcount: A:0.10, C:0.01, G:0.27, T:0.62
Consensus pattern (22 bp):
TTTTTTGGAGGAGGTTTTTTTT
Found at i:10557056 original size:3 final size:3
Alignment explanation
Indices: 10557042--10557121 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
10557032 GAGCTTTGTT
* *
10557042 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
10557085 TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA -TA TTA T
1 T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA T
10557122 ATATGCCCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:10557111 original size:12 final size:12
Alignment explanation
Indices: 10557045--10557123 Score: 72
Period size: 12 Copynumber: 6.5 Consensus size: 12
10557035 CTTTGTTTTA
*
10557045 TTATTTTATTAT
1 TTATATTATTAT
* *
10557057 TTTTACTATTAT
1 TTATATTATTAT
10557069 TTATATTATTA-
1 TTATATTATTAT
* *
10557080 TTAT-TTCTCAT
1 TTATATTATTAT
10557091 GTATATATTATTAT
1 -T-TATATTATTAT
10557105 TTATATTATTAT
1 TTATATTATTAT
10557117 ATTATAT
1 -TTATAT
10557124 ATGCCCTCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
10 4 0.08
11 4 0.08
12 30 0.57
13 10 0.19
14 5 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:10563703 original size:21 final size:21
Alignment explanation
Indices: 10563679--10563722 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
10563669 TTCAGTTTTA
10563679 CTGTATTTATCTTTTATAAGT
1 CTGTATTTATCTTTTATAAGT
10563700 CTGTATTTATCTTTTATAAGT
1 CTGTATTTATCTTTTATAAGT
10563721 CT
1 CT
10563723 TCTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (21 bp):
CTGTATTTATCTTTTATAAGT
Found at i:10565640 original size:14 final size:13
Alignment explanation
Indices: 10565621--10565650 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
10565611 CCAGAAAAGT
10565621 AAATCATTTTCCAG
1 AAATCATTTTCC-G
10565635 AAATCATTTTCCG
1 AAATCATTTTCCG
10565648 AAA
1 AAA
10565651 AACATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (13 bp):
AAATCATTTTCCG
Found at i:10569767 original size:28 final size:28
Alignment explanation
Indices: 10569736--10569809 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
10569726 TCAATGCCTT
*
10569736 GCACACTATGTGCCATACTC-AATATCTC
1 GCACACTAAGTGCCATACTCGAA-ATCTC
*
10569764 GCACACTAAGTGCCACACTCGAAATCTC
1 GCACACTAAGTGCCATACTCGAAATCTC
*
10569792 GTACACTAAGTGCCATAC
1 GCACACTAAGTGCCATAC
10569810 ATAGCCGAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.95
29 2 0.05
ACGTcount: A:0.31, C:0.32, G:0.14, T:0.23
Consensus pattern (28 bp):
GCACACTAAGTGCCATACTCGAAATCTC
Found at i:10569842 original size:40 final size:40
Alignment explanation
Indices: 10569794--10570008 Score: 313
Period size: 40 Copynumber: 5.4 Consensus size: 40
10569784 GAAATCTCGT
* * *
10569794 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCGC
*
10569834 ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCAC
1 ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCGC
* * * *
10569874 ACACTAAGTGTCATACATAGCCGAAGCTATCTCAAATCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCGC
* * *
10569914 ACACTAAGTGTCATATATAGCCGACGCTATGTCGAATCAC
1 ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCGC
* *
10569954 ACACTAAGTGCCATTTATAGCCGAAGCTATGTCGTATCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCGC
10569994 ACACTAAGTGCCATA
1 ACACTAAGTGCCATA
10570009 AATAACGGAT
Statistics
Matches: 155, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 155 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAATCGC
Found at i:10569929 original size:80 final size:80
Alignment explanation
Indices: 10569794--10570008 Score: 358
Period size: 80 Copynumber: 2.7 Consensus size: 80
10569784 GAAATCTCGT
10569794 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCATATATAGCCGAA
1 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCATATATAGCCGAA
10569859 GCTATGTCGAATCAC
66 GCTATGTCGAATCAC
* * *
10569874 ACACTAAGTGTCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGTCATATATAGCCGAC
1 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCATATATAGCCGAA
10569939 GCTATGTCGAATCAC
66 GCTATGTCGAATCAC
** * **
10569954 ACACTAAGTGCCATTTATAGCCGAAGCTATGTCGTATCGCACACTAAGTGCCATA
1 ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCATA
10570009 AATAACGGAT
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 125 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (80 bp):
ACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCCATATATAGCCGAA
GCTATGTCGAATCAC
Found at i:10572780 original size:6 final size:6
Alignment explanation
Indices: 10572766--10572811 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
10572756 CAAAATGAGG
* **
10572766 ATATGT ATATAT ATATGT ATACAT ATATGT ATATGT ATATGT ATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATAT
10572812 AAGTGGATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:10572783 original size:12 final size:12
Alignment explanation
Indices: 10572766--10572812 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
10572756 CAAAATGAGG
10572766 ATATGTATATAT
1 ATATGTATATAT
*
10572778 ATATGTATACAT
1 ATATGTATATAT
*
10572790 ATATGTATATGT
1 ATATGTATATAT
10572802 ATATGTATATA
1 ATATGTATATA
10572813 AGTGGATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:10575458 original size:22 final size:22
Alignment explanation
Indices: 10575433--10575477 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
10575423 ATGGACATTG
10575433 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
10575455 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
10575477 T
1 T
10575478 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:10579236 original size:22 final size:22
Alignment explanation
Indices: 10579208--10579252 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
10579198 AGGGGGAGTG
10579208 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
10579230 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
10579252 T
1 T
10579253 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:10583912 original size:28 final size:28
Alignment explanation
Indices: 10583880--10583936 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
10583870 AAAACATAGA
*
10583880 GGTAGAAAGGAATAGTTTCAATTGATAT
1 GGTAGAAAGGAATAATTTCAATTGATAT
10583908 GGTAGAAAGGAATAATTTCAATTGATAT
1 GGTAGAAAGGAATAATTTCAATTGATAT
10583936 G
1 G
10583937 AAAATTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (28 bp):
GGTAGAAAGGAATAATTTCAATTGATAT
Found at i:10597139 original size:6 final size:6
Alignment explanation
Indices: 10597109--10597147 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
10597099 TCCAACAACC
* *
10597109 AAAATA GAAAATA AAAGTC AAAATA AAAATA AAAATA AA
1 AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA AA
10597148 TAGTTATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:10607387 original size:24 final size:24
Alignment explanation
Indices: 10607347--10607392 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
10607337 TCAGATACCA
10607347 CTAAATGTAACACCCAAATCTGGC
1 CTAAATGTAACACCCAAATCTGGC
*
10607371 CTAAATGTTAAGA-CCAAATCTG
1 CTAAATG-TAACACCCAAATCTG
10607393 AAGAGTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (24 bp):
CTAAATGTAACACCCAAATCTGGC
Found at i:10608503 original size:62 final size:61
Alignment explanation
Indices: 10608433--10608575 Score: 196
Period size: 62 Copynumber: 2.3 Consensus size: 61
10608423 TTAAATCACA
* * * *
10608433 AATAGTGAGTCATATGACCTGGACACACGCCCGTGTCTCTGGCCCATGTGGTCTTTAATAGT
1 AATAGTGAGTCACACGACCTGGACACACGCCCGTGTCTCTAG-CCATGTGGTCTCTAATAGT
* ** *
10608495 AGTAGTGAGTCACACGACCTGGACACACGCTTGTGTCTCTAGCCGTGTGGTCTCTAATAGT
1 AATAGTGAGTCACACGACCTGGACACACGCCCGTGTCTCTAGCCATGTGGTCTCTAATAGT
*
10608556 AACAGTGAGTCACACGACCT
1 AATAGTGAGTCACACGACCT
10608576 ACCACATGGC
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
61 35 0.49
62 36 0.51
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (61 bp):
AATAGTGAGTCACACGACCTGGACACACGCCCGTGTCTCTAGCCATGTGGTCTCTAATAGT
Found at i:10608568 original size:61 final size:62
Alignment explanation
Indices: 10608436--10608575 Score: 192
Period size: 61 Copynumber: 2.3 Consensus size: 62
10608426 AATCACAAAT
* * * * **
10608436 AGTGAGTCATATGACCTGGACACACGCCCGTGTCTCTGGCCCATGTGGTCTTTAATAGTAGT
1 AGTGAGTCACACGACCTGGACACACGCCCGTGTCTCTAGCCCATGTGGTCTCTAATAGTAAC
** *
10608498 AGTGAGTCACACGACCTGGACACACGCTTGTGTCTCTAG-CCGTGTGGTCTCTAATAGTAAC
1 AGTGAGTCACACGACCTGGACACACGCCCGTGTCTCTAGCCCATGTGGTCTCTAATAGTAAC
10608559 AGTGAGTCACACGACCT
1 AGTGAGTCACACGACCT
10608576 ACCACATGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
61 35 0.51
62 34 0.49
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (62 bp):
AGTGAGTCACACGACCTGGACACACGCCCGTGTCTCTAGCCCATGTGGTCTCTAATAGTAAC
Found at i:10609819 original size:12 final size:12
Alignment explanation
Indices: 10609804--10609836 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
10609794 TGAACAAAAT
10609804 AAAATCATGGAC
1 AAAATCATGGAC
10609816 AAAATCATGGAC
1 AAAATCATGGAC
10609828 AAAATCATG
1 AAAATCATG
10609837 ATTATCTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (12 bp):
AAAATCATGGAC
Found at i:10610987 original size:5 final size:5
Alignment explanation
Indices: 10610977--10611002 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
10610967 AATTTAGAAA
10610977 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
10611003 CGAGTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:10616808 original size:27 final size:26
Alignment explanation
Indices: 10616768--10616823 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
10616758 AAGAAAGAAA
*
10616768 AAGAAAAAGAGAAGAGACAAGATTTT
1 AAGAAAAAGAGAAGAGACAAGATTAT
10616794 AAGAAAAATGAGAAGAGACAAGATTAT
1 AAGAAAAA-GAGAAGAGACAAGATTAT
10616821 AAG
1 AAG
10616824 GGCATAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.59, C:0.04, G:0.23, T:0.14
Consensus pattern (26 bp):
AAGAAAAAGAGAAGAGACAAGATTAT
Found at i:10618340 original size:29 final size:31
Alignment explanation
Indices: 10618264--10618322 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
10618254 ACTCAAGTGT
10618264 GAGTGTCAAATGTGATTATGTGCCCAACCAA
1 GAGTGTCAAATGTGATTATGTGCCCAACCAA
10618295 GAGTGTCAAATGTGATTATGTGCCCAAC
1 GAGTGTCAAATGTGATTATGTGCCCAAC
10618323 TAAATGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (31 bp):
GAGTGTCAAATGTGATTATGTGCCCAACCAA
Found at i:10623880 original size:21 final size:21
Alignment explanation
Indices: 10623845--10623897 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 21
10623835 ACAGCATCCC
10623845 TAGAGTTAGTCTGTTTCCTAGTA
1 TAGAGTT--TCTGTTTCCTAGTA
10623868 TAGAGTTTCTGTTTCCTAGTA
1 TAGAGTTTCTGTTTCCTAGTA
10623889 TAGAGTTTC
1 TAGAGTTTC
10623898 CTAAGTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 23 0.77
23 7 0.23
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (21 bp):
TAGAGTTTCTGTTTCCTAGTA
Found at i:10625702 original size:33 final size:33
Alignment explanation
Indices: 10625660--10625750 Score: 173
Period size: 33 Copynumber: 2.8 Consensus size: 33
10625650 TTTCTTCTTG
*
10625660 ACATTCCAGCTGCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
10625693 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
10625726 ACATTCCAGCTCCTGTCCAGCAACC
1 ACATTCCAGCTCCTGTCCAGCAACC
10625751 TGAAACAGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.19
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
Found at i:10627742 original size:21 final size:21
Alignment explanation
Indices: 10627716--10627757 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10627706 AGAGTTAGTT
10627716 TGTTTCCTAGTATAGAGTTTC
1 TGTTTCCTAGTATAGAGTTTC
10627737 TGTTTCCTAGTATAGAGTTTC
1 TGTTTCCTAGTATAGAGTTTC
10627758 CTAAGTTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (21 bp):
TGTTTCCTAGTATAGAGTTTC
Found at i:10630964 original size:12 final size:12
Alignment explanation
Indices: 10630947--10631003 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
10630937 CACGAACAAG
10630947 CTCGTTTATTGA
1 CTCGTTTATTGA
*
10630959 CTCGTTTA-TAA
1 CTCGTTTATTGA
* *
10630970 GCTTGCTTATTGA
1 -CTCGTTTATTGA
10630983 CTCGTTTA-TGA
1 CTCGTTTATTGA
*
10630994 CTCATTTATT
1 CTCGTTTATT
10631004 TATTAATGAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 12 0.34
12 21 0.60
13 2 0.06
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:10631302 original size:23 final size:23
Alignment explanation
Indices: 10631259--10631303 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
10631249 ATATGTTCAC
* *
10631259 GAACATGTTCGATTAATTTAAAT
1 GAACATGTTCGATGAAATTAAAT
10631282 GAACATGTTCG-TGAACATTAAA
1 GAACATGTTCGATGAA-ATTAAA
10631304 CAAACAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (23 bp):
GAACATGTTCGATGAAATTAAAT
Found at i:10632376 original size:9 final size:8
Alignment explanation
Indices: 10632361--10632385 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10632351 CTATCATCCT
10632361 TAAAAAAA
1 TAAAAAAA
10632369 TAAAAAAA
1 TAAAAAAA
10632377 TAAAAAAA
1 TAAAAAAA
10632385 T
1 T
10632386 CCCTATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:10642570 original size:12 final size:12
Alignment explanation
Indices: 10642553--10642578 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10642543 AAAATAGGGC
10642553 TTTAGCGGCGTT
1 TTTAGCGGCGTT
10642565 TTTAGCGGCGTT
1 TTTAGCGGCGTT
10642577 TT
1 TT
10642579 ATTAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Done.