Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 30
Found at i:3631938 original size:29 final size:29
Alignment explanation
Indices: 3631906--3631991 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
3631896 TGAGATCTCC
3631906 TGTGTTATGAATTAATTATTAAAATGTCA
1 TGTGTTATGAATTAATTATTAAAATGTCA
** * *
3631935 TGTGTTCGGAATTAAATATTGAAATGTCCA
1 TGTGTTATGAATTAATTATTAAAATGT-CA
*
3631965 -GTGTTAT-ATATTTATTATTAAAATGTC
1 TGTGTTATGA-ATTAATTATTAAAATGTC
3631992 CAATGCTAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.04
29 42 0.91
30 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (29 bp):
TGTGTTATGAATTAATTATTAAAATGTCA
Found at i:3631992 original size:29 final size:29
Alignment explanation
Indices: 3631915--3632020 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 29
3631905 CTGTGTTATG
* * * *
3631915 AATTAATTATTAAAATGT-CATGTGTTCGG
1 AATTAATTATTAAAATGTCCA-ATGCTAGA
* * * * *
3631944 AATTAAATATTGAAATGTCCAGTGTTATA
1 AATTAATTATTAAAATGTCCAATGCTAGA
* *
3631973 TATTTATTATTAAAATGTCCAATGCTAGA
1 AATTAATTATTAAAATGTCCAATGCTAGA
*
3632002 AATTAATTATTCAAATGTC
1 AATTAATTATTAAAATGTC
3632021 TACGGATTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 59 0.97
30 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (29 bp):
AATTAATTATTAAAATGTCCAATGCTAGA
Found at i:3635965 original size:27 final size:27
Alignment explanation
Indices: 3635919--3636026 Score: 130
Period size: 28 Copynumber: 4.0 Consensus size: 27
3635909 TTTACACTAC
3635919 CTGTTTCGAAATTAATTTTTAAAATTT
1 CTGTTTCGAAATTAATTTTTAAAATTT
*
3635946 CATGTTTCGAAATTAATTTTTAAATTTT
1 C-TGTTTCGAAATTAATTTTTAAAATTT
* * *
3635974 CTGTTTC-AGAATTAACTATTAACATTTT
1 CTGTTTCGA-AATTAATTTTTAA-AATTT
*
3636002 CTGTTTCGGAATTAA-TTTTAAAATT
1 CTGTTTCGAAATTAATTTTTAAAATT
3636027 CATGATTCAG
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.06
27 23 0.32
28 44 0.62
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.50
Consensus pattern (27 bp):
CTGTTTCGAAATTAATTTTTAAAATTT
Found at i:3640003 original size:3 final size:3
Alignment explanation
Indices: 3639995--3640020 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3639985 TGTGTCTTTT
3639995 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3640021 TCTCTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3642716 original size:16 final size:17
Alignment explanation
Indices: 3642683--3642716 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3642673 CCTTCAATTT
*
3642683 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
3642700 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
3642716 T
1 T
3642717 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:3643798 original size:35 final size:35
Alignment explanation
Indices: 3643748--3643861 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 35
3643738 ATTCGAAACC
*
3643748 TTAAATTGAAGTATTTTAGAATTTGGGGTTTAAAA
1 TTAAATTGAATTATTTTAGAATTTGGGGTTTAAAA
* *
3643783 TTTAATTGAATTATTTT-GAAATTTAGGGTTTAAAA
1 TTAAATTGAATTATTTTAG-AATTTGGGGTTTAAAA
** * * *
3643818 TTAAATTGAATTGCTTTAAAAATTGGGGTTTAGAA
1 TTAAATTGAATTATTTTAGAATTTGGGGTTTAAAA
*
3643853 TGAAATTGA
1 TTAAATTGA
3643862 GGACTGTTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 1 0.02
35 65 0.98
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (35 bp):
TTAAATTGAATTATTTTAGAATTTGGGGTTTAAAA
Found at i:3647124 original size:16 final size:16
Alignment explanation
Indices: 3647103--3647135 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3647093 TAATAAATAA
3647103 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3647119 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
3647135 A
1 A
3647136 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:3647241 original size:20 final size:20
Alignment explanation
Indices: 3647212--3647251 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3647202 ATTTAAATGA
*
3647212 TAAACAAACATAAACGAACG
1 TAAACAAACACAAACGAACG
*
3647232 TAAACGAACACAAACGAACG
1 TAAACAAACACAAACGAACG
3647252 AACATAAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (20 bp):
TAAACAAACACAAACGAACG
Found at i:3647241 original size:24 final size:23
Alignment explanation
Indices: 3647214--3647273 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
3647204 TTAAATGATA
* *
3647214 AACAAACATAAACGAACGTAAACG
1 AACAAA-ACAAACGAACATAAACG
*
3647238 AACACAAACGAACGAACATAAACG
1 AACA-AAACAAACGAACATAAACG
*
3647262 AACAATACAAAC
1 AACAAAACAAAC
3647274 ACAAAAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 6 0.20
24 22 0.73
25 2 0.07
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (23 bp):
AACAAAACAAACGAACATAAACG
Found at i:3647253 original size:14 final size:14
Alignment explanation
Indices: 3647234--3647273 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3647224 AACGAACGTA
3647234 AACGAACACAAACG
1 AACGAACACAAACG
*
3647248 AACGAACATAAACG
1 AACGAACACAAACG
*
3647262 AAC-AATACAAAC
1 AACGAACACAAAC
3647274 ACAAAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.60, C:0.25, G:0.10, T:0.05
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:3647265 original size:10 final size:10
Alignment explanation
Indices: 3647211--3647250 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
3647201 CATTTAAATG
*
3647211 ATAAACAAAC
1 ATAAACGAAC
3647221 ATAAACGAAC
1 ATAAACGAAC
*
3647231 GTAAACGAAC
1 ATAAACGAAC
*
3647241 ACAAACGAAC
1 ATAAACGAAC
3647251 GAACATAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3647558 original size:14 final size:14
Alignment explanation
Indices: 3647539--3647566 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3647529 GAACATAAAT
3647539 GAACATAAATGAAC
1 GAACATAAATGAAC
3647553 GAACATAAATGAAC
1 GAACATAAATGAAC
3647567 ATGTAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:3649247 original size:2 final size:2
Alignment explanation
Indices: 3649236--3649269 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3649226 TACGTAACCT
3649236 TA TA -A TA TA TA TA -A 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
3649270 AGTACCACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3649320 original size:12 final size:12
Alignment explanation
Indices: 3649303--3649327 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3649293 AAAGTAACTC
3649303 ATAATAAAATAA
1 ATAATAAAATAA
3649315 ATAATAAAATAA
1 ATAATAAAATAA
3649327 A
1 A
3649328 ATCGAAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAATAAAATAA
Found at i:3650904 original size:180 final size:182
Alignment explanation
Indices: 3650602--3650970 Score: 697
Period size: 180 Copynumber: 2.0 Consensus size: 182
3650592 AAAAAAGATA
3650602 TCAAAATTGCTCCAATCGTTTATTTGAAGCCTCCAGAGAATGAACCACTTTGTCATCGTTGGCTT
1 TCAAAATTGCTCCAATCGTTTATTTGAAGCCTCCAGAGAATGAACCACTTTGTCATCGTTGGCTT
3650667 CAAAATTTCTCAGGAATCAAGTCATACCAACCCTTCCCCATTTGTAAAAGCCTGAACTTGTAAGG
66 CAAAATTTCTCAGGAATCAAGTCATACCAACCCTTCCCCATTTGTAAAAGCCTGAACTTGTAAGG
3650732 ATTATCAAACTTAACCCA-TTCTCATGTTCCAACACAAATGAACGAGT-CCT
131 ATTATCAAACTTAACCCACTTCTCATGTTCCAACACAAATGAACGAGTCCCT
3650782 TCAAAATTGCTCCAATCGTTTATTTGAAGCCTCCAGAGAATGAACCACTTTGTCATCGTTGGCTT
1 TCAAAATTGCTCCAATCGTTTATTTGAAGCCTCCAGAGAATGAACCACTTTGTCATCGTTGGCTT
3650847 CAAAATTTCTCAGGAATCAAGTCATACCAACCCTTCCCCATTTGTAAAAGCCTGAACTTGTAAGG
66 CAAAATTTCTCAGGAATCAAGTCATACCAACCCTTCCCCATTTGTAAAAGCCTGAACTTGTAAGG
3650912 ATTATCAAACTTAACCCATTCCTTCTCATGTTCCAACACAAATGAACGAGTCCCT
131 ATTATCAAACTTAACCCA---CTTCTCATGTTCCAACACAAATGAACGAGTCCCT
3650967 TCAA
1 TCAA
3650971 GATTTTTCCG
Statistics
Matches: 184, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
180 148 0.80
184 29 0.16
185 7 0.04
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (182 bp):
TCAAAATTGCTCCAATCGTTTATTTGAAGCCTCCAGAGAATGAACCACTTTGTCATCGTTGGCTT
CAAAATTTCTCAGGAATCAAGTCATACCAACCCTTCCCCATTTGTAAAAGCCTGAACTTGTAAGG
ATTATCAAACTTAACCCACTTCTCATGTTCCAACACAAATGAACGAGTCCCT
Found at i:3655359 original size:81 final size:81
Alignment explanation
Indices: 3655256--3655450 Score: 245
Period size: 81 Copynumber: 2.4 Consensus size: 81
3655246 GGGAAATCCA
* * *
3655256 CTCCACTATTCTTTCAGGGGAGATCAA-TCTTGA-TATGTTCCAT-TTTTTC-GAGTAGTCAAAT
1 CTCCACTCTTCTTTCA-AGGAGAT-AAGACTTGACT-TGTTCC-TCTTTTTCAG-GTAGTCAAAT
*
3655317 CAATTTTGGAAGACGGGTCTG
61 CAATTTTGGAAGACAGGTCTG
* *
3655338 CTCCACTCTTCTTTCAAGGAGATAAGACTTGACTTGTTTCTCTTTTTCAGGTATTCAAATCAATT
1 CTCCACTCTTCTTTCAAGGAGATAAGACTTGACTTGTTCCTCTTTTTCAGGTAGTCAAATCAATT
3655403 TTGGAAGACAGGTCTG
66 TTGGAAGACAGGTCTG
* *
3655419 TTCCACTCTTCTTTCACGGAGATAAGACTTGA
1 CTCCACTCTTCTTTCAAGGAGATAAGACTTGA
3655451 GAAGTCTTTG
Statistics
Matches: 101, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
80 3 0.03
81 81 0.80
82 17 0.17
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (81 bp):
CTCCACTCTTCTTTCAAGGAGATAAGACTTGACTTGTTCCTCTTTTTCAGGTAGTCAAATCAATT
TTGGAAGACAGGTCTG
Found at i:3655679 original size:89 final size:89
Alignment explanation
Indices: 3655468--3655831 Score: 423
Period size: 89 Copynumber: 4.1 Consensus size: 89
3655458 TTGGAAAACG
* * * *
3655468 AAATCTGAAATAAGAAGAATTTGCTCCACCACTTTTTCGGGGAGATCAGACTCAAGATTGATTTG
1 AAATCTGAAATAAGAAGAATCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTG
*
3655533 CTTCGCTA--C--TCGGGAAGACT
66 CTTCGCTACTCTTTCGGGAAGACA
* * * * *
3655553 GAATCTGAAATAAGAAGAAACTGCTCCACTACTCTTTCGGGGGGATTATACTCGAGATTGATTTG
1 AAATCTGAAATAAGAAGAATCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTG
3655618 CTTCGCTACTCTTTCCGGG-AGACA
66 CTTCGCTACTCTTT-CGGGAAGACA
* ** * *
3655642 AAATATGAAATAAGAAGAATCTGCTCCTTTACTCTTTCGGGGATATAAGACTCGAGATTGATTTG
1 AAATCTGAAATAAGAAGAATCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTG
* * *
3655707 CTTCTCTACTATTTCGGGAAGACC
66 CTTCGCTACTCTTTCGGGAAGACA
* * * * * *
3655731 AAATCTGAAGTAAGTAGAATCTACTCCTCTACTCTTCCGGGGAGATCAGACTTGAGATTGATTTG
1 AAATCTGAAATAAGAAGAATCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTG
* ** *
3655796 CTTCACTACTCTTTCAAGAAGACC
66 CTTCGCTACTCTTTCGGGAAGACA
*
3655820 AAATCTAAAATA
1 AAATCTGAAATA
3655832 TTGACTTCTC
Statistics
Matches: 236, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
85 64 0.27
87 1 0.00
88 4 0.02
89 163 0.69
90 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (89 bp):
AAATCTGAAATAAGAAGAATCTGCTCCACTACTCTTTCGGGGAGATCAGACTCGAGATTGATTTG
CTTCGCTACTCTTTCGGGAAGACA
Found at i:3655943 original size:99 final size:100
Alignment explanation
Indices: 3655832--3656022 Score: 271
Period size: 99 Copynumber: 1.9 Consensus size: 100
3655822 ATCTAAAATA
* * * *
3655832 TTGACTTCTCTTCACAAGGAAGTCAATGATTGACTCTGTTGGGGAA-TCAGGGATAACAAATA-T
1 TTGACTTCTCTTCACAAGAAAGTCAAGGATTGACTCTGCT-GGGAAGTCAGGAATAACAAA-AGT
*
3655895 TTACTT-TCTTCACGAGAAAGTCAAGAATAACAAAGG
64 TGACTTCTCTTCACGAGAAAGTCAAGAATAACAAAGG
*
3655931 TTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTGCTGGGAAGTCAGGAATAACAAAAGTTG
1 TTGACTTCTCTTCACAAGAAAGTCAAGGATTGACTCTGCTGGGAAGTCAGGAATAACAAAAGTTG
* *
3655996 ACTTCTCTTCATGAGGAAGTCAAGAAT
66 ACTTCTCTTCACGAGAAAGTCAAGAAT
3656023 TGACTCTGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
98 6 0.07
99 55 0.68
100 20 0.25
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (100 bp):
TTGACTTCTCTTCACAAGAAAGTCAAGGATTGACTCTGCTGGGAAGTCAGGAATAACAAAAGTTG
ACTTCTCTTCACGAGAAAGTCAAGAATAACAAAGG
Found at i:3656016 original size:62 final size:62
Alignment explanation
Indices: 3655912--3656080 Score: 250
Period size: 62 Copynumber: 2.7 Consensus size: 62
3655902 CTTCACGAGA
* * * *
3655912 AAGTCAAGAATAACAAAGGTTGACTTCTCTTCACGAGAAAGTCAAGGATTGACTCTGCTGGG
1 AAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGAATTGACTCTGCTGGG
* *
3655974 AAGTCAGGAATAACAAAAGTTGACTTCTCTTCATGAGGAAGTCAAGAATTGACTCTGTTGGG
1 AAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGAATTGACTCTGCTGGG
* *
3656036 GAGTCAGGAATAAC-AAAGATTGACTTCTCTTCACAAGGAAGTCAA
1 AAGTCAGGAATAACAAAAG-TTGACTTCTCTTCACGAGGAAGTCAA
3656081 AAATAATAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
61 4 0.04
62 93 0.96
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (62 bp):
AAGTCAGGAATAACAAAAGTTGACTTCTCTTCACGAGGAAGTCAAGAATTGACTCTGCTGGG
Found at i:3656661 original size:42 final size:42
Alignment explanation
Indices: 3656597--3656693 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
3656587 AGGTCTTATA
* * * * *
3656597 AATGGCCCGAATGACTT-ATCATCTTGCTTGAAAGACTGA-T
1 AATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTGACT
* *
3656637 AGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACT
1 A-ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTGACT
3656680 AATGACCCGAAGGA
1 AATGACCCGAAGGA
3656694 CTTACTAAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
40 1 0.02
41 12 0.26
42 31 0.67
43 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (42 bp):
AATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTGACT
Found at i:3656714 original size:258 final size:258
Alignment explanation
Indices: 3656151--3657568 Score: 2036
Period size: 258 Copynumber: 5.5 Consensus size: 258
3656141 AATTTTCCTT
* * * * * *
3656151 GAAAGACTTATTGATGACCCAAAAGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAGACTC
1 GAAAGACTTACTGATGACCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACTT
* **
3656216 TGGTAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTAAA
66 TGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTAAA
* * * * *
3656281 AATCGCTTTCTCATTTTTTTGAAAATCATGTGAAAACATCTTGCCCTAAGGTCTTATAGAAGGCC
131 AATCACTTTCTCA-TTTTTCGAAAATCACGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCC
* * * * *
3656346 CGAATGACTTATCATCTTGCTCGAAAGACTGACAGATAACCCGAAGGATTTAATAATCATGGTC
195 CGAATGACTTATCATCTTGCTTGAAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTC
* * * * * *
3656410 GAAAGACTTACTGATGGCCCGAATGTCTTACTAATTTTGGAAATAGTTTAATGGGTAAGAAACTT
1 GAAAGACTTACTGATGACCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACTT
*
3656475 TGAAAAT-AGCTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTAA
66 TGGAAATCA-CTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTAA
* * * *
3656539 AAATCACTTTCTCATTTTTCGAAAACCATGTGAAAACATCTTACCCGAAGGTCTTATAAATGGCC
130 AAATCACTTTCTCATTTTTCGAAAATCACGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCC
*
3656604 CGAATGACTTATCATCTTGCTTGAAAGACTGATAGATGACCTGAAGGATTTAATCATCATGCTC
195 CGAATGACTTATCATCTTGCTTGAAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTC
* * * *
3656668 GAAAGACTTACTAATGACCCGAAGGACTTACTAAGTTTGAAAATAGTTTACTAGGTAAGAAACTT
1 GAAAGACTTACTGATGACCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACTT
* * * *
3656733 TGGTAATCATTTTCTTACTTGTCAAAAAATTCATTTTCTAAAAACATTAAATGAGAAACTTTAAA
66 TGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTAAA
* * *
3656798 AATTACTTTCTCATTTTTCAAAAATCACGTGAAAACATCTTGCCCAAAGGTCTTATAGATGGCCC
131 AATCACTTTCTCATTTTTCGAAAATCACGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCCC
* * *
3656863 GAATGACTTATCATCTTTCTTGAAAGACTTACAAATGACCCT-AAGGATTTAATCATCATGCTC
196 GAATGACTTATCATCTTGCTTGAAAGACTGACAGATGA-CCTGAAGGATTTAATCATCATGCTC
* * * *
3656926 GAAAGACTTACTGATAACTCGAAGGACTTACAAATTTTGGAAATAGTTTTCTAGGTAAGAAAATT
1 GAAAGACTTACTGATGACCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACTT
*
3656991 TGGAAATCACTTTCTTACTTTTCAAAACTTTCATTTTCTAAAAACATTAAATGAGAAACTTTAAA
66 TGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTAAA
* * * *
3657056 AACCGCTTTCTCATTTTTCGAAAATCACGTGAAAGCATCTTGCCTGAAGGTCTTATAGATGGCCC
131 AATCACTTTCTCATTTTTCGAAAATCACGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCCC
* * *
3657121 GAAGGACTTATCATCTTGCTCGAAAGAGTGACAGATGA-CTCGAAGGATTTAATCATCATGCTC
196 GAATGACTTATCATCTTGCTTGAAAGACTGACAGATGACCT-GAAGGATTTAATCATCATGCTC
*
3657184 GAAAGACTTACTGATCG-CTCGAAGGACTTACAAATATTT-GAAATAGTTTACTAGGTAAGAAAC
1 GAAAGACTTACTGAT-GACCCGAAGGACTTACAAAT-TTTGGAAATAGTTTACTAGGTAAGAAAC
* * * * *
3657247 TTTGGTAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAATATTAAATGATAAACCTTA
64 TTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTA
* *
3657312 AAAATTACTTTCTCATTTTTCAAAAATCACGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGC
129 AAAATCACTTTCTCATTTTTCGAAAATCACGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGC
* * * * * *
3657377 CCAAAGGACTTATCATCTTGCTTGAAAGACTGACAGATAACCCGAAAGATTTAATCATCATGCTT
194 CCGAATGACTTATCATCTTGCTTGAAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTC
* * * *
3657442 GAAAGACTTACTAATGGCCTGAAGAACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACTT
1 GAAAGACTTACTGATGACCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACTT
* * * *
3657507 TGGAAATCACTTTCTTACTTTTAAAAAATTTCATTTTCTATAAAGATTAAATAAGAAACTTT
66 TGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTT
3657569 GGTTATTGCT
Statistics
Matches: 1037, Mismatches: 112, Indels: 21
0.89 0.10 0.02
Matches are distributed among these distances:
256 2 0.00
257 4 0.00
258 897 0.86
259 134 0.13
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (258 bp):
GAAAGACTTACTGATGACCCGAAGGACTTACAAATTTTGGAAATAGTTTACTAGGTAAGAAACTT
TGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAACTTTAAA
AATCACTTTCTCATTTTTCGAAAATCACGTGAAAACATCTTGCCCGAAGGTCTTATAGATGGCCC
GAATGACTTATCATCTTGCTTGAAAGACTGACAGATGACCTGAAGGATTTAATCATCATGCTC
Found at i:3657205 original size:42 final size:41
Alignment explanation
Indices: 3657120--3657213 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
3657110 ATAGATGGCC
* *
3657120 CGAAGGACTTATCATCTTGCTCGAAAGAGTGACAGATGACT
1 CGAAGGACTTATCATCATGCTCGAAAGACTGACAGATGACT
* * *
3657161 CGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATCG-CT
1 CGAAGGACTT-ATCATCATGCTCGAAAGACTGACAGAT-GACT
3657203 CGAAGGACTTA
1 CGAAGGACTTA
3657214 CAAATATTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 10 0.22
42 34 0.76
43 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (41 bp):
CGAAGGACTTATCATCATGCTCGAAAGACTGACAGATGACT
Found at i:3660473 original size:99 final size:99
Alignment explanation
Indices: 3660302--3660500 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
3660292 ACTTAATCGG
3660302 ATGTTACACATCGTTTTTTGACCACTCAAGTTCGTCATCCACTGTTCCAATAATCATTTTGTCAA
1 ATGTTACACATCGTTTTTTGACCACTCAAGTTCGTCATCCACTGTTCCAATAATCATTTTGTCAA
3660367 TGTCCCATTTTCAATAAGAATCTCTATTTTCTTT
66 TGTCCCATTTTCAATAAGAATCTCTATTTTCTTT
3660401 ATGTTACACATCGTTTTTTGACCACTCAAGTTCGTCATCCACTGTTCCAATAATCATTTTGTCAA
1 ATGTTACACATCGTTTTTTGACCACTCAAGTTCGTCATCCACTGTTCCAATAATCATTTTGTCAA
3660466 TGTCCCATTTTCAATAAGAATCTCTATTTTCTTT
66 TGTCCCATTTTCAATAAGAATCTCTATTTTCTTT
3660500 A
1 A
3660501 ACAGTGGCCT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (99 bp):
ATGTTACACATCGTTTTTTGACCACTCAAGTTCGTCATCCACTGTTCCAATAATCATTTTGTCAA
TGTCCCATTTTCAATAAGAATCTCTATTTTCTTT
Found at i:3664550 original size:17 final size:16
Alignment explanation
Indices: 3664509--3664550 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
3664499 AAATATCTTT
3664509 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
3664525 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
3664542 TAAAA-AATT
1 TAAAATAATT
3664551 GATATGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:3664858 original size:7 final size:7
Alignment explanation
Indices: 3664824--3664873 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
3664814 TTTTAGATAC
3664824 AATAAAT
1 AATAAAT
3664831 ATATAAA-
1 A-ATAAAT
3664838 AATAAAAT
1 AAT-AAAT
*
3664846 ATTAAAT
1 AATAAAT
3664853 AATAAAT
1 AATAAAT
3664860 AATAAAT
1 AATAAAT
3664867 AATAAAT
1 AATAAAT
3664874 TTAATAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 2 0.05
7 29 0.76
8 7 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAAAT
Found at i:3676094 original size:20 final size:20
Alignment explanation
Indices: 3676057--3676095 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3676047 GTTCGAACAG
*
3676057 AACAAAAAAAGTAGAAAAAC
1 AACAAAAAAAATAGAAAAAC
3676077 AACAAAGAAAAATA-AAAAA
1 AACAAA-AAAAATAGAAAAA
3676096 AATTGAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.79, C:0.08, G:0.08, T:0.05
Consensus pattern (20 bp):
AACAAAAAAAATAGAAAAAC
Found at i:3678076 original size:74 final size:74
Alignment explanation
Indices: 3677998--3678148 Score: 302
Period size: 74 Copynumber: 2.0 Consensus size: 74
3677988 TAAGGCCGTG
3677998 AAGTTTGAGTAATTTCTTCATCAATTTTGATCAAAATTGTCTTGGTTTCATCATATAAAATTTAA
1 AAGTTTGAGTAATTTCTTCATCAATTTTGATCAAAATTGTCTTGGTTTCATCATATAAAATTTAA
3678063 GCATGTTCC
66 GCATGTTCC
3678072 AAGTTTGAGTAATTTCTTCATCAATTTTGATCAAAATTGTCTTGGTTTCATCATATAAAATTTAA
1 AAGTTTGAGTAATTTCTTCATCAATTTTGATCAAAATTGTCTTGGTTTCATCATATAAAATTTAA
3678137 GCATGTTCC
66 GCATGTTCC
3678146 AAG
1 AAG
3678149 AAGCAACATC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (74 bp):
AAGTTTGAGTAATTTCTTCATCAATTTTGATCAAAATTGTCTTGGTTTCATCATATAAAATTTAA
GCATGTTCC
Found at i:3679084 original size:2 final size:2
Alignment explanation
Indices: 3679074--3679106 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3679064 AAAAAATACA
3679074 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3679107 TGTATATGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3685293 original size:35 final size:35
Alignment explanation
Indices: 3685247--3685317 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3685237 GATTTTCCAC
3685247 AAATTCACTAATTTGTCTTTCTTTTGAGGAAAAAT
1 AAATTCACTAATTTGTCTTTCTTTTGAGGAAAAAT
3685282 AAATTCACTAATTTGTCTTTCTTTTGAGGAAAAAT
1 AAATTCACTAATTTGTCTTTCTTTTGAGGAAAAAT
3685317 A
1 A
3685318 GTAACCTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (35 bp):
AAATTCACTAATTTGTCTTTCTTTTGAGGAAAAAT
Found at i:3686268 original size:20 final size:20
Alignment explanation
Indices: 3686243--3686283 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3686233 AAATCAAGTT
3686243 TTGAAATTACTACCCCTTAC
1 TTGAAATTACTACCCCTTAC
*
3686263 TTGAAATTACTCCCCCTTAC
1 TTGAAATTACTACCCCTTAC
3686283 T
1 T
3686284 CGAACACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.37
Consensus pattern (20 bp):
TTGAAATTACTACCCCTTAC
Found at i:3686298 original size:21 final size:20
Alignment explanation
Indices: 3686245--3686301 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
3686235 ATCAAGTTTT
* *
3686245 GAAATTACTACCCCTTACTT
1 GAAATTACTCCCCCTTACTC
3686265 GAAATTACTCCCCCTTACTC
1 GAAATTACTCCCCCTTACTC
3686285 GAACACTT-CTCCCCCTT
1 GAA-A-TTACTCCCCCTT
3686302 TTTGTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 21 0.64
21 10 0.30
22 2 0.06
ACGTcount: A:0.25, C:0.39, G:0.05, T:0.32
Consensus pattern (20 bp):
GAAATTACTCCCCCTTACTC
Found at i:3686446 original size:13 final size:13
Alignment explanation
Indices: 3686428--3686452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3686418 AGCCATTAGT
3686428 TTCATAATCAATA
1 TTCATAATCAATA
3686441 TTCATAATCAAT
1 TTCATAATCAAT
3686453 GTGACATGGT
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:3686631 original size:28 final size:28
Alignment explanation
Indices: 3686596--3686653 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
3686586 GTAAAAATTC
3686596 AACATTCAAAAAAAATCTAAACATCCAA
1 AACATTCAAAAAAAATCTAAACATCCAA
*
3686624 AACATTCAAAATAAATCTAAACATCCAA
1 AACATTCAAAAAAAATCTAAACATCCAA
3686652 AA
1 AA
3686654 ATCCAAGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (28 bp):
AACATTCAAAAAAAATCTAAACATCCAA
Found at i:3688577 original size:22 final size:21
Alignment explanation
Indices: 3688533--3688633 Score: 123
Period size: 22 Copynumber: 4.7 Consensus size: 21
3688523 CAGACCCTGT
* *
3688533 GGGGGTATCGATTCCC-TCAA
1 GGGGGAATCGGTTCCCTTCAA
3688553 GGGGGAATCGGTTCCCATTCAA
1 GGGGGAATCGGTTCCC-TTCAA
3688575 GGGGGAATCGGTTCCCATTCAA
1 GGGGGAATCGGTTCCC-TTCAA
*
3688597 AGGGGAATCGGTTTCCCTTCAA
1 GGGGGAATCGG-TTCCCTTCAA
* *
3688619 GGGGGTATCGATTCC
1 GGGGGAATCGGTTCC
3688634 TCCTGCACTA
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
20 14 0.19
21 4 0.06
22 49 0.68
23 5 0.07
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTTCAA
Found at i:3688607 original size:44 final size:42
Alignment explanation
Indices: 3688533--3688633 Score: 141
Period size: 44 Copynumber: 2.4 Consensus size: 42
3688523 CAGACCCTGT
*
3688533 GGGGGTATCGATTCCCTCAAGGGGGAATCGG-TTCCCATTCAA
1 GGGGGTATCGATTCCCTCAAAGGGGAATCGGTTTCCC-TTCAA
* *
3688575 GGGGGAATCGGTTCCCATTCAAAGGGGAATCGGTTTCCCTTCAA
1 GGGGGTATCGATTCCC--TCAAAGGGGAATCGGTTTCCCTTCAA
3688619 GGGGGTATCGATTCC
1 GGGGGTATCGATTCC
3688634 TCCTGCACTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 14 0.27
44 32 0.63
45 5 0.10
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.25
Consensus pattern (42 bp):
GGGGGTATCGATTCCCTCAAAGGGGAATCGGTTTCCCTTCAA
Found at i:3695551 original size:46 final size:46
Alignment explanation
Indices: 3695498--3695621 Score: 203
Period size: 46 Copynumber: 2.7 Consensus size: 46
3695488 CACCCAGTTG
* *
3695498 TTTAGAAGGTTGAAGAGCATGGGGAATGTTGATCCTCAAACTGCTA
1 TTTAGAAGGTTGGAGAGCATGGGGAATGTTGATCCTCAAACTACTA
* * *
3695544 TTTAGAAGGTTGGAGAGCATGAGGAGTGTTGATCCTCAAACTACTG
1 TTTAGAAGGTTGGAGAGCATGGGGAATGTTGATCCTCAAACTACTA
3695590 TTTAGAAGGTTGGAGAGCATGGGGAATGTTGA
1 TTTAGAAGGTTGGAGAGCATGGGGAATGTTGA
3695622 GAAATTATAG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.28
Consensus pattern (46 bp):
TTTAGAAGGTTGGAGAGCATGGGGAATGTTGATCCTCAAACTACTA
Found at i:3701153 original size:3 final size:3
Alignment explanation
Indices: 3701145--3701169 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3701135 GTGGGTAGGG
3701145 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3701170 TTTTAACCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3711095 original size:23 final size:23
Alignment explanation
Indices: 3711059--3711110 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3711049 CATCTTATAT
* *
3711059 GGCACTTCGATGCATTTCTATGC
1 GGCACTTCGATGCAATTCTACGC
*
3711082 GGCACTTC-AGTGCAATTCTACGT
1 GGCACTTCGA-TGCAATTCTACGC
3711105 GGCACT
1 GGCACT
3711111 CGGTGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (23 bp):
GGCACTTCGATGCAATTCTACGC
Found at i:3717705 original size:23 final size:23
Alignment explanation
Indices: 3717674--3717761 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
3717664 GACATCTTAT
*
3717674 ATGGCACTTCGGTGTATTTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
* *
3717697 ATGGGACTTTGGTGCATTTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
* * *
3717720 ACGACACTTCGGTGCAATTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
* * *
3717743 GTGGCACTTCAGTGTATTT
1 ATGGCACTTCGGTGCATTT
3717762 ATACGAGCTT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
ATGGCACTTCGGTGCATTTCTAC
Found at i:3720787 original size:22 final size:22
Alignment explanation
Indices: 3720762--3720833 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 22
3720752 AAAAGATATA
*
3720762 ATATATAGTTTTGAAAACATTT
1 ATATATAGTTTTTAAAACATTT
* *
3720784 ATATAGTATATTTTTAAAACTTATAT
1 ATATA-TA-GTTTTTAAAAC--ATTT
3720810 AGTATATAGTTTTTTAAAACATTT
1 A-TATATAG-TTTTTAAAACATTT
3720834 TTGAAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
22 5 0.13
23 2 0.05
24 12 0.31
26 16 0.41
27 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
ATATATAGTTTTTAAAACATTT
Found at i:3720797 original size:24 final size:22
Alignment explanation
Indices: 3720765--3720816 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 22
3720755 AGATATAATA
3720765 TATAGTTTTGAAAACATTTATATAG
1 TATA-TTTTGAAAAC--TTATATAG
*
3720790 TATATTTTTAAAACTTATATAG
1 TATATTTTGAAAACTTATATAG
3720812 TATAT
1 TATAT
3720817 AGTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 13 0.50
24 9 0.35
25 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (22 bp):
TATATTTTGAAAACTTATATAG
Found at i:3720817 original size:24 final size:25
Alignment explanation
Indices: 3720757--3720832 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 25
3720747 GTTTAAAAAG
*
3720757 ATATAATATATAGTTTTGAAAACATT
1 ATAT-ATATATAGTTTTTAAAACATT
3720783 -TATATAGTATA-TTTTTAAAAC-TT
1 ATATATA-TATAGTTTTTAAAACATT
3720806 ATATAGTATATAGTTTTTTAAAACATT
1 ATATA-TATATAG-TTTTTAAAACATT
3720833 TTTGAAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
23 2 0.05
24 20 0.47
25 9 0.21
26 10 0.23
27 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (25 bp):
ATATATATATAGTTTTTAAAACATT
Found at i:3720865 original size:36 final size:37
Alignment explanation
Indices: 3720820--3721024 Score: 234
Period size: 36 Copynumber: 5.8 Consensus size: 37
3720810 AGTATATAGT
*
3720820 TTTTTAAAACATTTTTGAAAAATTATATAATATATAG
1 TTTTAAAAACATTTTTGAAAAATTATATAATATATAG
*
3720857 -TTTAAAAACATTTTTAAAAAATTATATAATATATAG
1 TTTTAAAAACATTTTTGAAAAATTATATAATATATAG
*
3720893 TTTTAAAAACATTTTTGAAAACTTATATAAT-T-T--
1 TTTTAAAAACATTTTTGAAAAATTATATAATATATAG
*
3720926 TTTT-AAAACATTTTTTG-AAAACTATATAATATATAG
1 TTTTAAAAACA-TTTTTGAAAAATTATATAATATATAG
*
3720962 TTTTAAAAAC-TTTTT-TAAAA--ATATAATATATAG
1 TTTTAAAAACATTTTTGAAAAATTATATAATATATAG
* * * *
3720995 CTTAAAAAATATTTTTGAAATATATATATA
1 TTTTAAAAACATTTTTGAAAAAT-TATATA
3721025 TTATTTTTAT
Statistics
Matches: 144, Mismatches: 11, Indels: 25
0.80 0.06 0.14
Matches are distributed among these distances:
32 17 0.12
33 31 0.22
34 6 0.04
35 13 0.09
36 39 0.27
37 33 0.23
38 5 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTAAAAACATTTTTGAAAAATTATATAATATATAG
Found at i:3721010 original size:69 final size:70
Alignment explanation
Indices: 3720805--3721025 Score: 233
Period size: 69 Copynumber: 3.2 Consensus size: 70
3720795 TTTTAAAACT
* *
3720805 TATATAGTATATAGTTTTTTAAAACATTTTTGAAAAATTATATAATATATAGTTTAAAAACATTT
1 TATATAATATATAG-TTTTAAAAACATTTTT-AAAAA-TATATAATATATAGTTTAAAAA-ATTT
** *
3720870 TTAAAAAAT
62 TTTGAAAAC
* * *
3720879 TATATAATATATAGTTTTAAAAACATTTTTGAAAACTTATATAAT-T-T-TTTTAAAACATTTTT
1 TATATAATATATAGTTTTAAAAACATTTTT-AAAA-ATATATAATATATAGTTTAAAAAATTTTT
3720941 TGAAAAC
64 TGAAAAC
* *
3720948 TATATAATATATAGTTTTAAAAAC-TTTTTTAAAA-ATATAATATATAGCTTAAAAAATATTTTT
1 TATATAATATATAGTTTTAAAAACATTTTTAAAAATATATAATATATAGTTTAAAAAAT-TTTTT
3721011 G-AAA-
65 GAAAAC
3721015 TATAT-ATATAT
1 TATATAATATAT
3721026 TATTTTTATT
Statistics
Matches: 129, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
65 7 0.05
66 7 0.05
67 9 0.07
68 16 0.12
69 40 0.31
70 7 0.05
71 1 0.01
72 1 0.01
73 28 0.22
74 13 0.10
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (70 bp):
TATATAATATATAGTTTTAAAAACATTTTTAAAAATATATAATATATAGTTTAAAAAATTTTTTG
AAAAC
Found at i:3721044 original size:14 final size:15
Alignment explanation
Indices: 3721025--3721059 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3721015 TATATATATA
3721025 TTATTTT-TATTTAT
1 TTATTTTCTATTTAT
3721039 TTATTTTCTATTTAT
1 TTATTTTCTATTTAT
*
3721054 TAATTT
1 TTATTT
3721060 CTTGTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTCTATTTAT
Found at i:3722281 original size:20 final size:17
Alignment explanation
Indices: 3722250--3722296 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 17
3722240 TTTTTTAAAA
3722250 TATTTTTTTCTTTCATTTT
1 TATTTTTTTCTTTC--TTT
3722269 TATTTTGTTTCTTTCTTT
1 TATTTT-TTTCTTTCTTT
3722287 TATTTATTTT
1 TATTT-TTTT
3722297 TATTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 8 0.31
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.79
Consensus pattern (17 bp):
TATTTTTTTCTTTCTTT
Found at i:3722901 original size:29 final size:29
Alignment explanation
Indices: 3722814--3722888 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
3722804 TAACATTACC
* *
3722814 ATAATTATTTTATAATAATTCATAAATTA
1 ATAATTATTTTATAACAATCCATAAATTA
3722843 ATAATTATTTTATAACAATCCATAAATTA
1 ATAATTATTTTATAACAATCCATAAATTA
3722872 ATAATTATTTTATAACA
1 ATAATTATTTTATAACA
3722889 TCTGAAAGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (29 bp):
ATAATTATTTTATAACAATCCATAAATTA
Found at i:3726708 original size:13 final size:13
Alignment explanation
Indices: 3726690--3726725 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
3726680 CGAACGGATG
3726690 TAAACGAACACAA
1 TAAACGAACACAA
3726703 TAAACGAACACAA
1 TAAACGAACACAA
*
3726716 TAAATGAACA
1 TAAACGAACA
3726726 TAAACGAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.61, C:0.19, G:0.08, T:0.11
Consensus pattern (13 bp):
TAAACGAACACAA
Found at i:3726955 original size:24 final size:24
Alignment explanation
Indices: 3726917--3726997 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
3726907 AGATTGTGAT
**
3726917 AAACATAAATGAACACACATAAAC
1 AAACATAAACAAACACACATAAAC
* **
3726941 GAACATAAACAAACAGGCATAAAC
1 AAACATAAACAAACACACATAAAC
* *
3726965 AAACATAAACAAATGA-ACATAAAT
1 AAACATAAACAAA-CACACATAAAC
3726989 AAACATAAA
1 AAACATAAA
3726998 TGAATGAACA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 46 0.98
25 1 0.02
ACGTcount: A:0.64, C:0.17, G:0.06, T:0.12
Consensus pattern (24 bp):
AAACATAAACAAACACACATAAAC
Found at i:3727003 original size:24 final size:24
Alignment explanation
Indices: 3726933--3727019 Score: 95
Period size: 24 Copynumber: 3.6 Consensus size: 24
3726923 AAATGAACAC
* *
3726933 ACATAAACGAACATAAACAAA-CA
1 ACATAAACAAACATAAACAAATGA
*
3726956 GGCATAAACAAACATAAACAAATGA
1 -ACATAAACAAACATAAACAAATGA
* **
3726981 ACATAAATAAACATAAATGAATGA
1 ACATAAACAAACATAAACAAATGA
*
3727005 ACATAAACGAACATA
1 ACATAAACAAACATA
3727020 TTACCGAACG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 52 0.98
25 1 0.02
ACGTcount: A:0.62, C:0.16, G:0.08, T:0.14
Consensus pattern (24 bp):
ACATAAACAAACATAAACAAATGA
Found at i:3728313 original size:26 final size:26
Alignment explanation
Indices: 3728283--3728339 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
3728273 TATTGCTTTT
*
3728283 GTTCAGTTATTATCATAATGCTTCTC
1 GTTCAGTTATTATCATAATGCTCCTC
3728309 GTTCAGTTATTATCATAATGCTCCTC
1 GTTCAGTTATTATCATAATGCTCCTC
3728335 GTTCA
1 GTTCA
3728340 ATACCATCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (26 bp):
GTTCAGTTATTATCATAATGCTCCTC
Found at i:3734592 original size:5 final size:5
Alignment explanation
Indices: 3734577--3734619 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
3734567 GCTGCCGCCG
* * *
3734577 TCGTC -CGTC TCGTC TCGTC TCGTC TTGTC TCGGC TCGGC TCGT
1 TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGT
3734620 GGTTGTGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 4 0.12
5 29 0.88
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (5 bp):
TCGTC
Found at i:3736500 original size:22 final size:22
Alignment explanation
Indices: 3736475--3736518 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3736465 AAAATTCACC
3736475 CAAGATTACAAGACTTAAATAT
1 CAAGATTACAAGACTTAAATAT
3736497 CAAGATTACAAGACTTAAATAT
1 CAAGATTACAAGACTTAAATAT
3736519 TTATCTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (22 bp):
CAAGATTACAAGACTTAAATAT
Found at i:3737548 original size:42 final size:40
Alignment explanation
Indices: 3737501--3737602 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 40
3737491 TATATTTTAT
* *
3737501 AATAATATATTTATAATTATTTACTATATTTTAAATTATTAA
1 AATAATATATTTATAATAATTT-CTATATTTTAAATAATT-A
* *
3737543 AATAATATATTATATAATAATTTTTATATTTTTAATAATTA
1 AATAATATATT-TATAATAATTTCTATATTTTAAATAATTA
*
3737584 AAGAATATATTT-TAATAAT
1 AATAATATATTTATAATAAT
3737603 ATAAAAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
39 7 0.13
40 1 0.02
41 11 0.20
42 25 0.46
43 10 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (40 bp):
AATAATATATTTATAATAATTTCTATATTTTAAATAATTA
Found at i:3737563 original size:15 final size:15
Alignment explanation
Indices: 3737469--3737563 Score: 67
Period size: 15 Copynumber: 6.7 Consensus size: 15
3737459 TCGGACCTAA
*
3737469 ATATATTAATAT-TT
1 ATATAATAATATATT
*
3737483 -TAAAATAATATATT
1 ATATAATAATATATT
*
3737497 TTATAATAATATATT
1 ATATAATAATATATT
* * *
3737512 -TATAATTATTTACT
1 ATATAATAATATATT
**
3737526 ATATTTTAA-ATTATT
1 ATATAATAATA-TATT
3737541 A-A-AATAATATATT
1 ATATAATAATATATT
3737554 ATATAATAAT
1 ATATAATAAT
3737564 TTTTATATTT
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
13 17 0.28
14 16 0.26
15 28 0.46
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATAATAATATATT
Found at i:3737596 original size:21 final size:22
Alignment explanation
Indices: 3737567--3737611 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3737557 TAATAATTTT
3737567 TATATTTTTAATAAT-TAAAGAA
1 TATATTTTTAATAATATAAA-AA
3737589 TATA-TTTTAATAATATAAAAA
1 TATATTTTTAATAATATAAAAA
3737610 TA
1 TA
3737612 AAAATCCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATATAAAAA
Found at i:3737976 original size:17 final size:17
Alignment explanation
Indices: 3737956--3737991 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3737946 TTTTTATCCA
*
3737956 TTATTTATTTTTATTAT
1 TTATTTACTTTTATTAT
3737973 TTATTTACTTTTATTAT
1 TTATTTACTTTTATTAT
3737990 TT
1 TT
3737992 CTAAATTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTATTTACTTTTATTAT
Found at i:3739567 original size:19 final size:20
Alignment explanation
Indices: 3739545--3739585 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3739535 TGTTATTTGC
3739545 AAATGAA-AATGTTGTGGAA
1 AAATGAAGAATGTTGTGGAA
*
3739564 AAATGAATGGATGTTGTGGAA
1 AAATGAA-GAATGTTGTGGAA
3739585 A
1 A
3739586 TTGTCTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (20 bp):
AAATGAAGAATGTTGTGGAA
Found at i:3741013 original size:20 final size:20
Alignment explanation
Indices: 3740984--3741022 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3740974 ATTCCACCAC
*
3740984 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3741004 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
3741023 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3742659 original size:22 final size:22
Alignment explanation
Indices: 3742631--3742674 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3742621 CTCCCTAGCC
*
3742631 AGTTGTGCGTCGAAGTTAAGCT
1 AGTTGTGCGTCAAAGTTAAGCT
*
3742653 AGTTGTGCGTCAAAGTTTAGCT
1 AGTTGTGCGTCAAAGTTAAGCT
3742675 TCTTGATTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.34
Consensus pattern (22 bp):
AGTTGTGCGTCAAAGTTAAGCT
Found at i:3762766 original size:18 final size:18
Alignment explanation
Indices: 3762743--3762778 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3762733 TCAAGAATGG
3762743 TAAGATAGGGGACACTAA
1 TAAGATAGGGGACACTAA
3762761 TAAGATAGGGGACACTAA
1 TAAGATAGGGGACACTAA
3762779 CACTGCTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (18 bp):
TAAGATAGGGGACACTAA
Found at i:3765308 original size:41 final size:41
Alignment explanation
Indices: 3765237--3765349 Score: 163
Period size: 41 Copynumber: 2.8 Consensus size: 41
3765227 CTTCACTCAG
* * * *
3765237 TTCCATCATATAAGAAGTTGGATCAGCATCACTTTGCTTGA
1 TTCCATCACATAAGGAGTTAGATCAACATCACTTTGCTTGA
*
3765278 TTCCATCACATAAGGAGTTAGATTAACATCACTTTGCTTGA
1 TTCCATCACATAAGGAGTTAGATCAACATCACTTTGCTTGA
* *
3765319 TTCCATCACATAAGGAGTTGGATCAGCATCA
1 TTCCATCACATAAGGAGTTAGATCAACATCA
3765350 GCCCGCCTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (41 bp):
TTCCATCACATAAGGAGTTAGATCAACATCACTTTGCTTGA
Found at i:3767331 original size:12 final size:12
Alignment explanation
Indices: 3767292--3767339 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
3767282 ACGGATATAT
*
3767292 CAGAAATCAAAA
1 CAGAAATCAGAA
* * *
3767304 CAGAATTTAGAT
1 CAGAAATCAGAA
*
3767316 CAGATATCAGAA
1 CAGAAATCAGAA
3767328 CAGAAATCAGAA
1 CAGAAATCAGAA
3767340 ATCAGAACGG
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:3772849 original size:2 final size:2
Alignment explanation
Indices: 3772842--3772895 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3772832 ATGGATCTTT
3772842 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
3772884 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3772896 GAATATTGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3777008 original size:24 final size:22
Alignment explanation
Indices: 3776957--3777012 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
3776947 TAGCATGTTT
*
3776957 AAAAATAAAACTTAAAATAAAG
1 AAAAAGAAAACTTAAAATAAAG
3776979 TAAAAACGAAAACTTGAAAATAAA-
1 -AAAAA-GAAAACTT-AAAATAAAG
3777003 AGAAAAGAAA
1 A-AAAAGAAA
3777013 TAACTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 10 0.34
24 11 0.38
25 8 0.28
ACGTcount: A:0.71, C:0.05, G:0.09, T:0.14
Consensus pattern (22 bp):
AAAAAGAAAACTTAAAATAAAG
Found at i:3779026 original size:17 final size:17
Alignment explanation
Indices: 3779006--3779045 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3778996 TTAATTAATT
3779006 AAACTAGTTCATTCATC
1 AAACTAGTTCATTCATC
* *
3779023 AAACTAGTTCATTTATT
1 AAACTAGTTCATTCATC
3779040 AAACTA
1 AAACTA
3779046 ACTCTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (17 bp):
AAACTAGTTCATTCATC
Found at i:3783092 original size:17 final size:17
Alignment explanation
Indices: 3783052--3783094 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3783042 TAGTTAGTTA
3783052 ATTAAACTAGTTCATTC
1 ATTAAACTAGTTCATTC
*
3783069 ATCAAACTAGTTCATAT-
1 ATTAAACTAGTTCAT-TC
3783086 ATTAAACTA
1 ATTAAACTA
3783095 ACTCTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (17 bp):
ATTAAACTAGTTCATTC
Found at i:3783299 original size:18 final size:18
Alignment explanation
Indices: 3783276--3783310 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3783266 ATTATTCGTA
3783276 TGTCTTTTATCTTTCCAC
1 TGTCTTTTATCTTTCCAC
3783294 TGTCTTTTATCTTTCCA
1 TGTCTTTTATCTTTCCA
3783311 ACGCCTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57
Consensus pattern (18 bp):
TGTCTTTTATCTTTCCAC
Found at i:3786767 original size:13 final size:13
Alignment explanation
Indices: 3786749--3786776 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3786739 AACGTGTGTC
3786749 GATCTTAATAGAG
1 GATCTTAATAGAG
3786762 GATCTTAATAGAG
1 GATCTTAATAGAG
3786775 GA
1 GA
3786777 ATGCTAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (13 bp):
GATCTTAATAGAG
Found at i:3788580 original size:32 final size:32
Alignment explanation
Indices: 3788539--3788627 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
3788529 TCGAGGGTTG
*
3788539 CCTATGTCCTTCGGGACGTATGGACAAGAATA
1 CCTATGTCCTTCGGGACATATGGACAAGAATA
* * * * * *
3788571 CCTATGTCCTTCAGAACATAAGGATAGGATTA
1 CCTATGTCCTTCGGGACATATGGACAAGAATA
*
3788603 CCTATGTCTTTCGGGACATATGGAC
1 CCTATGTCCTTCGGGACATATGGAC
3788628 TGGTCCTTCG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.28
Consensus pattern (32 bp):
CCTATGTCCTTCGGGACATATGGACAAGAATA
Found at i:3790742 original size:18 final size:18
Alignment explanation
Indices: 3790719--3790753 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3790709 ATTGGGATTT
3790719 GAATAAGGGTTT-TGCAAA
1 GAATAA-GGTTTGTGCAAA
3790737 GAATAAGGTTTGTGCAA
1 GAATAAGGTTTGTGCAA
3790754 GTAGTGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.06, G:0.29, T:0.29
Consensus pattern (18 bp):
GAATAAGGTTTGTGCAAA
Found at i:3796438 original size:12 final size:12
Alignment explanation
Indices: 3796423--3796448 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3796413 CAATCCTTTC
3796423 GATATGATCACT
1 GATATGATCACT
3796435 GATATGATCACT
1 GATATGATCACT
3796447 GA
1 GA
3796449 CAAAGTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (12 bp):
GATATGATCACT
Found at i:3798301 original size:23 final size:23
Alignment explanation
Indices: 3798271--3798314 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3798261 AATTTTTTAA
3798271 ATCTCTTCGAGTAGTCATAGAAT
1 ATCTCTTCGAGTAGTCATAGAAT
3798294 ATCTCTTCGAGTAGTCATAGA
1 ATCTCTTCGAGTAGTCATAGA
3798315 GTGACACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (23 bp):
ATCTCTTCGAGTAGTCATAGAAT
Found at i:3804514 original size:30 final size:30
Alignment explanation
Indices: 3804450--3804552 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 30
3804440 GAAAGCAAAC
* * * *
3804450 CAAAGAAAGAAGAAACCCACCACAAC-AAAC
1 CAAAGAAACAA-AAGCCCATCACAACAAAAA
* * * *
3804480 CAAAGAAAACAAAATCCC-TCACAGCAGAAG
1 CAAAG-AAACAAAAGCCCATCACAACAAAAA
3804510 CAAAGGAAACAAAAGCCCATCACAACAAAAA
1 CAAA-GAAACAAAAGCCCATCACAACAAAAA
3804541 CAAAGAAACAAA
1 CAAAGAAACAAA
3804553 TATAGGGGTA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
29 5 0.08
30 35 0.59
31 19 0.32
ACGTcount: A:0.60, C:0.26, G:0.11, T:0.03
Consensus pattern (30 bp):
CAAAGAAACAAAAGCCCATCACAACAAAAA
Found at i:3809914 original size:17 final size:17
Alignment explanation
Indices: 3809892--3809938 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
3809882 TACAGAGCCT
3809892 TTGAATCATTCAGGTCA
1 TTGAATCATTCAGGTCA
*
3809909 TTGAATCACTCAGGTCA
1 TTGAATCATTCAGGTCA
3809926 TTGAATCATTCAG
1 TTGAATCATTCAG
3809939 CGCTTAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (17 bp):
TTGAATCATTCAGGTCA
Found at i:3813417 original size:22 final size:22
Alignment explanation
Indices: 3813392--3813447 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3813382 CACTATCATG
* *
3813392 GGTTTAAAATACCTATATGTTC
1 GGTTCAAAATACCTATATGGTC
* * *
3813414 GGTTCGATATACCTATATGGTG
1 GGTTCAAAATACCTATATGGTC
3813436 GGTTCAAAATAC
1 GGTTCAAAATAC
3813448 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (22 bp):
GGTTCAAAATACCTATATGGTC
Found at i:3814865 original size:22 final size:22
Alignment explanation
Indices: 3814840--3814895 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
3814830 CACTATCATG
* *
3814840 GGTTTAAAATACCTATATGTTC
1 GGTTCAAAATACCTATATGGTC
* * *
3814862 GGTTCGATATACCTATATGGTG
1 GGTTCAAAATACCTATATGGTC
3814884 GGTTCAAAATAC
1 GGTTCAAAATAC
3814896 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (22 bp):
GGTTCAAAATACCTATATGGTC
Found at i:3816340 original size:22 final size:22
Alignment explanation
Indices: 3816285--3816340 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3816275 CACTATCATT
* **
3816285 GGTTTAAAATACCTATATTTTC
1 GGTTCAAAATACCTATATGGTC
* * *
3816307 GGTTCGATATACCTATATGGTG
1 GGTTCAAAATACCTATATGGTC
3816329 GGTTCAAAATAC
1 GGTTCAAAATAC
3816341 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (22 bp):
GGTTCAAAATACCTATATGGTC
Found at i:3825089 original size:26 final size:26
Alignment explanation
Indices: 3825059--3825115 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
3825049 TAGTAAAAAT
* *
3825059 ATTTAATTTTTATTTGAACCCTTAAA
1 ATTTAATTTTCATTAGAACCCTTAAA
3825085 ATTTAATTTTCATTAGAACCCTTAAA
1 ATTTAATTTTCATTAGAACCCTTAAA
3825111 ATTTA
1 ATTTA
3825116 TATTATTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (26 bp):
ATTTAATTTTCATTAGAACCCTTAAA
Found at i:3833537 original size:19 final size:19
Alignment explanation
Indices: 3833488--3833529 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3833478 CAATGAGAAG
*
3833488 GTCAACGG-ACAGGTCAAA
1 GTCAACGGTTCAGGTCAAA
*
3833506 GTCAACGGTTCAGGTCAAG
1 GTCAACGGTTCAGGTCAAA
3833525 GTCAA
1 GTCAA
3833530 TGAGTCAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (19 bp):
GTCAACGGTTCAGGTCAAA
Found at i:3836553 original size:20 final size:21
Alignment explanation
Indices: 3836528--3836566 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3836518 TATAGTATTT
3836528 AGGATTTAGA-TCAAATTATC
1 AGGATTTAGAGTCAAATTATC
*
3836548 AGGATTTCGAGTCAAATTA
1 AGGATTTAGAGTCAAATTA
3836567 AACTAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (21 bp):
AGGATTTAGAGTCAAATTATC
Found at i:3837895 original size:18 final size:19
Alignment explanation
Indices: 3837874--3837915 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3837864 TAACGGGCAG
3837874 GTCAAC-GATCAGGTCAAA
1 GTCAACGGATCAGGTCAAA
* *
3837892 GTCAACGGTTCAGGTCAAG
1 GTCAACGGATCAGGTCAAA
3837911 GTCAA
1 GTCAA
3837916 AGTGTCTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (19 bp):
GTCAACGGATCAGGTCAAA
Found at i:3838640 original size:28 final size:28
Alignment explanation
Indices: 3838600--3838658 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
3838590 TTAGTCGTAA
3838600 ATATTGACCTAGGCTAAATGGTAGAGTG
1 ATATTGACCTAGGCTAAATGGTAGAGTG
*
3838628 ATATTGACCTAGGCTAGATGGTAGAGTG
1 ATATTGACCTAGGCTAAATGGTAGAGTG
3838656 ATA
1 ATA
3838659 GTTGGCCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (28 bp):
ATATTGACCTAGGCTAAATGGTAGAGTG
Found at i:3841744 original size:6 final size:6
Alignment explanation
Indices: 3841733--3841765 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3841723 TAATCAGCGT
3841733 TTTATA TTTATA TTTATA TTTAT- TTTAT- TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTAT
3841766 TGACAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTATA
Found at i:3842194 original size:16 final size:17
Alignment explanation
Indices: 3842175--3842210 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
3842165 TAATTTAAAA
3842175 TTTAAAATATTT-ATAT
1 TTTAAAATATTTAATAT
3842191 TTTAAAATATTTAATAT
1 TTTAAAATATTTAATAT
3842208 TTT
1 TTT
3842211 TCTCAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAAATATTTAATAT
Found at i:3842747 original size:305 final size:299
Alignment explanation
Indices: 3842198--3842805 Score: 1146
Period size: 298 Copynumber: 2.0 Consensus size: 299
3842188 TATTTTAAAA
3842198 TATTTAATATTTTTCTCAAGTGTTGAAATACAATCTCTTATTAGCGTAAATGCATTTCCATACAT
1 TATTTAATATTTTTCTCAAGTGTTGAAATACAATCTCTTATTAGCGTAAATGCATTTCCATACAT
3842263 TATTTGGGCTCCATCGAAATATGATCGATTGCCTCTCCTCTCAGTCAAGAAACTGAGACACCTTT
66 TATTTGGGCTCCATCGAAATATGATCGATTGCCTCTCCTCTCAGTCAAGAAACTGAGACACCTTT
3842328 GTTCAATACAATAAATATTCGTTCTATATATGATGTCGGGATACCTTCATCAACAAAAAGATGAT
131 GTTCAATACAATAAATATTCGTTCTATATATGATGTCGGGATACCTTCATCAACAAAAAGATGAT
3842393 TCTACCTTCTAAAAAGAGAAATGAGCAATCTCTGTCCCAACAGTGAGAGTG-TGAGATGTCTTCA
196 TCTACCTTCTAAAAAGAGAAATGAGCAATCTCTGTCCCAACAGTGAGAGTGTTGAGATGTCTTCA
3842457 CCATCTAACAAAACCAAGAAGGATTGTTATATTTTTTAG
261 CCATCTAACAAAACCAAGAAGGATTGTTATATTTTTTAG
3842496 TATTTAATATTTTTCTCAAGTGTTGAAATACAATCTCTTATTAGCGTAAATGCATTTCCATACAT
1 TATTTAATATTTTTCTCAAGTGTTGAAATACAATCTCTTATTAGCGTAAATGCATTTCCATACAT
3842561 TATTTGGGCTCCATCGAAATATGATCGATTGCCTCTCCTCTCAGGTCAAGAGAACTGAGACACCT
66 TATTTGGGCTCCATCGAAATATGATCGATTGCCTCTCCTCTCA-GTCAAGA-AACTGAGACACCT
3842626 TTGTTTCAATAACAATAAAATATTCGTTGTCTATATATGATGTCGGGATACCTTCATCAACAAAA
129 TTG-TTCAAT-ACAAT-AAATATTCG-T-TCTATATATGATGTCGGGATACCTTCATCAACAAAA
3842691 AGATGATTCTACCTTCTAAAAAGAGAAATGAGCAATCTCTGTCCCAACAGTGAGAGTGTTGAGAT
189 AGATGATTCTACCTTCTAAAAAGAGAAATGAGCAATCTCTGTCCCAACAGTGAGAGTGTTGAGAT
3842756 GTCTTCACCATCTAACAAAACCAAGAAGGATTGTTATATTTTTTAG
254 GTCTTCACCATCTAACAAAACCAAGAAGGATTGTTATATTTTTTAG
3842802 TATT
1 TATT
3842806 AGTCTAGGAT
Statistics
Matches: 302, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
298 108 0.36
299 7 0.02
300 16 0.05
301 6 0.02
302 5 0.02
303 9 0.03
304 1 0.00
305 94 0.31
306 56 0.19
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (299 bp):
TATTTAATATTTTTCTCAAGTGTTGAAATACAATCTCTTATTAGCGTAAATGCATTTCCATACAT
TATTTGGGCTCCATCGAAATATGATCGATTGCCTCTCCTCTCAGTCAAGAAACTGAGACACCTTT
GTTCAATACAATAAATATTCGTTCTATATATGATGTCGGGATACCTTCATCAACAAAAAGATGAT
TCTACCTTCTAAAAAGAGAAATGAGCAATCTCTGTCCCAACAGTGAGAGTGTTGAGATGTCTTCA
CCATCTAACAAAACCAAGAAGGATTGTTATATTTTTTAG
Found at i:3843122 original size:3 final size:3
Alignment explanation
Indices: 3843114--3843181 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
3843104 TTTTAGGTTA
3843114 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3843162 TAT TAT TAT AAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
3843182 CAAAAAAACC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3850761 original size:7 final size:7
Alignment explanation
Indices: 3850749--3850778 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3850739 CTTTACATCA
3850749 TATTCTT
1 TATTCTT
*
3850756 TATTCTA
1 TATTCTT
3850763 TATTCTT
1 TATTCTT
3850770 TATTCTT
1 TATTCTT
3850777 TA
1 TA
3850779 CATTCCAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTCTT
Found at i:3854283 original size:8 final size:8
Alignment explanation
Indices: 3854266--3854349 Score: 64
Period size: 9 Copynumber: 10.1 Consensus size: 8
3854256 TATGCCTAAT
3854266 AAAATAAA
1 AAAATAAA
*
3854274 AAAATGAA
1 AAAATAAA
*
3854282 AAATTAAA
1 AAAATAAA
*
3854290 AAGGAA-AGA
1 AA--AATAAA
* *
3854299 GAAA-AAG
1 AAAATAAA
3854306 AAAATAAA
1 AAAATAAA
3854314 AAAATAAGA
1 AAAATAA-A
3854323 AAAATAAGA
1 AAAATAA-A
3854332 AAAATAAGA
1 AAAATAA-A
3854341 AAAATAAA
1 AAAATAAA
3854349 A
1 A
3854350 GGAAAAGAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
7 6 0.10
8 26 0.42
9 29 0.47
10 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:3854327 original size:9 final size:9
Alignment explanation
Indices: 3854306--3854347 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
3854296 AGAGAAAAAG
3854306 AAAATAA-A
1 AAAATAAGA
3854314 AAAATAAGA
1 AAAATAAGA
3854323 AAAATAAGA
1 AAAATAAGA
3854332 AAAATAAGA
1 AAAATAAGA
3854341 AAAATAA
1 AAAATAA
3854348 AAGGAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 7 0.21
9 26 0.79
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (9 bp):
AAAATAAGA
Found at i:3855469 original size:52 final size:52
Alignment explanation
Indices: 3855345--3855469 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
3855335 GAGGGAGAAG
* * *
3855345 AAGTTCATATTGAGAAGAACGTGTTCAACCCTGGCCCAACATTTCCAGTGGA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCATGGCCCAACATTTCCAGTGGA
*
3855397 GAGTTCATAATGAGAAGAACTTGTTCAACCATGGCCCAACATTTCCAGTGGA
1 AAGTTCATAATGAGAAGAACTTGTTCAACCATGGCCCAACATTTCCAGTGGA
*
3855449 AAGTTCATAATAAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
3855470 CGTCCAACGA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (52 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCATGGCCCAACATTTCCAGTGGA
Found at i:3856053 original size:31 final size:31
Alignment explanation
Indices: 3856018--3856085 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
3856008 CAGTTACGTC
**
3856018 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTAAAAACAGACTAAATGTTG
**
3856049 GGGGACCATATTAAAAATGGACTAAATGTTG
1 GGGGACCATATTAAAAACAGACTAAATGTTG
3856080 GGGGAC
1 GGGGAC
3856086 TGTATTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.22
Consensus pattern (31 bp):
GGGGACCATATTAAAAACAGACTAAATGTTG
Found at i:3856361 original size:23 final size:24
Alignment explanation
Indices: 3856327--3856381 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
3856317 CATAATGAAA
*
3856327 AATTAAATATTG-ATTTTAAAGTAT
1 AATTAAATATTGAATATTAAA-TAT
*
3856351 AATTAAA-ATTGAATATTGAATAT
1 AATTAAATATTGAATATTAAATAT
3856374 AATTAAAT
1 AATTAAAT
3856382 TATTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (24 bp):
AATTAAATATTGAATATTAAATAT
Found at i:3857014 original size:2 final size:2
Alignment explanation
Indices: 3857007--3857037 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3856997 GCCTAAGCTT
3857007 TA TA TA TA TA -A 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
3857038 AATAATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3857022 original size:9 final size:9
Alignment explanation
Indices: 3857008--3857071 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
3856998 CCTAAGCTTT
3857008 ATATATATA
1 ATATATATA
3857017 ATATATAT-
1 ATATATATA
3857025 ATATATAT-
1 ATATATATA
*
3857033 ATATAAATA
1 ATATATATA
3857042 ATA-ATAATA
1 ATATAT-ATA
3857051 ATA-ATAATA
1 ATATAT-ATA
3857060 ATA-ATAATA
1 ATATAT-ATA
3857069 ATA
1 ATA
3857072 AGGGTAAAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.31
9 35 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATATATA
Found at i:3857046 original size:3 final size:3
Alignment explanation
Indices: 3857038--3857072 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3857028 TATATATATA
3857038 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3857073 GGGTAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3857275 original size:31 final size:31
Alignment explanation
Indices: 3857201--3857267 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
3857191 CAGTTATGTC
3857201 GGGGACCATATTGCAAACATACTAAATGTTG
1 GGGGACCATATTGCAAACATACTAAATGTTG
3857232 GGGGACCATATTGCAAACATACTAAATGTTG
1 GGGGACCATATTGCAAACATACTAAATGTTG
3857263 GGGGA
1 GGGGA
3857268 TTGTATTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACATACTAAATGTTG
Found at i:3864136 original size:22 final size:22
Alignment explanation
Indices: 3864108--3864156 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
3864098 GCTAAGTAAT
3864108 AATTGTTGGGAAACATACTAAC
1 AATTGTTGGGAAACATACTAAC
3864130 AATTGTTGGGAAACATACTAAC
1 AATTGTTGGGAAACATACTAAC
3864152 AATTG
1 AATTG
3864157 ATAATATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (22 bp):
AATTGTTGGGAAACATACTAAC
Found at i:3865932 original size:243 final size:243
Alignment explanation
Indices: 3865504--3865988 Score: 925
Period size: 243 Copynumber: 2.0 Consensus size: 243
3865494 ACTAGCAATG
3865504 TTGATGAAGTTCCTAAATTTAAAGCAAGGTGATCGAGCTTTTCATGAATTTGAGGCAAAATACTA
1 TTGATGAAGTTCCTAAATTTAAAGCAAGGTGATCGAGCTTTTCATGAATTTGAGGCAAAATACTA
*
3865569 CAAGTTGAGCCGTTTTACTACTGATATTGTGCCAAATGATAAGGCCAAGCGTGATTGATTCATAG
66 CAAGTTGAACCGTTTTACTACTGATATTGTGCCAAATGATAAGGCCAAGCGTGATTGATTCATAG
* *
3865634 AGGGTTTAAGGTCAAATCTGAAAGAAATGATGATGGTTTTGAATTTTTTCGAGTCTGCAAGAAGT
131 AGGGTTTAAGGTCAAAGCTGAAAGAAATGATGATAGTTTTGAATTTTTTCGAGTCTGCAAGAAGT
*
3865699 GATAAATAAAGCTAAAGCCATTGAAAGAGCTCAGGAGGAAACCTTAGC
196 GATAAACAAAGCTAAAGCCATTGAAAGAGCTCAGGAGGAAACCTTAGC
3865747 TTGATGAAGTTCCTAAATTTAAAGCAAGGTGATCGAGCTTTTCATGAATTTGAGGCAAAATACTA
1 TTGATGAAGTTCCTAAATTTAAAGCAAGGTGATCGAGCTTTTCATGAATTTGAGGCAAAATACTA
*
3865812 CAAGTTGAACCGTTTTACTACTGATATTGTGCCAAATGATAAGGCCAATCGTGATTGATTCATAG
66 CAAGTTGAACCGTTTTACTACTGATATTGTGCCAAATGATAAGGCCAAGCGTGATTGATTCATAG
3865877 AGGGTTTAAGGTCAAAGCTGAAAGAAATGATGATAGTTTTGAATTTTTTCGAGTCTGCAAGAAGT
131 AGGGTTTAAGGTCAAAGCTGAAAGAAATGATGATAGTTTTGAATTTTTTCGAGTCTGCAAGAAGT
3865942 GATAAACAAAGCTAAAGCCATTGAAAGAGCTCAGGAGGAAACCTTAG
196 GATAAACAAAGCTAAAGCCATTGAAAGAGCTCAGGAGGAAACCTTAG
3865989 TAGCGGAACA
Statistics
Matches: 237, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
243 237 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (243 bp):
TTGATGAAGTTCCTAAATTTAAAGCAAGGTGATCGAGCTTTTCATGAATTTGAGGCAAAATACTA
CAAGTTGAACCGTTTTACTACTGATATTGTGCCAAATGATAAGGCCAAGCGTGATTGATTCATAG
AGGGTTTAAGGTCAAAGCTGAAAGAAATGATGATAGTTTTGAATTTTTTCGAGTCTGCAAGAAGT
GATAAACAAAGCTAAAGCCATTGAAAGAGCTCAGGAGGAAACCTTAGC
Found at i:3870611 original size:65 final size:63
Alignment explanation
Indices: 3870542--3870663 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
3870532 CGATACACTC
* * *
3870542 TTAAATGAAAAATCATCGAATGCAATAAGTGTATCGATATATAGGCAGTGTATCGATACCCCCTT
1 TTAAATG-AAAAT-ATCGAATGCAATAACTGTACCGATACATAGGCAGTGTATCGATACCCCCTT
* * * **
3870607 TTAAATGAAAATTTTGAATGTAATTTCTGTACCGATACATAGGCAGTGTATCGATAC
1 TTAAATGAAAATATCGAATGCAATAACTGTACCGATACATAGGCAGTGTATCGATAC
3870664 ACCATTTAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 37 0.76
64 5 0.10
65 7 0.14
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (63 bp):
TTAAATGAAAATATCGAATGCAATAACTGTACCGATACATAGGCAGTGTATCGATACCCCCTT
Found at i:3871344 original size:45 final size:45
Alignment explanation
Indices: 3871160--3871412 Score: 284
Period size: 45 Copynumber: 5.7 Consensus size: 45
3871150 TTAAAAAGGA
* * * * *
3871160 AAATGCATATGGGTGCATTCTCAATAGAAAAATATA-CTAAAGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTA-AGCTAAAGTTG
*
3871205 AAATGTATATGGGTACATTATCAACAG--AAGTATGCTAAAGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTAAGCTAAAGTTG
*
3871248 AAATGTATATGGGTACATTATCAACAG--AAGTATGCTAAAGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTAAGCTAAAGTTG
* * **
3871291 AAAAGTATATGGGTACATTATCGACAGAAAAGTAAGCTATGGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTAAGCTAAAGTTG
* * * * * *
3871336 AGATGTATACGAGTACATTTTCAACATAAAAGTATA-CTATAGTTG
1 AAATGTATATGGGTACATTATCAACAGAAAAGTA-AGCTAAAGTTG
*
3871381 AAATGTATATGGGTGCATTATCAACAGAAAAG
1 AAATGTATATGGGTACATTATCAACAGAAAAG
3871413 ATGTTAGAAT
Statistics
Matches: 179, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
43 81 0.45
45 97 0.54
46 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (45 bp):
AAATGTATATGGGTACATTATCAACAGAAAAGTAAGCTAAAGTTG
Found at i:3871499 original size:13 final size:13
Alignment explanation
Indices: 3871481--3871506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3871471 AAAAGAAAGA
3871481 ATCATGATAAATG
1 ATCATGATAAATG
3871494 ATCATGATAAATG
1 ATCATGATAAATG
3871507 GGGATTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
ATCATGATAAATG
Found at i:3874335 original size:50 final size:50
Alignment explanation
Indices: 3874273--3874369 Score: 142
Period size: 50 Copynumber: 1.9 Consensus size: 50
3874263 GATGAAGATG
*
3874273 CATCTCCCTTGGCCGAATGGTGATATGCTT-GTTCATCTTGGCGCCAAAGT
1 CATCTCCCTTGGCCGAATGGTGATATG-TTGGTTCATCTTGGCCCCAAAGT
* * *
3874323 CATCTTCCTTGGCCGAATGGTGTTGTGTTGGTTCATCTTGGCCCCAA
1 CATCTCCCTTGGCCGAATGGTGATATGTTGGTTCATCTTGGCCCCAA
3874370 TTTCTTCATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 2 0.05
50 40 0.95
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.34
Consensus pattern (50 bp):
CATCTCCCTTGGCCGAATGGTGATATGTTGGTTCATCTTGGCCCCAAAGT
Found at i:3875424 original size:22 final size:23
Alignment explanation
Indices: 3875392--3875452 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
3875382 ATTAGAATAT
3875392 ATTTATAAAATAAATAAAAT-TTA
1 ATTTA-AAAATAAATAAAATCTTA
*
3875415 ATTTAAAAAT-ATTAAAATCTTA
1 ATTTAAAAATAAATAAAATCTTA
* *
3875437 AATTAAATATAAATAA
1 ATTTAAAAATAAATAA
3875453 TTTTTGTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 7 0.22
22 16 0.50
23 9 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTAAAAATAAATAAAATCTTA
Found at i:3875562 original size:113 final size:113
Alignment explanation
Indices: 3875310--3875622 Score: 488
Period size: 112 Copynumber: 2.8 Consensus size: 113
3875300 GGGTCACATC
* * *
3875310 AATATTAAAATCTTAAATTAAATATTAATAATTTGTTA-TTTTTTTAGCAATTTAAGTGTTATCA
1 AATATTAAAATCTTAAATTAAATATAAATAATTTTTTAGATTTTTTAGCAATTTAAGTGTTATCA
* *
3875374 TATTCTCAATTAGAATATATTTATAAAATAAATAAAATTTAATTTAAA
66 TATTCTCAATTGGCATATATTTATAAAATAAATAAAATTTAATTTAAA
*
3875422 AATATTAAAATCTTAAATTAAATATAAATAATTTTTGTAGATTTTTAAGCAATTTAAGTGTTATC
1 AATATTAAAATCTTAAATTAAATATAAATAATTTTT-TAGATTTTTTAGCAATTTAAGTGTTATC
*
3875487 ATATTCTCAATTGGCATAGATTTATAAAATAAAT-AAATTTAATTTAAA
65 ATATTCTCAATTGGCATATATTTATAAAATAAATAAAATTTAATTTAAA
* *
3875535 AATATTAAAATCATAAATTAAAAATAAAT-ATTTTTTAGATTTTTTTAGCAATTTAAGTGTTATC
1 AATATTAAAATCTTAAATTAAATATAAATAATTTTTTAGA-TTTTTTAGCAATTTAAGTGTTATC
* *
3875599 ATATTTTCAATTGGCGTATATTTA
65 ATATTCTCAATTGGCATATATTTA
3875623 CGTACTCACT
Statistics
Matches: 185, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
111 4 0.02
112 84 0.45
113 43 0.23
114 54 0.29
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (113 bp):
AATATTAAAATCTTAAATTAAATATAAATAATTTTTTAGATTTTTTAGCAATTTAAGTGTTATCA
TATTCTCAATTGGCATATATTTATAAAATAAATAAAATTTAATTTAAA
Found at i:3876831 original size:52 final size:51
Alignment explanation
Indices: 3876735--3876841 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 51
3876725 GAAAAATAAG
*
3876735 AAAACAAAACAAATAGCATCATCTTAATGTTCCAAGCTATACACTTAAACA
1 AAAACAAAACAAATAGCATCATCATAATGTTCCAAGCTATACACTTAAACA
* * * *
3876786 AAAATAAAAGCAAATAGCATCATCATAAT-TTTCAAGTTGTGACACTTAAACA
1 AAAACAAAA-CAAATAGCATCATCATAATGTTCCAAGCTAT-ACACTTAAACA
3876838 AAAA
1 AAAA
3876842 ACTAAATGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 16 0.33
52 33 0.67
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.24
Consensus pattern (51 bp):
AAAACAAAACAAATAGCATCATCATAATGTTCCAAGCTATACACTTAAACA
Found at i:3886377 original size:23 final size:24
Alignment explanation
Indices: 3886334--3886388 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
3886324 TGTTTGTTTG
** *
3886334 TTTATTTTT-ATTTGTTTTATTTC
1 TTTATTTTTAATTTGTAATATTAC
3886357 TTTATTTTTAATTT-TAATATTAC
1 TTTATTTTTAATTTGTAATATTAC
3886380 TTT-TTTTTA
1 TTTATTTTTA
3886389 GGACAAAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.21
23 18 0.64
24 4 0.14
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTATTTTTAATTTGTAATATTAC
Found at i:3888609 original size:22 final size:23
Alignment explanation
Indices: 3888584--3888630 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3888574 GGTGGTTGGG
*
3888584 TTAATGG-ATTTTTAACTTTATT
1 TTAATGGTATATTTAACTTTATT
*
3888606 TTAATGGTATATTTAAGTTTATT
1 TTAATGGTATATTTAACTTTATT
3888629 TT
1 TT
3888631 GGTTCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.60
Consensus pattern (23 bp):
TTAATGGTATATTTAACTTTATT
Found at i:3889878 original size:24 final size:24
Alignment explanation
Indices: 3889851--3889905 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
3889841 CCGGTCCAGC
*
3889851 CGAGCCAAGCCAAGTGATCCAAGT
1 CGAGCCAAGCCAAGTGAACCAAGT
* ** *
3889875 CGAGTCGTGCCAAGTGAACCGAGT
1 CGAGCCAAGCCAAGTGAACCAAGT
*
3889899 CAAGCCA
1 CGAGCCA
3889906 GTCGAATCGA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (24 bp):
CGAGCCAAGCCAAGTGAACCAAGT
Found at i:3889976 original size:18 final size:18
Alignment explanation
Indices: 3889950--3889984 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3889940 TGAGCCATTG
*
3889950 ACCGTTGATCAGTCGTTA
1 ACCGGTGATCAGTCGTTA
*
3889968 ACCGGTGATCGGTCGTT
1 ACCGGTGATCAGTCGTT
3889985 GACTGCCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (18 bp):
ACCGGTGATCAGTCGTTA
Found at i:3897023 original size:2 final size:2
Alignment explanation
Indices: 3897016--3897069 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3897006 TACAACTTTA
3897016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3897058 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3897070 GATGAATGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3897672 original size:23 final size:23
Alignment explanation
Indices: 3897629--3897786 Score: 89
Period size: 23 Copynumber: 6.7 Consensus size: 23
3897619 CCCTTAAACC
3897629 TATAATATATTATATATTATAAG
1 TATAATATATTATATATTATAAG
* **
3897652 TATAATGTATTATATGA-TATACT
1 TATAATATATTATAT-ATTATAAG
3897675 TAT-ATA-AGTGTATA-ATTATAAG
1 TATAATATA-T-TATATATTATAAG
*
3897697 TATACATTATATATATATATATATATATA
1 TATA-A-TATAT-TATATAT-TATA-A-G
3897726 TATAATATA-TATATA-TATATA-
1 TATAATATATTATATATTATA-AG
*
3897747 TATATATATATATATATATATAAAAG
1 TATA-ATATAT-TATATAT-TATAAG
*
3897773 TAT-ATATATAATAT
1 TATAATATATTATAT
3897787 TTCATAACTA
Statistics
Matches: 107, Mismatches: 10, Indels: 36
0.70 0.07 0.24
Matches are distributed among these distances:
21 6 0.06
22 15 0.14
23 35 0.33
24 14 0.13
25 14 0.13
26 9 0.08
27 8 0.07
28 2 0.02
29 4 0.04
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (23 bp):
TATAATATATTATATATTATAAG
Found at i:3897698 original size:45 final size:46
Alignment explanation
Indices: 3897639--3897781 Score: 140
Period size: 45 Copynumber: 3.2 Consensus size: 46
3897629 TATAATATAT
3897639 TATATATTATAAGTATA-ATGTAT-TATATGATATACT-TATATAAGTG
1 TATATATTATAAGTATACAT-TATATATAT-ATATA-TATATATAAGTG
*
3897685 TATA-ATTATAAGTATACATTATATATATATATATATATAT-A-TA
1 TATATATTATAAGTATACATTATATATATATATATATATATAAGTG
* * *
3897728 TA-ATATATATATA-TATATATATATATATATATATATATATAAAAGTA
1 TATATAT-TATA-AGTATACAT-TATATATATATATATATATATAAGTG
3897775 TATATAT
1 TATATAT
3897782 AATATTTCAT
Statistics
Matches: 84, Mismatches: 3, Indels: 18
0.80 0.03 0.17
Matches are distributed among these distances:
42 1 0.01
43 5 0.06
44 12 0.14
45 46 0.55
46 12 0.14
47 4 0.05
48 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (46 bp):
TATATATTATAAGTATACATTATATATATATATATATATATAAGTG
Found at i:3897711 original size:2 final size:2
Alignment explanation
Indices: 3897704--3897786 Score: 127
Period size: 2 Copynumber: 42.5 Consensus size: 2
3897694 AAGTATACAT
3897704 TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
*
3897745 TA TA TA TA TA TA TA TA TA TA TA TA -A AA GTA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
3897786 T
1 T
3897787 TTCATAACTA
Statistics
Matches: 76, Mismatches: 1, Indels: 8
0.89 0.01 0.09
Matches are distributed among these distances:
1 3 0.04
2 72 0.95
3 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3898533 original size:2 final size:2
Alignment explanation
Indices: 3898526--3898560 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3898516 GTTAGAAATA
3898526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3898561 ATTTATTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3898957 original size:11 final size:11
Alignment explanation
Indices: 3898926--3898976 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
3898916 TCAATATTAA
*
3898926 ATATCTAATAC
1 ATATATAATAC
3898937 ATA-ATCAATAC
1 ATATAT-AATAC
3898948 ATATATAATAC
1 ATATATAATAC
* *
3898959 -TATATATTAT
1 ATATATAATAC
3898969 ATATATAA
1 ATATATAA
3898977 AAATAGCTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 9 0.27
11 22 0.67
12 2 0.06
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATATAATAC
Found at i:3902678 original size:16 final size:16
Alignment explanation
Indices: 3902657--3902687 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3902647 AATAATAATA
*
3902657 TAAAAAAATTAATAAG
1 TAAAAAAATAAATAAG
3902673 TAAAAAAATAAATAA
1 TAAAAAAATAAATAA
3902688 CCAGAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
TAAAAAAATAAATAAG
Found at i:3902682 original size:29 final size:27
Alignment explanation
Indices: 3902633--3902687 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
3902623 GAAAAGAAAG
* * *
3902633 AAAATAATAATTATAATAATAATATAAA
1 AAAATAATAAGTAAAAAAATAA-ATAAA
3902661 AAAATTAATAAGTAAAAAAATAAATAA
1 AAAA-TAATAAGTAAAAAAATAAATAA
3902688 CCAGAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (27 bp):
AAAATAATAAGTAAAAAAATAAATAAA
Found at i:3903184 original size:134 final size:133
Alignment explanation
Indices: 3902809--3903828 Score: 1098
Period size: 134 Copynumber: 7.7 Consensus size: 133
3902799 GAAATATGAC
* * *
3902809 GAGGGATCTGTTATGCTTCTTCTTGAGGG-AAATCAGATATGGGGATGTTGATTCATTCCACTGT
1 GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATTCATTCCACTTT
* * * * * *
3902873 CACTCAAGGAAGATTGAATCGAGACAGACTTGCTCCACTGTTATTCAGGGAATATCAAATATTAA
66 CACTC-AGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGA
*
3902938 AATA
130 AAGA
* * * * *
3902942 GAGGGATTTGTTCTACTTCTTCCTGAGGGAAAATCAGATAC--GGGATGTTGATTCATT-CAATT
1 GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGAT-CTGGGGATGTTGATTCATTCCACTT
*
3903004 GTCACTCAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTATCACTCAGGGAATATCAAATCTT
65 -TCACTC-AGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTT
3903069 GAAAGA
128 GAAAGA
* * *
3903075 GAGGGATATGTTTTTCTTTTTCTTGAGGGAAAATCAGATCTGGGGGA-GTTGATTCATTCCACTT
1 GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCT-GGGGATGTTGATTCATTCCACTT
* * *
3903139 TCATTCACGGAAGATTAAATTGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
65 TCACTCA-GGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
3903204 AAAGA
129 AAAGA
* * * * * * * *
3903209 GATGGATCTATTCTGTTTCTTCTTGAGGGAATATCATATATGAGGGA-GTTGATTCATTCCACTA
1 GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTG-GGGATGTTGATTCATTCCACTT
* ** *
3903273 TCACTTAGAGAAGATTGAATCGAGATAGACTTGTTCCACTATCACTCAGGGAATATCAAATCTTG
65 TCACTCAG-GAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
*
3903338 AAAAA
129 AAAGA
* * * * *
3903343 GAAGGATCTGTTCTGCTTCTTCTTGAGGGAAGATCATATCTGGAGATGTTGATTCATTCCACTGT
1 GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATTCATTCCACT-T
* * * * * *
3903408 T-ACTCAGAGAAGATTGGATCGAGGTAGACTTATTTCTCTTTCACTCAGGGAATATCAAATCTTG
65 TCACTCAG-GAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
3903472 AAAGA
129 AAAGA
* **
3903477 GAGGGA-CTTGTTTCGCTTCTTCTTGAGGGAAAATCAGATCCAGGGATGTTGATTCATTCCA-TT
1 GAGGGATC-TGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATTCATTCCACTT
* * * * *
3903540 GGCACTTAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATATT
65 -TCACTCA-GGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTT
3903605 GAAAGA
128 GAAAGA
* ** * * * * * * *
3903611 GATGGATCTGTTCCGCTTTTTCTTGAGGAAAAATCAGATATGGAGACGTTGATTCATTCTACTGT
1 GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATTCATTCCACTTT
* * *
3903676 CACTCAGGGAAGATTGAATCGAGG-ATGACTTGTTCCATTGTTACTCAGGGAATATCAAATCTAG
66 CACTCA-GGAAGATTGAATCGAGGCA-GACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTG
3903740 AAAGA
129 AAAGA
* * ** * * * *
3903745 GATGGATCTATTTCACTTTTTCTTGAGGGAAAATAAGATTTGGGGATGCT-A---ATTCCACTGT
1 GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATTCATTCCACT-T
*
3903806 TC-CTTAGGGAAGATTGAATCGAG
65 TCACTCA-GGAAGATTGAATCGAG
3903829 CTCGATTCAT
Statistics
Matches: 763, Mismatches: 104, Indels: 43
0.84 0.11 0.05
Matches are distributed among these distances:
130 27 0.04
131 2 0.00
132 5 0.01
133 147 0.19
134 570 0.75
135 12 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (133 bp):
GAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATTCATTCCACTTT
CACTCAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAA
AGA
Found at i:3903598 original size:402 final size:401
Alignment explanation
Indices: 3902825--3903783 Score: 1251
Period size: 402 Copynumber: 2.4 Consensus size: 401
3902815 TCTGTTATGC
*
3902825 TTCTTCTTGAGGGAAATCAGATATGGGGATGTTGATTCATTCCACTGTCACTCA-AGGAAGATTG
1 TTCTTCTTGAGGGAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACTCAGA-GAAGATTG
* * * * * *
3902889 AATCGAGACAGACTTGCTCCACTGTTATTCAGGGAATATCAAATATT-AAAATAGAGGGATTTGT
65 AATCGAGATAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAA-AGAAGGATCTGT
* *
3902953 TCTACTTCTTCCTGAGGGAAAATCAGATACGGGATGTTGATTCATTCAATTGTCACTCAAGGAAG
129 TCTACTTCTTCTTGAGGGAAAATCAGATACGGGATGTTGATTCATTCAACTGTCACTCAAGGAAG
*
3903018 ATTGAATCGAGGCAGACTTGTTCCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
194 ATTGAATCGAGGCAGACTTATTCCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
** * ** *
3903083 TGTTTTTCTTTTTCTTGAGGGAAAATCAGATCTGGGGGAGTTGATTCATTCCACTTTCATTCACG
259 TGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTCAGGGAGTTGATTCATTCCACTTGCATTCACG
* *
3903148 GAAGATTAAATTGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGATG
324 GAAGATTAAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATATTGAAAGAGATG
*
3903213 GATCTATTCTG-T
389 GATCTATTCCGCT
* * *
3903225 TTCTTCTTGAGGGAATATCATATATGAGGGA-GTTGATTCATTCCACTATCACTTAGAGAAGATT
1 TTCTTCTTGAGGGAA-ATCAGATATG-GGGACGTTGATTCATTCCACTGTCACTCAGAGAAGATT
* *
3903289 GAATCGAGATAGACTTGTTCCACTATCACTCAGGGAATATCAAATCTTGAAAAAGAAGGATCTGT
64 GAATCGAGATAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAAAGAAGGATCTGT
* * * * *
3903354 TCTGCTTCTTCTTGAGGGAAGATCATAT-CTGGAGATGTTGATTCATTCCACTGTTACTC-AGAG
129 TCTACTTCTTCTTGAGGGAAAATCAGATAC-GG-GATGTTGATTCATTCAACTGTCACTCAAG-G
* * * * *
3903417 AAGATTGGATCGAGGTAGACTTATTTCTCTTTCACTCAGGGAATATCAAATCTTGAAAGAGAGGG
191 AAGATTGAATCGAGGCAGACTTATTCCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGG
3903482 ACT-TGTTTCGCTTCTTCTTGAGGGAAAATCAGATC-CAGGGATGTTGATTCATTCCA-TTGGCA
256 A-TATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTCAGGGA-GTTGATTCATTCCACTT-GCA
* * * *
3903544 CTT-AGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATATTGAA
318 -TTCACGGAAGATTAAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATATTGAA
*
3903608 AGAGATGGATCTGTTCCGCT
382 AGAGATGGATCTATTCCGCT
* * * *
3903628 TT-TTCTTGAGGAAAAATCAGATATGGAGACGTTGATTCATTCTACTGTCACTCAGGGAAGATTG
1 TTCTTCTTGAGG-GAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACTCAGAGAAGATTG
* * * * *
3903692 AATCGAGGAT-GACTTGTTCCATTGTTACTCAGGGAATATCAAATCTAGAAAGAGATGGATCTAT
65 AATCGA-GATAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAAAGAAGGATCTGT
* *
3903756 T-TCACTTTTTCTTGAGGGAAAATAAGAT
129 TCT-ACTTCTTCTTGAGGGAAAATCAGAT
3903784 TTGGGGATGC
Statistics
Matches: 486, Mismatches: 57, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
400 16 0.03
401 128 0.26
402 331 0.68
403 11 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (401 bp):
TTCTTCTTGAGGGAAATCAGATATGGGGACGTTGATTCATTCCACTGTCACTCAGAGAAGATTGA
ATCGAGATAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAAAGAAGGATCTGTTC
TACTTCTTCTTGAGGGAAAATCAGATACGGGATGTTGATTCATTCAACTGTCACTCAAGGAAGAT
TGAATCGAGGCAGACTTATTCCACTATCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATG
TTTCGCTTCTTCTTGAGGGAAAATCAGATCTCAGGGAGTTGATTCATTCCACTTGCATTCACGGA
AGATTAAATCGAGGCAGACTTGTTCCACTGTCACTCAGGGAATATCAAATATTGAAAGAGATGGA
TCTATTCCGCT
Done.