Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008958.1 Hibiscus syriacus cultivar Beakdansim tig00112289_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: 2490255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1054563 original size:16 final size:16
Alignment explanation
Indices: 1054542--1054603 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
1054532 ACCAAAGTAA
1054542 AATTAAATAAATTAGG
1 AATTAAATAAATTAGG
**
1054558 AATTAAA-AAATATATAA
1 AATTAAATAAAT-TA-GG
1054575 AATTAAATAAATTAGG
1 AATTAAATAAATTAGG
*
1054591 AATATAAAAAAAT
1 AAT-TAAATAAAT
1054604 ATATCTACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
15 4 0.11
16 12 0.32
17 17 0.46
18 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AATTAAATAAATTAGG
Found at i:1054577 original size:33 final size:35
Alignment explanation
Indices: 1054539--1054607 Score: 124
Period size: 33 Copynumber: 2.0 Consensus size: 35
1054529 TTTACCAAAG
1054539 TAAAATTAAATAAATTAGGAAT-T-AAAAAATATA
1 TAAAATTAAATAAATTAGGAATATAAAAAAATATA
1054572 TAAAATTAAATAAATTAGGAATATAAAAAAATATA
1 TAAAATTAAATAAATTAGGAATATAAAAAAATATA
1054607 T
1 T
1054608 CTACTCTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 22 0.65
34 1 0.03
35 11 0.32
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (35 bp):
TAAAATTAAATAAATTAGGAATATAAAAAAATATA
Found at i:1054650 original size:26 final size:27
Alignment explanation
Indices: 1054591--1054652 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
1054581 ATAAATTAGG
*
1054591 AATATAAAAAAATATATCTACTCTGTA
1 AATATAAAAAAATATATCTACTCGGTA
*
1054618 AACATAAAAAAAT-TATC-ACT-GGTA
1 AATATAAAAAAATATATCTACTCGGTA
1054642 TCAATATAAAA
1 --AATATAAAA
1054653 GAAACACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 3 0.10
25 3 0.10
26 12 0.40
27 12 0.40
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (27 bp):
AATATAAAAAAATATATCTACTCGGTA
Found at i:1055525 original size:24 final size:24
Alignment explanation
Indices: 1055497--1055562 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
1055487 TTCAGTGACT
1055497 CTCTTTTCTTTCTTTTTTTCTCTC
1 CTCTTTTCTTTCTTTTTTTCTCTC
* *
1055521 CTCTTTTCTTT-TTTCTTCCT-TC
1 CTCTTTTCTTTCTTTTTTTCTCTC
1055543 C-CTTTTC--TCTTTTTTTCTCT
1 CTCTTTTCTTTCTTTTTTTCTCT
1055563 GTTTTTTCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 1 0.03
20 7 0.19
21 7 0.19
22 3 0.08
23 7 0.19
24 11 0.31
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (24 bp):
CTCTTTTCTTTCTTTTTTTCTCTC
Found at i:1055555 original size:22 final size:22
Alignment explanation
Indices: 1055497--1055562 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
1055487 TTCAGTGACT
1055497 CTCTTTTCTTTCTTTTTTTCTCTC
1 CTCTTTTC--TCTTTTTTTCTCTC
1055521 CTCTTTTCT-TTTTTCTTC-CTTC
1 CTCTTTTCTCTTTTT-TTCTC-TC
1055543 C-CTTTTCTCTTTTTTTCTCT
1 CTCTTTTCTCTTTTTTTCTCT
1055563 GTTTTTTCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
21 17 0.45
22 13 0.34
24 8 0.21
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (22 bp):
CTCTTTTCTCTTTTTTTCTCTC
Found at i:1055569 original size:11 final size:11
Alignment explanation
Indices: 1055545--1055579 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1055535 CTTCCTTCCC
1055545 TTTTCTCT-TT
1 TTTTCTCTGTT
1055555 TTTTCTCTGTT
1 TTTTCTCTGTT
*
1055566 TTTTCTGTGTT
1 TTTTCTCTGTT
1055577 TTT
1 TTT
1055580 ATGTATGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (11 bp):
TTTTCTCTGTT
Found at i:1061027 original size:23 final size:23
Alignment explanation
Indices: 1061001--1061064 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1060991 CAGCTCATAT
1061001 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1061024 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1061047 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1061065 TTTAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1061259 original size:103 final size:103
Alignment explanation
Indices: 1061075--1061297 Score: 428
Period size: 103 Copynumber: 2.2 Consensus size: 103
1061065 TTTAATAATG
*
1061075 TCCCAAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
*
1061140 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAAACTTCACACATGTTCCAAAGAATACATATATA
1061178 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1061243 CACCAAACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAAACTTCACACATGTTCCAAAGAATACATATATA
1061281 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
1061298 GACCCTCGAC
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAAACTTCACACATGTTCCAAAGAATACATATATA
Found at i:1062142 original size:64 final size:64
Alignment explanation
Indices: 1062035--1062258 Score: 242
Period size: 64 Copynumber: 3.5 Consensus size: 64
1062025 TAATGAAGGT
* * * * * *
1062035 ATGCATCGATGCACTAC-GATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTT-TCATTATTAATGGG
* * *
1062098 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
* **
1062162 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCATTATTAATGGG
** *
1062225 AGTGCATCGATGCACTACCAATGCATTGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
1062259 CTTCAAACAA
Statistics
Matches: 137, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
62 1 0.01
63 17 0.12
64 114 0.83
65 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:1066761 original size:23 final size:23
Alignment explanation
Indices: 1066735--1066798 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1066725 CAGCTCATAT
1066735 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1066758 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1066781 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1066799 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1066988 original size:103 final size:103
Alignment explanation
Indices: 1066809--1067031 Score: 437
Period size: 103 Copynumber: 2.2 Consensus size: 103
1066799 TATAATAATG
1066809 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1066874 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
1066912 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
*
1066977 CACCAGACTTCACACATGTTCCAAAGAATATATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
1067015 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
1067032 GACCCTCGAC
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:1067891 original size:64 final size:64
Alignment explanation
Indices: 1067783--1068007 Score: 244
Period size: 64 Copynumber: 3.5 Consensus size: 64
1067773 TAATGAAGGT
* * * * *
1067783 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGAATTCGATGTT-TCATTATTAATGG
1067846 G
64 G
* * *
1067847 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGAATTCGATGTTTCATTATTAATGGG
* * **
1067911 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGAATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGAATTCGATGT-TTCATTATTAATGGG
**
1067974 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
1068008 CTTCAAACAA
Statistics
Matches: 139, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 4 0.03
64 129 0.93
65 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGAATTCGATGTTTCATTATTAATGGG
Found at i:1072723 original size:59 final size:59
Alignment explanation
Indices: 1072656--1072770 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 59
1072646 CAATTAGGCC
1072656 CTTAACTATTTAATTATATTCAATTAAACCACATGCCGTTAATATTTAACAGAAGTCCA
1 CTTAACTATTTAATTATATTCAATTAAACCACATGCCGTTAATATTTAACAGAAGTCCA
* ** **
1072715 CTTAACTATTTAATTATATTCAATTAAGCCGTATGTTGTTAATATTTAACAGAAGT
1 CTTAACTATTTAATTATATTCAATTAAACCACATGCCGTTAATATTTAACAGAAGT
1072771 GTTGAGGTGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (59 bp):
CTTAACTATTTAATTATATTCAATTAAACCACATGCCGTTAATATTTAACAGAAGTCCA
Found at i:1073342 original size:18 final size:18
Alignment explanation
Indices: 1073311--1073353 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1073301 TATAATTTTA
*
1073311 AATTGAATATTTTTAATTT
1 AATT-AATAATTTTAATTT
*
1073330 AATTAATAATTTTATTTT
1 AATTAATAATTTTAATTT
*
1073348 TATTAA
1 AATTAA
1073354 AAATAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATTAATAATTTTAATTT
Found at i:1073520 original size:18 final size:18
Alignment explanation
Indices: 1073493--1073534 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1073483 TGTGCATTTT
1073493 AATT-TTAATAAAAATAA
1 AATTATTAATAAAAATAA
*
1073510 AATTATTAATAAAATTAA
1 AATTATTAATAAAAATAA
*
1073528 AAGTATT
1 AATTATT
1073535 GAGTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AATTATTAATAAAAATAA
Found at i:1076492 original size:42 final size:42
Alignment explanation
Indices: 1076427--1076513 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
1076417 GAAAAGTTTG
1076427 AATATCAAATTAAACTCACTGAGTAGCATAAATAATAAATGA
1 AATATCAAATTAAACTCACTGAGTAGCATAAATAATAAATGA
* * * *
1076469 AATATCAAATTAAATTTATTGAGTAGCCTAAATAATAAATGA
1 AATATCAAATTAAACTCACTGAGTAGCATAAATAATAAATGA
1076511 AAT
1 AAT
1076514 GCCATTCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (42 bp):
AATATCAAATTAAACTCACTGAGTAGCATAAATAATAAATGA
Found at i:1078167 original size:20 final size:19
Alignment explanation
Indices: 1078133--1078299 Score: 208
Period size: 20 Copynumber: 8.5 Consensus size: 19
1078123 TCAATATTAA
1078133 TTTTAGGTTGGAACCTGAT
1 TTTTAGGTTGGAACCTGAT
*
1078152 TTTTAAGTTGGGAACCTGAT
1 TTTTAGGTT-GGAACCTGAT
*
1078172 TTTTAGGTTGGAACATGAAT
1 TTTTAGGTTGGAACCTG-AT
* *
1078192 TTTTAGGTTAGAACCTAAT
1 TTTTAGGTTGGAACCTGAT
* *
1078211 TTTTAAGTTGGAAACATGAAT
1 TTTTAGGTTGG-AACCTG-AT
*
1078232 TTTTAGGTTGGAACCTGAC
1 TTTTAGGTTGGAACCTGAT
*
1078251 TTTTAAGTTGGAAACCTGAT
1 TTTTAGGTTGG-AACCTGAT
*
1078271 TTTTAGGTTGGAACCTAAT
1 TTTTAGGTTGGAACCTGAT
1078290 TTTTAGGTTG
1 TTTTAGGTTG
1078300 AAAACCATAT
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
19 54 0.43
20 60 0.48
21 12 0.10
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (19 bp):
TTTTAGGTTGGAACCTGAT
Found at i:1078185 original size:39 final size:40
Alignment explanation
Indices: 1078133--1078304 Score: 217
Period size: 39 Copynumber: 4.4 Consensus size: 40
1078123 TCAATATTAA
* * *
1078133 TTTTAGGTTGG-AACCTG-ATTTTTAAGTTGGGAACCTGAT
1 TTTTAGGTTGGAAACATGAATTTTTAGGTT-GGAACCTAAT
*
1078172 TTTTAGGTTGG-AACATGAATTTTTAGGTTAGAACCTAAT
1 TTTTAGGTTGGAAACATGAATTTTTAGGTTGGAACCTAAT
* * *
1078211 TTTTAAGTTGGAAACATGAATTTTTAGGTTGGAACCTGAC
1 TTTTAGGTTGGAAACATGAATTTTTAGGTTGGAACCTAAT
* *
1078251 TTTTAAGTTGGAAACCTG-ATTTTTAGGTTGGAACCTAAT
1 TTTTAGGTTGGAAACATGAATTTTTAGGTTGGAACCTAAT
*
1078290 TTTTAGGTTGAAAAC
1 TTTTAGGTTGGAAAC
1078305 CATATTCCAG
Statistics
Matches: 118, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 66 0.56
40 52 0.44
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.40
Consensus pattern (40 bp):
TTTTAGGTTGGAAACATGAATTTTTAGGTTGGAACCTAAT
Found at i:1078261 original size:79 final size:79
Alignment explanation
Indices: 1078133--1078304 Score: 233
Period size: 79 Copynumber: 2.2 Consensus size: 79
1078123 TCAATATTAA
* * *
1078133 TTTTAGGTTGG-AACCTGATTTTTAAGTTGGGAACCTGATTTTTAGGTTGG-AACATGAATTTTT
1 TTTTAGGTTGGAAACATGATTTTTAAGTTGGGAACCTGACTTTTAAGTTGGAAACATG-ATTTTT
1078196 AGGTTAGAACCTAAT
65 AGGTTAGAACCTAAT
* * *
1078211 TTTTAAGTTGGAAACATGAATTTTTAGGTT-GGAACCTGACTTTTAAGTTGGAAACCTGATTTTT
1 TTTTAGGTTGGAAACATG-ATTTTTAAGTTGGGAACCTGACTTTTAAGTTGGAAACATGATTTTT
*
1078275 AGGTTGGAACCTAAT
65 AGGTTAGAACCTAAT
*
1078290 TTTTAGGTTGAAAAC
1 TTTTAGGTTGGAAAC
1078305 CATATTCCAG
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
78 10 0.12
79 57 0.70
80 15 0.18
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.40
Consensus pattern (79 bp):
TTTTAGGTTGGAAACATGATTTTTAAGTTGGGAACCTGACTTTTAAGTTGGAAACATGATTTTTA
GGTTAGAACCTAAT
Found at i:1078339 original size:19 final size:19
Alignment explanation
Indices: 1078315--1078366 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1078305 CATATTCCAG
1078315 ATTTTAGGTTGCAAGCCAA
1 ATTTTAGGTTGCAAGCCAA
* * *
1078334 ATTTTAAGTTGTAATCCAA
1 ATTTTAGGTTGCAAGCCAA
*
1078353 AATTTAGGTTGCAA
1 ATTTTAGGTTGCAA
1078367 CCCAGTTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (19 bp):
ATTTTAGGTTGCAAGCCAA
Found at i:1078513 original size:40 final size:39
Alignment explanation
Indices: 1078399--1078650 Score: 122
Period size: 40 Copynumber: 6.3 Consensus size: 39
1078389 CAGGTTTTTA
* * *
1078399 AATTACAAGCAAGGTGATGTATCGTACGTGGTACA-ACC
1 AATTATAAGCAAGGTGATGTATTGTACGGGGTACACACC
* * * *
1078437 TAAATATAA--AAGTGGTGATGTATTGTTCTGGATACACACTC
1 -AATTATAAGCAA--GGTGATGTATTGTACGGGGTACACAC-C
*
1078478 AATTATAAGCAAGGTGATGTATTGTATGGGGTACACACC
1 AATTATAAGCAAGGTGATGTATTGTACGGGGTACACACC
* * * * *
1078517 TAA--ATATGAAAGTGATGATGTATTATACGGGATACACTCCC
1 -AATTATAAGCAAG-G-TGATGTATTGTACGGGGTACAC-ACC
* * * * * * *
1078558 AATTACAATCAATGTGATGTATCGTATGGGGTATACACTT
1 AATTATAAGCAAGGTGATGTATTGTACGGGGTACACAC-C
* * * *
1078598 AAATATGAA--AGTGGTGATGTATTATACGAGGTACACACCC
1 AATTAT-AAGCA-AGGTGATGTATTGTACGGGGTACACA-CC
*
1078638 AATTACAAGCAAG
1 AATTATAAGCAAG
1078651 AATCAGAGGT
Statistics
Matches: 152, Mismatches: 43, Indels: 35
0.66 0.19 0.15
Matches are distributed among these distances:
37 2 0.01
38 7 0.05
39 30 0.20
40 99 0.65
41 8 0.05
42 6 0.04
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (39 bp):
AATTATAAGCAAGGTGATGTATTGTACGGGGTACACACC
Found at i:1078550 original size:80 final size:80
Alignment explanation
Indices: 1078399--1078650 Score: 346
Period size: 80 Copynumber: 3.2 Consensus size: 80
1078389 CAGGTTTTTA
* * * *
1078399 AATTACAAGCAAGGTGATGTATCGTACGTGGTACA-ACCTAAATATAAAAGTGGTGATGTATTGT
1 AATTACAAGCAAGGTGATGTATCGTATGGGGTACACACCTAAATATGAAAGTGGTGATGTATTAT
* * *
1078463 TCTGGATACACACTC
66 ACGGGATACACACCC
* * *
1078478 AATTATAAGCAAGGTGATGTATTGTATGGGGTACACACCTAAATATGAAAGTGATGATGTATTAT
1 AATTACAAGCAAGGTGATGTATCGTATGGGGTACACACCTAAATATGAAAGTGGTGATGTATTAT
*
1078543 ACGGGATACACTCCC
66 ACGGGATACACACCC
* * * *
1078558 AATTACAATCAATGTGATGTATCGTATGGGGTATACACTTAAATATGAAAGTGGTGATGTATTAT
1 AATTACAAGCAAGGTGATGTATCGTATGGGGTACACACCTAAATATGAAAGTGGTGATGTATTAT
1078623 ACGAGG-TACACACCC
66 ACG-GGATACACACCC
1078638 AATTACAAGCAAG
1 AATTACAAGCAAG
1078651 AATCAGAGGT
Statistics
Matches: 150, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 31 0.21
80 117 0.78
81 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (80 bp):
AATTACAAGCAAGGTGATGTATCGTATGGGGTACACACCTAAATATGAAAGTGGTGATGTATTAT
ACGGGATACACACCC
Found at i:1079051 original size:2 final size:2
Alignment explanation
Indices: 1079044--1079074 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1079034 TTTGAACTAC
1079044 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
1079075 GGATCATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1084184 original size:22 final size:22
Alignment explanation
Indices: 1084159--1084204 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1084149 ACGAACCTGC
1084159 TTTTTTT--GTTGGAACATGAT
1 TTTTTTTAGGTTGGAACATGAT
**
1084179 TTTTTTTAGGTTGGAATGTGAT
1 TTTTTTTAGGTTGGAACATGAT
1084201 TTTT
1 TTTT
1084205 AAGTTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (22 bp):
TTTTTTTAGGTTGGAACATGAT
Found at i:1084225 original size:40 final size:39
Alignment explanation
Indices: 1084181--1084284 Score: 127
Period size: 40 Copynumber: 2.6 Consensus size: 39
1084171 AACATGATTT
* ** * **
1084181 TTTTTAGGTTGGAATGTGATTTTTAAGTTTGAAACCTGAA
1 TTTTTAAGTTGGAACCTAATTTTTAAGTGGGAAACCTG-A
* *
1084221 TTTTTACGTTAGAACCTAATTTTTAAGTGGGAAACCTGA
1 TTTTTAAGTTGGAACCTAATTTTTAAGTGGGAAACCTGA
1084260 TTTTTAAGTTGGAACCTAATTTTTA
1 TTTTTAAGTTGGAACCTAATTTTTA
1084285 GGTTGAAAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
39 24 0.44
40 31 0.56
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (39 bp):
TTTTTAAGTTGGAACCTAATTTTTAAGTGGGAAACCTGA
Found at i:1084236 original size:20 final size:20
Alignment explanation
Indices: 1084199--1084295 Score: 108
Period size: 19 Copynumber: 4.9 Consensus size: 20
1084189 TTGGAATGTG
*
1084199 ATTTTTAAGTTTGAAACCTGA
1 ATTTTTAAGTTGGAAACCT-A
* *
1084220 ATTTTTACGTTAG-AACCTA
1 ATTTTTAAGTTGGAAACCTA
* *
1084239 ATTTTTAAGTGGGAAACCTG
1 ATTTTTAAGTTGGAAACCTA
1084259 ATTTTTAAGTTGG-AACCTA
1 ATTTTTAAGTTGGAAACCTA
* *
1084278 ATTTTTAGGTTGAAAACC
1 ATTTTTAAGTTGGAAACC
1084296 AGGTTTTAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
19 27 0.42
20 26 0.41
21 11 0.17
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (20 bp):
ATTTTTAAGTTGGAAACCTA
Found at i:1084289 original size:19 final size:19
Alignment explanation
Indices: 1084181--1084289 Score: 92
Period size: 20 Copynumber: 5.6 Consensus size: 19
1084171 AACATGATTT
** *
1084181 TTTTTAGGTTGGAATGTGA
1 TTTTTAGGTTGGAACCTAA
* *
1084200 TTTTTAAGTTTGAAACCTGAA
1 TTTTT-AGGTTGGAACCT-AA
* *
1084221 TTTTTACGTTAGAACCTAA
1 TTTTTAGGTTGGAACCTAA
* * *
1084240 TTTTTAAGTGGGAAACCTGA
1 TTTTTAGGTTGG-AACCTAA
*
1084260 TTTTTAAGTTGGAACCTAA
1 TTTTTAGGTTGGAACCTAA
1084279 TTTTTAGGTTG
1 TTTTTAGGTTG
1084290 AAAACCAGGT
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
19 32 0.45
20 33 0.46
21 6 0.08
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (19 bp):
TTTTTAGGTTGGAACCTAA
Found at i:1084302 original size:19 final size:19
Alignment explanation
Indices: 1084280--1084359 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 19
1084270 GGAACCTAAT
* *
1084280 TTTTAGGTTGAAAACCAGG
1 TTTTAGGTTGCAAACCAGA
* *
1084299 TTTTAGGTTGCCAGCCAGA
1 TTTTAGGTTGCAAACCAGA
* *
1084318 TTTTAGGTTGCAAGCCAAA
1 TTTTAGGTTGCAAACCAGA
* *
1084337 TTTTAGATTGTAAACCAGA
1 TTTTAGGTTGCAAACCAGA
1084356 TTTT
1 TTTT
1084360 TAAATTACAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (19 bp):
TTTTAGGTTGCAAACCAGA
Found at i:1084497 original size:40 final size:39
Alignment explanation
Indices: 1084376--1084602 Score: 154
Period size: 40 Copynumber: 5.7 Consensus size: 39
1084366 ACAAGCAAGA
* * * *
1084376 TGATGTATCGTACGGGGTATACACCTAACTATGAAAATGG
1 TGATGTATTGTACGGGATACACACCTAAATATG-AAATGG
* * * * * *
1084416 TGATGTATT-TACAGAATGCACACCCAATTACAAGAAA-GG
1 TGATGTATTGTACGGGATACACACCTAA--ATATGAAATGG
*
1084455 TGATGTATTGTACGGGGTACACACCTAAATATGAAAGTGG
1 TGATGTATTGTACGGGATACACACCTAAATATGAAA-TGG
* * *
1084495 TGATGTATTGTACGGGATACACTCCCAATTATAAGAAA-GG
1 TGATGTATTGTACGGGATACACACCTAA--ATATGAAATGG
** * * * * * *
1084535 TTTTGTATCGCATGGGGTACACAACTAAATATGAAAATGA
1 TGATGTATTGTACGGGATACACACCTAAATATG-AAATGG
* *
1084575 TGATGTATTTTATGGGATACACACCTAA
1 TGATGTATTGTACGGGATACACACCTAA
1084603 TTACATGCAA
Statistics
Matches: 139, Mismatches: 39, Indels: 18
0.71 0.20 0.09
Matches are distributed among these distances:
38 10 0.07
39 26 0.19
40 94 0.68
41 2 0.01
42 7 0.05
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (39 bp):
TGATGTATTGTACGGGATACACACCTAAATATGAAATGG
Found at i:1084552 original size:80 final size:79
Alignment explanation
Indices: 1084362--1084607 Score: 303
Period size: 80 Copynumber: 3.1 Consensus size: 79
1084352 CAGATTTTTA
* * * *
1084362 AATTACAAGCAAGATGATGTATCGTACGGGGTATACACCTAACTATGAAAATGGTGATGTATTTA
1 AATTACAAGAAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAATGGTGATGTATTTA
* * *
1084427 CAGAATGCACACCC
66 CGGGATACACACCC
* *
1084441 AATTACAAGAAAGGTGATGTATTGTACGGGGTACACACCTAAATATGAAAGTGGTGATGTATTGT
1 AATTACAAGAAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAATGGTGATGTATT-T
*
1084506 ACGGGATACACTCCC
65 ACGGGATACACACCC
* ** * * * *
1084521 AATTATAAGAAAGGTTTTGTATCGCATGGGGTACACAACTAAATATGAAAATGATGATGTATTTT
1 AATTACAAGAAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAATGGTGATGTA-TTT
* *
1084586 ATGGGATACACACCT
65 ACGGGATACACACCC
1084601 AATTACA
1 AATTACA
1084608 TGCAAGAATC
Statistics
Matches: 142, Mismatches: 23, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
79 57 0.40
80 83 0.58
81 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (79 bp):
AATTACAAGAAAGGTGATGTATCGTACGGGGTACACACCTAAATATGAAAATGGTGATGTATTTA
CGGGATACACACCC
Found at i:1088542 original size:11 final size:11
Alignment explanation
Indices: 1088526--1088558 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1088516 TGATCAGCAG
1088526 TGATCCAGAGC
1 TGATCCAGAGC
1088537 TGATCCAGAGC
1 TGATCCAGAGC
1088548 TGATCCAGAGC
1 TGATCCAGAGC
1088559 AACGTACGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (11 bp):
TGATCCAGAGC
Found at i:1089079 original size:22 final size:23
Alignment explanation
Indices: 1089023--1089082 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
1089013 ATATTTTTAC
1089023 AAAAATTATATTA-AATAATTATA
1 AAAAATTAT-TTATAATAATTATA
*
1089046 AAAAGTTATATTTATAAT-ATTATA
1 AAAA-AT-TATTTATAATAATTATA
1089070 AAAAATTATTTAT
1 AAAAATTATTTAT
1089083 TTTTTATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 7 0.22
23 5 0.16
24 14 0.44
25 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AAAAATTATTTATAATAATTATA
Found at i:1089293 original size:21 final size:20
Alignment explanation
Indices: 1089255--1089301 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
1089245 TTATTTCAAA
1089255 TAAATAAATAAAAATATTTT
1 TAAATAAATAAAAATATTTT
1089275 TAAA-AAATAAATTAATATTTT
1 TAAATAAATAAA--AATATTTT
1089296 TAAATA
1 TAAATA
1089302 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 12 0.50
22 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAAATAAAAATATTTT
Found at i:1090876 original size:16 final size:16
Alignment explanation
Indices: 1090855--1090889 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1090845 TAATATATCC
1090855 TTAAGGTGGCCTTTGG
1 TTAAGGTGGCCTTTGG
1090871 TTAAGGTGGCCTTTGG
1 TTAAGGTGGCCTTTGG
1090887 TTA
1 TTA
1090890 GATGGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.34, T:0.40
Consensus pattern (16 bp):
TTAAGGTGGCCTTTGG
Found at i:1093322 original size:51 final size:50
Alignment explanation
Indices: 1093235--1093352 Score: 175
Period size: 51 Copynumber: 2.4 Consensus size: 50
1093225 TTCATACTAC
* * *
1093235 AAAAAATGTAGCACTT-ACACATATTTACACTGGTGTAAGTGAATAAAAT
1 AAAAAATGTAGCACTTAATACATACTTACACTAGTGTAAGTGAATAAAAT
* *
1093284 AAATAAGTGTATCACTTAATACATACTTACACTAGTGTAAGTGAATAAAAT
1 AAA-AAATGTAGCACTTAATACATACTTACACTAGTGTAAGTGAATAAAAT
1093335 AAAAAATGTAGCACTTAA
1 AAAAAATGTAGCACTTAA
1093353 CGCATAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 3 0.05
50 24 0.40
51 33 0.55
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (50 bp):
AAAAAATGTAGCACTTAATACATACTTACACTAGTGTAAGTGAATAAAAT
Found at i:1093363 original size:20 final size:20
Alignment explanation
Indices: 1093338--1093378 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1093328 ATAAAATAAA
1093338 AAATGTAGCACTTAACGCAT
1 AAATGTAGCACTTAACGCAT
1093358 AAATGTAGCACTTAACGCAT
1 AAATGTAGCACTTAACGCAT
1093378 A
1 A
1093379 CTTATACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTAGCACTTAACGCAT
Found at i:1093612 original size:20 final size:20
Alignment explanation
Indices: 1093545--1093652 Score: 71
Period size: 20 Copynumber: 5.4 Consensus size: 20
1093535 GAACTCCAAT
**
1093545 TTCGCAACTC-AGTTTCCAAA
1 TTCGCAACTCGA-TTTCTGAA
* *
1093565 TTCGCAACACTGAATTTC-AAA
1 TTCGCAACTC-G-ATTTCTGAA
1093586 TTCGCAACTCGATTTCTGAA
1 TTCGCAACTCGATTTCTGAA
* * **
1093606 TTTGCAACACGAATTT-TGTT
1 TTCGCAACTCG-ATTTCTGAA
*
1093626 TTCACAACTCGATTTC-GAA
1 TTCGCAACTCGATTTCTGAA
1093645 TTCGCAAC
1 TTCGCAAC
1093653 ACGAATTTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 13
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.25
20 31 0.45
21 16 0.23
22 4 0.06
23 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (20 bp):
TTCGCAACTCGATTTCTGAA
Found at i:1093613 original size:41 final size:39
Alignment explanation
Indices: 1093523--1093671 Score: 149
Period size: 40 Copynumber: 3.8 Consensus size: 39
1093513 ATGACCAACA
* * * * *
1093523 AATTTGCAACGCGAACTCCAATTTCGCAACTC-AGTTTCCA
1 AATTCGCAACACGAATTTCAATTTCGCAACTCGA-TTT-CG
*
1093563 AATTCGCAACACTGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCGCAACAC-GAATTTCAATTTCGCAACTCGATTTC-G
* *** *
1093604 AATTTGCAACACGAATTTTGTTTTCACAACTCGATTTCG
1 AATTCGCAACACGAATTTCAATTTCGCAACTCGATTTCG
1093643 AATTCGCAACACGAATTT-AATTTCGCAAC
1 AATTCGCAACACGAATTTCAATTTCGCAAC
1093672 AAGTTTTAGT
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
38 8 0.09
39 18 0.20
40 32 0.36
41 31 0.34
42 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (39 bp):
AATTCGCAACACGAATTTCAATTTCGCAACTCGATTTCG
Found at i:1093667 original size:19 final size:20
Alignment explanation
Indices: 1093523--1093672 Score: 89
Period size: 19 Copynumber: 7.6 Consensus size: 20
1093513 ATGACCAACA
* * *
1093523 AATTT-GCAACGCGAACTCC
1 AATTTCGCAACACGAATTTC
* *
1093542 AATTTCGCAACTC-AGTTTCC
1 AATTTCGCAACACGAATTT-C
*
1093562 AAATTCGCAACACTGAATTTC
1 AATTTCGCAACAC-GAATTTC
* *
1093583 AAATTCGCAACTCG-ATTTC
1 AATTTCGCAACACGAATTTC
*
1093602 TGAATTT-GCAACACGAATTTT
1 --AATTTCGCAACACGAATTTC
** * *
1093623 GTTTTCACAACTCG-ATTTC
1 AATTTCGCAACACGAATTTC
1093642 GAA-TTCGCAACACGAATTT-
1 -AATTTCGCAACACGAATTTC
1093661 AATTTCGCAACA
1 AATTTCGCAACA
1093673 AGTTTTAGTT
Statistics
Matches: 100, Mismatches: 20, Indels: 22
0.70 0.14 0.15
Matches are distributed among these distances:
18 2 0.02
19 37 0.37
20 36 0.36
21 21 0.21
22 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (20 bp):
AATTTCGCAACACGAATTTC
Found at i:1094461 original size:12 final size:12
Alignment explanation
Indices: 1094440--1094473 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1094430 ACCACATTTC
*
1094440 CAATACCAAACA
1 CAATATCAAACA
1094452 CAATATCAAACA
1 CAATATCAAACA
*
1094464 CAATCTCAAA
1 CAATATCAAA
1094474 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1094626 original size:24 final size:24
Alignment explanation
Indices: 1094593--1094652 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1094583 TAGTCAGTAT
*
1094593 TCGAAATTTGATCTTGGTCAATAC
1 TCGAACTTTGATCTTGGTCAATAC
*
1094617 TCGGACTTTGATCTTGGTCAATAC
1 TCGAACTTTGATCTTGGTCAATAC
*
1094641 TCGAATTTTGAT
1 TCGAACTTTGAT
1094653 GATGTTTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (24 bp):
TCGAACTTTGATCTTGGTCAATAC
Found at i:1096646 original size:23 final size:23
Alignment explanation
Indices: 1096620--1096685 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
1096610 CACCACAGCT
* *
1096620 CGTATAATTGCACCGAAGTGTCA
1 CGTAGAATTGCACCGAAGTGGCA
* *
1096643 CGTAGAATTGCACCGGAGTGGCG
1 CGTAGAATTGCACCGAAGTGGCA
* *
1096666 CTTAGAATTGCACCGTAGTG
1 CGTAGAATTGCACCGAAGTG
1096686 CCATATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGGCA
Found at i:1097367 original size:21 final size:21
Alignment explanation
Indices: 1097343--1097385 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1097333 TCATATTCGT
* *
1097343 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
1097364 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
1097385 T
1 T
1097386 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:1103453 original size:23 final size:23
Alignment explanation
Indices: 1103427--1103495 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1103417 CACCACAACT
*
1103427 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * * *
1103450 CGTAGAATTACACCGGAGTGGCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
1103473 CTTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1103496 TATAATAATG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1105787 original size:12 final size:12
Alignment explanation
Indices: 1105770--1105810 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1105760 AGCAAAAGGA
*
1105770 AATCAAAATCGC
1 AATCAAAATCAC
*
1105782 AATCAAAATCAA
1 AATCAAAATCAC
*
1105794 AATCAAAATCTC
1 AATCAAAATCAC
1105806 AATCA
1 AATCA
1105811 CAACCGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:1105791 original size:6 final size:6
Alignment explanation
Indices: 1105769--1105803 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1105759 AAGCAAAAGG
* *
1105769 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
1105804 TCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:1106268 original size:64 final size:64
Alignment explanation
Indices: 1106160--1106293 Score: 205
Period size: 64 Copynumber: 2.1 Consensus size: 64
1106150 ATTTAAAACA
*
1106160 ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
1 ACAAATCAATTAAACAAGCAAAAAAGAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
* *** * *
1106224 ACAAATCAATTATACAAGCAAAAAAGAATTCTTATTTCCTCATCAATTAAACAAATCAACTTTT
1 ACAAATCAATTAAACAAGCAAAAAAGAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
1106288 ACAAAT
1 ACAAAT
1106294 ACATCAATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.28
Consensus pattern (64 bp):
ACAAATCAATTAAACAAGCAAAAAAGAAGAATTATTTACACATCAATTAAACAAATCAACTTTT
Found at i:1107671 original size:21 final size:21
Alignment explanation
Indices: 1107642--1107756 Score: 106
Period size: 21 Copynumber: 5.5 Consensus size: 21
1107632 GTGAATCGGG
* * *
1107642 CTCTCGAACGGTGGGAGAGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
1107663 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
1107684 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
**
1107705 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
1107726 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
*
1107747 CTCGTGAACG
1 CTCTTGAACG
1107757 ATGACAGGTG
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 2 0.03
21 72 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.37, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:1107708 original size:42 final size:42
Alignment explanation
Indices: 1107642--1107764 Score: 174
Period size: 42 Copynumber: 2.9 Consensus size: 42
1107632 GTGAATCGGG
* *
1107642 CTCTCGAACGGTGGGAGAGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
* * *
1107684 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
* * *
1107726 CTCTTGAACGATAGGAGAGGCCTCGTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGG
1107765 TGAATTGGGC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.19
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
Found at i:1108132 original size:21 final size:21
Alignment explanation
Indices: 1108108--1108151 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1108098 ATTGTCATCG
1108108 CGTAAA-ACCTCTACCTCACCA
1 CGTAAAGACC-CTACCTCACCA
* *
1108129 CGTAAAGACCGTACCTCATCA
1 CGTAAAGACCCTACCTCACCA
1108150 CG
1 CG
1108152 CCATGCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.32, C:0.39, G:0.11, T:0.18
Consensus pattern (21 bp):
CGTAAAGACCCTACCTCACCA
Found at i:1109916 original size:20 final size:20
Alignment explanation
Indices: 1109893--1109955 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1109883 TCTGAAACTA
*
1109893 AAAATCGCAATGCGAAAATG
1 AAAATCGCAACGCGAAAATG
1109913 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
1109933 AAACTCGCAACACGAAAAT-
1 AAAATCGCAACGCGAAAATG
1109952 AAAA
1 AAAA
1109956 CTTGAATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.54, C:0.19, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1109956 original size:20 final size:20
Alignment explanation
Indices: 1109886--1109957 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1109876 AATAGTTTCT
* * *
1109886 GAAACTAAAAATCGCAATGC
1 GAAAATAAAACTCGCAACGC
1109906 GAAAATGAAAA-TCGCAACGC
1 GAAAAT-AAAACTCGCAACGC
* *
1109926 GAAAATGAAACTCGCAACAC
1 GAAAATAAAACTCGCAACGC
1109946 GAAAATAAAACT
1 GAAAATAAAACT
1109958 TGAATGAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 3 0.07
20 38 0.84
21 4 0.09
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.12
Consensus pattern (20 bp):
GAAAATAAAACTCGCAACGC
Found at i:1110290 original size:22 final size:22
Alignment explanation
Indices: 1110264--1110340 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
1110254 GGAGATAGAT
* *
1110264 GGATTTTGCCAGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
1110286 GGATTTCGCTGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
* *
1110308 GGATTTCGTCGGAGATGGGGAT
1 GGATTTCGCCGGAGATGGGGAC
*
1110330 GGATGTCGCCG
1 GGATTTCGCCG
1110341 TAGAGAGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.18, C:0.14, G:0.44, T:0.23
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAC
Found at i:1110478 original size:17 final size:18
Alignment explanation
Indices: 1110444--1110478 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1110434 GTTTCGAATT
1110444 CGAAAATAAATTCGCGTTG
1 CGAAAATAAA-TCGCGTTG
1110463 CGAAAATAAA-CGCGTT
1 CGAAAATAAATCGCGTT
1110479 TTGCGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (18 bp):
CGAAAATAAATCGCGTTG
Found at i:1110522 original size:20 final size:20
Alignment explanation
Indices: 1110496--1110547 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1110486 TTTGACTTTT
1110496 GCATTGCGAATTACAAATTC
1 GCATTGCGAATTACAAATTC
* * *
1110516 GCGTTGCGATTTACATATTC
1 GCATTGCGAATTACAAATTC
1110536 GCATTGCGAATT
1 GCATTGCGAATT
1110548 TGGAAAATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
GCATTGCGAATTACAAATTC
Found at i:1110792 original size:52 final size:51
Alignment explanation
Indices: 1110733--1110983 Score: 208
Period size: 52 Copynumber: 4.9 Consensus size: 51
1110723 TTATTTTCTC
** *
1110733 AATAAAAAATGTAGCAAACTTAATGCATACTTACACAGGTGTAAGTGAAAAA
1 AATAAAAAATGTAGCAAACTTAAAACATACTTACAC-GGTGTAAGTGAATAA
* *
1110785 AATAAAAAAATATATC--ACTTAAAACATACTTACATCGGTGTAAGTGAATAA
1 AAT-AAAAAATGTAGCAAACTTAAAACATACTTACA-CGGTGTAAGTGAATAA
* * *
1110836 AACAAATAATGTAGCAAACTTAAAACATACTTACACCGGTATAAGTGAATAA
1 AATAAAAAATGTAGCAAACTTAAAACATACTTACA-CGGTGTAAGTGAATAA
* * * * ** *
1110888 AATAAAAAATATA-TAACACTTAACACATTCTTACACCAATTTAAGT-AATTAA
1 AATAAAAAATGTAGCAA-ACTTAAAACATACTTACA-CGGTGTAAGTGAA-TAA
*** * *
1110940 AATAAAATGCGTAGC--ACTTAACACATATTTACATCGGTGTAAGT
1 AATAAAAAATGTAGCAAACTTAAAACATACTTACA-CGGTGTAAGT
1110984 ATGTACATCT
Statistics
Matches: 161, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
50 32 0.20
51 36 0.22
52 83 0.52
53 10 0.06
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (51 bp):
AATAAAAAATGTAGCAAACTTAAAACATACTTACACGGTGTAAGTGAATAA
Found at i:1112591 original size:20 final size:20
Alignment explanation
Indices: 1112568--1112607 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1112558 GAGACAACAG
1112568 TTGACCTAAAAATCTAAAGA
1 TTGACCTAAAAATCTAAAGA
*
1112588 TTGACCTGAAAATCTAAAGA
1 TTGACCTAAAAATCTAAAGA
1112608 CTGGCCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (20 bp):
TTGACCTAAAAATCTAAAGA
Found at i:1113519 original size:22 final size:20
Alignment explanation
Indices: 1113479--1113524 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
1113469 TTATATATTT
*
1113479 AAATTAATTTTAAATATAAA
1 AAATTAATTTTAAAAATAAA
1113499 AAATTAATTAATTAAAAATAAA
1 AAATTAATT--TTAAAAATAAA
1113521 AAAT
1 AAAT
1113525 AAACGTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.39
22 14 0.61
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATTAATTTTAAAAATAAA
Found at i:1113846 original size:31 final size:31
Alignment explanation
Indices: 1113776--1113846 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1113766 GATTTTTAGA
* *
1113776 TCGGGTTAATATCATATCGGTTGGCTTCAGG
1 TCGGGTCAATATCAGATCGGTTGGCTTCAGG
* * * *
1113807 TCGAGTCAATATCGGATCGGTTGGCTTCTGT
1 TCGGGTCAATATCAGATCGGTTGGCTTCAGG
1113838 TCGGGTCAA
1 TCGGGTCAA
1113847 CAATTAGATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (31 bp):
TCGGGTCAATATCAGATCGGTTGGCTTCAGG
Found at i:1116489 original size:20 final size:19
Alignment explanation
Indices: 1116460--1116497 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1116450 AAAAACCCAT
1116460 ATCTACAAAATAAATCTAAA
1 ATCTACAAAATAAA-CTAAA
*
1116480 ATCTATAAAATAAACTAA
1 ATCTACAAAATAAACTAA
1116498 TAAAGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (19 bp):
ATCTACAAAATAAACTAAA
Found at i:1117092 original size:6 final size:6
Alignment explanation
Indices: 1117081--1117113 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1117071 ATCCCCCTTC
1117081 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCC
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCC
1117114 GCTCGTCTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTCT
Found at i:1117973 original size:83 final size:84
Alignment explanation
Indices: 1117872--1118038 Score: 309
Period size: 84 Copynumber: 2.0 Consensus size: 84
1117862 TCAAACGGTT
* *
1117872 CACAAATGATTTGCTGAATATTCCGTTTGTTTACA-GCTGGTGTGGTTTTCTAATAGATTCATAT
1 CACAAATGATTTGCTGAATATTCCGTTTGTTTAAAGGCTGGTGTGGTTTTCTAATAGATTCACAT
1117936 ACTGTGATATTGTCTATTA
66 ACTGTGATATTGTCTATTA
1117955 CACAAATGATTTGCTGAATATTCCGTTTGTTTAAAGGCTGGTGTGGTTTTCTAATAGATTCACAT
1 CACAAATGATTTGCTGAATATTCCGTTTGTTTAAAGGCTGGTGTGGTTTTCTAATAGATTCACAT
1118020 ACTGTGATATTGTCTATTA
66 ACTGTGATATTGTCTATTA
1118039 GGCTTCAGCT
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
83 34 0.42
84 47 0.58
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.43
Consensus pattern (84 bp):
CACAAATGATTTGCTGAATATTCCGTTTGTTTAAAGGCTGGTGTGGTTTTCTAATAGATTCACAT
ACTGTGATATTGTCTATTA
Found at i:1120939 original size:19 final size:20
Alignment explanation
Indices: 1120901--1120944 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1120891 AAACCATTCA
1120901 GGGGGGAATCGGTACCCCCTT
1 GGGGGGAATCGGTA-CCCCTT
* *
1120922 GGGGGGAATCGGTTCCCTTT
1 GGGGGGAATCGGTACCCCTT
1120942 GGG
1 GGG
1120945 CAATCTGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.11, C:0.23, G:0.43, T:0.23
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCTT
Found at i:1121585 original size:10 final size:10
Alignment explanation
Indices: 1121570--1121594 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1121560 AATCATCCAA
1121570 AAACAAATTC
1 AAACAAATTC
1121580 AAACAAATTC
1 AAACAAATTC
1121590 AAACA
1 AAACA
1121595 TCCAACAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (10 bp):
AAACAAATTC
Found at i:1121615 original size:31 final size:31
Alignment explanation
Indices: 1121556--1121616 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1121546 TATAAATAAG
* *
1121556 TTCAAATCATCCAAAAACAAATTCAAACAAA
1 TTCAAATCATCCAAAAACAAAGTAAAACAAA
*
1121587 TTCAAA-CATCCAACAACCAAAGTAAAACAA
1 TTCAAATCATCCAA-AAACAAAGTAAAACAA
1121617 TCCAAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.57, C:0.25, G:0.02, T:0.16
Consensus pattern (31 bp):
TTCAAATCATCCAAAAACAAAGTAAAACAAA
Found at i:1123922 original size:20 final size:21
Alignment explanation
Indices: 1123867--1123922 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1123857 TAGTGCATGA
*
1123867 GGAATCGATACCCCCTTGTAG
1 GGAATCGATACCCCCTTGGAG
* **
1123888 GGAACCGATTTCCCC-TGGAG
1 GGAATCGATACCCCCTTGGAG
1123908 GGAATCGATACCCCC
1 GGAATCGATACCCCC
1123923 CATGGGTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.20
Consensus pattern (21 bp):
GGAATCGATACCCCCTTGGAG
Found at i:1131242 original size:8 final size:8
Alignment explanation
Indices: 1131229--1131254 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1131219 ATTAACCTCC
1131229 AATGAGCA
1 AATGAGCA
1131237 AATGAGCA
1 AATGAGCA
1131245 AATGAGCA
1 AATGAGCA
1131253 AA
1 AA
1131255 GTACTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.12
Consensus pattern (8 bp):
AATGAGCA
Found at i:1133535 original size:24 final size:24
Alignment explanation
Indices: 1133508--1133553 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1133498 TTTAAAAATC
*
1133508 TTATTTTTTATTATTTACTTTAAT
1 TTATTTTTTATTATTTAATTTAAT
*
1133532 TTATTTTTTATTTTTTAATTTA
1 TTATTTTTTATTATTTAATTTA
1133554 TTATTTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (24 bp):
TTATTTTTTATTATTTAATTTAAT
Found at i:1133552 original size:8 final size:7
Alignment explanation
Indices: 1133508--1133559 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
1133498 TTTAAAAATC
1133508 TTATTTT
1 TTATTTT
*
1133515 TTATTAT
1 TTATTTT
1133522 TTACTTTAAT
1 TTA-TTT--T
1133532 TTATTTT
1 TTATTTT
1133539 TTATTTT
1 TTATTTT
*
1133546 TTAATTTA
1 TT-ATTTT
1133554 TTATTT
1 TTATTT
1133560 CATATAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 23 0.61
8 8 0.21
9 3 0.08
10 4 0.11
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (7 bp):
TTATTTT
Found at i:1137882 original size:184 final size:182
Alignment explanation
Indices: 1137413--1137869 Score: 518
Period size: 184 Copynumber: 2.5 Consensus size: 182
1137403 ATGCCACTAA
* * * *
1137413 TAATAGGGTTCGCATATAGCAGCGTTTTGGTAACAAACGCAGCAAATAATTCGTACTTTAGTGGC
1 TAATAGGGTTCACATATAGCGGCGTTTTGGTAACAAACGCCGCAAATTATTCGTACTTTAGTGGC
* *
1137478 GTTTTAACAAAAAATGCCACAAATGTTTTTTATTTAAACGCCATTAACTTTAGACATATACGACA
66 GTTTTGACAAAAAATGCCACATATG--TTTTATTTAAACGCCATTAACTTTAGACATATACGACA
** *
1137543 TTTTTTAATAAACGCTGCAACATATGAGTACTATAGCAACATTTTGAAATACCG
129 TTTTTTAATAAACGCCACAACAGATGAGTACTATAGCAACATTTTGAAATACCG
* ** * * * * * *
1137597 CAATAATGTTAACATATACCGGTGTATTGGTAACAAACGCCGCAAAATATTCGTACATTAGTGGC
1 TAATAGGGTTCACATATAGCGGCGTTTTGGTAACAAACGCCGCAAATTATTCGTACTTTAGTGGC
* * *
1137662 GTTTTGACAAAAAATGCCACAAATATTTTTTATTTAAACGTCATTAACTTTAGACATATAGCGGC
66 GTTTTGACAAAAAATGCCAC--ATATGTTTTATTTAAACGCCATTAACTTTAGACATATA-CGAC
* * * **** **
1137727 ATTTTTTAATAAATGCCACAACAGATTAGTACTTTAGCGGTGTTTTGATAAAAATGTCG
128 ATTTTTTAATAAACGCCACAACAGATGAGTACTATAGCAACATTTTG----AAATACCG
* * * * *
1137786 TAATAGGGTTCACATATAGCGGCATTTTAGTAATAAACGCCGTAAATTATTCATACTTTAGTGGC
1 TAATAGGGTTCACATATAGCGGCGTTTTGGTAACAAACGCCGCAAATTATTCGTACTTTAGTGGC
1137851 GTTTTGACAAAAAATGCCA
66 GTTTTGACAAAAAATGCCA
1137870 TAGATTTATT
Statistics
Matches: 222, Mismatches: 44, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
184 103 0.46
185 40 0.18
186 3 0.01
189 76 0.34
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (182 bp):
TAATAGGGTTCACATATAGCGGCGTTTTGGTAACAAACGCCGCAAATTATTCGTACTTTAGTGGC
GTTTTGACAAAAAATGCCACATATGTTTTATTTAAACGCCATTAACTTTAGACATATACGACATT
TTTTAATAAACGCCACAACAGATGAGTACTATAGCAACATTTTGAAATACCG
Found at i:1151051 original size:196 final size:198
Alignment explanation
Indices: 1150681--1151079 Score: 759
Period size: 197 Copynumber: 2.0 Consensus size: 198
1150671 CAACTATTGG
1150681 TTGATAGCAGCAAGTTAGGCGGACATCGAATCCTTAGAATCTAGCTCGAAAGCTCCATGTGATTT
1 TTGATAGCAGCAAGTTAGGCGGACATCGAATCCTTAGAATCTAGCTCGAAAGCTCCATGTGATTT
1150746 TCTCCCACTGCCAATCCTGTAGATGAAAATTGGTAATCGTTGGTGGCAATCCTATCCAGAATGTC
66 TCTCCCACTGCCAATCCTGTAGATGAAAATTGGTAATCGTTGGTGGCAATCCTATCCAGAATGTC
1150811 AAATGCCTATGCTGATGATTTCAAGTAATGTCCATTTGCCGAGGCATCTAGCATCA-TCGTGGGT
131 AAATGCCTATGCTGATGATTTCAAGTAATGTCCATTTGCCGAGGCATCTAGCATCACTCGTGGGT
1150875 GCA
196 GCA
1150878 TTGATAGCAGCAAGTTAGG-GGACATCGAATCCTTAGAATCTAGCTCGAAAGCTCCATGTGATTT
1 TTGATAGCAGCAAGTTAGGCGGACATCGAATCCTTAGAATCTAGCTCGAAAGCTCCATGTGATTT
1150942 TCTCCCACTGCCAATCCTTGTAGATGAAAATTGGTAATCGTTGGTGGCAATCCTATCCAGAATGT
66 TCTCCCACTGCCAATCC-TGTAGATGAAAATTGGTAATCGTTGGTGGCAATCCTATCCAGAATGT
1151007 CAAATGCCTATGCTGATGATTTCAAGTAATGTCCATTT-CCGAGGCATCTAGCATCATCTCGTGG
130 CAAATGCCTATGCTGATGATTTCAAGTAATGTCCATTTGCCGAGGCATCTAGCATCA-CTCGTGG
1151071 GTGCA
194 GTGCA
1151076 TTGA
1 TTGA
1151080 CTCCATTATA
Statistics
Matches: 199, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
196 80 0.40
197 104 0.52
198 15 0.08
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (198 bp):
TTGATAGCAGCAAGTTAGGCGGACATCGAATCCTTAGAATCTAGCTCGAAAGCTCCATGTGATTT
TCTCCCACTGCCAATCCTGTAGATGAAAATTGGTAATCGTTGGTGGCAATCCTATCCAGAATGTC
AAATGCCTATGCTGATGATTTCAAGTAATGTCCATTTGCCGAGGCATCTAGCATCACTCGTGGGT
GCA
Found at i:1160434 original size:6 final size:6
Alignment explanation
Indices: 1160420--1160463 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
1160410 ACCATATAAG
* * *
1160420 ATATAC ATATGC ATACAC ATATAC ATACAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC AT
1160464 GCACATGCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (6 bp):
ATATAC
Found at i:1160443 original size:18 final size:18
Alignment explanation
Indices: 1160420--1160475 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
1160410 ACCATATAAG
**
1160420 ATATACATATGCATACAC
1 ATATACATACACATACAC
*
1160438 ATATACATACACATATAC
1 ATATACATACACATACAC
* *
1160456 ATATACATGCACATGCAC
1 ATATACATACACATACAC
1160474 AT
1 AT
1160476 GCACGTGCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (18 bp):
ATATACATACACATACAC
Found at i:1160500 original size:6 final size:6
Alignment explanation
Indices: 1160477--1160521 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1160467 CATGCACATG
* ** *
1160477 CACGTG CACGTA CACGTA CACGTA CATATA CACATA CACGTA CAC
1 CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CACGTA CAC
1160522 ATATTTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.36, C:0.33, G:0.13, T:0.18
Consensus pattern (6 bp):
CACGTA
Found at i:1160522 original size:12 final size:12
Alignment explanation
Indices: 1160431--1160524 Score: 71
Period size: 12 Copynumber: 7.8 Consensus size: 12
1160421 TATACATATG
*
1160431 CATACACATATA
1 CATACACATACA
*
1160443 CATACACATATA
1 CATACACATACA
* *
1160455 CATATACATGCA
1 CATACACATACA
* *
1160467 CATGCACATGCA
1 CATACACATACA
* * *
1160479 CGTGCACGTACA
1 CATACACATACA
* *
1160491 CGTACACGTACA
1 CATACACATACA
*
1160503 TATACACATACA
1 CATACACATACA
*
1160515 CGTACACATA
1 CATACACATA
1160525 TTTCTTTATA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 68 1.00
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (12 bp):
CATACACATACA
Found at i:1160934 original size:119 final size:119
Alignment explanation
Indices: 1160804--1161044 Score: 393
Period size: 118 Copynumber: 2.0 Consensus size: 119
1160794 ATAGTGGTAT
1160804 AAGAGCATGTGGTTCAAATTTGAT-AAAAAATGGATACAAATGAAAGATGAATTGAAG-AA-AAA
1 AAGAGCATGTGGTTCAAA-TTGATAAAAAAATGGATACAAATG-AAGATGAATTGAAGAAATAAA
1160866 GAAATCA-GAAAAAAGTTGAGGGACTAAATTATT-AAAAAAATTGTTATAACAAAGAGA
64 GAAATCATG---AAAGTTGAGGGACTAAATTATTAAAAAAAATTGTTATAACAAAGAGA
1160923 AAGAGCATGTGGTTCAAATTGATAAAAAAATGGATACAAATGAAGATGAATTGAAGAAATAAAGA
1 AAGAGCATGTGGTTCAAATTGATAAAAAAATGGATACAAATGAAGATGAATTGAAGAAATAAAGA
1160988 AATCATGAAAGTTGAGGGACTAAATTATTAAAAAAAAATTGTTATAACAAAGAGA
66 AATCATGAAAGTTGAGGGACTAAATTATT-AAAAAAAATTGTTATAACAAAGAGA
1161043 AA
1 AA
1161045 TTAAAAGAAC
Statistics
Matches: 116, Mismatches: 0, Indels: 11
0.91 0.00 0.09
Matches are distributed among these distances:
118 41 0.35
119 38 0.33
120 36 0.31
121 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.23
Consensus pattern (119 bp):
AAGAGCATGTGGTTCAAATTGATAAAAAAATGGATACAAATGAAGATGAATTGAAGAAATAAAGA
AATCATGAAAGTTGAGGGACTAAATTATTAAAAAAAATTGTTATAACAAAGAGA
Found at i:1171322 original size:30 final size:30
Alignment explanation
Indices: 1171279--1171339 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1171269 GGACCTGTCT
* *
1171279 AGAGGTTACAAAGAACCCCGGTAACTATCC
1 AGAGGTCACAAAGAACCCCGGCAACTATCC
* * *
1171309 AGAGGTCATAAAGATCCTCGGCAACTATCC
1 AGAGGTCACAAAGAACCCCGGCAACTATCC
1171339 A
1 A
1171340 TGTTCCTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (30 bp):
AGAGGTCACAAAGAACCCCGGCAACTATCC
Found at i:1175206 original size:20 final size:20
Alignment explanation
Indices: 1175181--1175220 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1175171 TATTTCCAAA
1175181 ACATATGAACTTTATGACTT
1 ACATATGAACTTTATGACTT
*
1175201 ACATATGAATTTTATGACTT
1 ACATATGAACTTTATGACTT
1175221 TCTTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
ACATATGAACTTTATGACTT
Found at i:1177993 original size:13 final size:13
Alignment explanation
Indices: 1177975--1178001 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1177965 ACTGTGAAGC
1177975 TCGACAGAAGCTT
1 TCGACAGAAGCTT
1177988 TCGACAGAAGCTT
1 TCGACAGAAGCTT
1178001 T
1 T
1178002 TCTTGTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (13 bp):
TCGACAGAAGCTT
Found at i:1190286 original size:32 final size:32
Alignment explanation
Indices: 1190235--1190347 Score: 118
Period size: 32 Copynumber: 3.5 Consensus size: 32
1190225 ATACCACATA
* * *
1190235 TACAAAAATAATGGCATAATACATATTATATG
1 TACATAAATAATGACATAATACATATCATATG
* * *
1190267 TACATAAGTAATGATATAATATATATCATATG
1 TACATAAATAATGACATAATACATATCATATG
* * * *
1190299 TACATAAATGATGACATAATACATGTCACATA
1 TACATAAATAATGACATAATACATATCATATG
* *
1190331 CACATAAATGATGACAT
1 TACATAAATAATGACAT
1190348 GATGAGCATA
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (32 bp):
TACATAAATAATGACATAATACATATCATATG
Found at i:1191538 original size:49 final size:49
Alignment explanation
Indices: 1191466--1191563 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
1191456 TAAACCCTAA
1191466 AAACCAATGGGAAAAATGTATGTGAGGGAGGCAGCTACAGCTGTCTTAT
1 AAACCAATGGGAAAAATGTATGTGAGGGAGGCAGCTACAGCTGTCTTAT
*
1191515 AAACCAATGGG-AAAATGTCATGTGAGGTAGGCAGCTACAGCTGTCTTAT
1 AAACCAATGGGAAAAATGT-ATGTGAGGGAGGCAGCTACAGCTGTCTTAT
1191564 TATTATTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 7 0.15
49 40 0.85
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (49 bp):
AAACCAATGGGAAAAATGTATGTGAGGGAGGCAGCTACAGCTGTCTTAT
Found at i:1191626 original size:15 final size:15
Alignment explanation
Indices: 1191606--1191638 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1191596 GAAGCAATCA
1191606 AAATTTAAAGCTATT
1 AAATTTAAAGCTATT
1191621 AAATTTAAAGCTATT
1 AAATTTAAAGCTATT
1191636 AAA
1 AAA
1191639 ACGTATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
AAATTTAAAGCTATT
Found at i:1191926 original size:24 final size:24
Alignment explanation
Indices: 1191868--1191926 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1191858 AAATATAAAT
*
1191868 AATTATTAAGATATTCAATACATTA
1 AATTATTAAAATATT-AATACATTA
* *
1191893 AA-TATAAAAATATT-ATGCAGTTA
1 AATTATTAAAATATTAATACA-TTA
1191916 AATTATTAAAA
1 AATTATTAAAA
1191927 AGTTCAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 4 0.14
23 5 0.18
24 17 0.61
25 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (24 bp):
AATTATTAAAATATTAATACATTA
Found at i:1193680 original size:2 final size:2
Alignment explanation
Indices: 1193673--1193700 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1193663 AATAAACAAT
1193673 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
1193701 AAGTTTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1199436 original size:19 final size:20
Alignment explanation
Indices: 1199412--1199459 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1199402 AATGATTTTC
* * *
1199412 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
1199431 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
1199451 TTTTGAAAA
1 TTTTGAAAA
1199460 ATAATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:1204413 original size:36 final size:36
Alignment explanation
Indices: 1204360--1204485 Score: 119
Period size: 36 Copynumber: 3.5 Consensus size: 36
1204350 TTTCAAACAT
** * ***
1204360 TATTTTTGAAAGTATATAGTATAT-GCTTTGAAGCCG
1 TATTTTTGAAAACATATAATATATAGCTTTGAA-AAA
* *
1204396 TATTTTTGAAAACATATAATATATAGTTTTTAAAAA
1 TATTTTTGAAAACATATAATATATAGCTTTGAAAAA
** *
1204432 TATTTTTGAAAACATATAATATATATATTTAAAAAA
1 TATTTTTGAAAACATATAATATATAGCTTTGAAAAA
*
1204468 CGATTTTTGAAAACATAT
1 -TATTTTTGAAAACATAT
1204486 TTTTTGAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
36 54 0.71
37 22 0.29
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.42
Consensus pattern (36 bp):
TATTTTTGAAAACATATAATATATAGCTTTGAAAAA
Found at i:1204483 original size:37 final size:36
Alignment explanation
Indices: 1204397--1204485 Score: 135
Period size: 36 Copynumber: 2.4 Consensus size: 36
1204387 TTGAAGCCGT
* *
1204397 ATTTTTGAAAACATATAATATATAGTTTTTAAAAAT
1 ATTTTTGAAAACATATAATATATAGTTTTAAAAAAG
1204433 ATTTTTGAAAACATATAATATATA-TATTTAAAAAACG
1 ATTTTTGAAAACATATAATATATAGT-TTTAAAAAA-G
1204470 ATTTTTGAAAACATAT
1 ATTTTTGAAAACATAT
1204486 TTTTTGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
35 1 0.02
36 32 0.65
37 16 0.33
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (36 bp):
ATTTTTGAAAACATATAATATATAGTTTTAAAAAAG
Found at i:1204517 original size:5 final size:5
Alignment explanation
Indices: 1204507--1204558 Score: 51
Period size: 5 Copynumber: 11.4 Consensus size: 5
1204497 ACATTATGGG
* *
1204507 TTATT TTA-T TTA-T TTA-T TTATT TCATT TTATT TT-TT AT-TT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
1204552 TTATT TT
1 TTATT TT
1204559 TAGGTCCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 18 0.44
5 23 0.56
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:1204560 original size:17 final size:20
Alignment explanation
Indices: 1204507--1204559 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 20
1204497 ACATTATGGG
1204507 TTATTTTATTTATTTATTTAT
1 TTATTTTATTT-TTTATTTAT
1204528 TTCATTTTATTTTTTA-TT-T
1 TT-ATTTTATTTTTTATTTAT
1204547 TTATTTTATTTTT
1 TTATTTTATTTTT
1204560 AGGTCCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.35
19 3 0.10
20 2 0.06
21 6 0.19
22 9 0.29
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (20 bp):
TTATTTTATTTTTTATTTAT
Found at i:1208611 original size:15 final size:15
Alignment explanation
Indices: 1208568--1208613 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1208558 GATATTTTGC
* *
1208568 TGTAATTTGATACGT
1 TGTAATTTGATTCGA
1208583 TGTAATTTGA-TCGA
1 TGTAATTTGATTCGA
*
1208597 TGTAATTTAATTCGA
1 TGTAATTTGATTCGA
1208612 TG
1 TG
1208614 ATGTTATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.46
Consensus pattern (15 bp):
TGTAATTTGATTCGA
Found at i:1211339 original size:174 final size:176
Alignment explanation
Indices: 1211049--1211399 Score: 679
Period size: 174 Copynumber: 2.0 Consensus size: 176
1211039 TATACGCGGT
1211049 TGAGTTTGTATGACAAAGCGGAAGAGATTATCGGCTTCATGAGAGAAGATAAAGTCACATTGAAA
1 TGAGTTTGTATGACAAAGCGGAAGAGATTATCGGCTTCATGAGAGAAGATAAAGTCACATTGAAA
1211114 CAGCTCGGGTTCAAGCCTAACTCGTCCAACTTGGACACGCTACTAACTTTTCAAG-AAAGTACGA
66 CAGCTCGGGTTCAAGCCTAACTCGTCCAACTTGGACACGCTACTAACTTTTCAAGAAAAGTACGA
1211178 GGATGAAGAGGGTGCC-CAGAACACTTGATGATATGCTCAAGATGA
131 GGATGAAGAGGGTGCCACAGAACACTTGATGATATGCTCAAGATGA
1211223 TGAGTTTGTATGACAAAGCGGAAGAGATTATCGGCTTCATGAGAGAAGATAAAGTCACATTGAAA
1 TGAGTTTGTATGACAAAGCGGAAGAGATTATCGGCTTCATGAGAGAAGATAAAGTCACATTGAAA
1211288 CAGCTCGGGTTCAAGCCTAACTCGTCCAACTTGGACACGCTACTAACTTTTCAAGAAAAGTACGA
66 CAGCTCGGGTTCAAGCCTAACTCGTCCAACTTGGACACGCTACTAACTTTTCAAGAAAAGTACGA
1211353 GGATGAAGAGGGTGCCATCAGAACACTTGATGATATGCTCAAGATGA
131 GGATGAAGAGGGTGCCA-CAGAACACTTGATGATATGCTCAAGATGA
1211400 GGTGACAACA
Statistics
Matches: 174, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
174 120 0.69
175 25 0.14
177 29 0.17
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (176 bp):
TGAGTTTGTATGACAAAGCGGAAGAGATTATCGGCTTCATGAGAGAAGATAAAGTCACATTGAAA
CAGCTCGGGTTCAAGCCTAACTCGTCCAACTTGGACACGCTACTAACTTTTCAAGAAAAGTACGA
GGATGAAGAGGGTGCCACAGAACACTTGATGATATGCTCAAGATGA
Found at i:1213425 original size:30 final size:30
Alignment explanation
Indices: 1213385--1213445 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1213375 GGCATAATAC
* * *
1213385 ATATTATATGTACATAAGTAATGATATAAT
1 ATATCATATGTACATAAATAATGACATAAT
*
1213415 ATATCATATGTACATAAATGATGACATAAT
1 ATATCATATGTACATAAATAATGACATAAT
1213445 A
1 A
1213446 CATGTCACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (30 bp):
ATATCATATGTACATAAATAATGACATAAT
Found at i:1214644 original size:49 final size:50
Alignment explanation
Indices: 1214569--1214667 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 50
1214559 TAAACCCTAA
1214569 AAACCAATGGGAAAAATGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
1 AAACCAATGGGAAAAATGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
*
1214619 AAACCAATGGG-AAAATGTCATGTGAGGTAGGCAGCTACAGCTGTCTTAT
1 AAACCAATGGGAAAAATGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
1214668 TATTATTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 37 0.77
50 11 0.23
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.23
Consensus pattern (50 bp):
AAACCAATGGGAAAAATGTCATGTGAGGGAGGCAGCTACAGCTGTCTTAT
Found at i:1214730 original size:15 final size:15
Alignment explanation
Indices: 1214710--1214742 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1214700 GAAGCAATCA
1214710 AAATTTAAAGCTATT
1 AAATTTAAAGCTATT
1214725 AAATTTAAAGCTATT
1 AAATTTAAAGCTATT
1214740 AAA
1 AAA
1214743 ACGTATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
AAATTTAAAGCTATT
Found at i:1215036 original size:24 final size:24
Alignment explanation
Indices: 1214978--1215036 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
1214968 AAATATAAAT
*
1214978 AATTATTAAGATATTCAATACATTA
1 AATTATTAAAATATT-AATACATTA
* *
1215003 AA-TATAAAAATATT-ATGCAGTTA
1 AATTATTAAAATATTAATACA-TTA
1215026 AATTATTAAAA
1 AATTATTAAAA
1215037 AGTTCAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 4 0.14
23 5 0.18
24 17 0.61
25 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (24 bp):
AATTATTAAAATATTAATACATTA
Found at i:1218248 original size:18 final size:19
Alignment explanation
Indices: 1218225--1218263 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1218215 TTTAAATAAT
*
1218225 AATAAAAATTATTAAA-TA
1 AATAAAAACTATTAAAGTA
*
1218243 AATAAAAGCTATTAAAGTA
1 AATAAAAACTATTAAAGTA
1218262 AA
1 AA
1218264 AATAAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (19 bp):
AATAAAAACTATTAAAGTA
Found at i:1226253 original size:16 final size:16
Alignment explanation
Indices: 1226215--1226252 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1226205 CTTTTTCACG
*
1226215 TCTTTCTTCTCTTCTT
1 TCTTTTTTCTCTTCTT
1226231 TCTTTTTTCTCTT-TT
1 TCTTTTTTCTCTTCTT
1226246 T-TTTTTT
1 TCTTTTTT
1226253 TGAACATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TCTTTTTTCTCTTCTT
Found at i:1226264 original size:17 final size:16
Alignment explanation
Indices: 1226244--1226287 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1226234 TTTTTCTCTT
1226244 TTTTTTTTTTGAACATC
1 TTTTTTTTTTGAAC-TC
* *
1226261 TTTTTTTTTCGAACTG
1 TTTTTTTTTTGAACTC
1226277 TTGTTTTTTTT
1 TT-TTTTTTTT
1226288 TTTTTTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.70
Consensus pattern (16 bp):
TTTTTTTTTTGAACTC
Found at i:1230848 original size:31 final size:31
Alignment explanation
Indices: 1230810--1230996 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
1230800 CCCGAAGGAC
* * *
1230810 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1230841 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1230872 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1230903 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1230934 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1230965 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1230996 C
1 C
1230997 CCTCGACCCT
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1231889 original size:21 final size:21
Alignment explanation
Indices: 1231863--1231908 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1231853 AATTCTGTCG
* *
1231863 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
1231884 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
1231905 CTTG
1 CTTG
1231909 CCCAGAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:1238606 original size:16 final size:17
Alignment explanation
Indices: 1238587--1238621 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1238577 GGAAAAATAG
*
1238587 AAAATAAGA-AATAAAT
1 AAAATAAGATAAAAAAT
1238603 AAAATAAGATAAAAAAT
1 AAAATAAGATAAAAAAT
1238620 AA
1 AA
1238622 TTGAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATAAGATAAAAAAT
Found at i:1238835 original size:5 final size:5
Alignment explanation
Indices: 1238733--1238820 Score: 56
Period size: 5 Copynumber: 17.0 Consensus size: 5
1238723 CTAAAAAACT
* * * *
1238733 AAAT- AAATA ATAATA AAATA AAGTA AAATA AAACA ATATTTA AAAGGA
1 AAATA AAATA A-AATA AAATA AAATA AAATA AAATA A-A-ATA AAA-TA
*
1238781 AAAT- AAAT- AAATA AATAGA TAAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AA-ATA -AAATA AAATA AAATA AAATA
1238821 GCAACCTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
4 12 0.18
5 35 0.53
6 15 0.23
7 4 0.06
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:1239912 original size:14 final size:14
Alignment explanation
Indices: 1239893--1239940 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
1239883 AAAATAAGTT
1239893 ATAATAATAAATAA
1 ATAATAATAAATAA
*
1239907 ATAATAATGAATAA
1 ATAATAATAAATAA
*
1239921 ATAATTATAATAATAA
1 ATAATAAT-A-AATAA
1239937 ATAA
1 ATAA
1239941 AAAATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 20 0.69
16 9 0.31
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
ATAATAATAAATAA
Found at i:1240092 original size:29 final size:30
Alignment explanation
Indices: 1240029--1240103 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
1240019 CAAAATGTTT
1240029 TTTTAAAAACTATATAATTTTCAAAAAAAA
1 TTTTAAAAACTATATAATTTTCAAAAAAAA
* * **
1240059 ATTTAAAAACTATATACTTTTC-AAAAATG
1 TTTTAAAAACTATATAATTTTCAAAAAAAA
*
1240088 TTTTAAAAATTATATA
1 TTTTAAAAACTATATA
1240104 TTACATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (30 bp):
TTTTAAAAACTATATAATTTTCAAAAAAAA
Found at i:1240112 original size:38 final size:38
Alignment explanation
Indices: 1240069--1240341 Score: 310
Period size: 38 Copynumber: 7.2 Consensus size: 38
1240059 ATTTAAAAAC
* *
1240069 TATATACTTTTCAAAAATGTTTTAAAAATTATATATTA
1 TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTA
* *
1240107 CATATAAGTTTTCAAAAATGTTTTCAAAAAACTATATATTT
1 TATAT-AGTTTTCAAAAATGTTTT--AAAAACTATATATTA
*
1240148 TATA-AGTTTTCAAAAATGTTTTCAAAACCTATATATTA
1 TATATAGTTTTCAAAAATGTTTT-AAAAACTATATATTA
1240186 TATA-AGTTTTC-AAAATGATTTTAAAAACTATATATTA
1 TATATAGTTTTCAAAAATG-TTTTAAAAACTATATATTA
1240223 TATATA-TTTTCTAAAAATGTTTTAAAAACTATATA-T-
1 TATATAGTTTTC-AAAAATGTTTTAAAAACTATATATTA
** *
1240259 TATATAGTTTTCAAATGTATTTTAAAAACTATATATTA
1 TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTA
* **
1240297 TATACA-TTTTCAAAAATCG-TTTGCAAACTATAATATATA
1 TATATAGTTTTCAAAAAT-GTTTTAAAAACTAT-ATAT-TA
1240336 TATATA
1 TATATA
1240342 TATATATATA
Statistics
Matches: 203, Mismatches: 19, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
36 26 0.13
37 55 0.27
38 58 0.29
39 48 0.24
41 16 0.08
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATAGTTTTCAAAAATGTTTTAAAAACTATATATTA
Found at i:1240119 original size:39 final size:37
Alignment explanation
Indices: 1240076--1240318 Score: 314
Period size: 38 Copynumber: 6.4 Consensus size: 37
1240066 AACTATATAC
*
1240076 TTTTCAAAAATGTTTTAAAAATTATATATTACATATAAG
1 TTTTCAAAAATGTTTTAAAAACTATATATT--ATATAAG
*
1240115 TTTTCAAAAATGTTTTCAAAAAACTATATATTTTATAAG
1 TTTTCAAAAATGTTTT--AAAAACTATATATTATATAAG
*
1240154 TTTTCAAAAATGTTTTCAAAACCTATATATTATATAAG
1 TTTTCAAAAATGTTTT-AAAAACTATATATTATATAAG
1240192 TTTTC-AAAATGATTTTAAAAACTATATATTATATATA-
1 TTTTCAAAAATG-TTTTAAAAACTATATATTATATA-AG
1240229 TTTTCTAAAAATGTTTTAAAAACTATATATTATAT-AG
1 TTTTC-AAAAATGTTTTAAAAACTATATATTATATAAG
** *
1240266 TTTTCAAATGTATTTTAAAAACTATATATTATATACA-
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATA-AG
1240303 TTTTCAAAAATCGTTT
1 TTTTCAAAAAT-GTTT
1240319 GCAAACTATA
Statistics
Matches: 182, Mismatches: 12, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
36 27 0.15
37 43 0.24
38 55 0.30
39 44 0.24
41 13 0.07
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTCAAAAATGTTTTAAAAACTATATATTATATAAG
Found at i:1240336 original size:2 final size:2
Alignment explanation
Indices: 1240325--1240395 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
1240315 GTTTGCAAAC
1240325 TA TA -A 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
*
1240366 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1240396 AAATAAAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1241024 original size:79 final size:81
Alignment explanation
Indices: 1240934--1241092 Score: 189
Period size: 79 Copynumber: 2.0 Consensus size: 81
1240924 ATTTTGTTGA
* **
1240934 CAGATAGCCCTTCTT-GCCTTGAGCTATGTCGTTAACGAT-GTGCC-TTGAGCTGAATGGAATCA
1 CAGATAACCCTT-TTAGCCTTGAGCTATGTCGCAAACGATAGTGCCTTTGAGCTGAATGGAATCA
1240996 AACTCAAAGGTCTTTGG
65 AACTCAAAGGTCTTTGG
* * * * * * *
1241013 CAGATAACCCTTTTAGCCTTGAGTTATGTTGCAAATGATAGTGCCTTTGAGCTGAGTGTAGTCGA
1 CAGATAACCCTTTTAGCCTTGAGCTATGTCGCAAACGATAGTGCCTTTGAGCTGAATGGAATCAA
*
1241078 ACTCGAAGGTCTTTG
66 ACTCAAAGGTCTTTG
1241093 TGTTTCAAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
78 2 0.03
79 30 0.45
80 5 0.08
81 29 0.44
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (81 bp):
CAGATAACCCTTTTAGCCTTGAGCTATGTCGCAAACGATAGTGCCTTTGAGCTGAATGGAATCAA
ACTCAAAGGTCTTTGG
Found at i:1241175 original size:33 final size:33
Alignment explanation
Indices: 1241134--1241216 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
1241124 TCTTTTTGTG
1241134 TGTGTTTCAAGAGAAACGATTTCAAAAGTTTTT
1 TGTGTTTCAAGAGAAACGATTTCAAAAGTTTTT
* *
1241167 TGTGTTTCAAGTGAAACGATTTCAAAGGTTTTT
1 TGTGTTTCAAGAGAAACGATTTCAAAAGTTTTT
1241200 TGTGTTTCAAGAGAAAC
1 TGTGTTTCAAGAGAAAC
1241217 TGTCTCCAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (33 bp):
TGTGTTTCAAGAGAAACGATTTCAAAAGTTTTT
Found at i:1241320 original size:37 final size:36
Alignment explanation
Indices: 1241269--1241544 Score: 245
Period size: 37 Copynumber: 7.8 Consensus size: 36
1241259 CAAAGATTGG
1241269 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
1241306 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1241340 TGTTTCAAGAGAAAGTGTCTCAAAAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
1241377 AG-TGCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
1241413 TGTTTCAAGGAAAAAATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATT
* *
1241442 TGTTTCAAGGGAAACTGTCTCAGGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1241478 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
1241515 TGTTT--TGAGTAAACTAGTCTCAAGCGAGAC
1 TGTTTCAAGAG-AAACT-GTCTCAAGAGAGAC
1241545 GACCCCTTGT
Statistics
Matches: 192, Mismatches: 30, Indels: 34
0.75 0.12 0.13
Matches are distributed among these distances:
28 6 0.03
29 13 0.07
31 1 0.01
32 2 0.01
33 2 0.01
34 29 0.15
35 6 0.03
36 50 0.26
37 83 0.43
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1241349 original size:19 final size:19
Alignment explanation
Indices: 1241288--1241351 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
1241278 AGAAACTGTC
1241288 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGAC--AA-TTTGTT
* *
1241310 TCAAG-G-GA-AA-CTGTC
1 TCAAGAGAGACAATTTGTT
1241325 TCAAGAGAGACAATTTGTT
1 TCAAGAGAGACAATTTGTT
1241344 TCAAGAGA
1 TCAAGAGA
1241352 AAGTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
15 8 0.24
16 1 0.03
17 4 0.12
18 2 0.06
19 11 0.32
20 2 0.06
21 1 0.03
22 5 0.15
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (19 bp):
TCAAGAGAGACAATTTGTT
Found at i:1241359 original size:71 final size:72
Alignment explanation
Indices: 1241269--1241519 Score: 272
Period size: 71 Copynumber: 3.6 Consensus size: 72
1241259 CAAAGATTGG
1241269 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1241334 AC-AATT
66 ACAAATT
* * * * ** *
1241340 TGTTTCAAGAGAAAGTGTCTCAAAAGAGACAAAACTTAG-TGCTAAAAGAAACTGTCTCAAGGGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTC-AAGGGAAACTGTCTCAAGAGA
1241404 GACGAAATT
65 GAC-AAATT
* ** * *
1241413 TGTTTCAAG-GAAA-------AA-ATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-ACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
1241469 GACAAAATT
65 GAC-AAATT
*
1241478 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1241520 TGAGTAAACT
Statistics
Matches: 143, Mismatches: 23, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
64 6 0.04
65 40 0.28
66 6 0.04
70 2 0.01
71 57 0.40
72 4 0.03
73 23 0.16
74 5 0.03
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (72 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
ACAAATT
Found at i:1241492 original size:36 final size:37
Alignment explanation
Indices: 1241440--1241544 Score: 128
Period size: 36 Copynumber: 2.9 Consensus size: 37
1241430 ATTCAAAGAT
*
1241440 TTTGTTTCAAGGGAAACTGTCTC-AGGAGAGACAAAA-
1 TTTGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAAC
1241476 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC
1 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC
* *
1241513 TTTGTTT--TGAGTAAACTAGTCTCAAGCGAGAC
1 TTTGTTTCAAGAG-AAACT-GTCTCAAGGGAGAC
1241545 GACCCCTTGT
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
35 3 0.05
36 36 0.58
37 23 0.37
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (37 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAC
Found at i:1243024 original size:95 final size:95
Alignment explanation
Indices: 1242826--1243088 Score: 321
Period size: 95 Copynumber: 2.7 Consensus size: 95
1242816 GGCTAGCTGA
* * *
1242826 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAAAGGGACAACTTAATATCATTGTATAG-AT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAAAGGGACAAC-TCA-AGC-TT-TATTGTAT
*
1242890 ATTATAATCACTTTTATCAGGCTAGATGAATATT
62 ATTATAATCACCTTTATCAGGCTAGATGAATATT
* * * * * *
1242924 ATCCATAAAGCTGGGGCATTTAACCAAATGCTCTACAGGGATAACTCAAGCTTTATTGTACATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCAAGCTTTATTGTATATTA
* *
1242989 TAATCACCTTTATCAGGCTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGATGAATATT
* * * * *
1243019 ATCCATAAAGCCGGGGCGTTTAACCAATTTCTTTAGAGAGACATCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCAAGCTTTATTGTATAT-T
1243084 ATAAT
65 ATAAT
1243089 ATTATAATCT
Statistics
Matches: 141, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
94 4 0.03
95 87 0.62
96 8 0.06
97 2 0.01
98 40 0.28
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAAAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGATGAATATT
Found at i:1246793 original size:28 final size:29
Alignment explanation
Indices: 1246743--1246798 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
1246733 CGATATTAAA
* *
1246743 AAAGGGAAAAAATGATAACATAATAAATC
1 AAAGGGAAAAAATGATAAAATAAGAAATC
*
1246772 AAAGGGGAAAAAT-ATAAAATAAGAAAT
1 AAAGGGAAAAAATGATAAAATAAGAAAT
1246799 AAATAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.64, C:0.04, G:0.16, T:0.16
Consensus pattern (29 bp):
AAAGGGAAAAAATGATAAAATAAGAAATC
Found at i:1246818 original size:16 final size:15
Alignment explanation
Indices: 1246778--1246820 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1246768 AATCAAAGGG
1246778 GAAAAATATAAAATAA
1 GAAAAA-ATAAAATAA
1246794 GAAATAAATAAAATAA
1 GAAA-AAATAAAATAA
*
1246810 GGTAAAAATAA
1 -GAAAAAATAA
1246821 TAATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (15 bp):
GAAAAAATAAAATAA
Found at i:1246960 original size:19 final size:18
Alignment explanation
Indices: 1246923--1247016 Score: 72
Period size: 18 Copynumber: 5.3 Consensus size: 18
1246913 AAGCCTCTAA
1246923 AAAACTAAATAAA-AAAAT
1 AAAA-TAAATAAATAAAAT
*
1246941 AATAATAAATAAGTAAAAT
1 AA-AATAAATAAATAAAAT
* ** *
1246960 AAAA-CAATATTTAAAAGG
1 AAAATAAATAAATAAAA-T
1246978 AAAATAAATAAAT-AAAT
1 AAAATAAATAAATAAAAT
*
1246995 --AATATATAAATAAAAT
1 AAAATAAATAAATAAAAT
1247011 AAAATA
1 AAAATA
1247017 GCAAACTAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
15 10 0.17
16 4 0.07
17 9 0.15
18 22 0.37
19 14 0.24
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAATAAATAAAAT
Found at i:1246968 original size:24 final size:23
Alignment explanation
Indices: 1246936--1246985 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1246926 ACTAAATAAA
* *
1246936 AAAATAATAATAAATAAGTAAAAT
1 AAAACAATAATAAA-AAGGAAAAT
* *
1246960 AAAACAATATTTAAAAGGAAAAT
1 AAAACAATAATAAAAAGGAAAAT
1246983 AAA
1 AAA
1246986 TAAATAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (23 bp):
AAAACAATAATAAAAAGGAAAAT
Found at i:1248101 original size:3 final size:3
Alignment explanation
Indices: 1248093--1248132 Score: 53
Period size: 3 Copynumber: 12.3 Consensus size: 3
1248083 AAAATAAGTT
1248093 ATA ATA ATAA ATA ATA ATA ATGA ATAA ATA ATA ATA ATA A
1 ATA ATA AT-A ATA ATA ATA AT-A AT-A ATA ATA ATA ATA A
1248133 ATATTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
3 25 0.74
4 9 0.26
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1248106 original size:10 final size:10
Alignment explanation
Indices: 1248093--1248135 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
1248083 AAAATAAGTT
1248093 ATAATAATAA
1 ATAATAATAA
1248103 ATAATAAT-A
1 ATAATAATAA
1248112 ATGAATAA-ATA
1 AT-AATAATA-A
1248123 ATAATAATAA
1 ATAATAATAA
1248133 ATA
1 ATA
1248136 TTTAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 3 0.10
10 22 0.76
11 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
ATAATAATAA
Done.