Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 10 of 206
Found at i:2970884 original size:18 final size:18
Alignment explanation
Indices: 2970861--2970895 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2970851 ATAAATTTTT
2970861 TTTTTACAAT-TTTTATAA
1 TTTTTA-AATATTTTATAA
2970879 TTTTTAAATATTTTATA
1 TTTTTAAATATTTTATA
2970896 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATATTTTATAA
Found at i:2971689 original size:36 final size:36
Alignment explanation
Indices: 2971649--2971720 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
2971639 TATCGCTATA
*
2971649 AAATTTAATATTATTTTATACTAAACACAGTTAAAC
1 AAATTTAATATTATTTTACACTAAACACAGTTAAAC
2971685 AAATTTAATATTATTTTACACTAAACACAGTTAAAC
1 AAATTTAATATTATTTTACACTAAACACAGTTAAAC
2971721 GGACCGCTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (36 bp):
AAATTTAATATTATTTTACACTAAACACAGTTAAAC
Found at i:2973419 original size:56 final size:56
Alignment explanation
Indices: 2973352--2973463 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
2973342 TATAAATTTC
* *
2973352 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCGTGTGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
2973408 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
1 ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
2973464 CATTACATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.36
Consensus pattern (56 bp):
ATTTTACCCATTCTCCACTCCACTCTCCCCATTCCATTATCATATGTCAATTCAAA
Found at i:2979923 original size:18 final size:18
Alignment explanation
Indices: 2979900--2979944 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
2979890 AAAATTCATG
2979900 TTTAATTTTACATAAATT
1 TTTAATTTTACATAAATT
*
2979918 TTTAA-TATACATAAATT
1 TTTAATTTTACATAAATT
*
2979935 TTTACTTTTA
1 TTTAATTTTA
2979945 TCGTAAGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATTTTACATAAATT
Found at i:2982924 original size:2 final size:2
Alignment explanation
Indices: 2982917--2982941 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2982907 TATGTTATCG
2982917 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 A
2982942 AACACAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2984143 original size:22 final size:22
Alignment explanation
Indices: 2984116--2984170 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2984106 ATAATAACAA
*
2984116 CAAAATAGTAACAATACAATAG
1 CAAAATAGTAACAAAACAATAG
*
2984138 CGAAAT-GATAACAAAACAATAG
1 CAAAATAG-TAACAAAACAATAG
*
2984160 CAAAAAAGTAA
1 CAAAATAGTAA
2984171 AACAACAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.15
Consensus pattern (22 bp):
CAAAATAGTAACAAAACAATAG
Found at i:2987361 original size:27 final size:27
Alignment explanation
Indices: 2987311--2987389 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
2987301 TTGGGGTCTT
* **
2987311 CCTCATCTTCTTCCTCAGTTGAAGAC-
1 CCTCTTCTTCTTCCTCAGAAGAAGACA
*
2987337 CCTTCTTCTTCTTCCTCAGAAGAAGTCA
1 CC-TCTTCTTCTTCCTCAGAAGAAGACA
* * *
2987365 CCTCTTCATCTTCTTCAGAGGAAGA
1 CCTCTTCTTCTTCCTCAGAAGAAGA
2987390 AGCGGCTGGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
26 2 0.05
27 39 0.91
28 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
CCTCTTCTTCTTCCTCAGAAGAAGACA
Found at i:2987886 original size:9 final size:9
Alignment explanation
Indices: 2987872--2987938 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
2987862 TTTGGTTAAA
2987872 AATTAACCG
1 AATTAACCG
*
2987881 AATTAACCT
1 AATTAACCG
*
2987890 AATTACCCG
1 AATTAACCG
2987899 AATTAACCG
1 AATTAACCG
*
2987908 AATTAACCA
1 AATTAACCG
*
2987917 AATTACCCG
1 AATTAACCG
*
2987926 AATTAACCA
1 AATTAACCG
2987935 AATT
1 AATT
2987939 GAATCACTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:2987910 original size:27 final size:27
Alignment explanation
Indices: 2987872--2987938 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
2987862 TTTGGTTAAA
*
2987872 AATTAACCGAATTAACCTAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
2987899 AATTAACCGAATTAACCAAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
*
2987926 AATTAACCAAATT
1 AATTAACCGAATT
2987939 GAATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.25
Consensus pattern (27 bp):
AATTAACCGAATTAACCAAATTACCCG
Found at i:2988073 original size:18 final size:18
Alignment explanation
Indices: 2988033--2988076 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2988023 AATTTTTATG
**
2988033 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
2988051 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
2988069 CTTGGGTT
1 ATTGGGTT
2988077 TGGATTGGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:2988619 original size:10 final size:9
Alignment explanation
Indices: 2988594--2988806 Score: 65
Period size: 9 Copynumber: 22.2 Consensus size: 9
2988584 ATGATTAAAA
*
2988594 ATAAAAATCA
1 ATAAAAAT-T
*
2988604 ATAAAAGTT
1 ATAAAAATT
2988613 ATAAAAATT
1 ATAAAAATT
**
2988622 ATTAAATTTT
1 A-TAAAAATT
2988632 AATAAAAAATT
1 -AT-AAAAATT
2988643 ATAAAAA-T
1 ATAAAAATT
2988651 ATTAAAAATT
1 A-TAAAAATT
* *
2988661 AGAAAAGTT
1 ATAAAAATT
* *
2988670 TTAAAATTAT
1 ATAAAAAT-T
2988680 ATAAAAATT
1 ATAAAAATT
* *
2988689 GTAAAAAATG
1 AT-AAAAATT
2988699 AT-AAAATAT
1 ATAAAAAT-T
*
2988708 ATAGAAATAT
1 ATAAAAAT-T
*
2988718 AGGAAAAATTT
1 A-TAAAAA-TT
*
2988729 TTAAAATATT
1 ATAAAA-ATT
* *
2988739 AT-AAAGTC
1 ATAAAAATT
2988747 ATAAGAAAATT
1 AT-A-AAAATT
*
2988758 ATAAAAAAT
1 ATAAAAATT
* *
2988767 GTAAAGAAAT
1 ATAAA-AATT
2988777 AT-AAAATT
1 ATAAAAATT
*
2988785 CGTAAAAAATT
1 -AT-AAAAATT
*
2988796 ATAAACATT
1 ATAAAAATT
2988805 AT
1 AT
2988807 CGTACTAAAA
Statistics
Matches: 149, Mismatches: 35, Indels: 39
0.67 0.16 0.17
Matches are distributed among these distances:
8 13 0.09
9 58 0.39
10 53 0.36
11 24 0.16
12 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2988842 original size:11 final size:10
Alignment explanation
Indices: 2988823--2988858 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
2988813 AAAAGAAGCA
2988823 TTTTATAATT
1 TTTTATAATT
2988833 TTTCTATAA-T
1 TTT-TATAATT
2988843 TTTTATAATT
1 TTTTATAATT
2988853 TTTTAT
1 TTTTAT
2988859 TTTTTCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 5 0.21
10 14 0.58
11 5 0.21
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:2989002 original size:10 final size:10
Alignment explanation
Indices: 2988989--2989047 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 10
2988979 TTTTTATGCA
2988989 TTTTATAATT
1 TTTTATAATT
*
2988999 TTTTATCA-T
1 TTTTATAATT
**
2989008 TTTTATAAAA
1 TTTTATAATT
2989018 TTTTAT-A-T
1 TTTTATAATT
2989026 TTTTAT-ATT
1 TTTTATAATT
*
2989035 TTTTCTAATT
1 TTTTATAATT
2989045 TTT
1 TTT
2989048 ATATTTTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
8 7 0.17
9 15 0.37
10 19 0.46
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:2989002 original size:19 final size:19
Alignment explanation
Indices: 2988978--2989054 Score: 81
Period size: 18 Copynumber: 4.2 Consensus size: 19
2988968 TAAATGACAT
2988978 TTTTTTATGCA-TTTTATAA
1 TTTTTTAT-CATTTTTATAA
2988997 TTTTTTATCATTTTTATAA
1 TTTTTTATCATTTTTATAA
**
2989016 AATTTTAT-ATTTTTAT-A
1 TTTTTTATCATTTTTATAA
* *
2989033 TTTTTTCTAATTTTTAT-A
1 TTTTTTATCATTTTTATAA
2989051 TTTT
1 TTTT
2989055 ACATTTTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.12
18 23 0.45
19 22 0.43
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (19 bp):
TTTTTTATCATTTTTATAA
Found at i:2989008 original size:18 final size:18
Alignment explanation
Indices: 2988978--2989038 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
2988968 TAAATGACAT
2988978 TTTTTTATGCATTTTATAA
1 TTTTTTAT-CATTTTATAA
2988997 TTTTTTATCATTTTTATAA
1 TTTTTTATCA-TTTTATAA
**
2989016 AATTTTAT-ATTTT-TATA
1 TTTTTTATCATTTTATA-A
2989033 TTTTTT
1 TTTTTT
2989039 CTAATTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.06
17 9 0.25
18 3 0.08
19 22 0.61
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTTATCATTTTATAA
Found at i:2989029 original size:8 final size:8
Alignment explanation
Indices: 2988998--2989064 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 8
2988988 ATTTTATAAT
2988998 TTTTTATCA
1 TTTTTAT-A
2989007 TTTTTATAAA
1 TTTTTAT--A
*
2989017 ATTTTATA
1 TTTTTATA
2989025 TTTTTATA
1 TTTTTATA
*
2989033 TTTTTTCTAA
1 -TTTTTAT-A
2989043 TTTTTATA
1 TTTTTATA
*
2989051 -TTTTACA
1 TTTTTATA
2989058 TTTTTAT
1 TTTTTAT
2989065 TAAAATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
7 6 0.13
8 14 0.30
9 19 0.40
10 8 0.17
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTTATA
Found at i:2989035 original size:26 final size:26
Alignment explanation
Indices: 2988988--2989111 Score: 101
Period size: 25 Copynumber: 4.6 Consensus size: 26
2988978 TTTTTTATGC
2988988 ATTTTATAATTTTTTATCATTTTTATAAA
1 ATTTTAT-A-TTTTTAT-ATTTTTATAAA
**
2989017 ATTTTATATTTTTATATTTTT-TCTA
1 ATTTTATATTTTTATATTTTTATAAA
*
2989042 ATTTT-TATATTTTACATTTTTATTAAA
1 ATTTTATAT-TTTTATATTTTTA-TAAA
* * **
2989069 ATTTAATATTTTTTATAACTTTTATTTA
1 ATTTTATA-TTTTTAT-ATTTTTATAAA
2989097 ATTTTAT-TTTTTATA
1 ATTTTATATTTTTATA
2989112 AATTTTTTGC
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
24 3 0.04
25 19 0.24
26 13 0.17
27 13 0.17
28 16 0.21
29 14 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (26 bp):
ATTTTATATTTTTATATTTTTATAAA
Found at i:2989105 original size:52 final size:51
Alignment explanation
Indices: 2988999--2989110 Score: 138
Period size: 52 Copynumber: 2.1 Consensus size: 51
2988989 TTTTATAATT
*
2988999 TTTTATCATTTTTATAAAATTTTATATTTTTATATTTTTTCTAATTTTTATA
1 TTTTATCATTTTTATAAAATTTAATATTTTTATATTTTTTCTAA-TTTTATA
*
2989051 TTTTA-CATTTTTATTAAAATTTAATATTTTTTATAACTTTTATT-TAATTTTATT
1 TTTTATCATTTTTA-TAAAATTTAATA-TTTTTAT-A-TTTT-TTCTAATTTTATA
2989105 TTTTAT
1 TTTTAT
2989111 AAATTTTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
51 8 0.15
52 16 0.31
53 7 0.13
54 12 0.23
55 7 0.13
56 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (51 bp):
TTTTATCATTTTTATAAAATTTAATATTTTTATATTTTTTCTAATTTTATA
Found at i:2989112 original size:26 final size:27
Alignment explanation
Indices: 2988996--2989118 Score: 105
Period size: 26 Copynumber: 4.6 Consensus size: 27
2988986 GCATTTTATA
*
2988996 ATTTTTTATCATTTTTA-TAAAATTTT
1 ATTTTTTATAATTTTTATTAAAATTTT
*
2989022 ATATTTTTAT-ATTTTT-TCT-AATTTTT
1 AT-TTTTTATAATTTTTAT-TAAAATTTT
* *
2989048 ATATTTTA-CATTTTTATTAAAATTTAAT
1 ATTTTTTATAATTTTTATTAAAATTT--T
* *
2989076 ATTTTTTATAACTTTTATT-TAATTTT
1 ATTTTTTATAATTTTTATTAAAATTTT
2989102 ATTTTTTATAAATTTTT
1 ATTTTTTAT-AATTTTT
2989119 TGCCACATGG
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
25 12 0.15
26 32 0.41
27 14 0.18
28 13 0.16
29 8 0.10
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTTTATAATTTTTATTAAAATTTT
Found at i:2989338 original size:92 final size:89
Alignment explanation
Indices: 2989223--2989499 Score: 278
Period size: 93 Copynumber: 3.0 Consensus size: 89
2989213 CCAAAGAGCC
* *
2989223 TTTTTGATGCA-TTTGACAGTTCAAGTACCTAATTGAGTG-AAAAACAAAATCAGGAGCTTAATT
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGCAAAAA-AAAAT-AGGAGCTTAATT
*
2989286 ATTTTATTTTTTTGAAAAGTTTGA-GGCT
64 ACTTT-TTTTTTT--AAAGTTTGAGGGCT
* * *
2989314 TTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAAAGCAATGGCTTAA
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGC-AAAAAAAAATAG-GA--GCTTAA
* *
2989379 TTGCTTTTTTTTTTAAAGTTTGAGGGTT
62 TTACTTTTTTTTTTAAAGTTTGAGGGCT
* * * *
2989407 TTTTTTATGCATTTTAAAAGTTTAAGTA-CTCAATTGAATGCAAAAAAAAAAGTTGGAGCTTAAT
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCT-AATTGAGTGC-AAAAAAAAA-TAGGAGCTTAAT
* *
2989471 TAC-TTTTTTTTT-AATTTTGAGGGCA
63 TACTTTTTTTTTTAAAGTTTGAGGGCT
2989496 TTTT
1 TTTT
2989500 ACATACTTAA
Statistics
Matches: 158, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
89 14 0.09
90 9 0.06
91 19 0.12
92 39 0.25
93 53 0.34
94 13 0.08
95 11 0.07
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (89 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGCAAAAAAAAATAGGAGCTTAATTAC
TTTTTTTTTTAAAGTTTGAGGGCT
Found at i:2989480 original size:93 final size:95
Alignment explanation
Indices: 2989223--2989482 Score: 260
Period size: 92 Copynumber: 2.8 Consensus size: 95
2989213 CCAAAGAGCC
* * * * * **
2989223 TTTTTGATGCA-TTTGACAGTTCAAGTACCTAATTGAGTG--AAAAACAAAATCA-GGAGCTTAA
1 TTTTTTATGCATTTTAAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAAGAATGGAGCTTAA
2989284 TTA-TTTTATTTTTTTGAAAAGTTTGAGGCT
66 TTACTTTT-TTTTTTTGAAAAGTTTGAGGCT
*
2989314 TTTTTTATGCATTTTGAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAAAGCAAT-G-GCTT
1 TTTTTTATGCATTTTAAAAGTTCAAGTACCTAATTAAGTGC-AAAAAAAAAAAG-AATGGAGCTT
* *
2989377 AATTGC-TTTTTTTTTT--AAAGTTTGAGGGTT
64 AATTACTTTTTTTTTTTGAAAAGTTTGA-GGCT
* *
2989407 TTTTTTATGCATTTTAAAAGTTTAAGTA-CTCAATTGAA-TGC-AAAAAAAAAAG-TTGGAGCTT
1 TTTTTTATGCATTTTAAAAGTTCAAGTACCT-AATT-AAGTGCAAAAAAAAAAAGAATGGAGCTT
2989468 AATTACTTTTTTTTT
64 AATTACTTTTTTTTT
2989483 AATTTTGAGG
Statistics
Matches: 144, Mismatches: 12, Indels: 25
0.80 0.07 0.14
Matches are distributed among these distances:
89 1 0.01
90 1 0.01
91 30 0.21
92 45 0.31
93 36 0.25
94 9 0.06
95 20 0.14
96 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (95 bp):
TTTTTTATGCATTTTAAAAGTTCAAGTACCTAATTAAGTGCAAAAAAAAAAAGAATGGAGCTTAA
TTACTTTTTTTTTTTGAAAAGTTTGAGGCT
Found at i:3000400 original size:90 final size:90
Alignment explanation
Indices: 3000306--3000474 Score: 234
Period size: 90 Copynumber: 1.9 Consensus size: 90
3000296 ATTTAGTGGC
* * * *
3000306 TCATCCTATAAATTCGGT-AGGTTTATCAAGTCTGTCTCAATAGGACCACCCAAACTCT-AGGCT
1 TCATCCTATAAATTCGGTGA-ATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGA-GCA
*
3000369 GTGAACTCATTAAGAGCTTCTGGTAGT
64 ATGAACTCATTAAGAGCTTCTGGTAGT
* * *
3000396 TCATCCTATAAATTTGGTGAATTCATCAAGTCCGTCTTAGTAGGACCACCCAAACTCTGAGCAAT
1 TCATCCTATAAATTCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGAGCAAT
3000461 GAACTCATTAAGAG
66 GAACTCATTAAGAG
3000475 TAACAAACTC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 67 0.97
91 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (90 bp):
TCATCCTATAAATTCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGAGCAAT
GAACTCATTAAGAGCTTCTGGTAGT
Found at i:3000917 original size:15 final size:15
Alignment explanation
Indices: 3000893--3000922 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3000883 ATTTTATGGT
3000893 GGAGCAAGCAACACA
1 GGAGCAAGCAACACA
*
3000908 GGAGCGAGCAACACA
1 GGAGCAAGCAACACA
3000923 CGTCTGTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.30, T:0.00
Consensus pattern (15 bp):
GGAGCAAGCAACACA
Found at i:3024833 original size:6 final size:6
Alignment explanation
Indices: 3024822--3024854 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3024812 TTACACTATG
3024822 CTTTTT CTTTTT C-TTTT C-TTTT CTTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
3024855 ATATCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:3024845 original size:16 final size:16
Alignment explanation
Indices: 3024824--3024854 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3024814 ACACTATGCT
3024824 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
3024840 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
3024855 ATATCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:3030227 original size:15 final size:16
Alignment explanation
Indices: 3030217--3030249 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3030207 CAAAAATTAT
3030217 ATTTTTTAAAA-AATA
1 ATTTTTTAAAATAATA
3030232 ATTTTTTAAAATAA-A
1 ATTTTTTAAAATAATA
3030247 ATT
1 ATT
3030250 CTAAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTTTAAAATAATA
Found at i:3030227 original size:16 final size:15
Alignment explanation
Indices: 3030203--3030242 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3030193 ATTTATAAAA
* *
3030203 TTTTCAAAAATTATAT
1 TTTTTAAAAAATA-AT
3030219 TTTTTAAAAAATAAT
1 TTTTTAAAAAATAAT
3030234 TTTTTAAAA
1 TTTTTAAAA
3030243 TAAAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTTAAAAAATAAT
Found at i:3030282 original size:18 final size:18
Alignment explanation
Indices: 3030259--3030297 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3030249 TCTAAATAAT
3030259 ATATAAAGAAAATT-AAAA
1 ATATAAA-AAAATTCAAAA
3030277 ATATAAAAAAATTCAAAA
1 ATATAAAAAAATTCAAAA
3030295 ATA
1 ATA
3030298 ATATTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
ATATAAAAAAATTCAAAA
Found at i:3039359 original size:10 final size:10
Alignment explanation
Indices: 3039346--3039372 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3039336 AATTTAATTT
3039346 TGAAAGTATC
1 TGAAAGTATC
3039356 TGAAAGTATC
1 TGAAAGTATC
3039366 TGAAAGT
1 TGAAAGT
3039373 TTTTAAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (10 bp):
TGAAAGTATC
Found at i:3039911 original size:12 final size:11
Alignment explanation
Indices: 3039894--3039927 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
3039884 TTAATACAAA
3039894 AAATATGATTTT
1 AAATAT-ATTTT
3039906 AAATATA-TTT
1 AAATATATTTT
3039916 AAATATATTTT
1 AAATATATTTT
3039927 A
1 A
3039928 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 5 0.24
12 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
AAATATATTTT
Found at i:3041435 original size:35 final size:35
Alignment explanation
Indices: 3041396--3041467 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3041386 AATTTCGAAG
3041396 AAGAAATGTGATTATCATTATTTAATTTGGGAACA
1 AAGAAATGTGATTATCATTATTTAATTTGGGAACA
3041431 AAGAAATGTGATTATCATTATTTAATTTGGGAACA
1 AAGAAATGTGATTATCATTATTTAATTTGGGAACA
3041466 AA
1 AA
3041468 AATTGTGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (35 bp):
AAGAAATGTGATTATCATTATTTAATTTGGGAACA
Found at i:3046203 original size:2 final size:2
Alignment explanation
Indices: 3046150--3046191 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3046140 TAACTATCTC
3046150 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
3046192 TCTTAAATAT
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):
AT
Found at i:3049530 original size:6 final size:6
Alignment explanation
Indices: 3049519--3049558 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
3049509 GACACCGATC
*
3049519 TTCCCT TTCCCT TTCCCT TTCCC- TTCCCT TTCCCC TTCCC
1 TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT TTCCC
3049559 CTCCCCCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
TTCCCT
Found at i:3049547 original size:17 final size:17
Alignment explanation
Indices: 3049518--3049563 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
3049508 AGACACCGAT
3049518 CTTCCCTTTCCCTTTCCC
1 CTTCCC-TTCCCTTTCCC
*
3049536 TTTCCCTTCCCTTTCCC
1 CTTCCCTTCCCTTTCCC
*
3049553 CTTCCCCTCCC
1 CTTCCCTTCCC
3049564 CCTATCCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (17 bp):
CTTCCCTTCCCTTTCCC
Found at i:3052462 original size:22 final size:22
Alignment explanation
Indices: 3052434--3052477 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3052424 TTTCTGTTTA
3052434 ATATATAAATTTATTAATATAT
1 ATATATAAATTTATTAATATAT
3052456 ATATATAAATTTATTAATATAT
1 ATATATAAATTTATTAATATAT
3052478 GTAAAAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATATAAATTTATTAATATAT
Found at i:3052590 original size:25 final size:26
Alignment explanation
Indices: 3052562--3052610 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
3052552 CAAATTCTAG
*
3052562 AAAAGTAAATCA-TTTTCAGAAAAGT
1 AAAAGTAAATAATTTTTCAGAAAAGT
3052587 AAAAGTAAATAATTTTTCAGAAAA
1 AAAAGTAAATAATTTTTCAGAAAA
3052611 CATTTTACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (26 bp):
AAAAGTAAATAATTTTTCAGAAAAGT
Found at i:3052794 original size:12 final size:12
Alignment explanation
Indices: 3052777--3052801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3052767 GGTGTTCATT
3052777 CGGTTAACCGAC
1 CGGTTAACCGAC
3052789 CGGTTAACCGAC
1 CGGTTAACCGAC
3052801 C
1 C
3052802 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:3053025 original size:9 final size:9
Alignment explanation
Indices: 3052962--3053029 Score: 66
Period size: 9 Copynumber: 7.4 Consensus size: 9
3052952 TTTGGTTAAA
3052962 AATTACCCG
1 AATTACCCG
* *
3052971 AATTAACTG
1 AATTACCCG
3052980 AATTACCCG
1 AATTACCCG
* *
3052989 AATTAACCA
1 AATTACCCG
3052998 AATTA-CCG
1 AATTACCCG
*
3053006 AAAAATACCCG
1 --AATTACCCG
3053017 AATTACCCG
1 AATTACCCG
3053026 AATT
1 AATT
3053030 TTTTTATTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
8 2 0.04
9 38 0.81
10 4 0.09
11 3 0.06
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:3060770 original size:5 final size:5
Alignment explanation
Indices: 3060760--3060790 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3060750 TGAGCATTCG
3060760 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
3060791 AATTTTCGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:3061830 original size:9 final size:9
Alignment explanation
Indices: 3061816--3061852 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3061806 TATAGTTTGA
3061816 TATTCGAAT
1 TATTCGAAT
3061825 TATTCGAAT
1 TATTCGAAT
*
3061834 TATTCGAGT
1 TATTCGAAT
3061843 TATTCGAAT
1 TATTCGAAT
3061852 T
1 T
3061853 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3063365 original size:41 final size:37
Alignment explanation
Indices: 3063320--3063452 Score: 115
Period size: 37 Copynumber: 3.4 Consensus size: 37
3063310 GTTTGAGTTT
* *
3063320 ATGAGACACTGGGTGTCAATCTATCACTTCAGATTT-ATTCG
1 ATGAGGCACTGGGTGTCAAT-T-T-ACTTC-GATTTAACT-G
* * *
3063361 ATGAGGCACTAGGTGCCAATTTACTTCGGTTTAACTG
1 ATGAGGCACTGGGTGTCAATTTACTTCGATTTAACTG
* *
3063398 ATGAGGCACTGGGTGTCAATTTACTGCTTCGAATTATCTG
1 ATGAGGCACTGGGTGTCAATTTA---CTTCGATTTAACTG
*
3063438 ATGAGGCACTAGGTG
1 ATGAGGCACTGGGTG
3063453 CCAAATTGGT
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
37 26 0.34
38 7 0.09
39 1 0.01
40 26 0.34
41 17 0.22
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (37 bp):
ATGAGGCACTGGGTGTCAATTTACTTCGATTTAACTG
Found at i:3063401 original size:37 final size:38
Alignment explanation
Indices: 3063360--3063456 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 38
3063350 AGATTTATTC
**
3063360 GATGAGGCACTAGGTGCCAATTTA-CTTCGGTTTAACT
1 GATGAGGCACTAGGTGCCAATTTACCTTCGAATTAACT
* * *
3063397 GATGAGGCACTGGGTGTCAATTTACTGCTTCGAATTATCT
1 GATGAGGCACTAGGTGCCAATTTAC--CTTCGAATTAACT
3063437 GATGAGGCACTAGGTGCCAA
1 GATGAGGCACTAGGTGCCAA
3063457 ATTGGTGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 22 0.44
40 28 0.56
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (38 bp):
GATGAGGCACTAGGTGCCAATTTACCTTCGAATTAACT
Found at i:3072405 original size:27 final size:27
Alignment explanation
Indices: 3072367--3072421 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3072357 ACAATTAGAG
3072367 TTAGTTTTTCTTCCTCTGCTTGTCATA
1 TTAGTTTTTCTTCCTCTGCTTGTCATA
3072394 TTAGTTTTTCTTCCTCTGCTTGTCATA
1 TTAGTTTTTCTTCCTCTGCTTGTCATA
3072421 T
1 T
3072422 CTGGGGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.11, C:0.22, G:0.11, T:0.56
Consensus pattern (27 bp):
TTAGTTTTTCTTCCTCTGCTTGTCATA
Found at i:3078833 original size:20 final size:21
Alignment explanation
Indices: 3078808--3078857 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
3078798 TGACTCGAAT
3078808 GTATCGATACCCTTAACAA-A
1 GTATCGATACCCTTAACAACA
* *
3078828 GTATCGATACCTTTCACAACA
1 GTATCGATACCCTTAACAACA
3078849 GTATCGATA
1 GTATCGATA
3078858 TCATGCCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (21 bp):
GTATCGATACCCTTAACAACA
Found at i:3080901 original size:2 final size:2
Alignment explanation
Indices: 3080894--3080923 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3080884 TATTGATAAT
3080894 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
3080924 AATGAAACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3082674 original size:20 final size:19
Alignment explanation
Indices: 3082645--3082682 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3082635 ATATATCTTG
*
3082645 ATATTTTTTAGTTAAAATT
1 ATATTTTTTAATTAAAATT
3082664 ATATATTTTTAATTAAAAT
1 ATAT-TTTTTAATTAAAAT
3082683 AATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATTTTTTAATTAAAATT
Found at i:3082692 original size:21 final size:20
Alignment explanation
Indices: 3082649--3082688 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3082639 ATCTTGATAT
* * *
3082649 TTTTTAGTTAAAATTATATA
1 TTTTTAATTAAAATAATAAA
3082669 TTTTTAATTAAAATAATAAA
1 TTTTTAATTAAAATAATAAA
3082689 ATTTACAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTAATTAAAATAATAAA
Found at i:3086355 original size:3 final size:3
Alignment explanation
Indices: 3086347--3086381 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3086337 GCTAGAATGT
3086347 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CT
3086382 TCAGTGGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
CTG
Found at i:3091886 original size:15 final size:15
Alignment explanation
Indices: 3091862--3091894 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3091852 AACATTGGGG
3091862 TAAT-ATTAAATATA
1 TAATAATTAAATATA
3091876 TAATAATTAAATATA
1 TAATAATTAAATATA
3091891 -AATA
1 TAATA
3091895 CAATGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAATTAAATATA
Found at i:3099174 original size:2 final size:2
Alignment explanation
Indices: 3099167--3099204 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3099157 TTTTCTTTTC
3099167 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
3099205 TAAGGACCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3100226 original size:3 final size:3
Alignment explanation
Indices: 3100218--3100248 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3100208 AGCTCGTTGC
3100218 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3100249 CCAATTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3100990 original size:2 final size:2
Alignment explanation
Indices: 3100983--3101007 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3100973 ATTACAATGT
3100983 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 T
3101008 TATTTATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3109813 original size:3 final size:3
Alignment explanation
Indices: 3109787--3109841 Score: 53
Period size: 3 Copynumber: 18.0 Consensus size: 3
3109777 ATTAGCAATT
3109787 TTA TTA TTTA GTTAA TTA TT- TTA TTA TTA TT- TTCA TTA TTA -TA TTA
1 TTA TTA -TTA -TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
3109833 TTA TTA TTA
1 TTA TTA TTA
3109842 GTTTTATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
2 6 0.13
3 29 0.64
4 9 0.20
5 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3109813 original size:23 final size:22
Alignment explanation
Indices: 3109787--3109851 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
3109777 ATTAGCAATT
3109787 TTATTATTTAGTTAATTATTTTA
1 TTATTATTTAGTT-ATTATTTTA
*
3109810 TTATTATTTTCA-TTATTATATTA
1 TTATTA-TTT-AGTTATTATTTTA
3109833 TTATTA-TTAGTT-TTATTTT
1 TTATTATTTAGTTATTATTTT
3109852 CCTTTCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 7 0.19
21 4 0.11
23 20 0.54
24 5 0.14
25 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (22 bp):
TTATTATTTAGTTATTATTTTA
Found at i:3115063 original size:30 final size:30
Alignment explanation
Indices: 3115027--3115084 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
3115017 GTAGTCCAAG
3115027 GTGTTCTTATATATATACATATATATTGAA
1 GTGTTCTTATATATATACATATATATTGAA
3115057 GTGTTCTTATATATATACATATATATTG
1 GTGTTCTTATATATATACATATATATTG
3115085 TATATTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (30 bp):
GTGTTCTTATATATATACATATATATTGAA
Found at i:3122148 original size:19 final size:19
Alignment explanation
Indices: 3122116--3122153 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3122106 ATATAATTAA
* *
3122116 ATAAATTATTAAAAAAATC
1 ATAAAATATAAAAAAAATC
3122135 ATAAAATATAAAAAAAATC
1 ATAAAATATAAAAAAAATC
3122154 TAGTTCAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAATATAAAAAAAATC
Found at i:3123884 original size:20 final size:20
Alignment explanation
Indices: 3123821--3123885 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
3123811 AGAGATGAAT
* *
3123821 TGATTATTATAAGAATCGGG
1 TGATTATTAAAAGAATCGAG
**
3123841 TGAGCAGTTATAAAGAGATC-AG
1 TGATTA-TTA-AAAGA-ATCGAG
*
3123863 TGATTATTACAAGAATCGAG
1 TGATTATTAAAAGAATCGAG
3123883 TGA
1 TGA
3123886 GTAGTTATAC
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 13 0.38
21 6 0.18
22 9 0.26
23 3 0.09
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (20 bp):
TGATTATTAAAAGAATCGAG
Found at i:3125751 original size:17 final size:17
Alignment explanation
Indices: 3125729--3125763 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3125719 ATTCTTAGTC
*
3125729 CTATTATTAGTGCATGT
1 CTATTATTAGTCCATGT
3125746 CTATTATTAGTCCATGT
1 CTATTATTAGTCCATGT
3125763 C
1 C
3125764 ATTGAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (17 bp):
CTATTATTAGTCCATGT
Found at i:3133403 original size:82 final size:81
Alignment explanation
Indices: 3133253--3133561 Score: 375
Period size: 82 Copynumber: 4.0 Consensus size: 81
3133243 TACGTATGAT
* * * *
3133253 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCTCTT
3133316 GATCAGATAAGTGTAG
66 GATCAGATAAGTGTAG
3133332 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCTCT
* *
3133397 TAATCAGATAAGTTTAG
65 TGATCAGATAAGTGTAG
*
3133414 CACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T-A---ACCACTTATCACTTTGTTTCTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCTCTT
*
3133471 GATCAGATAAGTGTAAC
66 GATCAGATAAGTGT-AG
** *
3133488 CACTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-AG---CCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCTCTT
3133545 GATCAGATAAGTGTAG
66 GATCAGATAAGTGTAG
3133561 C
1 C
3133562 TAAAACTACC
Statistics
Matches: 210, Mismatches: 15, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
73 35 0.17
74 67 0.32
76 1 0.00
78 1 0.00
79 11 0.05
80 7 0.03
81 20 0.10
82 68 0.32
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (81 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCTCTT
GATCAGATAAGTGTAG
Found at i:3133560 original size:37 final size:37
Alignment explanation
Indices: 3133377--3133561 Score: 291
Period size: 37 Copynumber: 5.0 Consensus size: 37
3133367 GCTAAAGCTA
* *
3133377 CCACTTATCACTTTGTCTCTTAATCAGATAAGTTTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
3133414 -CACTTATCACTTTGTCACTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
* *
3133450 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3133487 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
*
3133524 CCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
3133561 C
1 C
3133562 TAAAACTACC
Statistics
Matches: 138, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
36 32 0.23
37 106 0.77
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
Found at i:3139808 original size:13 final size:13
Alignment explanation
Indices: 3139783--3139815 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3139773 TTCTAAAAAT
3139783 ATTAATT-AATTA
1 ATTAATTCAATTA
3139795 ATTAATTCAATTA
1 ATTAATTCAATTA
*
3139808 AATAATTC
1 ATTAATTC
3139816 TCTAAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTAATTCAATTA
Found at i:3140032 original size:27 final size:27
Alignment explanation
Indices: 3140002--3140064 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
3139992 GGTAATCGAA
3140002 AGGCGGCACCAAAGGTGCCTTTC-CGAT
1 AGGCGGCACCAAAGGTGCCTTTCTC-AT
* *
3140029 AGGCGGCACCGATGGTGCCTTTCTCAT
1 AGGCGGCACCAAAGGTGCCTTTCTCAT
*
3140056 AGGTGGCAC
1 AGGCGGCAC
3140065 AAGACTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.21
Consensus pattern (27 bp):
AGGCGGCACCAAAGGTGCCTTTCTCAT
Found at i:3140300 original size:27 final size:27
Alignment explanation
Indices: 3140244--3140306 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
3140234 TTTTAGTCCT
3140244 GTGCCGCCTATGAGAAAGGCACCATCG
1 GTGCCGCCTATGAGAAAGGCACCATCG
* * *
3140271 GTGTCGCCTATCG-GAAAGGCACCTTTG
1 GTGCCGCCTAT-GAGAAAGGCACCATCG
3140298 GTGCCGCCT
1 GTGCCGCCT
3140307 TTCCATTACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (27 bp):
GTGCCGCCTATGAGAAAGGCACCATCG
Found at i:3140390 original size:28 final size:28
Alignment explanation
Indices: 3140328--3140405 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
3140318 TCCTTCAGCC
3140328 TTTTTTTTTTTG-TATTATTTTGGTAAAT
1 TTTTTTTTTTTGTTATTATTTTGGT-AAT
*** *
3140356 AAATTTTTTTTGTATATTATTTTGGTATT
1 TTTTTTTTTTTGT-TATTATTTTGGTAAT
3140385 TTTTTTTCTTTTG-TATTATTT
1 TTTTTTT-TTTTGTTATTATTT
3140406 CAGTAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 17 0.43
29 6 0.15
30 17 0.43
ACGTcount: A:0.18, C:0.01, G:0.09, T:0.72
Consensus pattern (28 bp):
TTTTTTTTTTTGTTATTATTTTGGTAAT
Found at i:3141955 original size:12 final size:12
Alignment explanation
Indices: 3141938--3141962 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3141928 CAGCAGAAAG
3141938 GAGTGAAGAGAA
1 GAGTGAAGAGAA
3141950 GAGTGAAGAGAA
1 GAGTGAAGAGAA
3141962 G
1 G
3141963 GCATTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:3146791 original size:11 final size:11
Alignment explanation
Indices: 3146777--3146801 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3146767 ATCTTTCTCC
3146777 CCTAATTTTTT
1 CCTAATTTTTT
3146788 CCTAATTTTTT
1 CCTAATTTTTT
3146799 CCT
1 CCT
3146802 TATGGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (11 bp):
CCTAATTTTTT
Found at i:3154549 original size:2 final size:2
Alignment explanation
Indices: 3154542--3154581 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
3154532 GACTTTGTTT
*
3154542 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA -A CA 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
3154582 CATTTTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3156501 original size:24 final size:24
Alignment explanation
Indices: 3156474--3156520 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
3156464 AGAGGAAAGT
3156474 TTAAAGAACATAAAAGAAAAAAAA
1 TTAAAGAACATAAAAGAAAAAAAA
** * *
3156498 TTAAATTACTTAAAAGGAAAAAA
1 TTAAAGAACATAAAAGAAAAAAA
3156521 TATGGGGATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.68, C:0.04, G:0.09, T:0.19
Consensus pattern (24 bp):
TTAAAGAACATAAAAGAAAAAAAA
Found at i:3160932 original size:27 final size:25
Alignment explanation
Indices: 3160902--3160960 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
3160892 GGCCAATCAC
*
3160902 ATTGGCGGCACCAAAGGTGCCAAAGTG
1 ATTGGCGG-ACCAAA-GTGCCAAAGAG
*
3160929 ATTGGCCTGACCAAAGTGCCAAAGAG
1 ATTGG-CGGACCAAAGTGCCAAAGAG
3160955 ATTGGC
1 ATTGGC
3160961 CTGGCCGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 15 0.52
27 11 0.38
28 2 0.07
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.17
Consensus pattern (25 bp):
ATTGGCGGACCAAAGTGCCAAAGAG
Found at i:3160957 original size:26 final size:27
Alignment explanation
Indices: 3160911--3160963 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
3160901 CATTGGCGGC
*
3160911 ACCAAAGGTGCCAAAGTGATTGGCCTG
1 ACCAAAGGTGCCAAAGAGATTGGCCTG
3160938 ACCAAA-GTGCCAAAGAGATTGGCCTG
1 ACCAAAGGTGCCAAAGAGATTGGCCTG
3160964 GCCGGACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (27 bp):
ACCAAAGGTGCCAAAGAGATTGGCCTG
Found at i:3161724 original size:18 final size:17
Alignment explanation
Indices: 3161695--3161729 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3161685 GTAATGTTTC
*
3161695 AAAAAATGTTTTTAGGA
1 AAAAAATGTTTTAAGGA
3161712 AAAAAATGTTTTTAAGGA
1 AAAAAATG-TTTTAAGGA
3161730 GAAGTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (17 bp):
AAAAAATGTTTTAAGGA
Found at i:3162124 original size:27 final size:27
Alignment explanation
Indices: 3162091--3162142 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
3162081 TCAGGCTAAT
3162091 CTTTGGCACCTTTGGTGCCGCCAATCA
1 CTTTGGCACCTTTGGTGCCGCCAATCA
3162118 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCTTTGGTGCCGCCAAT
3162143 GTGATTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.13, C:0.33, G:0.23, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCTTTGGTGCCGCCAATCA
Found at i:3162198 original size:16 final size:15
Alignment explanation
Indices: 3162168--3162196 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3162158 AGGCTGTTGT
3162168 CAGGTTTTTTTTTTG
1 CAGGTTTTTTTTTTG
3162183 CAGGTTTTTTTTTT
1 CAGGTTTTTTTTTT
3162197 TGTTTTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (15 bp):
CAGGTTTTTTTTTTG
Found at i:3162261 original size:28 final size:27
Alignment explanation
Indices: 3162206--3162270 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 27
3162196 TTGTTTTGAT
****
3162206 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAAAAGATA
3162233 ATATTTTGGTAAATAAAAAAAAAAGATA
1 ATATTTTGGTAAAT-AAAAAAAAAGATA
*
3162261 ACATTTTGGT
1 ATATTTTGGT
3162271 TATTTTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAAAGATA
Found at i:3165038 original size:30 final size:30
Alignment explanation
Indices: 3165002--3165069 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
3164992 CTTAACTAAA
* *
3165002 AAAAGTTACAATTTGA-TCACTAAACAATTC
1 AAAAGTTAC-ATTTAAGTCACCAAACAATTC
* *
3165032 AAAAGTTTTCATTTAAGTCACCAAACTATTC
1 AAAAG-TTACATTTAAGTCACCAAACAATTC
3165063 AAAAGTT
1 AAAAGTT
3165070 TTGATTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (30 bp):
AAAAGTTACATTTAAGTCACCAAACAATTC
Found at i:3165065 original size:31 final size:32
Alignment explanation
Indices: 3165018--3165084 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
3165008 TACAATTTGA
*
3165018 TCACTAAACAATTCAAAAGTTTTCA-TTTAAG
1 TCACCAAACAATTCAAAAGTTTTCATTTTAAG
* *
3165049 TCACCAAACTATTCAAAAGTTTTGATTTTAAG
1 TCACCAAACAATTCAAAAGTTTTCATTTTAAG
3165081 TCAC
1 TCAC
3165085 AAGGTTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (32 bp):
TCACCAAACAATTCAAAAGTTTTCATTTTAAG
Found at i:3170801 original size:6 final size:6
Alignment explanation
Indices: 3170790--3170815 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3170780 GATCTTCATT
3170790 ATTCTC ATTCTC ATTCTC ATTCTC AT
1 ATTCTC ATTCTC ATTCTC ATTCTC AT
3170816 GTACCGTACT
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:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTCTC
Found at i:3179497 original size:22 final size:22
Alignment explanation
Indices: 3179469--3179621 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
3179459 TTTATTGTTC
*
3179469 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
3179491 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
3179513 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
3179535 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
3179557 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
3179579 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
3179601 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
3179622 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:3186335 original size:2 final size:2
Alignment explanation
Indices: 3186328--3186367 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3186318 ATTAGGTCTG
3186328 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
3186368 GGGTAAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3196294 original size:9 final size:9
Alignment explanation
Indices: 3196282--3196373 Score: 54
Period size: 9 Copynumber: 10.4 Consensus size: 9
3196272 TTTATTTTTT
3196282 AAAATTATA
1 AAAATTATA
3196291 AAAATT-TA
1 AAAATTATA
*
3196299 AAAAATATAA
1 AAAATTAT-A
*
3196309 AAATATTTTTA
1 AAA-A-TTATA
3196320 AAAATT-T-
1 AAAATTATA
3196327 AAAATT-T-
1 AAAATTATA
3196334 AAAATT-T-
1 AAAATTATA
* *
3196341 AAAATCATT
1 AAAATTATA
3196350 AAAATTATTAA
1 AAAATTA-T-A
3196361 AAAATTATA
1 AAAATTATA
3196370 AAAA
1 AAAA
3196374 CCAAAATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
7 19 0.28
8 9 0.13
9 20 0.29
10 7 0.10
11 12 0.17
12 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:3196372 original size:8 final size:7
Alignment explanation
Indices: 3196320--3196355 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
3196310 AATATTTTTA
3196320 AAAATTT
1 AAAATTT
3196327 AAAATTT
1 AAAATTT
3196334 AAAATTT
1 AAAATTT
3196341 AAAATCATT
1 AAAAT--TT
3196350 AAAATT
1 AAAATT
3196356 ATTAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 20 0.74
9 7 0.26
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (7 bp):
AAAATTT
Found at i:3197522 original size:12 final size:12
Alignment explanation
Indices: 3197502--3197545 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
3197492 ACACCTCTTA
*
3197502 TGTTTAAATTGC
1 TGTTCAAATTGC
3197514 TGTTCAAATTGC
1 TGTTCAAATTGC
3197526 TGTTCAAATTGC
1 TGTTCAAATTGC
3197538 TGTTCAAA
1 TGTTCAAA
3197546 CTGGCACTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (12 bp):
TGTTCAAATTGC
Found at i:3198689 original size:24 final size:23
Alignment explanation
Indices: 3198631--3198690 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
3198621 CTCCCACAGT
*
3198631 TTGGACTTCTTTGAAATTAACAA
1 TTGGACTTTTTTGAAATTAACAA
* * * *
3198654 TTGGAACCTTTTTGGAATTAATAG
1 TTGG-ACTTTTTTGAAATTAACAA
3198678 TTGGAGCTTTTTT
1 TTGGA-CTTTTTT
3198691 TAAAAATAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (23 bp):
TTGGACTTTTTTGAAATTAACAA
Found at i:3203503 original size:50 final size:50
Alignment explanation
Indices: 3203445--3204403 Score: 804
Period size: 50 Copynumber: 19.3 Consensus size: 50
3203435 GGGATCTGAC
* *
3203445 TTGTAGCTTCAATATTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * *
3203495 TTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTC-AGGGAAGTAAGATCCGCTG
3203545 TTGTAGCTTCAATCTTCTT-AATTGCAATGTCAGGGAAGTAAGATCCGCTG
1 TTGTAGCTTCAATCTT-TTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * ** *
3203595 TTGTAGCTTCAATCTGTTCCACTGCAA-CACTAGGAAAGTAAGATCCGCTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTC-AGGGAAGTAAGATCCGCTG
*
3203645 TTGTAGCTTCAATCTTCTT-AATTGCAATGTCAGGGAAGTAATATCCGCTG
1 TTGTAGCTTCAATCTT-TTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * ** ** * * *
3203695 TTGTAGCTTCAATCTGTTCCACTGCACCG-CCTGGAAATAAGATTCGCCG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * *
3203744 TTGTGGCCTCAATCTTTT-GATTGCAATGTCAGGGAAGTGAGATCTGCTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * * *
3203793 TTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGATCCACTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTC-AGGGAAGTAAGATCCGCTG
* * *
3203843 TT-TAGCTTTAATCTTCTT-AATTGCAACGTCAGGGAAGTAAGATCTGCTG
1 TTGTAGCTTCAATCTT-TTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * ** ** * * *
3203892 TTGTAGCTTCAATCTGTTCCACTGCACCG-CCTGGAAATAAGATTCGCCG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * * *
3203941 TTGTGGCATCAATCTTTT-GATTGCAATGTTAGGGAAGTGAGATCTGCTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * * *
3203990 TTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGATCCACTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTC-AGGGAAGTAAGATCCGCTG
*
3204040 TTGTAGCTTCAATCTTCTT-AATTGCAATGTCAGGGAAGTAAGATTCGCTG
1 TTGTAGCTTCAATCTT-TTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * ** * * *
3204090 TTGTAGCTTCAATCTGTTCCACTGCACTG-CCTGGAAATAAGATTCGCCG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * * ***
3204139 TTGTGGCCTCAATCTTTT-AATTACAATGTCAGGGAAGTGAGCTCTATTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * *
3204188 TTGTAGCTTCAATCTGTTCCAA-TGCAATG-CTAGGAAAGTAAGATTCGCTG
1 TTGTAGCTTCAATCT-TTTCAATTGCAATGTC-AGGGAAGTAAGATCCGCTG
* * * ** * * * **
3204238 TTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAAGTAAGATTTGCTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
*
3204288 TTGTAGCTTCAATCTTCTT-AATTGCAATGTCAGGGAAGTAAGATCTGCTG
1 TTGTAGCTTCAATCTT-TTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
* * * * *
3204338 TTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCTG
1 TTGTAGCTTCAATCTTTTCAATTGCAATGTC-AGGGAAGTAAGATCCGCTG
3204388 TTGTAGCTTCAATCTT
1 TTGTAGCTTCAATCTT
3204404 CTTAATTACA
Statistics
Matches: 709, Mismatches: 170, Indels: 60
0.76 0.18 0.06
Matches are distributed among these distances:
48 18 0.03
49 222 0.31
50 455 0.64
51 14 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
TTGTAGCTTCAATCTTTTCAATTGCAATGTCAGGGAAGTAAGATCCGCTG
Found at i:3203618 original size:100 final size:99
Alignment explanation
Indices: 3203445--3204402 Score: 1173
Period size: 100 Copynumber: 9.6 Consensus size: 99
3203435 GGGATCTGAC
*
3203445 TTGTAGCTTCAATATTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAAT-CTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
3203510 GTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTG
65 GTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTG
3203545 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTT-TTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
*
3203610 GTTCCACTGCAACACTAGGAAAGTAAGATCCGCTG
65 GTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTG
*
3203645 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAATATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTT-TTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
* * *
3203710 GTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCG
65 GTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCTG
* * * * *
3203744 TTGTGGCCTCAATCTTTTGATTGCAATGTCAGGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTG
1 TTGTAGCTTCAATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTG
*
3203809 TTCCACTGCAACGCTAGGAAAGTAAGATCCACTG
66 TTCCACTGCAACGCTAGGAAAGTAAGATCCGCTG
* * *
3203843 TT-TAGCTTTAATCTTCTTAATTGCAACGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTT-TTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
* * *
3203907 GTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCG
65 GTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCTG
* * * * * *
3203941 TTGTGGCATCAATCTTTTGATTGCAATGTTAGGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTG
1 TTGTAGCTTCAATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTG
*
3204006 TTCCACTGCAACGCTAGGAAAGTAAGATCCACTG
66 TTCCACTGCAACGCTAGGAAAGTAAGATCCGCTG
*
3204040 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTT-TTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
* *
3204105 GTTCCACTGC-ACTGCCT-GGAAA-TAAGATTCGCCG
65 GTTCCACTGCAAC-G-CTAGGAAAGTAAGATCCGCTG
* * * * * ***
3204139 TTGTGGCCTCAATCTTTTAATTACAATGTCAGGGAAGTGAGCTCTATTGTTGTAGCTTCAATCTG
1 TTGTAGCTTCAATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTG
* * *
3204204 TTCCAATGCAATGCTAGGAAAGTAAGATTCGCTG
66 TTCCACTGCAACGCTAGGAAAGTAAGATCCGCTG
** * ** * * * **
3204238 TTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAAGTAAGATTTGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCT-TTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
** * * * *
3204303 -TCTTAATTGCAATG-TCAGGGAAGTAAGATCTGCTG
65 GT-TCCACTGCAACGCT-AGGAAAGTAAGATCCGCTG
** * * *
3204338 TTGTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATC
1 TTGTAGCTTCAATCT-TTTAATTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATC
3204402 T
64 T
3204403 TCTTAATTAC
Statistics
Matches: 753, Mismatches: 86, Indels: 38
0.86 0.10 0.04
Matches are distributed among these distances:
97 6 0.01
98 201 0.27
99 186 0.25
100 356 0.47
101 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (99 bp):
TTGTAGCTTCAATCTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTG
TTCCACTGCAACGCTAGGAAAGTAAGATCCGCTG
Found at i:3204145 original size:198 final size:198
Alignment explanation
Indices: 3203445--3204302 Score: 1301
Period size: 198 Copynumber: 4.3 Consensus size: 198
3203435 GGGATCTGAC
* * *
3203445 TTGTAGCTTCAATATTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
* * * * *
3203510 GTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATG
66 GTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCGTTGTGGCCTCAATCTT-TTAATTGCAATG
* * *
3203574 TCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGAT
128 TCAGGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGAT
*
3203639 CCGCTG
193 CCACTG
* *
3203645 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAATATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
*
3203710 GTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCA
66 GTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCA
3203775 GGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCA
131 GGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCA
3203840 CTG
196 CTG
* *
3203843 TT-TAGCTTTAATCTTCTTAATTGCAACGTCAGGGAAGTAAGA-TCTGCTGTTGTAGCTTCAATC
1 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTC-GCTGTTGTAGCTTCAATC
* * *
3203906 TGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCATCAATCTTTTGATTGCAATGTT
65 TGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTC
3203971 AGGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCC
130 AGGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCC
3204036 ACTG
195 ACTG
3204040 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
* *
3204105 GTTCCACTGCACTGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTACAATGTCA
66 GTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCA
* ** * * * *
3204170 GGGAAGTGAGCTCTATTGTTGTAGCTTCAATCTGTTCCAATGCAATGCTAGGAAAGTAAGATTCG
131 GGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCA
3204235 CTG
196 CTG
** * ** * * * *
3204238 TTGTAGCTTCAATCTGT-TCCACTGCACCGCCTGGAAAGTAAGATTTGCTGTTGTAGCTTCAATC
1 TTGTAGCTTCAATCT-TCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATC
3204302 T
65 T
3204303 TCTTAATTGC
Statistics
Matches: 611, Mismatches: 42, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
196 1 0.00
197 189 0.31
198 312 0.51
199 27 0.04
200 80 0.13
201 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (198 bp):
TTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
GTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTGCAATGTCA
GGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCA
CTG
Found at i:3204194 original size:395 final size:397
Alignment explanation
Indices: 3203445--3204402 Score: 1356
Period size: 395 Copynumber: 2.4 Consensus size: 397
3203435 GGGATCTGAC
* * *
3203445 TTGTAGCTTCAATATTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAAT-CTTTTAATTGCAACGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCT
* *
3203510 GTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGT
65 GTTCCACTGCAACGCTAGGAAAGTAAGATCCGCCGTTGTAGCATCAATCTTCTTAATTGCAATGT
3203575 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATC
130 CAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATC
* *
3203640 CGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAATATCCGCTGTTGTAGCTTC
195 CACTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTC
* *
3203705 AATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTGATTGCAA
260 AATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTACAA
* *
3203770 TGTCAGGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAG
325 TGTCAGGGAAGTGAGATCTACTGTTGTAGCTTCAATCTGTTCCAATGCAACGCTAGGAAAGTAAG
3203835 ATCCACTG
390 ATCCACTG
*
3203843 TT-TAGCTTTAATCTTCTTAATTGCAACGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCTT-TTAATTGCAACGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCT
* * * *
3203907 GTTCCACTGCACCGCCT-GGAAA-TAAGATTCGCCGTTGTGGCATCAATCTT-TTGATTGCAATG
65 GTTCCACTGCAACG-CTAGGAAAGTAAGATCCGCCGTTGTAGCATCAATCTTCTTAATTGCAATG
* * * *
3203969 TTAGGGAAGTGAGATCTGCTGTTGTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGAT
129 TCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGAT
*
3204034 CCACTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTT
194 CCACTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTT
*
3204099 CAATCTGTTCCACTGCACTGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTACA
259 CAATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTACA
* * *
3204164 ATGTCAGGGAAGTGAGCTCTATTGTTGTAGCTTCAATCTGTTCCAATGCAATGCTAGGAAAGTAA
324 ATGTCAGGGAAGTGAGATCTACTGTTGTAGCTTCAATCTGTTCCAATGCAACGCTAGGAAAGTAA
* *
3204229 GATTCGCTG
389 GATCCACTG
** * * * * * *
3204238 TTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAAGTAAGATTTGCTGTTGTAGCTTCAATCT
1 TTGTAGCTTCAATCT-TTTAATTGCAACGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCT
** * * * * * * ** *
3204303 -TCTTAATTGCAATG-TCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTGT-TCCACTGCAA
65 GT-TCCACTGCAACGCT-AGGAAAGTAAGATCCGCCGTTGTAGCATCAATCT-TCTTAATTGCAA
* *
3204365 CG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT
127 TGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCT
3204403 TCTTAATTAC
Statistics
Matches: 495, Mismatches: 55, Indels: 20
0.87 0.10 0.04
Matches are distributed among these distances:
394 1 0.00
395 266 0.54
396 88 0.18
397 96 0.19
398 44 0.09
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (397 bp):
TTGTAGCTTCAATCTTTTAATTGCAACGTCAGGGAAGTAAGATCTGCTGTTGTAGCTTCAATCTG
TTCCACTGCAACGCTAGGAAAGTAAGATCCGCCGTTGTAGCATCAATCTTCTTAATTGCAATGTC
AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGTAAGATCC
ACTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCA
ATCTGTTCCACTGCACCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTTAATTACAAT
GTCAGGGAAGTGAGATCTACTGTTGTAGCTTCAATCTGTTCCAATGCAACGCTAGGAAAGTAAGA
TCCACTG
Found at i:3217013 original size:16 final size:16
Alignment explanation
Indices: 3216992--3217033 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3216982 GAAATAAAAC
3216992 CAATAACAATGAATAA
1 CAATAACAATGAATAA
*
3217008 CAATAACGATG-ATAA
1 CAATAACAATGAATAA
*
3217023 CATTAA-AATGA
1 CAATAACAATGA
3217034 TGAACACAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 9 0.41
16 10 0.45
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.21
Consensus pattern (16 bp):
CAATAACAATGAATAA
Found at i:3218831 original size:20 final size:20
Alignment explanation
Indices: 3218808--3218849 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
3218798 CAATTTAACC
*
3218808 TTTTATTAATTATTTTATTAT
1 TTTTATT-ATTATTATATTAT
3218829 TTTTATTATTATTATATTAT
1 TTTTATTATTATTATATTAT
3218849 T
1 T
3218850 CATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTATTATTATATTAT
Found at i:3218837 original size:3 final size:3
Alignment explanation
Indices: 3218810--3218861 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
3218800 ATTTAACCTT
*
3218810 TTA TTAA TTA TT- TTA TTA TTT TTA TTA TTA TTA -TA TTA TTCA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
*
3218855 TTT TTA T
1 TTA TTA T
3218862 CATCATCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3218840 original size:27 final size:27
Alignment explanation
Indices: 3218810--3218861 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
3218800 ATTTAACCTT
*
3218810 TTATTA-ATTATTTTATTATTTTTATTA
1 TTATTATATTA-TTCATTATTTTTATTA
3218837 TTATTATATTATTCATTATTTTTAT
1 TTATTATATTATTCATTATTTTTAT
3218862 CATCATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (27 bp):
TTATTATATTATTCATTATTTTTATTA
Found at i:3218854 original size:18 final size:18
Alignment explanation
Indices: 3218810--3218880 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 18
3218800 ATTTAACCTT
*
3218810 TTATTAATTA-TTTTATTA
1 TTATTCATTATTTTTA-TA
* *
3218828 TT-TTTATTATTATTATA
1 TTATTCATTATTTTTATA
3218845 TTATTCATTATTTTTATCA
1 TTATTCATTATTTTTAT-A
*
3218864 TCA-TCATTATTTTTATA
1 TTATTCATTATTTTTATA
3218881 CACTTACACG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.24
18 31 0.69
19 3 0.07
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTCATTATTTTTATA
Found at i:3218911 original size:23 final size:23
Alignment explanation
Indices: 3218868--3218911 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
3218858 TTATCATCAT
*
3218868 CATTATTTTTATACACTTACACG
1 CATTATTTTTATACAATTACACG
*
3218891 CATT-TTTTTATATAATATACA
1 CATTATTTTTATACAAT-TACA
3218912 TATACATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (23 bp):
CATTATTTTTATACAATTACACG
Found at i:3221103 original size:19 final size:20
Alignment explanation
Indices: 3221063--3221106 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3221053 GTCTCTTTTC
* *
3221063 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
3221082 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
3221101 GCATTA
1 GCATTA
3221107 AACACCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:3223089 original size:12 final size:13
Alignment explanation
Indices: 3223071--3223103 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
3223061 AGTTCAGATT
3223071 CAAAAAAACAAAA
1 CAAAAAAACAAAA
3223084 -AAAAAAACAAAA
1 CAAAAAAACAAAA
3223096 CAAAAAAA
1 CAAAAAAA
3223104 ATGAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAACAAAA
Found at i:3223112 original size:17 final size:16
Alignment explanation
Indices: 3223072--3223104 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3223062 GTTCAGATTC
3223072 AAAAAAACAAAAAAAA
1 AAAAAAACAAAAAAAA
3223088 AAACAAAACAAAAAAAA
1 AAA-AAAACAAAAAAAA
3223105 TGAAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAAAAAA
Found at i:3224480 original size:50 final size:50
Alignment explanation
Indices: 3224350--3224885 Score: 274
Period size: 50 Copynumber: 10.7 Consensus size: 50
3224340 ACCATAGATT
* * *
3224350 TTACTTCCTTAGCAGTGCAGTAGAACAGATTGAAGCTACGACGGCGGATC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
*** * * * * ** * *
3224400 TGGTTTCCCT-GATATTGCAATTAAAAAGATTGAAGCCACAACGGCAGATC
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
* * * **
3224450 TTACTTCTTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGTAGATC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
*** * * * * ** * * *
3224500 TGGTTTCCCT-GATATTGCAATTAAAAAGATTGAAGTCACAACGGTGGATC
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
** * * *
3224550 TTACTTTTTTAGCAGTGCAGTGGAACCGATTGAAGCCACAACGGTGGACC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
* * * * * * * ** *
3224600 TGATTTCCCT-GATATTGTAATTAAAAAGATTGAAGCCACAACGGCGGATC
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
**
3224650 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGTTACAACGGCGGATC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
*** * ** * ** * * *
3224700 TGGTTTCCCTAATATTGCCA-TTAAAAAGATTGAAGCCATAACGACGGATC
1 TTACTTCCTTAGCAGTG-CAGTGGAACAGATTGAAGCCACAACGGCGGATC
* * * * *
3224750 TTACTTCTTTAGCAGTGTAGTGGAACAGATTGAAGCTACGATGGCGGATC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
*** * * * ** * *
3224800 TGGTTTCCCT-GATATTGCTA-TTAAAAAGATTGAAGCCACAACGGCGAATC
1 TTACTTCCTTAG-CAGTGC-AGTGGAACAGATTGAAGCCACAACGGCGGATC
* **
3224850 TTACTTCCTTAGCAGTGCAATGGAGTAGATTGAAGC
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGC
3224886 TGCGGCAGTG
Statistics
Matches: 334, Mismatches: 140, Indels: 24
0.67 0.28 0.05
Matches are distributed among these distances:
49 6 0.02
50 321 0.96
51 7 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (50 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCCACAACGGCGGATC
Found at i:3224523 original size:100 final size:100
Alignment explanation
Indices: 3224350--3225011 Score: 847
Period size: 100 Copynumber: 6.7 Consensus size: 100
3224340 ACCATAGATT
*
3224350 TTACTTCCTTAGCAGTGCAGTAGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
3224415 TGCAATTAAAAAGATTGAAGCCACAACGGCAGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* **
3224450 TTACTTCTTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGTAGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* *
3224515 TGCAATTAAAAAGATTGAAGTCACAACGGTGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
** * * * * * *
3224550 TTACTTTTTTAGCAGTGCAGTGGAACCGATTGAAGCCACAACGGTGGACCTGATTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
3224615 TGTAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
3224650 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGTTACAACGGCGGATCTGGTTTCCCTAATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* * *
3224715 TGCCATTAAAAAGATTGAAGCCATAACGACGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
3224750 TTACTTCTTTAGCAGTGTAGTGGAACAGATTGAAGCTACGATGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* *
3224815 TGCTATTAAAAAGATTGAAGCCACAACGGCGAATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* ** * * * * * * *
3224850 TTACTTCCTTAGCAGTGCAATGGAGTAGATTGAAGCTGCGGCAGTGGATCTAGTTTTCCTGACAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
3224915 TGCAATT-------TTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * * * * *
3224943 TTACTTCCCT-G-ATGGTGCGGTGGAATAGATTGAAGCTACGACGACAGATCTGGTTTCCCCGAC
1 TTACTTCCTTAGCA--GTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
3225006 ATTGCA
64 ATTGCA
3225012 GTTGAACAAA
Statistics
Matches: 492, Mismatches: 68, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
91 1 0.00
92 1 0.00
93 72 0.15
100 418 0.85
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:3224993 original size:93 final size:92
Alignment explanation
Indices: 3224829--3225011 Score: 208
Period size: 93 Copynumber: 2.0 Consensus size: 92
3224819 ATTAAAAAGA
* * * *
3224829 TTGAAGCCACAACGGCGAATCTTACTTCCTTAGCAGTGCAATGGAGTAGATTGAAGCTGCGGCAG
1 TTGAAGCCACAACGGCGAATCTTACTTCCTGAG-AGTGCAATGGAATAGATTGAAGCTACGACAG
** * *
3224894 TGGATCTAGTTTTCCTGACATTGCAATT
65 CAGATCTAGTTTCCCCGACATTGCAATT
* **
3224922 TTGAAGCCACAACGGCGGATCTTACTTCCCTGATG-GTGCGGTGGAATAGATTGAAGCTACGAC-
1 TTGAAGCCACAACGGCGAATCTTACTT-CCTGA-GAGTGCAATGGAATAGATTGAAGCTACGACA
*
3224985 GACAGATCTGGTTTCCCCGACATTGCA
64 G-CAGATCTAGTTTCCCCGACATTGCA
3225012 GTTGAACAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
92 1 0.01
93 69 0.92
94 4 0.05
95 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (92 bp):
TTGAAGCCACAACGGCGAATCTTACTTCCTGAGAGTGCAATGGAATAGATTGAAGCTACGACAGC
AGATCTAGTTTCCCCGACATTGCAATT
Found at i:3226491 original size:9 final size:9
Alignment explanation
Indices: 3226477--3226518 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3226467 TTATTAACTA
3226477 TTTTATTAT
1 TTTTATTAT
3226486 TTTTATTAT
1 TTTTATTAT
*
3226495 TATTA-TAT
1 TTTTATTAT
*
3226503 TATTCATTAT
1 T-TTTATTAT
3226513 TTTTAT
1 TTTTAT
3226519 CATCATCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 4 0.15
9 19 0.70
10 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTATTAT
Found at i:3226511 original size:18 final size:18
Alignment explanation
Indices: 3226479--3226537 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
3226469 ATTAACTATT
3226479 TTATTAT-TT-TT-ATTA
1 TTATTATATTATTCATTA
3226494 TTATTATATTATTCATTA
1 TTATTATATTATTCATTA
* *
3226512 TTTTTATCATCA-TCATTA
1 TTATTAT-ATTATTCATTA
*
3226530 TTTTTATA
1 TTATTATA
3226538 CACTTACACG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.18
16 2 0.05
17 3 0.08
18 23 0.61
19 3 0.08
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATATTATTCATTA
Found at i:3227741 original size:3 final size:3
Alignment explanation
Indices: 3227733--3227786 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
3227723 GGTTTCGACA
* * *
3227733 ATT ATT ATT ATC ATT ATT ATT ATT ATC ATT ATT ATT ATT ACT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
3227779 ATT ATT AT
1 ATT ATT AT
3227787 CAGTTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:3227796 original size:15 final size:15
Alignment explanation
Indices: 3227733--3227786 Score: 83
Period size: 15 Copynumber: 3.5 Consensus size: 15
3227723 GGTTTCGACA
3227733 ATTATTATTATCATT
1 ATTATTATTATCATT
3227748 ATTATTATTATCATT
1 ATTATTATTATCATT
3227763 ATTATTATTA-CTATTT
1 ATTATTATTATC-A-TT
3227779 ATTATTAT
1 ATTATTAT
3227787 CAGTTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
14 1 0.03
15 26 0.70
16 10 0.27
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATTATTATCATT
Found at i:3228233 original size:2 final size:2
Alignment explanation
Indices: 3228178--3228218 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3228168 TGATGATTAT
*
3228178 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3228219 GTACAAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3228312 original size:36 final size:37
Alignment explanation
Indices: 3228271--3228347 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
3228261 TTTAAATATG
* *
3228271 TATACATACACATGT-TTTTTCATA-TTTTCATAATTT
1 TATACATACACATGTATATAT-ATATTTTTCATAATTT
* *
3228307 TATACATATATATGTATATATATATTTTTCATAATTT
1 TATACATACACATGTATATATATATTTTTCATAATTT
3228344 TATA
1 TATA
3228348 ATTTTTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 16 0.46
37 19 0.54
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.53
Consensus pattern (37 bp):
TATACATACACATGTATATATATATTTTTCATAATTT
Found at i:3228369 original size:18 final size:18
Alignment explanation
Indices: 3228325--3228361 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3228315 TATATGTATA
3228325 TATATATTTTTCATAATTT
1 TATA-ATTTTTCATAATTT
3228344 TATAATTTTT-ATAATTT
1 TATAATTTTTCATAATTT
3228361 T
1 T
3228362 GTTAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 6 0.33
19 4 0.22
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TATAATTTTTCATAATTT
Found at i:3231287 original size:7 final size:7
Alignment explanation
Indices: 3231270--3231319 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
3231260 TAGTGCCTAT
3231270 GGTTTATG
1 GGTTTA-G
3231278 GGTTTAG
1 GGTTTAG
3231285 GGTTTTAG
1 GG-TTTAG
3231293 GGTTTAG
1 GGTTTAG
*
3231300 TGTTTAG
1 GGTTTAG
**
3231307 AATTTAG
1 GGTTTAG
3231314 GGTTTA
1 GGTTTA
3231320 AGATTTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 23 0.64
8 13 0.36
ACGTcount: A:0.18, C:0.00, G:0.34, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:3231333 original size:21 final size:22
Alignment explanation
Indices: 3231287--3231333 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
3231277 GGGTTTAGGG
*
3231287 TTTTAGGGTTTAGTGTTTAGAA
1 TTTTAGGGTTTAGTATTTAGAA
3231309 -TTTAGGGTTTAAG-ATTTA-AA
1 TTTTAGGGTTT-AGTATTTAGAA
3231329 TTTTA
1 TTTTA
3231334 ATATTTTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 2 0.09
21 18 0.82
22 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (22 bp):
TTTTAGGGTTTAGTATTTAGAA
Found at i:3247976 original size:42 final size:43
Alignment explanation
Indices: 3247911--3248000 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
3247901 AGAATCCACC
* *
3247911 TTGAGAACTTAGTGGAAATTTCC-TTTTCTATTAAAATGATTT
1 TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
* *
3247953 TTGAAAACTTGGTGTAAAATTCCTTTTTCTATTAAAATGATTT
1 TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
3247996 TTGAA
1 TTGAA
3248001 CTAATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 19 0.44
43 24 0.56
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (43 bp):
TTGAAAACTTAGTGGAAAATTCCTTTTTCTATTAAAATGATTT
Found at i:3254006 original size:21 final size:21
Alignment explanation
Indices: 3253980--3254024 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3253970 GTTTTGGAAA
3253980 CCACCAAAGAAATTGCTGAAG
1 CCACCAAAGAAATTGCTGAAG
** **
3254001 CCACCATTGATCTTGCTGAAG
1 CCACCAAAGAAATTGCTGAAG
3254022 CCA
1 CCA
3254025 TTGGTGATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (21 bp):
CCACCAAAGAAATTGCTGAAG
Found at i:3255489 original size:23 final size:24
Alignment explanation
Indices: 3255434--3255497 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
3255424 TTGTTACTCC
*
3255434 AATAGTTGGGA-CTTCTTTGAAATT
1 AATAGTTGGAACCTT-TTTGAAATT
* *
3255458 AACATTTGGAACCTTTTTG-AATT
1 AATAGTTGGAACCTTTTTGAAATT
*
3255481 AATAGTTGGAGCCTTTT
1 AATAGTTGGAACCTTTT
3255498 AAAAAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
23 18 0.55
24 12 0.36
25 3 0.09
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (24 bp):
AATAGTTGGAACCTTTTTGAAATT
Found at i:3258341 original size:25 final size:25
Alignment explanation
Indices: 3258313--3258379 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
3258303 TCTCGAGCCA
*
3258313 TATAACGGGAAGCTCATGT-GAGCTG
1 TATAATGGGAAGCTCAT-TCGAGCTG
* *
3258338 TATAATGGGAAGCTTATTCGGGCTG
1 TATAATGGGAAGCTCATTCGAGCTG
*
3258363 TATAATGGGAACCTCAT
1 TATAATGGGAAGCTCAT
3258380 AAGAGTCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (25 bp):
TATAATGGGAAGCTCATTCGAGCTG
Found at i:3262392 original size:84 final size:86
Alignment explanation
Indices: 3262293--3262539 Score: 324
Period size: 84 Copynumber: 2.9 Consensus size: 86
3262283 TTGTCCGTTT
3262293 TCTTTTCAAATTGATCAATTTTAGTACCTAT-CTTTTAGAATTTTAAATTTTAATCTTGACTTGG
1 TCTTTTCAAATTGATCAATTTTAGTACCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTGG
*
3262357 TAACAGTTAAATTGTCCAATA
66 TAACAATTAAATTGTCCAATA
*
3262378 T-TTTTCAAATTGATCAA-TTTAG-ACCCTATACTTTTAGAATTTTTAATTTTAATCTTGACTTG
1 TCTTTTCAAATTGATCAATTTTAGTA-CCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTG
* *
3262440 GTAACAATTAAATTGTCCATTT
65 GTAACAATTAAATTGTCCAATA
* * ** * ** *
3262462 TCTTTTCAAATTAATCAATTTTAGT-CTCTGTGTTTTTAAAATTTTAAAACTTAATCTTAACTTG
1 TCTTTTCAAATTGATCAATTTTAGTAC-CTATACTTTTAGAATTTTAAATTTTAATCTTGACTTG
*
3262526 GTAACACTTAAATT
65 GTAACAATTAAATT
3262540 TGTTTAATTA
Statistics
Matches: 142, Mismatches: 14, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
82 1 0.01
83 10 0.07
84 67 0.47
85 17 0.12
86 47 0.33
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (86 bp):
TCTTTTCAAATTGATCAATTTTAGTACCTATACTTTTAGAATTTTAAATTTTAATCTTGACTTGG
TAACAATTAAATTGTCCAATA
Found at i:3263793 original size:15 final size:15
Alignment explanation
Indices: 3263770--3263828 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
3263760 TTTCTCATCT
*
3263770 TTATTATACTTATTA
1 TTATAATACTTATTA
*
3263785 TTATAATACTGATTA
1 TTATAATACTTATTA
* *
3263800 TCT-TAGTACTTATCA
1 T-TATAATACTTATTA
3263815 TTATAATACTTATT
1 TTATAATACTTATT
3263829 CCTCTTATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATAATACTTATTA
Found at i:3264667 original size:6 final size:7
Alignment explanation
Indices: 3264649--3264674 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3264639 TTCAGAGGAG
3264649 TAAAAAA
1 TAAAAAA
3264656 TAAAAAA
1 TAAAAAA
3264663 TAAAAAA
1 TAAAAAA
3264670 TAAAA
1 TAAAA
3264675 GTGCGTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:3265227 original size:23 final size:23
Alignment explanation
Indices: 3265197--3265244 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
3265187 AAAACATGAA
3265197 AATACGTTTAGTAATTTTTTTCT
1 AATACGTTTAGTAATTTTTTTCT
3265220 AATACGTTTAGTAATTTTTTTCT
1 AATACGTTTAGTAATTTTTTTCT
3265243 AA
1 AA
3265245 CATAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.54
Consensus pattern (23 bp):
AATACGTTTAGTAATTTTTTTCT
Found at i:3268059 original size:27 final size:27
Alignment explanation
Indices: 3268029--3268082 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
3268019 TTTCAAAGAA
* *
3268029 AAGGGAAAGAAGAGAGGATTTTTTTTT
1 AAGGCAAAGAAGAAAGGATTTTTTTTT
* * *
3268056 AAGGCAGAGAGGAAATGATTTTTTTTT
1 AAGGCAAAGAAGAAAGGATTTTTTTTT
3268083 TCTAAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (27 bp):
AAGGCAAAGAAGAAAGGATTTTTTTTT
Found at i:3268899 original size:14 final size:15
Alignment explanation
Indices: 3268870--3268901 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3268860 CTTTCATATT
3268870 TTATCATGCGCATTA
1 TTATCATGCGCATTA
3268885 TTATCATGC-CATTA
1 TTATCATGCGCATTA
3268899 TTA
1 TTA
3268902 CTACAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (15 bp):
TTATCATGCGCATTA
Found at i:3272935 original size:5 final size:5
Alignment explanation
Indices: 3272891--3272950 Score: 54
Period size: 5 Copynumber: 12.2 Consensus size: 5
3272881 TTTTTATGTT
* * *
3272891 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA ATATA TTATA TTGTA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
3272940 TTATA TTATA T
1 TTATA TTATA T
3272951 AAATTAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
3 1 0.02
4 8 0.17
5 33 0.72
7 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:3273140 original size:19 final size:19
Alignment explanation
Indices: 3273104--3273139 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3273094 TAAAAGAAAT
3273104 AAAGTAAAGTAAATAAAAG
1 AAAGTAAAGTAAATAAAAG
3273123 AAAGTAAAG-AAATAAAA
1 AAAGTAAAGTAAATAAAA
3273140 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAGTAAAGTAAATAAAAG
Done.