Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 9 of 335
Found at i:3052718 original size:16 final size:16
Alignment explanation
Indices: 3052684--3052721 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3052674 AAAAGTTAAC
**
3052684 AAAATATATGATAGTA
1 AAAATATATGATACAA
3052700 AAAATATATGATACAA
1 AAAATATATGATACAA
3052716 AAAATA
1 AAAATA
3052722 CCTGACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (16 bp):
AAAATATATGATACAA
Found at i:3055624 original size:46 final size:45
Alignment explanation
Indices: 3055557--3055731 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
3055547 TGTAACCCGC
3055557 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
*
3055603 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* * * * *
3055649 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGCTCG-GCATTCGCAT
* *
3055696 CCATAAGTGAACTCGGACTCAACTTAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
3055732 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 4 0.04
46 63 0.58
47 29 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:3055677 original size:93 final size:93
Alignment explanation
Indices: 3055565--3055735 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
3055555 GCCCATAAGT
*
3055565 GAACTCGGACTCAACTCAACGAGCTC-AGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGA-ACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3055629 ACGAGCTCGGATGCCTAGTTACATCTCAC
65 ACGAGCTCGGATGCCTAGTTACATCTCAC
* *
3055658 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTTAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3055723 CGAGTTCGGATGC
66 CGAGCTCGGATGC
3055736 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:3057878 original size:15 final size:15
Alignment explanation
Indices: 3057855--3057889 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
3057845 TTTATATATT
3057855 TTTTGTTTTT-TTTG
1 TTTTGTTTTTGTTTG
3057869 TTTTGTTTTTGTTTG
1 TTTTGTTTTTGTTTG
3057884 TTTTGT
1 TTTTGT
3057890 GTTTACACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (15 bp):
TTTTGTTTTTGTTTG
Found at i:3061820 original size:21 final size:20
Alignment explanation
Indices: 3061796--3061834 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3061786 CTTCCTATTT
3061796 TTTTATTTATTCTTATTTTTA
1 TTTTATTTATT-TTATTTTTA
3061817 TTTTATTTATTTTATTTT
1 TTTTATTTATTTTATTTT
3061835 CTTTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTATTTATTTTATTTTTA
Found at i:3061822 original size:5 final size:5
Alignment explanation
Indices: 3061796--3061882 Score: 65
Period size: 5 Copynumber: 16.8 Consensus size: 5
3061786 CTTCCTATTT
*
3061796 TTTTA -TTTA TTCTTA TTTTTA TTTTA -TTTA TTTTA TTTTC TTTTGA
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A
*
3061842 TTTTGA TTTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 TTTT-A -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
3061883 GAAAGACATA
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
3 3 0.04
4 8 0.12
5 30 0.44
6 21 0.31
7 6 0.09
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:3061827 original size:25 final size:25
Alignment explanation
Indices: 3061791--3061882 Score: 79
Period size: 25 Copynumber: 3.8 Consensus size: 25
3061781 TGAATCTTCC
3061791 TATTTT-TTTA-TTTATTCTTATTTT
1 TATTTTATTTATTTTATT-TTATTTT
*
3061815 TATTTTATTTATTTTATTTTCTTTT
1 TATTTTATTTATTTTATTTTATTTT
* *
3061840 GATTTTGA--T-TTTTATTTTCATTTC
1 TATTTT-ATTTATTTTATTTT-ATTTT
*
3061864 AATTTTA-TTATTTTATTTT
1 TATTTTATTTATTTTATTTT
3061883 GAAAGACATA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
23 10 0.18
24 16 0.28
25 24 0.42
26 7 0.12
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.75
Consensus pattern (25 bp):
TATTTTATTTATTTTATTTTATTTT
Found at i:3068862 original size:35 final size:35
Alignment explanation
Indices: 3068816--3068886 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3068806 AATAACAAGA
3068816 AGAATATAAAATGAATACCAGAACATCTGGTACAT
1 AGAATATAAAATGAATACCAGAACATCTGGTACAT
3068851 AGAATATAAAATGAATACCAGAACATCTGGTACAT
1 AGAATATAAAATGAATACCAGAACATCTGGTACAT
3068886 A
1 A
3068887 CTCTTGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (35 bp):
AGAATATAAAATGAATACCAGAACATCTGGTACAT
Found at i:3075249 original size:24 final size:22
Alignment explanation
Indices: 3075213--3075271 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
3075203 GTATTTTATT
3075213 TTTTAATAAAATAAGAA-ATAATATA
1 TTTTAA-AAAATAA-AATATAA-A-A
*
3075238 TTTTAAAAAATAAAATCTAAAA
1 TTTTAAAAAATAAAATATAAAA
3075260 TTTTAAAAAATA
1 TTTTAAAAAATA
3075272 CAAACAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 13 0.41
23 3 0.09
24 10 0.31
25 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTTAAAAAATAAAATATAAAA
Found at i:3075391 original size:151 final size:149
Alignment explanation
Indices: 3075217--3075656 Score: 656
Period size: 149 Copynumber: 2.9 Consensus size: 149
3075207 TTTATTTTTT
* * * *
3075217 AATAAAATAAG-AAATAATATATTTTAAAAAATAAAATCTAAAATTTTAAAAAATACAAACAAAA
1 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCAAAA--TAAAAAAATACAAACAAAA
*
3075281 GGGCCAAAATCAGGGTTATTTACTAAATTAATAAAAAAAATACTTAAATAATACATTTGAAACAT
64 GGGCCAAAATCAAGGTTATTTACTAAATTAAT-AAAAAAATACTTAAATAATACATTTGAAACAT
3075346 TATGTACTAAAATAATAT-AAA
128 TATGTACTAAAATAATATAAAA
* **
3075367 AATAAAATACGAAAATAGTATATTTTAAAAATTAAAATCCAAAAATAAAAAAATAGGAAC-AAAG
1 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCC-AAAATAAAAAAATACAAACAAAAG
* * * *
3075431 TGCCAAAATCAAGGTTATTTATTAAATTAGTATTAAAAATACTTAAATAATACATTTGAAACATT
65 GGCCAAAATCAAGGTTATTTACTAAATTAATA-AAAAAATACTTAAATAATACATTTGAAACATT
3075496 ATGTACTAAAATAATATAAAAA
129 ATGTACTAAAATAATAT-AAAA
*
3075518 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAAAATAAAAAAATATAAACAAAAG
1 AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCC-AAAATAAAAAAATACAAACAAAAG
*
3075583 GGCCAAAATCAAGGTTATTTACTAAATTAAT-AAAAAA-ACTTAAATAATACACTTGAAACATTA
65 GGCCAAAATCAAGGTTATTTACTAAATTAATAAAAAAATACTTAAATAATACATTTGAAACATTA
3075646 TGTACTAAAAT
130 TGTACTAAAAT
3075657 TGTAACATCC
Statistics
Matches: 263, Mismatches: 21, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
148 1 0.00
149 115 0.44
150 27 0.10
151 84 0.32
152 36 0.14
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (149 bp):
AATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCAAAATAAAAAAATACAAACAAAAGG
GCCAAAATCAAGGTTATTTACTAAATTAATAAAAAAATACTTAAATAATACATTTGAAACATTAT
GTACTAAAATAATATAAAA
Found at i:3077154 original size:44 final size:45
Alignment explanation
Indices: 3077059--3077173 Score: 133
Period size: 44 Copynumber: 2.6 Consensus size: 45
3077049 ACAGGACAGA
* ***
3077059 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGTTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGACATTGGAG
* *
3077105 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGACATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGACATTGGAG
* **
3077149 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
3077174 GTCAAAGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 33 0.56
46 26 0.44
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGACATTGGAG
Found at i:3078464 original size:13 final size:13
Alignment explanation
Indices: 3078427--3078464 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3078417 GGGGCGTTAC
3078427 AAAAATAATATA-
1 AAAAATAATATAT
*
3078439 AAAAATAAAATAT
1 AAAAATAATATAT
*
3078452 AAAAATAGTATAT
1 AAAAATAATATAT
3078465 TTTAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAAATAATATAT
Found at i:3078611 original size:2 final size:2
Alignment explanation
Indices: 3078604--3078659 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
3078594 TCAGATGTTG
3078604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3078646 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3078660 TTGAGGGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3083032 original size:93 final size:93
Alignment explanation
Indices: 3082918--3083089 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
3082908 CGCCCATAAG
* *
3082918 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3082983 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
3083011 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3083076 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
3083090 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:3083086 original size:46 final size:46
Alignment explanation
Indices: 3082911--3083086 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
3082901 TGTAACCCGC
* * *
3082911 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
3082957 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3083007 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3083050 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
3083087 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3092329 original size:15 final size:15
Alignment explanation
Indices: 3092309--3092376 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
3092299 AATCATCTTA
3092309 ATATTATTTTAATAT
1 ATATTATTTTAATAT
**
3092324 ATATTATAGTAATAT
1 ATATTATTTTAATAT
*
3092339 -TA-TATATTTAGTAT
1 ATATTAT-TTTAATAT
* *
3092353 AAATTTATTTTTATAAT
1 ATA-TTATTTTAAT-AT
3092370 ATATTAT
1 ATATTAT
3092377 AAATTACATA
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
13 3 0.08
14 7 0.18
15 14 0.36
16 8 0.21
17 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
ATATTATTTTAATAT
Found at i:3092403 original size:18 final size:19
Alignment explanation
Indices: 3092365--3092409 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3092355 ATTTATTTTT
* *
3092365 ATAATATATTATAAATTAC
1 ATAATATATTAAAAATAAC
3092384 ATAATATA-TAAAAATAAC
1 ATAATATATTAAAAATAAC
3092402 ATAATATA
1 ATAATATA
3092410 ATATTAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAATATATTAAAAATAAC
Found at i:3098230 original size:19 final size:18
Alignment explanation
Indices: 3098208--3098250 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3098198 AATTACAAAA
*
3098208 AAAAATCAAAATAATTTTT
1 AAAAATCAAAAT-ATTTAT
* *
3098227 AAAATTCAACATATTTAT
1 AAAAATCAAAATATTTAT
3098245 AAAAAT
1 AAAAAT
3098251 TTTAAACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATCAAAATATTTAT
Found at i:3099801 original size:2 final size:2
Alignment explanation
Indices: 3099796--3099832 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3099786 TTTTTTTCAG
3099796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3099833 AATTGCTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3102438 original size:3 final size:3
Alignment explanation
Indices: 3102430--3102482 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
3102420 ATTCAGATTA
*
3102430 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CGC C-C GCAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC -CAC CAC CAC
3102475 CAC CAC CA
1 CAC CAC CA
3102483 GCAGTCACTT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
2 1 0.02
3 45 0.96
4 1 0.02
ACGTcount: A:0.30, C:0.66, G:0.04, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:3104636 original size:8 final size:9
Alignment explanation
Indices: 3104619--3104643 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3104609 AGTAATTTAA
3104619 TTCTTTTTT
1 TTCTTTTTT
3104628 TTCTTTTTT
1 TTCTTTTTT
3104637 TTCTTTT
1 TTCTTTT
3104644 AAGTCCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:3104699 original size:17 final size:17
Alignment explanation
Indices: 3104667--3104700 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3104657 TCTTCTTCTC
* *
3104667 CCTTTAATTTTGGGATT
1 CCTTTAATTATAGGATT
3104684 CCTTTAATTATAGGATT
1 CCTTTAATTATAGGATT
3104701 TTATGCAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (17 bp):
CCTTTAATTATAGGATT
Found at i:3107003 original size:18 final size:19
Alignment explanation
Indices: 3106980--3107018 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3106970 TACAAATACA
*
3106980 AACATT-ACATAATTATTT
1 AACATTCACATAATGATTT
*
3106998 AACATTCACATCATGATTT
1 AACATTCACATAATGATTT
3107017 AA
1 AA
3107019 TCATATCGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (19 bp):
AACATTCACATAATGATTT
Found at i:3108661 original size:15 final size:16
Alignment explanation
Indices: 3108633--3108663 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3108623 TTCTGTTTCT
3108633 TTTGTTTCGTTTTATA
1 TTTGTTTCGTTTTATA
3108649 TTTGTTT-GTTTTATA
1 TTTGTTTCGTTTTATA
3108664 ATATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.71
Consensus pattern (16 bp):
TTTGTTTCGTTTTATA
Found at i:3108670 original size:5 final size:5
Alignment explanation
Indices: 3108660--3108692 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3108650 TTGTTTGTTT
*
3108660 TATAA TATAA TATAA TATAA AATAA TAT-A TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATA
3108693 CACTTAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:3109403 original size:46 final size:46
Alignment explanation
Indices: 3109343--3109654 Score: 444
Period size: 46 Copynumber: 7.0 Consensus size: 46
3109333 TTTGACATGA
* * * * * *
3109343 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** **
3109389 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
3109435 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
3109481 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
3109527 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
3109573 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C---TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
3109611 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
3109655 AGAGCACACT
Statistics
Matches: 242, Mismatches: 15, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
38 34 0.14
40 3 0.01
43 1 0.00
44 3 0.01
45 4 0.02
46 197 0.81
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:3109618 original size:38 final size:38
Alignment explanation
Indices: 3109567--3109642 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3109557 ACATTTTATA
3109567 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
3109605 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
3109643 ATTTCATATC
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:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:3111803 original size:11 final size:11
Alignment explanation
Indices: 3111787--3111838 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
3111777 TATACTAAAT
3111787 AAATAATAATA
1 AAATAATAATA
*
3111798 AAATAAT-ATT
1 AAATAATAATA
* *
3111808 AAATATCTCATA
1 AAATA-ATAATA
*
3111820 AAATATTAATA
1 AAATAATAATA
3111831 AAATAATA
1 AAATAATA
3111839 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:3117781 original size:48 final size:52
Alignment explanation
Indices: 3117662--3117851 Score: 151
Period size: 48 Copynumber: 3.7 Consensus size: 52
3117652 ATTAGGGTTT
* * * * *
3117662 AAGGATACCATGTAAGACCATG-CAAGGCATGGCAACTGGTAAGGTTTC-TAAGGC
1 AAGGCTACCATGTAAGACCATGTCAAGACATGGC-A-TTGTGA-G-CTCATAAGGC
** *
3117716 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATT-T-A-CT-ATAAGGC
1 AAGGCTACCATGTAAGACCATGTCAAGACATGGCATTGTGAGCTCATAAGGC
* * * *
3117764 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGCTACCATGTAAGACCATGTCAAGACATGGCATT-GTGAGCTCATAAGGC
* *
3117817 AAGGCTACCATGTAAGACAATGTCAAGATATGGCA
1 AAGGCTACCATGTAAGACCATGTCAAGACATGGCA
3117852 ATGGTAAGTT
Statistics
Matches: 111, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
48 34 0.31
49 4 0.04
50 1 0.01
51 2 0.02
52 6 0.05
53 33 0.30
54 21 0.19
55 10 0.09
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (52 bp):
AAGGCTACCATGTAAGACCATGTCAAGACATGGCATTGTGAGCTCATAAGGC
Found at i:3117833 original size:53 final size:53
Alignment explanation
Indices: 3117662--3117908 Score: 196
Period size: 49 Copynumber: 4.8 Consensus size: 53
3117652 ATTAGGGTTT
* *
3117662 AAGGATACCATGTAAGACCATG-CAAGGCATGGCAACTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGC-ATTGGTAA-G-TTCATAAGGC
* * *
3117716 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATT--T-A-CT-ATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * *
3117764 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * *
3117817 AAGGCTACCATGTAAGACAATGTCAAGATATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCAT-AAGGC
** * * *
3117866 AAGGATACCACATAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
3117909 GTACCCGCGT
Statistics
Matches: 158, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
48 34 0.22
49 40 0.25
50 1 0.01
51 3 0.02
52 8 0.05
53 40 0.25
54 22 0.14
55 10 0.06
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:3117850 original size:101 final size:102
Alignment explanation
Indices: 3117669--3117851 Score: 264
Period size: 101 Copynumber: 1.8 Consensus size: 102
3117659 TTTAAGGATA
*
3117669 CCATGTAAGACCATGCAAGGCATGGCAACTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGAC
1 CCATGTAAGACCATGCAAGGCATGGCAACTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
*
3117734 CATGTCAAGACATGGCATTTACTATAAGGCAAAGGTC
66 AATGTCAAGACATGGCATTTACTATAAGGCAAAGGTC
* * **
3117771 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGCTACCATGTAAG
1 CCATGTAAGACCATG-CAAGGCATGGCAACTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
3117833 ACAATGTCAAGATATGGCA
64 ACAATGTCAAGACATGGCA
3117852 ATGGTAAGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
100 3 0.04
101 37 0.51
102 21 0.29
103 11 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.21
Consensus pattern (102 bp):
CCATGTAAGACCATGCAAGGCATGGCAACTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGAC
AATGTCAAGACATGGCATTTACTATAAGGCAAAGGTC
Found at i:3117869 original size:101 final size:100
Alignment explanation
Indices: 3117662--3117910 Score: 256
Period size: 102 Copynumber: 2.4 Consensus size: 100
3117652 ATTAGGGTTT
*
3117662 AAGGATACCATGTAAGACCATGCAAGGCATGGCAACTGGTAAGGTTTCTAAGGCAAGGAAATCAT
1 AAGGATACCATGTAAGACCATGCAAGGCATGGCAA-TGGTAAGGTTTCTAAGGCAAGGAAACCAT
*
3117727 GTAAGACCATGTCAAGACATGGCATTTACTATAAGGCA
65 GTAAGACAATGTCAAGACATGGCA--TACTATAAGGCA
* * * **
3117765 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGA-G-TTCATAAGGCAAGGCTACCA
1 AAGGATACCATGTAAGACCATG-CAAGGCATGGCAATGGTAAGGTTTC-TAAGGCAAGGAAACCA
* * *
3117827 TGTAAGACAATGTCAAGATATGGCA-A-TGGTAAGTTTCAA
64 TGTAAGACAATGTCAAGACATGGCATACT-ATAAG--GC-A
** *
3117866 AAGGATACCACATAAGACCATGACAAGTCATGGCAATGGTAAGGT
1 AAGGATACCATGTAAGACCATG-CAAGGCATGGCAATGGTAAGGT
3117911 ACCCGCGTAT
Statistics
Matches: 120, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
97 1 0.01
98 5 0.04
100 4 0.03
101 42 0.35
102 51 0.43
103 17 0.14
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (100 bp):
AAGGATACCATGTAAGACCATGCAAGGCATGGCAATGGTAAGGTTTCTAAGGCAAGGAAACCATG
TAAGACAATGTCAAGACATGGCATACTATAAGGCA
Found at i:3118121 original size:16 final size:16
Alignment explanation
Indices: 3118100--3118130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3118090 ATAAATTTGA
3118100 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
3118116 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
3118131 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:3122287 original size:21 final size:21
Alignment explanation
Indices: 3122261--3122301 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3122251 TTTCTCTTTC
3122261 AAATTTTATTTTTTTAATTAT
1 AAATTTTATTTTTTTAATTAT
3122282 AAATTTTATTTTTTTAATTA
1 AAATTTTATTTTTTTAATTA
3122302 CAAGAGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
AAATTTTATTTTTTTAATTAT
Found at i:3124266 original size:20 final size:20
Alignment explanation
Indices: 3124243--3124287 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3124233 ATATTATATT
3124243 AAATTAT-TAAAATTTGGTA
1 AAATTATGTAAAATTTGGTA
* *
3124262 CAAATTTTGTAAAATTTTGTA
1 -AAATTATGTAAAATTTGGTA
3124283 AAATT
1 AAATT
3124288 TTATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (20 bp):
AAATTATGTAAAATTTGGTA
Found at i:3124278 original size:10 final size:10
Alignment explanation
Indices: 3124250--3124294 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
3124240 ATTAAATTAT
*
3124250 TAAAATTTGG
1 TAAAATTTTG
3124260 TACAAATTTTG
1 TA-AAATTTTG
3124271 TAAAATTTTG
1 TAAAATTTTG
*
3124281 TAAAATTTTA
1 TAAAATTTTG
3124291 TAAA
1 TAAA
3124295 TAATATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (10 bp):
TAAAATTTTG
Found at i:3125157 original size:8 final size:8
Alignment explanation
Indices: 3125144--3125172 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3125134 TTATGTTTAG
3125144 TATATTAT
1 TATATTAT
3125152 TATATTAT
1 TATATTAT
3125160 TATATTAT
1 TATATTAT
3125168 TATAT
1 TATAT
3125173 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:3126489 original size:15 final size:15
Alignment explanation
Indices: 3126469--3126525 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
3126459 CGATGAATTT
3126469 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
3126484 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
3126499 ATTGAATTTATATTG
1 ATTGAATTTATATTG
3126514 ATTGAA-TTATAT
1 ATTGAATTTATAT
3126526 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:3126948 original size:21 final size:21
Alignment explanation
Indices: 3126908--3126981 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
3126898 AGGCACTTTA
3126908 TGTGTCGTATTTCA-GCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
3126930 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* * * **
3126951 TGTGTCGTTTTAGGCACTTTA
1 TGTGTCGTATCAGGCACCTCG
3126972 TGTGTCGTAT
1 TGTGTCGTAT
3126982 ACTGATCAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 3 0.07
21 33 0.73
22 9 0.20
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.39
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:3128262 original size:2 final size:2
Alignment explanation
Indices: 3128255--3128296 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3128245 TTTAAATTGC
3128255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3128297 AAGGTTGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3129556 original size:6 final size:6
Alignment explanation
Indices: 3129517--3129544 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3129507 TTTATTTTAT
3129517 TTAATA TTAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAA
3129545 ATTTATTATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:3130314 original size:16 final size:17
Alignment explanation
Indices: 3130285--3130318 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3130275 ACATGTGGTA
*
3130285 AAAAAATTATAAAAAAT
1 AAAAAATTAGAAAAAAT
3130302 AAAAAA-TAGAAAAAAT
1 AAAAAATTAGAAAAAAT
3130318 A
1 A
3130319 TTTAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAAAATTAGAAAAAAT
Found at i:3130355 original size:9 final size:10
Alignment explanation
Indices: 3130332--3130388 Score: 60
Period size: 11 Copynumber: 5.4 Consensus size: 10
3130322 AAATTTTACT
*
3130332 AAAAATTAGGA
1 AAAAATTA-TA
3130343 AAAAATTATA
1 AAAAATTATA
*
3130353 AAAGAAATATA
1 AAA-AATTATA
*
3130364 AAAAATTGTA
1 AAAAATTATA
3130374 AAAAATATATA
1 AAAAAT-TATA
3130385 AAAA
1 AAAA
3130389 GGCATCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 15 0.38
11 24 0.62
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (10 bp):
AAAAATTATA
Found at i:3130368 original size:21 final size:21
Alignment explanation
Indices: 3130342--3130388 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3130332 AAAAATTAGG
3130342 AAAAAATTATAAAAGAA-ATAT
1 AAAAAATTATAAAA-AATATAT
*
3130363 AAAAAATTGTAAAAAATATAT
1 AAAAAATTATAAAAAATATAT
3130384 AAAAA
1 AAAAA
3130389 GGCATCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAAAATTATAAAAAATATAT
Found at i:3131793 original size:16 final size:17
Alignment explanation
Indices: 3131770--3131805 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3131760 GGAAATGAGA
*
3131770 ATTTTTAAATATTTAAT
1 ATTTTAAAATATTTAAT
3131787 ATTTTAAAAATATTTAAT
1 ATTTT-AAAATATTTAAT
3131805 A
1 A
3131806 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAAATATTTAAT
Found at i:3132054 original size:14 final size:13
Alignment explanation
Indices: 3132009--3132052 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
3131999 TTATATTAAT
3132009 AATATTAAAAATA
1 AATATTAAAAATA
3132022 AA-A-TAAAAATA
1 AATATTAAAAATA
*
3132033 ATATTTTAAAAATA
1 A-ATATTAAAAATA
3132047 AATATT
1 AATATT
3132053 TATTTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 9 0.35
12 2 0.08
13 6 0.23
14 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATTAAAAATA
Found at i:3141349 original size:15 final size:15
Alignment explanation
Indices: 3141317--3141358 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3141307 TTTTCCATAT
* *
3141317 TTAATTTCTCAACAC
1 TTAATTTTTCAGCAC
*
3141332 TTATTTTTTCAGCAC
1 TTAATTTTTCAGCAC
3141347 TTAATTTTTCAG
1 TTAATTTTTCAG
3141359 TTTATCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.50
Consensus pattern (15 bp):
TTAATTTTTCAGCAC
Found at i:3143720 original size:18 final size:18
Alignment explanation
Indices: 3143697--3143734 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3143687 TATCTGAAAC
3143697 TTAATTTTGAATATGATA
1 TTAATTTTGAATATGATA
3143715 TTAATTTTGAATATGATA
1 TTAATTTTGAATATGATA
3143733 TT
1 TT
3143735 CCTATTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
TTAATTTTGAATATGATA
Found at i:3170337 original size:19 final size:19
Alignment explanation
Indices: 3170314--3170369 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
3170304 TTTAATTAAT
3170314 TTTTTAAAATTTTAAAAACA
1 TTTTTAAAATTTTAAAAA-A
3170334 TTTTTTAAAA--TTAAAAAA
1 -TTTTTAAAATTTTAAAAAA
*
3170352 -ATTTAAAATTATTAAAAA
1 TTTTTAAAATT-TTAAAAA
3170370 GGTATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 7 0.23
18 1 0.03
19 14 0.45
21 9 0.29
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTTAAAATTTTAAAAAA
Found at i:3170351 original size:21 final size:21
Alignment explanation
Indices: 3170312--3170352 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3170302 CATTTAATTA
**
3170312 ATTTTTTAAAATTTTAAAAAC
1 ATTTTTTAAAATTAAAAAAAC
3170333 ATTTTTTAAAATTAAAAAAA
1 ATTTTTTAAAATTAAAAAAA
3170353 TTTAAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTTTTAAAATTAAAAAAAC
Found at i:3170724 original size:26 final size:26
Alignment explanation
Indices: 3170688--3170739 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3170678 CTACGCTATG
3170688 GAGATAGTTTGCAATTAGACAAAGCA
1 GAGATAGTTTGCAATTAGACAAAGCA
3170714 GAGATAGTTTGCAATTAGACAAAGCA
1 GAGATAGTTTGCAATTAGACAAAGCA
3170740 TTAGTTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (26 bp):
GAGATAGTTTGCAATTAGACAAAGCA
Found at i:3179276 original size:17 final size:16
Alignment explanation
Indices: 3179244--3179274 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3179234 TACTTAAAGT
*
3179244 TTTAGTTGTATTTTTG
1 TTTAGTTATATTTTTG
3179260 TTTAGTTATATTTTT
1 TTTAGTTATATTTTT
3179275 TGGTGCCCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (16 bp):
TTTAGTTATATTTTTG
Found at i:3183727 original size:21 final size:22
Alignment explanation
Indices: 3183688--3183734 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3183678 TAGTAAGAAT
*
3183688 AAAAATGTTTTCTAAAATT-TA
1 AAAAATGTTTGCTAAAATTGTA
* *
3183709 AAAAATGTTTGGTATAATTGTA
1 AAAAATGTTTGCTAAAATTGTA
3183731 AAAA
1 AAAA
3183735 TAATAATGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAAATGTTTGCTAAAATTGTA
Found at i:3186928 original size:21 final size:23
Alignment explanation
Indices: 3186877--3186928 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
3186867 GGGGGCCAAA
3186877 ATTAAATTATAACTTTTATAATAG
1 ATTAAA-TATAACTTTTATAATAG
*
3186901 -TAAAAATATAA-TTTT-TAATAG
1 AT-TAAATATAACTTTTATAATAG
3186922 ATTAAAT
1 ATTAAAT
3186929 CAAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 6 0.25
24 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTAAATATAACTTTTATAATAG
Found at i:3197091 original size:30 final size:31
Alignment explanation
Indices: 3197035--3197101 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
3197025 ACGAAGAGTA
3197035 AGTTTGGATCGGGATTTTCTTTTTTATTTTT
1 AGTTTGGATCGGGATTTTCTTTTTTATTTTT
3197066 AGTTTGGATCGGGATTTTC-TTTTTATTTTT
1 AGTTTGGATCGGGATTTTCTTTTTTATTTTT
*
3197096 ACTTTG
1 AGTTTG
3197102 TGTGTGGGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.13, C:0.07, G:0.19, T:0.60
Consensus pattern (31 bp):
AGTTTGGATCGGGATTTTCTTTTTTATTTTT
Found at i:3209800 original size:18 final size:18
Alignment explanation
Indices: 3209758--3209800 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3209748 TAATTGTTAA
*
3209758 ATTATAAAAATAAATTTC
1 ATTATTAAAATAAATTTC
*
3209776 ATAATTAAAATAAATTAT-
1 ATTATTAAAATAAATT-TC
3209794 ATTATTA
1 ATTATTA
3209801 GATGATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATTAAAATAAATTTC
Found at i:3210050 original size:14 final size:15
Alignment explanation
Indices: 3210025--3210062 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
3210015 TTTTTTAATA
3210025 TTATATTAATTTTGT
1 TTATATTAATTTTGT
*
3210040 TTATA-TAATTTTTT
1 TTATATTAATTTTGT
3210054 TTAATATTA
1 TT-ATATTA
3210063 GCAAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 8 0.40
16 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TTATATTAATTTTGT
Found at i:3211174 original size:20 final size:20
Alignment explanation
Indices: 3211151--3211188 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3211141 TAAATTTTCA
3211151 ATTTAATTATT-AAATTTAGT
1 ATTT-ATTATTAAAATTTAGT
*
3211171 ATTTTTTATTAAAATTTA
1 ATTTATTATTAAAATTTA
3211189 TCAACTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTATTATTAAAATTTAGT
Found at i:3216607 original size:42 final size:42
Alignment explanation
Indices: 3216544--3216626 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
3216534 GCCTGAACCG
*
3216544 TGAAGGGTGGGTAAAAGCTAAGAAGCTCCTAAAATGGCCAAA
1 TGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAAA
3216586 TGAAGGGTGGGTAGAAA-CTAAGAAGCTCCCAAAATGGCCAA
1 TGAAGGGTGGGTA-AAAGCTAAGAAGCTCCCAAAATGGCCAA
3216627 GTAAACCAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 36 0.92
43 3 0.08
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.16
Consensus pattern (42 bp):
TGAAGGGTGGGTAAAAGCTAAGAAGCTCCCAAAATGGCCAAA
Found at i:3220580 original size:28 final size:27
Alignment explanation
Indices: 3220520--3220582 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
3220510 TCAAATAACT
* *
3220520 AATTAA-TAAAATATTAATATTTTGAG
1 AATTAATTAAAATATTAATAATTTAAG
3220546 AATTTAATTAAAATATTTTAA-AATTTAAG
1 AA-TTAATTAAAATA--TTAATAATTTAAG
3220575 AATTAATT
1 AATTAATT
3220583 TCAAATTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 4 0.13
28 13 0.42
29 8 0.26
30 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
AATTAATTAAAATATTAATAATTTAAG
Found at i:3222315 original size:53 final size:52
Alignment explanation
Indices: 3222171--3222322 Score: 164
Period size: 52 Copynumber: 2.9 Consensus size: 52
3222161 CAGAAAAGAT
** * *
3222171 GTGATATGTGCACCCGCATAAGACCATATCTGGGCTATGGTATCGGTGCAAC
1 GTGATATGTGTTCCCGTATAAGACCATATCTGGGCTATGGCATCGGTGCAAC
* ** *
3222223 GTGATATGTGTTCCCGTATAAGACCATAAT-TGGGCTATGGCGTCGGTGTGAT
1 GTGATATGTGTTCCCGTATAAGACCAT-ATCTGGGCTATGGCATCGGTGCAAC
* **
3222275 GTGATAATGTGATT-TCGTATAAGACCATATCTGGAATATGGCATCGGT
1 GTGAT-ATGTG-TTCCCGTATAAGACCATATCTGGGCTATGGCATCGGT
3222323 ATTATATGTG
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
52 48 0.57
53 34 0.40
54 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (52 bp):
GTGATATGTGTTCCCGTATAAGACCATATCTGGGCTATGGCATCGGTGCAAC
Found at i:3226238 original size:6 final size:6
Alignment explanation
Indices: 3226227--3226277 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
3226217 GGAATACACT
* * *
3226227 GTAACG GTAACG GTAACA GTAACA GTAACA ATAACA GTAACA GTAACA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA
3226275 GTA
1 GTA
3226278 GTGGTACACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:3226359 original size:45 final size:47
Alignment explanation
Indices: 3226265--3226370 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 47
3226255 CAATAACAGT
* * * *
3226265 AACAGTAACAGTAGTGGTACACAGAGTACCTCGTCGGAAAAAATTCGG
1 AACAGTAACAGTAGAGGTA-ACAGAGTACCTAGTCAGAAAAAATCCGG
* **
3226313 AACAGTAACAGTA-AGGT-ACAGAGTACCTATTCAGAACGAATCCGG
1 AACAGTAACAGTAGAGGTAACAGAGTACCTAGTCAGAAAAAATCCGG
3226358 AACAGTAACAGTA
1 AACAGTAACAGTA
3226371 TAGTGTCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 35 0.69
47 3 0.06
48 13 0.25
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (47 bp):
AACAGTAACAGTAGAGGTAACAGAGTACCTAGTCAGAAAAAATCCGG
Found at i:3227658 original size:15 final size:16
Alignment explanation
Indices: 3227638--3227670 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3227628 TCTCAAATTG
*
3227638 TAATTAT-TTAATTAA
1 TAATTATCTTAATAAA
3227653 TAATTATCTTAATAAA
1 TAATTATCTTAATAAA
3227669 TA
1 TA
3227671 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTATCTTAATAAA
Found at i:3232761 original size:23 final size:22
Alignment explanation
Indices: 3232660--3232765 Score: 119
Period size: 21 Copynumber: 4.9 Consensus size: 22
3232650 TGATCAGTAG
* * *
3232660 ACGACACATAAAGTGCCT-AAA
1 ACGACACATGAGGTGCCTGAAT
*
3232681 ACGACACACGAGGTGCCTG-AT
1 ACGACACATGAGGTGCCTGAAT
3232702 ACGACACATGAGGTGCCTG-AT
1 ACGACACATGAGGTGCCTGAAT
*
3232723 ACGACACACGAGGTGCCTGAAAT
1 ACGACACATGAGGTGCCTG-AAT
* *
3232746 ACGACACATAAAGTGCCTGA
1 ACGACACATGAGGTGCCTGA
3232766 TTGATAAAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
21 54 0.74
22 1 0.01
23 18 0.25
ACGTcount: A:0.36, C:0.25, G:0.24, T:0.15
Consensus pattern (22 bp):
ACGACACATGAGGTGCCTGAAT
Found at i:3232763 original size:44 final size:42
Alignment explanation
Indices: 3232660--3232766 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
3232650 TGATCAGTAG
* *
3232660 ACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTGAT
1 ACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTGAT
* *
3232702 ACGACACATGAGGTGCCTGATACGACACACGAGGTGCCTGAAAT
1 ACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTG--AT
3232746 ACGACACATAAAGTGCCTGAT
1 ACGACACATAAAGTGCCTGAT
3232767 TGATAAAGCC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 36 0.63
44 21 0.37
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (42 bp):
ACGACACATAAAGTGCCTGATACGACACACGAGGTGCCTGAT
Found at i:3233161 original size:15 final size:15
Alignment explanation
Indices: 3233136--3233189 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
3233126 TCATATATAT
3233136 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
3233152 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
3233167 AATAATTTCAATCAA
1 TATAAATTCAATCAA
3233182 TATAAATT
1 TATAAATT
3233190 AATAAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:3234950 original size:22 final size:23
Alignment explanation
Indices: 3234925--3234970 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3234915 CAACCAAATC
3234925 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3234947 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3234970 A
1 A
3234971 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3234976 original size:23 final size:23
Alignment explanation
Indices: 3234932--3234976 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3234922 ATCAATTCAA
*
3234932 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
3234955 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
3234977 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:3237883 original size:42 final size:42
Alignment explanation
Indices: 3237820--3237946 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
3237810 CTTCGTTTTC
** * *
3237820 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
3237863 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
3237904 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
3237945 TC
1 TC
3237947 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:3238006 original size:47 final size:46
Alignment explanation
Indices: 3237905--3238028 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
3237895 ATTCATATAT
* * * * *
3237905 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * * *
3237951 TGATGCCATATCCCAGATATGGTATTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
3237998 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
3238029 GAAATCACTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 26 0.39
47 40 0.61
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:3238088 original size:31 final size:31
Alignment explanation
Indices: 3238053--3238201 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
3238043 CTTGTCACTT
* *
3238053 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
3238084 GTAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
3238115 GTAGCCGGAGCTGCCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
3238146 GTAGCAGAAGCTACCACTTTTCACTGATTAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
3238177 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
3238202 TGTCATTTAT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:3238283 original size:50 final size:51
Alignment explanation
Indices: 3238177--3238305 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
3238167 CACTGATTAA
* * * *
3238177 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTATCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTATCATTGATCAGATAAAT
*
3238228 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAAT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTATCATTGATCAGATAAAT
3238278 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
3238306 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 44 0.62
51 27 0.38
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTATCATTGATCAGATAAAT
Found at i:3242214 original size:13 final size:14
Alignment explanation
Indices: 3242198--3242233 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3242188 CAATCTCATA
3242198 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
3242211 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
3242224 TCTC-ATTTCA
1 TCTCAATTTCA
3242234 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:3242223 original size:18 final size:19
Alignment explanation
Indices: 3242185--3242225 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
3242175 TGGTTCATGT
3242185 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
3242204 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
3242222 TTTC
1 TTTC
3242226 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:3242415 original size:39 final size:38
Alignment explanation
Indices: 3242348--3242482 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
3242338 ACCAATATGG
* * *
3242348 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
3242387 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
3242425 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
3242466 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
3242483 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:3242745 original size:18 final size:19
Alignment explanation
Indices: 3242719--3242757 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3242709 TTTCAATTCA
3242719 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
3242738 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
3242756 AT
1 AT
3242758 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:3244023 original size:16 final size:17
Alignment explanation
Indices: 3244002--3244035 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
3243992 TTTCTCCCCT
3244002 GTTTCTTC-TCTGTTTC
1 GTTTCTTCATCTGTTTC
3244018 GTTTCTTCATTCTGTTTC
1 GTTTCTTCA-TCTGTTTC
3244036 TTATGTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.03, C:0.24, G:0.12, T:0.62
Consensus pattern (17 bp):
GTTTCTTCATCTGTTTC
Found at i:3244071 original size:5 final size:5
Alignment explanation
Indices: 3244063--3244103 Score: 73
Period size: 5 Copynumber: 8.0 Consensus size: 5
3244053 TTTATATAAT
3244063 ATATA ATATA ATATA ATATA ATATA ATATA ATATA TATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA
3244104 TATTTTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:3244106 original size:10 final size:10
Alignment explanation
Indices: 3244055--3244106 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 10
3244045 TTTACTTATT
3244055 TATATA-ATA
1 TATATATATA
3244064 TATA-ATATA
1 TATATATATA
3244073 -ATATA-ATA
1 TATATATATA
3244081 TA-ATATA-A
1 TATATATATA
3244089 TATA-ATATA
1 TATATATATA
3244098 TATATATAT
1 TATATATAT
3244107 TTTAACACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
8 16 0.44
9 16 0.44
10 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATATATA
Found at i:3244106 original size:15 final size:16
Alignment explanation
Indices: 3244056--3244103 Score: 80
Period size: 15 Copynumber: 3.0 Consensus size: 16
3244046 TTACTTATTT
3244056 ATATAATATATAATATA
1 ATATAATATAT-ATATA
3244073 ATATAATATA-ATATA
1 ATATAATATATATATA
3244088 ATATAATATATATATA
1 ATATAATATATATATA
3244104 TATTTTAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.50
16 5 0.17
17 10 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAATATATATATA
Found at i:3248629 original size:13 final size:14
Alignment explanation
Indices: 3248613--3248648 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3248603 CAATCTCATA
3248613 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
3248626 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
3248639 TCTC-ATTTCA
1 TCTCAATTTCA
3248649 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:3248638 original size:18 final size:19
Alignment explanation
Indices: 3248600--3248640 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
3248590 TGGTTCATGT
3248600 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
3248619 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
3248637 TTTC
1 TTTC
3248641 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:3248830 original size:39 final size:38
Alignment explanation
Indices: 3248763--3248897 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
3248753 ACCAATATGG
* * *
3248763 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
3248802 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
3248840 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
3248881 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
3248898 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:3249162 original size:18 final size:19
Alignment explanation
Indices: 3249136--3249174 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3249126 TTTCAATTCA
3249136 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
3249155 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
3249173 AT
1 AT
3249175 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:3250492 original size:5 final size:5
Alignment explanation
Indices: 3250484--3250523 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
3250474 TTTATATAAT
3250484 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
3250524 TATTTTAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:3250952 original size:41 final size:41
Alignment explanation
Indices: 3250862--3250945 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
3250852 TATTCGGGAT
3250862 TTATTGCCTAGCAAGCTTTGTGCCGGTGTATTAAATCAGGC
1 TTATTGCCTAGCAAGCTTTGTGCCGGTGTATTAAATCAGGC
* * *
3250903 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATTAGGC
1 TTATTGCCTAGCAAGCTTTGTGCCGGTGTATTAAATCAGGC
3250944 TT
1 TT
3250946 TGTGCCTGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
TTATTGCCTAGCAAGCTTTGTGCCGGTGTATTAAATCAGGC
Found at i:3254164 original size:42 final size:42
Alignment explanation
Indices: 3254101--3254260 Score: 168
Period size: 42 Copynumber: 3.7 Consensus size: 42
3254091 CTTTGTTTTC
** *
3254101 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACAT-A
* *
3254144 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
3254185 TCGATGCC----CCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATA
3254230 TCGATGCCATAGCCCAGCTATGGTCTTACAC
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC
3254261 GAATCACATA
Statistics
Matches: 98, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
38 19 0.19
41 4 0.04
42 40 0.41
43 1 0.01
44 1 0.01
45 14 0.14
49 19 0.19
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATA
Found at i:3254299 original size:46 final size:47
Alignment explanation
Indices: 3254193--3254350 Score: 149
Period size: 47 Copynumber: 3.3 Consensus size: 47
3254183 TATCGATGCC
* * * * *
3254193 CCCAGCTATGGTCTTACAC-GTAATCACATATCACATATCGATGCCATAG
1 CCCAGATATGGTCTTACACAG-AAGCACATATCAC--ACCGATGCCAAAT
* * * *
3254242 CCCAGCTATGGTCTTACAC-GAATCACATATCTCACTGATGCCAAAT
1 CCCAGATATGGTCTTACACAGAAGCACATATCACACCGATGCCAAAT
* * * * *
3254288 TCCAGATATGGTCTTATACAGTAGCATATATCACACCGATGCCATAT
1 CCCAGATATGGTCTTACACAGAAGCACATATCACACCGATGCCAAAT
3254335 CCCAGATATGGTCTTA
1 CCCAGATATGGTCTTA
3254351 TACGTAAATC
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
46 25 0.27
47 36 0.39
48 12 0.13
49 20 0.22
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (47 bp):
CCCAGATATGGTCTTACACAGAAGCACATATCACACCGATGCCAAAT
Found at i:3254414 original size:31 final size:31
Alignment explanation
Indices: 3254379--3254494 Score: 164
Period size: 31 Copynumber: 3.7 Consensus size: 31
3254369 CTTGTCACTT
*
3254379 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
3254410 GTAGCC-AGAGCTACCATTTTTCACTAATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
3254441 GTAGCAGAAGCTACTC-CTTTTCACTGATCAG
1 GTAGCCGAAGCTAC-CACTTTTCACTGATCAG
3254472 GTAGCCGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
3254495 GTTGTCATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
30 2 0.03
31 70 0.95
32 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:3254546 original size:7 final size:7
Alignment explanation
Indices: 3254534--3254568 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
3254524 TAGCCGCAGC
3254534 TATCACT
1 TATCACT
3254541 TATCACT
1 TATCACT
3254548 TATCACT
1 TATCACT
3254555 TATCACT
1 TATCACT
3254562 T-TCACT
1 TATCACT
3254568 T
1 T
3254569 GTCCTTGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.46
Consensus pattern (7 bp):
TATCACT
Found at i:3263218 original size:53 final size:53
Alignment explanation
Indices: 3263137--3263287 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
3263127 CTTACACGGT
* *
3263137 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
3263192 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
3263245 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
3263288 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:3270734 original size:53 final size:53
Alignment explanation
Indices: 3270653--3270803 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
3270643 CTTACACGGT
* *
3270653 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
3270708 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
3270761 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
3270804 GCACACTTGT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:3273357 original size:21 final size:20
Alignment explanation
Indices: 3273332--3273396 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
3273322 TAGCCTTCGG
3273332 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTT-TGT
* * *
3273353 GCTTCAG-TTAGC-CTTCGG
1 GCTTCCGTTTAGCACTTTGT
3273371 GCTTCCGTTTAGCACTTTTGT
1 GCTTCCGTTTAGCAC-TTTGT
3273392 GCTTC
1 GCTTC
3273397 AGTTAGATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
20 6 0.17
21 14 0.40
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.42
Consensus pattern (20 bp):
GCTTCCGTTTAGCACTTTGT
Found at i:3273410 original size:39 final size:39
Alignment explanation
Indices: 3273314--3273402 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
3273304 GCTCTGATGA
3273314 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
*
3273353 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTTTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
3273392 GCTTCAGTTAG
1 GCTTCAGTTAG
3273403 ATTTCGGGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:3276682 original size:121 final size:120
Alignment explanation
Indices: 3276467--3276745 Score: 420
Period size: 121 Copynumber: 2.3 Consensus size: 120
3276457 CATCCATTGT
* * * *
3276467 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAGAGTGAAGGCATTGGAAAAT
1 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGACAATGGAAAAT
3276532 CAACATTGAAATAAGTAGTTATAATTATTGTCAACTGTTTCCATAAATTAAATTCA
66 CAACATTGAAATAAGTAGTTATAATTATTGTCAACTGTTTCCATAAATTAAATT-A
* * *
3276588 TTTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGATAATGGACAAT
1 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGACAATGGAAAAT
* * *
3276653 TAACATTGAAATTAA-TAGTTATAATTATTGTCAACTGTTTCCCTAAATTCAATTA
66 CAACATTGAAA-TAAGTAGTTATAATTATTGTCAACTGTTTCCATAAATTAAATTA
*
3276708 ATTAGGAGAAAACAATTAATAAA-TTATA-TTATATTAAA
1 ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAA
3276746 ATTAGATTTA
Statistics
Matches: 145, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
118 10 0.07
119 4 0.03
120 23 0.16
121 105 0.72
122 3 0.02
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (120 bp):
ATTAGGAGAAAACAATTAATAAAGTAATAGTTATATTAAATGTTAAAGTAAAGACAATGGAAAAT
CAACATTGAAATAAGTAGTTATAATTATTGTCAACTGTTTCCATAAATTAAATTA
Found at i:3293569 original size:2 final size:2
Alignment explanation
Indices: 3293562--3293594 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3293552 CTTTTGCTTC
3293562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3293595 CTAAGCCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3299234 original size:21 final size:21
Alignment explanation
Indices: 3299208--3299251 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3299198 GATAAAATGC
3299208 TTAAATAATAATT-TAATATAA
1 TTAAATAATAATTATAAT-TAA
*
3299229 TTAAATCATAATTATAATTAA
1 TTAAATAATAATTATAATTAA
3299250 TT
1 TT
3299252 CTCTAAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTAAATAATAATTATAATTAA
Found at i:3306173 original size:75 final size:73
Alignment explanation
Indices: 3306085--3306256 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
3306075 GGTTTTCCTC
*** * * **
3306085 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
3306149 TCAGTATGG
65 TCAGTATGG
*
3306158 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
3306223 CTCAGTATGG
64 CTCAGTATGG
3306233 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
3306257 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:3306254 original size:35 final size:35
Alignment explanation
Indices: 3306090--3306256 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
3306080 TCCTCATTGA
*** *
3306090 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
3306125 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
3306165 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
3306200 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
3306235 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
3306257 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:3313668 original size:75 final size:73
Alignment explanation
Indices: 3313580--3313751 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
3313570 GGTTTTCCTC
*** * * **
3313580 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
3313644 TCAGTATGG
65 TCAGTATGG
*
3313653 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
3313718 CTCAGTATGG
64 CTCAGTATGG
3313728 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
3313752 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:3313749 original size:35 final size:35
Alignment explanation
Indices: 3313585--3313751 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
3313575 TCCTCATTGA
*** *
3313585 AATACCATACCTACATTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
3313620 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
3313660 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
3313695 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
3313730 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
3313752 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:3317924 original size:46 final size:44
Alignment explanation
Indices: 3317820--3317927 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3317810 TGTCTTTGAC
** * * *
3317820 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3317864 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3317910 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3317928 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3325398 original size:10 final size:9
Alignment explanation
Indices: 3325367--3325396 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3325357 CTACATATTC
*
3325367 TTTAGAATT
1 TTTATAATT
3325376 TTTATAATT
1 TTTATAATT
3325385 TTTATAATT
1 TTTATAATT
3325394 TTT
1 TTT
3325397 TAAAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTATAATT
Found at i:3325431 original size:18 final size:19
Alignment explanation
Indices: 3325405--3325442 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3325395 TTTAAAAATA
* *
3325405 TAAATTTTAGAAA-TATTT
1 TAAAATTTACAAATTATTT
3325423 TAAAATTTACAAATTATTT
1 TAAAATTTACAAATTATTT
3325442 T
1 T
3325443 GTAGTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TAAAATTTACAAATTATTT
Found at i:3330739 original size:37 final size:37
Alignment explanation
Indices: 3330689--3330763 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3330679 AAACATGACT
3330689 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
1 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
3330726 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
1 AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
3330763 A
1 A
3330764 TTATCCTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.37
Consensus pattern (37 bp):
AAGATTACATCCTAATCATTCTTGAAAATACTTCTTC
Found at i:3345706 original size:18 final size:16
Alignment explanation
Indices: 3345683--3345725 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
3345673 ATTCGTGGAC
*
3345683 TAATTGATCTAATTTTAT
1 TAATTGATC-AATATT-T
3345701 TAATTGAATCAATATTT
1 TAATTG-ATCAATATTT
3345718 TAATTGAT
1 TAATTGAT
3345726 TTTCAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 7 0.30
18 11 0.48
19 3 0.13
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (16 bp):
TAATTGATCAATATTT
Found at i:3350216 original size:3 final size:3
Alignment explanation
Indices: 3350208--3350236 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3350198 GCTGAGCCGA
3350208 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3350237 AGATCACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3350564 original size:4 final size:4
Alignment explanation
Indices: 3350555--3350594 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
3350545 TCAATATGAA
3350555 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
3350595 GTATGTGAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:3354940 original size:7 final size:8
Alignment explanation
Indices: 3354908--3354938 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
3354898 AATATTTCAG
3354908 GAAAAAAA
1 GAAAAAAA
3354916 GAAAAAAA
1 GAAAAAAA
3354924 GAAAAAAA
1 GAAAAAAA
3354932 GAAAAAA
1 GAAAAAA
3354939 GATTGTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:3355981 original size:20 final size:20
Alignment explanation
Indices: 3355943--3355983 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3355933 TTATCTGATA
*
3355943 AATTTATATTTTAGGAAATT
1 AATTTATATTTTAGAAAATT
3355963 AATTTAATATTTTA-AAAATT
1 AATTT-ATATTTTAGAAAATT
3355983 A
1 A
3355984 TAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AATTTATATTTTAGAAAATT
Found at i:3359434 original size:15 final size:15
Alignment explanation
Indices: 3359414--3359445 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3359404 AGCAATCTTG
3359414 TTCCAGTGTACCTGT
1 TTCCAGTGTACCTGT
3359429 TTCCAGTGTACCTGT
1 TTCCAGTGTACCTGT
3359444 TT
1 TT
3359446 AAGCAATGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (15 bp):
TTCCAGTGTACCTGT
Found at i:3381444 original size:27 final size:28
Alignment explanation
Indices: 3381413--3381467 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
3381403 TTTATAATGT
3381413 TATTCTAATTT-ATATTTTTTTTTCTAA
1 TATTCTAATTTAATATTTTTTTTTCTAA
*
3381440 TATTCTCATTTAAAATATTTTTTTTTCT
1 TATTCTAATTT--AATATTTTTTTTTCT
3381468 TTTTTACTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
30 14 0.58
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTCTAATTTAATATTTTTTTTTCTAA
Found at i:3389749 original size:43 final size:44
Alignment explanation
Indices: 3389681--3389809 Score: 147
Period size: 46 Copynumber: 2.9 Consensus size: 44
3389671 CTTTTATTCA
* * *
3389681 TTCACCGGCATT-TTGCCTGCTAGGCTCG-AGGCCTGATATCAT-
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGA-ATAATG
3389723 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAATG
1 TTCACCGGCATTATAGCCTGCTAGGCTCG-AAGGCCCGAATAATG
* * * *
3389768 TCTCACCGGCATAATAGCCTGCTAAGTTCAAAGGCCCGAATA
1 T-TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
3389810 TAATACCAGC
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 12 0.16
43 15 0.20
44 4 0.05
45 20 0.27
46 24 0.32
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAATG
Found at i:3389858 original size:38 final size:38
Alignment explanation
Indices: 3389802--3389964 Score: 227
Period size: 38 Copynumber: 4.2 Consensus size: 38
3389792 AGTTCAAAGG
* * * * *
3389802 CCCGAATATAATACCAGCACTAGGCCTACTGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
3389840 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
3389878 CCCGGATATATTACCAGCACGAAGCCTGTGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
3389916 CCCGGTTATATTACCAGCACGAAGCCTGCGGGATTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTTAA
3389955 GCCCGGATAT
1 -CCCGGATAT
3389965 CATATTTCGA
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
38 100 0.88
39 5 0.04
40 8 0.07
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:3395390 original size:43 final size:44
Alignment explanation
Indices: 3395322--3395450 Score: 156
Period size: 46 Copynumber: 2.9 Consensus size: 44
3395312 CTTTTATTCA
* * *
3395322 TTCACCGGCATT-TCGCCTGCTAGGCTCG-AGGCCTGATATCAT-
1 TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGA-ATAATG
3395364 TTCACCGGCATTATAGCCTGCTAGGCTCGAAAGGCCCGAATAATG
1 TTCACCGGCATTATAGCCTGCTAGGCTCG-AAGGCCCGAATAATG
* * *
3395409 TCTCACCGGCATAATAGCCTACTAGGCTCAAAGGCCCGAATA
1 T-TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
3395451 TAATACCAGC
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 12 0.16
43 15 0.20
44 4 0.05
45 20 0.26
46 25 0.33
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.23
Consensus pattern (44 bp):
TTCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAATG
Found at i:3396659 original size:35 final size:36
Alignment explanation
Indices: 3396615--3396781 Score: 196
Period size: 35 Copynumber: 4.6 Consensus size: 36
3396605 TCCTCATTGA
** *
3396615 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
* **
3396650 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGG----GAT
*
3396690 AATACCATACCTACATTTCACAGCTCAGTAT-GGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
3396725 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGGAT
* *
3396760 GATACCAAACCTACATTTCACA
1 AATACCATACCTACATTTCACA
3396782 CTTTGCCATG
Statistics
Matches: 116, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
35 86 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (36 bp):
AATACCATACCTACATTTCACAACTCAGTATGGGAT
Found at i:3396698 original size:75 final size:74
Alignment explanation
Indices: 3396611--3396781 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 74
3396601 GTTTTCCTCA
** * * **
3396611 TTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAACT
1 TTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAACT
3396675 CAGTATGGAT
65 CAGTATGGAT
*
3396685 TTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAACT
1 TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
3396750 CAGTATGGA-
65 CAGTATGGAT
*
3396759 -TG--ATACCAAACCTACATTTCACA
1 TTGAAATACCATACCTACATTTCACA
3396782 CTTTGCCATG
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 20 0.23
73 2 0.02
74 7 0.08
75 58 0.67
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (74 bp):
TTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACTC
AGTATGGAT
Found at i:3399850 original size:44 final size:45
Alignment explanation
Indices: 3399760--3399888 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
3399750 GACAGAACGA
*
3399760 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
3399806 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
3399850 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3399889 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:3406713 original size:35 final size:35
Alignment explanation
Indices: 3406669--3406835 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
3406659 TCCTCATTGA
** *
3406669 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
3406704 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
3406744 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
3406779 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
3406814 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
3406836 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Done.