Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 27
Found at i:1571103 original size:23 final size:23
Alignment explanation
Indices: 1571076--1571119 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1571066 TAAACATCAA
1571076 TTAATGAGCTCTTTAATAAAATT
1 TTAATGAGCTCTTTAATAAAATT
* *
1571099 TTAATGAGCTGTTTACTAAAA
1 TTAATGAGCTCTTTAATAAAA
1571120 AAATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (23 bp):
TTAATGAGCTCTTTAATAAAATT
Found at i:1572532 original size:12 final size:12
Alignment explanation
Indices: 1572515--1572554 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1572505 AATTCTAAAT
1572515 AATATTTTATAA
1 AATATTTTATAA
1572527 AATA-TTTA-AA
1 AATATTTTATAA
1572537 CAATATTTTATAA
1 -AATATTTTATAA
1572550 AATAT
1 AATAT
1572555 CTAAACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.08
11 8 0.32
12 13 0.52
13 2 0.08
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
AATATTTTATAA
Found at i:1572536 original size:23 final size:23
Alignment explanation
Indices: 1572504--1572563 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1572494 TGTTAAATTT
*
1572504 AAAT-TCTAAATAATATTTTATA
1 AAATATCTAAACAATATTTTATA
*
1572526 AAATATTTAAACAATATTTTATA
1 AAATATCTAAACAATATTTTATA
1572549 AAATATCTAAACAAT
1 AAATATCTAAACAAT
1572564 TAAATAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 4 0.12
23 30 0.88
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATCTAAACAATATTTTATA
Found at i:1573014 original size:73 final size:74
Alignment explanation
Indices: 1572771--1573274 Score: 655
Period size: 74 Copynumber: 6.9 Consensus size: 74
1572761 TTTAACCGGT
* * * *
1572771 TAAAATAAAGTAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTGAAGGATGATAATA
1 TAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAGGTTGCTAATA
*
1572836 ATATAAACGG
65 ATGTAAACGG
* * * * *
1572846 TTAAAAAAATAGACGCTACCTATTACATTAAAATACATATCGATTTTTTTTTAAGGTTGCTAATA
1 TAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTA-CCAGTTTTTTTTAAGGTTGCTAATA
*
1572911 ATGTAAATGG
65 ATGTAAACGG
*
1572921 TAAAAAAATATA--CGCTACCTATTACATTAAATTACCTACCAG-TTTTTTTAAGGTTGCTAATA
1 TAAAAAAA-ATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAGGTTGCTAATA
*
1572983 ATGTAAACGA
65 ATGTAAACGG
* * * *
1572993 TAAAAAAAATAGGCGCTACCTATTACATTAAAATACCAACC-GTTTTTTTTAAAGTTGTTAAAAA
1 TAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAGGTTGCTAATAA
1573057 TGTAAACGG
66 TGTAAACGG
* *
1573066 TAAAAAAAATAGGCGCTACCTATTACATTAAACTACTTACC-GTTTTTTTTAAAGGTTGCTAATA
1 TAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTT-AAGGTTGCTAATA
*
1573130 ATGTAAACAG
65 ATGTAAACGG
* * *
1573140 TAAAAAAATTAGGCGCTATCTATTACATTAAAATACCTACCAGTTTTTTTTAAAGTTGCTAATAA
1 TAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAGGTTGCTAATAA
1573205 TGTAAACGG
66 TGTAAACGG
* * * * * *
1573214 T--AAAAAATAAGCACTACCTATTACATTAAACTAACTGCC-GATTTTTTTAAGGTTGCTAATA
1 TAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAGGTTGCTAATA
1573275 TAATAGGTAA
Statistics
Matches: 376, Mismatches: 46, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
71 23 0.06
72 68 0.18
73 101 0.27
74 133 0.35
75 48 0.13
76 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (74 bp):
TAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAGGTTGCTAATAA
TGTAAACGG
Found at i:1573278 original size:147 final size:146
Alignment explanation
Indices: 1572784--1573274 Score: 631
Period size: 147 Copynumber: 3.4 Consensus size: 146
1572774 AATAAAGTAG
* * * * * * *
1572784 GCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTGAAGGATGATAATAATATAAACGGTTA
1 GCGCTACCTATTACATTAAACTAACTACCAGTTTTTTTAAAGGTTGCTAATAATGTAAAC-GATA
* * * * *
1572849 AAAAAATAGACGCTACCTATTACATTAAAATACATATCGATTTTTTTTTAAGGTTGCTAATAATG
65 AAAAAATAGGCGCTACCTATTACATTAAAATACCTA-CCAGTTTTTTTTAAAGTTGCTAATAATG
*
1572914 TAAATGGTAAAAAAATATA
129 TAAACGGTAAAAAAATA-A
* *
1572933 -CGCTACCTATTACATTAAATTACCTACCAGTTTTTTT-AAGGTTGCTAATAATGTAAACGATAA
1 GCGCTACCTATTACATTAAACTAACTACCAGTTTTTTTAAAGGTTGCTAATAATGTAAACGAT-A
* * *
1572996 AAAAAATAGGCGCTACCTATTACATTAAAATACCAACC-GTTTTTTTTAAAGTTGTTAAAAATGT
65 AAAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAAGTTGCTAATAATGT
*
1573060 AAACGGTAAAAAAAATAG
130 AAACGGT-AAAAAAATAA
1573078 GCGCTACCTATTACATTAAACT-ACTTACC-GTTTTTTTTAAAGGTTGCTAATAATGTAAAC-AG
1 GCGCTACCTATTACATTAAACTAAC-TACCAG-TTTTTTTAAAGGTTGCTAATAATGTAAACGA-
*
1573140 TAAAAAAATTAGGCGCTATCTATTACATTAAAATACCTACCAGTTTTTTTTAAAGTTGCTAATAA
63 TAAAAAAA-TAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAAGTTGCTAATAA
1573205 TGTAAACGGT-AAAAAATAA
127 TGTAAACGGTAAAAAAATAA
* *
1573224 GCACTACCTATTACATTAAACTAACTGCC-GATTTTTTT-AAGGTTGCTAATA
1 GCGCTACCTATTACATTAAACTAACTACCAG-TTTTTTTAAAGGTTGCTAATA
1573275 TAATAGGTAA
Statistics
Matches: 307, Mismatches: 25, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
145 43 0.14
146 91 0.30
147 106 0.35
148 67 0.22
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (146 bp):
GCGCTACCTATTACATTAAACTAACTACCAGTTTTTTTAAAGGTTGCTAATAATGTAAACGATAA
AAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTTTTTTTAAAGTTGCTAATAATGTA
AACGGTAAAAAAATAA
Found at i:1573649 original size:192 final size:182
Alignment explanation
Indices: 1573270--1573792 Score: 652
Period size: 192 Copynumber: 2.8 Consensus size: 182
1573260 TTAAGGTTGC
* * *
1573270 TAATATAATAGGTAAAAATATGATAAAACTGGTTTCATAATGACAAAACCGGTAAAGCGCTACCA
1 TAATATAACAGGTAAAAATATGATAAAACTGGTTTCATTATGACAAAACCGGTAAAGCGCTACCG
* * * *
1573335 AATATGTTAAAAGTATTGATTTCATTTAAATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGC
66 GATATGTTGAAAGTATT-AATTCATTTAAATAAGTATCGACACTTTTAGAATTTAAAAGAAAAAC
* *
1573400 AGTAATAGCACCTATAAAGCATCGATACTTTATAAAAATGTATCGATACATAA
130 AATAATAGCACCTATAAAGCATCAATACTTTATAAAAATGTATCGATACATAA
* * * * * *
1573453 TAATATAACAGGTAAAAAAATGACAAAATTGATTTTATTATGACAAAACCGGTAAAGCGCTATCG
1 TAATATAACAGGTAAAAATATGATAAAACTGGTTTCATTATGACAAAACCGGTAAAGCGCTACCG
* *
1573518 GATATGTTGAAAGTATTAATTCAATTTAAATAAGTATAGATACTTTTGGAATTTTTGGAATTTAA
66 GATATGTTGAAAGTATTAATTC-ATTTAAATAAGTATCGACACTTTT---A------GAATTTAA
* * *
1573583 AAGAAAAATAATAATAGCGCCTATAAAGTATCAAT-CTTTTATAAAAATGTATCGATACATAA
121 AAGAAAAACAATAATAGCACCTATAAAGCATCAATAC-TTTATAAAAATGTATCGATACATAA
* * * *
1573645 TAATATAACAGGTTAAAATATGATAAAACCGGTTTCATTATGATAAAACCGGTAAAACGCTACCG
1 TAATATAACAGGTAAAAATATGATAAAACTGGTTTCATTATGACAAAACCGGTAAAGCGCTACCG
** * * *
1573710 GATATGTTGAAAGTATCGATTCCATTCAAATAAGTATCGACACTTTTAAAATTTAAAAGAAAAGC
66 GATATGTTGAAAGTATTAATT-CATTTAAATAAGTATCGACACTTTTAGAATTTAAAAGAAAAAC
*
1573775 AATAATAGCGCCTATAAA
130 AATAATAGCACCTATAAA
1573793 AATGTATAGA
Statistics
Matches: 290, Mismatches: 38, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
182 4 0.01
183 125 0.43
186 1 0.00
189 1 0.00
191 1 0.00
192 157 0.54
193 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (182 bp):
TAATATAACAGGTAAAAATATGATAAAACTGGTTTCATTATGACAAAACCGGTAAAGCGCTACCG
GATATGTTGAAAGTATTAATTCATTTAAATAAGTATCGACACTTTTAGAATTTAAAAGAAAAACA
ATAATAGCACCTATAAAGCATCAATACTTTATAAAAATGTATCGATACATAA
Found at i:1576092 original size:18 final size:18
Alignment explanation
Indices: 1576057--1576095 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1576047 GTATATGACT
* *
1576057 AAAATATACGTTGAAGTA
1 AAAATATACCTAGAAGTA
*
1576075 AAAATATACCTAGGAGTA
1 AAAATATACCTAGAAGTA
1576093 AAA
1 AAA
1576096 CCATGTCTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAATATACCTAGAAGTA
Found at i:1578483 original size:21 final size:21
Alignment explanation
Indices: 1578459--1578498 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1578449 TCGTATTAGA
1578459 TATTTGATTAATAT-ATATTCT
1 TATTT-ATTAATATCATATTCT
*
1578480 TATTTATTGATATCATATT
1 TATTTATTAATATCATATT
1578499 GTTTAGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TATTTATTAATATCATATTCT
Found at i:1584968 original size:17 final size:17
Alignment explanation
Indices: 1584946--1584989 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
1584936 AATATGCTAG
1584946 AATAAAATAAATA-AACA
1 AATAAAATAAATATAA-A
1584963 AATAAAATAAATATAAA
1 AATAAAATAAATATAAA
1584980 AATAACAATA
1 AATAA-AATA
1584990 TCAAATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAAATAAATATAAA
Found at i:1588760 original size:3 final size:3
Alignment explanation
Indices: 1588752--1588776 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1588742 CTTAAACGCT
1588752 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
1588777 CTCTCTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1589313 original size:15 final size:16
Alignment explanation
Indices: 1589282--1589315 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1589272 TTCATAATAT
1589282 TTATTAAAATGATTAA
1 TTATTAAAATGATTAA
*
1589298 TTATTTAAAT-ATTAA
1 TTATTAAAATGATTAA
1589313 TTA
1 TTA
1589316 AAAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATTAAAATGATTAA
Found at i:1590899 original size:32 final size:30
Alignment explanation
Indices: 1590861--1590937 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
1590851 CGGGTCCACG
* *
1590861 GGGCCTACCTAAGAATACATCTTAGGGTCGC
1 GGGCCTACCTAAGAAT-CATCTCAGGGCCGC
* *
1590892 AGGGCCTATCC-GAGAATGATCTCAGGGCCGC
1 -GGGCCTA-CCTAAGAATCATCTCAGGGCCGC
1590923 GGAGCCTACCTAAGA
1 GG-GCCTACCTAAGA
1590938 GTCACACTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
30 4 0.11
31 19 0.51
32 12 0.32
33 2 0.05
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (30 bp):
GGGCCTACCTAAGAATCATCTCAGGGCCGC
Found at i:1596301 original size:23 final size:23
Alignment explanation
Indices: 1596236--1596309 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1596226 TATAAATTAG
* * *
1596236 TAATATATAAATTACTTAATTTTAT
1 TAATTTATAAATTA-ATAA-TTAAT
1596261 TAATTT-TAAA--AA-AATTAAT
1 TAATTTATAAATTAATAATTAAT
1596280 TAATTTATAAATTAATAATTAAT
1 TAATTTATAAATTAATAATTAAT
1596303 TAATTTA
1 TAATTTA
1596310 AAGATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
19 10 0.24
20 6 0.14
22 3 0.07
23 14 0.33
24 4 0.10
25 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTTATAAATTAATAATTAAT
Found at i:1596769 original size:17 final size:19
Alignment explanation
Indices: 1596747--1596785 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1596737 TATTTTTTTT
1596747 AAATTTT-TTTATAAT-AA
1 AAATTTTATTTATAATGAA
*
1596764 AAATTTTATTTTTAATGAA
1 AAATTTTATTTATAATGAA
1596783 AAA
1 AAA
1596786 AATTAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 7 0.37
19 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AAATTTTATTTATAATGAA
Found at i:1598232 original size:23 final size:23
Alignment explanation
Indices: 1598202--1598258 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1598192 AACCACCTAT
1598202 TGCGGCCAATATAACAATAAAAG
1 TGCGGCCAATATAACAATAAAAG
1598225 TGCGGCCAATATAACAATAAAAG
1 TGCGGCCAATATAACAATAAAAG
* *
1598248 TACGGCGAATA
1 TGCGGCCAATA
1598259 AACCAAACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (23 bp):
TGCGGCCAATATAACAATAAAAG
Found at i:1599701 original size:43 final size:43
Alignment explanation
Indices: 1599648--1599787 Score: 165
Period size: 43 Copynumber: 3.3 Consensus size: 43
1599638 TTTGTAACAA
* *** * *
1599648 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* **
1599691 AAACACCGCAATATGTGTTGATATTTAGTAGCGTTTTTCCAAC
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
* *
1599734 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTGTTTCCAA-
1 AAACACCGCAATAGGTGTTGATATTTAGCGGCGTT-TTTCCAAC
1599777 AAACACCGCAA
1 AAACACCGCAA
1599788 AAGATCTGGT
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 74 0.91
44 7 0.09
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
AAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
Found at i:1599814 original size:86 final size:87
Alignment explanation
Indices: 1599633--1599831 Score: 201
Period size: 86 Copynumber: 2.3 Consensus size: 87
1599623 TAAAGTTCGC
* *
1599633 AGCGTTTTGTAACAA-AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAACAAACAC
1 AGCGTTTT-TTACAACAAACGCCGCAATAGGTAACGAGATATAGCGGCGTTTGTCCAACAAACAC
* * *
1599697 CGCAATATGTGTTGATATTTAGT
65 CGCAATAAGTGCTGATATATAGT
* *** * *
1599720 AGCG-TTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTGTTTCCAA-AAACAC
1 AGCGTTTTTTACAACAAACGCCGCAATAGGTAACGAGATATAGCGGCGTT-TGTCCAACAAACAC
*
1599783 CGCAA-AAGAT-CTGGTATATAGT
65 CGCAATAAG-TGCTGATATATAGT
* *
1599805 GGCGTTTTTTTATAACAAACGCCGCAA
1 AGCG-TTTTTTACAACAAACGCCGCAA
1599832 AATGTCATAT
Statistics
Matches: 92, Mismatches: 15, Indels: 10
0.79 0.13 0.09
Matches are distributed among these distances:
85 18 0.20
86 45 0.49
87 29 0.32
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (87 bp):
AGCGTTTTTTACAACAAACGCCGCAATAGGTAACGAGATATAGCGGCGTTTGTCCAACAAACACC
GCAATAAGTGCTGATATATAGT
Found at i:1600007 original size:21 final size:20
Alignment explanation
Indices: 1599981--1600037 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 20
1599971 ATTTTCCAAT
*
1599981 AAACTTGACATCCATAACAA
1 AAACTTGAAATCCATAACAA
*
1600001 CAAACTTAAAATCCATAACAA
1 -AAACTTGAAATCCATAACAA
*
1600022 AAA-ATGAAATCCATAA
1 AAACTTGAAATCCATAA
1600038 TAAATCAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.34
20 3 0.09
21 18 0.56
ACGTcount: A:0.56, C:0.21, G:0.04, T:0.19
Consensus pattern (20 bp):
AAACTTGAAATCCATAACAA
Found at i:1600033 original size:19 final size:21
Alignment explanation
Indices: 1599990--1600037 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
1599980 TAAACTTGAC
*
1599990 ATCCATAACAACAAACTTAAA
1 ATCCATAACAACAAACATAAA
*
1600011 ATCCATAACAA-AAA-ATGAA
1 ATCCATAACAACAAACATAAA
1600030 ATCCATAA
1 ATCCATAA
1600038 TAAATCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 3 0.12
21 11 0.44
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (21 bp):
ATCCATAACAACAAACATAAA
Found at i:1603439 original size:52 final size:52
Alignment explanation
Indices: 1603369--1603527 Score: 309
Period size: 52 Copynumber: 3.1 Consensus size: 52
1603359 TTAACAACAA
1603369 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
1603421 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1603473 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1603525 ATA
1 ATA
1603528 TTGTTCAGTA
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 105 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:1604635 original size:38 final size:42
Alignment explanation
Indices: 1604587--1604738 Score: 199
Period size: 42 Copynumber: 3.7 Consensus size: 42
1604577 ATTACCACTC
** * *
1604587 TATTGCGGCG-TTTTGGTATAAACGCCGCTAAATGT-TA-AA
1 TATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCTACTA
1604626 TA-TGCGGCG-TTTTAGCTA-AAACGCCGCTACATGTCTACTA
1 TATTGCGGCGTTTTTA-CTATAAACGCCGCTACATGTCTACTA
*
1604666 TATTGCGGCGTTTTTACTATAAACGCTGCTACATGTCTACTA
1 TATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCTACTA
*
1604708 TATTGCGACGTTTTTACTATAAACGCCGCTA
1 TATTGCGGCGTTTTTACTATAAACGCCGCTA
1604739 TTGTTTAACC
Statistics
Matches: 100, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
38 26 0.26
39 6 0.06
40 3 0.03
41 10 0.10
42 55 0.55
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (42 bp):
TATTGCGGCGTTTTTACTATAAACGCCGCTACATGTCTACTA
Found at i:1609370 original size:2 final size:2
Alignment explanation
Indices: 1609357--1609398 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1609347 TTAAATAACA
* *
1609357 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1609398 A
1 A
1609399 AAATTTTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1609996 original size:42 final size:42
Alignment explanation
Indices: 1609949--1610031 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
1609939 CACTACCTAC
* *
1609949 ATCATATATGACTTTTTACATCCACACTCGCCCACAACCCAA
1 ATCATATATGACTTTTTACATCCACACCCGCCCAAAACCCAA
*
1609991 ATCATATATGATTTTTTACATCCACACCCGCCCAAAACCCA
1 ATCATATATGACTTTTTACATCCACACCCGCCCAAAACCCA
1610032 CTAAATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.35, G:0.05, T:0.27
Consensus pattern (42 bp):
ATCATATATGACTTTTTACATCCACACCCGCCCAAAACCCAA
Found at i:1617769 original size:11 final size:12
Alignment explanation
Indices: 1617739--1617769 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
1617729 CCACAGTATC
1617739 TAAAAAAATATA
1 TAAAAAAATATA
1617751 TAATAAAAATATA
1 TAA-AAAAATATA
1617764 TAAAAA
1 TAAAAA
1617770 GTTAGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAAAAAATATA
Found at i:1619025 original size:44 final size:44
Alignment explanation
Indices: 1618954--1619082 Score: 197
Period size: 44 Copynumber: 2.9 Consensus size: 44
1618944 TATAACAAAA
* *
1618954 ACAAAG-GAAATATATATTTTAACAAATGTAAACTTGTGAAGCTT
1 ACAAAGAG-AATATATATTTTAACAAATGCAAGCTTGTGAAGCTT
* *
1618998 ATAAAGAGAATATATATTTTAACAAATGCAAGCTTGTGAAACTT
1 ACAAAGAGAATATATATTTTAACAAATGCAAGCTTGTGAAGCTT
*
1619042 ACAAAGAGAATATATATTTTAATAAATGCAAGCTTGTGAAG
1 ACAAAGAGAATATATATTTTAACAAATGCAAGCTTGTGAAG
1619083 TTTGCTCACC
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 76 0.99
45 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.31
Consensus pattern (44 bp):
ACAAAGAGAATATATATTTTAACAAATGCAAGCTTGTGAAGCTT
Found at i:1626611 original size:8 final size:8
Alignment explanation
Indices: 1626600--1626640 Score: 50
Period size: 7 Copynumber: 5.1 Consensus size: 8
1626590 TGTTATCTAA
1626600 AAAAATAT
1 AAAAATAT
1626608 AAAAATA-
1 AAAAATAT
1626615 AAAAATA-
1 AAAAATAT
1626622 AAAAATAGAT
1 AAAAAT--AT
1626632 AAAAATAT
1 AAAAATAT
1626640 A
1 A
1626641 TTAAAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 13 0.43
8 10 0.33
9 1 0.03
10 6 0.20
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (8 bp):
AAAAATAT
Found at i:1626618 original size:7 final size:7
Alignment explanation
Indices: 1626599--1626628 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1626589 GTGTTATCTA
1626599 AAAAAAT
1 AAAAAAT
1626606 ATAAAAAT
1 A-AAAAAT
1626614 AAAAAAT
1 AAAAAAT
1626621 AAAAAAT
1 AAAAAAT
1626628 A
1 A
1626629 GATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:1626619 original size:15 final size:14
Alignment explanation
Indices: 1626599--1626628 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1626589 GTGTTATCTA
1626599 AAAAAATATAAAAAT
1 AAAAAATA-AAAAAT
1626614 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
1626628 A
1 A
1626629 GATAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAAAT
Found at i:1631601 original size:21 final size:21
Alignment explanation
Indices: 1631575--1631625 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1631565 TTGTGTGGTA
1631575 TCATGGTCTCTTACGTTGTGT
1 TCATGGTCTCTTACGTTGTGT
1631596 TCATGGTCTCTTACGTTGTGT
1 TCATGGTCTCTTACGTTGTGT
1631617 TCATGGTCT
1 TCATGGTCT
1631626 TCCCACCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.47
Consensus pattern (21 bp):
TCATGGTCTCTTACGTTGTGT
Found at i:1636189 original size:32 final size:30
Alignment explanation
Indices: 1636111--1636189 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
1636101 GGTTACTCGA
*
1636111 CTCGACTCGTTGCTCATT---AAAATTTTG
1 CTCGACTCATTGCTCATTAAGAAAATTTTG
*
1636138 CTCGACTCA-TGCTCGTTAAGAAAACTTATTG
1 CTCGACTCATTGCTCATTAAGAAAA-TT-TTG
*
1636169 TTCGACTCATTGCTCATTAAG
1 CTCGACTCATTGCTCATTAAG
1636190 CTCTTTACTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 7 0.17
27 8 0.19
29 4 0.10
30 2 0.05
31 11 0.26
32 10 0.24
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (30 bp):
CTCGACTCATTGCTCATTAAGAAAATTTTG
Found at i:1636216 original size:16 final size:16
Alignment explanation
Indices: 1636179--1636218 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1636169 TTCGACTCAT
**
1636179 TGCTCATTAAGCTCTT
1 TGCTCATTAAGCTCGA
*
1636195 TACTCATTAAGCTCGA
1 TGCTCATTAAGCTCGA
1636211 TGCTCATT
1 TGCTCATT
1636219 GCTCGCCTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (16 bp):
TGCTCATTAAGCTCGA
Found at i:1638037 original size:27 final size:30
Alignment explanation
Indices: 1638006--1638062 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1637996 CTTATGACAA
*
1638006 TTTTAAATTTT-TA-T-ATAATTTATTTAT
1 TTTTAAATTTTCTATTAATAATTTAGTTAT
*
1638033 TTTTATATTTTCTATTAATAATTTAGTTAT
1 TTTTAAATTTTCTATTAATAATTTAGTTAT
1638063 GTCATCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.40
28 2 0.08
29 1 0.04
30 12 0.48
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
TTTTAAATTTTCTATTAATAATTTAGTTAT
Found at i:1640553 original size:24 final size:24
Alignment explanation
Indices: 1640526--1640573 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1640516 ATTTTATGTT
* *
1640526 ACTAATAATGTAAGCGGTAAAATA
1 ACTAATAAGGTAAACGGTAAAATA
1640550 ACTAATAAGGTAAACGGTAAAATA
1 ACTAATAAGGTAAACGGTAAAATA
1640574 TTAATATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (24 bp):
ACTAATAAGGTAAACGGTAAAATA
Found at i:1640895 original size:75 final size:75
Alignment explanation
Indices: 1640621--1640874 Score: 382
Period size: 75 Copynumber: 3.4 Consensus size: 75
1640611 TAATAGAATA
* * * *
1640621 ACTAATAATGTAAACGGTAAAATAAAATAGGTGTTACTTATTACGTTAAACTATCTACCGGTTTG
1 ACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTG
*
1640686 TTTAAAGATT
66 TTTAAAGGTT
** * * *
1640696 ACTAATAATGTAAACAATAAAATAAAATAGGCACTACCTATTATGTTAAACTACATACCGGTTTG
1 ACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTG
1640761 TTTAAAGGTT
66 TTTAAAGGTT
* * *
1640771 ACTAATAATGTAAATGGTAATATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTG
1 ACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTG
1640836 TTTAAAGGTT
66 TTTAAAGGTT
*
1640846 AATAATAATGTAAACGGTAAAATAAAATA
1 ACTAATAATGTAAACGGTAAAATAAAATA
1640875 AACGTTATCT
Statistics
Matches: 158, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 158 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (75 bp):
ACTAATAATGTAAACGGTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTG
TTTAAAGGTT
Found at i:1640909 original size:23 final size:23
Alignment explanation
Indices: 1640870--1640921 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1640860 CGGTAAAATA
* **
1640870 AAATAAACGTTATCTATTTTGTT
1 AAATAAACGTTACCTATTACGTT
1640893 AAATAAAC-TCTACCTATTACGTT
1 AAATAAACGT-TACCTATTACGTT
1640916 AAATAA
1 AAATAA
1640922 GCGAAACCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (23 bp):
AAATAAACGTTACCTATTACGTT
Found at i:1641014 original size:121 final size:121
Alignment explanation
Indices: 1640810--1641111 Score: 428
Period size: 121 Copynumber: 2.5 Consensus size: 121
1640800 GGCGCTACCT
*
1640810 ATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAATA
1 ATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAATA
* * * * * *
1640875 AACGTTATCTATTTTGTTAAATAA-ACTCTACCTATTACGTTAAATAAGCGAAACCC
66 AACGCTATCCATTATGTTAAA-AAGACGCTACCTATAACGTTAAATAAGCGAAACAC
* *
1640931 ATTATGTTAAACTAGCTA-CTGATTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAAT
1 ATTACGTTAAACTAGCTACCAG-TTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAAT
*** * ** *
1640995 AGGTGCTATCCATTATGTTAAAAAGGCGCTACCTATAACGTTAAATAAGCGCTACAT
65 AAACGCTATCCATTATGTTAAAAAGACGCTACCTATAACGTTAAATAAGCGAAACAC
1641052 ATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATA
1 ATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATA
1641112 TATACAACTT
Statistics
Matches: 160, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
120 4 0.03
121 154 0.96
122 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (121 bp):
ATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAAATAAAATA
AACGCTATCCATTATGTTAAAAAGACGCTACCTATAACGTTAAATAAGCGAAACAC
Found at i:1641037 original size:23 final size:23
Alignment explanation
Indices: 1641011--1641062 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1641001 TATCCATTAT
*
1641011 GTTAAA-AAGGCGCTACCTATAAC
1 GTTAAATAA-GCGCTACATATAAC
*
1641034 GTTAAATAAGCGCTACATATTAC
1 GTTAAATAAGCGCTACATATAAC
1641057 GTTAAA
1 GTTAAA
1641063 CTAGCTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (23 bp):
GTTAAATAAGCGCTACATATAAC
Found at i:1642945 original size:29 final size:30
Alignment explanation
Indices: 1642908--1642970 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1642898 TTCTTATTTC
1642908 TTTAAATATATTTTGT-TTATTATCATTAT-
1 TTTAAATATATTTTGTATTATTAT-ATTATA
* *
1642937 TTTACATATATTTTTTATTATTATATTATA
1 TTTAAATATATTTTGTATTATTATATTATA
1642967 TTTA
1 TTTA
1642971 TTATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTAAATATATTTTGTATTATTATATTATA
Found at i:1642972 original size:24 final size:25
Alignment explanation
Indices: 1642914--1642972 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
1642904 TTTCTTTAAA
*
1642914 TATATTT-TGTTTATTATCATTATTT
1 TATATTTAT-TTTATTATCATTATAT
* * *
1642939 TACATATATTTT-TTATTATTATAT
1 TATATTTATTTTATTATCATTATAT
1642963 TATATTTATT
1 TATATTTATT
1642973 ATATATATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 18 0.67
25 8 0.30
26 1 0.04
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (25 bp):
TATATTTATTTTATTATCATTATAT
Found at i:1643066 original size:22 final size:23
Alignment explanation
Indices: 1643016--1643082 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 23
1643006 TGGGTTTGAT
1643016 TTGATTATTTTAATAGGTAGTGG
1 TTGATTATTTTAATAGGTAGTGG
* *
1643039 TTGATTATTTTAATATGTGGT-G
1 TTGATTATTTTAATAGGTAGTGG
1643061 TTGATTATTTTAATAGGTAGTG
1 TTGATTATTTTAATAGGTAGTG
1643083 ATTTGATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (23 bp):
TTGATTATTTTAATAGGTAGTGG
Found at i:1654694 original size:106 final size:106
Alignment explanation
Indices: 1654523--1655344 Score: 1401
Period size: 106 Copynumber: 7.7 Consensus size: 106
1654513 AGCCGGTATT
*
1654523 AACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
1654588 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
1654629 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
1654694 TGGTTGTCAACAAACAACCTCCCAATTTCAGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
*
1654735 AACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
1654800 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTT
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
*
1654841 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* *
1654906 TGGTTGTAAACAAACAACCTCCCAATTTCAGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* *
1654947 AACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCAC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
1655012 TGGTTGTCAACAAACAAACTTCCCAATTTCAGAACCAATTTC
66 TGGTTGTCAACAAAC-AACTTCCCAATTTCAGAGCCAATTTC
* * *
1655054 AACTTCACAGCGAATGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
1655119 TAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* *
1655160 AACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* * *
1655225 TGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCAATTTC
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* * * *
1655266 AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCGAGTTCAACTTCACGACGAATGGACGGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
*
1655331 TGGCTGTCAACAAA
66 TGGTTGTCAACAAA
1655345 ATTTCGGAGC
Statistics
Matches: 679, Mismatches: 36, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
106 580 0.85
107 99 0.15
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (106 bp):
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
Found at i:1655116 original size:425 final size:424
Alignment explanation
Indices: 1654523--1655344 Score: 1437
Period size: 425 Copynumber: 1.9 Consensus size: 424
1654513 AGCCGGTATT
* *
1654523 AACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCAC
* *
1654588 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
66 TGGTTGTCAACAAACAACTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGA
*
1654653 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACCTCCCA
131 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACCTCCCA
* *
1654718 ATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
196 ATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTT
*
1654783 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTTAACTTCA
261 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCA
* *
1654848 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGT
326 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGT
1654913 AAACAAACAACCTCCCAATTTCAGAGCCAATTTC
391 AAACAAACAACCTCCCAATTTCAGAGCCAATTTC
*
1654947 AACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCAC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCAC
* *
1655012 TGGTTGTCAACAAACAAACTTCCCAATTTCAGAACCAATTTCAACTTCACAGCGAATGATATTGG
66 TGGTTGTCAACAAAC-AACTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGG
* *
1655077 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCC
130 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACCTCCC
1655142 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
195 AATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
1655207 TCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCAATTTCAACTTC
260 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTC
* * * *
1655272 ACAGCGAAGGATATTGGACTCCAGACAACGCGAGTTCAACTTCACGACGAATGGACGGCTGGCTG
325 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGCTG
*
1655337 TCAACAAA
390 TAAACAAA
1655345 ATTTCGGAGC
Statistics
Matches: 375, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
424 77 0.21
425 298 0.79
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (424 bp):
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCAC
TGGTTGTCAACAAACAACTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACCTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGT
AAACAAACAACCTCCCAATTTCAGAGCCAATTTC
Found at i:1655431 original size:319 final size:311
Alignment explanation
Indices: 1654523--1655400 Score: 1357
Period size: 319 Copynumber: 2.8 Consensus size: 311
1654513 AGCCGGTATT
*
1654523 AACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1654588 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
66 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
1654653 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACCTCCCA
131 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT--ACAAACAA-----CA
* *
1654718 ATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
189 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTT
* * *
1654783 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTT
254 CACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
*
1654841 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* * * *
1654906 TGGTTGTAAACAAACAACCTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGA
66 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
*
1654971 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAAACTTCCC
131 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT--ACAAAC-AA-----C
* *
1655036 AATTTCAGAACCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACGCAAGTTCAACT
188 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACT
1655101 TCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
253 TCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
* *
1655160 AACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
1 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* * *
1655225 TGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
* * * * *
1655290 CTCCAGACAACGCGAGTTCAACTTCACGACGAATGGACGGCTGGCTGT-C-AACAA-AATTTCGG
131 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTACAAACAACAATTTCAG
* * *
1655352 AGCCGATTTCAACTTCACAGCGAAGGATATTGGCCTCGAAACAACGCAA
196 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAA
1655401 CTTACATTGG
Statistics
Matches: 524, Mismatches: 35, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
308 51 0.10
314 2 0.00
315 3 0.01
316 1 0.00
318 179 0.34
319 288 0.55
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (311 bp):
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAACAAACAACTTCCCAATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTACAAACAACAATTTCAG
AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTC
Found at i:1656842 original size:25 final size:25
Alignment explanation
Indices: 1656804--1656853 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1656794 ATTTCTTTAA
1656804 ATATATTTCATTTATTATTATTATTAC
1 ATATATTT-ATTTATTATTA-TATTAC
1656831 ATATATTT-TTTATTATTATATTA
1 ATATATTTATTTATTATTATATTA
1656854 TATTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
27 8 0.35
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATATTTATTTATTATTATATTAC
Found at i:1656862 original size:14 final size:15
Alignment explanation
Indices: 1656804--1656871 Score: 52
Period size: 17 Copynumber: 4.4 Consensus size: 15
1656794 ATTTCTTTAA
1656804 ATATATTTCATT-TAT
1 ATATATTT-ATTATAT
*
1656819 -TAT-TATTATTACAT
1 ATATAT-TTATTATAT
*
1656833 ATATTTTTTATTATTAT
1 ATA-TATTTATTA-TAT
1656850 ATTATATTTATTATAT
1 A-TATATTTATTATAT
1656866 ATATAT
1 ATATAT
1656872 GTTTTTTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
13 4 0.09
14 7 0.16
15 7 0.16
16 11 0.26
17 12 0.28
18 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATATTTATTATAT
Found at i:1656871 original size:20 final size:20
Alignment explanation
Indices: 1656818--1656863 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1656808 ATTTCATTTA
*
1656818 TTATTATTATTACA-TATAT
1 TTATTATTATTATATTATAT
*
1656837 TTTTTATTATTATATTATAT
1 TTATTATTATTATATTATAT
1656857 TTATTAT
1 TTATTAT
1656864 ATATATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTATTATTATATTATAT
Found at i:1656955 original size:22 final size:23
Alignment explanation
Indices: 1656905--1656971 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 23
1656895 TGGGTTTGAT
1656905 TTGATTATTTTAATAGGTAGTGG
1 TTGATTATTTTAATAGGTAGTGG
* *
1656928 TTGATTATTTTAATATGTGGT-G
1 TTGATTATTTTAATAGGTAGTGG
1656950 TTGATTATTTTAATAGGTAGTG
1 TTGATTATTTTAATAGGTAGTG
1656972 ATTTGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.51
23 19 0.49
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (23 bp):
TTGATTATTTTAATAGGTAGTGG
Found at i:1657125 original size:17 final size:19
Alignment explanation
Indices: 1657103--1657143 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1657093 TCCTTTATAC
1657103 TTTTTT-ATAT-TAATGTAT
1 TTTTTTCATATAT-ATGTAT
1657121 TTTTTTCATATATATGTAT
1 TTTTTTCATATATATGTAT
1657140 TTTT
1 TTTT
1657144 CACAATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 14 0.67
20 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTCATATATATGTAT
Found at i:1660021 original size:77 final size:78
Alignment explanation
Indices: 1659878--1660039 Score: 254
Period size: 77 Copynumber: 2.1 Consensus size: 78
1659868 CCTGCTGCTT
*
1659878 TTTTCCAGCTTACTTATTTTTCACAGCAATCATGGTAAAAAAGTTGACACCCCACTCTGAAGATT
1 TTTT-CAGCTTACTTATCTTTCACAGCAATCATGGTAAAAAAGTTGACACCCCACTCTGAAGATT
*
1659943 GGATAAACTTCCAA
65 GGACAAACTTCCAA
* * *
1659957 TTTTCAGCTTACTTATCTTTCACCGCGATCATGG-AAAAAAGTTGCCACCCCACTCTGAAGATTG
1 TTTTCAGCTTACTTATCTTTCACAGCAATCATGGTAAAAAAGTTGACACCCCACTCTGAAGATTG
*
1660021 GACAAACTTCTAA
66 GACAAACTTCCAA
1660034 TTTTCA
1 TTTTCA
1660040 CACGTTTTTC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
77 46 0.60
78 27 0.35
79 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (78 bp):
TTTTCAGCTTACTTATCTTTCACAGCAATCATGGTAAAAAAGTTGACACCCCACTCTGAAGATTG
GACAAACTTCCAA
Found at i:1661573 original size:15 final size:14
Alignment explanation
Indices: 1661547--1661605 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
1661537 TTTAGCGGTA
*
1661547 ATTTTTATTTATTT
1 ATTTTGATTTATTT
1661561 ATTTTGGATTTATTT
1 ATTTT-GATTTATTT
1661576 A-TTT-ATTTATTT
1 ATTTTGATTTATTT
* *
1661588 ATTTCGAATTTATGT
1 ATTTTG-ATTTATTT
1661603 ATT
1 ATT
1661606 CATTTATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.24
13 2 0.05
14 8 0.21
15 19 0.50
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.68
Consensus pattern (14 bp):
ATTTTGATTTATTT
Found at i:1661580 original size:23 final size:23
Alignment explanation
Indices: 1661550--1661733 Score: 122
Period size: 23 Copynumber: 7.7 Consensus size: 23
1661540 AGCGGTAATT
1661550 TTTATTTATTTATTTTGGATTTATTTA
1 TTTATTTATTTATTTT-GA---ATTTA
*
1661577 TTTATTTATTTATTTCGAATTTA
1 TTTATTTATTTATTTTGAATTTA
* *
1661600 TGTATTCATTTATTTCT-AATTTA
1 TTTATTTATTTATTT-TGAATTTA
*
1661623 TTTAATTATTTATTTTTG-ATTTA
1 TTTATTTATTTA-TTTTGAATTTA
* ** * **
1661646 ATTATTTAATCCA-CTCAAATTTA
1 TTTATTT-ATTTATTTTGAATTTA
*
1661669 TTTATTTATTTAGGTATTTCAGATTTA
1 TTTATTTATTTA--T-TTTGA-ATTTA
* * *
1661696 TTTATTTGTTTGTTTTGAAATTA
1 TTTATTTATTTATTTTGAATTTA
1661719 TTTATTTATTTATTT
1 TTTATTTATTTATTT
1661734 GAAGGGATAT
Statistics
Matches: 121, Mismatches: 26, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
22 4 0.03
23 72 0.60
24 10 0.08
25 1 0.01
26 4 0.03
27 30 0.25
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTATTTATTTATTTTGAATTTA
Found at i:1661584 original size:27 final size:27
Alignment explanation
Indices: 1661550--1661614 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
1661540 AGCGGTAATT
* * *
1661550 TTTATTTATTTATTTTGGATTTATTTA
1 TTTATTTATTTATTTCGAATTTATGTA
1661577 TTTATTTATTTATTTCGAATTTATGTA
1 TTTATTTATTTATTTCGAATTTATGTA
*
1661604 TTCATTTATTT
1 TTTATTTATTT
1661615 CTAATTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (27 bp):
TTTATTTATTTATTTCGAATTTATGTA
Found at i:1661673 original size:4 final size:4
Alignment explanation
Indices: 1661550--1661653 Score: 79
Period size: 4 Copynumber: 26.0 Consensus size: 4
1661540 AGCGGTAATT
**
1661550 TTTA TTTA TTTA TTT- TGGA TTTA TTTA TTTA TTTA TTTA TTTCGAA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT---A TTTA
* * * * * *
1661600 TGTA TTCA TTTA TTT- CTAA TTTA TTTA ATTA TTTA TTT- TTGA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
1661646 ATTA TTTA
1 TTTA TTTA
1661654 ATCCACTCAA
Statistics
Matches: 76, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
3 4 0.05
4 68 0.89
7 4 0.05
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:1661694 original size:27 final size:24
Alignment explanation
Indices: 1661663--1661730 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 24
1661653 AATCCACTCA
1661663 AATTTATTTATTTATTTAGGTATTTC
1 AATTTATTTATTTATTTA-GT-TTTC
* *
1661689 AGATTTATTTATTTGTTT-GTTTTG
1 A-ATTTATTTATTTATTTAGTTTTC
*
1661713 AAATTATTTATTTATTTA
1 AATTTATTTATTTATTTA
1661731 TTTGAAGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 14 0.39
24 4 0.11
25 2 0.06
26 1 0.03
27 15 0.42
ACGTcount: A:0.26, C:0.01, G:0.09, T:0.63
Consensus pattern (24 bp):
AATTTATTTATTTATTTAGTTTTC
Found at i:1663900 original size:30 final size:29
Alignment explanation
Indices: 1663838--1663900 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1663828 AAATTTGTAA
*
1663838 TTTTTTTAGTTATTCGAACTGTATTTTCT
1 TTTTTTTAGTTAATCGAACTGTATTTTCT
1663867 TTTTTTTAGTTAATCGAACT-TCATTTTCT
1 TTTTTTTAGTTAATCGAACTGT-ATTTTCT
1663896 TTTTT
1 TTTTT
1663901 GTTTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.63
Consensus pattern (29 bp):
TTTTTTTAGTTAATCGAACTGTATTTTCT
Found at i:1663988 original size:17 final size:17
Alignment explanation
Indices: 1663952--1663993 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
1663942 AAAAATTTTG
1663952 AAATTATTAATCAACTTT
1 AAATTATTAATC-ACTTT
1663970 AAATTATTAATTC-CTTT
1 AAATTATTAA-TCACTTT
*
1663987 AAGTTAT
1 AAATTAT
1663994 CCTTGAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 10 0.45
19 2 0.09
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATTATTAATCACTTT
Found at i:1667852 original size:2 final size:2
Alignment explanation
Indices: 1667845--1667873 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1667835 ACTGATAACG
1667845 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1667874 GTATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1672015 original size:20 final size:20
Alignment explanation
Indices: 1671990--1672041 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1671980 ACTTCGACTA
1671990 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1672010 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1672030 TCGCATTGCGAT
1 TCGCATTGCGAT
1672042 AGTCCAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1672059 original size:21 final size:21
Alignment explanation
Indices: 1672029--1672171 Score: 127
Period size: 21 Copynumber: 6.8 Consensus size: 21
1672019 GATTTACATA
*
1672029 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1672050 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
1672073 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1672092 TTCGCGTTGCGATTTATTCCAA-
1 TTCGCGTTGCGA--TAGTCCAAG
* *
1672114 TT-TCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1672134 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
1672157 TT--CGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
1672172 TAAAATCGCA
Statistics
Matches: 99, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
19 19 0.19
20 2 0.02
21 51 0.52
22 2 0.02
23 25 0.25
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1672093 original size:42 final size:42
Alignment explanation
Indices: 1672035--1672171 Score: 256
Period size: 42 Copynumber: 3.3 Consensus size: 42
1672025 CATATTCGCA
*
1672035 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
1672077 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1672119 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1672161 TTGCGATAGTC
1 TTGCGATAGTC
1672172 TAAAATCGCA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:1678764 original size:28 final size:28
Alignment explanation
Indices: 1678727--1678783 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1678717 TTTGTTTGCT
*
1678727 TAGGCAACATATGTCGGAGTCCAGCTGC
1 TAGGCAACATATGCCGGAGTCCAGCTGC
*
1678755 TAGGTAACATATGCCGGAGTCCAGCTGC
1 TAGGCAACATATGCCGGAGTCCAGCTGC
1678783 T
1 T
1678784 GAAGGTGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (28 bp):
TAGGCAACATATGCCGGAGTCCAGCTGC
Found at i:1685621 original size:36 final size:36
Alignment explanation
Indices: 1685571--1685647 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
1685561 CTTATTTCGC
*
1685571 CTAGTTTTCTTGACCATGAACACATACATAATTATA
1 CTAGTTTTCATGACCATGAACACATACATAATTATA
*
1685607 CTAGTTTTCATGACCATGAACACATACATAGTTATA
1 CTAGTTTTCATGACCATGAACACATACATAATTATA
1685643 CTAGT
1 CTAGT
1685648 GTTTTTGCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (36 bp):
CTAGTTTTCATGACCATGAACACATACATAATTATA
Found at i:1688459 original size:17 final size:17
Alignment explanation
Indices: 1688439--1688480 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1688429 CTAATGAGTT
*
1688439 AATTTTCCTATTGGGCC
1 AATTTTACTATTGGGCC
1688456 AATTTTACTATTGGGCC
1 AATTTTACTATTGGGCC
1688473 AATTTTAC
1 AATTTTAC
1688481 CGCCAATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (17 bp):
AATTTTACTATTGGGCC
Found at i:1693165 original size:24 final size:23
Alignment explanation
Indices: 1693138--1693185 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
1693128 CTAAACTCTT
1693138 TATCATCATCATTATCCCTAACAG
1 TATCATCATCATTATCCCT-ACAG
1693162 TATCATCATCATTATCCCTACAG
1 TATCATCATCATTATCCCTACAG
1693185 T
1 T
1693186 GAAATTACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (23 bp):
TATCATCATCATTATCCCTACAG
Found at i:1696244 original size:12 final size:12
Alignment explanation
Indices: 1696224--1696273 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1696214 AAAATCAATT
*
1696224 AAATCTATTTTA
1 AAATTTATTTTA
1696236 AAATTTATTTTA
1 AAATTTATTTTA
*
1696248 AAATATATATTT-
1 AAATTTAT-TTTA
1696260 --ATTTATTTTA
1 AAATTTATTTTA
1696270 AAAT
1 AAAT
1696274 ATAGATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
9 3 0.10
10 5 0.16
12 20 0.65
13 3 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATTTATTTTA
Found at i:1696691 original size:22 final size:22
Alignment explanation
Indices: 1696238--1696690 Score: 701
Period size: 22 Copynumber: 20.6 Consensus size: 22
1696228 CTATTTTAAA
** *
1696238 ATTTATTTTAAAATATATATTT
1 ATTTATTTTAAAATATGGATTG
*
1696260 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
1696282 ATTTATTTTAAAATATGAAAAAA
1 ATTTATTTTAAAATATG-GATTG
** *
1696305 AAATATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
1696327 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696349 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1696371 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* ***
1696393 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* *
1696415 AATTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
1696437 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696459 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696481 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696503 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696525 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696547 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1696569 ATTTATTTTAAAATAGGGATTG
1 ATTTATTTTAAAATATGGATTG
1696591 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696613 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1696635 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
1696657 ATTTATTTTAAAATATTAATTG
1 ATTTATTTTAAAATATGGATTG
1696679 ATTT-TTTTAAAA
1 ATTTATTTTAAAA
1696691 AAAAAATCAT
Statistics
Matches: 397, Mismatches: 33, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
21 8 0.02
22 374 0.94
23 15 0.04
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1697934 original size:49 final size:48
Alignment explanation
Indices: 1697884--1698071 Score: 242
Period size: 49 Copynumber: 3.9 Consensus size: 48
1697874 TAAGGTTATT
* * *
1697884 ATTTTAAAATAATTTATTAAAATATGGATTGATTTATTTTTAAATAATT-
1 ATTTTTAAATAATTTATT--AGTATGGATTGATTTATTTTAAAATAATTG
*
1697933 A-TTTTAAATAATTTATTAGTATGGATTGATTTATTTAAAAATAGATTG
1 ATTTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA-ATTG
*
1697981 ATTTTTTAAATAA-TTATTAGTATGGATTGATTTATTTTAAAATGGATTG
1 A-TTTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-AATTG
1698030 ATATTTTAAATAATTTATTAGTA-GGATTGA-TTATTTTAAAAT
1 AT-TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT
1698072 TAGATGTTAT
Statistics
Matches: 126, Mismatches: 6, Indels: 15
0.86 0.04 0.10
Matches are distributed among these distances:
46 23 0.18
47 3 0.02
48 29 0.23
49 52 0.41
50 19 0.15
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (48 bp):
ATTTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAATTG
Found at i:1697948 original size:14 final size:14
Alignment explanation
Indices: 1697915--1697949 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
1697905 ATATGGATTG
1697915 ATTTATTTTTAAATA
1 ATTTA-TTTTAAATA
1697930 A-TTATTTTAAATA
1 ATTTATTTTAAATA
1697943 ATTTATT
1 ATTTATT
1697950 AGTATGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.53
14 8 0.42
15 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1698034 original size:18 final size:19
Alignment explanation
Indices: 1698002--1698039 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
1697992 AATTATTAGT
1698002 ATGGATTGATTTATTTTAAA
1 ATGGATTGA-TTATTTTAAA
1698022 ATGGATTGA-TATTTTAAA
1 ATGGATTGATTATTTTAAA
1698040 TAATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (19 bp):
ATGGATTGATTATTTTAAA
Found at i:1698113 original size:73 final size:77
Alignment explanation
Indices: 1698022--1698299 Score: 296
Period size: 73 Copynumber: 3.6 Consensus size: 77
1698012 TTATTTTAAA
*
1698022 ATGGATTGA-TATTTTAAATAATTTATTAGTA-GGATTGATTATTTTAAAAT-TAGA-TG-TTAT
1 ATGGATTGATTATTTTAAATAATTTATTAGTATGAATTGATTATTTTAAAATATAGATTGATTAT
1698082 TA-TGTAGTTGT
66 TATTGTAGTTGT
*
1698093 ATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTATTTTAAAATATGGATTGATTA
1 ATGGATTGA-TTATTTTAAATAATTTATTAGTATGAATTGATTATTTTAAAATATAGATTGATTA
1698158 TTATTGTAGTTGT
65 TTATTGTAGTTGT
* *
1698171 ATGGATTGATTA-TTTAAAT-A---ATTAGTATGTATTGA-TA-TTTAAAATATGGATTGATTTA
1 ATGGATTGATTATTTTAAATAATTTATTAGTATGAATTGATTATTTTAAAATATAGATTGA-TTA
*
1698229 TTTTAAATAATTTA-TTAGT
65 --TT--AT--TGTAGTT-GT
* *
1698248 ATGCATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAA
1 ATGGATTGA-TTATTTTAAATAATTTATTAGTATGAATTGA-TTATTTTAAA
1698300 TAATTTATTA
Statistics
Matches: 178, Mismatches: 5, Indels: 33
0.82 0.02 0.15
Matches are distributed among these distances:
70 17 0.10
71 14 0.08
72 14 0.08
73 24 0.13
74 18 0.10
75 6 0.03
76 11 0.06
77 22 0.12
78 21 0.12
79 7 0.04
80 1 0.01
83 15 0.08
85 2 0.01
86 6 0.03
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (77 bp):
ATGGATTGATTATTTTAAATAATTTATTAGTATGAATTGATTATTTTAAAATATAGATTGATTAT
TATTGTAGTTGT
Found at i:1698256 original size:32 final size:32
Alignment explanation
Indices: 1698215--1698560 Score: 366
Period size: 32 Copynumber: 10.7 Consensus size: 32
1698205 ATATTTAAAA
1698215 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
1698247 TATGCATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
1698279 TATGTATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
1698311 TATGGATTGA-TTATTTTAAAATATGGATTGATT--
1 TATGGATTGATTTATTTT-AAATA---ATTTATTAG
* * * * * *
1698344 TAT-TATTGTAGTTATATGAATTGATTTATT--
1 TATGGATTG-ATTTATTTTAAATAATTTATTAG
* * * * * *
1698374 T-T-AAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATT--T-TA-AATAATTTA--TT--AG
1698412 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
1698444 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
1698476 TATAGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
1698508 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
1698540 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1698561 ATATATATTG
Statistics
Matches: 271, Mismatches: 25, Indels: 36
0.82 0.08 0.11
Matches are distributed among these distances:
28 5 0.02
29 3 0.01
30 8 0.03
31 8 0.03
32 204 0.75
33 7 0.03
34 9 0.03
35 6 0.02
36 7 0.03
37 2 0.01
38 2 0.01
39 1 0.00
40 9 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:1698423 original size:54 final size:54
Alignment explanation
Indices: 1698247--1698673 Score: 338
Period size: 54 Copynumber: 7.6 Consensus size: 54
1698237 AATTTATTAG
* *
1698247 TATGCATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * * **
1698300 TA---ATTTATTAGTATGGATTGATTATTTTA-AAATATGGATTGATTTATTATTGTAGTTA
1 TATGGATTGATT--TAT--TTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAA
* *
1698358 TATGAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1698412 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA
1698468 TTTATTAGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAAT
1 --TA-T-G----GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT--A-AA-
1698533 TTA
54 --A
* * ***
1698536 TTTGTATGGATTGATTTATTTT-AA-AA--TA-TA-TATTGATTTA-TTATTTTTAGTTG
1 ----TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTTA-AAA
1698589 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1698643 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
1698674 TTGTAGTTGT
Statistics
Matches: 302, Mismatches: 34, Indels: 75
0.73 0.08 0.18
Matches are distributed among these distances:
49 18 0.06
50 8 0.03
51 2 0.01
52 3 0.01
53 18 0.06
54 92 0.30
55 19 0.06
56 9 0.03
57 13 0.04
58 31 0.10
59 6 0.02
60 3 0.01
61 6 0.02
62 2 0.01
63 2 0.01
64 60 0.20
65 3 0.01
66 1 0.00
68 2 0.01
69 1 0.00
70 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:1698464 original size:197 final size:193
Alignment explanation
Indices: 1697977--1698528 Score: 792
Period size: 197 Copynumber: 2.8 Consensus size: 193
1697967 TTAAAAATAG
1697977 ATTGATT-TTTTAAATAATTATTAGTATGGATTGATTTATTTT-AAA-ATGGATTGA--TATTTT
1 ATTGATTATTTTAAATAATTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATTTT
1698037 AAATAATTTATTAGTA-GGATTGA-TTATTTTAAAATTAGATGTTATTATGTAGTTGTATGGATT
65 AAATAATTTATTAGTATGGATTGATTTATTTT-AAA-TA-AT-TTATTA-GTA--TG--T--ATT
*
1698100 GATTTATTTTAAATAATTTATTAGTATGAATTGATTATTTTAAAATATGGATTGATTATTATTGT
119 GATTTATTTTAAATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGATTATTATTGT
* *
1698165 AGTTGTATGG
184 AGTTATATGA
1698175 ATTGATTA-TTTAAAT-A--ATTAGTATGTATTGA--TA-TTTAAAATATGGATTGATTTATTTT
1 ATTGATTATTTTAAATAATTATTAGTATG-ATTGATTTATTTTAAAATATGGATTGATTTATTTT
*
1698233 AAATAATTTATTAGTATGCATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTA
65 AAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTA
1698298 AATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGATTTATTATTGTAGTTATATGA
130 AATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGA-TTATTATTGTAGTTATATGA
1698363 ATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTGA-TTATTTTAAATAA-TTATTAGTAT-GATTGATTTATTTTAAAATATGGATTGATTTATT
1698428 TTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATT
63 TTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTAT-GTATTGATTTATT
1698492 TTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
127 TTAAATAATTTATTAGTATGGATTGA-TTATTTTAAA
1698529 TAATTTATTT
Statistics
Matches: 328, Mismatches: 5, Indels: 42
0.87 0.01 0.11
Matches are distributed among these distances:
187 57 0.17
188 23 0.07
189 4 0.01
190 7 0.02
191 3 0.01
192 3 0.01
193 8 0.02
194 29 0.09
195 16 0.05
196 26 0.08
197 120 0.37
198 32 0.10
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (193 bp):
ATTGATTATTTTAAATAATTATTAGTATGATTGATTTATTTTAAAATATGGATTGATTTATTTTA
AATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTATTTTAAAATATGGATTGATTATTATTGTAGTTATATGA
Found at i:1698601 original size:81 final size:81
Alignment explanation
Indices: 1698507--1698658 Score: 277
Period size: 81 Copynumber: 1.9 Consensus size: 81
1698497 TAATTTATTA
* *
1698507 GTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATATATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
1698572 TTTATTATTTTTAGTT
66 TTTATTATTTTTAGTT
*
1698588 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
1698653 TTTATT
66 TTTATT
1698659 TTAAATAATT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (81 bp):
GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
TTTATTATTTTTAGTT
Found at i:1698646 original size:22 final size:22
Alignment explanation
Indices: 1698621--1698663 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1698611 AATTTATTAG
1698621 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1698643 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1698664 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1699237 original size:21 final size:21
Alignment explanation
Indices: 1699137--1699243 Score: 64
Period size: 21 Copynumber: 5.1 Consensus size: 21
1699127 AAAATAGCAT
1699137 ATTTTATAATAATATGTTT-ATA
1 ATTTTATAAT-ATAT-TTTAATA
*
1699159 ATTATT-TATTATATTTTAA-A
1 ATT-TTATAATATATTTTAATA
* * * *
1699179 CTATTAAAATAACATTTGATAATA
1 ATTTTATAAT-ATATTT--TAATA
*
1699203 ATTTT-T-ATA-CTTTTAATA
1 ATTTTATAATATATTTTAATA
1699221 ATTTTATAATATATTTTAATA
1 ATTTTATAATATATTTTAATA
1699242 AT
1 AT
1699244 ATAAAATATA
Statistics
Matches: 64, Mismatches: 11, Indels: 21
0.67 0.11 0.22
Matches are distributed among these distances:
18 10 0.16
19 3 0.05
20 13 0.20
21 21 0.33
22 8 0.12
23 5 0.08
24 4 0.06
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTATAATATATTTTAATA
Found at i:1699253 original size:20 final size:22
Alignment explanation
Indices: 1699208--1699253 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1699198 TAATAATTTT
* *
1699208 TATACTTTTAATAATTTTATAA
1 TATACTTTTAATAATTATAAAA
1699230 TATA-TTTTAATAA-TATAAAA
1 TATACTTTTAATAATTATAAAA
1699250 TATA
1 TATA
1699254 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 9 0.41
22 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TATACTTTTAATAATTATAAAA
Found at i:1699540 original size:2 final size:2
Alignment explanation
Indices: 1699533--1699559 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1699523 TTCAATATTC
1699533 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1699560 TGCGATCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1700668 original size:234 final size:234
Alignment explanation
Indices: 1700259--1700726 Score: 920
Period size: 234 Copynumber: 2.0 Consensus size: 234
1700249 CTGTGAAAAT
1700259 AACACGAACCCTTGTAAGAAGAGAGGGTTTGATATTGATCTGAACTTAACATTAGGTTCTTTTCT
1 AACACGAACCCTTGTAAGAAGAGAGGGTTTGATATTGATCTGAACTTAACATTAGGTTCTTTTCT
1700324 CGACGGCGGTGATGAGAGTGAAGAAAAATCTGACTGTGTAGCTGAAAACAGCTTCATTGAAGACA
66 CGACGGCGGTGATGAGAGTGAAGAAAAATCTGACTGTGTAGCTGAAAACAGCTTCATTGAAGACA
1700389 AAACAGCCACGGCCACGGCGACGGATGCTTCTTCTGATGTCACAAATGTTCAAAAAAAGCAAAGA
131 AAACAGCCACGGCCACGGCGACGGATGCTTCTTCTGATGTCACAAATGTTC-AAAAAAGCAAAGA
1700454 GCTCAAGAGCAGCAGCCACGGTG-AGTTAAAACGGCGACG
195 GCTCAAGAGCAGCAGCCACGGTGAAGTTAAAACGGCGACG
1700493 AACACGAACCCTTGTAAGAAGAGAGGGTTTGATATTGATCTGAACTTAACATTAGGTTCTTTTCT
1 AACACGAACCCTTGTAAGAAGAGAGGGTTTGATATTGATCTGAACTTAACATTAGGTTCTTTTCT
1700558 CGACGGCGGTGATGAGAGTGAAGAAAAATCTGACTGTGTAGCTGAAAACAGCTTCATTGAAGACA
66 CGACGGCGGTGATGAGAGTGAAGAAAAATCTGACTGTGTAGCTGAAAACAGCTTCATTGAAGACA
1700623 AAACAGCCACGGCCACGGCGACGGATGCTTCTTCTGATGTCACAAATGTTCAAAAAAGCAAAGAG
131 AAACAGCCACGGCCACGGCGACGGATGCTTCTTCTGATGTCACAAATGTTCAAAAAAGCAAAGAG
1700688 CTCAAGAGCAGCAGCCACGGTGAAGTTAAAACGGCGACG
196 CTCAAGAGCAGCAGCCACGGTGAAGTTAAAACGGCGACG
1700727 TCGGAGACGG
Statistics
Matches: 233, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
233 36 0.15
234 197 0.85
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (234 bp):
AACACGAACCCTTGTAAGAAGAGAGGGTTTGATATTGATCTGAACTTAACATTAGGTTCTTTTCT
CGACGGCGGTGATGAGAGTGAAGAAAAATCTGACTGTGTAGCTGAAAACAGCTTCATTGAAGACA
AAACAGCCACGGCCACGGCGACGGATGCTTCTTCTGATGTCACAAATGTTCAAAAAAGCAAAGAG
CTCAAGAGCAGCAGCCACGGTGAAGTTAAAACGGCGACG
Found at i:1701877 original size:12 final size:12
Alignment explanation
Indices: 1701857--1701886 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1701847 GTTATAGTTA
1701857 TATTATAAAAAT
1 TATTATAAAAAT
*
1701869 TATTTTAAAAAT
1 TATTATAAAAAT
1701881 TATTAT
1 TATTAT
1701887 TTCATATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTATAAAAAT
Found at i:1703824 original size:18 final size:18
Alignment explanation
Indices: 1703801--1703840 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1703791 AGAAACCTCA
*
1703801 TCAGAATCATCTTCATCC
1 TCAGAATCATCCTCATCC
* *
1703819 TCAGAATCCTCCTCCTCC
1 TCAGAATCATCCTCATCC
1703837 TCAG
1 TCAG
1703841 TTTTCTTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.40, G:0.07, T:0.30
Consensus pattern (18 bp):
TCAGAATCATCCTCATCC
Found at i:1705922 original size:3 final size:3
Alignment explanation
Indices: 1705914--1705944 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
1705904 TATATTATAC
1705914 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
1705945 ATACTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1707095 original size:2 final size:2
Alignment explanation
Indices: 1707088--1707127 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1707078 TTTAGTAGTA
1707088 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
1707128 TTTTCTTGTA
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:1707249 original size:25 final size:24
Alignment explanation
Indices: 1707171--1707249 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
1707161 TTTTTTTTAT
* *
1707171 TTTTATCTATATATTTTATTATTA
1 TTTTATTTATATTTTTTATTATTA
* *
1707195 TTATTATTTATATTTTTT-TCTCTTCT
1 TT-TTATTTATATTTTTTAT-TATT-A
*
1707221 TTTTATTTATGTTTTTTATTATTAA
1 TTTTATTTATATTTTTTATTATT-A
1707246 TTTT
1 TTTT
1707250 CTTCACGTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
24 3 0.07
25 37 0.86
26 3 0.07
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (24 bp):
TTTTATTTATATTTTTTATTATTA
Found at i:1715319 original size:196 final size:194
Alignment explanation
Indices: 1714967--1715413 Score: 614
Period size: 196 Copynumber: 2.3 Consensus size: 194
1714957 AAAATATTAT
*
1714967 TTTATTCAATAAAAATAGTGATTTAATTGGGAAAAAAATAATATATAGAGGAATATTATTGTAAT
1 TTTATTCAATAAAAA-AGTGATTTAATT-GGAAAAAAATAATATATAGAGGAATATTATTGTAAA
* * ** *
1715032 TATTCTTAAATATATAAGGTAAAATTAAATATTTTTTGGGGTCGGATCAGGTTTGATATTTTTCA
64 TATTCTTAAATATATAAGGTAAAAATAAATATTTTTTGGGGTCGAATCAGGTCGGATATTTGTCA
* *
1715097 ACATAAACCTGAATTATAACCAACCCGAACATCACATTTAAAAAATCAATCCGACTTAACACGA-
129 ACATAAACATGAACTATAACCAACCCGAACATCACATTTAAAAAATCAATCCGACTTAAC-CGAT
1715161 CTA
193 C-A
*
1715164 TTTATTCAATAAAAACAATGATTTAATTGGAAAAAAATAATATATAGAGGAATATTATTGTAAAT
1 TTTATTCAATAAAAA-AGTGATTTAATTGGAAAAAAATAATATATAGAGGAATATTATTGTAAAT
* ** * *
1715229 ATTTTTAAATATATAAGGTAAAAATATGTATTTTTTTGGGTTGAATCAGGTCGGATATTTGTCAA
65 ATTCTTAAATATATAAGGTAAAAATAAATATTTTTTGGGGTCGAATCAGGTCGGATATTTGTCAA
* ** * *
1715294 TATAAACATGAACTATATTCAACCCGAACATCATATTTAAAAAATCGATCCGACTTAACCGATCA
130 CATAAACATGAACTATAACCAACCCGAACATCACATTTAAAAAATCAATCCGACTTAACCGATCA
* * * *
1715359 TTTATTAAATAAAAAAGTGATTTAATTAG-AAAAAAT-ATA-CTAGAGGAGTATTATT
1 TTTATTCAATAAAAAAGTGATTTAATTGGAAAAAAATAATATATAGAGGAATATTATT
1715414 ATAATTTTGG
Statistics
Matches: 224, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
191 14 0.06
192 3 0.01
193 7 0.03
194 12 0.05
195 18 0.08
196 144 0.64
197 26 0.12
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (194 bp):
TTTATTCAATAAAAAAGTGATTTAATTGGAAAAAAATAATATATAGAGGAATATTATTGTAAATA
TTCTTAAATATATAAGGTAAAAATAAATATTTTTTGGGGTCGAATCAGGTCGGATATTTGTCAAC
ATAAACATGAACTATAACCAACCCGAACATCACATTTAAAAAATCAATCCGACTTAACCGATCA
Found at i:1715530 original size:156 final size:159
Alignment explanation
Indices: 1715262--1715579 Score: 606
Period size: 156 Copynumber: 2.0 Consensus size: 159
1715252 ATATGTATTT
1715262 TTTTGGGTTGAATCAGGTCGGATATTTGTCAATATAAACATGAACTATATTCAACCCGAACATCA
1 TTTTGGGTTGAATCAGGTCGGATATTTGTCAATATAAACATGAACTATATTCAACCCGAACATCA
1715327 TATTTAAAAAATCGATCCGACTTAACCGATCATTTATTAAATAAAAA-AGTGATTTAATTAGAAA
66 TATTTAAAAAATCGATCCGACTTAACCGATCATTTATTAAATAAAAACAGTGATTTAATTAGAAA
1715391 AAAT-ATAC-TAGAGGAGTATTATTATAA
131 AAATAATACATAGAGGAGTATTATTATAA
1715418 TTTTGGGTTGAATCAGGTCGGATATTTGTCAATATAAACATGAACTATATTCAACCCGAACATCA
1 TTTTGGGTTGAATCAGGTCGGATATTTGTCAATATAAACATGAACTATATTCAACCCGAACATCA
1715483 TATTTAAAAAATCGATCCGACTTAACCCGATCATTTATTAAATAAAAACAGTGATTTAATTAGAA
66 TATTTAAAAAATCGATCCGACTTAA-CCGATCATTTATTAAATAAAAACAGTGATTTAATTAGAA
1715548 AAAATAATACATAGAGGAGTATTATTATAA
130 AAAATAATACATAGAGGAGTATTATTATAA
1715578 TT
1 TT
1715580 ATTTTTAAAT
Statistics
Matches: 158, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
156 90 0.57
157 22 0.14
158 21 0.13
159 4 0.03
160 21 0.13
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (159 bp):
TTTTGGGTTGAATCAGGTCGGATATTTGTCAATATAAACATGAACTATATTCAACCCGAACATCA
TATTTAAAAAATCGATCCGACTTAACCGATCATTTATTAAATAAAAACAGTGATTTAATTAGAAA
AAATAATACATAGAGGAGTATTATTATAA
Found at i:1716573 original size:19 final size:19
Alignment explanation
Indices: 1716545--1716597 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1716535 ACCAACAAAA
*
1716545 TCGCAATGCGATCTCTAAT
1 TCGCATTGCGATCTCTAAT
1716564 TCGCATTGCGATCTCTAAT
1 TCGCATTGCGATCTCTAAT
1716583 TCGCATTGCGATCTC
1 TCGCATTGCGATCTC
1716598 CACTATCGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (19 bp):
TCGCATTGCGATCTCTAAT
Found at i:1716679 original size:20 final size:20
Alignment explanation
Indices: 1716610--1716681 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1716600 CTATCGCAAA
1716610 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* * ** *
1716630 TTCGCATTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
* *
1716651 ATAGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
1716671 TTCGCGTTGCG
1 TTCGCGTTGCG
1716682 GTAGTCTACA
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 24 0.65
21 13 0.35
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:1716701 original size:22 final size:22
Alignment explanation
Indices: 1716675--1716727 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1716665 TTCCATTTCG
* *
1716675 CGTTGCGGTAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAATTGT
*
1716697 TGTTGCGATAGTCTACAATTGT
1 CGTTGCGATAGTCTACAATTGT
1716719 CGTTGCGAT
1 CGTTGCGAT
1716728 TTTCCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAATTGT
Found at i:1716849 original size:6 final size:6
Alignment explanation
Indices: 1716828--1716866 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1716818 GACACGTATT
**
1716828 ACCACG ACCATT ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1716867 CGAGACGGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.49, G:0.13, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:1720254 original size:28 final size:27
Alignment explanation
Indices: 1720214--1720275 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
1720204 ACTATTTTTT
* ** * *
1720214 TAAACAAAAAAATGGAGTTTGATTAAC
1 TAAAAAAAAAAATACAGTTTAAATAAC
1720241 TAAAAAAAGAAAATACAGTTTAAATAAC
1 TAAAAAAA-AAAATACAGTTTAAATAAC
1720269 TAAAAAA
1 TAAAAAA
1720276 TACAAATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.23
Consensus pattern (27 bp):
TAAAAAAAAAAATACAGTTTAAATAAC
Found at i:1720278 original size:22 final size:22
Alignment explanation
Indices: 1720250--1720293 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1720240 CTAAAAAAAG
*
1720250 AAAATAC-AGTTTAAATAACTAA
1 AAAATACAAATTTAAA-AACTAA
1720272 AAAATACAAATTTAAAAACTAA
1 AAAATACAAATTTAAAAACTAA
1720294 TGATGCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATACAAATTTAAAAACTAA
Found at i:1720710 original size:20 final size:21
Alignment explanation
Indices: 1720685--1720724 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1720675 ATGCAAAATA
1720685 AGTATCGATACCAT-AGGCTT
1 AGTATCGATACCATCAGGCTT
*
1720705 AGTATCGATATCATCAGGCT
1 AGTATCGATACCATCAGGCT
1720725 CAACAGCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
AGTATCGATACCATCAGGCTT
Found at i:1722457 original size:20 final size:21
Alignment explanation
Indices: 1722421--1722472 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1722411 GTTGATAGTG
* *
1722421 GTATCGATA-CTGTAAGGCTA
1 GTATCGATACCCGTAAGGATA
*
1722441 GTATCGATACCCG-AAGGATG
1 GTATCGATACCCGTAAGGATA
1722461 GTATCGATACCC
1 GTATCGATACCC
1722473 TTAAAACATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (21 bp):
GTATCGATACCCGTAAGGATA
Found at i:1722583 original size:54 final size:54
Alignment explanation
Indices: 1722455--1722583 Score: 159
Period size: 54 Copynumber: 2.4 Consensus size: 54
1722445 CGATACCCGA
* * * *
1722455 AGGATGGTATCGATACCCTTAAAACATCGAATGCCAGATTGGTATCGGTACCTTG
1 AGGA-GGTATCGATACCCTTGAAACATCAAATGCCAGATTGATATCGGTACCATG
* ** **
1722510 AGGAGGTATCAATACCCTTGAAACATCAAATGTTATTTTGATATCGGTACCATG
1 AGGAGGTATCGATACCCTTGAAACATCAAATGCCAGATTGATATCGGTACCATG
*
1722564 AGGAGGTATTGATACCCTTG
1 AGGAGGTATCGATACCCTTG
1722584 TAGGGTAGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
54 59 0.94
55 4 0.06
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (54 bp):
AGGAGGTATCGATACCCTTGAAACATCAAATGCCAGATTGATATCGGTACCATG
Found at i:1723181 original size:21 final size:21
Alignment explanation
Indices: 1723155--1723211 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1723145 TCGAGGGTCT
1723155 TATGTGGTCATTCGGGACAAA
1 TATGTGGTCATTCGGGACAAA
*
1723176 TATGTGGTC-TTCCGGGATAAA
1 TATGTGGTCATT-CGGGACAAA
1723197 TATGTGG-CACTTCGG
1 TATGTGGTCA-TTCGG
1723212 TGCAAATTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 27 0.84
22 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACAAA
Found at i:1725154 original size:31 final size:31
Alignment explanation
Indices: 1725113--1725173 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1725103 AAAACATAAG
*
1725113 ATATGATCACTTTCAG-TTTTATTTAATTAAT
1 ATATGATCAC-TTAAGTTTTTATTTAATTAAT
*
1725144 ATATGGTCACTTAAGTTTTTATTTAATTAA
1 ATATGATCACTTAAGTTTTTATTTAATTAA
1725174 GCTAGAGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (31 bp):
ATATGATCACTTAAGTTTTTATTTAATTAAT
Found at i:1725326 original size:20 final size:21
Alignment explanation
Indices: 1725301--1725349 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1725291 TTTAAATAAA
*
1725301 TTTTAACAT-AAAAT-ATATAT
1 TTTTAA-ATAAAAATAAAATAT
1725321 TTTTAAATAAAAATAAAATAT
1 TTTTAAATAAAAATAAAATAT
1725342 TTTTAAAT
1 TTTTAAAT
1725350 TAAGTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 11 0.42
21 13 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTAAATAAAAATAAAATAT
Found at i:1725366 original size:27 final size:27
Alignment explanation
Indices: 1725332--1725419 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 27
1725322 TTTAAATAAA
1725332 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
1725359 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATTTTTAAATTAAGTTAAT
*
1725384 -ATAAAAATATTTTTAAGTTAA--T-AT
1 AAT-AAAATATTTTTAAATTAAGTTAAT
1725408 ATATAAAATATT
1 A-ATAAAATATT
1725420 AAGAATTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
24 4 0.08
25 28 0.53
26 5 0.09
27 16 0.30
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
AATAAAATATTTTTAAATTAAGTTAAT
Found at i:1725422 original size:22 final size:22
Alignment explanation
Indices: 1725348--1725408 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
1725338 ATATTTTTAA
1725348 ATTAAGTTAATAATAAAATATATTT
1 ATTAAGTTAAT-ATAAAA-ATA-TT
*
1725373 AATAAGTTAATATAAAAATATT
1 ATTAAGTTAATATAAAAATATT
*
1725395 TTTAAGTTAATATA
1 ATTAAGTTAATATA
1725409 TATAAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.42
23 3 0.09
24 6 0.18
25 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
ATTAAGTTAATATAAAAATATT
Found at i:1734815 original size:22 final size:22
Alignment explanation
Indices: 1734798--1734864 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
1734788 CTCGTATAAA
1734798 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1734820 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1734842 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1734864 T
1 T
1734865 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1735134 original size:30 final size:29
Alignment explanation
Indices: 1735067--1735144 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
1735057 CCGTAGTTCA
* * *
1735067 TATCACGTAGACATAGTATTTCCATAACTT
1 TATCACATAGGCATA-TATTTACATAACTT
* *
1735097 TAACACATAGGCATATCATTTACATACCTT
1 TATCACATAGGCATAT-ATTTACATAACTT
1735127 TATCACATAGTGCATATA
1 TATCACATAG-GCATATA
1735145 ACTTTTTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (29 bp):
TATCACATAGGCATATATTTACATAACTT
Found at i:1735200 original size:29 final size:29
Alignment explanation
Indices: 1735158--1735229 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1735148 TTTTCTGCAT
* **
1735158 ATTCATGTCATGTAATACGTATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
1735187 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
1735216 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1735230 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):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1735675 original size:67 final size:67
Alignment explanation
Indices: 1735530--1735680 Score: 189
Period size: 68 Copynumber: 2.2 Consensus size: 67
1735520 TCTTTTTCTG
* * *
1735530 GGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTAAAGCATTCTGGAATTTCTTATACGAT
1 GGGGTATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTAAAGCATTCTGGAAATTCTTATACGAT
*
1735595 GAG
65 GAA
*** *
1735598 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATT-T-CGT
1 GGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTAAAGCATTCTGGAAATTC-TTATACGA
1735661 TGAA
64 TGAA
1735665 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
1735681 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
67 29 0.40
68 42 0.58
69 2 0.03
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTAAAGCATTCTGGAAATTCTTATACGATG
AA
Found at i:1735690 original size:21 final size:21
Alignment explanation
Indices: 1735660--1735702 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1735650 ATTCATTTCG
* *
1735660 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1735681 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1735702 T
1 T
1735703 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1741761 original size:22 final size:22
Alignment explanation
Indices: 1741744--1741810 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
1741734 CTCGTATAAA
1741744 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1741766 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1741788 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1741810 T
1 T
1741811 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1742080 original size:30 final size:29
Alignment explanation
Indices: 1742013--1742090 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
1742003 CCGTAGTTCA
* * *
1742013 TATCACGTAGACATAGTATTTCCATAACTT
1 TATCACATAGGCATA-TATTTACATAACTT
* *
1742043 TAACACATAGGCATATCATTTACATACCTT
1 TATCACATAGGCATAT-ATTTACATAACTT
1742073 TATCACATAGTGCATATA
1 TATCACATAG-GCATATA
1742091 ACTTTTTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (29 bp):
TATCACATAGGCATATATTTACATAACTT
Found at i:1742146 original size:29 final size:29
Alignment explanation
Indices: 1742104--1742175 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1742094 TTTTCTGCAT
* **
1742104 ATTCATGTCATGTAATACGTATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
1742133 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
1742162 ATTCATGTCATGTA
1 ATTCATGTCATGTA
1742176 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):
ATTCATGTCATGTAATACATATAATACAA
Found at i:1742624 original size:67 final size:67
Alignment explanation
Indices: 1742479--1742629 Score: 189
Period size: 68 Copynumber: 2.2 Consensus size: 67
1742469 TTTTCTCATG
* * *
1742479 GGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTAAAGCATTCTGGAATTTCTTATACGAT
1 GGGGTATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTAAAGCATTCTGGAAATTCTTATACGAT
*
1742544 GAG
65 GAA
*** *
1742547 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATT-T-CGT
1 GGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTAAAGCATTCTGGAAATTC-TTATACGA
1742610 TGAA
64 TGAA
1742614 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
1742630 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
67 29 0.40
68 42 0.58
69 2 0.03
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTAAAGCATTCTGGAAATTCTTATACGATG
AA
Found at i:1742639 original size:21 final size:21
Alignment explanation
Indices: 1742609--1742651 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1742599 ATTCATTTCG
* *
1742609 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1742630 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1742651 T
1 T
1742652 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1745095 original size:11 final size:11
Alignment explanation
Indices: 1745079--1745109 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1745069 AAATGATCTT
1745079 GAGTTGTCCCG
1 GAGTTGTCCCG
1745090 GAGTTGTCCCG
1 GAGTTGTCCCG
1745101 GAGTTGTCC
1 GAGTTGTCC
1745110 TAGTCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.10, C:0.26, G:0.35, T:0.29
Consensus pattern (11 bp):
GAGTTGTCCCG
Found at i:1746935 original size:12 final size:12
Alignment explanation
Indices: 1746920--1746965 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1746910 CGGTTTTTTT
*
1746920 ACCGGATAAAAA
1 ACCGGTTAAAAA
1746932 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1746947 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1746959 ACCGGTT
1 ACCGGTT
1746966 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1746947 original size:15 final size:13
Alignment explanation
Indices: 1746926--1746966 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1746916 TTTTACCGGA
1746926 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1746939 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1746953 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1746966 T
1 T
1746967 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1749281 original size:21 final size:21
Alignment explanation
Indices: 1749257--1749296 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1749247 TTTATTTTAT
1749257 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1749278 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1749297 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1749344 original size:33 final size:33
Alignment explanation
Indices: 1749291--1749389 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1749281 TTTGTTTCAA
1749291 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1749323 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1749356 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1749389 T
1 T
1749390 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1749418 original size:13 final size:13
Alignment explanation
Indices: 1749375--1749429 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1749365 TTGGAAGTAT
1749375 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1749388 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1749402 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1749415 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1749428 TT
1 TT
1749430 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1749850 original size:15 final size:15
Alignment explanation
Indices: 1749825--1749880 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1749815 ATCTGGAATA
*
1749825 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1749840 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1749855 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1749872 TTAAAACCG
1 TTAAAACCG
1749881 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1749889 original size:21 final size:18
Alignment explanation
Indices: 1749844--1749877 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1749834 GTTTTTTTAT
1749844 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1749861 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1749878 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1749997 original size:15 final size:17
Alignment explanation
Indices: 1749971--1750002 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1749961 TTCTATGGGA
1749971 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1749987 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1750003 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1757998 original size:13 final size:13
Alignment explanation
Indices: 1757976--1758005 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1757966 TTTAAATATT
*
1757976 ATAAATATATTAA
1 ATAAAAATATTAA
1757989 ATAAAAATATTAA
1 ATAAAAATATTAA
1758002 ATAA
1 ATAA
1758006 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAAAAATATTAA
Done.