Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 125 of 167
Found at i:41857016 original size:57 final size:57
Alignment explanation
Indices: 41856946--41857059 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
41856936 GACTAAGCAA
*
41856946 GGAAATGACAAAGACAACGGGAGTTAGCTCGGAAATTACAGTTTGTATTTCTATAAT
1 GGAAATGAAAAAGACAACGGGAGTTAGCTCGGAAATTACAGTTTGTATTTCTATAAT
41857003 GGAAATGAAAAAGACAACGGGAGTTAGCTCGGAAATTACAGTTTGTATTTCTATAAT
1 GGAAATGAAAAAGACAACGGGAGTTAGCTCGGAAATTACAGTTTGTATTTCTATAAT
41857060 CCGAACTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (57 bp):
GGAAATGAAAAAGACAACGGGAGTTAGCTCGGAAATTACAGTTTGTATTTCTATAAT
Found at i:41857380 original size:20 final size:23
Alignment explanation
Indices: 41857331--41857385 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
41857321 AAGTGAATGA
*
41857331 AATTATATTGAATTGAAAATATAT
1 AATTA-ATTGAATTGAAAATATAG
41857355 AATTAATT-AATT-AAAATAT-G
1 AATTAATTGAATTGAAAATATAG
41857375 AATTAATTGAA
1 AATTAATTGAA
41857386 AACTGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
22 4 0.14
23 3 0.10
24 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (23 bp):
AATTAATTGAATTGAAAATATAG
Found at i:41857530 original size:12 final size:12
Alignment explanation
Indices: 41857513--41857537 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41857503 GCCGACTACT
41857513 GTTACTGTTACC
1 GTTACTGTTACC
41857525 GTTACTGTTACC
1 GTTACTGTTACC
41857537 G
1 G
41857538 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:41857640 original size:6 final size:6
Alignment explanation
Indices: 41857625--41857655 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
41857615 CTGTGTACCG
*
41857625 TACTGC TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
41857656 CTGACTTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:41857793 original size:19 final size:19
Alignment explanation
Indices: 41857771--41857822 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
41857761 AAAGATCGAC
41857771 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* * *
41857790 TGTTACTGCAT-ATCTGAT
1 TGTTACTGAATAATTTAAT
*
41857808 TTTTACTGAATAATT
1 TGTTACTGAATAATT
41857823 GACTATTACT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:41857917 original size:18 final size:18
Alignment explanation
Indices: 41857848--41857962 Score: 81
Period size: 18 Copynumber: 6.3 Consensus size: 18
41857838 ACCGATCAAT
*
41857848 TGATTGATACTGAATAAC
1 TGATTGTTACTGAATAAC
* * *
41857866 TGATTATTATTGAATAAT
1 TGATTGTTACTGAATAAC
**
41857884 TGATTGTTACCAAATAAC
1 TGATTGTTACTGAATAAC
* * *
41857902 TAACTGTTACTGAATAAA
1 TGATTGTTACTGAATAAC
* *
41857920 TAATTGTT-CT-AATTGAC
1 TGATTGTTACTGAA-TAAC
*
41857937 TGATTGTTAATGAATATTAC
1 TGATTGTTACTGAATA--AC
41857957 TGATTG
1 TGATTG
41857963 ATTAATTGCT
Statistics
Matches: 72, Mismatches: 20, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
16 2 0.03
17 11 0.15
18 49 0.68
19 2 0.03
20 8 0.11
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.41
Consensus pattern (18 bp):
TGATTGTTACTGAATAAC
Found at i:41864946 original size:13 final size:13
Alignment explanation
Indices: 41864928--41864952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41864918 TATTTGAGAA
41864928 AATAGTAAAATTC
1 AATAGTAAAATTC
41864941 AATAGTAAAATT
1 AATAGTAAAATT
41864953 GTGAAATGGT
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:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AATAGTAAAATTC
Found at i:41867595 original size:19 final size:20
Alignment explanation
Indices: 41867559--41867601 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
41867549 TATCTCTATC
41867559 TTTTTCAATTTTAATTATT-
1 TTTTTCAATTTTAATTATTA
*
41867578 TTTTTC-ATTTTATTTTATTA
1 TTTTTCAATTTTA-ATTATTA
41867598 TTTT
1 TTTT
41867602 ACAAGTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCAATTTTAATTATTA
Found at i:41871584 original size:28 final size:28
Alignment explanation
Indices: 41871552--41871609 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
41871542 CCAATAAGAG
41871552 TTAGAGTGATCATGATCAATCGGGTAAC
1 TTAGAGTGATCATGATCAATCGGGTAAC
41871580 TTAGAGTGATCATGATCAATCGGGTAAC
1 TTAGAGTGATCATGATCAATCGGGTAAC
41871608 TT
1 TT
41871610 CTTTTCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (28 bp):
TTAGAGTGATCATGATCAATCGGGTAAC
Found at i:41872585 original size:48 final size:49
Alignment explanation
Indices: 41872532--41872630 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
41872522 GAAGGAGAAG
* * *
41872532 TAAGGCAGTGCGTGGG-AAAGGGTCATTAAGGTGGAGAATAGGGATCAA
1 TAAGGCAGTGAGCGGGAAAAGAGTCATTAAGGTGGAGAATAGGGATCAA
*
41872580 TAAGGCAGTGAGCGGGAAAAGAGTCATTAAGGTGGATAATAGGGATCAA
1 TAAGGCAGTGAGCGGGAAAAGAGTCATTAAGGTGGAGAATAGGGATCAA
41872629 TA
1 TA
41872631 CGATGTGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 14 0.30
49 32 0.70
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.19
Consensus pattern (49 bp):
TAAGGCAGTGAGCGGGAAAAGAGTCATTAAGGTGGAGAATAGGGATCAA
Found at i:41875170 original size:40 final size:40
Alignment explanation
Indices: 41875139--41875350 Score: 243
Period size: 40 Copynumber: 5.3 Consensus size: 40
41875129 GGACTAAGAT
41875139 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
41875179 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
* *
41875219 CCGAAGGCCTTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
* * ** * *
41875259 CCGAAGGCATTCGTGCGAGTTGTTAAA-TCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCC
* * * * * *
41875299 CCGAAGGCA-TTGTGTGAGTTACTAAA-ACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
41875338 CCGAAGGCATTTG
1 CCGAAGGCATTTG
41875351 AACGAGGAGC
Statistics
Matches: 154, Mismatches: 14, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
39 32 0.21
40 119 0.77
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
Found at i:41875223 original size:80 final size:80
Alignment explanation
Indices: 41875086--41875350 Score: 272
Period size: 80 Copynumber: 3.3 Consensus size: 80
41875076 TTGAATGCTG
* * ** **
41875086 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGA-ATATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TGACA-A-ATCCGGGTTAAGCCCCGAAGGCA
41875148 TTTGTGCGAGATAC-AAA
63 TTTGTGCGAGATACTAAA
* *
41875165 TTCCGGGTTAAGCCCCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCT
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGGCAT
41875229 TTGTGCGAGATACTAAA
64 TTGTGCGAGATACTAAA
* * ** * *
41875246 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCA-TT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTT
* *
41875310 GTGTGAGTTACTAAA
66 GTGCGAGATACTAAA
* * *
41875325 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
41875351 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
79 38 0.24
80 102 0.65
81 16 0.10
82 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:41875368 original size:79 final size:80
Alignment explanation
Indices: 41875139--41875383 Score: 205
Period size: 80 Copynumber: 3.1 Consensus size: 80
41875129 GGACTAAGAT
* * * * ** *
41875139 CCGAAGG-CATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCATTTGTGCGA-GATA
1 CCGAAGGCCA-TTGTGCGAGATACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-G
*
41875201 C-AAATTCCGGGTTAAGCC
63 CTAAA-TCCGGGTTAAGTC
* * * ** ** *
41875219 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
41875284 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * * *
41875299 CCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
41875363 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
41875377 CCGAAGG
1 CCGAAGG
41875384 TACGTGATTT
Statistics
Matches: 137, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
78 14 0.10
79 49 0.36
80 67 0.49
81 7 0.05
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:41879430 original size:27 final size:27
Alignment explanation
Indices: 41879381--41879435 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
41879371 TCCTGATTGG
*
41879381 TTTATTGTTTTTTATTTGACTTATTTA
1 TTTATTGTTTGTTATTTGACTTATTTA
*
41879408 TTTATT-TTTGTTATTTGTTCTTATTTA
1 TTTATTGTTTGTTATTTG-ACTTATTTA
41879435 T
1 T
41879436 GGTTGATCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.16, C:0.04, G:0.07, T:0.73
Consensus pattern (27 bp):
TTTATTGTTTGTTATTTGACTTATTTA
Found at i:41880055 original size:11 final size:11
Alignment explanation
Indices: 41880039--41880073 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
41880029 TTTTTGATTA
41880039 TTCTTTTTCTT
1 TTCTTTTTCTT
41880050 TTCTTTCTTC-T
1 TTCTTT-TTCTT
41880061 TTCTTTTTCTT
1 TTCTTTTTCTT
41880072 TT
1 TT
41880074 TGGCAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.14
11 16 0.73
12 3 0.14
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:41898728 original size:46 final size:46
Alignment explanation
Indices: 41898636--41898756 Score: 179
Period size: 46 Copynumber: 2.6 Consensus size: 46
41898626 TACATTTCAC
* * *
41898636 GAACTCGGACTCAACACTCAACGAGCTCGAGCGTTCACATCAATAAGT
1 GAACTCGGACTC-A-ACTCAACGAGTTCGAACATTCACATCAATAAGT
* *
41898684 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGAACATTCACATCAATAAGT
41898730 GAACTCGGACTCAACTCAACGAGTTCG
1 GAACTCGGACTCAACTCAACGAGTTCG
41898757 GATGCTCAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
46 55 0.81
47 1 0.01
48 12 0.18
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGAACATTCACATCAATAAGT
Found at i:41898777 original size:46 final size:45
Alignment explanation
Indices: 41898581--41898769 Score: 136
Period size: 46 Copynumber: 4.1 Consensus size: 45
41898571 CGTAACCCGC
*
41898581 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG-GATGC-CTAGTTA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGACATGCGC-A---A
* * * * * * *
41898628 -CATTTCA-CGAACTCGGACTCAACACTCAACGAGCTCGAGCGTTCACAT
1 CCA--TAAGTGAACTCGGACTC-A-ACTCAACGAGTTCGA-CATGCGCAA
* * *
41898676 CAATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG-ACATGCGCAA
* *
41898722 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG-GATGCTCAA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGACATGCGCAA
41898766 CCAT
1 CCAT
41898770 CCTAGTGACA
Statistics
Matches: 114, Mismatches: 18, Indels: 23
0.74 0.12 0.15
Matches are distributed among these distances:
44 9 0.08
46 56 0.49
47 16 0.14
48 15 0.13
49 14 0.12
51 3 0.03
52 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGACATGCGCAA
Found at i:41899218 original size:30 final size:30
Alignment explanation
Indices: 41899184--41899243 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41899174 ATTTAATACG
41899184 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
41899214 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
41899244 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:41906617 original size:29 final size:29
Alignment explanation
Indices: 41906584--41906639 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
41906574 ATTTAATACG
41906584 AACTTTGGAAAAATTACACTTTTGCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCTA
* * *
41906613 AACTTTTGCACAATTACACTTTTGCCC
1 AACTTTGGAAAAATTACACTTTTGCCC
41906640 CTAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (29 bp):
AACTTTGGAAAAATTACACTTTTGCCCTA
Found at i:41913935 original size:47 final size:48
Alignment explanation
Indices: 41913866--41913999 Score: 159
Period size: 47 Copynumber: 2.9 Consensus size: 48
41913856 TGGGTAAAGT
*
41913866 GTCGATGCCATGTCCC-GAACATGGTCTTACACTAGCTCACAT-CTCAA
1 GTCGATGCCATGTCCCAG-ACATGGTCTTACACTAGCTCACATAATCAA
* * * ***
41913913 GTCGATGCCAAGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATCAA
*
41913961 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCACA
1 GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACA
41914000 AACAAATGAC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
46 16 0.22
47 50 0.68
48 8 0.11
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (48 bp):
GTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAATCAA
Found at i:41917607 original size:13 final size:13
Alignment explanation
Indices: 41917586--41917618 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41917576 TTTAGTTAAA
*
41917586 TTAGTTAATTAGT
1 TTAGATAATTAGT
41917599 TTAGATAATTAGT
1 TTAGATAATTAGT
41917612 TTA-ATAA
1 TTAGATAA
41917619 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:41919469 original size:46 final size:46
Alignment explanation
Indices: 41919383--41919599 Score: 178
Period size: 46 Copynumber: 4.7 Consensus size: 46
41919373 AGGGTCAGGT
* * *
41919383 GCCGATGCCATGTCCCAGACATGGTCGTACACTGAC-ACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTCATCTCGTAG
* *
41919429 GCCGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCTTG-AG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTCGTAG
* * * * * *
41919475 GCCGAAGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTC-AAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGC-TTCATCTCGTAG
* * *
41919521 GCTGATGCCATGTCCCAGACATGGTTTTACACTGGCTCTCATAAT-GT-G
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-CTCGTAG
41919569 GCCGATGCATG-CCCTAGACATGTCTTACACT
1 GCCGATGCATGTCCC-AGACATGTCTTACACT
41919600 AGCTCACACA
Statistics
Matches: 137, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
44 11 0.08
45 14 0.10
46 66 0.48
47 25 0.18
48 20 0.15
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTCGTAG
Found at i:41919572 original size:94 final size:92
Alignment explanation
Indices: 41919432--41919602 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 92
41919422 TCTCGTAGCC
* **
41919432 GATGCATGTCCTAGACATGTCTTACACTGGCTTACATCTTGAGGCCGAAGCATGTCCC-AGACAT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATAATGAGGCCGAAGCATG-CCCTAGACAT
41919496 GTCTTACACTAGCACTCGTCTCAATGCT
65 GTCTTACACTAGCACTCGTCTCAATGCT
* * *
41919524 GATGCCATGTCCCAGACATGGTTTTACACTGGCTCT-CATAATGTGGCCGATGCATGCCCTAGAC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATAATGAGGCCGAAGCATGCCCTAGAC
41919588 ATGTCTTACACTAGC
63 ATGTCTTACACTAGC
41919603 TCACACAAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
92 4 0.06
93 16 0.23
94 48 0.70
95 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACATAATGAGGCCGAAGCATGCCCTAGACATG
TCTTACACTAGCACTCGTCTCAATGCT
Found at i:41925771 original size:25 final size:23
Alignment explanation
Indices: 41925742--41925787 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
41925732 AATAAAAAAC
*
41925742 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
41925767 TTTAAAACATAAAAACAAATA
1 TTTAAAACATAAAAACAAATA
41925788 TTAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:41926707 original size:20 final size:20
Alignment explanation
Indices: 41926684--41926721 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41926674 ACTTAGGATA
41926684 AATATTAGTAAAATAAGTAG
1 AATATTAGTAAAATAAGTAG
41926704 AATATTAGTAAAATAAGT
1 AATATTAGTAAAATAAGT
41926722 GTTTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (20 bp):
AATATTAGTAAAATAAGTAG
Found at i:41928690 original size:12 final size:12
Alignment explanation
Indices: 41928673--41928697 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41928663 CATACACTCT
41928673 CGTGTGCTAGGC
1 CGTGTGCTAGGC
41928685 CGTGTGCTAGGC
1 CGTGTGCTAGGC
41928697 C
1 C
41928698 ATGCTAAACC
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:0.08, C:0.28, G:0.40, T:0.24
Consensus pattern (12 bp):
CGTGTGCTAGGC
Found at i:41932789 original size:30 final size:32
Alignment explanation
Indices: 41932725--41932789 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
41932715 TTCAATCTCA
*
41932725 ACATATACTAGGCCGAAGCCTTTACATTATTC
1 ACATATACTAGGCCGAAGCCTTTACATAATTC
* *
41932757 ACAT-TACTGGGCCGAAGCCTTT-TATAATTC
1 ACATATACTAGGCCGAAGCCTTTACATAATTC
41932787 ACA
1 ACA
41932790 ACTCATATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 9 0.30
31 17 0.57
32 4 0.13
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (32 bp):
ACATATACTAGGCCGAAGCCTTTACATAATTC
Found at i:41933056 original size:24 final size:25
Alignment explanation
Indices: 41933029--41933080 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
41933019 GCCTAGCCAC
41933029 TTTTAAT-AACTAGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
** * *
41933053 TTTTGGTAAATTGGGGCAAAGCCCT
1 TTTTAATAAACTAGGGCAAAGCCCT
41933078 TTT
1 TTT
41933081 GCACTTCCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTTAATAAACTAGGGCAAAGCCCT
Found at i:41933154 original size:20 final size:21
Alignment explanation
Indices: 41933129--41933176 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
41933119 AAATGAATAC
*
41933129 ATCATGTGCATATCATA-CAT
1 ATCATGTGCATATCATATCAA
41933149 ATCATGTGCATATCATATCAA
1 ATCATGTGCATATCATATCAA
41933170 ATCATGT
1 ATCATGT
41933177 ATATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAA
Found at i:41942624 original size:30 final size:32
Alignment explanation
Indices: 41942560--41942624 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
41942550 TTCAATCTCA
*
41942560 ACATATACTGGGCCGAAGCCTTTACATTATTC
1 ACATATACTGGGCCGAAGCCTTTACATAATTC
*
41942592 ACAT-TACTGGGCCGAAGCCTTT-TATAATTC
1 ACATATACTGGGCCGAAGCCTTTACATAATTC
41942622 ACA
1 ACA
41942625 ACTCATATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.29
31 18 0.58
32 4 0.13
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (32 bp):
ACATATACTGGGCCGAAGCCTTTACATAATTC
Found at i:41942903 original size:25 final size:25
Alignment explanation
Indices: 41942871--41942940 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
41942861 CTCTTTTAAT
*
41942871 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41942896 AATTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
41942921 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41942941 GCACTTCCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41975641 original size:5 final size:5
Alignment explanation
Indices: 41975631--41975676 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
41975621 ATGTGTGTGC
41975631 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
41975677 TCACAATCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:41976901 original size:21 final size:24
Alignment explanation
Indices: 41976877--41976926 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 24
41976867 AGAAATTTAA
41976877 AAAAAATT-CAAAA-TAAT-TTTT
1 AAAAAATTCCAAAATTAATATTTT
*
41976898 -AAAAATTCCAAAATTTATATTTT
1 AAAAAATTCCAAAATTAATATTTT
41976921 AAAAAA
1 AAAAAA
41976927 ATTATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 3 0.12
23 4 0.17
24 5 0.21
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAAAATTCCAAAATTAATATTTT
Found at i:41976920 original size:23 final size:20
Alignment explanation
Indices: 41976878--41976925 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
41976868 GAAATTTAAA
41976878 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
41976898 AAAAATTCCAAAATTTATATTTT
1 AAAAATT-CAAAA-TAAT-TTTT
41976921 AAAAA
1 AAAAA
41976926 AATTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 3 0.12
23 9 0.38
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:41976954 original size:20 final size:19
Alignment explanation
Indices: 41976916--41976955 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
41976906 CAAAATTTAT
*
41976916 ATTTTAAAAAAATTATAAA
1 ATTTTAAAAAAAATATAAA
*
41976935 ATTTTCAAAAAAAATCTAAA
1 ATTTT-AAAAAAAATATAAA
41976955 A
1 A
41976956 ATATATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTTTAAAAAAAATATAAA
Found at i:41981520 original size:18 final size:19
Alignment explanation
Indices: 41981492--41981527 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
41981482 GGGTAATAGT
41981492 CAAATTTAACAAAAAAAAC
1 CAAATTTAACAAAAAAAAC
41981511 CAAA-TTAACAAAAAAAA
1 CAAATTTAACAAAAAAAA
41981528 TTGTAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (19 bp):
CAAATTTAACAAAAAAAAC
Found at i:41982045 original size:21 final size:21
Alignment explanation
Indices: 41982021--41982062 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41982011 TCAAAAAAAC
* *
41982021 TCTCAAATTTCTCTTTAAATT
1 TCTCAAATATATCTTTAAATT
41982042 TCTCAAATATATCTTTAAATT
1 TCTCAAATATATCTTTAAATT
41982063 ACAATTTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (21 bp):
TCTCAAATATATCTTTAAATT
Found at i:41984077 original size:42 final size:43
Alignment explanation
Indices: 41984023--41984133 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 43
41984013 GATTTACGCA
* * *
41984023 TAAGAC-CATGTCTGGGACA-TCGGCATCG-TATTTGATTTCGTG
1 TAAGACAC-TGTCTGGGACAGT-GGCATCGACATTTGATTACATG
41984065 TAAGACACTGTCTGGGACAGTGGCATCGACATTTGATTACATG
1 TAAGACACTGTCTGGGACAGTGGCATCGACATTTGATTACATG
*
41984108 TAAAACCAC-GTCTGGGAC-GTTGGCAT
1 TAAGA-CACTGTCTGGGACAG-TGGCAT
41984134 TGTACGAGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
42 25 0.42
43 32 0.53
44 3 0.05
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (43 bp):
TAAGACACTGTCTGGGACAGTGGCATCGACATTTGATTACATG
Found at i:41985773 original size:18 final size:18
Alignment explanation
Indices: 41985750--41985787 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41985740 AATCATGGGC
41985750 TTAGTTTCGCTTTCCATT
1 TTAGTTTCGCTTTCCATT
41985768 TTAGTTTCGCTTTCCATT
1 TTAGTTTCGCTTTCCATT
41985786 TT
1 TT
41985788 TACATCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.21, G:0.11, T:0.58
Consensus pattern (18 bp):
TTAGTTTCGCTTTCCATT
Found at i:41985895 original size:12 final size:13
Alignment explanation
Indices: 41985878--41985913 Score: 65
Period size: 12 Copynumber: 2.8 Consensus size: 13
41985868 AGATTTAAAA
41985878 TAAAATTTTATGC
1 TAAAATTTTATGC
41985891 T-AAATTTTATGC
1 TAAAATTTTATGC
41985903 TAAAATTTTAT
1 TAAAATTTTAT
41985914 TTAATTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
TAAAATTTTATGC
Found at i:41986901 original size:34 final size:33
Alignment explanation
Indices: 41986843--41986911 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
41986833 CCCTTTACCC
*
41986843 TAATTTATTTTTTATAAACAATAAATCCTAATT
1 TAATTTATTTTTTATAAACAATAAACCCTAATT
41986876 TAATTTATTTTTTA-AAACATCATAAACCCTAATT
1 TAATTTATTTTTTATAAACA--ATAAACCCTAATT
41986910 TA
1 TA
41986912 TTTTCTCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 5 0.15
33 14 0.42
34 14 0.42
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (33 bp):
TAATTTATTTTTTATAAACAATAAACCCTAATT
Found at i:41987599 original size:22 final size:22
Alignment explanation
Indices: 41987574--41987619 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
41987564 CGGTGTTAGA
*
41987574 AAAATTCTAAATA-AATAAAAAT
1 AAAATT-TAAATATAACAAAAAT
*
41987596 AAAATTTTAATATAACAAAAAT
1 AAAATTTAAATATAACAAAAAT
41987618 AA
1 AA
41987620 TTGTTACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATTTAAATATAACAAAAAT
Found at i:41989816 original size:20 final size:20
Alignment explanation
Indices: 41989791--41989831 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41989781 GAAATAAATG
41989791 AAATATTTGGGCTTATATGA
1 AAATATTTGGGCTTATATGA
41989811 AAATATTTGGGCTTATATGA
1 AAATATTTGGGCTTATATGA
41989831 A
1 A
41989832 CTCCATGAAA
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:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (20 bp):
AAATATTTGGGCTTATATGA
Found at i:41990370 original size:43 final size:43
Alignment explanation
Indices: 41990318--41990444 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 43
41990308 ATAGGATTCT
*
41990318 GATATGTGATTTCGTGTAATACCATGTCTGGGACGTTGGCATC
1 GATATGTGATTTCGTGTAAGACCATGTCTGGGACGTTGGCATC
* * * *
41990361 GATTTGTGATTTACGTGTAAGACCCTATCTGGGACAG-TGACATC
1 GATATGTGATTT-CGTGTAAGACCATGTCTGGGAC-GTTGGCATC
* * * *
41990405 GATATGTGATTACATGTAAGACCACGTTTGGGACGTTGGC
1 GATATGTGATTTCGTGTAAGACCATGTCTGGGACGTTGGC
41990445 GTTGTACAAG
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.01
43 31 0.46
44 35 0.51
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (43 bp):
GATATGTGATTTCGTGTAAGACCATGTCTGGGACGTTGGCATC
Found at i:41991669 original size:26 final size:26
Alignment explanation
Indices: 41991640--41991747 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
41991630 TGGTACAAAT
41991640 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
41991666 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41991692 TGATAATGGGTTAGGTAAATGCTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41991718 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41991744 TGAT
1 TGAT
41991748 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41997280 original size:28 final size:28
Alignment explanation
Indices: 41997249--41997310 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
41997239 GTCAGTGTTT
* *
41997249 TTCAATATCAATCAATT-TATCAGTATCA
1 TTCAATAACAATCAATTAT-TCAGTAACA
*
41997277 TTCAGTAACAATCAATTATTCAGTAACA
1 TTCAATAACAATCAATTATTCAGTAACA
*
41997305 ATCAAT
1 TTCAAT
41997311 TATTCAGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (28 bp):
TTCAATAACAATCAATTATTCAGTAACA
Found at i:41997299 original size:18 final size:18
Alignment explanation
Indices: 41997276--41997373 Score: 142
Period size: 18 Copynumber: 5.4 Consensus size: 18
41997266 TATCAGTATC
41997276 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
41997294 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
* *
41997312 ATTCAGTAGCAATCAGTT
1 ATTCAGTAACAATCAATT
*
41997330 ATTCAGTAACAATCAATC
1 ATTCAGTAACAATCAATT
* * *
41997348 ATTCAGTAACAGTCAGTC
1 ATTCAGTAACAATCAATT
41997366 ATTCAGTA
1 ATTCAGTA
41997374 CCTTTATTCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 73 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (18 bp):
ATTCAGTAACAATCAATT
Found at i:41997325 original size:36 final size:36
Alignment explanation
Indices: 41997273--41997373 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
41997263 ATTTATCAGT
*
41997273 ATCATTCAGTAACAATCAATTATTCAGTAACAATCA
1 ATCATTCAGTAACAATCAGTTATTCAGTAACAATCA
* *
41997309 ATTATTCAGTAGCAATCAGTTATTCAGTAACAATCA
1 ATCATTCAGTAACAATCAGTTATTCAGTAACAATCA
* *
41997345 ATCATTCAGTAACAGTCAGTCATTCAGTA
1 ATCATTCAGTAACAATCAGTTATTCAGTA
41997374 CCTTTATTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (36 bp):
ATCATTCAGTAACAATCAGTTATTCAGTAACAATCA
Found at i:41997345 original size:54 final size:56
Alignment explanation
Indices: 41997267--41997373 Score: 164
Period size: 54 Copynumber: 1.9 Consensus size: 56
41997257 CAATCAATTT
* *
41997267 ATCAGTATCATTCAGTAACAATCAATTATTCAGTAACAATCAATTATTCAGTAGCA
1 ATCAGTATCATTCAGTAACAATCAATCATTCAGTAACAATCAATCATTCAGTAGCA
* *
41997323 ATCAGT-T-ATTCAGTAACAATCAATCATTCAGTAACAGTCAGTCATTCAGTA
1 ATCAGTATCATTCAGTAACAATCAATCATTCAGTAACAATCAATCATTCAGTA
41997374 CCTTTATTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
54 40 0.85
55 1 0.02
56 6 0.13
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (56 bp):
ATCAGTATCATTCAGTAACAATCAATCATTCAGTAACAATCAATCATTCAGTAGCA
Found at i:41997506 original size:47 final size:47
Alignment explanation
Indices: 41997437--41997537 Score: 123
Period size: 47 Copynumber: 2.1 Consensus size: 47
41997427 ACCAACACAC
* * **
41997437 CAGTACGGTACTCAGTGCCTCATCGGCTT-TGCCAAAGTAAACAGTAA
1 CAGTACGGTACTCAGTACCTCATCGGATTAAACCAAAGT-AACAGTAA
* * *
41997484 CAGTACGGTACTTAGTACCTCATTGGATTAAACCGAAGTAACAGTAA
1 CAGTACGGTACTCAGTACCTCATCGGATTAAACCAAAGTAACAGTAA
41997531 CAGTACG
1 CAGTACG
41997538 ACACACATGG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
47 40 0.87
48 6 0.13
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (47 bp):
CAGTACGGTACTCAGTACCTCATCGGATTAAACCAAAGTAACAGTAA
Found at i:41998743 original size:14 final size:13
Alignment explanation
Indices: 41998717--41998741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41998707 ATTTTCCTTC
41998717 TTTTTCTTTCCCT
1 TTTTTCTTTCCCT
41998730 TTTTTCTTTCCC
1 TTTTTCTTTCCC
41998742 CTACTACGTT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTCTTTCCCT
Found at i:41998788 original size:19 final size:19
Alignment explanation
Indices: 41998764--41998802 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41998754 TGCTATTCTG
41998764 TTCTTTAGTCTCTTT-TTTT
1 TTCTTTA-TCTCTTTCTTTT
*
41998783 TTCTTTATTTCTTTCTTTT
1 TTCTTTATCTCTTTCTTTT
41998802 T
1 T
41998803 ATTATTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (19 bp):
TTCTTTATCTCTTTCTTTT
Found at i:41998823 original size:5 final size:5
Alignment explanation
Indices: 41998816--41998846 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
41998806 ATTAAACTAT
*
41998816 TATAT TATAA TATAA TATAA TATAA TATAA T
1 TATAA TATAA TATAA TATAA TATAA TATAA T
41998847 TTATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TATAA
Found at i:41999110 original size:17 final size:17
Alignment explanation
Indices: 41999070--41999111 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
41999060 AAATAACCCA
*
41999070 AAGCCCAAACCTAACAG
1 AAGCCCAAACCCAACAG
* *
41999087 GACCCCAAACCCAACAG
1 AAGCCCAAACCCAACAG
41999104 AAGCCCAA
1 AAGCCCAA
41999112 CTCAAATACC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.40, G:0.12, T:0.02
Consensus pattern (17 bp):
AAGCCCAAACCCAACAG
Found at i:42000193 original size:17 final size:18
Alignment explanation
Indices: 42000171--42000243 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 18
42000161 TTTCTTTTAC
42000171 TACTATTTATTA-TATTT
1 TACTATTTATTATTATTT
*
42000188 TACTATTATAGTTATTTTTT
1 TACTATT-TA-TTATTATTT
* *
42000208 CTACTACTTTGTTATTATTG
1 -TACTA-TTTATTATTATTT
42000228 TACTA-TTATTATTATT
1 TACTATTTATTATTATT
42000244 GCCATTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
17 17 0.37
18 2 0.04
19 8 0.17
20 11 0.24
21 6 0.13
22 2 0.04
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (18 bp):
TACTATTTATTATTATTT
Found at i:42000242 original size:20 final size:20
Alignment explanation
Indices: 42000154--42000243 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
42000144 TTAGATAATT
*
42000154 TTATTATT-TTCTTTTACTA
1 TTATTATTATTATTTTACTA
*
42000173 CTATTTATTA-TATTTTACTA
1 TTA-TTATTATTATTTTACTA
*
42000193 TTA-TAGTTATTTTTTCTACTA
1 TTATTA-TTATTATTT-TACTA
* * *
42000214 CT-TTGTTATTATTGTACTA
1 TTATTATTATTATTTTACTA
42000233 TTATTATTATT
1 TTATTATTATT
42000244 GCCATTAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.04
19 11 0.20
20 34 0.63
21 7 0.13
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.63
Consensus pattern (20 bp):
TTATTATTATTATTTTACTA
Found at i:42000243 original size:40 final size:40
Alignment explanation
Indices: 42000154--42000243 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
42000144 TTAGATAATT
*
42000154 TTATTATT-TTCTTTTACTACTATTTATTATATTTTACTA
1 TTATTATTATTCTTTTACTACTATTTATTATATTGTACTA
*
42000193 TTA-TAGTTATT-TTTT-CTACTACTTTGTTATTATTGTACTA
1 TTATTA-TTATTCTTTTACTACTA-TTTATTA-TATTGTACTA
42000233 TTATTATTATT
1 TTATTATTATT
42000244 GCCATTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
38 8 0.18
39 15 0.34
40 19 0.43
41 2 0.05
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.63
Consensus pattern (40 bp):
TTATTATTATTCTTTTACTACTATTTATTATATTGTACTA
Found at i:42000305 original size:3 final size:3
Alignment explanation
Indices: 42000299--42000358 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
42000289 ATTATTTTCG
* * *
42000299 TAT TAT TAT CAT TAT TAC TAT TAT TA- TATT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
42000344 TAT TAT TAT ATAT TA
1 TAT TAT TAT -TAT TA
42000359 GTGTATATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.85
4 5 0.10
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:42000461 original size:3 final size:3
Alignment explanation
Indices: 42000453--42000494 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
42000443 TACATTTCTA
42000453 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42000495 ATAGTAGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42000867 original size:11 final size:11
Alignment explanation
Indices: 42000853--42000934 Score: 66
Period size: 11 Copynumber: 7.7 Consensus size: 11
42000843 ATATATTTCA
*
42000853 TATATATCATG
1 TATATATTATG
*
42000864 TATATA-TATA
1 TATATATTATG
* *
42000874 TATTTAATAT-
1 TATATATTATG
*
42000884 TATATTTTTATG
1 TATA-TATTATG
42000896 TATATATTATG
1 TATATATTATG
42000907 TATATATCT-T-
1 TATATAT-TATG
42000917 TA-ATATTATG
1 TATATATTATG
42000927 TATATATT
1 TATATATT
42000935 TTAATACCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 1 0.02
9 5 0.09
10 14 0.25
11 32 0.56
12 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (11 bp):
TATATATTATG
Found at i:42000887 original size:20 final size:20
Alignment explanation
Indices: 42000864--42000940 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
42000854 ATATATCATG
42000864 TATATATATATATTTAATAT
1 TATATATATATATTTAATAT
* *
42000884 TATAT-T-TTTATGTATATAT
1 TATATATATATATTTA-ATAT
* *
42000903 TATGTATATATCTTTAATAT
1 TATATATATATATTTAATAT
*
42000923 TATGTATATAT-TTTAATA
1 TATATATATATATTTAATA
42000941 CCATACATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
18 6 0.12
19 16 0.33
20 21 0.44
21 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (20 bp):
TATATATATATATTTAATAT
Found at i:42000893 original size:14 final size:15
Alignment explanation
Indices: 42000842--42000922 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 15
42000832 CTACATTATT
*
42000842 TATATATTTCATATA
1 TATATATTTAATATA
* *
42000857 TAT-CATGT-ATATA
1 TATATATTTAATATA
42000870 TATATATTTAATAT-
1 TATATATTTAATATA
*
42000884 TATAT-TTT--TATG
1 TATATATTTAATATA
*
42000896 TATATA-TT-ATGTA
1 TATATATTTAATATA
*
42000909 TATATCTTTAATAT
1 TATATATTTAATAT
42000923 TATGTATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
11 3 0.06
12 7 0.14
13 18 0.35
14 13 0.25
15 10 0.20
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (15 bp):
TATATATTTAATATA
Found at i:42000899 original size:26 final size:28
Alignment explanation
Indices: 42000837--42000903 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 28
42000827 AATAACTACA
* *
42000837 TTATTTATATATTTCATATATATCATGT
1 TTATATATATATTTAATATATATCATGT
* *
42000865 ATATATATATATTTAATAT-TAT-ATTT
1 TTATATATATATTTAATATATATCATGT
*
42000891 TTATGTATATATT
1 TTATATATATATT
42000904 ATGTATATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 14 0.42
27 3 0.09
28 16 0.48
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TTATATATATATTTAATATATATCATGT
Found at i:42000922 original size:39 final size:42
Alignment explanation
Indices: 42000841--42000925 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 42
42000831 ACTACATTAT
42000841 TTATATATTTCATATATATCATGTATATATATATATTTAATA
1 TTATATATTTCATATATATCATGTATATATATATATTTAATA
* * * *
42000883 TTATAT-TTTTATGTATAT-AT-TATGTATATATCTTTAATA
1 TTATATATTTCATATATATCATGTATATATATATATTTAATA
42000922 TTAT
1 TTAT
42000926 GTATATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
39 21 0.54
40 2 0.05
41 10 0.26
42 6 0.15
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (42 bp):
TTATATATTTCATATATATCATGTATATATATATATTTAATA
Found at i:42001030 original size:14 final size:15
Alignment explanation
Indices: 42001011--42001039 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42001001 TTCGTTATCA
42001011 TTGCCAT-TTTTATT
1 TTGCCATGTTTTATT
42001025 TTGCCATGTTTTATT
1 TTGCCATGTTTTATT
42001040 CACTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (15 bp):
TTGCCATGTTTTATT
Found at i:42007621 original size:33 final size:33
Alignment explanation
Indices: 42007582--42007645 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
42007572 ATTCAACCTG
42007582 AATTTGTATAAGCATGGGAAAAATATATACGCA
1 AATTTGTATAAGCATGGGAAAAATATATACGCA
*
42007615 AATTTGTATAAGCATGGGAGAAATATATACG
1 AATTTGTATAAGCATGGGAAAAATATATACG
42007646 AGATGGAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (33 bp):
AATTTGTATAAGCATGGGAAAAATATATACGCA
Found at i:42015068 original size:52 final size:52
Alignment explanation
Indices: 42015004--42015103 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
42014994 ACCCAATTAA
*
42015004 ATGTATCACATCCATAATGAACTCGGACCAACTTAACGAGCTCGGATGTCCC
1 ATGTATCACATCCATAATAAACTCGGACCAACTTAACGAGCTCGGATGTCCC
* *
42015056 ATGTATCGCATCCATTATAAACTCGGACCAACTTAACGAGCTCGGATG
1 ATGTATCACATCCATAATAAACTCGGACCAACTTAACGAGCTCGGATG
42015104 CTCACATCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (52 bp):
ATGTATCACATCCATAATAAACTCGGACCAACTTAACGAGCTCGGATGTCCC
Found at i:42015129 original size:44 final size:44
Alignment explanation
Indices: 42015064--42015148 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
42015054 CCATGTATCG
* * *
42015064 CATCCATTATAAACTCGGACCAACTTAACGAGCTCGGATGCTCA
1 CATCCATAATAAACTCAGACCAACTCAACGAGCTCGGATGCTCA
* *
42015108 CATCCATAATGAACTCAGACCAACTCAACGAGCTTGGATGC
1 CATCCATAATAAACTCAGACCAACTCAACGAGCTCGGATGC
42015149 CTCATACATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.21
Consensus pattern (44 bp):
CATCCATAATAAACTCAGACCAACTCAACGAGCTCGGATGCTCA
Found at i:42017582 original size:51 final size:51
Alignment explanation
Indices: 42017522--42017623 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
42017512 ATTGCTGCCA
*
42017522 TTTATCTTCATTTAAATCAGCCCTAAATCTGAAATCTTGAACCCCAAGATC
1 TTTATCTTCATTTAAATCAGCCCTAAATCTGAAATCTTGAACCACAAGATC
42017573 TTTATCTTCATTTAAATCAGCCCTAAATCTGAAATCTTGAACCACAAGATC
1 TTTATCTTCATTTAAATCAGCCCTAAATCTGAAATCTTGAACCACAAGATC
42017624 AATCCCGAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (51 bp):
TTTATCTTCATTTAAATCAGCCCTAAATCTGAAATCTTGAACCACAAGATC
Found at i:42019966 original size:42 final size:42
Alignment explanation
Indices: 42019907--42020050 Score: 150
Period size: 42 Copynumber: 3.4 Consensus size: 42
42019897 TCGAAAGCTT
*
42019907 AACAGAAGCTCGTAAGAGCTAAAAAGTAAC-CTATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAAAAGTAACTC-ATAAGAGTTG
* *
42019949 AACAGAAGCTCGTAAGAGCTGAACAAA--AACTCATATGAGTTA
1 AACAGAAGCTCGTAAGAGCT-AA-AAAGTAACTCATAAGAGTTG
* * * ** *
42019991 AATAGAAGCACATAAGAGCTAAACGGTAACTCATAAGAATTG
1 AACAGAAGCTCGTAAGAGCTAAAAAGTAACTCATAAGAGTTG
*
42020033 AACAGAAGCTCGAAAGAG
1 AACAGAAGCTCGTAAGAG
42020051 TTGAATGAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 73 0.89
43 3 0.04
44 3 0.04
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAAAAGTAACTCATAAGAGTTG
Found at i:42019971 original size:21 final size:21
Alignment explanation
Indices: 42019888--42020043 Score: 86
Period size: 21 Copynumber: 7.5 Consensus size: 21
42019878 GTATATCATT
* *
42019888 AACAGAAGCTC-GAA-AGCTT
1 AACAGAAGCTCATAAGAGCTG
* *
42019907 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
* * * *
42019928 AAAAGTAACCT-ATAAGGGTTG
1 AACAG-AAGCTCATAAGAGCTG
*
42019949 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * * * *
42019970 AACAAAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTG
* * *
42019991 AATAGAAGCACATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTG
* **
42020012 AACGGTAA-CTCATAAGAATTG
1 AACAG-AAGCTCATAAGAGCTG
42020033 AACAGAAGCTC
1 AACAGAAGCTC
42020044 GAAAGAGTTG
Statistics
Matches: 99, Mismatches: 32, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
19 11 0.11
20 8 0.08
21 74 0.75
22 6 0.06
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:42020062 original size:84 final size:84
Alignment explanation
Indices: 42019910--42020099 Score: 256
Period size: 84 Copynumber: 2.3 Consensus size: 84
42019900 AAAGCTTAAC
** ** *
42019910 AGAAGCTCGTAAGAGCTAAAAAGTAACCTATAAGGGTTGAACAGAAGCTCGTAAGAGCTGAACAA
1 AGAAGCTCGTAAGAGCTAAACGGTAACCTATAAGAATTGAACAGAAGCTCGAAAGAGCTGAACAA
42019975 AAACTCATATGAGTTAAAT
66 AAACTCATATGAGTTAAAT
* * * **
42019994 AGAAGCACATAAGAGCTAAACGGTAA-CTCATAAGAATTGAACAGAAGCTCGAAAGAGTTGAATG
1 AGAAGCTCGTAAGAGCTAAACGGTAACCT-ATAAGAATTGAACAGAAGCTCGAAAGAGCTGAACA
*
42020058 AAAACTCATATTAGTTAAAT
65 AAAACTCATATGAGTTAAAT
*
42020078 AGAAGCTCGTAAGAACTAAACG
1 AGAAGCTCGTAAGAGCTAAACG
42020100 AAAAGTAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 2 0.02
84 89 0.98
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (84 bp):
AGAAGCTCGTAAGAGCTAAACGGTAACCTATAAGAATTGAACAGAAGCTCGAAAGAGCTGAACAA
AAACTCATATGAGTTAAAT
Found at i:42020064 original size:42 final size:42
Alignment explanation
Indices: 42019946--42020103 Score: 120
Period size: 42 Copynumber: 3.8 Consensus size: 42
42019936 CCTATAAGGG
* * * *
42019946 TTGAACAGAAGCTCGTAAGAGCTGAACAAAAACTCATATGAG
1 TTGAACAGAAGCTCGAAAGAGCTGAACGAAAACTCATAAGAA
* * * * **
42019988 TTAAATAGAAGCAC-ATAAGAGCTAAACGGTAACTCATAAGAA
1 TTGAACAGAAGCTCGA-AAGAGCTGAACGAAAACTCATAAGAA
* * ** *
42020030 TTGAACAGAAGCTCGAAAGAGTTGAATGAAAACTCATATTAG
1 TTGAACAGAAGCTCGAAAGAGCTGAACGAAAACTCATAAGAA
* * * * *
42020072 TTAAATAGAAGCTCGTAAGAACTAAACGAAAA
1 TTGAACAGAAGCTCGAAAGAGCTGAACGAAAA
42020104 GTAAAACACG
Statistics
Matches: 86, Mismatches: 28, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
42 85 0.99
43 1 0.01
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (42 bp):
TTGAACAGAAGCTCGAAAGAGCTGAACGAAAACTCATAAGAA
Found at i:42025207 original size:21 final size:20
Alignment explanation
Indices: 42025159--42025221 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
42025149 CCAATACGCC
42025159 AACAGAAGCTCG-AA-AGCTG
1 AACA-AAGCTCGTAAGAGCTG
42025178 AAC-AAGCTCGTAAGAGCTG
1 AACAAAGCTCGTAAGAGCTG
*
42025197 AACAAAAGCTCATAAGAGCTG
1 AAC-AAAGCTCGTAAGAGCTG
42025218 AACA
1 AACA
42025222 TAAACTCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 7 0.18
18 2 0.05
19 11 0.28
20 1 0.03
21 18 0.46
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (20 bp):
AACAAAGCTCGTAAGAGCTG
Found at i:42025229 original size:21 final size:21
Alignment explanation
Indices: 42025173--42025232 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
42025163 GAAGCTCGAA
*
42025173 AGCTGAAC--AAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
42025192 AGCTGAACAAAAGCTCATAAG
1 AGCTGAACAAAAGCTCATAAG
42025213 AGCTGAACATAAA-CTCATAA
1 AGCTGAACA-AAAGCTCATAA
42025233 TTAAGAGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 8 0.22
21 26 0.70
22 3 0.08
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (21 bp):
AGCTGAACAAAAGCTCATAAG
Found at i:42032159 original size:39 final size:39
Alignment explanation
Indices: 42032134--42032998 Score: 1694
Period size: 39 Copynumber: 22.2 Consensus size: 39
42032124 GGACTTTAGC
* * * *
42032134 CCGGACATATTTCCAGCACATAGCCTGAGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032173 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032212 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032251 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032290 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032329 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032368 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032407 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032446 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032485 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032524 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032563 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032602 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032641 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032680 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032719 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032758 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032797 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032836 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032875 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032914 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032953 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
42032992 CCGGATA
1 CCGGATA
42032999 CACATCAAAT
Statistics
Matches: 822, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 822 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:42039548 original size:39 final size:39
Alignment explanation
Indices: 42039438--42039551 Score: 192
Period size: 39 Copynumber: 2.9 Consensus size: 39
42039428 CAGGACATAT
* * *
42039438 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCGAATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
*
42039477 TTCCAGCACATAGCCTGCAGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
42039516 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATA
42039552 CACATCAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:42052109 original size:30 final size:29
Alignment explanation
Indices: 42052065--42052140 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
42052055 TATCCATTAC
*
42052065 ATTATTTTTATTATTTTATATTTTACTTATAA
1 ATTATTATT-TTATTTTATATTTTA--TATAA
* *
42052097 ATTA-TATTTTATTATATATTTTATATAT
1 ATTATTATTTTATTTTATATTTTATATAA
*
42052125 ATTATTTTTTTATTTT
1 ATTATTATTTTATTTT
42052141 CTGTAAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
28 8 0.21
29 9 0.24
30 14 0.37
31 3 0.08
32 4 0.11
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (29 bp):
ATTATTATTTTATTTTATATTTTATATAA
Found at i:42052120 original size:19 final size:20
Alignment explanation
Indices: 42052072--42052122 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 20
42052062 TACATTATTT
42052072 TTAT-TATTTTATATTTTAC
1 TTATATATTTTATATTTTAC
*
42052091 TTATA-A-ATTATATTTTA-
1 TTATATATTTTATATTTTAC
42052108 TTATATATTTTATAT
1 TTATATATTTTATAT
42052123 ATATTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 5 0.19
18 11 0.41
19 11 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATATTTTATATTTTAC
Found at i:42052123 original size:28 final size:28
Alignment explanation
Indices: 42052065--42052137 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 28
42052055 TATCCATTAC
42052065 ATTATTTTTATTATTTTATATTTTACTTATAA
1 ATTATTTTTATTA---TATATTTTAC-TATAA
*
42052097 ATTATATTTTATTATATATTTTA-TATAT
1 ATTAT-TTTTATTATATATTTTACTATAA
42052125 ATTATTTTT-TTAT
1 ATTATTTTTATTAT
42052138 TTTCTGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 4 0.10
27 4 0.10
28 9 0.23
30 9 0.23
32 5 0.13
33 8 0.21
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (28 bp):
ATTATTTTTATTATATATTTTACTATAA
Found at i:42052125 original size:11 final size:12
Alignment explanation
Indices: 42052099--42052127 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42052089 ACTTATAAAT
42052099 TATATTTTATTA
1 TATATTTTATTA
42052111 TATATTTTA-TA
1 TATATTTTATTA
42052122 TATATT
1 TATATT
42052128 ATTTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:42052285 original size:17 final size:17
Alignment explanation
Indices: 42052263--42052295 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42052253 TATTTTATTT
42052263 ATATTTTATTACATATC
1 ATATTTTATTACATATC
*
42052280 ATATTTTATTATATAT
1 ATATTTTATTACATAT
42052296 TATTCCTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTTATTACATATC
Found at i:42052295 original size:12 final size:12
Alignment explanation
Indices: 42052251--42052354 Score: 58
Period size: 12 Copynumber: 8.7 Consensus size: 12
42052241 TTTATTTCAT
42052251 TATATTTTATT-
1 TATATTTTATTA
42052262 TATATTTTATTA
1 TATATTTTATTA
* **
42052274 CATATCATATT-
1 TATATTTTATTA
*
42052285 T-TATTATA-TA
1 TATATTTTATTA
42052295 T-TATTCCTTATGGTA
1 TATATT--TTAT--TA
*
42052310 T-TTTTTTATTA
1 TATATTTTATTA
*
42052321 TATATTATATTA
1 TATATTTTATTA
42052333 TATACTTCTTATTA
1 TATA-TT-TTATTA
42052347 TATATTTT
1 TATATTTT
42052355 TTTTATTACT
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
9 1 0.01
10 11 0.15
11 14 0.19
12 24 0.33
13 8 0.11
14 9 0.12
15 6 0.08
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:42052311 original size:27 final size:27
Alignment explanation
Indices: 42052252--42052352 Score: 80
Period size: 27 Copynumber: 3.6 Consensus size: 27
42052242 TTATTTCATT
*
42052252 ATATTTTATTTATATTTTATTACATATC
1 ATATTTTA-TTATATATTATTACATATC
* * *
42052280 ATATTTTATTATATATTATTCCTTATG
1 ATATTTTATTATATATTATTACATATC
* * *
42052307 GTATTTTTTTAT-TATATATTATATTAT-
1 ATATTTTATTATATAT-TATTACA-TATC
42052334 ATACTTCTTATTATATATT
1 ATA-TT-TTATTATATATT
42052353 TTTTTTATTA
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
26 3 0.05
27 31 0.54
28 13 0.23
29 7 0.12
30 3 0.05
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (27 bp):
ATATTTTATTATATATTATTACATATC
Found at i:42052372 original size:21 final size:19
Alignment explanation
Indices: 42052341--42052399 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 19
42052331 TATATACTTC
42052341 TTATTATATATTTTTTTTA
1 TTATTATATATTTTTTTTA
** *
42052360 TTACTTATCATATGGTTTATA
1 TTA-TTAT-ATATTTTTTTTA
*
42052381 TTATTATATATTTTGTTTA
1 TTATTATATATTTTTTTTA
42052400 CAAATTATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 11 0.35
20 8 0.26
21 12 0.39
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.64
Consensus pattern (19 bp):
TTATTATATATTTTTTTTA
Found at i:42053847 original size:45 final size:45
Alignment explanation
Indices: 42053770--42053879 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
42053760 CGACTACTAT
* **
42053770 TACTGTTACCGTTACTGTTACCGATTTGACACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACCGATTCAACACTTTGTGTGTCGAA
* * * *
42053815 TACTATTACTGTTACCGTTACCTATTCAACACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACCGATTCAACACTTTGTGTGTCGAA
42053860 TACTGTTACTGTTACTGTTA
1 TACTGTTACTGTTACTGTTA
42053880 TTGCTACCAT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACCGATTCAACACTTTGTGTGTCGAA
Found at i:42053875 original size:51 final size:50
Alignment explanation
Indices: 42053755--42053879 Score: 125
Period size: 45 Copynumber: 2.6 Consensus size: 50
42053745 CAGACACTTA
* * * * **
42053755 TGTGCCGACTACTATTACTGTTACCGTTACTGTTACCGATTTGACACTTTG
1 TGTGTCGAATACT-TTACTGTTACTGTTACCGTTACCGATTCAACACTTTG
*
42053806 TGTGTCGAATAC--TA---TTACTGTTACCGTTACCTATTCAACACTTTG
1 TGTGTCGAATACTTTACTGTTACTGTTACCGTTACCGATTCAACACTTTG
*
42053851 TGTGTTGAATACTGTTACTGTTACTGTTA
1 TGTGTCGAATACT-TTACTGTTACTGTTA
42053880 TTGCTACCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
45 37 0.62
48 4 0.07
51 19 0.32
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (50 bp):
TGTGTCGAATACTTTACTGTTACTGTTACCGTTACCGATTCAACACTTTG
Found at i:42056575 original size:40 final size:41
Alignment explanation
Indices: 42056515--42056618 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
42056505 AACACACCAG
* * *
42056515 TTTGGCACCCAGTGCCTCATCGGA-TAAT-TCGAAGTAATAA
1 TTTGACACCCAGTGTCTCATCGAATTAATCT-GAAGTAATAA
* *
42056555 TTTGACACCCAGTGTTTCATCGAATTAATCTGAAGTAGTAA
1 TTTGACACCCAGTGTCTCATCGAATTAATCTGAAGTAATAA
* *
42056596 ATTGACACCTAGTGTCTCATCGA
1 TTTGACACCCAGTGTCTCATCGA
42056619 CTTGAAGTCG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 20 0.37
41 33 0.61
42 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (41 bp):
TTTGACACCCAGTGTCTCATCGAATTAATCTGAAGTAATAA
Found at i:42057429 original size:16 final size:16
Alignment explanation
Indices: 42057404--42057446 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 16
42057394 ATTCTCCTTA
42057404 TTTTTCCTTTTCTTTCC
1 TTTTT-CTTTTCTTTCC
42057421 TTTTTC-TTTCTTTCC
1 TTTTTCTTTTCTTTCC
42057436 TTCTTTCTTTT
1 TT-TTTCTTTT
42057447 GTTCTATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.46
16 5 0.21
17 8 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCTTTTCTTTCC
Found at i:42057456 original size:16 final size:16
Alignment explanation
Indices: 42057437--42057469 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42057427 TTTCTTTCCT
42057437 TCTTTCT-TTTGTTCTA
1 TCTTTCTCTTT-TTCTA
42057453 TCTTTCTCTTTTTCTA
1 TCTTTCTCTTTTTCTA
42057469 T
1 T
42057470 TTTTATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.06, C:0.21, G:0.03, T:0.70
Consensus pattern (16 bp):
TCTTTCTCTTTTTCTA
Found at i:42057497 original size:21 final size:21
Alignment explanation
Indices: 42057471--42057510 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42057461 TTTTTCTATT
42057471 TTTATTTCTTTT-ATTTATTTG
1 TTTA-TTCTTTTAATTTATTTG
42057492 TTTATTCTTTTAATTTATT
1 TTTATTCTTTTAATTTATT
42057511 ATTATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTATTCTTTTAATTTATTTG
Found at i:42060768 original size:22 final size:22
Alignment explanation
Indices: 42060683--42060768 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
42060673 TGTTGAGCGA
* *
42060683 TAGGCATCAAAGTGCAAATCAG
1 TAGGCACCATAGTGCAAATCAG
* * *
42060705 TAGGCACTATAATGCAAATTAG
1 TAGGCACCATAGTGCAAATCAG
* * * **
42060727 TAGACACCGTACTGTGAATCAG
1 TAGGCACCATAGTGCAAATCAG
*
42060749 TAGGCACCATAGTGAAAATC
1 TAGGCACCATAGTGCAAATC
42060769 GTGTACAAGT
Statistics
Matches: 47, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (22 bp):
TAGGCACCATAGTGCAAATCAG
Found at i:42061552 original size:25 final size:25
Alignment explanation
Indices: 42061518--42061568 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42061508 GAAAGGGGTT
42061518 TCAAATTCACTTACATGCACATAGC
1 TCAAATTCACTTACATGCACATAGC
42061543 TCAAATTCACTTACATGCACATAGC
1 TCAAATTCACTTACATGCACATAGC
42061568 T
1 T
42061569 AAACTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (25 bp):
TCAAATTCACTTACATGCACATAGC
Found at i:42080167 original size:26 final size:26
Alignment explanation
Indices: 42080138--42080242 Score: 174
Period size: 26 Copynumber: 4.0 Consensus size: 26
42080128 TGGTACAAAT
42080138 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
42080164 TGATAATGGATTAAGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
42080190 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
42080216 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
42080242 T
1 T
42080243 CATGGGCATT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:42087270 original size:26 final size:26
Alignment explanation
Indices: 42087241--42087296 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
42087231 TGGTACAAAT
42087241 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
42087267 TGATAATGGTTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
42087293 TGAT
1 TGAT
42087297 GGGCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.39
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:42090200 original size:26 final size:27
Alignment explanation
Indices: 42090165--42090217 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
42090155 AATTTAAGTA
42090165 AAAATGGGTATG-AAAAGTATATGAAT
1 AAAATGGGTATGAAAAAGTATATGAAT
42090191 AAAATGGGTATGAAAAAGTATATGAAT
1 AAAATGGGTATGAAAAAGTATATGAAT
42090218 TTTTGTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (27 bp):
AAAATGGGTATGAAAAAGTATATGAAT
Found at i:42091830 original size:18 final size:18
Alignment explanation
Indices: 42091807--42091892 Score: 100
Period size: 18 Copynumber: 4.7 Consensus size: 18
42091797 GAATGATTAT
* *
42091807 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAATCAA
*
42091825 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
42091843 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
*
42091861 TTATTCAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
42091880 TTATTCAGTAACA
1 TTATTCAGTAACA
42091893 GTCGATCTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
18 41 0.73
19 15 0.27
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:42091848 original size:36 final size:37
Alignment explanation
Indices: 42091807--42091895 Score: 126
Period size: 36 Copynumber: 2.4 Consensus size: 37
42091797 GAATGATTAT
* *
42091807 TTATTCAGTAACAGTCAGTTATTCGGTAACAA-TCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
* * *
42091843 TTATTCAATAATAATCAGTTATTCAGTAACAATTAAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
42091880 TTATTCAGTAACAGTC
1 TTATTCAGTAACAGTC
42091896 GATCTTTCCA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 28 0.64
37 16 0.36
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (37 bp):
TTATTCAGTAACAGTCAGTTATTCAGTAACAATTAAA
Found at i:42092019 original size:6 final size:6
Alignment explanation
Indices: 42092008--42092032 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42091998 CTGAAGCCGA
42092008 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
42092033 GCAATACGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:42092112 original size:47 final size:47
Alignment explanation
Indices: 42092026--42092132 Score: 151
Period size: 47 Copynumber: 2.3 Consensus size: 47
42092016 CAGTAACAGT
* * * *
42092026 AACAGTAGCAATACGGTACATAAAGTACCTCTTCAGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAAAGTACCTCATCAGAACAAATCCGG
* * *
42092073 AACGGTAATAGTACGGTACACAAAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAAAGTACCTCATCAGAACAAATCCGG
42092120 AACAGTAACAGTA
1 AACAGTAACAGTA
42092133 ACGATAACAG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAAAGTACCTCATCAGAACAAATCCGG
Found at i:42097324 original size:27 final size:28
Alignment explanation
Indices: 42097289--42097343 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
42097279 TTTATATATG
42097289 ATATGTTATATGA-AT-TATATGATATTGA
1 ATATGTTATAT-ACATGTATATGA-ATTGA
42097317 ATAT-TTATATACATGTATATGAATTGA
1 ATATGTTATATACATGTATATGAATTGA
42097344 TGAAAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 1 0.04
27 13 0.52
28 11 0.44
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (28 bp):
ATATGTTATATACATGTATATGAATTGA
Found at i:42104006 original size:17 final size:16
Alignment explanation
Indices: 42103974--42104015 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
42103964 TTATAATTTA
42103974 TTAATAAAA-ATGATT
1 TTAATAAAATATGATT
*
42103989 TTAATTAAAATATTATT
1 TTAA-TAAAATATGATT
*
42104006 TCAATAAAAT
1 TTAATAAAAT
42104016 GTTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TTAATAAAATATGATT
Found at i:42121368 original size:28 final size:28
Alignment explanation
Indices: 42121323--42121405 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
42121313 ATGCCGTTGA
* * *
42121323 ATACTCAATATTTTGCACACTAAGTGCC
1 ATACTCGATATCTCGCACACTAAGTGCC
*
42121351 ATACTCGATATCTCGCACATTAAGTGCC
1 ATACTCGATATCTCGCACACTAAGTGCC
*
42121379 ATACTCGATGTCTCGCACACTAAGTGC
1 ATACTCGATATCTCGCACACTAAGTGC
42121406 TGTACATAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (28 bp):
ATACTCGATATCTCGCACACTAAGTGCC
Found at i:42124087 original size:24 final size:22
Alignment explanation
Indices: 42124040--42124088 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 22
42124030 TAAATTGAAC
*
42124040 AATTTTTGTATTAAATAAGTTA
1 AATTTTTGTATTAAATAAGATA
42124062 AATTTTT-TATTATATATCAAGATA
1 AATTTTTGTATTA-A-AT-AAGATA
42124086 AAT
1 AAT
42124089 GAGGCTCGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.22
22 8 0.35
23 2 0.09
24 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (22 bp):
AATTTTTGTATTAAATAAGATA
Found at i:42134987 original size:18 final size:19
Alignment explanation
Indices: 42134964--42135007 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
42134954 AAAGAAACGG
42134964 AGTAAG-CATTTAATGCTT
1 AGTAAGTCATTTAATGCTT
**
42134982 AGTAAGTTTTTTAATGCTT
1 AGTAAGTCATTTAATGCTT
42135001 AGTAAGT
1 AGTAAGT
42135008 TTGAGCCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (19 bp):
AGTAAGTCATTTAATGCTT
Found at i:42134996 original size:19 final size:19
Alignment explanation
Indices: 42134972--42135009 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42134962 GGAGTAAGCA
42134972 TTTAATGCTTAGTAAGTTT
1 TTTAATGCTTAGTAAGTTT
42134991 TTTAATGCTTAGTAAGTTT
1 TTTAATGCTTAGTAAGTTT
42135010 GAGCCATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (19 bp):
TTTAATGCTTAGTAAGTTT
Found at i:42135349 original size:39 final size:39
Alignment explanation
Indices: 42135305--42135414 Score: 112
Period size: 40 Copynumber: 2.8 Consensus size: 39
42135295 CCTTCGGAGT
* *
42135305 TTAGCCAGATATAGCCACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCAGATATAGCAACTAGCACAAATGCCTTCGGGAC
* * * * *
42135344 TTAGCCCGGTTATAGTAACTTGCACAAATTCCTTCGGGAC
1 TTAG-CCAGATATAGCAACTAGCACAAATGCCTTCGGGAC
* ** *
42135384 TTAGCCCGATATAATAACTCGCACAAATGCC
1 TTAGCCAGATATAGCAACTAGCACAAATGCC
42135415 CGCACAAATG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
39 26 0.45
40 32 0.55
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (39 bp):
TTAGCCAGATATAGCAACTAGCACAAATGCCTTCGGGAC
Found at i:42135372 original size:40 final size:40
Alignment explanation
Indices: 42135328--42135523 Score: 155
Period size: 40 Copynumber: 4.6 Consensus size: 40
42135318 GCCACTAGCT
*
42135328 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
* *
42135368 CAAATTCCTTCGGGACTTAGCCC-GATATAATAACTCGCACAAATGCCCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACT--------T----GCA
* *
42135419 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
* ** * *
42135459 CGAATGCCTTCGGGACTTAGCCCGGA-ATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTTGCA
42135499 CAAATG-CTCTCGGGACTTAGCCCGG
1 CAAATGCCT-TCGGGACTTAGCCCGG
42135524 TTATCATCCG
Statistics
Matches: 127, Mismatches: 14, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
39 13 0.10
40 78 0.61
47 1 0.01
51 25 0.20
52 10 0.08
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
Found at i:42135441 original size:51 final size:52
Alignment explanation
Indices: 42135365--42135466 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 52
42135355 ATAGTAACTT
*
42135365 GCACAAATTCCTTCGGGACTTAGCCC-GATATAATAACTCGCACAAATGCCC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATGCCC
* * *
42135416 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACGAATGCC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATGCC
42135467 TTCGGGACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 25 0.54
52 21 0.46
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (52 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAAATGCCC
Found at i:42143416 original size:39 final size:39
Alignment explanation
Indices: 42143372--42143520 Score: 145
Period size: 39 Copynumber: 3.8 Consensus size: 39
42143362 CCTTCGGAGT
** *
42143372 TTAGCCAGATATAGCCACTAGCTCAAATGCCTTCGGGAC
1 TTAGCCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
* * * *
42143411 TTAGCCCGGTTATAGTAACTTGCACAAATTCCTTCGGGAC
1 TTAG-CCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
* * * *
42143451 TTAGCCCGGTATAATAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
* * * * *
42143490 ATAGCCCGGTATAATAACTCGCACAAATGCC
1 TTAGCCAGATATAGTAACTAGCACAAATGCC
42143521 CGCACAAAGG
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 64 0.67
40 32 0.33
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (39 bp):
TTAGCCAGATATAGTAACTAGCACAAATGCCTTCGGGAC
Found at i:42143439 original size:40 final size:39
Alignment explanation
Indices: 42143395--42143520 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
42143385 GCCACTAGCT
* *
42143395 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAATAACTCGCA
*
42143435 CAAATTCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
*
42143474 CAAATGCCTTCGGGACATAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
42143513 CAAATGCC
1 CAAATGCC
42143521 CGCACAAAGG
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 57 0.70
40 24 0.30
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
Found at i:42152475 original size:26 final size:25
Alignment explanation
Indices: 42152446--42152503 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
42152436 CCCAATATAT
*
42152446 GGCTCTTCGTGAGCTTCCTGACTAAA
1 GGCTCTT-ATGAGCTTCCTGACTAAA
* * *
42152472 GGCTCATTATGAGCTTTCTGATTAAT
1 GGCTC-TTATGAGCTTCCTGACTAAA
42152498 GGCTCT
1 GGCTCT
42152504 CCAGAGCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 24 0.89
27 2 0.07
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (25 bp):
GGCTCTTATGAGCTTCCTGACTAAA
Found at i:42165040 original size:27 final size:27
Alignment explanation
Indices: 42165010--42165374 Score: 404
Period size: 27 Copynumber: 13.7 Consensus size: 27
42165000 TAATAAAGAG
42165010 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
42165037 AAATTACCGAAATACCCCCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * * *
42165064 AAGTTACCGAAATACCCTC-AATTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* *
42165090 AAGTTACTAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
42165117 AAATTACCGAAATACCCTAGA-TTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
42165143 AAATTACTGAAGTACCTTCGA-TTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
*
42165169 AAATTA-TCAAAATACCCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* *
42165196 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
42165223 AAATTATTGAAATACCCTCGA-TTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
*
42165249 AAATTA-TCGAAATACTCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* * * *
42165276 AAATTACTAAAATACCCCCGATTTATG
1 AAATTACTGAAATACCCTCGATTTGTA
* *
42165303 AAATTA-TCGAAACACCCTCAATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
*
42165330 AAATTACCGAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
42165357 AAATTA-TCGAAATACCCT
1 AAATTACT-GAAATACCCT
42165375 TGTAGTGTAA
Statistics
Matches: 283, Mismatches: 45, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.01
26 88 0.31
27 192 0.68
28 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:42165112 original size:53 final size:54
Alignment explanation
Indices: 42165010--42165401 Score: 386
Period size: 53 Copynumber: 7.3 Consensus size: 54
42165000 TAATAAAGAG
* * * *
42165010 AAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTA
1 AAATTACCGAAATACCCTCGAATTGTAAAATTACTGAAATACCCTCGATTTGTA
* * * *
42165064 AAGTTACCGAAATACCCTC-AATTGTGAAGTTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGAATTGTAAAATTACTGAAATACCCTCGATTTGTA
* * * * *
42165117 AAATTACCGAAATACCCTAG-ATTGTGAAATTACTGAAGTACCTTCGA-TTGTG
1 AAATTACCGAAATACCCTCGAATTGTAAAATTACTGAAATACCCTCGATTTGTA
* * * * *
42165169 AAATTATCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCAATTTGTA
1 AAATTACCGAAATACCCTCGAATTGTAAAATTACTGAAATACCCTCGATTTGTA
** *
42165223 AAATTATTGAAATACCCTCG-ATTGTAAAATTA-TCGAAATACTCTCGATTTGTA
1 AAATTACCGAAATACCCTCGAATTGTAAAATTACT-GAAATACCCTCGATTTGTA
** * * * * * *
42165276 AAATTACTAAAATACCCCCGATTTATGAAATTA-TCGAAACACCCTCAATTTGTA
1 AAATTACCGAAATACCCTCGAATTGTAAAATTACT-GAAATACCCTCGATTTGTA
* * *
42165330 AAATTACCGAAATACCCTCGATTTGTAAAATTA-TCGAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCTCGAATTGTAAAATTACT-GAAATACCCTCGAT-TTGTA
* *
42165384 AAATGACCGACATACCCT
1 AAATTACCGAAATACCCT
42165402 GTAGGGTAAA
Statistics
Matches: 281, Mismatches: 51, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
52 21 0.07
53 135 0.48
54 125 0.44
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (54 bp):
AAATTACCGAAATACCCTCGAATTGTAAAATTACTGAAATACCCTCGATTTGTA
Found at i:42165273 original size:80 final size:79
Alignment explanation
Indices: 42165010--42165374 Score: 419
Period size: 80 Copynumber: 4.6 Consensus size: 79
42165000 TAATAAAGAG
* * *
42165010 AAATTACTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCGATTTGTAAAGTTACCGAA
1 AAATTAC-GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCGAA
*
42165075 ATACCCTCAATTGTG
65 ATACCCTCAATTGTA
* * * *
42165090 AAGTTACTAAAATACCCTCGATTTGTAAAATTACCGAAATACCCT-AGA-TTGTGAAATTACTGA
1 AAATTAC-GAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCA-ATTTGTAAAATTACCGA
* * * *
42165153 AGTACCTTCGATTGTG
64 AATACCCTCAATTGTA
* **
42165169 AAATTATCAAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTATTGAA
1 AAATTA-CGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCGAA
*
42165234 ATACCCTCGATTGTA
65 ATACCCTCAATTGTA
* ** * * * * *
42165249 AAATTATCGAAATACTCTCGATTTGTAAAATTACTAAAATACCCCCGATTTATGAAATTATCGAA
1 AAATTA-CGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCGAA
*
42165314 ACACCCTCAATTTGTA
65 ATACCCTCAA-TTGTA
*
42165330 AAATTACCGAAATACCCTCGATTTGTAAAATTATCGAAATACCCT
1 AAATTA-CGAAATACCCTCGATTTGTAAAATTACCGAAATACCCT
42165375 TGTAGTGTAA
Statistics
Matches: 247, Mismatches: 33, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
79 68 0.28
80 135 0.55
81 44 0.18
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (79 bp):
AAATTACGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTCAATTTGTAAAATTACCGAAA
TACCCTCAATTGTA
Found at i:42165411 original size:26 final size:27
Alignment explanation
Indices: 42165327--42165413 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
42165317 CCCTCAATTT
* * **
42165327 GTAAAATTACCGAAATACCCTCG-ATTT
1 GTAAAATGACCGAAATACCCTTGTA-GG
* * *
42165354 GTAAAATTATCGAAATACCCTTGTAGT
1 GTAAAATGACCGAAATACCCTTGTAGG
*
42165381 GTAAAATGACCGACATACCC-TGTAGG
1 GTAAAATGACCGAAATACCCTTGTAGG
42165407 GTAAAAT
1 GTAAAAT
42165414 AACTGTTTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 12 0.23
27 39 0.75
28 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCTTGTAGG
Found at i:42173116 original size:33 final size:33
Alignment explanation
Indices: 42173079--42173144 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
42173069 CGATTTTTAC
42173079 TCTTTCCACAGCATACACCAAAGAGTTGTCTTT
1 TCTTTCCACAGCATACACCAAAGAGTTGTCTTT
* * *
42173112 TCTTTCCCCAGCATTCACCAAAGTGTTGTCTTT
1 TCTTTCCACAGCATACACCAAAGAGTTGTCTTT
42173145 CACATTGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (33 bp):
TCTTTCCACAGCATACACCAAAGAGTTGTCTTT
Found at i:42179196 original size:26 final size:26
Alignment explanation
Indices: 42179167--42179239 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
42179157 CCCAATATAT
*
42179167 GGCTTTTCGTGAGCTTCCCGATTAAA
1 GGCTTTTCATGAGCTTCCCGATTAAA
* *
42179193 GGCTCTTT-ATGAGCTTCCTGATTAAT
1 GGCT-TTTCATGAGCTTCCCGATTAAA
* *
42179219 GGCTCTCCA-GAGCTTCCCGAT
1 GGCTTTTCATGAGCTTCCCGAT
42179240 ATAGCTTGCT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 12 0.31
26 24 0.62
27 3 0.08
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (26 bp):
GGCTTTTCATGAGCTTCCCGATTAAA
Found at i:42179304 original size:25 final size:25
Alignment explanation
Indices: 42179276--42179385 Score: 75
Period size: 25 Copynumber: 4.5 Consensus size: 25
42179266 AGACTATCCG
*
42179276 GAGCTTCCTGATTAATGGCTCTCCA
1 GAGCTTCCCGATTAATGGCTCTCCA
* **
42179301 GAGCTTCCCGA-T-ATAGCT-TGCTT
1 GAGCTTCCCGATTAATGGCTCT-CCA
** * * * *
42179324 GAATTTCCCGACATAA-GACTATCCG
1 GAGCTTCCCGA-TTAATGGCTCTCCA
*
42179349 GAGCTTCCTGATTAATGGCTCTCCA
1 GAGCTTCCCGATTAATGGCTCTCCA
42179374 GAGCTTCCCGAT
1 GAGCTTCCCGAT
42179386 ATAGCTTGCT
Statistics
Matches: 61, Mismatches: 18, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
22 1 0.02
23 15 0.25
24 4 0.07
25 39 0.64
26 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTCCA
Found at i:42179451 original size:73 final size:73
Alignment explanation
Indices: 42179203--42179443 Score: 439
Period size: 73 Copynumber: 3.3 Consensus size: 73
42179193 GGCTCTTTAT
42179203 GAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATATAGCTTGCTTGAATTTCCCGACATAAG
1 GAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATATAGCTTGCTTGAATTTCCCGACATAAG
42179268 ACTATCCG
66 ACTATCCG
42179276 GAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATATAGCTTGCTTGAATTTCCCGACATAAG
1 GAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATATAGCTTGCTTGAATTTCCCGACATAAG
42179341 ACTATCCG
66 ACTATCCG
*
42179349 GAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATATAGCTTGCTTGAATTTCCTGACATAA-
1 GAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATATAGCTTGCTTGAATTTCCCGACATAAG
42179413 AGCTATCCG
66 A-CTATCCG
* *
42179422 AAGCTTCCTAATTAATGGCTCT
1 GAGCTTCCTGATTAATGGCTCT
42179444 TTAGAGCTAC
Statistics
Matches: 164, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
72 1 0.01
73 163 0.99
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (73 bp):
GAGCTTCCTGATTAATGGCTCTCCAGAGCTTCCCGATATAGCTTGCTTGAATTTCCCGACATAAG
ACTATCCG
Done.