Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015263.1 Kokia drynarioides strain JFW-HI SEQ_130308, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1369056
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 871 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:947082 original size:3 final size:3
Alignment explanation
Indices: 947016--947065 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
947006 CAATCACATA
*
947016 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
947064 AA
1 AA
947066 ATATATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:954316 original size:21 final size:21
Alignment explanation
Indices: 954292--954342 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
954282 GAAGTTTTTA
* *
954292 GTATCGGTAGAGGTGAAACTT
1 GTATCGGTAGAAGAGAAACTT
**
954313 GTATCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAGAAACTT
954334 GTATCGGTA
1 GTATCGGTA
954343 AAACTATCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.31, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGAAGAGAAACTT
Found at i:954352 original size:21 final size:21
Alignment explanation
Indices: 954309--954360 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
954299 TAGAGGTGAA
*
954309 ACTTGTATCGGTAGAAGAGTC
1 ACTTGTATCGGTAAAAGAGTC
*
954330 ACTTGTATCGGTAAAACTA-TC
1 ACTTGTATCGGTAAAA-GAGTC
954351 ACTTGTATCG
1 ACTTGTATCG
954361 ATAGAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAAAAGAGTC
Found at i:963278 original size:21 final size:21
Alignment explanation
Indices: 963254--963311 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
963244 TATAGATGAA
963254 ACTTGTATCGATAGAA-GAGTC
1 ACTTGTATCGATAGAACGA-TC
* *
963275 ACTTGTATCGGTAGAACTATC
1 ACTTGTATCGATAGAACGATC
963296 ACTTGTATCGATAGAA
1 ACTTGTATCGATAGAA
963312 ATCTACATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (21 bp):
ACTTGTATCGATAGAACGATC
Found at i:966069 original size:21 final size:21
Alignment explanation
Indices: 966045--966084 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
966035 CTAACTTTAT
966045 TATTCGAGC-TTCTAGCTCGAC
1 TATTCGAGCTTTC-AGCTCGAC
*
966066 TATTCGGGCTTTCAGCTCG
1 TATTCGAGCTTTCAGCTCG
966085 GCCTTCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.35
Consensus pattern (21 bp):
TATTCGAGCTTTCAGCTCGAC
Found at i:970636 original size:26 final size:26
Alignment explanation
Indices: 970606--970657 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
970596 ATTTTGGGCG
970606 CAATTCTGGACACGTTCATGCAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
* *
970632 CAATTCTGGACATGTTCATGTAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
970658 TATTCCTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
CAATTCTGGACACGTTCATGCAGCGA
Found at i:971879 original size:17 final size:16
Alignment explanation
Indices: 971839--971905 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
971829 AATATATATG
971839 AAAATGCAGTGACAATA
1 AAAATGCAG-GACAATA
* *
971856 TACATGCAGCGACAATA
1 AAAATGCAG-GACAATA
* *
971873 AAAATGCAAGTACAACA
1 AAAATGC-AGGACAATA
971890 AAAATGCAGGGACAAT
1 AAAATGCA-GGACAAT
971906 TATACTACAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
16 1 0.03
17 36 0.92
18 2 0.05
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGCAGGACAATA
Found at i:974971 original size:37 final size:37
Alignment explanation
Indices: 974858--974973 Score: 142
Period size: 37 Copynumber: 3.1 Consensus size: 37
974848 AGCGACGGTC
* * **
974858 TTGGGTGCATTCTGGAAATAATCATGCGACGACAGTT
1 TTGGGTGCAATCTGGAAGTGCTCATGCGACGACAGTT
* * **
974895 TTAGGTGCAATCTGGAAGTGCTCATACGGTGACAGTT
1 TTGGGTGCAATCTGGAAGTGCTCATGCGACGACAGTT
* *
974932 TTGGGTGTAATCTGGAAGTGCTCATGCGACGATAGTT
1 TTGGGTGCAATCTGGAAGTGCTCATGCGACGACAGTT
974969 TTGGG
1 TTGGG
974974 CACAAATTTG
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (37 bp):
TTGGGTGCAATCTGGAAGTGCTCATGCGACGACAGTT
Found at i:975770 original size:12 final size:11
Alignment explanation
Indices: 975747--975785 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
975737 TTCTAGTTTC
975747 TTTTTATTTTT
1 TTTTTATTTTT
*
975758 TATTTATTTTT
1 TTTTTATTTTT
975769 TTTGTTATTTTCT
1 TTT-TTATTTT-T
975782 TTTT
1 TTTT
975786 GAAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 12 0.50
12 8 0.33
13 4 0.17
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTATTTTT
Found at i:980107 original size:24 final size:25
Alignment explanation
Indices: 980054--980115 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
980044 GTTATTTTAC
* *
980054 GAACATATGTTGTATGTTGTAATGT
1 GAACCTATGTTGTATGATGTAATGT
*
980079 GAACCTATGTTGTGTGATGT-ATGT
1 GAACCTATGTTGTATGATGTAATGT
*
980103 GAACCTAAGTTGT
1 GAACCTATGTTGT
980116 TATGTGCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (25 bp):
GAACCTATGTTGTATGATGTAATGT
Found at i:985519 original size:43 final size:43
Alignment explanation
Indices: 985458--985546 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
985448 ATATTAATAA
985458 CATAAATTATTTTTTCCCTTTGAAGAGTTATCTTGAGAACTCT
1 CATAAATTATTTTTTCCCTTTGAAGAGTTATCTTGAGAACTCT
985501 CATAAATTATTTTTTCCCTTTGAAGAGTTATCTTGAGAACTCT
1 CATAAATTATTTTTTCCCTTTGAAGAGTTATCTTGAGAACTCT
985544 CAT
1 CAT
985547 TATTCTCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (43 bp):
CATAAATTATTTTTTCCCTTTGAAGAGTTATCTTGAGAACTCT
Found at i:985743 original size:22 final size:25
Alignment explanation
Indices: 985715--985760 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 25
985705 CGTGTTATAA
985715 AATAAAGAG-AT-AGAGAG-AAAAT
1 AATAAAGAGAATGAGAGAGCAAAAT
985737 AATAAAGAGAATGAGAGAGCAAAA
1 AATAAAGAGAATGAGAGAGCAAAA
985761 GAAAGAGCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 2 0.10
24 6 0.29
25 4 0.19
ACGTcount: A:0.63, C:0.02, G:0.24, T:0.11
Consensus pattern (25 bp):
AATAAAGAGAATGAGAGAGCAAAAT
Found at i:986678 original size:9 final size:9
Alignment explanation
Indices: 986656--986816 Score: 58
Period size: 9 Copynumber: 16.8 Consensus size: 9
986646 AATGATAGAA
*
986656 ATAAAAATCA
1 ATAAAAAT-T
986666 ATAAAAATT
1 ATAAAAATT
986675 ATAAAAATT
1 ATAAAAATT
**
986684 ATTAAATTTT
1 A-TAAAAATT
*
986694 AATAAAAAAT
1 -ATAAAAATT
986704 ATAGAAAA-T
1 ATA-AAAATT
* *
986713 ATTGAAAATAG
1 A-TAAAAAT-T
*
986724 AAAAAAATT
1 ATAAAAATT
986733 ATAAAAATCGT
1 ATAAAAAT--T
*
986744 ACAAAAATT
1 ATAAAAATT
986753 AT-AAAATT
1 ATAAAAATT
*
986761 TTATAAAATCGT
1 ATA-AAAAT--T
986773 A-AGAAAATT
1 ATA-AAAATT
*
986782 ATAAAAAAT
1 ATAAAAATT
* *
986791 GTAAAGAAAT
1 ATAAA-AATT
*
986801 ATAAAATTT
1 ATAAAAATT
*
986810 GTAAAAA
1 ATAAAAA
986817 AAAATATAAA
Statistics
Matches: 113, Mismatches: 24, Indels: 29
0.68 0.14 0.17
Matches are distributed among these distances:
8 7 0.06
9 46 0.41
10 43 0.38
11 16 0.14
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:986697 original size:29 final size:30
Alignment explanation
Indices: 986665--986740 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
986655 AATAAAAATC
* **
986665 AATAAAAATTATAAAAATTATT-AAATTTT
1 AATAAAAATTATAAAAATTATTGAAAATAG
*
986694 AATAAAAAATATAGAAAA-TATTGAAAATAG
1 AATAAAAATTATA-AAAATTATTGAAAATAG
986724 AA-AAAAATTATAAAAAT
1 AATAAAAATTATAAAAAT
986741 CGTACAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.10
29 25 0.64
30 10 0.26
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (30 bp):
AATAAAAATTATAAAAATTATTGAAAATAG
Found at i:986758 original size:29 final size:30
Alignment explanation
Indices: 986726--986788 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
986716 GAAAATAGAA
986726 AAAAATTATA-AAAATCGTACA-AAAATTAT
1 AAAAATTATATAAAATCGTA-AGAAAATTAT
*
986755 -AAAATTTTATAAAATCGTAAGAAAATTAT
1 AAAAATTATATAAAATCGTAAGAAAATTAT
986784 AAAAA
1 AAAAA
986789 ATGTAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 9 0.30
29 17 0.57
30 4 0.13
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (30 bp):
AAAAATTATATAAAATCGTAAGAAAATTAT
Found at i:986780 original size:21 final size:21
Alignment explanation
Indices: 986755--986827 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
986745 CAAAAATTAT
* *
986755 AAAATTTTATAAAATCGT-AAG
1 AAAATTATAAAAAAT-GTAAAG
986776 AAAATTATAAAAAATGTAAAG
1 AAAATTATAAAAAATGTAAAG
** *
986797 -AAA-TATAAAATTTGTAAAA
1 AAAATTATAAAAAATGTAAAG
*
986816 AAAAATATAAAA
1 AAAATTATAAAA
986828 TTTATGTACT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 13 0.30
20 8 0.18
21 23 0.52
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAATTATAAAAAATGTAAAG
Found at i:986790 original size:69 final size:69
Alignment explanation
Indices: 986677--986830 Score: 154
Period size: 69 Copynumber: 2.2 Consensus size: 69
986667 TAAAAATTAT
* **
986677 AAAAATTATTAAATTTTAATAAAAAATATAGAAAATATTGAAAATAG-AAAAAAATTATAAAAAT
1 AAAAATTATAAAATTTTAATAAAAAATATAGAAAATATAAAAAAT-GTAAAAAAA-TATAAAAAT
*
986741 CGT-AC
64 CGTAAA
** * *
986746 AAAAATTATAAAATTTT-ATAAAATCGTA-AGAAAATTATAAAAAATGTAAAGAAATATAAAATT
1 AAAAATTATAAAATTTTAATAAAA-AATATAGAAAA-TATAAAAAATGTAAAAAAATATAAAAAT
*
986809 TGTAAA
64 CGTAAA
*
986815 AAAAAATATAAAATTT
1 AAAAATTATAAAATTT
986831 ATGTACTAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
68 23 0.32
69 48 0.68
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (69 bp):
AAAAATTATAAAATTTTAATAAAAAATATAGAAAATATAAAAAATGTAAAAAAATATAAAAATCG
TAAA
Found at i:986812 original size:19 final size:20
Alignment explanation
Indices: 986762--986830 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 20
986752 TATAAAATTT
* * *
986762 TATAAAA-TCGTAAGAAAAT
1 TATAAAATTTGTAAAAAAAA
** *
986781 TATAAAAAATGT-AAAGAAA
1 TATAAAATTTGTAAAAAAAA
986800 TATAAAATTTGTAAAAAAAAA
1 TATAAAATTTGT-AAAAAAAA
986821 TATAAAATTT
1 TATAAAATTT
986831 ATGTACTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 21 0.54
20 2 0.05
21 16 0.41
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.29
Consensus pattern (20 bp):
TATAAAATTTGTAAAAAAAA
Found at i:987054 original size:9 final size:9
Alignment explanation
Indices: 987042--987155 Score: 58
Period size: 9 Copynumber: 12.7 Consensus size: 9
987032 AAAAATTTAC
987042 ATTTTTATA
1 ATTTTTATA
987051 ATTTTT-T-
1 ATTTTTATA
*
987058 ACTTTTATAA
1 ATTTTTAT-A
** *
987068 AAATTTCTA
1 ATTTTTATA
*
987077 ATTATTAATA
1 ATT-TTTATA
987087 A-TTTTATTAA
1 ATTTTTA-T-A
* *
987097 AATTTAATA
1 ATTTTTATA
*
987106 ATTTTTACA
1 ATTTTTATA
987115 ATTTTTATA
1 ATTTTTATA
*
987124 ACTTTTAT-
1 ATTTTTATA
*
987132 -TGATTTATA
1 AT-TTTTATA
987141 ATTTTTATA
1 ATTTTTATA
987150 ATTTTT
1 ATTTTT
987156 TTTGCCTCAT
Statistics
Matches: 77, Mismatches: 18, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
7 5 0.06
8 10 0.13
9 44 0.57
10 14 0.18
11 4 0.05
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.60
Consensus pattern (9 bp):
ATTTTTATA
Found at i:987117 original size:28 final size:27
Alignment explanation
Indices: 987045--987124 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
987035 AATTTACATT
987045 TTTATAATTTTTTAC--TTTTATAAAAA
1 TTTATAA-TTTTTACAATTTTATAAAAA
* * * *
987071 TTTCTAATTATTAATAATTTTATTAAAA
1 TTTATAATT-TTTACAATTTTATAAAAA
987099 TTTAATAATTTTTACAATTTTTATAA
1 TTT-ATAATTTTTACAA-TTTTATAA
987125 CTTTTATTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
25 2 0.05
26 9 0.22
28 18 0.44
29 12 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATAATTTTTACAATTTTATAAAAA
Found at i:987485 original size:84 final size:85
Alignment explanation
Indices: 987247--987485 Score: 209
Period size: 84 Copynumber: 2.8 Consensus size: 85
987237 AACTGTTAAT
* * * * * * *
987247 TTTTTAATGCATTTG-ACAGTTCAACTATCTAATTGAGTGCAAAAATAAATCATAAGTTTAATT-
1 TTTTTAAAGCATTTGAAAAGTTCAAGTACCCAATTGAGTG--AAAA-AAA-CAAAAGCTTAATTA
* * *
987310 TATTTTTCAAAAAAGTTTGAAGTAT
62 T-TTTTTTAAAAAAGTTTGAAGAAA
* * * * **
987335 TTTTTGATGCATTTGAAAAGTTCAAGTACCCAATTGAGTGAAAAAAATAAGAGCTTAA-TAGCTT
1 TTTTTAAAGCATTTGAAAAGTTCAAGTACCCAATTGAGTGAAAAAAACAAAAGCTTAATTATTTT
987399 TTTAAAAAAGTTTG-AGAACA
66 TTTAAAAAAGTTTGAAGAA-A
* ***
987419 TTTTTAAAGCATTTTAAAAGTTCAAGTATTTAATTGAGT-AAAAAAACAAAAGCTTAATTATTTT
1 TTTTTAAAGCATTTGAAAAGTTCAAGTACCCAATTGAGTGAAAAAAACAAAAGCTTAATTATTTT
987483 TTT
66 TTT
987486 TAAAGTTAAA
Statistics
Matches: 123, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
83 19 0.15
84 56 0.46
85 7 0.06
86 3 0.02
87 4 0.03
88 14 0.11
89 20 0.16
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (85 bp):
TTTTTAAAGCATTTGAAAAGTTCAAGTACCCAATTGAGTGAAAAAAACAAAAGCTTAATTATTTT
TTTAAAAAAGTTTGAAGAAA
Found at i:996971 original size:4 final size:5
Alignment explanation
Indices: 996910--996968 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
996900 ACTTGATATT
* * *
996910 TTTCA TTTCA TTTCA TTTCA TTTTCA TTTC- TCTCCT TTTCA TTTCT TTTCA
1 TTTCA TTTCA TTTCA TTTCA -TTTCA TTTCA T-TTCA TTTCA TTTCA TTTCA
996961 TTTC- TTTC
1 TTTCA TTTC
996969 TTTTTTCACA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
4 5 0.11
5 35 0.76
6 6 0.13
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTCA
Found at i:996997 original size:5 final size:5
Alignment explanation
Indices: 996909--997004 Score: 54
Period size: 5 Copynumber: 19.6 Consensus size: 5
996899 AACTTGATAT
* * * * * * *
996909 TTTTC ATTTC ATTTC ATTTC ATTTTC ATTTC TCTCC TTTTC ATTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
* ** * *
996960 ATTTC -TTTC TTTT- TTCAC ATTTC TTAT- TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT
997005 CAAACATAAC
Statistics
Matches: 68, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
4 9 0.13
5 55 0.81
6 4 0.06
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (5 bp):
TTTTC
Found at i:997642 original size:74 final size:74
Alignment explanation
Indices: 997547--997696 Score: 246
Period size: 74 Copynumber: 2.0 Consensus size: 74
997537 CTTTACAAAA
* * *
997547 TGAAAGTGAACAGCCATCATTCATCATTCATAAATGAATGTCTTGATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATAATTCATAAATGAATGTCTTGATTCATTTAAAAAATCTTGA
*
997612 ATGAAACAT
66 ATAAAACAT
* *
997621 TGAATGTGAACAACCATCATTCATAATTCATAAATGAATGTGTTGATTCATTTAAAAAATCTTGA
1 TGAAAGTGAACAACCATCATTCATAATTCATAAATGAATGTCTTGATTCATTTAAAAAATCTTGA
997686 ATAAAACAT
66 ATAAAACAT
997695 TG
1 TG
997697 TATCCCTCCA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (74 bp):
TGAAAGTGAACAACCATCATTCATAATTCATAAATGAATGTCTTGATTCATTTAAAAAATCTTGA
ATAAAACAT
Found at i:1003391 original size:5 final size:5
Alignment explanation
Indices: 1003336--1003426 Score: 67
Period size: 5 Copynumber: 18.0 Consensus size: 5
1003326 AACTTAATAA
* * * * * * *
1003336 TTTTC ATTTC ATTTC ATTTTC ATTTC -TTTC CTTCC TTTTC ATTTC ATTTC
1 TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
* * *
1003386 TTTTC TTTTT TTTTC GTTTC TTTTTT TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC
1003427 GTCCAAACAA
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
4 4 0.06
5 58 0.84
6 7 0.10
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTC
Found at i:1003399 original size:25 final size:25
Alignment explanation
Indices: 1003336--1003426 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
1003326 AACTTAATAA
* *
1003336 TTTTCATTTCATTTCATTTTCATTTC
1 TTTTCTTTTCTTTTCA-TTTCATTTC
* *
1003362 -TTTCCTTCCTTTTCATTTCATTTC
1 TTTTCTTTTCTTTTCATTTCATTTC
* * * *
1003386 TTTTCTTTTTTTTTCGTTTCTTTTTT
1 TTTTCTTTTCTTTTCATTTC-ATTTC
1003412 TTTTCTTTTCTTTTC
1 TTTTCTTTTCTTTTC
1003427 GTCCAAACAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 9 0.17
25 27 0.51
26 17 0.32
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.73
Consensus pattern (25 bp):
TTTTCTTTTCTTTTCATTTCATTTC
Found at i:1003400 original size:15 final size:15
Alignment explanation
Indices: 1003382--1003425 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 15
1003372 TTTCATTTCA
1003382 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
*
1003397 TTTCGTTTCTTTTTTT
1 TTTCTTTTC-TTTTTT
1003413 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
1003426 CGTCCAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:1003409 original size:35 final size:35
Alignment explanation
Indices: 1003336--1003425 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 35
1003326 AACTTAATAA
*
1003336 TTTTCATTTCATTTCATTTTC-ATTTCTTTCCTTCC
1 TTTTCATTTCATTTC-TTTTCTTTTTCTTTCCTTCC
* * *
1003371 TTTTCATTTCATTTCTTTTCTTTTTTTTTCGTTTC
1 TTTTCATTTCATTTCTTTTCTTTTTCTTTCCTTCC
1003406 TTTT--TTT--TTTCTTTTCTTTT
1 TTTTCATTTCATTTCTTTTCTTTT
1003426 CGTCCAAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 13 0.26
33 3 0.06
34 5 0.10
35 29 0.58
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (35 bp):
TTTTCATTTCATTTCTTTTCTTTTTCTTTCCTTCC
Found at i:1004060 original size:74 final size:74
Alignment explanation
Indices: 1003965--1004114 Score: 264
Period size: 74 Copynumber: 2.0 Consensus size: 74
1003955 CTTTACAAAA
*
1003965 TGAAAGTGAACAGCCATCATTCATCATTCATAAATGAATGTCTTGATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATGTCTTGATTCATTTAAAAACTCTTGA
1004030 ATGAAACAT
66 ATGAAACAT
* *
1004039 TGAATGTGAACAACCATCATTCATCATTCATAAATGAATGTGTTGATTCATTTAAAAACTCTTGA
1 TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATGTCTTGATTCATTTAAAAACTCTTGA
*
1004104 GTGAAACAT
66 ATGAAACAT
1004113 TG
1 TG
1004115 TATCCCTCCA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (74 bp):
TGAAAGTGAACAACCATCATTCATCATTCATAAATGAATGTCTTGATTCATTTAAAAACTCTTGA
ATGAAACAT
Found at i:1015471 original size:23 final size:22
Alignment explanation
Indices: 1015428--1015471 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1015418 ATTGCTACCT
*
1015428 TGTGCACCAAACTCCTAGGCCG
1 TGTGCACCAAACCCCTAGGCCG
*
1015450 TGTGCACCACACGCCCTAGGCC
1 TGTGCACCAAAC-CCCTAGGCC
1015472 CAAGCCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.20, C:0.41, G:0.23, T:0.16
Consensus pattern (22 bp):
TGTGCACCAAACCCCTAGGCCG
Found at i:1015629 original size:9 final size:9
Alignment explanation
Indices: 1015617--1015653 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
1015607 TTTTCTAATT
1015617 TTTAATTTA
1 TTTAATTTA
1015626 TTTAATTTA
1 TTTAATTTA
*
1015635 -TTAACTT-
1 TTTAATTTA
1015642 TTTAATTTA
1 TTTAATTTA
1015651 TTT
1 TTT
1015654 TAAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 12 0.50
9 12 0.50
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTAATTTA
Found at i:1015633 original size:16 final size:16
Alignment explanation
Indices: 1015607--1015652 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1015597 GAAATTTCTA
*
1015607 TTTTCTAATTT-TTAAT
1 TTTT-TAATTTATTAAC
1015623 TTATTTAATTTATTAAC
1 TT-TTTAATTTATTAAC
1015640 TTTTTAATTTATT
1 TTTTTAATTTATT
1015653 TTAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 19 0.70
17 8 0.30
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAATTTATTAAC
Found at i:1015655 original size:26 final size:25
Alignment explanation
Indices: 1015606--1015664 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 25
1015596 AGAAATTTCT
1015606 ATTTTCTAA-TTTTTAATTTATTT-A
1 ATTTT-TAACTTTTTAATTTATTTAA
1015630 ATTTATTAACTTTTTAATTTATTTTAA
1 ATTT-TTAACTTTTTAATTTA-TTTAA
1015657 ATTTTTAA
1 ATTTTTAA
1015665 TATTTTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.23
25 12 0.39
26 7 0.23
27 5 0.16
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTTTAACTTTTTAATTTATTTAA
Found at i:1015668 original size:16 final size:15
Alignment explanation
Indices: 1015606--1015671 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 15
1015596 AGAAATTTCT
1015606 ATTTTCTAATTTTTAA
1 ATTTT-TAATTTTTAA
*
1015622 TTTATTTAATTTATTAA
1 ATT-TTTAATTT-TTAA
*
1015639 CTTTTTAATTTATTTTAA
1 ATTTTTAA--T-TTTTAA
1015657 ATTTTTAATATTTTA
1 ATTTTTAAT-TTTTA
1015672 TACTAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
16 20 0.48
17 8 0.19
18 12 0.29
19 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTAATTTTTAA
Found at i:1021822 original size:20 final size:20
Alignment explanation
Indices: 1021797--1021845 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1021787 AAGTCCGGTG
*
1021797 GTATCGATATTTTTAGAA-AA
1 GTATCGATAATTTTA-AATAA
*
1021817 GTATCGATAATTTTAAATTA
1 GTATCGATAATTTTAAATAA
1021837 GTATCGATA
1 GTATCGATA
1021846 CCAAATTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (20 bp):
GTATCGATAATTTTAAATAA
Found at i:1043466 original size:21 final size:21
Alignment explanation
Indices: 1043442--1043481 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1043432 GTGGGTATTG
1043442 AGGAAGAGAAAGAA-GAAGACA
1 AGGAAGAGAAA-AAGGAAGACA
*
1043463 AGGAGGAGAAAAAGGAAGA
1 AGGAAGAGAAAAAGGAAGA
1043482 AAGAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.60, C:0.03, G:0.38, T:0.00
Consensus pattern (21 bp):
AGGAAGAGAAAAAGGAAGACA
Found at i:1043937 original size:17 final size:17
Alignment explanation
Indices: 1043917--1043955 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1043907 ATTGTGATCA
1043917 CATTTTAATTGTCCATG
1 CATTTTAATTGTCCATG
* **
1043934 CATTTTATTTGTTGATG
1 CATTTTAATTGTCCATG
1043951 CATTT
1 CATTT
1043956 GCATTGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.54
Consensus pattern (17 bp):
CATTTTAATTGTCCATG
Found at i:1054050 original size:26 final size:26
Alignment explanation
Indices: 1053991--1054053 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
1053981 ATTCACACAG
*
1053991 CGATAACTT-TGAACAAGTTCATGTAG
1 CGATAA-TTCTGAACAAGTTCATGTAA
* *
1054017 CGACAATTCTGAACAAGTTCTTGTAA
1 CGATAATTCTGAACAAGTTCATGTAA
*
1054043 TGATAATTCTG
1 CGATAATTCTG
1054054 GGTGTAATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (26 bp):
CGATAATTCTGAACAAGTTCATGTAA
Found at i:1054689 original size:21 final size:21
Alignment explanation
Indices: 1054664--1054720 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1054654 AGTGCAGTCC
* *
1054664 TCTACCGATACAAGTGGCAGT
1 TCTACCGATACAAGTGACACT
* *
1054685 TCTACCAATACAAGTGACTCT
1 TCTACCGATACAAGTGACACT
*
1054706 TCTACCGAAACAAGT
1 TCTACCGATACAAGT
1054721 CTTACTTCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (21 bp):
TCTACCGATACAAGTGACACT
Found at i:1055806 original size:52 final size:52
Alignment explanation
Indices: 1055467--1055805 Score: 466
Period size: 52 Copynumber: 6.6 Consensus size: 52
1055457 TTCATTTAAC
* * * * *
1055467 ACTCACGATAACACATAGTCATCGGACCTCTTAGTTCGTAAAGGATTCATGT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* *
1055519 ACTCACAATGACACAAAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* *
1055571 ACTCACGATGACAC--AGTCATTGGACCTCATAATCCGTATAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* *
1055621 ACTCATGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* * * * *
1055673 ACTCACAATGACACATAGTCATCGGATCTCATAATCCATAAAGTATTCTTAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* * ** * *
1055725 AATCATGATGGTACATAGTCATCGGACCTTATAATCCATAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
1055777 ACTCACGATGACACATAGTCATCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
1055806 TTTTGCATTT
Statistics
Matches: 251, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
50 47 0.19
52 204 0.81
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
Found at i:1059715 original size:5 final size:5
Alignment explanation
Indices: 1059691--1059729 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
1059681 TTTTATTGAA
* *
1059691 TTTAT TATTAT GTAAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1059730 TGTTTTTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:1060676 original size:2 final size:2
Alignment explanation
Indices: 1060669--1060696 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1060659 TATAGCTACT
1060669 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
1060697 GTTATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1066652 original size:52 final size:52
Alignment explanation
Indices: 1066424--1066651 Score: 357
Period size: 52 Copynumber: 4.4 Consensus size: 52
1066414 TCATTTGATA
* * * *
1066424 TCACGATGACACATAGTTATCGGACCTCATAATCTGAAAAGAATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
* *
1066476 TCACGATGAAACATAGTCATCGGACCCCATAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
*
1066528 TCACGATGGCACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
* * * *
1066580 CCACGTTGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCATGTAC
1 TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
1066632 TCACGATGACACATAGTCAT
1 TCACGATGACACATAGTCAT
1066652 TTGTCCTTTT
Statistics
Matches: 160, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 160 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (52 bp):
TCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATAC
Found at i:1069916 original size:22 final size:22
Alignment explanation
Indices: 1069891--1069934 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1069881 AGTTCATTAT
1069891 AGTATCATATAACTTTAGTCAA
1 AGTATCATATAACTTTAGTCAA
*
1069913 AGTATCGTATAACTTTAGTCAA
1 AGTATCATATAACTTTAGTCAA
1069935 TCTATTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (22 bp):
AGTATCATATAACTTTAGTCAA
Found at i:1071887 original size:52 final size:52
Alignment explanation
Indices: 1071790--1072023 Score: 317
Period size: 52 Copynumber: 4.5 Consensus size: 52
1071780 TCATTTGATA
* ** * * * *
1071790 TCACGATGACACATAGTCATCAGACTTCATAATCTGAAAACGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCACACAATCCGTAAAGGATTCATATAC
1071842 TCACGATGACACATAGTCATCGGACCACACAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCACACAATCCGTAAAGGATTCATATAC
** *
1071894 TCACGATGACACATAGTCATCGGACCTTACAATCCGTAAAGGATTCTTATAC
1 TCACGATGACACATAGTCATCGGACCACACAATCCGTAAAGGATTCATATAC
* *
1071946 TCACGATGACACATAGTTATCGGA-CATCATAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCGGACCA-CACAATCCGTAAAGGATTCATATAC
* * *
1071998 CCACAATGACACATAATCATCGGACC
1 TCACGATGACACATAGTCATCGGACC
1072024 TTTTGCATTT
Statistics
Matches: 161, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
51 1 0.01
52 159 0.99
53 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.24
Consensus pattern (52 bp):
TCACGATGACACATAGTCATCGGACCACACAATCCGTAAAGGATTCATATAC
Found at i:1073036 original size:16 final size:16
Alignment explanation
Indices: 1073012--1073042 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1073002 TTCTTACAAA
*
1073012 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
1073028 TTTAGTCCTTTAACA
1 TTTAGTCCTTTAACA
1073043 CTAAAATCAT
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:0.26, C:0.19, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:1077674 original size:16 final size:16
Alignment explanation
Indices: 1077650--1077682 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1077640 TCCTTACAAA
*
1077650 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
1077666 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
1077682 T
1 T
1077683 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:1083051 original size:18 final size:19
Alignment explanation
Indices: 1083010--1083051 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1083000 TATTTTTTCT
1083010 TTTTTCTTTTTTTTTTTGA
1 TTTTTCTTTTTTTTTTTGA
*
1083029 ATTTTC-TTTTTTTTTTGA
1 TTTTTCTTTTTTTTTTTGA
1083047 TTTTT
1 TTTTT
1083052 TTAATGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTTTTTTTTTGA
Found at i:1087006 original size:14 final size:14
Alignment explanation
Indices: 1086987--1087017 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1086977 ATTGTAAAAC
1086987 ATAAAATAAAGGAA
1 ATAAAATAAAGGAA
*
1087001 ATAAAATAAGGGAA
1 ATAAAATAAAGGAA
1087015 ATA
1 ATA
1087018 GATAGGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
ATAAAATAAAGGAA
Found at i:1093346 original size:38 final size:38
Alignment explanation
Indices: 1093303--1093380 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
1093293 ATTTGCTTGG
1093303 CCTTCGACCTCGTTATTGGGCCTTGAGAAAATTTGATC
1 CCTTCGACCTCGTTATTGGGCCTTGAGAAAATTTGATC
*
1093341 CCTTCGACCTCGTTATTGGGCCTTGAGAAACTTTGATC
1 CCTTCGACCTCGTTATTGGGCCTTGAGAAAATTTGATC
1093379 CC
1 CC
1093381 ATCACATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (38 bp):
CCTTCGACCTCGTTATTGGGCCTTGAGAAAATTTGATC
Found at i:1094181 original size:17 final size:18
Alignment explanation
Indices: 1094143--1094183 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1094133 GCAAATGCGT
*
1094143 TGACAAATAAAATACAGA
1 TGACAATTAAAATACAGA
*
1094161 -GACAATTAAAATATA-A
1 TGACAATTAAAATACAGA
1094177 TGACAAT
1 TGACAAT
1094184 GCAATTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (18 bp):
TGACAATTAAAATACAGA
Found at i:1102050 original size:21 final size:20
Alignment explanation
Indices: 1102009--1102052 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1101999 GAGTAAAGAA
* * *
1102009 AAATAAAACAAATTAGTAAC
1 AAATAAAAAAAATCAGAAAC
1102029 AAATAAAAAAAATCAGGAAAC
1 AAATAAAAAAAATCA-GAAAC
1102050 AAA
1 AAA
1102053 GAATAACTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.70, C:0.09, G:0.07, T:0.14
Consensus pattern (20 bp):
AAATAAAAAAAATCAGAAAC
Found at i:1114457 original size:20 final size:21
Alignment explanation
Indices: 1114419--1114458 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1114409 TAAATTAAGC
1114419 ATCACTAAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
1114440 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
1114459 TAAAAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:1135966 original size:43 final size:43
Alignment explanation
Indices: 1135901--1136003 Score: 161
Period size: 43 Copynumber: 2.4 Consensus size: 43
1135891 TACTAGACTG
* *
1135901 TGTGTCAATACTGACTTGGGTCAAACGATCGAGTCTCAGCCCA
1 TGTGTCTATACTGACTTAGGTCAAACGATCGAGTCTCAGCCCA
* * *
1135944 TGTGTCTATATTGACTTAGGTCACACGATCGAGTCTCAGCCCG
1 TGTGTCTATACTGACTTAGGTCAAACGATCGAGTCTCAGCCCA
1135987 TGTGTCTATACTGACTT
1 TGTGTCTATACTGACTT
1136004 GGGCCACATG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (43 bp):
TGTGTCTATACTGACTTAGGTCAAACGATCGAGTCTCAGCCCA
Found at i:1147201 original size:15 final size:16
Alignment explanation
Indices: 1147171--1147208 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1147161 AAATATTATA
1147171 AAATT-TAAAATAAAT
1 AAATTATAAAATAAAT
1147186 AAATTATAAAAT-AAT
1 AAATTATAAAATAAAT
1147201 AAA-TATAA
1 AAATTATAA
1147209 TATTGAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAATAAAT
Found at i:1147204 original size:23 final size:24
Alignment explanation
Indices: 1147165--1147210 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1147155 ACTTAAAAAT
*
1147165 ATTATAAAATTTAAAATA-AATAA
1 ATTATAAAATATAAAATATAATAA
1147188 ATTATAAAATA-ATAAATATAATA
1 ATTATAAAATATA-AAATATAATA
1147211 TTGAGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 15 0.75
24 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
ATTATAAAATATAAAATATAATAA
Found at i:1149943 original size:34 final size:34
Alignment explanation
Indices: 1149900--1150002 Score: 206
Period size: 34 Copynumber: 3.0 Consensus size: 34
1149890 TATATTATTG
1149900 GGTTTTATAAGTTTCTCCTTAGAATTAAAGCTTT
1 GGTTTTATAAGTTTCTCCTTAGAATTAAAGCTTT
1149934 GGTTTTATAAGTTTCTCCTTAGAATTAAAGCTTT
1 GGTTTTATAAGTTTCTCCTTAGAATTAAAGCTTT
1149968 GGTTTTATAAGTTTCTCCTTAGAATTAAAGCTTT
1 GGTTTTATAAGTTTCTCCTTAGAATTAAAGCTTT
1150002 G
1 G
1150003 ATCAATTAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (34 bp):
GGTTTTATAAGTTTCTCCTTAGAATTAAAGCTTT
Found at i:1153448 original size:15 final size:17
Alignment explanation
Indices: 1153428--1153460 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1153418 CTTATCAACA
1153428 AATTAAAC-TA-AAAAT
1 AATTAAACATATAAAAT
1153443 AATTAAACATATAAAAT
1 AATTAAACATATAAAAT
1153460 A
1 A
1153461 TAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AATTAAACATATAAAAT
Found at i:1156024 original size:16 final size:16
Alignment explanation
Indices: 1155978--1156024 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1155968 AATATATATT
1155978 TATATTATTTTATTTTA
1 TATATT-TTTTATTTTA
* *
1155995 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
1156011 TATATTTTTTATTT
1 TATATTTTTTATTT
1156025 ATTAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:1166014 original size:17 final size:18
Alignment explanation
Indices: 1165994--1166028 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1165984 ACAAGATCAA
1165994 AAGT-AAATCAAGTACTT
1 AAGTGAAATCAAGTACTT
*
1166011 AAGTGAAATCGAGTACTT
1 AAGTGAAATCAAGTACTT
1166029 CGTACTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (18 bp):
AAGTGAAATCAAGTACTT
Found at i:1175063 original size:35 final size:35
Alignment explanation
Indices: 1175005--1175072 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1174995 TCTTTTAAAA
* *
1175005 ATTTTAAAATTTTAAATTAATAAAATTGTAATTAC
1 ATTTTAAAATTTAAAAATAATAAAATTGTAATTAC
* * *
1175040 ATTTTAACATTTAAAAATGATAAAATTTTAATT
1 ATTTTAAAATTTAAAAATAATAAAATTGTAATT
1175073 TAATTTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (35 bp):
ATTTTAAAATTTAAAAATAATAAAATTGTAATTAC
Found at i:1175079 original size:35 final size:34
Alignment explanation
Indices: 1175004--1175101 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 34
1174994 ATCTTTTAAA
* *
1175004 AATTTTAAAATTTTAAATTAATAAAATTGTAATT
1 AATTTTAAAATTTAAAAATAATAAAATTGTAATT
* * *
1175038 ACATTTTAACATTTAAAAATGATAAAATTTTAATTT
1 A-ATTTTAAAATTTAAAAATAATAAAATTGTAA-TT
1175074 AATTTTTTAATAATTATAAAAAT-ATAAA
1 AA--TTTTAA-AATT-TAAAAATAATAAA
1175102 CTACTAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
34 1 0.02
35 27 0.52
36 3 0.06
37 6 0.12
38 8 0.15
39 7 0.13
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (34 bp):
AATTTTAAAATTTAAAAATAATAAAATTGTAATT
Found at i:1181962 original size:5 final size:5
Alignment explanation
Indices: 1181954--1181978 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1181944 AATCCAACCC
1181954 AATCA AATCA AATCA AATCA AATCA
1 AATCA AATCA AATCA AATCA AATCA
1181979 TCCATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AATCA
Found at i:1185944 original size:13 final size:13
Alignment explanation
Indices: 1185926--1185953 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1185916 TAGCCATTTC
1185926 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
1185939 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
1185952 AG
1 AG
1185954 GACATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:1192090 original size:2 final size:2
Alignment explanation
Indices: 1192083--1192109 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1192073 GTACTTTTAT
1192083 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1192110 GTGATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1197547 original size:18 final size:18
Alignment explanation
Indices: 1197524--1197558 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1197514 ATGCGCAGAG
*
1197524 ATAGCGGTCAATCCCAAT
1 ATAGCGGCCAATCCCAAT
1197542 ATAGCGGCCAATCCCAA
1 ATAGCGGCCAATCCCAA
1197559 GCTCTGTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (18 bp):
ATAGCGGCCAATCCCAAT
Found at i:1202927 original size:35 final size:35
Alignment explanation
Indices: 1202855--1202928 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
1202845 TATACAGTAG
** * * *
1202855 TGTGGTTTTGTTTACATTAACCATATATAGAGTAA
1 TGTGGTTTTGTTTACATTAAAAACACATAGAGCAA
*
1202890 TGTGGTTTTGTTTACATTAAAAACACATTGAGCAA
1 TGTGGTTTTGTTTACATTAAAAACACATAGAGCAA
1202925 TGTG
1 TGTG
1202929 CACATGCCGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (35 bp):
TGTGGTTTTGTTTACATTAAAAACACATAGAGCAA
Found at i:1204380 original size:53 final size:53
Alignment explanation
Indices: 1204333--1204495 Score: 299
Period size: 53 Copynumber: 3.1 Consensus size: 53
1204323 GGTGCGGAAC
* *
1204333 TAAATGTGCATTTGTCCAATCATGCATATAGGTTATGGTGTTGGGTGCAGTAG
1 TAAATGTGCATTCGTCCAATCATGCATATAGGTTACGGTGTTGGGTGCAGTAG
1204386 TAAATGTGCATTCGTCCAATCATGCATATAGGTTACGGTGTTGGGTGCAGTAG
1 TAAATGTGCATTCGTCCAATCATGCATATAGGTTACGGTGTTGGGTGCAGTAG
*
1204439 TAAATGTGCATCCGTCCAATCATGCATATAGGTTACGGTGTTGGGTGCAGTAG
1 TAAATGTGCATTCGTCCAATCATGCATATAGGTTACGGTGTTGGGTGCAGTAG
1204492 TAAA
1 TAAA
1204496 ACACATTGTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 107 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (53 bp):
TAAATGTGCATTCGTCCAATCATGCATATAGGTTACGGTGTTGGGTGCAGTAG
Found at i:1205560 original size:24 final size:24
Alignment explanation
Indices: 1205506--1205560 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1205496 TTCAATCAAT
* *
1205506 TTAATCAATTTTTAATCATAAAAA
1 TTAATAAATTTTTAATCAGAAAAA
*
1205530 TAAAATAAATTTTTAAT-AGAAAATA
1 T-TAATAAATTTTTAATCAGAAAA-A
1205555 TTAATA
1 TTAATA
1205561 TAGTAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TTAATAAATTTTTAATCAGAAAAA
Found at i:1214252 original size:228 final size:228
Alignment explanation
Indices: 1213855--1214723 Score: 988
Period size: 228 Copynumber: 3.8 Consensus size: 228
1213845 TAAGACTCTA
*
1213855 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAGGCCAAAAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
* * * *
1213920 CCAGGATAAGGAAGGCATCCCTCCAGACCAGCAGCGTCTGATCTTCGCCGGAAAACAGCTCGAAG
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCCGGAAAACAGCTCGAAG
* *
1213985 ACGGCCGGACTTTGGCCGATTACAACATCCAAAAGGAGTCAACTCTCCACCTTGTCCTCCGTTTG
131 ACGGCCGGACTTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTACGTTTG
* *
1214050 CGTGGTGGGATGCAAATCTTCGTGAAAACCTTG
196 CGAGGTGGGATGCAAATCTTCGTGAAGACCTTG
* * * * *
1214083 ACCGGCAAGACAATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTTAAGGCGAAGAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
* * *
1214148 CCAAGACAAGGAAGGCATCCCTCCAGATCAGCAACGTCTCATCTTCGCCGGAAAACAACTTGAAG
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCCGGAAAACAGCTCGAAG
* * * *
1214213 ACGGCCGTACCTTGGCCGACTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTTCGTTTG
131 ACGGCCGGACTTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTACGTTTG
* *
1214278 CGCGGCGGGATGCAAATCTTCGTGAAGACGCTT-
196 CGAGGTGGGATGCAAATCTTCGTGAAGAC-CTTG
* * *
1214311 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCTGATACGATAGACAACGTGAAAGCCAAAAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
* * * *
1214376 CCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTCATCTTCGCTGGAAAGCAGCTCGAGG
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCCGGAAAACAGCTCGAAG
* * * * * * * * *
1214441 ACGGGCGGACTTTAGCCGATTACAATATCCAGAAGGAATCGACTCTTCATCTGGTTCTACGTCTT
131 ACGGCCGGACTTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTACGT-TT
* * *
1214506 -CGAGGTGGGATGCAGATCTTCGTCAAGACTTTG
195 GCGAGGTGGGATGCAAATCTTCGTGAAGACCTTG
* * * * * * * * * * * *
1214539 ACCGGTAAGACGATTACTTTGGAAGTGGAGAGCTCGGATACGATTGATAACGTGAAAGCGAAGAT
1 ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
* * * * * * * * * * * * * * *
1214604 TCAGGACAAAGAAGGAATTCCACCAGATCAGCAAAGGT-TGATTTTTGCTGGGAAACAACTGGAA
66 CCAAGACAAGGAAGGCATCCCTCCAGACCAGC-AACGTCTCATCTTCGCCGGAAAACAGCTCGAA
* ** * * * * * *
1214668 GATGGAAGGACTTTGGCTGATTACAATATTCAAAAGGAGTCCACTCTTCACCTTGT
130 GACGGCCGGACTTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGT
1214724 TCTCCGTCTT
Statistics
Matches: 547, Mismatches: 90, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
227 2 0.00
228 536 0.98
229 9 0.02
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (228 bp):
ACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCCAAAAT
CCAAGACAAGGAAGGCATCCCTCCAGACCAGCAACGTCTCATCTTCGCCGGAAAACAGCTCGAAG
ACGGCCGGACTTTGGCCGATTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTACGTTTG
CGAGGTGGGATGCAAATCTTCGTGAAGACCTTG
Found at i:1214708 original size:456 final size:456
Alignment explanation
Indices: 1213830--1214723 Score: 1117
Period size: 456 Copynumber: 2.0 Consensus size: 456
1213820 AGCCAAACAA
* * * *
1213830 GATGCAGATCTTTGTTAAGACTCTAACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
1 GATGCAAATCTTCGTGAAGACGCTAACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
* * * * * * *
1213895 CGATCGACAACGTGAAGGCCAAAATCCAGGATAAGGAAGGCATCCCTCCAGACCAGCAGCGTCTG
66 CGATAGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC
* *
1213960 ATCTTCGCCGGAAAACAGCTCGAAGACGGCCGGACTTTGGCCGATTACAACATCCAAAAGGAGTC
131 ATCTTCGCCGGAAAACAGCTCGAAGACGGCCGGACTTTAGCCGATTACAACATCCAAAAGGAATC
* * * *
1214025 AACTCTCCACCTTGTCCTCCGTTTGCGTGGTGGGATGCAAATCTTCGTGAAAACCTTGACCGGCA
196 AACTCTCCACCTGGTCCTACGTTTGCGAGGTGGGATGCAAATCTTCGTCAAAACCTTGACCGGCA
* * *
1214090 AGACAATCACTCTCGAGGTCGAGAGCTCCGACACGATCGACAACGTTAAGGCGAAGATCCAAGAC
261 AGACAATCACTCTCGAAGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCGAAGATCCAAGAC
* * * * **
1214155 AAGGAAGGCATCCCTCCAGATCAGCAACGTCTCATCTTCGCCGGAAAACAACTTGAAGACGGCCG
326 AAAGAAGGAATCCCACCAGATCAGCAACGTCTCATCTTCGCCGGAAAACAACTGGAAGACGGAAG
* *
1214220 TACCTTGGCCGACTACAACATCCAGAAGGAGTCAACTCTCCACCTTGTCCTTCGTTTGCGCGGCG
391 GACCTTGGCCGACTACAACATCCAAAAGGAGTCAACTCTCCACCTTGTCCTTCGTTTGCGCGGCG
1214285 G
456 G
* * *
1214286 GATGCAAATCTTCGTGAAGACGCTTACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCTGATA
1 GATGCAAATCTTCGTGAAGACGCTAACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
1214351 CGATAGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC
66 CGATAGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC
* * * * * *
1214416 ATCTTCGCTGGAAAGCAGCTCGAGGACGGGCGGACTTTAGCCGATTACAATATCCAGAAGGAATC
131 ATCTTCGCCGGAAAACAGCTCGAAGACGGCCGGACTTTAGCCGATTACAACATCCAAAAGGAATC
* * * * * * * *
1214481 GACTCTTCATCTGGTTCTACGTCTT-CGAGGTGGGATGCAGATCTTCGTCAAGACTTTGACCGGT
196 AACTCTCCACCTGGTCCTACGT-TTGCGAGGTGGGATGCAAATCTTCGTCAAAACCTTGACCGGC
* * * * * * * * * * *
1214545 AAGACGATTACTTTGGAAGTGGAGAGCTCGGATACGATTGATAACGTGAAAGCGAAGATTCAGGA
260 AAGACAATCACTCTCGAAGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCGAAGATCCAAGA
* * * * * * * *
1214610 CAAAGAAGGAATTCCACCAGATCAGCAAAGGT-TGATTTTTGCTGGGAAACAACTGGAAGATGGA
325 CAAAGAAGGAATCCCACCAGATCAGC-AACGTCTCATCTTCGCCGGAAAACAACTGGAAGACGGA
* * * * * * *
1214674 AGGACTTTGGCTGATTACAATATTCAAAAGGAGTCCACTCTTCACCTTGT
389 AGGACCTTGGCCGACTACAACATCCAAAAGGAGTCAACTCTCCACCTTGT
1214724 TCTCCGTCTT
Statistics
Matches: 365, Mismatches: 71, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
456 359 0.98
457 6 0.02
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (456 bp):
GATGCAAATCTTCGTGAAGACGCTAACCGGCAAGACGATCACTCTCGAGGTCGAGAGCTCCGACA
CGATAGACAACGTGAAAGCCAAAATCCAAGACAAGGAAGGCATCCCGCCAGACCAGCAACGTCTC
ATCTTCGCCGGAAAACAGCTCGAAGACGGCCGGACTTTAGCCGATTACAACATCCAAAAGGAATC
AACTCTCCACCTGGTCCTACGTTTGCGAGGTGGGATGCAAATCTTCGTCAAAACCTTGACCGGCA
AGACAATCACTCTCGAAGTCGAGAGCTCCGACACGATCGACAACGTGAAAGCGAAGATCCAAGAC
AAAGAAGGAATCCCACCAGATCAGCAACGTCTCATCTTCGCCGGAAAACAACTGGAAGACGGAAG
GACCTTGGCCGACTACAACATCCAAAAGGAGTCAACTCTCCACCTTGTCCTTCGTTTGCGCGGCG
G
Found at i:1215215 original size:26 final size:25
Alignment explanation
Indices: 1215186--1215239 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1215176 AACTAATTAA
* *
1215186 ATTATTTAAAAATTTTCATTAAAATT
1 ATTATTCAAAAAGTTT-ATTAAAATT
*
1215212 ATTATTCAAAAAGTTTATTTAAATT
1 ATTATTCAAAAAGTTTATTAAAATT
1215237 ATT
1 ATT
1215240 GGACCGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTATTCAAAAAGTTTATTAAAATT
Found at i:1217912 original size:4 final size:4
Alignment explanation
Indices: 1217903--1217934 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1217893 TTTTGTCTTT
1217903 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1217935 TCAAAATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1218027 original size:15 final size:15
Alignment explanation
Indices: 1218007--1218036 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1217997 CAGATCACTT
1218007 TAATTGATGCCTTCA
1 TAATTGATGCCTTCA
1218022 TAATTGATGCCTTCA
1 TAATTGATGCCTTCA
1218037 ATCGTTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
TAATTGATGCCTTCA
Found at i:1231290 original size:23 final size:24
Alignment explanation
Indices: 1231231--1231310 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 24
1231221 AGCATGTTTC
*
1231231 GTGCCCTCTGT-TTAGTAC-T-GT
1 GTGCCCTCTGTATTAGCACTTCGT
* *
1231252 GTGTCCTCTGTTATTAGCAGTTCGT
1 GTGCCCTCTG-TATTAGCACTTCGT
*
1231277 GTGCCCTCTG-ATTAGCACTTTGT
1 GTGCCCTCTGTATTAGCACTTCGT
*
1231300 ATGCCCTCTGT
1 GTGCCCTCTGT
1231311 TACCCAGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 9 0.19
22 1 0.02
23 25 0.53
24 1 0.02
25 11 0.23
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.41
Consensus pattern (24 bp):
GTGCCCTCTGTATTAGCACTTCGT
Found at i:1233041 original size:4 final size:4
Alignment explanation
Indices: 1233025--1233054 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1233015 ACTTGAAATA
*
1233025 ATCT ATTT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT
1233055 ATATAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (4 bp):
ATCT
Found at i:1235884 original size:95 final size:95
Alignment explanation
Indices: 1235705--1235934 Score: 284
Period size: 95 Copynumber: 2.4 Consensus size: 95
1235695 TCTCTTGTCA
* * *
1235705 TGTCGTGTTGTGACATAAAATGATTAGTCAATTAATGTTTATTTCACA--TACATTCACTTGTGT
1 TGTCGTGTTGTGACATAAAATAATTAGTCAATTAA-----A-TTCA-ATGTGCATTCACTTGCGT
*
1235768 GCGACGACATAAGTCTTCACATATATCGATCCTGTTG
59 GCGACGACATAAGTCTTCACATATACCGATCCTGTTG
* * * *
1235805 TGTCGTGTTGTGACATAGAATAATTAGTCAGTTAAATTCAATGTGCATTCATTTGCGTGTGACGA
1 TGTCGTGTTGTGACATAAAATAATTAGTCAATTAAATTCAATGTGCATTCACTTGCGTGCGACGA
* *
1235870 CATAAGTTTTCACATATACCGATCTTGTTG
66 CATAAGTCTTCACATATACCGATCCTGTTG
*
1235900 TGTTGTGTTGTGACATAAAATAATTAGTCAATTAA
1 TGTCGTGTTGTGACATAAAATAATTAGTCAATTAA
1235935 TGTTTACTCT
Statistics
Matches: 115, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
93 1 0.01
94 4 0.03
95 78 0.68
100 32 0.28
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (95 bp):
TGTCGTGTTGTGACATAAAATAATTAGTCAATTAAATTCAATGTGCATTCACTTGCGTGCGACGA
CATAAGTCTTCACATATACCGATCCTGTTG
Found at i:1239021 original size:14 final size:13
Alignment explanation
Indices: 1238967--1239012 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1238957 TTTGTTCAAG
1238967 AAAA-AATATTTT
1 AAAATAATATTTT
* *
1238979 AAATTTCATA-TTT
1 AAA-ATAATATTTT
1238992 AAAATAATATTTT
1 AAAATAATATTTT
1239005 AAAATAAT
1 AAAATAAT
1239013 TTCTTTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 7 0.26
13 17 0.63
14 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATAATATTTT
Found at i:1240039 original size:30 final size:30
Alignment explanation
Indices: 1240005--1240104 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
1239995 CTTTCTTGTA
* * * * *
1240005 GCCTCTACTTCCCTCGCTTGCCTTGCTGTT
1 GCCTCTGCTTCCCTCGGTTCCCTCGCTGCT
*
1240035 GCCTCTGCTTCTCTCGGTTCCCTCGCTGCT
1 GCCTCTGCTTCCCTCGGTTCCCTCGCTGCT
1240065 GCCTCTGCTTCCCTCGGTTCCCTCGCTGCT
1 GCCTCTGCTTCCCTCGGTTCCCTCGCTGCT
1240095 GCCTCTGCTT
1 GCCTCTGCTT
1240105 TAAGTTGTAG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.01, C:0.43, G:0.19, T:0.37
Consensus pattern (30 bp):
GCCTCTGCTTCCCTCGGTTCCCTCGCTGCT
Found at i:1240188 original size:40 final size:40
Alignment explanation
Indices: 1240144--1240235 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
1240134 TTTAAATAAA
* ** * *
1240144 TTAGCGGTGCTTATTGGAAAGCGCTGCTAATGATCGATCT
1 TTAGCGGCGCTTAGGGGAAAGCGCCGCTAATGACCGATCT
*
1240184 TTAGCGGCGCTTGGGGGAAAGCGCCGCTAATGACCGATCT
1 TTAGCGGCGCTTAGGGGAAAGCGCCGCTAATGACCGATCT
*
1240224 TTAGCAGCGCTT
1 TTAGCGGCGCTT
1240236 GACCCGGCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (40 bp):
TTAGCGGCGCTTAGGGGAAAGCGCCGCTAATGACCGATCT
Found at i:1240236 original size:40 final size:40
Alignment explanation
Indices: 1240159--1240236 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
1240149 GGTGCTTATT
* * *
1240159 GGAAAGCGCTGCTAATGATCGATCTTTAGCGGCGCTTGGG
1 GGAAAGCGCCGCTAATGACCGATCTTTAGCAGCGCTTGGG
1240199 GGAAAGCGCCGCTAATGACCGATCTTTAGCAGCGCTTG
1 GGAAAGCGCCGCTAATGACCGATCTTTAGCAGCGCTTG
1240237 ACCCGGCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (40 bp):
GGAAAGCGCCGCTAATGACCGATCTTTAGCAGCGCTTGGG
Found at i:1240292 original size:41 final size:41
Alignment explanation
Indices: 1240235--1240313 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
1240225 TAGCAGCGCT
* *
1240235 TGACCCGGCCTTTAGCGGCGCTTGGGGGAAAGCGCCGCAAA
1 TGACCCGACCTTTAGCGGCGCTTAGGGGAAAGCGCCGCAAA
* *
1240276 TGACCCGACCTTTAGCGGCGCTTAGTGTAAAGCGCCGC
1 TGACCCGACCTTTAGCGGCGCTTAGGGGAAAGCGCCGC
1240314 TATTGCTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.18
Consensus pattern (41 bp):
TGACCCGACCTTTAGCGGCGCTTAGGGGAAAGCGCCGCAAA
Found at i:1246066 original size:5 final size:5
Alignment explanation
Indices: 1246056--1246080 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1246046 TAACGCAATT
1246056 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
1246081 CCAAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:1247113 original size:18 final size:17
Alignment explanation
Indices: 1247092--1247148 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
1247082 TTATCAAAAG
1247092 ATATATTAATTAATAATA
1 ATAT-TTAATTAATAATA
*
1247110 ATATTATAATAAATAATA
1 ATATT-TAATTAATAATA
* *
1247128 ATATTTTATTATTAATA
1 ATATTTAATTAATAATA
1247145 ATAT
1 ATAT
1247149 AAAATATAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.41
18 20 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTTAATTAATAATA
Found at i:1247126 original size:21 final size:20
Alignment explanation
Indices: 1247102--1247147 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1247092 ATATATTAAT
1247102 TAATAATAATATTATAATAAA
1 TAATAAT-ATATTATAATAAA
* * *
1247123 TAATAATATTTTATTATTAA
1 TAATAATATATTATAATAAA
1247143 TAATA
1 TAATA
1247148 TAAAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATAATATATTATAATAAA
Found at i:1254207 original size:16 final size:17
Alignment explanation
Indices: 1254168--1254211 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1254158 AGATAATTAC
*
1254168 ATTTATTTTTTAATTTA
1 ATTTATTATTTAATTTA
*
1254185 ATGTATTATTT-ATTTA
1 ATTTATTATTTAATTTA
*
1254201 TTTTATTATTT
1 ATTTATTATTT
1254212 CCACATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTATTATTTAATTTA
Found at i:1255193 original size:22 final size:22
Alignment explanation
Indices: 1255168--1255209 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1255158 TTTGATTGAG
* *
1255168 TTCGAGCTTAAATTTATTAGTA
1 TTCGAACTTAAATTAATTAGTA
*
1255190 TTCGAACTTAACTTAATTAG
1 TTCGAACTTAAATTAATTAG
1255210 AATCGAGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (22 bp):
TTCGAACTTAAATTAATTAGTA
Found at i:1267400 original size:23 final size:22
Alignment explanation
Indices: 1267373--1267418 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1267363 ATTAATATTT
1267373 TAATTAACATTTCTATTAAAAAA
1 TAATTAA-ATTTCTATTAAAAAA
* *
1267396 TAATTTAATTTCTTTTAAAAAA
1 TAATTAAATTTCTATTAAAAAA
1267418 T
1 T
1267419 TGATAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATTAAATTTCTATTAAAAAA
Found at i:1267800 original size:16 final size:16
Alignment explanation
Indices: 1267760--1267798 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1267750 AGTTAGTTAT
*
1267760 AATTTAAATGAATTTG
1 AATTTAAATGAATTTA
1267776 AATTTAAATG-ATTTA
1 AATTTAAATGAATTTA
1267791 AATTTAAA
1 AATTTAAA
1267799 ATCATTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
AATTTAAATGAATTTA
Found at i:1269561 original size:6 final size:6
Alignment explanation
Indices: 1269550--1269574 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1269540 CTGTTTGTAA
1269550 GCTCAT GCTCAT GCTCAT GCTCAT G
1 GCTCAT GCTCAT GCTCAT GCTCAT G
1269575 AGTTTACATG
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:0.16, C:0.32, G:0.20, T:0.32
Consensus pattern (6 bp):
GCTCAT
Found at i:1283920 original size:247 final size:249
Alignment explanation
Indices: 1283456--1283928 Score: 779
Period size: 247 Copynumber: 1.9 Consensus size: 249
1283446 TAGATTAGTG
* * * *
1283456 ATCACTGAGAAAGGAGTGTTATTTAACTGAAAAAAAAAACGAGGGAAGGAAGCAAAAAAAATATA
1 ATCACTGAGAAAGGAGAGTCATTTAACAGAAAAAAAAAACGAGGGAAGGAAGCAAAAAAAATACA
* * * *
1283521 GGGACCAAATTCTGAACTTTCAAAAAGTACAGGATTTATTACATATTTTAACCAAAAATGGATCG
66 GGGACCAAATTCTGAACTTTAAAAAAGTACAGGATTTATTACATATTTTAACAAAAAATGAATCC
1283586 AGTTGAACAGGGGACATGAACCCGACGTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACG
131 AGTTGAACAGGGGACATGAACCCGACGTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACG
*
1283651 CGCTACCATTGCGCCACGGATCCGTTGGCAACACTGAATAGCTTTGTAATTATT
196 CGCTACCATTGCGCCACGGATCCATTGGCAACACTGAATAGCTTTGTAATTATT
* * *
1283705 ATCACTGAG-AAGG-GAGTCATTTTACAGAAAAAAAAAGCGAGGGAAGGAAGCATAAAAAATACA
1 ATCACTGAGAAAGGAGAGTCATTTAACAGAAAAAAAAAACGAGGGAAGGAAGCAAAAAAAATACA
*
1283768 GGGACTAAATTCTGAACTTTAAAAAAGTACAGGATTTATTACATATTTTAACAAAAAATGAATCC
66 GGGACCAAATTCTGAACTTTAAAAAAGTACAGGATTTATTACATATTTTAACAAAAAATGAATCC
* * * *
1283833 AGTTGGACCGGGGTCTTGAACCCGACGTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACG
131 AGTTGAACAGGGGACATGAACCCGACGTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACG
1283898 CGCTACCATTGCGCCACGGATCCATTGGCAA
196 CGCTACCATTGCGCCACGGATCCATTGGCAA
1283929 TATTATTTAA
Statistics
Matches: 207, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
247 194 0.94
248 4 0.02
249 9 0.04
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (249 bp):
ATCACTGAGAAAGGAGAGTCATTTAACAGAAAAAAAAAACGAGGGAAGGAAGCAAAAAAAATACA
GGGACCAAATTCTGAACTTTAAAAAAGTACAGGATTTATTACATATTTTAACAAAAAATGAATCC
AGTTGAACAGGGGACATGAACCCGACGTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACG
CGCTACCATTGCGCCACGGATCCATTGGCAACACTGAATAGCTTTGTAATTATT
Found at i:1289286 original size:46 final size:46
Alignment explanation
Indices: 1289219--1289310 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
1289209 CACCCAAATG
1289219 CAAAACGACAACAAACCATAGGTATAAAACAAGAAATAGAATTACA
1 CAAAACGACAACAAACCATAGGTATAAAACAAGAAATAGAATTACA
*
1289265 CAAAACGACAACAAACCATAGGTATAAAACAATAAATAGAATTACA
1 CAAAACGACAACAAACCATAGGTATAAAACAAGAAATAGAATTACA
1289311 ACACCCAGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.14
Consensus pattern (46 bp):
CAAAACGACAACAAACCATAGGTATAAAACAAGAAATAGAATTACA
Found at i:1292565 original size:20 final size:20
Alignment explanation
Indices: 1292523--1292566 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1292513 AAATTATGAA
*
1292523 TTTTATCTGATTCAAATAGT
1 TTTTATCTGATTCAAATAAT
* *
1292543 TTTTATCTGATTCGACTAAT
1 TTTTATCTGATTCAAATAAT
1292563 TTTT
1 TTTT
1292567 TTACCAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.11, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTATCTGATTCAAATAAT
Found at i:1294590 original size:52 final size:52
Alignment explanation
Indices: 1294469--1294601 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 52
1294459 AAATTTAAAG
* *
1294469 TAAATAATAAAAAATTTTAATTTTAAAATATGTTTTAAAATTATTGTGTTACAAA
1 TAAATAAT-AAAAA--TTAAATTTAAAATATATTTTAAAATTATTGTGTTACAAA
1294524 TAAATAATAAAAATTAAATTTAAAATATATTTTAAAATTATTGT-TTACAAA
1 TAAATAATAAAAATTAAATTTAAAATATATTTTAAAATTATTGTGTTACAAA
*
1294575 T--A-AAT-AAATTTAAATTTAAAATATATT
1 TAAATAATAAAAATTAAATTTAAAATATATT
1294602 CCAACCGATA
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
47 21 0.28
48 3 0.04
49 1 0.01
51 8 0.11
52 29 0.39
54 5 0.07
55 8 0.11
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.43
Consensus pattern (52 bp):
TAAATAATAAAAATTAAATTTAAAATATATTTTAAAATTATTGTGTTACAAA
Found at i:1299801 original size:24 final size:24
Alignment explanation
Indices: 1299769--1299817 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1299759 AGGGAGGAGA
1299769 AAGCGGTGGGGTTTAGAACTGTTC
1 AAGCGGTGGGGTTTAGAACTGTTC
1299793 AAGCGGTGGGGTTTAGAACTGTTC
1 AAGCGGTGGGGTTTAGAACTGTTC
1299817 A
1 A
1299818 CCTTTGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.29
Consensus pattern (24 bp):
AAGCGGTGGGGTTTAGAACTGTTC
Found at i:1306675 original size:73 final size:73
Alignment explanation
Indices: 1306556--1306711 Score: 294
Period size: 73 Copynumber: 2.1 Consensus size: 73
1306546 TGTGAAAGAA
1306556 GTTCTATTTACACTTTAGTTAGGATTTAACAAACTCCCTGGGTTTTCCATATATAGTGTGCCACA
1 GTTCTATTTACACTTTAGTTAGGATTTAACAAACTCCCTGGGTTTTCCATATATAGTGTGCCACA
1306621 CTGCCATT
66 CTGCCATT
1306629 GTTCTATTTACACTTTAGTTAGGATTTAACAAACTCCCTGGGTTTTCCATATATAGTGTGCCACA
1 GTTCTATTTACACTTTAGTTAGGATTTAACAAACTCCCTGGGTTTTCCATATATAGTGTGCCACA
1306694 CTGCCATT
66 CTGCCATT
* *
1306702 GATGTATTTA
1 GTTCTATTTA
1306712 AATTTGGTGG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 81 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (73 bp):
GTTCTATTTACACTTTAGTTAGGATTTAACAAACTCCCTGGGTTTTCCATATATAGTGTGCCACA
CTGCCATT
Found at i:1307902 original size:22 final size:22
Alignment explanation
Indices: 1307876--1307925 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1307866 CCATTGCTTT
1307876 AATCGCTTTTGC-TTTTCCCAAC
1 AATCGCTTTT-CTTTTTCCCAAC
1307898 AATCGCTTTTCTTTTTCCCAAC
1 AATCGCTTTTCTTTTTCCCAAC
1307920 AATCGC
1 AATCGC
1307926 CTCCCCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.20, C:0.32, G:0.08, T:0.40
Consensus pattern (22 bp):
AATCGCTTTTCTTTTTCCCAAC
Found at i:1312052 original size:22 final size:22
Alignment explanation
Indices: 1312027--1312074 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1312017 TGTAATTCAC
1312027 TAAAGTTTTGTGAATCAAAATG
1 TAAAGTTTTGTGAATCAAAATG
1312049 TAAAGTTTTGTGAATCAAAATG
1 TAAAGTTTTGTGAATCAAAATG
1312071 TAAA
1 TAAA
1312075 ATCTCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (22 bp):
TAAAGTTTTGTGAATCAAAATG
Found at i:1313079 original size:75 final size:75
Alignment explanation
Indices: 1312928--1313760 Score: 854
Period size: 75 Copynumber: 11.1 Consensus size: 75
1312918 TTGCCTAGAT
* * * * * *
1312928 GAAGCCTGTTTACTGAACATGTTGAGTT-CAGTAGGTTCACAGGGTATGCCTTG-GTGCTCAGGT
1 GAAGCCTGTTTCCCGAACATGTTGA-TTCCAGTAGGTTCACAAGGCATGGCTTGAG-GTTCAGGT
* *
1312991 TCAAGAAACTTA
64 TCAGGAAATTTA
* * * * * *
1313003 GAAGCTTGTTTCCCGAACATGTTGAGTCCAGTGGGTTCACAAGGTATGGTTTGAGGTTCAGATTC
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
1313068 AGGAAATTTA
66 AGGAAATTTA
* * * * * * * *
1313078 GAAGCTTGTTTCCAGAAAATGTTTATTCCGGTGGGTTCACAAGACATGG-TTCGAAGTTCAGGTT
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTT-GAGGTTCAGGTT
*
1313142 CGGGAAATTTA
65 CAGGAAATTTA
* *
1313153 GAAGCCTGCTTCCC-AAAATTGTTGATTCCAGT-GGATTCACAAGGCATGGCTTGA-G----GG-
1 GAAGCCTGTTTCCCGAACA-TGTTGATTCCAGTAGG-TTCACAAGGCATGGCTTGAGGTTCAGGT
1313210 TCAGGAAATTTA
64 TCAGGAAATTTA
* * * * *
1313222 GATGCCTGCTTT-CCGAACATGTTGATTCCTGTTGTTTCACAAGGCATGGCTTGAGGTTCGGGTT
1 GAAGCCTG-TTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTT
1313286 CAGGAAATTTA
65 CAGGAAATTTA
* * * * *
1313297 GTAGCCTGTTTCCCGAAAATGTTGATTCCAGTTGGTTCAC-AGTGCATGGATTGAGTTTCAGGTT
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAG-GCATGGCTTGAGGTTCAGGTT
1313361 CAGGAAATTTA
65 CAGGAAATTTA
* * *
1313372 GAAGCCTGCTTT-CCAAACATGTTGATTCCAGCAGGTTCACAAGGCATGGCTAGAGGTTCAGGTT
1 GAAGCCTG-TTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTT
1313436 CAGGAAATTTA
65 CAGGAAATTTA
* * * ** * ** *
1313447 GAAGCCTGTTTTCCAAACACGTCAATTCCAATCTGTTCACAAGGTATGGCTTGAGGTTCAGGTTC
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
*
1313512 AGCAAATTTA
66 AGGAAATTTA
* * * * * *
1313522 GAAGCCTGCTTCCCGAACATGTGGATTCGAGCAGTTTCACAAGGCATGCCTTGAGGTTCAGGTTC
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
1313587 AGGAAATTTA
66 AGGAAATTTA
*
1313597 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGTCAGCATCGG-TTGAGTTTCAG
1 GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAG---GCAT-GGCTTGAGGTTCAG
1313661 GTTCAGGAAATTTA
62 GTTCAGGAAATTTA
* ** * ** *
1313675 GAAGGCC-GCTTT-CCAAACATGTTGATTCCACCAGGTTCACAGGGCATCACTTGAGGTTCAGGC
1 GAA-GCCTG-TTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGT
*
1313738 TCGGGAAATTTA
64 TCAGGAAATTTA
1313750 GAAGCCTGTTT
1 GAAGCCTGTTT
1313761 ACCAAAAACA
Statistics
Matches: 639, Mismatches: 91, Indels: 57
0.81 0.12 0.07
Matches are distributed among these distances:
69 51 0.08
70 9 0.01
74 26 0.04
75 479 0.75
76 8 0.01
78 59 0.09
79 7 0.01
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (75 bp):
GAAGCCTGTTTCCCGAACATGTTGATTCCAGTAGGTTCACAAGGCATGGCTTGAGGTTCAGGTTC
AGGAAATTTA
Found at i:1313369 original size:219 final size:217
Alignment explanation
Indices: 1312988--1313793 Score: 798
Period size: 219 Copynumber: 3.6 Consensus size: 217
1312978 TTGGTGCTCA
* * * * * * *
1312988 GGTTCAAGAAACTTAGAAGCTTG-TTTCCCGAACATGTTGAGTCCAGTGGGTTCACAAGGTATGG
1 GGTTCAGGAAATTTAGAAGCCTGCTTT-CCAAACATGTTGATTCCAGTTGGTTCACAAGGCATGG
* * * * * * *
1313052 TTTGAGGTTCAGATTCAGGAAATTTAGAAGCTTGTTTCCAGAAAATGTTTATTCCGGTGGGTTCA
65 CTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAAAATGTTGATTCCAGTAGGTTCA
* *
1313117 CAAGACATGGTTCGAAGTTCAGGTTCGGGAAATTTAGAAGCCTGCTTCCCAAAATTGTTGATTCC
130 CAAGGCATGGTT-G-AGTTCAGGTTCAGGAAATTTAGAAGCCTGCTTCCCAAAA-TGTTGATTCC
1313182 AGTGGATTCACAAGGCATGGCTTGAG-
192 AGTGG-TTCACAAGGCATGGCTTGAGT
* * * *
1313208 GG-TCAGGAAATTTAGATGCCTGCTTTCCGAACATGTTGATTCCTGTTGTTTCACAAGGCATGGC
1 GGTTCAGGAAATTTAGAAGCCTGCTTTCCAAACATGTTGATTCCAGTTGGTTCACAAGGCATGGC
* * *
1313272 TTGAGGTTCGGGTTCAGGAAATTTAGTAGCCTGTTTCCCGAAAATGTTGATTCCAGTTGGTTCAC
66 TTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAAAATGTTGATTCCAGTAGGTTCAC
*
1313337 -AGTGCATGGATTGAGTTTCAGGTTCAGGAAATTTAGAAGCCTGCTTTCCAAACATGTTGATTCC
131 AAG-GCATGG-TTGAG-TTCAGGTTCAGGAAATTTAGAAGCCTGCTTCCCAAA-ATGTTGATTCC
* *
1313401 AGCAGGTTCACAAGGCATGGCTAGAGGTT
192 AG-TGGTTCACAAGGCATGGCTTGA-G-T
* * ** * *
1313430 CAGGTTCAGGAAATTTAGAAGCCTGTTTTCCAAACACGTCAATTCCAATCT-GTTCACAAGGTAT
1 --GGTTCAGGAAATTTAGAAGCCTGCTTTCCAAACATGTTGATTCCAGT-TGGTTCACAAGGCAT
* * * * * * *
1313494 GGCTTGAGGTTCAGGTTCAGCAAATTTAGAAGCCTGCTTCCCGAACATGTGGATTCGAGCAGTTT
63 GGCTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAAAATGTTGATTCCAGTAGGTT
* * *
1313559 CACAAGGCATGCCTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAACATGTTGATT
128 CACAAGGCATG-GTTGA-GTTCAGGTTCAGGAAATTTAGAAGCCTGCTTCCC-AAAATGTTGATT
1313624 CCAGTAGGTTCACAAGTCAGCATCGG-TTGAGTTT
190 CCAGT-GGTTCACAAG---GCAT-GGCTTGAG--T
*** *
1313658 CAGGTTCAGGAAATTTAGAAGGCC-GCTTTCCAAACATGTTGATTCCACCAGGTTCACAGGGCAT
1 --GGTTCAGGAAATTTAGAA-GCCTGCTTTCCAAACATGTTGATTCCAGTTGGTTCACAAGGCAT
** * * * * ** ** *
1313722 CACTTGAGGTTCAGGCTCGGGAAATTTAGAAGCCTGTTTACCAAAAACATCAATTCCAGTGGGTT
63 GGCTTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAAAATGTTGATTCCAGTAGGTT
1313787 CACAAGG
128 CACAAGG
1313794 TATAGCTCGG
Statistics
Matches: 486, Mismatches: 75, Indels: 42
0.81 0.12 0.07
Matches are distributed among these distances:
218 4 0.01
219 175 0.36
220 11 0.02
224 2 0.00
225 168 0.35
226 6 0.01
227 1 0.00
228 114 0.23
229 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (217 bp):
GGTTCAGGAAATTTAGAAGCCTGCTTTCCAAACATGTTGATTCCAGTTGGTTCACAAGGCATGGC
TTGAGGTTCAGGTTCAGGAAATTTAGAAGCCTGTTTCCCGAAAATGTTGATTCCAGTAGGTTCAC
AAGGCATGGTTGAGTTCAGGTTCAGGAAATTTAGAAGCCTGCTTCCCAAAATGTTGATTCCAGTG
GTTCACAAGGCATGGCTTGAGT
Found at i:1317730 original size:31 final size:33
Alignment explanation
Indices: 1317689--1317762 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
1317679 ATTTTAATAA
* * *
1317689 TTTATAATTTTTGAAAGATTAAA-T-TAATTTT
1 TTTATTATTTTTGAGAAATTAAAATGTAATTTT
1317720 TTTATTATTTTTTGAGAAATTAAAATGTAATTTT
1 TTTATTA-TTTTTGAGAAATTAAAATGTAATTTT
*
1317754 ATTATTATT
1 TTTATTATT
1317763 AATTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 6 0.17
32 14 0.39
33 3 0.08
34 13 0.36
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (33 bp):
TTTATTATTTTTGAGAAATTAAAATGTAATTTT
Found at i:1317742 original size:32 final size:34
Alignment explanation
Indices: 1317696--1317762 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1317686 TAATTTATAA
*
1317696 TTTTTGAAAGATT-AAAT-TAATTTTTTTATTAT
1 TTTTTGAAAGATTAAAATGTAATTTTATTATTAT
1317728 TTTTTGAGAA-ATTAAAATGTAATTTTATTATTAT
1 TTTTTGA-AAGATTAAAATGTAATTTTATTATTAT
1317762 T
1 T
1317763 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 10 0.32
33 6 0.19
34 15 0.48
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (34 bp):
TTTTTGAAAGATTAAAATGTAATTTTATTATTAT
Found at i:1319094 original size:31 final size:29
Alignment explanation
Indices: 1319031--1319106 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
1319021 CTTTTAAAAT
* **
1319031 ATTTAAAATTTTTAAATTAATAATGATAAA
1 ATTT-AAATTTTTAAAATAATAAAAATAAA
*
1319061 ATTATAAATCTTTTAAAATAATAAAAATTAA
1 ATT-TAAAT-TTTTAAAATAATAAAAATAAA
1319092 ATTT-AATTTTTAAAA
1 ATTTAAATTTTTAAAA
1319107 AATTATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 8 0.20
29 3 0.08
30 8 0.20
31 21 0.52
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTTAAATTTTTAAAATAATAAAAATAAA
Found at i:1321138 original size:6 final size:6
Alignment explanation
Indices: 1321127--1321152 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1321117 ACATTGTATG
1321127 TATGTA TATGTA TATGTA TATGTA TA
1 TATGTA TATGTA TATGTA TATGTA TA
1321153 CATGCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:1322556 original size:2 final size:2
Alignment explanation
Indices: 1322549--1322574 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1322539 AAATTCGTAA
1322549 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
1322575 TCGAATCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1331357 original size:59 final size:59
Alignment explanation
Indices: 1331241--1331364 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 59
1331231 CATGGATCAG
* * ** *
1331241 AAAAAAGTTCAGGTCTCAATGTGAGAACAATTGCCAAATTCAGGGACGGACTAGGACAA
1 AAAAAAGTACAAGTCTCAATGTGAGAACAATTGCCAAATTCAAAGACGAACTAGGACAA
* * * ** *
1331300 ATAAAAGTACAAGTCTTAATGTGAGAACAATTGTCAGGTTCAAAGACGAACTTGGACAA
1 AAAAAAGTACAAGTCTCAATGTGAGAACAATTGCCAAATTCAAAGACGAACTAGGACAA
1331359 AAAAAA
1 AAAAAA
1331365 AATTAAGGCT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (59 bp):
AAAAAAGTACAAGTCTCAATGTGAGAACAATTGCCAAATTCAAAGACGAACTAGGACAA
Found at i:1343979 original size:61 final size:61
Alignment explanation
Indices: 1343910--1344038 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
1343900 GTATAGTGAG
** * *
1343910 AATTTTCAAAAA-TTTGAGGAGGGTTAACTAAAATTTT-TAAA-ATCTTCAAGAGATAAATGAA
1 AATTTTCAAAAATTTTGA-GA-GCCTAACTAAAATTTTCTAAATAT-TTCAAGAGAGAAATCAA
* *
1343971 AATTTTCAAAAATTTTGAGAGCCTAATTAAAATTTTCTAAATATTTCAAGGGAGAAATCAA
1 AATTTTCAAAAATTTTGAGAGCCTAACTAAAATTTTCTAAATATTTCAAGAGAGAAATCAA
1344032 AATTTTC
1 AATTTTC
1344039 CAATTTGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
60 13 0.22
61 39 0.66
62 7 0.12
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (61 bp):
AATTTTCAAAAATTTTGAGAGCCTAACTAAAATTTTCTAAATATTTCAAGAGAGAAATCAA
Found at i:1361444 original size:31 final size:31
Alignment explanation
Indices: 1361380--1361448 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1361370 TTACAAAATG
* * *
1361380 GTCATTTAATTATTTAAAAATTTTCATTTAA
1 GTCATTGAAGTATTTAAAAATTTTCATTCAA
* **
1361411 GTCATTGAAGTATTTGAAAATTTTTGTTCAA
1 GTCATTGAAGTATTTAAAAATTTTCATTCAA
1361442 GTCATTG
1 GTCATTG
1361449 GATTGTTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (31 bp):
GTCATTGAAGTATTTAAAAATTTTCATTCAA
Found at i:1367942 original size:23 final size:22
Alignment explanation
Indices: 1367807--1367953 Score: 107
Period size: 23 Copynumber: 6.5 Consensus size: 22
1367797 AGTGTTGAGG
*
1367807 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACATAGTGC
* * * *
1367829 AATCCAGTAGGCACACACAATGC
1 AA-ACAGTAAGCACACATAGTGC
* * *
1367852 AATCAGTAAGCGCACATAGCGC
1 AAACAGTAAGCACACATAGTGC
* * *
1367874 AAATCAGTAGGCGCACATAGCGC
1 AAA-CAGTAAGCACACATAGTGC
* *
1367897 AAATCAGTAGGCACACGA-GGTGC
1 AAA-CAGTAAGCACAC-ATAGTGC
1367920 GAAACAGTAAGCACACATAGTGC
1 -AAACAGTAAGCACACATAGTGC
*
1367943 TGAACAGTAAG
1 -AAACAGTAAG
1367954 TGCGCTAGCG
Statistics
Matches: 102, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.19
23 79 0.77
24 4 0.04
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.13
Consensus pattern (22 bp):
AAACAGTAAGCACACATAGTGC
Found at i:1368055 original size:24 final size:26
Alignment explanation
Indices: 1368017--1368064 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
1368007 TCTACATGGG
1368017 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
1368043 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
1368065 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.