Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 19
Found at i:3791576 original size:22 final size:22
Alignment explanation
Indices: 3791551--3791630 Score: 78
Period size: 24 Copynumber: 3.6 Consensus size: 22
3791541 ATAAATATGC
*
3791551 TTATT-TCATATGCTATATATAA
1 TTATTATCATAT-ATATATATAA
3791573 TTATTATCATATATATATATATA
1 TTATTATCATATATATATATA-A
3791596 TATATATAT-ATATATATATATATA
1 T-TAT-TATCATATATATATATA-A
3791620 TTA-TATC-TATA
1 TTATTATCATATA
3791631 GTTATTATGA
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
21 7 0.13
22 13 0.25
23 10 0.19
24 19 0.37
25 3 0.06
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.51
Consensus pattern (22 bp):
TTATTATCATATATATATATAA
Found at i:3801621 original size:134 final size:134
Alignment explanation
Indices: 3801381--3801648 Score: 536
Period size: 134 Copynumber: 2.0 Consensus size: 134
3801371 CGTCCGTAGG
3801381 GCTTACCCTAAGAACACATCAAAGGGAGCCAACCTAAGATGTGCCTTGGGGCCTATGGGCCTACC
1 GCTTACCCTAAGAACACATCAAAGGGAGCCAACCTAAGATGTGCCTTGGGGCCTATGGGCCTACC
3801446 CAAGGGTATCATTAGGTCCGTAAGGTCTTACCAGCTAGATCAGGGCTGTGCCTCCATACTCTAGA
66 CAAGGGTATCATTAGGTCCGTAAGGTCTTACCAGCTAGATCAGGGCTGTGCCTCCATACTCTAGA
3801511 ATCC
131 ATCC
3801515 GCTTACCCTAAGAACACATCAAAGGGAGCCAACCTAAGATGTGCCTTGGGGCCTATGGGCCTACC
1 GCTTACCCTAAGAACACATCAAAGGGAGCCAACCTAAGATGTGCCTTGGGGCCTATGGGCCTACC
3801580 CAAGGGTATCATTAGGTCCGTAAGGTCTTACCAGCTAGATCAGGGCTGTGCCTCCATACTCTAGA
66 CAAGGGTATCATTAGGTCCGTAAGGTCTTACCAGCTAGATCAGGGCTGTGCCTCCATACTCTAGA
3801645 ATCC
131 ATCC
3801649 TATCCATATA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (134 bp):
GCTTACCCTAAGAACACATCAAAGGGAGCCAACCTAAGATGTGCCTTGGGGCCTATGGGCCTACC
CAAGGGTATCATTAGGTCCGTAAGGTCTTACCAGCTAGATCAGGGCTGTGCCTCCATACTCTAGA
ATCC
Found at i:3807002 original size:27 final size:27
Alignment explanation
Indices: 3806972--3807029 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3806962 ATTCTTATCT
3806972 TTTTACAACATAAGGGTATTTTCATAA
1 TTTTACAACATAAGGGTATTTTCATAA
** **
3806999 TTTTACCCCATAAGGGTATTTTTGTAA
1 TTTTACAACATAAGGGTATTTTCATAA
3807026 TTTT
1 TTTT
3807030 GCCTAACTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (27 bp):
TTTTACAACATAAGGGTATTTTCATAA
Found at i:3814442 original size:18 final size:18
Alignment explanation
Indices: 3814415--3814452 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3814405 CAAGTTTATC
*
3814415 TTTTCGAAATTAAATTTA
1 TTTTCAAAATTAAATTTA
*
3814433 TTTTCAAAATTCAATTTA
1 TTTTCAAAATTAAATTTA
3814451 TT
1 TT
3814453 ATTTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTCAAAATTAAATTTA
Found at i:3815695 original size:3 final size:3
Alignment explanation
Indices: 3815687--3815716 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3815677 AATATATTTA
3815687 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3815717 TAGTCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3815868 original size:2 final size:2
Alignment explanation
Indices: 3815780--3815851 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
3815770 AAAAAAATCC
3815780 TA TA TA TA -A 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
3815821 TA 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 TA T
3815852 TGCTTTAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3818779 original size:15 final size:15
Alignment explanation
Indices: 3818759--3818798 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
3818749 TTTTGACAAG
*
3818759 ATAAAATAAAGTGCA
1 ATAAAATAAAGTACA
*
3818774 ATAAAATAACGTACA
1 ATAAAATAAAGTACA
3818789 ATAAAATAAA
1 ATAAAATAAA
3818799 ACAAAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
ATAAAATAAAGTACA
Found at i:3819174 original size:30 final size:30
Alignment explanation
Indices: 3819132--3819197 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
3819122 GTAAGTATTT
* *
3819132 GAAATTACAAGGACCAAAATTGGAAAAATA
1 GAAATTACAAGGACCAAAATAGAAAAAATA
3819162 GAAACTTA-AAGGACCAAAATAGAAAAAATA
1 GAAA-TTACAAGGACCAAAATAGAAAAAATA
3819192 GAAATT
1 GAAATT
3819198 CAAAAGACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 2 0.06
30 28 0.85
31 3 0.09
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.17
Consensus pattern (30 bp):
GAAATTACAAGGACCAAAATAGAAAAAATA
Found at i:3819211 original size:30 final size:30
Alignment explanation
Indices: 3819143--3819211 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
3819133 AAATTACAAG
* * *
3819143 GACCAAAATTGGAAAAATAGAAACTTAAAG
1 GACCAAAATAGAAAAAATAGAAACTTAAAA
3819173 GACCAAAATAGAAAAAATAGAAA-TTCAAAA
1 GACCAAAATAGAAAAAATAGAAACTT-AAAA
*
3819203 GACTAAAAT
1 GACCAAAAT
3819212 GGTATTAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (30 bp):
GACCAAAATAGAAAAAATAGAAACTTAAAA
Found at i:3820021 original size:15 final size:15
Alignment explanation
Indices: 3820001--3820040 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
3819991 TTTTGACAAG
*
3820001 ATAAAATAAAGTGCA
1 ATAAAATAAAGTACA
3820016 ATAAAATAAAGTACA
1 ATAAAATAAAGTACA
3820031 ATAAAATAAA
1 ATAAAATAAA
3820041 ACAAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (15 bp):
ATAAAATAAAGTACA
Found at i:3820430 original size:30 final size:30
Alignment explanation
Indices: 3820396--3820452 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3820386 CAAAAATTGG
*
3820396 AAAAATAGAAACTTAAAGGACCAAAATATA
1 AAAAATAGAAACTTAAAAGACCAAAATATA
* *
3820426 AAAAATAGAAATTTAAAAGACTAAAAT
1 AAAAATAGAAACTTAAAAGACCAAAAT
3820453 GGTATTAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.65, C:0.07, G:0.09, T:0.19
Consensus pattern (30 bp):
AAAAATAGAAACTTAAAAGACCAAAATATA
Found at i:3822176 original size:17 final size:17
Alignment explanation
Indices: 3822154--3822186 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3822144 AATTAAACAC
3822154 TTCATTCATCAAACTAG
1 TTCATTCATCAAACTAG
*
3822171 TTCATTCATTAAACTA
1 TTCATTCATCAAACTA
3822187 ACTCTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (17 bp):
TTCATTCATCAAACTAG
Found at i:3829409 original size:108 final size:108
Alignment explanation
Indices: 3829221--3829614 Score: 517
Period size: 108 Copynumber: 3.7 Consensus size: 108
3829211 GTACTACCTG
* * ** *
3829221 CACTAAGTGTAAAAACCACAGAA-TCATAATAAGTTTATGAACGATTGTATCGACACTAAGTGTG
1 CACTAAGTGTACAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTG
* * *
3829285 CAACCCAATG-AATTCATAATAAGTTTAAGAGCGACCGTATCGA
66 CAACCC-ACGAAATTCATAATAAGTTTATGAACGACCGTATCGA
* *
3829328 CACTAAGTATACAACCCACAGAATTCATATTAAGTTTATGAACGACCGTATCGGCACTAAGTGTG
1 CACTAAGTGTACAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTG
* *
3829393 CAACCCACGAAATTCATAATAAGTTTATGAACGACCGCATCGG
66 CAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGA
* * *
3829436 CACTAAGTGTACAACCCACGGAATTCATAATAAGTTTATGAATGACCGTATCCGCACTAAGTGTG
1 CACTAAGTGTACAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTG
* * *
3829501 CAACCCACGAAATTCATAATTAG-TTATGAATGATCGTATC-A
66 CAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGA
* * * ** *
3829542 GCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGGTCGTATCGGCACTACGTGT
1 -CACTAAGTGTACAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGT
*
3829607 GCACCCCA
65 GCAACCCA
3829615 AAGAACTTAT
Statistics
Matches: 254, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
107 100 0.39
108 154 0.61
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (108 bp):
CACTAAGTGTACAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTG
CAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGA
Found at i:3829420 original size:162 final size:161
Alignment explanation
Indices: 3829244--3829615 Score: 507
Period size: 162 Copynumber: 2.3 Consensus size: 161
3829234 AACCACAGAA
* * *
3829244 TCATAATAAGTTTATGAACGATTGTATCGACACTAAGTGTGCAACCCAATGAATTCATAATAAGT
1 TCATAATAAGTTTATGAACGATCGTATCGGCACTAAGTGTGCAACCCAAGGAATTCATAATAAGT
*
3829309 TTAAGAGCGACCGTAT-CGACACTAAGTATACAACCCAC-AGAATTCAT-ATTAAGTTTATGAAC
66 TTAAGAACGACCGTATCCG-CACTAAGTATACAACCCACGA-AATTCATAATT-AG-TTATGAAC
*
3829371 GACCGTATCGGCACTAAGTGTGCAACCCACGAAAT
127 GACCGTATCAGCACTAAGTGTGCAACCCACGAAAT
* * * *
3829406 TCATAATAAGTTTATGAACGACCGCATCGGCACTAAGTGTACAACCCACGGAATTCATAATAAGT
1 TCATAATAAGTTTATGAACGATCGTATCGGCACTAAGTGTGCAACCCAAGGAATTCATAATAAGT
* * * * * *
3829471 TTATGAATGACCGTATCCGCACTAAGTGTGCAACCCACGAAATTCATAATTAGTTATGAATGATC
66 TTAAGAACGACCGTATCCGCACTAAGTATACAACCCACGAAATTCATAATTAGTTATGAACGACC
*
3829536 GTATCAGCACTAAGTGTGCAACCCACGGAAT
131 GTATCAGCACTAAGTGTGCAACCCACGAAAT
* * * *
3829567 TCATAATGAGTTTATGAACGGTCGTATCGGCACTACGTGTGCACCCCAA
1 TCATAATAAGTTTATGAACGATCGTATCGGCACTAAGTGTGCAACCCAA
3829616 AGAACTTATA
Statistics
Matches: 183, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
161 80 0.44
162 97 0.53
163 6 0.03
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (161 bp):
TCATAATAAGTTTATGAACGATCGTATCGGCACTAAGTGTGCAACCCAAGGAATTCATAATAAGT
TTAAGAACGACCGTATCCGCACTAAGTATACAACCCACGAAATTCATAATTAGTTATGAACGACC
GTATCAGCACTAAGTGTGCAACCCACGAAAT
Found at i:3829629 original size:54 final size:54
Alignment explanation
Indices: 3829220--3829627 Score: 448
Period size: 54 Copynumber: 7.6 Consensus size: 54
3829210 TGTACTACCT
** * * **
3829220 GCACTAAGTGTAAAAACCACAGAA-TCATAATAAGTTTATGAACGATTGTATCG
1 GCACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCGTATCG
* * * *
3829273 ACACTAAGTGTGCAACCCAATGAATTCATAATAAGTTTAAGAGCGACCGTATCG
1 GCACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCGTATCG
* * * * *
3829327 ACACTAAGTATACAACCCACAGAATTCATATTAAGTTTATGAACGACCGTATCG
1 GCACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCGTATCG
* *
3829381 GCACTAAGTGTGCAACCC-ACGAAATTCATAATAAGTTTATGAACGACCGCATCG
1 GCACTAAGTGTGCAACCCAAAG-AATTCATAATAAGTTTATGAACGACCGTATCG
* ** * *
3829435 GCACTAAGTGTACAACCCACGGAATTCATAATAAGTTTATGAATGACCGTATCC
1 GCACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCGTATCG
* * * * *
3829489 GCACTAAGTGTGCAACCC-ACGAAATTCATAATTAG-TTATGAATGATCGTATCA
1 GCACTAAGTGTGCAACCCAAAG-AATTCATAATAAGTTTATGAACGACCGTATCG
** * **
3829542 GCACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGGTCGTATCG
1 GCACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCGTATCG
* *
3829596 GCACTACGTGTGCACCCCAAAGAACTT-ATAAT
1 GCACTAAGTGTGCAACCCAAAGAA-TTCATAAT
3829628 GATTTGAAAG
Statistics
Matches: 302, Mismatches: 46, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
53 66 0.22
54 233 0.77
55 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (54 bp):
GCACTAAGTGTGCAACCCAAAGAATTCATAATAAGTTTATGAACGACCGTATCG
Found at i:3836196 original size:54 final size:54
Alignment explanation
Indices: 3836132--3836586 Score: 567
Period size: 54 Copynumber: 8.4 Consensus size: 54
3836122 CTATGTGTAT
* * **
3836132 TATCGGCACTAAGTGTGCAACCCATGAAATTCATAATAAGTTTATGAACGATTG
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
3836186 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
* *
3836240 TATCGACACTAAGTGTGCGACCCACAAAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
* * * * *
3836294 TATCGACACTAACTGTACAACCCACGTAATTCATAATAAGTTTATCAACAACCG
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
* * * * *
3836348 TATCGGCACTACGGGTGCAACCCAC-ATAATTCATAATATGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCG
* * * * *
3836402 TATC-AGTACTAAGTGTGTAACCCAC-AGAATTGATAATAAGTTTATGAACAACTG
1 TATCGA-CACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCG
* * * * * *
3836456 TATTGACACTAAGTGTGCAACCTATGGAATTCATAATAAG-TTATGAATGATCG
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
* * *
3836509 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATGAGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
* *
3836563 TATCGGCACTAAGTGTGCACCCCA
1 TATCGACACTAAGTGTGCAACCCA
3836587 AAGAACTTAT
Statistics
Matches: 344, Mismatches: 52, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
53 45 0.13
54 298 0.87
55 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
Found at i:3841636 original size:65 final size:64
Alignment explanation
Indices: 3841558--3841681 Score: 212
Period size: 65 Copynumber: 1.9 Consensus size: 64
3841548 ACACACCTAT
*
3841558 TTTTATTGAACATCGAATGCTTCTGATGTATCGATGCACAAACCATGCATCGATGCACTACAGG
1 TTTTATTGAACATCGAATGCTTCTGATGTACCGATGCACAAACCATGCATCGATGCACTACAGG
* *
3841622 TTTTATTGAAACATCGAATGCTTTTGATGTACCGATGCACAGACCATGCATCGATGCACT
1 TTTTATTG-AACATCGAATGCTTCTGATGTACCGATGCACAAACCATGCATCGATGCACT
3841682 CCTGGCTCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
64 8 0.14
65 48 0.86
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (64 bp):
TTTTATTGAACATCGAATGCTTCTGATGTACCGATGCACAAACCATGCATCGATGCACTACAGG
Found at i:3841696 original size:65 final size:65
Alignment explanation
Indices: 3841560--3841706 Score: 208
Period size: 65 Copynumber: 2.3 Consensus size: 65
3841550 ACACCTATTT
* *
3841560 TTATTG-AACATCGAATGCTTCTGATGTATCGATGCACAAACCATGCATCGATGCACTACAGGTT
1 TTATTGAAACATCGAATGCTTCTGATGTACCGATGCACAAACCATGCATCGATGCACTACAGGTC
* * * *
3841624 TTATTGAAACATCGAATGCTTTTGATGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCT
1 TTATTGAAACATCGAATGCTTCTGATGTACCGATGCACAAACCATGCATCGATGCACTACAGG-T
3841689 C
65 C
*
3841690 TT-TTGAAACATTGAATG
1 TTATTGAAACATCGAATG
3841707 TAATTAGTGT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 6 0.08
65 65 0.88
66 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (65 bp):
TTATTGAAACATCGAATGCTTCTGATGTACCGATGCACAAACCATGCATCGATGCACTACAGGTC
Found at i:3841724 original size:65 final size:65
Alignment explanation
Indices: 3841560--3841726 Score: 184
Period size: 65 Copynumber: 2.6 Consensus size: 65
3841550 ACACCTATTT
3841560 TTATTG-AACATCGAATGCTTCT-GATGTATC-GATGCACAAACCATGCATCGATGCACTACAGG
1 TTATTGAAACATCGAATGCTT-TAGATGTA-CAGATGCACAAACCATGCATCGATGCACTACAGG
*
3841622 TT
64 TC
* * * * *
3841624 TTATTGAAACATCGAATGCTTTTGATGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCT
1 TTATTGAAACATCGAATGCTTTAGATGTACAGATGCACAAACCATGCATCGATGCACTACAGG-T
3841689 C
65 C
*
3841690 TT-TTGAAACATTGAATG-TAATTAG-TGTACAGATGCAC
1 TTATTGAAACATCGAATGCT--TTAGATGTACAGATGCAC
3841727 CCCAAGTGTA
Statistics
Matches: 90, Mismatches: 7, Indels: 11
0.83 0.06 0.10
Matches are distributed among these distances:
64 9 0.10
65 75 0.83
66 6 0.07
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (65 bp):
TTATTGAAACATCGAATGCTTTAGATGTACAGATGCACAAACCATGCATCGATGCACTACAGGTC
Found at i:3844116 original size:2 final size:2
Alignment explanation
Indices: 3844109--3844144 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3844099 ACTATAGATA
3844109 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
3844145 GAAAATAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3847013 original size:90 final size:89
Alignment explanation
Indices: 3846897--3847073 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 89
3846887 TAATCCTGAA
* * *
3846897 TATTTAATTTCAATTAATTAAATATAGATTTAGTTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
3846962 TAGAGTAACTTGGATATAAAAGGAT
65 TAGAGTAACTTGGATATAAAAGGAT
* * *
3846987 TATTAAATTCCAATTTATTAATTATAGATTTAATTAATTTTAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
* *
3847052 AGGGTAACTTGGCTATAAAAGG
66 AGAGTAACTTGGATATAAAAGG
3847074 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 33 0.42
90 46 0.58
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGAGTAACTTGGATATAAAAGGAT
Found at i:3850865 original size:2 final size:2
Alignment explanation
Indices: 3850858--3850883 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3850848 AATCATATGA
3850858 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
3850884 CTAATTCATG
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:3851823 original size:20 final size:20
Alignment explanation
Indices: 3851800--3851894 Score: 81
Period size: 20 Copynumber: 5.0 Consensus size: 20
3851790 AGGGATTATT
3851800 AGTGGTCCTTCGGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
*
3851820 AGTGGTCCTTCGGGAC--AT
1 AGTGGTCCTTCGGGACAAAC
* * * *
3851838 AGTGGTTCTTCAGAACAATC
1 AGTGGTCCTTCGGGACAAAC
* * *
3851858 AGTGGTCCTTTGAGAC--AT
1 AGTGGTCCTTCGGGACAAAC
*
3851876 AGTTGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
3851895 TATTCAGTGC
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
18 27 0.49
20 28 0.51
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAAAC
Found at i:3851843 original size:18 final size:18
Alignment explanation
Indices: 3851799--3851892 Score: 89
Period size: 18 Copynumber: 5.0 Consensus size: 18
3851789 GAGGGATTAT
3851799 TAGTGGTCCTTCGGGACAAA
1 TAGTGGTCCTTCGGGAC--A
*
3851819 CAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
* * *
3851837 TAGTGGTTCTTCAGAACAA
1 TAGTGGTCCTTCGGGAC-A
* *
3851856 TCAGTGGTCCTTTGAGACA
1 T-AGTGGTCCTTCGGGACA
*
3851875 TAGTTGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
3851893 AATATTCAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
18 28 0.47
19 4 0.07
20 27 0.46
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:3851861 original size:38 final size:38
Alignment explanation
Indices: 3851799--3851886 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
3851789 GAGGGATTAT
* * *
3851799 TAGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCAGAACAAACAGTGGTCCTTCGAGACA
* * *
3851837 TAGTGGTTCTTCAGAACAATCAGTGGTCCTTTGAGACA
1 TAGTGGTCCTTCAGAACAAACAGTGGTCCTTCGAGACA
*
3851875 TAGTTGTCCTTC
1 TAGTGGTCCTTC
3851887 GGGACAAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (38 bp):
TAGTGGTCCTTCAGAACAAACAGTGGTCCTTCGAGACA
Found at i:3852218 original size:23 final size:24
Alignment explanation
Indices: 3852166--3852221 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 24
3852156 ATTGTATATG
3852166 TTATATGATATGAGTACATGTTAAGA
1 TTATATGATATGAG-ACATG-TAAGA
3852192 -TATATGATATGA-ACATG-AGAGA
1 TTATATGATATGAGACATGTA-AGA
3852214 TTATATGA
1 TTATATGA
3852222 ACAAGAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
21 1 0.04
22 3 0.11
23 12 0.43
25 12 0.43
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.36
Consensus pattern (24 bp):
TTATATGATATGAGACATGTAAGA
Found at i:3853307 original size:2 final size:2
Alignment explanation
Indices: 3853295--3853341 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3853285 TCATAATAAC
*
3853295 TA TA GA 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
3853337 TA TA T
1 TA TA T
3853342 GAAAATAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3861423 original size:161 final size:162
Alignment explanation
Indices: 3861158--3861480 Score: 639
Period size: 161 Copynumber: 2.0 Consensus size: 162
3861148 ATCACCAGTA
3861158 GTCACCCCCTGAGGTTACTTGCGGGAGGTGTAGCATTAATTTCCTAATGAGTGAACATTGCCTTA
1 GTCACCCCCTGAGGTTACTTGCGGGAGGTGTAGCATTAATTTCCTAATGAGTGAACATTGCCTTA
3861223 AGTTTGAACATAGAGGGAACCTAGAGGTTCAAATTAAAGGCTTTTTCTAGCTTAAGGTGTC-AAT
66 AGTTTGAACATAGAGGGAACCTAGAGGTTCAAATTAAAGGCTTTTTCTAGCTTAAGGTGTCAAAT
3861287 TATGAAATTAAAGCAACCTAGAGGGTCAGACC
131 TATGAAATTAAAGCAACCTAGAGGGTCAGACC
3861319 GTCACCCCCTGAGGTTACTTGCGGGAGGTGTAGCATTAATTTCCTAATGAGTGAACATTGCCTTA
1 GTCACCCCCTGAGGTTACTTGCGGGAGGTGTAGCATTAATTTCCTAATGAGTGAACATTGCCTTA
3861384 AGTTTGAACATAGAGGGAACCTAGAGGTTCAAATTAAAGGCTTTTTCTAGCTTAAGGTGTCAAAT
66 AGTTTGAACATAGAGGGAACCTAGAGGTTCAAATTAAAGGCTTTTTCTAGCTTAAGGTGTCAAAT
3861449 TATGAAATTAAAGCAACCTAGAGGGTCAGACC
131 TATGAAATTAAAGCAACCTAGAGGGTCAGACC
3861481 TAAAAATGTA
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 126 0.78
162 35 0.22
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (162 bp):
GTCACCCCCTGAGGTTACTTGCGGGAGGTGTAGCATTAATTTCCTAATGAGTGAACATTGCCTTA
AGTTTGAACATAGAGGGAACCTAGAGGTTCAAATTAAAGGCTTTTTCTAGCTTAAGGTGTCAAAT
TATGAAATTAAAGCAACCTAGAGGGTCAGACC
Found at i:3862039 original size:18 final size:17
Alignment explanation
Indices: 3862028--3862062 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
3862018 TAAACTTAAT
3862028 TAAAAAAATAAAATAAA
1 TAAAAAAATAAAATAAA
3862045 TAAAAAACATAAAATAAA
1 TAAAAAA-ATAAAATAAA
3862063 AATAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (17 bp):
TAAAAAAATAAAATAAA
Found at i:3862080 original size:17 final size:15
Alignment explanation
Indices: 3862031--3862084 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 15
3862021 ACTTAATTAA
3862031 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
*
3862046 -AAAA-AACATAAAAT
1 AAAAATAAAAT-AAAT
3862060 AAAAATAAAATGAACAT
1 AAAAATAAAAT-AA-AT
3862077 AAAAATAA
1 AAAAATAA
3862085 GGACCTAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 4 0.12
14 8 0.25
15 4 0.12
16 6 0.19
17 10 0.31
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.17
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:3863717 original size:39 final size:39
Alignment explanation
Indices: 3863637--3863922 Score: 387
Period size: 39 Copynumber: 7.4 Consensus size: 39
3863627 AAGAAAAGGA
* * *
3863637 ATCTCAAGTGAGAT-AAATCTTTTGTTTCGAGTGAAATT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
3863675 ATCTCAAGCGAGATAAAATATTCTGTTTCGAGTGAAAAT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * * *
3863714 ATCTAAAGTGAGATAAAGTCTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * *
3863753 ATCTCAAGCAAGATAAAATTTTCTGTTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
3863792 ATCTCAAGCGAGATAAAATCTTCTGTTTTGAGCGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
3863831 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * * *
3863870 ATCTTAAGCGTGAT-AAATTTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
3863908 ATCTCAAGCAAGATA
1 ATCTCAAGCGAGATA
3863923 TTAATCCCTC
Statistics
Matches: 215, Mismatches: 31, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
38 46 0.21
39 169 0.79
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
Found at i:3864337 original size:42 final size:41
Alignment explanation
Indices: 3864236--3864351 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 41
3864226 ACCCGAAGGT
* * * *
3864236 CTTATGGATGGCCCGAAGGACTTATCATCTTGTTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* * *
3864277 CTTATAGATGACCTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
*
3864319 CTTACT-GATGGCCCGAAGGACTTACTCATCATG
1 CTTA-TAGATGGCCCGAAGGACTTA-GCATCATG
3864352 AAAGCCTTGA
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
41 20 0.33
42 40 0.66
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:3866047 original size:53 final size:54
Alignment explanation
Indices: 3865951--3866072 Score: 167
Period size: 53 Copynumber: 2.3 Consensus size: 54
3865941 TTATATAACT
3865951 GGGTGTATCGGTACACACCAGGTGTATCAGTTCCCAAATTACATTCGAAGTAAG
1 GGGTGTATCGGTACACACCAGGTGTATCAGTTCCCAAATTACATTCGAAGTAAG
** * *
3866005 GGGTGTATCGGTACACAGGA-GTGTATC-GATTCTCAAATTACATTCGAAGTAGG
1 GGGTGTATCGGTACACACCAGGTGTATCAG-TTCCCAAATTACATTCGAAGTAAG
**
3866058 GGGAATATCGGTACA
1 GGGTGTATCGGTACA
3866073 TCAATGAGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
52 1 0.02
53 42 0.69
54 18 0.30
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (54 bp):
GGGTGTATCGGTACACACCAGGTGTATCAGTTCCCAAATTACATTCGAAGTAAG
Found at i:3866269 original size:17 final size:18
Alignment explanation
Indices: 3866249--3866295 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
3866239 TGATATTTGA
3866249 ATAATTT-AATTGAATAT
1 ATAATTTAAATTGAATAT
3866266 ATAATTTAAAATTGAATAT
1 ATAATTT-AAATTGAATAT
*
3866285 AAAATCTTAAA
1 ATAAT-TTAAA
3866296 ATTCAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 7 0.27
19 17 0.65
20 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
ATAATTTAAATTGAATAT
Found at i:3866280 original size:19 final size:20
Alignment explanation
Indices: 3866256--3866303 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
3866246 TGAATAATTT
*
3866256 AATTGAATATATAAT-TTAA
1 AATTGAATATAAAATCTTAA
3866275 AATTGAATATAAAATCTTAA
1 AATTGAATATAAAATCTTAA
*
3866295 AATTCAATA
1 AATTGAATA
3866304 ATACTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
AATTGAATATAAAATCTTAA
Found at i:3873970 original size:54 final size:55
Alignment explanation
Indices: 3873912--3874031 Score: 172
Period size: 55 Copynumber: 2.2 Consensus size: 55
3873902 ATATGACCGA
**
3873912 GTGTATCGGTACACAC-T-AGGTGTATTGGTTCCCAAATTACATTCGAAGTAAGGG
1 GTGTATCGGTACACACATGA-GTGTATTAATTCCCAAATTACATTCGAAGTAAGGG
* * *
3873966 GTGTATTGGTACACACATGAGTGTATTAATTCCCAAATTACATTTGAAGTAGGGG
1 GTGTATCGGTACACACATGAGTGTATTAATTCCCAAATTACATTCGAAGTAAGGG
3874021 GTGTATCGGTA
1 GTGTATCGGTA
3874032 TATGAACGAG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
54 15 0.26
55 42 0.72
56 1 0.02
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (55 bp):
GTGTATCGGTACACACATGAGTGTATTAATTCCCAAATTACATTCGAAGTAAGGG
Found at i:3874246 original size:19 final size:20
Alignment explanation
Indices: 3874222--3874265 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3874212 TAATTTAAAC
*
3874222 GAATATATAAT-TTAAAATT
1 GAATATAAAATCTTAAAATT
3874241 GAATATAAAATCTTAAAATT
1 GAATATAAAATCTTAAAATT
*
3874261 CAATA
1 GAATA
3874266 ATACTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (20 bp):
GAATATAAAATCTTAAAATT
Found at i:3876938 original size:13 final size:13
Alignment explanation
Indices: 3876920--3876948 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3876910 TCGGGAATCA
3876920 CCTGTAGTCACCC
1 CCTGTAGTCACCC
3876933 CCTGTAGTCACCC
1 CCTGTAGTCACCC
3876946 CCT
1 CCT
3876949 AATAAGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.48, G:0.14, T:0.24
Consensus pattern (13 bp):
CCTGTAGTCACCC
Found at i:3877363 original size:24 final size:24
Alignment explanation
Indices: 3877336--3877388 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
3877326 ATATCGATTT
3877336 CTAAAAGATCTAAAAGCTTAGGAC
1 CTAAAAGATCTAAAAGCTTAGGAC
3877360 CTAAAAGATCTAAAAGCTTAGGAC
1 CTAAAAGATCTAAAAGCTTAGGAC
3877384 CTAAA
1 CTAAA
3877389 TCGATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
CTAAAAGATCTAAAAGCTTAGGAC
Found at i:3880230 original size:2 final size:2
Alignment explanation
Indices: 3880225--3880265 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3880215 TAAAAACAAT
3880225 TA TA TA -A T- 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
3880265 T
1 T
3880266 CTTGATTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3883603 original size:31 final size:31
Alignment explanation
Indices: 3883563--3883644 Score: 146
Period size: 31 Copynumber: 2.6 Consensus size: 31
3883553 GACACTCTTG
*
3883563 TGCACTATCTGAATGCAACATAACTTTGCTA
1 TGCATTATCTGAATGCAACATAACTTTGCTA
*
3883594 TGTATTATCTGAATGCAACATAACTTTGCTA
1 TGCATTATCTGAATGCAACATAACTTTGCTA
3883625 TGCATTATCTGAATGCAACA
1 TGCATTATCTGAATGCAACA
3883645 CTGGCTCTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (31 bp):
TGCATTATCTGAATGCAACATAACTTTGCTA
Found at i:3883670 original size:32 final size:32
Alignment explanation
Indices: 3883625--3883710 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
3883615 AACTTTGCTA
3883625 TGCATTATCTGAATGCAACACTGGCTCTATTG
1 TGCATTATCTGAATGCAACACTGGCTCTATTG
*
3883657 TGCATTATTTGAATGCAACACTGGCTCTATTG
1 TGCATTATCTGAATGCAACACTGGCTCTATTG
3883689 TGCATTATCTGAATGCAACACT
1 TGCATTATCTGAATGCAACACT
3883711 AACACTACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACACTGGCTCTATTG
Found at i:3883725 original size:19 final size:19
Alignment explanation
Indices: 3883701--3883743 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
3883691 CATTATCTGA
3883701 ATGCAACACTAACACTACT
1 ATGCAACACTAACACTACT
*
3883720 ATGCAACACTGACACTACT
1 ATGCAACACTAACACTACT
3883739 ATGCA
1 ATGCA
3883744 CAAGCTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (19 bp):
ATGCAACACTAACACTACT
Found at i:3885569 original size:21 final size:20
Alignment explanation
Indices: 3885525--3885570 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3885515 TTTTAAATGT
* *
3885525 TTTTCAAAACTAGTCGAACC
1 TTTTCAAAACTACTCGAACA
*
3885545 TTTTCAAAACATACTCGATCA
1 TTTTCAAAAC-TACTCGAACA
3885566 TTTTC
1 TTTTC
3885571 GCTCTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.37
Consensus pattern (20 bp):
TTTTCAAAACTACTCGAACA
Found at i:3885658 original size:20 final size:19
Alignment explanation
Indices: 3885626--3885685 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
3885616 ATTTCTTAGC
3885626 AAAAGGA-ATGATCCCATTGG
1 AAAAGGATA-GATCCC-TTGG
* *
3885646 CAAAGGATAGATCCCCTTGA
1 AAAAGGATAGAT-CCCTTGG
*
3885666 AAAAGGATCGATCCCTTGG
1 AAAAGGATAGATCCCTTGG
3885685 A
1 A
3885686 CAATAGTGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 7 0.21
20 22 0.67
21 4 0.12
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (19 bp):
AAAAGGATAGATCCCTTGG
Found at i:3885790 original size:41 final size:41
Alignment explanation
Indices: 3885738--3885842 Score: 165
Period size: 41 Copynumber: 2.6 Consensus size: 41
3885728 TCCCTTCCCC
* *
3885738 AAAAAGGATAGATCCCTTTGGTATAACGGTCGAAATATTTG
1 AAAAAGAATAGATCCCTTTGGTATAACGGCCGAAATATTTG
* *
3885779 AAAAATAATAGATCCCTTTGGTATAACGGCCGACATATTTG
1 AAAAAGAATAGATCCCTTTGGTATAACGGCCGAAATATTTG
*
3885820 AAAAAGAATTGATCCCTTTGGTA
1 AAAAAGAATAGATCCCTTTGGTA
3885843 AAAGGATCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (41 bp):
AAAAAGAATAGATCCCTTTGGTATAACGGCCGAAATATTTG
Found at i:3890980 original size:16 final size:16
Alignment explanation
Indices: 3890962--3890993 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3890952 ATATGAACCA
3890962 TATAT-TTATA-TATT
1 TATATCTTATATTATT
3890976 TATATCTTATATTATT
1 TATATCTTATATTATT
3890992 TA
1 TA
3890994 GCTTATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATCTTATATTATT
Found at i:3896555 original size:16 final size:16
Alignment explanation
Indices: 3896536--3896570 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3896526 CTATGAACAA
3896536 TATAT-TTATATATATT
1 TATATCTTATAT-TATT
3896552 TATATCTTATATTATT
1 TATATCTTATATTATT
3896568 TAT
1 TAT
3896571 CTTATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATCTTATATTATT
Found at i:3898175 original size:17 final size:18
Alignment explanation
Indices: 3898140--3898178 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3898130 GAAAAAACAT
*
3898140 AAATAGGTAAATGAAATAA
1 AAATAAGTAAATG-AATAA
3898159 AAATAAGTAAATG-ATAA
1 AAATAAGTAAATGAATAA
3898176 AAA
1 AAA
3898179 CAAAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
19 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.21
Consensus pattern (18 bp):
AAATAAGTAAATGAATAA
Found at i:3899687 original size:36 final size:37
Alignment explanation
Indices: 3899619--3899724 Score: 196
Period size: 36 Copynumber: 2.9 Consensus size: 37
3899609 ATGATTCTTC
3899619 AGATGGCTCCACTTTGCGAGTTTAAGTCATGTGCTTT
1 AGATGGCTCCACTTTGCGAGTTTAAGTCATGTGCTTT
*
3899656 AGATGGCTCCACTTTGTGAG-TTAAGTCATGTGCTTT
1 AGATGGCTCCACTTTGCGAGTTTAAGTCATGTGCTTT
3899692 AGATGGCTCCACTTTGCGAGTTTAAGTCATGTG
1 AGATGGCTCCACTTTGCGAGTTTAAGTCATGTG
3899725 AAATGATTCT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 35 0.53
37 31 0.47
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (37 bp):
AGATGGCTCCACTTTGCGAGTTTAAGTCATGTGCTTT
Found at i:3899946 original size:75 final size:76
Alignment explanation
Indices: 3899826--3900033 Score: 201
Period size: 76 Copynumber: 2.8 Consensus size: 76
3899816 CTTTGCGGTT
* * * * * * *
3899826 TAAGCCAGTCTT-AATTTTTTGGATTACTCCCCTTCGT-GAGTTTAAGCCAAATGAGA-CGTCTT
1 TAAGCCAATCTTGATTTTTTTGGATTATTCTCCTTCGTAG-GTTTAAGACAAATGAGATAGT-TC
* *
3899888 TTCTTCACGA-TT
64 CTCTTCACGAGTA
* * * * * *
3899900 TAATCCATTCTTTATTTTTTTGGA-TATTTTGTCTTCGTAGGTTTAAGTCAAATGAGATAGTTCC
1 TAAGCCAATCTTGATTTTTTTGGATTATTCT-CCTTCGTAGGTTTAAGACAAATGAGATAGTTCC
*
3899964 TCTTCGCGAGTA
65 TCTTCACGAGTA
*
3899976 TAAGCCAATCTTGATTTTTTTGGATTATTCTCCTTCGTAGGTTTAGGACAAATGAGAT
1 TAAGCCAATCTTGATTTTTTTGGATTATTCTCCTTCGTAGGTTTAAGACAAATGAGAT
3900034 GACTCCCGGA
Statistics
Matches: 108, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
74 13 0.12
75 41 0.38
76 49 0.45
77 5 0.05
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (76 bp):
TAAGCCAATCTTGATTTTTTTGGATTATTCTCCTTCGTAGGTTTAAGACAAATGAGATAGTTCCT
CTTCACGAGTA
Found at i:3901523 original size:37 final size:31
Alignment explanation
Indices: 3901484--3901548 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
3901474 AATAAGTTAT
3901484 TATCATTATAGTTATAGATGTAGTATATATA
1 TATCATTATAGTTATAGATGTAGTATATATA
3901515 TATCATTATAGTTATAGATGTAGTATATATA
1 TATCATTATAGTTATAGATGTAGTATATATA
3901546 TAT
1 TAT
3901549 ATGAATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.46
Consensus pattern (31 bp):
TATCATTATAGTTATAGATGTAGTATATATA
Found at i:3915885 original size:34 final size:34
Alignment explanation
Indices: 3915847--3915930 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 34
3915837 AATATAATTT
*
3915847 TAAATACAACAAACTTACAATAA-GTATTAAATGG
1 TAAATA-AACAAAATTACAATAACGTATTAAATGG
3915881 TAAATAAA-AAAATTACAATAACTGGTATTAAATGG
1 TAAATAAACAAAATTACAATAAC--GTATTAAATGG
3915916 T-AATAAACAAAATTA
1 TAAATAAACAAAATTA
3915931 ACAAAATTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
32 12 0.27
33 2 0.04
34 12 0.27
35 19 0.42
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (34 bp):
TAAATAAACAAAATTACAATAACGTATTAAATGG
Found at i:3915944 original size:13 final size:13
Alignment explanation
Indices: 3915926--3915950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3915916 TAATAAACAA
3915926 AATTAACAAAATT
1 AATTAACAAAATT
3915939 AATTAACAAAAT
1 AATTAACAAAAT
3915951 GTCCAACAAA
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAACAAAATT
Found at i:3918053 original size:14 final size:14
Alignment explanation
Indices: 3918036--3918074 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3918026 ACTCTTAAAC
*
3918036 CTAAACCCTAACCT
1 CTAAACACTAACCT
*
3918050 CTAAATACTAACCT
1 CTAAACACTAACCT
*
3918064 CTAATCACTAA
1 CTAAACACTAA
3918075 ATCATACCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (14 bp):
CTAAACACTAACCT
Found at i:3920530 original size:29 final size:29
Alignment explanation
Indices: 3920484--3920661 Score: 166
Period size: 29 Copynumber: 6.2 Consensus size: 29
3920474 ACAGATATAA
** * *
3920484 CACCCTTTTTAAAATAATTACCAAAATAG
1 CACCCTTTTCGAATTAATTCCCAAAATAG
* * * *
3920513 TACCCTTTTCGAATTAATTCCCGAAGTAT
1 CACCCTTTTCGAATTAATTCCCAAAATAG
*
3920542 CA--CTTTTCAAATTAAATTCCCAAAATAG
1 CACCCTTTTCGAATT-AATTCCCAAAATAG
3920570 CA-CCTTTTCGAATTAAATTCCCAAAATAG
1 CACCCTTTTCGAATT-AATTCCCAAAATAG
* *
3920599 CA-CATATTTCGAATTAATTCCTAAAATAG
1 CACCCT-TTTCGAATTAATTCCCAAAATAG
* ** *
3920628 CACCCATTTCGAATTAATTCTGAAAATAT
1 CACCCTTTTCGAATTAATTCCCAAAATAG
3920657 CACCC
1 CACCC
3920662 GGTCAAAGGT
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 10 0.08
28 13 0.10
29 91 0.73
30 10 0.08
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (29 bp):
CACCCTTTTCGAATTAATTCCCAAAATAG
Found at i:3927775 original size:30 final size:29
Alignment explanation
Indices: 3927739--3927924 Score: 203
Period size: 29 Copynumber: 6.3 Consensus size: 29
3927729 CATTTTACAG
* * *
3927739 AAATAGCATCCTTTTTTAAAATAATTACCA
1 AAATAGCA-CCTTTTTCAAATTAATTCCCA
*
3927769 AAATAGCACCCTTTTCAAATTAATTCCCA
1 AAATAGCACCTTTTTCAAATTAATTCCCA
* * *
3927798 AAGTATCA-CTTTTTCGAATTATATTCCCA
1 AAATAGCACCTTTTTCAAATTA-ATTCCCA
*
3927827 AAATAGCACCTTTTTCGAATTAAATTCCCA
1 AAATAGCACCTTTTTCAAATT-AATTCCCA
* *
3927857 AAATAGCACCTATTTCAAATTAATTCTCA
1 AAATAGCACCTTTTTCAAATTAATTCCCA
** * *
3927886 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCTTTTTCAAATTAATTCCCA
*
3927915 AAATATCACC
1 AAATAGCACC
3927925 CGGTCAACGG
Statistics
Matches: 135, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
28 11 0.08
29 77 0.57
30 46 0.34
31 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (29 bp):
AAATAGCACCTTTTTCAAATTAATTCCCA
Found at i:3927858 original size:88 final size:87
Alignment explanation
Indices: 3927739--3927924 Score: 223
Period size: 88 Copynumber: 2.1 Consensus size: 87
3927729 CATTTTACAG
* *
3927739 AAATAGCATCCTTTTTTAAAATAATTACCAAAATAGCACCCT-TTTCAAATTAATTCCCAAAGTA
1 AAATAGCA-CCTTTTTCAAAATAATTACCAAAATAGCA-CCTATTTCAAATTAATTCCCAAAATA
* ** *
3927803 TCA-CTTTTTCGAATTATATTCCCA
64 GCACCCATTTCGAATTA-ATTACCA
* * * *
3927827 AAATAGCACCTTTTTCGAATTAAATTCCCAAAATAGCACCTATTTCAAATTAATTCTCAAAATAG
1 AAATAGCACCTTTTTCAAAAT-AATTACCAAAATAGCACCTATTTCAAATTAATTCCCAAAATAG
3927892 CACCCATTTCGAATTAATTACCA
65 CACCCATTTCGAATTAATTACCA
*
3927915 AAATATCACC
1 AAATAGCACC
3927925 CGGTCAACGG
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
87 13 0.15
88 60 0.71
89 11 0.13
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (87 bp):
AAATAGCACCTTTTTCAAAATAATTACCAAAATAGCACCTATTTCAAATTAATTCCCAAAATAGC
ACCCATTTCGAATTAATTACCA
Found at i:3934309 original size:138 final size:138
Alignment explanation
Indices: 3934009--3934310 Score: 337
Period size: 138 Copynumber: 2.2 Consensus size: 138
3933999 AAACATATAT
* * *
3934009 GAATATTC-GATTTGGTCCTTGCTTTTTCCCAAGGTTTCATTTTTGTTATTCAAACAAACAATTT
1 GAAT-TTCTGATTTGGTCCTTGATTTTGCCCAAGGTTTCATTTTGGTTATTCAAACAAACAATTT
* ** *
3934073 GATTAAATTGATTAAGTTTTAATACTAGAGCCTCCATATTAGGATTAATTTCACTTTAGTCTTTC
65 GATAAAATTGAACAAGTTTTAATACTAAAGCCTCCATATTAGGATTAATTTCACTTTAGTCTTTC
*
3934138 AATTTAGGA
130 AATTTAAGA
* ** * * *
3934147 TAATTTCTGATTTCATCCTTGATTTTGCCCAAGG-TTCTATTTTGGTTATTCAATTC-GATAATT
1 GAATTTCTGATTTGGTCCTTGATTTTGCCCAAGGTTTC-ATTTTGGTTATTCAA-ACAAACAATT
* * *
3934210 TGATAAAATTGAACATGTTTTAATACTACAAG-CTCCATTTTAGGATTAATTTCACTTTATTCCT
64 TGATAAAATTGAACAAGTTTTAATACTA-AAGCCTCCATATTAGGATTAATTTCACTTTAGT-CT
3934274 TT-AATTTAAGA
127 TTCAATTTAAGA
* *
3934285 GAATTAT-TTATTTGGTCCTCGATTTT
1 GAATT-TCTGATTTGGTCCTTGATTTT
3934311 ACTTGAGGTT
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
137 6 0.04
138 122 0.90
139 8 0.06
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.45
Consensus pattern (138 bp):
GAATTTCTGATTTGGTCCTTGATTTTGCCCAAGGTTTCATTTTGGTTATTCAAACAAACAATTTG
ATAAAATTGAACAAGTTTTAATACTAAAGCCTCCATATTAGGATTAATTTCACTTTAGTCTTTCA
ATTTAAGA
Found at i:3935482 original size:12 final size:12
Alignment explanation
Indices: 3935465--3935493 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3935455 TCACATTATT
3935465 TATTTGCAATTG
1 TATTTGCAATTG
3935477 TATTTGCAATTG
1 TATTTGCAATTG
3935489 TATTT
1 TATTT
3935494 ACAGTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (12 bp):
TATTTGCAATTG
Found at i:3936373 original size:26 final size:26
Alignment explanation
Indices: 3936343--3936519 Score: 138
Period size: 26 Copynumber: 7.5 Consensus size: 26
3936333 AGGCCTTAAT
3936343 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
*
3936369 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
3936395 ACATCCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
* *
3936415 GCATCATTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
* *
3936435 GTATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
3936461 GCATCCTTTTATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
*
3936481 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAATTATG
3936507 GCATCCTTTCATG
1 GCATCCTTTCATG
3936520 TCTTAATGCA
Statistics
Matches: 122, Mismatches: 17, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
20 43 0.35
21 4 0.03
22 4 0.03
24 4 0.03
25 4 0.03
26 63 0.52
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAATTATG
Found at i:3936424 original size:20 final size:20
Alignment explanation
Indices: 3936396--3936531 Score: 110
Period size: 20 Copynumber: 6.2 Consensus size: 20
3936386 TTAGTTATGA
3936396 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
3936416 CATCATTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
3936436 TATCCTTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGC--CTTA---AT-G
*
3936462 CATCCTTTTATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
3936482 CATCCTTTCATGCATTTTAGTTATGG
1 CATCCTTTCATGC--CTTA---AT-G
*
3936508 CATCCTTTCATGTCTTAATG
1 CATCCTTTCATGCCTTAATG
3936528 CATC
1 CATC
3936532 ATTTTATGCA
Statistics
Matches: 93, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
20 48 0.52
21 4 0.04
22 6 0.06
24 6 0.06
25 4 0.04
26 25 0.27
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:3936465 original size:46 final size:46
Alignment explanation
Indices: 3936311--3936552 Score: 271
Period size: 46 Copynumber: 5.3 Consensus size: 46
3936301 TTATTTGCAA
* * * *
3936311 ATTTTAGATATGTCATCCTTTTAGGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
3936357 ATTTTAATTATGGCATCCTTTCATGCATTTTAGTTATGACATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC--CTTA---ATG-CATCCTTTCATGC
* * *
3936409 --CTTA---AT-GCATCATTTCATGCCTTAATGTATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
3936449 ATTTTAGTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
3936495 ATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATCATTTTATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
3936541 ATTTTAGTTATG
1 ATTTTAGTTATG
3936553 AATTCATTTT
Statistics
Matches: 166, Mismatches: 18, Indels: 24
0.80 0.09 0.12
Matches are distributed among these distances:
40 12 0.07
41 3 0.02
42 3 0.02
44 3 0.02
45 2 0.01
46 119 0.72
47 2 0.01
48 3 0.02
50 3 0.02
51 3 0.02
52 13 0.08
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:3936477 original size:66 final size:70
Alignment explanation
Indices: 3936311--3936519 Score: 264
Period size: 66 Copynumber: 3.0 Consensus size: 70
3936301 TTATTTGCAA
* * * *
3936311 ATTTTAGATATGTCATCCTTTTAGGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCT
1 ATTTTAGTTATGACATCCTTTTATGCCTTAATGCATCCTTTCATGCA-CTTAA-TATGGCATCCT
3936376 TTCATGC
64 TTCATGC
* * *
3936383 ATTTTAGTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC-CTT-A-AT-GTATCCTTT
1 ATTTTAGTTATGACATCCTTTTATGCCTTAATGCATCCTTTCATGCACTTAATATGGCATCCTTT
3936444 CATGC
66 CATGC
* * *
3936449 ATTTTAGTTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCT
1 ATTTTAGTTATGACATCCTTTTATGCCTTAATGCATCCTTTCATGCA-CTTA-ATATGGCATCCT
3936514 TTCATG
64 TTCATG
3936520 TCTTAATGCA
Statistics
Matches: 118, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
66 56 0.47
67 2 0.02
68 2 0.02
69 1 0.01
70 2 0.02
71 2 0.02
72 53 0.45
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (70 bp):
ATTTTAGTTATGACATCCTTTTATGCCTTAATGCATCCTTTCATGCACTTAATATGGCATCCTTT
CATGC
Found at i:3942479 original size:20 final size:20
Alignment explanation
Indices: 3942451--3942489 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3942441 TGCATTTTAA
3942451 TTATGGCATCATTTCATGCC
1 TTATGGCATCATTTCATGCC
*
3942471 TTATTGCATCATTTCATGC
1 TTATGGCATCATTTCATGC
3942490 ATTTTAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (20 bp):
TTATGGCATCATTTCATGCC
Found at i:3942479 original size:46 final size:46
Alignment explanation
Indices: 3942398--3942561 Score: 247
Period size: 46 Copynumber: 3.6 Consensus size: 46
3942388 TTATTCTTAA
* * *
3942398 ATTTTAATTATGGCATCCTTTTAGGTCTTAATGCATCCTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
3942444 ATTTTAATTATGGCATCATTTCATGCCTTATTGCATCATTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
3942490 ATTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
3942536 ATTTTAGTTATGGCATCCTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGC
3942562 ATTTTAGTTA
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 106 1.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (46 bp):
ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:3942552 original size:72 final size:72
Alignment explanation
Indices: 3942471--3942771 Score: 300
Period size: 72 Copynumber: 4.3 Consensus size: 72
3942461 ATTTCATGCC
* * * *
3942471 TTATTGCATCATTTCATGCATTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
1 TTATGGCATCCTTTCATGCATTTTAGTTATGGCATCATTTTATGCCTTAATGCATCCTTTCATGC
3942536 ATTTTAG
66 ATTTTAG
** * * *
3942543 TTATGGCATCCTTTCATGCATTTTAGTTATTACATCCTTTCATGCCTTAATGCATCATTTCATGC
1 TTATGGCATCCTTTCATGCATTTTAGTTATGGCATCATTTTATGCCTTAATGCATCCTTTCATGC
3942608 ATTTTAG
66 ATTTTAG
* * * ** * *
3942615 TTATGGCATCCTTTTATGCCTTAATGTA-TCATTTCATGTATTTTA-G--TT-ATGGTATCCTTT
1 TTATGGCATCCTTTCATGCATT--T-TAGTTATGGCAT-CATTTTATGCCTTAAT-GCATCCTTT
*
3942675 CATGC--CTTA-
61 CATGCATTTTAG
*
3942684 --AT-GCATCATTTCATGCATTTTAGTTATGGCATCATTTTATGCCTTAATGCATCCTTTCATGC
1 TTATGGCATCCTTTCATGCATTTTAGTTATGGCATCATTTTATGCCTTAATGCATCCTTTCATGC
3942746 ATTTTAG
66 ATTTTAG
**
3942753 TTATTACATCCTTTCATGC
1 TTATGGCATCCTTTCATGC
3942772 CTTAATGCAT
Statistics
Matches: 186, Mismatches: 27, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
63 8 0.04
64 8 0.04
66 29 0.16
67 4 0.02
68 3 0.02
70 3 0.02
71 4 0.02
72 112 0.60
74 9 0.05
75 6 0.03
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.47
Consensus pattern (72 bp):
TTATGGCATCCTTTCATGCATTTTAGTTATGGCATCATTTTATGCCTTAATGCATCCTTTCATGC
ATTTTAG
Found at i:3942584 original size:118 final size:118
Alignment explanation
Indices: 3942430--3942679 Score: 410
Period size: 118 Copynumber: 2.1 Consensus size: 118
3942420 AGGTCTTAAT
* *
3942430 GCATCCTTTCATGCATTTTAATTATGGCATCATTTCATGCCTTATTGCATCATTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCATTTCATGCATTTT
*
3942495 AGTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
66 AGTTATGGCATCCTTTAATGCCTTAATGCATCATTTCATGCATTTTAGTTATG
* * *
3942548 GCATCCTTTCATGCATTTTAGTTATTACATCCTTTCATGCCTTAATGCATCATTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCATTTCATGCATTTT
* * *
3942613 AGTTATGGCATCCTTTTATGCCTTAATGTATCATTTCATGTATTTTAGTTATG
66 AGTTATGGCATCCTTTAATGCCTTAATGCATCATTTCATGCATTTTAGTTATG
*
3942666 GTATCCTTTCATGC
1 GCATCCTTTCATGC
3942680 CTTAATGCAT
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 122 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (118 bp):
GCATCCTTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCATTTCATGCATTTT
AGTTATGGCATCCTTTAATGCCTTAATGCATCATTTCATGCATTTTAGTTATG
Found at i:3942598 original size:46 final size:46
Alignment explanation
Indices: 3942548--3942850 Score: 455
Period size: 46 Copynumber: 6.6 Consensus size: 46
3942538 TTTAGTTATG
* *
3942548 GCATCCTTTCATGCATTTTAGTTATTACATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAAT
* *
3942594 GCATCATTTCATGCATTTTAGTTATGGCATCCTTTTATGCCTTAAT
1 GCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAAT
* * **
3942640 GTATCATTTCATGTATTTTAGTTATGGTATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAAT
* * *
3942686 GCATCATTTCATGCATTTTAGTTATGGCATCATTTTATGCCTTAAT
1 GCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAAT
* *
3942732 GCATCCTTTCATGCATTTTAGTTATTACATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAAT
*
3942778 GCATCCTTTCATGCATTTTAGTTATGGA-ATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCATTTTAGTTAT-GACATCCTTTCATGCCTTAAT
*
3942824 GCATCATTTCTTGCATTTTAGTTATGA
1 GCATCATTTCATGCATTTTAGTTATGA
3942851 ATTTATTTTA
Statistics
Matches: 235, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
45 2 0.01
46 232 0.99
47 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (46 bp):
GCATCATTTCATGCATTTTAGTTATGACATCCTTTCATGCCTTAAT
Found at i:3942817 original size:210 final size:207
Alignment explanation
Indices: 3942398--3942791 Score: 587
Period size: 210 Copynumber: 1.9 Consensus size: 207
3942388 TTATTCTTAA
* *
3942398 ATTTTAATTATGGCATCCTTTTAGGTCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCAT
1 ATTTTAATTATGGCATCCTTTTAGGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCAT
* *
3942463 TTCATGCCTTATTGCATCATTTCATGCATTTTAGTTATGGCATCCTTTAATGCCTTAATGCATCC
66 TTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCATTTAATGCCTTAATGCATCC
* *
3942528 TTTCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGTTATTACATCCTTTCATGCCTTAA
131 TTTCATGCATTTTAGTTATGACATCCTTTCATGCA-CTTA--TATTACATCCTTTCATGCCTTAA
*
3942593 TGCATCATTTCATGC
193 TGAATCATTTCATGC
* * * * * * *
3942608 ATTTTAGTTATGGCATCCTTTTATGCCTTAATGTATCATTTCATGTATTTTAGTTATGGTATCCT
1 ATTTTAATTATGGCATCCTTTTAGGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCAT
*
3942673 TTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCATTTTATGCCTTAATGCATCC
66 TTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCATTTAATGCCTTAATGCATCC
* *
3942738 TTTCATGCATTTTAGTTATTACATCCTTTCATGC-CTTA-A-TGCATCCTTTCATGC
131 TTTCATGCATTTTAGTTATGACATCCTTTCATGCACTTATATTACATCCTTTCATGC
3942792 ATTTTAGTTA
Statistics
Matches: 168, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
204 14 0.08
205 1 0.01
208 3 0.02
210 150 0.89
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (207 bp):
ATTTTAATTATGGCATCCTTTTAGGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCAT
TTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCATTTAATGCCTTAATGCATCC
TTTCATGCATTTTAGTTATGACATCCTTTCATGCACTTATATTACATCCTTTCATGCCTTAATGA
ATCATTTCATGC
Found at i:3949408 original size:21 final size:21
Alignment explanation
Indices: 3949384--3949429 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3949374 AAGAAAAATC
*
3949384 GATCCCTTAAGGGAAATGATA
1 GATCCCTTAAGGGAAAGGATA
* * *
3949405 GATCTCTTAGGGGAAAGGATC
1 GATCCCTTAAGGGAAAGGATA
3949426 GATC
1 GATC
3949430 ATTTCCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (21 bp):
GATCCCTTAAGGGAAAGGATA
Found at i:3951877 original size:340 final size:337
Alignment explanation
Indices: 3951258--3951930 Score: 994
Period size: 340 Copynumber: 2.0 Consensus size: 337
3951248 CACTCAGCTA
* * *
3951258 GGTGTTTAGGAAATTGTCTAAAGCTAGACAGATCAGACATGACTTAAAGCCAAGGCATGACTTTG
1 GGTGTTTAGGAAATTGTCTAAAGATAGACAGATCAGACAGGACTTAAAGCCAAGGAATGACTTTG
* * * *
3951323 GAGTCTATTACGAGTATCACTAGGAGGAGAGCCATGAGATCTAGTGTTGCCCTGAATTTAGAGGC
66 GAATATATTACGAGTATCACTAGGAAGAGAGCCATGAGATCCAGTGTTGCCCTGAATTTAGAGGC
* * *
3951388 TTAATCTAGAACATGATGAATAATAAAGAAATATAGTTCTTCGAGAAGGATAGAGAAAAAAATAG
131 TTAATATAGAAAATAATGAATAATAAAGAAATATAGTTCTTCGAGAAGGATAGAGAAAAAAATAG
* * * * *
3951453 AAGTTGATATATGTACATTAGAGAGCTCCAAGTCTGCATATTGAGCAAACAAGCAGTAATCATCA
196 AAGTTAATATATGTACATTAGAGAGCTCCAAGCCTACATATGGAGCAAACAAGCAATAATCATCA
*
3951518 CTATGAGACCGAAAGAAGTGAATCTAGTATTAATAACCTTGAAAATCATGATTATAGCCCTCTCA
261 CTATGAGACCGAAAGAAGTGAATCTAGTATTAATAACCCTGAAAATCATGATTATAGCCCTCTCA
3951583 CCATTTCCGTTG
326 CCATTTCCGTTG
* *
3951595 GGTGTTTAGGAAATTGTCTAAAGAT-GGCTTGATCAGACAGGACTTAAAGCCAAGGTATAATGAC
1 GGTGTTTAGGAAATTGTCTAAAGATAGAC-AGATCAGACAGGACTTAAAGCCAAGG---AATGAC
* * *
3951659 TTTGGAATATATTACGAGTATCACTAGGAAGAGTGTCTTGAGATCCAGTGTTGCCCTGAATTTAG
62 TTTGGAATATATTACGAGTATCACTAGGAAGAGAGCCATGAGATCCAGTGTTGCCCTGAATTTAG
3951724 AGGCTTAATATAGAAAATAATGAATAATAAAGAAATATAGTTCTTCGAGAAGGA-A-AGAAAAAA
127 AGGCTTAATATAGAAAATAATGAATAATAAAGAAATATAGTTCTTCGAGAAGGATAGAGAAAAAA
* * * *
3951787 ATGATAAGTTAATCTATGTACATTTGAGAGCTTCAAGCCTACATATGGAGCAAACAAGCCAATAA
192 AT-AGAAGTTAATATATGTACATTAGAGAGCTCCAAGCCTACATATGGAGCAAACAAG-CAATAA
* * * *
3951852 TCATCATTATGAGACC-AAGAGAAGTGAATCTAGTATTAGTAACCCTGAAAATCCTGATTATATC
255 TCATCACTATGAGACCGAA-AGAAGTGAATCTAGTATTAATAACCCTGAAAATCATGATTATAGC
3951916 CCTCTCACCATTTCC
319 CCTCTCACCATTTCC
3951931 ATTCGATACC
Statistics
Matches: 300, Mismatches: 29, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
336 2 0.01
337 48 0.16
338 10 0.03
339 50 0.17
340 190 0.63
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (337 bp):
GGTGTTTAGGAAATTGTCTAAAGATAGACAGATCAGACAGGACTTAAAGCCAAGGAATGACTTTG
GAATATATTACGAGTATCACTAGGAAGAGAGCCATGAGATCCAGTGTTGCCCTGAATTTAGAGGC
TTAATATAGAAAATAATGAATAATAAAGAAATATAGTTCTTCGAGAAGGATAGAGAAAAAAATAG
AAGTTAATATATGTACATTAGAGAGCTCCAAGCCTACATATGGAGCAAACAAGCAATAATCATCA
CTATGAGACCGAAAGAAGTGAATCTAGTATTAATAACCCTGAAAATCATGATTATAGCCCTCTCA
CCATTTCCGTTG
Found at i:3953617 original size:2 final size:2
Alignment explanation
Indices: 3953610--3953641 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3953600 CTTCGCTTTC
3953610 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
3953642 ATTCAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3956439 original size:138 final size:137
Alignment explanation
Indices: 3956268--3956661 Score: 347
Period size: 138 Copynumber: 2.9 Consensus size: 137
3956258 GAGCGGTGAT
* * * * *
3956268 CAAATTAAAAA-TACTCCTAAATTAAAGTAATAAAGTGAAAATTAAACTGAAATGAAGGATCTAA
1 CAAATAAAAAACT-CTCCTAAATTAAAG-GATAAAGTGAAAATTAAACTAAAATGAAGGATATAG
*
3956332 TATTAAAACCTAATCAATTTTAATCAATTCTTAATTCGAATAACCAAAATGTAA-CATCAAG-AA
64 TATTAAAACCTAATCAATTTTAATCAATTCTTAATTCGAATAACCAAAATGGAATC-TCAAGCAA
*
3956395 AAAGAGAGGTC
128 AAA-AGAGGAC
* * * *
3956406 CAAATAAAAAAACTCTCCTAAAATAAAGGATAAAGTGAAAATT-ATCATAAAAT-ATAGGCTTTA
1 CAAAT-AAAAAACTCTCCTAAATTAAAGGATAAAGTGAAAATTAAAC-TAAAATGA-AGGATATA
* * * * * **
3956469 GTATTGAAGCCTAATCAATTTT-ATAAAATCATTGAA-TGGAATAACCAAAATGGAATCTCTGGC
63 GTATTAAAACCTAATCAATTTTAATCAATTC-TT-AATTCGAATAACCAAAATGGAATCTCAAGC
* *
3956532 AGAAACGAGGAC
126 AAAAAAGAGGAC
* * * *
3956544 CAAATCAGAAACTCTCCTAAATTAAAGGATTAAAGTG-AAATTAATCCTAAAATGGAGGATATAG
1 CAAATAAAAAACTCTCCTAAATTAAAGGA-TAAAGTGAAAATTAA-ACTAAAATGAAGGATATAG
* * * * **
3956608 TATTTAAACCTAACCAGTTTTAA-CAAATTATTGGTTCGAATAACCAAAATGGAA
64 TATTAAAACCTAATCAATTTTAATC-AATTCTTAATTCGAATAACCAAAATGGAA
3956662 CCTTGGGCAA
Statistics
Matches: 205, Mismatches: 36, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
137 35 0.17
138 139 0.68
139 30 0.15
140 1 0.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.27
Consensus pattern (137 bp):
CAAATAAAAAACTCTCCTAAATTAAAGGATAAAGTGAAAATTAAACTAAAATGAAGGATATAGTA
TTAAAACCTAATCAATTTTAATCAATTCTTAATTCGAATAACCAAAATGGAATCTCAAGCAAAAA
AGAGGAC
Found at i:3956877 original size:15 final size:15
Alignment explanation
Indices: 3956857--3956898 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3956847 AAATTAAGTA
*
3956857 TTGGAATTTAGA-GT
1 TTGGAATTTAAATGT
3956871 GTTGGAATTTAAATGT
1 -TTGGAATTTAAATGT
3956887 TTGGAA-TTAAAT
1 TTGGAATTTAAAT
3956899 AAAACAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 17 0.68
16 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (15 bp):
TTGGAATTTAAATGT
Found at i:3959356 original size:116 final size:116
Alignment explanation
Indices: 3959222--3959490 Score: 301
Period size: 116 Copynumber: 2.3 Consensus size: 116
3959212 TTAATGGACG
* * *
3959222 AGTTCTTCTCACTATGAAACCTTCCATTAGAAATGTTGATCCACCTCCTCCTCTGATAGATGAGC
1 AGTTCTTCTCATTATGAAACCTTCCATTAGAAATGTTGATCCACCTCATCCTCTGATAGATGAAC
* * ** *
3959287 AAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TCTCT-CCCTCTTCATATA
66 AAAGGTTGAACAAGTTCTTCTCAGTATGAACTTCT-TCTACCAT-AACATACA
* * * ** * *
3959338 AGTTTTTCTCATTATGAAA-ATCTCCATTAGAAATTTTGATCCACCTCATTTTGTGATGGATGAA
1 AGTTCTTCTCATTATGAAACCT-TCCATTAGAAATGTTGATCCACCTCATCCTCTGATAGATGAA
* * * *
3959402 CTAAGGTTGAACATGTTCTTCTTAGTATGAACTTCTTCTACCATAACATACG
65 CAAAGGTTGAACAAGTTCTTCTCAGTATGAACTTCTTCTACCATAACATACA
* *
3959454 AGTTCTTCTCATTATAAAACCTTCCATTATAAATGTT
1 AGTTCTTCTCATTATGAAACCTTCCATTAGAAATGTT
3959491 AGTTTGTCTT
Statistics
Matches: 125, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
115 1 0.01
116 119 0.95
117 5 0.04
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (116 bp):
AGTTCTTCTCATTATGAAACCTTCCATTAGAAATGTTGATCCACCTCATCCTCTGATAGATGAAC
AAAGGTTGAACAAGTTCTTCTCAGTATGAACTTCTTCTACCATAACATACA
Found at i:3960009 original size:25 final size:26
Alignment explanation
Indices: 3959981--3960041 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
3959971 TTCATTTATC
3959981 ATTTTCTTT-TACTTTC-TAATTTTTT
1 ATTTTCTTTCT-CTTTCTTAATTTTTT
* *
3960006 ATTTTCTTTCTTTTTCTTCATTTTTT
1 ATTTTCTTTCTCTTTCTTAATTTTTT
3960032 ATTTTTCTTT
1 A-TTTTCTTT
3960042 ACAATAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 13 0.42
26 10 0.32
27 8 0.26
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.75
Consensus pattern (26 bp):
ATTTTCTTTCTCTTTCTTAATTTTTT
Found at i:3982345 original size:125 final size:124
Alignment explanation
Indices: 3982141--3982389 Score: 383
Period size: 125 Copynumber: 2.0 Consensus size: 124
3982131 AAATGATTTG
* * *
3982141 GATGTTGATTTATTGAAAACAACGTCGATTTTTGGTGCTTTTAAGAATCTAAGAAATTAGTTTGT
1 GATGTTGATTTATTGAAAACAACATCGATTTTTGGTACTTTTAAGAATATAAGAAATTAGTTTGT
*
3982206 AAATGTTGATTTGTGCGGTTCTAGATGAGTTAAATATTGATTCTAGTTGTTGTTAATCA
66 AAATGTTAATTTGTGCGGTTCTAGATGAGTTAAATATTGATTCTAGTTGTTGTTAATCA
* * * * *
3982265 GATGTTGATTTATTGAAAACAACATTGATTTTTTTGTATTTTTAGGAATATGAG-AATTAGGTTT
1 GATGTTGATTTATTGAAAACAACATCGA-TTTTTGGTACTTTTAAGAATATAAGAAATTA-GTTT
*
3982329 GTAAATGTTAATTTGTGCGGTTCTAGCTGAGTTAAATATTGATTCTAGTTGTTGTTAATCA
64 GTAAATGTTAATTTGTGCGGTTCTAGATGAGTTAAATATTGATTCTAGTTGTTGTTAATCA
3982390 AATTCTAGTG
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
124 31 0.27
125 82 0.73
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.44
Consensus pattern (124 bp):
GATGTTGATTTATTGAAAACAACATCGATTTTTGGTACTTTTAAGAATATAAGAAATTAGTTTGT
AAATGTTAATTTGTGCGGTTCTAGATGAGTTAAATATTGATTCTAGTTGTTGTTAATCA
Found at i:3991669 original size:143 final size:143
Alignment explanation
Indices: 3991411--3991696 Score: 572
Period size: 143 Copynumber: 2.0 Consensus size: 143
3991401 CAAGGAGCTT
3991411 GGCATCGGTGTGATCAATCAAGGCTAACACATAAAGCTTTACGTATGTGTTGGGATAAATGATGA
1 GGCATCGGTGTGATCAATCAAGGCTAACACATAAAGCTTTACGTATGTGTTGGGATAAATGATGA
3991476 AGCTCAATTGAACAACCGAATATTGCCATGAGGGATTAAATTGACTTTTTGAGTTTAGGGAGTAA
66 AGCTCAATTGAACAACCGAATATTGCCATGAGGGATTAAATTGACTTTTTGAGTTTAGGGAGTAA
3991541 GGAGTATAGAAGA
131 GGAGTATAGAAGA
3991554 GGCATCGGTGTGATCAATCAAGGCTAACACATAAAGCTTTACGTATGTGTTGGGATAAATGATGA
1 GGCATCGGTGTGATCAATCAAGGCTAACACATAAAGCTTTACGTATGTGTTGGGATAAATGATGA
3991619 AGCTCAATTGAACAACCGAATATTGCCATGAGGGATTAAATTGACTTTTTGAGTTTAGGGAGTAA
66 AGCTCAATTGAACAACCGAATATTGCCATGAGGGATTAAATTGACTTTTTGAGTTTAGGGAGTAA
3991684 GGAGTATAGAAGA
131 GGAGTATAGAAGA
3991697 TAGAAAATTT
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (143 bp):
GGCATCGGTGTGATCAATCAAGGCTAACACATAAAGCTTTACGTATGTGTTGGGATAAATGATGA
AGCTCAATTGAACAACCGAATATTGCCATGAGGGATTAAATTGACTTTTTGAGTTTAGGGAGTAA
GGAGTATAGAAGA
Found at i:3993731 original size:21 final size:23
Alignment explanation
Indices: 3993705--3993746 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
3993695 CTTAACTTTA
3993705 AAATCAAT-ATTTT-ATTTTTTT
1 AAATCAATGATTTTGATTTTTTT
*
3993726 AAATCATTGATTTTGATTTTT
1 AAATCAATGATTTTGATTTTT
3993747 GAAAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (23 bp):
AAATCAATGATTTTGATTTTTTT
Found at i:3995827 original size:5 final size:5
Alignment explanation
Indices: 3995817--3995874 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
3995807 AACGGTCAAC
* *
3995817 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG
3995866 GGTCG GGTC
1 GGTCG GGTC
3995875 AGACCAGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:3995832 original size:17 final size:17
Alignment explanation
Indices: 3995810--3995875 Score: 83
Period size: 17 Copynumber: 4.3 Consensus size: 17
3995800 AACGGTCAAC
3995810 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
3995827 GGTCAACGGTCGGGTC-
1 GGTCAACGGTCGGGTCG
3995843 -G-----GGTCGGGTCG
1 GGTCAACGGTCGGGTCG
3995854 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
3995871 GGTCA
1 GGTCA
3995876 GACCAGTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.21
12 1 0.02
15 1 0.02
17 31 0.74
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:3995854 original size:27 final size:27
Alignment explanation
Indices: 3995817--3995874 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
3995807 AACGGTCAAC
3995817 GGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCGGGTCAACGGTCGGGTCG
3995844 GGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCGGGTCAACGGTCGGGTCG
3995871 GGTC
1 GGTC
3995875 AGACCAGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (27 bp):
GGTCGGGTCGGGTCAACGGTCGGGTCG
Found at i:3995893 original size:9 final size:9
Alignment explanation
Indices: 3995871--3995939 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
3995861 GGTCGGGTCG
*
3995871 GGTCAGACC
1 GGTCAAACC
*
3995880 AGTCAAACC
1 GGTCAAACC
3995889 GGTCAAACC
1 GGTCAAACC
*
3995898 GGTTCGAACC
1 GG-TCAAACC
*
3995908 GGTTCGAACC
1 GG-TCAAACC
3995918 GGTCAAACC
1 GGTCAAACC
3995927 GGTCAGAACC
1 GGTCA-AACC
3995937 GGT
1 GGT
3995940 TGAAAATCGG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
9 28 0.53
10 25 0.47
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3995909 original size:10 final size:9
Alignment explanation
Indices: 3995885--3995939 Score: 65
Period size: 10 Copynumber: 5.8 Consensus size: 9
3995875 AGACCAGTCA
*
3995885 AACCGGTCA
1 AACCGGTCG
3995894 AACCGGTTCG
1 AACCGG-TCG
3995904 AACCGGTTCG
1 AACCGG-TCG
*
3995914 AACCGGTCA
1 AACCGGTCG
3995923 AACCGGTCAG
1 AACCGGTC-G
3995933 AACCGGT
1 AACCGGT
3995940 TGAAAATCGG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
9 16 0.39
10 25 0.61
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (9 bp):
AACCGGTCG
Found at i:3995909 original size:19 final size:19
Alignment explanation
Indices: 3995882--3995960 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
3995872 GTCAGACCAG
3995882 TCAAACCGGTCAAACCGGT
1 TCAAACCGGTCAAACCGGT
* *
3995901 TCGAACCGGTTCGAACCGG-
1 TCAAACCGG-TCAAACCGGT
3995920 TCAAACCGGTCAGAACCGGT
1 TCAAACCGGTCA-AACCGGT
* * *
3995940 TGAAAATCGGTTAAACCGGT
1 T-CAAACCGGTCAAACCGGT
3995960 T
1 T
3995961 TCCAGCAGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.04
19 22 0.45
20 17 0.35
21 8 0.16
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (19 bp):
TCAAACCGGTCAAACCGGT
Found at i:3995918 original size:29 final size:29
Alignment explanation
Indices: 3995885--3995940 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
3995875 AGACCAGTCA
3995885 AACCGGTCAAACCGGTTC-GAACCGGTTCG
1 AACCGGTCAAACCGG-TCAGAACCGGTTCG
3995914 AACCGGTCAAACCGGTCAGAACCGGTT
1 AACCGGTCAAACCGGTCAGAACCGGTT
3995941 GAAAATCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (29 bp):
AACCGGTCAAACCGGTCAGAACCGGTTCG
Found at i:4000997 original size:47 final size:47
Alignment explanation
Indices: 4000928--4001021 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
4000918 TCAGTAGGAG
4000928 CTCCACCTATTCTCCCCCCAAAAGTTCTAACTCCATTGGCAATCAAA
1 CTCCACCTATTCTCCCCCCAAAAGTTCTAACTCCATTGGCAATCAAA
4000975 CTCCACCTATT-TCTCCCCCAAAAGTTCTAACTCCATTGGCAATCAAA
1 CTCCACCTATTCTC-CCCCCAAAAGTTCTAACTCCATTGGCAATCAAA
4001022 GTCTGCGAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 2 0.04
47 44 0.96
ACGTcount: A:0.30, C:0.37, G:0.06, T:0.27
Consensus pattern (47 bp):
CTCCACCTATTCTCCCCCCAAAAGTTCTAACTCCATTGGCAATCAAA
Found at i:4003048 original size:7 final size:7
Alignment explanation
Indices: 4003036--4003066 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4003026 GTCAAAGAAA
4003036 GTCAACG
1 GTCAACG
*
4003043 GTCAACA
1 GTCAACG
4003050 GTCAACG
1 GTCAACG
4003057 GTCAACG
1 GTCAACG
4003064 GTC
1 GTC
4003067 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:4003867 original size:2 final size:2
Alignment explanation
Indices: 4003860--4003885 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4003850 GACATATTTA
4003860 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
4003886 TTGAAGATTT
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:4009816 original size:23 final size:22
Alignment explanation
Indices: 4009760--4009890 Score: 92
Period size: 21 Copynumber: 6.0 Consensus size: 22
4009750 GCAATTTCGT
* *
4009760 AAGAGTATTTTGTGTAGT-T-G
1 AAGAGTACTTTGTGTACTATGG
*
4009780 AAGTACTACTTTGTGTACTATGG
1 AAG-AGTACTTTGTGTACTATGG
*
4009803 TAAGAGTACTTTGTGTA-TTTGG
1 -AAGAGTACTTTGTGTACTATGG
** *
4009825 ATTATTACTTTGTGTACTATGG
1 AAGAGTACTTTGTGTACTATGG
* *
4009847 CAAGAGTACTTTGCGTTCT-TGG
1 -AAGAGTACTTTGTGTACTATGG
* *
4009869 -AGTTGTACTTTGGGTACTATGG
1 AAG-AGTACTTTGTGTACTATGG
4009891 CACTTTATGT
Statistics
Matches: 86, Mismatches: 17, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
20 5 0.06
21 37 0.43
22 15 0.17
23 26 0.30
24 3 0.03
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (22 bp):
AAGAGTACTTTGTGTACTATGG
Found at i:4009834 original size:44 final size:44
Alignment explanation
Indices: 4009758--4009890 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 44
4009748 TTGCAATTTC
* * * *
4009758 GTAAGAGTATTTTGTGTAGTTGAAGTACTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTATTTGGATTACTACTTTGTGTACTATG
*
4009802 GTAAGAGTACTTTGTGTATTTGGATTATTACTTTGTGTACTATG
1 GTAAGAGTACTTTGTGTATTTGGATTACTACTTTGTGTACTATG
* * * *
4009846 GCAAGAGTACTTTGCGT-TCTTGGAGTT-GTACTTTGGGTACTATG
1 GTAAGAGTACTTTGTGTAT-TTGGA-TTACTACTTTGTGTACTATG
4009890 G
1 G
4009891 CACTTTATGT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.01
44 75 0.96
45 2 0.03
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (44 bp):
GTAAGAGTACTTTGTGTATTTGGATTACTACTTTGTGTACTATG
Found at i:4010036 original size:13 final size:13
Alignment explanation
Indices: 4010018--4010045 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4010008 TAGAATATAT
4010018 TGATTTATAAGTA
1 TGATTTATAAGTA
4010031 TGATTTATAAGTA
1 TGATTTATAAGTA
4010044 TG
1 TG
4010046 CTAGGCATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (13 bp):
TGATTTATAAGTA
Found at i:4010791 original size:67 final size:67
Alignment explanation
Indices: 4010683--4010821 Score: 269
Period size: 67 Copynumber: 2.1 Consensus size: 67
4010673 GCCCCATGTA
*
4010683 TTGATGGCCTTTTTGTTTCCTTCTTTAGAACCTTTTGGGATTTGCTTTGTAATGATCTTTTTATT
1 TTGATGGCCTTTTTGGTTCCTTCTTTAGAACCTTTTGGGATTTGCTTTGTAATGATCTTTTTATT
4010748 CT
66 CT
4010750 TTGATGGCCTTTTTGGTTCCTTCTTTAGAACCTTTTGGGATTTGCTTTGTAATGATCTTTTTATT
1 TTGATGGCCTTTTTGGTTCCTTCTTTAGAACCTTTTGGGATTTGCTTTGTAATGATCTTTTTATT
4010815 CT
66 CT
4010817 TTGAT
1 TTGAT
4010822 TAGATTTGGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (67 bp):
TTGATGGCCTTTTTGGTTCCTTCTTTAGAACCTTTTGGGATTTGCTTTGTAATGATCTTTTTATT
CT
Found at i:4021069 original size:23 final size:23
Alignment explanation
Indices: 4021043--4021121 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 23
4021033 CTGGAGTGCA
4021043 AAAAAGAAAGAAAAGACAAAAAG
1 AAAAAGAAAGAAAAGACAAAAAG
*
4021066 AAAAAGAAA-AAAA-ATCAAAAATC
1 AAAAAGAAAGAAAAGA-CAAAAA-G
4021089 AAAAA-AGAAGAAAAGA-AGAAAAG
1 AAAAAGA-AAGAAAAGACA-AAAAG
4021112 AAAAGAGAAA
1 AAAA-AGAAA
4021122 AAATTCAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
21 1 0.02
22 11 0.24
23 21 0.46
24 11 0.24
25 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.03
Consensus pattern (23 bp):
AAAAAGAAAGAAAAGACAAAAAG
Found at i:4021077 original size:8 final size:8
Alignment explanation
Indices: 4021042--4021124 Score: 57
Period size: 8 Copynumber: 10.6 Consensus size: 8
4021032 ACTGGAGTGC
4021042 AAAAAAGA
1 AAAAAAGA
4021050 AAGAAAAGA
1 AA-AAAAGA
*
4021059 CAAAAAG-
1 AAAAAAGA
4021066 -AAAAAGA
1 AAAAAAGA
4021073 AAAAAA-A
1 AAAAAAGA
* **
4021080 TCAAAAATC
1 -AAAAAAGA
4021089 AAAAAAGA
1 AAAAAAGA
*
4021097 AGAAAAGA
1 AAAAAAGA
*
4021105 AGAAAAG-
1 AAAAAAGA
*
4021112 AAAAGAGA
1 AAAAAAGA
4021120 AAAAA
1 AAAAA
4021125 TTCAAAAAGA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
6 6 0.10
7 6 0.10
8 40 0.68
9 7 0.12
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:4021121 original size:47 final size:46
Alignment explanation
Indices: 4021041--4021132 Score: 134
Period size: 46 Copynumber: 2.0 Consensus size: 46
4021031 AACTGGAGTG
4021041 CAAAAAAGAAAGAAAAGACAAAAAGAAAAAGAAAAAAAATCAAAAAT
1 CAAAAAAGAAAGAAAAGACAAAAAGAAAAAG-AAAAAAATCAAAAAT
*
4021088 CAAAAAAG-AAGAAAAGA-AGAAAAGAAAAGAGAAAAAATTCAAAAA
1 CAAAAAAGAAAGAAAAGACA-AAAAGAAAA-AGAAAAAAATCAAAAA
4021133 GAAAGCAAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 1 0.02
46 31 0.74
47 10 0.24
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.04
Consensus pattern (46 bp):
CAAAAAAGAAAGAAAAGACAAAAAGAAAAAGAAAAAAATCAAAAAT
Found at i:4026332 original size:22 final size:21
Alignment explanation
Indices: 4026292--4026332 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4026282 CATCTCCATT
*
4026292 TCATCATCAACACCATCAACA
1 TCATCATCAAAACCATCAACA
*
4026313 TCATCCATCAAAACCTTCAA
1 TCAT-CATCAAAACCATCAA
4026333 TTCTACATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (21 bp):
TCATCATCAAAACCATCAACA
Found at i:4032047 original size:153 final size:153
Alignment explanation
Indices: 4031769--4032074 Score: 612
Period size: 153 Copynumber: 2.0 Consensus size: 153
4031759 ACCCATGGCA
4031769 TGGTTAGTATCGGCAATGGCATGTACAATCCATGAGGCATAACTCTTGATTTTGCCTTTTTACAC
1 TGGTTAGTATCGGCAATGGCATGTACAATCCATGAGGCATAACTCTTGATTTTGCCTTTTTACAC
4031834 ACTGAGCACCTTTCACATACCTTTTCATCTTTGGACAAAAGAGGTGTTCTTTCAAGAGGCTAAGT
66 ACTGAGCACCTTTCACATACCTTTTCATCTTTGGACAAAAGAGGTGTTCTTTCAAGAGGCTAAGT
4031899 GTCATTTCAACGCCAAAGTGTCC
131 GTCATTTCAACGCCAAAGTGTCC
4031922 TGGTTAGTATCGGCAATGGCATGTACAATCCATGAGGCATAACTCTTGATTTTGCCTTTTTACAC
1 TGGTTAGTATCGGCAATGGCATGTACAATCCATGAGGCATAACTCTTGATTTTGCCTTTTTACAC
4031987 ACTGAGCACCTTTCACATACCTTTTCATCTTTGGACAAAAGAGGTGTTCTTTCAAGAGGCTAAGT
66 ACTGAGCACCTTTCACATACCTTTTCATCTTTGGACAAAAGAGGTGTTCTTTCAAGAGGCTAAGT
4032052 GTCATTTCAACGCCAAAGTGTCC
131 GTCATTTCAACGCCAAAGTGTCC
4032075 CGTAAGTCCC
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 153 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (153 bp):
TGGTTAGTATCGGCAATGGCATGTACAATCCATGAGGCATAACTCTTGATTTTGCCTTTTTACAC
ACTGAGCACCTTTCACATACCTTTTCATCTTTGGACAAAAGAGGTGTTCTTTCAAGAGGCTAAGT
GTCATTTCAACGCCAAAGTGTCC
Found at i:4034751 original size:21 final size:22
Alignment explanation
Indices: 4034726--4034773 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
4034716 GTGCTTTTAA
*
4034726 ATTTTCTTGCTTTTCTTTTCTTT
1 ATTTTCTT-CCTTTCTTTTCTTT
*
4034749 -TTTTCTTCCTTTGTTTTC-TT
1 ATTTTCTTCCTTTCTTTTCTTT
4034769 ATTTT
1 ATTTT
4034774 TAGTTCTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.09
21 13 0.59
22 7 0.32
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (22 bp):
ATTTTCTTCCTTTCTTTTCTTT
Found at i:4034755 original size:22 final size:22
Alignment explanation
Indices: 4034727--4034774 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4034717 TGCTTTTAAA
*
4034727 TTTTCTTGCTTTTCTTTTCTT-T
1 TTTTCTT-CCTTTCTTTTCTTAT
*
4034749 TTTTCTTCCTTTGTTTTCTTAT
1 TTTTCTTCCTTTCTTTTCTTAT
4034771 TTTT
1 TTTT
4034775 AGTTCTTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTCTTCCTTTCTTTTCTTAT
Found at i:4038347 original size:19 final size:19
Alignment explanation
Indices: 4038325--4038361 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4038315 AAAATTTCAT
*
4038325 TTTGATTTTTAAAATCAAC
1 TTTGATTTTCAAAATCAAC
*
4038344 TTTGGTTTTCAAAATCAA
1 TTTGATTTTCAAAATCAA
4038362 ATCATTTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (19 bp):
TTTGATTTTCAAAATCAAC
Found at i:4059630 original size:82 final size:82
Alignment explanation
Indices: 4059517--4059859 Score: 364
Period size: 82 Copynumber: 4.2 Consensus size: 82
4059507 TGGCATCATG
* * * * *
4059517 CAATAGTTCATCATTCAAATTGATTCAATCATGGTAGCGTGCAAAAATTCACCATTCAATTCAAT
1 CAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTCAAT
*
4059582 TCAATCATGAAAACATG
66 TCAATCATGAAAACATA
* * * * * *
4059599 CAATAGTTCATCATTCAACTTGATTCCATCATCGTATCATATAATAACTCACCATTCGATTTAAT
1 CAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTCAAT
* * *
4059664 TCAATCATGACAGCAAA
66 TCAATCATGAAAACATA
* * ** * * * * *
4059681 TAATAGTTCATCATTTAACAAGATTCGATCATGGTAGCATGCTATTATTCACCATTTGATTCAAT
1 CAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTCAAT
*
4059746 TCAATCATGGAAGA-ATA
66 TCAATCAT-GAAAACATA
* * * *
4059763 TAGTAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACTATTCGATTAAAT
1 CAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTCAAT
* ** *
4059828 TCATTCATGGCATCATA
66 TCAATCATGAAAACATA
*
4059845 CAATAGTTCACCATT
1 CAATAGTTCATCATT
4059860 TGATTCAATT
Statistics
Matches: 207, Mismatches: 52, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
81 1 0.00
82 204 0.99
83 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (82 bp):
CAATAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATAATTCACCATTCGATTCAAT
TCAATCATGAAAACATA
Found at i:4059822 original size:164 final size:163
Alignment explanation
Indices: 4059517--4059860 Score: 422
Period size: 164 Copynumber: 2.1 Consensus size: 163
4059507 TGGCATCATG
* * *
4059517 CAATAGTTCATCATTCAAATTGATTCAATCATGGTAGCGTGCAAAAATTCACCATTCAATTCAAT
1 CAATAGTTCATCATTTAAATAGATTCAATCATGGTAGCATGCAAAAATTCACCATTCAATTCAAT
* * *
4059582 TCAATCATGAAAACATGCAATAGTTCATCATTCAACTTGATTCCATCATCGTATCATATAATAAC
66 TCAATCATGAAAACAT-CAATAGTTCATCATTCAACTTGATTCAATCATCGTAGCATACAATAAC
*
4059647 TCACCATTCGATTTAATTCAATCATGACAGCAAA
130 TCACCATTCGATTAAATTCAATCATGACAGCAAA
* * * ** **
4059681 TAATAGTTCATCATTTAACA-AGATTCGATCATGGTAGCATGCTATTATTCACCATTTGATTCAA
1 CAATAGTTCATCATTTAA-ATAGATTCAATCATGGTAGCATGCAAAAATTCACCATTCAATTCAA
* * *
4059745 TTCAATCATGGAAGAATAT-AGTAGTTCATCATTCAACTTGATTCAATCATGGTAGCATACAATA
65 TTCAATCAT-GAA-AACATCAATAGTTCATCATTCAACTTGATTCAATCATCGTAGCATACAATA
* * * * * *
4059809 ATTCACTATTCGATTAAATTCATTCATGGCATCATA
128 ACTCACCATTCGATTAAATTCAATCATGACAGCAAA
*
4059845 CAATAGTTCACCATTT
1 CAATAGTTCATCATTT
4059861 GATTCAATTC
Statistics
Matches: 152, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
164 144 0.95
165 4 0.03
166 4 0.03
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (163 bp):
CAATAGTTCATCATTTAAATAGATTCAATCATGGTAGCATGCAAAAATTCACCATTCAATTCAAT
TCAATCATGAAAACATCAATAGTTCATCATTCAACTTGATTCAATCATCGTAGCATACAATAACT
CACCATTCGATTAAATTCAATCATGACAGCAAA
Found at i:4059881 original size:41 final size:41
Alignment explanation
Indices: 4059507--4059901 Score: 190
Period size: 41 Copynumber: 9.6 Consensus size: 41
4059497 AGTTCGATCT
* * * * *
4059507 TGGCATCATGCAATAGTTCATCATTCAAATT-GATTCAATCA
1 TGGCAGCATACAATAGTTCACCATTC-GATTCAATTCAATCA
* * * * * *
4059548 TGGTAGCGTGCAAAAATTCACCATTCAATTCAATTCAATCA
1 TGGCAGCATACAATAGTTCACCATTCGATTCAATTCAATCA
** * * * * * *
4059589 TGAAAACATGCAATAGTTCATCATTCAACTT-GATTCCATCA
1 TGGCAGCATACAATAGTTCACCATTCGA-TTCAATTCAATCA
* * * * ** *
4059630 TCGTATCATATAATAACTCACCATTCGATTTAATTCAATCA
1 TGGCAGCATACAATAGTTCACCATTCGATTCAATTCAATCA
* * * * * * *
4059671 TGACAGCAAATAATAGTTCATCATT-TA-ACAAGATTCGATCA
1 TGGCAGCATACAATAGTTCACCATTCGATTC-A-ATTCAATCA
* * * *
4059712 TGGTAGCATGCTATTA-TTCACCATTTGATTCAATTCAATCA
1 TGGCAGCATAC-AATAGTTCACCATTCGATTCAATTCAATCA
* * * * * * *
4059753 TGGAAGAATATAGTAGTTCATCATTCAACTT-GATTCAATCA
1 TGGCAGCATACAATAGTTCACCATTCGA-TTCAATTCAATCA
* * * * *
4059794 TGGTAGCATACAATAATTCACTATTCGATTAAATTCATTCA
1 TGGCAGCATACAATAGTTCACCATTCGATTCAATTCAATCA
* *
4059835 TGGCATCATACAATAGTTCACCATTTGATTCAATTCAATCA
1 TGGCAGCATACAATAGTTCACCATTCGATTCAATTCAATCA
* * * * *
4059876 AGGCATCATATAACAGTTCATCATTC
1 TGGCAGCATACAATAGTTCACCATTC
4059902 AACTTGATTT
Statistics
Matches: 262, Mismatches: 81, Indels: 22
0.72 0.22 0.06
Matches are distributed among these distances:
40 13 0.05
41 239 0.91
42 9 0.03
43 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (41 bp):
TGGCAGCATACAATAGTTCACCATTCGATTCAATTCAATCA
Found at i:4059959 original size:123 final size:123
Alignment explanation
Indices: 4059728--4059959 Score: 286
Period size: 123 Copynumber: 1.9 Consensus size: 123
4059718 CATGCTATTA
* **
4059728 TTCACCATTTGATTCAATTCAATCATGGAAGAATATAGTAGTTCATCATTCAACTTGATTCAATC
1 TTCACCATTTGATTCAATTCAATCAAGGAAGAATATAACAGTTCATCATTCAACTTGATTCAATC
* ** * * *
4059793 ATGGTAGCATACAATAATTCACTATTCGATTAAATTCATTCATGGCATCATACAATAG
66 ATGGTAGCATACAATAATTCACAAACCAAATAAATTCAATCATGGCATCATACAATAG
* ** **
4059851 TTCACCATTTGATTCAATTCAATCAAGGCATCATATAACAGTTCATCATTCAACTTGATTTGATC
1 TTCACCATTTGATTCAATTCAATCAAGGAAGAATATAACAGTTCATCATTCAACTTGATTCAATC
* * * *
4059916 ATGGTAGCATTCATTTATTCACAAACCAAATCAATT-AGATCATG
66 ATGGTAGCATACAATAATTCACAAACCAAATAAATTCA-ATCATG
4059960 ATAACATGTA
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
122 1 0.01
123 89 0.99
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (123 bp):
TTCACCATTTGATTCAATTCAATCAAGGAAGAATATAACAGTTCATCATTCAACTTGATTCAATC
ATGGTAGCATACAATAATTCACAAACCAAATAAATTCAATCATGGCATCATACAATAG
Found at i:4065623 original size:90 final size:89
Alignment explanation
Indices: 4065464--4065640 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
4065454 CCCAACACAC
*
4065464 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCCAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
4065529 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
4065553 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
4065618 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
4065641 TTTGGGATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 34 0.41
90 49 0.59
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:4069937 original size:17 final size:18
Alignment explanation
Indices: 4069893--4069941 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
4069883 TTTTCTCGGA
* *
4069893 GTGTTTGGAGAGAAACTT
1 GTGTTTGGTGAGGAACTT
4069911 GTGTTTGGTGAGGAACTT
1 GTGTTTGGTGAGGAACTT
4069929 GTG-TTGGTGAGGA
1 GTGTTTGGTGAGGA
4069942 TTTATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.20, C:0.04, G:0.41, T:0.35
Consensus pattern (18 bp):
GTGTTTGGTGAGGAACTT
Found at i:4070112 original size:25 final size:25
Alignment explanation
Indices: 4070080--4070127 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
4070070 TATTGGGGAG
4070080 GGAAGAAATGAGAACCATTTGAAGA
1 GGAAGAAATGAGAACCATTTGAAGA
4070105 GGAAGAAATGAGAACCATTTGAA
1 GGAAGAAATGAGAACCATTTGAA
4070128 AAGAAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.27, T:0.17
Consensus pattern (25 bp):
GGAAGAAATGAGAACCATTTGAAGA
Found at i:4070135 original size:25 final size:25
Alignment explanation
Indices: 4070082--4070135 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
4070072 TTGGGGAGGG
* *
4070082 AAGAAATGAGAACCATTTGAAGAGG
1 AAGAAATGAGAACCATTTGAAAAGA
4070107 AAGAAATGAGAACCATTTGAAAAGA
1 AAGAAATGAGAACCATTTGAAAAGA
4070132 AAGA
1 AAGA
4070136 TGACATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.24, T:0.15
Consensus pattern (25 bp):
AAGAAATGAGAACCATTTGAAAAGA
Found at i:4081692 original size:17 final size:17
Alignment explanation
Indices: 4081667--4081699 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4081657 ATCCTACCTT
4081667 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
*
4081684 TACCTTAACCATTTCT
1 TACCATAACCATTTCT
4081700 TTTTAAGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:4082667 original size:17 final size:17
Alignment explanation
Indices: 4082645--4082683 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
4082635 TGGTGTAAAT
4082645 GGCAATGAAGATTGAAA
1 GGCAATGAAGATTGAAA
4082662 GGCAATGAAGATTGAAA
1 GGCAATGAAGATTGAAA
4082679 GGCAA
1 GGCAA
4082684 CTAAAGAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (17 bp):
GGCAATGAAGATTGAAA
Found at i:4086500 original size:21 final size:21
Alignment explanation
Indices: 4086474--4086530 Score: 60
Period size: 27 Copynumber: 2.4 Consensus size: 21
4086464 GATGTGTACT
4086474 ATATGAGAATCATGAATGCAC
1 ATATGAGAATCATGAATGCAC
4086495 ATATGAGATTTAGAATCATGAATGCAC
1 ATAT--G----AGAATCATGAATGCAC
4086522 ATATGAGAA
1 ATATGAGAA
4086531 AGTACTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
21 8 0.27
23 1 0.03
25 1 0.03
27 20 0.67
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (21 bp):
ATATGAGAATCATGAATGCAC
Found at i:4090820 original size:50 final size:50
Alignment explanation
Indices: 4090766--4090860 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
4090756 GATAAAGATG
* *
4090766 CATCTCCCTTGGCCAAATGGTGA-TATGCTTGTTCATCTTGGTGCCAAAGT
1 CATCTCCCTTGGCCAAATGGT-ATTATGATGGTTCATCTTGGTGCCAAAGT
* * *
4090816 CATCTTCCTTGGTCAAATGGTATTGTGATGGTTCATCTTGGTGCC
1 CATCTCCCTTGGCCAAATGGTATTATGATGGTTCATCTTGGTGCC
4090861 CAAATTCTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 1 0.03
50 38 0.97
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (50 bp):
CATCTCCCTTGGCCAAATGGTATTATGATGGTTCATCTTGGTGCCAAAGT
Found at i:4095899 original size:17 final size:17
Alignment explanation
Indices: 4095866--4095937 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
4095856 AATTAAGAGT
* *
4095866 TAGTTTAATAAAGGAAC
1 TAGTTTAATGAATGAAC
* *
4095883 TTGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
4095900 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
4095917 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
4095935 TAG
1 TAG
4095938 ATGCATGAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
17 29 0.67
18 14 0.33
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:4095931 original size:18 final size:18
Alignment explanation
Indices: 4095893--4095936 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
4095883 TTGTTTGATG
*
4095893 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
4095910 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
4095927 CAATGAACTA
1 -AATGAACTA
4095937 GATGCATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:4102221 original size:17 final size:16
Alignment explanation
Indices: 4102144--4102241 Score: 56
Period size: 17 Copynumber: 5.8 Consensus size: 16
4102134 GCATGAAACA
*
4102144 ATTAA-GAATTAGTTT
1 ATTAATGAACTAGTTT
*
4102159 AATTAATGAACTAACTTT
1 -ATTAATGAACT-AGTTT
*
4102177 ATTAAATGAACTTGTAATT
1 ATT-AATGAACTAGT--TT
4102196 -TTGAATGAACTAGTTT
1 ATT-AATGAACTAGTTT
* *
4102212 GATTAATGAACCATTTT
1 -ATTAATGAACTAGTTT
*
4102229 AATGAATGAACTA
1 -ATTAATGAACTA
4102242 CTTAGTTAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
16 7 0.11
17 29 0.45
18 26 0.41
19 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (16 bp):
ATTAATGAACTAGTTT
Found at i:4106424 original size:17 final size:17
Alignment explanation
Indices: 4106401--4106529 Score: 100
Period size: 17 Copynumber: 7.5 Consensus size: 17
4106391 GGTTTTATGG
4106401 ATGAACTAGTTTAATTA
1 ATGAACTAGTTTAATTA
* * *
4106418 ATAAACTAACTTTATTTA
1 ATGAACT-AGTTTAATTA
**
4106436 ATGAACT--TGAAATCTTGA
1 ATGAACTAGTTTAA--TT-A
* *
4106454 ATGAACTAGTTTGATGA
1 ATGAACTAGTTTAATTA
* *
4106471 ATGAACTAGTTTGATGA
1 ATGAACTAGTTTAATTA
*
4106488 ATGAACTAGTTTAATAA
1 ATGAACTAGTTTAATTA
* *
4106505 ATAAACTAGTTTAATCA
1 ATGAACTAGTTTAATTA
4106522 ATGAACTA
1 ATGAACTA
4106530 CTTAGTTAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.02
17 63 0.70
18 23 0.26
20 2 0.02
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (17 bp):
ATGAACTAGTTTAATTA
Found at i:4106492 original size:34 final size:34
Alignment explanation
Indices: 4106451--4106529 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
4106441 CTTGAAATCT
* * * *
4106451 TGAATGAACTAGTTTGATGAATGAACTAGTTTGA
1 TGAATGAACTAGTTTAATAAATAAACTAGTTTAA
4106485 TGAATGAACTAGTTTAATAAATAAACTAGTTTAA
1 TGAATGAACTAGTTTAATAAATAAACTAGTTTAA
*
4106519 TCAATGAACTA
1 TGAATGAACTA
4106530 CTTAGTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (34 bp):
TGAATGAACTAGTTTAATAAATAAACTAGTTTAA
Found at i:4108963 original size:23 final size:23
Alignment explanation
Indices: 4108924--4108968 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4108914 ATAAATATGC
*
4108924 TTATTTCATATGTTATAATATAA
1 TTATTTCATATGATATAATATAA
*
4108947 TTATTATCATAT-ATATATTATA
1 TTATT-TCATATGATATAATATA
4108969 TCTATAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATTTCATATGATATAATATAA
Done.