Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 4 of 203
Found at i:1007590 original size:18 final size:18
Alignment explanation
Indices: 1007564--1007613 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1007554 CGGGCTTGGG
1007564 ATAGTTTGGGCTTGTTTA
1 ATAGTTTGGGCTTGTTTA
* * *
1007582 ATGGTTTGGGCCTATTTA
1 ATAGTTTGGGCTTGTTTA
*
1007600 TTAGTTTGGGCTTG
1 ATAGTTTGGGCTTG
1007614 GGCATATTTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.08, G:0.30, T:0.48
Consensus pattern (18 bp):
ATAGTTTGGGCTTGTTTA
Found at i:1008541 original size:83 final size:86
Alignment explanation
Indices: 1008445--1008621 Score: 234
Period size: 93 Copynumber: 2.0 Consensus size: 86
1008435 CCGAAGCAAC
* * *
1008445 TACAATTTCATTTCAATATT-C-AATCATGC-AAACAAAAATTGAGTTTTTAAAACTTCTAATAA
1 TACAATTTCATTTCAATATTACAAATCATGCAAAAAAAAAATTGAGTCTTTAAAACGTCTAATAA
1008507 CATTAATTGTTCAAATCCGGG
66 CATTAATTGTTCAAATCCGGG
1008528 TACAATTTCATTTCAATATTCAAAAGACAAATCATGCAAAAAAAAAAATTGAGTCTTTAAAACGT
1 TACAATTTCATTTCAATATT------ACAAATCATGC-AAAAAAAAAATTGAGTCTTTAAAACGT
*
1008593 CTAATAACATTAATTGTTCAAATCTGGG
59 CTAATAACATTAATTGTTCAAATCCGGG
1008621 T
1 T
1008622 TATAAATAGG
Statistics
Matches: 80, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
83 20 0.25
90 1 0.01
91 8 0.10
93 51 0.64
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (86 bp):
TACAATTTCATTTCAATATTACAAATCATGCAAAAAAAAAATTGAGTCTTTAAAACGTCTAATAA
CATTAATTGTTCAAATCCGGG
Found at i:1009560 original size:20 final size:20
Alignment explanation
Indices: 1009528--1009565 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1009518 TATCATGCCA
1009528 TATACCAACA-TTTAATTCT
1 TATACCAACATTTTAATTCT
1009547 TATACCATACATTTTAATT
1 TATACCA-ACATTTTAATT
1009566 ACATGGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 3 0.18
21 7 0.41
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (20 bp):
TATACCAACATTTTAATTCT
Found at i:1013907 original size:41 final size:41
Alignment explanation
Indices: 1013852--1013961 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
1013842 TTAATTTAAA
* * *
1013852 CAGATTCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
*
1013894 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
*
1013935 CAGTTCACCGGCACTTAGCCTGCTAGG
1 CAGATCACCGGCACTTAGCCTGCTAGG
1013962 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
41 59 0.94
42 4 0.06
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
Found at i:1028260 original size:39 final size:39
Alignment explanation
Indices: 1028001--1028408 Score: 300
Period size: 39 Copynumber: 10.5 Consensus size: 39
1027991 TGATTTGTTG
* ** *** *
1028001 ATTTACGATCACGACCTTCGACTTTTTTATAATATGCTA
1 ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
* * * * * *** * *
1028040 ATTTATGATCATGATCTTTGACTTTTTTACAATCCGCTA
1 ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
* * * *
1028079 ATTTACGATCACGACCTTCAATTTTTTTATGGTCCGCTT
1 ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
* * * *
1028118 ATTTACGATCACGACCTTTGATTTTCTTACGGTCCACTG
1 ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
** * * * * *
1028157 ATTTATTATCACGGCCTTCAACTTTCTTATAGTCCGCTA
1 ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
* * *
1028196 ATTTATGATCACAACCTTCGACTTTCTTATGGTACACTT
1 ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
* * *
1028235 ATTTAAGATCATGACCTTCGACTTTCTTATGGTCCACTG
1 ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
* * *
1028274 ATTTATGATCACGACC-TCTGACTTTCTTACGGTTCA-TT
1 ATTTACGATCACGACCTTC-GACTTTCTTATGGTCCACTT
* * * * *
1028312 GATTTACGATCATGACTTTCGGCTTTCTTACGGTTCA-TT
1 -ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
* * * * *
1028351 GATTTACGATCATGACTTTCGCCTTTCTTATGGTTCACTG
1 -ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
*
1028391 ATTTACGATCACGGCCTT
1 ATTTACGATCACGACCTT
1028409 TTACTTACAA
Statistics
Matches: 304, Mismatches: 61, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
38 3 0.01
39 298 0.98
40 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (39 bp):
ATTTACGATCACGACCTTCGACTTTCTTATGGTCCACTT
Found at i:1028447 original size:54 final size:53
Alignment explanation
Indices: 1028383--1028570 Score: 214
Period size: 54 Copynumber: 3.5 Consensus size: 53
1028373 CTTTCTTATG
* * ** *
1028383 GTTCACTGATTTACGATCACGGCCTTTTACTTACAAGATTTTATGAGTCTCGCA
1 GTTCGCTGATTTACGATCACGACCTTTTACTTACGGGATTTTATGAATCTCG-A
* *
1028437 GTTCGCTGATTTACGATCACGACCTTTTACTTACGGGATTTTACGAATCTCGT
1 GTTCGCTGATTTACGATCACGACCTTTTACTTACGGGATTTTATGAATCTCGA
* * * * *
1028490 GGTCTGCTGATTTACAATCACGACTTTTTACTTACGGGATTTTATGAATTTCGTG
1 GTTC-GCTGATTTACGATCACGACCTTTTACTTACGGGATTTTATGAATCTCG-A
* * *
1028545 GTTTGCTGATTTATGACCACGACCTT
1 GTTCGCTGATTTACGATCACGACCTT
1028571 CGGCTTTCTT
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 3 0.03
54 108 0.96
55 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.39
Consensus pattern (53 bp):
GTTCGCTGATTTACGATCACGACCTTTTACTTACGGGATTTTATGAATCTCGA
Found at i:1028615 original size:39 final size:39
Alignment explanation
Indices: 1028548--1028765 Score: 204
Period size: 39 Copynumber: 5.6 Consensus size: 39
1028538 TTTCGTGGTT
* * * *
1028548 TGCTGATTTATGACCACGACCTTCGGCTTTCTTATGACC
1 TGCTGATTTACGATCACAACCTTCGGCTTTCTTATGATC
* * * * *
1028587 CGTTGATTTACGATCACAAACTTTGGCTTTCTTATGGTC
1 TGCTGATTTACGATCACAACCTTCGGCTTTCTTATGATC
* * ** * * *
1028626 TGTTGATTTACGGTCACAGTCATCGGCTTTCTTATGGTT
1 TGCTGATTTACGATCACAACCTTCGGCTTTCTTATGATC
* * *
1028665 TGCTGGTTTACGATCACGACCTTTGGCTTTCTTAT-AGTC
1 TGCTGATTTACGATCACAACCTTCGGCTTTCTTATGA-TC
* * * *
1028704 TGCTGATTTACGATCACGACCTTCGACTTTCTTATGGTT
1 TGCTGATTTACGATCACAACCTTCGGCTTTCTTATGATC
*
1028743 TGCTGATTTATGATCACAACCTT
1 TGCTGATTTACGATCACAACCTT
1028766 TTACTTACAA
Statistics
Matches: 144, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
39 144 1.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.40
Consensus pattern (39 bp):
TGCTGATTTACGATCACAACCTTCGGCTTTCTTATGATC
Found at i:1028680 original size:78 final size:78
Alignment explanation
Indices: 1028548--1028766 Score: 251
Period size: 78 Copynumber: 2.8 Consensus size: 78
1028538 TTTCGTGGTT
* * * * **** * *
1028548 TGCTGATTTATGACCACGACCTTCGGCTTTCTTATGACCCGTTGATTTACGATCACAAACTTTGG
1 TGCTGATTTACGATCACGACCATCGACTTTCTTATGGTTTGCTGATTTACGATCACAACCTTTGG
*
1028613 CTTTCTTATGGTC
66 CTTTCTTATAGTC
* * * * * *
1028626 TGTTGATTTACGGTCAC-AGTCATCGGCTTTCTTATGGTTTGCTGGTTTACGATCACGACCTTTG
1 TGCTGATTTACGATCACGA-CCATCGACTTTCTTATGGTTTGCTGATTTACGATCACAACCTTTG
1028690 GCTTTCTTATAGTC
65 GCTTTCTTATAGTC
* *
1028704 TGCTGATTTACGATCACGACCTTCGACTTTCTTATGGTTTGCTGATTTATGATCACAACCTTT
1 TGCTGATTTACGATCACGACCATCGACTTTCTTATGGTTTGCTGATTTACGATCACAACCTTT
1028767 TACTTACAAG
Statistics
Matches: 116, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
77 1 0.01
78 114 0.98
79 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (78 bp):
TGCTGATTTACGATCACGACCATCGACTTTCTTATGGTTTGCTGATTTACGATCACAACCTTTGG
CTTTCTTATAGTC
Found at i:1028760 original size:117 final size:117
Alignment explanation
Indices: 1028543--1028760 Score: 285
Period size: 117 Copynumber: 1.9 Consensus size: 117
1028533 ATGAATTTCG
* *
1028543 TGGTTTGCTGATTTATGACCACGACCTTCGGCTTTCTTATGACCCGTTGATTTACGATCACAAAC
1 TGGTTTGCTGATTTACGACCACGACCTTCGGCTTTCTTATGACCCGCTGATTTACGATCACAAAC
* * * *
1028608 TTTGGCTTTCTTATGGTCTGTTGATTTACGGTCACAGTCATCGGCTTTCTTA
66 TTCGACTTTCTTATGGTCTGCTGATTTACGATCACAGTCATCGGCTTTCTTA
* * * * * * *
1028660 TGGTTTGCTGGTTTACGATCACGACCTTTGGCTTTCTTAT-AGTCTGCTGATTTACGATCACGAC
1 TGGTTTGCTGATTTACGACCACGACCTTCGGCTTTCTTATGA-CCCGCTGATTTACGATCACAAA
* *
1028724 CTTCGACTTTCTTATGGTTTGCTGATTTATGATCACA
65 CTTCGACTTTCTTATGGTCTGCTGATTTACGATCACA
1028761 ACCTTTTACT
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
116 1 0.01
117 84 0.99
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.41
Consensus pattern (117 bp):
TGGTTTGCTGATTTACGACCACGACCTTCGGCTTTCTTATGACCCGCTGATTTACGATCACAAAC
TTCGACTTTCTTATGGTCTGCTGATTTACGATCACAGTCATCGGCTTTCTTA
Found at i:1028808 original size:54 final size:54
Alignment explanation
Indices: 1028744--1028983 Score: 284
Period size: 54 Copynumber: 4.4 Consensus size: 54
1028734 CTTATGGTTT
* *
1028744 GCTGATTTATGATCACAACCTTTTACTTACAAGATTTTATGAATCTCACAGTCC
1 GCTGATTTATGATCACAACCTTTTACTTACGAGATTTTACGAATCTCACAGTCC
* ** **
1028798 GCTGATTTATGATCACAACCTTTTACTTATGAGATTTTACGAATCTC-GTGATAT
1 GCTGATTTATGATCACAACCTTTTACTTACGAGATTTTACGAATCTCACAG-TCC
* * * * **
1028852 GTTGATTTATGATCACGATCTTTTACTTACGGGATTTTACGAATCTTGCAGTCC
1 GCTGATTTATGATCACAACCTTTTACTTACGAGATTTTACGAATCTCACAGTCC
** ** *
1028906 ATTGATTTACAATCACAACCTTTTACTTACGGGATTTTACGAATCTCACAGTCC
1 GCTGATTTATGATCACAACCTTTTACTTACGAGATTTTACGAATCTCACAGTCC
* *
1028960 GCTGATTTACGATCACGACCTTTT
1 GCTGATTTATGATCACAACCTTTT
1028984 GCAATCTTAT
Statistics
Matches: 156, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
53 1 0.01
54 154 0.99
55 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (54 bp):
GCTGATTTATGATCACAACCTTTTACTTACGAGATTTTACGAATCTCACAGTCC
Found at i:1032328 original size:44 final size:44
Alignment explanation
Indices: 1032280--1032750 Score: 636
Period size: 44 Copynumber: 10.7 Consensus size: 44
1032270 GTAATTTTCA
* * * * * * *
1032280 ACCTACTCCACAGCTGCTCAGGGAGCTAGGACTTACAATCTTCT
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
* * *
1032324 ACCTATTCCACTGTTGGTCAGGGAGCTAGGACTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
* ** *
1032368 ACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
* * * ** *
1032412 GCCTATTCCACTGCTGTTCAGGGAGCTAGAACTTACAATCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
* **
1032456 ACCTATTCCACTGCTGGTTAGGGAACTAGGGCTTACAGTCTTTT
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
1032500 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
* * * * *
1032544 ACTTGTTCCACTGATAGTCAGGGAACTAGGGCTTGCAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
*
1032588 ACCTATTCCACTGCTGGTCAAGGAACTAGGGCTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
* * *
1032632 ACCTATTCCACTACTGGTTAGGGAACTAGGGCTTGCAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
* *
1032676 ACCTATTCCACAGCTGGTTAGGGAACTAGGGCTTACAGTCTTCC
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
1032720 ACCTATTCCACTGCTGGTCAGGGAACTAGGG
1 ACCTATTCCACTGCTGGTCAGGGAACTAGGG
1032751 TTTATGATTT
Statistics
Matches: 382, Mismatches: 45, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 382 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGGTCAGGGAACTAGGGCTTACAGTCTTCC
Found at i:1047705 original size:24 final size:24
Alignment explanation
Indices: 1047678--1047732 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1047668 ATTTTGTGGC
1047678 ATTTCTATAAATACAGTTCACAAT
1 ATTTCTATAAATACAGTTCACAAT
* * * *
1047702 ATTTTTGTAAATGCAGTTCACAGT
1 ATTTCTATAAATACAGTTCACAAT
*
1047726 AATTCTA
1 ATTTCTA
1047733 CAATACATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (24 bp):
ATTTCTATAAATACAGTTCACAAT
Found at i:1047776 original size:71 final size:71
Alignment explanation
Indices: 1047616--1047777 Score: 216
Period size: 71 Copynumber: 2.3 Consensus size: 71
1047606 TGGGTATTAC
* ** * *
1047616 AATACAGTTTGCAGTATTTCTGTAAATACAGTTCATTGTAATTCTACAATATATTTTGTGGCATT
1 AATACAGTTTGCAGTATTTTTGTAAATACAGTTCACAGTAATTCTACAATACATTTTGCGGCATT
1047681 TCTATA
66 TCTATA
** * *
1047687 AATACAGTTCACAATATTTTTGTAAATGCAGTTCACAGTAATTCTACAATACATTTTGCGGCATT
1 AATACAGTTTGCAGTATTTTTGTAAATACAGTTCACAGTAATTCTACAATACATTTTGCGGCATT
*
1047752 TCTGTA
66 TCTATA
* *
1047758 AATATAGTTTGCGGTATTTT
1 AATACAGTTTGCAGTATTTT
1047778 ACAACACAGT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 76 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (71 bp):
AATACAGTTTGCAGTATTTTTGTAAATACAGTTCACAGTAATTCTACAATACATTTTGCGGCATT
TCTATA
Found at i:1049051 original size:10 final size:10
Alignment explanation
Indices: 1049038--1049082 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
1049028 AATTTATTTT
1049038 AAAAAATATA
1 AAAAAATATA
1049048 AAAAAAT-TA
1 AAAAAATATA
1049057 AAAAATATATA
1 AAAAA-ATATA
1049068 AAAAAATATA
1 AAAAAATATA
1049078 AAAAA
1 AAAAA
1049083 GTTATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.21
10 19 0.58
11 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAAATATA
Found at i:1058397 original size:21 final size:21
Alignment explanation
Indices: 1058371--1058413 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1058361 TTTGGGAGGA
1058371 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
1058392 TCAGCTCTTACGAGCTTTTGT
1 TCAGCTCTTACGAGCTTCTGT
1058413 T
1 T
1058414 GGCGTATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:1060928 original size:39 final size:40
Alignment explanation
Indices: 1060833--1061055 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
1060823 TTGAATGATG
*
1060833 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
1060871 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
1060912 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1060951 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
1060990 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
1061029 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
1061056 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1061019 original size:79 final size:81
Alignment explanation
Indices: 1060833--1061055 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
1060823 TTGAATGATG
* * *
1060833 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
1060895 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
1060912 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
1060973 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
1060990 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
1061054 TG
66 TG
1061056 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:1061077 original size:79 final size:79
Alignment explanation
Indices: 1060833--1061088 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
1060823 TTGAATGATG
* * * *
1060833 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
1060894 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
1060912 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
1060976 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
1060990 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
1061053 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
1061070 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
1061089 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:1069069 original size:40 final size:40
Alignment explanation
Indices: 1069014--1069224 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
1069004 ATTTGAATGA
*
1069014 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
1069054 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * *
1069094 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * *
1069134 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
1069174 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
1069214 TATCC-GGCTAA
1 TATCCGGGCTAA
1069225 ATTCCGAAGA
Statistics
Matches: 156, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
39 7 0.04
40 146 0.94
41 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:1072065 original size:32 final size:32
Alignment explanation
Indices: 1072024--1072088 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1072014 CCTACTAAAC
1072024 CTGCTGATAGTGTGGGAAGTGTACGAAATGCT
1 CTGCTGATAGTGTGGGAAGTGTACGAAATGCT
1072056 CTGCTGATAGTGTGGGAAGTGTACGAAATGCT
1 CTGCTGATAGTGTGGGAAGTGTACGAAATGCT
1072088 C
1 C
1072089 CGAAGCCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.28
Consensus pattern (32 bp):
CTGCTGATAGTGTGGGAAGTGTACGAAATGCT
Found at i:1077023 original size:21 final size:21
Alignment explanation
Indices: 1076974--1077071 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
1076964 GGATCAACTT
*
1076974 TCACGAGCTTCTGTTAAGCTC
1 TCACGAGCTTCTGTTCAGCTC
*** *
1076995 TTTTGAGCTTCTGTTCTGCTC
1 TCACGAGCTTCTGTTCAGCTC
*
1077016 TCACGAGCTTTTGTTCAGCTC
1 TCACGAGCTTCTGTTCAGCTC
*
1077037 TCACGAGCTTTTGTTCA-CTC
1 TCACGAGCTTCTGTTCAGCTC
1077057 TCACGAGCTTCTGTT
1 TCACGAGCTTCTGTT
1077072 GGTGTATTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
20 17 0.26
21 49 0.74
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (21 bp):
TCACGAGCTTCTGTTCAGCTC
Found at i:1078160 original size:56 final size:56
Alignment explanation
Indices: 1078074--1078193 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
1078064 ACAAGGGATG
1078074 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
1078130 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1078186 ATGGGCAA
1 ATGGGCAA
1078194 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:1079463 original size:39 final size:40
Alignment explanation
Indices: 1079364--1079507 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
1079354 CGAATGATGT
* * *
1079364 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAA
* * *
1079404 CCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-A
*
1079444 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
*
1079483 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1079508 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 34 0.39
40 43 0.49
41 10 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
Found at i:1079521 original size:40 final size:39
Alignment explanation
Indices: 1079416--1079514 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
1079406 AGACTAAGAT
** * *
1079416 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGC
1 CCGAAGGCATTTGAACGAGTTACTATA-ACCGGGCTAAGC
** *
1079455 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAG-C
1079495 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGAACGAGT
1079515 AGCTATATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.62
40 20 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAGC
Found at i:1079526 original size:79 final size:80
Alignment explanation
Indices: 1079363--1079513 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
1079353 TCGAATGATG
*
1079363 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
**
1079428 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * * *
1079443 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCAGACTAAGAT-CCGAAGGCAT
1079505 TTGAACGAG
64 TTGAACGAG
1079514 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:1087615 original size:111 final size:111
Alignment explanation
Indices: 1087421--1087623 Score: 388
Period size: 111 Copynumber: 1.8 Consensus size: 111
1087411 NNNNNNNNNN
*
1087421 TTTTGAGTCTAGTTTCTATAGAAACAAACGACATCAGTATTGAAGCCCTGTGCAGGGAGATATCC
1 TTTTGAGTCTAGTTTCTATAGAAACAAACGACATCAGTATTGAAGCCCTGTACAGGGAGATATCC
1087486 AAGTCGTAATGCGCAAAGGTCAGTGTACATATATGAATAGATTCCT
66 AAGTCGTAATGCGCAAAGGTCAGTGTACATATATGAATAGATTCCT
*
1087532 TTTTGAGTCTAGTTTCTATAGAAACAAACGGCATCAGTATTGAAGCCCTGTACAGGGAGATATCC
1 TTTTGAGTCTAGTTTCTATAGAAACAAACGACATCAGTATTGAAGCCCTGTACAGGGAGATATCC
1087597 AAGTCGTAATGCGCAAAGGTCAGTGTA
66 AAGTCGTAATGCGCAAAGGTCAGTGTA
1087624 GTCGATCCCT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 90 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (111 bp):
TTTTGAGTCTAGTTTCTATAGAAACAAACGACATCAGTATTGAAGCCCTGTACAGGGAGATATCC
AAGTCGTAATGCGCAAAGGTCAGTGTACATATATGAATAGATTCCT
Found at i:1090399 original size:37 final size:37
Alignment explanation
Indices: 1090338--1090439 Score: 127
Period size: 37 Copynumber: 2.7 Consensus size: 37
1090328 AATATGCTCT
*
1090338 ATCGAGCCAAATCTTATTGTTATACTGAA-TGAAGCTTA
1 ATCGAG-CAAATCTTATCGTTATACTGAATTG-AGCTTA
* *
1090376 ATCGAGCAAGTCATATCGTTATACTGAATTGAGCTTA
1 ATCGAGCAAATCTTATCGTTATACTGAATTGAGCTTA
*
1090413 A-CTGAGCAAATCTTATCGATATACTGA
1 ATC-GAGCAAATCTTATCGTTATACTGA
1090440 CTGATGTTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
36 1 0.02
37 47 0.84
38 8 0.14
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (37 bp):
ATCGAGCAAATCTTATCGTTATACTGAATTGAGCTTA
Found at i:1097019 original size:14 final size:14
Alignment explanation
Indices: 1096983--1097019 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1096973 GAGAGCTCAA
1096983 GAACGACCAATAAT
1 GAACGACCAATAAT
*
1096997 GAACAACCAATAAT
1 GAACGACCAATAAT
*
1097011 GAATGACCA
1 GAACGACCA
1097020 TGATATATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACGACCAATAAT
Found at i:1102250 original size:39 final size:39
Alignment explanation
Indices: 1102186--1102283 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
1102176 TTTCATTCCA
* *
1102186 TTAGCTAATTTTTTTTAC-TTAATTTATGCTTTATTTTAT
1 TTAG-TAATTTTTATCACATTAATTTATGCTTTATTTTAT
*
1102225 TTATTAATTTTTATCACATTAATTTATGCTTTATTTTAT
1 TTAGTAATTTTTATCACATTAATTTATGCTTTATTTTAT
1102264 TTAGTAATTTTTATCACATT
1 TTAGTAATTTTTATCACATT
1102284 TTCCTTAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 11 0.20
39 43 0.80
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (39 bp):
TTAGTAATTTTTATCACATTAATTTATGCTTTATTTTAT
Found at i:1129057 original size:32 final size:32
Alignment explanation
Indices: 1129021--1129117 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
1129011 CGTGCTGAAG
1129021 ATGGTGGGGAAATGCATTCTTCTGCTGTGGAT
1 ATGGTGGGGAAATGCATTCTTCTGCTGTGGAT
* * *
1129053 ATGGT---G--A--CCTTGCTT-TGCGTGCTGAAG
1 ATGGTGGGGAAATGCATT-CTTCTGC-TG-TGGAT
1129080 ATGGTGGGGAAATGCATTCTTCTGCTGTGGAT
1 ATGGTGGGGAAATGCATTCTTCTGCTGTGGAT
1129112 ATGGTG
1 ATGGTG
1129118 ACCTTCAAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 22
0.63 0.08 0.29
Matches are distributed among these distances:
25 6 0.12
26 5 0.10
27 9 0.19
29 1 0.02
30 1 0.02
32 15 0.31
33 5 0.10
34 6 0.12
ACGTcount: A:0.18, C:0.13, G:0.35, T:0.34
Consensus pattern (32 bp):
ATGGTGGGGAAATGCATTCTTCTGCTGTGGAT
Found at i:1129075 original size:59 final size:59
Alignment explanation
Indices: 1129009--1129122 Score: 228
Period size: 59 Copynumber: 1.9 Consensus size: 59
1128999 GGAGAGAATA
1129009 TGCGTGCTGAAGATGGTGGGGAAATGCATTCTTCTGCTGTGGATATGGTGACCTTGCTT
1 TGCGTGCTGAAGATGGTGGGGAAATGCATTCTTCTGCTGTGGATATGGTGACCTTGCTT
1129068 TGCGTGCTGAAGATGGTGGGGAAATGCATTCTTCTGCTGTGGATATGGTGACCTT
1 TGCGTGCTGAAGATGGTGGGGAAATGCATTCTTCTGCTGTGGATATGGTGACCTT
1129123 CAAGGAGGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.18, C:0.15, G:0.34, T:0.33
Consensus pattern (59 bp):
TGCGTGCTGAAGATGGTGGGGAAATGCATTCTTCTGCTGTGGATATGGTGACCTTGCTT
Found at i:1135297 original size:21 final size:20
Alignment explanation
Indices: 1135259--1135298 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1135249 ATATCACTTG
* *
1135259 AAAGTAATTTTTTTAAATAT
1 AAAGTAATTTTGTAAAATAT
1135279 AAAGTGAATTTTGTAAAATA
1 AAAGT-AATTTTGTAAAATA
1135299 ATGTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (20 bp):
AAAGTAATTTTGTAAAATAT
Found at i:1135546 original size:30 final size:31
Alignment explanation
Indices: 1135502--1135559 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1135492 ACAAGAAAGT
1135502 GATTTTAAACTTTAA-AAAT-TATTTAAACAC
1 GATTTTAAACTTTAATAAATGT-TTTAAACAC
**
1135532 GATTTTAATTTTTAATAAATGTTTTAAA
1 GATTTTAAACTTTAATAAATGTTTTAAA
1135560 TGCATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.54
31 10 0.42
32 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
GATTTTAAACTTTAATAAATGTTTTAAACAC
Found at i:1136239 original size:2 final size:2
Alignment explanation
Indices: 1136232--1136256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1136222 ACATGATTGC
1136232 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 T
1136257 TTTGCTTTTA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1138192 original size:25 final size:25
Alignment explanation
Indices: 1138138--1138197 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
1138128 AACAATTATC
*
1138138 GTATTAATGTTATTTAAATTGAATT
1 GTATTAATATTATTTAAATTGAATT
*
1138163 TTATT-ATATTATTTATAATGTGAA-T
1 GTATTAATATTATTTA-AAT-TGAATT
*
1138188 GTATTGATAT
1 GTATTAATAT
1138198 ATAAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 9 0.31
25 12 0.41
26 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (25 bp):
GTATTAATATTATTTAAATTGAATT
Found at i:1141372 original size:24 final size:24
Alignment explanation
Indices: 1141345--1141463 Score: 93
Period size: 25 Copynumber: 4.8 Consensus size: 24
1141335 TCATTAGGGA
* *
1141345 TTACTGATTTTAGCTCATGAGAGC
1 TTACTGATTTCAGCTCGTGAGAGC
*
1141369 TTACCGATTCTCAGCTCGT-ATGAGC
1 TTACTGATT-TCAGCTCGTGA-GAGC
1141394 TTA-TCGATTTCAGCTCGTGAGAGC
1 TTACT-GATTTCAGCTCGTGAGAGC
* *
1141418 TTA-TCGATTCTCAGTTCAT-ATGAGC
1 TTACT-GATT-TCAGCTCGTGA-GAGC
*
1141443 TTACCGATTTACAGCTCGTGA
1 TTACTGATTT-CAGCTCGTGA
1141464 AAGCATACCG
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
24 33 0.43
25 43 0.56
26 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (24 bp):
TTACTGATTTCAGCTCGTGAGAGC
Found at i:1141393 original size:25 final size:25
Alignment explanation
Indices: 1141365--1141492 Score: 122
Period size: 25 Copynumber: 5.2 Consensus size: 25
1141355 TAGCTCATGA
1141365 GAGCTTACCGATTCTCAGCTCGTAT
1 GAGCTTACCGATTCTCAGCTCGTAT
*
1141390 GAGCTTATCGATT-TCAGCTCGTGA-
1 GAGCTTACCGATTCTCAGCTCGT-AT
* * *
1141414 GAGCTTATCGATTCTCAGTTCATAT
1 GAGCTTACCGATTCTCAGCTCGTAT
1141439 GAGCTTACCGATT-TACAGCTCGTGA-
1 GAGCTTACCGATTCT-CAGCTCGT-AT
* * *
1141464 AAGCATACCGATTCGT-AGCTCATAT
1 GAGCTTACCGATTC-TCAGCTCGTAT
1141489 GAGC
1 GAGC
1141493 ATACATGTAC
Statistics
Matches: 85, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
24 25 0.29
25 58 0.68
26 1 0.01
27 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGATTCTCAGCTCGTAT
Found at i:1141426 original size:49 final size:49
Alignment explanation
Indices: 1141345--1141492 Score: 190
Period size: 49 Copynumber: 3.0 Consensus size: 49
1141335 TCATTAGGGA
* * * *
1141345 TTACTGATTTTAGCTCATGAGAGCTTACCGATTCTCAGCTCGTATGAGC
1 TTACCGATTTCAGCTCGTGAGAGCTTACCGATTCTCAGCTCATATGAGC
* * *
1141394 TTATCGATTTCAGCTCGTGAGAGCTTATCGATTCTCAGTTCATATGAGC
1 TTACCGATTTCAGCTCGTGAGAGCTTACCGATTCTCAGCTCATATGAGC
* *
1141443 TTACCGATTTACAGCTCGTGAAAGCATACCGATTCGT-AGCTCATATGAGC
1 TTACCGATTT-CAGCTCGTGAGAGCTTACCGATTC-TCAGCTCATATGAGC
1141493 ATACATGTAC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
49 51 0.60
50 33 0.39
51 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (49 bp):
TTACCGATTTCAGCTCGTGAGAGCTTACCGATTCTCAGCTCATATGAGC
Found at i:1147392 original size:43 final size:42
Alignment explanation
Indices: 1147201--1147392 Score: 152
Period size: 43 Copynumber: 4.5 Consensus size: 42
1147191 TGTGACTTCG
* ** * *
1147201 TGTAAGACCACGTCTGGGACGTTGGCAT-TAATTTGAGATTTACG
1 TGTAAGACCAAGTCTGGGACAATGGCATCTTATTT-A-A-TTACA
* * * * * *
1147245 TGTAAGACCAAGTCTGGGATATTGGCGTCGTATATAATTACG
1 TGTAAGACCAAGTCTGGGACAATGGCATCTTATTTAATTACA
** *
1147287 TGTAAGACCCTGTCTGGGACAGTGGCATCGTTATTTAATTACA
1 TGTAAGACCAAGTCTGGGACAATGGCATC-TTATTTAATTACA
* ** * *
1147330 TGTAAAACCCTGTCTGGGACAATGGCTTCATTATTTGATTACA
1 TGTAAGACCAAGTCTGGGACAATGGCATC-TTATTTAATTACA
*
1147373 TGTAAGACCAAGTCCGGGAC
1 TGTAAGACCAAGTCTGGGAC
1147393 GTTGGCATTG
Statistics
Matches: 122, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
42 29 0.24
43 65 0.53
44 25 0.20
45 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCAAGTCTGGGACAATGGCATCTTATTTAATTACA
Found at i:1151722 original size:60 final size:61
Alignment explanation
Indices: 1151638--1151833 Score: 223
Period size: 60 Copynumber: 3.0 Consensus size: 61
1151628 CATTCTTGAG
*
1151638 TAATAGAAATTACTTAGCATTTACTCTGGCTTCTCTTGTC-TTTTTACTGTTCTTGCATTT
1 TAATAGAAATTACTTAGCATTTACTCTGGCTTCTCTTGTCTTTTTTACTATTCTTGCATTT
* * *
1151698 TAATAGAAATTACTTAGCAATTACTCTTGCTTCTCTTGTCTTTTTTTTACTATTCTTTCATTTTA
1 TAATAGAAATTACTTAGCATTTACTCTGGCTTCTCTTGTC--TTTTTTACTATTCTTGC------
1151763 ATTGTT
58 A-T-TT
*
1151769 GAGTAATAGAAATTACTTAGCATTTACTCTGGCTTCTCTTGTCTTTTTTACTTTTCTTGCATTT
1 ---TAATAGAAATTACTTAGCATTTACTCTGGCTTCTCTTGTCTTTTTTACTATTCTTGCATTT
1151833 T
1 T
1151834 TATCTTTCTA
Statistics
Matches: 114, Mismatches: 8, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
60 38 0.33
61 1 0.01
63 14 0.12
64 2 0.02
65 1 0.01
66 1 0.01
69 1 0.01
70 1 0.01
71 2 0.02
72 15 0.13
74 38 0.33
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (61 bp):
TAATAGAAATTACTTAGCATTTACTCTGGCTTCTCTTGTCTTTTTTACTATTCTTGCATTT
Found at i:1151785 original size:74 final size:72
Alignment explanation
Indices: 1151698--1151833 Score: 218
Period size: 74 Copynumber: 1.9 Consensus size: 72
1151688 TCTTGCATTT
* *
1151698 TAATAGAAATTACTTAGCAATTACTCTTGCTTCTCTTGTCTTTTTTTTACTATTCTTTCATTTTA
1 TAATAGAAATTACTTAGCAATTACTCTGGCTTCTCTTGTC--TTTTTTACTATTCTTGCATTTTA
1151763 ATTGTTGAG
64 ATTGTTGAG
* *
1151772 TAATAGAAATTACTTAGCATTTACTCTGGCTTCTCTTGTCTTTTTTACTTTTCTTGCATTTT
1 TAATAGAAATTACTTAGCAATTACTCTGGCTTCTCTTGTCTTTTTTACTATTCTTGCATTTT
1151834 TATCTTTCTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 20 0.34
74 38 0.66
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.53
Consensus pattern (72 bp):
TAATAGAAATTACTTAGCAATTACTCTGGCTTCTCTTGTCTTTTTTACTATTCTTGCATTTTAAT
TGTTGAG
Found at i:1167363 original size:40 final size:39
Alignment explanation
Indices: 1167265--1167527 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
1167255 TCCTCGTTCA
* * * *
1167265 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
1167304 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
1167343 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
1167383 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
1167423 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
1167463 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
1167504 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
1167528 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:1167487 original size:120 final size:119
Alignment explanation
Indices: 1167265--1167527 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
1167255 TCCTCGTTCA
* * *
1167265 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
1167330 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
1167383 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
1167448 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
1167504 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
1167528 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:1167536 original size:41 final size:41
Alignment explanation
Indices: 1167459--1167536 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
1167449 TTTGTATCTC
* * *
1167459 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
1167500 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
1167537 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:1175270 original size:40 final size:40
Alignment explanation
Indices: 1175222--1175489 Score: 419
Period size: 40 Copynumber: 6.7 Consensus size: 40
1175212 GCAAACACAT
* * *
1175222 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
1175262 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
1175302 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
1175342 TTGCCTTCGGGTCATAGCCCGGATATATTATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
** *
1175382 TTGCCTTCGGGTCACAGCCCGGATATATCAACTCGCATAG
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1175422 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1175462 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
1175490 TCCAATGCTC
Statistics
Matches: 215, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 215 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:1195122 original size:49 final size:50
Alignment explanation
Indices: 1195053--1195288 Score: 230
Period size: 51 Copynumber: 4.7 Consensus size: 50
1195043 ATCATTCGAC
1195053 ACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAAT
1 ACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAAT
* **
1195102 TCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
1 ACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTAC-AAT
* * * **
1195153 -CACGTAGTAGCCTTCACTTAGTACTACATACGTGCTCAAAGCTTCTT--GGT
1 ACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TT-TTACAAT
* * * * * *
1195203 ACACATAGTAGCCTTCACTTAGTACTACACATGTGACCGTAG-TTTACCAAG
1 ACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTA-CAAT
* * *
1195254 ACACGTGGTAGCATTCACACAGTACTACACACGTG
1 ACACGTAGTAGCCTTCACATAGTACTACACACGTG
1195289 TTCATCGATA
Statistics
Matches: 155, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
48 2 0.01
49 38 0.25
50 44 0.28
51 67 0.43
52 2 0.01
53 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (50 bp):
ACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAAT
Found at i:1195222 original size:51 final size:49
Alignment explanation
Indices: 1195058--1195238 Score: 197
Period size: 50 Copynumber: 3.6 Consensus size: 49
1195048 TCGACACACG
* *** *
1195058 TAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAATTCACG
1 TAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA-GGCTCACA
* *
1195107 TAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCTCACG
1 TAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTA-GGCTCACA
* *
1195157 TAGTAGCCTTCACTTAGTACTACATACGTGCTCAAAGCTTCTT-GG-TACACA
1 TAGTAGCCTTCACTTAGTACTACACACGTGATC-AAG-TT-TTAGGCT-CACA
*
1195208 TAGTAGCCTTCACTTAGTACTACACATGTGA
1 TAGTAGCCTTCACTTAGTACTACACACGTGA
1195239 CCGTAGTTTA
Statistics
Matches: 117, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
49 33 0.28
50 44 0.38
51 36 0.31
52 2 0.02
53 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (49 bp):
TAGTAGCCTTCACTTAGTACTACACACGTGATCAAGTTTTAGGCTCACA
Found at i:1199813 original size:12 final size:12
Alignment explanation
Indices: 1199796--1199820 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1199786 GGTGTTCATT
1199796 CGGTTAACCGAC
1 CGGTTAACCGAC
1199808 CGGTTAACCGAC
1 CGGTTAACCGAC
1199820 C
1 C
1199821 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:1199993 original size:9 final size:9
Alignment explanation
Indices: 1199979--1200032 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
1199969 TTTGGTTAAA
1199979 AATTACCCG
1 AATTACCCG
1199988 AATTACCCG
1 AATTACCCG
*
1199997 -ATTAACCG
1 AATTACCCG
1200005 AATTACCCG
1 AATTACCCG
*
1200014 AAAATTACCTG
1 --AATTACCCG
1200025 AATTACCC
1 AATTACCC
1200033 AAAAATTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
8 7 0.18
9 23 0.61
11 8 0.21
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:1200005 original size:17 final size:17
Alignment explanation
Indices: 1199980--1200014 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1199970 TTGGTTAAAA
*
1199980 ATTACCCGAATTACCCG
1 ATTAACCGAATTACCCG
1199997 ATTAACCGAATTACCCG
1 ATTAACCGAATTACCCG
1200014 A
1 A
1200015 AAATTACCTG
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:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (17 bp):
ATTAACCGAATTACCCG
Found at i:1200027 original size:20 final size:19
Alignment explanation
Indices: 1199977--1200042 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
1199967 TTTTTGGTTA
1199977 AAAATTACCCGAATTACCCG
1 AAAATTA-CCGAATTACCCG
1199997 ---ATTAACCGAATTACCCG
1 AAAATT-ACCGAATTACCCG
*
1200014 AAAATTACCTGAATTACCCA
1 AAAATTACC-GAATTACCCG
1200034 AAAATTACC
1 AAAATTACC
1200043 CAAAAGGTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 15 0.38
18 1 0.03
19 3 0.08
20 21 0.52
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (19 bp):
AAAATTACCGAATTACCCG
Found at i:1203029 original size:50 final size:49
Alignment explanation
Indices: 1202914--1203148 Score: 219
Period size: 51 Copynumber: 4.7 Consensus size: 49
1202904 TCATTCGATA
**
1202914 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTACAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTAC-GGT
*
1202963 CACGTAGTAGCTTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG-T
* *
1203013 CCCGTAGTAGCCTTCAC-TCAGTACTACACACGTGCTCAAAGCTTCTT--GGT
1 CACGTAGTAGCCTTCACAT-AGTACTACACACGTGATC-AAG-TT-TTACGGT
* * * * * *
1203063 ACACATAGTAGCCTTCACTTAGTACTACACATGTGACCGTAG-TTTACCGAGA
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTA-CG-GT
* * *
1203115 CACGTGGTAGCATTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
1203149 TTCATCGATA
Statistics
Matches: 154, Mismatches: 20, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
48 2 0.01
49 38 0.25
50 42 0.27
51 66 0.43
52 4 0.03
53 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (49 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGT
Found at i:1205994 original size:10 final size:10
Alignment explanation
Indices: 1205976--1206021 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
1205966 ATTTATTAGC
1205976 AAACACATTA
1 AAACACATTA
*
1205986 AAACGCATT-
1 AAACACATTA
1205995 AAACACATT-
1 AAACACATTA
* *
1206004 TAACACATTT
1 AAACACATTA
1206014 AAACACAT
1 AAACACAT
1206022 ATGTTTAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 16 0.52
10 15 0.48
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (10 bp):
AAACACATTA
Found at i:1206000 original size:19 final size:19
Alignment explanation
Indices: 1205976--1206021 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1205966 ATTTATTAGC
*
1205976 AAACACATTAAAACGCA-TT
1 AAACACATT-AAACACATTT
*
1205995 AAACACATTTAACACATTT
1 AAACACATTAAACACATTT
1206014 AAACACAT
1 AAACACAT
1206022 ATGTTTAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (19 bp):
AAACACATTAAACACATTT
Found at i:1206003 original size:9 final size:9
Alignment explanation
Indices: 1205976--1206021 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 9
1205966 ATTTATTAGC
1205976 AAACACATT
1 AAACACATT
*
1205985 AAAACGCATT
1 -AAACACATT
1205995 AAACACATT
1 AAACACATT
*
1206004 TAACACATTT
1 AAACACA-TT
1206014 AAACACAT
1 AAACACAT
1206022 ATGTTTAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (9 bp):
AAACACATT
Found at i:1206129 original size:19 final size:19
Alignment explanation
Indices: 1206105--1206197 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
1206095 AATAAATTAC
*
1206105 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
1206124 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * * *
1206143 TGC-T-GGAATAAATT-A-C
1 T-CATCTTAGTTAATTAAGT
1206159 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
* *
1206178 TCTTCTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
1206197 T
1 T
1206198 GCTGAAATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 7 0.12
18 7 0.12
19 38 0.68
20 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:1206150 original size:54 final size:54
Alignment explanation
Indices: 1206086--1206207 Score: 208
Period size: 54 Copynumber: 2.3 Consensus size: 54
1206076 ATAAGTATTT
*
1206086 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAGTTAATTA
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTA
* *
1206140 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCTTCTTAGTTAATTT
1 AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTA
*
1206194 AGTTGCTGAAATAA
1 AGTTGCTGGAATAA
1206208 TTTATTGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (54 bp):
AGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAGTTAATTA
Found at i:1206259 original size:14 final size:14
Alignment explanation
Indices: 1206226--1206265 Score: 73
Period size: 13 Copynumber: 2.9 Consensus size: 14
1206216 TGCATGTGTT
1206226 TTTAGTTTATTAAA
1 TTTAGTTTATTAAA
1206240 -TTAGTTTATTAAA
1 TTTAGTTTATTAAA
1206253 TTTAGTTTATTAA
1 TTTAGTTTATTAA
1206266 TTAAACTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTAGTTTATTAAA
Found at i:1215892 original size:24 final size:24
Alignment explanation
Indices: 1215864--1215910 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1215854 TATATATACC
1215864 AATTCAATCA-ATA-TAAATTCAATA
1 AATTC-ATCACATACTAAA-TCAATA
1215888 AATTCATCACATACTAAATCAAT
1 AATTCATCACATACTAAATCAAT
1215911 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCATCACATACTAAATCAATA
Found at i:1234752 original size:35 final size:34
Alignment explanation
Indices: 1234693--1234810 Score: 98
Period size: 33 Copynumber: 3.5 Consensus size: 34
1234683 TGAATTGACG
* * *
1234693 GATAAGACCATGGTTGGACCATGGCAATGTTTAAAT
1 GATAAGACCATAGTTGGGCTATGGCAAT-TTT-AAT
*
1234729 G-TAAGACCATAGCTGGGCTATGGC-ATTTTAAT
1 GATAAGACCATAGTTGGGCTATGGCAATTTTAAT
* * * ** *
1234761 GAAAAGACCATAATTGGGTTATGGCACCTTGAAT
1 GATAAGACCATAGTTGGGCTATGGCAATTTTAAT
*
1234795 G-TAAGACCATGGTTGG
1 GATAAGACCATAGTTGG
1234811 ACCATAGTAG
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
32 4 0.06
33 34 0.52
34 8 0.12
35 19 0.29
36 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (34 bp):
GATAAGACCATAGTTGGGCTATGGCAATTTTAAT
Found at i:1241130 original size:126 final size:126
Alignment explanation
Indices: 1240968--1241488 Score: 733
Period size: 126 Copynumber: 4.1 Consensus size: 126
1240958 GGCCAAGCAA
** **
1240968 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAAAAATTTTGCTAACAGCACATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
* * *
1241033 CTGCTTGACGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTTAG
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
* * * * *
1241094 GAACTACTGTAGAAAAAAAGTGTCCACGTGGAAGCTTTTTTCAGTAATTTTACTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
* * *
1241159 CTGCTTGAAGCGTTTTTGACACTATATTTTTCAAAATCGTCTTCTCAAAGTGA-TTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTAT-TTTTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
*
1241220 GAACT-CTGTAGAAAAAGAGTC-TCCACGTGGGAGCTTTTTTTTAGTAATTTTGCTAACAGTGCA
1 GAACTACTGTAGAAAAAGAG-CGTCCACGTGGGAGC-TTTTTTCAGTAATTTTGCTAACAGTGCA
* **
1241283 TCCTGCTTGAAGCGTTTTTGACACTAGTTTTTCAAAATTGTCTTCTCAAAATTATTTTTTCAG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
* * *
1241346 GAACTACTATAGAAAAAGAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
* * * * * *
1241411 CTGCTTGAAGTGTTTTTGACATTATCTTTTCAGAACCGTCTTCTCAAAATTAATTTTTCTG
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
*
1241472 AAACTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
1241489 AAAGTAAAAT
Statistics
Matches: 349, Mismatches: 40, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
125 49 0.14
126 252 0.72
127 48 0.14
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAATTATTTTTTCAG
Found at i:1241700 original size:33 final size:33
Alignment explanation
Indices: 1241573--1241711 Score: 135
Period size: 34 Copynumber: 4.3 Consensus size: 33
1241563 TAAACACAAA
1241573 AATTATTTT-TAAAAAA-T-TAAACCCTAATTT
1 AATTATTTTATAAAAAACTCTAAACCCTAATTT
* * *
1241603 AATTAATTTTCTTAAAAACGCTAAACCCTAATTT
1 AATT-ATTTTATAAAAAACTCTAAACCCTAATTT
* ** * * *
1241637 AATTAATTTATTTGAAATCCCTAAAACCTAATTT
1 AATTATTTTA-TAAAAAACTCTAAACCCTAATTT
*
1241671 AATTATTTTAAAAAAAACTCTAAACCCTAATTT
1 AATTATTTTATAAAAAACTCTAAACCCTAATTT
1241704 -ATT-TTTTA
1 AATTATTTTA
1241712 AAATTCTTAA
Statistics
Matches: 89, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
30 4 0.04
31 10 0.11
32 9 0.10
33 21 0.24
34 45 0.51
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (33 bp):
AATTATTTTATAAAAAACTCTAAACCCTAATTT
Found at i:1242169 original size:28 final size:28
Alignment explanation
Indices: 1242132--1242191 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
1242122 TACTAGCAGG
1242132 CCTAAACCCACCCAAG-CCCAAACTAAA
1 CCTAAACCCACCCAAGCCCCAAACTAAA
* *
1242159 CCTAATACCCACCTAAGCCCCAAACTAAC
1 CCTAA-ACCCACCCAAGCCCCAAACTAAA
1242188 CCTA
1 CCTA
1242192 GCCCAGCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 10 0.34
29 14 0.48
ACGTcount: A:0.40, C:0.45, G:0.03, T:0.12
Consensus pattern (28 bp):
CCTAAACCCACCCAAGCCCCAAACTAAA
Found at i:1244137 original size:19 final size:20
Alignment explanation
Indices: 1244093--1244138 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1244083 AATGTCTCTT
*
1244093 TATGCA-TTCATTTCATGCA
1 TATGCATTTCATTACATGCA
1244112 T-TCGCATTTCATTACAT-CA
1 TAT-GCATTTCATTACATGCA
1244131 TATGCATT
1 TATGCATT
1244139 AAACACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 12 0.52
20 10 0.43
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (20 bp):
TATGCATTTCATTACATGCA
Found at i:1246999 original size:7 final size:7
Alignment explanation
Indices: 1246974--1247015 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
1246964 AGTGATGTGA
1246974 AAAAATG
1 AAAAATG
1246981 AAAAGATG
1 AAAA-ATG
1246989 -AAAATG
1 AAAAATG
1246995 AAAAATG
1 AAAAATG
1247002 AAAAA-G
1 AAAAATG
1247008 TAAAAATG
1 -AAAAATG
1247016 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:1247013 original size:21 final size:21
Alignment explanation
Indices: 1246974--1247015 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1246964 AGTGATGTGA
*
1246974 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
1246995 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
1247016 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:1248363 original size:44 final size:45
Alignment explanation
Indices: 1248313--1248540 Score: 148
Period size: 44 Copynumber: 5.2 Consensus size: 45
1248303 TCTCGGAGAC
* * * *
1248313 AGTGGAGCAGGTTGAAGATTACAGATCTTGCCTCCCT-AAGCAGT
1 AGTGGAGCAGATCGAAGATGACAGATCTTACCTCCCTGAAGCAGT
* * **
1248357 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAAGTTGT
1 AGTGGAGCAGATCGAAGATGACAGATCTTACCTCCCTGAAGCAGT
* * * * * * *
1248402 AGTGGAGTATATTG-A-A-GCCAGTAAT-TCTACTTCCCTG-GGCAGC
1 AGTGGAGCAGATCGAAGATGACAG--ATCT-TACCTCCCTGAAGCAGT
* * ** *
1248445 AGCGGCA-TAGATCGAAGATTTCAGATCTTGCCTCCCT-AAGCAGT
1 AGTGG-AGCAGATCGAAGATGACAGATCTTACCTCCCTGAAGCAGT
* * **
1248489 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGAAGTTGT
1 AGTGGAGCAGATCGAAGATGACAGATCTTACCTCCCTGAAGCAGT
1248534 AGTGGAG
1 AGTGGAG
1248541 TATATTGAAG
Statistics
Matches: 138, Mismatches: 34, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
42 4 0.03
43 14 0.10
44 87 0.63
45 30 0.22
46 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (45 bp):
AGTGGAGCAGATCGAAGATGACAGATCTTACCTCCCTGAAGCAGT
Found at i:1248502 original size:132 final size:132
Alignment explanation
Indices: 1248324--1248887 Score: 794
Period size: 132 Copynumber: 4.3 Consensus size: 132
1248314 GTGGAGCAGG
* *
1248324 TTGAAGATTACAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACC
** * *
1248389 TCCCTGAAGTTGTAGTGGAGTATATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGCATA
66 TCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATA
1248454 GA
131 GA
* *
1248456 TCGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACC
** * *
1248521 TCCCTGAAGTTGTAGTGGAGTATATTGAAGCCAGTAATTCTACTTCCCTGGGTAGCAGCGGAATA
66 TCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATA
1248586 GA
131 GA
* * *
1248588 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTAGAGCAGATAAAAAATGGCAGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACC
* * * * * *
1248653 T-CATCGTAGTTACATTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGACAGCAGTGGAAT
66 TCCCT-GAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAAT
1248717 AGA
130 AGA
* * * * *
1248720 TTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAGTGGGGCAAATCAAAGATGG-TGAATTTTAC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAG-ATTTTAC
* * *
1248784 CTCTCTGTGAA--TACAGTGGAGTACATTGAAGCCAGTAATTCTACTTTCCTGGGCAGCAGTGGA
65 CTC-C-CTGAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGA
1248847 ATAGA
128 ATAGA
*
1248852 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGT
1248888 AGTGGAGTAT
Statistics
Matches: 393, Mismatches: 34, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
131 3 0.01
132 386 0.98
134 3 0.01
135 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACC
TCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCGGAATA
GA
Found at i:1248902 original size:90 final size:90
Alignment explanation
Indices: 1248798--1249421 Score: 1212
Period size: 90 Copynumber: 6.9 Consensus size: 90
1248788 CTGTGAATAC
* *
1248798 AGTGGAGTACATTGAAGCCAGTAATTCTACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1248863 AGATCTTGTCTCCCTAAGCAGTAGT
66 AGATCTTGTCTCCCTAAGCAGTAGT
1248888 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1248953 AGATCTTGTCTCCCTAAGCAGTAGT
66 AGATCTTGTCTCCCTAAGCAGTAGT
1248978 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1249043 AGATCTTGTCTCCCTAAGCAGTAGT
66 AGATCTTGTCTCCCTAAGCAGTAGT
1249068 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1249133 AGATCTTGTCTCCCTAAGCAGTAGT
66 AGATCTTGTCTCCCTAAGCAGTAGT
1249158 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1249223 AGATCTTGTCTCCCTAAGCAGTAGT
66 AGATCTTGTCTCCCTAAGCAGTAGT
1249248 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
1249313 AGATCTTGTCTCCCTAAGCAGTAGT
66 AGATCTTGTCTCCCTAAGCAGTAGT
*
1249338 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGTAGATTTC
1 AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
*
1249403 AGATCTTGTCTCCTTAAGC
66 AGATCTTGTCTCCCTAAGC
1249422 TGGCGTGAAG
Statistics
Matches: 530, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 530 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (90 bp):
AGTGGAGTATATTGAAGCCAGTAATTCGACTTTCCTGGGCAGCAGTGGAATAGATTGAAGATTTC
AGATCTTGTCTCCCTAAGCAGTAGT
Found at i:1249677 original size:132 final size:132
Alignment explanation
Indices: 1249473--1250023 Score: 863
Period size: 132 Copynumber: 4.2 Consensus size: 132
1249463 CATAGACAGC
* *
1249473 GAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATC-GTAGAGTACATTGAAGCCAGT
1 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTA-CAGTGGAGTACATTGAAGCCAGT
*
1249537 AATTCTACTTCCCTGGGCAGTAGTGGAATAGATTGAAGATTTCAGATCTTGTCTTCCTAAGCAGT
65 AATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTTCCTAAGCAGT
1249602 AGT
130 AGT
* *
1249605 GAAGCACATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGAA
1 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* *
1249670 ATTCTACTTTCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTGTCTTCCTAAGCAGTA
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTTCCTAAGCAGTA
1249735 GT
131 GT
1249737 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
** * *
1249802 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTCATCTCCCTAAACAGTA
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTTCCTAAGCAGTA
1249867 GT
131 GT
* * * * *
1249869 GGAGCAGATCGAAGATGACAGATTTTACCTCCATGTGGTTACAGTGGAGTATATTGAAGCCAGTA
1 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * * *
1249934 ATTCTACTTCCCTGGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTC-TCCTTAAGCTGG
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTTCC-TAAGCAGT
*
1249998 CGT
130 AGT
* *
1250001 GAAGTAGATCAAAGATAGCAGAT
1 GAAGCAGATCAAAGATGGCAGAT
1250024 CTTGCCTTCC
Statistics
Matches: 383, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 3 0.01
132 380 0.99
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTTCCTAAGCAGTA
GT
Found at i:1250146 original size:43 final size:44
Alignment explanation
Indices: 1250098--1250279 Score: 97
Period size: 44 Copynumber: 4.2 Consensus size: 44
1250088 AGTAGAGTAC
1250098 ATTGAAGCCAGT-AATTCTACTTCCCTGGGCAGCAGTGGAATAG
1 ATTGAAGCCAGTCAATTCTACTTCCCTGGGCAGCAGTGGAATAG
* ** ** * **
1250141 ATTGAAG--ATTTCAGA-TCTTGTCTCCCTAAGCAGTAGTGGAGCAG
1 ATTGAAGCCA-GTCA-ATTCTACT-TCCCTGGGCAGCAGTGGAATAG
** *** * * * * * *
1250185 ATCAAAGATGGTGAATTTTACCTCCCTGTGGTTA-CAGTGGAGTAC
1 ATTGAAGCCAGTCAATTCTACTTCCCTG-GG-CAGCAGTGGAATAG
*
1250230 ATTGAAGCCAG-AAATTCTACTTCCCTGGGCAGCAGTGGAATAG
1 ATTGAAGCCAGTCAATTCTACTTCCCTGGGCAGCAGTGGAATAG
1250273 ATTGAAG
1 ATTGAAG
1250280 ATTTCAGATC
Statistics
Matches: 95, Mismatches: 34, Indels: 20
0.64 0.23 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 30 0.32
44 42 0.44
45 19 0.20
46 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (44 bp):
ATTGAAGCCAGTCAATTCTACTTCCCTGGGCAGCAGTGGAATAG
Found at i:1250167 original size:44 final size:44
Alignment explanation
Indices: 1250119--1250299 Score: 111
Period size: 44 Copynumber: 4.1 Consensus size: 44
1250109 TAATTCTACT
1250119 TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
1 TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
** * ** ** * * * **
1250163 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGA-ATTTTACC
1 TCCCTGGGCAGCAGTGGAATAGATTGAAGAT-TTCAGATCTTGTC
* * * * ** *
1250207 TCCCTGTGGTTA-CAGTGGAGTACATTGAAG---CCAGAAATTCTAC
1 TCCCTG-GG-CAGCAGTGGAATAGATTGAAGATTTCAGATCTTGT-C
1250250 TTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
1 -TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
1250295 TCCCT
1 TCCCT
1250300 AAGCAGTAGT
Statistics
Matches: 94, Mismatches: 33, Indels: 20
0.64 0.22 0.14
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 19 0.20
44 45 0.48
45 17 0.18
46 8 0.09
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (44 bp):
TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
Found at i:1250189 original size:177 final size:177
Alignment explanation
Indices: 1249871--1250680 Score: 974
Period size: 177 Copynumber: 4.5 Consensus size: 177
1249861 ACAGTAGTGG
* * *
1249871 AGCAGATCGAAGATGACAGATTTTACCTCCATGTGGTTACAGTGGAGTATATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
1249936 TCTACTTCCCTGGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTCTCCTTAAGCTGGCGT
66 TCTACTTCCCTAGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTCTCCTTAAGCTGGCGT
1250001 GAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGA
131 GAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGA
*
1250048 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * * * **
1250113 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTAGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTCTCCTTAAGCTGGCGT
* * ** * * * * * *
1250178 GGAGCAGATCAAAGAT-GGTGAATTTTACCTCCCTG--TGGTTACAGTGG
131 GAAGTAGATCAAAGATAGCAG-ATCTTGCCTTCCTGCATAG--ACAGCGA
* * * *** * * * * * * *
1250225 AGTACATTGAAGCCAG-AAATTCTACTTCCCTG-GG-CAGCAGTGGAATAGATTGAAG--ATTTC
1 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTA-CAGTGGAGTACATTGAAGCCA-GT-
** * **
1250285 AGA-TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGTAGATTTCAGATCTTGTCT
63 A-ATTCTACT-TCCCTAGGCAACAGT-G-G-A-AT---AGAT--TGTAGATTTCAGATCTTGTCT
1250349 CCTTAAGCTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGA
117 CCTTAAGCTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGA
*
1250410 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
1250475 TCTACTTCCCTAGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTCTCCTTAAGTTGGCTT
66 TCTACTTCCCTAGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTCTCCTTAAGCTGGCGT
*
1250540 GAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTACATAGACAGCGA
131 GAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGA
* *
1250587 AGCAGATCGAAGATGGCTGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1250652 TCTA-TCTCCCTAGGCAACAGTGGAATAGA
66 TCTACT-TCCCTAGGCAACAGTGGAATAGA
1250681 ATAGTGGAAT
Statistics
Matches: 527, Mismatches: 79, Indels: 54
0.80 0.12 0.08
Matches are distributed among these distances:
173 1 0.00
174 2 0.00
175 24 0.05
176 29 0.06
177 329 0.62
178 1 0.00
179 5 0.01
180 2 0.00
182 2 0.00
183 5 0.01
184 1 0.00
185 71 0.13
186 28 0.05
187 24 0.05
188 2 0.00
189 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (177 bp):
AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTAGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTCTCCTTAAGCTGGCGT
GAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGCGA
Found at i:1250208 original size:132 final size:133
Alignment explanation
Indices: 1250048--1250336 Score: 519
Period size: 132 Copynumber: 2.2 Consensus size: 133
1250038 TAGACAGCGA
* * *
1250048 AGCAGATCGAAGATGG-CAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTAA
1 AGCAGATCAAAGATGGTGAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGAAA
1250112 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
1250177 TGG
131 TGG
*
1250180 AGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGAAA
1 AGCAGATCAAAGATGGTGAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGAAA
1250244 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
66 TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
1250309 TGG
131 TGG
1250312 AGCAGATCAAAGATGGTGTAGATTT
1 AGCAGATCAAAGATGGTG-AGATTT
1250337 CAGATCTTGT
Statistics
Matches: 150, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
132 144 0.96
133 2 0.01
134 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (133 bp):
AGCAGATCAAAGATGGTGAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGAAA
TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
TGG
Found at i:1250296 original size:309 final size:309
Alignment explanation
Indices: 1249737--1250303 Score: 992
Period size: 309 Copynumber: 1.8 Consensus size: 309
1249727 AAGCAGTAGT
*
1249737 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTA
1249802 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTCATCTCCCTAAACAGTA
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTCATCTCCCTAAACAGTA
* *
1249867 GTGGAGCAGATCGAAGATGACAGATTTTACCTCCATGTGGTTACAGTGGAGTATATTGAAGCCAG
131 GTGGAGCAGATCAAAGATGACAGATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCAG
* * *
1249932 TAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGTAGATTTCAGATCTTGTCTCCTTAAGCTG
196 AAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCTG
1249997 GCGTGAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGC
261 GCGTGAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGC
*
1250046 GAAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTA
1 GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTA
** *
1250111 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
66 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTCATCTCCCTAAACAGTA
** *
1250176 GTGGAGCAGATCAAAGATG-GTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA
131 GTGGAGCAGATCAAAGATGACAG-ATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCA
*
1250240 GAAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
195 GAAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
1250304 AGTAGTGGAG
Statistics
Matches: 243, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
308 1 0.00
309 242 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (309 bp):
GAAGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAGTA
ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTCATCTCCCTAAACAGTA
GTGGAGCAGATCAAAGATGACAGATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCAG
AAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCTG
GCGTGAAGTAGATCAAAGATAGCAGATCTTGCCTTCCTGCATAGACAGC
Found at i:1250372 original size:53 final size:53
Alignment explanation
Indices: 1250278--1250378 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 53
1250268 AATAGATTGA
* *
1250278 AGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGT
1 AGATTTCAGATCTTGTCTCCCTAAGCAGGAGTGAAGCAGATCAAAGATGGTGT
* * * *
1250331 AGATTTCAGATCTTGTCTCCTTAAGCTGGCGTGAAGTAGATCAAAGAT
1 AGATTTCAGATCTTGTCTCCCTAAGCAGGAGTGAAGCAGATCAAAGAT
1250379 AGCAGATCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (53 bp):
AGATTTCAGATCTTGTCTCCCTAAGCAGGAGTGAAGCAGATCAAAGATGGTGT
Found at i:1250887 original size:44 final size:46
Alignment explanation
Indices: 1250824--1250921 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 46
1250814 CAGTGGAATC
** *
1250824 GATCGAA-AAGAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTA
1 GATCGAAGAAGAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTA
* *
1250868 GATCGAAGAA-AGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTA
1 GATCGAAGAAGAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTA
1250913 GATCGAAGA
1 GATCGAAGA
1250922 TACAAGTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
44 28 0.60
45 19 0.40
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (46 bp):
GATCGAAGAAGAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTA
Found at i:1251453 original size:28 final size:28
Alignment explanation
Indices: 1251416--1251475 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
1251406 TACTAGCAGG
1251416 CCTAAACCCACCCAAG-CCCAAACTAAA
1 CCTAAACCCACCCAAGCCCCAAACTAAA
* *
1251443 CCTAATACCCACCTAAGCCCCAAACTAAC
1 CCTAA-ACCCACCCAAGCCCCAAACTAAA
1251472 CCTA
1 CCTA
1251476 GCCCAGCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 5 0.17
28 10 0.34
29 14 0.48
ACGTcount: A:0.40, C:0.45, G:0.03, T:0.12
Consensus pattern (28 bp):
CCTAAACCCACCCAAGCCCCAAACTAAA
Found at i:1253973 original size:10 final size:10
Alignment explanation
Indices: 1253960--1254022 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
1253950 AAAAATCATT
1253960 AAAATTATAA
1 AAAATTATAA
*
1253970 AAAATTATAG
1 AAAATTATAA
* * *
1253980 AAACTCATAG
1 AAAATTATAA
1253990 AAAATTATAA
1 AAAATTATAA
1254000 AAATATT-T-A
1 AAA-ATTATAA
1254009 AAAATATATAA
1 AAAAT-TATAA
1254020 AAA
1 AAA
1254023 TATATGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
8 2 0.05
9 5 0.12
10 29 0.67
11 7 0.16
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:1254023 original size:10 final size:10
Alignment explanation
Indices: 1253990--1254027 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1253980 AAACTCATAG
1253990 AAAAT-TATA
1 AAAATATATA
*
1253999 AAAATATTTA
1 AAAATATATA
1254009 AAAATATATA
1 AAAATATATA
1254019 AAAATATAT
1 AAAATATAT
1254028 GAAAGTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 5 0.19
10 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAATATATA
Found at i:1266448 original size:16 final size:17
Alignment explanation
Indices: 1266417--1266449 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1266407 TAAAATTTTA
1266417 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
1266435 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
1266450 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:1266656 original size:52 final size:52
Alignment explanation
Indices: 1266600--1266702 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 52
1266590 TAAATTATTA
1266600 TATTACTAATACATAAAATAATAAAATAAAATAAAATA-AATATATATATAAC
1 TATTACTAATACATAAAATAATAAAATAAAATAAAATATAATATA-ATATAAC
* * * *
1266652 TATTACTAATACATAATATAATATAATATAATATAATATAATATAATATAA
1 TATTACTAATACATAAAATAATAAAATAAAATAAAATATAATATAATATAA
1266703 TATAATATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 40 0.87
53 6 0.13
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (52 bp):
TATTACTAATACATAAAATAATAAAATAAAATAAAATATAATATAATATAAC
Found at i:1266735 original size:5 final size:5
Alignment explanation
Indices: 1266612--1266716 Score: 108
Period size: 5 Copynumber: 20.6 Consensus size: 5
1266602 TTACTAATAC
* * * *
1266612 ATAAA ATAAT AAAAT AAAAT AAAAT A-AAT ATATAT ATAACT AT--T ACTAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAA-T ATAAT A-TAAT
1266662 ACATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 --ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1266714 ATA
1 ATA
1266717 GTATTACATG
Statistics
Matches: 90, Mismatches: 2, Indels: 16
0.83 0.02 0.15
Matches are distributed among these distances:
3 2 0.02
4 5 0.06
5 69 0.77
6 9 0.10
7 4 0.04
8 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:1266897 original size:17 final size:16
Alignment explanation
Indices: 1266875--1266908 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1266865 AACTAGCATA
1266875 ATAATAAATAATGATAT
1 ATAATAAATAAT-ATAT
*
1266892 ATAATAAGTAATATAT
1 ATAATAAATAATATAT
1266908 A
1 A
1266909 ATGTACGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATAATAAATAATATAT
Found at i:1267108 original size:225 final size:229
Alignment explanation
Indices: 1266755--1267365 Score: 654
Period size: 225 Copynumber: 2.6 Consensus size: 229
1266745 TCAAGGCATA
* *
1266755 TATATATATAAACTATTCATATATTAT-ATGATATGATATAGCATTATATAATATAGAAAGAAGG
1 TATATATATAAACTATT-A-ATA-TATGAT-ATATGATATAGCATTATATAATATAGTAAGAGGG
* * * *
1266819 TTAACTTTTAAATGTATAAAAAGTATAGGAACTTAGAACATATTTCAACTAGCATAATAATAAAT
62 TTAACTTTCAAATGTATGAAAAGTATAGGAACTTAGAGCATATTTCAACTAGTATAATAATAAAT
* *
1266884 AATGATATATAATA-AGTAATATA-TAATGTACG-ACTGTTA-TATA-TA-ACTATTAGT-AT-A
127 AAT-ATATATAATATA-TAATATATTAATATACGAACTATTATTATATTATA-TATTA-TAATAA
* * * * * * *
1266941 ATATAGAGTGTTACTTGATATTATAATGTTTAATCATTTATG
188 ATATAGAATATTACATAATATTATAATATTTAACCATTGATG
*
1266983 TATATATATAAACTATTAATATATGAT-TATGATATAGCATTATATAATATAGTAGGAGGGTTAA
1 TATATATATAAACTATTAATATATGATATATGATATAGCATTATATAATATAGTAAGAGGGTTAA
* * *
1267047 CTTTCAAATTGTATGAAATGTATATGAACTTAGAGCATATTTTAACTAGTATAATAATAAATAAT
66 CTTTCAAA-TGTATGAAAAGTATAGGAACTTAGAGCATATTTCAACTAGTATAATAATAAATAAT
* * *
1267112 AATATGTAATATATAATATACTTTTATTATATGTAACTATTATTATATTATATATTATAATAAAA
130 -ATATATAATATATAATATA---TTAATATACG-AACTATTATTATATTATATATTATAAT-AAA
*
1267177 TATATAATATTACATAATATTATAATATTTAACCATTGATG
189 TATAGAATATTACATAATATTATAATATTTAACCATTGATG
* * *
1267218 GATATATATAAACTATTAATATATTGTATACTAT-ATGATATGATATTATATAATATAGTACGAG
1 TATATATATAAACTATTAATATA-TG-ATA-TATGAT-ATA-G-CATTATATAATATAGTAAGAG
* * * * * *
1267282 GGCTAACTTTCAAATGTATGAAAAATATAGGGACTTAGAGCATATTTCAACCAATATAATAATAT
60 GGTTAACTTTCAAATGTATGAAAAGTATAGGAACTTAGAGCATATTTCAACTAGTATAATAATAA
1267347 AT-A-ATATATAATATATAAT
125 ATAATATATATAATATATAAT
1267366 GTACTACTCT
Statistics
Matches: 324, Mismatches: 37, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
224 41 0.13
225 69 0.21
226 6 0.02
227 1 0.00
228 17 0.05
229 6 0.02
231 6 0.02
232 5 0.02
233 9 0.03
234 1 0.00
235 57 0.18
236 2 0.01
237 17 0.05
238 2 0.01
239 7 0.02
240 46 0.14
241 32 0.10
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (229 bp):
TATATATATAAACTATTAATATATGATATATGATATAGCATTATATAATATAGTAAGAGGGTTAA
CTTTCAAATGTATGAAAAGTATAGGAACTTAGAGCATATTTCAACTAGTATAATAATAAATAATA
TATATAATATATAATATATTAATATACGAACTATTATTATATTATATATTATAATAAATATAGAA
TATTACATAATATTATAATATTTAACCATTGATG
Found at i:1267352 original size:7 final size:7
Alignment explanation
Indices: 1267334--1267365 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1267324 TATTTCAACC
1267334 AATATAAT
1 AATAT-AT
1267342 AATATAT
1 AATATAT
1267349 AATATAT
1 AATATAT
1267356 AATATAT
1 AATATAT
1267363 AAT
1 AAT
1267366 GTACTACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:1267406 original size:241 final size:234
Alignment explanation
Indices: 1266756--1267379 Score: 593
Period size: 235 Copynumber: 2.7 Consensus size: 234
1266746 CAAGGCATAT
* * * *
1266756 ATATATATAAACTATTCATATATTAT-ATGATATGATATAGCATTATATAATATAGAAAGAAGGT
1 ATATATATAAACTATT-A-ATA-TATGAT--TATGATATAGCATTATATAATATAGTACGAGGGC
* * * **
1266820 TAACTTTTAAA-TGTAT-AAAAAGTATAGGAACTTAGAACATATTTCAACTAGCATAATAAT-A-
61 TAACTTTCAAATTGTATGAAAAA-TATAGGAACTTAGAGCATATTTCAACCAATATAATAATAAT
* * * *
1266881 AATAATGATAT-ATA-ATAAGTA-A--TATA-TA-ATGT-ACGACTGTTATA-TATA-ACTATTA
125 AATAAT-ATATAATATATAA-TATACTTCTACTATATGTAACGATTATTATATTATATATTA-TA
* * * * * * * * * * *
1266936 GTATAATATAGAGTGTTACTTGATATTATAATGTTTAATCATTTATGT
187 ATAAAATATATAATATTACATAATATTATAATATTTAACCATTGATGG
* *
1266984 ATATATATAAACTATTAATATATGATTATGATATAGCATTATATAATATAGTAGGAGGGTTAACT
1 ATATATATAAACTATTAATATATGATTATGATATAGCATTATATAATATAGTACGAGGGCTAACT
** * * * *
1267049 TTCAAATTGTATGAAATGTATATGAACTTAGAGCATATTTTAACTAGTATAATAATAAATAATAA
66 TTCAAATTGTATGAAAAATATAGGAACTTAGAGCATATTTCAACCAATATAATAAT-AATAATAA
* * * *
1267114 TATGTAATATATAATATACTTTTATTATATGTAACTATTATTATATTATATATTATAATAAAATA
130 TATATAATATATAATATACTTCTACTATATGTAACGATTATTATATTATATATTATAATAAAATA
1267179 TATAATATTACATAATATTATAATATTTAACCATTGATGG
195 TATAATATTACATAATATTATAATATTTAACCATTGATGG
*
1267219 ATATATATAAACTATTAATATATTGTATACTAT-ATGATATGATATTATATAATATAGTACGAGG
1 ATATATATAAACTATTAATATA-TG-AT--TATGAT-ATA-G-CATTATATAATATAGTACGAGG
*
1267283 GCTAACTTTCAAA-TGTATGAAAAATATAGGGACTTAGAGCATATTTCAACCAATATAATAAT-A
59 GCTAACTTTCAAATTGTATGAAAAATATAGGAACTTAGAGCATATTTCAACCAATATAATAATAA
*
1267346 T-ATAATATATAATATATAATGTACTACTCTACTA
124 TAATAATATATAATATATAATATACT--TCTACTA
1267380 CTATTGTATG
Statistics
Matches: 330, Mismatches: 41, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
224 41 0.12
225 42 0.13
226 8 0.02
227 5 0.02
228 27 0.08
229 5 0.02
231 3 0.01
232 2 0.01
233 4 0.01
234 9 0.03
235 65 0.20
236 5 0.02
237 24 0.07
238 4 0.01
239 11 0.03
240 43 0.13
241 32 0.10
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (234 bp):
ATATATATAAACTATTAATATATGATTATGATATAGCATTATATAATATAGTACGAGGGCTAACT
TTCAAATTGTATGAAAAATATAGGAACTTAGAGCATATTTCAACCAATATAATAATAATAATAAT
ATATAATATATAATATACTTCTACTATATGTAACGATTATTATATTATATATTATAATAAAATAT
ATAATATTACATAATATTATAATATTTAACCATTGATGG
Found at i:1268031 original size:25 final size:24
Alignment explanation
Indices: 1267998--1268058 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
1267988 GTAATCATAT
* *
1267998 AAAAGTAAAATGAATTATTACATT-C
1 AAAATTAAAAT-AATTATAAC-TTAC
*
1268023 AAAATTAAAATATTTATAACTTAC
1 AAAATTAAAATAATTATAACTTAC
1268047 AAAATTCAAAAT
1 AAAATT-AAAAT
1268059 TATCTAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 2 0.06
24 14 0.45
25 15 0.48
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (24 bp):
AAAATTAAAATAATTATAACTTAC
Found at i:1268684 original size:15 final size:15
Alignment explanation
Indices: 1268661--1268690 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1268651 CTATATTATA
*
1268661 ATTAGTTGTAATCCC
1 ATTAATTGTAATCCC
1268676 ATTAATTGTAATCCC
1 ATTAATTGTAATCCC
1268691 CTAATTCTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (15 bp):
ATTAATTGTAATCCC
Found at i:1276531 original size:28 final size:28
Alignment explanation
Indices: 1276470--1276531 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1276460 AACGTAGTTT
* *
1276470 TAATTTATTTCAAATTTTTATTTATGTA
1 TAATTTATTTCAAATTTTTATTAATATA
* *
1276498 TTATTTATTTTAAATTTATT-TTAATATA
1 TAATTTATTTCAAATTT-TTATTAATATA
1276526 TAATTT
1 TAATTT
1276532 CCTTTCTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 26 0.93
29 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TAATTTATTTCAAATTTTTATTAATATA
Found at i:1287746 original size:44 final size:44
Alignment explanation
Indices: 1287666--1287949 Score: 245
Period size: 44 Copynumber: 6.5 Consensus size: 44
1287656 CCTGAGCAAT
* * * *
1287666 AGCGGAGCAGATCGAAGATGGTGAATCTTATCTCCCTGAGATTAC
1 AGCGGAGCAGATTGAAAATAGT-AATCCTATCTCCCTGAGATTAC
** *
1287711 AGCGGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTAC
1 AGCGGAGCAGATTGAAAATAGTAATCCTATCTCCCTGAGATTAC
* * * * *
1287755 AGTGGAGCGGATT-AAAATAAAG-GATCTTATCTCCCTAAGATTAC
1 AGCGGAGCAGATTGAAAAT--AGTAATCCTATCTCCCTGAGATTAC
** * *
1287799 AGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1 AGCGGAGCAGATTGAAAATAGTAATCCTATCTCCCTGAGATTAC
* * * * *
1287843 AGTGGAGCGGATT-AAAATAAAG-GATCTTATCTCCCTAAGATTAC
1 AGCGGAGCAGATTGAAAAT--AGTAATCCTATCTCCCTGAGATTAC
** * *
1287887 AGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1 AGCGGAGCAGATTGAAAATAGTAATCCTATCTCCCTGAGATTAC
* *
1287931 AGTGGAGCGGATT-AAAATA
1 AGCGGAGCAGATTGAAAATA
1287950 AAGGATCTTA
Statistics
Matches: 187, Mismatches: 44, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
43 14 0.07
44 144 0.77
45 29 0.16
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (44 bp):
AGCGGAGCAGATTGAAAATAGTAATCCTATCTCCCTGAGATTAC
Found at i:1287976 original size:88 final size:88
Alignment explanation
Indices: 1287690--1287963 Score: 512
Period size: 88 Copynumber: 3.1 Consensus size: 88
1287680 AAGATGGTGA
* * * *
1287690 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1287755 AGTGGAGCGGATTAAAATAAAGG
66 AGTGGAGCGGATTAAAATAAAGG
1287778 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1287843 AGTGGAGCGGATTAAAATAAAGG
66 AGTGGAGCGGATTAAAATAAAGG
1287866 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1287931 AGTGGAGCGGATTAAAATAAAGG
66 AGTGGAGCGGATTAAAATAAAGG
1287954 ATCTTATCTC
1 ATCTTATCTC
1287964 TCTGAATTTA
Statistics
Matches: 182, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 182 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (88 bp):
ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
AGTGGAGCGGATTAAAATAAAGG
Found at i:1288120 original size:219 final size:219
Alignment explanation
Indices: 1287866--1288272 Score: 636
Period size: 219 Copynumber: 1.9 Consensus size: 219
1287856 AAAATAAAGG
* *
1287866 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATTCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATCCTATTGCCCTGAGATTAC
**
1287931 AGTGG-AGCGGATTAAAATAAAGGATCTTATCTCTCTGAATTTACAGTAGAGTAGATCGCATCAG
66 AGTGGAAG-GGATTAAAATAAAGGATCTTATCTCTCTGAAGATACAGTAGAGTAGATCGCATCAG
* *
1287995 GTCTTATCTCCCTAAGATTACACTGGAATAGATCGAAGAATTCCAGATCTTATCTCCCTAAGCAA
130 GTCTTATCTCCCTAAGATTACACTGGAATAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAA
1288060 TAGTGGAGCTAATCGAAAATGGTGA
195 TAGTGGAGCTAATCGAAAATGGTGA
* * * * * *
1288085 ATCTTATCTCCTTGATATTACAGTGGAGTAGATTGAAGCCAGTAATCCTATTGCCCTGAGATTAC
1 ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATCCTATTGCCCTGAGATTAC
*
1288150 AGTGGAAGGGATTAAATTAAAGGATCTTATCTCTCTGAAGATACAGTAGAGTAGATCGCATCAGG
66 AGTGGAAGGGATTAAAATAAAGGATCTTATCTCTCTGAAGATACAGTAGAGTAGATCGCATCAGG
* * * * *
1288215 TCTTCTCTCCCTGAGATTATAGTGGAATAGACCGAAGAATTACAGATCTTATTTCCCT
131 TCTTATCTCCCTAAGATTACACTGGAATAGACCGAAGAATTACAGATCTTATCTCCCT
1288273 TACGGTGCAG
Statistics
Matches: 169, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
219 167 0.99
220 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (219 bp):
ATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAACCAGTAATCCTATTGCCCTGAGATTAC
AGTGGAAGGGATTAAAATAAAGGATCTTATCTCTCTGAAGATACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTAAGATTACACTGGAATAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAAT
AGTGGAGCTAATCGAAAATGGTGA
Found at i:1289864 original size:3 final size:3
Alignment explanation
Indices: 1289852--1289911 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
1289842 ATTACTTAAC
* * * * *
1289852 TAT T-T TAT TAT TAT TAT TGT TAT TAT TAT TAA TGT TAC TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1289899 TAG TAT TAT TAT T
1 TAT TAT TAT TAT T
1289912 TGTATTAGTT
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1289876 original size:15 final size:15
Alignment explanation
Indices: 1289852--1289911 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
1289842 ATTACTTAAC
1289852 TATT-TTATTATTAT
1 TATTGTTATTATTAT
1289866 TATTGTTATTATTAT
1 TATTGTTATTATTAT
* * *
1289881 TAATGTTACTATAAT
1 TATTGTTATTATTAT
1289896 TATTAG-TATTATTAT
1 TATT-GTTATTATTAT
1289911 T
1 T
1289912 TGTATTAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 4 0.11
15 33 0.87
16 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (15 bp):
TATTGTTATTATTAT
Found at i:1289911 original size:12 final size:12
Alignment explanation
Indices: 1289856--1289918 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
1289846 CTTAACTATT
*
1289856 TTATTATTATTA
1 TTATTATTAGTA
* *
1289868 TTGTTATTATTA
1 TTATTATTAGTA
* * *
1289880 TTAATGTTACTA
1 TTATTATTAGTA
*
1289892 TAATTATTAGTA
1 TTATTATTAGTA
*
1289904 TTATTATTTGTA
1 TTATTATTAGTA
1289916 TTA
1 TTA
1289919 GTTCATGTGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (12 bp):
TTATTATTAGTA
Found at i:1295096 original size:40 final size:39
Alignment explanation
Indices: 1295059--1295236 Score: 198
Period size: 40 Copynumber: 4.5 Consensus size: 39
1295049 ATATCCGGAC
1295059 TAAGATCCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGT
* *
1295099 TAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * *
1295139 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGT
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
* * * *
1295179 TAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGC
1 TAAGT-CCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
*
1295218 TATGTCCCGAAGGCATTTG
1 TAAGT-CCGAAGGCATTTG
1295237 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
39 33 0.27
40 85 0.70
41 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGT
Found at i:1295149 original size:80 final size:79
Alignment explanation
Indices: 1295065--1295236 Score: 229
Period size: 80 Copynumber: 2.2 Consensus size: 79
1295055 GGACTAAGAT
*
1295065 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
1295129 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * *
1295145 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
1295210 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
1295224 CCGAAGGCATTTG
1 CCGAAGGCATTTG
1295237 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
79 38 0.47
80 39 0.49
81 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:1295254 original size:79 final size:80
Alignment explanation
Indices: 1295092--1295269 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
1295082 AGATACAAAT
* * * *
1295092 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
1295157 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
1295172 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
1295236 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
1295251 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
1295270 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:1303000 original size:40 final size:40
Alignment explanation
Indices: 1302917--1303259 Score: 467
Period size: 40 Copynumber: 8.6 Consensus size: 40
1302907 TTGAATGCTG
* * * * * *
1302917 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
1302957 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
1302997 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1303037 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
1303077 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
1303117 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
1303157 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1303197 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1303236 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1303260 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:1305165 original size:25 final size:26
Alignment explanation
Indices: 1305137--1305194 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1305127 TTTGAAATGC
*
1305137 ATAATATATGGAA-AACATAAAATAA
1 ATAATATATAGAACAACATAAAATAA
**
1305162 ATAATA-ATAGAACAATTTAAAATAA
1 ATAATATATAGAACAACATAAAATAA
*
1305187 ATCATATA
1 ATAATATA
1305195 AGTTCAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 5 0.19
25 21 0.78
26 1 0.04
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAATATATAGAACAACATAAAATAA
Found at i:1305914 original size:4 final size:4
Alignment explanation
Indices: 1305905--1305947 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
1305895 GTTTTCTTTG
* * *
1305905 AAAT AAAT AAAT AAAAC AAAT AAAT AAAT GAAC AAAT AAAT AA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1305948 GCCAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:1305940 original size:16 final size:17
Alignment explanation
Indices: 1305905--1305947 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
1305895 GTTTTCTTTG
1305905 AAATAAATAAATAAAAC
1 AAATAAATAAATAAAAC
*
1305922 AAATAAATAAAT-GAAC
1 AAATAAATAAATAAAAC
1305938 AAATAAATAA
1 AAATAAATAA
1305948 GCCAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (17 bp):
AAATAAATAAATAAAAC
Found at i:1312996 original size:22 final size:22
Alignment explanation
Indices: 1312971--1313014 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1312961 TCATTGTCCC
1312971 AACATCATGAGTTGTATATTTT
1 AACATCATGAGTTGTATATTTT
*
1312993 AACATCGTGAGTTGTATATTTT
1 AACATCATGAGTTGTATATTTT
1313015 TACAGGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (22 bp):
AACATCATGAGTTGTATATTTT
Found at i:1314219 original size:17 final size:16
Alignment explanation
Indices: 1314197--1314230 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1314187 ATTATATAAT
1314197 TAATGATAATTAAATTA
1 TAATGAT-ATTAAATTA
*
1314214 TAATGATATTATATTA
1 TAATGATATTAAATTA
1314230 T
1 T
1314231 TAAATAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATATTAAATTA
Found at i:1315379 original size:40 final size:41
Alignment explanation
Indices: 1315295--1315382 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 41
1315285 AATTATGGAA
* * * * *
1315295 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTATAAAAT
*
1315336 TACTGAATATTG-TTATGTGTACT-ACATTGAACTATAAAAT
1 TACTGAATATTGTTTATGAGTACTGA-ATTGAACTATAAAAT
1315376 TACTGAA
1 TACTGAA
1315383 GTAATGAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.03
40 27 0.68
41 12 0.30
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTATAAAAT
Found at i:1315672 original size:43 final size:44
Alignment explanation
Indices: 1315586--1315684 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 44
1315576 GCCGACTACT
** * *
1315586 GTTACTGTTACCTATTCGACACTTTGTGTGTTGAATACTGTTACC
1 GTTACTGTTACAAATTCAACAC-TTGTATGTTGAATACTGTTACC
*
1315631 GTTACTGTTACAAATTCAACAC-TGTATGTTGAATACTGTTACT
1 GTTACTGTTACAAATTCAACACTTGTATGTTGAATACTGTTACC
*
1315674 GTTACTATTAC
1 GTTACTGTTAC
1315685 TGCTATCGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 29 0.60
45 19 0.40
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (44 bp):
GTTACTGTTACAAATTCAACACTTGTATGTTGAATACTGTTACC
Found at i:1325767 original size:16 final size:16
Alignment explanation
Indices: 1325746--1325795 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1325736 CTGTAGATGA
1325746 TTCAATTTTTATAATT
1 TTCAATTTTTATAATT
1325762 TTCAATATTTT-TAATT
1 TTCAAT-TTTTATAATT
*
1325778 TT-GATTTTTAATAATT
1 TTCAATTTTT-ATAATT
1325794 TT
1 TT
1325796 ATTTGTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.13
15 2 0.07
16 20 0.67
17 4 0.13
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (16 bp):
TTCAATTTTTATAATT
Found at i:1328606 original size:45 final size:44
Alignment explanation
Indices: 1328544--1328638 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
1328534 TAGAAAAGTT
* * * *
1328544 AAAAATAAATAGTATAAATTAAGTTATTTTTTTATTAACAAACAA
1 AAAAATAAATAGTATAAAATAAATTA-TTCTTTATGAACAAACAA
*
1328589 AAAAATAAATAGTATAAAATAAATTATTCTTTATGAATAAACAA
1 AAAAATAAATAGTATAAAATAAATTATTCTTTATGAACAAACAA
*
1328633 ATAAAT
1 AAAAAT
1328639 TAAGTGATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 20 0.45
45 24 0.55
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (44 bp):
AAAAATAAATAGTATAAAATAAATTATTCTTTATGAACAAACAA
Found at i:1328992 original size:130 final size:126
Alignment explanation
Indices: 1328747--1329004 Score: 331
Period size: 130 Copynumber: 2.0 Consensus size: 126
1328737 TACATTAGAA
* * *
1328747 TAGTTGTCATGTAATGTAGCAACACAACTTAAGCTAATAATAGTGTTATTAAAAAAAAAGATATC
1 TAGTTGTCATGCAATGTAGCAACACAACTTAAGCCAATAATAGTGTTATGAAAAAAAAAGATATC
* * *
1328812 AATAAATGACACAATCTATGACAATAGTTAATTGCCTATTAGCAATAGCTATATGTAGCAT
66 AATAAATGACACAATCTATGACAATAATTAAGTGCCTATTAGCAAAAGCTATATGTAGCAT
* *
1328873 TAGTTGTGACATGCAATGTAGCAACACAATTTAAGCCAATAATTA-TGTTATGAAAAGACATACA
1 TAGTTGT--CATGCAATGTAGCAACACAACTTAAGCCAATAA-TAGTGTTATGAAAA-A-A-AAA
* * * * *
1328937 -ATATCATTAAATGACATAATTTATGACAATAATTAAGTGCTTGTTAGCAAAAGCTATATGTAGC
60 GATATCAATAAATGACACAATCTATGACAATAATTAAGTGCCTATTAGCAAAAGCTATATGTAGC
1329001 AT
125 AT
1329003 TA
1 TA
1329005 TTTAAGAATT
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
126 7 0.06
128 40 0.35
129 3 0.03
130 61 0.54
131 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (126 bp):
TAGTTGTCATGCAATGTAGCAACACAACTTAAGCCAATAATAGTGTTATGAAAAAAAAAGATATC
AATAAATGACACAATCTATGACAATAATTAAGTGCCTATTAGCAAAAGCTATATGTAGCAT
Found at i:1330790 original size:6 final size:6
Alignment explanation
Indices: 1330779--1330805 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1330769 TTTTCATAAA
1330779 CCAATT CCAATT CCAATT CCAATT CCA
1 CCAATT CCAATT CCAATT CCAATT CCA
1330806 TTAAATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (6 bp):
CCAATT
Found at i:1339647 original size:198 final size:197
Alignment explanation
Indices: 1339309--1339704 Score: 765
Period size: 198 Copynumber: 2.0 Consensus size: 197
1339299 CCATGATTTC
1339309 TGAAAGGTTTTTGCACACTCATACTCTCTGATAATTTCTCTGCTTATATATATGGAAACTTATCT
1 TGAAAGGTTTTTGCACACTCATACTCTCTGATAATTTCTCTGCTTATATATATGGAAACTTATCT
1339374 TATTGATTTAATTCCAATAAATCTGATTAAAAATTTAAATCAAATTGATTTAATGACAGATTTTG
66 TATTGATTTAATTCCAATAAATCTGATTAAAAATTTAAATCAAATTGATTTAATGACAGATTTTG
*
1339439 TGGATATTTTTTTTTTCCAAAATTCCAACACTCTCCATGCTTATAAAAGGCCATGATTTCTGAAG
131 TGGATA-TTTTTTTTTCCAAAATTCCAAAACTCTCCATGCTTATAAAAGGCCATGATTTCTGAAG
1339504 GGT
195 GGT
1339507 TGAAAGGTTTTTGCACACTCATACTCTCTGATAATTTCTCTGCTTATATATATGGAAACTTATCT
1 TGAAAGGTTTTTGCACACTCATACTCTCTGATAATTTCTCTGCTTATATATATGGAAACTTATCT
1339572 TATTGATTTAATTCCAATAAATCTGATTAAAAATTTAAATCAAATTGATTTAATGACAGATTTTG
66 TATTGATTTAATTCCAATAAATCTGATTAAAAATTTAAATCAAATTGATTTAATGACAGATTTTG
*
1339637 TGGATATTTTTTTTTCCAAAATTTCAAAACTCTCCATGCTTATAAAAGGCCATGATTTCTGAAGG
131 TGGATATTTTTTTTTCCAAAATTCCAAAACTCTCCATGCTTATAAAAGGCCATGATTTCTGAAGG
1339702 GT
196 GT
1339704 T
1 T
1339705 TTTGCACGCT
Statistics
Matches: 196, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
197 60 0.31
198 136 0.69
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (197 bp):
TGAAAGGTTTTTGCACACTCATACTCTCTGATAATTTCTCTGCTTATATATATGGAAACTTATCT
TATTGATTTAATTCCAATAAATCTGATTAAAAATTTAAATCAAATTGATTTAATGACAGATTTTG
TGGATATTTTTTTTTCCAAAATTCCAAAACTCTCCATGCTTATAAAAGGCCATGATTTCTGAAGG
GT
Found at i:1341919 original size:5 final size:5
Alignment explanation
Indices: 1341909--1341933 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1341899 ATAATAATCC
1341909 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
1341934 CAGATGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1346440 original size:21 final size:22
Alignment explanation
Indices: 1346414--1346454 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1346404 TTAGATGCAT
* *
1346414 ATATTT-AATTAAAATTTAAGA
1 ATATTTGAATAAAAAATTAAGA
1346435 ATATTTGAATAAAAAATTAA
1 ATATTTGAATAAAAAATTAA
1346455 TACGCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
ATATTTGAATAAAAAATTAAGA
Found at i:1346960 original size:12 final size:13
Alignment explanation
Indices: 1346930--1346962 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1346920 AAAACATTTT
*
1346930 AATAAATAAATCA
1 AATATATAAATCA
1346943 AATATATAAATC-
1 AATATATAAATCA
1346955 AATATATA
1 AATATATA
1346963 TTTTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (13 bp):
AATATATAAATCA
Found at i:1349521 original size:5 final size:5
Alignment explanation
Indices: 1349511--1349557 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
1349501 TAATAACTAA
*
1349511 ATTGT ATTGT ATTGT ATTGT ATTGT ATT-T -TCTGA ATTGT ATTGT ATT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT AT-TGT ATTGT ATTGT ATT
1349558 TTCTTCTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 1 0.03
4 2 0.05
5 33 0.89
6 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.17, T:0.60
Consensus pattern (5 bp):
ATTGT
Found at i:1350933 original size:25 final size:27
Alignment explanation
Indices: 1350886--1350935 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1350876 GTGAGTTATG
*
1350886 TATATATAAATTATATGTAAATTATTT
1 TATATATAAATTATATATAAATTATTT
*
1350913 TATATATATATTATA-AT-AATTAT
1 TATATATAAATTATATATAAATTAT
1350936 AAGTTAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 1 0.05
27 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TATATATAAATTATATATAAATTATTT
Found at i:1357469 original size:27 final size:25
Alignment explanation
Indices: 1357439--1357499 Score: 59
Period size: 27 Copynumber: 2.4 Consensus size: 25
1357429 AAGCATGAGA
1357439 TAGTCCACCGAGACAACAAACACGGGG
1 TAGTCCACCGAGACAACAAACAC--GG
* * * **
1357466 TAGTGCACCTAGATAGTAAACACGG
1 TAGTCCACCGAGACAACAAACACGG
1357491 TAGTCCACC
1 TAGTCCACC
1357500 AGGACACTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
25 10 0.36
27 18 0.64
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (25 bp):
TAGTCCACCGAGACAACAAACACGG
Found at i:1358832 original size:15 final size:15
Alignment explanation
Indices: 1358812--1358851 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
1358802 TTTCATTTAA
1358812 TTCACGATTCTCATG
1 TTCACGATTCTCATG
1358827 TTCACGATTCTCATG
1 TTCACGATTCTCATG
1358842 TTCACGATTC
1 TTCACGATTC
1358852 AATTCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (15 bp):
TTCACGATTCTCATG
Found at i:1360231 original size:45 final size:45
Alignment explanation
Indices: 1360159--1360244 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
1360149 ACTCAGTGAT
* *
1360159 TCAGGACATAGCAACCACCTTATTAATCAATGATGTCCGGTGGAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
*
1360204 TCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
1360245 TTACATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
Done.