Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 147 of 187
Found at i:43854377 original size:15 final size:14
Alignment explanation
Indices: 43854327--43854378 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 14
43854317 TTAAAAGATG
43854327 TTTTTAAATAACTAT
1 TTTTTAAA-AACTAT
43854342 TTTTTAAAAAAGCTATTT
1 TTTTT-AAAAA-CTA--T
43854360 TTTTTAAAAACTACT
1 TTTTTAAAAACTA-T
43854375 TTTT
1 TTTT
43854379 GTTTATGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 12 0.38
16 9 0.28
17 5 0.16
18 6 0.19
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (14 bp):
TTTTTAAAAACTAT
Found at i:43854811 original size:21 final size:19
Alignment explanation
Indices: 43854777--43854816 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
43854767 TTTACTTTTT
*
43854777 TTAAATTTTTTTAATATTGA
1 TTAAATTATTTTAAT-TTGA
43854797 TTAAATCTATTTTAATTTGA
1 TTAAAT-TATTTTAATTTGA
43854817 GAAATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
TTAAATTATTTTAATTTGA
Found at i:43857125 original size:19 final size:21
Alignment explanation
Indices: 43857101--43857146 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
43857091 ATCTTGAAAC
43857101 ATTTTAAAATTT-TAAAA-TA
1 ATTTTAAAATTTATAAAATTA
43857120 ATTTT--AATTTATAAAATTA
1 ATTTTAAAATTTATAAAATTA
43857139 ATTTTAAA
1 ATTTTAAA
43857147 TAATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 5 0.22
18 5 0.22
19 12 0.52
21 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTAAAATTTATAAAATTA
Found at i:43858343 original size:23 final size:22
Alignment explanation
Indices: 43858308--43858350 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
43858298 AATGTTTTAT
43858308 ATTATAAAATATGAATATTTCA
1 ATTATAAAATATGAATATTTCA
*
43858330 ATTATATAAATATGAGTATTT
1 ATTATA-AAATATGAATATTT
43858351 GTTTTAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTATAAAATATGAATATTTCA
Found at i:43858363 original size:37 final size:37
Alignment explanation
Indices: 43858322--43858395 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
43858312 TAAAATATGA
43858322 ATATTTCAATTATATAAATATGAGTATTTGTTTTAGT
1 ATATTTCAATTATATAAATATGAGTATTTGTTTTAGT
*
43858359 ATATTTTAATTATATAAATATGAGTATTTGTTTTAGT
1 ATATTTCAATTATATAAATATGAGTATTTGTTTTAGT
43858396 CTTGCTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (37 bp):
ATATTTCAATTATATAAATATGAGTATTTGTTTTAGT
Found at i:43861266 original size:29 final size:30
Alignment explanation
Indices: 43861234--43861292 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
43861224 ATAGTTTTTA
*
43861234 AATT-AATTTCTAAT-AATTTTTATAAATTT
1 AATTAAATTT-TAATAAATTTTAATAAATTT
43861263 AATTAAATTTTAATAAATTTTAATAAATTT
1 AATTAAATTTTAATAAATTTTAATAAATTT
43861293 TTATGTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTAAATTTTAATAAATTTTAATAAATTT
Found at i:43861276 original size:11 final size:10
Alignment explanation
Indices: 43861238--43861293 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
43861228 TTTTTAAATT
43861238 AATTTCTAAT-
1 AATTT-TAATA
*
43861248 AATTTTTATA
1 AATTTTAATA
43861258 AA-TTTAATTA
1 AATTTTAA-TA
43861268 AATTTTAATA
1 AATTTTAATA
43861278 AATTTTAATA
1 AATTTTAATA
43861288 AATTTT
1 AATTTT
43861294 TATGTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
9 7 0.17
10 29 0.71
11 5 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (10 bp):
AATTTTAATA
Found at i:43862429 original size:18 final size:18
Alignment explanation
Indices: 43862408--43862445 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
43862398 ATAAAATAAG
43862408 ATAGTATGATAAATTTGA
1 ATAGTATGATAAATTTGA
43862426 ATAGTATGATAAATTTGA
1 ATAGTATGATAAATTTGA
43862444 AT
1 AT
43862446 TGTTAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (18 bp):
ATAGTATGATAAATTTGA
Found at i:43879428 original size:26 final size:27
Alignment explanation
Indices: 43879392--43879453 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
43879382 ACATATTTTC
*
43879392 TCAAAATTTTATCT-TGGGAAAAATC-A
1 TCAAAATTTTA-CTACGGGAAAAATCGA
*
43879418 TCAAAATTTTACTACGGGTAAAATCGA
1 TCAAAATTTTACTACGGGAAAAATCGA
43879445 -CAAAATTTT
1 TCAAAATTTT
43879454 GTTAGGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 29 0.91
27 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (27 bp):
TCAAAATTTTACTACGGGAAAAATCGA
Found at i:43879462 original size:26 final size:26
Alignment explanation
Indices: 43879392--43879467 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
43879382 ACATATTTTC
* *
43879392 TCAAAATTTTATCT-TGGGAAAAATCA
1 TCAAAATTTTA-CTACGGGTAAAATCA
43879418 TCAAAATTTTACTACGGGTAAAATCGA
1 TCAAAATTTTACTACGGGTAAAATC-A
** *
43879445 -CAAAATTTTGTTAGGGGTAAAAT
1 TCAAAATTTTACTACGGGTAAAAT
43879468 AGGGATGAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
25 2 0.05
26 40 0.93
27 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACTACGGGTAAAATCA
Found at i:43884990 original size:3 final size:3
Alignment explanation
Indices: 43884969--43885006 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
43884959 TAATAGCTCC
* *
43884969 ATT ATT TTT ATT ATC ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43885007 TTTTTAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:43896051 original size:16 final size:16
Alignment explanation
Indices: 43896040--43896099 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
43896030 TGTATTAGAT
* *
43896040 TAGAGGTGTATTGGAT
1 TAGAGGTGTAATGGAA
43896056 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATGGAA
43896072 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATGGAA
43896088 TAGAGGTGTAAT
1 TAGAGGTGTAAT
43896100 AGCAAATCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (16 bp):
TAGAGGTGTAATGGAA
Found at i:43896183 original size:39 final size:43
Alignment explanation
Indices: 43896078--43896187 Score: 111
Period size: 45 Copynumber: 2.6 Consensus size: 43
43896068 GGAATAGAGG
43896078 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
*** * ***
43896123 TGTAATGGAATAGATACGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
43896163 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
43896188 TAATGGAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
39 18 0.34
40 2 0.04
43 1 0.02
44 11 0.21
45 21 0.40
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:43896386 original size:16 final size:15
Alignment explanation
Indices: 43896361--43896407 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
43896351 TATAATTTAA
43896361 TAAAATTCTTAACAT
1 TAAAATTCTTAACAT
*
43896376 TAAATATTCTT-ATA-
1 TAAA-ATTCTTAACAT
43896390 T-AAATTCTTAACAT
1 TAAAATTCTTAACAT
43896404 TAAA
1 TAAA
43896408 TATAATTGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 2 0.08
15 8 0.31
16 6 0.23
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATTCTTAACAT
Found at i:43896407 original size:14 final size:14
Alignment explanation
Indices: 43896363--43896408 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 14
43896353 TAATTTAATA
43896363 AAATTCTTAACATT
1 AAATTCTTAACATT
*
43896377 AAATATTCTT-ATA-T
1 -AA-ATTCTTAACATT
43896391 AAATTCTTAACATT
1 AAATTCTTAACATT
43896405 AAAT
1 AAAT
43896409 ATAATTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 6 0.23
15 4 0.15
16 6 0.23
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTCTTAACATT
Found at i:43908092 original size:87 final size:87
Alignment explanation
Indices: 43907936--43908291 Score: 613
Period size: 87 Copynumber: 4.1 Consensus size: 87
43907926 AGATCAGTGA
* *
43907936 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGA
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
43908001 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
*
43908023 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGACCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
43908088 CTTCCTGCGTTAATAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
43908110 AGATTGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
43908175 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
*
43908197 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* ** *
43908262 CCTCCTGCGTCGACAGTGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
43908284 AGATCGAA
1 AGATCGAA
43908292 GATTACAAGT
Statistics
Matches: 254, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 254 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:43908440 original size:44 final size:44
Alignment explanation
Indices: 43908392--43908680 Score: 152
Period size: 44 Copynumber: 6.7 Consensus size: 44
43908382 AAATCAATCC
* *
43908392 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAACAATAGATCT
** * * *
43908436 TATCTCCCT-AAGCAGTAGTGGAGCAGATCG----C-ATCGGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAACAAT-AGATCT
**
43908476 TATCTCCCTGAAGTTGCAACGGAGCAGACTGAGAAA-ACA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TGA-AAACA-ATAGATCT
* * * * *
43908520 TATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGA-AGTAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAACAATAGATCT
* * * ** * *
43908564 TATCTCCCTGAGGTTACAGTGGAGCATATCGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAACAATAGATCT
** * **
43908608 TATCTCCCTGAAGTTTTAGTGGAGC-GTATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATGAAAACAATAGATCT
* * * *
43908652 CATCTCTCTGAAGTTTCAGTAGAGCAGAT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT
43908681 CGCATCAAGT
Statistics
Matches: 184, Mismatches: 43, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
39 2 0.01
40 14 0.08
41 14 0.08
42 1 0.01
43 25 0.14
44 123 0.67
45 4 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAACAATAGATCT
Found at i:43909477 original size:13 final size:13
Alignment explanation
Indices: 43909461--43909494 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
43909451 TTTTTTCCTT
43909461 TTTTCTTTTTCGG
1 TTTTCTTTTTCGG
43909474 TTTTC-TTTTCGG
1 TTTTCTTTTTCGG
*
43909486 TTTTGTTTT
1 TTTTCTTTT
43909495 GATTCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.74
Consensus pattern (13 bp):
TTTTCTTTTTCGG
Found at i:43913588 original size:41 final size:41
Alignment explanation
Indices: 43913526--43913718 Score: 158
Period size: 41 Copynumber: 4.7 Consensus size: 41
43913516 TTGAGTCCAA
* * *
43913526 CAGGCTTCATGTCGGTGTATATTATTAGGCTTTGTGCCTAG
1 CAGGTTTCATGCCGGTGTATATTATCAGGCTTTGTGCCTAG
* ** * *
43913567 TAGGTTTCATGTTGGTTTATATTATCAGGCTTTGTGCCTGG
1 CAGGTTTCATGCCGGTGTATATTATCAGGCTTTGTGCCTAG
* * *
43913608 CAAGCTTCATGCCGGTGTATATTATCAGCCTTTGTGCCTAG
1 CAGGTTTCATGCCGGTGTATATTATCAGGCTTTGTGCCTAG
* * * ** *
43913649 CAGGCTTTGA-GCTGGTGTAT-TGTATTAGGCTTTGAACCTAA
1 CAGG-TTTCATGCCGGTGTATAT-TATCAGGCTTTGTGCCTAG
* * *
43913690 CAGGCTTCTTGCCAGTGTAT-TGTATCAGG
1 CAGGTTTCATGCCGGTGTATAT-TATCAGG
43913719 TAACTTGTAC
Statistics
Matches: 120, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
40 3 0.03
41 114 0.95
42 3 0.03
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (41 bp):
CAGGTTTCATGCCGGTGTATATTATCAGGCTTTGTGCCTAG
Found at i:43913697 original size:82 final size:82
Alignment explanation
Indices: 43913507--43913717 Score: 205
Period size: 82 Copynumber: 2.6 Consensus size: 82
43913497 GGAGATAGTG
* * * * * *
43913507 TATCAGGCCTTGAGTCC-AACAGGCTTCATGTCGGTGTATATTATTAGGCTTTGTGCCTAGTAGG
1 TATCAGGCTTTGA-ACCTAACAGGCTTCATGCCGGTGTATATTATCAGCCTTTGTGCCTAGCAGG
* *
43913571 TTTCATGTTGGTTTATAT
65 TTTCATGCTGGTGTATAT
** ** *
43913589 TATCAGGCTTTGTGCCTGGCAAGCTTCATGCCGGTGTATATTATCAGCCTTTGTGCCTAGCAGGC
1 TATCAGGCTTTGAACCTAACAGGCTTCATGCCGGTGTATATTATCAGCCTTTGTGCCTAGCAGG-
*
43913654 TTTGA-GCTGGTGTAT-T
65 TTTCATGCTGGTGTATAT
* * *
43913670 GTATTAGGCTTTGAACCTAACAGGCTTCTTGCCAGTGTAT-TGTATCAG
1 -TATCAGGCTTTGAACCTAACAGGCTTCATGCCGGTGTATAT-TATCAG
43913718 GTAACTTGTA
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
81 4 0.04
82 96 0.92
83 4 0.04
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (82 bp):
TATCAGGCTTTGAACCTAACAGGCTTCATGCCGGTGTATATTATCAGCCTTTGTGCCTAGCAGGT
TTCATGCTGGTGTATAT
Found at i:43921632 original size:16 final size:18
Alignment explanation
Indices: 43921598--43921634 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
43921588 TGTTCAGATC
43921598 TTATATTTAATATAATTGT
1 TTATATTTAATAT-ATTGT
43921617 TTATATTT-ATAT-TTGT
1 TTATATTTAATATATTGT
43921633 TT
1 TT
43921635 TGTCCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATATTTAATATATTGT
Found at i:43922890 original size:20 final size:19
Alignment explanation
Indices: 43922846--43922900 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 19
43922836 GAGAATACCA
43922846 AACCTAAAAATATGATGAAG
1 AACC-AAAAATATGATGAAG
*
43922866 TACCAAAAATTATGA-GAAAG
1 AACCAAAAA-TATGATG-AAG
43922886 AACCAGAAAATATGA
1 AACCA-AAAATATGA
43922901 AGGAAAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 6 0.20
20 20 0.67
21 4 0.13
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (19 bp):
AACCAAAAATATGATGAAG
Found at i:43922930 original size:20 final size:21
Alignment explanation
Indices: 43922905--43922944 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
43922895 ATATGAAGGA
43922905 AAGAGAATACC-AAAACTACT
1 AAGAGAATACCAAAAACTACT
*
43922925 AAGAGAGTACCAAAAACTAC
1 AAGAGAATACCAAAAACTAC
43922945 GAGGAAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.12
Consensus pattern (21 bp):
AAGAGAATACCAAAAACTACT
Found at i:43923206 original size:20 final size:21
Alignment explanation
Indices: 43923181--43923233 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
43923171 TACGAGGGAG
43923181 GAAGTATCAAAAATTTTA-AA
1 GAAGTATCAAAAATTTTATAA
* *
43923201 GAAGTAT-TAAAA-TTTATGA
1 GAAGTATCAAAAATTTTATAA
43923220 GAA-TATCAAAAATT
1 GAAGTATCAAAAATT
43923234 ACGAAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 7 0.26
19 12 0.44
20 8 0.30
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (21 bp):
GAAGTATCAAAAATTTTATAA
Found at i:43924061 original size:21 final size:22
Alignment explanation
Indices: 43924032--43924072 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
43924022 TATATAATTT
*
43924032 TTTTTATTATGA-TTAATATAA
1 TTTTAATTATGATTTAATATAA
43924053 TTTTAATTATGATTTAATAT
1 TTTTAATTATGATTTAATAT
43924073 CAAATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTTAATTATGATTTAATATAA
Found at i:43926097 original size:21 final size:22
Alignment explanation
Indices: 43926064--43926104 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
43926054 GGTTTCATCT
*
43926064 ATTTAACTTTATTTTTTTATAA
1 ATTTAACTTTATTTATTTATAA
43926086 ATTTAA-TTTATTTATTTAT
1 ATTTAACTTTATTTATTTAT
43926105 CGTAACTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTAACTTTATTTATTTATAA
Found at i:43928598 original size:31 final size:32
Alignment explanation
Indices: 43928560--43928635 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
43928550 ATGGTTCAAA
* *
43928560 GTTTCAATTTTTCTTT-TTTCTTTTTCTAAAG
1 GTTTCAATCTTTCTTTCTTTCTTTTTCAAAAG
*
43928591 GTTTCAATCTTTCTTTCTTTTTTTTTCAAAAG
1 GTTTCAATCTTTCTTTCTTTCTTTTTCAAAAG
43928623 GTTTCAATCTTTC
1 GTTTCAATCTTTC
43928636 ATAGATTTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 15 0.37
32 26 0.63
ACGTcount: A:0.17, C:0.16, G:0.07, T:0.61
Consensus pattern (32 bp):
GTTTCAATCTTTCTTTCTTTCTTTTTCAAAAG
Found at i:43931092 original size:29 final size:30
Alignment explanation
Indices: 43931050--43931113 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 30
43931040 GACAGTTTCG
*
43931050 AGAATGTCGTATGTGCCATAGAAGAGTC-A
1 AGAATGTCGTATGTACCATAGAAGAGTCAA
43931079 AGAATGTCGTATGTACCATAGAAGAGTCAA
1 AGAATGTCGTATGTACCATAGAAGAGTCAA
43931109 AGAAT
1 AGAAT
43931114 CTAGCAACGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.23
Consensus pattern (30 bp):
AGAATGTCGTATGTACCATAGAAGAGTCAA
Found at i:43934687 original size:24 final size:24
Alignment explanation
Indices: 43934655--43934704 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
43934645 TTAAATAAAC
43934655 TTAAATGAAAAGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
43934679 TTAAATGAAAAGTCAAGAGTTATG
1 TTAAATGAAAAGTCAAGAGTTATG
43934703 TT
1 TT
43934705 TTTTAATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (24 bp):
TTAAATGAAAAGTCAAGAGTTATG
Found at i:43934888 original size:17 final size:17
Alignment explanation
Indices: 43934866--43934898 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
43934856 GATATAGAAT
43934866 GTGAACAATTTTACATA
1 GTGAACAATTTTACATA
43934883 GTGAACAATTTTACAT
1 GTGAACAATTTTACAT
43934899 TTAGATGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
GTGAACAATTTTACATA
Found at i:43941334 original size:22 final size:22
Alignment explanation
Indices: 43941297--43941339 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43941287 GTTATCAATG
*
43941297 GCAGTTTATCTACAAACCAGTA
1 GCAGTTTACCTACAAACCAGTA
* *
43941319 GCAGTTTACCTGCAAATCAGT
1 GCAGTTTACCTACAAACCAGT
43941340 GGTGGCTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (22 bp):
GCAGTTTACCTACAAACCAGTA
Found at i:43950076 original size:189 final size:189
Alignment explanation
Indices: 43949838--43950180 Score: 580
Period size: 189 Copynumber: 1.8 Consensus size: 189
43949828 TCCAATATCA
* *
43949838 ATACTTTTCATATGGTATTGATAAAAGTCCATTTGTATTGATATCTTTAGCTCCAACGGTCTCTG
1 ATACTTTTCATATGGTATCGATAAAAGTCCATTTGTATTGATATCTTTAGCTCCAACGGTCACTG
* * * *
43949903 AAGTTTGCATTAAGTGCTAATAGTATTGATACTCGTAGACAAAGTATCAATACCTTTTGTTGCAG
66 AACTTTGCATTAAATGCTAATAGTATTGATACTCATAGACAAAGTATCAATACCTTTTGTTGCAA
*
43949968 GTGAATTTAATGATATGGTATTTTTACATTTTGTTTTCAACCAATTTAGCTAAGTACTG
131 GTAAATTTAATGATATGGTATTTTTACATTTTGTTTTCAACCAATTTAGCTAAGTACTG
*
43950027 ATACTTTTCCTA-GGTATCGATAAAAGTCCATTTGTATTCGATATCTTTAGCTCCAACGGTCACT
1 ATACTTTTCATATGGTATCGATAAAAGTCCATTTGTATT-GATATCTTTAGCTCCAACGGTCACT
*
43950091 GAACTTTGCATTAAATGCTAATAGTATTGATACTCATAGACAAAGTATCGATACCTTTTGTTGCA
65 GAACTTTGCATTAAATGCTAATAGTATTGATACTCATAGACAAAGTATCAATACCTTTTGTTGCA
*
43950156 AGTAAATTTAATGATCTGGTATTTT
130 AGTAAATTTAATGATATGGTATTTT
43950181 CATCTCCAAC
Statistics
Matches: 143, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
188 25 0.17
189 118 0.83
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.40
Consensus pattern (189 bp):
ATACTTTTCATATGGTATCGATAAAAGTCCATTTGTATTGATATCTTTAGCTCCAACGGTCACTG
AACTTTGCATTAAATGCTAATAGTATTGATACTCATAGACAAAGTATCAATACCTTTTGTTGCAA
GTAAATTTAATGATATGGTATTTTTACATTTTGTTTTCAACCAATTTAGCTAAGTACTG
Found at i:43950596 original size:29 final size:29
Alignment explanation
Indices: 43950554--43950611 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
43950544 AAGGGAGATT
43950554 GTGAGGTTAAACCTTGTCCTCAAAAGTTG
1 GTGAGGTTAAACCTTGTCCTCAAAAGTTG
43950583 GTGAGGTTAAACCTTGTCCTCAAAAGTTG
1 GTGAGGTTAAACCTTGTCCTCAAAAGTTG
43950612 TTAACTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (29 bp):
GTGAGGTTAAACCTTGTCCTCAAAAGTTG
Found at i:43951160 original size:33 final size:35
Alignment explanation
Indices: 43951123--43951198 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 35
43951113 AAGATTGACT
*
43951123 TTTGCTATTGAATT-ACCTGTTATAAGCATATT-A
1 TTTGCTATTGAATTGAACTGTTATAAGCATATTGA
* * *
43951156 TTTGCTACTGTATTGAACTGTTATAGGCATATTGA
1 TTTGCTATTGAATTGAACTGTTATAAGCATATTGA
43951191 -TTGCTATT
1 TTTGCTATT
43951199 ATATTGTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 12 0.33
34 23 0.64
35 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (35 bp):
TTTGCTATTGAATTGAACTGTTATAAGCATATTGA
Found at i:43951584 original size:97 final size:97
Alignment explanation
Indices: 43951372--43951572 Score: 305
Period size: 97 Copynumber: 2.1 Consensus size: 97
43951362 TTGCTCAACT
* * ** *
43951372 AGTGGTTCATCCACAACGTATTAGCAGCTTTTATTTACACAGACGGATGGTTTATCCACAAATAT
1 AGTGGTTCATCCACAACATATTAGCAGCTTTTATCTACACAGACAAATAGTTTATCCACAAATAT
* *
43951437 ATTCTTATCATTAGCAGTCATCTGTAATGATC
66 ATTCTTATCATTAACAGTCATCTGCAATGATC
*
43951469 AGTGGTTCATCCACAACATATTAGCAGCTTTTATCTGCACAGACAAATAGTTTATCCACAAATAT
1 AGTGGTTCATCCACAACATATTAGCAGCTTTTATCTACACAGACAAATAGTTTATCCACAAATAT
*
43951534 ATT-TTATCATTAACAATTCATCTGCAATGATC
66 ATTCTTATCATTAAC-AGTCATCTGCAATGATC
43951566 AGTGGTT
1 AGTGGTT
43951573 TATTCATAAC
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
96 10 0.11
97 84 0.89
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (97 bp):
AGTGGTTCATCCACAACATATTAGCAGCTTTTATCTACACAGACAAATAGTTTATCCACAAATAT
ATTCTTATCATTAACAGTCATCTGCAATGATC
Found at i:43952704 original size:42 final size:42
Alignment explanation
Indices: 43952602--43952708 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
43952592 CATGTTTATA
* **
43952602 CTTCGATTTAT-TCGATGATGCACTTACATGCTAGTATATTTG
1 CTTCGGTTTATCT-GATGATGCACTTACATGAAAGTATATTTG
** ** **
43952644 CTTCGGTACATCCAATGATGCACTTATGTGAAAGTATATTTG
1 CTTCGGTTTATCTGATGATGCACTTACATGAAAGTATATTTG
43952686 CTTCGGTTTATCTGATGATGCAC
1 CTTCGGTTTATCTGATGATGCAC
43952709 AATGTGTGCC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (42 bp):
CTTCGGTTTATCTGATGATGCACTTACATGAAAGTATATTTG
Found at i:43952746 original size:43 final size:43
Alignment explanation
Indices: 43952634--43952837 Score: 137
Period size: 43 Copynumber: 4.8 Consensus size: 43
43952624 CTTACATGCT
* * * * * * **
43952634 AGTATATTTGCTTCGGTACATCCAATGATGCAC-TTATGTGAA
1 AGTATAATTGCTTCGATTCATCCGATGATGCACAATGTGTGCC
* * * *
43952676 AGTATATTTGCTTCGGTTTATCTGATGATGCACAATGTGTGCC
1 AGTATAATTGCTTCGATTCATCCGATGATGCACAATGTGTGCC
* **
43952719 AGTATAATTGCTTCGATTCGTCCGATGATGCACCTTGTGTGCC
1 AGTATAATTGCTTCGATTCATCCGATGATGCACAATGTGTGCC
* * * * *
43952762 AGTATAATTGTTTTGGCTTGC-T-CGATGATGCACTATGTGTGCT
1 AGTATAATTG-CTTCGATT-CATCCGATGATGCACAATGTGTGCC
** * *
43952805 AGTATCTTTCCTTCGATAT-ATCCAATGATGCAC
1 AGTATAATTGCTTCGAT-TCATCCGATGATGCAC
43952838 TATGATGCTA
Statistics
Matches: 128, Mismatches: 28, Indels: 11
0.77 0.17 0.07
Matches are distributed among these distances:
42 34 0.27
43 87 0.68
44 6 0.05
45 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (43 bp):
AGTATAATTGCTTCGATTCATCCGATGATGCACAATGTGTGCC
Found at i:43952833 original size:86 final size:85
Alignment explanation
Indices: 43952613--43952837 Score: 222
Period size: 86 Copynumber: 2.6 Consensus size: 85
43952603 TTCGATTTAT
*** * *
43952613 TCGATGATGCACT-TACATGCTAGTATATTTGCTTCGGTACATCCAATGATGCA-CTTATGTGAA
1 TCGATGATGCACTATGTGTGCTAGTATATTTGCTTCGATATATCCAATGATGCACCTTATGTGAA
* *
43952676 AGTATATTTGCTTCGGTTTA
66 AGTATAATTGCTTCGGTTGA
* * * * * *
43952696 TCTGATGATGCACAATGTGTGCCAGTATAATTGCTTCGAT-TCGTCCGATGATGCACCTTGTGTG
1 TC-GATGATGCACTATGTGTGCTAGTATATTTGCTTCGATAT-ATCCAATGATGCACCTTATGTG
** * * *
43952760 CCAGTATAATTGTTTTGGCTTGC
64 AAAGTATAATTGCTTCGG-TTGA
* *
43952783 TCGATGATGCACTATGTGTGCTAGTATCTTTCCTTCGATATATCCAATGATGCAC
1 TCGATGATGCACTATGTGTGCTAGTATATTTGCTTCGATATATCCAATGATGCAC
43952838 TATGATGCTA
Statistics
Matches: 111, Mismatches: 25, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
83 2 0.02
84 10 0.09
85 30 0.27
86 64 0.58
87 5 0.05
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (85 bp):
TCGATGATGCACTATGTGTGCTAGTATATTTGCTTCGATATATCCAATGATGCACCTTATGTGAA
AGTATAATTGCTTCGGTTGA
Found at i:43964061 original size:5 final size:5
Alignment explanation
Indices: 43964053--43964102 Score: 82
Period size: 5 Copynumber: 9.8 Consensus size: 5
43964043 AGGTTTTCAT
*
43964053 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TCTTC TTTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTT
43964103 TGTTGTAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 38 0.90
6 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:43973764 original size:21 final size:21
Alignment explanation
Indices: 43973738--43973780 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
43973728 TAGACCAAGT
*
43973738 GGGGGTCAACATACCCATGTG
1 GGGGGTCAACACACCCATGTG
*
43973759 GGGGGTCAACACATCCATGTG
1 GGGGGTCAACACACCCATGTG
43973780 G
1 G
43973781 ATGAGGCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (21 bp):
GGGGGTCAACACACCCATGTG
Found at i:43974502 original size:15 final size:15
Alignment explanation
Indices: 43974482--43974512 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43974472 ACGTCCAAAG
43974482 AAAATAAAAATAATC
1 AAAATAAAAATAATC
43974497 AAAATAAAAATAATC
1 AAAATAAAAATAATC
43974512 A
1 A
43974513 TAACAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAAAATAATC
Found at i:43975048 original size:5 final size:5
Alignment explanation
Indices: 43975038--43975076 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
43975028 ATTAATTAAT
43975038 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
43975077 TTATTTCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:43979587 original size:44 final size:44
Alignment explanation
Indices: 43979482--43979587 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
43979472 TTGACCCGCT
* * * *
43979482 CCACTGCAACCTCAGGGAAATCGGACTCATATCTTCAACTGGTC
1 CCACTGCAACTTCAGGGGAATCGAACCCATATCTTCAACTGGTC
43979526 CCACTGCAACTTCAGGGGAATCGAACCCATATCTTCAACTGG-C
1 CCACTGCAACTTCAGGGGAATCGAACCCATATCTTCAACTGGTC
43979569 CCTACTGCAACTTCAGGGG
1 CC-ACTGCAACTTCAGGGG
43979588 GATAAGATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
43 3 0.05
44 54 0.95
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGGAATCGAACCCATATCTTCAACTGGTC
Found at i:43979901 original size:33 final size:33
Alignment explanation
Indices: 43979859--43979924 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
43979849 CTCAGGGAGA
43979859 AAGGATTCGTGGCTTAAATCTGCTTCCTTACAC
1 AAGGATTCGTGGCTTAAATCTGCTTCCTTACAC
43979892 AAGGATTCGTGGCTTAAATCTGCTTCCTTACAC
1 AAGGATTCGTGGCTTAAATCTGCTTCCTTACAC
43979925 TTGAAGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (33 bp):
AAGGATTCGTGGCTTAAATCTGCTTCCTTACAC
Found at i:43980060 original size:128 final size:128
Alignment explanation
Indices: 43979904--43980159 Score: 417
Period size: 128 Copynumber: 2.0 Consensus size: 128
43979894 GGATTCGTGG
* * * *
43979904 CTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTG-TCGTCTTCGATCTGCTCTGCTACTGCT
1 CTTAAATCTGATTCCTTACACTTAAAGATAAGATTCGCT-GTCTCCGATCTGCTCTGCTACTGCT
* * *
43979968 TAGGGAGGCGAGATCTGTAATTT-TCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGA
65 TAGGGAGACAAGATCTGTAATTTCT-AACCTATTCCACTGCTGGTCAAGGACATAGGACTTGTGA
43980032 CTTAAATCTGATTCCTTACACTTAAAGATAAGATTCGCTGTCTCCGATCTGCTCTGCTACTGCTT
1 CTTAAATCTGATTCCTTACACTTAAAGATAAGATTCGCTGTCTCCGATCTGCTCTGCTACTGCTT
43980097 AGGGAGACAAGATCTGTAATTTCTAACCTATTCCACTGCTGGTCAAGGACATAGGACTTGTGA
66 AGGGAGACAAGATCTGTAATTTCTAACCTATTCCACTGCTGGTCAAGGACATAGGACTTGTGA
43980160 TTTCACCGAT
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
128 117 0.98
129 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (128 bp):
CTTAAATCTGATTCCTTACACTTAAAGATAAGATTCGCTGTCTCCGATCTGCTCTGCTACTGCTT
AGGGAGACAAGATCTGTAATTTCTAACCTATTCCACTGCTGGTCAAGGACATAGGACTTGTGA
Found at i:43981393 original size:6 final size:6
Alignment explanation
Indices: 43981384--43981417 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
43981374 CATTTTTACT
43981384 TTTTCA TTTTTCA TTTCTCA TTTTCA TTTTCA TT
1 TTTTCA -TTTTCA TTT-TCA TTTTCA TTTTCA TT
43981418 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCA
Found at i:43981407 original size:13 final size:12
Alignment explanation
Indices: 43981384--43981417 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
43981374 CATTTTTACT
43981384 TTTTCATTTTTCA
1 TTTTCA-TTTTCA
43981397 TTTCTCATTTTCA
1 TTT-TCATTTTCA
43981410 TTTTCATT
1 TTTTCATT
43981418 CTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 12 0.60
14 3 0.15
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTCATTTTCA
Found at i:43982337 original size:35 final size:35
Alignment explanation
Indices: 43982297--43982387 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 35
43982287 TTCTTATTTC
43982297 TTTTTCTCTTATTTTCATTTT-GACATTGATTTTGA
1 TTTTTCT-TTATTTTCATTTTCGACATTGATTTTGA
* ***
43982332 TTTTTCTTTTTTCTTC-TTTTCGTTTTTGATTTTGA
1 TTTTTCTTTATT-TTCATTTTCGACATTGATTTTGA
*
43982367 TTTTTTTTTATTTTTCATTTT
1 TTTTTCTTTA-TTTTCATTTT
43982388 TTTATTTTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
34 8 0.17
35 32 0.70
36 6 0.13
ACGTcount: A:0.11, C:0.10, G:0.07, T:0.73
Consensus pattern (35 bp):
TTTTTCTTTATTTTCATTTTCGACATTGATTTTGA
Found at i:43982370 original size:29 final size:31
Alignment explanation
Indices: 43982326--43982403 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 31
43982316 TTGACATTGA
**
43982326 TTTTGATTTTTCTTTTTTCTT-CTTTTC-GT
1 TTTTGATTTTGATTTTTTCTTACTTTTCAGT
* * *
43982355 TTTTGATTTTGATTTTTTTTTATTTTTCATT
1 TTTTGATTTTGATTTTTTCTTACTTTTCAGT
*
43982386 TTTTTATTTTGATTTTTT
1 TTTTGATTTTGATTTTTT
43982404 TCATCTAGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 18 0.44
30 5 0.12
31 18 0.44
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.78
Consensus pattern (31 bp):
TTTTGATTTTGATTTTTTCTTACTTTTCAGT
Found at i:43982372 original size:15 final size:14
Alignment explanation
Indices: 43982354--43982404 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
43982344 CTTCTTTTCG
*
43982354 TTTTTGATTTTGATTT
1 TTTTTTATTTTGA--T
*
43982370 TTTTTTATTTTTCAT
1 TTTTTTA-TTTTGAT
43982385 TTTTTTATTTTGAT
1 TTTTTTATTTTGAT
43982399 TTTTTT
1 TTTTTT
43982405 CATCTAGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 12 0.39
15 8 0.26
16 6 0.19
17 5 0.16
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTTGAT
Found at i:43982485 original size:142 final size:142
Alignment explanation
Indices: 43982235--43982517 Score: 512
Period size: 143 Copynumber: 2.0 Consensus size: 142
43982225 TTTTTGTCCT
43982235 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTCATTCTTATTTCTTT
1 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTCATTCTTATTTCTTT
43982300 TTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTCTTTTCGTTTTTGATTTT
66 TTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTCTTTTCGTTTTTGATTTT
43982365 GATTTTTTTTTA
131 GATTTTTTTTTA
*
43982377 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTTCATTCTTCTTTCTT
1 TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTC-TTTTTTCATTCTTATTTCTT
* * * *
43982442 TTTCTCTTATTTTTATTTTGACCTTGATTTTGATTTTTCTTTTTTCTTCTTTTTGTTTTTTATTT
65 TTTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTCTTTTCGTTTTTGATTT
43982507 TGATTTTTTTT
130 TGATTTTTTTT
43982518 GAATTGGATC
Statistics
Matches: 135, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
142 44 0.33
143 91 0.67
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.72
Consensus pattern (142 bp):
TTTTTCATTTTTTTATTTTGATTTTTTTCATCTAGATTTTTCTCTTTTTTCATTCTTATTTCTTT
TTCTCTTATTTTCATTTTGACATTGATTTTGATTTTTCTTTTTTCTTCTTTTCGTTTTTGATTTT
GATTTTTTTTTA
Found at i:43984559 original size:20 final size:20
Alignment explanation
Indices: 43984534--43984571 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43984524 ATTCGCTCTA
43984534 ATTTTTCCAACCTTTGTTCT
1 ATTTTTCCAACCTTTGTTCT
*
43984554 ATTTTTCTAACCTTTGTT
1 ATTTTTCCAACCTTTGTT
43984572 TGGATACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTTCCAACCTTTGTTCT
Found at i:43986964 original size:3 final size:3
Alignment explanation
Indices: 43986949--43986978 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
43986939 AAAATAAAAC
*
43986949 TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43986979 CATTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:43986967 original size:15 final size:15
Alignment explanation
Indices: 43986941--43987004 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
43986931 AATAAAGGAA
*
43986941 AATAA-AACTAATAAC
1 AATAATAAC-AATAAT
*
43986956 AATAATAATAATAAT
1 AATAATAACAATAAT
*
43986971 AATAATAACATTAA-
1 AATAATAACAATAAT
*
43986985 AATAATTAACTA-AAT
1 AATAA-TAACAATAAT
43987000 AATAA
1 AATAA
43987005 AATTGCTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 7 0.17
15 31 0.77
16 2 0.05
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAATAACAATAAT
Found at i:43989543 original size:9 final size:9
Alignment explanation
Indices: 43989514--43989543 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
43989504 ATGTGTAGGA
43989514 TTATTTTTT
1 TTATTTTTT
43989523 TTATCTTTTT
1 TTAT-TTTTT
43989533 TTATTTTTT
1 TTATTTTTT
43989542 TT
1 TT
43989544 TGTCTGCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (9 bp):
TTATTTTTT
Found at i:44007079 original size:18 final size:20
Alignment explanation
Indices: 44007053--44007089 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
44007043 CAGACACTCC
44007053 ATGTGC-TTTCT-TCTTTTT
1 ATGTGCTTTTCTCTCTTTTT
*
44007071 ATGTTCTTTTCTCTCTTTT
1 ATGTGCTTTTCTCTCTTTT
44007090 ATAACGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 5 0.31
20 6 0.38
ACGTcount: A:0.05, C:0.19, G:0.08, T:0.68
Consensus pattern (20 bp):
ATGTGCTTTTCTCTCTTTTT
Found at i:44007209 original size:18 final size:18
Alignment explanation
Indices: 44007188--44007239 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
44007178 TATCAATAGA
*
44007188 ATAAATTTAATTTTATTT
1 ATAAATTTAATTTAATTT
44007206 ATAAATTT-ATTTAATTT
1 ATAAATTTAATTTAATTT
*
44007223 ATTAAATATAATTTAAT
1 A-TAAATTTAATTTAAT
44007240 GGTTGTGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 9 0.30
18 14 0.47
19 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAAATTTAATTTAATTT
Found at i:44008847 original size:3 final size:3
Alignment explanation
Indices: 44008841--44008885 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
44008831 ATTATTAAGT
44008841 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44008886 TTAAAAGAAA
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):
ATA
Found at i:44008967 original size:17 final size:18
Alignment explanation
Indices: 44008945--44008978 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44008935 AGCAAAACGG
44008945 GAAAAAAGA-AAAGAAAA
1 GAAAAAAGAGAAAGAAAA
*
44008962 GAAAAAGGAGAAAGAAA
1 GAAAAAAGAGAAAGAAA
44008979 CAACGAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAGAAAGAAAA
Found at i:44015884 original size:26 final size:26
Alignment explanation
Indices: 44015828--44015884 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
44015818 AGACGGCTTT
*
44015828 GAATTGATTAAATTGATAATTGATAC
1 GAATTGATTAAATTGACAATTGATAC
* * *
44015854 AAATTGGTTAAATTGACGATTGA-ATC
1 GAATTGATTAAATTGACAATTGATA-C
44015880 GAATT
1 GAATT
44015885 TTTTTTGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (26 bp):
GAATTGATTAAATTGACAATTGATAC
Found at i:44017353 original size:19 final size:19
Alignment explanation
Indices: 44017329--44017374 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
44017319 TTGAACTTGA
*
44017329 AAATTGGACCTGAGATCGT
1 AAATTGGACATGAGATCGT
*
44017348 AAATTGGGCATGAGATCGT
1 AAATTGGACATGAGATCGT
44017367 AAATTGGA
1 AAATTGGA
44017375 TCTGGGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (19 bp):
AAATTGGACATGAGATCGT
Found at i:44021388 original size:3 final size:3
Alignment explanation
Indices: 44021380--44021418 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
44021370 TATCTGGTAC
44021380 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
44021419 ATAAAGATGA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:44024235 original size:3 final size:3
Alignment explanation
Indices: 44024229--44024289 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
44024219 TATCATTATT
* *
44024229 TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC -TC TGC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
44024276 TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TT
44024290 TTATTTCCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:44038434 original size:47 final size:47
Alignment explanation
Indices: 44038316--44038470 Score: 256
Period size: 47 Copynumber: 3.2 Consensus size: 47
44038306 GTGAGTATGC
* *
44038316 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGACAGAGGAGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTC-G--AGATGAGAGT
*
44038366 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCTCGAGATGAGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
44038413 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
44038460 CAGTGTAAGAC
1 CAGTGTAAGAC
44038471 NNNNNNNNNN
Statistics
Matches: 101, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
47 66 0.65
49 1 0.01
50 34 0.34
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.20
Consensus pattern (47 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGAGT
Found at i:44041717 original size:23 final size:23
Alignment explanation
Indices: 44041691--44041736 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
44041681 TGGTATTCAC
44041691 CTTTTACAAGAAAAAAATATTAA
1 CTTTTACAAGAAAAAAATATTAA
44041714 CTTTTACAAGAAAAAAATATTAA
1 CTTTTACAAGAAAAAAATATTAA
44041737 ATTAATCATA
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:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (23 bp):
CTTTTACAAGAAAAAAATATTAA
Found at i:44049113 original size:22 final size:23
Alignment explanation
Indices: 44049070--44049113 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
44049060 AAACACGCAA
*
44049070 AGTAGAAGAAAATAATGCAAAAC
1 AGTAGAAGAAAATAATGAAAAAC
44049093 AGTAGAA-AAAATAGAT-AAAAA
1 AGTAGAAGAAAATA-ATGAAAAA
44049114 TATATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.14
Consensus pattern (23 bp):
AGTAGAAGAAAATAATGAAAAAC
Found at i:44049263 original size:22 final size:22
Alignment explanation
Indices: 44049230--44049272 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44049220 GATTCAAAGG
*
44049230 TTGCTTTCTTATTTTTGTTTTT
1 TTGCTTTCTTATTTTTATTTTT
44049252 TTGC-TTCGTTATTTTTATTTT
1 TTGCTTTC-TTATTTTTATTTT
44049273 ATTTTCGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.07, C:0.09, G:0.09, T:0.74
Consensus pattern (22 bp):
TTGCTTTCTTATTTTTATTTTT
Found at i:44050205 original size:62 final size:59
Alignment explanation
Indices: 44050127--44050251 Score: 169
Period size: 62 Copynumber: 2.1 Consensus size: 59
44050117 TCTATACATA
* * *
44050127 TTTTTAATTTTCATATATACATACTTTATATCTTACATCATTATATATCTTTATATACGCAT
1 TTTTTAATTTTCATATATACATACCTTACATCTT--AT-ATTATATATCTTTATACACGCAT
* * *
44050189 TTTTTAATTTTCATATATATATACCTTGCATCTTATATTATATATCTTTATACACGTAT
1 TTTTTAATTTTCATATATACATACCTTACATCTTATATTATATATCTTTATACACGCAT
44050248 TTTT
1 TTTT
44050252 AAACTCATGT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 25 0.44
60 2 0.04
62 30 0.53
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.54
Consensus pattern (59 bp):
TTTTTAATTTTCATATATACATACCTTACATCTTATATTATATATCTTTATACACGCAT
Found at i:44050432 original size:2 final size:2
Alignment explanation
Indices: 44050427--44050451 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44050417 TATTTTAAAC
44050427 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 A
44050452 AATTATCATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44051263 original size:107 final size:106
Alignment explanation
Indices: 44051117--44051314 Score: 290
Period size: 107 Copynumber: 1.9 Consensus size: 106
44051107 AATAATAATA
* * *
44051117 AAGGCAATATTTTGCATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGTTGGGTTTCAATTTTTT
1 AAGGCAATATTTTGAATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTAGGTTTCAATTTTTT
* *
44051182 TGTTCGACCGAATAGCCAAATATCCTTTAAAATTTCAAAGT
66 CGTTCGACCAAATAGCCAAATATCCTTTAAAATTTCAAAGT
* **
44051223 AAGGCAATATTTTGAAGTTTGGAAATTCGAGGAAA-TGTGCCCTAATGTGCTAGGTTTTGATTTT
1 AAGGCAATATTTTGAA-TTTGGAAATTCGA-GAAAGCGTGCCCTAATGTGCTAGGTTTCAATTTT
*
44051287 TTCGTTTGACCAAATAGCCAAATATCCT
64 TTCGTTCGACCAAATAGCCAAATATCCT
44051315 CTTATATCTT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
106 15 0.19
107 62 0.77
108 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (106 bp):
AAGGCAATATTTTGAATTTGGAAATTCGAGAAAGCGTGCCCTAATGTGCTAGGTTTCAATTTTTT
CGTTCGACCAAATAGCCAAATATCCTTTAAAATTTCAAAGT
Found at i:44064165 original size:3 final size:3
Alignment explanation
Indices: 44064157--44064255 Score: 180
Period size: 3 Copynumber: 33.0 Consensus size: 3
44064147 ACAAAATTGC
44064157 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
44064205 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44064253 ATT
1 ATT
44064256 TGTGTGTGTG
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44073518 original size:23 final size:23
Alignment explanation
Indices: 44073469--44073522 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
44073459 TAGCTTGTAT
* * *
44073469 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGTCTCAGCTCAACA
*
44073492 GAGCTTACCGTCTCAGCTCAATA
1 GAGCTTACCGTCTCAGCTCAACA
44073515 GAGCTTAC
1 GAGCTTAC
44073523 TGTTTATCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (23 bp):
GAGCTTACCGTCTCAGCTCAACA
Found at i:44074292 original size:2 final size:2
Alignment explanation
Indices: 44074285--44074338 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
44074275 GGTATTTTGG
44074285 TA TA TA TA TA 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 TA TA TA TA TA
44074327 TA TA TA TA TA TA
1 TA TA TA TA TA TA
44074339 AATGCCTTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44076585 original size:66 final size:65
Alignment explanation
Indices: 44076464--44076586 Score: 142
Period size: 66 Copynumber: 1.9 Consensus size: 65
44076454 TGATGCGTGT
** * * **
44076464 ACAACCCAATTTTGCCCAGACCCAAATGGCCCATTACCTAATAACCCACCTAAACCCAACAAACA
1 ACAACCCAATTCGGCCCAAACCCAAATGGCCCATTACCTAATAACCAACAGAAACCCAACAAACA
*
44076529 ACAACCCAATTCGGCCCAAAACCCGAATGGCCCATTAACCT-A-AACCTAACAGAAACCC
1 ACAACCCAATTCGGCCC-AAACCCAAATGGCCCATT-ACCTAATAACC-AACAGAAACCC
44076587 TAGCAGAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
65 19 0.40
66 25 0.52
67 4 0.08
ACGTcount: A:0.40, C:0.38, G:0.08, T:0.14
Consensus pattern (65 bp):
ACAACCCAATTCGGCCCAAACCCAAATGGCCCATTACCTAATAACCAACAGAAACCCAACAAACA
Found at i:44076911 original size:13 final size:13
Alignment explanation
Indices: 44076876--44076924 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
44076866 ATAAGCTCTA
*
44076876 TTTTCCCTTTTAT
1 TTTTCCTTTTTAT
**
44076889 TTTTTATTTTTAT
1 TTTTCCTTTTTAT
44076902 TTTTCCTTTTT-T
1 TTTTCCTTTTTAT
44076914 TCTTTCCTTTT
1 T-TTTCCTTTT
44076925 AAAACTGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 2 0.07
13 28 0.93
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCCTTTTTAT
Found at i:44076924 original size:25 final size:25
Alignment explanation
Indices: 44076874--44076925 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
44076864 GTATAAGCTC
*
44076874 TATTTTCCCTTTTATTTTTTATTTT
1 TATTTTCCCTTTTATTTTTTACTTT
* *
44076899 TATTTTTCCTTTT-TTTCTTTCCTTT
1 TATTTTCCCTTTTATTT-TTTACTTT
44076924 TA
1 TA
44076926 AAACTGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (25 bp):
TATTTTCCCTTTTATTTTTTACTTT
Found at i:44076966 original size:17 final size:17
Alignment explanation
Indices: 44076941--44076978 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
44076931 GTTTGCTTTC
*
44076941 TTTATTTTTATTTTATT
1 TTTACTTTTATTTTATT
*
44076958 TTTACTTTTCTTTTATT
1 TTTACTTTTATTTTATT
44076975 TTTA
1 TTTA
44076979 AAAAAACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTACTTTTATTTTATT
Found at i:44079751 original size:19 final size:20
Alignment explanation
Indices: 44079711--44079754 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
44079701 GTCTCTTTAG
* *
44079711 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
44079730 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
44079749 GCATTA
1 GCATTA
44079755 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:44082466 original size:6 final size:6
Alignment explanation
Indices: 44082457--44082499 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
44082447 AAAATAGAAA
44082457 AAAAAG AAAAAAG AAAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG -AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
44082500 AAGGAGAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.64
7 13 0.36
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:44082466 original size:7 final size:7
Alignment explanation
Indices: 44082456--44082500 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
44082446 AAAAATAGAA
44082456 AAAAAAG
1 AAAAAAG
44082463 AAAAAAG
1 AAAAAAG
44082470 AAAAAAG
1 AAAAAAG
44082477 -AAAAAG
1 AAAAAAG
44082483 -AAAAAG
1 AAAAAAG
44082489 -AAAAAG
1 AAAAAAG
44082495 AAAAAA
1 AAAAAA
44082501 AGGAGAGGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 18 0.49
7 19 0.51
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:44082473 original size:12 final size:11
Alignment explanation
Indices: 44082446--44082499 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 11
44082436 AATCAAAGCC
*
44082446 AAAAATAGAAA
1 AAAAAAAGAAA
44082457 AAAAAGAA-AAA
1 AAAAA-AAGAAA
44082468 AGAAAAAAGAAA
1 A-AAAAAAGAAA
44082480 AAGAAAAAGAAA
1 AA-AAAAAGAAA
44082492 AAGAAAAA
1 AA-AAAAA
44082500 AAGGAGAGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 12 0.32
12 26 0.68
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:44084647 original size:85 final size:85
Alignment explanation
Indices: 44084504--44084903 Score: 604
Period size: 85 Copynumber: 4.7 Consensus size: 85
44084494 AGAACAAATT
* *
44084504 AGCAGATCGAAAACAAGCCTTGCATTCATTGGTTACAGTGGAGTTGGTTAAAGAAGCAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTG
*
44084569 CCTTCCTGCGTTAACAGTGA
66 CCTTCCTGCGTTAACAGCGA
*
44084589 AGCAGATCGAAAACAAGCATTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTG
*
44084654 CCTTCCTGC-ATAACAGCGA
66 CCTTCCTGCGTTAACAGCGA
* * *
44084673 AGCAGATCGAAAACAAAGTCTTGCCTTCATTGGTTACAATGGAGCTGGTTAAAGAAGTAGATCTT
1 AGCAGATCGAAAAC-AAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTT
44084738 GCCTTCCTGCGTTAACAGCGA
65 GCCTTCCTGCGTTAACAGCGA
* * *
44084759 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGTTTAAAGAAGTAGATCTTG
1 AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTG
* *
44084824 CCTTCCTGCATTAACAGTGA
66 CCTTCCTGCGTTAACAGCGA
* * * * *
44084844 AGCAGATCGAAAACAAATCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTGAAGATAGCA
1 AGCAGATCGAAAAC-AAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGA-AGCA
44084904 NNNNNNNNNN
Statistics
Matches: 289, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
84 22 0.08
85 206 0.71
86 58 0.20
87 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (85 bp):
AGCAGATCGAAAACAAGCCTTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGATCTTG
CCTTCCTGCGTTAACAGCGA
Found at i:44084657 original size:43 final size:43
Alignment explanation
Indices: 44084522--44084828 Score: 177
Period size: 43 Copynumber: 7.2 Consensus size: 43
44084512 GAAAACAAGC
* * *
44084522 CTTGCATTCATTGGTTACAGTGGAGTTGGTTAAAGAAGCAGAT
1 CTTGCCTTCATTGGTTACAGTGGAGCTGATTAAAGAAGCAGAT
* * * ** *
44084565 CTTGCCTTC-CTGCGTTAACAGTGAAGCAGATCGAA-AA-CA-AG
1 CTTGCCTTCATTG-GTT-ACAGTGGAGCTGATTAAAGAAGCAGAT
*
44084606 CATTGCCTTCATTGGTTACAGTGGAGCTGGTTAAAGAAGCAGAT
1 C-TTGCCTTCATTGGTTACAGTGGAGCTGATTAAAGAAGCAGAT
* * * * * * ** *
44084650 CTTGCCTTC-CTGCATAACAGCGAAGCAGATCGAA-AA-CAAAGT
1 CTTGCCTTCATTG-GTTACAGTGGAGCTGATTAAAGAAGCAGA-T
* * *
44084692 CTTGCCTTCATTGGTTACAATGGAGCTGGTTAAAGAAGTAGAT
1 CTTGCCTTCATTGGTTACAGTGGAGCTGATTAAAGAAGCAGAT
* * * * ** *
44084735 CTTGCCTTC-CTGCGTTAACAGCGAAGCAGATCGAA-AA-CA-AGC
1 CTTGCCTTCATTG-GTT-ACAGTGGAGCTGATTAAAGAAGCAGA-T
* * *
44084777 CTTGCCTTCATTGGTTGCAGTGGAGCTGTTTAAAGAAGTAGAT
1 CTTGCCTTCATTGGTTACAGTGGAGCTGATTAAAGAAGCAGAT
44084820 CTTGCCTTC
1 CTTGCCTTC
44084829 CTGCATTAAC
Statistics
Matches: 187, Mismatches: 58, Indels: 38
0.66 0.20 0.13
Matches are distributed among these distances:
41 30 0.16
42 60 0.32
43 69 0.37
44 28 0.15
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
CTTGCCTTCATTGGTTACAGTGGAGCTGATTAAAGAAGCAGAT
Found at i:44084867 original size:43 final size:42
Alignment explanation
Indices: 44084563--44084869 Score: 162
Period size: 43 Copynumber: 7.2 Consensus size: 42
44084553 AAAGAAGCAG
44084563 ATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAAC-A
1 ATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAA
* * * * * ** *
44084604 AGCATTGCCTTCATTG-GTT-ACAGTGGAGCTGGTTAAAGAAGCAG
1 ATC-TTGCCTTC-CTGCGTTAACAGTGAAGCAGATCGAA-AA-CAA
* *
44084648 ATCTTGCCTTCCTGC-ATAACAGCGAAGCAGATCGAAAACAA
1 ATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAA
* * * * * ** * *
44084689 AGTCTTGCCTTCATTG-GTT-ACAATGGAGCTGGTTAAAGAAGTAG
1 A-TCTTGCCTTC-CTGCGTTAACAGTGAAGCAGATCGAA-AA-CAA
*
44084733 ATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAA
1 ATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAA
** * * * * * ** * *
44084775 GCCTTGCCTTCATTG-GTT-GCAGTGGAGCTGTTTAAAGAAGTAG
1 ATCTTGCCTTC-CTGCGTTAACAGTGAAGCAGATCGAA-AA-CAA
*
44084818 ATCTTGCCTTCCTGCATTAACAGTGAAGCAGATCGAAAACAA
1 ATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAA
44084860 ATCCTTGCCT
1 AT-CTTGCCT
44084870 CCATCGGTTG
Statistics
Matches: 183, Mismatches: 63, Indels: 38
0.64 0.22 0.13
Matches are distributed among these distances:
41 29 0.16
42 61 0.33
43 66 0.36
44 27 0.15
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
ATCTTGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAA
Found at i:44085853 original size:88 final size:88
Alignment explanation
Indices: 44085704--44086789 Score: 1612
Period size: 88 Copynumber: 12.4 Consensus size: 88
44085694 NNNNNNCGAC
*
44085704 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGTAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
*
44085769 GACACAAACCTTGCCTCTCTCGA
66 GACACAAACCTTGCCTCTCTCGG
* *
44085792 TTGTGATGGAGCTGGTTTAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCAAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
44085857 GACACAAACCTTGCCTCTCTCGG
66 GACACAAACCTTGCCTCTCTCGG
*
44085880 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
44085945 GACACAAACCTTGCCTCTCTCGG
66 GACACAAACCTTGCCTCTCTCGG
* * *
44085968 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTTTGTATTTACAGTGAAGCAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
*
44086033 GATACAAACCTTGCCTCTCTCGG
66 GACACAAACCTTGCCTCTCTCGG
* *
44086056 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
*
44086121 AACACAAACCTTGCCTC-CATCGG
66 GACACAAACCTTGCCTCTC-TCGG
* * ** *** * *
44086144 TTG-CAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTTCTACGTTAACAGCGAAGCAGATCGA
1 TTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGA
*
44086208 A-A-ACAAACCTTGCCTCTCTCAG
65 AGACACAAACCTTGCCTCTCTCGG
* *
44086230 TTGTGATGGAGCTGGTTGAAGACAAATGATCTTGCCTTTCTGTATTGACAGCGAAGTAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
*
44086295 GACACAAACCTTGCCTCTCTCGA
66 GACACAAACCTTGCCTCTCTCGG
* * *
44086318 TTTTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCAAAGCAGGTCAAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
*
44086383 AACACAAACCTTGCCTCTCTCGG
66 GACACAAACCTTGCCTCTCTCGG
*
44086406 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
44086471 GACACAAACCTTGCCTCTCTCGG
66 GACACAAACCTTGCCTCTCTCGG
*
44086494 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTTACAGCGAAGCAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
*
44086559 GATACAAACCTTGCCTCTCTCGG
66 GACACAAACCTTGCCTCTCTCGG
* * *
44086582 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAAGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
*
44086647 AACACAAACCTTGCCTC-CATCGG
66 GACACAAACCTTGCCTCTC-TCGG
* * * ** * * *** * * *
44086670 TTG-CAGTGGAGTTGGTTGAAGATAGCAGATATTGCCTTCCTACGTTAATAGCGAAGCAGATCGA
1 TTGTGA-TGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGA
*
44086734 A-A-ACAAACCTTGCCTCTCTCAG
65 AGACACAAACCTTGCCTCTCTCGG
* *
44086756 TTGTGATAGAGCTGGTTGAAGACAAATGATCTTG
1 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTG
44086790 TTTCAAATCA
Statistics
Matches: 904, Mismatches: 84, Indels: 22
0.90 0.08 0.02
Matches are distributed among these distances:
86 110 0.12
87 11 0.01
88 783 0.87
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (88 bp):
TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGCAGGTCGAA
GACACAAACCTTGCCTCTCTCGG
Found at i:44086696 original size:526 final size:526
Alignment explanation
Indices: 44085704--44086789 Score: 2055
Period size: 526 Copynumber: 2.1 Consensus size: 526
44085694 NNNNNNCGAC
*
44085704 TTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTGACAGCGAAGTAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAATGATCTTGCCTTTCTGTATTGACAGCGAAGTAGGTCGAA
*
44085769 GACACAAACCTTGCCTCTCTCGATTGTGATGGAGCTGGTTTAAGACAAAAGATCTTGCCTTTCTG
66 GACACAAACCTTGCCTCTCTCGATTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTG
* *
44085834 TATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGA
131 TATTGACAGCAAAGCAGGTCAAAAACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGA
44085899 AGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
196 AGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
* *
44085964 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTTTGTATTTACAGTGAAGCAGGT
261 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTTACAGCGAAGCAGGT
44086029 CGAAGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
326 CGAAGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
*
44086094 CCTGCATTGACAGCGAAGCAGGTCGAAAACACAAACCTTGCCTCCATCGGTTGCAGTGGAGCTGG
391 CCTGCATTGACAGCGAAGCAAGTCGAAAACACAAACCTTGCCTCCATCGGTTGCAGTGGAGCTGG
* *
44086159 TTGAAGATAGCAGATCTTGCCTTTCTACGTTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTC
456 TTGAAGATAGCAGATATTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTC
44086224 TCTCAG
521 TCTCAG
44086230 TTGTGATGGAGCTGGTTGAAGACAAATGATCTTGCCTTTCTGTATTGACAGCGAAGTAGGTCGAA
1 TTGTGATGGAGCTGGTTGAAGACAAATGATCTTGCCTTTCTGTATTGACAGCGAAGTAGGTCGAA
*
44086295 GACACAAACCTTGCCTCTCTCGATTTTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTG
66 GACACAAACCTTGCCTCTCTCGATTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTG
44086360 TATTGACAGCAAAGCAGGTCAAAAACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGA
131 TATTGACAGCAAAGCAGGTCAAAAACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGA
44086425 AGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
196 AGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
44086490 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTTACAGCGAAGCAGGT
261 TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTTACAGCGAAGCAGGT
44086555 CGAAGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
326 CGAAGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
*
44086620 CCTGCATTGACAGCGAAGCAAGTCGAAAACACAAACCTTGCCTCCATCGGTTGCAGTGGAGTTGG
391 CCTGCATTGACAGCGAAGCAAGTCGAAAACACAAACCTTGCCTCCATCGGTTGCAGTGGAGCTGG
*
44086685 TTGAAGATAGCAGATATTGCCTTCCTACGTTAATAGCGAAGCAGATCGAAAACAAACCTTGCCTC
456 TTGAAGATAGCAGATATTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTC
44086750 TCTCAG
521 TCTCAG
*
44086756 TTGTGATAGAGCTGGTTGAAGACAAATGATCTTG
1 TTGTGATGGAGCTGGTTGAAGACAAATGATCTTG
44086790 TTTCAAATCA
Statistics
Matches: 547, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
526 547 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (526 bp):
TTGTGATGGAGCTGGTTGAAGACAAATGATCTTGCCTTTCTGTATTGACAGCGAAGTAGGTCGAA
GACACAAACCTTGCCTCTCTCGATTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTG
TATTGACAGCAAAGCAGGTCAAAAACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGA
AGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
TCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGTATTTACAGCGAAGCAGGT
CGAAGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTT
CCTGCATTGACAGCGAAGCAAGTCGAAAACACAAACCTTGCCTCCATCGGTTGCAGTGGAGCTGG
TTGAAGATAGCAGATATTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAACCTTGCCTC
TCTCAG
Found at i:44087619 original size:154 final size:155
Alignment explanation
Indices: 44087339--44087649 Score: 579
Period size: 154 Copynumber: 2.0 Consensus size: 155
44087329 TAAATTCCAC
*
44087339 TTTCAAACTCTGAAATCCAAGTTGAATCCAGGCAATGGGAACTCAGTTAATAAGTTTGAAACTCT
1 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTCAGTTAATAAGTTTGAAACTCT
44087404 TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAA-TTTT
66 TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
44087468 AAAAAAAATTATATACTGAAATAGG
131 AAAAAAAATTATATACTGAAATAGG
* *
44087493 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTGAGTTAATAGGTTTGAAACTCT
1 TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTCAGTTAATAAGTTTGAAACTCT
*
44087558 TCAACACCCAGTTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
66 TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
44087623 AAAAAAAATTATATACTGAAATAGG
131 AAAAAAAATTATATACTGAAATAGG
44087648 TT
1 TT
44087650 GTCAGATAGA
Statistics
Matches: 152, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
154 121 0.80
155 31 0.20
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (155 bp):
TTTCAAACTCTGAAATCCAAGTTGAATCCAGACAATGGGAACTCAGTTAATAAGTTTGAAACTCT
TCAACACCCAGCTACATTGCGGGGTCGACATTTATATTACCGGGTTTTTTACTGGAATAATTTTT
AAAAAAAATTATATACTGAAATAGG
Found at i:44087761 original size:49 final size:50
Alignment explanation
Indices: 44087679--44087787 Score: 166
Period size: 49 Copynumber: 2.2 Consensus size: 50
44087669 GAAATGGTCT
44087679 TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATT-A
1 TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATTAA
* * * * *
44087728 TTTTTTTAATGGCGCCTATCTGATAGGCTCCAATGAATTTTTTATATTAA
1 TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATTAA
44087778 TTTTTTTAAT
1 TTTTTTTAAT
44087788 AAAATGTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 43 0.80
50 11 0.20
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (50 bp):
TTTTTTTAATGGAGCCTATCTGAAAAGCGCCAATGAATATTTTATATTAA
Found at i:44088686 original size:60 final size:60
Alignment explanation
Indices: 44088622--44088740 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
44088612 ATACTAAACT
* * ** * *
44088622 AAACATAACAATTTATAATTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACGAACAAATTAATTTTAAAATAATTAC
44088682 AAACACAAAAATTTATAACATAATCCTAAATTACGAACAAATTAATTTTAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACGAACAAATTAATTTTAAAATAATTA
44088741 TAAAAAACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACGAACAAATTAATTTTAAAATAATTAC
Found at i:44088934 original size:14 final size:13
Alignment explanation
Indices: 44088909--44088972 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 13
44088899 CATTACCTTT
44088909 TTTTTCTTTCTTC
1 TTTTTCTTTCTTC
44088922 TTTTTCTTCTCTTC
1 TTTTTCTT-TCTTC
*
44088936 TTCTTCTCTTCTTC
1 TTTTTCT-TTCTTC
*
44088950 TCCTTTCTCTTTTTTC
1 T--TTT-TCTTTCTTC
44088966 TTTTTCT
1 TTTTTCT
44088973 ACCATGGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 11 0.26
14 20 0.47
15 1 0.02
16 8 0.19
17 3 0.07
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTCTTTCTTC
Found at i:44088939 original size:11 final size:11
Alignment explanation
Indices: 44088916--44088950 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
44088906 TTTTTTTTCT
44088916 TTCTTCT-TT-
1 TTCTTCTCTTC
44088925 TTCTTCTCTTC
1 TTCTTCTCTTC
44088936 TTCTTCTCTTC
1 TTCTTCTCTTC
44088947 TTCT
1 TTCT
44088951 CCTTTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.29
10 2 0.08
11 15 0.62
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
TTCTTCTCTTC
Found at i:44089145 original size:24 final size:25
Alignment explanation
Indices: 44089100--44089147 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
44089090 TTTATATTTA
*
44089100 AATATTTTTAATAAAAATAAAAAAT
1 AATATTTTTAATAAAAACAAAAAAT
* *
44089125 AATA-TTTTAATCAAACCAAAAAA
1 AATATTTTTAATAAAAACAAAAAA
44089148 AAATTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATTTTTAATAAAAACAAAAAAT
Found at i:44089788 original size:45 final size:45
Alignment explanation
Indices: 44089738--44089877 Score: 208
Period size: 45 Copynumber: 3.0 Consensus size: 45
44089728 CGGAGGGAAA
* * *
44089738 GGAGGGTATGGAGGTGGGCACGGAGGGTATGGTGGTGGTGGCCAC
1 GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
44089783 GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
1 GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
* *
44089828 GGAGGATACGGTGGTGGTGGCCACGGAGGATACGGTGGTGGTGGCCAC
1 GGAGGGTA---TGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
44089876 GG
1 GG
44089878 CGGTCACGGT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
45 49 0.56
48 38 0.44
ACGTcount: A:0.16, C:0.14, G:0.53, T:0.18
Consensus pattern (45 bp):
GGAGGGTATGGTGGTGGCCACGGAGGATATGGTGGTGGTGGCCAC
Found at i:44089889 original size:24 final size:24
Alignment explanation
Indices: 44089750--44089877 Score: 190
Period size: 24 Copynumber: 5.5 Consensus size: 24
44089740 AGGGTATGGA
* * *
44089750 GGTGGGCACGGAGGGTATGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
*
44089774 GGTGGCCACGGAGGGTA---TGGT
1 GGTGGCCACGGAGGATACGGTGGT
*
44089795 GGTGGCCACGGAGGATATGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
44089819 GGTGGCCACGGAGGATACGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
44089843 GGTGGCCACGGAGGATACGGTGGT
1 GGTGGCCACGGAGGATACGGTGGT
44089867 GGTGGCCACGG
1 GGTGGCCACGG
44089878 CGGTCACGGT
Statistics
Matches: 98, Mismatches: 3, Indels: 6
0.92 0.03 0.06
Matches are distributed among these distances:
21 20 0.20
24 78 0.80
ACGTcount: A:0.15, C:0.15, G:0.52, T:0.18
Consensus pattern (24 bp):
GGTGGCCACGGAGGATACGGTGGT
Found at i:44094819 original size:16 final size:16
Alignment explanation
Indices: 44094798--44094831 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
44094788 CAAAATCTCA
44094798 ATTTAATT-TTTAATTT
1 ATTTAATTATTT-ATTT
44094814 ATTTAATTATTTATTT
1 ATTTAATTATTTATTT
44094830 AT
1 AT
44094832 GATGTTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTAATTATTTATTT
Found at i:44096208 original size:5 final size:5
Alignment explanation
Indices: 44096182--44096239 Score: 89
Period size: 5 Copynumber: 11.4 Consensus size: 5
44096172 ATGTTTTAAA
* *
44096182 TATAT TAATAT TTTAA TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
44096233 TATAT TA
1 TATAT TA
44096240 AATAAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 43 0.90
6 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:44096859 original size:23 final size:24
Alignment explanation
Indices: 44096824--44096868 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
44096814 AATATGGCAA
44096824 GAAATTAAGTAGAAAAG-AAGTAT
1 GAAATTAAGTAGAAAAGTAAGTAT
44096847 GAAA-TAAGCTAGAAAAGTAAGT
1 GAAATTAAG-TAGAAAAGTAAGT
44096869 GAGCTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (24 bp):
GAAATTAAGTAGAAAAGTAAGTAT
Found at i:44104823 original size:19 final size:19
Alignment explanation
Indices: 44104799--44104849 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
44104789 GGCTTATTTA
*
44104799 ATTATTAATAATATTTGAG
1 ATTATTAATAAAATTTGAG
*
44104818 ATTATT--TAAAATTTGAT
1 ATTATTAATAAAATTTGAG
*
44104835 A-TATTAATAAGATTT
1 ATTATTAATAAAATTT
44104850 TATAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 7 0.26
19 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (19 bp):
ATTATTAATAAAATTTGAG
Found at i:44136708 original size:98 final size:100
Alignment explanation
Indices: 44136524--44136728 Score: 306
Period size: 98 Copynumber: 2.0 Consensus size: 100
44136514 TTGGTGCCAC
44136524 CAATCTCATTGGCACCTTTGGCAGCAATTCACTTTCAAAATTCAAAATCGTAAATTTACATGTCA
1 CAATCTCATTGGCACCTTTGGCAGCAATTCAC-TT----ATTCAAAATCGTAAATTTACATGTCA
*
44136589 GGTCTTTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
61 GGTCCTTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
* *
44136629 CAATCTCATTGGCACCTTTGGCAGCAATTCAC-T-TTCAAAATGGTAAATTTGCATGTCAGGTCC
1 CAATCTCATTGGCACCTTTGGCAGCAATTCACTTATTCAAAATCGTAAATTTACATGTCAGGTCC
* *
44136692 TTAAAACTGTAGAAAGTTACATTTTAGTCCTTTGG
66 TTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
44136727 CA
1 CA
44136729 CCATTGGTGC
Statistics
Matches: 95, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
98 62 0.65
103 1 0.01
105 32 0.34
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (100 bp):
CAATCTCATTGGCACCTTTGGCAGCAATTCACTTATTCAAAATCGTAAATTTACATGTCAGGTCC
TTAAAACTGTAAAAAGTTACATTTTAGTCATTTGG
Found at i:44136762 original size:27 final size:27
Alignment explanation
Indices: 44136723--44136781 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
44136713 TTTTAGTCCT
44136723 TTGGCACCATTGGTGCCGCCAATCTCA
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * * *
44136750 TTGGCACCTTTGGTGCCTCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
44136777 TTGGC
1 TTGGC
44136782 CTGATCAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.25, T:0.31
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:44136862 original size:28 final size:29
Alignment explanation
Indices: 44136831--44136897 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
44136821 TTTTTTTAGT
* **
44136831 ATATTTTGGTAAACAAAA-AAATTTTATA
1 ATATTTTGATAAACAAAATAAAAGTTATA
*
44136859 ATATTTTGATAAATAAAATAAAAGTTATA
1 ATATTTTGATAAACAAAATAAAAGTTATA
44136888 ATATTTTGAT
1 ATATTTTGAT
44136898 TATTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.47
29 18 0.53
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (29 bp):
ATATTTTGATAAACAAAATAAAAGTTATA
Found at i:44142584 original size:15 final size:14
Alignment explanation
Indices: 44142558--44142595 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
44142548 TTAAAAAAGT
*
44142558 AAATTATTTTTTAG
1 AAATTATTTTTTTG
44142572 AAATTATTTTTTTG
1 AAATTATTTTTTTG
*
44142586 AAAATATTTT
1 AAATTATTTT
44142596 ACTGCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
AAATTATTTTTTTG
Found at i:44143425 original size:34 final size:34
Alignment explanation
Indices: 44143350--44143426 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 34
44143340 TTACTATAAT
* * * * * *
44143350 TAATAATTAGTTATTAATTAATATTTTTTTACTT
1 TAATGATTAGTTAGTAATTAACATCTTTCTACTG
* *
44143384 TATTGATTGGTTAGTAATTAACATCTTTCTACTG
1 TAATGATTAGTTAGTAATTAACATCTTTCTACTG
44143418 TAATGATTA
1 TAATGATTA
44143427 AGAATTAGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.52
Consensus pattern (34 bp):
TAATGATTAGTTAGTAATTAACATCTTTCTACTG
Found at i:44143520 original size:27 final size:26
Alignment explanation
Indices: 44143490--44143565 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 26
44143480 ATATTTTTAT
44143490 TATTGTATTATTATTAAATATTATAAG
1 TATT-TATTATTATTAAATATTATAAG
* *
44143517 TATTATTATTATCATTAAAGA-TATAAG
1 TA-T-TTATTATTATTAAATATTATAAG
44143544 TA-TTATTATTATTCAACATATT
1 TATTTATTATTATT-AA-ATATT
44143566 TTTATTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
24 10 0.25
25 2 0.05
26 2 0.05
27 11 0.28
28 14 0.35
29 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (26 bp):
TATTTATTATTATTAAATATTATAAG
Found at i:44143574 original size:27 final size:25
Alignment explanation
Indices: 44143480--44143576 Score: 70
Period size: 27 Copynumber: 3.6 Consensus size: 25
44143470 ATTGTTAAAC
44143480 ATATTTTTATTATTGTATTATTATTAA
1 ATATTTTTATTA-T-TATTATTATTAA
* *
44143507 ATATTATAAGTATTATTATTATCATTAA
1 ATATT-T--TTATTATTATTATTATTAA
* * * *
44143535 AGA-TATAAGTATTATTATTATTCAA
1 ATATTTTTATTATTATTATTATT-AA
44143560 CATATTTTTATTATTAT
1 -ATATTTTTATTATTAT
44143577 AGGATTATTG
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
24 13 0.25
25 2 0.04
26 2 0.04
27 15 0.29
28 14 0.27
29 1 0.02
30 5 0.10
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (25 bp):
ATATTTTTATTATTATTATTATTAA
Found at i:44146983 original size:18 final size:19
Alignment explanation
Indices: 44146960--44147004 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
44146950 AAATGTACTA
*
44146960 ATTAATTT-TTTGGACCGC
1 ATTAATTTGTTTGGACCAC
*
44146978 ATTAATTTGTTTGGACCAT
1 ATTAATTTGTTTGGACCAC
44146997 ATTAATTT
1 ATTAATTT
44147005 AAGATCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (19 bp):
ATTAATTTGTTTGGACCAC
Found at i:44152177 original size:21 final size:21
Alignment explanation
Indices: 44152153--44152193 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44152143 TAATACTCAC
44152153 CCTACAACACCTAATTCTTAA
1 CCTACAACACCTAATTCTTAA
*
44152174 CCTACAACACCTACTTCTTA
1 CCTACAACACCTAATTCTTA
44152194 GTTTAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (21 bp):
CCTACAACACCTAATTCTTAA
Found at i:44156162 original size:17 final size:17
Alignment explanation
Indices: 44156140--44156172 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
44156130 TTCTATTGTA
44156140 TTTCATTTAAATAAAAC
1 TTTCATTTAAATAAAAC
44156157 TTTCATTTAAATAAAA
1 TTTCATTTAAATAAAA
44156173 AATTGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTCATTTAAATAAAAC
Found at i:44156391 original size:2 final size:2
Alignment explanation
Indices: 44156384--44156448 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
44156374 ATGCAATCTT
44156384 TA TA TA TA TA 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 TA TA TA TA TA
44156426 TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
44156449 CTCCATCTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44157796 original size:5 final size:5
Alignment explanation
Indices: 44157781--44157828 Score: 87
Period size: 5 Copynumber: 9.4 Consensus size: 5
44157771 ATATAGCTAG
44157781 TTATAT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
44157829 TATGAGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 38 0.90
6 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:44170315 original size:30 final size:30
Alignment explanation
Indices: 44170279--44170335 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
44170269 TGTCCACTTC
*
44170279 TCCCAGATTGGTACTTAAGGTTTTTTTTTG
1 TCCCAGATTAGTACTTAAGGTTTTTTTTTG
44170309 TCCCAGATTAGTACTTAAGGTTTTTTT
1 TCCCAGATTAGTACTTAAGGTTTTTTT
44170336 CCGTTAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (30 bp):
TCCCAGATTAGTACTTAAGGTTTTTTTTTG
Found at i:44170648 original size:26 final size:26
Alignment explanation
Indices: 44170612--44170669 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
44170602 ACTTTTTTGG
*
44170612 CTCCAAAGTGGCTCTTAGTTGTTTCT
1 CTCCATAGTGGCTCTTAGTTGTTTCT
44170638 CTCCATAGTGGCTCTTAGTTGTTTCT
1 CTCCATAGTGGCTCTTAGTTGTTTCT
44170664 CTCCAT
1 CTCCAT
44170670 TCCCTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (26 bp):
CTCCATAGTGGCTCTTAGTTGTTTCT
Found at i:44175628 original size:26 final size:26
Alignment explanation
Indices: 44175577--44175628 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
44175567 TAGGATGATT
* **
44175577 ATATTAAAAAATTTCTTATATTATAA
1 ATATTAAAAAATTTATTATAAAATAA
44175603 ATATT-AAAAATTATATTATAAAATAA
1 ATATTAAAAAATT-TATTATAAAATAA
44175629 TTTATGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATTAAAAAATTTATTATAAAATAA
Found at i:44176786 original size:38 final size:39
Alignment explanation
Indices: 44176731--44176832 Score: 145
Period size: 41 Copynumber: 2.6 Consensus size: 39
44176721 CACTCTACTA
44176731 AGTACATGTTGAA-CATGTCTACTACTAC-TGTTGAATTG
1 AGTACATGTT-AAGCATGTCTACTACTACTTGTTGAATTG
44176769 AGTACATGTTAAGCATGTCTACTACTACTATTGTTGAATTG
1 AGTACATGTTAAGCATGTCTACTACTAC--TTGTTGAATTG
* *
44176810 AATACATGTTAAGCATGGCTACT
1 AGTACATGTTAAGCATGTCTACT
44176833 GTTTCTGCAC
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
37 2 0.03
38 25 0.43
41 31 0.53
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (39 bp):
AGTACATGTTAAGCATGTCTACTACTACTTGTTGAATTG
Found at i:44180470 original size:9 final size:9
Alignment explanation
Indices: 44180456--44180484 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
44180446 ATAGTTGCAC
44180456 TAAATTATT
1 TAAATTATT
44180465 TAAATTATT
1 TAAATTATT
44180474 TAAATTATT
1 TAAATTATT
44180483 TA
1 TA
44180485 TAATACCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAAATTATT
Found at i:44180495 original size:18 final size:18
Alignment explanation
Indices: 44180455--44180499 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
44180445 TATAGTTGCA
*
44180455 CTAAATTATTTAAATTAT
1 CTAAATTATTTAAATTAC
*
44180473 TTAAATTATTTATAA-TAC
1 CTAAATTATTTA-AATTAC
44180491 CTAAATTAT
1 CTAAATTAT
44180500 CCCTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
CTAAATTATTTAAATTAC
Found at i:44181025 original size:15 final size:15
Alignment explanation
Indices: 44181001--44181038 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
44180991 AAAACCCTAA
*
44181001 AAACCTTAAAATCTT
1 AAACCCTAAAATCTT
44181016 AAACCCTAAAATCTT
1 AAACCCTAAAATCTT
*
44181031 AAAACCTA
1 AAACCCTA
44181039 CAAGTCAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACCCTAAAATCTT
Found at i:44181523 original size:18 final size:19
Alignment explanation
Indices: 44181500--44181537 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
44181490 CTGTTTAACT
*
44181500 TATAAA-AAAAAGAAATTA
1 TATAAATAAAAACAAATTA
*
44181518 TATAAATCAAAACAAATTA
1 TATAAATAAAAACAAATTA
44181537 T
1 T
44181538 CCCTTCGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (19 bp):
TATAAATAAAAACAAATTA
Found at i:44190158 original size:3 final size:3
Alignment explanation
Indices: 44190150--44190191 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
44190140 AAACACCAAA
44190150 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
44190192 TGATAGGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44198631 original size:26 final size:26
Alignment explanation
Indices: 44198585--44198662 Score: 70
Period size: 26 Copynumber: 2.9 Consensus size: 26
44198575 TTAAAAATTA
*
44198585 AAAAATTA-AAAAATATATAATTATTT
1 AAAAATTATAAAAAAAT-TAATTATTT
44198611 AAAAATTATAAAAAAATTAATGT-TTT
1 AAAAATTATAAAAAAATTAAT-TATTT
* * *
44198637 TAATATTTTAAAAAATAATTAATTAT
1 AAAAATTAT-AAAAA-AATTAATTAT
44198663 CAACGTAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 21 0.49
27 14 0.33
28 8 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
AAAAATTATAAAAAAATTAATTATTT
Done.