Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 21
Found at i:2682169 original size:24 final size:25
Alignment explanation
Indices: 2682064--2682169 Score: 64
Period size: 24 Copynumber: 4.4 Consensus size: 25
2682054 AAACGGAGAT
* *
2682064 ATCAGAAATCAAAACAG-ATTTCAG
1 ATCAGAAATCAGAACAGAATTTAAG
* *
2682088 ATCAGATATCAGAA-AGAATCT-AG
1 ATCAGAAATCAGAACAGAATTTAAG
* *
2682111 ATCAGAAATC-GAAACA-AAATTCAG
1 ATCAGAAATCAG-AACAGAATTTAAG
* * *
2682135 GTAATG-TATCAGAACAGAATTTAAG
1 ATCA-GAAATCAGAACAGAATTTAAG
2682160 -TCAGAAATCA
1 ATCAGAAATCA
2682170 AATAAAATAT
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
22 1 0.02
23 19 0.31
24 33 0.54
25 8 0.13
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTTAAG
Found at i:2683812 original size:21 final size:21
Alignment explanation
Indices: 2683767--2683814 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2683757 AACGGACCCC
* * *
2683767 AAAAACATATTCAGGACGTTA
1 AAAAACAGATTCAGGACATCA
*
2683788 AAAAACAGATTCAGGACATCG
1 AAAAACAGATTCAGGACATCA
2683809 AAAAAC
1 AAAAAC
2683815 GTCAGAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (21 bp):
AAAAACAGATTCAGGACATCA
Found at i:2693980 original size:30 final size:30
Alignment explanation
Indices: 2693923--2693980 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
2693913 TTTAAATAAT
*
2693923 TTCTTAATTTTTCTAGAAAAATTAATTAAG
1 TTCTTAATTTTTCTAGAAAAATCAATTAAG
2693953 TTCTTAAATTTTT-TA-AAAGAATCAATTA
1 TTCTT-AATTTTTCTAGAAA-AATCAATTA
2693981 GGCCATCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 15 0.60
31 7 0.28
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (30 bp):
TTCTTAATTTTTCTAGAAAAATCAATTAAG
Found at i:2694750 original size:19 final size:19
Alignment explanation
Indices: 2694723--2694760 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2694713 ACGTTTTTCA
*
2694723 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
2694742 AACTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
2694761 TTTAAAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:2706196 original size:153 final size:153
Alignment explanation
Indices: 2705913--2706215 Score: 561
Period size: 153 Copynumber: 2.0 Consensus size: 153
2705903 TTTTTTCTTT
2705913 TAAGCCGAAGGCTAAAGCGAAGGCTCAATCCCAAACGTGAGAATTCATATTCGACTTTCCGAGAA
1 TAAGCCGAAGGCTAAAGCGAAGGCTCAATCCCAAACGTGAGAATTCATATTCGACTTTCCGAGAA
* *
2705978 CACACTTAGCAAAATTGTTTGCTAAGAGGAAATTGAGATCGGAACCAGTTATTGTTGAAACAACA
66 CACACTTAGCAAAATTGTTTGCTAAGAGGAAACTGAGATCGGAACCAGTTATTGTTGAAAAAACA
2706043 TAATCCAAGTCGACAACGAAGAA
131 TAATCCAAGTCGACAACGAAGAA
* *
2706066 TAAGCCGAAGGCTAAAGCGAAGGCTCAGTCCCAAACGTGAGAATTCATATTTGACTTTCCGAGAA
1 TAAGCCGAAGGCTAAAGCGAAGGCTCAATCCCAAACGTGAGAATTCATATTCGACTTTCCGAGAA
2706131 CACACTTAGCAAAATTGTTTGCTAAGAGGAAACTGAGATCGGAACCAGTTATTGTTGAAAAAACA
66 CACACTTAGCAAAATTGTTTGCTAAGAGGAAACTGAGATCGGAACCAGTTATTGTTGAAAAAACA
*
2706196 TAATCCGAGTCGACAACGAA
131 TAATCCAAGTCGACAACGAA
2706216 AAATTGACCT
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 145 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (153 bp):
TAAGCCGAAGGCTAAAGCGAAGGCTCAATCCCAAACGTGAGAATTCATATTCGACTTTCCGAGAA
CACACTTAGCAAAATTGTTTGCTAAGAGGAAACTGAGATCGGAACCAGTTATTGTTGAAAAAACA
TAATCCAAGTCGACAACGAAGAA
Found at i:2706370 original size:18 final size:18
Alignment explanation
Indices: 2706347--2706389 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2706337 CTTTAGATTA
*
2706347 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
2706365 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
2706383 TTTATTT
1 TTTATTT
2706390 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:2706477 original size:16 final size:16
Alignment explanation
Indices: 2706459--2706488 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2706449 TATTTTACTT
2706459 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
2706474 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
2706489 CCCATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:2706516 original size:15 final size:16
Alignment explanation
Indices: 2706496--2706525 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2706486 TTTCCCATTT
2706496 TTTTAC-TTTATTTTG
1 TTTTACTTTTATTTTG
2706511 TTTTACTTTTATTTT
1 TTTTACTTTTATTTT
2706526 CTCTTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTACTTTTATTTTG
Found at i:2707268 original size:23 final size:23
Alignment explanation
Indices: 2707231--2707277 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2707221 ATGTTCACTT
2707231 TACATAACTTAAAATGA-AAAAAA
1 TACATAACTTAAAAT-ATAAAAAA
2707254 TACATAAC-TACAAATATAAAAAA
1 TACATAACTTA-AAATATAAAAAA
2707277 T
1 T
2707278 TTATATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (23 bp):
TACATAACTTAAAATATAAAAAA
Found at i:2708929 original size:16 final size:17
Alignment explanation
Indices: 2708902--2708937 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2708892 GATATGATAA
2708902 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
2708919 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
2708935 AAA
1 AAA
2708938 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:2710690 original size:17 final size:16
Alignment explanation
Indices: 2710668--2710743 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 16
2710658 AAGCTTAAAT
2710668 AAAATAATTAAAAAAAC
1 AAAATAA-TAAAAAAAC
*
2710685 AAAATAATAATAAAAAT
1 AAAATAATAA-AAAAAC
2710702 AAAA-AGAGTAAAAAAAC
1 AAAATA-A-TAAAAAAAC
* *
2710719 AACATAGAATAAAAAAAT
1 AA-A-ATAATAAAAAAAC
2710737 AAAATAA
1 AAAATAA
2710744 GTACAAGGAC
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
16 7 0.14
17 25 0.51
18 14 0.29
19 2 0.04
20 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (16 bp):
AAAATAATAAAAAAAC
Found at i:2710702 original size:34 final size:35
Alignment explanation
Indices: 2710664--2710746 Score: 109
Period size: 34 Copynumber: 2.4 Consensus size: 35
2710654 TAATAAGCTT
* *
2710664 AAATAAAATAATTAAAAAAACAA-A-ATAATAATAA
1 AAATAAAATAAGTAAAAAAACAACATAGAATAA-AA
2710698 AAATAAAA-AGAGTAAAAAAACAACATAGAATAAAA
1 AAATAAAATA-AGTAAAAAAACAACATAGAATAAAA
2710733 AAATAAAATAAGTA
1 AAATAAAATAAGTA
2710747 CAAGGACCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
33 1 0.02
34 20 0.47
35 15 0.35
36 7 0.16
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.17
Consensus pattern (35 bp):
AAATAAAATAAGTAAAAAAACAACATAGAATAAAA
Found at i:2710731 original size:18 final size:16
Alignment explanation
Indices: 2710676--2710740 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 16
2710666 ATAAAATAAT
*
2710676 TAAAAAAACAAAATAA
1 TAAAAAAACAAAAGAA
* *
2710692 TAATAAAAATAAAAAGAG
1 TAA-AAAAA-CAAAAGAA
2710710 TAAAAAAACAACATAGAA
1 TAAAAAAACAA-A-AGAA
*
2710728 TAAAAAAATAAAA
1 TAAAAAAACAAAA
2710741 TAAGTACAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.15
17 12 0.31
18 21 0.54
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (16 bp):
TAAAAAAACAAAAGAA
Found at i:2716424 original size:20 final size:20
Alignment explanation
Indices: 2716401--2716458 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2716391 GTACTGTATG
*
2716401 AATAGCACCGATACTGTGCA
1 AATAGTACCGATACTGTGCA
* **
2716421 AATAGTACCTATGTTGTGCA
1 AATAGTACCGATACTGTGCA
*
2716441 AATAGTATCGATACTGTG
1 AATAGTACCGATACTGTG
2716459 TGAACAGTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (20 bp):
AATAGTACCGATACTGTGCA
Found at i:2717741 original size:16 final size:16
Alignment explanation
Indices: 2717720--2717753 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2717710 CCTTTAGGAG
2717720 TGTACCGATACACTCA
1 TGTACCGATACACTCA
2717736 TGTACCGATACACTCA
1 TGTACCGATACACTCA
2717752 TG
1 TG
2717754 GTGTATCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (16 bp):
TGTACCGATACACTCA
Found at i:2717763 original size:19 final size:17
Alignment explanation
Indices: 2717718--2717765 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
2717708 TTCCTTTAGG
2717718 AGTGTACCGATACACTC
1 AGTGTACCGATACACTC
2717735 A-TGTACCGATACACTC
1 AGTGTACCGATACACTC
*
2717751 ATGGTGTATCGATAC
1 A--GTGTACCGATAC
2717766 CTAAATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 16 0.59
17 1 0.04
19 10 0.37
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (17 bp):
AGTGTACCGATACACTC
Found at i:2722112 original size:18 final size:18
Alignment explanation
Indices: 2722089--2722125 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2722079 CTCTCGATAA
2722089 ATTCTAAGAGTTAAAAAC
1 ATTCTAAGAGTTAAAAAC
2722107 ATTCTAAGAGTTAAAAAC
1 ATTCTAAGAGTTAAAAAC
2722125 A
1 A
2722126 AATTATCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (18 bp):
ATTCTAAGAGTTAAAAAC
Found at i:2723520 original size:19 final size:21
Alignment explanation
Indices: 2723496--2723541 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
2723486 CGTTTTAGTA
2723496 ATATTT-AA-ATTATCAATAT
1 ATATTTAAACATTATCAATAT
2723515 ATATTTTAAAACATTATCAATAT
1 ATA-TTT-AAACATTATCAATAT
2723538 ATAT
1 ATAT
2723542 CATATAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.13
20 3 0.13
22 3 0.13
23 14 0.61
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATTTAAACATTATCAATAT
Found at i:2726077 original size:2 final size:2
Alignment explanation
Indices: 2726070--2726100 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2726060 ATATCTGGCA
2726070 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 A
2726101 ATCCAATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2726206 original size:15 final size:15
Alignment explanation
Indices: 2726186--2726216 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2726176 AAGTTTTGAT
2726186 AGTCTAGGTAATTAA
1 AGTCTAGGTAATTAA
2726201 AGTCTAGGTAATTAA
1 AGTCTAGGTAATTAA
2726216 A
1 A
2726217 TTATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
AGTCTAGGTAATTAA
Found at i:2728187 original size:16 final size:16
Alignment explanation
Indices: 2728166--2728197 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2728156 AATAAATAAG
2728166 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2728182 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2728198 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:2728212 original size:71 final size:71
Alignment explanation
Indices: 2728137--2728268 Score: 228
Period size: 71 Copynumber: 1.9 Consensus size: 71
2728127 AACGGATGTA
* *
2728137 TGTTCATGTTCATTCATTTAATAAATAAGCGAACATAAACGAACACGAACATAAACGAACAAATT
1 TGTTCATGTTCATTCATTTAACAAATAAACGAACATAAACGAACACGAACATAAACGAACAAATT
2728202 TTTTTT
66 TTTTTT
* *
2728208 TGTTCATGTTCGTTCATTTAACAAATAAACGAACATAAACGAACACGAACATAAATGAACA
1 TGTTCATGTTCATTCATTTAACAAATAAACGAACATAAACGAACACGAACATAAACGAACA
2728269 CGAACATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (71 bp):
TGTTCATGTTCATTCATTTAACAAATAAACGAACATAAACGAACACGAACATAAACGAACAAATT
TTTTTT
Found at i:2728247 original size:10 final size:10
Alignment explanation
Indices: 2728232--2728290 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
2728222 CATTTAACAA
2728232 ATAAACGAAC
1 ATAAACGAAC
2728242 ATAAACGAAC
1 ATAAACGAAC
** *
2728252 ACGAAC-ATAA
1 ATAAACGA-AC
2728262 ATGAACACGAAC
1 AT-AA-ACGAAC
2728274 ATAAACGAAC
1 ATAAACGAAC
2728284 ATAAACG
1 ATAAACG
2728291 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2728257 original size:16 final size:16
Alignment explanation
Indices: 2728236--2728284 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
2728226 TAACAAATAA
2728236 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
2728252 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2728268 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2728284 A
1 A
2728285 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2729862 original size:24 final size:24
Alignment explanation
Indices: 2729801--2729862 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
2729791 TATTAGGTTA
*
2729801 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
2729825 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
2729849 AACATAACCGAACG
1 AACATAACTGAACG
2729863 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:2730769 original size:14 final size:14
Alignment explanation
Indices: 2730752--2730795 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2730742 TGAACGCACA
2730752 TAAACGAACATAAC
1 TAAACGAACATAAC
2730766 TAAACG--CAT-A-
1 TAAACGAACATAAC
2730776 TAAACGAACATAAC
1 TAAACGAACATAAC
*
2730790 TGAACG
1 TAAACG
2730796 TTCACGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
10 6 0.24
11 1 0.04
12 6 0.24
13 1 0.04
14 11 0.44
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.16
Consensus pattern (14 bp):
TAAACGAACATAAC
Found at i:2730771 original size:24 final size:24
Alignment explanation
Indices: 2730734--2730795 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
2730724 TATTAGGTTA
*
2730734 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
2730758 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
2730782 AACATAACTGAACG
1 AACATAACTGAACG
2730796 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:2731042 original size:933 final size:933
Alignment explanation
Indices: 2729236--2731102 Score: 3689
Period size: 933 Copynumber: 2.0 Consensus size: 933
2729226 ATCCAGCAGC
2729236 GCTCCACTGACCACGCCACTTTCTTCCCCCACTAGAGGATATAAGCGCAAATCTGACTGGGACTC
1 GCTCCACTGACCACGCCACTTTCTTCCCCCACTAGAGGATATAAGCGCAAATCTGACTGGGACTC
2729301 CCTAAGGGCAACTCTAACGCGGATGATTGGGCAACGAGGGGTGGGCTGGAGAAGACCGACTGGTC
66 CCTAAGGGCAACTCTAACGCGGATGATTGGGCAACGAGGGGTGGGCTGGAGAAGACCGACTGGTC
*
2729366 GAATGCACCGTTCATAGCGGCGTACAAGGGGATCCACATCGTTCAAGATGCCACAAAAAATCCCT
131 GAATGCACCGTTCATAGCGGCGTACAAGGGGATCCACATCGTTCAAAATGCCACAAAAAATCCCT
2729431 AAATTCACACCCCAAAATTAACAGACCAAAAAGAAATTCAAATTATTTACCTTATGAAATCACGT
196 AAATTCACACCCCAAAATTAACAGACCAAAAAGAAATTCAAATTATTTACCTTATGAAATCACGT
*
2729496 TCAAGAAGGGAAAGAGATGAATCTCTGTCGAATCGTTGTAGTTGAAGACTTGAAGCTCCGTCGAA
261 TCAAGAAGGGAAAGAGATGAATCTCTGTCGAATCGTTGCAGTTGAAGACTTGAAGCTCCGTCGAA
2729561 TCGTTGCAGAAATGAAAATTGTGGAGGGTGGGGAGAGTTGAGAATCAAGAACAGCTGAATGACGG
326 TCGTTGCAGAAATGAAAATTGTGGAGGGTGGGGAGAGTTGAGAATCAAGAACAGCTGAATGACGG
2729626 GTTGGAGAAGAGTTGAGAAAATATTGCTTTTAGATTTAGGGTTTTTTGTATTACCGCTTAATCAG
391 GTTGGAGAAGAGTTGAGAAAATATTGCTTTTAGATTTAGGGTTTTTTGTATTACCGCTTAATCAG
2729691 GCTGTAAAATTGGGTTAATTATGAAGTTGGTCATCAAAATATCATATTAATTAATATTTTTAAGA
456 GCTGTAAAATTGGGTTAATTATGAAGTTGGTCATCAAAATATCATATTAATTAATATTTTTAAGA
*
2729756 TACATACAAATTGGTCACCAAAATTGATTTAAGAATATTAGGTTAAACATAAATGAACGCACATA
521 TACATACAAATTGGTCACCAAAATTGATTCAAGAATATTAGGTTAAACATAAATGAACGCACATA
2729821 AACGAACATAACTAAACGCATATAAACGAACATAACCGAACGTTCACGAACGTAAATGAACGAAC
586 AACGAACATAACTAAACGCATATAAACGAACATAACCGAACGTTCACGAACGTAAATGAACGAAC
*
2729886 GAGACCTATGTTCATGTTCGTTTATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCAT
651 GAGACCTATGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCAT
2729951 TTAATAAATAAACGCACATAAACGAACTTCCCGCCGCACGGTTCATGAACGGTTCGCTGAACGTT
716 TTAATAAATAAACGCACATAAACGAACTTCCCGCCGCACGGTTCATGAACGGTTCGCTGAACGTT
2730016 CAGTTCATTTACAGGCCTACTAATCAATTTCACAGCCAATGACAACCATTTCAGGGGTCCAATAC
781 CAGTTCATTTACAGGCCTACTAATCAATTTCACAGCCAATGACAACCATTTCAGGGGTCCAATAC
2730081 CCAAAGACTTGAAAAATTGCAGCAGCCTTAAAAGAATGCGCCTTGAAAGAAACAGGCTGACTTGA
846 CCAAAGACTTGAAAAATTGCAGCAGCCTTAAAAGAATGCGCCTTGAAAGAAACAGGCTGACTTGA
2730146 AATACATCAGAAGATTTTGGAGT
911 AATACATCAGAAGATTTTGGAGT
2730169 GCTCCACTGACCACGCCACTTTCTTCCCCCACTAGAGGATATAAGCGCAAATCTGACTGGGACTC
1 GCTCCACTGACCACGCCACTTTCTTCCCCCACTAGAGGATATAAGCGCAAATCTGACTGGGACTC
2730234 CCTAAGGGCAACTCTAACGCGGATGATTGGGCAACGAGGGGTGGGCTGGAGAAGACCGACTGGTC
66 CCTAAGGGCAACTCTAACGCGGATGATTGGGCAACGAGGGGTGGGCTGGAGAAGACCGACTGGTC
2730299 GAATGCACCGTTCATAGCGGCGTACAAGGGGATCCACATCGTTCAAAATGCCACAAAAAATCCCT
131 GAATGCACCGTTCATAGCGGCGTACAAGGGGATCCACATCGTTCAAAATGCCACAAAAAATCCCT
2730364 AAATTCACACCCCAAAATTAACAGACCAAAAAGAAATTCAAATTATTTACCTTATGAAATCACGT
196 AAATTCACACCCCAAAATTAACAGACCAAAAAGAAATTCAAATTATTTACCTTATGAAATCACGT
2730429 TCAAGAAGGGAAAGAGATGAATCTCTGTCGAATCGTTGCAGTTGAAGACTTGAAGCTCCGTCGAA
261 TCAAGAAGGGAAAGAGATGAATCTCTGTCGAATCGTTGCAGTTGAAGACTTGAAGCTCCGTCGAA
2730494 TCGTTGCAGAAATGAAAATTGTGGAGGGTGGGGAGAGTTGAGAATCAAGAACAGCTGAATGACGG
326 TCGTTGCAGAAATGAAAATTGTGGAGGGTGGGGAGAGTTGAGAATCAAGAACAGCTGAATGACGG
2730559 GTTGGAGAAGAGTTGAGAAAATATTGCTTTTAGATTTAGGGTTTTTTGTATTACCGCTTAATCAG
391 GTTGGAGAAGAGTTGAGAAAATATTGCTTTTAGATTTAGGGTTTTTTGTATTACCGCTTAATCAG
2730624 GCTGTAAAATTGGGTTAATTATGAAGTTGGTCATCAAAATATCATATTAATTAATATTTTTAAGA
456 GCTGTAAAATTGGGTTAATTATGAAGTTGGTCATCAAAATATCATATTAATTAATATTTTTAAGA
2730689 TACATACAAATTGGTCACCAAAATTGATTCAAGAATATTAGGTTAAACATAAATGAACGCACATA
521 TACATACAAATTGGTCACCAAAATTGATTCAAGAATATTAGGTTAAACATAAATGAACGCACATA
*
2730754 AACGAACATAACTAAACGCATATAAACGAACATAACTGAACGTTCACGAACGTAAATGAACGAAC
586 AACGAACATAACTAAACGCATATAAACGAACATAACCGAACGTTCACGAACGTAAATGAACGAAC
2730819 GAGACCTATGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCAT
651 GAGACCTATGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCAT
2730884 TTAATAAATAAACGCACATAAACGAACTTCCCGCCGCACGGTTCATGAACGGTTCGCTGAACGTT
716 TTAATAAATAAACGCACATAAACGAACTTCCCGCCGCACGGTTCATGAACGGTTCGCTGAACGTT
2730949 CAGTTCATTTACAGGCCTACTAATCAATTTCACAGCCAATGACAACCATTTCAGGGGTCCAATAC
781 CAGTTCATTTACAGGCCTACTAATCAATTTCACAGCCAATGACAACCATTTCAGGGGTCCAATAC
2731014 CCAAAGACTTGAAAAATTGCAGCAGCCTTAAAAGAATGCGCCTTGAAAGAAACAGGCTGACTTGA
846 CCAAAGACTTGAAAAATTGCAGCAGCCTTAAAAGAATGCGCCTTGAAAGAAACAGGCTGACTTGA
2731079 AATACATCAGAAGATTTTGGAGT
911 AATACATCAGAAGATTTTGGAGT
2731102 G
1 G
2731103 TATCCTAGCT
Statistics
Matches: 929, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
933 929 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (933 bp):
GCTCCACTGACCACGCCACTTTCTTCCCCCACTAGAGGATATAAGCGCAAATCTGACTGGGACTC
CCTAAGGGCAACTCTAACGCGGATGATTGGGCAACGAGGGGTGGGCTGGAGAAGACCGACTGGTC
GAATGCACCGTTCATAGCGGCGTACAAGGGGATCCACATCGTTCAAAATGCCACAAAAAATCCCT
AAATTCACACCCCAAAATTAACAGACCAAAAAGAAATTCAAATTATTTACCTTATGAAATCACGT
TCAAGAAGGGAAAGAGATGAATCTCTGTCGAATCGTTGCAGTTGAAGACTTGAAGCTCCGTCGAA
TCGTTGCAGAAATGAAAATTGTGGAGGGTGGGGAGAGTTGAGAATCAAGAACAGCTGAATGACGG
GTTGGAGAAGAGTTGAGAAAATATTGCTTTTAGATTTAGGGTTTTTTGTATTACCGCTTAATCAG
GCTGTAAAATTGGGTTAATTATGAAGTTGGTCATCAAAATATCATATTAATTAATATTTTTAAGA
TACATACAAATTGGTCACCAAAATTGATTCAAGAATATTAGGTTAAACATAAATGAACGCACATA
AACGAACATAACTAAACGCATATAAACGAACATAACCGAACGTTCACGAACGTAAATGAACGAAC
GAGACCTATGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATCTTGTTCATGTTCGTTCAT
TTAATAAATAAACGCACATAAACGAACTTCCCGCCGCACGGTTCATGAACGGTTCGCTGAACGTT
CAGTTCATTTACAGGCCTACTAATCAATTTCACAGCCAATGACAACCATTTCAGGGGTCCAATAC
CCAAAGACTTGAAAAATTGCAGCAGCCTTAAAAGAATGCGCCTTGAAAGAAACAGGCTGACTTGA
AATACATCAGAAGATTTTGGAGT
Found at i:2733507 original size:14 final size:14
Alignment explanation
Indices: 2733488--2733538 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
2733478 GATTATATGC
2733488 TCATTTATGTTCGT
1 TCATTTATGTTCGT
2733502 TCATTTATG-TC--
1 TCATTTATGTTCGT
2733513 T-ATTTATGTTCGT
1 TCATTTATGTTCGT
2733526 TCATTTATGTTCG
1 TCATTTATGTTCG
2733539 AACAGAGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 7 0.21
11 3 0.09
13 3 0.09
14 20 0.61
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TCATTTATGTTCGT
Found at i:2733517 original size:24 final size:25
Alignment explanation
Indices: 2733473--2733535 Score: 94
Period size: 24 Copynumber: 2.5 Consensus size: 25
2733463 CGTTCGTGAA
2733473 CGTTCGATTATATG-CTCATTTATGTT
1 CGTTC-ATT-TATGTCTCATTTATGTT
2733499 CGTTCATTTATGTCT-ATTTATGTT
1 CGTTCATTTATGTCTCATTTATGTT
2733523 CGTTCATTTATGT
1 CGTTCATTTATGT
2733536 TCGAACAGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 26 0.72
25 5 0.14
26 5 0.14
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.54
Consensus pattern (25 bp):
CGTTCATTTATGTCTCATTTATGTT
Found at i:2733815 original size:13 final size:14
Alignment explanation
Indices: 2733794--2733873 Score: 71
Period size: 13 Copynumber: 5.9 Consensus size: 14
2733784 GTTTTTTTAT
*
2733794 GTTTGTGTT-GTTC
1 GTTTATGTTCGTTC
*
2733807 GTTTATGTTCATT-
1 GTTTATGTTCGTTC
2733820 -TATTATGTTCGTTC
1 GT-TTATGTTCGTTC
*
2733834 GTTTATGTTCATT-
1 GTTTATGTTCGTTC
2733847 -TATTATGTTCGTTC
1 GT-TTATGTTCGTTC
*
2733861 GTTTGTGTTCGTT
1 GTTTATGTTCGTT
2733874 TATCATTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.04
13 28 0.52
14 22 0.41
15 2 0.04
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.60
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:2733833 original size:27 final size:27
Alignment explanation
Indices: 2733799--2733876 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
2733789 TTTATGTTTG
2733799 TGTT-GTTCGTTTATGTTCATTTATTA
1 TGTTCGTTCGTTTATGTTCATTTATTA
2733825 TGTTCGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTCGTTTATGTTCATTTATTA
* *
2733852 TGTTCGTTCGTTTGTGTTCGTTTAT
1 TGTTCGTTCGTTTATGTTCATTTAT
2733877 CATTTAAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 4 0.08
27 45 0.92
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (27 bp):
TGTTCGTTCGTTTATGTTCATTTATTA
Found at i:2740623 original size:16 final size:16
Alignment explanation
Indices: 2740602--2740655 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
2740592 CATACAAAAC
*
2740602 ATTTAAATCATTCAAT
1 ATTTAAATCATTTAAT
*
2740618 ATTTAAATCATTTAAA
1 ATTTAAATCATTTAAT
*
2740634 ATTTAAATTATTTAAT
1 ATTTAAATCATTTAAT
2740650 ATTTAA
1 ATTTAA
2740656 TCCTTCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAAATCATTTAAT
Found at i:2740630 original size:9 final size:9
Alignment explanation
Indices: 2740601--2740648 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
2740591 TCATACAAAA
2740601 CATTTAAAT
1 CATTTAAAT
*
2740610 CA-TTCAAT
1 CATTTAAAT
2740618 -ATTTAAAT
1 CATTTAAAT
2740626 CATTTAAA-
1 CATTTAAAT
2740634 -ATTTAAAT
1 CATTTAAAT
*
2740642 TATTTAA
1 CATTTAA
2740649 TATTTAATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 8 0.24
8 10 0.30
9 15 0.45
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (9 bp):
CATTTAAAT
Found at i:2747547 original size:35 final size:34
Alignment explanation
Indices: 2747462--2747548 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2747452 AATATAATTT
*
2747462 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
2747496 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
2747534 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2747549 ACTAAATACA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:2747780 original size:3 final size:3
Alignment explanation
Indices: 2747774--2747818 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
2747764 TCATCATCAC
* * * *
2747774 CGT CGT CGT CAT CGT CGT CGT CGT CAT CGC CGT CGT CAT CGT CGT
1 CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT CGT
2747819 TTTCGTCCTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.07, C:0.36, G:0.27, T:0.31
Consensus pattern (3 bp):
CGT
Found at i:2747792 original size:15 final size:15
Alignment explanation
Indices: 2747774--2747818 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
2747764 TCATCATCAC
2747774 CGTCGTCGTCATCGT
1 CGTCGTCGTCATCGT
2747789 CGTCGTCGTCATCG-
1 CGTCGTCGTCATCGT
2747803 C--CGTCGTCATCGT
1 CGTCGTCGTCATCGT
2747816 CGT
1 CGT
2747819 TTTCGTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 11 0.41
13 1 0.04
14 1 0.04
15 14 0.52
ACGTcount: A:0.07, C:0.36, G:0.27, T:0.31
Consensus pattern (15 bp):
CGTCGTCGTCATCGT
Found at i:2749798 original size:17 final size:18
Alignment explanation
Indices: 2749778--2749818 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2749768 AAATTATATT
2749778 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
2749795 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
2749813 ATTAAA
1 AGTAAA
2749819 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:2751778 original size:33 final size:33
Alignment explanation
Indices: 2751731--2751801 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
2751721 ACAAAGTTTA
* *
2751731 CGAT-AATTGAAATACTTAAATACTTCCAAGCT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGCT
*
2751763 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGCT
2751796 CGATAA
1 CGATAA
2751802 TTGAAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGCT
Found at i:2751821 original size:21 final size:21
Alignment explanation
Indices: 2751796--2751837 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2751786 CTTCCAAGTT
2751796 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
2751817 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
2751838 AAAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2751874 original size:14 final size:15
Alignment explanation
Indices: 2751855--2751884 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2751845 ACTATATCGC
2751855 CATCTTTT-CTTTTT
1 CATCTTTTCCTTTTT
2751869 CATCTTTTCCTTTTT
1 CATCTTTTCCTTTTT
2751884 C
1 C
2751885 GTTTGGAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (15 bp):
CATCTTTTCCTTTTT
Found at i:2755517 original size:22 final size:22
Alignment explanation
Indices: 2755489--2755536 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2755479 AACTTTTTGA
*
2755489 TCAAAGTCAACGT-TGGTCAAAT
1 TCAAAGTCAAC-TCTGGTCAAAG
2755511 TCAAAGTCAACTCTGGTCAAAG
1 TCAAAGTCAACTCTGGTCAAAG
2755533 TCAA
1 TCAA
2755537 TGGCCATGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (22 bp):
TCAAAGTCAACTCTGGTCAAAG
Found at i:2755600 original size:13 final size:13
Alignment explanation
Indices: 2755582--2755606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2755572 GATTTTGTTC
2755582 AGTTGACTCAACG
1 AGTTGACTCAACG
2755595 AGTTGACTCAAC
1 AGTTGACTCAAC
2755607 TAGACCTAGT
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
AGTTGACTCAACG
Found at i:2759568 original size:19 final size:19
Alignment explanation
Indices: 2759546--2759612 Score: 50
Period size: 19 Copynumber: 3.6 Consensus size: 19
2759536 TATTTAATTC
2759546 ATTAAATATTATTATTATT
1 ATTAAATATTATTATTATT
* **
2759565 ATTATATA-TATTAATTAAA
1 ATTAAATATTATT-ATTATT
* *
2759584 ATAAAATATT-TTAATATT
1 ATTAAATATTATTATTATT
2759602 -TTAAAATATTA
1 ATT-AAATATTA
2759613 AATAATTATT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.40
19 19 0.54
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAAATATTATTATTATT
Found at i:2770069 original size:29 final size:30
Alignment explanation
Indices: 2770026--2770094 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
2770016 ATGCCATGAC
2770026 TATGGTGGTTGAAGGAGAGAAGAGGCGCTG
1 TATGGTGGTTGAAGGAGAGAAGAGGCGCTG
* *
2770056 TATGGT-GTTGAAGGAGAGAAGCGGCTCTG
1 TATGGTGGTTGAAGGAGAGAAGAGGCGCTG
* *
2770085 TTTGTTGGTT
1 TATGGTGGTT
2770095 ATGGGTTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.22, C:0.07, G:0.42, T:0.29
Consensus pattern (30 bp):
TATGGTGGTTGAAGGAGAGAAGAGGCGCTG
Found at i:2770754 original size:12 final size:12
Alignment explanation
Indices: 2770737--2770761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2770727 GATTAAGGGT
2770737 AATACACTTTTA
1 AATACACTTTTA
2770749 AATACACTTTTA
1 AATACACTTTTA
2770761 A
1 A
2770762 TTTAAAATTG
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
AATACACTTTTA
Found at i:2779136 original size:22 final size:21
Alignment explanation
Indices: 2779110--2779176 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
2779100 TCGCACTTAG
2779110 TAAGTCTTTCGAGCATGATGCT
1 TAAGTCTTTCGAGCATGATG-T
* * *
2779132 TAAGTCCTTCGGACCATTA-G-
1 TAAGTCTTTC-GAGCATGATGT
*
2779152 TAAGTCTTTCGAGTATGATGAT
1 TAAGTCTTTCGAGCATGATG-T
2779174 TAA
1 TAA
2779177 ATCCTTCGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 5 0.15
20 10 0.29
22 13 0.38
23 6 0.18
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGT
Found at i:2779170 original size:42 final size:42
Alignment explanation
Indices: 2779106--2779389 Score: 186
Period size: 42 Copynumber: 6.9 Consensus size: 42
2779096 AATTTCGCAC
* *
2779106 TTAGTAAGTCTTTCGAGCATGATGCTTAAGTCCTTCGGACCA
1 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGACCA
* ***
2779148 TTAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAA
1 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGACCA
** * * * * * **** ** *
2779190 TTTTTAAG-CCTTC-A-C-GGAAGAGT-AGTGAAGCAAATCCG
1 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGA-CCA
* * * *
2779228 TCAGTAAGTCTTTCGAGCATGATGA-TGAATCCTTTGGTCCA
1 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGACCA
* * **
2779269 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA
1 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGACCA
* * **
2779311 TCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCA
1 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGACCA
* * * *
2779353 TTTGTGAGTCTCTCGAGCAAGATGA-TAAATCCTTCGG
1 TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
2779390 GTAGGATATT
Statistics
Matches: 182, Mismatches: 53, Indels: 15
0.73 0.21 0.06
Matches are distributed among these distances:
37 3 0.02
38 10 0.05
39 4 0.02
40 2 0.01
41 45 0.25
42 118 0.65
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (42 bp):
TTAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGACCA
Found at i:2779285 original size:41 final size:41
Alignment explanation
Indices: 2779228--2779391 Score: 222
Period size: 42 Copynumber: 4.0 Consensus size: 41
2779218 AGCAAATCCG
* *
2779228 TCAGTAAGTCTTTCGAGCATGATGATGAATCCTT-TGGTCCA
1 TCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGT-CA
2779269 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA
1 TCAGTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGTCA
*
2779311 TCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCA
1 TCAGTAAGTCTTTCGAGCATGATGA-TAAATCCTTCGGGTCA
** * * *
2779353 TTTGTGAGTCTCTCGAGCAAGATGATAAATCCTTCGGGT
1 TCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGT
2779392 AGGATATTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
41 40 0.36
42 67 0.60
43 4 0.04
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
TCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGTCA
Found at i:2779324 original size:83 final size:83
Alignment explanation
Indices: 2779228--2779391 Score: 224
Period size: 83 Copynumber: 2.0 Consensus size: 83
2779218 AGCAAATCCG
* * * * *
2779228 TCAGTAAGTCTTTCGAGCATGATGA-TGAATCCTT-TGGTCCATCAGTAAGTCTTTCGAGCATGA
1 TCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGT-CATCAGTAAGTCTCTCGAGCAAGA
2779291 TGATGAAATCCTTCGGGTCA
65 TGAT-AAATCCTTCGGGTCA
** *
2779311 TCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTGTGAGTCTCTCGAGCAAGAT
1 TCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGCAAGAT
2779376 GATAAATCCTTCGGGT
66 GATAAATCCTTCGGGT
2779392 AGGATATTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
83 37 0.52
84 31 0.44
85 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (83 bp):
TCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGCAAGAT
GATAAATCCTTCGGGTCA
Found at i:2779761 original size:53 final size:53
Alignment explanation
Indices: 2779692--2780007 Score: 402
Period size: 53 Copynumber: 5.9 Consensus size: 53
2779682 AGAATCACAC
2779692 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* * * *
2779745 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCGAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* * *
2779798 CAGAAGATTGTTCGAGTTCTACTCCCCGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* *
2779851 CAAAAGATTGTTCGAGTTCTACACCCTGAAGCAAGAGGGAGCGAACCCGTA-A
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* * * * * * ***
2779903 GTAGAAGATTATTCGAGTTCTACGCTCTGAAGCAAAAGGGAGCGAACTCGTTTT
1 -CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
* * *
2779957 TAGAAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCAAACCCGT
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
2780008 CATTTGAAGA
Statistics
Matches: 231, Mismatches: 28, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
53 206 0.89
54 17 0.07
55 8 0.03
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGA
Found at i:2781808 original size:28 final size:26
Alignment explanation
Indices: 2781758--2781820 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
2781748 GCATGGTTTA
*
2781758 TATATTTTTTTAATTAAAAATATATG
1 TATAATTTTTTAATTAAAAATATATG
2781784 TATAATTTTTTAATTAAAAATATATG
1 TATAATTTTTTAATTAAAAATATATG
2781810 TATAATTTTTT
1 TATAATTTTTT
2781821 GTATGTCACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TATAATTTTTTAATTAAAAATATATG
Found at i:2784040 original size:31 final size:33
Alignment explanation
Indices: 2783982--2784043 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
2783972 TCAATGAAAA
2783982 TTGAATTAAATAAGAAAAGAAAAGATAAAATCT
1 TTGAATTAAATAAGAAAAGAAAAGATAAAATCT
2784015 TTGAATTAAATAA-AAAAG-AAAGATAAAAT
1 TTGAATTAAATAAGAAAAGAAAAGATAAAAT
2784044 GAAAGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 11 0.38
32 5 0.17
33 13 0.45
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (33 bp):
TTGAATTAAATAAGAAAAGAAAAGATAAAATCT
Found at i:2789652 original size:12 final size:12
Alignment explanation
Indices: 2789635--2789659 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2789625 AAGTTAAAAT
2789635 AATAAAATTTAA
1 AATAAAATTTAA
2789647 AATAAAATTTAA
1 AATAAAATTTAA
2789659 A
1 A
2789660 TTTTATTAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAAAATTTAA
Found at i:2792063 original size:18 final size:18
Alignment explanation
Indices: 2792042--2792077 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2792032 GCCACCGCGG
*
2792042 CCATTTATGATGCCGCAA
1 CCATATATGATGCCGCAA
2792060 CCATATATGATGCCGCAA
1 CCATATATGATGCCGCAA
2792078 TCGCCTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (18 bp):
CCATATATGATGCCGCAA
Found at i:2792434 original size:12 final size:12
Alignment explanation
Indices: 2792417--2792443 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2792407 TGTTCAGGAC
2792417 GACGACGACGAT
1 GACGACGACGAT
2792429 GACGACGACGAT
1 GACGACGACGAT
2792441 GAC
1 GAC
2792444 AGCGAGGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.26, G:0.33, T:0.07
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:2792748 original size:38 final size:37
Alignment explanation
Indices: 2792668--2792748 Score: 85
Period size: 38 Copynumber: 2.1 Consensus size: 37
2792658 TTTTGTTTAT
**
2792668 TACCATTTAATATCAGTTATTGTAATTTGGTTATTATT
1 TACCATTTAATATCA-TTATTGTAATTTGGTTATTAAA
*
2792706 TACCATTTAAT-TC-TTATTGTAAGTTTGTTGTATTTAAA
1 TACCATTTAATATCATTATTGTAA-TTTGGT-TA-TTAAA
2792744 TACCA
1 TACCA
2792749 AATTATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 9 0.24
36 5 0.14
37 4 0.11
38 19 0.51
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.51
Consensus pattern (37 bp):
TACCATTTAATATCATTATTGTAATTTGGTTATTAAA
Found at i:2795203 original size:90 final size:91
Alignment explanation
Indices: 2795064--2795228 Score: 269
Period size: 90 Copynumber: 1.8 Consensus size: 91
2795054 AAACTTTACA
* * * *
2795064 TCTCTTTTCTTTTCTTCAGAATTGTCACTAACAACCAAAACTATATTTTGAGTAAACAAACAAAG
1 TCTCTTTTCTTTTCTTCAGAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
*
2795129 CGAGGAGCAAATAAACTTCAAAAACT
66 CAAGGAGCAAATAAACTTCAAAAACT
*
2795155 TCTCTTTTCTTTT-TTCATAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
1 TCTCTTTTCTTTTCTTCAGAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
2795219 CAAGGAGCAA
66 CAAGGAGCAA
2795229 TATAGTATGG
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 55 0.81
91 13 0.19
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (91 bp):
TCTCTTTTCTTTTCTTCAGAAATGACACTAAAAACCAAAACTACATTTTGAGTAAACAAACAAAG
CAAGGAGCAAATAAACTTCAAAAACT
Found at i:2795989 original size:31 final size:31
Alignment explanation
Indices: 2795954--2796012 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2795944 AGCTTAAAAG
*
2795954 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
2795985 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2796013 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2796061 original size:22 final size:22
Alignment explanation
Indices: 2796036--2796485 Score: 692
Period size: 22 Copynumber: 20.6 Consensus size: 22
2796026 ATAATAAATT
*
2796036 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
2796058 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2796080 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2796102 TTTTAAAATAATTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
2796124 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
*
2796146 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
2796168 TTTTTAAAATAAATTTTTCCATA
1 -TTTTAAAATAAATCAATCCATA
2796191 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2796213 TTTTAAAATAAAT-AATCCCTA
1 TTTTAAAATAAATCAATCCATA
2796234 TTTT-AAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2796255 TTTTAAAA-AAATC-ATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2796275 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
2796297 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2796319 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
2796341 TTTTAAAATAATTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
2796363 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
*
2796385 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
2796407 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
2796429 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
2796451 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
2796473 TTTTAAAATAAAT
1 TTTTAAAATAAAT
2796486 TTTAAAAAAG
Statistics
Matches: 392, Mismatches: 31, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
20 23 0.06
21 32 0.08
22 319 0.81
23 18 0.05
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:2797779 original size:3 final size:3
Alignment explanation
Indices: 2797771--2797796 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2797761 GAATAAGGTT
2797771 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2797797 ATAAGGGCAG
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2800724 original size:17 final size:17
Alignment explanation
Indices: 2800675--2800726 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2800665 ATCAAAGAGT
2800675 TAGTTTAATT-ATGAAC
1 TAGTTTAATTAATGAAC
* **
2800691 TAGTTAAACGAATGAAC
1 TAGTTTAATTAATGAAC
*
2800708 TAGTTTAATTAAAGAAC
1 TAGTTTAATTAATGAAC
2800725 TA
1 TA
2800727 ACTTTATTGA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2803695 original size:389 final size:386
Alignment explanation
Indices: 2802986--2803760 Score: 1291
Period size: 389 Copynumber: 2.0 Consensus size: 386
2802976 TTGTAAATTA
*
2802986 GCATACAACTTTTCATTCTTAAAACAATAAAATTAAAACTTTGTTTTAAACGATGTTCCGTTCCT
1 GCATACAACTTTTCATTCTTAAAACAATAAAATTAAAACTTTGTTTTAAACGATGTTCCGTTCAT
2803051 CATCATCCCGTATCCTTATTTGGTGGTAGCCACTCTTAATCAATCGTAATATGATTTCTACTCGA
66 CATCATCCCGTATCCTTATTTGGTGGTAGCCACTCTTAATCAATCGTAATATGATTTCTACTCGA
2803116 CATCCACAACATGTGCCATATCCATCATTCTTTGGCACAAGTAACACCGGCACGACACAAGAACT
131 CATCCACAACATGTGCCATATCCATCATTCTTTGGCACAAGTAACACCGGCACGACACAAGAACT
*
2803181 AAGACTCTCCCTACATATCCTTTTGCCATCAACTAATTCACTTGTCTTGCAAGTGTTGGTTTCCT
196 AAGACTCTACCTACATATCCTTTTGCCATCAACTAATTCACTTGTCTTGCAAGTGTTGGTTTCCT
*
2803246 ACGGATTGCTTCGATAAGCTGGTCATTTAGGAATGATGGCACAGTGTACAAAATCTATTTGATG-
261 ACGGATTGCTTCGATAAGCTGGTCAGTTAGGAATGATGGCACAGTGTACAAAATCTATTTGATGT
*
2803310 TTC-ATT-C-CGGA-TGGTCACAACCCACTTGGTATTTCTTGCAGAAATAATTCGTCAAAT
326 TTCAATTCCACGGATTGGTCACAACCCACTTGGTATTTCCTGCAGAAATAATTCGTCAAAT
2803367 GCATACAACTTTTCATTCTT-AAACAATAAAAATTAAAAC-TTGTTTTAAACGATGTTATCCGTT
1 GCATACAACTTTTCATTCTTAAAACAAT-AAAATTAAAACTTTGTTTTAAACGATG-T-TCCGTT
2803430 CATCATCATCCCGTATCCTTATTTGGT-GTAGCCACTCTTAAGATCAATCGTAATATGATTTACT
63 CATCATCATCCCGTATCCTTATTTGGTGGTAGCCACTCTT-A-ATCAATCGTAATATGATTT-CT
* *
2803494 ACTC-ACAATCCACAAACATGTGCCAATATCCATCATTCTTTGGCACGAGTAACACTGGCAC-AG
125 ACTCGAC-ATCCAC-AACATGTGCC-ATATCCATCATTCTTTGGCACAAGTAACACCGGCACGA-
*
2803557 CACAAGGACTAAGACTCTACCTCACATATCCTTTTGCCATCAACTAATTCACTTGTCTTTGCAAG
186 CACAAGAACTAAGACTCTACCT-ACATATCCTTTTGCCATCAACTAATTCACTTGTC-TTGCAAG
*
2803622 TGTTTGGTTTCCTACGGATTGCTTCGATAAGCTGGTCAGTTAGGAATGATGGCACATTGTACAAA
249 TG-TTGGTTTCCTACGGATTGCTTCGATAAGCTGGTCAGTTAGGAATGATGGCACAGTGTACAAA
2803687 ATCTATTTGATGTTTCAATTCCACGGATTGGTCACAACCCACTTGGTATTTCCTGCAGAAATAAT
313 ATCTATTTGATGTTTCAATTCCACGGATTGGTCACAACCCACTTGGTATTTCCTGCAGAAATAAT
2803752 TCGTCAAAT
378 TCGTCAAAT
2803761 TACTCCATTT
Statistics
Matches: 368, Mismatches: 8, Indels: 23
0.92 0.02 0.06
Matches are distributed among these distances:
380 22 0.06
381 44 0.12
382 33 0.09
383 21 0.06
384 12 0.03
385 11 0.03
386 54 0.15
387 34 0.09
388 9 0.02
389 72 0.20
390 3 0.01
391 3 0.01
392 1 0.00
393 4 0.01
394 45 0.12
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (386 bp):
GCATACAACTTTTCATTCTTAAAACAATAAAATTAAAACTTTGTTTTAAACGATGTTCCGTTCAT
CATCATCCCGTATCCTTATTTGGTGGTAGCCACTCTTAATCAATCGTAATATGATTTCTACTCGA
CATCCACAACATGTGCCATATCCATCATTCTTTGGCACAAGTAACACCGGCACGACACAAGAACT
AAGACTCTACCTACATATCCTTTTGCCATCAACTAATTCACTTGTCTTGCAAGTGTTGGTTTCCT
ACGGATTGCTTCGATAAGCTGGTCAGTTAGGAATGATGGCACAGTGTACAAAATCTATTTGATGT
TTCAATTCCACGGATTGGTCACAACCCACTTGGTATTTCCTGCAGAAATAATTCGTCAAAT
Found at i:2804129 original size:14 final size:15
Alignment explanation
Indices: 2804110--2804143 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2804100 CTCTACCATA
*
2804110 AGTACTAA-TACATT
1 AGTACTAACAACATT
2804124 AGTACTAACAACATT
1 AGTACTAACAACATT
2804139 AGTAC
1 AGTAC
2804144 AACTACCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (15 bp):
AGTACTAACAACATT
Found at i:2805758 original size:2 final size:2
Alignment explanation
Indices: 2805751--2805790 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2805741 GTAAGATGTA
2805751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2805791 AAGAAGAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2807148 original size:17 final size:17
Alignment explanation
Indices: 2807118--2807153 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2807108 ATCAAAGAGT
* *
2807118 TAGTTTAATTAATGAAC
1 TAGTTAAATGAATGAAC
2807135 TAGTTAAATGAATGAAC
1 TAGTTAAATGAATGAAC
2807152 TA
1 TA
2807154 ATTTAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (17 bp):
TAGTTAAATGAATGAAC
Found at i:2816113 original size:64 final size:58
Alignment explanation
Indices: 2815976--2816113 Score: 143
Period size: 61 Copynumber: 2.3 Consensus size: 58
2815966 ATTATCCTAA
* * *
2815976 TAATATTC-AAATTAAATAATATATTTAATTTGCAATAGACAAAAGGTAAACTCCTTT
1 TAATATTCAAAATTAAACAATATATTTAATTTGAAATAGACAAAAGATAAACTCCTTT
* * * * *
2816033 TACTATTCAAACTTAAACATATATTATTTTAATTTGAAATATACAAAAGTATATAATTATCTTT
1 TAATATTCAAAATTAAACA-ATA-TA-TTTAATTTGAAATAGACAAAAG-ATA-AACT-CCTTT
2816097 TAATATTCAAAATTAAA
1 TAATATTCAAAATTAAA
2816114 AAGATAACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
57 7 0.11
58 8 0.12
59 3 0.05
60 2 0.03
61 20 0.31
62 2 0.03
63 3 0.05
64 19 0.30
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (58 bp):
TAATATTCAAAATTAAACAATATATTTAATTTGAAATAGACAAAAGATAAACTCCTTT
Found at i:2816795 original size:26 final size:26
Alignment explanation
Indices: 2816759--2816811 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2816749 ATGCAATTAT
2816759 GTTGTCCCTTTGAACCTAAATATTGG
1 GTTGTCCCTTTGAACCTAAATATTGG
* *
2816785 GTTGTCCCTTTGAACCTAGATCTTGG
1 GTTGTCCCTTTGAACCTAAATATTGG
2816811 G
1 G
2816812 ATCTCCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (26 bp):
GTTGTCCCTTTGAACCTAAATATTGG
Found at i:2818920 original size:131 final size:131
Alignment explanation
Indices: 2818700--2818940 Score: 428
Period size: 131 Copynumber: 1.8 Consensus size: 131
2818690 CTTCACTATA
* * *
2818700 GTTAATTAAAACTCAAACCATCAAGATTCAAGGTGTGCCCCACAAAGTGTGCAACAACAGAGATC
1 GTTAATCAAAACCCAAACCATCAAGATTCAAGGTGTGCCCAACAAAGTGTGCAACAACAGAGATC
* *
2818765 TTGCAAAGATATTCGAATCTAATTTGAAATCATAAATTCAAAAATTGAAGGATTAAACTCACCAT
66 TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAATTGAAGGATTAAACTCACCAT
2818830 T
131 T
*
2818831 GTTAATCAAAACCCAAACCATCAAGATTCAAGGTGTGCCCAACAAAGTGTGCAACAAGAGAGATC
1 GTTAATCAAAACCCAAACCATCAAGATTCAAGGTGTGCCCAACAAAGTGTGCAACAACAGAGATC
2818896 TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAAT
66 TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAAT
2818941 CCTCTTGATT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 104 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (131 bp):
GTTAATCAAAACCCAAACCATCAAGATTCAAGGTGTGCCCAACAAAGTGTGCAACAACAGAGATC
TTGCAAAGATATTCAAATCCAATTTGAAATCATAAATTCAAAAATTGAAGGATTAAACTCACCAT
T
Found at i:2821647 original size:2 final size:2
Alignment explanation
Indices: 2821640--2821668 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2821630 TTATCCTTAT
2821640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2821669 TAAAAAGTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2824374 original size:31 final size:31
Alignment explanation
Indices: 2824331--2824389 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
2824321 CATTATTTCC
*
2824331 AAGTGACTAAAACTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACGT
2824362 AAGTGACCAAAACTTAATAAAACGATAA
1 AAGTGACCAAAACTTAATAAAACGATAA
2824390 AATAAGTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAACGT
Found at i:2824396 original size:31 final size:31
Alignment explanation
Indices: 2824331--2824396 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
2824321 CATTATTTCC
* **
2824331 AAGTGACTAAAACTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAAAAT
2824362 AAGTGACCAAAACTTAATAAAACGATAAAAT
1 AAGTGACCAAAACTTAATAAAACGATAAAAT
2824393 AAGT
1 AAGT
2824397 TACTAGAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAAAAT
Found at i:2825214 original size:29 final size:31
Alignment explanation
Indices: 2825156--2825217 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
2825146 TCAAAAAACA
* *
2825156 TAATATATGGTCATTTTTATTTGTATTTAAT
1 TAATATATGGTCACTTTCATTTGTATTTAAT
*
2825187 TAATATATGGTCACTTTCGTTT-T-TTTAAT
1 TAATATATGGTCACTTTCATTTGTATTTAAT
2825216 TA
1 TA
2825218 GGATGTGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 1 0.04
31 19 0.68
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.56
Consensus pattern (31 bp):
TAATATATGGTCACTTTCATTTGTATTTAAT
Found at i:2827514 original size:22 final size:22
Alignment explanation
Indices: 2827489--2827530 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2827479 GACTGACTAC
2827489 TATGCCCCGAAGGACCACTGTA
1 TATGCCCCGAAGGACCACTGTA
* *
2827511 TATGTCCCGAAGGACTACTG
1 TATGCCCCGAAGGACCACTG
2827531 ATAATCCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (22 bp):
TATGCCCCGAAGGACCACTGTA
Found at i:2828524 original size:12 final size:12
Alignment explanation
Indices: 2828507--2828531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2828497 TGATGACAAG
2828507 TCAAATTTAACT
1 TCAAATTTAACT
2828519 TCAAATTTAACT
1 TCAAATTTAACT
2828531 T
1 T
2828532 ATCAAATCTT
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTTAACT
Found at i:2832939 original size:18 final size:18
Alignment explanation
Indices: 2832912--2832984 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
2832902 ACTGTATATT
2832912 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
2832930 TGTCCGGAAGAACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
2832949 TTTATCCCAAAGGACCACTA
1 --TGTCCCGAAGGACCACTA
*
2832969 TGT-CCTAAGGACCACT
1 TGTCCCGAAGGACCACT
2832985 CCTTAAGAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
17 12 0.27
18 17 0.39
19 1 0.02
20 1 0.02
21 13 0.30
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:2843098 original size:19 final size:19
Alignment explanation
Indices: 2843074--2843113 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2843064 AATAAATTTA
2843074 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
2843093 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
2843112 AT
1 AT
2843114 ACCCGGCCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:2843142 original size:12 final size:12
Alignment explanation
Indices: 2843112--2843166 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
2843102 AAATATATAT
*
2843112 ATACCCGGCCCG
1 ATACCCGGCCCA
*
2843124 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
2843136 ATACCCGACCCA
1 ATACCCGGCCCA
*
2843148 ATACCCAGCCCA
1 ATACCCGGCCCA
2843160 ATACCCG
1 ATACCCG
2843167 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.25, C:0.49, G:0.15, T:0.11
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:2852146 original size:21 final size:21
Alignment explanation
Indices: 2852113--2852152 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2852103 TTGAGTGGAC
2852113 ATAAATATGATTTTTTAATGT
1 ATAAATATGATTTTTTAATGT
2852134 ATAAGATAT-ATTTTTTAAT
1 ATAA-ATATGATTTTTTAAT
2852153 AACTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
ATAAATATGATTTTTTAATGT
Found at i:2857747 original size:16 final size:16
Alignment explanation
Indices: 2857723--2857759 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2857713 ACGCTCGGCA
*
2857723 AATACCGATGAGCACC
1 AATAACGATGAGCACC
2857739 AATAACGATGAGCACC
1 AATAACGATGAGCACC
*
2857755 GATAA
1 AATAA
2857760 ATTAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (16 bp):
AATAACGATGAGCACC
Found at i:2858251 original size:39 final size:39
Alignment explanation
Indices: 2858174--2858324 Score: 211
Period size: 39 Copynumber: 3.8 Consensus size: 39
2858164 AGTATTTGTC
*
2858174 TTAACTTATTAAATATTATATATTTTTTATTTTATCTCTGTAT
1 TTAACTTATT-AA-A-TATATA-TTTTTATTTTATCTCTATAT
2858217 TTAACTTATTAAATATATATTTTTATTTTATCTCTATCA-
1 TTAACTTATTAAATATATATTTTTATTTTATCTCTAT-AT
*
2858256 TTAACTTATTAAATAT-T-TTTTTA-TTTATCTCTATCT
1 TTAACTTATTAAATATATATTTTTATTTTATCTCTATAT
2858292 TTAACTTATTAAATATATATTTTTATTTTATCT
1 TTAACTTATTAAATATATATTTTTATTTTATCT
2858325 TTTTCATAAC
Statistics
Matches: 101, Mismatches: 2, Indels: 14
0.86 0.02 0.12
Matches are distributed among these distances:
36 27 0.27
37 7 0.07
38 7 0.07
39 40 0.40
40 7 0.07
41 1 0.01
42 2 0.02
43 10 0.10
ACGTcount: A:0.31, C:0.09, G:0.01, T:0.60
Consensus pattern (39 bp):
TTAACTTATTAAATATATATTTTTATTTTATCTCTATAT
Found at i:2861668 original size:22 final size:21
Alignment explanation
Indices: 2861643--2861683 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2861633 AATCATATTG
2861643 TTAAA-AATATTTATAATTTTAC
1 TTAAAGAA-ATTTAT-ATTTTAC
2861665 TTAAAGAAATTTATATTTT
1 TTAAAGAAATTTATATTTT
2861684 GTTCTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 11 0.61
23 2 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAAAGAAATTTATATTTTAC
Found at i:2862798 original size:14 final size:14
Alignment explanation
Indices: 2862782--2862812 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
2862772 TAAAAAGCTT
2862782 AAAAATATATATGTA
1 AAAAAT-TATATGTA
2862797 AAAAATTATATGTA
1 AAAAATTATATGTA
2862811 AA
1 AA
2862813 GGGTGAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (14 bp):
AAAAATTATATGTA
Found at i:2863061 original size:17 final size:17
Alignment explanation
Indices: 2862991--2863063 Score: 51
Period size: 17 Copynumber: 4.1 Consensus size: 17
2862981 AAATAATAAT
2862991 AATAATAAATATTA-TAA
1 AATAAT-AATATTATTAA
*
2863008 AATTAGAT-ATATTAATAA
1 AA-TA-ATAATATTATTAA
* *
2863026 CTATATTAATTACTTATTAA
1 -AATAATAA-TA-TTATTAA
2863046 AATAATAATATTATTAA
1 AATAATAATATTATTAA
2863063 A
1 A
2863064 GTATTAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
17 17 0.39
18 10 0.23
19 11 0.25
20 6 0.14
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (17 bp):
AATAATAATATTATTAA
Found at i:2863191 original size:43 final size:43
Alignment explanation
Indices: 2863144--2863233 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
2863134 ATTTTTATTG
*
2863144 AAATAAAAGTATAATATTATATATTAT-AATA-ATATAATTATAA
1 AAATAAAAGTATAATATTA-AAATTATCAATATATATAATT-TAA
* * * *
2863187 AAATAATATTATATTGTTAAAATTATCAATATATATAATTTAA
1 AAATAAAAGTATAATATTAAAATTATCAATATATATAATTTAA
2863230 AAAT
1 AAAT
2863234 TAATATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 6 0.15
43 26 0.65
44 8 0.20
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (43 bp):
AAATAAAAGTATAATATTAAAATTATCAATATATATAATTTAA
Found at i:2863249 original size:42 final size:42
Alignment explanation
Indices: 2863166--2863265 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
2863156 AATATTATAT
*
2863166 ATTATAATAATATAATTATAAAAATAATATTATATTGTTAAA
1 ATTATAATAATATAATTATAAAAATAATATTATATTATTAAA
2863208 ATTATCAATATATATAATT-TAAAAATTAATATT-T-TTATTAAA
1 ATTAT-AATA-ATATAATTATAAAAA-TAATATTATATTATTAAA
* * *
2863250 ATGATACTAAAATAAT
1 ATTATAATAATATAAT
2863266 AAATTGACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
40 6 0.12
41 3 0.06
42 16 0.31
43 11 0.22
44 15 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
ATTATAATAATATAATTATAAAAATAATATTATATTATTAAA
Found at i:2870987 original size:8 final size:8
Alignment explanation
Indices: 2870971--2871179 Score: 305
Period size: 8 Copynumber: 25.9 Consensus size: 8
2870961 ATGTGTATGT
*
2870971 GTGTATGC
1 GTGTGTGC
2870979 GTGTGTGC
1 GTGTGTGC
2870987 --GTGTGC
1 GTGTGTGC
2870993 GTGTGTGC
1 GTGTGTGC
2871001 GTGTGTGC
1 GTGTGTGC
2871009 GTGTGTGC
1 GTGTGTGC
2871017 GTGTGTGC
1 GTGTGTGC
*
2871025 GTGTGCGTGT
1 GTGT--GTGC
*
2871035 GTGTGTGT
1 GTGTGTGC
2871043 GTGTGTGC
1 GTGTGTGC
2871051 GTGTGTGC
1 GTGTGTGC
2871059 GTGTGTGTGC
1 --GTGTGTGC
2871069 GTGTGTGC
1 GTGTGTGC
2871077 GTGTGTGC
1 GTGTGTGC
2871085 GTGTGTGC
1 GTGTGTGC
2871093 GTGTGTGC
1 GTGTGTGC
2871101 GTGTGTGC
1 GTGTGTGC
2871109 GTGTGTGC
1 GTGTGTGC
2871117 GTGTGTGC
1 GTGTGTGC
2871125 GTGTGTGC
1 GTGTGTGC
2871133 GTGTGTGC
1 GTGTGTGC
*
2871141 GTGTGTGT
1 GTGTGTGC
*
2871149 GTGTGTGT
1 GTGTGTGC
*
2871157 GTGTGTGT
1 GTGTGTGC
*
2871165 GTGTGTGT
1 GTGTGTGC
2871173 GTGTGTG
1 GTGTGTG
2871180 TGTATGTATG
Statistics
Matches: 191, Mismatches: 4, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
6 6 0.03
8 170 0.89
10 15 0.08
ACGTcount: A:0.00, C:0.10, G:0.50, T:0.40
Consensus pattern (8 bp):
GTGTGTGC
Found at i:2871203 original size:8 final size:8
Alignment explanation
Indices: 2870962--2871202 Score: 257
Period size: 8 Copynumber: 30.1 Consensus size: 8
2870952 TGAATATATA
*
2870962 TGTGTATG
1 TGTGTGTG
*
2870970 TGTGTATG
1 TGTGTGTG
*
2870978 CGTGTGTG
1 TGTGTGTG
* *
2870986 CGTGTGCG
1 TGTGTGTG
*
2870994 TGTGTGCG
1 TGTGTGTG
*
2871002 TGTGTGCG
1 TGTGTGTG
*
2871010 TGTGTGCG
1 TGTGTGTG
*
2871018 TGTGTGCG
1 TGTGTGTG
*
2871026 TGTGCGTG
1 TGTGTGTG
2871034 TGTGTGTG
1 TGTGTGTG
2871042 TGTGTGTG
1 TGTGTGTG
*
2871050 CGTGTGTG
1 TGTGTGTG
*
2871058 CGTGTGTG
1 TGTGTGTG
*
2871066 TGCGTGTG
1 TGTGTGTG
*
2871074 TGCGTGTG
1 TGTGTGTG
*
2871082 TGCGTGTG
1 TGTGTGTG
*
2871090 TGCGTGTG
1 TGTGTGTG
*
2871098 TGCGTGTG
1 TGTGTGTG
*
2871106 TGCGTGTG
1 TGTGTGTG
*
2871114 TGCGTGTG
1 TGTGTGTG
*
2871122 TGCGTGTG
1 TGTGTGTG
*
2871130 TGCGTGTG
1 TGTGTGTG
*
2871138 TGCGTGTG
1 TGTGTGTG
2871146 TGTGTGTG
1 TGTGTGTG
2871154 TGTGTGTG
1 TGTGTGTG
2871162 TGTGTGTG
1 TGTGTGTG
2871170 TGTGTGTG
1 TGTGTGTG
*
2871178 TGTGTATG
1 TGTGTGTG
*
2871186 TATGTGTG
1 TGTGTGTG
*
2871194 TATGTGTG
1 TGTGTGTG
2871202 T
1 T
2871203 AAAGGTTCAT
Statistics
Matches: 219, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 219 1.00
ACGTcount: A:0.02, C:0.08, G:0.48, T:0.42
Consensus pattern (8 bp):
TGTGTGTG
Found at i:2871506 original size:119 final size:119
Alignment explanation
Indices: 2871306--2871612 Score: 346
Period size: 119 Copynumber: 2.5 Consensus size: 119
2871296 GGAAAGGTTC
* * * * * * *
2871306 ATCCACCTCCTTTTGTGATGGAATCGAACAAAGGTTGAACAATTTTTTCTTATTATGAACTTCTT
1 ATCCAACTCCTTATGTGATGAAATCGAAC--AGGTTGAAAAAGTTCTTCTCATTATGAA---CTT
* * * * *
2871371 CTCTCGGAAACATTGACCCAACTCCTTATGTGATAGAATTAAATGTAGTGATGGTGCTG
61 CTCTCGGAAACATTGACCCAACTCCTTACGTGATAGAATCAAACGTAGTGATGCTACTG
* *
2871430 ATCCAACTCTTTATGTGATGAAATCGAGC-GCGTTGAAAAAGTTCTTCTCATTATGAACTTCTCT
1 ATCCAACTCCTTATGTGATGAAATCGAACAG-GTTGAAAAAGTTCTTCTCATTATGAACTTCTCT
* * * *
2871494 CGGAAACGTTGACCCAACTCCTTACGTGATGGAATCAAACGTAGTGCTGCTACTT
65 CGGAAACATTGACCCAACTCCTTACGTGATAGAATCAAACGTAGTGATGCTACTG
* * *
2871549 ATCCAACTCCTTATGTGATGGAATCGAACAAAGGTTGAACAAGTTTTTCTCATTATGAACTTCT
1 ATCCAACTCCTTATGTGATGAAATCGAAC--AGGTTGAAAAAGTTCTTCTCATTATGAACTTCT
2871613 TCTCTCTCAT
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
119 79 0.51
121 30 0.19
122 23 0.15
124 24 0.15
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (119 bp):
ATCCAACTCCTTATGTGATGAAATCGAACAGGTTGAAAAAGTTCTTCTCATTATGAACTTCTCTC
GGAAACATTGACCCAACTCCTTACGTGATAGAATCAAACGTAGTGATGCTACTG
Found at i:2873097 original size:54 final size:53
Alignment explanation
Indices: 2873023--2873350 Score: 320
Period size: 54 Copynumber: 6.1 Consensus size: 53
2873013 TTATAGTTAT
* * * *
2873023 CATCACGAAACCCCTAAAAATTAGGCTTAGGTTGTTTAAAAATTCATTTGAATA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAA-A
* * * * * * *
2873077 CATCAAGAAACCCTTGAAAATTAGACCTAGCTTCTTTCAAAATCCATTTGTAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTG-AAA
* * * *
2873131 CATTAAGAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATCCATTTGTAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTG-AAA
* * *
2873185 CATCAAGAAACCCCTAAAAATCTA-GTTTAG-TTCCTCT-AAAATTCATTTAAAAA
1 CATCAAGAAACCCCTAAAAATC-AGGCTTAGCTT-CTTTAAAAATTCATTT-GAAA
* * * * * *
2873238 CATTAAGAAACTCTTAAAAATCAGGTTTATCTCCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTG-AAA
* * *
2873292 CATTAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAAATTCATTTGAAGA
1 CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAA-A
2873346 CATCA
1 CATCA
2873351 TATTGTTTGG
Statistics
Matches: 227, Mismatches: 38, Indels: 18
0.80 0.13 0.06
Matches are distributed among these distances:
52 1 0.00
53 43 0.19
54 180 0.79
55 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (53 bp):
CATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTAAAAATTCATTTGAAA
Found at i:2873272 original size:107 final size:108
Alignment explanation
Indices: 2873029--2873340 Score: 346
Period size: 107 Copynumber: 2.9 Consensus size: 108
2873019 TTATCATCAC
* * ** *
2873029 GAAACCCCTAAAAATTAGGCTTAGGTTGTTTAAAAATTCATTTGAATACATCAAGAAACCCTTGA
1 GAAACCCCTAAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAA-ACATCAAGAAACCCCTGA
* **
2873094 AAAT-TAGACCTAGCTTCTTTCAAAATCCATTTGTAAACATTAA
65 AAATCTAGACCTAGCTTCTCTCAAAATCCATTTAAAAACATTAA
* * *
2873137 GAAACCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATCCATTTGTAAACATCAAGAAACCCCTAA
1 GAAACCCCTAAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTG-AAACATCAAGAAACCCCTGA
** *
2873202 AAATCTAG-TTTAG-TTC-CTCTAAAATTCATTTAAAAACATTAA
65 AAATCTAGACCTAGCTTCTCTC-AAAATCCATTTAAAAACATTAA
* * * * *
2873244 GAAACTCTTAAAAATCAGGTTTATCTCCTTTAAAAATTCATTTGAAAACATTAAGAAACCCCTGA
1 GAAACCCCTAAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTG-AAACATCAAGAAACCCCTGA
* * * *
2873309 AAATC-AGGCTTAGCTTCTTTCAAAATTCATTT
65 AAATCTAGACCTAGCTTCTCTCAAAATCCATTT
2873341 GAAGACATCA
Statistics
Matches: 173, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
106 4 0.02
107 87 0.50
108 75 0.43
109 7 0.04
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (108 bp):
GAAACCCCTAAAAATCAGGCTTAGCTCCTTTAAAAATTCATTTGAAACATCAAGAAACCCCTGAA
AATCTAGACCTAGCTTCTCTCAAAATCCATTTAAAAACATTAA
Found at i:2875403 original size:16 final size:16
Alignment explanation
Indices: 2875382--2875415 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2875372 ACTTGATATG
*
2875382 TTTTCTTTTTCCCTTT
1 TTTTCTTATTCCCTTT
2875398 TTTTCTTATTCCCTTT
1 TTTTCTTATTCCCTTT
2875414 TT
1 TT
2875416 CTTTGCTTTA
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:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCTTATTCCCTTT
Found at i:2875473 original size:19 final size:19
Alignment explanation
Indices: 2875441--2875492 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2875431 TCCTTTTCTA
*
2875441 TTTTTCTT-TATTTTTTTAT
1 TTTTTCTTCT-TTTTTATAT
2875460 TTTTTCTTCTTTTTTATAT
1 TTTTTCTTCTTTTTTATAT
* *
2875479 CTTCTCTTCTTTTT
1 TTTTTCTTCTTTTT
2875493 CGTCCTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTTCTTTTTTATAT
Found at i:2876930 original size:20 final size:20
Alignment explanation
Indices: 2876888--2876939 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2876878 TGAAAGTGTG
*
2876888 AATGCAAAGATGCGAACACA
1 AATGTAAAGATGCGAACACA
**
2876908 AATGTAAAGATGCGAACGTA
1 AATGTAAAGATGCGAACACA
*
2876928 AATATAAAGATG
1 AATGTAAAGATG
2876940 TGAATGCGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (20 bp):
AATGTAAAGATGCGAACACA
Found at i:2883924 original size:19 final size:19
Alignment explanation
Indices: 2883897--2883941 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2883887 TAAATATTCT
* *
2883897 TGATTTTTATAGTAAACTG
1 TGATATTTATAGTAAACTA
2883916 TGATATTTATAGTAAACTA
1 TGATATTTATAGTAAACTA
2883935 TGATATT
1 TGATATT
2883942 GATTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (19 bp):
TGATATTTATAGTAAACTA
Found at i:2886209 original size:45 final size:45
Alignment explanation
Indices: 2886158--2886251 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
2886148 TTTTAATTAG
* *
2886158 AATTTGTGTTATATGTTAAATGAAGTTAAGTTGTGTTTTGGTATT
1 AATTTGTGCTATATGTTAAATGAAATTAAGTTGTGTTTTGGTATT
* *
2886203 AATTTGTGCTATTTGTTGAATGAAATTAAGTTGTGTTTTGGTATT
1 AATTTGTGCTATATGTTAAATGAAATTAAGTTGTGTTTTGGTATT
2886248 AATT
1 AATT
2886252 AAGTGTCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.51
Consensus pattern (45 bp):
AATTTGTGCTATATGTTAAATGAAATTAAGTTGTGTTTTGGTATT
Found at i:2886517 original size:40 final size:40
Alignment explanation
Indices: 2886473--2886597 Score: 107
Period size: 40 Copynumber: 3.1 Consensus size: 40
2886463 ATTAAACTAT
*
2886473 TGAAAGATCATCAACAAACCATAAATCAGAGTGAATGACA
1 TGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
* * * * *
2886513 TGAAATAACTATTC-A-AAACCGCAAA--AGAG-GATTAAGCTA
1 TGAAAGATC-A-TCAACAAACCACAAATCAGAGTGAATGA-C-A
*
2886552 TTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACC
1 -TGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
2886593 TGAAA
1 TGAAA
2886598 TAACTATTCA
Statistics
Matches: 63, Mismatches: 12, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
37 4 0.06
38 7 0.11
39 3 0.05
40 36 0.57
41 2 0.03
42 7 0.11
43 4 0.06
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (40 bp):
TGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
Found at i:2886617 original size:80 final size:80
Alignment explanation
Indices: 2886448--2886607 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
2886438 ATCAGCAAAC
* *
2886448 AAACCGCTAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCATAAATCAGAGTGAATGACA
1 AAACCGCAAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
2886513 TGAAATAACTATTCA
66 TGAAATAACTATTCA
* *
2886528 AAACCGCAAAAGAGGATTAAGCTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACC
1 AAACCGCAAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
2886593 TGAAATAACTATTCA
66 TGAAATAACTATTCA
2886608 TAAATGCAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (80 bp):
AAACCGCAAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
TGAAATAACTATTCA
Found at i:2894270 original size:21 final size:21
Alignment explanation
Indices: 2894219--2894271 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2894209 ATTATTACTA
2894219 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
2894240 TTGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2894261 TCGCAATGCGA
1 TCGCAATGCGA
2894272 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2894286 original size:20 final size:21
Alignment explanation
Indices: 2894261--2894312 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2894251 TTTTCCCAAT
*
2894261 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2894281 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2894302 TCGCAATGCGA
1 TCGCAATGCGA
2894313 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2894291 original size:41 final size:42
Alignment explanation
Indices: 2894246--2894353 Score: 96
Period size: 41 Copynumber: 2.6 Consensus size: 42
2894236 AATTTTGCGT
* *
2894246 TGCGATTTTCCCAATTCGCAATGCGAATA-AGTA-AATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATACTG-ACAATCGCAA
* ** * *
2894287 TGCGAATTTGGAAAATCGCAATGCG-ATACTGACTATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATACTGACAATCGCAA
* * *
2894328 TGCAATTTTCCTAATTCGCATTGCGA
1 TGCGATTTTCCAAATTCGCAATGCGA
2894354 TTTACGTATT
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
40 4 0.08
41 46 0.92
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (42 bp):
TGCGATTTTCCAAATTCGCAATGCGAATACTGACAATCGCAA
Found at i:2894356 original size:21 final size:20
Alignment explanation
Indices: 2894322--2894375 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2894312 ATACTGACTA
* * *
2894322 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTACCT-AT
*
2894343 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACCTAT
*
2894363 TCGCGTTGCGATT
1 TCGCATTGCGATT
2894376 AAGTAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCTAT
Found at i:2894392 original size:20 final size:20
Alignment explanation
Indices: 2894369--2894434 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2894359 GTATTCGCGT
2894369 TGCGATTAAGTAAATCGCAA
1 TGCGATTAAGTAAATCGCAA
* *
2894389 TGCGAATTAGGAAAATCGCAA
1 TGCG-ATTAAGTAAATCGCAA
** * *
2894410 TGTAAATATGTAAATCGCAA
1 TGCGATTAAGTAAATCGCAA
2894430 TGCGA
1 TGCGA
2894435 ATCTGACTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (20 bp):
TGCGATTAAGTAAATCGCAA
Found at i:2894404 original size:21 final size:21
Alignment explanation
Indices: 2894380--2894436 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
2894370 GCGATTAAGT
2894380 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * * *
2894401 AAATCGCAATG-TAAATATGT
1 AAATCGCAATGCGAATTAGGA
2894421 AAATCGCAATGCGAAT
1 AAATCGCAATGCGAAT
2894437 CTGACTATCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:2894427 original size:102 final size:103
Alignment explanation
Indices: 2894218--2894432 Score: 258
Period size: 102 Copynumber: 2.1 Consensus size: 103
2894208 GATTATTACT
* * * *
2894218 ATCGCAATGCGATTTTCCAATTTTGCGTTGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATC
1 ATCGCAATGCAATTTTCCAATTTCGCATTGCGATTTTACCAATTCGCAATGCGAATAAGTAAATC
* ** *
2894283 GCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT
66 GCAATGCGAATTAGGAAAATCGCAATGAAATACTGACA
** ** *
2894321 ATCGCAATGCAATTTTCCTAA-TTCGCATTGCGA-TTTACGTATTCGCGTTGCGATTAAGTAAAT
1 ATCGCAATGCAATTTTCC-AATTTCGCATTGCGATTTTACCAATTCGCAATGCGAATAAGTAAAT
2894384 CGCAATGCGAATTAGGAAAATCGCAATGTAAATA-TGTA-A
65 CGCAATGCGAATTAGGAAAATCGCAATG-AAATACTG-ACA
2894423 ATCGCAATGC
1 ATCGCAATGC
2894433 GAATCTGACT
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
102 63 0.66
103 31 0.32
104 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (103 bp):
ATCGCAATGCAATTTTCCAATTTCGCATTGCGATTTTACCAATTCGCAATGCGAATAAGTAAATC
GCAATGCGAATTAGGAAAATCGCAATGAAATACTGACA
Found at i:2895041 original size:19 final size:19
Alignment explanation
Indices: 2894977--2895064 Score: 105
Period size: 19 Copynumber: 4.8 Consensus size: 19
2894967 TAGTTTCGAG
2894977 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
2894997 AATGACTATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
2895013 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
2895030 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
2895049 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
2895065 AGATAATCGC
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.16
15 1 0.02
16 2 0.03
17 1 0.02
18 2 0.03
19 31 0.53
20 12 0.21
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:2895060 original size:52 final size:53
Alignment explanation
Indices: 2894977--2895094 Score: 175
Period size: 52 Copynumber: 2.2 Consensus size: 53
2894967 TAGTTTCGAG
**
2894977 AATGAAAATCGCAACGCGGAAATGACTATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
* *
2895030 AATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGATAATCGCAATGCGA
1 AATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
**
2895082 AACCAAAATCGCA
1 AATGAAAATCGCA
2895095 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 42 0.71
53 17 0.29
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (53 bp):
AATGAAAATCGCAACGCGGAAATGAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:2895112 original size:19 final size:19
Alignment explanation
Indices: 2895090--2895196 Score: 90
Period size: 19 Copynumber: 6.1 Consensus size: 19
2895080 GAAACCAAAA
*
2895090 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2895109 TCGCGTTGCG--TTTC---
1 TCGCGTTGCGATTTTCATT
*
2895123 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2895142 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2895156 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2895175 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
2895195 TC
1 TC
2895197 AACCAAAAGA
Statistics
Matches: 69, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.28
16 6 0.09
17 7 0.10
19 21 0.30
20 16 0.23
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2895137 original size:33 final size:33
Alignment explanation
Indices: 2895095--2895188 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
2895085 CAAAATCGCA
*
2895095 TTGCGATTTTCATTTCGCGTTGCGTTTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2895128 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
2895161 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
2895189 TTCATTTCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 45 0.79
34 12 0.21
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2896476 original size:18 final size:18
Alignment explanation
Indices: 2896453--2896501 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
2896443 CTCCACTTCG
2896453 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
2896471 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
2896489 AGAGCCATCACCT
1 AGAGCCATCACCT
2896502 GATCGACCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.47, G:0.12, T:0.12
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:2897094 original size:94 final size:94
Alignment explanation
Indices: 2896907--2897211 Score: 521
Period size: 94 Copynumber: 3.3 Consensus size: 94
2896897 TAGATTGCTT
* *
2896907 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAA-T-TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2896968 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
2896997 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2897062 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2897091 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2897156 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
2897185 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
2897212 GAAACTATTC
Statistics
Matches: 206, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
90 34 0.17
91 1 0.00
92 3 0.01
93 22 0.11
94 146 0.71
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2899276 original size:19 final size:19
Alignment explanation
Indices: 2899254--2899371 Score: 58
Period size: 19 Copynumber: 6.7 Consensus size: 19
2899244 CGAAACTAAA
2899254 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
2899273 TTCGCTTTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2899288 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
2899306 TTCGTATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2899321 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2899339 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2899358 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
2899372 AGACATTAAG
Statistics
Matches: 69, Mismatches: 19, Indels: 21
0.63 0.17 0.19
Matches are distributed among these distances:
14 15 0.22
16 6 0.09
17 6 0.09
19 33 0.48
20 9 0.13
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2899300 original size:33 final size:34
Alignment explanation
Indices: 2899258--2899351 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
2899248 ACTAAATTCG
*
2899258 CGTTGCGATTTTCATTTCGCT-TTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCTATTGCGATTCCCT
*
2899291 CGTTGCGATTTTCATTTCG-TATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCTATTGCGATTCCCT
2899324 CGTTGCGATTTTCATTTCGC-ATTGCGAT
1 CGTTGCGATTTTCATTTCGCTATTGCGAT
2899352 AGTAATTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCTATTGCGATTCCCT
Found at i:2899624 original size:12 final size:12
Alignment explanation
Indices: 2899609--2899633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2899599 ATTTTAAAGA
2899609 TGATTGCCTTTT
1 TGATTGCCTTTT
2899621 TGATTGCCTTTT
1 TGATTGCCTTTT
2899633 T
1 T
2899634 CTTGACACCA
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:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (12 bp):
TGATTGCCTTTT
Found at i:2901697 original size:12 final size:12
Alignment explanation
Indices: 2901680--2901704 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2901670 TCTTCGGGGA
2901680 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2901692 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2901704 C
1 C
2901705 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2901913 original size:24 final size:24
Alignment explanation
Indices: 2901879--2901925 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2901869 CTGAAACATC
2901879 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAT
* *
2901903 ATCAAAGTCCGGGTATTGACCAA
1 ATCAAAATCCGAGTATTGACCAA
2901926 GACCAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAT
Found at i:2901932 original size:24 final size:24
Alignment explanation
Indices: 2901881--2901932 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2901871 GAAACATCAT
* *
2901881 CAAAATCCGAGTATTGACCAATAT
1 CAAAATCCGAGTATTGACCAAGAC
* *
2901905 CAAAGTCCGGGTATTGACCAAGAC
1 CAAAATCCGAGTATTGACCAAGAC
2901929 CAAA
1 CAAA
2901933 TTTCGAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (24 bp):
CAAAATCCGAGTATTGACCAAGAC
Found at i:2902774 original size:20 final size:20
Alignment explanation
Indices: 2902674--2902832 Score: 158
Period size: 20 Copynumber: 7.7 Consensus size: 20
2902664 AATTATGTAT
*
2902674 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2902694 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2902714 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2902734 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
2902754 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
2902774 TAAAATTCGCATTGCGATTTTGT-AT
1 T---A-TCGCGTTGCGA--TAGTCAG
*
2902799 TATTGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2902819 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2902833 TTTCCAAATT
Statistics
Matches: 118, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.03
20 89 0.75
21 9 0.08
22 1 0.01
23 1 0.01
24 10 0.08
25 2 0.02
26 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2902851 original size:41 final size:43
Alignment explanation
Indices: 2902761--2902853 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 43
2902751 CAGTATCGCG
** * *
2902761 TTGCGATAGTCAGTAAAATTCGCATTGCGATTTTGTATTATTGCG
1 TTGCGATAGTCAGT--AATTCGCATTGCGATTTTCAAATATTGCA
2902806 TTGCGATAGTCAGT-A-TCGCATTGCGATTTTCCAAAT-TTGCA
1 TTGCGATAGTCAGTAATTCGCATTGCGATTTT-CAAATATTGCA
2902847 TTGCGAT
1 TTGCGAT
2902854 TTACTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
41 26 0.60
42 3 0.07
45 14 0.33
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (43 bp):
TTGCGATAGTCAGTAATTCGCATTGCGATTTTCAAATATTGCA
Found at i:2902869 original size:20 final size:21
Alignment explanation
Indices: 2902821--2902872 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2902811 ATAGTCAGTA
*
2902821 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
2902842 TTGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2902862 TCGCATTGCGA
1 TCGCATTGCGA
2902873 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Done.