Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009350.1 Hibiscus syriacus cultivar Beakdansim tig00113145_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: 2139524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1708422 original size:15 final size:15
Alignment explanation
Indices: 1708390--1708418 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1708380 ATAAATACTG
1708390 GTAAAACTAAACTAA
1 GTAAAACTAAACTAA
1708405 GTAAAA-TAAACTAA
1 GTAAAACTAAACTAA
1708419 AGTAGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (15 bp):
GTAAAACTAAACTAA
Found at i:1709201 original size:17 final size:17
Alignment explanation
Indices: 1709179--1709230 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
1709169 AATCTACGTA
*
1709179 TGATAACTGTAAACATT
1 TGATAACTGTAAATATT
* *
1709196 TGATAACTGAAAATATC
1 TGATAACTGTAAATATT
*
1709213 TGATAACTATAAATATT
1 TGATAACTGTAAATATT
1709230 T
1 T
1709231 AGAATTCACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (17 bp):
TGATAACTGTAAATATT
Found at i:1712197 original size:21 final size:21
Alignment explanation
Indices: 1712173--1712212 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1712163 CTGTAACACC
*
1712173 CATTCCCCATATACCCTTCTG
1 CATTCCACATATACCCTTCTG
1712194 CATTCCACATATACCCTTC
1 CATTCCACATATACCCTTC
1712213 CGTACATGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.42, G:0.03, T:0.33
Consensus pattern (21 bp):
CATTCCACATATACCCTTCTG
Found at i:1712805 original size:48 final size:47
Alignment explanation
Indices: 1712712--1712873 Score: 191
Period size: 47 Copynumber: 3.4 Consensus size: 47
1712702 TATATTAACA
* * *
1712712 CATCCATTT-ATGCATTTTAATATACATGGCATCCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTAA-AT-TATGACATCCATTCATGCCTTAATG
* *
1712761 CATCTTTTTCATGCATTTTAAATTATGACATTCATTCATGCCTTAATG
1 CATC-CTTTCATGCATTTTAAATTATGACATCCATTCATGCCTTAATG
* * * *
1712809 CATCCTTTCATACATTTTCAATTATGGCATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAAATTATGACATCCATTCATGCCTTAATG
*
1712856 CATCCTTTCATGTATTTT
1 CATCCTTTCATGCATTTT
1712874 CATTTACGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
47 53 0.54
48 25 0.26
49 9 0.09
50 11 0.11
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTAAATTATGACATCCATTCATGCCTTAATG
Found at i:1713297 original size:20 final size:22
Alignment explanation
Indices: 1713265--1713321 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 22
1713255 GTTCCAGGCT
*
1713265 CTATAGTATCGATACTTCTAT-
1 CTATAGTACCGATACTTCTATA
1713286 CT-TAGTACCGATACTTCTATA
1 CTATAGTACCGATACTTCTATA
*
1713307 CTATGGTACCGATAC
1 CTATAGTACCGATAC
1713322 CCCCTTCCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 17 0.53
21 4 0.12
22 11 0.34
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (22 bp):
CTATAGTACCGATACTTCTATA
Found at i:1713433 original size:95 final size:96
Alignment explanation
Indices: 1713294--1713510 Score: 287
Period size: 95 Copynumber: 2.3 Consensus size: 96
1713284 ATCTTAGTAC
* * * ** * **
1713294 CGATACTTCTATACTATGGTACCGATACCCCCTTCCGGTATCGATACCGAAATTAGCTTCGATGT
1 CGATACTACTATAATATGGTATCGATACCCCCTTAAGGTATCGATACCAAAATTAGAATCGATGT
* * *
1713359 TT-TATGGTATCGTTACCCTTACCACGGTAT
66 TTACATGGTATCGATACCCTTACAACGGTAT
1713389 CGATACTACTATAATATGGTATCGATACCCCCTTAAGGTATCGATACCAAAATTAGAATCGATGT
1 CGATACTACTATAATATGGTATCGATACCCCCTTAAGGTATCGATACCAAAATTAGAATCGATGT
*
1713454 TTACATGGTATCGATACCCTTACAATGGTAT
66 TTACATGGTATCGATACCCTTACAACGGTAT
* *
1713485 CGATACTGC-ATCA-ATGGTATCGATAC
1 CGATACTACTATAATATGGTATCGATAC
1713511 TGATTGAATC
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
94 13 0.12
95 62 0.58
96 32 0.30
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (96 bp):
CGATACTACTATAATATGGTATCGATACCCCCTTAAGGTATCGATACCAAAATTAGAATCGATGT
TTACATGGTATCGATACCCTTACAACGGTAT
Found at i:1713512 original size:20 final size:21
Alignment explanation
Indices: 1713458--1713512 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1713448 CGATGTTTAC
* *
1713458 ATGGTATCGATAC-CCTTACA
1 ATGGTATCGATACTGCATACA
1713478 ATGGTATCGATACTGCAT-CA
1 ATGGTATCGATACTGCATACA
1713498 ATGGTATCGATACTG
1 ATGGTATCGATACTG
1713513 ATTGAATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATGGTATCGATACTGCATACA
Found at i:1719739 original size:27 final size:27
Alignment explanation
Indices: 1719709--1719787 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
1719699 TGCATCCTTC
1719709 CATGCATTTTCAATTATGGCATTCGTT
1 CATGCATTTTCAATTATGGCATTCGTT
* * *
1719736 CATGC--CTT-AA-TAT---ATCCTTT
1 CATGCATTTTCAATTATGGCATTCGTT
1719756 CATGCATTTTCAATTATGGCATTCGTT
1 CATGCATTTTCAATTATGGCATTCGTT
*
1719783 TATGC
1 CATGC
1719788 CTTAATGCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
20 10 0.26
22 2 0.05
23 5 0.13
24 5 0.13
25 2 0.05
27 14 0.37
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (27 bp):
CATGCATTTTCAATTATGGCATTCGTT
Found at i:1719741 original size:47 final size:47
Alignment explanation
Indices: 1719631--1719960 Score: 446
Period size: 47 Copynumber: 7.0 Consensus size: 47
1719621 TAATATGCAA
* * * *
1719631 GGCATCCTTTCATGCCTTAATGCATCCTTTTCATGCTTTTTTATTTAT
1 GGCATCCGTTCATGCCTTAATGCATCC-TTTCATGCATTTTCAATTAT
* *
1719679 GGCATCCGTTTATGCCTTAATGCATCCTTCCATGCATTTTCAATTAT
1 GGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
* **
1719726 GGCATTCGTTCATGCCTTAATATATCCTTTCATGCATTTTCAATTAT
1 GGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
* * * *
1719773 GGCATTCGTTTATGCCTTAATGCATCCTTTCACGCATTTTTAATTAT
1 GGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
** *
1719820 GGCATATGTTCATGCCTTAATGCATCTTTTCATGCA-TTTCAATTAT
1 GGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
* * *
1719866 GACATCCGTTCATACCTTAATGCATCCTTTCATGCATTTTCAATTAC
1 GGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
** *
1719913 ATCATCCGTTCATGCCTTAATGCATCCTTTCATTCATTTTCAATTAT
1 GGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
1719960 G
1 G
1719961 AATTTGATTT
Statistics
Matches: 247, Mismatches: 34, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
46 40 0.16
47 182 0.74
48 25 0.10
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (47 bp):
GGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
Found at i:1719907 original size:140 final size:141
Alignment explanation
Indices: 1719598--1719960 Score: 453
Period size: 140 Copynumber: 2.6 Consensus size: 141
1719588 TTTTCACGTA
* * *
1719598 TTAACACATCCATTT-ATGCATTTT-AATATGCAAGGCATCCTTTCATGCCTTAATGCATCCTTT
1 TTAATACATCC-TTTCATGCATTTTCAAT-TAC-A-GCATCCGTTCATGCCTTAATGCATCC-TT
* * * *
1719661 TCATGCTTTTTTATTTATGGCATCCGTTTATGCCTTAATGCATCCTTCCATGCATTTTCAATTAT
61 TCATGCATTTTTAATTATGGCATACGTTCATGCCTTAATGCATCCTTCCATGCATTTTCAATTAT
* * *
1719726 GGCATTCGTTCATGCC
126 GACATCCGTTCATACC
* ** * * *
1719742 TTAATATATCCTTTCATGCATTTTCAATTATGGCATTCGTTTATGCCTTAATGCATCCTTTCACG
1 TTAATACATCCTTTCATGCATTTTCAATTACAGCATCCGTTCATGCCTTAATGCATCCTTTCATG
* * *
1719807 CATTTTTAATTATGGCATATGTTCATGCCTTAATGCATCTTTTCATGCA-TTTCAATTATGACAT
66 CATTTTTAATTATGGCATACGTTCATGCCTTAATGCATCCTTCCATGCATTTTCAATTATGACAT
1719871 CCGTTCATACC
131 CCGTTCATACC
* * *
1719882 TTAATGCATCCTTTCATGCATTTTCAATTACATCATCCGTTCATGCCTTAATGCATCCTTTCATT
1 TTAATACATCCTTTCATGCATTTTCAATTACAGCATCCGTTCATGCCTTAATGCATCCTTTCATG
*
1719947 CATTTTCAATTATG
66 CATTTTTAATTATG
1719961 AATTTGATTT
Statistics
Matches: 188, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
140 92 0.49
141 48 0.26
142 23 0.12
143 3 0.02
144 19 0.10
145 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (141 bp):
TTAATACATCCTTTCATGCATTTTCAATTACAGCATCCGTTCATGCCTTAATGCATCCTTTCATG
CATTTTTAATTATGGCATACGTTCATGCCTTAATGCATCCTTCCATGCATTTTCAATTATGACAT
CCGTTCATACC
Found at i:1720376 original size:20 final size:20
Alignment explanation
Indices: 1720347--1720384 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1720337 TCAGGCTCCA
*
1720347 TAGTATCGATACTTCTATCC
1 TAGTAACGATACTTCTATCC
1720367 TAGTAACGATACTTCTAT
1 TAGTAACGATACTTCTAT
1720385 ACTATGGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (20 bp):
TAGTAACGATACTTCTATCC
Found at i:1720515 original size:95 final size:95
Alignment explanation
Indices: 1720373--1720569 Score: 263
Period size: 95 Copynumber: 2.1 Consensus size: 95
1720363 ATCCTAGTAA
* * * * *
1720373 CGATACTTCTATACTATGGTACCGATACCCCCTTCCAGTATCGATACCGAAATTAGCTTCGATGT
1 CGATACTACTATACTATAGTACCGATACCCCCTTCAAGTATCGATACCAAAATTAG-ATCGATGT
* *
1720438 TT-CATGGTGTCGATACCCTTACCACGGTAT
65 TTGCATGGTATCGATACCCTTACAACGGTAT
* *
1720468 TGATACTACTATACTATAGTACCGATACCCTCTT-AAGGTATCGATACCAAAATTAGATCGATGT
1 CGATACTACTATACTATAGTACCGATACCCCCTTCAA-GTATCGATACCAAAATTAGATCGATGT
* *
1720532 TTGCATGGTATTGATACCCTTACAATGGTAT
65 TTGCATGGTATCGATACCCTTACAACGGTAT
1720563 CGATACT
1 CGATACT
1720570 GCATCAACGA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
94 10 0.11
95 78 0.89
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (95 bp):
CGATACTACTATACTATAGTACCGATACCCCCTTCAAGTATCGATACCAAAATTAGATCGATGTT
TGCATGGTATCGATACCCTTACAACGGTAT
Found at i:1735867 original size:19 final size:20
Alignment explanation
Indices: 1735820--1735870 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1735810 GAAACCCCTT
**
1735820 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1735840 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1735859 TGAAGATACATG
1 TGAAAATACATG
1735871 TTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1739193 original size:19 final size:20
Alignment explanation
Indices: 1739150--1739200 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1739140 GAAACCCCTT
**
1739150 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1739170 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
1739189 TGAAAATACATG
1 TGAAAATACATG
1739201 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1749718 original size:45 final size:46
Alignment explanation
Indices: 1749669--1749769 Score: 141
Period size: 47 Copynumber: 2.2 Consensus size: 46
1749659 TATAAAATCT
1749669 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1749714 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT-AATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
1749761 CTTGCCATT
1 CTTACCATT
1749770 ATTTCGTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
45 10 0.20
47 39 0.80
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1749954 original size:38 final size:39
Alignment explanation
Indices: 1749899--1749978 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 39
1749889 ACCGTAGTGC
*
1749899 TACACATAAGGTCGTGCCCACCATAT-ACCTAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATAACCGAAGTGTAT
*
1749937 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATA-ACCGAAGTGTAT
1749977 TA
1 TA
1749979 TAAACCTGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 25 0.66
40 13 0.34
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (39 bp):
TACACATAAGGTCGTGCCCACCATATAACCGAAGTGTAT
Found at i:1754360 original size:29 final size:30
Alignment explanation
Indices: 1754320--1754384 Score: 123
Period size: 29 Copynumber: 2.2 Consensus size: 30
1754310 ACTTAGCGAG
1754320 ACATAATAATTTGAAGGAATTGTAATTCAT
1 ACATAATAATTTGAAGGAATTGTAATTCAT
1754350 A-ATAATAATTTGAAGGAATTGTAATTCAT
1 ACATAATAATTTGAAGGAATTGTAATTCAT
1754379 ACATAA
1 ACATAA
1754385 GTATAAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.85
30 5 0.15
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (30 bp):
ACATAATAATTTGAAGGAATTGTAATTCAT
Found at i:1755690 original size:45 final size:46
Alignment explanation
Indices: 1755641--1755741 Score: 141
Period size: 47 Copynumber: 2.2 Consensus size: 46
1755631 TATAAAATCT
1755641 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1755686 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT-AATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
1755733 CTTGCCATT
1 CTTACCATT
1755742 ATTCCGTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
45 10 0.20
47 39 0.80
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1759730 original size:12 final size:11
Alignment explanation
Indices: 1759706--1759816 Score: 75
Period size: 12 Copynumber: 9.2 Consensus size: 11
1759696 TGAAATATTT
1759706 TTTTTCATTTCTC
1 TTTTTC-TTT-TC
1759719 ATTTTT-TTTCTC
1 -TTTTTCTTT-TC
1759731 TTTTTCTTTTC
1 TTTTTCTTTTC
1759742 TTTTTCATTTTC
1 TTTTTC-TTTTC
1759754 ATTTTTTTCTTCTTC
1 ---TTTTTCTT-TTC
*
1759769 GTTTTCATTTTC
1 TTTTTC-TTTTC
1759781 TTTTTCTATTT-
1 TTTTTCT-TTTC
1759792 TTTTTCTTCTTC
1 TTTTTCTT-TTC
1759804 TGTTTT-TTTTC
1 T-TTTTCTTTTC
1759815 TT
1 TT
1759817 ATAATATATA
Statistics
Matches: 84, Mismatches: 2, Indels: 26
0.75 0.02 0.23
Matches are distributed among these distances:
10 2 0.02
11 27 0.32
12 33 0.39
13 6 0.07
14 7 0.08
15 9 0.11
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:1759740 original size:6 final size:6
Alignment explanation
Indices: 1759706--1759816 Score: 68
Period size: 6 Copynumber: 18.3 Consensus size: 6
1759696 TGAAATATTT
* * *
1759706 TTTTTC ATTTCTC ATTTTT- TTTCTC TTTTTC -TTTTC TTTTTC ATTTTCATT
1 TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTT--TC
* * * * *
1759757 TTTTTC TTCTTC GTTTTC ATTTTC TTTTTC TATTT- TTTTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
1759804 TGTTT- TTTTTC TT
1 TTTTTC TTTTTC TT
1759817 ATAATATATA
Statistics
Matches: 80, Mismatches: 17, Indels: 15
0.71 0.15 0.13
Matches are distributed among these distances:
5 17 0.21
6 44 0.55
7 14 0.17
8 4 0.05
9 1 0.01
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:1759761 original size:21 final size:21
Alignment explanation
Indices: 1759737--1759787 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1759727 TCTCTTTTTC
*
1759737 TTTTCTTTTTCATTTTCATTT
1 TTTTCTTCTTCATTTTCATTT
*
1759758 TTTTCTTCTTCGTTTTCATTT
1 TTTTCTTCTTCATTTTCATTT
1759779 TCTTT-TTCT
1 T-TTTCTTCT
1759788 ATTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTCTTCTTCATTTTCATTT
Found at i:1759780 original size:27 final size:25
Alignment explanation
Indices: 1759724--1759785 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 25
1759714 TTCTCATTTT
* *
1759724 TTTTCTCTTTTTCTTTTCTTTTTCA
1 TTTTCTTTTTTTCTTTTCGTTTTCA
1759749 TTTTCATTTTTTTCTTCTTCGTTTTCA
1 TTTTC-TTTTTTTCTT-TTCGTTTTCA
1759776 TTTTCTTTTT
1 TTTTCTTTTT
1759786 CTATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 5 0.15
26 14 0.42
27 14 0.42
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTCTTTTTTTCTTTTCGTTTTCA
Found at i:1759792 original size:34 final size:33
Alignment explanation
Indices: 1759703--1759816 Score: 110
Period size: 33 Copynumber: 3.4 Consensus size: 33
1759693 AAGTGAAATA
* *
1759703 TTTT-TTTTCATTTCTCATTTTTTTTCTCTTTTTC-
1 TTTTCTTTTC-TTTTTCA-TTTTTTT-TCTTCTTCG
*
1759737 TTTTCTTTTTCATTTTCA-TTTTTTTCTTCTTCG
1 TTTTC-TTTTCTTTTTCATTTTTTTTCTTCTTCG
1759770 TTTTCATTTTCTTTTTCTATTTTTTTTCTTCTTCTG
1 TTTTC-TTTTCTTTTTC-ATTTTTTTTCTTCTTC-G
1759806 TTTT-TTTTCTT
1 TTTTCTTTTCTT
1759817 ATAATATATA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
32 7 0.10
33 21 0.30
34 12 0.17
35 19 0.28
36 10 0.14
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (33 bp):
TTTTCTTTTCTTTTTCATTTTTTTTCTTCTTCG
Found at i:1759794 original size:21 final size:20
Alignment explanation
Indices: 1759723--1759794 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1759713 TTTCTCATTT
*
1759723 TTTTTCTCTTTTTC-TTTTC
1 TTTTTCTTTTTTTCATTTTC
*
1759742 TTTTTC--ATTTTCATTTT-
1 TTTTTCTTTTTTTCATTTTC
*
1759759 TTTCTTCTTCGTTTTCATTTTC
1 TTT-TTCTT-TTTTTCATTTTC
1759781 TTTTTCTATTTTTT
1 TTTTTCT-TTTTTT
1759795 TTCTTCTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
17 8 0.19
18 7 0.16
19 6 0.14
21 18 0.42
22 4 0.09
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTTTCTTTTTTTCATTTTC
Found at i:1759798 original size:17 final size:17
Alignment explanation
Indices: 1759701--1759816 Score: 89
Period size: 17 Copynumber: 6.8 Consensus size: 17
1759691 ACAAGTGAAA
*
1759701 TATTTTTTTTC-ATTTC
1 TATTTTTTTTCTTTTTC
1759717 TCATTTTTTTTCTCTTTTTC
1 T-A-TTTTTTT-TCTTTTTC
*
1759737 T-TTTCTTTTTCATTTTC
1 TATTT-TTTTTCTTTTTC
*
1759754 -A-TTTTTTTCTTCTTC
1 TATTTTTTTTCTTTTTC
*
1759769 GT-TTTCATTTTCTTTTTC
1 -TATTT-TTTTTCTTTTTC
*
1759787 TATTTTTTTTCTTCTTC
1 TATTTTTTTTCTTTTTC
*
1759804 TGTTTTTTTTCTT
1 TATTTTTTTTCTT
1759817 ATAATATATA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
15 10 0.12
16 3 0.04
17 36 0.45
18 24 0.30
19 2 0.03
20 5 0.06
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTTTTTTTCTTTTTC
Found at i:1759802 original size:38 final size:37
Alignment explanation
Indices: 1759706--1759816 Score: 110
Period size: 36 Copynumber: 3.1 Consensus size: 37
1759696 TGAAATATTT
*
1759706 TTTTTCATTTCTCATTTT-TT-TTC-TCTTTTTCTTTTC
1 TTTTTCATTT-T-ATTTTCTTCTTCTTCGTTTTCTTTTC
*
1759742 TTTTTCATTTTCATTTTTTTCTTCTTCGTTTTCATTTTC
1 TTTTTCATTTT-ATTTTCTTCTTCTTCGTTTTC-TTTTC
1759781 TTTTTCTATTTT-TTTTCTTCTTC-T-GTTTT-TTTTC
1 TTTTTC-ATTTTATTTTCTTCTTCTTCGTTTTCTTTTC
1759815 TT
1 TT
1759817 ATAATATATA
Statistics
Matches: 68, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
34 7 0.10
35 7 0.10
36 17 0.25
37 4 0.06
38 17 0.25
39 11 0.16
40 5 0.07
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (37 bp):
TTTTTCATTTTATTTTCTTCTTCTTCGTTTTCTTTTC
Found at i:1759831 original size:35 final size:34
Alignment explanation
Indices: 1759757--1759831 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 34
1759747 CATTTTCATT
* ** *
1759757 TTTTTCTTCTTCGTTTTCATTTTCTTTTTCTATTT
1 TTTTTCTTCTTCGTTTT-ATTTTCTTATAATATTA
1759792 TTTTTCTTCTTCTGTTTT-TTTTCTTATAATATATA
1 TTTTTCTTCTTC-GTTTTATTTTCTTATAATAT-TA
1759827 TTTTT
1 TTTTT
1759832 AGCTCTTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
34 11 0.32
35 18 0.53
36 5 0.15
ACGTcount: A:0.11, C:0.13, G:0.03, T:0.73
Consensus pattern (34 bp):
TTTTTCTTCTTCGTTTTATTTTCTTATAATATTA
Found at i:1762674 original size:47 final size:45
Alignment explanation
Indices: 1762599--1762724 Score: 137
Period size: 47 Copynumber: 2.8 Consensus size: 45
1762589 TATAAAATCT
1762599 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * * * *
1762644 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
* * * * *
1762691 CTTGCCA-TTATTCCGTAAACTCAAAAGCTTATTT
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTT
1762725 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
44 21 0.30
45 10 0.14
46 2 0.03
47 36 0.52
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTACCAAAATA
Found at i:1762873 original size:40 final size:40
Alignment explanation
Indices: 1762829--1762910 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1762819 ACCGTAGTGC
*
1762829 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1762869 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1762909 TA
1 TA
1762911 TAAATCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1764964 original size:112 final size:111
Alignment explanation
Indices: 1764763--1764971 Score: 310
Period size: 112 Copynumber: 1.9 Consensus size: 111
1764753 TCGAAGTGTC
* *
1764763 GAAATGTTCATTCACCTTTTATGAATACCATGAGTGGCACCTTTTATGCCGATAATGCATCGTTA
1 GAAATGGTAATTCACCTTTTATGAATACCATGAGTGGCACCTTTTATGCCGATAATGCATCGTTA
*
1764828 TACATTAAACAAAATCGATCGATAATCTTTCATACATGAAGTATGTT
66 TACATTAAACAAAATCAATCGATAA-CTTTCATACATGAAGTATGTT
* * * ** *
1764875 GAAATGGTAATTCACCTTTTATTAATACCATGGGTGGCACCTTTTATTCTTATAATGCATTGTTA
1 GAAATGGTAATTCACCTTTTATGAATACCATGAGTGGCACCTTTTATGCCGATAATGCATCGTTA
* *
1764940 TGCATTAAACAAAATCAATTGATAACTTTCAT
66 TACATTAAACAAAATCAATCGATAACTTTCAT
1764972 TAGTGGCACC
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
111 7 0.08
112 79 0.92
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (111 bp):
GAAATGGTAATTCACCTTTTATGAATACCATGAGTGGCACCTTTTATGCCGATAATGCATCGTTA
TACATTAAACAAAATCAATCGATAACTTTCATACATGAAGTATGTT
Found at i:1765002 original size:20 final size:18
Alignment explanation
Indices: 1764985--1765018 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1764975 TGGCACCTAT
1764985 TATG-CTCTCAATGCACC
1 TATGACTCTCAATGCACC
1765002 TATGACTCTCAATGCAC
1 TATGACTCTCAATGCAC
1765019 ATACAATCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.29
Consensus pattern (18 bp):
TATGACTCTCAATGCACC
Found at i:1765419 original size:34 final size:34
Alignment explanation
Indices: 1765376--1765445 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
1765366 CTACACAAGC
*
1765376 ATCCATTATGTACATATACCAAACCCATGTTAGT
1 ATCCATTATGTACACATACCAAACCCATGTTAGT
*
1765410 ATCCATTATGTACACATACCATACCCATGTTAGT
1 ATCCATTATGTACACATACCAAACCCATGTTAGT
1765444 AT
1 AT
1765446 ACTCTCTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33
Consensus pattern (34 bp):
ATCCATTATGTACACATACCAAACCCATGTTAGT
Found at i:1765700 original size:21 final size:21
Alignment explanation
Indices: 1765674--1765746 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
1765664 ACCCACACAA
1765674 TATCGATACTAATTGCATCAG
1 TATCGATACTAATTGCATCAG
*
1765695 TATCGATACTAATTGCATCAA
1 TATCGATACTAATTGCATCAG
* *
1765716 TATCGATACTAATTACATTAG
1 TATCGATACTAATTGCATCAG
1765737 TATCGATACT
1 TATCGATACT
1765747 GTTCATCCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (21 bp):
TATCGATACTAATTGCATCAG
Found at i:1768481 original size:47 final size:47
Alignment explanation
Indices: 1768414--1768576 Score: 245
Period size: 47 Copynumber: 3.5 Consensus size: 47
1768404 CATACACCCT
* * *
1768414 TTTCAAGCATTTCCAATTATGACATCCGTTCATGCCTTAATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* * * *
1768461 TTTCATGCAATTTAAATTATGGCATCTGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
* *
1768508 TTTCATGCATTTTCAATTATGGCATTCGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
1768555 TTTCATGCATTTTCAATTATGA
1 TTTCATGCATTTTCAATTATGA
1768577 AAATGATCTA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 104 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (47 bp):
TTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTTATGCATCC
Found at i:1768512 original size:20 final size:20
Alignment explanation
Indices: 1768489--1768562 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
1768479 ATGGCATCTG
1768489 TTCATGCCTTTATGCATCCT
1 TTCATGCCTTTATGCATCCT
* * *
1768509 TTCATGCATTTTCAATTATGGCATTCG
1 TTCATGC-----C-TTTAT-GCATCCT
1768536 TTCATGCCTTTATGCATCCT
1 TTCATGCCTTTATGCATCCT
1768556 TTCATGC
1 TTCATGC
1768563 ATTTTCAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
20 19 0.46
21 4 0.10
22 1 0.02
25 1 0.02
26 4 0.10
27 12 0.29
ACGTcount: A:0.18, C:0.26, G:0.12, T:0.45
Consensus pattern (20 bp):
TTCATGCCTTTATGCATCCT
Found at i:1769083 original size:21 final size:21
Alignment explanation
Indices: 1769059--1769098 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1769049 TTTTAGGAGG
* *
1769059 AGGAGGAATAAGAAGAAGAAA
1 AGGAAGAAGAAGAAGAAGAAA
*
1769080 AGGAAGAGGAAGAAGAAGA
1 AGGAAGAAGAAGAAGAAGA
1769099 GGAAGAAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.03
Consensus pattern (21 bp):
AGGAAGAAGAAGAAGAAGAAA
Found at i:1769091 original size:18 final size:18
Alignment explanation
Indices: 1769070--1769104 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1769060 GGAGGAATAA
1769070 GAAGAAGAAAAGGAAGAG
1 GAAGAAGAAAAGGAAGAG
*
1769088 GAAGAAGAAGAGGAAGA
1 GAAGAAGAAAAGGAAGA
1769105 AAAGAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAAAGGAAGAG
Found at i:1769097 original size:12 final size:12
Alignment explanation
Indices: 1769061--1769109 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
1769051 TTAGGAGGAG
*
1769061 GAGGAATAAGAA
1 GAGGAAGAAGAA
*
1769073 GAAGAA-AAGGAA
1 GAGGAAGAA-GAA
1769085 GAGGAAGAAGAA
1 GAGGAAGAAGAA
1769097 GAGGAAGAA-AA
1 GAGGAAGAAGAA
1769108 GA
1 GA
1769110 AGTAACCTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 6 0.18
12 25 0.76
13 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (12 bp):
GAGGAAGAAGAA
Found at i:1769098 original size:27 final size:27
Alignment explanation
Indices: 1769053--1769108 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1769043 GTGAGATTTT
* * *
1769053 AGGAGGAGGAGGAATAAGAAGAAGAAA
1 AGGAAGAGGAAGAAGAAGAAGAAGAAA
*
1769080 AGGAAGAGGAAGAAGAAGAGGAAGAAA
1 AGGAAGAGGAAGAAGAAGAAGAAGAAA
1769107 AG
1 AG
1769109 AAGTAACCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.41, T:0.02
Consensus pattern (27 bp):
AGGAAGAGGAAGAAGAAGAAGAAGAAA
Found at i:1773348 original size:14 final size:16
Alignment explanation
Indices: 1773312--1773343 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1773302 AGAATATACT
1773312 AATATTATAAACATAAC
1 AATATTATAAACA-AAC
1773329 AATATTATAAACAAA
1 AATATTATAAACAAA
1773344 ATATTTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (16 bp):
AATATTATAAACAAAC
Found at i:1774572 original size:10 final size:10
Alignment explanation
Indices: 1774559--1774614 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
1774549 AATTGGTAGA
1774559 AATTGGATTT
1 AATTGGATTT
*
1774569 AATTTGG-TTGA
1 AA-TTGGATT-T
1774580 AATTGGATTT
1 AATTGGATTT
* *
1774590 AATTTGATTGA
1 AATTGGATT-T
1774601 AATTGGATTT
1 AATTGGATTT
1774611 AATT
1 AATT
1774615 TGATGTTATG
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
10 20 0.56
11 16 0.44
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (10 bp):
AATTGGATTT
Found at i:1774617 original size:21 final size:21
Alignment explanation
Indices: 1774557--1774618 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
1774547 GAAATTGGTA
*
1774557 GAAATTGGATTTAATTTGGTT
1 GAAATTGGATTTAATTTGATT
1774578 GAAATTGGATTTAATTTGATT
1 GAAATTGGATTTAATTTGATT
1774599 GAAATTGGATTTAATTTGAT
1 GAAATTGGATTTAATTTGAT
1774619 GTTATGATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (21 bp):
GAAATTGGATTTAATTTGATT
Found at i:1777714 original size:17 final size:18
Alignment explanation
Indices: 1777681--1777715 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1777671 ATGCGGTTTG
1777681 AAATTTCAGCTCTCAACA
1 AAATTTCAGCTCTCAACA
*
1777699 AAATTTTAGC-CTCAACA
1 AAATTTCAGCTCTCAACA
1777716 TGTTTTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATTTCAGCTCTCAACA
Found at i:1778764 original size:21 final size:21
Alignment explanation
Indices: 1778717--1778764 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1778707 AGTCTTCAGT
1778717 TGGAGTGGGTTGTGCAAGAAC
1 TGGAGTGGGTTGTGCAAGAAC
** * *
1778738 AAGAGTGGGTTGTGTAGGAAC
1 TGGAGTGGGTTGTGCAAGAAC
1778759 TGGAGT
1 TGGAGT
1778765 TTGGCTTTGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.44, T:0.25
Consensus pattern (21 bp):
TGGAGTGGGTTGTGCAAGAAC
Found at i:1780260 original size:15 final size:16
Alignment explanation
Indices: 1780240--1780271 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1780230 CACCTTCAAC
1780240 AAATAAAG-AAAACAG
1 AAATAAAGTAAAACAG
1780255 AAATAAAGTAAAACAG
1 AAATAAAGTAAAACAG
1780271 A
1 A
1780272 GGTATGGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.72, C:0.06, G:0.12, T:0.09
Consensus pattern (16 bp):
AAATAAAGTAAAACAG
Found at i:1788924 original size:15 final size:15
Alignment explanation
Indices: 1788893--1788921 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1788883 ATAAATACAT
1788893 GTAAAACTAAACTAA
1 GTAAAACTAAACTAA
1788908 GTAAAA-TAAACTAA
1 GTAAAACTAAACTAA
1788922 AGTTGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.21
Consensus pattern (15 bp):
GTAAAACTAAACTAA
Found at i:1789709 original size:18 final size:17
Alignment explanation
Indices: 1789686--1789726 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1789676 AATCTATGTC
1789686 TGATAACTATAAAACATA
1 TGATAACTAT-AAACATA
* *
1789704 TGATAACTGTAAACATC
1 TGATAACTATAAACATA
1789721 TGATAA
1 TGATAA
1789727 TTGAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (17 bp):
TGATAACTATAAACATA
Found at i:1789752 original size:18 final size:18
Alignment explanation
Indices: 1789684--1789752 Score: 86
Period size: 18 Copynumber: 3.9 Consensus size: 18
1789674 TTAATCTATG
* *
1789684 TCTGATAACTATAAAACA
1 TCTGATAACTGTAAATCA
*
1789702 TATGATAACTGTAAA-CA
1 TCTGATAACTGTAAATCA
* *
1789719 TCTGATAATTGAAAATCA
1 TCTGATAACTGTAAATCA
1789737 TCTGATAACTGTAAAT
1 TCTGATAACTGTAAAT
1789753 ATTTAGAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.33
18 29 0.67
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (18 bp):
TCTGATAACTGTAAATCA
Found at i:1791094 original size:29 final size:28
Alignment explanation
Indices: 1791009--1791095 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
1790999 TAAAATAAAT
*
1791009 AACTTTTAAAATTAAAATTTAGGTC-CTTA
1 AACTTTTAAAATTATAATTTA-GTCAC-TA
* **
1791038 AACTTTTAAAATTTATACTTTAACCACTA
1 AACTTTTAAAA-TTATAATTTAGTCACTA
*
1791067 AACTTTTAAAACTTATATTTTAGTCACTA
1 AACTTTTAAAA-TTATAATTTAGTCACTA
1791096 GATAAATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 39 0.81
30 9 0.19
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (28 bp):
AACTTTTAAAATTATAATTTAGTCACTA
Found at i:1797878 original size:19 final size:19
Alignment explanation
Indices: 1797811--1797886 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
1797801 CTGAACCGAT
* *
1797811 CTGACCCGTTGAATTTGAC
1 CTGACCAGTTGACTTTGAC
* **
1797830 CCGACTTGTTGAC-TTGAC
1 CTGACCAGTTGACTTTGAC
1797848 TCT-ACCCA-TTGACTTTGAC
1 -CTGA-CCAGTTGACTTTGAC
*
1797867 CTGACCAGTTGACTTGGAC
1 CTGACCAGTTGACTTTGAC
1797886 C
1 C
1797887 AGAATTAACC
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
18 16 0.36
19 28 0.64
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (19 bp):
CTGACCAGTTGACTTTGAC
Found at i:1798390 original size:13 final size:13
Alignment explanation
Indices: 1798372--1798400 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1798362 TGTATGCAAG
1798372 ATAACTATTTTAA
1 ATAACTATTTTAA
1798385 ATAACTATTTTAA
1 ATAACTATTTTAA
1798398 ATA
1 ATA
1798401 TCTGTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAACTATTTTAA
Found at i:1803111 original size:27 final size:29
Alignment explanation
Indices: 1803072--1803131 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
1803062 GAAACTGTCT
* *
1803072 AAATAGAGACAAA-A-TTTGTTTCAAGGG
1 AAATAGACACAAAGATTTTGTTTCAAGAG
*
1803099 AAATAGACTCAAAGATTTTTGTTTCAAGAG
1 AAATAGACACAAAGA-TTTTGTTTCAAGAG
1803129 AAA
1 AAA
1803132 CTGTCTCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.41
28 1 0.04
30 15 0.56
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.28
Consensus pattern (29 bp):
AAATAGACACAAAGATTTTGTTTCAAGAG
Found at i:1803129 original size:66 final size:67
Alignment explanation
Indices: 1803050--1803196 Score: 242
Period size: 67 Copynumber: 2.2 Consensus size: 67
1803040 TCGTTAGGGA
* *
1803050 TTTGTTTCAAGAGAAACTGTCTAAATAGAGACAAAA-TTTGTTTCAAGGGAAATAGACTCAAAGA
1 TTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGA
1803114 TT
66 TT
* * *
1803116 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATACTCAAATA
1 TTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGA
1803181 TT
66 TT
1803183 TTTGTTTCAAGAGA
1 TTTGTTTCAAGAGA
1803197 GACAAGATTT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 34 0.45
67 41 0.55
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (67 bp):
TTTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGA
TT
Found at i:1803244 original size:50 final size:52
Alignment explanation
Indices: 1803137--1803246 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 52
1803127 AGAAACTGTC
* **
1803137 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATACTCAAATATTTTTGTT
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATACTCAAAGATTGATGTT
* *
1803189 TCAAGAGAGACAAGA-TTTGTTTGAAGGGAAACGAT-CTCAAAGA-TGATGTT
1 TCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-ATACTCAAAGATTGATGTT
1803239 TCAAGAGA
1 TCAAGAGA
1803247 AACTGTCTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
50 13 0.25
51 23 0.44
52 16 0.31
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (52 bp):
TCAAGAGAGACAAAACTTTGTTTCAAGGGAAACATACTCAAAGATTGATGTT
Found at i:1803262 original size:117 final size:118
Alignment explanation
Indices: 1803076--1803313 Score: 363
Period size: 117 Copynumber: 2.0 Consensus size: 118
1803066 CTGTCTAAAT
**
1803076 AGAGACAAAATTTGTTTCAAGGGAAATAGACTCAAAGATTTTTGTTTCAAGAGAAACTGTCTCAA
1 AGAGACAAAATTTGTTTCAAGGGAAATAGACTCAAAGATTGATGTTTCAAGAGAAACTGTCTCAA
* * *
1803141 GAGAGACAAAACTTTGTTTCAAGGGAAACATACTCAAATATTTTTGTTTCAAG
66 GAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATCTTTGTTTCAAG
* * *
1803194 AGAGACAAGATTTGTTTGAAGGGAAA-CGATCTCAAAGA-TGATGTTTCAAGAGAAACTGTCTCA
1 AGAGACAAAATTTGTTTCAAGGGAAATAGA-CTCAAAGATTGATGTTTCAAGAGAAACTGTCTCA
* *
1803257 AGAGAGACAAAATTTTGTTTTAAGGGAAACAAACTCAAAGATCTTTGTTTCAAG
65 AGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATCTTTGTTTCAAG
1803311 AGA
1 AGA
1803314 AATTGTCTCA
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
117 77 0.71
118 32 0.29
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (118 bp):
AGAGACAAAATTTGTTTCAAGGGAAATAGACTCAAAGATTGATGTTTCAAGAGAAACTGTCTCAA
GAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATCTTTGTTTCAAG
Found at i:1803276 original size:37 final size:36
Alignment explanation
Indices: 1803235--1803352 Score: 95
Period size: 37 Copynumber: 3.4 Consensus size: 36
1803225 TCAAAGATGA
1803235 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAATTT
* * *** *
1803272 TGTTTTAAGGGAAACAAACTCAA-AGA-TC----TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATTT
*
1803302 TGTTTCAAGAGAAATTGTCTCAAGAGAGACTAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAATTT
* *
1803339 CGTTTCAAGGGAAA
1 TGTTTCAAGAGAAA
1803353 TAATTTCCAA
Statistics
Matches: 59, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
30 19 0.32
31 3 0.05
32 1 0.02
35 1 0.02
36 3 0.05
37 32 0.54
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATTT
Found at i:1803294 original size:66 final size:67
Alignment explanation
Indices: 1803189--1803352 Score: 224
Period size: 67 Copynumber: 2.5 Consensus size: 67
1803179 TATTTTTGTT
* * * *
1803189 TCAAGAGAGACAAGA-TTTGTTTGAAGGGAAACGATCTCAAAGAT-GATGTTTCAAGAGAAACTG
1 TCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAAACTCAAAGATCGATGTTTCAAGAGAAACTG
1803252 TC
66 TC
* ** *
1803254 TCAAGAGAGACAAAATTTTGTTTTAAGGGAAACAAACTCAAAGATCTTTGTTTCAAGAGAAATTG
1 TCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAAACTCAAAGATCGATGTTTCAAGAGAAACTG
1803319 TC
66 TC
* *
1803321 TCAAGAGAGACTAAATTTCGTTTCAAGGGAAA
1 TCAAGAGAGACAAAATTTTGTTTCAAGGGAAA
1803353 TAATTTCCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 14 0.16
66 26 0.30
67 47 0.54
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (67 bp):
TCAAGAGAGACAAAATTTTGTTTCAAGGGAAACAAACTCAAAGATCGATGTTTCAAGAGAAACTG
TC
Found at i:1803814 original size:37 final size:37
Alignment explanation
Indices: 1803647--1803821 Score: 185
Period size: 37 Copynumber: 4.8 Consensus size: 37
1803637 CATCTCAAAG
* * **
1803647 GAAAAATGTCTCAAGCGAGATGAAATTT-GTTTT-GA
1 GAAAACTGTCTCAAGTGAGACAAAATTTGGTTTTAGA
* * * *
1803682 TAGAAATTATCTCAAGTAAGACAAAATTTGGTTTTAGA
1 GA-AAACTGTCTCAAGTGAGACAAAATTTGGTTTTAGA
*
1803720 GAAAACTGTCTCAAGTTAGACAAAATTTGGTTTTAGA
1 GAAAACTGTCTCAAGTGAGACAAAATTTGGTTTTAGA
*
1803757 GAAAACTGTCTCAAGTGAGACAAAATTTGTTTTTCA-A
1 GAAAACTGTCTCAAGTGAGACAAAATTTGGTTTT-AGA
* * * *
1803794 GAAAATTGTCTCGAGCGAGACAACATTT
1 GAAAACTGTCTCAAGTGAGACAAAATTT
1803822 TGTTCTGAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
35 1 0.01
36 20 0.17
37 94 0.79
38 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.31
Consensus pattern (37 bp):
GAAAACTGTCTCAAGTGAGACAAAATTTGGTTTTAGA
Found at i:1803815 original size:74 final size:73
Alignment explanation
Indices: 1803647--1803844 Score: 202
Period size: 74 Copynumber: 2.7 Consensus size: 73
1803637 CATCTCAAAG
** * *
1803647 GAAAAATGTCTCAAGCGAGATGAAATTTGTTTTGATAGAAATTATCTCAAGTAAGACAAAATTTG
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAACTATCTCAAGTAAGACAAAATTTG
1803712 GTTTTAGA
66 GTTTTAGA
* ** * *
1803720 GAAAACTGTCTCAAGTTAGACAAAATTTGGTTTT-AGAGAAAACTGTCTCAAGTGAGACAAAATT
1 GAAAAATGTCTCAAGCGAGACAAAATTT-GTTTTGAGAG-AAACTATCTCAAGTAAGACAAAATT
*
1803784 TGTTTTTCA-A
64 TGGTTTT-AGA
* * * * * *
1803794 GAAAATTGTCTCGAGCGAGACAACATTTTGTTCTGAAAGAAACAATCTCAA
1 GAAAAATGTCTCAAGCGAGACAA-AATTTGTTTTGAGAGAAACTATCTCAA
1803845 AAGTGACTGA
Statistics
Matches: 101, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
73 26 0.26
74 67 0.66
75 8 0.08
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (73 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTGAGAGAAACTATCTCAAGTAAGACAAAATTTG
GTTTTAGA
Found at i:1806208 original size:22 final size:22
Alignment explanation
Indices: 1806178--1806219 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1806168 CTTTTTTCTC
1806178 TTTTCTCTTTGTTT-TTCTTTGA
1 TTTTCTC-TTGTTTATTCTTTGA
*
1806200 TTTTTTCTTGTTTATTCTTT
1 TTTTCTCTTGTTTATTCTTT
1806220 TAACTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (22 bp):
TTTTCTCTTGTTTATTCTTTGA
Found at i:1809779 original size:3 final size:3
Alignment explanation
Indices: 1809771--1809800 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1809761 TAAAAGAACT
1809771 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1809801 TAAATTGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1814742 original size:25 final size:25
Alignment explanation
Indices: 1814648--1814744 Score: 162
Period size: 25 Copynumber: 3.9 Consensus size: 25
1814638 ATTGAGGGGA
*
1814648 TTAGGG-TTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
1814672 TTAGGGTTTGAAACCCTAATC-GATT
1 TTAGGGTTTGAAACCCTAATCTG-TT
1814697 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
1814722 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
1814745 ATGGGTTGGG
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
24 7 0.10
25 61 0.88
26 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:1814868 original size:3 final size:3
Alignment explanation
Indices: 1814860--1814941 Score: 146
Period size: 3 Copynumber: 27.3 Consensus size: 3
1814850 ATGTAAATTA
1814860 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1814908 AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1814942 TACAAAAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1815333 original size:41 final size:42
Alignment explanation
Indices: 1815276--1815600 Score: 225
Period size: 46 Copynumber: 7.6 Consensus size: 42
1815266 TATCTATGGT
*
1815276 TGACATGGCTCCTACGTGATGAGGAGATCT-G-ATCTGGGGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGCATCTGGGG-A
* * * *
1815317 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGG-CATCT---GGGGA
* * * * ** *
1815363 TAACACGGTTCCTACGTGATGAGGACGGT-TGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAGGA-GATCTGG-CATCTGGGGA
1815406 TGACACGGCTCCTACGTGATGAGGAGATCTGG--TCTGGGGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGCATCTGGGG-A
* * * * *
1815447 TGACACGGCTCATACGTGATGAAGAGTTTTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGG-CATCT---GGGGA
* * * * ** *
1815493 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAGGA-GATCTGG-CATCTGGGGA
*
1815536 TGACACGGCTCCTACGTGATGAGGAGATCTGG--TCTGGTGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGCATCTGGGGA
* *
1815576 TGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGA
1815601 CGGCTGGCCA
Statistics
Matches: 219, Mismatches: 48, Indels: 35
0.73 0.16 0.12
Matches are distributed among these distances:
40 32 0.15
41 54 0.25
42 4 0.02
43 55 0.25
44 7 0.03
46 58 0.26
47 9 0.04
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (42 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGCATCTGGGGA
Found at i:1815396 original size:130 final size:129
Alignment explanation
Indices: 1815141--1815597 Score: 648
Period size: 130 Copynumber: 3.5 Consensus size: 129
1815131 CGTCTAAGGG
* * * *
1815141 TGACATGGTTCCTACGTGATGAGGAAATCT-AGTC-GAGGGATGACACTGCTCATACATGATGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGA-TCTG-GGGATGACACGGCTCATACATGATGAA
* * * *
1815204 GAGTTATTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTATGTGATGGGGACGACTGGTTAT
64 GAGTT-TTGGCCATC--TA--AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT
1815269 CTATGGT
123 CTATGGT
* *
1815276 TGACATGGCTCCTACGTGATGAGGAGATCTGATCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGG-ATGACACGGCTCATACATGATGAAG
* *
1815341 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTATGGT
65 AGTTTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* *
1815406 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGG-ATGACACGGCTCATACATGATGAAG
1815471 AGTTTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
65 AGTTTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * *
1815536 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGA
1815598 GGACGGCTGG
Statistics
Matches: 301, Mismatches: 18, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
129 20 0.07
130 207 0.69
131 2 0.01
133 2 0.01
135 41 0.14
136 29 0.10
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACATGATGAAGA
GTTTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:1815423 original size:43 final size:42
Alignment explanation
Indices: 1815242--1815568 Score: 207
Period size: 43 Copynumber: 7.5 Consensus size: 42
1815232 ATAACTCGGT
* * * *
1815242 TCCTATGTGATGGGGACGACTGGTTATCTATGGTTGACATGGC
1 TCCTACGTGATGAGGA-GATTGGTTATCTATGGTTGACACGGC
** *
1815285 TCCTACGTGATGAGGAGATCT-G--ATCTGGGGAATGACACGGC
1 TCCTACGTGATGAGGAGAT-TGGTTATCTATGG-TTGACACGGC
* * * ** * * *
1815326 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAGAT-TGGTTATCT-ATGGT--TGACACGGC
*
1815372 TCCTACGTGATGAGGACGGTTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATTGGTTATCTATGGTTGACACGGC
** *
1815415 TCCTACGTGATGAGGAGATCTGG---TCTGGGGAATGACACGGC
1 TCCTACGTGATGAGGAGAT-TGGTTATCTATGG-TTGACACGGC
* * * ** * * *
1815456 TCATACGTGATGAAGAGTTTTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAGGAG-ATTGGTTATCT-ATGGT--TGACACGGC
**
1815502 TCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAGGA-GATTGGTTATCTATGGTTGACACGGC
1815545 TCCTACGTGATGAGGAGATCTGGT
1 TCCTACGTGATGAGGAGAT-TGGT
1815569 CTGGTGATGA
Statistics
Matches: 218, Mismatches: 46, Indels: 40
0.72 0.15 0.13
Matches are distributed among these distances:
40 11 0.05
41 53 0.24
42 8 0.04
43 68 0.31
44 7 0.03
45 12 0.06
46 56 0.26
47 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (42 bp):
TCCTACGTGATGAGGAGATTGGTTATCTATGGTTGACACGGC
Found at i:1815707 original size:28 final size:28
Alignment explanation
Indices: 1815646--1815707 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1815636 AAACCAAATT
1815646 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* * *
1815674 AGAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
1815702 AAAGAT
1 AAAGAT
1815708 GATATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.93
29 2 0.07
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:1815895 original size:37 final size:38
Alignment explanation
Indices: 1815845--1815933 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 38
1815835 AAGATTAGTG
* *
1815845 TTTCGAGAGAAACAAACTCAAAGA-TGTT-TTT-TTTTT
1 TTTCAAGAAAAACAAACTCAAAGACT-TTGTTTGTTTTT
* *
1815881 GTTTTAAGAAAAACATACTCAAAGACTTTGTTTGTTTTT
1 -TTTCAAGAAAAACAAACTCAAAGACTTTGTTTGTTTTT
1815920 TTTCAAGAAAAACA
1 TTTCAAGAAAAACA
1815934 TATTCAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
37 22 0.50
38 17 0.39
39 5 0.11
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.39
Consensus pattern (38 bp):
TTTCAAGAAAAACAAACTCAAAGACTTTGTTTGTTTTT
Found at i:1815934 original size:38 final size:37
Alignment explanation
Indices: 1815843--1815946 Score: 113
Period size: 38 Copynumber: 2.8 Consensus size: 37
1815833 CAAAGATTAG
* * *
1815843 TGTTTCGAGAGAAACAAACTCAAAGATGTTTTTTTTT
1 TGTTTCAAGAAAAACATACTCAAAGATGTTTTTTTTT
*
1815880 TGTTTTAAGAAAAACATACTCAAAGACT-TTGTTTGTTTT
1 TGTTTCAAGAAAAACATACTCAAAGA-TGTT-TTT-TTTT
*
1815919 T-TTTCAAGAAAAACATATTCAAATGATG
1 TGTTTCAAGAAAAACATACTCAAA-GATG
1815947 GTAAAATTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
37 24 0.43
38 25 0.45
39 7 0.12
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (37 bp):
TGTTTCAAGAAAAACATACTCAAAGATGTTTTTTTTT
Found at i:1816249 original size:15 final size:15
Alignment explanation
Indices: 1816225--1816268 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1816215 AAGATGATCT
*
1816225 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
1816240 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
1816255 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
1816269 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:1816321 original size:31 final size:30
Alignment explanation
Indices: 1816257--1816331 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
1816247 AGAGAAAATG
*
1816257 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
1816288 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
1816319 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
1816332 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:1816497 original size:63 final size:63
Alignment explanation
Indices: 1816425--1816549 Score: 180
Period size: 64 Copynumber: 2.0 Consensus size: 63
1816415 AATGTGGGTA
* * *
1816425 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
* * *
1816487 TTTTCCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTT-CAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
1816550 GGATCCCATC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 4 0.07
63 13 0.24
64 38 0.69
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:1816785 original size:37 final size:36
Alignment explanation
Indices: 1816744--1816856 Score: 112
Period size: 37 Copynumber: 3.2 Consensus size: 36
1816734 GAGAAACTGT
1816744 CTCAAGAGATACAAAATTTTGTTTCCAAAGAAACAAA
1 CTCAA-AGATACAAAATTTTGTTTCCAAAGAAACAAA
** * *
1816781 CTCAAAGAT------TTTTGTTTTAAAAGAAACTAT
1 CTCAAAGATACAAAATTTTGTTTCCAAAGAAACAAA
* *
1816811 CTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAA
1 CTCAA-AGATACAAAATTTTGTTTCCAAAGAAACAAA
1816848 CTCAAAGAT
1 CTCAAAGAT
1816857 TTTTTTCAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
30 21 0.37
31 3 0.05
36 7 0.12
37 26 0.46
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (36 bp):
CTCAAAGATACAAAATTTTGTTTCCAAAGAAACAAA
Found at i:1816818 original size:67 final size:65
Alignment explanation
Indices: 1816717--1816880 Score: 238
Period size: 67 Copynumber: 2.5 Consensus size: 65
1816707 ATGAACATAT
** * * *
1816717 TCAAAGATTTAATTCAAGAGAAACTGTCTCAAGAGATACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTTTTTCAAAAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
* *
1816782 TCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1816847 AC
64 AC
*
1816849 TCAAAGATTTTTTTCAAAAGAAACAATCTCAA
1 TCAAAGATTTTTTTCAAAAGAAACTATCTCAA
1816881 AGATTTTTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 25 0.29
66 7 0.08
67 55 0.63
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (65 bp):
TCAAAGATTTTTTTCAAAAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
Found at i:1816887 original size:27 final size:28
Alignment explanation
Indices: 1816822--1816890 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
1816812 TTAAGAGAGA
*
1816822 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
1816850 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
1816878 CAAAGATTTTTTT
1 CAAAGATTTTTTT
1816891 TTCACAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:1817006 original size:26 final size:25
Alignment explanation
Indices: 1816977--1817088 Score: 89
Period size: 29 Copynumber: 4.1 Consensus size: 25
1816967 CAAAACTTTG
* *
1816977 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
1817003 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
1817030 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGA--TT
* *
1817059 TATTCTAAAGGAACAAACTCAAAGATT
1 T-TTCAAAAGAAAC-AACTCAAAGATT
1817086 TTT
1 TTT
1817089 TTCAAGAGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
25 8 0.11
26 14 0.19
27 8 0.11
28 11 0.15
29 33 0.45
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:1817060 original size:29 final size:29
Alignment explanation
Indices: 1816992--1817243 Score: 144
Period size: 29 Copynumber: 8.7 Consensus size: 29
1816982 AAATAAATAG
*
1816992 ACTCAAAGA--TTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
1817017 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
1817046 ACTCCAAGATTTTTATTCTAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
1817075 ACTCAAAGATTTTT-TTCAAGAGAAACTGTCTCAAGA
1 ACTCAAAGATTTTTATTCAAAAGGAA------C-A-A
** * ** *** * ** * *
1817111 GAGACAAAAAAATCGTTTTAAAATAAATAG
1 -ACTCAAAGATTTTTATTCAAAAGGAACAA
*
1817141 ACTCAAAGA--TTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
1817166 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
1817195 ACTCCAAGATTTTTATTCTAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
1817224 ACTCAAAGATTTTTTTTCAA
1 ACTCAAAGATTTTTATTCAA
1817244 GAGAAACTGT
Statistics
Matches: 173, Mismatches: 36, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
25 18 0.10
26 9 0.05
27 7 0.04
28 30 0.17
29 90 0.52
31 1 0.01
34 1 0.01
35 1 0.01
36 1 0.01
37 7 0.04
38 8 0.05
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:1817153 original size:149 final size:150
Alignment explanation
Indices: 1816948--1817283 Score: 613
Period size: 149 Copynumber: 2.3 Consensus size: 150
1816938 GATTTTTCAT
* ** * *
1816948 GAAATTGTCTCAAGAGAGAC-AAAACTTTGTTTCAAAATAAATAGACTCAAAGATTTTTCAAAAG
1 GAAACTGTCTCAAGAGAGACAAAAAAATCGTTTTAAAATAAATAGACTCAAAGATTTTTCAAAAG
1817012 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCTAAAGGAACAAAC
66 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCTAAAGGAACAAAC
1817077 TCAAAGA-TTTTTTTCAAGA
131 TCAAAGATTTTTTTTCAAGA
1817096 GAAACTGTCTCAAGAGAGACAAAAAAATCGTTTTAAAATAAATAGACTCAAAGATTTTTCAAAAG
1 GAAACTGTCTCAAGAGAGACAAAAAAATCGTTTTAAAATAAATAGACTCAAAGATTTTTCAAAAG
1817161 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCTAAAGGAACAAAC
66 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCTAAAGGAACAAAC
1817226 TCAAAGATTTTTTTTCAAGA
131 TCAAAGATTTTTTTTCAAGA
1817246 GAAACTGTCTCAAGAGAGACAAAAAAATCGTTTTAAAA
1 GAAACTGTCTCAAGAGAGACAAAAAAATCGTTTTAAAA
1817284 GATTCAAATA
Statistics
Matches: 181, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 19 0.10
149 112 0.62
150 50 0.28
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (150 bp):
GAAACTGTCTCAAGAGAGACAAAAAAATCGTTTTAAAATAAATAGACTCAAAGATTTTTCAAAAG
AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCTAAAGGAACAAAC
TCAAAGATTTTTTTTCAAGA
Found at i:1817608 original size:36 final size:34
Alignment explanation
Indices: 1817492--1817627 Score: 121
Period size: 33 Copynumber: 3.9 Consensus size: 34
1817482 AGAAAATGAT
* * * * *
1817492 GTCTCAAGCGAGACGAAATTTGCTTTAAGATATA
1 GTCTCAAACGAGACAAAATTTGTTTTTAGAAATA
* * * *
1817526 GTCTCAAATGAGACAAAGTTTCTTTTT-GATATA
1 GTCTCAAACGAGACAAAATTTGTTTTTAGAAATA
* *
1817559 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAACGAGACAAAATTTGTTTTT--AGAAATA
* *
1817595 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 GTCTCAAACGAGACAAAATTTGTTTTT-AGAAA
1817628 CGATCTCAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
33 31 0.36
34 20 0.24
35 6 0.07
36 28 0.33
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (34 bp):
GTCTCAAACGAGACAAAATTTGTTTTTAGAAATA
Found at i:1817615 original size:69 final size:67
Alignment explanation
Indices: 1817492--1817623 Score: 165
Period size: 69 Copynumber: 1.9 Consensus size: 67
1817482 AGAAAATGAT
* * * *
1817492 GTCTCAAGCGAGACGAAATTTGCTTTAAGATATAGTCTCAAATGAGACAAAGTTTCTTTTTGATA
1 GTCTCAAACGAGACAAAATTTGCTTTAAGAAATAGTCTCAAACGAGACAAAGTTTCTTTTTGATA
1817557 TA
66 TA
* * * * *
1817559 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTTGA
1 GTCTCAAACGAGACAAAATTTG-CTTTA-AGAAATAGTCTCAAACGAGACAAAGTTTCTTTTTGA
1817624 GAAACGATCT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 19 0.35
68 4 0.07
69 31 0.57
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (67 bp):
GTCTCAAACGAGACAAAATTTGCTTTAAGAAATAGTCTCAAACGAGACAAAGTTTCTTTTTGATA
TA
Found at i:1817635 original size:35 final size:33
Alignment explanation
Indices: 1817525--1817642 Score: 128
Period size: 33 Copynumber: 3.4 Consensus size: 33
1817515 TTTAAGATAT
* * * *
1817525 AGTCTCAAATGAGACAAAGTTTCTTTTTGATAT
1 AGTCTCAAGTGAGACAAAGTTTGTTTTTGAGAA
* *
1817558 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAA
1 AGTCTCAAGTGAGACAAAGTTTGTTTTT-GAGAA
*
1817592 ATTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAA
1 A--GTCTCAAGTGAGACAAAGTTTGTTTTTGAGAA
1817627 ACGATCTCAAGTGAGA
1 A-G-TCTCAAGTGAGA
1817643 TCAACTTTGT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
33 26 0.36
34 5 0.07
35 17 0.24
36 24 0.33
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (33 bp):
AGTCTCAAGTGAGACAAAGTTTGTTTTTGAGAA
Found at i:1817705 original size:101 final size:99
Alignment explanation
Indices: 1817595--1817822 Score: 250
Period size: 101 Copynumber: 2.3 Consensus size: 99
1817585 TAGAGAAATT
* *
1817595 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AGAAAC--GATCTCAA-GTGAGATCAACTTTGTTTA
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACATCT-AAGGTGAGAT----TTTGTTTA
* *
1817656 -ATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
60 TA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
1817696 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTTTGTTTTTAGT
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAAC-ATCTAAGGTGAGATTTTGTTTATAGT
* * *
1817761 GAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
64 GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
1817797 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
1817823 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
100 5 0.05
101 85 0.77
102 7 0.06
104 2 0.02
105 11 0.10
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (99 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACATCTAAGGTGAGATTTTGTTTATAGTGA
AACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:1817985 original size:36 final size:36
Alignment explanation
Indices: 1817945--1818043 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
1817935 AAAGGGAAAA
**
1817945 TGTCTCAAATGAGACAAAATTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
1817981 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
1818017 TGTCTCAAGCGAGACAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTT
1818044 TAGAAAAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTGAAATAAAT
Found at i:1818408 original size:4 final size:4
Alignment explanation
Indices: 1818399--1818458 Score: 84
Period size: 4 Copynumber: 15.0 Consensus size: 4
1818389 TTTATGTATC
* * * *
1818399 ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ACGT ATGT ATAT ACGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1818447 ATGT ATGT ATGT
1 ATGT ATGT ATGT
1818459 GTATACTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:1819657 original size:12 final size:11
Alignment explanation
Indices: 1819635--1819757 Score: 77
Period size: 12 Copynumber: 10.5 Consensus size: 11
1819625 TTTGTCCTCT
1819635 TTTTGTTCTTTG
1 TTTT-TTCTTTG
1819647 CTTTTTTCTTTG
1 -TTTTTTCTTTG
* *
1819659 ACTTTTGCTTTG
1 -TTTTTTCTTTG
*
1819671 ATTTTTCTTTG
1 TTTTTTCTTTG
*
1819682 TTTTTGCTTTG
1 TTTTTTCTTTG
*
1819693 ATTTTTT-TTCTC
1 -TTTTTTCTT-TG
* **
1819705 TCTGCTCTTTG
1 TTTTTTCTTTG
1819716 TTTTTTTCTTTG
1 -TTTTTTCTTTG
1819728 CTCTTTTCTCTTTG
1 -T-TTTT-TCTTTG
*
1819742 ATTTTTCTTTG
1 TTTTTTCTTTG
1819753 TTTTT
1 TTTTT
1819758 GATTGGATCT
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
11 34 0.40
12 37 0.44
13 8 0.09
14 6 0.07
ACGTcount: A:0.03, C:0.15, G:0.11, T:0.72
Consensus pattern (11 bp):
TTTTTTCTTTG
Found at i:1819675 original size:11 final size:11
Alignment explanation
Indices: 1819649--1819697 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
1819639 GTTCTTTGCT
*
1819649 TTTTTCTTTGA
1 TTTTGCTTTGA
1819660 CTTTTGCTTTGA
1 -TTTTGCTTTGA
* *
1819672 TTTTTCTTTGT
1 TTTTGCTTTGA
1819683 TTTTGCTTTGA
1 TTTTGCTTTGA
1819694 TTTT
1 TTTT
1819698 TTTTCTCTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (11 bp):
TTTTGCTTTGA
Found at i:1819686 original size:22 final size:22
Alignment explanation
Indices: 1819649--1819758 Score: 96
Period size: 23 Copynumber: 4.7 Consensus size: 22
1819639 GTTCTTTGCT
*
1819649 TTTTTCTTTGACTTTTGCTTTGA
1 TTTTTCTTTG-TTTTTGCTTTGA
1819672 TTTTTCTTTGTTTTTGCTTTGA
1 TTTTTCTTTGTTTTTGCTTTGA
* * * *
1819694 TTTTT-TTTCTCTCTGCTCTTTGTT
1 TTTTTCTTTGTTTTTG--CTTTG-A
*
1819718 TTTTTCTTTGCTCTTTTCTCTTTGA
1 TTTTTCTTTG-T-TTTT-GCTTTGA
1819743 TTTTTCTTTGTTTTTG
1 TTTTTCTTTGTTTTTG
1819759 ATTGGATCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
21 7 0.10
22 16 0.23
23 19 0.28
24 6 0.09
25 13 0.19
26 6 0.09
27 2 0.03
ACGTcount: A:0.04, C:0.15, G:0.11, T:0.71
Consensus pattern (22 bp):
TTTTTCTTTGTTTTTGCTTTGA
Found at i:1819692 original size:34 final size:34
Alignment explanation
Indices: 1819640--1819758 Score: 84
Period size: 34 Copynumber: 3.4 Consensus size: 34
1819630 CCTCTTTTTG
*
1819640 TTCTTTGCTTTTTTCTTTGACTTTTGCTTTGATTT
1 TTCTTTGCTTTTTGCTTTGACTTTT-CTTTGATTT
**
1819675 TTCTTTG-TTTTTGCTTTGA-TTTT-TTTTCTCTCT
1 TTCTTTGCTTTTTGCTTTGACTTTTCTTTGAT-T-T
* * * *
1819708 GCTCTTTGTTTTTTTCTTTGCTCTTTTCTCTTTGATTT
1 -TTCTTTGCTTTTTGCTTTG-AC-TTT-TCTTTGATTT
1819746 TTCTTTG-TTTTTG
1 TTCTTTGCTTTTTG
1819759 ATTGGATCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
31 4 0.06
32 1 0.02
33 5 0.08
34 17 0.26
35 17 0.26
36 5 0.08
37 6 0.09
38 4 0.06
39 2 0.03
40 4 0.06
ACGTcount: A:0.03, C:0.15, G:0.11, T:0.71
Consensus pattern (34 bp):
TTCTTTGCTTTTTGCTTTGACTTTTCTTTGATTT
Found at i:1819729 original size:19 final size:21
Alignment explanation
Indices: 1819695--1819733 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1819685 TTGCTTTGAT
1819695 TTTTTTTCTCTCTGCTCTTTG
1 TTTTTTTCTCTCTGCTCTTTG
1819716 TTTTTTTCT-T-TGCTCTTT
1 TTTTTTTCTCTCTGCTCTTT
1819734 TCTCTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.72
Consensus pattern (21 bp):
TTTTTTTCTCTCTGCTCTTTG
Found at i:1826565 original size:25 final size:25
Alignment explanation
Indices: 1826471--1826567 Score: 162
Period size: 25 Copynumber: 3.9 Consensus size: 25
1826461 ATTGAGGGGA
*
1826471 TTAGGG-TTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
1826495 TTAGGGTTTGAAACCCTAATC-GATT
1 TTAGGGTTTGAAACCCTAATCTG-TT
1826520 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
1826545 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
1826568 ATGGGTTGGG
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
24 7 0.10
25 61 0.88
26 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:1826691 original size:3 final size:3
Alignment explanation
Indices: 1826683--1826728 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
1826673 ATGTAAATTA
* *
1826683 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1826729 TACAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1828187 original size:4 final size:4
Alignment explanation
Indices: 1828180--1828208 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1828170 ACAATTCTCT
1828180 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1828209 ATTCATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1832194 original size:14 final size:16
Alignment explanation
Indices: 1832158--1832189 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1832148 AGAATATACT
1832158 AATATTATAAACATAAC
1 AATATTATAAACA-AAC
1832175 AATATTATAAACAAA
1 AATATTATAAACAAA
1832190 ATATTTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (16 bp):
AATATTATAAACAAAC
Found at i:1837451 original size:16 final size:16
Alignment explanation
Indices: 1837430--1837466 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1837420 GTGTAGGGAG
1837430 ATATGTCAATCTCTGA
1 ATATGTCAATCTCTGA
1837446 ATATGTCAATCTCTGA
1 ATATGTCAATCTCTGA
1837462 ATATG
1 ATATG
1837467 AGATGGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (16 bp):
ATATGTCAATCTCTGA
Found at i:1840523 original size:124 final size:124
Alignment explanation
Indices: 1840303--1840634 Score: 477
Period size: 124 Copynumber: 2.7 Consensus size: 124
1840293 GTATAACATA
* *
1840303 CTTTTATACCGATAATGCACCCATATGCATTTCAGCTATGGCATCATTTCATGCCAATAATGAAC
1 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
* * ** *
1840368 CCATATACATTATTCTTTTGACTTCCTTTCATGCTGATAATGCACTCATATACATTATT
66 CCATATGCATTATTCTTTTGACATCCTTTCATGCCAATAATGCACCCATATACATTATT
* *
1840427 CTTTTATGCCGACAATGCACCCATATGCATTTCAGCTATGACATCATTTCATGCCAATAATGCAC
1 CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
* * *
1840492 CCATATGCATTACTCTTTTGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATT
66 CCATATGCATTATTCTTTTGACATCCTTTCATGCCAATAATGCACCCATATACATTATT
* * * * *
1840551 CTTTTATGTCGATAATGCACACATTTGCATTT-ATGCTATGGTATCCTTTCATGCCAATAATGCA
1 CTTTTATGCCGATAATGCACCCATATGCATTTCA-GCTATGGCATCATTTCATGCCAATAATGCA
* *
1840615 TCCATATGTATTATTCTTTT
65 CCCATATGCATTATTCTTTT
1840635 ATGCCGATAA
Statistics
Matches: 185, Mismatches: 22, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
123 1 0.01
124 184 0.99
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (124 bp):
CTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
CCATATGCATTATTCTTTTGACATCCTTTCATGCCAATAATGCACCCATATACATTATT
Found at i:1840554 original size:45 final size:45
Alignment explanation
Indices: 1840440--1840555 Score: 162
Period size: 45 Copynumber: 2.6 Consensus size: 45
1840430 TTATGCCGAC
* * * *
1840440 AATGCACCCATATGCATTTCAGC-TATGACATCATTTCATGCCAAT
1 AATGCACCCATATGCATTAC-TCTTTTGGCATCATTTCATGCCAAT
*
1840485 AATGCACCCATATGCATTACTCTTTTGGCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTACTCTTTTGGCATCATTTCATGCCAAT
*
1840530 AATGCACCCATATGCATTATTCTTTT
1 AATGCACCCATATGCATTACTCTTTT
1840556 ATGTCGATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 1 0.02
45 63 0.98
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (45 bp):
AATGCACCCATATGCATTACTCTTTTGGCATCATTTCATGCCAAT
Found at i:1840566 original size:34 final size:34
Alignment explanation
Indices: 1840517--1840660 Score: 108
Period size: 34 Copynumber: 3.9 Consensus size: 34
1840507 TTTTGGCATC
* *
1840517 CTTTCATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCGATAATGCACCCATATGCATTATT
* *
1840551 CTTTTATGTCGATAATGCACACATTTGCATTTATGCTATGGTATC
1 CTTTTATGCCGATAATGCAC-C-----CA--TATGC-AT--TATT
* * * *
1840596 CTTTCATGCCAATAATGCATCCATATGTATTATT
1 CTTTTATGCCGATAATGCACCCATATGCATTATT
*
1840630 CTTTTATGCCGATAATACACCCATATGCATT
1 CTTTTATGCCGATAATGCACCCATATGCATT
1840661 TCAACTATGA
Statistics
Matches: 84, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
34 46 0.55
35 1 0.01
36 2 0.02
37 4 0.05
39 2 0.02
40 2 0.02
42 5 0.06
43 2 0.02
44 1 0.01
45 19 0.23
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (34 bp):
CTTTTATGCCGATAATGCACCCATATGCATTATT
Found at i:1840566 original size:79 final size:80
Alignment explanation
Indices: 1840477--1840789 Score: 378
Period size: 79 Copynumber: 4.0 Consensus size: 80
1840467 ACATCATTTC
* *
1840477 ATGCCAATAATGCACCCATATGCA-TTAC-TCTTTTGGCATCCTTTCATGCCAATAATGCACCCA
1 ATGCCGATAATGCACCCATATGCAGTTACATC-TATGGCATCCTTTCATGCCAATAATGCACCCA
1840540 TATGCATTATTCTTTT
65 TATGCATTATTCTTTT
* * * * * *
1840556 ATGTCGATAATGCACACATTTGCA-TT-TATGCTATGGTATCCTTTCATGCCAATAATGCATCCA
1 ATGCCGATAATGCACCCATATGCAGTTACAT-CTATGGCATCCTTTCATGCCAATAATGCACCCA
*
1840619 TATGTATTATTCTTTT
65 TATGCATTATTCTTTT
* * * * *
1840635 ATGCCGATAATACACCCATATGCA-TTTCAACTATGACATCCTTTCATGCCAATAATGTACCCAT
1 ATGCCGATAATGCACCCATATGCAGTTACATCTATGGCATCCTTTCATGCCAATAATGCACCCAT
1840699 ATGC---A-T-TTTT
66 ATGCATTATTCTTTT
* *
1840709 ATGCCGATAATGCACCCATATGCAGTT-CAGCTATGGCATCTTTTCATGCCAATAATGCACCCAT
1 ATGCCGATAATGCACCCATATGCAGTTACATCTATGGCATCCTTTCATGCCAATAATGCACCCAT
*
1840773 ATGCGTTATTCTTTT
66 ATGCATTATTCTTTT
1840788 AT
1 AT
1840790 TCATTCGTTC
Statistics
Matches: 200, Mismatches: 25, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
74 64 0.32
75 3 0.01
76 1 0.00
77 1 0.00
78 1 0.00
79 128 0.64
80 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (80 bp):
ATGCCGATAATGCACCCATATGCAGTTACATCTATGGCATCCTTTCATGCCAATAATGCACCCAT
ATGCATTATTCTTTT
Found at i:1842978 original size:23 final size:23
Alignment explanation
Indices: 1842952--1842999 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1842942 CAATCGAGTA
*
1842952 CCCAATGCCTTATGCAACGACTT
1 CCCAATGCCTTAGGCAACGACTT
1842975 CCCAATGCCTTAGGCAACGACTT
1 CCCAATGCCTTAGGCAACGACTT
1842998 CC
1 CC
1843000 AAAACCTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.23
Consensus pattern (23 bp):
CCCAATGCCTTAGGCAACGACTT
Found at i:1843007 original size:22 final size:23
Alignment explanation
Indices: 1842959--1843007 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1842949 GTACCCAATG
* **
1842959 CCTTATGCAACGACTTCCCAATG
1 CCTTAGGCAACGACTTCCCAAAA
1842982 CCTTAGGCAACGACTT-CCAAAA
1 CCTTAGGCAACGACTTCCCAAAA
1843004 CCTT
1 CCTT
1843008 GAAGTAAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.24
Consensus pattern (23 bp):
CCTTAGGCAACGACTTCCCAAAA
Found at i:1844487 original size:21 final size:19
Alignment explanation
Indices: 1844453--1844528 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 19
1844443 TATATATATA
*
1844453 TTTTTAATTATAT-TTTTT
1 TTTTTATTTATATATTTTT
* *
1844471 TATTTATTTACTATATTCCTT
1 TTTTTATTTA-TATATT-TTT
1844492 TTTTTATTTATATTATATTTT
1 TTTTTATTTATA-TAT-TTTT
1844513 TTTTTATTTTATATAT
1 TTTTTA-TTTATATAT
1844529 CTTATATCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 8 0.17
19 3 0.06
20 4 0.09
21 25 0.53
22 7 0.15
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTATTTATATATTTTT
Found at i:1844499 original size:25 final size:21
Alignment explanation
Indices: 1844465--1844528 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 21
1844455 TTTAATTATA
1844465 TTTTTTTATTTATTTACTATATT
1 TTTTTTTATTTA--TACTATATT
*
1844488 CCTTTTTTTATTTATATTATATT
1 --TTTTTTTATTTATACTATATT
1844511 TTTTTTTATTT-TA-TATAT
1 TTTTTTTATTTATACTATAT
1844529 CTTATATCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 11 0.29
23 8 0.21
25 12 0.32
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTTATTTATACTATATT
Found at i:1844512 original size:17 final size:17
Alignment explanation
Indices: 1844492--1844704 Score: 97
Period size: 17 Copynumber: 12.3 Consensus size: 17
1844482 TATATTCCTT
1844492 TTTTTATTTATATTATA
1 TTTTTATTTATATTATA
* *
1844509 TTTTTTTTTATTTTATA
1 TTTTTATTTATATTATA
*
1844526 TATCTTA--TATCATTATA
1 T-TTTTATTTAT-ATTATA
* *
1844543 TATATATATATATATATATA
1 T-T-TTTATTTATAT-TATA
* *
1844563 TATATATATTATA-TATA
1 TTTTTAT-TTATATTATA
1844580 TTTTT-TCTTAATATTATA
1 TTTTTAT-TT-ATATTATA
*
1844598 TTTTATACGTTTTTATATATA
1 TTTT-TA--TTTATAT-TATA
* * *
1844619 TATTTTGTTAATATTCTA
1 T-TTTTATTTATATTATA
* *
1844637 TTTTTGTTTTTATT-TA
1 TTTTTATTTATATTATA
1844653 --TTTATTTATATTATA
1 TTTTTATTTATATTATA
1844668 TTTTTACTTTAT-TT-TA
1 TTTTTA-TTTATATTATA
1844684 -TTTT-TTTATATTATTA
1 TTTTTATTTATATTA-TA
1844700 TTTTT
1 TTTTT
1844705 CTTAATATCA
Statistics
Matches: 152, Mismatches: 21, Indels: 46
0.69 0.10 0.21
Matches are distributed among these distances:
13 5 0.03
14 12 0.08
15 6 0.04
16 12 0.08
17 55 0.36
18 27 0.18
19 12 0.08
20 11 0.07
21 8 0.05
22 4 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (17 bp):
TTTTTATTTATATTATA
Found at i:1844527 original size:2 final size:2
Alignment explanation
Indices: 1844522--1844580 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
1844512 TTTTTTATTT
*
1844522 TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1844563 TA TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1844581 TTTTTCTTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
1 3 0.06
2 47 0.90
3 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1844598 original size:39 final size:38
Alignment explanation
Indices: 1844550--1844638 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 38
1844540 ATATATATAT
*
1844550 ATATATATATATATATA-TATATTATATATATTTTTTCTTA
1 ATAT-TATAT-TATATACT-TATTATATATATATTTTCTTA
* * *
1844590 ATATTATATTTTATACGTTTTTATATATATATTTTGTTA
1 ATATTATATTATATAC-TTATTATATATATATTTTCTTA
*
1844629 ATATTCTATT
1 ATATTATATT
1844639 TTTGTTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
38 5 0.12
39 32 0.76
40 5 0.12
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (38 bp):
ATATTATATTATATACTTATTATATATATATTTTCTTA
Found at i:1844659 original size:36 final size:38
Alignment explanation
Indices: 1844571--1844659 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 38
1844561 TATATATATA
*
1844571 TTATATATATTTTTTCTTAATATTATATTTTATACGTTT
1 TTATATATATATTTTCTTAATATTATATTTTATA-GTTT
* *
1844610 TTATATATATATTTTGTTAATATTCTATTTT-T-GTTT
1 TTATATATATATTTTCTTAATATTATATTTTATAGTTT
* *
1844646 TTATTTATTTATTT
1 TTATATATATATTT
1844660 ATATTATATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 16 0.36
38 1 0.02
39 28 0.62
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (38 bp):
TTATATATATATTTTCTTAATATTATATTTTATAGTTT
Found at i:1844664 original size:31 final size:31
Alignment explanation
Indices: 1844645--1844704 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1844635 TATTTTTGTT
1844645 TTTA-TTTATTTATTTATATTATATTTTTAC
1 TTTATTTTATTTATTTATATTATATTTTTAC
*
1844675 TTTATTTTATTTTTTTATATTATTATTTTT
1 TTTATTTTATTTATTTATATTA-TATTTTT
1844705 CTTAATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 16 0.59
32 7 0.26
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTATTTTATTTATTTATATTATATTTTTAC
Found at i:1844682 original size:10 final size:8
Alignment explanation
Indices: 1844643--1844704 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
1844633 TCTATTTTTG
1844643 TTTTTATT
1 TTTTTATT
*
1844651 TATTTATT
1 TTTTTATT
* *
1844659 TATATTATA
1 T-TTTTATT
1844668 TTTTTACTT
1 TTTTTA-TT
1844677 TATTTTATT
1 T-TTTTATT
*
1844686 TTTTTATA
1 TTTTTATT
*
1844694 TTATTATT
1 TTTTTATT
1844702 TTT
1 TTT
1844705 CTTAATATCA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
8 26 0.63
9 10 0.24
10 5 0.12
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTATT
Found at i:1844712 original size:18 final size:17
Alignment explanation
Indices: 1844658--1844708 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
1844648 ATTTATTTAT
1844658 TTATATTA-TATTTTTAC
1 TTATATTATTATTTTT-C
1844675 TT-TATT-TTATTTTT-
1 TTATATTATTATTTTTC
1844689 TTATATTATTATTTTTC
1 TTATATTATTATTTTTC
1844706 TTA
1 TTA
1844709 ATATCATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.07
15 4 0.13
16 19 0.63
17 5 0.17
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATATTATTATTTTTC
Found at i:1844837 original size:18 final size:17
Alignment explanation
Indices: 1844805--1844849 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1844795 TGTACACATT
1844805 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
*
1844822 ATTTCTTTTACCTTTTTT
1 ATTT-TTTTACCTTTTTA
1844840 ATTTTTTTAC
1 ATTTTTTTAC
1844850 TCCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:1844847 original size:17 final size:17
Alignment explanation
Indices: 1844803--1844849 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1844793 TATGTACACA
1844803 TTATTTTTATT-CCTTTT
1 TTATTTTT-TTACCTTTT
*
1844820 TAATTTCTTTTACCTTTT
1 TTATTT-TTTTACCTTTT
1844838 TTATTTTTTTAC
1 TTATTTTTTTAC
1844850 TCCATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTTTTTACCTTTT
Found at i:1848085 original size:27 final size:25
Alignment explanation
Indices: 1848033--1848096 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
1848023 ACAAAAAGAG
*
1848033 AAAAAAGCAAAGAGAAAATAAAAAA
1 AAAAAAACAAAGAGAAAATAAAAAA
1848058 ATAAAAAACAAAG-GAAAATTGAAGAAAA
1 A-AAAAAACAAAGAGAAAA-T-AA-AAAA
*
1848086 AAGAAAACAAA
1 AAAAAAACAAA
1848097 ATGCATATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 6 0.18
26 11 0.33
27 11 0.33
28 5 0.15
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.06
Consensus pattern (25 bp):
AAAAAAACAAAGAGAAAATAAAAAA
Found at i:1849776 original size:36 final size:36
Alignment explanation
Indices: 1849678--1849796 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
1849668 TATGTTTTAT
* * *
1849678 TTGAAACAAATTTCATCTCCCTTAAGACAGTTTCTT
1 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
* * **
1849714 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 TTGAAAC-AAATTTCATCTCTCTTGAGACAGTTTCTC
1849751 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTC-C
1 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
1849786 ATTGAAACAAA
1 -TTGAAACAAA
1849797 ATCTTTGAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 1 0.01
36 40 0.57
37 29 0.41
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
Found at i:1849891 original size:67 final size:67
Alignment explanation
Indices: 1849766--1849937 Score: 197
Period size: 67 Copynumber: 2.6 Consensus size: 67
1849756 ACAAATTTCA
* **
1849766 TCTCTCTTGAGACAGTTTC-CATTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAAACAAAAT
1 TCTCCCTTGAGACAGTTTCTC-TTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACAAAAT
1849828 TTG
65 TTG
* * *
1849831 TCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAGAACAAATTT
1 TCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACAAAATT
1849896 TG
66 TG
* * * * *
1849898 TTTCCCTTTAGACTGTTTTTCATGAAACAACAAATATCTT
1 TCTCCCTTGAGACAGTTTCTCTTGAAAC-ACAAA-ATCTT
1849938 TGAGATTGTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 21 0.23
66 3 0.03
67 57 0.63
68 5 0.05
69 5 0.05
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (67 bp):
TCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAACAAAATT
TG
Found at i:1850846 original size:110 final size:106
Alignment explanation
Indices: 1850647--1850902 Score: 325
Period size: 110 Copynumber: 2.4 Consensus size: 106
1850637 TCCGAATTTT
* * *
1850647 AGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAATACAACACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAA
* *
1850712 CGAAGGGGCGACTGATTGTCAACAAACAACTTTTC-AGTTTCATTC
66 CGAAGGGGCGACTGATTGTAAACAAACAA-TTTCCTAG-TTC---C
* * *
1850757 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAA
* * *
1850822 CGAAGGGGTGGCTGGTTGTAAACAAACAATTTCCTAGTTCC
66 CGAAGGGGCGACTGATTGTAAACAAACAATTTCCTAGTTCC
* * * *
1850863 AGAGGCAATTTCAACTTCACGGTGGAGGATATTGGACTCG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
1850903 GAACAATACT
Statistics
Matches: 129, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
106 36 0.28
109 7 0.05
110 86 0.67
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAA
CGAAGGGGCGACTGATTGTAAACAAACAATTTCCTAGTTCC
Found at i:1852477 original size:18 final size:18
Alignment explanation
Indices: 1852432--1852492 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
1852422 CTATTTTTGT
* *
1852432 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
1852449 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
1852467 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
1852485 TTTT-TTTT
1 TTTTATTTT
1852493 CTTAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:1852625 original size:18 final size:17
Alignment explanation
Indices: 1852593--1852637 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
1852583 TGCACACATT
1852593 ATTTTTATT-CCTTTTTA
1 ATTTTT-TTACCTTTTTA
1852610 ATTTCTTTTACCTTTTTA
1 ATTT-TTTTACCTTTTTA
1852628 ATTTTTTTAC
1 ATTTTTTTAC
1852638 TCCATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTTACCTTTTTA
Found at i:1852729 original size:26 final size:26
Alignment explanation
Indices: 1852700--1852763 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1852690 TTTTGTTTAT
**
1852700 TTTTATTTATT-TTTATTTTTTACGTG
1 TTTTATTTATTATCCATTTTTT-CGTG
* *
1852726 TTTT-GTTATTATCCATTTTTTCTTG
1 TTTTATTTATTATCCATTTTTTCGTG
1852751 TTTTATTTATTAT
1 TTTTATTTATTAT
1852764 TCTCACGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (26 bp):
TTTTATTTATTATCCATTTTTTCGTG
Found at i:1856075 original size:34 final size:34
Alignment explanation
Indices: 1856031--1856302 Score: 177
Period size: 45 Copynumber: 7.1 Consensus size: 34
1856021 GCATCATTTC
1856031 ATGCCAATAATGCACCCATATGCATTATTCTTTT
1 ATGCCAATAATGCACCCATATGCATTATTCTTTT
* *
1856065 ATGCCGATAATGCACCCATATACATTTCAGCTATGGCATCATTT
1 ATGCCAATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT
1856109 CATGCCAATAATGCACCCATATGCATTATTCTTTT
1 -ATGCCAATAATGCACCCATATGCATTATTCTTTT
* *
1856144 ATGCCGATAATGCAACCATATGCATTTCAGCTATGGCATCCTTT
1 ATGCCAATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT
*
1856188 CATGCCAATAATTCACCCATATGCATTATT-TTTT
1 -ATGCCAATAATGCACCCATATGCATTATTCTTTT
*
1856222 ATGCCGATAATGCACCCATATGCATTTCATCTATGACATCCTTT
1 ATGCCAATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT
*
1856266 CATGCCAATAATGCATCCATATGCATTATTCTTTT
1 -ATGCCAATAATGCACCCATATGCATTATTCTTTT
1856301 AT
1 AT
1856303 TCATTCGTTC
Statistics
Matches: 191, Mismatches: 13, Indels: 68
0.70 0.05 0.25
Matches are distributed among these distances:
33 22 0.12
34 51 0.27
35 11 0.06
36 3 0.02
37 3 0.02
38 5 0.03
39 2 0.01
40 3 0.02
41 5 0.03
42 3 0.02
43 3 0.02
44 15 0.08
45 65 0.34
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.36
Consensus pattern (34 bp):
ATGCCAATAATGCACCCATATGCATTATTCTTTT
Found at i:1856100 original size:79 final size:79
Alignment explanation
Indices: 1855964--1856302 Score: 518
Period size: 79 Copynumber: 4.3 Consensus size: 79
1855954 ATAAATGTAA
* * ** * * ** *
1855964 CACCTATATGCATTATTCTTTTCTGTTGATAATGTACGCATATTTATTTTAGCTATGGCATCATT
1 CACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATT
1856029 TCATGCCAATAATG
66 TCATGCCAATAATG
*
1856043 CACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATACATTTCAGCTATGGCATCATT
1 CACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATT
1856108 TCATGCCAATAATG
66 TCATGCCAATAATG
* *
1856122 CACCCATATGCATTATTCTTTTATGCCGATAATGCAACCATATGCATTTCAGCTATGGCATCCTT
1 CACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATT
*
1856187 TCATGCCAATAATT
66 TCATGCCAATAATG
* * *
1856201 CACCCATATGCATTATT-TTTTATGCCGATAATGCACCCATATGCATTTCATCTATGACATCCTT
1 CACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATT
1856265 TCATGCCAATAATG
66 TCATGCCAATAATG
*
1856279 CATCCATATGCATTATTCTTTTAT
1 CACCCATATGCATTATTCTTTTAT
1856303 TCATTCGTTC
Statistics
Matches: 241, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
78 73 0.30
79 168 0.70
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (79 bp):
CACCCATATGCATTATTCTTTTATGCCGATAATGCACCCATATGCATTTCAGCTATGGCATCATT
TCATGCCAATAATG
Done.