Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008092.1 Hibiscus syriacus cultivar Beakdansim tig00110607_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: 2324158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:1979268 original size:21 final size:22
Alignment explanation
Indices: 1979233--1979278 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1979223 ATAACAGTAT
1979233 TGTAGCAGAGGAATCGGTACCC
1 TGTAGCAGAGGAATCGGTACCC
*
1979255 TGTAGCAG-GGAATCGGTTCCC
1 TGTAGCAGAGGAATCGGTACCC
1979276 TGT
1 TGT
1979279 TTGTAATCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.24
Consensus pattern (22 bp):
TGTAGCAGAGGAATCGGTACCC
Found at i:1979846 original size:20 final size:21
Alignment explanation
Indices: 1979818--1979869 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1979808 AGCCAGATTT
* *
1979818 GGTACCGATACTCAAGGG-TC
1 GGTATCGATACTAAAGGGCTC
* *
1979838 GGTATCGATTCTAAAGGGCTT
1 GGTATCGATACTAAAGGGCTC
*
1979859 AGTATCGATAC
1 GGTATCGATAC
1979870 CATCATACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
GGTATCGATACTAAAGGGCTC
Found at i:1980518 original size:65 final size:64
Alignment explanation
Indices: 1980393--1980548 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 64
1980383 ACACCCTAAT
* * * * *
1980393 TCGAATGCATTTTGTGTACCGATGTACATCCATGCATCGATGCACTCTTGATTTTATTGAAACA
1 TCGAATGCATTTTATTTACCGATGCACATCCATGCATCGATACACTCTTGATCTTATTGAAACA
* *
1980457 TCGAATGCATTTTATTTACCGATGCATATACCATGCATCGATACACTCTTGGCTCTT-TTGAAAC
1 TCGAATGCATTTTATTTACCGATGCACAT-CCATGCATCGATACACTCTT-GATCTTATTGAAAC
1980521 A
64 A
* *
1980522 TCGAATGTA-ATTAGTTTACCGATGCAC
1 TCGAATGCATTTTA-TTTACCGATGCAC
1980549 CCCAAGTGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 28 0.35
65 47 0.59
66 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (64 bp):
TCGAATGCATTTTATTTACCGATGCACATCCATGCATCGATACACTCTTGATCTTATTGAAACA
Found at i:1987114 original size:20 final size:18
Alignment explanation
Indices: 1987089--1987126 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
1987079 GGAGAAATCT
1987089 CAATGGAACATCAACAACAA
1 CAATGGAAC-T-AACAACAA
1987109 CAATGGAACTAACAACAA
1 CAATGGAACTAACAACAA
1987127 TGAATCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.55, C:0.24, G:0.11, T:0.11
Consensus pattern (18 bp):
CAATGGAACTAACAACAA
Found at i:1991056 original size:17 final size:16
Alignment explanation
Indices: 1991028--1991059 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1991018 ATACTATCAG
1991028 AAAATAATATATGATA
1 AAAATAATATATGATA
1991044 AAAATATATATATGAT
1 AAAATA-ATATATGAT
1991060 TTAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAAATAATATATGATA
Found at i:1992766 original size:25 final size:26
Alignment explanation
Indices: 1992734--1992792 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
1992724 TTGTTGGAAT
1992734 TAATTAATTTATT-TTAATATATATAA
1 TAATTAATTTATTATTAATAT-TATAA
*
1992760 T-ATTAA-TTATTATTATTATTATAA
1 TAATTAATTTATTATTAATATTATAA
1992784 TAATTAATT
1 TAATTAATT
1992793 GAATTTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 11 0.38
25 16 0.55
26 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATTAATTTATTATTAATATTATAA
Found at i:1996514 original size:18 final size:18
Alignment explanation
Indices: 1996493--1996533 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1996483 GGCAGTATTT
* *
1996493 ATTTTTTATTACTTTATA
1 ATTTTTTAATAATTTATA
*
1996511 ATTTTTTAATAATTTATT
1 ATTTTTTAATAATTTATA
1996529 ATTTT
1 ATTTT
1996534 ATAGCTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTTTAATAATTTATA
Found at i:1996608 original size:23 final size:23
Alignment explanation
Indices: 1996577--1996622 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1996567 TTAATAGTTT
*
1996577 TTTAGTTTTAATAATTTTTAATA
1 TTTAGTTTTAATAATTTTGAATA
* * *
1996600 TTTATTTTTTATACTTTTGAATA
1 TTTAGTTTTAATAATTTTGAATA
1996623 ATTTTGTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
TTTAGTTTTAATAATTTTGAATA
Found at i:1996625 original size:33 final size:31
Alignment explanation
Indices: 1996574--1996645 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 31
1996564 TCATTAATAG
*
1996574 TTTTTTAGTTTTAATAATTTT-TAATATTTAT
1 TTTTTTACTTTTAATAATTTTGTAA-ATTTAT
1996605 TTTTTATACTTTTGAATAATTTTGTAAATTTAACT
1 TTTTT-TACTTTT-AATAATTTTGTAAATTT-A-T
1996640 TTTTTT
1 TTTTTT
1996646 TTTTAAAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 5 0.14
32 6 0.17
33 13 0.37
34 5 0.14
35 6 0.17
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (31 bp):
TTTTTTACTTTTAATAATTTTGTAAATTTAT
Found at i:2001425 original size:36 final size:35
Alignment explanation
Indices: 2001354--2001466 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 35
2001344 AAAACAATCC
* * *
2001354 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
*
2001389 TCAATTTCATTCTAAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCT-AAACCCCAAATTCTAAAATAAT
** *
2001425 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
2001460 TCAATTT
1 TCAATTT
2001467 AAGGTTTAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 39 0.57
36 29 0.43
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:2003299 original size:35 final size:35
Alignment explanation
Indices: 2003225--2003335 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
2003215 TCTAAACCTT
* * *
2003225 AAATTGAAGTATTTTAGAA-TTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
* * *
2003259 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
*
2003294 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATA
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
2003329 AAATTGA
1 AAATTGA
2003336 GGACTGTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
34 16 0.24
35 51 0.76
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATA
Found at i:2005948 original size:26 final size:26
Alignment explanation
Indices: 2005908--2005961 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2005898 TATTTGTCTC
* *
2005908 ATTGAATTGACACACTGAAAGAACAT
1 ATTGAAATGAAACACTGAAAGAACAT
*
2005934 ATTGAAATGAAACACTGAGAGAACAT
1 ATTGAAATGAAACACTGAAAGAACAT
2005960 AT
1 AT
2005962 CAAAACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (26 bp):
ATTGAAATGAAACACTGAAAGAACAT
Found at i:2006783 original size:21 final size:20
Alignment explanation
Indices: 2006759--2006797 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2006749 TCCTCAATCG
*
2006759 TATTTACGCTCACTCACTTTT
1 TATTCACGCTCACT-ACTTTT
2006780 TATTCACGCTCACTACTT
1 TATTCACGCTCACTACTT
2006798 CACACCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.44
Consensus pattern (20 bp):
TATTCACGCTCACTACTTTT
Found at i:2006938 original size:160 final size:160
Alignment explanation
Indices: 2006650--2006970 Score: 617
Period size: 160 Copynumber: 2.0 Consensus size: 160
2006640 TCAATATTAC
2006650 AATACTGCAATACTAGCTGCTGCTAGTTTACAAACTCACCAATATATTTAAAGCTTTGCTAAGCT
1 AATACTGCAATACTAGCTGCTGCTAGTTTACAAACTCACCAATATATTTAAAGCTTTGCTAAGCT
2006715 TCACAATATATCTCTCAAATCTTTATTTTTTTACTCCTCAATCGTATTTACGCTCACTCACTTTT
66 TCACAATATATCTCTCAAATCTTTATTTTTTTACTCCTCAATCGTATTTACGCTCACTCACTTTT
2006780 TATTCACGCTCACTACTTCACACCAACTAA
131 TATTCACGCTCACTACTTCACACCAACTAA
2006810 AATACTGCAATACTAGCTGCTGCTAGTTTACAAACTCACCAATATATTTAAAGCTTTGCTAAGCT
1 AATACTGCAATACTAGCTGCTGCTAGTTTACAAACTCACCAATATATTTAAAGCTTTGCTAAGCT
*
2006875 TCACAATATATCTCTCAAAATCTTTTTTTTTTTACTCCTCAATCGTATTTACGCTCA-TCACTTT
66 TCACAATATATCTCTC-AAATCTTTATTTTTTTACTCCTCAATCGTATTTACGCTCACTCACTTT
2006939 TTATTCACGCTCACTACTTCACACCAACTAA
130 TTATTCACGCTCACTACTTCACACCAACTAA
2006970 A
1 A
2006971 GGCTAAGCAC
Statistics
Matches: 159, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
160 120 0.75
161 39 0.25
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (160 bp):
AATACTGCAATACTAGCTGCTGCTAGTTTACAAACTCACCAATATATTTAAAGCTTTGCTAAGCT
TCACAATATATCTCTCAAATCTTTATTTTTTTACTCCTCAATCGTATTTACGCTCACTCACTTTT
TATTCACGCTCACTACTTCACACCAACTAA
Found at i:2018669 original size:29 final size:29
Alignment explanation
Indices: 2018628--2018703 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
2018618 AGGCCTCCAT
* * *
2018628 TTTTTTGTATTTATAATTAGGGACCCC-AA
1 TTTTTTATATTTATAACTAAGG-CCCCTAA
2018657 TTTTTTATATTTATAACTAAGGCCCCTAA
1 TTTTTTATATTTATAACTAAGGCCCCTAA
2018686 TTTTTTATAATTTCATAA
1 TTTTTTAT-ATTT-ATAA
2018704 AATTTCTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
28 4 0.10
29 29 0.71
30 4 0.10
31 4 0.10
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (29 bp):
TTTTTTATATTTATAACTAAGGCCCCTAA
Found at i:2018790 original size:118 final size:118
Alignment explanation
Indices: 2018653--2018888 Score: 361
Period size: 118 Copynumber: 2.0 Consensus size: 118
2018643 ATTAGGGACC
*
2018653 CCAATTTTTTATATTTATAACTAAGGCCCCTAATTTTTTATAATTTCATAAAAT-TTCTAGTTTT
1 CCAATTTTTTATATTTATAACTAAGGCCCCTAA-TTTTTAGAATTTCATAAAATGTT-TAGTTTT
*
2018717 TTA-CCT-CTTTTACCATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAA
64 TGACCCTCCTTTT-CCATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAA
* * *
2018771 CCAATTTTTTATATTTATAATTAGGGCCCTTAATTTTTAGAATTTCATAAAATGTTTAGTTTTTG
1 CCAATTTTTTATATTTATAACTAAGGCCCCTAATTTTTAGAATTTCATAAAATGTTTAGTTTTTG
* *
2018836 ACCCTCCTTTTCCATTTCTCTTATTTATTCATTGAATTTTGAATTAAATTTAA
66 ACCCTCCTTTTCCATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAA
2018889 TCATAATTTT
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
117 28 0.26
118 75 0.69
119 5 0.05
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (118 bp):
CCAATTTTTTATATTTATAACTAAGGCCCCTAATTTTTAGAATTTCATAAAATGTTTAGTTTTTG
ACCCTCCTTTTCCATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAA
Found at i:2021490 original size:28 final size:29
Alignment explanation
Indices: 2021433--2021487 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
2021423 ATATATGGGT
*
2021433 TAAATTGATTTTTTTTTAAGTTTGAAGGC
1 TAAATTGATTTTTTTTTAAGTTTCAAGGC
2021462 TAAATTGA-TTTTTTTTAAG-TTCAAGG
1 TAAATTGATTTTTTTTTAAGTTTCAAGG
2021488 GCTTATTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.24
28 11 0.44
29 8 0.32
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (29 bp):
TAAATTGATTTTTTTTTAAGTTTCAAGGC
Found at i:2021501 original size:28 final size:28
Alignment explanation
Indices: 2021433--2021501 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
2021423 ATATATGGGT
*
2021433 TAAATTGATTTTTTTTTAAGTTTGAAGGC
1 TAAATTG-TTTTTTTTTAAGTTTCAAGGC
*
2021462 TAAATTGATTTTTTTTAAG-TTCAAGGGC
1 TAAATTGTTTTTTTTTAAGTTTCAA-GGC
* *
2021490 TTATTTGTTTTT
1 TAAATTGTTTTT
2021502 AAATTACAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 4 0.12
28 23 0.68
29 7 0.21
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (28 bp):
TAAATTGTTTTTTTTTAAGTTTCAAGGC
Found at i:2022053 original size:23 final size:21
Alignment explanation
Indices: 2022006--2022053 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
2021996 TTAATGATGT
* *
2022006 TTTTATATTTAACTTAATATT
1 TTTTATATTTAACTTAAAATA
*
2022027 TTTTATATTTTCAATTTAAAATA
1 TTTTATA-TTT-AACTTAAAATA
2022050 TTTT
1 TTTT
2022054 TTAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 7 0.32
22 3 0.14
23 12 0.55
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTATATTTAACTTAAAATA
Found at i:2023661 original size:29 final size:29
Alignment explanation
Indices: 2023628--2023688 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2023618 CCAACAATAC
2023628 AACTCACCTGGTTGATGCATGTATTGTGA
1 AACTCACCTGGTTGATGCATGTATTGTGA
2023657 AACTCACCTGGTTGATGCATGTATTGTGA
1 AACTCACCTGGTTGATGCATGTATTGTGA
2023686 AAC
1 AAC
2023689 ACGTCCAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (29 bp):
AACTCACCTGGTTGATGCATGTATTGTGA
Found at i:2037588 original size:2 final size:2
Alignment explanation
Indices: 2037581--2037635 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2037571 AGTAGCATTG
2037581 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
2037623 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2037636 ATAAAATGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2038275 original size:21 final size:21
Alignment explanation
Indices: 2038251--2038318 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
2038241 CTATGTGATC
2038251 CTTCGGGACAATTATGTGGCA
1 CTTCGGGACAATTATGTGGCA
* *
2038272 CTTCGGTG-CAAACCTATGTAGTC-
1 CTTCGG-GAC-AA-TTATGT-GGCA
*
2038295 CTCCGGGACAATTATGTGGCA
1 CTTCGGGACAATTATGTGGCA
2038316 CTT
1 CTT
2038319 TGGTGCAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
20 2 0.06
21 14 0.40
22 6 0.17
23 11 0.31
24 2 0.06
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (21 bp):
CTTCGGGACAATTATGTGGCA
Found at i:2038302 original size:44 final size:44
Alignment explanation
Indices: 2038241--2038327 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
2038231 GTCGAGGGTT
*
2038241 CTATGTGATCCTTCGGGACAATTATGTGGCACTTCGGTGCAAAC
1 CTATGTGATCCTCCGGGACAATTATGTGGCACTTCGGTGCAAAC
*
2038285 CTATGT-AGTCCTCCGGGACAATTATGTGGCACTTTGGTGCAAA
1 CTATGTGA-TCCTCCGGGACAATTATGTGGCACTTCGGTGCAAA
2038328 TTACGAGCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (44 bp):
CTATGTGATCCTCCGGGACAATTATGTGGCACTTCGGTGCAAAC
Found at i:2039056 original size:16 final size:17
Alignment explanation
Indices: 2039027--2039062 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2039017 GAATTTTAGT
2039027 TGTTTTGTAAAAGTAAA
1 TGTTTTGTAAAAGTAAA
*
2039044 TGTTTTG-AAAAGTCAA
1 TGTTTTGTAAAAGTAAA
2039060 TGT
1 TGT
2039063 GACACCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (17 bp):
TGTTTTGTAAAAGTAAA
Found at i:2039144 original size:21 final size:21
Alignment explanation
Indices: 2039119--2039171 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
2039109 AGACAACCCT
2039119 TTACCGGCACCCACGACAAGC
1 TTACCGGCACCCACGACAAGC
*
2039140 TTACCGGTACCCACGACAAGC
1 TTACCGGCACCCACGACAAGC
2039161 TTACCGGCACC
1 TTACCGGCACC
2039172 ATGAAAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.42, G:0.19, T:0.13
Consensus pattern (21 bp):
TTACCGGCACCCACGACAAGC
Found at i:2039748 original size:16 final size:17
Alignment explanation
Indices: 2039719--2039754 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2039709 GAATTTTAGT
2039719 TGTTTTGTAAAAGTAAA
1 TGTTTTGTAAAAGTAAA
*
2039736 TGTTTTG-AAAAGTTAA
1 TGTTTTGTAAAAGTAAA
2039752 TGT
1 TGT
2039755 GACACCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.44
Consensus pattern (17 bp):
TGTTTTGTAAAAGTAAA
Found at i:2041403 original size:13 final size:13
Alignment explanation
Indices: 2041330--2041408 Score: 54
Period size: 13 Copynumber: 5.9 Consensus size: 13
2041320 TATTACAAAC
2041330 TAAATAATAAAAA-
1 TAAATAA-AAAAAT
2041343 T-AATAAAAACAAT
1 TAAATAAAAA-AAT
** *
2041356 TAAATTGAAACAT
1 TAAATAAAAAAAT
**
2041369 TAAATACAAATGAT
1 TAAATA-AAAAAAT
*
2041383 ACAAATAAAAAAAT
1 -TAAATAAAAAAAT
2041397 TAAATAAAAAAA
1 TAAATAAAAAAA
2041409 CATTAACAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
11 3 0.06
12 7 0.14
13 20 0.40
14 15 0.30
15 5 0.10
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (13 bp):
TAAATAAAAAAAT
Found at i:2041931 original size:21 final size:21
Alignment explanation
Indices: 2041890--2041931 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2041880 AAACCTTATG
* *
2041890 GTGGTGGCATCTGAACCGGCT
1 GTGGTGGCATCTAAAACGGCT
*
2041911 GTGGTGGCATCTAAAATGGCT
1 GTGGTGGCATCTAAAACGGCT
2041932 ACAGTGGTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (21 bp):
GTGGTGGCATCTAAAACGGCT
Found at i:2048563 original size:3 final size:3
Alignment explanation
Indices: 2048555--2048631 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
2048545 TTTTTACCCA
*
2048555 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2048603 TAT TAC TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2048632 AATATATATT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2049201 original size:15 final size:15
Alignment explanation
Indices: 2049181--2049222 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2049171 ACCACTCAGC
2049181 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
2049196 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
2049211 AAAGAAGAGAAA
1 AAAGAAAAGAAA
2049223 CTTACTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:2049206 original size:20 final size:20
Alignment explanation
Indices: 2049181--2049222 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2049171 ACCACTCAGC
*
2049181 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
2049201 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
2049221 AA
1 AA
2049223 CTTACTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:2050097 original size:13 final size:13
Alignment explanation
Indices: 2050081--2050120 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2050071 ATATAATAAA
2050081 TAAATATTTATTT
1 TAAATATTTATTT
*
2050094 TAAATAAATTATTT
1 TAAAT-ATTTATTT
2050108 T-AATATTTATTT
1 TAAATATTTATTT
2050120 T
1 T
2050121 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:2050798 original size:17 final size:17
Alignment explanation
Indices: 2050769--2050812 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2050759 TTAATTTTTT
*
2050769 AATTTTT-TCTTTTCAA
1 AATTTTTATATTTTCAA
*
2050785 AATTTTTATATTTTCAT
1 AATTTTTATATTTTCAA
*
2050802 AATATTTATAT
1 AATTTTTATAT
2050813 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTATATTTTCAA
Found at i:2050836 original size:15 final size:13
Alignment explanation
Indices: 2050816--2050853 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
2050806 TTTATATGTT
2050816 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
2050831 TTATTTTATTTCA
1 TTATTTTATTTCA
2050844 TTA-TTTATTT
1 TTATTTTATTT
2050854 TGTCAGAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:2054105 original size:16 final size:16
Alignment explanation
Indices: 2054086--2054119 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2054076 TTTGGGATCA
*
2054086 ATACCTTTTTGCATAC
1 ATACATTTTTGCATAC
2054102 ATACATTTTTGCATAC
1 ATACATTTTTGCATAC
2054118 AT
1 AT
2054120 TCATCATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (16 bp):
ATACATTTTTGCATAC
Found at i:2061413 original size:7 final size:7
Alignment explanation
Indices: 2061391--2061445 Score: 71
Period size: 7 Copynumber: 8.1 Consensus size: 7
2061381 AGAAAAAGTG
2061391 AAGAAGAA
1 AAGAA-AA
2061399 AA-AAAA
1 AAGAAAA
2061405 AAGAAAA
1 AAGAAAA
2061412 AA-AAAA
1 AAGAAAA
*
2061418 GAGAAAA
1 AAGAAAA
2061425 AAGAAAA
1 AAGAAAA
2061432 AAG-AAA
1 AAGAAAA
2061438 AAGAAAA
1 AAGAAAA
2061445 A
1 A
2061446 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 15 0.36
7 25 0.60
8 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:2061422 original size:27 final size:28
Alignment explanation
Indices: 2061392--2061446 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
2061382 GAAAAAGTGA
2061392 AGAAGAAAA-AAAAAAGAAAAA-AAAAAG
1 AGAA-AAAAGAAAAAAGAAAAAGAAAAAG
2061419 AGAAAAAAGAAAAAAGAAAAAGAAAAAG
1 AGAAAAAAGAAAAAAGAAAAAGAAAAAG
2061447 GGGGTCAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 4 0.15
27 16 0.62
28 6 0.23
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (28 bp):
AGAAAAAAGAAAAAAGAAAAAGAAAAAG
Found at i:2061424 original size:20 final size:20
Alignment explanation
Indices: 2061391--2061445 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
2061381 AGAAAAAGTG
*
2061391 AAGAAGAAAAAAAAAAGAAAA
1 AAGAA-AAAGAAAAAAGAAAA
2061412 AA-AAAAGAGAAAAAAGAAAA
1 AAGAAAA-AGAAAAAAGAAAA
2061432 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
2061446 GGGGGTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 2 0.06
20 23 0.74
21 6 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAGAAAAAGAAAAAAGAAAA
Found at i:2061783 original size:16 final size:16
Alignment explanation
Indices: 2061757--2061801 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2061747 TTTGAATACA
*
2061757 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
2061774 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
2061789 ATTCAATTTATTT
1 ATTCAATTTATTT
2061802 TTGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:2062868 original size:83 final size:83
Alignment explanation
Indices: 2062585--2063302 Score: 1313
Period size: 83 Copynumber: 8.7 Consensus size: 83
2062575 CATTAAATGA
*
2062585 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-TA-A
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2062648 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
2062666 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTGG-TA-
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTGGACAG
2062729 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
2062748 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2062813 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
2062831 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2062896 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
2062914 AAGATGAATTTGCCAATAGAATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2062979 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
2062997 AAGATGAATTTGCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2063062 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
2063080 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
2063145 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
2063163 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-TA-
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
2063226 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
2063245 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
2063303 TGGTAGGAAC
Statistics
Matches: 625, Mismatches: 8, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
81 61 0.10
82 156 0.25
83 404 0.65
84 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (83 bp):
AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACCAATCATTGAATTTAG
Found at i:2064482 original size:116 final size:116
Alignment explanation
Indices: 2064034--2064704 Score: 913
Period size: 116 Copynumber: 5.9 Consensus size: 116
2064024 ATTCAAATCT
* * *
2064034 ATCATTTGATGGATTATCTTTT-CCAGAGAAGGTTCATAATGAGAAGAACTCATCATCTGAAGGA
1 ATCACTTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
*
2064098 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTC
* *
2064150 ATCACTTGATGGATTATTTTTGCCAAAGAA-GTTCATAATGAGAAGAA--C-TCATTTGAAGAAG
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
* * *
2064211 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTC
* * * *
2064262 ATCAAATTGATGGATTAGCTTTT-CCAGAAAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGA
1 ATC-ACTTGATGGATTA-TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTCATCTGAAGA
*
2064323 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
64 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTC
*
2064376 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTTGTCATCTGAAGAAG
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
* *
2064441 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
66 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTC
* * *** *
2064492 ATCATTTGATGGATCAACGTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTCGTCATCTGAAGAA
*
2064556 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG---GAATTC
65 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTC
* *** *
2064605 ATCA-TTGGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 ATCACTT-GATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTCGTCATCTGAAGA
*
2064668 AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
64 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
2064705 TAATTCTATC
Statistics
Matches: 512, Mismatches: 32, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
112 69 0.13
113 155 0.30
114 86 0.17
115 24 0.05
116 178 0.35
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (116 bp):
ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTGAATTC
Found at i:2064642 original size:229 final size:227
Alignment explanation
Indices: 2064034--2064704 Score: 955
Period size: 229 Copynumber: 2.9 Consensus size: 227
2064024 ATTCAAATCT
* *
2064034 ATCATTTGATGGATTATCTTTTCCAGAGAAG-GTTCATAATGAGAAGAACTCATCATCTGAAGGA
1 ATCATTTGATGGATTAACTTTTCCAG-GAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
2064098 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGA
64 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG--TGAATTCATCACTTGATGGA
*
2064163 TTATTTTTGCCAA-AGAAGTTCATAATGAGAAGAAC--TCATTTGAAGAAGGAAGAAGAAGTTCA
127 TTATTTTTGCCAAGAG-AGTTCATAATGAGAAGAACTGTCATCTGAAGAAGGAAGAAGAAGTTCA
*
2064225 TAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
191 TAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTC
* * * *
2064262 ATCAAATTGATGGATTAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA--CTCATCTGAAGAAG
1 ATC-ATTTGATGGATTAACTTTTCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
2064325 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGAT
65 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG--TGAATTCATCACTTGATGGAT
2064390 TATTTTTGCC-AGAGAAGGTTCATAATGAGAAGAACTTGTCATCTGAAGAAGGAAGAAGAAGTTC
128 TATTTTTGCCAAGAG-A-GTTCATAATGAGAAGAAC-TGTCATCTGAAGAAGGAAGAAGAAGTTC
* *
2064454 ATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTC
190 ATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTC
* * * *
2064492 ATCATTTGATGGATCAACGTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCATTTGATGGATTAACTTTTCCAGGAAGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAG
* * *
2064557 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG-GAATTCATCA-TTGGATGGATC
65 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTGAATTCATCACTT-GATGGATT
***
2064620 AACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCAT
129 ATTTTTGCCAAG-AGAGTTCATAATGAGAAGAACT-GTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
2064685 AATAAGAAGAACTTGTTCAA
192 AATGAGAAGAACTTGTTCAA
2064705 TAATTCTATC
Statistics
Matches: 405, Mismatches: 24, Indels: 27
0.89 0.05 0.06
Matches are distributed among these distances:
225 1 0.00
226 91 0.22
227 19 0.05
228 8 0.02
229 164 0.40
230 66 0.16
231 3 0.01
232 53 0.13
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (227 bp):
ATCATTTGATGGATTAACTTTTCCAGGAAGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTGAATTCATCACTTGATGGATTAT
TTTTGCCAAGAGAGTTCATAATGAGAAGAACTGTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTTTATTTGAATTC
Found at i:2065029 original size:3 final size:3
Alignment explanation
Indices: 2065021--2065100 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
2065011 TTTTTACCCA
*
2065021 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2065069 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2065101 AATATATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2065670 original size:15 final size:15
Alignment explanation
Indices: 2065650--2065691 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
2065640 ACCACTCAGC
2065650 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
2065665 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
2065680 AAAGAAGAGAAA
1 AAAGAAAAGAAA
2065692 CTTACTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:2065675 original size:20 final size:20
Alignment explanation
Indices: 2065650--2065691 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2065640 ACCACTCAGC
*
2065650 AAAGAAACAGAAAAGAA-AGA
1 AAAGAAAAAG-AAAGAAGAGA
2065670 AAAGAAAAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAGA
2065690 AA
1 AA
2065692 CTTACTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAGAAGAGA
Found at i:2065878 original size:10 final size:10
Alignment explanation
Indices: 2065863--2065888 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2065853 GCCACCGGAT
2065863 GCGGTGGCCG
1 GCGGTGGCCG
2065873 GCGGTGGCCG
1 GCGGTGGCCG
2065883 GCGGTG
1 GCGGTG
2065889 ACAGTCACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.62, T:0.12
Consensus pattern (10 bp):
GCGGTGGCCG
Found at i:2066296 original size:28 final size:30
Alignment explanation
Indices: 2066245--2066300 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
2066235 TATATTTAGG
2066245 ATAAATAATAGATTTAATCCCTTAATTTTA
1 ATAAATAATAGATTTAATCCCTTAATTTTA
*
2066275 ATAAATAATA-TTTTAAT-CCTTAATTT
1 ATAAATAATAGATTTAATCCCTTAATTT
2066301 ATATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 9 0.36
29 6 0.24
30 10 0.40
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (30 bp):
ATAAATAATAGATTTAATCCCTTAATTTTA
Found at i:2066575 original size:13 final size:13
Alignment explanation
Indices: 2066559--2066598 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2066549 ATATAATAAA
2066559 TAAATATTTATTT
1 TAAATATTTATTT
*
2066572 TAAATAAATTATTT
1 TAAAT-ATTTATTT
2066586 T-AATATTTATTT
1 TAAATATTTATTT
2066598 T
1 T
2066599 TCAATATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:2067010 original size:13 final size:14
Alignment explanation
Indices: 2066994--2067022 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2066984 TGATGTTTTC
2066994 TTAAAAAAAA-AAT
1 TTAAAAAAAATAAT
2067007 TTAAAAAAAATAAT
1 TTAAAAAAAATAAT
2067021 TT
1 TT
2067023 TTAGGTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAAAAAATAAT
Found at i:2070312 original size:37 final size:37
Alignment explanation
Indices: 2070262--2070388 Score: 236
Period size: 37 Copynumber: 3.4 Consensus size: 37
2070252 TATACATACA
*
2070262 TGTTGATGAAATGTGTTGAAAATTACAATGAAGAAGG
1 TGTTGATAAAATGTGTTGAAAATTACAATGAAGAAGG
*
2070299 TGTTGATGAAATGTGTTGAAAATTACAATGAAGAAGG
1 TGTTGATAAAATGTGTTGAAAATTACAATGAAGAAGG
2070336 TGTTGATAAAATGTGTTGAAAATTACAATGAAGAAGG
1 TGTTGATAAAATGTGTTGAAAATTACAATGAAGAAGG
2070373 TGTTGATAAAATGTGT
1 TGTTGATAAAATGTGT
2070389 GAGAGACACA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 89 1.00
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.31
Consensus pattern (37 bp):
TGTTGATAAAATGTGTTGAAAATTACAATGAAGAAGG
Found at i:2072819 original size:9 final size:9
Alignment explanation
Indices: 2072807--2072879 Score: 67
Period size: 9 Copynumber: 7.6 Consensus size: 9
2072797 TTTATTATTT
2072807 TTATTAATA
1 TTATTAATA
2072816 TTATTAATA
1 TTATTAATA
2072825 TTATTAATA
1 TTATTAATA
2072834 TT-TTACTACTA
1 TTATTA--A-TA
2072845 TTATTAGTATTA
1 TTATTA--A-TA
2072857 TTATTAATA
1 TTATTAATA
* *
2072866 ATAATAATA
1 TTATTAATA
2072875 TTATT
1 TTATT
2072880 TACAATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
8 3 0.06
9 32 0.59
10 2 0.04
11 4 0.07
12 13 0.24
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (9 bp):
TTATTAATA
Found at i:2072879 original size:3 final size:3
Alignment explanation
Indices: 2072798--2072862 Score: 60
Period size: 3 Copynumber: 22.0 Consensus size: 3
2072788 TGTCTCGTTT
* * * * * *
2072798 TTA TTA TTT TTA TTA ATA TTA TTA ATA TTA TTA ATA TT- TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2072845 TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
2072863 ATAATAATAA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2077758 original size:20 final size:21
Alignment explanation
Indices: 2077735--2077781 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2077725 TTGCATTCGT
2077735 ATTTTTT-TCATTACATTTGC
1 ATTTTTTATCATTACATTTGC
** *
2077755 ATTTTTTATGTTTGCATTTGC
1 ATTTTTTATCATTACATTTGC
2077776 ATTTTT
1 ATTTTT
2077782 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.64
Consensus pattern (21 bp):
ATTTTTTATCATTACATTTGC
Found at i:2077793 original size:20 final size:20
Alignment explanation
Indices: 2077749--2077816 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
2077739 TTTTCATTAC
*
2077749 ATTTGCATTTTT-TATGTTTGC
1 ATTTGCATTTTTATAT-TTT-T
2077770 ATTTGCATTTTTATATTTTT
1 ATTTGCATTTTTATATTTTT
* * *
2077790 ATTTACATTTTCAT-TTTAT
1 ATTTGCATTTTTATATTTTT
2077809 ATTTGCAT
1 ATTTGCAT
2077817 CTTTGCATTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 11 0.27
20 12 0.29
21 15 0.37
22 3 0.07
ACGTcount: A:0.21, C:0.09, G:0.07, T:0.63
Consensus pattern (20 bp):
ATTTGCATTTTTATATTTTT
Found at i:2077822 original size:47 final size:47
Alignment explanation
Indices: 2077716--2077825 Score: 127
Period size: 47 Copynumber: 2.3 Consensus size: 47
2077706 CCTTTGGTCC
*
2077716 ATTTGCATTTTGCATTCGTATTTTTTTCATTACATTTGCATTTTTTAT
1 ATTTGCATTTTGCATTCGTATATTTTTCATTACATTTGCA-TTTTTAT
* ** *
2077764 GTTTGCA-TTTGCATTTTTATATTTTT-ATTTACATTTTCA-TTTTAT
1 ATTTGCATTTTGCATTCGTATATTTTTCA-TTACATTTGCATTTTTAT
2077809 ATTTGCATCTTTGCATT
1 ATTTGCAT-TTTGCATT
2077826 GAACAATTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 12 0.23
46 1 0.02
47 34 0.64
48 6 0.11
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.61
Consensus pattern (47 bp):
ATTTGCATTTTGCATTCGTATATTTTTCATTACATTTGCATTTTTAT
Found at i:2082254 original size:75 final size:75
Alignment explanation
Indices: 2082131--2082307 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
2082121 AGCAAGAAGA
* * * *
2082131 AAATGTTGGGGCATGCTGAAAACCCATTTTAATCAGAATCAATAATATTGACACATTTTAAATGT
1 AAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATATTAACACATTTTAAACGT
*
2082196 TTGCATCAGC
66 TTGCATCAAC
* * * * * *
2082206 AAATGATGGGGCATACTGAAAGCCCATTTCAATCAGAAAT-TAGAATATTAACTCATTTTGAACG
1 AAATGTTGGGGCATGCTGAAAACCCATTTCAATCAG-AATCAAGAATATTAACACATTTTAAACG
* *
2082270 TTTGTATTAAC
65 TTTGCATCAAC
*
2082281 AAATGTTGGGGCATGCTGAAGACCCAT
1 AAATGTTGGGGCATGCTGAAAACCCAT
2082308 ATCATCTTAT
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
75 81 0.96
76 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATATTAACACATTTTAAACGT
TTGCATCAAC
Found at i:2083262 original size:54 final size:54
Alignment explanation
Indices: 2083176--2083283 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
2083166 CTAACCAAAA
* *
2083176 ATCTGTATAGAAGCCACAGGAAAGGATAAATGTGTTATCAAATATTTTACGAAC
1 ATCTGTACAAAAGCCACAGGAAAGGATAAATGTGTTATCAAATATTTTACGAAC
* * *
2083230 ATCTGTACAAAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGTACAAAAGCCACAGGAAAGGATAAATGTGTTATCAAATATTTTACGAAC
2083284 CAGTGATTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (54 bp):
ATCTGTACAAAAGCCACAGGAAAGGATAAATGTGTTATCAAATATTTTACGAAC
Found at i:2084615 original size:30 final size:30
Alignment explanation
Indices: 2084581--2084647 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
2084571 CCCGAATGAC
2084581 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
*
2084611 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
2084641 CTATCCA
1 CTATCCA
2084648 TACGTCCCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:2087217 original size:2 final size:2
Alignment explanation
Indices: 2087210--2087235 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2087200 CTAATCAAAG
2087210 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
2087236 TCCCCAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2089974 original size:30 final size:30
Alignment explanation
Indices: 2089940--2090012 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
2089930 CCCAAATGAC
2089940 CTATCCAGAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGTAA
*
2089970 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCATCGGTAA
* *
2090000 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2090013 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCATCGGTAA
Found at i:2090036 original size:31 final size:31
Alignment explanation
Indices: 2089998--2090062 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
2089988 GATCCTCGGT
*
2089998 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
2090029 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
2090060 AAC
1 AAC
2090063 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:2091685 original size:22 final size:22
Alignment explanation
Indices: 2091654--2091720 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
2091644 AGGATGTTAC
* *
2091654 AGATTCTCTCTTTAAAAATTAT
1 AGATTCTCTCTTCAAAAATGAT
*
2091676 AGATTATCTCTTCAAAAATGAT
1 AGATTCTCTCTTCAAAAATGAT
*
2091698 AGATTCTCTCTTCAAAGATGAT
1 AGATTCTCTCTTCAAAAATGAT
2091720 A
1 A
2091721 AATCCTCTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
AGATTCTCTCTTCAAAAATGAT
Found at i:2091728 original size:22 final size:22
Alignment explanation
Indices: 2091682--2091740 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
2091672 TTATAGATTA
* * *
2091682 TCTCTTCAAAAATGATAGATTC
1 TCTCTTCAAAGATGATAAATCC
2091704 TCTCTTCAAAGATGATAAATCC
1 TCTCTTCAAAGATGATAAATCC
* *
2091726 TCTTTTTAAAGATGA
1 TCTCTTCAAAGATGA
2091741 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (22 bp):
TCTCTTCAAAGATGATAAATCC
Found at i:2092461 original size:45 final size:45
Alignment explanation
Indices: 2092397--2092918 Score: 873
Period size: 45 Copynumber: 11.6 Consensus size: 45
2092387 CTATTTCTCA
* *
2092397 CATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
2092442 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
2092487 CATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
2092532 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
2092577 CATCTATAAGCCCTTCAGTGCATGATGTTTTGAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * * *
2092622 CATATGTAGGCTCTTCAGTGCATGATGTTTTCAAAACTTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
**
2092667 CATCTGTAAGCCCTTCAGTGCATGATACTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
2092712 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
2092757 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
2092802 TATATGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
2092847 CATCTGTAAGCCCTTCAGTGCATGGTGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
2092892 CATCTGTAAGACCTACAGTGCAAGATG
1 CATCTGTAAGCCCTTCAGTGCATGATG
2092919 ATAAGAACTG
Statistics
Matches: 444, Mismatches: 33, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 444 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:2093099 original size:45 final size:45
Alignment explanation
Indices: 2093040--2093129 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
2093030 AGATGATAAG
** * *
2093040 ACCTTAGGGCCATCCATAAGATTTATAGTGCATGATGTTTTCAAA
1 ACCTTAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAA
* *
2093085 ACCTTCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAA
1 ACCTTAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAA
2093130 TGAGATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
ACCTTAGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAA
Found at i:2093410 original size:3 final size:3
Alignment explanation
Indices: 2093388--2093468 Score: 83
Period size: 3 Copynumber: 27.0 Consensus size: 3
2093378 TATCTCGTTT
* * * * *
2093388 TTA TTA TTT TTA TTA ATA TTA TTA ATA TT- TTA TTA CTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2093435 TTA TTA TTA ATA ATA TTA TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
2093469 AATAAATATA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.92
4 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2095794 original size:17 final size:17
Alignment explanation
Indices: 2095772--2095805 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2095762 TGAATGAGTG
2095772 ACATGTTAATCATGTGT
1 ACATGTTAATCATGTGT
2095789 ACATGTTAATCATGTGT
1 ACATGTTAATCATGTGT
2095806 GCTGATGCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
ACATGTTAATCATGTGT
Found at i:2107932 original size:2 final size:2
Alignment explanation
Indices: 2107925--2107977 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2107915 ATTTTTCTTT
2107925 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
2107967 TA TA TA TA TA T
1 TA TA TA TA TA T
2107978 GGGTAAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2109412 original size:25 final size:25
Alignment explanation
Indices: 2109384--2109447 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
2109374 GCCCAAGGCC
*
2109384 GTTACAATAAACTAAACTAACTTTA
1 GTTACAACAAACTAAACTAACTTTA
* *
2109409 GTTACAACAAACTCAACTAATTTTA
1 GTTACAACAAACTAAACTAACTTTA
2109434 GTTACAACAAACTA
1 GTTACAACAAACTA
2109448 GTTACTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (25 bp):
GTTACAACAAACTAAACTAACTTTA
Found at i:2113415 original size:4 final size:4
Alignment explanation
Indices: 2113406--2113519 Score: 77
Period size: 4 Copynumber: 28.5 Consensus size: 4
2113396 TTTAACGTGT
* * *
2113406 TATA TATA TATA TATA TATA TATA TATA TATA TATA TGTA TGTA TGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * * * * * * *
2113454 TGTA TGTA TGTA TGTA TGTA TATA GA-A GAGTA TATG TGTG TGTG TATA
1 TATA TATA TATA TATA TATA TATA TATA TA-TA TATA TATA TATA TATA
2113502 TATA TATA TATA TATA TA
1 TATA TATA TATA TATA TA
2113520 AAACAAGATC
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
3 3 0.03
4 95 0.95
5 2 0.02
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (4 bp):
TATA
Found at i:2120068 original size:20 final size:20
Alignment explanation
Indices: 2120043--2120080 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2120033 ATCCTATTCC
2120043 CTGGTAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
*
2120063 CTGGTAATCTTCCATTCC
1 CTGGTAATCTTACATTCC
2120081 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:2120745 original size:44 final size:45
Alignment explanation
Indices: 2120695--2120787 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 45
2120685 ATCGATATTG
* *
2120695 GTATCGAGACTGCAGTGTATTTTTACACATTAGTATCAGTA-CCT
1 GTATCGAGACTACAATGTATTTTTACACATTAGTATCAGTATCCT
*
2120739 GTATCGATACTACAATGTATTTTTACACATTAGTATCAGTATCCT
1 GTATCGAGACTACAATGTATTTTTACACATTAGTATCAGTATCCT
2120784 -TATC
1 GTATC
2120788 AATTCTACAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 42 0.93
45 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (45 bp):
GTATCGAGACTACAATGTATTTTTACACATTAGTATCAGTATCCT
Found at i:2120796 original size:44 final size:44
Alignment explanation
Indices: 2120710--2120796 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
2120700 GAGACTGCAG
*
2120710 TGTATTTTTACACATTAGTATCAGTACCTGTATCGATACTACAA
1 TGTATTTTTACACATTAGTATCAGTACCTGTATCAATACTACAA
*
2120754 TGTATTTTTACACATTAGTATCAGTATCCT-TATCAATTCTACA
1 TGTATTTTTACACATTAGTATCAGTA-CCTGTATCAATACTACA
2120797 TGAACATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 37 0.93
45 3 0.08
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.41
Consensus pattern (44 bp):
TGTATTTTTACACATTAGTATCAGTACCTGTATCAATACTACAA
Found at i:2129122 original size:2 final size:2
Alignment explanation
Indices: 2129115--2129143 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2129105 GATTGTATCA
2129115 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2129144 GCACTAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2130403 original size:31 final size:31
Alignment explanation
Indices: 2130368--2130427 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2130358 AACTTAAAAG
* * *
2130368 AGTTTTGCAATACTTAGATTAAAATAATTTC
1 AGTTTTACAATACTGAAATTAAAATAATTTC
*
2130399 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTAAAATAATT
2130428 CATACAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTAAAATAATTTC
Found at i:2130897 original size:16 final size:16
Alignment explanation
Indices: 2130878--2130927 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
2130868 AAATAATTAA
2130878 AATAATATAAAATTTT
1 AATAATATAAAATTTT
2130894 AATAATATATAAATAATTT
1 AATAATATA-AAAT--TTT
*
2130913 ATATGATATAAAATT
1 A-ATAATATAAAATT
2130928 AAATATCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
19 8 0.28
20 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
AATAATATAAAATTTT
Found at i:2133968 original size:105 final size:106
Alignment explanation
Indices: 2133756--2134396 Score: 863
Period size: 105 Copynumber: 6.1 Consensus size: 106
2133746 AAATGCAAGC
* * * * * * * *
2133756 TGCGTTGTTTTGAGGCCAATATCCTCCGCTGTGAACTTGAAATTGGCTCTGAAATTGAGAAGTTA
1 TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGAGAAATTG
* * *
2133821 TTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACT
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * * * *
2133862 TGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGAGAAATTG
*
2133927 -TTGTTGACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACT
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
2133967 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTG-GGAA--G
1 TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGAGAAATTG
* * *
2134029 -TTG-T--CAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACT
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * * * * *
2134066 TGTGCTGTCTCGAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGATCCGAAATTGGGAAA-TG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGAGAAATTG
*
2134130 TTTATTGACAACCAGCGGTCCCTTCGTCGT-ACAGTTGAACT
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGA-AGTTGAACT
* * *
2134171 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG-AATTGGCTCTGAAATTGAGAAGTTG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGAGAAATTG
2134235 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* * *
2134276 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGAGAAATTG
*
2134341 TTTGTTGACAACCAGCGGTCCTTTCGTCGTGAAGTTGAACT
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
*
2134382 TGCGTTGTCTTGAGT
1 TGCGTTGTCTGGAGT
2134397 GGCACGATAT
Statistics
Matches: 476, Mismatches: 49, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
99 80 0.17
100 3 0.01
101 2 0.00
102 6 0.01
103 1 0.00
104 22 0.05
105 229 0.48
106 133 0.28
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGAGAAATTG
TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
Found at i:2134113 original size:204 final size:208
Alignment explanation
Indices: 2133756--2134396 Score: 929
Period size: 204 Copynumber: 3.1 Consensus size: 208
2133746 AAATGCAAGC
* * * * * *
2133756 TGCGTTGTTTTGAGGCCAATATCCTCCGCTGTGAACTTGAAATTGGCTCTGAAATTGAGAAGTTA
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG---
2133821 TTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCC
63 TTTGTT-ACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCC
2133886 TTCGCTGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTG-TTGTTGACAACCAGCGGTCCCTT
127 TTCGCTGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTT
2133950 TGTCGTGAAGTTGAACT
192 TGTCGTGAAGTTGAACT
* *
2133967 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAG-TT
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTT
2134031 G-T-CAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCG
66 GTTACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCG
* * *
2134094 CCGTGAAGTTGAAATTGGATCCGAAATTGGGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTC
131 CTGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTTGTC
2134158 GT-ACAGTTGAACT
196 GTGA-AGTTGAACT
2134171 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG-AATTGGCTCTGAAATTGAGAAGTTG
1 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---G
* * * * * *
2134235 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
63 TTTGTT-ACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCC
* * * * *
2134300 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGT-CCTT
127 TTCGCTGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTT
2134364 TCGTCGTGAAGTTGAACT
192 T-GTCGTGAAGTTGAACT
*
2134382 TGCGTTGTCTTGAGT
1 TGCGTTGTCTGGAGT
2134397 GGCACGATAT
Statistics
Matches: 390, Mismatches: 28, Indels: 24
0.88 0.06 0.05
Matches are distributed among these distances:
203 22 0.06
204 169 0.43
206 2 0.01
207 6 0.02
208 1 0.00
210 87 0.22
211 102 0.26
212 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (208 bp):
TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTT
GTTACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGATCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTTGTC
GTGAAGTTGAACT
Found at i:2134752 original size:36 final size:35
Alignment explanation
Indices: 2134636--2134975 Score: 115
Period size: 37 Copynumber: 9.9 Consensus size: 35
2134626 AATTGTGTTG
* * * *
2134636 TTTCAAGAGAAACTGTCTCAAGGGAGATAAACTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTA
* ** ** *
2134671 GTTCAAAAGAAACTGTCTCAAG-G-GACGAACTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTA
*
2134705 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT-A
* * *** *
2134741 TTTCAAGGGAAA-TGTTTTC-A-A-TG--TTTA-TG
1 TTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTA
* * * *
2134770 TTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAA-ATTA
*
2134806 TTTCAAGGGAAACTATCTC-A-AGAGACAAAATTCA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT-A
* * *** *
2134840 TTTCAAGGGAAA-TGTTTTC--GA-TG--TTTA-TG
1 TTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTA
* * *
2134869 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TTA
* *
2134906 TTTCAA-GAAGAACTGACTCAAGAGAGACAAAACTTA
1 TTTCAAGGGA-AACTGTCTCAAGAGAGACAAAA-TTA
* ** *
2134942 GTTCCAAAAGAAACTGTCTCAAGGGAGACAAAAT
1 -TTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
2134976 GTGTTTTAAG
Statistics
Matches: 219, Mismatches: 58, Indels: 55
0.66 0.17 0.17
Matches are distributed among these distances:
29 28 0.13
30 7 0.03
31 3 0.01
32 2 0.01
33 7 0.03
34 49 0.22
35 28 0.13
36 41 0.19
37 53 0.24
38 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (35 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTA
Found at i:2134843 original size:99 final size:101
Alignment explanation
Indices: 2134672--2134937 Score: 418
Period size: 99 Copynumber: 2.7 Consensus size: 101
2134662 ATAAACTTAG
* * *
2134672 TTCAAAAGAAACTGTCTCAA-GG-GACGAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
2134735 AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
66 AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
2134771 TTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTGTTTCAAGGGAAACTATCTC-A-AGAGACAA
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
*
2134834 AATTCATTTCAAGGGAAATGTTTTCGATGTTTATGT
66 AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
*
2134870 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAA-GAAGAACTGA-CTCAAGAGAGA
1 TTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTGTTTCAAGGGA-AACT-ATCTCAAGAGAGA
2134933 CAAAA
63 CAAAA
2134938 CTTAGTTCCA
Statistics
Matches: 155, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
99 91 0.59
100 24 0.15
101 30 0.19
102 10 0.06
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (101 bp):
TTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAA
AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:2134920 original size:37 final size:38
Alignment explanation
Indices: 2134867--2134991 Score: 152
Period size: 37 Copynumber: 3.4 Consensus size: 38
2134857 TCGATGTTTA
2134867 TGTTTCAAG-AGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
2134904 TGTTTCAAGAAG-AACTGACTCAAGAGAGACAAAACTT
1 TGTTTCAAGAAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
2134941 AGTTCCAA-AAGAAACTGTCTCAAGGGAGACAAAA-TG
1 TGTTTCAAGAAGAAACTGTCTCAAGGGAGACAAAATTT
*
2134977 TGTTTTAAGAA-AAAC
1 TGTTTCAAGAAGAAAC
2134992 AATCTTGAGT
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
36 13 0.18
37 59 0.80
38 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (38 bp):
TGTTTCAAGAAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:2136518 original size:21 final size:20
Alignment explanation
Indices: 2136494--2136553 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 20
2136484 TGCATGTGCT
2136494 TTTTGTCCCTTTTTCTTTTG
1 TTTTGTCCCTTTTTCTTTTG
*
2136514 ATTTTG-CTCTTTTTTCCTTTTG
1 -TTTTGTC-CCTTTTT-CTTTTG
* *
2136536 TTTGTTTCTCTTTTTCTT
1 TTT-TGTCCCTTTTTCTT
2136554 AGTTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.03
21 17 0.55
22 12 0.39
23 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.08, T:0.72
Consensus pattern (20 bp):
TTTTGTCCCTTTTTCTTTTG
Found at i:2136528 original size:22 final size:23
Alignment explanation
Indices: 2136503--2136550 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2136493 TTTTTGTCCC
2136503 TTTTT-CTTTTGATT-TTGCTCT
1 TTTTTCCTTTTGATTGTTGCTCT
* *
2136524 TTTTTCCTTTTGTTTGTTTCTCT
1 TTTTTCCTTTTGATTGTTGCTCT
2136547 TTTT
1 TTTT
2136551 CTTAGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 8 0.35
23 10 0.43
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (23 bp):
TTTTTCCTTTTGATTGTTGCTCT
Found at i:2136551 original size:22 final size:21
Alignment explanation
Indices: 2136502--2136551 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2136492 CTTTTTGTCC
2136502 CTTTTT-CTTTTGATTTTGCT
1 CTTTTTCCTTTTGATTTTGCT
* *
2136522 CTTTTTTCCTTTTGTTTGTTTCT
1 C-TTTTTCCTTTTGATT-TTGCT
2136545 CTTTTTC
1 CTTTTTC
2136552 TTAGTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 5 0.20
22 14 0.56
23 5 0.20
ACGTcount: A:0.02, C:0.18, G:0.08, T:0.72
Consensus pattern (21 bp):
CTTTTTCCTTTTGATTTTGCT
Found at i:2137405 original size:105 final size:105
Alignment explanation
Indices: 2137223--2137429 Score: 405
Period size: 105 Copynumber: 2.0 Consensus size: 105
2137213 AGGTCTAATC
2137223 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
1 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
2137288 GAAGAACTAAAGATTAAAATTTATTCAATTGCTCCACCTT
66 GAAGAACTAAAGATTAAAATTTATTCAATTGCTCCACCTT
2137328 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
1 TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
*
2137393 GAAGAACTAAAGATTAAAATTTGTTCAATTGCTCCAC
66 GAAGAACTAAAGATTAAAATTTATTCAATTGCTCCAC
2137430 TTTAGAAAGT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (105 bp):
TTGTCATATGTCAAAAATCTATAATTCTTGAAGAGTTAAAAGAATCCTTAATTCATTTAATATTC
GAAGAACTAAAGATTAAAATTTATTCAATTGCTCCACCTT
Found at i:2138702 original size:36 final size:35
Alignment explanation
Indices: 2138631--2138702 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
2138621 AAAACGAAAA
2138631 TCCTACCCCACATGATATCTACCCGCATGCTTAAT
1 TCCTACCCCACATGATATCTACCCGCATGCTTAAT
* *
2138666 TCCTACCCGGACATGATCTCTATCCCGCATGC-TAAT
1 TCCTACCC-CACATGATATCTA-CCCGCATGCTTAAT
2138702 T
1 T
2138703 TCACACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 8 0.24
36 16 0.48
37 9 0.27
ACGTcount: A:0.24, C:0.36, G:0.11, T:0.29
Consensus pattern (35 bp):
TCCTACCCCACATGATATCTACCCGCATGCTTAAT
Found at i:2139310 original size:98 final size:99
Alignment explanation
Indices: 2139134--2139332 Score: 357
Period size: 98 Copynumber: 2.0 Consensus size: 99
2139124 TCTGAAATCA
2139134 TTAGAAAATAGTTAGTAAAACTATTACTTGAAAAAAAATAATCAAAGATAAATAATTGGAATCGA
1 TTAGAAAATAGTTAGTAAAACTATTACTTGAAAAAAAATAATCAAAGA-AAATAATTGGAATCGA
2139199 ATAAATAAATTAAAATTTAAACTTGTAA-TTTCGC
65 ATAAATAAATTAAAATTTAAACTTGTAATTTTCGC
*
2139233 TTAGAAAATAGTTAGTACAACTATTTACTTGAAAAAAAATAATCAAAG-AAATAATTGGAATCGA
1 TTAGAAAATAGTTAGTAAAACTA-TTACTTGAAAAAAAATAATCAAAGAAAATAATTGGAATCGA
2139297 ATAAATAAATTAAAATTTAAACTTGTAATTTTCGC
65 ATAAATAAATTAAAATTTAAACTTGTAATTTTCGC
2139332 T
1 T
2139333 AAAAAAGACA
Statistics
Matches: 97, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
98 44 0.45
99 29 0.30
100 24 0.25
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (99 bp):
TTAGAAAATAGTTAGTAAAACTATTACTTGAAAAAAAATAATCAAAGAAAATAATTGGAATCGAA
TAAATAAATTAAAATTTAAACTTGTAATTTTCGC
Found at i:2141465 original size:30 final size:31
Alignment explanation
Indices: 2141399--2141484 Score: 138
Period size: 30 Copynumber: 2.8 Consensus size: 31
2141389 ATGTAAATAC
* *
2141399 ATTATATAATGTAACGACATTAAAAGACATAT
1 ATTATATAATGCAACAACATTAAAAGACA-AT
2141431 ATTATATAATGCAACAACATTAAAAGAC-AT
1 ATTATATAATGCAACAACATTAAAAGACAAT
2141461 ATTATATAATGCAACAACATTAAA
1 ATTATATAATGCAACAACATTAAA
2141485 GGATAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
30 26 0.50
32 26 0.50
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (31 bp):
ATTATATAATGCAACAACATTAAAAGACAAT
Found at i:2150013 original size:16 final size:16
Alignment explanation
Indices: 2149989--2150022 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2149979 TATCGTCGAC
*
2149989 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2150005 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2150021 CG
1 CG
2150023 CGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2151257 original size:14 final size:14
Alignment explanation
Indices: 2151238--2151295 Score: 77
Period size: 14 Copynumber: 4.3 Consensus size: 14
2151228 CGTTTTGTTA
2151238 TATATTTATTATAG
1 TATATTTATTATAG
*
2151252 TATATTTATTGT-G
1 TATATTTATTATAG
2151265 TATATATTA-TATAG
1 TATAT-TTATTATAG
2151279 TATATTTATTATA-
1 TATATTTATTATAG
2151292 TATA
1 TATA
2151296 ATAGTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 15 0.38
14 24 0.62
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TATATTTATTATAG
Found at i:2151295 original size:27 final size:27
Alignment explanation
Indices: 2151236--2151304 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
2151226 AGCGTTTTGT
*
2151236 TATATAT-TTATTATAGTATATTTATTG
1 TATATATATTA-TATAGTATATTTATTA
*
2151263 TGTATATATTATATAGTATATTTATTA
1 TATATATATTATATAGTATATTTATTA
*
2151290 TATATAATAGTATAT
1 TATAT-ATATTATAT
2151305 TATATACTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 25 0.69
28 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (27 bp):
TATATATATTATATAGTATATTTATTA
Found at i:2156228 original size:60 final size:60
Alignment explanation
Indices: 2156135--2156255 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
2156125 ATGTAATATC
2156135 TAGTACTCGAACCTGAAACCTCTAAGAACAATAATTATTCCTTTAATCACTAAGGTAATT
1 TAGTACTCGAACCTGAAACCTCTAAGAACAATAATTATTCCTTTAATCACTAAGGTAATT
2156195 TAGTACTCGAACCTGAAACCTCTAAGAACAATAATTATTCCTTTAATCACTAAGGTAATT
1 TAGTACTCGAACCTGAAACCTCTAAGAACAATAATTATTCCTTTAATCACTAAGGTAATT
2156255 T
1 T
2156256 GATCAATGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (60 bp):
TAGTACTCGAACCTGAAACCTCTAAGAACAATAATTATTCCTTTAATCACTAAGGTAATT
Found at i:2156586 original size:26 final size:25
Alignment explanation
Indices: 2156557--2156613 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
2156547 TAGACACATG
*
2156557 ATTTTATGTAAAAATAAA-TCAATAAA
1 ATTTTAAG-AAAAATAAACT-AATAAA
* *
2156583 ATTTTAAGGAAAATAAACTTATAAA
1 ATTTTAAGAAAAATAAACTAATAAA
2156608 ATTTTA
1 ATTTTA
2156614 GATAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 19 0.70
26 8 0.30
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (25 bp):
ATTTTAAGAAAAATAAACTAATAAA
Found at i:2157196 original size:25 final size:23
Alignment explanation
Indices: 2157168--2157215 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
2157158 TTCTAATTTA
2157168 AAATACAAAAATATTAAATATAAAT
1 AAATACAAAAATA-TAAAT-TAAAT
*
2157193 AAATATAAAAATATAAATTAAAT
1 AAATACAAAAATATAAATTAAAT
2157216 TACTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.23
24 5 0.23
25 12 0.55
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATACAAAAATATAAATTAAAT
Found at i:2157206 original size:18 final size:21
Alignment explanation
Indices: 2157183--2157229 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 21
2157173 CAAAAATATT
2157183 AAATATAAA-TAAA-TA-TAA
1 AAATATAAATTAAATTACTAA
2157201 AAATATAAATTAAATTACTAA
1 AAATATAAATTAAATTACTAA
2157222 AAAT-TAAA
1 AAATATAAA
2157230 AGTATATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.35
19 4 0.15
20 6 0.23
21 7 0.27
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATATAAATTAAATTACTAA
Found at i:2157338 original size:12 final size:12
Alignment explanation
Indices: 2157323--2157347 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2157313 TATATTTAAC
2157323 TCTAATTGTATT
1 TCTAATTGTATT
2157335 TCTAATTGTATT
1 TCTAATTGTATT
2157347 T
1 T
2157348 TATTAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTAATTGTATT
Found at i:2157737 original size:23 final size:23
Alignment explanation
Indices: 2157695--2157746 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2157685 ATTCAATTTT
2157695 TATTT-TTATTTTTATATTCATA
1 TATTTATTATTTTTATATTCATA
2157717 TATTTATT-TTTTCTATATTCATA
1 TATTTATTATTTT-TATATTCATA
2157740 TAGTTTA
1 TA-TTTA
2157747 AATTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.33
23 14 0.52
24 4 0.15
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (23 bp):
TATTTATTATTTTTATATTCATA
Found at i:2163673 original size:35 final size:35
Alignment explanation
Indices: 2163626--2163695 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
2163616 TATGTTCGAC
* * *
2163626 GTGGACATATTTTTTTAAA-AATATAATTTAATATT
1 GTGGACACA-TTTTTTAAAGAAAACAATTTAATATT
2163661 GTGGACACATTTTTTAAAGAAAACAATTTAATATT
1 GTGGACACATTTTTTAAAGAAAACAATTTAATATT
2163696 ACATTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (35 bp):
GTGGACACATTTTTTAAAGAAAACAATTTAATATT
Found at i:2164061 original size:18 final size:18
Alignment explanation
Indices: 2164040--2164103 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
2164030 ATTTATTGTT
2164040 TTTATTTTGAATTATTTA
1 TTTATTTTGAATTATTTA
* *
2164058 TTTATTTCGAATCATTTA
1 TTTATTTTGAATTATTTA
* *
2164076 TTTA-TTT-ACTTATTCA
1 TTTATTTTGAATTATTTA
2164092 TTTATTTTGAAT
1 TTTATTTTGAAT
2164104 AAATTAGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 10 0.27
17 5 0.14
18 22 0.59
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTATTTTGAATTATTTA
Found at i:2164079 original size:22 final size:20
Alignment explanation
Indices: 2164051--2164098 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
2164041 TTATTTTGAA
2164051 TTATTTATTTATTTCGAATCAT
1 TTATTTATTTATTT--AATCAT
* *
2164073 TTATTTATTTACTTATTCAT
1 TTATTTATTTATTTAATCAT
2164093 TTATTT
1 TTATTT
2164099 TGAATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
22 13 0.54
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (20 bp):
TTATTTATTTATTTAATCAT
Found at i:2164125 original size:30 final size:26
Alignment explanation
Indices: 2164079--2164154 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
2164069 TCATTTATTT
* * *
2164079 ATTTACTTATTCATTTATTTTGAATAA
1 ATTTATTTATTTATTTATTTCGAA-AA
*
2164106 ATTAGTGATTTATTTATTTATTTCGGAAA
1 ATT--T-ATTTATTTATTTATTTCGAAAA
2164135 ATTTATTTATTTATTTATTT
1 ATTTATTTATTTATTTATTT
2164155 GAAGGGGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 16 0.38
27 4 0.10
29 6 0.14
30 16 0.38
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (26 bp):
ATTTATTTATTTATTTATTTCGAAAA
Found at i:2164151 original size:34 final size:34
Alignment explanation
Indices: 2164051--2164154 Score: 110
Period size: 34 Copynumber: 3.2 Consensus size: 34
2164041 TTATTTTGAA
* *
2164051 TTATTTATTTATTTCGAATCATTTATTTATTTAC
1 TTATTTATTTATTTCGAATAATTTATTTATTTAT
* * * *
2164085 TTATTCATTTATTTTGAATAA---A-TTAGTGAT
1 TTATTTATTTATTTCGAATAATTTATTTATTTAT
2164115 TTATTTATTTATTTCGGAA-AATTTATTTATTTAT
1 TTATTTATTTATTTC-GAATAATTTATTTATTTAT
2164149 TTATTT
1 TTATTT
2164155 GAAGGGGTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
30 20 0.36
31 4 0.07
33 1 0.02
34 30 0.55
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.61
Consensus pattern (34 bp):
TTATTTATTTATTTCGAATAATTTATTTATTTAT
Found at i:2164511 original size:17 final size:16
Alignment explanation
Indices: 2164475--2164512 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
2164465 ATAATAAATA
2164475 AATTTTAAAATTTATT
1 AATTTTAAAATTTATT
2164491 AATTTTGAATAATTT-TT
1 AATTTT-AA-AATTTATT
2164508 AATTT
1 AATTT
2164513 ATTAGTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTTTAAAATTTATT
Found at i:2172236 original size:22 final size:23
Alignment explanation
Indices: 2172192--2172236 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2172182 GCATTATATC
**
2172192 ATTTTTATTATAATATATTAAAT
1 ATTTTTATTATAATATACGAAAT
2172215 ATTTTTATT-TAATATACGAAAT
1 ATTTTTATTATAATATACGAAAT
2172237 GTGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTTATTATAATATACGAAAT
Found at i:2173544 original size:18 final size:17
Alignment explanation
Indices: 2173521--2173672 Score: 83
Period size: 18 Copynumber: 9.1 Consensus size: 17
2173511 ATAATATAAA
2173521 ATTATAAACTATATTTAT
1 ATTATAAACTATA-TTAT
* *
2173539 ATTATAAACTATGTAATT
1 ATTATAAACTATATTA-T
2173557 ATTAT-AA-TATA-TAT
1 ATTATAAACTATATTAT
*
2173571 A-TATAAATTATATT-T
1 ATTATAAACTATATTAT
* *
2173586 A-TGTGAAC--TA-TAT
1 ATTATAAACTATATTAT
*
2173599 A-TATAAACTATGTATATAAA
1 ATTATAAACTA--TAT-T-AT
2173619 ATTATAAACTATATTTAT
1 ATTATAAACTATA-TTAT
*
2173637 ATTATAAACTATATAATT
1 ATTATAAACTATATTA-T
*
2173655 ATTATAAGCTATA-TAT
1 ATTATAAACTATATTAT
2173671 AT
1 AT
2173673 AAATTATGTT
Statistics
Matches: 105, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
12 1 0.01
13 12 0.11
14 4 0.04
15 11 0.10
16 7 0.07
17 9 0.09
18 45 0.43
19 4 0.04
20 3 0.03
21 9 0.09
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTATAAACTATATTAT
Found at i:2173623 original size:98 final size:98
Alignment explanation
Indices: 2173514--2173716 Score: 352
Period size: 98 Copynumber: 2.1 Consensus size: 98
2173504 TATATATATA
* *
2173514 ATATAAAATTATAAACTATATTTATATTATAAACTATGTAATTATTATAATATATATATATAAAT
1 ATATAAAATTATAAACTATATTTATATTATAAACTATATAATTATTATAAGATATATATATAAAT
*
2173579 TATATTTATGTGAACTATATATATAAACTATGT
66 TATATTTATGCGAACTATATATATAAACTATGT
*
2173612 ATATAAAATTATAAACTATATTTATATTATAAACTATATAATTATTATAAGCTATATATATAAAT
1 ATATAAAATTATAAACTATATTTATATTATAAACTATATAATTATTATAAGATATATATATAAAT
* *
2173677 TATGTTTATGCGAATTATATATATAAACTATGT
66 TATATTTATGCGAACTATATATATAAACTATGT
2173710 ATATAAA
1 ATATAAA
2173717 CTATATATGT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (98 bp):
ATATAAAATTATAAACTATATTTATATTATAAACTATATAATTATTATAAGATATATATATAAAT
TATATTTATGCGAACTATATATATAAACTATGT
Found at i:2173712 original size:15 final size:15
Alignment explanation
Indices: 2173692--2173736 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2173682 TTATGCGAAT
2173692 TATATATATAAAC--
1 TATATATATAAACTA
*
2173705 TATGTATATAAACTA
1 TATATATATAAACTA
*
2173720 TATATGTATAAACTA
1 TATATATATAAACTA
2173735 TA
1 TA
2173737 AAAAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 12 0.44
15 15 0.56
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (15 bp):
TATATATATAAACTA
Found at i:2173736 original size:13 final size:13
Alignment explanation
Indices: 2173566--2173736 Score: 85
Period size: 13 Copynumber: 12.3 Consensus size: 13
2173556 TATTATAATA
*
2173566 TATATATATAAAT
1 TATATATATAAAC
* *
2173579 TATATTTATGTGAAC
1 TATA--TATATAAAC
2173594 TATATATATAAAC
1 TATATATATAAAC
* *
2173607 TATGTATATAAAA
1 TATATATATAAAC
* *
2173620 T-TATAAACTATA-
1 TATATATA-TAAAC
*
2173632 TTTATATTATAAAC
1 TATATA-TATAAAC
2173646 TATATAATTATTATAAGC
1 TATAT-A-TA-TA-AA-C
*
2173664 TATATATATAAAT
1 TATATATATAAAC
* * * *
2173677 TATGTTTATGCGAAT
1 TATATATAT--AAAC
2173692 TATATATATAAAC
1 TATATATATAAAC
*
2173705 TATGTATATAAAC
1 TATATATATAAAC
2173718 TATATATGTATAAAC
1 TATATA--TATAAAC
2173733 TATA
1 TATA
2173737 AAAAATATAT
Statistics
Matches: 121, Mismatches: 23, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
12 5 0.04
13 59 0.49
14 7 0.06
15 37 0.31
16 4 0.03
17 3 0.02
18 6 0.05
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:2173749 original size:18 final size:18
Alignment explanation
Indices: 2173726--2173765 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2173716 ACTATATATG
2173726 TATAAACTATAAAAAATA
1 TATAAACTATAAAAAATA
*
2173744 TATAAACTATAAAAAGTA
1 TATAAACTATAAAAAATA
2173762 TATA
1 TATA
2173766 GTTTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (18 bp):
TATAAACTATAAAAAATA
Found at i:2173825 original size:53 final size:53
Alignment explanation
Indices: 2173742--2173857 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 53
2173732 CTATAAAAAA
* * *
2173742 TATATAAACTATAAAAAGTATATAGTTTATAAAATATTATTTATATTAATATAG
1 TATATATA-TATAAAAACTATATAGTTTATAAAATATAATTTATATTAATATAG
* ***
2173796 TATATATATATATAAACTATATAGTTTATATGTTATAATTTATATTAATATAG
1 TATATATATATAAAAACTATATAGTTTATAAAATATAATTTATATTAATATAG
2173849 TATATATAT
1 TATATATAT
2173858 GTATGCATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 48 0.87
54 7 0.13
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (53 bp):
TATATATATATAAAAACTATATAGTTTATAAAATATAATTTATATTAATATAG
Found at i:2173978 original size:2 final size:2
Alignment explanation
Indices: 2173973--2174020 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
2173963 TTATATAGTT
** *
2173973 TA TA TA TA TA TA TA TA GG TA TA TA TA TA TA TA GTT 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
2174016 CTA TA
1 -TA TA
2174021 CATGGTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 35 0.92
3 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2173996 original size:16 final size:15
Alignment explanation
Indices: 2173975--2174020 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
2173965 ATATAGTTTA
2173975 TATATATATATATAGG
1 TATATATATATATA-G
2173991 TATATATATATATAG
1 TATATATATATATAG
*
2174006 TTTATATATACTATA
1 TATATATATA-TATA
2174021 CATGGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (15 bp):
TATATATATATATAG
Found at i:2174020 original size:20 final size:20
Alignment explanation
Indices: 2173959--2174036 Score: 76
Period size: 20 Copynumber: 4.2 Consensus size: 20
2173949 ATAAGTAATT
*
2173959 TACTTTATATAGTTTATATA
1 TACTATATATAGTTTATATA
*
2173979 TA-TATATATAG---GTATA
1 TACTATATATAGTTTATATA
2173995 TA-TATATATAGTTTATATA
1 TACTATATATAGTTTATATA
* * *
2174014 TACTATACATGGTTTATACA
1 TACTATATATAGTTTATATA
2174034 TAC
1 TAC
2174037 ATTAGGGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 15 0.31
19 14 0.29
20 19 0.40
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.47
Consensus pattern (20 bp):
TACTATATATAGTTTATATA
Found at i:2174123 original size:21 final size:21
Alignment explanation
Indices: 2174038--2174124 Score: 77
Period size: 21 Copynumber: 4.1 Consensus size: 21
2174028 TATACATACA
*
2174038 TTAGGGTTTAGGGTTTAAGGT
1 TTAGAGTTTAGGGTTTAAGGT
* * ** * *
2174059 TTATAGCTTATTGTTTATGAT
1 TTAGAGTTTAGGGTTTAAGGT
*
2174080 TTAAAGTTTAGGGTTT-AGAGT
1 TTAGAGTTTAGGGTTTAAG-GT
*
2174101 TTAGAGTTTAGAGTTTAAGGT
1 TTAGAGTTTAGGGTTTAAGGT
2174122 TTA
1 TTA
2174125 TATAAACTAT
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 46 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.47
Consensus pattern (21 bp):
TTAGAGTTTAGGGTTTAAGGT
Found at i:2174406 original size:17 final size:19
Alignment explanation
Indices: 2174370--2174408 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2174360 CTAGATTTCC
2174370 CAATTTCGCTCTAAATTCT
1 CAATTTCGCTCTAAATTCT
*
2174389 CAATTTC-C-CTATATTCT
1 CAATTTCGCTCTAAATTCT
2174406 CAA
1 CAA
2174409 AATTTCTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (19 bp):
CAATTTCGCTCTAAATTCT
Found at i:2174530 original size:22 final size:22
Alignment explanation
Indices: 2174502--2174548 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
2174492 CACTTTATAT
2174502 ATATATATATATATAATTAAAC
1 ATATATATATATATAATTAAAC
*
2174524 ATATATATTTATATAATTAAAC
1 ATATATATATATATAATTAAAC
2174546 ATA
1 ATA
2174549 AGTGACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATATATATATATAATTAAAC
Found at i:2175461 original size:2 final size:2
Alignment explanation
Indices: 2175454--2175498 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2175444 TATGTTTAAT
2175454 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
2175496 TA T
1 TA T
2175499 TATTCAAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2175652 original size:19 final size:20
Alignment explanation
Indices: 2175611--2175686 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 20
2175601 GAATATATGG
*
2175611 AAATTGAG-AATTTAGA-TA
1 AAATTGAGAAATTTAGAGGA
2175629 AAATTGAG-AATTTAGAGGA
1 AAATTGAGAAATTTAGAGGA
* *
2175648 AAATTGGGAAATTTAGAGGG
1 AAATTGAGAAATTTAGAGGA
* *
2175668 AATTTGGGAAATTTAGAGG
1 AAATTGAGAAATTTAGAGG
2175687 GAATAGAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.31
19 8 0.15
20 28 0.54
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.29
Consensus pattern (20 bp):
AAATTGAGAAATTTAGAGGA
Found at i:2175687 original size:20 final size:20
Alignment explanation
Indices: 2175637--2175690 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2175627 TAAAATTGAG
* *
2175637 AATTTAGAGGAAAATTGGGA
1 AATTTAGAGGGAATTTGGGA
2175657 AATTTAGAGGGAATTTGGGA
1 AATTTAGAGGGAATTTGGGA
2175677 AATTTAGAGGGAAT
1 AATTTAGAGGGAAT
2175691 AGAAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (20 bp):
AATTTAGAGGGAATTTGGGA
Found at i:2176486 original size:16 final size:16
Alignment explanation
Indices: 2176444--2176498 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
2176434 CGGATCATTT
2176444 ACAGGTCAGGTT-AAA
1 ACAGGTCAGGTTGAAA
* *
2176459 AGCATGTTAGGTTGAAA
1 A-CAGGTCAGGTTGAAA
2176476 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
2176492 ACAGGTC
1 ACAGGTC
2176499 GGGTAATACC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.03
16 29 0.85
17 4 0.12
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.22
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Done.