Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1967576 original size:3 final size:3
Alignment explanation
Indices: 1967568--1967612 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1967558 CGACTGCCCC
1967568 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1967613 GGGTAAACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1969786 original size:19 final size:19
Alignment explanation
Indices: 1969754--1969802 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
1969744 CTGGAGGAAA
* * *
1969754 AAAATATATGAAATTAAAT
1 AAAATAAATAAAATAAAAT
* *
1969773 TAAATTAATAAAATAAAAT
1 AAAATAAATAAAATAAAAT
1969792 AAAATAAATAA
1 AAAATAAATAA
1969803 TATGATATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAATAAAATAAAAT
Found at i:1969812 original size:19 final size:18
Alignment explanation
Indices: 1969790--1969829 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1969780 ATAAAATAAA
1969790 ATAAAATAAATAATATGAT
1 ATAAAATAAATAATAT-AT
* *
1969809 ATAAACTATATAATATAT
1 ATAAAATAAATAATATAT
1969827 ATA
1 ATA
1969830 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATAATATAT
Found at i:1969959 original size:38 final size:35
Alignment explanation
Indices: 1969811--1970190 Score: 217
Period size: 38 Copynumber: 10.5 Consensus size: 35
1969801 AATATGATAT
* *
1969811 AAACTATATAATATAT-ATATTTCAAAAATACGTTTTAGA
1 AAACTATATATTATATAAT-TTTC-AAAAT--GTTTT-TA
* * *
1969850 AAACTATATATTACATAGTTTTCAAAACG-TTTTA
1 AAACTATATATTATATAATTTTCAAAATGTTTTTA
*
1969884 AAAATAT-TATATATATAAGTTTTCAAAAATGTTTTTA
1 AAACTATATAT-TATATAA-TTTTC-AAAATGTTTTTA
*
1969921 AAACTATATATTATATAATTTCACAAAAAATGTTTTTA
1 AAACTATATATTATATAATTT-TC--AAAATGTTTTTA
* * * *
1969959 AAACTATATACTATATATGTTTTCAAAGTGTTTTAA
1 AAACTATATATTATATA-ATTTTCAAAATGTTTTTA
* * *
1969995 AAATTATATAATATATAAACGTTTTCAAAATGTTTTCA
1 AAACTATATATTATAT-AA--TTTTCAAAATGTTTTTA
*
1970033 AAACTATATA-T-TAT-A---T---AATGTTTTAA
1 AAACTATATATTATATAATTTTCAAAATGTTTTTA
* * *
1970059 AAACTATATAATATATAAACGTTTCCAAAATGTTTTCA
1 AAACTATATATTATAT-AA--TTTTCAAAATGTTTTTA
** * *
1970097 AAACTATATATTATATATATTTAAAAAAATATTTTCAA
1 AAACTATATATTATATA-ATTT-TCAAAATGTTTT-TA
* *
1970135 AAACTATATAATATATAAATTTTCGAAAATCATTTTCTGA
1 AAACTATATATTATAT-AATTTTC-AAAAT-GTTTT-T-A
*
1970175 AAATTATATATTATAT
1 AAACTATATATTATAT
1970191 TTTGTCAAAA
Statistics
Matches: 274, Mismatches: 36, Indels: 61
0.74 0.10 0.16
Matches are distributed among these distances:
26 19 0.07
27 1 0.00
28 3 0.01
29 1 0.00
30 1 0.00
33 3 0.01
34 13 0.05
35 8 0.03
36 39 0.14
37 31 0.11
38 111 0.41
39 28 0.10
40 16 0.06
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (35 bp):
AAACTATATATTATATAATTTTCAAAATGTTTTTA
Found at i:1970011 original size:74 final size:73
Alignment explanation
Indices: 1969811--1970201 Score: 273
Period size: 74 Copynumber: 5.4 Consensus size: 73
1969801 AATATGATAT
* * * * *
1969811 AAACTATATAATATATAT-ATTTCAAAAATACGTTTTAGAAAACTATAT-AT-TACATAGTTTTC
1 AAACTATAT-ATATATATGTTTTCAAAAAT--GTTTTA-AAAACTATATAATATATAAACTTTAC
*
1969873 AAAACG-TTTTA
62 AAAATGTTTTTA
* * * *
1969884 AAAATATTATATATATAAGTTTTCAAAAATGTTTTTAAAACTATATATTATAT-AA-TTTCACAA
1 AAACTA-TATATATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACTTT-AC--
1969947 AAAATGTTTTTA
62 AAAATGTTTTTA
* * *
1969959 AAACTATATACTATATATGTTTTC-AAAGTGTTTTAAAAATTATATAATATATAAACGTTTTCAA
1 AAACTATATA-TATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAAC-TTTACAA
*
1970023 AATGTTTTCA
64 AATGTTTTTA
*
1970033 AAACTATATAT-TATA-----T----AATGTTTTAAAAACTATATAATATATAAACGTTTCCAAA
1 AAACTATATATATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAAC-TTTACAAA
*
1970088 ATGTTTTCA
65 ATGTTTTTA
* ** * *
1970097 AAACTATATATTATATATATTTAAAAAAATATTTTCAAAAACTATATAATATATAAA-TTTTCGA
1 AAACTATATA-TATATATGTTTTCAAAAATGTTTT-AAAAACTATATAATATATAAACTTTAC-A
*
1970161 AAATCATTTTCTGA
63 AAAT-GTTTT-T-A
*
1970175 AAATTATATAT-TATAT-TTTGTCAAAAA
1 AAACTATATATATATATGTTT-TCAAAAA
1970202 CATTTTTACA
Statistics
Matches: 261, Mismatches: 28, Indels: 55
0.76 0.08 0.16
Matches are distributed among these distances:
64 55 0.21
65 1 0.00
66 4 0.02
67 1 0.00
71 13 0.05
72 12 0.05
73 15 0.06
74 71 0.27
75 39 0.15
76 36 0.14
77 4 0.02
78 10 0.04
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.42
Consensus pattern (73 bp):
AAACTATATATATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACTTTACAAAA
TGTTTTTA
Found at i:1970052 original size:26 final size:26
Alignment explanation
Indices: 1970023--1970076 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1970013 ACGTTTTCAA
* *
1970023 AATGTTTTCAAAACTATATATTATAT
1 AATGTTTTAAAAACTATATAATATAT
1970049 AATGTTTTAAAAACTATATAATATAT
1 AATGTTTTAAAAACTATATAATATAT
1970075 AA
1 AA
1970077 ACGTTTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (26 bp):
AATGTTTTAAAAACTATATAATATAT
Found at i:1970070 original size:64 final size:64
Alignment explanation
Indices: 1969987--1970113 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
1969977 GTTTTCAAAG
* *
1969987 TGTTTTAAAAATTATATAATATATAAACGTTTTCAAAATGTTTTCAAAACTATATATTATATAA
1 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATAA
1970051 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATA
1 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATA
1970114 TATTTAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (64 bp):
TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATAA
Found at i:1970088 original size:28 final size:26
Alignment explanation
Indices: 1970028--1970088 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1970018 TTCAAAATGT
* *
1970028 TTTC-AAAACTATATATTATATAATG
1 TTTCAAAAACTATATAATATATAACG
*
1970053 TTTTAAAAACTATATAATATATAAACG
1 TTTCAAAAACTATATAATATAT-AACG
*
1970080 TTTCCAAAA
1 TTTCAAAAA
1970089 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 3 0.10
26 16 0.55
27 10 0.34
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (26 bp):
TTTCAAAAACTATATAATATATAACG
Found at i:1970089 original size:138 final size:140
Alignment explanation
Indices: 1969911--1970190 Score: 340
Period size: 138 Copynumber: 2.0 Consensus size: 140
1969901 AGTTTTCAAA
* * *
1969911 AATGTTTTTAAAACTATATATTATATAATTTCACAAAAAATGTTTTTAAAACTATATACTATATA
1 AATGTTTTAAAAACTATATAATATATAATTTCAC-AAAAATGTTTTCAAAACTATATACTATATA
* ** * * * *
1969976 TGTTT-TCAAAGTGTTTT-AAAAATTATATAATATATAAACGTTTTC-AAAAT-GTTTTC-AAAA
65 TATTTAAAAAAATATTTTCAAAAACTATATAATATATAAA--TTTTCGAAAATCATTTTCGAAAA
1970036 CTATATATTATAT
128 CTATATATTATAT
*
1970049 AATGTTTTAAAAACTATATAATATATAAACGTTTC-C-AAAATGTTTTCAAAACTATATATTATA
1 AATGTTTTAAAAACTATATAATATAT-AA--TTTCACAAAAATGTTTTCAAAACTATATACTATA
1970112 TATATTTAAAAAAATATTTTCAAAAACTATATAATATATAAATTTTCGAAAATCATTTTCTGAAA
63 TATATTTAAAAAAATATTTTCAAAAACTATATAATATATAAATTTTCGAAAATCATTTTC-GAAA
*
1970177 ATTATATATTATAT
127 ACTATATATTATAT
1970191 TTTGTCAAAA
Statistics
Matches: 121, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
138 60 0.50
139 15 0.12
140 26 0.21
141 4 0.03
142 16 0.13
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (140 bp):
AATGTTTTAAAAACTATATAATATATAATTTCACAAAAATGTTTTCAAAACTATATACTATATAT
ATTTAAAAAAATATTTTCAAAAACTATATAATATATAAATTTTCGAAAATCATTTTCGAAAACTA
TATATTATAT
Found at i:1970987 original size:82 final size:82
Alignment explanation
Indices: 1970880--1971154 Score: 304
Period size: 82 Copynumber: 3.3 Consensus size: 82
1970870 CTTTTGGTCA
* *
1970880 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAATCA
1 CAGATAACCCTTCTAGACTTAAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAATCA
1970945 AACTCAAAGGTCTTTAG
66 AACTCAAAGGTCTTTAG
* * * * * * * **** *
1970962 CAGATAACCCTTCTTGACTTAAGCTATGCTGCAA--ATGATGTGCCT-TGGAGCTGAGCGGAGTC
1 CAGATAACCCTTCTAGACTTAAGCTATTCTGTAAGCTTGATTTGCCTCT-AAGTTGAATATAATC
* * *
1971024 GAACTCGAAGGTCTTTTGG
65 AAACTCAAAGGTC-TTTAG
* *
1971043 TCACAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAA
1 ---CAGATAACCCTTCTAGACTTAAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAA
1971108 TCAAACTCAAAGGTCTTTAG
63 TCAAACTCAAAGGTCTTTAG
*
1971128 CAGATAACCCTTCTTGACTTAAGCTAT
1 CAGATAACCCTTCTAGACTTAAGCTAT
1971155 GCTGCAAATG
Statistics
Matches: 148, Mismatches: 37, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
79 1 0.01
80 28 0.19
81 4 0.03
82 53 0.36
84 29 0.20
85 4 0.03
86 28 0.19
87 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (82 bp):
CAGATAACCCTTCTAGACTTAAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAATCA
AACTCAAAGGTCTTTAG
Found at i:1971071 original size:84 final size:82
Alignment explanation
Indices: 1970815--1971664 Score: 771
Period size: 84 Copynumber: 10.2 Consensus size: 82
1970805 GATTTGCCTC
*
1970815 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCAG-AGTCGAACTCGAAGGTCTTTTGGTC
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGC-GTAGTCGAACTCAAAGGTC-TTTGGTC
*
1970879 ACAGATAACCCTTCTAGCCT
63 ACAGATAACCCTTCTAGACT
* * * * * * * *** * * *
1970899 TGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAATCAAACTCAAAGGTCTTTAG--
1 TAAGCTATGCTGCAA--ATGATGTGCCT-TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTC
*
1970962 -CAGATAACCCTTCTTGACT
63 ACAGATAACCCTTCTAGACT
* *
1970981 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTCA
*
1971046 CAGATAACCCTTCTAGCCT
64 CAGATAACCCTTCTAGACT
* * * * * * * *** * * *
1971065 TGAGCTATTCTGTAAGCTTGATTTGCCTCTAAGTTGAATATAATCAAACTCAAAGGTCTTTAG--
1 TAAGCTATGCTGCAA--ATGATGTGCCT-TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTC
*
1971128 -CAGATAACCCTTCTTGACT
63 ACAGATAACCCTTCTAGACT
* *
1971147 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTCA
*
1971212 CAGATAACCCTTCTAGCCT
64 CAGATAACCCTTCTAGACT
* * * * **
1971231 TGAGCTATTCTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGG
1 TAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTCA
*
1971296 CAGACAACCCTTCTAGACT
64 CAGATAACCCTTCTAGACT
* * ** * * **
1971315 TAAGTTGTATTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTGGTTGG
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG-TCA
* *
1971380 CAGATAGCCCTTCTCGACT
64 CAGATAACCCTTCTAGACT
* * * * **
1971399 TAAGCTATGCCGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAAACTCAAAGGTCTTTTGTTGG
1 TAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTCA
*
1971464 CAGACAACCCTTCTAGACT
64 CAGATAACCCTTCTAGACT
* * * * *
1971483 TAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTCAC
1 TAAGCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTCAC
*
1971548 AGATAACCCTTCTAGCCT
65 AGATAACCCTTCTAGACT
* * **
1971566 TGAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTGGTGGC
1 TAAGCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTCAC
* * * *
1971630 AGGTAGCCCTTCTGGCCT
65 AGATAACCCTTCTAGACT
* *
1971648 TGAGCTAAGCTGCAAAT
1 TAAGCTATGCTGCAAAT
1971665 AGTTTGTTCA
Statistics
Matches: 615, Mismatches: 127, Indels: 50
0.78 0.16 0.06
Matches are distributed among these distances:
79 2 0.00
80 56 0.09
81 8 0.01
82 94 0.15
83 78 0.13
84 303 0.49
85 16 0.03
86 56 0.09
87 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (82 bp):
TAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTCACA
GATAACCCTTCTAGACT
Found at i:1971418 original size:168 final size:166
Alignment explanation
Indices: 1970815--1971623 Score: 1017
Period size: 166 Copynumber: 4.9 Consensus size: 166
1970805 GATTTGCCTC
1970815 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC-AGAGTCGAACTCGAAGGTCTTTTGGTC
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGA-AGTCGAACTCGAAGGTCTTTTGGTC
* * * * ** *
1970879 ACAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCC-TCTAAGTTGAATATAAT
65 ACAGATAACCCTTCTAGCCTTGAGCTATTCTGTAA--ATGATGTGCCGT-TGAGCTGAACGTAGT
* *
1970943 CAAACTCAAAGGTC--TTTAGCAGATAACCCTTCTTGACT
127 CAAACTCAAAGGTCTTTTTAGCAGACAACCCTTCTAGACT
*
1970981 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTCA
* * * * ** *
1971046 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAGCTTGATTTGCC-TCTAAGTTGAATATAATC
66 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAA--ATGATGTGCCGT-TGAGCTGAACGTAGTC
* *
1971110 AAACTCAAAGGTC--TTTAGCAGATAACCCTTCTTGACT
128 AAACTCAAAGGTCTTTTTAGCAGACAACCCTTCTAGACT
*
1971147 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCA
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTCA
* *
1971212 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
66 CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAATGATGTGCCGTTGAGCTGAACGTAGTCAAA
*
1971277 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACT
131 CTCAAAGGTC-TTT-TTAGCAGACAACCCTTCTAGACT
* * ** *
1971315 TAAGTTGTATTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTC-TTTGGTTG
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGG-TC
* * * * * * * * *
1971379 GCAGATAGCCCTTCTCGACTTAAGCTATGCCGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAA
65 ACAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAATGATGTGCCGTTGAGCTGAACGTAGTCAA
*
1971444 ACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACT
130 ACTCAAAGGTC-TTT-TTAGCAGACAACCCTTCTAGACT
* * *
1971483 TAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGC-ATAGTCGAACTCGAAGGTC-TTTGGTC
1 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGA-AGTCGAACTCGAAGGTCTTTTGGTC
* * * * *
1971546 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGA
65 ACAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAATGATGTGCCGTTGAGCTGAACGTAGTCAA
1971611 ACTCAAAGGTCTT
130 ACTCAAAGGTCTT
1971624 GGTGGCAGGT
Statistics
Matches: 593, Mismatches: 42, Indels: 16
0.91 0.06 0.02
Matches are distributed among these distances:
164 30 0.05
165 1 0.00
166 265 0.45
167 75 0.13
168 222 0.37
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (166 bp):
TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGAAGTCGAACTCGAAGGTCTTTTGGTCA
CAGATAACCCTTCTAGCCTTGAGCTATTCTGTAAATGATGTGCCGTTGAGCTGAACGTAGTCAAA
CTCAAAGGTCTTTTTAGCAGACAACCCTTCTAGACT
Found at i:1975069 original size:18 final size:19
Alignment explanation
Indices: 1975028--1975072 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1975018 AGTTAATGTG
1975028 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
1975047 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
1975065 AATGCAAA
1 AATGCAAA
1975073 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:1978409 original size:19 final size:19
Alignment explanation
Indices: 1978377--1978425 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
1978367 CTGGAGGAAA
* * *
1978377 AAAATATATGAAATTAAAT
1 AAAATAAATAAAATAAAAT
* *
1978396 TAAATTAATAAAATAAAAT
1 AAAATAAATAAAATAAAAT
1978415 AAAATAAATAA
1 AAAATAAATAA
1978426 TATGATATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATAAATAAAATAAAAT
Found at i:1978435 original size:19 final size:18
Alignment explanation
Indices: 1978413--1978452 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1978403 ATAAAATAAA
1978413 ATAAAATAAATAATATGAT
1 ATAAAATAAATAATAT-AT
* *
1978432 ATAAACTATATAATATAT
1 ATAAAATAAATAATATAT
1978450 ATA
1 ATA
1978453 TTTCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
ATAAAATAAATAATATAT
Found at i:1978585 original size:38 final size:35
Alignment explanation
Indices: 1978434--1978789 Score: 246
Period size: 38 Copynumber: 9.8 Consensus size: 35
1978424 AATATGATAT
*
1978434 AAACTATATAATATAT-ATATTTCAAAAATACGTTTTAGA
1 AAACTATATATTATATAAT-TTTC-AAAAT--GTTTTA-A
* * *
1978473 AAACTATATATTACATAGTTTTCAAAACGTTTTAAA
1 AAACTATATATTATATAATTTTCAAAATGTTTT-AA
* *
1978509 AATATTATATATTATATAAGTTTTCAAAAATGTTTTTA
1 AA-ACTATATATTATATAA-TTTTC-AAAATGTTTTAA
* *
1978547 AAACTATATATTATATAATTTCACAAAAAATGTTTTTA
1 AAACTATATATTATATAATTT-TC--AAAATGTTTTAA
* * *
1978585 AAACTATATACTATATATGTTTTCAAAGTGTTTTAA
1 AAACTATATATTATATA-ATTTTCAAAATGTTTTAA
* * *
1978621 AAATTATATAATATATAAACGTTTTCAAAATGTTTTCA
1 AAACTATATATTATAT-AA--TTTTCAAAATGTTTTAA
1978659 AAACTATATA-T-TAT-A---T---AATGTTTTAA
1 AAACTATATATTATATAATTTTCAAAATGTTTTAA
* * *
1978685 AAACTATATAATATATAAACGTTTCCAAAATGTTTTCA
1 AAACTATATATTATAT-AA--TTTTCAAAATGTTTTAA
** *
1978723 AAACTATATATTATATATATTTAAAAAATATTTTCAA
1 AAACTATATATTATATA-ATTTTCAAAATGTTTT-AA
*
1978760 AAACTATATAATATATAAATTTTCGAAAAT
1 AAACTATATATTATAT-AATTTTC-AAAAT
1978790 CATTTTCTGA
Statistics
Matches: 257, Mismatches: 33, Indels: 55
0.74 0.10 0.16
Matches are distributed among these distances:
26 19 0.07
27 1 0.00
28 3 0.01
29 1 0.00
30 1 0.00
34 1 0.00
36 50 0.19
37 53 0.21
38 97 0.38
39 30 0.12
40 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (35 bp):
AAACTATATATTATATAATTTTCAAAATGTTTTAA
Found at i:1978630 original size:74 final size:74
Alignment explanation
Indices: 1978434--1978815 Score: 280
Period size: 74 Copynumber: 5.2 Consensus size: 74
1978424 AATATGATAT
* * * * * *
1978434 AAACTATATAATATATAT-ATTTCAAAAATACGTTTTAGAAAACTATAT-AT-TACATAGTTTTC
1 AAACTATATATTATATATGTTTTCAAAAAT--GTTTTA-AAAACTATATAATATATAAACTTTAC
* *
1978496 AAAACGTTTTAAA
63 AAAATGTTTT-CA
* * * *
1978509 AATATTATATATTATATAAGTTTTCAAAAATGTTTTTAAAACTATATATTATAT-AA-TTTCACA
1 AA-ACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACTTT-AC-
*
1978572 AAAAATGTTTTTA
63 -AAAATGTTTTCA
* * * *
1978585 AAACTATATACTATATATGTTTTC-AAAGTGTTTTAAAAATTATATAATATATAAACGTTTTCAA
1 AAACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAAC-TTTACAA
1978649 AATGTTTTCA
65 AATGTTTTCA
*
1978659 AAACTATATA-T-TATA-----T----AATGTTTTAAAAACTATATAATATATAAACGTTTCCAA
1 AAACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAAC-TTTACAA
1978713 AATGTTTTCA
65 AATGTTTTCA
* * * *
1978723 AAACTATATATTATATAT-ATTTAAAAAATATTTTCAAAAACTATATAATATATAAA-TTTTCGA
1 AAACTATATATTATATATGTTTTCAAAAATGTTTT-AAAAACTATATAATATATAAACTTTAC-A
*
1978786 AAATCATTTTCTGA
64 AAAT-GTTTTC--A
*
1978800 AAATTATATATTATAT
1 AAACTATATATTATAT
1978816 TTTGTCAAAA
Statistics
Matches: 255, Mismatches: 27, Indels: 48
0.77 0.08 0.15
Matches are distributed among these distances:
64 55 0.22
65 1 0.00
66 4 0.02
67 1 0.00
70 1 0.00
72 4 0.02
73 5 0.02
74 70 0.27
75 57 0.22
76 19 0.07
77 38 0.15
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (74 bp):
AAACTATATATTATATATGTTTTCAAAAATGTTTTAAAAACTATATAATATATAAACTTTACAAA
ATGTTTTCA
Found at i:1978671 original size:112 final size:112
Alignment explanation
Indices: 1978434--1978677 Score: 325
Period size: 112 Copynumber: 2.2 Consensus size: 112
1978424 AATATGATAT
* * *
1978434 AAACTATATAATATATATATTTCAAAAATACGTTTTAGAAAACTATATATTACATAGTTTTCAAA
1 AAACTATATATTATATA-ATTTCAAAAAAACGTTTTAGAAAACTATATACTACATAGTTTTCAAA
* *
1978499 ACGTTTTAAAAATATTATATATTATATAAGTTTTCAAAAATGTTTTTA
65 ACGTTTTAAAAATATTATATAATATATAAGTTTTCAAAAATGTTTTCA
* * *
1978547 AAACTATATATTATATAATTTCACAAAAAATGTTTT-TAAAACTATATACTATATATGTTTTCAA
1 AAACTATATATTATATAATTTCA-AAAAAACGTTTTAGAAAACTATATACTACATA-GTTTTCAA
**
1978611 AGTGTTTT-AAAA-ATTATATAATATATAAACGTTTTC-AAAATGTTTTCA
64 AACGTTTTAAAAATATTATATAATATAT-AA-GTTTTCAAAAATGTTTTCA
1978659 AAACTATATATTATATAAT
1 AAACTATATATTATATAAT
1978678 GTTTTAAAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
111 13 0.11
112 58 0.50
113 46 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (112 bp):
AAACTATATATTATATAATTTCAAAAAAACGTTTTAGAAAACTATATACTACATAGTTTTCAAAA
CGTTTTAAAAATATTATATAATATATAAGTTTTCAAAAATGTTTTCA
Found at i:1978678 original size:26 final size:26
Alignment explanation
Indices: 1978649--1978702 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1978639 ACGTTTTCAA
* *
1978649 AATGTTTTCAAAACTATATATTATAT
1 AATGTTTTAAAAACTATATAATATAT
1978675 AATGTTTTAAAAACTATATAATATAT
1 AATGTTTTAAAAACTATATAATATAT
1978701 AA
1 AA
1978703 ACGTTTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (26 bp):
AATGTTTTAAAAACTATATAATATAT
Found at i:1978696 original size:64 final size:64
Alignment explanation
Indices: 1978613--1978739 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 64
1978603 GTTTTCAAAG
* *
1978613 TGTTTTAAAAATTATATAATATATAAACGTTTTCAAAATGTTTTCAAAACTATATATTATATAA
1 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATAA
1978677 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATA
1 TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATA
1978740 TATTTAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.43
Consensus pattern (64 bp):
TGTTTTAAAAACTATATAATATATAAACGTTTCCAAAATGTTTTCAAAACTATATATTATATAA
Found at i:1978714 original size:28 final size:26
Alignment explanation
Indices: 1978654--1978714 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1978644 TTCAAAATGT
* *
1978654 TTTC-AAAACTATATATTATATAATG
1 TTTCAAAAACTATATAATATATAACG
*
1978679 TTTTAAAAACTATATAATATATAAACG
1 TTTCAAAAACTATATAATATAT-AACG
*
1978706 TTTCCAAAA
1 TTTCAAAAA
1978715 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 3 0.10
26 16 0.55
27 10 0.34
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (26 bp):
TTTCAAAAACTATATAATATATAACG
Found at i:1991649 original size:20 final size:21
Alignment explanation
Indices: 1991624--1991665 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1991614 ACCCTTAAAT
1991624 CCACAACCATAAC-CTCAAAA
1 CCACAACCATAACTCTCAAAA
*
1991644 CCACAACCATAGCTCTCAAAA
1 CCACAACCATAACTCTCAAAA
1991665 C
1 C
1991666 AACCATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.45, C:0.40, G:0.02, T:0.12
Consensus pattern (21 bp):
CCACAACCATAACTCTCAAAA
Found at i:2001669 original size:231 final size:231
Alignment explanation
Indices: 2001266--2001729 Score: 775
Period size: 231 Copynumber: 2.0 Consensus size: 231
2001256 CGACGTAATG
2001266 TAAACAGAGATTCGATCCATAAAATAAAACTCAAACGGTTTTAAGATTATATTTTATCATATCCC
1 TAAACAGAGATTCGATCCATAAAATAAAACTCAAACGGTTTTAAGATTATATTTTATCATATCCC
* * * * * *
2001331 AGTGAGCATCTTAATGTCCAGCTGAGACGTTCGCTAATTATTTAATTGAAAATGATGAGTTTAGA
66 AATGAGCATCTTAACGTCCAACTCAGACGGTCGCTAATTATTTAACTGAAAATGATGAGTTTAGA
*
2001396 ACATATAAATAATCATGTGAATATTTTAAAAATTTTAATAATCGGGGACTCAACAATGCATCACT
131 ACATATAAATAATCATGTGAATATTTTAAAAATTTTAATAATCGAGGACTCAACAATGCATCACT
*
2001461 TTATAGTTAAAGGATTATTGTGTAACTTTCAATAGT
196 TTATAGTTAAAAGATTATTGTGTAACTTTCAATAGT
* * *
2001497 TAAACAGATATTCGATCCATAAAATATAGCTCAAACGGTTTTAAGATTATATTTTATCATATCCC
1 TAAACAGAGATTCGATCCATAAAATAAAACTCAAACGGTTTTAAGATTATATTTTATCATATCCC
* *
2001562 AATGAGCATCTTAACGTCCAATTCAGACGGTCGCTAATTATTTAACTGAAAATGATGAGTTTATA
66 AATGAGCATCTTAACGTCCAACTCAGACGGTCGCTAATTATTTAACTGAAAATGATGAGTTTAGA
* * * *
2001627 ACATATAAATAATCATGTGACTATTTTATAATTTTTAATAATCGAGGATTCAACAATGCATCACT
131 ACATATAAATAATCATGTGAATATTTTAAAAATTTTAATAATCGAGGACTCAACAATGCATCACT
2001692 TTATAGTTAAAAGATTATTGTGTAACTTTCAATAGT
196 TTATAGTTAAAAGATTATTGTGTAACTTTCAATAGT
2001728 TA
1 TA
2001730 GGGGACAAGA
Statistics
Matches: 216, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
231 216 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (231 bp):
TAAACAGAGATTCGATCCATAAAATAAAACTCAAACGGTTTTAAGATTATATTTTATCATATCCC
AATGAGCATCTTAACGTCCAACTCAGACGGTCGCTAATTATTTAACTGAAAATGATGAGTTTAGA
ACATATAAATAATCATGTGAATATTTTAAAAATTTTAATAATCGAGGACTCAACAATGCATCACT
TTATAGTTAAAAGATTATTGTGTAACTTTCAATAGT
Found at i:2002654 original size:27 final size:24
Alignment explanation
Indices: 2002624--2002677 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
2002614 TAAAAAAGTC
*
2002624 AAAAAGATTAGATAGAATAAAATAATA
1 AAAAAGATTAAATA-AA-AAAATAA-A
*
2002651 AAAAATATTAAATAAAAAAATAAA
1 AAAAAGATTAAATAAAAAAATAAA
2002675 AAA
1 AAA
2002678 TAATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 7 0.28
26 2 0.08
27 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (24 bp):
AAAAAGATTAAATAAAAAAATAAA
Found at i:2002667 original size:22 final size:24
Alignment explanation
Indices: 2002639--2002699 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
2002629 GATTAGATAG
2002639 AATAAAATAATAAAAAAT-AT-TA
1 AATAAAATAATAAAAAATAATATA
*
2002661 AATAAAAAAATAAAAAATAATAATA
1 AATAAAATAATAAAAAATAAT-ATA
*
2002686 AATGAAATAATAAA
1 AATAAAATAATAAA
2002700 TTTAAGGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.52
23 2 0.06
25 14 0.42
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (24 bp):
AATAAAATAATAAAAAATAATATA
Found at i:2002670 original size:25 final size:24
Alignment explanation
Indices: 2002624--2002699 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
2002614 TAAAAAAGTC
* *
2002624 AAAAAGATTAGATAGAATAAAATAATA
1 AAAAATATTAAATA-AA-AAAATAA-A
2002651 AAAAATATTAAATAAAAAAATAAA
1 AAAAATATTAAATAAAAAAATAAA
* * *
2002675 AAATAATAATAAATGAAATAATAAA
1 AAA-AATATTAAATAAAAAAATAAA
2002700 TTTAAGGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
24 4 0.09
25 25 0.58
26 2 0.05
27 12 0.28
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.22
Consensus pattern (24 bp):
AAAAATATTAAATAAAAAAATAAA
Found at i:2002678 original size:15 final size:15
Alignment explanation
Indices: 2002639--2002699 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
2002629 GATTAGATAG
2002639 AATAAAATAAT-AAAA
1 AATAAAA-AATAAAAA
**
2002654 AATATTAAATAAAAA
1 AATAAAAAATAAAAA
2002669 AATAAAAAATAATAATA
1 AATAAAAAATAA-AA-A
*
2002686 AATGAAATAATAAA
1 AAT-AAAAAATAAA
2002700 TTTAAGGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
14 3 0.08
15 19 0.51
16 2 0.05
17 5 0.14
18 8 0.22
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAAAAAATAAAAA
Found at i:2002731 original size:46 final size:46
Alignment explanation
Indices: 2002666--2002776 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
2002656 TATTAAATAA
2002666 AAAAATAAAAAATAATAATAAATGAAATAATAAATTTAAGGGAAAC
1 AAAAATAAAAAATAATAATAAATGAAATAATAAATTTAAGGGAAAC
2002712 AAAAATAAAAAATAATAATAAATGAAATAATAAATTTAAGGGAAAC
1 AAAAATAAAAAATAATAATAAATGAAATAATAAATTTAAGGGAAAC
2002758 -AAAATAAAATAATTAATAA
1 AAAAATAAAA-AA-TAATAA
2002777 AGGAAAATTA
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
45 9 0.14
46 48 0.76
47 6 0.10
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (46 bp):
AAAAATAAAAAATAATAATAAATGAAATAATAAATTTAAGGGAAAC
Found at i:2004086 original size:9 final size:9
Alignment explanation
Indices: 2004070--2004098 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2004060 AAATTAAATT
2004070 AAAT-AAAA
1 AAATAAAAA
2004078 AAATAAAAA
1 AAATAAAAA
2004087 AAATAAAAA
1 AAATAAAAA
2004096 AAA
1 AAA
2004099 ATAATATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAATAAAAA
Found at i:2004087 original size:10 final size:10
Alignment explanation
Indices: 2004074--2004102 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2004064 TAAATTAAAT
2004074 AAAAAAAT-A
1 AAAAAAATAA
2004083 AAAAAAATAA
1 AAAAAAATAA
2004093 AAAAAAATAA
1 AAAAAAATAA
2004103 TATACTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:2004090 original size:22 final size:20
Alignment explanation
Indices: 2004049--2004099 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
2004039 CCTGGACCAG
* * *
2004049 AAAAACAAAATAAATTAAATT
1 AAAAAAAAAATAAA-AAAAAT
2004070 AAATAAAAAAATAAAAAAAAT
1 AAA-AAAAAAATAAAAAAAAT
2004091 AAAAAAAAA
1 AAAAAAAAA
2004100 TAATATACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 6 0.23
21 10 0.38
22 10 0.38
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAAAAAATAAAAAAAAT
Found at i:2004156 original size:28 final size:27
Alignment explanation
Indices: 2004125--2004206 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
2004115 AATATAATAT
2004125 AAACTATATAATATATATATTTCAAAAA
1 AAACTATATAATATATAT-TTTCAAAAA
*
2004153 AAACTATATACTATAT-TTTT-AAAAA
1 AAACTATATAATATATATTTTCAAAAA
* * *
2004178 AAAGTTTTATATTATATAGTTTTCAAAAA
1 AAA-CTATATAATATATA-TTTTCAAAAA
2004207 TGATTTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 8 0.17
26 13 0.28
27 1 0.02
28 19 0.41
29 5 0.11
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (27 bp):
AAACTATATAATATATATTTTCAAAAA
Found at i:2004176 original size:24 final size:23
Alignment explanation
Indices: 2004135--2004180 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2004125 AAACTATATA
2004135 ATATATATATTTCAAAAAAAACT
1 ATATATATATTTCAAAAAAAACT
*
2004158 ATATACTATATTTTTAAAAAAAA
1 ATATA-TATA-TTTCAAAAAAAA
2004181 GTTTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 11 0.55
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATATATATTTCAAAAAAAACT
Found at i:2004460 original size:37 final size:37
Alignment explanation
Indices: 2004185--2004459 Score: 347
Period size: 37 Copynumber: 7.6 Consensus size: 37
2004175 AAAAAAGTTT
* *
2004185 TATATTATAT-AGTTTTCAAAAATG-ATTT-AAA--A
1 TATATTATATAATTTTTCAAAAATGTTTTTAAAACTA
*
2004217 -ATATTATATAAGTTTTCAAAAATGTTTTTAAAACTA
1 TATATTATATAATTTTTCAAAAATGTTTTTAAAACTA
*
2004253 TATATTATATAATTTTTCAAAAATATTTTTAAAACTA
1 TATATTATATAATTTTTCAAAAATGTTTTTAAAACTA
2004290 TATATTATATAATTTTTCAAAAATGTTTTTAAAACTA
1 TATATTATATAATTTTTCAAAAATGTTTTTAAAACTA
**
2004327 TATATTATATAAGTTTTTTTAAAATG-TTTTAAAAGCTA
1 TATATTATATAA-TTTTTCAAAAATGTTTTTAAAA-CTA
* *
2004365 TATATTATATAAGTTTTTTC-AAAATGTTTTAAAAACCA
1 TATATTATATAA--TTTTTCAAAAATGTTTTTAAAACTA
*
2004403 TATATTATAT-A-TTTTCAAAATATTTTTTTAAAACTA
1 TATATTATATAATTTTTCAAAA-ATGTTTTTAAAACTA
2004439 TATATTATATAA-TTTTCAAAA
1 TATATTATATAATTTTTCAAAA
2004460 TGACTTCAAA
Statistics
Matches: 217, Mismatches: 13, Indels: 21
0.86 0.05 0.08
Matches are distributed among these distances:
31 9 0.04
32 14 0.06
33 3 0.01
34 8 0.04
35 3 0.01
36 23 0.11
37 101 0.47
38 44 0.20
39 12 0.06
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (37 bp):
TATATTATATAATTTTTCAAAAATGTTTTTAAAACTA
Found at i:2005404 original size:2 final size:2
Alignment explanation
Indices: 2005399--2005430 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2005389 AATCTTAAAA
2005399 AT AT AT -T AT -T 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
2005431 TGTGTGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2007315 original size:18 final size:17
Alignment explanation
Indices: 2007301--2007351 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
2007291 ATATAATCTG
2007301 AATTCTTTTTATAA-TA
1 AATTCTTTTTATAATTA
2007317 AATTCTTTTTATAA-T-
1 AATTCTTTTTATAATTA
* *
2007332 AATT-TTTATATAATTT
1 AATTCTTTTTATAATTA
2007348 AATT
1 AATT
2007352 TATCGAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 8 0.25
15 5 0.16
16 19 0.59
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTCTTTTTATAATTA
Found at i:2007322 original size:16 final size:15
Alignment explanation
Indices: 2007301--2007345 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 15
2007291 ATATAATCTG
2007301 AATTCTTTTTATAAT
1 AATTCTTTTTATAAT
2007316 AAATTCTTTTTATAAT
1 -AATTCTTTTTATAAT
*
2007332 AATT-TTTATATAAT
1 AATTCTTTTTATAAT
2007346 TTAATTTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 9 0.32
15 4 0.14
16 15 0.54
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTCTTTTTATAAT
Found at i:2009606 original size:22 final size:23
Alignment explanation
Indices: 2009581--2009631 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
2009571 ACTATATTAC
2009581 ATATATTATATTTTC-AAAAACT
1 ATATATTATATTTTCAAAAAACT
* * *
2009603 ATATAATATTTTTTCAAAAAAGT
1 ATATATTATATTTTCAAAAAACT
2009626 ATATAT
1 ATATAT
2009632 ATTACATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATATTATATTTTCAAAAAACT
Found at i:2009704 original size:14 final size:14
Alignment explanation
Indices: 2009668--2009704 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2009658 ATTATATATG
2009668 TTTTAAAAAAACGT
1 TTTTAAAAAAACGT
*
2009682 TTTCAAAAAAACGTT
1 TTTTAAAAAAACG-T
2009697 TTTTAAAA
1 TTTTAAAA
2009705 CTATATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (14 bp):
TTTTAAAAAAACGT
Found at i:2009735 original size:37 final size:37
Alignment explanation
Indices: 2009680--2009802 Score: 185
Period size: 37 Copynumber: 3.3 Consensus size: 37
2009670 TTAAAAAAAC
*
2009680 GTTTTCAAAAAAACGTTTTTTAAAACTATATATTATAT
1 GTTTTC-AAAAACCGTTTTTTAAAACTATATATTATAT
* *
2009718 GTTTTCAAAAACCGTTTTTAAAAATTATATATTATAT
1 GTTTTCAAAAACCGTTTTTTAAAACTATATATTATAT
2009755 GTTTTC-AAAACCGTTTTTTTAAAACTATATATTATAT
1 GTTTTCAAAAACCG-TTTTTTAAAACTATATATTATAT
*
2009792 GCTTTCAAAAA
1 GTTTTCAAAAA
2009803 TATTTTCAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
36 7 0.09
37 60 0.78
38 10 0.13
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.45
Consensus pattern (37 bp):
GTTTTCAAAAACCGTTTTTTAAAACTATATATTATAT
Found at i:2010510 original size:19 final size:19
Alignment explanation
Indices: 2010469--2010511 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2010459 TTAGTATAGC
* *
2010469 ATATAATAATTAATATTGT
1 ATATTATAATTAATATTGA
2010488 ATATTATAATTAA-ATTTGA
1 ATATTATAATTAATA-TTGA
2010507 ATATT
1 ATATT
2010512 TTTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
ATATTATAATTAATATTGA
Found at i:2013814 original size:2 final size:2
Alignment explanation
Indices: 2013807--2013849 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2013797 TTTGGTTGTA
2013807 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2013849 A
1 A
2013850 CGGACAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2014048 original size:2 final size:2
Alignment explanation
Indices: 2014043--2014085 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2014033 ATATATAGGC
2014043 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
2014085 A
1 A
2014086 CACACAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2014096 original size:2 final size:2
Alignment explanation
Indices: 2014091--2014142 Score: 61
Period size: 2 Copynumber: 25.5 Consensus size: 2
2014081 ATATACACAC
* *
2014091 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG ACT AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG
2014133 ACG AG AG AG A
1 A-G AG AG AG A
2014143 TGGTGGGCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
1 1 0.02
2 39 0.91
3 3 0.07
ACGTcount: A:0.46, C:0.04, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:2015453 original size:6 final size:6
Alignment explanation
Indices: 2015442--2015468 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2015432 TTCCATGTCG
2015442 ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATA
2015469 ATTGTGTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:2016668 original size:16 final size:17
Alignment explanation
Indices: 2016643--2016685 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
2016633 AAATTTAAAA
2016643 AAAAATTAA-TATAATTT
1 AAAAATTAATTATAA-TT
2016660 AAAAA-TAATTATAATT
1 AAAAATTAATTATAATT
2016676 AAAATATTAA
1 AAAA-ATTAA
2016686 GGAGAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.39
17 11 0.48
18 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATTAATTATAATT
Found at i:2024615 original size:10 final size:10
Alignment explanation
Indices: 2024600--2024624 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2024590 AACAAGAATG
2024600 GGACCAAAAT
1 GGACCAAAAT
2024610 GGACCAAAAT
1 GGACCAAAAT
2024620 GGACC
1 GGACC
2024625 TAGCAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (10 bp):
GGACCAAAAT
Found at i:2025476 original size:359 final size:358
Alignment explanation
Indices: 2024775--2025491 Score: 1425
Period size: 359 Copynumber: 2.0 Consensus size: 358
2024765 GGGGGGGGGG
2024775 GCTCAACTAATGTCAAATTTCAATTCCAATTGAAATTTCTCGCACACTATAAAAAATAAAAAACC
1 GCTCAACTAATGTCAAATTTCAATTCCAATTGAAATTTCTCGCACACTATAAAAAATAAAAAACC
2024840 CAAAACCACCATTGAAAAAAAATTATTGAACCACTTTATATAATGTTTTGATATAACAATTTAAG
66 CAAAACCACCATTGAAAAAAAATTATTGAACCACTTTATATAATGTTTTGATATAACAATTTAAG
2024905 CCAAAATAATTTTCGACTTGAATTGAATTTATTCAAAGTTTTCAAAATAATTTAAAGTCAATTAA
131 CCAAAATAATTTTCGACTTGAATTGAATTTATTCAAAGTTTTCAAAATAATTTAAAGTCAATTAA
2024970 AAGTGAATTTGAGCACAAAAGTGATTTTCTCGTACGTAATACTGATATTGTTCTTACATTATCGA
196 AAGTGAATTTGAGCACAAAAGTGATTTTCTCGTACGTAATACTGATATTGTTCTTACATTATCGA
2025035 CATTATATGAACAATACTGATACTTTTCATGTGGTATCAATAGCCTAGATAAGAGAAGTATCGAT
261 CATTATATGAACAATACTGATACTTTTCATGTGGTATCAATAGCCTAGATAAGAGAAGTATCGAT
2025100 ACACTCTAGTTAGTACAGATACTATCATCTCAA
326 ACACTCTAGTTAGTACAGATACTATCATCTCAA
2025133 GCTCAACTAATGTCAAATTTCAATTCCAATTGAAATTTCTCGCACACTATAAAAAATAAAAAACC
1 GCTCAACTAATGTCAAATTTCAATTCCAATTGAAATTTCTCGCACACTATAAAAAATAAAAAACC
2025198 CAAAACCACCATTGAAAAAAAATTATTGAACCACTTTATATAATGTTTTGATATAACAATTTAAG
66 CAAAACCACCATTGAAAAAAAATTATTGAACCACTTTATATAATGTTTTGATATAACAATTTAAG
2025263 CCAAAATAATTTTCGACTTGAATTGAATTTATTCAAAGTTTTCAAAAATAATTTAAAGTCAATTA
131 CCAAAATAATTTTCGACTTGAATTGAATTTATTCAAAGTTTTC-AAAATAATTTAAAGTCAATTA
2025328 AAAGTGAATTTGAGCACAAAAGTGATTTTCTCGTACGTAATACTGATATTGTTCTTACATTATCG
195 AAAGTGAATTTGAGCACAAAAGTGATTTTCTCGTACGTAATACTGATATTGTTCTTACATTATCG
2025393 ACATTATATGAACAATACTGATACTTTTCATGTGGTATCAATAGCCTAGATAAGAGAAGTATCGA
260 ACATTATATGAACAATACTGATACTTTTCATGTGGTATCAATAGCCTAGATAAGAGAAGTATCGA
2025458 TACACTCTAGTTAGTACAGATACTATCATCTCAA
325 TACACTCTAGTTAGTACAGATACTATCATCTCAA
2025492 ATTCCAGAAT
Statistics
Matches: 358, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
358 173 0.48
359 185 0.52
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (358 bp):
GCTCAACTAATGTCAAATTTCAATTCCAATTGAAATTTCTCGCACACTATAAAAAATAAAAAACC
CAAAACCACCATTGAAAAAAAATTATTGAACCACTTTATATAATGTTTTGATATAACAATTTAAG
CCAAAATAATTTTCGACTTGAATTGAATTTATTCAAAGTTTTCAAAATAATTTAAAGTCAATTAA
AAGTGAATTTGAGCACAAAAGTGATTTTCTCGTACGTAATACTGATATTGTTCTTACATTATCGA
CATTATATGAACAATACTGATACTTTTCATGTGGTATCAATAGCCTAGATAAGAGAAGTATCGAT
ACACTCTAGTTAGTACAGATACTATCATCTCAA
Found at i:2030883 original size:22 final size:22
Alignment explanation
Indices: 2030858--2030913 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
2030848 TATTAAGAGT
*
2030858 GTAATTTTTTAGGTTGAATAGA
1 GTAATTTTTTAGGTTAAATAGA
* * *
2030880 GTAACTTCTTAAGTTAAATAGA
1 GTAATTTTTTAGGTTAAATAGA
2030902 GTAATTTTTTAG
1 GTAATTTTTTAG
2030914 ATTGGACATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.45
Consensus pattern (22 bp):
GTAATTTTTTAGGTTAAATAGA
Found at i:2031419 original size:20 final size:21
Alignment explanation
Indices: 2031394--2031442 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
2031384 TATCTATTTA
2031394 TAATATTT-TATATATCATGT
1 TAATATTTATATATATCATGT
2031414 TAATATTTTATATATATCATGT
1 TAATA-TTTATATATATCATGT
2031436 TAATATT
1 TAATATT
2031443 ATCTTCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.19
21 5 0.19
22 17 0.63
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
TAATATTTATATATATCATGT
Found at i:2031771 original size:16 final size:17
Alignment explanation
Indices: 2031752--2031792 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2031742 CACTTATTTT
2031752 CATTTTCTAAAAGAAC-
1 CATTTTCTAAAAGAACA
* *
2031768 CATTTTCTAACATAACA
1 CATTTTCTAAAAGAACA
2031785 CATTTTCT
1 CATTTTCT
2031793 TTAATATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (17 bp):
CATTTTCTAAAAGAACA
Found at i:2035071 original size:31 final size:31
Alignment explanation
Indices: 2035028--2035095 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
2035018 AGGAGAAATG
*
2035028 GTCCCTAATGTTATCAATCCATTTGATTTTA
1 GTCCCTAATGTTAACAATCCATTTGATTTTA
* *
2035059 GTCCTTAATGTTAACGATCCATTTGATTTTA
1 GTCCCTAATGTTAACAATCCATTTGATTTTA
2035090 GTCCCT
1 GTCCCT
2035096 CAGCTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (31 bp):
GTCCCTAATGTTAACAATCCATTTGATTTTA
Found at i:2038251 original size:37 final size:35
Alignment explanation
Indices: 2038173--2038252 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
2038163 GAAAAACACC
* *
2038173 ACCACATTAAAATGGAAGTTCAAATAATCTACTCA
1 ACCACATTAAAATGAAAGTTCAAATAATCTAATCA
*
2038208 ACCACATTAAAATGAAAATTTCAAA-ATATCTTAATCA
1 ACCACATTAAAATG-AAAGTTCAAATA-ATC-TAATCA
*
2038245 ATCACATT
1 ACCACATT
2038253 CATGAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 15 0.39
36 11 0.29
37 12 0.32
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (35 bp):
ACCACATTAAAATGAAAGTTCAAATAATCTAATCA
Found at i:2041171 original size:28 final size:28
Alignment explanation
Indices: 2041122--2041193 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
2041112 TTTTCACCCT
2041122 AAACCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGAATATCACACTTAAAA
* * *
2041150 AAGCTCGACCCGAATATTACACTTAAAA
1 AAACCCGACCCGAATATCACACTTAAAA
2041178 AAACCCGACCCGAATA
1 AAACCCGACCCGAATA
2041194 CCAAAAGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.44, C:0.31, G:0.10, T:0.15
Consensus pattern (28 bp):
AAACCCGACCCGAATATCACACTTAAAA
Found at i:2062918 original size:28 final size:30
Alignment explanation
Indices: 2062857--2062919 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
2062847 AACTTTCAAA
* *
2062857 TTATTCATATTTTAATCGTTATAGTTTATT
1 TTATTAATATTTTAATCGTTATAGTGTATT
*
2062887 TTATTAATATTTT-AT-GTTGTAGTGTATT
1 TTATTAATATTTTAATCGTTATAGTGTATT
2062915 TTATT
1 TTATT
2062920 GTTACTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 16 0.53
29 2 0.07
30 12 0.40
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (30 bp):
TTATTAATATTTTAATCGTTATAGTGTATT
Found at i:2065384 original size:2 final size:2
Alignment explanation
Indices: 2065377--2065429 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
2065367 TTAACCCTTT
2065377 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
2065418 TA CA AA TA TA TA
1 TA TA TA TA TA TA
2065430 ATGAATAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2066988 original size:20 final size:20
Alignment explanation
Indices: 2066965--2067029 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
2066955 TATCGCGTTG
*
2066965 CGATAGTCAGAATCGTGTTA
1 CGATAGTCAAAATCGTGTTA
**
2066985 CGATTATGT-ATTATC-TCGTTA
1 CGA-TA-GTCAAAATCGT-GTTA
*
2067006 CGATAGTCAAAATCGTGTTG
1 CGATAGTCAAAATCGTGTTA
2067026 CGAT
1 CGAT
2067030 TTTGTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
19 2 0.06
20 17 0.49
21 14 0.40
22 2 0.06
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (20 bp):
CGATAGTCAAAATCGTGTTA
Found at i:2066995 original size:41 final size:41
Alignment explanation
Indices: 2066944--2067050 Score: 169
Period size: 41 Copynumber: 2.6 Consensus size: 41
2066934 AATCGCATTG
*
2066944 CGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGTGTTA
1 CGATTTTGTATTATCGCGTTGCGATAGTCAAAATCGTGTTA
* * * *
2066985 CGATTATGTATTATCTCGTTACGATAGTCAAAATCGTGTTG
1 CGATTTTGTATTATCGCGTTGCGATAGTCAAAATCGTGTTA
2067026 CGATTTTGTATTATCGCGTTGCGAT
1 CGATTTTGTATTATCGCGTTGCGAT
2067051 TTACATATTC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
CGATTTTGTATTATCGCGTTGCGATAGTCAAAATCGTGTTA
Found at i:2067041 original size:21 final size:21
Alignment explanation
Indices: 2066941--2067052 Score: 63
Period size: 21 Copynumber: 5.4 Consensus size: 21
2066931 GAAAATCGCA
*
2066941 TTGCGATTTTGTATTATCGCG
1 TTGCGATTTTGTATTATCGTG
* **
2066962 TTGCGA--TAGTCAGAATCGTG
1 TTGCGATTTTGT-ATTATCGTG
* *
2066982 TTACGATTATGTATTATC-TCG
1 TTGCGATTTTGTATTATCGT-G
* * **
2067003 TTACGA--TAGTCAAAATCGTG
1 TTGCGATTTTGT-ATTATCGTG
*
2067023 TTGCGATTTTGTATTATCGCG
1 TTGCGATTTTGTATTATCGTG
2067044 TTGCGATTT
1 TTGCGATTT
2067053 ACATATTCGC
Statistics
Matches: 65, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
19 5 0.08
20 22 0.34
21 33 0.51
22 5 0.08
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTGTATTATCGTG
Found at i:2067068 original size:41 final size:41
Alignment explanation
Indices: 2066932--2067073 Score: 160
Period size: 41 Copynumber: 3.5 Consensus size: 41
2066922 GTAAATTTGG
2066932 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTC
1 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTC
* ** * * * *
2066973 AGAATCGTGTTACGATTATGTATTATCTCGTTACGATAGTC
1 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTC
** *
2067014 AAAATCGTGTTGCGATTTTGTATTATCGCGTTGCGAT-TTAC
1 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGT-C
* *
2067055 ATATTCGCATTGCGATTTT
1 AAAATCGCATTGCGATTTT
2067074 CTAAAATCGC
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 1 0.01
41 82 0.99
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (41 bp):
AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTC
Found at i:2067172 original size:40 final size:40
Alignment explanation
Indices: 2067126--2067259 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
2067116 GCGATAGTCA
*
2067126 AAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGG
1 AAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGG
* * * * * **
2067166 ATATCGCGTTGCG-AT-TTACATATTCGCA-TTGCGATAGTCA
1 AAATCGCGTTGCGAATCTGA-AAACT-G-ATTTGCGATACTGG
2067206 AAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGG
1 AAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGG
* *
2067246 AGATCGTGTTGCGA
1 AAATCGCGTTGCGA
2067260 TTTAGAGATC
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
38 1 0.01
39 6 0.08
40 56 0.79
41 6 0.08
42 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (40 bp):
AAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGG
Found at i:2067257 original size:80 final size:80
Alignment explanation
Indices: 2067115--2067263 Score: 271
Period size: 80 Copynumber: 1.9 Consensus size: 80
2067105 AAAATCACAA
* *
2067115 TGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACTGATTTGCGATACTGGATATCGCGTTGCGA
1 TGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGGAGATCGCGTTGCGA
2067180 TTTACATATTCGCAT
66 TTTACATATTCGCAT
*
2067195 TGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGGAGATCGTGTTGCGA
1 TGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGGAGATCGCGTTGCGA
2067260 TTTA
66 TTTA
2067264 GAGATCGCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (80 bp):
TGCGATAGTCAAAATCGCGTTGCGAATCTGAAAACTGATTTGCGATACTGGAGATCGCGTTGCGA
TTTACATATTCGCAT
Found at i:2070743 original size:24 final size:24
Alignment explanation
Indices: 2070716--2070822 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
2070706 AAACGGAGAT
*
2070716 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
2070740 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
2070764 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
2070788 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
2070812 ATCAGAAATCA
1 ATCAGAAATCA
2070823 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:2070822 original size:48 final size:48
Alignment explanation
Indices: 2070716--2070824 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
2070706 AAACGGAGAT
* * * *
2070716 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
2070764 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2070812 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2070825 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:2071972 original size:18 final size:18
Alignment explanation
Indices: 2071951--2071986 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2071941 GTTCCATCCG
*
2071951 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2071969 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2071987 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2073289 original size:10 final size:9
Alignment explanation
Indices: 2073276--2073325 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
2073266 GTCAAAGTTT
2073276 TGGTCAACAG
1 TGGTCAAC-G
2073286 TGGTCAACG
1 TGGTCAACG
2073295 TGGGTCAAC-
1 T-GGTCAACG
2073304 -GGTCAACG
1 TGGTCAACG
2073312 TGGGTCAACG
1 T-GGTCAACG
2073322 -GGTC
1 TGGTC
2073326 GGGTCAACGG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.19
8 4 0.11
9 2 0.06
10 23 0.64
ACGTcount: A:0.22, C:0.22, G:0.36, T:0.20
Consensus pattern (9 bp):
TGGTCAACG
Found at i:2073309 original size:17 final size:17
Alignment explanation
Indices: 2073287--2073322 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2073277 GGTCAACAGT
2073287 GGTCAACGTGGGTCAAC
1 GGTCAACGTGGGTCAAC
2073304 GGTCAACGTGGGTCAAC
1 GGTCAACGTGGGTCAAC
2073321 GG
1 GG
2073323 GTCGGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (17 bp):
GGTCAACGTGGGTCAAC
Found at i:2073317 original size:27 final size:29
Alignment explanation
Indices: 2073277--2073335 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
2073267 TCAAAGTTTT
2073277 GGTCAACAGTGGTCAAC-GT-GGGTCAAC
1 GGTCAACAGTGGTCAACGGTCGGGTCAAC
2073304 GGTCAAC-GTGGGTCAACGGGTCGGGTCAAC
1 GGTCAACAGT-GGTCAAC-GGTCGGGTCAAC
2073334 GG
1 GG
2073336 GTCGGGTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 2 0.07
27 14 0.50
29 2 0.07
30 10 0.36
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (29 bp):
GGTCAACAGTGGTCAACGGTCGGGTCAAC
Found at i:2073331 original size:13 final size:13
Alignment explanation
Indices: 2073313--2073388 Score: 71
Period size: 13 Copynumber: 5.5 Consensus size: 13
2073303 CGGTCAACGT
2073313 GGGTCAACGGGTC
1 GGGTCAACGGGTC
2073326 GGGTCAACGGGTCGGGTC
1 GGGTCAA-----CGGGTC
* *
2073344 GGGTCAACTGGCC
1 GGGTCAACGGGTC
*
2073357 GGGTAAACGGGTC
1 GGGTCAACGGGTC
*
2073370 GGGTAAACGGGTC
1 GGGTCAACGGGTC
2073383 GGGTCA
1 GGGTCA
2073389 GGTTATGACC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 39 0.75
18 13 0.25
ACGTcount: A:0.17, C:0.21, G:0.46, T:0.16
Consensus pattern (13 bp):
GGGTCAACGGGTC
Found at i:2073351 original size:31 final size:31
Alignment explanation
Indices: 2073313--2073373 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2073303 CGGTCAACGT
* *
2073313 GGGTCAACGGGTCGGGTCAACGGGTCGGGTC
1 GGGTCAACGGGCCGGGTAAACGGGTCGGGTC
*
2073344 GGGTCAACTGGCCGGGTAAACGGGTCGGGT
1 GGGTCAACGGGCCGGGTAAACGGGTCGGGT
2073374 AAACGGGTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.48, T:0.16
Consensus pattern (31 bp):
GGGTCAACGGGCCGGGTAAACGGGTCGGGTC
Found at i:2073359 original size:18 final size:18
Alignment explanation
Indices: 2073320--2073360 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2073310 CGTGGGTCAA
*
2073320 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGC
*
2073338 CGGGTCGGGTCAACTGGC
1 CGGGTCGGGTCAACGGGC
2073356 CGGGT
1 CGGGT
2073361 AAACGGGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.24, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGC
Found at i:2075136 original size:19 final size:19
Alignment explanation
Indices: 2075112--2075176 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
2075102 TTTTTCATTT
2075112 AGGGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
*
2075131 AGGGGGAATCTG-T--TCCC
1 AGGGGGAATC-GATACCCCC
2075148 --GGGGAATCGATACTCCCC
1 AGGGGGAATCGATAC-CCCC
2075166 AGGGGGGAATC
1 A-GGGGGAATC
2075177 TGTTCTCCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.25
17 3 0.08
18 3 0.08
19 11 0.31
20 1 0.03
21 8 0.22
ACGTcount: A:0.23, C:0.26, G:0.35, T:0.15
Consensus pattern (19 bp):
AGGGGGAATCGATACCCCC
Found at i:2075157 original size:34 final size:36
Alignment explanation
Indices: 2075114--2075181 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
2075104 TTTCATTTAG
2075114 GGGGAATCGATAC-CCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCGATACTCCCCAGGGGGGAATCTGTTCCC
2075148 GGGGAATCGATACTCCCCAGGGGGGAATCTGTTC
1 GGGGAATCGATACTCCCCAGGGGGGAATCTGTTC
2075182 TCCCTGCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 13 0.41
35 5 0.16
36 14 0.44
ACGTcount: A:0.21, C:0.26, G:0.34, T:0.19
Consensus pattern (36 bp):
GGGGAATCGATACTCCCCAGGGGGGAATCTGTTCCC
Found at i:2083981 original size:17 final size:17
Alignment explanation
Indices: 2083940--2083982 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2083930 AAAATAATTG
* *
2083940 AAATTTATATAATTTTA
1 AAATTTAAATAATATTA
*
2083957 AAACTTAAATAATATTA
1 AAATTTAAATAATATTA
*
2083974 TAATTTAAA
1 AAATTTAAA
2083983 ATATACATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTAAATAATATTA
Found at i:2090598 original size:12 final size:12
Alignment explanation
Indices: 2090581--2090609 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2090571 TCTGAATTCT
2090581 CAATTCTATTTC
1 CAATTCTATTTC
2090593 CAATTCTATTTC
1 CAATTCTATTTC
2090605 CAATT
1 CAATT
2090610 TCTTAATCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
CAATTCTATTTC
Found at i:2103411 original size:14 final size:14
Alignment explanation
Indices: 2103392--2103441 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
2103382 ATAAAAATTG
2103392 ATATTAAATTATAA
1 ATATTAAATTATAA
2103406 ATATTAAAATT-TAA
1 ATATT-AAATTATAA
*
2103420 ATATAAAATCTACTAA
1 ATATTAAAT-TA-TAA
2103436 ATATTA
1 ATATTA
2103442 CATCTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 4 0.13
14 13 0.43
15 5 0.17
16 8 0.27
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATTAAATTATAA
Found at i:2109526 original size:30 final size:30
Alignment explanation
Indices: 2109490--2109546 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2109480 TATTAAATTT
*
2109490 ATAGTTTAGTTACTAGACGAGTCAAAACTG
1 ATAGTTTAGTTACTAAACGAGTCAAAACTG
*
2109520 ATAGTTTAGTTACTAAACGAGTTAAAA
1 ATAGTTTAGTTACTAAACGAGTCAAAA
2109547 TTTTAACGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (30 bp):
ATAGTTTAGTTACTAAACGAGTCAAAACTG
Found at i:2111330 original size:7 final size:7
Alignment explanation
Indices: 2111314--2111346 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2111304 AGGCAACTTC
2111314 GTTTTTT
1 GTTTTTT
*
2111321 GTTTTCT
1 GTTTTTT
2111328 GTTTTTT
1 GTTTTTT
2111335 -TTTTTT
1 GTTTTTT
2111341 GTTTTT
1 GTTTTT
2111347 GGTCTGCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (7 bp):
GTTTTTT
Found at i:2112349 original size:34 final size:34
Alignment explanation
Indices: 2112310--2112378 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
2112300 GTTTTGGTGA
*
2112310 TTTCATCTGTGTGTATAATGATAAAGGATAGATT
1 TTTCATCTGTGTATATAATGATAAAGGATAGATT
*
2112344 TTTCATCTGTGTATATAATGATAAAGGATGGATT
1 TTTCATCTGTGTATATAATGATAAAGGATAGATT
2112378 T
1 T
2112379 CTCGTTTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (34 bp):
TTTCATCTGTGTATATAATGATAAAGGATAGATT
Found at i:2130061 original size:43 final size:42
Alignment explanation
Indices: 2129954--2130066 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 42
2129944 TTTATCTTGT
2129954 TAAAATATATT-TTTTAATTA-TTAAAA-ATAAAAAAAATTA
1 TAAAATATATTATTTTAATTATTTAAAATATAAAAAAAATTA
* * * ** *
2129993 TAAAATATGTTATTTTAACTGTTTAAAATATAATTCATAATTA
1 TAAAATATATTATTTTAATTATTTAAAATATAA-AAAAAATTA
2130036 T-AAATATATTATTTTAATTATTTTAAAATAT
1 TAAAATATATTATTTTAATTA-TTTAAAATAT
2130067 TAACATATTC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
39 10 0.17
40 7 0.12
41 6 0.10
42 20 0.33
43 17 0.28
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (42 bp):
TAAAATATATTATTTTAATTATTTAAAATATAAAAAAAATTA
Found at i:2131139 original size:16 final size:16
Alignment explanation
Indices: 2131091--2131139 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
2131081 AATTTACGAC
* *
2131091 TATTATTGTAAATTTT
1 TATTATTTTAAATATT
2131107 TATTATAATTTAGAATATT
1 TATTAT--TTTA-AATATT
2131126 TATTATTTTAAATA
1 TATTATTTTAAATA
2131140 AAATTAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 10 0.36
17 4 0.14
18 3 0.11
19 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (16 bp):
TATTATTTTAAATATT
Found at i:2136561 original size:13 final size:13
Alignment explanation
Indices: 2136543--2136567 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2136533 GTCATAACCC
2136543 GACCCGACCCGTT
1 GACCCGACCCGTT
2136556 GACCCGACCCGT
1 GACCCGACCCGT
2136568 CCCGTTGACC
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:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2136562 original size:18 final size:18
Alignment explanation
Indices: 2136539--2136580 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2136529 ACCAGTCATA
2136539 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2136557 ACCCGACCCGTCCCGTTG
1 ACCCGACCCGACCCGTTG
2136575 ACCCGA
1 ACCCGA
2136581 TCTGACCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2141047 original size:60 final size:60
Alignment explanation
Indices: 2140943--2141073 Score: 174
Period size: 60 Copynumber: 2.2 Consensus size: 60
2140933 AATTTAGGAT
* *
2140943 AAAGTGTA-AAAATGATCCATTAATCATAGGATATTGTTTGATTGAGCCCATCGACTATTA
1 AAAGT-TATAAAATGATCCATCAATCATAGGAAATTGTTTGATTGAGCCCATCGACTATTA
* * * * **
2141003 AAATTTATAAAATGATCCATCGATTATAGGAAATTGTTTTATTGAGTTCATCGACTATTA
1 AAAGTTATAAAATGATCCATCAATCATAGGAAATTGTTTGATTGAGCCCATCGACTATTA
2141063 AAAGTTATAAA
1 AAAGTTATAAA
2141074 TTGGTCACCC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.03
60 59 0.97
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (60 bp):
AAAGTTATAAAATGATCCATCAATCATAGGAAATTGTTTGATTGAGCCCATCGACTATTA
Found at i:2143581 original size:31 final size:31
Alignment explanation
Indices: 2143539--2143631 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
2143529 AAGTGTTCTA
2143539 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
*
2143570 TACGAGTTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
2143601 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
2143632 ATGCGCTATG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.24
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:2143688 original size:22 final size:22
Alignment explanation
Indices: 2143662--2143724 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
2143652 GAGGTCTCCT
**
2143662 GCATGCAGTGGGGAGCAAGCGA
1 GCATGCAACGGGGAGCAAGCGA
2143684 GCATGCAACGGGGAGCAAGCGA
1 GCATGCAACGGGGAGCAAGCGA
2143706 GCATGCAACGGGGAGCAAG
1 GCATGCAACGGGGAGCAAG
2143725 GCGCAGGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.43, T:0.06
Consensus pattern (22 bp):
GCATGCAACGGGGAGCAAGCGA
Found at i:2143769 original size:29 final size:29
Alignment explanation
Indices: 2143736--2143819 Score: 123
Period size: 29 Copynumber: 2.9 Consensus size: 29
2143726 CGCAGGACAT
*
2143736 GGTCGCCCAGCGTGCATGGCGACCTACAA
1 GGTCGCCCGGCGTGCATGGCGACCTACAA
*
2143765 GGTCGCCTGGCGTGCATGGCGACCTACAA
1 GGTCGCCCGGCGTGCATGGCGACCTACAA
* * *
2143794 GGTCGCCCGGAGGGCATGACGACCTA
1 GGTCGCCCGGCGTGCATGGCGACCTA
2143820 TGCTGAGAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.19, C:0.32, G:0.35, T:0.14
Consensus pattern (29 bp):
GGTCGCCCGGCGTGCATGGCGACCTACAA
Found at i:2145792 original size:27 final size:27
Alignment explanation
Indices: 2145735--2145792 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2145725 ATTTAAATTT
* * * *
2145735 AAATTAAAAAAGAGAATTTATTTTATT
1 AAATTAAAAAAGAAAATTCAATTTATA
2145762 AAATTAAAAAAGAAAATTGCAATTTA-A
1 AAATTAAAAAAGAAAATT-CAATTTATA
2145789 AAAT
1 AAAT
2145793 AATTATGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (27 bp):
AAATTAAAAAAGAAAATTCAATTTATA
Found at i:2146081 original size:2 final size:2
Alignment explanation
Indices: 2146076--2146110 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2146066 ATATATATAT
2146076 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG A- AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2146111 AAGACGGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2151277 original size:13 final size:13
Alignment explanation
Indices: 2151259--2151283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2151249 TGGCTGTTTG
2151259 TGTTCCGAAATCC
1 TGTTCCGAAATCC
2151272 TGTTCCGAAATC
1 TGTTCCGAAATC
2151284 AACAGCAACT
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:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTTCCGAAATCC
Found at i:2157727 original size:11 final size:11
Alignment explanation
Indices: 2157711--2157735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2157701 GCCTTTGGTT
2157711 TCCCCTCCAAC
1 TCCCCTCCAAC
2157722 TCCCCTCCAAC
1 TCCCCTCCAAC
2157733 TCC
1 TCC
2157736 ACCCATGCCT
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:0.64, G:0.00, T:0.20
Consensus pattern (11 bp):
TCCCCTCCAAC
Found at i:2159671 original size:2 final size:2
Alignment explanation
Indices: 2159664--2159692 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2159654 CACATCTGTG
2159664 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 T
2159693 CATACGACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2160982 original size:16 final size:16
Alignment explanation
Indices: 2160961--2160992 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2160951 GGTCCCCGCA
2160961 CCTATGAATATTAGGG
1 CCTATGAATATTAGGG
2160977 CCTATGAATATTAGGG
1 CCTATGAATATTAGGG
2160993 TAAATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
CCTATGAATATTAGGG
Found at i:2161116 original size:35 final size:34
Alignment explanation
Indices: 2161072--2161184 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
2161062 AAAACAATTC
*
2161072 TCAATTTCATTCTAAACCACAAATTCTAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCTAAAATAAT
*
2161107 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCTAAAATAAT
* * *
2161142 TCAATTACATTCTAAAACTCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCTAAAATAAT
2161177 TCAATTTC
1 TCAATTTC
2161185 TGTCTTTTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.91
36 5 0.07
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCTAAAATAAT
Found at i:2162263 original size:35 final size:35
Alignment explanation
Indices: 2162208--2162319 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
2162198 ATTTCTCCTT
* *
2162208 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAAA-G
1 AAATTGAATTATTTTGGAATTTGGGGTTTA-AAATG
* * *
2162243 TAATTTAATTATTTTGGAATTTAGGGTTTAAAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * * * *
2162278 AAATTGAATTACTTTGAAATTTGAGATTTATAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
2162313 AAATTGA
1 AAATTGA
2162320 GGAATGTTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
34 3 0.05
35 60 0.95
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
Found at i:2165109 original size:41 final size:41
Alignment explanation
Indices: 2165062--2165139 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
2165052 AAATCCCACA
* * *
2165062 TTTGTTTTATGTAATTCGTTTTTCGGAAAATGTTTTCCCGT
1 TTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCGT
2165103 TTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
1 TTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
2165140 TAGTATTTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (41 bp):
TTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCGT
Found at i:2165380 original size:8 final size:8
Alignment explanation
Indices: 2165367--2165432 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
2165357 TATTAATAGT
2165367 TATAATAA
1 TATAATAA
2165375 TATAATAA
1 TATAATAA
**
2165383 TAT-ATTT
1 TATAATAA
*
2165390 TA-AATAT
1 TATAATAA
2165397 TATAATAA
1 TATAATAA
*
2165405 AATAATCAA
1 TATAAT-AA
*
2165414 T-T-ATAT
1 TATAATAA
2165420 TATAATAA
1 TATAATAA
2165428 TATAA
1 TATAA
2165433 GATATTATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 2 0.04
7 12 0.27
8 29 0.64
9 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (8 bp):
TATAATAA
Found at i:2165485 original size:26 final size:27
Alignment explanation
Indices: 2165456--2165519 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
2165446 TATTTTAATA
2165456 AATATATAATAAT-TT-TTTATATATTT
1 AATAT-TAATAATATTATTTATATATTT
2165482 AATATTTAATAATATTATTTATATATTT
1 AATA-TTAATAATATTATTTATATATTT
2165510 AATATTAATA
1 AATATTAATA
2165520 TAATAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.31
27 9 0.26
28 15 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATATTAATAATATTATTTATATATTT
Found at i:2165488 original size:7 final size:7
Alignment explanation
Indices: 2165471--2165520 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
2165461 ATAATAATTT
2165471 TTTATATA
1 TTTA-ATA
2165479 TTTAATA
1 TTTAATA
2165486 TTTAATA
1 TTTAATA
* *
2165493 -ATATTA
1 TTTAATA
2165499 TTTATATA
1 TTTA-ATA
2165507 TTTAATA
1 TTTAATA
2165514 -TTAATA
1 TTTAATA
2165520 T
1 T
2165521 AATAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
6 10 0.29
7 15 0.43
8 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAATA
Found at i:2165565 original size:23 final size:23
Alignment explanation
Indices: 2165539--2165583 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2165529 AATAATATTT
2165539 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
2165562 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
2165584 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:2165608 original size:13 final size:13
Alignment explanation
Indices: 2165481--2165609 Score: 64
Period size: 13 Copynumber: 10.2 Consensus size: 13
2165471 TTTATATATT
2165481 TAATATTTAATAA
1 TAATATTTAATAA
* *
2165494 TATTATTTATATATT
1 TAATATTTA-ATA-A
2165509 TAATA-TTAAT-A
1 TAATATTTAATAA
*
2165520 TAATA-ATAA-AA
1 TAATATTTAATAA
2165531 TAATATTTTAATAA
1 TAATA-TTTAATAA
2165545 -AGATATTTAA-AA
1 TA-ATATTTAATAA
*
2165557 T-ATA-CTAATTAA
1 TAATATTTAA-TAA
*
2165569 T-ATTTTTAA-AA
1 TAATATTTAATAA
*
2165580 T-ATAATTATAAAAA
1 TAAT-ATT-TAATAA
2165594 TAATATTTAATAA
1 TAATATTTAATAA
2165607 TAA
1 TAA
2165610 ATAAATCATT
Statistics
Matches: 90, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
10 3 0.03
11 22 0.24
12 9 0.10
13 33 0.37
14 17 0.19
15 6 0.07
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (13 bp):
TAATATTTAATAA
Found at i:2165813 original size:14 final size:14
Alignment explanation
Indices: 2165794--2165827 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2165784 AAATGTAATT
2165794 CATTTTACGGAAAA
1 CATTTTACGGAAAA
*
2165808 CATTTTCCGGAAAA
1 CATTTTACGGAAAA
*
2165822 CGTTTT
1 CATTTT
2165828 TCAGAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:2165852 original size:14 final size:14
Alignment explanation
Indices: 2165835--2165877 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
2165825 TTTTCAGAAA
2165835 TATAATTCATTTTC
1 TATAATTCATTTTC
** *
2165849 TATAATTCAAATTA
1 TATAATTCATTTTC
2165863 TAGTAATTCATTTTC
1 TA-TAATTCATTTTC
2165878 CAAAAAACCA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (14 bp):
TATAATTCATTTTC
Found at i:2169568 original size:14 final size:14
Alignment explanation
Indices: 2169549--2169575 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2169539 TATGAATCTC
2169549 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
2169563 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
2169576 AGTTTCATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:2170236 original size:15 final size:15
Alignment explanation
Indices: 2170216--2170245 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2170206 TGTCTGTTTG
2170216 GGGTGCCGCTGGTTC
1 GGGTGCCGCTGGTTC
*
2170231 GGGTGCTGCTGGTTC
1 GGGTGCCGCTGGTTC
2170246 CATTGGTAAT
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:0.00, C:0.23, G:0.47, T:0.30
Consensus pattern (15 bp):
GGGTGCCGCTGGTTC
Found at i:2177899 original size:2 final size:2
Alignment explanation
Indices: 2177892--2177928 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2177882 AAGACGATTT
2177892 TA TA 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 T
2177929 TTTTTAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2179208 original size:21 final size:20
Alignment explanation
Indices: 2179122--2179279 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
2179112 AAATGACCAA
**
2179122 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2179141 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2179161 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2179181 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2179202 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2179223 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2179243 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2179264 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2179280 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2179311 original size:20 final size:20
Alignment explanation
Indices: 2179246--2179495 Score: 241
Period size: 20 Copynumber: 12.5 Consensus size: 20
2179236 CGATTTTCCA
** *
2179246 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
2179266 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
2179286 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2179306 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* * *
2179326 AAATCACAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2179346 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
2179366 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2179386 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
2179406 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
2179426 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
2179446 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* * *
2179466 AAATCACAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
2179486 AAATCACAAC
1 AAATCGCAAC
2179496 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:2179477 original size:40 final size:40
Alignment explanation
Indices: 2179285--2179495 Score: 266
Period size: 40 Copynumber: 5.3 Consensus size: 40
2179275 CGCGAACACA
* * * * *
2179285 TAAATCGCAACG-TGTATCCGTATATCGCAACGCGTATCCG
1 TAAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTG
* * * * *
2179325 TAAATCACAATGCG-T-ATCCGTATATCGCAACGCGTATCCG
1 TAAATCGCAA--CGATAATCCGTAAATCGCAACGAGAATCTG
2179365 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
2179405 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
*
2179445 TAAATCGCAACGATAATCCGTAAATCACAACGAGAATCTG
1 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
*
2179485 TAAATCACAAC
1 TAAATCGCAAC
2179496 ACTGAAATTT
Statistics
Matches: 159, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
38 2 0.01
39 1 0.01
40 153 0.96
42 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (40 bp):
TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
Found at i:2180217 original size:24 final size:24
Alignment explanation
Indices: 2180178--2180224 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2180168 AAATTTGGTC
2180178 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2180202 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2180225 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2180416 original size:12 final size:12
Alignment explanation
Indices: 2180399--2180423 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2180389 ATATAATCCT
2180399 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2180411 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2180423 G
1 G
2180424 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2182798 original size:19 final size:19
Alignment explanation
Indices: 2182758--2182874 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
2182748 GATTCTCTCG
2182758 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2182778 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2182797 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2182811 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2182830 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2182849 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2182868 TTGCGAT
1 TTGCGAT
2182875 AGTCAATTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 7 0.08
19 55 0.61
20 15 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2182820 original size:33 final size:35
Alignment explanation
Indices: 2182777--2182874 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 35
2182767 TCATTTCCGC
2182777 ATTGCGATTTTCATTTCGCATTGCGATTC-TCTCG
1 ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
*
2182811 -TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCGCATTGCGA--TTCATCTCG
2182847 CATTGCGATTTTCATTTCGCATTGCGAT
1 -ATTGCGATTTTCATTTCGCATTGCGAT
2182875 AGTCAATTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
33 25 0.43
35 3 0.05
36 5 0.09
38 25 0.43
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (35 bp):
ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
Found at i:2182852 original size:52 final size:53
Alignment explanation
Indices: 2182739--2182856 Score: 229
Period size: 53 Copynumber: 2.2 Consensus size: 53
2182729 GAAATGAAAA
2182739 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2182792 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2182844 TCGCATTGCGATT
1 TCGCATTGCGATT
2182857 TTCATTTCGC
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 31 0.48
53 34 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:2182985 original size:33 final size:33
Alignment explanation
Indices: 2182933--2183094 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
2182923 CCATTACATT
2182933 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
2182967 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
2182999 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
2183038 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
*
2183071 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
2183095 TTGCGATTCT
Statistics
Matches: 105, Mismatches: 12, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 54 0.51
34 10 0.10
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:2182989 original size:19 final size:19
Alignment explanation
Indices: 2182933--2183100 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
2182923 CCATTACATT
2182933 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
2182953 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
2182967 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
2182986 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
2183005 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
2183019 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
2183038 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
2183057 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
2183071 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
2183090 TCGCATTGCGA
1 TCGCAATGCGA
2183101 TTCTCCCATT
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.24
15 3 0.02
16 6 0.05
17 5 0.04
18 4 0.03
19 71 0.57
20 6 0.05
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:2183012 original size:52 final size:52
Alignment explanation
Indices: 2182933--2183100 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
2182923 CCATTACATT
2182933 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
2182986 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
2183038 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
2183090 TCGCATTGCGA
1 TCGCAATGCGA
2183101 TTCTCCCATT
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 104 0.92
53 9 0.08
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:2183149 original size:19 final size:19
Alignment explanation
Indices: 2183107--2183206 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
2183097 GCGATTCTCC
2183107 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
2183127 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
2183146 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
2183162 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
2183179 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
2183198 CATTGCGAT
1 CATTGCGAT
2183207 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:2183203 original size:52 final size:53
Alignment explanation
Indices: 2183090--2183206 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
2183080 GAAATTAAAA
2183090 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
2183143 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
2183195 TCGCATTGCGAT
1 TCGCATTGCGAT
2183207 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:2183310 original size:332 final size:332
Alignment explanation
Indices: 2182776--2183598 Score: 1528
Period size: 332 Copynumber: 2.5 Consensus size: 332
2182766 TTCATTTCCG
* * * * *
2182776 CATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGAT
1 CATTGCGATTTTCATTTCCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGAT
2182837 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATAGTCAATTTTGCCTTCAACATAATGCA
63 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATAGTCAATTTTGCCTTCAACATAATGCA
2182902 GATTGAAATCAACAAAATCAACCATTACATTTCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
128 GATTGAAATCAACAAAATCAACCATTACATTTCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
2182967 TCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAA
193 TCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAA
2183032 TGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATT
258 TGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATT
2183097 GCGATTCTCC
323 GCGATTCTCC
2183107 CATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTT
1 CATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTT
2183172 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATAGTCAATTTTGCCTTCAACATAATGCAGAT
66 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATAGTCAATTTTGCCTTCAACATAATGCAGAT
*
2183237 TGAAATCAACAAAATCAACCATTACATTTCGCAATGCGGAAATGAAAATCGCAACGAGATAATCG
131 TGAAATCAACAAAATCAACCATTACATTTCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
2183302 CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
196 CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
2183367 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCG
261 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCG
2183432 ATTCTCC
326 ATTCTCC
*
2183439 CATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCACATTGCGATTCTCTCGTTGCGATTTT
1 CATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTT
2183504 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATAGTCAATTTTGCCTTCAACATAATGCAGAT
66 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATAGTCAATTTTGCCTTCAACATAATGCAGAT
2183569 TGAAATCAACAAAATCAACCATTACATTTC
131 TGAAATCAACAAAATCAACCATTACATTTC
2183599 AATCAATTAA
Statistics
Matches: 481, Mismatches: 7, Indels: 7
0.97 0.01 0.01
Matches are distributed among these distances:
330 9 0.02
331 22 0.05
332 450 0.94
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (332 bp):
CATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTT
CATTTCGCATTGCGATTTTCATTTCGCATTGCGATAGTCAATTTTGCCTTCAACATAATGCAGAT
TGAAATCAACAAAATCAACCATTACATTTCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG
CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCG
ATTCTCC
Done.