Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000572.1 Hibiscus syriacus cultivar Beakdansim tig00001120_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: 2399138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1333808 original size:149 final size:149
Alignment explanation
Indices: 1333628--1333942 Score: 571
Period size: 149 Copynumber: 2.1 Consensus size: 149
1333618 GAGTCGAGGG
*
1333628 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1333693 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
*
1333757 ATATGGCACTACGTTGCAAT
130 ATATGGCACTACGGTGCAAT
1333777 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1333842 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
1333907 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1333926 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1333943 TGTAATTATA
Statistics
Matches: 161, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
150 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1333943 original size:23 final size:23
Alignment explanation
Indices: 1333910--1333954 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1333900 ATCATTATAT
*
1333910 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1333933 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTATACG
1333955 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1336683 original size:5 final size:5
Alignment explanation
Indices: 1336673--1336798 Score: 252
Period size: 5 Copynumber: 25.2 Consensus size: 5
1336663 TTTTCTTCTC
1336673 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1336723 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1336773 TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA T
1336799 GTTTGAGGAT
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 121 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:1336947 original size:23 final size:23
Alignment explanation
Indices: 1336857--1336947 Score: 76
Period size: 23 Copynumber: 3.8 Consensus size: 23
1336847 AATGATAAGT
*
1336857 AATATTAAATTAATTTATAAAACATTA
1 AATA-TAAATTAA-TTA-AAAATA-TA
* *
1336884 AATTATAAAGT-ATTAAACATATA
1 AA-TATAAATTAATTAAAAATATA
* *
1336907 ATTATAAATTAATTAAAAATCTA
1 AATATAAATTAATTAAAAATATA
*
1336930 AATATAATTTAATTAAAA
1 AATATAAATTAATTAAAA
1336948 TACAATATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
22 7 0.13
23 29 0.55
24 4 0.08
25 3 0.06
26 1 0.02
27 7 0.13
28 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (23 bp):
AATATAAATTAATTAAAAATATA
Found at i:1337115 original size:27 final size:27
Alignment explanation
Indices: 1337067--1337127 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1337057 TCCCGCCGTC
* *
1337067 ACTGTCACCATCGCTACTGTTATAATT
1 ACTGTCACCACCGCTACCGTTATAATT
* * *
1337094 ACTGTCACCACCGTTGCCGTTATCATT
1 ACTGTCACCACCGCTACCGTTATAATT
*
1337121 ACCGTCA
1 ACTGTCA
1337128 TAACCGTCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.33
Consensus pattern (27 bp):
ACTGTCACCACCGCTACCGTTATAATT
Found at i:1337390 original size:22 final size:23
Alignment explanation
Indices: 1337355--1337403 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1337345 CATTTAGATT
1337355 TTTAACTAATTTATAA-TTATACA
1 TTTAACTAATTTATAATTTA-ACA
*
1337378 TTTAA-TACTTTATAATTTAACA
1 TTTAACTAATTTATAATTTAACA
1337400 TTTA
1 TTTA
1337404 TAAATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAACTAATTTATAATTTAACA
Found at i:1354143 original size:21 final size:21
Alignment explanation
Indices: 1354113--1354160 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1354103 TAATTTTCAA
*
1354113 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1354134 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1354155 ACATTG
1 ACATTG
1354161 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1358763 original size:21 final size:21
Alignment explanation
Indices: 1358733--1358780 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1358723 TAATTTTCAA
* *
1358733 ACATTATTGCATCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1358754 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
1358775 ACATTG
1 ACATTG
1358781 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:1359195 original size:21 final size:21
Alignment explanation
Indices: 1359169--1359221 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1359159 GTTTCCAGAT
*
1359169 TCGCAACGCGAACATT-GACTA
1 TCGCAACGCGAAC-TTCAACTA
*
1359190 TCGCAACGCAAACTTCAACTA
1 TCGCAACGCGAACTTCAACTA
*
1359211 TCGCAATGCGA
1 TCGCAACGCGA
1359222 TTTTTCCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCAACTA
Found at i:1359260 original size:21 final size:21
Alignment explanation
Indices: 1359234--1359482 Score: 244
Period size: 21 Copynumber: 11.8 Consensus size: 21
1359224 TTTCCAAATT
1359234 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1359255 CGTTGCGATTTATTCCAAATTCG
1 CGTTGCGA--TAGTCCAAGTTCG
* *
1359278 CGTTGCAATAGTCCAAGTTTG
1 CGTTGCGATAGTCCAAGTTCG
*
1359299 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
1359320 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
1359341 CATTGCGATTTATTTCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
1359362 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1359383 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
1359404 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
1359425 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
1359446 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
1359467 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
1359483 AATCGCAACG
Statistics
Matches: 189, Mismatches: 23, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
19 34 0.18
21 100 0.53
23 55 0.29
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:1359275 original size:42 final size:42
Alignment explanation
Indices: 1359217--1359433 Score: 346
Period size: 42 Copynumber: 5.1 Consensus size: 42
1359207 ACTATCGCAA
1359217 TGCGATTT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* *
1359258 TGCGATTTATTCCAAATTCGCGTTGCAATAGTCCAAGTTTGCGT
1 TGCGATTTATTCCAAATT--CGTTGCGATAGTCCAAGTTCGCGT
* *
1359302 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCAT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
* * *
1359344 TGCGATTTATTTCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1359386 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1359428 TGCGAT
1 TGCGAT
1359434 AGTCCAAGTT
Statistics
Matches: 161, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
41 8 0.05
42 114 0.71
44 39 0.24
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1359450 original size:42 final size:41
Alignment explanation
Indices: 1359217--1359475 Score: 308
Period size: 42 Copynumber: 6.1 Consensus size: 41
1359207 ACTATCGCAA
* *
1359217 TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* * *
1359258 TGCGATTTATTCCAAATTCGCGTTGCAATAGTCCAAGTTTGCGT
1 TGCGA-TTATTCCAAGTT--CGTTGCGATAGTCCAAGTTCGCGT
*
1359302 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCAT
1 TGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* *
1359344 TGCGATTTATTTCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
*
1359386 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGA-TTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
* *
1359428 TGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT--CGT
1 TGCGATTATTCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGT
1359470 TGCGAT
1 TGCGAT
1359476 AGTCCAAAAT
Statistics
Matches: 194, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
40 9 0.05
41 5 0.03
42 131 0.68
44 49 0.25
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
TGCGATTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1359450 original size:84 final size:85
Alignment explanation
Indices: 1359217--1359475 Score: 359
Period size: 84 Copynumber: 3.1 Consensus size: 85
1359207 ACTATCGCAA
*
1359217 TGCGATTT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCGCGT
* *
1359281 TGCAATAGTCCAAGTTTGCGT
65 TGCGATAGTCCAAGTTCGCGT
* * *
1359302 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGCATTGCGATTTATTTCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAGTTCGCGT
*
1359365 TGCGATAGTCGAAGTTCGCGT
65 TGCGATAGTCCAAGTTCGCGT
*
1359386 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TAGTCCAAGTTCGCGTT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTTCGCGTT
*
1359450 GCGATTTATTCCAAGTT--CGT
66 GCGA--TAGTCCAAGTTCGCGT
1359470 TGCGAT
1 TGCGAT
1359476 AGTCCAAAAT
Statistics
Matches: 156, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
82 9 0.06
84 83 0.53
85 8 0.05
86 56 0.36
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (85 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAGTTCGCGTT
GCGATAGTCCAAGTTCGCGT
Found at i:1360400 original size:42 final size:40
Alignment explanation
Indices: 1360338--1360809 Score: 331
Period size: 42 Copynumber: 11.3 Consensus size: 40
1360328 CGTTGCGATT
1360338 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
* * *
1360380 TTCGACTATCGCAACGAACTTGGACT--ATCGCAATGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
*
1360418 TTGGAATAAATCGCAACGCGAACTT-GAACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAA-TAAATCGCAACGAAC
* * *
1360460 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
* * * *
1360502 TTGGAATAAATCGCAACGCGAACTTCGACT--ATCTCAACGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGAAC
* *
1360544 TTGGACTATCGCAACGCGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAACTTGGAATAAATCGCAA--CGAAC
*
1360588 TTGGACTATCGCAACGAACTTGGAATAAATCGTAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
* *
1360630 TTCGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
* * *
1360670 TTGGAATAAATCGCAATGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
* * * *
1360714 TTCGACTATCGCAATGAACTTGG-A-CAATCGCAACGAAT
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
* * * *
1360752 TTGTAATAAATCGCAACGCGAACTTTGACT--ATCGCAACGCAAAC
1 TTGGACT--ATCGCAA--CGAACTTGGAATAAATCGCAACG--AAC
1360796 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1360810 TGCGAATATG
Statistics
Matches: 370, Mismatches: 38, Indels: 44
0.82 0.08 0.10
Matches are distributed among these distances:
38 17 0.05
40 56 0.15
41 3 0.01
42 256 0.69
43 2 0.01
44 36 0.10
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (40 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGAAC
Found at i:1360502 original size:84 final size:81
Alignment explanation
Indices: 1360345--1360809 Score: 400
Period size: 84 Copynumber: 5.6 Consensus size: 81
1360335 ATTTTGGACT
*
1360345 ATCGCAA--CGAACTTGGAA-TAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTA
1 ATCGCAACGCGAACTTGGAACT--ATCGCAA--CGAACTTGGACTATCGCAACGAACTTGGACTA
*
1360407 TCGCAATGAACTTGGAATAA
62 TCGCAACGAACTTGGAATAA
* *
1360427 ATCGCAACGCGAACTT-GAACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTA
1 ATCGCAACGCGAACTTGGAACTATCGCAACGAACTTGGACT--ATCGCAA--CGAACTTGGACTA
1360491 TCGCAACGAACTTGGAATAA
62 TCGCAACGAACTTGGAATAA
* * * * *
1360511 ATCGCAACGCGAACTTCG-ACTATCTCAACGAACTTGGACTATCGCAACGCGAATTTGTAATAAA
1 ATCGCAACGCGAACTTGGAACTATCGCAACGAACTTGGACTATCGCAA--CGAACTTGGACT--A
*
1360575 TCGCAACGCGAACTTGGACT--
62 TCGCAA--CGAACTTGGAATAA
* * * *
1360595 ATCGCAA--CGAACTTGGAA-TAAATCGTAACGCGAACTTCGACTATCGCAACGAATTTGGAATA
1 ATCGCAACGCGAACTTGGAACT--ATCGCAA--CGAACTTGGACTATCGCAACGAACTTGGACT-
1360657 AATCGCAACGAACTTGGAATAA
61 -ATCGCAACGAACTTGGAATAA
* * * * *
1360679 ATCGCAA--TGAATTTGGAA-TAAATCGCAACGCGAACTTCGACTATCGCAATGAACTTGGACAA
1 ATCGCAACGCGAACTTGGAACT--ATCGCAA--CGAACTTGGACTATCGCAACGAACTTGGACTA
* *
1360741 TCGCAACGAATTTGTAATAA
62 TCGCAACGAACTTGGAATAA
*
1360761 ATCGCAACGCGAACTTTG-ACTATCGCAACGCAAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTGGAACTATCGCAACG--AACTTGGACTATCGCAA
1360810 TGCGAATATG
Statistics
Matches: 329, Mismatches: 30, Indels: 48
0.81 0.07 0.12
Matches are distributed among these distances:
80 12 0.04
82 107 0.33
83 5 0.02
84 175 0.53
85 1 0.00
86 29 0.09
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (81 bp):
ATCGCAACGCGAACTTGGAACTATCGCAACGAACTTGGACTATCGCAACGAACTTGGACTATCGC
AACGAACTTGGAATAA
Found at i:1360515 original size:63 final size:60
Alignment explanation
Indices: 1360338--1360809 Score: 370
Period size: 61 Copynumber: 7.5 Consensus size: 60
1360328 CGTTGCGATT
* * * *
1360338 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT--ATCGCAA-CGAAC
1 TTGGACTATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACCGAAC
* * *
1360399 TTGGACTATCGCAATGAACTTGGAATAAATCGCAACGCGAACTT-GAACT--ATCGCAA-CGAAC
1 TTGGACTATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAA-TAAATCGCAACCGAAC
* * *
1360460 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAAC-CGAAC
* * *
1360525 TTCGACTATCTCAACGAACTTGGACTATCGCAACGCGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGACTATCGCAA--CGAATTTGGAATAAATCGCAAC-CGAAC
* * * * * *
1360588 TTGGACTATCGCAACGAACTTGGAATAAATCGTAACGCGAACTTCGACT--ATCGCAA-CGAAT
1 TTGGACTATCGCAACGAACTTGGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACCGAAC
* * *
1360649 TTGGAATAAATCGCAACGAACTTGGAATAAATCGCAATGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGAACTTGGACT--ATCGCAACGAATTTGGAATAAATCGCAAC-CGAAC
* * * *
1360714 TTCGACTATCGCAATGAACTTGGACAATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAAC-CGAAC
*
1360775 TTTGACTATCGCAACGCAAACTTGGACTATCGCAA
1 TTGGACTATCGCAACG--AACTTGGACTATCGCAA
1360810 TGCGAATATG
Statistics
Matches: 351, Mismatches: 38, Indels: 42
0.81 0.09 0.10
Matches are distributed among these distances:
60 2 0.01
61 153 0.44
62 3 0.01
63 149 0.42
65 44 0.13
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (60 bp):
TTGGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACCGAAC
Found at i:1360598 original size:105 final size:103
Alignment explanation
Indices: 1360338--1360685 Score: 488
Period size: 105 Copynumber: 3.3 Consensus size: 103
1360328 CGTTGCGATT
1360338 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
* * * *
1360403 ACT--ATCGCAA--TGAACTTGGAATAAATCGCAACGCGAAC
66 AATAAATCGCAACGCGAACTTCGACT--ATCGCAA--CGAAC
*
1360441 TTGAACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
*
1360506 AATAAATCGCAACGCGAACTTCGACTATCTCAACGAAC
66 AATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
* * *
1360544 TTGGACTATCGCAACGCGAATTTGTAATAAATCGCAACGCGAACTTGGACTATCGCAACGAACTT
1 TTGGACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTT
* *
1360609 GGAATAAATCGTAACGCGAACTTCGACTATCGCAACGAAT
64 GGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
*
1360649 TTGGAATAAATCGCAACGAACTTGGAATAAATCGCAA
1 TTGGACT--ATCGCAACGAACTTGGAATAAATCGCAA
1360686 TGAATTTGGA
Statistics
Matches: 221, Mismatches: 16, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
103 84 0.38
105 121 0.55
107 16 0.07
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (103 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG
AATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
Found at i:1360704 original size:105 final size:104
Alignment explanation
Indices: 1360345--1360809 Score: 440
Period size: 105 Copynumber: 4.5 Consensus size: 104
1360335 ATTTTGGACT
* *
1360345 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACT--AT
1 ATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTGGACTATCGCAACGAACTTGGAATAAAT
* * * *
1360408 CGCAA--TGAACTTGGAATAAATCGCAACGCGAACTT-GAACT--
65 CGCAACGCGAACTTCGACT--ATCGCAA--CGAATTTGGAA-TAA
*
1360448 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTGGACTATCGCAACGAACTTGGAATAAAT
* * *
1360513 CGCAACGCGAACTTCGACTATCTCAACGAACTTGGACT--
65 CGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* *
1360551 ATCGCAACGCGAATTTGTAATAAATCGCAACGCGAACTTGGACTATCGCAACGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAAATCGCAAC-CGAACTTGGACTATCGCAACGAACTTGGAATAA
*
1360616 ATCGTAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
63 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* * * * *
1360658 ATCGCAACGAACTTGGAATAAATCGCAA-TGAATTTGGAATAAATCGCAACGCGAACTTCGACT-
1 ATCGCAACGAACTTGGAATAAATCGCAACCGAACTTGGACT--ATCGCAA--CGAACTTGGAATA
* * * *
1360721 -ATCGCAA--TGAACTTGGACAATCGCAACGAATTTGTAATAA
62 AATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* * *
1360761 ATCGCAACGCGAACTTTGACT--ATCGCAACGCAAACTTGGACTATCGCAA
1 ATCGCAA--CGAACTTGGAATAAATCGCAAC-CGAACTTGGACTATCGCAA
1360810 TGCGAATATG
Statistics
Matches: 314, Mismatches: 31, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
103 134 0.43
104 2 0.01
105 152 0.48
107 26 0.08
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (104 bp):
ATCGCAACGAACTTGGAATAAATCGCAACCGAACTTGGACTATCGCAACGAACTTGGAATAAATC
GCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
Found at i:1360785 original size:21 final size:19
Alignment explanation
Indices: 1360770--1360809 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1360760 AATCGCAACG
*
1360770 CGAACTTTGACTATCGCAA
1 CGAACTTGGACTATCGCAA
1360789 CGCAAACTTGGACTATCGCAA
1 CG--AACTTGGACTATCGCAA
1360810 TGCGAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
21 16 0.89
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:1362453 original size:3 final size:3
Alignment explanation
Indices: 1362445--1362474 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1362435 ATTTTAAACG
1362445 TTA TTA TTA TTA TTA TTA TTA TTA TGTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
1362475 TGAAGAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1367176 original size:22 final size:22
Alignment explanation
Indices: 1367148--1367382 Score: 321
Period size: 22 Copynumber: 10.5 Consensus size: 22
1367138 ATTTTAAAAT
1367148 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
*
1367170 TTTATTTTAAAATATGGATTGG
1 TTTATTTTAAAATATGGATTGA
1367192 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
* ***
1367214 TTTATTTTAAAATATGAAAAAAAAA
1 TTTATTTTAAAATATG---GATTGA
*
1367239 ATTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
1367261 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
1367282 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
1367305 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGGATTGA
**
1367327 TTTATTTTAAAATATGGA-AAA
1 TTTATTTTAAAATATGGATTGA
1367348 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGGATTGA
1367371 TTTATTTTAAAA
1 TTTATTTTAAAA
1367383 AATTTATTAT
Statistics
Matches: 186, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.01
22 165 0.89
23 2 0.01
25 17 0.09
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TTTATTTTAAAATATGGATTGA
Found at i:1367218 original size:66 final size:66
Alignment explanation
Indices: 1367143--1367382 Score: 365
Period size: 66 Copynumber: 3.6 Consensus size: 66
1367133 AATCTATTTT
*
1367143 AAAATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGGTTTATTTTAAAATATG
1 AAAATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATG
1367208 G
66 G
** * *** *
1367209 ATTGA-TTTATTTTAAAATATGAAAAAAAAAATTATTTTAAAATATGGATTGATTTATTTTAAAA
1 A-AAATTTTATTTTAAAATATG---GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1367273 TATGG
62 TATGG
1367278 AAAATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATG
1 AAAATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATG
1367343 G
66 G
1367344 AAAATTTTATTTTAAAATATGGATTGATTTATTTTAAAA
1 AAAATTTTATTTTAAAATATGGATTGATTTATTTTAAAA
1367383 AATTTATTAT
Statistics
Matches: 154, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
66 96 0.62
67 1 0.01
68 1 0.01
69 56 0.36
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (66 bp):
AAAATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATG
G
Found at i:1375305 original size:213 final size:213
Alignment explanation
Indices: 1374935--1375364 Score: 734
Period size: 213 Copynumber: 2.0 Consensus size: 213
1374925 TAAAAGCTTC
* * * *
1374935 AGATAAGAAAAGTGGCACAAATAAAGCTCATTCCAGTGACTCTGATGCACTTGGAAAGGACTCGA
1 AGATAAGAAAAGTGGCACAAATAAAGCTCATTCCAATGACTCCGATGCACATGGAAAGGACTCAA
* *
1375000 AAGAGGTAACAGTCGCACCTGAAGCAACTCAACAAACTGCTATGGTTGATGATTCCAAAGACATC
66 AAGAGGTAACAGTCGCACCCGAAGCAACTCAACAAACTGCTATGGTCGATGATTCCAAAGACATC
* *
1375065 CAAGAGTTGCAGAGTACTACTTCGATCGTAACACCTGAAGAAAATGAAATATCTCAAAGCTCCAA
131 CAAGAGTTGCAGAGTACTACATCGATCGTAACACCCGAAGAAAATGAAATATCTCAAAGCTCCAA
*
1375130 GGGGAACCATCTTATTGA
196 GGGGAACCATCTTACTGA
*
1375148 AGATAAGAAAAGTGGCACAGATAAAGCTCATTCCAATGACTCCGATGCACATGGAAAGGACTCAA
1 AGATAAGAAAAGTGGCACAAATAAAGCTCATTCCAATGACTCCGATGCACATGGAAAGGACTCAA
* * *
1375213 AAGAGGTAACAGTCGCACCCGAAGCAACTCAGCAAACTGCTATTGTCGATGATTCCGAAGACATC
66 AAGAGGTAACAGTCGCACCCGAAGCAACTCAACAAACTGCTATGGTCGATGATTCCAAAGACATC
*
1375278 CAAGAGTTGCAGAGTACTACATCGATCGTAACACCCGAAGAAAATGAAATTTCTCAAAGCTCCAA
131 CAAGAGTTGCAGAGTACTACATCGATCGTAACACCCGAAGAAAATGAAATATCTCAAAGCTCCAA
1375343 GGGGAACCATCTTACTGA
196 GGGGAACCATCTTACTGA
1375361 AGAT
1 AGAT
1375365 GACAAGCCAG
Statistics
Matches: 203, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
213 203 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (213 bp):
AGATAAGAAAAGTGGCACAAATAAAGCTCATTCCAATGACTCCGATGCACATGGAAAGGACTCAA
AAGAGGTAACAGTCGCACCCGAAGCAACTCAACAAACTGCTATGGTCGATGATTCCAAAGACATC
CAAGAGTTGCAGAGTACTACATCGATCGTAACACCCGAAGAAAATGAAATATCTCAAAGCTCCAA
GGGGAACCATCTTACTGA
Found at i:1376271 original size:3 final size:3
Alignment explanation
Indices: 1376263--1376335 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
1376253 ATTGTAATTG
1376263 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1376311 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
1376336 GCTTATTTAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1377579 original size:19 final size:19
Alignment explanation
Indices: 1377533--1377579 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1377523 CATTAATTTG
*
1377533 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
1377553 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
1377573 TATATTT
1 TATATTT
1377580 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:1380028 original size:31 final size:32
Alignment explanation
Indices: 1379992--1380053 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1379982 ATTTTACATG
1379992 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
1380023 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1380054 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:1383710 original size:14 final size:15
Alignment explanation
Indices: 1383691--1383722 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1383681 AAGAGAAGAC
1383691 AAATTTG-TGGGGCA
1 AAATTTGATGGGGCA
1383705 AAATTTGATGGGGCA
1 AAATTTGATGGGGCA
1383720 AAA
1 AAA
1383723 AAAATTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.25
Consensus pattern (15 bp):
AAATTTGATGGGGCA
Found at i:1384523 original size:106 final size:103
Alignment explanation
Indices: 1384364--1384559 Score: 288
Period size: 106 Copynumber: 1.9 Consensus size: 103
1384354 AATTTATCTT
* *
1384364 AAAACAAATTTCTCTCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTT-CACTTG
1 AAAACAAATTTCTCTCTTGAGACATTTTTCCTCTGAGATACAAATTTTAAATTTG-TTGCACTTG
*
1384428 AAACAAAATTAATCTCACTTGAGATTGTTGTTTTTTAAA
65 AAACAAAATTAATATCACTTGAGATTGTTGTTTTTTAAA
* *
1384467 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTTCTCTGAGATACAAA-TTTAAATTTGTTGTAC
1 AAAACAAATTTC-TCT--CTTGAGACA-TTTTTCCTCTGAGATACAAATTTTAAATTTGTTGCAC
1384531 TTGAAACAAAATTAATATCACTTGAGATT
62 TTGAAACAAAATTAATATCACTTGAGATT
1384560 TTCAAAGCTG
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
103 12 0.14
104 3 0.04
105 2 0.02
106 48 0.58
107 18 0.22
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (103 bp):
AAAACAAATTTCTCTCTTGAGACATTTTTCCTCTGAGATACAAATTTTAAATTTGTTGCACTTGA
AACAAAATTAATATCACTTGAGATTGTTGTTTTTTAAA
Found at i:1384757 original size:28 final size:30
Alignment explanation
Indices: 1384726--1384801 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
1384716 TTGTGAGACA
*
1384726 GTTTCTCTTG-AA-ATAAATCTTTGAGTCT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
*
1384754 GTTTCTTTTGAAACAAAAATCTTTGAGTCT
1 GTTTCTCTTGAAACAAAAATCTTTGAGTCT
1384784 GTTTCT-TTGGAAACAAAA
1 GTTTCTCTT-GAAACAAAA
1384802 TTTTGTCTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 9 0.21
29 4 0.09
30 30 0.70
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (30 bp):
GTTTCTCTTGAAACAAAAATCTTTGAGTCT
Found at i:1384802 original size:29 final size:30
Alignment explanation
Indices: 1384740--1384801 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1384730 CTCTTGAAAT
*
1384740 AAATCTTTGAGTCTGTTTCTTTTGAAACAA
1 AAATCTTTGAGTCTGTTTCTTTGGAAACAA
1384770 AAATCTTTGAGTCTGTTTCTTTGGAAACAA
1 AAATCTTTGAGTCTGTTTCTTTGGAAACAA
1384800 AA
1 AA
1384802 TTTTGTCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (30 bp):
AAATCTTTGAGTCTGTTTCTTTGGAAACAA
Found at i:1384860 original size:26 final size:25
Alignment explanation
Indices: 1384822--1384939 Score: 59
Period size: 26 Copynumber: 4.6 Consensus size: 25
1384812 CTTAAGACAA
*
1384822 TTTCTTTTGAAAAAATCTTTGAGTCTG
1 TTTCTCTT-AAAAAATCTTTGAGT-TG
*
1384849 TTTCTCTT--AAAA----TGAGATAG
1 TTTCTCTTAAAAAATCTTTGAG-TTG
*
1384869 TTTCTCTTGAAATAAATCTTTGAATATG
1 TTTCTCTT-AAA-AAATCTTTGAGT-TG
* * *
1384897 TTCCTTTTGAAAAATCTTTGAGTTTG
1 TTTCTCTTAAAAAATCTTTGAG-TTG
*
1384923 CTTCTCTTAACAAAATC
1 TTTCTCTTAA-AAAATC
1384940 ATCTTTGAGT
Statistics
Matches: 67, Mismatches: 12, Indels: 24
0.65 0.12 0.23
Matches are distributed among these distances:
20 13 0.19
21 1 0.01
23 1 0.01
24 7 0.10
26 18 0.27
27 17 0.25
28 10 0.15
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (25 bp):
TTTCTCTTAAAAAATCTTTGAGTTG
Found at i:1385792 original size:35 final size:35
Alignment explanation
Indices: 1385752--1385860 Score: 126
Period size: 35 Copynumber: 3.3 Consensus size: 35
1385742 CTTTGAGTCG
1385752 TTCCCTTTAACGAATTTTGTCTCATTTGAGACAGT
1 TTCCCTTTAACGAATTTTGTCTCATTTGAGACAGT
* *
1385787 TTCCCTTT-A--AA---CGTCGTC-TTTGAGTC-GT
1 TTCCCTTTAACGAATTTTGTC-TCATTTGAGACAGT
1385815 TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGT
1 TTCCCTTT-AACGAATTTTGTCTCATTTGAGACAGT
1385851 TTCCCTTTAA
1 TTCCCTTTAA
1385861 ACGTCGTCTT
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
28 10 0.17
29 10 0.17
30 3 0.05
32 4 0.07
34 3 0.05
35 20 0.33
36 10 0.17
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (35 bp):
TTCCCTTTAACGAATTTTGTCTCATTTGAGACAGT
Found at i:1385854 original size:64 final size:64
Alignment explanation
Indices: 1385690--1385914 Score: 404
Period size: 64 Copynumber: 3.6 Consensus size: 64
1385680 TTGAGATCAA
1385690 TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTCCC-TTAAACGTCGTCTTTGAGTCG-
1 TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTCCCTTTAAACGTCGTCTTTGAGTCGT
1385752 TTCCCTTT-AACGAATTTTGTCTCATTTGAGACAGTTTCCCTTTAAACGTCGTCTTTGAGTCGT
1 TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTCCCTTTAAACGTCGTCTTTGAGTCGT
*
1385815 TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTCCCTTTAAACGTCGTCTTTGAGTTGT
1 TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTCCCTTTAAACGTCGTCTTTGAGTCGT
*
1385879 TTCCCTTAAAACGAATTTTGTCTC-TTTGAGACAGTT
1 TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTT
1385915 GCTTTAAAAT
Statistics
Matches: 158, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
61 32 0.20
62 29 0.18
63 20 0.13
64 77 0.49
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (64 bp):
TTCCCTTTAAACGAATTTTGTCTCATTTGAGACAGTTTCCCTTTAAACGTCGTCTTTGAGTCGT
Found at i:1385959 original size:28 final size:27
Alignment explanation
Indices: 1385928--1385988 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
1385918 TTAAAATATC
1385928 ATCTTTGAGTTTATTT-TTCTTGAAACAA
1 ATCTTTGAGTTTATTTCTT-TTGAAAC-A
* *
1385956 ATCTTTGGGTTTGTTTCTTTTGAAACA
1 ATCTTTGAGTTTATTTCTTTTGAAACA
1385983 ATCTTT
1 ATCTTT
1385989 AATTTGGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 7 0.23
28 21 0.70
29 2 0.07
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.52
Consensus pattern (27 bp):
ATCTTTGAGTTTATTTCTTTTGAAACA
Found at i:1386089 original size:40 final size:40
Alignment explanation
Indices: 1386034--1386397 Score: 143
Period size: 40 Copynumber: 8.6 Consensus size: 40
1386024 TGGCCAGCCG
*
1386034 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
* * ** *
1386074 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGATC
* * *
1386116 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATC
* * *
1386163 TCTTCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGATC
* * * * *
1386203 TCTTCATCACGTATGAGCTGTAGTCA-CCCTAGATACCAG-TC
1 TCCTCATCACGTAGGAACCGT-GTCATCCCCAG--ACCAGATC
* * * *
1386244 GTCCTCATCACGTAGCCG-AGC-TATCACCACTCCTAAAGATGGCCAG-CC
1 -TCCTCATCACGTAG--GAACCGTGTCATC-C-CC---AGA---CCAGATC
* *
1386292 GTCCTCAACACGTAGGAACCGTGTCATCCCTC-GACCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATCCC-CAGACCAGATC
* * * * * *
1386333 TCTTCATCACGTATGAGCAGTGTCAACCCTC-GACCAGATT
1 TCCTCATCACGTAGGAACCGTGTCATCCC-CAGACCAGATC
*
1386373 TCCTCATCACGTAGGAACCATGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
1386398 CCCTTAGACG
Statistics
Matches: 247, Mismatches: 45, Indels: 64
0.69 0.13 0.18
Matches are distributed among these distances:
39 3 0.01
40 110 0.45
41 10 0.04
42 20 0.08
43 35 0.14
44 3 0.01
45 1 0.00
46 32 0.13
47 9 0.04
48 24 0.10
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
Found at i:1386362 original size:130 final size:129
Alignment explanation
Indices: 1386013--1386386 Score: 426
Period size: 129 Copynumber: 2.9 Consensus size: 129
1386003 TGAAACCATA
* *
1386013 ACTCCTAAAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCT
1 ACTCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCC-GACCAGATCTCTT
* * * * * *
1386078 CATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTAT
65 CATCACGTATGAGCAGTGTCAACCCTAGAT-ACCAGTCGTCCTCATCACGTA-G-ACCGAGCTAT
1386143 CAC
127 CAC
* * * * *
1386146 -CT--T-TAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCT
1 ACTCCTAAAGATGGCCAG-CCGTCCTCATCACGTAGGAACCGTGTCA-TCCCCGACCAGATCTCT
*
1386206 TCATCACGTATGAGCTGTAGTC-ACCCTAGATACCAGTCGTCCTCATCACGTAG-CCGAGCTATC
64 TCATCACGTATGAGCAGT-GTCAACCCTAGATACCAGTCGTCCTCATCACGTAGACCGAGCTATC
1386269 ACC
128 A-C
* *
1386272 ACTCCTAAAGATGGCCAGCCGTCCTCAACACGTAGGAACCGTGTCATCCCTCGACCAGAACTCTT
1 ACTCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCC-CGACCAGATCTCTT
* *
1386337 CATCACGTATGAGCAGTGTCAACCCTCG--ACCAGAT-TTCCTCATCACGTAG
65 CATCACGTATGAGCAGTGTCAACCCTAGATACCAG-TCGTCCTCATCACGTAG
1386387 GAACCATGTC
Statistics
Matches: 206, Mismatches: 23, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
125 9 0.04
126 1 0.00
127 3 0.01
128 39 0.19
129 76 0.37
130 76 0.37
132 2 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (129 bp):
ACTCCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCGACCAGATCTCTTC
ATCACGTATGAGCAGTGTCAACCCTAGATACCAGTCGTCCTCATCACGTAGACCGAGCTATCAC
Found at i:1386617 original size:3 final size:3
Alignment explanation
Indices: 1386609--1386669 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
1386599 ATTGTAATTG
1386609 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1386657 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
1386670 GCTTATTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1387892 original size:19 final size:19
Alignment explanation
Indices: 1387846--1387892 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1387836 CATTAATTTG
*
1387846 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
1387866 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
1387886 TATATTT
1 TATATTT
1387893 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:1390175 original size:37 final size:37
Alignment explanation
Indices: 1390120--1390191 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
1390110 TAGCTCCATA
1390120 TGATTACTGTCTTCGTCCTCGATCTCATTGCTTTTTT
1 TGATTACTGTCTTCGTCCTCGATCTCATTGCTTTTTT
*
1390157 TGATTACTGTCTTTGTCCTCGATCTCATTGCTTTT
1 TGATTACTGTCTTCGTCCTCGATCTCATTGCTTTT
1390192 GGTTTAGCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.14, T:0.51
Consensus pattern (37 bp):
TGATTACTGTCTTCGTCCTCGATCTCATTGCTTTTTT
Found at i:1391548 original size:9 final size:8
Alignment explanation
Indices: 1391518--1391548 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1391508 TTTCGCATTC
1391518 TTTAAAAT
1 TTTAAAAT
1391526 TTTAAAAT
1 TTTAAAAT
1391534 TTTAAAAT
1 TTTAAAAT
1391542 ATTTAAA
1 -TTTAAA
1391549 TTTCTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1394628 original size:27 final size:28
Alignment explanation
Indices: 1394598--1394660 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
1394588 TTATAAACCC
** * **
1394598 TAAATCTTAATTA-TAATTTCTAAATTT
1 TAAATCTTAAACACTAAATTCTAAATCA
1394625 TAAAT-TTAAACACTAAATTCTAAATCA
1 TAAATCTTAAACACTAAATTCTAAATCA
1394652 TAAATCTTA
1 TAAATCTTA
1394661 CTATCCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 5 0.17
27 21 0.72
28 3 0.10
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (28 bp):
TAAATCTTAAACACTAAATTCTAAATCA
Found at i:1403674 original size:29 final size:29
Alignment explanation
Indices: 1403625--1403728 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
1403615 ACATTCAACT
* * *
1403625 ATTACAAAAATAGCACATTTTTAAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
*
1403654 ATTACCAAAATATCACCTTTTTCAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
* *
1403683 ATTACTAAAATATCACCTTTTTTAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
*
1403712 ATTCCCAAAATATCACC
1 ATTACCAAAATATCACC
1403729 AGGGCGGGTC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (29 bp):
ATTACCAAAATATCACCTTTTTAAAAATA
Found at i:1404509 original size:10 final size:10
Alignment explanation
Indices: 1404494--1404520 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1404484 TTTAATTTAG
1404494 TCACCAAATT
1 TCACCAAATT
1404504 TCACCAAATT
1 TCACCAAATT
1404514 TCACCAA
1 TCACCAA
1404521 TTTAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (10 bp):
TCACCAAATT
Found at i:1411084 original size:30 final size:30
Alignment explanation
Indices: 1411044--1411146 Score: 122
Period size: 29 Copynumber: 3.5 Consensus size: 30
1411034 ACATTCAACT
* * *
1411044 ATTACGAAAATAACACATTTTTTAAAAATG
1 ATTACCAAAATATCACATTTTTTAAAAATA
* *
1411074 ATTACCAAAATATCAC-CTTTTTCAAAATA
1 ATTACCAAAATATCACATTTTTTAAAAATA
*
1411103 ATTACTAAAATATCACATTTTTT-AAAATA
1 ATTACCAAAATATCACATTTTTTAAAAATA
1411132 ATT-CTCAAAATATCA
1 ATTAC-CAAAATATCA
1411147 TCGGGGCGGG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 43 0.68
30 19 0.30
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.36
Consensus pattern (30 bp):
ATTACCAAAATATCACATTTTTTAAAAATA
Found at i:1417820 original size:54 final size:54
Alignment explanation
Indices: 1417754--1417863 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 54
1417744 CCTCAGTGTC
* *
1417754 TATCATTGATTTTAATGATTGTTTACCACA-TATCTCAGTACCTAGTGAAAATGA
1 TATCATTGATTTTAATGATTGTTTACCACAGT-TCCCAGCACCTAGTGAAAATGA
*
1417808 TATCATTTATTTTAATGATTGTTTACCACAGTTCCCAGCACCTAGTGAAAATGA
1 TATCATTGATTTTAATGATTGTTTACCACAGTTCCCAGCACCTAGTGAAAATGA
1417862 TA
1 TA
1417864 ACAACTTTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 51 0.98
55 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (54 bp):
TATCATTGATTTTAATGATTGTTTACCACAGTTCCCAGCACCTAGTGAAAATGA
Found at i:1420059 original size:29 final size:30
Alignment explanation
Indices: 1420001--1420072 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
1419991 TTTCTCTCTT
* *
1420001 ATTTCAATCACTATATTTTTAATTTTTTTC
1 ATTTTAATCACTACATTTTTAATTTTTTTC
1420031 ATTTTAATCACTACATTTTTAA-TTTTTTC
1 ATTTTAATCACTACATTTTTAATTTTTTTC
*
1420060 AATTTAATCACTA
1 ATTTTAATCACTA
1420073 AACTTTATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTAATCACTACATTTTTAATTTTTTTC
Found at i:1420351 original size:33 final size:33
Alignment explanation
Indices: 1420307--1420395 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
1420297 CGACCATGAT
* *
1420307 CCCTTTTCTTTCCGACCACCCTCCGTC-AACTGG
1 CCCTTTCCTTTCCGACCACACTCCGTCAAAC-GG
*
1420340 TCCTTTCCTTTCCGACCACACTCCGTCAAACGG
1 CCCTTTCCTTTCCGACCACACTCCGTCAAACGG
* *
1420373 CCCTTTCCTTTTCGACCATACTC
1 CCCTTTCCTTTCCGACCACACTC
1420396 TGTCCACTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 46 0.94
34 3 0.06
ACGTcount: A:0.15, C:0.44, G:0.10, T:0.31
Consensus pattern (33 bp):
CCCTTTCCTTTCCGACCACACTCCGTCAAACGG
Found at i:1422942 original size:29 final size:28
Alignment explanation
Indices: 1422889--1422994 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 28
1422879 CAGTGTTGCC
*
1422889 GTAGGTCGCCAGGGCATC-CCAGCGACATG
1 GTAGGTCGCCA-TGCA-CGCCAGCGACATG
1422918 GTAGGTCGCCATGCACGCCAGGCGACATG
1 GTAGGTCGCCATGCACGCCA-GCGACATG
* * * * *
1422947 GTAGGTCGTCATGCACTCCCAACGACCTT
1 GTAGGTCGCCATGCAC-GCCAGCGACATG
*
1422976 ATAGGTCGCCATGCACGCC
1 GTAGGTCGCCATGCACGCC
1422995 CGACGTCCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 8 0.12
29 53 0.82
30 3 0.05
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (28 bp):
GTAGGTCGCCATGCACGCCAGCGACATG
Found at i:1423544 original size:27 final size:29
Alignment explanation
Indices: 1423480--1423544 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
1423470 TATATTAAAA
1423480 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* * *
1423509 -AGTATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1423535 AAATAGTTAA
1 AAATAATTAA
1423545 GTTATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.03
27 15 0.50
28 14 0.47
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1423633 original size:27 final size:28
Alignment explanation
Indices: 1423603--1423660 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
1423593 AGTTTATTAG
*
1423603 TAGTTTA-AGTTTTA-TTATAATAAAAAA
1 TAGTTTATAGTTTAAGTTAT-ATAAAAAA
1423630 TAGTTTATTAGTTTAAGTTATATAAAAAA
1 TAGTTTA-TAGTTTAAGTTATATAAAAAA
1423659 TA
1 TA
1423661 ATTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
29 16 0.59
30 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (28 bp):
TAGTTTATAGTTTAAGTTATATAAAAAA
Found at i:1426167 original size:59 final size:58
Alignment explanation
Indices: 1426033--1426151 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 58
1426023 AAAAATATAT
*
1426033 TAAATAAT-ATT-TTAAATCATTAGTATCAAATAATTAAATATTAATAATAAATCATTA
1 TAAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATT-ATAATAAATCATTA
* *
1426090 TTAATAATAATTAGTAAATCATTAGTATCAAATCATTAAATATT-TAA-AAATCATTAA
1 TAAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATT-A
1426147 TAAAT
1 TAAAT
1426152 TCGACTATGT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
56 8 0.15
57 15 0.27
58 3 0.05
59 29 0.53
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (58 bp):
TAAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATTA
Found at i:1426306 original size:14 final size:14
Alignment explanation
Indices: 1426228--1426500 Score: 164
Period size: 14 Copynumber: 20.1 Consensus size: 14
1426218 ATTAGTAATA
1426228 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1426242 AGTATTAAATCATT
1 ATTATTAAATCATT
*
1426256 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
1426267 ATTACTAAAT-A--
1 ATTATTAAATCATT
* *
1426278 ATTACTAAATAATT
1 ATTATTAAATCATT
*
1426292 ACTATTAAATCATT
1 ATTATTAAATCATT
* * *
1426306 ATTATCATTATTATT
1 ATTATTA-AATCATT
1426321 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1426335 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1426347 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1426361 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1426373 ATTATCAAATCATT
1 ATTATTAAATCATT
* *
1426387 ACTAAATCATCAAATTATT
1 A-T---T-ATTAAATCATT
*
1426406 AAATATTTAAATCATT
1 -ATTA-TTAAATCATT
*
1426422 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1426434 ATTACTAAATCATT
1 ATTATTAAATCATT
*
1426448 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1426460 ATTATCAAATCATT
1 ATTATTAAATCATT
*
1426474 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1426486 ATTATCAAATCATT
1 ATTATTAAATCATT
1426500 A
1 A
1426501 CTAAATATCA
Statistics
Matches: 204, Mismatches: 32, Indels: 46
0.72 0.11 0.16
Matches are distributed among these distances:
11 16 0.08
12 55 0.27
13 11 0.05
14 85 0.42
15 16 0.08
16 9 0.04
18 1 0.00
19 10 0.05
20 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1426314 original size:9 final size:9
Alignment explanation
Indices: 1426300--1426339 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
1426290 TTACTATTAA
1426300 ATCATTATT
1 ATCATTATT
1426309 ATCATTATT
1 ATCATTATT
*
1426318 ATTATTATT
1 ATCATTATT
1426327 AAATCATTATT
1 --ATCATTATT
1426338 AT
1 AT
1426340 AATGATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 19 0.70
11 8 0.30
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (9 bp):
ATCATTATT
Found at i:1426324 original size:26 final size:26
Alignment explanation
Indices: 1426204--1426490 Score: 172
Period size: 26 Copynumber: 11.3 Consensus size: 26
1426194 CTCATTTGTT
* * *
1426204 ATTATTCT-ATAATTATTAGT-AATA
1 ATTATTATAATAATTATTATTAAATC
* *
1426228 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATAATTATTATTAAATC
* * *
1426253 ATTATTATAA-AATCATTACTAAATA
1 ATTATTATAATAATTATTATTAAATC
* *
1426278 ATTACTA-AATAATTACTATTAAATC
1 ATTATTATAATAATTATTATTAAATC
*
1426303 ATTATTATCATTATTATTATTATTAAATC
1 ATTATTAT-A--ATAATTATTATTAAATC
* *
1426332 ATTATTATAATGATTATTACTAAATC
1 ATTATTATAATAATTATTATTAAATC
* *
1426358 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATAATTATTATTAAATC
* * *
1426384 ATTACTA-AATCATCAAATTATTAAAT-
1 ATTATTATAATAAT--TATTATTAAATC
* *
1426410 A-T-TTA-AATCATTATTA-T-AATG
1 ATTATTATAATAATTATTATTAAATC
* *
1426431 ATTATTACT-A-AATCATTATTATAATG
1 ATTATTA-TAATAATTATTATTA-AATC
* * *
1426457 ATTATTATCA-AATCATTATTATAATG
1 ATTATTATAATAATTATTATTA-AATC
1426483 ATTATTAT
1 ATTATTAT
1426491 CAAATCATTA
Statistics
Matches: 214, Mismatches: 30, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
20 3 0.01
21 2 0.01
22 5 0.02
23 9 0.04
24 27 0.13
25 50 0.23
26 84 0.39
27 10 0.05
28 1 0.00
29 23 0.11
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATTATAATAATTATTATTAAATC
Found at i:1426347 original size:20 final size:20
Alignment explanation
Indices: 1426309--1426347 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1426299 AATCATTATT
* *
1426309 ATCATTATTATTATTATTAA
1 ATCATTATTATAATGATTAA
1426329 ATCATTATTATAATGATTA
1 ATCATTATTATAATGATTA
1426348 TTACTAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
ATCATTATTATAATGATTAA
Found at i:1426427 original size:87 final size:81
Alignment explanation
Indices: 1426239--1426500 Score: 309
Period size: 87 Copynumber: 3.2 Consensus size: 81
1426229 TTATTAAATC
* * * * * * * *
1426239 ATTAGTATTAAATCATTATTATAA-AATCATTACTAAATAATTACTA-AATAATTACTATTAAAT
1 ATTAATATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAAT
* *
1426302 CATTATTATCATTATT
66 CATTATAATCATAATT
*
1426318 ATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAAT
1 ATTAATATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAAT
1426383 CATTACTAAATCATCAAATT
66 CATTA-T-AATCAT--AATT
1426403 ATTAAATATTTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAA
1 ATT-AATA-TTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAA
*
1426468 ATCATTAT--T-ATAATG
64 ATCATTATAATCATAATT
* *
1426483 ATTATTATCAAATCATTA
1 ATTAATATTAAATCATTA
1426501 CTAAATATCA
Statistics
Matches: 161, Mismatches: 14, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
78 10 0.06
79 26 0.16
80 24 0.15
81 19 0.12
82 3 0.02
83 6 0.04
85 6 0.04
86 4 0.02
87 63 0.39
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (81 bp):
ATTAATATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAAT
CATTATAATCATAATT
Found at i:1426434 original size:12 final size:12
Alignment explanation
Indices: 1426419--1426490 Score: 90
Period size: 12 Copynumber: 5.7 Consensus size: 12
1426409 TATTTAAATC
1426419 ATTATTATAATG
1 ATTATTATAATG
*
1426431 ATTATTACTAAATC
1 ATTATTA-T-AATG
1426445 ATTATTATAATG
1 ATTATTATAATG
*
1426457 ATTATTATCAAATC
1 ATTATTAT--AATG
1426471 ATTATTATAATG
1 ATTATTATAATG
1426483 ATTATTAT
1 ATTATTAT
1426491 CAAATCATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
12 29 0.56
13 2 0.04
14 21 0.40
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (12 bp):
ATTATTATAATG
Found at i:1426470 original size:113 final size:112
Alignment explanation
Indices: 1426228--1426513 Score: 380
Period size: 113 Copynumber: 2.5 Consensus size: 112
1426218 ATTAGTAATA
* * * *
1426228 ATTATTAAATCATTAGTATTAAATCATTATTATAAAATCATTACTAAATAATTACTAAATAATTA
1 ATTATCAAATCATTATTA-T-AATGATTATTATCAAATCATTACTAAAT-A-T-C-AAATAATTA
* * *
1426293 CTATTAAATCATTATTATCATTATTATTATTATTAAATCATTATTATAATGATT
60 ATATTAAATCATTATTATCA-TATGATTATTACTAAATCATTATTATAATGATT
*
1426347 ATTA-CTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATTATTAAATA
1 ATTATC-AAATCATTATTATAATGATTATTATCAAATCATTACTAAAT-ATCAAATAATT-AATA
1426411 TTTAAATCATTATTAT-A-ATGATTATTACTAAATCATTATTATAATGATT
63 -TTAAATCATTATTATCATATGATTATTACTAAATCATTATTATAATGATT
1426460 ATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATATCAAAT
1 ATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATATCAAAT
1426514 CTATCATAAT
Statistics
Matches: 154, Mismatches: 9, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
112 7 0.05
113 75 0.49
114 8 0.05
115 5 0.03
116 16 0.10
117 27 0.18
118 1 0.01
119 15 0.10
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (112 bp):
ATTATCAAATCATTATTATAATGATTATTATCAAATCATTACTAAATATCAAATAATTAATATTA
AATCATTATTATCATATGATTATTACTAAATCATTATTATAATGATT
Found at i:1426491 original size:26 final size:26
Alignment explanation
Indices: 1426414--1426500 Score: 158
Period size: 26 Copynumber: 3.3 Consensus size: 26
1426404 TTAAATATTT
1426414 AAATCATTATTATAATGATTATTA-C
1 AAATCATTATTATAATGATTATTATC
1426439 TAAATCATTATTATAATGATTATTATC
1 -AAATCATTATTATAATGATTATTATC
1426466 AAATCATTATTATAATGATTATTATC
1 AAATCATTATTATAATGATTATTATC
1426492 AAATCATTA
1 AAATCATTA
1426501 CTAAATATCA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
26 59 0.98
27 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (26 bp):
AAATCATTATTATAATGATTATTATC
Found at i:1426799 original size:12 final size:12
Alignment explanation
Indices: 1426782--1426840 Score: 79
Period size: 12 Copynumber: 5.1 Consensus size: 12
1426772 GTTCATTAAA
1426782 TATTAAATTCAT
1 TATTAAATTCAT
*
1426794 TATTAAATTTAT
1 TATTAAATTCAT
1426806 TATTAAA-TCAT
1 TATTAAATTCAT
1426817 TATTTAAATT-AT
1 TA-TTAAATTCAT
1426829 TATTAAA-TCAT
1 TATTAAATTCAT
1426840 T
1 T
1426841 TTTATGGTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 1 0.02
11 13 0.31
12 27 0.64
13 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:1426820 original size:23 final size:23
Alignment explanation
Indices: 1426782--1426844 Score: 94
Period size: 23 Copynumber: 2.7 Consensus size: 23
1426772 GTTCATTAAA
1426782 TATTAAATTCATTA-TTAAATTTAT
1 TATTAAA-TCATTATTTAAA-TTAT
1426806 TATTAAATCATTATTTAAATTAT
1 TATTAAATCATTATTTAAATTAT
1426829 TATTAAATCATT-TTTA
1 TATTAAATCATTATTTA
1426845 TGGTTAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.11
23 22 0.58
24 12 0.32
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTAAATCATTATTTAAATTAT
Found at i:1427141 original size:93 final size:94
Alignment explanation
Indices: 1426983--1427212 Score: 374
Period size: 93 Copynumber: 2.4 Consensus size: 94
1426973 ATTAAATCAT
* *
1426983 TATTATTATCAAATCATTAAATATTAATAAT-ATTCATTATTACTAATCATTACTATCAAATCAT
1 TATTACTATCAAATCATTAAAAATTAATAATAATTCATTATTACTAATCATTACTATCAAATCAT
1427047 TAAATATTAATAATAATTTCACTATTAC-
66 TAAATATTAATAATAATTTCACTATTACA
1427075 TATTACTATCAAATCATTAAAAATTAATAATAATTCATTATTACTAATCATTACTATCAAATCAT
1 TATTACTATCAAATCATTAAAAATTAATAATAATTCATTATTACTAATCATTACTATCAAATCAT
*
1427140 TAAATATTAATAATAATTTCATTATTACTAA
66 TAAATATTAATAATAATTTCACTATTAC--A
*
1427171 TCATTACTATCAAATTATTAAAAATTAATAATAATTTCATTA
1 T-ATTACTATCAAATCATTAAAAATTAATAATAA-TTCATTA
1427213 ATATTAGTTA
Statistics
Matches: 128, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
92 29 0.23
93 60 0.47
96 1 0.01
97 31 0.24
98 7 0.05
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (94 bp):
TATTACTATCAAATCATTAAAAATTAATAATAATTCATTATTACTAATCATTACTATCAAATCAT
TAAATATTAATAATAATTTCACTATTACA
Found at i:1427180 original size:49 final size:49
Alignment explanation
Indices: 1426984--1427212 Score: 364
Period size: 49 Copynumber: 4.8 Consensus size: 49
1426974 TTAAATCATT
*
1426984 ATTATTATCAAATCATTAAATATTAATAAT-A-TTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
1427031 ATTACTATCAAATCATTAAATATTAATAATAATTTCACTATTAC---T-
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
1427076 ATTACTATCAAATCATTAAAAATTAATAATAA-TTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1427124 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
* *
1427173 ATTACTATCAAATTATTAAAAATTAATAATAATTTCATTA
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTA
1427213 ATATTAGTTA
Statistics
Matches: 168, Mismatches: 7, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
44 10 0.06
45 31 0.18
46 1 0.01
47 30 0.18
48 32 0.19
49 64 0.38
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:1429707 original size:5 final size:5
Alignment explanation
Indices: 1429697--1429723 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1429687 AAGTTATTGC
1429697 TCCTT TCCTT TCCTT TCCTT TCCTT TC
1 TCCTT TCCTT TCCTT TCCTT TCCTT TC
1429724 TTGTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
TCCTT
Found at i:1430085 original size:45 final size:42
Alignment explanation
Indices: 1429996--1430096 Score: 130
Period size: 45 Copynumber: 2.3 Consensus size: 42
1429986 GTTTAAACAC
* *
1429996 ACTAACAAATTAATTAAATATTTTTTACATTTAATAACTTAA
1 ACTAACAAATTAATTAAATATTTTTTAAATCTAATAACTTAA
* * *
1430038 ACTAAGAAACTAATTAACTAATTTTTTATAATCTATATAACTTAA
1 ACTAACAAATTAATTAAAT-ATTTTTTA-AATCTA-ATAACTTAA
1430083 ACTAACAAATTAAT
1 ACTAACAAATTAAT
1430097 ATAATTTAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 16 0.33
43 8 0.16
44 4 0.08
45 21 0.43
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40
Consensus pattern (42 bp):
ACTAACAAATTAATTAAATATTTTTTAAATCTAATAACTTAA
Found at i:1430891 original size:29 final size:29
Alignment explanation
Indices: 1430836--1430913 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
1430826 ATTGGACGCC
*
1430836 GGGCGTGCATGGCGACCTATAAGGTCGCT
1 GGGCGTGCATGGCGACCTACAAGGTCGCT
* *
1430865 GGGCGTGCATGGCGACCTACCATGTCGCT
1 GGGCGTGCATGGCGACCTACAAGGTCGCT
* *
1430894 GGG-ATGCCCTGGCGACCTAC
1 GGGCGTG-CATGGCGACCTAC
1430914 GGCAACACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 2 0.05
29 41 0.95
ACGTcount: A:0.15, C:0.29, G:0.36, T:0.19
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTACAAGGTCGCT
Found at i:1432279 original size:16 final size:16
Alignment explanation
Indices: 1432245--1432283 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1432235 GGAAATTCCA
1432245 GGTACCC-AGAAATCG
1 GGTACCCGAGAAATCG
1432260 GGTACCCGA-AAATCCG
1 GGTACCCGAGAAAT-CG
1432276 GGTACCCG
1 GGTACCCG
1432284 GATTTGCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.13
Consensus pattern (16 bp):
GGTACCCGAGAAATCG
Found at i:1437705 original size:24 final size:24
Alignment explanation
Indices: 1437659--1437719 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1437649 TATATCTGCT
* * *
1437659 TAAAATAATATTGACGTTCTCTCC
1 TAAAATAATAATAACGTTATCTCC
*
1437683 TAAAATAATAATAATGTTATCTCC
1 TAAAATAATAATAACGTTATCTCC
*
1437707 TACAATAACTAAT
1 TAAAATAA-TAAT
1437720 GCTAACGTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (24 bp):
TAAAATAATAATAACGTTATCTCC
Found at i:1440167 original size:39 final size:39
Alignment explanation
Indices: 1440123--1440221 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
1440113 CAATTGCCTA
1440123 AATCCCTAATTCCCCATTTTCATTTCCC-TATCGTACCCC
1 AATCCCTAATTCCCCATTTTCATTTCCCAT-TCGTACCCC
* ** * * * *
1440162 GATCCCTAATTCCCTTTTTTTATTTCTCATTCGTATCGC
1 AATCCCTAATTCCCCATTTTCATTTCCCATTCGTACCCC
*
1440201 AATCCCTAATTCACCATTTTC
1 AATCCCTAATTCCCCATTTTC
1440222 CACTTCGTTT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
39 46 0.98
40 1 0.02
ACGTcount: A:0.20, C:0.34, G:0.04, T:0.41
Consensus pattern (39 bp):
AATCCCTAATTCCCCATTTTCATTTCCCATTCGTACCCC
Found at i:1445102 original size:65 final size:65
Alignment explanation
Indices: 1444942--1445102 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
1444932 TTATTTAAGG
* * * ** *
1444942 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
1445005 A
65 A
*
1445006 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
1445070 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1445103 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:1446696 original size:149 final size:149
Alignment explanation
Indices: 1446523--1446837 Score: 517
Period size: 149 Copynumber: 2.1 Consensus size: 149
1446513 GAGTCGAGGG
* **
1446523 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
1446588 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCTTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATT
* *
1446652 ATATGGCACTACGGTGTAAT
130 ATATGGCACTACAGTGCAAT
*
1446672 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1446737 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
1446802 TATGGCACTACAGTGCAAT
131 TATGGCACTACAGTGCAAT
1446821 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1446838 TGCAATTATA
Statistics
Matches: 155, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
148 1 0.01
149 153 0.99
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
TATGGCACTACAGTGCAAT
Found at i:1446840 original size:23 final size:23
Alignment explanation
Indices: 1446805--1446849 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1446795 ATTATTATAT
*
1446805 GGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTATACGC
* *
1446828 GGCACTTCGGTGCAATTATACG
1 GGCACTACAGTGCAATTATACG
1446850 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGC
Found at i:1448702 original size:39 final size:39
Alignment explanation
Indices: 1448658--1448756 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
1448648 CAATTGCCTG
1448658 AATCCCTAATTCCCCATTTTCATTTC-CCTCTCGCACCCC
1 AATCCCTAATTCCCCATTTTCATTTCTCCT-TCGCACCCC
* ** * *
1448697 GATCCCTAATTCCCTTTTTTCATTTCTCCTTCGCATCTC
1 AATCCCTAATTCCCCATTTTCATTTCTCCTTCGCACCCC
*
1448736 AATCCCTAATTCACCATTTTC
1 AATCCCTAATTCCCCATTTTC
1448757 CTCTTCGTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 47 0.94
40 3 0.06
ACGTcount: A:0.18, C:0.39, G:0.03, T:0.39
Consensus pattern (39 bp):
AATCCCTAATTCCCCATTTTCATTTCTCCTTCGCACCCC
Found at i:1449720 original size:13 final size:13
Alignment explanation
Indices: 1449702--1449728 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1449692 CTGACCACAT
1449702 TGTCCGCACCTAC
1 TGTCCGCACCTAC
1449715 TGTCCGCACCTAC
1 TGTCCGCACCTAC
1449728 T
1 T
1449729 TTGGTGGAAC
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:0.15, C:0.44, G:0.15, T:0.26
Consensus pattern (13 bp):
TGTCCGCACCTAC
Found at i:1449827 original size:131 final size:131
Alignment explanation
Indices: 1449593--1449849 Score: 514
Period size: 131 Copynumber: 2.0 Consensus size: 131
1449583 TGTCGTCTCT
1449593 CTACTTTGGTGGAACAGGCTCGTTGATCTTAGCATCTTCCATCTCTTTAAAATTTTGTTCACTTC
1 CTACTTTGGTGGAACAGGCTCGTTGATCTTAGCATCTTCCATCTCTTTAAAATTTTGTTCACTTC
1449658 CAACAGGCTCACAACATCCCGATTCGCACCTTGGCTGACCACATTGTCCGCACCTACTGTCCGCA
66 CAACAGGCTCACAACATCCCGATTCGCACCTTGGCTGACCACATTGTCCGCACCTACTGTCCGCA
1449723 C
131 C
1449724 CTACTTTGGTGGAACAGGCTCGTTGATCTTAGCATCTTCCATCTCTTTAAAATTTTGTTCACTTC
1 CTACTTTGGTGGAACAGGCTCGTTGATCTTAGCATCTTCCATCTCTTTAAAATTTTGTTCACTTC
1449789 CAACAGGCTCACAACATCCCGATTCGCACCTTGGCTGACCACATTGTCCGCACCTACTGTC
66 CAACAGGCTCACAACATCCCGATTCGCACCTTGGCTGACCACATTGTCCGCACCTACTGTC
1449850 AGGCTGATGG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 126 1.00
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.31
Consensus pattern (131 bp):
CTACTTTGGTGGAACAGGCTCGTTGATCTTAGCATCTTCCATCTCTTTAAAATTTTGTTCACTTC
CAACAGGCTCACAACATCCCGATTCGCACCTTGGCTGACCACATTGTCCGCACCTACTGTCCGCA
C
Found at i:1452402 original size:22 final size:22
Alignment explanation
Indices: 1452377--1452438 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
1452367 TTAATACAAT
1452377 ATTTCTAAAATAATAACAA-ATA
1 ATTT-TAAAATAATAACAATATA
* **
1452399 ATTTAAAAAATAAATATTAATATA
1 ATTT-TAAAAT-AATAACAATATA
1452423 ATTTTAAAATATATAA
1 ATTTTAAAATA-ATAA
1452439 TTAAATTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 10 0.32
23 14 0.45
24 7 0.23
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTTTAAAATAATAACAATATA
Found at i:1452447 original size:19 final size:19
Alignment explanation
Indices: 1452410--1452447 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1452400 TTTAAAAAAT
*
1452410 AAATATTAATATAATTTTA
1 AAATATTAATATAAATTTA
1452429 AAATATATAAT-TAAATTTA
1 AAATAT-TAATATAAATTTA
1452448 TTAAATTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATATTAATATAAATTTA
Found at i:1460356 original size:3 final size:3
Alignment explanation
Indices: 1460341--1460383 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1460331 TACTGGCCGC
* *
1460341 CAT CAT CAC CAT CAT CAT CAT CAT CA- CTAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C-AT CAT CAT CAT CAT C
1460384 GAACTCCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:1460424 original size:12 final size:12
Alignment explanation
Indices: 1460341--1460425 Score: 57
Period size: 12 Copynumber: 6.8 Consensus size: 12
1460331 TACTGGCCGC
* *
1460341 CATCATCACCAT
1 CATCATCATCTT
*
1460353 CATCATCATCAT
1 CATCATCATCTT
1460365 CA-CTATCATCTT
1 CATC-ATCATCTT
*
1460377 CATCATCGAACTCCT
1 CATCATC--A-TCTT
1460392 CATCGA-CATCTT
1 CATC-ATCATCTT
* *
1460404 CCTCGTCATCTT
1 CATCATCATCTT
1460416 CATCATCATC
1 CATCATCATC
1460426 AAATCCGTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
11 1 0.02
12 45 0.78
13 2 0.03
14 1 0.02
15 8 0.14
16 1 0.02
ACGTcount: A:0.26, C:0.38, G:0.04, T:0.33
Consensus pattern (12 bp):
CATCATCATCTT
Found at i:1461212 original size:60 final size:60
Alignment explanation
Indices: 1461084--1461225 Score: 182
Period size: 60 Copynumber: 2.4 Consensus size: 60
1461074 TGAGGTGGCG
* * *
1461084 AAAGGCGTATCCCCGTAGACGCGCTTTACCTGGTTTTACGCTGAGTTGGTTGCCACGTGTG
1 AAAGGCGCATCCCCGTAGACGCGCTTTACCT-GTTTTACGCTGAGTTAGTTGCCACGTGTA
**
1461145 AAAGGCGCATCCCCGTAGACGCGCTTTACCT-TTATTTTGCTGA-TTCAGTTGCCACGTGTA
1 AAAGGCGCATCCCCGTAGACGCGCTTTACCTGTT-TTACGCTGAGTT-AGTTGCCACGTGTA
*
1461205 AAAGGCGCATCCCAG-AGACGC
1 AAAGGCGCATCCCCGTAGACGC
1461226 ACCTTTCAGT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
59 10 0.14
60 33 0.45
61 30 0.41
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (60 bp):
AAAGGCGCATCCCCGTAGACGCGCTTTACCTGTTTTACGCTGAGTTAGTTGCCACGTGTA
Found at i:1461472 original size:30 final size:32
Alignment explanation
Indices: 1461437--1461512 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 32
1461427 ATAGTTATTA
1461437 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTATATTAAATAATAATTATATAAATAT
* * *
1461467 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATAATTATATAAATAT
1461500 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
1461513 TTATTAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 14 0.36
31 2 0.05
32 7 0.18
33 16 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTTTATATTAAATAATAATTATATAAATAT
Found at i:1461501 original size:33 final size:30
Alignment explanation
Indices: 1461422--1461532 Score: 86
Period size: 33 Copynumber: 3.6 Consensus size: 30
1461412 AGTTATTTTT
* *
1461422 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTT-TATTAATATA
* *
1461454 ATTATATAAATATTATTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTATT--AAT-ATA
*
1461487 TTTATATAATTATTATTTATTTA--AATTTA
1 TTTATATAATTATTATTT-TTTATTAATATA
*
1461516 TTAAT-TAATTATT-TTTT
1 TTTATATAATTATTATTTT
1461533 GTGCTAATTA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
26 1 0.01
27 3 0.04
28 8 0.12
29 6 0.09
30 7 0.10
31 4 0.06
32 15 0.22
33 19 0.28
34 4 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTATATAATTATTATTTTTTATTAATATA
Found at i:1461701 original size:26 final size:25
Alignment explanation
Indices: 1461672--1461727 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1461662 GTTATGTTTA
**
1461672 ATTTAAATTTATTATGAATTTATATT
1 ATTTAAATTTATTAT-AATGCATATT
* *
1461698 ATTTTAATTTTTTATAATGCATATT
1 ATTTAAATTTATTATAATGCATATT
1461723 ATTTA
1 ATTTA
1461728 TGATACTGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (25 bp):
ATTTAAATTTATTATAATGCATATT
Found at i:1463363 original size:21 final size:21
Alignment explanation
Indices: 1463312--1463363 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1463302 TATGTCATCT
*
1463312 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
1463333 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1463354 CCGCAGGGTT
1 CCGCAGGGTT
1463364 TTATACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:1463918 original size:34 final size:34
Alignment explanation
Indices: 1463875--1463981 Score: 142
Period size: 34 Copynumber: 3.1 Consensus size: 34
1463865 ATAAATGTTT
1463875 TTAAAATACAAATTATAATATTCGAAATTTAAAA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
* * * *
1463909 TTAAAATACAAATAATATTATTTGAAATTTAAAT
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
* * * *
1463943 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
1463977 TTAAA
1 TTAAA
1463982 TTTAAGTTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 62 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAATATTCGAAATTTAAAA
Found at i:1464632 original size:127 final size:127
Alignment explanation
Indices: 1464404--1464911 Score: 867
Period size: 127 Copynumber: 4.0 Consensus size: 127
1464394 GCGCTTTAAA
1464404 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* *
1464469 CAATGATAACATATTATCTGACAAAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTTCATG
66 CAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
1464531 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCAGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
*
1464596 CAATGATAACATATTATCTGACAAAATAATGGAAGGCACGCCCCCGGGAACGCGCCTTCACG
66 CAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
1464658 GTCCCCTAAGAAATAATAGGTATTGACATAAATAGTTCAT-GGGGGACATAAGTGACATAATAGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTC-TCGGGGGACATAAGTGACATAATAGG
*
1464722 GCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGC-CCTCCCGGGAACGCGCCTTCACG
65 GCAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCC-CCCGGGAACGCGCCTTCACG
1464785 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
* * * * *
1464850 CAATGATAATATATTCTCTGATAAAATAATAGAAGGCGCGCCCCCGAGAACGCGCCTTCACG
66 CAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
1464912 TGAATAGTAC
Statistics
Matches: 360, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
126 3 0.01
127 355 0.99
128 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
CAATGATAACATATTATCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:1468945 original size:2 final size:2
Alignment explanation
Indices: 1468938--1468969 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1468928 ACTGATGTAA
1468938 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
1468970 CACATGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1476343 original size:23 final size:23
Alignment explanation
Indices: 1476317--1476372 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1476307 TTAGTTTAGG
*
1476317 GAAGAAAATAGTTGTTAGGTTGC
1 GAAGAAAATAGTTATTAGGTTGC
* *
1476340 GAAGAAAATGGTTATTTGGTTGC
1 GAAGAAAATAGTTATTAGGTTGC
*
1476363 TAAGAAAATA
1 GAAGAAAATA
1476373 AGGGGAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.27, T:0.30
Consensus pattern (23 bp):
GAAGAAAATAGTTATTAGGTTGC
Found at i:1476928 original size:3 final size:3
Alignment explanation
Indices: 1476920--1477019 Score: 200
Period size: 3 Copynumber: 33.3 Consensus size: 3
1476910 AGAGCAACGC
1476920 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1476968 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1477016 ATA A
1 ATA A
1477020 AAAGAACATG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1478035 original size:2 final size:2
Alignment explanation
Indices: 1478030--1478073 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1478020 AAACTAATAG
* * *
1478030 GA GA GA AA GA GA GA GG GA GG GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1478072 GA
1 GA
1478074 CGAACACCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1479936 original size:24 final size:22
Alignment explanation
Indices: 1479895--1479973 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 22
1479885 GAATGTGATT
1479895 AGTGCATCGATGCA---TAAGG
1 AGTGCATCGATGCACTGTAAGG
1479914 AGTGCATCGATGCACATGTTAAGG
1 AGTGCATCGATGCAC-TG-TAAGG
*
1479938 -GATGCATCGATACACTGT-A-G
1 AG-TGCATCGATGCACTGTAAGG
*
1479958 AATGCATCGATGCACT
1 AGTGCATCGATGCACT
1479974 TCAAGGGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
19 14 0.28
20 14 0.28
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.34
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (22 bp):
AGTGCATCGATGCACTGTAAGG
Found at i:1480636 original size:23 final size:24
Alignment explanation
Indices: 1480602--1480650 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1480592 CAGGATATAC
*
1480602 AGTGGTCTTTCGGGAC-ATTTCAT
1 AGTGGTCTTTCGGGACAAATTCAT
1480625 AGTGGT-TCTTCGGGACAAATTCAT
1 AGTGGTCT-TTCGGGACAAATTCAT
1480649 AG
1 AG
1480651 CCCTAGTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 1 0.04
23 14 0.61
24 8 0.35
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (24 bp):
AGTGGTCTTTCGGGACAAATTCAT
Found at i:1483971 original size:21 final size:21
Alignment explanation
Indices: 1483945--1484001 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1483935 ATTATGGGCT
1483945 ATGTGCATCGATGCACATTCA
1 ATGTGCATCGATGCACATTCA
1483966 ATGTGCATCGATGCACATTCA
1 ATGTGCATCGATGCACATTCA
* *
1483987 ATGTGTACCGATGCA
1 ATGTGCATCGATGCA
1484002 TCAAGGGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
ATGTGCATCGATGCACATTCA
Found at i:1484134 original size:24 final size:22
Alignment explanation
Indices: 1484107--1484171 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
1484097 CACCGGTGCA
1484107 TAAGGAGTGCATCGATGCACATG
1 TAAGGAGTGCATCGATGCAC-TG
*
1484130 TTAAGG-GATGCATCGATACACTG
1 -TAAGGAG-TGCATCGATGCACTG
*
1484153 T-A-GAATGCATCGATGCACT
1 TAAGGAGTGCATCGATGCACT
1484172 TCAAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 14 0.39
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.47
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (22 bp):
TAAGGAGTGCATCGATGCACTG
Found at i:1484811 original size:20 final size:22
Alignment explanation
Indices: 1484783--1484839 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
1484773 AGGGTTCATA
*
1484783 GGTCATTCGGGACA-T-ACAGT
1 GGTCTTTCGGGACATTCACAGT
*
1484803 GGTCTTTCGGGACATTTCATAGT
1 GGTCTTTCGGGACA-TTCACAGT
1484826 GGTCTTTCGGGACA
1 GGTCTTTCGGGACA
1484840 AATTCATAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 13 0.41
22 1 0.03
23 18 0.56
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (22 bp):
GGTCTTTCGGGACATTCACAGT
Found at i:1484830 original size:23 final size:24
Alignment explanation
Indices: 1484800--1484848 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
1484790 CGGGACATAC
*
1484800 AGTGGTCTTTCGGGAC-ATTTCAT
1 AGTGGTCTTTCGGGACAAATTCAT
1484823 AGTGGTCTTTCGGGACAAATTCAT
1 AGTGGTCTTTCGGGACAAATTCAT
1484847 AG
1 AG
1484849 CCCCTAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (24 bp):
AGTGGTCTTTCGGGACAAATTCAT
Found at i:1488986 original size:22 final size:22
Alignment explanation
Indices: 1488958--1489001 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1488948 AACTTTGGGG
1488958 ACTTGTTTACAAGTTCTTAAAT
1 ACTTGTTTACAAGTTCTTAAAT
*
1488980 ACTTGTTTACAATTTCTTAAAT
1 ACTTGTTTACAAGTTCTTAAAT
1489002 GAAGAAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (22 bp):
ACTTGTTTACAAGTTCTTAAAT
Found at i:1500574 original size:27 final size:24
Alignment explanation
Indices: 1500533--1500585 Score: 61
Period size: 27 Copynumber: 2.1 Consensus size: 24
1500523 CTAATTAGTA
1500533 ATGAAAAAGAAAAAAGTATTATAAAAC
1 ATGAAAAAGAAAAAA--ATTA-AAAAC
* *
1500560 ATGAAAAATACAAAAATTAAAAAC
1 ATGAAAAAGAAAAAAATTAAAAAC
1500584 AT
1 AT
1500586 CATTAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 4 0.17
27 13 0.54
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.19
Consensus pattern (24 bp):
ATGAAAAAGAAAAAAATTAAAAAC
Found at i:1505748 original size:38 final size:38
Alignment explanation
Indices: 1505697--1505772 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1505687 TATGATGAAG
1505697 GTTGTTTAGTAATAATGGAATGAATTAAAGGGTAAAAT
1 GTTGTTTAGTAATAATGGAATGAATTAAAGGGTAAAAT
1505735 GTTGTTTAGTAATAATGGAATGAATTAAAGGGTAAAAT
1 GTTGTTTAGTAATAATGGAATGAATTAAAGGGTAAAAT
1505773 TGTCATTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (38 bp):
GTTGTTTAGTAATAATGGAATGAATTAAAGGGTAAAAT
Found at i:1506915 original size:15 final size:17
Alignment explanation
Indices: 1506895--1506926 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1506885 TTTAAGTGTC
1506895 CATGAT-ATATG-TATA
1 CATGATAATATGATATA
1506910 CATGATAATATGATATA
1 CATGATAATATGATATA
1506927 AATTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (17 bp):
CATGATAATATGATATA
Found at i:1507375 original size:24 final size:22
Alignment explanation
Indices: 1507341--1507398 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
1507331 TACCTATGTT
*
1507341 CTTCGGAACATATGGAAAGTGGTC
1 CTTCGGGACATAT--AAAGTGGTC
*
1507365 CTTCGGGACATATACAGTGGTC
1 CTTCGGGACATATAAAGTGGTC
*
1507387 CTTCAGGACATA
1 CTTCGGGACATA
1507399 GTGGTCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 19 0.61
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
CTTCGGGACATATAAAGTGGTC
Found at i:1507413 original size:18 final size:18
Alignment explanation
Indices: 1507380--1507414 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1507370 GGACATATAC
*
1507380 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTACAGGACAT
*
1507398 AGTGGTCCTACGGGACA
1 AGTGGTCCTACAGGACA
1507415 AATTCTACGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACAGGACAT
Found at i:1510721 original size:20 final size:20
Alignment explanation
Indices: 1510679--1510721 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1510669 ATTATTCAGT
*
1510679 GTGTATCGATGCACTACAGA
1 GTGTATCGATGCACTACAAA
*
1510699 GTGTATCGATGCACTTCAAA
1 GTGTATCGATGCACTACAAA
1510719 GTG
1 GTG
1510722 AAAATGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
GTGTATCGATGCACTACAAA
Found at i:1511732 original size:18 final size:18
Alignment explanation
Indices: 1511709--1511748 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1511699 GGTCATAACC
1511709 CGACCCAACCCGTTGACT
1 CGACCCAACCCGTTGACT
* *
1511727 CGACCCGACCTGTTGACT
1 CGACCCAACCCGTTGACT
1511745 CGAC
1 CGAC
1511749 AAGTTGATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.17
Consensus pattern (18 bp):
CGACCCAACCCGTTGACT
Found at i:1511775 original size:15 final size:15
Alignment explanation
Indices: 1511751--1511785 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1511741 GACTCGACAA
*
1511751 GTTGATCCGTTGACC
1 GTTGACCCGTTGACC
*
1511766 GTTGACCCGTTGACT
1 GTTGACCCGTTGACC
1511781 GTTGA
1 GTTGA
1511786 TCGGCGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.23, G:0.29, T:0.34
Consensus pattern (15 bp):
GTTGACCCGTTGACC
Found at i:1514345 original size:72 final size:72
Alignment explanation
Indices: 1514266--1514416 Score: 191
Period size: 72 Copynumber: 2.1 Consensus size: 72
1514256 GATTTTCGAT
* *
1514266 TTGAATTCTGATCTGATACTTGA-CATGGA-TTATGATCTGATA-TCTGACATGGATTCTGATCT
1 TTGAATTCTGATCTGATACTTGATC-T-GATTTATGATATGATACT-TGACATGGATTCTGATAT
1514328 GATACTTGAC
63 GATACTTGAC
* * * *
1514338 TTGAATTCTGATCTGTTACTTGATCTGATTTCTGATATGATACTTGACCTGGATTTTGATATGAT
1 TTGAATTCTGATCTGATACTTGATCTGATTTATGATATGATACTTGACATGGATTCTGATATGAT
1514403 ACTTGAC
66 ACTTGAC
*
1514410 ATGAATT
1 TTGAATT
1514417 ATGTTTTGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
71 2 0.03
72 65 0.94
73 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (72 bp):
TTGAATTCTGATCTGATACTTGATCTGATTTATGATATGATACTTGACATGGATTCTGATATGAT
ACTTGAC
Found at i:1514426 original size:24 final size:24
Alignment explanation
Indices: 1514267--1514416 Score: 169
Period size: 24 Copynumber: 6.2 Consensus size: 24
1514257 ATTTTCGATT
1514267 TGAATTCTGATCTGATACTTGACA
1 TGAATTCTGATCTGATACTTGACA
* *
1514291 TGGATTATGATCTGATA-TCTGACA
1 TGAATTCTGATCTGATACT-TGACA
* *
1514315 TGGATTCTGATCTGATACTTGACT
1 TGAATTCTGATCTGATACTTGACA
*
1514339 TGAATTCTGATCTGTTACTTGATC-
1 TGAATTCTGATCTGATACTTGA-CA
* * *
1514363 TGATTTCTGATATGATACTTGACC
1 TGAATTCTGATCTGATACTTGACA
* * *
1514387 TGGATTTTGATATGATACTTGACA
1 TGAATTCTGATCTGATACTTGACA
1514411 TGAATT
1 TGAATT
1514417 ATGTTTTGAT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.02
24 104 0.96
25 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (24 bp):
TGAATTCTGATCTGATACTTGACA
Found at i:1514589 original size:43 final size:43
Alignment explanation
Indices: 1514528--1514622 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
1514518 GGGCCTTACT
* *
1514528 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACACTA
1514571 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACACTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACACTA
1514614 TGGTGTGTT
1 TGGTGTGTT
1514623 CGGTTGGAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.16, C:0.12, G:0.37, T:0.36
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACACTA
Found at i:1516067 original size:22 final size:22
Alignment explanation
Indices: 1516042--1516102 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
1516032 GAACATTTGG
*
1516042 ACAGTGGTCATTCGGGACATAT
1 ACAGTGGTCCTTCGGGACATAT
*
1516064 ACAGTGGTCCTTCGAGACATAT
1 ACAGTGGTCCTTCGGGACATAT
1516086 ACAGTGGTCCTTCGGGA
1 ACAGTGGTCCTTCGGGA
1516103 TATAGTAGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (22 bp):
ACAGTGGTCCTTCGGGACATAT
Found at i:1517338 original size:59 final size:59
Alignment explanation
Indices: 1517246--1517364 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
1517236 TTCTATTATT
1517246 AGTCACAGATAAAATTATCTTAATGGTTAAATAATTTATTGTTATTTTGAAGATGTTGG
1 AGTCACAGATAAAATTATCTTAATGGTTAAATAATTTATTGTTATTTTGAAGATGTTGG
1517305 AGTCACAGATAAAATTATCTTAATGGTTAAATAATTTATTGTTATTTTGAAGATGTTGG
1 AGTCACAGATAAAATTATCTTAATGGTTAAATAATTTATTGTTATTTTGAAGATGTTGG
1517364 A
1 A
1517365 TTCAAGCATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (59 bp):
AGTCACAGATAAAATTATCTTAATGGTTAAATAATTTATTGTTATTTTGAAGATGTTGG
Found at i:1519538 original size:35 final size:35
Alignment explanation
Indices: 1519499--1519569 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
1519489 AAAATACTTT
*
1519499 AATTTAGGTTTTAGAATATAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
* * *
1519534 AATTTGGGGTTTAGAATATAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
1519569 A
1 A
1519570 TTTTTGAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTAAAGTATTTTGG
Found at i:1521810 original size:31 final size:31
Alignment explanation
Indices: 1521768--1521827 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1521758 AACGTTATAG
* *
1521768 TCACTCACATTATTAATTTATAATTTTTTTA
1 TCACTCACATTATCAATTTATAATATTTTTA
*
1521799 TCACTCGCATTATCAATTTATAATATTTT
1 TCACTCACATTATCAATTTATAATATTTT
1521828 AGCCACTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.02, T:0.52
Consensus pattern (31 bp):
TCACTCACATTATCAATTTATAATATTTTTA
Found at i:1525056 original size:20 final size:20
Alignment explanation
Indices: 1525031--1525073 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1525021 GTGTATATAT
1525031 ATATATTGTTGTACTATGTG
1 ATATATTGTTGTACTATGTG
1525051 ATATATTGTTGTACTATGTG
1 ATATATTGTTGTACTATGTG
1525071 ATA
1 ATA
1525074 CCTTACTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (20 bp):
ATATATTGTTGTACTATGTG
Found at i:1526772 original size:18 final size:18
Alignment explanation
Indices: 1526744--1526787 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1526734 GTATGTCATT
*
1526744 TTTTGCTTTAAATTGAATC
1 TTTT-CTTTAAACTGAATC
*
1526763 TTTTCTTTAAGCTGAATC
1 TTTTCTTTAAACTGAATC
1526781 -TTTCTTT
1 TTTTCTTT
1526788 TCCCTGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (18 bp):
TTTTCTTTAAACTGAATC
Found at i:1533960 original size:33 final size:33
Alignment explanation
Indices: 1533918--1533984 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1533908 AAAGAAGCCT
*
1533918 GACCCTGTTCCTGATTCTACTTCAGTAGCTCAA
1 GACCCTGTTCCTGAATCTACTTCAGTAGCTCAA
* *
1533951 GACCCTGTTCCTGAATCTCCTTCAGTAGTTCAA
1 GACCCTGTTCCTGAATCTACTTCAGTAGCTCAA
1533984 G
1 G
1533985 CTTTTGGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (33 bp):
GACCCTGTTCCTGAATCTACTTCAGTAGCTCAA
Found at i:1536902 original size:2 final size:2
Alignment explanation
Indices: 1536895--1536923 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1536885 GCATAAAAAT
1536895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1536924 GATTCATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1545608 original size:24 final size:24
Alignment explanation
Indices: 1545555--1545609 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1545545 TTTAATTCGT
*
1545555 AAAATATTTTTTAATTAATTTAAA
1 AAAATATTTTATAATTAATTTAAA
* *
1545579 ATAAATA-TTTATATATTATTTTATA
1 A-AAATATTTTATA-ATTAATTTAAA
1545604 AAAATA
1 AAAATA
1545610 ACTGTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AAAATATTTTATAATTAATTTAAA
Found at i:1547237 original size:17 final size:19
Alignment explanation
Indices: 1547187--1547237 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
1547177 TAAGAATGAT
1547187 AATATTTATTAAATAAATC
1 AATATTTATTAAATAAATC
*
1547206 AACATTATATATAAAT-AAT-
1 AATATT-TAT-TAAATAAATC
*
1547225 TATATTTATTAAA
1 AATATTTATTAAA
1547238 AGAACAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 4 0.15
18 3 0.11
19 9 0.33
20 6 0.22
21 5 0.19
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTTATTAAATAAATC
Found at i:1547251 original size:29 final size:29
Alignment explanation
Indices: 1547218--1547284 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 29
1547208 CATTATATAT
1547218 AAATAATTATATTTATTAAAAGAACAAAC
1 AAATAATTATATTTATTAAAAGAACAAAC
1547247 --A-AA-TATATTTATTAAAAGAACAAAC
1 AAATAATTATATTTATTAAAAGAACAAAC
1547272 AAATATATT-TATT
1 AAATA-ATTATATT
1547285 GTTAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
25 22 0.67
26 2 0.06
27 2 0.06
28 1 0.03
29 5 0.15
30 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATAATTATATTTATTAAAAGAACAAAC
Found at i:1547257 original size:25 final size:25
Alignment explanation
Indices: 1547225--1547284 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
1547215 TATAAATAAT
1547225 TATATTTATTAAAAGAACAAACAAA
1 TATATTTATTAAAAGAACAAACAAA
1547250 TATATTTATTAAAAGAACAAACAAA
1 TATATTTATTAAAAGAACAAACAAA
1547275 TATATTTATT
1 TATATTTATT
1547285 GTTAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (25 bp):
TATATTTATTAAAAGAACAAACAAA
Done.