Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_pilon, whole genome shotgun sequence
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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 17
Found at i:3229327 original size:13 final size:13
Alignment explanation
Indices: 3229309--3229333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3229299 AATTTTCCTT
3229309 TTTTTTCTTTTTA
1 TTTTTTCTTTTTA
3229322 TTTTTTCTTTTT
1 TTTTTTCTTTTT
3229334 TTCTCTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTCTTTTTA
Found at i:3229333 original size:23 final size:23
Alignment explanation
Indices: 3229301--3229346 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3229291 TTTTCTTTAA
*
3229301 TTTTCCTTTTTTTTCTTTTTATT
1 TTTTCCTTTTTTCTCTTTTTATT
*
3229324 TTTTCTTTTTTTCTCTTTTTATT
1 TTTTCCTTTTTTCTCTTTTTATT
3229347 CTGATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTCCTTTTTTCTCTTTTTATT
Found at i:3232582 original size:18 final size:17
Alignment explanation
Indices: 3232550--3232596 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
3232540 TATTAATGAA
3232550 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
3232567 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
3232585 G-AATAAAAATAA
1 GTAA-AAAAATAA
3232597 TGTGTACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:3232722 original size:18 final size:18
Alignment explanation
Indices: 3232696--3232757 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 18
3232686 TGATATTAAG
3232696 AAAAA-AAAATAATAGAA
1 AAAAATAAAATAATAGAA
*
3232713 AAAAATAAAATAA-AG-T
1 AAAAATAAAATAATAGAA
* *
3232729 AAAAATATAATATATATAA
1 AAAAATAAAATA-ATAGAA
*
3232748 ATAAATAAAA
1 AAAAATAAAA
3232758 ACAAAAATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 11 0.31
17 8 0.23
18 8 0.23
19 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAAATAAAATAATAGAA
Found at i:3232947 original size:20 final size:20
Alignment explanation
Indices: 3232911--3232949 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3232901 TAATATAATA
*
3232911 TAAATAAAAAACGAATATAG
1 TAAATAAAAAACAAATATAG
3232931 TAAATAAATAAA-AAATATA
1 TAAATAAA-AAACAAATATA
3232950 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAATAAAAAACAAATATAG
Found at i:3233962 original size:2 final size:2
Alignment explanation
Indices: 3233955--3233979 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3233945 TACAATTGGT
3233955 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
3233980 CATTTGTTAA
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:3235019 original size:16 final size:16
Alignment explanation
Indices: 3234985--3235091 Score: 85
Period size: 17 Copynumber: 6.6 Consensus size: 16
3234975 AACCTAAATG
*
3234985 ATAAAA-ATT-TTTGA
1 ATAAAATATTATTTTA
3234999 ATAAAATATTATTTTA
1 ATAAAATATTATTTTA
* *
3235015 ATAAAATAATAATTTAA
1 ATAAAAT-ATTATTTTA
**
3235032 GAGTTTAATATTATTTTA
1 -A-TAAAATATTATTTTA
*
3235050 ATAAAATGTTATTTTTA
1 ATAAAATATTA-TTTTA
*
3235067 ATAAAATATTA-ATTA
1 ATAAAATATTATTTTA
*
3235082 TTAAAATATT
1 ATAAAATATT
3235092 TAAAATATAT
Statistics
Matches: 74, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
14 6 0.08
15 15 0.20
16 18 0.24
17 23 0.31
18 8 0.11
19 4 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
ATAAAATATTATTTTA
Found at i:3235096 original size:24 final size:24
Alignment explanation
Indices: 3235068--3235114 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3235058 TTATTTTTAA
3235068 TAAAATATTAATTATTAA-AATATT
1 TAAAATA-TAATTATTAATAATATT
*
3235092 TAAAATATATTTATTAATAATAT
1 TAAAATATAATTATTAATAATAT
3235115 AATATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAATATAATTATTAATAATATT
Found at i:3235137 original size:22 final size:20
Alignment explanation
Indices: 3235095--3235139 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
3235085 AAATATTTAA
*
3235095 AATATATTTATTAATAATAT
1 AATATATTTATTAATATTAT
3235115 AATATATTTATTTTAATATTAT
1 AATATATTTA--TTAATATTAT
3235137 AAT
1 AAT
3235140 TTCAATACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATATTTATTAATATTAT
Found at i:3239044 original size:24 final size:24
Alignment explanation
Indices: 3239008--3239069 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
3238998 CCATACTCAA
*
3239008 GGAGTATCAATACTACTTTACACG
1 GGAGTATCGATACTACTTTACACG
3239032 GGAGTATCGATACTACTTTACACG
1 GGAGTATCGATACTACTTTACACG
*
3239056 GTAGTATCGATACT
1 GGAGTATCGATACT
3239070 GTTGAACTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (24 bp):
GGAGTATCGATACTACTTTACACG
Found at i:3242974 original size:9 final size:9
Alignment explanation
Indices: 3242960--3242986 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3242950 TATATCACTT
3242960 TAAAACTCA
1 TAAAACTCA
3242969 TAAAACTCA
1 TAAAACTCA
3242978 TAAAACTCA
1 TAAAACTCA
3242987 ATCATAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
TAAAACTCA
Found at i:3243192 original size:19 final size:20
Alignment explanation
Indices: 3243140--3243194 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
3243130 TTAATAATGA
3243140 ATAATATTATTTT-ATACAT
1 ATAATATTATTTTAATACAT
* *
3243159 ATAATATTAATTTAATA-GT
1 ATAATATTATTTTAATACAT
*
3243178 CTAATATTATTTTAATA
1 ATAATATTATTTTAATA
3243195 AAATATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 28 0.90
20 3 0.10
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAATATTATTTTAATACAT
Found at i:3259471 original size:55 final size:55
Alignment explanation
Indices: 3259320--3259790 Score: 688
Period size: 55 Copynumber: 8.7 Consensus size: 55
3259310 CGTTTGATGG
*
3259320 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATT-TATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGT-TGA
* *
3259375 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
*
3259428 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
3259483 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
3259538 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * *
3259593 AGATTG-T-GGGTCTTATACTCCCTGAAGAAATAGGGGGCAGACACGATTGTTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* *
3259646 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * * *
3259701 AGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
* * *
3259754 AGATTGTCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGG
3259791 AGCGAACCAG
Statistics
Matches: 378, Mismatches: 30, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
53 142 0.38
54 7 0.02
55 229 0.61
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTGA
Found at i:3259775 original size:163 final size:162
Alignment explanation
Indices: 3259320--3259790 Score: 714
Period size: 163 Copynumber: 2.9 Consensus size: 162
3259310 CGTTTGATGG
* *
3259320 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
**
3259385 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACTC
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTG-TCGAGTCTTATACTC
*
3259450 TCTGAAGAAATAGGGGACAGACGCGATTGTTGA
130 TCTGAAGAAATAGGGGACAGACACGATTGTTGA
* * *
3259483 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACACGATTGTTGAAGATTGCTCG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-G
* *
3259548 AGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGA-TGAAGATTGT-GGGTCTTATAC
64 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATT-ATTGAAGATTGTCGAGTCTTATAC
* *
3259611 TCCCTGAAGAAATAGGGGGCAGACACGATTGTTGA
128 TCTCTGAAGAAATAGGGGACAGACACGATTGTTGA
*
3259646 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
* *
3259711 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTCCGAGT-TCTATACT
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTGT-CGAGTCT-TATACT
* *
3259775 CTCTAAAGAAAGAGGG
129 CTCTGAAGAAATAGGG
3259791 AGCGAACCAG
Statistics
Matches: 278, Mismatches: 23, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
160 1 0.00
161 48 0.17
162 2 0.01
163 177 0.64
164 2 0.01
165 48 0.17
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (162 bp):
AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTATTGAAGATTGTCGAGTCTTATACTCT
CTGAAGAAATAGGGGACAGACACGATTGTTGA
Found at i:3259813 original size:108 final size:108
Alignment explanation
Indices: 3259320--3259790 Score: 757
Period size: 108 Copynumber: 4.3 Consensus size: 108
3259310 CGTTTGATGG
* * *
3259320 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATTTATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
* *
3259385 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGA
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
* * *
3259428 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGTTGAAGATTGTTCG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-G
* *
3259493 AGTCTTATACTCTCTGAAGAAATAAGGGGCAGACACGATTGTTGA
64 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
3259538 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
*
3259603 TCTTATACTCCCTGAAGAAATAGGGGGCAGACACGATTGTTGA
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
3259646 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
1 AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
* *
3259711 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGA
66 TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
* *
3259754 AGATTG-TCCGAGT-TCTATACTCTCTAAAGAAAGAGGG
1 AGATTGCT-CGAGTCT-TATACTCTCTGAAGAAATAGGG
3259791 AGCGAACCAG
Statistics
Matches: 340, Mismatches: 19, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
107 2 0.01
108 236 0.69
109 2 0.01
110 100 0.29
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
AGATTGCTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGG
TCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGTTGA
Found at i:3266682 original size:108 final size:108
Alignment explanation
Indices: 3266493--3266706 Score: 347
Period size: 108 Copynumber: 2.0 Consensus size: 108
3266483 AAAAGATAGT
* * * *
3266493 CTATCTTAGGAAGTGAGTAACGGTTCTTAATGGTTAACTTATTCAACTGCTTGTAGTTGACATAC
1 CTATCTTAGAAAGTGAGTAACGATTCTTAATGGTTAACTTATGCAACTGCCTGTAGTTGACATAC
* *
3266558 AACCTCATTGACCCATCATTCTTCTTACTAAAAAAGTTTGACG
66 AACCTCATTGACCCATCATTCTTCTTAATAAAAAAGATTGACG
* * *
3266601 CTATCTTAGAAAGTGGGTAACGATTCTTGATGGTTAACTTATGCAACTGCCTGTAGTTGATATAC
1 CTATCTTAGAAAGTGAGTAACGATTCTTAATGGTTAACTTATGCAACTGCCTGTAGTTGACATAC
3266666 AACCTCATTGACCCATCATTCTTCTTAATAAAAAAGATTGA
66 AACCTCATTGACCCATCATTCTTCTTAATAAAAAAGATTGA
3266707 TGCTCCCTAC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (108 bp):
CTATCTTAGAAAGTGAGTAACGATTCTTAATGGTTAACTTATGCAACTGCCTGTAGTTGACATAC
AACCTCATTGACCCATCATTCTTCTTAATAAAAAAGATTGACG
Found at i:3269258 original size:3 final size:3
Alignment explanation
Indices: 3269246--3269281 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3269236 TATATAATTT
*
3269246 TTA TTA -TA TTA TTA TTA TTA TTA CTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3269282 ATACTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3276903 original size:63 final size:62
Alignment explanation
Indices: 3276804--3277115 Score: 273
Period size: 63 Copynumber: 5.0 Consensus size: 62
3276794 TACATACATT
* * * * *
3276804 TTGACTTCTTCATTAA-AAAAAGTCAACCTTTGTTATTTACTGACTCCTCAGTAAAGTCAATCC
1 TTGACTTCTTCGTGAAGAGAAA-TCAACTTTTGTTATTT-CTGACTCCTCAGTAGAGTCAATCC
* * * * *
3276867 TTGACTTCTTCATGAAGAGAAATCAACTTTTGTTATTCCCTAACTCCTCAATAGAGTCAATCT
1 TTGACTTCTTCGTGAAGAGAAATCAACTTTTGTTATT-TCTGACTCCTCAGTAGAGTCAATCC
3276930 TTGACTT-TCTCGTGAAGA-AAAGTCATA-TTTTGTTATTTCCTGACTCCTCAGTAGAGTCAA-C
1 TTGACTTCT-TCGTGAAGAGAAA-TCA-ACTTTTGTTATTT-CTGACTCCTCAGTAGAGTCAATC
*
3276991 TT
62 -C
* * *
3276993 TTGACTTCCTT-GTAAAGAGAAGTCAA-TCTTTGTTATTTTTCGACTCCTCAGTAGAGTCAA-CC
1 TTGACTT-CTTCGTGAAGAGAAATCAACT-TTTGTTATTTCT-GACTCCTCAGTAGAGTCAATCC
* * * * *
3277055 TTTGACTTCCTT-GTGAAGAGAAGTCAACATATATTATTTTTGACTCCTCAGTAGAGTCAAT
1 -TTGACTT-CTTCGTGAAGAGAAATCAACTTTTGTTATTTCTGACTCCTCAGTAGAGTCAAT
3277116 ATTCAACTTC
Statistics
Matches: 214, Mismatches: 20, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
62 27 0.13
63 178 0.83
64 8 0.04
65 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (62 bp):
TTGACTTCTTCGTGAAGAGAAATCAACTTTTGTTATTTCTGACTCCTCAGTAGAGTCAATCC
Found at i:3277028 original size:126 final size:125
Alignment explanation
Indices: 3276803--3277115 Score: 330
Period size: 126 Copynumber: 2.5 Consensus size: 125
3276793 ATACATACAT
* * * * * *
3276803 TTTGACTTCTTCATTAAAAAAAGTCAACCTTTGTTATTTACTGACTCCTCAGTAAAGTCAATCCT
1 TTTGACTTCCTCGTGAAGAAAAGTCAACATTTGTTATTT-CTGACTCCTCAGTAGAGTCAATCCT
* *
3276868 TGACTTCTTCATGAAGAGAAATCAACTTTTGTTATTCC-CTAACTCCTCAATAGAGTCAATC
65 TGACTTCTTCATAAAGAGAAATCAACTTTTGTTATTCCTC-AACTCCTCAATAGAGTCAACC
* *
3276929 TTTGACTTTCTCGTGAAGAAAAGTCATA-TTTTGTTATTTCCTGACTCCTCAGTAGAGTCAA-CT
1 TTTGACTTCCTCGTGAAGAAAAGTCA-ACATTTGTTATTT-CTGACTCCTCAGTAGAGTCAATC-
* * * ** * *
3276992 TTTGACTTCCTT-GTAAAGAGAAGTCAA-TCTTTGTTATTTTTCGACTCCTCAGTAGAGTCAACC
63 CTTGACTT-CTTCATAAAGAGAAATCAACT-TTTGTTATTCCTCAACTCCTCAATAGAGTCAACC
* * * * *
3277055 TTTGACTTCCTTGTGAAGAGAAGTCAACATATATTATTTTTGACTCCTCAGTAGAGTCAAT
1 TTTGACTTCCTCGTGAAGAAAAGTCAACATTTGTTATTTCTGACTCCTCAGTAGAGTCAAT
3277116 ATTCAACTTC
Statistics
Matches: 156, Mismatches: 24, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
125 23 0.15
126 128 0.82
127 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (125 bp):
TTTGACTTCCTCGTGAAGAAAAGTCAACATTTGTTATTTCTGACTCCTCAGTAGAGTCAATCCTT
GACTTCTTCATAAAGAGAAATCAACTTTTGTTATTCCTCAACTCCTCAATAGAGTCAACC
Found at i:3277378 original size:82 final size:82
Alignment explanation
Indices: 3277277--3277470 Score: 280
Period size: 82 Copynumber: 2.4 Consensus size: 82
3277267 TTTTTTATTT
* * *
3277277 CAGTCTGATCTCCCTTGAATGAATAGTGGAGTAGATACATCTTCAAAAATTGATCTGAATACTCG
1 CAGTCTGATCTCCCCTGAATGAATAGTGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCG
*
3277342 AAAAAGAGGCACATATC
66 AAAAAGAGGCACAGATC
* * * *
3277359 CAGTCTGATCTCCCCTGAATGAAAAGTGGAGCATATACGTCTTCAAAAATTGATCTGGATACCCG
1 CAGTCTGATCTCCCCTGAATGAATAGTGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCG
*
3277424 AAAAAGTGGCACAGATC
66 AAAAAGAGGCACAGATC
* * *
3277441 CAGTCTGATCTTCTCTGAATAAATAGTGGA
1 CAGTCTGATCTCCCCTGAATGAATAGTGGA
3277471 ACAAATTCTT
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 99 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (82 bp):
CAGTCTGATCTCCCCTGAATGAATAGTGGAGCAGATACATCTTCAAAAATTGATCTGAATACCCG
AAAAAGAGGCACAGATC
Found at i:3277536 original size:35 final size:35
Alignment explanation
Indices: 3277491--3277735 Score: 307
Period size: 35 Copynumber: 6.9 Consensus size: 35
3277481 CTTATTTCAT
*
3277491 ATCCAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
1 ATCCAACCTTCACAAAAGAGTAGTGAAGCAATGCA
* * *
3277526 ATACAACCTTCAAAAAAGAGTAGTGAAGTAATGCA
1 ATCCAACCTTCACAAAAGAGTAGTGAAGCAATGCA
3277561 ATCCAACCTTCACAAAAGAGTAGTGAAGCAATGCA
1 ATCCAACCTTCACAAAAGAGTAGTGAAGCAATGCA
* *
3277596 ATCCAGCCTTCACAAAAGAGTAGTGAAG-AATTCA
1 ATCCAACCTTCACAAAAGAGTAGTGAAGCAATGCA
*
3277630 GATCCAGCCTTCACAAAAGAGTAGTGAAGCAATGCA
1 -ATCCAACCTTCACAAAAGAGTAGTGAAGCAATGCA
* * * *
3277666 ATCTAGCCTTCATAAAAAGAGTAGTGAAGAAAAT-CAAA
1 ATCCAACCTTCA-CAAAAGAGTAGTGAAG-CAATGC--A
*
3277704 AT-CAAGCCTTCACAAAAAAGTAGTGAAGCAAT
1 ATCCAA-CCTTCACAAAAGAGTAGTGAAGCAAT
3277736 ATAATATCAA
Statistics
Matches: 185, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
34 5 0.03
35 129 0.70
36 24 0.13
37 18 0.10
38 9 0.05
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (35 bp):
ATCCAACCTTCACAAAAGAGTAGTGAAGCAATGCA
Found at i:3279086 original size:2 final size:2
Alignment explanation
Indices: 3279079--3279129 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3279069 CATTAGCCTT
3279079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3279121 TA TA TA TA T
1 TA TA TA TA T
3279130 TAGTATATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3280058 original size:24 final size:24
Alignment explanation
Indices: 3280030--3280083 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3280020 CATCCTAATT
*
3280030 GTTATTGTTTTTAACTGTTCAACG
1 GTTATTGTTTTTAACTATTCAACG
3280054 GTTATTGTTTTTAACTATTCAACG
1 GTTATTGTTTTTAACTATTCAACG
3280078 GTTATT
1 GTTATT
3280084 ACTGTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (24 bp):
GTTATTGTTTTTAACTATTCAACG
Found at i:3282747 original size:17 final size:18
Alignment explanation
Indices: 3282727--3282771 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
3282717 CTTCTACGAT
3282727 ACATCATCTC-GATCAAA-
1 ACATCATC-CAGATCAAAG
3282744 ACATCATCCAGATCAAAG
1 ACATCATCCAGATCAAAG
3282762 ACATCATCCA
1 ACATCATCCA
3282772 AGTAATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.04
17 15 0.58
18 10 0.38
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.20
Consensus pattern (18 bp):
ACATCATCCAGATCAAAG
Found at i:3283374 original size:20 final size:21
Alignment explanation
Indices: 3283344--3283387 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3283334 TAAACAGTAC
*
3283344 ATATATGTTCATGTGGTACCG
1 ATATATGTTCATGTGGTACAG
3283365 ATAT-TGTTCATGTGGTACAG
1 ATATATGTTCATGTGGTACAG
3283385 ATA
1 ATA
3283388 CCCTAGGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (21 bp):
ATATATGTTCATGTGGTACAG
Found at i:3283631 original size:21 final size:20
Alignment explanation
Indices: 3283606--3283644 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3283596 GCAGAGAAAA
3283606 ATCCCAAAACGGCTAGAAATC
1 ATCCC-AAACGGCTAGAAATC
*
3283627 ATCCCCAACGGCTAGAAA
1 ATCCCAAACGGCTAGAAA
3283645 CGGCCACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.41, C:0.31, G:0.15, T:0.13
Consensus pattern (20 bp):
ATCCCAAACGGCTAGAAATC
Found at i:3285226 original size:17 final size:18
Alignment explanation
Indices: 3285201--3285240 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3285191 AAAAAATAGA
*
3285201 AATAGAAATATA-ATTAT
1 AATAAAAATATATATTAT
*
3285218 AATAAAAATATATTTTAT
1 AATAAAAATATATATTAT
3285236 AATAA
1 AATAA
3285241 CTCACTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
AATAAAAATATATATTAT
Found at i:3290316 original size:20 final size:20
Alignment explanation
Indices: 3290293--3290332 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3290283 TCAAACTCAA
3290293 ATTACTATT-TTATTCTATTT
1 ATTACTATTATTATT-TATTT
*
3290313 ATTATTATTATTATTTATTT
1 ATTACTATTATTATTTATTT
3290333 GCCTTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTACTATTATTATTTATTT
Found at i:3290789 original size:41 final size:40
Alignment explanation
Indices: 3290731--3290818 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 40
3290721 GAAAAAGTTT
3290731 AAAAAAAAACTATTCACT-ATTCGAACAACAAAAAAAGTAAA
1 AAAAAAAAACTATTCACTGATTCGAACAAC-AAAAAAG-AAA
* * *
3290772 AAGAAAAAAA-TGTTCACTGTTTTGAACAACAAAAAAGAAA
1 AA-AAAAAAACTATTCACTGATTCGAACAACAAAAAAGAAA
3290812 AAAAAAA
1 AAAAAAA
3290819 GACAGAAACT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 5 0.12
40 5 0.12
41 16 0.38
42 16 0.38
ACGTcount: A:0.64, C:0.11, G:0.08, T:0.17
Consensus pattern (40 bp):
AAAAAAAAACTATTCACTGATTCGAACAACAAAAAAGAAA
Found at i:3292559 original size:17 final size:18
Alignment explanation
Indices: 3292524--3292562 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3292514 CAAATTACTA
*
3292524 TTTTATTCTATTTATTAT
1 TTTTATTCTATTTAGTAT
*
3292542 TTTTATTTTATTT-GTAT
1 TTTTATTCTATTTAGTAT
3292559 TTTT
1 TTTT
3292563 CTTATTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTATTCTATTTAGTAT
Found at i:3296032 original size:29 final size:28
Alignment explanation
Indices: 3296000--3296069 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
3295990 TCCTTTACCT
*
3296000 TACTATTTCTTATACTATTTCTTTTATTG
1 TACTATTTCTT-TACTAATTCTTTTATTG
3296029 TACTATTTCTCTTACTAATTCTTTTATTG
1 TACTATTTCT-TTACTAATTCTTTTATTG
* *
3296058 TTCTATATCTTT
1 TACTATTTCTTT
3296070 TAGTATATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.05
29 34 0.92
30 1 0.03
ACGTcount: A:0.20, C:0.16, G:0.03, T:0.61
Consensus pattern (28 bp):
TACTATTTCTTTACTAATTCTTTTATTG
Found at i:3296378 original size:32 final size:32
Alignment explanation
Indices: 3296318--3296379 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
3296308 TGACACATTT
* **
3296318 AGTGCCCTGTGATTGCACGATAGGTGCAGCTC
1 AGTGCCCTGTGATTGCACCATAAATGCAGCTC
* *
3296350 AGTGTCCTGTGATTGCACCCTAAATGCAGC
1 AGTGCCCTGTGATTGCACCATAAATGCAGC
3296380 ATATTTAGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (32 bp):
AGTGCCCTGTGATTGCACCATAAATGCAGCTC
Found at i:3296400 original size:36 final size:35
Alignment explanation
Indices: 3296350--3296440 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 35
3296340 GGTGCAGCTC
* *
3296350 AGTGTCCTGTGATTGCACCCTAAATGCAGCATATTT
1 AGTG-CCTGTGATTGCACCCTAAATGCAACACATTT
* * * *
3296386 AGTGACCTATGATTGCATCGTAGATGCAACACATTT
1 AGTG-CCTGTGATTGCACCCTAAATGCAACACATTT
3296422 AGTGCCATGTGATTGCACC
1 AGTGCC-TGTGATTGCACC
3296441 ATAGGTGTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 2 0.04
36 43 0.96
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (35 bp):
AGTGCCTGTGATTGCACCCTAAATGCAACACATTT
Found at i:3296756 original size:28 final size:28
Alignment explanation
Indices: 3296712--3296765 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
3296702 ATACTTTTAC
3296712 TAATATAATAAATTCATATT-CGTATAAA
1 TAATATAATAAATTCAT-TTACGTATAAA
*
3296740 TAATCTAA-AAATATCATTTACGTATA
1 TAATATAATAAAT-TCATTTACGTATA
3296766 TTCAATACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (28 bp):
TAATATAATAAATTCATTTACGTATAAA
Found at i:3307363 original size:22 final size:22
Alignment explanation
Indices: 3307337--3307381 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3307327 CTCGAATAAC
**
3307337 ATTCATGATAATTATCATATAT
1 ATTCATGATAAACATCATATAT
*
3307359 ATTCATTATAAACATCATATAT
1 ATTCATGATAAACATCATATAT
3307381 A
1 A
3307382 ATAACCAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.42
Consensus pattern (22 bp):
ATTCATGATAAACATCATATAT
Found at i:3309649 original size:17 final size:17
Alignment explanation
Indices: 3309627--3309660 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3309617 AATAAAGGAG
* *
3309627 CTAGTTTGATTAATGAA
1 CTAGTTTAATGAATGAA
3309644 CTAGTTTAATGAATGAA
1 CTAGTTTAATGAATGAA
3309661 TGAGTTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (17 bp):
CTAGTTTAATGAATGAA
Found at i:3310353 original size:114 final size:112
Alignment explanation
Indices: 3310153--3310360 Score: 271
Period size: 114 Copynumber: 1.8 Consensus size: 112
3310143 CCCTATTTTA
* *
3310153 TGATGGATTTGAGAAAAATGTTGAATAAGTTCTTCTCATCATGAACTTCTCTCTTATGAATGAGT
1 TGATGGATTTGAGAAAAATGTTGAACAAGTTCTTCTCATCATGAACTTCTCCCTTATGAATGAG-
*
3310218 TTTTCTCATTATGAATTCCTCATTGAAAAAATTGATCCACATCCTTCTG
65 -TTTCTCATTATGAATCCCTCATTGAAAAAATTGATCCACATCCTTCTG
* *
3310267 TGATGGATTTGAGCAAAA-GCTTGAACAAGTTCTTCTCATTATGAACTTCCCATCCCTTTAT-AG
1 TGATGGATTTGAGAAAAATG-TTGAACAAGTTCTTCTCATCATGAACTT--C-TCCC-TTATGA-
3310330 ATGAG-TTCTCATTATGAA-CCCTCATTGAAAA
60 ATGAGTTTCTCATTATGAATCCCTCATTGAAAA
3310361 GATCAATTTG
Statistics
Matches: 83, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
113 1 0.01
114 55 0.66
115 13 0.16
116 1 0.01
117 4 0.05
118 9 0.11
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (112 bp):
TGATGGATTTGAGAAAAATGTTGAACAAGTTCTTCTCATCATGAACTTCTCCCTTATGAATGAGT
TTCTCATTATGAATCCCTCATTGAAAAAATTGATCCACATCCTTCTG
Found at i:3313082 original size:69 final size:69
Alignment explanation
Indices: 3312890--3313119 Score: 241
Period size: 69 Copynumber: 3.3 Consensus size: 69
3312880 ATAATAATAA
* * * *** *
3312890 ATGATTAGGTGCTCCCGTGTGTGTCACTCTAATCCTTCGGGGATCTTGTGTGAGACACCCAGAAT
1 ATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTGGGGCTCGCATGCGAGACACCCAGAAT
*
3312955 AACC
66 AGCC
* * * * *
3312959 ATGATTAGGCGTTCTCGTGCGAGTCACTCTAATCCTTTGGGGCTCTCGCA--CGAGACACCCAGG
1 ATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTGGGG--CTCGCATGCGAGACACCCAGA
3313022 ATAGCC
64 ATAGCC
* * * *
3313028 ACGATTAGGTGCTCCCATGTGAGTCACTCTAATCCTTTGGAGCTAC-CATGCGAGACACCCAAAA
1 ATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTGGGGCT-CGCATGCGAGACACCCAGAA
3313092 TAGCC
65 TAGCC
* *
3313097 ATAAATAGGTGCTCCCGTGTGAG
1 ATGATTAGGTGCTCCCGTGTGAG
3313120 ACACCAAAAA
Statistics
Matches: 130, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
67 4 0.03
68 1 0.01
69 123 0.95
71 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (69 bp):
ATGATTAGGTGCTCCCGTGTGAGTCACTCTAATCCTTTGGGGCTCGCATGCGAGACACCCAGAAT
AGCC
Found at i:3313225 original size:2 final size:2
Alignment explanation
Indices: 3313220--3313262 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3313210 TTATGGTTTT
*
3313220 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3313262 T
1 T
3313263 TTTTTGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3313361 original size:3 final size:3
Alignment explanation
Indices: 3313330--3313384 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
3313320 TTGAAGTATA
3313330 TAT TA- TAT ATAT TA- TAT T-T TAT ATAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
3313374 TAT TAT TAT TA
1 TAT TAT TAT TA
3313385 CTCTCATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.13
3 35 0.74
4 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3314148 original size:16 final size:17
Alignment explanation
Indices: 3314104--3314156 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
3314094 TAAGGAATTA
3314104 AATAAAGGAATAAAAATG
1 AATAAAGGAA-AAAAATG
*
3314122 -ATAAA-GAAAAATA-G
1 AATAAAGGAAAAAAATG
*
3314136 AATAAAGGAAAAAAATT
1 AATAAAGGAAAAAAATG
3314153 AATA
1 AATA
3314157 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 9 0.31
16 10 0.34
17 9 0.31
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (17 bp):
AATAAAGGAAAAAAATG
Found at i:3315239 original size:4 final size:4
Alignment explanation
Indices: 3315230--3315286 Score: 71
Period size: 4 Copynumber: 14.0 Consensus size: 4
3315220 AATAATAATA
* *
3315230 AAAT AAAT AAAT -AAT AAAT GAAAT AAAAT AAAT AAAT AAAT ACAT AGAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
3315279 AAAT AAAT
1 AAAT AAAT
3315287 TAAAAACATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 3 0.06
4 36 0.77
5 8 0.17
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3315244 original size:16 final size:15
Alignment explanation
Indices: 3315223--3315286 Score: 78
Period size: 16 Copynumber: 4.2 Consensus size: 15
3315213 AACAAATAAT
3315223 AATAATAAAATAAATA
1 AATAAT-AAATAAATA
3315239 AATAATAAATGAAAT-
1 AATAATAAAT-AAATA
3315254 AA-AATAAATAAATA
1 AATAATAAATAAATA
*
3315268 AATACATAGATAAATA
1 AATA-ATAAATAAATA
3315284 AAT
1 AAT
3315287 TAAAAACATT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
13 4 0.09
14 9 0.21
15 7 0.16
16 23 0.53
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (15 bp):
AATAATAAATAAATA
Found at i:3315280 original size:25 final size:22
Alignment explanation
Indices: 3315216--3315286 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 22
3315206 GACCTGAAAC
3315216 AAATAATAATAATAAAATAAAT
1 AAATAATAATAATAAAATAAAT
3315238 AAATAATAAATGAAATAAAATAAAT
1 AAATAAT-AAT--AATAAAATAAAT
3315263 AAATAAATACATAGAT-AAATAAAT
1 AAAT-AATA-ATA-ATAAAATAAAT
3315287 TAAAAACATT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
22 7 0.16
23 3 0.07
24 9 0.21
25 19 0.44
26 5 0.12
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (22 bp):
AAATAATAATAATAAAATAAAT
Found at i:3315365 original size:38 final size:38
Alignment explanation
Indices: 3315286--3315558 Score: 394
Period size: 38 Copynumber: 7.3 Consensus size: 38
3315276 GATAAATAAA
* * * *
3315286 TTAAAAAC-ATTTTTTAAAACTATA-CA-ATATATGTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
* *
3315321 TTAAAAAATAATTTTCAAAACCATATAATATATAT-TT
1 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
* * *
3315358 TAAAAAAATAATTTTCAATACTATATAATATATATATTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATATA-TT
3315397 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
3315435 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
3315473 TTAAAAACTAATTTTCAAAACTATATAATATATAT-TT
1 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
* *
3315510 TTAAAAAGTAATTTTCAAAACTATATAATATATATGTTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATAT-ATT
3315549 TTAAAAACTA
1 TTAAAAACTA
3315559 TGTATTATAT
Statistics
Matches: 218, Mismatches: 13, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
35 7 0.03
36 13 0.06
37 71 0.33
38 81 0.37
39 46 0.21
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (38 bp):
TTAAAAACTAATTTTCAAAACTATATAATATATATATT
Found at i:3315428 original size:37 final size:37
Alignment explanation
Indices: 3315426--3315558 Score: 223
Period size: 37 Copynumber: 3.5 Consensus size: 37
3315416 ACTATATAAT
3315426 ATATATATTT-TAAAAACTAATTTTCAAAACTATATA
1 ATATATATTTTTAAAAACTAATTTTCAAAACTATATA
3315462 ATATATATATTTTAAAAACTAATTTTCAAAACTATATA
1 ATATATAT-TTTTAAAAACTAATTTTCAAAACTATATA
*
3315500 ATATATATTTTTAAAAAGTAATTTTCAAAACTATATA
1 ATATATATTTTTAAAAACTAATTTTCAAAACTATATA
3315537 ATATATATGTTTTTAAAAACTA
1 ATATATA--TTTTTAAAAACTA
3315559 TGTATTATAT
Statistics
Matches: 91, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
36 8 0.09
37 37 0.41
38 34 0.37
39 12 0.13
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (37 bp):
ATATATATTTTTAAAAACTAATTTTCAAAACTATATA
Found at i:3315555 original size:26 final size:26
Alignment explanation
Indices: 3315521--3315570 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3315511 TAAAAAGTAA
*
3315521 TTTTCAAAACTATATAATATATATGT
1 TTTTAAAAACTATATAATATATATGT
* *
3315547 TTTTAAAAACTATGTATTATATAT
1 TTTTAAAAACTATATAATATATAT
3315571 ATTTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (26 bp):
TTTTAAAAACTATATAATATATATGT
Found at i:3315580 original size:26 final size:26
Alignment explanation
Indices: 3315526--3315581 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
3315516 AGTAATTTTC
* **
3315526 AAAACTATATAATATATATGTTTTTA
1 AAAACTATATAATATATATATTTAAA
* *
3315552 AAAACTATGTATTATATATATTTAAA
1 AAAACTATATAATATATATATTTAAA
3315578 AAAA
1 AAAA
3315582 AGTTTTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
AAAACTATATAATATATATATTTAAA
Found at i:3315604 original size:35 final size:36
Alignment explanation
Indices: 3315565--3315645 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 36
3315555 ACTATGTATT
3315565 ATATATATTTAAAAAAAAGTTTTCA-AAACAATATA
1 ATATATATTTAAAAAAAAGTTTTCAGAAACAATATA
** * *
3315600 ATATATATTTTCAAAAATGTTTTCAGAAACTATATA
1 ATATATATTTAAAAAAAAGTTTTCAGAAACAATATA
*
3315636 TTATATATTT
1 ATATATATTT
3315646 TCAAAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 22 0.55
36 18 0.45
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (36 bp):
ATATATATTTAAAAAAAAGTTTTCAGAAACAATATA
Found at i:3315635 original size:36 final size:35
Alignment explanation
Indices: 3315565--3315651 Score: 120
Period size: 36 Copynumber: 2.5 Consensus size: 35
3315555 ACTATGTATT
**
3315565 ATATATATTTAAAAAAAAGTTTTCAAAACAATATA
1 ATATATATTTTCAAAAAAGTTTTCAAAACAATATA
* *
3315600 ATATATATTTTCAAAAATGTTTTCAGAAACTATATA
1 ATATATATTTTCAAAAAAGTTTTCA-AAACAATATA
*
3315636 TTATATATTTTCAAAA
1 ATATATATTTTCAAAA
3315652 TATTTAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 22 0.48
36 24 0.52
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (35 bp):
ATATATATTTTCAAAAAAGTTTTCAAAACAATATA
Found at i:3315713 original size:36 final size:34
Alignment explanation
Indices: 3315553--3315714 Score: 105
Period size: 36 Copynumber: 4.5 Consensus size: 34
3315543 ATGTTTTTAA
* ** * *
3315553 AAACTATGTATTATATATATTTAAAAAAAAGTTTTC
1 AAACTATATATTATATA-ATTT-TCAAAATGATTTC
* * *
3315589 AAAACAATATAATATAT-ATTTTCAAAAATGTTTTC
1 -AAACTATATATTATATAATTTTC-AAAATGATTTC
*
3315624 AGAAACTATATATTATAT-ATTTTCAAAAT-ATTTAAA
1 --AAACTATATATTATATAATTTTCAAAATGATTT--C
*
3315660 AAACCCCATATATTATATAATTTTCAAAATGATTTC
1 AAA--CTATATATTATATAATTTTCAAAATGATTTC
3315696 AAACTATAATATATATATA
1 AAACTAT-ATAT-TATATA
3315715 TATATAATGG
Statistics
Matches: 101, Mismatches: 14, Indels: 21
0.74 0.10 0.15
Matches are distributed among these distances:
34 9 0.09
35 23 0.23
36 41 0.41
37 24 0.24
38 4 0.04
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (34 bp):
AAACTATATATTATATAATTTTCAAAATGATTTC
Found at i:3316390 original size:84 final size:84
Alignment explanation
Indices: 3316296--3316640 Score: 366
Period size: 84 Copynumber: 4.2 Consensus size: 84
3316286 CCCTCTTTCT
* * ** ** *
3316296 TTAAGTTATGCTGCAAATGATAGTGCCTAAGAGCTGAGCGTTGTTGAACTCGAAGGTCTTT-GAA
1 TTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTCGAA
*
3316360 GACAAATAACCCTTCTTGAC
66 G-CAAATAACCCTTCTCGAC
* * ** * *
3316380 TGAAGCTATGCTGTAAATGATGGTGCCTTTGAGCTGAGTATAATCGAAATCGAAGATCTTT-G--
1 TTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTCGAA
* *
3316442 GCAGAT-AGCCTTCTCGAC
66 GCAAATAACCCTTCTCGAC
* * * * * *
3316460 TTAAGCTATGCTGTAAATAAT-GTGCCTTGGAGCTAAGCGTAATCGAACTCGAAGGTCTTTGGTT
1 TTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTCG-A
*
3316524 GGCAAATAACCCTTCTCGAC
65 AGCAAATAACCCTTCTCGAC
* * * *
3316544 TTAAGTTATGCTGCAAATGTTGGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTCGAA
1 TTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTCGAA
3316609 G---ATAACCCTTCTCGAC
66 GCAAATAACCCTTCTCGAC
3316625 TTAAGCTATGCTGCAA
1 TTAAGCTATGCTGCAA
3316641 TCTTTGGTGA
Statistics
Matches: 217, Mismatches: 38, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
79 33 0.15
80 30 0.14
81 34 0.16
82 1 0.00
83 5 0.02
84 78 0.36
85 36 0.17
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (84 bp):
TTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTCTTTCGAA
GCAAATAACCCTTCTCGAC
Found at i:3316535 original size:164 final size:165
Alignment explanation
Indices: 3316296--3316640 Score: 451
Period size: 164 Copynumber: 2.1 Consensus size: 165
3316286 CCCTCTTTCT
* * * ** *
3316296 TTAAGTTATGCTGCAAATGATAGTGCCTAAGAGCTGAGCGTTGTTGAACTCGAAGGTCTTTGAAG
1 TTAAGCTATGCTGCAAATAATAGTGCCTAAGAGCTAAGCGTAATCGAACTCGAAGGTCTTTGAAG
* *
3316361 ACAAATAACCCTTCTTGACTGAAGCTATGCTGTAAATGATGGTGCCTTTGAGCTGAGTATAATCG
66 ACAAATAACCCTTCTCGACTGAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTATAATCG
* * *
3316426 AAATCGAAGATCTTTGGCAGAT-AGCCTTCTCGAC
131 AAATCGAAGATCTTTCGAAGATAACCCTTCTCGAC
* ** **
3316460 TTAAGCTATGCTGTAAATAAT-GTGCCTTGGAGCTAAGCGTAATCGAACTCGAAGGTCTTTGGTT
1 TTAAGCTATGCTGCAAATAATAGTGCCTAAGAGCTAAGCGTAATCGAACTCGAAGGTCTTT-GAA
* * * * * *
3316524 GGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGTTGGTTCCTTTGAGCTGAGTGTAATC
65 GACAAATAACCCTTCTCGACTGAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTATAATC
* *
3316589 GAACTCGAAGGTCTTTCGAAGATAACCCTTCTCGAC
130 GAAATCGAAGATCTTTCGAAGATAACCCTTCTCGAC
3316625 TTAAGCTATGCTGCAA
1 TTAAGCTATGCTGCAA
3316641 TCTTTGGTGA
Statistics
Matches: 154, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
163 33 0.21
164 95 0.62
165 26 0.17
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (165 bp):
TTAAGCTATGCTGCAAATAATAGTGCCTAAGAGCTAAGCGTAATCGAACTCGAAGGTCTTTGAAG
ACAAATAACCCTTCTCGACTGAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTATAATCG
AAATCGAAGATCTTTCGAAGATAACCCTTCTCGAC
Found at i:3316854 original size:84 final size:82
Alignment explanation
Indices: 3316651--3317240 Score: 469
Period size: 84 Copynumber: 7.2 Consensus size: 82
3316641 TCTTTGGTGA
* * ** *** * * *
3316651 CAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCAAAGCTGAGTGTAATTAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCAA
* *
3316716 ACTCGAGGGTCTTTG--G
65 ACTCGAAGGTTTTTGTTG
* * * * * *
3316732 CAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAA
*
3316797 CTCGAAGGTATTTTGATG
66 CTCGAAGGT-TTTTGTTG
* * * * * * * *
3316815 ATAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGA-CTGTAATC
1 -CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGC-GTAGTC
**
3316879 AAACTCG-AGAGTCATTG--G
63 AAACTCGAAG-GTTTTTGTTG
* * *
3316897 CAGAT-ACCCTTCTCA-ACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAA
* *
3316960 ACTCAAAGGTCTTTGGTTAG
65 ACTCGAAGGT-TTTTGTT-G
* * ** * * *
3316980 AAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACATGACTTAGAGCTGAGCATAGTCAAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAA
*
3317045 CTCGAAGGTCTTTGTTGG
66 CTCGAAGGTTTTTGTT-G
* * * * ** * * * *
3317063 CAAATAACCCTTATAGCCTTGAGTTATAATGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCAA
*
3317128 ACTCGGAGGTTTTT-TTG
65 ACTCGAAGGTTTTTGTTG
* * * *
3317145 CAGATAGCCCTTCTCGACTTAAGATATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAA
* * *
3317210 CTCGAAGGTCTTGGTGG
66 CTCGAAGGTTTTTGTTG
*
3317227 CAGATAGCCCTTCT
1 CAGATAACCCTTCT
3317241 GGCCTTGAGC
Statistics
Matches: 394, Mismatches: 97, Indels: 35
0.75 0.18 0.07
Matches are distributed among these distances:
79 22 0.06
80 57 0.14
81 73 0.19
82 51 0.13
83 46 0.12
84 122 0.31
85 23 0.06
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (82 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAA
CTCGAAGGTTTTTGTTG
Found at i:3316932 original size:80 final size:80
Alignment explanation
Indices: 3316675--3316939 Score: 234
Period size: 80 Copynumber: 3.2 Consensus size: 80
3316665 AGCCTTGAGT
* * * * * *
3316675 TATGCTATAAATGATGTGCCCTCAAAGCTGAGTGTAATTAAACTCGAGGGTCTTTGGCAGATAGC
1 TATGCTACAAATGATGTGCCCTCGAAGCTGACTGTAATCAAACTCGAGAGTCATTGGCAGATA-C
*
3316740 CCTTCTCGACTTAAGC
65 CCTTCTCAACTTAAGC
* * * * * *
3316756 TATGCTACAAATGATATG-CCTTGGAGCTGAGC-GTAGTCGAACTCGA-AGGT-ATTTTGATGAT
1 TATGCTACAAATGATGTGCCCTCGAAGCTGA-CTGTAATCAAACTCGAGA-GTCA--TTG--G-C
* * *
3316817 AGATAACCCTTCT-AGCCTTGAGT
59 AGAT-ACCCTTCTCA-ACTTAAGC
* **
3316840 TATGTTGTAAATGATGTGCCCTCGAAGCTGACTGTAATCAAACTCGAGAGTCATTGGCAGATACC
1 TATGCTACAAATGATGTGCCCTCGAAGCTGACTGTAATCAAACTCGAGAGTCATTGGCAGATACC
3316905 CTTCTCAACTTAAGC
66 CTTCTCAACTTAAGC
3316920 TATGCTACAAATGATGTGCC
1 TATGCTACAAATGATGTGCC
3316940 TTGGAGCTGA
Statistics
Matches: 139, Mismatches: 31, Indels: 29
0.70 0.16 0.15
Matches are distributed among these distances:
80 52 0.37
81 24 0.17
82 1 0.01
83 1 0.01
84 34 0.24
85 25 0.18
86 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (80 bp):
TATGCTACAAATGATGTGCCCTCGAAGCTGACTGTAATCAAACTCGAGAGTCATTGGCAGATACC
CTTCTCAACTTAAGC
Found at i:3316990 original size:164 final size:165
Alignment explanation
Indices: 3316643--3317017 Score: 558
Period size: 164 Copynumber: 2.3 Consensus size: 165
3316633 TGCTGCAATC
* * *
3316643 TTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCAAAGCTGAG
1 TTTGGATGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAC
* * * *
3316707 TGTAATTAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATA
66 TGTAATCAAACTCGAGAGTCATTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTACAAATGATA
*
3316772 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
131 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTA
* * *
3316807 TTTTGATGATAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAC
1 TTTGGATGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAC
*
3316872 TGTAATCAAACTCGAGAGTCATTGGCAGATA-CCCTTCTCAACTTAAGCTATGCTACAAATGATG
66 TGTAATCAAACTCGAGAGTCATTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTACAAATGATA
*
3316936 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
131 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTA
* * * * *
3316971 TTTGGTTAGA-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TTTGGAT-GATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
3317018 CATGACTTAG
Statistics
Matches: 189, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
164 105 0.56
165 84 0.44
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.30
Consensus pattern (165 bp):
TTTGGATGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAC
TGTAATCAAACTCGAGAGTCATTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTACAAATGATA
TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTA
Found at i:3318602 original size:95 final size:94
Alignment explanation
Indices: 3318434--3318619 Score: 248
Period size: 95 Copynumber: 2.0 Consensus size: 94
3318424 ATACATAAAC
* * * * * * *
3318434 ACCTTTATCAGGTTAGCTAAATCTTATCCATAAAGTCGGGGTGTTTAACCAATTTCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCAGAGCGTTTAACCAATTGCCTTAGAGGG
* *
3318499 ATAGCTCAAGCTTTATTGTATAGTATAATT
66 ACAACTCAAGCTTTATTGTATA-TATAATT
* *
3318529 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCAGAGCGTTTAGCCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCAGAGCGTTTAACCAATTGCCT-TAGAGG
3318593 GACAACTCAAGCTTTATTGTATATATA
65 GACAACTCAAGCTTTATTGTATATATA
3318620 TAATATTATA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 6 0.08
95 73 0.92
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (94 bp):
ACCTTTATCAGGCTAGCTAAATATTATCCATAAAGCCAGAGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATATATAATT
Found at i:3321287 original size:28 final size:27
Alignment explanation
Indices: 3321205--3321293 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 27
3321195 TAAAAAGAAT
*
3321205 AAAAATAAATAAGGAATTAAATA-AATA-
1 AAAAATAAATAAGGAA-AAAATATAA-AG
3321232 AATAAATAAATAAGGAAAAAATGATAAAG
1 AA-AAATAAATAAGGAAAAAAT-ATAAAG
*
3321261 AAAAATAGAATAAAGGAAAAAAT-TAAAT
1 AAAAATA-AAT-AAGGAAAAAATATAAAG
3321289 AAAAA
1 AAAAA
3321294 ATATATATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
27 6 0.11
28 30 0.56
29 7 0.13
30 11 0.20
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (27 bp):
AAAAATAAATAAGGAAAAAATATAAAG
Found at i:3321312 original size:19 final size:20
Alignment explanation
Indices: 3321290--3321332 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3321280 AAATTAAATA
3321290 AAAAAT-AT-ATATATAAAAG
1 AAAAATGATAATATA-AAAAG
*
3321309 AAAAATGATAATTTAAAAAG
1 AAAAATGATAATATAAAAAG
3321329 AAAA
1 AAAA
3321333 TAGTGAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAAATGATAATATAAAAAG
Found at i:3322629 original size:4 final size:4
Alignment explanation
Indices: 3322620--3322686 Score: 82
Period size: 4 Copynumber: 16.0 Consensus size: 4
3322610 AATAATAATA
3322620 AAAT AAAT AAAT AAAT -AAT AAAT AAAAT AAAAT AAAAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT -AAAT AAAT
*
3322667 AGAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT
3322687 TAAAAACATT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
3 3 0.05
4 37 0.63
5 19 0.32
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3322659 original size:39 final size:41
Alignment explanation
Indices: 3322609--3322691 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 41
3322599 GACCTAAAAC
3322609 AAATAATAATAAAATAAATAAATAAAT-AATAAATAAAATA
1 AAATAATAATAAAATAAATAAATAAATAAATAAATAAAATA
* *
3322649 AAATAA-AATAAAATAAATAGATAAATAAATAAATAAATTA
1 AAATAATAATAAAATAAATAAATAAATAAATAAATAAAATA
3322689 AAA
1 AAA
3322692 ACATTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 19 0.47
40 21 0.52
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (41 bp):
AAATAATAATAAAATAAATAAATAAATAAATAAATAAAATA
Found at i:3322663 original size:35 final size:34
Alignment explanation
Indices: 3322609--3322691 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 34
3322599 GACCTAAAAC
3322609 AAATAATAATAAAATAAATAAATAAAT-AATAAAT
1 AAATAA-AATAAAATAAATAAATAAATAAATAAAT
*
3322643 AAAATAAAATAAAATAAAATAAATAGATAAATAAAT
1 -AAATAAAATAAAAT-AAATAAATAAATAAATAAAT
*
3322679 AAATAAATTAAAA
1 AAATAAAATAAAA
3322692 ACATTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 8 0.18
35 29 0.66
36 7 0.16
ACGTcount: A:0.75, C:0.00, G:0.01, T:0.24
Consensus pattern (34 bp):
AAATAAAATAAAATAAATAAATAAATAAATAAAT
Found at i:3322760 original size:37 final size:37
Alignment explanation
Indices: 3322696--3323023 Score: 389
Period size: 39 Copynumber: 8.9 Consensus size: 37
3322686 TTAAAAACAT
* * *
3322696 TTTTTAAAACTATACAATATAT-GTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
*
3322732 TTTTCAAAACCATATAATATATATTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
*
3322769 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATAT-A-ATATATATTTTTAAAAAATAA
*
3322808 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATAT-A-ATATATATTTTTAAAAAATAA
*
3322847 TTTTCAAAACTATATAATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
* * *
3322884 TTTTCAAAACTATATAATATATATGTTTTTCAAAGATAT
1 TTTTCAAAACTATATAATATATA--TTTTTAAAAAATAA
* *
3322923 TTTTAAAAACTATAT-ATATATA--TTTAAAAAA-AG
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
* * *
3322956 TTTTCAAAACAATATAATATATA-TTTTCAAAAATAT
1 TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
* * * *
3322992 TTTTTAAAACTATGTATTATATATTTTCAAAA
1 TTTTCAAAACTATATAATATATATTTTTAAAA
3323024 TATTTAAAAA
Statistics
Matches: 259, Mismatches: 24, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
33 14 0.05
34 14 0.05
35 8 0.03
36 39 0.15
37 77 0.30
38 9 0.03
39 98 0.38
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (37 bp):
TTTTCAAAACTATATAATATATATTTTTAAAAAATAA
Found at i:3322816 original size:76 final size:75
Alignment explanation
Indices: 3322696--3323023 Score: 381
Period size: 76 Copynumber: 4.4 Consensus size: 75
3322686 TTAAAAACAT
* * * * *
3322696 TTTTTAAAACTATACA-ATATAT-GTTTTAAAAAATAATTTTCAAAACCATATAATATATATTTT
1 TTTTCAAAACTATATATATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATTTT
3322759 TAAAAAATAA
66 TAAAAAATAA
3322769 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
1 TTTTCAAAACTATAT-ATATATATATTTTTAAAAACTAATTTTCAAAACTATAT-A-ATATATAT
*
3322834 TTTTAAAAACTAA
63 TTTTAAAAAATAA
3322847 TTTTCAAAACTATATA-ATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATGTT
1 TTTTCAAAACTATATATATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATA--TT
* * *
3322911 TTTCAAAGATAT
64 TTTAAAAAATAA
* *
3322923 TTTTAAAAAC--TATATATATATA--TTTAAAAA--AAGTTTTCAAAACAATATAATATATA-TT
1 TTTTCAAAACTATATATATATATATTTTTAAAAACTAA-TTTTCAAAACTATATAATATATATTT
* *
3322981 TTCAAAAATAT
65 TTAAAAAATAA
* * *
3322992 TTTTTAAAACTATGTAT-TATATATTTTCAAAA
1 TTTTCAAAACTATATATATATATATTTTTAAAA
3323024 TATTTAAAAA
Statistics
Matches: 226, Mismatches: 16, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
69 21 0.09
70 6 0.03
71 6 0.03
72 28 0.12
73 21 0.09
74 12 0.05
75 14 0.06
76 81 0.36
77 2 0.01
78 35 0.15
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (75 bp):
TTTTCAAAACTATATATATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATTTT
TAAAAAATAA
Found at i:3323045 original size:35 final size:36
Alignment explanation
Indices: 3322788--3323050 Score: 148
Period size: 39 Copynumber: 7.2 Consensus size: 36
3322778 CTATATAATA
* * *
3322788 TATATATTTTTAAAAACTAATTTT-CAAAACTATATAAT
1 TATATATTTTCAAAAA-T-ATTTTAAAAAACCATAT-AT
* * * *
3322826 ATATATATTTTTAAAAACTAATTTT-CAAAACTATATAA
1 -TATATATTTTCAAAAA-T-ATTTTAAAAAACCATATAT
* * *
3322864 TATATATTTTTAAAAACTAATTTT-CAAAACTATATAAT
1 TATATATTTTCAAAAA-T-ATTTTAAAAAACCATAT-AT
* * * *
3322902 ATATATGTTTTTCAAAGATATTTTTAAAAACTATATA-
1 -TATAT-ATTTTCAAAAATATTTTAAAAAACCATATAT
* * * *
3322939 TATATA-TTT-AAAAAAAGTTTT-CAAAACAATATAA
1 TATATATTTTCAAAAATA-TTTTAAAAAACCATATAT
** * *
3322973 TATATATTTTCAAAAATATTTTTTAAAACTATGTAT
1 TATATATTTTCAAAAATATTTTAAAAAACCATATAT
3323009 TATATATTTTC-AAAATA-TTTAAAAAACCCATATAT
1 TATATATTTTCAAAAATATTTTAAAAAA-CCATATAT
3323044 TATATAT
1 TATATAT
3323051 ATTATATATA
Statistics
Matches: 194, Mismatches: 20, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
33 15 0.08
34 20 0.10
35 26 0.13
36 31 0.16
37 35 0.18
38 8 0.04
39 51 0.26
40 8 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.44
Consensus pattern (36 bp):
TATATATTTTCAAAAATATTTTAAAAAACCATATAT
Found at i:3324022 original size:4 final size:4
Alignment explanation
Indices: 3324013--3324067 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
3324003 GTTTTGCATC
* * * * *
3324013 ATTT ATTT ATTT GTTT GTTC ATTT ATTT ATTT ATTT -TTC ATTT ATCT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3324060 -TTT ATTT A
1 ATTT ATTT A
3324068 AATTCCTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 4 0.10
4 37 0.90
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:3324036 original size:20 final size:19
Alignment explanation
Indices: 3324011--3324066 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
3324001 TAGTTTTGCA
*
3324011 TCATTTATTTATTTGTTTGT
1 TCATTTATTTATTTATTT-T
3324031 TCATTTATTTATTTATTTT
1 TCATTTATTTATTTATTTT
*
3324050 TCATTTATCT-TTTATTT
1 TCATTTATTTATTTATTT
3324067 AAATTCCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.21
19 10 0.29
20 17 0.50
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (19 bp):
TCATTTATTTATTTATTTT
Found at i:3325855 original size:31 final size:29
Alignment explanation
Indices: 3325797--3325855 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3325787 TTTTGGTTAG
*
3325797 TGGCCAAAATATAAAATTTGAAAGTTTAT
1 TGGCCAAAATATAAAATTGGAAAGTTTAT
*
3325826 TGGCCAAAGTATAAAATTGGGAAAAGTTTA
1 TGGCCAAAATATAAAATT-GG-AAAGTTTA
3325856 GGGACCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 1 0.04
31 8 0.31
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.31
Consensus pattern (29 bp):
TGGCCAAAATATAAAATTGGAAAGTTTAT
Found at i:3327043 original size:11 final size:11
Alignment explanation
Indices: 3327029--3327056 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3327019 GGTTGTTGTG
3327029 TAATTGTTCTA
1 TAATTGTTCTA
3327040 TAATTGTTCTA
1 TAATTGTTCTA
3327051 TAATTG
1 TAATTG
3327057 ATGTACTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54
Consensus pattern (11 bp):
TAATTGTTCTA
Found at i:3335428 original size:40 final size:39
Alignment explanation
Indices: 3335362--3335456 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 39
3335352 ACAGTACAAC
* * *
3335362 ACACTACGGTG--TATAAGGTGGGCAAGGCCCGGCCTCA
1 ACACTACGGTGCATATTAGGTGAGCAAGGCCCGACCTCA
*
3335399 ACACTACGGTGCATTATTAGGTGAGCAAGGCTCGACCTCA
1 ACACTACGGTGCA-TATTAGGTGAGCAAGGCCCGACCTCA
* *
3335439 GCACTACTGTGCAATATT
1 ACACTACGGTGC-ATATT
3335457 TGACTCCTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
37 11 0.23
40 36 0.75
41 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.22
Consensus pattern (39 bp):
ACACTACGGTGCATATTAGGTGAGCAAGGCCCGACCTCA
Found at i:3336287 original size:24 final size:24
Alignment explanation
Indices: 3336260--3336359 Score: 87
Period size: 24 Copynumber: 4.2 Consensus size: 24
3336250 GATATCAAAA
*
3336260 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
3336284 ATCATAACAGAATCCATG-TTAGGA-
1 ATCAAAACAGAATTCA-GATCA-GAT
* *
3336308 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
3336332 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
3336356 ATCA
1 ATCA
3336360 GATAAAATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.05
24 52 0.90
25 3 0.05
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:3336359 original size:48 final size:48
Alignment explanation
Indices: 3336253--3336361 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
3336243 AAACGGAGAT
* * * * *
3336253 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
3336301 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3336349 ATCAGAAATCAGA
1 ATCAGAAATCAGA
3336362 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3337522 original size:18 final size:18
Alignment explanation
Indices: 3337501--3337536 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3337491 CTTTCATCCG
*
3337501 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
3337519 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
3337537 GTCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3338885 original size:13 final size:13
Alignment explanation
Indices: 3338880--3338928 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
3338870 GTCAACGGGT
*
3338880 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
3338893 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
3338906 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
3338919 CGGGTCGGGT
1 CGGGTCGGGT
3338929 TATGACCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:3338890 original size:18 final size:18
Alignment explanation
Indices: 3338867--3338902 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3338857 AACGGGTCAA
3338867 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
3338885 CGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGT
3338903 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:3338898 original size:8 final size:7
Alignment explanation
Indices: 3338831--3338877 Score: 67
Period size: 7 Copynumber: 6.4 Consensus size: 7
3338821 TGGTCAACTC
3338831 CGGTCAA
1 CGGTCAA
3338838 CGGTCAA
1 CGGTCAA
3338845 CGGTCAA
1 CGGTCAA
*
3338852 CAGTCAA
1 CGGTCAA
3338859 CGGGTCAA
1 C-GGTCAA
3338867 CGGGTCAA
1 C-GGTCAA
3338875 CGG
1 CGG
3338878 GTCGGGTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 23 0.62
8 14 0.38
ACGTcount: A:0.28, C:0.28, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:3341152 original size:48 final size:48
Alignment explanation
Indices: 3341047--3341154 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
3341037 AAACGGAGAT
* * * *
3341047 ATCAAAAATCA-AACATAATTCAGATCAGATATCATAACAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
3341094 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3341142 ATCAGAAATCAGA
1 ATCAGAAATCAGA
3341155 TAAAATATTC
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
47 7 0.15
48 40 0.85
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3342315 original size:17 final size:17
Alignment explanation
Indices: 3342293--3342327 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3342283 CTTTCATCCG
*
3342293 ATCTTATTATTTAATTC
1 ATCTTATCATTTAATTC
*
3342310 ATCTTATCATTTACTTC
1 ATCTTATCATTTAATTC
3342327 A
1 A
3342328 GTCATTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (17 bp):
ATCTTATCATTTAATTC
Found at i:3343643 original size:15 final size:15
Alignment explanation
Indices: 3343623--3343672 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
3343613 GGTCAACTCC
3343623 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
3343638 GGTCAACAGTCAACG
1 GGTCAACGGTCAACG
3343653 GGTCAACGGGTCAACG
1 GGTCAAC-GGTCAACG
3343669 GGTC
1 GGTC
3343673 GGGTCGGGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.14
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:3343660 original size:23 final size:22
Alignment explanation
Indices: 3343624--3343667 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
3343614 GTCAACTCCG
3343624 GTCAACGGTCAACGGGTCAACA
1 GTCAACGGTCAACGGGTCAACA
3343646 GTCAACGGGTCAACGGGTCAAC
1 GTCAAC-GGTCAACGGGTCAAC
3343668 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.30, C:0.27, G:0.30, T:0.14
Consensus pattern (22 bp):
GTCAACGGTCAACGGGTCAACA
Found at i:3343677 original size:13 final size:13
Alignment explanation
Indices: 3343672--3343720 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
3343662 GTCAACGGGT
*
3343672 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
*
3343685 CTGGTCGGGTAAA
1 CGGGTCGGGTAAA
3343698 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
3343711 CGGGTCGGGT
1 CGGGTCGGGT
3343721 TATGACCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:3343682 original size:18 final size:18
Alignment explanation
Indices: 3343659--3343694 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3343649 AACGGGTCAA
3343659 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
3343677 CGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGT
3343695 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:3343690 original size:8 final size:8
Alignment explanation
Indices: 3343623--3343672 Score: 77
Period size: 8 Copynumber: 6.5 Consensus size: 8
3343613 GGTCAACTCC
3343623 GGTCAAC-
1 GGTCAACG
3343630 GGTCAACG
1 GGTCAACG
3343638 GGTCAAC-
1 GGTCAACG
*
3343645 AGTCAACG
1 GGTCAACG
3343653 GGTCAACG
1 GGTCAACG
3343661 GGTCAACG
1 GGTCAACG
3343669 GGTC
1 GGTC
3343673 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
7 13 0.33
8 26 0.67
ACGTcount: A:0.26, C:0.26, G:0.34, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:3346030 original size:27 final size:27
Alignment explanation
Indices: 3345992--3346054 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
3345982 GAGGTAACTT
*
3345992 TTCGTGCACACTCTCAACTCTCCCTTC
1 TTCGAGCACACTCTCAACTCTCCCTTC
3346019 TTCGAGCACACTCTCAACTCTCCCTTC
1 TTCGAGCACACTCTCAACTCTCCCTTC
3346046 TTCGAGCAC
1 TTCGAGCAC
3346055 TTGTTAGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.43, G:0.10, T:0.30
Consensus pattern (27 bp):
TTCGAGCACACTCTCAACTCTCCCTTC
Found at i:3349581 original size:69 final size:69
Alignment explanation
Indices: 3349470--3349686 Score: 213
Period size: 69 Copynumber: 3.1 Consensus size: 69
3349460 TAATAAATGC
* * * *
3349470 TTAGGTGCTC-CCATGCAAGTTACTCTAATACTTTAGGGCTCCCGTGCGAGACGCCCAAAATAGC
1 TTAGGTGCTCATC-TGCAAGTCACTCTAATACTTCAGGGCTCCCATGCGAGACGCCCAAAATAGC
3349534 TATGA
65 TATGA
* ** * * * *** *
3349539 TTAGGTGCTCTTCTGTGAGTCACTCTAATACTTCAGGGCTCCCCTGTGAGATGCCTGGAATAGCC
1 TTAGGTGCTCATCTGCAAGTCACTCTAATACTTCAGGGCTCCCATGCGAGACGCCCAAAATAGCT
3349604 ATGA
66 ATGA
* * * * * *
3349608 TTAGGTGCTCATGTGCAAGTCACTCTAATCCTTC-GGGATTCCCATGCGAGACACTCAAAATAAC
1 TTAGGTGCTCATCTGCAAGTCACTCTAATACTTCAGGG-CTCCCATGCGAGACGCCCAAAATAGC
*
3349672 TACGA
65 TATGA
3349677 TTAGGTGCTC
1 TTAGGTGCTC
3349687 CCGTGTGAGA
Statistics
Matches: 117, Mismatches: 29, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
68 3 0.03
69 113 0.97
70 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (69 bp):
TTAGGTGCTCATCTGCAAGTCACTCTAATACTTCAGGGCTCCCATGCGAGACGCCCAAAATAGCT
ATGA
Found at i:3349834 original size:69 final size:68
Alignment explanation
Indices: 3349693--3349844 Score: 164
Period size: 69 Copynumber: 2.2 Consensus size: 68
3349683 GCTCCCGTGT
* * * * * *
3349693 GAGACACCTAAAATAGCCACAATTAGGTGTCCCATTCGAGTCACTGTAGTCCTTTATGGCTCCCG
1 GAGACACCCAAAATAGCCACAATTAAGTGTCCCATGCGAGTCACTCTAATCCTTTATGGCTCCCA
*
3349758 TGC
66 TAC
* * *
3349761 GAGACACCCATAATAGCCACAATTAAGT-TCTCTAGTGCGAGTCACTCTAATCCTTTA-GAGCTT
1 GAGACACCCAAAATAGCCACAATTAAGTGTC-CCA-TGCGAGTCACTCTAATCCTTTATG-GCTC
3349824 CCATAC
63 CCATAC
*
3349830 GAGACACTCAAAATA
1 GAGACACCCAAAATA
3349845 ATTATTTGTA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
67 2 0.03
68 28 0.41
69 39 0.57
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (68 bp):
GAGACACCCAAAATAGCCACAATTAAGTGTCCCATGCGAGTCACTCTAATCCTTTATGGCTCCCA
TAC
Found at i:3353636 original size:36 final size:36
Alignment explanation
Indices: 3353589--3353982 Score: 499
Period size: 36 Copynumber: 10.9 Consensus size: 36
3353579 GTGCGCTACA
*
3353589 TCCTTCCGTTCGACTTGAATCGGAAGTGTCAATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
*
3353625 TCCTTCTGTTCGACTTGAATCGGAAGTGT-GCATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCG-ATGCT
* * *
3353661 TCCTTCCGTTCGACTTGAATCAGAAGTGACTATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* * * *
3353697 TCCTTTCGTTAGACTTGAATCGGAAGTGCCAATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
*
3353733 TCCTTCCGTTCGACTTGAATCGGAAGTGTGGATG-T
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* * * *
3353768 CTCATTCCGTTTGACTTGAATCGGAAGTGCCTATGCCT
1 -TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATG-CT
* * *
3353806 T-CTTCCGTTCGACTTGAATCGGAAGTGCCTATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* *
3353841 TCTTTCCGTTCGACTTGAATCGGAAGTGTCGATGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* * *
3353877 TCCTTCCGTTCGACTTGAATCGAAAGTGAT-GACGCC
1 TCCTTCCGTTCGACTTGAATCGGAAGTG-TCGATGCT
*
3353913 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
* *
3353949 TTCTTCCGTTCGACTTGAATCGGAAGTGTAGATG
1 TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATG
3353983 AAATCACAAA
Statistics
Matches: 313, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
35 3 0.01
36 307 0.98
37 2 0.01
38 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (36 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGTCGATGCT
Found at i:3353778 original size:108 final size:106
Alignment explanation
Indices: 3353589--3353982 Score: 549
Period size: 108 Copynumber: 3.7 Consensus size: 106
3353579 GTGCGCTACA
* *
3353589 TCCTTCCGTTCGACTTGAATCGGAAGTGTCAATGCTTCCTTCTGTTCGACTTGAATCGGAAGTGT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
*
3353654 GCATGCTTCCTTCCGTTCGACTTGAATCAGAAGTGACTATGCT
66 GGATGC-TCCTTCCGTTCGACTTGAATC-GAAGTGACTATGCT
* *
3353697 TCCTTTCGTTAGACTTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
* * *
3353762 GGATGTCTCATTCCGTTTGACTTGAATCGGAAGTGCCTATGCCT
66 GGATG-CTCCTTCCGTTCGACTTGAATC-GAAGTGACTATG-CT
* * *
3353806 T-CTTCCGTTCGACTTGAATCGGAAGTGCCTATGCCTCTTTCCGTTCGACTTGAATCGGAAGTGT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
* * *
3353870 CGATGCCTCCTTCCGTTCGACTTGAATCGAAAGTGA-TGACGCC
66 GGATG-CTCCTTCCGTTCGACTTGAATCG-AAGTGACT-ATGCT
* *
3353913 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTTCTTCCGTTCGACTTGAATCGGAAGTGT
1 TCCTTCCGTTCGACTTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
*
3353978 AGATG
66 GGATG
3353983 AAATCACAAA
Statistics
Matches: 255, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
107 4 0.02
108 247 0.97
109 4 0.02
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (106 bp):
TCCTTCCGTTCGACTTGAATCGGAAGTGCCAATGCTTCCTTCCGTTCGACTTGAATCGGAAGTGT
GGATGCTCCTTCCGTTCGACTTGAATCGAAGTGACTATGCT
Found at i:3359187 original size:19 final size:19
Alignment explanation
Indices: 3359152--3359192 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3359142 TAAACAATAT
** *
3359152 AAAAGAAATAACCATAAGG
1 AAAAGAAATAAAAATAAAG
3359171 AAAAGAAATAAAAATAAAG
1 AAAAGAAATAAAAATAAAG
3359190 AAA
1 AAA
3359193 TAAACAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.73, C:0.05, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAGAAATAAAAATAAAG
Found at i:3359256 original size:31 final size:30
Alignment explanation
Indices: 3359221--3359297 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
3359211 TATGGTAAAT
3359221 AAATAAATAAATAAGAACAAGAAGAAAATAA
1 AAATAAATAAATAA-AACAAGAAGAAAATAA
* * *
3359252 AAATAAATAAATAAAATATGAAGCAAATAA
1 AAATAAATAAATAAAACAAGAAGAAAATAA
*
3359282 AAACAAATGAAATAAA
1 AAATAAAT-AAATAAA
3359298 GGCAAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 20 0.49
31 21 0.51
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.16
Consensus pattern (30 bp):
AAATAAATAAATAAAACAAGAAGAAAATAA
Found at i:3359527 original size:17 final size:20
Alignment explanation
Indices: 3359441--3359543 Score: 70
Period size: 20 Copynumber: 5.0 Consensus size: 20
3359431 AAACTCATGG
3359441 AAAAATAAAAAATAATATAT
1 AAAAATAAAAAATAATATAT
* * * *
3359461 ACACATAAATAA-AATATCT
1 AAAAATAAAAAATAATATAT
3359480 AAAAATATGACAAAAAATAATATAT
1 -AAAA-AT---AAAAAATAATATAT
3359505 AAAAATAAAAAA-AATA-A-
1 AAAAATAAAAAATAATATAT
* *
3359522 AAAAATAATAGATATATATAT
1 AAAAATAAAAAATA-ATATAT
3359543 A
1 A
3359544 TATCGTAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 19
0.68 0.11 0.21
Matches are distributed among these distances:
17 10 0.16
18 2 0.03
19 13 0.21
20 18 0.29
21 3 0.05
23 2 0.03
24 9 0.14
25 6 0.10
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAATAAAAAATAATATAT
Found at i:3361497 original size:124 final size:124
Alignment explanation
Indices: 3361342--3361902 Score: 897
Period size: 124 Copynumber: 4.5 Consensus size: 124
3361332 GTTGACAGAC
* * * * **
3361342 ACCCCTTCGCTATGAAGTTGAGCTTTGAATTGGATATCCTTCGTTGTGAAGTCAAAATCCAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
* * * * * * *
3361407 AGAGATGGATGTTGCTAGTGGGCACGATATCCTTCGTCATGAAGTTGAAATCGTGGATG
66 AAAGATGAATGTTGCTGGTGAGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATG
* *
3361466 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTGAAATCTAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
* * *
3361531 AAAGATGAATGTTGTTGGTGAGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATG
66 AAAGATGAATGTTGCTGGTGAGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATG
* *
3361590 GCCCCTTCGTTTTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
3361655 AAAGATGAATGTTGCTGGTGAGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATG
66 AAAGATGAATGTTGCTGGTGAGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATG
* *
3361714 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGAGAATTTGAAATCCAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
*
3361779 AAAGATGAATGTTGCTGGTGGGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATG
66 AAAGATGAATGTTGCTGGTGAGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATG
* *
3361838 GCCCCTTCGCTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
3361903 CGAGTAAATT
Statistics
Matches: 407, Mismatches: 30, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 407 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (124 bp):
ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
AAAGATGAATGTTGCTGGTGAGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATG
Found at i:3362231 original size:147 final size:147
Alignment explanation
Indices: 3361988--3362262 Score: 408
Period size: 147 Copynumber: 1.9 Consensus size: 147
3361978 TCTTTCACTG
* *
3361988 TGAAGTTGAGATTTGAATTGGATATCTTTCGTTTTGAAGTTGAAATCCAATCTTGTCTTCTTTTA
1 TGAAGTTGAGATTTGAATTGGATATCTTTCGTTGTGAAGTTGAAATCCAATCTTGTCTTCTTTCA
* * * *
3362053 AGTCCAATATCCTTCGTCGTGAAGTTAAAATTGACTCTGAATAAAACTGGAAAGTTATTTGTTGA
66 AGTCCAAGATCATTCGCCGTGAAGTTAAAATTGACTATGAATAAAACTGGAAAGTTATTTGTTGA
3362118 CAGACGCCCCTCCGCTA
131 CAGACGCCCCTCCGCTA
* * *
3362135 TGAAGTTGAGCTTTGAATTGGATATAC-TTCGTTGTGAAGTTGAAATCCAATCTTGTGTTGTTTC
1 TGAAGTTGAGATTTGAATTGGATAT-CTTTCGTTGTGAAGTTGAAATCCAATCTTGTCTTCTTTC
* * * * *
3362199 GAGTCCAAGATCATTTGCCGTGAAGTTGAAATTGACTATGGATGAAACTGGAAAGTTATTTGTT
65 AAGTCCAAGATCATTCGCCGTGAAGTTAAAATTGACTATGAATAAAACTGGAAAGTTATTTGTT
3362263 AAGTCCAATA
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
147 112 0.99
148 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (147 bp):
TGAAGTTGAGATTTGAATTGGATATCTTTCGTTGTGAAGTTGAAATCCAATCTTGTCTTCTTTCA
AGTCCAAGATCATTCGCCGTGAAGTTAAAATTGACTATGAATAAAACTGGAAAGTTATTTGTTGA
CAGACGCCCCTCCGCTA
Found at i:3362364 original size:64 final size:64
Alignment explanation
Indices: 3362218--3362365 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
3362208 ATCATTTGCC
* *
3362218 GTGAAGTTGAAATTGACTATGGATGAAACTGGAAAGTTATTTGTTAAGTCCAATATCCTTCTCT
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTAAGTCCAATATCCTTCTCT
* * *
3362282 GTGAAGTTGAAATTGACTCTGAATGAAACTGGAACGTTGTTTGTTGAGTCCAATATCCTTCAT-T
1 GTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTAAGTCCAATATCCTTC-TCT
3362346 GTGAAGTTGAAATTGACTCT
1 GTGAAGTTGAAATTGACTCT
3362366 AAAAGCTAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 77 0.99
65 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (64 bp):
GTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTTAAGTCCAATATCCTTCTCT
Found at i:3367344 original size:19 final size:19
Alignment explanation
Indices: 3367320--3367360 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3367310 TAAACAACAT
* *
3367320 AAAAGAAATAACAATAAGG
1 AAAAGAAATAAAAATAAAG
3367339 AAAAGAAATAAAAATAAAG
1 AAAAGAAATAAAAATAAAG
3367358 AAA
1 AAA
3367361 TAAACAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAGAAATAAAAATAAAG
Found at i:3367437 original size:26 final size:26
Alignment explanation
Indices: 3367385--3367452 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
3367375 AATAAATGGT
*
3367385 AAATAAATAAGAACAAGAAGAAAATAA
1 AAATAAATAA-AATAAGAAGAAAATAA
* *
3367412 AAATAAATAAAATATGAAGCAAATAA
1 AAATAAATAAAATAAGAAGAAAATAA
* *
3367438 AAACAAATGAAATAA
1 AAATAAATAAAATAA
3367453 AGGCAAAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 25 0.71
27 10 0.29
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (26 bp):
AAATAAATAAAATAAGAAGAAAATAA
Found at i:3367647 original size:26 final size:26
Alignment explanation
Indices: 3367616--3367677 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 26
3367606 ATATATACAC
* *
3367616 ATAAATAAAATATCTAAAAAT-AT-G
1 ATAAATAAAATATATAAAAATAATAA
3367640 ATAAA-AATAATATATAAAAATAATAA
1 ATAAATAA-AATATATAAAAATAATAA
3367666 ATAAATAAAATA
1 ATAAATAAAATA
3367678 ATAGATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 17 0.53
25 2 0.06
26 9 0.28
27 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (26 bp):
ATAAATAAAATATATAAAAATAATAA
Found at i:3367658 original size:13 final size:13
Alignment explanation
Indices: 3367634--3367670 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3367624 AATATCTAAA
3367634 AATATGATAAAAAT
1 AATAT-ATAAAAAT
3367648 AATATATAAAAAT
1 AATATATAAAAAT
*
3367661 AATAAATAAA
1 AATATATAAA
3367671 TAAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (13 bp):
AATATATAAAAAT
Found at i:3367664 original size:16 final size:17
Alignment explanation
Indices: 3367645--3367690 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
3367635 ATATGATAAA
3367645 AATAATATATA-AAAAT
1 AATAATATATATAAAAT
*
3367661 AATAA-ATAAATAAAAT
1 AATAATATATATAAAAT
3367677 AATAGATATATATA
1 AATA-ATATATATA
3367691 TATTGTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 4 0.16
16 14 0.56
17 1 0.04
18 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAATATATATAAAAT
Found at i:3369450 original size:17 final size:17
Alignment explanation
Indices: 3369423--3369456 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3369413 AAAATCGATC
3369423 GAAACAATAAGAACAAAA
1 GAAACAATAAGAA-AAAA
3369441 GAAA-AATAAGAAAAAA
1 GAAACAATAAGAAAAAA
3369457 TAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (17 bp):
GAAACAATAAGAAAAAA
Found at i:3370884 original size:160 final size:156
Alignment explanation
Indices: 3370317--3371011 Score: 805
Period size: 157 Copynumber: 4.4 Consensus size: 156
3370307 TCTGGTATAT
** ** *
3370317 GAGCATGTGGTTCATTTTTTGGTAAAAAC-CGACTTAAAAT-AAGGATGAATTGAAGAAATGAGG
1 GAGCATGTGGTTCA-AATTTGGTAAAAACAATACTTAAAATAAAGGATGAATTGAAGAAATAAGG
* * *
3370380 AAATTATGAAAAATTGAGGGACTAAATTGAAAAATAAAAAATTTTATCAAAAAGAGGAATTGAAA
65 AAATTATAAAAAATTGACGGACTAAATTGAAAAATAGAAAATTTTATCAAAAAGAGGAATTGAAA
* *
3370445 GTAAATATGTATTCTACGATGGTTCAA
130 GTACATATGTATTCTACGATGGTTTAA
* *
3370472 GAGCATGTGGTTCAAATTTGGTAAAAACAA-ACTTAAACTAAATGATGAATTGAAGAAATAAGGA
1 GAGCATGTGGTTCAAATTTGGTAAAAACAATACTTAAAATAAAGGATGAATTGAAGAAATAAGGA
* * * * *
3370536 AATTATAAAAAGTTGACGGACCAAATTGAAAAATATAAAACTATTTATCAAAAATAGAAATTGAA
66 AATTATAAAAAATTGACGGACTAAATTGAAAAATAGAAAA-T-TTTATCAAAAAGAGGAATTGAA
*
3370601 AGTACATATGTATTCTACAATGGTTTAA
129 AGTACATATGTATTCTACGATGGTTTAA
*
3370629 GAGCATGTGGTTCAAATTTGGTAAAAA-TATACTTAAAATAAAGGATGAATTGAAGAAATAAGGA
1 GAGCATGTGGTTCAAATTTGGTAAAAACAATACTTAAAATAAAGGATGAATTGAAGAAATAAGGA
** * * *
3370693 AATTATAAAATGTTAACGGACTAAATTGAAAAATAGAAAATTTGTCATCAAAAAGAGGAATTTAG
66 AATTATAAAAAATTGACGGACTAAATTGAAAAATAGAAAATTT-T-ATCAAAAAGAGGAATTGAA
* * *
3370758 AGTACCTATGTATTCTATGATGGTTTAG
129 AGTACATATGTATTCTACGATGGTTTAA
*
3370786 GAGCAT-TGGTTCAAATTTGTTAAAAAACAATAGGCTTAAAATAAAGGATGAATTGAAGAAATAA
1 GAGCATGTGGTTCAAATTTGGT-AAAAACAATA--CTTAAAATAAAGGATGAATTGAAGAAATAA
* * *
3370850 GGAAATTATAAAAAAATGA-GGAACTAAATTGAAAATTAGAAAATTTGTTATCAAAAAGATGAAT
63 GGAAATTATAAAAAATTGACGG-ACTAAATTGAAAAATAGAAAA-TT-TTATCAAAAAGAGGAAT
* * * * *
3370914 TGAAAGTAAATAT-TTTGTCTAAGATGG-GTAG
125 TGAAAGTACATATGTAT-TCTACGATGGTTTAA
* * * * * * * * * *
3370945 GAACTTTTGGTTCAAATTTTGTAAAAA-TAGAGTTAAAATAAATGATGAATTGAAGGAATAATGA
1 GAGCATGTGGTTCAAATTTGGTAAAAACAATACTTAAAATAAAGGATGAATTGAAGAAATAAGGA
3371009 AAT
66 AAT
3371012 CAGGGATTAA
Statistics
Matches: 468, Mismatches: 56, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
154 20 0.04
155 73 0.16
156 50 0.11
157 190 0.41
158 5 0.01
159 16 0.03
160 110 0.24
161 3 0.01
162 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (156 bp):
GAGCATGTGGTTCAAATTTGGTAAAAACAATACTTAAAATAAAGGATGAATTGAAGAAATAAGGA
AATTATAAAAAATTGACGGACTAAATTGAAAAATAGAAAATTTTATCAAAAAGAGGAATTGAAAG
TACATATGTATTCTACGATGGTTTAA
Found at i:3378948 original size:23 final size:23
Alignment explanation
Indices: 3378922--3379023 Score: 154
Period size: 23 Copynumber: 4.4 Consensus size: 23
3378912 GGTTCTACGC
3378922 GGTCCTTCAGGACATTTCTATGT
1 GGTCCTTCAGGACATTTCTATGT
3378945 GGTCCTTCAGGACATTTCTATGT
1 GGTCCTTCAGGACATTTCTATGT
*
3378968 GGTCCTTCGGGACATTTCTATGT
1 GGTCCTTCAGGACATTTCTATGT
*
3378991 GGTCCTTC-GAGACATTTGTATGT
1 GGTCCTTCAG-GACATTTCTATGT
3379014 GG-CACTTCAG
1 GGTC-CTTCAG
3379024 TGCATATTCT
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
22 2 0.03
23 71 0.96
24 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (23 bp):
GGTCCTTCAGGACATTTCTATGT
Found at i:3384180 original size:20 final size:20
Alignment explanation
Indices: 3384151--3384211 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
3384141 CTCATATCGT
*
3384151 TGCACCGGAAGAGATAGAAG
1 TGCACTGGAAGAGATAGAAG
3384171 TGCACTGGAAGAGATAGAAG
1 TGCACTGGAAGAGATAGAAG
3384191 TGCACCT-GAAGAGATAGAAG
1 TGCA-CTGGAAGAGATAGAAG
3384211 T
1 T
3384212 TTAACCTGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 37 0.95
21 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.33, T:0.15
Consensus pattern (20 bp):
TGCACTGGAAGAGATAGAAG
Found at i:3395131 original size:19 final size:20
Alignment explanation
Indices: 3395088--3395131 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3395078 AATAAAGTCC
* * *
3395088 TATTGAATTTTAAAATTTTA
1 TATTCAATTTCAAAATTTGA
3395108 TATTCAATTTCAAAA-TTGA
1 TATTCAATTTCAAAATTTGA
3395127 TATTC
1 TATTC
3395132 GAGTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (20 bp):
TATTCAATTTCAAAATTTGA
Found at i:3396937 original size:23 final size:22
Alignment explanation
Indices: 3396911--3396954 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3396901 AACGATTTAG
3396911 AGCTCTCAAAAATAAAATTTGAA
1 AGCTCTCAAAAA-AAAATTTGAA
* *
3396934 AGCTTTGAAAAAAAAATTTGA
1 AGCTCTCAAAAAAAAATTTGA
3396955 TTTGAAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (22 bp):
AGCTCTCAAAAAAAAATTTGAA
Found at i:3404467 original size:26 final size:27
Alignment explanation
Indices: 3404413--3404467 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3404403 CCTTGCTATG
*
3404413 TATCGATACACTATGAATGTGTATCGA
1 TATCGATACACTATGAATGTGTACCGA
*
3404440 TATCGATACACTCA-GGA-GTGTACCGA
1 TATCGATACACT-ATGAATGTGTACCGA
3404466 TA
1 TA
3404468 CACTCGTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
27 14 0.56
28 1 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (27 bp):
TATCGATACACTATGAATGTGTACCGA
Found at i:3406348 original size:10 final size:10
Alignment explanation
Indices: 3406333--3406366 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
3406323 TGTTAAAACA
3406333 TTTTGGATGT
1 TTTTGGATGT
3406343 TTTTGGAATTGT
1 TTTTGG-A-TGT
3406355 TTTTGGATGT
1 TTTTGGATGT
3406365 TT
1 TT
3406367 CAATATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 11 0.50
11 2 0.09
12 9 0.41
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.62
Consensus pattern (10 bp):
TTTTGGATGT
Found at i:3407921 original size:24 final size:24
Alignment explanation
Indices: 3407889--3407934 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3407879 GCATGATATG
3407889 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
*
3407913 GTACATAGATGTTTTTTACATC
1 GTACATAGATGTTTTATACATC
3407935 ATCTGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:3409155 original size:13 final size:14
Alignment explanation
Indices: 3409125--3409160 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3409115 GGAGTAAACA
3409125 ATTTTCAAA-ATTG
1 ATTTTCAAAGATTG
3409138 A-TTTCAAAGA-TG
1 ATTTTCAAAGATTG
3409150 ATTTTCAAAGA
1 ATTTTCAAAGA
3409161 AAATATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (14 bp):
ATTTTCAAAGATTG
Found at i:3409669 original size:21 final size:21
Alignment explanation
Indices: 3409643--3409682 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3409633 ATTTTACACT
3409643 GAGTGTACCGATACACCTAGA
1 GAGTGTACCGATACACCTAGA
*
3409664 GAGTGTACCGATAGACCTA
1 GAGTGTACCGATACACCTA
3409683 TGCTCCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (21 bp):
GAGTGTACCGATACACCTAGA
Found at i:3414367 original size:22 final size:23
Alignment explanation
Indices: 3414341--3414384 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3414331 CGGTAAGGGG
*
3414341 TATCGGTACCATAG-AAGGGTAA
1 TATCGATACCATAGTAAGGGTAA
*
3414363 TATCGATACTATAGTAAGGGTA
1 TATCGATACCATAGTAAGGGTA
3414385 TCGATACCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (23 bp):
TATCGATACCATAGTAAGGGTAA
Found at i:3414481 original size:95 final size:95
Alignment explanation
Indices: 3414287--3414486 Score: 235
Period size: 95 Copynumber: 2.1 Consensus size: 95
3414277 ATGATAAGGG
* * *
3414287 GTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCGATATCGGTAAGGGGTATCGGTACCA
1 GTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCGATACCCGTAAGGGGTATCGGTACCA
* * *
3414352 TAGAAGGGTAATATCGATACTATAGTAAGG
66 TAGAAGAGTAATATCGATACTAGAGTAAGA
* * *
3414382 GTATCGATACCAGGAAACATCGAACCTATTTTTGGTATCGATACCCG-AAGGGGGTATTGGTACC
1 GTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCGATACCCGTAA-GGGGTATCGGTACC
* * * *
3414446 ATAGTATAG-AAGTATCGGTACTAGGGT-AGTA
65 ATAGAAGAGTAA-TATCGATACTAGAGTAAG-A
3414477 GTATCGATAC
1 GTATCGATAC
3414487 TATGGAGCCA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
94 6 0.07
95 83 0.93
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (95 bp):
GTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCGATACCCGTAAGGGGTATCGGTACCA
TAGAAGAGTAATATCGATACTAGAGTAAGA
Found at i:3415159 original size:54 final size:54
Alignment explanation
Indices: 3414809--3415134 Score: 510
Period size: 54 Copynumber: 6.1 Consensus size: 54
3414799 ACCAAATCGA
* * *
3414809 CACTAAGTGTGCATTTCACGGAGTTCATCCTATGTGGATGAATAAACGTTTCGG
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* *
3414863 CACTAAGTGTACATTTCAC-GAATTCATCCTATGTGGATGAATAACTGTTTCGG
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* *
3414916 CACTAAGTGTGCATTTCACGGAATTCATACTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* * *
3414970 CACTAAGTGTGCATTTCACAGAATTCATCCTATATGGATGAATAATCGTTTCGA
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
*
3415024 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATAAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
** * *
3415078 CACTAAGTGTGCATTTCATGGAATTCATCCTGTGTGGATGAATAATCGTTTCGG
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
3415132 CAC
1 CAC
3415135 CATGACTGCA
Statistics
Matches: 250, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
53 49 0.20
54 201 0.80
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGG
Found at i:3424118 original size:22 final size:23
Alignment explanation
Indices: 3424087--3424130 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
3424077 ACCTTGGCTC
3424087 AGAGAGAAAAAAAACTAAGTTAA
1 AGAGAGAAAAAAAACTAAGTTAA
3424110 AGAGA-AAAAAAAACTAAGTTA
1 AGAGAGAAAAAAAACTAAGTTA
3424131 TTCTACTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.14
Consensus pattern (23 bp):
AGAGAGAAAAAAAACTAAGTTAA
Found at i:3434566 original size:23 final size:23
Alignment explanation
Indices: 3434538--3434656 Score: 79
Period size: 23 Copynumber: 5.0 Consensus size: 23
3434528 ACAATCTGTC
3434538 CATCACCATTATCA-CACCTATAT
1 CATCACCATTATCATCACC-ATAT
3434561 CATCACCA-TAGTCCATCACCATTAT
1 CATCACCATTA-T-CATCACCA-TAT
*
3434586 CAT-GCC-TATATCATCACCATAGT
1 CATCACCAT-TATCATCACCATA-T
*
3434609 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
3434633 CAACACCA-TATTCTATCACCATAT
1 CATCACCATTA-TC-ATCACCATAT
3434657 AACGCCTATA
Statistics
Matches: 77, Mismatches: 5, Indels: 27
0.71 0.05 0.25
Matches are distributed among these distances:
22 6 0.08
23 27 0.35
24 18 0.23
25 25 0.32
26 1 0.01
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:3434579 original size:13 final size:11
Alignment explanation
Indices: 3434538--3434656 Score: 82
Period size: 11 Copynumber: 10.0 Consensus size: 11
3434528 ACAATCTGTC
3434538 CATCACCATTAT
1 CATCACCA-TAT
3434550 CA-CACCTATAT
1 CATCACC-ATAT
3434561 CATCACCATAGT
1 CATCACCATA-T
3434573 CCATCACCATTAT
1 -CATCACCA-TAT
*
3434586 CATGC-CTATAT
1 CAT-CACCATAT
3434597 CATCACCATAGT
1 CATCACCATA-T
3434609 CCATCACCATTAT
1 -CATCACCA-TAT
*
3434622 CA-CGCCTATAT
1 CATCACC-ATAT
*
3434633 CAACACCATATT
1 CATCACCATA-T
3434645 CTATCACCATAT
1 C-ATCACCATAT
3434657 AACGCCTATA
Statistics
Matches: 88, Mismatches: 5, Indels: 28
0.73 0.04 0.23
Matches are distributed among these distances:
10 1 0.01
11 33 0.38
12 23 0.26
13 27 0.31
14 4 0.05
ACGTcount: A:0.33, C:0.34, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:3434582 original size:36 final size:36
Alignment explanation
Indices: 3434535--3434675 Score: 212
Period size: 36 Copynumber: 3.9 Consensus size: 36
3434525 GATACAATCT
*
3434535 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
3434571 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
3434607 GTCCATCACCATTATCACGCCTATATCAACACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
3434643 TTCTATCACCA-TATAACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
3434676 ACTTATAAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 19 0.20
36 77 0.80
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:3440310 original size:23 final size:23
Alignment explanation
Indices: 3440282--3440400 Score: 70
Period size: 23 Copynumber: 5.0 Consensus size: 23
3440272 ACAATCTGTC
*
3440282 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCACC-ATAT
3440305 CATCACCA-TAGTCCATCACCAT-T
1 CATCACCATTA-T-CATCACCATAT
*
3440328 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCACCATA-T
*
3440353 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCACC-ATAT
*
3440377 CAACACCA-TATTCTATCACCATAT
1 CATCACCATTA-TC-ATCACCATAT
3440401 AACGCCTATA
Statistics
Matches: 76, Mismatches: 6, Indels: 27
0.70 0.06 0.25
Matches are distributed among these distances:
22 9 0.12
23 29 0.38
24 14 0.18
25 17 0.22
26 2 0.03
27 5 0.07
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCACCATAT
Found at i:3440323 original size:13 final size:11
Alignment explanation
Indices: 3440282--3440400 Score: 73
Period size: 11 Copynumber: 10.0 Consensus size: 11
3440272 ACAATCTGTC
3440282 CATCACCATTAT
1 CATCACCA-TAT
*
3440294 CA-CGCCTATAT
1 CATCACC-ATAT
3440305 CATCACCATAGT
1 CATCACCATA-T
3440317 CCATCACCATTAT
1 -CATCACCA-TAT
*
3440330 CA-CGCCTATAT
1 CATCACC-ATAT
3440341 CATCACCATAGT
1 CATCACCATA-T
3440353 CCATCACCATTAT
1 -CATCACCA-TAT
*
3440366 CA-CGCCTATAT
1 CATCACC-ATAT
*
3440377 CAACACCATATT
1 CATCACCATA-T
3440389 CTATCACCATAT
1 C-ATCACCATAT
3440401 AACGCCTATA
Statistics
Matches: 86, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
11 33 0.38
12 23 0.27
13 26 0.30
14 4 0.05
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:3440326 original size:36 final size:36
Alignment explanation
Indices: 3440279--3440419 Score: 230
Period size: 36 Copynumber: 3.9 Consensus size: 36
3440269 GATACAATCT
3440279 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
3440315 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
3440351 GTCCATCACCATTATCACGCCTATATCAACACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
3440387 TTCTATCACCA-TATAACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
3440420 ACTTATAAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.19
36 80 0.81
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Done.