Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 43
Found at i:1004683 original size:20 final size:20
Alignment explanation
Indices: 1004658--1004695 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1004648 CCCCCTTTGA
*
1004658 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
1004678 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
1004696 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:1006629 original size:17 final size:17
Alignment explanation
Indices: 1006604--1006637 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1006594 TTGAATATTT
*
1006604 TGGAATGTTTGATTTTG
1 TGGAATGTTGGATTTTG
*
1006621 TGGATTGTTGGATTTTG
1 TGGAATGTTGGATTTTG
1006638 GATTTATGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.53
Consensus pattern (17 bp):
TGGAATGTTGGATTTTG
Found at i:1018170 original size:19 final size:20
Alignment explanation
Indices: 1018128--1018170 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1018118 TTTCTTTTTT
*
1018128 CTTTCATTATTAATTTTTCA
1 CTTTCATTATTAATTTTACA
1018148 CTTTCATT-TTAACTTTTAC-
1 CTTTCATTATTAA-TTTTACA
1018167 CTTT
1 CTTT
1018171 TCTCTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (20 bp):
CTTTCATTATTAATTTTACA
Found at i:1026146 original size:20 final size:20
Alignment explanation
Indices: 1026104--1026152 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1026094 TAACTTTTTC
1026104 TTTTATCTTTCATTTTTAAT
1 TTTTATCTTTCATTTTTAAT
* *
1026124 TTTTCTCTTTCA-TTTTAAC
1 TTTTATCTTTCATTTTTAAT
*
1026143 TTTTACCTTT
1 TTTTATCTTT
1026153 TCTCTTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATCTTTCATTTTTAAT
Found at i:1026146 original size:26 final size:26
Alignment explanation
Indices: 1026091--1026159 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
1026081 CCCTCCTAAA
* *
1026091 TTTTAACTTTTTCT-TTTATCTTTCAT
1 TTTTAA-TTTTTCTCTTTATCTTTAAC
1026117 TTTTAATTTTTCTCTTTCAT-TTTAAC
1 TTTTAATTTTTCTCTTT-ATCTTTAAC
**
1026143 TTTTACCTTTTCTCTTT
1 TTTTAATTTTTCTCTTT
1026160 GTTTCATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.19
26 28 0.76
27 2 0.05
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTAATTTTTCTCTTTATCTTTAAC
Found at i:1029995 original size:8 final size:9
Alignment explanation
Indices: 1029967--1030001 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
1029957 CACGTGAGGA
1029967 TTATTTTCTT
1 TTATTTT-TT
1029977 CTTATTTTTT
1 -TTATTTTTT
1029987 TTATTTTTT
1 TTATTTTTT
1029996 TTATTT
1 TTATTT
1030002 ACTGTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 2 0.08
11 7 0.29
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (9 bp):
TTATTTTTT
Found at i:1031330 original size:8 final size:9
Alignment explanation
Indices: 1031312--1031346 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
1031302 TAAAGACAGT
1031312 AAATAAAAA
1 AAATAAAAA
1031321 AAATAAAAA
1 AAATAAAAA
1031330 AAATAAGAAGA
1 AAATAA-AA-A
1031341 AAATAA
1 AAATAA
1031347 TCCTCACGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 2 0.08
11 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (9 bp):
AAATAAAAA
Found at i:1044550 original size:53 final size:53
Alignment explanation
Indices: 1044449--1044553 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
1044439 AAACTATATT
* * * * *
1044449 ATATTTTTCATTTAAGTACTCAAAGTAATTTTTGTTAAAAGTAGTATTTAAAC
1 ATATTTGTCATCTAAGTACTAAAAGTAATTTTTATTAAAAGTAATATTTAAAC
*
1044502 ATATTTGTCATCTAAGTACTAAAAGTATTTTTTATTAAAA-TAAATATTTAAA
1 ATATTTGTCATCTAAGTACTAAAAGTAATTTTTATTAAAAGT-AATATTTAAA
1044554 GTATACTGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 1 0.02
53 44 0.98
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (53 bp):
ATATTTGTCATCTAAGTACTAAAAGTAATTTTTATTAAAAGTAATATTTAAAC
Found at i:1050964 original size:8 final size:8
Alignment explanation
Indices: 1050537--1052156 Score: 300
Period size: 8 Copynumber: 203.0 Consensus size: 8
1050527 TCAATAATTT
1050537 GGTCATTC
1 GGTCATTC
* *
1050545 TGTCATTA
1 GGTCATTC
*
1050553 GCTCATTC
1 GGTCATTC
*
1050561 AGTCATTC
1 GGTCATTC
***
1050569 AACCATTC
1 GGTCATTC
* **
1050577 GATCATGA
1 GGTCATTC
*
1050585 GATCATTC
1 GGTCATTC
*
1050593 AGTCATTC
1 GGTCATTC
* * *
1050601 GCTTAATC
1 GGTCATTC
* *
1050609 GCTCATTA
1 GGTCATTC
*
1050617 GGTTATTC
1 GGTCATTC
1050625 GGTCATTC
1 GGTCATTC
*** *
1050633 AACCATTG
1 GGTCATTC
*
1050641 GGTCTTTC
1 GGTCATTC
1050649 GGTCATTC
1 GGTCATTC
* *
1050657 AGTCATTT
1 GGTCATTC
1050665 GGTCATTC
1 GGTCATTC
*
1050673 GGTCATCC
1 GGTCATTC
* *
1050681 AGTCATTA
1 GGTCATTC
*
1050689 GGTTATTC
1 GGTCATTC
*
1050697 GATCATTC
1 GGTCATTC
** *
1050705 AATAATTC
1 GGTCATTC
* *
1050713 AGTCATTA
1 GGTCATTC
1050721 GGTCATTAC
1 GGTCATT-C
*
1050730 -GTCATTT
1 GGTCATTC
1050737 GGTCATTC
1 GGTCATTC
* *
1050745 GATCATTT
1 GGTCATTC
*
1050753 TGTCATTC
1 GGTCATTC
*
1050761 GGTCATTT
1 GGTCATTC
*
1050769 TGTCATTC
1 GGTCATTC
*
1050777 GATCATTC
1 GGTCATTC
* *
1050785 GTTCATTA
1 GGTCATTC
1050793 GGTCATTC
1 GGTCATTC
* *
1050801 GATCAGTC
1 GGTCATTC
* *
1050809 AGTCATTG
1 GGTCATTC
*
1050817 GGGCATTC
1 GGTCATTC
** *
1050825 AATCATTT
1 GGTCATTC
1050833 GGTCATTC
1 GGTCATTC
*
1050841 GGTCATTA
1 GGTCATTC
**
1050849 ACTCATTC
1 GGTCATTC
* *
1050857 GGTTATTT
1 GGTCATTC
* * *
1050865 GATTATTT
1 GGTCATTC
1050873 GGTCATTAC
1 GGTCATT-C
*
1050882 -GTCATTA
1 GGTCATTC
*
1050889 GGTCATTT
1 GGTCATTC
* *
1050897 GGTTATCC
1 GGTCATTC
* *
1050905 AGTCATTA
1 GGTCATTC
* *
1050913 GGTTATTT
1 GGTCATTC
*
1050921 GGGCATTC
1 GGTCATTC
* *
1050929 GATCATTA
1 GGTCATTC
* *
1050937 GGTCGTTT
1 GGTCATTC
*
1050945 GGCCATTC
1 GGTCATTC
*
1050953 GGTCATTG
1 GGTCATTC
1050961 GGTCA-TC
1 GGTCATTC
** *
1050968 AATCATTT
1 GGTCATTC
**
1050976 AATCATT-
1 GGTCATTC
* *
1050983 AGTCATTA
1 GGTCATTC
*** * *
1050991 AACCTTTA
1 GGTCATTC
*
1050999 GGTCATTG
1 GGTCATTC
1051007 GGTCATTC
1 GGTCATTC
* *
1051015 AGTCATTA
1 GGTCATTC
* *
1051023 GGTTATTT
1 GGTCATTC
*
1051031 GGTCATCC
1 GGTCATTC
1051039 GGTCATTC
1 GGTCATTC
** *
1051047 AATCATTA
1 GGTCATTC
1051055 GGTCATTC
1 GGTCATTC
*
1051063 GGTCATTA
1 GGTCATTC
*
1051071 GGCCATTC
1 GGTCATTC
* * *
1051079 AGTCTTTT
1 GGTCATTC
1051087 GGTCATTC
1 GGTCATTC
* *
1051095 GATCATTT
1 GGTCATTC
*
1051103 GATCATTC
1 GGTCATTC
* *
1051111 AGTCATTT
1 GGTCATTC
* * *
1051119 AGTCAATA
1 GGTCATTC
* *
1051127 AGTCATTA
1 GGTCATTC
*
1051135 GGCCATTC
1 GGTCATTC
* * *
1051143 GATCCTTT
1 GGTCATTC
1051151 GGTCATTC
1 GGTCATTC
** *
1051159 AATCATTA
1 GGTCATTC
1051167 GGTCATTC
1 GGTCATTC
*
1051175 GGTCCTTC
1 GGTCATTC
** *
1051183 TATCATTA
1 GGTCATTC
* *
1051191 GATCATTT
1 GGTCATTC
1051199 GGTCATTC
1 GGTCATTC
*
1051207 AGTCAATT-
1 GGTC-ATTC
*
1051215 GATCATTC
1 GGTCATTC
*
1051223 GATCATTTC
1 GGTCA-TTC
* *
1051232 GGTTATTA
1 GGTCATTC
*
1051240 GGTCATTG
1 GGTCATTC
** *
1051248 GGTTTTTA
1 GGTCATTC
*
1051256 GGTCATTT
1 GGTCATTC
*
1051264 GTTCATTC
1 GGTCATTC
** **
1051272 AATGGTTC
1 GGTCATTC
**
1051280 TTTCATTC
1 GGTCATTC
*
1051288 GGTCATTT
1 GGTCATTC
* *
1051296 GTTCATTA
1 GGTCATTC
*
1051304 GATCACTT-
1 GGTCA-TTC
* *
1051312 GATCTTTC
1 GGTCATTC
* *
1051320 AGTCATTT
1 GGTCATTC
1051328 GGTCATTC
1 GGTCATTC
*
1051336 GGTCATTAA
1 GGTCATT-C
*
1051345 GG-CCTTC
1 GGTCATTC
* *
1051352 AGTCATTT
1 GGTCATTC
*
1051360 GGCCATTC
1 GGTCATTC
*
1051368 GGTTATAT-
1 GGTCAT-TC
*
1051376 GATCATTC
1 GGTCATTC
** *
1051384 AATCATTT
1 GGTCATTC
* *
1051392 GTTCATTT
1 GGTCATTC
*
1051400 AGTCATTC
1 GGTCATTC
1051408 GGTCATTC
1 GGTCATTC
** * *
1051416 AATAATTT
1 GGTCATTC
* *
1051424 GGCCATTA
1 GGTCATTC
* *
1051432 GGTTATTT
1 GGTCATTC
*
1051440 GATCATTC
1 GGTCATTC
* *
1051448 AGTCATTT
1 GGTCATTC
* * *
1051456 AGTAATTA
1 GGTCATTC
*
1051464 GGTCATTT
1 GGTCATTC
1051472 GGTCATTC
1 GGTCATTC
* *
1051480 AGTCATTA
1 GGTCATTC
1051488 GGTCATTC
1 GGTCATTC
1051496 GGTCAGTT-
1 GGTCA-TTC
* *
1051504 GTTTATTC
1 GGTCATTC
*
1051512 AGTCATTC
1 GGTCATTC
* *
1051520 TGTCATTA
1 GGTCATTC
*
1051528 GGTCA-CC
1 GGTCATTC
* *
1051535 AGTTCATTG
1 -GGTCATTC
*
1051544 GGTCATTA
1 GGTCATTC
* * *
1051552 GGTTAGTA
1 GGTCATTC
1051560 GGTCATTC
1 GGTCATTC
* *
1051568 GATTATTC
1 GGTCATTC
* *
1051576 AGTCATTA
1 GGTCATTC
*
1051584 GGTTATTC
1 GGTCATTC
*
1051592 GATCATTC
1 GGTCATTC
* *
1051600 GATCATTT
1 GGTCATTC
*
1051608 GGCCATTC
1 GGTCATTC
**
1051616 ATTCATTC
1 GGTCATTC
*
1051624 GGTCATCC
1 GGTCATTC
**
1051632 GAACATTC
1 GGTCATTC
* *
1051640 GATCATTA
1 GGTCATTC
* *
1051648 GATCATTA
1 GGTCATTC
* *
1051656 GGT-TTTT
1 GGTCATTC
*
1051663 AG-CATTC
1 GGTCATTC
1051670 GGTCATTC
1 GGTCATTC
*
1051678 TGTCATTC
1 GGTCATTC
1051686 GGTCATTC
1 GGTCATTC
** *
1051694 AATCATTT
1 GGTCATTC
* *
1051702 AGTCATTA
1 GGTCATTC
*
1051710 GGACATTC
1 GGTCATTC
** *
1051718 AATCATTT
1 GGTCATTC
*
1051726 GGTCTTTTC
1 GGTC-ATTC
*
1051735 -TTCATTC
1 GGTCATTC
* *
1051742 GATCATTA
1 GGTCATTC
*
1051750 GGTCATTT
1 GGTCATTC
* *
1051758 GATCATTT
1 GGTCATTC
*
1051766 GATCATTC
1 GGTCATTC
* *
1051774 GATCATTA
1 GGTCATTC
1051782 GGTCATTC
1 GGTCATTC
* *
1051790 AGTCATTA
1 GGTCATTC
*
1051798 GATCATTC
1 GGTCATTC
** *
1051806 AATCATTT
1 GGTCATTC
*
1051814 GGTAATTC
1 GGTCATTC
* *
1051822 AGTCATTA
1 GGTCATTC
*
1051830 GGTCATTG
1 GGTCATTC
**
1051838 GGTCATGA
1 GGTCATTC
* *
1051846 GTTCATTA
1 GGTCATTC
*
1051854 GCTCATTC
1 GGTCATTC
* *
1051862 GATCATTA
1 GGTCATTC
1051870 GGTCA-TC
1 GGTCATTC
** *
1051877 ATTCATTA
1 GGTCATTC
*
1051885 GCTCATTC
1 GGTCATTC
*
1051893 GGTCATTT
1 GGTCATTC
**
1051901 AATCATTC
1 GGTCATTC
* *
1051909 GATCATTT
1 GGTCATTC
1051917 GGTCATTC
1 GGTCATTC
*
1051925 GATCATTC
1 GGTCATTC
**
1051933 GACCATTC
1 GGTCATTC
* *
1051941 AGTCATTA
1 GGTCATTC
*
1051949 GGTCATTT
1 GGTCATTC
*
1051957 AGTCATTC
1 GGTCATTC
*
1051965 TGTCATT-
1 GGTCATTC
*
1051972 GGACCATTC
1 GG-TCATTC
*
1051981 GATCATTC
1 GGTCATTC
* * *
1051989 GATTATTA
1 GGTCATTC
1051997 GGTCATTC
1 GGTCATTC
*** *
1052005 TAACATTT
1 GGTCATTC
* *
1052013 GGTCGTTA
1 GGTCATTC
* *
1052021 GGTTATTA
1 GGTCATTC
*
1052029 GGTCATTA
1 GGTCATTC
* *
1052037 AGTCATTA
1 GGTCATTC
* * *
1052045 GATTATTA
1 GGTCATTC
*
1052053 GATCATTC
1 GGTCATTC
* *
1052061 AGTCATTA
1 GGTCATTC
* * *
1052069 GATTATTA
1 GGTCATTC
*
1052077 GATCATTC
1 GGTCATTC
* *
1052085 AGTCATTA
1 GGTCATTC
* *
1052093 TGTCAATC
1 GGTCATTC
** *
1052101 AATTATTC
1 GGTCATTC
1052109 GGTCATTC
1 GGTCATTC
*
1052117 GATCATTC
1 GGTCATTC
*
1052125 GGTCATTG
1 GGTCATTC
1052133 GGTCATTC
1 GGTCATTC
* *
1052141 AGTTATTC
1 GGTCATTC
*
1052149 GATCATTC
1 GGTCATTC
1052157 AGCCATTCCA
Statistics
Matches: 1107, Mismatches: 479, Indels: 52
0.68 0.29 0.03
Matches are distributed among these distances:
7 33 0.03
8 1055 0.95
9 19 0.02
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (8 bp):
GGTCATTC
Found at i:1051882 original size:31 final size:32
Alignment explanation
Indices: 1051832--1051899 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
1051822 AGTCATTAGG
* *
1051832 TCATTGGGTCATGAGTTCATTAGCTCATTCGA
1 TCATTAGGTCATCAGTTCATTAGCTCATTCGA
*
1051864 TCATTAGGTCATCA-TTCATTAGCTCATTCGG
1 TCATTAGGTCATCAGTTCATTAGCTCATTCGA
1051895 TCATT
1 TCATT
1051900 TAATCATTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.40
Consensus pattern (32 bp):
TCATTAGGTCATCAGTTCATTAGCTCATTCGA
Found at i:1052250 original size:24 final size:24
Alignment explanation
Indices: 1051858--1052259 Score: 84
Period size: 24 Copynumber: 16.8 Consensus size: 24
1051848 TCATTAGCTC
*
1051858 ATTCGATCATTAGGTCA-TC-ATT
1 ATTCGATCATTTGGTCATTCGATT
* * * ** *
1051880 CATTAGCTCATTCGGTCATTTAATC
1 -ATTCGATCATTTGGTCATTCGATT
*
1051905 ATTCGATCATTTGGTCATTCGATC
1 ATTCGATCATTTGGTCATTCGATT
* ** * * *
1051929 ATTCGACCATTCAGTCATTAGGTC
1 ATTCGATCATTTGGTCATTCGATT
* * **
1051953 ATT-TAGTCATTCT-GTCATTGGACC
1 ATTCGA-TCATT-TGGTCATTCGATT
* * * * * *
1051977 ATTCGATCATTCGATTATTAGGTC
1 ATTCGATCATTTGGTCATTCGATT
* * * * *
1052001 ATTCTAACATTTGGTCGTTAGGTT
1 ATTCGATCATTTGGTCATTCGATT
* * ** *
1052025 ATTAGGTCATTAAGTCATTAGATT
1 ATTCGATCATTTGGTCATTCGATT
* ** *
1052049 ATTAGATCATTCAGTCATTAGATT
1 ATTCGATCATTTGGTCATTCGATT
* **
1052073 ATTAGATCATTCAGTCATT--ATGT
1 ATTCGATCATTTGGTCATTCGAT-T
* * * * *
1052096 CAATCAATTATTCGGTCATTCGATC
1 -ATTCGATCATTTGGTCATTCGATT
* *
1052121 ATTCGGTCATTGGGTCATTC-AGTT
1 ATTCGATCATTTGGTCATTCGA-TT
** * *
1052145 ATTCGATCATTCAGCCATTCCA-T
1 ATTCGATCATTTGGTCATTCGATT
* * *** * * *
1052168 AGTTAGGTCATTCAATCATTTGGTC
1 A-TTCGATCATTTGGTCATTCGATT
* *
1052193 AATCGATCATTTGATCATTCGATT
1 ATTCGATCATTTGGTCATTCGATT
* *
1052217 TTTCGATCATTTGGTCATTCTATT
1 ATTCGATCATTTGGTCATTCGATT
*
1052241 ATTC-AGTCATTAGGTCATT
1 ATTCGA-TCATTTGGTCATT
1052260 ATGTCATTGG
Statistics
Matches: 281, Mismatches: 83, Indels: 29
0.72 0.21 0.07
Matches are distributed among these distances:
22 2 0.01
23 20 0.07
24 252 0.90
25 5 0.02
26 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (24 bp):
ATTCGATCATTTGGTCATTCGATT
Found at i:1052257 original size:8 final size:8
Alignment explanation
Indices: 1052246--1052325 Score: 54
Period size: 8 Copynumber: 10.0 Consensus size: 8
1052236 CTATTATTCA
1052246 GTCATTAG
1 GTCATTAG
*
1052254 GTCATTAT
1 GTCATTAG
*
1052262 GTCATTGG
1 GTCATTAG
1052270 GTCATTAG
1 GTCATTAG
* * *
1052278 ATTATTAA
1 GTCATTAG
* *
1052286 ATCATTTG
1 GTCATTAG
* *
1052294 ATAATTAG
1 GTCATTAG
1052302 GTCATTAG
1 GTCATTAG
*
1052310 GTTATTCA-
1 GTCATT-AG
1052318 GTCATTAG
1 GTCATTAG
1052326 TTGATTTGGT
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
7 1 0.02
8 52 0.96
9 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (8 bp):
GTCATTAG
Found at i:1052291 original size:32 final size:33
Alignment explanation
Indices: 1052255--1052324 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
1052245 AGTCATTAGG
* *
1052255 TCATTATG-TCATTGGGTCATTAGATTATTAAA
1 TCATTATGATAATTAGGTCATTAGATTATTAAA
* * *
1052287 TCATT-TGATAATTAGGTCATTAGGTTATTCAG
1 TCATTATGATAATTAGGTCATTAGATTATTAAA
1052319 TCATTA
1 TCATTA
1052325 GTTGATTTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (33 bp):
TCATTATGATAATTAGGTCATTAGATTATTAAA
Found at i:1052324 original size:24 final size:24
Alignment explanation
Indices: 1052241--1052325 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
1052231 TCATTCTATT
*
1052241 ATTCAGTCATTAGGTCATTATGTC
1 ATTCAGTCATTAGGTCATTAAGTC
** * * *
1052265 ATTGGGTCATTAGATTATTAAATC
1 ATTCAGTCATTAGGTCATTAAGTC
* * * *
1052289 ATT-TGATAATTAGGTCATTAGGTT
1 ATTCAG-TCATTAGGTCATTAAGTC
1052313 ATTCAGTCATTAG
1 ATTCAGTCATTAG
1052326 TTGATTTGGT
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
23 1 0.02
24 42 0.95
25 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (24 bp):
ATTCAGTCATTAGGTCATTAAGTC
Found at i:1052864 original size:14 final size:15
Alignment explanation
Indices: 1052840--1052868 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1052830 CTCTAAAAAA
1052840 ATTTAATTTTTATTT
1 ATTTAATTTTTATTT
1052855 ATTT-ATTTTTATTT
1 ATTTAATTTTTATTT
1052869 TTAAACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTAATTTTTATTT
Found at i:1059070 original size:9 final size:9
Alignment explanation
Indices: 1059056--1059159 Score: 73
Period size: 10 Copynumber: 10.8 Consensus size: 9
1059046 GGCTGCTGGA
1059056 AACCGGTTT
1 AACCGGTTT
1059065 AACCGGTTTT
1 AACCGG-TTT
1059075 CAACCGGTTCT
1 -AACCGGTT-T
*
1059086 GACCGGTTT
1 AACCGGTTT
*
1059095 CAACCGGTTCG
1 -AACCGGTT-T
1059106 AACCGGTTT
1 AACCGGTTT
* *
1059115 GACCGGTCTG
1 AACCGGT-TT
1059125 AACCGGTTT
1 AACCGGTTT
* *
1059134 GACCGGTCTG
1 AACCGGT-TT
*
1059144 AGCCGGTTT
1 AACCGGTTT
*
1059153 GACCGGT
1 AACCGGT
1059160 CTGACCCGAC
Statistics
Matches: 73, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
9 26 0.36
10 40 0.55
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1059081 original size:20 final size:21
Alignment explanation
Indices: 1059056--1059114 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1059046 GGCTGCTGGA
1059056 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
1059076 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
1059096 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
1059115 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:1059092 original size:10 final size:10
Alignment explanation
Indices: 1059077--1059165 Score: 77
Period size: 10 Copynumber: 9.3 Consensus size: 10
1059067 CCGGTTTTCA
1059077 ACCGGTTCTG
1 ACCGGTTCTG
*
1059087 ACCGGTT-TCA
1 ACCGGTTCT-G
1059097 ACCGGTTC-G
1 ACCGGTTCTG
1059106 AACCGGTT-TG
1 -ACCGGTTCTG
1059116 ACCGG-TCTG
1 ACCGGTTCTG
1059125 AACCGGTT-TG
1 -ACCGGTTCTG
1059135 ACCGG-TCTG
1 ACCGGTTCTG
1059144 AGCCGGTT-TG
1 A-CCGGTTCTG
1059154 ACCGG-TCTG
1 ACCGGTTCTG
1059163 ACC
1 ACC
1059166 CGACCCGACC
Statistics
Matches: 66, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
8 3 0.05
9 25 0.38
10 36 0.55
11 2 0.03
ACGTcount: A:0.15, C:0.29, G:0.30, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:1059121 original size:19 final size:20
Alignment explanation
Indices: 1059077--1059163 Score: 112
Period size: 19 Copynumber: 4.5 Consensus size: 20
1059067 CCGGTTTTCA
*
1059077 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
1059097 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
1059116 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
1059135 ACCGG-TCTGAGCCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
1059154 ACCGG-TCTGA
1 ACCGGTTCTGA
1059164 CCCGACCCGA
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.03
19 45 0.71
20 16 0.25
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:1059164 original size:9 final size:9
Alignment explanation
Indices: 1059107--1059165 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
1059097 ACCGGTTCGA
*
1059107 ACCGGTTTG
1 ACCGGTCTG
1059116 ACCGGTCTG
1 ACCGGTCTG
*
1059125 AACCGGTTTG
1 -ACCGGTCTG
1059135 ACCGGTCTG
1 ACCGGTCTG
*
1059144 AGCCGGTTTG
1 A-CCGGTCTG
1059154 ACCGGTCTG
1 ACCGGTCTG
1059163 ACC
1 ACC
1059166 CGACCCGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 27 0.63
10 16 0.37
ACGTcount: A:0.14, C:0.29, G:0.32, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:1059183 original size:17 final size:17
Alignment explanation
Indices: 1059161--1059214 Score: 108
Period size: 17 Copynumber: 3.2 Consensus size: 17
1059151 TTGACCGGTC
1059161 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1059178 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1059195 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1059212 TGA
1 TGA
1059215 TCGTTGACCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.19, C:0.44, G:0.24, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1059221 original size:7 final size:7
Alignment explanation
Indices: 1059206--1059236 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1059196 GACCCGACCC
1059206 GACCGTT
1 GACCGTT
*
1059213 GATCGTT
1 GACCGTT
1059220 GACCGTT
1 GACCGTT
1059227 GACCGTT
1 GACCGTT
1059234 GAC
1 GAC
1059237 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:1066213 original size:20 final size:21
Alignment explanation
Indices: 1066188--1066246 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1066178 GGCTGCTGGA
1066188 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
1066208 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
1066228 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
1066247 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:1066224 original size:10 final size:10
Alignment explanation
Indices: 1066209--1066278 Score: 62
Period size: 10 Copynumber: 7.3 Consensus size: 10
1066199 CCGGTTTTCA
1066209 ACCGGTTCTG
1 ACCGGTTCTG
*
1066219 ACCGGTT-TCA
1 ACCGGTTCT-G
1066229 ACCGGTTC-G
1 ACCGGTTCTG
1066238 AACCGGTT-TG
1 -ACCGGTTCTG
1066248 ACCGG-TCTG
1 ACCGGTTCTG
1066257 AGCCGGTT-TG
1 A-CCGGTTCTG
1066267 ACCGG-TCTG
1 ACCGGTTCTG
1066276 ACC
1 ACC
1066279 CGACCCGACC
Statistics
Matches: 50, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
8 2 0.04
9 18 0.36
10 29 0.58
11 1 0.02
ACGTcount: A:0.14, C:0.30, G:0.30, T:0.26
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:1066225 original size:30 final size:29
Alignment explanation
Indices: 1066189--1066253 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
1066179 GCTGCTGGAA
1066189 ACCGGTTT-AACCGGTTTTC-AACCGGTTCTG
1 ACCGGTTTCAACCGG--TTCGAACCGGTT-TG
1066219 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1066248 ACCGGT
1 ACCGGT
1066254 CTGAGCCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:1066253 original size:19 final size:20
Alignment explanation
Indices: 1066209--1066276 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
1066199 CCGGTTTTCA
*
1066209 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
1066229 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
1066248 ACCGG-TCTGAGCCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
1066267 ACCGG-TCTGA
1 ACCGGTTCTGA
1066277 CCCGACCCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
18 2 0.05
19 26 0.59
20 16 0.36
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:1066277 original size:9 final size:9
Alignment explanation
Indices: 1066239--1066278 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
1066229 ACCGGTTCGA
*
1066239 ACCGGTTTG
1 ACCGGTCTG
1066248 ACCGGTCTG
1 ACCGGTCTG
*
1066257 AGCCGGTTTG
1 A-CCGGTCTG
1066267 ACCGGTCTG
1 ACCGGTCTG
1066276 ACC
1 ACC
1066279 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:1066285 original size:5 final size:5
Alignment explanation
Indices: 1066275--1066327 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
1066265 TGACCGGTCT
* *
1066275 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
1066324 GACC
1 GACC
1066328 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:1066296 original size:17 final size:17
Alignment explanation
Indices: 1066274--1066334 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
1066264 TTGACCGGTC
1066274 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1066291 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
1066313 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1066330 TGACC
1 TGACC
1066335 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 22 0.56
22 17 0.44
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1066301 original size:22 final size:22
Alignment explanation
Indices: 1066275--1066341 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
1066265 TGACCGGTCT
1066275 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1066297 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
1066319 GACCCGACCGTTGACCGTTGACC
1 GACCCGACC--CGACCGTTGACC
1066342 GTTGACCGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 31 0.74
24 11 0.26
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1066334 original size:7 final size:7
Alignment explanation
Indices: 1066324--1066350 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1066314 GACCCGACCC
1066324 GACCGTT
1 GACCGTT
1066331 GACCGTT
1 GACCGTT
1066338 GACCGTT
1 GACCGTT
1066345 GACCGT
1 GACCGT
1066351 CTTTGACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1071976 original size:23 final size:23
Alignment explanation
Indices: 1071935--1071978 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1071925 CTAAAGAATT
1071935 ATAGTATATTAAAATATATAAAA
1 ATAGTATATTAAAATATATAAAA
*
1071958 ATAGTTATTTTAAAA-ATATAA
1 ATAG-TATATTAAAATATATAA
1071979 TGTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
ATAGTATATTAAAATATATAAAA
Found at i:1073184 original size:20 final size:20
Alignment explanation
Indices: 1073159--1073198 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1073149 TTTTTTATTG
1073159 ATTATTATT-TATATTATTAT
1 ATTATTATTATAT-TTATTAT
1073179 ATTATTATTATATTTATTAT
1 ATTATTATTATATTTATTAT
1073199 TAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTATTATTATATTTATTAT
Found at i:1073189 original size:23 final size:24
Alignment explanation
Indices: 1073154--1073200 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1073144 ACTAGTTTTT
1073154 TATTGATTATTAT-TTATATTATTA
1 TATTGATTATTATATT-TATTATTA
1073178 TATT-ATTATTATATTTATTATTA
1 TATTGATTATTATATTTATTATTA
1073201 AATAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TATTGATTATTATATTTATTATTA
Found at i:1075402 original size:10 final size:10
Alignment explanation
Indices: 1075387--1075428 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
1075377 TTTATTTACT
1075387 TATTATTTTA
1 TATTATTTTA
1075397 TATTATTTTA
1 TATTATTTTA
*
1075407 TATTATTTATT
1 TATTATTT-TA
1075418 TATTATTTTA
1 TATTATTTTA
1075428 T
1 T
1075429 TCATGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTATTTTA
Found at i:1075442 original size:20 final size:20
Alignment explanation
Indices: 1075398--1075449 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1075388 ATTATTTTAT
* * *
1075398 ATTATTTTATATTATTTATTT
1 ATTATTTTAT-TCATGTATTA
1075419 ATTATTTTATTCATGTATTA
1 ATTATTTTATTCATGTATTA
1075439 ATTATTTTATT
1 ATTATTTTATT
1075450 TGTCTGTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTATTTTATTCATGTATTA
Found at i:1075443 original size:31 final size:31
Alignment explanation
Indices: 1075378--1075450 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
1075368 TTCAATTTTT
* *
1075378 TTATTTACTTATTATTTTATATTATTTTATA
1 TTATTTATTTATTATTTTATATCATTTTATA
1075409 TTATTTATTTATTATTTTAT-TCATGTATTA-A
1 TTATTTATTTATTATTTTATATCAT-T-TTATA
1075440 TTATTTTATTT
1 TTA-TTTATTT
1075451 GTCTGTTAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 3 0.08
31 24 0.65
32 10 0.27
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.68
Consensus pattern (31 bp):
TTATTTATTTATTATTTTATATCATTTTATA
Found at i:1085165 original size:54 final size:54
Alignment explanation
Indices: 1085083--1085232 Score: 148
Period size: 54 Copynumber: 2.9 Consensus size: 54
1085073 CAATGATTGA
* * * * *
1085083 GAACATCTGAGCATAAATCACAGGAAAGGGTGAATGTGTTGTCAAATGCTTTAC
1 GAACATCTGAGCAGAAACCACAGAAAAGGATGAAGGTGTTGTCAAATGCTTTAC
* * *
1085137 GAACATCTGAGCAGAAGCCACAGAAAAGGATGAAGGTGTTGTCAAGTGTTTTAC
1 GAACATCTGAGCAGAAACCACAGAAAAGGATGAAGGTGTTGTCAAATGCTTTAC
* * * *
1085191 -ATC-TC-GA-CAAAAACCACAGGAAAA-GATGAATGTATTGTCAAA
1 GAACATCTGAGCAGAAACCACA-GAAAAGGATGAAGGTGTTGTCAAA
1085233 AATTTTACGA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
50 24 0.30
51 7 0.09
52 2 0.02
53 2 0.02
54 46 0.57
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGAAAAGGATGAAGGTGTTGTCAAATGCTTTAC
Found at i:1085614 original size:22 final size:21
Alignment explanation
Indices: 1085563--1085614 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
1085553 ATCTGCACTC
1085563 TTCAAAGATGATAGATTATTT
1 TTCAAAGATGATAGATTATTT
*
1085584 TT--AAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTAT-TT
1085604 TTCAAAGATGA
1 TTCAAAGATGA
1085615 AAGTTTTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 14 0.52
20 4 0.15
21 2 0.07
22 7 0.26
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (21 bp):
TTCAAAGATGATAGATTATTT
Found at i:1086308 original size:20 final size:20
Alignment explanation
Indices: 1086285--1086330 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1086275 TTCATAATGA
1086285 GAAGAACTCATCTGAAGAAG
1 GAAGAACTCATCTGAAGAAG
*
1086305 GAAGAACTCATCTGAAGAAT
1 GAAGAACTCATCTGAAGAAG
1086325 GAAGAA
1 GAAGAA
1086331 GAAGTTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.13, G:0.24, T:0.15
Consensus pattern (20 bp):
GAAGAACTCATCTGAAGAAG
Found at i:1086315 original size:133 final size:133
Alignment explanation
Indices: 1086172--1086443 Score: 438
Period size: 133 Copynumber: 2.0 Consensus size: 133
1086162 TTCATAATGA
*
1086172 GAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
1 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* * *
1086237 GAATTCATCACTT-GATGGATCAATATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAA
66 GAATTCATCA-TTCGATGGATCAACATTGCCAGAAAGAGTTCATAATAAGAAGAACTCATCTGAA
1086301 GAAG
130 GAAG
* *
1086305 GAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACTTTTCGCTT
1 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
* ***
1086370 GAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAG
66 GAATTCATCATTCGATGGATCAACATTGCCAGAAAGAGTTCATAATAAGAAGAACTCATCTGAAG
1086435 AAG
131 AAG
1086438 GAAGAA
1 GAAGAA
1086444 GAAGTTCATA
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
132 2 0.02
133 126 0.98
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (133 bp):
GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
GAATTCATCATTCGATGGATCAACATTGCCAGAAAGAGTTCATAATAAGAAGAACTCATCTGAAG
AAG
Found at i:1086329 original size:113 final size:110
Alignment explanation
Indices: 1086017--1087484 Score: 1190
Period size: 113 Copynumber: 12.9 Consensus size: 110
1086007 AGTTCAAATC
* * *
1086017 CATCATTCAATGGATCAACATTTCTAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATT-GATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
1086081 AGAATAAGTTCATAATGAGAAGAACTTGTTTAACTTTTCGCTTGAATT
65 AGAA-AAATTCATAATGAGAAGAACTTGTTCAACTTTT-GCTTGAATT
** * ***
1086129 TTTCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATT-GATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1086194 AGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
65 AGAA-AAATTCATAATGAGAAGAACTTGTTCAACTTTT-GCTTGAATT
**
1086242 CATCACTTGATGGATCAATATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCA-TTGATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** * * *** * *
1086307 AGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACTTTTCG-CTT
65 AGAA-AAAT-T-CATAATG-AGAAGAA---C-T--T--GTTCAAC-T-TTT-GC--TT-GAATT
* * *** *
1086370 GAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAG
1 -C----ATCATT-GATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * ** *
1086435 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACTTTTTGCTCAAATC
60 AAGGAAGAA-AAATTCATAATGAGAAGAACTTGTTCAAC-TTTTGCTTGAATT
** * * *
1086488 CATCATCTGATGGATCAGTTTTTCTAGAAAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCAT-TGATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * ** *
1086553 AGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATC
65 AGAA-AAATTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATT
* *
1086601 CATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCAT-TGATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* ** *
1086666 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
65 AGAA-AAATTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATT
*
1086714 CATCATCTGATGGATCAGCATTTCCAGAATA-TGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCAT-TGATGGATCAGCATTTCCAGAA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* ** *
1086778 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
64 AAGAA-AAATTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATT
* *
1086827 CATCATCTGATGGATCATCATTTCCAGAAATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCAT-TGATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
1086892 AGAAGAAGTTCATAATGAGAAGAAATTGTTCAACTTTTCGCTTGAATT
65 AGAA-AAATTCATAATGAGAAGAACTTGTTCAACTTTT-GCTTGAATT
* *** *
1086940 CATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
1 CATCATT-GATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
1087005 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACTTTTTGCTTGAATT
65 AGAA-AAATTCATAATGAGAAGAACTTGTTCAAC-TTTTGCTTGAATT
* *
1087053 CATCACTTGATGGATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAAAAGG
1 CATCA-TTGATGGATCAGCATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * *
1087117 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACTTTAG--T---TT
64 AAGAA-AAATTCATAATGAGAAGAACTTGTTCAACTTTTGCTTGAATT
* * * * * *
1087160 GATC---GACGGATCAACATTTCCA-TAA-AGTTCATAATGAGAAGAACTTATCTAAAG-AGGAA
1 CATCATTGATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * * *
1087219 GAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AACT
66 GAA-AAATTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATT
** * *
1087265 CTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTT
1 C-AT--C---A-TTGATGGATCAG---C-A--TTTCCAGA-AAGAGTTCATAATGAGAAGAACTC
* * * * * *
1087329 ATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTTAACCTTTTG-TTTAACT
52 ATCTGAAGAAGGAAGAA-AAATTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATT
** * **
1087388 CTATCACAGAAGCAGAT-AG-A-TTCCAG-AATTGTTCATAATGAGAAGAACTCATCTG-A-AA-
1 C-ATCATTGATG--GATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* * *
1087446 -AAGAATAAGTTCATAATGAGAAGAATTTCTTCAACTTTT
63 GAAGAA-AAATTCATAATGAGAAGAACTTGTTCAACTTTT
1087485 TGCTAGATTA
Statistics
Matches: 1169, Mismatches: 125, Indels: 131
0.82 0.09 0.09
Matches are distributed among these distances:
100 35 0.03
101 33 0.03
103 18 0.02
105 6 0.01
106 31 0.03
107 5 0.00
108 5 0.00
109 24 0.02
110 7 0.01
112 32 0.03
113 737 0.63
114 12 0.01
115 12 0.01
116 7 0.01
117 3 0.00
118 6 0.01
119 5 0.00
120 2 0.00
121 10 0.01
122 8 0.01
123 80 0.07
124 5 0.00
125 1 0.00
126 5 0.00
127 1 0.00
128 4 0.00
129 1 0.00
130 7 0.01
131 5 0.00
132 3 0.00
133 59 0.05
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (110 bp):
CATCATTGATGGATCAGCATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAAAATTCATAATGAGAAGAACTTGTTCAACTTTTGCTTGAATT
Found at i:1086954 original size:339 final size:335
Alignment explanation
Indices: 1086305--1087488 Score: 1342
Period size: 339 Copynumber: 3.5 Consensus size: 335
1086295 TCTGAAGAAG
*
1086305 GAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA-CTTTTCGCT
1 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTT-GCT
* * * * *** *
1086369 TGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGA-GTTCATAATAAGAAGAACTCATCTGA
65 TAAATCCATCACT-GATGGATCAGCATTTCCA-GAATATGTTCATAATGAGAAGAACTCATCTGA
* *
1086433 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACTTTTTGCTCAAATCCATCATCTGA
128 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCTGA
* * * *
1086498 TGGATCAGT-TTTTCTAGAAAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
193 TGGATCA-TCATTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * *
1086562 TCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCATCTGATGGATCAGCTTTTCCA
256 TCATAATGAGAAGAAATTGTTCAACCTTTTGCT-TAATTCATCATC-GATGGATCAGCTTTTCCA
*
1086627 GAAAAAGTTCATAATGA
319 GAGAAAGTTCATAATGA
* * * *
1086644 GAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
1 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
1086709 AAATCCATCATCTGATGGATCAGCATTTCCAGAATATGTTCATAATGAGAAGAACTCATCTGAAG
66 AAATCCATCA-CTGATGGATCAGCATTTCCAGAATATGTTCATAATGAGAAGAACTCATCTGAAG
* *
1086774 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCTGATG
130 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCTGATG
1086839 GATCATCATTTCCAGAAATAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
195 GATCATCATTTCCAGAAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
1086904 TAATGAGAAGAAATTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGG
259 TAATGAGAAGAAATTGTTCAACCTTTT-GCTT-AATTCATCA-TCGATGGATCAGCTTTTCCAGA
** *
1086968 GCGAGTTCATAATAA
321 GAAAGTTCATAATGA
*
1086983 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACTTTTTGCTT
1 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
* * * *
1087048 GAATTCATCACTTGATGGATCAACATTTCCAGAGA-AAGTTCATAATGAGAAGAACTCATCTGAA
66 AAATCCATCAC-TGATGGATCAGCATTTCCAGA-ATATGTTCATAATGAGAAGAACTCATCTGAA
* * * * *
1087112 AAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCGA-CTTTAG-T----T---TGATC-GAC
129 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCTGAT
* * * *
1087167 GGATCAACATTTCCA-TAAAGTTCATAATGAGAAGAACTTATCTAAAG-AGGAAGAAGAAGTTCA
194 GGATCATCATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
** * *
1087230 TAATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCA-CAGAAGGAGATAGATCAGCATCA
259 TAATGAGAAGAAATTGTTCAACCTTTTGCTTAATTC-ATCATC-------GAT-G----G-ATCA
*
1087294 ACTTTTCCAGAGAAAGTTCATAATGA
310 GCTTTTCCAGAGAAAGTTCATAATGA
* * * *
1087320 GAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGTTT
1 GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
* * * *
1087384 AACTCTATCACAGAAGCAGAT-AG-A-TTCCAGAAT-TGTTCATAATGAGAAGAACTCATCTG-A
66 AAATCCATCACTGATG--GATCAGCATTTCCAGAATATGTTCATAATGAGAAGAACTCATCTGAA
* * * *
1087444 -AA--AAGAATAAGTTCATAATGAGAAGAATTTCTTCAACTTTTTGCT
129 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
1087489 AGATTACATC
Statistics
Matches: 733, Mismatches: 82, Indels: 68
0.83 0.09 0.08
Matches are distributed among these distances:
324 1 0.00
325 4 0.01
326 42 0.06
327 32 0.04
328 2 0.00
329 46 0.06
330 8 0.01
331 6 0.01
332 2 0.00
333 27 0.04
334 7 0.01
335 4 0.01
336 52 0.07
337 43 0.06
338 17 0.02
339 431 0.59
340 9 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (335 bp):
GAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTT
AAATCCATCACTGATGGATCAGCATTTCCAGAATATGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGG
ATCATCATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAAATTGTTCAACCTTTTGCTTAATTCATCATCGATGGATCAGCTTTTCCAGAGAAAG
TTCATAATGA
Found at i:1087240 original size:100 final size:102
Alignment explanation
Indices: 1087064--1087248 Score: 311
Period size: 100 Copynumber: 1.8 Consensus size: 102
1087054 ATCACTTGAT
1087064 GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTC
1 GGATCAACATTTCCA-AGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTC
1087129 ATAATGAGAAGAACTTGTTCGACTTTAGTTTGATCGAC
65 ATAATGAGAAGAACTTGTTCGACTTTAGTTTGATCGAC
* * *
1087167 GGATCAACATTTCC-ATAAAGTTCATAATGAGAAGAACTTATCT-AAAGAGGAAGAAGAAGTTCA
1 GGATCAACATTTCCAAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCA
*
1087230 TAATGAGAAGAGCTTGTTC
66 TAATGAGAAGAACTTGTTC
1087249 AACCTTTTGC
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 37 0.47
101 27 0.35
103 14 0.18
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (102 bp):
GGATCAACATTTCCAAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCGACTTTAGTTTGATCGAC
Found at i:1087314 original size:123 final size:123
Alignment explanation
Indices: 1087183--1087408 Score: 398
Period size: 123 Copynumber: 1.8 Consensus size: 123
1087173 ACATTTCCAT
*
1087183 AAAGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAAGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATT
*
1087248 CAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAG
66 CAACCTTTTGCATAACTCTATCACAGAAGCAGATAGATCAGCATCAACTTTTCCAGAG
*
1087306 AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATT
1 AAAGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATT
* **
1087371 TAACCTTTTGTTTAACTCTATCACAGAAGCAGATAGAT
66 CAACCTTTTGCATAACTCTATCACAGAAGCAGATAGAT
1087409 TCCAGAATTG
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 97 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (123 bp):
AAAGTTCATAATGAGAAGAACTTATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATT
CAACCTTTTGCATAACTCTATCACAGAAGCAGATAGATCAGCATCAACTTTTCCAGAG
Found at i:1087511 original size:106 final size:108
Alignment explanation
Indices: 1087309--1087511 Score: 252
Period size: 106 Copynumber: 1.9 Consensus size: 108
1087299 TCCAGAGAAA
* * *
1087309 GTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTTAA
1 GTTCATAATGAGAAGAACTCATCTGAAGA-GAAGAAGAAGTTCATAATGAGAAGAACTTATTCAA
* *
1087374 CCTTTTGTTTAACTCTATCACAGAAGCAGATAGATTCCAGAATT
65 CCTTTTGTCTAACTCTATCACAGAAGAAGATAGATTCCAGAATT
* * *
1087418 GTTCATAATGAGAAGAACTCATCTGAA-A-AAGAATAAGTTCATAATGAGAAGAATTTCTTCAAC
1 GTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAAC
* * *
1087481 TTTTTG-CTAGATTAC-ATCATAGAAGAAGATA
66 CTTTTGTCTA-ACT-CTATCACAGAAGAAGATA
1087512 AATTGTCATC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
105 2 0.02
106 51 0.63
107 1 0.01
108 1 0.01
109 26 0.32
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (108 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAGAAGTTCATAATGAGAAGAACTTATTCAAC
CTTTTGTCTAACTCTATCACAGAAGAAGATAGATTCCAGAATT
Found at i:1087700 original size:3 final size:3
Alignment explanation
Indices: 1087694--1087737 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
1087684 TTTTTATTTG
*
1087694 ATT ATT ATT -TAT ATT ATT ATT ATT ATT ATG ATAT ATT ATT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT A
1087738 AATAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 32 0.89
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1089332 original size:21 final size:21
Alignment explanation
Indices: 1089302--1089342 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1089292 CATTTTCTGA
*
1089302 TATTTCTAAATAAATAAATTT
1 TATTTATAAATAAATAAATTT
*
1089323 TATTTATAAATATATAAATT
1 TATTTATAAATAAATAAATT
1089343 AATATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTTATAAATAAATAAATTT
Found at i:1092025 original size:42 final size:41
Alignment explanation
Indices: 1091990--1092142 Score: 127
Period size: 41 Copynumber: 3.7 Consensus size: 41
1091980 AATATAGTGG
*
1091990 TAAA-TTAGCGGCG-TTTATACCACAAACACTACAATAGAGTA
1 TAAATTTAGCGGCGATTTA-ACCA-AAACGCTACAATAGAGTA
* * **
1092031 TAAATTTTGCGGCGATTTAGCCAAAACGCCGCAATAGAGTA
1 TAAATTTAGCGGCGATTTAACCAAAACGCTACAATAGAGTA
* * * *
1092072 TAAATTTTA-CGGCGATTGAGCCAAAACGCTACAATATAGTGG
1 TAAA-TTTAGCGGCGATTTAACCAAAACGCTACAATAGAGT-A
*
1092114 TAAA-TTAGCGGTG-TTTATACCACAAACGC
1 TAAATTTAGCGGCGATTTA-ACCA-AAACGC
1092143 CATAATATAT
Statistics
Matches: 91, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
40 6 0.07
41 57 0.63
42 24 0.26
43 4 0.04
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (41 bp):
TAAATTTAGCGGCGATTTAACCAAAACGCTACAATAGAGTA
Found at i:1092107 original size:41 final size:41
Alignment explanation
Indices: 1092013--1092107 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
1092003 TTTATACCAC
* * *
1092013 AAACACTACAATAGAGTATAAATTTTGCGGCGATTTAGCCA
1 AAACGCTACAATAGAGTATAAATTTTACGGCGATTGAGCCA
**
1092054 AAACGCCGCAATAGAGTATAAATTTTACGGCGATTGAGCCA
1 AAACGCTACAATAGAGTATAAATTTTACGGCGATTGAGCCA
1092095 AAACGCTACAATA
1 AAACGCTACAATA
1092108 TAGTGGTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (41 bp):
AAACGCTACAATAGAGTATAAATTTTACGGCGATTGAGCCA
Found at i:1092380 original size:41 final size:43
Alignment explanation
Indices: 1092184--1092379 Score: 257
Period size: 41 Copynumber: 4.8 Consensus size: 43
1092174 TCCTCAAATG
* *
1092184 CTGCAATAGTGATAATCAATAGTGGCG-GTTTTAGACAAACGT
1 CTGCAATAGTGTTAATCAATAGTGGCGTTTTTTAGACAAACGT
* * *
1092226 C-GCAATAGTGTTAATCAATAATGGCG-TTTTTAGAAAAACGC
1 CTGCAATAGTGTTAATCAATAGTGGCGTTTTTTAGACAAACGT
*
1092267 CT-CAATAGTGTTAATCAATAGTGGC-CTTTTTAGACAAACG-
1 CTGCAATAGTGTTAATCAATAGTGGCGTTTTTTAGACAAACGT
*
1092307 CTGCAATAGTGTTAATCAATAGTAGCGTTTTTTA-ACAAACGT
1 CTGCAATAGTGTTAATCAATAGTGGCGTTTTTTAGACAAACGT
*
1092349 CAG-AATAGTG-TAATCAATAGTGGCGTTTTTT
1 CTGCAATAGTGTTAATCAATAGTGGCGTTTTTT
1092380 TGTATAAACA
Statistics
Matches: 138, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
40 22 0.16
41 107 0.78
42 9 0.07
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (43 bp):
CTGCAATAGTGTTAATCAATAGTGGCGTTTTTTAGACAAACGT
Found at i:1093127 original size:41 final size:42
Alignment explanation
Indices: 1093055--1093157 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 42
1093045 GGATACAAAT
* * *
1093055 GCCGCAATAGAGTTGTT-ATTAGGTGGCGTTTT-TTAATAAAC
1 GCCGCAATAGAGTAGTTCCTTAGGTGGCGTTTTCGTAA-AAAC
* * *
1093096 GCCGCAATAGAATAGTTCCTTA-GTGGTGTTTTCGTAAAAAT
1 GCCGCAATAGAGTAGTTCCTTAGGTGGCGTTTTCGTAAAAAC
*
1093137 GCAGCAATAGAGTAGTTCCTT
1 GCCGCAATAGAGTAGTTCCTT
1093158 TGCGGCGTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
41 46 0.88
42 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (42 bp):
GCCGCAATAGAGTAGTTCCTTAGGTGGCGTTTTCGTAAAAAC
Found at i:1096059 original size:21 final size:21
Alignment explanation
Indices: 1096035--1096089 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1096025 ATGAAACAAG
*
1096035 GGAAGCAGAGAGAGCAGCAAT
1 GGAAGCAGAGAGAGCAGCAAC
* *
1096056 GGAAGCA-ACCAGAGCAGCAGC
1 GGAAGCAGA-GAGAGCAGCAAC
1096077 GGAAGCAGAGAGA
1 GGAAGCAGAGAGA
1096090 AAAGCAGCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.42, C:0.18, G:0.38, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAAC
Found at i:1096115 original size:21 final size:21
Alignment explanation
Indices: 1096066--1096178 Score: 102
Period size: 21 Copynumber: 5.4 Consensus size: 21
1096056 GGAAGCAACC
* * * *
1096066 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAA
* *
1096087 AGAAAAGCAGCGGCAGCATAA
1 AGAGAAGCAGCGGCAGCACAA
**
1096108 AGAGAAGCAATGGCAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
*
1096129 AGAGAAGCAGCGAC-GACACAA
1 AGAGAAGCAGCGGCAG-CACAA
* * *
1096150 AGAGAAACGGCGGTAGCACAA
1 AGAGAAGCAGCGGCAGCACAA
1096171 AGAGAAGC
1 AGAGAAGC
1096179 CGCGAACTTT
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 1 0.01
21 71 0.97
22 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.33, T:0.03
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAA
Found at i:1097546 original size:15 final size:15
Alignment explanation
Indices: 1097526--1097560 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1097516 TGAGTCATTA
1097526 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
1097541 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
1097556 CCCGC
1 CCCGC
1097561 ATCCGCCCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.06, C:0.69, G:0.20, T:0.06
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1106164 original size:29 final size:26
Alignment explanation
Indices: 1106132--1106197 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
1106122 ATTAAAATTT
*
1106132 ATAAAAATTAATTAAGTAAAATTATAAAA
1 ATAAAAATTAATTAAATAAAA--AT-AAA
*
1106161 ATAAAAA-TAAATAAATAAAAATAAA
1 ATAAAAATTAATTAAATAAAAATAAA
*
1106186 ATAATAATTAAT
1 ATAAAAATTAAT
1106198 AATATTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 9 0.28
26 5 0.16
28 11 0.34
29 7 0.22
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (26 bp):
ATAAAAATTAATTAAATAAAAATAAA
Found at i:1106175 original size:24 final size:24
Alignment explanation
Indices: 1106124--1106175 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1106114 ATTATAAAAT
* * *
1106124 TAAAATTTATAAAAATTAATTAAG
1 TAAAATTTATAAAAATAAAATAAA
1106148 TAAAA-TTATAAAAATAAAAATAAA
1 TAAAATTTATAAAAAT-AAAATAAA
1106172 TAAA
1 TAAA
1106176 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
TAAAATTTATAAAAATAAAATAAA
Found at i:1106191 original size:14 final size:14
Alignment explanation
Indices: 1106112--1106192 Score: 58
Period size: 14 Copynumber: 5.6 Consensus size: 14
1106102 ATCTCCAATT
* *
1106112 AAATTATAAAATTA
1 AAATAATAAAAATA
* *
1106126 AAATTTATAAAAATT
1 AAA-TAATAAAAATA
* *
1106141 AATTAAGTAAAATTA
1 AAATAA-TAAAAATA
1106156 TAAA-AATAAAAAT-
1 -AAATAATAAAAATA
1106169 AAATAAATAAAAATA
1 AAAT-AATAAAAATA
1106184 AAATAATAA
1 AAATAATAA
1106193 TTAATAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
12 3 0.06
14 25 0.47
15 23 0.43
16 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (14 bp):
AAATAATAAAAATA
Found at i:1106999 original size:14 final size:13
Alignment explanation
Indices: 1106972--1107006 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1106962 GGTTAGATAT
1106972 TTAATAAAATAAAA
1 TTAA-AAAATAAAA
1106986 TTAAAAAATAAAA
1 TTAAAAAATAAAA
*
1106999 ATAAAAAA
1 TTAAAAAA
1107007 GTATTCTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TTAAAAAATAAAA
Found at i:1110937 original size:15 final size:15
Alignment explanation
Indices: 1110917--1110949 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1110907 CGCCGCCGTC
*
1110917 CGTCTCGTCTCGGGT
1 CGTCTCGTCTCGAGT
1110932 CGTCTCGTCTCGAGT
1 CGTCTCGTCTCGAGT
1110947 CGT
1 CGT
1110950 GGTCGTGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.33, G:0.30, T:0.33
Consensus pattern (15 bp):
CGTCTCGTCTCGAGT
Found at i:1110956 original size:6 final size:6
Alignment explanation
Indices: 1110945--1110982 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
1110935 CTCGTCTCGA
* *
1110945 GTCGTG GTCGTG ATCGTG GTCGCG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1110983 AATACGTGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.03, C:0.18, G:0.47, T:0.32
Consensus pattern (6 bp):
GTCGTG
Found at i:1111103 original size:21 final size:19
Alignment explanation
Indices: 1111078--1111222 Score: 83
Period size: 21 Copynumber: 7.0 Consensus size: 19
1111068 GATTTTAGAC
1111078 TATCGCAACGAATTTGGAA
1 TATCGCAACGAATTTGGAA
* **
1111097 TAAATCGCAACGCAAACTTGGGC
1 T--ATCGCAACG--AATTTGGAA
* **
1111120 TATCACAATTAATTTGGAA
1 TATCGCAACGAATTTGGAA
* *
1111139 TAAATCGCAACGCGAACTTGGAC
1 T--ATCGCAA--CGAATTTGGAA
1111162 TATCGCAACGAATTTGGAA
1 TATCGCAACGAATTTGGAA
* * *
1111181 TAAATCGCAACACGAACTTCGAC
1 T--ATCGC-A-ACGAATTTGGAA
1111204 TATCGCAACGAATTTGGAA
1 TATCGCAACGAATTTGGAA
1111223 AACAACAACG
Statistics
Matches: 92, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
19 27 0.29
20 1 0.01
21 38 0.41
22 1 0.01
23 25 0.27
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (19 bp):
TATCGCAACGAATTTGGAA
Found at i:1111290 original size:21 final size:21
Alignment explanation
Indices: 1111142--1111297 Score: 101
Period size: 21 Copynumber: 7.6 Consensus size: 21
1111132 TTTGGAATAA
1111142 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* *
1111163 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
* *
1111182 AAATCGCAACACGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
* *
1111205 ATCGCAA--CGAATTTGGA-A
1 ATCGCAACGCGAACTTGGACT
* * *
1111223 AACAACAACGCGAACTTCGACT
1 ATC-GCAACGCGAACTTGGACT
* * * **
1111245 ATCGCAA--TGAATTTAGAAA
1 ATCGCAACGCGAACTTGGACT
1111264 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
1111285 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1111298 TATGTAAATC
Statistics
Matches: 99, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
18 2 0.02
19 35 0.35
21 51 0.52
22 2 0.02
23 9 0.09
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:1111293 original size:40 final size:42
Alignment explanation
Indices: 1111075--1111291 Score: 291
Period size: 42 Copynumber: 5.3 Consensus size: 42
1111065 TGCGATTTTA
*
1111075 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
* * **
1111117 GGCTATCACAATTAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
* *
1111159 GACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
* *
1111201 GACTATCGCAACGAATTTGG-A-AAA-CAACAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATC-GCAACGCGAACTTG
* *
1111241 GACTATCGCAATGAATTTAG-A-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1111281 GACTATCGCAA
1 GACTATCGCAA
1111292 TGCGAATATG
Statistics
Matches: 156, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 60 0.38
41 2 0.01
42 93 0.60
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
Found at i:1111354 original size:21 final size:21
Alignment explanation
Indices: 1111306--1111355 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1111296 AATATGTAAA
*
1111306 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAAT
* * *
1111327 TCACATTGCGGTAGTCGAAAT
1 TCGCATTGCGATAGTCCAAAT
1111348 TCGCATTG
1 TCGCATTG
1111356 TAAATTTGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:1130290 original size:14 final size:14
Alignment explanation
Indices: 1130271--1130298 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1130261 ACCTCATCTT
1130271 ATTTTAAAATATGG
1 ATTTTAAAATATGG
1130285 ATTTTAAAATATGG
1 ATTTTAAAATATGG
1130299 TTTAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
ATTTTAAAATATGG
Found at i:1131781 original size:19 final size:20
Alignment explanation
Indices: 1131739--1131788 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1131729 TGAGCCATTC
*
1131739 AGTATCGATA-CTACCCGTG
1 AGTATCGATACCCACCCGTG
*
1131758 AGTATCGATACCCACCCTTG
1 AGTATCGATACCCACCCGTG
*
1131778 -GTATTGATACC
1 AGTATCGATACC
1131789 AAAAAATGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTATCGATACCCACCCGTG
Found at i:1134623 original size:19 final size:20
Alignment explanation
Indices: 1134583--1134623 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1134573 TGATAGAATT
*
1134583 TTTAAATTTGAAAGATTTAA
1 TTTAAATTTGAAAGATTCAA
1134603 TTTAAA-TT-AAATGATTCAA
1 TTTAAATTTGAAA-GATTCAA
1134622 TT
1 TT
1134624 ATAATGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 3 0.16
19 10 0.53
20 6 0.32
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (20 bp):
TTTAAATTTGAAAGATTCAA
Found at i:1150281 original size:18 final size:17
Alignment explanation
Indices: 1150258--1150300 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1150248 GAAGAACAAG
1150258 TGATATGAAATGTATAAA
1 TGATATGAAATGT-TAAA
** *
1150276 TGATATGCCATGTTATA
1 TGATATGAAATGTTAAA
1150293 TGATATGA
1 TGATATGA
1150301 GAGCTAGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (17 bp):
TGATATGAAATGTTAAA
Found at i:1150750 original size:34 final size:35
Alignment explanation
Indices: 1150711--1150781 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
1150701 TATAAGAATA
1150711 TGGATAGTGGAAT-AGGTTAGTAATGGAAATAGTG
1 TGGATAGTGGAATAAGGTTAGTAATGGAAATAGTG
1150745 TGGATAGTGGAATAAGGTTAGTAATGGAAATAGTG
1 TGGATAGTGGAATAAGGTTAGTAATGGAAATAGTG
1150780 TG
1 TG
1150782 AGATGATGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 13 0.36
35 23 0.64
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (35 bp):
TGGATAGTGGAATAAGGTTAGTAATGGAAATAGTG
Found at i:1153651 original size:24 final size:20
Alignment explanation
Indices: 1153619--1153676 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1153609 GCTTGGATAG
1153619 TGCATCGATGCACATGTTAAGGAA
1 TGCATCGATGCAC-TG-T-A-GAA
1153643 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
1153663 TGTATCGATGCACT
1 TGCATCGATGCACT
1153677 TCAAAGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1154403 original size:27 final size:27
Alignment explanation
Indices: 1154365--1154430 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
1154355 CTTAAGGAGT
1154365 GGTCCTTCGGGATAAATACAATACATA
1 GGTCCTTCGGGATAAATACAATACATA
* * * *
1154392 GGTCATTCGGGATAAATATAGTATATA
1 GGTCCTTCGGGATAAATACAATACATA
1154419 GGTCCTTCGGGA
1 GGTCCTTCGGGA
1154431 CAAAATTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (27 bp):
GGTCCTTCGGGATAAATACAATACATA
Found at i:1157664 original size:24 final size:20
Alignment explanation
Indices: 1157637--1157694 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1157627 GCATGGATAG
1157637 TGCATCGATGCACATGTTAAGGAA
1 TGCATCGATGCAC-TG-T-A-GAA
1157661 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
1157681 TGTATCGATGCACT
1 TGCATCGATGCACT
1157695 TCAAAGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1158588 original size:8 final size:8
Alignment explanation
Indices: 1158575--1158600 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1158565 TATGAATTGC
1158575 ATTATATG
1 ATTATATG
1158583 ATTATATG
1 ATTATATG
1158591 ATTATATG
1 ATTATATG
1158599 AT
1 AT
1158601 GATGTGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATTATATG
Found at i:1161017 original size:29 final size:29
Alignment explanation
Indices: 1160965--1161045 Score: 126
Period size: 29 Copynumber: 2.7 Consensus size: 29
1160955 GATAAATCTT
*
1160965 CATACTTCTTCTTCTTCTTCTTCTCCATTTC
1 CATA-TTCTTATTC-TCTTCTTCTCCATTTC
1160996 CATATTCTTATTCTCTTCTTCTCCATTTC
1 CATATTCTTATTCTCTTCTTCTCCATTTC
*
1161025 CATCTTCTTATTCTCTTCTTC
1 CATATTCTTATTCTCTTCTTC
1161046 AAGTTTACTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 36 0.75
30 8 0.17
31 4 0.08
ACGTcount: A:0.11, C:0.33, G:0.00, T:0.56
Consensus pattern (29 bp):
CATATTCTTATTCTCTTCTTCTCCATTTC
Found at i:1164813 original size:15 final size:14
Alignment explanation
Indices: 1164777--1164810 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1164767 AATAAAAATT
*
1164777 TAAAAATAAATTAA
1 TAAAAATTAATTAA
1164791 TAAAAATTAATTAA
1 TAAAAATTAATTAA
1164805 TAAAAA
1 TAAAAA
1164811 ATTTACCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAAATTAATTAA
Found at i:1171137 original size:15 final size:15
Alignment explanation
Indices: 1171103--1171145 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1171093 TGTTATCATA
* *
1171103 TAATTGAAAGTTTTTT
1 TAATTTAAA-TTTATT
1171119 TAATTTAAATTTATT
1 TAATTTAAATTTATT
*
1171134 TAATTTTAATTT
1 TAATTTAAATTT
1171146 TTTTTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TAATTTAAATTTATT
Found at i:1171777 original size:4 final size:4
Alignment explanation
Indices: 1171768--1171883 Score: 89
Period size: 4 Copynumber: 29.8 Consensus size: 4
1171758 GGAGTTAATT
* * *
1171768 TTTA TTTA TTTA CTTTGA ATTA TTTA TTTA -TT- TTTA ATAA TTTA TTTA
1 TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * **
1171816 TTTA TGTA ATAA TTTA -TT- TTTA TTTA TTTA TTTA TTT- TGAA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
1171861 GTTA TTTA TTCA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
1171884 GAAGGGATAT
Statistics
Matches: 85, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
3 9 0.11
4 70 0.82
5 5 0.06
6 1 0.01
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:1171793 original size:22 final size:20
Alignment explanation
Indices: 1171762--1171880 Score: 106
Period size: 18 Copynumber: 6.2 Consensus size: 20
1171752 AAATCTGGAG
1171762 TTAATT-TTTATTTATTTACT
1 TTAATTATTTATTTATTTA-T
1171782 TTGAATTATTTATTTA-TT-T
1 TT-AATTATTTATTTATTTAT
*
1171801 TTAATAATTTATTTATTTAT
1 TTAATTATTTATTTATTTAT
* *
1171821 GTAATAATTTA-TT-TTTAT
1 TTAATTATTTATTTATTTAT
* **
1171839 TTATTTATTTATTT-TGAAT
1 TTAATTATTTATTTATTTAT
* *
1171858 TTAGTTATTTATTCATTTAT
1 TTAATTATTTATTTATTTAT
1171878 TTA
1 TTA
1171881 TTTGAAGGGA
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
18 25 0.30
19 24 0.29
20 19 0.23
21 6 0.07
22 8 0.10
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (20 bp):
TTAATTATTTATTTATTTAT
Found at i:1171876 original size:31 final size:29
Alignment explanation
Indices: 1171793--1171883 Score: 92
Period size: 34 Copynumber: 2.9 Consensus size: 29
1171783 TGAATTATTT
* *
1171793 ATTTATTTTTAATAATTTATTTATTTATGTAATA
1 ATTTATTTTTATTCATTTATTTATTT-TG----A
*
1171827 ATTTATTTTTATTTATTTATTTATTTTGA
1 ATTTATTTTTATTCATTTATTTATTTTGA
1171856 ATTTAGTTATTTATTCATTTATTTATTT
1 ATTTA-TT-TTTATTCATTTATTTATTT
1171884 GAAGGGATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
29 6 0.12
30 2 0.04
31 18 0.35
33 2 0.04
34 24 0.46
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (29 bp):
ATTTATTTTTATTCATTTATTTATTTTGA
Found at i:1172343 original size:14 final size:15
Alignment explanation
Indices: 1172324--1172353 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1172314 TAAATCTATG
1172324 TTTATTTATTT-TAA
1 TTTATTTATTTATAA
1172338 TTTATTTATTTATAA
1 TTTATTTATTTATAA
1172353 T
1 T
1172354 ATTTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATTTATTTATAA
Found at i:1174098 original size:18 final size:18
Alignment explanation
Indices: 1174075--1174125 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
1174065 TTTCAATTTG
1174075 TTTAAATTATTAATTAAC
1 TTTAAATTATTAATTAAC
*
1174093 TTTAAATTATTAATTAAG
1 TTTAAATTATTAATTAAC
1174111 TTTAAATTATTAATT
1 TTTAAATTATTAATT
1174126 TGTTTATCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTATTAATTAAC
Found at i:1176526 original size:15 final size:15
Alignment explanation
Indices: 1176496--1176537 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1176486 TTTGAACTAC
*
1176496 ATAATTC-TATAAAA
1 ATAATTCATATATAA
1176510 ATAATTCATATATAA
1 ATAATTCATATATAA
*
1176525 ATAATTTATATAT
1 ATAATTCATATAT
1176538 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 7 0.28
15 18 0.72
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTCATATATAA
Found at i:1178172 original size:23 final size:25
Alignment explanation
Indices: 1178124--1178174 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1178114 TATTTTAAAA
*
1178124 TATTTATTTAATTTTTAGAATCATAT
1 TATTTATTTAATTTTAAGAA-CATAT
1178150 TATTTATTT-ATTTTAAGAA-ATAT
1 TATTTATTTAATTTTAAGAACATAT
1178173 TA
1 TA
1178175 ACTTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
25 9 0.38
26 9 0.38
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
TATTTATTTAATTTTAAGAACATAT
Found at i:1178377 original size:22 final size:21
Alignment explanation
Indices: 1178322--1178390 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1178312 TAAGAACAAT
* *
1178322 ATTATTTCAAATATATAAATAA
1 ATTATTTTAAAAATAT-AATAA
*
1178344 TATTATTTTAAAAATTTAATAA
1 -ATTATTTTAAAAATATAATAA
*
1178366 ATTTTTTATAAAAATAT-ATAA
1 ATTATTT-TAAAAATATAATAA
1178387 ATTA
1 ATTA
1178391 ATGAATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 13 0.33
22 13 0.33
23 13 0.33
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTTTAAAAATATAATAA
Found at i:1178900 original size:9 final size:10
Alignment explanation
Indices: 1178877--1178901 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1178867 AAATTAAATA
1178877 AAAAATAATG
1 AAAAATAATG
1178887 AAAAATAATG
1 AAAAATAATG
1178897 AAAAA
1 AAAAA
1178902 AGTGATGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (10 bp):
AAAAATAATG
Found at i:1182421 original size:18 final size:18
Alignment explanation
Indices: 1182398--1182435 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1182388 TTGGCATGAC
* *
1182398 ATTTTTTAATTATTTTTT
1 ATTTTTAAATTATTATTT
1182416 ATTTTTAAATTATTATTT
1 ATTTTTAAATTATTATTT
1182434 AT
1 AT
1182436 ATTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTAAATTATTATTT
Found at i:1182434 original size:12 final size:12
Alignment explanation
Indices: 1182414--1182447 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1182404 TAATTATTTT
1182414 TTATT-TTTAAA
1 TTATTATTTAAA
*
1182425 TTATTATTTATA
1 TTATTATTTAAA
1182437 TTATTATTTAA
1 TTATTATTTAA
1182448 CTAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTATTTAAA
Found at i:1187240 original size:27 final size:27
Alignment explanation
Indices: 1187181--1187249 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 27
1187171 TAATTTATGT
*
1187181 AATTTTAAAATATTTT---ATATGATA
1 AATTATAAAATATTTTAAAATATGATA
*
1187205 AATTTTAAAATATTTTAAAATATGATA
1 AATTATAAAATATTTTAAAATATGATA
*
1187232 AGA-TATAAAA-CTTTTAAA
1 A-ATTATAAAATATTTTAAA
1187250 CTCACAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 16 0.41
26 7 0.18
27 15 0.38
28 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (27 bp):
AATTATAAAATATTTTAAAATATGATA
Found at i:1187384 original size:23 final size:23
Alignment explanation
Indices: 1187339--1187384 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1187329 ATTATAGCAA
* * *
1187339 AAAAATATTAAAATTTTAGTTTT
1 AAAAATATAAAAATTATAATTTT
*
1187362 AAAAGTATAAAAATTATAATTTT
1 AAAAATATAAAAATTATAATTTT
1187385 TACATTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AAAAATATAAAAATTATAATTTT
Found at i:1194431 original size:132 final size:132
Alignment explanation
Indices: 1194194--1194579 Score: 682
Period size: 132 Copynumber: 2.9 Consensus size: 132
1194184 TTATATCTAA
* * * *
1194194 TTTACCCCCGAAACTTTTTTATTTGAAAACAGAAGAGACTATATCCACCCTTATCGGATTAAAAC
1 TTTACCCCTGAAACTTTTTTAATTGAAAACAGAAGAGACTATATCCATCCTTATCGGATAAAAAC
*
1194259 AACAATATATAGCTAACACCAAGAATTATGAGCAAAAGTGAAGCAAGTTTATGATTGTTTCTTCA
66 AACAACATATAGCTAACACCAAGAATTATGAGCAAAAGTGAAGCAAGTTTATGATTGTTTCTTCA
1194324 GC
131 GC
* *
1194326 TTTACCCCTGAACCTTTTTTAATTGAAAACAGAAGATACTATATCCATCCTTATCGGATAAAAAC
1 TTTACCCCTGAAACTTTTTTAATTGAAAACAGAAGAGACTATATCCATCCTTATCGGATAAAAAC
*
1194391 AACAACATATAGCTAACACCAAGAATTATGAGCAAAAGTGAAGCAAGTTTATGATTTTTTCTTCA
66 AACAACATATAGCTAACACCAAGAATTATGAGCAAAAGTGAAGCAAGTTTATGATTGTTTCTTCA
1194456 GC
131 GC
1194458 TTTACCCCTGAAACTTTTTTAATTGAAAACAGAAGAGACTATATCCATCCTTATCGGATAAAAAC
1 TTTACCCCTGAAACTTTTTTAATTGAAAACAGAAGAGACTATATCCATCCTTATCGGATAAAAAC
* *
1194523 AACAACATACAGCTAACACCAAAAATTATGAGCAAAAGTGAAGCAAGTTTATGATTG
66 AACAACATATAGCTAACACCAAGAATTATGAGCAAAAGTGAAGCAAGTTTATGATTG
1194580 AGTTCACCTT
Statistics
Matches: 241, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 241 1.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.29
Consensus pattern (132 bp):
TTTACCCCTGAAACTTTTTTAATTGAAAACAGAAGAGACTATATCCATCCTTATCGGATAAAAAC
AACAACATATAGCTAACACCAAGAATTATGAGCAAAAGTGAAGCAAGTTTATGATTGTTTCTTCA
GC
Found at i:1195324 original size:14 final size:14
Alignment explanation
Indices: 1195305--1195331 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1195295 TTTATGTTCG
1195305 TTCATTTGTTTATA
1 TTCATTTGTTTATA
1195319 TTCATTTGTTTAT
1 TTCATTTGTTTAT
1195332 GTTCTCCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (14 bp):
TTCATTTGTTTATA
Found at i:1195518 original size:14 final size:14
Alignment explanation
Indices: 1195492--1195522 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1195482 TTTTATGTGC
1195492 GTTCGTTTATGTTT
1 GTTCGTTTATGTTT
*
1195506 GTTCGTTTGTGTTT
1 GTTCGTTTATGTTT
1195520 GTT
1 GTT
1195523 TACGTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.06, G:0.26, T:0.65
Consensus pattern (14 bp):
GTTCGTTTATGTTT
Found at i:1195523 original size:24 final size:24
Alignment explanation
Indices: 1195496--1195549 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1195486 ATGTGCGTTC
*
1195496 GTTTATGTTTGTTCGTTTGTGTTT
1 GTTTATGTTTGTTCATTTGTGTTT
*
1195520 GTTTACGTTTGTTCATTTGTGTTT
1 GTTTATGTTTGTTCATTTGTGTTT
1195544 GTTTAT
1 GTTTAT
1195550 CTTTAAACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.07, C:0.06, G:0.22, T:0.65
Consensus pattern (24 bp):
GTTTATGTTTGTTCATTTGTGTTT
Found at i:1203524 original size:21 final size:21
Alignment explanation
Indices: 1203464--1203525 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
1203454 CCATGAACAG
* *
1203464 TGCTACATTGCATCGATGAAT
1 TGCTACAGTGCATCGATGCAT
1203485 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAT
*
1203506 TGCTACAGTGCACCGATGCA
1 TGCTACAGTGCATCGATGCA
1203526 CTAAAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAT
Found at i:1206484 original size:20 final size:21
Alignment explanation
Indices: 1206446--1206485 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1206436 AAACCATTAA
1206446 GGGGGGAATCGGTACTCCCTTG
1 GGGGGGAATCGGTA-TCCCTTG
1206468 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
1206486 CTGAGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTATCCCTTG
Found at i:1208593 original size:21 final size:20
Alignment explanation
Indices: 1208564--1208645 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 20
1208554 GAACCCGTCA
*
1208564 GGGGTATCGATTCCCTCAAG
1 GGGGAATCGATTCCCTCAAG
*
1208584 GAGGGAATCGGTTCCCAATCAAAG
1 G-GGGAATCGATTCCC--TC-AAG
* * *
1208608 GGGGAATCGGTTCCCTTATGG
1 GGGGAATCGATTCCCTCA-AG
*
1208629 GGGGTATCGATTCCCTC
1 GGGGAATCGATTCCCTC
1208646 TGCCAAATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
20 2 0.04
21 28 0.56
23 16 0.32
24 4 0.08
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGAATCGATTCCCTCAAG
Found at i:1215112 original size:20 final size:20
Alignment explanation
Indices: 1215075--1215113 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1215065 GCCAAACCAT
1215075 GGGGGAATCGGTACTCCCTTG
1 GGGGGAATCGGTA-TCCCTTG
1215096 GGGGGAAATCGGT-TCCCT
1 GGGGG-AATCGGTATCCCT
1215114 CTGAGCATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGGTATCCCTTG
Found at i:1218595 original size:8 final size:8
Alignment explanation
Indices: 1218582--1218622 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1218572 ATCATTTTCA
1218582 GAGAATTT
1 GAGAATTT
1218590 GAGAATTT
1 GAGAATTT
*
1218598 -AGAGTTT
1 GAGAATTT
*
1218605 GGGAATTT
1 GAGAATTT
1218613 GAGAATTT
1 GAGAATTT
1218621 GA
1 GA
1218623 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1219039 original size:34 final size:34
Alignment explanation
Indices: 1219000--1219107 Score: 139
Period size: 34 Copynumber: 3.1 Consensus size: 34
1218990 TAAGTTGAAA
*
1219000 TTTAATGTTAAATTTCGAA-AACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAA-TATAATTTATAT
* *
1219034 TTTAATTTTTAAATTTCGAATAATATTATTTTTTAT
1 TTTAA-TTTTAAATTTCGAATAATA-TAATTTATAT
*
1219070 TTT-ATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
1219103 TTTAA
1 TTTAA
1219108 AACATTTATC
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
33 11 0.17
34 25 0.38
35 16 0.25
36 13 0.20
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:1219674 original size:21 final size:21
Alignment explanation
Indices: 1219615--1219687 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
1219605 TATAGTATGA
*
1219615 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1219636 AA-CCTGGCGTGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
1219657 AACCCTACGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1219678 AACCCTGCGG
1 AACCCTGCGG
1219688 AGATGGCATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1221110 original size:16 final size:16
Alignment explanation
Indices: 1221089--1221119 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1221079 ACAAAAAAAT
*
1221089 TAATAATTCTAAATAA
1 TAATAATTATAAATAA
1221105 TAATAATTATAAATA
1 TAATAATTATAAATA
1221120 TTATTTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAATTATAAATAA
Found at i:1221463 original size:51 final size:51
Alignment explanation
Indices: 1221364--1221463 Score: 114
Period size: 51 Copynumber: 2.0 Consensus size: 51
1221354 TAATGGAAGG
* * * **
1221364 CGCGTTCCCGGGAATGCGCTTTCCACACGTGGCAGTCGAGCTGGCGAAAGA
1 CGCGTTCCCGGGAATGCGCCTTCCACACGTGGCAGTCCAACTAACGAAAGA
*
1221415 CGCG-TCCCTGGGGATGCGCCTTCCACACGTGGCA-TCCAACTCAACGAAA
1 CGCGTTCCC-GGGAATGCGCCTTCCACACGTGGCAGTCCAACT-AACGAAA
1221464 ACACGGGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
50 9 0.22
51 32 0.78
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (51 bp):
CGCGTTCCCGGGAATGCGCCTTCCACACGTGGCAGTCCAACTAACGAAAGA
Found at i:1222568 original size:21 final size:21
Alignment explanation
Indices: 1222515--1222568 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
1222505 GATTCTGACT
1222515 ATCGCATTGCGATTTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
*
1222536 ATTCGCATTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTTCCCAA
*
1222558 ATCGCAATGCG
1 ATCGCATTGCG
1222569 GTTACGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCCAA
Found at i:1222580 original size:20 final size:20
Alignment explanation
Indices: 1222555--1222603 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1222545 GCGATTTTCC
*
1222555 TAAATCGCAATGCGGTTACG
1 TAAATCACAATGCGGTTACG
1222575 TAAATCACAATGCGGTTACG
1 TAAATCACAATGCGGTTACG
1222595 TAAATCACA
1 TAAATCACA
1222604 TTACGATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
TAAATCACAATGCGGTTACG
Found at i:1223545 original size:24 final size:24
Alignment explanation
Indices: 1223494--1223547 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1223484 GTATTCGAAA
*
1223494 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1223518 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1223542 TTTGAT
1 TTTGAT
1223548 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1226085 original size:20 final size:19
Alignment explanation
Indices: 1226018--1226110 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 19
1226008 GGCATTCATT
1226018 TGACTATCGCAACACAGAAA
1 TGACTATCGCAACAC-GAAA
**
1226038 TGACGT-TCGCAATCATCTTAA
1 TGAC-TATCGCAA-CA-CGAAA
*
1226059 TGTCTATCGCAACACGGAAA
1 TGACTATCGCAACAC-GAAA
**
1226079 TGACTATCGCAATGCGAAA
1 TGACTATCGCAACACGAAA
**
1226098 TGAAAATCGCAAC
1 TGACTATCGCAAC
1226111 GAGGGAATCG
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
19 15 0.26
20 27 0.47
21 14 0.25
22 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (19 bp):
TGACTATCGCAACACGAAA
Found at i:1226106 original size:19 final size:18
Alignment explanation
Indices: 1226084--1226148 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
1226074 GGAAATGACT
1226084 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
1226103 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
1226117 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
1226136 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
1226149 TTTAGTTTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
14 7 0.19
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 19 0.53
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:1226209 original size:33 final size:33
Alignment explanation
Indices: 1226158--1226222 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1226148 ATTTAGTTTC
* * *
1226158 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTT
1 GCGTTGCGAATCTCTCGTTGCGATTTTCATTTT
1226191 GCGTTGCGAATCTCTCGTTGCGATTTTCATTT
1 GCGTTGCGAATCTCTCGTTGCGATTTTCATTT
1226223 CGCATTTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
GCGTTGCGAATCTCTCGTTGCGATTTTCATTTT
Found at i:1226359 original size:14 final size:14
Alignment explanation
Indices: 1226340--1226376 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1226330 CATCAATTAA
1226340 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1226354 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1226368 ACAAATCAA
1 ACAAATCAA
1226377 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1227810 original size:42 final size:42
Alignment explanation
Indices: 1227764--1227843 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1227754 CGATGACAGT
* * *
1227764 GGCCTCTTGAACGGTGGGAATGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAATGGACTCTCGAGGAATGATAGG
* * *
1227806 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAATGGACTCTCGAGGAATGA
1227844 CAGGCGATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAATGGACTCTCGAGGAATGATAGG
Found at i:1228284 original size:19 final size:19
Alignment explanation
Indices: 1228268--1228328 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
1228258 AAAAATGACT
1228268 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1228287 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1228301 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1228320 ATCGCAACG
1 ATCGCAACG
1228329 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1228310 original size:33 final size:33
Alignment explanation
Indices: 1228268--1228362 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
1228258 AAAAATGACT
* *
1228268 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1228301 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* **
1228334 ATCGCAACGTGAAACCAAAAATCGCAACG
1 ATCGCAACGCGAAA-TGAAAATCGCAACG
1228363 CGATTATAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 44 0.79
34 12 0.21
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1228435 original size:19 final size:19
Alignment explanation
Indices: 1228411--1228467 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
1228401 GCGATTCTCT
1228411 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1228430 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
1228450 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
1228468 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 18 0.50
20 18 0.50
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1228455 original size:20 final size:20
Alignment explanation
Indices: 1228404--1228465 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
1228394 TCGCGTTGCG
1228404 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1228424 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1228443 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1228463 ATT
1 ATT
1228466 TCAACCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1228757 original size:94 final size:94
Alignment explanation
Indices: 1228556--1228929 Score: 602
Period size: 94 Copynumber: 4.1 Consensus size: 94
1228546 ATGAATTGCA
* * *
1228556 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATAATAACTTCAGAGTATTAAAGAAT--ACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1228618 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1228647 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1228712 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1228741 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1228806 TTAGCAGAATTGGTAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1228835 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
1228895 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1228925 TTACT
1 TTACT
1228930 AAGCAATCTA
Statistics
Matches: 269, Mismatches: 9, Indels: 10
0.93 0.03 0.03
Matches are distributed among these distances:
90 40 0.15
91 4 0.01
92 50 0.19
93 19 0.07
94 156 0.58
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1230640 original size:40 final size:38
Alignment explanation
Indices: 1230596--1230708 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 38
1230586 TCTTTTGGTT
*
1230596 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGTG
1 GAAATGAAAATCGCAACG-GAGAATGAAAATCGCAACG-C
**
1230636 GAAATGACTATCGCAAC-GAG-A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGGAGAATGAAAATCGCAACGC
*
1230669 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACG-GAGAATGAAAATCGCAACGC
1230707 GA
1 GA
1230709 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
33 15 0.25
34 10 0.16
35 3 0.05
36 2 0.03
37 1 0.02
38 15 0.25
40 15 0.25
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGGAGAATGAAAATCGCAACGC
Found at i:1230682 original size:19 final size:19
Alignment explanation
Indices: 1230596--1230708 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
1230586 TCTTTTGGTT
*
1230596 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1230615 GAGAATGAAAATCGCAACGTG
1 GA-AATGAAAATCGCAACG-C
**
1230636 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1230653 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1230669 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1230688 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1230707 GA
1 GA
1230709 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 35 0.44
20 28 0.35
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1231093 original size:25 final size:26
Alignment explanation
Indices: 1231035--1231086 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
1231025 TTTCCATTTC
*
1231035 TGAATGATTGTGAGGGATTTCTGACCG
1 TGAATGGTTGTGAGGGATTTC-GACCG
1231062 TGAATGGTTGTGAGGGATTTC-ACCG
1 TGAATGGTTGTGAGGGATTTCGACCG
1231087 GCGATGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.17
27 20 0.83
ACGTcount: A:0.21, C:0.12, G:0.35, T:0.33
Consensus pattern (26 bp):
TGAATGGTTGTGAGGGATTTCGACCG
Found at i:1231334 original size:20 final size:20
Alignment explanation
Indices: 1231311--1231401 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
1231301 CGATAGTCAG
1231311 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1231331 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
* *
1231351 AATTCGCATTGTGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
1231372 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1231392 ATTCGCATTG
1 ATTCGCATTG
1231402 TGAATTAGGA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 42 0.71
21 17 0.29
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Done.