Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008183.1 Hibiscus syriacus cultivar Beakdansim tig00110783_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: 2364390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1591873 original size:24 final size:23
Alignment explanation
Indices: 1591829--1591885 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
1591819 AAAAATAAAA
1591829 ATTAAACGAACTTATAAATGAATC
1 ATTAAACGAACTTATAAATGAA-C
* **
1591853 ATTAAACGAACTTGTTCATGAAC
1 ATTAAACGAACTTATAAATGAAC
1591876 A-TAAACGAAC
1 ATTAAACGAAC
1591886 GAGTCAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 9 0.30
23 2 0.07
24 19 0.63
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (23 bp):
ATTAAACGAACTTATAAATGAAC
Found at i:1600465 original size:4 final size:4
Alignment explanation
Indices: 1600456--1600482 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1600446 TTCAACTATG
1600456 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
1600483 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1608089 original size:20 final size:20
Alignment explanation
Indices: 1608064--1608116 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1608054 GACCAACAAA
1608064 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
1608084 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
1608104 TTCGCAACGCGAA
1 TTCGCAACGCGAA
1608117 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:1608154 original size:21 final size:21
Alignment explanation
Indices: 1608125--1608167 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1608115 AATATGTAAA
1608125 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
1608146 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
1608167 T
1 T
1608168 TGCAACGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1608194 original size:20 final size:20
Alignment explanation
Indices: 1608169--1608213 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1608159 TTCCAAATTT
1608169 GCAACGCAAATATGTAAATC
1 GCAACGCAAATATGTAAATC
*
1608189 GCAACGCAAATTTGTAAATC
1 GCAACGCAAATATGTAAATC
1608209 GCAAC
1 GCAAC
1608214 ACAGAAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (20 bp):
GCAACGCAAATATGTAAATC
Found at i:1608235 original size:20 final size:20
Alignment explanation
Indices: 1608210--1608248 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1608200 TTGTAAATCG
*
1608210 CAACACAGAAGTCAAATTCA
1 CAACACAAAAGTCAAATTCA
1608230 CAACACAAAAGTCAAATTC
1 CAACACAAAAGTCAAATTC
1608249 GCAATGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.26, G:0.08, T:0.15
Consensus pattern (20 bp):
CAACACAAAAGTCAAATTCA
Found at i:1608303 original size:20 final size:20
Alignment explanation
Indices: 1608280--1608340 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
1608270 CATAATTGAA
1608280 TTTCAAATTCGCAACTAGAT
1 TTTCAAATTCGCAACTAGAT
* *
1608300 TTTCGAATTCGCAAC-ACGAA
1 TTTCAAATTCGCAACTA-GAT
*
1608320 TTT-AATTTCGCAA-TAGAT
1 TTTCAAATTCGCAACTAGAT
1608338 TTT
1 TTT
1608341 AGTTTCGCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 5 0.15
19 10 0.29
20 19 0.56
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
TTTCAAATTCGCAACTAGAT
Found at i:1608341 original size:18 final size:18
Alignment explanation
Indices: 1608287--1608350 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1608277 GAATTTCAAA
1608287 TTCGCAACTAGATTTTCGAA-
1 TTCGCAA-TAGATTTT--AAT
* *
1608307 TTCGCAACACGAATTTAAT
1 TTCGCAATA-GATTTTAAT
*
1608326 TTCGCAATAGATTTTAGT
1 TTCGCAATAGATTTTAAT
1608344 TTCGCAA
1 TTCGCAA
1608351 CATAAATGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 16 0.43
19 9 0.24
20 12 0.32
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (18 bp):
TTCGCAATAGATTTTAAT
Found at i:1608525 original size:16 final size:15
Alignment explanation
Indices: 1608490--1608528 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1608480 TCCCCGTCTC
*
1608490 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1608505 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1608521 TAATTTTT
1 TAATTTTT
1608529 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1609145 original size:12 final size:12
Alignment explanation
Indices: 1609124--1609157 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1609114 ACCACATTTC
*
1609124 CAATACCAAACA
1 CAATATCAAACA
1609136 CAATATCAAACA
1 CAATATCAAACA
*
1609148 CAATCTCAAA
1 CAATATCAAA
1609158 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:1609310 original size:24 final size:24
Alignment explanation
Indices: 1609283--1609336 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1609273 GCATTCGAAA
1609283 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1609307 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1609331 TTTGAT
1 TTTGAT
1609337 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1611619 original size:18 final size:18
Alignment explanation
Indices: 1611596--1611631 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1611586 AAGCAAAAGG
*
1611596 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1611614 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1611632 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1611983 original size:20 final size:20
Alignment explanation
Indices: 1611960--1612000 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1611950 GCGTTGCGAT
*
1611960 AGTCAAATTCGTAACACGAA
1 AGTCAAATTCGCAACACGAA
*
1611980 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACACGAA
1612000 A
1 A
1612001 TCGCAAACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
AGTCAAATTCGCAACACGAA
Found at i:1612256 original size:27 final size:28
Alignment explanation
Indices: 1612208--1612264 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
1612198 ATAATTCGTA
*
1612208 TTTACACATCAAATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
1612236 TTTACAAATC-AATTAAACAAATCAACT
1 TTTACAAATCAAATTAAACAAATCAACT
1612263 TT
1 TT
1612265 CAATGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAACT
Found at i:1612257 original size:13 final size:13
Alignment explanation
Indices: 1612219--1612260 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1612209 TTACACATCA
1612219 AATTAAACAAATC
1 AATTAAACAAATC
**
1612232 AACTTTTACAAATC
1 AA-TTAAACAAATC
1612246 AATTAAACAAATC
1 AATTAAACAAATC
1612259 AA
1 AA
1612261 CTTTCAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (13 bp):
AATTAAACAAATC
Found at i:1613687 original size:21 final size:21
Alignment explanation
Indices: 1613607--1613681 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
1613597 GTGAATCGGG
* * *
1613607 CTCTTGAACGGTGGGCGGGAC
1 CTCTTGAACGATGAGAGGGAC
*
1613628 CTCTTGAACGATGACAGGGAC
1 CTCTTGAACGATGAGAGGGAC
* * *
1613649 CTCTTCAATGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGAC
1613670 CTCTTGAACGAT
1 CTCTTGAACGAT
1613682 AGGAGGCGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGAC
Found at i:1616202 original size:21 final size:21
Alignment explanation
Indices: 1616177--1616239 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1616167 CCGTTTGACA
*
1616177 GGGGGAAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
1616198 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
**
1616219 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
1616240 AGCAATCTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.17, C:0.29, G:0.38, T:0.16
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:1617715 original size:19 final size:20
Alignment explanation
Indices: 1617668--1617715 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1617658 TCTAAATCCT
*
1617668 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* * *
1617688 CTTTGAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1617707 TTTTCAAAA
1 TTTTCAAAA
1617716 GAAAATCGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1618527 original size:23 final size:23
Alignment explanation
Indices: 1618501--1618553 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1618491 AATGCACCGA
1618501 AGTGCCACATAGAATTGCACAGT
1 AGTGCCACATAGAATTGCACAGT
* *
1618524 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACAGT
1618547 AGTGCCA
1 AGTGCCA
1618554 TATAATAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACAGT
Found at i:1618754 original size:103 final size:102
Alignment explanation
Indices: 1618569--1618785 Score: 389
Period size: 103 Copynumber: 2.1 Consensus size: 102
1618559 TAATGTCCAT
* *
1618569 AAGGACCACATACCATTCCTTAAGAATCATATACATATACTAGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATACCATTCCTTAAGAATCATACACATATACAAGGATCAAGTATGTGTCTCACCAG
1618634 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1618671 AAGGACCACATATCATTCCTTAAGAATCATACACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATACCATTCCTTAAGAATCATACACATAT-ACAAGGATCAAGTATGTGTCTCACCA
1618736 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1618774 AAGGACCACATA
1 AAGGACCACATA
1618786 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 36 0.33
103 74 0.67
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (102 bp):
AAGGACCACATACCATTCCTTAAGAATCATACACATATACAAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1623703 original size:23 final size:23
Alignment explanation
Indices: 1623669--1623729 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1623659 CTCGTGTAAA
*
1623669 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
1623692 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1623715 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1623730 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1623924 original size:103 final size:102
Alignment explanation
Indices: 1623745--1623960 Score: 405
Period size: 103 Copynumber: 2.1 Consensus size: 102
1623735 TAATGTCCAT
*
1623745 AGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGATCAAGTATGTGTCTCACCAGA
1 AGGACCACATATCATTCCTTAAGAATCATATACATATACAAGGATCAAGTATGTGTCTCACCAGA
1623810 CTTCACACATGTTCCAAAGAATACATATATGTCCCGA
66 CTTCACACATGTTCCAAAGAATACATATATGTCCCGA
*
1623847 AGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGGATCAAGTATGTGTCTCACCAG
1623912 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGA
65 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGA
1623950 AGGACCACATA
1 AGGACCACATA
1623961 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 37 0.33
103 74 0.67
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (102 bp):
AGGACCACATATCATTCCTTAAGAATCATATACATATACAAGGATCAAGTATGTGTCTCACCAGA
CTTCACACATGTTCCAAAGAATACATATATGTCCCGA
Found at i:1625663 original size:21 final size:21
Alignment explanation
Indices: 1625639--1625683 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1625629 TTTTGTTCGT
* *
1625639 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1625660 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1625681 TTG
1 TTG
1625684 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1627634 original size:21 final size:21
Alignment explanation
Indices: 1627608--1627649 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1627598 CCATTTGACA
*
1627608 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGATACCCCCTG
*
1627629 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCGATACCCCCTG
1627650 AGCAATCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.29, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGGGAATCGATACCCCCTG
Found at i:1628087 original size:19 final size:20
Alignment explanation
Indices: 1628049--1628089 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1628039 ACTTAAATTA
*
1628049 GCAATGCGAAAATAAAAATC
1 GCAACGCGAAAATAAAAATC
*
1628069 GCAACGCGAAACT-AAAATC
1 GCAACGCGAAAATAAAAATC
1628088 GC
1 GC
1628090 GTTGTGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (20 bp):
GCAACGCGAAAATAAAAATC
Found at i:1628503 original size:22 final size:22
Alignment explanation
Indices: 1628475--1628533 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
1628465 AGATGGAGAT
1628475 AGACGGATTTCGCCGGAGATAG
1 AGACGGATTTCGCCGGAGATAG
** *
1628497 AGACGGATTTCATCGGAGATGG
1 AGACGGATTTCGCCGGAGATAG
* *
1628519 GGACGGATGTCGCCG
1 AGACGGATTTCGCCG
1628534 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATAG
Found at i:1628665 original size:20 final size:20
Alignment explanation
Indices: 1628640--1628748 Score: 125
Period size: 20 Copynumber: 5.5 Consensus size: 20
1628630 ATTGTGTTTT
1628640 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
*
1628660 GCGTTGCGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTTC
* * *
1628680 GTGTTGCAAATTTGACTATC
1 GCGTTGCGAATTTGACTTTC
1628700 GCGTTGCGAATTTGAC-TTC
1 GCGTTGCGAATTTGACTTTC
*
1628719 TGTGTTGCG-ATTT-ACATATTC
1 -GCGTTGCGAATTTGAC-T-TTC
1628740 GCGTTGCGA
1 GCGTTGCGA
1628749 TTTACAGATT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 63 0.85
21 3 0.04
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:1628680 original size:40 final size:40
Alignment explanation
Indices: 1628636--1628748 Score: 158
Period size: 40 Copynumber: 2.8 Consensus size: 40
1628626 TAATATTGTG
*
1628636 TTTTGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGAC
1 TTTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGAC
* *
1628676 TTTTGTGTTGCAAATTTGACTATCGCGTTGCGAATTTGAC
1 TTTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGAC
*
1628716 TTCTGTGTTGCG-ATTT-ACATATTCGCGTTGCGA
1 TTTTGTGTTGCGAATTTGAC-T-TTCGCGTTGCGA
1628749 TTTACAGATT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 58 0.89
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (40 bp):
TTTTGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGAC
Found at i:1628749 original size:20 final size:20
Alignment explanation
Indices: 1628722--1628768 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1628712 TGACTTCTGT
* *
1628722 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGA
1628742 GTTGCGATTTACAGATTCGA
1 GTTGCGATTTACAGATTCGA
1628762 GTTGCGA
1 GTTGCGA
1628769 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGA
Found at i:1629963 original size:250 final size:250
Alignment explanation
Indices: 1629522--1630023 Score: 977
Period size: 250 Copynumber: 2.0 Consensus size: 250
1629512 CCACCAGGAA
1629522 AAGCTTGTCCATTCAAGAATATAATGCAAGAAGATCGACATCGTATGCAGTCCATTCGAAACGAT
1 AAGCTTGTCCATTCAAGAATATAATGCAAGAAGATCGACATCGTATGCAGTCCATTCGAAACGAT
1629587 TAACATCCATTTATGGGAAACCGAAAATGTCATTATCTTTAACTGGAATGCTCAAATTATTTCAA
66 TAACATCCATTTATGGGAAACCGAAAATGTCATTATCTTTAACTGGAATGCTCAAATTATTTCAA
1629652 GATTGGCCACACAAGTGCACAAACTAAGACAATTGTTCAACAAAGAAATCTTATGCTCTGCAACA
131 GATTGGCCACACAAGTGCACAAACTAAGACAATTGTTCAACAAAGAAATCTTATGCTCTGCAACA
*
1629717 TGTTGTGCAGTCTACCTCACCTAACCTTCTTTTTCTGGCTTTGGCTCTGCACCGC
196 TGTTGTGCAGTCTACCTCACCTAACCTTCTTTTTCTGCCTTTGGCTCTGCACCGC
1629772 AAGCTTGTCCATTCAAGAATATAATGCAAGAAGATCGACATCGTATGCAGTCCATTCGAAACGAT
1 AAGCTTGTCCATTCAAGAATATAATGCAAGAAGATCGACATCGTATGCAGTCCATTCGAAACGAT
1629837 TAACATCCATTTATGGGAAACCGAAAATGTCATTATCTTTAACTGGAATGCTCAAATTATTTCAA
66 TAACATCCATTTATGGGAAACCGAAAATGTCATTATCTTTAACTGGAATGCTCAAATTATTTCAA
*
1629902 GATTGGCCACACAAGTGCACAAACTAAGACAATTGTTCAAGAAAGAAATCTTATGCTCTGCAACA
131 GATTGGCCACACAAGTGCACAAACTAAGACAATTGTTCAACAAAGAAATCTTATGCTCTGCAACA
*
1629967 TGTTGTGCAGTCTACCTCACCTAACCTTCTTTTTCTGCCTTTGGCTCTGCACTGC
196 TGTTGTGCAGTCTACCTCACCTAACCTTCTTTTTCTGCCTTTGGCTCTGCACCGC
1630022 AA
1 AA
1630024 ACGAAATTTT
Statistics
Matches: 249, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
250 249 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (250 bp):
AAGCTTGTCCATTCAAGAATATAATGCAAGAAGATCGACATCGTATGCAGTCCATTCGAAACGAT
TAACATCCATTTATGGGAAACCGAAAATGTCATTATCTTTAACTGGAATGCTCAAATTATTTCAA
GATTGGCCACACAAGTGCACAAACTAAGACAATTGTTCAACAAAGAAATCTTATGCTCTGCAACA
TGTTGTGCAGTCTACCTCACCTAACCTTCTTTTTCTGCCTTTGGCTCTGCACCGC
Found at i:1635248 original size:25 final size:25
Alignment explanation
Indices: 1635227--1635275 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1635217 TTTATTTTTA
1635227 TTTTC-TAAAATTTTATAAATTTATT
1 TTTTCTTAAAA-TTTATAAATTTATT
*
1635252 TTTTCTTTAAATTTATAAATTTAT
1 TTTTCTTAAAATTTATAAATTTAT
1635276 CCCTTCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTCTTAAAATTTATAAATTTATT
Found at i:1636895 original size:36 final size:36
Alignment explanation
Indices: 1636848--1636920 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1636838 AAATTCCCCC
1636848 TCGCTTATCTCATGCTTGTCCTCAAGTATGATATAA
1 TCGCTTATCTCATGCTTGTCCTCAAGTATGATATAA
1636884 TCGCTTATCTCATGCTTGTCCTCAAGTATGATATAA
1 TCGCTTATCTCATGCTTGTCCTCAAGTATGATATAA
1636920 T
1 T
1636921 TAAATAAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (36 bp):
TCGCTTATCTCATGCTTGTCCTCAAGTATGATATAA
Found at i:1639239 original size:15 final size:14
Alignment explanation
Indices: 1639219--1639279 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 14
1639209 TGCTTCATTG
1639219 AAATAAAATGAAATA
1 AAATAAAAT-AAATA
1639234 AAATAAAATAAAT-
1 AAATAAAATAAATA
* * *
1639247 AAA-CAAACAAACA
1 AAATAAAATAAATA
1639260 AAAT-AAATAAAT-
1 AAATAAAATAAATA
1639272 AAATAAAA
1 AAATAAAA
1639280 ATATAACGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 10 0.26
13 15 0.39
14 4 0.11
15 9 0.24
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:1644741 original size:42 final size:43
Alignment explanation
Indices: 1644686--1644768 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
1644676 CATATTTGAT
1644686 TAGTTAAATATTAATA-TATAAGTATGAGCTAAGCAATCTTAG
1 TAGTTAAATATTAATATTATAAGTATGAGCTAAGCAATCTTAG
*
1644728 TAGTTAAATATTAATATTATAAGTATTAGCTAAGCAATCTT
1 TAGTTAAATATTAATATTATAAGTATGAGCTAAGCAATCTT
1644769 GTAAATTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 16 0.41
43 23 0.59
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (43 bp):
TAGTTAAATATTAATATTATAAGTATGAGCTAAGCAATCTTAG
Found at i:1659442 original size:3 final size:3
Alignment explanation
Indices: 1659434--1659459 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1659424 TTACTTGCTT
1659434 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
1659460 TTCACATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1659869 original size:13 final size:14
Alignment explanation
Indices: 1659845--1659873 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1659835 CAAACATTAT
1659845 TTGAATTTTTTTAG
1 TTGAATTTTTTTAG
1659859 TTGAA-TTTTTTAG
1 TTGAATTTTTTTAG
1659872 TT
1 TT
1659874 TATGTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (14 bp):
TTGAATTTTTTTAG
Found at i:1660378 original size:3 final size:3
Alignment explanation
Indices: 1660370--1660421 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
1660360 ACCCTCTTTC
* * * * *
1660370 TCA TCA TCA TCA TCA TCA TCG TCG CCA TCA TAA TCA TCA TCA TCT TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1660418 TCA T
1 TCA T
1660422 GGGTTTAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1671726 original size:3 final size:3
Alignment explanation
Indices: 1671718--1671758 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1671708 TTATCTATAT
1671718 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1671759 TGTTAAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1677037 original size:13 final size:13
Alignment explanation
Indices: 1677019--1677043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1677009 TTTTTCTCCA
1677019 AACCGGTTAAAAT
1 AACCGGTTAAAAT
1677032 AACCGGTTAAAA
1 AACCGGTTAAAA
1677044 AAAATCCGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
AACCGGTTAAAAT
Found at i:1689118 original size:17 final size:17
Alignment explanation
Indices: 1689096--1689132 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1689086 AATTCGCCCC
1689096 CATAGCATAAAATATTA
1 CATAGCATAAAATATTA
1689113 CATAGCATAAAATATTA
1 CATAGCATAAAATATTA
1689130 CAT
1 CAT
1689133 TCATCCCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (17 bp):
CATAGCATAAAATATTA
Found at i:1692447 original size:22 final size:24
Alignment explanation
Indices: 1692421--1692479 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 24
1692411 TTTAATCACT
1692421 TTAATA-TTTTTTA-A-AGTTTAGG
1 TTAATAGTTTTTTACATAG-TTAGG
1692443 TTAATTAGTTTTTTTACATAGTTAGG
1 TTAA-TAG-TTTTTTACATAGTTAGG
1692469 TTAATTAGTTT
1 TTAA-TAGTTT
1692480 GATTATAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
25 10 0.31
26 14 0.44
27 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.56
Consensus pattern (24 bp):
TTAATAGTTTTTTACATAGTTAGG
Found at i:1694076 original size:16 final size:18
Alignment explanation
Indices: 1694038--1694079 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
1694028 AAATAAATAT
1694038 TAAATAAATTGAAGAAAGA
1 TAAA-AAATTGAAGAAAGA
1694057 -AAAAAATTG-AGAAA-A
1 TAAAAAATTGAAGAAAGA
1694072 TAAAAAAT
1 TAAAAAAT
1694080 AAGGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.05
16 12 0.55
17 6 0.27
18 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (18 bp):
TAAAAAATTGAAGAAAGA
Found at i:1695776 original size:164 final size:162
Alignment explanation
Indices: 1695570--1696772 Score: 1238
Period size: 164 Copynumber: 7.3 Consensus size: 162
1695560 AGGTCTTCGG
* * * * * * * * *
1695570 TTGGCAGATAGCCCTTCTAGACTTAGGCTATACTGTAAATGATATGGCTTGGAGATGAGTGTAAT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * *
1695635 CGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAAGCTATGCTGTAAATGATGTG
66 CGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
* *
1695700 CCTTGGAGCTGAACATAGTCGAACTCGAAGGTCT
130 CCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * *
1695734 TTGGCAGATAGCCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGACGTT-GAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
* * * * * *
1695798 TTGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
65 TCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
1695863 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
129 GCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * * * *
1695898 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
1 TT-G-G-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCG
* ** * * *
1695963 TAATCGAACTCG--GGGGTAT-TTGGCAGATAGCCCTTCTAGACTTAAGTTATGCTGCAAATGAT
62 TAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGAT
* *
1696025 GTGCCATTGAGCTGAGCGTAGTCTAACTCAAAGGTCTTTT
127 GTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTC---T
* * *
1696065 GTTGGCATACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
1 -TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * * * *
1696130 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAG-TCATGCTGTAAATGATAT
65 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGCT-ATGCTGCAAATGATGT
* * * * **
1696194 GCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCT
129 G-CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * * * *
1696230 TTGACAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTT-GAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
* * * * *
1696294 TCGAACTCAAAGATCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
65 TCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
1696359 GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCT
129 GCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * * * *
1696394 TTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
1 TTG--G-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCG
* ** * *
1696459 TAATCGAACTCGGGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
62 TAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGAT
*
1696521 GTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCT
127 GTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCT
* * * * * *
1696558 TTGGCATATAGCCCTTCTCGACTTAA-TCTATGTTGCAAATGATGTGCCTTGGAGCTTAGCGTAG
1 TTGGCAGATAACCCTTCTAGACTTAAGT-TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * *
1696622 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTACAAATGATGT
65 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
*
1696687 GCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCT
129 GCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCT
** * * *
1696722 TTGGTGACAGATAACCCTTCTATCCTTGAGTTATACTGTAAATGATATGCC
1 TT-G-G-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC
1696773 CTCGAAGCTG
Statistics
Matches: 857, Mismatches: 147, Indels: 67
0.80 0.14 0.06
Matches are distributed among these distances:
160 26 0.03
161 32 0.04
162 2 0.00
164 476 0.56
165 98 0.11
166 11 0.01
167 149 0.17
168 63 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (162 bp):
TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGC
CTTGAGCTGAGCGTAGTCGAACTCGAAGGTCT
Found at i:1695988 original size:248 final size:248
Alignment explanation
Indices: 1695550--1696713 Score: 1606
Period size: 248 Copynumber: 4.7 Consensus size: 248
1695540 GTGAATGTAA
** ** * * * * * *
1695550 TTGAACTCGGAGGTCTTCGGTTGGCAGATAGCCCTTCTAGACTTAGGCTATACTGTAAATGATAT
1 TTGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
* * * * * * * * * *
1695615 GGCTTGGAGATGAGTGTAATCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGA
* * * * *** * **
1695680 GCTATGCTGTAAATGATGTG-CCTTGGAGCTGAACATAGTCGAACTCGAAGGTCTTTGGCAGATA
130 GTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
* * *
1695744 GCCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGACGTTGAGCTGAGCGTAG
195 GCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
*
1695798 TTGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TTGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1695863 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
*
1695928 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTATTTGGCAGATAG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
* * *
1695993 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCATTGAGCTGAGCGTAG
196 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
* *
1696046 TCT-AACTCAAAGGTCTTTTGTTGGCATACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATA
1 T-TGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATA
*
1696110 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGA
65 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGA
* * *
1696175 GTCATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGACAGATA
130 GTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATA
*
1696240 GCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAG
195 GCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
* *
1696294 TCGAACTCAAAGATCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TTGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
* *
1696359 GCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
1696424 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
1696489 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
196 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
* * * * * * *
1696542 TCGAACTCAAAGGTC---T-TTGGCATATAGCCCTTCTCGACTTAA-TCTATGTTGCAAATGATG
1 TTGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGT-TGTGCTGCAAATGATA
* * * * * *
1696602 TGCCTTGGAGCTTAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
65 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTG
* ** * * * * *
1696667 AGCTATGCTACAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTC
129 AGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
1696714 AAAGGTCTTT
Statistics
Matches: 834, Mismatches: 77, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
243 1 0.00
244 90 0.11
245 42 0.05
247 38 0.05
248 662 0.79
249 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (248 bp):
TTGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAG
CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
Found at i:1696900 original size:116 final size:116
Alignment explanation
Indices: 1696677--1696889 Score: 300
Period size: 117 Copynumber: 1.8 Consensus size: 116
1696667 AGCTATGCTA
* * *
1696677 CAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTC
1 CAAATGATATGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGACAGACAACCCTTC
** * *
1696742 TATCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCG
66 TAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCG
* * * *
1696793 CAAATGATATGTCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGCAGACAACCTTT
1 CAAATGATATGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTC-TTTGGTGACAGACAACCCTT
* *
1696858 CTAGACTTAAGTTGTGCTGCAAATGATATGCC
65 CTAGACTTAAGTTATACTGCAAATGATATGCC
1696890 TGAGAGCTGA
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
116 41 0.49
117 42 0.51
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (116 bp):
CAAATGATATGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTGACAGACAACCCTTC
TAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCG
Found at i:1696936 original size:200 final size:200
Alignment explanation
Indices: 1696592--1696992 Score: 626
Period size: 200 Copynumber: 2.0 Consensus size: 200
1696582 AATCTATGTT
* * * *
1696592 GCAAATGATGTGCCTTGGAGCTTAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCT
1 GCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAACCCT
* * *
1696657 TCTCGACTTAAGCTATGCTACAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCT
66 TCTAGACTTAAGCTATGCTACAAATGATATGCCGTAGAGCTGAGCGTAGTCGAACTCAAAGGTCT
*
1696722 TTGGTGACAGATAACCCTTCTATCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTG
131 TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTG
1696787 TAATC
196 TAATC
* * *
1696792 GCAAATGATATGTCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGCAGACAACCT
1 GCAAATGATATG-CCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAACCC
* * * *
1696856 TTCTAGACTTAAGTTGTGCTGCAAATGATATGCC-TGAGAGCTGAGCGTAGTCGAACTCGAAGGT
65 TTCTAGACTTAAGCTATGCTACAAATGATATGCCGT-AGAGCTGAGCGTAGTCGAACTCAAAGGT
*
1696920 CTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAG
129 CTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAG
1696985 TGTAATC
194 TGTAATC
1696992 G
1 G
1696993 AACTTGGGGG
Statistics
Matches: 183, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
199 1 0.01
200 179 0.98
201 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (200 bp):
GCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAACCCT
TCTAGACTTAAGCTATGCTACAAATGATATGCCGTAGAGCTGAGCGTAGTCGAACTCAAAGGTCT
TTGGTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTG
TAATC
Found at i:1697119 original size:84 final size:83
Alignment explanation
Indices: 1696792--1697130 Score: 310
Period size: 84 Copynumber: 4.1 Consensus size: 83
1696782 GAGTGTAATC
* * * * *
1696792 GCAAATGATATGTCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGCAGACAACCT
1 GCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCC
* * *
1696856 TTCTAGACTTAAGTTGTGCT
64 TTCTAGACTTAAGCTATACT
* **
1696876 GCAAATGATATGCC-TGAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGATAGATAACCCT
1 GCAAATGATATGCCTTG-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCT
* * *
1696940 TCTAGCCTTGAGTTATACT
65 TCTAGACTTAAGCTATACT
* * * * * * ** *
1696959 GTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTC--T-TTGGCAGATAGCCCT
1 GCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCT
* *
1697021 TCTCGACTTAAGCTATGCT
65 TCTAGACTTAAGCTATACT
* * *
1697040 GCAAATGATGTGCCTTGGAGATGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCT
1 GCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCT
* * * *
1697105 TCTTGTCTTGAGCTATATT
65 TCTAGACTTAAGCTATACT
1697124 GCAAATG
1 GCAAATG
1697131 TTGTCTTAAA
Statistics
Matches: 201, Mismatches: 46, Indels: 16
0.76 0.17 0.06
Matches are distributed among these distances:
80 25 0.12
81 35 0.17
82 2 0.01
83 42 0.21
84 96 0.48
85 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (83 bp):
GCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTT
CTAGACTTAAGCTATACT
Found at i:1704557 original size:60 final size:60
Alignment explanation
Indices: 1704493--1704636 Score: 209
Period size: 60 Copynumber: 2.4 Consensus size: 60
1704483 GAGTCCTGTG
* * *
1704493 ACTATTAAATGTTTCGAAATGGTCTCAT-GACTATAAGACGTTATTTTGTTGAGTCATCTA
1 ACTATTAAAAGTTTCAAAATAGTCTC-TCGACTATAAGACGTTATTTTGTTGAGTCATCTA
* *
1704553 ACTATTAAAAGTTTCAAAATAGTCTCTCGACTATAAGACGTTATTTTGTTGTGTCCTCTA
1 ACTATTAAAAGTTTCAAAATAGTCTCTCGACTATAAGACGTTATTTTGTTGAGTCATCTA
**
1704613 ACTATTAAAAGTTAAAAAATAGTC
1 ACTATTAAAAGTTTCAAAATAGTC
1704637 ATATGATTAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
59 1 0.01
60 75 0.99
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (60 bp):
ACTATTAAAAGTTTCAAAATAGTCTCTCGACTATAAGACGTTATTTTGTTGAGTCATCTA
Found at i:1705988 original size:19 final size:19
Alignment explanation
Indices: 1705964--1706008 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1705954 CAATAAGATG
1705964 AAGAAAATAGAAGAGATTA
1 AAGAAAATAGAAGAGATTA
1705983 AAGAAAATAGAAGAGATTA
1 AAGAAAATAGAAGAGATTA
1706002 AAGAAAA
1 AAGAAAA
1706009 GATGAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (19 bp):
AAGAAAATAGAAGAGATTA
Found at i:1707257 original size:28 final size:28
Alignment explanation
Indices: 1707216--1707279 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
1707206 AAGATTCGAG
1707216 GGTTCTACGTGGTCCTACGGGACATA-T
1 GGTTCTACGTGGTCCTACGGGACATAGT
* *
1707243 GTGTTCTATGTGGTCCTTCGGGACATAGT
1 G-GTTCTACGTGGTCCTACGGGACATAGT
1707272 GGTTCTAC
1 GGTTCTAC
1707280 AGGACAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 29 0.91
29 2 0.06
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (28 bp):
GGTTCTACGTGGTCCTACGGGACATAGT
Found at i:1710084 original size:29 final size:29
Alignment explanation
Indices: 1710052--1710222 Score: 222
Period size: 29 Copynumber: 5.9 Consensus size: 29
1710042 ACTAACATAC
*
1710052 TTTTAAAAATATTTACGAAAATATCACCT
1 TTTTAAAAATATTTACGAAAATAGCACCT
*
1710081 TTTTAAGAATATTTACGAAAAATAGCA--T
1 TTTTAAAAATATTTACG-AAAATAGCACCT
*
1710109 TTTTAAAAATATTTAC-AAAATAACACACT
1 TTTTAAAAATATTTACGAAAATAGCAC-CT
* * *
1710138 TTTAAAAAATATTTATGAAAATAGCACCA
1 TTTTAAAAATATTTACGAAAATAGCACCT
* *
1710167 TTTTAAAAATATTTACAAAAATAGCACCA
1 TTTTAAAAATATTTACGAAAATAGCACCT
*
1710196 TTTCAAAAATATTTACGAAAATAGCAC
1 TTTTAAAAATATTTACGAAAATAGCAC
1710223 TGGGTCTGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
26 8 0.06
28 16 0.13
29 83 0.67
30 17 0.14
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.33
Consensus pattern (29 bp):
TTTTAAAAATATTTACGAAAATAGCACCT
Found at i:1719761 original size:45 final size:45
Alignment explanation
Indices: 1719706--1719791 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
1719696 GAGAGTTCGC
* *
1719706 ATAGGTCATAAACTCACAAATGGTAACAAAAGA-AATTAAATTCAT
1 ATAGGGCATAAACTCACAAATGATAACAAAA-ATAATTAAATTCAT
* *
1719751 ATAGGGCATAAGCTCACAAGTGATAACAAAAATAATTAAAT
1 ATAGGGCATAAACTCACAAATGATAACAAAAATAATTAAAT
1719792 ATTAATTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (45 bp):
ATAGGGCATAAACTCACAAATGATAACAAAAATAATTAAATTCAT
Found at i:1721718 original size:2 final size:2
Alignment explanation
Indices: 1721711--1721744 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1721701 CATTTAAACA
1721711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1721745 GAGAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1721977 original size:20 final size:21
Alignment explanation
Indices: 1721952--1722003 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1721942 TTTTCCCAAT
*
1721952 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
**
1721972 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGAAAAA
1721993 TCGCAATGCGA
1 TCGCAATGCGA
1722004 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:1721982 original size:41 final size:41
Alignment explanation
Indices: 1721937--1722194 Score: 134
Period size: 41 Copynumber: 6.3 Consensus size: 41
1721927 AATTTCGCGT
**
1721937 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
* * * * * *
1721978 TGCGAATTTGAAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * * **
1722019 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCATAATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
1722060 TGTGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
* * * * *
1722101 CGCGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCA-TAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * * ** *
1722142 TGCGA-ATACGTAAATCGCAATGCGAAT-CTTACTATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGTA-AATCGCAA
*
1722182 TGCGATTTACATA
1 TGCGATTTTCATA
1722195 GCGCCATTCG
Statistics
Matches: 161, Mismatches: 45, Indels: 22
0.71 0.20 0.10
Matches are distributed among these distances:
39 6 0.04
40 36 0.22
41 116 0.72
42 1 0.01
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (41 bp):
TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:1722047 original size:21 final size:21
Alignment explanation
Indices: 1721910--1722085 Score: 76
Period size: 21 Copynumber: 8.5 Consensus size: 21
1721900 ATTATGACTA
*
1721910 TCGCAATGCGATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
** **
1721931 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1721952 TCGCAATGCGA--ATAAGTAAA
1 TCGCAATGCGATTTTCA-TAAT
* * * *
1721972 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGATTTTCATAAT
** *
1721993 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
1722013 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1722034 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
** *
1722054 TCGCGTTGTGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
1722075 TCGCAATGCGA
1 TCGCAATGCGA
1722086 ATACGTAAAT
Statistics
Matches: 113, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
19 2 0.02
20 43 0.38
21 66 0.58
22 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:1722100 original size:20 final size:20
Alignment explanation
Indices: 1722075--1722186 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
1722065 TTTTCATAAT
1722075 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1722095 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1722115 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1722136 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1722156 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
1722176 TCGCAATGCGA
1 TCGCAATGCGA
1722187 TTTACATAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1722850 original size:52 final size:54
Alignment explanation
Indices: 1722780--1722930 Score: 234
Period size: 52 Copynumber: 2.8 Consensus size: 54
1722770 CGATTTTCAT
1722780 TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGAT-TC
1 TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATATC
*
1722833 -TCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTC
1 TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATA-TC
*
1722887 ATTTCGCGTTGCGATTTTCATTATCTCGTTGCGATTTTCATTTC
1 --TTCGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATTTC
1722931 AACCAAAAGA
Statistics
Matches: 89, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
52 49 0.55
54 2 0.02
57 18 0.20
58 20 0.22
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (54 bp):
TTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATATC
Found at i:1722889 original size:71 final size:73
Alignment explanation
Indices: 1722767--1722930 Score: 260
Period size: 71 Copynumber: 2.2 Consensus size: 73
1722757 CAAAATCGCA
**
1722767 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGA-T
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCGCGTTGCGATT
1722831 TC-TCTCG
66 TCATCTCG
1722838 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCGCGTTGCGA-T
1722903 TTCATTATCTCG
65 TTC---ATCTCG
1722915 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1722931 AACCAAAAGA
Statistics
Matches: 85, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
71 61 0.72
73 3 0.04
77 21 0.25
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.47
Consensus pattern (73 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCGCGTTGCGATT
TCATCTCG
Found at i:1722891 original size:24 final size:19
Alignment explanation
Indices: 1722762--1722930 Score: 249
Period size: 19 Copynumber: 9.1 Consensus size: 19
1722752 GAAACCAAAA
*
1722762 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1722781 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1722800 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1722819 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1722833 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1722852 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1722871 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1722890 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1722909 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1722929 TC
1 TC
1722931 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
14 10 0.07
16 3 0.02
17 3 0.02
19 102 0.75
20 18 0.13
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1725101 original size:42 final size:42
Alignment explanation
Indices: 1725025--1725143 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
1725015 GACTCGCCTG
* * * *
1725025 TCATCCCTC-AAGA-GTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
1725067 TCATTCCTCG-AGA-GTCCCATCCCACCGTTCAAGAGGCCACTT
1 TCA-TCCTCGAAGAGGTCCC-TCCCACCGTTCAAGAGGCCACTA
* * *
1725109 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAG
1725144 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 5 0.08
42 53 0.83
43 6 0.09
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1726475 original size:14 final size:14
Alignment explanation
Indices: 1726456--1726491 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1726446 ATTGTTTAAT
1726456 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1726470 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1726484 TGATTTGT
1 TGATTTGT
1726492 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1726640 original size:33 final size:32
Alignment explanation
Indices: 1726598--1726695 Score: 94
Period size: 32 Copynumber: 3.0 Consensus size: 32
1726588 AAAAATTACT
1726598 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACGA-A
** *
1726631 ATCGCAATGC-AGGTCAAAATCGCAACGACTAA
1 ATCGCAATGCGAAAT-AAAATCGCAACGACGAA
* *
1726663 ATTGCAACGCGAAACTAAAATCGCAACG-CGAA
1 ATCGCAATGCGAAA-TAAAATCGCAACGACGAA
1726695 A
1 A
1726696 CTAAATTCGC
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
32 28 0.53
33 24 0.45
34 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATAAAATCGCAACGACGAA
Found at i:1726712 original size:19 final size:19
Alignment explanation
Indices: 1726661--1726705 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1726651 CGCAACGACT
*
1726661 AAATTGCAACGCGAAACTA
1 AAATCGCAACGCGAAACTA
1726680 AAATCGCAACGCGAAACTA
1 AAATCGCAACGCGAAACTA
*
1726699 AATTCGC
1 AAATCGC
1726706 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (19 bp):
AAATCGCAACGCGAAACTA
Found at i:1726723 original size:19 final size:19
Alignment explanation
Indices: 1726701--1726851 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
1726691 CGAAACTAAA
1726701 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1726720 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1726735 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1726753 TTCACATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1726768 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
1726786 TTCGCGTTGCGA--TT-A-
1 TTCGCGTTGCGATTTTCAT
*
1726801 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1726819 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1726838 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1726852 AGATATTAAG
Statistics
Matches: 99, Mismatches: 17, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 27 0.27
16 9 0.09
17 9 0.09
19 44 0.44
20 10 0.10
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1726747 original size:33 final size:33
Alignment explanation
Indices: 1726705--1726831 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1726695 ACTAAATTCG
* *
1726705 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1726738 CGTTGCGATTTTCATTTCACATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1726771 CGTTGCGATTTTCATTTCGCGTTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1726804 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1726832 AGTAATTTCC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1726897 original size:20 final size:20
Alignment explanation
Indices: 1726825--1726897 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
1726815 TCATTTCGCA
* *
1726825 TTGCGATAGTAATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
**
1726845 TTGCGATAG--ATATTAAGATG
1 TTGCGATAGTCAT-TTCCG-TG
1726865 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
1726886 TTGCGATAGTCA
1 TTGCGATAGTCA
1726898 AATGATTGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 21 0.51
21 10 0.24
22 3 0.07
23 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:1729176 original size:12 final size:12
Alignment explanation
Indices: 1729159--1729183 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1729149 TCTTCGGGGA
1729159 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1729171 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1729183 C
1 C
1729184 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1729397 original size:24 final size:24
Alignment explanation
Indices: 1729370--1729416 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1729360 CAAAATCCGA
*
1729370 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1729394 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1729417 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1729425 original size:24 final size:24
Alignment explanation
Indices: 1729374--1729425 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1729364 ATCCGAGTAT
* ** *
1729374 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1729398 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1729422 TGAC
1 TGAC
1729426 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1730248 original size:20 final size:20
Alignment explanation
Indices: 1730215--1730293 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1730205 GAATAAGTAA
* *
1730215 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
1730235 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
1730256 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
1730276 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
1730294 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:1730300 original size:20 final size:20
Alignment explanation
Indices: 1730253--1730302 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1730243 GAGATAATAC
1730253 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
1730273 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
1730293 AAAATCGCAA
1 AAAATCGCAA
1730303 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:1730549 original size:20 final size:20
Alignment explanation
Indices: 1730520--1730583 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
1730510 GGGGAAATCA
1730520 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
* ***
1730540 CAATGCGAAAATGAAAATCG
1 CAACGCGAAAATGGCTATCG
1730560 CAACGCGAAAATGGCTATCG
1 CAACGCGAAAATGGCTATCG
1730580 CAAC
1 CAAC
1730584 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAATGGCTATCG
Found at i:1730589 original size:20 final size:20
Alignment explanation
Indices: 1730520--1730591 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1730510 GGGGAAATCA
*
1730520 CAACGCGAAAATGGCTATCG
1 CAACTCGAAAATGGCTATCG
***
1730540 CAA-TGCGAAAATGAAAATCG
1 CAACT-CGAAAATGGCTATCG
*
1730560 CAACGCGAAAATGGCTATCG
1 CAACTCGAAAATGGCTATCG
*
1730580 CAACTAGAAAAT
1 CAACTCGAAAAT
1730592 CGCAATGCGG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (20 bp):
CAACTCGAAAATGGCTATCG
Found at i:1730590 original size:40 final size:40
Alignment explanation
Indices: 1730514--1730591 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
1730504 CGCAACGGGG
*
1730514 AAATCACAACGCGAAAATGGCTATCGCAATGCGAAAATGA
1 AAATCACAACGCGAAAATGGCTATCGCAATGAGAAAATGA
*
1730554 AAATCGCAACGCGAAAATGGCTATCGCAACT-AGAAAAT
1 AAATCACAACGCGAAAATGGCTATCGCAA-TGAGAAAAT
1730592 CGCAATGCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (40 bp):
AAATCACAACGCGAAAATGGCTATCGCAATGAGAAAATGA
Found at i:1730595 original size:34 final size:34
Alignment explanation
Indices: 1730500--1730596 Score: 95
Period size: 40 Copynumber: 2.7 Consensus size: 34
1730490 ATTCATTTGA
** * *
1730500 CTATCGCAACGGGGAAATCACAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
1730534 CTATCGCAATGCGAAAATGAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C---AA-GAAAATCGCAACGCGAAAATGG
*
1730574 CTATCGCAACTAGAAAATCGCAA
1 CTATCGCAACAAGAAAATCGCAA
1730597 TGCGGAATGA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
34 20 0.38
35 1 0.02
36 1 0.02
38 1 0.02
40 29 0.56
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.14
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:1732263 original size:41 final size:42
Alignment explanation
Indices: 1732209--1732300 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
1732199 CCTCTTCAAC
* *
1732209 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
1732250 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
1732292 GATGACAGG
1 GATGACAGG
1732301 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:1732265 original size:21 final size:21
Alignment explanation
Indices: 1732236--1732296 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1732226 GAACGGTGGG
*
1732236 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
1732257 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
1732278 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1732297 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1732669 original size:20 final size:20
Alignment explanation
Indices: 1732644--1732696 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1732634 TAGTTTACTT
1732644 TCGCAATGCGAAAATGACTA
1 TCGCAATGCGAAAATGACTA
* * *
1732664 TCGCAATGTGGAAATGGCTA
1 TCGCAATGCGAAAATGACTA
1732684 TCGCAATGCGAAA
1 TCGCAATGCGAAA
1732697 TGAAAATCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAAAATGACTA
Found at i:1732758 original size:19 final size:19
Alignment explanation
Indices: 1732736--1732818 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
1732726 GAAACACAAA
1732736 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1732755 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
* *
1732771 TCG--TTGCAATTTTTATT
1 TCGCATTGCGATTTTCATT
1732788 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1732807 TCACATTGCGAT
1 TCGCATTGCGAT
1732819 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
14 5 0.10
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 33 0.63
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1732857 original size:20 final size:20
Alignment explanation
Indices: 1732803--1732846 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1732793 TTGCGATTTT
*
1732803 CATTT-CACATTGCGATAGC
1 CATTTCCACGTTGCGATAGC
*
1732822 CATTTCCACGTTGCGATAGT
1 CATTTCCACGTTGCGATAGC
1732842 CATTT
1 CATTT
1732847 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (20 bp):
CATTTCCACGTTGCGATAGC
Found at i:1733439 original size:18 final size:18
Alignment explanation
Indices: 1733392--1733439 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1733382 CGGGTCGATC
*
1733392 AGGTGATGGATCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1733410 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1733428 AGGTGATGGCTC
1 AGGTGATGGCTC
1733440 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.10, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1734807 original size:20 final size:20
Alignment explanation
Indices: 1734759--1734817 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1734749 AATAGTTTCT
* *
1734759 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1734779 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
1734799 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
1734818 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1735079 original size:20 final size:21
Alignment explanation
Indices: 1735054--1735101 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
1735044 TCTGAGAGAT
1735054 GGAGATA-GACGGATTTCGCC
1 GGAGATAGGACGGATTTCGCC
*
1735074 GGAGATAGGGACGGATTTCGTC
1 GGAGATA-GGACGGATTTCGCC
1735096 GGAGAT
1 GGAGAT
1735102 GGGTGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.28
22 18 0.72
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.21
Consensus pattern (21 bp):
GGAGATAGGACGGATTTCGCC
Found at i:1735377 original size:21 final size:22
Alignment explanation
Indices: 1735346--1735450 Score: 89
Period size: 21 Copynumber: 5.0 Consensus size: 22
1735336 AGTTGCGAAA
1735346 GTCAGTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
* *
1735368 GT-ATTATCGCGTTGCGA--TA
1 GTCAGTATCGCGTTGCGATTTT
1735387 GTCAGTATCGCGTTGCGATTTT
1 GTCAGTATCGCGTTGCGATTTT
* *
1735409 -CCA-AATTCGCGTTGCGATTTT
1 GTCAGTA-TCGCGTTGCGATTTT
* *
1735430 -CCAAGT-TCGCATTGCGATTTT
1 GTC-AGTATCGCGTTGCGATTTT
1735451 CCAAATTCGC
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
19 3 0.04
20 15 0.22
21 47 0.68
22 4 0.06
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (22 bp):
GTCAGTATCGCGTTGCGATTTT
Found at i:1735390 original size:41 final size:41
Alignment explanation
Indices: 1735277--1735408 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 41
1735267 AAAAATCGTA
* * * *
1735277 TTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATTGAG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
** * * *
1735318 TTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGTATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
*
1735358 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
1735399 TTGCGATTTT
1 TTGCGATTTT
1735409 CCAAATTCGC
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 32 0.43
41 43 0.57
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.37
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
Found at i:1735405 original size:20 final size:20
Alignment explanation
Indices: 1735291--1735404 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1735281 GATTATGTAT
*
1735291 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
1735311 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1735331 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1735351 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1735372 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1735392 TATCGCGTTGCGA
1 TATCGCGTTGCGA
1735405 TTTTCCAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1735419 original size:41 final size:41
Alignment explanation
Indices: 1735337--1735467 Score: 149
Period size: 41 Copynumber: 3.2 Consensus size: 41
1735327 TAAGTATCGA
* ** *
1735337 GTTGCGAAAGTCAGTATCGCGTTGCGATTTT-GTATTATCGC
1 GTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGC
1735378 GTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGC
1 GTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGC
** *
1735419 GTTGCGATTTTCCAAGT-TCGCATTGCGATTTTCCAAATTCGC
1 GTTGCGATAGT-C-AGTATCGCGTTGCGATTTTCCAAATTCGC
*
1735461 ATTGCGA
1 GTTGCGA
1735468 ATTGGGAAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 43 0.54
42 33 0.42
43 3 0.04
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.36
Consensus pattern (41 bp):
GTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGC
Found at i:1735451 original size:21 final size:21
Alignment explanation
Indices: 1735394--1735467 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
1735384 ATAGTCAGTA
*
1735394 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1735415 TCGCGTTGCGATTTTCCAAGT
1 TCGCATTGCGATTTTCCAAAT
1735436 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
1735457 TCGCATTGCGA
1 TCGCATTGCGA
1735468 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1735481 original size:21 final size:20
Alignment explanation
Indices: 1735457--1735509 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
1735447 TTTTCCAAAT
1735457 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
**
1735478 TCGCAACGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
1735499 TCGCATTGCGA
1 TCGCATTGCGA
1735510 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.81
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1735482 original size:42 final size:42
Alignment explanation
Indices: 1735393--1735482 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
1735383 GATAGTCAGT
* * * * *
1735393 ATCGCGTTGCGATTTTCCAAATTCGCGTTGCGATTTTCCAAG
1 ATCGCATTGCGATTTTCCAAATTCGCATTGCGAATTGCCAAA
* **
1735435 TTCGCATTGCGATTTTCCAAATTCGCATTGCGAATTGGGAAA
1 ATCGCATTGCGATTTTCCAAATTCGCATTGCGAATTGCCAAA
1735477 ATCGCA
1 ATCGCA
1735483 ACGCGAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
ATCGCATTGCGATTTTCCAAATTCGCATTGCGAATTGCCAAA
Found at i:1735859 original size:2 final size:2
Alignment explanation
Indices: 1735852--1735884 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1735842 TAAATTTATC
1735852 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 A
1735885 CTTCTCAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1736156 original size:63 final size:63
Alignment explanation
Indices: 1736057--1736307 Score: 441
Period size: 63 Copynumber: 4.0 Consensus size: 63
1736047 AGACCAGCAT
* *
1736057 CCACCATACTCTCGTCCCTAAGGCTTCTCATTGGCCCAAAGCCTATTAACTCACATTCGACAC
1 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCGACAC
* *
1736120 CCACCATACTCTCGTCACTAAGGCTTCTTATTGGCCCAAAGCTCATTAACTCACATTCGACA-
1 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCGACAC
*
1736182 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCAACAC
1 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCGACAC
*
1736245 CCACCATACTCTCGTCACTAAGGCATCTCATTGGCCCAAAGCCCATTAACTCACATTCGACAC
1 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCGACAC
1736308 TAGGTTGACC
Statistics
Matches: 178, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
62 59 0.33
63 119 0.67
ACGTcount: A:0.27, C:0.37, G:0.11, T:0.25
Consensus pattern (63 bp):
CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCGACAC
Found at i:1736279 original size:125 final size:125
Alignment explanation
Indices: 1736057--1736307 Score: 448
Period size: 125 Copynumber: 2.0 Consensus size: 125
1736047 AGACCAGCAT
* * *
1736057 CCACCATACTCTCGTCCCTAAGGCTTCTCATTGGCCCAAAGCCTATTAACTCACATTCGACACCC
1 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCAACACCC
* * *
1736122 ACCATACTCTCGTCACTAAGGCTTCTTATTGGCCCAAAGCTCATTAACTCACATTCGACA
66 ACCATACTCTCGTCACTAAGGCATCTCATTGGCCCAAAGCCCATTAACTCACATTCGACA
1736182 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCAACACCC
1 CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCAACACCC
1736247 ACCATACTCTCGTCACTAAGGCATCTCATTGGCCCAAAGCCCATTAACTCACATTCGACA
66 ACCATACTCTCGTCACTAAGGCATCTCATTGGCCCAAAGCCCATTAACTCACATTCGACA
1736307 C
1 C
1736308 TAGGTTGACC
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.27, C:0.37, G:0.11, T:0.25
Consensus pattern (125 bp):
CCACCATACTCTCGTCACTAAGGCTTCTCATTGGCCCAAAGCCCATTAACTCACATTCAACACCC
ACCATACTCTCGTCACTAAGGCATCTCATTGGCCCAAAGCCCATTAACTCACATTCGACA
Found at i:1738196 original size:14 final size:12
Alignment explanation
Indices: 1738177--1738228 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 12
1738167 ATTTTAAATT
1738177 TTAAAATATATATA
1 TTAAAATA-ATA-A
1738191 TTAAAATAATAA
1 TTAAAATAATAA
*
1738203 TAAAAATAATAAA
1 TTAAAATAAT-AA
*
1738216 TTATAAATTATAA
1 TTA-AAATAATAA
1738229 AAATGGCTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 10 0.30
13 9 0.27
14 14 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAAAATAATAA
Found at i:1738223 original size:26 final size:26
Alignment explanation
Indices: 1738179--1738228 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1738169 TTTAAATTTT
*
1738179 AAAATATATATATTAAAATAATAATA
1 AAAATATATAAATTAAAATAATAATA
*
1738205 AAAATA-ATAAATTATAAATTATAA
1 AAAATATATAAATTA-AAATAATAA
1738229 AAATGGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AAAATATATAAATTAAAATAATAATA
Found at i:1746234 original size:12 final size:12
Alignment explanation
Indices: 1746217--1746255 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1746207 TTACTACTAA
1746217 TTTAATAATATT
1 TTTAATAATATT
1746229 TTTAATAATAATT
1 TTTAATAAT-ATT
*
1746242 TATTATTAATATT
1 T-TTAATAATATT
1746255 T
1 T
1746256 AATGATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 9 0.38
13 8 0.33
14 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAATAATATT
Found at i:1746263 original size:21 final size:20
Alignment explanation
Indices: 1746234--1746299 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
1746224 ATATTTTTAA
1746234 TAATAATTTATTATTAATATT
1 TAAT-ATTTATTATTAATATT
1746255 TAATGATTTGA-TATTAATAATT
1 TAAT-ATTT-ATTATTAAT-ATT
* * *
1746277 TAATAATGATTATTAATAAT
1 TAATATTTATTATTAATATT
1746297 TAA
1 TAA
1746300 ATTATAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.16
21 24 0.63
22 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATATTTATTATTAATATT
Found at i:1746296 original size:24 final size:24
Alignment explanation
Indices: 1746218--1746360 Score: 125
Period size: 24 Copynumber: 6.0 Consensus size: 24
1746208 TACTACTAAT
*
1746218 TTAATAATATTTTTAATAATAATTTA
1 TTAATAATA-ATTTAATAATAA-TTA
* *
1746244 TTATTAAT-ATTTAATGAT--TTGA
1 TTAATAATAATTTAATAATAATT-A
* *
1746266 -TATTAATAATTTAATAATGATTA
1 TTAATAATAATTTAATAATAATTA
*
1746289 TTAATAATTAAATT-ATAATAATTA
1 TTAATAA-TAATTTAATAATAATTA
* *
1746313 ATAAAAATAATTTAATAATAATTA
1 TTAATAATAATTTAATAATAATTA
* *
1746337 TTAATAATTATTTAATAATGATTA
1 TTAATAATAATTTAATAATAATTA
1746361 AATATTTCAA
Statistics
Matches: 96, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
21 9 0.09
22 10 0.10
23 6 0.06
24 59 0.61
25 5 0.05
26 7 0.07
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (24 bp):
TTAATAATAATTTAATAATAATTA
Found at i:1746312 original size:21 final size:21
Alignment explanation
Indices: 1746267--1746355 Score: 71
Period size: 21 Copynumber: 4.4 Consensus size: 21
1746257 ATGATTTGAT
* * *
1746267 ATTAATAATTTAATAATGATT
1 ATTAATAATTAAATAATAATA
*
1746288 ATTAATAATTAAATTATAATA
1 ATTAATAATTAAATAATAATA
*
1746309 ATTAATAA--AAATAAT-TTA
1 ATTAATAATTAAATAATAATA
*
1746327 A-TAATAATT-ATTAATAATTA
1 ATTAATAATTAAATAATAA-TA
*
1746347 TTTAATAAT
1 ATTAATAAT
1746356 GATTAAATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
17 6 0.11
18 8 0.15
19 6 0.11
20 2 0.04
21 32 0.59
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
ATTAATAATTAAATAATAATA
Found at i:1746321 original size:27 final size:27
Alignment explanation
Indices: 1746291--1746343 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1746281 AATGATTATT
*
1746291 AATAATTAAATTATAATAATTAATAAA
1 AATAATTAAATAATAATAATTAATAAA
* *
1746318 AATAATTTAATAATAATTATTAATAA
1 AATAATTAAATAATAATAATTAATAA
1746344 TTATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATAATTAAATAATAATAATTAATAAA
Found at i:1746364 original size:11 final size:10
Alignment explanation
Indices: 1746266--1746361 Score: 67
Period size: 10 Copynumber: 9.6 Consensus size: 10
1746256 AATGATTTGA
1746266 TATTAATAATT
1 TATTAATAA-T
* *
1746277 TAATAATGAT
1 TATTAATAAT
1746287 TATTAATAAT
1 TATTAATAAT
1746297 TAAATT-ATAAT
1 T--ATTAATAAT
*
1746308 AATTAATAA-
1 TATTAATAAT
1746317 -A--AATAATT
1 TATTAATAA-T
*
1746325 TAATAATAAT
1 TATTAATAAT
1746335 TATTAATAAT
1 TATTAATAAT
1746345 TATTTAATAAT
1 TA-TTAATAAT
*
1746356 GATTAA
1 TATTAA
1746362 ATATTTCAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
6 5 0.07
8 1 0.01
9 4 0.06
10 30 0.43
11 26 0.38
12 3 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (10 bp):
TATTAATAAT
Found at i:1746438 original size:22 final size:22
Alignment explanation
Indices: 1746413--1746454 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1746403 ATAGTTTAAC
1746413 TTATAACA-AGTCGAATTTATAT
1 TTATAA-ATAGTCGAATTTATAT
1746435 TTATAAATAGTCGAATTTAT
1 TTATAAATAGTCGAATTTAT
1746455 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (22 bp):
TTATAAATAGTCGAATTTATAT
Found at i:1747673 original size:17 final size:15
Alignment explanation
Indices: 1747651--1747690 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
1747641 TGGGGTTATG
1747651 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
1747667 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
1747683 TTAAATAT
1 TTAAATAT
1747691 GCATGTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:1747831 original size:16 final size:16
Alignment explanation
Indices: 1747831--1747873 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1747821 TATTTATAAA
1747831 TATAAATTCGACTTGT
1 TATAAATTCGACTTGT
* *
1747847 TATAAGTTCAACTAT-T
1 TATAAATTCGACT-TGT
1747863 TATAAATTCGA
1 TATAAATTCGA
1747874 TTTAAATTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (16 bp):
TATAAATTCGACTTGT
Found at i:1747835 original size:22 final size:22
Alignment explanation
Indices: 1747810--1747851 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1747800 TTTAAAAAGA
1747810 ATAAATTCGACTAT-TTATAAAT
1 ATAAATTCGACT-TGTTATAAAT
1747832 ATAAATTCGACTTGTTATAA
1 ATAAATTCGACTTGTTATAA
1747852 GTTCAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (22 bp):
ATAAATTCGACTTGTTATAAAT
Found at i:1747935 original size:24 final size:22
Alignment explanation
Indices: 1747896--1747984 Score: 90
Period size: 24 Copynumber: 3.8 Consensus size: 22
1747886 AAATTTTATT
1747896 TAATTATT-TAATCATTATTAAA
1 TAATTATTATAATCATTATT-AA
*
1747918 TAATTATTAGTAATCATTATTAG
1 TAATTATTA-TAATCATTATTAA
* *
1747941 TAATTATTATAATTTAATTATTAC
1 TAATTATTATAA--TCATTATTAA
1747965 TAATTATTATTAAATCATTA
1 TAATTATTA-T-AATCATTA
1747985 GTATCAAATC
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.19
23 10 0.18
24 33 0.58
25 1 0.02
26 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATTATTATAATCATTATTAA
Found at i:1747938 original size:13 final size:13
Alignment explanation
Indices: 1747904--1747950 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
1747894 TTTAATTATT
1747904 TAATCATTATTA-
1 TAATCATTATTAG
*
1747916 -AATAATTATTAG
1 TAATCATTATTAG
1747928 TAATCATTATTAG
1 TAATCATTATTAG
*
1747941 TAATTATTAT
1 TAATCATTAT
1747951 AATTTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.33
13 20 0.67
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (13 bp):
TAATCATTATTAG
Found at i:1747960 original size:14 final size:15
Alignment explanation
Indices: 1747941--1747969 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1747931 TCATTATTAG
1747941 TAATTATTA-TAATT
1 TAATTATTACTAATT
1747955 TAATTATTACTAATT
1 TAATTATTACTAATT
1747970 ATTATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATTACTAATT
Found at i:1747975 original size:13 final size:13
Alignment explanation
Indices: 1747920--1747976 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
1747910 TTATTAAATA
*
1747920 ATTATTAGTAATC
1 ATTATTAGTAATT
1747933 ATTATTAGTAATT
1 ATTATTAGTAATT
*
1747946 ATTA-TA--ATTT
1 ATTATTAGTAATT
*
1747956 AATTATTACTAATT
1 -ATTATTAGTAATT
1747970 ATTATTA
1 ATTATTA
1747977 AATCATTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.08
11 4 0.11
12 4 0.11
13 23 0.62
14 3 0.08
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (13 bp):
ATTATTAGTAATT
Found at i:1748014 original size:21 final size:22
Alignment explanation
Indices: 1747973--1748019 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
1747963 ACTAATTATT
* *
1747973 ATTAAATCATTAGTATCAAATC
1 ATTAAATCATTAATATCAAATA
1747995 ATTAAAT-ATTAATAAT-AAATA
1 ATTAAATCATTAAT-ATCAAATA
1748016 ATTA
1 ATTA
1748020 TTAATAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
ATTAAATCATTAATATCAAATA
Found at i:1754959 original size:21 final size:21
Alignment explanation
Indices: 1754935--1754974 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1754925 CAATGGGATT
*
1754935 AGGATTAGGAATTGGATTTTG
1 AGGATTAGGAAGTGGATTTTG
*
1754956 AGGATTTGGAAGTGGATTT
1 AGGATTAGGAAGTGGATTT
1754975 GGTTGACGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.38
Consensus pattern (21 bp):
AGGATTAGGAAGTGGATTTTG
Found at i:1759576 original size:22 final size:21
Alignment explanation
Indices: 1759534--1759573 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1759524 GAGCTTATTT
*
1759534 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1759555 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1759574 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1763822 original size:3 final size:3
Alignment explanation
Indices: 1763814--1763844 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1763804 ATGAAAATCA
1763814 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1763845 GAACCTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1764697 original size:41 final size:41
Alignment explanation
Indices: 1764651--1764791 Score: 135
Period size: 41 Copynumber: 3.4 Consensus size: 41
1764641 GTTTATAGCT
*
1764651 CAAACGCCGCAATAGAGATGTTTATAGTGGCGTTTTTTCAA
1 CAAACGACGCAATAGAGATGTTTATAGTGGCGTTTTTTCAA
* * * * *
1764692 TAAACGCCGCAATAGAG-TGGTAATT-TAGCGGTG-TTTTTAAA
1 CAAACGACGCAATAGAGAT-GT--TTATAGTGGCGTTTTTTCAA
* * * *
1764733 CAAACGACGCTATAGTGTTGTTTATAGTGGCGTTTGTTCAA
1 CAAACGACGCAATAGAGATGTTTATAGTGGCGTTTTTTCAA
*
1764774 CAAACGACGCTATAGAGA
1 CAAACGACGCAATAGAGA
1764792 AGTAATTTCG
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
39 2 0.03
40 7 0.09
41 62 0.77
42 7 0.09
43 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
CAAACGACGCAATAGAGATGTTTATAGTGGCGTTTTTTCAA
Found at i:1764706 original size:82 final size:80
Alignment explanation
Indices: 1764608--1764867 Score: 254
Period size: 82 Copynumber: 3.2 Consensus size: 80
1764598 TGTTTTTTTA
* * *
1764608 AACAAACGCCGTAATAGAG-GGTAATTTAGCAGCGTTTATAGCTCAAACGCCGCAATAGAGATGT
1 AACAAACGCCGCAATAGAGAGGTAATTTAGC-GCGTTTATA--ACAAACGCCGCAATAGAGTTGT
*
1764672 TTATAGTGGCGTTTTTTC
63 TTATAGTGGCGTTTGTTC
* * * * * * *
1764690 AATAAACGCCGCAATAGAGTGGTAATTTAGCGGTGTTTTTAAACAAACGACGCTATAGTGTTGTT
1 AACAAACGCCGCAATAGAGAGGTAATTTAGC-GCGTTTAT-AACAAACGCCGCAATAGAGTTGTT
1764755 TATAGTGGCGTTTGTTC
64 TATAGTGGCGTTTGTTC
* * * * * *
1764772 AACAAACGACGCTATAGAGAAGTAATTTCGCGACGTTTAATAAAAAATGCCGCAATAGTA-TTGT
1 AACAAACGCCGCAATAGAGAGGTAATTTAGCG-CGTTT-ATAACAAACGCCGCAATAG-AGTTGT
* *
1764836 TTATAGTGACGTTTGTGC
63 TTATAGTGGCGTTTGTTC
*
1764854 AAAAAACGCCGCAA
1 AACAAACGCCGCAA
1764868 AAATATGAAC
Statistics
Matches: 144, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
81 1 0.01
82 124 0.86
83 18 0.12
84 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (80 bp):
AACAAACGCCGCAATAGAGAGGTAATTTAGCGCGTTTATAACAAACGCCGCAATAGAGTTGTTTA
TAGTGGCGTTTGTTC
Found at i:1765316 original size:22 final size:23
Alignment explanation
Indices: 1765268--1765322 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1765258 GTGTTTTTTT
*
1765268 GCTTTCGAATAGAAAAATAATTA
1 GCTTTCGAAAAGAAAAATAATTA
*
1765291 -CTTTCGAAAAGGAAAATAA-TA
1 GCTTTCGAAAAGAAAAATAATTA
*
1765312 GCTTTTGAAAA
1 GCTTTCGAAAA
1765323 CGTGAATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (23 bp):
GCTTTCGAAAAGAAAAATAATTA
Found at i:1766258 original size:15 final size:15
Alignment explanation
Indices: 1766226--1766276 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1766216 TGTAGAGCCT
1766226 AAATAAAATA-TT-TA
1 AAATAAAA-AGTTATA
**
1766240 AAATATCAAGTTATA
1 AAATAAAAAGTTATA
1766255 AAATAAAAAGTTATA
1 AAATAAAAAGTTATA
1766270 AAATAAA
1 AAATAAA
1766277 GGTCATTAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 1 0.03
14 8 0.26
15 22 0.71
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (15 bp):
AAATAAAAAGTTATA
Found at i:1766505 original size:83 final size:83
Alignment explanation
Indices: 1766366--1766519 Score: 195
Period size: 83 Copynumber: 1.8 Consensus size: 83
1766356 AGGTTTACTG
* * * *
1766366 TATAGTGGCGTTTTATGAAGAAACGACACAAAATATTTTTACTTTTCCTGT-TTTTTTATACAAA
1 TATAGTGGCGTTTGATGAACAAACGACACAAAATATTTATACTTTTCCGGTATTTTTTA-ACAAA
1766430 CGCCGCCATAGCTGTAATC
65 CGCCGCCATAGCTGTAATC
* * * *
1766449 TATAGTGGCGTTTGGTTAACAAACGCCACAAAATATTTATA-TTTTAGCGGTATTTTTTCAACAA
1 TATAGTGGCGTTTGATGAACAAACGACACAAAATATTTATACTTTT-CCGGTATTTTTT-AACAA
1766513 ACGCCGC
64 ACGCCGC
1766520 AAATATTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
82 4 0.07
83 38 0.63
84 17 0.28
85 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (83 bp):
TATAGTGGCGTTTGATGAACAAACGACACAAAATATTTATACTTTTCCGGTATTTTTTAACAAAC
GCCGCCATAGCTGTAATC
Found at i:1766546 original size:41 final size:42
Alignment explanation
Indices: 1766466--1766546 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 42
1766456 GCGTTTGGTT
** *
1766466 AACAAACGCCACAAAATATTTATATTTTAGCGGTATTTTTTC
1 AACAAACGCCACAAAATATTTATAAATTAGCGGCATTTTTTC
* *
1766508 AACAAACGCCGC-AAATATTTATAAATTAGCGGCGTTTTT
1 AACAAACGCCACAAAATATTTATAAATTAGCGGCATTTTT
1766547 GTACAAACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 23 0.68
42 11 0.32
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (42 bp):
AACAAACGCCACAAAATATTTATAAATTAGCGGCATTTTTTC
Done.