Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 14 of 427
Found at i:3843478 original size:8 final size:8
Alignment explanation
Indices: 3843465--3843489 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3843455 TTAAAATCTT
3843465 AGACATTA
1 AGACATTA
3843473 AGACATTA
1 AGACATTA
3843481 AGACATTA
1 AGACATTA
3843489 A
1 A
3843490 TTAATCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (8 bp):
AGACATTA
Found at i:3849757 original size:51 final size:51
Alignment explanation
Indices: 3849701--3849873 Score: 148
Period size: 51 Copynumber: 3.2 Consensus size: 51
3849691 TGGCAACCAG
3849701 GAAAACATTTTCCGGAAAATGTTTTCCTGGTTTTACGTTGTTTGGTAACCT
1 GAAAACATTTTCCGGAAAATGTTTTCCTGGTTTTACGTTGTTTGGTAACCT
* ** * * * ** * * * *
3849752 GAAAACATTTTCAGGAACACGGGTAAAATTGCTTGCTTTTTGGCTCCGTTTAGCAACCAG
1 GAAAACATTTTCCGGAA-A-ATGT----TTTCCTGGTTTTACG-T-TGTTTGGTAACC-T
*
3849812 GAAAACATTTTCCGGAAAATGTTTTCCTAGTTTTACGTTGTTTGGTAACCT
1 GAAAACATTTTCCGGAAAATGTTTTCCTGGTTTTACGTTGTTTGGTAACCT
3849863 GAAAACATTTT
1 GAAAACATTTT
3849874 ACCTACGGAA
Statistics
Matches: 88, Mismatches: 25, Indels: 18
0.67 0.19 0.14
Matches are distributed among these distances:
51 27 0.31
52 10 0.11
53 3 0.03
54 9 0.10
57 10 0.11
58 3 0.03
59 10 0.11
60 16 0.18
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (51 bp):
GAAAACATTTTCCGGAAAATGTTTTCCTGGTTTTACGTTGTTTGGTAACCT
Found at i:3851032 original size:15 final size:14
Alignment explanation
Indices: 3851007--3851066 Score: 84
Period size: 14 Copynumber: 4.2 Consensus size: 14
3850997 AGTAAATCAA
3851007 TTTCCAGAAATTAT
1 TTTCCAGAAATTAT
3851021 TTTCCAAGAAATTAT
1 TTTCC-AGAAATTAT
*
3851036 TTTCCAGAAATCAT
1 TTTCCAGAAATTAT
* *
3851050 TTTCCAAAAAATAT
1 TTTCCAGAAATTAT
3851064 TTT
1 TTT
3851067 ACCTGCAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 27 0.66
15 14 0.34
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (14 bp):
TTTCCAGAAATTAT
Found at i:3851042 original size:29 final size:28
Alignment explanation
Indices: 3851007--3851066 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
3850997 AGTAAATCAA
* *
3851007 TTTCCAGAAATTATTTTCCAAGAAATTAT
1 TTTCCAGAAATCATTTTCCAA-AAAATAT
3851036 TTTCCAGAAATCATTTTCCAAAAAATAT
1 TTTCCAGAAATCATTTTCCAAAAAATAT
3851064 TTT
1 TTT
3851067 ACCTGCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (28 bp):
TTTCCAGAAATCATTTTCCAAAAAATAT
Found at i:3851221 original size:3 final size:3
Alignment explanation
Indices: 3851213--3851257 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3851203 TGTATTTCCA
3851213 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3851258 TTTAAGGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3851964 original size:3 final size:3
Alignment explanation
Indices: 3851956--3851986 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3851946 AAATTGGTCT
3851956 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3851987 AGCTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3863505 original size:9 final size:9
Alignment explanation
Indices: 3863491--3863517 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3863481 CACACACTAA
3863491 TAATAATAG
1 TAATAATAG
3863500 TAATAATAG
1 TAATAATAG
3863509 TAATAATAG
1 TAATAATAG
3863518 AAAGATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (9 bp):
TAATAATAG
Found at i:3863769 original size:21 final size:21
Alignment explanation
Indices: 3863744--3863792 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
3863734 TATATATCCG
* *
3863744 TAATATATAAAAACGTATATA
1 TAATATATAAAAACATATACA
*
3863765 TAATAT-T-AAAACATTTACA
1 TAATATATAAAAACATATACA
3863784 TAATATATA
1 TAATATATA
3863793 CACACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 15 0.65
20 2 0.09
21 6 0.26
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (21 bp):
TAATATATAAAAACATATACA
Found at i:3863890 original size:17 final size:18
Alignment explanation
Indices: 3863868--3863901 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3863858 ATATACCTAC
*
3863868 ATATATATATAC-TAAAG
1 ATATATACATACATAAAG
3863885 ATATATACATACATAAA
1 ATATATACATACATAAA
3863902 ACATATACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATATACATACATAAAG
Found at i:3863907 original size:19 final size:17
Alignment explanation
Indices: 3863866--3863908 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
3863856 ATATATACCT
*
3863866 ACATATATATATACTAA
1 ACATATATACATACTAA
*
3863883 AGATATATACATACATAAA
1 ACATATATACATAC-T-AA
3863902 ACATATA
1 ACATATA
3863909 CTAAGATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 12 0.57
18 1 0.05
19 8 0.38
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (17 bp):
ACATATATACATACTAA
Found at i:3863915 original size:29 final size:29
Alignment explanation
Indices: 3863856--3863912 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
3863846 TATTACATAA
* * *
3863856 ATATATACCTACATATATATATACTAAAG
1 ATATATACATACATAAACATATACTAAAG
3863885 ATATATACATACATAAAACATATACTAA
1 ATATATACATACAT-AAACATATACTAA
3863913 GATTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.32
Consensus pattern (29 bp):
ATATATACATACATAAACATATACTAAAG
Found at i:3864188 original size:26 final size:25
Alignment explanation
Indices: 3864140--3864194 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
3864130 AAATATGCAT
**
3864140 ACAATATTATAAAATATTTATAACTA
1 ACAATATTATAAAATATACATAAC-A
3864166 ACAATATTA-AAATATATACATAACA
1 ACAATATTATAAA-ATATACATAACA
3864191 ACAA
1 ACAA
3864195 AAGTATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (25 bp):
ACAATATTATAAAATATACATAACA
Found at i:3864476 original size:25 final size:25
Alignment explanation
Indices: 3864440--3864492 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3864430 TAAGAGGAAT
*
3864440 AATAAAAAAACAATAATAATATAAA
1 AATAAAAAAACAAAAATAATATAAA
* * *
3864465 AATAAAATAACAAAAATGATATGAA
1 AATAAAAAAACAAAAATAATATAAA
3864490 AAT
1 AAT
3864493 GAACTTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (25 bp):
AATAAAAAAACAAAAATAATATAAA
Found at i:3869413 original size:22 final size:22
Alignment explanation
Indices: 3869388--3869431 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3869378 ATGTATAGGA
3869388 CTAATTTGCTCATTTTTTTAGT
1 CTAATTTGCTCATTTTTTTAGT
3869410 CTAATTTGCTCATTTTTTTAGT
1 CTAATTTGCTCATTTTTTTAGT
3869432 AAAGGGGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.59
Consensus pattern (22 bp):
CTAATTTGCTCATTTTTTTAGT
Found at i:3872954 original size:16 final size:16
Alignment explanation
Indices: 3872930--3872967 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
3872920 GAAAATAAAA
*
3872930 TTATTGGTTTATTTAT
1 TTATGGGTTTATTTAT
3872946 TTATGGGTTTATTTAT
1 TTATGGGTTTATTTAT
3872962 TTATGG
1 TTATGG
3872968 ATTAGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (16 bp):
TTATGGGTTTATTTAT
Found at i:3880610 original size:18 final size:18
Alignment explanation
Indices: 3880587--3880622 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3880577 AACATGTATG
3880587 CGTCGCGGGGCTAGAACA
1 CGTCGCGGGGCTAGAACA
3880605 CGTCGCGGGGCTAGAACA
1 CGTCGCGGGGCTAGAACA
3880623 TGCGTGTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.39, T:0.11
Consensus pattern (18 bp):
CGTCGCGGGGCTAGAACA
Found at i:3887390 original size:215 final size:215
Alignment explanation
Indices: 3886873--3887438 Score: 703
Period size: 217 Copynumber: 2.6 Consensus size: 215
3886863 AACTTGTAAG
* *
3886873 TTACGACCAGAAACTTTAGGCCTCAGATTTGTAAG-TTTTAATCTCATCAGACTGAAGGTCTGAC
1 TTACGACCAGCAACTTTAGGCCTCAGATTTGT-AGTTTTTATTCTCATCAGACTGAAGGTCTGAC
* * * * *
3886937 AATGTAGGCAATTATTAATCATCATAAGCCTCTAAAAGCATAGATTAATTAATAATTACATCATT
65 AATGTAGGCAATTCTTAATCATCATAAGCCTCAAAAAGCATAGATT-CTTACTAATTACATCACT
* * * * * *
3887002 CAAAACAAAGCTATATACAGACTACATGCATGTTTTAATGTAGGGAGAAAATGAAATTGGTTGGT
129 C-AAACAAAGCAATACACAGACTACATACATG-TATAATGAAGGGAGAAAATGAAATTGGTTGAT
* * *
3887067 CCACCATCACAAATAAGTCTTAAG
192 CCACCAACAAAAATAAGTCTTAAA
* * * * * *
3887091 TTATGACCGGCAACTTTAGGCCTCAGATTTGCA-TTTCTATTTTCATCAGACTAAAGGTCTGACA
1 TTACGACCAGCAACTTTAGGCCTCAGATTTGTAGTTTTTATTCTCATCAGACTGAAGGTCTGACA
*
3887155 ATGTAGGCAATTCTTAATCATCATAAGCCTCAAAAAGCATAGGTTCTTCACTAATTACATCACTC
66 ATGTAGGCAATTCTTAATCATCATAAGCCTCAAAAAGCATAGATTCTT-ACTAATTACATCACTC
*
3887220 AAACAAAGCAATACACAGAGTACATACATG-AT-AT-AAGGG-GAAAATGAAATTGGTTGATCCA
130 AAACAAAGCAATACACAGACTACATACATGTATAATGAAGGGAGAAAATGAAATTGGTTGATCCA
*
3887281 CCAACAAAAAATAAGTTTTTTAAA
195 CCAAC-AAAAATAAG--TCTTAAA
*** * * *
3887305 TTACGACCATTGACTTTAGGCCTCAGATTTGTAGTTTTTGTTGTCTTCAGACTGAAGGTCTGACA
1 TTACGACCAGCAACTTTAGGCCTCAGATTTGTAGTTTTTATTCTCATCAGACTGAAGGTCTGACA
* *
3887370 ATGTAGGCAATTCTTAATCATCATAAGCCTCTAAAAAGAATAGATTCTTTACAAATTACATCACT
66 ATGTAGGCAATTCTTAATCATCATAAGCCTC-AAAAAGCATAGATTC-TTACTAATTACATCACT
3887435 CAAA
129 CAAA
3887439 ACAATGATAT
Statistics
Matches: 301, Mismatches: 39, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
211 25 0.08
212 12 0.04
213 2 0.01
214 33 0.11
215 57 0.19
216 59 0.20
217 85 0.28
218 28 0.09
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (215 bp):
TTACGACCAGCAACTTTAGGCCTCAGATTTGTAGTTTTTATTCTCATCAGACTGAAGGTCTGACA
ATGTAGGCAATTCTTAATCATCATAAGCCTCAAAAAGCATAGATTCTTACTAATTACATCACTCA
AACAAAGCAATACACAGACTACATACATGTATAATGAAGGGAGAAAATGAAATTGGTTGATCCAC
CAACAAAAATAAGTCTTAAA
Found at i:3890206 original size:11 final size:11
Alignment explanation
Indices: 3890175--3890213 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
3890165 ACTATTTTCC
3890175 TATTATTTTAT
1 TATTATTTTAT
3890186 TATTA-TTTAT
1 TATTATTTTAT
3890196 TATTATTTTAT
1 TATTATTTTAT
*
3890207 TGTTATT
1 TATTATT
3890214 GTTTAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:3892440 original size:74 final size:74
Alignment explanation
Indices: 3892348--3892485 Score: 213
Period size: 74 Copynumber: 1.9 Consensus size: 74
3892338 TAAATCATTT
* * * *
3892348 ATGCCACCAGTATATTTGTTATCAAATGATCATTCATTTAAGTAGTATATTATCTTACTTTATAC
1 ATGCCACCAATATATTTGTTACCAAATGATCATTCATGTAAATAGTATATTATCTTACTTTATAC
3892413 CGGTCAACC
66 CGGTCAACC
* * *
3892422 ATGCCATCAATATATTTGTTACCAAGTGATCATTCATGTAAATAGTATATTATCTTGCTTTATA
1 ATGCCACCAATATATTTGTTACCAAATGATCATTCATGTAAATAGTATATTATCTTACTTTATA
3892486 TCGGGTAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 57 1.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (74 bp):
ATGCCACCAATATATTTGTTACCAAATGATCATTCATGTAAATAGTATATTATCTTACTTTATAC
CGGTCAACC
Found at i:3894511 original size:19 final size:19
Alignment explanation
Indices: 3894487--3894532 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3894477 GAACATCCAG
3894487 TCACACAAAGTGAGTGAGC
1 TCACACAAAGTGAGTGAGC
3894506 TCACACAAAGTGAGTGAGC
1 TCACACAAAGTGAGTGAGC
*
3894525 GCACACAA
1 TCACACAA
3894533 TCCTCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.13
Consensus pattern (19 bp):
TCACACAAAGTGAGTGAGC
Found at i:3903931 original size:21 final size:21
Alignment explanation
Indices: 3903916--3903958 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3903906 TCTTTTTATT
3903916 GTTCTTTTGTTACTTTTTTCA
1 GTTCTTTTGTTACTTTTTTCA
*
3903937 GTTCTTTTGTTGCTTTTTTCA
1 GTTCTTTTGTTACTTTTTTCA
3903958 G
1 G
3903959 CATAAATTGC
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:0.07, C:0.14, G:0.14, T:0.65
Consensus pattern (21 bp):
GTTCTTTTGTTACTTTTTTCA
Found at i:3909703 original size:230 final size:234
Alignment explanation
Indices: 3909234--3909745 Score: 616
Period size: 230 Copynumber: 2.2 Consensus size: 234
3909224 ACTCTTGCTC
* * *
3909234 AATTTTTCATCAATAATTTAACAGCAAAATTATAAAATAAGAAAAAAAAATTAACTTGGCAGACA
1 AATTTTTCATCAATAATTTAACAGCAAAATTATAAAACAAGAAAAAAAAATGAACTTGACAGACA
* * *
3909299 AGAACTTGATTATATATCATGCAAACAGAAGATTAGATTAAAACAAGAGATTTAACTGCCTCAAA
66 AGAACTTGATTATATATCATGCAAACACAAGATTAGATTAAAACAAGAGATTAAACTACCTCAAA
** * *
3909364 GTCATCTAATTTCATCTAACACTACAAGTTTAAAGCAGTGACCAACATAAAACAATATAACAAAG
131 GTCATCTAATTTCATAAAACACTACAAGTTTAAAGCAGTGACCAACATAAAACAACATAACAAAA
* *
3909429 AATTCTCAACAACTATTAATCTTTTCTTCTCCCTGATCA
196 AATTCTCAACAACTATTAATCTTCTCTTCTCACTGATCA
* * * *
3909468 AA-TTTTCATCAATAATTTAACATCAAGATTAT-CAACAA-AAAAAAAAA-GAACTTTACA-A-A
1 AATTTTTCATCAATAATTTAACAGCAAAATTATAAAACAAGAAAAAAAAATGAACTTGACAGACA
* *
3909527 TAGAACTTGATTATTTGATCATGCAAACACAAGATTCAG-TTAAAACAATAGATTAAA-TCACCT
66 -AGAACTTGATTATAT-ATCATGCAAACACAAGATT-AGATTAAAACAAGAGATTAAACT-ACCT
* *
3909590 CAAAGTCA-CTTAATTTCATAAAACACTACGAGTTTAAAGCAGTGATCC-ACATGAAACAACATA
127 CAAAGTCATC-TAATTTCATAAAACACTACAAGTTTAAAGCAGTGA-CCAACATAAAACAACATA
* * * *
3909653 ACTAAAAAAATT-TCAACAATTATTCATCTTCTCTTTTTACTGAT-A
190 AC--AAAAAATTCTCAACAACTATTAATCTTCTCTTCTCACTGATCA
* * * *
3909698 AATTTTTCATTAATAATTTAACAGCAAAATTATTAAATAAGGAAAAAA
1 AATTTTTCATCAATAATTTAACAGCAAAATTATAAAACAAGAAAAAAA
3909746 TTCACTTGAC
Statistics
Matches: 237, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
228 1 0.00
229 17 0.07
230 102 0.43
231 66 0.28
232 15 0.06
233 34 0.14
234 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (234 bp):
AATTTTTCATCAATAATTTAACAGCAAAATTATAAAACAAGAAAAAAAAATGAACTTGACAGACA
AGAACTTGATTATATATCATGCAAACACAAGATTAGATTAAAACAAGAGATTAAACTACCTCAAA
GTCATCTAATTTCATAAAACACTACAAGTTTAAAGCAGTGACCAACATAAAACAACATAACAAAA
AATTCTCAACAACTATTAATCTTCTCTTCTCACTGATCA
Found at i:3910148 original size:443 final size:439
Alignment explanation
Indices: 3909334--3910148 Score: 984
Period size: 443 Copynumber: 1.8 Consensus size: 439
3909324 CAGAAGATTA
*
3909334 GATTAAAACAAGAGATTTAACTGCCTCAAAGTCATCTAATTTCATCTAACACTACAAGTTTAAAG
1 GATTAAAACAAGAGATTAAACTGCCTCAAAGTCATCTAATTTCATCTAACACTACAAGTTTAAAG
* *
3909399 CAGTGACCAACATAAAACAATATAACAAAGAATTCTCAACAACTATTAATCTTTTCTTCTCCCTG
66 CAGTGACCAACATAAAACAACATAACAAAGAATTCTCAACAACTATTAATCTTTTCTTCTCCCTA
** * *
3909464 ATCAAATTTTCATCAATAATTTAACATCAAGATTATCAACAAAAAAAAAAAGAACTTTACAAATA
131 ATCAAATTTTCATCAATAATAGAACATCAAGATTATCAACAAAAAAAAAAAGAACTTGACAAACA
* * * * * *
3909529 GAACTTGATTATTTGATCATGCAAACACAAGATTCAGTTAAAACAATAGATTAAATCACCTCAAA
196 AAACTCGATTATATGATCATGCAAACACAACATTCAGTCAAAACAAGAGATTAAATCACCTCAAA
* *
3909594 GTCACTTAATTTCATAAAACACTACGAGTTTAAAGCAGTGATCCACATGAAACAACATAACTAAA
261 GTCACTTAATTTCATAAAACACTACGAATTTAAAGCAGTGATCCACATGAAACAACAGAACTAAA
* *
3909659 AAAATTTCAACAATTATTCATCTTCTCTTTTTACTGATAAATTTTTCATTAATAATTTAACAGCA
326 AAAATTTCAACAATTATTCATCTTCTCATTTTACTAATAAATTTTTCATTAATAATTTAACAGCA
3909724 AAATTATTAAATAAGGAAAAAATTCACTTGACAAACAAAACTTGGGTTC
391 AAATTATTAAATAAGGAAAAAATTCACTTGACAAACAAAACTTGGGTTC
* * *
3909773 GATTAAAATAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAA-TTTAAA
1 GATTAAAACAAGAGATTAAACTGCCTCAAAGTCATCTAATTTCATCTAACACTAC-AAGTTTAAA
* * * * ** * * * *
3909837 GCAGTGATCAGCATGAAACAACGTAGTTAAAGAATTTTCTACAATTATTAATCTTTTCATT-TTC
65 GCAGTGACCAACATAAAACAACATA-ACAAAGAATTCTCAACAACTATTAATCTTTTC-TTCTCC
* ** ***
3909901 CTAATCAATTTTTTTTCCAATAATAGAACCA-CAA-ATTTATCAA-ATAAGGGGAAAAAGAACAT
128 CTAATCAAATTTTCAT-CAATAATAGAA-CATCAAGA-TTATCAACA-AA-AAAAAAAAGAAC-T
3909963 TGACAAACAAAACTCGATTATATGATCATGCAAACACAACATT-AGATCAAAACAAGAGATTAAA
187 TGACAAACAAAACTCGATTATATGATCATGCAAACACAACATTCAG-TCAAAACAAGAGATTAAA
** ** * * * *
3910027 TTGCCTCAAAGTCA-TCTAATTTCATCTAGCACTTCTAATTTAAAGCGGTGAT-CAGCATGAAAC
251 TCACCTCAAAGTCACT-TAATTTCATAAAACACTACGAATTTAAAGCAGTGATCCA-CATGAAAC
* * * * * *
3910090 AACGGAATTAAAGAATTTTCTAA-AATTATTCATCTT-TCATTTTCCTAATCATATTTTTC
314 AACAGAACTAAAAAAATTTC-AACAATTATTCATCTTCTCATTTTACTAAT-AAATTTTTC
3910149 CAATAATAGA
Statistics
Matches: 312, Mismatches: 50, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
439 77 0.25
440 45 0.14
441 23 0.07
442 26 0.08
443 139 0.45
444 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (439 bp):
GATTAAAACAAGAGATTAAACTGCCTCAAAGTCATCTAATTTCATCTAACACTACAAGTTTAAAG
CAGTGACCAACATAAAACAACATAACAAAGAATTCTCAACAACTATTAATCTTTTCTTCTCCCTA
ATCAAATTTTCATCAATAATAGAACATCAAGATTATCAACAAAAAAAAAAAGAACTTGACAAACA
AAACTCGATTATATGATCATGCAAACACAACATTCAGTCAAAACAAGAGATTAAATCACCTCAAA
GTCACTTAATTTCATAAAACACTACGAATTTAAAGCAGTGATCCACATGAAACAACAGAACTAAA
AAAATTTCAACAATTATTCATCTTCTCATTTTACTAATAAATTTTTCATTAATAATTTAACAGCA
AAATTATTAAATAAGGAAAAAATTCACTTGACAAACAAAACTTGGGTTC
Found at i:3910330 original size:229 final size:234
Alignment explanation
Indices: 3909770--3910279 Score: 780
Period size: 234 Copynumber: 2.2 Consensus size: 234
3909760 AAAACTTGGG
*
3909770 TTCGATTAAAATAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTA
1 TTCGATTAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTA
* *
3909835 AAGCAGTGATCAGCATGAAACAACGTAGTTAAAGAATTTTCTACAATTATTAATCTTTTCATTTT
66 AAGCAGTGATCAGCATGAAACAACGTAATTAAAGAATTTTCTAAAATTATTAATCTTTTCATTTT
* *
3909900 CCTAATCAATTTTTTTTCCAATAATAGAACCACAAATTTATCAAATAAGGGGAAAAAGAACATTG
131 CCTAATCAATTATTTTTCCAATAATAGAACCACAAACTTATCAAATAAGGGGAAAAAGAACATTG
*
3909965 ACAAACAAAACTCGATTATATGATCATGCAAACACAACA
196 ACAAACAAAACTCGATTATATGATCATGCAAACAAAACA
* * *
3910004 TTAGATCAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTTCTAATTTA
1 TTCGATTAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTA
* * *
3910069 AAGCGGTGATCAGCATGAAACAACGGAATTAAAGAATTTTCTAAAATTATTCATC-TTTCATTTT
66 AAGCAGTGATCAGCATGAAACAACGTAATTAAAGAATTTTCTAAAATTATTAATCTTTTCATTTT
** *
3910133 CCTAATC-A-TATTTTTCCAATAATAGAA-CATCAAACTTATCAAATAAGGGG-GGAA-AACTTT
131 CCTAATCAATTATTTTTCCAATAATAGAACCA-CAAACTTATCAAATAAGGGGAAAAAGAACATT
* *
3910193 GACAAACAAAACTCTATTATATGATCATGCAAACAAAAGA
195 GACAAACAAAACTCGATTATATGATCATGCAAACAAAACA
* * * *
3910233 TTCGATTAAAACAAAAGATTATACTGCCTCAAATTCATCTAATTTCA
1 TTCGATTAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCA
3910280 GCAAACACAA
Statistics
Matches: 252, Mismatches: 23, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
229 83 0.33
230 4 0.02
231 37 0.15
232 1 0.00
233 16 0.06
234 111 0.44
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (234 bp):
TTCGATTAAAACAAGAGATTAAATTGCCTCAAAGTCATCTAATTTCATCTAGCACTACTAATTTA
AAGCAGTGATCAGCATGAAACAACGTAATTAAAGAATTTTCTAAAATTATTAATCTTTTCATTTT
CCTAATCAATTATTTTTCCAATAATAGAACCACAAACTTATCAAATAAGGGGAAAAAGAACATTG
ACAAACAAAACTCGATTATATGATCATGCAAACAAAACA
Found at i:3910677 original size:11 final size:11
Alignment explanation
Indices: 3910663--3910695 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3910653 ATTAAAAGGC
3910663 AAAAA-AAAGA
1 AAAAATAAAGA
3910673 AAAAATAAAGA
1 AAAAATAAAGA
*
3910684 GAAAATAAAGA
1 AAAAATAAAGA
3910695 A
1 A
3910696 GATCAGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (11 bp):
AAAAATAAAGA
Found at i:3913007 original size:13 final size:12
Alignment explanation
Indices: 3912985--3913021 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3912975 TTAATTAAAT
3912985 TATTGT-AATAA
1 TATTGTAAATAA
3912996 TATTTGTAAATAA
1 TA-TTGTAAATAA
3913009 TATT-TAAATAA
1 TATTGTAAATAA
3913020 TA
1 TA
3913022 AAATATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.46
12 6 0.25
13 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (12 bp):
TATTGTAAATAA
Found at i:3936711 original size:3 final size:3
Alignment explanation
Indices: 3936703--3936738 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3936693 GTAGTTTACG
3936703 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3936739 TTTTGATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3937145 original size:21 final size:20
Alignment explanation
Indices: 3937119--3937167 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
3937109 TTACCATTTT
3937119 AATAGTGTTAT-ATATACATAA
1 AATAGTGTT-TCATATA-ATAA
*
3937140 AATAGTAATTTCATATAATAA
1 AATAGT-GTTTCATATAATAA
3937161 AATAGTG
1 AATAGTG
3937168 CAAATTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (20 bp):
AATAGTGTTTCATATAATAA
Found at i:3940023 original size:15 final size:17
Alignment explanation
Indices: 3939991--3940026 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
3939981 TTAAAAATCA
3939991 AAATAATTATTCAAATT
1 AAATAATTATTCAAATT
3940008 AAAT-ATTATT-AAATT
1 AAATAATTATTCAAATT
3940023 AAAT
1 AAAT
3940027 CTCAACTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 6 0.32
17 4 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATAATTATTCAAATT
Found at i:3943374 original size:21 final size:20
Alignment explanation
Indices: 3943331--3943374 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3943321 TTAAATCCAA
*
3943331 AAAAAAAAATTAAATTCATT
1 AAAAAAAAATTAAATTCACT
* *
3943351 AAAATAAAATGTAAATTGACT
1 AAAAAAAAAT-TAAATTCACT
3943372 AAA
1 AAA
3943375 TTCTAATTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAAAAAATTAAATTCACT
Found at i:3949987 original size:50 final size:52
Alignment explanation
Indices: 3949927--3950025 Score: 148
Period size: 50 Copynumber: 1.9 Consensus size: 52
3949917 AGATAATTTT
* *
3949927 ATTTCGGGTTTAGGTCAATTC-AGATCATTTGGA-TATGTCAGTTGGGTATC
1 ATTTCAGGTTTAGGTCAATTCAAGATCATTTGGAGTATCTCAGTTGGGTATC
* *
3949977 ATTTCAGGTTTAGGTCCATTCAAGATCATTTTGAGTATCTCAGTTGGGT
1 ATTTCAGGTTTAGGTCAATTCAAGATCATTTGGAGTATCTCAGTTGGGT
3950026 CATTTAAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 19 0.44
51 11 0.26
52 13 0.30
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.40
Consensus pattern (52 bp):
ATTTCAGGTTTAGGTCAATTCAAGATCATTTGGAGTATCTCAGTTGGGTATC
Found at i:3954651 original size:5 final size:5
Alignment explanation
Indices: 3954631--3954666 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
3954621 TGAATTAGGT
3954631 AAAAG AAAAAG CAAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAA
3954667 AAGTGCTGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 19 0.66
6 10 0.34
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3962914 original size:19 final size:20
Alignment explanation
Indices: 3962856--3962901 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3962846 CTTTAATGTG
* *
3962856 TGCATGCGTGTCTTCATTTT
1 TGCATGCATTTCTTCATTTT
3962876 TGCATGCATTTCTTCATTTT
1 TGCATGCATTTCTTCATTTT
3962896 TGCATG
1 TGCATG
3962902 TGTTTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (20 bp):
TGCATGCATTTCTTCATTTT
Found at i:3968519 original size:224 final size:218
Alignment explanation
Indices: 3968124--3968566 Score: 649
Period size: 224 Copynumber: 2.0 Consensus size: 218
3968114 GAACTGGTAA
*
3968124 TTATTTCTTAGAGACTGAAAAGTTTAATTCATTCTTTGCAGATTCTTCAAAATCAACTTCTGGAC
1 TTATTTCTTAGAGACTGAAAAGTTTAATTCATTCTTTGCAGAATCTTCAAAATCAACTTCTGGAC
* *
3968189 ATTTCAACAGAAAGGGATGAACTAAAGACACATATCGAGGAACTGACCAGCAAATTATCCTGCCT
66 ATTTCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACCAGCAAATTATCCTGCCT
** * *
3968254 CGGAAAGGAAAATCTTAAAAACGATTCTAATGAGGTGGTTGGTTATTTTTAAAAATGAC-TCTTT
131 CGGAAAGGAAAATCTTAAAAACGATTCTAATGACATGGTTGGTT-GTTTAAAAAATGACAT-TTT
*
3968318 TCTTGCTAGCAATCTAACTAGGTTGGGAAT
194 T-TT--T--CAATCTAACTAGGTTAGGAAT
* *
3968348 TTATTTCTTAGAGACTGAAAAGTTTATTTCATTCTTTGCAGAATCTT-AAAGATCAACTTCTGTA
1 TTATTTCTTAGAGACTGAAAAGTTTAATTCATTCTTTGCAGAATCTTCAAA-ATCAACTTCTGGA
* * *
3968412 CATTTCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACTAGCAGATTATCCTGCG
65 CATTTCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACCAGCAAATTATCCTGCC
* *
3968477 TC-GAAGCGGAAAATCTTAAAAATGATTCTAATGACATGGTTGGTTGTTTAAAAAATGACATTTT
130 TCGGAA-AGGAAAATCTTAAAAACGATTCTAATGACATGGTTGGTTGTTTAAAAAATGACATTTT
3968541 TTTTCAATCTAACTAGGTTAGGAAT
194 TTTTCAATCTAACTAGGTTAGGAAT
3968566 T
1 T
3968567 ATCTGATATC
Statistics
Matches: 201, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
218 21 0.10
220 1 0.00
222 2 0.01
223 22 0.11
224 155 0.77
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (218 bp):
TTATTTCTTAGAGACTGAAAAGTTTAATTCATTCTTTGCAGAATCTTCAAAATCAACTTCTGGAC
ATTTCAACAGAAAGGGATAAACTAAAGACACAAATCGAGGAACTGACCAGCAAATTATCCTGCCT
CGGAAAGGAAAATCTTAAAAACGATTCTAATGACATGGTTGGTTGTTTAAAAAATGACATTTTTT
TTCAATCTAACTAGGTTAGGAAT
Found at i:3973680 original size:2 final size:2
Alignment explanation
Indices: 3973673--3973701 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3973663 AATTGCCATC
3973673 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3973702 TGTCAAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3974128 original size:31 final size:30
Alignment explanation
Indices: 3974092--3974176 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
3974082 TTTGGAAGAT
3974092 CTAATTAAAAATTTTAAAACTTTTAGAAGGCA
1 CTAATTAAAAATTTTAAAACTTTTAG--GGCA
* * *
3974124 -TAATT-AAAATTTCTAAAAATCTTAGGGTA
1 CTAATTAAAAATTT-TAAAACTTTTAGGGCA
*
3974153 TCTAATTAAAACTTTTAAAACTTT
1 -CTAATTAAAAATTTTAAAACTTT
3974177 CAAACGGCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
29 3 0.07
30 7 0.16
31 27 0.63
32 6 0.14
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (30 bp):
CTAATTAAAAATTTTAAAACTTTTAGGGCA
Found at i:3977971 original size:49 final size:49
Alignment explanation
Indices: 3977899--3978002 Score: 199
Period size: 49 Copynumber: 2.1 Consensus size: 49
3977889 ATGGAGAATA
3977899 TTCTTTTGCAGATTATATTGTTTATTAATACTTTTTCACTTACCATCTC
1 TTCTTTTGCAGATTATATTGTTTATTAATACTTTTTCACTTACCATCTC
3977948 TTCTTTTGCAGATTATATTGTTTATTAATACTTTTTCACTTACCATCTC
1 TTCTTTTGCAGATTATATTGTTTATTAATACTTTTTCACTTACCATCTC
*
3977997 TGCTTT
1 TTCTTT
3978003 AAAGGATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.54
Consensus pattern (49 bp):
TTCTTTTGCAGATTATATTGTTTATTAATACTTTTTCACTTACCATCTC
Found at i:3978043 original size:29 final size:28
Alignment explanation
Indices: 3978007--3978065 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
3977997 TGCTTTAAAG
*
3978007 GATTAACTTAGTCACTCTTTTTTTTTTAT
1 GATTAACTTAGTCACTC-TCTTTTTTTAT
3978036 GATTAACTTAGTCACTCTCTTTTTTTAT
1 GATTAACTTAGTCACTCTCTTTTTTTAT
3978064 GA
1 GA
3978066 ATATATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.54
Consensus pattern (28 bp):
GATTAACTTAGTCACTCTCTTTTTTTAT
Found at i:3978661 original size:22 final size:23
Alignment explanation
Indices: 3978618--3978661 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
3978608 CATTTTTAAG
* *
3978618 TTTATAATATTTTATATTATTTT
1 TTTATAATATATTATATAATTTT
*
3978641 TTTAT-ATATATTATGTAATTT
1 TTTATAATATATTATATAATTT
3978662 AGGACACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTATAATATATTATATAATTTT
Found at i:3979609 original size:26 final size:26
Alignment explanation
Indices: 3979573--3979624 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
3979563 GACCTTGCCA
3979573 GCACTCCTAACTTCACTACTGAAGGG
1 GCACTCCTAACTTCACTACTGAAGGG
3979599 GCACTCCTAACTTCACTACTGAAGGG
1 GCACTCCTAACTTCACTACTGAAGGG
3979625 ATTATTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (26 bp):
GCACTCCTAACTTCACTACTGAAGGG
Found at i:3981439 original size:11 final size:11
Alignment explanation
Indices: 3981423--3981448 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3981413 GTATACAGCA
3981423 TTTCTTTTTTG
1 TTTCTTTTTTG
3981434 TTTCTTTTTTG
1 TTTCTTTTTTG
3981445 TTTC
1 TTTC
3981449 CATATTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.81
Consensus pattern (11 bp):
TTTCTTTTTTG
Found at i:3984177 original size:18 final size:20
Alignment explanation
Indices: 3984154--3984191 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3984144 ACGTGACAGT
3984154 CCAAC-TAGATTT-TAAATG
1 CCAACTTAGATTTCTAAATG
3984172 CCAACTTAGATTTCTAAATG
1 CCAACTTAGATTTCTAAATG
3984192 AGACGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
CCAACTTAGATTTCTAAATG
Found at i:3984228 original size:17 final size:17
Alignment explanation
Indices: 3984208--3984241 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3984198 AAATAGATTT
3984208 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
*
3984225 TTAATTAAAATTTTTAA
1 TTAATTAAAAATTTTAA
3984242 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:3984401 original size:17 final size:17
Alignment explanation
Indices: 3984381--3984414 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3984371 AGGTTTAGGT
3984381 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
3984398 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
3984415 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:3991083 original size:34 final size:34
Alignment explanation
Indices: 3991043--3991110 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
3991033 ACAAAAGAAG
3991043 AATAAATCTAAAAAGTTGAAGAATTATTGGCAAT
1 AATAAATCTAAAAAGTTGAAGAATTATTGGCAAT
3991077 AATAAATCTAAAAAGTTGAAGAATTATTGGCAAT
1 AATAAATCTAAAAAGTTGAAGAATTATTGGCAAT
3991111 CTTACTACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (34 bp):
AATAAATCTAAAAAGTTGAAGAATTATTGGCAAT
Found at i:3996130 original size:2 final size:2
Alignment explanation
Indices: 3996089--3996115 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3996079 TATATGTAAA
3996089 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3996116 GTGTTAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3996137 original size:25 final size:26
Alignment explanation
Indices: 3996099--3996156 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
3996089 ATATATATAT
3996099 ATATATATATATATATAGTGTTAGAA
1 ATATATATATATATATAGTGTTAGAA
*
3996125 ATATAT-TATATATATAGTGTTTGAA
1 ATATATATATATATATAGTGTTAGAA
*
3996150 GTATATA
1 ATATATA
3996157 CATGAGATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 23 0.79
26 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (26 bp):
ATATATATATATATATAGTGTTAGAA
Found at i:4006123 original size:32 final size:32
Alignment explanation
Indices: 4006068--4006148 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
4006058 GTTTTTAGGT
* * *
4006068 AAAA-TAATAAAATAAAATTTTAAGTTCC-TTA
1 AAAATTAAAAAAAAAAAATATTAAG-TCCTTTA
* *
4006099 AAAGTTAAAAGAAAAAAATATTAAGTCCTTTA
1 AAAATTAAAAAAAAAAAATATTAAGTCCTTTA
4006131 AAAATTAAAAAAAAAAAA
1 AAAATTAAAAAAAAAAAA
4006149 AAATAGAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 6 0.15
32 35 0.85
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAATTAAAAAAAAAAAATATTAAGTCCTTTA
Found at i:4007454 original size:10 final size:11
Alignment explanation
Indices: 4007435--4007467 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
4007425 AGTCAACAAA
4007435 TATTTAAAAAT
1 TATTTAAAAAT
4007446 TATTTAAAAAT
1 TATTTAAAAAT
4007457 TA-TTAAAAAT
1 TATTTAAAAAT
4007467 T
1 T
4007468 GTAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATTTAAAAAT
Found at i:4008543 original size:18 final size:19
Alignment explanation
Indices: 4008512--4008549 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4008502 TTTTATTTAG
* *
4008512 ATTTTTATATAATTTTAAT
1 ATTTTAATATAATTTGAAT
4008531 ATTTTAATA-AATTTGAAT
1 ATTTTAATATAATTTGAAT
4008549 A
1 A
4008550 ATTGTTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTTAATATAATTTGAAT
Found at i:4013435 original size:2 final size:2
Alignment explanation
Indices: 4013391--4013422 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4013381 TTGATATAAC
4013391 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
4013423 GTGTGTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4022670 original size:17 final size:16
Alignment explanation
Indices: 4022639--4022680 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
4022629 TGAATATAGC
**
4022639 AATATATTTTTTTAAAT
1 AATATATTTAGTT-AAT
4022656 AATATATTTAGTTAAT
1 AATATATTTAGTTAAT
4022672 AA-ATATTTA
1 AATATATTTA
4022681 TAAATTGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATATATTTAGTTAAT
Found at i:4023443 original size:23 final size:23
Alignment explanation
Indices: 4023406--4023449 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4023396 AAATAAAAGA
*
4023406 AAAAAAAACTCAAAATTTTCTAT
1 AAAAAAAACTCAAAATCTTCTAT
* *
4023429 AAAAAAACCTTAAAATCTTCT
1 AAAAAAAACTCAAAATCTTCT
4023450 GTCGAGTGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAAAAAACTCAAAATCTTCTAT
Found at i:4023943 original size:49 final size:49
Alignment explanation
Indices: 4023871--4023969 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
4023861 TGATGTATGG
4023871 TTGAAAAGATTGAACTTAGTCATGATAATAGAACAAAATTATTTTTCAA
1 TTGAAAAGATTGAACTTAGTCATGATAATAGAACAAAATTATTTTTCAA
4023920 TTGAAAAGATTGAACTTAGTCATGATAATAGAACAAAATTATTTTTCAA
1 TTGAAAAGATTGAACTTAGTCATGATAATAGAACAAAATTATTTTTCAA
4023969 T
1 T
4023970 CTTTTTCTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.35
Consensus pattern (49 bp):
TTGAAAAGATTGAACTTAGTCATGATAATAGAACAAAATTATTTTTCAA
Found at i:4026012 original size:19 final size:19
Alignment explanation
Indices: 4025980--4026024 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
4025970 TTTTTTGAAT
* *
4025980 TTTTTATAAATATTTT-TA
1 TTTTTAAAAATATTTTAAA
4025998 TTTTTAAAAATTATTTTAAA
1 TTTTTAAAAA-TATTTTAAA
4026018 TTTTTAA
1 TTTTTAA
4026025 TTTTTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
20 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAAAAATATTTTAAA
Found at i:4030914 original size:11 final size:11
Alignment explanation
Indices: 4030898--4030927 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4030888 TAACATTAAG
4030898 AATATATATAT
1 AATATATATAT
*
4030909 AATATAAATAT
1 AATATATATAT
4030920 AATATATA
1 AATATATA
4030928 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:4031775 original size:15 final size:16
Alignment explanation
Indices: 4031742--4031777 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4031732 TTTTCTTCTT
*
4031742 TTTTTTTGGGGTTAGG
1 TTTTTTTGGGGTTAAG
4031758 TTTTTTTGGGG-TAAG
1 TTTTTTTGGGGTTAAG
4031773 TTTTT
1 TTTTT
4031778 CTTTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.61
Consensus pattern (16 bp):
TTTTTTTGGGGTTAAG
Found at i:4031791 original size:15 final size:15
Alignment explanation
Indices: 4031773--4031807 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
4031763 TTGGGGTAAG
4031773 TTTTTCTTT-TCTTTT
1 TTTTTCTTTGT-TTTT
4031788 TTTTTCTTTGTTTTT
1 TTTTTCTTTGTTTTT
4031803 TTTTT
1 TTTTT
4031808 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:4032558 original size:88 final size:83
Alignment explanation
Indices: 4032451--4033028 Score: 290
Period size: 88 Copynumber: 7.0 Consensus size: 83
4032441 AACAGACATT
** * *
4032451 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
4032516 TTGATTTTTTGAAACTTAACTTG
65 TTGATTTTTTGAAA---AAC-TG
* * * ** *
4032539 AAAAGCAGATTTTGAAAATACCTCGATATGTGA-CTGGAGGTTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
*
4032603 GTTGA-TTTTTGAAAAACAG
64 GTTGATTTTTTGAAAAACTG
* * * * ** *** *
4032622 AAATTAAAAGA--CT-CAACTCAACTCTCGCA-GAAATTAAAAAGCTCAACTCACCTCTCGCAAT
1 AAA--AACAGATTTTGAAAAT--AC-CTCGCACGTGA-GCCAAGGCTCAACTCACCTCTCGCAAT
4032683 ATGAGTTGAATTTTTTTG-AAAA---
60 ATGAGTTG-A-TTTTTTGAAAAACTG
** * *
4032705 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
*
4032770 TTGA-TTTTTGAAAACAGAATTTG
65 TTGATTTTTTG--AA-A-AA-CTG
* * * * * * *
4032793 AAAAATAGATTTTGAAAATACCTCGACATGTAACCCGAGGCTCAACTCACATCTCGCAATGTGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
4032858 TTGATTTTTTTGAAAAA-T-
65 TTGA-TTTTTTGAAAAACTG
* *** *** * *
4032876 --ATA-A-ATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
4032936 GTTGATTTTTTTG--AAA--G
64 GTTGA-TTTTTTGAAAAACTG
* * * * * * *
4032953 ATAGA-A-A--TTGAAAATAGCTCAGCGCATGAGCCAAGGGTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
4033014 TTGATTTTTTGAAAA
65 TTGATTTTTTGAAAA
4033029 CAGAAATTGA
Statistics
Matches: 383, Mismatches: 70, Indels: 84
0.71 0.13 0.16
Matches are distributed among these distances:
76 9 0.02
77 47 0.12
78 2 0.01
79 64 0.17
80 3 0.01
81 11 0.03
82 38 0.10
83 14 0.04
84 41 0.11
85 9 0.02
86 6 0.02
87 19 0.05
88 114 0.30
90 6 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (83 bp):
AAAAACAGATTTTGAAAATACCTCGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAAACTG
Found at i:4032655 original size:30 final size:30
Alignment explanation
Indices: 4032619--4032680 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
4032609 TTTTGAAAAA
4032619 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
4032649 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
4032679 CA
1 CA
4032681 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:4033000 original size:77 final size:75
Alignment explanation
Indices: 4032830--4033169 Score: 370
Period size: 72 Copynumber: 4.5 Consensus size: 75
4032820 ATGTAACCCG
* * * *
4032830 AGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTG--AAAATACCT
* *
4032895 CAGTGTGTGATCTGA
63 CA--GCGTGATCTCA
* *
4032910 A-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAAAATAGCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
*
4032974 GCGCATGAGC-CA
65 GCG--TGATCTCA
* * * *
4032986 AGGGTCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTTAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
**
4033050 CGTG-TCTTG
66 CGTGATCTCA
** * *
4033059 AGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
* *
4033122 CGTG-TCCCG
66 CGTGATCTCA
4033131 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
4033170 TTTGAAAGGC
Statistics
Matches: 224, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
72 65 0.29
73 30 0.13
74 4 0.02
75 22 0.10
76 12 0.05
77 42 0.19
78 3 0.01
79 45 0.20
80 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (75 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAG
CGTGATCTCA
Found at i:4033318 original size:74 final size:75
Alignment explanation
Indices: 4033195--4033356 Score: 222
Period size: 74 Copynumber: 2.1 Consensus size: 75
4033185 TTGAAAAATG
*
4033195 GAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCGACGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
4033260 TTTTGACAACA
65 TTTTGACAACA
* * *
4033271 GAAATTGAAATTACCTC-AGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCGA-CGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
4033334 TTTTGA-AAGGCA
65 TTTTGACAA--CA
*
4033346 AAAATTGAAAA
1 GAAATTGAAAA
4033357 ACGGAAATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
73 2 0.03
74 42 0.55
75 12 0.16
76 21 0.27
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (75 bp):
GAAATTGAAAATACCTCGACGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAACA
Found at i:4033411 original size:165 final size:165
Alignment explanation
Indices: 4033025--4033683 Score: 924
Period size: 165 Copynumber: 4.0 Consensus size: 165
4033015 TGATTTTTTG
* ** * ** *
4033025 AAAACAGAAATTGAAAATACCTTAACGTGT--CTTGAGGCTCAACTCATTTCTCGCAATATGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
*
4033088 TGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
66 TGATATTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
4033152 ATATGAGTTGATTTTTTTTTTGAAAGGCAGAAATTGA
131 ATATGAGTTGA--TTTTTTTTGAAAGGCAGAAATTGA
* *
4033189 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* *
4033254 TGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TATTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
*
4033319 AATATGAGTTGA-TTTTTTTGAAAGGCAAAAATTGA
130 AATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGA
* * *
4033354 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * *
4033419 TGATTTTTTTGACAACAGAAATTGAAATTATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TATTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
*
4033484 AATATGAGTTGATTTTTTTTTGAAAGACAGAAATTGA
130 AATATGAGTTGA-TTTTTTTTGAAAGGCAGAAATTGA
* *
4033521 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* *** * * *
4033586 TGAAATTAAAACATA-A-AAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTAGT
66 TGATATTTTGACA-ACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGC
4033648 AATATGAGTTGA-TTTTTTTGACAA--CAGAAATTGA
130 AATATGAGTTGATTTTTTTTGA-AAGGCAGAAATTGA
4033682 AA
1 AA
4033684 TTACCTCAGC
Statistics
Matches: 454, Mismatches: 33, Indels: 19
0.90 0.07 0.04
Matches are distributed among these distances:
161 12 0.03
162 9 0.02
163 2 0.00
164 59 0.13
165 177 0.39
166 37 0.08
167 89 0.20
168 69 0.15
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (165 bp):
AAAACGGAAATTGAAAATACCTCGACGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGT
TGATATTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGA
Found at i:4033483 original size:74 final size:77
Alignment explanation
Indices: 4033350--4033523 Score: 228
Period size: 74 Copynumber: 2.3 Consensus size: 77
4033340 AAGGCAAAAA
* * * *
4033350 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATAC
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATAC
4033415 GAGTTGA-TTTTT
65 GAGTTGATTTTTT
* * * * *
4033427 TTGACA-ACAGAAATTGAAATTATCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACG
4033490 AGTTGATTTTTTT
66 AGTTGA-TTTTTT
4033503 TTGAAAGACAGAAATTGAAAA
1 TTGAAAGACAGAAATTGAAAA
4033524 ACGGAAATTG
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
74 33 0.39
76 33 0.39
77 18 0.21
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (77 bp):
TTGAAAGACAGAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACG
AGTTGATTTTTT
Found at i:4033522 original size:14 final size:14
Alignment explanation
Indices: 4033503--4033537 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4033493 TGATTTTTTT
*
4033503 TTGAAAGACAGAAA
1 TTGAAAAACAGAAA
*
4033517 TTGAAAAACGGAAA
1 TTGAAAAACAGAAA
4033531 TTGAAAA
1 TTGAAAA
4033538 TACCTCGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.20, T:0.17
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:4033750 original size:73 final size:72
Alignment explanation
Indices: 4033517--4033756 Score: 247
Period size: 74 Copynumber: 3.3 Consensus size: 72
4033507 AAGACAGAAA
** * * * *
4033517 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATAC
1 TTGAAAAATAGAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCACAATAT
**
4033582 GAGTTGAAA
64 GAGTTGATT
* * *
4033591 TT-AAAACATAAAAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCT-AGTAATAT
1 TTGAAAA-ATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCA-CAATAT
4033653 GAGTTGATTTTT
64 GAGTTGA---TT
* * *
4033665 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGA
1 TTGAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGA
4033729 GTTGATT
66 GTTGATT
4033736 TTGAAAAAGTAGAAATT-AAAA
1 TTGAAAAA-TAGAAATTGAAAA
4033757 GGTTCAACCT
Statistics
Matches: 136, Mismatches: 20, Indels: 22
0.76 0.11 0.12
Matches are distributed among these distances:
71 35 0.26
72 6 0.04
73 34 0.25
74 60 0.44
75 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (72 bp):
TTGAAAAATAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGA
GTTGATT
Found at i:4033934 original size:70 final size:71
Alignment explanation
Indices: 4033513--4033965 Score: 236
Period size: 74 Copynumber: 6.3 Consensus size: 71
4033503 TTGAAAGACA
** * * * * *
4033513 GAAATTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCA
1 GAAATT-AAAAACAAAAATTGAAAATACCTCAGC--GTGACCTCAAGCTCAACTCACCTCTAGCA
*
4033578 ATACGAGTT
63 ATATGAGTT
* * *
4033587 GAAATTAAAACATAAAAATTGAAAATACCTCAGCGTG-CC-CGAGGCTCAACTCACCTCTAGTAA
1 GAAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCTC-AAGCTCAACTCACCTCTAGCAA
4033650 TATGAGTT
64 TATGAGTT
** * * * * * * *
4033658 GATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCA-C
1 GA---AATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCTCAAGCTCAACTCACCTCT-AGC
4033722 AATATGAGTT
62 AATATGAGTT
** * * *** * * ** * * *
4033732 GATTTTGAAAAAGTAGAAATT-AAAA-GGTTCAACCT-ACCTCTCGCAAT-ATGAGTTGA-TTCT
1 GAAATT-AAAAA-CAAAAATTGAAAATACCTCAGCGTGACCTCAAGC--TCA--A-CTCACCTCT
* *
4033792 TG-AACA--ACG-T
59 AGCAATATGA-GTT
* * * * *
4033802 -AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATA
1 GAAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCTCAAGCTCAACTCACCTCTAGCAATA
4033866 TGAGTT
66 TGAGTT
4033872 GAAATTAAAACACAAAAATTGAAAATACCTCAGCGTG-CC-CAAGCTCAACTCACCTCTAGCAAT
1 GAAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCTCAAGCTCAACTCACCTCTAGCAAT
4033935 ATGAGTT
65 ATGAGTT
**
4033942 GATTTTGAAAAACAAAAATT-AAAA
1 GAAATT-AAAAACAAAAATTGAAAA
4033966 GGCTTAACTC
Statistics
Matches: 290, Mismatches: 60, Indels: 63
0.70 0.15 0.15
Matches are distributed among these distances:
66 2 0.01
67 12 0.04
68 12 0.04
69 14 0.05
70 56 0.19
71 55 0.19
72 38 0.13
73 38 0.13
74 62 0.21
75 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (71 bp):
GAAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCTCAAGCTCAACTCACCTCTAGCAATA
TGAGTT
Found at i:4034060 original size:122 final size:122
Alignment explanation
Indices: 4033842--4034086 Score: 352
Period size: 122 Copynumber: 2.0 Consensus size: 122
4033832 GCGTGACCTG
* *
4033842 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
4033907 TGCCCAAGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 TGCCCAAGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG-AAAACAAAAATTAAA
* * * * *
4033965 AGGCTTAACTCACCTCTCGCAATATGAG-T-CAATTTAAA-ACATAAACTAAAAATACCTCAGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
* * *
4034027 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
66 TG-CCC-AAGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
4034086 A
1 A
4034087 ATACCTCAAC
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
120 22 0.20
121 26 0.24
122 35 0.32
123 27 0.25
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (122 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAACTAAAAATACCTCAGCG
TGCCCAAGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAAAAATTAAA
Found at i:4034186 original size:70 final size:70
Alignment explanation
Indices: 4033965--4034366 Score: 331
Period size: 71 Copynumber: 5.5 Consensus size: 70
4033955 AAAAATTAAA
* ** * * * * *
4033965 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAA-ACATAAACTAAAAATACCTCAGTGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
4034029 CCCCG
66 CCCCG
* * * *
4034034 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAACG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
* **
4034098 TGTCTTG
64 TGCCCCG
*
4034105 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
4034170 CCCCG
66 CCCCG
* * ** ** * ** *
4034175 AGGCTCAACTCACTTCTAGCAATATGAGTTGATTCTTGAACAACGTAAATTGAAAACAGAAATTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-T-TAAAAC-ACAAAAATTG-AAA-A-TACCTC
*** *
4034240 AAAATACCTCAGCGTG
60 AGCGTGCC-C--C--G
4034256 ACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCT
1 A---G--GCTCAACTCACCTCTCGCAATATGAGTTG--ATTAAAACACAAAAATTGAAAATACCT
4034321 CAGCGTGCCCCG
59 CAGCGTGCCCCG
*
4034333 AGGCTCAACTCACCTCTAGCAATATGAGTTGATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATT
4034367 TTGAAAAACA
Statistics
Matches: 262, Mismatches: 50, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
69 33 0.13
70 58 0.22
71 60 0.23
72 32 0.12
73 8 0.03
74 4 0.02
75 1 0.00
76 6 0.02
77 3 0.01
79 2 0.01
81 3 0.01
82 6 0.02
83 1 0.00
84 4 0.02
85 8 0.03
86 31 0.12
87 1 0.00
88 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (70 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
CCCCG
Found at i:4034354 original size:158 final size:155
Alignment explanation
Indices: 4034068--4034371 Score: 518
Period size: 158 Copynumber: 1.9 Consensus size: 155
4034058 TGAGTTGATT
* * *
4034068 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
4034133 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTAGCAAT
66 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
4034198 ATGAGTTGATTCTTGAACAACGTAAA
131 ATGAGTTGATT-TTGAACAACGTAAA
* * *
4034224 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
4034289 TTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
66 TTG--ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCA
4034354 ATATGAGTTGATTTTGAA
129 ATATGAGTTGATTTTGAA
4034372 AAACAAAAAT
Statistics
Matches: 139, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
156 62 0.45
157 5 0.04
158 72 0.52
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (155 bp):
TTGAAAACAAAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
ATGAGTTGATTTTGAACAACGTAAA
Found at i:4034355 original size:72 final size:71
Alignment explanation
Indices: 4034221--4034386 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
4034211 TGAACAACGT
* * * *
4034221 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
4034286 GAGTTG
66 GAGTTG
*
4034292 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
4034357 TGAGTTG
65 TGAGTTG
**
4034364 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
4034387 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:4034531 original size:73 final size:71
Alignment explanation
Indices: 4034386--4034651 Score: 342
Period size: 73 Copynumber: 3.7 Consensus size: 71
4034376 AAAAATTAAA
* * * * *
4034386 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAACAAAAATTAAAAATACCTCAGCGT
4034449 GCCCCG
66 GCCCCG
* * *
4034455 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAACAAAAAATAAAAATACCTCAAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT--AAAAACAAAAATTAAAAATACCTCAGC
* **
4034520 GTGTCTTG
64 GTGCCCCG
* *
4034528 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAA-ACAAAAATTAAAAATACCTCAGCG
4034591 TGCCCCG
65 TGCCCCG
*
4034598 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-AAAAACAAAAATTAAAA
4034652 GGCTTAACTC
Statistics
Matches: 168, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
69 30 0.18
70 60 0.36
71 2 0.01
72 14 0.08
73 62 0.37
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAACAAAAATTAAAAATACCTCAGCGT
GCCCCG
Found at i:4042986 original size:15 final size:16
Alignment explanation
Indices: 4042953--4042988 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
4042943 TTTTCTTCTT
*
4042953 TTTTTTTGGGGTTAGG
1 TTTTTTTGGGGTTAAG
4042969 TTTTTTTGGGG-TAAG
1 TTTTTTTGGGGTTAAG
4042984 TTTTT
1 TTTTT
4042989 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.61
Consensus pattern (16 bp):
TTTTTTTGGGGTTAAG
Found at i:4042995 original size:6 final size:6
Alignment explanation
Indices: 4042984--4043016 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4042974 TTGGGGTAAG
4042984 TTTTTC TTTTTC TTTTT- TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
4043017 TTTGGGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTTC
Found at i:4043004 original size:11 final size:11
Alignment explanation
Indices: 4042984--4043016 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
4042974 TTGGGGTAAG
4042984 TTTTTCTTTTTC
1 TTTTT-TTTTTC
4042996 TTTTTTTTTTC
1 TTTTTTTTTTC
4043007 TTTTTTTTTT
1 TTTTTTTTTT
4043017 TTTGGGTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:4043006 original size:17 final size:16
Alignment explanation
Indices: 4042984--4043019 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
4042974 TTGGGGTAAG
4042984 TTTTTCTTTTTCTTTTT
1 TTTTTCTTTTT-TTTTT
4043001 TTTTTCTTTTTTTTTT
1 TTTTTCTTTTTTTTTT
4043017 TTT
1 TTT
4043020 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTT
Found at i:4044651 original size:17 final size:17
Alignment explanation
Indices: 4044629--4044662 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4044619 ATTTTAGTTT
4044629 TTATTTGAA-AAAAAATA
1 TTATTT-AATAAAAAATA
4044646 TTATTTAATAAAAAATA
1 TTATTTAATAAAAAATA
4044663 AATTTCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TTATTTAATAAAAAATA
Found at i:4048866 original size:22 final size:23
Alignment explanation
Indices: 4048838--4048881 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
4048828 TTAAAAAAGG
4048838 TAAAAAAAATG-AAGGGTTATTA
1 TAAAAAAAATGAAAGGGTTATTA
4048860 TAAAAAAAATGAAAGGGTTATT
1 TAAAAAAAATGAAAGGGTTATT
4048882 TTTGTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (23 bp):
TAAAAAAAATGAAAGGGTTATTA
Found at i:4049379 original size:24 final size:23
Alignment explanation
Indices: 4049339--4049385 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4049329 AAATATTGTC
4049339 AATACATCAAAGAACATAATGAAA
1 AATACATCAAAGAACAT-ATGAAA
*
4049363 AATACATCAACA-TACATATGAAA
1 AATACATCAA-AGAACATATGAAA
4049386 GTGACATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 14 0.67
25 1 0.05
ACGTcount: A:0.60, C:0.15, G:0.06, T:0.19
Consensus pattern (23 bp):
AATACATCAAAGAACATATGAAA
Found at i:4049412 original size:22 final size:23
Alignment explanation
Indices: 4049366--4049414 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
4049356 AATGAAAAAT
* *
4049366 ACATCAACATACATATGAAAGTG
1 ACATAAACATACACATGAAAGTG
*
4049389 ACATAAACAT-CACATGCAAGTG
1 ACATAAACATACACATGAAAGTG
4049411 ACAT
1 ACAT
4049415 TAATTTCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (23 bp):
ACATAAACATACACATGAAAGTG
Found at i:4051105 original size:5 final size:5
Alignment explanation
Indices: 4051095--4051119 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4051085 TTTGGTTTCT
4051095 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
4051120 AATGTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:4055234 original size:239 final size:239
Alignment explanation
Indices: 4054535--4055285 Score: 885
Period size: 238 Copynumber: 3.1 Consensus size: 239
4054525 TGTCATCCAA
* * * * *
4054535 GGAAAGAATGGTATTATATTGACTGAAAGATTTGCATCGTGATATAGAACCATTAATT-TTCTCC
1 GGAAAGAAT-ATA-TATGTTGACTGAAAGGTTCGCATCGTGATATAGAACCATTCATTATTCTCC
* * * * * *
4054599 TCTGTAGGTGTTAAGGTTGTATGGATATGTTCAATAGTTACCTGTCTCTGATTGCACGTCGAGTT
64 TTTGTAGGTGTTAAGGTTGTAT---TATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTT
* * * * *
4054664 TGCAATTCTAAGATGGGCGAAGGAGAATTCATGGTTTTTTATGTTCATTATAAGTATAGGAGGGG
126 TGCAATTCTAAGATGAGCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAGGAAGGG
* * * *
4054729 GACAAGTCTGGGAGTTAATGTATTGTTTCGTTATCAGCTTGTCATATGT
191 GACGAGTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
** * * * * * * *
4054778 GGAAAG------TATGTTGACCAAAAGGTTCTCATCATGTTTTA-AAGCCTTTCCTTTATTTTCC
1 GGAAAGAATATATATGTTGACTGAAAGGTTCGCATCGTGATATAGAA-CCATT-CATTATTCT-C
*
4054836 CTTTGTAGGTGTTAAGGTTGTATGGTTATATTCAATAATTGCCCGTCTCTGAGTGCACTTCGAGT
63 CTTTGTAGGTGTTAAGGTTGTA---TTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGT
* * * * ** *
4054901 TTGCCATTTTGAGAT-AGGCGAAGGAGAATTTGTTAC-TTTTATGTTAGTTATAAGTATAGGAAG
125 TTGCAATTCTAAGATGA-GCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAGGAAG
* * *
4054964 GAGACGAGTGTGGAAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
189 GGGACGAGTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
* *
4055015 GGAAAGAATCATATATGTTGGCTGAAAGGTTCGCATCGTGATATAGAACCGTT-ATTATTCTCCT
1 GGAAAGAAT-ATATATGTTGACTGAAAGGTTCGCATCGTGATATAGAACCATTCATTATTCTCCT
4055079 TTGTAGGTGTTAAGGTTGTATTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTTGCA
65 TTGTAGGTGTTAAGGTTGTATTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTTGCA
* *
4055144 ATTCTAAGATGAGCGAAGCAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAGGAAGGGGATG
130 ATTCTAAGATGAGCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAGGAAGGGGACG
*
4055209 AGTCTGGGACTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
195 AGTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
*
4055254 AGAAAGAATAATATATGTTGACTGAAAGGTTC
1 GGAAAGAAT-ATATATGTTGACTGAAAGGTTC
4055286 ATGTACTGTT
Statistics
Matches: 424, Mismatches: 66, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
234 2 0.00
235 27 0.06
236 2 0.00
237 77 0.18
238 147 0.35
239 102 0.24
241 24 0.06
242 6 0.01
243 6 0.01
244 29 0.07
245 2 0.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (239 bp):
GGAAAGAATATATATGTTGACTGAAAGGTTCGCATCGTGATATAGAACCATTCATTATTCTCCTT
TGTAGGTGTTAAGGTTGTATTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTTGCAA
TTCTAAGATGAGCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAGGAAGGGGACGA
GTCTGGGAGTTAATATATTGTTTCGTTGTCAACTTGTCATATGT
Found at i:4060543 original size:15 final size:16
Alignment explanation
Indices: 4060514--4060543 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4060504 ATAATATTGA
4060514 AATTTTCATTTAATCC
1 AATTTTCATTTAATCC
4060530 AATTTTCA-TTAATC
1 AATTTTCATTTAATC
4060544 ACCAACATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTCATTTAATCC
Found at i:4062794 original size:19 final size:20
Alignment explanation
Indices: 4062748--4062796 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
4062738 GCAAAATGGA
*
4062748 TAATAATTAATTTTTTTTAAT
1 TAATAA-TAATTTTTTATAAT
*
4062769 TGGATAATAATTTTTTAT-AT
1 T-AATAATAATTTTTTATAAT
4062789 TAATAATA
1 TAATAATA
4062797 TTTAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 11 0.46
22 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TAATAATAATTTTTTATAAT
Found at i:4063147 original size:22 final size:23
Alignment explanation
Indices: 4063103--4063149 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4063093 TTATGAATAG
4063103 ATTTAGTTAAAAACCAACAAAAA
1 ATTTAGTTAAAAACCAACAAAAA
4063126 ATTTAGTTAAAAACCAACAAAAA
1 ATTTAGTTAAAAACCAACAAAAA
4063149 A
1 A
4063150 CCATACTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.13, G:0.04, T:0.21
Consensus pattern (23 bp):
ATTTAGTTAAAAACCAACAAAAA
Found at i:4071595 original size:2 final size:2
Alignment explanation
Indices: 4071588--4071614 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4071578 TCTTAGAATA
4071588 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4071615 CTGCTTAGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4077054 original size:159 final size:157
Alignment explanation
Indices: 4076750--4077069 Score: 435
Period size: 159 Copynumber: 2.0 Consensus size: 157
4076740 CTAACTATTC
* ** *
4076750 CATTTTTAACATTCAAAACCACTGAAAACAAAACACTACCCTTTACTGAACTCAGATGACAAAAG
1 CATTTGTAACATTCAAAACCAAAGAAAACAAAACACTACCCTTTACTGAACTCAGATGACAAAAC
4076815 CAGGCTCATTTTCACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTACCT
66 CAGGCTCATTTTCACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTACCT
*
4076880 TCTCAATAACCAAACAGGAAGTGAACT
131 TCTCAATAACAAAACAGGAAGTGAACT
* * * * *
4076907 CATTTGTAACATTTAAAACCAAAGAAAACATAATACTACCCTTTAGTGAACACTCGGATGACAAA
1 CATTTGTAACATTCAAAACCAAAGAAAACAAAACACTACCCTTTACTG-A-ACTCAGATGACAAA
* ** * *
4076972 ACCAGGTTC-TTTTGCACAGTGAAATGATCGTTTCAACTTTCCCTTTTCCTCCAATTTTCCTTTA
64 ACCAGGCTCATTTT-CACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTA
* ***
4077036 CTTTCTTGGTAACAAAACAGGAAGTGAACT
128 CCTTCTCAATAACAAAACAGGAAGTGAACT
4077066 CATT
1 CATT
4077070 GCAGTAAAAG
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
157 41 0.29
158 5 0.04
159 95 0.67
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (157 bp):
CATTTGTAACATTCAAAACCAAAGAAAACAAAACACTACCCTTTACTGAACTCAGATGACAAAAC
CAGGCTCATTTTCACAGTGAAACAATCATTTCAACTTTCCATTTTCCTCCAATTTTCCTTTACCT
TCTCAATAACAAAACAGGAAGTGAACT
Found at i:4078495 original size:11 final size:10
Alignment explanation
Indices: 4078477--4078501 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4078467 TCTGATTAGC
4078477 TCTTTTTTTT
1 TCTTTTTTTT
4078487 TCTTTTTTTT
1 TCTTTTTTTT
4078497 TCTTT
1 TCTTT
4078502 CAAATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:4079480 original size:81 final size:81
Alignment explanation
Indices: 4079345--4079509 Score: 330
Period size: 81 Copynumber: 2.0 Consensus size: 81
4079335 AGTGATGTTG
4079345 TGTCATCATGTTTTTAAGATGGTCAATTGCTATGACAAGGAGACCTATGGTAGAAGTATAACATA
1 TGTCATCATGTTTTTAAGATGGTCAATTGCTATGACAAGGAGACCTATGGTAGAAGTATAACATA
4079410 TACTATCTGTATTAAT
66 TACTATCTGTATTAAT
4079426 TGTCATCATGTTTTTAAGATGGTCAATTGCTATGACAAGGAGACCTATGGTAGAAGTATAACATA
1 TGTCATCATGTTTTTAAGATGGTCAATTGCTATGACAAGGAGACCTATGGTAGAAGTATAACATA
4079491 TACTATCTGTATTAAT
66 TACTATCTGTATTAAT
4079507 TGT
1 TGT
4079510 GTTTTAAACT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (81 bp):
TGTCATCATGTTTTTAAGATGGTCAATTGCTATGACAAGGAGACCTATGGTAGAAGTATAACATA
TACTATCTGTATTAAT
Found at i:4081618 original size:18 final size:19
Alignment explanation
Indices: 4081577--4081619 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4081567 AGGTCTACCC
*
4081577 AAAAAATAGATGGTTTGAG
1 AAAAAATAGATGGTTTGAA
* *
4081596 TAAAAATATA-GGTTTGAA
1 AAAAAATAGATGGTTTGAA
4081614 AAAAAA
1 AAAAAA
4081620 AATAAGGCCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.26
Consensus pattern (19 bp):
AAAAAATAGATGGTTTGAA
Found at i:4087269 original size:30 final size:30
Alignment explanation
Indices: 4087200--4087258 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4087190 TTAATTTGAC
4087200 ATAATTTAGTCCTCTATTATTTATAATGTG
1 ATAATTTAGTCCTCTATTATTTATAATGTG
4087230 ATAATTTAGTCCTCTATTATTTATAATGT
1 ATAATTTAGTCCTCTATTATTTATAATGT
4087259 TATTAATTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (30 bp):
ATAATTTAGTCCTCTATTATTTATAATGTG
Found at i:4104886 original size:13 final size:13
Alignment explanation
Indices: 4104862--4104910 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
4104852 ACACTTAAAT
*
4104862 TTTTCCAAAGCAC
1 TTTTCAAAAGCAC
*
4104875 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
4104888 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
4104901 TTTTCAAAAG
1 TTTTCAAAAG
4104911 AACTGGCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:4124404 original size:97 final size:97
Alignment explanation
Indices: 4124277--4124467 Score: 242
Period size: 97 Copynumber: 2.0 Consensus size: 97
4124267 TATTCGGAGT
* * ** *
4124277 TGAATATCGGTTTTTAACTCATTGGGTGATAGATTTTGATTTATAGTTTCTTTGGAGGATTCTTT
1 TGAATATCAGTTTTAAACTCATTGCATGATAGATTTTGATTGATAGTTTCTTTGGAGGATTCTTT
*
4124342 TGACT-GAATTATTCGGATTCGAGTGTGAGGGA
66 TAACTAG-ATTATTCGGATTCGAGTGTGAGGGA
* * *
4124374 TGAATATCAGTTTTAAACAT-ATTGCATGATAGTTTTTTATTGATAGTTTCTTTGTAGGATTCTT
1 TGAATATCAGTTTTAAAC-TCATTGCATGATAGATTTTGATTGATAGTTTCTTTGGAGGATTCTT
* * *
4124438 TTAACTAGGTTATTTGGATTTGAGTGTGAG
65 TTAACTAGATTATTCGGATTCGAGTGTGAG
4124468 TGTTCATTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
97 78 0.98
98 2 0.03
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (97 bp):
TGAATATCAGTTTTAAACTCATTGCATGATAGATTTTGATTGATAGTTTCTTTGGAGGATTCTTT
TAACTAGATTATTCGGATTCGAGTGTGAGGGA
Found at i:4124706 original size:99 final size:100
Alignment explanation
Indices: 4124535--4124719 Score: 284
Period size: 99 Copynumber: 1.9 Consensus size: 100
4124525 GATTCACTTG
* *
4124535 GATTCGAGTGTGAGCGTTAAATACCGGTTTTTAACGAATTGCCTTTGGGGGTTTGTTTCAATGAT
1 GATTCGAATGTGAGCGTTAAATACCGGTTTTTAACGAATTGCCTTTGGGAGTTTGTTTCAATGAT
4124600 AGTTTC-TTTGGAGGATTCTAAAAAATGTTATTCA
66 AGTTTCTTTTGGAGGATTCTAAAAAATGTTATTCA
* * * *
4124634 GATTCGAATGTGAGTGTTGAATACTGGTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGA
1 GATTCGAATGTGAGCGTTAAATACCGGTTTTTAACGAATTGCC-TTTGGGAGTTTGTTTCAATGA
4124699 TAG-TTCTTTTTGGAGGATTCT
65 TAGTTTC-TTTTGGAGGATTCT
4124720 TAACTAAGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
99 42 0.55
100 22 0.29
101 13 0.17
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.42
Consensus pattern (100 bp):
GATTCGAATGTGAGCGTTAAATACCGGTTTTTAACGAATTGCCTTTGGGAGTTTGTTTCAATGAT
AGTTTCTTTTGGAGGATTCTAAAAAATGTTATTCA
Found at i:4124761 original size:99 final size:99
Alignment explanation
Indices: 4124560--4124764 Score: 254
Period size: 101 Copynumber: 2.1 Consensus size: 99
4124550 GTTAAATACC
*
4124560 GGTTTTTAACGAATTGCCTTTGGGGGTTTGTTTCAATGATAGTTTCTTTGGAGGATTCTAAAAAA
1 GGTTTTTAACGAATTGCCTTTGGGAGTTTGTTTCAATGATAGTTTCTTTGGAGGATTCTAAAAAA
* * * *
4124625 TGTTATTCAGATTCGAATGTGAGTGTTGAATACT
66 TGTTATTCAGATTCGAATATGAGCGCTGAATAAT
* * *
4124659 GGTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGATAGTTCTTTTTGGAGGATTCTTAAC
1 GGTTTTTAACGAATTGCC-TTTGGGAGTTTGTTTCAATGATAGTT-TCTTTGGAGGATTC-TAAA
* * * *
4124724 TAA-GTTATTCGGATTTGAGTATGAGCGCT-AA-AAT
63 AAATGTTATTCAGATTCGAATATGAGCGCTGAATAAT
4124758 GGTTTTT
1 GGTTTTT
4124765 TAACTACTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
99 27 0.30
100 26 0.29
101 33 0.36
102 5 0.05
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.43
Consensus pattern (99 bp):
GGTTTTTAACGAATTGCCTTTGGGAGTTTGTTTCAATGATAGTTTCTTTGGAGGATTCTAAAAAA
TGTTATTCAGATTCGAATATGAGCGCTGAATAAT
Found at i:4124793 original size:54 final size:54
Alignment explanation
Indices: 4124719--4124822 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
4124709 TGGAGGATTC
* *
4124719 TTAACTAAGTTATTCGGATTTGAGTATGAGCGCTAAAAT-GGTTTTTTAACTACT
1 TTAACTAAGCTATTCAGATTTGAGTATGAGCG-TAAAATCGGTTTTTTAACTACT
* * * *
4124773 TTAACTATGCTATTCAGATTTGGGTGTGAGCGTTAAATCGGTTTTTTAAC
1 TTAACTAAGCTATTCAGATTTGAGTATGAGCGTAAAATCGGTTTTTTAAC
4124823 ATATTGCCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 5 0.12
54 38 0.88
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (54 bp):
TTAACTAAGCTATTCAGATTTGAGTATGAGCGTAAAATCGGTTTTTTAACTACT
Found at i:4127917 original size:15 final size:15
Alignment explanation
Indices: 4127889--4127923 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4127879 TGAGTTGAGT
*
4127889 GTTTTGTAGGGTTCG
1 GTTTTATAGGGTTCG
*
4127904 GTTTTATAGTGTTCG
1 GTTTTATAGGGTTCG
4127919 GTTTT
1 GTTTT
4127924 GTATTCATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.06, G:0.31, T:0.54
Consensus pattern (15 bp):
GTTTTATAGGGTTCG
Found at i:4136644 original size:2 final size:2
Alignment explanation
Indices: 4136633--4136666 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4136623 CACTTCAAGA
4136633 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4136667 AAAGATTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4138029 original size:2 final size:2
Alignment explanation
Indices: 4138022--4138060 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4138012 GGTCTAGATT
4138022 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
4138061 TAAGTTGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4139005 original size:31 final size:31
Alignment explanation
Indices: 4138970--4139031 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
4138960 TTATAACTTT
4138970 ATAATAATTTTA-ATGATTTTT-AATTTTTAAA
1 ATAAT-ATTTTATAT-ATTTTTAAATTTTTAAA
* *
4139001 ATAATTTTTTATATTTTTTTAAATTTTTAAA
1 ATAATATTTTATATATTTTTAAATTTTTAAA
4139032 TTTAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (31 bp):
ATAATATTTTATATATTTTTAAATTTTTAAA
Found at i:4139016 original size:28 final size:27
Alignment explanation
Indices: 4138947--4139018 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
4138937 AACATTTAAT
* *
4138947 TAATTTTTAATATTTATAACTTTATAA
1 TAATTTTTAATATTTTTAACTTTAAAA
*
4138974 TAA-TTTTAATGATTTTTAATTTTTAAAA
1 TAATTTTTAAT-ATTTTTAA-CTTTAAAA
*
4139002 TAATTTTTTATATTTTT
1 TAATTTTTAATATTTTT
4139019 TTAAATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 7 0.18
27 10 0.26
28 15 0.39
29 6 0.16
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (27 bp):
TAATTTTTAATATTTTTAACTTTAAAA
Found at i:4142407 original size:170 final size:174
Alignment explanation
Indices: 4142089--4142421 Score: 478
Period size: 176 Copynumber: 1.9 Consensus size: 174
4142079 AAAAAAGTAA
* * * *
4142089 AGTGAAAATGCAATGATTCAGATCTAAATACTAAATATATACAGAGATTTGCGATCTAATATCCA
1 AGTGAAAATGCAATGATTCAGATCGAAATACTAAACATATACACAGATTTGCGATCTAATATACA
*
4142154 AGGCATTCAAATTTAACAGAGGCAATGAAGAATTGCAGATTTCAACAAAACTTAATTTCCGAAAG
66 AGGCATTCAAATTTAACAGAGG-AATG-ACAATTGCAGATTTCAACAAAACTTAATTTCCGAAAG
4142219 CCACCAAAAGAAATCCAACAAAAAGATGATGATAAAGAAAACATCG
129 CCACCAAAAGAAATCCAACAAAAAGATGATGATAAAGAAAACATCG
* * * * *
4142265 AGTGAATATGCGATGCTTCAGATCGAAATACTAAACATATCCACATATTTGCGATCTAATATACA
1 AGTGAAAATGCAATGATTCAGATCGAAATACTAAACATATACACAGATTTGCGATCTAATATACA
* * *
4142330 AGGTATTCAAATATTAACAGA-G-A-G-CAA-TGCAGATTTCAACAGAACTTAGTTTCCGAAAGC
66 AGGCATTCAAAT-TTAACAGAGGAATGACAATTGCAGATTTCAACAAAACTTAATTTCCGAAAGC
*
4142390 TACCAAAAGAAATCCAACAAAAAGATGATGAT
130 CACCAAAAGAAATCCAACAAAAAGATGATGAT
4142422 GTTGATGATG
Statistics
Matches: 142, Mismatches: 14, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
170 62 0.44
171 2 0.01
173 1 0.01
174 1 0.01
176 68 0.48
177 8 0.06
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.24
Consensus pattern (174 bp):
AGTGAAAATGCAATGATTCAGATCGAAATACTAAACATATACACAGATTTGCGATCTAATATACA
AGGCATTCAAATTTAACAGAGGAATGACAATTGCAGATTTCAACAAAACTTAATTTCCGAAAGCC
ACCAAAAGAAATCCAACAAAAAGATGATGATAAAGAAAACATCG
Found at i:4143141 original size:4 final size:4
Alignment explanation
Indices: 4143112--4143160 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
4143102 TATCAATGGA
* * * *
4143112 AGTG AGCG AGCG AGCG AGTG AATG AGTG AGTG AGTG AGTG AGTTG AGTG
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AGTG AG-TG AGTG
4143161 GTTGTCTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 36 0.90
5 4 0.10
ACGTcount: A:0.27, C:0.06, G:0.47, T:0.20
Consensus pattern (4 bp):
AGTG
Found at i:4144015 original size:2 final size:2
Alignment explanation
Indices: 4144008--4144039 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4143998 TGAAAACTTT
4144008 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4144040 AAATCGACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4144286 original size:23 final size:20
Alignment explanation
Indices: 4144245--4144287 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
4144235 TATATTATGT
*
4144245 AATTTATATTAAATAAAATA
1 AATTTATATTAAACAAAATA
4144265 AATTTATTATTATAACATAAATA
1 AATTTA-TATTA-AACA-AAATA
4144288 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 5 0.26
22 3 0.16
23 5 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTATATTAAACAAAATA
Found at i:4146504 original size:29 final size:29
Alignment explanation
Indices: 4146461--4146518 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
4146451 ATTCTAAAAT
* *
4146461 TATTATTTTATAAAATTTGTAAATTTTTA
1 TATTATTTTAAAAAATTTATAAATTTTTA
* *
4146490 TATTTTTTTAAAAAATTTATAATTTTTTA
1 TATTATTTTAAAAAATTTATAAATTTTTA
4146519 AAAACACAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TATTATTTTAAAAAATTTATAAATTTTTA
Found at i:4146508 original size:19 final size:19
Alignment explanation
Indices: 4146486--4146522 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4146476 TTTGTAAATT
*
4146486 TTTATATTTTTTTAAAAAA
1 TTTATAATTTTTTAAAAAA
4146505 TTTATAATTTTTTAAAAA
1 TTTATAATTTTTTAAAAA
4146523 CACAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATAATTTTTTAAAAAA
Found at i:4146559 original size:18 final size:18
Alignment explanation
Indices: 4146535--4146597 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
4146525 CAAATTTTAG
*
4146535 AATTTTTATAAATATTTTT
1 AATTTTTA-ATATATTTTT
* *
4146554 AATTTTTAATTTTTTTTT
1 AATTTTTAATATATTTTT
* * *
4146572 AATTTTTGATTTTTTTTGT
1 AATTTTTAATATATTTT-T
4146591 AATTTTT
1 AATTTTT
4146598 GTTAAGAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 23 0.59
19 16 0.41
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
AATTTTTAATATATTTTT
Found at i:4146598 original size:19 final size:18
Alignment explanation
Indices: 4146549--4146598 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
4146539 TTTATAAATA
*
4146549 TTTTTAATTTTTAATTTT
1 TTTTTAATTTTTGATTTT
4146567 TTTTTAATTTTTGATTTT
1 TTTTTAATTTTTGATTTT
4146585 TTTTGTAATTTTTG
1 TTTT-TAATTTTTG
4146599 TTAAGAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTTTAATTTTTGATTTT
Found at i:4146745 original size:12 final size:12
Alignment explanation
Indices: 4146728--4146753 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4146718 AATCCAAAAT
4146728 TTCTTATTTGAG
1 TTCTTATTTGAG
4146740 TTCTTATTTGAG
1 TTCTTATTTGAG
4146752 TT
1 TT
4146754 GACTCAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (12 bp):
TTCTTATTTGAG
Found at i:4153547 original size:30 final size:30
Alignment explanation
Indices: 4153513--4153575 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
4153503 TAAAAATAAC
4153513 TTAAAAAT-TCTATATACAAAATATATATT-T
1 TTAAAAATAT-TATATA-AAAATATATATTAT
* *
4153543 TTAAAAATATTATATAAAAGTATTTATTAT
1 TTAAAAATATTATATAAAAATATATATTAT
4153573 TTA
1 TTA
4153576 TTATTTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.34
30 18 0.62
31 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
TTAAAAATATTATATAAAAATATATATTAT
Found at i:4155721 original size:31 final size:32
Alignment explanation
Indices: 4155654--4155721 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
4155644 AATATGCTAC
* *
4155654 AAGTCCCTATACTATTCGAATATTTAGAATTT
1 AAGTCCCTATACTATTCGAATATTAAAAATTT
* *
4155686 -AGTCCCTCTACTTTTCGAAT-TTAAAAATTT
1 AAGTCCCTATACTATTCGAATATTAAAAATTT
4155716 AAGTCC
1 AAGTCC
4155722 AATTAGTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (32 bp):
AAGTCCCTATACTATTCGAATATTAAAAATTT
Found at i:4165727 original size:3 final size:3
Alignment explanation
Indices: 4165719--4165757 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
4165709 CGCTCTTCCT
4165719 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4165758 ATGTTAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4170892 original size:85 final size:84
Alignment explanation
Indices: 4170789--4171003 Score: 238
Period size: 85 Copynumber: 2.5 Consensus size: 84
4170779 TAGCTGAGTG
* * *
4170789 TAACTATCAA-TATAATTTACCCTAATTAATTAAATTCGTCTCGACTCTATTTTTGTAT-TTTTG
1 TAACTAT-AAGTATAATTTACCCTAATTAATTAAATTCGGCTCGACTCAATTTTTGTATCTTCTG
*
4170852 TGACAAATCATCAGTAACCGAA
65 TGACAAATC-T-AATAACCGAA
* * *
4170874 TAACTATAAGTATAATTTACCCATTATTAATTAAATTTGGCTTGACTCAATTTTTGTATCTTCTG
1 TAACTATAAGTATAATTTACCC-TAATTAATTAAATTCGGCTCGACTCAATTTTTGTATCTTCTG
* *
4170939 TGATAAATCTAATAATCGAA
65 TGACAAATCTAATAACCGAA
*** *
4170959 TAACTACCGGTATAATTTA-TCTATTATTAATTAAATTCGGCTCGA
1 TAACTATAAGTATAATTTACCCTA--ATTAATTAAATTCGGCTCGA
4171004 TTCGATTCGA
Statistics
Matches: 109, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
83 1 0.01
84 3 0.03
85 61 0.56
86 32 0.29
87 12 0.11
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (84 bp):
TAACTATAAGTATAATTTACCCTAATTAATTAAATTCGGCTCGACTCAATTTTTGTATCTTCTGT
GACAAATCTAATAACCGAA
Found at i:4171316 original size:2 final size:2
Alignment explanation
Indices: 4171309--4171333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4171299 AGCTCAATAA
4171309 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 T
4171334 TTTTTAACAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4172160 original size:4 final size:4
Alignment explanation
Indices: 4172151--4172181 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4172141 TAGGCTCATA
*
4172151 TATG TATG TATG TATG TTTG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
4172182 TATTCATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (4 bp):
TATG
Found at i:4178986 original size:60 final size:60
Alignment explanation
Indices: 4178894--4179010 Score: 168
Period size: 60 Copynumber: 1.9 Consensus size: 60
4178884 GAACTTGGTA
* *
4178894 ACTATTTTTACATTGGGTTTGAATTTTCTTTTTTGTTT-AAGTTAGGTCT-TGAATTTGGCG
1 ACTATTTTCACATTGGGTTTGAATTATCTTTTTTGTTTGAA-TTA-GTCTCTGAATTTGGCG
4178954 ACTATTTTCACATTAGGGTTTGAATTAT-TTTTTTGTTTGAATTAGTCTCTGAATTTG
1 ACTATTTTCACATT-GGGTTTGAATTATCTTTTTTGTTTGAATTAGTCTCTGAATTTG
4179011 ACAATTGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
59 4 0.08
60 34 0.65
61 14 0.27
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.53
Consensus pattern (60 bp):
ACTATTTTCACATTGGGTTTGAATTATCTTTTTTGTTTGAATTAGTCTCTGAATTTGGCG
Found at i:4181754 original size:24 final size:25
Alignment explanation
Indices: 4181727--4181773 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
4181717 ACTGTCAAAT
*
4181727 TTCAA-GACTAAAGTGGAAAAATAA
1 TTCAAGGACTAAAGTGAAAAAATAA
*
4181751 TTCAAGGACTAAATTGAAAAAAT
1 TTCAAGGACTAAAGTGAAAAAAT
4181774 TACCATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (25 bp):
TTCAAGGACTAAAGTGAAAAAATAA
Found at i:4184415 original size:123 final size:122
Alignment explanation
Indices: 4184277--4184502 Score: 346
Period size: 123 Copynumber: 1.8 Consensus size: 122
4184267 ATTGATATGA
*
4184277 GGGATTCATTTGAACAACAATGAATTTGTGTTGGGGTATTTCAAAAATATTGATCCATG-AAATA
1 GGGATTCATTTGAACAACAATGAATTTGTGTTGGGGTAATTCAAAAATATTGATCCATGAAAATA
* *
4184341 CATATTTGTTTTGGGGTAATTCTTCTCCCATTGCAGCATTTATTTGATGCCATTAAGAG
66 CATATTTGTTTTAGGGTAA--ATTCTCCCATTGCAGCATTTATTTGATGCCATTAAGAG
* * * * *
4184400 GGGATTCATTTGAACAACCATGAATTTGTTTTGGGGTAATTCGATATTATTGATCCATGAAAATA
1 GGGATTCATTTGAACAACAATGAATTTGTGTTGGGGTAATTCAAAAATATTGATCCATGAAAATA
*
4184465 CATATTTGTTTTAGGTTAAATTCTCCCATTGCAGCATT
66 CATATTTGTTTTAGGGTAAATTCTCCCATTGCAGCATT
4184503 GATCCACGAA
Statistics
Matches: 93, Mismatches: 9, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
122 18 0.19
123 53 0.57
124 22 0.24
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (122 bp):
GGGATTCATTTGAACAACAATGAATTTGTGTTGGGGTAATTCAAAAATATTGATCCATGAAAATA
CATATTTGTTTTAGGGTAAATTCTCCCATTGCAGCATTTATTTGATGCCATTAAGAG
Found at i:4189278 original size:19 final size:19
Alignment explanation
Indices: 4189251--4189287 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4189241 AGACTGTAAC
4189251 AATGATGTTTGAAAACTTT
1 AATGATGTTTGAAAACTTT
*
4189270 AATGTTGTTTGAAAACTT
1 AATGATGTTTGAAAACTT
4189288 AGTTATATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.43
Consensus pattern (19 bp):
AATGATGTTTGAAAACTTT
Done.