Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007859.1 Hibiscus syriacus cultivar Beakdansim tig00110221_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: 3538007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2739938 original size:18 final size:18
Alignment explanation
Indices: 2739875--2739943 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 18
2739865 AGTTATTTTG
2739875 AATAATAAATTA-ATTTA-
1 AATAA-AAATTAGATTTAT
*
2739892 AAT-AAAATTGGTAATTTATT
1 AATAAAAATTAG--ATTTA-T
*
2739912 AAAAAAAATTAGATTTAT
1 AATAAAAATTAGATTTAT
2739930 AATAAAAATGTAGA
1 AATAAAAAT-TAGA
2739944 AAGTTTAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
15 5 0.12
16 1 0.02
17 3 0.07
18 14 0.34
19 9 0.22
20 2 0.05
21 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
AATAAAAATTAGATTTAT
Found at i:2740306 original size:30 final size:30
Alignment explanation
Indices: 2740270--2740329 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2740260 TACGAGATTA
2740270 ATATAAAAATTTGATAACAAATTCTAACAC
1 ATATAAAAATTTGATAACAAATTCTAACAC
*
2740300 ATATAAAATTTTGATAACAAATTCTAACAC
1 ATATAAAAATTTGATAACAAATTCTAACAC
2740330 GTATTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (30 bp):
ATATAAAAATTTGATAACAAATTCTAACAC
Found at i:2740594 original size:32 final size:31
Alignment explanation
Indices: 2740558--2740657 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 31
2740548 CTTGACCTAA
2740558 CCGAAAATCAATCGATCTGATATTGACCCGAC
1 CCGAAAATCAATCGATCT-ATATTGACCCGAC
*
2740590 CCG-AAATCTAAAT-GATCTAGTATTAACCCGAC
1 CCGAAAATC--AATCGATCTA-TATTGACCCGAC
* * * * *
2740622 CCAAAAACCAACCGATCCAATATTGACCCAAC
1 CCGAAAATCAATCGAT-CTATATTGACCCGAC
2740654 CCGA
1 CCGA
2740658 TATTGACCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
31 8 0.15
32 37 0.69
33 9 0.17
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (31 bp):
CCGAAAATCAATCGATCTATATTGACCCGAC
Found at i:2749767 original size:44 final size:43
Alignment explanation
Indices: 2749717--2750192 Score: 504
Period size: 43 Copynumber: 10.9 Consensus size: 43
2749707 GAAGTATTTT
* *
2749717 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTATCGTTACCGC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCC-C
* * * * *
2749761 AGGCTCCTCTGTTATGTGCAAGGGTAAATCCTTATCGTTATCGC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTT-TCCC
* * *
2749805 AGGCTCCTCTGCTATGTGAAAGGGTAAGTCCTTACCGTTACCTC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCC-C
2749849 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
* * * *
2749892 AAGCT-CTTCTTCTATGTGCAAGGTTAAGTCCTTACCGTTACCGC
1 AGGCTCCTT-TGCTATGTGCAAGGGTAAGTCCTTACCGTTTCC-C
*
2749936 AGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
* * * * * *
2749979 AGGTTCCTTTGCTGTATGAAAGGGTAAGACCTTACAGTTTTCCCC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCG-TTT-CCC
* * * * * **
2750024 AAGTTCCTTTGCTATGTGTAAGGATAAGACCTTATAGTTTCCC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
* * * **
2750067 AGGTTCCTTTGCTATGTACAAGGGTAAGACCTTATAGTTTCCC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
* ** *
2750110 AGGCTCTTTTTTTATGTGCAAGGGTAAGACCTTACCGTTTCCC
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
* * * **
2750153 AAGCTCTTTTGTTATGTGCAAGGGTAAACCCTTACCGTTT
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTT
2750193 TTGTATGCTC
Statistics
Matches: 374, Mismatches: 51, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
42 3 0.01
43 181 0.48
44 153 0.41
45 37 0.10
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (43 bp):
AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
Found at i:2749866 original size:88 final size:87
Alignment explanation
Indices: 2749717--2750191 Score: 483
Period size: 88 Copynumber: 5.4 Consensus size: 87
2749707 GAAGTATTTT
* * * *
2749717 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTATCGTTACCGCAGGCTCCTCTGTTATGTGCAA
1 AGGCTCCTTTGCTATGTGAAAGGGTAAGTCCTTACCGTTACCGCAGGCTCCTTTGCTATGTGCAA
* *
2749782 GGGTAAATCCTTATCGTTATCGC
66 GGGTAAATCCTTACCGTT-TCCC
* *
2749805 AGGCTCCTCTGCTATGTGAAAGGGTAAGTCCTTACCGTTACCTCAGGCTCCTTTGCTATGTGCAA
1 AGGCTCCTTTGCTATGTGAAAGGGTAAGTCCTTACCGTTACCGCAGGCTCCTTTGCTATGTGCAA
*
2749870 GGGTAAGTCCTTACCGTTTCCC
66 GGGTAAATCCTTACCGTTTCCC
* * * * *
2749892 AAGCT-CTTCTTCTATGTGCAAGGTTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCA
1 AGGCTCCTT-TGCTATGTGAAAGGGTAAGTCCTTACCGTTACCGCAGGCTCCTTTGCTATGTGCA
*
2749956 AGGGTAAGTCCTTACCGTTTCCC
65 AGGGTAAATCCTTACCGTTTCCC
* * * * * * * * * *
2749979 AGGTTCCTTTGCTGTATGAAAGGGTAAGACCTTACAGTTTTCCCCAAGTTCCTTTGCTATGTGTA
1 AGGCTCCTTTGCTATGTGAAAGGGTAAGTCCTTACCG-TTACCGCAGGCTCCTTTGCTATGTGCA
* **
2750044 AGGATAAGA-CCTTATAGTTTCCC
65 AGGGTAA-ATCCTTACCGTTTCCC
* * ** * * **
2750067 AGGTTCCTTTGCTATGT-ACAAGGGTAAGACCTTATAGTTTCC-CAGGCTCTTTTTTTATGTGCA
1 AGGCTCCTTTGCTATGTGA-AAGGGTAAGTCCTTACCGTTACCGCAGGCTCCTTTGCTATGTGCA
2750130 AGGGTAAGA-CCTTACCGTTTCCC
65 AGGGTAA-ATCCTTACCGTTTCCC
* * * * **
2750153 AAGCTCTTTTGTTATGTGCAAGGGTAAACCCTTACCGTT
1 AGGCTCCTTTGCTATGTGAAAGGGTAAGTCCTTACCGTT
2750192 TTTGTATGCT
Statistics
Matches: 325, Mismatches: 56, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
86 66 0.20
87 110 0.34
88 149 0.46
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (87 bp):
AGGCTCCTTTGCTATGTGAAAGGGTAAGTCCTTACCGTTACCGCAGGCTCCTTTGCTATGTGCAA
GGGTAAATCCTTACCGTTTCCC
Found at i:2750224 original size:131 final size:130
Alignment explanation
Indices: 2749717--2750216 Score: 547
Period size: 131 Copynumber: 3.8 Consensus size: 130
2749707 GAAGTATTTT
* * * * * *
2749717 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTATCGTTACCGCAGGCTCCTCTGTTATGTGCAA
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTTCC-CAAGCTCCTTTGCTATGTGCAA
* * *
2749782 GGGTAAATCCTTATCGTTATCGCAGGCTCCTCTGCTATGTGAAAGGGTAAGTCCTTACCGTTACC
65 GGGTAAATCCTTACCGTTATCGCAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCC
2749847 TC
130 -C
* *
2749849 AGGCTCCTTTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCCAAGCT-CTTCTTCTATGTGCAA
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTTCCCAAGCTCCTT-TGCTATGTGCAA
* * *
2749913 GGTTAAGTCCTTACCGTTACCGCAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCC
65 GGGTAAATCCTTACCGTTATCGCAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCC
2749978 C
130 C
* * * * * * *
2749979 AGGTTCCTTTGCTGTATGAAAGGGTAAGACCTTACAGTTTTCCCCAAGTTCCTTTGCTATGTGTA
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCG-TTT-CCCAAGCTCCTTTGCTATGTGCA
* ** * * * * * **
2750044 AGGATAAGA-CCTTATAGTT-TCCCAGGTTCCTTTGCTATGTACAAGGGTAAGACCTTATAGTTT
64 AGGGTAA-ATCCTTACCGTTATCGCAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTT
2750107 CCC
128 CCC
* ** * *
2750110 AGGCTCTTTTTTTATGTGCAAGGGTAAGACCTTACCGTTTCCCAAGCTCTTTTGTTATGTGCAAG
1 AGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTTCCCAAGCTCCTTTGCTATGTGCAAG
* * * * * *
2750175 GGTAAACCCTTACCGTTTTTGTATGCTCCTCTGCTTTGTGCA
66 GGTAAATCCTTACCGTTATCGCAGGCTCCTCTGCTATGTGCA
2750217 CATGGTAAAT
Statistics
Matches: 305, Mismatches: 56, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
128 1 0.00
129 33 0.11
130 53 0.17
131 145 0.48
132 70 0.23
133 3 0.01
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (130 bp):
AGGCTCCTTTGCTATGTGCAAGGGTAAGACCTTACCGTTTCCCAAGCTCCTTTGCTATGTGCAAG
GGTAAATCCTTACCGTTATCGCAGGCTCCTCTGCTATGTGCAAGGGTAAGTCCTTACCGTTTCCC
Found at i:2751641 original size:39 final size:39
Alignment explanation
Indices: 2751587--2751697 Score: 127
Period size: 39 Copynumber: 2.8 Consensus size: 39
2751577 TTTAATATTT
* **
2751587 TAATAATATTATTATTTTAATAAGTAAATAATATAATTAA
1 TAAT-ATATTTTTATTTTAATAAAAAAATAATATAATTAA
*
2751627 TAATATATTTTTATTTTAATAAAAAAATAATATAATTTA
1 TAATATATTTTTATTTTAATAAAAAAATAATATAATTAA
*
2751666 TAATA-ATTTTGT-TTTTAGTAAAATACAATAAT
1 TAATATATTTT-TATTTTAATAAAA-A-AATAAT
2751698 TTTAATATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
38 15 0.24
39 38 0.60
40 10 0.16
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (39 bp):
TAATATATTTTTATTTTAATAAAAAAATAATATAATTAA
Found at i:2751671 original size:42 final size:40
Alignment explanation
Indices: 2751587--2751672 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 40
2751577 TTTAATATTT
**
2751587 TAATAATATTATTATTTTAATAAGTAAATAATATAATTAA
1 TAATAATATTATTATTTTAATAAAAAAATAATATAATTAA
* *
2751627 TAAT-ATATTTTTATTTTAATAAAAAAATAATATAATTTA
1 TAATAATATTATTATTTTAATAAAAAAATAATATAATTAA
2751666 TAATAAT
1 TAATAAT
2751673 TTTGTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 35 0.85
40 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (40 bp):
TAATAATATTATTATTTTAATAAAAAAATAATATAATTAA
Found at i:2751697 original size:35 final size:31
Alignment explanation
Indices: 2751650--2751720 Score: 81
Period size: 35 Copynumber: 2.2 Consensus size: 31
2751640 TTTTAATAAA
*
2751650 AAAATAATATAATTTATAATAATTTTGTTTTTAGT
1 AAAATAATATAATTT-TAAT-ATTTT-TATTTA-T
2751685 AAAATACA-ATAATTTTAATATTTTTATTTAT
1 AAAATA-ATATAATTTTAATATTTTTATTTAT
2751716 AAAAT
1 AAAAT
2751721 TGTAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
31 6 0.18
32 5 0.15
33 5 0.15
34 4 0.12
35 13 0.38
36 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (31 bp):
AAAATAATATAATTTTAATATTTTTATTTAT
Found at i:2751795 original size:25 final size:23
Alignment explanation
Indices: 2751753--2751821 Score: 59
Period size: 25 Copynumber: 2.9 Consensus size: 23
2751743 TAATATTTCC
*
2751753 ATAA-ATTATTATAATATTTTCAAA
1 ATAATATTATTATTATATTTT--AA
* *
2751777 ATAATATTATTATTTTATTAGTAA
1 ATAATATTATTATTATATT-TTAA
*
2751801 ATAATATTATTTATTGTATTT
1 ATAATATTA-TTATTATATTT
2751822 GATGTTTATA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 15 0.41
25 21 0.57
26 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (23 bp):
ATAATATTATTATTATATTTTAA
Found at i:2754798 original size:12 final size:13
Alignment explanation
Indices: 2754774--2754813 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2754764 TCAAAACAAC
2754774 AACATGATCCAAA
1 AACATGATCCAAA
*
2754787 AACA-GCTCCAAA
1 AACATGATCCAAA
2754799 CAACATGATCCAAA
1 -AACATGATCCAAA
2754813 A
1 A
2754814 TCCACTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 7 0.30
13 9 0.39
14 7 0.30
ACGTcount: A:0.53, C:0.28, G:0.07, T:0.12
Consensus pattern (13 bp):
AACATGATCCAAA
Found at i:2754803 original size:13 final size:14
Alignment explanation
Indices: 2754771--2754812 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2754761 CATTCAAAAC
2754771 AACAACATGATCCA
1 AACAACATGATCCA
*
2754785 AA-AACA-GCTCCA
1 AACAACATGATCCA
2754797 AACAACATGATCCA
1 AACAACATGATCCA
2754811 AA
1 AA
2754813 ATCCACTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.52, C:0.29, G:0.07, T:0.12
Consensus pattern (14 bp):
AACAACATGATCCA
Found at i:2758626 original size:26 final size:26
Alignment explanation
Indices: 2758566--2758626 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
2758556 GTGGACTTTG
*
2758566 GATCATATTGTTTGGAGCTGTTTGGA
1 GATCATGTTGTTTGGAGCTGTTTGGA
* * **
2758592 GCTGC-TGTTGTTTGGAGTTGTTTTTA
1 GAT-CATGTTGTTTGGAGCTGTTTGGA
2758618 GATCATGTT
1 GATCATGTT
2758627 ACTGTTTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
25 1 0.04
26 25 0.93
27 1 0.04
ACGTcount: A:0.15, C:0.08, G:0.30, T:0.48
Consensus pattern (26 bp):
GATCATGTTGTTTGGAGCTGTTTGGA
Found at i:2758957 original size:15 final size:15
Alignment explanation
Indices: 2758937--2758968 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2758927 GTGGTTTCTC
*
2758937 TGTCTTTTGTGTATT
1 TGTCTTTTGTATATT
2758952 TGTCTTTTGTATATT
1 TGTCTTTTGTATATT
2758967 TG
1 TG
2758969 GTTGACAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.19, T:0.66
Consensus pattern (15 bp):
TGTCTTTTGTATATT
Found at i:2759262 original size:44 final size:44
Alignment explanation
Indices: 2759199--2759324 Score: 243
Period size: 44 Copynumber: 2.9 Consensus size: 44
2759189 TAATGTGAGA
*
2759199 AAACTTTACAAGCTTGCATTTGTTAAAATATATATTCTTTTTGT
1 AAACTTCACAAGCTTGCATTTGTTAAAATATATATTCTTTTTGT
2759243 AAACTTCACAAGCTTGCATTTGTTAAAATATATATTCTTTTTGT
1 AAACTTCACAAGCTTGCATTTGTTAAAATATATATTCTTTTTGT
2759287 AAACTTCACAAGCTTGCATTTGTTAAAATATATATTCT
1 AAACTTCACAAGCTTGCATTTGTTAAAATATATATTCT
2759325 CTTTACTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 81 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (44 bp):
AAACTTCACAAGCTTGCATTTGTTAAAATATATATTCTTTTTGT
Found at i:2759264 original size:23 final size:23
Alignment explanation
Indices: 2759238--2759309 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 23
2759228 ATATATTCTT
2759238 TTTGTAAACTTCACAAGCTTGCA
1 TTTGTAAACTTCACAAGCTTGCA
* * **
2759261 TTTGTTAAAATAT-ATATTCTT---
1 TTTG-TAAACT-TCACAAGCTTGCA
2759282 TTTGTAAACTTCACAAGCTTGCA
1 TTTGTAAACTTCACAAGCTTGCA
2759305 TTTGT
1 TTTGT
2759310 TAAAATATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
19 1 0.03
20 10 0.29
21 4 0.11
23 9 0.26
24 10 0.29
25 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (23 bp):
TTTGTAAACTTCACAAGCTTGCA
Found at i:2760973 original size:41 final size:41
Alignment explanation
Indices: 2760913--2760996 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
2760903 GCAGAGGATC
2760913 TAATGTGATTGTAACTATAAGCAAAAACAATAGGTTACGAG
1 TAATGTGATTGTAACTATAAGCAAAAACAATAGGTTACGAG
*
2760954 TAATGTGATTGTAATTATAAGCAAAAACAATAGGTTACGAG
1 TAATGTGATTGTAACTATAAGCAAAAACAATAGGTTACGAG
2760995 TA
1 TA
2760997 GATAATTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (41 bp):
TAATGTGATTGTAACTATAAGCAAAAACAATAGGTTACGAG
Found at i:2764578 original size:20 final size:21
Alignment explanation
Indices: 2764553--2764592 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2764543 TGTTTACTGT
2764553 TGAATG-GAACCATTCAGCGC
1 TGAATGTGAACCATTCAGCGC
*
2764573 TGAATGTTGAACCGTTCAGC
1 TGAATG-TGAACCATTCAGC
2764593 ATTCAGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
TGAATGTGAACCATTCAGCGC
Found at i:2766353 original size:22 final size:20
Alignment explanation
Indices: 2766317--2766369 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
2766307 ACATGCGGAT
*
2766317 GTATCGATACTCTTAAAGGGTG
1 GTATCGATACCCTT--AGGGTG
*
2766339 GTATCGGTACCCTTAGGGTG
1 GTATCGATACCCTTAGGGTG
*
2766359 GTACCGATACC
1 GTATCGATACC
2766370 TTCAAGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
22 12 0.44
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCTTAGGGTG
Found at i:2773860 original size:21 final size:21
Alignment explanation
Indices: 2773834--2773920 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
2773824 CGAGGGTCTT
*
2773834 TGTGGTCCTTCGGGACAATTA
1 TGTGGTCCTTCGGGACAAATA
* *
2773855 TGTGGTTCTACGGGACAAATA
1 TGTGGTCCTTCGGGACAAATA
*
2773876 TGTGG-CACTTCGGTG-CAACCCTA
1 TGTGGTC-CTTCGG-GACAA--ATA
* *
2773899 TGTGGTCCTTCAGGACGAATA
1 TGTGGTCCTTCGGGACAAATA
2773920 T
1 T
2773921 ATAGCACTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
21 34 0.67
22 2 0.04
23 14 0.27
24 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (21 bp):
TGTGGTCCTTCGGGACAAATA
Found at i:2773920 original size:44 final size:44
Alignment explanation
Indices: 2773853--2773937 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
2773843 TCGGGACAAT
* * * * *
2773853 TATGTGGTTCTACGGGACAAATATGTGGCACTTCGGTGCAACCC
1 TATGTGGTCCTACAGGACAAATATATAGCACTTCGATGCAACCC
* *
2773897 TATGTGGTCCTTCAGGACGAATATATAGCACTTCGATGCAA
1 TATGTGGTCCTACAGGACAAATATATAGCACTTCGATGCAA
2773938 ATTACGAGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (44 bp):
TATGTGGTCCTACAGGACAAATATATAGCACTTCGATGCAACCC
Found at i:2774522 original size:42 final size:42
Alignment explanation
Indices: 2774476--2774563 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
2774466 AATAAATTTT
2774476 AAATTTATTCCTATTTGTGAATTTCTTATATTTTGAAAAGTC
1 AAATTTATTCCTATTTGTGAATTTCTTATATTTTGAAAAGTC
* *
2774518 AAATTTATTCTTATTTGTGAATTTCTTATGTTTTGAAAAGTC
1 AAATTTATTCCTATTTGTGAATTTCTTATATTTTGAAAAGTC
2774560 AAAT
1 AAAT
2774564 GTGACACCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (42 bp):
AAATTTATTCCTATTTGTGAATTTCTTATATTTTGAAAAGTC
Found at i:2778321 original size:3 final size:3
Alignment explanation
Indices: 2778313--2778370 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
2778303 CATAAATTTG
2778313 TAA 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 TAA
*
2778361 T-T TAA TAA TA
1 TAA TAA TAA TA
2778371 TGTTTTTGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 51 0.98
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2778973 original size:136 final size:135
Alignment explanation
Indices: 2778736--2779078 Score: 493
Period size: 136 Copynumber: 2.6 Consensus size: 135
2778726 GACTTGAAAG
* ** *
2778736 GAACAAGTTCTTCTCATTATGAAC-TTTCT-CCT-T-TAAGACGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
* * *
2778797 T-T-TTGGAAATGTCAATCCCTCTAACGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGAT
66 TCTATTGGAAATATCAATCCCTCTAACGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTGAT
2778860 AGATC
131 AGATC
*
2778865 GAACAGGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTT-TTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
2778930 CTCTATTGGAAATATTAATCCCTC-AAGCGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTG
65 CTCTATTGGAAATATCAATCCCTCTAA-CGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTG
*
2778994 ATAGGTC
129 ATAGATC
* *
2779001 GAACAAGCTATTCCCATTATGAACTTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAAC-TTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
*
2779066 CTCCATTGGAAAT
65 CTCTATTGGAAAT
2779079 GTTGATCCAT
Statistics
Matches: 191, Mismatches: 14, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
129 22 0.12
130 1 0.01
131 4 0.02
132 3 0.02
133 1 0.01
134 26 0.14
135 3 0.02
136 129 0.68
137 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
TCTATTGGAAATATCAATCCCTCTAACGAGGTGTCACTGATTCGAAATGCCATGAATCGAGTGAT
AGATC
Found at i:2779983 original size:18 final size:17
Alignment explanation
Indices: 2779960--2780023 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
2779950 CTCATTTTTC
2779960 TCTTTTCATTTTTTTATT
1 TCTTTTC-TTTTTTTATT
*
2779978 TC-TTT-TGTTTTTATT
1 TCTTTTCTTTTTTTATT
* *
2779993 TTTTTTCATCTTTTTATT
1 TCTTTTC-TTTTTTTATT
*
2780011 T-GTTTCTTTTTTT
1 TCTTTTCTTTTTTT
2780024 CTTCAAGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
15 10 0.26
16 9 0.24
17 7 0.18
18 12 0.32
ACGTcount: A:0.08, C:0.09, G:0.03, T:0.80
Consensus pattern (17 bp):
TCTTTTCTTTTTTTATT
Found at i:2793762 original size:43 final size:43
Alignment explanation
Indices: 2793701--2793793 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
2793691 TGGCTCAGGA
*
2793701 GTTGACGGCGTGACTCACATTCACGGCTGAAAGCTGAACATGT
1 GTTGACGGCGCGACTCACATTCACGGCTGAAAGCTGAACATGT
2793744 GTTGACGGCGCGACTCACATTCACGGCTGAAAGCTGAACATGT
1 GTTGACGGCGCGACTCACATTCACGGCTGAAAGCTGAACATGT
2793787 GTTGACG
1 GTTGACG
2793794 ACTGTTGAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.23
Consensus pattern (43 bp):
GTTGACGGCGCGACTCACATTCACGGCTGAAAGCTGAACATGT
Found at i:2794023 original size:3 final size:3
Alignment explanation
Indices: 2794015--2794048 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2794005 ATATTTGTAT
*
2794015 TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2794049 TTTTTTTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2794929 original size:20 final size:22
Alignment explanation
Indices: 2794878--2794923 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2794868 CAATATCTAA
2794878 TTTAAA-TATAAAAATAATTAT
1 TTTAAATTATAAAAATAATTAT
*
2794899 TTTAAATTATAAAAATAATTTT
1 TTTAAATTATAAAAATAATTAT
2794921 TTT
1 TTT
2794924 TTTATAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAAATTATAAAAATAATTAT
Found at i:2805861 original size:12 final size:12
Alignment explanation
Indices: 2805841--2805872 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2805831 AGATGAGATG
*
2805841 TCAGGTATGCTT
1 TCAGCTATGCTT
2805853 TCAGCTATGCTT
1 TCAGCTATGCTT
2805865 TCAGCTAT
1 TCAGCTAT
2805873 CTCAGTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (12 bp):
TCAGCTATGCTT
Found at i:2813614 original size:16 final size:16
Alignment explanation
Indices: 2813580--2813621 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2813570 TGTTACTTCA
* *
2813580 GAATGATT-AAGTGCT
1 GAATGATTCAAATACT
2813595 GAATGATTCAAATACT
1 GAATGATTCAAATACT
2813611 GAATG-TTCAAA
1 GAATGATTCAAA
2813622 GGCTCTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (16 bp):
GAATGATTCAAATACT
Found at i:2826200 original size:26 final size:24
Alignment explanation
Indices: 2826152--2826200 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
2826142 AGATAAATTT
* *
2826152 AATCTAATTGTTTTATATTTTTAA
1 AATCTAATTGTTGTATATGTTTAA
2826176 AATCGTAATTGTCTGTATATGTTTA
1 AATC-TAATTGT-TGTATATGTTTA
2826201 GCAATGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 7 0.33
26 10 0.48
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (24 bp):
AATCTAATTGTTGTATATGTTTAA
Found at i:2830139 original size:21 final size:20
Alignment explanation
Indices: 2830053--2830210 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
2830043 AAATGACCAA
**
2830053 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2830072 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2830092 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2830112 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
2830133 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2830154 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2830174 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
2830195 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2830211 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2830203 original size:20 final size:20
Alignment explanation
Indices: 2830178--2830371 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2830168 GATTTTCAAT
* *
2830178 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2830198 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2830218 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2830238 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2830258 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2830278 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2830298 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2830318 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2830339 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2830359 AATCGCAACGCGA
1 AATCGCAACGCGA
2830372 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2830223 original size:40 final size:39
Alignment explanation
Indices: 2830178--2830371 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
2830168 GATTTTCAAT
* ** *
2830178 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
2830218 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
2830258 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
2830298 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
2830339 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
2830372 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:2830261 original size:60 final size:60
Alignment explanation
Indices: 2830178--2830370 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2830168 GATTTTCAAT
* ** * *
2830178 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2830238 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2830298 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2830359 AATCGCAACGCG
1 AATCGCAACGCG
2830371 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2830791 original size:33 final size:33
Alignment explanation
Indices: 2830752--2830822 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2830742 TTCACTTAGA
*
2830752 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2830785 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2830818 TTTCA
1 TTTCA
2830823 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2830962 original size:14 final size:14
Alignment explanation
Indices: 2830943--2830997 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2830933 AGAATGACTG
2830943 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2830957 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2830976 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2830990 TCGCAACG
1 TCGCAACG
2830998 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2830980 original size:33 final size:33
Alignment explanation
Indices: 2830943--2831013 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2830933 AGAATGACTG
**
2830943 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2830976 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2831009 TCGCA
1 TCGCA
2831014 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2831031 original size:19 final size:19
Alignment explanation
Indices: 2831009--2831106 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2830999 GAAACCAAAA
*
2831009 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2831028 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2831042 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2831061 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2831075 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2831094 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2831107 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2831050 original size:14 final size:14
Alignment explanation
Indices: 2831031--2831120 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2831021 TTTCATTTCG
2831031 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2831045 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2831064 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2831078 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2831095 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2831111 CGTTGCGATT
1 CGTTGCGATT
2831121 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2831056 original size:33 final size:33
Alignment explanation
Indices: 2831014--2831128 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2831004 CAAAATCGCA
2831014 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2831047 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2831080 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2831113 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2831129 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2833032 original size:92 final size:93
Alignment explanation
Indices: 2832826--2833204 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
2832816 TAGATTGCTT
*
2832826 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2832891 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2832919 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2832983 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2833011 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2833075 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2833103 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2833168 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2833196 AGTAAATTT
1 AGTAAATTT
2833205 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2833056 original size:185 final size:185
Alignment explanation
Indices: 2832826--2833206 Score: 737
Period size: 185 Copynumber: 2.1 Consensus size: 185
2832816 TAGATTGCTT
2832826 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
2832891 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2832956 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2833011 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
2833076 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
2833141 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2833196 AGTAAATTTAT
1 AGTAAATTTAT
2833207 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 101 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2833288 original size:19 final size:19
Alignment explanation
Indices: 2833248--2833376 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2833238 TAGTTTACTT
* *
2833248 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2833268 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2833287 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2833306 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2833320 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2833339 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2833353 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2833372 TCGCA
1 TCGCA
2833377 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2833327 original size:33 final size:32
Alignment explanation
Indices: 2833284--2833376 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2833274 CGCGAAACCA
**
2833284 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2833316 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2833349 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2833377 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2833374 original size:52 final size:52
Alignment explanation
Indices: 2833248--2833376 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2833238 TAGTTTACTT
**
2833248 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2833300 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2833353 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2833377 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2833394 original size:19 final size:19
Alignment explanation
Indices: 2833372--2833506 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2833362 GAAACCAAAA
*
2833372 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2833391 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2833407 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2833424 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2833440 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2833457 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2833476 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2833496 TCGTGTTGCGA
1 TCGCGTTGCGA
2833507 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2833413 original size:14 final size:14
Alignment explanation
Indices: 2833394--2833450 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2833384 TTTCATTTCG
2833394 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2833408 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2833425 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2833441 CGTTGCGATT
1 CGTTGCGATT
2833451 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2833419 original size:33 final size:33
Alignment explanation
Indices: 2833377--2833469 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2833367 CAAAATCGCA
*
2833377 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2833410 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2833443 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2833470 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2834970 original size:14 final size:14
Alignment explanation
Indices: 2834951--2834986 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2834941 ATTGTTTAAT
2834951 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2834965 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2834979 TGATTTGT
1 TGATTTGT
2834987 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2835161 original size:20 final size:19
Alignment explanation
Indices: 2835093--2835175 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
2835083 AAAAATGACT
2835093 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2835112 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2835126 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2835145 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2835165 ATCGCAATGCG
1 ATCGCAATGCG
2835176 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2835228 original size:19 final size:19
Alignment explanation
Indices: 2835204--2835477 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
2835194 GATTATCTCG
2835204 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2835223 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2835242 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2835256 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2835275 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2835294 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2835313 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2835332 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2835351 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2835365 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2835384 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2835403 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2835417 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2835437 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2835451 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2835470 TTGCGATT
1 TTGCGATT
2835478 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 137 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2835244 original size:52 final size:52
Alignment explanation
Indices: 2835182--2835449 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
2835172 TGCGTTTATA
*
2835182 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2835234 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2835286 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
2835343 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2835395 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2835448 AT
1 AT
2835450 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 131 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2835333 original size:109 final size:105
Alignment explanation
Indices: 2835182--2835449 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
2835172 TGCGTTTATA
2835182 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
2835246 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2835286 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
2835351 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2835395 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
2835450 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 19 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 95 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2837776 original size:12 final size:12
Alignment explanation
Indices: 2837759--2837783 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2837749 TCTTCGGGGA
2837759 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2837771 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2837783 C
1 C
2837784 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2837992 original size:24 final size:24
Alignment explanation
Indices: 2837958--2838004 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2837948 CTGAAACATC
2837958 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2837982 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2838005 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2838709 original size:20 final size:20
Alignment explanation
Indices: 2838681--2839070 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
2838671 AAATTTCAGT
* * * *
2838681 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2838701 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2838721 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2838741 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2838761 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2838781 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2838801 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2838821 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2838841 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2838861 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2838881 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
2838901 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
2838922 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2838942 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2838962 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2838982 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2839002 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2839022 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2839042 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2839062 GTTGCGATT
1 GTTGCGATT
2839071 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2841870 original size:135 final size:134
Alignment explanation
Indices: 2841609--2841851 Score: 387
Period size: 135 Copynumber: 1.8 Consensus size: 134
2841599 TAATAGATTA
* * *
2841609 ATATATAATTTTAAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGT
1 ATATATAATTTTAAAAATAAGATATTTATTTAATTAAAAATATCAGAAAATGGACATCCAGTTGC
* **
2841674 TTTAAGACTGCAATTTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTAAATATATAT
66 TTTAAGACTGCAATTTCTTAATATTAAAAAATAAATAAACATTAATAAAACATCGAAATATATAT
2841739 ATAT
131 ATAT
* *
2841743 ATATATAATTTATAAAAATAAGATGTTTATTTAATTAAAAATATCAGAAAATGGATATCCAGTTG
1 ATATATAATTT-TAAAAATAAGATATTTATTTAATTAAAAATATCAGAAAATGGACATCCAGTTG
* *
2841808 CTTTAAGACTGCACTTTCTTAATATTTAAAAATAAATAAACATT
65 CTTTAAGACTGCAATTTCTTAATATTAAAAAATAAATAAACATT
2841852 GCTATCTAAT
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
134 11 0.11
135 89 0.89
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (134 bp):
ATATATAATTTTAAAAATAAGATATTTATTTAATTAAAAATATCAGAAAATGGACATCCAGTTGC
TTTAAGACTGCAATTTCTTAATATTAAAAAATAAATAAACATTAATAAAACATCGAAATATATAT
ATAT
Found at i:2843521 original size:3 final size:3
Alignment explanation
Indices: 2843513--2843551 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
2843503 ATTTATTTAT
*
2843513 ATA ATA ATA ATA ATA TATA TTA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT
2843552 TTTAATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:2843526 original size:22 final size:22
Alignment explanation
Indices: 2843513--2843557 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2843503 ATTTATTTAT
2843513 ATAATAATAATAATATATATTA
1 ATAATAATAATAATATATATTA
*
2843535 ATAATAATAATAATA-ATTTTA
1 ATAATAATAATAATATATATTA
2843556 AT
1 AT
2843558 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAATAATAATAATATATATTA
Found at i:2843529 original size:16 final size:16
Alignment explanation
Indices: 2843510--2843551 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
2843500 GTAATTTATT
2843510 TATATAATAATAATAA
1 TATATAATAATAATAA
*
2843526 TATATATTAATAATAA
1 TATATAATAATAATAA
2843542 TA-ATAATAAT
1 TATATAATAAT
2843552 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATAATAATAATAA
Found at i:2844552 original size:30 final size:30
Alignment explanation
Indices: 2844516--2844845 Score: 173
Period size: 30 Copynumber: 10.9 Consensus size: 30
2844506 TTAACTTTTA
2844516 AAAAATATATTTTATTTTTATCTTAAACTT
1 AAAAATATATTTTATTTTTATCTTAAACTT
* *
2844546 AAAAATATATATTT-TTCTTATTTTAAA-TT
1 AAAAATATAT-TTTATTTTTATCTTAAACTT
* *** *
2844575 AAAAATACATTTTAGCCTTATCTT-AATTT
1 AAAAATATATTTTATTTTTATCTTAAACTT
* * *
2844604 AAACAATATAATATATTTTTATCTT-ACCTTTT
1 AAA-AATATATTTTATTTTTATCTTAAAC--TT
* * * * * **
2844636 AAAAATATTTTTTATCTTAATGGGGATCAATTTT
1 AAAAATATATTTTATTTTTAT----CTTAAACTT
*
2844670 AAAAAATATATTTTATTTTTATATTAAA-TT
1 -AAAAATATATTTTATTTTTATCTTAAACTT
* *
2844700 ATTAAATATA-TTTATTCTTATCTTAACTTAACTT
1 A-AAAATATATTTTATTTTTATCTT-A---AACTT
* * *
2844734 AAAAAATATATTTTACTCTTAT-TTTAACTT
1 -AAAAATATATTTTATTTTTATCTTAAACTT
*
2844764 -AAAA-ATA-TTTAGTTTTATCTT-AACTT
1 AAAAATATATTTTATTTTTATCTTAAACTT
* **
2844790 AAAAAATATATGTTT-TTCTTATCTT-ATTTT
1 -AAAAATATAT-TTTATTTTTATCTTAAACTT
2844820 AAAAATATATTTTATTTTTATCTTAA
1 AAAAATATATTTTATTTTTATCTTAA
2844846 TTTAAAACTA
Statistics
Matches: 231, Mismatches: 41, Indels: 56
0.70 0.12 0.17
Matches are distributed among these distances:
26 14 0.06
27 5 0.02
28 16 0.07
29 58 0.25
30 64 0.28
31 23 0.10
32 5 0.02
33 2 0.01
34 13 0.06
35 30 0.13
36 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (30 bp):
AAAAATATATTTTATTTTTATCTTAAACTT
Found at i:2844587 original size:59 final size:59
Alignment explanation
Indices: 2844516--2844845 Score: 201
Period size: 59 Copynumber: 5.4 Consensus size: 59
2844506 TTAACTTTTA
*
2844516 AAAAATATATTTTATTTTTATCTTAAACTTAAAAATATATATTTTTCTTATTTTAAATT
1 AAAAATATATTTTATTTTTATCTTAAACTTAAAAATATATATTTTTCTTATCTTAAATT
* *** * * **
2844575 AAAAATACATTTTAGCCTTATCTT-AATTTAAACAATATAATATATTT-TTATCTTACCTTTT
1 AAAAATATATTTTATTTTTATCTTAAACTTAAA-AATAT-ATATTTTTCTTATCTTA--AATT
* * * * * ** * *
2844636 AAAAATATTTTTTATCTTAATGGGGATCAATTTTAAAAA-ATATATTTTATTTTTATATTAAATT
1 AAAAATATATTTTATTTTTAT----CTTAAACTTAAAAATATATA-TTT-TTCTTATCTTAAATT
* * * *
2844700 ATTAAATATA-TTTATTCTTATCTTAACTTAACTTAAAAA-ATATATTTTACTCTTATTTTAACT
1 A-AAAATATATTTTATTTTTATCTT-A---AACTTAAAAATATATATTTT--TCTTATCTTAAAT
2844763 T
59 T
* * **
2844764 -AAAA-ATA-TTTAGTTTTATCTT-AACTTAAAAAATATATGTTTTTCTTATCTTATTTT
1 AAAAATATATTTTATTTTTATCTTAAACTT-AAAAATATATATTTTTCTTATCTTAAATT
2844820 AAAAATATATTTTATTTTTATCTTAA
1 AAAAATATATTTTATTTTTATCTTAA
2844846 TTTAAAACTA
Statistics
Matches: 205, Mismatches: 41, Indels: 49
0.69 0.14 0.17
Matches are distributed among these distances:
56 16 0.08
57 9 0.04
58 18 0.09
59 45 0.22
60 9 0.04
61 34 0.17
62 4 0.02
63 6 0.03
64 39 0.19
65 11 0.05
66 14 0.07
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (59 bp):
AAAAATATATTTTATTTTTATCTTAAACTTAAAAATATATATTTTTCTTATCTTAAATT
Found at i:2844742 original size:64 final size:61
Alignment explanation
Indices: 2844668--2844791 Score: 169
Period size: 64 Copynumber: 2.0 Consensus size: 61
2844658 GGGATCAATT
* *
2844668 TTAAAAAATATATTTTATTTTTATATTAAATTATTAAATATATTTA-TTCTTATCTTAACTTAAC
1 TTAAAAAATATATTTTACTCTTATATTAAATTA--AAA-ATATTTAGTT-TTATCTTAACTTAAC
* *
2844732 TTAAAAAATATATTTTACTCTTATTTTAACTTAAAAATATTTAGTTTTATCTTAACTTAA
1 TTAAAAAATATATTTTACTCTTATATTAAATTAAAAATATTTAGTTTTATCTTAACTTAA
2844792 AAAATATATG
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
61 21 0.38
62 5 0.09
64 29 0.53
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (61 bp):
TTAAAAAATATATTTTACTCTTATATTAAATTAAAAATATTTAGTTTTATCTTAACTTAAC
Found at i:2844795 original size:155 final size:154
Alignment explanation
Indices: 2844511--2844798 Score: 363
Period size: 155 Copynumber: 1.9 Consensus size: 154
2844501 AATTATTAAC
* **
2844511 TTTTAAAAAATATATTTTATTTTTATCTTAAACTTAAAAATATATATTTTTCTTATTTTAAATTA
1 TTTTAAAAAATATATTTTATTTTTATATTAAACTTAAAAATATATATTTTTCTTAACTTAAATTA
* * * *
2844576 AAAATACATTTTAGCCTTATCTTAATTTAAACAATATAATATATTTTTATCTTACCTTTTAAAAA
66 AAAATACATTTTAGCCTTATCTTAACTTAAACAATAT-ATATAGTTTTATCTTAACTTTAAAAAA
2844641 TATTTTTTATCTTAATGGGGATCAA
130 TATTTTTTATCTTAATGGGGATCAA
*
2844666 TTTTAAAAAATATATTTTATTTTTATATTAAA-TTATTAAATATATTTATTCTTATCTTAACTTA
1 TTTTAAAAAATATATTTTATTTTTATATTAAACTTA--AAA-ATATATATT-TT-TCTTAACTTA
* * *
2844730 ACTTAAAAAATATATTTTA-CTCTTATTTTAACTTAAA-AATAT-T-TAGTTTTATCTTAAC-TT
61 AATT-AAAAATACATTTTAGC-CTTATCTTAACTTAAACAATATATATAGTTTTATCTTAACTTT
2844790 AAAAAATAT
124 AAAAAATAT
2844799 ATGTTTTTCT
Statistics
Matches: 115, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
154 3 0.03
155 41 0.36
156 16 0.14
157 9 0.08
158 2 0.02
159 17 0.15
160 27 0.23
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (154 bp):
TTTTAAAAAATATATTTTATTTTTATATTAAACTTAAAAATATATATTTTTCTTAACTTAAATTA
AAAATACATTTTAGCCTTATCTTAACTTAAACAATATATATAGTTTTATCTTAACTTTAAAAAAT
ATTTTTTATCTTAATGGGGATCAA
Found at i:2844809 original size:25 final size:27
Alignment explanation
Indices: 2844726--2844815 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 27
2844716 CTTATCTTAA
* *
2844726 CTTAACTTAAAAAATATATTTTACTCTTAT
1 CTTAACTTAAAAAATATA---TAGTTTTAT
* *
2844756 TTTAACTT-AAAAATATTTAGTTTTAT
1 CTTAACTTAAAAAATATATAGTTTTAT
2844782 CTTAACTTAAAAAATATAT-GTTTT-T
1 CTTAACTTAAAAAATATATAGTTTTAT
*
2844807 CTTATCTTA
1 CTTAACTTA
2844816 TTTTAAAAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
25 9 0.17
26 19 0.37
27 9 0.17
29 8 0.15
30 7 0.13
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (27 bp):
CTTAACTTAAAAAATATATAGTTTTAT
Found at i:2844824 original size:29 final size:29
Alignment explanation
Indices: 2844516--2844852 Score: 204
Period size: 29 Copynumber: 11.1 Consensus size: 29
2844506 TTAACTTTTA
* *
2844516 AAAAATATATTTTATTTTTATCTTAAACTT
1 AAAAATATATTTTATTCTTATCTT-AATTT
* *
2844546 AAAAATATATATTT-TTCTTATTTTAAATT
1 AAAAATATAT-TTTATTCTTATCTTAATTT
* **
2844575 AAAAATACATTTTAGCCTTATCTTAATTT
1 AAAAATATATTTTATTCTTATCTTAATTT
* * * *
2844604 AAACAATATAATATATTTTTATCTTACCTTTT
1 AAA-AATATATTTTATTCTTATCTTA--ATTT
* * *
2844636 AAAAATATTTTTTA-TCTTAATGGGGATCAATTTT
1 AAAAATATATTTTATTCTT-AT----CTTAA-TTT
* * *
2844670 AAAAAATATATTTTATTTTTATATTAAATT
1 -AAAAATATATTTTATTCTTATCTTAATTT
*
2844700 ATTAAATATA-TTTATTCTTATCTTAACTTAACTT
1 A-AAAATATATTTTATTCTTATCTTAA--T---TT
* * *
2844734 AAAAAATATATTTTACTCTTATTTTAACTT
1 -AAAAATATATTTTATTCTTATCTTAATTT
*
2844764 -AAAA-ATA-TTTAGTT-TTATCTTAACTTA
1 AAAAATATATTTTA-TTCTTATCTTAA-TTT
*
2844791 AAAAATATATGTTT-TTCTTATCTTATTTT
1 AAAAATATAT-TTTATTCTTATCTTAATTT
*
2844820 AAAAATATATTTTATTTTTATCTTAATTT
1 AAAAATATATTTTATTCTTATCTTAATTT
2844849 AAAA
1 AAAA
2844853 CTATTCAATA
Statistics
Matches: 236, Mismatches: 42, Indels: 59
0.70 0.12 0.18
Matches are distributed among these distances:
26 12 0.05
27 5 0.02
28 14 0.06
29 76 0.32
30 56 0.24
31 20 0.08
32 6 0.03
34 12 0.05
35 32 0.14
36 3 0.01
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (29 bp):
AAAAATATATTTTATTCTTATCTTAATTT
Found at i:2847985 original size:133 final size:131
Alignment explanation
Indices: 2847680--2847962 Score: 287
Period size: 133 Copynumber: 2.2 Consensus size: 131
2847670 TTGACCTTAT
** * * ** *
2847680 ATAATTGAGGCCCCAAATTTTGTAATCTCACTTT-TAACTTTA-TAATTGAGGCTTTTAA-G--T
1 ATAATTGA-GCCCCCTATTTTTTAATCTCATTTTCTAACTTTATTAA-TGAGGCCCTAAAGGTTT
* * *
2847740 TTTTTCAACCTCACTTTCTACCTTTTCAATTGAGGCCCCTAAGTTTCTTCATCTCAATTTCTACT
64 TTTTTCAACCTCACTTTCTAACTTTTCAATTGAGGACCCTAAGTTTCTTCATCTCAATTTCAACT
*
2847805 TTT
129 TTA
*
2847808 ATAATTGAGCCCCCTATTTTTTAATCTCATTTTTTTTAACTTTATTAATGAGGCCCTAAAGGTTT
1 ATAATTGAGCCCCCTATTTTTTAATCTCA--TTTTCTAACTTTATTAATGAGGCCCTAAAGGTTT
* * *
2847873 TTTTTTAATCTCACTTTCTAAC-TTTCTAATTTAGGACCCTAAGGTTT-TTCGATCTCAATTAT-
64 TTTTTCAACCTCACTTTCTAACTTTTC-AATTGAGGACCCTAA-GTTTCTTC-ATCTCAATT-TC
2847935 AAC-TTA
125 AACTTTA
*
2847941 ATAATTGAGGCCCCTATTTTTT
1 ATAATTGAGCCCCCTATTTTTT
2847963 TCAATCTCGA
Statistics
Matches: 129, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
127 18 0.14
128 8 0.06
129 3 0.02
130 17 0.13
131 4 0.03
132 4 0.03
133 59 0.46
134 15 0.12
135 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.46
Consensus pattern (131 bp):
ATAATTGAGCCCCCTATTTTTTAATCTCATTTTCTAACTTTATTAATGAGGCCCTAAAGGTTTTT
TTTCAACCTCACTTTCTAACTTTTCAATTGAGGACCCTAAGTTTCTTCATCTCAATTTCAACTTT
A
Found at i:2847988 original size:43 final size:43
Alignment explanation
Indices: 2847589--2847995 Score: 211
Period size: 43 Copynumber: 9.4 Consensus size: 43
2847579 CTTTATTTTT
* *
2847589 CTTTATAATTGAGG-TCCTAA-TATTATTCAATCTCACTTAT-TA
1 CTTTATAATTGAGGCCCCTAAGT-TTTTTCAATCTCACTT-TCTA
* * * * ** *
2847631 TCTTTACAATTGAAGTCTCTAA-TTTTTTCAATCT-TTTTTTTGA
1 -CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCT-A
* *
2847674 CCTTATATAATTGAGGCCCC-AAATTTTGT-AATCTCACTTT-TAA
1 -CTT-TATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCT-A
*** *
2847717 CTTTATAATTGAGGCTTTTAAGTTTTTTCAACCTCACTTTCTA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTA
* *
2847760 CCTTT-TCAATTGAGGCCCCTAAGTTTCTTC-ATCTCAATTTCTA
1 -CTTTAT-AATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTA
* * *
2847803 CTTTTATAATTGAGCCCCCT-A-TTTTTT-AATCTCATTTTTTTTAA
1 C-TTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCA--CTTTCT-A
*
2847847 CTTTATTAA-TGAGG-CCCTAAAGGTTTTTTTTTAATCTCACTTTCTAA
1 CTTTA-TAATTGAGGCCCCT-AA-G--TTTTTTCAATCTCACTTTCT-A
* * * * * * *
2847894 CTTTCTAATTTAGGACCCTAAGGTTTTTCGATCTCAATTAT-AA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTT-TCTA
* *
2847937 CTTAATAATTGAGGCCCCT-ATTTTTTTCAATCTCGA-TTTCTA
1 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTC-ACTTTCTA
*
2847979 CTTTTATAATTAAGGCC
1 C-TTTATAATTGAGGCC
2847996 TTTAACTTTT
Statistics
Matches: 281, Mismatches: 52, Indels: 62
0.71 0.13 0.16
Matches are distributed among these distances:
41 25 0.09
42 35 0.12
43 115 0.41
44 68 0.24
45 1 0.00
46 4 0.01
47 16 0.06
48 10 0.04
49 7 0.02
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (43 bp):
CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCACTTTCTA
Found at i:2847995 original size:133 final size:131
Alignment explanation
Indices: 2847739--2847995 Score: 276
Period size: 133 Copynumber: 1.9 Consensus size: 131
2847729 GGCTTTTAAG
* * *
2847739 TTTTTTCAACCTCACTTTCTACCTTTTCAATTGAGGCCCCTAAGTTTCTTCATCTCAATTTCTAC
1 TTTTTTCAACCTCACTTTCTAACTTTTCAATTGAGGACCCTAAGTTTCTTCATCTCAATTTCAAC
* * *
2847804 TTTTATAATTGAGCCCCCTATTTTTTAATCTCATTTTTTTTAACTTTATTAATGAGGCCCTAAAG
66 TTTAATAATTGAGCCCCCTATTTTTTAATCTCA--TTTTCTAACTTTATTAATAAGGCCCTAAAG
2847869 GTT
129 GTT
* * *
2847872 TTTTTTTAATCTCACTTTCTAAC-TTTCTAATTTAGGACCCTAAGGTTT-TTCGATCTCAATTAT
1 TTTTTTCAACCTCACTTTCTAACTTTTC-AATTGAGGACCCTAA-GTTTCTTC-ATCTCAATT-T
*
2847935 -AAC-TTAATAATTGAGGCCCCTATTTTTTTCAATCTCGA-TTTCT-ACTTT-TATAATTAAGGC
62 CAACTTTAATAATTGAGCCCCCTA-TTTTTT-AATCTC-ATTTTCTAACTTTAT-TAA-TAAGGC
2847995 C
122 C
2847996 TTTAACTTTT
Statistics
Matches: 105, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
131 1 0.01
132 12 0.11
133 63 0.60
134 21 0.20
135 7 0.07
136 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (131 bp):
TTTTTTCAACCTCACTTTCTAACTTTTCAATTGAGGACCCTAAGTTTCTTCATCTCAATTTCAAC
TTTAATAATTGAGCCCCCTATTTTTTAATCTCATTTTCTAACTTTATTAATAAGGCCCTAAAGGT
T
Found at i:2849101 original size:22 final size:21
Alignment explanation
Indices: 2849055--2849101 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2849045 AATGGATTCT
* *
2849055 TTTAGAAAGTTTAAAATTGTT
1 TTTAGAAAGTTTAAAACTGTA
2849076 TTTAGAAAGTTTGAAAAACT-TA
1 TTTAGAAAGTTT--AAAACTGTA
2849098 TTTA
1 TTTA
2849102 ATTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (21 bp):
TTTAGAAAGTTTAAAACTGTA
Found at i:2852083 original size:16 final size:16
Alignment explanation
Indices: 2852059--2852126 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 16
2852049 AAGAGTTTTT
*
2852059 TAAAAATTATTTATTA
1 TAAATATTATTTATTA
*
2852075 TAAATATTAAATTTAATA
1 TAAATATT--ATTTATTA
*
2852093 AATAATATTATTTATT-
1 TA-AATATTATTTATTA
*
2852109 TGAATATTATTT-TTA
1 TAAATATTATTTATTA
2852124 TAA
1 TAA
2852127 TTTTATTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
14 2 0.05
15 12 0.29
16 7 0.17
17 6 0.15
18 8 0.20
19 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (16 bp):
TAAATATTATTTATTA
Found at i:2852269 original size:23 final size:23
Alignment explanation
Indices: 2852220--2852282 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
2852210 GTGTTATATT
* **
2852220 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
2852243 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
2852266 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
2852283 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:2852310 original size:19 final size:20
Alignment explanation
Indices: 2852258--2852310 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2852248 TTAAATATCT
2852258 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
2852277 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
2852298 TTATTAAATATAT
1 TTATTAAATATAT
2852311 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:2852323 original size:30 final size:29
Alignment explanation
Indices: 2852266--2852421 Score: 100
Period size: 30 Copynumber: 5.5 Consensus size: 29
2852256 CTTTATTAAA
2852266 ATATTATTTAAATATATAAA-TAATATTAT
1 ATATTA-TTAAATATATAAATTAATATTAT
**
2852295 -TCATTATTAAATATATAAATTTTTTATTAT
1 AT-ATTATTAAATATATAAA-TTAATATTAT
*
2852325 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAAT-TAATAT-TAT
** *
2852354 ATATTATTATAATATAATTGATT-ATTTTAT
1 ATATTATTA-AATAT-ATAAATTAATATTAT
*
2852384 ATAATATTAAA-A-AT--ATT-ATATTAT
1 ATATTATTAAATATATAAATTAATATTAT
2852408 ATTATTA-TAAATAT
1 A-TATTATTAAATAT
2852422 TAATAAATAA
Statistics
Matches: 102, Mismatches: 12, Indels: 29
0.71 0.08 0.20
Matches are distributed among these distances:
24 14 0.14
25 5 0.05
26 2 0.02
28 16 0.16
29 27 0.26
30 31 0.30
31 4 0.04
32 3 0.03
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
ATATTATTAAATATATAAATTAATATTAT
Found at i:2852675 original size:42 final size:42
Alignment explanation
Indices: 2852617--2852736 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 42
2852607 ATGAATTACA
* *
2852617 TTCCGGAAAACCAATTACGTTAAACAAACATAGGAAAACATT
1 TTCCGGAAAACGAATTACGTTAAACAAACACAGGAAAACATT
* *
2852659 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTTAAACAAACACAGGAAAACATT
* * *
2852701 TTCAGGAAAACGAATTAC-TTGAAACACACACGGGAA
1 TTCCGGAAAACGAATTACGTT-AAACAAACACAGGAA
2852737 TTCGGAGAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 69 0.99
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTTAAACAAACACAGGAAAACATT
Found at i:2854680 original size:64 final size:65
Alignment explanation
Indices: 2854576--2854705 Score: 199
Period size: 64 Copynumber: 2.0 Consensus size: 65
2854566 GTCACCGCCA
* * *
2854576 CCTCCAGTCGAAGCTCTGCGACCGTCCGACCAAAACCCCTAAGGTCGATCATC-AAAGTCGTCGT
1 CCTCCAGACGAAGCTCTGCAACCGTCCGACCAAAACCCCTAAGGTCGATCATCAAAAGCCGTCGT
* * *
2854640 CCTCCAGACGAAGCTCTGTAACCGTCCGACCAAAATCCCTAAGGTCGATCGTCAAAAGCCGTCGT
1 CCTCCAGACGAAGCTCTGCAACCGTCCGACCAAAACCCCTAAGGTCGATCATCAAAAGCCGTCGT
2854705 C
1 C
2854706 GTTCGCTGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
64 48 0.81
65 11 0.19
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.18
Consensus pattern (65 bp):
CCTCCAGACGAAGCTCTGCAACCGTCCGACCAAAACCCCTAAGGTCGATCATCAAAAGCCGTCGT
Found at i:2855786 original size:31 final size:31
Alignment explanation
Indices: 2855739--2855834 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
2855729 GAACTTCGAC
* *
2855739 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
2855770 AACTATCCATATGTCCCGTAGAATATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
*
2855801 AACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
2855832 AAC
1 AAC
2855835 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 1 0.02
31 54 0.98
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:2861134 original size:31 final size:31
Alignment explanation
Indices: 2861086--2861182 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
2861076 AAAACCTCGG
* * *
2861086 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
1 AAACTATCCATATGTCCCGAAGAACATAGGT
* * *
2861117 AAACTATTCATATGTCCCGTAGAATATAGGT
1 AAACTATCCATATGTCCCGAAGAACATAGGT
* *
2861148 AAATTGTCCATATGTCCCGAA-AGACATAGGT
1 AAACTATCCATATGTCCCGAAGA-ACATAGGT
2861179 AAAC
1 AAAC
2861183 CCTCGATTCT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 1 0.02
31 52 0.98
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (31 bp):
AAACTATCCATATGTCCCGAAGAACATAGGT
Found at i:2862960 original size:12 final size:12
Alignment explanation
Indices: 2862943--2862977 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
2862933 CGAGTCAGTC
2862943 GAGTCAACTCAT
1 GAGTCAACTCAT
*
2862955 GAGTCAACTCGT
1 GAGTCAACTCAT
2862967 GAGTCAACTCA
1 GAGTCAACTCA
2862978 GACAGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (12 bp):
GAGTCAACTCAT
Found at i:2863020 original size:19 final size:19
Alignment explanation
Indices: 2862996--2863033 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2862986 CAACCCGACT
* *
2862996 CGACCCGTTGACTTTGACC
1 CGACCCGTAGACTCTGACC
2863015 CGACCCGTAGACTCTGACC
1 CGACCCGTAGACTCTGACC
2863034 AGAGTTGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.39, G:0.21, T:0.21
Consensus pattern (19 bp):
CGACCCGTAGACTCTGACC
Found at i:2866864 original size:31 final size:31
Alignment explanation
Indices: 2866829--2866909 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
2866819 ATATATAACA
* *
2866829 TTAGTAACCATTTTGTTATAAATCGATAATG
1 TTAGTAACCAATTTGTTACAAATCGATAATG
* *
2866860 TTAGTGACCAATTTGTTACAAATCGATAATA
1 TTAGTAACCAATTTGTTACAAATCGATAATG
* * *
2866891 TTAATGATCAATTTGTTAC
1 TTAGTAACCAATTTGTTAC
2866910 TTTTGAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (31 bp):
TTAGTAACCAATTTGTTACAAATCGATAATG
Found at i:2869340 original size:20 final size:20
Alignment explanation
Indices: 2869315--2869353 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2869305 TTAATTTCGC
*
2869315 AACGCGAATCTGTACATCGA
1 AACGCGAATCTGTAAATCGA
*
2869335 AACGCGAATTTGTAAATCG
1 AACGCGAATCTGTAAATCG
2869354 CAACACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
AACGCGAATCTGTAAATCGA
Found at i:2869388 original size:20 final size:20
Alignment explanation
Indices: 2869351--2869408 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
2869341 AATTTGTAAA
*
2869351 TCGCAACAC-AAA-TCAAAT
1 TCGCAACGCGAAAGTCAAAT
* *
2869369 TCGTAACGCGATAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
2869389 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
2869409 GTTTTTACGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 7 0.21
19 2 0.06
20 24 0.73
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAT
Found at i:2869875 original size:19 final size:20
Alignment explanation
Indices: 2869851--2869893 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2869841 AAATCGCAAC
*
2869851 GCGA-TTTCATTTTTGCGTT
1 GCGATTTTCATTTTGGCGTT
*
2869870 GCGATTTTTATTTTGGCGTT
1 GCGATTTTCATTTTGGCGTT
2869890 GCGA
1 GCGA
2869894 ATTTAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (20 bp):
GCGATTTTCATTTTGGCGTT
Found at i:2869898 original size:19 final size:20
Alignment explanation
Indices: 2869854--2869898 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2869844 TCGCAACGCG
*
2869854 ATTTCATTTTTGCGTTGCGAT
1 ATTT-ATTTTGGCGTTGCGAT
*
2869875 TTTTATTTTGGCGTTGCGA-
1 ATTTATTTTGGCGTTGCGAT
2869894 ATTTA
1 ATTTA
2869899 AGTTTCAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 14 0.67
21 3 0.14
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (20 bp):
ATTTATTTTGGCGTTGCGAT
Found at i:2871832 original size:12 final size:12
Alignment explanation
Indices: 2871815--2871856 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2871805 TTTTTCGTCA
*
2871815 TTATTTATTTAT
1 TTATTTATTAAT
*
2871827 TTATTTACTAAT
1 TTATTTATTAAT
*
2871839 TTATGTATTAAT
1 TTATTTATTAAT
2871851 TTATTT
1 TTATTT
2871857 TCAGCGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:2872047 original size:42 final size:42
Alignment explanation
Indices: 2872000--2872098 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
2871990 GATGCACCTA
* ***
2872000 TCATCATTCAAGAGGCGCCTCCTTTCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
2872042 TCATCA-TCAAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
2872084 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
2872099 TCCTATCCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:2872054 original size:21 final size:21
Alignment explanation
Indices: 2872028--2872098 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
2872018 CTCCTTTCGT
2872028 TCAAGAGGCCCCTCTCATC-A
1 TCAAGAGGCCCCTCTCATCGA
* * * *
2872048 TCAAAGAAGCCCCTCCCACCGT
1 TC-AAGAGGCCCCTCTCATCGA
* *
2872070 TCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCTCATCGA
2872091 TCAAGAGG
1 TCAAGAGG
2872099 TCCTATCCGT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.25, C:0.37, G:0.20, T:0.18
Consensus pattern (21 bp):
TCAAGAGGCCCCTCTCATCGA
Found at i:2873490 original size:19 final size:19
Alignment explanation
Indices: 2873468--2873504 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2873458 TTTTACATTG
2873468 AAAGTTGATTTGTTTAATA
1 AAAGTTGATTTGTTTAATA
2873487 AAAGTTGATTTGTTTAAT
1 AAAGTTGATTTGTTTAAT
2873505 TTGATGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (19 bp):
AAAGTTGATTTGTTTAATA
Found at i:2873672 original size:20 final size:20
Alignment explanation
Indices: 2873649--2873708 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
2873639 GGTTTTCAGT
2873649 TTGCGAATTTGACTTTCGCA
1 TTGCGAATTTGACTTTCGCA
* **
2873669 TTGCGAATTTTACTTTCGTG
1 TTGCGAATTTGACTTTCGCA
*
2873689 TTGCGAATTTGACTATCGCA
1 TTGCGAATTTGACTTTCGCA
2873709 ACGCTTATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCA
Found at i:2873975 original size:39 final size:39
Alignment explanation
Indices: 2873921--2874007 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
2873911 TCAAGTTGTA
2873921 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
* *
2873960 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
2873999 GATTTTGAT
1 GATTTTGAT
2874008 AAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
Found at i:2874340 original size:18 final size:18
Alignment explanation
Indices: 2874317--2874353 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2874307 CAAAATTTAT
2874317 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2874335 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2874353 A
1 A
2874354 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2874804 original size:20 final size:20
Alignment explanation
Indices: 2874775--2874824 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2874765 AAATAATGTA
* *
2874775 CAACATGAAAGTTAAATTCG
1 CAACACGAAAGTCAAATTCG
*
2874795 CAACGCGAAAGTCAAATTCG
1 CAACACGAAAGTCAAATTCG
2874815 CAACACGAAA
1 CAACACGAAA
2874825 TTAGCGTTGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.22, G:0.16, T:0.16
Consensus pattern (20 bp):
CAACACGAAAGTCAAATTCG
Found at i:2877272 original size:3 final size:3
Alignment explanation
Indices: 2877264--2877291 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2877254 TCTTCGGGGA
2877264 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2877292 AGGGTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2877666 original size:12 final size:12
Alignment explanation
Indices: 2877645--2877678 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2877635 GGTTGTGGGT
*
2877645 TTTGAGATTGTG
1 TTTGATATTGTG
2877657 TTTGATATTGTG
1 TTTGATATTGTG
*
2877669 TTTGGTATTG
1 TTTGATATTG
2877679 GAAATGTAGT
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:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2878267 original size:14 final size:15
Alignment explanation
Indices: 2878231--2878268 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2878221 GAAATCATTG
2878231 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
2878246 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
2878261 AAAAATTA
1 AAAAATTA
2878269 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:2878453 original size:19 final size:19
Alignment explanation
Indices: 2878425--2878496 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
2878415 ACTAAAACCT
* *
2878425 GTTGCGAATTGGAAATTCA
1 GTTGCAAATTTGAAATTCA
2878444 GTTGCAAATTTGAAATTCA
1 GTTGCAAATTTGAAATTCA
* *
2878463 GTTGCGAATTTGAAATTTCGC
1 GTTGCAAATTTGAAA-TTC-A
2878484 GTTGCAAATTTGA
1 GTTGCAAATTTGA
2878497 CTTTGTGTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 31 0.67
20 3 0.07
21 12 0.26
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (19 bp):
GTTGCAAATTTGAAATTCA
Found at i:2878507 original size:40 final size:40
Alignment explanation
Indices: 2878424--2878555 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 40
2878414 AACTAAAACC
* * ** *
2878424 TGTTGCGAATTGGAAA-TTC-AGTTGCAAATTTGAAATTC
1 TGTTGCGAATTTGAAATTTCGCGTTGCAAATTTGACTTTG
*
2878462 AGTTGCGAATTTGAAATTTCGCGTTGCAAATTTGACTTTG
1 TGTTGCGAATTTGAAATTTCGCGTTGCAAATTTGACTTTG
* * * *
2878502 TGTTGCGAATTTG-ACTATCGCGTTGCGAATTTGACTATCG
1 TGTTGCGAATTTGAAATTTCGCGTTGCAAATTTGACT-TTG
* *
2878542 CGTTACGAATTTGA
1 TGTTGCGAATTTGA
2878556 CTTCTATGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
38 14 0.18
39 23 0.30
40 40 0.52
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (40 bp):
TGTTGCGAATTTGAAATTTCGCGTTGCAAATTTGACTTTG
Found at i:2878513 original size:59 final size:60
Alignment explanation
Indices: 2878444--2878569 Score: 141
Period size: 59 Copynumber: 2.1 Consensus size: 60
2878434 TGGAAATTCA
* * * *
2878444 GTTGCAAATTTGAA-ATTC-AGTTGCGAATTTGAAATTTCGCGTTGCAAATTTGACTT-TGT
1 GTTGCGAATTTGAATA-TCGAGTTGCGAATTTG-AATATCGCGTTACAAATTTGACTTCTAT
* * * *
2878503 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTAT
1 GTTGCGAATTTGAATATCGAGTTGCGAATTTGAATATCGCGTTACAAATTTGACTTCTAT
2878563 GTTGCGA
1 GTTGCGA
2878570 TTTACAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 34 0.61
60 22 0.39
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (60 bp):
GTTGCGAATTTGAATATCGAGTTGCGAATTTGAATATCGCGTTACAAATTTGACTTCTAT
Found at i:2878528 original size:20 final size:20
Alignment explanation
Indices: 2878463--2878557 Score: 120
Period size: 20 Copynumber: 4.8 Consensus size: 20
2878453 TTGAAATTCA
* *
2878463 GTTGCGAATTTGAAATTTCGC
1 GTTGCGAATTTG-ACTATCGC
* * *
2878484 GTTGCAAATTTGACT-TTGT
1 GTTGCGAATTTGACTATCGC
2878503 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
2878523 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
2878543 GTTACGAATTTGACT
1 GTTGCGAATTTGACT
2878558 TCTATGTTGC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.25
20 38 0.58
21 11 0.17
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:2878588 original size:60 final size:60
Alignment explanation
Indices: 2878464--2878590 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
2878454 TGAAATTCAG
* * * * *
2878464 TTGCGAATTTGAAATTTCGCGTTGCAAATTTGACTTTGTGTTGCGAATTTGACTATCGCG
1 TTGCGAATTTGAAATATCGCGTTACAAATTTGACTTTATGTTGCGAATTTGACAATCGCA
* *
2878524 TTGCGAATTTG-ACTATCGCGTTACGAATTTGACTTCTATGTTGCG-ATTT-ACAAATTCGCA
1 TTGCGAATTTGAAATATCGCGTTACAAATTTGACTT-TATGTTGCGAATTTGAC-AA-TCGCA
2878584 TTGCGAA
1 TTGCGAA
2878591 ATTGGAATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
58 2 0.04
59 25 0.44
60 30 0.53
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.39
Consensus pattern (60 bp):
TTGCGAATTTGAAATATCGCGTTACAAATTTGACTTTATGTTGCGAATTTGACAATCGCA
Found at i:2878626 original size:20 final size:19
Alignment explanation
Indices: 2878577--2878632 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
2878567 CGATTTACAA
*
2878577 ATTCGCATTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
* *
2878596 AATCTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
2878616 AGTTCGCGTTGC-AAATT
1 A-TTCGCGTTGCGAAATT
2878633 TGTTGGTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.27
20 20 0.67
21 2 0.07
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:2879422 original size:83 final size:82
Alignment explanation
Indices: 2879247--2879434 Score: 241
Period size: 83 Copynumber: 2.3 Consensus size: 82
2879237 AATGATACTT
* * * * * * *
2879247 TAGTGGCGTTTTTTCAACAAACGCCGCAATAGAGTAGTAATTTAGTAGCATTTTTATATAAATGC
1 TAGTGGCGTTTGTCCAACAAACGACGCAATAGAGTAATAATTTAGCAGCATTTTCAAATAAATGC
*
2879312 CGCAATAGGGTTGTCTA
66 CGCAATAGAGTTGTCTA
* * *
2879329 TAGTGGCGTTTGTCCAACAAACGACGCTATAGAGTAATAATTTAGCGGCGTTTATCAAATAAATG
1 TAGTGGCGTTTGTCCAACAAACGACGCAATAGAGTAATAATTTAGCAGCATTT-TCAAATAAATG
*
2879394 CCGCAATAGAGTTGTTTA
65 CCGCAATAGAGTTGTCTA
* *
2879412 TAGTGACGTTTGTGCAACAAACG
1 TAGTGGCGTTTGTCCAACAAACG
2879435 CTGTAAAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
82 45 0.49
83 46 0.51
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (82 bp):
TAGTGGCGTTTGTCCAACAAACGACGCAATAGAGTAATAATTTAGCAGCATTTTCAAATAAATGC
CGCAATAGAGTTGTCTA
Found at i:2879891 original size:23 final size:22
Alignment explanation
Indices: 2879841--2879889 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2879831 GTGTTTTTCT
*
2879841 GCTTTCGAATAGAAAAATAATA
1 GCTTTGGAATAGAAAAATAATA
*
2879863 GCTTTGGAATAGGAAAATAATA
1 GCTTTGGAATAGAAAAATAATA
2879885 GCTTT
1 GCTTT
2879890 TGAAAATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (22 bp):
GCTTTGGAATAGAAAAATAATA
Found at i:2881013 original size:86 final size:83
Alignment explanation
Indices: 2880858--2881022 Score: 222
Period size: 86 Copynumber: 2.0 Consensus size: 83
2880848 GCGTTTTTCT
* * * *
2880858 ACAAACGCCGTAATAGTCTACCCCTATAGTGGCCTTTTTCAATAAATGCCGCAAAAGAGTATTAC
1 ACAAACGCCGTAATAGTCTACCCCTATAGTCGCCTTTTTCAATAAACGCCGCAAAAGAGTAGTAA
2880923 TTTAGCGGCATTTTCCCA
66 TTTAGCGGCATTTTCCCA
* * * *
2880941 ACAAACGCCGTAATAGTGTACCCCCTATAGTCGCGTTTTATTCAATACACGTCGCAAAAGAGTAG
1 ACAAACGCCGTAATAGTCTA-CCCCTATAGTCGC-CTTT-TTCAATAAACGCCGCAAAAGAGTAG
*
2881006 TAATTTAGCGGCGTTTT
63 TAATTTAGCGGCATTTT
2881023 TTTATAAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
83 19 0.27
84 12 0.17
85 3 0.04
86 36 0.51
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (83 bp):
ACAAACGCCGTAATAGTCTACCCCTATAGTCGCCTTTTTCAATAAACGCCGCAAAAGAGTAGTAA
TTTAGCGGCATTTTCCCA
Found at i:2881104 original size:42 final size:41
Alignment explanation
Indices: 2881058--2881267 Score: 158
Period size: 42 Copynumber: 5.0 Consensus size: 41
2881048 GGACAGTAGT
*
2881058 GGCGTTTTATAGGTAAACGCCACGATAGAGTTGAACTATAGA
1 GGCGTTTTATA-GTAAACGCCGCGATAGAGTTGAACTATAGA
* * * *
2881100 GGCGTTTTCATA-CAAACGCCGCTATAGAGTTGGAC-ATTAGT
1 GGCGTTTT-ATAGTAAACGCCGCGATAGAGTTGAACTA-TAGA
* * *
2881141 GGCATTTTATATGTAAAC-ACGACGATATAGTTGAACTATAGA
1 GGCGTTTTATA-GTAAACGCCG-CGATAGAGTTGAACTATAGA
* * * * * * * *
2881183 GGCGTTTTCGTA-AAAATGCCGCTATAGAATTGGACAATAGT
1 GGCGTTTT-ATAGTAAACGCCGCGATAGAGTTGAACTATAGA
* * *
2881224 GGCGTTTTATAAGTAAACGCCGCGATAAAATTAAACTATAGA
1 GGCGTTTTAT-AGTAAACGCCGCGATAGAGTTGAACTATAGA
2881266 GG
1 GG
2881268 TATTTTGTAC
Statistics
Matches: 126, Mismatches: 32, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
40 5 0.04
41 57 0.45
42 58 0.46
43 6 0.05
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (41 bp):
GGCGTTTTATAGTAAACGCCGCGATAGAGTTGAACTATAGA
Found at i:2881129 original size:41 final size:40
Alignment explanation
Indices: 2881022--2881286 Score: 140
Period size: 42 Copynumber: 6.4 Consensus size: 40
2881012 AGCGGCGTTT
* * * * * *
2881022 TTTTATAAAAATGCCGCTACAGAGTTGGAC-AGTAGTGGCG
1 TTTTATACAAACGCCGCGATAGAGTTGAACTA-TAGAGGCG
* *
2881062 TTTTATAGGTAAACGCCACGATAGAGTTGAACTATAGAGGCG
1 TTTTATA--CAAACGCCGCGATAGAGTTGAACTATAGAGGCG
* * * *
2881104 TTTTCATACAAACGCCGCTATAGAGTTGGAC-ATTAGTGGCA
1 TTTT-ATACAAACGCCGCGATAGAGTTGAACTA-TAGAGGCG
* * *
2881145 TTTTATATGTAAAC-ACGACGATATAGTTGAACTATAGAGGCG
1 TTTTATA--CAAACGCCG-CGATAGAGTTGAACTATAGAGGCG
* * * * * * * *
2881187 TTTTCGTAAAAATGCCGCTATAGAATTGGACAATAGTGGCG
1 TTTT-ATACAAACGCCGCGATAGAGTTGAACTATAGAGGCG
* * * * **
2881228 TTTTATAAGTAAACGCCGCGATAAAATTAAACTATAGAGGTA
1 TTTTAT-A-CAAACGCCGCGATAGAGTTGAACTATAGAGGCG
*
2881270 TTTTGTACAAACGCCGC
1 TTTTATACAAACGCCGC
2881287 TATAAACGCC
Statistics
Matches: 169, Mismatches: 43, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
40 21 0.12
41 58 0.34
42 83 0.49
43 7 0.04
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (40 bp):
TTTTATACAAACGCCGCGATAGAGTTGAACTATAGAGGCG
Found at i:2881130 original size:83 final size:83
Alignment explanation
Indices: 2881034--2881290 Score: 336
Period size: 83 Copynumber: 3.1 Consensus size: 83
2881024 TTATAAAAAT
* * * *
2881034 GCCGCTACAGAGTTGGACAGTAGTGGCGTTTTATAGGTAAACGCCACGATAGAGTTGAACTATAG
1 GCCGCTATAGAGTTGGACAATAGTGGCGTTTTATAAGTAAACGCCACGATAAAGTTGAACTATAG
*
2881099 AGGCGTTTTCATACAAAC
66 AGGCGTTTTCGTACAAAC
* * * * * *
2881117 GCCGCTATAGAGTTGGACATTAGTGGCATTTTATATGTAAACACGACGATATAGTTGAACTATAG
1 GCCGCTATAGAGTTGGACAATAGTGGCGTTTTATAAGTAAACGCCACGATAAAGTTGAACTATAG
* *
2881182 AGGCGTTTTCGTAAAAAT
66 AGGCGTTTTCGTACAAAC
* * * *
2881200 GCCGCTATAGAATTGGACAATAGTGGCGTTTTATAAGTAAACGCCGCGATAAAATTAAACTATAG
1 GCCGCTATAGAGTTGGACAATAGTGGCGTTTTATAAGTAAACGCCACGATAAAGTTGAACTATAG
**
2881265 AGGTATTTT-GTACAAAC
66 AGGCGTTTTCGTACAAAC
2881282 GCCGCTATA
1 GCCGCTATA
2881291 AACGCCGCTA
Statistics
Matches: 150, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
82 15 0.10
83 135 0.90
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (83 bp):
GCCGCTATAGAGTTGGACAATAGTGGCGTTTTATAAGTAAACGCCACGATAAAGTTGAACTATAG
AGGCGTTTTCGTACAAAC
Found at i:2884751 original size:21 final size:21
Alignment explanation
Indices: 2884725--2884778 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
2884715 GCGTTGCATT
2884725 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
2884746 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
2884767 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2884779 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:2884792 original size:20 final size:20
Alignment explanation
Indices: 2884767--2884925 Score: 189
Period size: 20 Copynumber: 7.9 Consensus size: 20
2884757 TAGTTGAAAA
*
2884767 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
2884787 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* * *
2884807 TCACGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCAGT
2884827 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
2884847 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* * *
2884867 TTGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
2884889 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
2884910 T--CGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCA
2884926 AATTCGTTGC
Statistics
Matches: 122, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
18 1 0.01
19 14 0.11
20 87 0.71
21 4 0.03
22 16 0.13
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:2884842 original size:60 final size:61
Alignment explanation
Indices: 2884767--2884964 Score: 221
Period size: 60 Copynumber: 3.3 Consensus size: 61
2884757 TAGTTGAAAA
* * * *
2884767 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCACGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAGTTCACGTTGCGATATCTACAGT
* **
2884827 TCGCGTTGCGATTTTCCAGTTCGCGTTGCGATTTTCCAGTTTGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAGTTCACGTTGCGATA-TCTACAGT
*
2884889 T-GTCGTTGCGATTTTCCAAATT--CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGT
1 TCG-CGTTGCGATTTTCC-AATTCGCGTTGCGATTTTCC-AGTTCACGTTGCGATA-TCTACAGT
2884949 T-GTCGTTGCGATTTTC
1 TCG-CGTTGCGATTTTC
2884965 TAAATTCATT
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
60 84 0.67
61 15 0.12
62 23 0.18
63 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAGTTCACGTTGCGATATCTACAGT
Found at i:2885007 original size:20 final size:20
Alignment explanation
Indices: 2884982--2885033 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2884972 ATTGCGAAAA
* *
2884982 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCAGT
2885002 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*
2885022 TCGTGTTGCGAT
1 TCGCGTTGCGAT
2885034 AGTTGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:2885052 original size:21 final size:21
Alignment explanation
Indices: 2885026--2885072 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2885016 TCCAGTTCGT
*
2885026 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCAC
2885047 GTTGCGATAGTTGAAAATCAC
1 GTTGCGATAGTTGAAAATCAC
2885068 GTTGC
1 GTTGC
2885073 CTTTGACAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
GTTGCGATAGTTGAAAATCAC
Found at i:2888974 original size:65 final size:63
Alignment explanation
Indices: 2888855--2889060 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 63
2888845 TTTATCAAAG
* * * * *
2888855 TGATGCACCGATGCACCAATCCACGCATCGATGCACCATGA-ATTAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACCAA-CCATGCACCGATGCACTAGGATATT---TTGAAACATCGAATGCA
2888918 TT
62 TT
*
2888920 TCATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCACCGATGCACT-AGGATATTT-TG-AAACATCGAATGCA
2888983 TT
62 TT
* * ** * *
2888985 TGATGCATCGATGCACCAGCCATGCATCGATGCACTTTGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTAGGATATTTTGAAACATCGAATGCATT
2889048 TGATGCATCGATG
1 TGATGCATCGATG
2889061 AACTCTTAGT
Statistics
Matches: 120, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 30 0.25
64 20 0.17
65 67 0.56
66 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACCAACCATGCACCGATGCACTAGGATATTTTGAAACATCGAATGCATT
Found at i:2889147 original size:21 final size:21
Alignment explanation
Indices: 2889121--2889173 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
2889111 TTTTACACCG
2889121 ATGCACCGATGCACCATGGGT
1 ATGCACCGATGCACCATGGGT
2889142 ATGCACCGATGCACCATGGGT
1 ATGCACCGATGCACCATGGGT
*
2889163 ATGCATCGATG
1 ATGCACCGATG
2889174 TACTGACGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (21 bp):
ATGCACCGATGCACCATGGGT
Found at i:2889986 original size:17 final size:17
Alignment explanation
Indices: 2889961--2890042 Score: 74
Period size: 17 Copynumber: 4.6 Consensus size: 17
2889951 CGTATAAATG
2889961 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
* ** *
2889978 TCTCGAAGGATGTCATCTGTG
1 TCCCGAAGGACCT-ATC---A
*
2889999 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
*
2890016 TCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCA
2890033 TCCCGAAGGA
1 TCCCGAAGGA
2890043 TGTAATCTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
17 37 0.71
18 3 0.06
20 2 0.04
21 10 0.19
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.21
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:2890010 original size:38 final size:39
Alignment explanation
Indices: 2889959--2890034 Score: 118
Period size: 38 Copynumber: 1.9 Consensus size: 39
2889949 CTCGTATAAA
*
2889959 TGTCCCGAAGGACCTATCATCTCGAAGGA-TGTCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGACTGTCATCTG
*
2889997 TGTCCCGAAGGACCTGTCATCCCGAAGGACCTGTCATC
1 TGTCCCGAAGGACCTATCATCCCGAAGGA-CTGTCATC
2890035 CCGAAGGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 27 0.79
40 7 0.21
ACGTcount: A:0.22, C:0.30, G:0.24, T:0.24
Consensus pattern (39 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGACTGTCATCTG
Found at i:2890027 original size:55 final size:55
Alignment explanation
Indices: 2889961--2890071 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
2889951 CGTATAAATG
* * *
2889961 TCCCGAAGGACCTATCATCTCGAAGGATGTCATCTGTGTCCCGAAGGACCTGTCA
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTGTCCCGAAGGACCTATCA
* *
2890016 TCCCGAAGGACCTGTCATCCCGAAGGATGTAATCTGTGTCCCGTAGGACCTATCA
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTGTCCCGAAGGACCTATCA
2890071 T
1 T
2890072 ATGTCTTATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (55 bp):
TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTGTCCCGAAGGACCTATCA
Found at i:2890756 original size:35 final size:37
Alignment explanation
Indices: 2890697--2890765 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
2890687 TTTCATTTAG
2890697 GGGGAATCGATACCCCCCCAGGGGGG-ATCTGTTCCC
1 GGGGAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
2890733 GGGGAATCGATA-CCCCCCAGGGGGGAATCTGTT
1 GGGGAATCGATACCCCCCCAGGGGGGAATCTGTT
2890766 TCCCCTGCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.17
Consensus pattern (37 bp):
GGGGAATCGATACCCCCCCAGGGGGGAATCTGTTCCC
Done.