Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:1573158 original size:19 final size:18
Alignment explanation
Indices: 1573136--1573177 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 18
1573126 ACGGGTCGTG
1573136 ACCGTTCAAACCGGTCAAA
1 ACCGTT-AAACCGGTCAAA
1573155 ACCGGTTAAACCGGTCAAA
1 ACC-GTTAAACCGGTCAAA
1573174 ACCG
1 ACCG
1573178 GTTTCCAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (18 bp):
ACCGTTAAACCGGTCAAA
Found at i:1573178 original size:19 final size:19
Alignment explanation
Indices: 1573143--1573180 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1573133 GTGACCGTTC
1573143 AAACCGGTCAAAACCGGTT
1 AAACCGGTCAAAACCGGTT
1573162 AAACCGGTCAAAACCGGTT
1 AAACCGGTCAAAACCGGTT
1573181 TCCAGCGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (19 bp):
AAACCGGTCAAAACCGGTT
Found at i:1574116 original size:18 final size:18
Alignment explanation
Indices: 1574095--1574132 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1574085 TCCTCCTTAT
*
1574095 TTCCACCTTCTTTTCTTC
1 TTCCACCATCTTTTCTTC
*
1574113 TTCCTCCATCTTTTCTTC
1 TTCCACCATCTTTTCTTC
1574131 TT
1 TT
1574133 TATAGTTTTT
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:0.05, C:0.37, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCCACCATCTTTTCTTC
Found at i:1574365 original size:33 final size:32
Alignment explanation
Indices: 1574316--1574381 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 32
1574306 CCATCTTAAG
*
1574316 TTCACCCTCAATACCTCAACTTCTTTCACCAC
1 TTCACCCTCAACACCTCAACTTCTTTCACCAC
1574348 TTCACCACTCAACACCTCAACTTCTTTCACCAC
1 TTCACC-CTCAACACCTCAACTTCTTTCACCAC
1574381 T
1 T
1574382 CCATCTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.26, C:0.44, G:0.00, T:0.30
Consensus pattern (32 bp):
TTCACCCTCAACACCTCAACTTCTTTCACCAC
Found at i:1574440 original size:21 final size:21
Alignment explanation
Indices: 1574415--1574458 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1574405 CCCCTTATGC
*
1574415 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCAACT
*
1574436 CTCTCAAGTTTCTCTTCAACT
1 CTCTCAAGTGTCTCTTCAACT
1574457 CT
1 CT
1574459 TTATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.34, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCAACT
Found at i:1574560 original size:15 final size:15
Alignment explanation
Indices: 1574540--1574572 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1574530 ACTCTATTTT
1574540 CCCTCACTGTCATCC
1 CCCTCACTGTCATCC
1574555 CCCTCACTGTCATCC
1 CCCTCACTGTCATCC
1574570 CCC
1 CCC
1574573 AATACAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.58, G:0.06, T:0.24
Consensus pattern (15 bp):
CCCTCACTGTCATCC
Found at i:1574879 original size:22 final size:23
Alignment explanation
Indices: 1574851--1574906 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
1574841 AGCTTGCATT
1574851 TATAATAAAAT-TTATAATTTTA
1 TATAATAAAATATTATAATTTTA
* *
1574873 TATAATAACTATATTATCATTTTA
1 TATAATAA-AATATTATAATTTTA
1574897 TATAA-AAAAT
1 TATAATAAAAT
1574907 CGTTCTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
23 4 0.14
24 15 0.52
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TATAATAAAATATTATAATTTTA
Found at i:1577161 original size:182 final size:182
Alignment explanation
Indices: 1576854--1577345 Score: 736
Period size: 182 Copynumber: 2.7 Consensus size: 182
1576844 TACGCCTACT
* * * *
1576854 TATTAAAGTATCGACACTTTCAATAAATCCGGTAG-TGGTTTACCGGTTTTGTCATTTCGAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCT-CTTTACCGGTTTTGTCATTTAGAGACC
* *
1576918 GGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAGTATCGACAC
65 GGTTTTTTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACAC
**
1576983 TTTATACGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTA
130 TTTATAAACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTA
* * *
1577036 TATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTTTACCGGTTTTGTCATTTAGAGACCG
* * ** *
1577101 GTTTTTTCATATTTATACATGTTATATCGTTGTTAATCGATACATTGTTATAAAGTATCGACACT
66 GTTTTTTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
* *
1577166 TTATAAACGCTAAAATTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
131 TTATAAACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTA
* * *
1577218 TATTAAAGTATCGACACTTTCAATATATCCGGTAC-CACTTTACCGGTTTTGTCTTTTTGAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGT-CGCTCTTTACCGGTTTTGTCATTTAGAGACC
* * *
1577282 GGTTTTTTCATATTTTTACCTGTTATATTGATGTGGATCGATACATTTTTATAAATTATCGACA
65 GGTTTTTTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACA
1577346 TAAACCGACA
Statistics
Matches: 277, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
182 275 0.99
183 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTCGCTCTTTACCGGTTTTGTCATTTAGAGACCG
GTTTTTTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
TTATAAACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCAATACTTA
Found at i:1582013 original size:18 final size:19
Alignment explanation
Indices: 1581979--1582014 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1581969 GCATTTTTCA
1581979 GAAAGATTTACCTACAGAT
1 GAAAGATTTACCTACAGAT
*
1581998 GAAAGA-TTATCTACAGA
1 GAAAGATTTACCTACAGA
1582015 CGAATCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (19 bp):
GAAAGATTTACCTACAGAT
Found at i:1582993 original size:36 final size:38
Alignment explanation
Indices: 1582945--1583015 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 38
1582935 GGGAAGGATG
* * *
1582945 ACATGTTTTCTTTTGCGGTAT-TTAATTTA-ATGCTTC
1 ACATGTTCTCTTTTGCAGTATGTAAATTTATATGCTTC
1582981 ACATGTTCTCTTTTGCAGTATGTAAATTTATATGC
1 ACATGTTCTCTTTTGCAGTATGTAAATTTATATGC
1583016 ATGCTTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 19 0.63
37 7 0.23
38 4 0.13
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (38 bp):
ACATGTTCTCTTTTGCAGTATGTAAATTTATATGCTTC
Found at i:1587971 original size:57 final size:57
Alignment explanation
Indices: 1587901--1588012 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
1587891 TAATTCACGG
*
1587901 CTGCAGCCGAACGTCAGTCTGGTTCGATACACCAAACTGATTTCGCGAGAAAATCGA
1 CTGCAGCAGAACGTCAGTCTGGTTCGATACACCAAACTGATTTCGCGAGAAAATCGA
* *
1587958 CTGCAGCAGAACGTCAGTCTGGTTGGATACACCAATCTGATTTCGCGAGAAAATC
1 CTGCAGCAGAACGTCAGTCTGGTTCGATACACCAAACTGATTTCGCGAGAAAATC
1588013 AAGAATTGCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (57 bp):
CTGCAGCAGAACGTCAGTCTGGTTCGATACACCAAACTGATTTCGCGAGAAAATCGA
Found at i:1591385 original size:20 final size:21
Alignment explanation
Indices: 1591357--1591398 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1591347 ATAATGTATC
*
1591357 AAAATTAATTAATTTT-ATTA
1 AAAAATAATTAATTTTGATTA
*
1591377 AAAAATAATTATTTTTGATTA
1 AAAAATAATTAATTTTGATTA
1591398 A
1 A
1591399 GCTGATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAAATAATTAATTTTGATTA
Found at i:1591808 original size:73 final size:73
Alignment explanation
Indices: 1591680--1591817 Score: 179
Period size: 73 Copynumber: 1.9 Consensus size: 73
1591670 ACACAAATGA
* * * * *
1591680 ATTTCTTGATGAATGGTAAGTTAAAGGTTCGGTTCGTTTATATTTTTAGTTGTGGGGTTCCGTCT
1 ATTTCTTGATGAATGGTAAGTTAAACGTTCGGTTCATTTATATCTCTAGTCGTGGGGTTCCGTCT
1591745 TTGTTTCT
66 TTGTTTCT
** * *
1591753 ATTTCTTGATGAACT-GTTCGTTAAACGTTTGGTTCATTTATATCTCTAGTCGTGGGGTTCTGTC
1 ATTTCTTGATGAA-TGGTAAGTTAAACGTTCGGTTCATTTATATCTCTAGTCGTGGGGTTCCGTC
1591817 T
65 T
1591818 CCATGAAGCG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
73 54 0.98
74 1 0.02
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (73 bp):
ATTTCTTGATGAATGGTAAGTTAAACGTTCGGTTCATTTATATCTCTAGTCGTGGGGTTCCGTCT
TTGTTTCT
Found at i:1592068 original size:20 final size:20
Alignment explanation
Indices: 1591947--1592104 Score: 90
Period size: 20 Copynumber: 7.8 Consensus size: 20
1591937 AAATAACCAA
1591947 CAAATTCGCAACGCG-ATTT
1 CAAATTCGCAACGCGAATTT
* ** * *
1591966 CAAATTTGCAACATGAACTA
1 CAAATTCGCAACGCGAATTT
* * *
1591986 CAATTTCGCAACAC-AGTTT
1 CAAATTCGCAACGCGAATTT
*
1592005 CCAAATTCGCAAAGCGAATTT
1 -CAAATTCGCAACGCGAATTT
* * *
1592026 CCCAAATTCGTAACTC-AGTTTT
1 --CAAATTCGCAACGCGA-ATTT
*
1592048 CAAATTCGCAACTCGAATTT
1 CAAATTCGCAACGCGAATTT
***
1592068 CTTTTTCGCAACGC-AATTTT
1 CAAATTCGCAACGCGAA-TTT
1592088 CCAAATTCGCAACGCGA
1 -CAAATTCGCAACGCGA
1592105 GTCCTTTTCG
Statistics
Matches: 102, Mismatches: 28, Indels: 15
0.70 0.19 0.10
Matches are distributed among these distances:
19 16 0.16
20 53 0.52
21 17 0.17
22 16 0.16
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:1592277 original size:22 final size:22
Alignment explanation
Indices: 1592252--1592298 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1592242 TCTCTACGGT
*
1592252 GACATCCGTCCCCATCTCCGAC
1 GACATCCGTCCCCATATCCGAC
*
1592274 GACATCCGTCCCCATATCCGGC
1 GACATCCGTCCCCATATCCGAC
1592296 GAC
1 GAC
1592299 CCCCCTCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.47, G:0.17, T:0.17
Consensus pattern (22 bp):
GACATCCGTCCCCATATCCGAC
Found at i:1592678 original size:14 final size:15
Alignment explanation
Indices: 1592659--1592691 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1592649 GCGATTTTAG
1592659 TTTTCGCGTTGCG-A
1 TTTTCGCGTTGCGAA
*
1592673 TTTTCGTGTTGCGAA
1 TTTTCGCGTTGCGAA
1592688 TTTT
1 TTTT
1592692 ATTTTCGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.52
Consensus pattern (15 bp):
TTTTCGCGTTGCGAA
Found at i:1592697 original size:34 final size:35
Alignment explanation
Indices: 1592648--1592730 Score: 116
Period size: 34 Copynumber: 2.4 Consensus size: 35
1592638 AAATTCGCAA
* * *
1592648 TGCG-ATTTTAGTTTTCGCGTTGCGATTTTCGTGT
1 TGCGAATTTTAGTTTTCGAGTTGCAATTTTCATGT
1592682 TGCGAATTTTA-TTTTCGAGTTGCAATTTTCATGT
1 TGCGAATTTTAGTTTTCGAGTTGCAATTTTCATGT
*
1592716 TGCGAATTTAAGTTT
1 TGCGAATTTTAGTTT
1592731 CAAGAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 34 0.79
35 9 0.21
ACGTcount: A:0.17, C:0.12, G:0.22, T:0.49
Consensus pattern (35 bp):
TGCGAATTTTAGTTTTCGAGTTGCAATTTTCATGT
Found at i:1592710 original size:19 final size:20
Alignment explanation
Indices: 1592672--1592710 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1592662 TCGCGTTGCG
*
1592672 ATTTTCGTGTTGCGAATTTT
1 ATTTTCGAGTTGCGAATTTT
1592692 ATTTTCGAGTTGC-AATTTT
1 ATTTTCGAGTTGCGAATTTT
1592711 CATGTTGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (20 bp):
ATTTTCGAGTTGCGAATTTT
Found at i:1594298 original size:42 final size:42
Alignment explanation
Indices: 1594232--1594397 Score: 176
Period size: 42 Copynumber: 4.0 Consensus size: 42
1594222 CACCACTTTT
* * **
1594232 TCATCGAGTCGATTCTTCAGTTCGACACCGAGATCCATCACC
1 TCATCGAGCCGATTCTACACCTCGACACCGAGATCCATCACC
* * * **
1594274 TCATCGAGTCGATTCTCCACTTCGACACCGAGATTTATCACC
1 TCATCGAGCCGATTCTACACCTCGACACCGAGATCCATCACC
* *
1594316 TGATCGAGCCGATTCTACACCTCGACACCGAGAGCCATCA--
1 TCATCGAGCCGATTCTACACCTCGACACCGAGATCCATCACC
* * * *
1594356 TC-TCTAGCCGACTCTATACCTCGACACCGAGACCCATCACC
1 TCATCGAGCCGATTCTACACCTCGACACCGAGATCCATCACC
1594397 T
1 T
1594398 ATTCCATCAC
Statistics
Matches: 106, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 33 0.31
40 1 0.01
41 1 0.01
42 71 0.67
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (42 bp):
TCATCGAGCCGATTCTACACCTCGACACCGAGATCCATCACC
Found at i:1594522 original size:21 final size:21
Alignment explanation
Indices: 1594497--1594687 Score: 95
Period size: 21 Copynumber: 9.1 Consensus size: 21
1594487 ACCTCCATGG
*
1594497 GATGATTTAGGTGCTTTACGT
1 GATGAGTTAGGTGCTTTACGT
*
1594518 GATGAGGTCA-GTGCTTTACGT
1 GATGA-GTTAGGTGCTTTACGT
*
1594539 GATGAGGTAGGTGCTTTACGT
1 GATGAGTTAGGTGCTTTACGT
* * **
1594560 GATGA-TAATGGTGCATGGCGT
1 GATGAGTTA-GGTGCTTTACGT
** *
1594581 GATGAGGCAGG-GTCTTTACAT
1 GATGAGTTAGGTG-CTTTACGT
* * *
1594602 GGTGACG-TAGTTGTTTTACGT
1 GATGA-GTTAGGTGCTTTACGT
***
1594623 GAT-AACAATGGTGCTTTACGT
1 GATGAGTTA-GGTGCTTTACGT
* * * *
1594644 GGTGAGATAGCTGCTTTATGT
1 GATGAGTTAGGTGCTTTACGT
* * *
1594665 GATGAGGTGGGTGCTCTACGT
1 GATGAGTTAGGTGCTTTACGT
1594686 GA
1 GA
1594688 GATTGTTTCG
Statistics
Matches: 123, Mismatches: 37, Indels: 20
0.68 0.21 0.11
Matches are distributed among these distances:
20 6 0.05
21 110 0.89
22 7 0.06
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.34
Consensus pattern (21 bp):
GATGAGTTAGGTGCTTTACGT
Found at i:1594582 original size:63 final size:63
Alignment explanation
Indices: 1594514--1594687 Score: 172
Period size: 63 Copynumber: 2.8 Consensus size: 63
1594504 TAGGTGCTTT
* *
1594514 ACGTGATGAGGTCAGTGCTTTACGTGATGAGGTAGGTGCTTTACGTGATGATAATGGTGCATG
1 ACGTGATGAGGTCAGTGCTTTACGTGATGAGGTAGGTGCTTTACGTGATAACAATGGTGCATG
* * * * * * * * *
1594577 GCGTGATGAGG-CAGGGTCTTTACATGGTGACGTAGTTGTTTTACGTGATAACAATGGTGCTTT
1 ACGTGATGAGGTCAGTG-CTTTACGTGATGAGGTAGGTGCTTTACGTGATAACAATGGTGCATG
* * * * *
1594640 ACGTGGTGAGAT-AGCTGCTTTATGTGATGAGGTGGGTGCTCTACGTGA
1 ACGTGATGAGGTCAG-TGCTTTACGTGATGAGGTAGGTGCTTTACGTGA
1594688 GATTGTTTCG
Statistics
Matches: 85, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
62 4 0.05
63 80 0.94
64 1 0.01
ACGTcount: A:0.21, C:0.12, G:0.34, T:0.33
Consensus pattern (63 bp):
ACGTGATGAGGTCAGTGCTTTACGTGATGAGGTAGGTGCTTTACGTGATAACAATGGTGCATG
Found at i:1594678 original size:42 final size:41
Alignment explanation
Indices: 1594506--1594687 Score: 127
Period size: 42 Copynumber: 4.3 Consensus size: 41
1594496 GGATGATTTA
* *
1594506 GGTGCTTTACGTGATGAGGTCAGTGCTTTACGTGATGAGGTA
1 GGTGCTTTACGTGATGAGAT-AGTGCTTTACGTGATGAGGTG
* * * ** *
1594548 GGTGCTTTACGTGATGATAATGGTGCATGGCGTGATGAGGCAG
1 GGTGCTTTACGTGATGA-GATAGTGCTTTACGTGATGAGG-TG
* * * * **
1594591 GGT-CTTTACATGGTGACG-TAGTTGTTTTACGTGATAACAAT-
1 GGTGCTTTACGTGATGA-GATAG-TGCTTTACGTGATGA-GGTG
* *
1594632 GGTGCTTTACGTGGTGAGATAGCTGCTTTATGTGATGAGGTG
1 GGTGCTTTACGTGATGAGATAG-TGCTTTACGTGATGAGGTG
*
1594674 GGTGCTCTACGTGA
1 GGTGCTTTACGTGA
1594688 GATTGTTTCG
Statistics
Matches: 103, Mismatches: 30, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
41 7 0.07
42 92 0.89
43 4 0.04
ACGTcount: A:0.20, C:0.12, G:0.35, T:0.34
Consensus pattern (41 bp):
GGTGCTTTACGTGATGAGATAGTGCTTTACGTGATGAGGTG
Found at i:1595045 original size:42 final size:42
Alignment explanation
Indices: 1594998--1595114 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
1594988 AGGATCCACA
* * * *
1594998 TCCCATTGTTCATGATTCACCTCTCATCGTTCAAGAGGCATC
1 TCCCATCGTTCATGATCCACCTCCCATCGTTCAAGAGGCACC
* *
1595040 TCCCATCGTTCAAT-AGGCC-CCTCCCATCGTTCAAGAGGCCCC
1 TCCCATCGTTC-ATGA-TCCACCTCCCATCGTTCAAGAGGCACC
* * *
1595082 TCCCATCGTTCAGGATCCACCTCCTATCTTTCA
1 TCCCATCGTTCATGATCCACCTCCCATCGTTCA
1595115 GGATCCACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
41 3 0.05
42 55 0.90
43 3 0.05
ACGTcount: A:0.20, C:0.38, G:0.14, T:0.29
Consensus pattern (42 bp):
TCCCATCGTTCATGATCCACCTCCCATCGTTCAAGAGGCACC
Found at i:1595046 original size:21 final size:21
Alignment explanation
Indices: 1595017--1595093 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
1595007 TCATGATTCA
* *
1595017 CCTCTCATCGTTCAAGAGGCA
1 CCTCCCATCGTTCAAGAGGCC
* *
1595038 TCTCCCATCGTTCAATAGGCC
1 CCTCCCATCGTTCAAGAGGCC
1595059 CCTCCCATCGTTCAAGAGGCC
1 CCTCCCATCGTTCAAGAGGCC
1595080 CCTCCCATCGTTCA
1 CCTCCCATCGTTCA
1595094 GGATCCACCT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.19, C:0.40, G:0.16, T:0.25
Consensus pattern (21 bp):
CCTCCCATCGTTCAAGAGGCC
Found at i:1595104 original size:21 final size:21
Alignment explanation
Indices: 1594985--1595122 Score: 100
Period size: 21 Copynumber: 6.6 Consensus size: 21
1594975 CCTACAACCA
* * *
1594985 TTCAGGATCCACATCCCATTG
1 TTCAAGATCCACCTCCCATCG
* * *
1595006 TTCATGATTCACCTCTCATCG
1 TTCAAGATCCACCTCCCATCG
** *
1595027 TTCAAGAGGCATCTCCCATCG
1 TTCAAGATCCACCTCCCATCG
* *
1595048 TTCAATAGGCC-CCTCCCATCG
1 TTCAAGA-TCCACCTCCCATCG
*
1595069 TTCAAGAGGCC-CCTCCCATCG
1 TTCAAGA-TCCACCTCCCATCG
* * *
1595090 TTCAGGATCCACCTCCTATCT
1 TTCAAGATCCACCTCCCATCG
*
1595111 TTCAGGATCCAC
1 TTCAAGATCCAC
1595123 ATTCCATACT
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
20 2 0.02
21 93 0.96
22 2 0.02
ACGTcount: A:0.21, C:0.37, G:0.14, T:0.28
Consensus pattern (21 bp):
TTCAAGATCCACCTCCCATCG
Found at i:1596682 original size:20 final size:20
Alignment explanation
Indices: 1596682--1596777 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1596672 AACGCGAAAA
* * *
1596682 TCGCAACTCGATATTCAAAT
1 TCGCAACACGAAAATCAAAT
* **
1596702 TCGCAACATGAAAATCGGAT
1 TCGCAACACGAAAATCAAAT
****
1596722 TCGCAACACGAAAATTGGTT
1 TCGCAACACGAAAATCAAAT
**
1596742 TCGCAATTCGAAAATCAAAT
1 TCGCAACACGAAAATCAAAT
*
1596762 TCGCAACAAGAAAATC
1 TCGCAACACGAAAATC
1596778 GCGTTGCGAA
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
TCGCAACACGAAAATCAAAT
Found at i:1596745 original size:40 final size:40
Alignment explanation
Indices: 1596701--1596776 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1596691 GATATTCAAA
** *
1596701 TTCGCAACAT-GAAAATCGGATTCGCAACACGAAAATTGGT
1 TTCGCAA-ATCGAAAATCAAATTCGCAACAAGAAAATTGGT
*
1596741 TTCGCAATTCGAAAATCAAATTCGCAACAAGAAAAT
1 TTCGCAAATCGAAAATCAAATTCGCAACAAGAAAAT
1596777 CGCGTTGCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 30 0.97
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (40 bp):
TTCGCAAATCGAAAATCAAATTCGCAACAAGAAAATTGGT
Found at i:1596799 original size:40 final size:40
Alignment explanation
Indices: 1596711--1596789 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
1596701 TTCGCAACAT
** * * *
1596711 GAAAATCGGATTCGCAACACGAAAATTGGTTTCGCAATTC
1 GAAAATCAAATTCGCAACAAGAAAATCGGTTGCGCAATTC
1596751 GAAAATCAAATTCGCAACAAGAAAATCGCGTTGCG-AATT
1 GAAAATCAAATTCGCAACAAGAAAATCG-GTTGCGCAATT
1596790 TTAATATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 28 0.85
41 5 0.15
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (40 bp):
GAAAATCAAATTCGCAACAAGAAAATCGGTTGCGCAATTC
Found at i:1596829 original size:20 final size:20
Alignment explanation
Indices: 1596804--1596842 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1596794 TATCAAGTTG
* *
1596804 CGATTTTCGTGTTGCGAATA
1 CGATTTTCGCGTTCCGAATA
1596824 CGATTTTCGCGTTCCGAAT
1 CGATTTTCGCGTTCCGAAT
1596843 TTGAGTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
CGATTTTCGCGTTCCGAATA
Found at i:1599497 original size:24 final size:24
Alignment explanation
Indices: 1599431--1599489 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1599421 TGAAACAATC
1599431 TCAAAATTCGAGTATTGACCAAGA
1 TCAAAATTCGAGTATTGACCAAGA
* *
1599455 TCAAAGTTCGGGTATTGACCAAGA
1 TCAAAATTCGAGTATTGACCAAGA
*
1599479 TCAAATTTCGA
1 TCAAAATTCGA
1599490 ATACTGACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TCAAAATTCGAGTATTGACCAAGA
Found at i:1600430 original size:20 final size:20
Alignment explanation
Indices: 1600401--1600570 Score: 153
Period size: 20 Copynumber: 8.4 Consensus size: 20
1600391 AAAAATTCGT
1600401 GTTGCGAAAAAGAAAATCGA
1 GTTGCGAAAAAGAAAATCGA
* * *
1600421 GTTCCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAAATCGA
* *
1600441 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAAATCGA
**
1600461 GTTGCGAATTCA-AAAATCGA
1 GTTGCGAA-AAAGAAAATCGA
** * *
1600481 GTTGCGAAATTGTAAATCAA
1 GTTGCGAAAAAGAAAATCGA
* *
1600501 GTTGCGAAAAAGAAATTCGT
1 GTTGCGAAAAAGAAAATCGA
** *
1600521 GTTGCGAAATTGTTAAAAACGA
1 GTTGCGAAAAAG--AAAATCGA
*
1600543 GTTGCGAAAAAGAAATTCGA
1 GTTGCGAAAAAGAAAATCGA
1600563 GTTGCGAA
1 GTTGCGAA
1600571 TCTGAAAATT
Statistics
Matches: 118, Mismatches: 28, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
20 102 0.86
21 1 0.01
22 15 0.13
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
GTTGCGAAAAAGAAAATCGA
Found at i:1600437 original size:40 final size:40
Alignment explanation
Indices: 1600393--1600570 Score: 189
Period size: 40 Copynumber: 4.4 Consensus size: 40
1600383 TATACCCAAA
*
1600393 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTCCGAAAAAG
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAG
* * *
1600433 AAATTCGTGTTGCGAAAAAGAAATTCGTGTTGCGAATTCAA-
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAA--AAAG
* ** * *
1600474 AAA-TCGAGTTGCGAAATTGTAAATCAAGTTGCGAAAAAG
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAG
** *
1600513 AAATTCGTGTTGCGAAATTGTTAAAAACGAGTTGCGAAAAAG
1 AAATTCGTGTTGCGAAAAAG--AAAATCGAGTTGCGAAAAAG
*
1600555 AAATTCGAGTTGCGAA
1 AAATTCGTGTTGCGAA
1600571 TCTGAAAATT
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.02
39 3 0.03
40 73 0.63
41 3 0.03
42 34 0.30
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (40 bp):
AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAG
Found at i:1600466 original size:60 final size:60
Alignment explanation
Indices: 1600393--1600570 Score: 216
Period size: 60 Copynumber: 2.9 Consensus size: 60
1600383 TATACCCAAA
* *
1600393 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTCCGAAAAAGAAATTCGTGTTGCGAAAAAG
1 AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAGAAATTCGAGTTGCGAAAAAG
** ** *
1600453 AAATTCGTGTTGCGAATTCA-AAAATCGAGTTGCGAAATTGTAAA-TCAAGTTGCGAAAAAG
1 AAATTCGTGTTGCGAA-AAAGAAAATCGAGTTGCGAAAAAG-AAATTCGAGTTGCGAAAAAG
** *
1600513 AAATTCGTGTTGCGAAATTGTTAAAAACGAGTTGCGAAAAAGAAATTCGAGTTGCGAA
1 AAATTCGTGTTGCGAAAAAG--AAAATCGAGTTGCGAAAAAGAAATTCGAGTTGCGAA
1600571 TCTGAAAATT
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
60 63 0.64
61 7 0.07
62 28 0.29
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (60 bp):
AAATTCGTGTTGCGAAAAAGAAAATCGAGTTGCGAAAAAGAAATTCGAGTTGCGAAAAAG
Found at i:1600577 original size:20 final size:19
Alignment explanation
Indices: 1600432--1600592 Score: 74
Period size: 20 Copynumber: 8.0 Consensus size: 19
1600422 TTCCGAAAAA
* **
1600432 GAAATTCGTGTTGCGAAAAA
1 GAAATTCGAGTTGCG-AATT
*
1600452 GAAATTCGTGTTGCGAATT
1 GAAATTCGAGTTGCGAATT
* *
1600471 CAAAAATCGAGTTGCGAAATT
1 -GAAATTCGAGTTGCG-AATT
* **
1600492 GTAAA-TCAAGTTGCGAAAAA
1 G-AAATTCGAGTTGCG-AATT
*
1600512 GAAATTCGTGTTGCGAAATT
1 GAAATTCGAGTTGCG-AATT
** **
1600532 GTTAAAAACGAGTTGCGAAAAA
1 G--AAATTCGAGTTGCG-AATT
1600554 GAAATTCGAGTTGCGAATCT
1 GAAATTCGAGTTGCGAAT-T
*
1600574 GAAAATT-GAGTTGCAAATT
1 G-AAATTCGAGTTGCGAATT
1600593 TGGAAACTGT
Statistics
Matches: 110, Mismatches: 23, Indels: 17
0.73 0.15 0.11
Matches are distributed among these distances:
19 8 0.07
20 75 0.68
21 12 0.11
22 15 0.14
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (19 bp):
GAAATTCGAGTTGCGAATT
Found at i:1600606 original size:20 final size:20
Alignment explanation
Indices: 1600583--1600653 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
1600573 TGAAAATTGA
1600583 GTTGCAAATTTGGAAACTGT
1 GTTGCAAATTTGGAAACTGT
**
1600603 GTTGCGAAA-TTGG-AGTTCGT
1 GTTGC-AAATTTGGAAACT-GT
* *
1600623 GTTGCAAATTT-GAAACCGC
1 GTTGCAAATTTGGAAACTGT
*
1600642 GTTGCGAATTTG
1 GTTGCAAATTTG
1600654 TTGGTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
19 17 0.44
20 19 0.49
21 3 0.08
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCAAATTTGGAAACTGT
Found at i:1602788 original size:31 final size:32
Alignment explanation
Indices: 1602731--1602791 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1602721 TTGAGTAAAC
*
1602731 TATGTATTTAATATATAACTTGTTAATTTTGT
1 TATGTATTTAATATATAAATTGTTAATTTTGT
*
1602763 TATGT-TTTAATATTTAAATCT-TTAATTTT
1 TATGTATTTAATATATAAAT-TGTTAATTTT
1602792 TAAAGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (32 bp):
TATGTATTTAATATATAAATTGTTAATTTTGT
Found at i:1603547 original size:7 final size:7
Alignment explanation
Indices: 1603535--1603593 Score: 55
Period size: 7 Copynumber: 7.7 Consensus size: 7
1603525 TATTTTGATT
1603535 ATATTTA
1 ATATTTA
1603542 ATATTTA
1 ATATTTA
*
1603549 ATATTTT
1 ATATTTA
*
1603556 GTATTTA
1 ATATTTA
1603563 ATTTATTTA
1 A--TATTTA
1603572 AGTATTTAA
1 A-TATTT-A
1603581 ATTATTTA
1 A-TATTTA
1603589 ATATT
1 ATATT
1603594 GTATTTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 22 0.51
8 7 0.16
9 14 0.33
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:1603597 original size:21 final size:21
Alignment explanation
Indices: 1603536--1603601 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 21
1603526 ATTTTGATTA
1603536 TATTT-AA-TATTTAATATTTTG
1 TATTTAAATTATTTAATA--TTG
*
1603557 TATTTAATTTATTT-A-A--G
1 TATTTAAATTATTTAATATTG
1603574 TATTTAAATTATTTAATATTG
1 TATTTAAATTATTTAATATTG
1603595 TATTTAA
1 TATTTAA
1603602 TTAATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
17 14 0.38
18 1 0.03
19 1 0.03
21 14 0.38
22 2 0.05
23 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTTAAATTATTTAATATTG
Found at i:1606230 original size:20 final size:20
Alignment explanation
Indices: 1606206--1606276 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1606196 TTGTAAATCA
1606206 AGTTGCGAAAAAGAAATTCG
1 AGTTGCGAAAAAGAAATTCG
* ** **
1606226 TGTTGCGAAATTGTTAAAAACG
1 AGTTGCGAAAAAG--AAATTCG
1606248 AGTTGCGAAAAAGAAATTCG
1 AGTTGCGAAAAAGAAATTCG
1606268 AGTTGCGAA
1 AGTTGCGAA
1606277 TCTGAAAATT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
20 24 0.62
22 15 0.38
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (20 bp):
AGTTGCGAAAAAGAAATTCG
Found at i:1606258 original size:42 final size:40
Alignment explanation
Indices: 1606189--1606276 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 40
1606179 TCTCGTTATA
* *
1606189 TGCGAAATTGTAAATCAAGTTGCGAAAAAGAAATTCGTGT
1 TGCGAAATTGTAAAACAAGTTGCGAAAAAGAAATTCGAGT
*
1606229 TGCGAAATTGTTAAAAACGAGTTGCGAAAAAGAAATTCGAGT
1 TGCGAAATTG-T-AAAACAAGTTGCGAAAAAGAAATTCGAGT
1606271 TGCGAA
1 TGCGAA
1606277 TCTGAAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 10 0.23
41 1 0.02
42 32 0.74
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (40 bp):
TGCGAAATTGTAAAACAAGTTGCGAAAAAGAAATTCGAGT
Found at i:1606283 original size:20 final size:21
Alignment explanation
Indices: 1606206--1606293 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 21
1606196 TTGTAAATCA
1606206 AGTTGCGAAAAAG-AAATTCG
1 AGTTGCGAAAAAGAAAATTCG
* ** *
1606226 TGTTGCGAAATTGTTAAAA-ACG
1 AGTTGCGAAAAAG--AAAATTCG
1606248 AGTTGCGAAAAAG-AAATTCG
1 AGTTGCGAAAAAGAAAATTCG
***
1606268 AGTTGCGAATCTGAAAATT-G
1 AGTTGCGAAAAAGAAAATTCG
1606288 AGTTGC
1 AGTTGC
1606294 AAATTTGGAA
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
19 3 0.06
20 29 0.56
21 5 0.10
22 12 0.23
23 3 0.06
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (21 bp):
AGTTGCGAAAAAGAAAATTCG
Found at i:1606312 original size:20 final size:20
Alignment explanation
Indices: 1606289--1606359 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
1606279 TGAAAATTGA
1606289 GTTGCAAATTTGGAAACTGT
1 GTTGCAAATTTGGAAACTGT
**
1606309 GTTGCGAAA-TTGG-AGTTCGT
1 GTTGC-AAATTTGGAAACT-GT
* *
1606329 GTTGCAAATTT-GAAACCGC
1 GTTGCAAATTTGGAAACTGT
*
1606348 GTTGCGAATTTG
1 GTTGCAAATTTG
1606360 TTGGTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
19 17 0.44
20 19 0.49
21 3 0.08
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCAAATTTGGAAACTGT
Found at i:1608492 original size:31 final size:32
Alignment explanation
Indices: 1608435--1608495 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1608425 TTGAGTAAAC
*
1608435 TATGTATTTAATATATAACTTGTTAATTTTGT
1 TATGTATTTAATATATAAATTGTTAATTTTGT
*
1608467 TATGT-TTTAATATTTAAATCT-TTAATTTT
1 TATGTATTTAATATATAAAT-TGTTAATTTT
1608496 TAAAGTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (32 bp):
TATGTATTTAATATATAAATTGTTAATTTTGT
Found at i:1609250 original size:7 final size:7
Alignment explanation
Indices: 1609238--1609296 Score: 55
Period size: 7 Copynumber: 7.7 Consensus size: 7
1609228 TATTTTGATT
1609238 ATATTTA
1 ATATTTA
1609245 ATATTTA
1 ATATTTA
*
1609252 ATATTTT
1 ATATTTA
*
1609259 GTATTTA
1 ATATTTA
1609266 ATTTATTTA
1 A--TATTTA
1609275 AGTATTTAA
1 A-TATTT-A
1609284 ATTATTTA
1 A-TATTTA
1609292 ATATT
1 ATATT
1609297 GTATTTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 22 0.51
8 7 0.16
9 14 0.33
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:1609300 original size:21 final size:21
Alignment explanation
Indices: 1609239--1609304 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 21
1609229 ATTTTGATTA
1609239 TATTT-AA-TATTTAATATTTTG
1 TATTTAAATTATTTAATA--TTG
*
1609260 TATTTAATTTATTT-A-A--G
1 TATTTAAATTATTTAATATTG
1609277 TATTTAAATTATTTAATATTG
1 TATTTAAATTATTTAATATTG
1609298 TATTTAA
1 TATTTAA
1609305 TTAATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
17 14 0.38
18 1 0.03
19 1 0.03
21 14 0.38
22 2 0.05
23 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTTAAATTATTTAATATTG
Found at i:1616886 original size:21 final size:21
Alignment explanation
Indices: 1616860--1616901 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1616850 TCTAATGCTT
*
1616860 CTAGTGTTGCAACGAGTTCTA
1 CTAGTGTTGCAACAAGTTCTA
*
1616881 CTAGTGTTGCCACAAGTTCTA
1 CTAGTGTTGCAACAAGTTCTA
1616902 ATGCTTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (21 bp):
CTAGTGTTGCAACAAGTTCTA
Found at i:1617040 original size:27 final size:27
Alignment explanation
Indices: 1616996--1617047 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1616986 CTACTTCTAG
*
1616996 TGGTGTTGCAGCTGGTTTGAATGCTGA
1 TGGTGTTGCAGATGGTTTGAATGCTGA
*
1617023 TGGTGTTGCAGAAT-GTTTTAATGCT
1 TGGTGTTGCAG-ATGGTTTGAATGCT
1617048 TCCAGTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (27 bp):
TGGTGTTGCAGATGGTTTGAATGCTGA
Found at i:1629550 original size:7 final size:7
Alignment explanation
Indices: 1629538--1629643 Score: 70
Period size: 7 Copynumber: 15.1 Consensus size: 7
1629528 AATGTTATTC
1629538 AAACCCT
1 AAACCCT
1629545 AAACCCT
1 AAACCCT
**
1629552 AAACTAT
1 AAACCCT
*
1629559 AAACTCT
1 AAACCCT
*
1629566 AAATCCT
1 AAACCCT
1629573 AAACCCT
1 AAACCCT
* *
1629580 AAGCTCT
1 AAACCCT
*
1629587 -AACTCAT
1 AAAC-CCT
1629594 AAACCCT
1 AAACCCT
**
1629601 AAATTCT
1 AAACCCT
*
1629608 AAATCCT
1 AAACCCT
**
1629615 AAACTAT
1 AAACCCT
* *
1629622 AAATCAT
1 AAACCCT
1629629 AAACCCT
1 AAACCCT
1629636 AAACCCT
1 AAACCCT
1629643 A
1 A
1629644 TCACATAATT
Statistics
Matches: 75, Mismatches: 22, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
6 2 0.03
7 70 0.93
8 3 0.04
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (7 bp):
AAACCCT
Found at i:1629567 original size:21 final size:21
Alignment explanation
Indices: 1629538--1629640 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
1629528 AATGTTATTC
* *
1629538 AAACCCTAAACCCTAAACTAT
1 AAACTCTAAACCCTAAACCAT
* *
1629559 AAACTCTAAATCCTAAACCCT
1 AAACTCTAAACCCTAAACCAT
* * *
1629580 AAGCTCT-AACTCATAAACCCT
1 AAACTCTAAAC-CCTAAACCAT
* * *
1629601 AAATTCTAAATCCTAAACTAT
1 AAACTCTAAACCCTAAACCAT
1629622 AAA-TCATAAACCCTAAACC
1 AAACTC-TAAACCCTAAACC
1629641 CTATCACATA
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
20 4 0.06
21 58 0.91
22 2 0.03
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (21 bp):
AAACTCTAAACCCTAAACCAT
Found at i:1629596 original size:35 final size:35
Alignment explanation
Indices: 1629538--1629643 Score: 124
Period size: 35 Copynumber: 3.0 Consensus size: 35
1629528 AATGTTATTC
* *
1629538 AAACCCTAAACCCTAAACT-ATAAACTCTAAATCCT
1 AAACCCTAAACTCT-AACTCATAAACCCTAAATCCT
* *
1629573 AAACCCTAAGCTCTAACTCATAAACCCTAAATTCT
1 AAACCCTAAACTCTAACTCATAAACCCTAAATCCT
* * * *
1629608 AAATCCTAAACTATAAATCATAAACCCTAAACCCT
1 AAACCCTAAACTCTAACTCATAAACCCTAAATCCT
1629643 A
1 A
1629644 TCACATAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 4 0.07
35 56 0.93
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (35 bp):
AAACCCTAAACTCTAACTCATAAACCCTAAATCCT
Found at i:1630242 original size:25 final size:26
Alignment explanation
Indices: 1630197--1630251 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1630187 AAAAATTATT
1630197 TATTAAAAATATTATCATTAGA-AATA
1 TATTAAAAATATTATCATTAGATAA-A
* *
1630223 TATTAAATAT-TTGTCATTAGATAAA
1 TATTAAAAATATTATCATTAGATAAA
1630248 TATT
1 TATT
1630252 TTTTTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (26 bp):
TATTAAAAATATTATCATTAGATAAA
Found at i:1630593 original size:14 final size:14
Alignment explanation
Indices: 1630574--1630603 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1630564 TATAATTATC
*
1630574 AATAATGTATTTTT
1 AATAATGTAATTTT
1630588 AATAATGTAATTTT
1 AATAATGTAATTTT
1630602 AA
1 AA
1630604 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:1631478 original size:183 final size:187
Alignment explanation
Indices: 1631114--1631505 Score: 625
Period size: 183 Copynumber: 2.1 Consensus size: 187
1631104 ATTTTGAATT
* * *
1631114 TATATAA-AAATTAAATATTTTTTTAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAT
1631178 AATTATAAAATAAAAATTTTATACAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
66 AATTATAAAATAAAAATTTTATA-AAAATTTTT-ATTAATTAATATTGATTTAAGTTTAAAAGTT
*
1631243 ATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAACTCATATG-T-TA
129 ATTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAACTCATATGTTATA
* * *
1631300 TATATAATATATTTAATCTTTTTTTAATTTAAAAAAATAGTTTACAATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAT
* *
1631365 AATTATAAAATAAAAATTTTAT-ATAATTTTT-TTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 AATTATAAAATAAAAATTTTATAAAAATTTTTATTAATTAATATTGATTTAAGTTTAAAAGTTAT
1631428 TGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGC-TAAGCTCATATGTTATA
131 TGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAA-CTCATATGTTATA
*
1631485 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
1631506 AATTTCGGTT
Statistics
Matches: 191, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
182 3 0.02
183 78 0.41
184 1 0.01
185 29 0.15
186 7 0.04
187 73 0.38
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (187 bp):
TATATAATATATTTAATATTTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATAT
AATTATAAAATAAAAATTTTATAAAAATTTTTATTAATTAATATTGATTTAAGTTTAAAAGTTAT
TGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTTAACTCATATGTTATA
Found at i:1633936 original size:31 final size:31
Alignment explanation
Indices: 1633888--1634041 Score: 245
Period size: 31 Copynumber: 5.0 Consensus size: 31
1633878 CCCGAAGGAC
* * *
1633888 CAGTCCATAGGTCCCGAATAACCTAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1633919 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1633950 CAGTCCATATGTCCCGAAGAACATACGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1633981 CAGTCCATATGTCCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1634012 CAGTTCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1634042 CCCTCGACTC
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 114 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1635376 original size:21 final size:21
Alignment explanation
Indices: 1635329--1635376 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1635319 TACAAAGTCT
1635329 TATAAAAAATAAAATTTAAAGG
1 TATAAAAAATAAAATTT-AAGG
*
1635351 T-TAAAAAATTAAAATTT-ATG
1 TATAAAAAA-TAAAATTTAAGG
1635371 TATAAA
1 TATAAA
1635377 TTATCATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 11 0.48
22 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (21 bp):
TATAAAAAATAAAATTTAAGG
Found at i:1635403 original size:18 final size:19
Alignment explanation
Indices: 1635368--1635405 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1635358 ATTAAAATTT
**
1635368 ATGTATAAATTATCATAAA
1 ATGTATAAATTAAAATAAA
1635387 ATGTAT-AATTAAAATAAA
1 ATGTATAAATTAAAATAAA
1635405 A
1 A
1635406 AAAATAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (19 bp):
ATGTATAAATTAAAATAAA
Found at i:1636427 original size:26 final size:24
Alignment explanation
Indices: 1636391--1636461 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
1636381 GAGATATTAG
*
1636391 AAATCAAAACAGAATTAAGA-AAA
1 AAATCAGAACAGAATTAAGATAAA
* **
1636414 TATATATCAGAACATAATCCAGATAAA
1 -A-A-ATCAGAACAGAATTAAGATAAA
*
1636441 AAATCAGAACAGAATTCAGAT
1 AAATCAGAACAGAATTAAGAT
1636462 CATTTATCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 18 0.47
25 2 0.05
26 15 0.39
27 3 0.08
ACGTcount: A:0.58, C:0.13, G:0.10, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTAAGATAAA
Found at i:1639874 original size:19 final size:20
Alignment explanation
Indices: 1639850--1639889 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1639840 TTGGGTAATA
1639850 TATTTTTCA-AATTAATTTT
1 TATTTTTCATAATTAATTTT
* *
1639869 TATTTTTGATATTTAATTTT
1 TATTTTTCATAATTAATTTT
1639889 T
1 T
1639890 TTATATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTTTTCATAATTAATTTT
Found at i:1642889 original size:18 final size:18
Alignment explanation
Indices: 1642866--1643001 Score: 107
Period size: 18 Copynumber: 7.6 Consensus size: 18
1642856 TACAAATATG
1642866 TTTTTAGGTTGTAACCTA
1 TTTTTAGGTTGTAACCTA
* * ***
1642884 TTTTTAAGTTATAATGGGA
1 TTTTTAGGTTGTAA-CCTA
1642903 -TTTTAGGTTGTAACCTA
1 TTTTTAGGTTGTAACCTA
* * ***
1642920 TTTTTAAGTTATAATGGGA
1 TTTTTAGGTTGTAA-CCTA
*
1642939 -TTTTAGGTTGTAACCTT
1 TTTTTAGGTTGTAACCTA
* *
1642956 TTTTTAGGTTATAACGTGA
1 TTTTTAGGTTGTAACCT-A
1642975 -TTTTAGGTTGTAACCTA
1 TTTTTAGGTTGTAACCTA
1642992 TTTTTAGGTT
1 TTTTTAGGTT
1643002 ATAAGGGGAT
Statistics
Matches: 86, Mismatches: 26, Indels: 12
0.69 0.21 0.10
Matches are distributed among these distances:
17 2 0.02
18 82 0.95
19 2 0.02
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (18 bp):
TTTTTAGGTTGTAACCTA
Found at i:1642979 original size:54 final size:54
Alignment explanation
Indices: 1642903--1643131 Score: 212
Period size: 54 Copynumber: 4.3 Consensus size: 54
1642893 TATAATGGGA
* * * *
1642903 TTTTAGGTTGTAACCT-ATTTTTAAGTTATAATGGGATTTTAGGTTGTAACCTTT
1 TTTTAGGTTATAACGTGA-TTTTAGGTTATAATGGGATTTTAGGTTGTAACCTGT
* *** * *** *
1642957 TTTTAGGTTATAACGTGATTTTAGGTTGTAA-CCTATTTTTAGGTTATAAGGGGA
1 TTTTAGGTTATAACGTGATTTTAGGTTATAATGGGA-TTTTAGGTTGTAACCTGT
* * * *
1643011 TTTTAGGTTATAACATG-TTTTAGGTTATAATGGGATTTTAGGTGGTATCCTAT
1 TTTTAGGTTATAACGTGATTTTAGGTTATAATGGGATTTTAGGTTGTAACCTGT
* * * ** *
1643064 TTTTAGGTTATAATGGGATTTTAGGTTGTAATTAGATTTTAGGTTGTAACATGT
1 TTTTAGGTTATAACGTGATTTTAGGTTATAATGGGATTTTAGGTTGTAACCTGT
1643118 TTTTAGGTTATAAC
1 TTTTAGGTTATAAC
1643132 TGGGTTGGTA
Statistics
Matches: 134, Mismatches: 37, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
53 37 0.28
54 96 0.72
55 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.48
Consensus pattern (54 bp):
TTTTAGGTTATAACGTGATTTTAGGTTATAATGGGATTTTAGGTTGTAACCTGT
Found at i:1643014 original size:18 final size:18
Alignment explanation
Indices: 1642885--1643131 Score: 133
Period size: 18 Copynumber: 13.8 Consensus size: 18
1642875 TGTAACCTAT
* *
1642885 TTTTAAGTTATAATGGGA
1 TTTTAGGTTATAACGGGA
* **
1642903 TTTTAGGTTGTAAC-CTA
1 TTTTAGGTTATAACGGGA
* *
1642920 TTTTTAAGTTATAATGGGA
1 -TTTTAGGTTATAACGGGA
* ****
1642939 TTTTAGGTTGTAACCTTT
1 TTTTAGGTTATAACGGGA
*
1642957 TTTTAGGTTATAACGTGA
1 TTTTAGGTTATAACGGGA
* **
1642975 TTTTAGGTTGTAAC-CTA
1 TTTTAGGTTATAACGGGA
*
1642992 TTTTTAGGTTATAAGGGGA
1 -TTTTAGGTTATAACGGGA
**
1643011 TTTTAGGTTATAACATG-
1 TTTTAGGTTATAACGGGA
*
1643028 TTTTAGGTTATAATGGGA
1 TTTTAGGTTATAACGGGA
** * **
1643046 TTTTAGGTGGTATC-CTA
1 TTTTAGGTTATAACGGGA
*
1643063 TTTTTAGGTTATAATGGGA
1 -TTTTAGGTTATAACGGGA
* ***
1643082 TTTTAGGTTGTAATTAGA
1 TTTTAGGTTATAACGGGA
* ** *
1643100 TTTTAGGTTGTAACATGT
1 TTTTAGGTTATAACGGGA
1643118 TTTTAGGTTATAAC
1 TTTTAGGTTATAAC
1643132 TGGGTTGGTA
Statistics
Matches: 168, Mismatches: 54, Indels: 14
0.71 0.23 0.06
Matches are distributed among these distances:
17 17 0.10
18 148 0.88
19 3 0.02
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.47
Consensus pattern (18 bp):
TTTTAGGTTATAACGGGA
Found at i:1643108 original size:36 final size:36
Alignment explanation
Indices: 1642867--1643094 Score: 352
Period size: 36 Copynumber: 6.4 Consensus size: 36
1642857 ACAAATATGT
*
1642867 TTTTAGGTTGTAACCTATTTTTAAGTTATAATGGGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGGGA
*
1642903 TTTTAGGTTGTAACCTATTTTTAAGTTATAATGGGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGGGA
* * *
1642939 TTTTAGGTTGTAACCTTTTTTTAGGTTATAACGTGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGGGA
*
1642975 TTTTAGGTTGTAACCTATTTTTAGGTTATAAGGGGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGGGA
*
1643011 TTTTAGGTTATAA-C-ATGTTTTAGGTTATAATGGGA
1 TTTTAGGTTGTAACCTAT-TTTTAGGTTATAATGGGA
* *
1643046 TTTTAGGTGGTATCCTATTTTTAGGTTATAATGGGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGGGA
1643082 TTTTAGGTTGTAA
1 TTTTAGGTTGTAA
1643095 TTAGATTTTA
Statistics
Matches: 175, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
34 2 0.01
35 28 0.16
36 143 0.82
37 2 0.01
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.47
Consensus pattern (36 bp):
TTTTAGGTTGTAACCTATTTTTAGGTTATAATGGGA
Found at i:1644017 original size:42 final size:42
Alignment explanation
Indices: 1643929--1644018 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
1643919 AAACATATTG
* ** ** * *
1643929 TCACTATTCTTAATTGGTGATTTGTGACGATTATTGTTTTTG
1 TCACTAGTCTTAATTGGTGATTTGTGACGACAATAATTTGTA
* *
1643971 TCACTAGTCTTAGTTGGTGATTTGTGACGGCAATAATTTGTA
1 TCACTAGTCTTAATTGGTGATTTGTGACGACAATAATTTGTA
1644013 TCACTA
1 TCACTA
1644019 TTAAAGTGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (42 bp):
TCACTAGTCTTAATTGGTGATTTGTGACGACAATAATTTGTA
Found at i:1646291 original size:36 final size:36
Alignment explanation
Indices: 1646250--1646479 Score: 205
Period size: 36 Copynumber: 6.4 Consensus size: 36
1646240 ATGATTCTTT
* * *
1646250 GCATGATATACTTGTGCTGGTTACTGATGATTATAA
1 GCATGATATACATGTGCTTGCTACTGATGATTATAA
* * *
1646286 ACATGATATACATGTGCTTGCTACTGATTATTATGA
1 GCATGATATACATGTGCTTGCTACTGATGATTATAA
* * * * *
1646322 GTC-GGATATATATATGCTTGCTACTTATTATTATGAA
1 G-CATGATATACATGTGCTTGCTACTGATGATTAT-AA
* * *
1646359 -CATGATATACATGTGCTTGCTATTGATTATTATGA
1 GCATGATATACATGTGCTTGCTACTGATGATTATAA
** *
1646394 GCATGATATACATGTAATTGCTACTGATGATTATAT
1 GCATGATATACATGTGCTTGCTACTGATGATTATAA
* * * * *
1646430 GCATGATACACATGTG-TCGGTTAATGATGATTATAT
1 GCATGATATACATGTGCT-TGCTACTGATGATTATAA
*
1646466 GCATGGTATACATG
1 GCATGATATACATG
1646480 CGCTGGTTAA
Statistics
Matches: 158, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
35 3 0.02
36 153 0.97
37 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (36 bp):
GCATGATATACATGTGCTTGCTACTGATGATTATAA
Found at i:1646488 original size:36 final size:36
Alignment explanation
Indices: 1646418--1646504 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
1646408 TAATTGCTAC
*
1646418 TGATGATTATATGCATGATACACATGTGTCGGTTAA
1 TGATGATTATATGCATGATACACATGCGTCGGTTAA
* *
1646454 TGATGATTATATGCATGGTATACATGCG-CTGGTTAA
1 TGATGATTATATGCATGATACACATGCGTC-GGTTAA
*
1646490 TGAGGATTATATGCA
1 TGATGATTATATGCA
1646505 CAATATTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 1 0.02
36 45 0.98
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (36 bp):
TGATGATTATATGCATGATACACATGCGTCGGTTAA
Found at i:1648761 original size:21 final size:21
Alignment explanation
Indices: 1648735--1648805 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
1648725 TGTCCATTAT
*
1648735 AATGTTGATGTGACGATTCAC
1 AATGTTGATGTGACGATTCAA
* *
1648756 AATGTTAATGTGACGATTCAT
1 AATGTTGATGTGACGATTCAA
** *
1648777 AATGTTGACATGATGATTCAA
1 AATGTTGATGTGACGATTCAA
1648798 AATGTTGA
1 AATGTTGA
1648806 CATGATAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (21 bp):
AATGTTGATGTGACGATTCAA
Found at i:1648806 original size:21 final size:21
Alignment explanation
Indices: 1648770--1648811 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1648760 TTAATGTGAC
*
1648770 GATTCATAATGTTGACATGAT
1 GATTCAAAATGTTGACATGAT
1648791 GATTCAAAATGTTGACATGAT
1 GATTCAAAATGTTGACATGAT
1648812 AATTTATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (21 bp):
GATTCAAAATGTTGACATGAT
Found at i:1649083 original size:40 final size:44
Alignment explanation
Indices: 1648990--1649090 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 44
1648980 AATATTCAAA
*
1648990 TATTCAAAAAATTAAATATAATAAATAATAAAAATAAAAATTAAT
1 TATT-AAAAAATTAAATATAATAAATAATAAAAATAAAAATTAAC
* * *
1649035 TTTCTAAAAAATTAAATAT-AT-ATTAATAATAATAAAAA-T-AC
1 TAT-TAAAAAATTAAATATAATAAATAATAAAAATAAAAATTAAC
*
1649076 TATTAAAAATTTAAA
1 TATTAAAAAATTAAA
1649091 AATTAAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
40 11 0.22
41 3 0.06
42 1 0.02
43 15 0.31
44 2 0.04
45 16 0.33
46 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (44 bp):
TATTAAAAAATTAAATATAATAAATAATAAAAATAAAAATTAAC
Found at i:1649701 original size:22 final size:22
Alignment explanation
Indices: 1649645--1649716 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
1649635 TTATTTTGAT
* * *
1649645 TATTTTTGTCTAAGTCTGGATG
1 TATTTTTGTCTAAGTTTGCATA
*
1649667 TA-TTTTGTTTAAGTTTGCATA
1 TATTTTTGTCTAAGTTTGCATA
*
1649688 TATTTTTGTCTAAGTTTTCATA
1 TATTTTTGTCTAAGTTTGCATA
1649710 TATTTTT
1 TATTTTT
1649717 AAAAATCTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.40
22 26 0.60
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.58
Consensus pattern (22 bp):
TATTTTTGTCTAAGTTTGCATA
Found at i:1650218 original size:16 final size:16
Alignment explanation
Indices: 1650197--1650227 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1650187 CATATCGGTG
1650197 CATATCATTAGTGGTA
1 CATATCATTAGTGGTA
1650213 CATATCATTAGTGGT
1 CATATCATTAGTGGT
1650228 GCACATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (16 bp):
CATATCATTAGTGGTA
Found at i:1650546 original size:2 final size:2
Alignment explanation
Indices: 1650539--1650564 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1650529 ATAACTTATG
1650539 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1650565 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1650613 original size:21 final size:21
Alignment explanation
Indices: 1650562--1650614 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
1650552 TATATATATA
**
1650562 TATTATTTTTTAATAGTATTTT
1 TATT-TTTTTTAATAGTAAATT
*
1650584 TATTATTTTTAATA-TAAATT
1 TATTTTTTTTAATAGTAAATT
*
1650604 TAGTTTTTTTA
1 TATTTTTTTTA
1650615 GTAATTTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 13 0.50
21 9 0.35
22 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (21 bp):
TATTTTTTTTAATAGTAAATT
Found at i:1657136 original size:18 final size:18
Alignment explanation
Indices: 1657113--1657150 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1657103 GAGTAGGGTC
*
1657113 AATTTGAAAATCTTGTAG
1 AATTTGAAAATCTTATAG
*
1657131 AATTTGAAATTCTTATAG
1 AATTTGAAAATCTTATAG
1657149 AA
1 AA
1657151 ATGCTTTTTG
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:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (18 bp):
AATTTGAAAATCTTATAG
Found at i:1658380 original size:17 final size:17
Alignment explanation
Indices: 1658342--1658400 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
1658332 TAATTTGTTT
* *
1658342 AATATCATAATTAT-AT
1 AATATTATAATTATAAA
*
1658358 AATATTTTAATTATAAA
1 AATATTATAATTATAAA
1658375 AATATTATAATTATAAA
1 AATATTATAATTATAAA
1658392 AATAATTAT
1 AAT-ATTAT
1658401 TAAGGAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.32
17 20 0.54
18 5 0.14
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTATAATTATAAA
Found at i:1658833 original size:24 final size:24
Alignment explanation
Indices: 1658806--1658853 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1658796 CGTTCGTGAA
* *
1658806 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCATTTATGTT
*
1658830 CGTTTGATTATGTTCATTTATGTT
1 CGTTCGATTATGTTCATTTATGTT
1658854 TAACCCAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.10, G:0.21, T:0.56
Consensus pattern (24 bp):
CGTTCGATTATGTTCATTTATGTT
Found at i:1675622 original size:29 final size:30
Alignment explanation
Indices: 1675585--1675648 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
1675575 AGTGACTTGA
1675585 ACAGTGCATCGATACGCTACAGT-ACTGCT
1 ACAGTGCATCGATACGCTACAGTAACTGCT
*
1675614 ACAGTGCATCGATACGCTATAGTAACTGCT
1 ACAGTGCATCGATACGCTACAGTAACTGCT
*
1675644 GCAGT
1 ACAGT
1675649 TACTGCTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (30 bp):
ACAGTGCATCGATACGCTACAGTAACTGCT
Found at i:1676249 original size:40 final size:40
Alignment explanation
Indices: 1676205--1676326 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
1676195 ACCGTAGTAC
1676205 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
* *
1676245 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAA
1 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1676285 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1676325 TA
1 TA
1676327 TAAACCTATA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
Found at i:1689161 original size:2 final size:2
Alignment explanation
Indices: 1689154--1689178 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1689144 AACTACGACC
1689154 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1689179 GTGTTTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1689869 original size:35 final size:35
Alignment explanation
Indices: 1689818--1689884 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
1689808 AAATGATATA
* *
1689818 AAAATCGTTTATGCTAAACGGGAATGGGGACGGGG
1 AAAACCGTTTATGCTAAACGGGAACGGGGACGGGG
*
1689853 AAAACCGTTTATGCTAAACGGGGACGGGGACG
1 AAAACCGTTTATGCTAAACGGGAACGGGGACG
1689885 AGTTTGGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.36, T:0.18
Consensus pattern (35 bp):
AAAACCGTTTATGCTAAACGGGAACGGGGACGGGG
Found at i:1690012 original size:23 final size:24
Alignment explanation
Indices: 1689981--1690029 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
1689971 AATAAATTTA
*
1689981 ATTTAAATTAAAAAATATTTATAT
1 ATTTAAATTAAAAAATATATATAT
* *
1690005 ATTT-AATTTAAATATATATATAT
1 ATTTAAATTAAAAAATATATATAT
1690028 AT
1 AT
1690030 CCGGCCCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAAATTAAAAAATATATATAT
Found at i:1690027 original size:29 final size:29
Alignment explanation
Indices: 1689957--1690027 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1689947 ATTATTATAT
1689957 ATATATATAATATTAATAAATTTAATTTAA
1 ATATATAT-ATATTAATAAATTTAATTTAA
* * * *
1689987 AT-TAAAAAATATTTATATATTTAATTTAA
1 ATAT-ATATATATTAATAAATTTAATTTAA
1690016 ATATATATATAT
1 ATATATATATAT
1690028 ATCCGGCCCG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
29 28 0.85
30 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATATATATATATTAATAAATTTAATTTAA
Found at i:1692211 original size:14 final size:14
Alignment explanation
Indices: 1692186--1692226 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1692176 TTTTATCTTT
1692186 AAATTAATTTTTTAA
1 AAATT-ATTTTTTAA
1692201 AAATTA-TTTTTAA
1 AAATTATTTTTTAA
*
1692214 AAGTTATTTTTTA
1 AAATTATTTTTTA
1692227 GGTATTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 12 0.50
14 7 0.29
15 5 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
AAATTATTTTTTAA
Found at i:1696765 original size:39 final size:37
Alignment explanation
Indices: 1696675--1696774 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 37
1696665 ACTCTAATCC
*
1696675 TTCTT-AGACTCATTTCCCTAGAAACTTGTTTTAGTCT
1 TTCTTAAGACT-ATTTCCCTAGAAACTTGTTTCAGTCT
*
1696712 TTCTTAAGATTATTTTCCCTAGAAACCTTG-TTCACGTCT
1 TTCTTAAGACTA-TTTCCCTAGAAA-CTTGTTTCA-GTCT
* *
1696751 TT-TCTATGACTATTTCTCTAGAAA
1 TTCT-TAAGACTATTTCCCTAGAAA
1696775 TCAACTTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
37 6 0.11
38 31 0.58
39 16 0.30
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (37 bp):
TTCTTAAGACTATTTCCCTAGAAACTTGTTTCAGTCT
Found at i:1702531 original size:64 final size:61
Alignment explanation
Indices: 1702451--1702572 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 61
1702441 AGGTATTTAT
*
1702451 TATCTATTTAACTTTGAATATTAAAAGATAATTATTATCATTTTAAATATTTTAAATTAAATAA
1 TATCTATTTAACTTTGAATAGTAAAAGATAATTA-TATC-TTTTAAAT-TTTTAAATTAAATAA
* * * ** *
1702515 TATCTATTTAAGTTTGAATGGTAAAAGGTGTTTATATCTTTTGAATTTTTAAATTAAA
1 TATCTATTTAACTTTGAATAGTAAAAGATAATTATATCTTTTAAATTTTTAAATTAAA
1702573 AGATATTATC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 12 0.24
62 7 0.14
63 4 0.08
64 28 0.55
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (61 bp):
TATCTATTTAACTTTGAATAGTAAAAGATAATTATATCTTTTAAATTTTTAAATTAAATAA
Found at i:1704576 original size:14 final size:14
Alignment explanation
Indices: 1704557--1704584 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1704547 AGTGAGAATC
1704557 TCAATTTTTCTTCT
1 TCAATTTTTCTTCT
1704571 TCAATTTTTCTTCT
1 TCAATTTTTCTTCT
1704585 ATTGTTGTCT
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:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
TCAATTTTTCTTCT
Found at i:1705410 original size:149 final size:147
Alignment explanation
Indices: 1705252--1705547 Score: 468
Period size: 149 Copynumber: 2.0 Consensus size: 147
1705242 TAAATGAAAA
*
1705252 GAGATAAAAGACACGACAAATAAAGAAAAATGACTAAATTGTAACATGAATAAAACCAGGGAATC
1 GAGATAAAAGACACGACAAATAAAGAAAAATGACTAAATTCTAACATGAATAAAACCAGGGAATC
* * *
1705317 AAATTTAAAGAAACAAAAATACAAAAAGACCAAAATGAATTTGCAATCAAAAGGAGGGACATCA-
66 AAAATTAAAGAAACAAAAA-A-AAAAAGACCAAAATGAATTTGCAATCAAAAAGAGAGACAT-AG
1705381 ACAATGATCTACCCATATAC
128 ACAATGATCTACCCATATAC
* *
1705401 GAGATAAAAGTCACGACAAATAAAGAAATATGACTAAATTCTAACATGAATAAAACCAGGGAATC
1 GAGATAAAAGACACGACAAATAAAGAAAAATGACTAAATTCTAACATGAATAAAACCAGGGAATC
* * *
1705466 AAAATTAAAGAAACAAGAAAAAAAAGATCAAAATGAATTTGCAATCAAAAAGAGAGACCTAGACA
66 AAAATTAAAGAAACAAAAAAAAAAAGACCAAAATGAATTTGCAATCAAAAAGAGAGACATAGACA
*
1705531 ATGATTTACCCATATAC
131 ATGATCTACCCATATAC
1705548 ACTAAGAGGA
Statistics
Matches: 136, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
146 1 0.01
147 55 0.40
148 1 0.01
149 79 0.58
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (147 bp):
GAGATAAAAGACACGACAAATAAAGAAAAATGACTAAATTCTAACATGAATAAAACCAGGGAATC
AAAATTAAAGAAACAAAAAAAAAAAGACCAAAATGAATTTGCAATCAAAAAGAGAGACATAGACA
ATGATCTACCCATATAC
Found at i:1707841 original size:18 final size:18
Alignment explanation
Indices: 1707820--1707860 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1707810 TTTGTGATAA
*
1707820 TTTGCTTATGTTGAATAT
1 TTTGATTATGTTGAATAT
* *
1707838 TTTGATTTTGTTGGATAT
1 TTTGATTATGTTGAATAT
1707856 TTTGA
1 TTTGA
1707861 ATTACATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.02, G:0.20, T:0.59
Consensus pattern (18 bp):
TTTGATTATGTTGAATAT
Found at i:1708550 original size:20 final size:20
Alignment explanation
Indices: 1708497--1708543 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1708487 AAGTTTTGAT
*
1708497 ACTTTCA-AATAGTTTCGAA
1 ACTTTCATAAGAGTTTCGAA
*
1708516 ACTATC-TAAAGAGTTTCGAA
1 ACTTTCAT-AAGAGTTTCGAA
1708536 ACTTTCAT
1 ACTTTCAT
1708544 TAAAGTTACG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (20 bp):
ACTTTCATAAGAGTTTCGAA
Found at i:1710243 original size:7 final size:7
Alignment explanation
Indices: 1710231--1710255 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1710221 GGTCAAAGGA
1710231 GGTCAAC
1 GGTCAAC
1710238 GGTCAAC
1 GGTCAAC
1710245 GGTCAAC
1 GGTCAAC
1710252 GGTC
1 GGTC
1710256 GGGTCAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:1710289 original size:9 final size:9
Alignment explanation
Indices: 1710257--1710304 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1710247 TCAACGGTCG
*
1710257 GGTCAGACC
1 GGTCAAACC
*
1710266 GGTTCGAACC
1 GG-TCAAACC
*
1710276 GGTCAAATC
1 GGTCAAACC
1710285 GGTCAAAACC
1 GGTC-AAACC
1710295 GGTCAAACC
1 GGTCAAACC
1710304 G
1 G
1710305 ATTTTCCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 17 0.53
10 15 0.47
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1716495 original size:20 final size:20
Alignment explanation
Indices: 1716442--1716488 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1716432 AAGTTTTGAT
*
1716442 ACTTTCA-AATAGTTTCGAA
1 ACTTTCATAAGAGTTTCGAA
*
1716461 ACTATC-TAAAGAGTTTCGAA
1 ACTTTCAT-AAGAGTTTCGAA
1716481 ACTTTCAT
1 ACTTTCAT
1716489 TAAAGTTACG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 5 0.23
20 16 0.73
21 1 0.05
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (20 bp):
ACTTTCATAAGAGTTTCGAA
Found at i:1723559 original size:2 final size:2
Alignment explanation
Indices: 1723552--1723578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1723542 TAATAGTGTT
1723552 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1723579 TTTTTTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1723825 original size:10 final size:10
Alignment explanation
Indices: 1723810--1723890 Score: 83
Period size: 10 Copynumber: 7.6 Consensus size: 10
1723800 TTAATATTTT
*
1723810 TGTTGAGATA
1 TGTTGAAATA
1723820 TGTTGAAATA
1 TGTTGAAATA
1723830 TGCTATGAAATA
1 TG-T-TGAAATA
1723842 TGTT-AAGATA
1 TGTTGAA-ATA
1723852 TGCTGTTGAAATA
1 ---TGTTGAAATA
*
1723865 TGTTGAGATA
1 TGTTGAAATA
1723875 TGTTGAAATA
1 TGTTGAAATA
1723885 TGTTGA
1 TGTTGA
1723891 GACCATTTGA
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
9 2 0.03
10 39 0.64
11 2 0.03
12 9 0.15
13 7 0.11
14 2 0.03
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (10 bp):
TGTTGAAATA
Found at i:1723861 original size:35 final size:33
Alignment explanation
Indices: 1723820--1723886 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1723810 TGTTGAGATA
1723820 TGTTGAAATATGCTATGAAATATGTT-AAGATATGC
1 TGTTGAAATATG-T-TGAAATATGTTGAA-ATATGC
*
1723855 TGTTGAAATATGTTGAGATATGTTGAAATATG
1 TGTTGAAATATGTTGAAATATGTTGAAATATG
1723887 TTGAGACCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 15 0.50
34 3 0.10
35 12 0.40
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (33 bp):
TGTTGAAATATGTTGAAATATGTTGAAATATGC
Found at i:1723880 original size:20 final size:20
Alignment explanation
Indices: 1723810--1723892 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 20
1723800 TTAATATTTT
* *
1723810 TGTTGAGATATGTTGAAATA
1 TGTTGAAATATGTTGAGATA
*
1723830 TGCTATGAAATATGTTAAGATA
1 TG-T-TGAAATATGTTGAGATA
1723852 TGCTGTTGAAATATGTTGAGATA
1 ---TGTTGAAATATGTTGAGATA
1723875 TGTTGAAATATGTTGAGA
1 TGTTGAAATATGTTGAGA
1723893 CCATTTGAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 20 0.37
21 1 0.02
22 14 0.26
23 16 0.30
24 1 0.02
25 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (20 bp):
TGTTGAAATATGTTGAGATA
Found at i:1726328 original size:17 final size:18
Alignment explanation
Indices: 1726300--1726365 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 18
1726290 TTCATTGAAA
1726300 AACCGAAAAAACGAACCG
1 AACCGAAAAAACGAACCG
1726318 AACCG-AAAAAC---CCG
1 AACCGAAAAAACGAACCG
1726332 AACCGTTAAAAAACCCGAACCG
1 AACCG--AAAAAA--CGAACCG
1726354 AACCGAAAAAAC
1 AACCGAAAAAAC
1726366 CGGTTTCGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
14 8 0.20
17 11 0.28
18 6 0.15
19 1 0.03
20 6 0.15
22 8 0.20
ACGTcount: A:0.53, C:0.30, G:0.14, T:0.03
Consensus pattern (18 bp):
AACCGAAAAAACGAACCG
Found at i:1726912 original size:73 final size:73
Alignment explanation
Indices: 1726792--1726947 Score: 294
Period size: 73 Copynumber: 2.1 Consensus size: 73
1726782 TGCAACACAA
1726792 AATTAATAAATATTAGCATTTATTTTATACTTATATATTGACATTCATATACTTATATTAATACT
1 AATTAAT-AATATTAGCATTTATTTTATACTTATATATTGACATTCATATACTTATATTAATACT
1726857 AATTGATCT
65 AATTGATCT
*
1726866 AATTAATAATATTAGCATTTATTTTATATTTATATATTGACATTCATATACTTATATTAATACTA
1 AATTAATAATATTAGCATTTATTTTATACTTATATATTGACATTCATATACTTATATTAATACTA
1726931 ATTGATCT
66 ATTGATCT
1726939 AATTAATAA
1 AATTAATAA
1726948 ATGTAATATA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 74 0.91
74 7 0.09
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.47
Consensus pattern (73 bp):
AATTAATAATATTAGCATTTATTTTATACTTATATATTGACATTCATATACTTATATTAATACTA
ATTGATCT
Found at i:1727766 original size:21 final size:21
Alignment explanation
Indices: 1727739--1727798 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
1727729 TGTCCGAGTT
1727739 ACCCGCGACGGTCGCAATAGC
1 ACCCGCGACGGTCGCAATAGC
* **
1727760 GCCCGCGACGACCGCAATAGC
1 ACCCGCGACGGTCGCAATAGC
*
1727781 ACCCGCGACAGTCGCAAT
1 ACCCGCGACGGTCGCAAT
1727799 CACGGTAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.40, G:0.27, T:0.08
Consensus pattern (21 bp):
ACCCGCGACGGTCGCAATAGC
Found at i:1735330 original size:17 final size:17
Alignment explanation
Indices: 1735308--1735365 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1735298 TATTTTTTAT
1735308 TATTATATTTATATAAA
1 TATTATATTTATATAAA
* *
1735325 TATTATTTTTTTATTAAA
1 TATTATATTTATA-TAAA
* * *
1735343 AATAATATTTATATAAT
1 TATTATATTTATATAAA
1735360 TATTAT
1 TATTAT
1735366 TTATTTTAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATATTTATATAAA
Found at i:1735330 original size:20 final size:19
Alignment explanation
Indices: 1735305--1735371 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
1735295 TTATATTTTT
1735305 TATTATTATATTTATATAAA
1 TATTATT-TATTTATATAAA
*
1735325 TATTATTTTTTTAT-TAAA
1 TATTATTTATTTATATAAA
* * *
1735343 -AATA-ATATTTATATAAT
1 TATTATTTATTTATATAAA
1735360 TATTATTTATTT
1 TATTATTTATTT
1735372 TAAATTAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
16 6 0.16
17 6 0.16
18 7 0.19
19 11 0.30
20 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTTATTTATATAAA
Found at i:1739531 original size:139 final size:139
Alignment explanation
Indices: 1738224--1739556 Score: 1803
Period size: 139 Copynumber: 9.6 Consensus size: 139
1738214 TGCGTCTCCG
* * * * * * *
1738224 GGGACATGACTCACATAATAGGGCAATTATAACATATTCTCTGACATAACAATCGAAGGCGCGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
* * * * * * *
1738289 CCGAG-AATGCGCTTTCACCACTTTGCTAATTCCCCTCAAATATAATAAGTACTAACATGAATAG
66 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
**
1738353 TTCCCCTAA
131 TTCCCCCGA
* * * * * * * *
1738362 TGAACATGAATGACATAACAAGGCAATGATAACATATTATTTGACAAAATAATGGAAGGCGCGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
* * * * *
1738427 TCCAGAAACGCGCTTTCACCACTTTGCCACA-TCCCTTAAAAAATGATAGGTACTGAC-TGAATA
66 CCCAGAAACGCGCTTTCACCACTTTGCCA-AGTCCCCTCAAACATAATAGGTACTGACATGAATA
*
1738490 GTTCCCCAGA
130 GTTCCCCCGA
* * * *
1738500 GGGACATGAGTGGCATAATAGGGCAATGATAACATATTCTCTGACAAAATAATAGAAGGCACGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
*** * *
1738565 CTTGGAAACGCGCTTTCAGCACTTTTCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
66 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
*
1738630 TTCCCCCAA
131 TTCCCCCGA
*
1738639 GGGACATGAGTGACATAATAGGGCAATGATATCATATTCTCTGACAAAATAATGGAAGACGCGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
* * * *
1738704 CCCGGAAACACGCTTTCACCACTTTGCCAAATCCCCTCAAACATAATAGGTACTGACATGAATTG
66 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
*
1738769 TGCCCCCGA
131 TTCCCCCGA
* *
1738778 GGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGACGCACC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
*
1738843 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTACCCTCAAACATAATAGGTACTGACATGAATAG
66 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
* *
1738908 TGCCTCCGA
131 TTCCCCCGA
* *
1738917 GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATGGAAGGCGCGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
*
1738982 CCCAGAAACGCGCTTTCACCACTTTGCCACA-TCCCCTCAAACATGATAGGTACTGACATGAATA
66 CCCAGAAACGCGCTTTCACCACTTTGCCA-AGTCCCCTCAAACATAATAGGTACTGACATGAATA
* **
1739046 GTTTCCTAGA
130 GTTCCCCCGA
* * * * *
1739056 GGGACATGAGTGGCATAATAGGGCTATGATAACATATTCTCTGAAAAAATAATGGAAGGCACGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
** *
1739121 CCTGGAAACGCGCTTTCACCACTTTTCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
66 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
* *
1739186 TTCTCCCAA
131 TTCCCCCGA
* * **
1739195 GGGACATGAGTGACATAATATGGCAATGATATCATATTCTCTGACAAAATAATGGAAGACGCTTC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
* * * * *
1739260 CCCGGAAACACGCTTTCACCACTTTTCCAAATCCCCTCAAACATAATAGGTACTGACATGAATTG
66 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
*
1739325 TGCCCCCGA
131 TTCCCCCGA
* * *
1739334 GGGACATGAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGACACTCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
* * *
1739399 CCTAGAAACGCGCTTTCACCACTTTTCCAAGTCCCCTCAAACATAATAGGTACT-AGTATGAATA
66 CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGA-CATGAATA
*
1739463 GTGCCCCCGA
130 GTTCCCCCGA
* *
1739473 GGGACATGAGTGACATAATAGGGCAATGATAGCATATTCTCTGACAAAATAATGGAAGACGTGCC
1 GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
* * *
1739538 CCCGGGAACGCGCCTTCAC
66 CCCAGAAACGCGCTTTCAC
1739557 GTAAATAGTA
Statistics
Matches: 1058, Mismatches: 130, Indels: 13
0.88 0.11 0.01
Matches are distributed among these distances:
137 1 0.00
138 172 0.16
139 883 0.83
140 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (139 bp):
GGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGACGCGCC
CCCAGAAACGCGCTTTCACCACTTTGCCAAGTCCCCTCAAACATAATAGGTACTGACATGAATAG
TTCCCCCGA
Found at i:1741447 original size:21 final size:21
Alignment explanation
Indices: 1741423--1741462 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1741413 TGTCCTAAAA
*
1741423 ATGTATTCATACCTATATTGT
1 ATGTATTAATACCTATATTGT
*
1741444 ATGTATTAATACTTATATT
1 ATGTATTAATACCTATATT
1741463 TAAAACTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
ATGTATTAATACCTATATTGT
Found at i:1741571 original size:75 final size:75
Alignment explanation
Indices: 1741478--1741660 Score: 271
Period size: 75 Copynumber: 2.4 Consensus size: 75
1741468 CTTAACCGGT
* *
1741478 TAAAATAAAATA-AGAGCTACCTATTATGTTAAACTACCTACCGGTTTGTTTGAAGGTTACTAAT
1 TAAAATAAAATAGA-AGCTACCTATTATGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAAT
1741542 AATGTAAACGG
65 AATGTAAACGG
* * *
1741553 TAAAATAAAATAGAAGCTACCTATTACGTTAAAATACTTACTGGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGAAGCTACCTATTATGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
1741618 ATGTAAACGG
66 ATGTAAACGG
* *
1741628 TAAAATAAAATAGGCA-CTACCTTTTATGTTAAA
1 TAAAATAAAATA-GAAGCTACCTATTATGTTAAA
1741661 TAGGCACTAC
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
75 95 0.97
76 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (75 bp):
TAAAATAAAATAGAAGCTACCTATTATGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:1741664 original size:23 final size:23
Alignment explanation
Indices: 1741635--1741706 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
1741625 CGGTAAAATA
*
1741635 AAATAGGCACTACCTTTTATGTT
1 AAATAGGCACTACCTATTATGTT
*
1741658 AAATAGGCACTACCTATTACGTT
1 AAATAGGCACTACCTATTATGTT
* * *
1741681 AAATAAGCGCTATCTATTATGTT
1 AAATAGGCACTACCTATTATGTT
1741704 AAA
1 AAA
1741707 CTACCTACCG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (23 bp):
AAATAGGCACTACCTATTATGTT
Found at i:1741813 original size:75 final size:75
Alignment explanation
Indices: 1741689--1741849 Score: 232
Period size: 75 Copynumber: 2.1 Consensus size: 75
1741679 TTAAATAAGC
* * * * *
1741689 GCTATCTATTATGTTAAACTACCTACCGGTATGTTTGAAGGTTACTAATAATATAAATGGAAAAA
1 GCTACCTATTACGTTAAAATACCTACCGGTATGTTTAAAAGTTACTAATAATATAAATGGAAAAA
*
1741754 TAAAATAGTT
66 TAAAATAGAT
* * * *
1741764 GCTACCTATTACGTTAAAATACCTATCGGTTTGTTTAAAAGTTATTAATAATATAAATGGTAAAA
1 GCTACCTATTACGTTAAAATACCTACCGGTATGTTTAAAAGTTACTAATAATATAAATGGAAAAA
1741829 TAAAATAGAT
66 TAAAATAGAT
1741839 GCTACCTATTA
1 GCTACCTATTA
1741850 TATTAAGTAG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (75 bp):
GCTACCTATTACGTTAAAATACCTACCGGTATGTTTAAAAGTTACTAATAATATAAATGGAAAAA
TAAAATAGAT
Found at i:1741868 original size:23 final size:23
Alignment explanation
Indices: 1741838--1741901 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
1741828 ATAAAATAGA
1741838 TGCTACCTATTATATTAAGTAGG
1 TGCTACCTATTATATTAAGTAGG
*
1741861 TGCTACCTATTTTATTAAGTAGG
1 TGCTACCTATTATATTAAGTAGG
*
1741884 TGCTACCTATTATGTTAA
1 TGCTACCTATTATATTAA
1741902 ATAAACGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (23 bp):
TGCTACCTATTATATTAAGTAGG
Found at i:1741869 original size:196 final size:196
Alignment explanation
Indices: 1741485--1741902 Score: 577
Period size: 196 Copynumber: 2.1 Consensus size: 196
1741475 GGTTAAAATA
* *
1741485 AAATAAGAGCTACCTATTATGTTAAACTACCTACCGGTTTGTTTGAAGGTTACTAATAATGTAAA
1 AAATAAGAGCTACCTATTATGTTAAACTACCTACCGGTATGTTTGAAGGTTACTAATAATATAAA
* * *
1741550 CGGTAAAATAAAATAGAAGCTACCTATTACGTTAAAATACTTACTGGTTTGTTTAAAGGTTACTA
66 CGGAAAAATAAAATAGAAGCTACCTATTACGTTAAAATACCTACTGGTTTGTTTAAAAGTTACTA
* * * *
1741615 ATAATGTAAACGGTAAAATAAAATAGGCACTACCTTTTATGTTAAATAGGCACTACCTATTACGT
131 ATAATATAAACGGTAAAATAAAATAGACACTACCTATTATATTAAATAGGCACTACCTATTACGT
1741680 T
196 T
* *
1741681 AAATAAGCGCTATCTATTATGTTAAACTACCTACCGGTATGTTTGAAGGTTACTAATAATATAAA
1 AAATAAGAGCTACCTATTATGTTAAACTACCTACCGGTATGTTTGAAGGTTACTAATAATATAAA
* ** *
1741746 TGGAAAAATAAAATAGTTGCTACCTATTACGTTAAAATACCTA-TCGGTTTGTTTAAAAGTTATT
66 CGGAAAAATAAAATAGAAGCTACCTATTACGTTAAAATACCTACT-GGTTTGTTTAAAAGTTACT
* ** * ** ***
1741810 AATAATATAAATGGTAAAATAAAATAGATGCTACCTATTATATTAAGTAGGTGCTACCTATTTTA
130 AATAATATAAACGGTAAAATAAAATAGACACTACCTATTATATTAAATAGGCACTACCTATTACG
1741875 TT
195 TT
* * *
1741877 AAGTAGGTGCTACCTATTATGTTAAA
1 AAATAAGAGCTACCTATTATGTTAAA
1741903 TAAACGGTAC
Statistics
Matches: 193, Mismatches: 28, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
195 1 0.01
196 192 0.99
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (196 bp):
AAATAAGAGCTACCTATTATGTTAAACTACCTACCGGTATGTTTGAAGGTTACTAATAATATAAA
CGGAAAAATAAAATAGAAGCTACCTATTACGTTAAAATACCTACTGGTTTGTTTAAAAGTTACTA
ATAATATAAACGGTAAAATAAAATAGACACTACCTATTATATTAAATAGGCACTACCTATTACGT
T
Found at i:1742669 original size:108 final size:108
Alignment explanation
Indices: 1742468--1742745 Score: 344
Period size: 108 Copynumber: 2.6 Consensus size: 108
1742458 TGATAATATT
* * ** * * * *
1742468 TATTTATAACAAAATAA-TAAATTAACCTATTTTATTGTCGTGTGATTTCAAAGTCCCTATCAGC
1 TATTAATAACAAAATAAGT-AATTAACCTATTTTATTATCGTCAGATTTCTAAGGCCCAATCAAC
* * * *
1742532 TTAAACTTTAGTAACATTTAAGGCGCTACCTAATGTGTTGATAA
65 ATAAACTTTAGTAACATTTAAGGCACTACCTAATATATTGATAA
* *
1742576 TATTAATAACAAAATAAGTAATTAACCTATTTTTTTATCATCAGATTTCTAAGGCCCAATCAACA
1 TATTAATAACAAAATAAGTAATTAACCTATTTTATTATCGTCAGATTTCTAAGGCCCAATCAACA
* *
1742641 TAAACTTT-GATAATATTTTAGGCACTACCTAATATATTGATAA
66 TAAACTTTAG-TAACATTTAAGGCACTACCTAATATATTGATAA
* * * *
1742684 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCA
1 TATTAATAACAAAATAAGTAATTAACCTATTTTATTATCGTCAGATTTCTAAGGCCCAATCA
1742746 GCTTTAAAAG
Statistics
Matches: 147, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
107 1 0.01
108 145 0.99
109 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (108 bp):
TATTAATAACAAAATAAGTAATTAACCTATTTTATTATCGTCAGATTTCTAAGGCCCAATCAACA
TAAACTTTAGTAACATTTAAGGCACTACCTAATATATTGATAA
Found at i:1742848 original size:226 final size:226
Alignment explanation
Indices: 1742592--1743074 Score: 706
Period size: 226 Copynumber: 2.1 Consensus size: 226
1742582 TAACAAAATA
* * *
1742592 AGTAATTAACCTATTTTTTTATCA-TCAGATTTCTAAGGC-CCAATCAACATAAAC-TTTGATAA
1 AGTAATTAATCTATTTTGTTAT-AGTCAGATTTCCAAGGCTCC-ATCAACATAAACTTTTG-TAA
* *
1742654 TATTTTAGGCACTACCTAATATATTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGT
63 CATTTTAGGCACTACCTAATATATTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGT
*
1742719 TATCGTC-AGATTTCTAAGGCCCCATCAGCTTTAAAAGGGCGCTACCTATTACATTAAATAAGCG
128 TATCGTCGA-ATTTCTAAGGCCCCATCAGCTTTAAAAGGGCACTACCTATTACATTAAATAAGCG
1742783 CTACTTGTTATATTATTATGATTGATAATGTTTCC
192 CTACTTGTTATATTATTATGATTGATAATGTTTCC
* * *
1742818 AGTAATTAATCTATTTTGTTATAGTCAGATTTCCAAGGCTCCATTAGCTTAAACTTTTGTAACAT
1 AGTAATTAATCTATTTTGTTATAGTCAGATTTCCAAGGCTCCATCAACATAAACTTTTGTAACAT
* *
1742883 TTTAGGCTCTACCTAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCACTACCTAATATATTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTAT
* * * *
1742948 CGTCGAATTTCTAAGGTCCCATCAGCTTTAAAGGGGCACTACCTATTACGTTACATAAGCGCTAC
131 CGTCGAATTTCTAAGGCCCCATCAGCTTTAAAAGGGCACTACCTATTACATTAAATAAGCGCTAC
* *
1743013 TTGTTATGTTATTATGGTTGATAATGTTTCC
196 TTGTTATATTATTATGATTGATAATGTTTCC
* ** *
1743044 AATAATTAATCGGTTATGTTATAGTCA-ATTT
1 AGTAATTAATCTATTTTGTTATAGTCAGATTT
1743075 TTTTTGACGC
Statistics
Matches: 232, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
225 5 0.02
226 220 0.95
227 7 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (226 bp):
AGTAATTAATCTATTTTGTTATAGTCAGATTTCCAAGGCTCCATCAACATAAACTTTTGTAACAT
TTTAGGCACTACCTAATATATTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTAT
CGTCGAATTTCTAAGGCCCCATCAGCTTTAAAAGGGCACTACCTATTACATTAAATAAGCGCTAC
TTGTTATATTATTATGATTGATAATGTTTCC
Found at i:1744256 original size:36 final size:36
Alignment explanation
Indices: 1744180--1744306 Score: 148
Period size: 36 Copynumber: 3.5 Consensus size: 36
1744170 AAGGAAATTG
* * *
1744180 TCTCAAGTGAGACAAAATTTGTTTTTTAA-AAAAACAA
1 TCTCAAGTGAGATAAAA-TT-TATTTTAAGAAAAAAAA
* * *
1744217 TCTCAAGTAAAATAAAATTTATTTTGAGAAAAAAAA
1 TCTCAAGTGAGATAAAATTTATTTTAAGAAAAAAAA
* * *
1744253 TCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAAATTTATTTTAAGAAAAAAAA
1744289 TCTCAAGTGAGATAAAAT
1 TCTCAAGTGAGATAAAAT
1744307 CTTTAGTGAA
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
35 6 0.08
36 56 0.74
37 14 0.18
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (36 bp):
TCTCAAGTGAGATAAAATTTATTTTAAGAAAAAAAA
Found at i:1744745 original size:116 final size:115
Alignment explanation
Indices: 1744440--1744834 Score: 451
Period size: 116 Copynumber: 3.4 Consensus size: 115
1744430 TATGAACTTC
* * ** *
1744440 TTCTCCTTCAT-GAGACGAGTTCTTCTCATTATGAACCCTTCCGCTGGAAATGTTGATCCACCTC
1 TTCTCCCTCATCG-GACGAGTTCTTCTCATTATGAACCTTTCCATTGGAAATGTTGATCCACTTC
* * * *
1744504 CTTTTGTGATGGATGAACCAAGGTTGAACAAGTTATTCTTATTAGGAACTTT
65 CTTCTGTGATGGACGAGCCAAGGTTGAACAAGTTATTCTCATTAGGAA-TTT
* * *
1744556 TTCTCCCTCATCGGACAAG---TTCTCATTATGAACCATTCCATTGGAAATGCTGATCCACCTT-
1 TTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACCTTTCCATTGGAAATGTTGATCCA-CTTC
* * *
1744617 ATTCTG-GCATGGACGAGCCAAGGTTGAATAAGTTATTCTCATGAGGAATTT
65 CTTCTGTG-ATGGACGAGCCAAGGTTGAACAAGTTATTCTCATTAGGAATTT
* * * * *
1744668 AATCTCCCTTATCAGATGAGTTCTTCTCATTATGAACCTTTCCATTGGAAATATTGATCCACTTC
1 -TTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACCTTTCCATTGGAAATGTTGATCCACTTC
* * *
1744733 CTTCTGTGATGGACGAGCCAAGGTTGAACAAGTTTTTCTCATTAAGAACTTC
65 CTTCTGTGATGGACGAGCCAAGGTTGAACAAGTTATTCTCATTAGGAA-TTT
* * * *
1744785 TTCTCCCTCATCGGACGAGTTCATCTTATTATGAACATTTCAATTGGAAA
1 TTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACCTTTCCATTGGAAA
1744835 AGCAGGTATG
Statistics
Matches: 233, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
112 4 0.02
113 87 0.37
114 2 0.01
115 3 0.01
116 133 0.57
117 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (115 bp):
TTCTCCCTCATCGGACGAGTTCTTCTCATTATGAACCTTTCCATTGGAAATGTTGATCCACTTCC
TTCTGTGATGGACGAGCCAAGGTTGAACAAGTTATTCTCATTAGGAATTT
Found at i:1747429 original size:2 final size:2
Alignment explanation
Indices: 1747409--1747456 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
1747399 ATTATAGTTA
* *
1747409 AT AT AT GT AT AT TT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1747452 AT AT A
1 AT AT A
1747457 ATTTAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 40 0.98
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1747567 original size:26 final size:25
Alignment explanation
Indices: 1747534--1747585 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
1747524 TGAATATTTA
1747534 ATTTGAAATAATTAAATAAGACTTT
1 ATTTGAAATAATTAAATAAGACTTT
*
1747559 ATTTCGAAATAATTAAATAAGATTTT
1 ATTT-GAAATAATTAAATAAGACTTT
1747585 A
1 A
1747586 ATTAATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
ATTTGAAATAATTAAATAAGACTTT
Found at i:1753758 original size:27 final size:27
Alignment explanation
Indices: 1753718--1753771 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1753708 TTTTCACGGG
* *
1753718 ATCTCTGATTATGATCGAGAAATCCGA
1 ATCTCTGATCATGACCGAGAAATCCGA
1753745 ATCTCTGATCATGACCGAGAAATCCGA
1 ATCTCTGATCATGACCGAGAAATCCGA
1753772 CTGGATCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (27 bp):
ATCTCTGATCATGACCGAGAAATCCGA
Found at i:1757432 original size:24 final size:24
Alignment explanation
Indices: 1757405--1757523 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
1757395 TTCGATTTGA
1757405 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
1757429 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
1757453 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1757477 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
1757501 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
1757524 AATTATGTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
23 1 0.01
24 86 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:1757702 original size:43 final size:43
Alignment explanation
Indices: 1757641--1757733 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
1757631 GCCTTACTTA
*
1757641 GTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTATG
1 GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATG
1757684 GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATG
1 GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATG
1757727 GTGTGTT
1 GTGTGTT
1757734 CGGTTGGAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.16, C:0.11, G:0.37, T:0.37
Consensus pattern (43 bp):
GTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTATG
Found at i:1771563 original size:98 final size:98
Alignment explanation
Indices: 1771341--1771615 Score: 266
Period size: 98 Copynumber: 2.8 Consensus size: 98
1771331 ATCATGATAT
* * * *
1771341 ATTTACTCCACTACTCTTCAGGGTAGGTCAAATCTAGAGAAGAA-ATGGAATATGCTCTGCTACT
1 ATTTTCTCCGCTACTCTTCAGGGTAGGTCAAATCTAAAGAA-AAGAT-G-ATATGCTCCGCTACT
* * * * *
1771405 CTTCAAGGAAGGTCATATTTAGAGAAAAATAAAGGGG
63 CTT-TAGGTAGGTCAGATCTAGAGAAAAATAAAGGAG
* * * ** *
1771442 ATTTTCTCCTCTGCTCTTAAGGGTAAATCAAATCTAAAGAAAAGATGATATGCTCCGCTATTCTT
1 ATTTTCTCCGCTACTCTTCAGGGTAGGTCAAATCTAAAGAAAAGATGATATGCTCCGCTACTCTT
* * *
1771507 TAGGGTAGGTCAGATCTATAG-GAAATAAATGAG
66 TA-GGTAGGTCAGATCTAGAGAAAAATAAAGGAG
* * * * * * *
1771540 ATTTTTTTCGCTACTCTTCAGGGTAGGTCAGATCTAAAGAAAAGATGATCTGCTTCGTTGCTCTT
1 ATTTTCTCCGCTACTCTTCAGGGTAGGTCAAATCTAAAGAAAAGATGATATGCTCCGCTACTCTT
1771605 TAGGTAGGTCA
66 TAGGTAGGTCA
1771616 AATCAAGGTA
Statistics
Matches: 142, Mismatches: 30, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
97 9 0.06
98 64 0.45
99 30 0.21
100 3 0.02
101 36 0.25
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (98 bp):
ATTTTCTCCGCTACTCTTCAGGGTAGGTCAAATCTAAAGAAAAGATGATATGCTCCGCTACTCTT
TAGGTAGGTCAGATCTAGAGAAAAATAAAGGAG
Found at i:1771718 original size:93 final size:92
Alignment explanation
Indices: 1771586--1771872 Score: 297
Period size: 93 Copynumber: 3.1 Consensus size: 92
1771576 AAGAAAAGAT
* * * * **
1771586 GATCTGCTTCGTTGCTCTTTAGGTAGGTCAAATCAAGGTAGATTTACTCTACTTTTCTTTAGAGT
1 GATCTGCTTCGTTTCTCTTAAGGTAGGTCATATCAAGGTAGATTTGCTCTACTGCTCTTTAGAGT
* *
1771651 AGGTCAAATATAGAGAACATAAAGGGG
66 AGGTCAAATATAGAGAAAAGAAAGGGG
* * * *
1771678 GATCTGCTCCGTTTCTCTTCAAGGTAGGTCATACCTAGGTAGATTTGCTCTACTGCTCTTTAGGG
1 GATCTGCTTCGTTTCTCTT-AAGGTAGGTCATATCAAGGTAGATTTGCTCTACTGCTCTTTAGAG
** *
1771743 TAGGTTTAATCTAGAGAAAAGAAAGGGG
65 TAGGTCAAATATAGAGAAAAGAAAGGGG
* * * * * * *
1771771 GATCTGCTTTGTTTCTCTTTAGGGTAGATCATATCAAGGTAGATTTGCTCTAATGATATTCA-AG
1 GATCTGCTTCGTTTCTC-TTAAGGTAGGTCATATCAAGGTAGATTTGCTCTACTGCTCTTTAGA-
* * * *
1771835 GTAGGTTAAATCTAGAGAAAAGAATGGGA
64 GTAGGTCAAATATAGAGAAAAGAAAGGGG
*
1771864 GATATGCTT
1 GATCTGCTT
1771873 AGCGACTCTT
Statistics
Matches: 162, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
92 17 0.10
93 143 0.88
94 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (92 bp):
GATCTGCTTCGTTTCTCTTAAGGTAGGTCATATCAAGGTAGATTTGCTCTACTGCTCTTTAGAGT
AGGTCAAATATAGAGAAAAGAAAGGGG
Found at i:1773325 original size:18 final size:18
Alignment explanation
Indices: 1773304--1773345 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1773294 CTTGAGACCT
1773304 CCTTTGATTTTAAAACGC
1 CCTTTGATTTTAAAACGC
1773322 CCTTTGATTTTAAAACGC
1 CCTTTGATTTTAAAACGC
1773340 CCTTTG
1 CCTTTG
1773346 CAGATTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (18 bp):
CCTTTGATTTTAAAACGC
Found at i:1776450 original size:157 final size:157
Alignment explanation
Indices: 1776013--1776682 Score: 757
Period size: 155 Copynumber: 4.3 Consensus size: 157
1776003 TTAAATCCAA
* * * *
1776013 CTTTTATTTTAAGTATGTTTTTACCAAATTTAAACCACATGCTCTTAAGACATCGTAAAATACAT
1 CTTTTATTTTAAGTCTGTTTTTACCAAATTTAAACCACATGCTCATAAAACATCGTAGAATACAT
* * * *
1776078 ATGTACTTTCAATTTCTC-TTTTAGATAATAAATTTTATAATTTTCAATTTAGGCCTTCAATTTT
66 ATGTACTTTCAATTTCTCTTTTTA-ATAACAAATTTTATATTTTTCAATTTAGTCCCTCAATTTT
* *
1776142 TCATAATTTCCATATTTCTTCAATACAT
130 TCATAATTTCCTTATTTCTTCAATTCAT
* * * *
1776170 CCTTTATTTTAAGAT-T-ATTTTACCAAATTTGAACCACATGCTCGT-AAACAATCGTAGAA-AC
1 CTTTTATTTTAAG-TCTGTTTTTACCAAATTTAAACCACATGCTCATAAAAC-ATCGTAGAATAC
* * * * *
1776231 ATATGTACTTTCAATTTATCTTTTTGATAACAAATTTTCTAATTTTCAATTTAATCCCTCAATTT
64 ATATGTACTTTCAATTTCTCTTTTTAATAACAAATTTTATATTTTTCAATTTAGTCCCTCAATTT
* * * * *
1776296 TTCATATTTTTCGTATTTATTCAATTTAT
129 TTCATAATTTCCTTATTTCTTCAATTCAT
* ** * * * * * *
1776325 CTTTTATTTTAAGTCTATTTTTATTAAATTTGAACTACATACCCCTAAAACATCATAGAATACAT
1 CTTTTATTTTAAGTCTGTTTTTACCAAATTTAAACCACATGCTCATAAAACATCGTAGAATACAT
* * * * *
1776390 ATTTACTTTCAATTTCTATTTTTAATAAAAAAATATT-TATTTTTCAATTTAGTCCATCAATTTT
66 ATGTACTTTCAATTTCTCTTTTTAAT-AACAAATTTTATATTTTTCAATTTAGTCCCTCAATTTT
*
1776454 TAATAATTTCCTTATTTCTTCAATTCAT
130 TCATAATTTCCTTATTTCTTCAATTCAT
* * *
1776482 -TATTTATTTTAAGTCTGTTTTTAACAAATTTAAACCGCATGCTCATAAACCA-CTGTAGAATAC
1 CT-TTTATTTTAAGTCTGTTTTTACCAAATTTAAACCACATGCTCATAAAACATC-GTAGAATAC
* * * *
1776545 ATATGTTCTTTCAA--TCTCTTTTTGATAACAAATTTTATATTTTTCTATTTAGTCCCTCAAATT
64 ATATGTACTTTCAATTTCTCTTTTTAATAACAAATTTTATATTTTTCAATTTAGTCCCTCAATTT
*
1776608 TTCATAATTTCCTTATTTCCTCAATTCAT
129 TTCATAATTTCCTTATTTCTTCAATTCAT
* * * *
1776637 CCTTTATTTTAAATTTGTTTTTATCAAATTTAAACCACATGCTCAT
1 CTTTTATTTTAAGTCTGTTTTTACCAAATTTAAACCACATGCTCAT
1776683 GTATCGTAAT
Statistics
Matches: 431, Mismatches: 70, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
154 9 0.02
155 194 0.45
156 70 0.16
157 149 0.35
158 9 0.02
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (157 bp):
CTTTTATTTTAAGTCTGTTTTTACCAAATTTAAACCACATGCTCATAAAACATCGTAGAATACAT
ATGTACTTTCAATTTCTCTTTTTAATAACAAATTTTATATTTTTCAATTTAGTCCCTCAATTTTT
CATAATTTCCTTATTTCTTCAATTCAT
Done.