Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 39
Found at i:2994132 original size:23 final size:23
Alignment explanation
Indices: 2994106--2994169 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2994096 CAGCTCGTAT
2994106 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
2994129 AATTGCACCGTAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
*
2994152 AAATGCACCGAAGTGCCA
1 AATTGCACCGAAGTGCCA
2994170 TATAAGATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:2995770 original size:21 final size:21
Alignment explanation
Indices: 2995746--2995788 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2995736 TCTGGTTAGT
* * *
2995746 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2995767 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2995788 T
1 T
2995789 ATCCCAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2999447 original size:23 final size:23
Alignment explanation
Indices: 2999421--2999488 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
2999411 CAGCTCGTAT
*
2999421 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATATAG
* * **
2999444 AATTGCACTGTAGTGCCGCATAG
1 AATTGCACCGAAGTGCCATATAG
* *
2999467 AAATGTACCGAAGTGCCATATA
1 AATTGCACCGAAGTGCCATATA
2999489 AGATGTCCCT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATATAG
Found at i:3007197 original size:17 final size:17
Alignment explanation
Indices: 3007175--3007208 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3007165 TGAACTTATT
3007175 AGTCTCGTGTGTGAATC
1 AGTCTCGTGTGTGAATC
3007192 AGTCTCGTGTGTGAATC
1 AGTCTCGTGTGTGAATC
3007209 GTAAGCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.29, T:0.35
Consensus pattern (17 bp):
AGTCTCGTGTGTGAATC
Found at i:3021291 original size:12 final size:12
Alignment explanation
Indices: 3021274--3021298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3021264 AAATTTTATT
3021274 GATTTTTTAAAA
1 GATTTTTTAAAA
3021286 GATTTTTTAAAA
1 GATTTTTTAAAA
3021298 G
1 G
3021299 TTATATTATT
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (12 bp):
GATTTTTTAAAA
Found at i:3021346 original size:24 final size:24
Alignment explanation
Indices: 3021301--3021359 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
3021291 TTTAAAAGTT
*
3021301 ATATTATTTAAATAATTATTTTGA
1 ATATTATTAAAATAATTATTTTGA
* *
3021325 ATATTATATAAAATTATT-TTTTTA
1 ATATTAT-TAAAATAATTATTTTGA
3021349 CAT-TTATTAAA
1 -ATATTATTAAA
3021360 TCGCAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATATTATTAAAATAATTATTTTGA
Found at i:3025123 original size:60 final size:58
Alignment explanation
Indices: 3024950--3025137 Score: 148
Period size: 60 Copynumber: 3.2 Consensus size: 58
3024940 AAATACTATC
* * * * * *
3024950 CTCAAATTATGACCCTTATTTAAATTGATC-TCTAAATTCTTAAACATTTTAATTTCAT
1 CTCAAATTATGACACTCATTTAAATTGGTCTTC-AAATTTTTGATCATTTTAATTTCAT
* * * * * * *
3025008 CTCTAAATTATGACTCTCAATCTAATTTAGT-TCTCAAACTTTTCGAT-ATTATAATTTCGTT
1 CTC-AAATTATGACACTC-ATTTAAATTGGTCT-TCAAA-TTTTTGATCATTTTAATTTC-AT
* *
3025069 CTCAAACTATGACACTCATTTTAAATTGGTCTTCAAATTTTTGATCATTTTAATTTTAT
1 CTCAAATTATGACACTCA-TTTAAATTGGTCTTCAAATTTTTGATCATTTTAATTTCAT
*
3025128 CCCAAATTAT
1 CTCAAATTAT
3025138 CAATATATAC
Statistics
Matches: 98, Mismatches: 23, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 55 0.56
61 11 0.11
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (58 bp):
CTCAAATTATGACACTCATTTAAATTGGTCTTCAAATTTTTGATCATTTTAATTTCAT
Found at i:3032243 original size:16 final size:16
Alignment explanation
Indices: 3032222--3032255 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3032212 TTTTTACATG
3032222 AACCAAAA-TACTATTA
1 AACCAAAATTA-TATTA
3032238 AACCAAAATTATATTA
1 AACCAAAATTATATTA
3032254 AA
1 AA
3032256 TATATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (16 bp):
AACCAAAATTATATTA
Found at i:3035873 original size:13 final size:13
Alignment explanation
Indices: 3035857--3035894 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
3035847 AATATTAAGT
3035857 AATAATAAAAATA
1 AATAATAAAAATA
*
3035870 AATAATAATAATA
1 AATAATAAAAATA
3035883 AATACATAAAAA
1 AATA-ATAAAAA
3035895 CAAAAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:3037553 original size:5 final size:5
Alignment explanation
Indices: 3037432--3037549 Score: 211
Period size: 5 Copynumber: 23.8 Consensus size: 5
3037422 TCCTTTTTAT
3037432 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
3037482 TTTCA TTTCA TTTCA TTTCA TTTCA -TTCA TTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
* *
3037531 TTTCA TTTCT TTTCT TTTC
1 TTTCA TTTCA TTTCA TTTC
3037550 TTTTTCCTCT
Statistics
Matches: 111, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
4 4 0.04
5 107 0.96
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCA
Found at i:3046131 original size:2 final size:2
Alignment explanation
Indices: 3046124--3046165 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3046114 TTAAACCAAA
* *
3046124 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A- AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3046165 A
1 A
3046166 ATAATGAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3047591 original size:9 final size:9
Alignment explanation
Indices: 3047567--3047633 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
3047557 TTAGGGTTTT
3047567 ATAATATT-
1 ATAATATTA
3047575 -TAAT-TTA
1 ATAATATTA
3047582 ATAATATTA
1 ATAATATTA
3047591 ATAATA-TA
1 ATAATATTA
*
3047599 TATATATAATA
1 -ATA-ATATTA
*
3047610 ATAATAATA
1 ATAATATTA
*
3047619 ATAATTTTA
1 ATAATATTA
*
3047628 AAAATA
1 ATAATA
3047634 ACAATTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
6 2 0.04
7 4 0.08
8 6 0.12
9 29 0.59
10 6 0.12
11 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATAATATTA
Found at i:3047595 original size:3 final size:3
Alignment explanation
Indices: 3047580--3047623 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
3047570 ATATTTAATT
*
3047580 TAA TAA TAT TAA TAA T-A TATA TATA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA T
3047624 TTTAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 28 0.76
4 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:3047929 original size:76 final size:76
Alignment explanation
Indices: 3047807--3049114 Score: 2145
Period size: 76 Copynumber: 17.3 Consensus size: 76
3047797 CTTAAAAAAT
* * ** * *
3047807 ATCATGCACTGAAGGGCTTACAGATGACCCTAAGATTTTGAAAACATCAAAAAGCTCCCGAATGT
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
3047872 TTTTTGGAAAT
66 TTTTTGGAAAC
* * * *
3047883 ATCATGCACTGTAGGACTTACAAATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGAAGGG
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3047948 TTTTTGGAAAC
66 TTTTTGGAAAC
*
3047959 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048024 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
3048035 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAACCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048100 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
3048111 ATCATGCACTGTAGAACTTATAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
3048176 TTTTTGAAAAC
66 TTTTTGGAAAC
*
3048187 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048252 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
3048263 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGT
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
3048328 TTTTTGAAAAC
66 TTTTTGGAAAC
*
3048339 ATCAGGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048404 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
3048415 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCTGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048480 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
3048491 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATTAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
3048556 TTTTTGGAATC
66 TTTTTGGAAAC
*
3048567 ATCATGCACTGTATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048632 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
3048643 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048708 TTTTTGGAAAC
66 TTTTTGGAAAC
*
3048719 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3048784 TTTTTGGAAAC
66 TTTTTGGAAAC
*
3048795 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
3048860 TTTTTAGAAAC
66 TTTTTGGAAAC
* *
3048871 ATCATACACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
3048936 TTTTTGAAAAC
66 TTTTTGGAAAC
*
3048947 ATCAGGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
3049012 TTTTTGGAAAC
66 TTTTTGGAAAC
3049023 ATCATGCAC--T--G-----CAG--GA-CCTAAGGCTTTGAAAACATCAAAAAAGCTCCCGAAGG
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGG
3049076 CTTTTTTGGAAAC
65 C-TTTTTGGAAAC
3049089 ATCATGCACTGTAGGACTTACAGATG
1 ATCATGCACTGTAGGACTTACAGATG
3049115 TGGGAAATAG
Statistics
Matches: 1149, Mismatches: 70, Indels: 25
0.92 0.06 0.02
Matches are distributed among these distances:
64 20 0.02
65 19 0.02
66 20 0.02
67 3 0.00
68 1 0.00
70 1 0.00
72 1 0.00
74 1 0.00
75 3 0.00
76 1079 0.94
77 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (76 bp):
ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAAC
Found at i:3049105 original size:66 final size:64
Alignment explanation
Indices: 3048975--3049105 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 64
3048965 TACAGATGAC
3048975 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGA
1 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGA
*
3049039 CCTAAGGCTTTGAAAACATCAAAAAAGCTCCCGAAGGCTTTTTTGGAAACATCATGCACTGTAGG
1 CCTAAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGCAGG
3049104 A
64 A
3049105 C
1 C
3049106 TTACAGATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
64 20 0.31
65 17 0.27
66 27 0.42
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (64 bp):
CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGA
Found at i:3049767 original size:22 final size:22
Alignment explanation
Indices: 3049742--3049818 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
3049732 AATAAAGCTT
*
3049742 TCATCTTTGAAAAGAGACTCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3049764 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3049786 CCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3049808 TCATATTTGAA
1 TCATCTTTGAA
3049819 GAGTGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3054517 original size:17 final size:18
Alignment explanation
Indices: 3054495--3054531 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3054485 CTTGATTCAA
3054495 TTTCC-TTTTCCTTTTTT
1 TTTCCTTTTTCCTTTTTT
3054512 TTTCCTTTTTTCCTTTTTT
1 TTTCC-TTTTTCCTTTTTT
3054531 T
1 T
3054532 ACCTAATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
19 13 0.72
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCCTTTTTCCTTTTTT
Found at i:3056390 original size:12 final size:12
Alignment explanation
Indices: 3056373--3056400 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3056363 ACAAACGTAA
3056373 AAATGCAAATGT
1 AAATGCAAATGT
3056385 AAATGCAAATGT
1 AAATGCAAATGT
3056397 AAAT
1 AAAT
3056401 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:3058897 original size:2 final size:2
Alignment explanation
Indices: 3058892--3058957 Score: 102
Period size: 2 Copynumber: 34.5 Consensus size: 2
3058882 TATTTAAACC
*
3058892 AT AT AT A- AT AT AT CT AT AT AT AT AT AT AT -T 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
3058932 AT -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3058958 ATGAAAGTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 56 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3058979 original size:36 final size:36
Alignment explanation
Indices: 3058892--3058981 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
3058882 TATTTAAACC
* * * * *
3058892 ATATATAATATATCTATATATATATATATTATATAT
1 ATATATTATACATATATATATATATATATAATAAAT
*
3058928 ATATATTATATATATATATATATATATATAATGAAAGT
1 ATATATTATACATATATATATATATATATAAT-AAA-T
3058966 ATA-ATT-TACATATATA
1 ATATATTATACATATATA
3058982 AAAGTAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 38 0.81
37 5 0.11
38 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (36 bp):
ATATATTATACATATATATATATATATATAATAAAT
Found at i:3073076 original size:88 final size:88
Alignment explanation
Indices: 3072927--3073096 Score: 297
Period size: 88 Copynumber: 1.9 Consensus size: 88
3072917 ACACACCCTT
3072927 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
3072992 ATTAATTGAATTTAATAATCCTC
66 ATTAATTGAAATTAATAATCCTC
* *
3073015 TTATATCCAAGTTACCCTTATCATATTAGGGATTTTATTATTTCAAATT-ATTAAATCTATATTT
1 TTATAACCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
3073079 AATTAATTGAAATTAATA
65 AATTAATTGAAATTAATA
3073097 TTCAGGATTA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
88 61 0.78
89 17 0.22
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:3079836 original size:90 final size:89
Alignment explanation
Indices: 3079684--3079856 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
3079674 ACATACCCTT
3079684 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATATTTA
1 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATATTTA
* *
3079749 ATTAATTGTAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
3079773 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAACCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATCAAATCTATATTT
3079838 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
3079857 TTCAGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.44
Consensus pattern (89 bp):
TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:3082921 original size:18 final size:18
Alignment explanation
Indices: 3082898--3082967 Score: 104
Period size: 18 Copynumber: 3.9 Consensus size: 18
3082888 TATGTGATAT
*
3082898 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCAGGACATA
*
3082916 GTGGTCCGTCAGGACATA
1 GTGGTCCTTCAGGACATA
3082934 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGGACATA
* *
3082952 ATGGTCCTTCGGGACA
1 GTGGTCCTTCAGGACA
3082968 AATTCTAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCAGGACATA
Found at i:3085613 original size:23 final size:24
Alignment explanation
Indices: 3085587--3085651 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
3085577 TAGATTTATG
3085587 CCGAAGGACTGCGTAGAA-TTGCC
1 CCGAAGGACTGCGTAGAATTTGCC
* * **
3085610 CCGAAGGACCGCGTAAAATTTGTT
1 CCGAAGGACTGCGTAGAATTTGCC
*
3085634 CCGAAGGACTACGTAGAA
1 CCGAAGGACTGCGTAGAA
3085652 CCCTTGAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (24 bp):
CCGAAGGACTGCGTAGAATTTGCC
Found at i:3085648 original size:24 final size:23
Alignment explanation
Indices: 3085587--3085648 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
3085577 TAGATTTATG
*
3085587 CCGAAGGACTGCGTAGAATTGCC
1 CCGAAGGACTGCGTAAAATTGCC
* **
3085610 CCGAAGGACCGCGTAAAATTTGTT
1 CCGAAGGACTGCGTAAAA-TTGCC
*
3085634 CCGAAGGACTACGTA
1 CCGAAGGACTGCGTA
3085649 GAACCCTTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.19
Consensus pattern (23 bp):
CCGAAGGACTGCGTAAAATTGCC
Found at i:3085858 original size:29 final size:30
Alignment explanation
Indices: 3085807--3085864 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
3085797 ATTTAAGGAA
**
3085807 AAAATGTTTTTGGGTTTGAATTGAATTTAC
1 AAAATGTTTTTGGACTTGAATTGAATTTAC
3085837 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
3085865 TTCAAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:3085970 original size:21 final size:21
Alignment explanation
Indices: 3085944--3086021 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
3085934 AGGGGGTCAA
*
3085944 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCATAC
**
3085965 AGTGCATCCATGCACCTGTAC
1 AGTGCATCCATGCACCCATAC
* * *
3085986 TAGTGCATCGATGCA-TCATGC
1 -AGTGCATCCATGCACCCATAC
3086007 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3086022 TCAAACACCG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 13 0.28
21 21 0.45
22 13 0.28
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATAC
Found at i:3086012 original size:20 final size:19
Alignment explanation
Indices: 3085987--3086097 Score: 70
Period size: 20 Copynumber: 5.8 Consensus size: 19
3085977 CACCTGTACT
3085987 AGTGCATCGATGCATCATGC
1 AGTGCATCGATGCATCAT-C
*
3086007 AGTGCATCCATGCA-C-TC
1 AGTGCATCGATGCATCATC
** *
3086024 A-AACACCGAATGCA--ATC
1 AGTGCATCG-ATGCATCATC
*
3086041 AGTGCATCGATGCATCCTTC
1 AGTGCATCGATGCAT-CATC
* *
3086061 TGTGCATCGATGCATCAAGGC
1 AGTGCATCGATGCATC-A-TC
*
3086082 TGTGCATCGATGCATC
1 AGTGCATCGATGCATC
3086098 TTGTTGTGCA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
16 3 0.04
17 15 0.21
18 5 0.07
19 2 0.03
20 29 0.41
21 17 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCATCATC
Found at i:3086086 original size:21 final size:20
Alignment explanation
Indices: 3086042--3086097 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
3086032 AATGCAATCA
***
3086042 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGGCT
3086062 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-AGGCT
3086083 GTGCATCGATGCATC
1 GTGCATCGATGCATC
3086098 TTGTTGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGCT
Found at i:3086089 original size:41 final size:41
Alignment explanation
Indices: 3086042--3086124 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
3086032 AATGCAATCA
*
3086042 GTGCATCGATGCATCCTT-CTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCAT-CTTGCTGTGCATCCATGCA-CGAAGGCT
*
3086083 GTGCATCGATGCATCTTGTTGTGCATCCATGCACGAAGGCT
1 GTGCATCGATGCATCTTGCTGTGCATCCATGCACGAAGGCT
3086124 G
1 G
3086125 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCTTGCTGTGCATCCATGCACGAAGGCT
Found at i:3086107 original size:20 final size:20
Alignment explanation
Indices: 3086042--3086115 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
3086032 AATGCAATCA
3086042 GTGCATCGATGCATCCTT-CT
1 GTGCATCGATGCAT-CTTGCT
**
3086062 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-TTGCT
*
3086083 GTGCATCGATGCATCTTGTT
1 GTGCATCGATGCATCTTGCT
*
3086103 GTGCATCCATGCA
1 GTGCATCGATGCA
3086116 CGAAGGCTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 28 0.61
21 17 0.37
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCTTGCT
Found at i:3089444 original size:29 final size:30
Alignment explanation
Indices: 3089373--3089432 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
3089363 AAATTTAAGG
3089373 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
3089404 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
3089433 TTCAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:3089538 original size:21 final size:21
Alignment explanation
Indices: 3089512--3089569 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
3089502 AGGGTGTCAA
*
3089512 AGTGCATCCATGTACCCCTAC
1 AGTGCATCCATGCACCCCTAC
* *
3089533 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
3089554 AGTGCATTCATGCACC
1 AGTGCATCCATGCACC
3089570 TGCACTAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:3089661 original size:20 final size:20
Alignment explanation
Indices: 3089638--3089704 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
3089628 TTAGTGCAAT
*
3089638 GATGCATCCTTCTGTGCATC
1 GATGCATCCTGCTGTGCATC
**
3089658 GATGCATCAAGGCTGTGCATC
1 GATGCATC-CTGCTGTGCATC
3089679 GATGCATCCTGCTGTGCATC
1 GATGCATCCTGCTGTGCATC
*
3089699 CATGCA
1 GATGCA
3089705 CGAAGGCTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.28
Consensus pattern (20 bp):
GATGCATCCTGCTGTGCATC
Found at i:3089675 original size:21 final size:21
Alignment explanation
Indices: 3089649--3089713 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
3089639 ATGCATCCTT
3089649 CTGTGCATCGATGCATCAAGG
1 CTGTGCATCGATGCATCAAGG
**
3089670 CTGTGCATCGATGCATC-CTG
1 CTGTGCATCGATGCATCAAGG
*
3089690 CTGTGCATCCATGCA-CGAAGG
1 CTGTGCATCGATGCATC-AAGG
3089711 CTG
1 CTG
3089714 CAACGGCTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.41
21 21 0.57
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (21 bp):
CTGTGCATCGATGCATCAAGG
Found at i:3090111 original size:34 final size:32
Alignment explanation
Indices: 3090072--3090141 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3090062 TTTTGTAAAG
* * *
3090072 GGGAAAGGTTCTAGCTTATCCCATGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCA-G-AAAAACTA
*
3090106 GGGAAAGGTTATAGTTTAGCCCAGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCAGAAAAACTA
3090138 GGGA
1 GGGA
3090142 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCAGAAAAACTA
Found at i:3101831 original size:24 final size:24
Alignment explanation
Indices: 3101759--3101823 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
3101749 TGTCACATAG
* * * *
3101759 ATTTGTCTCGAAGGATCGCGCAGA
1 ATTTGTCTCGAATGACCACACAGA
3101783 ATTTGTCTCGAATGACCACACAGA
1 ATTTGTCTCGAATGACCACACAGA
3101807 ATTTGT-TCCGAATGACC
1 ATTTGTCT-CGAATGACC
3101824 GCTTAGAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (24 bp):
ATTTGTCTCGAATGACCACACAGA
Found at i:3115611 original size:2 final size:2
Alignment explanation
Indices: 3115604--3115629 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3115594 ACTTTGGTGC
3115604 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
3115630 CCGATTATTT
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:3118919 original size:15 final size:16
Alignment explanation
Indices: 3118899--3118932 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3118889 ACTTGATTTA
3118899 TTCTTTTTCT-TCTTT
1 TTCTTTTTCTCTCTTT
3118914 TTCTTTTTCTCTCTTT
1 TTCTTTTTCTCTCTTT
3118930 TTC
1 TTC
3118933 GAATATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTCTCTCTTT
Found at i:3119664 original size:33 final size:33
Alignment explanation
Indices: 3119627--3119689 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
3119617 GACTTTATTT
* *
3119627 CCTCAAAGATAGGTAAAGGTATGATTTTGGGTG
1 CCTCAAAGAGAGGTAAAGGTATGACTTTGGGTG
*
3119660 CCTCAAAGAGAGGTAATGGTATGACTTTGG
1 CCTCAAAGAGAGGTAAAGGTATGACTTTGG
3119690 TGACTCAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (33 bp):
CCTCAAAGAGAGGTAAAGGTATGACTTTGGGTG
Found at i:3125272 original size:13 final size:13
Alignment explanation
Indices: 3125254--3125280 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3125244 ACACACACAC
3125254 ATATATATATATA
1 ATATATATATATA
3125267 ATATATATATATA
1 ATATATATATATA
3125280 A
1 A
3125281 ATAAGTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATATATATA
Found at i:3125649 original size:39 final size:39
Alignment explanation
Indices: 3125606--3125683 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
3125596 GATTTGTCGT
3125606 CCCGTATCCCGACTCGGATGTTGCAGGTACCCGAAATTC
1 CCCGTATCCCGACTCGGATGTTGCAGGTACCCGAAATTC
3125645 CCCGTATCCCGACTCGGATGTTGCAGGTACCCGAAATTC
1 CCCGTATCCCGACTCGGATGTTGCAGGTACCCGAAATTC
3125684 GGGTACCGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (39 bp):
CCCGTATCCCGACTCGGATGTTGCAGGTACCCGAAATTC
Found at i:3128717 original size:19 final size:19
Alignment explanation
Indices: 3128678--3128723 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3128668 ATACATTTTC
3128678 ATGAACAGTACTATACGGT
1 ATGAACAGTACTATACGGT
* **
3128697 ATGAATAGTACTATATTGT
1 ATGAACAGTACTATACGGT
3128716 ATGAACAG
1 ATGAACAG
3128724 CACCGTAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (19 bp):
ATGAACAGTACTATACGGT
Found at i:3128794 original size:21 final size:21
Alignment explanation
Indices: 3128764--3128803 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3128754 ACATGTTACT
3128764 GTGTACCGATGCACTGCTATA
1 GTGTACCGATGCACTGCTATA
*
3128785 GTGTATCGATGCACTGCTA
1 GTGTACCGATGCACTGCTA
3128804 CAGTAACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTATA
Found at i:3129650 original size:22 final size:22
Alignment explanation
Indices: 3129613--3129668 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3129603 TGAAATTTTT
* * *
3129613 TCCCAAAGGACTTATGTATTTG
1 TCCCGAAGGACCTATGCATTTG
*
3129635 TCCCGAATGACCTATGCATTTG
1 TCCCGAAGGACCTATGCATTTG
3129657 TCCCGAAGGACC
1 TCCCGAAGGACC
3129669 GCGTAGAACC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (22 bp):
TCCCGAAGGACCTATGCATTTG
Found at i:3131447 original size:29 final size:29
Alignment explanation
Indices: 3131414--3131509 Score: 111
Period size: 29 Copynumber: 3.3 Consensus size: 29
3131404 TAATTCATGA
* *
3131414 TGCTATTTTGGGAATTAATTCAAAAAGGG
1 TGCTATTTTGGTAATTAATTTAAAAAGGG
* * *
3131443 TGCTAATTTGGTAATTAATTTGAAAAGTG
1 TGCTATTTTGGTAATTAATTTAAAAAGGG
* * *
3131472 TGCTATCTTGGTTATTATTTTAAAAAGGGG
1 TGCTATTTTGGTAATTAATTTAAAAA-GGG
3131502 TGCTATTT
1 TGCTATTT
3131510 ATGTAAAATG
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
29 45 0.83
30 9 0.17
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.42
Consensus pattern (29 bp):
TGCTATTTTGGTAATTAATTTAAAAAGGG
Found at i:3132243 original size:24 final size:24
Alignment explanation
Indices: 3132216--3132276 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3132206 TACCTGATTG
3132216 TTGACCTGGATTCAAATATGATAC
1 TTGACCTGGATTCAAATATGATAC
* ***
3132240 TTGACCTGAATTTTTATATGATAC
1 TTGACCTGGATTCAAATATGATAC
*
3132264 TTGACATGGATTC
1 TTGACCTGGATTC
3132277 TGATTTGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (24 bp):
TTGACCTGGATTCAAATATGATAC
Found at i:3138109 original size:22 final size:21
Alignment explanation
Indices: 3138083--3138130 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
3138073 TTTGACCGAT
3138083 CCGACCCGACCCGACCATTGA
1 CCGACCCGACCCGACCATTGA
*
3138104 CTCGACCCGACCCGACCGTTGA
1 C-CGACCCGACCCGACCATTGA
3138126 CCGAC
1 CCGAC
3138131 TATATTCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (21 bp):
CCGACCCGACCCGACCATTGA
Found at i:3138194 original size:29 final size:29
Alignment explanation
Indices: 3138132--3138268 Score: 96
Period size: 29 Copynumber: 4.7 Consensus size: 29
3138122 TTGACCGACT
** **
3138132 ATATTCTGGGAATTAATTCGATTTTGGTG
1 ATATTCTGGGAATTAATTCGAAATAAGTG
3138161 ATATTCTGGGAATTAATTCGAAATAAGTG
1 ATATTCTGGGAATTAATTCGAAATAAGTG
* * * ** *
3138190 TTATTTTGGTAATTGTTTCGAAAAAAAGGGTG
1 ATATTCTGGGAATTAATTCG-AAATAA--GTG
* * *
3138222 ATATTATGGGAATTAATTTGAAATGA-TG
1 ATATTCTGGGAATTAATTCGAAATAAGTG
* * *
3138250 CTATTTTAGGAATTAATTC
1 ATATTCTGGGAATTAATTC
3138269 AAAAAGGGTG
Statistics
Matches: 83, Mismatches: 22, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
28 17 0.20
29 40 0.48
30 5 0.06
31 4 0.05
32 17 0.20
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (29 bp):
ATATTCTGGGAATTAATTCGAAATAAGTG
Found at i:3138292 original size:29 final size:29
Alignment explanation
Indices: 3138212--3138342 Score: 115
Period size: 28 Copynumber: 4.6 Consensus size: 29
3138202 TTGTTTCGAA
* * *
3138212 AAAAAGGGTGATATTATGGGAATTAATTT
1 AAAAAGGGTGCTATTTTGGTAATTAATTT
* * * *
3138241 -GAAATGATGCTATTTTAGG-AATTAATTC
1 AAAAAGGGTGCTATTTT-GGTAATTAATTT
*
3138269 AAAAAGGGTGGTATTTTGGTAATTAATTT
1 AAAAAGGGTGCTATTTTGGTAATTAATTT
* * *
3138298 GAAAA-GGTGCTATTTTGGTTATTATTTT
1 AAAAAGGGTGCTATTTTGGTAATTAATTT
*
3138326 AAAAAGGGGTGTTATTT
1 AAAAA-GGGTGCTATTT
3138343 ATGTAAAATG
Statistics
Matches: 80, Mismatches: 17, Indels: 9
0.75 0.16 0.08
Matches are distributed among these distances:
28 45 0.56
29 26 0.32
30 9 0.11
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.40
Consensus pattern (29 bp):
AAAAAGGGTGCTATTTTGGTAATTAATTT
Found at i:3139070 original size:24 final size:24
Alignment explanation
Indices: 3139043--3139122 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
3139033 TACCTGATTG
*
3139043 TTGACCTGGATTCAAATATGATAT
1 TTGACCTGGATTCAAATATGATAC
***
3139067 TTGACCTGGATTTTTATATGATAC
1 TTGACCTGGATTCAAATATGATAC
* ** * *
3139091 TTGACATGGATTCTGATTTGTTAC
1 TTGACCTGGATTCAAATATGATAC
3139115 TTGACCTG
1 TTGACCTG
3139123 AATTATGTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (24 bp):
TTGACCTGGATTCAAATATGATAC
Found at i:3144569 original size:13 final size:14
Alignment explanation
Indices: 3144551--3144579 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3144541 TGGGACCATT
3144551 GACATCTT-CGGAG
1 GACATCTTCCGGAG
3144564 GACATCTTCCGGAG
1 GACATCTTCCGGAG
3144578 GA
1 GA
3144580 GATTTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (14 bp):
GACATCTTCCGGAG
Found at i:3145664 original size:19 final size:20
Alignment explanation
Indices: 3145638--3145680 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
3145628 TTCTTTTTGA
3145638 TTTA-TTCCTT-TCTTTTA-T
1 TTTATTTCCTTAT-TTTTACT
3145656 TTTATTTCCTTATTTTTACT
1 TTTATTTCCTTATTTTTACT
3145676 TTTAT
1 TTTAT
3145681 CTCTCCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 11 0.50
20 7 0.32
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTTCCTTATTTTTACT
Found at i:3156755 original size:25 final size:25
Alignment explanation
Indices: 3156719--3156769 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3156709 AAACATTAAC
*
3156719 CATAGAATCTCAAGTAGTTATCAAT
1 CATAGAAGCTCAAGTAGTTATCAAT
3156744 CATAGAAGCTCAAGTAGTTATCAAT
1 CATAGAAGCTCAAGTAGTTATCAAT
3156769 C
1 C
3156770 CATAAGCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (25 bp):
CATAGAAGCTCAAGTAGTTATCAAT
Found at i:3158764 original size:23 final size:23
Alignment explanation
Indices: 3158738--3158828 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
3158728 ACATGTTCCC
*
3158738 GAACGTTAAATAAACATATTCGT
1 GAACGTTAAATAAACATATTCAT
* * * **
3158761 GAACATATAAATGAATATATAAAT
1 GAACGT-TAAATAAACATATTCAT
*
3158785 GAACGTTAAATAAACATGTTCAT
1 GAACGTTAAATAAACATATTCAT
* * **
3158808 TAATGTTAAACGAACATATTC
1 GAACGTTAAATAAACATATTC
3158829 GCAAACATTA
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
23 33 0.66
24 17 0.34
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (23 bp):
GAACGTTAAATAAACATATTCAT
Found at i:3158775 original size:12 final size:12
Alignment explanation
Indices: 3158760--3158801 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3158750 AACATATTCG
3158760 TGAACATATAAA
1 TGAACATATAAA
*
3158772 TGAATATATAAA
1 TGAACATATAAA
*
3158784 TGAACGT-TAAA
1 TGAACATATAAA
*
3158795 TAAACAT
1 TGAACAT
3158802 GTTCATTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (12 bp):
TGAACATATAAA
Found at i:3158943 original size:41 final size:40
Alignment explanation
Indices: 3158860--3158948 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
3158850 ACAAATACCT
**
3158860 TAAA-AAA-ATAAATGAACATGAACACGATATTAAAAATT
1 TAAACAAACATAAATGAACATGAACACGATATTAAAAAAA
* * *
3158898 TAAACGAACATAAACTGAACATGAACAC-CTTTTAAAAAGAA
1 TAAACAAACATAAA-TGAACATGAACACGATATTAAAAA-AA
3158939 TAAACAAACA
1 TAAACAAACA
3158949 AACGCAAACA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
38 4 0.10
39 2 0.05
40 13 0.32
41 22 0.54
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.20
Consensus pattern (40 bp):
TAAACAAACATAAATGAACATGAACACGATATTAAAAAAA
Found at i:3163167 original size:28 final size:28
Alignment explanation
Indices: 3163121--3163189 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
3163111 GGGGTGTTCT
*
3163121 AATTAATCCAT-TACCGTTAATCATAAC
1 AATTAATCGATGTACCGTTAATCATAAC
3163148 AATTAATCGATGTACCGTTAATCATAAC
1 AATTAATCGATGTACCGTTAATCATAAC
3163176 AATTAATCGATGTA
1 AATTAATCGATGTA
3163190 ATTGCTACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 10 0.25
28 30 0.75
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (28 bp):
AATTAATCGATGTACCGTTAATCATAAC
Found at i:3166652 original size:43 final size:43
Alignment explanation
Indices: 3166532--3166625 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 43
3166522 TTAATTACCG
*
3166532 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAAGTCCCTTTGCTGTGTGCAAGGGTAAGCC
*
3166575 TTACAGTTCCCCCAAGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAAGTCCCTTTGCTGTGTGCAAGGGTAAGCC
3166618 TTACAGTT
1 TTACAGTT
3166626 TCCCTAGGCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.31
Consensus pattern (43 bp):
TTACAGTTCCCCCAAGTCCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:3167890 original size:21 final size:21
Alignment explanation
Indices: 3167864--3167905 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3167854 AATCAAGAAT
3167864 GTTAGCTCTCTATCTATAGGG
1 GTTAGCTCTCTATCTATAGGG
3167885 GTTAGCTCTCTATCTATAGGG
1 GTTAGCTCTCTATCTATAGGG
3167906 ATTCTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
GTTAGCTCTCTATCTATAGGG
Found at i:3168037 original size:67 final size:65
Alignment explanation
Indices: 3167926--3168149 Score: 218
Period size: 68 Copynumber: 3.3 Consensus size: 65
3167916 ATGATTTACT
* * * * *
3167926 TATTCAAATTTAAATATATAATAATATCTTTTAATTTTAGATATTCAAAAT-ATATATATACATT
1 TATTCAAAGTAAAAAATA-AATAATATCTTTTAATTTTAAATATTTAAAATAATATA-AT-C-TT
3167990 TTAA
62 TTAA
*
3167994 TATTCAAAGTAAAAAATAAATAATATCTTTTAATTTAAAATATTTAAAATAATATAATCTTTTAA
1 TATTCAAAGTAAAAAATAAATAATATCTTTTAATTTTAAATATTTAAAATAATATAATCTTTTAA
* * * **
3168059 TAGTCAAAGTTAAATAGAT-AATAAATATCTTTTTAATTTTAATTATTTAAAATAATAATTGTCC
1 TATTCAAAG-TAAA-AAATAAAT-AATATC-TTTTAATTTTAAATATTTAAAATAAT-ATAAT-C
*
3168123 TATTAA
60 TTTTAA
*
3168129 TATTCAAATTAAAAACATAAA
1 TATTCAAAGTAAAAA-ATAAA
3168150 AAGATAAATA
Statistics
Matches: 131, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
65 14 0.11
66 8 0.06
67 40 0.31
68 45 0.34
69 9 0.07
70 15 0.11
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (65 bp):
TATTCAAAGTAAAAAATAAATAATATCTTTTAATTTTAAATATTTAAAATAATATAATCTTTTAA
Found at i:3168106 original size:68 final size:69
Alignment explanation
Indices: 3167929--3168115 Score: 219
Period size: 67 Copynumber: 2.8 Consensus size: 69
3167919 ATTTACTTAT
* * *
3167929 TCAAATTTAAATATATAAT-AATATCTTTTAATTTTAGATATTCAAAAT-ATATATATACATTTT
1 TCAAAGTTAAATAAATAATAAATATCTTTTAATTTTA-ATATTTAAAATAATATATATACATTTT
*
3167992 AATAT
65 AATAG
*
3167997 TCAAAG-TAAA-AAATAA-ATAATATCTTTTAATTTAAAATATTTAAAATAATATA-AT-C-TTT
1 TCAAAGTTAAATAAATAATA-AATATCTTTTAATTT-TAATATTTAAAATAATATATATACATTT
3168056 TAATAG
64 TAATAG
*
3168062 TCAAAGTTAAATAGATAATAAATATCTTTTTAATTTTAATTATTTAAAATAATA
1 TCAAAGTTAAATAAATAATAAATATC-TTTTAATTTTAA-TATTTAAAATAATA
3168116 ATTGTCCTAT
Statistics
Matches: 103, Mismatches: 7, Indels: 18
0.80 0.05 0.14
Matches are distributed among these distances:
65 14 0.14
66 10 0.10
67 44 0.43
68 35 0.34
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (69 bp):
TCAAAGTTAAATAAATAATAAATATCTTTTAATTTTAATATTTAAAATAATATATATACATTTTA
ATAG
Found at i:3170462 original size:14 final size:14
Alignment explanation
Indices: 3170445--3170478 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3170435 AACGATACTG
3170445 GAAAATAATTTTTA
1 GAAAATAATTTTTA
3170459 G-AAATAATTTTTA
1 GAAAATAATTTTTA
*
3170472 TAAAATA
1 GAAAATA
3170479 TAATTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
GAAAATAATTTTTA
Found at i:3176097 original size:2 final size:2
Alignment explanation
Indices: 3176092--3176124 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3176082 GTGTGTGTGA
*
3176092 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3176125 CTTCGAAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3179878 original size:30 final size:30
Alignment explanation
Indices: 3179844--3179903 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3179834 ATAAAATATG
3179844 AAATATGAGTTATGTGTAACAAATACAGTT
1 AAATATGAGTTATGTGTAACAAATACAGTT
3179874 AAATATGAGTTATGTGTAACAAATACAGTT
1 AAATATGAGTTATGTGTAACAAATACAGTT
3179904 TTGGACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (30 bp):
AAATATGAGTTATGTGTAACAAATACAGTT
Found at i:3182310 original size:4 final size:4
Alignment explanation
Indices: 3182301--3182327 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3182291 CAATGCATGT
3182301 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
3182328 CATGGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:3185207 original size:32 final size:32
Alignment explanation
Indices: 3185171--3185258 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
3185161 ATGGAATATT
* * *
3185171 TTAGGGCCTGAGAGCCTACCTAA-AATAGTATC
1 TTAGGGCCTAAGAGCCTACCCAAGAA-AGTACC
*
3185203 TTAGGGCCTAAGAGCATACCCAAGAAAGTACC
1 TTAGGGCCTAAGAGCCTACCCAAGAAAGTACC
* *
3185235 TTGGGGCCTTAGAGCCTACCCAAG
1 TTAGGGCCTAAGAGCCTACCCAAG
3185259 GAAATGTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 46 0.96
33 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (32 bp):
TTAGGGCCTAAGAGCCTACCCAAGAAAGTACC
Found at i:3185270 original size:32 final size:31
Alignment explanation
Indices: 3185201--3185291 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
3185191 TAAAATAGTA
* *
3185201 TCTTAGGGCCTAAGAGCATACCCAA-GAAAG
1 TCTTGGGGCCTTAGAGCATACCCAAGGAAAG
*
3185231 TACCTTGGGGCCTTAGAGCCTACCCAAGGAAATG
1 T--CTTGGGGCCTTAGAGCATACCCAAGGAAA-G
*
3185265 TCTTGGGGCCTTAGAG-TTACCCAAGGA
1 TCTTGGGGCCTTAGAGCATACCCAAGGA
3185292 CACCTTAGGC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
30 1 0.02
31 10 0.19
32 36 0.68
33 4 0.08
34 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (31 bp):
TCTTGGGGCCTTAGAGCATACCCAAGGAAAG
Found at i:3186347 original size:27 final size:27
Alignment explanation
Indices: 3186317--3186379 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3186307 CCAGAGCTTG
3186317 GGGGTATTTAGGTCATTTCT-CACTTCA
1 GGGGTATTTAGGTCATTT-TACACTTCA
* * *
3186344 GGGGAATTTTGGTCATTTTACAGTTCA
1 GGGGTATTTAGGTCATTTTACACTTCA
*
3186371 AGGGTATTT
1 GGGGTATTT
3186380 CAATAATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (27 bp):
GGGGTATTTAGGTCATTTTACACTTCA
Found at i:3187067 original size:2 final size:2
Alignment explanation
Indices: 3187060--3187135 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
3187050 AATCTAATCT
3187060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3187102 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3187136 AATAAATTAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3187343 original size:19 final size:19
Alignment explanation
Indices: 3187307--3187350 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3187297 CCTTTTTGGT
*
3187307 CAGTCAACGGGTAGGTCAA
1 CAGTCAACGGGCAGGTCAA
* *
3187326 CAGTCAATGGGCATGTCAA
1 CAGTCAACGGGCAGGTCAA
*
3187345 CGGTCA
1 CAGTCA
3187351 TATCAAAGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.18
Consensus pattern (19 bp):
CAGTCAACGGGCAGGTCAA
Found at i:3187363 original size:30 final size:30
Alignment explanation
Indices: 3187322--3187395 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
3187312 AACGGGTAGG
3187322 TCAACAGTCAATGGGCATGTCAACGGTCATA
1 TCAA-AGTCAATGGGCATGTCAACGGTCATA
* *
3187353 TCAAAGTCAATGGGCATGTCAGCGGTCATG
1 TCAAAGTCAATGGGCATGTCAACGGTCATA
3187383 TCAAAGTCAATGG
1 TCAAAGTCAATGG
3187396 TTCGGGTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 37 0.90
31 4 0.10
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (30 bp):
TCAAAGTCAATGGGCATGTCAACGGTCATA
Found at i:3191012 original size:19 final size:19
Alignment explanation
Indices: 3190985--3191059 Score: 80
Period size: 19 Copynumber: 4.0 Consensus size: 19
3190975 CGAACCGGTT
3190985 TGACACATTGACTTTGACC
1 TGACACATTGACTTTGACC
* *
3191004 TGACCCATTGA-ATTGACC
1 TGACACATTGACTTTGACC
* ***
3191022 CGACGTGTTGACTTTGACC
1 TGACACATTGACTTTGACC
*
3191041 TGACTCATTGACTTTGACC
1 TGACACATTGACTTTGACC
3191060 AGAGTTAACC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
18 13 0.30
19 31 0.70
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.32
Consensus pattern (19 bp):
TGACACATTGACTTTGACC
Found at i:3192613 original size:13 final size:13
Alignment explanation
Indices: 3192595--3192619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3192585 TCCAGATTTC
3192595 TCTTCTTCTCCAT
1 TCTTCTTCTCCAT
3192608 TCTTCTTCTCCA
1 TCTTCTTCTCCA
3192620 CCGTGAAGCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (13 bp):
TCTTCTTCTCCAT
Found at i:3193205 original size:64 final size:64
Alignment explanation
Indices: 3193137--3193258 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
3193127 ATTGTTCAAG
* * * * * * *
3193137 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTACCGATGCAAAAGAAGTGCATCGATACACCCCCTTAAAATAAAAACATCGAATGCCATCA
* *
3193201 GTGTACCGATGCAAAAGTAGTGCATCGATACACCCCCTTAAAATACAAACATCGAATG
1 GTGTACCGATGCAAAAGAAGTGCATCGATACACCCCCTTAAAATAAAAACATCGAATG
3193259 GGATTTATGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (64 bp):
GTGTACCGATGCAAAAGAAGTGCATCGATACACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:3193936 original size:23 final size:23
Alignment explanation
Indices: 3193906--3193978 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
3193896 AGAACTACGA
3193906 TGCAATTCTACGCGACACTTCGG
1 TGCAATTCTACGCGACACTTCGG
3193929 TGCAATTCTACGCGACACTTCGG
1 TGCAATTCTACGCGACACTTCGG
* *
3193952 TGCAATTCTACGTGGCACTTCGG
1 TGCAATTCTACGCGACACTTCGG
3193975 TGCA
1 TGCA
3193979 TTTATATGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (23 bp):
TGCAATTCTACGCGACACTTCGG
Found at i:3194208 original size:3 final size:3
Alignment explanation
Indices: 3194200--3194225 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3194190 CAATTCCTTG
3194200 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3194226 TTGCCTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3200189 original size:64 final size:64
Alignment explanation
Indices: 3200079--3200215 Score: 179
Period size: 64 Copynumber: 2.1 Consensus size: 64
3200069 TTCAAGGTGT
* *
3200079 ATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGCACAAG-TAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGCA-AAGATAGTGC
* ** * *
3200143 ATCGATGCACCCCCTTAAAATAAAAACATTGAATGGGATTTA-TGTATCGATGCATAGATAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCA-TCAGTGTATCGATGCAAAGATAGTGC
3200207 ATCGATGCA
1 ATCGATGCA
3200216 GCCGTCAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
63 2 0.03
64 60 0.94
65 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
ATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGCAAAGATAGTGC
Found at i:3204075 original size:23 final size:23
Alignment explanation
Indices: 3204049--3204106 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
3204039 TCTTATTGTT
* * **
3204049 TGACACATTTTTCTCTGTCTTTA
1 TGACACGTTTTTATCTACCTTTA
*
3204072 TGACACGTTTTTATCTACCTTTG
1 TGACACGTTTTTATCTACCTTTA
3204095 TGACACGTTTTT
1 TGACACGTTTTT
3204107 TATTTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.12, T:0.50
Consensus pattern (23 bp):
TGACACGTTTTTATCTACCTTTA
Found at i:3205201 original size:2 final size:2
Alignment explanation
Indices: 3205190--3205220 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3205180 TTTTTTTTTT
*
3205190 TG TG TC TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3205221 TGGGGATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3211125 original size:18 final size:18
Alignment explanation
Indices: 3211098--3211132 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3211088 CTTGTATAAA
*
3211098 TGCACTGAAGTGCCATAG
1 TGCACCGAAGTGCCATAG
3211116 TGCACCGAAGTGCCATA
1 TGCACCGAAGTGCCATA
3211133 TAAAATTGTC
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:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (18 bp):
TGCACCGAAGTGCCATAG
Found at i:3213808 original size:20 final size:21
Alignment explanation
Indices: 3213770--3213808 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3213760 AAAACATATG
*
3213770 TTTTGTTAAATTATAGATGAT
1 TTTTGTTAAACTATAGATGAT
*
3213791 TTTTTTTAAACTAT-GATG
1 TTTTGTTAAACTATAGATG
3213809 CAAAACATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (21 bp):
TTTTGTTAAACTATAGATGAT
Found at i:3219005 original size:40 final size:40
Alignment explanation
Indices: 3218950--3219028 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
3218940 ACTTACGGTG
* *
3218950 AGTTAACGACTACAACTTCCCCGTTGAAAACTAAAAATTC
1 AGTTAACGACTACAACTTACCCATTGAAAACTAAAAATTC
*
3218990 AGTTAACGACTACAACTTACCCATTGAAAATTAAAAATT
1 AGTTAACGACTACAACTTACCCATTGAAAACTAAAAATT
3219029 AAAATTTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.27
Consensus pattern (40 bp):
AGTTAACGACTACAACTTACCCATTGAAAACTAAAAATTC
Found at i:3219139 original size:11 final size:11
Alignment explanation
Indices: 3219123--3219147 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3219113 AATTTGGATC
3219123 TATATTAAAAA
1 TATATTAAAAA
3219134 TATATTAAAAA
1 TATATTAAAAA
3219145 TAT
1 TAT
3219148 TATGATGGTG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATATTAAAAA
Found at i:3219969 original size:12 final size:12
Alignment explanation
Indices: 3219952--3219985 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3219942 TAATAATTTA
3219952 ATATATTTTAAT
1 ATATATTTTAAT
3219964 ATATATTTTAAT
1 ATATATTTTAAT
* *
3219976 TTTTATTTTA
1 ATATATTTTA
3219986 TATGCATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATATTTTAAT
Found at i:3224109 original size:21 final size:21
Alignment explanation
Indices: 3224085--3224146 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
3224075 GTAAATCACA
3224085 TTGCGATTTTCCGAATTCGCT
1 TTGCGATTTTCCGAATTCGCT
*
3224106 TTGCGATTTTCCGAATTCGTT
1 TTGCGATTTTCCGAATTCGCT
*
3224127 TTGCGATTTTCCAAATTCGC
1 TTGCGATTTTCCGAATTCGC
3224147 AACGCGAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
TTGCGATTTTCCGAATTCGCT
Found at i:3224189 original size:20 final size:20
Alignment explanation
Indices: 3224140--3224189 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3224130 CGATTTTCCA
*
3224140 AATTCGCAACGCGAATCTGT
1 AATTCGCAACGAGAATCTGT
* * *
3224160 AAATCACAACGAGAATTTGT
1 AATTCGCAACGAGAATCTGT
3224180 AATTCGCAAC
1 AATTCGCAAC
3224190 ACATAAGTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
AATTCGCAACGAGAATCTGT
Found at i:3224203 original size:20 final size:20
Alignment explanation
Indices: 3224180--3224224 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3224170 GAGAATTTGT
*
3224180 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
3224200 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
3224220 AATTC
1 AATTC
3224225 ACAAAGCGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:3224438 original size:20 final size:21
Alignment explanation
Indices: 3224397--3224440 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
3224387 GTCTCCATCG
3224397 CCGACGAAATCCGTCCCTATCT
1 CCGACGAAATCCGT-CCTATCT
3224419 CCGACGAAATCCGT-CTATCT
1 CCGACGAAATCCGTCCTATCT
3224439 CC
1 CC
3224441 ATCTCTCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.23, C:0.41, G:0.14, T:0.23
Consensus pattern (21 bp):
CCGACGAAATCCGTCCTATCT
Found at i:3224794 original size:20 final size:20
Alignment explanation
Indices: 3224771--3224811 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3224761 AAACTTAAAT
3224771 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
**
3224791 TCGCAAGGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
3224811 T
1 T
3224812 TGCGTTGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.17, G:0.20, T:0.12
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:3224837 original size:19 final size:20
Alignment explanation
Indices: 3224813--3224851 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
3224803 AATGAAAATT
3224813 GCGTTGCGATTTT-AGTTTC
1 GCGTTGCGATTTTAAGTTTC
3224832 GCGTTGCGATTTTAAGTTTC
1 GCGTTGCGATTTTAAGTTTC
3224852 AGAAACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.46
Consensus pattern (20 bp):
GCGTTGCGATTTTAAGTTTC
Found at i:3226571 original size:21 final size:21
Alignment explanation
Indices: 3226522--3226571 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3226512 GTTAGGGGAG
*
3226522 TTACGTGATGAGGTCAATACT
1 TTACGTGAGGAGGTCAATACT
* *
3226543 TTGCGTGAGGAGGTCAATATT
1 TTACGTGAGGAGGTCAATACT
*
3226564 TTATGTGA
1 TTACGTGA
3226572 CGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:3226629 original size:21 final size:21
Alignment explanation
Indices: 3226588--3226725 Score: 63
Period size: 21 Copynumber: 6.6 Consensus size: 21
3226578 TGGTGCATGG
*
3226588 CGTGATGAGGTACGGTCTTTA
1 CGTGATGAGGTAAGGTCTTTA
*
3226609 CGTGGTGAGGTAGAGGT-TTTA
1 CGTGATGAGGTA-AGGTCTTTA
* *
3226630 CGCGATGA--CAATGGTTCTTTA
1 CGTGATGAGGTAA-GG-TCTTTA
* **
3226651 CGTGGTGAGGT-ATCTACTTTA
1 CGTGATGAGGTAAGGT-CTTTA
* **
3226672 CGTGGTGAGGT-ATCTACTTTA
1 CGTGATGAGGTAAGGT-CTTTA
* **
3226693 CGTGGTGAGGT-ATCTACTTTA
1 CGTGATGAGGTAAGGT-CTTTA
3226714 CGTGATGAGGTA
1 CGTGATGAGGTA
3226726 GCCGCTCTAC
Statistics
Matches: 98, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 2 0.02
21 88 0.90
22 4 0.04
ACGTcount: A:0.20, C:0.13, G:0.32, T:0.35
Consensus pattern (21 bp):
CGTGATGAGGTAAGGTCTTTA
Found at i:3226672 original size:42 final size:42
Alignment explanation
Indices: 3226603--3226722 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 42
3226593 TGAGGTACGG
***** * *
3226603 TCTTTACGTGGTGAGGTAGAGGTTTTACGCGATGA-CAATGGT
1 TCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGCAAT-CT
* **
3226645 TCTTTACGTGGTGAGGTATCTACTTTACGTGGTGAGGTATCT
1 TCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGCAATCT
*
3226687 ACTTTACGTGGTGAGGTATCTACTTTACGTGATGAG
1 TCTTTACGTGGTGAGGTATCTACTTTACGTGATGAG
3226723 GTAGCCGCTC
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 63 0.97
43 2 0.03
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (42 bp):
TCTTTACGTGGTGAGGTATCTACTTTACGTGATGAGCAATCT
Found at i:3226723 original size:42 final size:42
Alignment explanation
Indices: 3226646--3226725 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
3226636 GACAATGGTT
*
3226646 CTTTACGTGGTGAGGTATCTACTTTACGTGGTGAGGTATCTA
1 CTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTATCTA
3226688 CTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTA
1 CTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTA
3226726 GCCGCTCTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.38
Consensus pattern (42 bp):
CTTTACGTGGTGAGGTATCTACTTTACGTGATGAGGTATCTA
Found at i:3226737 original size:42 final size:42
Alignment explanation
Indices: 3226649--3226738 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
3226639 AATGGTTCTT
* * * *
3226649 TACGTGGTGAGGTATCTACTTTACGTGGTGAGGTATCTACTT
1 TACGTGGTGAGGTATCTACTTTACGTGATGAGGTAGCCACTC
*
3226691 TACGTGGTGAGGTATCTACTTTACGTGATGAGGTAGCCGCTC
1 TACGTGGTGAGGTATCTACTTTACGTGATGAGGTAGCCACTC
3226733 TACGTG
1 TACGTG
3226739 AGATTGTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (42 bp):
TACGTGGTGAGGTATCTACTTTACGTGATGAGGTAGCCACTC
Found at i:3227048 original size:21 final size:20
Alignment explanation
Indices: 3227018--3227078 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
3227008 TCAGATTCAC
3227018 CTATCATCGTTCAAGAGGCCT
1 CTAT-ATCGTTCAAGAGGCCT
*
3227039 CTTATATCGTTCAAAAGG-CT
1 C-TATATCGTTCAAGAGGCCT
*
3227059 CTATAGTCCTTCAAGAGGCC
1 CTATA-TCGTTCAAGAGGCC
3227079 CCTCCCACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 14 0.41
22 3 0.09
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (20 bp):
CTATATCGTTCAAGAGGCCT
Found at i:3227094 original size:21 final size:21
Alignment explanation
Indices: 3227068--3227137 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
3227058 TCTATAGTCC
*
3227068 TTCAAGAGGCCCCTCCCACCT
1 TTCAAGAGGCCCCTCCCACCG
* ** *
3227089 TTCAAGAGGCCCATGTCATCG
1 TTCAAGAGGCCCCTCCCACCG
**
3227110 TTCAAGAGGTTCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
3227131 TTCAAGA
1 TTCAAGA
3227138 ACCCGATTCA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:3228004 original size:22 final size:23
Alignment explanation
Indices: 3227979--3228022 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3227969 AATTAAGTTT
3227979 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
3228001 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
3228023 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:3233829 original size:20 final size:20
Alignment explanation
Indices: 3233804--3233841 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3233794 TTTTGGTGCA
*
3233804 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
3233824 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
3233842 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:3237908 original size:14 final size:14
Alignment explanation
Indices: 3237889--3237922 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3237879 TGTTTAATTT
3237889 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
3237903 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
3237917 ATTTGT
1 ATTTGT
3237923 TTAATTGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:3237958 original size:78 final size:78
Alignment explanation
Indices: 3237870--3238061 Score: 312
Period size: 78 Copynumber: 2.5 Consensus size: 78
3237860 TGGGTACACT
*
3237870 TTTTTTGCTTGTTTAATTTATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAG
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAG
3237935 GAAATAAAAATTA
66 GAAATAAAAATTA
* *
3237948 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGGTTTGTTTAATTGATGTG
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAG
* ***
3238013 TAAATAATTCTTA
66 GAAATAAAAATTA
*
3238026 TATTTTGCTTGTTTAATTGATTTGTAAAAGTTGATT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATT
3238062 GATGTTTTAA
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 106 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (78 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAG
GAAATAAAAATTA
Found at i:3237983 original size:14 final size:14
Alignment explanation
Indices: 3237964--3238000 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3237954 GCTTGTTTAA
3237964 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
3237978 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
3237992 TTGGTTTGT
1 TTGATTTGT
3238001 TTAATTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:3238015 original size:41 final size:41
Alignment explanation
Indices: 3237878--3238016 Score: 123
Period size: 41 Copynumber: 3.5 Consensus size: 41
3237868 CTTTTTTTGC
* * *
3237878 TTGTTTAATTTATTTGTAAAAGTTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATGTGTAAAAGTTGATTTGTAAAAGTTGGT
* * *
3237919 TTGTTTAATTGATGAGGAAATAAAAATT-ATTT-T-----TT-GC
1 TTGTTTAATTGATG-TG---TAAAAGTTGATTTGTAAAAGTTGGT
*
3237956 TTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGGT
1 TTGTTTAATTGATGTGTAAAAGTTGATTTGTAAAAGTTGGT
3237997 TTGTTTAATTGATGTGTAAA
1 TTGTTTAATTGATGTGTAAA
3238017 TAATTCTTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
33 7 0.09
34 4 0.05
35 1 0.01
36 1 0.01
37 13 0.17
38 2 0.03
40 2 0.03
41 32 0.43
42 1 0.01
43 1 0.01
44 4 0.05
45 7 0.09
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.49
Consensus pattern (41 bp):
TTGTTTAATTGATGTGTAAAAGTTGATTTGTAAAAGTTGGT
Found at i:3238237 original size:29 final size:29
Alignment explanation
Indices: 3238195--3238251 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3238185 TTTTGTGTTT
3238195 CGAATTTGACTTTCGCAACAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
*
3238224 CGAATTTGACTTTCGCAATAATCGCAAC
1 CGAATTTGACTTTCGCAACAATCGCAAC
3238252 AAAAAATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAACG
Found at i:3240793 original size:24 final size:24
Alignment explanation
Indices: 3240742--3240793 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3240732 ATCCGAGTAT
** *
3240742 TGACCAAGATCAAAGTCTGGGTAT
1 TGACCAAGATCAAAGTCTGAATAC
* *
3240766 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTCTGAATAC
3240790 TGAC
1 TGAC
3240794 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCTGAATAC
Found at i:3240925 original size:12 final size:12
Alignment explanation
Indices: 3240904--3240937 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3240894 TGTTGTGGGT
*
3240904 TTTGAAATTGTG
1 TTTGATATTGTG
3240916 TTTGATATTGTG
1 TTTGATATTGTG
*
3240928 TTTGGTATTG
1 TTTGATATTG
3240938 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:3241804 original size:21 final size:20
Alignment explanation
Indices: 3241780--3241939 Score: 85
Period size: 20 Copynumber: 7.9 Consensus size: 20
3241770 TGTGCAAAAA
3241780 AAATTCGCGTTGCGAATTCAG
1 AAATTCGCGTTGCGAATT-AG
* *
3241801 AAA-TCGAGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTAG
*
3241820 AAATTCAGCGTTGCGAATTTGG
1 AAATTC-GCGTTGCGAA-TTAG
***
3241842 AAA-TCGCAACGCGAATTTAG
1 AAATTCGCGTTGCGAA-TTAG
* ** * * *
3241862 AAAATCGCAATGTGATTTAC
1 AAATTCGCGTTGCGAATTAG
* *
3241882 ATATTCGCGTTGCGAATTTGG
1 AAATTCGCGTTGCGAA-TTAG
*
3241903 AAATT-GAGTTGCGAAATT-G
1 AAATTCGCGTTGCG-AATTAG
* *
3241922 GAGTTCGCGTTGCGAATT
1 AAATTCGCGTTGCGAATT
3241940 TGTTGGTCAT
Statistics
Matches: 107, Mismatches: 25, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
19 12 0.11
20 58 0.54
21 31 0.29
22 6 0.06
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTAG
Found at i:3241824 original size:40 final size:38
Alignment explanation
Indices: 3241728--3241847 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 38
3241718 ACTAAAACCT
* *
3241728 GTTGCGAAATTAAAATTCGTGTTGTGAATTCGAAAATCGA
1 GTTGCG-AATTAAAATTCGCGTTGCGAATTCG-AAATCGA
* **
3241768 GTTGTGCAAAAAAAATTCGCGTTGCGAATTCAGAAATCGA
1 GTTGCG-AATTAAAATTCGCGTTGCGAATTC-GAAATCGA
* *
3241808 GTTGCGAATTTGAAATTCAGCGTTGCGAATTTGGAAATCG
1 GTTGCGAA-TTAAAATTC-GCGTTGCGAA-TTCGAAATCG
3241848 CAACGCGAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
39 2 0.03
40 43 0.66
41 18 0.28
42 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (38 bp):
GTTGCGAATTAAAATTCGCGTTGCGAATTCGAAATCGA
Found at i:3241856 original size:41 final size:41
Alignment explanation
Indices: 3241780--3241869 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
3241770 TGTGCAAAAA
**
3241780 AAATTCGCGTTGCGAATTCAGAAATCGAGTTGCGAATTT-G
1 AAATTCGCGTTGCGAATTCAGAAATCGAGACGCGAATTTAG
**
3241820 AAATTCAGCGTTGCGAATTTGGAAATCGCA-ACGCGAATTTAG
1 AAATTC-GCGTTGCGAATTCAGAAATCG-AGACGCGAATTTAG
*
3241862 AAAATCGC
1 AAATTCGC
3241870 AATGTGATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
40 6 0.14
41 29 0.69
42 7 0.17
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (41 bp):
AAATTCGCGTTGCGAATTCAGAAATCGAGACGCGAATTTAG
Found at i:3241880 original size:20 final size:21
Alignment explanation
Indices: 3241832--3241871 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3241822 ATTCAGCGTT
*
3241832 GCGAATTT-GGAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
3241852 GCGAATTTAGAAAATCGCAA
1 GCGAATTTAGAAAATCGCAA
3241872 TGTGATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:3242879 original size:21 final size:21
Alignment explanation
Indices: 3242834--3242896 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
3242824 ATTCTCAATT
* *
3242834 ATTTTTTTACTTATTATTTATAC
1 ATTTTTTTA-TAATTA-TTAGAC
3242857 ATTTTTTTATAATTATTAGAC
1 ATTTTTTTATAATTATTAGAC
*
3242878 ATTATTTTT-GAATTATTAG
1 ATT-TTTTTATAATTATTAG
3242897 CACAATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 17 0.47
22 10 0.28
23 9 0.25
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTTTTTTATAATTATTAGAC
Found at i:3245048 original size:11 final size:11
Alignment explanation
Indices: 3245032--3245059 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3245022 AAGTATTTAT
3245032 ATATTTATATC
1 ATATTTATATC
3245043 ATATTTATATC
1 ATATTTATATC
3245054 ATATTT
1 ATATTT
3245060 CAGTTAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATTTATATC
Found at i:3247805 original size:18 final size:18
Alignment explanation
Indices: 3247782--3247941 Score: 230
Period size: 18 Copynumber: 8.9 Consensus size: 18
3247772 GCGCGAAATT
*
3247782 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3247800 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
3247818 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
3247836 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
3247854 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
* *
3247872 TGTCCCGGAGGACCACTG
1 TGTCCCGAAGGACCACTA
* *
3247890 TGTCCCAAAGGACCACTC
1 TGTCCCGAAGGACCACTA
*
3247908 TGTCCAGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3247926 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
3247942 ATAGACCCTC
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 124 1.00
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3248736 original size:20 final size:22
Alignment explanation
Indices: 3248711--3248768 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
3248701 TTCCCCTTGA
3248711 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
3248731 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
3248754 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3248769 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:3250155 original size:20 final size:19
Alignment explanation
Indices: 3250130--3250169 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3250120 TTCAATCCCT
*
3250130 TTCATTTCTTTATTCCATTA
1 TTCATTTATTTATTCC-TTA
3250150 TTCATTTATTTATTCCTTA
1 TTCATTTATTTATTCCTTA
3250169 T
1 T
3250170 ACACAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (19 bp):
TTCATTTATTTATTCCTTA
Found at i:3251323 original size:28 final size:28
Alignment explanation
Indices: 3251292--3251373 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
3251282 AAATCTTATT
3251292 CTATTAGCAAGAAAACATACTCCTTACA
1 CTATTAGCAAGAAAACATACTCCTTACA
* ** *
3251320 CTATCAG--ATCAAA-AT--T--TTTCA
1 CTATTAGCAAGAAAACATACTCCTTACA
3251341 TCTATTAGCAAGAAAACATACTCCTTACA
1 -CTATTAGCAAGAAAACATACTCCTTACA
3251370 CTAT
1 CTAT
3251374 CAGATCAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 16
0.61 0.13 0.26
Matches are distributed among these distances:
21 4 0.11
22 6 0.16
23 1 0.03
24 4 0.11
25 4 0.11
26 4 0.11
27 1 0.03
28 10 0.26
29 4 0.11
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.30
Consensus pattern (28 bp):
CTATTAGCAAGAAAACATACTCCTTACA
Found at i:3251350 original size:50 final size:50
Alignment explanation
Indices: 3251291--3251390 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
3251281 CAAATCTTAT
3251291 TCTATTAGCAAGAAAACATACTCCTTACACTATCAGATCAAAATTTTTCA
1 TCTATTAGCAAGAAAACATACTCCTTACACTATCAGATCAAAATTTTTCA
3251341 TCTATTAGCAAGAAAACATACTCCTTACACTATCAGATCAAAATTTTTCA
1 TCTATTAGCAAGAAAACATACTCCTTACACTATCAGATCAAAATTTTTCA
3251391 CTTTTAGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (50 bp):
TCTATTAGCAAGAAAACATACTCCTTACACTATCAGATCAAAATTTTTCA
Found at i:3252139 original size:18 final size:18
Alignment explanation
Indices: 3252116--3252273 Score: 221
Period size: 18 Copynumber: 8.9 Consensus size: 18
3252106 GCGCGAAATT
*
3252116 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
3252134 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
3252152 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
3252170 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
3252188 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
3252206 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
* *
3252224 TGTCCCAAAGGA-C-CTC
1 TGTCCCGAAGGACCACTA
*
3252240 TGTCCAGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3252258 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
3252274 ATAGACCCTC
Statistics
Matches: 122, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
16 12 0.10
17 2 0.02
18 108 0.89
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3253031 original size:20 final size:22
Alignment explanation
Indices: 3253006--3253061 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 22
3252996 TTCCCCTTGA
3253006 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
3253026 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
3253049 A-TGCATCGATGCA
1 AGTGCATCGATGCA
3253062 CTACCCTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.52
22 13 0.39
23 3 0.09
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Done.