Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 2 of 38
Found at i:218678 original size:22 final size:23
Alignment explanation
Indices: 218641--218684 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
218631 TCTCTCCCTC
218641 TTTTTTGTTTTCAAAATAATCTT
1 TTTTTTGTTTTCAAAATAATCTT
218664 TTTTTTGTTTT-AAAATAATCT
1 TTTTTTGTTTTCAAAATAATCT
218685 CCCCCTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTTTTGTTTTCAAAATAATCTT
Found at i:222467 original size:13 final size:13
Alignment explanation
Indices: 222449--222473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
222439 ACTTTTTACC
222449 ATGTATCGATACA
1 ATGTATCGATACA
222462 ATGTATCGATAC
1 ATGTATCGATAC
222474 TTTTCACTTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:222532 original size:20 final size:20
Alignment explanation
Indices: 222503--222557 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
222493 CTGCTAATTT
*
222503 CATGTGTCGATACAATTAAG
1 CATGTATCGATACAATTAAG
* *
222523 CATGTATCGATATAA-TGAG
1 CATGTATCGATACAATTAAG
*
222542 CATGTATCAATACAAT
1 CATGTATCGATACAAT
222558 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTAAG
Found at i:223211 original size:21 final size:21
Alignment explanation
Indices: 223187--223228 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
223177 TTCAATAAAA
223187 CTCCCCCTTAATAAAATAATT
1 CTCCCCCTTAATAAAATAATT
*
223208 CTCCCCCTTGATAAAATAATT
1 CTCCCCCTTAATAAAATAATT
223229 AAAGCTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (21 bp):
CTCCCCCTTAATAAAATAATT
Found at i:229722 original size:3 final size:3
Alignment explanation
Indices: 229708--229745 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
229698 CATGTCAACT
* *
229708 TCA TCA TTA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
229746 TTCACCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:229746 original size:9 final size:9
Alignment explanation
Indices: 229720--229749 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
229710 ATCATTATCA
*
229720 TCATCATCA
1 TCATCATCT
229729 TCATCATCT
1 TCATCATCT
229738 TCATCATCT
1 TCATCATCT
229747 TCA
1 TCA
229750 CCATTTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (9 bp):
TCATCATCT
Found at i:231437 original size:19 final size:19
Alignment explanation
Indices: 231394--231449 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
231384 CTGCTAGTTT
*
231394 CATGTATCAATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
231414 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
*
231433 CATGTATGGATACAATG
1 CATGTATCGATACAATG
231450 TATCGATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:233225 original size:16 final size:18
Alignment explanation
Indices: 233182--233239 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 18
233172 TTTTGATAAT
*
233182 TTGTTT-TGAATAATCTTG
1 TTGTTTGTGATTAAT-TTG
*
233200 TATTTTTGTGATT-A-TTG
1 T-TGTTTGTGATTAATTTG
*
233217 TTGTTTGTGCTTAATTTG
1 TTGTTTGTGATTAATTTG
233235 TTGTT
1 TTGTT
233240 AATTTGATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 9 0.28
19 5 0.16
20 4 0.12
ACGTcount: A:0.16, C:0.03, G:0.19, T:0.62
Consensus pattern (18 bp):
TTGTTTGTGATTAATTTG
Found at i:234924 original size:21 final size:21
Alignment explanation
Indices: 234894--234945 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
234884 TTATCAGTGC
* *
234894 ATAGATCAACGCTTCGACACA
1 ATAGAGCAACGCTTAGACACA
*
234915 ATAGAGCAACGCTTAGATACA
1 ATAGAGCAACGCTTAGACACA
234936 AT-GAGTCAAC
1 ATAGAG-CAAC
234946 AACTAGAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (21 bp):
ATAGAGCAACGCTTAGACACA
Found at i:235325 original size:22 final size:24
Alignment explanation
Indices: 235300--235352 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
235290 TGTTTTTATA
235300 AAAAGGGAGATTATTTT-G-AAAC-
1 AAAAGGGAGATT-TTTTCGAAAACG
* *
235322 AAAAAGAAGATTTTTTCGAAAACG
1 AAAAGGGAGATTTTTTCGAAAACG
235346 AAAAGGG
1 AAAAGGG
235353 GGAAATTTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 4 0.17
22 11 0.46
23 4 0.17
24 5 0.21
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (24 bp):
AAAAGGGAGATTTTTTCGAAAACG
Found at i:235325 original size:23 final size:24
Alignment explanation
Indices: 235299--235352 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
235289 TTGTTTTTAT
235299 AAAAAGGGAGATTATTTT-G-AAAC
1 AAAAAGGGAGATT-TTTTCGAAAAC
*
235322 AAAAA-GAAGATTTTTTCGAAAAC
1 AAAAAGGGAGATTTTTTCGAAAAC
*
235345 GAAAAGGG
1 AAAAAGGG
235353 GGAAATTTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 13 0.52
24 1 0.04
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (24 bp):
AAAAAGGGAGATTTTTTCGAAAAC
Found at i:237395 original size:10 final size:10
Alignment explanation
Indices: 237376--237406 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
237366 GTATCGATAC
237376 ATGAACAGTG
1 ATGAACAGTG
*
237386 ATGAATAGTG
1 ATGAACAGTG
237396 ATGAACAGTG
1 ATGAACAGTG
237406 A
1 A
237407 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:237619 original size:21 final size:21
Alignment explanation
Indices: 237593--237633 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
237583 GTCAACCTTG
237593 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
237614 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
237634 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:240228 original size:20 final size:20
Alignment explanation
Indices: 240203--240243 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
240193 AAAAGGAAGA
240203 GATATTTTTGAAATAAATTT
1 GATATTTTTGAAATAAATTT
240223 GATATTTTTGAAATAAATTT
1 GATATTTTTGAAATAAATTT
240243 G
1 G
240244 TTTTGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (20 bp):
GATATTTTTGAAATAAATTT
Found at i:241034 original size:19 final size:20
Alignment explanation
Indices: 240991--241028 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
240981 ACACCCAGAT
*
240991 GTATCGATACATATTTCTTA
1 GTATCGATACATAGTTCTTA
241011 GTATCGATACAT-GTTCTT
1 GTATCGATACATAGTTCTT
241029 GATATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (20 bp):
GTATCGATACATAGTTCTTA
Found at i:241959 original size:16 final size:18
Alignment explanation
Indices: 241926--241962 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
241916 TAAGAAATGA
241926 GAAAAGAAGACTAAAAAGT
1 GAAAAGAAGACT-AAAAGT
241945 GAAAAGAAGA-T-AAAGT
1 GAAAAGAAGACTAAAAGT
241961 GA
1 GA
241963 TGAATTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.62, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAGACTAAAAGT
Found at i:248715 original size:42 final size:42
Alignment explanation
Indices: 248660--248778 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
248650 TTTTTCTCTC
* * *
248660 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
*
248702 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
* *
248744 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
248779 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
Found at i:248719 original size:12 final size:11
Alignment explanation
Indices: 248693--248768 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
248683 TCTATTATCT
*
248693 CTCCTGTCTCTC
1 CTCCTATCTC-C
248705 CTCCTATCATCC
1 CTCCTATC-TCC
248717 CTCCTATCT--
1 CTCCTATCTCC
*
248726 CTACTATCT--
1 CTCCTATCTCC
248735 CTCCTATCTCTC
1 CTCCTATCTC-C
248747 CTCCTATCATCC
1 CTCCTATC-TCC
*
248759 CTCCTCTCTC
1 CTCCTATCTC
248769 TTCTTTCTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
9 16 0.29
11 3 0.05
12 32 0.58
13 4 0.07
ACGTcount: A:0.11, C:0.49, G:0.01, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:248746 original size:9 final size:9
Alignment explanation
Indices: 248688--248748 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
248678 CTCTCTCTAT
248688 TATCTCTCC
1 TATCTCTCC
*
248697 TGTCTCTCC
1 TATCTCTCC
* *
248706 T-CCTAT-C
1 TATCTCTCC
*
248713 -ATCCCTCC
1 TATCTCTCC
*
248721 TATCTCTAC
1 TATCTCTCC
248730 TATCTCTCC
1 TATCTCTCC
248739 TATCTCTCC
1 TATCTCTCC
248748 T
1 T
248749 CCTATCATCC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.11, C:0.44, G:0.02, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:252366 original size:179 final size:179
Alignment explanation
Indices: 252066--252426 Score: 695
Period size: 179 Copynumber: 2.0 Consensus size: 179
252056 ATTGCCCAAG
*
252066 GTGTATGACATAAAAGAAGAGCTTGCTAGGGTAAAGCCATAAAGTAATATGTATTAATTATGTTT
1 GTGTATGACATAAAAGAAGAGCTTGCTAGGGTAAAGACATAAAGTAATATGTATTAATTATGTTT
252131 TTGCATGTGTGTCTATATGCGAGCGTGTGTGTGTGTGTGTGTGCATGTATATATACATACATAAT
66 TTGCATGTGTGTCTATATGCGAGCGTGTGTGTGTGTGTGTGTGCATGTATATATACATACATAAT
252196 AAGCTTAAGACATAAATTTGACAATAAACTCTAAAGAATGGTTTAGTTT
131 AAGCTTAAGACATAAATTTGACAATAAACTCTAAAGAATGGTTTAGTTT
252245 GTGTATGACATAAAAGAAGAGCTTGCTAGGGTAAAGACATAAAGTAATATGTATTAATTATGTTT
1 GTGTATGACATAAAAGAAGAGCTTGCTAGGGTAAAGACATAAAGTAATATGTATTAATTATGTTT
*
252310 TTGCATGTGTGTCTATATGCGAGCGTGTGTGTGTGTGTGTGTGCATGTATATATACATATATAAT
66 TTGCATGTGTGTCTATATGCGAGCGTGTGTGTGTGTGTGTGTGCATGTATATATACATACATAAT
*
252375 AAGCTTAAGACATAAATTTGACAATAAACTCTAACGAATGGTTTAGTTT
131 AAGCTTAAGACATAAATTTGACAATAAACTCTAAAGAATGGTTTAGTTT
252424 GTG
1 GTG
252427 CAACAAAATA
Statistics
Matches: 179, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 179 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (179 bp):
GTGTATGACATAAAAGAAGAGCTTGCTAGGGTAAAGACATAAAGTAATATGTATTAATTATGTTT
TTGCATGTGTGTCTATATGCGAGCGTGTGTGTGTGTGTGTGTGCATGTATATATACATACATAAT
AAGCTTAAGACATAAATTTGACAATAAACTCTAAAGAATGGTTTAGTTT
Found at i:255606 original size:49 final size:47
Alignment explanation
Indices: 255551--255678 Score: 125
Period size: 50 Copynumber: 2.6 Consensus size: 47
255541 AAATTTCGCA
255551 TAACCTTAAAGACTCAGTTTGGGTTGGTTTCGACGAAAAGTACTAAAAC
1 TAACCTTAAAGACTC-GTTTGGGTTGGTTTCGACGAAAAGTAC-AAAAC
* * * *
255600 TAACCTTAGAA-AGCTCGATTGTGGTTGGTTTTGATGGAAAGTACAAAAC
1 TAACCTTA-AAGA-CTCGTTTG-GGTTGGTTTCGACGAAAAGTACAAAAC
* *
255649 -AACCCTAAAGAACTCGATTTTGGTTGGTTT
1 TAACCTTAAAG-ACTCG-TTTGGGTTGGTTT
255679 TGATAGAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
47 2 0.03
48 19 0.29
49 21 0.32
50 24 0.36
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (47 bp):
TAACCTTAAAGACTCGTTTGGGTTGGTTTCGACGAAAAGTACAAAAC
Found at i:255677 original size:48 final size:48
Alignment explanation
Indices: 255572--255708 Score: 150
Period size: 48 Copynumber: 2.8 Consensus size: 48
255562 ACTCAGTTTG
* * * * *
255572 GGTTGGTTTCGACGAAAAGTACTAAAACTAACCTTAGAAAGCTCGATTGT
1 GGTTGGTTTTGATGGAAAGTAC-AAAACTAACCCTA-AAAACTCGATTGT
*
255622 GGTTGGTTTTGATGGAAAGTACAAAAC-AACCCTAAAGAACTCGATTTT
1 GGTTGGTTTTGATGGAAAGTACAAAACTAACCCTAAA-AACTCGATTGT
* * * *
255670 GGTTGGTTTTGATAGAAAGCACAAAGCTAATCCTAAAAA
1 GGTTGGTTTTGATGGAAAGTACAAAACTAACCCTAAAAA
255709 ACTCTAAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.03
48 41 0.55
49 13 0.17
50 19 0.25
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (48 bp):
GGTTGGTTTTGATGGAAAGTACAAAACTAACCCTAAAAACTCGATTGT
Found at i:255832 original size:49 final size:49
Alignment explanation
Indices: 255770--255871 Score: 154
Period size: 49 Copynumber: 2.1 Consensus size: 49
255760 TTAAATGACC
* *
255770 CTAAAATGAATGAAATTACAAAATGATC-CTTATATCATAAAAAATAACT
1 CTAAAATGAATGAAATTACAAAATAATCTC-TAAATCATAAAAAATAACT
*
255819 CTAAAATGCATGAAATTACAAAATAATCTCTAAATCATAAAAAATAACT
1 CTAAAATGAATGAAATTACAAAATAATCTCTAAATCATAAAAAATAACT
255868 -TAAA
1 CTAAA
255872 TGACCCTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
48 4 0.08
49 44 0.90
50 1 0.02
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (49 bp):
CTAAAATGAATGAAATTACAAAATAATCTCTAAATCATAAAAAATAACT
Found at i:255901 original size:107 final size:106
Alignment explanation
Indices: 255704--255928 Score: 265
Period size: 107 Copynumber: 2.1 Consensus size: 106
255694 AGCTAATCCT
* ** * * * * * *
255704 AAAA-AACTCTAAAATATATGAAATTGTATAATAATCCCTAAATTATGATAAATGATTTAAATGA
1 AAAATAACTCTAAAATACATGAAATTACAAAATAATCCCTAAATCATAAAAAATAACTTAAATGA
* *
255768 CCCTAAAATGAATGAAATTACAAAATGATCCTTATATCATAA
66 CCCTAAAATGAATGAAATTACAAAATG-TCCCTAAATCATAA
* *
255810 AAAATAACTCTAAAATGCATGAAATTACAAAATAATCTCTAAATCATAAAAAATAACTTAAATGA
1 AAAATAACTCTAAAATACATGAAATTACAAAATAATCCCTAAATCATAAAAAATAACTTAAATGA
* * * *
255875 CCCTAAAATGCATGAAATTCCCAAATGTCCCTAAATCATAG
66 CCCTAAAATGAATGAAATTACAAAATGTCCCTAAATCATAA
*
255916 AAAATGACT-TAAA
1 AAAATAACTCTAAA
255929 TGACCTTATG
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
105 4 0.04
106 23 0.23
107 73 0.73
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (106 bp):
AAAATAACTCTAAAATACATGAAATTACAAAATAATCCCTAAATCATAAAAAATAACTTAAATGA
CCCTAAAATGAATGAAATTACAAAATGTCCCTAAATCATAA
Found at i:255926 original size:57 final size:58
Alignment explanation
Indices: 255819--255933 Score: 169
Period size: 57 Copynumber: 2.0 Consensus size: 58
255809 AAAAATAACT
*
255819 CTAAAATGCATGAAATTACAAAATAATCTCTAAATCATAAAAAATAACTTAAATGACC
1 CTAAAATGCATGAAATTACAAAATAATCCCTAAATCATAAAAAATAACTTAAATGACC
* * * * *
255877 CTAAAATGCATGAAATTCCCAAAT-GTCCCTAAATCATAGAAAATGACTTAAATGACC
1 CTAAAATGCATGAAATTACAAAATAATCCCTAAATCATAAAAAATAACTTAAATGACC
255934 TTATGTTAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 29 0.57
58 22 0.43
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.25
Consensus pattern (58 bp):
CTAAAATGCATGAAATTACAAAATAATCCCTAAATCATAAAAAATAACTTAAATGACC
Found at i:256331 original size:12 final size:13
Alignment explanation
Indices: 256302--256337 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
256292 AACTTACTCA
256302 GTATCGATACAAT
1 GTATCGATACAAT
*
256315 GTATCGAT-CATT
1 GTATCGATACAAT
256327 GTATCGATACA
1 GTATCGATACA
256338 TGGTGAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:257325 original size:13 final size:13
Alignment explanation
Indices: 257307--257332 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
257297 CAATTTTTGG
257307 TGTATCGATACAT
1 TGTATCGATACAT
257320 TGTATCGATACAT
1 TGTATCGATACAT
257333 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:257344 original size:32 final size:33
Alignment explanation
Indices: 257287--257350 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
257277 TACAAGCCAA
**
257287 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
257320 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
257351 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:257357 original size:19 final size:18
Alignment explanation
Indices: 257287--257357 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
257277 TACAAGCCAA
257287 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
257307 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
257320 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
257339 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
257358 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:260050 original size:13 final size:13
Alignment explanation
Indices: 260032--260090 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
260022 ATAATCACCC
260032 TGTATCGATACAA
1 TGTATCGATACAA
260045 TGTATCGATACAA
1 TGTATCGATACAA
*
260058 ---A--G-TAAAA
1 TGTATCGATACAA
260065 TGTATCGATACAA
1 TGTATCGATACAA
260078 TGTATCGATACAA
1 TGTATCGATACAA
260091 AGTAAAATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 4 0.11
8 1 0.03
10 2 0.05
12 1 0.03
13 30 0.79
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:260068 original size:20 final size:20
Alignment explanation
Indices: 260043--260109 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
260033 GTATCGATAC
260043 AATGTATCGATACAAAGTAA
1 AATGTATCGATACAAAGTAA
260063 AATGTATCGATAC-------
1 AATGTATCGATACAAAGTAA
260076 AATGTATCGATACAAAGTAA
1 AATGTATCGATACAAAGTAA
260096 AATGTATCGATACA
1 AATGTATCGATACA
260110 TTGAATTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.32
20 27 0.68
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGTAA
Found at i:260074 original size:33 final size:33
Alignment explanation
Indices: 260032--260109 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
260022 ATAATCACCC
260032 TGTATCGATACAATGTATCGATACAAAGTAAAA
1 TGTATCGATACAATGTATCGATACAAAGTAAAA
260065 TGTATCGATACAATGTATCGATACAAAGTAAAA
1 TGTATCGATACAATGTATCGATACAAAGTAAAA
260098 TGTATCGATACA
1 TGTATCGATACA
260110 TTGAATTTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAATGTATCGATACAAAGTAAAA
Found at i:263661 original size:13 final size:13
Alignment explanation
Indices: 263643--263668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263633 TACAGCAAGT
263643 ATGTATCGATACA
1 ATGTATCGATACA
263656 ATGTATCGATACA
1 ATGTATCGATACA
263669 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:266274 original size:15 final size:15
Alignment explanation
Indices: 266254--266284 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
266244 TAAAAATATC
*
266254 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
266269 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
266284 C
1 C
266285 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:268381 original size:13 final size:13
Alignment explanation
Indices: 268363--268401 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
268353 ACATTTTTCT
268363 TTGTATCGATACA
1 TTGTATCGATACA
268376 TTGTATCGATACA
1 TTGTATCGATACA
*
268389 CTGTATCGATACA
1 TTGTATCGATACA
268402 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:270966 original size:13 final size:13
Alignment explanation
Indices: 270948--270973 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
270938 TACAGCAAGT
270948 ATGTATCGATACA
1 ATGTATCGATACA
270961 ATGTATCGATACA
1 ATGTATCGATACA
270974 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:272481 original size:21 final size:21
Alignment explanation
Indices: 272452--272496 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
272442 AAGTTTTTAT
*
272452 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
272472 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
272494 TTT
1 TTT
272497 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:274737 original size:13 final size:13
Alignment explanation
Indices: 274719--274744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
274709 CAATTTTTGG
274719 TGTATCGATACAT
1 TGTATCGATACAT
274732 TGTATCGATACAT
1 TGTATCGATACAT
274745 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:274756 original size:32 final size:33
Alignment explanation
Indices: 274699--274762 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
274689 TACAAGCCAA
**
274699 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
274732 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
274763 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:274769 original size:19 final size:18
Alignment explanation
Indices: 274699--274769 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
274689 TACAAGCCAA
274699 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
274719 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
274732 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
274751 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
274770 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:276527 original size:3 final size:3
Alignment explanation
Indices: 276519--276564 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
276509 TCAACCATCA
*
276519 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATA ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
276565 AGTTGACTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:280959 original size:26 final size:27
Alignment explanation
Indices: 280922--280987 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 27
280912 ATTTCTCAAA
280922 ATGTATCGATACATTTGGAAAACC-AG
1 ATGTATCGATACATTTGGAAAACCTAG
*
280948 ATGTATCAATACATTTGGAAAACCTAG
1 ATGTATCGATACATTTGGAAAACCTAG
280975 ATGTATCGATACA
1 ATGTATCGATACA
280988 ATGATCTTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
26 23 0.62
27 14 0.38
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (27 bp):
ATGTATCGATACATTTGGAAAACCTAG
Found at i:282052 original size:13 final size:13
Alignment explanation
Indices: 282031--282060 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
282021 CGATACATGG
*
282031 TACATTGTATCGA
1 TACAATGTATCGA
282044 TACAATGTATCGA
1 TACAATGTATCGA
282057 TACA
1 TACA
282061 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:282058 original size:33 final size:33
Alignment explanation
Indices: 282016--282078 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
282006 TACCACTATT
*
282016 TGTATCGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTGTATCGATACAA
282049 TGTATCGATACATGATGAATTGTATCGATA
1 TGTATCGATACATGATGAATTGTATCGATA
282079 AATTGCTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:288237 original size:13 final size:13
Alignment explanation
Indices: 288219--288245 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
288209 ACAATATTCC
288219 TTGTATCGATACA
1 TTGTATCGATACA
288232 TTGTATCGATACA
1 TTGTATCGATACA
288245 T
1 T
288246 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:288409 original size:20 final size:21
Alignment explanation
Indices: 288373--288412 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
288363 TTACAAATTT
*
288373 CTTCATTTTTACTTCAAAATA
1 CTTCATTTTTACATCAAAATA
288394 CTTCATTTTT-CATCAAAAT
1 CTTCATTTTTACATCAAAAT
288413 CACCAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (21 bp):
CTTCATTTTTACATCAAAATA
Found at i:290828 original size:13 final size:13
Alignment explanation
Indices: 290807--290836 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
290797 CGATACATGG
*
290807 TACATTGTATCGA
1 TACAATGTATCGA
290820 TACAATGTATCGA
1 TACAATGTATCGA
290833 TACA
1 TACA
290837 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:290847 original size:33 final size:33
Alignment explanation
Indices: 290792--290854 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
290782 TACCACTGTT
*
290792 TGTATCGATACATGGTACATTGTATCGATACAA
1 TGTATCGATACATGATACATTGTATCGATACAA
*
290825 TGTATCGATACATGATGA-ATTGTATTGATA
1 TGTATCGATACATGAT-ACATTGTATCGATA
290855 AATTGCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTATCGATACATGATACATTGTATCGATACAA
Found at i:295327 original size:12 final size:11
Alignment explanation
Indices: 295307--295344 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 11
295297 CATTTCATTT
295307 TTTTTCTTTTC
1 TTTTTCTTTTC
295318 TTTTTGCTTTTC
1 TTTTT-CTTTTC
295330 TTTTTCTTTT-
1 TTTTTCTTTTC
295340 TTTTT
1 TTTTT
295345 TTGGTTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.19
11 10 0.38
12 11 0.42
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:295345 original size:12 final size:12
Alignment explanation
Indices: 295304--295346 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
295294 TCCCATTTCA
295304 TTTTTTTTCTTT
1 TTTTTTTTCTTT
* *
295316 TCTTTTTGC-TT
1 TTTTTTTTCTTT
*
295327 TTCTTTTTCTTT
1 TTTTTTTTCTTT
295339 TTTTTTTT
1 TTTTTTTT
295347 GGTTTTTGCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:295353 original size:12 final size:12
Alignment explanation
Indices: 295304--295345 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
295294 TCCCATTTCA
295304 TTTTTTTT-CTT
1 TTTTTTTTGCTT
*
295315 TTCTTTTTGCTT
1 TTTTTTTTGCTT
*
295327 TTCTTTTT-CTT
1 TTTTTTTTGCTT
295338 TTTTTTTT
1 TTTTTTTT
295346 TGGTTTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (12 bp):
TTTTTTTTGCTT
Found at i:298830 original size:67 final size:65
Alignment explanation
Indices: 298687--298830 Score: 153
Period size: 67 Copynumber: 2.2 Consensus size: 65
298677 TGATTTTTGT
* * * * *** * *
298687 TATTCAGAAAGATATAGGTTTTTTTTTTTGGCTTGTTCAGAAGGATACAAGTTTGGCTCTTAACC
1 TATTCAGAAAGACATAGGTTTTTTTTTTTGACTTATTCAAAAGGATACAAGTTCAACCCTTAACA
* * *
298752 TATTTAGAAAGACATAGGTTTGATTTTTTTTGACTTATTCAAAAGGATATAAGTTCAACCCTTTA
1 TATTCAGAAAGACATAGGTTT--TTTTTTTTGACTTATTCAAAAGGATACAAGTTCAACCCTTAA
298817 CA
64 CA
*
298819 TATTCAAAAAGA
1 TATTCAGAAAGA
298831 TACAAGTTTG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
65 19 0.30
67 44 0.70
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (65 bp):
TATTCAGAAAGACATAGGTTTTTTTTTTTGACTTATTCAAAAGGATACAAGTTCAACCCTTAACA
Found at i:299604 original size:30 final size:31
Alignment explanation
Indices: 299570--299628 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
299560 CCTTACAACA
*
299570 CTATCTTTTGA-AGGCTAAGACAGAACCTCC
1 CTATCTTTTCACAGGCTAAGACAGAACCTCC
*
299600 CTATCTTTTCACAGGCTAAGATAGAACCT
1 CTATCTTTTCACAGGCTAAGACAGAACCT
299629 TTTCTCTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (31 bp):
CTATCTTTTCACAGGCTAAGACAGAACCTCC
Found at i:300191 original size:21 final size:22
Alignment explanation
Indices: 300148--300191 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
300138 AATTTGAATA
300148 TGTATCGATACAATCATAGGGT
1 TGTATCGATACAATCATAGGGT
*
300170 TGTATCGATATAATCA-AGGGT
1 TGTATCGATACAATCATAGGGT
300191 T
1 T
300192 AGGTACTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (22 bp):
TGTATCGATACAATCATAGGGT
Found at i:300954 original size:12 final size:12
Alignment explanation
Indices: 300937--300961 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
300927 GCAATATTAT
300937 ACAATTTCTCCA
1 ACAATTTCTCCA
300949 ACAATTTCTCCA
1 ACAATTTCTCCA
300961 A
1 A
300962 TTTCTCCTTT
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:0.32, G:0.00, T:0.32
Consensus pattern (12 bp):
ACAATTTCTCCA
Found at i:302715 original size:21 final size:20
Alignment explanation
Indices: 302691--302746 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
302681 GATAGGGAAA
*
302691 TGAAGGAATTTGATGAGTAAT
1 TGAAGGAATTTGATGAAT-AT
*
302712 TGAAGAAATTTGATGAATAT
1 TGAAGGAATTTGATGAATAT
* *
302732 TGGATGAATTTGATG
1 TGAAGGAATTTGATG
302747 TTTTGAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.36
Consensus pattern (20 bp):
TGAAGGAATTTGATGAATAT
Found at i:303656 original size:21 final size:20
Alignment explanation
Indices: 303607--303662 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
303597 GTTGGGCCAA
303607 ATATATCGATACAATTCTTC
1 ATATATCGATACAATTCTTC
* *
303627 ATGTATCGATACAATT-TTAAT
1 ATATATCGATACAATTCTT--C
303648 ATATATCGATACAAT
1 ATATATCGATACAAT
303663 CATAGGGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.06
20 15 0.48
21 14 0.45
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATATCGATACAATTCTTC
Found at i:303692 original size:21 final size:22
Alignment explanation
Indices: 303651--303692 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
303641 TTTTAATATA
* *
303651 TATCGATACAATCATAGGGTTG
1 TATCGATAAAATCAGAGGGTTG
303673 TATCGATAAAATC-GAGGGTT
1 TATCGATAAAATCAGAGGGTT
303693 AGCTACTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (22 bp):
TATCGATAAAATCAGAGGGTTG
Found at i:312126 original size:52 final size:52
Alignment explanation
Indices: 312056--312176 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
312046 GAAAATTTAT
* *
312056 CTGCATGTATTGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
312108 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
312160 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
312177 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:312189 original size:52 final size:52
Alignment explanation
Indices: 312056--312196 Score: 187
Period size: 52 Copynumber: 2.7 Consensus size: 52
312046 GAAAATTTAT
* *
312056 CTGCATGTATTGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *** *
312108 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
312160 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
312197 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 4 0.05
52 74 0.95
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:312203 original size:13 final size:13
Alignment explanation
Indices: 312185--312209 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312175 CAAAGATCAG
312185 TGTATCGATACAA
1 TGTATCGATACAA
312198 TGTATCGATACA
1 TGTATCGATACA
312210 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:312292 original size:13 final size:13
Alignment explanation
Indices: 312274--312298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312264 CAAAAAAATA
312274 TGTATCGATACAT
1 TGTATCGATACAT
312287 TGTATCGATACA
1 TGTATCGATACA
312299 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:312294 original size:33 final size:33
Alignment explanation
Indices: 312252--312318 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
312242 AGTAGCTTAA
312252 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
312285 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
312318 A
1 A
312319 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:313514 original size:15 final size:15
Alignment explanation
Indices: 313494--313528 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
313484 ATATAGTAAT
*
313494 AAAAAACAAAAAATA
1 AAAAAACAAAAAAGA
*
313509 AAAAAATAAAAAAGA
1 AAAAAACAAAAAAGA
313524 AAAAA
1 AAAAA
313529 TCATGAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.89, C:0.03, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAAACAAAAAAGA
Found at i:314278 original size:93 final size:93
Alignment explanation
Indices: 314164--314334 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
314154 CTAGGAAGAA
** *
314164 AAAAAGAAAGCACGAGCAGCTCGTAGCAACAAAGAATGAAGAAGAAAG-AAGCATGTGCAACGTG
1 AAAAAGAAAGCACGAGCAGCTCACAACAACAAAGAATGAAGAA-AAAGAAAGCATGTGCAACGTG
314228 AAAAGGAGTAGCCAACAGTAGCTAGAAAG
65 AAAAGGAGTAGCCAACAGTAGCTAGAAAG
* * *
314257 AAAAAGAAAGCAC-AGGGAGCTCACAACAATAAGGAATGAAGAAAAAGAAAGCATGTGCAACGTG
1 AAAAAGAAAGCACGA-GCAGCTCACAACAACAAAGAATGAAGAAAAAGAAAGCATGTGCAACGTG
314321 AAAAGGAGTAGCCA
65 AAAAGGAGTAGCCA
314335 GCAGCAGCAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
92 5 0.07
93 65 0.93
ACGTcount: A:0.50, C:0.15, G:0.26, T:0.09
Consensus pattern (93 bp):
AAAAAGAAAGCACGAGCAGCTCACAACAACAAAGAATGAAGAAAAAGAAAGCATGTGCAACGTGA
AAAGGAGTAGCCAACAGTAGCTAGAAAG
Found at i:314978 original size:23 final size:22
Alignment explanation
Indices: 314946--314991 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
314936 AGAATAAAGC
314946 AAAAACAGC-AGTTGATACGAACA
1 AAAAACAGCAAG--GATACGAACA
*
314969 AAAAATAGCAAGGATACGAACA
1 AAAAACAGCAAGGATACGAACA
314991 A
1 A
314992 GAAGAGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 8 0.38
24 2 0.10
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (22 bp):
AAAAACAGCAAGGATACGAACA
Found at i:315086 original size:35 final size:35
Alignment explanation
Indices: 315035--315186 Score: 182
Period size: 35 Copynumber: 4.3 Consensus size: 35
315025 GTGTTGGCAA
*
315035 CAAAACAAGAGGCAGCAATGGCATCGAAACAGCAG
1 CAAAACAAGAGGCAGCAACGGCATCGAAACAGCAG
** * *
315070 CAAAACAAGAAACAGCAATGGCATCGAAACAACAG
1 CAAAACAAGAGGCAGCAACGGCATCGAAACAGCAG
*
315105 CAAAACAAGAGGCAGCAACGGCATCGAAATAGCAAG
1 CAAAACAAGAGGCAGCAACGGCATCGAAACAGC-AG
* * *
315141 -AAAATAAGAGGCAGCAACGACATCGAAGCAGCAAG
1 CAAAACAAGAGGCAGCAACGGCATCGAAACAGC-AG
*
315176 -AAAATAAGAGG
1 CAAAACAAGAGG
315187 AAGAATGAGC
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 102 0.98
36 2 0.02
ACGTcount: A:0.50, C:0.20, G:0.24, T:0.06
Consensus pattern (35 bp):
CAAAACAAGAGGCAGCAACGGCATCGAAACAGCAG
Found at i:315244 original size:34 final size:33
Alignment explanation
Indices: 315197--315275 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 33
315187 AAGAATGAGC
* *
315197 AGCAAAA-AGCAGCTGAAGATGATAGCAAAGCA
1 AGCAAAACAGCAGCTGAAGACGACAGCAAAGCA
*
315229 AGCAAGAACAGCAGCTGAAGACGGCAGCAAAGCA
1 AGCAA-AACAGCAGCTGAAGACGACAGCAAAGCA
315263 AGCAATAACAGCA
1 AGCAA-AACAGCA
315276 ACAAAGCAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 5 0.12
33 2 0.05
34 34 0.83
ACGTcount: A:0.48, C:0.20, G:0.25, T:0.06
Consensus pattern (33 bp):
AGCAAAACAGCAGCTGAAGACGACAGCAAAGCA
Found at i:320710 original size:22 final size:22
Alignment explanation
Indices: 320684--320743 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
320674 CAAAATTATG
*
320684 AAAAATTCAAAAGCAAAAGAACA
1 AAAAATTCAAAAGCAAAACAA-A
* *
320707 AAAAA-TGAAAAGAAAAACAAA
1 AAAAATTCAAAAGCAAAACAAA
*
320728 AAAAAGTGCAAAAGCA
1 AAAAA-TTCAAAAGCA
320744 GCATAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 6 0.21
22 12 0.41
23 11 0.38
ACGTcount: A:0.72, C:0.10, G:0.12, T:0.07
Consensus pattern (22 bp):
AAAAATTCAAAAGCAAAACAAA
Found at i:323236 original size:71 final size:70
Alignment explanation
Indices: 323109--323453 Score: 283
Period size: 73 Copynumber: 4.8 Consensus size: 70
323099 CAGATAGGTA
* * *
323109 CCACCAACTTGTGTGGACTTTAAGAA-AGAAAAGAAGTCCTACTCTTTGAGGACTAAAATGATAA
1 CCACCAACTTGTGTGGGCTTTAA-AAGA-AAAAG-TGTCCTACTCTTTAAGGACTAAAA-GATAA
323173 AAAAGTATG
62 AAAAGTATG
* * * *
323182 CCACCAAATTGTGTGGGCTTTAAAAGAAAAAGTGTCTTGCTCTTTAAAGACTAAAAGGATAAAAA
1 CCACCAACTTGTGTGGGCTTTAAAAGAAAAAGTGTCCTACTCTTTAAGGACTAAAA-GATAAAAA
* *
323247 CGTGTG
65 AGTATG
* * * * * *
323253 CTACCAACTTATATGGGATTTAAAAAGAAAAAAGTGTCCTGCTCTTTAAGGACAAAAAGAATAAA
1 CCACCAACTTGTGTGGGCTTT-AAAAG-AAAAAGTGTCCTACTCTTTAAGGACTAAAAG-ATAAA
*
323318 AAAGTGTG
63 AAAGTATG
* * * *
323326 CCACTAACTTGTGTGGGCTTTAGAA-AAAAAG-GCATCATACTCTTTGAGGACTAATAAGAT--A
1 CCACCAACTTGTGTGGGCTTTAAAAGAAAAAGTG--TCCTACTCTTTAAGGACTAA-AAGATAAA
323387 AAAG-ATG
63 AAAGTATG
* ** * *
323394 CCACTAGTTTGTGTGGGCTTTAAAAAGAAAAAG-GCATCCTACTCTTTGAGGA-TAGAAGAT
1 CCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGTG--TCCTACTCTTTAAGGACTAAAAGAT
323454 GCCACCAGCT
Statistics
Matches: 228, Mismatches: 35, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
68 26 0.11
69 11 0.05
70 30 0.13
71 65 0.29
72 19 0.08
73 77 0.34
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (70 bp):
CCACCAACTTGTGTGGGCTTTAAAAGAAAAAGTGTCCTACTCTTTAAGGACTAAAAGATAAAAAA
GTATG
Found at i:323378 original size:144 final size:144
Alignment explanation
Indices: 323127--323389 Score: 331
Period size: 144 Copynumber: 1.8 Consensus size: 144
323117 TTGTGTGGAC
* *
323127 TTTAAGAAAGAAAAGAAGTCCTACTCTTTGAGGACTAAAATGATAAAAAAGTATGCCACCAAATT
1 TTTAAGAAAGAAAAGAAGTCCTACTCTTTAAGGACTAAAAAGATAAAAAAGTATGCCACCAAATT
* *
323192 GTGTGGGCTTTAAAAGAAAAAGTGTCTTGCTCTTTAAAGACTAA-AAGGATAAAAACGTGTGCTA
66 GTGTGGGCTTTAAAAGAAAAAGTGTCATACTCTTTAAAGACTAATAA-GATAAAAACGTGTGCTA
323256 CCAACTTATATGGGA
130 CCAACTTATATGGGA
* * *
323271 TTTAA-AAAGAAAA-AAGTGTCCTGCTCTTTAAGGAC-AAAAAGAATAAAAAAGTGTGCCACTAA
1 TTTAAGAAAGAAAAGAA--GTCCTACTCTTTAAGGACTAAAAAG-ATAAAAAAGTATGCCACCAA
* * * *
323333 CTTGTGTGGGCTTTAGAA-AAAAAG-GCATCATACTCTTTGAGGACTAATAAGATAAAA
63 ATTGTGTGGGCTTTAAAAGAAAAAGTG--TCATACTCTTTAAAGACTAATAAGATAAAA
323390 GATGCCACTA
Statistics
Matches: 102, Mismatches: 11, Indels: 12
0.82 0.09 0.10
Matches are distributed among these distances:
142 3 0.03
143 19 0.19
144 78 0.76
145 2 0.02
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (144 bp):
TTTAAGAAAGAAAAGAAGTCCTACTCTTTAAGGACTAAAAAGATAAAAAAGTATGCCACCAAATT
GTGTGGGCTTTAAAAGAAAAAGTGTCATACTCTTTAAAGACTAATAAGATAAAAACGTGTGCTAC
CAACTTATATGGGA
Found at i:323443 original size:70 final size:71
Alignment explanation
Indices: 323109--323577 Score: 341
Period size: 71 Copynumber: 6.7 Consensus size: 71
323099 CAGATAGGTA
* *
323109 CCACCAACTTGTGTGGACTTTAAGAAAG-AAAA-GAAGTCCTACTCTTTGAGGACTAAAATGATA
1 CCACCAACTTGTGTGGGCTTTAA-AAAGAAAAAGGCA-TCCTACTCTTTGAGGACTAAAA-GAT-
323172 AAAAAGTATG
62 AAAAAGTATG
* * * * *
323182 CCACCAAATTGTGTGGGCTTT-AAAAGAAAAAGTG--TCTTGCTCTTTAAAGACTAAAAGGATAA
1 CCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG-GCATCCTACTCTTTGAGGACTAAAA-GATAA
*
323244 AAACGTGTG
64 AAA-GTATG
* * * * * ** * * *
323253 CTACCAACTTATATGGGATTTAAAAAGAAAAAAGTGTCCTGCTCTTTAAGGACAAAAAGAATAAA
1 CCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAG-AT-AA
*
323318 AAAGTGTG
64 AAAGTATG
* * *
323326 CCACTAACTTGTGTGGGCTTT-AGAA-AAAAAGGCATCATACTCTTTGAGGACTAATAAGAT-AA
1 CCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAA-AAGATAAA
323388 AAG-ATG
65 AAGTATG
* **
323394 CCACTAGTTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGA-T---AG-----A
1 CCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGATAAAA
323450 AG-ATG
66 AGTATG
* * * * * * * *
323455 CCACCAGCTTATGTGGGCTTTAAAAAGAAAAAGGCATCTTGCTTTTTAAGGACTAACAGGAT-AG
1 CCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAA-AAGATAAA
323519 AAG-ATG
65 AAGTATG
** * * *
323525 CCACCAGTTTGTGTGGGATTTAAAAAAGGAAATGGCATCCTACTCTTTGAGGA
1 CCACCAACTTGTGTGGGCTTT-AAAAAGAAAAAGGCATCCTACTCTTTGAGGA
323578 TGAAAAGGTG
Statistics
Matches: 322, Mismatches: 52, Indels: 46
0.77 0.12 0.11
Matches are distributed among these distances:
61 51 0.16
62 1 0.00
65 2 0.01
66 1 0.00
68 21 0.07
69 9 0.03
70 53 0.16
71 95 0.30
72 22 0.07
73 61 0.19
74 6 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (71 bp):
CCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGATAAAA
AGTATG
Found at i:323454 original size:61 final size:61
Alignment explanation
Indices: 323383--323613 Score: 219
Period size: 61 Copynumber: 3.6 Consensus size: 61
323373 GGACTAATAA
* * *
323383 GATAAAAGATGCCACTAGTTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAG
1 GATAAAAGATGCCACCAGCTTATGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAG
* * * *
323444 GATAGAAGATGCCACCAGCTTATGTGGGCTTTAAAAAGAAAAAGGCATCTTGCTTTTTAAGGACT
1 GATAAAAGATGCCACCAGCTTATGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTT---G---
323509 AACAG
60 ---AG
* * * * * *
323514 GATAGAAGATGCCACCAGTTTGTGTGGGATTTAAAAAAGGAAATGGCATCCTACTCTTTGAG
1 GATAAAAGATGCCACCAGCTTATGTGGGCTTT-AAAAAGAAAAAGGCATCCTACTCTTTGAG
* * *
323576 GATGAAAAGGTGCCATCAGCTTATATGGGCTTTAAAAA
1 GAT-AAAAGATGCCACCAGCTTATGTGGGCTTTAAAAA
323614 AAAGGGAAAA
Statistics
Matches: 137, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
61 51 0.37
62 10 0.07
63 22 0.16
64 1 0.01
68 1 0.01
70 31 0.23
71 21 0.15
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (61 bp):
GATAAAAGATGCCACCAGCTTATGTGGGCTTTAAAAAGAAAAAGGCATCCTACTCTTTGAG
Found at i:323828 original size:105 final size:106
Alignment explanation
Indices: 323560--323828 Score: 289
Period size: 104 Copynumber: 2.6 Consensus size: 106
323550 AAGGAAATGG
* * * *
323560 CATCCTACTCTTTGAGGATGAAAAGGTGCCA-TCAGCTTATATGGGCTTT--AAA-AAAAAGGGA
1 CATCCTGCTCTTTAAGGAT-AAAAGGTGCCACT-AGCTTATGTGGGCTTTAAAAAGAAAAAAGGA
* * * *
323621 AAAAAAGTGCTACCAACTTGTGTAGGCTTTGAAAAGAAAAAGG
64 AAAAAAGTGCCACCAACTTGTGTAAGCTTGGAAAAGAAAAAGA
* * * * *
323664 CATCCTGCTCTTTAAAGACTAAAATGTACGACTAGCTTAAGTGGGCTTTAAAAAG-AAAAAGG-A
1 CATCCTGCTCTTTAAGGA-TAAAAGGTGCCACTAGCTTATGTGGGCTTTAAAAAGAAAAAAGGAA
** *
323727 AAAGGGTGCCACCAACTTGTGTAAGCTTGGAAAAGAAAAATA
65 AAAAAGTGCCACCAACTTGTGTAAGCTTGGAAAAGAAAAAGA
** * *
323769 TGTCTTGCTCTTTAAGGATAAAAGGTGCCACTAGCTTGTGTGGGCTTTAAAAAGAAAAAA
1 CATCCTGCTCTTTAAGGATAAAAGGTGCCACTAGCTTATGTGGGCTTTAAAAAGAAAAAA
323829 AGCATCTTGC
Statistics
Matches: 134, Mismatches: 25, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
104 68 0.51
105 57 0.43
106 9 0.07
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (106 bp):
CATCCTGCTCTTTAAGGATAAAAGGTGCCACTAGCTTATGTGGGCTTTAAAAAGAAAAAAGGAAA
AAAAGTGCCACCAACTTGTGTAAGCTTGGAAAAGAAAAAGA
Found at i:323841 original size:62 final size:63
Alignment explanation
Indices: 323771--323889 Score: 188
Period size: 62 Copynumber: 1.9 Consensus size: 63
323761 GAAAAATATG
*
323771 TCTTGCTCTTTAAGGA-TAAAAGGTGCCACTAGCTTGTGTGGGC-TTTAAAAAGAAAAAAAGCA
1 TCTTGCTCTTTAAGGATTAAAAGGTGCCACCA-CTTGTGTGGGCTTTTAAAAAGAAAAAAAGCA
* *
323833 TCTTGCTCTTTGAGGATTAAAATGTGCCACCACTTGTGTGGGCTTTTAAAAAGAAAA
1 TCTTGCTCTTTAAGGATTAAAAGGTGCCACCACTTGTGTGGGCTTTTAAAAAGAAAA
323890 GGCGTTCTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
62 26 0.50
63 26 0.50
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (63 bp):
TCTTGCTCTTTAAGGATTAAAAGGTGCCACCACTTGTGTGGGCTTTTAAAAAGAAAAAAAGCA
Found at i:323881 original size:63 final size:62
Alignment explanation
Indices: 323722--323889 Score: 191
Period size: 61 Copynumber: 2.7 Consensus size: 62
323712 TAAAAAGAAA
* * ** ** *
323722 AAGGA-AAAGGGTGCCACCAACTTGTGTAAGCTTGGAAAAGAAAAATATG--TCTTGCTCTTT
1 AAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAA-AAGCATCTTGCTCTTT
*
323782 AAGGATAAAAGGTGCCACTAGCTTGTGTGGGCTTTAAAAAGAAAAAAAGCATCTTGCTCTTT
1 AAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAAAGCATCTTGCTCTTT
* *
323844 GAGGATTAAAATGTGCCACCA-CTTGTGTGGGCTTTTAAAAAGAAAA
1 AAGGA-TAAAAGGTGCCACCAGCTTGTGTGGGC-TTTAAAAAGAAAA
323890 GGCGTTCTGC
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
60 7 0.08
61 33 0.36
62 26 0.28
63 26 0.28
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (62 bp):
AAGGATAAAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAAGAAAAAAAGCATCTTGCTCTTT
Found at i:331387 original size:20 final size:21
Alignment explanation
Indices: 331340--331392 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
331330 GCCAATGACC
*
331340 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
331361 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
331381 TGTATCGATACA
1 TGTATCGATACA
331393 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:331398 original size:13 final size:13
Alignment explanation
Indices: 331380--331404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331370 ACATTTGGTC
331380 ATGTATCGATACA
1 ATGTATCGATACA
331393 ATGTATCGATAC
1 ATGTATCGATAC
331405 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:332044 original size:20 final size:20
Alignment explanation
Indices: 332019--332058 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
332009 TAATCATATA
332019 TTTCTTTCTCCCCCTTAAAC
1 TTTCTTTCTCCCCCTTAAAC
*
332039 TTTCTTTCTCCCTCTTAAAC
1 TTTCTTTCTCCCCCTTAAAC
332059 ATAAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTCTTTCTCCCCCTTAAAC
Found at i:333899 original size:13 final size:13
Alignment explanation
Indices: 333881--333916 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
333871 ATAGACCCTT
*
333881 TGTATCGATACAC
1 TGTATCGATACAA
333894 TGTATCGATACAA
1 TGTATCGATACAA
333907 TGTATCGATA
1 TGTATCGATA
333917 TAGAGAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:340106 original size:20 final size:21
Alignment explanation
Indices: 340059--340111 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
340049 GCCAATGACC
*
340059 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
340080 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
340100 TGTATCGATACA
1 TGTATCGATACA
340112 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:340117 original size:13 final size:13
Alignment explanation
Indices: 340099--340123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340089 ACATTTGGTC
340099 ATGTATCGATACA
1 ATGTATCGATACA
340112 ATGTATCGATAC
1 ATGTATCGATAC
340124 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:346925 original size:11 final size:11
Alignment explanation
Indices: 346909--346935 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
346899 AGAAAAGTTT
346909 GAAATTCAAAA
1 GAAATTCAAAA
346920 GAAATTCAAAA
1 GAAATTCAAAA
346931 GAAAT
1 GAAAT
346936 AGGGTTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.19
Consensus pattern (11 bp):
GAAATTCAAAA
Found at i:347384 original size:82 final size:79
Alignment explanation
Indices: 347110--347392 Score: 336
Period size: 80 Copynumber: 3.5 Consensus size: 79
347100 TCCTCGAGAA
* * * * * *
347110 GAAAATTTTAATATTTTAGAAGTCAAAATAGGGTTGGAGTCT-CCATTCAAAAATGATGGGGTTG
1 GAAAAATTCAATATTTTGGAAGTAAAAATAGGGTTGGAGTATCCCCTT-AAAAATGATGGGGTTG
* *
347174 GAGTATCCCAATTGT
65 GAGTATCCCGATAGT
* * *
347189 GAAAAATTCAATATTTTGGAAGTAAAAAT-GGAGTTCGAGTATCTCCTGAAAAATGATGGGGTTG
1 GAAAAATTCAATATTTTGGAAGTAAAAATAGG-GTTGGAGTATCCCCTTAAAAATGATGGGGTTG
347253 GAGTATCCCTGATAGT
65 GAGTATCCC-GATAGT
* * * **
347269 GAAAAATTCAATATTTTGGAAGTAAAAACAGGGTTGGAGTATCCCCTTAAAAATAATAGGGTTAA
1 GAAAAATTCAATATTTTGGAAGTAAAAATAGGGTTGGAGTATCCCCTTAAAAATGATGGGGTTGG
* *
347334 AATATCCTCGATGGT
66 AGTATCC-CGATAGT
347349 GAAAAAAATTCAATATTTTGGAAGTAAAAATAGGGTTGGAGTAT
1 G--AAAAATTCAATATTTTGGAAGTAAAAATAGGGTTGGAGTAT
347393 GTCGTAACGT
Statistics
Matches: 175, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
78 2 0.01
79 58 0.33
80 72 0.41
81 3 0.02
82 40 0.23
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (79 bp):
GAAAAATTCAATATTTTGGAAGTAAAAATAGGGTTGGAGTATCCCCTTAAAAATGATGGGGTTGG
AGTATCCCGATAGT
Found at i:350543 original size:52 final size:52
Alignment explanation
Indices: 350462--350582 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
350452 TGAAGAGTTA
*
350462 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
350514 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
350566 CTGCATATATCGATACA
1 CTGCATGTATCGATACA
350583 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:350595 original size:52 final size:52
Alignment explanation
Indices: 350462--350602 Score: 187
Period size: 52 Copynumber: 2.7 Consensus size: 52
350452 TGAAGAGTTA
* *
350462 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATATATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *** *
350514 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATATATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
350566 CTGCATATATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATATATCGATACATAAGAT-AGTGTATCGATACA
350603 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 4 0.05
52 76 0.95
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATATATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:350609 original size:13 final size:13
Alignment explanation
Indices: 350591--350615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
350581 CAAAGATCAG
350591 TGTATCGATACAA
1 TGTATCGATACAA
350604 TGTATCGATACA
1 TGTATCGATACA
350616 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:350698 original size:13 final size:13
Alignment explanation
Indices: 350680--350704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
350670 CAAAAAAATA
350680 TGTATCGATACAT
1 TGTATCGATACAT
350693 TGTATCGATACA
1 TGTATCGATACA
350705 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:350700 original size:33 final size:33
Alignment explanation
Indices: 350658--350724 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
350648 AGTAGCTTAA
350658 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
350691 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
350724 A
1 A
350725 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:351755 original size:43 final size:45
Alignment explanation
Indices: 351694--351827 Score: 191
Period size: 43 Copynumber: 2.9 Consensus size: 45
351684 GATGGAAAAT
351694 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G-
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATGA
* *
351737 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-ATG-A
*
351785 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
351828 AATGATGATG
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 37 0.46
44 2 0.03
45 1 0.01
46 1 0.01
47 1 0.01
48 3 0.04
49 35 0.44
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATGA
Found at i:351793 original size:49 final size:49
Alignment explanation
Indices: 351651--351837 Score: 233
Period size: 49 Copynumber: 3.9 Consensus size: 49
351641 GATGTCAACG
* *
351651 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
351703 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
351746 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
351795 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATG
351838 AGAAGAGTGA
Statistics
Matches: 119, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
43 36 0.30
44 2 0.02
45 1 0.01
46 1 0.01
48 2 0.02
49 46 0.39
50 1 0.01
51 2 0.02
52 28 0.24
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:351824 original size:92 final size:94
Alignment explanation
Indices: 351650--351827 Score: 306
Period size: 92 Copynumber: 1.9 Consensus size: 94
351640 GGATGTCAAC
351650 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAA-GTGCCAATATGCTGATTCAAG
*
351715 GCCAGCTATATTGGACTTAAAGGTGCCAAT
65 GCCAGCGATATTGGACTTAAAGGTGCCAAT
* *
351745 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA-TGCCAATATGCTGATTCAAGG
1 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTGCCAATATGCTGATTCAAGG
351808 CCAGCGATATTGGACTTAAA
66 CCAGCGATATTGGACTTAAA
351828 AATGATGATG
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
92 40 0.50
94 4 0.05
95 36 0.45
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (94 bp):
GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTGCCAATATGCTGATTCAAGG
CCAGCGATATTGGACTTAAAGGTGCCAAT
Found at i:351949 original size:55 final size:52
Alignment explanation
Indices: 351889--352871 Score: 514
Period size: 49 Copynumber: 20.0 Consensus size: 52
351879 CGATATTGGG
* *
351889 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
351944 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
351996 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
352039 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
352088 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
352131 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * * *
352180 CTTAAAGAT-G--AAGGTGCCAATGTGTTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
352229 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* ** * * * * * *
352278 CTTAAAATGATGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGG
1 CTT-AAA-GATG--GA-AAAGGTG--CCA-A---C---ATGCTGATTCAAGGCCAGCTACATTGA
*
352343 G
52 A
* *
352344 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
352399 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
352451 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
352494 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
352543 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
352586 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
352635 CTTAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
352684 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * *
352727 CTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
352776 CTTAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* *
352825 CTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTG
352872 GGCTTAGAAG
Statistics
Matches: 777, Mismatches: 93, Indels: 122
0.78 0.09 0.12
Matches are distributed among these distances:
43 189 0.24
44 5 0.01
46 2 0.00
48 3 0.00
49 404 0.52
50 3 0.00
51 5 0.01
52 62 0.08
53 10 0.01
54 3 0.00
55 40 0.05
57 4 0.01
58 1 0.00
59 1 0.00
60 1 0.00
61 1 0.00
62 1 0.00
63 5 0.01
64 7 0.01
65 3 0.00
66 27 0.03
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
Found at i:351987 original size:266 final size:266
Alignment explanation
Indices: 351513--352093 Score: 1108
Period size: 266 Copynumber: 2.2 Consensus size: 266
351503 TTTTAGAGAT
* * *
351513 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAA
351578 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
351643 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
351708 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
196 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
351773 CTTAAA
261 CTTAAA
* *
351779 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAGA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAA
*
351844 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
351909 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
351974 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
196 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
352039 CTTAAA
261 CTTAAA
352045 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
352094 GGTGCCAATG
Statistics
Matches: 309, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 309 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (266 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
CTTAAA
Found at i:352090 original size:92 final size:92
Alignment explanation
Indices: 351916--352877 Score: 804
Period size: 92 Copynumber: 10.3 Consensus size: 92
351906 GGATGTCAAC
* * *
351916 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATATGCTGATTCAAG
*
351981 GCCAGCTATATTGGACTTAAAGGTGCCAAT
63 GCCAGCGATATTGGACTTAAAGGTGCCAAT
*
352011 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
352076 AGCGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
352103 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
352168 AGCGATATTGGACTTAAAGATGAAGGTGCCAAT
66 AGCGATATTGGACTT----A--AAGGTGCCAAT
*
352201 GTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
**
352266 AGCGATATTGGACTTAAAATGATGATGAGAA-
66 AGCGATATTGGACTT-AAA-G--G-TGCCAAT
** * * ** * * *** * * *
352297 AAG-TGA-TAAAGATGCCA-ATATGTT-GA-TTCATGGCCAACGAT----AT-TG-GGCTT-AAA
1 GTGCTGAGTCAAG--GCCAGCTACATTGGACTTAAAGATGAA-GATGCCAATATGCTGATTCAAG
* * ** * * **
352350 G--ATGAGAAAAAGGA-TGTCAACGTGCTGAT
63 GCCA-GCGATATTGGACT-TAAAGGTGCCAAT
* * * * * *
352379 -T-C-AAGGCCA-GCTACA-TTGA-ACTTAAAGA-TGGAAA-AT---G-TGCCAATATGCTGATT
1 GTGCTGAGTCAAGGC--CAGCT-ACA-TT--GGACT-TAAAGATGAAGATGCCAATATGCTGATT
*
352432 CAAGGCCAGCTATATTGGACTTAAAGGTGCCAAT
59 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
*
352466 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
352531 AGCGATATTGGACTTAAAGGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
352558 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
352623 AGCGATATTGGACTTAAAGATGAAGGTGCCAAT
66 AGCGATATTGGACTT----A--AAGGTGCCAAT
* *
352656 GTGCTGAGTCAAGGCCAGCTACATTGGACTT-AA-A-G--G-TGCCAATGTGCTGAGTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
352715 AGCTACATTGGACTTAAAGATAAAGGTGCCAAT
66 AGCGATATTGGAC-T-----TAAAGGTGCCAAT
* * * * * *
352748 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
* *
352813 AGCTACATTGGACTTAAAGATAAAGGTGCCAAT
66 AGCGATATTGGAC-T-----TAAAGGTGCCAAT
* * * *
352846 ATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTA
352878 GAAGGGTTGC
Statistics
Matches: 729, Mismatches: 72, Indels: 129
0.78 0.08 0.14
Matches are distributed among these distances:
78 2 0.00
79 1 0.00
80 5 0.01
81 7 0.01
82 1 0.00
83 2 0.00
84 5 0.01
85 8 0.01
86 11 0.02
87 23 0.03
88 9 0.01
89 8 0.01
90 7 0.01
91 3 0.00
92 327 0.45
93 12 0.02
94 16 0.02
95 46 0.06
96 9 0.01
97 7 0.01
98 220 0.30
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (92 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGGTGCCAAT
Found at i:352198 original size:141 final size:138
Alignment explanation
Indices: 351955--352877 Score: 626
Period size: 141 Copynumber: 6.7 Consensus size: 138
351945 TTAAAGATGG
* * * *
351955 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AAA-GGTGCCAATGTGCTGA
1 AAAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAATGGTGCCAATATGCTGA
* *
352018 TTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATA
66 TTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
352083 TTGGACTT
131 TTGGACTT
*
352091 -AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATG
1 AAAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAA-ATG--G-TGCCAATATG
* * * *
352155 CTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGTTGAGTCAAGGCCAGC
62 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGC
* *
352220 TACATTGGACTT
127 GATATTGGACTT
* * * **
352232 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAA
1 AAA-A-G--G-TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAATG--G-TGCCAA
* * * * * **** * * *
352297 -AAG-TGA-TAAAGATGCCA-ATATGTT-GA-TT---CATG--GCCAACGATATTG-GGCTT-AA
58 TATGCTGATTCAAG--GCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA-TGCTGATTCAA
* * * **
352349 AG--ATGAGAAAAAGGA-TGT
120 GGCCA-GCGATATTGGACT-T
* * ** * * * * * *
352367 -CAACGTGCTGAT-T-C-AAGGCCA-GCTACA-TTGA-ACTTAAAGA-TGGAAAAT-GTGCCAAT
1 AAAAGGTGCCAATATGCTGAGTCAAGGC--CAGCT-ACA-TT--GGACT-TAAAATGGTGCCAAT
*
352423 ATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCC
59 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
* *
352482 AGCTACATTGGACTT
124 AGCGATATTGGACTT
* * * *
352497 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAA-GGTGCCAATGT
1 AAA-A-G--G-TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAATGGTGCCAATAT
* * *
352560 GCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAG
61 GCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAG
352625 CGATATTGGACTT
126 CGATATTGGACTT
* *
352638 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAA-GGTGCCAATGT
1 --A-A--AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAATGGTGCCAATAT
* * *
352701 GCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAG
61 GCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAG
*
352766 CTATATTGGACTT
126 CGATATTGGACTT
*
352779 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCA
1 --A-A--AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAA-AT---GGTGCCA
*
352844 ATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
57 ATATGCTGATTCAAGGCCAGCTATATTGGACTTA
352878 GAAGGGTTGC
Statistics
Matches: 616, Mismatches: 103, Indels: 125
0.73 0.12 0.15
Matches are distributed among these distances:
125 6 0.01
126 11 0.02
127 16 0.03
128 16 0.03
129 17 0.03
130 8 0.01
131 3 0.00
132 1 0.00
133 1 0.00
134 3 0.00
135 86 0.14
136 12 0.02
137 9 0.01
138 9 0.01
139 8 0.01
140 3 0.00
141 288 0.47
142 7 0.01
143 9 0.01
144 10 0.02
145 7 0.01
146 12 0.02
147 74 0.12
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (138 bp):
AAAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAATGGTGCCAATATGCTGA
TTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
TTGGACTT
Found at i:352371 original size:455 final size:455
Alignment explanation
Indices: 351650--352882 Score: 1957
Period size: 455 Copynumber: 2.8 Consensus size: 455
351640 GGATGTCAAC
* * *
351650 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATATGCTGATTCAAG
* *
351715 GCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
63 GCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
351774 TTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGA
128 TTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAATGATGATGA
*
351839 GAAGAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAA
192 GAAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAA
351904 AAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
257 AAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
351969 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
322 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACA
352034 TTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
387 TTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGC
352099 CAAT
452 CAAT
352103 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
*
352168 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTA
66 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
352233 AAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAA
131 AAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAA
352298 AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
196 AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
352363 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCT
261 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCT
352428 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
326 GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
352493 ACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
391 ACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
352558 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
352623 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-
66 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
* * * *
352687 AA-A-G--G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT--AA--A-GAT----AA
131 AAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAA
* * * * *
352738 A--G-----G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG
196 AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
* * * * *
352790 -TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATATGCT
261 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCT
*
352851 GATTCAAGGCCAGCTATATTGGGCTTAGAAGG
326 GATTCAAGGCCAGCTATATTGGACTTA-AAGG
352883 GTTGCCACCG
Statistics
Matches: 750, Mismatches: 23, Indels: 43
0.92 0.03 0.05
Matches are distributed among these distances:
423 42 0.06
424 4 0.01
426 40 0.05
427 4 0.01
430 1 0.00
432 39 0.05
433 1 0.00
438 1 0.00
440 3 0.00
444 3 0.00
445 1 0.00
447 2 0.00
449 34 0.05
450 38 0.05
452 5 0.01
453 36 0.05
454 3 0.00
455 404 0.54
456 89 0.12
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (455 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
AAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAA
AGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
ACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAAT
Found at i:352514 original size:49 final size:49
Alignment explanation
Indices: 352362--352877 Score: 636
Period size: 49 Copynumber: 10.8 Consensus size: 49
352352 TGAGAAAAAG
* * *
352362 GATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAA
* * *
352412 AATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--
1 GA--TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
352458 G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
* * *
352506 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
*
352550 G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
* * *
352598 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
* *
352647 GGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AA-A-G--
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
* *
352691 G-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
* * *
352739 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
* * *
352788 GGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
* * * *
352837 GGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
352878 GAAGGGTTGC
Statistics
Matches: 408, Mismatches: 38, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
43 108 0.26
44 8 0.02
45 3 0.01
46 4 0.01
47 2 0.00
48 8 0.02
49 238 0.58
50 2 0.00
51 2 0.00
52 33 0.08
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
Found at i:352921 original size:33 final size:33
Alignment explanation
Indices: 352877--352949 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
352867 TATTGGGCTT
352877 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
352910 AGAAGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
352943 A-AAGGGT
1 AGAAGGGT
352950 GAAAGATGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 5 0.13
33 33 0.87
ACGTcount: A:0.21, C:0.16, G:0.36, T:0.27
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:353061 original size:34 final size:34
Alignment explanation
Indices: 352951--353865 Score: 1011
Period size: 33 Copynumber: 27.1 Consensus size: 34
352941 AGAAAGGGTG
* * * *
352951 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
352984 CAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAA-GG-AA
353020 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
353054 AAAGAGTGCCACGAAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
353088 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
353122 AAAGAGTACCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
353155 AAAGTGTGCCACAGAGTTGTGGGCTTTA-AAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
* *
353189 AAAGAATGCCACAGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
353222 AAAGAGTGCCACGTAATTGTGGGCTTTA-AAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
353255 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
353288 AAAGAGTGCCACGTAATTGTGGGCTTTA-AAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
*
353321 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
353354 AAAGTGTGCCACAGAGTTGTGGGCTTTA-AAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
*
353388 AAAGAATGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
353421 AAAGAGTGCCACGTAATTGTGGGCTTTA-AAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
353454 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
353487 AAAGAGTGCCACGTAATTGTGGGCTTTA-AAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
*
353520 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AGAA-GGAA
* * * *
353557 AAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
353591 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
353624 AAAGAGTGCCACGTAATTGTGGGCTTTA-AAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
* *
353657 AAAGAGTGTCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AGAA-GGAA
* * * *
353694 AAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
* * ** *
353729 AAAGTGTGCCACAGAGTTGTGGGCTTTTAA-AAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
353762 AAAG-GTGCCACGGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
*
353793 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AGAA-GGAA
* * *
353829 AAAGAGTGCCACAGAGTTGTGGGCTTTGAAGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
353863 AAA
1 AAA
353866 TGTCACTGAG
Statistics
Matches: 777, Mismatches: 72, Indels: 65
0.85 0.08 0.07
Matches are distributed among these distances:
31 25 0.03
32 34 0.04
33 353 0.45
34 211 0.27
35 36 0.05
36 29 0.04
37 89 0.11
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
Found at i:353292 original size:66 final size:65
Alignment explanation
Indices: 352951--354067 Score: 1105
Period size: 66 Copynumber: 16.8 Consensus size: 65
352941 AGAAAGGGTG
* * * *
352951 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAACAA-AGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGAGTGCCACG-AGTTGTGGGCTTTAAAGGAA-AAGAGTGCCACGGAGTTGTGGGC-TTAGAA
353014 GGGAAA
63 -GG--A
*
353020 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAGAA
1 AAAGAGTGCCAC-GAGTTGTGGGCTTTA-AAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
353084 GGAA
63 GG-A
*
353088 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTACCACGGAGTTGTGGGCTTAGAA
1 AAAGAGTGCCAC-GAGTTGTGGGCTTTA-AAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
353152 GGA
63 GGA
* * * *
353155 AAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAATGCCACAGAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCAC-GAGTTGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
353220 GA
64 GA
*
353222 AAAGAGTGCCACGTAATTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
1 AAAGAGTGCCACG-AGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
353287 A
65 A
* *
353288 AAAGAGTGCCACGTAATTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAGG
1 AAAGAGTGCCACG-AGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
353353 A
65 A
* * *
353354 AAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAATGCCACGGAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCAC-GAGTTGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
353419 GA
64 GA
*
353421 AAAGAGTGCCACGTAATTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
1 AAAGAGTGCCACG-AGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
353486 A
65 A
* *
353487 AAAGAGTGCCACGTAATTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
1 AAAGAGTGCCACG-AGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGC-TT-AGAA
353552 GGGAA
63 -GG-A
* *
353557 AAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCAC-GAGTTGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
353622 GA
64 GA
* * *
353624 AAAGAGTGCCACGTAATTGTGGGCTTTAAAGGAAAAGAGTGTCACGGAGTTGTGGGCTTTGAAAA
1 AAAGAGTGCCACG-AGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGC-TT-AGAA
353689 GGGAA
63 -GG-A
* * * * **
353694 AAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTTAA
1 AAAGAGTGCCAC-GAGTTGTGGGCTTT--AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
**
353759 AAA
63 GGA
*
353762 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAA--AAAAG-GTGCCACGGAGTTGTGGGCTTTGAAA
1 AAAGAGTGCCAC-GAGTTGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGTTGTGGGC-TT-AGA
353823 AGGGAA
62 A-GG-A
* * * * * * *
353829 AAAGAGTGCCACAGAGTTGTGGGCTTTGAA-GAAAA-AATGTCACTGAGTCGTGGACTTTG-A-G
1 AAAGAGTGCCAC-GAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
353890 A
65 A
** * * * * * *
353891 CAAA-A-TGCCACTGAGTCATGGACTTTGAAGGAAAAGA-TGCCACTGAGTCGTGGACTTTG-A-
1 -AAAGAGTGCCAC-GAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
353951 GA
64 GA
* * * * *
353953 CAAA-A-TGCCACTGAGTTGTGGACTTTAAAGGAAAAGA-TGCCACTGAGTCGTGGACTTTG-A-
1 -AAAGAGTGCCAC-GAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAG
354013 GA
64 GA
* * * * *
354015 CAAA-A-TGCCACTGAGTCGTGGACTTTAAAGAAAAAGA-TGCCACTGAGTCGTGG
1 -AAAGAGTGCCAC-GAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGG
354068 ACTTTGAGCA
Statistics
Matches: 939, Mismatches: 74, Indels: 77
0.86 0.07 0.07
Matches are distributed among these distances:
61 20 0.02
62 141 0.15
63 23 0.02
64 7 0.01
65 3 0.00
66 252 0.27
67 195 0.21
68 123 0.13
69 17 0.02
70 77 0.08
71 55 0.06
72 26 0.03
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (65 bp):
AAAGAGTGCCACGAGTTGTGGGCTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGA
Found at i:353903 original size:30 final size:30
Alignment explanation
Indices: 353835--354103 Score: 319
Period size: 30 Copynumber: 8.7 Consensus size: 30
353825 GGAAAAAGAG
* * * *
353835 TGCCACAGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTG-AGACAAAA
*
353866 TGTCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
*
353896 TGCCACTGAGTCATGGACTTTGAAGGA-AAAGA
1 TGCCACTGAGTCGTGGACTTTG-A-GACAAA-A
353928 TGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
353958 TGCCACTGAGTTGTGGACTTTAAAGGA-AAAGA
1 TGCCACTGAGTCGTGGACTTT-GA-GACAAA-A
353990 TGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
354020 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTT-GAGACAAA-A
*
354052 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
354083 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
354104 TTTTTTTTTT
Statistics
Matches: 209, Mismatches: 17, Indels: 24
0.84 0.07 0.10
Matches are distributed among these distances:
30 75 0.36
31 64 0.31
32 70 0.33
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:353939 original size:62 final size:62
Alignment explanation
Indices: 353835--354103 Score: 407
Period size: 62 Copynumber: 4.3 Consensus size: 62
353825 GGAAAAAGAG
* * * * * *
353835 TGCCACAGAGTTGTGGGCTTTGAA-GAAAAAATGTCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
353896 TGCCACTGAGTCATGGACTTTGAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
*
353958 TGCCACTGAGTTGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
354020 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
354083 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
354104 TTTTTTTTTT
Statistics
Matches: 193, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
61 22 0.11
62 149 0.77
63 22 0.11
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (62 bp):
TGCCACTGAGTCGTGGACTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:355159 original size:15 final size:15
Alignment explanation
Indices: 355139--355172 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
355129 CTCACCGAGA
*
355139 TTTTCTGTTTTGTTT
1 TTTTCTGTTTTCTTT
*
355154 TTTTCTTTTTTCTTT
1 TTTTCTGTTTTCTTT
355169 TTTT
1 TTTT
355173 TGTGTTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTCTGTTTTCTTT
Found at i:362440 original size:52 final size:52
Alignment explanation
Indices: 362359--362479 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
362349 TGAAGAGTTA
*
362359 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
362411 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
362463 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
362480 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:362492 original size:52 final size:51
Alignment explanation
Indices: 362359--362499 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
362349 TGAAGAGTTA
362359 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
362411 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
362463 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
362500 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:362506 original size:13 final size:13
Alignment explanation
Indices: 362488--362512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362478 CAAAGATCAG
362488 TGTATCGATACAA
1 TGTATCGATACAA
362501 TGTATCGATACA
1 TGTATCGATACA
362513 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:362595 original size:13 final size:13
Alignment explanation
Indices: 362577--362601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
362567 CAAAAAAATA
362577 TGTATCGATACAT
1 TGTATCGATACAT
362590 TGTATCGATACA
1 TGTATCGATACA
362602 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:362597 original size:33 final size:33
Alignment explanation
Indices: 362555--362621 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
362545 AGTAGCTTAA
362555 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
362588 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
362621 A
1 A
362622 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:367718 original size:14 final size:14
Alignment explanation
Indices: 367676--367718 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
367666 AGTAAAAGTC
*
367676 AAAAGTTAACAAGTA
1 AAAAGTTAACTA-TA
* *
367691 AAAAGTCAATTATA
1 AAAAGTTAACTATA
367705 AAAAGTTAACTATA
1 AAAAGTTAACTATA
367719 TTGGCTAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (14 bp):
AAAAGTTAACTATA
Found at i:369352 original size:13 final size:13
Alignment explanation
Indices: 369334--369364 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
369324 ACATTTCTTC
369334 ATGTATCGATACA
1 ATGTATCGATACA
369347 ATGTATCGATACA
1 ATGTATCGATACA
*
369360 TTGTA
1 ATGTA
369365 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:369352 original size:33 final size:33
Alignment explanation
Indices: 369314--369380 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
369304 GTTACAAGCT
369314 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
369347 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
369380 A
1 A
369381 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:369435 original size:21 final size:19
Alignment explanation
Indices: 369409--369482 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
369399 CTGCCAGTTT
**
369409 CATGTATCGATACAATTTGGC
1 CATGTATCGATACAA--TGAA
*
369430 CATGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
*
369449 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAATG-AA
369469 CATGTATCGATACA
1 CATGTATCGATACA
369483 TCTGTGTGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 17 0.36
20 16 0.34
21 14 0.30
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:369454 original size:19 final size:20
Alignment explanation
Indices: 369430--369482 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
369420 ACAATTTGGC
* *
369430 CATGTATCGATATAATG-AA
1 CATGTATCGATACAAAGCAA
369449 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAAAGCAA
369469 CATGTATCGATACA
1 CATGTATCGATACA
369483 TCTGTGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (20 bp):
CATGTATCGATACAAAGCAA
Found at i:370056 original size:36 final size:36
Alignment explanation
Indices: 370007--370081 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
369997 TCGTCGTTTT
* *
370007 TCTCCCCTCAAAAATATTCTCCCCCTTAAATGATTA
1 TCTCCCCTAAAAAAAATTCTCCCCCTTAAATGATTA
*
370043 TCTCCTCTAAAAAAAATTCTCCCCCTTAAATGATTA
1 TCTCCCCTAAAAAAAATTCTCCCCCTTAAATGATTA
370079 TCT
1 TCT
370082 TCTTCCCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.35
Consensus pattern (36 bp):
TCTCCCCTAAAAAAAATTCTCCCCCTTAAATGATTA
Found at i:377711 original size:28 final size:28
Alignment explanation
Indices: 377671--377726 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
377661 CAACCTATTA
377671 ATCTCTTTGAGAACTATACCCCAAGTTC
1 ATCTCTTTGAGAACTATACCCCAAGTTC
377699 ATCTCTTTGAGAACTATACCCCAAGTTC
1 ATCTCTTTGAGAACTATACCCCAAGTTC
377727 CTAAGAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.32
Consensus pattern (28 bp):
ATCTCTTTGAGAACTATACCCCAAGTTC
Found at i:378271 original size:21 final size:20
Alignment explanation
Indices: 378245--378300 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
378235 CTGCCAGTTT
**
378245 CATGTATCGATACAATTTGGC
1 CATGTATCGATACAA-TTGAA
*
378266 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
378285 CATGTATCGATACAAT
1 CATGTATCGATACAAT
378301 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.53
21 14 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:378304 original size:13 final size:13
Alignment explanation
Indices: 378286--378312 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
378276 TATAATGAAC
378286 ATGTATCGATACA
1 ATGTATCGATACA
378299 ATGTATCGATACA
1 ATGTATCGATACA
378312 A
1 A
378313 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:378330 original size:33 final size:32
Alignment explanation
Indices: 378267--378331 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
378257 CAATTTGGCC
* *
378267 ATGTATCGATATAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
* *
378299 ATGTATCGATACAAAGCAGCATGTATTGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
378332 TCTGTGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:381949 original size:76 final size:75
Alignment explanation
Indices: 381807--381951 Score: 186
Period size: 76 Copynumber: 1.9 Consensus size: 75
381797 AAGTATCTAT
* * * * *
381807 CTAAGGTCATATGGAACGTCCATGTCAAAACATGTCCATTAGAGGTATTTCGGTTATAGTATCTT
1 CTAAGGTCATATGGAACCTCCATATCAAAACATGTCCATTAGAGGTATTTAGGTTATAATAACTT
381872 AAAATCGAGG
66 AAAATCGAGG
* *
381882 CTAAGGTCATATGGGAACCTTCATATTAAAACATGTCCATTA-AGGGTATTTAGG-TAGTAATAA
1 CTAAGGTCATAT-GGAACCTCCATATCAAAACATGTCCATTAGA-GGTATTTAGGTTA-TAATAA
381945 CTTAAAA
63 CTTAAAA
381952 CTGAATCTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
75 15 0.25
76 45 0.75
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (75 bp):
CTAAGGTCATATGGAACCTCCATATCAAAACATGTCCATTAGAGGTATTTAGGTTATAATAACTT
AAAATCGAGG
Done.