Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 5 of 135
Found at i:1741945 original size:101 final size:101
Alignment explanation
Indices: 1741816--1742043 Score: 422
Period size: 101 Copynumber: 2.3 Consensus size: 101
1741806 TGAATTGACG
1741816 GATAAGACCATAACTAGGTTATGGCATTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTAGGTTATGGCATTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
*
1741881 ATATGTAAGACCATAGTTGGGCTATTG-CATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTA-TGACATTCTGAT
1741917 GATAAGACCATAACTAGGTTATGGCATTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTAGGTTATGGCATTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
*
1741982 ATATGTAAGACCATAGCTGGGCTATGACATTTTGAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
1742018 GATAAGACCATAACTAGGTTATGGCA
1 GATAAGACCATAACTAGGTTATGGCA
1742044 CTACGAATGT
Statistics
Matches: 124, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
100 2 0.02
101 122 0.98
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (101 bp):
GATAAGACCATAACTAGGTTATGGCATTATGAACATAAGACCATGGTTGGACCATGGCAGTGTTT
ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
Found at i:1742028 original size:33 final size:33
Alignment explanation
Indices: 1741816--1742043 Score: 127
Period size: 33 Copynumber: 6.8 Consensus size: 33
1741806 TGAATTGACG
* * * * *
1741816 GATAAGACCATAACTAGGTTATGGCATTATGAA
1 GATAAGACCATAGCTGGGCTATGGCATTTTGAT
* * * * * *
1741849 CATAAGACCATGGTTGGACCATGGCAGTGTTTATAT
1 GATAAGACCATAGCTGGGCTATGGCA-T-TTT-GAT
* * *
1741885 G-TAAGACCATAGTTGGGCTATTGCATTCTGAT
1 GATAAGACCATAGCTGGGCTATGGCATTTTGAT
* * * * *
1741917 GATAAGACCATAACTAGGTTATGGCATTATGAA
1 GATAAGACCATAGCTGGGCTATGGCATTTTGAT
* * * * * *
1741950 CATAAGACCATGGTTGGACCATGGCAGTGTTTATAT
1 GATAAGACCATAGCTGGGCTATGGCA-T-TTT-GAT
*
1741986 G-TAAGACCATAGCTGGGCTATGACATTTTGAT
1 GATAAGACCATAGCTGGGCTATGGCATTTTGAT
* * *
1742018 GATAAGACCATAACTAGGTTATGGCA
1 GATAAGACCATAGCTGGGCTATGGCA
1742044 CTACGAATGT
Statistics
Matches: 140, Mismatches: 47, Indels: 16
0.69 0.23 0.08
Matches are distributed among these distances:
32 6 0.04
33 85 0.61
34 4 0.03
35 43 0.31
36 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (33 bp):
GATAAGACCATAGCTGGGCTATGGCATTTTGAT
Found at i:1742356 original size:21 final size:21
Alignment explanation
Indices: 1742332--1742374 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1742322 TATTTTAAGG
1742332 GTAGAATAATCTAGAAACTAA
1 GTAGAATAATCTAGAAACTAA
*
1742353 GTAGAATAATTTAGAAACTAA
1 GTAGAATAATCTAGAAACTAA
1742374 G
1 G
1742375 GAAAATGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (21 bp):
GTAGAATAATCTAGAAACTAA
Found at i:1744627 original size:29 final size:31
Alignment explanation
Indices: 1744593--1744652 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
1744583 TAACCAGTAT
*
1744593 ATAAAAATTAATAAATAAATT-A-TAAGGTG
1 ATAAAAATTAATAAAAAAATTGATTAAGGTG
*
1744622 ATAAAAGTTAATAAAAAAATTGATTAAGGTG
1 ATAAAAATTAATAAAAAAATTGATTAAGGTG
1744653 GGCAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
30 1 0.04
31 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (31 bp):
ATAAAAATTAATAAAAAAATTGATTAAGGTG
Found at i:1746490 original size:45 final size:45
Alignment explanation
Indices: 1746440--1746591 Score: 175
Period size: 45 Copynumber: 3.4 Consensus size: 45
1746430 GTAACGGTAG
* * *
1746440 CAGTAATAGTAACAGTATT-GAACACACAAAGTGCTGAATTTGTAA
1 CAGTAACAGTAACAGTATTCG-ACACACAAAGTGCCGAATTCGTAA
*
1746485 CAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAA-TCGATAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTCG-TAA
** *
1746530 CAGTAACAACAACAGTATTCGACACACAGAGTGCCGAA-TCGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTC-GTAA
* *
1746575 CAGTAACAATAATAGTA
1 CAGTAACAGTAACAGTA
1746592 GTCGGCATAT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
44 2 0.02
45 90 0.96
46 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTCGTAA
Found at i:1760493 original size:77 final size:81
Alignment explanation
Indices: 1760336--1760493 Score: 198
Period size: 78 Copynumber: 2.0 Consensus size: 81
1760326 AATTGAACTG
** *
1760336 GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACGGATGTGAATGAATTATTTAT
1 GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACAAATGTGAATGAATGATTTAT
1760401 AAGACAAGTTCAATCT
66 AAGACAAGTTCAATCT
* * * * * *
1760417 GATAGAGTAACTG-AGGG-TTGTTCTGC-AAAAAGCATTGTCACAAATGTGAATGAATGA-TTGT
1 GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACAAATGTGAATGAATGATTTAT
*
1760478 AAGCCAAGTTCAATCT
66 AAGACAAGTTCAATCT
1760494 TCAGTAAAGT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 18 0.27
78 25 0.37
79 8 0.12
80 4 0.06
81 12 0.18
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.27
Consensus pattern (81 bp):
GATAGAGTAAATGAAGGGCTTGCTCTGCAAAAAAACACTGACACAAATGTGAATGAATGATTTAT
AAGACAAGTTCAATCT
Found at i:1778898 original size:15 final size:15
Alignment explanation
Indices: 1778878--1778910 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1778868 AATATGATAT
1778878 TTAATTAT-TAAAATA
1 TTAATTATGTAAAA-A
1778893 TTAATTATGTAAAAA
1 TTAATTATGTAAAAA
1778908 TTA
1 TTA
1778911 CAACTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TTAATTATGTAAAAA
Found at i:1778946 original size:27 final size:28
Alignment explanation
Indices: 1778895--1778950 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1778885 TTAAAATATT
*
1778895 AATTATGTAAAAATTACAACTAATATAA
1 AATTATGTAAAAATTACAACAAATATAA
* *
1778923 AATTATTTAAAATTTAC-ACAAATATAA
1 AATTATGTAAAAATTACAACAAATATAA
1778950 A
1 A
1778951 TAAATCCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (28 bp):
AATTATGTAAAAATTACAACAAATATAA
Found at i:1784099 original size:198 final size:199
Alignment explanation
Indices: 1783761--1784160 Score: 793
Period size: 198 Copynumber: 2.0 Consensus size: 199
1783751 TTTTCTAATG
1783761 ATTTTTTAAAAGTTATTTTATGCCATAATATTTTTCTTTTTTTGTTCTTCAAATCGTGTTTGAGA
1 ATTTTTTAAAAGTTATTTTATGCCATAATATTTTTCTTTTTTTGTTCTTCAAATCGTGTTTGAGA
1783826 TTTTTGGGAATGTTTAGGTAAAATAATATTTAACGAGCGAAAAATAAATAGGTTTCGAATATAGA
66 TTTTTGGGAATGTTTAGGTAAAATAATATTTAACGAGCGAAAAATAAATAGGTTTCGAATATAGA
1783891 TTGAGCTCGTATTTTAATATTTGAAATTTAAATTCTATCTAATTTAATTATAAATATG-TATAAC
131 TTGAGCTCGTATTTTAATATTTGAAATTTAAATTCTATCTAATTTAATTATAAATATGTTATAAC
1783955 TTAT
196 TTAT
1783959 ATTTTTTAAAAGTTATTTTATGCCATAATATTTTTCTTTTTTTGTTCTTCAAATCGTGTTTGAGA
1 ATTTTTTAAAAGTTATTTTATGCCATAATATTTTTCTTTTTTTGTTCTTCAAATCGTGTTTGAGA
1784024 TTTTTGGGAATGTTTAGGTAAAATAATATTTAACGAGCGAAAAATAAATAGGTTTCGAATATAGA
66 TTTTTGGGAATGTTTAGGTAAAATAATATTTAACGAGCGAAAAATAAATAGGTTTCGAATATAGA
1784089 TTGAGCTCGTATTTTAATATTTGAAATTTAAATTCTATCTAATTTAATTATAAATATGTTATAAC
131 TTGAGCTCGTATTTTAATATTTGAAATTTAAATTCTATCTAATTTAATTATAAATATGTTATAAC
1784154 TTAT
196 TTAT
1784158 ATT
1 ATT
1784161 ATATTAAATT
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
198 188 0.94
199 13 0.06
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (199 bp):
ATTTTTTAAAAGTTATTTTATGCCATAATATTTTTCTTTTTTTGTTCTTCAAATCGTGTTTGAGA
TTTTTGGGAATGTTTAGGTAAAATAATATTTAACGAGCGAAAAATAAATAGGTTTCGAATATAGA
TTGAGCTCGTATTTTAATATTTGAAATTTAAATTCTATCTAATTTAATTATAAATATGTTATAAC
TTAT
Found at i:1786411 original size:21 final size:21
Alignment explanation
Indices: 1786383--1786501 Score: 96
Period size: 21 Copynumber: 5.7 Consensus size: 21
1786373 TCTCACGAGG
1786383 TTCTGTTTAACTCTTATGGGT
1 TTCTGTTTAACTCTTATGGGT
* * * * *
1786404 TTCCGTTTAGCTCTTTTGAGC
1 TTCTGTTTAACTCTTATGGGT
* *
1786425 TTCTATTTAACCCTTATGGGT
1 TTCTGTTTAACTCTTATGGGT
* * * * *
1786446 TTCTGTTCAGCTTTTACGAGCT
1 TTCTGTTTAACTCTTATG-GGT
* *
1786468 TTC-GTTCAACCCTTATGGGT
1 TTCTGTTTAACTCTTATGGGT
1786488 TTCTGTTTAACTCT
1 TTCTGTTTAACTCT
1786502 CATGAGCTTT
Statistics
Matches: 70, Mismatches: 26, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
20 5 0.07
21 60 0.86
22 5 0.07
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (21 bp):
TTCTGTTTAACTCTTATGGGT
Found at i:1786434 original size:42 final size:42
Alignment explanation
Indices: 1786361--1786517 Score: 163
Period size: 42 Copynumber: 3.7 Consensus size: 42
1786351 TCGTATTTAC
* *
1786361 TTTCCGTTTAGCTCTCACGAGGTTCTGTTTAACTCTTATGGG
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGG
*** *
1786403 TTTCCGTTTAGCTCTTTTGAGCTTCTATTTAACCCTTATGGG
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGG
* * * * *
1786445 TTTCTGTTCAGCTTTTACGAGCTT-TCGTTCAACCCTTATGGG
1 TTTCCGTTTAGCTCTCACGAGCTTCT-GTTTAACCCTTATGGG
* * * *
1786487 TTTCTGTTTAACTCTCATGAGCTTTTGTTTA
1 TTTCCGTTTAGCTCTCACGAGCTTCTGTTTA
1786518 GCCTTCGGGC
Statistics
Matches: 94, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
41 1 0.01
42 92 0.98
43 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (42 bp):
TTTCCGTTTAGCTCTCACGAGCTTCTGTTTAACCCTTATGGG
Found at i:1792471 original size:22 final size:22
Alignment explanation
Indices: 1792408--1792474 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
1792398 ACTGATTAAC
*
1792408 AGAGAGCACTAAAGTGCT-ATGC
1 AGAGAGCACTAAAGTGCTAAT-A
*
1792430 GGAGAGCAC-AAATGTGCTAATA
1 AGAGAGCACTAAA-GTGCTAATA
*
1792452 AGAGAGCACTAACGTGCTAATA
1 AGAGAGCACTAAAGTGCTAATA
1792474 A
1 A
1792475 TCAGAGAGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 3 0.08
22 31 0.82
23 4 0.11
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.18
Consensus pattern (22 bp):
AGAGAGCACTAAAGTGCTAATA
Found at i:1802322 original size:22 final size:22
Alignment explanation
Indices: 1802259--1802325 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
1802249 ACTGATTAAC
*
1802259 AGAGAGCACTAAAGTGCT-ATGC
1 AGAGAGCACTAAAGTGCTAAT-A
*
1802281 GGAGAGCAC-AAATGTGCTAATA
1 AGAGAGCACTAAA-GTGCTAATA
*
1802303 AGAGAGCACTAACGTGCTAATA
1 AGAGAGCACTAAAGTGCTAATA
1802325 A
1 A
1802326 TCAGAGAGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 3 0.08
22 31 0.82
23 4 0.11
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.18
Consensus pattern (22 bp):
AGAGAGCACTAAAGTGCTAATA
Found at i:1805523 original size:16 final size:16
Alignment explanation
Indices: 1805504--1805535 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1805494 TTGATGTATT
*
1805504 ATATATAAAAATAATA
1 ATATAAAAAAATAATA
1805520 ATATAAAAAAATAATA
1 ATATAAAAAAATAATA
1805536 TAGATGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATAAAAAAATAATA
Found at i:1805532 original size:13 final size:14
Alignment explanation
Indices: 1805506--1805537 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1805496 GATGTATTAT
1805506 ATATAAAAATAATA
1 ATATAAAAATAATA
1805520 ATATAAAAA-AATA
1 ATATAAAAATAATA
1805533 ATATA
1 ATATA
1805538 GATGAACTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATATAAAAATAATA
Found at i:1823130 original size:411 final size:411
Alignment explanation
Indices: 1822368--1823197 Score: 1414
Period size: 411 Copynumber: 2.0 Consensus size: 411
1822358 AAATATGAGG
* *
1822368 ACCTTCAGGGTAAGTTTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
1 ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
* *
1822433 AGGAACCACTTGTTGCAAAAATGGGAGGAGCTTTTGGATGGAATCAACATGCCCTCACAAATGCA
66 AGGAACCACTTGGTGCAAAAATGGGAGGAACTTTTGGATGGAATCAACATGCCCTCACAAATGCA
*
1822498 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGTTTACAGAGGCTAATCATGAAA
131 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGATTACAGAGGCTAATCATGAAA
*
1822563 CAAATTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
196 CAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
* **
1822628 GAGGGTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGATCTTCAATCAGTTATGCTTGAGAGGGA
261 GAGGGTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGACCTTCAATCAGTTACACTTGAGAGGGA
* * *
1822693 TCAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAATC-TTTCGGCGAAGGCAGCT
326 TAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAA-CGTTTCAGCAAAGGCAGCT
1822757 CGA-TTTGAAGTTGAGAATGAAA
390 C-ATTTTGAAGTTGAGAATGAAA
* *
1822779 ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAACTGTTGGAACAATCCTTAATGGAA
1 ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
* * * *
1822844 AGGAGCCACTTGGTGCAAAAATGGGTGGAACTTTTGGATGGAATCGACATGCCTTCACAAATGCA
66 AGGAACCACTTGGTGCAAAAATGGGAGGAACTTTTGGATGGAATCAACATGCCCTCACAAATGCA
* *
1822909 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTCGGGAGGGCGATTACAGAGGCTAATCATGAAA
131 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGATTACAGAGGCTAATCATGAAA
*
1822974 GAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
196 CAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
*
1823039 GAGGAGT-CAGAAAAGAGAGTAGCTGATCTTGGGGCAGACCTTCAATCAGTTACACTTGAGAGGG
261 GAGG-GTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGACCTTCAATCAGTTACACTTGAGAGGG
1823103 ATAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAACGTTTCAGCAAAGGCAGCT
325 ATAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAACGTTTCAGCAAAGGCAGCT
1823168 CATTTTGAAGTTGAGAATGAAA
390 CATTTTGAAGTTGAGAATGAAA
1823190 ACCTTCAG
1 ACCTTCAG
1823198 ATTAGAGTCA
Statistics
Matches: 394, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
410 2 0.01
411 390 0.99
412 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (411 bp):
ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
AGGAACCACTTGGTGCAAAAATGGGAGGAACTTTTGGATGGAATCAACATGCCCTCACAAATGCA
ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGATTACAGAGGCTAATCATGAAA
CAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
GAGGGTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGACCTTCAATCAGTTACACTTGAGAGGGA
TAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAACGTTTCAGCAAAGGCAGCTC
ATTTTGAAGTTGAGAATGAAA
Found at i:1830121 original size:12 final size:13
Alignment explanation
Indices: 1830095--1830124 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1830085 ACATCATCTT
1830095 CGTACATACAGTA
1 CGTACATACAGTA
1830108 CGTACATA-AGTA
1 CGTACATACAGTA
1830120 CGTAC
1 CGTAC
1830125 GTATGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (13 bp):
CGTACATACAGTA
Found at i:1831849 original size:1 final size:1
Alignment explanation
Indices: 1831845--1831869 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1831835 ACACCCCCCC
1831845 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1831870 CCAACTGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1841662 original size:81 final size:83
Alignment explanation
Indices: 1841532--1841696 Score: 316
Period size: 81 Copynumber: 2.0 Consensus size: 83
1841522 AATGATTATA
1841532 TACGTGGATTGTACGAAAGATTTGATAGGAGAACTTATAAGATAAAGATTTTATGATTATTTTAT
1 TACGTGGATTGTACGAAAGATTTGATAGGAGAACTTATAAGATAAAGATTTTATGATTATTTTAT
1841597 TA-TT-TATTAAGATTTT
66 TATTTATATTAAGATTTT
1841613 TACGTGGATTGTACGAAAGATTTGATAGGAGAACTTATAAGATAAAGATTTTATGATTATTTTAT
1 TACGTGGATTGTACGAAAGATTTGATAGGAGAACTTATAAGATAAAGATTTTATGATTATTTTAT
1841678 TATTTATATTAAGATTTT
66 TATTTATATTAAGATTTT
1841696 T
1 T
1841697 TTTTGTGTTG
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
81 67 0.82
82 2 0.02
83 13 0.16
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.44
Consensus pattern (83 bp):
TACGTGGATTGTACGAAAGATTTGATAGGAGAACTTATAAGATAAAGATTTTATGATTATTTTAT
TATTTATATTAAGATTTT
Found at i:1852295 original size:14 final size:15
Alignment explanation
Indices: 1852278--1852315 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1852268 ATTTTCTAGT
*
1852278 AAATCATTTTTC-AA
1 AAATCATTTTCCGAA
1852292 AAATCATTTTCCGAA
1 AAATCATTTTCCGAA
1852307 AAA-CATTTT
1 AAATCATTTT
1852316 ACTGTCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (15 bp):
AAATCATTTTCCGAA
Found at i:1853833 original size:21 final size:21
Alignment explanation
Indices: 1853809--1853852 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1853799 TTACAAACAC
*
1853809 AAAATTACAATATTCATATAA
1 AAAATTACAATATTCATACAA
1853830 AAAATTACAATATTCATACAA
1 AAAATTACAATATTCATACAA
1853851 AA
1 AA
1853853 TACTAATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATTACAATATTCATACAA
Found at i:1853905 original size:19 final size:19
Alignment explanation
Indices: 1853886--1853923 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1853876 AAATTTAATT
1853886 ATAAAATAATTACAATATTA
1 ATAAAA-AATTACAATATTA
*
1853906 ATACAAAATTACAATATT
1 ATAAAAAATTACAATATT
1853924 CATTGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAATTACAATATTA
Found at i:1855073 original size:10 final size:10
Alignment explanation
Indices: 1855058--1855223 Score: 332
Period size: 10 Copynumber: 16.6 Consensus size: 10
1855048 ATTTTAAAAA
1855058 TAAAAAATTT
1 TAAAAAATTT
1855068 TAAAAAATTT
1 TAAAAAATTT
1855078 TAAAAAATTT
1 TAAAAAATTT
1855088 TAAAAAATTT
1 TAAAAAATTT
1855098 TAAAAAATTT
1 TAAAAAATTT
1855108 TAAAAAATTT
1 TAAAAAATTT
1855118 TAAAAAATTT
1 TAAAAAATTT
1855128 TAAAAAATTT
1 TAAAAAATTT
1855138 TAAAAAATTT
1 TAAAAAATTT
1855148 TAAAAAATTT
1 TAAAAAATTT
1855158 TAAAAAATTT
1 TAAAAAATTT
1855168 TAAAAAATTT
1 TAAAAAATTT
1855178 TAAAAAATTT
1 TAAAAAATTT
1855188 TAAAAAATTT
1 TAAAAAATTT
1855198 TAAAAAATTT
1 TAAAAAATTT
1855208 TAAAAAATTT
1 TAAAAAATTT
1855218 TAAAAA
1 TAAAAA
1855224 TAAAAAAAAT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 156 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAAAAATTT
Found at i:1859344 original size:16 final size:16
Alignment explanation
Indices: 1859323--1859356 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1859313 AAATTAATAC
1859323 TTTTATAATATTCATT
1 TTTTATAATATTCATT
1859339 TTTTATAATATTCATT
1 TTTTATAATATTCATT
1859355 TT
1 TT
1859357 CTTTAAATTT
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:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATAATATTCATT
Found at i:1860501 original size:199 final size:200
Alignment explanation
Indices: 1860161--1860559 Score: 791
Period size: 199 Copynumber: 2.0 Consensus size: 200
1860151 ATTTGAGAAA
1860161 CCATTATAATTTGTGAGTACTACTAAATTGAGTATAATTAGAGCTTCCAATTACGCTTTTCAATT
1 CCATTATAATTTGTGAGTACTACTAAATTGAGTATAATTAGAGCTTCCAATTACGCTTTTCAATT
1860226 TTTAGGGGTGAGAATTAGAGTAATCACACAAGTAATTACCCTTAAATTTAATTTTAAAAAGTTAT
66 TTTAGGGGTGAGAATTAGAGTAATCACACAAGTAATTACCCTTAAATTTAATTTTAAAAAGTTAT
1860291 TTTCTATACAAGTTTAAGTTATAAATTTTTATATTATAAACATGAATATGTATGAGTA-TTGGGA
131 TTTCTATACAAGTTTAAGTTATAAATTTTTATATTATAAACATGAATATGTATGAGTATTTGGGA
1860355 TGATT
196 TGATT
1860360 CCATTATAATTTGTGAGTACTACTAAATTGAGTATAATTAGAGCTTCCAATTACGCTTTTCAATT
1 CCATTATAATTTGTGAGTACTACTAAATTGAGTATAATTAGAGCTTCCAATTACGCTTTTCAATT
1860425 TTTAGGGGTGAGAATTAGAGTAATCACACAAGTAATTACCCTTAAATTTAATTTTAAAAAGTTAT
66 TTTAGGGGTGAGAATTAGAGTAATCACACAAGTAATTACCCTTAAATTTAATTTTAAAAAGTTAT
1860490 TTTCTATACAAGTTTAAGTTATAAATTTTTATATTATAAACATGAATATGTATGAGTATTTGGGA
131 TTTCTATACAAGTTTAAGTTATAAATTTTTATATTATAAACATGAATATGTATGAGTATTTGGGA
1860555 TGATT
196 TGATT
1860560 ATGAAAAAAT
Statistics
Matches: 199, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
199 188 0.94
200 11 0.06
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (200 bp):
CCATTATAATTTGTGAGTACTACTAAATTGAGTATAATTAGAGCTTCCAATTACGCTTTTCAATT
TTTAGGGGTGAGAATTAGAGTAATCACACAAGTAATTACCCTTAAATTTAATTTTAAAAAGTTAT
TTTCTATACAAGTTTAAGTTATAAATTTTTATATTATAAACATGAATATGTATGAGTATTTGGGA
TGATT
Found at i:1860589 original size:23 final size:25
Alignment explanation
Indices: 1860557--1860612 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
1860547 ATTTGGGATG
*
1860557 ATTATGAAAAAAT-ATTTAT-TATAT
1 ATTAT-AAAAAATAATTTATGTACAT
1860581 ATTAT-AAAAATAATTTATGTACAT
1 ATTATAAAAAATAATTTATGTACAT
*
1860605 TTTATAAA
1 ATTATAAA
1860613 GTTGTAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 6 0.22
23 6 0.22
24 13 0.48
25 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (25 bp):
ATTATAAAAAATAATTTATGTACAT
Found at i:1860592 original size:22 final size:24
Alignment explanation
Indices: 1860564--1860612 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1860554 ATGATTATGA
*
1860564 AAAAAT-ATTTAT-TATATATTAT
1 AAAAATAATTTATGTACATATTAT
*
1860586 AAAAATAATTTATGTACATTTTAT
1 AAAAATAATTTATGTACATATTAT
1860610 AAA
1 AAA
1860613 GTTGTAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 6 0.26
24 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
AAAAATAATTTATGTACATATTAT
Found at i:1863215 original size:40 final size:40
Alignment explanation
Indices: 1863169--1863244 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
1863159 TGAAAATTTA
1863169 AAAGCTTTTCTTTTCATCTTTTTAATATGTAAAATTTTTG
1 AAAGCTTTTCTTTTCATCTTTTTAATATGTAAAATTTTTG
1863209 AAAGCTTTTCTTTTCATCTTTTTAATATGTAAAATT
1 AAAGCTTTTCTTTTCATCTTTTTAATATGTAAAATT
1863245 CTATCAACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.54
Consensus pattern (40 bp):
AAAGCTTTTCTTTTCATCTTTTTAATATGTAAAATTTTTG
Found at i:1871618 original size:18 final size:18
Alignment explanation
Indices: 1871586--1871633 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1871576 TTTAACTAAT
* *
1871586 TTAATAAATAATATA-AA
1 TTAATAAATATTTTATAA
*
1871603 TT-ATGAATATTTTATAA
1 TTAATAAATATTTTATAA
1871620 TTAATAAATATTTT
1 TTAATAAATATTTT
1871634 CGATCTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TTAATAAATATTTTATAA
Found at i:1881791 original size:182 final size:183
Alignment explanation
Indices: 1881484--1881848 Score: 723
Period size: 182 Copynumber: 2.0 Consensus size: 183
1881474 TATGGAAGGG
1881484 CCCCTAGATGCAGGGTGCCAATTAATCTCATTTTGATGAAGGTAGTCGATGGTAAAAGTGTGCTT
1 CCCCTAGATGCAGGGTGCCAATTAATCTCATTTTGATGAAGGTAGTCGATGGTAAAAGTGTGCTT
1881549 AATAGGGTGATTTGCAAAGGTGGTATAACACGTATTATATATTATAATAACATAGTTATATATAA
66 AATAGGGTGATTTGCAAAGGTGGTATAACACGTATTATATATTATAATAACATAGTTATATATAA
1881614 TGATATATATCAATAATAATTTACCTTAAATATATAAAGTT-ATTTATTTATA
131 TGATATATATCAATAATAATTTACCTTAAATATATAAAGTTAATTTATTTATA
1881666 CCCCTAGATGCAGGGTGCCAATTAATCTCATTTTGATGAAGGTAGTCGATGGTAAAAGTGTGCTT
1 CCCCTAGATGCAGGGTGCCAATTAATCTCATTTTGATGAAGGTAGTCGATGGTAAAAGTGTGCTT
1881731 AATAGGGTGATTTGCAAAGGTGGTATAACACGTATTATATATTATAATAACATAGTTATATATAA
66 AATAGGGTGATTTGCAAAGGTGGTATAACACGTATTATATATTATAATAACATAGTTATATATAA
1881796 TGATATATATCAATAATAATTTACCTTAAATATATAAAGTTAATTTATTTATA
131 TGATATATATCAATAATAATTTACCTTAAATATATAAAGTTAATTTATTTATA
1881849 TATTTATCAT
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
182 171 0.94
183 11 0.06
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (183 bp):
CCCCTAGATGCAGGGTGCCAATTAATCTCATTTTGATGAAGGTAGTCGATGGTAAAAGTGTGCTT
AATAGGGTGATTTGCAAAGGTGGTATAACACGTATTATATATTATAATAACATAGTTATATATAA
TGATATATATCAATAATAATTTACCTTAAATATATAAAGTTAATTTATTTATA
Found at i:1894377 original size:13 final size:13
Alignment explanation
Indices: 1894359--1894386 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1894349 TATTGCATTA
1894359 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
1894372 TTTGTTTCGGTTC
1 TTTGTTTCGGTTC
1894385 TT
1 TT
1894387 GCCTGTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.21, T:0.64
Consensus pattern (13 bp):
TTTGTTTCGGTTC
Found at i:1895647 original size:30 final size:30
Alignment explanation
Indices: 1895611--1895677 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
1895601 GGCTAAATAG
*
1895611 TTTGTTTCGGTTCTTGCCTGTATTGCATTA
1 TTTGTTTCGGTTCTTGCCTATATTGCATTA
1895641 TTTGTTTCGGTTCTTGCCTATATTGCATTA
1 TTTGTTTCGGTTCTTGCCTATATTGCATTA
1895671 TTTGTTT
1 TTTGTTT
1895678 GAGTTAATCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.10, C:0.15, G:0.18, T:0.57
Consensus pattern (30 bp):
TTTGTTTCGGTTCTTGCCTATATTGCATTA
Found at i:1920084 original size:333 final size:333
Alignment explanation
Indices: 1919478--1920143 Score: 1323
Period size: 333 Copynumber: 2.0 Consensus size: 333
1919468 AAATTCAAGT
1919478 GCTAGGTACCCGTAATGATAACGGAAAGATGAGTAATGTACTCTTAATGGACCCATAACATAAAT
1 GCTAGGTACCCGTAATGATAACGGAAAGATGAGTAATGTACTCTTAATGGACCCATAACATAAAT
1919543 ATATTAGAGTGTTATAATTACGGTAACACTTTTGATGAGATCTACCTATGTGAGTGGAAGTGTGA
66 ATATTAGAGTGTTATAATTACGGTAACACTTTTGATGAGATCTACCTATGTGAGTGGAAGTGTGA
1919608 CCGCTTTCTAGGAGCTTAAGGGCTTGGCTCTAACAACACTTATGAAAAGAGGATATAGACACATG
131 CCGCTTTCTAGGAGCTTAAGGGCTTGGCTCTAACAACACTTATGAAAAGAGGATATAGACACATG
1919673 GCCATAATAGTGTCCCTAGATACTATGCATTGACTGATGTTGAAATCATTGTGTGAGATGTGTCT
196 GCCATAATAGTGTCCCTAGATACTATGCATTGACTGATGTTGAAATCATTGTGTGAGATGTGTCT
*
1919738 AGTTAATCAAATGGAATAGTTGGTTCAAAGCTTAGTCTACCATGCAATTTCTATTAACTTTAACA
261 AGTTAATCAAATGGAATAGTTGGTTCAAAGCTTAGTCTACCATGCAATTTCGATTAACTTTAACA
1919803 TGTTTTCA
326 TGTTTTCA
1919811 GCTAGGTACCCGTAATGATAACGGAAAGATGAGTAATGTACTCTTAATGGACCCATAACATAAAT
1 GCTAGGTACCCGTAATGATAACGGAAAGATGAGTAATGTACTCTTAATGGACCCATAACATAAAT
1919876 ATATTAGAGTGTTATAATTACGGTAACACTTTTGATGAGATCTACCTATGTGAGTGGAAGTGTGA
66 ATATTAGAGTGTTATAATTACGGTAACACTTTTGATGAGATCTACCTATGTGAGTGGAAGTGTGA
1919941 CCGCTTTCTAGGAGCTTAAGGGCTTGGCTCTAACAACACTTATGAAAAGAGGATATAGACACATG
131 CCGCTTTCTAGGAGCTTAAGGGCTTGGCTCTAACAACACTTATGAAAAGAGGATATAGACACATG
1920006 GCCATAATAGTGTCCCTAGATACTATGCATTGACTGATGTTGAAATCATTGTGTGAGATGTGTCT
196 GCCATAATAGTGTCCCTAGATACTATGCATTGACTGATGTTGAAATCATTGTGTGAGATGTGTCT
1920071 AGTTAATCAAATGGAATAGTTGGTTCAAAGCTTAGTCTACCATGCAATTTCGATTAACTTTAACA
261 AGTTAATCAAATGGAATAGTTGGTTCAAAGCTTAGTCTACCATGCAATTTCGATTAACTTTAACA
1920136 TGTTTTCA
326 TGTTTTCA
1920144 CTAAGTGAAG
Statistics
Matches: 332, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
333 332 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (333 bp):
GCTAGGTACCCGTAATGATAACGGAAAGATGAGTAATGTACTCTTAATGGACCCATAACATAAAT
ATATTAGAGTGTTATAATTACGGTAACACTTTTGATGAGATCTACCTATGTGAGTGGAAGTGTGA
CCGCTTTCTAGGAGCTTAAGGGCTTGGCTCTAACAACACTTATGAAAAGAGGATATAGACACATG
GCCATAATAGTGTCCCTAGATACTATGCATTGACTGATGTTGAAATCATTGTGTGAGATGTGTCT
AGTTAATCAAATGGAATAGTTGGTTCAAAGCTTAGTCTACCATGCAATTTCGATTAACTTTAACA
TGTTTTCA
Found at i:1924011 original size:30 final size:30
Alignment explanation
Indices: 1923975--1924032 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1923965 GCATTTGTAC
* *
1923975 AAGACCATAAGTTCCAATTTGCTATGACAT
1 AAGACCATAAGTACCAACTTGCTATGACAT
1924005 AAGACCATAAGTACCAACTTGCTATGAC
1 AAGACCATAAGTACCAACTTGCTATGAC
1924033 TGGCATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (30 bp):
AAGACCATAAGTACCAACTTGCTATGACAT
Found at i:1924976 original size:34 final size:35
Alignment explanation
Indices: 1924910--1924976 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1924900 CAAACACCAG
* *
1924910 AAAATATTTTCCAGTAAATCATATTATAGAAAAGT
1 AAAACATTTTCCAGTAAATCATATTACAGAAAAGT
* *
1924945 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATATTACAGAAAA
1924977 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATATTACAGAAAAGT
Found at i:1948270 original size:17 final size:17
Alignment explanation
Indices: 1948248--1948281 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1948238 TTAACCGAAC
1948248 TTAATTATGTAATGTTT
1 TTAATTATGTAATGTTT
1948265 TTAATTATGTAATGTTT
1 TTAATTATGTAATGTTT
1948282 CAAGACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (17 bp):
TTAATTATGTAATGTTT
Found at i:1953182 original size:18 final size:18
Alignment explanation
Indices: 1953161--1953212 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
1953151 TTTATTATTA
1953161 TTTTTATTAATTTTATGT
1 TTTTTATTAATTTTATGT
*
1953179 TTTTTAGT-ATTTTATTGT
1 TTTTTATTAATTTTA-TGT
1953197 TTTATT-TTAATTTTAT
1 TTT-TTATTAATTTTAT
1953213 ATAATTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 6 0.21
18 15 0.52
19 8 0.28
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (18 bp):
TTTTTATTAATTTTATGT
Found at i:1953236 original size:45 final size:44
Alignment explanation
Indices: 1953146--1953236 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 44
1953136 ATATTATACC
* *
1953146 TATTTTTTATTATTATTTTTATTAATTTTATGTTTTTTAGTATTT
1 TATTTTTTATTATTAATTTTATTAATTTTATATTTTTTA-TATTT
*
1953191 TATTGTTTTATT-TTAATTTTATATAATTTTCTAATTTTTT-TATTT
1 TATT-TTTTATTATTAATTTTAT-TAATTTTAT-ATTTTTTATATTT
1953236 T
1 T
1953237 TAATTTATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
45 19 0.47
46 15 0.38
47 6 0.15
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (44 bp):
TATTTTTTATTATTAATTTTATTAATTTTATATTTTTTATATTT
Found at i:1958042 original size:30 final size:30
Alignment explanation
Indices: 1957986--1958048 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
1957976 AATAAAAAAA
* * *
1957986 TTTGGACCCCTTAAAAGTTAAAAAAAGCTT
1 TTTGGACCCATTAAAAGTGAAAAAAAGATT
**
1958016 TTTGGACCCATTAAAAGTGAGTAAAAGATT
1 TTTGGACCCATTAAAAGTGAAAAAAAGATT
1958046 TTT
1 TTT
1958049 CTTGGCCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (30 bp):
TTTGGACCCATTAAAAGTGAAAAAAAGATT
Found at i:1968223 original size:15 final size:15
Alignment explanation
Indices: 1968199--1968232 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1968189 TAAATTAGAA
1968199 ATTACCATTATTATT
1 ATTACCATTATTATT
*
1968214 ATTACTATTATTATT
1 ATTACCATTATTATT
1968229 ATTA
1 ATTA
1968233 TATATAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTACCATTATTATT
Found at i:1978124 original size:33 final size:33
Alignment explanation
Indices: 1978055--1978124 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1978045 AATTTAAAAA
* *
1978055 TTTTAATCCGTTTTATGATCCTTTCAAGGTACT
1 TTTTAATCCGTTTTATGATCCTTTAAAGATACT
* *
1978088 TTTTAATCCGTTTTATGATCCTTTAAATATATT
1 TTTTAATCCGTTTTATGATCCTTTAAAGATACT
1978121 TTTT
1 TTTT
1978125 GACTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (33 bp):
TTTTAATCCGTTTTATGATCCTTTAAAGATACT
Found at i:1979301 original size:2 final size:2
Alignment explanation
Indices: 1979296--1979320 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1979286 GGCATTTTTG
1979296 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 T
1979321 TTTTGGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2040054 original size:15 final size:16
Alignment explanation
Indices: 2040024--2040056 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2040014 ATTTAGAATT
*
2040024 TATTTAATCTTTAAAA
1 TATTTAATCATTAAAA
2040040 TATTTAAT-ATTAAAA
1 TATTTAATCATTAAAA
2040055 TA
1 TA
2040057 ATACAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATCATTAAAA
Found at i:2041700 original size:17 final size:18
Alignment explanation
Indices: 2041665--2041718 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
2041655 ATTTATATAA
*
2041665 AAAAATAAAACTCAAATTT
1 AAAAATTAAACT-AAATTT
2041684 -AAAATTAAACTAAATTT
1 AAAAATTAAACTAAATTT
* *
2041701 AAAAAATAAAGTAAATTT
1 AAAAATTAAACTAAATTT
2041719 GTAAGTTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.19
18 25 0.81
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAAATTAAACTAAATTT
Found at i:2055567 original size:2 final size:2
Alignment explanation
Indices: 2055560--2055589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2055550 TAAGAGCTTT
2055560 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2055590 CAGAGCAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2058109 original size:18 final size:19
Alignment explanation
Indices: 2058078--2058113 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2058068 GTATGTATGT
2058078 ATAATAACTAATTTCTACA
1 ATAATAACTAATTTCTACA
2058097 ATAATAA-TAATTTCTAC
1 ATAATAACTAATTTCTAC
2058114 TAGTGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATAACTAATTTCTACA
Found at i:2073674 original size:20 final size:19
Alignment explanation
Indices: 2073642--2073681 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2073632 GTAACTTTGT
*
2073642 TTTGTATTTTATTAAACTA
1 TTTGTATTGTATTAAACTA
*
2073661 TTTGTTATTGTATTAATCTA
1 TTTG-TATTGTATTAAACTA
2073681 T
1 T
2073682 GGCTTATGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTGTATTGTATTAAACTA
Found at i:2081440 original size:18 final size:18
Alignment explanation
Indices: 2081417--2081456 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
2081407 TGTTTTGCTG
2081417 TCACTTGACACATTATTA
1 TCACTTGACACATTATTA
2081435 TCACTTGACACATTATTA
1 TCACTTGACACATTATTA
2081453 TCAC
1 TCAC
2081457 ATGCAATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (18 bp):
TCACTTGACACATTATTA
Found at i:2089203 original size:47 final size:46
Alignment explanation
Indices: 2089112--2089204 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 46
2089102 CTTATTCCAA
* * *
2089112 ACTTATCATACCGAAATAAATTTTTGTGTGTGTGTTAGATAGGTGT
1 ACTTATCATACCGAAATAAATTTTTGTGTATGTGTTAAAAAGGTGT
* *
2089158 ACTTATCATACTGAAATAAATTTTTTTTGTATGTGTTAAAAAGGTGT
1 ACTTATCATACCGAAATAAA-TTTTTGTGTATGTGTTAAAAAGGTGT
2089205 TTTTAAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
46 19 0.46
47 22 0.54
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (46 bp):
ACTTATCATACCGAAATAAATTTTTGTGTATGTGTTAAAAAGGTGT
Found at i:2096017 original size:75 final size:75
Alignment explanation
Indices: 2095938--2096113 Score: 255
Period size: 75 Copynumber: 2.3 Consensus size: 75
2095928 TTGTTCCGGT
* *
2095938 CTCCCCCTCCCCCACCACCACTCCCTCCATCCTCAGCTACATCTCCATCTTCTT-CTGTAAAGAA
1 CTCCCCCTCCCCCTCCACCACTCCCTCCATCCTCAGCTACATCTCCATCTT-TTACCGTAAAGAA
* *
2096002 TTCGTTTTCAG
65 TTCATCTTCAG
* * * *
2096013 CTCCCCCTCCCCCTCCCCCACTCCCTCCTTTCTCAGCTATATCTCCATCTTTTACCGTAAAGAAT
1 CTCCCCCTCCCCCTCCACCACTCCCTCCATCCTCAGCTACATCTCCATCTTTTACCGTAAAGAAT
2096078 TCATCTTCAG
66 TCATCTTCAG
*
2096088 CTCCCCCTCCTCCTCCACCACTCCCT
1 CTCCCCCTCCCCCTCCACCACTCCCT
2096114 AACGTGGCTT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 2 0.02
75 88 0.98
ACGTcount: A:0.16, C:0.49, G:0.05, T:0.30
Consensus pattern (75 bp):
CTCCCCCTCCCCCTCCACCACTCCCTCCATCCTCAGCTACATCTCCATCTTTTACCGTAAAGAAT
TCATCTTCAG
Found at i:2098612 original size:17 final size:18
Alignment explanation
Indices: 2098590--2098627 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2098580 AAAAAAAAGT
*
2098590 TAATACCATGAA-CAAAA
1 TAATACCATAAATCAAAA
*
2098607 TAATACCCTAAATCAAAA
1 TAATACCATAAATCAAAA
2098625 TAA
1 TAA
2098628 AAGAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (18 bp):
TAATACCATAAATCAAAA
Found at i:2099800 original size:14 final size:14
Alignment explanation
Indices: 2099766--2099810 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
2099756 GTTAGGGGAC
*
2099766 ACCATAAACCATAA
1 ACCATAAACCCTAA
2099780 ACCATAAACCCTAA
1 ACCATAAACCCTAA
* * *
2099794 GCTATAAACTCTAA
1 ACCATAAACCCTAA
2099808 ACC
1 ACC
2099811 CCATCCTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (14 bp):
ACCATAAACCCTAA
Found at i:2119786 original size:6 final size:6
Alignment explanation
Indices: 2119775--2119801 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2119765 ATATATCAAT
2119775 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
2119802 GTGTGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:2122574 original size:5 final size:5
Alignment explanation
Indices: 2122559--2122591 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
2122549 GAAAGCTATA
2122559 ATGCT -TGCT ATGCT ATGCT ATGCT ATGCT ATGC
1 ATGCT ATGCT ATGCT ATGCT ATGCT ATGCT ATGC
2122592 AGTGGTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (5 bp):
ATGCT
Found at i:2130510 original size:21 final size:21
Alignment explanation
Indices: 2130484--2130528 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2130474 ACCAGATTCT
2130484 GCTAGATTCAGGTGAAAGCAA
1 GCTAGATTCAGGTGAAAGCAA
2130505 GCTAGATTCAGGTGAAAGCAA
1 GCTAGATTCAGGTGAAAGCAA
2130526 GCT
1 GCT
2130529 CCAAGCAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.20
Consensus pattern (21 bp):
GCTAGATTCAGGTGAAAGCAA
Found at i:2130537 original size:21 final size:21
Alignment explanation
Indices: 2130492--2130537 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2130482 CTGCTAGATT
* **
2130492 CAGGTGAAAGCAAGCTAGATT
1 CAGGTGAAAGCAAGCTACAAG
*
2130513 CAGGTGAAAGCAAGCTCCAAG
1 CAGGTGAAAGCAAGCTACAAG
2130534 CAGG
1 CAGG
2130538 ACGAATTTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.30, T:0.13
Consensus pattern (21 bp):
CAGGTGAAAGCAAGCTACAAG
Found at i:2134708 original size:45 final size:45
Alignment explanation
Indices: 2134634--2134730 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 45
2134624 TTATTTTCCT
*
2134634 AAATAAAATTAAAAACGACCTAAATACCTAATTAATATATAATGA
1 AAATAAAATTAAAAACGACCTAAACACCTAATTAATATATAATGA
* *
2134679 AAATGAAATTAAAAACGACTTAAACACCTAATTAATATATAATGA
1 AAATAAAATTAAAAACGACCTAAACACCTAATTAATATATAATGA
2134724 AAATAAA
1 AAATAAA
2134731 GTTTAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (45 bp):
AAATAAAATTAAAAACGACCTAAACACCTAATTAATATATAATGA
Found at i:2145307 original size:118 final size:119
Alignment explanation
Indices: 2145099--2145335 Score: 467
Period size: 118 Copynumber: 2.0 Consensus size: 119
2145089 CATTAGAATT
2145099 GGATTTGCCCCCACTCTTAAGAGGCTTACCCTTAGATTGGGACGAAATTTTGGGGGTTTCCTGCT
1 GGATTTGCCCCCACTCTTAAGAGGCTTACCCTTAGATTGGGACGAAATTTTGGGGGTTTCCTGCT
2145164 TGGAATTGCCCGTCTTTGGAACGTCTTGTTTTAACTTTGAGG-AGCTTTTGGTG
66 TGGAATTGCCCGTCTTTGGAACGTCTTGTTTTAACTTTGAGGAAGCTTTTGGTG
2145217 GGATTTGCCCCCACTCTTAAGAGGCTTACCCTTAGATTGGGACGAAATTTTGGGGGTTTCCTGCT
1 GGATTTGCCCCCACTCTTAAGAGGCTTACCCTTAGATTGGGACGAAATTTTGGGGGTTTCCTGCT
2145282 TGGAATTGCCCGTCTTTGGAACGTCTTGTTTTAACTTTGAGGAAGCTTTTGGTG
66 TGGAATTGCCCGTCTTTGGAACGTCTTGTTTTAACTTTGAGGAAGCTTTTGGTG
2145336 TGGCACTTCC
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
118 107 0.91
119 11 0.09
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.36
Consensus pattern (119 bp):
GGATTTGCCCCCACTCTTAAGAGGCTTACCCTTAGATTGGGACGAAATTTTGGGGGTTTCCTGCT
TGGAATTGCCCGTCTTTGGAACGTCTTGTTTTAACTTTGAGGAAGCTTTTGGTG
Found at i:2154670 original size:38 final size:38
Alignment explanation
Indices: 2154618--2154730 Score: 163
Period size: 39 Copynumber: 2.9 Consensus size: 38
2154608 GACTTAGAGT
*
2154618 TAGACTTTAGTTTTATTTTTATTGGGTTGGTAATTGGA
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGA
* * *
2154656 TAGACTTTAATTTTAGTTTTATTGGGTTGGGCAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTT-GGTAATTGGA
*
2154695 TAGACTTCAGTTTTAGTTTTATTGGGTTGGATAATT
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGG-TAATT
2154731 TTATTTATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 28 0.42
39 38 0.58
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.50
Consensus pattern (38 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGA
Found at i:2162528 original size:134 final size:135
Alignment explanation
Indices: 2162288--2162556 Score: 531
Period size: 134 Copynumber: 2.0 Consensus size: 135
2162278 CAACTCTTTG
2162288 GTACAAAGGCAAAAACTCTAAACCCAATGTGATCCTAACGCCTGGCATCAATAATAAAGGAAAAG
1 GTACAAAGGCAAAAACTCTAAACCCAATGTGATCCTAACGCCTGGCATCAATAATAAAGGAAAAG
2162353 GAAAAAAAACTATATCTATATAAAAAAGGTATCGTAACCCTACAAAGTACAACCACTAT-AACTG
66 GAAAAAAAACTATATCTATATAAAAAAGGTATCGTAACCCTACAAAGTACAACCACTATAAACTG
2162417 CATTA
131 CATTA
2162422 GTACAAAGGCAAAAACTCTAAACCCAATGTGATCCTAACGCCTGGCATCAATAATAAAGGAAAAG
1 GTACAAAGGCAAAAACTCTAAACCCAATGTGATCCTAACGCCTGGCATCAATAATAAAGGAAAAG
2162487 GAAAAAAAACTATATCTATATAAAAAAGGTATCGTAACCCTACAAAGTACAACCACTATAAACTG
66 GAAAAAAAACTATATCTATATAAAAAAGGTATCGTAACCCTACAAAGTACAACCACTATAAACTG
2162552 CATTA
131 CATTA
2162557 ACTACGAATA
Statistics
Matches: 134, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
134 124 0.93
135 10 0.07
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (135 bp):
GTACAAAGGCAAAAACTCTAAACCCAATGTGATCCTAACGCCTGGCATCAATAATAAAGGAAAAG
GAAAAAAAACTATATCTATATAAAAAAGGTATCGTAACCCTACAAAGTACAACCACTATAAACTG
CATTA
Found at i:2172178 original size:23 final size:23
Alignment explanation
Indices: 2172151--2172203 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
2172141 TGCATTTATT
2172151 AGACGTTTTGTAGGTATTTAGGA
1 AGACGTTTTGTAGGTATTTAGGA
2172174 AGACGTTTTGTAGGTATTTAGGA
1 AGACGTTTTGTAGGTATTTAGGA
2172197 AGACGTT
1 AGACGTT
2172204 CGACGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (23 bp):
AGACGTTTTGTAGGTATTTAGGA
Found at i:2172812 original size:13 final size:13
Alignment explanation
Indices: 2172794--2172820 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2172784 TGGTACCACG
2172794 ATTATATCATCAA
1 ATTATATCATCAA
2172807 ATTATATCATCAA
1 ATTATATCATCAA
2172820 A
1 A
2172821 ATATCATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTATATCATCAA
Found at i:2175706 original size:37 final size:37
Alignment explanation
Indices: 2175614--2175785 Score: 173
Period size: 37 Copynumber: 4.5 Consensus size: 37
2175604 CACCAGTTTA
* **
2175614 GCACCCAGTGCCTCATCGGATAATTCGAAGTAATAATATG
1 GCACCCAGTGCCTCATCGGCTAAACCGAAGT-A-AAT-TG
* *
2175654 ACACCCAGTGTCTCATCGGCTAAACCGAAGTAAATTG
1 GCACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTG
** * *
2175691 GCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTG
1 GCACCCAGTGCCTCATCG-GCTAAACC---GAAGTAAATTG
* * *
2175732 ACACCCAGTGTCTCATTGGCTAAACCGAAGTAAATTG
1 GCACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTG
2175769 GCACCCAGTGCCTCATC
1 GCACCCAGTGCCTCATC
2175786 AAATTAATCC
Statistics
Matches: 107, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
37 42 0.39
38 8 0.07
39 1 0.01
40 31 0.29
41 25 0.23
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (37 bp):
GCACCCAGTGCCTCATCGGCTAAACCGAAGTAAATTG
Found at i:2175737 original size:41 final size:39
Alignment explanation
Indices: 2175615--2175830 Score: 165
Period size: 41 Copynumber: 5.5 Consensus size: 39
2175605 ACCAGTTTAG
* *
2175615 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAAT-AATATGA
1 CACCCAGTGCCTCATC-GACTAA-TCCAAGTAGTAAAT-TGA
* * * * *
2175655 CACCCAGTGTCTCATCGGCTAAACC--GAAGTAAATTGG
1 CACCCAGTGCCTCATCGACTAATCCAAGTAGTAAATTGA
*
2175692 CACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCG-ACTAATCC-AAGTAGTAAATTGA
* * * * * *
2175733 CACCCAGTGTCTCATTGGCTAAACC--GAAGTAAATTGG
1 CACCCAGTGCCTCATCGACTAATCCAAGTAGTAAATTGA
* *
2175770 CACCCAGTGCCTCATCAAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATC-GACTAATCC-AAGTAGTAAATTGA
* *
2175811 CACCCAGTGTCTCATTGACT
1 CACCCAGTGCCTCATCGACT
2175831 CAAAGTCGAA
Statistics
Matches: 134, Mismatches: 32, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
37 45 0.34
38 13 0.10
39 2 0.01
40 25 0.19
41 49 0.37
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGACTAATCCAAGTAGTAAATTGA
Found at i:2175826 original size:78 final size:78
Alignment explanation
Indices: 2175614--2175827 Score: 351
Period size: 78 Copynumber: 2.8 Consensus size: 78
2175604 CACCAGTTTA
* * * * *
2175614 GCACCCAGTGCCTCATCGGA-TAATTCGAAGTAAT-AATATGACACCCAGTGTCTCATCGGCTAA
1 GCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAAT-TGACACCCAGTGTCTCATTGGCTAA
2175677 ACCGAAGTAAATTG
65 ACCGAAGTAAATTG
2175691 GCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGACACCCAGTGTCTCATTGGCTAAA
1 GCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGACACCCAGTGTCTCATTGGCTAAA
2175756 CCGAAGTAAATTG
66 CCGAAGTAAATTG
*
2175769 GCACCCAGTGCCTCATCAAATTAATCCAAAGTAGTAAATTGACACCCAGTGTCTCATTG
1 GCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGACACCCAGTGTCTCATTG
2175828 ACTCAAAGTC
Statistics
Matches: 129, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
77 19 0.15
78 107 0.83
79 3 0.02
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (78 bp):
GCACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGACACCCAGTGTCTCATTGGCTAAA
CCGAAGTAAATTG
Found at i:2176029 original size:24 final size:24
Alignment explanation
Indices: 2175984--2176030 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2175974 TATATATACC
2175984 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
2176008 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
2176031 TCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:2176713 original size:6 final size:6
Alignment explanation
Indices: 2176696--2176726 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2176686 CCTTTCTTTC
*
2176696 TTTCTT TCTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
2176727 CTTTCCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:2176802 original size:5 final size:5
Alignment explanation
Indices: 2176792--2176819 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2176782 ATTTATTTGT
2176792 TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TAT
2176820 TTTAACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:2193599 original size:16 final size:17
Alignment explanation
Indices: 2193568--2193600 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2193558 TAAAAAAATC
*
2193568 TATTAAAAATAGTGGTA
1 TATTAAAAAGAGTGGTA
2193585 TATTAAAAAGA-TGGTA
1 TATTAAAAAGAGTGGTA
2193601 ACAATCAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.33
Consensus pattern (17 bp):
TATTAAAAAGAGTGGTA
Found at i:2195798 original size:21 final size:21
Alignment explanation
Indices: 2195772--2195816 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2195762 ATATTTGGTA
2195772 TGTAGGCAATGCTGTTCAATT
1 TGTAGGCAATGCTGTTCAATT
2195793 TGTAGGCAATGCTGTTCAATT
1 TGTAGGCAATGCTGTTCAATT
2195814 TGT
1 TGT
2195817 TGTCAGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.40
Consensus pattern (21 bp):
TGTAGGCAATGCTGTTCAATT
Found at i:2196702 original size:13 final size:13
Alignment explanation
Indices: 2196682--2196716 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2196672 CTCAAATGTC
*
2196682 TCAAAAGCACTTT
1 TCAAAAGCACTTG
*
2196695 TGAAAAGCACTTG
1 TCAAAAGCACTTG
2196708 TCAAAAGCA
1 TCAAAAGCA
2196717 ATAAGAACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTG
Found at i:2196835 original size:134 final size:135
Alignment explanation
Indices: 2196595--2196863 Score: 515
Period size: 134 Copynumber: 2.0 Consensus size: 135
2196585 TTAAATACAT
2196595 ATTTGTTACTTTATAATCTCATGTCTAAAATGGACATTTTATCTTTCAAAAGTATTTTTTGACAG
1 ATTTGTTACTTTATAATCTCATGTCTAAAATGGACATTTTATCTTTCAAAAGTATTTTTTGACAG
2196660 CAATGTCAAACACTCAAATGTCTCAAAAGCACTTTTGAAAAGCACTTGTCAAAAGCAAT-AAGAA
66 CAATGTCAAACACTCAAATGTCTCAAAAGCACTTTTGAAAAGCACTTGTCAAAAGCAATGAAGAA
2196724 CTGGC
131 CTGGC
2196729 ATTTGTTACTTTATAATCTCATGTCTAAAATGGACATTTTATAC-TTCAAAAGTATTTTTTGACA
1 ATTTGTTACTTTATAATCTCATGTCTAAAATGGACATTTTAT-CTTTCAAAAGTATTTTTTGACA
2196793 GCAATGTCAAACACTCAAATGTCTCAAAAGCACTTTTGAAAAGCACTTGTCAAAAGCAATGAAGA
65 GCAATGTCAAACACTCAAATGTCTCAAAAGCACTTTTGAAAAGCACTTGTCAAAAGCAATGAAGA
2196858 ACTGGC
130 ACTGGC
2196864 CTTCTTCTCC
Statistics
Matches: 133, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
134 122 0.92
135 11 0.08
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (135 bp):
ATTTGTTACTTTATAATCTCATGTCTAAAATGGACATTTTATCTTTCAAAAGTATTTTTTGACAG
CAATGTCAAACACTCAAATGTCTCAAAAGCACTTTTGAAAAGCACTTGTCAAAAGCAATGAAGAA
CTGGC
Found at i:2196836 original size:13 final size:13
Alignment explanation
Indices: 2196816--2196850 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2196806 CTCAAATGTC
*
2196816 TCAAAAGCACTTT
1 TCAAAAGCACTTG
*
2196829 TGAAAAGCACTTG
1 TCAAAAGCACTTG
2196842 TCAAAAGCA
1 TCAAAAGCA
2196851 ATGAAGAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (13 bp):
TCAAAAGCACTTG
Found at i:2208204 original size:96 final size:96
Alignment explanation
Indices: 2208035--2208227 Score: 314
Period size: 96 Copynumber: 2.0 Consensus size: 96
2208025 ATGAGCCAAG
* * *
2208035 ATTACCAGGAATATAACTTCCCTGTCGCCTAGGTTGGACTATAAGATACCCTTCCTTTTCAATGA
1 ATTACCAGGAATATAAATTCCCTGTCGCCTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
2208100 CCGATGGTTCCATAGCAAAGTTTTCACCTTC
66 CCGATGGTTCCATAGCAAAGTTTTCACCTTC
* * *
2208131 ATTATCAGGAATGTAAATTCCCTGTCGGCTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
1 ATTACCAGGAATATAAATTCCCTGTCGCCTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
* *
2208196 CTGATGGTTCCATAGCTAAGTTTTCACCTTC
66 CCGATGGTTCCATAGCAAAGTTTTCACCTTC
2208227 A
1 A
2208228 CTACACTTGA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (96 bp):
ATTACCAGGAATATAAATTCCCTGTCGCCTAGGTTGGACCATAAGATACCCTTCCTTTTCAATAA
CCGATGGTTCCATAGCAAAGTTTTCACCTTC
Found at i:2209530 original size:3 final size:3
Alignment explanation
Indices: 2209522--2209547 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2209512 ATCTCAAATC
2209522 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2209548 GGTTGCTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2212084 original size:2 final size:2
Alignment explanation
Indices: 2212077--2212104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2212067 TTTAGTTCTC
2212077 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
2212105 CATTAATAAG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2251705 original size:5 final size:5
Alignment explanation
Indices: 2251692--2251725 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
2251682 AGGGGAAGAC
*
2251692 CATGA CATGG CATGG CATGG CATGG CATGG CATG
1 CATGG CATGG CATGG CATGG CATGG CATGG CATG
2251726 CACTGCACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.21
Consensus pattern (5 bp):
CATGG
Found at i:2258135 original size:229 final size:230
Alignment explanation
Indices: 2257734--2258192 Score: 902
Period size: 229 Copynumber: 2.0 Consensus size: 230
2257724 CTAAGGGATT
2257734 TAGGCAGTCAGCTAGCCAGGCTGGTTCTTTGAATTTTTTGGAAACCCCATACCACTTATCCCATC
1 TAGGCAGTCAGCTAGCCAGGCTGGTTCTTTGAATTTTTTGGAAACCCCATACCACTTATCCCATC
2257799 ATTAGTTTTGACATGAAAATGATATCCCATAATCTCCATGTGATCATGTCACTGTTTTGTTTCTC
66 ATTAGTTTTGACATGAAAATGATATCCCATAATCTCCATGTGATCATGTCACTGTTTTGTTTCTC
2257864 TGACCCTTTTAGCTACCATATATACGTTGATTACTACTGTAATGAATTTAAACAAATATATATAT
131 TGACCCTTTTAGCTACCATATATACGTTGATTACTACTGTAATGAATTTAAACAAATATATATAT
2257929 ATATATATATTAGAA-TTAAAAATTTAAAACAATA
196 ATATATATATTAGAATTTAAAAATTTAAAACAATA
2257963 TAGGCAGTCAGCTAGCCAGGCTGGTTCTTTGAATTTTTTGGAAACCCCATACCACTTATCCCATC
1 TAGGCAGTCAGCTAGCCAGGCTGGTTCTTTGAATTTTTTGGAAACCCCATACCACTTATCCCATC
2258028 ATTAGTTTTGACATGAAAATGATATCCCATAATCTCCATGTGATCATGTCACTGTTTTGTTTCTC
66 ATTAGTTTTGACATGAAAATGATATCCCATAATCTCCATGTGATCATGTCACTGTTTTGTTTCTC
2258093 TGACCCTTTTAGCTACCATATATACGTTGATTACTACTGTAATGAATTTAAACAAATATATATAT
131 TGACCCTTTTAGCTACCATATATACGTTGATTACTACTGTAATGAATTTAAACAAATATATATAT
*
2258158 ATATATATATTAGAATTTAAAATTTTAAAACAATA
196 ATATATATATTAGAATTTAAAAATTTAAAACAATA
2258193 GACTTAATTA
Statistics
Matches: 228, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
229 210 0.92
230 18 0.08
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (230 bp):
TAGGCAGTCAGCTAGCCAGGCTGGTTCTTTGAATTTTTTGGAAACCCCATACCACTTATCCCATC
ATTAGTTTTGACATGAAAATGATATCCCATAATCTCCATGTGATCATGTCACTGTTTTGTTTCTC
TGACCCTTTTAGCTACCATATATACGTTGATTACTACTGTAATGAATTTAAACAAATATATATAT
ATATATATATTAGAATTTAAAAATTTAAAACAATA
Found at i:2272475 original size:162 final size:162
Alignment explanation
Indices: 2272195--2272518 Score: 612
Period size: 162 Copynumber: 2.0 Consensus size: 162
2272185 AAACCCTTAA
2272195 ATTTATTGTAAAATTCGATGCTTTACGCTTTCCTAATAAATATGCTAAGAATTAGTATGTGAAAA
1 ATTTATTGTAAAATTCGATGCTTTACGCTTTCCTAATAAATATGCTAAGAATTAGTATGTGAAAA
* * *
2272260 TGTTCGTCAAAGGATGTTGTTGGCATGTTGTTTTACTATCTTAAAAGGTTAAAACCGTAAATAAA
66 TGTTCGTCAAAGGATGTTGTTGGCATGTTGTTTTACTATATTAAAAAGTTAAAACCCTAAATAAA
2272325 TATCAATTTTTGAGTCTTCAATAGTCTTTTTC
131 TATCAATTTTTGAGTCTTCAATAGTCTTTTTC
2272357 ATTTATTGTAAAATTCGATGCTTTACGCTTTCCTAATAAATATGCTAAGAATTAGTATGTGAAAA
1 ATTTATTGTAAAATTCGATGCTTTACGCTTTCCTAATAAATATGCTAAGAATTAGTATGTGAAAA
*
2272422 TGTTCGTCAAGGGATGTTGTTGGCATGTTGTTTTACTATATTAAAAAGTTAAAACCCTAAATAAA
66 TGTTCGTCAAAGGATGTTGTTGGCATGTTGTTTTACTATATTAAAAAGTTAAAACCCTAAATAAA
2272487 TATCAATTTTTGAGTCTTCAATAGTCTTTTTC
131 TATCAATTTTTGAGTCTTCAATAGTCTTTTTC
2272519 CTTTCATTTC
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 158 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (162 bp):
ATTTATTGTAAAATTCGATGCTTTACGCTTTCCTAATAAATATGCTAAGAATTAGTATGTGAAAA
TGTTCGTCAAAGGATGTTGTTGGCATGTTGTTTTACTATATTAAAAAGTTAAAACCCTAAATAAA
TATCAATTTTTGAGTCTTCAATAGTCTTTTTC
Found at i:2276148 original size:13 final size:13
Alignment explanation
Indices: 2276126--2276158 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2276116 ACAGAGAAGG
*
2276126 AGAAAGGAAAGAA
1 AGAAAAGAAAGAA
2276139 AGAAAAGAAAGAA
1 AGAAAAGAAAGAA
2276152 AGAAAAG
1 AGAAAAG
2276159 GGAATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAAAAGAAAGAA
Found at i:2281662 original size:24 final size:24
Alignment explanation
Indices: 2281628--2281679 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2281618 TTTCTAGAAG
* *
2281628 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
* *
2281652 ATTTAGCATTTATTAGCATCATAT
1 ATTTAGCATTTATGAGCATAATAT
2281676 ATTT
1 ATTT
2281680 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:2283568 original size:15 final size:15
Alignment explanation
Indices: 2283548--2283578 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2283538 CCCCCCCCCC
2283548 CCAAAAAAAAAAAAA
1 CCAAAAAAAAAAAAA
2283563 CCAAAAAAAAAAAAA
1 CCAAAAAAAAAAAAA
2283578 C
1 C
2283579 AACAACAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (15 bp):
CCAAAAAAAAAAAAA
Found at i:2286489 original size:2 final size:2
Alignment explanation
Indices: 2286482--2286511 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2286472 AGTACTTTTC
2286482 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
2286512 GTACTTGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2287562 original size:20 final size:19
Alignment explanation
Indices: 2287532--2287571 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
2287522 TTTCTTTTGT
2287532 TCCACGAACAAAATAATTA
1 TCCACGAACAAAATAATTA
*
2287551 TCCACTGAACAAAGTAATTA
1 TCCAC-GAACAAAATAATTA
2287571 T
1 T
2287572 TTCTGGCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (19 bp):
TCCACGAACAAAATAATTA
Found at i:2288140 original size:27 final size:25
Alignment explanation
Indices: 2288110--2288180 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 25
2288100 ATATTTTCAA
*
2288110 AATAATAAAAAAATTAAATTCTATATT
1 AATATTAAAAAAATTAAA-T-TATATT
*
2288137 AATATTAAATAAA-TATAATTATATT
1 AATATTAAAAAAATTA-AATTATATT
2288162 AATATTAAATAAAATTAAA
1 AATATTAAA-AAAATTAAA
2288181 ATCTCCACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 15 0.39
26 8 0.21
27 15 0.39
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (25 bp):
AATATTAAAAAAATTAAATTATATT
Found at i:2288172 original size:21 final size:19
Alignment explanation
Indices: 2288138--2288178 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2288128 TTCTATATTA
*
2288138 ATATTAAATAAATATAATT
1 ATATTAAATAAATAAAATT
2288157 ATATTAATATTAAATAAAATT
1 ATATTAA-A-TAAATAAAATT
2288178 A
1 A
2288179 AAATCTCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATTAAATAAATAAAATT
Found at i:2289676 original size:19 final size:17
Alignment explanation
Indices: 2289628--2289679 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
2289618 TTTTTACATT
*
2289628 TTTAAAATATTATGAAAA
1 TTTAAAATTTTAT-AAAA
*
2289646 TTTGAAATTTTTATAAATA
1 TTT-AAAATTTTATAAA-A
2289665 CTTTAAAATTTTATA
1 -TTTAAAATTTTATA
2289680 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.21
19 19 0.68
20 3 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (17 bp):
TTTAAAATTTTATAAAA
Found at i:2300747 original size:11 final size:11
Alignment explanation
Indices: 2300720--2300749 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
2300710 TTTTATAAAA
2300720 AATTAATTTTT
1 AATTAATTTTT
2300731 AA-TAATTTTT
1 AATTAATTTTT
2300741 AATTAATTT
1 AATTAATTT
2300750 AATATTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AATTAATTTTT
Found at i:2302289 original size:3 final size:3
Alignment explanation
Indices: 2302281--2302314 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2302271 CTTAACTATT
2302281 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
2302315 GTACACTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:2314471 original size:76 final size:76
Alignment explanation
Indices: 2314385--2314650 Score: 176
Period size: 76 Copynumber: 3.2 Consensus size: 76
2314375 TAACAATATT
2314385 TAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAATATATTAATAACA
1 TAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAATATATTAATAACA
2314450 TTATTAATTAG
66 TTATTAATTAG
* * * * * * *
2314461 TAAGATTTAAA-TACTACTCTAATAATTTCAAAAT-TTTAGATTTTATAAAAAGGCAAGTGTTAT
1 TAAGATTTAAATTA-TATTTTAAT--TTTTAAAATCTTCA-A--AT-TAAAAA--TAA---TAAT
* * *
2314524 ACCCTATAAAATAACATTTGAGATAATTATAACAATAT
54 A---TAT-TAATAACA--T----T-A-T-T-A-ATTAG
2314562 TTAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAATATATTAATAAC
1 T-AAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAATATATTAATAAC
2314627 ATTATTAATTAG
65 ATTATTAATTAG
2314639 TAAGATTTAAAT
1 TAAGATTTAAAT
2314651 ACTCACTCTA
Statistics
Matches: 140, Mismatches: 20, Indels: 60
0.64 0.09 0.27
Matches are distributed among these distances:
75 2 0.01
76 29 0.21
77 7 0.05
78 10 0.07
79 1 0.01
80 2 0.01
81 7 0.05
82 1 0.01
83 2 0.01
86 5 0.04
88 7 0.05
89 6 0.04
90 7 0.05
92 5 0.04
95 2 0.01
96 1 0.01
97 7 0.05
98 2 0.01
99 1 0.01
100 10 0.07
101 7 0.05
102 17 0.12
103 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (76 bp):
TAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAATATATTAATAACA
TTATTAATTAG
Found at i:2314607 original size:178 final size:179
Alignment explanation
Indices: 2314308--2314664 Score: 707
Period size: 178 Copynumber: 2.0 Consensus size: 179
2314298 TCTTTTTATT
2314308 TTTCAAAATTTTAGATTTTATAAAAAGGCAAGTGTTATACCCTATAAAATAACATTTGAGATAAT
1 TTTCAAAATTTTAGATTTTATAAAAAGGCAAGTGTTATACCCTATAAAATAACATTTGAGATAAT
2314373 TATAACAATATTTAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAAT
66 TATAACAATATTTAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAAT
2314438 ATATTAATAACATTATTAATTAGTAAGATTTAAATACT-ACTCTAATAA
131 ATATTAATAACATTATTAATTAGTAAGATTTAAATACTCACTCTAATAA
2314486 TTTCAAAATTTTAGATTTTATAAAAAGGCAAGTGTTATACCCTATAAAATAACATTTGAGATAAT
1 TTTCAAAATTTTAGATTTTATAAAAAGGCAAGTGTTATACCCTATAAAATAACATTTGAGATAAT
2314551 TATAACAATATTTAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAAT
66 TATAACAATATTTAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAAT
2314616 ATATTAATAACATTATTAATTAGTAAGATTTAAATACTCACTCTAATAA
131 ATATTAATAACATTATTAATTAGTAAGATTTAAATACTCACTCTAATAA
2314665 AGTTTATAAA
Statistics
Matches: 178, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 168 0.94
179 10 0.06
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (179 bp):
TTTCAAAATTTTAGATTTTATAAAAAGGCAAGTGTTATACCCTATAAAATAACATTTGAGATAAT
TATAACAATATTTAAGATTTAAATTATATTTTAATTTTTAAAATCTTCAAATTAAAAATAATAAT
ATATTAATAACATTATTAATTAGTAAGATTTAAATACTCACTCTAATAA
Found at i:2320996 original size:93 final size:93
Alignment explanation
Indices: 2320837--2321022 Score: 345
Period size: 93 Copynumber: 2.0 Consensus size: 93
2320827 GGTGATGACA
* *
2320837 AGACCATCAAGGTTAGTTATGATTGAATAGTTATTTCTTTATTGATATGAAGAAAAATAGATCTT
1 AGACCATCAAGGTTAGTTATGATTGAATAGTTATTTATTCATTGATATGAAGAAAAATAGATCTT
2320902 CTACACTGATTGCTTGAGTTTAGGTGTG
66 CTACACTGATTGCTTGAGTTTAGGTGTG
2320930 AGACCATCAAGGTTAGTTATGATTGAATAGTTATTTATTCATTGATATGAAGAAAAATAGATCTT
1 AGACCATCAAGGTTAGTTATGATTGAATAGTTATTTATTCATTGATATGAAGAAAAATAGATCTT
*
2320995 CTACACTGATTTCTTGAGTTTAGGTGTG
66 CTACACTGATTGCTTGAGTTTAGGTGTG
2321023 GGACGTAGAT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (93 bp):
AGACCATCAAGGTTAGTTATGATTGAATAGTTATTTATTCATTGATATGAAGAAAAATAGATCTT
CTACACTGATTGCTTGAGTTTAGGTGTG
Found at i:2326348 original size:21 final size:21
Alignment explanation
Indices: 2326311--2326350 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2326301 GAGGATGAGA
*
2326311 AAGATGAAGCAGGAGATGATC
1 AAGATGAAGCAGCAGATGATC
2326332 AAGATGAAG-ATGCAGATGA
1 AAGATGAAGCA-GCAGATGA
2326351 GGAGGATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.45, C:0.07, G:0.33, T:0.15
Consensus pattern (21 bp):
AAGATGAAGCAGCAGATGATC
Found at i:2326444 original size:15 final size:15
Alignment explanation
Indices: 2326424--2326458 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2326414 TGCCAGTGGA
2326424 GACGAGGATGACGAC
1 GACGAGGATGACGAC
*
2326439 GACGAGGATGATGAC
1 GACGAGGATGACGAC
2326454 GACGA
1 GACGA
2326459 TGACGACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.40, T:0.09
Consensus pattern (15 bp):
GACGAGGATGACGAC
Found at i:2326462 original size:9 final size:9
Alignment explanation
Indices: 2326424--2326470 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
2326414 TGCCAGTGGA
*
2326424 GACGAGGAT
1 GACGACGAT
*
2326433 GACGACGAC
1 GACGACGAT
* *
2326442 GAGGATGAT
1 GACGACGAT
2326451 GACGACGAT
1 GACGACGAT
2326460 GACGACGAT
1 GACGACGAT
2326469 GA
1 GA
2326471 TGGTGAGGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.38, T:0.11
Consensus pattern (9 bp):
GACGACGAT
Found at i:2326487 original size:9 final size:9
Alignment explanation
Indices: 2326478--2326524 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
2326468 TGATGGTGAG
*
2326478 GAAGAGGAG
1 GAAGAGGAA
*
2326487 GAAGAAGAA
1 GAAGAGGAA
2326496 GAAGAGGAA
1 GAAGAGGAA
* *
2326505 GACGAGGAT
1 GAAGAGGAA
2326514 GAAGAGGAA
1 GAAGAGGAA
2326523 GA
1 GA
2326525 GCTTCAGCCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.51, C:0.02, G:0.45, T:0.02
Consensus pattern (9 bp):
GAAGAGGAA
Found at i:2326511 original size:24 final size:24
Alignment explanation
Indices: 2326475--2326525 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2326465 CGATGATGGT
*
2326475 GAGGAAGAGGAGGAAGAAGAAGAA
1 GAGGAAGACGAGGAAGAAGAAGAA
* *
2326499 GAGGAAGACGAGGATGAAGAGGAA
1 GAGGAAGACGAGGAAGAAGAAGAA
2326523 GAG
1 GAG
2326526 CTTCAGCCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02
Consensus pattern (24 bp):
GAGGAAGACGAGGAAGAAGAAGAA
Found at i:2331392 original size:30 final size:30
Alignment explanation
Indices: 2331356--2331415 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2331346 TCAACTGGTT
2331356 ATCCTGAATAACTATAGAGTTAAAACATCA
1 ATCCTGAATAACTATAGAGTTAAAACATCA
2331386 ATCCTGAATAACTATAGAGTTAAAACATCA
1 ATCCTGAATAACTATAGAGTTAAAACATCA
2331416 TTTGCAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (30 bp):
ATCCTGAATAACTATAGAGTTAAAACATCA
Found at i:2332091 original size:21 final size:21
Alignment explanation
Indices: 2332065--2332106 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2332055 CTCACAAATG
2332065 ATTGTTAACAAACAGGGTTGT
1 ATTGTTAACAAACAGGGTTGT
2332086 ATTGTTAACAAACAGGGTTGT
1 ATTGTTAACAAACAGGGTTGT
2332107 TCACTTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
ATTGTTAACAAACAGGGTTGT
Found at i:2335287 original size:20 final size:20
Alignment explanation
Indices: 2335264--2335303 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2335254 AAGTATTTCA
*
2335264 ATTAAATTCATGTTATTAAC
1 ATTAAATTCATATTATTAAC
* *
2335284 ATTAATTTTATATTATTAAC
1 ATTAAATTCATATTATTAAC
2335304 TCAGTTTTTT
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:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTAAATTCATATTATTAAC
Found at i:2338529 original size:11 final size:12
Alignment explanation
Indices: 2338507--2338539 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2338497 CATGAATTTG
2338507 ATTTATAAAATT
1 ATTTATAAAATT
2338519 ATTTA-AAAATT
1 ATTTATAAAATT
*
2338530 ATTTTTAAAA
1 ATTTATAAAA
2338540 ATAATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTATAAAATT
Found at i:2339700 original size:2 final size:2
Alignment explanation
Indices: 2339695--2339757 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
2339685 CCCCTTTTTT
2339695 TC TC TC TC TC 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 TC
2339737 TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC T
2339758 AACAGATCGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2362693 original size:16 final size:16
Alignment explanation
Indices: 2362669--2362706 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2362659 TTTTAAAATA
*
2362669 CTTTTAAAATATTTTT
1 CTTTAAAAATATTTTT
2362685 CTTTAAAAATATTTTT
1 CTTTAAAAATATTTTT
*
2362701 ATTTAA
1 CTTTAA
2362707 TTTTTTTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
CTTTAAAAATATTTTT
Found at i:2371455 original size:43 final size:42
Alignment explanation
Indices: 2371369--2371524 Score: 197
Period size: 43 Copynumber: 3.7 Consensus size: 42
2371359 CCGAGATTAT
* *
2371369 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGAATTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGTGATTTC
* *
2371411 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGTGATTTC
** * *
2371454 GTGTAAGACCATGGCTGGGATATTGGCATCGATACAGT-ATTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATA-TGTGATTTC
*
2371497 ATGTAAGACCATATCTGGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
2371525 TGTTACGATA
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
42 26 0.26
43 73 0.72
44 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGTGATTTC
Found at i:2371514 original size:86 final size:84
Alignment explanation
Indices: 2371369--2371524 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 84
2371359 CCGAGATTAT
* * * *
2371369 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGAATTCGTGTAAGACCATGTCTGGGACAT
1 GTGTAAGACCATAGCTGGGATATGGCATCGATATCAGAATTCATGTAAGACCATATCTGGGACA-
2371434 TGGCATCGATATGTGATTTC
65 TGGCATCGATATGTGATTTC
* * *
2371454 GTGTAAGACCATGGCTGGGATATTGGCATCGATA-CAGTATTACATGTAAGACCATATCTGGGAT
1 GTGTAAGACCATAGCTGGGATA-TGGCATCGATATCAGAATT-CATGTAAGACCATATCTGGGAC
2371518 ATGGCAT
64 ATGGCAT
2371525 TGTTACGATA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
85 31 0.50
86 31 0.50
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCATAGCTGGGATATGGCATCGATATCAGAATTCATGTAAGACCATATCTGGGACAT
GGCATCGATATGTGATTTC
Found at i:2391256 original size:14 final size:15
Alignment explanation
Indices: 2391234--2391310 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
2391224 CAATCAAACA
2391234 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
2391248 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
2391263 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
2391283 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
2391297 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
2391311 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:2391275 original size:20 final size:20
Alignment explanation
Indices: 2391250--2391289 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2391240 AATATTTTCC
*
2391250 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2391270 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2391290 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2391295 original size:34 final size:35
Alignment explanation
Indices: 2391238--2391304 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2391228 CAAACACCAG
*
2391238 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2391273 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2391305 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2403952 original size:27 final size:27
Alignment explanation
Indices: 2403914--2403965 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2403904 GGCTAATCAC
2403914 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
2403941 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
2403966 GACTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:2404830 original size:27 final size:27
Alignment explanation
Indices: 2404789--2404840 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2404779 CATTTTAGTC
2404789 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
2404816 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
2404841 GTGATTGGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.33, G:0.23, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:2404848 original size:27 final size:27
Alignment explanation
Indices: 2404791--2404849 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
2404781 TTTTAGTCCT
*
2404791 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * *
2404818 TTGGCACCTTTGGTGCCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
2404845 TTGGC
1 TTGGC
2404850 CTGATTAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.27, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:2404929 original size:26 final size:28
Alignment explanation
Indices: 2404900--2404960 Score: 108
Period size: 26 Copynumber: 2.2 Consensus size: 28
2404890 GTTTTTTTGT
2404900 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
2404926 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
2404954 ATATTTT
1 ATATTTT
2404961 AGTTATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 14 0.42
27 7 0.21
28 12 0.36
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:2405038 original size:4 final size:4
Alignment explanation
Indices: 2405029--2405067 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
2405019 AAGATATATC
*
2405029 ATGT ATGT ATGT AAGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
2405068 AGTAATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:2409957 original size:25 final size:25
Alignment explanation
Indices: 2409927--2409978 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
2409917 TTTTTTCTTT
* *
2409927 TAAAAATATTTAAAATTATTAATATA
1 TAAAAA-ATTTAAAAATATTAAAATA
2409953 TAAAAAATTTAAAAATATTAAAATA
1 TAAAAAATTTAAAAATATTAAAATA
2409978 T
1 T
2409979 TAATATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAAAATTTAAAAATATTAAAATA
Found at i:2409968 original size:8 final size:9
Alignment explanation
Indices: 2409926--2409981 Score: 55
Period size: 8 Copynumber: 6.4 Consensus size: 9
2409916 ATTTTTTCTT
2409926 TTAAAAATA
1 TTAAAAATA
*
2409935 TTTAAAATTA
1 -TTAAAAATA
*
2409945 TT-AATATA
1 TTAAAAATA
*
2409953 TAAAAAAT-
1 TTAAAAATA
2409961 TTAAAAATA
1 TTAAAAATA
2409970 TT-AAAATA
1 TTAAAAATA
2409978 TTAA
1 TTAA
2409982 TATAAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
8 20 0.54
9 9 0.24
10 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTAAAAATA
Found at i:2409989 original size:13 final size:14
Alignment explanation
Indices: 2409966--2409997 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2409956 AAAATTTAAA
2409966 AATATTAAAATATT
1 AATATTAAAATATT
2409980 AATA-TAAAATATT
1 AATATTAAAATATT
2409993 -ATATT
1 AATATT
2409998 TTCATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATTAAAATATT
Found at i:2410087 original size:13 final size:14
Alignment explanation
Indices: 2410071--2410112 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
2410061 TTTTAATTTT
2410071 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
2410084 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
2410099 ATTTTAAATAATAT
1 ATTTT-AATAATAT
2410113 TCTTTACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:2410097 original size:16 final size:16
Alignment explanation
Indices: 2410075--2410111 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2410065 AATTTTATTT
2410075 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
2410092 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
2410107 TAATA
1 TAATA
2410112 TTCTTTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:2449420 original size:16 final size:16
Alignment explanation
Indices: 2449397--2449430 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2449387 TACCTATTGG
2449397 AATTTTTTT-ATTTAT
1 AATTTTTTTAATTTAT
*
2449412 AATTTTTTTAATTTTT
1 AATTTTTTTAATTTAT
2449428 AAT
1 AAT
2449431 GATTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
AATTTTTTTAATTTAT
Found at i:2463906 original size:82 final size:81
Alignment explanation
Indices: 2463762--2463914 Score: 202
Period size: 82 Copynumber: 1.9 Consensus size: 81
2463752 GCAGCTTGCT
* * *
2463762 TACTGATTCCTACATGTTAGCAAGGTTTGGCATGACGTTGTCTACCATAAGAATTGGATTACCTT
1 TACTGATTCCTACATGTTAGCAAGGTTTGGCATGACATAG-CTACCATAAGAATTAGATTACCTT
2463827 GAAATCGCCCTCTTGTG
65 GAAATCGCCCTCTTGTG
* **
2463844 TACTGATTCCTACATGTTAGCTAGGTTTGGCATGACATAG-TACTGTGACA-AATTAGATTTACC
1 TACTGATTCCTACATGTTAGCAAGGTTTGGCATGACATAGCTACCAT-A-AGAATTAGA-TTACC
2463907 TTGAAATC
63 TTGAAATC
2463915 AGTCCAAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
80 4 0.06
81 7 0.11
82 51 0.82
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (81 bp):
TACTGATTCCTACATGTTAGCAAGGTTTGGCATGACATAGCTACCATAAGAATTAGATTACCTTG
AAATCGCCCTCTTGTG
Done.