Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 72 of 135
Found at i:23778111 original size:251 final size:250
Alignment explanation
Indices: 23777641--23778114 Score: 813
Period size: 251 Copynumber: 1.9 Consensus size: 250
23777631 ATTGAGGTGT
23777641 GTTGAAGTTCAACTATTGATTTACATCAGCTTAATGCATTACTTTAGTAAAATATGATTATATGA
1 GTTGAAGTTCAACTATTGATTTACATCAGCTTAATGCATTACTTTAGTAAAATATGATTATATGA
* * *
23777706 AATAATAAGATGTGATAAACTACGATAAATAATCAGAAAGACACCGGGACCCTAACCGACGATGG
66 AATAATAAGATGTGATAAACTACGATAAATAATCAGAAAAACACCAGGACCCTAACCGACGACGG
* *
23777771 TATCGAGTTTTGGGTGTTACATTTAGTGGTATCAAAGCTTACGATTTAGCCGTTTCTCGGACAGT
131 TATCGAGTTTTAGGTGTTACATTTAGTGGTATCAAAGCTTACGATTTAACCGTTTCTCGGACAGT
23777836 TATGTTTGTATTAAATGATTTAGTAGTAAAATAAGATTTAGTATTAAATAATTTA
196 TATGTTTGTATTAAATGATTTAGTAGTAAAATAAGATTTAGTATTAAATAATTTA
* *
23777891 GTTGATGTTCAATTATTGATTTACATCGAGCTTAATGCATTACTTTAGTAAAATATGATTATATG
1 GTTGAAGTTCAACTATTGATTTACATC-AGCTTAATGCATTACTTTAGTAAAATATGATTATATG
* ** * *
23777956 AAATAATAAGATGTGATAAACTACGATAAATGATCAGAAAAACATTAGGATCCTAACCGATGACG
65 AAATAATAAGATGTGATAAACTACGATAAATAATCAGAAAAACACCAGGACCCTAACCGACGACG
* *
23778021 GTATCGAGTTTTAGGTGTTACATTTAGTGGTATCAAAGCTTACGGTTTAACTGTTTCTCGGACAG
130 GTATCGAGTTTTAGGTGTTACATTTAGTGGTATCAAAGCTTACGATTTAACCGTTTCTCGGACAG
23778086 TTATGTTTGTATTAAATGATTTAGTAGTA
195 TTATGTTTGTATTAAATGATTTAGTAGTA
23778115 CATGCCATAT
Statistics
Matches: 209, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
250 25 0.12
251 184 0.88
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (250 bp):
GTTGAAGTTCAACTATTGATTTACATCAGCTTAATGCATTACTTTAGTAAAATATGATTATATGA
AATAATAAGATGTGATAAACTACGATAAATAATCAGAAAAACACCAGGACCCTAACCGACGACGG
TATCGAGTTTTAGGTGTTACATTTAGTGGTATCAAAGCTTACGATTTAACCGTTTCTCGGACAGT
TATGTTTGTATTAAATGATTTAGTAGTAAAATAAGATTTAGTATTAAATAATTTA
Found at i:23786602 original size:80 final size:80
Alignment explanation
Indices: 23786469--23786641 Score: 231
Period size: 80 Copynumber: 2.2 Consensus size: 80
23786459 ACTAGAGATT
*
23786469 GATTATATGGACCCTCCGATGGCTAAGATCCTACATATGTTGCTGATTCTTGACAAATTATGTGA
1 GATTATATGGACCCTCCAATGGCTAAGATCCTACATATGTTGCTGATTCTTGACAAATTATGTGA
23786534 GCAGCATCGTGAGTA
66 GCAGCATCGTGAGTA
* ** * ** *
23786549 GATTATATGGACCCTCTAATGGCTAAGATGTTGCATATGTTG-TGGATTCTTGACAGCTTGTGTG
1 GATTATATGGACCCTCCAATGGCTAAGATCCTACATATGTTGCT-GATTCTTGACAAATTATGTG
* *
23786613 AGCAGTATCGTGAGTG
65 AGCAGCATCGTGAGTA
*
23786629 GATAATATGGACC
1 GATTATATGGACC
23786642 ATATCGATGG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
79 1 0.01
80 80 0.99
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (80 bp):
GATTATATGGACCCTCCAATGGCTAAGATCCTACATATGTTGCTGATTCTTGACAAATTATGTGA
GCAGCATCGTGAGTA
Found at i:23786755 original size:25 final size:25
Alignment explanation
Indices: 23786726--23786789 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
23786716 ATTCTATTTG
23786726 GGCTCGTAAGAGCGATATACTGTCT
1 GGCTCGTAAGAGCGATATACTGTCT
* * *
23786751 GGCTCGTAAGGGCAATATTCTGTCT
1 GGCTCGTAAGAGCGATATACTGTCT
*
23786776 GGCTTGTAAGAGCG
1 GGCTCGTAAGAGCG
23786790 TGGTTCTGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (25 bp):
GGCTCGTAAGAGCGATATACTGTCT
Found at i:23791909 original size:80 final size:80
Alignment explanation
Indices: 23791761--23791959 Score: 222
Period size: 80 Copynumber: 2.5 Consensus size: 80
23791751 ACTGTATATT
* * * ** * * *
23791761 GATTATATAGACCCTCAAATGGCTGAGATCCTGCATATGTTATGGATTCTTGATAGCTTATATAA
1 GATTATATGGACCCTCAGATGGCTGAGATCCTACATATGTTACAGATTCTTGACAACTAATATAA
23791826 GCAGCATCGTGAGTA
66 GCAGCATCGTGAGTA
* * *
23791841 GATTATATGGACCCTCCGATGGCTGAGATCCTACATATGTTACAGATTCTTGACAAC-AAGTGTG
1 GATTATATGGACCCTCAGATGGCTGAGATCCTACATATGTTACAGATTCTTGACAACTAA-TATA
*
23791905 AGCAGCATCGTGAGTT
65 AGCAGCATCGTGAGTA
* * *
23791921 GATAATATGGACCGT-ATTGATGGCTGGGATCCTACATAT
1 GATTATATGGACCCTCA--GATGGCTGAGATCCTACATAT
23791960 TGTGTAGTTT
Statistics
Matches: 100, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 1 0.01
80 79 0.79
81 20 0.20
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (80 bp):
GATTATATGGACCCTCAGATGGCTGAGATCCTACATATGTTACAGATTCTTGACAACTAATATAA
GCAGCATCGTGAGTA
Found at i:23791976 original size:81 final size:79
Alignment explanation
Indices: 23791765--23791996 Score: 198
Period size: 80 Copynumber: 2.9 Consensus size: 79
23791755 TATATTGATT
* ** * * * * * * *
23791765 ATATAGACCCTCAAATGGCTGAGATCCTGCATATGTTATGGATTCTTGATAGCTTA-TATAAGCA
1 ATATGGACCCTCCGATGGCTGAGATCCTACATATGTTA-AGATTCCTGACAAC-AAGTGTAAGCA
*
23791829 GCATCGTGAGTAGATT
64 GCATCGTGAGTAGATA
* *
23791845 ATATGGACCCTCCGATGGCTGAGATCCTACATATGTTACAGATTCTTGACAACAAGTGTGAGCAG
1 ATATGGACCCTCCGATGGCTGAGATCCTACATATGTTA-AGATTCCTGACAACAAGTGTAAGCAG
*
23791910 CATCGTGAGTTGATA
65 CATCGTGAGTAGATA
* ** * * * **
23791925 ATATGGACCGTATTGATGGCTGGGATCCTACATATTGTGT-AGTTTCCTGACAGCTTGTGTAAGC
1 ATATGGACCCT-CCGATGGCTGAGATCCTACATA-TGT-TAAGATTCCTGACAACAAGTGTAAGC
23791989 AGCATCGT
63 AGCATCGT
23791997 ATACTGGTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
79 1 0.01
80 75 0.60
81 45 0.36
82 3 0.02
83 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (79 bp):
ATATGGACCCTCCGATGGCTGAGATCCTACATATGTTAAGATTCCTGACAACAAGTGTAAGCAGC
ATCGTGAGTAGATA
Found at i:23792052 original size:25 final size:25
Alignment explanation
Indices: 23792014--23792080 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
23792004 TTAAATTCTT
*
23792014 TCTAGGCTCATAAGAGCAATATACTG
1 TCTA-GCTCGTAAGAGCAATATACTG
* ** *
23792040 TCTAGCTCGTAAGCGTGATATTCTG
1 TCTAGCTCGTAAGAGCAATATACTG
* *
23792065 TCTGGCTTGTAAGAGC
1 TCTAGCTCGTAAGAGC
23792081 GTGATTCTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
25 28 0.88
26 4 0.12
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (25 bp):
TCTAGCTCGTAAGAGCAATATACTG
Found at i:23797930 original size:22 final size:22
Alignment explanation
Indices: 23797905--23797962 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
23797895 AAAAAAATAT
*
23797905 TCAATTAAATTGGCGCAATCTA
1 TCAATTAAATTGGCGCAATCAA
*
23797927 TCAATTAAATTGGTGCAATCAA
1 TCAATTAAATTGGCGCAATCAA
*
23797949 TCAATTATATTGGC
1 TCAATTAAATTGGC
23797963 ATATTACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (22 bp):
TCAATTAAATTGGCGCAATCAA
Found at i:23799783 original size:19 final size:19
Alignment explanation
Indices: 23799752--23799790 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
23799742 TTAAATTCTA
23799752 ATTTAACCCAAAA-TATTT
1 ATTTAACCCAAAATTATTT
*
23799770 ATTTTACCCAAAAATTATTT
1 ATTTAACCC-AAAATTATTT
23799790 A
1 A
23799791 AAACCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAACCCAAAATTATTT
Found at i:23801753 original size:37 final size:37
Alignment explanation
Indices: 23801562--23801760 Score: 249
Period size: 37 Copynumber: 5.4 Consensus size: 37
23801552 ATTTAAATAA
* *
23801562 TCGGGCTTTATGCCTACTAGGCTTTGTGCCGGTGTAT
1 TCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTAT
*
23801599 TCGAG-TTATGTGCCTAGTAGGCTTTGTGCCGGTGTAT
1 TCGGGCTT-TGTGCCTAGTAGGCTTTGTGCCGGTGTAT
* * * *
23801636 TCAGGCTATT-TGCCTAGTAGGCTCTGTGCCAGTATAT
1 TCGGGCT-TTGTGCCTAGTAGGCTTTGTGCCGGTGTAT
* *
23801673 TCGGGCTATGTGCCTAGTAGGCTTAGTGCCGGTGTAT
1 TCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTAT
* * *
23801710 TTGGGCTTTGTGCCTAGTAGGCTTTGTGCCAGTGTTT
1 TCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTAT
*
23801747 TCGGGCTTTATGCC
1 TCGGGCTTTGTGCC
23801761 AATGAATCAG
Statistics
Matches: 137, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
36 3 0.02
37 131 0.96
38 2 0.01
39 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.31, T:0.37
Consensus pattern (37 bp):
TCGGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTAT
Found at i:23806564 original size:16 final size:16
Alignment explanation
Indices: 23806543--23806574 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23806533 TTACCTGTAT
23806543 CGCCAAAGAAGAAGGA
1 CGCCAAAGAAGAAGGA
23806559 CGCCAAAGAAGAAGGA
1 CGCCAAAGAAGAAGGA
23806575 TTCTATCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.31, T:0.00
Consensus pattern (16 bp):
CGCCAAAGAAGAAGGA
Found at i:23808849 original size:37 final size:37
Alignment explanation
Indices: 23808799--23808997 Score: 272
Period size: 37 Copynumber: 5.4 Consensus size: 37
23808789 ATTTAAATAA
* * * *
23808799 TCGGGCTTTGTGCCTAGTAAGCTTTATGCCGGTGTAT
1 TCGGGCTATGTGCCTAGTAGGCTTTGTGTCGGTGTAT
*
23808836 TCGGGCTATGTGCCTAGTAGGCTTTGTGTCAGTGTAT
1 TCGGGCTATGTGCCTAGTAGGCTTTGTGTCGGTGTAT
* * *
23808873 TCGGGTTATGTACCTAGTAGGTTTTGTGTCGGTGTAT
1 TCGGGCTATGTGCCTAGTAGGCTTTGTGTCGGTGTAT
* * *
23808910 TCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGTAT
1 TCGGGCTATGTGCCTAGTAGGCTTTGTGTCGGTGTAT
* *
23808947 TCGGGTTATGTACCTAGTAGGCTTTGTGTCGGTGTAT
1 TCGGGCTATGTGCCTAGTAGGCTTTGTGTCGGTGTAT
*
23808984 TCGGGCTTTGTGCC
1 TCGGGCTATGTGCC
23808998 GGTGTTTTCG
Statistics
Matches: 139, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 139 1.00
ACGTcount: A:0.13, C:0.17, G:0.32, T:0.39
Consensus pattern (37 bp):
TCGGGCTATGTGCCTAGTAGGCTTTGTGTCGGTGTAT
Found at i:23808908 original size:74 final size:74
Alignment explanation
Indices: 23808811--23808997 Score: 311
Period size: 74 Copynumber: 2.5 Consensus size: 74
23808801 GGGCTTTGTG
* * * *
23808811 CCTAGTAAGCTTTATGCCGGTGTATTCGGGCTATGTGCCTAGTAGGCTTTGTGTCAGTGTATTCG
1 CCTAGTAGGCTTTGTGTCGGTGTATTCGGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGTATTCG
23808876 GGTTATGTA
66 GGTTATGTA
* *
23808885 CCTAGTAGGTTTTGTGTCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGTATTCG
1 CCTAGTAGGCTTTGTGTCGGTGTATTCGGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGTATTCG
23808950 GGTTATGTA
66 GGTTATGTA
*
23808959 CCTAGTAGGCTTTGTGTCGGTGTATTCGGGCTTTGTGCC
1 CCTAGTAGGCTTTGTGTCGGTGTATTCGGGCTATGTGCC
23808998 GGTGTTTTCG
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 104 1.00
ACGTcount: A:0.14, C:0.17, G:0.31, T:0.39
Consensus pattern (74 bp):
CCTAGTAGGCTTTGTGTCGGTGTATTCGGGCTATGTGCCTAGTAGGCTTTGTGCCAGTGTATTCG
GGTTATGTA
Found at i:23808990 original size:21 final size:21
Alignment explanation
Indices: 23808966--23809018 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
23808956 GTACCTAGTA
23808966 GGCTTTGTGTCGGTGTATTCG
1 GGCTTTGTGTCGGTGTATTCG
* *
23808987 GGCTTTGTGCCGGTGTTTTCG
1 GGCTTTGTGTCGGTGTATTCG
*
23809008 GGTTTTGTGTC
1 GGCTTTGTGTC
23809019 TAGTAGGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.02, C:0.15, G:0.38, T:0.45
Consensus pattern (21 bp):
GGCTTTGTGTCGGTGTATTCG
Found at i:23809038 original size:58 final size:58
Alignment explanation
Indices: 23808929--23809038 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 58
23808919 GTGCCTAGTA
**
23808929 GGCTTTGTGCCAGTGTATTCGGGTTATGTACCTAGTAGGCTTTGTGTCGGTGTATTCG
1 GGCTTTGTGCCAGTGTATTCGGGTTATGTACCTAGTAGGCTTTGTACCGGTGTATTCG
* * * **
23808987 GGCTTTGTGCCGGTGTTTTCGGGTTTTGTGTCTAGTAGGCTTTGTACCGGTG
1 GGCTTTGTGCCAGTGTATTCGGGTTATGTACCTAGTAGGCTTTGTACCGGTG
23809039 AATCAAGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (58 bp):
GGCTTTGTGCCAGTGTATTCGGGTTATGTACCTAGTAGGCTTTGTACCGGTGTATTCG
Found at i:23810484 original size:30 final size:30
Alignment explanation
Indices: 23810449--23810551 Score: 145
Period size: 30 Copynumber: 3.5 Consensus size: 30
23810439 CTAAGTTTTT
*
23810449 AAAAATTCAAATTTGACCCCCAAAATTTCT
1 AAAAATTCAAATTTGACCCCCAAAATTTCC
* *
23810479 AAAAATTCAAATTTCACCCTC-AAATTTCC
1 AAAAATTCAAATTTGACCCCCAAAATTTCC
* * *
23810508 AAAAATTCAAATTTAATCCCCAAAGTTTCC
1 AAAAATTCAAATTTGACCCCCAAAATTTCC
23810538 AAAAATTCAAATTT
1 AAAAATTCAAATTT
23810552 AGCCCCCGTT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 25 0.38
30 40 0.62
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (30 bp):
AAAAATTCAAATTTGACCCCCAAAATTTCC
Found at i:23811466 original size:13 final size:13
Alignment explanation
Indices: 23811448--23811472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23811438 GTGATTATAG
23811448 CATGTTGATATTA
1 CATGTTGATATTA
23811461 CATGTTGATATT
1 CATGTTGATATT
23811473 TTTGCATACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (13 bp):
CATGTTGATATTA
Found at i:23822380 original size:52 final size:50
Alignment explanation
Indices: 23822253--23822380 Score: 166
Period size: 50 Copynumber: 2.5 Consensus size: 50
23822243 CTTTTACCCT
* * * *
23822253 TAAAGCTATGGAGGTGCAGATTGAAACCGCAATGGAAAATCTCATACACC
1 TAAAGCTGTAGAGGAGCAGATTGAAGCCGCAATGGAAAATCTCATACACC
* * *
23822303 TAAAGCTGTAGAGGAGCAGAATGAAGCCGCAATGGCAAATCTCATTCACC
1 TAAAGCTGTAGAGGAGCAGATTGAAGCCGCAATGGAAAATCTCATACACC
*
23822353 TATAAAGTTGTAGAGGAGCAGATTGAAG
1 --TAAAGCTGTAGAGGAGCAGATTGAAG
23822381 TCACAAGGAC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 43 0.64
52 24 0.36
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (50 bp):
TAAAGCTGTAGAGGAGCAGATTGAAGCCGCAATGGAAAATCTCATACACC
Found at i:23822535 original size:40 final size:40
Alignment explanation
Indices: 23822433--23822730 Score: 347
Period size: 39 Copynumber: 7.4 Consensus size: 40
23822423 AAGTTACAAC
* *
23822433 ATCCAATC-TTTACCCTAACCAGAGGGCAGATTAAAG-CA
1 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA
* * *
23822471 ATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACC
1 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA
*
23822511 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTAAAG-CA
1 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA
* ** * * *
23822550 ATCCAATATTTTACCCCGATCATG-GGGCTGATTGAAAACT
1 ATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAAGACA
* *
23822590 ATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG-CA
1 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA
23822629 ATCCAATCTTTTACCCTAATCAGAGGGCAGATT-AAGGACA
1 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAA-GACA
*
23822669 ATCCAATCTTTTACCCCTAAAATTATAGAGGGGCAGATTGAAGACA
1 ATCCAATCTTTTA-CCCT--AA-T-CAGA-GGGCAGATTGAAGACA
23822715 ATCCAATCTTTTACCC
1 ATCCAATCTTTTACCC
23822731 CTAAAGTTAT
Statistics
Matches: 221, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
38 9 0.04
39 90 0.41
40 81 0.37
41 4 0.02
43 2 0.01
44 1 0.00
45 6 0.03
46 26 0.12
47 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (40 bp):
ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA
Found at i:23822537 original size:79 final size:79
Alignment explanation
Indices: 23822432--23822730 Score: 361
Period size: 79 Copynumber: 3.7 Consensus size: 79
23822422 AAAGTTACAA
* *
23822432 CATCCAATC-TTTACCCTAACCAGAGGGCAGATTAAAGCAATCTAATCTTTTACCCTAACCAGAG
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTAAAGCAATCCAATCTTTTACCCTAATCAGAG
23822496 GGCAGATTGAAGAC
66 GGCAGATTGAAGAC
* * **
23822510 CATCCAATCTTTTACCCTAATCAGAGGGCAGATTAAAGCAATCCAATATTTTACCCCGATCATG-
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTAAAGCAATCCAATCTTTTACCCTAATCA-GA
* *
23822574 GGGCTGATTGAAAAC
65 GGGCAGATTGAAGAC
* * *
23822589 TATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATCAGAG
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTAAAGCAATCCAATCTTTTACCCTAATCAGAG
23822654 GGCAGATT-AAGGAC
66 GGCAGATTGAA-GAC
* ** *
23822668 AATCCAATCTTTTACCCCTAAAATTATAGAGGGGCAGATTGAAGACAATCCAATCTTTTACCC
1 CATCCAATCTTTTA-CCCT--AA--CCAGA-GGGCAGATTAAAG-CAATCCAATCTTTTACCC
23822731 CTAAAGTTAT
Statistics
Matches: 189, Mismatches: 21, Indels: 14
0.84 0.09 0.06
Matches are distributed among these distances:
78 12 0.06
79 137 0.72
80 5 0.03
82 2 0.01
84 2 0.01
85 13 0.07
86 18 0.10
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (79 bp):
CATCCAATCTTTTACCCTAACCAGAGGGCAGATTAAAGCAATCCAATCTTTTACCCTAATCAGAG
GGCAGATTGAAGAC
Found at i:23822783 original size:50 final size:46
Alignment explanation
Indices: 23822652--23822806 Score: 166
Period size: 46 Copynumber: 3.3 Consensus size: 46
23822642 CCCTAATCAG
* * * *
23822652 AGGGCAGATTAAGGACAATCCAATCTTTTACCCCTAAAATTATAGA
1 AGGGCAGATTAAAGACAAGCAAATCTTTTACCCCTAAAGTTATAGA
* * * * *
23822698 GGGGCAGATTGAAGACAATCCAATCTTTTACCCCTAAAGTTATAAA
1 AGGGCAGATTAAAGACAAGCAAATCTTTTACCCCTAAAGTTATAGA
* *
23822744 AGGGCAGATTAAAGCTACAAAAGCAAATCTTATACCCCTAAAGTAATAGA
1 AGGGCAGATTAAAG--AC--AAGCAAATCTTTTACCCCTAAAGTTATAGA
*
23822794 AGGACAGATTAAA
1 AGGGCAGATTAAA
23822807 ACTCACAGTA
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
46 53 0.58
48 2 0.02
50 37 0.40
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (46 bp):
AGGGCAGATTAAAGACAAGCAAATCTTTTACCCCTAAAGTTATAGA
Found at i:23824535 original size:30 final size:30
Alignment explanation
Indices: 23824491--23824638 Score: 201
Period size: 30 Copynumber: 4.9 Consensus size: 30
23824481 TGACCCCTCT
23824491 AAGTTTTCAAAAATTCAAATTTAACCCCCA
1 AAGTTTTCAAAAATTCAAATTTAACCCCCA
* *
23824521 AA-TTTTCTAAAAATTCAAATTTCACCCCTA
1 AAGTTTTC-AAAAATTCAAATTTAACCCCCA
*
23824551 AA-TTTTCCAAAAATTCAAATTTAATCCCCA
1 AAGTTTT-CAAAAATTCAAATTTAACCCCCA
* **
23824581 AAGTTTGCAAAAATTCAAATTTAACCCTTA
1 AAGTTTTCAAAAATTCAAATTTAACCCCCA
*
23824611 AAGTTTTCAAAAATTAAAATTTAACCCC
1 AAGTTTTCAAAAATTCAAATTTAACCCC
23824639 ATTTTAATGT
Statistics
Matches: 103, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.05
30 94 0.91
31 4 0.04
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (30 bp):
AAGTTTTCAAAAATTCAAATTTAACCCCCA
Found at i:23838548 original size:18 final size:17
Alignment explanation
Indices: 23838512--23838550 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
23838502 AAATGTTCTA
* *
23838512 ACAAATGAAATGTAGTG
1 ACAAATGAAATGCAATG
23838529 ACAAATGAAAATGCAATG
1 ACAAATG-AAATGCAATG
23838547 ACAA
1 ACAA
23838551 CTAAATAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.54, C:0.10, G:0.18, T:0.18
Consensus pattern (17 bp):
ACAAATGAAATGCAATG
Found at i:23850823 original size:18 final size:18
Alignment explanation
Indices: 23850777--23850823 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
23850767 GGCGGAACCT
*
23850777 GAAGAGAAGAAGGAAAAT
1 GAAGAGAAGAAGGAAAAA
23850795 GAAGA-AGAGAAGGAAAAA
1 GAAGAGA-AGAAGGAAAAA
*
23850813 GAGGAGAAGAA
1 GAAGAGAAGAA
23850824 TGAAGAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (18 bp):
GAAGAGAAGAAGGAAAAA
Found at i:23850829 original size:15 final size:16
Alignment explanation
Indices: 23850776--23850830 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 16
23850766 AGGCGGAACC
*
23850776 TGAAGAGAAGAAGGAAAA
1 TGAAGAGGAGAAGG--AA
*
23850794 TGAAGAAGAGAAGGAA
1 TGAAGAGGAGAAGGAA
*
23850810 -AAAGAGGAGAA-GAA
1 TGAAGAGGAGAAGGAA
23850824 TGAAGAG
1 TGAAGAG
23850831 AAGGAAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.10
15 14 0.45
16 2 0.06
18 12 0.39
ACGTcount: A:0.58, C:0.00, G:0.36, T:0.05
Consensus pattern (16 bp):
TGAAGAGGAGAAGGAA
Found at i:23857792 original size:56 final size:56
Alignment explanation
Indices: 23857669--23857796 Score: 166
Period size: 56 Copynumber: 2.3 Consensus size: 56
23857659 TTGAGTATAA
* *
23857669 AAAAAGGTGATGTCAACCATGGCTTGCCAAACACCCAAAAAATATTTTTTAATCTG
1 AAAAAGGTGGTGTCAACCATGACTTGCCAAACACCCAAAAAATATTTTTTAATCTG
** * * * * * *
23857725 GGAAAGATGGTGTCGACCATGACTTGCCAAACACCCGAAAAATATTTTTTTATGTT
1 AAAAAGGTGGTGTCAACCATGACTTGCCAAACACCCAAAAAATATTTTTTAATCTG
23857781 AAAAAGGTGGTGTCAA
1 AAAAAGGTGGTGTCAA
23857797 TCATTGGGTC
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (56 bp):
AAAAAGGTGGTGTCAACCATGACTTGCCAAACACCCAAAAAATATTTTTTAATCTG
Found at i:23862213 original size:20 final size:20
Alignment explanation
Indices: 23862185--23862224 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23862175 CCCTTGCTTT
23862185 TAAAATTTTCAATTTTCTTC
1 TAAAATTTTCAATTTTCTTC
* **
23862205 TAAACTTTTTGATTTTCTTC
1 TAAAATTTTCAATTTTCTTC
23862225 AAATGAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.57
Consensus pattern (20 bp):
TAAAATTTTCAATTTTCTTC
Found at i:23866096 original size:43 final size:43
Alignment explanation
Indices: 23866035--23866486 Score: 200
Period size: 43 Copynumber: 10.5 Consensus size: 43
23866025 TATATTTTCA
* * * *
23866035 TCGGTTTATCTGATGATGCACTGTGTGTGCCAGTATAGTTGCT
1 TCGGTTTATCCGATGATGCACTATGTATGCCAGTATAGTTACT
* * * *
23866078 TCGGTTTATCCGACGATGCACTATGTGTGCTAGTATGGTTAC-
1 TCGGTTTATCCGATGATGCACTATGTATGCCAGTATAGTTACT
* * * * * * * *
23866120 TCTAGTATATCCGATGACGCACTATGTTTGCTAGTGTATTTTCT
1 TC-GGTTTATCCGATGATGCACTATGTATGCCAGTATAGTTACT
* * * ** * **
23866164 TTGGTTTATTCGATGATTCACTATACATACCAGTATACATACT
1 TCGGTTTATCCGATGATGCACTATGTATGCCAGTATAGTTACT
* * * * * *
23866207 TTGGTTTATTCGATGATGCACTGTATATGCCAGTATATTTTCT
1 TCGGTTTATCCGATGATGCACTATGTATGCCAGTATAGTTACT
* * ** *
23866250 TTGGTTTATCCGATGATGCAC--TGTACGCGTCAGTATACATGCT
1 TCGGTTTATCCGATGATGCACTATGTATGC--CAGTATAGTTACT
* * * * * * * *
23866293 ACGATATATTCGATGATGCATTAATTGTTTTGCCAGTATATTTTCT
1 TCGGTTTATCCGATGATGCACT-A-TG-TATGCCAGTATAGTTACT
* * *** * *
23866339 TTGGTTTATTCGATGATGCACTATACGTGCAAGTAT-GCATACT
1 TCGGTTTATCCGATGATGCACTATGTATGCCAGTATAG-TTACT
* * * * * * *
23866382 TCAGTATATCCAATGATGC-CTCATATGTGCAAGTATA-TTTCT
1 TCGGTTTATCCGATGATGCACT-ATGTATGCCAGTATAGTTACT
* **
23866424 TCGGTTTATCCGATGATGCAC--TGTACGTGCCAATATACATACT
1 TCGGTTTATCCGATGATGCACTATGTA--TGCCAGTATAGTTACT
* *
23866467 TCGGTATACCCGATGATGCA
1 TCGGTTTATCCGATGATGCA
23866487 TTGTTTGCAT
Statistics
Matches: 308, Mismatches: 85, Indels: 32
0.72 0.20 0.08
Matches are distributed among these distances:
40 2 0.01
41 5 0.02
42 31 0.10
43 235 0.76
44 2 0.01
45 1 0.00
46 27 0.09
47 2 0.01
48 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (43 bp):
TCGGTTTATCCGATGATGCACTATGTATGCCAGTATAGTTACT
Found at i:23866199 original size:86 final size:86
Alignment explanation
Indices: 23866062--23866466 Score: 278
Period size: 86 Copynumber: 4.7 Consensus size: 86
23866052 GCACTGTGTG
* * * * *** * * ***
23866062 TGCCAGTATAGTTGCTTCGGTTTATCCGACGATGCACTATGTGTGCTAGTATGGTTACTCTAGTA
1 TGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTATACATACCAGTATACATACTCTAGTA
* *
23866127 TATCCGATGACGCACTATGTT
66 TATCCGATGACGCACTATATA
* * * * * * *
23866148 TGCTAGTGTATTTTCTTTGGTTTATTCGATGATTCACTATACATACCAGTATACATACTTTGGTT
1 TGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTATACATACCAGTATACATACTCTAGTA
* * *
23866213 TATTCGATGATGCACTGTATA
66 TATCCGATGACGCACTATATA
* **** * *
23866234 TGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTACGCGTCAGTATACATGCTACGA-T
1 TGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTATACATACCAGTATACATACT-CTAGT
* * * * *
23866298 ATATTCGATGATGCATTAATTGTTT
65 ATATCCGATGACGCACT-A-T-ATA
* * * * *
23866323 TGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATACGTGCAAGTATGCATACT-TCAGT
1 TGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTATACATACCAGTATACATACTCT-AGT
* * *
23866387 ATATCCAATGATGC-CTCATATG
65 ATATCCGATGACGCACT-ATATA
* * * * * *
23866409 TGCAAGTATA-TTTCTTCGGTTTATCCGATGATGCACTGTACGTGCCAATATACATACT
1 TGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTATACATACCAGTATACATACT
23866467 TCGGTATACC
Statistics
Matches: 250, Mismatches: 63, Indels: 13
0.77 0.19 0.04
Matches are distributed among these distances:
85 42 0.17
86 137 0.55
87 1 0.00
88 4 0.02
89 66 0.26
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (86 bp):
TGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTATACATACCAGTATACATACTCTAGTA
TATCCGATGACGCACTATATA
Found at i:23866353 original size:89 final size:86
Alignment explanation
Indices: 23866125--23866486 Score: 282
Period size: 86 Copynumber: 4.2 Consensus size: 86
23866115 GTTACTCTAG
* * * * * * *
23866125 TATATCCGATGACGCACTATGTTTGCTAGTGTATTTTCTTTGGTTTATTCGATGATTCACTATAC
1 TATATTCGATGATGCACTGTATTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATAC
** ** *
23866190 ATACCAGTATACATACTTTGG
66 GCACCAGTATACATACTACGA
* * * *
23866211 TTTATTCGATGATGCACTGTATATGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTAC
1 TATATTCGATGATGCACTGTATTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATAC
** *
23866276 GCGTCAGTATACATGCTACGA
66 GCACCAGTATACATACTACGA
*
23866297 TATATTCGATGATGCATTAATTGT-TTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACT
1 TATATTCGATGATGC----ACTGTATTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACT
** * * *
23866361 ATACGTGCAAGTATGCATACTTC-A
62 ATACGCACCAGTATACATACTACGA
* * * * * * * *
23866385 GTATATCCAATGATGC-CTCATATGTGCAAGTATA-TTTCTTCGGTTTATCCGATGATGCACTGT
1 -TATATTCGATGATGCACT-GTATTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTAT
** * * *
23866448 ACGTGCCAATATACATACTTCGG
64 ACGCACCAGTATACATACTACGA
**
23866471 TATACCCGATGATGCA
1 TATATTCGATGATGCA
23866487 TTGTTTGCAT
Statistics
Matches: 222, Mismatches: 45, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
84 1 0.00
85 58 0.26
86 91 0.41
88 1 0.00
89 67 0.30
90 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (86 bp):
TATATTCGATGATGCACTGTATTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATAC
GCACCAGTATACATACTACGA
Found at i:23866400 original size:175 final size:174
Alignment explanation
Indices: 23866146--23866488 Score: 445
Period size: 175 Copynumber: 2.0 Consensus size: 174
23866136 ACGCACTATG
* * * * **
23866146 TTTGCTAGTGTATTTTCTTTGGTTTATTCGATGATTCACTATACATACCAGTATACATACTTTGG
1 TTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATACATACAAGTATACATACTTCAG
* * * * * *
23866211 TTTATTCGATGATGCACT-GTATATGCCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTA
66 TATATCCAATGATGC-CTCATATATGCAAGTATA-TTTCTTCGGTTTATCCGATGATGCACTGTA
* * * **
23866275 CGCGTCAGTATACATGCTACGATATATTCGATGATGCATTAATTGT
129 CGCGCCAATATACATACTACGATATACCCGATGATGCATTAATTGT
* * *
23866321 TTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATACGTGCAAGTATGCATACTTCAG
1 TTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATACATACAAGTATACATACTTCAG
*
23866386 TATATCCAATGATGCCTCATATGTGCAAGTATATTTCTTCGGTTTATCCGATGATGCACTGTACG
66 TATATCCAATGATGCCTCATATATGCAAGTATATTTCTTCGGTTTATCCGATGATGCACTGTACG
* * *
23866451 TGCCAATATACATACTTCGGTATACCCGATGATGCATT
131 CGCCAATATACATACTACGATATACCCGATGATGCATT
23866489 GTTTGCATGC
Statistics
Matches: 143, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
174 63 0.44
175 80 0.56
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (174 bp):
TTTGCCAGTATATTTTCTTTGGTTTATTCGATGATGCACTATACATACAAGTATACATACTTCAG
TATATCCAATGATGCCTCATATATGCAAGTATATTTCTTCGGTTTATCCGATGATGCACTGTACG
CGCCAATATACATACTACGATATACCCGATGATGCATTAATTGT
Found at i:23867933 original size:9 final size:9
Alignment explanation
Indices: 23867921--23867954 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
23867911 CCCAAAATCT
*
23867921 TTCATCACC
1 TTCATCAAC
23867930 TTCATCAAC
1 TTCATCAAC
23867939 TTCATCAAC
1 TTCATCAAC
23867948 TTC-TCAA
1 TTCATCAA
23867955 AACATGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 4 0.17
9 20 0.83
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
TTCATCAAC
Found at i:23868753 original size:23 final size:23
Alignment explanation
Indices: 23868723--23869093 Score: 526
Period size: 23 Copynumber: 16.1 Consensus size: 23
23868713 CTTATATCTA
*
23868723 TGCTTAAATATTAATGTAATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23868746 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
23868769 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23868792 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23868815 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
23868838 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23868861 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
23868884 TGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23868907 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23868930 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23868953 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23868976 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
23868999 TGCTCAAATATTAATGTGGTTTA
1 TGCTTAAATATTAATGTGATTTG
*
23869022 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * * *
23869045 TGCTCAAGTATTAATGTGGTTTA
1 TGCTTAAATATTAATGTGATTTG
*
23869068 TGCTTAAATATTAATGTTATTTG
1 TGCTTAAATATTAATGTGATTTG
23869091 TGC
1 TGC
23869094 ATAGACATAA
Statistics
Matches: 308, Mismatches: 40, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 308 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:23869191 original size:36 final size:36
Alignment explanation
Indices: 23869151--23869290 Score: 226
Period size: 36 Copynumber: 3.9 Consensus size: 36
23869141 TGTGAAAGTG
*
23869151 AATATGTGGGTATGTTCTTCATGCCATGTGACAGAT
1 AATATGTGGGTATGTTCTTCATGCCATGTGACAGAA
* *
23869187 AATATGTGGGTATGTTCTTCATGCCATGAGATAGAA
1 AATATGTGGGTATGTTCTTCATGCCATGTGACAGAA
* * *
23869223 AATATGTGGGCATGTTCTTCATGTCATGTGACAAAA
1 AATATGTGGGTATGTTCTTCATGCCATGTGACAGAA
23869259 AATATGTGGGTATGTTCTTCATGCCATGTGAC
1 AATATGTGGGTATGTTCTTCATGCCATGTGAC
23869291 TTATTATATT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 94 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (36 bp):
AATATGTGGGTATGTTCTTCATGCCATGTGACAGAA
Found at i:23876000 original size:5 final size:5
Alignment explanation
Indices: 23875984--23876038 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
23875974 ACATGGGTTG
* *
23875984 AAAAT AACAT AAAAT AAAAT ATTAAAT AAACA- AAAAT GAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A--AAAT AAA-AT AAAAT AAAAT AAAAT
23876031 AAAA- AAAA
1 AAAAT AAAA
23876039 GGGATTCAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
4 5 0.12
5 31 0.74
6 1 0.02
7 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:23876010 original size:22 final size:22
Alignment explanation
Indices: 23875985--23876038 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
23875975 CATGGGTTGA
23875985 AAAT-AACATAAAATAAAATATT
1 AAATAAACA-AAAATAAAATATT
*
23876007 AAATAAACAAAAATGAAATA--
1 AAATAAACAAAAATAAAATATT
23876027 AAATAAA-AAAAA
1 AAATAAACAAAAA
23876039 GGGATTCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 7 0.23
22 14 0.47
23 4 0.13
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAACAAAAATAAAATATT
Found at i:23879537 original size:16 final size:17
Alignment explanation
Indices: 23879516--23879550 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
23879506 AATTTAAATT
*
23879516 AATTAATTAA-TTTCTC
1 AATTAAATAATTTTCTC
23879532 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
23879549 AA
1 AA
23879551 CTAGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:23881288 original size:14 final size:15
Alignment explanation
Indices: 23881262--23881295 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
23881252 AAGAAAATTG
23881262 GAAAACAATTTTAAT
1 GAAAACAATTTTAAT
*
23881277 TAAAAC-ATTTTAAT
1 GAAAACAATTTTAAT
23881291 GAAAA
1 GAAAA
23881296 ATAAACGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (15 bp):
GAAAACAATTTTAAT
Found at i:23881434 original size:5 final size:5
Alignment explanation
Indices: 23881418--23881473 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
23881408 ACACGGGTTG
* *
23881418 AAAAT AACAT AAAAT AAAAT ATTAAAT -AAAT AAAAA AGAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A--AAAT AAAAT AAAAT A-AAAT AAAAT
23881465 AAAAT AAAA
1 AAAAT AAAA
23881474 AAGATTCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 4 0.09
5 31 0.72
6 4 0.09
7 4 0.09
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:23881450 original size:16 final size:17
Alignment explanation
Indices: 23881426--23881471 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
23881416 TGAAAATAAC
**
23881426 ATAAAATAAAATATTAA
1 ATAAAATAAAATAAGAA
23881443 AT-AAATAAAA-AAGAA
1 ATAAAATAAAATAAGAA
23881458 ATAAAATAAAATAA
1 ATAAAATAAAATAA
23881472 AAAAGATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 5 0.20
16 16 0.64
17 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
ATAAAATAAAATAAGAA
Found at i:23881459 original size:11 final size:11
Alignment explanation
Indices: 23881445--23881477 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
23881435 AATATTAAAT
23881445 AAATAAAAAAG
1 AAATAAAAAAG
*
23881456 AAATAAAATA-
1 AAATAAAAAAG
23881466 AAATAAAAAAG
1 AAATAAAAAAG
23881477 A
1 A
23881478 TTCAATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (11 bp):
AAATAAAAAAG
Found at i:23883316 original size:12 final size:12
Alignment explanation
Indices: 23883299--23883323 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23883289 GAATGAAAAA
23883299 ATTATTTACTTT
1 ATTATTTACTTT
23883311 ATTATTTACTTT
1 ATTATTTACTTT
23883323 A
1 A
23883324 CTTTCAGTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATTTACTTT
Found at i:23888316 original size:28 final size:30
Alignment explanation
Indices: 23888252--23888318 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
23888242 TAAAAAAATT
* *
23888252 TCAAAATATTGTTTTCTAATTTTTAAAGGG
1 TCAAAAAATTGTTTTCTAACTTTTAAAGGG
* *
23888282 TC-TAAAATT-TTTTTTAACTTTTAAA-GG
1 TCAAAAAATTGTTTTCTAACTTTTAAAGGG
23888309 TCAAAAAATT
1 TCAAAAAATT
23888319 ACCAATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 4 0.13
28 20 0.65
29 5 0.16
30 2 0.06
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.46
Consensus pattern (30 bp):
TCAAAAAATTGTTTTCTAACTTTTAAAGGG
Found at i:23891230 original size:17 final size:17
Alignment explanation
Indices: 23891210--23891341 Score: 108
Period size: 17 Copynumber: 7.9 Consensus size: 17
23891200 CCACACATTG
*
23891210 ACACAGTTCGCATATAA
1 ACACAGCTCGCATATAA
* *
23891227 ACACA--TACACATTTAA
1 ACACAGCT-CGCATATAA
* *
23891243 ACATAGCTAGCATATAA
1 ACACAGCTCGCATATAA
*
23891260 ACATAGCT-GCATATAA
1 ACACAGCTCGCATATAA
* * *
23891276 GCACAACTCTCATATAA
1 ACACAGCTCGCATATAA
* *
23891293 ACATAGCTAGCATATAA
1 ACACAGCTCGCATATAA
* *
23891310 ACACAACTCGTATATAA
1 ACACAGCTCGCATATAA
*
23891327 ACACAACTCGCATAT
1 ACACAGCTCGCATAT
23891342 TCAAGTAATC
Statistics
Matches: 91, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
15 1 0.01
16 24 0.26
17 65 0.71
18 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.23
Consensus pattern (17 bp):
ACACAGCTCGCATATAA
Found at i:23891290 original size:33 final size:35
Alignment explanation
Indices: 23891253--23891329 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 35
23891243 ACATAGCTAG
*
23891253 CATATAAACATAGCT-GCATATAAGCACAACTC-T
1 CATATAAACATAGCTAGCATATAAACACAACTCGT
23891286 CATATAAACATAGCTAGCATATAAACACAACTCGT
1 CATATAAACATAGCTAGCATATAAACACAACTCGT
23891321 -ATATAAACA
1 CATATAAACA
23891330 CAACTCGCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 15 0.37
34 25 0.61
35 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.08, T:0.23
Consensus pattern (35 bp):
CATATAAACATAGCTAGCATATAAACACAACTCGT
Found at i:23891297 original size:50 final size:51
Alignment explanation
Indices: 23891217--23891341 Score: 157
Period size: 50 Copynumber: 2.5 Consensus size: 51
23891207 TTGACACAGT
* * * *
23891217 TCGCATATAAACAC-A-TACACATTTAAACATAGCTAGCATATAAACATAGC
1 TCGCATATAAACACAACT-CGCATATAAACATAGCTAGCATATAAACACAAC
* *
23891267 T-GCATATAAGCACAACTCTCATATAAACATAGCTAGCATATAAACACAAC
1 TCGCATATAAACACAACTCGCATATAAACATAGCTAGCATATAAACACAAC
*
23891317 TCGTATATAAACACAACTCGCATAT
1 TCGCATATAAACACAACTCGCATAT
23891342 TCAAGTAATC
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
49 11 0.17
50 32 0.50
51 21 0.33
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (51 bp):
TCGCATATAAACACAACTCGCATATAAACATAGCTAGCATATAAACACAAC
Found at i:23894200 original size:24 final size:23
Alignment explanation
Indices: 23894149--23894202 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
23894139 TTGAGAAATA
*
23894149 ATTT-TTTAATTAAACTTTGTTT
1 ATTTGTTTAATTAAACTCTGTTT
*
23894171 AATTGTTTCAATTAAACTCTGTTT
1 ATTTGTTT-AATTAAACTCTGTTT
23894195 ATTTGTTT
1 ATTTGTTT
23894203 GAGTCAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 21 0.78
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (23 bp):
ATTTGTTTAATTAAACTCTGTTT
Found at i:23896210 original size:24 final size:24
Alignment explanation
Indices: 23896142--23896216 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
23896132 AGAAATAATC
* *
23896142 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
23896166 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
23896190 TTTCAATTAAACTCTGTTTATATG
1 TTTCAATTAAACTCTGTTTATTTG
23896214 TTT
1 TTT
23896217 GAGTCAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:23896867 original size:3 final size:3
Alignment explanation
Indices: 23896848--23896897 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
23896838 TAGTTTTTAG
* *
23896848 ATT ATG ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23896896 AT
1 AT
23896898 GGAGTGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:23898290 original size:31 final size:32
Alignment explanation
Indices: 23898253--23898324 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
23898243 GAGATTTTGG
* *
23898253 TTTAGGTTTTAAAATTTT-GGGA-TTTTCGGA
1 TTTAGGTTTCAAAATTTTGGGGATTTTTAGGA
23898283 TTTTAGGTTTCAAAATTTTGGGGATTTTTAGGA
1 -TTTAGGTTTCAAAATTTTGGGGATTTTTAGGA
23898316 TTTAGGTTT
1 TTTAGGTTT
23898325 GGATATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 17 0.46
32 13 0.35
33 7 0.19
ACGTcount: A:0.22, C:0.03, G:0.24, T:0.51
Consensus pattern (32 bp):
TTTAGGTTTCAAAATTTTGGGGATTTTTAGGA
Found at i:23898829 original size:19 final size:20
Alignment explanation
Indices: 23898787--23898829 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
23898777 ATTGTCTACT
23898787 ATTG-TGATTATGTTTTGATC
1 ATTGTTGATTATGTTTT-ATC
23898807 -TTGTTGATTATGTTTT-TC
1 ATTGTTGATTATGTTTTATC
23898825 ATTGT
1 ATTGT
23898830 CCCCATTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.10
19 7 0.33
20 12 0.57
ACGTcount: A:0.16, C:0.05, G:0.19, T:0.60
Consensus pattern (20 bp):
ATTGTTGATTATGTTTTATC
Found at i:23899285 original size:16 final size:16
Alignment explanation
Indices: 23899264--23899316 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 16
23899254 AAAAATTAAA
23899264 ATTATTTAATAATTTT
1 ATTATTTAATAATTTT
*
23899280 ATTATTTCAAAAATTTT
1 ATTATTT-AATAATTTT
23899297 -TT-TTTAATAATTTT
1 ATTATTTAATAATTTT
23899311 A-TATTT
1 ATTATTT
23899317 TAAAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 9 0.28
15 6 0.19
16 9 0.28
17 8 0.25
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATTTAATAATTTT
Found at i:23899292 original size:28 final size:27
Alignment explanation
Indices: 23899261--23899328 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 27
23899251 ATTAAAAATT
23899261 AAAATTATTTAATAATTTTATTATTTCA
1 AAAATTATTTAATAATTTTA-TATTTCA
* *
23899289 AAAATTTTTTTTTAATAATTTTATATTTTA
1 AAAA---TTATTTAATAATTTTATATTTCA
*
23899319 AAAAATATTT
1 AAAATTATTT
23899329 TAAAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
27 4 0.12
28 4 0.12
30 10 0.30
31 15 0.45
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
AAAATTATTTAATAATTTTATATTTCA
Found at i:23899323 original size:31 final size:31
Alignment explanation
Indices: 23899268--23899329 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
23899258 ATTAAAATTA
* *
23899268 TTTAATAATTTTATTATTTCAAAAATTTTTT
1 TTTAATAATTTTATTATTTAAAAAATATTTT
23899299 TTTAATAATTTTA-TATTTTAAAAAATATTTT
1 TTTAATAATTTTATTA-TTTAAAAAATATTTT
23899330 AAAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTAAAAAATATTTT
Found at i:23899341 original size:13 final size:12
Alignment explanation
Indices: 23899311--23899344 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
23899301 TAATAATTTT
23899311 ATATTTTAAAAA
1 ATATTTTAAAAA
23899323 ATATTTTAAAAA
1 ATATTTTAAAAA
23899335 ATAATTTTAA
1 AT-ATTTTAA
23899345 TATTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATTTTAAAAA
Found at i:23899870 original size:25 final size:24
Alignment explanation
Indices: 23899841--23899950 Score: 82
Period size: 24 Copynumber: 4.3 Consensus size: 24
23899831 ATTGTATTAC
23899841 TATTATATATAACTATTATAATATA
1 TATTATATATAA-TATTATAATATA
*
23899866 TATTATA-ATAAAATATATAATATTA
1 TATTATATATAATAT-TATAATA-TA
*
23899891 CATTATATTATAATATT-TAATAT-
1 TATTATA-TATAATATTATAATATA
*
23899914 TGATATACATATAATATTAATATATTATA
1 T-AT-TATATATAATATT-ATA-A-TATA
*
23899943 TACTATAT
1 TATTATAT
23899951 GATATGATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
23 2 0.03
24 23 0.34
25 23 0.34
26 3 0.04
27 11 0.16
28 4 0.06
29 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (24 bp):
TATTATATATAATATTATAATATA
Found at i:23899881 original size:15 final size:15
Alignment explanation
Indices: 23899858--23899905 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
23899848 TATAACTATT
*
23899858 ATAATATATATTATA
1 ATAAAATATATTATA
*
23899873 ATAAAATATATAATA
1 ATAAAATATATTATA
* * *
23899888 TTACATTATATTATA
1 ATAAAATATATTATA
23899903 ATA
1 ATA
23899906 TTTAATATTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAATATATTATA
Found at i:23899923 original size:30 final size:30
Alignment explanation
Indices: 23899863--23899937 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
23899853 CTATTATAAT
23899863 ATATATTATAATA-AAATATATAATATTAC
1 ATATATTATAATATAAATATATAATATTAC
* *
23899892 ATTATATTATAATATTTAATAT-TGATA-TAC
1 A-TATATTATAATA-TAAATATATAATATTAC
*
23899922 ATATAATATTAATATA
1 ATATATTA-TAATATA
23899938 TTATATACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 8 0.21
30 21 0.55
31 4 0.11
32 5 0.13
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
ATATATTATAATATAAATATATAATATTAC
Found at i:23900076 original size:247 final size:255
Alignment explanation
Indices: 23899606--23900077 Score: 550
Period size: 247 Copynumber: 1.9 Consensus size: 255
23899596 TCATTATACC
* *
23899606 TATAGATTATAATAACATATATAGTATTACATGATATTATAATATTTAATCATTGATGCATATAC
1 TATAGATTATAATAAAATATATAATATTACATGATATTATAATATTTAATCATT-ATGCATATAC
* * * * * * * *
23899671 ATTTATTTATGTAAAACTATTAATATATTATGTTATATGATGTGGTATTATATAATATACTAGGA
65 ATATATATATGTAAAACTATTAATATACTATATGATATGATATAGCATTATATAATATACTAGGA
* * * * * * *
23899736 GGACTAACTTTCAACTGTACAAAAAATATATAAATTTAGAGCATATTTTAACTAGTATAATAATA
130 GGACTAACTTTCAAATGTACAAAAAATATATAAACTTACAACATATTTCAACCAATATAATAATA
*
23899801 AACTATAATATATAATAATAAGTAATATATATTGTATTACTATTATATATAACTATTATAA
195 AACAATAATATATAATAATAAGTAATATATATTGTATTACTATTATATATAACTATTATAA
* *
23899862 TATATATTATAATAAAATATATAATATTACATTATATTATAATATTTAAT-A-T-TG-ATATACA
1 TATAGATTATAATAAAATATATAATATTACATGATATTATAATATTTAATCATTATGCATATACA
* *
23899923 TATA-ATAT-TAATA-TATT-ATATACTATATGATATGATATAGCATTATATAATATAGTAGGA-
66 TATATATATGTAAAACTATTAATATACTATATGATATGATATAGCATTATATAATATACTAGGAG
* * ** * * *
23899983 GATCTAATTTTTAAATGTACGGAAAGTATA-ACGACTTACAATATATTTCAACCAATATAATAAT
131 GA-CTAACTTTCAAATGTACAAAAAATATATA-AACTTACAACATATTTCAACCAATATAATAAT
* * * *
23900047 AACCAATAATATATGATTATAATTAATATAT
194 AAACAATAATATATAATAATAAGTAATATAT
23900078 TATGTACTAC
Statistics
Matches: 181, Mismatches: 33, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
246 3 0.02
247 107 0.59
248 4 0.02
249 4 0.02
250 3 0.02
251 10 0.06
252 2 0.01
254 1 0.01
255 1 0.01
256 46 0.25
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (255 bp):
TATAGATTATAATAAAATATATAATATTACATGATATTATAATATTTAATCATTATGCATATACA
TATATATATGTAAAACTATTAATATACTATATGATATGATATAGCATTATATAATATACTAGGAG
GACTAACTTTCAAATGTACAAAAAATATATAAACTTACAACATATTTCAACCAATATAATAATAA
ACAATAATATATAATAATAAGTAATATATATTGTATTACTATTATATATAACTATTATAA
Found at i:23900677 original size:15 final size:15
Alignment explanation
Indices: 23900657--23900709 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
23900647 AAAGTAAAAT
*
23900657 AAATTATTATATTTA
1 AAATTATAATATTTA
*
23900672 AAATTAAAATATTTA
1 AAATTATAATATTTA
* *
23900687 TAACTTATAAAATTTA
1 -AAATTATAATATTTA
23900703 AAATTAT
1 AAATTAT
23900710 TTGAATCCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTATAATATTTA
Found at i:23901858 original size:14 final size:13
Alignment explanation
Indices: 23901806--23901871 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
23901796 ATTTATTCAA
*
23901806 TTTTAATTTTGTT
1 TTTTAATTTTATT
*
23901819 TGTTTATTTTTATT
1 T-TTTAATTTTATT
* *
23901833 GTGTTAAATTTATT
1 -TTTTAATTTTATT
23901847 TTTTATATTTTATT
1 TTTTA-ATTTTATT
23901861 TATTTGAATTT
1 T-TTT-AATTT
23901872 AGTTATTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
13 5 0.12
14 27 0.66
15 8 0.20
16 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (13 bp):
TTTTAATTTTATT
Found at i:23908180 original size:22 final size:22
Alignment explanation
Indices: 23908152--23908204 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
23908142 TCAAGAATTG
23908152 TCGATACTTGGCAAAAAAGGTA
1 TCGATACTTGGCAAAAAAGGTA
23908174 TCGATACTTGGCAAAAAAGGTA
1 TCGATACTTGGCAAAAAAGGTA
23908196 TCGATACTT
1 TCGATACTT
23908205 TTTGGTCTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (22 bp):
TCGATACTTGGCAAAAAAGGTA
Found at i:23908284 original size:20 final size:20
Alignment explanation
Indices: 23908219--23908309 Score: 58
Period size: 20 Copynumber: 4.5 Consensus size: 20
23908209 GTCTGGAACT
* *
23908219 ATTTTGACTTGTTTGAAAAAC
1 ATTTTGACTTGGTT-AAAATC
* ** *
23908240 ATTTTAAAGT-GTTAAAATG
1 ATTTTGACTTGGTTAAAATC
* * *
23908259 AATTTGACTTGGTTCAAATT
1 ATTTTGACTTGGTTAAAATC
* *
23908279 ATTTTGACATGTTTAAAATC
1 ATTTTGACTTGGTTAAAATC
*
23908299 ATTTTAACTTG
1 ATTTTGACTTG
23908310 ATTTTAAAAT
Statistics
Matches: 50, Mismatches: 19, Indels: 3
0.69 0.26 0.04
Matches are distributed among these distances:
19 10 0.20
20 33 0.66
21 7 0.14
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATC
Found at i:23910554 original size:20 final size:20
Alignment explanation
Indices: 23910531--23910580 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
23910521 TTTTTTTGCG
*
23910531 AGTATCGATATTTTTATAA-A
1 AGTATCGATAGTTTTA-AATA
* *
23910551 AGTATTGATAGTTTTAAATC
1 AGTATCGATAGTTTTAAATA
23910571 AGTATCGATA
1 AGTATCGATA
23910581 CCAAATTGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (20 bp):
AGTATCGATAGTTTTAAATA
Found at i:23916787 original size:20 final size:20
Alignment explanation
Indices: 23916723--23916812 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
23916713 TCTGGAGCTG
* *
23916723 TTTTGACTTGTTTGAAAAACA
1 TTTTGACTTGGTT-AAAATCA
**
23916744 TTTTGAAGT-GTTAAAA-CGA
1 TTTTGACTTGGTTAAAATC-A
* *
23916763 TTTTGACTTGGTTCAAATTA
1 TTTTGACTTGGTTAAAATCA
* *
23916783 TTTTGACATGTTTAAAATCA
1 TTTTGACTTGGTTAAAATCA
*
23916803 TTTTAACTTG
1 TTTTGACTTG
23916813 ATTTTAAAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
18 1 0.02
19 12 0.23
20 33 0.62
21 7 0.13
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (20 bp):
TTTTGACTTGGTTAAAATCA
Found at i:23920860 original size:20 final size:20
Alignment explanation
Indices: 23920823--23920870 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
23920813 CTCCAGTGAG
* * *
23920823 ACTTCTTCCGGTAGAACTCC
1 ACTTCTACCGATAGAACTAC
*
23920843 ACTTCTACCGATATAACTAC
1 ACTTCTACCGATAGAACTAC
*
23920863 AGTTCTAC
1 ACTTCTAC
23920871 TAATACCTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.31
Consensus pattern (20 bp):
ACTTCTACCGATAGAACTAC
Found at i:23922162 original size:15 final size:17
Alignment explanation
Indices: 23922130--23922170 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
23922120 AATTCATGAT
23922130 AAGAGCAAG-ATTTGAAG
1 AAGAG-AAGAATTTGAAG
23922147 AAGA-AAGAATTT-AAG
1 AAGAGAAGAATTTGAAG
23922162 AAGAGAAGA
1 AAGAGAAGA
23922171 GAAAGTAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.45
16 8 0.36
17 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.15
Consensus pattern (17 bp):
AAGAGAAGAATTTGAAG
Found at i:23931610 original size:18 final size:18
Alignment explanation
Indices: 23931576--23931609 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
23931566 CATTTATAAA
23931576 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAAGAAAAG
23931594 AAAAGAA-AAAAGAAAA
1 AAAAGAAGAAAAGAAAA
23931610 ATATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAGAAGAAAAGAAAAG
Found at i:23931958 original size:13 final size:13
Alignment explanation
Indices: 23931940--23931964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23931930 CCCATTTTAT
23931940 CATTTTTAGCATG
1 CATTTTTAGCATG
23931953 CATTTTTAGCAT
1 CATTTTTAGCAT
23931965 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:23933288 original size:27 final size:27
Alignment explanation
Indices: 23933258--23933331 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
23933248 GAATGGAAAG
**
23933258 TAGCACTTCATTGCTCTCTATTCAAAT
1 TAGCACTTCGGTGCTCTCTATTCAAAT
* *
23933285 TAGCACTTTGGTGCTCTCTATTCTAAT
1 TAGCACTTCGGTGCTCTCTATTCAAAT
23933312 TAGCACTTCGGTGCTCTCTA
1 TAGCACTTCGGTGCTCTCTA
23933332 ATTTACACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.41
Consensus pattern (27 bp):
TAGCACTTCGGTGCTCTCTATTCAAAT
Found at i:23934635 original size:23 final size:23
Alignment explanation
Indices: 23934606--23934838 Score: 281
Period size: 23 Copynumber: 10.1 Consensus size: 23
23934596 TATATCTATA
*
23934606 CTTAAATATTAATATGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* * * *
23934629 CTCAAATTTTAATGTGATTTATA
1 CTTAAATATTAATGTGATTTGTG
*
23934652 TTTAAATATTAACT-TGATTTGTG
1 CTTAAATATTAA-TGTGATTTGTG
*
23934675 CTTAAATATTAATGTTG-TTTATG
1 CTTAAATATTAATG-TGATTTGTG
23934698 CTTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* *
23934721 TTTAAATATTAATGTGATTTATG
1 CTTAAATATTAATGTGATTTGTG
* * *
23934744 TTTAAATAATAATGTGATTTGTA
1 CTTAAATATTAATGTGATTTGTG
*
23934767 CTTAAGTATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
* * *
23934790 CTTAAATATTAATATTATTTATG
1 CTTAAATATTAATGTGATTTGTG
*
23934813 ATTAAATATTAATGTGATTTGTG
1 CTTAAATATTAATGTGATTTGTG
23934836 CTT
1 CTT
23934839 GAAGAATTAA
Statistics
Matches: 175, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
22 3 0.02
23 169 0.97
24 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (23 bp):
CTTAAATATTAATGTGATTTGTG
Found at i:23944519 original size:17 final size:18
Alignment explanation
Indices: 23944497--23944536 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
23944487 TAATTTCATA
23944497 CATTTT-TATTGTCATCG
1 CATTTTATATTGTCATCG
* *
23944514 CATTTTATTTTGTCATTG
1 CATTTTATATTGTCATCG
23944532 CATTT
1 CATTT
23944537 CTTTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (18 bp):
CATTTTATATTGTCATCG
Found at i:23947797 original size:26 final size:29
Alignment explanation
Indices: 23947768--23947822 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 29
23947758 CCTCAAATGA
*
23947768 GAAGAATCAA-GC-TGAATT-CACAGATG
1 GAAGAATCAACGCAGGAATTCCACAGATG
*
23947794 GAAGCATCAACGCAGGAATTCCACAGATG
1 GAAGAATCAACGCAGGAATTCCACAGATG
23947823 TAGCTGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 2 0.08
28 5 0.21
29 8 0.33
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (29 bp):
GAAGAATCAACGCAGGAATTCCACAGATG
Found at i:23963683 original size:52 final size:52
Alignment explanation
Indices: 23963601--23963838 Score: 352
Period size: 52 Copynumber: 4.6 Consensus size: 52
23963591 TTTCATTTAG
* * * * *
23963601 TACTCACGGTGACACATAGTCATCGTACCTCACAATCCGTAAAGGATTCCTT
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATA
* *
23963653 TACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGAATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATA
*
23963705 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAATGATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATA
* * *
23963757 CACTCACGATGACACATAGACATCAGACCTCATAATCCGTATAA-GATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTA-AAGGATTCATA
*
23963809 TACTCATGATGACACATAGTCATCGGACCT
1 TACTCACGATGACACATAGTCATCGGACCT
23963839 TTTTACATTT
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 166 0.99
53 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (52 bp):
TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATA
Found at i:23970756 original size:22 final size:21
Alignment explanation
Indices: 23970709--23970756 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
23970699 AATGATCATA
*
23970709 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* *
23970730 TTTAACATTAATTAATCCTATT
1 ATTAAC-TTAATTAATCATATT
23970752 ATTAA
1 ATTAA
23970757 TCAATATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:23976188 original size:22 final size:24
Alignment explanation
Indices: 23976144--23976189 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
23976134 ATTAGTACAG
**
23976144 TCAATTTCATACAAATACTCAAAA
1 TCAATTTCATACAAATAAGCAAAA
23976168 TCAATTT-ATA-AAATAAGCAAAA
1 TCAATTTCATACAAATAAGCAAAA
23976190 ACAGTTCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 3 0.15
24 7 0.35
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.28
Consensus pattern (24 bp):
TCAATTTCATACAAATAAGCAAAA
Found at i:23977881 original size:23 final size:23
Alignment explanation
Indices: 23977850--23978155 Score: 425
Period size: 23 Copynumber: 13.3 Consensus size: 23
23977840 CTTATATCTA
* *
23977850 TGCTTAAATATTACTATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
23977873 TGCTCAAATTTTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23977896 TACTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23977919 TGCTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23977942 TGCTTAAATAATAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
23977965 T-CTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
23977987 TGTTTAAATATTAATTTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23978010 TGCTTAAATAATAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23978033 TGCTTAAATATTAATGTAATTTG
1 TGCTTAAATATTAATGTGATTTG
23978056 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
**
23978079 TAATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
23978102 TGCTTAAATATTAATATTATTTA
1 TGCTTAAATATTAATGTGATTTG
**
23978125 TAATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
23978148 TGCTTAAA
1 TGCTTAAA
23978156 AAATTAAGAT
Statistics
Matches: 244, Mismatches: 38, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
22 21 0.09
23 223 0.91
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:23978265 original size:36 final size:36
Alignment explanation
Indices: 23978225--23978301 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
23978215 TGATGACTGT
** *
23978225 TGTGAAAGTGAATATGTGGGTATGTTCTTCATGCCA
1 TGTGAAAGAAAATATGTGGATATGTTCTTCATGCCA
* *
23978261 TGTGACAGAAAATATGTGGATATGTTCTTCATGCTA
1 TGTGAAAGAAAATATGTGGATATGTTCTTCATGCCA
23978297 TGTGA
1 TGTGA
23978302 CTGGTTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.36
Consensus pattern (36 bp):
TGTGAAAGAAAATATGTGGATATGTTCTTCATGCCA
Found at i:23984278 original size:15 final size:14
Alignment explanation
Indices: 23984246--23984272 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23984236 AATTATTGAA
23984246 AAAATTATTTTTTG
1 AAAATTATTTTTTG
23984260 AAAATTATTTTTT
1 AAAATTATTTTTT
23984273 TTAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
AAAATTATTTTTTG
Found at i:23985376 original size:2 final size:2
Alignment explanation
Indices: 23985363--23985402 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
23985353 TTTAGTTGGT
*
23985363 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
23985403 AATTCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:23988552 original size:16 final size:16
Alignment explanation
Indices: 23988531--23988593 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
23988521 TAAACAATTG
23988531 ATTACAACTCTATTCT
1 ATTACAACTCTATTCT
* * *
23988547 ATTACAATTCTGTTCC
1 ATTACAACTCTATTCT
* *
23988563 ATTACAATTTTATT-T
1 ATTACAACTCTATTCT
23988578 CATTACAACTCTATTC
1 -ATTACAACTCTATTC
23988594 AATTTCAGTA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTACAACTCTATTCT
Found at i:23992134 original size:2 final size:2
Alignment explanation
Indices: 23992127--23992160 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
23992117 AAATGGGAGG
23992127 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
23992161 ATCTGGCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23993762 original size:18 final size:18
Alignment explanation
Indices: 23993716--23993764 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
23993706 TACATAGTCA
*
23993716 ATTGCAACCACAATCACG
1 ATTGCAACCACAATCAAG
* **
23993734 ATTACCGCCACAATCAAG
1 ATTGCAACCACAATCAAG
*
23993752 CTTGCAACCACAA
1 ATTGCAACCACAA
23993765 ATGCAAGGAC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.35, G:0.10, T:0.16
Consensus pattern (18 bp):
ATTGCAACCACAATCAAG
Found at i:24018423 original size:3 final size:3
Alignment explanation
Indices: 24018415--24018472 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
24018405 CACATCCCAC
24018415 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24018463 ATT ATT ATT A
1 ATT ATT ATT A
24018473 GTGCAAGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:24019910 original size:36 final size:38
Alignment explanation
Indices: 24019845--24019923 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 38
24019835 GAGCCAACCA
**
24019845 ACCCAAACCAGAAGCCCAAATTTGAGACCCAATATTTG
1 ACCCAAACCAGAAGCCCAAATTTGAGACCCAATACCTG
*
24019883 ACCCAAA-CA-AAGGCCCAATTTTG-GACCCAATACCTG
1 ACCCAAACCAGAA-GCCCAAATTTGAGACCCAATACCTG
24019919 ACCCA
1 ACCCA
24019924 TTTTAATACC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 18 0.49
37 12 0.32
38 7 0.19
ACGTcount: A:0.38, C:0.33, G:0.13, T:0.16
Consensus pattern (38 bp):
ACCCAAACCAGAAGCCCAAATTTGAGACCCAATACCTG
Found at i:24019964 original size:23 final size:24
Alignment explanation
Indices: 24019933--24019979 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
24019923 ATTTTAATAC
24019933 CCAAGCTAAG-A-CCCAAAACCAAG
1 CCAAGCTAAGAAGCCC-AAACCAAG
*
24019956 CCAATCTAAGAAGCCCAAACCAAG
1 CCAAGCTAAGAAGCCCAAACCAAG
24019980 GCCCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 9 0.43
25 3 0.14
ACGTcount: A:0.47, C:0.34, G:0.13, T:0.06
Consensus pattern (24 bp):
CCAAGCTAAGAAGCCCAAACCAAG
Found at i:24019991 original size:85 final size:85
Alignment explanation
Indices: 24019884--24020059 Score: 298
Period size: 85 Copynumber: 2.1 Consensus size: 85
24019874 CAATATTTGA
* * * * *
24019884 CCCAAACAAAGGCCCAATTTTGGACCCAATACCTGACCCATTTTAATACCCAAGCTAAGACCCAA
1 CCCAAACAAAGGCCCAAATTTGGACCAAATACCTCACCCATTTAAATACCCAACCTAAGACCCAA
24019949 AACCAAGCCAATCTAAGAAG
66 AACCAAGCCAATCTAAGAAG
*
24019969 CCCAAACCAAGGCCCAAATTTGGACCAAATACCTCACCCATTTAAATACCCAACCTAAGACCCAA
1 CCCAAACAAAGGCCCAAATTTGGACCAAATACCTCACCCATTTAAATACCCAACCTAAGACCCAA
24020034 AACCAAGCCAATCTAAGAAG
66 AACCAAGCCAATCTAAGAAG
24020054 CCCAAA
1 CCCAAA
24020060 TTGACCCATG
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.41, C:0.34, G:0.10, T:0.15
Consensus pattern (85 bp):
CCCAAACAAAGGCCCAAATTTGGACCAAATACCTCACCCATTTAAATACCCAACCTAAGACCCAA
AACCAAGCCAATCTAAGAAG
Found at i:24033988 original size:51 final size:51
Alignment explanation
Indices: 24033924--24034159 Score: 330
Period size: 51 Copynumber: 4.6 Consensus size: 51
24033914 CGAAAGAGTT
* *
24033924 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAGGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTC
* * *
24033975 CAATAACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTC
* * * * *
24034026 TGATTACTAAGTGCCATCGTGAGTAAACGAATCCTCTACGGATTAAAAGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTC
* *
24034077 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCAT-GACGAATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCC-TCTACGGATTAAAGGTC
* *
24034128 CGATGACTCAGTGTCATCGTGAGTATATGAAT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAAT
24034160 TTTTAAACCG
Statistics
Matches: 165, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
51 164 0.99
52 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATTAAAGGTC
Found at i:24034814 original size:21 final size:24
Alignment explanation
Indices: 24034789--24034845 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 24
24034779 TACTTGAGTT
24034789 GTATCGGTAGTTAAAT-TAT-G-A
1 GTATCGGTAGTTAAATGTATAGAA
**
24034810 GTATCGGTAGTTGTATGTATAGAA
1 GTATCGGTAGTTAAATGTATAGAA
24034834 GTATCGGTAGTT
1 GTATCGGTAGTT
24034846 TGCATGCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 14 0.45
22 3 0.10
23 1 0.03
24 13 0.42
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.39
Consensus pattern (24 bp):
GTATCGGTAGTTAAATGTATAGAA
Found at i:24055986 original size:18 final size:19
Alignment explanation
Indices: 24055954--24055989 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24055944 TGGATAGGAA
24055954 ATTTTATAAAATATGCATC
1 ATTTTATAAAATATGCATC
*
24055973 ATTTT-TAAAGTATGCAT
1 ATTTTATAAAATATGCAT
24055990 TAACATGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (19 bp):
ATTTTATAAAATATGCATC
Found at i:24059272 original size:547 final size:546
Alignment explanation
Indices: 24058250--24059322 Score: 1388
Period size: 547 Copynumber: 2.0 Consensus size: 546
24058240 GTTTCGTACT
* * **
24058250 TAGCAGATTGAACTTATTTCCACATTTGATGAGCTTGAAATCGAGTAATTTCATTTATATTTTTG
1 TAGCAGATTGAACTTATTTCCACATTTGATAAACTTGAAATAAAGTAATTTCATTTATATTTTTG
* * ** * * *
24058315 CATTTTTAATCTACTTTTTGTTTTATGATAAAATGTACTAAGAATGTTGTATTATTGGTTTTAAG
66 CATTTTTAATATACGTTTCATTTTATAATAAAATGTACTAAGAAGGTTGTATTATTGCTTTTAAG
* * *
24058380 GCCAAATGAGGCCTAAAGATTAGCTAACATACTTCGTGAGTGCACAGGAGACTACTAATAGCAAG
131 GCCAAATGAGGCCAAAAGATTAGCTAACATACTTAGTGAGTGCACAGGAGACTACTAACAGCAAG
* * * * * **
24058445 CCATAGTGATACTGATCACTTCGTCACAACATAGACAGCTCTATGCTGCAACACAGGGATCAGCA
196 CCAGAGTGAAACTGACCACTTCGTCACAACATAGACAGCTCTATGCTGCAAAAAAAAGATCAGCA
* *
24058510 ACGAAGAATTCAAGGACTACCTGCAACGTCGCGACACAAGTCCTAGTGTGTCGCGACATCAACCT
261 ACGAAGAATTCAAGGACTACCTACAACGTCGCGACACAAGGCCTAGTGTGTCGCGACATCAACCT
* * ** * *
24058575 CAGACTCCAACTCTACATCTTGCGAGGGGCGTTTTCATCTTCACAATGCAACTTACACACGAAGG
326 CAGACTCCAACTATACATCCTGCGAAAGGCGTTTTCATCTTCACAATGCAACTTAAACACGAAGA
* * * * * * *
24058640 ACGATAGTTGACTTAGGGTTAAGGAGAAATGACCATGTAAAGCTATAAATATGACCTTTAGGACT
391 ACGATAGCTAACTTAAGGTTAAGAAAAAATGACCATGTAAAGCTATAAATAGGACCTTTAGCACT
* * * * ** *
24058705 AGGGTTTATACACAATTACTTAGCTTTTAATTTTTAGTTTTAGTTTTATTTATTTTTTTCTTTTG
456 AGGATTGAGACACAATTACTTAGCTTTCAATTTTTAGTTTTAG-TTTATTTATTTTTAGCCTTTG
24058770 AAACGAGTGATCTATCGGTTTAAAACC
520 AAACGAGTGATCTATCGGTTTAAAACC
* *
24058797 TAGCAGATTGAACTTATTTCTACATTTGATAAACTTGAAATAAAGT-ATATTCCTTTATATTTTA
1 TAGCAGATTGAACTTATTTCCACATTTGATAAACTTGAAATAAAGTAAT-TTCATTTATATTTT-
* * *
24058861 TGCATTTTTCATATA-GTTTCATTTTCTAATAAAATGTGCTAA-ATAGGTTGTATTATTGCTTTT
64 TGCATTTTTAATATACGTTTCATTTTATAATAAAATGTACTAAGA-AGGTTGTATTATTGCTTTT
* * *
24058924 AAGGCC-AATCGAGGCCAAAATG-TTAGCTAACATACTTAGTGAGTGCATAGGAGACTAGTAGCA
128 AAGGCCAAAT-GAGGCCAAAA-GATTAGCTAACATACTTAGTGAGTGCACAGGAGACTACTAACA
* **
24058987 GCAAGCTAGAGTGAAACTGACCACTTCGTCATGACATAGACAGCTCTATG-TCGCAAAAAAAAGA
191 GCAAGCCAGAGTGAAACTGACCACTTCGTCACAACATAGACAGCTCTATGCT-GCAAAAAAAAGA
* * * * * *
24059051 TCAGCAGCGAGGAATTCCAA-GACTGCCTACTACGTCGCGACACAAGGCCTGGTGTGTTGCGACA
255 TCAGCAACGAAGAATT-CAAGGACTACCTACAACGTCGCGACACAAGGCCTAGTGTGTCGCGACA
* * * * *
24059115 TCGACCTCAGACTCCAACTATGCATCCTGCGAAAGGTGTTTTCGTCTTCATAATGCAACTTAAAC
319 TCAACCTCAGACTCCAACTATACATCCTGCGAAAGGCGTTTTCATCTTCACAATGCAACTTAAAC
* * *
24059180 ACGAAGAACGATAGCTAATTTAAGGTTGAGAAAAAATGGCCATGTAAAAGCTATAAATAGGA-CT
384 ACGAAGAACGATAGCTAACTTAAGGTTAAGAAAAAATGACCATGT-AAAGCTATAAATAGGACCT
*
24059244 TTAGCACTAGGATTGAGACACCATTACTTAGCTTTCAATTTTTAGTTTTAGTTTATTTATTTTTA
448 TTAGCACTAGGATTGAGACACAATTACTTAGCTTTCAATTTTTAGTTTTAGTTTATTTATTTTTA
24059309 GCCTTTGAAACGAG
513 GCCTTTGAAACGAG
24059323 ATTGTAGAAA
Statistics
Matches: 449, Mismatches: 69, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
546 32 0.07
547 385 0.86
548 32 0.07
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (546 bp):
TAGCAGATTGAACTTATTTCCACATTTGATAAACTTGAAATAAAGTAATTTCATTTATATTTTTG
CATTTTTAATATACGTTTCATTTTATAATAAAATGTACTAAGAAGGTTGTATTATTGCTTTTAAG
GCCAAATGAGGCCAAAAGATTAGCTAACATACTTAGTGAGTGCACAGGAGACTACTAACAGCAAG
CCAGAGTGAAACTGACCACTTCGTCACAACATAGACAGCTCTATGCTGCAAAAAAAAGATCAGCA
ACGAAGAATTCAAGGACTACCTACAACGTCGCGACACAAGGCCTAGTGTGTCGCGACATCAACCT
CAGACTCCAACTATACATCCTGCGAAAGGCGTTTTCATCTTCACAATGCAACTTAAACACGAAGA
ACGATAGCTAACTTAAGGTTAAGAAAAAATGACCATGTAAAGCTATAAATAGGACCTTTAGCACT
AGGATTGAGACACAATTACTTAGCTTTCAATTTTTAGTTTTAGTTTATTTATTTTTAGCCTTTGA
AACGAGTGATCTATCGGTTTAAAACC
Found at i:24066852 original size:14 final size:15
Alignment explanation
Indices: 24066833--24066862 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
24066823 ATAGCAAACA
24066833 TCTTTTTC-TTCTTT
1 TCTTTTTCTTTCTTT
24066847 TCTTTTTCTTTCTTT
1 TCTTTTTCTTTCTTT
24066862 T
1 T
24066863 TCTCATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTTCTTTCTTT
Found at i:24066865 original size:24 final size:25
Alignment explanation
Indices: 24066833--24066879 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
24066823 ATAGCAAACA
24066833 TCTTTTTCTTC-TTTTC-TTTTTCTT
1 TCTTTTTC-TCATTTTCATTTTTCTT
24066857 TCTTTTTCTCATTTTCATTTTTC
1 TCTTTTTCTCATTTTCATTTTTC
24066880 AAGTGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 2 0.10
24 13 0.62
25 6 0.29
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (25 bp):
TCTTTTTCTCATTTTCATTTTTCTT
Found at i:24075153 original size:85 final size:85
Alignment explanation
Indices: 24075010--24075180 Score: 306
Period size: 85 Copynumber: 2.0 Consensus size: 85
24075000 TTTTAAGTGT
* *
24075010 TCTCTTGCGTCTTCATGAGGAAAACCAGAATACTGCCCATTTGAATTTAACATCTGAAACATCAC
1 TCTCTTGCGTCTTCATGAGGAAAACCAGAATACTACCCATTTAAATTTAACATCTGAAACATCAC
24075075 TAGTTTCAGCTCGAAATTAC
66 TAGTTTCAGCTCGAAATTAC
*
24075095 TCTCTTGCGTCTTCATGAGGAAAACCAGAATACTACCCATTTAAATTTAATATCTGAAACATCAC
1 TCTCTTGCGTCTTCATGAGGAAAACCAGAATACTACCCATTTAAATTTAACATCTGAAACATCAC
*
24075160 TGGTTTCAGCTCGAAATTAC
66 TAGTTTCAGCTCGAAATTAC
24075180 T
1 T
24075181 AGCTTGAATA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (85 bp):
TCTCTTGCGTCTTCATGAGGAAAACCAGAATACTACCCATTTAAATTTAACATCTGAAACATCAC
TAGTTTCAGCTCGAAATTAC
Found at i:24093054 original size:51 final size:51
Alignment explanation
Indices: 24092962--24093199 Score: 255
Period size: 51 Copynumber: 4.6 Consensus size: 51
24092952 GCTATAAACG
*
24092962 AAAGGATCCGATGACTAAGTGTCATCGTGAGT-AATGAATCCTTTACGGATT
1 AAAGG-TCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
24093013 AAAGGTCCGATGACTAGGTGTAATCATGAGTAAATGAATCCTTTACGAATT
1 AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * *
24093064 ACAGGTTCGATGACTAGGTATCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * **
24093115 AAAGGTCCGATGACTCA-GTGTTATCGTGAGTATATGAATTCCTATACGGAAC
1 AAAGGTCCGATGACT-AGGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
* ** *
24093167 AAGAGGTCCGATAACTATATGCCATCGTGAGTA
1 AA-AGGTCCGATGACTAGGTGTCATCGTGAGTA
24093200 TTAAATGAAC
Statistics
Matches: 154, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
50 23 0.15
51 96 0.62
52 11 0.07
53 24 0.16
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAGGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:24097787 original size:18 final size:17
Alignment explanation
Indices: 24097735--24097788 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
24097725 CGACAAAAAT
* *
24097735 TTCTTCCTC-CTCATTC
1 TTCTTCCTCTTTCCTTC
*
24097751 TT-TTCCTTTTTCCTT-
1 TTCTTCCTCTTTCCTTC
24097766 TTCTTCCTCTTTCTCTTC
1 TTCTTCCTCTTTC-CTTC
24097784 TTCTT
1 TTCTT
24097789 TGTCTTCCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 7 0.23
16 15 0.50
17 3 0.10
18 5 0.17
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (17 bp):
TTCTTCCTCTTTCCTTC
Found at i:24106921 original size:18 final size:17
Alignment explanation
Indices: 24106900--24106945 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
24106890 AAAAATAACA
*
24106900 ATAAAATAATAAGAGCT
1 ATAAAACAATAAGAGCT
*
24106917 GATAATACAATAAGAGCT
1 -ATAAAACAATAAGAGCT
*
24106935 ATAATACAATA
1 ATAAAACAATA
24106946 TTGTGCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.24
Consensus pattern (17 bp):
ATAAAACAATAAGAGCT
Found at i:24106940 original size:17 final size:18
Alignment explanation
Indices: 24106907--24106945 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
24106897 ACAATAAAAT
24106907 AATAAGAGCTGATAATAC
1 AATAAGAGCTGATAATAC
24106925 AATAAGAGCT-ATAATAC
1 AATAAGAGCTGATAATAC
24106942 AATA
1 AATA
24106946 TTGTGCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (18 bp):
AATAAGAGCTGATAATAC
Found at i:24114965 original size:3 final size:3
Alignment explanation
Indices: 24114957--24115013 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
24114947 GTATTGAGGT
*
24114957 AGA AGA AGA AGAA AGA A-A AGA AGA AGA AAA AGA AG- AGA AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
*
24115002 AAA AGA AGA AGA
1 AGA AGA AGA AGA
24115014 CATTGCCCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 6 0.13
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:24114980 original size:18 final size:17
Alignment explanation
Indices: 24114957--24115013 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
24114947 GTATTGAGGT
24114957 AGAAGAAGAAGAAAGAAA
1 AGAAGAAGAA-AAAGAAA
*
24114975 AGAAGAAGAAAAAGAAG
1 AGAAGAAGAAAAAGAAA
24114992 AGAAGGAAGAAAAAGAAGA
1 AGAA-GAAGAAAAAGAA-A
24115011 AGA
1 AGA
24115014 CATTGCCCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
17 10 0.29
18 22 0.63
19 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAAAAGAAA
Found at i:24114983 original size:21 final size:23
Alignment explanation
Indices: 24114957--24115013 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
24114947 GTATTGAGGT
24114957 AGAAGAAGAAGAA-AGAA-AAGA
1 AGAAGAAGAAGAAGAGAAGAAGA
*
24114978 AGAAGAAAAAGAAGAGAAGGAAGA
1 AGAAGAAGAAGAAGAGAA-GAAGA
*
24115002 AAAAGAAGAAGA
1 AGAAGAAGAAGA
24115014 CATTGCCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.40
22 4 0.13
24 14 0.47
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAAGAAGAGAAGAAGA
Found at i:24124209 original size:23 final size:21
Alignment explanation
Indices: 24124173--24124224 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
24124163 ATGGATACAG
24124173 TTTTATTTTATTTTATTTATT
1 TTTTATTTTATTTTATTTATT
* *
24124194 TTTTATATTTAGTTTTCTTTACT
1 TTTTAT-TTTA-TTTTATTTATT
*
24124217 CTTTATTT
1 TTTTATTT
24124225 AATTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 6 0.23
23 14 0.54
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTATTTTATTTTATTTATT
Found at i:24132853 original size:22 final size:22
Alignment explanation
Indices: 24132807--24132853 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
24132797 TCATTGCACC
* *
24132807 ACATAGCTCTCCCCATGTCATG
1 ACATAGCTCTCCCCATATCACG
*
24132829 ACATAGCTCTCCCCATATTACG
1 ACATAGCTCTCCCCATATCACG
24132851 ACA
1 ACA
24132854 ACGAGTTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.36, G:0.11, T:0.26
Consensus pattern (22 bp):
ACATAGCTCTCCCCATATCACG
Found at i:24136070 original size:16 final size:17
Alignment explanation
Indices: 24136039--24136072 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24136029 GTGACAAAAT
*
24136039 AAAATGCATAGGAACTA
1 AAAATGCATAGAAACTA
24136056 AAAATGCATA-AAACTA
1 AAAATGCATAGAAACTA
24136072 A
1 A
24136073 TTAAAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATGCATAGAAACTA
Found at i:24138355 original size:20 final size:21
Alignment explanation
Indices: 24138330--24138368 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24138320 ACAAGGAATT
24138330 TGAAACA-ACAAAAGTAAAAG
1 TGAAACATACAAAAGTAAAAG
*
24138350 TGAAACATATAAAAGTAAA
1 TGAAACATACAAAAGTAAA
24138369 TAAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (21 bp):
TGAAACATACAAAAGTAAAAG
Found at i:24144074 original size:13 final size:14
Alignment explanation
Indices: 24144056--24144085 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24144046 GTCAATGCAA
24144056 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
24144069 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
24144083 TCA
1 TCA
24144086 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:24150992 original size:23 final size:24
Alignment explanation
Indices: 24150965--24151016 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
24150955 AGTCATAAAC
*
24150965 CAAAATTA-ATTAAATAAAGAAAA
1 CAAAATTACAATAAATAAAGAAAA
*
24150988 CAAAA-TACAATAAATAAATAAAA
1 CAAAATTACAATAAATAAAGAAAA
*
24151011 TAAAAT
1 CAAAAT
24151017 CATATCTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (24 bp):
CAAAATTACAATAAATAAAGAAAA
Found at i:24157652 original size:39 final size:39
Alignment explanation
Indices: 24157598--24157677 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
24157588 AAACTTGGGC
24157598 TTAAAATTTTATATATATAATTATACTAAATCAAAGCTT
1 TTAAAATTTTATATATATAATTATACTAAATCAAAGCTT
24157637 TTAAAATTTTATATATATAATTATACTAAATCAAAGCTT
1 TTAAAATTTTATATATATAATTATACTAAATCAAAGCTT
24157676 TT
1 TT
24157678 GATAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (39 bp):
TTAAAATTTTATATATATAATTATACTAAATCAAAGCTT
Found at i:24158596 original size:2 final size:2
Alignment explanation
Indices: 24158589--24158616 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24158579 AAGAAAACAT
24158589 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
24158617 AAAGAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24160233 original size:16 final size:16
Alignment explanation
Indices: 24160212--24160245 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
24160202 AAAAAAATTC
24160212 TATATGGTGGGATGCT
1 TATATGGTGGGATGCT
24160228 TATATGGTGGGATGCT
1 TATATGGTGGGATGCT
24160244 TA
1 TA
24160246 GGGATAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.35, T:0.38
Consensus pattern (16 bp):
TATATGGTGGGATGCT
Found at i:24162330 original size:20 final size:19
Alignment explanation
Indices: 24162287--24162340 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
24162277 TGATAAGCAC
* *
24162287 AATTTTAATAATATTAATA
1 AATTTTAATAACATGAATA
24162306 AATTTTTAATAACATGAA-A
1 AA-TTTTAATAACATGAATA
24162325 ATATTTTAATTAACAT
1 A-ATTTTAA-TAACAT
24162341 TAAATCCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTTTAATAACATGAATA
Found at i:24162345 original size:19 final size:18
Alignment explanation
Indices: 24162304--24162345 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
24162294 ATAATATTAA
24162304 TAAATTTTTAATAACATG
1 TAAATTTTTAATAACATG
*
24162322 AAAATATTTTAATTAACAT-
1 TAAAT-TTTTAA-TAACATG
24162341 TAAAT
1 TAAAT
24162346 CCACACCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAATTTTTAATAACATG
Found at i:24164040 original size:27 final size:26
Alignment explanation
Indices: 24163992--24164042 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
24163982 CAAGAAAATA
**
24163992 AAAAAGAAAACAAAAGCGAACACGAT
1 AAAAAGAAAACAAAAGAAAACACGAT
*
24164018 AAAAATAAAACGAAAAGAAAACACG
1 AAAAAGAAAAC-AAAAGAAAACACG
24164043 CAACTAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.69, C:0.14, G:0.14, T:0.04
Consensus pattern (26 bp):
AAAAAGAAAACAAAAGAAAACACGAT
Found at i:24168332 original size:17 final size:17
Alignment explanation
Indices: 24168293--24168422 Score: 84
Period size: 17 Copynumber: 7.5 Consensus size: 17
24168283 ACATAATCAA
*
24168293 GGGTTCGCATAATATAT
1 GGGTTCGCATAACATAT
** * *
24168310 ATGTTCGGATGACATAT
1 GGGTTCGCATAACATAT
24168327 GGGTTCGCATAACATAT
1 GGGTTCGCATAACATAT
*
24168344 GGGTTCACATGACACATAT
1 GGGTTCGCAT-A-ACATAT
* *
24168363 -AGTTCTCATAAC-TGAT
1 GGGTTCGCATAACAT-AT
* * * **
24168379 GGTTTCACACATGATAT
1 GGGTTCGCATAACATAT
24168396 AGGGTTCGCATAACATAT
1 -GGGTTCGCATAACATAT
*
24168414 GCGTTCGCA
1 GGGTTCGCA
24168423 CATGATATAG
Statistics
Matches: 83, Mismatches: 24, Indels: 12
0.70 0.20 0.10
Matches are distributed among these distances:
15 1 0.01
16 4 0.05
17 51 0.61
18 21 0.25
19 6 0.07
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (17 bp):
GGGTTCGCATAACATAT
Found at i:24168362 original size:19 final size:17
Alignment explanation
Indices: 24168321--24168442 Score: 70
Period size: 17 Copynumber: 7.0 Consensus size: 17
24168311 TGTTCGGATG
*
24168321 ACATATGGGTTCGCATA
1 ACATATGGGTTCACATA
24168338 ACATATGGGTTCACATGA
1 ACATATGGGTTCACAT-A
* *
24168356 CACATAT-AGTTCTCATA
1 -ACATATGGGTTCACATA
* *
24168373 AC-TGATGGTTTCACACA
1 ACAT-ATGGGTTCACATA
** *
24168390 TGATATAGGGTTCGCATA
1 ACATAT-GGGTTCACATA
* *
24168408 ACATATGCGTTCGCACATG
1 ACATATGGGTT--CACATA
*
24168427 ATATA-GGGTTCACATA
1 ACATATGGGTTCACATA
24168443 CATTATAAGG
Statistics
Matches: 77, Mismatches: 20, Indels: 17
0.68 0.18 0.15
Matches are distributed among these distances:
15 1 0.01
16 9 0.12
17 28 0.36
18 25 0.32
19 14 0.18
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (17 bp):
ACATATGGGTTCACATA
Found at i:24168449 original size:18 final size:18
Alignment explanation
Indices: 24168428--24168504 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
24168418 TCGCACATGA
*
24168428 TATAGGGTTCACATACAT
1 TATAGGGCTCACATACAT
* * *
24168446 TATAAGGC-CTGCATACAA
1 TATAGGGCTC-ACATACAT
*
24168464 TATAGGGCTCACATAAAT
1 TATAGGGCTCACATACAT
* *
24168482 TATAGGGCTCACACACAC
1 TATAGGGCTCACATACAT
24168500 TATAG
1 TATAG
24168505 CAGCCTTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
17 1 0.02
18 44 0.96
19 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (18 bp):
TATAGGGCTCACATACAT
Found at i:24171316 original size:194 final size:195
Alignment explanation
Indices: 24170964--24171318 Score: 459
Period size: 194 Copynumber: 1.8 Consensus size: 195
24170954 GAAACTGACG
* * * * * * * *
24170964 CGATGGCTGAGGTACTGCATATGTTACGAGTCCTTGATAGCTCGTGTGAGTAGCATCATGAGTTG
1 CGATGCCTGAGGTACCGCATATGTTACGAGTCCTCGACAACTCGTGTGAGAAACATCATGAGATG
* * * *
24171029 GGAAATGAGAAATGAATCCAAGAATGGATTACAGGCCTTACGGTGGTTGAGATTTATGCATAAGT
66 AGAAAAGAGAAATGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATTTATGCATAAGT
*
24171094 GCATATTCTCGATAATTTGTGTGAGCAGCATTGTTAGGGAACAATTATATGCACAGATACCATAT
131 GCATATTCTCGATAATCTGTGTGAGCAGCATTGTTAGGGAACAATTATATGCACAGATACCATAT
* * *
24171159 CGATGCCTGAGGTACCGCATATGTTATGAGTCCTCGACAACTCGTGTGAGAAATATCGTGAGAT-
1 CGATGCCTGAGGTACCGCATATGTTACGAGTCCTCGACAACTCGTGTGAGAAACATCATGAGATG
* * *
24171223 AGAAAAGA-AATATGAAATCCAA-AATGGATTATAGGCCCTACGATGGTTGGGATTTATGCTTGA
66 AGAAAAGAGAA-ATG-AATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATTTATGCAT-A
*
24171286 A-TGCATATTCTCGATAGCTCT-TGTGAGCAGCAT
128 AGTGCATATTCTCGATA-ATCTGTGTGAGCAGCAT
24171319 CTTTAGAGGA
Statistics
Matches: 136, Mismatches: 20, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
193 2 0.01
194 70 0.51
195 64 0.47
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (195 bp):
CGATGCCTGAGGTACCGCATATGTTACGAGTCCTCGACAACTCGTGTGAGAAACATCATGAGATG
AGAAAAGAGAAATGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATTTATGCATAAGT
GCATATTCTCGATAATCTGTGTGAGCAGCATTGTTAGGGAACAATTATATGCACAGATACCATAT
Found at i:24180248 original size:15 final size:15
Alignment explanation
Indices: 24180230--24180272 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
24180220 AACTTCCTCT
*
24180230 TTTTCTTCTTCTTTC
1 TTTTCTTCTTCTTCC
*
24180245 TTTTTTTCTTCTTCC
1 TTTTCTTCTTCTTCC
*
24180260 TTCTCTTCCTTCT
1 TTTTCTT-CTTCT
24180273 CCTCCTCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCTTCTTCTTCC
Found at i:24180252 original size:18 final size:18
Alignment explanation
Indices: 24180229--24180263 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24180219 AAACTTCCTC
*
24180229 TTTTTCTTCTTCTTTCTT
1 TTTTTCTTCTTCCTTCTT
24180247 TTTTTCTTCTTCCTTCT
1 TTTTTCTTCTTCCTTCT
24180264 CTTCCTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTCTTCTTCCTTCTT
Found at i:24190345 original size:17 final size:16
Alignment explanation
Indices: 24190323--24190382 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
24190313 CATTAATTTA
24190323 CAATGACAAATGAAATG
1 CAATGAC-AATGAAATG
24190340 CAATGACAATGCAAATG
1 CAATGACAATG-AAATG
* * *
24190357 TAGTGACAATTATAATG
1 CAATGACAATGA-AATG
24190374 CAATGACAA
1 CAATGACAA
24190383 AGGGGATGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.14
17 31 0.86
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (16 bp):
CAATGACAATGAAATG
Found at i:24190397 original size:34 final size:34
Alignment explanation
Indices: 24190336--24190402 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
24190326 TGACAAATGA
*
24190336 AATGCAATGACAATGCAAATGTAGTGACAATTAT
1 AATGCAATGACAAAGCAAATGTAGTGACAATTAT
*** *
24190370 AATGCAATGACAAAGGGGATGTGGTGACAATTA
1 AATGCAATGACAAAGCAAATGTAGTGACAATTA
24190403 AATTTCGACT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (34 bp):
AATGCAATGACAAAGCAAATGTAGTGACAATTAT
Done.