Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 128 of 433
Found at i:39257346 original size:28 final size:28
Alignment explanation
Indices: 39257239--39257352 Score: 104
Period size: 28 Copynumber: 4.0 Consensus size: 28
39257229 GTGAGCATGA
* **
39257239 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATAGGCC
*
39257267 ATATAAATGTGATTTGGGCCTAATAGGCC
1 ATATGAATGTGA-TTGGGCCTAATAGGCC
* * **
39257296 ATAT-ACAGGTGATTTGGAATAATAGGCC
1 ATATGA-ATGTGATTGGGCCTAATAGGCC
* * *
39257324 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATAGGCC
39257352 A
1 A
39257353 GATACAGGTA
Statistics
Matches: 69, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
28 46 0.67
29 23 0.33
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATAGGCC
Found at i:39258368 original size:21 final size:21
Alignment explanation
Indices: 39258330--39258377 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
39258320 GTAACTGAAA
**
39258330 GGTTTCTTTTTTAGTTAATTAG
1 GGTTTCTTTTTTA-TTAAGAAG
39258352 GGTTTCTTTTATT-TTAAGAAG
1 GGTTTCTTTT-TTATTAAGAAG
39258373 GGTTT
1 GGTTT
39258378 TCAATGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 11 0.48
22 10 0.43
23 2 0.09
ACGTcount: A:0.19, C:0.04, G:0.21, T:0.56
Consensus pattern (21 bp):
GGTTTCTTTTTTATTAAGAAG
Found at i:39265254 original size:40 final size:40
Alignment explanation
Indices: 39265210--39265397 Score: 272
Period size: 40 Copynumber: 4.7 Consensus size: 40
39265200 GCTACTAGCT
39265210 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
39265250 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCC
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
39265290 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * ** *
39265330 CAAATGCCTTCAGG-CTTAGCCCGG-AATTAGCCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
39265369 CAAATGCCTTCGGGACTTGGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
39265398 CAATCCGAAT
Statistics
Matches: 133, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
38 1 0.01
39 32 0.24
40 99 0.74
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:39266606 original size:54 final size:52
Alignment explanation
Indices: 39266530--39266654 Score: 223
Period size: 54 Copynumber: 2.4 Consensus size: 52
39266520 CTCAAAGCTC
39266530 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGC--TTT
*
39266584 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAATAACATGAGAGCTTT
1 TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTT
39266636 TTTTTCTTTCTTTTTCTTT
1 TTTTTCTTTCTTTTTCTTT
39266655 TTTCATCATC
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 22 0.31
54 48 0.69
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.55
Consensus pattern (52 bp):
TTTTTCTTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTT
Found at i:39268676 original size:34 final size:33
Alignment explanation
Indices: 39268631--39268742 Score: 116
Period size: 34 Copynumber: 3.3 Consensus size: 33
39268621 TTTTGATCTT
* * *
39268631 ATATGAAATTCTAATTTAACATATGCTTCTGGAA
1 ATATGACATTCTAATTT-ATATATGTTTCTGGAA
* * *
39268665 ATATGACATTCTAATCTGATATATGTTTTTGAAA
1 ATATGACATTCTAAT-TTATATATGTTTCTGGAA
* * *
39268699 ATATGACATTTTGATCTTATATATGTTTCTGGTA
1 ATATGACATTCTAAT-TTATATATGTTTCTGGAA
39268733 ATATGACATT
1 ATATGACATT
39268743 TTGATATTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 64 0.98
35 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (33 bp):
ATATGACATTCTAATTTATATATGTTTCTGGAA
Found at i:39268743 original size:34 final size:34
Alignment explanation
Indices: 39268651--39268754 Score: 136
Period size: 34 Copynumber: 3.1 Consensus size: 34
39268641 CTAATTTAAC
* * * *
39268651 ATATGCTTCTGGAAATATGACATTCTAATCTGAT
1 ATATGTTTCTGGAAATATGACATTTTGATCTTAT
* *
39268685 ATATGTTTTTGAAAATATGACATTTTGATCTTAT
1 ATATGTTTCTGGAAATATGACATTTTGATCTTAT
* *
39268719 ATATGTTTCTGGTAATATGACATTTTGATATTAT
1 ATATGTTTCTGGAAATATGACATTTTGATCTTAT
39268753 AT
1 AT
39268755 TTGTATTTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 60 1.00
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (34 bp):
ATATGTTTCTGGAAATATGACATTTTGATCTTAT
Found at i:39271300 original size:5 final size:5
Alignment explanation
Indices: 39271290--39271323 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
39271280 TCTTAATATC
*
39271290 TTTTA TTTTA TATTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
39271324 TCAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:39273804 original size:24 final size:24
Alignment explanation
Indices: 39273776--39273825 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
39273766 AAATTTTCCT
39273776 CATGGTATCATAATAAAAAAAATA
1 CATGGTATCATAATAAAAAAAATA
* *
39273800 CATGGTTTCATAATAAAAAACATA
1 CATGGTATCATAATAAAAAAAATA
39273824 CA
1 CA
39273826 GACATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (24 bp):
CATGGTATCATAATAAAAAAAATA
Found at i:39275205 original size:28 final size:28
Alignment explanation
Indices: 39275138--39275227 Score: 134
Period size: 28 Copynumber: 3.4 Consensus size: 28
39275128 TATGACGTTC
*
39275138 TGCTAAGTGAAATAAGACCATGGC-AT-
1 TGCTAAGTGAAATAAGTCCATGGCAATG
39275164 T--TAAGTGAAATAAGTCCATGGCAATG
1 TGCTAAGTGAAATAAGTCCATGGCAATG
*
39275190 TGCTAAGTGAAATAAGTCCATGGCATTG
1 TGCTAAGTGAAATAAGTCCATGGCAATG
39275218 TGCTAAGTGA
1 TGCTAAGTGA
39275228 GAAATTTCCC
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
24 20 0.34
25 2 0.03
26 2 0.03
28 34 0.59
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (28 bp):
TGCTAAGTGAAATAAGTCCATGGCAATG
Found at i:39275331 original size:51 final size:51
Alignment explanation
Indices: 39275251--39275449 Score: 292
Period size: 51 Copynumber: 3.9 Consensus size: 51
39275241 TGAACCTTGG
* *
39275251 GAATAAAATAGCTTTGGACACAAGCGTGGTACTATGTGAAGGCCATTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * *
39275302 GAATATAATAGCTTTGGACACATGTGTGGTACTATGTGAACGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* * *
39275353 GAATTAAATAGCTTTGGACATAAGTGTGGTACTAGGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* *
39275404 GAATAAAATAGCTTT-GACTACAAGGGTGGTACTATATGAAGGCCAC
1 GAATAAAATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGGCCAC
39275450 CGTGTATCCG
Statistics
Matches: 131, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
50 3 0.02
51 128 0.98
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:39282411 original size:20 final size:20
Alignment explanation
Indices: 39282388--39282430 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
39282378 CACTTTAAAC
39282388 TTTGATGACCCAATTTAGAA
1 TTTGATGACCCAATTTAGAA
39282408 TTTGATGACCCAATTTAGAA
1 TTTGATGACCCAATTTAGAA
39282428 TTT
1 TTT
39282431 AAGTCATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
TTTGATGACCCAATTTAGAA
Found at i:39283592 original size:3 final size:3
Alignment explanation
Indices: 39283584--39283617 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
39283574 CTATCTTGTC
39283584 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
39283618 AACTACTCTG
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:39295355 original size:15 final size:15
Alignment explanation
Indices: 39295335--39295402 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
39295325 ATACTACAAA
39295335 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
39295350 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
39295367 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
39295384 ATA-TTAATATTAA-
1 ATATTTATTATTAAT
39295397 ATATTT
1 ATATTT
39295403 TCAATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.25
15 12 0.27
16 1 0.02
17 7 0.16
18 1 0.02
19 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:39295452 original size:16 final size:16
Alignment explanation
Indices: 39295421--39295457 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
39295411 ATGTGAATAA
39295421 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
39295437 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
39295453 TATTA
1 TATTA
39295458 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:39295498 original size:20 final size:22
Alignment explanation
Indices: 39295469--39295525 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
39295459 AATAAAATTG
*
39295469 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
39295489 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* *
39295511 TATTAAT-AATTATAT
1 AAATAATAAATTATAT
39295526 GACTAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.28
21 10 0.31
22 13 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:39296258 original size:28 final size:28
Alignment explanation
Indices: 39296227--39296280 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
39296217 TTCCTTCCTA
39296227 AATTCTCAATTCTCAATAC-TCAATTTCT
1 AATTCTCAATTCTCAAT-CTTCAATTTCT
* * *
39296255 AATTTTCTATTTTCAATCTTCAATTT
1 AATTCTCAATTCTCAATCTTCAATTT
39296281 TCAATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.05
28 21 0.95
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (28 bp):
AATTCTCAATTCTCAATCTTCAATTTCT
Found at i:39301745 original size:43 final size:42
Alignment explanation
Indices: 39301574--39301746 Score: 156
Period size: 43 Copynumber: 4.0 Consensus size: 42
39301564 CATAGGATTT
*
39301574 TCGATATGTGATTCCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATAT-TGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
* * * * *
39301617 TCGAT-TTGAGATTTACGTGTAAGATCATGTCTGGGACATCGTCA
1 TCGATATT--GA-TTACGTGTAAGACCACGTCTGGGACGTTGGCA
* *
39301661 TC-ATATTTGATTTCGTGTAAGACC-CTGTCTGGGTCAG-TGGCA
1 TCGATA-TTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* *
39301703 TCGATACTTGATTACATGTAAGACCACGTCTGTGACGTTGGCA
1 TCGATA-TTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
39301746 T
1 T
39301747 TGTACAAGCT
Statistics
Matches: 102, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
41 1 0.01
42 27 0.26
43 43 0.42
44 29 0.28
45 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
TCGATATTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:39303339 original size:39 final size:41
Alignment explanation
Indices: 39303262--39303341 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 41
39303252 ACTGATGCAT
** *
39303262 ACTGTATCTGAGATAGGCTAAGGCCCTAATTTTTATTTGAA
1 ACTGTATCTGAGATAGGCTAAGGCCCTAAACTATATTTGAA
*
39303303 ACTGTATCTGA-ATGGGCTAAGG-CCTAAACTATATTTGAA
1 ACTGTATCTGAGATAGGCTAAGGCCCTAAACTATATTTGAA
39303342 TCTATAATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 14 0.40
40 10 0.29
41 11 0.31
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (41 bp):
ACTGTATCTGAGATAGGCTAAGGCCCTAAACTATATTTGAA
Found at i:39305794 original size:14 final size:15
Alignment explanation
Indices: 39305765--39305793 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39305755 TAAAATTAAA
39305765 AAAAATTAATATTTT
1 AAAAATTAATATTTT
39305780 AAAAATTAATATTT
1 AAAAATTAATATTT
39305794 ACTTTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAAATTAATATTTT
Found at i:39308603 original size:120 final size:119
Alignment explanation
Indices: 39308386--39308607 Score: 302
Period size: 120 Copynumber: 1.8 Consensus size: 119
39308376 CCAAAATACG
* **
39308386 CTTTAGCCAACTCTTTCATAAGTGTTGGGATATGCAAGCCTAAAGCAACGCTTTTATAAGAGTTG
1 CTTTAGCCAACTCTTTCATAAGGGTTGGGATATGCAAGCCTAAAGCAACGCTTAAATAAGAGTTG
39308451 GTAAAAGTCTAATCCTAAGACGACACTTTTGGGGCAAGTGTTGGTATAGACTGGA
66 GT-AAAGTCTAATCCTAAGACGACACTTTTGGGGCAAGTGTTGGTATAGACTGGA
* * * *
39308506 CTTTAGCCAACTCTTTGTATAAGGGTTGGTATATGCATGCCTAAAGCAATGCTTAAATAAGAGTT
1 CTTTAGCCAACTCTTT-CATAAGGGTTGGGATATGCAAGCCTAAAGCAACGCTTAAATAAGAGTT
** * **
39308571 GGCT-TTGTCTAGTTTTAAGACGACACTTTTGGGGCAA
65 GG-TAAAGTCTAATCCTAAGACGACACTTTTGGGGCAA
39308608 CACTTTCCTA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
120 44 0.50
121 43 0.49
122 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (119 bp):
CTTTAGCCAACTCTTTCATAAGGGTTGGGATATGCAAGCCTAAAGCAACGCTTAAATAAGAGTTG
GTAAAGTCTAATCCTAAGACGACACTTTTGGGGCAAGTGTTGGTATAGACTGGA
Found at i:39308706 original size:91 final size:91
Alignment explanation
Indices: 39308525--39308716 Score: 287
Period size: 91 Copynumber: 2.1 Consensus size: 91
39308515 ACTCTTTGTA
* **
39308525 TAAGGGTTGGTATATGCATGCCTAAAGCAATGCTTAAATAAGAGTTGGCTTTGTCTAGTTTTAAG
1 TAAGGGTTGGTATATGCATGCCTAAAGCAACGCTTAAATAAGAGTTGGCTTTGTCTAGTCCTAAG
39308590 ACGACACTTTTGGGGCAACACTTTCC
66 ACGACACTTTTGGGGCAACACTTTCC
* * * *
39308616 TAAGGGTTGGTATATGTATGCCTATAGCAACGCTTGAATAAGAGTTGGTTTTTGTCTAGTCCTAA
1 TAAGGGTTGGTATATGCATGCCTAAAGCAACGCTTAAATAAGAGTTGG-CTTTGTCTAGTCCTAA
*
39308681 GACGACACTTTTGTGGCAACA-TTTCC
65 GACGACACTTTTGGGGCAACACTTTCC
*
39308707 TAAGTGTTGG
1 TAAGGGTTGG
39308717 GATAGACTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 58 0.64
92 33 0.36
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (91 bp):
TAAGGGTTGGTATATGCATGCCTAAAGCAACGCTTAAATAAGAGTTGGCTTTGTCTAGTCCTAAG
ACGACACTTTTGGGGCAACACTTTCC
Found at i:39308782 original size:131 final size:132
Alignment explanation
Indices: 39308616--39309085 Score: 606
Period size: 132 Copynumber: 3.5 Consensus size: 132
39308606 AACACTTTCC
* * *
39308616 TAAGGGTTGGTATATGTATGCCTATA-GCAACGCTTGAATAAGAGTTGGTTTTTGTCTAGTCCTA
1 TAAGGGTTGGTATATGTATGCCTA-AGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTA
*
39308680 AGACGACACTTTTGTGGCAACA-TTTCCTAAGTGTTGGGATAGACTTTGCTTTGGCCAACTCTTT
65 AGACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTTTGCTTTGGCCAACTCTTT
39308744 GTA
130 GTA
*
39308747 TAAGGGTTGGTATATGTATGCCTAAGGCAATGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAA
1 TAAGGGTTGGTATATGTATGCCTAAGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAA
* * * *
39308812 GACGACACTTTTGTGGCGACATTTTACTAAGTGTTGGTATAGACTATGCTTTGGCCAACTCTTTG
66 GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTTTGCTTTGGCCAACTCTTTG
39308877 TA
131 TA
* * *
39308879 TAAGGGTTGGGATATGTATGACTCAGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAA
1 TAAGGGTTGGTATATGTATGCCTAAGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAA
* * * *
39308944 GACGACACTTTTTTGGTGACACTTTCCGAAGTGTTGGGATAGACTGGCCAACTTATGCTTTAGCC
66 GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGAT--A---G---ACTT-TGCTTTGGCC
39309009 AACTCTTTGTA
122 AACTCTTTGTA
* * * * * * **
39309020 TAAGGGTTGG-ATATGCATGCCAAAGACAACACTTAAATAAGAGTTGGC-TTTGTCCAGTCCTAA
1 TAAGGGTTGGTATATGTATGCCTAAGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAA
39309083 GAC
66 GAC
39309086 AATATATATT
Statistics
Matches: 298, Mismatches: 30, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
130 1 0.00
131 79 0.27
132 137 0.46
134 1 0.00
137 1 0.00
139 16 0.05
140 33 0.11
141 30 0.10
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (132 bp):
TAAGGGTTGGTATATGTATGCCTAAGGCAACGCTTGAATAAAAGTTGGCTTTTGTATAGTCCTAA
GACGACACTTTTGTGGCGACACTTTCCTAAGTGTTGGGATAGACTTTGCTTTGGCCAACTCTTTG
TA
Found at i:39309547 original size:29 final size:29
Alignment explanation
Indices: 39309505--39309572 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
39309495 AGCTTCTATA
*
39309505 TTTAGGATTTAGGGTTTAT-GATTTAAGAG
1 TTTAGGATTTAGGGTGTATGGATTTAAG-G
* *
39309534 TTTAGGCTTTAGGGTGTATGGTTTTAAGG
1 TTTAGGATTTAGGGTGTATGGATTTAAGG
39309563 TTTAGGATTT
1 TTTAGGATTT
39309573 TATGGTCTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.47
Consensus pattern (29 bp):
TTTAGGATTTAGGGTGTATGGATTTAAGG
Found at i:39309573 original size:15 final size:13
Alignment explanation
Indices: 39309505--39309612 Score: 54
Period size: 15 Copynumber: 7.5 Consensus size: 13
39309495 AGCTTCTATA
*
39309505 TTTAGGATTTAGGG
1 TTTAGG-TTTAAGG
*
39309519 TTTATGATTTAAGAG
1 TTTA-GGTTTAAG-G
*
39309534 TTTAGGCTTTAGGG
1 TTTAGG-TTTAAGG
*
39309548 TGTATGGTTTTAAGG
1 TTTA-GG-TTTAAGG
*
39309563 TTTAGGATTTTATGG
1 TTTAGG--TTTAAGG
39309578 TCTTGAGGTTTAAGG
1 T-TT-AGGTTTAAGG
*
39309593 TTTGTGGTTTAAGG
1 TTT-AGGTTTAAGG
*
39309607 CTTAGG
1 TTTAGG
39309613 GTTTTGATAA
Statistics
Matches: 74, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
13 2 0.03
14 30 0.41
15 37 0.50
16 2 0.03
17 3 0.04
ACGTcount: A:0.20, C:0.03, G:0.31, T:0.45
Consensus pattern (13 bp):
TTTAGGTTTAAGG
Found at i:39312266 original size:15 final size:16
Alignment explanation
Indices: 39312243--39312275 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39312233 TTAGTTAACC
39312243 TTTTCTTTTCC-TTTT
1 TTTTCTTTTCCGTTTT
*
39312258 TTTTTTTTTCCGTTTT
1 TTTTCTTTTCCGTTTT
39312274 TT
1 TT
39312276 AGATTTAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTCCGTTTT
Found at i:39312389 original size:26 final size:26
Alignment explanation
Indices: 39312342--39312392 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
39312332 TAGATATTAT
** *
39312342 TTGTCATAAATTTTAATATTATTTAA
1 TTGTCATAAAGATAAATATTATTTAA
*
39312368 TTGTCATAAAGATAAATTTTATTTA
1 TTGTCATAAAGATAAATATTATTTA
39312393 TTTTAATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (26 bp):
TTGTCATAAAGATAAATATTATTTAA
Found at i:39314788 original size:41 final size:41
Alignment explanation
Indices: 39314743--39314910 Score: 119
Period size: 41 Copynumber: 4.1 Consensus size: 41
39314733 CCTTCGGAAT
* * *
39314743 CAAGCCCGATTCTTAGCACTGGCTCAAAAGCCCTTCAAGAC
1 CAAGCCTGATTATGAGCACTGGCTCAAAAGCCCTTCAAGAC
* * * * *
39314784 CAAGCTCGGATTA-GACCACTGGCTCGAAGGCCCTTC-GGAAC
1 CAAGC-CTGATTATGAGCACTGGCTCAAAAGCCCTTCAAG-AC
* * * * *
39314825 TAAGTCTGGTTATGA-CACTGGCTCTAAAGCCCCTCGAA-AC
1 CAAGCCTGATTATGAGCACTGGCTCAAAAGCCCTTC-AAGAC
* * * * *
39314865 TAAGTCTGGTTATTAGCACTGGCTCAAAAGCCCTTCGAGAC
1 CAAGCCTGATTATGAGCACTGGCTCAAAAGCCCTTCAAGAC
39314906 CAAGC
1 CAAGC
39314911 TCGGATTTAG
Statistics
Matches: 99, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
40 40 0.40
41 54 0.55
42 5 0.05
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (41 bp):
CAAGCCTGATTATGAGCACTGGCTCAAAAGCCCTTCAAGAC
Found at i:39314866 original size:40 final size:41
Alignment explanation
Indices: 39314757--39314902 Score: 165
Period size: 41 Copynumber: 3.6 Consensus size: 41
39314747 CCCGATTCTT
*
39314757 AGCACTGGCTCAAAAGCCCTTC-AAGACCAAG-CTCGGATTA-G
1 AGCACTGGCTCAAAAGCCCTTCGAA-ACTAAGTCT-GG-TTATG
* * * *
39314798 ACCACTGGCTCGAAGGCCCTTCGGAACTAAGTCTGGTTATG
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTCTGGTTATG
* * *
39314839 A-CACTGGCTCTAAAGCCCCTCGAAACTAAGTCTGGTTATT
1 AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTCTGGTTATG
39314879 AGCACTGGCTCAAAAGCCCTTCGA
1 AGCACTGGCTCAAAAGCCCTTCGA
39314903 GACCAAGCTC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
40 38 0.43
41 48 0.54
42 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (41 bp):
AGCACTGGCTCAAAAGCCCTTCGAAACTAAGTCTGGTTATG
Found at i:39321249 original size:14 final size:14
Alignment explanation
Indices: 39321230--39321259 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39321220 GGATATTTCC
39321230 TTGGGCTATTTTTT
1 TTGGGCTATTTTTT
*
39321244 TTGGGCTGTTTTTT
1 TTGGGCTATTTTTT
39321258 TT
1 TT
39321260 CAAATATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.07, G:0.23, T:0.67
Consensus pattern (14 bp):
TTGGGCTATTTTTT
Found at i:39325678 original size:38 final size:38
Alignment explanation
Indices: 39325512--39325931 Score: 169
Period size: 38 Copynumber: 11.4 Consensus size: 38
39325502 AGATAGGTCA
* * * * * *
39325512 ATCCCAACCTTTGCTAAAA-GTCGCCTTAGATAAGATAT
1 ATCCCAACATTT-TTAAAAGGTTGCCTTAGACAATATCT
* *
39325550 ATACCAACATTTTT--AAGGTTACCTTAGA-AGA-ATCT
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACA-ATATCT
* * * * *
39325585 ATCGCAACCTTTTT--AACGTTGCTTTAAACAAGTA--T
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACAA-TATCT
* **
39325620 ATCCCAACCTTTTTTTAAGGTTGCCTTAGACAATATCT
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACAATATCT
* * * **
39325658 ATTCTAACATTTTTAAAAGGTTGCCTTAAAC-ATGCCT
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACAATATCT
* * *
39325695 ATCCCAACCTTTCCT-AAAGGTTGCCTTAGACAAGATCT
1 ATCCCAACATTT-TTAAAAGGTTGCCTTAGACAATATCT
* * * * ** *
39325733 ATCCCAACTTTTTTAAAAAGTTGCTTTAGATAAGGTTT
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACAATATCT
* ** * * * ***
39325771 ATACCAATTTTTTTTAAGGGTTGCTTTAGACAAGGCCT
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACAATATCT
* * *
39325809 ATCTCAACCTTTTT--AAGGTTGCCTT--A-AATGAGTCA
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACAAT-A-TCT
* * **
39325844 ATCCCAAC-CTTTT-AAAGGTTGCCATAGAC-GGATCT
1 ATCCCAACATTTTTAAAAGGTTGCCTTAGACAATATCT
* * *
39325879 ATCCCAACTATTCTTAAAA-GTTGCCTTAGACAAGAACT
1 ATCCCAAC-ATTTTTAAAAGGTTGCCTTAGACAATATCT
* *
39325917 ATACCAACCTTTTTA
1 ATCCCAACATTTTTA
39325932 TAGTTGCCTT
Statistics
Matches: 288, Mismatches: 72, Indels: 45
0.71 0.18 0.11
Matches are distributed among these distances:
33 2 0.01
34 5 0.02
35 70 0.24
36 23 0.08
37 65 0.23
38 123 0.43
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (38 bp):
ATCCCAACATTTTTAAAAGGTTGCCTTAGACAATATCT
Found at i:39325883 original size:35 final size:35
Alignment explanation
Indices: 39325439--39325947 Score: 204
Period size: 35 Copynumber: 14.0 Consensus size: 35
39325429 TTGGAAAAGG
* * * *
39325439 TCTATCCCAACCTTTTTAGGGTTG-CTGTAAACAGG
1 TCTATCCCAACCTTTTAAAGGTTGCCT-TAGACAGA
** * * * * * *
39325474 TCTATTTCAACATTTTTAACGTTGTCTTAGATAGG
1 TCTATCCCAACCTTTTAAAGGTTGCCTTAGACAGA
* * * *
39325509 TCAATCCCAACCTTTGCTAAAAGTCGCCTTAGATAAGA
1 TCTATCCCAACCTTT--TAAAGGTTGCCTTAGA-CAGA
* * * * *
39325547 TATATACCAACATTTTTAAGGTTACCTTAGA-AGAA
1 TCTATCCCAACCTTTTAAAGGTTGCCTTAGACAG-A
* * * * *
39325582 TCTATCGCAACCTTTTTAACGTTGCTTTAAACA-A
1 TCTATCCCAACCTTTTAAAGGTTGCCTTAGACAGA
* * *
39325616 GTATATCCCAACCTTTTTTTAAGGTTGCCTTAGACAATA
1 -TCTATCCCAACC--TTTTAAAGGTTGCCTTAGAC-AGA
* * * *
39325655 TCTATTCTAACATTTTTAAAAGGTTGCCTTAAACATG-
1 TCTATCCCAAC-CTTTT-AAAGGTTGCCTTAGACA-GA
*
39325692 CCTATCCCAACCTTTCCTAAAGGTTGCCTTAGACAAGA
1 TCTATCCCAACCTTT--TAAAGGTTGCCTTAGAC-AGA
* * * * *
39325730 TCTATCCCAACTTTTTTAAAAAGTTGCTTTAGATAAGG
1 TCTATCCCAAC-CTTTT-AAAGGTTGCCTTAGA-CAGA
* * ** * * *
39325768 TTTATACCAATTTTTTTTAAGGGTTGCTTTAGACAAGG
1 TCTATCCCAA--CCTTTTAAAGGTTGCCTTAGAC-AGA
* * *
39325806 CCTATCTCAACCTTTTTAAGGTTGCCTTA-A-ATGA
1 TCTATCCCAACCTTTTAAAGGTTGCCTTAGACA-GA
* * *
39325840 GTCAATCCCAACCTTTTAAAGGTTGCCATAGACGGA
1 -TCTATCCCAACCTTTTAAAGGTTGCCTTAGACAGA
* *
39325876 TCTATCCCAACTATTCTTAAAAGTTGCCTTAGACAAGA
1 TCTATCCCAAC-CTT-TTAAAGGTTGCCTTAGAC-AGA
* * * *
39325914 ACTATACCAACCTTTTTATA-GTTGCCTTATACAG
1 TCTATCCCAACC-TTTTAAAGGTTGCCTTAGACAG
39325948 GTTTATAACA
Statistics
Matches: 354, Mismatches: 88, Indels: 64
0.70 0.17 0.13
Matches are distributed among these distances:
33 1 0.00
34 4 0.01
35 107 0.30
36 48 0.14
37 79 0.22
38 106 0.30
39 9 0.03
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (35 bp):
TCTATCCCAACCTTTTAAAGGTTGCCTTAGACAGA
Found at i:39326509 original size:2 final size:2
Alignment explanation
Indices: 39326497--39326530 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39326487 ATCAAAATAA
39326497 AT AT A- 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
39326531 AAAGTGAAAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39328651 original size:43 final size:44
Alignment explanation
Indices: 39328521--39328685 Score: 164
Period size: 43 Copynumber: 3.8 Consensus size: 44
39328511 TTCCGGTATG
* *
39328521 TGATTTTGTGTAAGACCACGTCTGGGA-TGTTGGCATCGAT-TT
1 TGATTTCGTGTAAGACCACGTCTGGGACAGTTGGCATCGATATT
* * * *
39328563 GAGATTTACGTGTAAAACCATGTTTGGGACA-TTGGCATCG-TATT
1 -TGATTT-CGTGTAAGACCACGTCTGGGACAGTTGGCATCGATATT
*
39328607 TGATTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATTGATATT
1 TGATTTCGTGTAAGACCAC-GTCTGGGACAGTTGGCATCGATATT
** *
39328650 TGATAACATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 TGATTTCGTGTAAGACCACGTCTGGGACAGTTGGCAT
39328686 TGTACGAGTT
Statistics
Matches: 100, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
42 27 0.27
43 44 0.44
44 29 0.29
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (44 bp):
TGATTTCGTGTAAGACCACGTCTGGGACAGTTGGCATCGATATT
Found at i:39329360 original size:22 final size:22
Alignment explanation
Indices: 39329326--39329378 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
39329316 AATTGCCATC
* *
39329326 TTGA-TATGATTTGGTAGTTAAA
1 TTGAGTATGATTTGATA-TGAAA
*
39329348 TTG-GTATGCTTTGATATGAAA
1 TTGAGTATGATTTGATATGAAA
39329369 TTGAGTATGA
1 TTGAGTATGA
39329379 AATTCATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (22 bp):
TTGAGTATGATTTGATATGAAA
Found at i:39334581 original size:43 final size:43
Alignment explanation
Indices: 39334533--39334618 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
39334523 GATGAATTTT
39334533 GGATAATGGCTATGCAAGAAGAATTAAATCAATTTGAAAAAAA
1 GGATAATGGCTATGCAAGAAGAATTAAATCAATTTGAAAAAAA
39334576 GGATAATGGCTATGCAAGAAGAATTAAATCAATTTGAAAAAAA
1 GGATAATGGCTATGCAAGAAGAATTAAATCAATTTGAAAAAAA
39334619 AATCAAGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (43 bp):
GGATAATGGCTATGCAAGAAGAATTAAATCAATTTGAAAAAAA
Found at i:39344577 original size:46 final size:45
Alignment explanation
Indices: 39344519--39344671 Score: 123
Period size: 48 Copynumber: 3.3 Consensus size: 45
39344509 TGGCATTGGT
39344519 GGACATGCATCGGCCT-CAAGATGTAAGCCAGTGTAAGA-CATATCTG
1 GGACATGCATCGG-CTACAAGATGT--GCCAGTGTAAGACCATATCTG
* * * *
39344565 GGACATGTATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCTG
1 GGACATGCATCGGCTACAAGATGTGCCAGTGTAAGACCATATCTG
** * * * *
39344610 GGATGTGGCATTGGC-ACCTATAGAGGTGCCAGTGTAAGACCATGTCTA
1 GGACAT-GCATCGGCTA-C-A-AGATGTGCCAGTGTAAGACCATATCTG
39344658 GGACATGGCATCGG
1 GGACAT-GCATCGG
39344672 TATGGATATG
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
44 11 0.13
45 14 0.16
46 26 0.30
48 35 0.41
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (45 bp):
GGACATGCATCGGCTACAAGATGTGCCAGTGTAAGACCATATCTG
Found at i:39344704 original size:50 final size:49
Alignment explanation
Indices: 39344639--39344769 Score: 149
Period size: 50 Copynumber: 2.7 Consensus size: 49
39344629 ATAGAGGTGC
* * *
39344639 CAGTGTAAGACCATGTCTAGGACATGGCATCGGTATGGATATGT-GAGAG-
1 CAGTATAAGACCATGTCTAGGACATGGCATCGGCATCGAT-T-TCGAGAGT
* * *
39344688 CTAGTATAAGACCATGTCTAGGACATGGCGTCGGCCTCGATTTCGATAGT
1 C-AGTATAAGACCATGTCTAGGACATGGCATCGGCATCGATTTCGAGAGT
* *
39344738 CAGTGTAAGACCATGTCTGGGACATGGCATCG
1 CAGTATAAGACCATGTCTAGGACATGGCATCG
39344770 ACTTGATGGA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.01
49 34 0.49
50 35 0.50
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (49 bp):
CAGTATAAGACCATGTCTAGGACATGGCATCGGCATCGATTTCGAGAGT
Found at i:39347638 original size:210 final size:210
Alignment explanation
Indices: 39347276--39347697 Score: 790
Period size: 210 Copynumber: 2.0 Consensus size: 210
39347266 ATTTTCAACA
*
39347276 AGATTTCCACCAAAGTCTCCACATTTCCCATATTTTTAAAGTAAACCCTAAAATTTCATTTTTTA
1 AGATTTCCACCAAAGTCTCCACATTTCCCATATTTTTAAAGTAAACCCTAAAATCTCATTTTTTA
* *
39347341 TTTCAAAATCATACTAGCTTTAGAATACAACTTTTTATAAATATATTGTTTTAAATTGAACATAT
66 TTTCAAAATCATACTAGCTTTAGAAGACAACTTTTTATAAATATATTATTTTAAATTGAACATAT
*
39347406 ATAACTTTTACATATATACATATTTTTGTTACTGTACATATTTTAGATATATATACGTATCAAAT
131 ATAACTTTTACATATATACATATTTTCGTTACTGTACATATTTTAGATATATATACGTATCAAAT
39347471 AAAAAAATTACTTTC
196 AAAAAAATTACTTTC
*
39347486 AGATTTCCACCAAAGTCTCCACATTTCCCATATTTTTAAGGTAAACCCTAAAATCTCATTTTTTA
1 AGATTTCCACCAAAGTCTCCACATTTCCCATATTTTTAAAGTAAACCCTAAAATCTCATTTTTTA
39347551 TTTCAAAATCATACTAGCTTTAGAAGACAACTTTTTATAAATATATTATTTTAAATTGAACATAT
66 TTTCAAAATCATACTAGCTTTAGAAGACAACTTTTTATAAATATATTATTTTAAATTGAACATAT
*
39347616 ATAACTTTTACATATATACATATTTTCGTTACTGTACATATTTTAGATCTATATACGTATCAAAT
131 ATAACTTTTACATATATACATATTTTCGTTACTGTACATATTTTAGATATATATACGTATCAAAT
39347681 AAAAAAATTACTTTC
196 AAAAAAATTACTTTC
39347696 AG
1 AG
39347698 TTTGCCCTTT
Statistics
Matches: 206, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
210 206 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (210 bp):
AGATTTCCACCAAAGTCTCCACATTTCCCATATTTTTAAAGTAAACCCTAAAATCTCATTTTTTA
TTTCAAAATCATACTAGCTTTAGAAGACAACTTTTTATAAATATATTATTTTAAATTGAACATAT
ATAACTTTTACATATATACATATTTTCGTTACTGTACATATTTTAGATATATATACGTATCAAAT
AAAAAAATTACTTTC
Found at i:39358627 original size:13 final size:14
Alignment explanation
Indices: 39358609--39358641 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39358599 GGTGAGAATA
39358609 AAAAATAATTTA-T
1 AAAAATAATTTATT
*
39358622 AAAAATATTTTATT
1 AAAAATAATTTATT
39358636 AAAAAT
1 AAAAAT
39358642 TATATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAAAATAATTTATT
Found at i:39363675 original size:17 final size:18
Alignment explanation
Indices: 39363640--39363676 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39363630 TTTGTTAATC
39363640 TATTTTTAGTAAATTTTA
1 TATTTTTAGTAAATTTTA
39363658 TATTTTT-G-AAATTGTTA
1 TATTTTTAGTAAATT-TTA
39363675 TA
1 TA
39363677 GCTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 6 0.33
18 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (18 bp):
TATTTTTAGTAAATTTTA
Found at i:39365260 original size:54 final size:54
Alignment explanation
Indices: 39365178--39365286 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
39365168 TCAACCTAGA
39365178 GTCAGTTGCTTTGACTCTCGAAAGAGATATTAACATAATTTAGGGATTTCTATG
1 GTCAGTTGCTTTGACTCTCGAAAGAGATATTAACATAATTTAGGGATTTCTATG
*
39365232 GTCAGTTGCTTTTACTCTCGAAAGAGATATTAACATAATTTAGGGATTTCTATG
1 GTCAGTTGCTTTGACTCTCGAAAGAGATATTAACATAATTTAGGGATTTCTATG
39365286 G
1 G
39365287 ATCAAGACAC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (54 bp):
GTCAGTTGCTTTGACTCTCGAAAGAGATATTAACATAATTTAGGGATTTCTATG
Found at i:39365318 original size:40 final size:40
Alignment explanation
Indices: 39365266--39365346 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
39365256 AGATATTAAC
39365266 ATAATTTAGGGATTTCTATGGATCAAGACACAAGTGAATA
1 ATAATTTAGGGATTTCTATGGATCAAGACACAAGTGAATA
*
39365306 ATAATTTAGGGATTTCTATGGATCAGGACACAAGTGAATA
1 ATAATTTAGGGATTTCTATGGATCAAGACACAAGTGAATA
39365346 A
1 A
39365347 ATCGTTTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (40 bp):
ATAATTTAGGGATTTCTATGGATCAAGACACAAGTGAATA
Found at i:39366302 original size:21 final size:21
Alignment explanation
Indices: 39366264--39366304 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39366254 GTAAGTCTAC
* **
39366264 TTATTTTATGGATGAATGCAT
1 TTATATTATGGACAAATGCAT
39366285 TTATATTATGGACAAATGCA
1 TTATATTATGGACAAATGCA
39366305 CTAACTTGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (21 bp):
TTATATTATGGACAAATGCAT
Found at i:39375974 original size:6 final size:6
Alignment explanation
Indices: 39375960--39376004 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
39375950 ATAATTTTGG
* * * *
39375960 AGATGA AGATTA AGATGG ACATGG AGATGA AGATGA AGATGA AGA
1 AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGA
39376005 AGATGAGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.47, C:0.02, G:0.33, T:0.18
Consensus pattern (6 bp):
AGATGA
Found at i:39378262 original size:26 final size:26
Alignment explanation
Indices: 39378204--39378265 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
39378194 CAATAATAGA
* *
39378204 CTAAATGCTTTCTCAATAAAGATATG
1 CTAAATTCTTTCTCAATAAAAATATG
39378230 CTAAATTCTTTCTCAATAAAAATATG
1 CTAAATTCTTTCTCAATAAAAATATG
39378256 CTAAATTCTT
1 CTAAATTCTT
39378266 ACCAATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (26 bp):
CTAAATTCTTTCTCAATAAAAATATG
Found at i:39388825 original size:13 final size:13
Alignment explanation
Indices: 39388807--39388831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39388797 AATAAAGTAG
39388807 GACACAGCCGTGC
1 GACACAGCCGTGC
39388820 GACACAGCCGTG
1 GACACAGCCGTG
39388832 TGCACCAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.36, G:0.32, T:0.08
Consensus pattern (13 bp):
GACACAGCCGTGC
Found at i:39395091 original size:22 final size:22
Alignment explanation
Indices: 39395066--39395112 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
39395056 TGGGATAGAG
*
39395066 TATATGTATCGAAAAATGAACT
1 TATATGTAACGAAAAATGAACT
39395088 TATATGTAACGAAAAATGAACT
1 TATATGTAACGAAAAATGAACT
39395110 TAT
1 TAT
39395113 TCAGAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (22 bp):
TATATGTAACGAAAAATGAACT
Found at i:39404852 original size:29 final size:29
Alignment explanation
Indices: 39404828--39404921 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
39404818 TCGCACAGCC
*
39404828 AGTGCCGTATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
39404857 AGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
39404886 AGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
39404915 AGTGCCA
1 AGTGCCA
39404922 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (29 bp):
AGTGCCATATATTTCCAGCATGCACACTT
Found at i:39404853 original size:58 final size:58
Alignment explanation
Indices: 39404791--39404921 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
39404781 ATTTAAGCCC
* * * *
39404791 GCACACATAGTGCCATACCCTTCGAGC-TCGCACAGC-CAGTGCCGTATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCAT-GCACA-CTCAGTGCCATATATTTCCAGCAT
* * *
39404849 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
39404907 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
39404922 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
57 1 0.02
58 62 0.97
59 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (58 bp):
GCACACTTAGTGCCATACACTTCCAGCATGCACACTCAGTGCCATATATTTCCAGCAT
Found at i:39408332 original size:64 final size:64
Alignment explanation
Indices: 39408231--39408358 Score: 195
Period size: 64 Copynumber: 2.0 Consensus size: 64
39408221 ACTTATAACT
* * *
39408231 ATTCGAGTGGGAATTAACCAATTATTATCATTCTCAACTATAGTTAAACATCTCTTCTTTGGAA
1 ATTCGAGTGGGAATTAACCAATTATTATCATTCTCAACTACAGGTAAACATCCCTTCTTTGGAA
* *
39408295 ATTCGAGTGGGAGTTAACTC-ATTATTATCATTCTCAACTACAGGTAGACATCCCTTCTTTGGAA
1 ATTCGAGTGGGAATTAAC-CAATTATTATCATTCTCAACTACAGGTAAACATCCCTTCTTTGGAA
39408359 CACGCTGGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 57 0.98
65 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (64 bp):
ATTCGAGTGGGAATTAACCAATTATTATCATTCTCAACTACAGGTAAACATCCCTTCTTTGGAA
Found at i:39412967 original size:81 final size:81
Alignment explanation
Indices: 39412832--39412989 Score: 298
Period size: 81 Copynumber: 2.0 Consensus size: 81
39412822 GTGAGATAGG
39412832 CATAAGACTGAATTGGACAAAATAAAACCATACCTTTGCTAATAAGGTCAAGTATTCTCTGCGAC
1 CATAAGACTGAATTGGACAAAATAAAACCATACCTTTGCTAATAAGGTCAAGTATTCTCTGCGAC
*
39412897 AAGTATGAGTCCCAGA
66 AACTATGAGTCCCAGA
*
39412913 CATAAGACTGAATTGGACAAAATAAAACCATACCTTTGCTAATAAGGTCAAGTATTCTCTGTGAC
1 CATAAGACTGAATTGGACAAAATAAAACCATACCTTTGCTAATAAGGTCAAGTATTCTCTGCGAC
39412978 AACTATGAGTCC
66 AACTATGAGTCC
39412990 TGTGTTTTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (81 bp):
CATAAGACTGAATTGGACAAAATAAAACCATACCTTTGCTAATAAGGTCAAGTATTCTCTGCGAC
AACTATGAGTCCCAGA
Found at i:39413879 original size:7 final size:7
Alignment explanation
Indices: 39413867--39413893 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39413857 TATAAAAATT
39413867 AATATAA
1 AATATAA
39413874 AATATAA
1 AATATAA
39413881 AATATAA
1 AATATAA
39413888 AATATA
1 AATATA
39413894 TTAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATATAA
Found at i:39417509 original size:36 final size:36
Alignment explanation
Indices: 39417462--39417534 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
39417452 TTATTCTTTA
39417462 ACTTAGAATAATTAAATCTTTGTTCATGTTGTTACG
1 ACTTAGAATAATTAAATCTTTGTTCATGTTGTTACG
39417498 ACTTAGAATAATTAAATCTTTGTTCATGTTGTTACG
1 ACTTAGAATAATTAAATCTTTGTTCATGTTGTTACG
39417534 A
1 A
39417535 ATAATTTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (36 bp):
ACTTAGAATAATTAAATCTTTGTTCATGTTGTTACG
Found at i:39427326 original size:48 final size:47
Alignment explanation
Indices: 39427226--39427330 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 47
39427216 ATTGATAAGT
* * *
39427226 ACTATACCATGGCCTGTAGCCAAATCAAGGTAACTTATCCCAGAGTA
1 ACTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAGAATA
* * ***
39427273 CCTATACCATGGCCCGTAGCCAAATCAAAGGTAACTCCTCTTTGAATA
1 ACTATACCATGGCCCGTAGCCAAATC-AAGGTAACTCATCCCAGAATA
39427321 ACTATACCAT
1 ACTATACCAT
39427331 AGGTCGCAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
47 24 0.50
48 24 0.50
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (47 bp):
ACTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAGAATA
Found at i:39434304 original size:12 final size:12
Alignment explanation
Indices: 39434287--39434311 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39434277 CTTATCACAT
39434287 ATATACACTTTC
1 ATATACACTTTC
39434299 ATATACACTTTC
1 ATATACACTTTC
39434311 A
1 A
39434312 CATTCATCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATACACTTTC
Found at i:39434305 original size:59 final size:50
Alignment explanation
Indices: 39434299--39434456 Score: 198
Period size: 49 Copynumber: 3.4 Consensus size: 50
39434289 ATACACTTTC
39434299 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC-ATAT
1 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATAT
39434348 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT--C-----
1 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATAT
*
39434391 ----ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTC-ATAT
1 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATAT
* *
39434436 TTATACACATTCACATTCATC
1 ATATACACTTTCACATTCATC
39434457 GCGTAAAATC
Statistics
Matches: 98, Mismatches: 1, Indels: 20
0.82 0.01 0.17
Matches are distributed among these distances:
39 38 0.39
41 1 0.01
47 1 0.01
49 58 0.59
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.34
Consensus pattern (50 bp):
ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATAT
Found at i:39434353 original size:49 final size:49
Alignment explanation
Indices: 39434136--39434456 Score: 332
Period size: 47 Copynumber: 6.7 Consensus size: 49
39434126 CCCTTCGGGA
* * * * *
39434136 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39434183 CCTATCACATA-A-ATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39434230 CTTATCAC--ATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39434277 CTTATCACATATATACACTTTCATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----AT--A---T-ATATACACTTTCACATTCATCACATCGGCCATTAGGC
39434336 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39434385 CTTAT--C--------ACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39434424 CTTATCTCATATTTATACACATTCACATTCATC
1 CTTATCACATATATATACACTTTCACATTCATC
39434457 GCGTAAAATC
Statistics
Matches: 238, Mismatches: 10, Indels: 50
0.80 0.03 0.17
Matches are distributed among these distances:
39 38 0.16
41 1 0.00
45 1 0.00
46 1 0.00
47 89 0.37
49 58 0.24
50 1 0.00
53 1 0.00
55 3 0.01
58 1 0.00
59 44 0.18
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39434359 original size:61 final size:59
Alignment explanation
Indices: 39434240--39434393 Score: 220
Period size: 49 Copynumber: 2.8 Consensus size: 59
39434230 CTTATCACAT
39434240 ATATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 ATATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
*
39434299 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC----AT--A---T-
1 ATATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
*
39434348 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
1 ATATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
39434394 CTTTCACATT
Statistics
Matches: 93, Mismatches: 1, Indels: 11
0.89 0.01 0.10
Matches are distributed among these distances:
49 45 0.48
50 1 0.01
53 1 0.01
55 2 0.02
59 44 0.47
ACGTcount: A:0.31, C:0.30, G:0.08, T:0.32
Consensus pattern (59 bp):
ATATACACCTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
Found at i:39434396 original size:39 final size:39
Alignment explanation
Indices: 39434352--39434429 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
39434342 ACATATATAT
39434352 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
39434391 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
39434430 TCATATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (39 bp):
ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
Found at i:39434406 original size:106 final size:106
Alignment explanation
Indices: 39434195--39434393 Score: 344
Period size: 108 Copynumber: 1.9 Consensus size: 106
39434185 TATCACATAA
* *
39434195 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACCTTCACATTCAT
1 ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACCTTCACATTCAT
*
39434260 CACATCGGCCATTAGGCCTTATCACATATATACACTTTCAT
66 CACATCGGCCATTAGGCCTTATCACATATATACACATTCAT
*
39434301 ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTC
1 ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACCTTCACATTC
39434366 ATCACATCGGCCATTAGGCCTTATCACA
64 ATCACATCGGCCATTAGGCCTTATCACA
39434394 CTTTCACATT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 41 0.47
108 47 0.53
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (106 bp):
ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACCTTCACATTCAT
CACATCGGCCATTAGGCCTTATCACATATATACACATTCAT
Found at i:39442249 original size:42 final size:42
Alignment explanation
Indices: 39442202--39442323 Score: 138
Period size: 43 Copynumber: 2.9 Consensus size: 42
39442192 TACCATACCA
* * * * *
39442202 ATGCCATATCCCAGATATGGTCTTACATGAGATCTTATATCG
1 ATGCCATATCCTAGATATGGTCTTACACGAAATCTCACATCG
* * *
39442244 ATGCCAATAGCCTAGCTATAGTCTTACACGAAATCTCACATCG
1 ATGCC-ATATCCTAGATATGGTCTTACACGAAATCTCACATCG
*
39442287 ATGCCATATCCTAGATACGGTCTTACAC-ATAATCTCA
1 ATGCCATATCCTAGATATGGTCTTACACGA-AATCTCA
39442324 ACTAACCATA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 1 0.02
42 31 0.47
43 34 0.52
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCTAGATATGGTCTTACACGAAATCTCACATCG
Found at i:39447673 original size:20 final size:20
Alignment explanation
Indices: 39447647--39447692 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
39447637 TAGGGACTAA
* *
39447647 AATGAAAAGTTGTAAAATTT
1 AATGAAAAATTCTAAAATTT
*
39447667 GATGAAAAATTCTAAAATTT
1 AATGAAAAATTCTAAAATTT
39447687 AATGAA
1 AATGAA
39447693 TACATGTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGAAAAATTCTAAAATTT
Found at i:39451474 original size:42 final size:42
Alignment explanation
Indices: 39451424--39451530 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
39451414 ACATCGATGT
** ** * *
39451424 CATATCCCAGATATGGTCTTGTACGAGTTCTCATTTCGACGC
1 CATATCCCAGATATGGTCTTACACGAAATCTCATATCAACGC
* **
39451466 CATGTCCCAGACGTGGTCTTACACGAAATCTCATATCAACGC
1 CATATCCCAGATATGGTCTTACACGAAATCTCATATCAACGC
*
39451508 CATATCCCGGATATGGTCTTACA
1 CATATCCCAGATATGGTCTTACA
39451531 TGATAACTCA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (42 bp):
CATATCCCAGATATGGTCTTACACGAAATCTCATATCAACGC
Found at i:39453161 original size:28 final size:28
Alignment explanation
Indices: 39453129--39453227 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
39453119 GCAATAAGCC
*
39453129 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
39453157 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
39453185 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
39453214 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39453228 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:39460843 original size:28 final size:28
Alignment explanation
Indices: 39460811--39460909 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
39460801 GCAATAAGCC
*
39460811 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
39460839 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
39460867 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
39460896 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39460910 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:39466884 original size:40 final size:41
Alignment explanation
Indices: 39466825--39467005 Score: 257
Period size: 40 Copynumber: 4.6 Consensus size: 41
39466815 AACCCAAGTA
* *
39466825 CCTTC-GGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
* *
39466863 CCTTCGGGTCTTAGCCCGGATATAGTCAA-TAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
*
39466903 CCTTCGGGACTTAGCCCGGATATAGTC-TCTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
* *
39466943 CCTTCGGGACTTAGCCCGGATATAGT-TACTAGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
39466983 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
39467006 CATTTGAATA
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
38 5 0.04
39 6 0.05
40 115 0.89
41 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
Found at i:39467527 original size:2 final size:2
Alignment explanation
Indices: 39467520--39467549 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39467510 CACCATACGC
39467520 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
39467550 TTTCTCTAGT
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:39468465 original size:14 final size:14
Alignment explanation
Indices: 39468443--39468485 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
39468433 TTTCATTTTG
39468443 TAACATAAAATTAT
1 TAACATAAAATTAT
*
39468457 TAGCATAAAA-TAT
1 TAACATAAAATTAT
* *
39468470 TAACACAAAATAAT
1 TAACATAAAATTAT
39468484 TA
1 TA
39468486 TAATATGCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (14 bp):
TAACATAAAATTAT
Found at i:39468479 original size:13 final size:13
Alignment explanation
Indices: 39468443--39468481 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
39468433 TTTCATTTTG
39468443 TAACATAAAATTAT
1 TAACATAAAA-TAT
*
39468457 TAGCATAAAATAT
1 TAACATAAAATAT
*
39468470 TAACACAAAATA
1 TAACATAAAATA
39468482 ATTATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (13 bp):
TAACATAAAATAT
Found at i:39477806 original size:39 final size:40
Alignment explanation
Indices: 39477748--39477848 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
39477738 AAATTGAATG
* *
39477748 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
39477787 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
39477827 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
39477849 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:39477841 original size:40 final size:40
Alignment explanation
Indices: 39477748--39477898 Score: 180
Period size: 40 Copynumber: 3.8 Consensus size: 40
39477738 AAATTGAATG
* * * * *
39477748 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
39477787 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
39477827 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* *
39477867 AAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
39477899 AAATCGTGAT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
39 32 0.33
40 62 0.65
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:39477913 original size:40 final size:38
Alignment explanation
Indices: 39477744--39477915 Score: 161
Period size: 40 Copynumber: 4.4 Consensus size: 38
39477734 TGAGAAATTG
* *
39477744 AATG-ATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-A
1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA
* * *
39477783 AAT-TATATCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
39477820 AGTAGCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
39477860 AGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 A-ATG-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
39477900 AATCGTGATATCCGGG
1 AAT-GT-ATATCCGGG
39477916 TAAAGTCCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
36 2 0.02
37 4 0.04
38 2 0.02
39 26 0.24
40 74 0.68
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (38 bp):
AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:39480569 original size:20 final size:20
Alignment explanation
Indices: 39480541--39480581 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39480531 ACAATCCGAA
*
39480541 TATCAATACTCGGGCCAAGG
1 TATCAATACTCGAGCCAAGG
* *
39480561 TATCGATACTTGAGCCAAGG
1 TATCAATACTCGAGCCAAGG
39480581 T
1 T
39480582 GCCATTCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (20 bp):
TATCAATACTCGAGCCAAGG
Found at i:39482205 original size:35 final size:35
Alignment explanation
Indices: 39482134--39482287 Score: 107
Period size: 35 Copynumber: 4.4 Consensus size: 35
39482124 CAAGGTTCAT
*
39482134 TATATCATCACATAAGGCCAAATATACAAGTACAA
1 TATATCATCACATAAGACCAAATATACAAGTACAA
* * *
39482169 TATATCATCATATATGACCTAATATACAAGCT-CAA
1 TATATCATCACATAAGACCAAATATACAAG-TACAA
* * * * * **
39482204 TAAAACATCACATGTAG-TCAAATATTCAAGTTTAA
1 TATATCATCACAT-AAGACCAAATATACAAGTACAA
* ** * *
39482239 TACAAT-ATCACATGTGGCCAAATATACAAGTTCAA
1 TA-TATCATCACATAAGACCAAATATACAAGTACAA
*
39482274 TATGTCATCACATA
1 TATATCATCACATA
39482288 TGTACATACC
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
34 3 0.03
35 84 0.92
36 4 0.04
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (35 bp):
TATATCATCACATAAGACCAAATATACAAGTACAA
Found at i:39483076 original size:30 final size:30
Alignment explanation
Indices: 39483022--39483078 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39483012 TAATCCATAT
*
39483022 ATTTCATTTATTTTTCATTTTAGTCCTTCA
1 ATTTCATTTATTTTTCAATTTAGTCCTTCA
*
39483052 ATTT-ATTTTTTTTTGCAATTTAGTCCT
1 ATTTCATTTATTTTT-CAATTTAGTCCT
39483079 AATAATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.61
Consensus pattern (30 bp):
ATTTCATTTATTTTTCAATTTAGTCCTTCA
Found at i:39490365 original size:35 final size:35
Alignment explanation
Indices: 39490318--39490478 Score: 160
Period size: 35 Copynumber: 4.6 Consensus size: 35
39490308 ATACTTAAGT
*
39490318 TTCATTATATCATCACATATGGCCAAATATACAAG
1 TTCAATATATCATCACATATGGCCAAATATACAAG
* ** * * *
39490353 TACAATATATCATCTTATATGACCTAATACACAAG
1 TTCAATATATCATCACATATGGCCAAATATACAAG
* * * * * * * *
39490388 CTCAATAAAACATCACATGTAGTCAAATATTCATG
1 TTCAATATATCATCACATATGGCCAAATATACAAG
* * *
39490423 TTTAATATAACATCACATGTGGCCAAATATACAAG
1 TTCAATATATCATCACATATGGCCAAATATACAAG
39490458 TTCAATATATCATCACATATG
1 TTCAATATATCATCACATATG
39490479 TACATACCTA
Statistics
Matches: 95, Mismatches: 31, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
35 95 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (35 bp):
TTCAATATATCATCACATATGGCCAAATATACAAG
Found at i:39492150 original size:42 final size:42
Alignment explanation
Indices: 39492091--39492174 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
39492081 ATCATCAAAG
39492091 GATAGTTTTCACAGGCTTTATTAGCTAACACATACTGACCTA
1 GATAGTTTTCACAGGCTTTATTAGCTAACACATACTGACCTA
*
39492133 GATAGTTTTTACAGGCTTTATTAGCTAACACATACTGACCTA
1 GATAGTTTTCACAGGCTTTATTAGCTAACACATACTGACCTA
39492175 AAGGGTTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (42 bp):
GATAGTTTTCACAGGCTTTATTAGCTAACACATACTGACCTA
Found at i:39507420 original size:22 final size:22
Alignment explanation
Indices: 39507395--39507449 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
39507385 TCTATTTTTA
39507395 ATGTCACGACAACAGCCATAAG
1 ATGTCACGACAACAGCCATAAG
* *
39507417 ATGTCGCGACAACAGCCATAGG
1 ATGTCACGACAACAGCCATAAG
39507439 ATGTCACGACA
1 ATGTCACGACA
39507450 CCGACCTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.15
Consensus pattern (22 bp):
ATGTCACGACAACAGCCATAAG
Found at i:39512537 original size:40 final size:40
Alignment explanation
Indices: 39512493--39512593 Score: 177
Period size: 40 Copynumber: 2.5 Consensus size: 40
39512483 CTCGTTCAAC
39512493 TGCCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAA
1 TGCCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAA
*
39512533 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
1 TGCCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAA
39512573 TGCCTTC-GAGACTTAGCCCGG
1 TGCCTTCGGA-ACTTAGCCCGG
39512594 TTGTCATCTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
39 1 0.02
40 57 0.98
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
TGCCTTCGGAACTTAGCCCGGATATAGTAACTCGCACAAA
Found at i:39519657 original size:40 final size:40
Alignment explanation
Indices: 39519587--39519684 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
39519577 AAACCAAGTA
* * ** *
39519587 CCTTCGAGATTTAG-CCGGATATAGCTACTCGTTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
39519626 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATG
39519666 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39519685 TTGTCATCCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 13 0.25
40 39 0.75
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
Found at i:39522960 original size:13 final size:13
Alignment explanation
Indices: 39522942--39522966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39522932 TTTATCTATG
39522942 TTTAATTGATAGT
1 TTTAATTGATAGT
39522955 TTTAATTGATAG
1 TTTAATTGATAG
39522967 CCCTATGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTTAATTGATAGT
Found at i:39528162 original size:2 final size:2
Alignment explanation
Indices: 39528155--39528185 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39528145 AGTGTCGACT
39528155 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 T
39528186 GTTAAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39532997 original size:35 final size:35
Alignment explanation
Indices: 39532951--39533028 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
39532941 CAGAAATCAT
39532951 TTCTCATGAGTTTGACATACATACCTGTGTTAATA
1 TTCTCATGAGTTTGACATACATACCTGTGTTAATA
39532986 TTCTCATGAGTTTGACATACATACCTGTGTTAATA
1 TTCTCATGAGTTTGACATACATACCTGTGTTAATA
*
39533021 TGCTCATG
1 TTCTCATG
39533029 TACTTTACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (35 bp):
TTCTCATGAGTTTGACATACATACCTGTGTTAATA
Found at i:39533443 original size:49 final size:49
Alignment explanation
Indices: 39533383--39533499 Score: 157
Period size: 49 Copynumber: 2.4 Consensus size: 49
39533373 GTCTTGTCCT
39533383 AGACAGGTCTTACACTGACT-TTCATATATCGAG-GCTGATGCCATATCCC
1 AGACAGGTCTTACACTGACTCTT-ATATATCG-GTGCTGATGCCATATCCC
* * * *
39533432 AGACAGGTCTTACACTGGCTCTTATCTATCGGTGTTGATGCCATGTCCC
1 AGACAGGTCTTACACTGACTCTTATATATCGGTGCTGATGCCATATCCC
*
39533481 AGATAGGTCTTACACTGAC
1 AGACAGGTCTTACACTGAC
39533500 ACACAACAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
48 1 0.02
49 57 0.95
50 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (49 bp):
AGACAGGTCTTACACTGACTCTTATATATCGGTGCTGATGCCATATCCC
Found at i:39534383 original size:20 final size:20
Alignment explanation
Indices: 39534358--39534396 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39534348 ACAAATTCAA
39534358 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
39534378 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
39534397 AATAGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:39541872 original size:12 final size:12
Alignment explanation
Indices: 39541855--39541879 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39541845 CTTGAATCAA
39541855 TCCGAGTAAAAC
1 TCCGAGTAAAAC
39541867 TCCGAGTAAAAC
1 TCCGAGTAAAAC
39541879 T
1 T
39541880 TTTAGCAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TCCGAGTAAAAC
Found at i:39542048 original size:20 final size:20
Alignment explanation
Indices: 39542025--39542078 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
39542015 ATACCCTAAA
* *
39542025 TGAAGTATCGATACTTTGGC
1 TGAAGTATCGATACCTTGAC
*
39542045 TGAAATATCGATACCTTGAC
1 TGAAGTATCGATACCTTGAC
*
39542065 TGAAGTATCAATAC
1 TGAAGTATCGATAC
39542079 ATTTCTCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (20 bp):
TGAAGTATCGATACCTTGAC
Found at i:39542162 original size:30 final size:30
Alignment explanation
Indices: 39542126--39542186 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
39542116 TGCCAAAGTA
*
39542126 TGATTTGTTGTTCCAGAATAAGAGAAAATT
1 TGATTTGTTGTTCCAAAATAAGAGAAAATT
*
39542156 TGATTTGTTGTTCTAAAATAAGAGAAAATT
1 TGATTTGTTGTTCCAAAATAAGAGAAAATT
39542186 T
1 T
39542187 ACTTTAGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (30 bp):
TGATTTGTTGTTCCAAAATAAGAGAAAATT
Found at i:39542673 original size:39 final size:39
Alignment explanation
Indices: 39542630--39542709 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
39542620 CCTCCTCTTC
*
39542630 AATCCATATCTTTATTGTACGTATATAAGATTCTTAGTA
1 AATCCATATCTTTATTGTACGCATATAAGATTCTTAGTA
39542669 AATCCATATCTTTATTGTACGCATATAAGATTCTTAGTA
1 AATCCATATCTTTATTGTACGCATATAAGATTCTTAGTA
39542708 AA
1 AA
39542710 ATTTAGCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (39 bp):
AATCCATATCTTTATTGTACGCATATAAGATTCTTAGTA
Found at i:39545693 original size:6 final size:6
Alignment explanation
Indices: 39545682--39545731 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
39545672 ATTTCTGTTA
* *
39545682 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATATAT ATATAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
39545730 AT
1 AT
39545732 GCTATTCGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (6 bp):
ATACAT
Found at i:39546151 original size:25 final size:23
Alignment explanation
Indices: 39546116--39546174 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
39546106 TTCTTAATGA
*
39546116 ATATTTGAATTTAATATTTAATAAT
1 ATATTTTAATTTAATATTT--TAAT
*
39546141 ATATTTTAA-TTGATATTTTAAT
1 ATATTTTAATTTAATATTTTAAT
*
39546163 -TTTTTTAATTTA
1 ATATTTTAATTTA
39546175 TAATATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 7 0.24
22 6 0.21
24 8 0.28
25 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (23 bp):
ATATTTTAATTTAATATTTTAAT
Found at i:39547924 original size:55 final size:56
Alignment explanation
Indices: 39547857--39547972 Score: 141
Period size: 55 Copynumber: 2.1 Consensus size: 56
39547847 AAGCCCCTAC
* * *
39547857 TTTTATTAAAAATTA-AAATATATATATAAATCATA-A-AAAAATAAAAATTTGTAAAA
1 TTTTATTAAAAATCATAAAT-TAT-TATAAAT-ATATAGAAAAATAAAAAATTATAAAA
*
39547913 TTTTA-TAAAAATCATAAATTATTATAAATATATAGAAATATAAAAAATTATAAAA
1 TTTTATTAAAAATCATAAATTATTATAAATATATAGAAAAATAAAAAATTATAAAA
39547968 TTTTA
1 TTTTA
39547973 CAAAGTCATT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
53 3 0.06
54 8 0.15
55 33 0.62
56 9 0.17
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (56 bp):
TTTTATTAAAAATCATAAATTATTATAAATATATAGAAAAATAAAAAATTATAAAA
Found at i:39548195 original size:21 final size:20
Alignment explanation
Indices: 39548171--39548275 Score: 69
Period size: 20 Copynumber: 5.3 Consensus size: 20
39548161 AGGGGCCATT
39548171 AAATTTTTAATGATTTTTATA
1 AAATTTTTAAT-ATTTTTATA
*
39548192 AAA-TTTTACA-ATTTTTTTA
1 AAATTTTTA-ATATTTTTATA
* **
39548211 CAATTTTTAATAAATTT-T-
1 AAATTTTTAATATTTTTATA
39548229 AAATTGTTT-ATATTTTTATTA
1 AAATT-TTTAATATTTTTA-TA
* *
39548250 AAA-TTTAAATAATTTTTCTA
1 AAATTTTTAAT-ATTTTTATA
39548270 AAATTT
1 AAATTT
39548276 ATTATTTATT
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
18 10 0.15
19 17 0.26
20 23 0.35
21 15 0.23
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (20 bp):
AAATTTTTAATATTTTTATA
Found at i:39548459 original size:21 final size:23
Alignment explanation
Indices: 39548425--39548467 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
39548415 GCTTAATTAT
39548425 TTTTTTAATAAA-TTTGAGAGTA
1 TTTTTTAATAAATTTTGAGAGTA
*
39548447 TTTTTT-ATGAATTTTGAGAGT
1 TTTTTTAATAAATTTTGAGAGT
39548468 TCAAGTGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.53
Consensus pattern (23 bp):
TTTTTTAATAAATTTTGAGAGTA
Found at i:39548481 original size:88 final size:89
Alignment explanation
Indices: 39548324--39548523 Score: 203
Period size: 88 Copynumber: 2.2 Consensus size: 89
39548314 TAAGAGCAGG
* *
39548324 GGCTTAATTGTTTTTTTGAAAAATTTTGAGGATCATTTTTTGTATATTTTGAAAGCTCAAGTACC
1 GGCTTAATTATTTTTTT-AAAAATTTTGAGGATCATTTTTTATATATTTTGAAAGCTCAAGTACC
*
39548389 CAATTGAGT-AAAAAAAAAAAGCAAA
65 CAATTGAATGAAAAAAAAAAAG-AAA
* * *
39548414 GGCTTAATTATTTTTTTAATAAA-TTTGA-GAGT-ATTTTTTATGA-ATTTTGAGAGTTCAAGTG
1 GGCTTAATTATTTTTTTAA-AAATTTTGAGGA-TCATTTTTTAT-ATATTTTGAAAGCTCAAGTA
** ** *
39548475 TTCAATTGAATGCCAAAAAAAAAGAAT
63 CCCAATTGAATGAAAAAAAAAAAGAAA
* *
39548502 GACTTAATTACTTTTTTAAAAA
1 GGCTTAATTATTTTTTTAAAAA
39548524 AAATTAAAGA
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
87 3 0.03
88 52 0.56
89 19 0.20
90 19 0.20
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (89 bp):
GGCTTAATTATTTTTTTAAAAATTTTGAGGATCATTTTTTATATATTTTGAAAGCTCAAGTACCC
AATTGAATGAAAAAAAAAAAGAAA
Found at i:39549194 original size:84 final size:79
Alignment explanation
Indices: 39549103--39549254 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 79
39549093 ATCGGCTAAG
* *
39549103 TACTTGAATTTAGTAAATACAAGATTAAAAATAAAATTTAAAAAAACAAAACAAATAATGAGTTC
1 TACTTGAATTTAATAAATACAA-ATT-AAAA-AAAATTT-AAAAAA-AAAACAAATAATGAATTC
39549168 GAATATTCAAATAAGATAA
61 GAATATTCAAATAAGATAA
* *
39549187 TACTTGAATTTAATAAATACAAATTTAAAAAAATTTAAAAAAAAAACAAATATTGAATTCGAATA
1 TACTTGAATTTAATAAATACAAATTAAAAAAAATTTAAAAAAAAAACAAATAATGAATTCGAATA
39549252 TTC
66 TTC
39549255 GAATCCACAT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
79 24 0.38
80 6 0.09
81 7 0.11
82 3 0.05
83 3 0.05
84 21 0.33
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (79 bp):
TACTTGAATTTAATAAATACAAATTAAAAAAAATTTAAAAAAAAAACAAATAATGAATTCGAATA
TTCAAATAAGATAA
Found at i:39552435 original size:3 final size:3
Alignment explanation
Indices: 39552427--39552457 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
39552417 ACAAAATTTA
39552427 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
39552458 CTATCAACTC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39554075 original size:182 final size:189
Alignment explanation
Indices: 39553568--39554087 Score: 811
Period size: 194 Copynumber: 2.8 Consensus size: 189
39553558 TAAGTAACAA
* * * *
39553568 TAGAAGATTTAAGTAGAGCAAATCTGCAATTACAACAGAGATCTTCAACACCAACTAAACAGCTT
1 TAGAAGTTTTAAGTAGAGCAAATCTGCAATGAGAACAGAGATCTTCAACATCAACTAAACAGCTT
*
39553633 AATGCATTTCTCTTCACATTGATCTACTCTTTCCTAAAATCAAACATGAAATTCTCACTCTTTCT
66 AATGCATTTCTCTTCACATTGATCTACTCTTACCTAAAATCAAACATGAAATTCTCACTCTTTCT
*
39553698 CTGGAAACAAACAAACAATAAACACTAACCAACTTAGTGAAAAGAAAAAAGAAACGAGTAAGAC
131 CAGGAAACAAACAAACAATAAACACTAACCAA--TAGT---AAGAAAAAAGAAACGAGTAAGAC
* *
39553762 TAGAAGTTTTAAGTAGAGCACATCTGCAACGAGAACAGAGATCTTCAACATCAACTAAACAGCTT
1 TAGAAGTTTTAAGTAGAGCAAATCTGCAATGAGAACAGAGATCTTCAACATCAACTAAACAGCTT
* *
39553827 AACGCATTTCTCTTCACATTGATCTACTATTACCTAAAATCAAACATGAAATTCTCACTCTTTCT
66 AATGCATTTCTCTTCACATTGATCTACTCTTACCTAAAATCAAACATGAAATTCTCACTCTTTCT
**
39553892 CAGGAAACAAACAAACAATAAACACTAACCAA-AGT-AGTGAAAA-AAACGAGT-A-A-
131 CAGGAAACAAACAAACAATAAACACTAACCAATAGTAAGAAAAAAGAAACGAGTAAGAC
*
39553945 TAG-ATTTTTAAGTAGAGCAAATCTGCAATGAGAACAGAGATCTTCAACATCAACTAAACAGCTT
1 TAGAAGTTTTAAGTAGAGCAAATCTGCAATGAGAACAGAGATCTTCAACATCAACTAAACAGCTT
*
39554009 AATGCATTTCTCTTCACATTGATCTACTCTTACCTAAAATCAAACATGAAAATCTCACTCTTTCT
66 AATGCATTTCTCTTCACATTGATCTACTCTTACCTAAAATCAAACATGAAATTCTCACTCTTTCT
*
39554074 CAGGAAACAGACAA
131 CAGGAAACAAACAA
39554088 GCAACAATTT
Statistics
Matches: 307, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
182 133 0.43
183 3 0.01
184 1 0.00
185 1 0.00
186 8 0.03
187 6 0.02
191 3 0.01
194 152 0.50
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (189 bp):
TAGAAGTTTTAAGTAGAGCAAATCTGCAATGAGAACAGAGATCTTCAACATCAACTAAACAGCTT
AATGCATTTCTCTTCACATTGATCTACTCTTACCTAAAATCAAACATGAAATTCTCACTCTTTCT
CAGGAAACAAACAAACAATAAACACTAACCAATAGTAAGAAAAAAGAAACGAGTAAGAC
Found at i:39557493 original size:22 final size:21
Alignment explanation
Indices: 39557462--39557516 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
39557452 TTAAAAAAAG
*
39557462 TTAAACTTTA-AAATCATTTTT
1 TTAAATTTTATAAAT-ATTTTT
*
39557483 ATTGAATTTTAATAAATATTTTT
1 -TTAAATTTT-ATAAATATTTTT
39557506 TTAAATTTTAT
1 TTAAATTTTAT
39557517 TTTATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 15 0.54
23 7 0.25
24 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAAATTTTATAAATATTTTT
Found at i:39561863 original size:28 final size:28
Alignment explanation
Indices: 39561831--39561916 Score: 172
Period size: 28 Copynumber: 3.1 Consensus size: 28
39561821 TTGTAGAGTG
39561831 TAGCAAAAGACTTATGGTGTAACCAACT
1 TAGCAAAAGACTTATGGTGTAACCAACT
39561859 TAGCAAAAGACTTATGGTGTAACCAACT
1 TAGCAAAAGACTTATGGTGTAACCAACT
39561887 TAGCAAAAGACTTATGGTGTAACCAACT
1 TAGCAAAAGACTTATGGTGTAACCAACT
39561915 TA
1 TA
39561917 TTTGAGATCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (28 bp):
TAGCAAAAGACTTATGGTGTAACCAACT
Found at i:39562230 original size:49 final size:49
Alignment explanation
Indices: 39562154--39562276 Score: 156
Period size: 49 Copynumber: 2.5 Consensus size: 49
39562144 TGGGCCACTT
* * **
39562154 GTAAGGCATGGTAGTTGCTAACTAGATTGGTGTATGTGTTGGACTACTG
1 GTAAGGCATGTTAGTTGCTAACCAGATTGGCATATGTGTTGGACTACTG
* ** *
39562203 GTAAGGCATGTTAATTGCTAACCAGATTGGCATATGTGTTGGGTTATTG
1 GTAAGGCATGTTAGTTGCTAACCAGATTGGCATATGTGTTGGACTACTG
* *
39562252 ATAGGGCATGTTAGTTGCTAACCAG
1 GTAAGGCATGTTAGTTGCTAACCAG
39562277 TCTGGCGTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.34
Consensus pattern (49 bp):
GTAAGGCATGTTAGTTGCTAACCAGATTGGCATATGTGTTGGACTACTG
Found at i:39567272 original size:37 final size:36
Alignment explanation
Indices: 39567222--39567308 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
39567212 TACGAAGTCT
39567222 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
39567258 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
39567295 TCACCCGGAACATA
1 T-ACCCGG-ACATA
39567309 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:39567446 original size:49 final size:49
Alignment explanation
Indices: 39567377--39567835 Score: 684
Period size: 49 Copynumber: 9.4 Consensus size: 49
39567367 TTTACCACAT
* * *
39567377 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
* *
39567426 ATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
* * * *
39567475 ATATACATATACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
* * * * *
39567524 ATATACATATACTTTCGCATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
* * *
39567573 ATATATATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
* *
39567622 ATATATATACATTTTCGCATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
* *
39567671 ATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
* * *
39567720 ATATATATACATTTTCACATTCATCGCATCGGCCATTAGGCCTTATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
*
39567769 ATATACATACATTTTCACATTCATCACATCGACCATTAGGCCTCATCAC
1 ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
*
39567818 ATATATATACATTTTCAC
1 ATATACATACATTTTCAC
39567836 GAATCTTGAT
Statistics
Matches: 387, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 387 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (49 bp):
ATATACATACATTTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
Found at i:39567694 original size:27 final size:27
Alignment explanation
Indices: 39567615--39567695 Score: 64
Period size: 27 Copynumber: 3.2 Consensus size: 27
39567605 CCATTAGGCC
*
39567615 TCATCACATATATATACATTTTCGCAT
1 TCATCACATATACATACATTTTCGCAT
*** ** *
39567642 TCATCAC--AT-CGGCCA-TTAGGC-C
1 TCATCACATATACATACATTTTCGCAT
39567664 TCATCACATATACATACATTTTCGCAT
1 TCATCACATATACATACATTTTCGCAT
39567691 TCATC
1 TCATC
39567696 GCATCGGCCA
Statistics
Matches: 36, Mismatches: 13, Indels: 10
0.61 0.22 0.17
Matches are distributed among these distances:
22 7 0.19
23 4 0.11
24 4 0.11
25 5 0.14
26 4 0.11
27 12 0.33
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (27 bp):
TCATCACATATACATACATTTTCGCAT
Found at i:39578064 original size:38 final size:40
Alignment explanation
Indices: 39578020--39578225 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
39578010 TGAATGATAC
* ** *
39578020 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCTAGTTGTTATAT
39578059 -CGGGCTAAGACCCGAAGGCATTCGTG-TGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCT-AGTTGTTATAT
*
39578098 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCTAGTTGTTATAT
* * *** *
39578138 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCTAGTTGTTATAT
* * *
39578178 CCGGGTTAAGACCCGAAGGCAATT-GTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGC-ATTCGTGCTAGTTGTTATAT
39578218 CC-GGCTAA
1 CCGGGCTAA
39578226 ATTCCGAAGA
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
37 1 0.01
38 25 0.18
39 12 0.08
40 101 0.71
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCTAGTTGTTATAT
Found at i:39586176 original size:40 final size:40
Alignment explanation
Indices: 39586121--39586341 Score: 300
Period size: 40 Copynumber: 5.5 Consensus size: 40
39586111 TGAATGATAC
* ** * *
39586121 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATCATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
39586161 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
* *
39586201 CCAGGCTAAGACCCGAAGGAATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
39586241 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
* * *** *
39586281 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
*
39586321 CCGGGTTAAGACCCGAAGGCA
1 CCGGGCTAAGACCCGAAGGCA
39586342 ATTGTGCTTG
Statistics
Matches: 164, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 162 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
Found at i:39586378 original size:120 final size:120
Alignment explanation
Indices: 39586121--39586369 Score: 306
Period size: 120 Copynumber: 2.1 Consensus size: 120
39586111 TGAATGATAC
* ** * *
39586121 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATCATATCCGGGCTAAGACCCGAAGGCATTC
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATCCGGGCTAAGACCCGAAGGCATTC
* *** * *
39586185 GTGCGAGTTGTTATATCCAGGCTAAGACCCGAAGGAATTCGTGCGAGTTGTTATAT
65 GTGCAAGTTACCAAATCCAGGCTAAGACCCGAAGGAATTCGTGCGAGTGGTTATAT
*
39586241 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTCG
* * **
39586306 TGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATT-GTGCTTGTGGATTATAT
66 TGCAAGTTACCAAATCCAGGCTAAGACCCGAAGG-AATTCGTGCGAGTGG-TTATAT
39586362 CC-GGCTAA
1 CCGGGCTAA
39586370 ATTCCGAAGA
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
120 96 0.87
121 14 0.13
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (120 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTCG
TGCAAGTTACCAAATCCAGGCTAAGACCCGAAGGAATTCGTGCGAGTGGTTATAT
Found at i:39590902 original size:48 final size:47
Alignment explanation
Indices: 39590828--39591007 Score: 216
Period size: 48 Copynumber: 3.8 Consensus size: 47
39590818 AGGGTAAATT
* * * *
39590828 GCCGATGCCATATCCCAGACATGGTCTTACATTAGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT-GAG
* * * * * *
39590876 GCTGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTCTTAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATGAG
* *
39590924 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATGAG
*
39590972 GCCGATGCCATGTCCCAGACATAGTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
39591008 ACACCTAACA
Statistics
Matches: 111, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 110 0.99
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATGAG
Found at i:39590999 original size:96 final size:96
Alignment explanation
Indices: 39590827--39591007 Score: 265
Period size: 96 Copynumber: 1.9 Consensus size: 96
39590817 GAGGGTAAAT
* * *
39590827 TGCCGATGCCATATCCCAGACATGGTCTTACATTAGCTCACATGTCGAGGCTGATGCCATGTCCC
1 TGCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCC
*
39590892 AAACATGGTCTTACACTAGCTCTCGTCTTAA
66 AAACATAGTCTTACACTAGCTCTCGTCTTAA
* * * *
39590923 TGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATAAT-GTGGCCGATGCCATGTCC
1 TGCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCACAT-ATCGAGGCCGATGCCATGTCC
*
39590987 CAGACATAGTCTTACACTAGC
65 CAAACATAGTCTTACACTAGC
39591008 ACACCTAACA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
96 74 0.99
97 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (96 bp):
TGCCGATGCCATATCCCAGACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCC
AAACATAGTCTTACACTAGCTCTCGTCTTAA
Found at i:39593276 original size:25 final size:24
Alignment explanation
Indices: 39593242--39593329 Score: 108
Period size: 24 Copynumber: 3.6 Consensus size: 24
39593232 TTTGAAAGTC
39593242 CGCACACATAGTGCTCTTAC-TTAT-T
1 CGCACACATAGTGC-C--ACGTTATCT
*
39593267 CGCACACATAGTGCCACGTTTTCT
1 CGCACACATAGTGCCACGTTATCT
* *
39593291 CGCACACATAGTGCCATGTAATCT
1 CGCACACATAGTGCCACGTTATCT
39593315 CGCACACATAGTGCC
1 CGCACACATAGTGCC
39593330 GCATAGCCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
22 2 0.04
23 3 0.05
24 38 0.67
25 14 0.25
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (24 bp):
CGCACACATAGTGCCACGTTATCT
Found at i:39593298 original size:24 final size:24
Alignment explanation
Indices: 39593266--39593352 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
39593256 TCTTACTTAT
**
39593266 TCGCACACATAGTGCCACGTTTTC
1 TCGCACACATAGTGCCACGTAATC
*
39593290 TCGCACACATAGTGCCATGTAATC
1 TCGCACACATAGTGCCACGTAATC
* * **
39593314 TCGCACACATAGTGCCGCATAGCC
1 TCGCACACATAGTGCCACGTAATC
*
39593338 TTGCACACATAGTGC
1 TCGCACACATAGTGC
39593353 TGTATTTTCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (24 bp):
TCGCACACATAGTGCCACGTAATC
Found at i:39601959 original size:48 final size:48
Alignment explanation
Indices: 39601827--39601962 Score: 175
Period size: 48 Copynumber: 2.8 Consensus size: 48
39601817 GGTAAATTGT
* * *
39601827 CGATACCATGTCCTAGACATGGTCTTACGCTGGCTCACATGTCGAAGC
1 CGATACCATGTCCTAGACATGGTCTTACACTGGCTCTCATCTCGAAGC
* * *
39601875 CGATACCATGTCCTGGACATGGTCTTACACTAGCTCTCGTCTC-AATGC
1 CGATACCATGTCCTAGACATGGTCTTACACTGGCTCTCATCTCGAA-GC
** *
39601923 CGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCAT
1 CGATACCATGTCCTAGACATGGTCTTACACTGGCTCTCAT
39601963 AATGTGGCCG
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
47 2 0.03
48 73 0.97
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (48 bp):
CGATACCATGTCCTAGACATGGTCTTACACTGGCTCTCATCTCGAAGC
Found at i:39601973 original size:48 final size:47
Alignment explanation
Indices: 39601827--39602001 Score: 149
Period size: 48 Copynumber: 3.7 Consensus size: 47
39601817 GGTAAATTGT
* * * * * *
39601827 CGATACCATGTCCTAGACATGGTCTTACGCTGGCTCACAT-GTCGAAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-G-TGC
* ** * *
39601875 CGATACCATGTCCTGGACATGGTCTTACACTAGCTCTCGTCTCAA--TGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--AT-AATGTGC
*
39601923 CGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-GC
* *
39601971 CGATGCCACGTCCCAGACATGGTCTTGCACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
39602002 AGCACACCTA
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
45 2 0.02
46 1 0.01
47 1 0.01
48 99 0.95
50 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGC
Found at i:39605917 original size:23 final size:23
Alignment explanation
Indices: 39605891--39605936 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
39605881 AATAATTTGA
39605891 AAGTCAATATGTTACTTTAATAT
1 AAGTCAATATGTTACTTTAATAT
39605914 AAGTCAATATGTTACTTTAATAT
1 AAGTCAATATGTTACTTTAATAT
39605937 TCTTTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (23 bp):
AAGTCAATATGTTACTTTAATAT
Found at i:39606580 original size:2 final size:2
Alignment explanation
Indices: 39606573--39606598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39606563 CTTAGACAAA
39606573 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
39606599 CATAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39607685 original size:10 final size:10
Alignment explanation
Indices: 39607658--39607686 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
39607648 AAGTGTTTAG
39607658 TAAAAAAA-T
1 TAAAAAAATT
39607667 TAAAAAAATT
1 TAAAAAAATT
39607677 TAAAAAAATT
1 TAAAAAAATT
39607687 CTTTCCAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:39608653 original size:16 final size:16
Alignment explanation
Indices: 39608599--39608654 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
39608589 CGTTTGGTTG
*
39608599 GCTGTAATGGAATAAA
1 GCTGTAATGGAATAGA
* * *
39608615 GTTATAATTGAATAGA
1 GCTGTAATGGAATAGA
*
39608631 GCCGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
39608647 GGTGTAAT
1 GCTGTAAT
39608655 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.05, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:39608956 original size:58 final size:58
Alignment explanation
Indices: 39608839--39608961 Score: 167
Period size: 58 Copynumber: 2.1 Consensus size: 58
39608829 TTTTAATAAG
* * *
39608839 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATTTTAACATA
1 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTCAACATA
* * * *
39608897 ATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATAAAATTCTCAATATA
1 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATT-TCAACATA
39608955 ATTATTA
1 ATTATTA
39608962 CTATATGAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 22 0.39
58 35 0.61
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACAAAATTTCAACATA
Found at i:39612345 original size:18 final size:17
Alignment explanation
Indices: 39612318--39612360 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
39612308 ATATTTTAAG
*
39612318 TATAAGATATTTAATATA
1 TATAATATA-TTAATATA
*
39612336 TATAATATATTATTATA
1 TATAATATATTAATATA
39612353 -ATAATATA
1 TATAATATA
39612361 ATATAATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 7 0.30
18 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATAATATATTAATATA
Found at i:39612359 original size:21 final size:21
Alignment explanation
Indices: 39612324--39612382 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
39612314 TAAGTATAAG
39612324 ATATT-TAATATATATAATATA
1 ATATTATAATA-ATATAATATA
*
39612345 TTATTATAATAATATAATATA
1 ATATTATAATAATATAATATA
*
39612366 ATAGTTAAAATAA-ATAA
1 ATA-TTATAATAATATAA
39612383 AAGAAACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATTATAATAATATAATATA
Done.