Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000121.1 Hibiscus syriacus cultivar Beakdansim tig00000218_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: 2099483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1860176 original size:23 final size:23
Alignment explanation
Indices: 1860150--1860195 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1860140 CACCACAGCT
*
1860150 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1860173 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1860196 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1860436 original size:151 final size:149
Alignment explanation
Indices: 1860173--1860479 Score: 569
Period size: 151 Copynumber: 2.0 Consensus size: 149
1860163 CGAAGTGCCA
1860173 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
1860238 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
1860303 TATATATATCCCGAAGGACCG
129 TATATATATCCCGAAGGACCG
*
1860324 CGTAGAATTGTACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
1860389 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCATAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1860454 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1860473 CGTAGAA
1 CGTAGAA
1860480 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
149 31 0.20
150 1 0.01
151 121 0.79
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1861959 original size:64 final size:63
Alignment explanation
Indices: 1861821--1861982 Score: 159
Period size: 64 Copynumber: 2.5 Consensus size: 63
1861811 TCTTTTAATG
* * *
1861821 AAGGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTAC
1 AAGG-ATGCATCGATGCA-TACTGATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAA
* * * *
1861886 TAGGATGCATCGATGCATGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTA
1 AAGGATGCATCGATGCAT-ACTGATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTA
1861949 A
63 A
**
1861950 AA-GAGTGCATCGATGCATTACCAATGCATCGAT
1 AAGGA-TGCATCGATGCA-TACTGATGCATCGAT
1861983 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
63 3 0.04
64 67 0.83
65 11 0.14
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
AAGGATGCATCGATGCATACTGATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAA
Found at i:1862965 original size:18 final size:19
Alignment explanation
Indices: 1862942--1862982 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1862932 ATAACCTCAA
*
1862942 TCCATTTCT-TTTCTTTAT
1 TCCATTTCTCTTTATTTAT
1862960 TCCATTTCTCCTTTATTTAT
1 TCCATTTCT-CTTTATTTAT
1862980 TCC
1 TCC
1862983 TTATACACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (19 bp):
TCCATTTCTCTTTATTTAT
Found at i:1864769 original size:21 final size:22
Alignment explanation
Indices: 1864743--1864790 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1864733 ACATTGAACT
1864743 TATTCAAAACGTT-TACAA-AAA
1 TATTCAAAAC-TTATACAATAAA
*
1864764 TATTCAAAACTTATACAATATA
1 TATTCAAAACTTATACAATAAA
1864786 TATTC
1 TATTC
1864791 TTTTGATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 7 0.29
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (22 bp):
TATTCAAAACTTATACAATAAA
Found at i:1865331 original size:23 final size:23
Alignment explanation
Indices: 1865305--1865350 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1865295 CACCACAGCT
*
1865305 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1865328 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1865351 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1865567 original size:149 final size:149
Alignment explanation
Indices: 1865328--1865632 Score: 583
Period size: 149 Copynumber: 2.0 Consensus size: 149
1865318 CGAAGTGCCA
1865328 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
1865393 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATATTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATATTCCACAGAATATA
1865458 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
*
1865477 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGATT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
1865542 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATATTCCACAGAATATA
1865607 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1865626 CGTAGAA
1 CGTAGAA
1865633 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATATTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1880392 original size:126 final size:126
Alignment explanation
Indices: 1880168--1880420 Score: 490
Period size: 126 Copynumber: 2.0 Consensus size: 126
1880158 AGGAACAACA
1880168 ATGAAGACAAAGAGGAACAATCTTCTTTGAAGTTCAGCATGATGGAAGCAGTACAAACTCCAAGA
1 ATGAAGACAAAGAGGAACAATCTTCTTTGAAGTTCAGCATGATGGAAGCAGTACAAACTCCAAGA
1880233 TGAGGCCATGTGATTGAGGCTTTTATATATAGC-TTTAACCACAATAACACTATTTTAATT
66 TGAGGCCATGTGATTGAGGCTTTTATATATAGCTTTTAACCACAATAACACTATTTTAATT
1880293 ATGAAGACAAAGAGGAACAATCTTCTTTGAAGTTCAGCATGATTGGAAGCAGTACAAACTCCAAG
1 ATGAAGACAAAGAGGAACAATCTTCTTTGAAGTTCAGCATGA-TGGAAGCAGTACAAACTCCAAG
1880358 ATGAGGCCATGTGATTGAGGCTTTTATATATAGCTTTTAACCACAATAACACTATTTTAATT
65 ATGAGGCCATGTGATTGAGGCTTTTATATATAGCTTTTAACCACAATAACACTATTTTAATT
1880420 A
1 A
1880421 CCTACAAAAG
Statistics
Matches: 126, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
125 42 0.33
126 56 0.44
127 28 0.22
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (126 bp):
ATGAAGACAAAGAGGAACAATCTTCTTTGAAGTTCAGCATGATGGAAGCAGTACAAACTCCAAGA
TGAGGCCATGTGATTGAGGCTTTTATATATAGCTTTTAACCACAATAACACTATTTTAATT
Found at i:1882442 original size:18 final size:18
Alignment explanation
Indices: 1882419--1882459 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1882409 AATTACTAGA
1882419 AACATTATCAACCATAAT
1 AACATTATCAACCATAAT
1882437 AACATTATCAACCATAAT
1 AACATTATCAACCATAAT
1882455 AACAT
1 AACAT
1882460 AACAAATAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (18 bp):
AACATTATCAACCATAAT
Found at i:1883638 original size:200 final size:200
Alignment explanation
Indices: 1883012--1883756 Score: 986
Period size: 200 Copynumber: 3.8 Consensus size: 200
1883002 TTATGCATGT
* * ** * * *
1883012 GTATTGATACTT-GT-TTTACGCTTATTATCATTATACTAGTATATTTTTATCGTTTTCATTGTA
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGATTTTTACCGTTTACATTGTA
* * * **
1883075 AATTAACCTATTACGTTAAAGTAATATGTTTCGAAATTATAAGTATCGATACTTTATATATGTGT
66 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
* * *
1883140 ATCGATA-TATTTTGCGTGCAATTTGTTTGAGAAGCATACTGGAATAAAAGTATTGATACCTATA
131 ATCGATACT-TTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATA
* *
1883204 TAGACA
195 TAAAAA
* **
1883210 GTATCGATACTTGGTATTTACGCCTATTATCAATATAATGGTAGA--TTT---GTTTACATTGTA
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGATTTTTACCGTTTACATTGTA
* * * * * * *
1883270 AATTTACCTATTACTTTAAAGTAATCGGTTTCGAAATTTCGAGTATCAATATTTTGTACATGTGT
66 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
* *
1883335 ATCGATACATTTTGCGTGCAAATTG-TTGAGAAGCATACTGGACTAAAAGTATCGATACATATAT
131 ATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATAT
*
1883399 ATAAA
196 AAAAA
* * * * * * * * *
1883404 GTATCGATACTTGGTATATACACTTAGTATCATTATACCGGTAAACTTTTACCCTTTATATTGTT
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGATTTTTACCGTTTACATTGTA
* * *
1883469 AATTTACCTATTACTTTATAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTGTAAATGTGT
66 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
* *
1883534 ATCGATACTTTTTACGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATGTAT
131 ATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATAT
1883599 AAAAA
196 AAAAA
* * * *
1883604 GTATCGATACTTTGTGTTTACGCCTATTATCATTAAACCGATAGATTTTTACCGTTTACATTGTA
1 GTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGATTTTTACCGTTTACATTGTA
1883669 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
66 AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
1883734 ATCGATACTTTTTGCGTGCAAAT
131 ATCGATACTTTTTGCGTGCAAAT
1883757 AACCGATAAC
Statistics
Matches: 473, Mismatches: 65, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
194 76 0.16
195 87 0.18
196 3 0.01
198 14 0.03
199 92 0.19
200 201 0.42
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (200 bp):
GTATCGATACTTGGTATTTACGCCTATTATCATTATACCGGTAGATTTTTACCGTTTACATTGTA
AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATATATGTGT
ATCGATACTTTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATCGATACATATAT
AAAAA
Found at i:1886507 original size:21 final size:19
Alignment explanation
Indices: 1886483--1886538 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
1886473 TCGATCGCAA
*
1886483 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAATT--CGT
*
1886504 TGCGATTTATTCCAAATTCGT
1 TGCGA--TAGTCCAAATTCGT
1886525 TGCGATAGTCCAAA
1 TGCGATAGTCCAAA
1886539 ATCGCAACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.27
21 13 0.43
23 9 0.30
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (19 bp):
TGCGATAGTCCAAATTCGT
Found at i:1887171 original size:6 final size:6
Alignment explanation
Indices: 1887155--1887192 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1887145 TCTCGTCTTG
1887155 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1887193 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1887334 original size:21 final size:21
Alignment explanation
Indices: 1887310--1887425 Score: 130
Period size: 21 Copynumber: 5.6 Consensus size: 21
1887300 TTTGAAATAA
*
1887310 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1887331 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
1887352 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
1887372 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
* *
1887393 ATCGCAACGCGAACTTCCACT
1 ATCGCAATGCGAACTTCGACT
*
1887414 ATCGCATTGCGA
1 ATCGCAATGCGA
1887426 TTTACATATT
Statistics
Matches: 81, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
20 17 0.21
21 64 0.79
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1887393 original size:62 final size:63
Alignment explanation
Indices: 1887282--1887425 Score: 186
Period size: 62 Copynumber: 2.3 Consensus size: 63
1887272 CGTTGCGATT
* *
1887282 TTGGACTATCGCAA--CGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAATATG--ATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
* *
1887345 TTGGACTATCGCAATGCGAATATG-TAAATCGCAATGCGAACTTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAATATGATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
** *
1887407 TTCCACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
1887426 TTTACATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
62 51 0.71
63 14 0.19
65 7 0.10
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (63 bp):
TTGGACTATCGCAATGCGAATATGATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
Found at i:1887460 original size:21 final size:21
Alignment explanation
Indices: 1887434--1887571 Score: 167
Period size: 21 Copynumber: 6.6 Consensus size: 21
1887424 GATTTACATA
1887434 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
1887455 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
*
1887476 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
1887496 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
*
1887517 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
1887538 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
**
1887559 TTCGTGTTGCGAT
1 TTCGCATTGCGAT
1887572 TTATTCCAAA
Statistics
Matches: 102, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
20 17 0.17
21 84 0.82
22 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:1887460 original size:83 final size:84
Alignment explanation
Indices: 1887310--1887551 Score: 239
Period size: 83 Copynumber: 2.9 Consensus size: 84
1887300 TTTGAAATAA
* * *
1887310 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGAC-TA-TCGCAATGCGAATA-T-GTA
1 ATCGCAACGCGAACTTCGACTATCGCATTGCG-A-TT-TACATATTCGCATTGCG-ATAGTCG-A
* * ***
1887371 A-ATCGCAATGCGA-ACTTGGACT
61 AGTTCGCATTGCGATACTCCAACT
*
1887393 ATCGCAACGCGAACTTCCACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTC
1 ATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTC
* *
1887458 GCATTGCGATAGTCCAAGT
66 GCATTGCGATACTCCAACT
** * *
1887477 -TCGCATTGCGATA-GTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTT
1 ATCGCAACGCGA-ACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTT
1887540 CGCATTGCGATA
65 CGCATTGCGATA
1887552 GTCGAAGTTC
Statistics
Matches: 136, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
80 2 0.01
81 7 0.05
82 13 0.10
83 109 0.80
84 5 0.04
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (84 bp):
ATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTC
GCATTGCGATACTCCAACT
Found at i:1887552 original size:83 final size:83
Alignment explanation
Indices: 1887411--1887571 Score: 286
Period size: 83 Copynumber: 1.9 Consensus size: 83
1887401 GCGAACTTCC
*
1887411 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAG
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
1887476 TTCGCATTGCGATAGTCG
66 TTCGCATTGCGATAGTCG
*
1887494 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
**
1887559 TTCGTGTTGCGAT
66 TTCGCATTGCGAT
1887572 TTATTCCAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (83 bp):
ACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
TTCGCATTGCGATAGTCG
Found at i:1887840 original size:18 final size:18
Alignment explanation
Indices: 1887817--1887859 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1887807 TAGTCGGTTT
*
1887817 AATTTGATAAAATGGTAA
1 AATTTGATAAAATGATAA
1887835 AATTTGATAAAATGATAA
1 AATTTGATAAAATGATAA
*
1887853 AAATTGA
1 AATTTGA
1887860 GACTTTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (18 bp):
AATTTGATAAAATGATAA
Found at i:1894954 original size:22 final size:22
Alignment explanation
Indices: 1894923--1894964 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1894913 AATGATTTCC
* *
1894923 CCCCTCTCTTTCTCTTTCTCTT
1 CCCCTCTCTTCCCCTTTCTCTT
*
1894945 CCCCTTTCTTCCCCTTTCTC
1 CCCCTCTCTTCCCCTTTCTC
1894965 ATCAACATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (22 bp):
CCCCTCTCTTCCCCTTTCTCTT
Found at i:1895380 original size:27 final size:29
Alignment explanation
Indices: 1895327--1895384 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 29
1895317 CAAACAGAAC
1895327 AAAAGCAAGAGGGAGGGGGGAAGAAGATG
1 AAAAGCAAGAGGGAGGGGGGAAGAAGATG
1895356 AAAA-CAAGAGGGA-GGGGGAAGAAGATG
1 AAAAGCAAGAGGGAGGGGGGAAGAAGATG
1895383 AA
1 AA
1895385 CAAGTGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 16 0.55
28 9 0.31
29 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.45, T:0.03
Consensus pattern (29 bp):
AAAAGCAAGAGGGAGGGGGGAAGAAGATG
Found at i:1896383 original size:29 final size:28
Alignment explanation
Indices: 1896350--1896449 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 28
1896340 AATAATATAT
* * *
1896350 GTAAATGAATTATCTAAAAATTATTTTAC
1 GTAAATGAATTACCTGAAAA-TGTTTTAC
*
1896379 GTAAATGAATTACCCGAAAATGTTTTAC
1 GTAAATGAATTACCTGAAAATGTTTTAC
*
1896407 TTAAAATGAATTACCTGAAAACTGTTTTAC
1 GT-AAATGAATTACCTGAAAA-TGTTTTAC
*
1896437 ATACAATGAATTA
1 GTA-AATGAATTA
1896450 TATCTTCTCG
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
28 8 0.13
29 35 0.57
30 18 0.30
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (28 bp):
GTAAATGAATTACCTGAAAATGTTTTAC
Found at i:1896579 original size:29 final size:29
Alignment explanation
Indices: 1896547--1896615 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
1896537 TAAATTTATG
* *
1896547 AAAAATAATTTACATAAATTGAA-TACTTT
1 AAAAATAATTTACATAAAATGAATTA-TTA
* * *
1896576 AAAATTGATTTACGTAAAATGAATTATTA
1 AAAAATAATTTACATAAAATGAATTATTA
1896605 AAAAATAATTT
1 AAAAATAATTT
1896616 CTAGAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
29 30 0.94
30 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAAATAATTTACATAAAATGAATTATTA
Found at i:1900893 original size:130 final size:130
Alignment explanation
Indices: 1900701--1900960 Score: 415
Period size: 130 Copynumber: 2.0 Consensus size: 130
1900691 ATGGAACATG
*
1900701 AGCTATGTGAAAATAAGTAGTAATTACATGTGCAAATGGAATGTTATGTGAAAAGTTATGTGGCT
1 AGCTATGTGAAAATAAGTAGTAATTACATGTGCAAATGAAATGTTATGTGAAAAGTTATGTGGCT
1900766 ATGTGAAGATGTGTAATGGTATAAAGAT-ATGCCCATG-TATGTGA-ATGAGAGCTAGGGGTATA
66 ATGTGAAGA-GTGTAATGGTATAAAGATAATGCCCATGTTATGTGATATGAGA-C-AGGGGTATA
1900828 GTT
128 GTT
1900831 AGCTATGTG-AAAT-AGTTAAGTAATTACATGTGCAAATGTAAATGTTATGTGAAAAGTT-TGTG
1 AGCTATGTGAAAATAAG-T-AGTAATTACATGTGCAAATG-AAATGTTATGTGAAAAGTTATGTG
1900893 GCTATGTGAAGAGTGTAATGGTATAAAGATAATGCCCATGTTATGTGATATGAGACAGGGGTATA
63 GCTATGTGAAGAGTGTAATGGTATAAAGATAATGCCCATGTTATGTGATATGAGACAGGGGTATA
1900958 GTT
128 GTT
1900961 GACATGCCAA
Statistics
Matches: 123, Mismatches: 1, Indels: 12
0.90 0.01 0.09
Matches are distributed among these distances:
128 2 0.02
129 23 0.19
130 66 0.54
131 26 0.21
132 6 0.05
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (130 bp):
AGCTATGTGAAAATAAGTAGTAATTACATGTGCAAATGAAATGTTATGTGAAAAGTTATGTGGCT
ATGTGAAGAGTGTAATGGTATAAAGATAATGCCCATGTTATGTGATATGAGACAGGGGTATAGTT
Found at i:1901012 original size:20 final size:20
Alignment explanation
Indices: 1900987--1901063 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
1900977 AGGGATTATT
1900987 AGTGGTCCTTCGGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
* *
1901007 AATGGTCCTTCGGGAC--AT
1 AGTGGTCCTTCGGGACAAAC
* * *
1901025 AGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACAAAC
1901045 AGTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
1901064 TATTCAGTGC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.31
20 31 0.69
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAAAC
Found at i:1901037 original size:38 final size:38
Alignment explanation
Indices: 1900986--1901061 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
1900976 GAGGGATTAT
*
1900986 TAGTGGTCCTTCGGGACAAACAATGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGAACAAACAATGGTCCTTCGGGACA
* * *
1901024 TAGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGAACAAACAATGGTCCTTCGGGACA
1901062 AATATTCAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (38 bp):
TAGTGGTCCTTCGGAACAAACAATGGTCCTTCGGGACA
Found at i:1901434 original size:4 final size:4
Alignment explanation
Indices: 1901427--1901655 Score: 309
Period size: 4 Copynumber: 57.5 Consensus size: 4
1901417 TGATAATGAC
* * *
1901427 ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATAT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
1901475 ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT A--T ATAT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
1901521 ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
1901569 ATGT ATGT ATGT ATGC ATGT ATTAT ATAT ATGT ATGT ATGT ATGT ATAT
1 ATGT ATGT ATGT ATGT ATGT A-TGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
1901618 ATGT ATGT ATGT ATAT ATGT ATGT ATGC ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1901656 ATAATGTATT
Statistics
Matches: 199, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.01
4 194 0.97
5 3 0.02
ACGTcount: A:0.31, C:0.01, G:0.19, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:1903641 original size:13 final size:13
Alignment explanation
Indices: 1903623--1903648 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1903613 ACTGAATATT
1903623 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
1903636 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
1903649 CACTATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
TGTCCCGAAGGAC
Found at i:1904062 original size:18 final size:18
Alignment explanation
Indices: 1904035--1904126 Score: 121
Period size: 18 Copynumber: 4.9 Consensus size: 18
1904025 ACTGAATATT
1904035 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1904053 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1904071 TGCCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
1904089 TGCCCCGAAGGACCATTGATA
1 TGTCCCGAAGGACCA---CTA
1904110 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1904127 GATAATCCCT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
18 49 0.75
21 16 0.25
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1905770 original size:19 final size:17
Alignment explanation
Indices: 1905746--1905789 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
1905736 TAATGGGTGT
1905746 ATCGATGCACTCCCTATGC
1 ATCGATGCACT-CCT-TGC
*
1905765 ATCGATGTACTCCTTGC
1 ATCGATGCACTCCTTGC
1905782 ATTCGATG
1 A-TCGATG
1905790 TTCATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (17 bp):
ATCGATGCACTCCTTGC
Found at i:1905789 original size:18 final size:19
Alignment explanation
Indices: 1905746--1905790 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1905736 TAATGGGTGT
*
1905746 ATCGATGCACTCCCTATGC
1 ATCGATGTACTCCCTATGC
1905765 ATCGATGTACT-CCT-TGC
1 ATCGATGTACTCCCTATGC
1905782 ATTCGATGT
1 A-TCGATGT
1905791 TCATTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 10 0.42
19 10 0.42
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (19 bp):
ATCGATGTACTCCCTATGC
Found at i:1913197 original size:2 final size:2
Alignment explanation
Indices: 1913190--1913240 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1913180 AGAGTAGTAA
1913190 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1913231 AT AT AT AT AT
1 AT AT AT AT AT
1913241 CTAATTCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1914246 original size:20 final size:20
Alignment explanation
Indices: 1914180--1914294 Score: 125
Period size: 18 Copynumber: 6.0 Consensus size: 20
1914170 TCGAGGGATT
*
1914180 ATCAGTGGTCATTCGGGACA
1 ATCAGTGGTCCTTCGGGACA
* *
1914200 AACATTGGTCCTTCGGGAC-
1 ATCAGTGGTCCTTCGGGACA
* *
1914219 AT-AGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACA
1914238 ATCAGTGGTCCTTCGGGAC-
1 ATCAGTGGTCCTTCGGGACA
*
1914257 AT-AGTGGTCCTTTGGGAC-
1 ATCAGTGGTCCTTCGGGACA
*
1914275 AT-AGTGGTCCTTTGGGACA
1 ATCAGTGGTCCTTCGGGACA
1914294 A
1 A
1914295 ATATTCAGTG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
18 46 0.56
19 6 0.07
20 30 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (20 bp):
ATCAGTGGTCCTTCGGGACA
Found at i:1914247 original size:38 final size:38
Alignment explanation
Indices: 1914183--1914293 Score: 138
Period size: 38 Copynumber: 3.0 Consensus size: 38
1914173 AGGGATTATC
* *
1914183 AGTGG-TCATTCGGGACAAACATTGGTCCTTCGGGACAT
1 AGTGGTTC-TTCGGGACAATCAGTGGTCCTTCGGGACAT
*
1914221 AGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACAT
1 AGTGGTTCTTCGGGACAATCAGTGGTCCTTCGGGACAT
* * *
1914259 AGTGGTCCTTTGGGAC-AT-AGTGGTCCTTTGGGACA
1 AGTGGTTCTTCGGGACAATCAGTGGTCCTTCGGGACA
1914294 AATATTCAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 16 0.25
37 2 0.03
38 45 0.69
39 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (38 bp):
AGTGGTTCTTCGGGACAATCAGTGGTCCTTCGGGACAT
Found at i:1914678 original size:4 final size:4
Alignment explanation
Indices: 1914661--1914747 Score: 122
Period size: 4 Copynumber: 21.8 Consensus size: 4
1914651 TAATGACATA
* * *
1914661 TATG TATA TATG TATG TATG TATA TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
1914709 TATG TATG TATG TATG TATG TATA TATG TA-G TAGTG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TA-TG TAT
1914748 TTGTTACATG
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
3 3 0.04
4 67 0.92
5 3 0.04
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1915437 original size:35 final size:36
Alignment explanation
Indices: 1915398--1915528 Score: 162
Period size: 35 Copynumber: 3.7 Consensus size: 36
1915388 GCCTTAGATC
* *
1915398 TATAAGGAATTACCAGC-TGATCGGTACTGAACCTA
1 TATAAGGAATTACCAACTTGATCAGTACTGAACCTA
* *
1915433 TATAAGGAATTACCAAC-CGATCAGTGCTGAACCTGA
1 TATAAGGAATTACCAACTTGATCAGTACTGAACCT-A
1915469 -ATAAGGAATTACCAACTTGATCAG-AGCTGAACCTA
1 TATAAGGAATTACCAACTTGATCAGTA-CTGAACCTA
* *
1915504 TATAAGGAATTACTAGCTTGATCAG
1 TATAAGGAATTACCAACTTGATCAG
1915529 AGCTAAACCT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
35 47 0.56
36 37 0.44
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (36 bp):
TATAAGGAATTACCAACTTGATCAGTACTGAACCTA
Found at i:1915498 original size:36 final size:35
Alignment explanation
Indices: 1915398--1915539 Score: 171
Period size: 36 Copynumber: 4.0 Consensus size: 35
1915388 GCCTTAGATC
* *
1915398 TATAAGGAATTACCAGCTGATCGGTA-CTGAACCTA
1 TATAAGGAATTACCAACTGATCAG-AGCTGAACCTA
* *
1915433 TATAAGGAATTACCAACCGATCAGTGCTGAACCTGA
1 TATAAGGAATTACCAACTGATCAGAGCTGAACCT-A
1915469 -ATAAGGAATTACCAACTTGATCAGAGCTGAACCTA
1 TATAAGGAATTACCAAC-TGATCAGAGCTGAACCTA
* * *
1915504 TATAAGGAATTACTAGCTTGATCAGAGCTAAACCTA
1 TATAAGGAATTACCAAC-TGATCAGAGCTGAACCTA
1915540 CAGAGAATTC
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
35 46 0.49
36 48 0.51
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (35 bp):
TATAAGGAATTACCAACTGATCAGAGCTGAACCTA
Found at i:1917195 original size:23 final size:23
Alignment explanation
Indices: 1917168--1917227 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
1917158 CAAAGTCAAC
*
1917168 GGTCAACAGTTAACTATAGTCAT
1 GGTCAACAGTCAACTATAGTCAT
1917191 GGTCAACAGTCAACTATAGTCAT
1 GGTCAACAGTCAACTATAGTCAT
*
1917214 AGTCAACAGTCAAC
1 GGTCAACAGTCAAC
1917228 GGGTCAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (23 bp):
GGTCAACAGTCAACTATAGTCAT
Found at i:1917240 original size:14 final size:15
Alignment explanation
Indices: 1917215--1917245 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1917205 TATAGTCATA
1917215 GTCAACAGTCAACGG
1 GTCAACAGTCAACGG
1917230 GTCAA-AGTCAACGG
1 GTCAACAGTCAACGG
1917244 GT
1 GT
1917246 TGACTCAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (15 bp):
GTCAACAGTCAACGG
Found at i:1917261 original size:14 final size:15
Alignment explanation
Indices: 1917239--1917280 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1917229 GGTCAAAGTC
*
1917239 AACGGGTTGACTCAG
1 AACGAGTTGACTCAG
1917254 -ACGAGTTGACTC-G
1 AACGAGTTGACTCAG
1917267 AACGAGTTGACTCA
1 AACGAGTTGACTCA
1917281 ACATGACCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (15 bp):
AACGAGTTGACTCAG
Found at i:1925856 original size:2 final size:2
Alignment explanation
Indices: 1925849--1925883 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1925839 CATAATTCGA
1925849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1925884 AAATATTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1931706 original size:79 final size:79
Alignment explanation
Indices: 1931618--1931768 Score: 257
Period size: 79 Copynumber: 1.9 Consensus size: 79
1931608 ACGCTAGAAA
1931618 AAGTTTAATAGTTTTTATATGATTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
1 AAGTTTAATAGTTTTTATATGATTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
1931683 TTATTTTCGTTAAG
66 TTATTTTCGTTAAG
* * * * *
1931697 AAGTTTAATAGTTTTTATATGGTTTGTTAATGTCATGTTAAATTAATTGTTCAAAGTAAGAGAAT
1 AAGTTTAATAGTTTTTATATGATTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
1931762 TTATTTT
66 TTATTTT
1931769 TTAGTTTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 67 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (79 bp):
AAGTTTAATAGTTTTTATATGATTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
TTATTTTCGTTAAG
Found at i:1933453 original size:41 final size:41
Alignment explanation
Indices: 1933408--1933486 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
1933398 CAAATTAATA
**
1933408 TTTTAAAAGTTTTAAGGATCTAAAATTAAAATTTTCAATTT
1 TTTTAAAAAATTTAAGGATCTAAAATTAAAATTTTCAATTT
*
1933449 TTTTAAAAAATTTAAGGGTCTAAAATTAAAATTTTCAA
1 TTTTAAAAAATTTAAGGATCTAAAATTAAAATTTTCAA
1933487 AATTTTAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (41 bp):
TTTTAAAAAATTTAAGGATCTAAAATTAAAATTTTCAATTT
Found at i:1940364 original size:3 final size:3
Alignment explanation
Indices: 1940358--1940422 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
1940348 TTTTTATCCA
*
1940358 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1940406 TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1940423 AATATATTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1953264 original size:8 final size:8
Alignment explanation
Indices: 1953251--1953310 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
1953241 TGAAGAGAAA
1953251 AAAAAAAG
1 AAAAAAAG
1953259 AAAAAAAAG
1 -AAAAAAAG
*
1953268 AAAAGAAAA
1 AAAA-AAAG
1953277 AAAGAAAAG
1 AAA-AAAAG
*
1953286 AAAAAAAT
1 AAAAAAAG
* *
1953294 AGAAAATG
1 AAAAAAAG
1953302 AAAAAAAG
1 AAAAAAAG
1953310 A
1 A
1953311 GAAGAAAAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
8 20 0.49
9 20 0.49
10 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1953264 original size:9 final size:9
Alignment explanation
Indices: 1953250--1953299 Score: 66
Period size: 9 Copynumber: 5.4 Consensus size: 9
1953240 TTGAAGAGAA
1953250 AAAAAAAAG
1 AAAAAAAAG
1953259 AAAAAAAAG
1 AAAAAAAAG
1953268 AAAAGAAAA-
1 AAAA-AAAAG
*
1953277 AAAGAAAAG
1 AAAAAAAAG
1953286 AAAAAAATAG
1 AAAAAAA-AG
1953296 AAAA
1 AAAA
1953300 TGAAAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 4 0.11
9 22 0.61
10 10 0.28
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1953271 original size:14 final size:14
Alignment explanation
Indices: 1953243--1953324 Score: 98
Period size: 13 Copynumber: 5.9 Consensus size: 14
1953233 ATTATGCTTG
*
1953243 AAGAGAAAAAA-AA
1 AAGAAAAAAAAGAA
1953256 AAGAAAAAAAAGAA
1 AAGAAAAAAAAGAA
1953270 AAG-AAAAAAAGAA
1 AAGAAAAAAAAGAA
1953283 AAGAAAAAAATAGAA
1 AAGAAAAAAA-AGAA
*
1953298 AATG-AAAAAAAGAG
1 AA-GAAAAAAAAGAA
1953312 AAGAAAAAGAAAG
1 AAGAAAAA-AAAG
1953325 GGGGTCAAGG
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
13 24 0.39
14 20 0.33
15 16 0.26
16 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:1953304 original size:29 final size:27
Alignment explanation
Indices: 1953243--1953324 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 27
1953233 ATTATGCTTG
1953243 AAGAGAAAAAA-AAAAGAAAAAAAAGAA
1 AAGA-AAAAAAGAAAAGAAAAAAAAGAA
1953270 AAGAAAAAAAGAAAAGAAAAAAATAGAA
1 AAGAAAAAAAGAAAAGAAAAAAA-AGAA
*
1953298 AATGAAAAAAAGAGAAGAAAAAGAAAG
1 AA-GAAAAAAAGAAAAGAAAAA-AAAG
1953325 GGGGTCAAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
26 6 0.12
27 16 0.32
28 6 0.12
29 20 0.40
30 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (27 bp):
AAGAAAAAAAGAAAAGAAAAAAAAGAA
Found at i:1954641 original size:83 final size:82
Alignment explanation
Indices: 1954446--1954708 Score: 438
Period size: 82 Copynumber: 3.2 Consensus size: 82
1954436 AAACATTAAA
*
1954446 TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
*
1954511 AGAACATTCATTGAATT
66 AGAACAATCATTGAATT
* * *
1954528 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATA-
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAG
* *
1954592 TAGAACCAAGCATTGAATT
65 CAGAA-CAATCATTGAATT
1954611 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1 TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
1954676 AGAACAATCATTGAATT
66 AGAACAATCATTGAATT
1954693 TGGAAGATGAATTTGC
1 TGGAAGATGAATTTGC
1954709 TCATAGTAAA
Statistics
Matches: 166, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
82 91 0.55
83 75 0.45
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (82 bp):
TGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGC
AGAACAATCATTGAATT
Found at i:1955521 original size:113 final size:113
Alignment explanation
Indices: 1955322--1955869 Score: 875
Period size: 113 Copynumber: 4.8 Consensus size: 113
1955312 TAGCAAAGAT
* * * *
1955322 TTGAATCCATCATTTGATGGAACAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1955387 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
1955435 CTGAATCCGTCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
1955500 AGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
1955548 TTAAATTCATCATTTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1955613 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1955661 TTGAATCCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
1955725 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1955774 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
*
1955838 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1955870 CTCATCAAGA
Statistics
Matches: 406, Mismatches: 28, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
112 1 0.00
113 405 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
TTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1956126 original size:3 final size:3
Alignment explanation
Indices: 1956120--1956202 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
1956110 TTTTTATCCA
*
1956120 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1956168 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1956203 AATATATTAA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1958662 original size:8 final size:8
Alignment explanation
Indices: 1958649--1958679 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1958639 ACATACATGA
1958649 ATGCATAC
1 ATGCATAC
1958657 ATGCATAC
1 ATGCATAC
1958665 ATGCATAC
1 ATGCATAC
1958673 ATGCATA
1 ATGCATA
1958680 GTTTGCATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (8 bp):
ATGCATAC
Found at i:1959222 original size:10 final size:10
Alignment explanation
Indices: 1959183--1959232 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
1959173 TTCATCACAC
1959183 CAAATTCTCT
1 CAAATTCTCT
*
1959193 CAATTTCTCT
1 CAAATTCTCT
*
1959203 CAACTTCTCT
1 CAAATTCTCT
*
1959213 CAAATACTCT
1 CAAATTCTCT
* *
1959223 TATATTCTCT
1 CAAATTCTCT
1959233 GTTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1959281 original size:9 final size:9
Alignment explanation
Indices: 1959269--1959302 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1959259 TAATATTTTG
1959269 TATTTAATT
1 TATTTAATT
*
1959278 TATTTAA-G
1 TATTTAATT
1959286 TATTTAATT
1 TATTTAATT
1959295 TATTTAAT
1 TATTTAAT
1959303 ATTTACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1959290 original size:17 final size:17
Alignment explanation
Indices: 1959268--1959307 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1959258 TTAATATTTT
1959268 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1959285 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1959302 -TATTTA
1 GTATTTA
1959308 CTTATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1962767 original size:20 final size:20
Alignment explanation
Indices: 1962742--1962782 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1962732 CGTTACACAG
*
1962742 GGGGAATTGGTATCCC-CTGA
1 GGGGAATCGGT-TCCCTCTGA
1962762 GGGGAATCGGTTCCCTCTGA
1 GGGGAATCGGTTCCCTCTGA
1962782 G
1 G
1962783 CATTCTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGAATCGGTTCCCTCTGA
Found at i:1963178 original size:13 final size:14
Alignment explanation
Indices: 1963160--1963191 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1963150 GATTTTCTAA
1963160 TTGAAAATAAA-TT
1 TTGAAAATAAAGTT
1963173 TTG-AAATAAAGTT
1 TTGAAAATAAAGTT
1963186 TTGAAA
1 TTGAAA
1963192 TTACTCCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 8 0.47
14 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (14 bp):
TTGAAAATAAAGTT
Found at i:1963181 original size:12 final size:13
Alignment explanation
Indices: 1963164--1963192 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1963154 TTCTAATTGA
1963164 AAATAAA-TTTTG
1 AAATAAAGTTTTG
1963176 AAATAAAGTTTTG
1 AAATAAAGTTTTG
1963189 AAAT
1 AAAT
1963193 TACTCCCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (13 bp):
AAATAAAGTTTTG
Found at i:1963221 original size:21 final size:21
Alignment explanation
Indices: 1963195--1963245 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1963185 TTTGAAATTA
1963195 CTCCCCCTTACTTTAACACTT
1 CTCCCCCTTACTTTAACACTT
* *
1963216 CTCCCCCTAATTTTAACACTT
1 CTCCCCCTTACTTTAACACTT
1963237 CTCCCCCTT
1 CTCCCCCTT
1963246 TTTGTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.45, G:0.00, T:0.37
Consensus pattern (21 bp):
CTCCCCCTTACTTTAACACTT
Found at i:1963266 original size:14 final size:14
Alignment explanation
Indices: 1963247--1963274 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1963237 CTCCCCCTTT
1963247 TTGTTAAATCAAAA
1 TTGTTAAATCAAAA
1963261 TTGTTAAATCAAAA
1 TTGTTAAATCAAAA
1963275 AGACTCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
TTGTTAAATCAAAA
Found at i:1965449 original size:22 final size:22
Alignment explanation
Indices: 1965408--1965482 Score: 98
Period size: 23 Copynumber: 3.4 Consensus size: 22
1965398 CGTGGGTGGT
1965408 ATCGATT-CCCTCCAAGGGGGA
1 ATCGATTCCCCTCCAAGGGGGA
*
1965429 ATCGATTCCCCTTCAAAGGGGGA
1 ATCGATTCCCC-TCCAAGGGGGA
* * *
1965452 ATCGGTTCCCCTGCAAGGGGGT
1 ATCGATTCCCCTCCAAGGGGGA
1965474 ATCGATTCC
1 ATCGATTCC
1965483 TCTTGCACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 7 0.15
22 19 0.41
23 20 0.43
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (22 bp):
ATCGATTCCCCTCCAAGGGGGA
Found at i:1965451 original size:23 final size:22
Alignment explanation
Indices: 1965408--1965482 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
1965398 CGTGGGTGGT
*
1965408 ATCGATT-CCCTCCAAGGGGGA
1 ATCGATTCCCCTTCAAGGGGGA
1965429 ATCGATTCCCCTTCAAAGGGGGA
1 ATCGATTCCCCTTC-AAGGGGGA
* * *
1965452 ATCGGTTCCCCTGCAAGGGGGT
1 ATCGATTCCCCTTCAAGGGGGA
1965474 ATCGATTCC
1 ATCGATTCC
1965483 TCTTGCACTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
21 7 0.15
22 20 0.43
23 20 0.43
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (22 bp):
ATCGATTCCCCTTCAAGGGGGA
Found at i:1968201 original size:27 final size:27
Alignment explanation
Indices: 1968170--1968221 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1968160 ATCCAGGCGG
1968170 ATTTCTCGGTCATGATCAGAGATCCGA
1 ATTTCTCGGTCATGATCAGAGATCCGA
*
1968197 ATTTCTCGGTCATGGTCAGAGATCC
1 ATTTCTCGGTCATGATCAGAGATCC
1968222 CATGAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
ATTTCTCGGTCATGATCAGAGATCCGA
Found at i:1968488 original size:20 final size:20
Alignment explanation
Indices: 1968451--1968493 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1968441 ATTCCACCAC
*
1968451 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1968471 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1968491 ATG
1 ATG
1968494 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1973117 original size:27 final size:27
Alignment explanation
Indices: 1973086--1973140 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1973076 CTGATCCAGG
1973086 CAGATTTCTCGGTCATGATCAGAGATC
1 CAGATTTCTCGGTCATGATCAGAGATC
*
1973113 CAGATTTCTCGGTCATGGTCAGAGATC
1 CAGATTTCTCGGTCATGATCAGAGATC
1973140 C
1 C
1973141 CGTGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (27 bp):
CAGATTTCTCGGTCATGATCAGAGATC
Found at i:1978080 original size:23 final size:24
Alignment explanation
Indices: 1978040--1978085 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1978030 AAACCATTCA
1978040 GGGGGAATCGGTACCCCT-TTGGG
1 GGGGGAATCGGTACCCCTCTTGGG
*
1978063 GGGGAGAATCGGT-TCCCTCTTGG
1 GGGG-GAATCGGTACCCCTCTTGG
1978086 CAATCTGCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.13, C:0.22, G:0.41, T:0.24
Consensus pattern (24 bp):
GGGGGAATCGGTACCCCTCTTGGG
Found at i:1981843 original size:105 final size:104
Alignment explanation
Indices: 1981662--1981850 Score: 299
Period size: 105 Copynumber: 1.8 Consensus size: 104
1981652 CTTTGTCTTA
*
1981662 CTAGCTGAAGGAATCTATCAATAAAGCCAGGGTTTTAACCAATTACTTTAGTAGAATAGCTCAAC
1 CTAGCTGAAGGAATCTATCAATAAAGCCAGGGTTTTAACCAATTACTTTAGTAGAATAACTCAAC
*
1981727 TTTATTGTATATATGTATAGTTTCTTTGACTTTATTTGG
66 TTTATTGTATATATATATAGTTTCTTTGACTTTATTTGG
* * * *
1981766 CTAGCTGAAGGAGTCTATCTATAAAGCCAGGGCTTTTAACTAATTCCTTTAG-AGGAATAACTCA
1 CTAGCTGAAGGAATCTATCAATAAAGCCAGGG-TTTTAACCAATTACTTTAGTA-GAATAACTCA
1981830 ACTTTATTGTATATATATATA
64 ACTTTATTGTATATATATATA
1981851 CATACACACA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
104 31 0.40
105 46 0.60
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (104 bp):
CTAGCTGAAGGAATCTATCAATAAAGCCAGGGTTTTAACCAATTACTTTAGTAGAATAACTCAAC
TTTATTGTATATATATATAGTTTCTTTGACTTTATTTGG
Found at i:2007050 original size:59 final size:59
Alignment explanation
Indices: 2006987--2007336 Score: 274
Period size: 59 Copynumber: 6.0 Consensus size: 59
2006977 ATGGCATTTT
*
2006987 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATAT-GGAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGG-GCACTAA
* * * *
2007046 GTGTGCT-AAATGATAATGAAATCATATTGAAAT-TATGGATTTTCAGATAGGGCA-TATTA
1 GTGTGCTAAAATGATAAGGAAATCATACTG-AGTGTATGGATTTCCAGATAGGGCACTA--A
* * **
2007105 -TGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATAGG-TTTCCAGATAAAGCACTAAA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTAT-GGATTTCCAGATAGGGCACT-AA
* * *** *
2007164 G-GTACT-AAATGATAAGGAAATCATATTGAAAATATGGATTTCCATATAGGGCA-TATTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCACTA--A
** * * ** **
2007222 -TGTGCTAAAATGATAACAAAATCATACTAATTGTATGGATTT-TTGAATAGGGCACTTT
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAG-ATAGGGCACTAA
* * * * *
2007280 GTGTGCTAAAATGAAAAGGGAAGCATACTAAGTGTAT-GATTTTCCAGATAGAGCACT
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGA-TTTCCAGATAGGGCACT
2007337 GATAGTGCTA
Statistics
Matches: 226, Mismatches: 45, Indels: 40
0.73 0.14 0.13
Matches are distributed among these distances:
56 1 0.00
57 5 0.02
58 86 0.38
59 128 0.57
60 5 0.02
61 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCACTAA
Found at i:2007185 original size:117 final size:117
Alignment explanation
Indices: 2006979--2007263 Score: 394
Period size: 117 Copynumber: 2.4 Consensus size: 117
2006969 ATTACCGAAT
* * * **
2006979 GGCATTTTGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACT
1 GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACT
* * * *
2007044 AAGTGTGCTAAATGATAATGAAATCATATTGAAATTATGGATTTTCAGATAG
66 AAGTGTACTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAG
* *
2007096 GGCATATTATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATAGG-TTTCCAGATAAAGCAC
1 GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTAT-GGATTTCCAGATAAAGCAC
*
2007160 TAAAG-GTACTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCATATAG
65 T-AAGTGTACTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAG
** * *
2007213 GGCATATTATGTGCTAAAATGATAACAAAATCATACTAATTGTATGGATTT
1 GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTT
2007264 TTGAATAGGG
Statistics
Matches: 147, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
116 2 0.01
117 140 0.95
118 5 0.03
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (117 bp):
GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCACT
AAGTGTACTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAG
Found at i:2007287 original size:176 final size:175
Alignment explanation
Indices: 2006995--2007336 Score: 419
Period size: 176 Copynumber: 1.9 Consensus size: 175
2006985 TTGTGTGCTA
***
2006995 AAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTAAGTGTGCTAAATGAT
1 AAATGATAAGGAAATCATACTGAAAATATGGATTTCCATATGGAGCACTAAGTGTGCTAAATGAT
** * **
2007060 AATGAAATCATATTGAAATTATGGATTTTCAGATAGGGCATATTATGTGCTAAAATGGTAAGGGA
66 AACAAAATCATACTGAAATTATGGATTTTCAGATAGGGCATATTATGTGCTAAAATGAAAAGGGA
* *
2007125 ATCATACTGAGTGTAT-AGGTTTCCAGATAAAGCACTAAAGGTACT
131 AGCATACTAAGTGTATGA-GTTTCCAGATAAAGCACTAAAGGTACT
*
2007170 AAATGATAAGGAAATCATATTGAAAATATGGATTTCCATATAGG-GCA-TATTA-TGTGCTAAAA
1 AAATGATAAGGAAATCATACTGAAAATATGGATTTCCATAT-GGAGCACTA--AGTGTGCT-AAA
* * *
2007232 TGATAACAAAATCATACT-AATTGTATGGATTTT-TGAATAGGGCACT-TTGTGTGCTAAAATGA
62 TGATAACAAAATCATACTGAAAT-TATGGATTTTCAG-ATAGGGCA-TATTATGTGCTAAAATGA
* *
2007294 AAAGGGAAGCATACTAAGTGTATGATTTTCCAGATAGAGCACT
124 AAAGGGAAGCATACTAAGTGTATGAGTTTCCAGATAAAGCACT
2007337 GATAGTGCTA
Statistics
Matches: 143, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
174 2 0.01
175 50 0.35
176 89 0.62
177 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (175 bp):
AAATGATAAGGAAATCATACTGAAAATATGGATTTCCATATGGAGCACTAAGTGTGCTAAATGAT
AACAAAATCATACTGAAATTATGGATTTTCAGATAGGGCATATTATGTGCTAAAATGAAAAGGGA
AGCATACTAAGTGTATGAGTTTCCAGATAAAGCACTAAAGGTACT
Found at i:2007289 original size:117 final size:116
Alignment explanation
Indices: 2006979--2007298 Score: 367
Period size: 117 Copynumber: 2.7 Consensus size: 116
2006969 ATTACCGAAT
* * *
2006979 GGCATTTTGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGA-TTTCCATATGGAGCAC
1 GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTTCAATA-GG-GCAC
* * *
2007043 TAAGTGTGCTAAATGATAATGAAATCATATTGAAATTATGGATTTTCAGATAG
64 TAAGTGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAG
* * * **
2007096 GGCATATTATGTGCTAAAATGGTAAGGGAATCATACTGAGTGTATAGG-TTTCCAGATAAAGCAC
1 GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTAT-GGATTTTCA-ATAGGGCAC
* *
2007160 TAAAG-GTACTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCATATAG
64 T-AAGTGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAG
** * * *
2007213 GGCATATTATGTGCTAAAATGATAACAAAATCATACTAATTGTATGGATTTTTGAATAGGGCACT
1 GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGA-TTTTCAATAGGGCACT
** *
2007278 TTGTGTGCTAAAATGAAAAGG
65 AAGTGTGCT-AAATGATAAGG
2007299 GAAGCATACT
Statistics
Matches: 168, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
116 3 0.02
117 140 0.83
118 22 0.13
119 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (116 bp):
GGCATATTATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTTCAATAGGGCACTA
AGTGTGCTAAATGATAAGGAAATCATATTGAAAATATGGATTTCCAGATAG
Found at i:2008354 original size:34 final size:34
Alignment explanation
Indices: 2008309--2008383 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
2008299 ATGGTATTGA
* *
2008309 TACCAACCCTTTCAGTATCGTTACCCACTTTTAG
1 TACCAATCCTTTCAGTATCGTTACCCACTCTTAG
*
2008343 TACCAATCCTTTCAGTATCGTTACCCACTCTTGG
1 TACCAATCCTTTCAGTATCGTTACCCACTCTTAG
2008377 TACCAAT
1 TACCAAT
2008384 ATCAAAATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (34 bp):
TACCAATCCTTTCAGTATCGTTACCCACTCTTAG
Found at i:2020910 original size:18 final size:18
Alignment explanation
Indices: 2020887--2020922 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2020877 TTTTTCTATG
2020887 TTTTATAATAAAATTTAT
1 TTTTATAATAAAATTTAT
* *
2020905 TTTTATATTAATATTTAT
1 TTTTATAATAAAATTTAT
2020923 ATGTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTATAATAAAATTTAT
Found at i:2022471 original size:20 final size:20
Alignment explanation
Indices: 2022446--2022484 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2022436 TATATCATAA
2022446 AGACTTGATGGACTCAAATC
1 AGACTTGATGGACTCAAATC
2022466 AGACTTGATGGACTCAAAT
1 AGACTTGATGGACTCAAAT
2022485 TAAACTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGACTTGATGGACTCAAATC
Found at i:2022491 original size:20 final size:20
Alignment explanation
Indices: 2022448--2022492 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2022438 TATCATAAAG
*
2022448 ACTTGATGGACTCAAATCAG
1 ACTTGATGGACTCAAATCAA
*
2022468 ACTTGATGGACTCAAATTAA
1 ACTTGATGGACTCAAATCAA
2022488 ACTTG
1 ACTTG
2022493 GAAATCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
ACTTGATGGACTCAAATCAA
Found at i:2036757 original size:29 final size:29
Alignment explanation
Indices: 2036724--2036815 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 29
2036714 TCCAAATTTC
2036724 ACATGCCATAGAAACTCTCCCTAATTGAT
1 ACATGCCATAGAAACTCTCCCTAATTGAT
* *
2036753 ACATGCC-TTGCATAA-TCT-CCAAATT--T
1 ACATGCCATAG-A-AACTCTCCCTAATTGAT
2036779 CACATGCCATAGAAACTCTCCCTAATTGAT
1 -ACATGCCATAGAAACTCTCCCTAATTGAT
2036809 ACATGCC
1 ACATGCC
2036816 TTGCATAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
26 3 0.06
27 11 0.22
28 16 0.31
29 18 0.35
30 3 0.06
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.28
Consensus pattern (29 bp):
ACATGCCATAGAAACTCTCCCTAATTGAT
Found at i:2036798 original size:27 final size:27
Alignment explanation
Indices: 2036712--2036799 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
2036702 CAAAAGTCAT
2036712 TCTCCAAATTTCACATGCCATAGAAAC
1 TCTCCAAATTTCACATGCCATAGAAAC
* *
2036739 TCTCCCTAATTGAT-ACATGCC-TTGCATAA-
1 TCT-CCAAATT--TCACATGCCATAG-A-AAC
2036768 TCTCCAAATTTCACATGCCATAGAAAC
1 TCTCCAAATTTCACATGCCATAGAAAC
2036795 TCTCC
1 TCTCC
2036800 CTAATTGATA
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
26 3 0.06
27 16 0.33
28 16 0.33
29 11 0.22
30 3 0.06
ACGTcount: A:0.32, C:0.31, G:0.08, T:0.30
Consensus pattern (27 bp):
TCTCCAAATTTCACATGCCATAGAAAC
Found at i:2036798 original size:56 final size:56
Alignment explanation
Indices: 2036712--2036823 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
2036702 CAAAAGTCAT
2036712 TCTCCAAATTTCACATGCCATAGAAACTCTCCCTAATTGATACATGCCTTGCATAA
1 TCTCCAAATTTCACATGCCATAGAAACTCTCCCTAATTGATACATGCCTTGCATAA
2036768 TCTCCAAATTTCACATGCCATAGAAACTCTCCCTAATTGATACATGCCTTGCATAA
1 TCTCCAAATTTCACATGCCATAGAAACTCTCCCTAATTGATACATGCCTTGCATAA
2036824 GAGCGCTGCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.30
Consensus pattern (56 bp):
TCTCCAAATTTCACATGCCATAGAAACTCTCCCTAATTGATACATGCCTTGCATAA
Found at i:2038725 original size:11 final size:11
Alignment explanation
Indices: 2038690--2038741 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
2038680 GTTCACGAAC
2038690 ATGTTCGTTTA
1 ATGTTCGTTTA
* * *
2038701 GTGTACATTTTA
1 ATGTTC-GTTTA
2038713 ATGTTCGTTTA
1 ATGTTCGTTTA
*
2038724 ATGTTCCTTTA
1 ATGTTCGTTTA
2038735 TATGTTC
1 -ATGTTC
2038742 AATTTTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 18 0.56
12 14 0.44
ACGTcount: A:0.19, C:0.12, G:0.15, T:0.54
Consensus pattern (11 bp):
ATGTTCGTTTA
Found at i:2062564 original size:2 final size:2
Alignment explanation
Indices: 2062559--2062588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2062549 AAATGAAGAA
2062559 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
2062589 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2062593 original size:2 final size:2
Alignment explanation
Indices: 2062588--2062614 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2062578 TATATATATA
2062588 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2062615 ATTGTATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2071055 original size:24 final size:24
Alignment explanation
Indices: 2071028--2071073 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2071018 ATAAATTTAA
2071028 TTTAAAT-TAAAAAATATATTATCT
1 TTTAAATGTAAAAAAT-TATTATCT
*
2071052 TTTAAATGTATAAAATTATTAT
1 TTTAAATGTAAAAAATTATTAT
2071074 TGTAGGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTAAATGTAAAAAATTATTATCT
Found at i:2072046 original size:21 final size:21
Alignment explanation
Indices: 2072000--2072049 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
2071990 CGCGGTTTTT
*
2072000 CCCGATTACACGATGGGGATC
1 CCCGTTTACACGATGGGGATC
*
2072021 CCCGTTTACCCGATGGGGATC
1 CCCGTTTACACGATGGGGATC
2072042 CCCGTTTA
1 CCCGTTTA
2072050 AATCTCTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (21 bp):
CCCGTTTACACGATGGGGATC
Found at i:2073096 original size:18 final size:19
Alignment explanation
Indices: 2073061--2073097 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2073051 CACGAAATGT
2073061 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2073081 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2073098 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2073270 original size:15 final size:15
Alignment explanation
Indices: 2073252--2073282 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2073242 AAATTCTAAA
2073252 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
2073267 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
2073282 T
1 T
2073283 CTATTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:2087956 original size:2 final size:2
Alignment explanation
Indices: 2087949--2087974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2087939 TAAGATGTGC
2087949 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
2087975 CAACTTTTTA
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:2092058 original size:51 final size:50
Alignment explanation
Indices: 2092003--2092129 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 50
2091993 TTAGCAGTAA
** *
2092003 AGCGCGCCCCTTGCACCGCGCTATACGATGATTTGGCGTCACGTGGGGTAT
1 AGCGCGCCCCTTGCACCGCGCTATACGATGAGATGGCGCCACGT-GGGTAT
* *
2092054 AGCGCGCCCCTTGCACTGCGCTATACGGTGAGATGGCGCCACGTGGGTAT
1 AGCGCGCCCCTTGCACCGCGCTATACGATGAGATGGCGCCACGTGGGTAT
* *
2092104 AGCGCGGCCGC-TGCAGCGCGCTATAC
1 AGCGC-GCCCCTTGCACCGCGCTATAC
2092130 CTGTATATCT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 24 0.36
51 43 0.64
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCTTGCACCGCGCTATACGATGAGATGGCGCCACGTGGGTAT
Found at i:2092341 original size:13 final size:14
Alignment explanation
Indices: 2092313--2092341 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2092303 ATATTTTATA
2092313 ATGTTTTTACTATT
1 ATGTTTTTACTATT
2092327 ATGTTTTTACT-TT
1 ATGTTTTTACTATT
2092340 AT
1 AT
2092342 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
ATGTTTTTACTATT
Found at i:2092555 original size:105 final size:99
Alignment explanation
Indices: 2092416--2092619 Score: 275
Period size: 105 Copynumber: 2.0 Consensus size: 99
2092406 TGGAAATCAT
* *
2092416 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAAATTATTAATAATATTT
1 ATATCTCGACACTTTGATGATACGGTAACATTTTAACGTTTTAATTT-AA-T-TT-A-AATA-TT
* * * *
2092481 AGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
60 A-TTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
*
2092521 ATATCTCGATACTTTGATGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATATTATTGAT
1 ATATCTCGACACTTTGATGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATATTATTGAT
2092586 TCATTTAATACATGATTATTAGATTAAGAATTAA
66 TCATTTAATACATGATTATTAGATTAAGAATTAA
2092620 TTTTTGTAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
98 2 0.02
99 35 0.38
100 4 0.04
101 1 0.01
102 2 0.02
103 1 0.01
104 2 0.02
105 44 0.48
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (99 bp):
ATATCTCGACACTTTGATGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATATTATTGAT
TCATTTAATACATGATTATTAGATTAAGAATTAA
Found at i:2093300 original size:26 final size:24
Alignment explanation
Indices: 2093228--2093300 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
2093218 TTATATTTGT
2093228 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
2093253 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
2093276 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
2093301 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:2096942 original size:47 final size:48
Alignment explanation
Indices: 2096838--2096943 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 48
2096828 TTATACAAAA
2096838 CGGTACCTGCCCCGCGCTATATAAATTATGTCAGGAGTAAAGGTATGTCG
1 CGGTACCTGCCCCGCGCTATATAAATTATGTC--GAGTAAAGGTATGTCG
2096888 CGGTACCTGCCCCGCGCTATATAAAATTATG-C-AGTAAAGGTATAG-CG
1 CGGTACCTGCCCCGCGCTATAT-AAATTATGTCGAGTAAAGGTAT-GTCG
*
2096935 TGGTACCTG
1 CGGTACCTG
2096944 ATCCGTGCTA
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
47 21 0.40
48 1 0.02
50 23 0.43
51 8 0.15
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25
Consensus pattern (48 bp):
CGGTACCTGCCCCGCGCTATATAAATTATGTCGAGTAAAGGTATGTCG
Done.