Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 40 of 79
Found at i:13064952 original size:16 final size:17
Alignment explanation
Indices: 13064931--13064964 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13064921 ACTATTAAAA
13064931 AACTTAA-ATATCATTT
1 AACTTAATATATCATTT
*
13064947 AACTTAATTTATCATTT
1 AACTTAATATATCATTT
13064964 A
1 A
13064965 GTTTACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
AACTTAATATATCATTT
Found at i:13070773 original size:22 final size:22
Alignment explanation
Indices: 13070748--13070808 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
13070738 AGCTTGCTAG
*
13070748 GCACTAAGCCTAAATAACACAA
1 GCACTAAGCCTGAATAACACAA
* *
13070770 GCACTAAGCCTGAATAACCCCA
1 GCACTAAGCCTGAATAACACAA
13070792 GCACTAAGCCTGAATAA
1 GCACTAAGCCTGAATAA
13070809 TACCTCATTT
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:0.43, C:0.30, G:0.13, T:0.15
Consensus pattern (22 bp):
GCACTAAGCCTGAATAACACAA
Found at i:13074450 original size:25 final size:25
Alignment explanation
Indices: 13074398--13074483 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
13074388 TCATGTACAT
* * * * *
13074398 GTATGCTCATACGAGCTGTGAATTG
1 GTATGCTCACACAAGCTATAAATCG
* * * *
13074423 GTATGCTCACTCAAGTTGTAGATCG
1 GTATGCTCACACAAGCTATAAATCG
* *
13074448 GTATGCTCTCACGAGCTATAAATCG
1 GTATGCTCACACAAGCTATAAATCG
13074473 GTATGCTCACA
1 GTATGCTCACA
13074484 TGAGTTGTGG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (25 bp):
GTATGCTCACACAAGCTATAAATCG
Found at i:13074897 original size:16 final size:17
Alignment explanation
Indices: 13074866--13074898 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13074856 ATACGGATAA
13074866 ATTTATCTCAATTCAAT
1 ATTTATCTCAATTCAAT
*
13074883 ATTTATTTC-ATTCAAT
1 ATTTATCTCAATTCAAT
13074899 TTACCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTATCTCAATTCAAT
Found at i:13080071 original size:40 final size:36
Alignment explanation
Indices: 13079998--13080071 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
13079988 TGGAGTAGAT
*
13079998 TAGTATATCATTAACAAACACAACCACAAATCTATC
1 TAGTATATCATTAACAAACAAAACCACAAATCTATC
* *
13080034 TAGTATATTATTAATAAACAAAACCACAAATCTATC
1 TAGTATATCATTAACAAACAAAACCACAAATCTATC
13080070 TA
1 TA
13080072 ATTGAGGCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (36 bp):
TAGTATATCATTAACAAACAAAACCACAAATCTATC
Found at i:13083519 original size:24 final size:24
Alignment explanation
Indices: 13083406--13083532 Score: 91
Period size: 24 Copynumber: 5.2 Consensus size: 24
13083396 TCCAAATAAT
*
13083406 TGGCTCT-TATGAGCTACCTGATTAA
1 TGGCTCTCTA-GAGCTTCCTG-TTAA
* *
13083431 TGGCTCTCTAGAGCTTCCTGATAT
1 TGGCTCTCTAGAGCTTCCTGTTAA
* * * *
13083455 TGGCT-TACTTGAACTTCTTGTTAT
1 TGGCTCT-CTAGAGCTTCCTGTTAA
* * *
13083479 TGGCTC-GTATGATCTTCCCGTTAA
1 TGGCTCTCTA-GAGCTTCCTGTTAA
13083503 TGGCTCTCTAGAGCTT-CTGTTACA
1 TGGCTCTCTAGAGCTTCCTGTTA-A
13083527 TGGCTC
1 TGGCTC
13083533 ACATGAGCTT
Statistics
Matches: 80, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
23 7 0.09
24 53 0.66
25 18 0.22
26 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (24 bp):
TGGCTCTCTAGAGCTTCCTGTTAA
Found at i:13089002 original size:24 final size:24
Alignment explanation
Indices: 13088974--13089021 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
13088964 TGCCATATAA
13088974 ACCAGAATATACGCTGCAAAAGTT
1 ACCAGAATATACGCTGCAAAAGTT
13088998 ACCAGAATATACGCTGCAAAAGTT
1 ACCAGAATATACGCTGCAAAAGTT
13089022 GGATAGTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (24 bp):
ACCAGAATATACGCTGCAAAAGTT
Found at i:13090507 original size:20 final size:20
Alignment explanation
Indices: 13090472--13090520 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
13090462 ATCATGGTCT
*
13090472 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
13090491 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
13090511 TTGCTTACTT
1 TTGCTTACTT
13090521 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:13090783 original size:49 final size:50
Alignment explanation
Indices: 13090723--13090859 Score: 154
Period size: 49 Copynumber: 2.8 Consensus size: 50
13090713 GATAATAGCA
* * * *
13090723 TGCCAAAGCCATGTCCTATACATGGTCTTACATGGGATGTT-TCATGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCAT-AACG
* *
13090772 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATAACGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATAAC-G
* * *
13090822 TGCCCATGCCATGTCCCAGACATGATCTTATATGGGAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
13090860 CTCATTCCCC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
48 5 0.07
49 36 0.49
50 32 0.44
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATAACG
Found at i:13092196 original size:21 final size:21
Alignment explanation
Indices: 13092170--13092210 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13092160 AAGCTCGAAG
*
13092170 GCTAAACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
* *
13092191 GCTAAATAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
13092211 GGTTGAACGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.15
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:13095814 original size:68 final size:68
Alignment explanation
Indices: 13095739--13095875 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
13095729 ATCATACCTT
*
13095739 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACCACACATCGTAGC
1 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTAGC
13095804 ACC
66 ACC
*
13095807 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTATC
1 TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTAGC
13095872 ACC
66 ACC
13095875 T
1 T
13095876 TTCAGTTGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (68 bp):
TAACTTTCAACTGATAATACTCAGATCTAAGGTTTATCTTCGAGAACACCACAACACATCGTAGC
ACC
Found at i:13100889 original size:5 final size:5
Alignment explanation
Indices: 13100851--13100886 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
13100841 TACTGAACCT
*
13100851 AACAC AACAC AACAC AACAC AACAC AACAC ATCAC A
1 AACAC AACAC AACAC AACAC AACAC AACAC AACAC A
13100887 TCAAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.58, C:0.39, G:0.00, T:0.03
Consensus pattern (5 bp):
AACAC
Found at i:13104935 original size:49 final size:48
Alignment explanation
Indices: 13104862--13104986 Score: 126
Period size: 49 Copynumber: 2.5 Consensus size: 48
13104852 CTTATAAGCG
*
13104862 TCCCGATAATTGGCTCTTCAGAGCTTCTCGATAAC-TGGCTCGTATGAGCT
1 TCCCGATAA-TGGCTCTT-AGAGCTTCCCG-TAACATGGCTCGTATGAGCT
* * *
13104912 TCCCGTTAATGGCTCTCTAGAGCTTCCCGTTACATGGTTCGTATGAGCT
1 TCCCGATAATGGCTCT-TAGAGCTTCCCGTAACATGGCTCGTATGAGCT
* * *
13104961 TCTCGGTATATGGCTCTGAAGAGCTT
1 TCCCGATA-ATGGCTCT-TAGAGCTT
13104987 TCTATTTACA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.05
49 37 0.58
50 24 0.38
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (48 bp):
TCCCGATAATGGCTCTTAGAGCTTCCCGTAACATGGCTCGTATGAGCT
Found at i:13104943 original size:24 final size:24
Alignment explanation
Indices: 13104862--13104940 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
13104852 CTTATAAGCG
*
13104862 TCCCGATAATTGGCTCTTCAGAGCT
1 TCCCGATAACTGGCTCTT-AGAGCT
* *
13104887 TCTCGATAACTGGCTCGTATGAGCT
1 TCCCGATAACTGGCTCTTA-GAGCT
*
13104912 TCCCGTTAA-TGGCTCTCTAGAGCT
1 TCCCGATAACTGGCTCT-TAGAGCT
13104936 TCCCG
1 TCCCG
13104941 TTACATGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
24 17 0.37
25 29 0.63
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.32
Consensus pattern (24 bp):
TCCCGATAACTGGCTCTTAGAGCT
Found at i:13104959 original size:25 final size:26
Alignment explanation
Indices: 13104900--13104977 Score: 92
Period size: 25 Copynumber: 3.1 Consensus size: 26
13104890 CGATAACTGG
13104900 CTCGTATGAGCTTCCCGTTAATGGCT
1 CTCGTATGAGCTTCCCGTTAATGGCT
13104926 CTC-TA-GAGCTTCCCGTTACATGG-T
1 CTCGTATGAGCTTCCCGTTA-ATGGCT
* *
13104950 -TCGTATGAGCTTCTCGGTATATGGCT
1 CTCGTATGAGCTTCCCGTTA-ATGGCT
13104976 CT
1 CT
13104978 GAAGAGCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.05
24 16 0.36
25 21 0.48
26 4 0.09
27 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (26 bp):
CTCGTATGAGCTTCCCGTTAATGGCT
Found at i:13115237 original size:45 final size:44
Alignment explanation
Indices: 13115171--13115302 Score: 153
Period size: 45 Copynumber: 3.0 Consensus size: 44
13115161 TACGTGTACT
* *
13115171 GGGTACCATTGATTATAAAGGTGGTTGCTGTGTGTTGATTCCACC
1 GGGTACTATTGATTAT-AAGGTGGTTGCTATGTGTTGATTCCACC
*
13115216 GGGTACTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCCACC
1 GGGTACTATTGATTAT-AAGGTGGTTGCTATGTGTTGATTCCACC
** *
13115261 GATTA-TCATTGACTATAAGGTTGG-TGCTATGTGTTGA-TCCAC
1 GGGTACT-ATTGATTATAAGG-TGGTTGCTATGTGTTGATTCCAC
13115303 TGTGTATCTG
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
43 5 0.06
44 17 0.22
45 55 0.71
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.36
Consensus pattern (44 bp):
GGGTACTATTGATTATAAGGTGGTTGCTATGTGTTGATTCCACC
Found at i:13127350 original size:25 final size:25
Alignment explanation
Indices: 13127289--13127476 Score: 90
Period size: 25 Copynumber: 7.6 Consensus size: 25
13127279 ACACATAGAA
* * *
13127289 GCTCTTATAAGCGTCCCGATAATTG
1 GCTCTTATGAGCTTCCCGATAACTG
13127314 GCTCTTCA-GAGCTTCCCGATAACTG
1 GCTCTT-ATGAGCTTCCCGATAACTG
* **
13127339 GCTCTTATGAGCTACTTGATTAA-TG
1 GCTCTTATGAGCTTCCCGA-TAACTG
*
13127364 GCT-TTCTGGAGCTTCCCGAT-ACTG
1 GCTCTTAT-GAGCTTCCCGATAACTG
* * * * *
13127388 CCTCACT-TGAACTTCCC-ATTATTG
1 GCTC-TTATGAGCTTCCCGATAACTG
*
13127412 GCTCGTATGAGCTTCCC-ATTAA-TG
1 GCTCTTATGAGCTTCCCGA-TAACTG
* *
13127436 GCTCTCTA-GAGCTTCTCG-TTACATG
1 GCTCT-TATGAGCTTCCCGATAAC-TG
**
13127461 GCTCACATGAGCTTCC
1 GCTCTTATGAGCTTCC
13127477 TGTTACATGG
Statistics
Matches: 124, Mismatches: 24, Indels: 30
0.70 0.13 0.17
Matches are distributed among these distances:
23 6 0.05
24 48 0.39
25 65 0.52
26 5 0.04
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.34
Consensus pattern (25 bp):
GCTCTTATGAGCTTCCCGATAACTG
Found at i:13127447 original size:24 final size:24
Alignment explanation
Indices: 13127357--13127464 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
13127347 GAGCTACTTG
* *
13127357 ATTAATGGCTTTCTGGAGCTTCCC
1 ATTAATGGCTCTCTAGAGCTTCCC
* * * * *
13127381 GA-TACTGCCTCACTTGAACTTCCC
1 -ATTAATGGCTCTCTAGAGCTTCCC
* *
13127405 ATTATTGGCTC-GTATGAGCTTCCC
1 ATTAATGGCTCTCTA-GAGCTTCCC
*
13127429 ATTAATGGCTCTCTAGAGCTTCTC
1 ATTAATGGCTCTCTAGAGCTTCCC
*
13127453 GTTACATGGCTC
1 ATTA-ATGGCTC
13127465 ACATGAGCTT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
23 2 0.03
24 52 0.81
25 10 0.16
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (24 bp):
ATTAATGGCTCTCTAGAGCTTCCC
Found at i:13127481 original size:25 final size:25
Alignment explanation
Indices: 13127418--13127501 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
13127408 ATTGGCTCGT
** *
13127418 ATGAGCTTCCCATTA-ATGGCTCTC
1 ATGAGCTTCCTGTTACATGGCTCAC
13127442 -TAGAGCTT-CTCGTTACATGGCTCAC
1 AT-GAGCTTCCT-GTTACATGGCTCAC
13127467 ATGAGCTTCCTGTTACATGGCTCAC
1 ATGAGCTTCCTGTTACATGGCTCAC
*
13127492 ATAAGCTTCC
1 ATGAGCTTCC
13127502 CGGTTTATGG
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.04
24 9 0.18
25 37 0.73
26 3 0.06
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCTGTTACATGGCTCAC
Found at i:13127511 original size:25 final size:24
Alignment explanation
Indices: 13127421--13127532 Score: 84
Period size: 25 Copynumber: 4.5 Consensus size: 24
13127411 GGCTCGTATG
* * *
13127421 AGCTTCCCATTAATGGCTCTC-TA
1 AGCTTCCCGTTTATGGCTCACATA
* * *
13127444 GAGCTTCTCGTTACATGGCTCACATG
1 -AGCTTCCCGTT-TATGGCTCACATA
* *
13127470 AGCTTCCTGTTACATGGCTCACATA
1 AGCTTCCCGTT-TATGGCTCACATA
*
13127495 AGCTTCCCGGTTTATGGCTCA-AAA
1 AGCTTCCC-GTTTATGGCTCACATA
13127519 GAGCTTCCCGTTTA
1 -AGCTTCCCGTTTA
13127533 CAAGTCTGCA
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
24 16 0.22
25 53 0.73
26 4 0.05
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (24 bp):
AGCTTCCCGTTTATGGCTCACATA
Found at i:13132500 original size:22 final size:23
Alignment explanation
Indices: 13132472--13132517 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
13132462 GGATACACGG
13132472 ATCCAACCAAACACA-CCAGAAT
1 ATCCAACCAAACACACCCAGAAT
*
13132494 ATCCAACCTAACACACCCAGAAT
1 ATCCAACCAAACACACCCAGAAT
13132517 A
1 A
13132518 ATATAAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.48, C:0.37, G:0.04, T:0.11
Consensus pattern (23 bp):
ATCCAACCAAACACACCCAGAAT
Found at i:13136399 original size:48 final size:48
Alignment explanation
Indices: 13136263--13136436 Score: 217
Period size: 48 Copynumber: 3.6 Consensus size: 48
13136253 ATAGTATAAC
*** * * * **
13136263 TATGGTCTTACAC-ATCGTCACATATCACACACTGAAGCCATAGCTCAGC
1 TATGGTCTTACACGAAAATCACATATCACAC-C-GATGCCATATCCCATA
*
13136312 TATGGTCTTACACGAAAA-CACATATCACACTGATGCCATATCCCATA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCATA
* *
13136359 TATGGTCTTACATGAAAATCACGTATCACACCGATGCCATATCCCATA
1 TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCATA
13136407 TATGGTCTTACACGAAAATCACATATCACA
1 TATGGTCTTACACGAAAATCACATATCACA
13136437 TCACACTGAT
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
47 28 0.26
48 55 0.50
49 25 0.23
50 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (48 bp):
TATGGTCTTACACGAAAATCACATATCACACCGATGCCATATCCCATA
Found at i:13142362 original size:7 final size:7
Alignment explanation
Indices: 13142350--13142392 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
13142340 CTAATTAGAT
13142350 ATTTTTA
1 ATTTTTA
13142357 ATTTTTA
1 ATTTTTA
13142364 TATTTTTTAA
1 -A-TTTTT-A
13142374 ATTTTTA
1 ATTTTTA
*
13142381 AATTTTA
1 ATTTTTA
13142388 ATTTT
1 ATTTT
13142393 AACATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 18 0.58
8 6 0.19
9 6 0.19
10 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:13142368 original size:15 final size:15
Alignment explanation
Indices: 13142348--13142392 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
13142338 CTCTAATTAG
13142348 ATATTTTTAATTTTT
1 ATATTTTTAATTTTT
13142363 ATATTTTTTAAATTTTT
1 ATA-TTTTT-AATTTTT
*
13142380 A-AATTTTAATTTT
1 ATATTTTTAATTTT
13142393 AACATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 6 0.22
17 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATTTTTAATTTTT
Found at i:13146981 original size:56 final size:55
Alignment explanation
Indices: 13146914--13147067 Score: 186
Period size: 53 Copynumber: 2.8 Consensus size: 55
13146904 AGTAGTTACG
* * * *
13146914 TAAGAATCAAATTGCTAAAAGATAACATTCCATAATAATATCCTATAATATCTCAT
1 TAAGAATCAAATTGCTAAAAGATAA-ATTCCATAATAATATCCTACAAAATCCCAC
* ** *
13146970 TAAGAATCAAATTGTTAAGGGAT-AATT-CATAATAATATCTTACAAAATCCCAC
1 TAAGAATCAAATTGCTAAAAGATAAATTCCATAATAATATCCTACAAAATCCCAC
* *
13147023 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTA
1 TAAGAATCAAATTGCTAAAAGATAA-ATTCCATAATAATATCCTA
13147068 ACACCCCCTT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
53 40 0.49
54 4 0.05
55 3 0.04
56 34 0.42
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.31
Consensus pattern (55 bp):
TAAGAATCAAATTGCTAAAAGATAAATTCCATAATAATATCCTACAAAATCCCAC
Found at i:13148436 original size:16 final size:16
Alignment explanation
Indices: 13148412--13148453 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
13148402 TGATTCACTA
* *
13148412 TAATGGAATAGGGTTG
1 TAATGGAATAGAGCTG
*
13148428 TAATTGAATAGAGCTG
1 TAATGGAATAGAGCTG
13148444 TAATGGAATA
1 TAATGGAATA
13148454 AAACTGCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.31
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:13158021 original size:14 final size:14
Alignment explanation
Indices: 13158002--13158029 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13157992 CCAGTTTATT
13158002 AATGAATTATTAAA
1 AATGAATTATTAAA
13158016 AATGAATTATTAAA
1 AATGAATTATTAAA
13158030 TATAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:13163788 original size:11 final size:11
Alignment explanation
Indices: 13163772--13163796 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13163762 GGTCATGTAG
13163772 AATAGACTTGT
1 AATAGACTTGT
13163783 AATAGACTTGT
1 AATAGACTTGT
13163794 AAT
1 AAT
13163797 GGCATAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (11 bp):
AATAGACTTGT
Found at i:13163859 original size:73 final size:73
Alignment explanation
Indices: 13163737--13163896 Score: 275
Period size: 73 Copynumber: 2.2 Consensus size: 73
13163727 TAGGGTATTC
* *
13163737 CATTGAACCAAACAACTATTTGTGTGGTCATGTAGAATAGACTTGTAATAGACTTGTAATGGCAT
1 CATTGAACCAAACAACTATTTGTGTGGGCATGTAGAATAGACTTATAATAGACTTGTAATGGCAT
13163802 AGCCATTA
66 AGCCATTA
* * *
13163810 CATTGAACCAAACAACTGTTTGTGTGGGCCTGTAGAATATACTTATAATAGACTTGTAATGGCAT
1 CATTGAACCAAACAACTATTTGTGTGGGCATGTAGAATAGACTTATAATAGACTTGTAATGGCAT
13163875 AGCCATTA
66 AGCCATTA
13163883 CATTGAACCAAACA
1 CATTGAACCAAACA
13163897 TTACCTAAGT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 82 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (73 bp):
CATTGAACCAAACAACTATTTGTGTGGGCATGTAGAATAGACTTATAATAGACTTGTAATGGCAT
AGCCATTA
Found at i:13182372 original size:15 final size:15
Alignment explanation
Indices: 13182352--13182384 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
13182342 TAACTATTTT
*
13182352 TATTATTATTGTTAC
1 TATTATTAATGTTAC
13182367 TATTATTAATGTTAC
1 TATTATTAATGTTAC
13182382 TAT
1 TAT
13182385 AACTATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (15 bp):
TATTATTAATGTTAC
Found at i:13182409 original size:18 final size:18
Alignment explanation
Indices: 13182388--13182426 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13182378 TTACTATAAC
13182388 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
*
13182406 TATTAGTTTATATGTTTA
1 TATTAGTTTATATATTTA
13182424 TAT
1 TAT
13182427 ACCTATGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:13183718 original size:13 final size:13
Alignment explanation
Indices: 13183652--13183722 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
13183642 ATATCTATCT
*
13183652 ATATAAACATTTC
1 ATATAATCATTTC
*
13183665 GTATAATCACTTT-
1 ATATAATCA-TTTC
13183678 ATATAA-CTATTTCC
1 ATATAATC-ATTT-C
* **
13183692 ATTTAATCGGTTC
1 ATATAATCATTTC
13183705 ATATAATCATTTC
1 ATATAATCATTTC
13183718 ATATA
1 ATATA
13183723 CCGAATTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
12 4 0.09
13 29 0.66
14 10 0.23
15 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (13 bp):
ATATAATCATTTC
Found at i:13189201 original size:28 final size:26
Alignment explanation
Indices: 13189170--13189232 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
13189160 ACAGAATTTT
* *
13189170 CCACTAAGTATTCATTTAGCAGAGATCC
1 CCACAAAGGATTCATTT--CAGAGATCC
* *
13189198 CCACAAAGGCTTCCTTTCAGAGATCC
1 CCACAAAGGATTCATTTCAGAGATCC
13189224 CCACAAAGG
1 CCACAAAGG
13189233 CTTTTATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 18 0.58
28 13 0.42
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (26 bp):
CCACAAAGGATTCATTTCAGAGATCC
Found at i:13189258 original size:29 final size:29
Alignment explanation
Indices: 13189190--13189318 Score: 108
Period size: 29 Copynumber: 4.7 Consensus size: 29
13189180 TTCATTTAGC
* * *
13189190 AGAGATCCCCACAAAGGCTTC-CTTT--C
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
* *
13189216 AGAGATCCCCACAAAGGCTTTTATTTAAT
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
* *
13189245 AGAGATTGTCACAAAGGCTTCTATTTAAT
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
* * * *
13189274 AGTGATCGCCATAAAGGCTTC-ACTTCAT
1 AGAGATCGCCACAAAGGCTTCTATTTAAT
*
13189302 AGATAT--CCACAAAGGCT
1 AGAGATCGCCACAAAGGCT
13189319 CACTTATACT
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
26 30 0.36
27 3 0.04
28 9 0.11
29 42 0.50
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (29 bp):
AGAGATCGCCACAAAGGCTTCTATTTAAT
Found at i:13189574 original size:30 final size:30
Alignment explanation
Indices: 13189538--13189599 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
13189528 GAATCATACT
* *
13189538 TGATAGACTCATTCACATTTGACTTGGTCA
1 TGATAGACTCATTCACAATAGACTTGGTCA
* * *
13189568 TGATAGAGTCTTTCACAATAGACTTGTTCA
1 TGATAGACTCATTCACAATAGACTTGGTCA
13189598 TG
1 TG
13189600 TCATTAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (30 bp):
TGATAGACTCATTCACAATAGACTTGGTCA
Found at i:13192064 original size:27 final size:27
Alignment explanation
Indices: 13192002--13192064 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
13191992 AGCATAGTTT
*
13192002 TCGCCAAATCACATCTGGAAGCACAGC
1 TCGCCAAATCACATATGGAAGCACAGC
* *
13192029 TCACTAAATCACATATGTG-AGCACAGC
1 TCGCCAAATCACATATG-GAAGCACAGC
13192056 TCGCCAAAT
1 TCGCCAAAT
13192065 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (27 bp):
TCGCCAAATCACATATGGAAGCACAGC
Found at i:13192694 original size:27 final size:28
Alignment explanation
Indices: 13192628--13192698 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
13192618 TGATTACAGA
*
13192628 TCGCCAAGCCCACTGGCGAATCCCCAGC
1 TCGCCAAGCCCACTGGCGAATCACCAGC
* *
13192656 TCGCCAGGCCCACTGGCG-ATCACTA-C
1 TCGCCAAGCCCACTGGCGAATCACCAGC
*
13192682 TTCGCCAATCCCACTGG
1 -TCGCCAAGCCCACTGG
13192699 TGATTATAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.51
28 17 0.46
ACGTcount: A:0.20, C:0.44, G:0.21, T:0.15
Consensus pattern (28 bp):
TCGCCAAGCCCACTGGCGAATCACCAGC
Found at i:13196021 original size:21 final size:23
Alignment explanation
Indices: 13195996--13196040 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
13195986 AACAAGGTAG
*
13195996 ATAAAAAT-A-GAACAAAATAAA
1 ATAAAAATAATGAAAAAAATAAA
13196017 ATAAAAATAATGAAAAAAATAAA
1 ATAAAAATAATGAAAAAAATAAA
13196040 A
1 A
13196041 ATTACTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 1 0.05
23 12 0.57
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (23 bp):
ATAAAAATAATGAAAAAAATAAA
Found at i:13196477 original size:28 final size:28
Alignment explanation
Indices: 13196412--13196465 Score: 92
Period size: 28 Copynumber: 1.9 Consensus size: 28
13196402 TTAATTAAAC
13196412 TAATTAAATTAATTATCCTAAAATAATA
1 TAATTAAATTAATTATCCTAAAATAATA
13196440 TAATTAAATTAATTAATCC-AAAATAA
1 TAATTAAATTAATT-ATCCTAAAATAA
13196466 CTTAATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (28 bp):
TAATTAAATTAATTATCCTAAAATAATA
Found at i:13202954 original size:430 final size:430
Alignment explanation
Indices: 13202154--13203013 Score: 1720
Period size: 430 Copynumber: 2.0 Consensus size: 430
13202144 GAAATAGAGC
13202154 ACCCCTTCCCTATTCATTCCAAAATCTTTGGTATTCCCACTCTCAACCTGTCGAAAACAAAGTCC
1 ACCCCTTCCCTATTCATTCCAAAATCTTTGGTATTCCCACTCTCAACCTGTCGAAAACAAAGTCC
13202219 CAACGACTCATCCTCTATCTGCTTACCCTTAATCTGCTCTACCCATGTCAATTTAACTTGAAGTT
66 CAACGACTCATCCTCTATCTGCTTACCCTTAATCTGCTCTACCCATGTCAATTTAACTTGAAGTT
13202284 GGGCCAACAGACTACCATCATCAAATAAACTGAGGCAAACAAACATCACTCTCAGGTCAGTCATA
131 GGGCCAACAGACTACCATCATCAAATAAACTGAGGCAAACAAACATCACTCTCAGGTCAGTCATA
13202349 GCTCTACGGCTCAGTGCGTCAGCTACCACATTAGCCTTACCAGGGTGGTATTCAATAGTACAGTC
196 GCTCTACGGCTCAGTGCGTCAGCTACCACATTAGCCTTACCAGGGTGGTATTCAATAGTACAGTC
13202414 ATAGTCTTCAAGTAGCTCAATCCATCTACGCTGCCTAAGATTCAGCTCCTTCTGAGTGAGGAGGT
261 ATAGTCTTCAAGTAGCTCAATCCATCTACGCTGCCTAAGATTCAGCTCCTTCTGAGTGAGGAGGT
13202479 ACTTAAGGCTCTTGTGATCAGTGTAAATGATACACTTCTAACCAAACAAGTAATGCCTCCAGATT
326 ACTTAAGGCTCTTGTGATCAGTGTAAATGATACACTTCTAACCAAACAAGTAATGCCTCCAGATT
13202544 TTCAGTACGAATACCACTGCGGCCAACTTCAAGTCATGCG
391 TTCAGTACGAATACCACTGCGGCCAACTTCAAGTCATGCG
13202584 ACCCCTTCCCTATTCATTCCAAAATCTTTGGTATTCCCACTCTCAACCTGTCGAAAACAAAGTCC
1 ACCCCTTCCCTATTCATTCCAAAATCTTTGGTATTCCCACTCTCAACCTGTCGAAAACAAAGTCC
13202649 CAACGACTCATCCTCTATCTGCTTACCCTTAATCTGCTCTACCCATGTCAATTTAACTTGAAGTT
66 CAACGACTCATCCTCTATCTGCTTACCCTTAATCTGCTCTACCCATGTCAATTTAACTTGAAGTT
13202714 GGGCCAACAGACTACCATCATCAAATAAACTGAGGCAAACAAACATCACTCTCAGGTCAGTCATA
131 GGGCCAACAGACTACCATCATCAAATAAACTGAGGCAAACAAACATCACTCTCAGGTCAGTCATA
13202779 GCTCTACGGCTCAGTGCGTCAGCTACCACATTAGCCTTACCAGGGTGGTATTCAATAGTACAGTC
196 GCTCTACGGCTCAGTGCGTCAGCTACCACATTAGCCTTACCAGGGTGGTATTCAATAGTACAGTC
13202844 ATAGTCTTCAAGTAGCTCAATCCATCTACGCTGCCTAAGATTCAGCTCCTTCTGAGTGAGGAGGT
261 ATAGTCTTCAAGTAGCTCAATCCATCTACGCTGCCTAAGATTCAGCTCCTTCTGAGTGAGGAGGT
13202909 ACTTAAGGCTCTTGTGATCAGTGTAAATGATACACTTCTAACCAAACAAGTAATGCCTCCAGATT
326 ACTTAAGGCTCTTGTGATCAGTGTAAATGATACACTTCTAACCAAACAAGTAATGCCTCCAGATT
13202974 TTCAGTACGAATACCACTGCGGCCAACTTCAAGTCATGCG
391 TTCAGTACGAATACCACTGCGGCCAACTTCAAGTCATGCG
13203014 TCGGATAATT
Statistics
Matches: 430, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
430 430 1.00
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (430 bp):
ACCCCTTCCCTATTCATTCCAAAATCTTTGGTATTCCCACTCTCAACCTGTCGAAAACAAAGTCC
CAACGACTCATCCTCTATCTGCTTACCCTTAATCTGCTCTACCCATGTCAATTTAACTTGAAGTT
GGGCCAACAGACTACCATCATCAAATAAACTGAGGCAAACAAACATCACTCTCAGGTCAGTCATA
GCTCTACGGCTCAGTGCGTCAGCTACCACATTAGCCTTACCAGGGTGGTATTCAATAGTACAGTC
ATAGTCTTCAAGTAGCTCAATCCATCTACGCTGCCTAAGATTCAGCTCCTTCTGAGTGAGGAGGT
ACTTAAGGCTCTTGTGATCAGTGTAAATGATACACTTCTAACCAAACAAGTAATGCCTCCAGATT
TTCAGTACGAATACCACTGCGGCCAACTTCAAGTCATGCG
Found at i:13211538 original size:26 final size:26
Alignment explanation
Indices: 13211509--13211561 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
13211499 CGAGAGAGAT
13211509 TGATCATGCCTTAATCTTTTAAATTA
1 TGATCATGCCTTAATCTTTTAAATTA
13211535 TGATCATGCCTTAATCTTTTAAATTA
1 TGATCATGCCTTAATCTTTTAAATTA
13211561 T
1 T
13211562 CTATGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (26 bp):
TGATCATGCCTTAATCTTTTAAATTA
Found at i:13211670 original size:6 final size:6
Alignment explanation
Indices: 13211659--13211686 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
13211649 CTCTCGCAAC
13211659 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
13211687 CAAATTTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:13234304 original size:25 final size:25
Alignment explanation
Indices: 13234272--13234389 Score: 89
Period size: 25 Copynumber: 4.8 Consensus size: 25
13234262 CCCTCTCTTC
13234272 AGCCATATAACGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATGTG
* * *
13234297 AGCCATATAATGGGAAGCTTATCT-
1 AGCCATATAACGGGAAGCTCATGTG
* * **
13234321 AGGCAGTATAATGGGAAGCTCATAAG
1 AGCCA-TATAACGGGAAGCTCATGTG
* ** *
13234347 AGCCATAT-TCAAGAAGCTCATGCG
1 AGCCATATAACGGGAAGCTCATGTG
* *
13234371 AGCC-TATAACAGGTAGCTC
1 AGCCATATAACGGGAAGCTC
13234390 TGAAGAGCCA
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
23 3 0.04
24 26 0.36
25 40 0.55
26 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATGTG
Found at i:13234500 original size:26 final size:26
Alignment explanation
Indices: 13234466--13234520 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
13234456 AGCTCTGGCA
*
13234466 AGCCATTAATCGGGAAGCTTACAAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
* *
13234492 AGCCTTTAATCGGGAAGCTCACGAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
13234518 AGC
1 AGC
13234521 TATATAACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
AGCCATTAATCGGGAAGCTCACAAAG
Found at i:13234531 original size:26 final size:26
Alignment explanation
Indices: 13234470--13234548 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
13234460 CTGGCAAGCC
*
13234470 ATTAATCGGGAAGCTTACAAAGAGCCT
1 ATTAATCGGGAAGCTCACAAAGAG-CT
*
13234497 -TTAATCGGGAAGCTCACGAAGAGCT
1 ATTAATCGGGAAGCTCACAAAGAGCT
*
13234522 ATATAA-CGGGACA-CTCA-TAAGAGCT
1 AT-TAATCGGGA-AGCTCACAAAGAGCT
13234547 AT
1 AT
13234549 GGTGTGTCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 11 0.24
26 31 0.67
27 4 0.09
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (26 bp):
ATTAATCGGGAAGCTCACAAAGAGCT
Found at i:13235181 original size:20 final size:20
Alignment explanation
Indices: 13235156--13235196 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13235146 AGCCCATGTA
*
13235156 TTTCATAAATTTTATAACTT
1 TTTCATAAATTTTACAACTT
*
13235176 TTTCATGAATTTTACAACTT
1 TTTCATAAATTTTACAACTT
13235196 T
1 T
13235197 ACAATTTAGT
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:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTCATAAATTTTACAACTT
Found at i:13236444 original size:21 final size:21
Alignment explanation
Indices: 13236420--13236462 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13236410 ATTTTGGTTC
13236420 ATGCCAAAATAGGCTAAAACA
1 ATGCCAAAATAGGCTAAAACA
13236441 ATGCCAAAATAGGCTAAAACA
1 ATGCCAAAATAGGCTAAAACA
13236462 A
1 A
13236463 CCTATACGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.14, T:0.14
Consensus pattern (21 bp):
ATGCCAAAATAGGCTAAAACA
Found at i:13259156 original size:17 final size:17
Alignment explanation
Indices: 13259134--13259185 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
13259124 TAAAAAATTG
13259134 TTTTAAAAATATAAATA
1 TTTTAAAAATATAAATA
*
13259151 TTTTAAAAATTATAAAAA
1 TTTTAAAAA-TATAAATA
*
13259169 TTATAAATAA-ATAAATA
1 TTTTAAA-AATATAAATA
13259186 ATTAATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.50
18 13 0.43
19 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTTAAAAATATAAATA
Found at i:13259159 original size:18 final size:18
Alignment explanation
Indices: 13259134--13259185 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
13259124 TAAAAAATTG
13259134 TTTT-AAAAATATAAATA
1 TTTTAAAAAATATAAATA
* *
13259151 TTTTAAAAATTATAAAAA
1 TTTTAAAAAATATAAATA
* *
13259169 TTATAAATAA-ATAAATA
1 TTTTAAAAAATATAAATA
13259186 ATTAATTACT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTTAAAAAATATAAATA
Found at i:13259166 original size:9 final size:9
Alignment explanation
Indices: 13259137--13259175 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
13259127 AAAATTGTTT
13259137 TAAAAA-TA
1 TAAAAATTA
* *
13259145 TAAATATTT
1 TAAAAATTA
13259154 TAAAAATTA
1 TAAAAATTA
13259163 TAAAAATTA
1 TAAAAATTA
13259172 TAAA
1 TAAA
13259176 TAAATAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 5 0.19
9 21 0.81
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:13259188 original size:27 final size:26
Alignment explanation
Indices: 13259137--13259189 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
13259127 AAAATTGTTT
**
13259137 TAAAAATATAAATATTTTAAAAATTA
1 TAAAAATATAAATATAATAAAAATTA
13259163 TAAAAATTATAAATA-AATAAATAATTA
1 TAAAAA-TATAAATATAATAAA-AATTA
13259190 ATTACTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAAAATATAAATATAATAAAAATTA
Found at i:13259642 original size:7 final size:7
Alignment explanation
Indices: 13259630--13259661 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
13259620 AAAGTATTTT
13259630 AAAATTA
1 AAAATTA
13259637 AAAATTA
1 AAAATTA
*
13259644 AAAAATA
1 AAAATTA
13259651 AAAATTA
1 AAAATTA
13259658 AAAA
1 AAAA
13259662 ATATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAATTA
Found at i:13259652 original size:14 final size:14
Alignment explanation
Indices: 13259630--13259664 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
13259620 AAAGTATTTT
*
13259630 AAAATTAAAAATTA
1 AAAAATAAAAATTA
13259644 AAAAATAAAAATTA
1 AAAAATAAAAATTA
13259658 AAAAATA
1 AAAAATA
13259665 TATTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAAAAATTA
Found at i:13259892 original size:20 final size:22
Alignment explanation
Indices: 13259867--13259920 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
13259857 TATTAATCTT
13259867 TTTATAATTTTTC-TCTAA-TA
1 TTTATAATTTTTCTTCTAATTA
* *
13259887 TTTAT-ATATCTCTTCTAATTTA
1 TTTATAATTTTTCTTCTAA-TTA
13259909 TTTATAATTTTT
1 TTTATAATTTTT
13259921 AAACAATCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 5 0.19
20 10 0.38
22 7 0.27
23 4 0.15
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTATAATTTTTCTTCTAATTA
Found at i:13267249 original size:2 final size:2
Alignment explanation
Indices: 13267244--13267291 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
13267234 TATTATATAC
13267244 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13267286 AG AG AG
1 AG AG AG
13267292 TTTGTGCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13268556 original size:12 final size:12
Alignment explanation
Indices: 13268516--13268557 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
13268506 TAGTTAACAA
* *
13268516 TTTTATTATAAA
1 TTTTAATATAAT
13268528 TTTTAAT-TAATT
1 TTTTAATATAA-T
13268540 TTTTAATATAAT
1 TTTTAATATAAT
13268552 TTTTAA
1 TTTTAA
13268558 AATTACTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAATATAAT
Found at i:13272859 original size:53 final size:53
Alignment explanation
Indices: 13272779--13272893 Score: 194
Period size: 53 Copynumber: 2.2 Consensus size: 53
13272769 TCAAAAAGAA
* *
13272779 ACAAAAACGAAACCCAAAAAAGCAGAGTCAACAAAGATAGTCGAAGCAAGTTC
1 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
*
13272832 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATATTCGAACCAAGTTC
1 ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
13272885 ACGAAAAAC
1 AC-AAAAAC
13272894 AGAGCCCCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 52 0.90
54 6 0.10
ACGTcount: A:0.55, C:0.22, G:0.14, T:0.10
Consensus pattern (53 bp):
ACAAAAACGAAACCCAAAAAAACAGAGTCAACAAAGATAGTCGAACCAAGTTC
Found at i:13275244 original size:33 final size:33
Alignment explanation
Indices: 13275180--13275254 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
13275170 GGAAGTAATC
*
13275180 TTAGGAACAACTAACCTTGGGAACGATATTATG
1 TTAGGAACAACTAACCTTGGGAACGACATTATG
* *
13275213 TTAGGAACAACTAACTTTTGGAAC-AGCATTATG
1 TTAGGAACAACTAACCTTGGGAACGA-CATTATG
* *
13275246 GTGGGAACA
1 TTAGGAACA
13275255 CTTTGGAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (33 bp):
TTAGGAACAACTAACCTTGGGAACGACATTATG
Found at i:13276042 original size:23 final size:22
Alignment explanation
Indices: 13276016--13276058 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
13276006 AGATCGAAAG
13276016 AAGAAAAGAAAAGAGAGAAAACA
1 AAGAAAAGAAAAGAG-GAAAACA
* *
13276039 AAGAAGAGAGAAGAGGAAAA
1 AAGAAAAGAAAAGAGGAAAA
13276059 TTTCATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.70, C:0.02, G:0.28, T:0.00
Consensus pattern (22 bp):
AAGAAAAGAAAAGAGGAAAACA
Found at i:13282620 original size:30 final size:30
Alignment explanation
Indices: 13282562--13282623 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
13282552 AAAACTCTTG
* * * * *
13282562 AATAAAATAAAAGTTTTTTTTTTGAAACAA
1 AATAAAATAAAAGATTTATGTATCAAACAA
13282592 AATAAAATAAAAGATTTATGTATCAAACAA
1 AATAAAATAAAAGATTTATGTATCAAACAA
13282622 AA
1 AA
13282624 GGGATGTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.32
Consensus pattern (30 bp):
AATAAAATAAAAGATTTATGTATCAAACAA
Found at i:13286081 original size:17 final size:19
Alignment explanation
Indices: 13286061--13286101 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
13286051 ATATAATTTT
*
13286061 AAAATATA-T-AATACATC
1 AAAATATACTAAAAACATC
13286078 AAAA-ATACTAAAAACATC
1 AAAATATACTAAAAACATC
13286096 AAAATA
1 AAAATA
13286102 AATATTTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 5 0.25
18 11 0.55
19 1 0.05
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATATACTAAAAACATC
Found at i:13286226 original size:30 final size:30
Alignment explanation
Indices: 13286182--13286241 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
13286172 ACTTAACAAG
13286182 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
13286212 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
13286242 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:13292358 original size:23 final size:23
Alignment explanation
Indices: 13292315--13292360 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13292305 TCATGTGAGC
*
13292315 ATTAATGTAAAGGAAAGACTATG
1 ATTAATGTAAAGGAAACACTATG
*
13292338 ATTATATGTAAAGG-CACACTATG
1 ATTA-ATGTAAAGGAAACACTATG
13292361 TGTGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (23 bp):
ATTAATGTAAAGGAAACACTATG
Found at i:13301831 original size:19 final size:19
Alignment explanation
Indices: 13301809--13301864 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
13301799 TAAAAATTAG
*
13301809 TAATTTTGTTATATTTATA
1 TAATTTTGTAATATTTATA
* *
13301828 TAATTTTTTGTAATCTTTTTA
1 TAA--TTTTGTAATATTTATA
13301849 TAATTTTGTAATATTT
1 TAATTTTGTAATATTT
13301865 TTAGTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
TAATTTTGTAATATTTATA
Found at i:13301865 original size:19 final size:19
Alignment explanation
Indices: 13301809--13301867 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
13301799 TAAAAATTAG
* *
13301809 TAATTTTGTTATATTTATA
1 TAATTTTGTAATATTTTTA
*
13301828 TAATTTTTTGTAATCTTTTTA
1 TAA--TTTTGTAATATTTTTA
13301849 TAATTTTGTAATATTTTTA
1 TAATTTTGTAATATTTTTA
13301868 GTTTATACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
TAATTTTGTAATATTTTTA
Found at i:13302995 original size:25 final size:25
Alignment explanation
Indices: 13302962--13303018 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
13302952 CGTTGACATG
13302962 GTCG-TTAACAGATGCCACGCTAAT
1 GTCGATTAACAGATGCCACGCTAAT
13302986 GTCGATTAACAGATGCCACGCTAAT
1 GTCGATTAACAGATGCCACGCTAAT
*
13303011 GTTGATTA
1 GTCGATTA
13303019 CTAACATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (25 bp):
GTCGATTAACAGATGCCACGCTAAT
Found at i:13305808 original size:18 final size:18
Alignment explanation
Indices: 13305766--13305801 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13305756 TGCCAAGTGC
13305766 ATATCCTAACCCTTATAT
1 ATATCCTAACCCTTATAT
13305784 ATATCCTAACCCTTATAT
1 ATATCCTAACCCTTATAT
13305802 GTTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATCCTAACCCTTATAT
Found at i:13306316 original size:62 final size:59
Alignment explanation
Indices: 13306200--13306320 Score: 136
Period size: 62 Copynumber: 2.0 Consensus size: 59
13306190 TTGTACAAAC
* * ****
13306200 TATTTTTATATTGTTTCATTTAATAAAATAGAAGTTGTTTTAAATATTTTAATAGTAAAT
1 TATTTTTATATTGTTTCATTTAATAAAATAGAAGCTCTTTTAAATAAGGCAATAG-AAAT
*
13306260 TATTTTTATATT-TTATCCTATTTAATAAAATAGAAGCTCTTTTGAATAAGGCAATAGAAAT
1 TATTTTTATATTGTT-T-C-ATTTAATAAAATAGAAGCTCTTTTAAATAAGGCAATAGAAAT
13306321 GATGCAACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 5 0.10
62 31 0.61
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (59 bp):
TATTTTTATATTGTTTCATTTAATAAAATAGAAGCTCTTTTAAATAAGGCAATAGAAAT
Found at i:13309496 original size:28 final size:27
Alignment explanation
Indices: 13309450--13309518 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
13309440 TTTTTGACAC
* *
13309450 TATTTTTTCAGAACTGTCTTCTCAAAAT
1 TATTTTTTTAGAACCGTCTTCTC-AAAT
* *
13309478 TATTTTTTTAGAGCCGTCTTTTCAAAT
1 TATTTTTTTAGAACCGTCTTCTCAAAT
*
13309505 TTTTTTTTTCAGAA
1 TATTTTTTT-AGAA
13309519 ACTACTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.52
Consensus pattern (27 bp):
TATTTTTTTAGAACCGTCTTCTCAAAT
Found at i:13309698 original size:125 final size:124
Alignment explanation
Indices: 13309478--13309782 Score: 407
Period size: 125 Copynumber: 2.4 Consensus size: 124
13309468 TTCTCAAAAT
* * * * *
13309478 TATTTTTTTAGAGCCGTCTTTTCAAATTTTTTTTTTCAGAAACTAC--TAAAAAAAGTGCGTCAA
1 TATTTTTTTAGAACCGTCTTTTCAAA-ATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGTCAA
* * * *
13309541 GTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGCATCTTGCTTGAAGTGTTTTTGACAC
65 GTGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
*
13309601 TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGTCCAC
1 TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGT-CAA
*
13309666 GTGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGGCAC
65 GTGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
* * * * * *
13309726 TATTTTTTCAGAACTGTCTTCTCAAAATTAATTTTTTAGAAATTACTGGACGAAAAA
1 TATTTTTTTAGAACCGTCTTTTCAAAATT-ATTTTTCAGAAACTACTGTA-GAAAAA
13309783 AAGACAAAAT
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
122 17 0.11
123 25 0.16
124 12 0.08
125 83 0.52
126 17 0.11
127 6 0.04
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (124 bp):
TATTTTTTTAGAACCGTCTTTTCAAAATTATTTTTCAGAAACTACTGTAGAAAAAGAGCGTCAAG
TGGGAGCTTCTTTCAATACTTTTGCTGATAGTGCATCCTGCTTGAAGCGTTTTTGACAC
Found at i:13309914 original size:33 final size:32
Alignment explanation
Indices: 13309871--13309958 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 32
13309861 TACAAAATTA
*
13309871 TTTTTAAAAACCCTAAACCCTAATTTAATTTAT
1 TTTTTTAAAACCCTAAACCCT-ATTTAATTTAT
**
13309904 TTTTTTAAAACAATAAA-CC---TTAATTTAT
1 TTTTTTAAAACCCTAAACCCTATTTAATTTAT
**
13309932 TTTTTTAAATTCCTAAACCCTGATTTA
1 TTTTTTAAAACCCTAAACCCT-ATTTA
13309959 TTTTTTAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
28 22 0.51
29 2 0.05
32 2 0.05
33 17 0.40
ACGTcount: A:0.38, C:0.16, G:0.01, T:0.45
Consensus pattern (32 bp):
TTTTTTAAAACCCTAAACCCTATTTAATTTAT
Found at i:13309962 original size:27 final size:28
Alignment explanation
Indices: 13309896--13309974 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 28
13309886 AACCCTAATT
* ** *
13309896 TAATTTATTTTTTTAAAACAATAAACCT
1 TAATTTATTTTTTTAAATCCCTAAACCC
*
13309924 TAATTTATTTTTTTAAATTCCTAAACCC
1 TAATTTATTTTTTTAAATCCCTAAACCC
*
13309952 TGATTTA-TTTTTTAAATCCCTAA
1 TAATTTATTTTTTTAAATCCCTAA
13309975 CCCATAACCC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 15 0.34
28 29 0.66
ACGTcount: A:0.35, C:0.14, G:0.01, T:0.49
Consensus pattern (28 bp):
TAATTTATTTTTTTAAATCCCTAAACCC
Found at i:13318448 original size:25 final size:25
Alignment explanation
Indices: 13318412--13318526 Score: 117
Period size: 25 Copynumber: 4.6 Consensus size: 25
13318402 CGGACACACC
*
13318412 ACAGCTCGTATGAGCTTCTTAATTT
1 ACAGCTCGTATGAGCTTCTCAATTT
* *
13318437 ACAGCTCATATGAGCTTCTCGATTT
1 ACAGCTCGTATGAGCTTCTCAATTT
* *
13318462 ACAGCTCGTATGAGCTTCCCAATTC
1 ACAGCTCGTATGAGCTTCTCAATTT
* * *
13318487 ATAGCTCGTGA-GAGCATACT-GATTT
1 ACAGCTCGT-ATGAGC-TTCTCAATTT
*
13318512 AGAGCTCGTATGAGC
1 ACAGCTCGTATGAGC
13318527 ATGCATGAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.01
25 70 0.95
26 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCTCAATTT
Found at i:13318493 original size:50 final size:50
Alignment explanation
Indices: 13318412--13318526 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
13318402 CGGACACACC
** * *
13318412 ACAGCTCGTATGAGCTTCTTAATTTACAGCTCAT-ATGAGC-TTCTCGATTT
1 ACAGCTCGTATGAGCTTCCCAATTCACAGCTCATGA-GAGCATACT-GATTT
* *
13318462 ACAGCTCGTATGAGCTTCCCAATTCATAGCTCGTGAGAGCATACTGATTT
1 ACAGCTCGTATGAGCTTCCCAATTCACAGCTCATGAGAGCATACTGATTT
*
13318512 AGAGCTCGTATGAGC
1 ACAGCTCGTATGAGC
13318527 ATGCATGAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 52 0.93
51 4 0.07
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (50 bp):
ACAGCTCGTATGAGCTTCCCAATTCACAGCTCATGAGAGCATACTGATTT
Found at i:13321836 original size:59 final size:58
Alignment explanation
Indices: 13321750--13321863 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
13321740 ATAATCAAAG
* * * *
13321750 TTTCTTGTCATCACAGTTCATAGTAGGTGAGTCTATACTCAAACAAGAATATGATCAT
1 TTTCCTGTCATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGATCAT
* *
13321808 TTTCCTGTCAATCACAGTTCACAATAGGTAAGTTTATACTTAAACAAGAATATGAT
1 TTTCCTGTC-ATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGAT
13321864 TATTCATTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 8 0.16
59 41 0.84
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (58 bp):
TTTCCTGTCATCACAGTTCACAATAGGTAAGTCTATACTCAAACAAGAATATGATCAT
Found at i:13330854 original size:7 final size:6
Alignment explanation
Indices: 13330829--13330853 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13330819 GATTAGTTAT
13330829 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
13330854 ACTAAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:13343736 original size:20 final size:20
Alignment explanation
Indices: 13343692--13343789 Score: 106
Period size: 20 Copynumber: 4.8 Consensus size: 20
13343682 CAAAACACAT
* * *
13343692 CAGAGAGCATCGAAATGCTAA
1 CAGAG-GCACCGAAGTGCAAA
*
13343713 CAGAGGCACCGTAGTGCAAA
1 CAGAGGCACCGAAGTGCAAA
13343733 CAGAGGCACCGAAGTGCAAA
1 CAGAGGCACCGAAGTGCAAA
* * * *
13343753 CAGATGCATCAAAATGCAAA
1 CAGAGGCACCGAAGTGCAAA
*
13343773 CAAAGGCACCGAAGTGC
1 CAGAGGCACCGAAGTGC
13343790 GATCCCATAC
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
20 58 0.92
21 5 0.08
ACGTcount: A:0.41, C:0.23, G:0.26, T:0.10
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCAAA
Found at i:13351571 original size:40 final size:40
Alignment explanation
Indices: 13351475--13351578 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
13351465 ACCAAAATCC
* *
13351475 TTATTATAATTATTGTAATTATAA--TTTACGATCGAATA
1 TTATTATAATTATTGTAATTATAATTTTTACGATCAAACA
* * *
13351513 TTATTATAATTATTGTAATTGTAATTTTTTCGGTCAAACA
1 TTATTATAATTATTGTAATTATAATTTTTACGATCAAACA
*
13351553 TTATTATAATTATGGTAATTATAATT
1 TTATTATAATTATTGTAATTATAATT
13351579 ATAATATTCG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 23 0.40
40 34 0.60
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.50
Consensus pattern (40 bp):
TTATTATAATTATTGTAATTATAATTTTTACGATCAAACA
Found at i:13362398 original size:28 final size:29
Alignment explanation
Indices: 13362366--13362425 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
13362356 GATTTAATAT
13362366 TTATAAAAATATTCA-AAAAA-TAAAAAAA
1 TTATAAAAA-ATTCATAAAAATTAAAAAAA
* *
13362394 TTATAAAAAGTTCATAAAAATTCAAAAAA
1 TTATAAAAAATTCATAAAAATTAAAAAAA
13362423 TTA
1 TTA
13362426 GTATGAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.14
28 14 0.50
29 10 0.36
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (29 bp):
TTATAAAAAATTCATAAAAATTAAAAAAA
Found at i:13362401 original size:17 final size:17
Alignment explanation
Indices: 13362368--13362423 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
13362358 TTTAATATTT
*
13362368 ATAAAAATATTCAAAAA
1 ATAAAAAAATTCAAAAA
13362385 ATAAAAAAATT-ATAAAA
1 ATAAAAAAATTCA-AAAA
*
13362402 AGTTCATAAAAATTCAAAAA
1 A--T-AAAAAAATTCAAAAA
13362422 AT
1 AT
13362424 TAGTATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.03
17 15 0.47
18 1 0.03
19 1 0.03
20 13 0.41
21 1 0.03
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (17 bp):
ATAAAAAAATTCAAAAA
Found at i:13371720 original size:73 final size:73
Alignment explanation
Indices: 13371582--13371737 Score: 253
Period size: 73 Copynumber: 2.2 Consensus size: 73
13371572 GAAGAAAAGG
13371582 AAAATA-AATAAGTAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTTA
1 AAAATATAATAAGTAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTTA
*
13371646 ACAAATGA
66 ACAAATAA
* * *
13371654 AAAATATAATACGTTAAAAAGAAAAAAATTTAAATTGTT-TAAAAAAAGTATAATGATTAGTTTT
1 AAAATATAATAAG-TAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTT
13371718 AACAAATAA
65 AACAAATAA
13371727 AAAATATAATA
1 AAAATATAATA
13371738 TATTAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
72 6 0.08
73 47 0.60
74 25 0.32
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (73 bp):
AAAATATAATAAGTAAAAAGAAAAAAATTTAAATTGTTCAAAAAAAAGTATAAGGATTAGTTTTA
ACAAATAA
Found at i:13373012 original size:13 final size:13
Alignment explanation
Indices: 13372965--13373022 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
13372955 AAATCCAAAA
13372965 TATAAAAAA-AAT
1 TATAAAAAATAAT
13372977 TAT-AAAAATAA-
1 TATAAAAAATAAT
**
13372988 TATGAAGCAATAAT
1 TAT-AAAAAATAAT
*
13373002 TATAAAAAATATT
1 TATAAAAAATAAT
*
13373015 TTTAAAAA
1 TATAAAAA
13373023 TTATAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 8 0.22
12 5 0.14
13 20 0.56
14 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (13 bp):
TATAAAAAATAAT
Found at i:13375657 original size:23 final size:23
Alignment explanation
Indices: 13375630--13375673 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
13375620 CTGAAAATTA
13375630 TAGATATGACTTTTATTTTTAAT
1 TAGATATGACTTTTATTTTTAAT
* *
13375653 TAGATTTGATTTTTATTTTTA
1 TAGATATGACTTTTATTTTTA
13375674 TTTACCTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (23 bp):
TAGATATGACTTTTATTTTTAAT
Found at i:13377310 original size:22 final size:22
Alignment explanation
Indices: 13377281--13377333 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
13377271 CCAAACCTCA
*
13377281 TTTT-TTTGTTG-GTAAGTTTG
1 TTTTCTTTGTTGTGTAAGTTCG
*
13377301 CTTTTCTTTG-TGTGTTAGTTCG
1 -TTTTCTTTGTTGTGTAAGTTCG
13377323 TTTTCTTTGTT
1 TTTTCTTTGTT
13377334 ATTTATTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.06, C:0.08, G:0.21, T:0.66
Consensus pattern (22 bp):
TTTTCTTTGTTGTGTAAGTTCG
Found at i:13382500 original size:15 final size:16
Alignment explanation
Indices: 13382468--13382500 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13382458 AGAGAATACT
*
13382468 GAATTTGATCATGAAA
1 GAATTTGATCAAGAAA
13382484 GAATTTG-TCAAGAAA
1 GAATTTGATCAAGAAA
13382499 GA
1 GA
13382501 GGTTATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (16 bp):
GAATTTGATCAAGAAA
Found at i:13390209 original size:18 final size:18
Alignment explanation
Indices: 13390177--13390212 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13390167 TTAAGTTAGT
*
13390177 GGAAACAAATAAAACAAA
1 GGAAACAAAGAAAACAAA
*
13390195 GGAAACAAAGGAAACAAA
1 GGAAACAAAGAAAACAAA
13390213 TAGCTTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.11, G:0.17, T:0.03
Consensus pattern (18 bp):
GGAAACAAAGAAAACAAA
Found at i:13391139 original size:74 final size:75
Alignment explanation
Indices: 13391046--13391304 Score: 310
Period size: 74 Copynumber: 3.5 Consensus size: 75
13391036 AAAATAAATA
* * * * * *
13391046 ACTATTTATTTGTCGGTTTATTCGACTAGTGCTGGGCG-TAATTCTCATTGGTAAATCCAACTAG
1 ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTAG
*
13391110 AGTTTGGCTC
66 AGTTAGGCTC
* * * * *
13391120 ACTATTTATTCGTTGGTTTA-ACGGACTAGCGCTGGGTGCAAATAC-CGTTGGTATATCCAACTA
1 ACTAATTATTTGTCGGTTTATTC-GACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTA
*
13391183 GAGCTAGGCTC
65 GAGTTAGGCTC
* * *
13391194 ACTAATTATTTGTCGATTTATTCGACTAGCGCTGGACGCAAATACT-GTTGGTATATCCAACTTG
1 ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTAG
*
13391258 AGTTGGGCTC
66 AGTTAGGCTC
* *
13391268 CCTAATTATTTGTCGGTTTATTCGACTAGCGTTGGGC
1 ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGC
13391305 ACAACTTTCG
Statistics
Matches: 156, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
73 1 0.01
74 150 0.96
75 5 0.03
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (75 bp):
ACTAATTATTTGTCGGTTTATTCGACTAGCGCTGGGCGCAAATACTCGTTGGTATATCCAACTAG
AGTTAGGCTC
Found at i:13392376 original size:25 final size:25
Alignment explanation
Indices: 13392344--13392423 Score: 126
Period size: 25 Copynumber: 3.2 Consensus size: 25
13392334 TCAGTGAGTT
*
13392344 ACACGGCTTGGCACAC-GGACGTGTG
1 ACACGGCTTTGCACACGGGA-GTGTG
*
13392369 ACATGGCTTTGCACACGGGAGTGTG
1 ACACGGCTTTGCACACGGGAGTGTG
13392394 ACACGGCTTTGCACACGGGAGTGTG
1 ACACGGCTTTGCACACGGGAGTGTG
13392419 ACACG
1 ACACG
13392424 ACTGCGTGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
25 48 0.94
26 3 0.06
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (25 bp):
ACACGGCTTTGCACACGGGAGTGTG
Found at i:13403731 original size:30 final size:30
Alignment explanation
Indices: 13403673--13403731 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
13403663 TTGAAAAGGT
* *
13403673 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
13403703 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
13403732 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:13426175 original size:21 final size:21
Alignment explanation
Indices: 13426129--13426179 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
13426119 ATGAAACTAT
* *
13426129 TTACTATGTCGTGACACGCCC
1 TTACTATGTCGCGACACGCAC
*
13426150 CTACTATGTCGCGACAC-CAAC
1 TTACTATGTCGCGACACGC-AC
13426171 TTACTATGT
1 TTACTATGT
13426180 TGCAACATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (21 bp):
TTACTATGTCGCGACACGCAC
Found at i:13441923 original size:12 final size:12
Alignment explanation
Indices: 13441906--13441945 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
13441896 AGTGAAAAGC
13441906 AAAAAGAGATTG
1 AAAAAGAGATTG
*
13441918 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
13441930 AAAGAGAGCTTG
1 AAAAAGAGATTG
13441942 AAAA
1 AAAA
13441946 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:13443035 original size:80 final size:80
Alignment explanation
Indices: 13442902--13443142 Score: 482
Period size: 80 Copynumber: 3.0 Consensus size: 80
13442892 TGTTTTCGTA
13442902 AATCTTTTCGAACAAAATTTAAAGGGTTTGCTTGTTTGAATTTGAGTATGCTAACACCCTCGTTG
1 AATCTTTTCGAACAAAATTTAAAGGGTTTGCTTGTTTGAATTTGAGTATGCTAACACCCTCGTTG
13442967 CCATTTGGATCGAGT
66 CCATTTGGATCGAGT
13442982 AATCTTTTCGAACAAAATTTAAAGGGTTTGCTTGTTTGAATTTGAGTATGCTAACACCCTCGTTG
1 AATCTTTTCGAACAAAATTTAAAGGGTTTGCTTGTTTGAATTTGAGTATGCTAACACCCTCGTTG
13443047 CCATTTGGATCGAGT
66 CCATTTGGATCGAGT
13443062 AATCTTTTCGAACAAAATTTAAAGGGTTTGCTTGTTTGAATTTGAGTATGCTAACACCCTCGTTG
1 AATCTTTTCGAACAAAATTTAAAGGGTTTGCTTGTTTGAATTTGAGTATGCTAACACCCTCGTTG
13443127 CCATTTGGATCGAGT
66 CCATTTGGATCGAGT
13443142 A
1 A
13443143 GTCAAAATCA
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 161 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (80 bp):
AATCTTTTCGAACAAAATTTAAAGGGTTTGCTTGTTTGAATTTGAGTATGCTAACACCCTCGTTG
CCATTTGGATCGAGT
Found at i:13451099 original size:20 final size:19
Alignment explanation
Indices: 13451050--13451100 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
13451040 ATATAAGTGT
*
13451050 TTAATTTGTCTTGTTTTAG
1 TTAATTTGTCTTGTTTCAG
*
13451069 TTAAATGTGTCTTGATTTCA-
1 TT-AATTTGTCTTG-TTTCAG
13451089 TTAAGTTTGTCT
1 TTAA-TTTGTCT
13451101 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.15
20 18 0.69
21 4 0.15
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.57
Consensus pattern (19 bp):
TTAATTTGTCTTGTTTCAG
Found at i:13458345 original size:17 final size:16
Alignment explanation
Indices: 13458295--13458347 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 16
13458285 GGGTGAGAAG
13458295 TAAAAGTTTAGGGGGAAAA
1 TAAAAGTTTA-GGGG--AA
*
13458314 TAAAAAGTTTTGGGGAA
1 T-AAAAGTTTAGGGGAA
13458331 TAAAAGTTTGAGGGGAA
1 TAAAAGTTT-AGGGGAA
13458348 AGTAAATGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 8 0.27
17 9 0.30
19 5 0.17
20 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTAGGGGAA
Found at i:13459690 original size:16 final size:16
Alignment explanation
Indices: 13459665--13459698 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13459655 AGGTGGTGGT
*
13459665 AGGCGACGGCGTCAGA
1 AGGCGACGGCGGCAGA
*
13459681 AGGCGGCGGCGGCAGA
1 AGGCGACGGCGGCAGA
13459697 AG
1 AG
13459699 TTCAACAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.50, T:0.03
Consensus pattern (16 bp):
AGGCGACGGCGGCAGA
Found at i:13460237 original size:6 final size:6
Alignment explanation
Indices: 13460226--13460261 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
13460216 AATAGTTATA
13460226 TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT
13460262 AAATCATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:13460581 original size:6 final size:6
Alignment explanation
Indices: 13460570--13460605 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
13460560 TGAATAGTTA
13460570 TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT
13460606 AAATCATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:13462644 original size:2 final size:2
Alignment explanation
Indices: 13462637--13462664 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13462627 TAATTCCTAA
13462637 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
13462665 TTCCATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13463307 original size:106 final size:106
Alignment explanation
Indices: 13463115--13463319 Score: 281
Period size: 106 Copynumber: 1.9 Consensus size: 106
13463105 AAGGAAAAAT
* * *
13463115 TTTCAAATTAAGGCAATATTTTGCGTTGGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTCT
1 TTTCAAAGTAAGGCAATATTTTACGTTAGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTCT
*
13463180 CGATTTCTCGTCTGATCAAATAGCCGAATATCCTTTCGAAA
66 CGATTTCTCGTCTGATCAAATAGCCAAATATCCTTTCGAAA
* * * *
13463221 TTTCAAAGTGAGGCAATATTTTACGTTTAG-AAATTCGAGAGAACGTGCCCTAACGTGCTGGGTT
1 TTTCAAAGTAAGGCAATATTTTACG-TTAGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTC
*
13463285 TCGATTTCTCGT-TCGA-CTAAATAGGCAAATATCCT
65 TCGATTTCTCGTCT-GATC-AAATAGCCAAATATCCT
13463320 CTTAAATCTC
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 2 0.02
106 82 0.94
107 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (106 bp):
TTTCAAAGTAAGGCAATATTTTACGTTAGAAAATTCGAGAAAACGTGCCCTAACGTACTGGGTCT
CGATTTCTCGTCTGATCAAATAGCCAAATATCCTTTCGAAA
Found at i:13463702 original size:126 final size:127
Alignment explanation
Indices: 13463556--13463809 Score: 501
Period size: 126 Copynumber: 2.0 Consensus size: 127
13463546 AATCATTTTA
13463556 CGAGGTGACCCGATTACACCTCATCAAAAAAGATTGTTGTCGACACTCCCATGTTCATTTTTTTA
1 CGAGGTGACCCGATTACACCTCATCAAAAAAGATTGTTGTCGACACTCCCATGTTCATTTTTTTA
13463621 TTATTAAAACCCAAGTCGACCCCGTTTTCACGAAAAAATGATGTCAACATTTACCAATATAG
66 TTATTAAAACCCAAGTCGACCCCGTTTTCACGAAAAAATGATGTCAACATTTACCAATATAG
13463683 CGAGGTGA-CCGATTACACCTCATCAAAAAAGATTGTTGTCGACACTCCCATGTTCATTTTTTTA
1 CGAGGTGACCCGATTACACCTCATCAAAAAAGATTGTTGTCGACACTCCCATGTTCATTTTTTTA
13463747 TTATTAAAACCCAAGTCGACCCCGTTTTCACGAAAAAATGATGTCAACATTTACCAATATAG
66 TTATTAAAACCCAAGTCGACCCCGTTTTCACGAAAAAATGATGTCAACATTTACCAATATAG
13463809 C
1 C
13463810 CCTTATTTTC
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 119 0.94
127 8 0.06
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (127 bp):
CGAGGTGACCCGATTACACCTCATCAAAAAAGATTGTTGTCGACACTCCCATGTTCATTTTTTTA
TTATTAAAACCCAAGTCGACCCCGTTTTCACGAAAAAATGATGTCAACATTTACCAATATAG
Found at i:13465397 original size:69 final size:69
Alignment explanation
Indices: 13465163--13465407 Score: 264
Period size: 69 Copynumber: 3.6 Consensus size: 69
13465153 AGTATGTTAC
* * * *
13465163 ACTTAAAAACAGTAGCAAAATCTTAGATATTTAAGAACATATGGCAAACCAACACTCAACTAAAA
1 ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAAA
13465228 CAAG
66 CAAG
* * * * * *** * ** *
13465232 ACTTAGAAACAGTAGCAAAACATTAGATATTTGAGAACATAAGA-AAATTTTGACATATGTTACA
1 ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTA-ACTAAA
13465296 AC-AG
65 ACAAG
* * *
13465300 -TTTACAAACAGTAGCCAAAA-AGTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAA
1 ACTTAAAAACAGTAG-CAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAA
13465363 ACAAG
65 ACAAG
*
13465368 ACTTAAAAACAATAGCAAAATATTAGATATTTAAGAACAT
1 ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACAT
13465408 GTGAAATTTT
Statistics
Matches: 137, Mismatches: 33, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
67 37 0.27
68 28 0.20
69 72 0.53
ACGTcount: A:0.51, C:0.15, G:0.11, T:0.24
Consensus pattern (69 bp):
ACTTAAAAACAGTAGCAAAATATTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAAA
CAAG
Found at i:13465419 original size:136 final size:136
Alignment explanation
Indices: 13465169--13465431 Score: 393
Period size: 136 Copynumber: 1.9 Consensus size: 136
13465159 TTACACTTAA
** *
13465169 AAACAGTAGCAAAATCTTAGATATTTAAGAACATATGGCAAACCAACACTCAACTAAAACAAGAC
1 AAACAGTAGCAAAATAGTAGATATTTAAGAACATATGACAAACCAACACTCAACTAAAACAAGAC
* * *
13465234 TTAGAAACAGTAGCAAAACATTAGATATTTGAGAACATAAGAAAATTTTGACATATGTTACAACA
66 TTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATATGTTACAACA
13465299 GTTTAC
131 GTTTAC
* *
13465305 AAACAGTAGCCAAAA-AGTAGATATTTAAGAACATATGACAAACTAACACTTAACTAAAACAAGA
1 AAACAGTAG-CAAAATAGTAGATATTTAAGAACATATGACAAACCAACACTCAACTAAAACAAGA
* ** * *
13465369 CTTAAAAACAATAGCAAAATATTAGATATTTAAGAACATGTGAAATTTTTGGCATATGTTACA
65 CTTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATATGTTACA
13465432 CTTTAAAACA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
136 108 0.96
137 5 0.04
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (136 bp):
AAACAGTAGCAAAATAGTAGATATTTAAGAACATATGACAAACCAACACTCAACTAAAACAAGAC
TTAAAAACAATAGCAAAACATTAGATATTTAAGAACATAAGAAAATTTTGACATATGTTACAACA
GTTTAC
Found at i:13465558 original size:39 final size:39
Alignment explanation
Indices: 13465515--13465592 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
13465505 AACTACACTT
* * **
13465515 AAAAACAGTAGTAAAACATTAGATATTTAAGAACATATG
1 AAAAAAAGTAGCAAAACATTAGATAAGTAAGAACATATG
* *
13465554 AAAAAAAGTAGCAAATCATTATATAAGTAAGAACATATG
1 AAAAAAAGTAGCAAAACATTAGATAAGTAAGAACATATG
13465593 GCAAACCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (39 bp):
AAAAAAAGTAGCAAAACATTAGATAAGTAAGAACATATG
Found at i:13471782 original size:20 final size:21
Alignment explanation
Indices: 13471743--13471782 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13471733 TTTCTTCCCT
*
13471743 CAAAAACACCACTTTCTCCTA
1 CAAAAACACCACTTTATCCTA
*
13471764 CAAAAACA-CATTTTATCCT
1 CAAAAACACCACTTTATCCT
13471783 GAAACTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.28
Consensus pattern (21 bp):
CAAAAACACCACTTTATCCTA
Found at i:13481422 original size:14 final size:14
Alignment explanation
Indices: 13481403--13481435 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
13481393 TTGTTGTAGT
13481403 GTGGACTAAATATA
1 GTGGACTAAATATA
*
13481417 GTGGACTACATATA
1 GTGGACTAAATATA
13481431 GTGGA
1 GTGGA
13481436 ATTACTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (14 bp):
GTGGACTAAATATA
Found at i:13486517 original size:20 final size:21
Alignment explanation
Indices: 13486479--13486521 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
13486469 AATCGCTTCC
13486479 TTAAAATCAAAAAATTTTTAA
1 TTAAAATCAAAAAATTTTTAA
*
13486500 TTAAAATCAAAATATTTTTAA
1 TTAAAATCAAAAAATTTTTAA
13486521 T
1 T
13486522 CACCAAAGTG
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:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAATCAAAAAATTTTTAA
Found at i:13500846 original size:59 final size:59
Alignment explanation
Indices: 13500779--13500892 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
13500769 GTGTAGAGTG
13500779 CCCTTTTTTGTCCTCTCATCACAACAAGAACCCTACGAGAAACTGTTAAGCCATTACTA
1 CCCTTTTTTGTCCTCTCATCACAACAAGAACCCTACGAGAAACTGTTAAGCCATTACTA
* * *
13500838 CCCTTTTTTGTCCTCTCATTACAACAAGAACCCTATGAGAAACTTTTAAGCCATT
1 CCCTTTTTTGTCCTCTCATCACAACAAGAACCCTACGAGAAACTGTTAAGCCATT
13500893 TGACTCAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (59 bp):
CCCTTTTTTGTCCTCTCATCACAACAAGAACCCTACGAGAAACTGTTAAGCCATTACTA
Found at i:13502911 original size:15 final size:16
Alignment explanation
Indices: 13502881--13502913 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
13502871 AAAGAGAGAG
13502881 AGGTGTGTGGGAATGA
1 AGGTGTGTGGGAATGA
*
13502897 AGGTGTGT-TGAATGA
1 AGGTGTGTGGGAATGA
13502912 AG
1 AG
13502914 TAGAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (16 bp):
AGGTGTGTGGGAATGA
Found at i:13506791 original size:67 final size:66
Alignment explanation
Indices: 13506669--13506892 Score: 211
Period size: 67 Copynumber: 3.3 Consensus size: 66
13506659 CCTCAAAAAA
* * * * *
13506669 GGTTCAAGGTGTAAGGCCTTAGCTTGGCTAAT-GTAACCAATAAAGTCCGCAAGGATGTTAAACA
1 GGTTCAAGGTGTAAGACCAT-GCTTAGCT-ATGGTAACCAATAGAGTCAGCAAGGATGTTAAACA
13506733 TGG
64 TGG
*
13506736 GGTTACAAGGTGTAAGACCATGCTTAGCTATGGTAACCAATAGAGTCAG-ACAGGATGTTAAATA
1 GGTT-CAAGGTGTAAGACCATGCTTAGCTATGGTAACCAATAGAGTCAGCA-AGGATGTTAAACA
13506800 TGG
64 TGG
** * * * * * * *
13506803 GGTTACAAGGTGTAAGACCACAACTCAACTATGGCAACCAATAGAGTCTGCTATGAGGTTAAACA
1 GGTT-CAAGGTGTAAGACCA-TGCTTAGCTATGGTAACCAATAGAGTCAGCAAGGATGTTAAACA
13506868 T-G
64 TGG
*
13506870 GGTTCAGACTGTGTAAGACCATG
1 GGTTCA-A-GGTGTAAGACCATG
13506893 GCTCGGCTAT
Statistics
Matches: 131, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
66 5 0.04
67 67 0.51
68 59 0.45
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (66 bp):
GGTTCAAGGTGTAAGACCATGCTTAGCTATGGTAACCAATAGAGTCAGCAAGGATGTTAAACATG
G
Found at i:13514116 original size:44 final size:44
Alignment explanation
Indices: 13513936--13514132 Score: 161
Period size: 44 Copynumber: 4.5 Consensus size: 44
13513926 TGTTGATCTG
* *
13513936 CTCCACTACTGCTTAGGGGGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAACCTA
* * *
13513980 CTCCACTACTGCTTAGGGTGATAGAA-CTA-ATATCTTAAATCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTACA-ATCTTCAACCTA
* * ** * * * ** * *
13514023 CTTTTCCACTA-T-ATTCGGAAGATAAGATTC-ACCATCTTTGATCTG
1 C---TCCACTACTGCTTAGGGTGA-CAGAATCTACAATCTTCAACCTA
*
13514068 CTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAACCTA
13514112 CTCCACTACTGCTTAGGGTGA
1 CTCCACTACTGCTTAGGGTGA
13514133 TAGGACTAAT
Statistics
Matches: 117, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
42 8 0.07
43 19 0.16
44 67 0.57
45 15 0.13
46 8 0.07
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGTGACAGAATCTACAATCTTCAACCTA
Found at i:13514150 original size:132 final size:132
Alignment explanation
Indices: 13513928--13514228 Score: 512
Period size: 132 Copynumber: 2.3 Consensus size: 132
13513918 TTCGTTATTG
* * *
13513928 TTGATCTGCTCCACTACTGCTTAGGGGGACAGAATCTGCAATCTTCAACCTACTCCACTACTGCT
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCAACCTACTCCACTACTGCT
* *
13513993 TAGGGTGATAGAACTAATATCTTAAATCTACTTTTCCACTATATTCGGAAGATAAGATTCACCAT
66 TAGGGTGATAGAACTAATAGCTTAAATCTACTTCTCCACTATATTCGGAAGATAAGATTCACCAT
13514058 CT
131 CT
13514060 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCAACCTACTCCACTACTGCT
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCAACCTACTCCACTACTGCT
* * * * *
13514125 TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCAT
66 TAGGGTGATAGAACTAATAGCTTAAATCTACTTCTCCACTATATTCGGAAGATAAGATTCACCAT
13514190 CT
131 CT
13514192 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
1 TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCT
13514229 GATTCGTAGC
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 159 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (132 bp):
TTGATCTGCTCCACTACTGATTAGGGTGACAGAATCTACAATCTTCAACCTACTCCACTACTGCT
TAGGGTGATAGAACTAATAGCTTAAATCTACTTCTCCACTATATTCGGAAGATAAGATTCACCAT
CT
Found at i:13514862 original size:100 final size:100
Alignment explanation
Indices: 13514631--13515932 Score: 1025
Period size: 100 Copynumber: 13.2 Consensus size: 100
13514621 GGATTGGCTT
* * ** * *
13514631 CTTCAATATGTTT-AATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCC
1 CTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCC
** * * * * *
13514695 ATTACACCGCCAGGGAAAGTAAGATTCGTCGTTGTGG
65 GCTGCATCGCCTGGG-AAGTAAGATTCGCCGTTGTAG
* * * * **
13514732 CCTCAATCTATTTAACCA-T--AATGTCAGGGAAACAAGATTCGCCGTTTTAGCTTCAATCTGTT
1 CTTCAATCT-TTTAA--ATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTT
* * * * * *
13514794 CCGTTGCACCGCTTGGAAAGTAAGATTCGCCATTGCAG
63 CCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * *
13514832 CTTCAATCTTTTAAATTGCAATG-CTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCT
1 CTTCAATCTTTTAAATTGCAATGTC-GGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCC
* * *
13514896 G-TCGCATCTCCTGGG-AGTAAGATTCGTCGTTGTGG
65 GCT-GCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * *
13514931 CCTCAATCTTTTAAATTGCAATGTTGGGGAAGC-ATGATTCGCCGTTGTAGCTTCAATCTGTTCC
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGA-GATTCGCCGTCGTAGCTTCAATCTGTTCC
* * *
13514995 GCTGCACCGCCT-GAAAGGTAAGATTCGCTGTTGTAG
65 GCTGCATCGCCTGGGAA-GTAAGATTCGCCGTTGTAG
* * * * * * * *
13515031 CTTCAATCTTTGAAACTGCAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTAATCTGTTCTG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * * *
13515096 TTGCATCGTCT-GGAAGTAGGATTCACCGTTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* *
13515130 CTTCAATCTTTT-AATTGCAATGTCGGGGAAGTGAGATTCGCTGTCGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * *
13515194 CTGTATCACCTGGGAAGTAAGATTCACCGTTGTTG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * * * *
13515229 CTTCGATCTTTTGAATTGCAATGTCGAGGAAGGGAGATTCGCTGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * *
13515294 CTGCATCGCCTGGGAAGTAAGATTCACCGTTATGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * ** *
13515329 CTTCGATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGATGTCGTAGCTTTAATCTGTTCCG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
*
13515394 CTGCATCTCCTGGGAAGTAAGATTCGCCGTTGTAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * *
13515429 CCTCAATCTTTTAAATTGCAATGTTGGGGAAGC-AGGATTCGTCGTTGTAGCTTCAATCTATTCC
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGA-GATTCGCCGTCGTAGCTTCAATCTGTTCC
* * * * **
13515493 GTTACACCGCCT-GAAAGGTAAGATTCGCTATTGTAG
65 GCTGCATCGCCTGGGAA-GTAAGATTCGCCGTTGTAG
* * * * * * * *
13515529 CTTCAATCTTTGAAACTACAATGTCGAGGAAGTGAGATTCGCCGTCGTAGCTTTAATCTATTTCG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
*
13515594 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
** * * * * * * *
13515629 CTTTGATCTTTTGAATTGC-----CAGAGAAGCAAGA-TCTGCTG-CTGTAGCTTCAATCCGTTT
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTC-GCCGTC-GTAGCTTCAATCTGTTC
* * * * * *
13515687 CACTGCAAC-ACTAGGAAAATAAGA-TCTGCTGTTGTAG
64 CGCTGCATCGCCT-GGGAAGTAAGATTC-GCCGTTGTAG
* * * * * *
13515724 CTTCAATCTTTTTAA---C--TGTCGGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * * *
13515784 CTGCAAC-ACTAGGAAAGTAAGATCCGCTGTTGTAG
66 CTGCATCGCCT-GGGAAGTAAGATTCGCCGTTGTAG
* * * * * * *
13515819 CTTCAATCTTTTTAA---C--TGTCGGGGAAGCAAGATCCGCTGTTGTAGCCTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * * *
13515879 CTGCAACG-ATAGGAAAGTAAGATCCGCTGTTGTAG
66 CTGCATCGCCT-GGGAAGTAAGATTCGCCGTTGTAG
*
13515914 CTTCAATCTTTTTAATTGC
1 CTTCAATCTTTTAAATTGC
13515933 CATCTATGGT
Statistics
Matches: 997, Mismatches: 170, Indels: 71
0.81 0.14 0.06
Matches are distributed among these distances:
92 1 0.00
94 7 0.01
95 231 0.23
96 2 0.00
97 1 0.00
98 54 0.05
99 149 0.15
100 487 0.49
101 62 0.06
102 1 0.00
103 1 0.00
104 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
Found at i:13515578 original size:498 final size:499
Alignment explanation
Indices: 13514631--13515647 Score: 1321
Period size: 498 Copynumber: 2.0 Consensus size: 499
13514621 GGATTGGCTT
*
13514631 CTTCAATATGTTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCT-TTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCA
* * ** *
13514696 TTACACCGCCAGGGAAAGTAAGATTCGTCGTTGTGGCCTCAATCTATTTAACCATAATGTCAGGG
65 CTACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTATTTAACCACAATGTCAGGG
** * ** * *
13514761 AAACAAGATTCGCCGTTTTAGCTTCAATCTGTTCCGTTGCACCGCTTGGAAAGTAAGATTCGCCA
130 AAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCTGGAAAGTAAGATTCACCA
*
13514826 TTGCAGCTTCAATCTTTTAAATTGCAATGCTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCT
195 TTACAGCTTCAATCTTTTAAATTGCAATGCTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCT
* * *
13514891 GTTCTGTCGCATCTCCTGGGAGTAAGATTCGTCGTTGTGGCCTCAATCTTTTAAATTGCAATGTT
260 GTTCCGTCGCATCTCCTGGGAGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCAATGTT
* * *
13514956 GGGGAAGCATGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCTGAAAGGTAAGATTC
325 GGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTATTCCGCTACACCGCCTGAAAGGTAAGATTC
* *
13515021 GCTGTTGTAGCTTCAATCTTTGAAACTGCAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTA
390 GCTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTA
* * * *
13515086 ATCT-GTTCTGTTGCATCGTCT-GGAAGTAGGATTCACCGTTGTGG
455 ATCTATTTC-GCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGG
* * * *
13515130 CTTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGATTCGCTGTCGTAGCTTCAATCTGTTCCGC
1 CTTCAATCTTTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCAC
** * * * * * ***
13515195 TGTATCACCTGGG-AAGTAAGATTCACCGTTGTTGCTTCGATCT-TTTGAATTGCAATGTC-GAG
66 TACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTATTT-AACCACAATGTCAG-G
*** * * *
13515257 GAAGGGAGATTCGCTGTCGTAGCTTCAATCTATTCCACTGCATCGCCTGGGAAGTAAGATTCACC
129 GAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCTGGAAAGTAAGATTCACC
* ** * * ** * *
13515322 GTTATGGCTTCGATCTTTTGAATTGCAATG-TCGGGGAAGTGAGATTCGA-TGTCGTAGCTTTAA
194 ATTACAGCTTCAATCTTTTAAATTGCAATGCT-GGGGAAACGAGATTC-ACCGTCGTAGCTTCAA
13515385 TCTGTTCCG-CTGCATCTCCTGGGAAGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCA
257 TCTGTTCCGTC-GCATCTCCTGGG-AGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCA
* *
13515449 ATGTTGGGGAAGCAGGATTCGTCGTTGTAGCTTCAATCTATTCCGTTACACCGCCTGAAAGGTAA
320 ATGTTGGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTATTCCGCTACACCGCCTGAAAGGTAA
** * *
13515514 GATTCGCTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGTGAGATTCGCCGTCGTAG
385 GATTCGCTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGCAAGATACACCGTCGTAG
*
13515579 CTTTAATCTATTTCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
450 CTTTAATCTATTTCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGG
**
13515629 CTTTGATCTTTTGAATTGC
1 CTTCAATCTTTT-AATTGC
13515648 CAGAGAAGCA
Statistics
Matches: 445, Mismatches: 64, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
496 6 0.01
497 155 0.35
498 236 0.53
499 42 0.09
500 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (499 bp):
CTTCAATCTTTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCAC
TACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTATTTAACCACAATGTCAGGGA
AACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCTGGAAAGTAAGATTCACCAT
TACAGCTTCAATCTTTTAAATTGCAATGCTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCTG
TTCCGTCGCATCTCCTGGGAGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCAATGTTG
GGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTATTCCGCTACACCGCCTGAAAGGTAAGATTCG
CTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTAA
TCTATTTCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGG
Found at i:13515632 original size:50 final size:49
Alignment explanation
Indices: 13514765--13515640 Score: 318
Period size: 50 Copynumber: 17.6 Consensus size: 49
13514755 TCAGGGAAAC
* * * * * *
13514765 AAGATTCGCCGTTTTAGCTTCAATCTGTTCCGTTGCACCGCTTGGAAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* * *** **
13514815 AAGATTCGCCATTGCAGCTTCAATCTTTTAAATTGCAAT-G-CTGGGGAAAC
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT-CGCTGC-ATCGCCT-GGGAAGT
* * * * *
13514865 GAGATTCACCGTCGTAGCTTCAATCTGTTCTG-TCGCATCTCCTGGG-AGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTC-GCT-GCATCGCCTGGGAAGT
* * * *** * *
13514914 AAGATTCGTCGTTGTGGCCTCAATCTTTTAAATTGCAAT-G-TTGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT-CGCTGC-ATCGCCT-GGGAAGT
* * * *
13514964 ATGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCT-GAAAGGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAA-GT
* *** * *
13515014 AAGATTCGCTGTTGTAGCTTCAATCTTTGAAACTGCAAT-GTC-GAGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTTT-TCGCTGC-ATCGCCTG-GGAAGT
* * * * * * *
13515064 AAGATACACCGTCGTAGCTTTAATCTGTTCTGTTGCATCGTCT-GGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTC-GCTGCATCGCCTGGGAAGT
* * * *** * *
13515113 AGGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAAT-GTCGGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTCGCTGC-ATCGCCTGGGAAGT
* * * * * *
13515162 GAGATTCGCTGTCGTAGCTTCAATCTGTTCCGCTGTATCACCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* * * * * *
13515212 AAGATTCACCGTTGTTGCTTCGATCTTTT-GAATTGCAAT-GTC-GAGGAAGG
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTCG--CTGC-ATCGCCTG-GGAAGT
* * * * *
13515262 GAGATTCGCTGTCGTAGCTTCAATCTATTCCACTGCATCGCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* * * * * * *
13515312 AAGATTCACCGTTATGGCTTCGATCTTTT-GAATTGCAAT-GTCGGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTCG--CTGC-ATCGCCTGGGAAGT
* ** * * * *
13515362 GAGATTCGATGTCGTAGCTTTAATCTGTTCCGCTGCATCTCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* *** * *
13515412 AAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCAAT-G-TTGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT-CGCTGC-ATCGCCT-GGGAAGT
* * * * * * *
13515462 AGGATTCGTCGTTGTAGCTTCAATCTATTCCGTTACACCGCCT-GAAAGGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAA-GT
** *** * *
13515512 AAGATTCGCTATTGTAGCTTCAATCTTTGAAACTACAAT-GTC-GAGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTT-TCGCTGC-ATCGCCTG-GGAAGT
* * *
13515562 GAGATTCGCCGTCGTAGCTTTAATCTATTTCGCTGCATCGCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* **
13515612 AAGATTCGCCGTTGTGGCTTTGATCTTTT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT
13515641 GAATTGCCAG
Statistics
Matches: 584, Mismatches: 187, Indels: 111
0.66 0.21 0.13
Matches are distributed among these distances:
48 9 0.02
49 123 0.21
50 420 0.72
51 31 0.05
52 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (49 bp):
AAGATTCGCCGTTGTAGCTTCAATCTTTTCGCTGCATCGCCTGGGAAGT
Found at i:13515710 original size:95 final size:95
Alignment explanation
Indices: 13515608--13515934 Score: 458
Period size: 95 Copynumber: 3.4 Consensus size: 95
13515598 ATCGCCTGGG
* * * ** * * * * *
13515608 AAGTAAGATTCGCCGTTGTGGCTTTGATCTTTTGAATTGCCAGAGAAGCAAGATCTGCTGCTGTA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
* *
13515673 GCTTCAATCCGTTTCACTGCAACACTAGGA
66 GCTTCAATCTGTTCCACTGCAACACTAGGA
* * * *
13515703 AAATAAGATCTGCTGTTGTAGCTTCAATCTTTTTAACTGTCGGGGAAGCAAGATCCGCTGTTGTA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
13515768 GCTTCAATCTGTTCCACTGCAACACTAGGA
66 GCTTCAATCTGTTCCACTGCAACACTAGGA
* *
13515798 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGTCGGGGAAGCAAGATCCGCTGTTGTA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
*
13515863 GCCTCAATCTGTTCCACTGCAACGA-TAGGA
66 GCTTCAATCTGTTCCACTGCAAC-ACTAGGA
*
13515893 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCCA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCA
13515935 TCTATGGTTT
Statistics
Matches: 209, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
95 208 1.00
96 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (95 bp):
AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
GCTTCAATCTGTTCCACTGCAACACTAGGA
Found at i:13515820 original size:50 final size:50
Alignment explanation
Indices: 13515657--13515922 Score: 266
Period size: 50 Copynumber: 5.5 Consensus size: 50
13515647 CCAGAGAAGC
* * * *
13515657 AAGATCTGCTGCTGTAGCTTCAATCCGTTTCACTGCAACACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
* * * * * * *
13515707 AAGATCTGCTGTTGTAGCTTCAATCTTTTTAACTG----TC-GGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
*
13515752 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
* * * * * *
13515802 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG----TC-GGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
* *
13515847 AAGATCCGCTGTTGTAGCCTCAATCTGTTCCACTGCAACGA-TAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAAC-ACTAGGAAAGT
13515897 AAGATCCGCTGTTGTAGCTTCAATCT
1 AAGATCCGCTGTTGTAGCTTCAATCT
13515923 TTTTAATTGC
Statistics
Matches: 172, Mismatches: 33, Indels: 22
0.76 0.15 0.10
Matches are distributed among these distances:
45 71 0.41
46 2 0.01
49 1 0.01
50 98 0.57
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (50 bp):
AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
Found at i:13517050 original size:8 final size:8
Alignment explanation
Indices: 13517039--13517081 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
13517029 CCATTTTTAC
*
13517039 TTTTTCTT
1 TTTTTCAT
13517047 TTTTTCAT
1 TTTTTCAT
13517055 TTTTTCA-
1 TTTTTCAT
*
13517062 TTATTCATT
1 TTTTTCA-T
13517071 TTTTTCAT
1 TTTTTCAT
13517079 TTT
1 TTT
13517082 CATCATCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 6 0.20
8 18 0.60
9 6 0.20
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:13517082 original size:22 final size:22
Alignment explanation
Indices: 13517045--13517095 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
13517035 TTACTTTTTC
*
13517045 TTTTTTTCATTTTTTCATTATTCA
1 TTTTTTTCA-TTTTTCATCA-TCA
13517069 TTTTTTTCA-TTTTCATCATCA
1 TTTTTTTCATTTTTCATCATCA
13517090 TTTTTT
1 TTTTTT
13517096 GACCCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
24 9 0.35
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTCATTTTTCATCATCA
Found at i:13517083 original size:15 final size:15
Alignment explanation
Indices: 13517048--13517084 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
13517038 CTTTTTCTTT
13517048 TTTTCA-TTTTTTCA
1 TTTTCATTTTTTTCA
13517062 TTATTCATTTTTTTCA
1 TT-TTCATTTTTTTCA
13517078 TTTTCAT
1 TTTTCAT
13517085 CATCATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 9 0.43
16 10 0.48
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTTTTTCA
Found at i:13517910 original size:5 final size:6
Alignment explanation
Indices: 13517894--13517922 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
13517884 TTGACCTCTC
13517894 CTTTTT CTTTTT CTTTTT C-TTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
13517923 TTGACTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Done.