Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 60 of 66
Found at i:22843837 original size:27 final size:28
Alignment explanation
Indices: 22843802--22843863 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
22843792 TTTTATTTTT
* *
22843802 AAATATTAATAATTTATAA-TTAATTAA
1 AAATATTAATAATTAATAATTTAAATAA
*
22843829 AAATATTAATAATTAATAATTTAAATAT
1 AAATATTAATAATTAATAATTTAAATAA
22843857 AAATATT
1 AAATATT
22843864 TTAATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 18 0.58
28 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATTAATAATTAATAATTTAAATAA
Found at i:22843886 original size:25 final size:25
Alignment explanation
Indices: 22843844--22843922 Score: 126
Period size: 25 Copynumber: 3.2 Consensus size: 25
22843834 TTAATAATTA
*
22843844 ATAATTTAAATA-TAAATATTTTAAT
1 ATAATTTAATTACT-AATATTTTAAT
22843869 ATAATTTAATTACTAATATTTTAAT
1 ATAATTTAATTACTAATATTTTAAT
22843894 ATAATTTAATTACTAATATTTTAAT
1 ATAATTTAATTACTAATATTTTAAT
22843919 -TAAT
1 ATAAT
22843923 AATATTTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
24 4 0.08
25 47 0.90
26 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (25 bp):
ATAATTTAATTACTAATATTTTAAT
Found at i:22843893 original size:15 final size:15
Alignment explanation
Indices: 22843873--22843931 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
22843863 TTTAATATAA
22843873 TTTAATTACTAATAT
1 TTTAATTACTAATAT
22843888 TTTAA-TA-T-A-A-
1 TTTAATTACTAATAT
22843898 TTTAATTACTAATAT
1 TTTAATTACTAATAT
*
22843913 TTTAATTAATAATAT
1 TTTAATTACTAATAT
22843928 TTTA
1 TTTA
22843932 TTTATAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 5 0.13
11 3 0.08
12 2 0.05
13 2 0.05
14 3 0.08
15 23 0.61
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATTACTAATAT
Found at i:22843943 original size:22 final size:22
Alignment explanation
Indices: 22843910--22843979 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
22843900 TAATTACTAA
22843910 TATTT-TAA-TTAATAATATTT
1 TATTTATAATTTAATAATATTT
*
22843930 TATTTATAATTTAATATTATTAT
1 TATTTATAATTTAATAATATT-T
* *
22843953 TATTAAAAATATTAATAAT-TTT
1 TATTTATAAT-TTAATAATATTT
22843975 TATTT
1 TATTT
22843980 TTATATTCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
20 5 0.12
21 3 0.07
22 15 0.37
23 11 0.27
24 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTATAATTTAATAATATTT
Found at i:22844021 original size:25 final size:25
Alignment explanation
Indices: 22843799--22844021 Score: 101
Period size: 25 Copynumber: 9.0 Consensus size: 25
22843789 TTATTTTATT
*
22843799 TTTAA-ATATTAATAATTTATAATTAA
1 TTTAATATATTAATAA-TT-TAATAAA
* *
22843825 TTAAAAATATTAATAA-TTAAT-AA
1 TTTAATATATTAATAATTTAATAAA
* *
22843848 TTTAA-ATATAAATATTTTAATATAA
1 TTTAATATATTAATAATTTAATA-AA
* *
22843873 TTTAAT-TACTAATATTTTAATATAA
1 TTTAATATATTAATAATTTAATA-AA
* * *
22843898 TTTAAT-TACTAATATTTTAATTAA
1 TTTAATATATTAATAATTTAATAAA
* * * *
22843922 TAATATTTTATTTATAATTTAAT--A
1 T-TTAATATATTAATAATTTAATAAA
* *
22843946 -TTATTATTATTAAAAATATTAAT-AA
1 TTTAATA-TATTAATAAT-TTAATAAA
* * * *
22843971 TTT-TTATTTTTATATTCATTAA-AAA
1 TTTAATATATTAATAAT--TTAATAAA
22843996 TTTAATATATTAATAATTTAATAAA
1 TTTAATATATTAATAATTTAATAAA
22844021 T
1 T
22844022 AAAACATTAA
Statistics
Matches: 158, Mismatches: 24, Indels: 31
0.74 0.11 0.15
Matches are distributed among these distances:
22 12 0.08
23 19 0.12
24 23 0.15
25 67 0.42
26 27 0.17
27 10 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTAATATATTAATAATTTAATAAA
Found at i:22866789 original size:7 final size:7
Alignment explanation
Indices: 22866777--22866813 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
22866767 TGTCTCTTCC
22866777 TCTCACT
1 TCTCACT
22866784 TCTCACT
1 TCTCACT
22866791 TCTCACT
1 TCTCACT
22866798 TCTCACT
1 TCTCACT
22866805 TCTCACT
1 TCTCACT
22866812 TC
1 TC
22866814 ACTTCCAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
TCTCACT
Found at i:22866817 original size:12 final size:12
Alignment explanation
Indices: 22866786--22866829 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
22866776 CTCTCACTTC
22866786 TCACTTCTCACTT
1 TCACTTCTCAC-T
22866799 CTCACTTCTCACT
1 -TCACTTCTCACT
22866812 TCACTTC-CAACT
1 TCACTTCTC-ACT
22866824 TCACTT
1 TCACTT
22866830 AACTTGCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.03
12 16 0.55
13 1 0.03
14 11 0.38
ACGTcount: A:0.18, C:0.41, G:0.00, T:0.41
Consensus pattern (12 bp):
TCACTTCTCACT
Found at i:22866843 original size:2 final size:2
Alignment explanation
Indices: 22866836--22866860 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22866826 ACTTAACTTG
22866836 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
22866861 CACCATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:22881124 original size:2 final size:2
Alignment explanation
Indices: 22881119--22881166 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
22881109 AAATTTTTTA
* *
22881119 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT GT 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
22881161 AT AT AT
1 AT AT AT
22881167 GCAAATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22881920 original size:95 final size:93
Alignment explanation
Indices: 22881749--22881922 Score: 224
Period size: 95 Copynumber: 1.8 Consensus size: 93
22881739 CTTTCTTTTC
* *
22881749 TAATTGTGCAGAGTTCTCATTATTGACTTGTTATCACTCATAAAAAAGATGGACCATCTTGATCC
1 TAATCGTGCAGAGTTCTCATTATTCACTTGTTATCACTCATAAAAAAGAT-GACCATCTTGATCC
*
22881814 CTATCTATTTCAATTCTAATATTTCCACT
65 CGATCTATTTCAATTCTAATATTTCCACT
* * * *
22881843 TAATCGTGTAGAGTTCTCATTATTCACTTTTTTTCTACTCATTAAAAAGAT-ATCTCATCTTGAT
1 TAATCGTGCAGAGTTCTCATTATTCACTTGTTATC-ACTCATAAAAAAGATGA-C-CATCTTGAT
* *
22881907 CCGGATTTATTTCAAT
63 CCCGATCTATTTCAAT
22881923 CATAGTATCT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
93 1 0.01
94 31 0.46
95 36 0.53
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (93 bp):
TAATCGTGCAGAGTTCTCATTATTCACTTGTTATCACTCATAAAAAAGATGACCATCTTGATCCC
GATCTATTTCAATTCTAATATTTCCACT
Found at i:22890218 original size:3 final size:3
Alignment explanation
Indices: 22890210--22890242 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
22890200 TAGAAGGAGT
22890210 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA
22890243 AACTAGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GTA
Found at i:22903841 original size:20 final size:19
Alignment explanation
Indices: 22903812--22903851 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
22903802 ACCAAAGAAG
*
22903812 CTTTTTTTTTT-AATATTT
1 CTTTTTTTTTTCAAAATTT
22903830 CTTTTTTCTTTTCAAAATTT
1 CTTTTTT-TTTTCAAAATTT
22903850 CT
1 CT
22903852 ACTATTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTTTTTTCAAAATTT
Found at i:22914972 original size:19 final size:20
Alignment explanation
Indices: 22914931--22914979 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
22914921 TTAATGCTAT
*
22914931 AGAAACAAAAGAAGAGAGAG
1 AGAAACAAAAGAAGAGACAG
* *
22914951 AGAAGCAAAAG-AGAGACTG
1 AGAAACAAAAGAAGAGACAG
22914970 AGAAA-AAAAG
1 AGAAACAAAAG
22914980 GGCTGTATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 5 0.20
19 10 0.40
20 10 0.40
ACGTcount: A:0.63, C:0.06, G:0.29, T:0.02
Consensus pattern (20 bp):
AGAAACAAAAGAAGAGACAG
Found at i:22917699 original size:2 final size:2
Alignment explanation
Indices: 22917692--22917716 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22917682 CTCTAGACAT
22917692 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
22917717 GACAGGCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22929798 original size:30 final size:30
Alignment explanation
Indices: 22929741--22929797 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
22929731 ATCATAAAGT
* *
22929741 TTTATTTGATTTAAAATAAAAATAAAAATA
1 TTTATTTGACTCAAAATAAAAATAAAAATA
22929771 TTTATTTGACTCAAAAT-AAAATAAAAA
1 TTTATTTGACTCAAAATAAAAATAAAAA
22929798 ACTTGATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (30 bp):
TTTATTTGACTCAAAATAAAAATAAAAATA
Found at i:22944740 original size:14 final size:14
Alignment explanation
Indices: 22944721--22944748 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22944711 TTCCAAGTCC
22944721 TAATTAAGTCATCT
1 TAATTAAGTCATCT
22944735 TAATTAAGTCATCT
1 TAATTAAGTCATCT
22944749 CTATAACCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TAATTAAGTCATCT
Found at i:22973799 original size:42 final size:42
Alignment explanation
Indices: 22973716--22973844 Score: 138
Period size: 42 Copynumber: 3.1 Consensus size: 42
22973706 TTTTTCCCAA
* * * *
22973716 TCTCTGGAAGCCT-AGGGGACTGAACTCCACCA-CTCAGTTTGT
1 TCTCTGG-AGCCTGGGGGGATTGAACTCCACTATCTGA-TTTGT
**
22973758 TCTCTGGGAGCCT-GGGGGATTGAACTCCTGTATCTGATTTGT
1 TCTCT-GGAGCCTGGGGGGATTGAACTCCACTATCTGATTTGT
* *
22973800 TCTCTTGAGGCTGGGGGGATTGAACTCCACTATCTGATTTGT
1 TCTCTGGAGCCTGGGGGGATTGAACTCCACTATCTGATTTGT
22973842 TCT
1 TCT
22973845 TGTGAACAGC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 5 0.07
42 64 0.86
43 5 0.07
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.33
Consensus pattern (42 bp):
TCTCTGGAGCCTGGGGGGATTGAACTCCACTATCTGATTTGT
Found at i:22978094 original size:24 final size:26
Alignment explanation
Indices: 22978067--22978116 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
22978057 GTTTTATTTT
* *
22978067 AAATTTT-TATTTTTAT-TTTTTAAA
1 AAATTTTATAGTTTCATCTTTTTAAA
22978091 AAATTTTATAGTTTCATCTTTTTAAA
1 AAATTTTATAGTTTCATCTTTTTAAA
22978117 TATTTCCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (26 bp):
AAATTTTATAGTTTCATCTTTTTAAA
Found at i:22978121 original size:25 final size:22
Alignment explanation
Indices: 22978063--22978121 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 22
22978053 CTCTGTTTTA
*
22978063 TTTTAAAT-TTTTATTTTTATT
1 TTTTAAATATTTTATTTTCATT
*
22978084 TTTTAAAAAATTTTATAGTTTCATCT
1 TTTT-AAATATTTTAT--TTTCAT-T
22978110 TTTTAAATATTT
1 TTTTAAATATTT
22978122 CCTCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 6 0.20
25 12 0.40
26 5 0.17
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTAAATATTTTATTTTCATT
Found at i:22978180 original size:32 final size:32
Alignment explanation
Indices: 22978130--22978192 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
22978120 TTCCTCAAAA
* * *
22978130 TTTTAAAAAATTATAATTTTGTCTTTGTTTTG
1 TTTTAAAAAATTAAAATTTTATCTTTATTTTG
*
22978162 TTTTAAAAATTTAAAATTTTATCTTTATTTT
1 TTTTAAAAAATTAAAATTTTATCTTTATTTT
22978193 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (32 bp):
TTTTAAAAAATTAAAATTTTATCTTTATTTTG
Found at i:22979854 original size:33 final size:33
Alignment explanation
Indices: 22979793--22979855 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
22979783 TCTTCGACCG
* *
22979793 TCTTCCTCTCCTCTCTCAACCGGCCTTCCCTCA
1 TCTTCATCTCCTCTCTCAACCGACCTTCCCTCA
*
22979826 TCTTCATCTCCTCTCTCAACCGATCTTCCC
1 TCTTCATCTCCTCTCTCAACCGACCTTCCC
22979856 CTGTGTTCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.11, C:0.49, G:0.05, T:0.35
Consensus pattern (33 bp):
TCTTCATCTCCTCTCTCAACCGACCTTCCCTCA
Found at i:22988808 original size:2 final size:2
Alignment explanation
Indices: 22988801--22988870 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
22988791 AGGAGGTTTA
* * *
22988801 AT AT AT AT AC AC AC 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
22988843 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
22988871 TTTTACGAAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:22994489 original size:2 final size:2
Alignment explanation
Indices: 22994482--22994515 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22994472 TTTACTTATG
22994482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22994516 ATGTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22994598 original size:2 final size:2
Alignment explanation
Indices: 22994591--22994621 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22994581 NNNNNNNNNN
22994591 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22994622 GTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22996887 original size:23 final size:22
Alignment explanation
Indices: 22996844--22996887 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
22996834 AAATACAAAC
* **
22996844 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
22996866 ATATTTTGTATTAGAAGATAAT
1 ATATTTT-TATTAGAAGATAAT
22996888 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:23001836 original size:2 final size:2
Alignment explanation
Indices: 23001829--23001853 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23001819 GACTACCTCA
23001829 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
23001854 TCTGACTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23001930 original size:2 final size:2
Alignment explanation
Indices: 23001923--23001956 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
23001913 CTTCTAAGCG
*
23001923 CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
23001957 TCTGACTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:23002002 original size:103 final size:103
Alignment explanation
Indices: 23001829--23002023 Score: 381
Period size: 103 Copynumber: 1.9 Consensus size: 103
23001819 GACTACCTCA
23001829 ACACACACACACACACACACACACATCTGACTCTAGGTAAAGAAGTTGGAAGTCAAAGCCAAAAA
1 ACACACACACACACACACACACACATCTGACTCTAGGTAAAGAAGTTGGAAGTCAAAGCCAAAAA
23001894 GGTAAATGAGGATAGGTTTCTTCTAAGCGCACACACAC
66 GGTAAATGAGGATAGGTTTCTTCTAAGCGCACACACAC
*
23001932 ACACACACACACACACACATACACATCTGACTCTAGGTAAAGAAGTTGGAAGTCAAAGCCAAAAA
1 ACACACACACACACACACACACACATCTGACTCTAGGTAAAGAAGTTGGAAGTCAAAGCCAAAAA
23001997 GGTAAATGAGGATAGGTTTCTTCTAAG
66 GGTAAATGAGGATAGGTTTCTTCTAAG
23002024 AGTTGTGATC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (103 bp):
ACACACACACACACACACACACACATCTGACTCTAGGTAAAGAAGTTGGAAGTCAAAGCCAAAAA
GGTAAATGAGGATAGGTTTCTTCTAAGCGCACACACAC
Found at i:23005893 original size:11 final size:11
Alignment explanation
Indices: 23005874--23005906 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
23005864 TCACGTCAGC
23005874 ATAATTAATAT
1 ATAATTAATAT
23005885 -TAGATTAATAT
1 ATA-ATTAATAT
23005896 ATAATTAATAT
1 ATAATTAATAT
23005907 CATATCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
ATAATTAATAT
Found at i:23005916 original size:22 final size:22
Alignment explanation
Indices: 23005874--23005918 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
23005864 TCACGTCAGC
* *
23005874 ATAATTAATATTAGATTAATAT
1 ATAATTAATATCAGATCAATAT
*
23005896 ATAATTAATATCATATCAATAT
1 ATAATTAATATCAGATCAATAT
23005918 A
1 A
23005919 AAAGTATCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATTAATATCAGATCAATAT
Found at i:23008601 original size:6 final size:6
Alignment explanation
Indices: 23008590--23008653 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
23008580 AGAGTCTTGA
* * * *
23008590 CAACAG CAACAG CAGCAG CAACAA CAACAG AAACAG CAACGGCGG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAA---CAG CAACAG
*
23008641 CAACAG CCACAG C
1 CAACAG CAACAG C
23008654 CGACAGCACC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
6 41 0.89
9 5 0.11
ACGTcount: A:0.45, C:0.34, G:0.20, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:23012501 original size:2 final size:2
Alignment explanation
Indices: 23012494--23012530 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
23012484 CCTGTATCAC
*
23012494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23012531 AATTTGCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:23028793 original size:12 final size:11
Alignment explanation
Indices: 23028776--23028809 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
23028766 TTTGTCGGAC
23028776 TATATAT-ATA
1 TATATATAATA
23028786 TATATATAATA
1 TATATATAATA
23028797 TA-ATATAATA
1 TATATATAATA
23028807 TAT
1 TAT
23028810 TTCACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 17 0.77
11 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATATAATA
Found at i:23031892 original size:2 final size:2
Alignment explanation
Indices: 23031875--23032096 Score: 161
Period size: 2 Copynumber: 116.5 Consensus size: 2
23031865 AGCTACATAC
* * * *
23031875 AT AT AC AT AC AT AT AT AT AT AT AT AC AT AC 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
* *
23031917 AT AT AC AT AC 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
* ** *
23031959 AT AT AT AT CAT A- AT AT AT AT AT AT AT AT AT A- AT A- AG CC AG
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
23031999 AN A- AT GAT -T GAT -T A- AT AC CT -T AT AT AT AT AT AT AT -T AT
1 AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23032037 AT AT A- AT A- AT A- AT A- AT ACT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
23032075 AT A- AC AT ACT -T AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT A
23032097 AAGCATTTCT
Statistics
Matches: 178, Mismatches: 21, Indels: 42
0.74 0.09 0.17
Matches are distributed among these distances:
1 16 0.09
2 154 0.87
3 8 0.04
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:23031913 original size:22 final size:22
Alignment explanation
Indices: 23031875--23031987 Score: 178
Period size: 22 Copynumber: 5.2 Consensus size: 22
23031865 AGCTACATAC
23031875 ATATACATAC--ATATATATAT
1 ATATACATACATATATATATAT
23031895 ATATACATACATATATATATAT
1 ATATACATACATATATATATAT
23031917 ATATACATACATATATATATAT
1 ATATACATACATATATATATAT
* *
23031939 ATATATATATATATATATATAT
1 ATATACATACATATATATATAT
23031961 ATATATCATA-ATATATATATAT
1 ATATA-CATACATATATATATAT
23031983 ATATA
1 ATATA
23031988 TAATAAGCCA
Statistics
Matches: 87, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
20 10 0.11
22 74 0.85
23 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATACATACATATATATATAT
Found at i:23039686 original size:127 final size:127
Alignment explanation
Indices: 23039460--23039844 Score: 752
Period size: 127 Copynumber: 3.0 Consensus size: 127
23039450 TAGTCAATAA
23039460 GAACTTAATTTCAAGAAGAACATCAATTGTAGTCAAGCAGGTGGCATCGGTTATCAGTCACTGCT
1 GAACTTAATTTCAAGAAGAACATCAATTGTAGTCAAGCAGGTGGCATCGGTTATCAGTCACTGCT
23039525 GGCTCTTGAAGCGATTTTCATGTAAAGAGATTGCTATTGTTGAAGTAGATCTACAACATTGG
66 GGCTCTTGAAGCGATTTTCATGTAAAGAGATTGCTATTGTTGAAGTAGATCTACAACATTGG
23039587 GAACTTAATTTCAAGAAGAACATCAATTGTAGTCAAGCAGGTGGCATCGGTTATCAGTCACTGCT
1 GAACTTAATTTCAAGAAGAACATCAATTGTAGTCAAGCAGGTGGCATCGGTTATCAGTCACTGCT
23039652 GGCTCTTGAAGCGATTTTCATGTAAAGAGATTGCTATTGTTGAAGTAGATCTACAACATTGG
66 GGCTCTTGAAGCGATTTTCATGTAAAGAGATTGCTATTGTTGAAGTAGATCTACAACATTGG
*
23039714 GAACTTAATTTCAAGAAGAACATCAATTGTAGTCAAGCAGGTGGCATCAGTTATCAGTCACTGCT
1 GAACTTAATTTCAAGAAGAACATCAATTGTAGTCAAGCAGGTGGCATCGGTTATCAGTCACTGCT
*
23039779 GGCTCTTGAAGCGATTTTCATGTAAAGAGATCGCTATTGTTGAAGTAGATCTACAACATTGG
66 GGCTCTTGAAGCGATTTTCATGTAAAGAGATTGCTATTGTTGAAGTAGATCTACAACATTGG
23039841 GAAC
1 GAAC
23039845 ATGTTCAATG
Statistics
Matches: 256, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 256 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (127 bp):
GAACTTAATTTCAAGAAGAACATCAATTGTAGTCAAGCAGGTGGCATCGGTTATCAGTCACTGCT
GGCTCTTGAAGCGATTTTCATGTAAAGAGATTGCTATTGTTGAAGTAGATCTACAACATTGG
Found at i:23057238 original size:13 final size:13
Alignment explanation
Indices: 23057220--23057249 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
23057210 GATTTCAAAC
23057220 TGCATAGAGAGAT
1 TGCATAGAGAGAT
23057233 TGCATAGAGAGAT
1 TGCATAGAGAGAT
23057246 TGCA
1 TGCA
23057250 GGGATTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.30, T:0.23
Consensus pattern (13 bp):
TGCATAGAGAGAT
Found at i:23067571 original size:26 final size:24
Alignment explanation
Indices: 23067513--23067578 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 24
23067503 TTATTTAAAA
23067513 ATTTTAAATAAAATTTTATTTTTT
1 ATTTTAAATAAAATTTTATTTTTT
* *
23067537 ATTAGTTAAATCAAATTTATGTATTTTT
1 ATT--TTAAATAAAATTT-TAT-TTTTT
*
23067565 ATTTTAAATTAAAT
1 ATTTTAAATAAAAT
23067579 AAGTCTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 3 0.09
26 22 0.63
27 2 0.06
28 8 0.23
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (24 bp):
ATTTTAAATAAAATTTTATTTTTT
Found at i:23079422 original size:45 final size:45
Alignment explanation
Indices: 23079218--23079424 Score: 254
Period size: 45 Copynumber: 4.6 Consensus size: 45
23079208 ATGACGTGTT
* * *
23079218 ACAGATTTTTGTACATGGCGTGTAATACACTAACCATGGCTTGTC
1 ACAGATTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTC
* * * ** **
23079263 ACAGGTTTTTGTACATGGCTTGTAACACGCTAATTATGATTTGTC
1 ACAGATTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTC
*
23079308 ACA-AGCTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTC
1 ACAGA-TTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTC
* * * *
23079353 ACAGATTTTTGTACATGACGTGTCATACGCTAACTATAGCTTGTC
1 ACAGATTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTC
*
23079398 ACAGATTTTTGTACATGGCTTGTCACA
1 ACAGATTTTTGTACATGGCGTGTCACA
23079425 GGCTTTTGTA
Statistics
Matches: 136, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
45 135 0.99
46 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (45 bp):
ACAGATTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTC
Found at i:23079422 original size:69 final size:69
Alignment explanation
Indices: 23079342--23079493 Score: 234
Period size: 69 Copynumber: 2.2 Consensus size: 69
23079332 ACACGCTAAC
* *
23079342 CATGGCTTGTCACAGATTTTTGTACATGACGTGTCATACGCTAACTATAGCTTGTCAC-AGATTT
1 CATGGCTTGTCACAGACTTTTGTACATGACGTGTCATACGCTAACCATAGCTTGTCACAAG-TTT
*
23079406 TTGTA
65 TTATA
* *
23079411 CATGGCTTGTCACAGGCTTTTGTACATGACGTGTCATACGCTAACCATAGCTTGTCATAAGTTTT
1 CATGGCTTGTCACAGACTTTTGTACATGACGTGTCATACGCTAACCATAGCTTGTCACAAGTTTT
23079476 TATA
66 TATA
*
23079480 CATGGCGTGTCACA
1 CATGGCTTGTCACA
23079494 CGCTAATCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
69 74 0.97
70 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (69 bp):
CATGGCTTGTCACAGACTTTTGTACATGACGTGTCATACGCTAACCATAGCTTGTCACAAGTTTT
TATA
Found at i:23079423 original size:24 final size:24
Alignment explanation
Indices: 23079391--23079438 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
23079381 GCTAACTATA
*
23079391 GCTTGTCACAGATTTTTGTACATG
1 GCTTGTCACAGACTTTTGTACATG
*
23079415 GCTTGTCACAGGCTTTTGTACATG
1 GCTTGTCACAGACTTTTGTACATG
23079439 ACGTGTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (24 bp):
GCTTGTCACAGACTTTTGTACATG
Found at i:23079445 original size:24 final size:24
Alignment explanation
Indices: 23079394--23079446 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
23079384 AACTATAGCT
* * *
23079394 TGTCACAGATTTTTGTACATGGCT
1 TGTCACAGACTTTTGTACATGACG
*
23079418 TGTCACAGGCTTTTGTACATGACG
1 TGTCACAGACTTTTGTACATGACG
23079442 TGTCA
1 TGTCA
23079447 TACGCTAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (24 bp):
TGTCACAGACTTTTGTACATGACG
Found at i:23079464 original size:45 final size:44
Alignment explanation
Indices: 23079415--23079538 Score: 158
Period size: 45 Copynumber: 2.8 Consensus size: 44
23079405 TTTGTACATG
* * *
23079415 GCTTGTCACAGGCTTTTGTACATGACGTGTCATACGCTAACCAT
1 GCTTGTCACAAGTTTTTGTACATGACGTGTCACACGCTAACCAT
* * * *
23079459 AGCTTGTCATAAGTTTTTATACATGGCGTGTCACACGCTAATCAT
1 -GCTTGTCACAAGTTTTTGTACATGACGTGTCACACGCTAACCAT
*
23079504 GATTTGTCACAAGTTTTTGTACATGACGTGTCACA
1 G-CTTGTCACAAGTTTTTGTACATGACGTGTCACA
23079539 AATTTTTGTA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
44 1 0.01
45 66 0.99
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (44 bp):
GCTTGTCACAAGTTTTTGTACATGACGTGTCACACGCTAACCAT
Found at i:23079535 original size:24 final size:24
Alignment explanation
Indices: 23079508--23079558 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
23079498 AATCATGATT
*
23079508 TGTCACAAGTTTTTGTACATGACG
1 TGTCACAAATTTTTGTACATGACG
23079532 TGTCACAAATTTTTGTACATGACG
1 TGTCACAAATTTTTGTACATGACG
23079556 TGT
1 TGT
23079559 AACACGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
TGTCACAAATTTTTGTACATGACG
Found at i:23079599 original size:114 final size:114
Alignment explanation
Indices: 23079304--23079603 Score: 392
Period size: 114 Copynumber: 2.6 Consensus size: 114
23079294 AATTATGATT
* *
23079304 TGTCACAAGCTTTTGTACATGGCGTGTCACACGCTAACCATGGCTTGTCACAGATTTTTGTACAT
1 TGTCACAAGCTTTTGTACATGACGTGTCACACGCTAACCATGGCTTGTCACAGATTTTTATACAT
* * * *
23079369 GACGTGTCATACGCTAACTATAGCTTGTCACAGATTTTTGTACATGGCT
66 GGCGTGTCACACGCTAACTATAGCTTGTCACAGATTTTTGTACATGACG
* * * *
23079418 TGTCACAGGCTTTTGTACATGACGTGTCATACGCTAACCATAGCTTGTCATA-AGTTTTTATACA
1 TGTCACAAGCTTTTGTACATGACGTGTCACACGCTAACCATGGCTTGTCACAGA-TTTTTATACA
*
23079482 TGGCGTGTCACACGCTAA-TCAT-GATTTGTCACA-AGTTTTTGTACATGACG
65 TGGCGTGTCACACGCTAACT-ATAG-CTTGTCACAGA-TTTTTGTACATGACG
** * * *
23079532 TGTCACAAATTTTTGTACATGACGTGTAACACGCTAACCATGGCTTGTCACAGATTTTTTTATAT
1 TGTCACAAGCTTTTGTACATGACGTGTCACACGCTAACCATGGCTTGTCACAGATTTTTATACAT
23079597 GGCGTGT
66 GGCGTGT
23079604 AACATCATAG
Statistics
Matches: 161, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
113 4 0.02
114 156 0.97
115 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (114 bp):
TGTCACAAGCTTTTGTACATGACGTGTCACACGCTAACCATGGCTTGTCACAGATTTTTATACAT
GGCGTGTCACACGCTAACTATAGCTTGTCACAGATTTTTGTACATGACG
Found at i:23117098 original size:13 final size:13
Alignment explanation
Indices: 23117080--23117118 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
23117070 AATTGGTATA
23117080 ATATTTAAAAAAT
1 ATATTTAAAAAAT
23117093 ATATTT---AAAT
1 ATATTTAAAAAAT
23117103 -TATTTAAAAAAT
1 ATATTTAAAAAAT
23117115 ATAT
1 ATAT
23117119 AATTAAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
9 5 0.23
10 4 0.18
12 4 0.18
13 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTTAAAAAAT
Found at i:23117170 original size:13 final size:13
Alignment explanation
Indices: 23117152--23117195 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
23117142 CATTCAATCA
23117152 ATTTTATATTTTT
1 ATTTTATATTTTT
* *
23117165 ATTTTAAATAATTT
1 ATTTTATAT-TTTT
23117179 -TTTTATATTTTT
1 ATTTTATATTTTT
23117191 ATTTT
1 ATTTT
23117196 GAATCAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 19 0.76
14 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTTATATTTTT
Found at i:23125902 original size:14 final size:14
Alignment explanation
Indices: 23125883--23125912 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
23125873 CTAAAATTAT
23125883 AACTTATAAAAAAG
1 AACTTATAAAAAAG
23125897 AACTTATAAAAAAG
1 AACTTATAAAAAAG
23125911 AA
1 AA
23125913 ATTTACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (14 bp):
AACTTATAAAAAAG
Found at i:23130232 original size:37 final size:36
Alignment explanation
Indices: 23130191--23130261 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 36
23130181 AAATTCTAAT
*
23130191 TAGTGGAGTCCTAATAAAATGGGAGTTGTTAGTAGCA
1 TAGTGGAGTCCTAATAAAATGGG-GTGGTTAGTAGCA
23130228 TAGTGGAGTCCTAATAAAATGGGGTGGTTAGTAG
1 TAGTGGAGTCCTAATAAAATGGGGTGGTTAGTAG
23130262 TAGAGTCCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.31, C:0.07, G:0.32, T:0.30
Consensus pattern (36 bp):
TAGTGGAGTCCTAATAAAATGGGGTGGTTAGTAGCA
Found at i:23136564 original size:18 final size:19
Alignment explanation
Indices: 23136524--23136565 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
23136514 ATAGTTTTTG
*
23136524 AAAAGTTTTTTAAAAAAGT
1 AAAATTTTTTTAAAAAAGT
23136543 --AATTTTTTTAAAAAA-T
1 AAAATTTTTTTAAAAAAGT
23136559 AAAATTT
1 AAAATTT
23136566 AAAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
AAAATTTTTTTAAAAAAGT
Found at i:23140301 original size:26 final size:26
Alignment explanation
Indices: 23140272--23140352 Score: 67
Period size: 29 Copynumber: 3.0 Consensus size: 26
23140262 TGCAATTATC
23140272 CATTTTTTATTATTAATTATTATTTT
1 CATTTTTTATTATTAATTATTATTTT
* *
23140298 CATTTTATTTTATTTTTTATTATCATATTTT
1 CA--TT-TTTTATTATTAATTAT--TATTTT
* *
23140329 C-TATTTT-TTACTAATTATTATTTT
1 CATTTTTTATTATTAATTATTATTTT
23140353 TTTATACTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
24 6 0.14
26 10 0.23
27 4 0.09
28 3 0.07
29 14 0.32
31 7 0.16
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (26 bp):
CATTTTTTATTATTAATTATTATTTT
Found at i:23140319 original size:29 final size:31
Alignment explanation
Indices: 23140276--23140335 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
23140266 ATTATCCATT
23140276 TTTTATTATTAATTAT-TATTTTC-ATTTTA
1 TTTTATTATTAATTATATATTTTCTATTTTA
* *
23140305 TTTTATTTTTTATTATCATATTTTCTATTTT
1 TTTTATTATTAATTAT-ATATTTTCTATTTT
23140336 TTACTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
31 7 0.27
32 5 0.19
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTATTATTAATTATATATTTTCTATTTTA
Found at i:23140323 original size:23 final size:23
Alignment explanation
Indices: 23140276--23140338 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
23140266 ATTATCCATT
* * *
23140276 TTTTATTATTAATTATTATTTTCA
1 TTTTATT-TTATTTTTTATTATCA
23140300 TTTTATTTTATTTTTTATTATCA
1 TTTTATTTTATTTTTTATTATCA
* *
23140323 TATT-TTCTATTTTTTA
1 TTTTATTTTATTTTTTA
23140339 CTAATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 11 0.32
23 16 0.47
24 7 0.21
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTATTTTATTTTTTATTATCA
Found at i:23140464 original size:10 final size:10
Alignment explanation
Indices: 23140449--23140526 Score: 68
Period size: 10 Copynumber: 7.6 Consensus size: 10
23140439 GTGACAAAAA
23140449 TTTTATATTT
1 TTTTATATTT
*
23140459 TTTTATTTTT
1 TTTTATATTT
23140469 ATTTTATATTT
1 -TTTTATATTT
* *
23140480 TTATATCTTT
1 TTTTATATTT
* *
23140490 GTATATATTTT
1 TTTTATA-TTT
23140501 TTCTTATATTT
1 TT-TTATATTT
23140512 TTTTAT-TTT
1 TTTTATATTT
*
23140521 TATTAT
1 TTTTAT
23140527 TATCATATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
9 8 0.14
10 26 0.46
11 18 0.32
12 4 0.07
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.76
Consensus pattern (10 bp):
TTTTATATTT
Found at i:23144833 original size:12 final size:12
Alignment explanation
Indices: 23144818--23144852 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
23144808 TTCTCTTTCT
*
23144818 TTTTTTTTTTTA
1 TTTTTTTTTTAA
23144830 TTTTTTTTTTAA
1 TTTTTTTTTTAA
23144842 TTATTTTTTTT
1 TT-TTTTTTTT
23144853 GTTTCTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:23144835 original size:15 final size:15
Alignment explanation
Indices: 23144817--23144852 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
23144807 TTTCTCTTTC
23144817 TTTTTTTTTT--TTA
1 TTTTTTTTTTAATTA
23144830 TTTTTTTTTTAATTA
1 TTTTTTTTTTAATTA
23144845 TTTTTTTT
1 TTTTTTTT
23144853 GTTTCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
15 11 0.52
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTAATTA
Found at i:23144852 original size:19 final size:20
Alignment explanation
Indices: 23144825--23144862 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
23144815 TCTTTTTTTT
* *
23144825 TTTTATTTTTTTTTTAATTA
1 TTTTATTTTGTTTCTAATTA
23144845 TTTT-TTTTGTTTCTAATT
1 TTTTATTTTGTTTCTAATT
23144863 TTATTACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTATTTTGTTTCTAATTA
Found at i:23151176 original size:18 final size:18
Alignment explanation
Indices: 23151153--23151188 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23151143 TTTAATTAAA
23151153 TTAAAAATATATAAAAAT
1 TTAAAAATATATAAAAAT
*
23151171 TTAAAATTATATAAAAAT
1 TTAAAAATATATAAAAAT
23151189 AATTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAATATATAAAAAT
Found at i:23151199 original size:28 final size:29
Alignment explanation
Indices: 23151154--23151210 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
23151144 TTAATTAAAT
23151154 TAAAAATATATAAAAATT-TAAAATTATA
1 TAAAAATATATAAAAATTATAAAATTATA
*
23151182 TAAAAATA-ATTAATAATTAATAAAATTAT
1 TAAAAATATA-TAAAAATT-ATAAAATTAT
23151211 CTATTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 15 0.60
30 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAAAATATATAAAAATTATAAAATTATA
Found at i:23153967 original size:2 final size:2
Alignment explanation
Indices: 23153962--23154023 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
23153952 TATACTTCAA
* *
23153962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT CT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
23154002 AT AT AT AT AT -T AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
23154024 AAAATATTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23158050 original size:28 final size:29
Alignment explanation
Indices: 23157995--23158048 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
23157985 TTTGTTTTTT
*
23157995 ATTTTTTAAAATAATAATATTTATTTTAA
1 ATTTTTAAAAATAATAATATTTATTTTAA
23158024 ATTTTTAAAAAT-ATAA-ATTTATTTT
1 ATTTTTAAAAATAATAATATTTATTTT
23158049 TATTAAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 4 0.17
29 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTTTTAAAAATAATAATATTTATTTTAA
Found at i:23173947 original size:17 final size:17
Alignment explanation
Indices: 23173925--23173959 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
23173915 TCAGTAGCAG
23173925 AAAGAAAAAAAAAAAGA
1 AAAGAAAAAAAAAAAGA
*
23173942 AAAGAAAAGAAAAAAGA
1 AAAGAAAAAAAAAAAGA
23173959 A
1 A
23173960 CGTTAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAAAAAGA
Found at i:23174358 original size:21 final size:21
Alignment explanation
Indices: 23174315--23174359 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
23174305 TTTATATGAA
*
23174315 ATGCACATGATATTACACTTT
1 ATGCACATGATATTACACGTT
* * *
23174336 ATGCATATGATGTTGCACGTT
1 ATGCACATGATATTACACGTT
23174357 ATG
1 ATG
23174360 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (21 bp):
ATGCACATGATATTACACGTT
Found at i:23174451 original size:26 final size:25
Alignment explanation
Indices: 23174415--23174502 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 25
23174405 CGTTATGTAT
23174415 AAAAATATATTACATATCATGATTAAA
1 AAAAAT-TATTACATATCATG-TTAAA
** *
23174442 AAAAATTATTACACGTAATGTTGAAA
1 AAAAATTATTACATATCATGTT-AAA
* *
23174468 AAATATTATTATTATATATCATGTTTAA
1 AAA-A--ATTATTACATATCATGTTAAA
23174496 AAAAATT
1 AAAAATT
23174503 CTGTTACATT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
25 5 0.10
26 17 0.35
27 8 0.16
28 5 0.10
29 14 0.29
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (25 bp):
AAAAATTATTACATATCATGTTAAA
Found at i:23190508 original size:103 final size:102
Alignment explanation
Indices: 23190329--23190544 Score: 263
Period size: 103 Copynumber: 2.1 Consensus size: 102
23190319 GACGTGACAC
* * * *
23190329 TACCACATCATCACAAAAAGCGACATGACATTGCCACATCACACTTTGAATTCAAGTATTGATAT
1 TACCACATCATCACAAAAAGCGACATGACATTACCACATCACACTTTGAATTCAAGTACTAACAT
* * * * * *
23190394 GGCAATGCCACATCACTCTTGTTATCCTGATGTGGCAT
66 GGCAATACCACATCA-TCCTGTCATCCTAACGTAGCAT
* ** *
23190432 TACCACATCATCACAAAAAGTGATGTGACATTACCACATCACACTTT-AAGTTCAAGTACTAACG
1 TACCACATCATCACAAAAAGCGACATGACATTACCACATCACACTTTGAA-TTCAAGTACTAACA
* *
23190496 TGGCACTACCACATCATCCTGTCATGCTAACGTAGCAT
65 TGGCAATACCACATCATCCTGTCATCCTAACGTAGCAT
23190534 TACCACATCAT
1 TACCACATCAT
23190545 AATTTGGGTT
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
102 29 0.30
103 67 0.70
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (102 bp):
TACCACATCATCACAAAAAGCGACATGACATTACCACATCACACTTTGAATTCAAGTACTAACAT
GGCAATACCACATCATCCTGTCATCCTAACGTAGCAT
Found at i:23190589 original size:23 final size:23
Alignment explanation
Indices: 23190563--23190607 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
23190553 TTCGAGATGT
*
23190563 CACATAGCACACCCAGAGGTTGC
1 CACATAGCACACCAAGAGGTTGC
* *
23190586 CACATGGCACACCAAGATGTTG
1 CACATAGCACACCAAGAGGTTG
23190608 ACATGTGGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (23 bp):
CACATAGCACACCAAGAGGTTGC
Found at i:23197270 original size:21 final size:21
Alignment explanation
Indices: 23197246--23197285 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23197236 TGGACATTCC
23197246 ATTATCGATAT-TATATTAATG
1 ATTATC-ATATCTATATTAATG
*
23197267 ATTATCTTATCTATATTAA
1 ATTATCATATCTATATTAA
23197286 ATAAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
ATTATCATATCTATATTAATG
Found at i:23197527 original size:21 final size:21
Alignment explanation
Indices: 23197503--23197542 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
23197493 TGGACATTCC
23197503 ATTATCGATAT-TATATTAATG
1 ATTATC-ATATCTATATTAATG
*
23197524 ATTATCTTATCTATATTAA
1 ATTATCATATCTATATTAA
23197543 ATAAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
ATTATCATATCTATATTAATG
Found at i:23197602 original size:257 final size:257
Alignment explanation
Indices: 23197146--23197659 Score: 958
Period size: 257 Copynumber: 2.0 Consensus size: 257
23197136 CGAAATTCGA
* *
23197146 ATTAAGACCCTCTCATCATACTAGTGGAGTCTTAATCGAAATCCTTAACCTAAGGAAATTCACTC
1 ATTAAGACCCTCTCATCATACTAGTAGAGTCTTAATCGAAATCCTTAACCTAAGAAAATTCACTC
23197211 GAAATTGCGACTCTCGCGTTTCGAATGGACATTCCATTATCGATATTATATTAATGATTATCTTA
66 GAAATTGCGACTCTCGCGTTTCGAATGGACATTCCATTATCGATATTATATTAATGATTATCTTA
23197276 TCTATATTAAATAAATTCATTTTTATCCCATTTTCATCATATCTTTATTTTTTATAAAACTATCT
131 TCTATATTAAATAAATTCATTTTTATCCCATTTTCATCATATCTTTATTTTTTATAAAACTATCT
23197341 CTTTGAACTAGTTTATTATCCATAAATGAAAATTTTATTTATTTATTTATTA-TATTACTTT
196 CTTTGAACTAGTTTATTATCCATAAATGAAAATTTTATTTATTTATTTATTATTATTACTTT
* * * *
23197402 NATTAAGACCCTCTCATCGTACTGGTAGAGTTTTAATCGAAATCTTTAACCTAAGAAAATTCACT
1 -ATTAAGACCCTCTCATCATACTAGTAGAGTCTTAATCGAAATCCTTAACCTAAGAAAATTCACT
23197467 CGAAATTGCGACTCTCGCGTTTCGAATGGACATTCCATTATCGATATTATATTAATGATTATCTT
65 CGAAATTGCGACTCTCGCGTTTCGAATGGACATTCCATTATCGATATTATATTAATGATTATCTT
23197532 ATCTATATTAAATAAATTCATTTTTATCCCATTTTCATCATATCTTTATTTTTTATAAAACTATC
130 ATCTATATTAAATAAATTCATTTTTATCCCATTTTCATCATATCTTTATTTTTTATAAAACTATC
23197597 TCTTTGAACTAGTTTATTATCCATAAATGAAAATTTTATTTATTTATTTATTATTATTACTTT
195 TCTTTGAACTAGTTTATTATCCATAAATGAAAATTTTATTTATTTATTTATTATTATTACTTT
23197660 TATTTATCAT
Statistics
Matches: 250, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
257 241 0.96
258 9 0.04
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (257 bp):
ATTAAGACCCTCTCATCATACTAGTAGAGTCTTAATCGAAATCCTTAACCTAAGAAAATTCACTC
GAAATTGCGACTCTCGCGTTTCGAATGGACATTCCATTATCGATATTATATTAATGATTATCTTA
TCTATATTAAATAAATTCATTTTTATCCCATTTTCATCATATCTTTATTTTTTATAAAACTATCT
CTTTGAACTAGTTTATTATCCATAAATGAAAATTTTATTTATTTATTTATTATTATTACTTT
Found at i:23198743 original size:14 final size:14
Alignment explanation
Indices: 23198724--23198768 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
23198714 CTCCAGCTTC
23198724 TTTTTTATTTTTAT
1 TTTTTTATTTTTAT
*
23198738 TTTTTTATTTTGGAT
1 TTTTTTATTTT-TAT
23198753 TTTTTTATTATTTAT
1 TTTTTTATT-TTTAT
23198768 T
1 T
23198769 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 11 0.41
15 14 0.52
16 2 0.07
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:23198754 original size:15 final size:14
Alignment explanation
Indices: 23198724--23198761 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
23198714 CTCCAGCTTC
*
23198724 TTTTTTATTTTTAT
1 TTTTTTATTTTGAT
23198738 TTTTTTATTTTGGAT
1 TTTTTTATTTT-GAT
23198753 TTTTTTATT
1 TTTTTTATT
23198762 ATTTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (14 bp):
TTTTTTATTTTGAT
Found at i:23198770 original size:10 final size:9
Alignment explanation
Indices: 23198734--23198779 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
23198724 TTTTTTATTT
23198734 TTATTTTT-
1 TTATTTTTA
*
23198742 TTATTTTGGA
1 TTATTTT-TA
23198752 TT-TTTTTA
1 TTATTTTTA
23198760 TTATTTATTA
1 TTATTT-TTA
23198770 TTATTTTTA
1 TTATTTTTA
23198779 T
1 T
23198780 ATTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
8 10 0.31
9 11 0.34
10 11 0.34
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (9 bp):
TTATTTTTA
Found at i:23198782 original size:18 final size:18
Alignment explanation
Indices: 23198727--23198782 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
23198717 CAGCTTCTTT
* *
23198727 TTTATTTTTATTTTTTTA
1 TTTATTATTATTTTTATA
*
23198745 TTT-TGGATT-TTTTTATTA
1 TTTAT-TATTATTTTTA-TA
23198763 TTTATTATTATTTTTATA
1 TTTATTATTATTTTTATA
23198781 TT
1 TT
23198783 ATATATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
17 6 0.20
18 17 0.57
19 7 0.23
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTATTATTATTTTTATA
Found at i:23199916 original size:22 final size:21
Alignment explanation
Indices: 23199858--23199950 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 21
23199848 AGAGAAGAAA
*
23199858 AAAGAAAAAGGAGAAAGA-AG
1 AAAGAAAAAGGAGAAAAAGAG
*
23199878 AAAGAGAAAAGAAGAAAAAGAG
1 AAAGA-AAAAGGAGAAAAAGAG
* *
23199900 AAAGAAATAAGGGGAAAAAGGG
1 AAAGAAA-AAGGAGAAAAAGAG
*
23199922 GAAGAAGGAGAAGGAGAAAGAA-AG
1 AAAGAA--A-AAGGAGAAA-AAGAG
23199946 AAAGA
1 AAAGA
23199951 GAGAAGAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
20 5 0.09
21 13 0.23
22 23 0.40
24 14 0.25
25 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAGGAGAAAAAGAG
Found at i:23199919 original size:52 final size:52
Alignment explanation
Indices: 23199846--23199965 Score: 135
Period size: 52 Copynumber: 2.3 Consensus size: 52
23199836 TATAGCTGGG
*
23199846 AGAGAGAAGAAAAA--AGAAAAAGGAGAAAGAA-GA-AA-GAGAAAAGAAGAAAA
1 AGAGAGAAGAAAAAGGGGAAAAAGG-GAAAGAAGGAGAAGGAG-AAAGAA-AAAA
* *
23199896 AGAGA-AAGAAATAAGGGGAAAAAGGGGAAGAAGGAGAAGGAGAAAGAAAGAA
1 AGAGAGAAGAAA-AAGGGGAAAAAGGGAAAGAAGGAGAAGGAGAAAGAAAAAA
23199948 AGAGAGAAGAAAAAGGGG
1 AGAGAGAAGAAAAAGGGG
23199966 GGAGCGGTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
49 6 0.10
50 7 0.12
51 6 0.10
52 24 0.40
53 14 0.23
54 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (52 bp):
AGAGAGAAGAAAAAGGGGAAAAAGGGAAAGAAGGAGAAGGAGAAAGAAAAAA
Found at i:23199956 original size:22 final size:22
Alignment explanation
Indices: 23199847--23199952 Score: 71
Period size: 22 Copynumber: 4.8 Consensus size: 22
23199837 ATAGCTGGGA
23199847 GAGAGAAGAAA-AAAGA-AAAAG
1 GAGA-AAGAAAGAAAGAGAAAAG
23199868 GAGAAAG-AAGAAAGAGAAAAG
1 GAGAAAGAAAGAAAGAGAAAAG
*
23199889 AAGAAA-AAGAGAAAGA-AATAAG
1 GAGAAAGAA-AGAAAGAGAA-AAG
* * * *
23199911 GGGAAA-AAGGGGAAGAAGGAGAAG
1 GAGAAAGAA-AGAAAG-A-GAAAAG
23199935 GAGAAAGAAAGAAAGAGA
1 GAGAAAGAAAGAAAGAGA
23199953 GAAGAAAAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.03
20 8 0.12
21 17 0.25
22 23 0.34
23 2 0.03
24 12 0.18
25 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (22 bp):
GAGAAAGAAAGAAAGAGAAAAG
Found at i:23200009 original size:23 final size:22
Alignment explanation
Indices: 23199982--23200033 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
23199972 GTTGGGAGAG
*
23199982 AAGAAGAA-AGCAAAAGCAAAAGA
1 AAGAAGAACAGAAAAAG-AAAA-A
23200005 AAGAAAGAACAGAAAAAGAAAAA
1 AAG-AAGAACAGAAAAAGAAAAA
23200028 AAGAAG
1 AAGAAG
23200034 GAAAAGGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 3 0.12
23 7 0.27
24 9 0.35
25 7 0.27
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (22 bp):
AAGAAGAACAGAAAAAGAAAAA
Found at i:23200021 original size:19 final size:19
Alignment explanation
Indices: 23199985--23200032 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
23199975 GGGAGAGAAG
*
23199985 AAGAAAGCAAAAGCAAAAGA
1 AAGAAAG-AAAAGAAAAAGA
*
23200005 AAGAAAGAACAGAAAAAGA
1 AAGAAAGAAAAGAAAAAGA
*
23200024 AAAAAAGAA
1 AAGAAAGAA
23200033 GGAAAAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAAAGAAAAAGA
Found at i:23200419 original size:38 final size:36
Alignment explanation
Indices: 23200376--23200470 Score: 91
Period size: 38 Copynumber: 2.5 Consensus size: 36
23200366 TATAAAAATT
* *
23200376 ATAAAAAATAAAAATAAATTATGAAGAAGAATAAAGAA
1 ATAAAAAATAAAAATAAATAAT-AACAAGAA-AAAGAA
* * *
23200414 ATAAAAAAGAAAAAACATAATAATAACAAGAAATAGAA
1 ATAAAAAA-TAAAAATA-AATAATAACAAGAAAAAGAA
*
23200452 ATAATAAATAAATAATAAA
1 ATAAAAAATAAA-AATAAA
23200471 ATATACATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
37 5 0.11
38 23 0.50
39 13 0.28
40 5 0.11
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (36 bp):
ATAAAAAATAAAAATAAATAATAACAAGAAAAAGAA
Found at i:23200651 original size:7 final size:7
Alignment explanation
Indices: 23200641--23200673 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
23200631 ATATAAAATG
23200641 AAATAAT
1 AAATAAT
23200648 AAATAA-
1 AAATAAT
23200654 AAATAAT
1 AAATAAT
23200661 AAATAAT
1 AAATAAT
23200668 AAATAA
1 AAATAA
23200674 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:23200657 original size:13 final size:14
Alignment explanation
Indices: 23200641--23200673 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
23200631 ATATAAAATG
23200641 AAATAATAAATAA-
1 AAATAATAAATAAT
23200654 AAATAATAAATAAT
1 AAATAATAAATAAT
23200668 AAATAA
1 AAATAA
23200674 ATTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAATAAATAAT
Found at i:23202045 original size:13 final size:13
Alignment explanation
Indices: 23202029--23202081 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
23202019 ATATAAAATG
23202029 AAATAATAAATAA
1 AAATAATAAATAA
23202042 AAATAATAAATAA
1 AAATAATAAATAA
*
23202055 ATAATAA-AAAGAA
1 A-AATAATAAATAA
*
23202068 AAAAAAT-AATAA
1 AAATAATAAATAA
23202080 AA
1 AA
23202082 TAGCAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 10 0.29
13 20 0.57
14 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:23202082 original size:26 final size:27
Alignment explanation
Indices: 23202014--23202083 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
23202004 ATAATTGTTT
*
23202014 AAAAAAT-ATAAAATGAAATAATAAATAA
1 AAAAAATAATAAAAT--AATAATAAAGAA
*
23202042 AAATAATAA-ATAAATAATAA-AAAGAA
1 AAAAAATAATA-AAATAATAATAAAGAA
23202068 AAAAAATAATAAAATA
1 AAAAAATAATAAAATA
23202084 GCAAATAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 18 0.50
27 6 0.17
28 7 0.19
29 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (27 bp):
AAAAAATAATAAAATAATAATAAAGAA
Found at i:23229984 original size:21 final size:21
Alignment explanation
Indices: 23229946--23229989 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
23229936 ACCGCAATTA
* *
23229946 AATTTGAAGAACAAAAAATCC
1 AATTTGAAAAACAAAAAACCC
* *
23229967 AATTTGAAAAATAGAAAACCC
1 AATTTGAAAAACAAAAAACCC
23229988 AA
1 AA
23229990 GTACAAACAA
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:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (21 bp):
AATTTGAAAAACAAAAAACCC
Found at i:23258584 original size:35 final size:35
Alignment explanation
Indices: 23258545--23258611 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
23258535 CAAAGGAAAA
*
23258545 GTCATGTCTATTGGAAATTAA-AAAATAAAGGATGG
1 GTCATGTCTATT-GAAAATAAGAAAATAAAGGATGG
* *
23258580 GTCATGTTTGTTGAAAATAAGAAAATAAAGGA
1 GTCATGTCTATTGAAAATAAGAAAATAAAGGA
23258612 ATTTGTTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.25
35 21 0.75
ACGTcount: A:0.45, C:0.04, G:0.22, T:0.28
Consensus pattern (35 bp):
GTCATGTCTATTGAAAATAAGAAAATAAAGGATGG
Found at i:23260469 original size:28 final size:28
Alignment explanation
Indices: 23260410--23260484 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
23260400 AAGCATTAAA
* * * *
23260410 GTGTAACAA-AATGTTTTTGAATATGTC
1 GTGTAACAACAATATTTTTTAACATGAC
*
23260437 ATGTAACAACAATATTTTTTAACATGAC
1 GTGTAACAACAATATTTTTTAACATGAC
23260465 GTGTAACAACAATATTTTTT
1 GTGTAACAACAATATTTTTT
23260485 TTTCAATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 8 0.20
28 33 0.80
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (28 bp):
GTGTAACAACAATATTTTTTAACATGAC
Found at i:23260619 original size:82 final size:82
Alignment explanation
Indices: 23260438--23260640 Score: 211
Period size: 82 Copynumber: 2.5 Consensus size: 82
23260428 GAATATGTCA
* * *
23260438 TGTAACAACAATATTTTTTAACATGACGTGTAACAACAATATTTTTTTTTCAATATAGCATGTAA
1 TGTAACAACAATATTTTTTTACATGGCGTGTAACAACAATATTTTTTTTTCAACATAGCATGTAA
* *
23260503 CAACCTTTTTTAATTATGACG
66 CAA----TTCTAATCATGACG
* * * *
23260524 TGT---AAC-ATGTTTTTTTACTTGGCGTGTAACAATAATATTTTTTTTTCAACATAGCGTGTAA
1 TGTAACAACAATATTTTTTTACATGGCGTGTAACAACAATATTTTTTTTTCAACATAGCATGTAA
23260585 CAA-TCTAATCATGGA-G
66 CAATTCTAATCAT-GACG
23260601 TGTAACAACAATATTTTTTTTCAACATGGCGTGTAACAAC
1 TGTAACAACAATA-TTTTTTT--ACATGGCGTGTAACAAC
23260641 TAAACCATGA
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
77 11 0.11
78 2 0.02
80 3 0.03
81 2 0.02
82 58 0.60
83 3 0.03
84 15 0.15
86 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (82 bp):
TGTAACAACAATATTTTTTTACATGGCGTGTAACAACAATATTTTTTTTTCAACATAGCATGTAA
CAATTCTAATCATGACG
Found at i:23260699 original size:21 final size:21
Alignment explanation
Indices: 23260670--23260710 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
23260660 TGTTTTTGTA
23260670 CATGACGTGTAACAACCTAAT
1 CATGACGTGTAACAACCTAAT
*
23260691 CATGGCGTGTAACAACCTAA
1 CATGACGTGTAACAACCTAA
23260711 CCATAGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (21 bp):
CATGACGTGTAACAACCTAAT
Found at i:23260732 original size:66 final size:66
Alignment explanation
Indices: 23260625--23260760 Score: 186
Period size: 66 Copynumber: 2.1 Consensus size: 66
23260615 TTTTTTTCAA
* *
23260625 CATGGCGTGTAACAACTAAACCATGACTTGTCACATGTTTTTGTACATGACGTGTAACAACCTAA
1 CATGGCGTGTAACAACTAAACCATGACTTGTCACATATTTTTGTACATGACGTATAACAACCTAA
*
23260690 T
66 C
* * *
23260691 CATGGCGTGTAACAACCT-AACCAT-AGTTTGTTACATATTTTTGTACATGGCGTATAACAACCT
1 CATGGCGTGTAACAA-CTAAACCATGA-CTTGTCACATATTTTTGTACATGACGTATAACAACCT
23260754 AAC
64 AAC
23260757 CATG
1 CATG
23260761 ACTTATCACA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
65 1 0.02
66 59 0.95
67 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (66 bp):
CATGGCGTGTAACAACTAAACCATGACTTGTCACATATTTTTGTACATGACGTATAACAACCTAA
C
Found at i:23260741 original size:111 final size:111
Alignment explanation
Indices: 23260624--23260871 Score: 374
Period size: 111 Copynumber: 2.2 Consensus size: 111
23260614 TTTTTTTTCA
* * *
23260624 ACATGGCGTGTAACAA-CTAAACCATGACTTGTCACATGTTTTTGTACATGACGTGTAACAACCT
1 ACATGGCGTATAACAACCT-AACCATGACTTATCACATATTTTTGTACATGACGTGTAACAACCT
* * * *
23260688 AATCATGGCGTGTAACAACCTAACCAT-AGTTTGTTACATATTTTTGT
65 AATCATGGCGTGTAACAACCTAACAATGA-CTTGTCACATATTTTTAT
23260735 ACATGGCGTATAACAACCTAACCATGACTTATCACATATTTTTGTACATGACGTGTAACAACCTA
1 ACATGGCGTATAACAACCTAACCATGACTTATCACATATTTTTGTACATGACGTGTAACAACCTA
*
23260800 ATCATGGTGTGTAACAACCTAACAATGACTTGTCACATATTTTTAT
66 ATCATGGCGTGTAACAACCTAACAATGACTTGTCACATATTTTTAT
**
23260846 ACATAACGTATAACAACCTAACCATG
1 ACATGGCGTATAACAACCTAACCATG
23260872 GCGTGCAATA
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
111 122 0.98
112 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (111 bp):
ACATGGCGTATAACAACCTAACCATGACTTATCACATATTTTTGTACATGACGTGTAACAACCTA
ATCATGGCGTGTAACAACCTAACAATGACTTGTCACATATTTTTAT
Found at i:23260755 original size:45 final size:45
Alignment explanation
Indices: 23260691--23260805 Score: 160
Period size: 45 Copynumber: 2.6 Consensus size: 45
23260681 ACAACCTAAT
* * *
23260691 CATGGCGTGTAACAACCTAACCAT-AGTTTGTTACATATTTTTGTA
1 CATGGCGTGTAACAACCTAACCATGA-CTTATCACATATTTTTGTA
*
23260736 CATGGCGTATAACAACCTAACCATGACTTATCACATATTTTTGTA
1 CATGGCGTGTAACAACCTAACCATGACTTATCACATATTTTTGTA
* *
23260781 CATGACGTGTAACAACCTAATCATG
1 CATGGCGTGTAACAACCTAACCATG
23260806 GTGTGTAACA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 61 0.98
46 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (45 bp):
CATGGCGTGTAACAACCTAACCATGACTTATCACATATTTTTGTA
Found at i:23260816 original size:66 final size:66
Alignment explanation
Indices: 23260736--23260875 Score: 208
Period size: 66 Copynumber: 2.1 Consensus size: 66
23260726 TATTTTTGTA
* * * *
23260736 CATGGCGTATAACAACCTAACCATGACTTATCACATATTTTTGTACATGACGTGTAACAACCTAA
1 CATGGCGTATAACAACCTAACAATGACTTATCACATATTTTTATACATAACGTATAACAACCTAA
*
23260801 T
66 C
* * *
23260802 CATGGTGTGTAACAACCTAACAATGACTTGTCACATATTTTTATACATAACGTATAACAACCTAA
1 CATGGCGTATAACAACCTAACAATGACTTATCACATATTTTTATACATAACGTATAACAACCTAA
23260867 C
66 C
23260868 CATGGCGT
1 CATGGCGT
23260876 GCAATATCAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (66 bp):
CATGGCGTATAACAACCTAACAATGACTTATCACATATTTTTATACATAACGTATAACAACCTAA
C
Found at i:23263455 original size:139 final size:138
Alignment explanation
Indices: 23263236--23263497 Score: 474
Period size: 139 Copynumber: 1.9 Consensus size: 138
23263226 TTTTAAAATT
23263236 ATGTAATGTGGAACTTTTTTAATGGTGTGATTTAATTTTTGAAATTGGACGCCCAACATGTCATA
1 ATGTAATGTGGAACTTTTTTAATGGTGTGATTTAATTTTTGAAATTGGACGCCCAACATGTCATA
23263301 ATGAAATATATTATATTTTTATTTTAGAATAAAATT-AGTAAAAATT-TCCAAAAGCAAATTTGA
66 ATGAAATATATTATATTTTTATTTTAGAATAAAATTCA-TAAAAATTCT-CAAAAGCAAATTTGA
23263364 AAATTAAAAA
129 AAATTAAAAA
23263374 ATGTAATGTGGAACTTTTTTAATGGTGTGATTTAATTTTTGAAATTGGTACGCCCAACATGTCAT
1 ATGTAATGTGGAACTTTTTTAATGGTGTGATTTAATTTTTGAAATTGG-ACGCCCAACATGTCAT
*
23263439 AATGGAATATATTATATTTTTATTTTAGAATAAAATTCATAAAAATTCTCAAAAGCAAA
65 AATGAAATATATTATATTTTTATTTTAGAATAAAATTCATAAAAATTCTCAAAAGCAAA
23263498 ACAACTATGA
Statistics
Matches: 120, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
138 48 0.40
139 70 0.58
140 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (138 bp):
ATGTAATGTGGAACTTTTTTAATGGTGTGATTTAATTTTTGAAATTGGACGCCCAACATGTCATA
ATGAAATATATTATATTTTTATTTTAGAATAAAATTCATAAAAATTCTCAAAAGCAAATTTGAAA
ATTAAAAA
Found at i:23265489 original size:21 final size:21
Alignment explanation
Indices: 23265463--23265505 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
23265453 ATGGCGTGTG
23265463 ACATCATATGCAC-TGCATATA
1 ACATCATATGCACTTG-ATATA
*
23265484 ACATCATGTGCACTTGATATA
1 ACATCATATGCACTTGATATA
23265505 A
1 A
23265506 AGAGATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (21 bp):
ACATCATATGCACTTGATATA
Found at i:23275036 original size:2 final size:2
Alignment explanation
Indices: 23275031--23275060 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23275021 GTGTGTGTGT
23275031 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
23275061 TACCTTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23278806 original size:21 final size:21
Alignment explanation
Indices: 23278780--23278822 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
23278770 GGAATTGCAA
23278780 GCCTCTGCCCCACATTTGGGT
1 GCCTCTGCCCCACATTTGGGT
23278801 GCCTCTGCCCCACATTTGGGT
1 GCCTCTGCCCCACATTTGGGT
23278822 G
1 G
23278823 TCTCAGCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.37, G:0.26, T:0.28
Consensus pattern (21 bp):
GCCTCTGCCCCACATTTGGGT
Found at i:23283412 original size:3 final size:3
Alignment explanation
Indices: 23283404--23283432 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23283394 TTATGATATT
23283404 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
23283433 TTAATCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:23292632 original size:24 final size:24
Alignment explanation
Indices: 23292603--23292656 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
23292593 TTCATTAATA
23292603 AAAATTTAATAAAATT-A-TAAAAT
1 AAAATTTAA-AAAATTAATTAAAAT
*
23292626 AATAATTTTAAAAATTAATTAAAAT
1 AA-AATTTAAAAAATTAATTAAAAT
23292651 AAAATT
1 AAAATT
23292657 ATCTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 8 0.30
24 11 0.41
25 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATTTAAAAAATTAATTAAAAT
Found at i:23296560 original size:15 final size:16
Alignment explanation
Indices: 23296530--23296561 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
23296520 ATTATTAATG
23296530 TTTAAAAATAAGATAA
1 TTTAAAAATAAGATAA
23296546 TTTAAAAATAA-ATAA
1 TTTAAAAATAAGATAA
23296561 T
1 T
23296562 CATAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TTTAAAAATAAGATAA
Found at i:23296600 original size:26 final size:26
Alignment explanation
Indices: 23296545--23296600 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
23296535 AAATAAGATA
*
23296545 ATTTAAAAATAAATAATCATAATAAC
1 ATTTAAAAATAAATAATAATAATAAC
* * *
23296571 ATTTAAATTATAAATAA-AATATTAAT
1 ATTTAAA-AATAAATAATAATAATAAC
23296597 ATTT
1 ATTT
23296601 TATAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTAAAAATAAATAATAATAATAAC
Found at i:23296651 original size:26 final size:27
Alignment explanation
Indices: 23296604--23296660 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
23296594 AATATTTTAT
* **
23296604 AATATTAATAATTAGATTATAA-ACAA
1 AATATTAATAATTAAAAAATAAGACAA
* *
23296630 AATATTAATATTTAAAAAATAAGATAA
1 AATATTAATAATTAAAAAATAAGACAA
23296657 AATA
1 AATA
23296661 AATAATCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (27 bp):
AATATTAATAATTAAAAAATAAGACAA
Found at i:23305211 original size:22 final size:22
Alignment explanation
Indices: 23305181--23305231 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
23305171 TAGTTACAAT
*
23305181 TTTTTATATGAAGAGACGTAAC
1 TTTTCATATGAAGAGACGTAAC
23305203 TTTTCATATGAAGAGACGTAAC
1 TTTTCATATGAAGAGACGTAAC
23305225 TTTTCAT
1 TTTTCAT
23305232 TTTGTTACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
TTTTCATATGAAGAGACGTAAC
Found at i:23310634 original size:22 final size:22
Alignment explanation
Indices: 23310609--23310655 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
23310599 AAACATTGAC
* * *
23310609 ATAGATTTACTATAGATTCATA
1 ATAGATTGACGATAAATTCATA
*
23310631 ATAGATTGACGATAAATTTATA
1 ATAGATTGACGATAAATTCATA
23310653 ATA
1 ATA
23310656 AAATTACACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (22 bp):
ATAGATTGACGATAAATTCATA
Found at i:23314120 original size:65 final size:65
Alignment explanation
Indices: 23314000--23314122 Score: 158
Period size: 65 Copynumber: 1.9 Consensus size: 65
23313990 AAACGAAATT
* * * * * *
23314000 TCCTCCCCTGGTTTTTGAAAATCAGGTGAAATTAAGGCGATGGGTGGTTTCCTTATCAGGAGCTC
1 TCCTCCCCTGGTTCTTGAAAATCAAGTCAAATTAAGGCGATGGCTGGCTGCCTTATCAGGAGCTC
* *
23314065 TCCTCCCCTGGTTCTTGAAAATCAAGTCAAATTAAGGTTG-TGGCTGGCTGGCTTATCA
1 TCCTCCCCTGGTTCTTGAAAATCAAGTCAAATTAAGG-CGATGGCTGGCTGCCTTATCA
23314123 CAAGAGCTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 48 0.98
66 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (65 bp):
TCCTCCCCTGGTTCTTGAAAATCAAGTCAAATTAAGGCGATGGCTGGCTGCCTTATCAGGAGCTC
Found at i:23314356 original size:2 final size:2
Alignment explanation
Indices: 23314349--23314407 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
23314339 TCAACTAACG
*
23314349 AT AT AT AT AT AT AT AT AT AT AG 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
23314391 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
23314408 CACAAATGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23349554 original size:23 final size:23
Alignment explanation
Indices: 23349528--23349832 Score: 75
Period size: 23 Copynumber: 13.6 Consensus size: 23
23349518 AAGTAAATAA
23349528 TAAAAATATTTTTTATTAAAATT
1 TAAAAATATTTTTTATTAAAATT
* * **
23349551 TAAATA-ATTTTTAATTAAAAAA
1 TAAAAATATTTTTTATTAAAATT
* * * *
23349573 TAAAAA-AATTATGATGAGAAA--
1 TAAAAATATTTTTTATTA-AAATT
23349594 T--AAATATTTTTTATTAAAATT
1 TAAAAATATTTTTTATTAAAATT
* * **
23349615 AAAAAAT-TTATTTTGTTAAAAAA
1 TAAAAATATT-TTTTATTAAAATT
** * *
23349638 TAAAAATATTTTAAGCAATAAAA-C
1 TAAAAATATTTT--TTATTAAAATT
** * *
23349662 T-AAAATAACTTTTACTATAA-T
1 TAAAAATATTTTTTATTAAAATT
* *
23349683 TAAATAATA-TTTTTATCAAAATA
1 TAAA-AATATTTTTTATTAAAATT
* * * *
23349706 TAAATATA-TATTTAATATAATT
1 TAAAAATATTTTTTATTAAAATT
* * **
23349728 TAATAATATTTTGTATTAAAAGA
1 TAAAAATATTTTTTATTAAAATT
* *
23349751 TAATTAA-ATTTTTTATT-ATA-T
1 TAA-AAATATTTTTTATTAAAATT
** **
23349772 TAAATAATATTTAATATTAAAAAA
1 TAAA-AATATTTTTTATTAAAATT
*
23349796 TAAATATATCTTTTTATT-AAATT
1 TAAAAATAT-TTTTTATTAAAATT
*
23349819 TAAATAATANTTTT
1 TAAA-AATATTTTT
23349833 AATAATATTA
Statistics
Matches: 197, Mismatches: 64, Indels: 42
0.65 0.21 0.14
Matches are distributed among these distances:
19 6 0.03
20 7 0.04
21 12 0.06
22 65 0.33
23 83 0.42
24 19 0.10
25 5 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAAAATATTTTTTATTAAAATT
Found at i:23349576 original size:22 final size:23
Alignment explanation
Indices: 23349521--23349649 Score: 65
Period size: 22 Copynumber: 5.8 Consensus size: 23
23349511 AAATAATAAG
* *
23349521 TAAATAATAAAAATATTTTTTAT
1 TAAAAAATAAAAATATTTTTAAT
** *
23349544 TAAAATTTAAATA-ATTTTTAAT
1 TAAAAAATAAAAATATTTTTAAT
* * *
23349566 TAAAAAATAAAAA-AATTATGA-
1 TAAAAAATAAAAATATTTTTAAT
* * *
23349587 TGAGAAAT--AAATATTTTTTAT
1 TAAAAAATAAAAATATTTTTAAT
* **
23349608 T-AAAATTAAAAA-ATTTATTTTGT
1 TAAAAAATAAAAATA-TT-TTTAAT
23349631 TAAAAAATAAAAATATTTT
1 TAAAAAATAAAAATATTTT
23349650 AAGCAATAAA
Statistics
Matches: 78, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
19 3 0.04
20 9 0.12
21 8 0.10
22 28 0.36
23 17 0.22
24 12 0.15
25 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
TAAAAAATAAAAATATTTTTAAT
Found at i:23349736 original size:22 final size:21
Alignment explanation
Indices: 23349671--23349739 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
23349661 CTAAAATAAC
* *
23349671 TTTTACTATAATTAAATAATA
1 TTTTAATATAATTTAATAATA
* * *
23349692 TTTTTATCAAAATATAA-ATATA
1 TTTTAAT-ATAATTTAATA-ATA
23349714 TATTTAATATAATTTAATAATA
1 T-TTTAATATAATTTAATAATA
23349736 TTTT
1 TTTT
23349740 GTATTAAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
21 9 0.25
22 21 0.58
23 6 0.17
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAATATAATTTAATAATA
Found at i:23349783 original size:45 final size:45
Alignment explanation
Indices: 23349521--23349833 Score: 180
Period size: 45 Copynumber: 7.0 Consensus size: 45
23349511 AAATAATAAG
* * * *
23349521 TAAATAATAAAAATATTTTTTATTAAAATTTAAATAAT-TTTTAAT
1 TAAAAAATAAATATATTTTTTATTATAA-TTAAATAATATTTTTAT
* * * * * * *
23349566 TAAAAAATAAA-AAAATTATGATGAGAAATAAAT-AT-TTTTTAT
1 TAAAAAATAAATATATTTTTTATTATAATTAAATAATATTTTTAT
* * * * * *
23349608 TAAAATTAAAAAATTTATTTTGTTA--AAAAATAAA-AATATTTTAAG
1 TAAAA--AATAAATATATTTT-TTATTATAATTAAATAATATTTTTAT
* ** *
23349653 CAATAAAACTAAA-ATAACTTTTACTATAATTAAATAATATTTTTAT
1 TAA-AAAA-TAAATATATTTTTTATTATAATTAAATAATATTTTTAT
* * * * *
23349699 CAAAATATAAATATA-TATTTAATATAATTTAATAATATTTTGTAT
1 TAAAAAATAAATATATTTTTTATTATAATTAAATAATATTTT-TAT
* * * *
23349744 TAAAAGATAATTAAATTTTTTATTAT-ATTAAATAATATTTAATAT
1 TAAAAAATAAATATATTTTTTATTATAATTAAATAATATTT-TTAT
*
23349789 TAAAAAATAAATATATCTTTTTATTA-AATTTAAATAATANTTTTA
1 TAAAAAATAAATATAT-TTTTTATTATAA-TTAAATAATATTTTTA
23349834 ATAATATTAT
Statistics
Matches: 205, Mismatches: 45, Indels: 35
0.72 0.16 0.12
Matches are distributed among these distances:
42 13 0.06
43 8 0.04
44 57 0.28
45 79 0.39
46 36 0.18
47 12 0.06
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (45 bp):
TAAAAAATAAATATATTTTTTATTATAATTAAATAATATTTTTAT
Found at i:23349866 original size:17 final size:17
Alignment explanation
Indices: 23349836--23349876 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
23349826 TANTTTTAAT
23349836 AATAT-TATATTATATGA
1 AATATATATATTATAT-A
23349853 AATATATATA-TATATA
1 AATATATATATTATATA
23349869 AATA-ATAT
1 AATATATAT
23349877 TTAAACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 5 0.22
17 10 0.43
18 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATATATATATTATATA
Found at i:23353479 original size:26 final size:26
Alignment explanation
Indices: 23353450--23353501 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
23353440 AAGGACCAGG
23353450 TGATGCCTAAGCCAATTGACCTGATA
1 TGATGCCTAAGCCAATTGACCTGATA
23353476 TGATGCCTAAGCCAATTGACCTGATA
1 TGATGCCTAAGCCAATTGACCTGATA
23353502 AAAGGTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (26 bp):
TGATGCCTAAGCCAATTGACCTGATA
Found at i:23357663 original size:14 final size:14
Alignment explanation
Indices: 23357644--23357674 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23357634 CAAACATCAA
23357644 GCAATCATACCATT
1 GCAATCATACCATT
23357658 GCAATCATACCATT
1 GCAATCATACCATT
23357672 GCA
1 GCA
23357675 TGACGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.26
Consensus pattern (14 bp):
GCAATCATACCATT
Found at i:23359033 original size:23 final size:23
Alignment explanation
Indices: 23359001--23359045 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
23358991 GACTGGAATA
23359001 GCATTACAGAGTCATTTTCTAAT
1 GCATTACAGAGTCATTTTCTAAT
*
23359024 GCATTCCAGAGTCATTTTCTAA
1 GCATTACAGAGTCATTTTCTAA
23359046 GGAGTGTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (23 bp):
GCATTACAGAGTCATTTTCTAAT
Found at i:23360396 original size:2 final size:2
Alignment explanation
Indices: 23360386--23360418 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23360376 TCTCTCTCTC
*
23360386 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23360419 GCAGAGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23389819 original size:7 final size:7
Alignment explanation
Indices: 23389807--23389831 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
23389797 TTAACCCTCT
23389807 CTCAGGC
1 CTCAGGC
23389814 CTCAGGC
1 CTCAGGC
23389821 CTCAGGC
1 CTCAGGC
23389828 CTCA
1 CTCA
23389832 CACTTTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (7 bp):
CTCAGGC
Found at i:23392131 original size:9 final size:9
Alignment explanation
Indices: 23392119--23392152 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
23392109 TAATAATTAA
23392119 TTTAAAATT
1 TTTAAAATT
*
23392128 TTTAAATAGT
1 TTTAAA-ATT
23392138 TTTAAAATT
1 TTTAAAATT
23392147 TTTAAA
1 TTTAAA
23392153 TATTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (9 bp):
TTTAAAATT
Found at i:23412686 original size:2 final size:2
Alignment explanation
Indices: 23412679--23412763 Score: 95
Period size: 2 Copynumber: 43.0 Consensus size: 2
23412669 ACTTACAATG
* *
23412679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GCT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
* *
23412721 GT AT -T ACT NT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23412762 AT
1 AT
23412764 TTATGCATGT
Statistics
Matches: 73, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
1 3 0.04
2 68 0.93
3 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:23415182 original size:27 final size:28
Alignment explanation
Indices: 23415126--23415188 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
23415116 TTTTATCATG
* * *
23415126 ACGTATAACAATTATATCTTTCTACATA
1 ACGTGTAACAATTAAATCTTTCGACATA
*
23415154 ACGTGTAACAATTAAAT-TTTCGATATA
1 ACGTGTAACAATTAAATCTTTCGACATA
*
23415181 ACCTGTAA
1 ACGTGTAA
23415189 TAATCACATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (28 bp):
ACGTGTAACAATTAAATCTTTCGACATA
Found at i:23451724 original size:75 final size:75
Alignment explanation
Indices: 23451630--23451821 Score: 251
Period size: 76 Copynumber: 2.5 Consensus size: 75
23451620 CAATATTTTT
* * *
23451630 TTTAACATGACGTATAACATGTTTTTGTACATGGCATGTAACAATAATATTTTTTTT-AATATGA
1 TTTAACATGACGTATAACATGTTTTTGTACATGACATGTAACAACAATATTTTTTTTCAACATGA
*
23451694 CGTGTAATAA
66 CGTGTAACAA
* * * * *
23451704 TTTAACCATGATGTGTAACATGTTTTTGTATATGACGTGTAACAACAGTATTTTTTTTCAACATG
1 TTTAA-CATGACGTATAACATGTTTTTGTACATGACATGTAACAACAATATTTTTTTTCAACATG
23451769 ACGTGTAACAA
65 ACGTGTAACAA
** *
23451780 CCTAATCATGACGTATTACATGTTTTTGTACATGACATGTAA
1 TTTAA-CATGACGTATAACATGTTTTTGTACATGACATGTAA
23451822 TAGCTTAATC
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 5 0.05
75 45 0.45
76 49 0.49
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (75 bp):
TTTAACATGACGTATAACATGTTTTTGTACATGACATGTAACAACAATATTTTTTTTCAACATGA
CGTGTAACAA
Found at i:23451845 original size:121 final size:121
Alignment explanation
Indices: 23451690--23451951 Score: 362
Period size: 121 Copynumber: 2.2 Consensus size: 121
23451680 TTTTTTTAAT
* * * *
23451690 ATGACGTGTAATAATTTAACCATGATGTGTAACATGTTTTTGTATATGACGTGTAACAACAGTAT
1 ATGACGTGTAATAACTTAACCATGATATGTAACATGTTTTTGTACATGACGTGTAACAACAATAT
* * *
23451755 TTTTTTTCAACATGACGTGTAACAACCTAATCATGACGTATTACATGTTTTTGTAC
66 TTTTTTTCAACATGACGTGTAACAACCTAACCATGACATATTACATATTTTTGTAC
* * * * * *
23451811 ATGACATGTAATAGCTTAATCATGGTATGTAACATGTTTTTGTACATGACGTGTAATAATAATAT
1 ATGACGTGTAATAACTTAACCATGATATGTAACATGTTTTTGTACATGACGTGTAACAACAATAT
* * ** *
23451876 TTTTTTTTAACATGACGTGTAATAATTTAACCATGATATATTACATATTTTTGTAC
66 TTTTTTTCAACATGACGTGTAACAACCTAACCATGACATATTACATATTTTTGTAC
23451932 ATGACGTGTAATAACTTAAC
1 ATGACGTGTAATAACTTAAC
23451952 TATAACGTAT
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (121 bp):
ATGACGTGTAATAACTTAACCATGATATGTAACATGTTTTTGTACATGACGTGTAACAACAATAT
TTTTTTTCAACATGACGTGTAACAACCTAACCATGACATATTACATATTTTTGTAC
Done.