Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008211.1 Hibiscus syriacus cultivar Beakdansim tig00110833_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: 2208279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1701051 original size:19 final size:20
Alignment explanation
Indices: 1701029--1701067 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1701019 ACAAGTATAG
*
1701029 ATTTAATTTAA-AAATTATT
1 ATTTAATATAAGAAATTATT
*
1701048 ATTTGATATAAGAAATTATT
1 ATTTAATATAAGAAATTATT
1701068 TCAAATACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTAATATAAGAAATTATT
Found at i:1701791 original size:2 final size:2
Alignment explanation
Indices: 1701784--1701823 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1701774 ACCATTAACA
1701784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1701824 TTAAAGGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1704094 original size:24 final size:24
Alignment explanation
Indices: 1704021--1704094 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 24
1704011 TGTTCATTTA
*
1704021 TTTAT-TGTTCACGAACATGTTCG
1 TTTATATGTTCACGAACGTGTTCG
* ** * *
1704044 CTTA-ATGTTCGTGAACGTGCTCA
1 TTTATATGTTCACGAACGTGTTCG
1704067 TTTATATGTTCACGAACGTGTTCG
1 TTTATATGTTCACGAACGTGTTCG
1704091 TTTA
1 TTTA
1704095 GCATTCACGA
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
23 19 0.50
24 19 0.50
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (24 bp):
TTTATATGTTCACGAACGTGTTCG
Found at i:1704117 original size:23 final size:23
Alignment explanation
Indices: 1704075--1704119 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1704065 CATTTATATG
* * *
1704075 TTCACGAACGTGTTCGTTTAGCA
1 TTCACGAACATATTCATTTAGCA
1704098 TTCACGAACATATTCATTTAGC
1 TTCACGAACATATTCATTTAGC
1704120 GTAAGATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (23 bp):
TTCACGAACATATTCATTTAGCA
Found at i:1704484 original size:2 final size:2
Alignment explanation
Indices: 1704477--1704502 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1704467 TATTTTTGTG
1704477 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
1704503 TAAAAAAGTT
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:1706883 original size:21 final size:21
Alignment explanation
Indices: 1706845--1706884 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1706835 ATGGCAATTT
*
1706845 AACTTGAATCCGATGGGTTCC
1 AACTTGAACCCGATGGGTTCC
1706866 AACTTG-ACCCGATAGGGTT
1 AACTTGAACCCGAT-GGGTT
1706885 GGATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (21 bp):
AACTTGAACCCGATGGGTTCC
Found at i:1707146 original size:32 final size:33
Alignment explanation
Indices: 1707089--1707151 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1707079 GGTCGTAGTC
1707089 GGTGGAGAGTATATATTTTTCGGGTCGGGTTCG
1 GGTGGAGAGTATATATTTTTCGGGTCGGGTTCG
* *
1707122 GGTGGAGGGTGTATATTTTT-GGGTCGGGTT
1 GGTGGAGAGTATATATTTTTCGGGTCGGGTT
1707152 GACCAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 10 0.36
33 18 0.64
ACGTcount: A:0.13, C:0.06, G:0.43, T:0.38
Consensus pattern (33 bp):
GGTGGAGAGTATATATTTTTCGGGTCGGGTTCG
Found at i:1718647 original size:27 final size:27
Alignment explanation
Indices: 1718609--1718675 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
1718599 CAAAACAGTG
*
1718609 CTGAATGATTCAGCACAGAAGTACATT
1 CTGAATGATTCAGCACAGAAATACATT
1718636 CTGAATGATTCAGCACAGAAATACATT
1 CTGAATGATTCAGCACAGAAATACATT
*
1718663 CCGAATGATTCAG
1 CTGAATGATTCAG
1718676 AGCCATTATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (27 bp):
CTGAATGATTCAGCACAGAAATACATT
Found at i:1722565 original size:77 final size:79
Alignment explanation
Indices: 1722391--1722635 Score: 261
Period size: 77 Copynumber: 3.2 Consensus size: 79
1722381 AAACTCGAAT
*
1722391 ACTTATACACCCTTGCATACATGGTGTTCAAACACGAGACCTCAAAGGAT-AAAGATTCTTAACC
1 ACTTATACACCCTTGCATACATGGTGCTCAAACACGAGACCTCAAAGGATAAAAGA-TCTTAACC
*
1722455 ATTAGACATTGAACG
65 ATTTGACATTGAACG
* * * * * * * *
1722470 A-TTACACACCCTTACATACATAGTACTCGAACCCGGGACCTCAAGGGATAAAAGA-CTTAACCA
1 ACTTATACACCCTTGCATACATGGTGCTCAAACACGAGACCTCAAAGGATAAAAGATCTTAACCA
*
1722533 TTTGACATTTAAC-
66 TTTGACATTGAACG
* * * *
1722546 ACTTATACA-CCTCTGCATACATGGTGCTCAAACTCGATACCTCAAAGAATAAAAGATTCTCAAC
1 ACTTATACACCCT-TGCATACATGGTGCTCAAACACGAGACCTCAAAGGATAAAAGA-TCTTAAC
* *
1722610 CATTTGACACTG-CCG
64 CATTTGACATTGAACG
1722625 -CTTATACACCC
1 ACTTATACACCC
1722636 CTATATGCAT
Statistics
Matches: 134, Mismatches: 25, Indels: 14
0.77 0.14 0.08
Matches are distributed among these distances:
76 4 0.03
77 59 0.44
78 48 0.36
79 23 0.17
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.25
Consensus pattern (79 bp):
ACTTATACACCCTTGCATACATGGTGCTCAAACACGAGACCTCAAAGGATAAAAGATCTTAACCA
TTTGACATTGAACG
Found at i:1722656 original size:155 final size:154
Alignment explanation
Indices: 1722391--1722674 Score: 358
Period size: 155 Copynumber: 1.8 Consensus size: 154
1722381 AAACTCGAAT
* * *
1722391 ACTTATACACCCTTGCATACATGGTGTTCAAACACGAGACCTCAAAGGATAAAGATTCTTAACCA
1 ACTTATACACCCTTGCATACATGGTGCTCAAACACGAGACCTCAAAGAATAAAGATTCTCAACCA
* * * * * *
1722456 TTAGACATTGAACGATTACACACCCTTACATACATAGTACTCGAACCCGGGACCTCAAGGGATAA
66 TTAGACACTGAACGATTACACACCCCTACATACATAGAACACGAACCCAGAACCT-AAGGGATAA
1722521 AAGACTTAACCATTTGACATTTAAC
130 AAGACTTAACCATTTGACATTTAAC
* *
1722546 ACTTATACA-CCTCTGCATACATGGTGCTCAAACTCGATACCTCAAAGAATAAAAGATTCTCAAC
1 ACTTATACACCCT-TGCATACATGGTGCTCAAACACGAGACCTCAAAGAAT-AAAGATTCTCAAC
* * * * * *
1722610 CATTTGACACTG-CCGCTTATACACCCCTATATGCAT-GAAGCACGAACCCAGAACCTAAGGGAT
64 CATTAGACACTGAACGATTACACACCCCTACATACATAGAA-CACGAACCCAGAACCTAAGGGAT
1722673 AA
128 AA
1722675 CAATAATCCC
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
154 14 0.13
155 73 0.67
156 22 0.20
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (154 bp):
ACTTATACACCCTTGCATACATGGTGCTCAAACACGAGACCTCAAAGAATAAAGATTCTCAACCA
TTAGACACTGAACGATTACACACCCCTACATACATAGAACACGAACCCAGAACCTAAGGGATAAA
AGACTTAACCATTTGACATTTAAC
Found at i:1727179 original size:18 final size:19
Alignment explanation
Indices: 1727138--1727180 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1727128 TCTCTCTAAA
*
1727138 AAAAATAAAATAAAATAAG
1 AAAAAGAAAATAAAATAAG
*
1727157 -TAAAGAAAATAAAA-AAG
1 AAAAAGAAAATAAAATAAG
1727174 AAAAAGA
1 AAAAAGA
1727181 TTGCTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (19 bp):
AAAAAGAAAATAAAATAAG
Found at i:1727578 original size:46 final size:46
Alignment explanation
Indices: 1727527--1727627 Score: 184
Period size: 46 Copynumber: 2.2 Consensus size: 46
1727517 TTAAATGATT
*
1727527 TATTAATGATTATTTTTTACTTTTATAGGGTGTTTAACAACAAGCA
1 TATTAATGATTAGTTTTTACTTTTATAGGGTGTTTAACAACAAGCA
*
1727573 TATTAATGATTAGTTTTTACTTTTATAGGGTGTTTAACAATAAGCA
1 TATTAATGATTAGTTTTTACTTTTATAGGGTGTTTAACAACAAGCA
1727619 TATTAATGA
1 TATTAATGA
1727628 AATAATTGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.46
Consensus pattern (46 bp):
TATTAATGATTAGTTTTTACTTTTATAGGGTGTTTAACAACAAGCA
Found at i:1728877 original size:17 final size:17
Alignment explanation
Indices: 1728847--1728879 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1728837 CTCGGGTTAG
1728847 TCAACATCAATTCAAAC
1 TCAACATCAATTCAAAC
1728864 TCAA-ATCAATTTCAAA
1 TCAACATCAA-TTCAAA
1728880 TCACCGCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
TCAACATCAATTCAAAC
Found at i:1733448 original size:30 final size:31
Alignment explanation
Indices: 1733414--1733473 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1733404 ATGGTAAATT
*
1733414 ACTTG-TTTAGTACTTAAACTATCAATTTTG
1 ACTTGTTTTAGAACTTAAACTATCAATTTTG
* *
1733444 ACTTGTTTTAGAACTTAAACTTTTAATTTT
1 ACTTGTTTTAGAACTTAAACTATCAATTTT
1733474 ATTTTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (31 bp):
ACTTGTTTTAGAACTTAAACTATCAATTTTG
Found at i:1734606 original size:105 final size:105
Alignment explanation
Indices: 1734482--1734676 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 105
1734472 AATTGTGTAT
* * * * *
1734482 TCAAATCTAACCATGAG-AAAAAGATAAACTAAAACAACAACCAACTGGCGGTAAACGTGCCATA
1 TCAAATCTAACCATAAGAAAAAAAATAAAC-AAAACAACAACCAAATGGCGGAAAACATGCCATA
* *
1734546 ATGATAAAGAAAAATATGTCATAAAGGTATAAAAAAATATA
65 ACGATAAAGAAAAACATGTCATAAAGGTATAAAAAAATATA
* * *
1734587 TCAAATCTAATCC-TAAGAAAAAAAATAAACAAAACAACGACCAAATGGCTGAAAACATGTCATA
1 TCAAATCTAA-CCATAAGAAAAAAAATAAACAAAACAACAACCAAATGGCGGAAAACATGCCATA
*
1734651 ACGATAAAGAAAAACATGTTATAAAG
65 ACGATAAAGAAAAACATGTCATAAAG
1734677 ATAGAAGAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
105 64 0.83
106 13 0.17
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.18
Consensus pattern (105 bp):
TCAAATCTAACCATAAGAAAAAAAATAAACAAAACAACAACCAAATGGCGGAAAACATGCCATAA
CGATAAAGAAAAACATGTCATAAAGGTATAAAAAAATATA
Found at i:1734665 original size:23 final size:23
Alignment explanation
Indices: 1734637--1734698 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1734627 CCAAATGGCT
*
1734637 GAAAACATGTCATAACGATA-AA
1 GAAAACATGTCATAAAGATAGAA
*
1734659 GAAAAACATGTTATAAAGATAGAA
1 G-AAAACATGTCATAAAGATAGAA
1734683 GAAAACATGTCATAAA
1 GAAAACATGTCATAAA
1734699 TATATAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.03
23 31 0.89
24 3 0.09
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (23 bp):
GAAAACATGTCATAAAGATAGAA
Found at i:1739627 original size:3 final size:3
Alignment explanation
Indices: 1739621--1739666 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
1739611 AAAAAACTCG
* * **
1739621 TAT TAT TAT TAT TGT TTT TAT TGG TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1739667 GATAATGTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1742409 original size:17 final size:17
Alignment explanation
Indices: 1742389--1742446 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
1742379 GAAAGTCAAC
1742389 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1742406 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
1742423 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1742440 GGTCAAC
1 GGTCAAC
1742447 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1742497 original size:19 final size:19
Alignment explanation
Indices: 1742440--1742504 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
1742430 AGTCGGGTCG
*
1742440 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* * *
1742459 AGTCAAACCGATTTAGACC
1 GGTCAAACCGGTTCAGACC
1742478 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
1742497 GGTTCAAA
1 GG-TCAAA
1742505 ACTGGTCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 1 0.03
19 31 0.84
20 5 0.14
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1749019 original size:17 final size:17
Alignment explanation
Indices: 1748999--1749056 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
1748989 GAAAGTTAAC
1748999 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1749016 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
1749033 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1749050 GGTCAAC
1 GGTCAAC
1749057 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1749074 original size:19 final size:19
Alignment explanation
Indices: 1749050--1749139 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
1749040 AGTCGGGTCG
*
1749050 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
1749069 GGTCAAACCGATTCAGACC
1 GGTCAAACCGGTTCAGACC
1749088 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
1749107 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
1749127 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1749140 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.75
20 15 0.24
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1749106 original size:10 final size:10
Alignment explanation
Indices: 1749052--1749139 Score: 85
Period size: 9 Copynumber: 9.1 Consensus size: 10
1749042 TCGGGTCGGG
*
1749052 TCAACCCGGT
1 TCAAACCGGT
*
1749062 TCAGACCGG-
1 TCAAACCGGT
*
1749071 TCAAACCGAT
1 TCAAACCGGT
*
1749081 TCAGACCGG-
1 TCAAACCGGT
1749090 TCAAACCGGT
1 TCAAACCGGT
*
1749100 TCGAACCGG-
1 TCAAACCGGT
1749109 TCAAACCGGT
1 TCAAACCGGT
*
1749119 TCAAAACTGG-
1 TC-AAACCGGT
1749129 TCAAACCGGT
1 TCAAACCGGT
1749139 T
1 T
1749140 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 29 0.47
10 27 0.44
11 6 0.10
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1749948 original size:31 final size:31
Alignment explanation
Indices: 1749902--1749962 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1749892 CTGTTAGTAA
*
1749902 CTTTTGTTTTCATTTAATTAAGATATTGTCG
1 CTTTCGTTTTCATTTAATTAAGATATTGTCG
*
1749933 CTTTCGTTTTTATTTAATTAAGATATTGTC
1 CTTTCGTTTTCATTTAATTAAGATATTGTC
1749963 ATTGAGAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.56
Consensus pattern (31 bp):
CTTTCGTTTTCATTTAATTAAGATATTGTCG
Found at i:1752112 original size:22 final size:23
Alignment explanation
Indices: 1752074--1752116 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1752064 CTATCTTTTA
1752074 TTTCTGTCTGCTATTAATGTGTT
1 TTTCTGTCTGCTATTAATGTGTT
*
1752097 TTTCTGT-TGCTTTTAATGTG
1 TTTCTGTCTGCTATTAATGTG
1752117 GTAGCGCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (23 bp):
TTTCTGTCTGCTATTAATGTGTT
Found at i:1754934 original size:10 final size:10
Alignment explanation
Indices: 1754918--1754954 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1754908 TCTCATCCTG
1754918 TTATATATAT
1 TTATATATAT
*
1754928 ATATATATAT
1 TTATATATAT
*
1754938 TTATATTTAT
1 TTATATATAT
1754948 TTATATA
1 TTATATA
1754955 AAGTGATTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATATATAT
Found at i:1766434 original size:11 final size:11
Alignment explanation
Indices: 1766418--1766443 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1766408 TATAAAATTT
1766418 TAAATGAAAAA
1 TAAATGAAAAA
1766429 TAAATGAAAAA
1 TAAATGAAAAA
1766440 TAAA
1 TAAA
1766444 AATATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (11 bp):
TAAATGAAAAA
Found at i:1766446 original size:17 final size:17
Alignment explanation
Indices: 1766419--1766456 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1766409 ATAAAATTTT
1766419 AAATGAAAAATAAATGAA
1 AAATGAAAAATAAAT-AA
*
1766437 AAAT-AAAAATATATAA
1 AAATGAAAAATAAATAA
1766453 AAAT
1 AAAT
1766457 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATGAAAAATAAATAA
Found at i:1770993 original size:21 final size:21
Alignment explanation
Indices: 1770969--1771010 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1770959 AATCCATAGG
1770969 TGGAAATTTATACTACAGATT
1 TGGAAATTTATACTACAGATT
1770990 TGGAAATTTATACTACAGATT
1 TGGAAATTTATACTACAGATT
1771011 CGAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
TGGAAATTTATACTACAGATT
Found at i:1782481 original size:2 final size:2
Alignment explanation
Indices: 1782436--1782461 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1782426 GTATTTGTGG
1782436 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
1782462 GAATAAGGTA
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:1783025 original size:23 final size:23
Alignment explanation
Indices: 1782957--1783025 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1782947 CAACCTTATA
1782957 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
1782980 CGGTACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
1783003 TGGCATTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1783026 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1789324 original size:13 final size:13
Alignment explanation
Indices: 1789306--1789333 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1789296 CAAGTATACC
1789306 TGAACTTATTAAA
1 TGAACTTATTAAA
1789319 TGAACTTATTAAA
1 TGAACTTATTAAA
1789332 TG
1 TG
1789334 GAATCAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (13 bp):
TGAACTTATTAAA
Found at i:1790854 original size:2 final size:2
Alignment explanation
Indices: 1790849--1790886 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1790839 AAAAATCAAA
1790849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1790887 TTGACACGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1795777 original size:20 final size:20
Alignment explanation
Indices: 1795705--1795771 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1795695 TATTCCCTGG
*
1795705 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCTCACTGA
*
1795725 TAATCTTTTATT-TCTACTGG
1 TAATCTTTTATTCTC-ACTGA
*
1795745 TAATATTTTATTCTCACTGA
1 TAATCTTTTATTCTCACTGA
1795765 TAATCTT
1 TAATCTT
1795772 ACATTCCGCG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.93
21 2 0.05
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (20 bp):
TAATCTTTTATTCTCACTGA
Found at i:1796041 original size:19 final size:21
Alignment explanation
Indices: 1796008--1796056 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
1795998 ATGTTAAAAT
* *
1796008 ATATTATTTAATTATTA-AAA
1 ATATTAATAAATTATTATAAA
1796028 ATA-TAATAAATTATTATAAA
1 ATATTAATAAATTATTATAAA
1796048 ATATTAATA
1 ATATTAATA
1796057 TATTTGAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 9 0.36
21 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTAATAAATTATTATAAA
Found at i:1797493 original size:31 final size:31
Alignment explanation
Indices: 1797449--1797535 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
1797439 TTTTTGGGTA
*
1797449 AAATTGGTATTTTATCCAAAGTTTAAGAG-TC
1 AAATTAGTATTTTATCCAAA-TTTAAGAGATC
* * * *
1797480 AAATTAGTGTTTTATCGAAATTTTAGAGATG
1 AAATTAGTATTTTATCCAAATTTAAGAGATC
* *
1797511 AAATTAATATTTTATCTAAAATTTA
1 AAATTAGTATTTTATC-CAAATTTA
1797536 TGAATTAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 7 0.16
31 32 0.71
32 6 0.13
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.43
Consensus pattern (31 bp):
AAATTAGTATTTTATCCAAATTTAAGAGATC
Found at i:1797546 original size:31 final size:30
Alignment explanation
Indices: 1797456--1797548 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
1797446 GTAAAATTGG
* * *
1797456 TATTTTATCCAAAGTTTAAGAGTCAAATTAG
1 TATTTTATCCAAAATTT-AGAATCAAATTAA
* * * *
1797487 TGTTTTATCGAAATTTTAGAGATGAAATTAA
1 TATTTTATCCAAAATTTAGA-ATCAAATTAA
* *
1797518 TATTTTATCTAAAATTTATGAATTAAATTAA
1 TATTTTATCCAAAATTTA-GAATCAAATTAA
1797549 AGATCAACTC
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 3 0.06
31 45 0.90
32 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (30 bp):
TATTTTATCCAAAATTTAGAATCAAATTAA
Found at i:1802011 original size:45 final size:45
Alignment explanation
Indices: 1801956--1802049 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
1801946 AGTTTGACAC
* *
1801956 CTAACATTTTTTTCGTTCTAGTTTGGTGCCTATCGTTTCATTCCG
1 CTAACATTTTTTTCGTTCTAGTTTGATGCCTAACGTTTCATTCCG
*
1802001 CTAACGTTTTTTTCGTTCTAGTTTGATGCCTAACGTTTCATTCCG
1 CTAACATTTTTTTCGTTCTAGTTTGATGCCTAACGTTTCATTCCG
1802046 -TAAC
1 CTAAC
1802050 TTAGTTTGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 4 0.09
45 42 0.91
ACGTcount: A:0.16, C:0.22, G:0.15, T:0.47
Consensus pattern (45 bp):
CTAACATTTTTTTCGTTCTAGTTTGATGCCTAACGTTTCATTCCG
Found at i:1803076 original size:57 final size:57
Alignment explanation
Indices: 1803003--1803115 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
1802993 TTATGGAATG
* ** * *
1803003 AAACGTTAAGCACCAAACTGGAATGAAAAAATGTTAGACACTAAACTAGAACGAAAA
1 AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGACACCAAACTAGAACGAAAA
* *
1803060 AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGGCACCAAATTAGAACGAAA
1 AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGACACCAAACTAGAACGAAA
1803116 GACATACGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.14
Consensus pattern (57 bp):
AAACGTTAAGCACCAAACTGAAACAAAAAAACGTTAGACACCAAACTAGAACGAAAA
Found at i:1803077 original size:29 final size:29
Alignment explanation
Indices: 1803003--1803115 Score: 126
Period size: 28 Copynumber: 4.0 Consensus size: 29
1802993 TTATGGAATG
* *
1803003 AAACGTTAAGCACCAAACTGGAATG-AAA
1 AAACGTTAAGCACCAAACTAGAACGAAAA
* *
1803031 AAATGTT-AGACACTAAACTAGAACGAAAA
1 AAACGTTAAG-CACCAAACTAGAACGAAAA
1803060 AAACGTTAAGCACCAAACT-GAAAC-AAAA
1 AAACGTTAAGCACCAAACTAG-AACGAAAA
* *
1803088 AAACGTTAGGCACCAAATTAGAACGAAA
1 AAACGTTAAGCACCAAACTAGAACGAAA
1803116 GACATACGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
27 2 0.03
28 43 0.61
29 24 0.34
30 2 0.03
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.14
Consensus pattern (29 bp):
AAACGTTAAGCACCAAACTAGAACGAAAA
Found at i:1804462 original size:40 final size:40
Alignment explanation
Indices: 1804404--1804483 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
1804394 GTAAGTCTGG
*
1804404 ATCAAAATACTATGAAGAGTGAAAGCATAAAATCCAATCC
1 ATCAAAATACTATCAAGAGTGAAAGCATAAAATCCAATCC
* *
1804444 ATCAAAATACTATCAAGAGTGAAAGCGTAAAATTCAATCC
1 ATCAAAATACTATCAAGAGTGAAAGCATAAAATCCAATCC
1804484 TACAAACATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.21
Consensus pattern (40 bp):
ATCAAAATACTATCAAGAGTGAAAGCATAAAATCCAATCC
Found at i:1809362 original size:30 final size:30
Alignment explanation
Indices: 1809317--1809426 Score: 89
Period size: 31 Copynumber: 3.5 Consensus size: 30
1809307 TTGGGCAGTA
*
1809317 CTCGACTCGTGCTCGTTAAAAAAATTTGTTG
1 CTCGACTCG-ACTCGTTAAAAAAATTTGTTG
* ***
1809348 CTCGATTCGACTCGTTGCTCGTTAAAA-TTG-TG
1 CTCGACTCGACTCG-T--T-AAAAAAATTTGTTG
*
1809380 CTCGACTCGTGCTCGTTAAAAAAATTTGTTG
1 CTCGACTCG-ACTCGTTAAAAAAATTTGTTG
*
1809411 CTCAACTCGACTCGTT
1 CTCGACTCGACTCGTT
1809427 GCTCGTTAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
29 4 0.07
30 14 0.23
31 19 0.32
32 11 0.18
33 8 0.13
34 4 0.07
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (30 bp):
CTCGACTCGACTCGTTAAAAAAATTTGTTG
Found at i:1809371 original size:37 final size:34
Alignment explanation
Indices: 1809318--1809435 Score: 126
Period size: 37 Copynumber: 3.5 Consensus size: 34
1809308 TGGGCAGTAC
1809318 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCGA
1 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTC-A
1809353 TTCGACTCGTTGCTCGTT---AAAA-TTG-TG--C-
1 -TCGACTCG-TGCTCGTTAAAAAAATTTGTTGCTCA
1809381 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAA
1 TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTC-A
1809416 CTCGACTCGTTGCTCGTTAA
1 -TCGACTCG-TGCTCGTTAA
1809436 GCTCACTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 23
0.75 0.00 0.25
Matches are distributed among these distances:
26 8 0.11
27 8 0.11
29 4 0.06
30 4 0.06
31 2 0.03
32 2 0.03
33 4 0.06
34 4 0.06
36 16 0.23
37 18 0.26
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (34 bp):
TCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCA
Found at i:1809421 original size:63 final size:63
Alignment explanation
Indices: 1809317--1809435 Score: 220
Period size: 63 Copynumber: 1.9 Consensus size: 63
1809307 TTGGGCAGTA
* *
1809317 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCGATTCGACTCGTTGCTCGTTAAAATTGTG
1 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAAAATTGTG
1809380 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAA
1 CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAA
1809436 GCTCACTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (63 bp):
CTCGACTCGTGCTCGTTAAAAAAATTTGTTGCTCAACTCGACTCGTTGCTCGTTAAAATTGTG
Found at i:1809560 original size:21 final size:21
Alignment explanation
Indices: 1809534--1809622 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
1809524 ATTAAAATAA
1809534 TATTATTAATTAATAATATTT
1 TATTATTAATTAATAATATTT
* * *
1809555 TATTATTAATTAAAAATAATA
1 TATTATTAATTAATAATATTT
* * *
1809576 GATTAGTTAACTTATTATTATTAT
1 TATTA-TTAA-TTAATAATATT-T
*
1809600 TATTTATTAATAAATTAATATTT
1 TA-TTATTAATTAA-TAATATTT
1809623 AATATTTAGA
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
21 22 0.44
22 4 0.08
23 10 0.20
24 11 0.22
25 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTATTAATTAATAATATTT
Found at i:1809568 original size:39 final size:43
Alignment explanation
Indices: 1809524--1809621 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 43
1809514 TTTTTTGGGT
1809524 ATTAAAATAATATTA-TTAA-TTAATAATATT-TTA-TTATTA
1 ATTAAAATAATATTAGTTAACTTAATAATATTATTATTTATTA
* *
1809563 ATTAAAAATAATAGATTAGTTAACTTATTATTATTATTATTTATTA
1 ATT-AAAATAAT--ATTAGTTAACTTAATAATATTATTATTTATTA
*
1809609 A-TAAATTAATATT
1 ATTAAAATAATATT
1809622 TAATATTTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
39 3 0.06
40 8 0.16
42 7 0.14
43 4 0.08
44 16 0.33
45 4 0.08
46 7 0.14
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (43 bp):
ATTAAAATAATATTAGTTAACTTAATAATATTATTATTTATTA
Found at i:1809689 original size:23 final size:23
Alignment explanation
Indices: 1809646--1809690 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1809636 ATTTTTTGAA
**
1809646 TAAAATAATTTTGAAGTAATTAC
1 TAAAATAATTTTGAAAAAATTAC
1809669 TAAAATATATTTT-AAAAAATTA
1 TAAAATA-ATTTTGAAAAAATTA
1809691 ATAAGATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TAAAATAATTTTGAAAAAATTAC
Found at i:1810384 original size:223 final size:223
Alignment explanation
Indices: 1809996--1810444 Score: 871
Period size: 223 Copynumber: 2.0 Consensus size: 223
1809986 GTACAAGGCA
*
1809996 CAAAAGAAGTGCAATGTAACCATGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
1 CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
*
1810061 CATTTGTGAAATGGCAAGGCTGCAAAGCAGTAATCATTATTGAAAAATAAATTACCTTCTTCATT
66 CATTTGTGAAATGGCAAGGCTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
1810126 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
131 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
1810191 TGAATCCATGTCGAACAAGGGTCTCTTT
196 TGAATCCATGTCGAACAAGGGTCTCTTT
1810219 CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
1 CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
*
1810284 CATTTGTGAAATGGCAAGGTTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
66 CATTTGTGAAATGGCAAGGCTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
1810349 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
131 TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
1810414 TGAATCCATGTCGAACAAGGGTCTCTTT
196 TGAATCCATGTCGAACAAGGGTCTCTTT
1810442 CAA
1 CAA
1810445 GACCTGAAAA
Statistics
Matches: 223, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
223 223 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (223 bp):
CAAAAGAAGTGCAATGTAACCAAGTAGTAGGACTAAATATTAAGTGCAAAAGCACTGGTATAATG
CATTTGTGAAATGGCAAGGCTGCAAAGCAATAATCATTATTGAAAAATAAATTACCTTCTTCATT
TGCTTTGTCAAAAACAAATTTGGCAAGCTTTGGTATTACTTCTGTGTCTGTTTCAGATTCAAAAG
TGAATCCATGTCGAACAAGGGTCTCTTT
Found at i:1824107 original size:2 final size:2
Alignment explanation
Indices: 1824100--1824126 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1824090 TAATCTTGAA
1824100 AT 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 AT A
1824127 AAGTTTAGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1827614 original size:19 final size:19
Alignment explanation
Indices: 1827590--1827626 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1827580 GAATGCTAGA
*
1827590 GGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCCAG
*
1827609 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1827627 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (19 bp):
GGGGAACCGATACCCCCAG
Found at i:1828331 original size:103 final size:103
Alignment explanation
Indices: 1828106--1828323 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1828096 GTAGAGGGTC
* * *
1828106 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1828171 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1828209 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1828274 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1828312 TATGTGGTCCTT
1 TATGTGGTCCTT
1828324 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1828373 original size:23 final size:23
Alignment explanation
Indices: 1828340--1828425 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
1828330 ATTATTATAT
*
1828340 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
1828363 GGCACTCCGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
1828386 GGCACTCCGGTGTAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
**
1828409 GGCACTTAGGTGCAATT
1 GGCACTCCGGTGCAATT
1828426 ATATGAGCTG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:1834503 original size:21 final size:21
Alignment explanation
Indices: 1834461--1834503 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1834451 TTTCTGGGCT
* *
1834461 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1834482 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1834503 A
1 A
1834504 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1835240 original size:103 final size:103
Alignment explanation
Indices: 1835051--1835268 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1835041 ATAGAGGGTC
* *
1835051 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACAAAC
*
1835116 TTGATCCTTGGTATATATATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
*
1835154 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACAAAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACAAAC
*
1835219 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
1835257 TATGTGGTCCTT
1 TATGTGGTCCTT
1835269 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACAAAC
TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
Found at i:1835318 original size:23 final size:23
Alignment explanation
Indices: 1835287--1835347 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1835277 TATTATATGT
1835287 CACTACGGTGCAATTCTACGCGG
1 CACTACGGTGCAATTCTACGCGG
* * *
1835310 CACTCCGGTGTAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGG
1835333 CACTTA-GGTGCAATT
1 CAC-TACGGTGCAATT
1835348 ATATGAGCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.28
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGG
Found at i:1836349 original size:31 final size:31
Alignment explanation
Indices: 1836311--1836404 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
1836301 AGGGTTGAGG
*
1836311 GTTTACCTATGTTTTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
*
1836342 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
** * * *
1836373 AATTACCTAGGTTCTTCGGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGATATATGGACT
1836404 G
1 G
1836405 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGATATATGGACT
Found at i:1841985 original size:96 final size:94
Alignment explanation
Indices: 1841797--1841987 Score: 348
Period size: 96 Copynumber: 2.0 Consensus size: 94
1841787 AAATATAGGT
1841797 CAATGATGGATCTCTACTTTATAACTGCAAGTAGACCGGACATTATGTTTAGTGTTTCTTATGTG
1 CAATGATGGATCTCTACTTTATAACTGCAAGTAGACCGGACATTATGTTTAGTGTTTCTTATGTG
1841862 CTAGATTTCAATCATGTCCTAAGGAATCA
66 CTAGATTTCAATCATGTCCTAAGGAATCA
1841891 CAATGATGGATCTCTACTTTATCTAACTGCAAGTAGACCGGACATTATGTTTAGTGTTTGCTTAT
1 CAATGATGGATCTCTACTTTA--TAACTGCAAGTAGACCGGACATTATGTTTAGTGTTT-CTTAT
1841956 GTGCTAGATTTCAATCATGTCCTAA-GAATCA
63 GTGCTAGATTTCAATCATGTCCTAAGGAATCA
1841987 C
1 C
1841988 TTACTAGCTG
Statistics
Matches: 94, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
94 21 0.22
96 43 0.46
97 30 0.32
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (94 bp):
CAATGATGGATCTCTACTTTATAACTGCAAGTAGACCGGACATTATGTTTAGTGTTTCTTATGTG
CTAGATTTCAATCATGTCCTAAGGAATCA
Found at i:1846844 original size:16 final size:17
Alignment explanation
Indices: 1846823--1846855 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1846813 TCAAGTACCT
1846823 ACAAAAG-AAAATAAAA
1 ACAAAAGCAAAATAAAA
1846839 ACAAAAGCAAAATAAAA
1 ACAAAAGCAAAATAAAA
1846856 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.79, C:0.09, G:0.06, T:0.06
Consensus pattern (17 bp):
ACAAAAGCAAAATAAAA
Found at i:1847389 original size:18 final size:18
Alignment explanation
Indices: 1847368--1847424 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
1847358 GATTGCCCAG
1847368 AGGGAACAGATTCCCCCC
1 AGGGAACAGATTCCCCCC
*
1847386 AGGGGGTATC-GATT--CCCC
1 A--GGG-AACAGATTCCCCCC
1847404 -GGGAACAGATTCCCCCC
1 AGGGAACAGATTCCCCCC
1847421 AGGG
1 AGGG
1847425 GTATCGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 2 0.07
15 7 0.23
17 4 0.13
18 8 0.27
20 7 0.23
21 2 0.07
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (18 bp):
AGGGAACAGATTCCCCCC
Found at i:1847426 original size:34 final size:35
Alignment explanation
Indices: 1847369--1847454 Score: 138
Period size: 34 Copynumber: 2.5 Consensus size: 35
1847359 ATTGCCCAGA
*
1847369 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCAC
*
1847404 GGGAACAGATTCCCCCCA-GGGGTATCGATTCCAT
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCAC
*
1847438 GGGTACAGATTCCCCCC
1 GGGAACAGATTCCCCCC
1847455 TTGCATGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 30 0.62
35 18 0.38
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.19
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCAC
Found at i:1848823 original size:19 final size:20
Alignment explanation
Indices: 1848799--1848846 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1848789 AACGATTTTC
*
1848799 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1848818 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1848838 TTTTGAAAA
1 TTTTGAAAA
1848847 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1850425 original size:21 final size:21
Alignment explanation
Indices: 1850399--1850440 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1850389 ATTTGAATAT
*
1850399 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1850420 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1850441 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1850502 original size:21 final size:21
Alignment explanation
Indices: 1850469--1850508 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1850459 TTTTTGCAGA
*
1850469 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1850491 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1850509 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1850762 original size:34 final size:32
Alignment explanation
Indices: 1850723--1850792 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1850713 TTTTGTAAAG
*
1850723 GGGAAAGGTTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* *
1850757 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
1850789 GGGA
1 GGGA
1850793 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:1855271 original size:103 final size:103
Alignment explanation
Indices: 1854948--1855263 Score: 578
Period size: 103 Copynumber: 3.1 Consensus size: 103
1854938 GGGTCTACGC
*
1854948 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
1855013 CCTTGGCATATGTATATAATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
*
1855051 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1855116 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
1855154 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
1855219 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
1855257 GGTCCTT
1 GGTCCTT
1855264 ATGGACATTA
Statistics
Matches: 206, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:1855317 original size:23 final size:23
Alignment explanation
Indices: 1855287--1855347 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1855277 TATGGAACTA
1855287 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* *
1855310 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
*
1855333 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
1855348 AGCTATGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:1857423 original size:18 final size:18
Alignment explanation
Indices: 1857400--1857438 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1857390 AAACAAAAAC
*
1857400 TAAATTTTAGGTATAGTT
1 TAAATTTTAGGTATAATT
1857418 TAAATTTTAGGTATAATT
1 TAAATTTTAGGTATAATT
1857436 TAA
1 TAA
1857439 GGTCTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
TAAATTTTAGGTATAATT
Found at i:1884833 original size:89 final size:88
Alignment explanation
Indices: 1884628--1884982 Score: 533
Period size: 89 Copynumber: 4.0 Consensus size: 88
1884618 GGAGGATTAG
*
1884628 TTTT-TTTTGGTGATCTCGACCTCGGTGGTTTCGTATGTAAGATTTACTGTTTTGATTGTTGATG
1 TTTTGTTTTGGTGATCTCGACCTCGGTGGTTTCATATGTAAGATTTACTGTTTTGATTGTTGATG
1884692 TTTGCGAGTCTCCTCCTTTTTCTGT
66 TTTGCGAGTCTCCT--TTTTTCTGT
* **
1884717 TTTTGTTTTGGTGATCTCGTCGACGGTGGTTTCATATGTAAGATTTACTGTTTTGATTG-TGATG
1 TTTTGTTTTGGTGATCTCGACCTCGGTGGTTTCATATGTAAGATTTACTGTTTTGATTGTTGATG
1884781 TTTGCGAGTCTCCTTATTTTCTGT
66 TTTGCGAGTCTCCTT-TTTTCTGT
* *
1884805 TTTGTGTTTTGTTGATCTCGACCTCGGTGGTTTCGTATGTAAGATTTACTGTTTTGATTGTTGAT
1 TTT-TGTTTTGGTGATCTCGACCTCGGTGGTTTCATATGTAAGATTTACTGTTTTGATTGTTGAT
1884870 GTTTGCGAGTCTCC-TTTTTCTGT
65 GTTTGCGAGTCTCCTTTTTTCTGT
*
1884893 TTTTGTTTTGGTGATCGTCG---GCGGTGGTTTCATATGTAAGATTTACTGTTTTGATTGTTGAT
1 TTTTGTTTTGGTGATC-TCGACCTCGGTGGTTTCATATGTAAGATTTACTGTTTTGATTGTTGAT
*
1884955 GTTTGCGAGTTTCCTTCATTTTCTGT
65 GTTTGCGAGTCTCCTT--TTTTCTGT
1884981 TT
1 TT
1884983 CGAGATTTAT
Statistics
Matches: 245, Mismatches: 13, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
85 53 0.22
86 1 0.00
87 13 0.05
88 35 0.14
89 75 0.31
90 68 0.28
ACGTcount: A:0.12, C:0.13, G:0.24, T:0.51
Consensus pattern (88 bp):
TTTTGTTTTGGTGATCTCGACCTCGGTGGTTTCATATGTAAGATTTACTGTTTTGATTGTTGATG
TTTGCGAGTCTCCTTTTTTCTGT
Found at i:1887980 original size:36 final size:36
Alignment explanation
Indices: 1887933--1888004 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1887923 TTCGATGTTG
1887933 CAATAAAATTATGAGACACTCTTTTCCTCCTTCCAA
1 CAATAAAATTATGAGACACTCTTTTCCTCCTTCCAA
1887969 CAATAAAATTATGAGACACTCTTTTCCTCCTTCCAA
1 CAATAAAATTATGAGACACTCTTTTCCTCCTTCCAA
1888005 TGCTCGACGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (36 bp):
CAATAAAATTATGAGACACTCTTTTCCTCCTTCCAA
Found at i:1896664 original size:31 final size:28
Alignment explanation
Indices: 1896629--1896700 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 28
1896619 TCAAAAAATA
1896629 TAAAATATATTTACTTTTATTTTTAATTAAT
1 TAAAATATATTTA-TTTTA--TTTAATTAAT
* *
1896660 TAAAAAATATTTATTTTATTTATTTAAT
1 TAAAATATATTTATTTTATTTAATTAAT
1896688 TAAAATATCATTT
1 TAAAATAT-ATTT
1896701 CGAGTTAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 16 0.43
29 4 0.11
30 5 0.14
31 12 0.32
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TAAAATATATTTATTTTATTTAATTAAT
Found at i:1896686 original size:24 final size:26
Alignment explanation
Indices: 1896644--1896695 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
1896634 TATATTTACT
1896644 TTTATTTTTAATTAATTAA-AAAATA
1 TTTATTTTTAATTAATTAATAAAATA
* *
1896669 TTTA-TTTTATTTATTTAATTAAAATA
1 TTTATTTTTAATTAATTAA-TAAAATA
1896695 T
1 T
1896696 CATTTCGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
25 4 0.17
26 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTATTTTTAATTAATTAATAAAATA
Found at i:1897049 original size:19 final size:20
Alignment explanation
Indices: 1897025--1897063 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1897015 CTGTAGTCTA
*
1897025 TTTATTAT-ATATTTTTATT
1 TTTATTATAAAATTTTTATT
*
1897044 TTTATTTTAAAATTTTTATT
1 TTTATTATAAAATTTTTATT
1897064 CATAATTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTATAAAATTTTTATT
Found at i:1897433 original size:26 final size:24
Alignment explanation
Indices: 1897407--1897476 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 24
1897397 TATATATAAT
1897407 ATAATTTTTATATATTAATTTAAA
1 ATAATTTTTATATATTAATTTAAA
*
1897431 AT-ATTTTT-TATATTAACTTATTAA
1 ATAATTTTTATATATTAA-TT-TAAA
*
1897455 AT-ATATTTTAT-TATTAACTTAA
1 ATAAT-TTTTATATATTAATTTAA
1897477 TTTAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 8 0.21
23 10 0.26
24 10 0.26
25 10 0.26
26 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAATTTTTATATATTAATTTAAA
Found at i:1897442 original size:22 final size:22
Alignment explanation
Indices: 1897410--1897495 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 22
1897400 ATATAATATA
1897410 ATTTTTATATATTAATTTAAAAT
1 ATTTTT-TATATTAATTTAAAAT
1897433 ATTTTTTATATTAACTTATTAAATAT
1 ATTTTTTATATTAA--T-TTAAA-AT
1897459 ATTTTATTATTAACTTAATTTAAAAAT
1 ATTTT-TTA-T-A-TTAATTT-AAAAT
1897486 ATTTATTTAT
1 ATTT-TTTAT
1897496 TTATTAAAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 17
0.76 0.00 0.24
Matches are distributed among these distances:
22 8 0.15
23 6 0.11
24 1 0.02
25 5 0.09
26 8 0.15
27 14 0.26
28 6 0.11
29 1 0.02
30 4 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTATATTAATTTAAAAT
Found at i:1897495 original size:27 final size:26
Alignment explanation
Indices: 1897421--1897496 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
1897411 TTTTTATATA
1897421 TTAATTT-AAAATATTTTTTATATTAAC
1 TTAATTTAAAAATA-TTTTT-TATTAAC
*
1897448 TT-A-TTAAATATATTTTATTATTAAC
1 TTAATTTAAAAATATTTT-TTATTAAC
1897473 TTAATTTAAAAATATTTATTTATT
1 TTAATTTAAAAATATTT-TTTATT
1897497 TATTAAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
25 15 0.36
26 8 0.19
27 18 0.43
28 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
TTAATTTAAAAATATTTTTTATTAAC
Found at i:1898843 original size:23 final size:23
Alignment explanation
Indices: 1898817--1898862 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1898807 CACCACAGCT
*
1898817 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1898840 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1898863 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1903612 original size:16 final size:17
Alignment explanation
Indices: 1903591--1903642 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
1903581 TTTTTAATTT
1903591 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
1903607 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
1903622 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
1903639 AATT
1 AATT
1903643 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:1905086 original size:21 final size:21
Alignment explanation
Indices: 1905060--1905103 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1905050 ATTCTGGGCT
* *
1905060 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
1905081 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
1905102 AG
1 AG
1905104 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1905174 original size:23 final size:22
Alignment explanation
Indices: 1905131--1905175 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1905121 ATGTCATGGG
*
1905131 GGAACCGATACCCCCACAGGAA
1 GGAACCGATACCCCCAAAGGAA
*
1905153 GGAACCGATTCCCCCTAAAGGAA
1 GGAACCGATACCCCC-AAAGGAA
1905176 AATTGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.36, C:0.33, G:0.22, T:0.09
Consensus pattern (22 bp):
GGAACCGATACCCCCAAAGGAA
Found at i:1905951 original size:31 final size:31
Alignment explanation
Indices: 1905867--1905988 Score: 117
Period size: 31 Copynumber: 3.9 Consensus size: 31
1905857 GAGTCGAGGG
1905867 TACCTATGTTCTACGGAACATATGGACAGA-A
1 TACCTATGTTCTACGGAACATATGGACA-ATA
*
1905898 TTACCTATG-TCTTTC-GAGACATATGGACAATA
1 -TACCTATGTTC-TACGGA-ACATATGGACAATA
* *
1905930 TACCTATGTTCTAAGGAACATATGGACAGT-
1 TACCTATGTTCTACGGAACATATGGACAATA
* * *
1905960 TCACCTAGGTTCTTCGGAACCTATGGACA
1 T-ACCTATGTTCTACGGAACATATGGACA
1905989 GTTGCCGAGG
Statistics
Matches: 76, Mismatches: 8, Indels: 13
0.78 0.08 0.13
Matches are distributed among these distances:
30 1 0.01
31 49 0.64
32 26 0.34
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAATA
Found at i:1906029 original size:30 final size:30
Alignment explanation
Indices: 1905978--1906049 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
1905968 GTTCTTCGGA
* * *
1905978 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
1906008 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
1906038 ACCTCTGGATAG
1 ACCTCTGGATAG
1906050 GTCCTGCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:1908082 original size:23 final size:23
Alignment explanation
Indices: 1908056--1908100 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1908046 CACCACAGCT
* *
1908056 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
* *
1908079 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
1908101 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:1908808 original size:21 final size:21
Alignment explanation
Indices: 1908784--1908824 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1908774 TTCATATTCG
* *
1908784 TTGAGGGGGTATCGATTCCCA
1 TTGAAGGGGTACCGATTCCCA
*
1908805 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
1908825 CTAGCCTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCA
Found at i:1915575 original size:19 final size:20
Alignment explanation
Indices: 1915538--1915575 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1915528 CTTTTTTTTA
*
1915538 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1915558 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1915576 TCTAACATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1919122 original size:21 final size:21
Alignment explanation
Indices: 1919096--1919139 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1919086 ATTCTGGGCT
* *
1919096 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
1919117 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
1919138 AG
1 AG
1919140 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1920027 original size:31 final size:30
Alignment explanation
Indices: 1919903--1920027 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 30
1919893 GAGTCGAGGG
1919903 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG--T
*
1919935 TACCTATG-TCTTTC-GAGACATATGGACAGT
1 TACCTATGTTC-TACGGA-ACATATGGACAGT
*
1919965 ATACCTATGTTCTAAGGAACATATGGACAGT
1 -TACCTATGTTCTACGGAACATATGGACAGT
* * *
1919996 TCACCTAGGTTCTTCGGAACCTATGGACAGT
1 T-ACCTATGTTCTACGGAACATATGGACAGT
1920027 T
1 T
1920028 GCCGAGGATC
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
30 2 0.03
31 52 0.65
32 26 0.32
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (30 bp):
TACCTATGTTCTACGGAACATATGGACAGT
Found at i:1931654 original size:29 final size:29
Alignment explanation
Indices: 1931615--1931673 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1931605 ATGTAAACAT
* *
1931615 CATACAATAAGAACAAAACAGCTGGGAAA
1 CATACAATAAGAACAAAACAACAGGGAAA
* *
1931644 CATACATTAAGAACAGAACAACAGGGAAA
1 CATACAATAAGAACAAAACAACAGGGAAA
1931673 C
1 C
1931674 CAGTTTGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.19, G:0.17, T:0.10
Consensus pattern (29 bp):
CATACAATAAGAACAAAACAACAGGGAAA
Found at i:1939869 original size:2 final size:2
Alignment explanation
Indices: 1939864--1939928 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1939854 TATACTTGTT
1939864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1939906 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1939929 CACACACACA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1940003 original size:28 final size:29
Alignment explanation
Indices: 1939945--1940008 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1939935 CACAAACAAC
1939945 AAAAACGAAAGTTAATCGCCCTTAAGAAA
1 AAAAACGAAAGTTAATCGCCCTTAAGAAA
1939974 AAAAACGAAAGTTAATCGCCCTTAAGAAA
1 AAAAACGAAAGTTAATCGCCCTTAAGAAA
1940003 AGAAAA
1 A-AAAA
1940009 GGGGAGTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16
Consensus pattern (29 bp):
AAAAACGAAAGTTAATCGCCCTTAAGAAA
Found at i:1940087 original size:29 final size:29
Alignment explanation
Indices: 1940046--1940101 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1940036 CACACAAATC
1940046 ATTTTTAGAAAATAAATCAGAACTATTTT
1 ATTTTTAGAAAATAAATCAGAACTATTTT
1940075 ATTTTT-GATAAATAAATCAGAACTATT
1 ATTTTTAGA-AAATAAATCAGAACTATT
1940102 ACTCCAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (29 bp):
ATTTTTAGAAAATAAATCAGAACTATTTT
Found at i:1944966 original size:21 final size:21
Alignment explanation
Indices: 1944942--1944984 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1944932 AATAAAATTA
1944942 GAACACTTGATAAGTTTACCT
1 GAACACTTGATAAGTTTACCT
1944963 GAACACTTGATAAGTTTACCT
1 GAACACTTGATAAGTTTACCT
1944984 G
1 G
1944985 TTCGATCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (21 bp):
GAACACTTGATAAGTTTACCT
Found at i:1946607 original size:19 final size:19
Alignment explanation
Indices: 1946583--1946668 Score: 73
Period size: 19 Copynumber: 4.2 Consensus size: 19
1946573 GCGATTTTGA
*
1946583 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
* * *
1946602 AAAATGTGTTACAAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
1946623 AAAAATGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
*
1946646 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
1946665 AAAA
1 AAAA
1946669 ATCCAAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
19 31 0.58
20 1 0.02
21 1 0.02
22 8 0.15
23 2 0.04
24 2 0.04
25 8 0.15
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:1946669 original size:19 final size:19
Alignment explanation
Indices: 1946633--1946669 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1946623 AAAAATGTGT
1946633 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
1946652 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
1946670 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:1946862 original size:6 final size:6
Alignment explanation
Indices: 1946851--1946877 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1946841 TCCCGTCTCG
1946851 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1946878 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1947196 original size:19 final size:19
Alignment explanation
Indices: 1947172--1947208 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1947162 CGCGATACTG
*
1947172 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1947191 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1947209 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1949063 original size:21 final size:21
Alignment explanation
Indices: 1949037--1949081 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1949027 GATTTCTGGG
*
1949037 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
1949058 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1949079 CAA
1 CAA
1949082 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1950179 original size:23 final size:23
Alignment explanation
Indices: 1950153--1950197 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1950143 CACCACAGCT
*
1950153 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1950176 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1950198 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1950447 original size:149 final size:149
Alignment explanation
Indices: 1950177--1950479 Score: 588
Period size: 149 Copynumber: 2.0 Consensus size: 149
1950167 GAAGTGCCCC
1950177 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1950242 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
66 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
1950307 ATATGTCCTAAAGAACCGA
131 ATATGTCCTAAAGAACCGA
*
1950326 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1950391 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
66 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
*
1950456 ATATGTCCTAAAGAACCGC
131 ATATGTCCTAAAGAACCGA
1950475 GTAGA
1 GTAGA
1950480 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (149 bp):
GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
ATATGTCCTAAAGAACCGA
Found at i:1950601 original size:30 final size:30
Alignment explanation
Indices: 1950567--1950625 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1950557 ATCGCGTAGT
* *
1950567 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
1950597 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
1950626 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:1950717 original size:29 final size:29
Alignment explanation
Indices: 1950647--1950718 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1950637 TTTTCTGCAT
* * *
1950647 ATTCATGTCATGCAATGCATATAATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
1950676 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
1950705 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1950719 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:1951056 original size:19 final size:20
Alignment explanation
Indices: 1951019--1951056 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1951009 TTTTTTCTCA
*
1951019 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1951039 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1951057 TCAAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1951166 original size:66 final size:67
Alignment explanation
Indices: 1951020--1951191 Score: 240
Period size: 67 Copynumber: 2.6 Consensus size: 67
1951010 TTTTTCTCAT
* * *
1951020 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
1951085 GA
66 GA
* * *
1951087 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
1951151 GA
66 GA
* *
1951153 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
1951192 AACCCAGAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
65 6 0.06
66 19 0.20
67 70 0.74
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
GA
Found at i:1957246 original size:23 final size:23
Alignment explanation
Indices: 1957220--1957264 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1957210 CACCACAGCT
*
1957220 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1957243 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1957265 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1957514 original size:149 final size:149
Alignment explanation
Indices: 1957244--1957546 Score: 588
Period size: 149 Copynumber: 2.0 Consensus size: 149
1957234 GAAGTGCCCC
1957244 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1957309 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
66 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
1957374 ATATGTCCTAAAGAACCGA
131 ATATGTCCTAAAGAACCGA
*
1957393 GTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
1957458 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
66 ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
*
1957523 ATATGTCCTAAAGAACCGC
131 ATATGTCCTAAAGAACCGA
1957542 GTAGA
1 GTAGA
1957547 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (149 bp):
GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATC
ATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATAC
ATATGTCCTAAAGAACCGA
Found at i:1957680 original size:30 final size:30
Alignment explanation
Indices: 1957635--1957693 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1957625 ATCGCGTAGT
* *
1957635 CATATTATTTCCATACCTTTATCACATAGG
1 CATATCATTTACATACCTTTATCACATAGG
1957665 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
1957694 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGG
Found at i:1957794 original size:34 final size:29
Alignment explanation
Indices: 1957715--1957786 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1957705 TTTTCTGCAT
* *
1957715 ATTCATGTCATGCAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
1957744 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
1957773 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1957787 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:1958124 original size:19 final size:20
Alignment explanation
Indices: 1958087--1958124 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1958077 TTTTTTCTCA
*
1958087 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1958107 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1958125 TCAAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1958234 original size:66 final size:67
Alignment explanation
Indices: 1958088--1958259 Score: 240
Period size: 67 Copynumber: 2.6 Consensus size: 67
1958078 TTTTTCTCAT
* * *
1958088 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
1958153 GA
66 GA
* * *
1958155 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
1958219 GA
66 GA
* *
1958221 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
1958260 AACCCAGAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
65 6 0.06
66 19 0.20
67 70 0.74
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCATTCTGGAAATTCATATACGAT
GA
Found at i:1959931 original size:23 final size:23
Alignment explanation
Indices: 1959905--1959994 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
1959895 TTATTATATA
*
1959905 GCACTTCGGTGCATTTCTACGCG
1 GCACTACGGTGCATTTCTACGCG
1959928 GCACTACGGTGCATTTCTACGCG
1 GCACTACGGTGCATTTCTACGCG
* * *
1959951 GCACTACGGTGCAATTCTATGTG
1 GCACTACGGTGCATTTCTACGCG
* *
1959974 GCACTTCGGTGCATTTATACG
1 GCACTACGGTGCATTTCTACG
1959995 AGCTGTGGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.30
Consensus pattern (23 bp):
GCACTACGGTGCATTTCTACGCG
Found at i:1960248 original size:20 final size:21
Alignment explanation
Indices: 1960225--1960264 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1960215 AAATGATTGT
1960225 ATATAA-ATATGTATGTTTTG
1 ATATAAGATATGTATGTTTTG
*
1960245 ATATAATGATATGTGTGTTT
1 ATATAA-GATATGTATGTTT
1960265 CTCGTGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (21 bp):
ATATAAGATATGTATGTTTTG
Found at i:1962638 original size:17 final size:17
Alignment explanation
Indices: 1962603--1962642 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1962593 GGTAATTAAA
1962603 GATTGA-TAAGGAATTT
1 GATTGATTAAGGAATTT
* *
1962619 GATTGATTAATGATTTT
1 GATTGATTAAGGAATTT
1962636 GATTGAT
1 GATTGAT
1962643 AAGAACTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (17 bp):
GATTGATTAAGGAATTT
Found at i:1963809 original size:21 final size:21
Alignment explanation
Indices: 1963783--1963827 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1963773 GAGTTCTGGG
* *
1963783 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1963804 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1963825 CAA
1 CAA
1963828 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1964696 original size:31 final size:31
Alignment explanation
Indices: 1964658--1964797 Score: 235
Period size: 31 Copynumber: 4.5 Consensus size: 31
1964648 CATGTCGAGG
1964658 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1964689 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1964720 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1964751 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1964782 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
1964798 TGGAATCTAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1964809 original size:31 final size:31
Alignment explanation
Indices: 1964658--1964813 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
1964648 CATGTCGAGG
*
1964658 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
1964689 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
1964720 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
1964751 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* * *
1964782 GATTACCTAGGTTCTTTGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
1964813 G
1 G
1964814 GTCCTTCGGG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:1967953 original size:21 final size:21
Alignment explanation
Indices: 1967927--1967971 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1967917 GAGTTCTGGG
* *
1967927 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1967948 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1967969 CAA
1 CAA
1967972 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1968847 original size:31 final size:31
Alignment explanation
Indices: 1968809--1968948 Score: 235
Period size: 31 Copynumber: 4.5 Consensus size: 31
1968799 AGGGTCGAGG
1968809 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1968840 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1968871 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1968902 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1968933 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
1968949 TGGAATCTAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1968960 original size:31 final size:31
Alignment explanation
Indices: 1968809--1968964 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
1968799 AGGGTCGAGG
*
1968809 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
1968840 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
1968871 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
1968902 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* * *
1968933 GATTACCTAGGTTCTTTGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
1968964 G
1 G
1968965 GTCCTTCAGG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:1971614 original size:23 final size:23
Alignment explanation
Indices: 1971588--1971655 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1971578 ATTATTATAT
1971588 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1971611 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1971634 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1971656 AGTTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1971909 original size:20 final size:21
Alignment explanation
Indices: 1971886--1971925 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1971876 AAATGATTAT
1971886 ATATAA-ATATGTATGTTTTG
1 ATATAAGATATGTATGTTTTG
*
1971906 ATATAATGATATGTGTGTTT
1 ATATAA-GATATGTATGTTT
1971926 CTCGTGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (21 bp):
ATATAAGATATGTATGTTTTG
Found at i:1974083 original size:31 final size:31
Alignment explanation
Indices: 1974018--1974091 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
1974008 ACTCAGATAA
*
1974018 CATTCAGGTAATGCACATCATGTCAGGGTTG
1 CATTCAGGTAATGCACATCATGTCAGGGTCG
* *
1974049 CATTCATGTAATGCACAGT-ATGTTA-GGTCCG
1 CATTCAGGTAATGCACA-TCATGTCAGGGT-CG
*
1974080 CATTCAGATAAT
1 CATTCAGGTAAT
1974092 ACCTACCATG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 3 0.08
31 32 0.89
32 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (31 bp):
CATTCAGGTAATGCACATCATGTCAGGGTCG
Found at i:1976221 original size:14 final size:13
Alignment explanation
Indices: 1976196--1976222 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1976186 TATCAAGATT
1976196 TTATTTAAAAAAA
1 TTATTTAAAAAAA
1976209 TTATTTAAAAAAA
1 TTATTTAAAAAAA
1976222 T
1 T
1976223 AAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTATTTAAAAAAA
Done.